bioRxiv directory

Ohene-Marfo, P.; Mohammed, S.; Jiang, C.; Bhaskaran, S.; Georgescu, C.; John, M.; Pham, K.; Tran, A.; Rao, C. V.; Gyu Oh, T.; Kinter, M.; Freeman, W. M.; Houchen, C.; Wren, J. D.; Deepa, S.

10.1101/2025.11.26.690789 — cancer biology — Posted on 2025-11-30

3 LaCONIC: A Label-Aware and Graph-Guided Contrastive Multi-Omics Collaborative Learning Model for Cancer Risk Prediction

Liu, P.; Liang, X.; Luo, J.

10.1101/2025.11.26.690662 — bioinformatics — Posted on 2025-11-30

4 Sample-level modeling of single-cell data at scale with tinydenseR

Milanez-Almeida, P.; Schildknecht, D.; Linder, M.; Brachmann, S. M.; Weiss, A.; Adler, F.; Lenticchia, S. C.; Meistertzheim, M.; Wild, S.; Cuttat, R.; Jayaraman, P.; Lee, L. H.; Mulvey, T.; Hassounah, N.; Crafts, G.; Quinn, D. S.; Orlando, E. J.

10.1101/2025.11.26.690752 — bioinformatics — Posted on 2025-11-30

5 Splice Isoform Induced Selective Inhibition of Vesicular Monoamine Transporter Assembly Revealed by Multi-level Combinatorial Analysis

Karagöl, A.; Karagöl, T.

10.1101/2025.11.29.691296 — biochemistry — Posted on 2025-11-30

6 Uncovering senescent fibroblast heterogeneity connects DNA damage response to idiopathic pulmonary fibrosis

Hughes, J.-W. B.; Pujari, A.; Sandholm, A.; Croll, D.; Monk, L. B.; Joshua, I.; Butterfield, R.; Horton, C.; Schneider, K.; Senchyna, F.; Brown, I.; Coelho, A. L.; Ho, T.-C.; Deguchi, H.; Le Saux, C. J.; Deinhardt-Emmer, S.; Ellerby, L. M.; Vitari, A.; Furman, D.; Hogoboam, C. M.; Laslavic, A.; Desprez, P.-Y.; Quarta, M.; Campisi, J.

10.1101/2025.11.26.690792 — cell biology — Posted on 2025-11-30

7 The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome

Shen, B. A.; Asfahl, K. L.; Lim, B.; Bertolli, S. K.; Minot, S. S.; Radey, M. C.; Penewit, K.; Ngo, B.; Salipante, S. J.; Johnston, C. D.; Peterson, S. B.; Goodman, A. D.; Mougous, J. D.

10.1101/2025.11.29.690828 — microbiology — Posted on 2025-11-30

8 Nuclear activities and interactome of the NS5 protein of Tick-Borne Encephalitis Virus

Chazal, M.; Sow, A.-A.; Le Seac'h, E.; Hawasheen, D.; Bonifacio, M.; Feracci, M.; Gracias, S.; Sogues, A.; Molho, M.; Pan, H.; Bonaventure, B.; Quivy, J.-P.; Almouzni, G.; Decroly, E.; Ramage, H.; Johnson, J. R.; Caval, v.; jouvenet, n.

10.1101/2025.11.29.691275 — microbiology — Posted on 2025-11-30

9 Structure and function of the nervous system in the stem of the siphonophore Nanomia septata: its role in swimming coordination.

Norekian, T. P.; Meech, R. W.

10.1101/2025.11.27.690755 — neuroscience — Posted on 2025-11-30

10 Modulation of metabolic, inflammatory, fibrotic and cell death pathways by Resmetirom in metabolic dysfunction-associated steatohepatitis (MASH): A transcriptomic profiling study

He, C.; Wang, Z.; Weng, J.; Xu, S.

10.1101/2025.11.26.690715 — pharmacology and toxicology — Posted on 2025-11-30

11 A clinical-stage oncology compound selectively targets drug-resistant cancers

Long, K.; Bhattacharjee, D.; Newman-Stonebraker, S. H.; Suhr, S.; Mercado, B. Q.; Tighe, A.; Romero, L.; Thompson, S. L.; Sausville, E. L.; John, K. M.; Julian, L.; Mishra, S.; Klingbeil, O.; Gupta, P.; Bhatt, U.; Gao, A. C.; Ricardo, S.; Vakoc, C. R.; Bornhauser, B. C.; Corsello, S. M.; Taylor, S. S.; Holland, P. L.; Sheltzer, J. M.

10.1101/2025.11.26.690878 — cancer biology — Posted on 2025-11-30

12 Active surface waves drive rippling in Myxococcus xanthus colonies

Bourque, A. R.; Hampshire, P. A. E.; Alert, R.; Shaevitz, J. W.

10.1101/2025.11.28.691037 — biophysics — Posted on 2025-11-30

13 Human spastin functions as an ATPase-independent microtubule nucleator via ring-stack formation

Liu, H.; Matsumoto, N.; Kaneshiro, T.; Kato, T.; Shigematsu, H.; Kikkawa, S.; Nitta, E.; Imasaki, T.; Nitta, R.

10.1101/2025.11.28.691112 — biophysics — Posted on 2025-11-30

14 Why PAR is not RNA: ion atmospheres, bridging interactions, and ion-induced structural collapse

Baidya, L.; Zhang, H.; Nguyen, H.

10.1101/2025.11.29.691228 — biophysics — Posted on 2025-11-30

15 Towards improved particle averaging for single-molecule localization microscopy using geometric deep learning

Mindroc-Filimon, D.; Helmerich, D.; Salome, P.; Sauer, M.; Kollmannsberger, P.

10.1101/2025.11.26.690737 — bioinformatics — Posted on 2025-11-30

16 SMOLM-LFM: ratiometric single molecule orientation without polarizers

Vesga, A. G.; Aleman-Castaneda, L.; Heil, H. S.; Daly, S.; Bruggeman, E.; Lee, S. F.; Brasselet, S.; Henriques, R.

10.1101/2025.11.26.690201 — bioengineering — Posted on 2025-11-30

17 ClpK as a Chaperone Hub: Computational Exploration of its Protein Interaction Landscape.

Ballim, T.; Achilonu, I.; Khoza, T.

10.1101/2025.11.28.691151 — biochemistry — Posted on 2025-11-30

18 Computational Repurposing and Phytochemical Screening of Inhibitors Against ClpK from Klebsiella pneumoniae.

Ballim, T.; Khoza, T.

10.1101/2025.11.28.691150 — biochemistry — Posted on 2025-11-30

19 A dynamical-nonequilibrium molecular dynamics (D-NEMD) alanine scanning approach for identifying allosteric positions in proteins

Balega, B.; Beer, M.; Pike, D. T. S.; Spencer, J.; Oliveira, A. S. F.; Mulholland, A. J.

10.1101/2025.11.29.691197 — biochemistry — Posted on 2025-11-30

20 Bayesian inference of population structure using identity-by-descent-based stochastic block models

Micheletti, S. J.; Bryc, K.; Esselmann, S. G. A.; Wilton, P. R.; Freyman, W. A.

10.1101/2025.11.26.690810 — genetics — Posted on 2025-11-30

21 Volatile but persistent co-existence of self-compatibility and self-incompatibility in plants

Jangid, A.; Feldheim, O. N.; Friedlander, T.

10.1101/2025.11.30.691363 — evolutionary biology — Posted on 2025-11-30

22 Experimental and field evidence indicate that islet-nesting tundra birds experience reduced nest predation and benefit indirectly from high snow goose densities

Beaudoin, M.; Beardsell, A.; Duchesne, E.; Corbeil-Robitaille, M.-Z.; Legagneux, P.; Berteaux, D.; Bety, J.

10.1101/2025.11.26.690446 — ecology — Posted on 2025-11-30

23 Eco-evolutionary feedback of adaptive evolution to a pesticide worsens the impact of a pesticide switch in a pivotal freshwater non-target species

Almeida, R. A.; Fajgenblat, M.; Lemmens, P.; Cuypers, K.; Maes, J.; Brans, K. I.; De Meester, L.

10.1101/2025.11.30.691396 — ecology — Posted on 2025-11-30

24 Identifying the internalization pathways of magnetotactic bacteria and magnetosomes by cancer cells

Gandarias, L.; Arana, L.; Gubieda, A. G.; Perez-Berna, A. J.; Abad-Diaz-de-Cerio, A.; Fdez-Gubieda, M. L.; Muela, A.; Garcia-Prieto, A.

10.1101/2025.11.26.690460 — cell biology — Posted on 2025-11-30

25 Protease secreting Nannochloropsis limnetica can valorise invasive plants through circular water-use and accumulate neutral lipids

Iyer, A.; Heneghan, P.; Dillon, E.; Modin, O.; Halim, R.

10.1101/2025.11.29.691304 — microbiology — Posted on 2025-11-30

26 Nanoscale imaging of native symbiotic animal tissue using amultimodal large volume imaging pipeline for cryo-electrontomography

Gundlach, K. A.; Schiotz, O. H.; Ladinsky, M. S.; Raimann, C.; Rheinberger, M.; Beck, F.; Guenduez, B.; Langelaan, R.; Ruecklin, M.; Limpens, R. W. A. L.; Ruby, E. G.; McFall-Ngai, M.; Plitzko, J. M.; Briegel, A.

10.1101/2025.11.30.691379 — microbiology — Posted on 2025-11-30

27 From minutes to bounds: A probabilistic UV-C control and a shape-only morphological fingerprint for postharvest Colletotrichum

Ahn, E.; Baek, I.; Lim, S.; Lovelace, A.; Cha, M.; Kim, M. S.; Park, S.; Meinhardt, L.

10.1101/2025.11.29.691312 — microbiology — Posted on 2025-11-30

28 Viral diversity, ecological interconnectedness, and the identification of mammalian chuviruses in Australian microbats

Ortiz-Baez, A. S.; Melade, J.; Van Brussel, K.; Lang, B.; Lachenauer, A.; Holmes, E. C.

10.1101/2025.11.29.691345 — microbiology — Posted on 2025-11-30

29 Epitope and functional classification of human neutralizing antibodies against SFTSV Gn

Wang, Q.; Li, H.; Jian, F.; Han, A.; Liu, Y.; Liu, J.; Yu, Y.; Wang, J.; Yu, L.; Wang, Y.; Sun, H.; Ma, M.; Shao, F.; Zhu, L.; Liu, W.; Cao, Y.

10.1101/2025.11.26.690690 — immunology — Posted on 2025-11-30

30 HDL-associated phosphatidylserine blunts myeloid activation and protects from atherosclerosis

Bernal, A.; Hamid, A.; Grao-Roldan, C.; Scarpa, A.; Sanchez, I.; Nicolas-Avila, J. A.; Pena-Couso, L.; Yaghmour, M. H.; Benguria, A.; Rosado, A.; Sanchez, L.; Torroja, C.; Dopazo, A.; Sanchez-Cabo, F.; Hidalgo, A.; Senders, M. L.; van Leent, M. M. T.; Seep, L.; Hasenauer, J.; Placek, K.; Thiele, C.; Netea, M. G.; Mulder, W. J. M.; Riksen, N. P.; Perez-Medina, C.

10.1101/2025.11.26.689708 — immunology — Posted on 2025-11-30

31 Reverse Spatiotemporal Hierarchy during Cross-modal Memory Recall and Imagery

Hu, Y.; Diedrichsen, J.; Mohsenzadeh, Y.

10.1101/2025.11.26.690759 — neuroscience — Posted on 2025-11-30

32 An ultra-low background far-red light-responsive optogenetic tool based on an engineered biliverdin-binding domain

Le, G. N. T.; Pham, L. M. T.; Xue, B.; Uppalapati, M.; Woolley, A.

10.1101/2025.11.29.691301 — synthetic biology — Posted on 2025-11-30

33 The allometry of discontinuous gas exchange cycles in Atta cephalotes leaf-cutter ants

Walthaus, O. K.; Labonte, D.

10.1101/2025.11.26.690668 — physiology — Posted on 2025-11-30

34 Peptide nanoparticles for systemic mRNA delivery in rodents and non-human primates

Lehto, T.; Sork, H.; Lorents, A.; Radler, J.; Bazaz, S.; Roudi, S.; Gustafsson, O.; Boukary, O.; Talgre, I. R.; Hallbrink, M.; Wiklander, O. P. B.; Saher, O.; Bost, J.; Ezzat, K.; Smith, C. E.; Gupta, D.; Lehto, T.; Andaloussi, S. E.

10.1101/2025.11.26.690657 — pharmacology and toxicology — Posted on 2025-11-30

35 Angiotensin II Induces Abdominal Aortic Branch Aneurysms in Fibrillin-1C1041G/+ Mice

Franklin, M. K.; Howatt, D. A.; Moorleghen, J. J.; Sheppard, M.; Sawada, H.; Lu, H. S.; Daugherty, A.

10.1101/2025.11.26.690689 — pathology — Posted on 2025-11-30

36 DYRK1A regulates cancer cell and cancer-associated fibroblast secretomes to foster an immunosuppressive microenvironment in pancreatic cancer

Pascual-Sabater, S.; Varhadi, S.; Di Vona, C.; Celma, M.; Fillat, C.; de la Luna, S.

10.1101/2025.11.26.690756 — cancer biology — Posted on 2025-11-30

37 Collagen I promotes cancer cell survival via amino acid import and mTORC1 activation

Nazemi, M.; Yanes, B.; Oyelade, I.; Walker, H.; Rainero, E.

10.1101/2025.11.26.690708 — cancer biology — Posted on 2025-11-30

38 Molecular interplay between the DNA damage checkpoint kinase Mec1-Ddc2 and its activator Dpb11 on gapped DNA

Beckwitt, E. C.; Chua, G. N. L.; Liu, S.; O'Donnell, M. E.

10.1101/2025.11.28.691181 — biophysics — Posted on 2025-11-30

39 Interactions with lipid membrane modulate the conformational dynamics and energy landscape of Tumor Necrosis Factor

Khelashvili, G.; Kolossvary, I.; Sherman, W.; Trovato, F.

10.1101/2025.11.28.690881 — biophysics — Posted on 2025-11-30

40 Butyrate Rescues Cardiac Metabolic Dysfunction in Hypertensive Heart Failure with Preserved Ejection Fraction

Kedziora, S. M.; Geisberger, S. Y.; Popp, O.; Frolova, A.; Uhrbach, A.; Kaeker, K.; Tagiyeva, N.; Kelm, M.; Berndt, N.; Zhang, Y. D.; Mastrobuoni, G.; Escrihuela-Branz, R.; Pixner, L.; Bartolomaeus, T. U.; Fahjen, P.; Kaufhold, G. N.; Parakkat, P.; Chitroceanu, A. M.; Tschoepe, C.; Edelmann, F.; Schiattarella, G. G.; Forslund, S. K.; Wilck, N.; Gotthardt, M.; Mertins, P.; Dechend, R.; Sawamiphak, S.; Kempa, S.; Muller, D. N.; Haase, N.

10.1101/2025.11.28.690152 — biochemistry — Posted on 2025-11-30

41 Deep Red Blood Cell Proteome Defines the Band 3 N-Terminus Interactome as a Regulator of Hypoxic Adaptation via BLVRB-Dependent S-Nitroso Transfer

Issaian, A. V.; Dzieciatkowska, M.; Bevers, S.; Zohreh, S.; Hay, A.; Saviola, A.; Redzic, J. S.; Reisz, J. A.; Keele, G. R.; Cendali, F. I.; Haiman, Z. B.; Nemkov, T.; Stephenson, D.; Lisk, C.; Vallese, F.; Palsson, B. O.; King, S. B.; Page, G. P.; Doctor, A.; Hudson, K. E.; Hansen, K. C.; Irwin, D. C.; Mohandas, N.; Zimring, J. C.; Eisenmesser, E. Z.; D'Alessandro, A.

10.1101/2025.11.29.691178 — biochemistry — Posted on 2025-11-30

42 Loss of STARD7 Impairs Mitochondrial Phospholipid Homeostasis and Contributes to Mitochondrial Myopathy

Horibata, Y.; Sato, T.; Ohyama, M.; Yuyama, S.; Itoh, M.; Miura, S.; Konishi, A.; Sugimoto, H.

10.1101/2025.11.27.691062 — biochemistry — Posted on 2025-11-30

43 Development of a New Approach Method to Monitor and Modify Caffeine Metabolism Correlated to CYP1A2 Expression

Chen, X.; Miyagi, M.; Tochtrop, G. P.

10.1101/2025.11.27.691042 — biochemistry — Posted on 2025-11-30

44 NET1/ARHGEF8 is a mechanosensitive Guanine Exchange Factor controlling vascular smooth muscle cells' contractility

Mrad, M.-A.; Batta, S. P. R.; Vignard, V.; Rio, M.; Gros, E.; Chadeuf, G.; Sauzeau, V.; Loirand, G.; Vion, A.-C.

10.1101/2025.11.26.690669 — cell biology — Posted on 2025-11-30

45 Cancers modulate p53 truncal neoantigen display to evade T cell detection

Haratani, K.; Reinhold, B.; Duke-Cohan, J. S.; Fahey, C. G.; Tan, K.; Mallis, R. J.; Gusev, A.; Kehl, K. L.; Luo, J.; Holliday, E. L.; Masi, D. J.; Karmazyn, A.; Zienkiewicz, K. J.; Hennessey, C. J.; Blasco, R. B.; Thai, T. C.; Gibbons, G. M.; Kivlehan, S.; Lizotte, P.; Paweletz, C. P.; Aguirre, A. J.; Ligon, K. L.; Chiarle, R.; Lang, M. J.; Barbie, D. A.; Reinherz, E. L.

10.1101/2025.11.26.690562 — immunology — Posted on 2025-11-30

46 Domain-specific decoupling of co-chaperone and ligase functions in STUB1 underlies biochemical and clinical heterogeneity in SCA48

Altinok, S.; Paulakonis, E.; Almeida, M. F.; Hwang, I.; Sanchez-Hodge, R.; DOvidio, C.; Roper, G.; Irons, G.; Vargas, E.; Peng, I.; Saeed, M.; Pathan, A.; Ronnebaum, S. M.; Shi, C.-h.; Ranek, M. J.; Scaglione, K. M.; Page, R. C.; Brown, N. G.; Schisler, J. C.

10.1101/2025.11.26.690709 — neuroscience — Posted on 2025-11-30

47 Loss of ESE3/EHF is sufficient to promote cell plasticity, transformation and androgen-independent status in the early stage of prostate carcinogenesis.

Albino, D.; Sandrini, G.; Musumeci, C.; Storelli, E.; Papa, G.; Impellizzieri, D.; Cacciatore, A.; Cassanmagnago, G. A.; Balla, A.; Mosole, S.; Civenni, G.; Rinaldi, A.; Jeronimo, C.; Henrique, R. M.; Bolis, M.; Catapano, C. V.; Carbone, G. M.

10.1101/2025.11.26.690649 — cancer biology — Posted on 2025-11-30

48 Orthosteric Molecular Glue Inhibits COP9 Signalosome with Substrate-Dependent Potency

Shi, H.; Wang, X.; Yu, C.; Mao, H.; Jiao, F.; Braitbard, M.; Shor, B.; Zhang, Z.; Hinds, T. R.; Cao, S.; Fan, E.; Schneidman-Duhovny, D.; Huang, L.; Zheng, N.

10.1101/2025.11.26.690573 — molecular biology — Posted on 2025-11-30

49 U7 small nuclear RNA splice-switching therapeutics for STMN2 and UNC13A in Amyotrophic Lateral Sclerosis

Mehta, P. R.; Solomon, T.; Pickles, S.; Harley, P.; Barioglio, M.; Schweingruber, C.; Marrero-Gagliardi, A.; Gao, Y.; Mattedi, F.; Barattucci, S.; Lin, L. T.-W.; Ryadnov, E.; Zanovello, M.; Cammack, A. J.; Isaacs, A.; Burrone, J.; Shaw, C. E.; Keuss, M. J.; Petrucelli, L.; Fratta, P.; Ruepp, M.-D.

10.1101/2025.11.26.690143 — neuroscience — Posted on 2025-11-30

50 Increasing TET expression and 5-hydroxymethylcytosine formation by a carbocyclic 5-aza-2'-deoxy-cytidine antimetabolite

Däther, M.; Peev, E.; Fröhlich, A.; Vick, B.; Fatourechi, S.; Gasparoni, G.; Heiss, M.; Pleintinger, C. C.; Bisong, E. A.; Hurmiz, H.; Guglielminotti, D.; Gärtner, Y. V.; Aumer, T.; Spiekermann, K.; Walter, J.; Jeremias, I.; Traube, F. R.; Carell, T.

10.1101/2025.11.26.690736 — cancer biology — Posted on 2025-11-30

51 UHRF1 Overexpression Generates Distinct Senescent States with Different Tp53 Dependencies

Magnani, E.; Chen, C.; Macchi, F.; Madakashira, B. P.; Randic, T.; McBain, I.; Sadler, K. C.

10.1101/2025.11.26.690503 — cancer biology — Posted on 2025-11-30

52 MAS cryoprobe enhances solid-state NMR signals of α-synuclein fibrils

Dickwella Widanage, M. C.; Perrone, B.; Saha, J.; Fu, R.; Struppe, J.; McGlinchey, R.; Lee, J.; Schurko, R.; Ramamoorthy, A.

10.1101/2025.09.20.677435 — biophysics — Posted on 2025-11-30

53 BeadBuddy: user-friendly, nanometer-scale registration of single-molecule imaging data

Clark, F. T.; Whitney, P. H.; Saiz, N.; Ziarno, A.; Lionnet, T.

10.1101/2025.11.25.690467 — biophysics — Posted on 2025-11-30

54 Somatostatin-expressing neurons regulate sleep deprivation and recovery

Kobayashi, K. T.; Taguchi, Y.-h.

10.1101/2025.10.10.681551 — bioinformatics — Posted on 2025-11-30

55 Clonal Hematopoiesis Associated with TP53 and DNMT3A Mutations Promotes Tissue Repair in Acute Cardiovascular Diseases

Pan, Y.; Meng, X.; Wang, C.; Zhou, W.; Zhou, Q.; Chi, J.; Barrier, B.; Martinez-Lemus, L.; Li, D.-P.; Liu, Z.; Kang, X.

10.1101/2025.11.23.690015 — cell biology — Posted on 2025-11-30

56 KANK2 at focal adhesion regulates their maintenance and dynamics, while at fibrillar adhesions it influences cell migration via microtubule-dependent mechanism

Stojanovic, N.; Rac, A.; Loncaric, M.; Tadijan, A.; Paradzik, M.; Acman, M.; Humphries, J. D.; Humphries, M. J.; Ambriovic-Ristov, A.

10.1101/2025.02.24.639831 — cell biology — Posted on 2025-11-30

57 In vivo functional profiling and structural characterisation of the human GLP1R A316T variant

El Eid, L.; Manchanda, Y.; Austin, G.; Deane-Alder, K.; Rujan, R.-M.; Mariam, Z.; Oqua, A. I.; Belousoff, M. J.; Bernardino de la Serna, J.; Sloop, K. W.; Rutter, G. A.; Montoya, A.; Withers, D. J.; Millership, S.; Bouzakri, K.; Jones, B.; Reynolds, C. A.; Sexton, P. M.; Wootten, D.; Deganutti, G.; Tomas, A.

10.1101/2024.10.19.619191 — cell biology — Posted on 2025-11-30

58 Progressive overfilling of readily releasable pool underlies short-term facilitation at recurrent excitatory synapses in layer 2/3 of the rat prefrontal cortex

Shin, J.; Lee, S. Y.; Kim, Y.; Lee, S.-H.

10.1101/2024.09.10.612266 — neuroscience — Posted on 2025-11-30

59 Oligodendrocyte precursor cells establish contacts with somata of active neurons

Sun, Y.; Jukkola, P.; Akinlaja, Y.; Garaschuk, O.; Pfeiffer, F.

10.1101/2025.03.28.646001 — neuroscience — Posted on 2025-11-30

60 Benign Taste Experience Enhances Cortical Response Reliability during Aversion Conditioning Towards a Novel Taste

Flores, V. L.; Barash, E.; Katz, D. B.; Lin, J.-Y.

10.1101/2023.12.19.572413 — neuroscience — Posted on 2025-11-30

61 Negative-Valence Neurons in the Larval Zebrafish Pallium

Smith, C. D.; Du, Z.; Dempsey, W. P.; Fraser, S. E.; Truong, T. V.; Arnold, D. B.

10.1101/2025.11.21.689820 — neuroscience — Posted on 2025-11-30

62 Designing minimal E. coli genomes using variational autoencoders

Shcherbakova, A.; Sharma, K.; Chen, Y.; Grierson, C.; Marucci, L.; Buchan, D.; Barnes, C. P.

10.1101/2024.10.22.619620 — synthetic biology — Posted on 2025-11-30

63 Mechanics and growth coordination define SOSEKI-based polarity fields

Piepers, M.; Reyes-Hernandez, B. J.; Ramos, J. R.; Boelke, N.; Schuetz, L.; Song, C.; Primc, A.; Bald, L.; Merks, R. M.; Weijers, D.; Maizel, A.

10.1101/2025.11.26.690761 — plant biology — Posted on 2025-11-30

64 HIF-1α and HIF-2α transcription factors differentially regulate lung alveolar macrophage function

Priego, E.; Adan-Barrientos, I.; Conde-Garrosa, R.; Martinez-Cano, S.; Sanchez, I.; Mananes, D.; Mastrangelo, A.; Amores, J.; Izquierdo, H. M.; Sancho, D.

10.1101/2025.11.25.690373 — physiology — Posted on 2025-11-30

65 Sketch, capture and layout phylogenies

Huson, D.

10.1101/2025.04.01.646633 — bioinformatics — Posted on 2025-11-30

66 TSAR, Thermal Shift Analysis in R, identifies endogenous molecules that interact with HIV-1 capsid hexamers

McFadden, W. M.; Gao, X.; Ye, Z.; Wen, X.; Lorson, Z. C.; Zhang, H.; Fahim, J.; Emanuelli, A.; Kirby, K. A.; Sarafianos, S. G.

10.1101/2023.11.29.569293 — biochemistry — Posted on 2025-11-30

67 Genetic prediction with ARG-powered linear algebra

Lee, H.; Pope, N. S.; Kelleher, J.; Gorjanc, G.; Ralph, P. L.

10.1101/2025.07.14.664631 — genomics — Posted on 2025-11-30

68 LoGicAl: Local ancestry and genotype calling uncertainty-aware ancestry-specific allele frequency estimation from admixed samples

Wang, J.; Zöllner, S.

10.1101/2025.07.01.662683 — genetics — Posted on 2025-11-30

69 Comparative genomics of Sympodiorosea identifies genome evolution mediated through selective pressure on the metabolic gene repertoire

Robinson, J. C.; Berasategui, A.; Montoya, Q.; Rodrigues, A.; Christopher, Y.; Fernandez-Marin, H.; Read, T. D.; Gerardo, N. M.

10.1101/2025.11.25.690603 — evolutionary biology — Posted on 2025-11-30

70 Genomic rearrangements rewire chromatin contacts and drive adaptive gene expression divergence in mammals

Bhattacharya, J.; Lal, M.; Sandhu, K. S.

10.1101/2025.08.10.669527 — evolutionary biology — Posted on 2025-11-30

71 Structural Genomic Variation and Its Potential Role In Deer Speciation

Azimi Chetabi, F.; Shafer, A.

10.1101/2025.04.23.650217 — evolutionary biology — Posted on 2025-11-30

72 Chromatin accessibility differences between the hybrids of nasuta-albomicans complex of Drosophila

Padma, R.; Patil, A. B.; Vijay, N.

10.1101/2025.06.26.661782 — evolutionary biology — Posted on 2025-11-30

73 Latent gene network expression underlies partial re-evolution of a polyphenic trait in the worker caste of ants

Vasquez-Correa, A.; Arnet, J.; Chen, T.; Abouheif, E.

10.1101/2025.11.19.689334 — evolutionary biology — Posted on 2025-11-30

74 Environmental fluctuations alter the competitive trade-offs of group size in a social primate

Jacobson, O. T.; Crofoot, M. C.; Finerty, G. E.; Barrett, B. J.; Perry, S. E.

10.1101/2025.08.12.669921 — ecology — Posted on 2025-11-30

75 Integrating fish biology, population genomics and fishery policies for informed management of interjurisdictional multi-species fisheries

Gangal, M.; Arthur, R.; Suri, V.; Pandit, A.; Tyagi, A.; Prakash, P.; Sule, M.; Majgaonkar, I.; Krishnaswamy, J.; Ramakrishnan, U.

10.1101/2024.07.12.603026 — ecology — Posted on 2025-11-30

76 NeMO: a flexible R package for nested multi-species occupancy modelling and eDNA study optimization

Mace, B.; Manel, S.; Valentini, A.; Rocle, M.; Roset, N.; Delrieu-Trottin, E.

10.1101/2025.05.23.655794 — ecology — Posted on 2025-11-30

77 Seasonality, land use, and host diversity shape microbiome-pathogen interactions in wild populations of Arabidopsis thaliana

Henry, L. P.; Rat, A.; Laderman, E.; Lion, R.; Mayjonade, B.; TEAM PATHOCOM, ; Roux, F.; Weigel, D.; Bergelson, J.

10.1101/2025.06.29.662221 — ecology — Posted on 2025-11-30

78 Progranulin deficiency aggravates aging-induced vascular injury

Luvizotto, R. A. M.; Nascimento, A. F.; Costa, R. M.; Pimenta, G. F.; Singh, S.; Awata, W. M. C.; Russ, A.; Haastrup, A.; Cuevas, R. A.; Behzadi, P.; St. Hilaire, C.; Roberts, J.; Bruder, A.; Bruder-Nascimento, T.

10.1101/2025.11.25.690611 — cell biology — Posted on 2025-11-30

79 PHD1-dependent hydroxylation of RepoMan (CDCA2) on P604 modulates the control of mitotic progression

Druker, J.; Jiang, H.; Shakir, D.; Child, F.; Alvarez, V.; Platani, M.; Corno, A.; Alabert, C.; Saurin, A. T.; Swedlow, J. R.; Rocha, S.; Lamond, A. I.

10.1101/2025.05.06.652400 — cell biology — Posted on 2025-11-30

80 Oscillatory and elevated flow distinctly regulate gene expression in human coronary artery endothelial cells

Vidotto, G.; Luzzi, S.; Humphries, J.; Beal, R.; McVey, D. G.; Nelson, C. P.; Webb, T. R.; Humphries, M.; Smith, G.; White, S. J.

10.1101/2025.10.10.681055 — cell biology — Posted on 2025-11-30

81 Rescue from pyridostatin-stabilized telomeric G-quadruplexes by DNA cleavage and microhomology-mediated end joining

Matmati, S.; Rao, S.; Lingner, J.

10.1101/2025.11.25.690390 — molecular biology — Posted on 2025-11-30

82 Dual function of ERH in primary miRNA biogenesis

Herzog, S.; Aschenwald, S.; Panda, A. K.; Wurzer, T.; Baumgaertner, S.; Ertl, V. S.; Hatzer, J.; Villunger, A.; Falk, S.

10.1101/2025.09.23.678008 — molecular biology — Posted on 2025-11-30

83 Environmentally mediated interactions predict community assembly and invasion success in a gut microbiota SynCom

van Leeuwen, P. T.; Gadaleta, P.; Brul, S.; Seppen, J.; Wortel, M. T.

10.1101/2024.07.15.603569 — microbiology — Posted on 2025-11-30

84 Reduced gravity and muon flus absence affect Caenorhabditis elegans life history traits and viral infection

Villena-Gimenez, A.; Castiglioni, V. G.; Legarda, E. G.; Munoz-Sanchez, J. C.; Gonzalez, R.; Elena, S. F.

10.1101/2024.10.03.616447 — microbiology — Posted on 2025-11-30

85 Metagenomic Profiling of Bacterial (16S) and Fungal (ITS) Communities on D'Anjou Pears during Long-Term Controlled Atmosphere Storage

Raad, R.; Mann, A.; Pal, A.; Parra, A.; Strawn, L.; Hamilton, A.; Critzer, F.; den Bakker, H. C.

10.1101/2025.11.26.690795 — microbiology — Posted on 2025-11-30

86 Enhancing microalgal productivity through bioactive substances, light, and CO2

Herrera, N.; Llanes, A.; Quinones, W.

10.1101/2025.11.26.690871 — microbiology — Posted on 2025-11-30

87 Undecaprenyl Pyrophosphate Phosphatase (UppP) is a pivotal element in Salmonella Intramacrophage Survival

Vij, R.; Mukherjee, D.; Parmar, K.; Nallamotu, K. C.; Reddy, M.; Chakravortty, D.

10.1101/2025.04.24.650467 — microbiology — Posted on 2025-11-30

88 Brainwide blood volume reflects opposing neural populations

Landemard, A.; Krumin, M.; Harris, K. D.; Carandini, M.

10.1101/2025.07.01.662538 — neuroscience — Posted on 2025-11-30

89 Delineating In-Vivo T1-Weighted Intensity Profiles Within the Human Insula Cortex Using 7-Tesla MRI

Dalby, C.; Dibble, A. J.; Carvalheiro, J.; Queirazza, F.; Sevegnani, M.; Harvey, M.; Svanera, M.; Fracasso, A.

10.1101/2024.08.05.605123 — neuroscience — Posted on 2025-11-30

90 Linking Electrophysiological Metrics to Oxidative Metabolism: Implications for EEG-fMRI Association

Zhong, X.; Van Lankveld, H.; Mathew, A.; Chen, J. J.

10.1101/2025.11.04.686568 — neuroscience — Posted on 2025-11-30

91 Preclinical Evaluation of a Zotarolimus-Eluting Stent for Intracranial Application: A 30-Day GLP Canine Study

Bhatti, I. A.; Jumah, F.; Gillani, S. A.; Nunna, R.; Khan,, I.; Rolfes, A.; Jagadeesan, B. D.; Hassan, A. E.; Qureshi, A. I.; Siddiq, F.

10.1101/2025.11.25.690612 — neuroscience — Posted on 2025-11-30

92 One-step induction of human GABAergic neurons promotes presynaptic development & synapse maturation

van Voorst, T. W.; van boven, M. A.; Marinus, K. I.; Colon-Mercado, J. M.; Schretzmeir, J.; Haag, C.; Toonen, R. F.; Koopmans, F.; Ward, M.; Smit, A. B.; van Kesteren, R. E.; Verhage, M.; Cornelisse, L. N.

10.1101/2025.06.30.662293 — neuroscience — Posted on 2025-11-30

93 Lack of Oncomodulin Increases ATP-Dependent Calcium Signaling and Susceptibility to Noise in Adult Mice

Yang, Y.; Jeng, J.-Y.; Murtha, K.; Climer, L.; Ceriani, F. E.; Sese, W. D.; Hornak, A. J.; Sleiman, K. C.; Stahl, I.; Liberman, M. C.; Marcotti, W.; Simmons, D. D.

10.1101/2024.06.10.598303 — neuroscience — Posted on 2025-11-30

94 Transcranial magnetic stimulation of the occipital cortex interferes with foot movements in acquired but not congenitally blind individuals

Ikegami, T.; Miura, G.; Hirashima, M.; Naito, E.; Hirose, S.

10.1101/2021.08.03.454870 — neuroscience — Posted on 2025-11-30

95 Task-optimized models of sensory uncertainty reproduce human confidence judgments

Govindarajan, L. N.; Alavilli, S.; McDermott, J. H.

10.1101/2025.10.31.685933 — neuroscience — Posted on 2025-11-30

96 Reinforcement learning enhances training efficiency in high-performance athletes

Magelssen, C.; Gilgien, M.; Tajet, S. L.; Losnegard, T.; Haugen, P.; Reid, R.; Frömer, R.

10.1101/2024.04.22.590558 — neuroscience — Posted on 2025-11-30

97 White matter microstructure and macrostructure brain charts across the human lifespan

Kim, M. E.; Gao, C.; Ramadass, K.; Newlin, N. R.; Kanakaraj, P.; Bogdanov, S.; Rudravaram, G.; Archer, D.; Hohman, T. J.; Jefferson, A. L.; Morgan, V. L.; Roche, A.; Englot, D. J.; Resnick, S. M.; Beason-Held, L. L.; Cutting, L.; Barquero, L. A.; D'arcangel, M. A.; Nguyen, T. Q.; Humphreys, K. L.; Niu, Y.; Vinci-Booher, S.; Cascio, C. J.; The HABS-HD Study Team, ; Alzheimers Disease Neuroimaging Initiative, ; The BIOCARD Study Team, ; Davis, L. T.; Li, Z.; Vandekar, S. N.; Zhang, P.; Gore, J. C.; Landman, B. A.; Schilling, K. G.

10.1101/2025.05.08.652953 — neuroscience — Posted on 2025-11-30

98 Attention to Speech Modulates Distortion Product Otoacoustic Emissions Evoked by Speech-derived Stimuli in Humans

Steinebach, J.; Reichenbach, T.

10.1101/2025.08.15.670505 — neuroscience — Posted on 2025-11-30

99 Investigating Age-Related Decline in Sensorimotor Control Using Robotic Tasks

Alvarez-Hidalgo, L.; Edlmann, E.; Schmidtmann, G.; Howard, I. S.

10.1101/2025.07.07.663471 — neuroscience — Posted on 2025-11-30

100 Navigating uncertainty: reward location variability induces reorganization of hippocampal spatial representations

Tessereau, C.; Xuan, F.; Chen, Z.; MELLOR, J. R.; Dayan, P.; Dombeck, D. A.

10.1101/2025.01.06.631465 — neuroscience — Posted on 2025-11-30

101 Individual Taste Preferences Predict Cortical Taste Dynamics but Are Modified by Experience

Maigler, K. C.; Lin, J.-Y.; Crouse, E.; Stone, B. T.; Craddock, A. E.; Katz, D. B.

10.1101/2024.04.02.587752 — neuroscience — Posted on 2025-11-30

102 CMV can spread through plant to plant contact: implications for experimental practices

Chateau, L.; Szadkowski, M.; Theodore, J.; Rimbaud, L.

10.1101/2025.07.30.667662 — plant biology — Posted on 2025-11-30

103 GABA Neurons in the Amygdala play a central Role in Urocortin-3-Mediated Stress Suppression of Reproduction

Yu, J.; Farjami, S.; Nechyporenko, K.; Li, X. F.; Yaseen, H.; Lin, Y.; Ye, J.; Hollings, O.; de Burgh, R.; Singh, B.; O'Byrne, K. T.; Tsaneva-Atanasova, K.; Voliotis, M.

10.1101/2025.01.06.631361 — physiology — Posted on 2025-11-30

104 CXCL16 mediates nociception and inflammation in murine post-traumatic osteoarthritis

Lammlin, L.; Redding, S.; Knights, A. J.; Mohan, A.; Newton, M. D.; Bergman, R. F.; Smith, I. J.; Howser, S. C.; Gonzalez-Nolde, S.; Rzeczycki, P. M.; Adamczyk, N. S.; Miller, R. E.; Maerz, T.

10.1101/2025.04.10.647297 — physiology — Posted on 2025-11-30

105 Brief and localized pulsed transcranial photobiomodulation cumulatively increases EEG power across the brain in healthy young adults

Mathew, A. A.; Van Lankveld, H.; Zhong, X. Z.; Chen, J. X.; Niculescu, S.; Zomorrodi, R.; Chen, J. J.

10.1101/2025.05.26.656199 — physiology — Posted on 2025-11-30

106 Inactivation of a protein hydroxylase complex impairs replication fork restart in cancer and neurodevelopmental disorders

Kennedy, T. J.; Fletcher, S.; Boora, U.; Fraser-Williams, E.; Kaur, A.; Hughes, G. W.; Hendrix, E.; Morris, J. R.; Smerdon, S. J.; Coleman, M.

10.1101/2025.11.22.689938 — cancer biology — Posted on 2025-11-30

107 Comparative analysis of morphological and acoustic correlates of bush-cricket tympanic membranes

Islam, M. N.; Holmes, L. B.; Rooke, D.; Sarria-S, F. A.; Montealegre-Z, F.

10.1101/2025.11.11.687687 — biophysics — Posted on 2025-11-30

108 Reliable Identification of Homodimers Using AlphaFold

Danielsson, S. N.; Elofsson, A.

10.1101/2025.11.27.691011 — bioinformatics — Posted on 2025-11-30

109 ORANGE: A Machine Learning Approach for Modeling Tissue-Specific Aging from Transcriptomic Data

Jalal, W.; Musarrat, M.; Samee, M. A. H.; Rahman, M. S.

10.1101/2025.05.02.651895 — bioinformatics — Posted on 2025-11-30

110 MIMEco: Multi-objective metabolic modeling to predict and explain pairwise interactions

Lambert, A.; Chaffron, S.; Eveillard, D.

10.1101/2025.11.25.690486 — bioinformatics — Posted on 2025-11-30

111 ELITE: E3 Ligase Inference for Tissue specific Elimination: A LLM Based E3 Ligase Prediction System for Precise Targeted Protein Degradation

Patjoshi, S.; Froehlich, H.; Madan, S.

10.1101/2025.11.05.686884 — bioinformatics — Posted on 2025-11-30

112 A Micro-Engineered Heart Tissue Model of Desmin-related Cardiomyopathy Caused by Mutant αB Crystalin

Kargar Gaz Kooh, Y.; Bahmani, B.; Zhao, C.; Malayath, G.; Hayem, L.; Jin, H.; Ramahdita, G.; Jiang, H.; Santiago Perez, J.; Chou, H.-Y.; Huang, Y.; Ma, X.; Genin, G. M.; Rawnsley, D.; Diwan, A.; Huebsch, N.

10.1101/2025.10.02.680018 — bioengineering — Posted on 2025-11-30

113 Structural insights into cobalamin loading and reactivation of human methionine synthase

Ferreira, D. S. M.; McLennan, K.; Diamond, C.; Vollmar, M.; Kiyani, W.; Froese, D. S.; Kopec, J.; Bailey, H. J.; Chalk, R.; Basle, A.; Elkins, J. M.; Coker, J. A.; Yue, W.; McCorvie, T. J.

10.1101/2025.11.10.687659 — biochemistry — Posted on 2025-11-30

114 Are human super-predators always super-scary? A meta-analysis of wild animal behavioural responses to human interactions

Dsouza, S.; Shanker, K.; Thaker, M.

10.1101/2024.08.27.609826 — animal behavior and cognition — Posted on 2025-11-30

115 Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations

Dillard, L. J.; Calabrese, G. M.; Mesner, L. D.; Farber, C. R.

10.1101/2024.05.20.594981 — genomics — Posted on 2025-11-30

116 Epigenomic and transcriptomic germ-free ageing atlas reveals sterile inflammation as an intrinsic ageing feature

Nijen Twilhaar, W.; Chang, J.-C.; Terooatea, T. W.; Yabukami, H.; Kato, S.; Hetherington, N.; Satoh-Takayama, N.; Ahmadi, A.; Hsieh, T.-H.; Jeyamohan, P.; Kageyama, T.; Lan, Y. J.; Kadono-Maekubo, N.; Maeda, S.; Miyajima, Y.; Mochizuki, M.; Motomura, Y.; Nakanishi, Y.; Rother, N.; Tahara, U.; Takeno, N.; Tsutsui, K.; Vilaseca Barcelo, M.; Wang, H.; Amagai, M.; Fujiwara, H.; Hon, C. C.; Matsui, T.; Moro, K.; Nourshargh, S.; Ohno, H.; Minoda, A.

10.1101/2025.11.19.689100 — genomics — Posted on 2025-11-30

117 The effects of host phylogenetic coverage and congruence metric on Monte Carlo-based null models of phylosymbiosis

DuBose, J. G.

10.1101/2025.02.07.637028 — evolutionary biology — Posted on 2025-11-30

118 Old growth attributes by chain saw: how between-patch heterogeneity changes the metacommunities of beetles in temperate forests

Mitesser, O.; Cadotte, M.; Mori, A. S.; van der Plas, F.; Chao, A.; Rothacher, J.; Baessler, C.; Bevanda, M.; Biedermann, P. H. W.; Bradler, P. M.; Gomez, A. C.; Decker, O.; Delory, B. M.; Dittrich, S.; Feldhaar, H.; Fichtner, A.; Kreis, A.; Koestler-Albert, L.; Lettenmaier, L.; von Oheimb, G.; Pflumm, L.; Pierick, K.; Jakob Schwalb-Willmann, J.; Thorn, S.; Vogelfaenger, L.; Weisser, W.; Wegmann, M.; Wild, C. M.; Mueller, J.

10.1101/2025.08.30.673209 — ecology — Posted on 2025-11-30

119 Large-scale identification of plasma membrane repair proteins revealed spatiotemporal cellular responses to plasma membrane damage

Yamazaki, Y.; Kono, K.

10.1101/2024.10.15.618344 — cell biology — Posted on 2025-11-30

120 The Senescence-Associated Secretory Phenotype constitutes HIF-1α activation but is independent of micronuclei-induced cGas/Sting activation

Ho, C.; Deng, L.; Picone, R.; Abderazzaq, F.; Flanagan, N.; Chua, D.; Low, B. C.; Wu, S. K.

10.1101/2024.09.25.615081 — cell biology — Posted on 2025-11-30

121 Membrane affinity difference between MinD monomer and dimer is not crucial for MinD gradient formation in Bacillus subtilis

Bohorquez, L.; Strahl, H.; Marenduzzo, D.; Thiele, M.; Burmann, F.; Hamoen, L. W.

10.1101/2024.06.11.598461 — microbiology — Posted on 2025-11-30

122 NDNF+ interneurons have a privileged role in regulating cortical excitability

Richardson, A.; Mercier, M. S.; Shimoda, Y.; Graham, R. T.; Leite, M.; Garcia, A.; Muller, M.; Bond, S. A.; Grodzdanova, M.; Wu, Q.; Lieb, A.; Kullmann, D. M.; Magloire, V.

10.1101/2025.11.27.690945 — neuroscience — Posted on 2025-11-30

123 A summary of intraspecific size variation for large mysticetes

McClure, J.

10.1101/2025.02.07.637173 — zoology — Posted on 2025-11-30

124 Structure, function and dynamics of mCoral, a pH responsive engineered variant of the mCherry fluorescent protein with improved hydrogen peroxide tolerance.

Zitti, A.; Aksakal, O.; Vitsupakorn, D.; Rizkallah, P.; Makolajeck, H.; Platts, J.; Menzies, G.; Jones, D.

10.1101/2025.11.26.690718 — biochemistry — Posted on 2025-11-30

125 An ancient transcription factor functions as the master regulator of primary cilia formation

Wang, W.; Zhang, X.; Qiu, Y.; Meng, X.; Cheng, S.; Chen, Y.; liu, S.; Chen, W.; Yi, J.; You, X.; Liu, H.; Xing, J.; Xu, C.; Jiang, H.; Wang, H.; Tian, G.; Hu, Z.

10.1101/2025.11.28.691250 — cell biology — Posted on 2025-11-29

126 Early-life stromal niches orchestrate B lymphopoiesis at the brain's borders

Walker, A. J.; Fisher, T. M.; Caldwell, S. K.; Gupte, A. S.; Colville-Reimertz, J. M.; Sabikunnahar, B.; Marsh, S. E.; de Soysa, Y.; Gazestani, V. H.; Walker, A. C.; Huang, Y.; Mavinkurve, A. V.; Barr, H. J.; Lanser, T. B.; Murphy, S.; Bowling, S.; Dissing-Olesen, L.; Camargo, F. D.; Stevens, B.

10.1101/2025.11.27.690844 — immunology — Posted on 2025-11-29

127 Predicting functional topography of the human visual cortex from cortical anatomy at scale

Ribeiro, F. L.; Satzger, R.; Hoffstaedter, F.; Burger, C.; Herholz, P.; Linhardt, D.; Benson, N. C.; Schwarzkopf, D. S.; Puckett, A. M.; Bollmann, S.; Hebart, M. N.

10.1101/2025.11.27.690210 — neuroscience — Posted on 2025-11-29

128 Top-down feedback can explain the existence of working memory traces in early visual cortex

Krause, N. N.; Compte, A.; Rademaker, R. L.

10.1101/2025.11.27.690959 — neuroscience — Posted on 2025-11-29

129 High-Frequency Activity Encodes the Temporal Dynamics of Hierarchical Prediction Errors in Humans: An Electrocorticography Study

Huang, Y. T.; Chen, Y.-Y.; Fujitani, S.; Shimada, S.; Koike, S.; Kunii, N.; Saito, N.; Chao, Z. C.

10.1101/2025.11.29.691270 — neuroscience — Posted on 2025-11-29

130 Flexible selection of working memory representations to reduce cognitive cost

Li, J.; Xu, A. Z.; Bao, C.; Albesa-Gonzalez, A.; Li, L.; Clopath, C.; Erlich, J. C.

10.1101/2025.11.28.691186 — neuroscience — Posted on 2025-11-29

131 Integrated proteogenomics uncovers ancestry-specific and shared molecular drivers in localized prostate cancer

Schafer, C. C.; Abulez, T. S.; Zhang, X.; Ho, K.-L.; Jiang, J.; Young, D.; Fox, J.; Conrads, K. A.; Hood, B. L.; Sukumar, G.; Nousome, D.; Raj-Kumar, P.-K.; Russo, M.; Shafi, A. A.; Su, X. A.; Dobi, A.; Ali, A.; Elsamanoudi, S.; Cullen, J.; Figg, W. D.; Petrovics, G.; Dalgard, C. L.; Wilkerson, M. D.; Bateman, N. W.; Conrads, T. P.; Sesterhenn, I. A.; APOLLO Research Network, ; Ellis, L.; Shriver, C. D.; Chesnut, G. T.; Tan, S.-H.

10.1101/2025.11.28.691220 — cancer biology — Posted on 2025-11-29

132 Optimizing marker density for maximizing the accuracy of genomic prediction and heritability estimates in three major North American and European spruce species

Soro, A.; Lenz, P.; Beaulieu, J.; Laverdiere, J.-P.; Nadeau, S.; Gagnon, F.; Ogut, F.; Wu, H.; Perron, M.; Bousquet, J.

10.1101/2025.11.28.691168 — genomics — Posted on 2025-11-29

133 Coexistence of piRNA and KZFP Defense Systems: Evolutionary Dynamics of Layered Defense against Transposable Elements

Nabeka, Y.; Innan, H.

10.1101/2025.11.27.690821 — evolutionary biology — Posted on 2025-11-29

134 Recurrent expansion and rapid evolution of the Drosophilid RNAi pathway in testis

Elicker, K.; Setia, G.; Quraishi, M.; Jiang, X. Y. Z.; Kan, L.; Flynt, A. S.; Wen, J.; Wahba, L.; Lai, E. C.

10.1101/2025.11.28.691189 — evolutionary biology — Posted on 2025-11-29

135 Gut microbiota variation across sympatric stingless bee species and honey bees in the Neotropics

Haag, K. L.; Stein, L. Q.; Nunes-Silva, C. G.; Mazel, F.; Prasad, A.; Engel, P.

10.1101/2025.11.29.691224 — ecology — Posted on 2025-11-29

136 Unraveling the archaeal virosphere: diversity, functional and virus-host interactions

Zhao, Y.; Liu, P.; Feng, M.; Wen, R.; Zhang, Z.; Zhang, X.; Huang, X.; Chi, H.

10.1101/2025.11.27.691053 — ecology — Posted on 2025-11-29

137 C-terminal lysine residues localise NLRP10 at lipid compartments and govern NLRP10 oligomer formation

Voss, T.-D.; Winterberg, C.; Beck, A.; Gottschild, C.; Mueller, L.; Enayat, S. M.; Geyer, M.; Kufer, T. A.

10.1101/2025.11.27.690698 — immunology — Posted on 2025-11-29

138 High-throughput phenomics of global ant biodiversity

Katzke, J.; Hita Garcia, F.; Loesel, P. D.; Azuma, F.; Farago, T.; Aibekova, L.; Casadei-Ferreira, A.; Gautam, S.; Richter, A.; Toulkeridou, E.; Bremer, S.; Hamann, E.; Hein, J.; Odar, J.; Sarkar, C.; Zuber, M.; Boomsma, J. J.; Feitosa, R. M.; Schrader, L.; Zhang, G.; Csosz, S.; Dong, M.; Evangelista, O.; Fischer, G.; Fisher, B. L.; Florez-Fernandez, J. A.; The GAGA Consortium, ; Garcia, F.; Gomez, K.; Grasso, D. A.; De Greef, S.; Guenard, B.; Hawkes, P. G.; Johnson, R. A.; Keller, R. A.; Larsen, R. S.; Linksvayer, T. A.; Liu, C.; Matte, A.; Ogasawara, M.; Ran, H.; Rodriguez, J.; Schifani, E.

10.1101/2025.11.29.689474 — zoology — Posted on 2025-11-29

139 Identifying phenotype-genotype-function coupling in 3D organoid imaging using Shape, Appearance and Motion Phenotype Observation Tool (SPOT)

Zhou, F. Y.; Jacobs, B.-A.; Norton-Steele, A.; Han, X.; Zhou, L.; Carroll, T. M.; Ruiz Puig, C.; Chadwick, J.; Qin, X.; Lisle, R.; Marsh, L.; Byrne, H.; Harrington, H.; Lu, X.

10.1101/2025.11.28.691111 — cancer biology — Posted on 2025-11-29

140 ATHENA: A deep learning-based AI for functional prediction of genomic mutations and synergistic vulnerabilities in prostate cancer

CHENG, S.; Jin, X.; Qian, J.; Jiang, Y.; Kim, I.; Deng, S.; Mu, P.

10.1101/2025.11.26.690813 — cancer biology — Posted on 2025-11-29

141 Estimating fitness effects of mutations in the presence of genetic linkage

Lagunov, S. V.; Rouzine, I. M.

10.1101/2025.11.26.690712 — genomics — Posted on 2025-11-29

142 Hierarchical taxonomic constraints shape bacterial nitrogen cycling across functional and molecular scales

Mingli, J.; Yanni, H.; Zhiming, W.; Qian, Z.; Qian, L.; Kaihua, P.; Mingliang, Z.; Liang, S.; Jiguo, Q.; Pengfa, L.; Yan, X.; Yiyong, Z.; qing, h.

10.1101/2025.11.26.690687 — genomics — Posted on 2025-11-29

143 Chromosome-Level Genome Assembly of Southern Africa Mozambique Tilapia (Oreochromis mossambicus) using PacBio HiFi and Omni-C sequencing

TSHILATE, T. S.; Nesengani, L. T.; Mdyogolo, S.; Smith, R. M.; Molotsi, A. H.; Masebe, T.; Mapholi, N.

10.1101/2025.11.27.690999 — genomics — Posted on 2025-11-29

144 Differential chromatin accessibility between pre- and post-natal stages highlights putative causal regulatory variants in pig skeletal muscle

Shishmani, E.; Rau, A.; Djebali, S.; Clark, E. L.; Estelle, J.; Palombo, V.; D'Andrea, M.; Giuffra, E.

10.1101/2025.11.27.690935 — genomics — Posted on 2025-11-29

145 Off-target effects as confounders of Cas13d-based lncRNA screens

Montero, J. J.; Trozzo, R.; Rad, R.

10.1101/2025.11.27.690751 — genomics — Posted on 2025-11-29

146 The genomic landscape of asymmetric introgression tracks chromosomal characteristics in tinamous (Aves: Tinamidae)

Musher, L. J.; Thom, G.; Catanach, T. A.; Valqui, T.; Brumfield, R. T.; Aleixo, A.; Johnson, K. P.; Weckstein, J. D.

10.1101/2025.11.26.690533 — genomics — Posted on 2025-11-29

147 Admixture in a butterfly species complex creates a genomic mosaic of ancestry with distinct histories for different chromosomes

Gompert, Z.; Lucas, L. K.; Donley, A.; Foriser, M. L.; Fordyce, J. A.; Nice, C. C.

10.1101/2025.11.28.691233 — evolutionary biology — Posted on 2025-11-29

148 Contrasting evolutionary forces of specialization and admixture underlie the genomic and phenotypic diversity of Yarrowia lipolytica

Izquierdo-Gea, S.; Vicente, J.; Pena, T. A.; Villarreal, P.; Cubillos, F. A.; Neuveglise, C.; Barriuso, J.; Belda, I.; Ruiz, J.

10.1101/2025.11.28.690175 — evolutionary biology — Posted on 2025-11-29

149 Splendid isolation with migration: Diversity dynamics of South American mammals

Pino, K.; Rodriguez-Serrano, E.; Carrillo, J. D.; Cooper, R. B.; Silvestro, D.

10.1101/2025.11.28.691169 — evolutionary biology — Posted on 2025-11-29

150 Gene flow weakens genomic clines while selection maintains adaptive loci: two decades of evolution in Drosophila melanogaster natural populations

Horvath Miranda, V.; da Silva Ribeiro, T.; Alves, J. M.; Eanes, W. F.; Brud, E.; Veeramah, K. R.; Pool, J. E.; Rodrigues, M. F.; Cogni, R.

10.1101/2025.11.28.691231 — evolutionary biology — Posted on 2025-11-29

151 Antibiotic production reduces the cost of resource cheaters in Streptomyces coelicolor

Theinert, L.; Norte, D.; Veugelers, B.; Veit, L.; Avitia-Dominguez, L. A.; Rozen, D.

10.1101/2025.11.28.691120 — evolutionary biology — Posted on 2025-11-29

152 Global gaps and priorities for shark and ray conservation: Integrating threat, function, and evolutionary distinctiveness

Mouton, T. L.; Silvestro, D.; Kocakova, K.; Spitznagel, D.; Leprieur, F.; Pimiento, C.

10.1101/2025.11.28.691085 — ecology — Posted on 2025-11-29

153 Development and Characterisation of Equine Gastric Organoids

Harte, T.; Todd, H.; Moore, J.; Burgess, S.; Wells, B.; Smith, D.

10.1101/2025.11.28.690112 — cell biology — Posted on 2025-11-29

154 Alternative Anastrozole Target CYP4V2 Impairs Neurons in Preclinical Models of Inherited Tauopathy

Pedicone, C.; Weitzman, S.; Orrick, J.; Pugh, D.; Goate, A. M.; Cagan, R.; Bowles, K.; Sonoshita, M.

10.1101/2025.11.29.689498 — neuroscience — Posted on 2025-11-29

155 AAV-mediated regeneration of neurons in injury-induced and inherited retinal degeneration

Yang, M.; Awad, S.; Chung, A.; Dang, J.; Chong, M.; Flickinger, Z.; Wong, K. W. Y.; Hoang, T.

10.1101/2025.11.28.688728 — neuroscience — Posted on 2025-11-29

156 ONCOchannelome: A computational framework to investigate altered ion channels across tumor types

Parthasarathi, K. T. S.; Ramu, S.; Jolly, M. K.; Sharma, J.

10.1101/2025.11.27.685767 — bioinformatics — Posted on 2025-11-29

157 Modular Nanobody Conjugates with Controlled Topology Using Genetically Encoded Non-canonical Amino Acids

Adomanis, R.; Phan, N.; Walter, G.; Kimmel, B. R.

10.1101/2025.11.27.691038 — bioengineering — Posted on 2025-11-29

158 Exploring the Persistence of Transgenes in Genetically Engineered Cyanobacteria

Barnes, C. L.; Lee, J. W.; Greene, L. H.

10.1101/2025.11.26.690176 — genomics — Posted on 2025-11-29

159 PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA

Del Vecchio, A.; Kapourani, C.-A.; Athar, A. M.; Dobrowolska, A.; Anighoro, A.; Tenmann, B.; Edwards, L.; Regep, C.

10.1101/2025.11.28.691095 — genomics — Posted on 2025-11-29

160 Quantitative Logics for Directed Evolution of an Asexual Population

Park, K.

10.1101/2025.11.27.690992 — evolutionary biology — Posted on 2025-11-29

161 Rooting the deep divergence of land plants

Chen, H.; de Vries, J.

10.1101/2025.11.29.691271 — evolutionary biology — Posted on 2025-11-29

162 sept-1/zina-1 is an Ancient Toxin-Antidote System in Caenorhabditis elegans

Liu, D.; Zheng, C.

10.1101/2025.11.28.691152 — evolutionary biology — Posted on 2025-11-29

163 Accessible AI Enhances Monitoring of Coral Seeding Devices in Reef Restoration

Stratford, J. E.; Toor, M.; Forster, R.; Larkey, E.; Martinez Balvanera, S.; Williams, B.; Alessi, C.; Cassidy, D.; Razak, T. B.; Humanes, A.; Lachs, L.; Martinez, H.; Jones, K. E.; Guest, J.; Ferarri, R.

10.1101/2025.11.27.688254 — ecology — Posted on 2025-11-29

164 Engineering Clostridium thermocellum for production of 2,3-butanediol from cellulose

Jilani, S. B.; Ashok, N.; Guss, A. M.; Olson, D. G.

10.1101/2025.11.28.691234 — synthetic biology — Posted on 2025-11-29

165 Optimization of heuristic logic synthesis by iteratively reducing circuit substructures using a database of optimal implementations

Tran, A. P.; Jatkar, D. D.; Ali Al-Radhawi, M.; Ernst, E. A.; Sontag, E. D.

10.1101/2025.11.28.691216 — synthetic biology — Posted on 2025-11-29

166 Old Collections, New Perspectives: Analytical Reassessment of One of Europe's Biggest Archaeological Broomcorn Millet Deposits (Romania)

Garcia-Vazquez, A.; Golea, M.; Mircea, C.; Carciumaru, M.; Sava, G.; Ilie, A.; Lazar, C.

10.1101/2025.11.26.690670 — paleontology — Posted on 2025-11-29

167 Can We Extract Physics-like Energies from Generative Protein Diffusion Models?

Sarma, S. S.; Truscott, H. H.; Xu, D.; Reid, K.; Chu, L.-S.; Chen, J.; Gray, J. J.

10.1101/2025.11.28.690021 — biophysics — Posted on 2025-11-29

168 Intermediate heterogeneity modulates coupling between chain compaction and structure formation during protein folding

Kaushik, A.; Udgaonkar, J.

10.1101/2025.11.26.690716 — biophysics — Posted on 2025-11-29

169 Scaling contact force parameters across body size, limb count, and number of contact spheres

van Bijlert, P. A.

10.1101/2025.11.26.690874 — biophysics — Posted on 2025-11-29

170 Small molecule activator of phosphatase PP2A remodels scaffold PR65 structural dynamics to promote holoenzyme assembly

Yilmaz, S. Z.; Banerjee, A.; Saha, S.; Ohlmeyer, M.; Gordon, R.; Itzhaki, L. S.; Bahar, I.; Gur, M.

10.1101/2025.11.26.690749 — biophysics — Posted on 2025-11-29

171 LorMe: a streamlined and interoperable R framework for end-to-end microbiome analysis

Wang, N.; Zhang, Y.; Yang, X.; Gao, Y.; Xia, H.; Xu, Y.; Shen, Q.; Jousset, A.; Jiang, G.; Wei, Z.

10.1101/2025.11.26.690896 — bioinformatics — Posted on 2025-11-29

172 Genetic diversity, predictive protein structures, and interaction networks of Cysteine-Rich Receptor-Like Kinases in Arabidopsis thaliana

Stouthamer, J.; Pereira, D.; Martin-Ramirez, S.; Mutte, S.; Mott, G. A.; Smakowska-Luzan, E.

10.1101/2025.11.26.690834 — bioinformatics — Posted on 2025-11-29

173 Biochemical characterization of ABHD14A, an outlying member of the metabolic serine hydrolase family

Gupta, S.; Kamat, S.

10.1101/2025.11.28.691245 — biochemistry — Posted on 2025-11-29

174 Characterization of the Mitomycin C Resistance Protein McrA

Tjallinks, G.; Dunleavy, T.; Jonker, T.; Angeleri, N.; Mattevi, A.; Fraaije, M.

10.1101/2025.11.28.691146 — biochemistry — Posted on 2025-11-29

175 Comparing DNA extraction methods for successful PacBio HiFi sequencing: a case study of the freshwater mussel Anodonta anatina (Bivalvia: Unionidae)

Giulio, M.; Lergster, U.; Feulner, P. G. D.; Weber, A. A.-T.

10.1101/2025.11.26.690746 — genomics — Posted on 2025-11-29

176 Functional Landscape of Zebrafish Gonadotropins and Receptors: A Comprehensive Genetic Analysis

ZENG, C.; ZHANG, Z.; ZHOU, L.; ZHOU, X.; AI, N.; Ge, W.

10.1101/2025.11.26.690707 — genetics — Posted on 2025-11-29

177 RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions

Laverre, A.; Latrille, T.; Robinson-Rechavi, M.

10.1101/2025.11.26.690685 — evolutionary biology — Posted on 2025-11-29

178 Developmental priming increases copper-tolerance in a model fish species via epigenetic-and microbiome-mediated mechanisms

Uren Webster, T. M.; Laing, L. V.; Onime, J.; Littler, H.; McFarling, R. J.; Paris, J. R.; Fitzgerald, J. A.; Lange, A.; Farbos, A.; Moore, K.; Hitchings, M. D.; van Aerle, R.; Bury, N. R.; Santos, E. M.

10.1101/2025.11.28.691212 — evolutionary biology — Posted on 2025-11-29

179 Influence of vegetation structure on lemur recolonization of post-fire habitats in northwestern Madagascar

Rabemananjara, N. R.; Rasolozaka, M.; Ravolanirina, M. O.; Marivola, R.; Randriamiarantsoa, S. H.; Rakotondravony, R.; Razafindraibe, H.; Schuessler, D.; Radespiel, U.

10.1101/2025.11.26.690642 — ecology — Posted on 2025-11-29

180 Azimuthal Segment Imaging in cryo-STEM Tomography

Kirchweger, P.; Seifer, S.; Wolf, S. G.; Varsano, N.; Zens, B.; Schur, F. K.; Elbaum, M.

10.1101/2025.11.26.690630 — cell biology — Posted on 2025-11-29

181 An optimised method for generation of murine CAR-T cells by CRISPR/Cas9.

Jackson, T.; Himsworth, C.; Munning-Tomes, S.; Alam, F.; Brezovjakova, H.; Donovan, L. K.; Erbe, A. K.; Sondel, P. M.; Chesler, L.; Anderson, J.

10.1101/2025.11.29.689298 — molecular biology — Posted on 2025-11-29

182 A simple, reversible and non-toxic anchor-away system for effective nuclear depletion of proteins

Esteban-Serna, S.; Widen, T.; Grosemans, H.; Farquhar, I.; Granneman, S.

10.1101/2025.11.28.691147 — molecular biology — Posted on 2025-11-29

183 Comparison of extracellular vesicles isolation methods reveals method-dependent protein and miRNA profiles in saliva

Simphor, E.; Boulestreau, J.; Marchal, R.; Molina, F.; Kahli, M.

10.1101/2025.11.26.690666 — molecular biology — Posted on 2025-11-29

184 Proteomic and phospho-proteomic longitudinal signatures of human skeletal muscle in lung cancer cachexia

Sorensen, J.; Voldstedlund, C. T.; Battey, E.; Ogueboule, Z.; Irazoki, A.; Modvig, J.; Knos, C.; Hammershoi, A.; Carl, C. S.; Raun, S. H.; Dmytriyeva, O.; Richter, E. A.; Langer, S. W.; Sylow, L.

10.1101/2025.11.26.690647 — molecular biology — Posted on 2025-11-29

185 Looping specificity of Polycomb response elements requires GAF and a combinatorial code of looping factors

Sabaris, G.; Di Stefano, M.; Denaud, S.; Fritsch, L.; Popmihaylova, A.-M.; Papadopoulos, G.-L.; Schuettengruber, B.; Cavalli, G.

10.1101/2025.11.28.691166 — molecular biology — Posted on 2025-11-29

186 Hyperthermia reduces antimicrobial tolerance of Mycobacterium marinum in biofilms and ex vivo zebrafish granulomas

Jokinen, A.; Hammaren, M. M.; Korhonen, R.; Parikka, M.

10.1101/2025.11.28.691154 — microbiology — Posted on 2025-11-29

187 Genome-wide CRISPR screen reveals PEX11B as a host restriction factor against ORFV through membrane fluidity regulation

Gao, X.; Hao, J.; Lu, S.; Wang, S.; Sun, Y.; Ke, X.; Gao, X.; Su, Y.; Sun, Y.; Tian, Y.; Yan, W.; Wang, J.; Hai, R.; Zhang, Q.; Wang, J.; Hu, W.; Wang, G.

10.1101/2025.11.28.691156 — microbiology — Posted on 2025-11-29

188 Integron-associated structures underlie the accumulation of antibiotic resistance genes on plasmids beyond cassette arrays

Mao, Y.; Zhang, G.; Han, Z.; Whitaker, R. J.; Nguyen, T. H.

10.1101/2025.11.28.691237 — microbiology — Posted on 2025-11-29

189 Cryptococcus neoformans adapts to host CO2 concentrations through the coordinated remodeling of central carbon metabolism, oxidative stress resistance, and membrane homeostasis.

Ristow, L. J.; Blackburn, E. E.; jezewski, a. J.; Lin, X.; Krysan, D. J.

10.1101/2025.11.28.691145 — microbiology — Posted on 2025-11-29

190 Aridity drives global convergence of desert microbiomes and biogeochemical activities

Leung, P. M.; Bay, S. K.; Wong, W. W.; Jirapanjawat, T.; Archer, S. D.; Beaman, J.; Cherif, A.; Chown, S. L.; Cowan, D. A.; Demergasso, C.; de los Rios, A.; DiRuggiero, J.; Elberling, B.; Frey, B.; Gillor, O.; Graham, D. W.; Gupta, P.; Hogg, I. D.; Juottonen, H.; Kytöviita, M.-M.; Makhalanyane, T.; Meredith, L. K.; Nguyen-Dinh, T.; Prieme, A.; Ramond, J.-B.; Siciliano, S. D.; Tan, G. Y. A.; Warren-Rhodes, K. A.; Wieler, N.; Cook, P. L. M.; Delgado-Baquerizo, M.; Greening, C.

10.1101/2025.11.29.691269 — microbiology — Posted on 2025-11-29

191 Peptacetobacter felis sp. nov., a novel bile acid-converting bacterial species isolated from the feces of healthy cats in the United States

Dione, N.; Mlaga, K. D.; Jospin, G.; Marfori, Z.; Liang, S.; Ganz, H. E.

10.1101/2025.11.28.691207 — microbiology — Posted on 2025-11-29

192 Kazal-type serine protease inhibitors from Arabidopsis thaliana and Toxoplasma gondii exhibit antimicrobial activity against plant pathogens

Sanchez, M. A.; Strack, K. N.; Mendoza-Morales, L. F.; Ramos Duarte, V. A.; Perez, E.; Sander, V. A.; Laguia Becher, M.; Pieckenstain, F. L.; Clemente, M.

10.1101/2025.11.28.691165 — microbiology — Posted on 2025-11-29

193 Distribution of carbon monoxide-oxidizing microorganisms along a chronosequence on Piton De La Fournaise volcano

Wildbur, C.; Dawson, R. A.; Roy, S.; Ah-Peng, C.; Espenberg, M.; Hernandez, M.

10.1101/2025.11.28.691264 — microbiology — Posted on 2025-11-29

194 Efficient in vivo mammalian neuron editing using peptide-mediated CRISPR enzyme delivery

Manohar, B. D.; Travis, M.; Munjal, V.; Baehr, C. M.; Rahnama, L. M. A.; Hyung Kang, M.; Haddad, R. F.; Asija, K.; Noel, E. A.; Peddireddy, N.; Chouhan, R. S.; Sharma, R.; Wyman, S. K.; Krishnappa, N.; Killebrew, D. A.; Hua Li, S.; Snow, K. J.; Byrne, A. K.; Boosani, C. S.; Otero, P. A.; Bringas, J. R.; O'Brien, A. A.; Rocco, M. T.; Zimmerly, M. P.; Gray, I.; Sran, G. K.; Patel, M. I.; Seidensticker, E. F.; Saville, E.; Gaitan, Y.; Schmelzle, A. L.; Subramanyam, P. N. B.; Samaranch, L.; Green, J. A.; Wells, K. D.; Ehrenberg, A. J.; Murray, S. A.; Clelland, C. D.; Murthy, N.; Lonser, R. R.; Had

10.1101/2025.11.26.690638 — neuroscience — Posted on 2025-11-29

195 Bifunctional Architecture Enables Substrate Catalysis and Channeling in Paracoccus TMAO Demethylase

Thach, T.; Dhanabalan, K.; Maurya, S.; Han-Hallett, Y.; Quan, S.; Allison, J.; Ramanathan, G.; Subramanian, R.

10.1101/2025.11.26.690739 — biophysics — Posted on 2025-11-29

196 Animal-Origin-Free Method for Generating Blood Vessel Organoids

Hoffmann, A.; Schorn, D.; Thoenig, J.; Yordanov, T. E.

10.1101/2025.11.26.690667 — bioengineering — Posted on 2025-11-29

197 Low-intensity focused ultrasound enables temporal modulation of human midbrain organoid differentiation

Jeong, J.; Jo, Y.; Lee, Y.; Jang, E.; Jeong, Y.; Heo, W. D.; Shin, J. H.; Lee, M.-O.; Lee, H. J.

10.1101/2025.08.29.672992 — developmental biology — Posted on 2025-11-29

198 Sense codon-misassociated eRF1 elicits ribosome stalling and induction of quality control

Han, P.; Mito, M.; Yamashita, A.; Ito, T.; Iwasaki, S.

10.1101/2024.09.01.610654 — molecular biology — Posted on 2025-11-29

199 Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli

Poudyal, P.; Sy, B. M.; Mediati, D. G.; Payne, M.; Nandel, V.; Norris, D.; McAteer, S. P.; Ullah, A.; Li, S.; Menz, L.; Waters, S.; Dallman, T.; Baker, M. A.; Lan, R.; Gally, D. L.; Tree, J. J.

10.1101/2025.11.27.690950 — microbiology — Posted on 2025-11-29

200 Unfolding the Black Box of Recurrent Neural Networks for Path Integration

Chu, T.; Wu, Y.; Burgess, N.; Ji, Z.; Wu, S.

10.1101/2025.10.25.684492 — neuroscience — Posted on 2025-11-29

201 Novel Biomaterial-Based Synovial Fluid Analysis Reveals Protective microRNA Signatures in a Mouse Model of Acute Synovitis-Driven Osteoarthritis

Takahata, K.; Arakawa, K.; Yasuda, T.; Enomoto, S.; Katashima, T.; Sakai, T.; Kokubun, T.

10.1101/2025.09.11.675532 — pathology — Posted on 2025-11-29

202 Drosophila midgut tumor-induced insulin resistance systemically remodels lymph gland hematopoiesis during cancer cachexia

Chowdhury, U.; Panzade, G.; Karnik, P. N.; Birwadkar, P.; Tashu, T.; Khadilkar, R. J.

10.1101/2025.11.24.690188 — cancer biology — Posted on 2025-11-29

203 Evaluating Physiological Indicators in Detecting Deception and Truthfulness using the Comparison Question Test (CQT)

Rashid, A. M. S.; Carmichael, B.; Su, C.; Shi, K.; Lim, K.; Kumar, P. S.; Wan, N. J.; Govil, E.; Yap, D.

10.1101/2024.09.01.609623 — bioengineering — Posted on 2025-11-29

204 Adaptive behavior is guided by integrated representations of controlled and non-controlled information

Huang, B.; Ritz, H.; Jiang, J.

10.1101/2025.08.07.669231 — neuroscience — Posted on 2025-11-29

205 Profiling presynaptic scaffolds using split-GFP reconstitution reveals cell-type-specific spatial configurations in the fly brain

Wu, H.; Maekawa, Y.; Eno, S.; Kondo, S.; Yamagata, N.; Tanimoto, H.

10.1101/2024.12.02.626511 — neuroscience — Posted on 2025-11-29

206 The functional divergence of two ethylene receptor subfamilies that exhibit Ca2+-permeable channel activity

Pan, C.; Cheng, J.; Lin, Z.; Hao, D.; Xiao, Z.; Ming, Y.; Song, W.; Liu, L.; Guo, H.

10.1101/2025.11.28.691086 — plant biology — Posted on 2025-11-29

207 Ethylene signal-driven plant-multitrophic synergy boosts crop performance

Baer, M.; Zhong, Y.; Yu, B.; Tian, T.; He, X.; Gu, L.; Huang, X.; Gallina, E.; Metzen, I. E.; Bucher, M.; Song, R.; Gutjahr, C.; SU, Z.; Moya, Y.; von Wiren, N.; Zhang, L.; Yuan, L.; Shi, Y.; Wang, S.; Qi, W.; Baer, M.; Zhao, Z.; Li, C.; Li, X.; Hochholdinger, F.; Yu, P.

10.1101/2025.11.28.690471 — plant biology — Posted on 2025-11-29

208 Polygenic resistance is associated with altered early immune timing and changes in transcriptome network structure

Hadlik, M.; Baranek, M.; Barankova, K.; Kovacova, V.

10.1101/2025.11.27.690962 — plant biology — Posted on 2025-11-29

209 Chloroplast-mitochondria synergy modulates responses to iron limitation in two Thalassiosira diatom species

ANGULO, J.; Uwizeye, C.; Albanese, P.; Menneteau, M.; Ravanel, S.; Jouneau, P.-H.; Finazzi, G.; Courtois, F.

10.1101/2025.11.28.691171 — plant biology — Posted on 2025-11-29

210 In situ GCIB Cryo-Sectioning Enables Subcellular Cryo-ToF-SIMS Imaging of Arabidopsis Seeds

Claire, S.; Moreau, B.; Boujard, M.; Eric, G.; Jouneau, P.-H.; Barnes, J.-P.

10.1101/2025.11.28.691143 — plant biology — Posted on 2025-11-29

211 Ultrafast CTCF dynamics control cohesin barrier function

Rudnizky, S.; Murray, P. J.; Sorensen, E. W.; Koenig, T. J. R.; Pangeni, S.; Merino-Urteaga, R.; Chhabra, H.; Caccianini, L.; Davidson, I. F.; Osorio-Valeriano, M.; Hook, P. W.; Meneses, P.; Hao, J.; Zarb, J. S.; Hatzakis, N. S.; Timp, W.; Farnung, L.; Vos, S. M.; Peters, J.-M.; Aksimentiev, A.; Ha, T.

10.1101/2025.11.25.690553 — biophysics — Posted on 2025-11-29

212 Evaluating an In Vivo Oxidative Stress sensor in cystic fibrosis rat epithelial tissues

Rout-Pitt, N.; Barnes, S.; Reyne, N.; McCarron, A.; Donnelley, M.; Kostecki, R.; Noschka, E.

10.1101/2025.11.25.690596 — biophysics — Posted on 2025-11-29

213 ClsDiff-AMP30: Generating Antimicrobial Peptides by a Classifier Guidance Noise Predictor

Yan, J.; Cai, J.; Li, Y.; Lin, Z.; Xian, W.; Wei, X.; Lei, I. F.; Zhou, M.; Campbell-Valois, F.-X.; Siu, S. W. I.

10.1101/2025.11.25.690620 — bioinformatics — Posted on 2025-11-29

214 Dynamic optimization of chemo-immunotherapy sequencing reveals phenotype-dependent regimens across tumor immune microenvironments

Gong, K.; Lu, T.; Wang, X.; Liu, X.

10.1101/2025.11.26.690636 — bioinformatics — Posted on 2025-11-29

215 Scalable integration and prediction of unpaired single-cell and spatial multi-omics via regularized disentanglement

Sun, J.; Liang, C.; Wei, R.; Zheng, P.; Yan, H.; Bai, L.; Zhang, K.; Ouyang, W.; Ye, P.

10.1101/2025.11.25.689803 — genomics — Posted on 2025-11-29

216 DNA-barcoded microneedle array patch enabling the profiling of in vivo spatiotemporal transcriptomics

Guo, Y.; Zhang, Y.; Li, X.; Kuang, J.; Cao, K.; Chen, F.; Fan, C.; Zhao, Y.

10.1101/2025.11.25.690619 — genomics — Posted on 2025-11-29

217 Progeny-based genomic selection reveals untapped genetic potential in an underutilized medicinal plant, Perilla frutescens

Kinoshita, S.; Sakurai, K.; Tsusaka, T.; Sakurai, M.; Shirasawa, K.; Isobe, S.; Iwata, H.

10.1101/2025.11.26.690889 — genetics — Posted on 2025-11-29

218 wQFM-GDL Enables Accurate Quartet-based Genome-scale Species Tree Inference Under Gene Duplication and Loss

Rafi, A.; Rumi, A. M. S.; Hakim, S. A.; Bayzid, M. S.

10.1101/2025.04.04.647228 — evolutionary biology — Posted on 2025-11-29

219 The bind of the burrow: space use is dominated by selection for burrow habitat over foraging habitat in an arid-adapted carnivore

Thorley, J.; Duncan, C.; Herdtle, A.; Manser, M.; Cram, D.; Clutton-Brock, T.

10.1101/2025.11.26.690549 — ecology — Posted on 2025-11-29

220 Evaluate and simulate the reproduction and survival of a reintroduced population in an endangered bird species Crested ibis (Nipponia nippon)

Xi, X.; He, Y.; Zeng, S.; Yang, S.; Pan, Z.; Zheng, J.; Wang, D.

10.1101/2025.11.25.690618 — ecology — Posted on 2025-11-29

221 Disrupted endothelial cell-cell dynamics in ALK1 and SMAD4 deficiency drive arteriovenous malformations

Hardman, D.; Oppenheim, O.; Giese, W.; Gerhardt, H.; Bernabeu, M. O.

10.1101/2025.11.26.690643 — cell biology — Posted on 2025-11-29

222 Spatial Transcriptomics Reveals CXCL12+ Fibroblasts as Central Immune Organizers through CXCR4 Signaling in Abdominal Aortic Aneurysm

Levy-Lambert, D.; Ramirez, J. L.; Shaikh, S.; De Jeronimo Diaz, C.; Huang, A. G.; Combes, A.; Fragiadakis, G.; Fidler, T.; Oskowitz, A.

10.1101/2025.11.24.690328 — cell biology — Posted on 2025-11-29

223 SIRP: A Self-Supervised Fluorescence Denoising method with Implicit Representation Priors

Li, Y.; Zhu, J.; Xu, P.; Guo, M.; Li, Y.; Liu, H.

10.1101/2025.11.25.690616 — cell biology — Posted on 2025-11-29

224 Molecular basis for cellular compartmentalization by an ancient membrane fission mechanism

Espadas, J.; Souza, D. P.; Hakala, M.; Garcia-Arcos, J. M.; Tran, J.; Kumar, A.; Marcuello, C.; Merino, A.; Colom, A.; Vanni, S.; Kaksonen, M.; Baum, B.; Toret, C. P.; Roux, A.

10.1101/2025.11.28.690958 — cell biology — Posted on 2025-11-29

225 Upregulation of MAM by C99 disrupts ACSL4 activity and phospholipid homeostasis in Alzheimer disease.

Montesinos, J.; Yun, T.; Salomon-Cruz, I. D.; Agudelo-castrillon, S.; Uceda, M.; Ferrer, A. C.; Anton-Barros, C.; Gomez-lopez, N.; Agrawal, R. R.; Larrea, D.; Velasco, K. R.; Fernandez-Bernal, A.; Benitez, E.; Zhu, X.; Schon, E. A.; Cardona-Gomez, G. P.; Area-Gomez, E.

10.1101/2025.11.25.690197 — molecular biology — Posted on 2025-11-29

226 Systematic yeast two-hybrid screening identifies novel functions for SET1C/COMPASS

Luciano, P.; Park, K.; Audebert, S.; Camoin, L.; Nino, C. A.; Park, D. K.; Maudlin, I. E.; Dubarry, M.; lee, l.; Oeffinger, M.; Beggs, J. D.; Kim, Y. H.; Kim, J.; Dichtl, B.; Geli, V.

10.1101/2025.11.23.690026 — molecular biology — Posted on 2025-11-29

227 Ecology of methyl-coenzyme M reductase encoding Thermoproteota

Jay, Z. J.; Kellom, M.; Eloe-Fadrosh, E.; Hatzenpichler, R.

10.1101/2025.10.16.682713 — microbiology — Posted on 2025-11-29

228 Characterize Oral-to-Blood Microbial DNA Translocation in Individuals with Cocaine Use Disorder

Johnson, d.; Sundararaj, K. P.; Subramanian, S.; Qiu, Y.; Samuel, I.; Cheng, D.; Salman, T.; Luo, Z.; Fitting, S.; Keen, L.; Call, E.; Maddi, A.; Stoops, W.; Hartley, A.; McKinnon, J. E.; Wan, Z.; Berto, S.; Jiang, W.

10.1101/2025.11.03.686400 — microbiology — Posted on 2025-11-29

229 Life Identification Numbers: A bacterial strain nomenclature approach

Palma, F.; Hennart, M.; Jolley, K. A.; Crestani, C.; Wyres, K. L.; Bridel, S.; Yeats, C. A.; Brancotte, B.; Raffestin, B.; David, S.; Lam, M. M. C.; Izdebski, R.; Passet, V.; Rodrigues, C.; Rethoret-Pasty, M.; Combary, A.; Cottis, S.; Maiden, M. C. J.; Aanensen, D. M.; Holt, K. E.; Criscuolo, A.; Brisse, S.

10.1101/2024.03.11.584534 — microbiology — Posted on 2025-11-29

230 PD-1 blockade during T cell priming enhances long-term protection against metastatic tumors by epigenetically tuning T cell exhaustion

Dinter, T.; Mackowiak, S.; Rogers, Z.; Bhandarkar, V.; Carney, M.; Zhang, Y.; Morgan, D.; Pop, L.; Chatterjee, F.; Lutz, E.; Jain, Y.; Radhakrishnan, A.; Lander, E.; Wittrup, K.; Love, J. C.; Meissner, A.; Spranger, S.

10.1101/2025.11.25.690601 — immunology — Posted on 2025-11-29

231 Fungal Mst3-proteins are involved in fungal innate immunity needed for the recognition of bacteria surrounding the hyphae, as well as for plant pathogenicity

Gong, S.; Lin, X.; Liu, S.; Olsson, S.; Lu, G.; Wang, Z.; Li, Y.

10.1101/2025.11.25.690610 — immunology — Posted on 2025-11-29

232 PKU tags, novel genetically encoded shape tags for cell labeling in light and electron microscopy

Sun, R.; Yang, P.; Wang, L.; Hu, Y.; Yang, Y.; Deng, F.; Li, S.; Fan, M.; Xia, X.; Li, Y.

10.1101/2025.11.25.690457 — neuroscience — Posted on 2025-11-29

233 ABA-responsive transcription factor CbNAC63 is involved in modulating biosynthesis of triterpenoid saponins in Conyza blinii

Yuan, Y.; Zhou, M.; Yang, M.; Wang, M.; Zhan, J.; Wang, T.; Chen, H.; Zheng, T.

10.1101/2025.11.27.690938 — plant biology — Posted on 2025-11-29

234 An inositol pyrophosphate interaction screen provides insight into the regulation of plant casein kinase II

Sturm, K.; Pri-Tal, O.; Rico-Resendiz, F.; Verma, Y.; Richter, A.; Chen, H.; Broger, L.; Hothorn, L. A.; Fiedler, D.; Panse, V. G.; Hothorn, M.

10.1101/2025.11.27.691040 — plant biology — Posted on 2025-11-29

235 AGO5 restricts virus vertical transmission in plant gametophytes

Hoffmann, G.; Sadhu, S. P.; Bradamante, G.; Diez Marulanda, J. C.; Proschwitz, A.; Wegscheider, T.; Turhan, I.; Bente, H.; Gutzat, R.; Incarbone, M.

10.1101/2025.11.28.691182 — plant biology — Posted on 2025-11-29

236 Increased versican and fibrosis in mesenteric lymph nodes disrupts immune surveillance and drives systemic bacterial dissemination in cirrhosis

Juneja, P.; Sharma, A.; SHarma, B.; KUMAR, G.; Jakhar, D.; Chauhan, N.; Khillan, V.; Mukund, A.; Tripathi, D. M.; Sarin, S. K.; Maiwall, R.; Kaur, S.

10.1101/2025.11.25.690350 — physiology — Posted on 2025-11-29

237 TRPV4 Promotes Histamine Receptor Signaling in Lymphatic Endothelial Cells

Retamal, J. S.; Peng, S.; Nguyen, T.-N.; Bandala-Sanchez, E.; Eriksson, E. M.; McCague, R. E.; Mahdavian, N. S.; Carbone, S. E.; Cao, E.; Gondin, A. B.; Veldhuis, N. A.; Poole, D. P.

10.1101/2025.11.25.690563 — pharmacology and toxicology — Posted on 2025-11-29

238 Regulation of Renal Transporters by Pro-inflammatory Cytokines in Human Proximal Tubular Epithelial Cells: Identification of the Perpetrator and Mechanisms

Tsang, Y. P.; Wang, K.; Kelly, E. J.; Mao, Q.; Unadkat, J. D.

10.1101/2025.11.25.690608 — pharmacology and toxicology — Posted on 2025-11-29

239 Anatomical Research on the Anterior Cruciate Ligament of the Knee

Zhang, D. Z.; Han, Z. Z.; Chi, Y.

10.1101/2025.11.23.690033 — pathology — Posted on 2025-11-29

240 BeadBuddy: user-friendly, nanometer-scale registration of single-molecule imaging data

Lionnet, T.; Clark, F. T.; Whitney, P. H.; Saiz, N.; Ziarno, A.

10.1101/2025.11.25.690467 — biophysics — Posted on 2025-11-29

241 Deep-brain thermo-endomicroscopy

Imamura, R.; Nakane, Y.; Kataoka, N.; Abe, H.; Ohshima, T.; Sotoma, S.; Sugi, T.

10.1101/2025.11.25.690615 — biophysics — Posted on 2025-11-29

242 Displacement-Optimized Tanglegrams for Trees and Networks

Huson, D.

10.1101/2025.11.26.690634 — bioinformatics — Posted on 2025-11-29

243 Evaluation of Anti-Fibrotic Therapeutics Using a Three-Dimensional In Vitro Liver Fibrosis Model

Gadre, M. A.; S.V., K.

10.1101/2025.11.24.690128 — bioengineering — Posted on 2025-11-29

244 Anatomical 3D Reconstruction of Murine Lymph Nodes for Visualization, Quantitation, and Numerical Simulation

Donzanti, M. J.; Moghadamnia, Y.; Kapinski, A. T.; Zurakowski, R.; Gleghorn, J. P.

10.1101/2025.11.25.690560 — bioengineering — Posted on 2025-11-29

245 In vitro design of intrathecal drug administration therapies

Ayansiji, A.; Gardner, C.; Dors, S.; Gehrke, D.; Moral-Pulido, F.; Slavin, K.; Linninger, A.

10.1101/2025.11.25.690590 — bioengineering — Posted on 2025-11-29

246 Transcription-induced mutation and gBGC at the Transcriptional Start Site impact the evolution of human protein-coding genes

Qiu, Y.; Hebraud, E.; Pouyet, F.; Palazzo, A. F.

10.1101/2025.11.24.690122 — evolutionary biology — Posted on 2025-11-29

247 Differential functions of multiple Wnts and receptors in cell polarity regulation in C. elegans

Sawa, H.; Asakawa, M.; Negishi, T.

10.1101/2025.11.25.690575 — developmental biology — Posted on 2025-11-29

248 Axon-specific mRNA translation shapes dopaminergic circuit development

Gora, C.; Frenette, B.; Gelon, P.; Sephton, C.; Hussein, S. M.; Metzakopian, E.; Levesque, M.

10.1101/2025.11.25.690389 — developmental biology — Posted on 2025-11-29

249 Developing a nuclear transplantation model for Australian amphibian conservation using a common species of Australian Frog (Limnodynastes peronii)

Patel, R.; Upton, R.; Clulow, S.; Nixon, B.; Gruber, B.; Archer, M.; Mahony, M.; Clulow, J.

10.1101/2025.11.25.690599 — developmental biology — Posted on 2025-11-29

250 Mechanical constraint causes lower turgor, thicker walls, and faster growth in Arabidopsis root hairs

Zambare, V.; Yi, H.; Anderson, C. T.

10.1101/2025.11.25.690544 — cell biology — Posted on 2025-11-29

251 Progranulin deficiency aggravates aging-induced vascular injury

Bruder-Nascimento, T.; Luvizotto, R. A. M.; Nascimento, A. F.; Pimenta, G. F.; Costa, R. M.; Singh, S.; Awata, W. M. C.; Russ, A.; Haastrup, A.; Cuevas, R. A.; Behzadi, P.; St. Hilaire, C.; Roberts, J.; Bruder, A.

10.1101/2025.11.25.690611 — cell biology — Posted on 2025-11-29

252 An Integrated Single-Cell Atlas Reveals Hepatic Stellate Cell Heterogeneity and Spatiotemporal Dynamics after Liver Injury

Wang, J.; Tao, J.; Xia, C.; Tang, M.; Stoica, A.-F.; Yuan, S.; Li, Y.; Guo, L.; Kong, X.; Wang, J.

10.1101/2025.11.25.690307 — cell biology — Posted on 2025-11-29

253 Synergistic role of riboflavin-auxotrophic Enterococcus for MR1 expression and intra-tumoral mucosal associated invariant T (MAIT) cell activation

Birla, P.; Yang, L.; Shan, W.; Minamisawa, S.; Dhaygude, O.; Manoj, H.; Zheng, Y.; Fan, H.; Beauregard, H.; Smith, K. N.; Shaikh, F. Y.; Sears, C. L.; Pardoll, D. M.; Housseau, F.

10.1101/2025.11.25.690539 — immunology — Posted on 2025-11-29

254 Systemic immune dysregulation in hypertensive disorders of pregnancy persists years after delivery

Sabayev, M.; Ganio, E. A.; Stelzer, I. A.; Sato, M.; Cambriel, A.; Bonham, T. A.; Juvan, Z. N.; Diop, M.; Iyer, P.; Sedan, O.; Aghaeepour, N.; Angst, M. S.; Shaw, G. M.; Stevenson, D. K.; Stefanick, M. L.; Boyd, H. A.; Melbye, M.; Hlatky, M. A.; Winn, V. D.; Gaudilliere, B.; Feyaerts, D.

10.1101/2025.11.25.690209 — immunology — Posted on 2025-11-29

255 Oligodendrocytes show enriched expression of amyloid precursor protein and GABA B receptor isoform 1a

Houmam, S.; Siodlak, D.; Montgomery, C.; Seshadri, M.; Pezant, N. P.; Hallum, G. B.; Salinas-Salinas, C.; Stanford, D. R.; Thomason, Y. M.; Rice, H. C.

10.1101/2025.11.25.690528 — neuroscience — Posted on 2025-11-29

256 Neuronal APOE4 alone is sufficient to drive tau pathology, neurodegeneration, and neuroinflammation in an Alzheimer's disease mouse model

Blumenfeld, J.; Li, Y.; Kim, M. J.; Yip, O.; Yao, L.; De Leon, S.; Fulthorpe, R.; Shostak, D.; Platow, Z.; Suan, K.; Hao, Y.; Koutsodendris, N.; Ellis, C.; Nguyen, J.; Huang, Y.

10.1101/2025.11.25.690488 — neuroscience — Posted on 2025-11-29

257 The Dominant Hand-Area Network: Task-Signal Mismatch and the Decoupling of BCI Skill from Global Efficiency in Postural Motor Imagery

Ayon, M. A. A. H.

10.1101/2025.11.23.690036 — neuroscience — Posted on 2025-11-29

258 Local homeostatic scaling supports stable rate propagation under noise and heterogeneity

Li, H.; McDougal, R. A.

10.1101/2025.11.25.689806 — neuroscience — Posted on 2025-11-29

259 Closed-loop anti-phase tACS over preSMA reduced oscillatory beta synchronization and modulated motor inhibition performance

Fang, Z.; Sack, A. T.; Leunissen, I.

10.1101/2025.11.25.690566 — neuroscience — Posted on 2025-11-29

260 Neuropeptide Y regulation of L-type Ca2+ channel activity is altered following chronic myocardial infarction

Fiore, C. M.; Agarwal, S. R.; Elasoru, S. E.; Ardell, J.; Ajijola, O.; Shivkumar, K.; Harvey, R. D.

10.1101/2025.11.25.690298 — pharmacology and toxicology — Posted on 2025-11-29

261 Neuronal innervation of breast cancer promotes metastatic dissemination

Schulte, A. J.; Andrechek, E.

10.1101/2025.11.25.690523 — cancer biology — Posted on 2025-11-29

262 Therapy-induced PSMA2 Sensitizes Prostate Cancer Cells to Residual Androgen and Promotes Neuroendocrine Lineage Transformation

Patterson, N.; Badoi, A.; Vadla, G. P.; Hasani, M.; Moyer, J.; Ramirez, C. D. L. N.; Chabu, C.

10.1101/2025.11.25.690552 — cancer biology — Posted on 2025-11-29

263 Antibody-Protein L Functionalized Microparticles for Detection of Surface Markers in Heterogeneous Colorectal Lesions

Ramezani, S.; Zacharias, N. M.; Norton, W.; Davis, J. S.; Dominic, A.; Armijo, R.; Wang, M.; Wendt, R. E.; Carson, D. D.; Harrington, D. A.; Farach-Carson, M. C.; Bhattacharya, P. K.

10.1101/2025.11.25.690572 — cancer biology — Posted on 2025-11-29

264 A Comparison of Computational Methods for Modeling Stochastic Collaborative DNA Methylation Dynamics

Lemus, M. A. G.; Read, E. L.

10.1101/2025.11.25.690568 — biophysics — Posted on 2025-11-29

265 Graft protection by myeloid progenitor cells using lethal or non-lethal preconditioning.

Li, Y.; Sun, L.; Martinez, E.; Sedello, A.; Fong, T.; Domen, J.

10.1101/2025.11.25.690526 — immunology — Posted on 2025-11-29

266 Incentive Salience, not Psychomotor Sensitization or Tolerance, Drives Escalation of Cocaine Self-Administration in Heterogeneous Stock Rats

Ramborger, J.; Mosquera, J.; Brennan, M.; Sichel, B.; Othman, D.; Plasil, S.; Sneddon, E. A.; Zahedi, S.; Morgan, A.; Chonwattanagul, S.; Bai, K.; China, L.; La, T.; Maturin, L.; Carrette, L. L. G.; George, O.

10.1101/2025.10.04.680105 — neuroscience — Posted on 2025-11-29

267 Dual Activation of MC3R and MC4R Drives Weight Loss and Reduces Food Intake in Obese Primates

Seiler, J. L.; Impastato, A. C.; Zhang, E. X.; Kelley, K. J.; Bennett, T. L.; Studnitzer, B.; Prindle, C. R.; Rajewski, B. H.; Badeau, B. A.; Jiang, X.; Potterfield, R.; Delev, J. Y.; Marks, D. L.

10.1101/2025.11.25.690554 — neuroscience — Posted on 2025-11-29

268 SLC4A1 MUTATIONS THAT CAUSE DISTAL RENAL TUBULAR ACIDOSIS ALTER CYTOPLASMIC PH AND CELLULAR AUTOPHAGY

Essuman, G.; Rizvi, M.; Almomani, E.; Ullah, S. A.; Hasib, S. M.; Chelangarimiyandoab, F.; Mungara, P.; Schmitt, M. J.; Hureaux, M.; Vargas-Poussou, R.; Touret, N.; Cordat, E.

10.1101/2024.10.23.619718 — physiology — Posted on 2025-11-29

269 Systematic characterization of site-specific proline hydroxylation using hydrophilic interaction chromatography and mass spectrometry

Jiang, H.; Druker, J.; Wilson, J. W.; Bensaddek, D.; Swedlow, J. R.; Rocha, S.; Lamond, A. I.

10.1101/2023.07.28.550951 — biochemistry — Posted on 2025-11-29

270 A Bayesian Informative Shrinkage Approach for Large-scale Multiple Hypothesis Testing (BISHOT): with Applications in Differential Analysis of Omics Data

Su, Y.; Clark, M. E. J. Z.; Wang, C.

10.1101/2025.09.11.675690 — genetics — Posted on 2025-11-29

271 A 3D Amphioxus Brain Atlas Illuminates the Blueprint of the Ancestral Chordate Brain

Lin, C.-Y.; Hsu, W.-H.; Lu, M.-Y. J.; Chen, Y.-H.; Chen, Y.-C.; Su, Y.-H.; Chou, S.-J.; Yu, J.-K.

10.1101/2025.11.27.690639 — evolutionary biology — Posted on 2025-11-29

272 Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs

Zhang, K.; Basak, M.; Zaher, Y.; Yao, E.; Wang, S.-A.; Aung, T.; Chuang, P.-T.

10.1101/2025.10.28.684989 — developmental biology — Posted on 2025-11-29

273 Targeting the cell membrane in established and emerging model organisms

Karapidaki, I.; Handberg-Thorsager, M.; Momose, T.; Yasuo, H.; Genikhovich, G.; Assaf, S.; Deleau, C.; Pang, Y.; Clayton, P.; Lohmann, B.; Rusciano, M. L.; Stranges, M.; Mathieu, J.; Zilliox, M.; Ustyantsev, K.; Salmon, B.; Laplace-Builhe, B.; Koenig, M.; Colgren, J. J.; Arnone, M. I.; Berezikov, E.; Brunet, T.; Bucher, G.; Burkhardt, P.; Dickinson, D. J.; Houliston, E.; Huisken, J.; Leclere, L.; Averof, M.

10.1101/2024.11.12.623055 — developmental biology — Posted on 2025-11-29

274 Chromatin Disruption After Prenatal Hypoxia Predicts Lasting Neuron Deficits

Cristancho, A. G.; Joseph, D. J.; Cassidy, M. M.; Chauhan, P. S.; Gadra, E. J.; Gadra, E. C.; Zarrinnegar, D.; Rodriguez, B. N.; Marsh, E. D.

10.1101/2025.11.28.691133 — neuroscience — Posted on 2025-11-29

275 Non-invasive modulation of brain activity and behavior by transcranial radio frequency stimulation

Yaghmazadeh, O.; Alon, L.; Arefin, T. M.; Ben Youss, Z.; Zhang, J.; Buzsaki, G.

10.1101/2025.11.27.691064 — neuroscience — Posted on 2025-11-29

276 Cross-Species Cortical Geometry Reveals Conserved Gradients Across Primates and Human-Specific Expansion

Wei, Y.; Wang, Y.; Wei, T.; Lu, X.; Li, D.; Sherwood, C. C.; Zhang, Y.; Cheng, C.; Jiang, T.; Fan, L.; Cheng, L.

10.1101/2025.11.28.691123 — neuroscience — Posted on 2025-11-29

277 An integrated platform for high-throughput phenospace learning of 3D multilineage organoid systems

Okuda, R.; Harmel, C.; Xu, Q.; Mary, H.; Schulz, P.; Steinacher, L.; D'Arcangelo, E.; Gjeta, B.; Signer, M.; Cubela, I.; Bickle, M.; Lutolf, M. P.; Cabon, L.; Lukonin, I.; Camp, G.

10.1101/2025.11.27.690952 — cancer biology — Posted on 2025-11-29

278 LARIS enables accurate and efficient ligand and receptor interaction analysis in spatial transcriptomics

Dai, M.; Torok, T.; Sun, D.; Shende, V.; Wang, G.; Lin, Y.; Wu, S. J.; Rukshin, A.; Fishell, G.; Chen, F.

10.1101/2025.11.26.690796 — bioinformatics — Posted on 2025-11-28

279 Palaeogenomics reveals 1,500 years of population history of the peoples of the Chonos Archipelago, Chile.

Davidson, R.; Reyes, O.; Roca-Rada, X.; Arango-Isaza, E.; Kassadjikova, K.; Barbieri, C.; Llamas, B.; Fehren-Schmitz, L.

10.1101/2025.11.26.690513 — genomics — Posted on 2025-11-28

280 Distinct developmental trajectories of externally- and internally-generated hippocampal sequences and assemblies

Leprince, E.; Filippi, C.; Mantez, M.; Dard, R. F.; Dichio, V.; Majnik, J.; Cretella, M.; Bocchio, M.; Picardo, M. A.; Monasson, R.; Platel, J.-C.; Cossart, R.

10.1101/2025.11.27.690943 — neuroscience — Posted on 2025-11-28

281 Medial Temporal Default Mode Network Selectively Encodes Autobiographical Visual Imagery

Anderson, A. J.; Turnbull, A. G.; Lin, F. V.

10.1101/2025.11.25.690576 — neuroscience — Posted on 2025-11-28

282 Prenatal maternal stress is associated with increased sensitivity to neuropathic pain and sex-specific epigenetic and transcriptomic dynamics in the prefrontal cortex

Vovk, A.; Gregoire, S.; Barel, Z.; Stone, L. S.; Lax, E.

10.1101/2025.11.27.691002 — neuroscience — Posted on 2025-11-29

283 A slow unpicking of the landscape thread? Changes in tropical savanna birds on a gradient of habitat modification over 12 years of monitoring

Kutt, A. S.

10.1101/2025.07.29.667582 — ecology — Posted on 2025-11-28

284 Serum Lipidome as an Early Peripheral Indicator in Familial Alzheimers Disease

Cardona Gomez, G. P.; Salomon Cruz, I. D.; Lozano Trujillo, L. A.; Galvis Garrido, N. D.; Agudelo Castrillon, S. C.; Barbosa Carvajal, J. P.; Hoyos Rios, M.; Trujillo Chacon, L. M.; Henao, E.; Fernandez, G. J.; Osorio, E.; Quiroz, Y. T.; Schon, E.; Lopera, F.; Villegas Lanau, C. A.; Aguirre Acevedo, D. C.; Arias Londono, J. D.; Aguillon Nino, D. F.; Area-Gomez, E.

10.1101/2025.11.25.690392 — neuroscience — Posted on 2025-11-28

285 Engineering the citrus phyllosphere microbiome for enhanced disease resistance to bacterial canker

Li, J.; Xu, J.; Lee, D.; Hendrich, C.; Pang, Z.; Wang, W.; Cruz, M. A.; Feng, Y.; Dalmendray, J.; Duan, Y.; Zhang, M.; Calovic, M.; Oswalt, C.; Wang, N.

10.1101/2025.11.25.690529 — plant biology — Posted on 2025-11-28

286 Anionic Lipid Trafficking and Cell Mechanics RegulateMembrane Electrical Potential in Non-Excitable Tissue Cells

Ge, Z.; Ni, Q.; Yan, Y.; Wu, Y.; Si, B. R.; Fu, J.; LIN, D.; Konstantopoulos, K.; Li, Y.; Sun, S.

10.1101/2025.11.25.690536 — biophysics — Posted on 2025-11-28

287 Structure of bacteriophage P1 head provides insight into capsid polymorphism

Sen, A.; Nakamura, T.; Terashi, G.; Kim, K.; Bhatt, V.; Chellam, S.; Tran, L.; Kihara, D.

10.1101/2025.11.26.689930 — biophysics — Posted on 2025-11-28

288 Spectral tuning and signaling of diverse and most red sensitive visual rhodopsins that drive high colour discrimination in Mantis Shrimp eyes

Brouillon, C.; Pushkarev, A.; Lienard, M. A.; Hwang, S.; Munhoven, A.; McDowell, R. J.; Lucas, R. J. J.; Porter, M.; Sun, H.; Hegemann, P.

10.1101/2025.11.25.690411 — biophysics — Posted on 2025-11-28

289 NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores In Single-Molecule Sensing

Liu, Y.; Su, Z.; Yang, W.; Li, D.; Zhang, J.; Zhang, Y.; Zeng, T.; Zhang, Y.; Li, Y.; Fan, G.; Ma, K.; Liu, S.; Xu, X.; Dong, Y.; Wang, Z.

10.1101/2025.11.25.690617 — bioinformatics — Posted on 2025-11-28

290 Ovo, an Open-Source Ecosystem for De Novo Protein Design

Prihoda, D.; Ancona, M.; Calounova, T.; Kral, A.; Polak, L.; Hrban, H.; Dickens, N. J.; Bitton, D. A.

10.1101/2025.11.27.691041 — bioinformatics — Posted on 2025-11-28

291 Deep-learning model guided discovery and characterization of bacterial unspecific peroxygenases

Shen, X.; Song, D.; Zhang, H.; Yang, Q.; Chen, B.

10.1101/2025.11.27.690923 — bioinformatics — Posted on 2025-11-28

292 Composite biomaterials of polyelectrolyte complex micelle nanoparticles in hyaluronic acid gels enable local, targeted miR-92a inhibition and enhanced angiogenesis in diabetic wound repair

Xi, B. J.; Wang, S.; Alpar, A. T.; Hubbell, J. A.; Fang, Y.; Tirrell, M. V.

10.1101/2025.11.25.690510 — bioengineering — Posted on 2025-11-28

293 Process optimization for enhanced enzymatic nylon deconstruction

Bourgery, C.; Zhang, L.; Carper, D. L.; Zhou, M.; Sacci, R.; Korey, M.; Wang, L.; Hemond, J.; Cahill, J. F.; Bocharova, V.; Michener, J. K.

10.1101/2025.11.26.690883 — biochemistry — Posted on 2025-11-28

294 D-BLUP: a differentiable genomic BLUP model with learnable variance and marker weights

Guhlin, J. G.; Dearden, P.

10.1101/2025.11.25.690542 — genomics — Posted on 2025-11-28

295 Robotic Handling Preserves Induced Pluripotent Stem Cell Derived Vascular Smooth Muscle Cells Differentiation using a Weekend-free, Automatable, Low-variability, Low-cost (WALL) Protocol

Bax, M. C.; Ramalingam, J.; Romanov, V.; Alsherbiny, M. A.; Junday, K.; Thorpe, J.; Hurley, E.; Lim, M.; Tarr, I.; Hesselson, S.; Giannoulatou, E.; Liu, R.; Hill, A.; Iismaa, S.; Graham, R. M.

10.1101/2025.11.25.690512 — developmental biology — Posted on 2025-11-28

296 The pos-1 3' untranslated region governs germline specification and proliferation to ensure reproductive robustness

Varderesian, H. V.; Utaegbulam, J. N.; Brown, H. E.; Ramirez, B.; Velcani, M.; Ryder, S. P.

10.1101/2025.11.26.690476 — developmental biology — Posted on 2025-11-28

297 CaRPOOL: A Pooled Calcium-Recording CRISPR Screening Platform Identifies CCR7 as a Modulator of Cellular Osmomechanosensing

Ouyang, M.; Wang, J.; Tian, R.

10.1101/2025.11.27.690909 — cell biology — Posted on 2025-11-28

298 Host-derived lipid transfer and metabolic reprogramming in a ciliate-algal symbiosis

Chen, Y.-J.; Wei, C.-Y.; Kamal, M. M.; Hsu, C.-W.; Hsiao, S.-Y.; Lee, D.-C.; Wang, P.-L.; Leu, J.-Y.

10.1101/2025.11.27.690892 — microbiology — Posted on 2025-11-28

299 From microbiome to sperm motility traits: An inside out perspective

Graziano, M.; Garbini, G. L.; Devigili, A.; Pinzoni, L.; Quagliariello, A.; Bosi, E.; Gasparini, C.; Fondi, M.; Martino, M. E.

10.1101/2025.11.28.691116 — microbiology — Posted on 2025-11-28

300 GPR37 activation erases spinal pain memory and resolves increased nociception in murine models

Hammond, R. M.; Wang, J.; Pariyar, R.; Koo, H.; La, J.-H.

10.1101/2025.11.25.690482 — neuroscience — Posted on 2025-11-28

301 Transcriptional response to chronic long-access fentanyl self-administration in rat habenula and amygdala

Magnard, R.; Gonzalez-Padilla, D.; Yalcinbas, E. A.; Chaloux-Pinette, E.; Eagles, N. J.; Totty, M. S.; Janak, P. H.; Collado-Torres, L.; Maynard, K. R.

10.1101/2025.11.25.690517 — neuroscience — Posted on 2025-11-28

302 Engineered symbiont biosensor maps micron-scale sugar gradients in the honeybee gut

Chhun, A.; Quinn, A.; Steiner, T.; Zoppi, F.; Nguyen, T. H. G.; Engel, P.; Schaerli, Y.

10.1101/2025.11.28.691108 — synthetic biology — Posted on 2025-11-28

303 Mammary Fibroblasts Secrete Damage Associated Molecular Patterns through Extracellular Vesicles in Response to Ionizing Radiation

Sanchez, G. B.; Patel, P.; Gomez-Crase, P.; Kim, C.; Rose, K. L.; Rafat, M.

10.1101/2025.11.25.690532 — cancer biology — Posted on 2025-11-28

304 Preserving Information and Integrity in Cryo-EM: A Fourier-Space Deposition Approach

Otwinowski, Z.; Bromberg, R.; Guo, Y.; Borek, D.

10.1101/2025.11.26.690836 — biophysics — Posted on 2025-11-28

305 A New Fight-or-Flight Pacemaker Mechanism via Ryanodine Receptor Abundance and Superclustering

Subirachs, V. V.; Syevda, T.; Maltsev, A. V.; Yang, D.; Lakatta, E. G.; Stern, M. D.; Maltsev, V. A.

10.1101/2025.11.26.690788 — biophysics — Posted on 2025-11-28

306 Rewriting protein alphabets with language models

Pantolini, L.; Studer, G.; Engist, L.; Pudziuvelyte, I.; Pommerening, F.; Waterhouse, A. M.; Tauriello, G.; Steinegger, M.; Schwede, T.; Durairaj, J.

10.1101/2025.11.27.690975 — bioinformatics — Posted on 2025-11-28

307 Fine-Tuning Protein Language Models Enhances the Identification and Interpretation of the Transcription Factors

Hassan, M. T.; Gaffar, S.; Zahid, H.; Lee, S. J.

10.1101/2025.11.27.691010 — bioinformatics — Posted on 2025-11-28

308 Transcriptional Profiling and Co-expression Integration for the Filtering of Relevant Bacterial sRNA-mRNA Interactions: Application to Staphylococcus aureus Biofilm

Ribeiro, C. A. M.; Quispe Saji, G. d. R.; Cerqueira e Costa, M. d. O.; Viana, A. S.; Carvalho, M. F.; Figueiredo, A. M. S.; Galan-Vasquez, E.; Martinez-Hernandez, J. E.; Nicolas, M. F.

10.1101/2025.11.26.690695 — bioinformatics — Posted on 2025-11-28

309 Single-molecule dynamics reveal ATP binding alone powers substrate translocation by an ABC transporter

Nocker, C.; Pecak, M.; Nocker, T.; Fahim, A.; Susac, L.; Tampe, R.

10.1101/2025.11.27.690960 — biochemistry — Posted on 2025-11-28

310 Unconventional DNA architecture in a dopamine-bound aptamer complex

Chao, E. H. P.; Largy, E.; Kaiyum, Y. A.; Nguyen, M.-D.; Dauphin-Ducharme, P.; Johnson, P. E.; Mackereth, C. D.

10.1101/2025.11.27.690961 — biochemistry — Posted on 2025-11-28

311 Interaction and co-phase separation of SARS-CoV-2 nucleocapsid protein and human hnRNPA1 and its implications for viral life cycle

Gupta, P.; Sahu, R.; Nandi, I.; Setty, S. R. G.; Das, S.; Singh, M.

10.1101/2025.11.28.691101 — biochemistry — Posted on 2025-11-28

312 Structure, function and dynamics of mCoral, a pH responsive engineered variant of the mCherry fluorescent protein with improved hydrogen peroxide tolerance.

Ziti, A.; Aksakal, O.; Vitsupakorn, D.; Rizkallah, P.; Makolajeck, H.; Platts, J.; Menzies, G.; Jones, D.

10.1101/2025.11.26.690718 — biochemistry — Posted on 2025-11-28

313 POLQ variants with aberrant DNA polymerase activity protect against UV-induced cell death.

Weicksel, S. E.; Thomas, C.; Hall, E.; Ray, S.; Towle-Weicksel, J. B.

10.1101/2025.11.26.690880 — biochemistry — Posted on 2025-11-28

314 Epigenetic control of nuclear mechanics and cellular migration via histone H3 lysine 9 methylation at Lamina-Associated Domains

Comunian, S.; Petit, V.; Velasco, G.; Zakharova, V.; Jebane, C.; Lahure, P.; Joliot, V.; Del Maestro, L.; Hennion, M.; Lamour, G.; Manneville, J.-B.; Helfer, E.; Boyarchuk, E.; Ait-Si-Ali, S.

10.1101/2025.11.28.690983 — molecular biology — Posted on 2025-11-28

315 The HMGN Proteins Are Transcriptional Regulatory Factors in Humans

Cruz-Becerra, G.; Zau, J.; Purow-Ruderman, R.; Dao, A.; Delatte, B.; Chapin, N.; Kassavetis, G. A.; Kadonaga, J. T.

10.1101/2025.11.27.690916 — molecular biology — Posted on 2025-11-28

316 Shift in pre-existing antibiotic heteroresistance explains AST change from susceptible to resistant during patient treatment

Kittleson, B.; Abbott, C.; Kaye, K.; Weiss, D. S.

10.1101/2025.11.27.690971 — microbiology — Posted on 2025-11-28

317 The phage {Phi}13-encoded transcriptional regulator Ltr controls phage assembly in Staphylococcus aureus

Wolz, C.; Dobritz, R.; Baecker, M.; Rohmer, C.; Korn, N.; Bisanzio, V.

10.1101/2025.11.28.691083 — microbiology — Posted on 2025-11-28

318 Structure of NO16, a marine non-tailed vibriophage with a global distribution

Otaegi-Ugartemendia, S.; Condezo, G. N.; Martinez, M.; Kalatzis, P. G.; Middelboe, M.; San Martin, C.

10.1101/2025.11.28.690173 — microbiology — Posted on 2025-11-28

319 Evaluating the Synergetic Effect of Nigella sativa Extract and Metal Oxide Nanoparticles Against Different Microbes

Jan, M. O.; Jan, A.

10.1101/2025.11.28.691110 — microbiology — Posted on 2025-11-28

320 Detection and isolation of H5N1 clade 2.3.4.4b high pathogenicity avian influenza virus from ticks (Ornithodoros maritimus) recovered from a naturally infected slender-billed gull (Chroicocephalus genei)

Andrieux, D.; Crispo, M.; Dirat, M.; Lebouteiller, L.; Walch, M.; Lienard, E.; CROVILLE, G.; Fusade-Boyer, M.; Palumbo, L.; Hirschinger, J.; Le Loc'h, G.; GUERIN, j.-l.; SOUBIES, S. M.; Gaide, N.

10.1101/2025.11.28.689408 — microbiology — Posted on 2025-11-28

321 Direct recruitment of RNA Polymerase II by NANOG to activated target genes

Mullin, N. P.; Barbieri, E.; Zhang, J.; Vojtek, M.; McGarvey, A.; Colby, D.; Tomlinson, S.; Chambers, I.

10.1101/2025.11.27.690710 — cell biology — Posted on 2025-11-28

322 The ERCC6L2-MRI-KU complex coordinates NHEJ at staggered DNA double-strand breaks.

Reichl, P. I.; Sonmez, C.; Sun, Y.; King, A.; Davies, B.; Wilkinson, A. C.; Lottersberger, F.; Chapman, J. R.

10.1101/2025.11.28.691009 — molecular biology — Posted on 2025-11-28

323 RNA degradation modulates unique aging-related gene expression in naked mole-rats

Matsubara, R.; Wu, J.; Ozeki, A. N.; Kawamura, Y.; Hamada, M.; Miura, K.; Akimitsu, N.

10.1101/2025.11.28.691058 — molecular biology — Posted on 2025-11-28

324 Extracellular electron transport in coral-algal symbiosis studied by chlorophyll fluorescence relaxation and ferricyanide reduction

Aslam, S. M.; Patil, P. P.; Kovacs, S.; Larkum, A. W. D.; Szabo, M.; Vass, I.

10.1101/2025.11.26.690407 — plant biology — Posted on 2025-11-28

325 Synthetic tools to redirect the ubiquitin E3 ligase activity of, PRT1, a plant-specific N-recognin.

Oldham, K. E. A.; Mabbitt, P. D.

10.1101/2025.11.27.690864 — plant biology — Posted on 2025-11-28

326 Evaluation of single-cell RNA profiling technologies using FFPE, fresh, and frozen ccRCC tumor specimens

Xirenayi, S.; Camp, S. Y.; Garza, A. E.; Rustagi, Y.; Pimenta, E.; Shannon, E.; Nag, A.; Betherman, A.; Anselmo, A.; Trowbridge, R.; Thorner, A. R.; Park, J.; Bi, K.; Van Allen, E. M.

10.1101/2025.11.25.690485 — cancer biology — Posted on 2025-11-28

327 DeepPathway: Predicting Pathway Expression from Histopathology Images

Ahsan, M. A.; Piper Hanley, K.; Fergie, M.; O'leary, C.; Borst, G.; Roncaroli, F.; Minhas, F.; Rattray, M.; Iqbal, M.; Baker, S. M.

10.1101/2025.07.21.665956 — bioinformatics — Posted on 2025-11-28

328 Clinical Implications of SRPK1 Expression in Human Tumours: A Comprehensive Pan-Cancer Analysis Based on Multi-Omics Databases

Duzgun, D.; Oltean, S.

10.1101/2025.11.25.690492 — bioinformatics — Posted on 2025-11-28

329 Multi-omics integrative approach of senescent endothelial cells and derived extracellular vesicles in a replicative senescence model

Milhano-Santos, F.; Ramirez-Carracedo, R.; Ciordia, S.; Clavain, L.; Hernandez-Fonseca, J. P.; Martin-Jouve, B.; Bodega, G.; Ramirez, R.; Ruiz-Torres, M. P.; Lopez-Granero, C.; Ruiz-Ortega, M.; Alique, M.

10.1101/2025.11.25.690417 — cell biology — Posted on 2025-11-28

330 FRG1 Regulates Nonsense-Mediated mRNA Decay by Modulating UPF1 Levels

Palo, A.; Mohapatra, T.; Singh, A.; T, S.; Mohanty, S.; Swain, R. K.; Dixit, M.

10.1101/2025.11.18.689056 — molecular biology — Posted on 2025-11-28

331 Reconstitution of glycan-driven MHC I recycling reveals calreticulin as mediator between TAPBPR and tapasin

Heinke, T. J.; Fahim, A.; Popovic, N.; Rath, T.; Morgner, N.; Trowitzsch, S.; Tampe, R.

10.1101/2025.11.25.690393 — immunology — Posted on 2025-11-28

332 Disabling a key viral innate immunity antagonist converts measles vaccine into RIG-I-driven cancer immunotherapy

Barinov, A.; Vera-Peralta, H.; Nader, J. S.; Najburg, V.; Combredet, C.; Arbabian, A.; Gracias, S.; Frantz, P. N.; Vibert, R.; Simard, E.; Coateval, M.; Pouliquen, D.; Petithomme, T.; Prot, M.; Simon-Loriere, E.; Hardy, D.; Louzili, S.; Brzezicha, B.; Hoffmann, J.; Riebbels, V.; Le Bigot, J.-F.; Gregoire, M.; Fonteneau, J.-F.; Komarova, A.; Boisgerault, N.; Tangy, F.

10.1101/2025.10.03.680227 — immunology — Posted on 2025-11-28

333 High-resolution MRI Guided Whole Mouse Brain Cell Type Atlas using Deep Learning

Han, X.; Hu, R.; Liu, Z.; Chen, J.; Jafry, M.; Song, H.; Zhao, Y.; Lin, M.; White, L. E.; Johnson, G. A.; Wang, N.

10.1101/2025.11.25.690475 — neuroscience — Posted on 2025-11-28

334 Quantitative modelling of biological response dynamics reveals novel patterns in plant volatile signalling

Waterman, J. M.; Moore, G. J.; Amdahl-Culleton, L. K.; Hoefer, S.; Erb, M.

10.1101/2025.11.26.690448 — plant biology — Posted on 2025-11-28

335 Mechanics and growth coordination define SOSEKI-based polarity fields

Piepers, M.; Reyes-Hernandez, B. J.; Ramos, J. R.; Boelke, N.; Schuetz, L.; Song, C.; Primc, A.; Bald, L.; Merks, R. M.; Maizel, A.

10.1101/2025.11.26.690761 — plant biology — Posted on 2025-11-28

336 Root meristem growth factor (RGF) peptide signaling as a molecular bridge between root development and non-lethal thermal stress adaptation

Hsiao, Y.-C.; Lai, J.-K.; Shiue, S.-Y.; YAMADA, M.

10.1101/2025.11.27.690926 — plant biology — Posted on 2025-11-28

337 Engineering sHsp17 and Hsp90 in Zea mays to Develop Thermotolerance

Babar, U.; Rana, I. A.

10.1101/2025.11.26.690697 — plant biology — Posted on 2025-11-28

338 Production of prolyl-hydroxylated human type III collagen in Physcomitrella photobioreactors

Bohlender, L. L.; Parsons, J.; Mitgau, A.; Hoernstein, S. N. W.; Grigolon, G.; Henes, B.; Decker, E. L.; Reski, R.

10.1101/2025.11.26.690659 — plant biology — Posted on 2025-11-28

339 CPIExtract: A software package to collect and harmonize small molecule and protein interactions

Piras, A.; Sebek, M. L.; Chenghao, S.; Ispirova, G.; Menichetti, G.

10.1101/2024.07.03.601957 — bioinformatics — Posted on 2025-11-28

340 Triad-LMF: A Hierarchical Low-Rank Multimodal Fusion Framework for Robust Cancer Subtype Classification Using Multi-Omics Data

Tan, X.; Chen, X.; Tian, R.; Cai, Q.; Jiang, M.; Yang, D.; Zhang, L.

10.1101/2025.05.15.653805 — bioinformatics — Posted on 2025-11-28

341 Language may be all omics needs: Harmonizing multimodal data for omics understanding with CellHermes

Gao, Y.; Wang, W.; Zhao, Y.; Dong, K.; Shan, C.; Zheng, W.; Richter, T.; Li, Z.; Chen, S.; Theis, F. J.; Liu, Q.

10.1101/2025.11.07.687322 — bioinformatics — Posted on 2025-11-28

342 Advancements in an Automated Breast Density Detection Technique for Breast Cancer Risk Prediction: a Synthetic Signal-dependent Noise Construct

Heine, J.; Fowler, E.; Schabath, M. B.; Egan, K. B.

10.1101/2025.11.25.690493 — bioengineering — Posted on 2025-11-28

343 Development of a Novel Methyl Cellulose Hydrogel with Physiologically-Relevant Controlled Ethanol Release for Cervical Dysplasia Ablation

Jankowski, A. M.; Imanoel, E.; Adhikari, G.; Mueller, J.; Maisel, K.

10.1101/2025.11.25.690497 — bioengineering — Posted on 2025-11-28

344 Mineralized Tissue-Targeting Expression System for Local Control of Gene Expression

Liu, J.; Chen, Q.; Yoon, I.-C.; Makkar, H.; Zhang, S.; Chen, Y.-C.; Li, Y.; Thussananutiyakul, J.; Xue, L.; Zhang, S.; Xu, J.; Luo, Y.; Chen, K.; MITCHELL, M.; Chen, C.; Vining, K. H.

10.1101/2025.11.25.690451 — bioengineering — Posted on 2025-11-28

345 Evolution of objectives can enable prosocial behaviour without social awareness

Meyer, B.; Yang, Y.

10.1101/2025.08.06.668887 — animal behavior and cognition — Posted on 2025-11-28

346 Adaptive Partial Conjunction Hypothesis: Identifying Pleiotropy Across Heterogeneous Effect Units

Li, Y.; Lu, Z.; Lin, X.

10.1101/2025.11.25.690340 — genetics — Posted on 2025-11-28

347 Local and Spatial Processes Shape the Collapse and Recovery of Mutualistic Networks

Bhandary, S.; Bascompte, J.

10.1101/2025.11.25.690369 — ecology — Posted on 2025-11-28

348 Optimizing crop clustering to minimize pathogen invasion in agriculture

Suprunenko, Y. F.; Gilligan, C. A.

10.1101/2025.03.07.642019 — ecology — Posted on 2025-11-28

349 Mitochondrial pull-out controls mitochondrial structure in response to mitochondrial activity

Kasmaie, A.; Gatti, P.; Ilamathi, H. S.; Gueye, S. M.; Brown, A. I.; Germain, M.

10.1101/2025.11.25.690431 — cell biology — Posted on 2025-11-28

350 Deubiquitinase USP-14 controls intestinal distension-induced immune activation in Caenorhabditis elegans via Wnt/β-catenin signaling

Ghosh, A.; Singh, J.

10.1101/2025.11.25.690479 — immunology — Posted on 2025-11-28

351 The fat-body secreted neuropeptide CCHa2 signals insulin-producing cells in the brain to promote sleep

Biglari, S.; Gong, S.; Wang, M. C.; Payne, C.; Kauffman, M. R.; DiAngelo, J. R. R.; Keene, A.

10.1101/2025.11.25.690337 — neuroscience — Posted on 2025-11-28

352 The molecular mechanism of uptake and cell-to-cell transmission of arginine-containing dipeptide repeat proteins.

Sutter, A. B.; Buksh, B. F.; Mojsilovic-Petrovic, J.; Dalton, C.; Till, N. A.; Morgan, D. C.; MacMillan, D. W. C.; Kalb, R. G.

10.1101/2025.11.25.690484 — neuroscience — Posted on 2025-11-28

353 Eating to survive...or not? feeding compensation and toxicity in a songbird exposed to thiamethoxam trated seeds

Poliserpi, M. B.; Fernandez-Vizcaino, E.; Brodeur, J.

10.1101/2025.11.25.690477 — zoology — Posted on 2025-11-28

354 Illuminating the Role of Asymmetric Mitochondrial Fission on Beta-Cell Health

Henning, P.; Schultz, J.; Baltrusch, S.; Uhrmacher, A. M.

10.1101/2025.11.25.690461 — systems biology — Posted on 2025-11-28

355 Gene duplication drove functional divergence of two effectors in the maize anthracnose pathogen

Garcia-Rodriguez, P.; Rodriguez-Monaco, L.; Fernandez-Cuevas, F. B.; Zambrano, S. D. B.; Gutierrez-Sanchez, S.; Jerez-Vanegas, A.; Rogerio, F.; Ortiz-Alvarez, J.; Baroncelli, R.; Espeso, E. A.; Thon, M.; Sukno, S. A.

10.1101/2025.11.26.690860 — plant biology — Posted on 2025-11-28

356 In vivo effects of Cisplatin and titanium dioxide nanoparticles combined treatment

Costa, C. N.; Ciapina, L. P.; Bahia, A. C.; Neto, V. B. d. S.; da Silva, F. A. B.; Lopes, F.

10.1101/2025.11.03.685613 — pharmacology and toxicology — Posted on 2025-11-28

357 Drug-Eluting, Radiopaque, Tumor-Casting Hydrogels for Endovascular Locoregional Therapy of Hepatocellular Carcinoma

Dong, Y. C.; Villasenor, K. E.; Yoon, S.; Islam, A.; Vasquez, L.; Gurevich, A.; McLaughlin, S.; Gade, T. P.; Cormode, D. P.

10.1101/2025.11.25.690505 — cancer biology — Posted on 2025-11-28

358 Proteostasis Modelling using Deuterated Water Metabolic Labeling and Data-Independent Acquisition Mass Spectrometry

Deberneh, H. M.; Wilkinson, D. J.; Crossland, H.; Basisty, N.; Smith, K.; Atherton, P. J.; Sadygov, R. G.

10.1101/2025.11.25.690247 — bioinformatics — Posted on 2025-11-28

359 scDNAm-GPT Captures Genome-wide CpG Dependencies in Single-cell DNA methylomes to Revolutionize Epigenetic Analysis

Liang, C.; Ye, P.; Yan, H.; Zheng, P.; Sun, J.; Wang, Y.; Li, Y.; Ren, Y.; Jiang, Y.; Wei, R.; Xiang, J.; Zhang, S.; Jiang, L.; Bai, W.; Ma, X.; Chen, T.; Zuo, W.; Bai, L.; Ouyang, W.; Li, J.

10.1101/2025.02.19.638959 — bioinformatics — Posted on 2025-11-28

360 Impact of multi-echo ICA modeling decisions on motor-task fMRI analysis

Reddy, N. A.; Medina, M. C.; Northrop, J. N.; Zou, C.; Clements, R. G.; Nehrujee, A.; Sandhu, M.; Bright, M. G.

10.1101/2025.11.25.690440 — bioengineering — Posted on 2025-11-28

361 mfSuSiE enables multi-cell-type fine-mapping and multi-omic integration of chromatin accessibility QTLs in aging brain.

Liu, A.; De Jager, P. L.; Bennett, D.; The Alzheimer's Disease Functional Genomics Consortium, ; Wang, G.; Denault, W. R. P.

10.1101/2025.11.25.690439 — genetics — Posted on 2025-11-28

362 Oncogenic Ppm1d mutations deregulate the p53 pathway in primary mouse gliomas

Valentine, V.; Groth, A. J.; Tolliver, J.; Saravanapavan, A.; Maingi, S. M.; Weidenhammer, L. B.; Williams, N. T.; Luo, L.; Waitkus, M. S.; Jacob, S.; Reitman, Z. J.

10.1101/2025.11.25.690483 — genetics — Posted on 2025-11-28

363 ER-phagy and mitophagy programs in human CD4+ memory T cells before and after activation

Morone, D.; Raimondi, A.; Molinari, M.

10.1101/2025.11.25.690386 — cell biology — Posted on 2025-11-28

364 Mini-agrin prevents calcium leakage and restores the dystrophin complex.

Aldharee, H.; Mierzejewski, B.; Kerr, A.; Bragg, L.; Bigot, A.; Reinhard, J. R.; Santoleri, S.; Roberts, N.; Das, R.; Mouly, V.; Ruegg, M. A.; Cossu, G.; Galli, F.

10.1101/2025.11.25.690165 — cell biology — Posted on 2025-11-28

365 Simulation based-inference of epidemiological and phylodynamic models via Neural Posterior Estimation

Pinotti, F.; Theze, J.; Bailly, X.; Fournie, G.

10.1101/2025.11.25.690436 — systems biology — Posted on 2025-11-28

366 The histone methyltransferase SDG26 shapes cold stress responses in Arabidopsis through chromatin-based regulation of ABA-dependent and ABA-independent pathways

Xue, Z.; Zumsteg, J.; Mathieu, E.; Shen, W.-H.; Berr, A.

10.1101/2025.11.25.690385 — plant biology — Posted on 2025-11-28

367 Reconnecting food production and consumption through redesigning food systems to support healthy diets

De Clerck, C.; Desmarez, T.; Delandmeter, M.; de Faccio Carvalho, P. C.; Dumont, B.; Bindelle, J.

10.1101/2025.11.25.690428 — plant biology — Posted on 2025-11-28

368 CLPC2 plays specific roles in CLP complex-mediated regulation of growth, photosynthesis, embryogenesis and response to growth-promoting microbial compounds

Leal-Lopez, J.; Bahaji, A.; De Diego, N.; Tarkowski, P.; Baroja-Fernandez, E.; Munoz, F. J.; Almagro, G.; Perez, C. E.; Bastidas-Parrado, L. A.; Loperfido, D.; Caporalli, E.; Ezquer, I.; Lopez-Serrano, L.; Ferez-Gomez, A.; Coca-Ruiz, V.; Pulido, P.; Morcillo, R. J. L.; Pozueta-Romero, J.

10.1101/2025.11.25.690394 — plant biology — Posted on 2025-11-28

369 HIF-1α and HIF-2α transcription factors differentially regulate lung alveolar macrophage function

Priego, E.; Adan-Barrientos, I.; Conde-Garrosa, R.; Martinez-Cano, S.; Sanchez, I.; Mananes, D.; Mastrangelo, A.; Amores, J.; Izquierdo, H. M.; Sancho, D.

10.1101/2025.11.25.690373 — physiology — Posted on 2025-11-28

370 Sex-Specific neurogenic and cognitive responses in a murine model of accelerated aging

Gomez-Oliva, R.; Chamorro-Francisco, A.; Atienza-Navarro, I.; Carrascal, L.; Freire-Aragon, M. D.; Hernandez-Galan, R.; Nunez-Abades, P.; Garcia-Alloza, M.; Castro, C.

10.1101/2025.11.25.690416 — pharmacology and toxicology — Posted on 2025-11-28

371 Extending digital biology: bacterial survival and morphological heterogeneity under antibiotic stress

Maikranz, E.; Aristov, A.; Le Quellec, L.; Baroud, C.

10.1101/2025.11.25.690353 — bioengineering — Posted on 2025-11-28

372 Antimetastatic Sulfonate-Functionalized Mesoporous Silica Nanoparticles Enhance Irinotecan Stability and Delivery for Colorectal Cancer Treatment

Wu, C.-H.; Chen, Z.-A.; Zhang, R.-L.; Sun, T. C.; Li, D.-W.; Lin, C. K.; Wu, S.-H.; Chen, P.; Mou, C.-Y.; Chen, Y.-P.

10.1101/2025.11.25.690433 — bioengineering — Posted on 2025-11-28

373 Inverse directions of association of higher physical activity and higher insulin resistance with human skeletal muscle cell type abundance and fiber type-level gene expression

Ciotlos, D. L.; Hanks, S. C.; Varshney, A.; Erdos, M. R.; Manickam, N.; Stringham, H. M.; Orchard, P.; Hill-Burns, E. M.; Narisu, N.; Bonnycastle, L. L.; Sweeney, M. D.; Saramies, J.; Laakso, M.; Tuomilehto, J.; Lakka, T. A.; Mohlke, K. L.; Boehnke, M.; Collins, F. S.; Koistinen, H. A.; Parker, S. C. J.; Scott, L. J.

10.1101/2025.10.27.683567 — genomics — Posted on 2025-11-28

374 Seasonal variation in insect assemblages at flowers of Balanites aegyptiaca, an ecologically and socially important tree species in the Ferlo region of Senegal's Great Green Wall corridor

MEDINA-SERRANO, N.; Bagneres, A.-G.; Ndiaye, M. M.; Vrecko, V.; McKey, D.; Hossaert, M.

10.1101/2025.03.26.645493 — ecology — Posted on 2025-11-28

375 Goldilocks conundrum explains cryoinjury in slow-cooled amphibian embryonic cells

Patel, R.; Upton, R.; Clulow, S.; Nixon, B.; Mahony, M.; Clulow, J.

10.1101/2025.11.24.690295 — developmental biology — Posted on 2025-11-28

376 Brush border intermicrovillar adhesion limits bacterial attachment to the small intestine brush border

Cowell, R. P.; Bickart, A. C.; Shashi, S. R.; Vasquez, A.; Brackman, L. C.; Abdel-Dayem, M. A.; Chen, W.; Bowman, D. M.; Krystofiak, E. S.; Essalki, Y.; Gross, I.; Harrison, D. G.; Wanjalla, C. N.; Algood, H. M.; Tyska, M. J.; Meenderink, L. M.

10.1101/2025.11.25.690363 — cell biology — Posted on 2025-11-28

377 Modulatory Effects of the Motor Imagery and Jendrassik Maneuver upon the Forearm H-Reflex and Electroencephalographic Activity

Starodubtseva, N. M.; Morozova, M. V.; Lebedev, M. A.

10.1101/2025.11.25.690346 — neuroscience — Posted on 2025-11-28

378 A developmentally inspired computational model of face recognition that learns continuously through generative memory replay

Abudarham, N.; Yovel, G.

10.1101/2025.11.25.690208 — neuroscience — Posted on 2025-11-28

379 Hippocampal network activity changes during early epileptogenesis predict subsequent epilepsy

Strueber, M.; Stoeber, T. M.; Schuetz, V.; Costard, L.; Neubert, V.; Bauer, S.; Pitsch, J.; Melzer, N.; Strzelczyk, A.; Triesch, J.; Siebenbrodt, K.; Rosenow, F.; Kienitz, R.

10.1101/2025.11.25.690377 — neuroscience — Posted on 2025-11-28

380 Encoding without generation in the medial prefrontal cortex during cautious goal-directed actions

Sajid, M. S.; Zhou, J.; Castro-Alamancos, M. A.

10.1101/2025.11.25.690391 — neuroscience — Posted on 2025-11-28

381 Evidence for separate processes underlying movement and decision vigor in a reward-oriented task

Conessa, A.; Boutin, A.; Berret, B.

10.1101/2025.11.25.690375 — neuroscience — Posted on 2025-11-28

382 Oxylipin carbonyl compositions in the chloroplast compartments

Khorobrykh, S. A.; Iijima, Y.; Shibata, D.; Mano, J.

10.1101/2025.11.25.690356 — plant biology — Posted on 2025-11-28

383 Integrative spatial multi-omics reveals prognostic tumor niches in female genital tumors

Xu, T.; Lin, S.; Wu, Y.; He, Y.; Zhang, Z.; Zhao, Y.; Zhang, P.; Zhao, L.; Yang, W.; Ye, M.; Zhang, R.; Wen, L.; Ren, P.; Luo, C.; Zhang, Z.; Zeng, Z.; Meng, Y.

10.1101/2025.11.24.690313 — genomics — Posted on 2025-11-28

384 Deep-mutational scanning libraries using tiled-region exchange mutagenesis

Kindree, K.; Chochinov, C. A.; Bhachu, K.; Cheng, Y.; Caron, A.; McDonald, M.; Mamai, Z.; Nguyen Ba, A. N.

10.1101/2025.09.05.674540 — molecular biology — Posted on 2025-11-28

385 Balancing Efficiency and Compensation: Age-related Theta and Alpha Dynamics in High-load Working Memory

Leon-Correa, E.; Ruhnau, P.; Balani, A.; Qureshi, A.; Tse, D.; MAKRIS, S.

10.1101/2025.11.26.690640 — neuroscience — Posted on 2025-11-28

386 A chronic state biostimuli-responsive therapeutic model system: applications to skin tissue repair and regeneration

Duncan, A.; Djakite, T.; Echalard, A.; Labat, B.

10.1101/2025.11.24.690306 — systems biology — Posted on 2025-11-28

387 Evolutionary rewiring of host metabolism and interferon signalling by SARS-CoV-2 variants

Somji, R.-A.; Brown, J. C.; Rowles-Khalid, S.; Abdullahi, T. B.; Luo, D.; Barthel, N.; Mulleder, M.; Ralser, M. S.; Barclay, W. S.; Rallis, C.; Giotis, E. S.

10.1101/2025.11.15.688605 — systems biology — Posted on 2025-11-28

388 Impact of Science Beliefs, Teaching Efficacy, and Incentives on Preschool Science Teaching: A Moderated-Mediation Model

Yanhui, F.; Wang, L.

10.1101/2025.11.26.690867 — scientific communication and education — Posted on 2025-11-28

389 COMPARATIVE ANALYSIS OF TWO-DIMENSIONAL AND THREE-DIMENSIONAL MRI RADIOMICS MODELS FOR PREDICTING MOLECULAR BIOMAKERS IN BREAST CANCER.

Wang, X.; Liu, X.; Wang, Z.

10.1101/2025.11.26.690866 — cancer biology — Posted on 2025-11-28

390 MARRVEL-MCP enables natural language variant interpretation through autonomous workflow construction

Everton, Z. J.; Botas, J.; Kim, S. Y.; Liu, Z.; Jeong, H.-H.

10.1101/2025.11.26.690887 — bioinformatics — Posted on 2025-11-28

391 Sensorineural regulation of skull healing implicates FGF1 signaling in non-healing bone

Horenberg, A. L.; Villapudua-Gastelum, C.; Xu, M.; Zeng, E.; Dias, S.; Sinha, T.; Archer, M.; Scheller, E. L.; Pathak, A.; James, A.; Grayson, W.

10.1101/2025.11.24.690319 — bioengineering — Posted on 2025-11-28

392 Observational epidemiological studies can mitigate genetic confounding with the genetic relatedness matrix

Patel, R. A.; Schraiber, J. G.; Pennell, M.; Edge, M. D.

10.1101/2025.11.24.690292 — genetics — Posted on 2025-11-28

393 Using General Algebra to Model the Directed Evolution of an Asexual Population

Park, K.

10.1101/2025.11.22.689897 — evolutionary biology — Posted on 2025-11-28

394 The Vaginal Microbiome in Women Recently Experiencing BV and UTI

Gilbert, N.; Whang, S. N.; Wang, X.; Thomas-White, K. J.; Olmschenk, G.; Garza, J. E.; Navarro, P.

10.1101/2025.11.27.690987 — microbiology — Posted on 2025-11-28

395 Sleep-like slow waves in wakefulness index post-stroke behavioural alterations

Pearce, D. J.; Biabani, M. J.; Chong, T. T.-J.; Demeyere, N.; Loughnane, G. M.; Mattingley, J. B.; Moore, M. J.; New, P. W.; O'Connell, R. G.; Rangelov, D.; Stolwyk, R. J.; Webb, S.; Brosnan, M. B.; Andrillon, T.; Bellgrove, M. A.

10.1101/2025.11.24.689850 — neuroscience — Posted on 2025-11-28

396 Spatio-temporal modelling of in vitro viral infection: the impact of defective interfering particles on type I interferon response

Li, Y.; Nielsen, B. F.; Levin, S. A.; te Velthuis, A. J. W.; Grenfell, B.

10.1101/2025.10.09.681519 — systems biology — Posted on 2025-11-28

397 Hippocampal CA3 Nex/Neurod6+ neuron-specific TNFR2 alleviates chronic neuropathic pain by sex-dependently engaging opioid and endocannabinoid pathways

Arnab, S.; Fathi, P.; Jones, E.; Meyyappan, A.; Nguyen, K. L.; Bracchi-Ricard, V.; Gupta, S.; Fischer, R.; Tom, V. J.; Bethea, J. R.

10.1101/2025.11.24.690195 — pharmacology and toxicology — Posted on 2025-11-28

398 Cirrhosis severity modulates proteomic and immune landscapes in hepatocellular carcinoma

Shastry, R. K. R.; Kale, A.; Tee, S. S.

10.1101/2025.11.24.690286 — cancer biology — Posted on 2025-11-28

399 Growth characteristics of Myco-Composites Produced Using Locally Isolated Ganoderma Species and Lignocellulosic Waste

Kumar Mishra, A.; B. Bhatt, S.; Kundanati, L.

10.1101/2025.11.24.690336 — bioengineering — Posted on 2025-11-28

400 Neuropeptides Involved in Elicited Reversal Speed Plasticity in C. elegans During Mechanosensory Habituation

Siu, A.; Kokan, N.; Rankin, C. H.

10.1101/2025.11.24.690280 — animal behavior and cognition — Posted on 2025-11-28

401 A Porcine Model of Intervertebral Disc Injury Recapitulates Human Discogenic Pain via Notochordal Cell Loss and Pain-inducing Nucleus Pulposus Cell Emergence

Kaneda, G.; Wechsler, J. T.; Chavez, M.; Sheyn, J.; Cheema, K.; Shen, C.; Rigo De Righi, D.; Avalos, P.; Xie, Y.; Tawackoli, W.; Floyd, C.; Li, D.; Sheyn, D.

10.1101/2025.11.24.690318 — developmental biology — Posted on 2025-11-28

402 Impaired synaptic inhibition and enhanced aversion encoding by lateral habenula neurons during Δ9-tetrahydrocannabinol withdrawal.

Hwang, E.-K.; Daphne, D.; Maddox, C. C.; Zapata, A.; Hoffman, A. F.; Lupica, C. R.

10.1101/2025.11.24.690244 — neuroscience — Posted on 2025-11-28

403 Subanesthetic Ketamine Disrupts Predictive Signaling in the Prefrontal Cortex

Corrigan, B. W.; Roussy, M.; Luna, R.; Gulli, R. A.; Schall, J. D.; Sachs, A. J.; Palaniyappan, L.; Martinez-Trujillo, J. C.

10.1101/2025.11.24.690250 — neuroscience — Posted on 2025-11-28

404 How human aging disrupts the head direction network: evidence from VR experiments and mechanistic models

Bernard, M.; Shine, J.; Bicanski, A.; Wolbers, T.

10.1101/2025.11.24.690256 — neuroscience — Posted on 2025-11-28

405 Multiplex imaging combined to machine learning enable automated profiling of cortical malformations applications in tuberous sclerosis complex

Martin, R. C.; Metais, A.; Carbone, F.; Bakouh, N.; Balducci, E.; Conrozier, D.; Ameur, S.; Varlet, P.; Nabbout, R.; Kabashi, E.; Zaidi, M.; Blauwblomme, T.; Ciura, S.

10.1101/2025.11.24.690101 — neuroscience — Posted on 2025-11-28

406 Contextual unfamiliarity during drug intake induces AMPA receptors linked to relapse vulnerability

Alles, H.; Huang, X.; Schlueter, O. M.

10.1101/2025.11.24.690243 — neuroscience — Posted on 2025-11-28

407 The Role of Sleep Duration and Age in Neural Reactivation and Episodic Memory Performance Across the Adult Lifespan

Seraji, M.; Mirjalili, S.; Wiafe, S.-L.; Duarte, A.; Calhoun, V.

10.1101/2025.11.24.690290 — neuroscience — Posted on 2025-11-28

408 Individuals matter: habitat factors and plant traits shape individual-level pollinator interactions in a semi-arid landscape

Michael, D.; Joshi, K.; Krishna, S.

10.1101/2025.07.26.666931 — ecology — Posted on 2025-11-28

409 Tripartite ER-Mitochondria-Lipid Droplets contact sites control adipocyte metabolic flexibility

Palard, M.; Chadeuf, G.; Carpentier, M.; Frey, S.; Croyal, M.; Shaaban, R.; Hadjadj, S.; Cloteau, C.; Elkhallouki, N.; Bomme, P.; Le Lay, S.; Combot, Y.; Marjouh, M.; Paul-Gilloteaux, P.; Antreou, A.; Le May, C.; Ducheix, S.; Cariou, B.; Giordano, F.; Rieusset, J.; Thiam, A. R.; Prieur, X.

10.1101/2025.09.16.676493 — cell biology — Posted on 2025-11-28

410 A fourth locus in the Plasmodium falciparum genome associated with sickle haemoglobin

Hamilton, W. L.; Forster, A. J.; Aniweh, Y.; Asoala, V.; Drury, E.; Rockett, K. A.; Awandare, G. A.; Kwiatkowski, D. P.; Band, G.; Amenga-Etego, L. N.

10.1101/2023.09.14.557461 — microbiology — Posted on 2025-11-28

411 Mitochondrial protein FgDML1 regulates DON toxin biosynthesis and cyazofamid sensitivity in Fusarium graminearum by affecting mitochondrial homeostasis

Wang, C.; Mao, X.; Cong, W.; Yang, L.; Hou, Y.

10.1101/2025.05.23.655648 — microbiology — Posted on 2025-11-28

412 Temporal Dynamics of Sensorimotor Integration for Auditory and Proprioceptive Target Information During Movement Preparation and Execution

Camponogara, I.

10.1101/2025.07.09.663821 — neuroscience — Posted on 2025-11-28

413 Developmental Trajectories of Addition and Subtraction in Early School-aged Children

Zhou, M.; Ji, S.; Zhang, Y.; Shen, H.; Huang, J.; Zhang, Q.; Li, Y.; Mei, H.; Kuang, R.; Lin, Y.; Song, Y.; Huang, J.; Dong, X.

10.1101/2025.11.27.691071 — neuroscience — Posted on 2025-11-28

414 The human neuroblastoma SH-SY5Y cell line as a model to assess β-amyloid neurotoxicity: A systematic review and meta-analysis

Reges Pinheiro, N.; Franca Dias Carneiro, C.; Scarcella Cancelliero, G.; Orlovski Nogueira, G.; Almeida, G.; Fernandes, N.; Wasilewska-Sampaio, A. P.; Martins, S.; Felix, A.; Amaral, O. B.; Sebollela, A.

10.1101/2025.10.20.683497 — neuroscience — Posted on 2025-11-28

415 Precision of reaches and proprioception in motor control and adaptation

Henriques, D. Y.; Gastrock, R. Q.; 't Hart, B. M.

10.1101/2025.06.14.659693 — neuroscience — Posted on 2025-11-28

416 Brief and localized pulsed transcranial photobiomodulation cumulatively increases EEG power across the brain in healthy young adults

Mathew, A. A.; Van Lankveld, H.; Zhong, X. Z.; Chen, J. X.; Niculescu, S.; Zomorrodi, R.; Chen, J. J.

10.1101/2025.05.26.656199 — physiology — Posted on 2025-11-28

417 Enhanced metagenomics-enabled transmission inference with TRACS

Tonkin-Hill, G.; Shao, Y.; Zarebski, A. E.; Mallawaarachchi, S.; Xie, O.; Maklin, T.; Thorpe, H. A.; Davies, M. R.; Bentley, S. D.; Lawley, T. D.; Corander, J.

10.1101/2024.08.19.608527 — bioinformatics — Posted on 2025-11-28

418 Prompt-to-Pill: Multi-Agent Drug Discovery and Clinical Simulation Pipeline

Vichentijevikj, I.; Mishev, K.; Simjanoska Misheva, M.

10.1101/2025.08.12.669861 — bioinformatics — Posted on 2025-11-28

419 A high-resolution analysis of arrestin2 interactions responsible for CCR5 endocytosis

Petrovic, I.; Desai, S.; Isaikina, P.; Abiko, L. A.; Spang, A.; Grzesiek, S.

10.1101/2024.11.04.621860 — biochemistry — Posted on 2025-11-28

420 The ABCs of Cyanobacterial Glycogen: In Vitro Modelling of Glycogen Synthesis and Functional Divergence of Glycogen Synthases in Synechocystis sp. PCC 6803

Lee, K.; Bekiari, D.; Doello, S.; Forchhammer, K.

10.1101/2025.11.13.688228 — biochemistry — Posted on 2025-11-28

421 Life history and infection susceptibility parameters of Drosophila species reared on a common diet

Sun, H.; Cole, M.; Ragnoni, E.; Johnson, J.; Jarvis, A.; Hedelin, L.; Westlake, H. E.; Longdon, B.; Hanson, M. A.

10.1101/2025.11.25.690557 — evolutionary biology — Posted on 2025-11-28

422 DNA methylation site loss for plasticity-led novel trait genetic fixation

Katsumura, T.; Sato, S.; Yamashita, K.; Oda, S.; Gakuhari, T.; Tanaka, S.; Fujitani, K.; Nishimaki, T.; Imai, T.; Yoshiura, Y.; Takeshima, H.; Hashiguchi, Y.; Sekita, Y.; Mitani, H.; Ogawa, M.; Takeuchi, H.; Oota, H.

10.1101/2020.07.09.194738 — evolutionary biology — Posted on 2025-11-28

423 Mutual Inhibition Model of pattern formation: The role of Wnt-Dickkopf interactions in driving Hydra body axis formation

Mercker, M.; Kazarnikov, A.; Tursch, A.; Richter, T.; Özbek, S.; Holstein, T. W.; Marciniak-Czochra, A.

10.1101/2021.09.13.460125 — developmental biology — Posted on 2025-11-28

424 HUMAN SPINAL CORD ORGANOIDS REVEAL CELL INTERCALATION AS A CONSERVED MECHANISM FOR SECONDARY NEURULATION

Blanco-Ameijeiras, J.; El Majzoub, Y.; Garcia-Valero, M.; Rebollo, E.; Macho-Rendon, J.; Corbacho, J.; Martinez-Morales, J. R.; Marti, E.

10.1101/2024.11.19.624296 — developmental biology — Posted on 2025-11-28

425 Experience-Dependent Plasticity of Thalamoprefrontal Circuitry Characterizes Learning Across Species

Elkinbard, I.; Sadeghzadeh, S.; Hedlund, M.; Tsai, V.; Ho, T.; Deisseroth, K.; Buch, V.

10.1101/2025.11.23.689976 — neuroscience — Posted on 2025-11-28

426 A flexible coding scheme underlying working memory generalization in human parietal and frontal cortices

Shi, D.; Shu, L.; Yu, Q.

10.1101/2025.11.26.690703 — neuroscience — Posted on 2025-11-28

427 A lateralized pathway for associating nutrients with flavors

Grove, J. C. R.; Hakimi, A. M.; Li, Q.; Zhang, J.; Backes, H.; Kuzmanovic, B.; Choi, J.; Ubadiah, V.; Qiu, L.; Liu, Z.; Small, D. M.; Tittgemeyer, M.; Knight, Z. A.

10.1101/2025.02.09.637334 — neuroscience — Posted on 2025-11-28

428 Early Arousal Signals Drive Reward Learning and Subsequent Choice Behaviour

Ban, K.; Fouragnan, E. F.; Philiastides, M. G.

10.1101/2025.11.25.690494 — neuroscience — Posted on 2025-11-28

429 Recurrent Emergence of Boundary Cell Types During Evolution of Floral Bullseye Patterns

Oud, S.; Zurowski, M. M.; van der Jagt, P. L.; Yeo, M. T. S.; Walker, J. F.; Moyroud, E.; Vroomans, R. M. A.

10.1101/2025.05.03.651954 — systems biology — Posted on 2025-11-28

430 Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics and organisation

McCarthy, L. A.; Way, L. E.; Dai, X.; Ren, Z.; Fuller, D. E. H.; Dhiman, I.; Larkin, L.; Sieben, J. J. D.; Westerlaken, I.; Abbondanzieri, E. A.; Hardy, G. G.; Meyer, A. S.; Wang, X.; Biteen, J. S.

10.1101/2025.08.31.673347 — biophysics — Posted on 2025-11-28

431 Missense mutations on SynGAP C2 domain impair membrane diffusion

Miotto, M.; Bo', L.; Ruocco, G.; Di Angelantonio, S.; Basilico, B.

10.1101/2025.11.27.690967 — biophysics — Posted on 2025-11-28

432 Pasta, a versatile transcriptomic clock, maps the chemical and genetic determinants of aging and rejuvenation

Salignon, J.; Tsiokou, M.; Marques, P.; Rodriguez-Diaz, E.; Ang, H.; Pietrocola, F.; Riedel, C. G.

10.1101/2025.06.04.657785 — bioinformatics — Posted on 2025-11-28

433 PARAS: high-accuracy machine-learning of substrate specificities in nonribosomal peptide synthetases

Terlouw, B. R.; Huang, C.; Meijer, D.; Cediel-Becerra, J. D. D.; He, R.; Rothe, M. L.; Jenner, M.; Zhou, S.; Zhang, Y.; Fage, C. D.; Tsunematsu, Y.; van Wezel, G. P.; Robinson, S. L.; Alberti, F. L.; Alkhalaf, L. M.; Chevrette, M. G.; Challis, G.; Medema, M. H.

10.1101/2025.01.08.631717 — bioinformatics — Posted on 2025-11-28

434 Intergenerational transmission of parental rejection effects on survival, behaviour, and miRNA expression in owl monkeys

Farinha, J.; Clausi Marroquin, M.; Pardo Chambi, F. O.; Sanchez, N.; Boot, J.; Mein, C. A.; Yip, P.; Paredes, U. M.

10.1101/2024.12.20.629709 — animal behavior and cognition — Posted on 2025-11-28

435 Improved spike-in normalization clarifies the relationship between active histone modifications and transcription

Patel, L.; Cao, Y.; Xu, T.; Modolo, E.; Dishon, T.; Zhang, L.; Mendenhall, E.; Heinz, S.; Simon, I.; Benner, C.; Goren, A.

10.1101/2025.11.25.690627 — genomics — Posted on 2025-11-28

436 Ddx3x regulates B-cell development and immunoglobulin rearrangement in mice

Liu, K.; Krishnamurthy, D.; Tuazon, J.; Mukhopadhyay, E.; Karmele, E. P.; Donmez, O. A.; Perlot, T.; Foong-Sobis, M.; Karns, R. A.; Mandal, M.; Reynaud, D.; Kottyan, L. C.; Weirauch, M. T.; Shao, W.-H.; Scofield, R. H.; Penninger, J. M.; Harley, J. B.; Waggoner, S. N.

10.1101/452086 — immunology — Posted on 2025-11-28

437 Regional brain age deviations reveal divergent developmental pathways in youth

Gagnon, A.; Brunet, M. A.; Descoteaux, M.; Takser, L.

10.1101/2025.11.27.690886 — neuroscience — Posted on 2025-11-28

438 Environmental dynamics shape human learning: change points versus random walks

Foucault, C.; Weber, L. A.; Hunt, L. T.

10.1101/2025.11.26.690700 — neuroscience — Posted on 2025-11-28

439 Flexible Steering and Conflict Resolution: Pro-Goal/Anti-Goal Gating in Drosophila Lateral Accessory Lobes

Liao, C.-C.; Chang, N.; Liu, Y.-S.; Lo, C.-C.

10.1101/2025.10.19.683286 — neuroscience — Posted on 2025-11-28

440 Susceptibility to Task-irrelevant Auditory Distractors in Relation to Visual Working Memory in Children With and Without ADHD

Kong, Y.; Zhou, M.; Yuan, X.; Luo, X.; Huang, J.; Li, Y.; Yang, L.; Wang, Y.; Sun, L.; Song, Y.

10.1101/2025.11.27.691069 — neuroscience — Posted on 2025-11-28

441 Distributed activity in the human posterior putamen distinguishes goal-directed from habitual control in humans

Johri, A.; Kluen, L. M.; Gera, R.; Man, V.; Perez, O. D.; Simon, J. P.; Ding, W.; Fransen, A.; Cho, S.; Oh, S.; Cockburn, J.; Feusner, J.; Tadayon-Nejad, R.; O'Doherty, J.

10.1101/2025.11.26.690863 — neuroscience — Posted on 2025-11-28

442 Indistinguishability domains of neural microcircuit motifs mapped through classification scores of postsynaptic spike counts

Naveen Kumar, A.; Ramakrishnan, R.

10.1101/2025.09.19.673918 — neuroscience — Posted on 2025-11-28

443 Variation in Synaptic Inputs Drives Functional Versatility for Sound Encoding in Globular Bushy Cells

Wang, C.; Ashida, G.; Keine, C.; Milenkovic, I.

10.1101/2025.08.27.672091 — neuroscience — Posted on 2025-11-28

444 miRNA modules for precise, tunable control of gene expression

Du, R.; Flynn, M. J.; Mahe, K.; Honsa, M.; Gu, B.; Li, D.; McGeary, S. E.; Gradinaru, V.; Jungmann, R.; Elowitz, M. B.

10.1101/2024.03.12.583048 — synthetic biology — Posted on 2025-11-28

445 Novel Dopamine 4 Receptor Ligands Differentially Ameliorate ADHD-like Behaviors in Spontaneously Hypertensive Rats

de la Pena, I.; Andino, S.; Amis, A.; Alkhatib, M. A.; Li, T.; Keck, T. M.; Boateng, C. A.

10.1101/2025.11.26.690786 — pharmacology and toxicology — Posted on 2025-11-28

446 Solid-state nanopore sensing reveals conformational changes induced by a mutation in a neuron-specific tRNAArg

Dutt, S.; Lai, L. B.; Mehta, R.; Karawdeniya, B. I.; Bandara, Y. M. N. D. Y.; Clulow, A. J.; Glatt, S.; Gopalan, V.; Kluth, P.

10.1101/2025.04.08.647894 — biophysics — Posted on 2025-11-28

447 High-Speed Multiplexed DNA-PAINT Imaging of Nuclear Organization Using an Expanded Sequence Repertoire

Banerjee, A.; Anand, M.; Srivastava, M.; Vidwath, V. S.; Ganji, M.

10.1101/2024.12.21.629871 — biophysics — Posted on 2025-11-28

448 Occupancy estimation of wild species in a palm oil plantation using unstructured data

van Strien, A. J.; Meijaard, E.; Nardiyono, N.; Suief, S.; Zaini, S.

10.1101/2025.07.11.664290 — bioinformatics — Posted on 2025-11-28

449 Mechanistic and Antigenic Boundaries of Henipavirus and Parahenipavirus Glycoproteins

May, A. J.; Lella, M.; Lindenberger, J.; Berkman, A.; Kumar, U.; Dutta, M.; Barr, M.; Parks, R.; Lu, X.; Berry, M.; Newman, A.; Huang, X.; Mrigwani, A.; Song, K.; Ilevbare, V.; Sammour, S.; Park, C. S.; Adhikari, R. D.; Devkota, P.; Janowska, K.; Liu, Y.; Scapellato, G.; Spence, T. N.; Mansouri, K.; Wiehe, K.; Edwards, R. J.; Saunders, K. O.; Haynes, B. F.; Acharya, P.

10.1101/2024.12.11.627382 — biochemistry — Posted on 2025-11-28

450 Triple-helical ligands selectively targeting the closed αI domain of integrin α2β1

Shibata, S. S.; Oki, H.; Kawahara, K.; Masuda, R.; Fujii, K. K.; Koide, T.

10.1101/2025.07.28.667101 — biochemistry — Posted on 2025-11-28

451 Casual Versus Fractal Modularity in Mammalian Social Organisation

Dunbar, R. I. M.

10.1101/2025.11.26.690800 — animal behavior and cognition — Posted on 2025-11-28

452 Multi-ancestry fine-mapping accounting for ancestral and environmental heterogeneity improves resolution and interpretation

Wang, S.; Ojewunmi, O.; Pirie, F.; Motala, A.; Ramsay, M.; Morris, A.; Fatumo, S.; Chikowore, T.; Asimit, J. L.

10.1101/2025.11.26.690727 — genetics — Posted on 2025-11-28

453 High cell-type specificity of eQTLs revealed by single-nucleus analyses of brain and blood

Vochteloo, M.; Kooijmans, A.; Bakker, J.; Oelen, R.; Niewold, J.; Kaptijn, D.; Bonder, M. J.; van der Wijst, M.; Huang, Y.; Bryois, J.; Tsai, E. A.; Franke, L.; Westra, H.-J.

10.1101/2025.11.26.689911 — genetics — Posted on 2025-11-28

454 Quantifying the fitness contribution of phagocytosis

Schavemaker, P. E.; Tam, K. S.; Lynch, M.

10.1101/2025.10.23.684244 — evolutionary biology — Posted on 2025-11-28

455 A mathematical model for bleb expansion clarifies the role of TalA in regulating blebbing

De Silva, S. H. D. S.; Movsumova, E.; Reznik, J.; Santiago, Z.; Asante-Asamani, E.; Brazill, D.

10.1101/2025.02.28.640705 — cell biology — Posted on 2025-11-28

456 Phosphorus stress and spatial confinement lower the threshold for quorum-sensing activation of redox-active metabolite production in Pseudomonas synxantha

Alcalde, R. E.; Jeckel, H.; Zhang, O.; Avila, R. L.; Dalleska, N.; Mavrodi, D.; Yang, C.; Newman, D. K.

10.1101/2025.11.11.687776 — microbiology — Posted on 2025-11-28

457 Two cortical mechanisms for natural audiovisual processing

Pushpita, S. N.; Wehbe, L.

10.1101/2025.11.05.686819 — neuroscience — Posted on 2025-11-28

458 NDNF+ interneurons have a privileged role in regulating cortical excitability

Richardson, A.; Mercier, M. S.; Shimoda, Y.; Graham, R. T.; Leite, M.; Garcia, A.; Muller, M.; Bond, S. A.; Grodzdanova, M.; Wu, Q.; Kullmann, D. M.; Magloire, V.

10.1101/2025.11.27.690945 — neuroscience — Posted on 2025-11-28

459 Dispersal evolution as a driver of island biodiversity

van Wunnik, S.; Kauai, F.; Bonte, D.

10.1101/2025.11.27.690991 — evolutionary biology — Posted on 2025-11-28

460 GRNITE: Gene Regulatory Network Inference with Text Embeddings

Azizpour, A.; Rao, N.; Segarra, S.; Nakhleh, L.; Sapoval, N.

10.1101/2025.11.25.690454 — bioinformatics — Posted on 2025-11-28

461 k-spaces: Mixtures of Gaussian latent variable models

Markarian, N.; Engelhardt, B. E.; Pierce, N. A.; Sternberg, P. W.; Pachter, L.

10.1101/2025.11.24.690254 — bioinformatics — Posted on 2025-11-28

462 Efficient Identification of Short Tandem Repeats via Context-Aware Motif Discovery and Ultra-Fast Sequence Alignment

Liao, X.; Wen, L.; Jing, M.; Li, X.; Chen, B.; Zhang, B.; Gao, X.; Shang, X.

10.1101/2025.11.25.690584 — bioinformatics — Posted on 2025-11-28

463 plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics

Syed, M.; Walter, C.; Meyer, H. V.

10.1101/2025.11.25.690541 — bioinformatics — Posted on 2025-11-28

464 SuSiE 2.0: improved methods and implementations for genetic fine-mapping and phenotype prediction

McCreight, A.; Cho, Y.; Li, R.; Nachun, D.; Gan, H.-Y.; Carbonetto, P.; Stephens, M.; Denault, W. R.; Wang, G.

10.1101/2025.11.25.690514 — bioinformatics — Posted on 2025-11-28

465 Is Evolution Predictable? Experiments in an Evolutionary Video Game

Martinet, K. M.; Dace, B.; Harmon, L. J.; Pearson, S.; Wischnowski, J.; Wright, L. R.; Soule, T.; Robison, B. D.

10.1101/2025.11.27.691019 — evolutionary biology — Posted on 2025-11-28

466 Quantifying the geographic mosaic of coevolutionary temperature: from coldspots to hotspots

Gawecka, K. A.; Pedraza, F.; Andreazzi, C. S.; Bascompte, J.

10.1101/2025.11.27.691007 — ecology — Posted on 2025-11-28

467 Resistance, heteroresistance and fitness costs drive colistin treatment failure during Acinetobacter baumannii murine pneumonia

Hernandez-Bird, J.; He, B.; VanOtterloo, L. M.; Billings, E. B.; Huo, W.; Teodoro, G. I. C.; Echlin, H.; Rosch, J. M.; Trent, M. S.; Isberg, R. R.

10.1101/2025.07.24.666669 — microbiology — Posted on 2025-11-27

468 Which are the most heat-tolerant animals? Insights from a Mediterranean lepismatid under thermal stress in the context of climate change

Fernandez Vizcaino, E.; Molero-Baltanas, R.; Carbonell, J. A.; Gaju-Ricart, M.; Camacho, A.

10.1101/2025.11.25.690525 — zoology — Posted on 2025-11-27

469 Antibody Responses to Melanoma Helper Peptide Vaccines May Enhance Antigen Opsonization Through Formation of Immune Complexes and are Modulated by Vaccine Adjuvants

Ashkani, E. G.; Dickinson, A. M.; Olson, W. C.; Taylor, J. J.; Slingluff, C. L.

10.1101/2025.11.24.690236 — cancer biology — Posted on 2025-11-27

470 Structural Insights into Biased Signaling at Chemokine Receptor CCR7

Tanaka, K.; Nishikawa, K.; Shiimura, Y.; Fujiyoshi, Y.; Tsutsumi, N.

10.1101/2025.11.24.690334 — biophysics — Posted on 2025-11-27

471 A composition-matching algorithm, MatchIDR, identifies prion-like domains that localize to stress granules

Cascarina, S. M.; Paul, K. R.; Ford, L. L.; Ross, E. D.

10.1101/2025.11.24.690216 — biochemistry — Posted on 2025-11-27

472 Ferrapoptosis: Discovery of a Hybrid Programmed Cell Death

Yang, Q.; Chen, Y.; Shen, Y.; Zhang, X.; Chen, X.; Zhao, X.; Yuan, R.; Li, M.; Xu, Y.; Lin, X.; Sun, Y.; Zuo, S.; Liu, X.; Li, Z.; Chen, Y.; Wang, S.; Lv, M.; Zhang, L.; Liang, W.; Chen, X.

10.1101/2025.11.25.690347 — cell biology — Posted on 2025-11-27

473 An unprecedented DNA recognition-mimicry switch governs induction in arbitrium phages

Chmielowska, C.; Zamora-Caballero, S.; Mancheno-Bonillo, J.; Li, Y.; Sin, D.; Borenstein, T.; Bendori, S. O.; Eldar, A.; Marina, A.; Penades, J.

10.1101/2025.11.27.690993 — molecular biology — Posted on 2025-11-27

474 Long-range mRNA folding shapes expression and sequence of bacterial genes

Gill, M. S.; Kim, I. A.; Xue, J. R.; Thappeta, Y.; Taggart, J. C.; Li, G.-W.

10.1101/2025.11.27.690947 — molecular biology — Posted on 2025-11-27

475 Cell heterogeneity contributes to the variable response of HIV-1 to latency reversing agents

Topno, R. K.; Karaki, H.; Mazzarda, F.; Pourcelot, O.; Philippe, M.; Zibara, K.; Radulescu, O.; Bertrand, E.

10.1101/2025.11.26.690455 — molecular biology — Posted on 2025-11-27

476 Acoziborole resistance associated mutations in trypanosome CPSF3

Ridgway, M.; Novotna, M.; Mendoza-Martinez, C.; Tinti, M.; Altmann, S.; Sloan, G.; Horn, D.

10.1101/2025.11.26.690711 — microbiology — Posted on 2025-11-27

477 Rapid and accurate quantification of viable Listeria monocytogenes with clonal specificity using microfluidic droplet digital PCR based technology

Song, C.; Gao, Z.; Cai, G.; Yu, Y.; Ding, R.; Feng, S.; Liu, Y.

10.1101/2025.11.27.690673 — microbiology — Posted on 2025-11-27

478 Photocaged chloroquine derivatives for the light-dependent inhibition of autophagy in cancer stem cells

Alonso-Manresa, S.; Serra, C.; Munoz, L.; Bataller, M.; Garcia-Mayea, Y.; Pajarin, M. E. L.; Prats, B. G.; Zamora, S. M.; Riascos, Z. V. D.; Llebaria, A.; Josa-Cullere, L.

10.1101/2025.11.24.690081 — cancer biology — Posted on 2025-11-27

479 Inorganic pyrophosphate disrupts amorphous hydrated bone mineral interfaces in hypophosphatasia

Dillon, S.; Armiger, A.; Murgoci, A.; Skingle, L.; Tabegna, F. G. A.; McDonald, S.; Mumm, S.; Whyte, M. P.; Garton, M.; Poole, K. E. S.; Duer, M. J.

10.1101/2025.11.24.689921 — biophysics — Posted on 2025-11-27

480 Slab-PTM: A Coarse-Grained Force Field Parameter Patch for Modeling Post-Translational Modification Effects on Biomolecular Condensates

Mu, J.; Lai, L.

10.1101/2025.11.24.690320 — biophysics — Posted on 2025-11-27

481 Reliable Identification of Homodimers Using AlphaFold

Danielsson, S. N.; Elofsson, A.

10.1101/2025.11.27.691011 — bioinformatics — Posted on 2025-11-27

482 Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: N160L, N160S, N160C, N160M, N160G

Li, N.; Vater, A.; Siegel, J. B.

10.1101/2025.11.24.690255 — bioengineering — Posted on 2025-11-27

483 Topological adaptation of heliorhodopsins enables exogenous second-antenna acquisition in monoderm phototrophs

Kornilov, D.; Bukhdruker, S.; Astashkin, R.; Tsybrov, F.; Shevtsov, M.; Bukhalovich, S.; Ivashchenko, S.; Mikhailov, A.; Zinovev, E.; Golybev, V.; Ryzhykau, Y.; Vlasov, A.; Rulev, M.; Borshchevskiy, V.; Kuzmichev, P.; Bamberg, E.; Gordeliy, V.

10.1101/2025.11.27.691015 — biochemistry — Posted on 2025-11-27

484 Effects of cell growth and temperature on mitochondrial physiology of Drosophila melanogaster embryonic cell line

Rosa, R. S.; Mendonca, A. P. M.; Oliveira, M. P.; Carvalho, D. B.; Vazquez, L.; Oliveira, M.

10.1101/2025.11.25.690158 — biochemistry — Posted on 2025-11-27

485 Multi-stem-loop constrained library enables accelerated SELEX for aptamers with superior kinetics and affinity

Wang, Q.; Zhao, Y.; Zhao, S.; Wu, A.; Hao, L.; Hong, T.; Hong, L.

10.1101/2025.11.27.690911 — biochemistry — Posted on 2025-11-27

486 Chromatin priming and Hunchback recruitment integrate spatial and temporal cues in Drosophila neuroblasts

Bhattacharya, A.; Rao, H.; Sen, S. Q.

10.1101/2025.11.25.690435 — developmental biology — Posted on 2025-11-27

487 Linear Z-line-like alignment of capping protein in obliquely striated muscle of the nematode C. elegans suggests that dense bodies are not equivalent to Z-lines

Ono, S.; Nickoloff-Bybel, E.; Kurimaru, K.; Ono, K.

10.1101/2025.11.24.690283 — cell biology — Posted on 2025-11-27

488 Role of the osaA transcription factor gene in development, secondary metabolism and virulence in the mycotoxigenic fungus Aspergillus flavus

Hossain, F. E.; Dabholkar, A.; Lohmar, J. M.; Lebar, M. D.; Mack, B. M.; Calvo, A. M.

10.1101/2025.11.26.690797 — molecular biology — Posted on 2025-11-27

489 i6A-seq maps N6-isopentenyladenosine and uncovers its role as a regulator of mRNA stability through recruitment of DIS3L2

Avrahami-Rozenblum, C.; Cohen Ben-Aderet, L.; Ashwal-Fluss, R.; Masoud, R.; Nayshool, O.; Zinger, T.; Sevilla-Sharon, M.; Glick-Saar, E.; Yahalom, A.; Coll-SanMartin, L.; Esteller, M.; Rechavi, G.; Dominissini, D.; Moshitch-Moshkovitz, S.

10.1101/2025.11.26.690722 — molecular biology — Posted on 2025-11-27

490 Regulatory Rewiring Drives Intraspecies Competition in Bacillus subtilis

Kalamara, M.; Bonsall, A.; Griffin, J.; Carneiro, J.; Stevenson, D.; Gierlinski, M.; Eigentler, L.; Wood, A.; Porter, M.; Dorfmueller, H. C.; MacPhee, C. E.; Abbott, J. C.; Stanley-Wall, N.

10.1101/2025.11.27.690801 — microbiology — Posted on 2025-11-27

491 The spatial proteome of the Plasmodium falciparum schizont illuminates the composition and evolutionary trajectories of its organelles

Chisholm, S. A.; Flores, V.; Kemp, A.; Breckels, L. M.; Koreny, L.; Dos Santos Pacheco, N.; Barylyuk, K.; Kuroshchenkova, A.; Lilley, K. S.; Rayner, J. C.; Waller, R. F.

10.1101/2025.11.27.690946 — microbiology — Posted on 2025-11-27

492 Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli

Poudyal, P.; Sy, B. M.; Mediati, D. G.; Payne, M.; Nandel, V.; Norris, D.; McAteer, S. P.; Ullah, A.; Li, S.; Menz, L.; Waters, S.; Dallman, T.; Baker, M. A.; Lan, R.; Gally, D. L.; Tree, J. J.

10.1101/2025.11.27.690950 — microbiology — Posted on 2025-11-27

493 NCY-I beta-lactamase activity correlates with antimicrobial susceptibility of a clinical strain of Nocardia cyriacigeorgica

Couston, J.; Le Marchand, A.; Hodille, E.; Genestet, C.; Joannard, B.; Jerome, F.; Benito, Y.; Dumitrescu, O.; Blaise, M.

10.1101/2025.11.27.690932 — microbiology — Posted on 2025-11-27

494 Redefining the role of the Plasmodium heme detoxification protein: From hemozoin formation to mitochondrial protein synthesis

Sarrazin, L.; Kloehn, J.; Ziesmann, T.; Schmitz, Y.; Sandtmann, A.-L.; Domenech-Eres, R.; Scholz-Hoehn, K.; Boulet, C.; Distler, U.; Matz, J. M.

10.1101/2025.11.27.690934 — microbiology — Posted on 2025-11-27

495 High-Resolution Imaging of the Rhizosphere Using Resin-Embedded Cross-Sectional Polishing and Scanning Electron Microscopy for Biological Samples (bioCP-SEM)

Toyooka, K.; Saito, Y.; Goto, Y.; Sato, M.

10.1101/2025.11.27.690849 — microbiology — Posted on 2025-11-27

496 Systematic Discovery of Novel Phosphoinositide-Binding Effectors in Legionella Reveals Conserved α-Helical Folds

Bolt, A. E.; Richardson, A. E.; Pike, C. M.; Noll, R. R.; Yu, Y.; Neunuebel, J. P.; LeMarchand, S.; Schmitz, K. R.; Neunuebel, M. R.

10.1101/2025.11.26.690877 — microbiology — Posted on 2025-11-27

497 Gut microbiota characterization in vegetarian adults from the adventist population living in coastal, highland, and jungle regions of Peru

Marcos Carbajal, P.; Medina ramirez, S.; Yareta Yareta, J.; Otiniano Trujillo, M.; Chambi Quispe, M.; Ruiz Panaifo, M.; Diaz Rengifo, P.; Sias Garay, C.; Tito, R.; Obregon-Tito, A.

10.1101/2025.11.26.690875 — microbiology — Posted on 2025-11-27

498 Iterative and modular expression of Botryococcus braunii genes enhances isoprenoid production in the diatom Phaeodactylum tricornutum

Morelli, L.; Jensen, C.; Arnspang, E. C.; Fabris, M.

10.1101/2025.11.27.690994 — synthetic biology — Posted on 2025-11-27

499 Paradoxical gene regulation explained by competition for genomic sites

Jatkar, D. D.; Aravind, K. M.; Sontag, E. D.; Del Vecchio, D.

10.1101/2025.11.27.691022 — synthetic biology — Posted on 2025-11-27

500 PhenoDEL as a Novel Screening Strategy Based on Intracellular Protein Degradation Activity

Onda, Y.; Ochi, Y.; Araki, T.; Kageoka, M.; Takeda, S.; Yamada, K.; Ueda, T.; Ohno, K.; Tanaka, M.; Sakai, D.; Hasegawa, M.; Tanaka, Y.

10.1101/2025.11.26.690606 — synthetic biology — Posted on 2025-11-27

501 A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow

Giuili, E.; Van de Velde, S.; Kint, S.; Ferro dos Santos, M. R.; Cornelli, L.; Roelandt, S.; Schoofs, K.; Imschoot, R.; Van Paemel, R.; Meuris, L.; Everaert, C.; De Preter, K.

10.1101/2025.11.27.688590 — bioinformatics — Posted on 2025-11-27

502 Molecular maps of diseases from omics data and network embeddings

Hu, D.; Schaap-Johansen, A.-L.; Villarroel, J.; Ekebjaerg, C. E.; Rasmussen, S.; Hansen, D. H.; Wernersson, R.; Jensen, L. J.

10.1101/2025.11.25.689280 — bioinformatics — Posted on 2025-11-27

503 Tracking ongoing chromosomal instability using single-cell whole-genome sequencing

Hernando, B.; Chaves-Urbano, B.; Escobar-Rey, M.; Torres-Lazaro, M.; Cadiz, A.; Fernandez-Sanroman, A.; Barrambana, S.; Lechuga, C. G.; Guerra, C.; Barbacid, M.; Gomez-Sanchez, D.; Sanchez-Vega, F.; Razavi, P.; Garcia-Perez, M.; Santamaria, P. G.; Macintyre, G.

10.1101/2025.11.26.690781 — genomics — Posted on 2025-11-27

504 Using pangenome variation graphs to improve mutation detection in a large DNA virus

Wright, C.; Tennakoon, C.; Lasecka-Dykes, L.; Downing, T.

10.1101/2025.11.26.690900 — genomics — Posted on 2025-11-27

505 Understanding Patterns of Interploidy Admixture in Polyploid Complexes: Insights from Thymus sect. Mastichina (Lamiaceae)

Garcia-Cardenas, F. J.; Ortiz, M. A.; del Valle, J. C.; Doblas, D.; de la Estrella, M.; Nieto-Lugilde, D.; Berjano, R.

10.1101/2025.11.27.690785 — evolutionary biology — Posted on 2025-11-27

506 Parent-offspring conflict over sex determination in non-Mendelian systems

Hitchcock, T. J.; Baird, R. B.

10.1101/2025.11.26.690632 — evolutionary biology — Posted on 2025-11-27

507 Wrapping it Up: Structural Basis of ADAMTS13 Global Latency

Geist, N.; Bonnez, Q.; Vanhoorelbeke, K.; Delcea, M.

10.1101/2025.11.26.689657 — molecular biology — Posted on 2025-11-27

508 TSP1/TGF-β1 drives arachidonic acid metabolism to orchestrate neutrophil swarming

Widera, L.; Spangenberg, P.; Siemes, D.; Bessler, S.; Bottek, J.; Voss, H.; Novak, A.; Hueser, D.; Richter, M.; Potthoff, A.; Siebels, B.; Moritz, M.; Gocke, A.; Thiebes, S.; Schaefer, S.; Chavakis, T.; Jablonska, J.; Laemmermann, T.; Gunzer, M.; Schlueter, H.; Hahn, J.; Grueneboom, A.; Soehnlein, O.; Dreisewerd, K.; Soltwisch, J.; Shevchuk, O.; Engel, D. R.

10.1101/2025.11.25.688397 — immunology — Posted on 2025-11-27

509 Dog brain atlas generated via spatially constrained spectral clustering

Hernandez-Perez, R.; Cuaya, L. V.; Boch, M.; Barrios, F. A.; Alcauter, S.; Huber, L.; Lamm, C.

10.1101/2025.11.25.690406 — neuroscience — Posted on 2025-11-27

510 The structured mRNA element 45ABC mediates auto- and cross-regulation of RBP45 genes via alternative splicing

Reinhardt, M.; Burgardt, R.; Engel, C.; Sack, M.; Weinberg, Z.; Wachter, A.

10.1101/2025.11.25.690383 — plant biology — Posted on 2025-11-27

511 Chromosome-scale haplotype genome assemblies for the Australian mango 'Kensington Pride' 1 and a wild relative, Mangifera laurina, provide insights into anthracnose-resistance and volatile 2 compound biosynthesis genes

Wijesundara, U. K.; Furtado, A.; Masouleh, A.; Dillon, N. L.; Smyth, H.; Henry, R. J.

10.1101/2025.11.24.690335 — plant biology — Posted on 2025-11-27

512 CHLOROPLAST GENOME AND PHYLOGENETIC ANALYSIS OF KATMON (Dillenia philippinensis Rolfe), A PHILIPPINE ENDEMIC FRUIT

Lucero, J. J. M.; Munoz, J. A. M.; Aglibot, L. Y.; Cardona, D. E. M.; Gueco, L. S.; Manalang, A. P.; Villanueva, J. C.; Alonday, R. C. S.

10.1101/2025.11.26.690882 — plant biology — Posted on 2025-11-27

513 COATswga: A Coverage Optimizing and Accurate Toolkit for fast primer design in selective whole genome amplification

Zuckerman, K.; Leonetti, A.; DeFeo, R.; Taropawala, O.; Simkin, A.; Fola, A. A.; Bailey, J. A.

10.1101/2025.11.26.688640 — bioinformatics — Posted on 2025-11-27

514 Haplotype-resolved diploid genome inference on pangenome graphs

Chandra, G.; Doan, W. T.; Gibney, D.

10.1101/2025.11.26.690754 — bioinformatics — Posted on 2025-11-27

515 Computer-guided enzyme engineering of PET hydrolase mutants towards improved PET affinity

Balola, A.; Ferreira, S.; Souza, C. S.; Lousa, D.; Correia, J. P.; Soares, C. M.; Rocha, I.

10.1101/2025.11.26.689686 — bioinformatics — Posted on 2025-11-27

516 Synthesis of stable isotope labeled analogs of phytanic acid for separate and combined tracing of alpha-, beta- and omega-oxidation

Broadrup, R. L.; Schwartz, A. C.; Smith, J.; von Trentini, D.; Snyder, N. W.

10.1101/2025.11.24.689497 — biochemistry — Posted on 2025-11-27

517 What Relative Neocortex Size Tells Us About Social Evolution

Dunbar, R. I. M.

10.1101/2025.11.26.690799 — animal behavior and cognition — Posted on 2025-11-27

518 Do DNA and cytometric measures agree on genome sizes?

Gilbert, D.

10.1101/2025.11.26.690794 — genomics — Posted on 2025-11-27

519 Tangerine: a Starship-like element in the genomes of Xanthoria lichen-forming fungi

Tagirdzhanova, G.; Bucknell, A.; Cameron, E. S.; Finn, R. D.; Blaxter, M.; McDonald, M. C.; Talbot, N. J.

10.1101/2025.11.25.690456 — genomics — Posted on 2025-11-27

520 Phylogenomic and comparative genome analysis of the Juglandaceae family reveals black walnut (Juglans nigra) as an ancient lineage of the Rhysocaryon section.

Ebrahimi, A.; Mathur, S.; Arab, M. M.; LaBonte, N.; Long, E.; Monroe, J. G.; Jacobs, D. F.

10.1101/2025.11.25.690472 — genomics — Posted on 2025-11-27

521 Accurate and robust 3D genome feature discovery from multiplexed DNA FISH

Yu, H.; Zhou, L.; Xie, L.; Strambio-De-Castillia, C.; Hu, M.; Li, Y.

10.1101/2025.11.26.690837 — genomics — Posted on 2025-11-27

522 Genome-wide association mapping for grain and forage quality traits in a subtropical oat germplasm collection adapted to highland regions of Eastern Africa

Gari, A. T.; Ashenafi, L.; Dejene, M.; Mohammed, K.; Mekonen, T.; Feyisa, F.; Lire, H.; Negawo, A. T.; Rahman, A.; De Vega, J. J.; Jones, C. S.; Barth, S.

10.1101/2025.11.26.690820 — genomics — Posted on 2025-11-27

523 Rodent Origins and Human-Mediated Evolutionary Dynamics of PRRSV

Novosel, D.; Jungic, A.; Rota Stabelli, O.; Cortey, M.; Curik, I.; Mateu, E.

10.1101/2025.11.25.690366 — evolutionary biology — Posted on 2025-11-27

524 Single-cell phylodynamics reveal rapid late-stage colorectal cancer expansions

Alves, J. M.; Chen, K.; Prado-Lopez, S.; Estevez-Gomez, N.; Alvarino, P.; Alonso, J.; Valecha, M.; Tomas, L.; Zwaans, A.; Stolz, U.; Stadler, T.; Chantada, D.; Cameselle-Teijeiro, J. M.; Drummond, A.; Posada, D.

10.1101/2025.11.25.690378 — evolutionary biology — Posted on 2025-11-27

525 Domestication of the ancient grain Amaranthus cruentus L.

Sulub-Tun, R. A.; Singh, A.; Cifuentes-Velasquez, R.; Stetter, M. G.; Sanchez-del Pino, I.

10.1101/2025.11.27.690906 — evolutionary biology — Posted on 2025-11-27

526 Bursts of reproduction can create genetic structure in frequently recombining bacterial populations

Jiang, C. J.; Weissman, D. B.

10.1101/2025.11.25.690602 — evolutionary biology — Posted on 2025-11-27

527 The heterogeneous selection landscape of genome evolution in prokaryotes

Kogay, R.; Karamycheva, S.; Rochman, N. D.; Wolf, Y. I.; Koonin, E. V.

10.1101/2025.11.26.690804 — evolutionary biology — Posted on 2025-11-27

528 The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum

Chavez, C. M.; Harrison, M.-C.; Danis, T.; Groenewald, M.; Hittinger, C. T.; Rokas, A.

10.1101/2025.11.26.690719 — evolutionary biology — Posted on 2025-11-27

529 charisma: An R package to perform reproducible color characterization of digital images for biological studies

Schwartz, S. T.; Tsai, W. L. E.; Karan, E. A.; Juhn, M. S.; Shultz, A. J.; McCormack, J. E.; Smith, T. B.; Alfaro, M. E.

10.1101/2025.11.25.690362 — evolutionary biology — Posted on 2025-11-27

530 Sex-specific modifications of gametogenesis in natural and lab-bred Fundulus spp. hybrids

Dedukh, D.; Obidena, K.; Majtanova, Z.; Ouellette, P.; Roussel, A.-J.; Horn, M. E.; Janko, K.; Dalziel, A. C.; Dion-Cote, A.-M.

10.1101/2025.11.26.690728 — evolutionary biology — Posted on 2025-11-27

531 Automated detection of macropods in Tasmania using drone surveys and convolutional neural networks (CNNs)

Teo, Y. V.; Turner, D.; Buettel, J. C.; Brook, B. W.

10.1101/2025.11.26.688741 — ecology — Posted on 2025-11-27

532 Combining artificial intelligence and local ecological knowledge to document the largest ever-counted Cape buffalo mega-herd

Bennitt, E.; Costelloe, B. R.; Koger, B.; Wielgus, E.; Masunga, G.; Caron, A.

10.1101/2025.11.26.689243 — ecology — Posted on 2025-11-27

533 Learning the mechanism of collective microbial function via random community-media pairing

Wang, L.; Kuehn, S.; Tikhonov, M.

10.1101/2025.11.25.690499 — ecology — Posted on 2025-11-27

534 Hyperdominance and rarity in Amazonian secondary forests

Elias, F.; Ferreira, J.; Berenguer, E.; Oliveira do Nascimento, R.; Miranda, L.; Vicente Silverio, D.; Vieira, I.; Aragao, L.; Schwartz, G.; Barlow, J.

10.1101/2025.11.25.690408 — ecology — Posted on 2025-11-27

535 A Natural Programmable Metamaterial Controls 3D Curvature of Compound Eyes

Garrido-Garcia, J.; Walther, R. F.; Torres-Tirado, J.; Andres-San Roman, J. A.; Sanz-Herrera, J. A.; Pichaud, F.; Casares, F.; Escudero, L. M.

10.1101/2025.11.25.689431 — developmental biology — Posted on 2025-11-27

536 Gene editing without a genome: generation and validation of F0 CRISPR mutants in gastropod mollusc Crepidula fornicata

Jordan, D. C.; Rivers, M. L.; Belmont, L.; Martin, S. A. M.; Bean, T. P.; Sleight, V. A.

10.1101/2025.11.26.690768 — developmental biology — Posted on 2025-11-27

537 Integrin β1-Talin1 at focal adhesions underpin uncontrolled endothelial cell enlargement in live cerebral cavernous malformation vasculature

Keyser, M. S.; Yordanov, T. E.; da Silva, J. A.; Chau, T. C.; Morris, E. K.; Paterson, S.; Bower, N.; Koltowska, K.; Baillie, G. J.; Simons, C.; Parton, R. G.; Smith, K. A.; Hogan, B. M.; Lagendijk, A. K.

10.1101/2025.11.25.688491 — cell biology — Posted on 2025-11-27

538 Homotypic endoplasmic reticulum membrane tethering is critical for flavivirus replication

Owen, J. E.; Bemis, C. L.; Wang, Q.; Varadan, A. C.; Vander Velden, J. W.; Andacic, L.; Uyar, O.; Gupta, M.; Scharer, C. D.; Chatel-Chaix, L.; Scaturro, P.; Suthar, M. S.; Neufeldt, C.

10.1101/2025.11.26.690702 — microbiology — Posted on 2025-11-27

539 Initial identification of genomic islands in Taylorella equigenitalis and Taylorella asinigenitalis and their distribution in isolates from around the world

Hicks, J. A.; Li, G.; Petry, S.; Duquesne, F.; Choi, J. G.; Overesh, G.; Lantz, K.; Robbe Austerman, S.; Huang, X.

10.1101/2025.11.26.686905 — microbiology — Posted on 2025-11-27

540 A conserved transcriptional backbone and rewiring of gene-regulatory networks in activated human CD4⁺ T cells

Mihai, I. S.; Nunez-Carpintero, I.; Cirillo, D.; Trygg, J.; Forsell, M. N.; Selinger, M.

10.1101/2025.11.25.687998 — immunology — Posted on 2025-11-27

541 namiRa: A Comprehensive, Manually Curated Database for MicroRNA Expression, Function, and Deregulation in Cancer

Mohebbi, S.; Dostmohammadi, A.; Amjadian, S.; Abdi, Z.; Torkian, H.; Ghavidel, M.; Rahbar, M.; Movahed, A. Y.; Rastidoust, N.; Mahdizad, F.; Akbari, A.; Farsi, S. M.; Azadedel, F.; Abdollahi, L.; Farhadnejad, R.; Salmanzadeh, N.; Sadeghi, H.; Moradi, S.

10.1101/2025.11.25.671411 — cancer biology — Posted on 2025-11-27

542 Experience from an HTS campaign: Investigation of susceptibility and rescue of SARS-CoV-2 nsp3 protease assay from metal contamination

Georgiou, I.; O'Neill, S.; Robinson, C.; Cunningham, F.; O'Byrne, S. N.; Gray, D.; Scott, D. E.; Gilbert, I. H.

10.1101/2025.11.27.690678 — biochemistry — Posted on 2025-11-27

543 Amaranth: Enhanced Single-Cell Transcript Assembly via Discriminative Modeling of UMI Reads and Internal Reads

Zang, X. C.; Zahin, T.; Khan, I. M.; Shi, Q.; Xing, Y.; Shao, M.

10.1101/2025.11.24.690228 — bioinformatics — Posted on 2025-11-27

544 mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing

Patro, R.; Bharti, S.; Singhania, P.; Dhakal, R.; Dahlstrom, T. J.; Groot Koerkamp, R.

10.1101/2025.11.24.690271 — bioinformatics — Posted on 2025-11-27

545 AmarylOmicBase: A unified transcriptome database to accelerate gene discovery in Amaryllidoideae species

Goncalves dos Santos, K. C.; Merindol, N.; Desgagne-Penix, I.

10.1101/2025.11.24.690262 — bioinformatics — Posted on 2025-11-27

546 Eduomics: a Nextflow pipeline to simulate -omics data for education

Sola, L.; Bagordo, D.; Carpanzano, S.; Santorsola, M.; Lescai, F.

10.1101/2025.11.24.690117 — bioinformatics — Posted on 2025-11-27

547 TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models

Liu, S.; Tang, J.; Ma, J.; Liang, S.

10.1101/2025.11.24.690325 — bioinformatics — Posted on 2025-11-27

548 Mapping spatial gradients in spatial transcriptomics data with score matching

Wang, A.; Geman, D.; Chitra, U.; Younes, L.

10.1101/2025.11.24.690257 — bioinformatics — Posted on 2025-11-27

549 Multi-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening

Hsieh, W.-H.; Hung, Y.-H.; Zhang, J.-H.; Chen, H.-Y.; Lin, L.-P.; He, M.-H.; Wang, Y.-C.; Ho, Y.-Y.; Fernandez, G.; Perkins-Veazie, P.; Le, B.; Li, X.; Hsieh, T.-F.; Lin, J.-Y.

10.1101/2025.11.24.690302 — genomics — Posted on 2025-11-27

550 Ribosomal RNA Synthesis is a Lethal Vulnerability During Reductive Stress In C. elegans

Rotti, J.; Ahsan, F.; Stuhr, N.; Emans, S.; Soukas, A.; Yerevanian, A.

10.1101/2025.11.24.690266 — genetics — Posted on 2025-11-27

551 MIMYR: Generative modeling of missing tissue in spatial transcriptomics

Deshpande, A.; Bei, Z.; Ma, J.; Krieger, S.

10.1101/2025.11.24.690239 — bioinformatics — Posted on 2025-11-27

552 Comparative Assessment of Large Language Models for Microbial Phenotype Annotation

Muench, P. C.; Safaei, N.; Han, Y.; Binder, M.; Robertson, G.; Mreches, R.; Franzosa, E. A.; Huttenhower, C.; McHardy, A. C.

10.1101/2025.11.24.690272 — bioinformatics — Posted on 2025-11-27

553 Expanding the RNA Virus Universe by Scalable Structure-Guided Discovery

Luo, G.; Zang, Z.; Yuan, L.; Zhou, J.; Dong, A.; Huang, Y.; Li, S. Z.; Ju, F.

10.1101/2025.11.24.690314 — bioinformatics — Posted on 2025-11-27

554 CodonTranslator: a conditional codon language model for codon optimization across all domains of life

Chen, Y.; Zhang, Y.; Li, J.; Tian, B.; Huang, H.

10.1101/2025.11.24.690310 — bioinformatics — Posted on 2025-11-27

555 Heterogeneous evolutionary history defines the rear edge of the North American herb Campanula americana

Perrier, A.; Lamb, K.; Galloway, L.

10.1101/2025.11.24.690277 — evolutionary biology — Posted on 2025-11-27

556 Fine-scale ecological biomonitoring in a large, complex agriculturally impacted watershed via eDNA metabarcoding

Silva, B. S. M. L. e.; Riley, A. C.; Craiovan, E.; Wright, M.; Watson, K.; Lapen, D. R.; Hajibabaei, M.

10.1101/2025.11.24.690238 — ecology — Posted on 2025-11-27

557 Nutrient stress activates Rab5b-mediated autophagy to remodel the synaptic proteome

Overhoff, M.; Ickert, L.; Marten, S.; Hill, A.; Tellkamp, F.; Ludwig, S. L.; Antczak, P.; Koehler, F.; Mueller, R.-U.; Krueger, M.; Kononenko, N.

10.1101/2025.11.25.690410 — neuroscience — Posted on 2025-11-27

558 Synaptopodin KO rat for assessing the dendritic spine apparatus and axonal cisternal organelle in synaptic plasticity, development, and behavior

Kuwajima, M.; Ostrovskaya, O. I.; Kirk, L. M.; Alario, A.; Yin, W.; Singh, S.; Xaymongkhol, A.; Li, A.; Prasad, E.; Harris, K. M.

10.1101/2025.11.25.690444 — neuroscience — Posted on 2025-11-27

559 Inferring Local Protein Structural Similarity from Sequence Alone

Ma, Z.; Herrera, J. E.; Bethel, N. P.; Jinich, A.

10.1101/2025.11.24.690129 — bioinformatics — Posted on 2025-11-27

560 CrossPPI: A Cross - Fusion Based Model for Protein - Protein Binding Affinity Prediction.

Singam, S. R.; Devarashetty, N. C. A.; Gogte, S.; Kondaparthi, V.

10.1101/2025.11.25.690371 — bioinformatics — Posted on 2025-11-27

561 The BRCA1- RAD51 Axis Regulates SCAI/REV3 Dependent Replication Fork Maintenance

Unterseher, C.; Tsuchida, H.; Bosire, R.; Jin, X.; Kieffer, S.; Adeyemi, R.

10.1101/2025.11.25.689574 — cell biology — Posted on 2025-11-27

562 De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology

Nyarko, P.; Quenu, M.; Guery, M.-A.; Cohen, C.; Girgis, S. T.; Makunin, A.; McCarthy, S. A.; Hamilton, W. L.; Lawniczak, M.; Claessens, A.

10.1101/2025.11.19.689036 — genomics — Posted on 2025-11-27

563 Fast Optimization of Robust Transcriptomics Embeddings using Probabilistic Inference Autoencoder Networks for multi-Omics

Wang, N.; Turner, D.; Feinberg, H.; Nieto Caballero, V. E.; Yuan, D.; Scott, N.; Cardenas, C.; DeBerardine, M.; Dan, S.; Caceres, L.; Schembri, J.; Yao, Z.; Lee, C.; Pillow, J. W.; Krienen, F. M.

10.1101/2025.11.16.686778 — neuroscience — Posted on 2025-11-27

564 Altered postnatal chromatin development in the nucleus accumbens primes lifelong stress sensitivity

Rashford, R. L.; Fang, L. Z.; DeBerardine, M.; Kim, H. J. J.; Hirschfield, L. W.; Cervi, E.; Barrett, M. R.; Thompson, J. M.; Creed, M. C.; Pena, C. J.

10.1101/2024.04.12.589272 — neuroscience — Posted on 2025-11-27

565 Piperine activates the thick filament of resting rat skeletal muscle, enhancing dynamic contractility in a fiber-type-dependent manner

Kruse, D. Z.; Herskind, J.; Kuehn, M. N.; Klotz, A. J.; Hessel, A. L.; Overgaard, K.

10.1101/2025.11.24.689918 — physiology — Posted on 2025-11-27

566 Dynamical buffering of reconfiguration dynamics in intrinsically disordered proteins

Ivanovic, M. T.; Holla, A.; Nüesch, M. F.; von Roten, V.; Schuler, B.; Best, R. B.

10.1101/2025.10.12.681911 — biophysics — Posted on 2025-11-27

567 Modular Noncovalent Functionalization of Electrospun Piezoelectric Scaffolds with Bioactive Nanocarriers

Bortel, S. P.; Chowdhury, S. S. J.; Cheng, J.; Uvaldo, D.; Wright, M.; Arinzeh, T. L.; Correa, S.

10.1101/2025.10.25.684210 — bioengineering — Posted on 2025-11-27

568 SWING domains prime chromatin for nuclear body mediated gene regulation

Yu, R.; Sas-Nowosielska, H.; Dessai, A. S.; Oubarri, A.; Kim, H.; Faunce, C.; Vanderkruk, B.; Alexander, K. A.; Nguyen, S. C.; Krantz, I. D.; Joyce, E. F.; Lakadamyali, M.; Berger, S. L.

10.1101/2025.10.01.679801 — genetics — Posted on 2025-11-27

569 The five divergent amino acids rule and evolution analysis of cytochrome c oxidase as new methods for Scolopendra Linnaeus, 1758 species differentiation (Chilopoda. Scolopendromorpha).

Domenech, C.; Barbera, V. M.; Larriba, E.

10.1101/2025.11.24.690109 — evolutionary biology — Posted on 2025-11-27

570 Cis-regulation of gene expression between sexes and life stages in Rumex hastatulus

Yuan, M.; Sacchi, B. M.; Choudhury, B. I.; Barrett, S. C. H.; Stinchcombe, J. R.; Wright, S. I.

10.1101/2025.06.16.659834 — evolutionary biology — Posted on 2025-11-27

571 map3k1 is required for spatial restriction of progenitor differentiation in planarians

Canales, B.; King, H. O.; Reddien, P. W.

10.1101/2025.03.04.641450 — developmental biology — Posted on 2025-11-27

572 An avidity-driven mechanism of extracellular BMP regulation by Twisted gastrulation

Moore, G.; Revici, R.; Forbes-Beadle, L.; Sutcliffe, C.; Birchenough, H. L.; Baldock, C.; Ashe, H. L.

10.1101/2024.07.08.602551 — developmental biology — Posted on 2025-11-27

573 Cellularization in chytrid fungi uses distinct mechanisms from conventional cytokinesis and cellularization in animals and yeast

Medina, E. M.; Elting, M. W.; Fritz-Laylin, L. K.

10.1101/2025.01.30.635136 — cell biology — Posted on 2025-11-27

574 A New Approach to Modeling LGMDR1: Pyrvinium-Treated capn3b crispant Zebrafish

Ruiz-Roldan, C.; Valls, A.; Immanuel, J.; De Santis, F.; Fernandez-Torron, R.; Lopez de Munain, A.; Saenz, A.

10.1101/2025.11.25.690358 — molecular biology — Posted on 2025-11-27

575 Measuring mtDNA turnover, synthesis, and supercoiling via selective bromodeoxyuridine incorporation

Deng, J.; Mohan, A.; Shutt, T.

10.1101/2023.10.24.563889 — molecular biology — Posted on 2025-11-27

576 Ataxin-2 knockdown is neuroprotective via cell-autonomous and non-cell-autonomous mechanisms

Gastaldo, D.; Vito, S.; Black, H.; Foreman, O.; Yang, Z.; Pham, V.; Zhu, Y.; Choi, M.; Jovicic, A.

10.1101/2025.11.24.690282 — neuroscience — Posted on 2025-11-27

577 Muscle-specific DNM2 overexpression improves Charcot-Marie-Tooth disease in vivo and reveals a narrow therapeutic window in skeletal muscle

Goret, M.; Piccolo, G.; Laporte, J.

10.1101/2025.11.25.690395 — neuroscience — Posted on 2025-11-27

578 Physiological alpha-synuclein S129 phosphorylation mediates postsynaptic and nuclear interactions in the human brain

Choi, S. G.; Duvernay, J.; Bahrami, A.; Tittle, T.; Muller, S.; Sani, S. S.; Kordower, J. H.; Killinger, B. A.

10.1101/2025.04.22.649861 — neuroscience — Posted on 2025-11-27

579 AKAP1 regulates mitochondrial and synaptic homeostasis to enable neuroprotection and repair in retinal ganglion cell degeneration

Bastola, T.; Kim, K.-Y.; Shen, Z.; Perkins, G. A.; Poudel, M.; Gomez, V.; Lim, Y.; Choi, H.; Won, J. Y.; Choi, S.-H.; Ellisman, M. H.; Weinreb, R. N.; Ju, W.-K.

10.1101/2025.11.24.689866 — neuroscience — Posted on 2025-11-27

580 Identification of gingipains in glioblastoma tumors and evidence that P. gingivalis infection drives IL-6 and PD-L1 expression in glioma cells

Moore, E. M.; Bekale, L. A.; Tun, Z. M. M.; Chen, J.; Ryder, M. I.; Ermini, F.; Dominy, S. S.; Barron, A. E.

10.1101/2025.11.13.686868 — neuroscience — Posted on 2025-11-27

581 AI-Driven and 3D-Bioprinted New Approach Methodology (NAM) Identifies NEO100 as Potent Ultrasound-Activated Therapeutic for Primary and Metastatic Brain Tumors

Majumder, R.; Datta, P.; Moolayadukkam, S.; Nakamura, B.; Izquierdo, U.; Joshi, R.; Sedighi, S.; Chen, T. C.; Neman, J.

10.1101/2025.11.25.690556 — cancer biology — Posted on 2025-11-27

582 An effect size-based screening approach to identify actigraphy markers of the submarine environment

Marques, D.; Fernandes, C.; Barbosa-Morais, N. L.; Reis, C.

10.1101/2025.06.16.659930 — bioinformatics — Posted on 2025-11-27

583 A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits

Roback, E. Y.; X, M.; Ricemeyer, E. S.; Warlen, A.; Carroll, R. A.; Elsik, C. G.; Keene, A. C.; Rohner, N.; McGaugh, S. E.; Warren, W. C.

10.1101/2025.11.25.690530 — evolutionary biology — Posted on 2025-11-27

584 High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation

Smiley-Rhodes, J. A.; Bitter, M. C.; Berardi, S.; Beltz, J. K.; Petrov, D. A.; Schmidt, P.

10.1101/2025.11.04.686622 — evolutionary biology — Posted on 2025-11-27

585 Evolution of multicellular reproduction through co-option of ecological interactions

Fernandes, A. P.; Vroomans, R. M.; Colizzi, E. S.

10.1101/2025.10.08.681199 — evolutionary biology — Posted on 2025-11-27

586 Fluctuating flooding motivates the facilitation of a wetland invader: a probe into the stress gradient hypothesis

Zhang, J.; Qu, Y.; Li, X.; Chen, W.; Xu, H.; Chen, J.; Yang, X.; Zhu, Y.; Wang, T.; Yang, L.

10.1101/2025.11.25.689875 — ecology — Posted on 2025-11-27

587 Seasonal and diel environment effects on host-seeking behaviour in the European tick vector, Ixodes ricinus

Noll, M.; Wall, R.; Makepeace, B. L.; Rose Vineer, H.

10.1101/2025.11.06.685884 — ecology — Posted on 2025-11-27

588 In situ mutational screening and CRISPR interference reveal that the apterous Early enhancer is required for developmental boundary positioning

Aguilar, G.; Sickmann, M. E.; Born, G.; Bieli, D.; Affolter, M.; Müller, M.

10.1101/2023.08.05.552106 — developmental biology — Posted on 2025-11-27

589 Both terminal misfolding and polymerisation contribute to disease-relevant phenotypic changes in cell models of alpha-1-antitrypsin deficiency-associated liver disease

Stylianou, P.; Adoni, K.; Nyon, M.-P.; Cryar, A.; Lee, N. O.; Haq, I.; Dickens, J. A.; Segeritz, C.-P.; Smith, G.; Ordonez, A.; Irving, J. A.; Lomas, D. A.; Leighton, K.-M.; Beasley, J.; Jones, A. W. E.; Rashid, S. T.; Vallier, L.; Thalassinos, K.; Gooptu, B.

10.1101/2025.09.30.679226 — cell biology — Posted on 2025-11-27

590 Probing metazoan polyphosphate biology using Drosophila reveals novel and conserved polyP functions

Sarkar, S.; Sharma, H.; Hosen, S. Y.; Ladke, J. S.; Moser, S.; Balasubramanian, D.; Raran-Kurussi, S.; Jessen, H. J.; Bhandari, R.; Jaiswal, M.

10.1101/2023.03.26.534266 — cell biology — Posted on 2025-11-27

591 Host oxidative stress primes mycobacteria for rapid antibiotic resistance evolution

Pepper-Tunick, E.; Srinivas, V.; Mast, F. D.; Li, S.; Russ, S.; Hanson, W.; Zamora, A. D.; Wu, W.-J.; Silcocks, M.; Ha, D. T. M.; Dunstan, S. J.; Thuong, T. N. T.; Turkarslan, S.; Aitchison, J. D.; Arrieta-Ortiz, M. L.; Baliga, N. S.

10.1101/2025.11.19.689367 — microbiology — Posted on 2025-11-27

592 Emergence of hypervirulent Klebsiella pneumoniae ST111 with a novel virulence plasmid causing pyogenic liver abscess

Feng, L.; Liu, K.; Liu, Y.; Ou, Y.; Dong, X.; Sun, Z.; Chen, L.; Shi, X.; Hao, M.

10.1101/2025.11.25.690365 — microbiology — Posted on 2025-11-27

593 Diverse infection models demonstrate robust resistance of Mycobacterium tuberculosis to innate immunity

Fairgrieve, M. R.; Brydon, E. C.; Chavez, R. A.; Kotov, D. I.; Vance, R.

10.1101/2025.11.20.687493 — immunology — Posted on 2025-11-27

594 Quantifying maternal antibody transfer to colostrum and cord blood reveals virus-specific selectivity in dogs

Teh, S.; Truyen, L. H.; Woodyear, S.; Palmeri, J.; Pimeta-Pereira, A. A.; Peprah, A. A.; Lanman, E.; Lonergan, T.; Reid, A. M.; Cheong, S. H.; caddy, S. L.

10.1101/2025.11.24.690260 — immunology — Posted on 2025-11-27

595 Oscillatory brain activity reflects semantic and phonological activation during sentence planning.

Meltzer, J. A.; Kielar, A.; Oppermann, F.

10.1101/2025.11.26.690808 — neuroscience — Posted on 2025-11-27

596 Reward impulsivity is linked to addictive-like behaviors towards sweet food and sugary drinks but not fatty food

Mohan, S.; Bobashev, G.; Moiseeva, V.; Shestakova, A.; Panidi, K.; Gutkin, B.

10.1101/2025.06.19.660563 — neuroscience — Posted on 2025-11-27

597 Setting priorities for the acquisition of primary plant occurrence data

Bystriakova, N.; De Melo, P. A. H.; Antonelli, A.; Bachman, S.; Bramley, G.; Brown, M.; Cespedes, G.; Cheek, M.; Darbyshire, I.; Demissew, S.; DeEgea, J.; Erst, A.; Forest, F.; Friis, I.; Fu, L.-F.; Fuentes, A.; Gogoi, R.; Jennings, L.; Jongkind, C. C. H.; Klitgaard, B.; Larridon, I.; Lucas, E.; Maldonado, C.; Martinez, M.; Moat, J.; Nic Lughadha, E.; Reynel, C.; Rustiami, H.; Santamaria Aguilar, D.; Tello, S.; Trethowan, L.; Utteridge, T. M. A.; Vorontsova, B.; Wei, Y.-G.; Wells, T.; Monro, A. K.

10.1101/2025.11.11.683036 — plant biology — Posted on 2025-11-27

598 TAGINE: Fast Taxonomy-based Feature Engineering for Microbiome Analysis

Baum, S.; Meshulam, I.; Peleg, O.; Algavi, Y.; Borenstein, E.

10.1101/2025.11.25.689983 — bioinformatics — Posted on 2025-11-27

599 Establishment of a Congenic Strain for the Oyster Mushroom Reveals the Structure and Evolution of Mating-Type Loci

Lee, Y.-Y.; Vidal-Diez de Ulzurrun, G.; Tay, R. J.; Hsueh, Y.-P.

10.1101/2025.11.21.689727 — genetics — Posted on 2025-11-26

600 Chemostat culturing reduces fecal eukaryotic virus load and delays diarrhea after virome transplantation

Offersen, S. M.; Adamberg, S.; Spiegelhauer, M. R.; Mao, X.; Rasmussen, T. S.; Larsen, F.; Zhong, J.; Nguyen, D. N.; Nielsen, D. S.; Aunsholt, L.; Thymann, T.; Adamberg, K.; Brunse, A.

10.1101/2024.11.20.624498 — microbiology — Posted on 2025-11-27

601 Enhanced pitch perception in early blind individuals and musicians is due to reduced internal noise

Park, W. J.; Awad, J.; Fine, I.

10.1101/2025.11.25.690447 — neuroscience — Posted on 2025-11-26

602 Early Arousal Signals Drive Reward Learning and Subsequent Choice Behaviour

Ban, K.; Fouragnan, E. F.; Philiastides, M. G.

10.1101/2025.11.25.690494 — neuroscience — Posted on 2025-11-26

603 A flexible coding scheme underlying working memory generalization in human parietal and frontal cortices

Shi, D.; Shu, L.; Yu, Q.

10.1101/2025.11.26.690703 — neuroscience — Posted on 2025-11-26

604 Ventral Hippocampal Temporoammonic and Schaffer Collateral Pathways Differentially Control Fear- and Anxiety-Related Behaviors

Kambali, M.; Wang, M.; Nagarajan, R.; Lyu, J.; Gritton, H.; Rudolph, U.

10.1101/2025.11.26.690696 — neuroscience — Posted on 2025-11-26

605 Dynamic brain states during encoding and their post-encoding reinstatement predicts episodic memory in children

Zeng, Y.; Chakravartti, S. P.; Ryali, S.; Qin, S.; Menon, V.

10.1101/2025.11.25.690570 — neuroscience — Posted on 2025-11-26

606 Inferential planning in the frontal cortex

Donnarumma, F.; Parr, T.; Friston, K.; Whittington, J.; Pezzulo, G.

10.1101/2025.11.26.690672 — neuroscience — Posted on 2025-11-26

607 Decoding the neural stages from action and object recognition to mentalizing

Wurm, M. F.; Lee, S.

10.1101/2025.11.25.690412 — neuroscience — Posted on 2025-11-26

608 A cholinergic mechanism orchestrating task-dependent computation across the cortex

Luo, J. K.; Tan, J.; Myhre, E.; Salvino, P.; Hark, A.; Pinto, L.

10.1101/2025.11.26.690825 — neuroscience — Posted on 2025-11-27

609 Language usage modulates the neural mechanisms ofselective attention in bilinguals

Theron-Grimaldi, S.; Schwarz, J.; Alex, P.; Bozic, M.

10.1101/2025.11.26.690745 — neuroscience — Posted on 2025-11-27

610 Coordinated multilaminar dynamics underlie multiplexed computation in motor cortex

Lopez-Galdo, L.; Nougaret, S.; Battaglia, D.; Kilavik, B. E.

10.1101/2025.11.26.690660 — neuroscience — Posted on 2025-11-27

611 Serotonin modulates nucleus accumbens circuits to suppress aggression

Zhang, Z.; Touponse, G. C.; Alderman, P. J.; Yassine, T.; Pomrenze, M. B.; Harris, T. W.; Shank, A. N.; Malenka, R. C.; Eshel, N.

10.1101/2025.11.26.690732 — neuroscience — Posted on 2025-11-27

612 Peripheral opioid tolerance involves skin keratinocytes and platelet-derived growth factor type B signaling

Posa, L.; Miracle, S. A.; Albers, K. M.; Fanelli, M. J.; Buton, A.; Le, T.; Khasnavis, A.; Martin, G.; MacDonald, A. K.; Gamble, M.; Freyberg, Z.; Logan, R.; Puig, S.; Fabri-Ruiz, S.

10.1101/2024.05.14.594040 — neuroscience — Posted on 2025-11-27

613 The metatranscriptomic response of the wheat rhizosphere to drought varies with growth stages.

Pande, P. M.; Tremblay, J.; St-Arnaud, M.; Yergeau, E.

10.1101/2025.11.26.690733 — microbiology — Posted on 2025-11-26

614 Energy-guided combinatorial co-optimization of antibody affinity and stability

Tennenhouse, A.; Mechaly, A.; Oldham, R. J.; Henry, J.; Elliott, I. G.; Kim, J.; Sirkis, Y. F.; Gaiduk, S.; Christ, D.; Cragg, M. S.; Fleishman, S. J.

10.1101/2025.11.26.690765 — synthetic biology — Posted on 2025-11-26

615 Effect of Lead Body and Helix Design Variables on Implantation Success, Insertion Depth, and Muscle Torque in Left Bundle Branch Area: Insights from An Ex-Vivo Porcine Model

Shah, A. R.; Puccio, A.; Yazaki, K.; Offei, E.; Castilo, M. S. R.; Jaroonpipatkul, S.; Vaziri, A. Y.; Khan, M. S.; Ranjan, R.; Hitchcock, R.; Dosdall, D.

10.1101/2025.11.25.690583 — bioengineering — Posted on 2025-11-26

616 TDP-43 controls RNA structure through high affinity lattice interactions

Vivek, R.; Kume, T.; Roschdi, S.; Record, T.; Hoskins, A.; BUTCHER, S.

10.1101/2025.11.26.690829 — biochemistry — Posted on 2025-11-26

617 Structural basis for ATP regulation of human 5-lipoxygenase

Teder, T.; Pozzani, F.; Schulte, T.; Hosseini, A. N.; Radmark, O.; Orellana, L.; Haeggstrom, J. Z.

10.1101/2025.11.26.690380 — biochemistry — Posted on 2025-11-26

618 GPR17 structure and agonism with small molecules and oxysterols

Metrick, C. M.; Zhang, L.; Hercher, M.; Dodge, G. J.; Cherry, D.; Vera Rebollar, J.; Brickelmaier, M.; Wang, J.; Martin, J. G.; Hronowski, X.; Kemp, M.; Capacci, A.; Arndt, J. W.; Silvian, L.; Conrad, K. S.; Silbereis, J.

10.1101/2025.11.26.690757 — biochemistry — Posted on 2025-11-26

619 Iron uptake mediated by TFRC and secretion of transferrin types stimulate thermogenic activation in human adipocytes

Alrifai, R.; Seo, M.; Karadsheh, G.; Mahendra, F. R.; Demeny, M. A.; Györy, F.; Motyan, J. A.; Fesüs, L.; Kristof, E.; Arianti, R.

10.1101/2025.11.24.690185 — cell biology — Posted on 2025-11-26

620 cAMP promotes acute lysosome biogenesis through TFEB nuclear import-export dynamics.

Bhatt, S.; Zaidi, M. A. A.; Woods, N. T. B.; Rozeveld, C. N.; Schott, M. B.

10.1101/2025.11.24.690233 — cell biology — Posted on 2025-11-26

621 Single-Molecule DNA Footprinting and Transcription Imaging Reveal the Molecular Mechanisms of Promoter Dynamics

Slaninova, V.; Mazzarda, F.; Dalakishvili, L.; Depierre, D.; Moene, C. J. I.; Topno, R. K.; Escudier, J.-M.; Robert, M.-C.; Cuvier, O.; Krebs, A.; Molina, N.; Radulescu, O.; Bertrand, E.

10.1101/2025.11.26.690466 — molecular biology — Posted on 2025-11-26

622 Dynamic changes in mRNA isoform usage during human retinal development

Keuthan, C. J.; Parthiban, S.; Chang, Y.-Y.; Shan, X.; Chang, X.; Yan, E.; Cavalier, S.; Timp, W.; Hicks, S. C.; Zack, D. J.

10.1101/2025.11.26.689062 — molecular biology — Posted on 2025-11-26

623 Tsa1-Mediated Regulation of PKA Tunes Trehalose Metabolism in Saccharomyces cerevisiae

Garrigos, V.; Dengler, L.; Henriques, D.; Matallana, E.; Picazo, C.; Ewald, J.; Aranda, A.

10.1101/2025.11.26.690464 — molecular biology — Posted on 2025-11-26

624 Rad18 suppresses the late step of human immunodeficiency virus type 1 replication

Ariumi, Y.; Zou, C.; Fukuda, H.; Tateishi, S.; Miyagi, E.; Strebel, K.

10.1101/2025.11.26.690725 — microbiology — Posted on 2025-11-26

625 A Validated Method for Detection of Bifidobacterium infantis Bi-26™ DNA in Stool by Quantitative Real-Time PCR

Godderz, M.; Sunshine, J.; Polke, M.; Rhyne, P.; Taylor, N.; Kiefer, A.; Yeung, N.; Wisplinghoff, H.; Zechner, U.; Frahm, N.

10.1101/2025.11.26.690772 — microbiology — Posted on 2025-11-26

626 Arachidonic acid modulates fluconazole-induced responses in Candida albicans biofilms

Fourie, R.; Kuloyo, O.; Ibe, C.; Kemp, G.; Naicker, P.; Govender, I.; Kruger, M.; Sebolai, O. M.; Albertyn, J.; Pohl, C. H.

10.1101/2025.11.25.690624 — microbiology — Posted on 2025-11-26

627 Quantifying antibiotic susceptibility and inoculum effects using transient dynamics of Pseudomonas aeruginosa

Sundius, S. A.; Farrell, J.; Eick, K.; Kuske, R.; Brown, S. P.

10.1101/2025.11.26.690803 — microbiology — Posted on 2025-11-26

628 Molecular and functional dissection of the AP2-I/BDP1 transcriptional complex of the malaria parasite reveals a role beyond the red blood cell stages

Le Berre, M.; Mellottee, L.; Salvi, A. R.; Touarin, P.; Auxilien, S.; Ropars, V.; Chaptal, M.; Ramiole, C.; Nessler, S.; Ramaprasad, A.; Santos, J. M.

10.1101/2025.11.26.690747 — microbiology — Posted on 2025-11-26

629 Malaria parasites adjust liver stage development to synchronise the blood stage of infection with host daily rhythms.

Herbert Mainero, A.; Schneider, P.; O'Donnell, A. J.; Reece, S. E.

10.1101/2025.11.26.690661 — microbiology — Posted on 2025-11-26

630 Moisture Matters: Unintended Consequences of Performing Wet Sanitation in Dry Environments.

Slaughter, C.; Chuang, S.; Daeschel, D.; McLandsborough, L. A.; Snyder, A. B.

10.1101/2025.11.26.690674 — microbiology — Posted on 2025-11-26

631 Revised 16S rRNA V4 hypervariable region targeting primers enhance detection of Patescibacteria and other lineages across diverse environments

Hu, H.; Karwautz, C.; Duszka, K.; Karner, T.; Wagner, I.; Grander, C.; Grander, W.; Steinwidder, L.; Boito, L.; Velde, V. V. d.; Bauters, M.; Boeckx, P.; Seki, D.; Glasl, B.; Thiele, S.; Schmidt, H.; Seneca, J.; Wagner, M.; Pjevac, P.

10.1101/2025.11.26.690684 — microbiology — Posted on 2025-11-26

632 Histological techniques for the visualisation and identification of polymicrobial communities in mucosal tissue

Giddings, H. J.; Teodosio, A.; Jones, J.; Butterworth, W.; Shannon-Lowe, C. D.; Cole, J. A.; Rossiter-Pearson, A. E.

10.1101/2025.11.26.690509 — microbiology — Posted on 2025-11-26

633 In search for the invisible: motor inhibition in monkey premotor cortex and its RNN replicas

Albore, N.; Galluzzi, A.; Pani, P.; Ferraina, S.; Mattia, M.

10.1101/2025.11.24.690225 — neuroscience — Posted on 2025-11-26

634 Decoding Gene Responsiveness to Synthetic Chromatin Reader-Actuators with Multi-Modal Epigenomic Profiling

Kim, S. H.; Enwerem-Lackland, I.; Williams, N. L.; Fisher, R.; Plaisier, C. L.; Haynes, K. A.

10.1101/2025.11.26.690833 — synthetic biology — Posted on 2025-11-26

635 Tuning Yeast Glycosylation Proximal to the FLS2-flg22 Binding Interface enables Functional Yeast Surface Display under Induced ER Stress

Dolgikh, B.; Schulte, S.; Woldring, D. R.

10.1101/2025.11.25.690463 — synthetic biology — Posted on 2025-11-26

636 KDM7-mediated oxygen sensing reprograms chromatin to enhance hypoxia tolerance in the root

Zhang, D.; Chirinos, X.; Del Chiaro, A.; Shukla, V.; Ryder, A.; Beltran, A. D. P.; Iacopino, S.; Bota, P.; Zivkovic, D.; Fioriti, F.; Telara, Y.; Ellison, C. J.; Costa, F.; Elliott, P. R.; Giorgi, F.; Giuntoli, B.; Flashman, E. G.; Abreu, I.; Licausi, F.

10.1101/2025.11.24.690241 — plant biology — Posted on 2025-11-26

637 Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain

Seo, L.; Farran, I.; Aslam, A.; Li, X.; Jaishankar, P.; Fraser, J. S.; Renslo, A.; Wankowicz, S. A.

10.1101/2025.11.25.690589 — biophysics — Posted on 2025-11-26

638 DNA Motors Powered by Exonuclease III for Autonomous Rolling Motion and Biosensing Applications

Imtiaz, Y.; Hardin, J.; Sheyitov, B.; Zhang, L.; Foote, A.; Rahman, M. H. b. A.; Jackson, K.; Piranej, S.; Bazrafshan, A.; Salaita, K.

10.1101/2025.11.26.690764 — biophysics — Posted on 2025-11-26

639 A multi-step filtering pipeline for human read removal enhances detection of Fusobacterium in WGS datasets with immunohistochemical confirmation in mucinous rectal cancer.

Frolova, M. S.; Maguire, B.; Duessmann, H.; Rayan, M.; Burke, C.; Korashy, H. M.; Raman, A.; Gallagher, W. M.; Burke, J. P.; Furney, S. J.; Prehn, J. H. M.

10.1101/2025.11.24.690231 — bioinformatics — Posted on 2025-11-26

640 Structural insights into autophosphorylation-mediated heat shock response by the protein-arginine kinase McsAB

Arifuzzaman, M.; Park, K.; Kwon, E.; Kim, D. Y.

10.1101/2025.11.26.690658 — biochemistry — Posted on 2025-11-26

641 Structural atlas of Pakpunavirus P7-1 reveals determinants of virion stability and genome ejection

Cingolani, G.; Li, F.; Bellis, N.; Lokareddy, R. K.; Hou, C.-F. D.; Yang, R.; Branston, S.; Kovach, Z.; Geiger, R.; Soriaga, A.; Sim, L.; Kyme, P.; Birx, D.; Lemire, S.

10.1101/2025.11.26.690771 — biochemistry — Posted on 2025-11-26

642 Mutant FUS perturbs m6A regulation by repressing ALKBH5, while restoring m6A levels alleviates ALS pathology in vivo

Di Timoteo, G.; Setti, A.; Margarita, F.; D'Angelo, A.; Giuliani, A.; Biagi, M. C.; Di Salvio, M.; Santini, T.; Cestra, G.; Bozzoni, I.

10.1101/2025.11.26.690809 — molecular biology — Posted on 2025-11-26

643 Staphylococcus aureus urease is controlled by a complex regulatory network and promotes dissemination during catheter-associated urinary tract infections (CAUTI)

Gomez, J.; Duran-Ramirez, J.; Alvarez, M.; Cristy, S. A.; Walker, J.

10.1101/2025.11.26.690714 — microbiology — Posted on 2025-11-26

644 Atmospheric hydrogen consumption is regulated by catabolite repression in mycobacteria

Kropp, A.; Archer, J.; Jespersen, M.; Watts, T.; Solari, J.; Huang, C.; Grinter, R.; Greening, C.

10.1101/2025.11.25.690588 — microbiology — Posted on 2025-11-26

645 Moisture and material shape microbial communities in the built environment through disturbance-productivity relationships

Nannini, K.; Krutkin, D. D.; Kelley, S. T.; Ortiz-Velez, A.; Brown, J. D.; Ogden, S. M.; Terrazas, F.; Barber, N. A.

10.1101/2025.11.25.690005 — microbiology — Posted on 2025-11-26

646 Spatial constraint drives negative frequency dependent selection of phage weaponization

Peng, Y.; Holt, J. D.; Dalia, T. N.; Dalia, A. B.; Nadell, C. D.

10.1101/2025.11.26.690769 — microbiology — Posted on 2025-11-26

647 Generation of an optimised Cumate toolkit for tuneable protein expression during in vitro and in vivo studies of Burkholderia cenocepacia

Tahir, H.; Karlic, K. I.; Mwiti, G.; Scott, N. E.

10.1101/2025.11.26.690688 — microbiology — Posted on 2025-11-26

648 3-Phenylpropionic acid, a microbiota-derived polyphenol metabolite linked to hippuric acid, ameliorates colitis as a colon-enriched PPAR-γ agonist

Zhu, Y.; Xiang, L.; Luo, W.; Zhang, W.; Lai, W.; Wu, X.; Zhuo, S.; Feng, B.; Chen, S.; Fang, S.; Chen, M.; Bai, P.; Feng, R.

10.1101/2025.11.25.690607 — microbiology — Posted on 2025-11-26

649 Sustained Humoral Activation through self-amplifying mRNA Vaccination Enhances Longitudinal Antibody Function in a Phase III Trial

Levine, K. S.; Blanc, R.; Wang, Q.; Malca, H.; Sekulovich, R.; Jin, H.; Liu, S.; Verhoeven, C.; Sullivan, B.; Smolenov, I.; McNamara, R. P.

10.1101/2025.11.25.690547 — immunology — Posted on 2025-11-26

650 Improved spike-in normalization clarifies the relationship between active histone modifications and transcription

Patel, L.; Cao, Y.; Xu, T.; Xu, T.; Dishon, T.; Zhang, L.; Mendenhall, E.; Heinz, S.; Simon, I.; Benner, C.; Goren, A.

10.1101/2025.11.25.690627 — genomics — Posted on 2025-11-26

651 Receptor stoichiometry predicts artery-typical vulnerability to altered Notch signaling during smooth muscle differentiation.

Sanlidag, S.; Virtanen, N.; Hoursan, H.; Ristori, T.; Sjoqvist, M.; Loerakker, S.; Sahlgren, C.

10.1101/2025.05.05.652186 — developmental biology — Posted on 2025-11-26

652 A non-canonical AKT1-TERT pathway coordinates autophagy and ERphagy

Babu, V. S.; Ghosh, S.; Bammidi, S.; Jiwon, R.; Sharma, R.; Meyer, D.; Hose, S.; Pattabiraman, P. P.; Sahel, J.-A.; Kidley, N. J.; Braz, N. F.; Slater, M. J.; Lang, S.; Ghosh, A.; Yi, J.; Sripathi, S.; Rangaramanujam, K.; Bharti, K.; Sinha, D.

10.1101/2025.11.24.690135 — cell biology — Posted on 2025-11-26

653 Injury-Induced Remodeling of Junctional Actin Bands in the Vestibular Maculae of Mice and Chicks: Implications for Sensory Regeneration

Warchol, M. E.

10.1101/2025.11.24.682866 — neuroscience — Posted on 2025-11-26

654 Global and selective effects of auditory attention on arousal: insights from pupil dilation

Grandjean, A.; Hoyer, R. S.; Mathieu, A.; Caclin, A.; Moulin, A.; Bidet-Caulet, A.

10.1101/2024.11.19.624303 — neuroscience — Posted on 2025-11-26

655 Protein-Independent Liquid - Liquid Phase Separation of Adenosine Triphosphate under Crowded Conditions

Dec, R.; Dzwolak, W.; Winter, R.

10.1101/2025.11.24.690196 — biophysics — Posted on 2025-11-26

656 Cross-chemical and cross-species toxicity prediction: benchmarkingand a novel 3D-structure-based deep learning model

Yuan, R.; Shaw, J.; Tang, H.; Ye, Y.

10.1101/2025.11.24.690199 — bioinformatics — Posted on 2025-11-26

657 Comparative metagenomics using pan-metagenomics graphs

Coleman, I.; Mametyarova, N.; Zaznaev, A.; Cai, P.; Yu, L.; Meydan, Y.; Litman, A.; Sharma, A.; He, L.; Simkhovich, A.; Seeram, D.; Park, H.; Nobel, Y. R.; Kav, A. B.; Pe'er, I.; Uhlemann, A.-C.; Korem, T.

10.1101/2025.11.24.690211 — bioinformatics — Posted on 2025-11-26

658 The role of fecundity dynamics and time of injury for femalereproductive fitness

Michalak, P.; Ferdy, J.-B.; Duneau, D.

10.1101/2025.11.12.687561 — evolutionary biology — Posted on 2025-11-26

659 Inhibition of eIF5A hypusination improves pancreatic islet transplantation outcomes by promoting ischemia tolerance

Ouahmi, H.; Massa, F.; Allart, E.; Cougnon, M.; Rouleau, M.; Van Obberghen, E.; Shkreli, M.; Sicard, A.; Pisani, D. F.

10.1101/2025.11.24.689446 — cell biology — Posted on 2025-11-26

660 RNA virus ecogenomics along a subarctic permafrost thaw gradient

Pratama, A. A.; Dominguez-Huerta, G.; Wainaina, J. M.; Bolduc, B.; Tian, F.; Ellenbogen, J.; Guo, J.; EMERGE Field Team, ; EMERGE Coordinators, ; Kuhn, J. H.; Wrighton, K. C.; Kusel, K.; Zayed, A. A.; Sullivan, M. B.

10.1101/2025.02.13.637936 — microbiology — Posted on 2025-11-26

661 Glomerulus-specific inhomogeneity of the basal activity map in the olfactory bulb supports olfactory-driven behavior

Fink, S.; Fomin-Thunemann, N.; Tzeng, W.-Y.; Figarella, K.; Kamari, F.; Kovalchuk, Y.; Garaschuk, O.

10.1101/2025.11.24.690198 — neuroscience — Posted on 2025-11-26

662 Modeling Psychophysical Data in R: A Comparative Study of Four Model Frameworks

Balestrucci, P.; Mezzetti, M.; La Scaleia, B.; Moscatelli, A.

10.1101/2025.11.17.688833 — neuroscience — Posted on 2025-11-26

663 SPOROCYTELESS/NOZZLE acts together with MADS-domain transcription factors to regulate an auxin-dependent network controlling the Megaspore Mother Cell development

Cavalleri, A.; Astori, C.; Manrique, S.; Bruzzaniti, G.; Smaczniak, C.; Mizzotti, C.; Ruiu, A.; Spano, M.; Movilli, A.; Gregis, V.; Xu, X.; Kaufmann, K.; Colombo, L.

10.1101/2025.03.11.641985 — plant biology — Posted on 2025-11-26

664 Immuno-Impaired Expression of Synaptophysin, GFAP and Nissl Substances in the Cerebral Cortex of Diabetic Wistar Rats; Evaluation of Andrographis Paniculata Effects

ONANUGA, I. O.; FOLARIN, R. O.; MUNIRU, E. T.; IBRAHIM, R. B.; USMAN, I. M.; JEGEDE, A. I.; AZU, O. O.; OBAYA, T. O.; KEHINDE, M. O.

10.1101/2025.11.22.689937 — pharmacology and toxicology — Posted on 2025-11-26

665 AI-driven discovery and optimization of antimicrobial peptides from extreme environments on global scale

Kang, Z.; Zhang, H.; Zhou, Q.; Liu, J.; Zhou, K.; Chen, P.; Liu, B.-F.; Ning, K.

10.1101/2025.11.13.688364 — bioinformatics — Posted on 2025-11-26

666 Progressive decoding of DNA-stored JPEG data with on-the-fly error correction

Nawaz, I.; Agarwal, P.; Heinis, T.

10.1101/2025.10.26.684640 — bioinformatics — Posted on 2025-11-26

667 A Hybrid Modeling Framework for Predictive Digital Twins of CHO Cell Culture

Richelle, A.; Andersson, D.; Antonakoudis, A.; Jakobsson, J.; Pijeaud, S.; Vernersson, A.; Trygg, J.

10.1101/2025.11.24.690194 — bioengineering — Posted on 2025-11-26

668 NanoBRET Tracer Development for Class I Bromodomain Target Engagement in Live Cells

Sneddon, M. S.; Tsou, C.-J.; Fu, X.; Shelat, A. A.; Pomerantz, W. C. K.

10.1101/2025.11.25.689777 — biochemistry — Posted on 2025-11-26

669 A flexible Janus head: molecular determinants of a viral protein's RNAi suppressor and capsid forming activities

Arendt, D.; Tamilarasan, S.; Golbik, R. P.; Thondorf, I.; Bender, J.; Lilie, H.; Gursinsky, T.; Parthier, C.; Schmidt, C.; Stubbs, M. T.; Behrens, S.-E.

10.1101/2025.11.26.690650 — biochemistry — Posted on 2025-11-26

670 Calibrated Variant Effect Prediction at the Residue Level Using Conditional Score Distributions

Passi, G.; Amittai, S.; Schneidman-Duhovny, D.

10.1101/2025.11.24.690189 — genomics — Posted on 2025-11-26

671 Interplay of structured and random interactions in complex ecosystems dynamics

Giral Martinez, J.; Barbier, M.; De Monte, S.

10.1101/2024.11.25.624858 — ecology — Posted on 2025-11-26

672 DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics

Hillary, L. S.; Knotts, T. A.; Adams, S. H.; Ali, M. R.; Olm, M. R.; Emerson, J. B.

10.1101/2025.11.25.690293 — microbiology — Posted on 2025-11-26

673 NLRP1 Shapes Immune and Inflammatory Signatures in Human Melanoma but Not in Mouse Models

Targhetta, V. P.; Vieira, R. d. S.; Ranfley, H.; de Souza Breda, C. N.; Camara, N. O. S.

10.1101/2025.11.24.690170 — immunology — Posted on 2025-11-26

674 Shared feedback control principles across standing and walking

Geng, Y.; van Dieen, J. H.; Bruijn, S. M.

10.1101/2025.11.24.690121 — neuroscience — Posted on 2025-11-26

675 Quantitative phosphoproteomics uncovers the signalling dynamics of hallucinogenic psychedelics

Lopez-Gimenez, J. F.; Cutillas, P. R.; Gonzalez-Maeso, J.; Martin-Guerrero, S. M.; Taddei-Tardon, M.; Maltman, J. L.; Potukanuma, S.

10.1101/2025.11.24.690190 — neuroscience — Posted on 2025-11-26

676 Spontaneous differentiation across cell lineages of separate germ layer origin during progenitor cell-mediated regeneration of the central nervous system

Chen, C. Z.; Yu, Y.; Murphy, N.; Cubillos, J. F.; Rawji, K. S.; Zhao, C.; Hill, M.; Arthur-Farraj, P.; Franklin, R. J. M.; Neumann, B.

10.1101/2025.11.24.690179 — neuroscience — Posted on 2025-11-26

677 Digital Spatial Pathway Mapping Reveals Prognostic Tumor States in Head and Neck Cancer

Hense, J.; Idaji, M. J.; Ciernik, L.; Dippel, J.; Ersan, F.; Knebel, M.; Pusztai, A.; Sendelhofert, A.; Buchstab, O.; Froehling, S.; Otto, S.; Hess, J.; Liokatis, P.; Klauschen, F.; Mueller, K.-R.; Mock, A.

10.1101/2025.11.24.689710 — pathology — Posted on 2025-11-26

678 Dual targeting of BTK and BCL2 enhances apoptosis in marginal zone lymphoma models: preclinical activity of BGB-16673 and sonrotoclax

Arribas, A. J.; Civanelli, E.; Scalise, C.; Cascione, L.; Rinaldi, A.; Rossi, D.; Zucca, E.; Carosella, L.; Raniolo, S.; Limongelli, V.; Bertoni, F.

10.1101/2025.11.24.690186 — cancer biology — Posted on 2025-11-26

679 Drosophila midgut tumor-induced insulin resistance systemically remodels lymph gland hematopoiesis during cancer cachexia

Khadilkar, R. J.; Chowdhury, U.; Panzade, G.; Karnik, P. N.; Birwadkar, P.; Tashu, T.

10.1101/2025.11.24.690188 — cancer biology — Posted on 2025-11-26

680 Benchmarking cell-type deconvolution in cross-platform transcriptomic data

Singh, A.; Cakmak, P.; Lun, J. H.; Macas, J.; Plate, K. H.; Reiss, Y.; Schupp, J.; Imkeller, K.

10.1101/2025.11.24.690141 — bioinformatics — Posted on 2025-11-26

681 RNA-X: Modeling RNA interactions to design binder RNA and simultaneously target multiple molecules of different types

Shukueian Tabrizi, S.; Hashemi Aghdam, H.; Cicek, A. E.

10.1101/2025.11.24.690191 — bioinformatics — Posted on 2025-11-26

682 Cellular Mechanisms Underlying Melanoma Brain Metastasis

Yavuz, B. R.; Jang, H.; Nussinov, R.

10.1101/2025.11.24.689301 — bioinformatics — Posted on 2025-11-26

683 To the homeRNAmax: Developing an Improved Blood Self-Collection and Stabilization Platform for Remote Transcriptomic Studies

Eakman, M.; Stefanovic, F.; Berthier, J.; Robinson, I. H.; Knudsen, L.; Nguyen, S. H.; Craig, C. A.; Leong, K. M.; Chan, D. W. H.; Adams, K. N.; Olanrewaju, A. O.; Thongpang, S.; Nicholson, T. M.; Berthier, E.; Theberge, A. B.; Haack, A. J.

10.1101/2025.11.24.690053 — bioengineering — Posted on 2025-11-26

684 Micellangelo: a Generative Model of Cell-Topography Interactions

Konshin, N.; Minartz, K.; de Boer, J.; Menkovski, V.

10.1101/2025.11.24.690184 — bioengineering — Posted on 2025-11-26

685 Phosphatidylinositol 5 phosphate 4 kinase regulates phosphatidylinositol 3,4 bisphosphate levels in vivo.

Venugopal, A.; Varma, S.; PADINJAT, R.

10.1101/2025.11.24.690171 — cell biology — Posted on 2025-11-26

686 Centrosomal P4.1-associated protein (CPAP) is a novel regulator of ESCRT pathway function during endosome maturation

Gudi, R. R.; Vasu, C.

10.1101/2025.08.09.669489 — cell biology — Posted on 2025-11-26

687 Generation of a HiBiT-expressing recombinant rat hepacivirus supporting both in vivo and in vitro infection

Akaike, Y.; Tanaka, T.; Kasai, H.; Yamashita, A.; Matsuura, Y.; Moriishi, K.

10.1101/2025.11.25.690605 — microbiology — Posted on 2025-11-26

688 NSUN2-dependent 5-methylcytosine Modification Regulates Influenza A virus Gene Expression and Genomic Packaging

Chen, H.; Hu, J.; Jiang, S.; You, W.; Hao, R.; Li, J.; Gong, S.; Xiao, X.; Zhao, H.; Liu, L.

10.1101/2025.11.26.690652 — microbiology — Posted on 2025-11-26

689 Mutational spectra reveal influenza virus transmission routes and adaptation

Ruis, C.; Rossi, A. D.; Sanderson, T.; Matuszewska, M.; Ntemourtsidou, M.; Mendes, V.; Torres, P. H. M.; Parkhill, J.; Peacock, T. P.; Floto, R. A.

10.1101/2025.11.26.690773 — microbiology — Posted on 2025-11-26

690 A Globally Representative Immunopeptidomics Approach to Identify Population-Wide Vaccine Candidates

Baker, T.; Song, L.; Cai, C.; Gu, S.; Foster, L.

10.1101/2025.11.25.690604 — immunology — Posted on 2025-11-26

691 Cued replay of experience in human infants

Postzich, C. M.; Finnemann, J.; Skeide, M. A.

10.1101/2025.06.12.659246 — neuroscience — Posted on 2025-11-26

692 STODE: A Deep Generative Framework for Continuous Spatiotemporal Dynamics in Spatial Transcriptomics

Majima, K.; Kojima, Y.; Shimamura, T.

10.1101/2025.11.24.690134 — bioinformatics — Posted on 2025-11-26

693 Generalizable and scalable protein stability prediction with rewired protein generative models

Li, Z.; Luo, Y.

10.1101/2025.02.13.638154 — bioinformatics — Posted on 2025-11-26

694 AI-Guided Stability Tuning of a Heterodimeric Linker for Programmable Protein Tube Architectures

Noji, M.; Suzuki, Y.

10.1101/2025.11.24.689909 — bioengineering — Posted on 2025-11-26

695 Improved De Novo Peptide Binder Design with Target-Conditioned Inverse Folding

Layne, E.; Kanawaty, A. K.; Broom, A.; Kitaygorodsky, A.; Nivedha, A. K.; Vora, P.; Woffindale, C.; Hailstone, S.; Sachouli, E.; Halcrow, E.; Donachie, G.; Adsett, M.; Butterfoss, G. L.; Fingerhuth, M.

10.1101/2025.10.28.685072 — bioengineering — Posted on 2025-11-26

696 Shear Difference: Flow Type Dictates Endothelial Flow-Responsive Gene Programs in a 3D-Printed in vitro Model

Shah, N. A.; Rye, K.-A.; Endre, Z. H.; Barber, T. J.; Erlich, J. H.; Cochran, B. J.

10.1101/2025.11.24.690338 — bioengineering — Posted on 2025-11-26

697 Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates

Salve, B. G.; H, S.; Vijay, N.

10.1101/2025.07.03.663111 — genomics — Posted on 2025-11-26

698 MetaBeeAI: an AI pipeline for full-text systematic reviews in biology

Parkinson, R. H.; Cerbone, H.; Mieskolainen, M.; Cao, S.; Wilson, A. D.; Albacete, S.; Armstrong, E. B.; Bass, C.; Botias, C.; Brown, A.; Hayward, A. J.; Herbertsson, L.; Jones, A. K.; Nagloo, N.; Nicholls, E.; Rigosi, E.; Sgolastra, F.; Siviter, H.; Stanley, D. A.; Straub, L.; Straw, E. A.; Tadei, R.; Walter, K.; Stevance, H. F.; Daniels, R. K.; Lambert, B.; Roberts, S.

10.1101/2025.11.24.690154 — ecology — Posted on 2025-11-26

699 Separating faces in ARMS metabarcoding improves marine biodiversity monitoring: a comparison across protocols, experimental designs, and photographic surveys

Chenuil, A.; Bouchereau, E.; Legrand, T.; Calvert, V.; Chemin, C.; Chenesseau, S.; Guillemain, D.; Gutierrez Ortega, J.-M.; Haguenauer, A.; Leduc, M.; Marschal, F.; Marschal, C.; Mirleau, F.; Selva, M.; Vanbostal, L.; Zuberer, F.; Mirleau, P.; Plaisance, L.; Rossi, V.; Ruitton, S.; Meglecz, E.; Dubut, V.

10.1101/2025.11.24.690150 — ecology — Posted on 2025-11-26

700 Thiamine transporter 2 and Janus kinase 2 inhibitor, fedratinib suppresses thermogenic activation of human neck area-derived adipocytes

Karadsheh, G.; Kovacs, E.; Alrifai, R.; Seo, M.; Györy, F.; Csatari-Kovacs, R.; Csösz, E.; Poliska, S.; Fesüs, L.; Arianti, R.; Kristof, E.

10.1101/2025.11.24.690155 — cell biology — Posted on 2025-11-26

701 Sexual dimorphism in zymosan-induced arthritis is linked with a higher IFN response in myeloid cell subsets that faithfully recapitulate RA synovial cell clusters

Bell, R. D.; Huang, M.; Yuan, R.; Wingert, C.; Mishra, B.; Seren, S.; Singh, T.; Maclauchlan, S.; Gravallese, E.; Singh, A.; Lakhanpal, A.; Bass, A.; Donlin, L.; Ivashkiv, L. B.

10.1101/2025.11.24.690174 — immunology — Posted on 2025-11-26

702 A mouse model of classical trigeminal neuralgia via intradural compression of the trigeminal nerve

Abdulrahim, M.; Xu, R.; Chen, Y.; Nair, S.; Xu, Q.; Zhang, Y.; Das, O.; Gensler, R.; Feghali, J.; Ahmad, A. K.; Jackson, C.; Huang, J.; Comair, Y.; Bettegowda, C.; Dong, X.

10.1101/2025.11.24.690061 — neuroscience — Posted on 2025-11-26

703 Fus depleted oligodendrocytes reduce neuronal damage and attenuate AD progression in the AppNL-G-F mouse

Tung, T.-H.; Babu, S.; Tang, X.; Sciutto, A. L.; Romer, M.; Racha, P.; Fiesler, V.; Saha, A.; Sado, T. C.; Saito, T.; Grinspan, J. B.; Mathys, H.; Kozai, T. D. Y.; Cambi, F.

10.1101/2025.11.24.689041 — neuroscience — Posted on 2025-11-26

704 Overlooked features lead to divergent neurobiological interpretations of brain-based machine learning biomarkers

Adkinson, B. D.; Rosenblatt, M.; Sun, H.; Dadashkarimi, J.; Tejavibulya, L.; Horien, C.; Westwater, M. L.; Noble, S.; Scheinost, D.

10.1101/2025.03.12.642878 — neuroscience — Posted on 2025-11-26

705 Old-New Recognition Memory Revisited

Wei, X.; Buckner, R. L.

10.1101/2025.11.11.687844 — neuroscience — Posted on 2025-11-26

706 Characterization of hippocampal subfields using histology-based annotated postmortem MRI: Lessons for in vivo segmentation II

Tucker, H. L.; Karat, B.; De Ruiter, A. T.; Parker, D. M.; Lim, S. A.; Denning, A. E.; Ittyerah, R.; Levorse, L. M.; Trotman, W.; Bahena, A.; Chung, E.; Prabhakaran, K.; Bedard, M. L.; Ohm, D. T.; Xie, L.; Das, S. R.; Pluta, J. B.; Schuck, T.; Liu, W.; Pickup, S.; Artacho-Perula, E.; Martin, M. M. I. d. O.; Munoz, M.; Romero, F. J.; Gonzalez, J. C. D.; Jimenez, M. A.; Rabal, M. M.; Serrano, A. I.; Gonzalez, N. V.; Sanchez, S. C.; de la Rosa, C.; Lee, E. B.; Detre, J. A.; Tisdall, D.; Irwin, D. J.; Wolk, D. A.; Adler, D. H.; de Flores, R.; Berron, D.; Ding, S.-L.; Yushkevich, P.; Hodgetts, C. J

10.1101/2025.11.21.689744 — neuroscience — Posted on 2025-11-26

707 Early Sleep-Dependent Sensory Gating in the Olfactory System

Serantes, D.; Gallo, D.; Garcia, A.; Gonzalez, J.; Mendoza, M.; Lagos, P.; Torterolo, P.; Cavelli, M. L.

10.1101/2025.11.04.686664 — neuroscience — Posted on 2025-11-26

708 Contralesional activity reflects compensation, while brainstem detour pathways support skilled motor recovery after stroke

Panzeri, M.; Thiem, N.; Hoffmann, C.; Schillinger, U.; Barapatre, N.; Musall, S.; Helmchen, F.; Wahl, A.-S.

10.1101/2025.11.24.690099 — neuroscience — Posted on 2025-11-26

709 Parabrachial Calcitonin Gene-Related Peptide Neurons Sex-Specifically Modulate Anxiety in Alcohol Withdrawal

Van Doorn, C. E.; Tyree, J. B.; Jaramillo, A. A.

10.1101/2025.11.24.690162 — neuroscience — Posted on 2025-11-26

710 Distinct Roles of Deep and Superficial Cortical Layers in Tone Prediction, Comparison, and Adaptation in Human Auditory Cortex

van Haren, J.; de Lange, F. P.; Kotz, S. A.; De Martino, F.

10.1101/2025.11.24.687809 — neuroscience — Posted on 2025-11-26

711 Thermal boundaries and underlying systems biology mechanisms in two waterbloom cyanobacteria

Zhang, T.; Liu, L.; Wang, Z.; Zhao, Z.; Guo, Y.; Cao, H.; Yang, Z.

10.1101/2025.11.24.690146 — systems biology — Posted on 2025-11-26

712 Stochastic Gene Expression under Sequestration: Noise Reduction and Emergent Distributions

Morozova, O.; Oravcova, I.; Zabaikina, I.; Bokes, P.; Singh, A.

10.1101/2025.11.24.690157 — systems biology — Posted on 2025-11-26

713 Role of CIA2 and CIL in the regulation of chloroplast photomorphogenesis in Arabidopsis

Zarrin Ghalami, R.; Burdiak, P.; Kamran, M.; Duszyn, M.; Rusaczonek, A.; Muszynska, E.; karpinski, s.

10.1101/2025.11.24.690140 — plant biology — Posted on 2025-11-26

714 The TUTase URT1 regulates the transcriptome of seeds and their primary dormancy

Peter, J.; Roignant, J.; Sacharowski, S.; Ubrig, E.; Lefevre, B.; Swiezewski, S.; Gagliardi, D.; Zuber, H.

10.1101/2024.12.19.629392 — plant biology — Posted on 2025-11-26

715 ANUBI: A Platform for Affinity Optimization of Proteins and Peptides in Drug Design

Buratto, D.; Wang, W.; Zhang, X.; Zhu, Q.; Meng, J.; Rigden, D. J.; Zhou, R.; Zonta, F.

10.1101/2025.10.20.683353 — biophysics — Posted on 2025-11-26

716 ASD: Antigen-Specific Antibody Database

Czerwinski, A.; Dudzic, P.; Wojtowicz, K.; Jaszczyszyn, I.; Bielska, W.; Wrobel, S.; Demharter, S.; Spreafico, R.; Greiff,, V.; Krawczyk, K.

10.1101/2025.11.24.690097 — bioinformatics — Posted on 2025-11-26

717 Discovery of molecular glues by modeling ternary complex conformational ensembles and thermodynamic stability

Izaguirre, J. A.; McDargh, Z.; Trovato, F.; Wu, Y.; Palpant, T.; Razavi, A. M.; Koh, C.; Xu, H.

10.1101/2025.01.13.632817 — bioinformatics — Posted on 2025-11-26

718 FusionProt: Fusing Sequence and Structural Information for Unified Protein Representation Learning

Kalifa, D.; Singer, U.; Radinsky, K.

10.1101/2025.08.06.668973 — bioinformatics — Posted on 2025-11-26

719 Disentangling Protein Function via Decoupled Information Theoretic Selection of Key Tuning Residues

Saeed, H.; Yang, A.; Huang, W.

10.1101/2025.05.28.653817 — bioinformatics — Posted on 2025-11-26

720 Repurposed endogenous virus-like vesicles mediate dendritic cell long-range antigen presentation and T cell activation for enhanced cancer vaccination

Gu, W.; Li, R.; Goodrich, H.; Artzi, D.; Cai, S.; Shi, A.; Tsai, Y.-C.; Qin, G.; Li, A.; Goldwasser, E.; Elkasri, N.; Luozhong, S.; Kamada, S.; Wu, Y.; Upadhayay, V.; Zhao, Y.; Yang, Y.; Lau, J.; Sultan, E.; Wirganowicz, A.; Cai, C.; Yu, Q.; Jiang, S.

10.1101/2025.11.23.690059 — bioengineering — Posted on 2025-11-26

721 Mapping Protein Occupancy on DNA with an Unnatural Cytosine Modification in Bio-orthogonal Contexts

Zhu, R.; Loo, C. E.; Hurley, C. M.; Parker, J. B.; Kohli, R. M.

10.1101/2025.11.24.690163 — biochemistry — Posted on 2025-11-26

722 eRNAkit: Expanding the Functional Atlas of human Enhancer RNAs Beyond the Nucleus

Benova, N.; Kuklinkova, R.; Eldahshoury, M. K.; Anene, C. A.

10.1101/2025.04.25.650683 — molecular biology — Posted on 2025-11-26

723 Flavobacteria buffer nitrous oxide emissions from partial denitrifiers in coastal sediments

Nguyen-Dinh, T.; Hutchinson, T.; Ricci, F.; Prayitno, H.; Jimenez, L.; Eate, V.; Leung, P. M.; Lappan, R.; Yoon, S.; Wong, W. W.; Cook, P.; Greening, C.

10.1101/2025.11.24.689969 — microbiology — Posted on 2025-11-26

724 Atypical endo-β-1,4-mannanases are necessary for normal glucomannan synthesis in Arabidopsis

Kikuchi, A.; Sato, E.; Yoshimi, Y.; Takasaki, H.; Nishigaki, N.; Atsuzawa, K.; Kaneko, Y.; Yamaguchi, M.; Takahashi, D.; Dupree, P.; Kotake, T.

10.1101/2025.02.21.639209 — plant biology — Posted on 2025-11-26

725 Curability Difference between Autochthonous Mouse Tumors and Their Transplants in Association with Immune Gene Expression

Tanooka, H.

10.1101/2025.11.23.690042 — cancer biology — Posted on 2025-11-26

726 AFM-Fold: Rapid Reconstruction of Protein Conformations from AFM Images

Kawai, T.; Matsunaga, Y.

10.1101/2025.11.17.688836 — biophysics — Posted on 2025-11-26

727 CHALLENGER: Detecting Copy Number Variants in Challenging Regions Using Whole Genome Sequencing Data

Yilmaz, M. A.; Ceylan, A. A.; Cicek, A. E.

10.1101/2025.11.23.690083 — bioinformatics — Posted on 2025-11-26

728 MELO-ED: learning locality-sensitive multi-embeddings for edit distance

Yuan, X.; Chen, K.; Ahmed, A. Y.; Shao, M.

10.1101/2025.11.23.689944 — bioinformatics — Posted on 2025-11-26

729 A Stretchable Wearable Doppler Ultrasound Patch for Continuous Vascular Monitoring

Li, Y.; Li, Z.; Peng, C.

10.1101/2025.11.23.690069 — bioengineering — Posted on 2025-11-26

730 Direct MRI of Collagen

Van Schoor, J. D.; Weiger, M.; Pruessmann, K. P.; Baadsvik, E. L.

10.1101/2025.11.24.690130 — bioengineering — Posted on 2025-11-26

731 Mapping galectin-3 ligands in tear fluid establishes spliceoform-dependent lacritin binding

Chang, V.; Lian, I.; Mahoney, K. E.; Romano, J.; Afshari, A. R.; Chen, R. J.; Chen, X.; Fineide, F.; Khan, A. Z.; Utheim, T. P.; Karlsson, N. G.; Laurie, G. W.; Malaker, S. A.

10.1101/2025.11.24.690288 — biochemistry — Posted on 2025-11-26

732 Neural encoding of innate preference to gravity-defying motion

Kobylkov, D.; Vallortigara, G.

10.1101/2025.11.24.690125 — animal behavior and cognition — Posted on 2025-11-26

733 CapuchinAI: Leveraging AI to study wild primate cognition

Sanchez Vargas, F.; Potluri, S. R.; Abernethy, J.; Benitez, M. E.

10.1101/2025.11.07.687266 — animal behavior and cognition — Posted on 2025-11-26

734 GM-CSF instructs vertebral emergency myelopoiesis in neuropathic pain

Cunha, T. M.

10.1101/2025.11.23.690022 — immunology — Posted on 2025-11-26

735 Absence of Local Retinotopy in the Mouse Optic Tract

Tripodi, M.; Asari, H.

10.1101/2025.11.23.690078 — neuroscience — Posted on 2025-11-26

736 Accurate evaluation of neural sensitivity to weak alternating electric fields requires protocols accounting for input dependence

Gaugain, G.; Modolo, J.; Nikolayev, D.

10.1101/2025.11.24.690108 — neuroscience — Posted on 2025-11-26

737 Intrabody-guided synapse proteomics defines pyramidal neuron input architecture and uncovers early remodeling in a mouse model of Alzheimer's disease

Dascenco, D.; Marcassa, G.; Mallopoulou, A.; Vandensteen, J.; Lefever, L.; Leysen, E.; Lorente-Echeverria, B.; Koumoundourou, A.; Daaboul, D.; Ghesquiere, B.; Magalhaes, P.; de Wit, J.

10.1101/2025.11.24.689247 — neuroscience — Posted on 2025-11-26

738 Coppice conversion of European beech (Fagus sylvatica L.): natural evolution, periodic thinning, regeneration cutting

Chianucci, F.; Bertini, G.; Tiberi, G.; Lazzerini, G.; Marchino, L.; Piovosi, M.; Cutini, A.

10.1101/2025.11.24.690100 — plant biology — Posted on 2025-11-26

739 High-Throughput Fragment Screening Identifies a New Small Molecule Scaffold that Modulates TREM2 Signaling

Fuchs, N.; El Gaamouch, F.; Nada, H.; Cho, S.; Gabr, M.

10.1101/2025.11.23.690065 — pharmacology and toxicology — Posted on 2025-11-26

740 Graded Notch Signaling Functions as a Rheostat of Lineage Plasticity and Therapy Resistance in Prostate Cancer

Jiang, Y.; Cheng, S.; Zhang, C. Y.; Jin, X.; Li, L.; Fraidenburg, M.; Wang, C.; Kim, I. Y.; Mu, P.

10.1101/2025.11.23.690056 — cancer biology — Posted on 2025-11-26

741 Optimized k-mer search across millions of bacterial genomes on laptops

Brunetti, F.; Brinda, K.

10.1101/2025.11.23.690050 — bioinformatics — Posted on 2025-11-26

742 Per-residue optimisation of protein structures:Rapid alternative to optimisation with constrainedalpha carbons

Schindler, O.; Bucekova, G.; Svoboda, T.; Svobodova, R.

10.1101/2025.11.24.690085 — bioinformatics — Posted on 2025-11-26

743 ExactCN: Predicting Exact Copy Numbers on Whole Exome Sequencing Data

FarhangKia, E.; Ceylan, A. A.; Gencturk, M.; Yilmaz, M. A.; Karademir, F.; Cicek, A. E.

10.1101/2025.11.24.690086 — bioinformatics — Posted on 2025-11-26

744 DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data

Li, R.; Yang, J.; Su, P.-C.; Jaffe, A.; Lindenbaum, O.; Kluger, Y.

10.1101/2025.11.23.689932 — bioinformatics — Posted on 2025-11-26

745 Glucocorticoid-induced proteome and phosphoproteome changes in breast cancer cell lines

Cho, H.; Olsen, J. V.

10.1101/2025.11.25.690354 — biochemistry — Posted on 2025-11-26

746 Structure-function studies on the serine protease domain of Factor VII activating protease (FSAP).

Kandanur, S. P. S.; Dalhus, B.; Emsley, J.; Kanse, S. M.

10.1101/2025.11.25.690424 — biochemistry — Posted on 2025-11-26

747 Integrative multi-omic analysis identifies key transcription factors and target proteins in renal cell carcinoma and its subtypes

Chhetri, S. B.; Winter, T. D.; Machiela, M. J.; Brown, K.; Battle, A.; Purdue, M. P.; Chanock, S. J.; Dutta, D.

10.1101/2025.11.23.690024 — genetics — Posted on 2025-11-26

748 Clonal Hematopoiesis Associated with TP53 Mutation Promotes Tissue Repair in Acute Cardiovascular Diseases

Pan, Y.; Meng, X.; Wang, C.; Zhou, W.; Zhou, Q.; Chi, J.; Barrier, B.; Martinez-Lemus, L.; Li, D.-P.; Liu, Z.; Kang, X.

10.1101/2025.11.23.690015 — cell biology — Posted on 2025-11-26

749 Internally twin-Strep tagged CD63 for rapid and efficient isolation of engineered extracellular vesicles encapsulating functional proteins

Pham, M. T.; Krohn, J. B.; Meyer, J.; Ritter, C.; Schneider, M.; Helm, D.; Frey, D.; Haselmann Weiss, U.; Leuschner, F.; Rohr, K.; Bartenschlager, R.

10.1101/2025.11.26.690653 — molecular biology — Posted on 2025-11-26

750 A dividing cell model for stable propagation and curing of bona fide human sporadic Creutzfeldt-Jakob Disease prions

Nihat, A.; Arora, P.; Schmidt, C.; Rayner, M.; Linehan, J.; Brandner, S.; Mead, S.; Collinge, J.; Jat, P.

10.1101/2025.11.23.690013 — neuroscience — Posted on 2025-11-26

751 Ventral Tegmental Area Glutamatergic Neurons Suppress Hippocampal Sharp-wave Ripples and Induce Head Movements in Mice

Subramaniyan, M.; Manivannan, S.; Zhou, M. S.; Dani, J. A.

10.1101/2025.11.23.690012 — neuroscience — Posted on 2025-11-26

752 Affiliative behavioural phenotype and microglial activation predict social decision-making following immune activation

Hammond, E.; MONARI, P.; Luebke, E.; Johnson, A.; Auger, A.; Marler, C.

10.1101/2025.11.23.690017 — neuroscience — Posted on 2025-11-26

753 A Mesoscale Framework for Psychedelic Drug Action in the Human Brain

Dai, R.; Cofre, R.; Timmermann, C.; Carhart-Harris, R. L.; Hudetz, A. G.; Huang, Z.; Mashour, G. A.

10.1101/2025.11.23.690016 — neuroscience — Posted on 2025-11-26

754 Pupil size reveals the perceptual quality and effortless nature of synesthesia

Strauch, C.; Leenaars, C.; Rouw, R.

10.1101/2025.11.24.690102 — neuroscience — Posted on 2025-11-26

755 Cytokinin-mediated trichome initiation in Nicotiana benthamiana upon Agrobacterium tumefaciens infiltration

Saebel, R.; Brand, A.; Balcke, G. U.; Syrowatka, F.; Horn, C.; Marillonnet, S.; Tissier, A. F.

10.1101/2025.11.23.690080 — plant biology — Posted on 2025-11-26

756 Association between KCNC1 gene polymorphism and blood lipid levels in determining the efficacy of high-intensity interval training

Lai, j.; gong, l.; liu, y.; li, y.; nie, j.; zhou, d.

10.1101/2025.11.23.690038 — physiology — Posted on 2025-11-26

757 Characterization of a water-soluble formulation of Passiflora incarnata and its effect on sperm motility: A novel male-centric contraceptive formulation

Chakraborty, S.; Singh, H. K.; Nagpal, K.; Saha, S.

10.1101/2025.11.23.687804 — physiology — Posted on 2025-11-26

758 Autoimmunity and H. pylori infection cooperatively promote epithelial tumorigenic differentiation and systemic immune modulation

Vazquez, E. N.; Lozano, C.; Honan, A. M.; Zaika, E.; Houghton, J.; El-Rifai, W.; Zaika, A.; Chen, Z.

10.1101/2025.11.23.690054 — cancer biology — Posted on 2025-11-26

759 Mechanistic insights into CFTR function from molecular dynamics analysis of electrostatic interactions

ELBAHNSI, A.; Mornon, J.-P.; Callebaut, I.

10.1101/2025.11.23.690003 — bioinformatics — Posted on 2025-11-26

760 Multi-tissue spatial transcriptomics reveals biological age hotspots in mouse and human aging

Vicente-Alvarez, V.; de Magalhaes, C. G.; Glubokov, D.; Moliere, A.; Tyshkovskiy, A.; Gladyshev, V.

10.1101/2025.11.23.689860 — bioinformatics — Posted on 2025-11-26

761 A Multi-Agent Approach to Generating Context-Rich Gene Sets

Makinde, E.; Maleki, F.; Ovens, K.

10.1101/2025.11.23.690073 — bioinformatics — Posted on 2025-11-26

762 Comparative Analysis of Pathology Foundation Models for Automated Detection of Tertiary Lymphoid Structures in H&E-Stained Digital Pathology Images

Guan, M.; Sun, Y.; Belete, M.; Muthuswamy, A.; Farma, M.; Kaufmann, J.; Lechpammer, M.; Sridhar, S.; Higgs, B.; Si, H.

10.1101/2025.11.23.688074 — bioinformatics — Posted on 2025-11-26

763 Mitochondrial Respiratory Chain Function is crucial for Muscle Toxicity in Facioscapulohumeral Muscular Dystrophy

Heher, P.; Pfeiffer-Vogl, J.; Ganassi, M.; Fulea, R.-C.; McGuire, L.; Engquist, E. N.; Tyszkiewicz, M.; Prueller, J.; Grillari, J.; Tasca, G.; Banerji, C. R.; Zammit, P. S.

10.1101/2025.11.25.690559 — biochemistry — Posted on 2025-11-26

764 G-Quadruplex and i-Motif Structures in the SHMT1 5UTR Modulate Gene Expression

Palumbo, R. M.; Kasaju, M.; Hershey, S. C.; McCann, M. E.; Woon, Z. H.; Heisler, D. B.; Mihailescu, M. R.

10.1101/2025.11.24.690261 — biochemistry — Posted on 2025-11-26

765 Charge segregation in the C-terminal linker of FtsZ enables Z-ring scaling with prokaryotic cell width

Kojic, M.; Megrian, D.; Loose, M.

10.1101/2025.11.25.690400 — biochemistry — Posted on 2025-11-26

766 How endosomal PIKfyve inhibition prevents viral membrane fusion and entry

Chow, N.; Saminathan, A.; Scanavachi, G.; Kirchhausen, T.

10.1101/2025.11.25.690586 — cell biology — Posted on 2025-11-26

767 EVtrace: tracing extracellular vesicles-associated proteins in recipient cells using stable isotope labeling

Kuipers, M. E.; Seras, J.; Damen, M.; Wubbolts, R.; Abasolo, I.; Stecker, K. E.; Nolte-'t Hoen, E. N. M.

10.1101/2025.11.23.690082 — molecular biology — Posted on 2025-11-26

768 eIF5A coordinates the transcription and translation of its target genes

Barba-Aliaga, M.; Chi, L.; Prieto-Diez, S.; Planells, J.; Garcia-Martinez, J.; Perez-Ortin, J. E.; Alepuz, P.

10.1101/2025.11.25.690413 — molecular biology — Posted on 2025-11-26

769 Probiotic lactic acid bacteria induce regulatory functions in γδ T cells

Saito, S.; Okuno, A.

10.1101/2025.11.21.689796 — immunology — Posted on 2025-11-26

770 TNF-α-Driven Systemic Inflammasome Hyperactivity Links Psoriatic Inflammation to monocyte inflammatory response and platelet activation

Verma, D.; Jeppsson, F.; Sjogren, F.; Andersson, B.; Eding, C. B.; Kasic, N.-K.; Moparthi, L.; Enerback, C.

10.1101/2025.11.24.690330 — immunology — Posted on 2025-11-26

771 Linking White-Matter Development to Clinical Variation in Autism: Longitudinal Normative Modelling of FA in the EU-AIMS LEAP Cohort

Cirstian, R.; Forde, N. J.; Buckova, B. R.; Dell'Acqua, F.; Charman, T.; Loth, E.; Oakley, B.; Molla, L. C.; Yorke, I.; Stones, R.; Banaschewski, T.; Murphy, D. G. M.; Buitelaar, J. K.; EU-AIMS LEAP Group, ; Beckmann, C. F.; Marquand, A. F.

10.1101/2025.11.25.690402 — neuroscience — Posted on 2025-11-26

772 Two views of the brain are reconciled by a unifying principle of maximal information processing

Fosque, L. J.; Shew, W.; Ching, S.; Hengen, K. B.

10.1101/2025.11.25.690580 — neuroscience — Posted on 2025-11-26

773 Subcortical control of reaching in humans

Contemori, S.; Loeb, G. E.; Corneil, B. D.; Wallis, G.; Carroll, T. J.

10.1101/2025.11.26.690644 — neuroscience — Posted on 2025-11-26

774 DECODING BRAIN DYNAMICS VIA CROSS-NETWORK NON-LINEAR TRAJECTORIES

Seraji, M.; Shultz, S.; Li, Q.; Ma, L.; Fu, Z.; Calhoun, V.

10.1101/2025.11.25.690593 — neuroscience — Posted on 2025-11-26

775 Interconnected axes of phenotypic plasticity drive coordinated cellular behaviour and worse clinical outcomes in breast cancer

Meena, R. K.; Fan, Y.; R, S.; Pandey, A. J.; Kannan, A.; Subramanian, Y.; Subramanian, Y.; George, J. T.; Jolly, M. K.

10.1101/2025.11.23.688595 — systems biology — Posted on 2025-11-26

776 Identification of a putative RBOHD-FERONIA-CRK10-PIP2;6 plasma membrane complex that interacts with phyB to regulate ROS production in Arabidopsis thaliana

Mohanty, D.; Fichman, Y.; Pelaez-Vico, M. A.; Myers, R. J.; Sealander, M.; Sinha, R.; Morrow, J.; Eckstein, R.; Olson, K.; Xu, C.; An, H.; Yoo, C. Y.; Zhu, J.-K.; Zhao, C.; Zandalinas, S. I.; Liscum, E.; Mittler, R.

10.1101/2025.11.23.689998 — plant biology — Posted on 2025-11-26

777 Oncogenic RAS activity is linked to immune priming and adenosine-driven immune evasion in lung adenocarcinoma

de Carne Trecesson, S.; East, P.; Pillsbury, C.; Silva dos Santos, M.; Cha, H.; Colliver, E.; Gilmore, T.; Rana, S.; Moore, C.; Lighterness, S.; Caswell, D. R.; Boumelha, J.; Tomaschko, M.; Baer, R.; Eyles, J.; Teixeira, B.; Saeed, M.; Litchfield, K.; Molina-Arcas, M.; Lee, S.-H.; MacRae, J.; Hobson, P.; Swanton, C.; Downward, J.

10.1101/2025.11.25.690426 — cancer biology — Posted on 2025-11-26

778 ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas

Denu, R. A.; Singh, A. K.; Jiang, Y.; Zheng, Z.; Ingram, D. R.; Wani, K. M.; Lazcano, R.; Ginn, M. P.; Anand, K.; Singh, B. K.; Ballard, J. C.; Kochat, V.; Chatterjee, B.; Padron, W.; Landers, S. M.; Bhalla, A.; Multani, A.; Dharmaiah, S.; Malgulwar, P. B.; Cai, Y.; Lin, H.; Huse, J. T.; Ying, H. T.; Keung, E. Z.; Wang, W.-L.; Conley, A. P.; Patel, S.; Somaiah, N.; Farooqi, A.; Lazar, A. J.; Nassif Haddad, E. F.; Torres, K. E.; Rai, K.

10.1101/2025.11.23.689992 — cancer biology — Posted on 2025-11-26

779 PULSAR: a Foundation Model for Multi-scale and Multicellular Biology

Pang, K.; Rosen, Y.; Kedzierska, K.; He, Z.; Rajagopal, A.; Gustafson, C. E.; Huynh, G.; Leskovec, J.

10.1101/2025.11.24.685470 — bioinformatics — Posted on 2025-11-26

780 ETSAM: Effectively Segmenting Cell Membranes in cryo-Electron Tomograms

Selvaraj, J.; Cheng, J.

10.1101/2025.11.23.689996 — bioinformatics — Posted on 2025-11-26

781 Conserved early steps of stemmadenine biosynthesis

Kamileen, M. O.; Nakamura, Y.; Sigmund, M.; Keshan, R.; Grabe, V.; Heinicke, S.; Kunert, M.; Hong, B.; Alam, R.; Kang, G.; Caputi, L.; O'Connor, S. E.

10.1101/2025.11.23.690000 — biochemistry — Posted on 2025-11-26

782 Deep-Pose-Tracker: a unified model for behavioural studies of Caenorhabditis elegans

Saha, D.; Chaudhary, S.; Vyas, D.; Ghosh-Roy, A.; Sharma, R.

10.1101/2025.11.23.689997 — animal behavior and cognition — Posted on 2025-11-26

783 Enterococcus faecalis alters antibiotic susceptibility in Pseudomonas aeruginosa mixed species biofilms.

Anderson, C.; Mattenberger, Y.; Parga Martinez, A.; Portalier, H.; Tan, C.; Esteban Henao, M.; Viollier, P. H.; Kline, K. A.

10.1101/2025.11.24.690246 — microbiology — Posted on 2025-11-26

784 The renin angiotensin system in cognitive flexibility: Effects of single-dose losartan on task-switching in healthy volunteers

Prasad, D.; Feltham, G.; De Giorgi, R.; Costi, S.; Fox, E.; Gillespie, A. L.; Reinecke, A.

10.1101/2025.11.23.689943 — neuroscience — Posted on 2025-11-26

785 Direct Training of Networks of Morris-Lecar Neurons withBackprop

Akbari, N.; Mason, K.; Gruber, A.; Nicola, W.

10.1101/2025.11.23.690009 — neuroscience — Posted on 2025-11-26

786 Defective insulin clearance plays a primary role in the pathogenesis of chronic kidney disease in mice with null deletion of Ceacam2 gene

Kumarasamy, S.; Belew, G.; Portuphy, A. O.; Abdolahipour, R.; Zaidi, S.; Yang, H.; Russo, L.; Ghanem, S. S.; Gohara, A. F.; Malgor, R.; Najjar, S. M.

10.1101/2025.11.23.690002 — physiology — Posted on 2025-11-26

787 What is the influence of knee joint movement on the maximal average mechanical power output of human quadriceps femoris muscle?

Reuvers, E. D. H. M.; van Soest, A. J. K.; Kistemaker, D. A.

10.1101/2025.11.23.689993 — physiology — Posted on 2025-11-26

788 SPARP-seq reveals poly(A) tail shortening as a hallmark of the active human translatome

Shu, Y.; Li, J.; Sun, Z.; Li, Y.; Lu, W.; Long, Y.; Chen, X.; Li, S.; Chen, W.; Zhai, J.

10.1101/2025.11.25.690357 — molecular biology — Posted on 2025-11-26

789 Engineering a Bright Near-Infrared Fluorescent Protein by Screening a Comprehensive Phenotypic Landscape

Kulhanek, D.; Wei, Q.; Head, J.; Hellinger, J.; Jansen, Z.; Gilmour, A.; Segall-Shapiro, T.; Brodbelt, J. S.; Usama, S. M.; Thyer, R.

10.1101/2025.11.25.690577 — synthetic biology — Posted on 2025-11-26

790 Signatures in CRISPR Mutational Spectra Reveal Role and Interplay of Genes in DNA Repair

Seale, C.; Barazas, M.; van Schendel, R.; Tijsterman, M.; Goncalves, J. P.

10.1101/2025.11.25.690381 — bioinformatics — Posted on 2025-11-26

791 Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast

Ackermann, L. M.; Ro, A.; Dunn, B.; Armstrong, J. O.; Dunham, M. J.

10.1101/2025.11.25.687580 — genetics — Posted on 2025-11-26

792 Life history and infection susceptibility parameters of Drosophila species reared on a common diet

Cole, M.; Sun, H.; Ragnoni, E.; Johnson, J.; Jarvis, A.; Hedelin, L.; Westlake, H. E.; Longdon, B.; Hanson, M. A.

10.1101/2025.11.25.690557 — evolutionary biology — Posted on 2025-11-26

793 Notebook-based alignment of human and agentic reasoning in single-cell biology

Fischer, D. S.

10.1101/2025.11.24.689256 — bioinformatics — Posted on 2025-11-26

794 Customizable FDM-based zebrafish embryo mold for live imaging

Rivera Pineda, M. X.; Lehtimäki, J.; Jacquemet, G.

10.1101/2025.11.24.689779 — cell biology — Posted on 2025-11-26

795 Infection Of Rhesus Macaques With Onyong-nyong Virus UVIR-O804 Recapitulates Key Aspects of Human Clinical Disease

Jaeger, H. K.; Denton, M.; Andoh, T. F.; Kreklywich, C. N.; Gao, L.; Pung, L. J.; Streblow, Z. J.; McMonigal, A.; Ray, K.; Graves, B.; Streblow, M. M.; Barber-Axthelm, A. M.; Zilverberg, G.; Terry, M.; Fei, S. S.; Hogan, G.; Schultz, D. C.; Cherry, S.; Axthelm, M. K.; Labriola, C. S.; Heise, M. T.; Streblow, D. N.

10.1101/2025.11.20.689439 — microbiology — Posted on 2025-11-26

796 Cumulative cgMLST provides increased discrimination of nested phylogenetic groups

Ovsepian, A.; Delgado-Blas, J.; Rethoret-Pasty, M.; Martin, M. J.; Lebreton, F.; Brisse, S.

10.1101/2025.11.25.689980 — microbiology — Posted on 2025-11-26

797 WITHDRAWN: Spatial Analysis of Placentae During Congenital Cytomegalovirus Infection Reveals Distinct Cellular Profiles in Immune Cells and Trophoblasts

Sintim-Aboagye, E.; Quach, H. Q.; Sherman, W.; Farnan, S.; Otrubova, K.; Verma, N.; Littlefield, D.; Punia, S.; Johnson, E.; Blackstad, M.; Schleiss, M.; Norgan, A.; Gray, C.; Enninga, E. A. L.; Chakraborty, R.

10.1101/2025.04.04.647170 — immunology — Posted on 2025-11-26

798 Calibration of MRI-based reference intervals to new samples

Chen, A. A.; Seidlitz, J.; Gardner, M.; Bethlehem, R. A. I.; Dorfschmidt, L.; Kafadar, E.; Lifespan Brain Chart Consortium, ; Benitez, A.; Jensen, J. H.; Vandekar, S.; Satterthwaite, T. D.; Alexander-Bloch, A. F.

10.1101/2025.11.25.690453 — neuroscience — Posted on 2025-11-26

799 Dietary inclusion of papaya seed powder significantly modulates reproductive function and growth dynamics in Nile tilapia cultured under controlled conditions.

Denagde, R. T.; Nuguse, M.

10.1101/2025.11.23.690043 — zoology — Posted on 2025-11-26

800 VSPGx: A High-Accuracy Pharmacogenomics Interpretation Software Solution with Automated CPIC Guideline Integration

Fortier, N.; Rudy, G.; Scherer, A.

10.1101/2025.11.24.690276 — bioinformatics — Posted on 2025-11-26

801 PathWeigh II: Graph Based Belief Propagation for Pathway Activity Analysis

Livne, D.

10.1101/2025.11.22.689915 — bioinformatics — Posted on 2025-11-26

802 β-Nicotinamide mononucleotide: a novel broad-spectrum CRISPR inhibitor

Wei, T.; Shen, W.; Li, W.; Song, Y.; Fa, Y.; An, J.; Sun, Y.; Li, H.

10.1101/2025.11.22.685598 — genetics — Posted on 2025-11-26

803 Evaluating Regulatory Module Function within Mitochondrial Pyruvate Dehydrogenase Complex

Keller, C.; Caseys, C.; Kliebenstein, D.

10.1101/2025.11.24.690278 — molecular biology — Posted on 2025-11-25

804 Endothelial-pericyte interactions activate insulin signaling and its implications for blood-brain barrier dysfunction in Alzheimers disease

Wang, Z.; Veerareddy, V.; Eberts, P. M.; Azarin, S. M.; Kandimalla, K. K.

10.1101/2025.11.24.690270 — molecular biology — Posted on 2025-11-25

805 A default-control network cortical gradient differentiates the imagination of social and solitary experiences

Anderson, A. J.; Turnbull, A. G.; Smallwood, J.; Lin, F. V.

10.1101/2025.11.25.690561 — neuroscience — Posted on 2025-11-25

806 Synaptic MEMOIR: mapping individual synapses of neurons with protein barcodes

Tischbirek, C. H.; Fang, L.; Chadly, D. M.; Lobbia, S.; Aguirre, J. D.; Takei, Y.; Chen, C.-H.; Sternberg, P. W.; Lois, C.; Elowitz, M. B.; Cai, L.

10.1101/2025.11.25.690442 — neuroscience — Posted on 2025-11-25

807 Understanding cortical computation through the lens of joint-embedding predictive architectures

Mohammadi, A. G.; Halvagal, M. S.; Zenke, F.

10.1101/2025.11.25.690220 — neuroscience — Posted on 2025-11-25

808 Modelling mental disorders in zebrafish. Neurexins severely modulate anxiety, social behaviours and aggression.

Nguyen, Q.; Guo, F.; Mowry, B.; Das, J.; Giacomotto, J.

10.1101/2025.11.24.690344 — neuroscience — Posted on 2025-11-25

809 Data-driven Cognitive Clusters in Persistent Developmental Dyslexia

Pinheiro-Chagas, P.; Kersey, M.; Bahar, N.; Inkelis, S.; Siebert, J. M.; Vonk, J. M. J.; Bogley, R.; Carpenter, E.; Martin-Moreno, D. V.; De Leon, J.; Tee, B. L.; Mandelli, M. L.; Pereira, C.; Miller, Z.; Gorno-Tempini, M. L.

10.1101/2025.11.24.690327 — neuroscience — Posted on 2025-11-25

810 Cognition Disconnected: The Influence of Domain-General Cognition (g) in Lesion-Deficit Mapping

Sozer, L.; Griffis, J.; Langbehn, K.; Bruss, J.; Olafson, E.; Manzel, K.; Corbetta, M.; Tranel, D.; Boes, A.; Bowren, M.

10.1101/2025.11.25.690275 — neuroscience — Posted on 2025-11-25

811 Melody: Decoding the Sequence Determinants of Locus-Specific DNA Methylation Across Human Tissues

Jin, J.; Wang, D.; Qiao, J.; Gao, W.; Liu, Y.; Chen, S.; Zou, Q.; Wu, S.; Su, R.; Wei, L.

10.1101/2025.11.23.689975 — bioinformatics — Posted on 2025-11-25

812 Transcriptome-wide profiling of alternative splicing regulators with CRISPore-seq

Müller, S.; Andrews, N.; Yan, R. E.; Sookdeo, A.; Burrell, W. H.; Dai, X.; Rughani, P.; Daniloski, Z.; Juul, S.; Sanjana, N. E.

10.1101/2025.11.25.690515 — genomics — Posted on 2025-11-25

813 Cell type-resolved long-read transcriptomics of the human cortex reveals pervasive alternative splicing and disease-relevant isoforms

Yang, A.; Rodriguez, M.; Kozlenkov, A.; Dracheva, S.; Humphrey, J.; Breen, M. S.

10.1101/2025.11.25.690524 — genomics — Posted on 2025-11-25

814 Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors

Wang, L.; Deng, Y.; Nielsen, R.

10.1101/2025.11.24.690249 — genetics — Posted on 2025-11-25

815 Neuroanatomical signatures of depression and anxiety in at-risk adolescents: A symptom-oriented perspective

Ding, Q.; Rakesh, D.; Peng, S.; Li, X.; Whittle, S.

10.1101/2025.11.23.689891 — neuroscience — Posted on 2025-11-25

816 Dysregulated lactate metabolism synergizes with ALS genetic risk factors to accelerate motor decline

Tendulkar, S.; Wu, T.; Strickland, A.; Hackett, A. R.; Sato-Yamada, Y.; Mao, X.; Sasaki, Y.; Milbrandt, J.; Bloom, J.; DiAntonio, A.

10.1101/2025.11.24.690227 — neuroscience — Posted on 2025-11-25

817 Sex-Specific Induction of H3K27me1 in the Prefrontal Cortex Mediates the Enduring Effects of Early Life Stress

Nguyen, J.; Byragoni, N.; Arinzeh, N.; Bortolami, A.; Sidoli, S.; Russo, S. J.; Nestler, E. J.; Torres-Berrio, A.

10.1101/2025.11.25.690167 — neuroscience — Posted on 2025-11-25

818 Synthesizing images to map neural networks to the human brain

Peng, K.; Norman, K. A.; Turk-Browne, N. B.; Wammes, J. D.

10.1101/2025.11.25.689428 — neuroscience — Posted on 2025-11-25

819 Memory traces bias new learning for hippocampal generalization

Qian, F. K.; Li, G.; Lipshutz, D.; Romani, S.; Magee, J. C.

10.1101/2025.11.24.690297 — neuroscience — Posted on 2025-11-25

820 Mapping the Developmental Trajectory of Functional Brain Networks in Early Infancy: Insights into Typical Maturation

Seraji, M.; Shultz, S.; Li, Q.; Fu, Z.; Iraji, A.; Calhoun, V.

10.1101/2025.11.25.690500 — neuroscience — Posted on 2025-11-25

821 Altered striatal dopamine dynamics and behavior in Grin2a mutant mice, a genetic mouse model of schizophrenia

Hall, A.; Jacoby, J.; Gangal, H.; Rochman, E.; Shephard, N.; Song, B.; Farsi, Z.; Datta, S. R.; Sheng, M.; Kunwar, P. S.

10.1101/2025.11.24.690326 — neuroscience — Posted on 2025-11-25

822 SPATIAL DISSIMILARITY TRAJECTORIES REVEAL RAPID FUNCTIONAL NETWORK REFINEMENT DURING EARLY INFANCY

Seraji, M.; Shultz, S.; Wiafe, S.-L.; Fu, Z.; Calhoun, V.

10.1101/2025.11.25.690597 — neuroscience — Posted on 2025-11-25

823 Sexual selection and flight as predictors of sexual size and shape dimorphism in stick and leaf insects

Boisseau, R. P.; Bradler, S.; Emlen, D. J.

10.1101/2025.11.25.690473 — evolutionary biology — Posted on 2025-11-25

824 A major selective sweep likely linked to insecticide resistance identified along altitudinal gradients in the pine processionary moth

Nouhaud, P.; Gautier, M.; Schifano, A.; Saune, L.; Kerdelhue, C.; Perrier, C.

10.1101/2025.11.24.690095 — evolutionary biology — Posted on 2025-11-25

825 The origins and adaptive consequences of polyploidy in a dominant prairie grass

Phillips, A. R.; AuBuchon-Elder, T.; Barry, K. W.; Stitzer, M. C.; Buckler, E. S.; Bukowski, R.; Cameron, B.; Cryan, E.; Forrestel, E.; Grabowski, P. P.; Grimwood, J.; Jenkins, J. W.; Shu, S.; Lipzen, A.; Lovell, J. T.; Minx, P.; Porter, J.; Runcie, D. E.; Schmutz, J.; Solomon, B.; Stephens, J.; Sun, Q.; Williams, M.; Yoshinaga, Y.; Flint-Garcia, S.; Romay, C.; Kellogg, E. A.; Ross-Ibarra, J.

10.1101/2025.11.25.690567 — plant biology — Posted on 2025-11-25

826 Genetic and environmental interactions outweigh mitonuclear coevolution for complex traits in Drosophila

Darwin, L. J.; Lemieux, F. A.; Bachtel, R. Z.; Blocker, J. H.; Brown, C. P.; Lerman, J. D.; Maule, O. C.; Raynes, Y.; Rand, D. M.

10.1101/2025.11.24.689096 — evolutionary biology — Posted on 2025-11-25

827 Historic Overexploitation, Genetic Erosion and Local extinction: Palaeogenomic Insights into the Decline of Eubalaena glacialis in the Northeast Atlantic

Themudo, G.; de la Iglesia, A. R.; dos Santos, I. M.; Netels, R. L. S. T.; Lopez, A.; Martinez-Cedeira, J.; da Fonseca, R. R.; Campos, P. F.

10.1101/2025.11.24.690181 — evolutionary biology — Posted on 2025-11-25

828 Genomic signature of repeated transitions to diurnality in spiders

Tong, C.; Fan, Z.; Wang, L.; Zhang, Z.

10.1101/2025.11.23.690066 — evolutionary biology — Posted on 2025-11-25

829 Risk to European birds from collisions with wind-energy facilities

Etard, A.; Jung, M.; Visconti, P.

10.1101/2025.11.24.685024 — ecology — Posted on 2025-11-25

830 Periodical cicadas suffer legacy effects of century-old forest removal

Chan, I.; Brown, G. E.; Castaneda-Santiago, F.; Chitty, J. S.; Elliott, T. A.; Gose, M. J.; Hanfland, C. M.; Hendrix, S. D.; Leerhoff, C. R.; Meerdink, S. K.; Skibbe, A. M.; Steffensen, M. J.; Weinrich, C. L.; Forbes, A. A.

10.1101/2025.11.24.690214 — ecology — Posted on 2025-11-25

831 Mechanisms behind facilitation-competition transition along rainfall gradients

Hollander, O.; Mau, Y.; DeMalach, N.

10.1101/2025.11.24.690218 — ecology — Posted on 2025-11-25

832 Notch and Wnt signalling interact for proper prosensory and non-sensory domain formation

Ray, N.; Lingamallu, S. M.; Guha, A.; Ladher, R. K.

10.1101/2025.11.24.690138 — developmental biology — Posted on 2025-11-25

833 The effects of rapid mitochondrial gene loss on organellar proteomes

Warren, J. M.; Broz, A. K.; Stikeleather, R.; Sloan, D. B.

10.1101/2025.11.24.690252 — molecular biology — Posted on 2025-11-25

834 Stage-specific screening reveals complex resilience pathways to cold stress in rice

Akter, F.; BISWAS, P. S.; Islam, A. A.; Raihan, M. S.; Rahman, M. M.; Iftekharuddaula, K. M.; Islam, M. R.; Platten, J. D.

10.1101/2025.11.23.690040 — plant biology — Posted on 2025-11-25

835 Tug-of-war between cortical and cytoplasmic forces shaping planar of 4-cell stage embryos

Caballero Mancebo, S.; Gonzalez Suarez, D.; Chenevert, J.; Ben-Aicha, S.; Besnardeau, L.; McDougall, A.; dumollard, r.

10.1101/2025.11.24.690087 — developmental biology — Posted on 2025-11-25

836 Shotgun sequencing data and SSR mining data of aibika (Abelmoschus manihot, Malvaceae)

Rivallan, R.; Garavito, A.; Lawac, F.; Robert, N.; Paofa, J.; Labouisse, J.-P.

10.1101/2025.11.23.689977 — molecular biology — Posted on 2025-11-25

837 Mapping Protein Occupancy on DNA with an Unnatural Cytosine Modification in Bio-orthogonal Contexts

Zhu, R.; Loo, C. E.; Hurley, C. M.; Parker, J. B.; Kohli, R. M.

10.1101/2025.11.24.690163 — biochemistry — Posted on 2025-11-25

838 Evidence of sheeppox in 17th-19th century France: a multi-disciplinary investigation of a sheep mass mortality assemblage

Binois Roman, A.; LHote, L.; Ferguson, R.; Daly, K. G.

10.1101/2025.11.24.690131 — genetics — Posted on 2025-11-25

839 Broad Effects of Activation of Alcohol Dehydrogenase 1 on Healthspan Extension

Sukienik, A.; Bernahu, S.; Ghaddar, A.; MacPhail, E.; O'Rourke, E.

10.1101/2025.11.23.687054 — cell biology — Posted on 2025-11-25

840 Mechanistic Investigation of LncRNA-ZMIZ1-AS1 in the Malignant Phenotype of Hepatocellular Carcinoma

Chen, G.; Tang, H.; Mao, C.; Wu, G.

10.1101/2025.11.23.690041 — molecular biology — Posted on 2025-11-25

841 4-HNE reduces phagocytosis through the expression of Synaptotagmin 1 in human monocyte-derived macrophages

Ioannidis, M.; den Ouden, M.; Dijt, S. J.; Incarnato, D.; Grijpstra, P.; Wortel, J.; Verhage, M.; Maassen, S.; van den Bogaart, G.

10.1101/2025.11.24.690103 — molecular biology — Posted on 2025-11-25

842 GC3 codons enhance protein production in diverse GC- and AT-rich plant species

Kaufman, I. D.; Wu, H.-Y. L.; Hsu, P. Y.

10.1101/2025.11.25.690434 — molecular biology — Posted on 2025-11-25

843 In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles

Seraj, Z.; Zottig, X.; Huang, C.; Loveland, A. B.; Diggs, S.; Sholi, E.; Grigorieff, N.; Korostelev, A. A.

10.1101/2025.11.25.690450 — molecular biology — Posted on 2025-11-25

844 Reductive death is averted by an ancient metabolic switch.

Ahsan, F. M.; Rotti, J. F.; Yerevanian, A. I.; Emans, S. W.; Stuhr, N. L.; Aceves-Salvador, J. A.; Wang, W.; Baker, D. J.; Pouli, D.; Skinner, O. S.; Blower, M. D.; Soukas, A. A.

10.1101/2025.11.24.690166 — molecular biology — Posted on 2025-11-25

845 Tracking HIV-1 DNA fate from Cell Culture to Humanized mice Tissues.

Diana, J.-S.; Tatirovsky, E.; Tomasini, C.; Cuche, C.; Ay, S.; Scoca, V.; Cavazzana, M.; Di Santo, J. P.; Di Nunzio, F.

10.1101/2025.11.25.690387 — microbiology — Posted on 2025-11-25

846 Four Decades of Genomic Stability and Adaptive Divergence in Xanthomonas arboricola pv. pruni-Infecting Phages: Defining Duraznoxanthovirus arenicola and Its Evolutionary Framework

D'Amico-Willman, K. M.; Joglekar, P.; Turner, D.; Flaherty, M.; Ritchie, D. F.; Huerta, A. I.

10.1101/2025.11.25.690537 — microbiology — Posted on 2025-11-25

847 Proteus mirabilis entails a switch from commensal to pathogen - Genomic insights from a blaTEM-1B-harboring novel isolate from India.

Acharya, S.; Kushwaha, P.; Desai, S.; Biswas, S.; Longjam, L. A.; Chatterjee, B.; Ruwali, M.; De, S.; Krishnaswamy, L.; Suravajhala, P.; Chaubey, G.

10.1101/2025.11.25.690331 — microbiology — Posted on 2025-11-25

848 Somatic mutations impose an entropic upper bound on human lifespan

Efimov, E.; Fedotov, V.; Malaev, L.; Khrameeva, E. E.; Kriukov, D.

10.1101/2025.11.23.689982 — systems biology — Posted on 2025-11-25

849 Transcriptome and hormone regulations shape drought stress-dependent Fusarium Head Blight susceptibility in different barley genotypes

Hoheneder, F.; Steidele, C. E.; Gigl, M.; Dawid, C.; Hueckelhoven, R.

10.1101/2025.11.23.689882 — plant biology — Posted on 2025-11-25

850 Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

Jung, H.; Lee, Y.; Yu, D.; Jeon, Y.; Kang, H.; Um, D.; Seo, M.; Park, D.; Kim, J.; Lee, S.-J.; Kim, J.; Escobedo, L.; Sun, Y.; Thomas, A.; Nam, K.; Kim, T.-K.

10.1101/2025.11.23.690049 — cancer biology — Posted on 2025-11-25

851 An Integrated Biophysical Fragment Screening Approach Identifies Novel Binders of the CD28 Immune Receptor

Calvo-Barreiro, L.; Nada, H.; Gabr, M.

10.1101/2025.11.23.690058 — biophysics — Posted on 2025-11-25

852 LoL-align: sensitive and fast probabilistic protein structure alignment

Reifenrath, L.; van Kempen, M.; Kim, G.; Kim, S. H.; Radnezhad, M.; Mirdita, M.; Steinegger, M.; Söding, J.

10.1101/2025.11.24.690091 — bioinformatics — Posted on 2025-11-25

853 Cas9-enriched nanopore sequencing enables comprehensive and multiplexed detection of repeat expansions

Lee, S.; Jung, C.; Kim, M.; Kim, N.; Hwang, G.-H.; Lee, S.-T.; Chu, K.; Lee, S. K.; Kim, H.-J.; Chae, J.-H.; Bae, S.; Moon, J.

10.1101/2025.11.24.690106 — bioengineering — Posted on 2025-11-25

854 AlphaFlex: Ensembles of the human proteome representing disordered regions

Liu, Z. H.; Zhang, O.; De Castro, S.; Sun, K.; Ghafouri, H.; Attafi, O. A.; Fawzi, N. L.; Tosatto, S. C. E.; Monzon, A. M.; Moses, A. M.; Head-Gordon, T.; Forman-Kay, J. D.

10.1101/2025.11.24.690279 — biochemistry — Posted on 2025-11-25

855 A Charge-reversal Point Mutation Completely Depletes Flavin Chromophore from European Robin Cryptochrome 4a Protein

Xu, J.; Rasmussen, E. S.; Berthias, F.; Schmidt, J.; Mouritsen, H.; Jensen, O. N.; Solovyov, I. A.

10.1101/2025.11.24.690116 — biochemistry — Posted on 2025-11-25

856 Anion supercharging enables structural assignment of oxidatively released O-glycans

Kelly, M. I.; Ashwood, C.

10.1101/2025.11.23.689986 — biochemistry — Posted on 2025-11-25

857 Transgenerational plasticity affects fitness and mediates local adaptation

Branch, H. A.; Moxley, D. R.; Angert, A. L.

10.1101/2025.11.23.690023 — evolutionary biology — Posted on 2025-11-25

858 The five divergent amino acids rule and evolution analysis of cytochrome c oxidase as new methods for Scolopendra Linnaeus, 1758 species differentiation (Chilopoda. Scolopendromorpha).

Domenech Perez, C.; Barber, V. M.; Larriba, E.

10.1101/2025.11.24.690109 — evolutionary biology — Posted on 2025-11-25

859 Identification of Entomopathogenic Nematode isolates from Nigeria and their pathogenicity against the invasive fall armyworm, Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae)

Okolo, C. T.; Claudius-Cole, A.; Grundler, F.; Borgemeister, C.

10.1101/2025.11.23.689995 — ecology — Posted on 2025-11-25

860 Genome organizer SATB1 restrains the BACH1-cMAF axis that drives autoimmunity

Papamatheakis, D. A.; Tzerpos, P.; Tsoukatou, D.; Morres, E.; Kapsetaki, M.; Balazs, D.; Igarashi, K.; Spilianakis, C.

10.1101/2025.11.25.690242 — molecular biology — Posted on 2025-11-25

861 Transcript-wide m6A methylation defines the efficiency of the cap-independent translation initiation

Smolin, E. A.; Buyan, A. I.; Buzdin, A. A.; Lyabin, D. N.; Kulakovskiy, I. V.; Eliseeva, I. A.

10.1101/2025.11.25.690160 — molecular biology — Posted on 2025-11-25

862 RAPMS 2.0 Improves Specificity and Throughput for Proteomic Identification of RNA Binding Proteins

Honson, D.; Deng, W.; Blanco, M.; Sha, J.; Plath, K.; Wohlschlegl, J. A.; Guttman, M.; Majumdar, D.

10.1101/2025.11.23.690051 — molecular biology — Posted on 2025-11-25

863 EXPRESSION OF CONJUGATION GENES IS CONTROLLED BY PROCESSIVE ANTITERMINATION AND A NOVEL ZIPPER-TYPE TRANSCRIPTIONAL ATTENUATION MECHANISM

Gonzalez-Alvarez, D.; Miguel-Arribas, A.; Ranaweera, S.; Freire-Gomez, F.; Abia, D.; de Jong, A.; Wu, L. J.; Babitzke, P.; Meijer, W. J. J.

10.1101/2025.11.24.689506 — molecular biology — Posted on 2025-11-25

864 Assessment of the Genetic Architecture at Early-Stage Drought Tolerance in Wheat Using UAV-Based Multispectral Imaging

Ullah, M. A.; Muqaddas, F.; Naeem, M. K.; ur Rehman, A.; Tabassum, J.; Rehman, S. U.; Sajjad, M.; Mahmood, Z.; Javed, M. A.; Khan, M. R.; Chen, J.

10.1101/2025.11.23.689999 — molecular biology — Posted on 2025-11-25

865 Structure of the Hibernating Francisella tularensis Ribosome and Mechanistic Insights into Its Inhibition by Antibiotics

Klima, M.; Silhan, J.; Pavlik, P.; Hercik, K.; Boura, E.

10.1101/2025.11.25.690415 — microbiology — Posted on 2025-11-25

866 Zoliflodacin and gepotidacin cross-resistance in Neisseria gonorrhoeae

Mukherjee, A.; Blomqvist, S. O.; Helekal, D.; Das, A. A.; Palace, S. G.; Grad, Y. H.

10.1101/2025.11.25.690462 — microbiology — Posted on 2025-11-25

867 Oligotrophy and organic carbon dissipation as trophic strategy in chernozem rare and uncultured taxa

Demin, K. A.; Sedova, V. V.; Krylov, K. I.; Mirko, P. A.; Kocharovskaya, Y. N.; Minkina, T. M.; Prazdnova, E. V.

10.1101/2025.11.25.690425 — microbiology — Posted on 2025-11-25

868 Rapid quantification of short-chain fatty acids by Fourier-transform infrared spectroscopy for microbiota quality assessment

Sayol-Altarriba, A.; Aira, A.; Martin-Lopez, E.; Villasante, A.; Albarracin, R.; Faneca, J.; Pitart, C.; Roca, I.; Casals, G.; Marco, S.; Villanueva-Canas, J. L.; Casals-Pascual, C.

10.1101/2025.11.25.690441 — microbiology — Posted on 2025-11-25

869 Biological insights and methodological challenges learned from working with a diverse heterotrophic marine bacterial library

Valiya Kalladi, W. B.; Osborne, M.; Scott, H.; Kratzl, F.; Martinez Gutierrez, C. A.; Forchielli, E. J.; Gurevich, N.; Velasquez-Reyes, J. M.; Sampat, K.; Zoccaratto, L.; Herbst, K.; Weissberg, O.; Grossart, H.-P.; Segre, D.; Sher, D. J.

10.1101/2025.11.25.689180 — microbiology — Posted on 2025-11-25

870 The small protein SbtC is a functional component of the CO2 concentrating mechanism of cyanobacteria

Walke, P.; Poppitz, C.; Menz, N.; Hess, W. R.; Burnap, R.; Hagemann, M.; Klaehn, S.

10.1101/2025.11.25.690420 — microbiology — Posted on 2025-11-25

871 MODY mutations in transcription factors HNF1A and HNF1B affect the production of interferon signaling proteins: evidence at the proteome level

Kuznetsova, K. G.; Vasicek, J.; Skiadopoulou, D.; Unger, L.; Nethala, R. A.; Wierer, M.; Ghila, L.; Johansson, S.; Njoelstad, P. R.; Chera, S.; Johansson, B. B.; Manning, A.; Vaudel, M.

10.1101/2025.11.24.690114 — systems biology — Posted on 2025-11-25

872 Synthetic niches enable co-culture bioprocessing but are prone to mutational escape

Vandenbroucke, V.; Martinez, J. A.; Henrion, L.; Zicler, A.; Telek, S.; Josselin, L.; Frank, D.

10.1101/2025.11.24.690348 — synthetic biology — Posted on 2025-11-25

873 The plant longevity gene AHL15 delays leaf senescence by repressing ORESARA1 and cytokinin degradation

Luden, T.; Amakorova, P.; Novak, O.; Balazadeh, S.; Offringa, R.

10.1101/2025.11.23.689984 — plant biology — Posted on 2025-11-25

874 Structure-Based Optimization of Pathogen Signal Sequences for Enhanced Antigen Expression in Humans for Vaccine Designs

Do, H. N.; Shanker, A.; Kidner, R. Q.; Montoya, M. M.; Kubicek-Sutherland, J. Z.; Gnanakaran, S.

10.1101/2025.11.25.690495 — biophysics — Posted on 2025-11-25

875 Structural basis of stereochemical promiscuity by an umami taste receptor ortholog, Tas1r1/Tas1r3 from pufferfish

Mizoguchi, R.; Toda, Y.; Nagae, M.; Yoshida, T.; Matsuura, H.; Hirata, K.; Miyanoiri, Y.; Hosotani, M.; Ashikawa, Y.; Ito, C.; Tsutsumi, N.; Yasui, N.; Ishimaru, Y.; Yamashita, A.

10.1101/2025.11.24.689453 — biochemistry — Posted on 2025-11-25

876 Kruppel-like factor 1 acts upstream of the SKN-1/Nrf transcription factors to modulate oxidative stress, lipid homeostasis and longevity

Castillo-Quan, J. I.; McCarty, A.; Kurdeikaite, U.; Gilmore, K.; Cabral, A.; Mejia, J.; Barrett, J.; La Terza, M.; Johnson, E.; Carroll, A.; Schaffer, J.; Moroz, N.

10.1101/2025.11.22.689963 — cell biology — Posted on 2025-11-25

877 Mechanics-dependent Global Nuclear Eviction and Site-Specific Recruitment of YAP Regulates DNA Damage Responses

Yagnik, S.; Mazumder, A.

10.1101/2025.11.23.690063 — cell biology — Posted on 2025-11-25

878 Physiological Significance of Bacterial Mn(II) Oxidation

Lin, H.; Bai, Y.

10.1101/2025.11.24.690301 — microbiology — Posted on 2025-11-25

879 Repurposing ethacridine as a potent MMPL3 Inhibitor for the treatment of tuberculosis

Kalia, N. P.; Agnivesh, P. K.; Roy, A.; Sau, S.; Meshram, S.; Dalal, A.; Sharma, A.

10.1101/2025.11.25.690360 — microbiology — Posted on 2025-11-25

880 Large differences in photorespiration and its temperature response among temperate trees

Tiwari, R.; David, P.; Muscarella, R.

10.1101/2025.11.22.689893 — plant biology — Posted on 2025-11-25

881 Oxymatrine Induces Ferroptosis in MKN28 Gastric Cancer Cells

Ma, L.; Mian, R.

10.1101/2025.11.22.689973 — cancer biology — Posted on 2025-11-25

882 WormSpot: a machine learning-powered viability scoring platform in C. elegans for Candida pathogenicity studies

Lee, J. G. W.; Ong, V. E. Y.; Zhang, D.

10.1101/2025.11.22.689965 — bioinformatics — Posted on 2025-11-25

883 Coral restoration is only practical when local human pressure levels are low

Brookson, C. B.; Greiner, A.

10.1101/2024.11.26.622858 — ecology — Posted on 2025-11-25

884 Transcriptomic insights into the tripartite plant-pathogen-mycoparasite interaction reveal novel mechanisms involving fungal secretomes and plant amino acid metabolism

Maeda, K.; Kouda, M.; Ohara, M.; Kawase, T.; Saito, K.; Iwao, E.; Sushida, H.; Suzuki, T.; Sumita, T.; Iida, Y.

10.1101/2025.11.24.690098 — microbiology — Posted on 2025-11-25

885 From rest to focus: Pharmacological modulation of the relationship between resting state dynamics and task-based brain activation

Biernacki, K.; Zhai, T.; Hill, J.; McConnell, E.; Salmeron, B.-J.; Kaiser, R.; Janes, A. C.

10.1101/2025.09.30.679567 — neuroscience — Posted on 2025-11-25

886 Neurodegeneration in the olfactory system in Niemann Pick type C1 disease

Fioriello, M. G.; Lobraico, D.; Gatta, R. P.; Lobasso, S.; Reisert, J.; Frigeri, A.; Dibattista, M.

10.1101/2025.11.22.689959 — neuroscience — Posted on 2025-11-25

887 Gene syntax defines supercoiling-mediated transcriptional feedback

Johnstone, C. P.; Love, K. S.; Kabaria, S. R.; Jones, R. D.; Blanch-Asensio, A.; Ploessl, D. S.; Peterman, E. L.; Lee, R.; Yun, J.; Oakes, C. G.; Mummery, C. L.; Davis, R. P.; DeKosky, B. J.; Zandstra, P. W.; Galloway, K. E.

10.1101/2025.01.19.633652 — synthetic biology — Posted on 2025-11-25

888 Flavoaffinins, elusive cellulose-binding natural products from an anaerobic bacterium

Kountz, D. J.; Yu, R.; Lee, J. H.; Maloney, K. N.; Balskus, E. P.

10.1101/2025.02.08.637243 — biochemistry — Posted on 2025-11-25

889 Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation

Horz, J. M.; Wolff, K.; Friedhoff, R.; Pucker, B.

10.1101/2024.02.14.580303 — genomics — Posted on 2025-11-25

890 High rate of mutation and efficient removal by selection of structural variants from natural populations of Caenorhabditis elegans

Saxena, A. S.; Baer, C. F.

10.1101/2025.03.22.644739 — genetics — Posted on 2025-11-25

891 No evidence for disassortative mating based on HLA in a small-scale, endogamous population

Meeks, G. L.; Scelza, B.; Kichula, K. M.; Berevoescu, C.; Hardy, K.; Farias, T. D.; Harrison, G. F.; Pollock, N. R.; Font-Porterias, N.; Prall, S.; Norman, P. J.; Henn, B. M.

10.1101/2025.05.06.652536 — evolutionary biology — Posted on 2025-11-25

892 Wetland soil history shapes microbial community composition, while hydrologic disturbance alters greenhouse gas fluxes

Bledsoe, R. B.; Finlay, C.; Peralta, A. L.

10.1101/2020.06.29.178533 — ecology — Posted on 2025-11-25

893 Aberrant cohesin function in Saccharomyces cerevisiae activates Mcd1 degradation to promote cell lethality

Singh, G.; Skibbens, R. V.

10.1101/2025.09.17.676868 — cell biology — Posted on 2025-11-25

894 Epimutations driven by RNAi or heterochromatin evoke transient antimicrobial drug resistance in fungi

Son, Y.-E.; Perez-Arques, C.; Heitman, J.

10.1101/2025.06.17.660219 — microbiology — Posted on 2025-11-25

895 Characterization of a hypersporulating strain derivative of Clostridioides difficile R20291

Cid-Rojas, F.; Paredes-Sabja, D.

10.1101/2025.11.25.690273 — microbiology — Posted on 2025-11-25

896 The Phosphate-Specific Transport System Gene pstA1 Contributes to Rifampin Tolerance in Mycobacterium tuberculosis

Danchik, C.; Chinmayi, G. V. A.; Lee, G. Y.; Bader, J. S.; Eoh, H.; Karakousis, P. C.

10.1101/2025.10.31.685634 — microbiology — Posted on 2025-11-25

897 Pandemic Response Box Screening Identified CRM1/XPO1 as an Anti-Mammarenavirus Druggable Target

Ofodile, C. A.; Cubitt, B.; Onyemelukwe, N.; Okwuanaso, C. B.; Witwit, H.; de la Torre, J. C.

10.1101/2025.11.24.690217 — microbiology — Posted on 2025-11-25

898 4-Hydroxynonenal suppresses IL-10 production during infection

Ioannidis, M.; Maassen, S.; Boekhoud, L.; den Ouden, M.; Simioniuc, M.; Grijpstra, P.; Incarnato, D.; Bianchi, F.; Bouma, H.; van den Bogaart, G.

10.1101/2025.11.24.690094 — immunology — Posted on 2025-11-25

899 Protein kinase CK2 alpha prime as a dual modulator of neuroimmune signaling and synaptic dysfunction in Tauopathy

White, A.; Gavrilyuk, P.; Gu, P.; Falcon Moya, R.; Thurston, R.; Fickak, A.; Rozema, N. B.; Keshavaram, P.; Vermilyea, S.; Schlichte, R.; Meints, J.; Zhang, Y.; Araque, A.; Lee, M. K.; Gomez-Pastor, R.

10.1101/2025.06.24.661391 — neuroscience — Posted on 2025-11-25

900 Old-New Recognition Memory Revisited

Wei, X.; Buckner, R. L.

10.1101/2025.11.11.687844 — neuroscience — Posted on 2025-11-25

901 ACMTF-R: supervised multi-omics data integration uncovering shared and distinct outcome-associated variation

van der Ploeg, G. R.; White, F.; Jakobsen, R. R.; Westerhuis, J.; Heintz-Buschart, A.; Smilde, A.

10.1101/2025.07.28.667162 — systems biology — Posted on 2025-11-25

902 A deep-time landscape of plant cis-regulatory sequence evolution

Amundson, K. R.; Hendelman, A.; Ciren, D.; Yang, H.; de Neve, A. E.; Tal, S.; Sulema, A.; Jackson, D.; Barlett, M. E.; Lippman, Z. B.; Efroni, I.

10.1101/2025.09.17.676453 — plant biology — Posted on 2025-11-25

903 Parkin overexpression attenuates muscle atrophy and improves mitochondrial bioenergetics but fails to improve key histological features in a mouse model of Duchenne Muscular Dystrophy

Reynaud, O.; Ayoub, M.-B.; Leduc-Gaudet, J.-P.; Cefis, M.; Lussier, M.; Hussain, S. N.; Gouspillou, G.

10.1101/2025.06.13.659533 — physiology — Posted on 2025-11-25

904 Glycolysis-stratified coordination of fatty acid and glutamine metabolism in pancreatic ductal adenocarcinoma

Fareed, S.

10.1101/2025.09.14.676164 — cancer biology — Posted on 2025-11-25

905 Easydecon: Efficient Cell Type Mapping and Deconvolution for High-Definition Spatial Transcriptomic Data

Umu, S. U.; Karlsen, V. T.; Baekkevold, E. S.; Jahnsen, F. L.; Domanska, D.

10.1101/2025.04.08.647764 — bioinformatics — Posted on 2025-11-25

906 Systematic discovery of single-cell protein networks in cancer with Shusi

Zhang, T.; Yu, J.; Lou, S.; Liang, Z.; Liang, Y.; Li, Z.; Wang, H.; Pei, S.; Shen, N.

10.1101/2025.04.27.649905 — bioinformatics — Posted on 2025-11-25

907 Rehabilitating the benefits of gene tree correction in the presence of incomplete lineage sorting

Lafond, M.; Scornavacca, C.

10.1101/2025.07.09.663893 — bioinformatics — Posted on 2025-11-25

908 A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome

Kim, A.-R.; Huang, K.; Johnson, J. L.; Yaron-Barir, T. M.; Wang, K.; Cantley, L. C.; Hu, Y.; Perrimon, N.

10.1101/2025.10.10.681672 — bioinformatics — Posted on 2025-11-25

909 Conkazal-M1 from the MKAVA family of conotoxins - a dual-function protease inhibitor and neuroactive peptide

Hackney, C. M.; Koch, T. L.; Ryding, N. L.; Rogalski, A.; Chase, K.; Giglio, M. L.; Espino, S. S.; Acyatan, Z. G.; Watkins, M.; Olivera, B. M.; Safavi-Hemami, H.; Teilum, K.; Ellgaard, L.

10.1101/2025.11.05.686841 — biochemistry — Posted on 2025-11-25

910 Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency

Nocente, M. C.; Della Rosa, M.; Malcolm, A. A.; Lister, G.; Savin, I.; Ray-Jones, H.; Elderkin, S.; Tian, R.; Andrews, S.; Bendall, A.; Semprich, C. I.; Kampmann, M.; Malysheva, V.; Rostovskaya, M.; Rugg-Gunn, P.; Spivakov, M.

10.1101/2025.10.02.679816 — genomics — Posted on 2025-11-25

911 Identity-by-descent captures Shared Environmental Factors at Biobank Scale

Marsico, F.; Buonaiuto, S.; Amos-Abanyie, E.; Chinthala, L.; Mohammed, A.; Zahr, R.; Regeneron Genetics Center, ; Rooney, R.; Williams, R. W.; Davis, R. L.; Finkel, T. H.; Brown, C. W.; Vacca, M.; Prins, P.; Colonna, V.

10.1101/2025.05.03.652048 — genomics — Posted on 2025-11-25

912 Predictive power of different Akkermansia phylogroups in clinical response to PD-1 blockade against non-small cell lung cancer

Fan, P.; Ni, M.; Fan, Y.; Ksiezarek, M.; Fang, G.

10.1101/2024.08.21.608814 — genomics — Posted on 2025-11-25

913 Ciliary ARLs drive renal cystogenesis

Van Sciver, R. E.; Forster, A.; Caspary, T.

10.1101/2025.11.20.689124 — genetics — Posted on 2025-11-25

914 Yeast de novo proteins integrate into cellular systems using ancient protein targeting and degradation pathways

Houghton, C. J.; Castilho Coelho, N.; Chiang, A.; Wacholder, A.; Hedayati, S.; Guyer, A.; Wankiiri-Hale, M.; Raza, H.; Lord, N.; Parikh, S. B.; Ozbaki-Yagan, N.; Iannotta, J.; Berger, A.; Wohlever, M. L.; Carvunis, A.-R.; O'Donnell, A. F.

10.1101/2024.08.28.610198 — evolutionary biology — Posted on 2025-11-25

915 Defective splicing of Y-chromosome-linked gigantic genes contributes to hybrid male sterility in Drosophila

Fontan, A.; Lannes, R.; Fingerhut, J.; Flynn, J.; Yamashita, Y. M.

10.1101/2025.05.22.655455 — evolutionary biology — Posted on 2025-11-25

916 Metabolic fluctuations explain allometric scaling diversity

Tabi, A.; Merbis, W.; Santos, F.; Sole, R.

10.1101/2025.11.06.686202 — ecology — Posted on 2025-11-25

917 Genetic and physical interactions reveal overlapping and distinct contributions to meiotic double-strand break formation in C. elegans

Raices, M.; Balmir, F.; Silva, N.; Li, W.; Grundy, M. K.; Hoffman, D. K.; Altendorfer, E.; Camacho, C. J.; Bernstein, K.; Colaiacovo, M. P.; Yanowitz, J.

10.1101/2024.02.23.581796 — developmental biology — Posted on 2025-11-25

918 Aggressive Cholesterol Lowering Normalizes Atherosclerosis Regression in Jak2V617F Mice

Hardaway, B. D.; Fidler, T. P.; Tavallaie, M.; Avrampou, K.; Hsu, C.-C.; Schiavone, S.; Xiao, T.; Wang, N.; Tall, A. R.

10.1101/2025.07.23.666334 — molecular biology — Posted on 2025-11-25

919 Tityus serrulatus venom: TsTX-κ beta a neurotoxin with anti-microbial activity and non-hemolytic

Oliveira, T. d. J.; Pereira, N.; Riciluca, K. C. T.; do Nascimento, S. M.; Castro de Oliveira, U.; Silva Junior, P. I.

10.1101/2022.10.09.511467 — microbiology — Posted on 2025-11-25

920 Macrophage chemotaxis steered by complex self-generated gradients of complement C5a

Kiran, A.; Thomason, P. A.; Versluis, D. M.; Paschke, P. I.; Donnelly, H.; Tweedy, L.; Lilla, S.; Bravo-Ferrer, I.; Shergold, A.; Devlin, R.; Roberts, E. W.; Insall, R. H.

10.1101/2025.11.05.686842 — immunology — Posted on 2025-11-25

921 A neural circuit framework for economic choice: from building blocks of valuation to compositionality in multitasking

Battista, A.; Padoa-Schioppa, C.; Wang, X.-J.

10.1101/2025.03.13.643098 — neuroscience — Posted on 2025-11-25

922 Context-Dependent Metabolic Adaptation in Microbial Communities: From Monocultures to Complex Ecological Interactions

Burrichter, A. G.; Zimmermann, J.; Meng, C.; Ludwig, C.; Kaleta, C.; Stecher, B.

10.1101/2025.10.22.683057 — systems biology — Posted on 2025-11-25

923 Suppressing the suppressor: Gallic acid induced asymmetric tetramerization of the pleotropic virulence factor SuhB from Pseudomonas aeruginosa abolishes its extragenic suppressor activities. A structure-based functional study

Yadav, V. K.; Jena, A. K.; Mukerji, M.; Bhattacharyya, S.

10.1101/2025.11.12.687946 — biophysics — Posted on 2025-11-25

924 Pangenome-Informed Language Models for Synthetic Genome Sequence Generation

Huang, P.; Charton, F.; Schmelzle, J.-N. M.; Darnell, S. S.; Prins, P.; Garrison, E.; Suh, G. E.

10.1101/2024.09.18.612131 — bioinformatics — Posted on 2025-11-25

925 Distinct NIR Reflectance Spectra Associated with Foliar Symptoms of Beech Leaf Disease

Moore, E. G.; Dabydeen, L. C.; Salha, R.; Bichler, J.; Borsuk, A. M.

10.1101/2025.11.22.689946 — plant biology — Posted on 2025-11-25

926 Consistent Neural Representation of Affective States between Watching and Recall using fNIRS

Park, C.; Kim, J.

10.1101/2025.11.22.689961 — neuroscience — Posted on 2025-11-25

927 Chronotype-specific impacts of sleep-wake schedule on behavioral, physiological and psychological parameters

Haga, T.; Iwama, S.; Ushiba, J.; Ushiyama, J.

10.1101/2025.11.22.684496 — neuroscience — Posted on 2025-11-25

928 WITHDRAWN: A painless nerve growth factor variant uncouples nociceptive and neurotrophic TrkA signaling

Kumar, S.; Jung, H. A.; Walker, G.; Rana, J. K.; Fu, R.; Hong, M. T.; Malerba, F.; Kumar, J.; Navratna, V.; Jung, W.; Miller, S. J.; Kruckenhauser, L. M.; Capsoni, S.; Hafler, B. P.; Cattaneo, A.; Krishnan, Y.; Mosalaganti, S.; Bhattacharyya, M.

10.1101/2025.11.18.686377 — neuroscience — Posted on 2025-11-25

929 A non-canonical MPK3-ACTPK1-RbcS signalling module fine-tunes photosynthesis in rice

Jonwal, S.; Banerjee, G.; Rengasamy, B.; Mohit, M.; Sharma, P.; Sinha, A. K.

10.1101/2025.11.22.689956 — plant biology — Posted on 2025-11-25

930 Overexpression of TPM4 promotes cancer progression through EMT in anaplastic thyroid cancer

Ying, H.; Zhou, Y.; Jiang, X.; Cui, W.; Chen, S.; Yao, X.; Feng, J.; Guo, D.; Qian, X.

10.1101/2025.11.22.689948 — cancer biology — Posted on 2025-11-25

931 MSICKB: A Curated Knowledgebase for Exploring Molecular Heterogeneity and Biomarker Discovery in Microsatellite Instability Cancers

Shen, B.; Zhang, Y.

10.1101/2025.11.22.689859 — bioinformatics — Posted on 2025-11-25

932 Spatial and Single-Cell Transcriptomics Decipher the Crosstalk Environment of DEFB1+ Cancer Cells and IFI30+ Macrophages in Intrahepatic Cholangiocarcinoma

Wang, G.; Meng, H.; Li, M.; Fang, X.; Zou, W.; Qu, H.

10.1101/2025.11.22.689892 — bioinformatics — Posted on 2025-11-25

933 Evolution in response to an abiotic stress shapes species coexistence

Fragata, I.; Godinho, D. P.; Rodrigues, L. R.; Cruz, M. A.; Zele, F.; Godoy, O.; Magalhaes, S.

10.1101/2023.05.06.539716 — evolutionary biology — Posted on 2025-11-25

934 Using General Algebra to Model the Directed Evolution of an Asexual Population

Park, K.

10.1101/2025.11.22.689897 — evolutionary biology — Posted on 2025-11-25

935 Mapping embryonic mouse lung development using enhanced spatial transcriptomics

Zhang, P.; Law, B. K.; Goodwin, K.; Chan, M. M.; Nelson, C. M.

10.1101/2025.11.22.688293 — developmental biology — Posted on 2025-11-25

936 RanBP2-dependent annulate lamellae drive nuclear pore assembly and nuclear expansion

Lin, J.; Agote-Aran, A.; Liao, Y.; Cloarec, M.; Andronov, L.; Schoch, R.; Ronchi, P.; Cochard, V.; Zhu, R.; Grandgirard, E.; Liu, X.; Lemee, M. V.; Kleiss, C.; Golzio, C.; Ruff, M.; Chevreux, G.; Schwab, Y.; Klaholz, B.; Sumara, I.

10.1101/2024.10.08.617205 — cell biology — Posted on 2025-11-25

937 General features of cognition gene polymorphism patterns in marine fish

Zhang, Z.; Zhang, S.; Xu, Y.; Guo, C.

10.1101/2025.11.22.689885 — molecular biology — Posted on 2025-11-25

938 Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis)

Cummins, C.; Sutton, W.; McLeod, T.; Dallas, J. W.; Ghotbi, M.; Vargas-Gastelum, L.; Alexander, N. R.; Rurik, A. J.; McGinnity, D.; Reinsch, S. D.; Sandonato, P.; Arbour, J.; Freake, M.; Ashley, A.; Ternes, W.; Culp, E.; Spatafora, J.; McPhail, K.; Stajich, J. E.; Hardman, R.; Walker, D. M.

10.1101/2025.11.24.690264 — microbiology — Posted on 2025-11-25

939 Endothelial cell MHC molecules are necessary and sufficient to reject 3D-printed human skin grafts in an advanced human immune system mouse

Tobiasova, Z.; Sefik, E.; Qin, L.; McNiff, J.; Davis, G.; Flavell, R.; Saltzman, W. M.; Pober, J. S.

10.1101/2025.11.24.689811 — immunology — Posted on 2025-11-25

940 Immunological Differences in Atopic Dermatitis Across Age Groups: Insights from Single-Cell Multi-Omics

Baldonado, G. C. L.; Kumar, S.; Jin, J.; Fang, X.; Ildardashty, A.; Braun, M.; Neuhaus, I. M.; Mathes, E.; Bhutani, T.; Liao, W.

10.1101/2025.11.22.689843 — immunology — Posted on 2025-11-25

941 Asymmetric blood flow within a shared capillary network links the nucleus of the solitary tract and area postrema

Carson, K. E.; Roy, R. K.; Stern, J. E.

10.1101/2025.11.22.689934 — neuroscience — Posted on 2025-11-25

942 Fronto-Parietal Oscillatory Dynamics of Emotion Regulation as a Function of Adult Attachment Orientations

Domic-Siede, M.; Figueroa-Cuevas, J.; Leiva-Cortes, K.; Lopez, D.; Guzman-Gonzalez, M.; Lau-Lemus, T.; Hernandez, S.; Ortiz, R.; Gonzalez, L.; Silva, J. R.

10.1101/2025.11.22.689931 — neuroscience — Posted on 2025-11-25

943 A system for high-throughput axonal imaging of induced pluripotent stem cell-derived human i3Neurons

Whittaker, S.; McKenna, E.; Sarbanes, S.; Fernandopulle, M.; Ward, M.; Roll-Mecak, A.

10.1101/2025.11.22.689945 — neuroscience — Posted on 2025-11-25

944 Immuno-Impaired Expression of Synaptophysin, GFAP and Nissl Substances in the Cerebral Cortex of Diabetic Wistar Rats; Evaluation of Andrographis Paniculata Effects

ONANUGA, I. O.; FOLARIN, R. O.; Muniru, E. T.; IBRAHIM, R. B.; USMAN, I. M.; JEGEDE, A. I.; AZU, O. O.; OBAYA, T. O.; KEHINDE, M. O.

10.1101/2025.11.22.689937 — pharmacology and toxicology — Posted on 2025-11-25

945 Inactivation of a protein hydroxylase complex impairs replication fork restart in cancer and neurodevelopmental disorders

Kennedy, T. J.; Fletcher, S.; Boora, U.; Fraser-Williams, E.; Hughes, G. W.; Morris, J. R.; Smerdon, S. J.; Coleman, M.

10.1101/2025.11.22.689938 — cancer biology — Posted on 2025-11-25

946 Extracting host-specific developmental signatures from longitudinal microbiome data

Erdos, B.; Chatzis, C.; Thorsen, J.; Stokholm, J.; Smilde, A. K.; Rasmussen, M. A.; Acar, E.

10.1101/2025.11.22.689760 — bioinformatics — Posted on 2025-11-25

947 CLEAR-AF: Improved Autofluorescence Subtraction for Multiplexed Tissue Imaging via Polar Transformation and Gaussian Mixture Models

Arnould, A.; De Moor, B.; De Smet, F.; Bosisio, F. M.; Antoranz, A.

10.1101/2025.11.22.689928 — bioinformatics — Posted on 2025-11-25

948 MORGaN: self-supervised multi-relational graph learning for drug target discovery

Occhetta, M.; Myatt, A.; Mudaliar, M. A. V.; Bessant, C.

10.1101/2025.09.10.675402 — bioinformatics — Posted on 2025-11-25

949 From Circles to Signals: Representation Learning on Ultra-Long Extrachromosomal Circular DNA

Li, J.; Liu, Z.; Zhang, Z.; Zhang, J.; Singh, R.

10.1101/2025.11.22.689941 — bioinformatics — Posted on 2025-11-25

950 A technical semi-field methodology to measure the effect of nutrition on honeybee brood rearing

Goncalves, R. F. d. S.; De Sousa, R. T.; Stabler, D.; Pinto, D. M. S.; Wright, G. A.; Shafir, S.

10.1101/2025.07.01.662504 — animal behavior and cognition — Posted on 2025-11-25

951 Apoptosis uncovers human evolutionary heritage sequestered in non-coding DNA

Joshi, R.; Roy, A.; Lopes, R.; Kata, L.; Selukar, R.; Markam, M.; Banerji, S.; Raghuram, G. V.; Shabrish, S.; Mittra, I.

10.1101/2025.11.13.688179 — evolutionary biology — Posted on 2025-11-25

952 Aspen-associated soil microbiomes reveal different strategies for nitrogen acquisition across ecosystems in Mexico and Canada

Fijarczyk, A.; Goessen, R.; Morency, M.-J.; Gagne, P.; Laganiere, J.; Wehenkel, C.; Hernandez-Velasco, J.; Porth, I.; Isabel, N.; Martineau, C.

10.1101/2025.03.05.641730 — evolutionary biology — Posted on 2025-11-25

953 Derivation of primed sheep embryonic stem cells and conversion to an intermediate naive-like state

TS, S.; Vasquez-Hidalgo, M. A.; Pillai, V. V.

10.1101/2025.11.22.689923 — developmental biology — Posted on 2025-11-25

954 Quantitative Dual Predation by a Wild-type Bdellovibrio-like Organism and Lytic Bacteriophage Reveals Host-Specific Synergy

Forteza, I. L.; Subong, B. J.; Hessari-Bahrami, M.

10.1101/2025.11.23.690044 — microbiology — Posted on 2025-11-25

955 In vitro liquid-liquid phase separation induced by respiratory syncytial virus proteins and RNA

Basse, V.; Agarwal, T.; Sneideris, T.; Richard, C.-A.; Troussier, J.; Vasseur, J.-J.; Debart, F.; Eleouet, J.-F.; de Csillery, E.; Knowles, T.; Galloux, M.

10.1101/2025.11.25.690368 — microbiology — Posted on 2025-11-25

956 Injury-induced tau pathology promotes aggressive behavior in Drosophila without neurodegeneration.

Maxson, R.; Smoyer, C. J.; Hampton, M. F.; Shen, Y.; Wiese, K.; Yee, C.; Singh, A.; Funtila, A.; McKenney, R. J.; Ori-McKenney, K. M.

10.1101/2025.11.22.689595 — neuroscience — Posted on 2025-11-25

957 Hypovolemia Evokes Conserved Inverse Neurovascular Coupling in the Supraoptic Nucleus Independent of Heart Failure

Roy, R. K.; Filosa, J. A.; Stern, J. E.

10.1101/2025.11.22.689917 — neuroscience — Posted on 2025-11-25

958 Exposure to Maternal Pre- and Postnatal Psychological Distress: Associations with Brain Structure in 5-year-old Children

Pulli, E. P.; Audah, H. K.; Svensk, A.; Rosberg, A.; Luotonen, S.; Juntunen, P.; Mariani Wigley, I. L.; Kumpulainen, V.; Silver, E.; Copeland, A.; Saukko, E.; Merisaari, H.; Kataja, E.-L.; Karlsson, L.; Karlsson, H.; Tuulari, J. J.

10.1101/2025.11.24.690168 — neuroscience — Posted on 2025-11-25

959 Executive Resources Shape the Impact of Language Predictability Across the Adult Lifespan

Schuckart, M. M.; Martin, S.; Tune, S.; Schmitt, L.-M.; Hartwigsen, G.; Obleser, J.

10.1101/2024.05.08.592872 — neuroscience — Posted on 2025-11-25

960 Managing Gaze Competition when Acting On and Monitoring the Environment in Parallel

Fooken, J.; Johansson, R. S.; Flanagan, J. R.

10.1101/2024.10.28.620734 — neuroscience — Posted on 2025-11-25

961 Aphid infestation induces plant-sex-specific changes in floral chemistry and pollinator behaviour in Silene latifolia

Zill, K. B.; Stegemann, T.; Kaltenegger, E.; Bilger, W. J.; Demetrowitsch, T. J.; Berndt, H.; Erfmeier, A.; Unsicker, S. B.; Schrieber, K.

10.1101/2025.07.22.666187 — plant biology — Posted on 2025-11-25

962 EGFR-Driven Phenotypes Dictate Differential Therapeutic Response to Radiotherapy and Temozolomide in Glioblastoma.

Castello-Pons, M.; Perales-Paton, M.; Italia, M.; Gomez-Soria, I.; Casero, A.; Belmonte-Beitia, J.; Perez-Garcia, V.; Sanchez-Gomez, P.

10.1101/2025.11.22.689881 — cancer biology — Posted on 2025-11-25

963 Co-targeting KRAS and Exportin1 as an effective therapeutic strategy for KRASG12D mutant pancreatic ductal adenocarcinoma

Khan, H. Y.; Al Hallak, M. N.; Aboukameel, A.; Bannoura, S. F.; Uddin, M. H.; Aboukameel, A. A.; Alkan, F. K.; Caglayan, A. B.; Alkan, H. K.; Bao, B.; Jimenez, H.; Johansen, A. M.; McGrath, C.; Barker, G.; Choucair, K.; Tubon, M.; Beal, E.; Kim, S.; Beydoun, R.; Dyson, G.; Shi, Y.; Nagasaka, M.; Atfi, A.; Korkaya, H.; Saif, M. W.; Philip, P. A.; El-Rayes, B.; Chen, H.; Shields, A. F.; Mohammad, R. M.; Pasche, B. C.; Azmi, A. S.

10.1101/2025.11.21.689857 — cancer biology — Posted on 2025-11-25

964 B-cell activating factor plays a critical role in CAR-T cell-associated cytokine release syndrome

Parameswaran, R.; Fritz, C.; Metheny, L.; Wald, D. N.; Caimi, P.

10.1101/2025.11.22.689920 — cancer biology — Posted on 2025-11-25

965 ApoE4 accelerates the condensate to amyloid transition of tau

V, V. K.; Garai, K.

10.1101/2025.11.22.689889 — biophysics — Posted on 2025-11-25

966 JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics

Guo, Y.; Liu, J.; Cheng, H.; Ma, Y.

10.1101/2025.11.21.689823 — bioinformatics — Posted on 2025-11-25

967 Molecular mechanism decipher of Alzheimer's disease based on single-cell RNA-seq information

Jiang, X.; Wei, D.; Ye, J.; Gilson, E.

10.1101/2025.11.22.689872 — bioinformatics — Posted on 2025-11-25

968 rnaends: an R package to study exact RNA ends at nucleotide resolution

Caetano, T.; Redder, P.; Fichant, G.; Barriot, R.

10.1101/2025.04.18.649472 — bioinformatics — Posted on 2025-11-25

969 STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes

Clifton, K.; Jiang, V.; Peixoto, R. d. S.; Singh, S.; Matsuura, R.; Rabb, H.; Fan, J.

10.1101/2025.11.21.689847 — bioinformatics — Posted on 2025-11-25

970 STELAR-X: Scaling Coalescent-Based Species Tree Inference to 100,000 Species and Beyond

Saha, A.; Bayzid, M. S.

10.1101/2025.11.22.689894 — bioinformatics — Posted on 2025-11-25

971 RoBep: A Region-Oriented Deep Learning Model for B-Cell Epitope Prediction

Xu, Y.; Wei, G.; Zhou, J.; Huang, Y.; Yu, W.; Lin, Z.; LIU, R.; Fan, X.

10.1101/2025.11.22.689912 — bioinformatics — Posted on 2025-11-25

972 Distinct networks of expressed genes are associated with neophobia in the hippocampus of male and female Eurasian tree sparrows (Passer montanus)

Lipshutz, S. E.; Bentz, A. B.; Cochran, E.; Krajcir, K.; Kimball, M.; Lattin, C. R.

10.1101/2025.09.04.674257 — animal behavior and cognition — Posted on 2025-11-25

973 A Marfan-Associated FBN1 Nonsense Mutation Mouse Model Reveals Adventitial Inflammation During Aneurysm Progression

Wu, S.; Zhao, J.; Ponce, A.; Pham, L.; Xie, D.; Ju, D.; Yin, S.; Hernandez, F.; Jones, S.; Li, C.; Chung, C. S.; Komnenov, D.; Rossi, N. F.; Mizrak, D.; Yang, B.; Yang, Z.; Yang, M.; Li, H.; Xie, Y.; Chen, K.; Zhang, K.; Li, L.

10.1101/2025.09.23.678101 — genetics — Posted on 2025-11-25

974 PRSNet-2: End-to-end genotype-to-phenotype prediction via hierarchical graph neural networks

Li, H.; Shan, Z.; Fu, H.; Du, Y.; Gao, S.; Gao, P.; Cooper-Knock, J.; Min, Y.; Xing, X.; Zhang, S.

10.1101/2025.11.22.689899 — genetics — Posted on 2025-11-25

975 Sex determination of Syrian hamster pups using placental tissues

Kumpanenko, Y.; Piessens, L.; Neven, V.; Dallmeier, K.; Alpizar, Y. A.

10.1101/2025.11.22.689895 — genetics — Posted on 2025-11-25

976 Longitudinal analysis of the hand microbiome in response to chlorine-based antiseptic use during a military field exercise

Glenna, S.; Birkeland, E. E.; Orr, R. J. S.; Gilfillan, G. D.; Dalland, M.; Okstad, O. A.; Voie, O. A.; Rounge, T. B.

10.1101/2025.11.20.689467 — microbiology — Posted on 2025-11-25

977 Restoration of MAIT cell function in healthcare-associated bacterial infections supports recovery of carbapenem efficacy against resistant bacteria

Xue, Y.; Karim, A. M.; Sia, W. R.; Han, F.; Chan, K. L.; Chua, N. G.; Hadadi, L.; Liu, Z.; Mak, J. Y.; Fairlie, D. P.; Wang, L.-F.; Sandberg, J. K.; Kwa, A. L.-H.; Leeansyah, E.

10.1101/2025.11.21.689870 — immunology — Posted on 2025-11-25

978 Nuclear factor kappa B subunits and IkappaB family are modulated in the ovine endometrium during early pregnancy

Du, Z.; Xu, Y.; Yang, H.; Zhu, H.; Zhang, L.; Yang, L.

10.1101/2025.11.22.689904 — immunology — Posted on 2025-11-25

979 Temporal Dynamics of Complement Activation and Outcome in Patients with Acute Ischemic Stroke

Wang, Y.; Westendorp, W. F.; Bijlsma, M. W.; Tanck, M.; Man, W. K.; Brouwer, M. C.; Mulder, I. A.; Coutinho, J. M.; van de Beek, D.

10.1101/2025.11.21.689862 — neuroscience — Posted on 2025-11-25

980 Vascular dementia increases levels of methylenetetrahydro-folate reductase and cystathionine β-synthase in female patients and changes gene expression of acetylcholine and glutamate clathrin-sculpted transport vesicles

Joshi, S.; McKee, A.; Ille, S.; Buss, K.; Beach, T.; Serrano, G. E.; Jadavji, N. M.

10.1101/2025.11.21.689865 — neuroscience — Posted on 2025-11-25

981 Sensory Circuit Dynamics in a Mouse Model of Epileptic Encephalopathy

Suchanek, D.; Williams, A.; Cao, T.; Todd, W. D.; Sun, Q.-Q.

10.1101/2025.11.22.689933 — neuroscience — Posted on 2025-11-25

982 Fluid-Structure Interaction Dynamics of Cervical Lymphatic Vessel Pumping and Valvular Function

Kim, D.; Tithof, J.

10.1101/2025.11.21.689846 — physiology — Posted on 2025-11-25

983 SAMP1 Facilitates Importin-Mediated Nuclear Translocation to Activate the PKA/CREB Pathway and Hepatic Gluconeogenesis

Schena, E.; Columbaro, M.

10.1101/2025.11.17.688768 — pathology — Posted on 2025-11-25

984 Multi-omics-driven kinetic modeling reveals metabolic adaptations and vulnerabilities in BRCA1-deficient ovarian cancer

Toumpe, I.; Masid, M.; Hatzimanikatis, V.; Miskovic, L.

10.1101/2025.10.22.682756 — cancer biology — Posted on 2025-11-25

985 A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion

Polovnikov, K. E.; Starkov, D.

10.1101/2025.09.04.674214 — biophysics — Posted on 2025-11-25

986 CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants

Huang, J.; Yang, Z.; Yin, M.; Li, C.; Li, J.; Wang, Y.; Huang, L.; Li, M.; Liang, C.; He, F.; Han, R.; Jiang, Y.

10.1101/2024.12.29.630569 — bioinformatics — Posted on 2025-11-25

987 Cis-TERN: a graph-based method to integrate single-cell chromatin accessibility with gene expression data to infer the pseudotime ordering of cells

Gokhale, A.; Przytycki, P. F.

10.1101/2025.11.21.689849 — bioinformatics — Posted on 2025-11-25

988 Modifications to the gut microbiome alter bone matrix proteomics and fracture toughness at the cellular scale

Hunt, N. K.; Liu, C.; Liu, J.; Tang, Q.; Stephen, S. J.; Wang, B.; Schurman, C. A.; King, C. D.; Liu, Q.; Vashishth, D.; Schilling, B.; Hassani, M.; Hernandez, C. J.

10.1101/2025.11.21.689836 — bioengineering — Posted on 2025-11-25

989 A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2

Zhan, S. H.; Wong, Y.; Ignatieva, A.; Eaton, K.; Guthrie, I.; Jeffery, B.; Palmer, D. S.; Murall, C. L.; Otto, S.; Kelleher, J.

10.1101/2023.06.08.544212 — evolutionary biology — Posted on 2025-11-25

990 Rapid turnover of sex chromosomes is associated with speciation in Neotropical armored catfish Harttia (Siluriformes, Loricariidae)

de Menezes Cavalcante Sassi, F.; Santos de Souza, F. H.; Shams, F.; Fernandez Perez, M.; Ezaz, T.; Deon, G. A.; Liehr, T.; Xu, L.; Cioffi, M. d. B.

10.1101/2025.08.06.668863 — evolutionary biology — Posted on 2025-11-25

991 Temperature stress disrupts reciprocal adaptation in a microbial predator-prey system

Plum, K.; Zufall, R.

10.1101/2025.11.21.689813 — evolutionary biology — Posted on 2025-11-25

992 Foraging behavior and ecology drive the evolution of humeral shape in hummingbirds

Rios-Orjuela, J. C.; Cadena, D.; Rico-Guevara, A.; Berberi, I.; Miner, L.; Dakin, R.

10.1101/2025.08.11.669688 — evolutionary biology — Posted on 2025-11-25

993 In situ mutational screening and CRISPR interference reveal that the apterous Early enhancer is required for developmental boundary positioning

Gustavo, G.; Sickmann, M. E.; Born, G.; Bieli, D.; Affolter, M.; Müller, M.

10.1101/2023.08.05.552106 — developmental biology — Posted on 2025-11-25

994 Chinmo defines the region-specific oncogenic competence in the Drosophila central nervous system

Nguyen, P.-K.; Froldi, F.; Marshall, O. J.; Southall, T.; Cheng, L.

10.1101/2025.05.20.655209 — developmental biology — Posted on 2025-11-25

995 Capsaicin acts as a novel NRF2 agonist to suppress ethanol induced gastric mucosa oxidative damage by directly disrupting the KEAP1-NRF2 interaction

Gao, X.; Guo, W.; Liu, P.; Yuwen, M.; Ren, H.; Hu, S.; Liu, Z.; Tan, R.; Liu, K.; Yang, Z.; Ba, J.; Bai, X.; Shama, S.; Tang, C.; Miao, K.; Pei, H.; Liu, L.; Zhu, C.; Wang, T.; Zhang, B.; Kang, J.

10.1101/2024.01.06.574490 — cell biology — Posted on 2025-11-25

996 Steady-state epithelial apical flatness is characterized by MLCK morphodynamics and asynchronous Ca2+ oscillations, but not underlying ECM geometry

Wu, H.; Herrmann, E. G.; Hyer, J. M.; Hua, L. L.; Mikawa, T.

10.1101/2025.11.21.688964 — cell biology — Posted on 2025-11-25

997 Identification of the C9-Hydrogenase for 9,17-Dioxo-1,2,3,4,10,19-Hexanorandrostan-5-oic Acid (9,17-DOHNA) and the 7α-Dehydratase Essential for Initiating β-Oxidation of the B-, C-, and D-Rings in Steroid Degradation by Comamonas testosteroni TA441

Horinouchi, M.

10.1101/2025.11.20.689525 — microbiology — Posted on 2025-11-25

998 Split-luciferin Assay for Real-time Measurement of Cytosolic Molecular Accumulation in Live Mycobacteria

Dash, R.; Spira, A.; Bhandari, S.; Newkirk, S.; Lucas, N.; Chordia, M.; Pires, M.

10.1101/2025.11.02.686125 — microbiology — Posted on 2025-11-25

999 Flavobacteria buffer nitrous oxide emissions from partial denitrifiers in coastal sediments

Nguyen-Dinh, T.; Hutchinson, T.; Ricci, F.; Prayitno, H.; Jimenez, L.; Eate, V.; Leung, P. M.; Lappan, R.; Yoon, S.; Wong, W. W.; Cook, P.; Greening, C.

10.1101/2025.11.24.689969 — microbiology — Posted on 2025-11-25

1000 Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation

Cheng, C.; Bennett, B. D.; Savalia, P.; Asrari, H.; Biel, C.; Evans, K. A.; Tang, R.; Thrash, C.

10.1101/2025.06.25.661606 — microbiology — Posted on 2025-11-25

1001 Glycosylated IgG antibodies contribute to the recovery of haemorrhagic fever with renal syndrome patients

Quan, C.; Wang, L.; Gao, J.; Li, Y.; Xu, X.; Li, H.; Gao, Z.; Ruan, W.; Liu, H.; Li, Q.; Xing, W.; Zhao, L.; Carr, M. J.; Shi, W.; Hou, H.

10.1101/2025.04.11.648365 — immunology — Posted on 2025-11-25

1002 The anticonvulsant and mood-stabilizing drug valproic acid attracts C. elegans and activates chemosensory neurons via a cGMP signaling pathway

Rogel-Hernandez, L. E.; Casademunt, H.; Samuel, A. D. T.; Goodman, M. B.

10.1101/2025.11.11.687732 — neuroscience — Posted on 2025-11-25

1003 Most early-born subplate neurons persist as Layer 6b neurons in the adult mouse neocortex

Sugita, Y.; Moriya-Ito, K.; Hanashima, C.; Ohtaka-Maruyama, C.

10.1101/2025.11.20.689634 — neuroscience — Posted on 2025-11-25

1004 Predicting Neural Activity from Connectome Embedding Spaces

Zhang, Z.; Zhang, H.; Mihalas, S.

10.1101/2025.05.09.653224 — neuroscience — Posted on 2025-11-25

1005 Identifying regulators of associative learning using a protein-labelling approach in C. elegans

Rahmani, A.; McMillen, A.; Allen, E.; Ansaar, R.; Green, R.; Johnson, M. E.; Poljak, A.; Chew, Y. L.

10.1101/2024.02.19.580416 — neuroscience — Posted on 2025-11-25

1006 Serial Imaging of Tumour and microEnvironment (SITE) platform for live-cell ex vivo modelling of primary and metastatic cancer dynamics

Murthy, V.; Makkawi, R.; Anderson, F.; Halsey, C.; Manalo-Hall, E.; Srikanth, S.; Tangkilisan, G.; Zheng, T.; McGann, J.; Birtwistle, M. R.; Copperman, J.; Davies, A. E.

10.1101/2025.09.08.674915 — cancer biology — Posted on 2025-11-25

1007 Structure and dynamics of a muti-domain nitric oxide synthase regulated by a C2 domain

Nair, D.; CRANE, B. R.

10.1101/2025.08.15.670619 — biophysics — Posted on 2025-11-25

1008 Slow Electromechanical Interference Links Division Geometry, Differentiation Bias, and Senescence-like Arrest

Bueno, A. D. M.

10.1101/2025.10.28.684574 — biophysics — Posted on 2025-11-25

1009 Structural Integrity of RyR2 Clusters Controls Cardiac Calcium Leak

Noren, A.; Shiferaw, Y.

10.1101/2025.11.07.687312 — biophysics — Posted on 2025-11-25

1010 Allosteric effects of the coupling cation in melibiose transporter MelB

Hariharan, P.; Shi, Y.; Amirhossein, B.; Liang, R.; Viner, R.; Guan, L.

10.1101/2025.07.10.664195 — biophysics — Posted on 2025-11-25

1011 Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet

Kim, J.; Rosen, B. D.; Fumagalli, S. E.; Kuhn, K. L.; Long, A.; Schoenebeck, J. J.; Schwartz, H.; Wu-Cavener, L.; Zimin, A. V.; Cavener, D.; Smith, T. P. L.; Phillippy, A. M.; Koren, S.; Rhie, A.

10.1101/2025.10.01.679366 — bioinformatics — Posted on 2025-11-25

1012 A translational transcriptomic signature of vaccine reactogenicity for the evaluation of novel formulations

Becker, J.; Roelens, M.; Reynaud, K.; Beloeil, L.

10.1101/2025.11.20.689650 — bioinformatics — Posted on 2025-11-25

1013 Autonomous Liquid-handling Robotics Scripting for Accessible and Responsible Protein Engineering

Yuan, G.; Luo, L.; Li, W.; Lan, Y.; Jiang, H.; Chen, Y.; Yi, X.; Li, B.; Alinejad-Rokny, H.; Wang, T.; Fu, L.; Yang, M.; Si, T.

10.1101/2025.09.30.679666 — bioengineering — Posted on 2025-11-25

1014 Social isolation reduces oxygen consumption, speed of movement and social preference in wild-type Zebrafish (Danio rerio)

Ghosh, A.; Rao, A. M.; Middha, P.; Rai, S.; Rajaraman, B. K.

10.1101/2024.11.22.624675 — ecology — Posted on 2025-11-25

1015 Alveolar epithelium propagates mechanical signals that control multi-cellular homeostasis in the lung

Shen, C.; Morley, M. P.; Schaefer, S. E.; Zhao, G.; Planer, J. D.; Chembazhi, U. V.; Jones, D. L.; Kim, M.; Ying, Y.; Zhou, S.; Li, S.; Hallquist, H.; Lange, A.; Basil, M. C.; Morrisey, E. E.

10.1101/2025.06.04.657878 — cell biology — Posted on 2025-11-25

1016 Gene expression analysis and proximity labeling reveal posttranscriptional functions of the yeast RNA Polymerase II regulator Def1

Akinniyi, O. T.; Kulkarni, S.; Hribal, M. M.; Keller, C. A.; Giardine, B.; Reese, J. C.

10.1101/2024.09.16.613278 — molecular biology — Posted on 2025-11-25

1017 Sensory integration, temporal prediction and rule discovery reflect interdependent inference processes

Benjamin, L.; Morillon, B.; Wyart, V.

10.1101/2025.04.29.651167 — neuroscience — Posted on 2025-11-25

1018 Striatal cell-type specific encoding stability and reorganization for agency and habit

Malvaez, M.; Liang, A.; Hall, B. S.; Giovanniello, J. R.; Paredes, N.; Gonzalez, J. Y.; Blair, G. J.; Sias, A. C.; Murphy, M. D.; Guo, W.; Wang, A.; Singh, M.; Griffin, N. K.; Bridges, S. P.; Wiener, A.; Pimenta, J. S.; Holley, S. M.; Cepeda, C.; Levine, M. S.; Balsam, P. D.; Blair, H. T.; Wikenheiser, A. M.; Wassum, K. M.

10.1101/2025.01.26.634924 — neuroscience — Posted on 2025-11-25

1019 WITHDRAWN: Large mRNA language foundation modeling with NUWA for unified sequence perception and generation

Zhong, Y.; Yan, W.; Zhang, Y.; Tan, K.; Bian, B.

10.1101/2025.11.01.686058 — bioinformatics — Posted on 2025-11-25

1020 WITHDRAWN: UFMylation of 14-3-3ϵ coordinates MAVS signaling complex assembly to promote antiviral innate immune induction

Gutierrez, I. V.; Park, M.; Sar, L.; Rodriguez, R. E.; Schmidt, H. M.; Snider, D. L.; Torres, G.; Scaglione, K. M.; Horner, S. M.

10.1101/2025.10.21.683613 — immunology — Posted on 2025-11-25

1021 Mapping high resolution, multidimensional phase diagrams of physiological protein condensates

Agarwal, T.; Sneideris, T.; Svara, F.; Jermakovs, K.; Coyle, H.; Qamar, S.; Kava, E.; Scrutton, R.; Pleschka, N.; Peres, P.; Cereghetti, G.; Andrzejewska, E.; Diaz-Barreiro, A.; Palmer, G.; Costa-Filho, A. J.; Krainer, G.; Knowles, T. P.; Nixon-Abell, J.

10.1101/2025.11.24.690258 — biophysics — Posted on 2025-11-25

1022 The architecture of allele-specific regulatory variant effects across five human genomes

Dura, K.; Siklenka, K.; Strouse, K.; Morrow, S.; Majoros, W.; Reddy, T. E.

10.1101/2025.11.22.689315 — genomics — Posted on 2025-11-25

1023 A Multi-omic Atlas of Human Choroid Plexus in Alzheimer's Disease

Philippe, T.; Avey, D. R.; Vasco, N. K.; Vyas, H.; Tissera, S. D.; Xu, J.; Ng, B.; Saunders, D. M.; Lagrimas, A. K.; Duong, D.; Seyfried, N. T.; Bennett, D. A.; Wang, Y.

10.1101/2025.11.23.690014 — genomics — Posted on 2025-11-25

1024 Coordinated shifts in gene expression and regulation during mole-rat evolution

Daunesse, M.; Liorzou, E.; Parey, E.; Villar Lozano, D.; BERTHELOT, C.

10.1101/2025.11.24.690111 — evolutionary biology — Posted on 2025-11-25

1025 Developmental and transcriptional programs that define the initiation of the forelimb

Ghatpande, V.; Lewis, A. J.; Windsor, K. E.; Lee, H.; Alcala, A. J.; Menke, D. B.; Cenik, C.; Vokes, S. A.

10.1101/2025.11.23.689776 — developmental biology — Posted on 2025-11-25

1026 Polarization Increases Nuclear Stiffness in Macrophages Despite Reduction in Lamin A/C Levels

Elpers, M. A.; Odell, J. D.; Shu, T.; Ambekar, Y. S.; Henretta, S. J.; Saadi, H.; Woodworth, G. F.; Zipfel, W. R.; Scarcelli, G.; Holt, L. J.; Lammerding, J.

10.1101/2025.11.22.689940 — cell biology — Posted on 2025-11-25

1027 A CROSS-SPECIES ANALYSIS OF CELL WALL MECHANOSENSORS

Municio-Diaz, C.; MINC, N.

10.1101/2025.11.24.690177 — cell biology — Posted on 2025-11-25

1028 AAV2 Bypasses Direct Endosomal Escape by Using AAVR to Access the Trans-Golgi Network en Route to the Nucleus.

Cabanes-Creus, M.; Liao, S.; Pardo-Pinon, M.; Rojas, A. L.; Kelich, J.; Coyne, J.; Knight, M.; Nazareth, D.; Roca-Pinilla, R.; Senapati, S.; Walsh, M. C.; Cejas, P. J.; Armour, S. M.; Hierro, A.; Lisowski, L.

10.1101/2025.11.22.689972 — cell biology — Posted on 2025-11-25

1029 The Actin regulator Mena promotes Wnt signalosome endocytosis and Wnt signalling.

Wu, S.-y.; Moreno, M. M.; Noble, A.; Azwan, A. H.; Guille, M.; Liu, K. J.; Krause, M.

10.1101/2025.11.24.690281 — cell biology — Posted on 2025-11-25

1030 Predictive Neural Signals during Natural Mandarin Speech Comprehension

Wang, Q.; Berlot, E.; Fazekas, J.; Szewczyk, J.; de Lange, F.

10.1101/2025.11.23.690006 — neuroscience — Posted on 2025-11-25

1031 Exposure to Maternal Pre- and Postnatal Psychological Distress: Associations with Brain Structure in 5-year-old Children

10.1101/2025.11.24.690168 — neuroscience — Posted on 2025-11-25

1032 Sex and experience dependent regulation of synaptic protein turnover

Heo, S.; Zhang, S.; Mun, D.-G.; Pandey, A.; Bygrave, A. M.; Huganir, R. L.

10.1101/2025.11.24.690161 — neuroscience — Posted on 2025-11-25

1033 Distinct Roles of Deep and Superficial Cortical Layers in Tone Prediction, Comparison, and Adaptation in Human Auditory Cortex

van Haren, J.; de Lange, F. P.; Kotz, S. A.; De Martino, F.

10.1101/2025.11.24.687809 — neuroscience — Posted on 2025-11-25

1034 The brain architecture of punishment learning

Gregory, A. V.; Jean-Richard-dit-Bressel, P.; Huang, N.; Diefenbach, J.; Choi, E.; Soo, J.; Chen, J.; Killcross, S.; McNally, G.

10.1101/2025.11.24.690287 — neuroscience — Posted on 2025-11-25

1035 Role of Bassoon-mediated active zone integrity at different types of brain synapses for brain activity and cortex-dependent memory formation

Oelschlegel, A. M.; Schicknick, H.; Annamneedi, A.; Montenegro-Venegas, C.; Fejtova, A.; Gundelfinger, E. D.; Goldschmidt, J.; Tischmeyer, W.

10.1101/2025.11.24.690204 — neuroscience — Posted on 2025-11-25

1036 Social Processing in the Amygdala: Single-Nucleus RNA-Sequencing Reveals Distinct Neuronal Responses to Dominant and Subordinate Cues

Dwortz, M. F.; Curley, J. P.; Hofmann, H. A.

10.1101/2025.11.24.690183 — neuroscience — Posted on 2025-11-25

1037 Experience-Dependent Plasticity of Thalamoprefrontal Circuitry Characterizes Learning Across Species

Elkinbard, I.; Sadeghzadeh, S.; Hedlund, M.; Tsai, V.; Ho, T.; Deisseroth, K.; Buch, V.

10.1101/2025.11.23.689976 — neuroscience — Posted on 2025-11-25

1038 Intrinsic excitability controls structural plasticity of cerebellar climbing fibers

Musto, M.; Bergamini, M.; La Terra, A.; Marte, A.; Marenco, G.; Lo Iacono, F.; Benfenati, F.; Grasselli, G.

10.1101/2025.11.24.690115 — neuroscience — Posted on 2025-11-25

1039 General-Purpose Large Language Models, such as DeepSeek V3.2, Have Evolved Protein Design Capabilities

Li, J.; Dong, X.

10.1101/2025.11.23.689994 — bioinformatics — Posted on 2025-11-24

1040 HIV Virion Capturing Liposomes for Therapeutic Vaccination

Kang, T. K.; Ang, C.; Canziani, G.; Elkateb, H.; Thomas, D.; Yang, D.; Smith, A. B. E.; Haddad, E. K.; Chaiken, I.; Deak, P. E.

10.1101/2025.11.24.690259 — bioengineering — Posted on 2025-11-24

1041 An ancient anthozoan protein reveals an alternative evolutionary path of antiviral signaling

Sharoni, T.; Jaimes-Becerra, A.; Birch, S.; Kwak, H.-J.; Aleshkina, D.; Lewandowska, M.; Surm, J. M.; Justin, H.; Aharoni, R.; Reitzel, A. M.; Moran, Y.

10.1101/2025.11.22.689925 — evolutionary biology — Posted on 2025-11-24

1042 Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances

Felce, C.; Cope, A. L.; Schraiber, J. G.; Krishnaswamy, M.; Pachter, L.; Pennell, M.

10.1101/2025.11.24.690267 — evolutionary biology — Posted on 2025-11-24

1043 Flavobacteria buffer nitrous oxide emissions from partial denitrifiers in coastal sediments

Nguyen-Dinh, T.; Hutchinson, T.; Ricci, F.; Prayitno, H.; Jimenez, L.; Eate, V.; Leung, P. M.; Lappan, R.; Yoon, S.; Wong, W. W.; Cook, P.; Greening, C.

10.1101/2025.11.24.689969 — microbiology — Posted on 2025-11-24

1044 Lignin degradation and valorization by Pseudomonas putida KT2440: a new role for glutathione peroxidase

Zhou, Q.; Fransen, A.; Innocenti, P.; Ram, A. F. J.; de Winde, J.

10.1101/2025.11.24.690113 — microbiology — Posted on 2025-11-24

1045 Glycerol suppresses lactose-dependent growth of Streptococcus pyogenes through a transcription-independent mechanism

Bando, A.; Hirose, Y.; Bertolla, O. M.; Takemoto, N.; Brouwer, S.; O'Donohue, J.; Ono, M.; Ikeda, E.; Nizet, V.; Walker, M. J.; Kawabata, S.

10.1101/2025.11.24.690200 — microbiology — Posted on 2025-11-24

1046 Bacteriophage genome-wide transposon mutagenesis

Chan, A. W.; Yee, W.-X.; Mozumdar, D.; Kokontis, C. Y.; Rojas-Montero, M.; Yuping, L.; Bondy-Denomy, J.; Yang, Y.

10.1101/2025.11.23.690004 — microbiology — Posted on 2025-11-24

1047 Histones and nucleoid-associated proteins in Methanosarcina acetivorans mediate recovery from stress and stasis

Nayak, D. D.; Baskevitch, A.

10.1101/2025.11.24.690127 — microbiology — Posted on 2025-11-24

1048 Antiviral and anti-inflammatory effects of Tabamide A derivative, TA25, against human rhinovirus and multiple zoonotic viruses in vitro and in silico

Kim, B.; Bat Ulzii, A.; Lim, T.; Kim, J. W.; Im, W. R.; Rajoriya, S.; Natasha, A.; Misra, D.; Hennisa, H.; Kwag, N. Y.; Yoon, D.; Jo, G.; Park, Y. B.; Park, J.; Lee, J. T.; Jeon, S. H.; Kim, W.-K.

10.1101/2025.11.23.690071 — microbiology — Posted on 2025-11-24

1049 Bacillus competence pili are efficient single - and double stranded DNA uptake machines

Kilb, A.; Dempwolff, F.; Graumann, P. L.

10.1101/2025.11.24.690153 — microbiology — Posted on 2025-11-24

1050 Scuticociliate Detection and Microbiome Composition in Museum Collections of Diadema Antillarum

Vilanova-Cuevas, B.; Hewson, I.

10.1101/2025.11.24.690235 — microbiology — Posted on 2025-11-24

1051 A programmable mRNA platform for miRNA detection via miRNA-mRNA2 triplex-mediated ribosomal frameshifting

Chen, Y.; Zhao, W.; Chen, H.; Zhou, H.; Fan, S.; Duan, H.; Dai, Y.; Lu, R.; Li, C.; Jiang, C.; Chan, E.; Chen, G.

10.1101/2025.11.24.690164 — synthetic biology — Posted on 2025-11-24

1052 Non-clinical safety of GRAd vector-based COVID-19 and HIV vaccines supports a platform regulatory approach

Capone, S.; Paalangara, R.; Gohin, S.; Menard, A.; Amy, C.; Berrabah, W.; Rogue, A.; Getz, M. A.; Alrubayyi, A.; Battella, S.; Raggioli, A.; Gentile, M.; Di Rita, A.; Noto, A.; Miselli, G.; Grazioli, F.; Napolitano, F.; Sowcik, D.; Soriani, M.; Chmielewski, B.; Molife, L.; Muturi-Kioi, V.; Makadzange, A. T.; Gaiha, G. D.; Ancian, P.; Ackland, J.; Folgori, A.; Colloca, S.

10.1101/2025.11.24.689034 — pharmacology and toxicology — Posted on 2025-11-24

1053 Sex-biased duplicates are rapidly generated during Drosophila tRNA repertoire evolution

Sosa, D.; Sobczyk, M.; Chen, J.-H.; Xia, S.; Pan, T.; Long, M.

10.1101/2025.11.24.689867 — evolutionary biology — Posted on 2025-11-24

1054 Characterization of a new laboratory colony of Anopheles funestus mosquitoes established in Ifakara, Tanzania

Hape, E. E.; Njalambaha, R. M.; Muyaga, L. L.; Nambunga, I. H.; Mgando, J. P.; Mwasheshi, D. D.; Nombo, N. K.; Mabula, D. M.; Zengenene, M. P.; Kahamba, N. F.; Odero, J. O.; Ngowo, H. S.; Mapua, S. A.; Chaki, P. P.; Govella, N. J.; Lyimo, I. N.; Kiware, S. S.; Lwetoijera, D. W.; Tarimo, B. B.; Kaindoa, E. W.; Selvaraj, P.; Tripet, F.; Wondji, C. S.; Baldini, F.; Koekemoer, L. L.; Ferguson, H. M.; Okumu, F. O.

10.1101/2025.11.23.690074 — ecology — Posted on 2025-11-24

1055 Lithocholic acid induces T3SS-dependent formation of invasion-competent Shigella flexneri aggregates

Lanier, J.; Skelly, J. J.; Salsbury, F.; Koseoglu, V. K.

10.1101/2025.11.24.690263 — microbiology — Posted on 2025-11-24

1056 Characterisation of novel bacteriophages against the cattle pathogen Moraxella bovis

Sampson, H. R.; Wegrzyn, M.; Josephs, T.; Ugokwe, N. I.; Kinsella, A.; Thanki, A. M.; Kalra, D. K.; Roux, A.; Patrick, H. L.; Swift, B. M.; Firth, G.; Odedra, R.; Millard, A. D.; Clokie, M. R.

10.1101/2025.11.24.690234 — microbiology — Posted on 2025-11-24

1057 A generalizable cross-continent prediction of esophageal squamous cell carcinoma using the oral microbiome

ElNaggar, S.; Chen, W. C.; Prodehl, L. M.; Marumo, T. K.; Khan, M. U.; Mathew, C. G.; Ruff, P.; Jin, Z.; Neugut, A. I.; Rustgi, A. K.; Uhlemann, A.-C.; Korem, T.; Abrams, J. A.

10.1101/2025.11.23.690048 — microbiology — Posted on 2025-11-24

1058 Thermal and non-thermal stress conditions activate the Plasmodium falciparum AP2-HS-dependent heat-shock response

Rafols, N.; Chillaron-Adan, M.; Tinto-Font, E.; Cortes, A.

10.1101/2025.11.24.690237 — microbiology — Posted on 2025-11-24

1059 Nomenclature updates to the hemagglutinin gene clade designations resulting from the continued evolution of high pathogenicity avian influenza A(H5) virus clades 2.3.2.1c and 2.3.4.4

Lam, T. T.-Y.; Davis, T.

10.1101/2025.11.23.690055 — microbiology — Posted on 2025-11-24

1060 Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins

Kabel, S.; Bendori, S. O.; Borenstein, T.; Guler, P.; del Sol, F. G.; Mancheno-Bonilla, J.; Marina, A.; Eldar, A.

10.1101/2025.11.23.689978 — microbiology — Posted on 2025-11-24

1061 Viral protease-mediated polyprotein processing in human astroviruses

Noyvert, D.; Neves, L. X.; Fominykh, K.; Hankinson, J.; Lindsey, G.; Lulla, A.; Emmott, E.; Lulla, V.

10.1101/2025.11.24.690148 — microbiology — Posted on 2025-11-24

1062 Comparative transcriptomic profiling of human conjunctival epithelial cells and macrophages in response to Chlamydia trachomatis genovars A and B in early- and mid-infection cycles

Ghasemian, E.; Holland, M. J.

10.1101/2025.11.24.689971 — microbiology — Posted on 2025-11-24

1063 Bifidobacterium- and Escherichia-dominant ecological guilds shape distinct microbial metabolism in the gut microbiome of tuberculosis patients

Yunusbaeva, M. M.; Sabirova, D. M.; Borodina, L. Y.; Khasanova, K. R.; Yunusbayeva, A. B.; Altinbaev, R. S.; Ganiev, I. R.; Yunusbayev, B. B.

10.1101/2025.11.24.690090 — microbiology — Posted on 2025-11-24

1064 Transcriptomic and Proteomic Analysis Reveals Nitrogen Recycling as a Core Mechanism for Prochlorococcus Prolonged Survival

Weissberg, O.; Aharonovich, D.; Sher, D. J.

10.1101/2025.11.24.690089 — microbiology — Posted on 2025-11-24

1065 Targeting Metabolic Vulnerabilities: Valinomycin Augments the Potency of Bioenergetic Inhibitors in Combatting Drug-Resistant and Dormant Mycobacterium tuberculosis

Roy, A.; Kushwah, S.; Sau, S.; Agnivesh, P. K.; Parida, K. K.; Divya, M.; Kalia, N. P.

10.1101/2025.11.23.690070 — microbiology — Posted on 2025-11-24

1066 A geothermal amoeba sets a new upper temperature limit for eukaryotes

Rappaport, H. B.; Petek-Seoane, N. A.; Tyml, T.; Mikus, F.; Labutti, K.; Ani, G.; Niblo, J. K.; MacVicar, E.; Shepherd, R. M.; de la Higuera, I.; Lord, S. J.; Dey, G.; Wolfe, G. V.; Dudin, O.; Sukenik, S.; Katz, L. A.; Stedman, K. M.; Skruber, K.; Schulz, F.; Mullins, R. D.; Oliverio, A. M.

10.1101/2025.11.24.690213 — microbiology — Posted on 2025-11-24

1067 Uncovering structural determinants of peptide recognition by public and private T-cell receptors

Akil, C.; Peng, Y.; McCarthy, J.; Zhu, Y.; Hardenbrook, N.; Dong, D.; Antoun, E.; Yao, X.; Liu, G.; Chen, J.-l.; balikci, E.; Cioaca, R.; Yang, Y.; Mentzer, A. J.; Knight, J. C.; Fernandes, R.; Dong, T.; Zhang, P.

10.1101/2025.11.23.690020 — immunology — Posted on 2025-11-24

1068 Creating an energy efficient central metabolism for boosting biosynthesis without compromising cell growth of yeast

Ni, X.; Wang, H.; Zhang, M.; Gao, N.; Gao, J.; Yang, F.; Zhou, Y.

10.1101/2025.11.22.689960 — synthetic biology — Posted on 2025-11-24

1069 Deciphering the Structure and Mechanism of SaGpx: A Non-Canonical Glutathione Peroxidase from Staphylococcus aureus

Maji, S.; Shukla, M.; Bhattacharyya, S.

10.1101/2025.11.24.690144 — biophysics — Posted on 2025-11-24

1070 Molecular motors orchestrate pause-and-run dynamics to facilitate intracellular transport

Shen, Y.; Ori-McKenney, K. M.

10.1101/2025.11.22.689936 — biophysics — Posted on 2025-11-24

1071 Fragment-Based Development of NSP14 Exonuclease Inhibitors Confounded by Batch-to-Batch Variability

Coker, J. A.; Sun, R.; Polzer, P. M.; Romigh, T.; Goins, C. M.; Wang, N. S.; Jung, J. U.; Stauffer, S. R.

10.1101/2025.11.21.689747 — biochemistry — Posted on 2025-11-24

1072 Key residues in SARS-CoV-2 NSP3 hyper variable region are necessary to modulate early stress granule activity.

Alvarado, R. E.; Lokugamage, K. G.; Garvanska, D.; Estes, L. K.; Ahearn, Y. P.; McLeland, A.; Moayyed, A.; Lopez-Mendez, B. D.; Plante, J. A.; Plante, K. S.; Johnson, B. A.; Nilsson, J. S.; Menachery, V. D.

10.1101/2025.11.22.689758 — microbiology — Posted on 2025-11-24

1073 BarTn7: Optimizing Bacterial Lineage Tracking at Sub-Species Resolution for Population Dynamics in Ecological and Evolutionary Studies

Herbert, R. A.; Deutschbauer, A.

10.1101/2025.11.24.690285 — microbiology — Posted on 2025-11-24

1074 Decoding the fibroblast/mast cell signaling pathway of acupuncture

Xue, X.; Wang, R.; Sheng, W.; Pang, J.; Lu, D.; Yu, M.; lan, T.; Tseng, Y.

10.1101/2025.11.20.688774 — cell biology — Posted on 2025-11-24

1075 Contemporary HIV-1 envelope pseudovirus panels for detecting and assessing B cell lineages with broadly neutralizing antibody potential

Korber, B.; Seaman, M. S.; Mkhize, N. N.; Greene, K.; Gao, H.; Shen, X.; Domin, E.; Tang, H.; Theiler, J.; Wagh, K.; Moore, P. L.; Williamson, C.; Mullins, J. I.; Doria-Rose, N. A.; Montefiori, D.; Giorgi, E. E.

10.1101/2025.11.21.689752 — immunology — Posted on 2025-11-24

1076 Neonatal Platelets Differentiate Monocytes to a Myeloid Derived Suppressor Cell Phenotype

Maurya, P.; O'Reilly, D.; Hilt, Z. T.; Livada, A.; McGrath, K.; Li, C.; Ture, S. K.; Malloy, M.; Tun, E. T.; Palis, J.; Morrell, C. N.

10.1101/2025.11.21.689809 — immunology — Posted on 2025-11-24

1077 Effects of a novel proteasome inhibitor, UR238 on the tumor immune microenvironment and growth in epithelial ovarian cancer

Miller, J. P.; Zhang, N.; Kim, K.; Snyder, C. W.; McDowell, J. L.; Whittum, M. E.; Khazan, N.; Singh, N.; Strawderman, M.; Moore, R.; Singh, R.; Rowswell-Turner, R. B.

10.1101/2025.11.21.689729 — immunology — Posted on 2025-11-24

1078 Blood-based Transcriptomics Reveal Sex- and Amyloid-Modulated Biology of Plasma pTau217 in Preclinical Alzheimer's Disease

Seto, M.; Klinger, H. M.; Clifton, M.; Janve, V. A.; Brown, J. A.; Birkenbihl, C.; Coughlan, G. T.; Townsend, D. L.; Wang, T.-C.; Properzi, M.; Hanseeuw, B.; Chhatwal, J.; Yang, H.-S.; Rissman, R.; Aisen, P.; Cuppels, M.; Donohue, M. C.; Raman, R.; Johnson, K. A.; Sperling, R. A.; Dumitrescu, L.; Hohman, T. J.; Buckley, R. F.

10.1101/2025.11.21.689770 — neuroscience — Posted on 2025-11-24

1079 Visual perceptual learning enhances functional connectivity in retinotopic space

Bejjanki, V. R.; Turk-Browne, N. B.

10.1101/2025.11.21.689780 — neuroscience — Posted on 2025-11-24

1080 Negative-Valence Neurons in the Larval Zebrafish Pallium

Smith, C. D.; Du, Z.; Dempsey, W. P.; Fraser, S. E.; Truong, T. V.; Arnold, D. B.

10.1101/2025.11.21.689820 — neuroscience — Posted on 2025-11-24

1081 TDP-43 suppression of ATP8A2 cryptic splicing implicates phosphatidylserine-driven neuroinflammation in ALS/FTD

O'Connor, J. T.; Loo, H. Q.; Guo, C.; Pickles, S.; Sundali, S.; Jawahar, V. M.; Dickson, D. W.; Bloom, A. J.; Petrucelli, L.; Gitler, A. D.; Milbrandt, J.; DiAntonio, A.

10.1101/2025.11.21.689833 — neuroscience — Posted on 2025-11-24

1082 'Dispersification' of Agalinis (Orobanchaceae) into South America is associated with hummingbird pollination and perennial life history shifts

Pezzi, P. H.; Soltis, P. S.; Soltis, D. E.; Latvis, M.

10.1101/2025.11.21.689784 — plant biology — Posted on 2025-11-24

1083 Exhaled breath condensate proteomics using amphipols improves protein detection but reveals statistical challenges in respiratory disease biomarker discovery

Schillebeeckx, E.; Argentini, A.; Raskin, J.; Vanmeerbeeck, J.; Gevaert, K.; Lamote, K.; Fernandez, E.

10.1101/2025.11.21.689702 — pathology — Posted on 2025-11-24

1084 TAp73 mediates anti-tumor immunity through regulation of lipid metabolism in the lung tumor microenvironment

Ackerman, H. D.; Rubio, V. Y.; Davis, A. J.; Lockhart, J. H.; Hackel, N.; Jimenez, R. V.; Sierra-Mondragon, R. A.; Baldwin, J. R.; Carr, C.; Reiser, M.; Napoli, M.; Yu, X.; Cheng, C.-H.; Stewart, P. A.; Acevedo-Acevedo, S.; Checker, R.; Grammatikakis, I.; Su, X.; Wu, Y.; Gould, T.; Bailey, A.; Robinson, L. A.; Haura, E. B.; Koomen, J. M.; Rodriguez, P. C.; Flores, E. R.

10.1101/2025.11.21.689807 — cancer biology — Posted on 2025-11-24

1085 In vivo assessment of differential toxicity of cancer treatment drugs in Fanconi Anemia

Grompe, M.; Dorrell, C.; Burtness, B.; Cruz-Gomez, S.; MacMillan, A.

10.1101/2025.11.21.689800 — cancer biology — Posted on 2025-11-24

1086 Multimodal Approach for Identification and Validation of Hepatocellular Carcinoma Targets for Radiotheranostics

Homan, P.; Chung, J.-Y.; Lee, W.; Nambiar, D. M.; Sheehan-Klenk, J.; Makala, H.; Fayn, S.; Jacobson, O.; King, A. P.; Kim, K.; Kim, J. W.; Lee, S. R.; Cam, M.; Hewitt, S. M.; Wang, X. W.; Ho, M.; Escorcia, F. E.

10.1101/2025.11.21.689799 — cancer biology — Posted on 2025-11-24

1087 Sphingosine-1-phosphate receptor modulators resensitize FLT3-ITD acute myeloid leukemia cells with NRAS mutations to FLT3 inhibitors

Baer, M. R.; Chatterjee, A.; Ali, M. K. M.; Bailey, C. M.; Liu, Y.; Small, D.; Smith, C. C.; Traer, E. C.; Wang, Y.; Silvestri, G.

10.1101/2025.11.21.689510 — cancer biology — Posted on 2025-11-24

1088 Sequence-to-graph alignment based copy number calling using a network flow formulation

Magalhaes, H.; Weber, J.; Klau, G. W.; Marschall, T.; Prodanov, T.

10.1101/2025.11.21.689771 — bioinformatics — Posted on 2025-11-24

1089 MiRformer: a dual-transformer-encoder framework for predicting microRNA-mRNA interactions from paired sequences

Gu, J.; Chen, C.; Li, Y.

10.1101/2025.11.21.689769 — bioinformatics — Posted on 2025-11-24

1090 Inferring virtual cell environments using multi-agent reinforcement learning

Kalafut, N. C.; He, C.; Sheng, J.; Chandrashekar, P. B.; Choi, J. J.; Wang, D.

10.1101/2025.11.21.689815 — bioinformatics — Posted on 2025-11-24

1091 Accurate Probabilistic Reconstruction of Cell Lineage Trees from SNVs and CNAs with ScisTreeCNA

Zhang, H.; Wu, Y.

10.1101/2025.11.21.689819 — bioinformatics — Posted on 2025-11-24

1092 Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics

Wissel, D.; Sheynkman, G. M.; Robinson, M. D.

10.1101/2025.11.21.689818 — bioinformatics — Posted on 2025-11-24

1093 Deconvolution of Sparse-count RNA Sequencing Data for Tumor Cells Using Embedded Negative Binomial Distributions

Montierth, M.; Yan, H.; Xie, L.; Nemeth, K.; Pan, X.; Li, R.; Ercan, C.; Yang, P.; Sinjab, A.; Zhou, T.; Peng, F.; Singh, M.; Wang, L.; Kopetz, S.; Kadara, H.; Yuan, Y.; Calin, G.; Wang, W.

10.1101/2025.11.21.689822 — bioinformatics — Posted on 2025-11-24

1094 Acute immune modulation with poly-salicylic acid particles ameliorates pain and structural damage in post-traumatic osteoarthritis

Felder, M. L.; Lammlin, L.; Giannone, A. A.; Guevara, M. V.; Howser, S. C.; Smith, I. J.; Maerz, T.; Eniola-Adefeso, O.

10.1101/2025.11.21.689790 — bioengineering — Posted on 2025-11-24

1095 Nanobodies targeting hnRNPA2/B1 and tau

Pirhanov, A.; Rodriguez, C.; Tashakori-Asfestani, F.; Gonsoulin, R.; Santiago, R.; Tobunluepop, K.; Erhunmwunsee, E.; Puri, S.; Arbaciauskaite, M.; He, W.; Wolozin, B.; Cho, Y.

10.1101/2025.11.21.689763 — bioengineering — Posted on 2025-11-24

1096 Bioreactor-Enabled Extracellular Vesicle Production for Downstream Functional Engineering

Tripp, T. L.; Vasile, K.; Terrizzi, M.; Cisneros, E.; Volpatti, L. R.; Hisey, C.

10.1101/2025.11.21.689817 — bioengineering — Posted on 2025-11-24

1097 From Scattered to Focused: Task-Dependent Connectivity in Honey Bees, with Midge Swarms and Bird Flocks

Ahmed, I.; Islam, M. S.; Faruque, I. A.

10.1101/2025.11.21.689829 — animal behavior and cognition — Posted on 2025-11-24

1098 Moments of the length of sample genealogy and their applications

Fu, Y.-X.

10.1101/2025.11.21.689774 — evolutionary biology — Posted on 2025-11-24

1099 The form and function of a multi-functional weapon system in male and female burying beetles (Nicrophorus vespilloides)

Smith, J. M. L.; Catherall-Ostler, A. M.; Püffel, F.; Labonte, D.; Kilner, R. M.

10.1101/2025.11.21.689795 — evolutionary biology — Posted on 2025-11-24

1100 Molecular evolution of CO2-sensing ab1C neurons underlies divergent sensory responses in the Drosophila suzukii species group

Gadau, A.; Mills, S.; Jiang, X. Y. Z.; Li, C.; Svetec, N.; Xu, Z.; Li, W.; Nagel, K. I.; Zhao, L.

10.1101/2025.11.21.689786 — evolutionary biology — Posted on 2025-11-24

1101 The discovery and patterns of the underlying long-standing mild-effect mutator alleles in S. cerevisiae populations

Jiang, P.; Sudhesh, V.; Phan, M. M.-N.; Bansal, I.; Wheeler, C.; Herr, A. J.; Dunham, M. J.; Harris, K.

10.1101/2025.11.22.689970 — evolutionary biology — Posted on 2025-11-24

1102 Social media posts as a source of ecological information over time: using Twitter (X) as a proof of principle

Milodrowski, R.; Extavour, C.; Ylla, G.

10.1101/2025.11.21.689797 — ecology — Posted on 2025-11-24

1103 Functional insights into nucleoside diphosphate kinases encoded by two ndk paralogs in Waddlia chondrophila

Ghazi-Soltani, G.; Beghdadi, C. K.; Adams, S. E.; Greub, G.

10.1101/2025.10.15.682642 — microbiology — Posted on 2025-11-24

1104 A model of the cerebellum generates gait adaptations in a reflex-based neuromusculoskeletal model during split-belt walking

Fleischmann, S.; Shanbhag, J.; Miehling, J.; Wartzack, S.; Ong, C.; Eskofier, B. M.; Koelewijn, A. D.

10.1101/2024.12.12.628122 — neuroscience — Posted on 2025-11-24

1105 PP2A methylesterase, PME-1, and PP2A methyltransferase, LCMT-1, control sensitivity to impairments caused by injury-related oligomeric tau

Sundaresh, S. N.; Vogel, E. W.; Hue, C. D.; Zhang, H.; Staniszewski, A.; Berman, H. L.; Gill, Z.; Asam, K.; Liang, S.; Shen, L.; Gnanaprakash, M.; Acquarone, E.; Fa, M.; Kanaan, N. M.; Morrison, B.; Arancio, O.; Nicholls, R. E.

10.1101/2025.06.05.657660 — neuroscience — Posted on 2025-11-24

1106 Slow synaptic plasticity from the hippocampus underlies gradual mapping and fragmentation of novel spaces by grid cells

chen, l.; Dong, L. L.; Shin, J. H.; Shahid, F.; Malone, T. J.; Ma, Y.; Vasu, S. O.; Tien, N.-W.; Cekada, K.; Zhang, K. J.; Anderson, L.; Chandra, S.; Fiete, I.; Alvarez, V. A.; Gu, Y.

10.1101/2025.07.30.667696 — neuroscience — Posted on 2025-11-24

1107 Exploring the multifactorial causes and therapeutic strategies for anabolic resistance in sarcopenia: A systems modeling study

McColl, T. J.; Moore, D. R.; Emberly, E.; Church, D. D.; Clarke, D. C.

10.1101/2025.09.12.675977 — systems biology — Posted on 2025-11-24

1108 Spatial analysis of IPMNs defines a paradoxical KRT17-positive, low-grade epithelial population harboring malignant features

Li, J.; Macchia, J.; Elhossiny, A. M.; Arya, N.; Liang, J.; Kadiyala, P.; Branch, G. L.; Peterson, N.; Kwon, R.; Machicado, J. D.; Wamsteker, E.-J.; Schulman, A.; Philips, G.; Menees, S.; Xia, J. Y.; Singhi, A. D.; Sahai, V.; Fang, J. M.; Frankel, T. L.; Bednar, F.; Pasca di Magliano, M.; Shi, J.; Carpenter, E. S.

10.1101/2025.03.18.643943 — cancer biology — Posted on 2025-11-24

1109 Oncogenic PI3Kα variants reveal graded conformational spectrum with mutation-specific cryptic pockets

Jang, H.; yavuz, b. R.; Zhang, M.; Liu, Y.; Nussinov, R.

10.1101/2025.06.26.661751 — biophysics — Posted on 2025-11-24

1110 Synthetic cargo adaptors reveal molecular features that can enhance dynein activation

Siva, A.; Gillies, J. P.; de Borchgrave, A.; Garrott, S. R.; Mishra, R.; El Jbeily, R.; Clarke, R.; Conklin, C.; Gibson, D.; Zang, J. L.; DeSantis, M. E.

10.1101/2025.06.06.658359 — biophysics — Posted on 2025-11-24

1111 Using Deep Learning with Different Architectures to Recognize RNA:DNA Triplex Structures from Histone Modification Features

Tsenum, J. L.

10.1101/2025.09.16.676231 — bioinformatics — Posted on 2025-11-24

1112 Transcripts enriched in codons that trigger the P-site tRNA-mediated mRNA decay possess stable mRNA

Carneiro, R. L.; Palhano, F. L.

10.1101/2025.04.10.648249 — bioinformatics — Posted on 2025-11-24

1113 Recognition of distinct sleep states in Drosophila uncovers previously obscured homeostatic and circadian control of sleep.

Abhilash, L.; Evans, R.; Shafer, O. T.

10.1101/2025.06.23.661143 — animal behavior and cognition — Posted on 2025-11-24

1114 Predator-prey scaling laws support a suspension feeding lifestyle in Cambrian luolishaniid lobopodians

Richards, J.; Ortega-Hernandez, J.

10.1101/2025.11.05.686786 — paleontology — Posted on 2025-11-24

1115 Predicting RNA:DNA Triplex Structures from Sequence Features Using Deep Learning Architectures

Tsenum, J. L.

10.1101/2025.09.16.676176 — bioinformatics — Posted on 2025-11-24

1116 Fluctuating Selection among Individuals (FSI) as a Novel Genetic Drift in Molecular Evolution

Gu, X.

10.1101/2025.11.10.687654 — evolutionary biology — Posted on 2025-11-24

1117 Gene regulatory network determinants of rapid recall in human memory CD4+ T cells

Katko, A.; Korinfskaya, S.; Bejjani, A. T.; Owoeye, S. M.; Yang, Z. F.; Rudrapatna, A.; Potter, S.; Wayman, J. A.; Kotliar, M.; Kottyan, L. C.; Barski, A.; Miraldi, E. R.

10.1101/2025.04.06.646912 — systems biology — Posted on 2025-11-24

1118 Glycolysis-stratified coordination of fatty acid and glutamine metabolism in pancreatic ductal adenocarcinoma

Fareed, S.

10.1101/2025.09.14.676164 — cancer biology — Posted on 2025-11-24

1119 Collective bacterial condensation is fundamentally constrained by the emergence of active turbulence

Livne, N.; Vaknin, A.

10.1101/2025.07.20.665738 — biophysics — Posted on 2025-11-24

1120 Systematic characterization of existing and novel inducible transgenic systems in human pluripotent stem cells after prolonged differentiation

Gallagher, M. D.; Khalil, A. S.; Liu, Q.; Lungjangwa, T.; Drews, A.; Hanan, B. F.; List, M.; Hardart, H.; Mooney, D. J.; Jaenisch, R.

10.1101/2025.10.17.683097 — bioengineering — Posted on 2025-11-24

1121 Understanding the Causal Impact of Elevated Maternal Stress During Pregnancy: A Systematic Literature Review of Guinea Pig Models

Wilson, R.; Messiah, C.; Louis-Jacques, A. F.

10.1101/2025.07.30.667555 — physiology — Posted on 2025-11-24

1122 Infected host competence overshadows heterogeneity in susceptibility in shaping experimental epizootics

Perez-Umphrey, A. A.; Langwig, K. E.; Adelman, J. S.; Childs, L. M.; Garrett-Larsen, J.; Hawley, D. M.; Fleming-Davies, A. E.

10.1101/2025.01.15.632224 — ecology — Posted on 2025-11-24

1123 Spontaneous spiking statistics form unique area-specific fingerprints and reflect the hierarchy of cerebral cortex

Morales-Gregorio, A.; Gutzen, R.; Paneri, S.; Sapountzis, P.; Kleinjohann, A.; Grün, S.; Riehle, A.; Chen, X.; Brochier, T.; Gregoriou, G. G.; Kilavik, B. E.; van Albada, S. J.

10.1101/2025.05.13.653871 — neuroscience — Posted on 2025-11-24

1124 Optimizing short-channel regression in fNIRS: an empirical evaluation with ecological audiovisual stimuli

Lemaire, Y.; Barone, P.; Strelnikov, K.; Deguine, O.; Caclin, A.; Ginzburg, J.

10.1101/2025.05.23.655796 — neuroscience — Posted on 2025-11-24

1125 A retinotopic reference frame for space throughout human visual cortex

Szinte, M.; de Hollander, G.; Aqil, M.; Verissimo, I.; Dumoulin, S.; Knapen, T.

10.1101/2024.02.05.578862 — neuroscience — Posted on 2025-11-24

1126 Alpha/Beta oscillations reflect the dynamics of the oculomotor system: a new perspective on subsequent memory effects

Wu, X.; Popov, T.; Beilner, T.; Fearns, N.; Vollmar, C.; Kaufmann, E.; Remi, J.; Staudigl, T.

10.1101/2025.07.29.667451 — neuroscience — Posted on 2025-11-24

1127 Modular nanostructure design of DX-tile DNA nano-stars (DX-DNAns) controls self-organization and force propagation of DX-based DNA Hydrogels yielding a soft matter metamaterial with programmable viscoelastic properties and integrated functionalization

Bush, J.

10.1101/2025.03.25.645358 — bioengineering — Posted on 2025-11-24

1128 Modeling cetacean eDNA distribution along the Washington coast using metabarcoding from opportunistic samples and generalized additive models

Valdivia-Carrillo, T.; Van Cise, A.; Shaffer, M.; Parsons, K.; Im, A.; Shelton, A.; Jacobson, E. K.; Wells, A.; Ramon-Laca, A.; Nichols, K. M.; Kelly, R. P.

10.1101/2025.11.21.689289 — genomics — Posted on 2025-11-24

1129 Ferroptosis governs lymphatic vessel growth and regression

Drekolia, M.-K.; Wang, D.; Chen, Y.; Du, Y.; Wittig, J.; Xu, R.; Schilling, D.; Aliraj, B.; Mettner, J.; Gupta, L.; Xu, C.; Guenther, S.; Cetic, R.; Matthess, Y.; Fleming, I.; Kaulich, M.; Dobreva, G.; Weigert, A.; Dick, T. P.; Dikic, I.; Stolz, A.; Yaniv, K.; Linkermann, A.; Hu, J.; Bibli, S.-I.

10.1101/2025.11.18.689033 — cell biology — Posted on 2025-11-24

1130 ACUTE AMYLOID-B 40 EXPOSURE DISRUPTS METABOLIC INSULIN SIGNALING IN BLOOD-BRAIN BARRIER ENDOTHELIAL CELLS

Nelson, D.; Kalari, K. R.; Kandimalla, K. K.

10.1101/2025.11.21.689761 — molecular biology — Posted on 2025-11-24

1131 The LacI hinge region balances binding stability against inducibility

Yuan, J.; Luking, M.; Zikrin, S.; Sen, B.; Marklund, E.; Spoel, D. v. d.; Fange, D.; Elf, J.

10.1101/2025.05.07.652604 — molecular biology — Posted on 2025-11-24

1132 Isoquinoline Alkaloids from Traditional Medicinal Plants of the Papaveraceae as a Third Line of Defense Against Bacterial Ocular Infections

Dziegielewska, M.; Zielinska, S.; Dudek, B.; Brozyna, M.; Kozlowska, W.; Matkowski, A.; Bartoszewicz, M.; Sun, Y.; Junka, A. F.

10.1101/2025.11.21.689706 — microbiology — Posted on 2025-11-24

1133 Escape from antimicrobial CRISPR-Cas9 in E. coli ST131 depends on the genetic context of the target gene.

Morros-Bernaus, C.; Westley, J.; Wyrsch, E. R.; Djordjevic, S. P.; Zhang, L.; Leonard, A.; Gaze, W.; Sünderhauf, D.; van Houte, S.

10.1101/2025.08.04.668416 — microbiology — Posted on 2025-11-24

1134 Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants

Robertson, S.; Mosca, A.; Ashraf, S.; Corral, A.; Alegria Terrazas, R.; Arnton, C.; Thorpe, P.; Morris, J.; Hedley, P. E.; Babbi, G.; Savojardo, C.; Martelli, P. L.; Moller, F.; Nielsen, H.; Leekitcharoenphon, P.; Aarestrup, F. M.; Halder, R.; Laczny, C. C.; Wilmes, P.; Pietrantonio, L.; Di Cillo, P.; Catara, V.; Abbott, J. C.; Bulgarelli, D.

10.1101/2025.07.14.664720 — plant biology — Posted on 2025-11-24

1135 Characterization of hippocampal subfields using histology-based annotated postmortem MRI: Lessons for in vivo segmentation II

10.1101/2025.11.21.689744 — neuroscience — Posted on 2025-11-24

1136 Genetic risk implicating endolysosomal network genes correlates with endolysosomal dysfunction across neural cell types in Alzheimer's disease

Mamde, S.; Rose, S.; Prater, K. E.; Cochoit, A.; Lin, Y. F.; Smith, I.; Johnson, C. S. C.; Reid, A.; Qiu, W.; Strohbehn, S.; Keene, C. D.; Rolf, B.; Lin, K.; Lee, S.-I.; Garden, G.; Blue, E.; Young, J. E.; Jayadev, S.

10.1101/2025.03.16.643481 — neuroscience — Posted on 2025-11-24

1137 Functional muscle networks reveal the mechanistic effects of post-stroke rehabilitation on motor impairment and therapeutic responsiveness

O'Reilly, D.; Pregnolato, G.; Turolla, A.; Kiper, P.; Delis, I.; Severini, G.

10.1101/2025.08.17.670726 — neuroscience — Posted on 2025-11-24

1138 Physics of low complexity polymers: patterning, polymer collapse and bulk microphases

Girard, M.

10.1101/2025.11.21.689704 — biophysics — Posted on 2025-11-24

1139 Use of High Pressure NMR Spectroscopy to Rapidly Identify Proteins with Internal Ligand-Binding Voids

Gagne, D.; Azad, R.; Aramini, J. M.; Xu, X.; Isiorho, E. A.; Edupuganti, U. R.; Williams, J. P.; Marcelino, L. P.; Johnson, B. A.; Akasaka, K.; Gardner, K. H.

10.1101/2020.08.25.267195 — biophysics — Posted on 2025-11-24

1140 Reinforcement learning for adaptive control of phenotypically heterogeneous bacterial populations

Kratz, J.; Wen, Z.; Banerjee, S.; Carja, O.

10.1101/2025.11.21.689767 — bioinformatics — Posted on 2025-11-24

1141 Continuous Motility Fingerprints from Gaussian Mixture Models Reveal Hidden Sperm Heterogeneity

Lamm, J.

10.1101/2025.11.20.689493 — bioinformatics — Posted on 2025-11-24

1142 Discovering the unseen: a performance comparison of taxonomic classification methods under unknown DNA barcodes

Orsholm, J.; Zito, A.; Somervuo, P.; Harrison, J. P.; Koskela, M.; Ovaskainen, O.; Braga, M. P.; Chazot, N.; Roslin, T.; Furneaux, B.

10.1101/2025.10.13.681976 — bioinformatics — Posted on 2025-11-24

1143 Public Cohort Analysis Identifies Thyroglobulin Variants as Hypothyroidism Risk Factors

Hermanson, J. N.; Hudson, A. D.; Plate, L.

10.1101/2025.11.21.689591 — biochemistry — Posted on 2025-11-24

1144 CpG-induced regions associated compositional stratification of human essential proteins through mathematical genomics

Singh, S.; Hungyo, K.; Hassan, S. S.; Uversky, V. N.

10.1101/2025.11.21.689746 — genomics — Posted on 2025-11-24

1145 Multi-omics Integration with GWAS Unveils Molecular Mechanistic Insights for Type 2 Diabetes

Abbas, M.; Toh, H.; Martin, P. M.; Lindsey, M. L.; Melese, M. T.; Oteng, A.-B.; Gaye, A.

10.1101/2025.11.21.689764 — genomics — Posted on 2025-11-24

1146 High-quality genome assembly and functional annotation of Hiroshima-derived Pacific oyster Magallana gigas

Imai, M.; Kanda, M.; Mino, M.; Koike, K.; Okuhara, K.; Bono, H.

10.1101/2025.11.20.688662 — genomics — Posted on 2025-11-24

1147 A scaling theory of trait evolution

Jennings, W. B.

10.1101/2025.11.18.689082 — evolutionary biology — Posted on 2025-11-24

1148 Chemogenetic modulation of luciferase emission color for imaging and sensing

Manirakiza, H.; Shpinov, Y.; Gontier, A.; El Hajji, L.; Jullien, L.; Gautier, A.

10.1101/2025.11.21.689291 — cell biology — Posted on 2025-11-24

1149 Machine Learning Analysis of the Human Initiator Reveals New Insights into the Interrelationships between the TATA box, Initiator, and DPR

Rhyne-Carrigg, T. E.; Vo ngoc, L.; Medrano, C.; Gillespie, K. E.; Kadonaga, J. T.

10.1101/2025.11.21.689830 — molecular biology — Posted on 2025-11-24

1150 Cryo-EM structure of a single-chain β1-adrenoceptor - AmpC β-lactamase fusion protein

Collu, G.; Mohammed, I.; Lafita, A.; Bierig, T.; Poghosyan, E.; Bliven, S.; Afanasyev, P.; Benoit, R. M.

10.1101/2021.09.25.461805 — molecular biology — Posted on 2025-11-24

1151 Alcohols inhibit glucose transporters noncompetitively at a constant membrane concentration according to lipid theory

Uesono, Y.

10.1101/2025.11.20.689647 — pharmacology and toxicology — Posted on 2025-11-24

1152 Evolution of a Pyroptosis-Apoptosis crosstalk drives non-canonical inflammasome signalling.

Grant, S.; Nicholson, E.; Chen, Z. H. X.; Robson, C.; Viswanathan, B.; Chang, Y.; Sung, A. W.; Patel, P.; Kleppen, J.; Ozdenya, T.; Chen, K.; Spicer, C. D.; Boucher, D.

10.1101/2025.11.01.685735 — biochemistry — Posted on 2025-11-24

1153 Identity-by-descent captures Shared Environmental Factors at Biobank Scale

10.1101/2025.05.03.652048 — genomics — Posted on 2025-11-24

1154 Single-cell disentangled representations for perturbation modeling and treatment effect estimation

Sun, J.; Stojanov, P.; Zhang, K.

10.1101/2025.11.21.689783 — genomics — Posted on 2025-11-24

1155 Exposure to a mixture of organic pollutants in a threatened freshwater turtle Emys orbicularis: effects of age, sex, and temporal variation

Merleau, L.-A.; Lourdais, O.; Olivier, A.; Vittecoq, M.; Alliot, F.; Traore, S.; Leray, C.; Goutte, A.

10.1101/2025.06.29.658864 — ecology — Posted on 2025-11-24

1156 Less is more: uncompensated gravity torques for intuitive EMG-based assistance with a robotic exoskeleton

Quesada, L.; Verdel, D.; Bruneau, O.; Berret, B.; Amorim, M.-A.; Vignais, N.

10.1101/2025.11.21.689589 — neuroscience — Posted on 2025-11-24

1157 Metabolic imbalance limits fermentation in microbes engineered for high-titer ethanol production

Sharma, B. D.; Thusoo, E.; Stevenson, D. M.; Amador-Noguez, D.; Lynd, L.; Olson, D. G.

10.1101/2025.11.21.689677 — systems biology — Posted on 2025-11-24

1158 Imputation strategy for population DNA methylation sequencing data

Duplan, A.; Brandt, S.; Garnier, A.; Tost, J.; Sanchez, L.; Duvaux, L.; Maury, S.; Durufle, H.

10.1101/2025.03.21.644107 — bioinformatics — Posted on 2025-11-24

1159 BoltzGen: Toward Universal Binder Design

Stark, H.; Faltings, F.; Choi, M.; Xie, Y.; Hur, E.; O'Donnell, T. J.; Bushuiev, A.; Ucar, T.; Passaro, S.; Mao, W.; Reveiz, M.; Bushuiev, R.; Pluskal, T.; Sivic, J.; Kreis, K.; Vahdat, A.; Ray, S.; Goldstein, J. T.; Savinov, A.; Hambalek, J. A.; Gupta, A.; Taquiri-Diaz, D. A.; Zhang, Y.; Hatstat, A. K.; Arada, A.; Kim, N. H.; Tackie-Yarboi, E.; Boselli, D.; Schnaider, L.; Liu, C. C.; Li, G.-W.; Hnisz, D.; Sabatini, D. M.; DeGrado, W. F.; Wohlwend, J.; Corso, G.; Barzilay, R.; Jaakkola, T.

10.1101/2025.11.20.689494 — bioengineering — Posted on 2025-11-24

1160 Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCF

Henikoff, S.; Henikoff, J. G.

10.1101/2025.11.10.687711 — genomics — Posted on 2025-11-24

1161 Unsupervised visual learning is revealed for task-irrelevant natural scenes due to reduced attentional suppression effects in visual areas

Watanabe, T.; Sasaki, Y.; Zama, T.; Matthews, J. R.; Ogawa, D.; Shibata, K.

10.1101/2024.07.31.605957 — neuroscience — Posted on 2025-11-24

1162 Palaeoproteomics reveals bovine carcass processing with 6,000-year-old flint tools

Burnett, A.; Halbrücker, E.; Engels, I.; Dennis, R. S.; De Groote, I.; Deforce, D.; Cristiani, E.; Crombe, P.; Dhaenens, M.

10.1101/2025.09.29.679186 — paleontology — Posted on 2025-11-24

1163 Thermally activated irreversible homogenization of G-quadruplexes in an ALS/FTD-associated nucleotide expansion

Ross, D.; Lewis, O.; McLean, O.; Bhanot, S.; Donahue, S.; Baker, R.; Dias, R.; Eagerton, D.; Mohanty, V.; Mohanty, B. K.

10.1101/2025.06.02.657482 — biophysics — Posted on 2025-11-24

1164 Accurate highly variable gene selection using RECODE in transcriptome data analysis

Imoto, Y.

10.1101/2025.06.23.661026 — bioinformatics — Posted on 2025-11-24

1165 InfluenceNet: Encoding Motif Influence for Interpretable Modeling of Cis-Regulatory Syntax

Hu, J.; Koes, D. R.; Chikina, M.

10.1101/2025.11.20.689553 — bioinformatics — Posted on 2025-11-24

1166 Relaxed selection diminishes social memory and expression of host defences against cuckoos

Tolman, D.; Rönkä, K.; Kluen, E.; Jolkkonen, J.; Di Bari, P.; Ientile, R.; Campobello, D.; Thorogood, R.

10.1101/2024.01.14.575589 — animal behavior and cognition — Posted on 2025-11-24

1167 Experimentally mimicking long term infections of Magallana gigas with the OsHV-1 virus reveals evolution through positive selection

Pelletier, C.; Faury, N.; Mege, M.; Degremont, L.; Hattinguais, M.; Vidal-Dupiol, J.; Chevignon, G.; Jacquot, M.; Morga, B.

10.1101/2025.02.07.637049 — evolutionary biology — Posted on 2025-11-24

1168 Uncoupling the TFIIH Core and Kinase Modules Leads To Misregulated RNA Polymerase II CTD Serine 5 Phosphorylation

Giordano, G.; Buratowski, R.; Jeronimo, C.; Poitras, C.; Robert, F.; Buratowski, S.

10.1101/2023.09.11.557269 — molecular biology — Posted on 2025-11-24

1169 Cellular and Spatial Drivers of Unresolved Injury and Functional Decline in the Human Kidney

Lake, B. B.; Melo Ferreira, R.; Hansen, J.; Menon, R.; Basta, J.; Thiessen Philbrook, H.; Reinert, S.; Fallegger, R.; Lagwankar, A. K.; Chen, X.; Maity, S.; Djambazova, K. V.; Gorman, B. L.; Lucarelli, N.; Gisch, D. L.; Schmidt, I. M.; Nair, V.; Alakwaa, F.; Kefaloyianni, E.; Zhang, B.; Knoten, A. L.; Kaushal, M.; Otto, E. A.; Farrow, M. A.; Diep, D.; Velickovic, D.; Sabo, A. R.; Cole, E.; Tamayo, I.; Tanevski, J.; Conklin, K. Y.; Sealfon, R. S. G.; He, Y.; Brennan, M.; Robbins, L.; Cheng, Y.-H.; Bitzer, M.; Surapaneni, A.; Menez, S.; Kharchenko, P. V.; Alpers, C. E.; Balis, U. G. J.; Barisoni

10.1101/2025.09.26.678707 — molecular biology — Posted on 2025-11-24

1170 Nutrient deprived growth of Streptomyces promotes foraging growth and enhanced antimicrobial activity

Soderholm, N.; Tanner, H.; Sandblad, L.

10.1101/2024.04.15.589617 — microbiology — Posted on 2025-11-24

1171 Corylus avellana disease management: using metagenomics to illuminate the rhizosphere microbiome of hazelnut

Robinson, J. K.; Steele, J.; Molnar, T. J.; Regan, S.; diCenzo, G. C.

10.1101/2025.10.22.684018 — microbiology — Posted on 2025-11-24

1172 Histone H2A Ubiquitination Mediates the Establishment of Reactivation-Competent HSV-1 Latent Infection

Boehlke, J. M.; Dochnal, S. A.; Misra, C. S.; Francois, A.; Boutell, C.; Cliffe, A. R.

10.1101/2025.11.23.690028 — microbiology — Posted on 2025-11-24

1173 Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression

Dearborn, J. S.; Frankiw, L.; Limoge, D. S.; Burns, C. H.; Vlach, L.; Milletich, P.; Kirch, T.; Miller, Z. D.; Dowell, W.; Languon, S.; Garcia-Flores, Y.; Cockrell, R. C.; Baltimore, D.; Majumdar, D.

10.1101/443796 — immunology — Posted on 2025-11-24

1174 BlueBerry: Closed-loop wireless optogenetic manipulation in freely moving animals

Nourizonoz, A.; Girard, B.; Guyoton, M.; Galinanes, G.; Thurnherr, R.; Pellat, S.; Bellone, C.; Huber, D.

10.1101/2025.01.30.635697 — neuroscience — Posted on 2025-11-24

1175 Two-photon characterisation of long-Stokes-shift dye ATTO 490LS for single-laser multicolour imaging

Cheung, K. Y.; Wu, Y.; Lee, S. Y.; Zhang, X.; Fukuda, M.; Suresh, D. D.; Claridge-Chang, A.

10.1101/2025.11.21.689649 — neuroscience — Posted on 2025-11-24

1176 Locomotion Selectively Amplifies Activity of Sensitizing Neurons in Primary Visual Cortex

Hinojosa, A.; Kosiachkin, Y.; Dominiak, S.; Evans, B.; Lagnado, L.

10.1101/2025.07.24.666602 — neuroscience — Posted on 2025-11-24

1177 Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage

Huang, Z.; Luo, S.; Wang, Z.; Zhang, Z.; Jiang, B.; Nie, Q.; Zhang, J.

10.1101/2024.07.10.602845 — systems biology — Posted on 2025-11-24

1178 In Silico Investigation of the Role of Local and Global Inflammation-Driven Feedback in Myelopoiesis and Clonal Cell Expansion

Umar, Y. J.; Savvopoulos, S. V.; Pitsalidis, C.; Mitroulis, I.; Hatzikirou, H.

10.1101/2025.08.15.670507 — systems biology — Posted on 2025-11-24

1179 The mRNA covalent modification dihydrouridine regulates transcript turnover and photosynthetic capacity during plant abiotic stress

Yu, L.; Melandri, G.; Dittrich, A. C.; Calleja, S.; Rozzi, B.; Ganguly, D. R.; Palos, K.; Srinivasan, A.; Brewer, E. K.; Fischer, H.; Obata, T.; Elgawad, H. A.; Beemster, G. T. S.; Henderson, R.; Garcia, C. D.; Zhang, X.; Stern, D.; Eveland, A.; Schroeder, S. J.; Skirycz, A.; Lyons, E.; Arnold, E. A.; Gregory, B. D.; Nelson, A. D. L.; Pauli, D.

10.1101/2025.01.17.633510 — plant biology — Posted on 2025-11-24

1180 Humanized glioblastoma patient-derived orthotopic xenografts recreate a locally immunosuppressed human immune ecosystem amenable to immunotherapeutic modulation

Moreno-Sanchez, P. M.; Oudin, A.; Kisakol, B.; Dussmann, H.; Klein, E.; Baus, V.; Rolin, C.; Seguin-Devaux, C.; Rezaeipour, M.; Poli, A.; Michelucci, A.; Paggetti, J.; Moussay, E.; Prehn, J. H.; Niclou, S. P.; Golebiewska, A.

10.1101/2025.11.20.689484 — cancer biology — Posted on 2025-11-24

1181 De novo identification of protein domains in cryo-electron tomography maps from AlphaFold2 models

Lu, Y.; Chen, G.; Sun, F.; Zhu, Y.; Zhang, Z.

10.1101/2024.11.21.623534 — biophysics — Posted on 2025-11-24

1182 BC-Design: A Biochemistry-Aware Framework for Inverse Protein Design

Tang, X.; Wu, F.; Liu, Y.; Ye, X.; Su, A.; Panescu, A.; Li, G.; Shao, Y.; Xu, D.; Gerstein, M.

10.1101/2024.10.28.620755 — bioinformatics — Posted on 2025-11-24

1183 Quantitative mapping of methionine sensitivity to oxidation in the copper-bound PcuC chaperone

Tarrago, L.; Molinelli, L.; Belghazi, M.; Tribout, M.; Lemaire, D.; Legrand, P.; Grosse, S.; Pignol, D.; Sabaty, M.; Tron, T.; Arnoux, P.

10.1101/2025.09.11.675508 — biochemistry — Posted on 2025-11-24

1184 A partner switch from CDS2 to RAB1A redirects MBOAT7 to inhibit DGAT2-mediated lipid droplet growth

Xu, J.; Zhang, J.; Wang, W.; Su, H.; Chen, S.; Ding, M.; Huang, X.

10.1101/2025.08.26.672501 — cell biology — Posted on 2025-11-24

1185 Pangenome Analysis of Proteus mirabilis Reveals Lineage-Specific Antimicrobial Resistance Profiles and Discordant Genotype-Phenotype Correlations

Deka, N.; Brauer, A. L.; Connerton, K.; Hanson, B. M.; Walker, J. N.; Armbruster, C. E.

10.1101/2025.11.21.689858 — microbiology — Posted on 2025-11-24

1186 High affinity cross-context cellular assays reveal novel protein-protein interactions of peripheral myelin protein of 22 kDa

Stausberg, D.; Moshkovskii, S.; Arlt, F. A.; Fledrich, R.; Stassart, R. M.; Nave, K.-A.; Urlaub, H.; Ewers, D.; Sereda, M. W.

10.1101/2025.09.03.673966 — neuroscience — Posted on 2025-11-24

1187 Tau, amyloid-beta and alpha-synuclein co-pathologies synergistically enhance neuroinflammation and neuropathology

Webster, J. M.; Yang, Y.-T.; Miller, A. T.; Zane, A.; Scholz, K.; Stone, W. J.; Corbin-Stein, N. J.; Mudium, N.; Won, W.-J.; Stoll, A. C.; Greathouse, K. M.; Cooper, N. H.; Long, L. F.; Manuel, P. N.; Herskowitz, J. H.; Yacoubian, T. A.; Tyrrell, D. J.; Sandoval, I. M.; Manfredsson, F. P.; Kordower, J. H.; Harms, A. S.

10.1101/2024.10.13.618101 — neuroscience — Posted on 2025-11-24

1188 Covert spatial attention is uniform across cardinal meridians despite differential adaptation

Lee, H.-H.; Carrasco, M.

10.1101/2025.09.30.676904 — neuroscience — Posted on 2025-11-24

1189 Characterizing neuronal population geometry with AI equation discovery

Tilbury, R.; Kwon, D.; Haydaroglu, A.; Ratliff, J.; Schmutz, V.; Carandini, M.; Miller, K. J.; Stachenfeld, K.; Harris, K. D.

10.1101/2025.11.12.688086 — neuroscience — Posted on 2025-11-24

1190 Small heat shock protein HSPB8 interacts with a pre-fibrillar TDP43 low complexity domain species to delay fibril formation

Jami, K. M.; Corbett, K.; Farb, D. C.; Osumi, K. M.; Shafer, C. C.; Criscione, S.; Murray, D. T.

10.1101/2025.01.28.635368 — biophysics — Posted on 2025-11-24

1191 scRegulate: Single-Cell Regulatory-Embedded Variational Inference of Transcription Factor Activity from Gene Expression

Zandigohar, M.; Rehman, J.; Dai, Y.

10.1101/2025.04.17.649372 — bioinformatics — Posted on 2025-11-24

1192 Identification of Distinct Topological Structures From High-Dimensional Data

Xu, B.; Braun, R.

10.1101/2025.08.26.672446 — bioinformatics — Posted on 2025-11-24

1193 fpocketR: A platform for identification and analysis of ligand-binding pockets in RNA

Veenbaas, S. D.; Felder, S.; Weeks, K. M.

10.1101/2025.03.25.645323 — bioinformatics — Posted on 2025-11-24

1194 Spatial Image Gradient Estimation from the Diffusion MRI Profile

Aganj, I.; Feiweier, T.; Kirsch, J. E.; Fischl, B. R.; van der Kouwe, A. J.

10.1101/2025.06.06.658348 — bioengineering — Posted on 2025-11-24

1195 Major histocompatibility complex class II-expressing bone marrow megakaryocytes activate CD4+ T cells and induce regulatory T cell fate

Camacho, V.; Wang, K. G.; Hanc, P.; Carminita, E.; Becker, I. C.; Lee, D. H.; Maggi, J.; Falchetti, M.; Barrachina, M. N.; von Andrian, U.; Carrascal, M.; Italiano, J. E.; Machlus, K. R.

10.1101/2025.11.21.689743 — immunology — Posted on 2025-11-24

1196 Regulatory logic of neuronal identity specification in Drosophila

Coyne, R.; Treese, M.; Chen, Y.-C.; Lake, C.; Tabi, O. B.; Rajesh, R.; Hassan, H.; Li, H.; Desplan, C.; Ozel, M. N.

10.1101/2025.09.01.673531 — neuroscience — Posted on 2025-11-24

1197 Integrating physiology and transcriptomics reveals the mechanisms underlying the differences in cotton (Gossypium hirsutum L.) growth and development under different photoperiods

Zhang, N.; Liu, Y.; Dai, H.; Yi, P.; Cheng, W.; Zhan, X.; Liu, A.; Tu, X.

10.1101/2025.11.21.689390 — physiology — Posted on 2025-11-24

1198 LongPhase-S: purity estimation and variant recalibration with somatic haplotying for long-read sequencing

Ho, M.-E.; Zheng, Z.; Luo, R.; Chiang, H.-H.; Huang, Y.-T.

10.1101/2025.11.20.689492 — bioinformatics — Posted on 2025-11-24

1199 Patient induced pluripotent stem cells identify specificities of a reticular pseudodrusen phenotype in age-related macular degeneration

Hall, J. C.; Sudhakar, K. K.; Daniszewski, M.; Senabouth, A.; Abbott, C. J.; Liang, H. H.; Kumar, H.; Lidgerwood, G. E.; Mirzaei, M.; Ma, J.; Atkinson, T.; Hirokawa, Y.; Nandrot, E. F.; Barnett, A.; Cazevieille, C.; Manes, G.; Mountford, S.; Thompson, P.; Fletcher, E. L.; Wu, Z.; Bahlo, M.; Ansell, B.; Paull, D.; Hewitt, A. W.; Guymer, R. H.; Powell, J.; Pebay, A.

10.1101/2025.11.19.689393 — genetics — Posted on 2025-11-24

1200 Brazil Seed Transfer Zones: Supporting Seed Sourcing for Climate-Resilient Ecosystem Restoration

Silva, M.; Junqueira, A.; Guimaraes, P.; Celentano, D.; Murer, B.; Fremout, T.; Thomas, E.; Kettle, C.; Damasceno, E.; Medeiros, A.; Dutra-Silva, R.; Borghetti, F.; Pina-Rodrigues, F.; Gomes, A.; Maioli, V.; Pennington, T.; Rowland, L.; Malta, E.

10.1101/2025.11.20.689464 — ecology — Posted on 2025-11-24

1201 Loss of SPECC1L in cranial neural crest cells results in increased hedgehog signaling and frontonasal dysplasia

Tran, A. J.; Hufft-Martinez, B. M.; Thalman, D. N.; Maili, L.; McKinney, S.; Goering, J. P.; Trainor, P. A.; Saadi, I.

10.1101/2025.11.21.689834 — developmental biology — Posted on 2025-11-24

1202 Cytokine and Immunoglobulin Dynamics in Phage Therapy: Insights from Clinical Cases

Ritter, S. R.; Clark, J. R.; Salazar, K. C.; Aslam, S.; Maresso, A. W.

10.1101/2025.11.21.689765 — microbiology — Posted on 2025-11-24

1203 Learning dynamically regulates stimulus discrimination of ventral striatal D1 receptor expressing neurons

Daw, T. B.; Cao, J.; Li, R.; Masmanidis, S. C.

10.1101/2025.11.21.689812 — neuroscience — Posted on 2025-11-24

1204 Spatial patterning of transcriptional and regulatory programs in the primate subcortex

Dan, S.; Turner, M. A.; DeBerardine, M.; Caceres, L.; Nieto, V. E.; Schembri, J.; Levandowski, K.; Cardenas, C.; Wang, N.; Li, C.; Basu, S.; Zheng, H.; Liu, X.; Hollt, T.; Feliciano, J.; Zhang, Q.; Nakamoto, R.; McMillen, D. A.; Martin, N.; Cuevas, N. V.; Olsen, P.; Nagra, J.; Campos, J.; VanNess, M. M.; Waters, J.; Ransford, S.; Juneau, Z.; Hastings, S.; Barta, S.; Ruiz, A.; Ariza, J.; Raphael, B. J.; Zeng, H.; Lein, E. S.; Lelieveldt, B.; Feng, G.; Long, B.; Krienen, F. M.

10.1101/2025.11.22.689869 — neuroscience — Posted on 2025-11-24

1205 A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia

Hewitt, M. N.; Turner, M. A.; Johansen, N.; McMillen, D. A.; Dan, S.; DeBerardine, M.; Ruiz, A.; Huang, M.; Quon, J.; Fu, Y.; Kapen, I.; Barta, S.; Martin, N.; Cuevas, N. V.; Olsen, P.; Nagra, J.; Campos, J.; VanNess, M. M.; Ransford, S.; Juneau, Z.; Hastings, S.; Ching, L.; Kunst, M.; Basu, S.; Hollt, T.; Li, C.; Lelieveldt, B.; Yazdani, F.; Zhang, Q.; Levandowski, K.; Feng, G.; Rosen, B.; Glasser, M. F.; Hayashi, T.; Garcia, A. D.; Kana, O.; Maltzer, Z. M.; Campagnola, L.; Jarsky, T.; Kruse, L.; Freiwald, W.; Keene, C. D.; Van Essen, D. C.; Ariza, J.; Waters, J.; Krienen, F. M.; Bakken, T. E

10.1101/2025.11.22.688128 — neuroscience — Posted on 2025-11-24

1206 Localized mRNAs and protein synthesis in cortical layer 1

Spano, T.; Nassim-Assir, B.; Kaulich, E.; Tushev, G.; Fürst, N.; Will, H.; Maric, L.; Ciirdaeva, E.; Schuman, E. M.

10.1101/2025.11.23.689989 — neuroscience — Posted on 2025-11-24

1207 Independent Lateralization of Language, Attention, and Numerical Cognition Across Task and Rest

Labache, L.; Hesling, I.; Zago, L.

10.1101/2025.11.23.690045 — neuroscience — Posted on 2025-11-24

1208 Proteogenomic profiling of soft tissue leiomyosarcoma reveals distinct molecular subtypes with divergent outcomes and therapeutic vulnerabilities

Tanaka, A.; Ogawa, M.; Otani, Y.; Hendrickson, R. C.; Zhuoning, L.; Agaram, N. P.; Klimstra, D. S.; Wang, J. Y.; Roehrl, M. H. A.

10.1101/2025.11.19.689365 — cancer biology — Posted on 2025-11-24

1209 Transcriptomic module fingerprint reveals heterogeneity of whole blood transcriptome in type 1 diabetic patients

Valentim, F. L.; Konza, O.; Velasquez, A.; Saadawi, A.; Patel, N.; Lorenzon, R.; Tchitchek, N. T.; Mariotti-Ferrandiz, E.; Klatzmann, D.; Six, A.

10.1101/2025.11.19.689306 — bioinformatics — Posted on 2025-11-24

1210 Determining gene specificity from multivariate single-cell RNA sequencing data

Swarna, N. P.; Booeshaghi, A. S.; Rebboah, E.; Gordon, M. G.; Kathail, P.; Li, T.; Alvarez, M.; Ye, C. J.; Wold, B. J.; Mortazavi, A.; Pachter, L.

10.1101/2025.11.21.689845 — bioinformatics — Posted on 2025-11-24

1211 Mapping the AI Life Sciences Landscape in Greece: A National Survey and Bibliometric Comparison with Global Trends

Adamidi, E.; Chatzopoulos, S.; Dimopoulos, A.; Krithara, A.; Nentidis, A.; Pechlivanis, N.; Psomopoulos, F. E.; Vergoulis, T.; Vichos, K.

10.1101/2025.11.19.689212 — bioinformatics — Posted on 2025-11-24

1212 MAGIC: Methylation Analysis with Genomic Inferred Contexts

Han, J.; Thompson, M.; Pellegrini, M.

10.1101/2025.11.19.689248 — bioinformatics — Posted on 2025-11-24

1213 Life-long behavioral screen reveals an architecture of vertebrate aging

Bedbrook, C. N.; Nath, R. D.; Zhang, L.; Linderman, S. W.; Brunet, A.; Deisseroth, K.

10.1101/2025.11.21.688112 — animal behavior and cognition — Posted on 2025-11-24

1214 Gene-transcription factor regulatory networks implicate primary cilia in the evolution of vertebrate sex determination and expand models of epigenetic regulation

Gessler, T. B.; Adams, D. C.; Valenzuela, N.

10.1101/2025.11.21.689810 — evolutionary biology — Posted on 2025-11-24

1215 WWOX deficiency uncovers a cell-autonomous mechanism impairing myelin repair

Abudiab, B.; Manenti, C.; Repudi, S.; Abu-Swai, S.; Akkawi, R.; Jebara, T.; Davila-Velderrain, J.; Aqeilan, R. I.

10.1101/2025.11.22.689900 — neuroscience — Posted on 2025-11-24

1216 Comparative Analysis of FOXP2 Expression in the Thalamus of Mice, Rats, and Macaques: Implications for the Evolution of Language Circuits.

Sanchez-Moreno, B.; Uceda-Heras, A.; de la Fuente-Fernandez, M.; Garcia-Cabezas, M. A.; Cavada, C.; Gilabert-Juan, J.

10.1101/2025.11.23.689322 — neuroscience — Posted on 2025-11-24

1217 Dynamic methylation changes in Alzheimers disease-related genes during mindfulness practice - a proof-of-concept study

Blanco-Luquin, I.; Macias, M.; Marro, I.; Puebla-Guedea, M.; Acha, B.; Alvarez-Jimenez, J.; Razquin-Sola, S.; Roldan, M.; Cabezon-Arteta, E.; Gonzalez-Villena, L.; Montero-Marin, J.; Garcia-Campayo, J.; Mendioroz, M.

10.1101/2025.11.17.688316 — neuroscience — Posted on 2025-11-24

1218 LsrL modulates Lsr2-induced chromatin structure to tune biosynthetic gene cluster regulation in Streptomyces venezuelae

Ramirez, V.; Tiller, L.; Szafran, M.; Zhang, X.; Jakimowicz, D.; Elliot, M.; Freddolino, L.

10.1101/2025.11.23.690019 — microbiology — Posted on 2025-11-23

1219 Lipid Nanoparticles Enable mRNA Delivery to Diverse Cell Types of the Inner Retina

Biswas, S.; Carpentiero, E.; Xhaferri, N.; Streckenbach, P.; Renigunta, V.; Lindner, M.

10.1101/2025.11.21.689792 — neuroscience — Posted on 2025-11-23

1220 Coordinated regulation of the metaboproteome by Hsp90 chaperones controls metabolic plasticity

Perez, R. F.; Mochi, G. L.; Burkacki, J. K.; Zoccoli-Rodriguez, V.; Arcadi, L. D.; Backe, S. J.; Wilmore, J. R.; Woodford, M. R.

10.1101/2025.11.21.689798 — biochemistry — Posted on 2025-11-23

1221 Fluorescent Biosensor-Guided Engineering of Enzyme Cascades for Electrochemical Applications

Ricks, N. J.; Brachi, M.; Arun, F.; Baiarashov, E.; Minteer, S.; Hammond, M.

10.1101/2025.11.21.689824 — biochemistry — Posted on 2025-11-23

1222 Sensitivity to TDP-43 loss and degradation resistance determine cryptic exon biomarker potential

Brown, A.-L.; Zanovello, M.; Mikheenko, A.; Dattilo, D.; Pellegrini, F.; Bryce-Smith, S.; Mattedi, F.; Mehta, P. R.; Vargas, J. N. S.; NYGC ALS Consortium, ; Humphrey, J.; Keuss, M.; Fratta, P.

10.1101/2025.11.23.689722 — molecular biology — Posted on 2025-11-23

1223 Mammalian PABPC4 is non-essential, but has roles in growth, post-natal survival and haematopoiesis.

Brook, M.; Lorbeer, M.; Scanlon, J. P.; Hrabalkova, L.; Nagy, B.; Ounapuu, T.; Michael, M.; Smith, R. C. L.; Henderson, J. J.; Martins, P. J. S.; Howard, S. E.; Irvine, L.; Gray, N. K.

10.1101/2025.11.22.689676 — molecular biology — Posted on 2025-11-23

1224 TXNDC5 Governs Extracellular Matrix Homeostasis in Pulmonary Hypertension

Chen, Z.; Kong, F.; Huang, L.; Wu, W.; Wang, Z.; Chen, H.; Zhang, J.; Deng, L.; Cao, C.; Zhang, X.; Liu, Z.; Yang, K.-C.; Chang, W.-T.; Bian, J.-S.; Nie, X.

10.1101/2025.11.21.689856 — molecular biology — Posted on 2025-11-23

1225 Multiple Quality Control Checkpoints Safeguard Small Nuclear RNA Biogenesis and Prevent Assembly of Aberrant Spliceosomes

Ma, T.; Huntington, C.; Song, Z.; Lardelli, R. M.; Van Nostrand, E. L.; Lykke-Anderson, J.

10.1101/2025.11.21.689835 — molecular biology — Posted on 2025-11-23

1226 Measurement of nitric oxide production in mouse tracheal epithelial cell cultures differentiated at the air liquid interface.

Iqbal, M.; Mahan, D.; Clark, A.; Bruce, A.; DeMartino, A.; Corti, P.

10.1101/2025.11.23.690029 — molecular biology — Posted on 2025-11-23

1227 Regulation of murine follicle-stimulating hormone β subunit transcription by newly identified enhancers

Jin, Y.; Schultz, H.; Ongaro, L.; Schang, G.; Zhou, X.; Alonso, C. A. I.; Zamojski, M.; Nudelman, G.; Mendelev, N.; Onuma, S.; Welt, C. K.; Bilezikjian, L. M.; Sealfon, S. C.; Ruf-Zamojski, F.; Bernard, D. J.

10.1101/2025.11.21.689832 — molecular biology — Posted on 2025-11-23

1228 Histone H2A Ubiquitination Mediates the Establishment of Reactivation-Competent HSV-1 Latent Infection

Boehlke, J. M.; Dochnal, S. A.; Misra, C. S.; Cliffe, A. R.; Boutell, C.; Francois, A.

10.1101/2025.11.23.690028 — microbiology — Posted on 2025-11-23

1229 The impact of N-terminal dimerization on formin homology 1 (FH1) domain polymer dynamics and actin assembly

Bogue, K.; Christian, B.; Quinlan, M. E.; Allard, J.

10.1101/2025.11.21.689827 — biophysics — Posted on 2025-11-23

1230 Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli

Yehya, N.; Bohrer, C. H.; Yu, Q.; Hathcock, D.; Goldberg, B. I.; Leng, S.; Harris, F. E.; Hendrix, H.; White, M.; Leng, F.; Meyer, S.; Tu, Y.; Xiao, J.

10.1101/2025.11.23.690031 — biophysics — Posted on 2025-11-23

1231 Mapping Bidirectional Allosteric Communication in Arf GTPases

Peters, E. V.; Koduru, T.; McCallum, S. A.; Yee, E. F.; Cherfils, J.; Royer, C. A.

10.1101/2025.11.21.689788 — biophysics — Posted on 2025-11-23

1232 Accurate Reconstruction of Circular RNAs from Complex Rolling Circular Long Reads with CircPlex

Zahin, T.; Khan, I. M.; Shao, M.

10.1101/2025.11.21.689841 — bioinformatics — Posted on 2025-11-23

1233 2D HSQC-derived "dark forest" image with enhanced local resolution via first derivative processing-logarithmic cosine transformation (FDP-LCT): Demonstration on per-O-ethylated kappa- and iota-carrageenans

Xing, X.; Tingley, J. P.; Bajwa, B.; Weiler, V.; Montina, T.; Cui, S. W.; Abbott, D. W.

10.1101/2025.11.21.689839 — biochemistry — Posted on 2025-11-23

1234 Systematic characterization of cancer-associated SPOP mutants reveals novel and reprogrammable degradative activities

Caldwell, A. G.; Parmar, H.; Jin, X.; Zhou, C.; Zhang, X.

10.1101/2025.11.21.689851 — biochemistry — Posted on 2025-11-23

1235 Early Host-Virus RNA Interactions Reveal SPEN-Driven m6A Regulation as a Major Determinant of Henipavirus Infection

Ascura, A.; Clarke, S.; Livingston, A. F.; Trotman, J. B.; Haigh, S.; Malek, M. C.; Calabrese, J. M.; Ascano, M.

10.1101/2025.11.21.689838 — biochemistry — Posted on 2025-11-23

1236 Engineered Transdermal Peptide-Recombinant Type III Collagen Hydrogel with Biological Efficacy in Cell Proliferation and Wound Healing

Hong, J.; Tan, W.; Liu, Y.

10.1101/2025.11.22.689886 — biochemistry — Posted on 2025-11-23

1237 Trans-acting mutations reveal non-nuclear modulators of both intrinsic and extrinsic gene expression noise in a eukaryote.

Martin, N.; Kleine-Schultjann, J.; Boussau, Q.; Dumont, A.; Duplus-Bottin, H.; Modolo, L.; Yvert, G.; Wittkopp, P. J.; Duveau, F.

10.1101/2025.11.22.689898 — genetics — Posted on 2025-11-23

1238 OPUS-ET: Resolving Compositional and Conformational Heterogeneities of Biomolecules in Cryo-Electron Tomography

Luo, Z.; Chen, X.; Wang, Q.; Ma, J.

10.1101/2025.11.21.688990 — molecular biology — Posted on 2025-11-23

1239 ZAKα is a sensor of mRNA stasis at the ribosomal exit channel

Vind, A. C.; Martinez, J. F.; Wu, Z.; Bugai, A.; Mordente, K. C.; Chen, Q.; Rasmussen, M.; He, D.; Svejstrup, J. Q.; Jensen, T. H.; Blasius, M.; Bekker-Jensen, S.

10.1101/2025.11.22.689755 — molecular biology — Posted on 2025-11-23

1240 The Ies6 subunit is essential for INO80-mediated nucleosome organization

Singh, A. K.; Mueller-Planitz, F.

10.1101/2025.11.21.689789 — molecular biology — Posted on 2025-11-23

1241 Priority effects determine community composition at the strain level in the honeybee gut microbiota

Prasad, A.; Santos-Matos, G.; Szigeti-Genoud, A.; Mazel, F.; Engel, P.

10.1101/2025.11.22.689826 — microbiology — Posted on 2025-11-23

1242 Characterizing JP-5 Biodegradation Potential in Hawaii Soil Microbiome: Phylogeny, Growth Kinetics, and Biosurfactant Production

Zou, Y.; Jeon, M. K.; Yan, T.

10.1101/2025.11.21.689844 — microbiology — Posted on 2025-11-23

1243 Stage-specific regulation of the Plasmodium falciparum proteasome activity reveals adaptive rewiring in artemisinin resistance

Subramanyaswamy, S. B.; Paul, G.; Ogunribido, D.; Mirauti, A.; Li, D.; Zhan, W.; Lin, G.; Kirkman, L.

10.1101/2025.11.21.689772 — microbiology — Posted on 2025-11-23

1244 Adaptation to a host-associated lifestyle drives convergent loss of flagellar motility in Pseudomonadota

Siani, R.; Gutjahr, C.; Schloter, M.

10.1101/2025.11.22.689265 — microbiology — Posted on 2025-11-23

1245 Chemical proteomics identifies signal peptidase IB (SpsB) as a target of the SOS response inhibitor OXF-077 and a regulator of quinolone resistance emergence in Staphylococcus aureus

Bradbury, J. D.; Walsh, T. R.; Lanyon-Hogg, T.

10.1101/2025.11.21.689737 — microbiology — Posted on 2025-11-23

1246 A divergent Plasmodium NEK4 acts as a key regulator driving the early events of meiosis

Yanase, R.; Hair, M.; Zeeshan, M.; Ferguson, D. J. P.; Brady, D.; Pasquarello, C.; Bottrill, A.; Bhanvadia, S.; Neal, A.; Tromer, E. C.; Le Roch, K. G.; Hainard, A.; Holder, A. A.; Vaughan, S.; Guttery, D. S.; Tewari, R.

10.1101/2025.11.21.689802 — microbiology — Posted on 2025-11-23

1247 Isolation of the first cultured representative from a deep-branching phylum in serpentinite-hosted ecosystems

Liu, G.; Zhu, J.; Sun, Y.; liu, r.; Gu, Y.; Yuan, S.; Wang, H.; Li, M.; Qi, H.; Peng, Q.; Wu, S.; Sun, C.

10.1101/2025.11.21.689855 — microbiology — Posted on 2025-11-23

1248 Magneto-Photonic Gene Circuit for Minimally Invasive Control of Gene Expression in Mammalian Cells

Franco, E. A. C.; Radawiec, R.; Slaviero, A.; Grady, C. J.; Ricker, B.; Pelled, G.; Hochgeschwender, U.; Kim, T.; Gilad, A.

10.1101/2025.11.21.688514 — synthetic biology — Posted on 2025-11-23

1249 Pan-cell type continuous chromatin state annotation of all epigenomes from the International Human Epigenome Consortium

Daneshpajouh, H.; Moghul, I.; Wiese, K. C.; Libbrecht, M. W.

10.1101/2025.02.06.636950 — genomics — Posted on 2025-11-23

1250 Sex chromosomes and chromosomal rearrangements are key to behavioural sexual isolation in Jaera albifrons marine isopods

Ribardiere, A.; Daguin-Thiebaut, C.; Coudret, J.; Le Corguille, G.; Avia, K.; Houbin, C.; Loisel, S.; Gagnaire, P.-A.; Broquet, T.

10.1101/2025.01.08.631900 — evolutionary biology — Posted on 2025-11-23

1251 Extracellular Particles Derived from Mesenchymal Stromal Cells Reduce Pseudomonas aeruginosa Lung Infection and Inflammation in Mice

Sarkar, S.; Barnaby, R.; Faber, Z.; Taub, L.; Roche, C.; Charpentier, L. A.; Hampton, T. H.; Vietje, B.; Taatjes, D. J.; Cho, B.-K.; Goo, Y. A.; Wargo, M. J.; Weiss, D. J.; Bonfield, T. L.; Kelley, T. J.; Stanton, B. A.

10.1101/2025.03.30.646208 — microbiology — Posted on 2025-11-23

1252 Direct Measure of DNA Damage in Huntington Disease Reveals Elevated Oxidative Genotoxic Stress and Dysfunctional DNA Repair

Bazan, C. A. B.; Laville-Dupuy, S.; Klepfish, M.; Cousineau, J.; Maiuri, T.; Peng, C. Y.; Osterlund, E. J.; Alpaugh, M.; Truant, R.

10.1101/2025.11.21.689804 — cell biology — Posted on 2025-11-23

1253 WITHDRAWN: An Evaluation of Representational Similarity Analysis for Model Selection and Assessment in Computational Neuroscience

Chen, L.

10.1101/2023.09.18.558316 — neuroscience — Posted on 2025-11-23

1254 Structural evolution of a fungal cell wall protein family for β-glucan-binding and cell separation

Schoppner, P.; Weitzel, V.; Veelders, M.; Korf, L.; Andras, J.; Wolf, K.; Bruckner, S.; Essen, L.-O.; Mosch, H.-U.

10.1101/2025.11.20.689653 — microbiology — Posted on 2025-11-23

1255 Galectin-1 induces macrophage immunometabolic reprogramming, modulates T cell immunity and attenuates atherosclerotic plaque formation

Li, Y.; Leberzammer, J.; Blanchet, X.; Duan, R.; Lacy, M.; Triantafyllidou, V.; Eckardt, V.; Briem, E.; Jung, A. S.; Su, R.; Guerra, J.; Jansen, Y.; Hristov, M.; Enard, W.; Weber, C.; Dorothee, A.; Doering, Y.; Santovito, D.; Kaltner, H.; Ludwig, A.-K.; von Hundelshausen, P.

10.1101/2025.11.21.689721 — immunology — Posted on 2025-11-23

1256 From Syllables to Words: EEG Evidence of Different Age Trajectories in Speech Tracking and Statistical Learning in Infants at High and Low Likelihood for Autism

Godel, M.; Flo, A.; Benjamin, L.; Dehaene-Lambertz, G.; Schaer, M.

10.1101/2025.11.20.689632 — neuroscience — Posted on 2025-11-23

1257 Alirocumab attenuated plaque inflammation and PCSK9-induced proinflammatory signalling in M1 macrophages independently of lipid lowering

Lorenzo, O.; Espadas, C.; Soto-Catalan, M.; Romero-Cote, M.; Lumpuy-Castillo, J.; Gomez-Garre, D.; Tunon, J.

10.1101/2025.11.20.689631 — biochemistry — Posted on 2025-11-23

1258 Apical and basolateral plasma membranes in epithelial cells have distinct lipidomes and biophysical properties

Shurer, C. R.; Levental, K. R.; Levental, I.

10.1101/2025.11.20.689573 — cell biology — Posted on 2025-11-23

1259 Characterizing drug activity with sensitive interactomes in human living cells

Kundlacz, C.; Sleiman, N. H.; Marmigere, F.; Gillet, B.; Hughes, S.; Gilquin, L.; Duplus-Bottin, H.; Dumont, A.; Yvert, G.; Bleicher, F.; Gautier, A.; Coste, I.; Renno, T.; Merabet, S.

10.1101/2025.11.20.689448 — molecular biology — Posted on 2025-11-23

1260 Phytophthora root rot induces compositional and functional changes in avocado rhizosphere bacterial communities

Alfaro-Garcia, R. G.; Vargas-Mejia, P.; Patino-Conde, V.; Rebollar, E. A.; Guerrero-Analco, J. A.; Vega-Arreguin, J. C.; Reverchon, F.; Mendez-Bravo, A.

10.1101/2025.11.20.689515 — microbiology — Posted on 2025-11-23

1261 The bacterial SOS response promotes the expression of the transposase encoded by ISCR mobile genetic elements

Lallement, C.; Jove, T.; Pasternak, C.; Da Re, S.; Ploy, M.-C.

10.1101/2025.11.21.689736 — microbiology — Posted on 2025-11-23

1262 Myeloid cell recruitment propels right ventricular dysfunction in HFpEF via sterile inflammation.

Jaeschke, L.; Kocana, C.; Chitroceanu, A. M.; Winkler, A.; Kleitke, H.; Fahjen, P.; Faidel, D.; Asmus, E.; Meiser, M.; Stamatiades, E. G.; Hublitz, K. W.; Zach, V.; Kretzler, L.; Zurkan, D.; Perret, P.-L.; von der Ohe, L. A.; Simmons, S.; Gillan, J. L.; Franz, K.; Alasfar, L.; Hahn, V. S.; Sharma, K.; Reynolds, E.; Schiattarella, G. G.; Van Linthout, S.; Pieske, B.; Hegemann, N.; Mertins, P.; Edelmann, F.; Kuebler, W. M.; Grune, J.

10.1101/2025.11.21.689863 — physiology — Posted on 2025-11-23

1263 NK2R signaling governs intestinal lipid mobilization and mucosal inflammation

Perez, P.; Liu, C.-C.; Ferrari, A.; Littlejohn, N. K.; Kennelly, J. P.; Robinson, E.; Nguyen-Tran, V. T. B.; Athanacio, J.; Joesph, S. B.; Amso, Z.; Tontonoz, P.; Srinivasan, S.

10.1101/2025.11.21.689675 — physiology — Posted on 2025-11-23

1264 Triclabendazole inhibits succinate dehydrogenase in vitro

Kämpfer, T.; Ancarola, M. E.; Zumstein, P.; Bernal, A.; Zumkehr, T.; Mühlemann, S.; Wiedemar, N.; Lundström-Stadelmann, B.

10.1101/2025.11.20.689426 — pharmacology and toxicology — Posted on 2025-11-23

1265 Genetic risk implicating endolysosomal network genes correlates with endolysosomal dysfunction across neural cell types in Alzheimer's disease

10.1101/2025.03.16.643481 — neuroscience — Posted on 2025-11-23

1266 Form and function of actin impacts actin health and aging.

Averbukh, M.; Nelson, H.; Wang, T.; Lange, C. M.; Alcala, A.; Nair, T.; Kim, J.; Suh, D.; Vega, M.; Gao, S. M.; Dutta, N.; Aviles Barahona, R.; Coakley, A. J.; Gerke, J. A.; Odron, S. F.; Clarke, J. G.; Singh, N.; Nickel, M. S.; Peterson, J. C.; Lam-Truong, H. L.; Moaddeli, D.; Castro Torres, T.; Oorloff, M.; Peruch, M.; Mehta, H.; Thorwald, M. A.; Curran, S. P.; Wang, M. C.; Johnson, T. A.; Crimmins, E. M.; Arpawong, T. E.; Kumsta, C.; Garcia, G.; Higuchi-Sanabria, R.

10.1101/2025.11.22.689949 — cell biology — Posted on 2025-11-23

1267 Selector: A General Python Library for Diverse Subset Selection

Meng, F.; Martinez Gonzalez, M.; Chuiko, V.; Tehrani, A.; Rahman Al Nabulsi, A.; Broscius, A.; Khaleel, H.; Lopez Perez, K. G.; Miranda Quintana, R. A.; Ayers, P.; Heidar-Zadeh, F.

10.1101/2025.11.21.689756 — bioinformatics — Posted on 2025-11-22

1268 X-Ray contrast-adjustable 3D printing for multimodal fusion of microCT and histology

Nolte, P.; Ackurat, C. J.; Brettmacher, M.; Reichardt, M.; Stammes, M. A.; Russmann, C.; Dullin, C.

10.1101/2025.11.21.689680 — bioengineering — Posted on 2025-11-22

1269 Integrated host phage RNA seq analysis of Mycobacteriophage D29 infection reveals dual arm balanced phage genome expression and inhibited expression of host transporter and VapC target genes.

Shaw, R.; Ghosh, S.; Dutta, S.; Ghosh, A.; Das Gupta, S. K. K.

10.1101/2025.11.21.689395 — microbiology — Posted on 2025-11-22

1270 Dissociating the neural codes for multiple pitch perception in humans

Graves, J. E.; Guest, D. R.; Starr, T. M.; Li, A.; Mehta, A. H.

10.1101/2025.11.21.689749 — neuroscience — Posted on 2025-11-22

1271 Unpouching Peracarida relationships with ultraconserved elements

Iwasa-Arai, T.; Linse, K.; Andrade, S. C. d. S.; Giribet, G.

10.1101/2025.11.21.689751 — zoology — Posted on 2025-11-22

1272 Skeletal Muscle Regeneration is Accelerated Following Injection of Time Release Ion Matrix in Injured Mice

Kendra, J. A.; Hao, J.; Harris, D. R.; Blatt, R. L.; Naman, A. G.; Goble, S. D.; Garcia, L. D.; Brow, R. K.; Morton, A. B.

10.1101/2025.11.21.689759 — physiology — Posted on 2025-11-22

1273 Genetic variation of human G6PD impacts Red Blood Cell transfusion efficacy

Karafin, M. S.; Issaian, A. V.; Bevers, S.; Reisz, J. A.; Hay, A.; Keele, G. R.; Dzieciatkowska, M.; Cendali, F. I.; Haiman, Z. B.; Key, A. M.; Nemkov, T.; Stephenson, D.; Marsh, E.; Moore, A.; Palha, M. S.; Legenzov, E. A.; Lamb, D. R.; Deng, X.; Stone, M.; Hansen, K.; Kleinman, S.; Norris, P. J.; Busch, M. P.; Vallese, F.; Palsson, B. O.; Spitalnik, S.; Kao, J. P.; Roubinian, N. H.; Janetzko, J.; Page, G. P.; Eisenmesser, E. Z.; Zimring, J. C.; Buehler, P. W.; D'Alessandro, A.

10.1101/2025.11.21.689741 — biochemistry — Posted on 2025-11-22

1274 Crossover formation and coordinated assembly of synaptonemal complex relies on a direct interaction between Zip1 and Zip3

MacQueen, A. J.; Sharmin, S.; Voelkel-Meiman, K.; Poppel, A. J.

10.1101/2025.11.21.689840 — genetics — Posted on 2025-11-22

1275 Pangenome Analysis of Proteus mirabilis Reveals Lineage-Specific Antimicrobial Resistance Profiles and Discordant Genotype-Phenotype Correlations

Deka, N.; Brauer, A. L.; Connerton, K.; Hanson, B. M.; Walker, J. N.; Armbruster, C. E.

10.1101/2025.11.21.689858 — microbiology — Posted on 2025-11-22

1276 Sex differences in gene regulation and its impact on cancer incidence

Lopes-Ramos, C. M.; Burkholz, R.; Ben Guebila, M.; Fanfani, V.; Saha, E.; Shutta, K. H.; Glass, K.; Quackenbush, J.; DeMeo, D. L.

10.1101/2025.11.21.689715 — systems biology — Posted on 2025-11-22

1277 Systemic immune alterations in a murine experimental model of osteoarthritis

Seillier, C.; Brochard, S.; Boumediene, K.; Vivien, D.; Le Mauff, B.; Toutirais, O.; BAUGE, C.

10.1101/2025.11.22.689773 — physiology — Posted on 2025-11-22

1278 FINS - A global occurrence dataset of fossil neoselachians from the Cretaceous to the Quaternary

Kocakova, K.; Villafana, J.; Gardiner, A.; Mathes, G.; Pimiento, C.

10.1101/2025.11.21.689757 — paleontology — Posted on 2025-11-22

1279 MIR17HG Expression Is Transcriptionally Regulated by PAX3::FOXO1 and MYCN 1 and is Necessary for Oncogenic Activity in Fusion-Positive Rhabdomyosarcoma

Zargar, S. A.; Raut, P. K.; Kim, H.; Hoffman, R. A.; Stanton, B.; Barr, F. G.

10.1101/2025.11.21.689335 — cancer biology — Posted on 2025-11-22

1280 AlterNet: Alternative splicing-aware gene regulatory networkinference

Hoffmann, J.; Wallnig, J.; Dai, Z.; Tsoy, O.; Blumenthal, D. B.; Hartebrodt, A.

10.1101/2025.11.21.689745 — bioinformatics — Posted on 2025-11-22

1281 Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs

Bhat, S. G.; Mahajan, D.; Jain, C.

10.1101/2025.11.21.689636 — bioinformatics — Posted on 2025-11-22

1282 CCK* (Convex Closure K*): A Suite of Algorithms for the De Novo Design of L- and D-peptide Binders

Childs, H.; McBride, A. C.; Donald, B. R.

10.1101/2025.11.21.689740 — bioinformatics — Posted on 2025-11-22

1283 Comparative genomics and interactions of vector thysanopterans and transmitted viruses

Catto, M. A.; Labadie, P. E.; Kennedy, G. G.; Jacobson, A. L.; Hunt, B. G.; Srinivasan, R.

10.1101/2025.11.21.689785 — bioinformatics — Posted on 2025-11-22

1284 Precision at Every Scale: Efficiency in AI-Driven De Novo Antibody Design

Cha, H.; Cho, K.; Gu, J.; Gwak, D.; Ham, S. W.; Hong, M.; Kwon, S.; Lee, C.; Lee, D. K.; Lee, D.; Lee, D.; Lim, J.; Noh, J.; Oh, S.; Park, E.; Park, S.; Park, T.; Ryu, E.; Ryu, S.; Sa, D. H.; Seok, C.; Song, M. Y.; Won, J.; Woo, H.; Yang, J.

10.1101/2025.11.21.689414 — bioengineering — Posted on 2025-11-22

1285 Dose- and outcome-dependent effects of bacterial infection on female fecundity in Drosophila melanogaster

Basu, A.; Tekade, K.; Prasad, N. G.

10.1101/2025.11.22.689874 — evolutionary biology — Posted on 2025-11-22

1286 Threatened bat species reduce their activity in presence of traffic noise playback, and may shout louder

Hart, A.; Monari, P.; Borkin, K.; Cain, K. E.; Prebble, T.; Cieraad, E.; Pattemore, D.

10.1101/2025.11.21.689748 — ecology — Posted on 2025-11-22

1287 Novel markers for haemogenic endothelium and haematopoietic progenitors in the mouse yolk sac

Diez-Pinel, G.; Muratore, A.; Ruhrberg, C.; Canu, G.

10.1101/2025.11.21.689693 — developmental biology — Posted on 2025-11-22

1288 Microbial metabolism of complex organic matter across diverse deep-sea ecosystems

Zheng, R.; Wang, C.; Sun, C.

10.1101/2025.11.21.689854 — microbiology — Posted on 2025-11-22

1289 Inter-areal coupling for cognition through coincident oscillatory transients

Siems, M.; Cao, Y.; Donner, T. H.; Tsetsos, K.; Engel, A. K.

10.1101/2025.11.21.689181 — neuroscience — Posted on 2025-11-22

1290 Cannabis-enriched oral Actinomyces induces anxiety-like behavior via impairing mitochondria and GABA signaling

Salman, T.; Luo, Z.; Johnson, D.; Noorani, A. A.; Wan, Z.; Bordieanu, B.; Ye, Z.-w.; Penrod-Martin, R.; Xian, H.; Fitting, S.; Kalivas, P.; Jiang, W.

10.1101/2025.11.21.689724 — neuroscience — Posted on 2025-11-22

1291 A gene expression atlas of a juvenile nervous system

Taylor, S. R.; Olson, C.; Ripoll-Sanchez, L.; Valperga, G.; McWhirter, R.; Barney, S. T.; Atkinson, A.; Goel, S.; Weinreb, A.; Hardin, A.; Rolfson, A.; Pattee, J.; Aguilar, G. R.; Merritt, D. M.; Eroglu, M.; Majeed, M.; Grundvig, E.; Child, E.; Vertes, P. E.; Schafer, W.; Varol, E.; Hammarlund, M.; Hobert, O.; Miller, D. M.

10.1101/2025.11.21.689793 — neuroscience — Posted on 2025-11-22

1292 Risky Choices After Frontal Brain Injury: Differential Effects in Self vs Other-Decision Contexts

Rostami, F.; Soltani, S.; Grafman, J.; Heyrani, R.; Yazdanpanah, A.; Jahanbakhshi, A.; Vahabie, A.-H.; Shariat, S. V.; Abdolalizadeh, A.; Mirfazeli, F. S.

10.1101/2025.11.21.689684 — neuroscience — Posted on 2025-11-22

1293 Observations of anisotropic paramagnetic and diamagnetic susceptibility in the primate brain

Chen, J.; Gkotsoulias, D. G.; Jaffe, J. E.; Grassle, T.; Jaeger, C.; Gone Bi, Z. B.; Crockford, C.; Wittig, R.; Moeller, H. E.; Liu, C.

10.1101/2025.11.21.689628 — neuroscience — Posted on 2025-11-22

1294 Increases in Plasma Viscosity Disrupt Microvascular Flow Dynamics

Franco, C. E.; Gonzales, A. L.

10.1101/2025.11.21.689861 — physiology — Posted on 2025-11-22

1295 Bias in genome-wide association test statistics due to omitted interactions

Yelmen, B.; Güler, M. N.; Estonian Biobank Research Team, ; Kollo, T.; Möls, M.; Charpiat, G.; Jay, F.

10.1101/2025.11.21.689603 — bioinformatics — Posted on 2025-11-22

1296 GBoost-CTL: A novel method in multi-tissue transcriptome-wide associations studies in cross-tissue learner incorporating GWAS information

Billah, M. M.; Wei, H.; Sun, F.; Zhang, K.

10.1101/2025.11.22.689782 — bioinformatics — Posted on 2025-11-22

1297 INS-17, an insulin-receptor ligand, confers specificity in adult IIS-regulated phenotypes in C. elegans

Leptich, E. J.; Vijayakumar, P.; Pietryk, E. W.; Williams, M. I.; Arey, R. N.

10.1101/2025.11.20.689590 — genetics — Posted on 2025-11-22

1298 Ecdysone-mediated intestinal growth contributes to microbiota-driven developmental plasticity under malnutrition

Bai, L.; Bellemin, S.; Guillemot, E.; Strigini, M.; Gillet, B.; Ramos, C. I.; Leulier, F.

10.1101/2025.02.07.637066 — developmental biology — Posted on 2025-11-22

1299 Leveraging mathematical models to predict and control T-cell activation

Barreiro, X. R.; Faro, J.; Villaverde, A. F.

10.1101/2025.11.20.689432 — immunology — Posted on 2025-11-22

1300 Development of patient-derived neuroprogenitor cells (hNPCs), neurons, and astrocytes to explore the etiology of Guam Parkinsonism-dementia complex (PDC)

Chlebowski-Giulietti, A.; Yang, Y.; Siddique, N. A.; Siddique, T.; Spencer, P. S.; Steele, J. C.; KISBY, G. E.

10.1101/2025.10.07.680309 — neuroscience — Posted on 2025-11-22

1301 Goal-directed shaping of cortical waves

Dogadov, A.; Shulz, D. E.; Ego-Stengel, V.; Ferezou, I.; Estebanez, L.

10.1101/2024.09.10.612344 — neuroscience — Posted on 2025-11-22

1302 RNA-based communication in heterogeneous populations of cell mimics

Lehr, F.-X.; Banlaki, I.; Bumueller, E.; Mercier, T.; Niederholtmeyer, H.

10.1101/2025.09.03.673985 — synthetic biology — Posted on 2025-11-22

1303 Blocking SHP2 benefits FGFR2 inhibitor and overcomes its resistance in FGFR2-amplified gastric cancer

Zhang, Y.; Wang, H.; Wei, Y.; Pan, Y.; Song, X.; Shao, J.; Yu, L.; Shi, T.; Wang, Y.

10.1101/2024.11.04.621870 — cancer biology — Posted on 2025-11-22

1304 Autonomous AI Agents Discover Aging Interventions from Millions of Molecular Profiles

Ying, K.; Tyshkovskiy, A.; Moldakozhayev, A.; Wang, H.; De Magalhaes, C. G.; Iqbal, S.; Garza, A. E.; Tskhay, A.; Poganik, J. R.; Huang, K.; Qu, Y.; Glubokov, D.; Jin, C.; Lee, D.; Liu, H.; Leote, C.; Trapp, A.; de Lima Camillo, L. P.; Kerepesi, C.; Moqri, M.; Zhang, O.; Jiang, K.; Galkin, F.; Zhavoronkov, A.; Van Raamsdonk, J. M.; Wang, M.; Cong, L.; Regev, A.; Leskovec, J.; Wyss-Coray, T.; Gladyshev, V. N.

10.1101/2023.02.28.530532 — bioinformatics — Posted on 2025-11-22

1305 Modular nanostructure design of DX-tile DNA nano-stars (DX-DNAns) controls self-organization and force propagation of DX-based DNA Hydrogels yielding a soft matter metamaterial with programmable viscoelastic properties and integrated functionalization

Bush, J.

10.1101/2025.03.25.645358 — bioengineering — Posted on 2025-11-22

1306 Cellulase catalysis on cell surfaces using Caulobacter S-layer display

Davenport, B.; Av-Shalom, T.; Ievdokymenko, K.; Hallam, S. J.

10.1101/2025.07.28.667093 — bioengineering — Posted on 2025-11-22

1307 Evidence for G6PD variant classification from multiplexed functional assays

Geck, R. C.; Wheelock, M. K.; Powell, R. L.; Wang, Z. R.; Holmes, D. L.; Fayer, S.; Boyle, G. E.; Vandi, A. J.; McGee, A. V.; Amorosi, C. J.; Moore, N.; Rubin, A. F.; Fowler, D. M.; Dunham, M. J.

10.1101/2025.08.11.669723 — genetics — Posted on 2025-11-22

1308 Major histocompatibility complex class II-expressing bone marrow megakaryocytes activate CD4+ T cells and induce regulatory T cell fate

Camacho, V.; Wang, K. G.; Hanc, P.; Carminita, E.; Becker, I. C.; Lee, D. H.; Maggi, J.; Falchetti, M.; Barrachina, M. N.; von Andrian, U.; Carrascal, M.; Italiano, J. E.; Machlus, K. R.

10.1101/2025.11.21.689743 — immunology — Posted on 2025-11-22

1309 Motor biases reflect a misalignment between visual and proprioceptive reference frames

Wang, T.; Morehead, R.; Jiang, A.; Ivry, R. B.; Tsay, J. S.

10.1101/2024.03.15.585272 — neuroscience — Posted on 2025-11-22

1310 Longitudinal three-photon imaging for tracking amyloid plaques and vascular degeneration in a mouse model of Alzheimer's disease

Stas, E.; Yang, M.; Schultz, S. R.; Go, M. A.

10.1101/2025.08.12.669914 — neuroscience — Posted on 2025-11-22

1311 High affinity cross-context cellular assays reveal novel protein-protein interactions of peripheral myelin protein of 22 kDa

Stausberg, D.; Moshkovskiy, S.; Arlt, F. A.; Fledrich, R.; Stassart, R. M.; Nave, K.-A.; Urlaub, H.; Ewers, D.; Sereda, M. W.

10.1101/2025.09.03.673966 — neuroscience — Posted on 2025-11-22

1312 Elevated synaptic PKA activity and abnormal striatal dopamine signaling in Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder

Song, B. J.; Ge, Y.; Nicolella, A.; Kwon, M. J.; Lodder, B.; Bonanno, K.; Valle-Tojeiro, A.; Hartley, N. D.; Mandell, K. P.; Adeleye, J.; Misri, D.; Geng, C.; Natarajan, S.; Picard, I.; Shepard, N.; Hall, A.; Tian, J.; Aryal, S.; Farsi, Z.; Liu, X.-M.; Morshed, N.; Nadaf, N. M.; Pribiag, H.; Simmons, S. K.; Mani, D. R.; Stevens, B.; Kunwar, P. S.; Fu, Z.; Macosko, E. Z.; Levin, J. Z.; Sabatini, B. L.; Carr, S. A.; Dejanovic, B.; Keshishian, H.; Granger, A. J.; Sheng, M.

10.1101/2024.09.24.614783 — neuroscience — Posted on 2025-11-22

1313 Cas9 Nickase-Mediated Contraction of CAG/CTG Repeats in Vivo is Accompanied by Improvements in Huntington's Disease Pathology

Murillo, A.; Alpaugh, M.; Durairaj, R. R.; Randall, E. L.; Larin, M.; Heraty, L.; Aston, A. N.; Taylor, A. S.; Monteys, A. M.; Stoberl, N.; Heuchan, A. E.; Aeschlimann, P.; Fears, K.; Landles, C.; Osborne, G. F.; Mangin, A.; Bhattacharyya, S.; Metzakopian, E.; Allen, N. D.; Puymirat, J.; Bates, G.; Davidson, B. L.; Chicchetti, F.; Lelos, M.; Dion, V.

10.1101/2024.02.19.580669 — neuroscience — Posted on 2025-11-22

1314 Expression of nano-engineered RNA organelles in bacteria

Ng, B.; Fan, C.; Dordevic, M.; Knirsch, A.; Malouf, L.; Fabrini, G.; Nuccio, S. P.; Rubio-Sanchez, R. M.; Christie, G.; Takinoue, M.; Cicuta, P.; Di Michele, L.

10.1101/2025.07.08.663582 — synthetic biology — Posted on 2025-11-22

1315 Intraductal Papillary Mucinous Neoplasm Cellular Plasticity is linked with Repeat Element Dysregulation

Pankaj, A.; Raabe, M. J.; Zhang, M. L.; Song, Y.; Patel, B. K.; Xu, K.; Kocher, J. R.; Lang, E.; Richieri, P.; Caldwell, N. J.; Ni, P.; Ganci, M. L.; Nieman, L. T.; Deshpande, V.; Bardeesy, N.; Fernandez Del-Castillo, C.; Aryee, M. J.; Mino-Kenudson, M.; Ting, D. T.; Hernandez-Barco, Y. G.

10.1101/2025.01.14.632658 — cancer biology — Posted on 2025-11-22

1316 Stall force measurement of the kinesin-3 motor KIF1A using a programmable DNA origami nanospring

Takamatsu, N.; Furumoto, H.; Ariga, T.; Iwaki, M.; Hayashi, K.

10.1101/2025.07.02.662715 — biophysics — Posted on 2025-11-22

1317 Demographic insights for coral restoration

Madin, J. S.; Oliver, T.; McWilliam, M.; Asbury, M.; Baird, A.; Chen, G. K.; Connolly, S. R.; Couch, C.; Drury, C.; Ehrenberg, J.; Jorissen, H.; Nims, A. D.; Reichert, J.; Rova, L.; Schiettekatte, N.; Toonen, R. J.; Wulstein, D.

10.1101/2025.10.21.683544 — ecology — Posted on 2025-11-22

1318 MAP7-driven cytoskeletal cross-talk establishes Sertoli cell polarity crucial for germ cell meiotic progression

Kikuchi, K.; Fujimori, T.; Nakagawa, M.; Ohta, K.; Shimada, R.; Fujimura, S.; Yasunaga, K.-i.; Usuki, S.; Tani, N.; Nakamura, A.; Araki, K.; Ishiguro, K.-i.

10.1101/2025.09.16.676497 — cell biology — Posted on 2025-11-22

1319 From Wiring to Firing: Collapse of embryonic identities and emergence of functional diversity during motor neuron maturation

Chen, Y.; Chi, H.-M.; Tian, A.; Miller, A.; Patel, T.

10.1101/2025.08.12.669897 — neuroscience — Posted on 2025-11-22

1320 Efficient Cell Factory Design by Combining Meta-Heuristic Algorithm with Enzyme Constrained Metabolic Models

Liao, W.; Gao, G.; Wang, H.; Fan, X.; Wang, L.; He, S.; Xiang, G.; Yan, X.; Lu, H.

10.1101/2025.06.12.659423 — bioinformatics — Posted on 2025-11-22

1321 MindSight: A Bio-Inspired Neural Architecture for Visual Restoration via Cortical Electrical Stimulation

Zou, Y.; Niu, H.; Zhao, B.; Yi, G.; Yang, M.; Ju, J.; Yin, J.; Li, C. T.

10.1101/2025.11.12.688136 — bioengineering — Posted on 2025-11-22

1322 Rapid prey capture learning drives a slow resetting of network activity in rodent binocular visual cortex

Leman, D. P.; Cary, B. A.; Bissen, D.; Wen, W.; Lane, B. J.; Shanley, M. R.; Wong, N. F.; Bhut, K. B.; Turrigiano, G. G.

10.1101/2025.04.11.648036 — neuroscience — Posted on 2025-11-22

1323 The unexpected dual role of S100A9 amyloid protein on neurodegeneration in progressive multiple sclerosis motor cortex

Pansieri, J.; Attwood, J.; Pisa, M.; Yates, R.; DeLuca, G. C.

10.1101/2025.11.21.689707 — neuroscience — Posted on 2025-11-22

1324 Microfluidic sieve-detector for rapid capture and detection of single molecules

Kim, G.; Shen, M. L.; Ng, A.; Juncker, D.

10.1101/2025.10.30.685461 — bioengineering — Posted on 2025-11-22

1325 Computational design of cysteine proteases

Choi, H.; Coventry, B.; Bauer, M. S.; Venkatesh, P.; Chen, A.; Kim, D.; Bera, A. K.; Kang, A.; Nguyen, H.; Joyce, E.; Shankaran, B.; Thompson, T. R.; Gershon, J.; Shida, A. F.; Lee, G. R.; Hilvert, D.; Pellock, S. J.; Baker, D.

10.1101/2025.11.21.689808 — biochemistry — Posted on 2025-11-22

1326 A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants

Cohen, R. O.; Chomentowska, A.; Cai, L.; Eaton, D. A. R.

10.1101/2025.11.20.689508 — evolutionary biology — Posted on 2025-11-22

1327 Single Cell RNA Sequencing Reveals Gene Expression Continuums Along the Spatial Hierarchy of the Pulmonary Circulation

Sveiven, S.; Knutsen, C.; Zanini, F.; Cornfield, D.; Alvira, C.

10.1101/2025.05.17.654540 — cell biology — Posted on 2025-11-22

1328 Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance

Shang, R.; Popitsch, N.; Lee, S.; Ameres, S.; Lai, E.

10.1101/2025.09.09.675111 — molecular biology — Posted on 2025-11-22

1329 Broadband synergy versus oscillatory redundancy in the visual cortex

Roberts, L.; Aijala, J.; Burger, F.; Uran, C.; Jensen, M. A.; Miller, K. J.; Ince, R. A. A.; Vinck, M.; Hermes, D.; Canales-Johnson, A.

10.1101/2025.02.27.640666 — neuroscience — Posted on 2025-11-22

1330 Achieving Micrometer-Scale 4D X-ray tomography of Living Leaf Tissue in the Laboratory

Siracusa, F.; Kristensen, E. V.; Szameitat, A.; Tobler, D. J.; Ertem, I.; Frank, M.; Wu, C.; Abdurrahmanoglu, R.; Pinna, A.; Minutello, F.; Husted, S.; Grivel, J.-C.; Mokso, R.

10.1101/2025.11.21.689754 — plant biology — Posted on 2025-11-22

1331 Achilles tendons of MRL/MpJ mice show scar-mediated healing after tenotomy

Tang, N.; Sivalingam, D. S.; Wilson, K.; Weldemarian, M. M.; Tian, H.; Hart, C. D.; Rammath, P.; Glazier, J.; Jiang, J.; Leong, N.; Lowe, T.; Kane, M. A.; Iwamoto, M.; Kuo, C. K.; Enomoto-Iwamoto, M.

10.1101/2025.05.13.653102 — pathology — Posted on 2025-11-22

1332 Hormone-induced thrombosis is mediated through non-canonical fibrin(ogen) aggregation and a novel estrogen target in zebrafish

Yu, X.; Yaman, M.; Zhao, Q. Y.; Emly, S. M.; Lee, J. K.; Su, H.; Ferguson, A. C.; Nagaswami, C.; Chaturantabut, S.; Goessling, W.; Weisel, J. W.; Auchus, R. J.; Shavit, J. A.

10.1101/2024.11.13.623199 — pathology — Posted on 2025-11-22

1333 A neoantigen-microbead platform for personalized T cell cancer vaccination

Jiang, L.; Akpinar, B.; Li, Y.; Sanaee, M.; Sanjaya, N. A.; Schmidt, K.; Woodbridge, A. F.; Nilsson, O. B.; Notari, L.; Kindler, C.; Rimke, I.; Thomas, O.; Kanatani, S.; Uhlen, P.; Widengren, J.; Graslund, T.; Wermeling, F.; Gronlund, H.

10.1101/2025.11.21.689667 — cancer biology — Posted on 2025-11-22

1334 Active regulation of the epidermal growth factor receptor by the membrane bilayer

Srinivasan, S.; Lin, X.; Chen, X.; Regmi, R.; Zhang, B.; Schlau-Cohen, G. S.

10.1101/2025.08.14.670284 — biophysics — Posted on 2025-11-22

1335 Quantum and Classical Graph Convolutional Neural Networks for Protein Ligand Dissociation Constant Prediction

Salamatov, A.; Atluri, G.

10.1101/2025.11.20.689635 — bioinformatics — Posted on 2025-11-22

1336 A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome

Kim, A.-R.; Huang, K.; Johnson, J. L.; Yaron-Barir, T. M.; Wang, K.; Cantley, L. C.; Hu, Y.; Perrimon, N.

10.1101/2025.10.10.681672 — bioinformatics — Posted on 2025-11-22

1337 Engineering Apical Integrin-binding Cellular Patches to Directed Cell Reprogramming via Mechanical Remodeling

Zhi, J.; Zhao, T.; Hou, W.; Zhang, Q.; Gao, Z.; Yu, J.; Wu, K.; Xu, C.; Hu, X.; Zhang, Y.

10.1101/2025.11.21.689608 — bioengineering — Posted on 2025-11-22

1338 Proof of concept study deploying CRISPR inhibition and activation opens new avenues for systematic biological exploration in zebrafish.

Barrientos, N. B.; Shoppell, E. A.; Boyd, R. J.; Culotta, V. C.; McCallion, A. S.

10.1101/2024.09.16.613289 — genetics — Posted on 2025-11-22

1339 Effects of intergenerational transmission of small intestinal bacteria cultured from stunted Bangladeshi children with enteropathy

Pruss, K. M.; Kao, C.; Byrne, A. E.; Chen, R. Y.; Di Luccia, B.; Karvelyte, L.; Coskun, R.; Lemieux, M.; Nepal, K.; Webber, D. M.; Hibberd, M. C.; Wang, Y.; Liu, H.; Rodionov, D. A.; Osterman, A.; Colonna, M.; Maueroder, C.; Ravichandran, K.; Barratt, M.; Ahmed, T.; Gordon, J.

10.1101/2024.11.01.621574 — microbiology — Posted on 2025-11-22

1340 Multiple longitudinal tracts in the cephalopod arm sensorimotor system

Olson, C. S.; Ragsdale, C. W.

10.1101/2025.11.20.689621 — neuroscience — Posted on 2025-11-22

1341 High extraversion enhances attentional control through dynamic network reorganization

Chen, J. C. C.; Nandi, B.; Campusano, R.; Jiang, F.; Ziegler, D.; Gazzaley, A.; Zanto, T.

10.1101/2025.11.20.689570 — neuroscience — Posted on 2025-11-22

1342 Neural dynamics outside task-coding dimensions drive decision trajectories through transient amplification

Pereira-Obilinovic, U.; Daie, K.; Chen, S.; Svoboda, K.; Darshan, R.

10.1101/2025.11.20.689599 — neuroscience — Posted on 2025-11-22

1343 Two-photon characterisation of long-Stokes-shift dye ATTO 490LS for single-laser multicolour imaging

Cheung, K. Y.; Wu, Y.; Lee, S. Y.; Zhang, X.; Fukuda, M.; Claridge-Chang, A.

10.1101/2025.11.21.689649 — neuroscience — Posted on 2025-11-22

1344 Cross-fostering affects microglia and cell death in the hippocampus of female and male degu pups

Attlas, G.; Duprey, M.; Carlson, C.; Arusha, K. S.; Boadi, K. D.; Ellah, S. S.; Kim, D.; Raineki, C.; Bauer, C. M.; Duarte-Guterman, P.

10.1101/2025.08.05.668723 — neuroscience — Posted on 2025-11-22

1345 Cell Trajectory Inference based on Optimal Transport and a mechanistic stochastic gene expression model

Fournie, C.; Ventre, E.; Herbach, U.; Baradat, A.; Gandrillon, O.; Crauste, F.

10.1101/2025.11.21.689689 — systems biology — Posted on 2025-11-22

1346 Shared PRAME Epitopes are T-Cell Targets in NUT Carcinoma

Jensen, J. L.; Peterson, S. K.; Sambade, M.; Alley, J. R.; Yu, S.; Kinjo, T.; Bennett, S. N.; Vensko, S.; Shabrang, M.; DeBetta, J. D.; Geyer, J. K.; Price, B. A.; Nickel, K. P.; Kimple, R. J.; Kotecha, R. S.; Herring, L. E.; Davis, I. J.; Wang, J. R.; French, C. A.; Kuhlman, B.; Weiss, J.; Rubinsteyn, A.; Vincent, B. G.

10.1101/2025.03.07.642090 — cancer biology — Posted on 2025-11-22

1347 Enhanced Processivity and Collective Force Production of Kinesin-1 at Low Radial Forces

Hensley, A. M.; Yildiz, A.

10.1101/2025.08.27.672644 — biophysics — Posted on 2025-11-22

1348 Probing the Structural Dynamics of the Unbound MAX Protein: Insights from Well-Tempered Metadynamics

Lu, H.; Marti, J.; Faraudo, J.

10.1101/2025.09.01.673476 — biophysics — Posted on 2025-11-22

1349 Autonomous AI Agents Discover Aging Interventions from Millions of Molecular Profiles

10.1101/2023.02.28.530532 — bioinformatics — Posted on 2025-11-22

1350 TAS1R3 regulates GTPase signaling in human skeletal muscle cells for glucose uptake.

Hoolachan, J. M.; Balakrishnan, R.; Merz, K. E.; Thurmond, D. C.; Veluthakal, R.

10.1101/2025.09.10.674099 — cell biology — Posted on 2025-11-22

1351 T cell fate is dictated by different antigen presenting cells in response to dietary versus gut epithelial self-antigen

Zhou, Y. D.; Brown, H.; Schaffer, E.; Taylor, G. M.; Fiske, K. L.; Komnick, M. R.; Lopez, S.; Dermody, T. S.; Esterhazy, D.

10.1101/2025.11.06.687030 — immunology — Posted on 2025-11-22

1352 Composing the value signal for dopamine-mediated learning

Mahajan, P.; Seymour, B.

10.1101/2025.10.10.681616 — neuroscience — Posted on 2025-11-22

1353 Balanced spatiotemporal color responses are fine-tuned to natural light spectrum in mice ventral retina

Quetu, T.; Louboutin, A.; Castellani, F.; Baroux, R.; Ferrari, U.; Goldin, M. A.

10.1101/2025.03.13.643035 — neuroscience — Posted on 2025-11-22

1354 MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements

Hera, M. R.; Koslicki, D.; Martinez, C.

10.1101/2025.11.11.687920 — bioinformatics — Posted on 2025-11-22

1355 Testing methodological and population-specific influences on the detection of Zipf's law of brevity in chimpanzee gestures

Safryghin, A.; Badihi, G.; Ferrer-i-Cancho, R.; Grund, C.; Hayashi, M.; Mielke, A.; Mine, J.; Rodrigues, E. D.; Soldati, A.; Zuberbuhler, K.; Zulberti, C.; Hobaiter, C.

10.1101/2025.11.21.689682 — animal behavior and cognition — Posted on 2025-11-21

1356 Neural Sensitivity to Word Frequency Modulated by Morphological Structure: Univariate and Multivariate fMRI Evidence from Korean

Kim, J.; Lee, S.; Nam, K.

10.1101/2025.11.20.689262 — neuroscience — Posted on 2025-11-21

1357 Most early-born subplate neurons persist as Layer 6b neurons in the adult mouse neocortex

Sugita, Y.; Moriya-Ito, K.; Hanashima, C.; Ohtaka-Maruyama, C.

10.1101/2025.11.20.689634 — neuroscience — Posted on 2025-11-21

1358 O-GlcNAc Transferase Regulates GABAergic Synapse Organization and Receptor Composition.

Bhattacharjee, M.; Han, L.; Elenska, P.; Del Pozo, M. P.; Druzin, M.; Lagerlof, O.

10.1101/2025.11.21.689700 — neuroscience — Posted on 2025-11-21

1359 Hippocampal sequences traverse a memory space

Ulrich, O. C.; Molinuevo-Gomez, D.; Lane, M. R.; Priestley, J. B.

10.1101/2025.11.21.689701 — neuroscience — Posted on 2025-11-21

1360 RNA at Lipid/Water Interfaces: Molecular Insights from Coarse-Grained Simulations and Reflectivity Data Predictions

Ibrahim, M.; Koefinger, J.; Zacharias, M.; Schneck, E.; Schwierz, N.

10.1101/2025.11.21.689668 — biophysics — Posted on 2025-11-21

1361 Rapid aging and disassembly of actin filaments from two evolutionary distant yeasts

Billault-Chaumartin, I.; Wioland, H.; Guillotin, A.; Michelot, A.; JEGOU, A.; Romet-Lemonne, G.

10.1101/2025.11.21.689671 — biochemistry — Posted on 2025-11-21

1362 Imputed transcriptional patterns in ancient genomes reveal molecular targets of selection

Andre, M.; Montinaro, F.; Zapparoli, E.; Provero, P.; Marnetto, d.

10.1101/2025.11.21.689732 — genomics — Posted on 2025-11-21

1363 Rising, falling, stalling: Complex biodiversity trajectories in UK rivers

Mungee, M.; Wilkes, M.; Bell, V.; Kunin, W. E.; Hassall, C.; Brown, L.

10.1101/2025.11.21.689659 — ecology — Posted on 2025-11-21

1364 Sub-sarcomeric regulation of thin and thick filaments in skeletal muscle myofibrils

Sliogeryte, K.; Fusi, L.

10.1101/2025.11.21.689690 — biophysics — Posted on 2025-11-21

1365 Accurate conformational ensembles of mixed folded proteins from NMR-guided simulations

Hobbs, B.; Limmer, N.; Clenshaw, G. L.; Ossa, F.; Karamanos, T. K.

10.1101/2025.11.21.689726 — biophysics — Posted on 2025-11-21

1366 Microsecond Time-Resolved Cryo-EM Based on Jet Vitrification

Haubner, M.; Williams, H. M.; Hruby, J.; Straub, M. S.; Guskov, A.; Kovalev, K.; Drabbels, M.; Lorenz, U. J.

10.1101/2025.11.21.689681 — biophysics — Posted on 2025-11-21

1367 Minimizer Density revisited: Models and Multiminimizers

Ingels, F.; Robidou, L.; Martayan, I.; Marchet, C.; Limasset, A.

10.1101/2025.11.21.689688 — bioinformatics — Posted on 2025-11-21

1368 Overriding bioprocess perturbations with a cell machine interface for reliable microbial stress-response control

Delvenne, M.; Martinez, J. A.; Haringa, C.; Noorman, H.; Minden, S.; Takors, R.; Frank, D.

10.1101/2025.11.21.689713 — bioengineering — Posted on 2025-11-21

1369 Design and analysis of synthetic carbon fixation pathways based on novel enzymatic reactions

Rainaldi, V.; D'Adamo, S.; Claassens, N. J.

10.1101/2025.11.21.689712 — biochemistry — Posted on 2025-11-21

1370 Structural and energetic insights into human rhomboid proteases reveal a unique lateral gating mechanism for orphan family members

Clifton, B. R.; Corey, R. A.; Grieve, A. G.

10.1101/2025.11.21.689725 — biochemistry — Posted on 2025-11-21

1371 Establishment of a Congenic Strain for the Oyster mushroom reveals the Structure and Evolution of Mating-Type Loci

Lee, Y.-Y.; Vidal-Diez de Ulzurrun, G.; Tay, R. J.; Hsueh, Y.-P.

10.1101/2025.11.21.689727 — genetics — Posted on 2025-11-21

1372 Phage toxin variants are linked to protection specificity in a defensive symbiont

Panossian, B.; Mclean, A. H. C.; Patel, V.; Wu, T.; Haider, M. B.; Oliver, K. M.; Henry, L. M.

10.1101/2025.11.21.689672 — evolutionary biology — Posted on 2025-11-21

1373 Stably coexisting communities deliver higher ecosystem multifunctionality

Daniel, C.; Godoy, O.; Pichon, N. A.; Gheno, M.; Allan, E.

10.1101/2025.11.21.689673 — ecology — Posted on 2025-11-21

1374 From Single Molecular Detail to Subcellular Dynamics: Real-Time Kinetics Study of dPA Uptake with Raman-based Spectroscopy

Borek-Dorosz, A.; Dawiec, P.; Temma, K.; Xi, H.; Yamamoto, I.; Brzozowski, K.; Profic-Paczkowska, J.; Li, M.; Cudak, M.; Siakala, K.; Qiao, J.; Majzner, K.; Fujita, K.; Baranska, M.; Nowakowska, A. M.

10.1101/2025.11.21.689687 — cell biology — Posted on 2025-11-21

1375 Trithorax balances ISC fate decisions via Ptx1-mediated repression of EE specification

Fasoulaki, V.; Eliopoulos, A.; Galaras, A.; Theodorou, V.; Hatzis, P.; Delidakis, C.; Veneti, Z.

10.1101/2025.11.21.689716 — cell biology — Posted on 2025-11-21

1376 Increased mannosylation of extracellular vesicles in Long COVID plasma provides a potential therapeutic target for Galanthus nivalis agglutinin (GNA) affinity resin

Pesqueira Sanchez, M. A.; de Necochea Campion, R.; Dalhuisen, T.; Fehrman, E. A.; Chhabra, P. S.; Kelly, J. D.; Martin, J. N.; Deeks, S. G.; Henrich, T. J.; Peluso, M. J.; LaRosa, S. P.

10.1101/2025.11.21.689519 — molecular biology — Posted on 2025-11-21

1377 SPRINT-MS: A high-throughput platform for identifying protein-protein interactions using pooled IP-MS and sparse signal recovery.

Street, L. A.; Majumdar, M.; Rothamel, K. L.; Gogus, E.; Brar, G. A.; Yeo, G. W.; Rube, T.; Jovanovic, M.

10.1101/2025.11.21.689547 — molecular biology — Posted on 2025-11-21

1378 Transglutaminase 2 predicts parasitic worm-mediated protection against hepatic steatosis in obese mice

Folami, S.; Sharma, M.; Sabaratnam, R.; Bidault, G.; Diaz-delCastillo, M.; Dale, M.; Myhill, L. J.; Kolnes, K. J.; Misra, V.; Juhl, C. B.; Vidal-Puig, A.; Hoejlund, K.; Palmfeldt, J.; Williams, A.; Nejsum, P.; Indira Chandran, V.

10.1101/2025.11.21.689654 — molecular biology — Posted on 2025-11-21

1379 Horizontal Gene Transfer of E. coli by direct DNA uptake from extracellular liquid phase

Wood, C.; Smith, Z.; Johnson, L.; Lee, J. W.

10.1101/2025.11.21.689801 — molecular biology — Posted on 2025-11-21

1380 N-terminal acetylation reduces α-synuclein pathology in models of Parkinson's disease

del Cid-Pellitero, E.; Goiran, T.; Al-Azzawi, Z. A. M.; Karpilovsky, N. C.; Jones-Tabah, J.; Mayo, J. J.; Larroquette, F.; Luo, W.; Shlaifer, I.; Thattikota, Y.; Bayne, A.; Trempe, J.-F.; Durcan, T.; Fon, E. A.

10.1101/2025.11.21.689703 — molecular biology — Posted on 2025-11-21

1381 Ecological distribution, environmental roles and drivers of Actinobacteriota in two Mid-Atlantic estuaries

Ahmed, M. A.; John, J.; Campbell, B. J.

10.1101/2025.11.21.689735 — microbiology — Posted on 2025-11-21

1382 Single-Cell Multi-Omics Dissects Transcript Isoform and Immune Repertoire Dynamics in Human Immunosenescence

Zheng, Y.; Ren, Z.-H.; Yang, Y.; Liu, W.; Li, F.; Zuo, Y.; Zeng, T.; Wang, X.; Lin, X.; Zhu, X.; Guan, B.; Zhou, W.; Huang, Y.; Li, W.; Feng, Y.; Yang, X.; Liu, X.; Jin, X.; Li, H.; Dong, Y.; Yang, X.; Xu, X.; Yin, J.; Liu, C.

10.1101/2025.11.21.689731 — immunology — Posted on 2025-11-21

1383 Identification and Characterization of a Small Molecule Ligand for the Huntingtin-HAP40 Complex

Leung, R.; Wolf, E.; Deme, J. C.; Balakrishnan, S.; Simoben, C. V.; Feng, S.; Macdonald, J. D.; Chandrasekaran, R.; Sun, J.; Wang, X.; Bolotokova, A.; Zou, Y.; Kannan, R.; Ackloo, S.; Wilson, D. J.; Lea, S.; Edwards, A.; Arrowsmith, C.; Peng, H.; Halabelian, L.; Schapira, M.; Harding, R. J.

10.1101/2025.11.21.689733 — pharmacology and toxicology — Posted on 2025-11-21

1384 Transcriptomic insights into developmental toxicity of per- and poly-fluoroalkyl substances (PFAS) in Caenorhabditis elegans: The potential key role of xenobiotic detoxification pathway

Cao, Z.; Zhou, C.; Zhao, Q.; Du, H.

10.1101/2025.11.21.689658 — pharmacology and toxicology — Posted on 2025-11-21

1385 Compressed inverted indexes for scalable sequence similarity

Ingels, F.; Vandamme, L.; Girard, M.; Agret, C.; Cazaux, B.; Limasset, A.

10.1101/2025.11.21.689685 — bioinformatics — Posted on 2025-11-21

1386 ASVNet: Inferring microbes from 16S rRNA amplicon sequencing data

Sanchez-Gil, J. J.; de Jonge, R.

10.1101/2025.11.21.689717 — bioinformatics — Posted on 2025-11-21

1387 ApoA-I dissociated from human HDL retains its acceptor properties in ABCA1-mediated cholesterol efflux from RAW 264.7 macrophages in coronary artery disease

Baserova, V. B.; Popov, M. A.; Dergunov, A. D.

10.1101/2025.11.21.689699 — biochemistry — Posted on 2025-11-21

1388 A stress-dependent TRIM28-ALKBH2 feedback loop modulates chemotherapy response

Zhao, Y.; Sun, Z.; Deng, Y.; Liu, Y.; Liu, Z.; Li, J.; Wu, L.; Zeng, L.; Feng, X.; Miao, L.; Sheng, Y.; Chen, B.; He, Y.; Liu, Y.

10.1101/2025.11.21.689678 — biochemistry — Posted on 2025-11-21

1389 Mechanical Disturbance of Trichomes Enhances Cd2+ Uptake via Malate-Mediated Stomatal Opening in Arabidopsis

Du, J.; Wei, H.; Shen, T.; Chang, X.; Hao, M.; Qi, Y.; Liu, N.; Cao, Z.; Dong, J.; Zhou, L. H.

10.1101/2025.11.20.689625 — plant biology — Posted on 2025-11-21

1390 Enterococcus faecium colonization and persistence in a model of diabetic wound infection

Jeyabalan, N.; Tanoto, F. R.; Antypas, H.; Yi, C. N. J.; Wen, R. T. J.; Pethe, K.; Becker, D. L.; Stocks, C. J.; Kline, K. A.

10.1101/2025.11.20.689639 — microbiology — Posted on 2025-11-21

1391 Extracellular vesicles as indicators of environmental stress response in Lactiplantibacillus plantarum: a multi-platform study

Razim, A.; Laimer-Digruber, A.; Schmid, A. M.; Edelbacher, T. V.; Paschal, M. E.; Weinmayer, T.; Thaler, M.; Skalska, M. E.; Migdal, P.; Morandi, M. I.; Daniel, C.; Srutkova, D.; Schwarzer, M.; Hrdy, J.; Ehling-Schulz, M.; Gorska, S.; Inic-Kanada, A.; Wiedermann, U.; Schabussova, I.

10.1101/2025.11.21.689665 — microbiology — Posted on 2025-11-21

1392 OspA Antibodies Inhibit the In vitro Transmigration of Borreliellia burgdorferi

Bhattacharyya, A.; MANTIS, N. J.

10.1101/2025.11.20.689610 — immunology — Posted on 2025-11-21

1393 mCytoCounter, a deployable somatic cell counting device for the assessment of mastitis in dairy farms

Khaware, N.; Elangovan, R.; Jeet, T.; Balasubramanian, P.; Schulze, H.; Bachmann, T. T.; Perumal, V.

10.1101/2025.11.19.689399 — immunology — Posted on 2025-11-21

1394 Lipid droplets promote the aberrant liquid-liquid phase separation of alpha-synuclein leading to impaired energy homeostasis

Cevallos, J.; Eubanks, E.; Jung, S.; Huang, Y.; Guadagno, E.; Suvvari, N. R.; Doshi, A.; Ravinutala, N.; Mosera, A.; Ramalingam, N.; Tripathi, A.; Bartels, T.; Dettmer, U.; Kara, E.

10.1101/2025.11.20.689615 — neuroscience — Posted on 2025-11-21

1395 Integrative Network Analysis Reveals Organizational Principles of the Endocannabinoid System

Shridhar, A.; Dixit, S.; Torres, A.; Gaudino, R.

10.1101/2025.10.28.685143 — systems biology — Posted on 2025-11-21

1396 Glutamine alters the response to stress in mice with diet-induced obesity in a sex-dependent manner.

Lefebvre, C.; Tiffay, A.; Breemeersch, C.-E.; Dreux, V.; Bole-Feysot, C.; Guerin, C.; Breton, J.; Langlois, L.; Maximin, E.; Monnoye, M.; Dechelotte, P.; Douard, V.; Goichon, A.; Coeffier, M.

10.1101/2025.11.21.689652 — pathology — Posted on 2025-11-21

1397 Theoretical estimates on the expected number of mutations for reconstructing clonal lineage trees

Bristy, N. A.; Schwartz, R.

10.1101/2025.11.20.689642 — cancer biology — Posted on 2025-11-21

1398 The fMRI response to transcranial photobiomodulation: the effect of wavelength, irradiance, frequency and skin tone on the BOLD and CBF response in healthy young adults

Van Lankveld, H.; Chen, J. X.; Zhong, X. Z.; Chen, J. J.

10.1101/2025.11.20.689588 — bioengineering — Posted on 2025-11-21

1399 Computational design of metalloproteases

Chen, A.; Wu, K.; Choi, H.; Venkatesh, P.; Pellock, S. J.; Hanikel, N.; Coventry, B.; Kim, D.; Woodbury, S. M.; Ji, P.; Honda, S.; Li, X.; Gerben, S.; Chang, L.; Yan, X.; Hyman, A. A.; Hilvert, D.; Baker, D.

10.1101/2025.11.20.689622 — biochemistry — Posted on 2025-11-21

1400 Acute Stress in Female Adolescent Rats Increases Anxiety-like but not Depression-like Behaviors

Xiong, J.; Giannakou, I.; O'Bryan, M.; Hartman, C.; Rempel-Clower, N.

10.1101/2025.11.20.689244 — animal behavior and cognition — Posted on 2025-11-21

1401 Antigen-reactive CD4+ T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation bias

Kocher, K.; Drost, F.; Schuelein, C.; Spriewald, B.; Schubert, B.; Schober, K.

10.1101/2025.11.19.688845 — immunology — Posted on 2025-11-21

1402 Deep White-Matter Pathways Mediate the Link Between Docosahexaenoic Acid (DHA) Status and Cognitive Performance in Adolescence

Figueroa-Vargas, A.; Valenzuela, R.; Soto-Icaza, P.; Zamorano, F.; Larrain, C.; Silva, C.; Guevara, P.; Navarrete, S.; Almagia, A.; Arancibia, V.; Barrera, C.; Ivanovic, D.; Billeke, P.

10.1101/2025.11.20.689543 — neuroscience — Posted on 2025-11-21

1403 Cognitive Performance and Brain-Predicted Age Difference in Bipolar Disorder

Ng, H. X.; Sutherland, A.; Eyler, L.

10.1101/2025.11.20.681142 — neuroscience — Posted on 2025-11-21

1404 Four new Duchenne muscular dystrophy mouse models with clinically relevant exon deletions in the human DMD gene

van Putten, M.; Linssen, M.; Tanganyika-de Winter, C.; Brouwers, C. M.; Claassens, J. W. C.; Verwey, N.; Walsh, M.; Stan, T. L.; Aartsma-Rus, A.; Hohenstein, P.

10.1101/2025.11.21.689489 — neuroscience — Posted on 2025-11-21

1405 Comparison of Brain Age Algorithms in Bipolar Disorder

Ng, H. X.; Eyler, L.

10.1101/2025.11.20.689600 — neuroscience — Posted on 2025-11-21

1406 Effects of Nanopore Confinement on the Conformational, Dynamical, and Self-Assembly Properties of an FG-Repeat Peptide

Zhao, W.; Yau, W.-M.; Tycko, R.

10.1101/2025.09.11.675621 — biophysics — Posted on 2025-11-21

1407 The Human-In-the-Loop Drug Design Framework with Equivariant Rectified Flow

Zhao, Y.; Huang, Y.; Peng, X.; Lin, H.; Xu, Q.; Shi, Y.; Liu, X.; Wang, Y.; Liu, Q.; Peng, J.; Ma, J.

10.1101/2025.11.20.689585 — bioinformatics — Posted on 2025-11-21

1408 3D pathology-guided microdissection

Hsieh, H.-C.; Gao, G.; Han, Q.; Brenes, D.; Baraznenok, E.; Yan, R.; Serafin, R.; Bishop, K. W.; Wang, R.; Konnick, E. Q.; Pritchard, C. C.; Figiel, S.; Hamdy, F. C.; Mills, I. G.; Reder, N. P.; Reddi, D. M.; Paulson, T. G.; Grady, W. M.; Valk, J. E.; True, L. D.; Haffner, M. C.; Rao, S. R.; Woodcock, D. J.; Liu, J. T. C.

10.1101/2025.11.20.689586 — bioengineering — Posted on 2025-11-21

1409 A multi-muscular, redundant strategy for free-flight roll stability

Ludlow, B. K.; Dhawan, S.; Whitehead, S. C.; Teoh, H. K.; Ehrhardt, E.; Cowan, N.; Dickerson, B. H.; Cohen, I.

10.1101/2025.09.29.679272 — animal behavior and cognition — Posted on 2025-11-21

1410 Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains

Garrido, C.; Gomez-Munoz, C.; Kornobis, E.; Agier, N.; Ilioaia, O.; Fischer, G.; Xu, Z.

10.1101/2025.05.13.653712 — genomics — Posted on 2025-11-21

1411 INS-17, an insulin-receptor ligand, confers specificity in adult IIS-regulated phenotypes in C. elegans

Leptich, E. J.; Vijayakumar, P.; Pietryk, E. W.; Williams, M. I.; Arey, R. N.

10.1101/2025.11.20.689590 — genetics — Posted on 2025-11-21

1412 Predicting the invasiveness of threshold-dependent gene drives

Kim, I. K.; Messer, P. W.

10.1101/2025.11.20.689598 — evolutionary biology — Posted on 2025-11-21

1413 Long-term surveillance reveals hybridization by nuclear reassortment and intercontinental spread as major evolutionary drivers in wheat yellow rust

Hovmoeller, M. S.; Thach, T.; Algaba, J. R.; Hansen, J. G.; Meyer, M.; Hodson, D.; Nazari, K.; Park, R. R.; Tam, R.; Moeller, M.; Schwessinger, B.; Rathjen, J. P.; Silva, P.; Riella, V.; Justesen, A. F.

10.1101/2025.05.22.655633 — evolutionary biology — Posted on 2025-11-21

1414 Evolutionary diversity and function of odorant receptors in birds

Driver, R. J.; Marie, M. A.; Ko, V. J.; Meesa, P.; Sun, W.; Li, R. J.; Brewer, M. S.; Lu, H.-Y.; Bennett, K. F. P.; Ojiro, I.; Mantha, N. E.; Matsunami, H.; Balakrishnan, C. N.

10.1101/2025.11.14.688425 — evolutionary biology — Posted on 2025-11-21

1415 Drug-induced phospholipidosis as an artifact in antiviral drug repurposing

Glenn, I. S.; Paris, L.; White, A. D.; Garda, V. G.; Montano, M.; Khalid, M. M.; Kao, A. W.; Ott, M.; Shoichet, B. K.

10.1101/2025.11.20.689520 — cell biology — Posted on 2025-11-21

1416 Specific GPCRs Elicit Unique Extracellular Vesicle MiRNA Array Signatures: An Exploratory Study

Shi, X.; Palumbo, M. C.; Benware, S.; Wiedrick, J.; Markwardt, S.; Janowsky, A. J.

10.1101/2025.06.16.659918 — cell biology — Posted on 2025-11-21

1417 Phosphorylation remodels the mitotic centrosome matrix to generate bipartite gamma-tubulin complex docking sites

Ohta, M.; Arakawa, O.; Gu, Y.; Tian, W.; Corbett, K. D.; Desai, A.; Oegema, K.

10.1101/2025.11.20.689565 — cell biology — Posted on 2025-11-21

1418 Airway injury induces alveolar epithelial responses mediated by macrophages

Wong, I. G.; Paschini, M.; Stark, J.; Vazquez, A. B.; Ya, V.; Moye, A. L.; Dang, S. M.; Trovero, M. F.; Thompson, E. L.; Ahmed, S.; Chaudhry, F. N.; Shehaj, A.; Rouhani, M. J.; Bronson, R.; Janes, S. M.; Rowbotham, S. P.; Zepp, J. A.; Franklin, R. A.; Kim, C. F.

10.1101/2024.04.02.587596 — cell biology — Posted on 2025-11-21

1419 An Asgard archaeon with internal membrane compartments

MacLeod, F. I.; von Kuegelgen, A.; Lechowska, M. K.; Parham, J.; Richard, I. A.; Aguilar-Pine, E. J.; Burns, B. P.; Baker, B. J.; Bharat, T.; Baum, B.

10.1101/2025.11.06.686947 — cell biology — Posted on 2025-11-21

1420 SF3B1 phosphorylation is an evolutionarily conserved step in spliceosome activation carried out by the divergent, OTS964-insensitive kinase CRK9 in trypanosomes

Machida, K.; Rattan, P.; Peterman, N.; Hao, B.; Gunzl, A.

10.1101/2025.11.20.689580 — molecular biology — Posted on 2025-11-21

1421 Structural basis for BCL7B-mediated ncBAF-nucleosome engagement

Sun, F.; Zou, B.; Li, H.; Xu, C.; Luo, Q.; Wang, C.; Xu, P.; Pei, D.; Chen, J.; Qin, D.; Zhang, Y.; He, J.

10.1101/2025.11.20.689410 — molecular biology — Posted on 2025-11-21

1422 Congenital CMV infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors

Levan, J.; Vaaben, A. V.; Tsui, J.; Davidson, B. R.; Olive, M. E.; Callaway, P. C.; Nguyen, C. B. T.; Ilala, M.; Patel, R. K.; Hunter, R. D.; Fragiadakis, G. K.; Combes, A. J.; Nankya, F.; Dorsey, G.; Kakuru, A.; Muhindo, M.; Feeney, M. E.

10.1101/2025.11.20.689355 — immunology — Posted on 2025-11-21

1423 Constraining inference of across-region interactions using neural activity perturbations

Basrai, D.; Lee, J.; Kristl, A. C.; Wang, P.; Miri, A.; Glaser, J. I.

10.1101/2025.11.20.689584 — neuroscience — Posted on 2025-11-21

1424 Impact of chronic alcohol and stress on mid-life cognition and locus coeruleus integrity

Revka, O.; Belculfine, S. J.; Fitts, L.; Nippert, K. E.; Teves, C. A.; Reis, P. M.; Tenney, S.; Packer, B. E.; Alvarez, I. G.; Milstein, O.; da Silva, M. C.; Moorman, D. E.; Vazey, E.

10.1101/2025.11.20.689500 — neuroscience — Posted on 2025-11-21

1425 The polypharmacological profiles of xanomeline and N-desmethylxanomeline

Sakamoto, K.; Huang, X.-P.; Albert, T.; Knobloch, P.; Folland, G.; Roth, B. L.

10.1101/2025.11.20.689572 — neuroscience — Posted on 2025-11-21

1426 Aging reveals divergent responses of AgRP/NPY neurons to diet in male and female mice.

Brothers, T.; Wei, W.; Korgan, A. C.; Bridges, Z.; O'Connell, K. M. S.

10.1101/2025.11.20.689576 — neuroscience — Posted on 2025-11-21

1427 Spatio-Temporal Multi-Omics Profiling of Mechanisms and Biomarkers in Inhaled Drug-Induced Lung Toxicity

Majumder, M. M.; Williams, E. C.; Lindvall, M. O.; Hamm, G.; Jarnuczak, A.; Setyo, L.; Di Poto, C.; Azim, A.; Chen, J.; Iannetta, A. A.; Touza, J. L.; Allman, E.; Miele, E.; Lindren, J.; Sand, E.; Anderberg, R. H.; Oag, S.; Franzen, L.; Costyson, A.; Keith, B. P.; Tan, J.; Jones, S.; Fitzpatrick, P.; Johansson, J.; Prasse, A.; Corkhill, D.; Borde, A.; Hess, S.; Terrilon, S.; Ostridge, K.; Stahl, P.; Aberg, P.; Hornberg, J.; Mohorianu, I.; Ollerstam, A.

10.1101/2025.11.20.689571 — systems biology — Posted on 2025-11-21

1428 Thermo-Flux: generation and analysis of comprehensive thermodynamic-stoichiometric metabolic network models

Smith, E. N.; Fargier, N.; Pedro, J.; Heinemann, M.

10.1101/2025.11.20.689566 — systems biology — Posted on 2025-11-21

1429 How do selective serotonin reuptake inhibitors effect metabolism? A lesson for teaching non-majors about enzymes and metabolic pathways

Tuma, T. T.; Johnson, A. M.; Brickman, P.

10.1101/2025.11.20.689583 — scientific communication and education — Posted on 2025-11-21

1430 Metabolomic analysis of Chinese chestnut (Castanea mollissima Bl.) leaves in response to Oligonychus ununguis feeding stress

Zhang, X.; Zhang, S.; Li, Y.; Guo, Y.; Liu, J.; Liu, J.; Fan, L.; Wang, G.

10.1101/2025.11.20.689536 — plant biology — Posted on 2025-11-21

1431 Unveiling Differential Epigenetic Regulation of ABC Transporter Genes in Wild and Domestic Rice in Response to Heavy Metal Stress

Mondal, S.; Sinha, D.; Bhattacharya, S.; Bose, B.

10.1101/2025.11.20.687438 — plant biology — Posted on 2025-11-21

1432 Seasonal plasticity of symbiotic strategies clarifies coral holobiont resistance and resilience

Huffmyer, A. S.; Strand, E. L.; Hackerott, S.; Wong, K. H.; Becker, D. M.; Conetta, D.; Terpis, K. X.; Pfab, F.; Wong, J. M.; Dellaert, Z.; Oliaro, F. J.; Cunning, R.; Eirin-Lopez, J. M.; Roberts, S. B.; Nisbet, R. M.; Putnam, H. M.

10.1101/2025.11.20.689604 — physiology — Posted on 2025-11-21

1433 Nuclear α1A-Adrenergic Receptor Regulation of cAMP Production by an Inside-Out MAP Kinase Signaling Pathway in Cardiac Myocytes

Fiore, C. M.; Rudokas, M.; Masuda, R.; Khamsopha, B.; Sherpa, R. T.; Moshal, K. S.; Agarwal, S. R.; Harvey, R. D.

10.1101/2025.11.20.687712 — pharmacology and toxicology — Posted on 2025-11-21

1434 Saxiphilin functions as a "toxin sponge" protein that counteracts the effects of saxitoxin poisoning

Nixon, S. A.; Zakrzewska, S.; Jang, S.; Huang, K.; Barra, A.; Chen, Z.; Goss, D. R.; Park, E.; Du Bois, J.; Minor, D. L.

10.1101/2025.11.20.689596 — pharmacology and toxicology — Posted on 2025-11-21

1435 Circadian clock regulates epidermal endocrine system in homeostatic skin pigmentation

Zhu, A.; Yang, L.; Lai, S.; Yang, F.; Tsuruta, D.; Katayama, I.

10.1101/2025.11.20.689605 — pathology — Posted on 2025-11-21

1436 TP53 and RB1 are predictive genetic biomarkers for sensitivity to cytarabine in gliomas

Laaniste, L.; Luginbuehl, J.; Trinh, M.; Watkins, R.; Lueg, G.; Neilson, G.; Burgers, M.; Kania, K.; Reynolds, R.; Smith, Z.; Kleniuk, J.; Gould, L.; Pregowska, D.; Mathiesen, S.; Johnson, M.; Muhammed, L.

10.1101/2025.11.20.688938 — cancer biology — Posted on 2025-11-21

1437 Identification of sialic acid linkage profiles in primary liver cancers

Ochoa-Rios, S.; Dressman, J. W.; Angel, P.; Drake, R. R.; Mehta, A. S.

10.1101/2025.11.20.689542 — cancer biology — Posted on 2025-11-21

1438 Progesterone receptors drive advanced breast cancer phenotypes including circulating tumor- and stem-like cell expansion in the context of ESR1 mutation

Truong, T.; Gillis, N. E.; Dwyer, A. R.; Huggins, R. J.; Hagen, K. M.; Posani, S. H.; Temiz, N. A.; Perez Kerkvliet, C.; Piepgras, E. M.; Ostrander, J. H.; Greene, G. L.; Lange, C. A.

10.1101/2025.11.20.689560 — cancer biology — Posted on 2025-11-21

1439 How minor sequence changes enable mechanistic diversity in MFS transporters? An atomic-level rationale for symport emergence in NarU

Dean, T. J.; Feng, J.; Shukla, D.

10.1101/2025.11.20.689225 — biophysics — Posted on 2025-11-21

1440 Torque-based immune cell chemotaxis in complex environments

Jakuszeit, T.; Deygas, M.; Bernard, M.; Mathur, A.; Wang, L.; Behrend, L.; Saez, P. J.; Vargas, P.; Voituriez, R.; Piel, M.

10.1101/2025.11.21.688683 — biophysics — Posted on 2025-11-21

1441 Force Scaling in Active Swarm of Microtubules via Magnetic Manipulation

Kakugo, A.; Rashid, M. R.; Akter, M.; Kabir, A. M. R.; Sada, K.; Hiraiwa, T.; Kuzuya, A.; Kawamata, I.; Tani, M.

10.1101/2025.11.20.689561 — biophysics — Posted on 2025-11-21

1442 Optimizing the membrane composition of immobilized giant vesicles for effective entrapment and observation of motile bacteria

Chu, P.; Yu, L.; Fradin, C.

10.1101/2025.11.20.689592 — biophysics — Posted on 2025-11-21

1443 biocentral: embedding-based protein predictions

Franz, S.; Olenyi, T.; Schloetermann, P.; Smaoui, A.; Jimenez Soto, L. F.; Rost, B.

10.1101/2025.11.21.689449 — bioinformatics — Posted on 2025-11-21

1444 Snail plots are badges of genome assembly quality

Challis, R. J.; Blaxter, M. L.

10.1101/2025.11.20.689594 — bioinformatics — Posted on 2025-11-21

1445 Transforming Biological Foundation Model Representations for Out-of-Distribution Data

Pratapa, A.; Tata, P. R.; Singh, R.

10.1101/2025.11.20.689462 — bioinformatics — Posted on 2025-11-21

1446 Ciliary ARLs drive renal cystogenesis

Van Sciver, R. E.; Forster, A.; Caspary, T.

10.1101/2025.11.20.689124 — genetics — Posted on 2025-11-21

1447 Leadership under risk: male vervet monkey's roles in group progression across high-risk terrain

Tankink, J. A.; van de Waal, E.; Bshary, R.; van Schaik, C.

10.1101/2025.11.21.689472 — evolutionary biology — Posted on 2025-11-21

1448 A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants

Cohen, R. O.; Chomentowska, A.; Cai, L.; Eaton, D. A. R.

10.1101/2025.11.20.689508 — evolutionary biology — Posted on 2025-11-21

1449 The LAST mile: Evaluating genetic biocontrol as a supplemental tool for eradicating invasive rodents on islands

Birand, A.; Hay, B.; Combs, M.; Gierus, L.; Horak, K. E.; Oh, K. P.; Robertson, L. J.; Thomas, P.; Velasquez-Escobar, A. M.; Will, D. J.; Maselko, M.; Piaggio, A. J.

10.1101/2025.11.20.688920 — ecology — Posted on 2025-11-21

1450 Morphogenesis of the Carapace from Phyllosoma to Puerulus in Spiny Lobsters

Adachi, H.; Morikawa, K.; Inoue, Y.; Kondo, S.

10.1101/2025.11.20.688360 — developmental biology — Posted on 2025-11-21

1451 Immune tracheal intercellular signalling coordinates the muscle injury response in Drosophila

Ammar, N.; Josse, O.; Guillou, A.; Perochon, J.; Boukhatmi, H.

10.1101/2025.06.25.661466 — developmental biology — Posted on 2025-11-21

1452 ZONAB regulates DNA methylation and mitochondrial function to control endothelial cell senescence

Jiang, W.; Lynam, E.; Delafosse, J.; Birdsey, G. M.; Randi, A. M.; Matter, K.; Balda, M. S.

10.1101/2025.11.20.689552 — cell biology — Posted on 2025-11-21

1453 Ku limits aberrant mRNA splicing promoted by intronic antisense Alu elements

Pascarella, G.; Mikhova, M.; Parkhi, G.; Godfrey, J.; Heyza, J.; Janovic, T.; Olive, A.; Carninci, P.; Schmidt, J. C.; Meek, K.

10.1101/2025.11.20.689478 — molecular biology — Posted on 2025-11-21

1454 Lipoprotein lipase requires a flexible lid and stable C-terminal, both maintained by ApoC-II peptide binding

Lietzke, E. E.; Rouse, M. S.; Oldham, D.; Dong, Z.; Eckel, R. H.; Sprenger, K. G.; Bruce, K. D.

10.1101/2025.11.20.689556 — molecular biology — Posted on 2025-11-21

1455 Dominant-negative TP53 mutations potentiated by the HSF1-regulatedproteostasis network

Halim, S.; Sebastian, R. M.; Liivak, K. E.; Patrick, J. E.; Hui, T.; Amici, D. R.; Giacomelli, A. O.; Rios, P.; Butty, V. L.; Hahn, W. C.; Sanchez-Rivera, F. J.; Mendillo, M. L.; Lin, Y.-S.; Shoulders, M. D.

10.1101/2024.11.01.621414 — molecular biology — Posted on 2025-11-21

1456 Time-resolved bottleneck analysis in bacterial infection dynamics

Vicente, S.; Boutillon, N.; Forien, R.; Mila, I.; Roques, L.; Peeters, N.

10.1101/2025.11.21.689558 — microbiology — Posted on 2025-11-21

1457 Genetic dissection of microglia cannibalism reveals an IL10 signaling axis controls microglia lifespan

Gordon, H.; Gan, D.; Dolojan, A.; Dennen, J.; Hoover, C. A.; Koh, Z. M.; Chau, K.; Avalos Arceo, R.; Cavanaugh, C.; Li, J.; Smith, C. J.

10.1101/2025.11.21.689277 — neuroscience — Posted on 2025-11-21

1458 Dissociation between physical reasoning and tool use in individuals with left hemisphere brain damage

Liu, S.; Karakose-Akbiyik, S.; Caramazza, A.; Sotero, F. D.; Buxbaum, L. J.; Wong, A. L.

10.1101/2025.11.20.688863 — neuroscience — Posted on 2025-11-21

1459 Engineering directional phosphoryl flow enables programmable signaling dynamics in bacteria

Nieves, M.; Valle, J. M.; Dalla Rizza, J.; Carrion, F.; Naranjo-Meneses, P.; Larrieux, N.; Bischofs, I.; Buschiazzo, A.; Trajtenberg, F.

10.1101/2025.11.17.688798 — systems biology — Posted on 2025-11-21

1460 Plant-specific tau class glutathione transferases safeguard against lipid oxidation stress through dual detoxification of lipid peroxides and reactive carbonyl species

Yamauchi, Y.; Matuura, N.; Kawaguchi, F.; Sakurai, C.; Nakasuga, R.; Ito, J.; Nakagawa, K.; Mizutani, M.; Sugimoto, Y.; Mano, J.

10.1101/2025.11.21.687491 — plant biology — Posted on 2025-11-21

1461 scSNViz: Visualization and Analysis of Cell-Specific Expressed SNVs

Martinez, S.; Sharma, T.; Johnson, L.; Kim, A.; Ballesteros Prieto, V.; Arestakesyan, H.; Harish, S.; Dias, J.; Goldfrank, J.; Edwards, N. J.; Horvath, A.

10.1101/2024.05.31.596816 — bioinformatics — Posted on 2025-11-21

1462 Continuous Motility Fingerprints from Gaussian Mixture Models Reveal Hidden Sperm Heterogeneity

Lamm, J.

10.1101/2025.11.20.689493 — bioinformatics — Posted on 2025-11-21

1463 Longitudinal Phylogenetic Inference of Copy Number Alterations and Single Nucleotide Variants from Single-Cell Sequencing

Kulman, E.; Kuang, R.; Morris, Q.

10.1101/2025.09.16.676596 — bioinformatics — Posted on 2025-11-21

1464 YibaoGaussian: Generate dynamic 3D models from text using Gaussian splatting as the explicit representation

Mingtong, L.; Huang, M.; Yang, C.; Ji, C.; Xie, M.

10.1101/2025.11.20.689534 — bioengineering — Posted on 2025-11-21

1465 Long-term evaluation of the association between dominance, bib size, sex and age

Silva, N. J.; Silva, L. R.; D'Amelio, P. B.; Ferreira, A. C.; Lucas, A.; Covas, R.; Doutrelant, C.

10.1101/2025.02.13.638048 — animal behavior and cognition — Posted on 2025-11-21

1466 Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability

Jocher, J.; Janssen, P.; Vieth, B.; Edenhofer, F. C.; Dietl, T.; Spurk, P.; Termeg, A.; Geuder, J.; Enard, W.; Hellmann, I.

10.1101/2024.12.12.628179 — evolutionary biology — Posted on 2025-11-21

1467 Ecology of the exotic macroalga Batophora occidentalis in Posidonia oceanica meadows and other native benthic habitats

Anton, A.; Paoletti, S.; Cucala-Garcia, L.; Morell, C.; Muniz-Quintana, S.

10.1101/2025.11.20.689540 — ecology — Posted on 2025-11-21

1468 Sexually dimorphic role of estrogen receptor α in preserving right ventricular endothelial integrity

Li, J.; Karoor, V.; Frump, A. L.; Zhao, H.; Liang, S.; Woodcock, C.-S. C.; Petrache, I.; Dai, Z.; Lahm, T.

10.1101/2025.11.20.689545 — cell biology — Posted on 2025-11-21

1469 Carbon and microbes in a degrading palsa mire are distinct from peatland and a wider connected sub-Arctic fluvial system

Tuomela, N.; Elovaara, S.; Hultman, J.; Kaartokallio, H.; Thomas, D.

10.1101/2025.05.07.652394 — microbiology — Posted on 2025-11-21

1470 Serum Exosomes from a Uniquely Defined Early-Adult Cohort Reprogram Endothelial Transcriptomes Linked to Alzheimer's Pathogenesis.

Packard, B. E.; Roux, P. F.; L'Heureux, S. E.; Zamboni, W. E.

10.1101/2025.11.20.689131 — neuroscience — Posted on 2025-11-21

1471 Mithra: An Open-Source and Cross-Platform Visualization Toolbox for Human Intracranial Recordings

Khalilian-Gourtani, A.; Esmaeili, Y.; Michalak, A. J.; Flinker, A.

10.1101/2025.11.20.689539 — neuroscience — Posted on 2025-11-21

1472 Development and characterisation of a promoter library for Sulfolobus acidocaldarius

Peeters, A. I.; Xu, Y.; Pijpstra, P.; Verheijen, P. J. T.; Peeters, E.; De Paepe, B.; De Mey, M.

10.1101/2025.11.20.689296 — synthetic biology — Posted on 2025-11-21

1473 Humanized glioblastoma patient-derived orthotopic xenografts recreate a locally immunosuppressed human immune ecosystem amenable to immunotherapeutic modulation

10.1101/2025.11.20.689484 — cancer biology — Posted on 2025-11-21

1474 Tom70-mediated mitochondria-nuclear envelope contacts regulate nuclear pore complex inheritance during gametogenesis

Ruediger, C. T.; Styler, B. S.; Sawyer, E. S.; Spiri, S.; King, G. A.; Walsh, M. E.; Brar, G. A.; Jorgens, D. M.; Ünal, E.

10.1101/2025.11.20.689567 — cell biology — Posted on 2025-11-21

1475 Targeting of human mitochondrial DNA with programmable pAgo nuclease

Rimskaya, B.; Kropocheva, E.; Shchukina, E.; Ulaschik, E.; Gelgenbein, D.; Lisitskaya, L.; Shmanai, V.; Smirnikhina, S.; Kulbachiskiy, A.; Mazunin, I.

10.1101/2025.11.20.689640 — molecular biology — Posted on 2025-11-21

1476 UFMylation of 14-3-3ϵ coordinates MAVS signaling complex assembly to promote antiviral innate immune induction

Gutierrez, I. V.; Park, M.; Sar, L.; Rodriguez, R.; Schmidt, H. M.; Snider, D. L.; Torres, G.; Scaglione, K. M.; Horner, S. M.

10.1101/2025.03.19.644084 — immunology — Posted on 2025-11-21

1477 Spike inference from calcium imaging data acquired with GCaMP8 indicators

Rupprecht, P.; Rozsa, M.; Fang, X.; Svoboda, K.; Helmchen, F.

10.1101/2025.03.03.641129 — neuroscience — Posted on 2025-11-21

1478 Defective Microhomology-Mediated End-joining in SMARCB1-Deficient Tumors

Zhu, G.; Asada, S.; Nguyen, H.; Hirohashi, Y.; Sun, L.; Mukkavalli, S.; Saravanapavan, A.; Shapiro, G. I.; D'Andrea, A. D.

10.1101/2025.11.20.689563 — cancer biology — Posted on 2025-11-21

1479 How small molecules stabilize oligomers of a phase-separating disordered protein

Zhu, J.; Sisk, T. R.; Mateos, B.; Bielskute-Garcia, S.; Salvatella, X.; Robustelli, P.

10.1101/2025.11.20.689623 — biophysics — Posted on 2025-11-21

1480 A chromosome-level genome assembly of the South African indigenous, Kolbroek pig, Sus scrofa domesticus

Smith, R. M.; Molotsi, A. H.; Nesengani, L. T.; Tshilate, T. S.; Mdyogolo, S.; Hlongwane, N. L.; Masebe, T. M.; Djikeng, A.; Mapholi, N. O.

10.1101/2025.11.20.689645 — genomics — Posted on 2025-11-21

1481 JAK-STAT pathway activation compromises nephrocyte function in a Drosophila high-fat diet model of chronic kidney disease

Zhao, Y.; Duan, J.; Seah, H.; van de Leemput, J.; Han, Z.

10.1101/2024.03.07.583967 — cell biology — Posted on 2025-11-21

1482 Calcitonin-Driven Reactivation of the Hippo Tumor-Suppressor Cascade Attenuates YAP/TAZ Oncogenic Signaling in Glioblastoma

Goswami, J.; Uttarasili, P.; Garg, L.; Prasasvi, K. R.; Chowdhury, A.; Saha, S.; Chatterjee, J.; Srivastava, A.; Somasundaram, K.

10.1101/2025.11.20.689524 — cancer biology — Posted on 2025-11-21

1483 Exaggerated male hindlegs function as pure weapons of male-male combat in thorny devil stick insects

Boisseau, R. P.; Emlen, D. J.

10.1101/2025.11.21.689692 — evolutionary biology — Posted on 2025-11-21

1484 Genome-wide analysis exploring mechanisms used by Shigella sonnei to survive long-term nutrient starvation

Matanza, X. M.; Leung, P. B.; Torraca, V.; Watson, J.; Dorman, M. J.; Thompson, N. R.; clements, a.

10.1101/2025.11.20.689435 — microbiology — Posted on 2025-11-21

1485 Glycolysis-dependent Sulfur Metabolism Orchestrates Morphological Plasticity and Virulence in Fungi

Shah, D.; Rewatkar, N.; M, A.; Gupta, S.; Mathivathanan, S.; Biswas, S.; Varahan, S.

10.1101/2025.05.14.654021 — microbiology — Posted on 2025-11-21

1486 EBV INFECTION OUTCOMES DETERMINED BY MONOCYTE AND TREG-DRIVEN IMMUNE DYNAMICS IN AN EX VIVO PBMC MODEL

Yoon, L.; MacMullen, L. N.; Castro Munoz, L. J.; Gu, A.; Bregman, J.; Campion, M. S.; Srivastava, A.; Xian, R. R.; Ambinder, R. F.; Kossenkov, A.; Soldan, S. S.; Lieberman, P. M.

10.1101/2025.11.20.689441 — immunology — Posted on 2025-11-21

1487 Developing a Stepwise Induction Protocol for Cisplatin-Resistant Human Cervical Cancer Cells

Vijayakumar, V.

10.1101/2025.11.20.687683 — cancer biology — Posted on 2025-11-21

1488 Clusters, Fingers, and Singles: A Mechanical Landscape of Tumor Invasion

Akeeb, S.; Marcus, A. I.; Jiang, Y.

10.1101/2025.11.20.689434 — cancer biology — Posted on 2025-11-21

1489 Causality-oriented regulatory inference and rational transcriptomic reprogramming design with CASCADE

Cao, Z.-J.; Guo, T.; Li, C.; Zhang, F.; Lu, P.; Gu, C.; Guo, F.; Gao, G.

10.1101/2025.11.20.689377 — bioinformatics — Posted on 2025-11-21

1490 The Pleiotropy Hypothesis of Molecular Evolution

Gu, X.

10.1101/2025.11.19.689358 — evolutionary biology — Posted on 2025-11-21

1491 Gelsolin Counteracts ER Stress-Driven Inflammatory Circuits in Psoriasis-like Dermatitis

Ori, D.; Okude, H.; Konishi, R.; Murase, M.; Hiroki, S.; Takahara, S.; Tanaka, T.; Toyodome, R.; Kano, N.; Kawasaki, T.; Ishii, K.; Kobiyama, K.; Nakashima, H.; Nakashima, K.; Sasai, M.; Yamamoto, M.; Kumagai, Y.; Tsuru, A.; Kohno, K.; Kawai, T.

10.1101/2025.11.20.689413 — immunology — Posted on 2025-11-21

1492 ATRX Deficiency Drives Aberrant Type I Interferon Signalling Through cGAS-Dependent Transcriptional Dysregulation

El-Daher, M.-T.; White, E. L.; Grimes, G.; Zhu, G.; Fellas, A.; Tait, T. A.; Uggenti, C.; Blair, N.; Nita, E.; Gautier, P.; Dunn-Davies, H.; Glen, S.; Dhir, S.; Rodero, M. P.; Rice, G. I.; Seabra, L.; Clark, R.; Fawkes, A.; Marsh, J. A.; Livingston, J. H.; Wassmer, E.; Naik, S.; Vogt, J.; Isidor, B.; Tillotson, R.; Lepelley, A.; Revy, P.; Gibbons, R. J.; Crow, Y. J.

10.1101/2025.11.19.685761 — immunology — Posted on 2025-11-21

1493 Leveraging mathematical models to predict and control T-cell activation

Barreiro, X. R.; Faro, J.; Villaverde, A. F.

10.1101/2025.11.20.689432 — immunology — Posted on 2025-11-21

1494 Orchestrating Spatial Transcriptomics Analysis with Bioconductor

Crowell, H. L.; Dong, Y.; Billato, I.; Cai, P.; Emons, M.; Gunz, S.; Guo, B.; Li, M.; Mahmoud, A.; Manukyan, A.; Pages, H.; Panwar, P.; Rao, S.; Sargeant, C. J.; Shepherd Kern, L.; Ramos, M.; Sun, J.; Totty, M.; Carey, V. J.; Chen, Y.; Collado-Torres, L.; Ghazanfar, S.; Hansen, K. D.; Martinowich, K.; Maynard, K. R.; Patrick, E.; Righelli, D.; Risso, D.; Tiberi, S.; Waldron, L.; Gottardo, R.; Robinson, M. D.; Hicks, S. C.; Weber, L. M.

10.1101/2025.11.20.688607 — bioinformatics — Posted on 2025-11-21

1495 Decrypting cellular engagement and recruitment from spatially resolved transcriptomics

Yao, J.; Shim, J. S.; Zhu, J.; Kang, S. W.; McCord, K.; Chang, W. Y.; Choi, J. M.; Lee, C.; Jang, H.-J.; Hudson, W. H.; Burt, B. M.; Yue, T.; Li, C.; Lee, H.-S.; Wang, T.

10.1101/2025.11.20.689581 — bioinformatics — Posted on 2025-11-21

1496 Preference-Based Fine-Tuning of Genomic Sequence Models for Personal Expression Prediction with Data Augmentation

Choi, M.; Cho, B.; Lee, S.

10.1101/2025.11.09.687505 — bioinformatics — Posted on 2025-11-21

1497 A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants

Cohen, R. O.; Chomentowska, A.; Cai, L.; Eaton, D. A. R.

10.1101/2025.11.20.689508 — evolutionary biology — Posted on 2025-11-21

1498 Over the hills and far away: linking landscape factors with cavity excavation on living forest trees by the Black woodpecker (Dryocopus martius, L. 1758)

Cabrera, C.; Monnet, J.-M.; Boutteaux, J.-J.; Doutau, B.; Denis, P.; Paillet, Y.

10.1101/2022.06.22.497197 — ecology — Posted on 2025-11-21

1499 Resprouting sustains cork oak seedlings while recent grazing limits resprouting and survival

Wadud, A. I.; Craveiro, J.; Erroi, S.; Alcobia, S.; Branco, M.; Bugalho, M. N.; Vaz, P. G.

10.1101/2025.11.20.689419 — ecology — Posted on 2025-11-21

1500 Pathophysiological remodeling of the skeletal muscle microenvironment in patients with lung cancer

Battey, E.; Irazoki, A.; Wang, J.; Sorensen, J.; Modvig, J.; Themsen, S.; Voldstedlund, C.; Knos, C.; Andersen, N.; Frank, E.; Kudahl, S.; Hahn, N.; Madsen, A.; Raun, S. H.; Gavaldi, C. P.; Dmitryev, O.; Ortenblad, N.; Farup, J.; Sylow, L.

10.1101/2025.11.19.689342 — molecular biology — Posted on 2025-11-21

1501 Mid-level visual features engage V4 to support sparse object recognition under uncertainty

Loued-Khenissi, L.; Scialom, E.; Lutti, A.; Herzog, M. H.; Draganski, B.

10.1101/2025.10.28.685033 — neuroscience — Posted on 2025-11-21

1502 Inhibition of oxytocin neurons during key periods of development has long-term behavioural and body composition effects.

Schaller, F.; Alifrangis, M.-S.; BARELLE, P.-Y.; Santos, C.; Tyzio, R.; Bertoni, A.; Omnes, F.; belaidouni, Y.; Bader, F.; Pallesi, E.; Gaiarsa, J.-L.; Bouret, S.; Muscatelli, F.

10.1101/2025.11.13.688271 — neuroscience — Posted on 2025-11-21

1503 Intertidal Gastropods (Gastropoda: Mollusca): Insights on diversity and distribution in the Mumbai Metropolitan Region, India

Ansari, R. M.; Patade, P.; Modi, S.

10.1101/2025.11.20.689409 — zoology — Posted on 2025-11-21

1504 Elevated CO2 drives epigenetic reprogramming andchromatin dynamics in Arabidopsis thaliana

Lewis, S.; Li, M.; Panda, K.; Harkess, A.; Slotkin, R. K.; Meyers, B. C.

10.1101/2025.11.20.689512 — plant biology — Posted on 2025-11-21

1505 A user-friendly machine-learning program to quantify stomatal features from fluorescence images

Angres, G. J.; Gillert, A.; Muroyama, A.

10.1101/2025.11.20.689597 — plant biology — Posted on 2025-11-21

1506 scDock: Streamlining drug discovery targeting cell-cell communication via scRNA-seq analy-sis and molecular docking

Huang, C.-H.; Oyang, Y.-J.; Huang, H.-C.; Juan, H.-F.

10.1101/2025.11.20.689638 — bioinformatics — Posted on 2025-11-21

1507 PertAdapt: Unlocking Single-Cell Foundation Models for Genetic Perturbation Prediction via Condition-Sensitive Adaptation

Bai, D.; Song, L.; Xing, E.

10.1101/2025.11.21.689655 — bioinformatics — Posted on 2025-11-21

1508 cpiVAE: Robust and Interpretable Cross-Platform Proteomics Imputation

Li, Y.; Duong, T.; Rooney, M. R.; Ballantyne, C. M.; Coresh, J.; Brody, J. A.; Sotoodehnia, N.; Arking, D. E.; Bader, J. S.

10.1101/2025.11.20.689433 — bioinformatics — Posted on 2025-11-21

1509 On the Comparison of LGT networks and Tree-based Networks

Marchand, B.; Tahiri, N.; Tremblay-Savard, O.; Lafond, M.

10.1101/2025.11.20.689557 — bioinformatics — Posted on 2025-11-21

1510 ARCADIA Reveals Spatially Dependent Transcriptional Programs through Integration of scRNA-seq and Spatial Proteomics

Rozenman, B.; Hoffer-Hawlik, K.; Djedjos, N.; Azizi, E.

10.1101/2025.11.20.689521 — bioinformatics — Posted on 2025-11-21

1511 SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data

Zhou, H.; Chen, H.; Rudnick, Z.; Baalbaki, S. I.; Lee, Y. J.; Lugo-Martinez, J.

10.1101/2025.11.20.689569 — bioinformatics — Posted on 2025-11-21

1512 Comparing the ability of embedding methods on metabolic hypergraphs for capturing taxonomy-based features

Cervellini, M.; Sinaimeri, B.; Matias, C.; Martino, A.

10.1101/2025.07.10.663860 — bioinformatics — Posted on 2025-11-21

1513 YOLito: A generalizable model for automated mosquito detection

Sar-Shalom, E.; Kassner, Z.; Sarig, A.; Vinauger, C.; Coutinho-Abreu, I.; Triana, M. F.; Bouzada, L. I.; Pitts, J.; Stensmyr, M. C.; Akbari, O.; Papathanos, P. A.; Bohbot, J. D.

10.1101/2025.11.20.689454 — animal behavior and cognition — Posted on 2025-11-21

1514 Bees attend primarily to costs, not benefits, to avoid exploitation by floral mimics

Novinger, A. N.; Hemingway, C.; Burrow, J. K.; Davis, C. C.; Russell, A. L.

10.1101/2025.11.20.689644 — animal behavior and cognition — Posted on 2025-11-21

1515 Reconstructing the network of horizontal gene exchange in bacteria to differentiate direct and indirect transfers

Sheinman, M.; Stentella, T.; Etheimer, P.; Massip, F.; Arndt, P. F.

10.1101/2025.11.20.689518 — genomics — Posted on 2025-11-21

1516 Exome Sequencing and Allele Dosage Analysis of Coast Redwood, a Hexaploid Conifer, Identifies a Major Population Break South of San Francisco Bay

Nikolaeva, A. S.; Santangelo, J.; Smith, L.; Dodd, R.; Nielsen, R.

10.1101/2025.11.20.689601 — ecology — Posted on 2025-11-21

1517 Crimean-Congo Haemorrhagic Fever Virus Circulates within Broad Ecological Networks of Ticks and Vertebrates

Estrada-Pena, A.; Carnell, O.; Wijburg, S. R.; Holding, M.; Sprong, H.

10.1101/2025.11.20.689440 — ecology — Posted on 2025-11-21

1518 Biofouling on aquaculture mesh: disentangling seasonal and environmental effects with eDNA

Tian, T.; Pochon, X.; Bell, P.; Wellenreuther, M.

10.1101/2025.11.20.689612 — ecology — Posted on 2025-11-21

1519 ARCADE: Controllable Codon Design from Foundation Models via Activation Engineering

Li, J.; Lai, H.-s.; Liang, L.; Du, S.; Tang, S.; Kingsford, C.

10.1101/2025.08.19.668819 — bioinformatics — Posted on 2025-11-21

1520 Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis

Jain, A.; Pham, T. M.; Laidlaw, D. H.; Ma, Y.; Singh, R.

10.1101/2025.11.20.689624 — bioinformatics — Posted on 2025-11-21

1521 HiC-SCA: A Spectral Clustering Method for Reliable A/B Compartment Assignment From Hi-C Data

Chan, J.; Kono, H.

10.1101/2025.09.22.677711 — genomics — Posted on 2025-11-21

1522 Group social conditions and environment predict foraging behavior in wild baboons

Creighton, M. J. A.; Fan, O.; Warutere, J. K.; Tung, J.; Archie, E. A.; Alberts, S. C.

10.1101/2025.11.20.689548 — ecology — Posted on 2025-11-21

1523 Spatiotemporal transcriptomic analyses reveal molecular gradient patterning during development and the tonotopic organization along cochlear axis

Yan, M.; Zhang, P.; Wang, Y.; Wang, H.; Li, J.; Guo, X.; Zeng, X.; Feng, Z.; Yun, Z.; Deng, F.; Wang, S.; Deng, D.; Ma, L.; Feng, Y.; Wu, H.-J.; Zhao, Y.; Li, J.

10.1101/2024.10.30.621022 — developmental biology — Posted on 2025-11-21

1524 Interleukin enhancer binding factor 2 (Ilf2) and kidney epithelial stress resilience

Cao, S.; Lopez-Cayuqueo, K.; Leiz, J.; Boivin, F. J.; Marko, L.; Hinze, C.; Schmidt-Ott, K. M.

10.1101/2025.08.12.667599 — cell biology — Posted on 2025-11-21

1525 Super-resolved imaging and Bayesian analysis of single exocytosis events reveals molecular-scale patterning by cortical microtubule arrays

Lindeboom, J.; Gutierrez, R.; Kirik, V.; Ehrhardt, D. W.

10.1101/2024.12.01.626273 — cell biology — Posted on 2025-11-21

1526 The repertoire of resistance mutations selected by a Pseudomonas aeruginosa type IV pilus-targeting lytic bacteriophage

Tran, V. N.; Harvey, H.; Lahane, T. S.; Burrows, L. L.

10.1101/2025.11.17.688846 — microbiology — Posted on 2025-11-21

1527 Autism-like behavior induced by conditional ablation of the Bassoon gene in GABAergic interneurons

Annamneedi, A.; Montenegro-Venegas, C.; Caliskan, G.; Marosi, E. L.; Blondiaux, A.; Tiwari, N.; Razzaq, M.; Kreutzmann, J. C.; Pellissier, L. P.; Fejtova, A.; Mikulovic, S.; Fendt, M.; Gundelfinger, E. D.; Stork, O.

10.1101/2025.11.20.689526 — neuroscience — Posted on 2025-11-21

1528 "Awe-scillations": EEG spectral and complexity representations of awe

Chen, J. C. C.; Mace, G.; Ostrand, A.; Valtierra, C.; Griffith, S.; Campusano, R.; Li, A.; Vinson, E.; Schlomberg, J.; Eshel, M.; Suntay, J. M.; Rahim, S.; Anguera, R.; Brown, D. A.; Swann, N. C.; Mazzucato, L.; Hu, X.; Zhang, D.; Timmermann, C.; Carhart-Harris, R.; Zanto, T.; Ziegler, D.; Gazzaley, A.; Pasquini, L.

10.1101/2025.11.20.689403 — neuroscience — Posted on 2025-11-21

1529 The fluctuation-based regime of thalamocortical circuitry

Jennings, L.; Hansel, D.; Priebe, N. J.

10.1101/2025.11.20.689511 — neuroscience — Posted on 2025-11-21

1530 Phase precession of spindle-slow oscillation coupling across the human brain

Bender, A. C.; Taubkin, M.; Bothwell, M. Y.; Pellerin, K.; Pavlova, M. K.; Sarkis, R. A.; Cash, S. S.; Lam, A. D.

10.1101/2025.11.20.689541 — neuroscience — Posted on 2025-11-21

1531 Perceptual processes as charting operators

Neri, P.

10.1101/2025.06.25.661475 — neuroscience — Posted on 2025-11-21

1532 A Modular Toolkit For Theophylline-Dependent Synthetic Auxotrophs Via Riboswitch-Gated Essential Genes

Gonzalez-Lopez, C.; Overly, A.; Singh, S.; Huang, C.; Lopez, G.

10.1101/2025.11.20.689564 — synthetic biology — Posted on 2025-11-21

1533 Terrain ruggedness and human activities influence the distribution of Grauer's gorillas (Gorilla beringei graueri) and eastern chimpanzees (Pan troglodytes schweinfurthii) in the Tayna Nature Reserve, Democratic Republic of Congo

Michel, A.; Mbeke, J. K.; Visando, B. K.; Kahlenberg, S.; Fawcett, K.; Caillaud, D.

10.1101/2025.07.28.667236 — ecology — Posted on 2025-11-21

1534 Cdh-2 modulates cortical F-actin distribution to establish stiffness gradients driving forebrain roof plate invagination

Sachdeva, M.; Sharma, P.; Gupta, P.; Zaidi, M. A. A.; Kushwaha, S.; Sen, J.

10.1101/2025.11.03.686203 — developmental biology — Posted on 2025-11-21

1535 Arterial vascular patterning: a crosstalk between angiogenic and shear stress signaling.

Chen, D.; Rukhlenko, O. S.; Joshi, D.; Rudnicki, M.; Coon, B. G.; Chakraborty, R.; Tuliakova, A.; Ioannou, E.; Martin, K. A.; Ruhrberg, C.; Kholodenko, B. N.; Schwartz, M. A.; Simons, M.

10.1101/2024.01.23.576920 — developmental biology — Posted on 2025-11-21

1536 Bacterial supplementation shapes honey bee gut microbiota, metabolism and proteome under controlled and field conditions

Lee, S.; Dobes, P.; Mascellani Bergo, A.; Marciniak, J.; Hurychova, J.; Sreibr, S.; Kamler, M.; Purnoch, V.; Killer, J.; Hlinakova, L.; Titera, D.; Cinek, O.; Carolan, J. C.; Hyrsl, P.; Havlik, J.

10.1101/2025.11.20.689477 — microbiology — Posted on 2025-11-20

1537 The PPE2 protein of Mycobacterium tuberculosis is responsible for the development of hyperglycemia and insulin resistance during tuberculosis

Bisht, M. K.; Maurya, V.; Dahiya, P.; Valluri, V. L.; Ghosh, S.; Mukhopadhyay, S.

10.1101/2025.08.13.670014 — microbiology — Posted on 2025-11-20

1538 The Type VI Secretion System Antifungal Effector Tfe2 Inhibits Protein Translation and Drives Hyperactivation of TORC1.

Trunk, K.; Pankov, G.; Anderton, A.; Stonys, V.; Frey, A.; Haggarty, J.; Leaves, I.; Papakyriacou, P.; Li, M.; Manthri, V.; Zimbres, F.; Denny, P. W.; Whitfield, P.; Hacker, C.; Gow, N. A. R.; Rickman, C.; Grant, C. M.; Trost, M.; Coulthurst, S. J.; Quinn, J.

10.1101/2025.11.20.689513 — microbiology — Posted on 2025-11-20

1539 mRNA-LNP Vaccines Encoding for Dengue Optimized prM/ENV Proteins Induce Protective Immunity without ADE

LaMontia-Hankin, E.; Wollner, C. J.; Stone, E. T.; Pena Rosado, A.; Pflugheber, J.; Zalla, A.; Nieto, S.; Pinto, A. K.; Brien, J. D.; Richner, J. M.

10.1101/2025.07.21.665855 — microbiology — Posted on 2025-11-21

1540 Nucleotide context models outperform protein language models for predicting antibody affinity maturation

Johnson, M. M.; Sung, K.; Haddox, H. K.; Vora, A. A.; Araki, T.; Victora, G. D.; Song, Y. S.; Fukuyama, J.; Matsen, F. A.

10.1101/2025.06.16.659977 — immunology — Posted on 2025-11-20

1541 Deep Mining of the Human Antibody Repertoire Identifies Frequent and Genetically Diverse CDRH3 Topologies Targetable by Vaccination

Habib, R.; Solieva, S. O.; Lin, Z. J.; Ghosh, S.; Bayruns, K.; Singh, M.; Agostino, C. J.; Tursi, N. J.; Sowers, K. J.; Huang, J.; Roark, R. S.; Purwar, M.; Park, Y.; Ayyanathan, K.; Li, H.; Carey, J. W.; Kim, A.; Park, J.; McCanna, M. E.; Skelly, A. N.; Chokkalingam, N.; Kriete, S.; Shupin, N.; Huynh, A.; Walker, S.; Sadeesh, R.; Laenger, N.; Du, J.; Cui, J.; Patel, A.; Escolano, A.; Kwong, P. D.; Shapiro, L.; Bowman, G. R.; Hahn, B. H.; Shaw, G. M.; Weiner, D. B.; Pallesen, J.; Kulp, D. W.

10.1101/2024.10.04.616739 — immunology — Posted on 2025-11-20

1542 The molecular and cellular underpinnings of human brain lateralization

Labache, L.; Chopra, S.; Zhang, X.-H.; Holmes, A. J.

10.1101/2025.04.11.648388 — neuroscience — Posted on 2025-11-20

1543 Gene dosage effects of 22q11.2 copy number variants on in-vivo measures of white matter axonal density and dispersion

Boen, R.; Villalon-Reina, J. E.; Kushan, L.; O'Hora, K. P.; Fung, H.; Parker, N.; Akkouh, I. A.; Alnaes, D.; O'Hara, R.; Marzelli, M. J.; Foland-Ross, L.; Chick, C. F.; Cotto, I.; Reiss, A. L.; Hallmayer, J.; Thompson, P. M.; Andreassen, O. A.; Sonderby, I. E.; Bearden, C. E.

10.1101/2025.05.29.656839 — neuroscience — Posted on 2025-11-20

1544 Working Memory Guides Perceptual Decisions Through Fast Capture and Slow Drift

Park, H.-B.; Zhang, W.

10.1101/2025.10.16.682875 — neuroscience — Posted on 2025-11-20

1545 Repeated Subconcussive Head Impacts Compromise White Matter Integrity and Bimanual Coordination in Collegiate Football Players

D'Amario, S.; Magee, B.; Champagne, A. A.; Wilson, M. E.; Ramirez-Garcia, G.; Coverdale, N. S.; Cook, D. J.

10.1101/2025.05.14.654080 — neuroscience — Posted on 2025-11-20

1546 Quantifying transmembrane water exchange by diffusion NMR methods: From yeast cells to optic nerve ex vivo

Scher, Y.; Reuveni, S.; Cohen, Y.

10.1101/2025.06.01.657299 — neuroscience — Posted on 2025-11-21

1547 STAMPS: Signal-peptide Transformer for Augmenting Mammalian Protein Secretion

Gabrielli, J.; Esposito, M.; Briliute, J.; Burrell, M.; Thom, G.; Kontoravdi, C.; Ceroni, F.

10.1101/2025.11.20.689577 — synthetic biology — Posted on 2025-11-20

1548 Causes and consequences of experimental variation in Nicotiana benthamiana transient expression

Tang, S. N.; Szarzanowicz, M.; Lanctot, A.; Sirirungruang, S.; Kirkpatrick, L. D.; Drako, K.; Alamos, S.; Cheng, L.; Waldburger, L. M.; Liu, S.; Huang, L.; Akyuz Turumtay, E.; Kazaz, S.; Baidoo, E.; Eudes, A.; Thompson, M.; Shih, P.

10.1101/2025.06.12.659391 — plant biology — Posted on 2025-11-20

1549 Proline transporters balance the salicylic acid-mediated trade-off between regeneration and immunity in plants

Xu, D.; Belew, Z. M.; Cassia Ferreira Dias, N.; Wang, L.; Zhang, A.; Chen, Y.-F. S.; Newton, C. J.; Kong, F.; Zheng, Y.; Yao, Y.; Brewer, M. T.; Teixeira, P. J. P. L.; Nour-Eldin, H. H.; Xu, D.; Yang, L.

10.1101/2025.11.20.689487 — plant biology — Posted on 2025-11-20

1550 Lymphotoxin-driven cancer cell eradication by tumoricidal CD8+ tumor-infiltrating lymphocytes

Xie, H.; Jiang, A.; Dey, A.; Dean, J. W.; Perera, J.; Smith, N.; Chen, C.-Y.; Anderson, S.; Cicerchia, A. M.; Sun, Yi, Y.; Michaud, W. A.; Florentin, M.; Fang, J.; Revach, O.-Y.; Sharova, T.; Lawless, A. R.; Xu, K. H.; Song, Y.; Patel, B.; Stevens, J. D.; Lane, W. J.; Keskin, D. B.; Cohen, S.; Lawrence, D. P.; Sullivan, R. J.; Flaherty, K. T.; Boland, G. M.; Nieman, L. T.; Sade-Feldman, M.; Hacohen, N.; Sen, D. R.; Wu, C.; Gastman, B.; Qi, R.; Yin, H.; Villani, A.-C.; Manguso, R. T.; Jenkins, R. W.

10.1101/2025.11.19.689204 — cancer biology — Posted on 2025-11-20

1551 Hidden-driver inference reveals synergistic brain-penetrant therapies for medulloblastoma

Liu, J.; Yang, X.; Zhu, M.; Dong, X.; Zhou, H.; Bianski, B.; Jonchere, B. M.; Lin, W.; Fu, X.; Yang, L.; Freeman, B. B.; Wang, A. S.; Jiang, R.; Chen, T.; Robinson, G. W.; Roussel, M. F.; Merchant, T. E.; Gajjar, A.; Yu, J.

10.1101/2025.11.20.689490 — cancer biology — Posted on 2025-11-20

1552 Decoupling Phase Separation and Fibrillization Preserves Activity of Biomolecular Condensates

Mahendran, T. S.; Singh, A.; Srinivasan, S.; Jennings, C. M.; Neureuter, C.; Gindra, B. H.; Parekh, S. H.; Banerjee, P. R.

10.1101/2025.03.18.643977 — biophysics — Posted on 2025-11-20

1553 Autonomous AI Agents Discover Aging Interventions from Millions of Molecular Profiles

10.1101/2023.02.28.530532 — bioinformatics — Posted on 2025-11-20

1554 CONCERT predicts niche-aware perturbation responses in spatial transcriptomics

Lin, X.; Kong, Z.; Ghosh, S.; Kellis, M.; Zitnik, M.

10.1101/2025.11.08.686890 — bioinformatics — Posted on 2025-11-20

1555 Computational Evaluation of Phytochemicals as Potential Anti-HIV Drugs Targeting CCR5 and CXCR4 Receptors

Nebir, S. S.; Al Arian, T.; Sarkar, B.; Moni, R.; Malek, S.; Sajidul Islam, S.; Zohora, U. S.; Rahman, M. S.

10.1101/2025.04.10.648243 — bioinformatics — Posted on 2025-11-20

1556 A comprehensive AMR genotype-phenotype database (CABBAGE)

Dickens, E.; Derelle, R.; Beardmore, R. E.; Suresh, A.; Uplekar, S.; Azov, A.; Gurbich, T. A.; El Houdaigui, B.; Keatley, J.; Ochkalova, S.; Koci, O.; Rahman, N. M.; Shivalikanjli, A.; Winterbottom, A.; Yordanova, G.; Parkinson, H.; Yates, A. D.; Finn, R. D.; Lees, J.; Chindelevitch, L.

10.1101/2025.11.12.688105 — genomics — Posted on 2025-11-20

1557 Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering

Sun, J.; Biharie, K.; Cai, P.; Mueller-Boetticher, N.; Kiessling, P.; Turner, M. A.; Helweg Dam, S.; Heyl, F.; Kathirchelvan, S.; Emons, M.; Gunz, S.; Twardziok, S.; El-Heliebi, A.; Zacharias, M.; SpaceHack 2.0 participants, ; Reinders, M.; Eils, R.; Gottardo, R.; Kuppe, C.; Long, B.; Mahfouz, A.; Robinson, M. D.; Ishaque, N.

10.1101/2025.06.23.660861 — genomics — Posted on 2025-11-20

1558 A predicted structural interactome reveals binding interference from intrinsically disordered regions

Peng, J.; Zhao, L.

10.1101/2025.08.15.670535 — genomics — Posted on 2025-11-20

1559 Inference of clonal hematopoiesis using the collective behaviour of DNA methylation states

Crofts, S.; Grenko, C.; Robertson, N.; Kirschner, K.; Chandra, T.

10.1101/2025.11.18.689122 — genetics — Posted on 2025-11-20

1560 Molecular Evolution under Macro-Perturbation Barrier and the Fixation Process of Polyploidization

Gu, X.

10.1101/2025.11.19.689354 — evolutionary biology — Posted on 2025-11-20

1561 Temporal dynamics of color polymorphism and hybridization in Colias butterflies

Jahner, J. P.; Forister, M.; Parchman, T.; Burdo, S.; McFarlane, S. E.; Buerkle, C. A.; Nice, C.; Fordyce, J.; Shapiro, A.

10.1101/2025.05.25.656022 — evolutionary biology — Posted on 2025-11-20

1562 Evolution of quantitative traits: exploring the ecological, social and genetic bases of adaptive polymorphism

Lehmann, L.; Mullon, C.

10.1101/2025.06.23.661088 — evolutionary biology — Posted on 2025-11-20

1563 Evolutionary diversity and function of odorant receptors in birds

Driver, R. J.; Marie, M. A.; Ko, V. J.; Meesa, P.; Sun, W.; Li, R. J.; Brewer, M. S.; Lu, H.-Y.; Bennett, K. F. P.; Ojiro, I.; Mantha, N. E.; Matsunami, H.; Balakrishnan, C. N.

10.1101/2025.11.14.688425 — evolutionary biology — Posted on 2025-11-20

1564 Early life adversity shapes life history trade-offs between growth and reproduction in free-ranging rhesus macaques

Petersen, R. M.; Patterson, S. K.; Widdig, A.; Turcotte, C. M.; Anton, S. C.; Williams, S. A.; Romero, A. N.; Bauman Surratt, S. E.; Ruiz Lambides, A. V.; The Cayo Biobank Research Unit, ; Montague, M. J.; Snyder-Mackler, N.; Brent, L. J. N.; Higham, J. P.; Lea, A. J.

10.1101/2025.09.11.675677 — evolutionary biology — Posted on 2025-11-20

1565 From blood to pluripotency: Fibrocytes as a reprogrammable somatic cell source for bovine iPSCs

Sylvester, H.; Koganti, P. P.; Gurung, S.; Pillai, V. V.; Selvaraj, V.

10.1101/2025.10.30.685680 — cell biology — Posted on 2025-11-20

1566 Substitution of a valine to glutamic acid in the omega-like loop of MSMEG_6194 of Mycobacterium smegmatis interchanges its activity from DD-carboxypeptidase to beta-lactamase

Panda, A. P.; Chatterjee, D.; Roy, A.; Biswal, S.; Ghosh, A. S.

10.1101/2025.11.20.689485 — molecular biology — Posted on 2025-11-20

1567 The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements

Koulle, A.; Ogundele, O.; Shah, D.; Baker, I.; Lopez, M.; Reynolds, N.; Ragheb, R.; Laue, E. D.; Hendrich, B.

10.1101/2025.08.29.672645 — molecular biology — Posted on 2025-11-20

1568 Glc7/PP1 triggers Paf1 complex dissociation from RNA polymerase II to enable transcription termination

Namjilsuren, S.; Arndt, K. M.

10.1101/2025.09.03.674035 — molecular biology — Posted on 2025-11-20

1569 Decoding Condensate Composition Reveals Tunable Interactomes and Functions of Disordered Proteins

Han, Q.; Zhong, Y.; Quan, B.; Wang, T.-Y.; Chou, T.-F.; Chong, S.

10.1101/2025.10.27.684971 — molecular biology — Posted on 2025-11-20

1570 HPV16 E6 oncoprotein promotes microhomology-mediated viral integration by upregulating POLQ expression

Zhu, G.; Asada, S.; Abeykoon, J. P.; Sun, L.; Mukkavalli, S.; D'Andrea, A. D.

10.1101/2025.11.20.689626 — molecular biology — Posted on 2025-11-20

1571 Temporal transcriptomics and molecular dynamics identify a serine-type endopeptidase as a key regulator of dengue virus infection in Aedes aegypti

Sapkota, S.; Yeasmin, F.; Hasnat, S.; Rahman, S.; Shahinuzzaman, A. D. A.; Hoque, M. N.

10.1101/2025.11.20.689538 — microbiology — Posted on 2025-11-20

1572 Rice stripe virus utilizes a Laodelphax striatellus salivary carbonic anhydrase to facilitate plant infection by direct molecular interaction

Zhao, J.; Meng, X.; Yang, J.; Fang, R.; Huo, Y.; Zhang, L.

10.1101/2023.04.04.535507 — microbiology — Posted on 2025-11-20

1573 Breaching the diatom frustule: Alteromonas macleodii triggers protoplast emergence and programmed necrotic-like cell death in the oceanic diatom Thalassiosira rotula

Short, I.; Martinez-Perez, C.; Stocker, R.; Alcolombri, U.

10.1101/2025.11.20.688403 — microbiology — Posted on 2025-11-20

1574 Intramammary infection of bovine H5N1 influenza virus in ferrets leads to transmission in suckling neonates

Baker, P. H.; Moyer, M.; Bai, Y.; Stafford, L. S.; Kelvin, A. A.; Lee, C.; Langel, S. N.

10.1101/2024.11.15.623885 — microbiology — Posted on 2025-11-20

1575 Active learning guides automated discovery of DNA delivery via electroporation for non-model microbes

Brumwell, S. L.; Lord, A.; Corts, A. D.; Harken, S.; Crits-Christoph, A.; Nguyen, M.-A.; Leung, J.; Mendler, K.; Esmurria, A.; Gilbert, C.; Ling, L.; Lee, H. H.; Ostrov, N.

10.1101/2025.11.18.689155 — microbiology — Posted on 2025-11-20

1576 Enhancing tumor-infiltrating T cells with an exclusive fuel source

Miller, M. L.; Thauland, T. J.; Nagarajan, R.; Zuo, W. E.; Moreno Lastre, M. A.; Butte, M. J.

10.1101/2024.05.20.595053 — immunology — Posted on 2025-11-20

1577 PyDecNef: An open-source framework for fMRI-based decoded neurofeedback

Margolles, P.; Abdennour, N.; Mei, N.; Elosegi, P.; Soto, D.

10.1101/2023.10.02.560503 — neuroscience — Posted on 2025-11-20

1578 Fast-conducting mechanonociceptors uniquely engage reflexive and affective pain circuitry to drive protective responses

Lezgiyeva, K.; Liu, J.; Nguyen, K.; DeLisle, M. M.; Ko, F. C.; Fullam, S.; Obeidat, A. M.; Turecek, J.; Alkislar, I.; Lehnert, B. P.; Martinez-Garcia, R. I.; Sivakumar, R.; Choi, J.; Mazor, O.; Garibyan, L.; Sharma, N.; Emanuel, A. J.; Malfait, A.-M.; Miller, R. E.; Ginty, D. D.

10.1101/2025.11.11.687663 — neuroscience — Posted on 2025-11-20

1579 Mobile Eye-Tracking Glasses Capture Ocular and Head Markers of Listening Effort

Cui, M. E.; Verno-Lavigne, E.; Saxena, S.; Fink, L. K.; Herrmann, B.

10.1101/2025.09.17.676957 — neuroscience — Posted on 2025-11-20

1580 Bayesian Causal Inference Accounts for Multisensory Filling-In at the Blind Spot

Chan, A.; Stiles, N. R. B.; Levitan, C. A.; Wu, D.-A.; Tanguay, A. R.; Shimojo, S.

10.1101/2024.11.15.623713 — neuroscience — Posted on 2025-11-20

1581 Active sensing during a visual perceptual decision-making task

Ghani, N.

10.1101/2025.08.27.672629 — neuroscience — Posted on 2025-11-20

1582 Intramolecular competition generates pulsatory protein activity shaped by light, temperature, and evolution

Huang, Z.; Forson, M.; Benman, W.; Gardner, K. H.; Bugaj, L. J.

10.1101/2025.04.08.647774 — systems biology — Posted on 2025-11-20

1583 EGFR suppression and drug-induced potentiation are widespread features of oncogenic RTK fusions

Gao, Y.; Gonzalez Martinez, D.; Wissert, S.; Bader, H.; Sahni, N.; Le, A.; Doebele, R.; Bugaj, L.

10.1101/2025.11.19.689362 — cancer biology — Posted on 2025-11-20

1584 Machine Learning-Driven Nanopore Sensing for Quantitative, Label-Free miRNA Detection

Koch, C.; Sakthimani, S.; Noakes, V.; Cretu, M.; Newman, D.; Gutierrez, R.; Bruce, M.; Gorelik, J.; Guerra, N.; Edel, J.; Ivanov, A.

10.1101/2025.11.17.688909 — biophysics — Posted on 2025-11-20

1585 Buoyant mass reveals distinct T cell states predictive of checkpoint response

Yu, J.; Zhang, Y.; Duquette, S. M.; Kimmerling, R. J.; Kostas, J. C.; Lum, K. K.; LaBella, R.; Olcum, S.; Vacha, M.; Wasserman, S. C.; Aikins, R.; Katsis, K.; Usherwood, T. R.; Cohen, S.; Dinter, T.; Lawless, A.; Sharova, T.; Stevens, M.; Yee, G. L.; Wu, W.; Spranger, S.; Miettinen, T.; Ileana M Cristea, I. M.; Boland, G. M.; Manalis, S. R.

10.1101/2024.09.26.615179 — biophysics — Posted on 2025-11-20

1586 MotifPeeker: Benchmarking epigenomic profiling methods using motifs

Dash, H.; Roberts, T.; Weinert, M.; Skene, N.

10.1101/2025.03.31.645756 — bioinformatics — Posted on 2025-11-20

1587 Measuring Genomic Data with PFP

Luca, S.; Masillo, F.; Liptak, Z.

10.1101/2025.02.21.639270 — bioinformatics — Posted on 2025-11-20

1588 Preference-Based Fine-Tuning of Genomic Sequence Models for Personal Expression Prediction with Data Augmentation

Choi, M.; Cho, B.; Lee, S.

10.1101/2025.11.09.687505 — bioinformatics — Posted on 2025-11-20

1589 Morphology-Guided Deep Learning for Nanoparticle Agglomeration Diagnostic Assays

Jhawar, K.; Chu, X.-L.; DeGrandchamp, J. B.; Yin, Y.; Peddibhotla, A. L.; Banu, S.; Mohd Hatta, F. N. N.; Wang, Y.; Torok, P.; Wang, L.

10.1101/2025.09.13.676051 — bioengineering — Posted on 2025-11-20

1590 A simple library preparation modification significantly reduces barcode crosstalk in ONT multiplexed sequencing

Dai, Q.; Gunsch, C. K.; Granek, J. A.

10.1101/2025.11.19.689316 — genomics — Posted on 2025-11-20

1591 Revealing year-round activity of cave-dwelling insectivorous bats with a sonotype classifier in data-deficient areas.

Labadie, M.; Morand, S.; Caron, A.; De Nys, H. M.; Niama, F. R.; Nguilili, F.; TOBI, N.-; Bourgarel, M.; Bas, Y.; Roemer, C.

10.1101/2025.02.22.639615 — ecology — Posted on 2025-11-20

1592 Desert Hedgehog mediates stem Leydig cell differentiation through Ptch2/Gli1/Sf1 signaling axis

Zhao, C.; Chen, Y.; Liu, L.; Liu, X.; Xiao, H.; Wang, F.; Huang, Q.; Dai, X.; Tao, W.; Wang, D.; Wei, J.

10.1101/2025.06.13.659479 — developmental biology — Posted on 2025-11-20

1593 Nuclear GAPDH cascade mediates stress-dependent pathological cardiac growth

Nakamura, S.; Zhang, M.; Numata, G.; Kariya, T.; Sasaki, H.; Sasaki, M.; Ramos, A.; Amiya, E.; Hatano, M.; Ando, M.; Yasunaga, Y.; Iwakiri, M.; Koitabashi, N.; Zhu, G.; Tsujimura, T.; Lee, D. I.; Tristan, C.; Shahani, N.; Tsuchiya, Y.; Jaaro-Peled, H.; Sasano, T.; Slusher, B.; Kass, D. A.; Ushiku, T.; Ono, M.; Saitoh, T.; Ishizuka, K.; Sawa, A.; Takimoto, E.

10.1101/844902 — molecular biology — Posted on 2025-11-20

1594 Rapidly and reproducibly building a comprehensive catalogueof resistance-associated variants for M. tuberculosis

Adlard, D.; Malone, K. M.; Westhead, J.; Hunt, M.; Thai, H.; Colpus, M.; Turner, R. D.; Omar, S. V.; Eyre, D. W.; Ismail, N.; Walker, T. M.; Peto, T. E.; Crook, D. W.; Iqbal, Z.; Fowler, P. W.

10.1101/2025.10.02.679941 — microbiology — Posted on 2025-11-20

1595 Inferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamics

Dominguez-Mirazo, M.; Tahan, R.; Kirzner, S.; Lindell, D.; Weitz, J. S.

10.1101/2025.03.25.645349 — microbiology — Posted on 2025-11-20

1596 CDK7, CDK9, or CDK11 Inhibition Reduces Neutrophil-Driven Inflammation and Tissue Damage in Experimental Autoimmune Models

Schlotfeldt, M.; Voss, L.; Mansini, A. P.; Mehlberg, D.; Johannisson, S.; Radziewitz, M.; Schneider, A.-K.; Vahabi, S. M.; Wang, Y.; Gainer, H.; Li, J.; Osterloh, C.; Ernst, N.; Visser, R.; Vidarsson, G.; Petersen, F.; Yu, X.; Ludwig, R. J.; Vorobyev, A.; Amber, K. T.; Lux, A.; Bieber, K.

10.1101/2025.11.19.689221 — immunology — Posted on 2025-11-20

1597 A reversible allosteric inhibitor of GlyT2 alleviates neuropathic pain without on-target side effects

Cantwell Chater, R. P.; Peiser-Oliver, J.; Pati, T. K.; Quinn, A. S.; Lotsaris, I.; Frangos, Z. J.; Anderson, K. E.; Tischer, A. E.; Williams-Noonan, B. J.; AUBREY, K. R.; O'Mara, M. L.; Michaelides, M.; Mohammadi, S. A.; Cioffi, C. L.; Vandenberg, R. J.; Shahsavar, A.

10.1101/2025.04.21.649698 — neuroscience — Posted on 2025-11-20

1598 Global signal regression reduces connectivity patterns related to physiological signals and does not alter EEG-derived connectivity

Porxas, A. X.; Kassinopoulos, M.; Prokopiou, P. C.; Boudrias, M.-H.; Mitsis, G. D.

10.1101/2024.04.18.590163 — neuroscience — Posted on 2025-11-20

1599 The Virtual Brain Ontology: A Digital Knowledge Framework for Reproducible Brain Network Modeling

Martin, L.; Buelau, K.; Pille, M.; Schmitt, R. A.; Huettl, C.; Meier, J. M.; Taher, H.; Perdikis, D.; Schirner, M.; Stefanovski, L.; Ritter, P.

10.1101/2025.11.19.689211 — neuroscience — Posted on 2025-11-20

1600 Defence recognition of a stripe rust fungal effector is uncoupled from disease outcomes in wheat

Pereira, E. C.; Dagvadorj, B.; Tam, R.; Li, H.; Baig, D. I.; Moller, M.; Raphael, M.; Williams, S. J.; Periyannan, S.; Danila, F. R.; Rathjen, J. P.; Schwessinger, B.

10.1101/2025.07.30.667774 — plant biology — Posted on 2025-11-20

1601 Diverse infection models demonstrate robust resistance of Mycobacterium tuberculosis to innate immunity

Fairgrieve, M. R.; Brydon, E. C.; Chavez, R. A.; Kotov, D. I.; Vance, R.

10.1101/2025.11.20.687493 — immunology — Posted on 2025-11-20

1602 Rubisco Dark Inhibition in Angiosperms Shows a Complex Distribution Pattern

Nehls-Ramos, C.; Carmo-Silva, E.; Orr, D. J.

10.1101/2025.11.20.689527 — plant biology — Posted on 2025-11-20

1603 Chrono-atlas of cell-type specific daily gene expression rhythms in the regenerating colon

Carmona-Alcocer, V.; Gobet, C.; MacDonald, J.; Taleb, Z.; Naef, F.; Karpowicz, P.

10.1101/2025.11.20.689502 — physiology — Posted on 2025-11-20

1604 Hidden-driver inference reveals synergistic brain-penetrant therapies for medulloblastoma

Liu, J.; Yang, X.; Zhu, M.; Dong, X.; Zhou, H.; Bianski, B.; Jonchere, B. M.; Lin, W.; Fu, X.; Yang, L.; Freeman, B. B.; Wang, A.; Jiang, R.; Chen, T.; Robinson, G. W.; Roussel, M. F.; Merchant, T. E.; Gajjar, A.; Yu, J.

10.1101/2025.11.20.689490 — cancer biology — Posted on 2025-11-20

1605 Dynamic Epigenetic Changes During Antidepressant Pharmacotherapy in Major Depressive Disorder

Mueller, S.; Frank, J.; Zillich, E.; Streit, F.; Koch, N.; Schiele, M. A.; Domschke, K.; Tadic, A.; Herzog, D. P.; Wagner, S.; Mueller, M. B.; Treccani, G.; Gassen, N. C.; Rietschel, M.; Witt, S. H.; Lieb, K.; Engelmann, J.; Zillich, L.

10.1101/2025.11.20.688229 — genomics — Posted on 2025-11-20

1606 Widespread loss of Y expression in the absence of transcriptional dosage compensation in Rumex hastatulus

Sacchi, B. M.; Yuan, M.; Pyne, C.; Choudhury, B.; Gong, Y.; Barrett, S. C. H.; Wright, S. I.

10.1101/2025.11.20.689509 — genomics — Posted on 2025-11-20

1607 Pelagic trophodynamics control invertebrate population dynamics

Bercial, L. B.; Taboada, F. G.; Pitt, J. M.; Welch, J. L.; Warren, T. M.

10.1101/2025.11.20.689514 — ecology — Posted on 2025-11-20

1608 Analyses of bent spindles reveal the mechanics of anaphase B in fission yeast

Real-Calderon, P.; Fai, T.; Daga, R.; Lemiere, J.; Chang, F.

10.1101/2025.11.20.689516 — cell biology — Posted on 2025-11-20

1609 The emerging role of receptor trafficking insignalosome formation and sustained long-termWnt/β-catenin signaling

Haack, F.; Burrage, K.; Uhrmacher, A. M.

10.1101/2025.11.20.689481 — systems biology — Posted on 2025-11-20

1610 Proline transporters balance the salicylic acid-mediated trade-off between regeneration and immunity in plants

Yang, L.; Xu, D.; Belew, Z. M.; Cassia Ferreira Dias, N.; Wang, L.; Zhang, A.; Chen, Y.-F. S.; Newton, C. J.; Kong, F.; Zheng, Y.; Yao, Y.; Brewer, M. T.; Teixeira, P. J. P. L.; Nour-Eldin, H. H.; Xu, D.

10.1101/2025.11.20.689487 — plant biology — Posted on 2025-11-20

1611 E3 ubiquitin-ligase Hakai induces LRP4 degradation and regulates Wnt/beta-catenin signalling in colorectal cancer cells

Rodriguez-Alonso, A.; Jove, L.; Alfonsin, G.; Tasende, M.; Jordens, I.; Maurice, M.; Figueroa, A.

10.1101/2025.11.20.689197 — cancer biology — Posted on 2025-11-20

1612 Environmental dipolar relaxation during excited state proton transfer in Green Fluorescent Protein

Kurttila, M.; Camacho, I. S.; Zitti, A.; Platts, J. A.; Garcia-Ruiz, J.; Clarke, R. W.; Pudney, C. R.; Jones, D. R.; Jones, A. R.

10.1101/2025.11.20.688880 — biophysics — Posted on 2025-11-20

1613 Inferring and Evaluating Network Medicine-Based Disease Modules with Nextflow

Kersting, J.; Spindler, L. M.; Bucheron, C.; Aguirre-Plans, J.; Manz, Q.; Pock, T.; Tan, M.; Delgado-Chaves, F. M.; Nogales, C.; Schmidt, H. H. H. W.; Menche, J.; Maier, A.; Baumbach, J.; Guney, E.; List, M.

10.1101/2025.11.20.687681 — bioinformatics — Posted on 2025-11-20

1614 Analyzing the Performance of Deep Learning Splice Prediction Algorithms

Fortier, N.; Rudy, G.; Scherer, A.

10.1101/2025.11.20.689501 — bioinformatics — Posted on 2025-11-20

1615 Metabolic engineering of Corynebacterium glutamicum for production of the low-caloric natural sweetener D-allulose via phosphorylated intermediates

Lehnert, A.; Deditius, M.; Wirtz, A.; Baumgart, M.; Bott, M.

10.1101/2025.11.20.689482 — bioengineering — Posted on 2025-11-20

1616 Social attraction mediates collective foraging decisions in invasive hornets

Lcaombrade, M.; Doussot, C.; Mahot-Castaing, B.; Gautrais, J.; Goulefert, L.; Ferrieu, E.; Bourg, A.; Thiery, D.; Vogelweith, F.; Lihoreau, M.

10.1101/2025.11.20.689504 — animal behavior and cognition — Posted on 2025-11-20

1617 Pera virus mimics bacteria to infect Pedopumella sp. a freshwater heterotrophic Chrysophyceae

Billard, H.; Balor, S.; Soldan, V.; Szczepaniak, C.; Sime-Ngando, T.; Colombet, J.

10.1101/2025.11.20.689488 — ecology — Posted on 2025-11-20

1618 Omicron evolution drives increased ciliated cell tropism and dysfunction in nasal epithelia.

Parry, R.; Mostafavi, H.; McCallum, G.; Sng, J. D. J.; Joensuu, M.; Short, K. R.; Slonchak, A.; Khromykh, A.

10.1101/2025.11.19.689397 — microbiology — Posted on 2025-11-20

1619 Pathogenic IgG from long COVID patients with neurological sequelae triggers sensitive but not cognitive impairments upon transfer into mice

Mignolet, M.; Deroux, C.; Florkin, T.; Bielarz, V.; De Swert, K.; Halloin, N.; Sprimont, L.; Ladang, A.; George, F.; Gilloteaux, J.; Abeloos, L.; Van Weyenbergh, J.; Jamoulle, M.; Diederich, C.; Gillet, N. A.; Bulpa, P.; Nicaise, C.

10.1101/2025.11.20.689423 — neuroscience — Posted on 2025-11-20

1620 Developmental deviations of structural connectivity in youths with ADHD predict symptom and treatment outcomes

Xu, X.; Fu, Z.; Xu, H.; Zhang, K.; Yang, H.; Li, Y.; Zhao, Y.; Zheng, X.; Keller, A.; Xu, T.; Chen, R.; Cai, W.; Cao, Q.; Yang, L.; Cui, Z.

10.1101/2025.11.20.689391 — neuroscience — Posted on 2025-11-20

1621 Epigenetic editing of Cartpt promotes acquisition and extinction of cocaine memory

Winter, J. J.; Hooks, M.; Krick, K. S.; Goldhamer, A.; DiTullio, R. W.; Czarnecki, K. S.; Ekobeni, C.-E.; Han, C.; Rodriguez-Acevedo, K. L.; Hughes, B. W.; Estill, M.; Teague, C. D.; Ramakrishnan, A. W.; Shen, L.; Nestler, E. J.; Heller, E. A.

10.1101/2025.11.20.689329 — neuroscience — Posted on 2025-11-20

1622 Synchronization of two active ears via binaural coupling

Whiley, R. E.; Ledo, F.; Fedoryk, O.; Bergevin, C.

10.1101/2025.11.20.689396 — neuroscience — Posted on 2025-11-20

1623 APOE E4 Alzheimer's Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex

Huuki-Myers, L. A.; Divecha, H. R.; Bach, S. V.; Valentine, M. R.; Eagles, N. J.; Mulvey, B.; Bharadwaj, R. A.; Zhang, R.; Evans, J. R.; Grant-Peters, M.; Miller, R. A.; Kleinman, J. E.; Han, S.; Hyde, T. M.; Page, S. C.; Weinberger, D. R.; Martinowich, K.; Ryten, M.; Maynard, K. R.; Collado-Torres, L.

10.1101/2025.11.20.689483 — neuroscience — Posted on 2025-11-20

1624 Intertidal Gastropods (Gastropoda: Mollusca): Insights on diversity and distribution in the Mumbai Metropolitan Region, India.

Ansari, R. M.; Modi, S.

10.1101/2025.11.20.689409 — zoology — Posted on 2025-11-20

1625 Conformational Diversity and Allosteric Network Enable Multi-Substrate Recognition in Laccase Enzyme

Mitra, S.; Biswas, R.; Chakrabarty, S.

10.1101/2025.11.20.689517 — biophysics — Posted on 2025-11-20

1626 A frameshift mutation in the methyltransferase rlmN is associated with increased linezolid resistance in Mycobacterium tuberculosis

Reimer, B. M.; Green, A. G.

10.1101/2025.11.20.689544 — bioinformatics — Posted on 2025-11-20

1627 CAcnesDB: A database of Cutibacterium acnes with Integrated Functional Insights derived from Multi-modal Genome Annotation

Pandia, B.; Regati, D.; Rathod, N.; Sankar, S.; Vasudevan, S.; R, S.; Chandra, N.

10.1101/2025.11.20.689451 — bioinformatics — Posted on 2025-11-20

1628 OSM-11 modulates salinity-stress tolerance in Caenorhabditis elegans

Zhang, P.; Xue, B.; Xie, Y.; Li, K.; Yang, H.; Sun, P.; Zhang, L.

10.1101/2025.11.20.689412 — genetics — Posted on 2025-11-20

1629 Distinct Programs Drive Organ Development and Regeneration

Ma, R.; Deng, Z.; Li, Y.; Chen, J.; Zhang, J.; Feng, D.; Xu, C.; Zhou, J.; Zhang, X.; Xia, K.; Lu, P.

10.1101/2025.11.20.689429 — cell biology — Posted on 2025-11-20

1630 Description of Gopheromyces tardescens, gen. nov., sp.nov., Gigasporangiomyces pilosus, gen. nov., sp.nov., Kelyphomyces adhaerens, gen. nov., sp. nov., proposal of Testudinimycetales ord. nov. and Testudinimycetaceae fam. nov., and emended description of the order Neocallimastigales.

Morris, A.; Mills, T.; Miller, S. L.; Pratt, C. J.; Wang, Y.; Elshahed, M. S.; Youssef, N. H.; Vinzelj, J.

10.1101/2025.11.20.689491 — microbiology — Posted on 2025-11-20

1631 Multiomic analysis reveals that polyamines alter G. vaginalis-induced cervicovaginal epithelial cell dysfunction

Anton, L.; Kholod, O.; Phatate, R.; Ferguson, B.; Klohonatz, K.; Goods, B. A.; Gerson, K. D.

10.1101/2025.11.20.689523 — microbiology — Posted on 2025-11-20

1632 Humoral immunity induced by LP.8.1 monovalent vaccines against a broad range of SARS-CoV-2 variants including XEC, NB.1.8.1, XFG, and BA.3.2

Kaku, Y.; Fujiwara, M.; Uriu, K.; Yo, M. S.; Kawakubo, S.; Ito, J.; Itoh, N.; Uwamino, Y.; Saito, F.; Satoh, H.; The Genotype to Phenotype Japan (G2P-Japan) Consortium, ; Sato, K.

10.1101/2025.11.18.689152 — microbiology — Posted on 2025-11-20

1633 Updated taxonomy of the family Rhizobiaceae with proposals for 10 novel genera and 35 novel combinations

Naranjo-Robayo, N.; Harrison, T. L.; Esme, O.; Menendez, E.; Kuzmanovic, N.; Peix, A.; Young, J. P. W.; diCenzo, G. C.

10.1101/2025.11.20.689363 — microbiology — Posted on 2025-11-20

1634 Rv3400 is a phosphoglucomutase required for trehalose metabolism in Mycobacterium tuberculosis

Liu, Y.; Ruecker, N.; Faulkner, V.; Rachineni, K.; Al-Saffar, N.; VillacampaTeixeira, P.; Dias da Costa, T.; Johnson, E.; Robertson, B. D.; Ehrt, S.; Larrouy-Maumus, G.

10.1101/2025.11.20.689507 — microbiology — Posted on 2025-11-20

1635 MicroRNA166-HD-ZIP III module impacts tuber shape, color and productivity in potato

Patil, N. S.; Vasav, A.; Kumari, J.; Arora, G.; Natarajan, B.; Banerjee, A. K.

10.1101/2025.11.20.685984 — plant biology — Posted on 2025-11-20

1636 Ex Vivo Testing of Inflatable Penile Prosthesis in Human Cadaveric Penis with Paired in Silico Model offering Surgical and Biomechanical Insights

Khorshidi, M. A.; Bose, S.; Cullen, I. C.; Sullivan, J.; Johnston, R.; Patterson, K.; Watschke, B.; Sinnott, T.; Mareena, E.; Lally, C.

10.1101/2025.11.20.689496 — bioengineering — Posted on 2025-11-20

1637 Structure knows best: predicting ecological interactions across space through pairwise integration of latent network patterns

Abramov, K.; Biton, B.; Galai, G.; Puzis, R.; Pilosof, S.

10.1101/2025.11.20.689463 — ecology — Posted on 2025-11-20

1638 ratioPCR delivers precise real-time quantification from multi-template PCR via mechanistic bias correction

Kinter, J.; Stiefvater, A.; Osterop, S.; Sinnreich, M.

10.1101/2025.11.20.686216 — molecular biology — Posted on 2025-11-20

1639 Metabolic cross-talk promotes persistence of Enterococcus in a model of polymicrobial catheter-associated urinary tract infection

Zou, Z.; Pinkner, J. S.; Obernuefemann, C. L. P.; Kleinschmidt, K. R.; Sanick, D. A.; Hickerson, S. M.; Dodson, K. W.; Henderson, J. P.; Hultgren, S. J.; Caparon, M. G.

10.1101/2025.11.19.689321 — microbiology — Posted on 2025-11-20

1640 The effect of vitamin D and calcium supplementation on gut microbiota composition in adolescents living with HIV in Southern Africa

Hauptmann, M.; Dzavakwa, N. V.; Tembo, M. J.; Mazombwe-Chisenga, M.; Leschczyk, C.; Thirumoolanathan, G.; Sichibalo, K.; Madanhire, T.; Rowland-Jones, S. L.; Kelly, P.; Kranzer, K.; Filteau, S.; Gregson, C. L.; Simms, V.; Kasonka, L.; Ferrand, R. A.; Schaible, U. E.

10.1101/2025.11.20.689294 — microbiology — Posted on 2025-11-20

1641 B-cell follicles of lymphatic tissues act as a critical microanatomical niche for sustained viral replication, virus-host interaction and damage during chronic SIV infection

Cheng, Y.; Zhao, M.; Chen, J.; Mandal, S.; Lewis, M. G.; Li, Q.

10.1101/2025.11.19.687931 — immunology — Posted on 2025-11-20

1642 Neural and Behavioral Responses to Social Norm Violations Across Trust and Fairness Contexts

Dwamena, D.; Stanley, J. M.; Wyngaarden, J. B.; Kos, M.; Sharp, C.; Yang, Y.; Jarcho, J.; Fareri, D.; Smith, D. V.

10.1101/2025.11.20.689349 — neuroscience — Posted on 2025-11-20

1643 Age-Dependent Effects of Paraquat-Induced Parkinsonism on Serum Alpha-Synuclein Expression, Substantia Nigra Histoarchitecture and Neurobehaviour in Male Wistar Rats

Ichie, K. E.; Asomugha, A. L.; Okafor, I. A.

10.1101/2025.11.20.689379 — neuroscience — Posted on 2025-11-20

1644 Cumulative timing-dependent changes in corticospinal excitability during suprathreshold paired-pulse transcranial magnetic stimulation

Suresh, S.; Biabani, M.; Liao, W.-Y.; Opie, G. M.; Fornito, A.; Goldsworthy, M. R.; Rogasch, N. C.

10.1101/2025.11.19.689398 — neuroscience — Posted on 2025-11-20

1645 Attractive and repulsive couplings between circadian pacemaker neurons promote entrainment to light-dark cycles with after-effect

Kitaguchi, Y.; Komori, S.; Tei, H.; Uriu, K.

10.1101/2025.11.20.689452 — physiology — Posted on 2025-11-20

1646 Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition

Radic-Sarikas, B.; Markovic, M.; Sturtzel, C.; Ilg, M.; Zylka, M. M.; Surdez, D.; Metzelder, M.; Distel, M.; Ovsianikov, A.; Halbritter, F.; Kovar, H.

10.1101/2025.11.20.689456 — cancer biology — Posted on 2025-11-20

1647 Clathrin adaptors drive phase separation in endocytosis and trafficking

Draper-Barr, G.; Schiller, J.; Veith, K.; Niebling, S.; Ruiz-Carrillo, D.; Huang, Z.; Tischer, C.; Thuenauer, R.; Defelipe, L.; Garcia-Alai, M. M.

10.1101/2025.11.20.689461 — biophysics — Posted on 2025-11-20

1648 MembraneBuilder: High-speed membrane construction for large molecular dynamics simulations

Hamilton, C. J.; Hart, G.

10.1101/2025.11.20.689436 — biophysics — Posted on 2025-11-20

1649 Generating Hybrid Proteins with the MSA-Transformer

Tule, S.; Davis, S.; Koludarov, I.; Mora, A.; Boden, M.

10.1101/2025.11.20.689447 — bioinformatics — Posted on 2025-11-20

1650 NUDT5 regulates the global efficacy of nucleoside analog drugs by coordinating purine synthesis and PRPP allocation

Valerie, N. C. K.; Alam, S.; Hormann, F. M.; Martens, U.; Lundgren, B.; Gaetani, M.; Boström, J.; Rudd, S. G.; Arvidsson, P. I.; Altun, M.

10.1101/2025.11.20.689348 — biochemistry — Posted on 2025-11-20

1651 Same-sex sexual behaviours in a wasp despite sex recognition cues: the broad mating filter hypothesis

Charrat, B.; Meiffren, G.; Allaine, D.; Amat, I.; Desouhant, E.

10.1101/2025.11.20.689450 — animal behavior and cognition — Posted on 2025-11-20

1652 Dissecting disgust and fear in chimpanzees: From facilitation to disruption of cognitive processes

Sarabian, C.; MacIntosh, A. J. J.; Goncalves, A.; Kawai, N.; Adachi, I.

10.1101/2025.11.20.689418 — animal behavior and cognition — Posted on 2025-11-20

1653 Dissecting sequence determinants of DNA methylation and in silico perturbation

Chen, F.; Zhang, Q.; Zhu, S.; Liang, J.; Zhong, S.; Zhang, Z.; Su, J.; Guo, Y.; Fan, X.; Zhang, Y.; Yu, F.

10.1101/2025.11.20.689274 — genomics — Posted on 2025-11-20

1654 Genomic evidence for co-evolution and sporadic host shifts in leishmaniaviruses

Heeren, S.; Motta Cantanhede, L.; Chourabi, K.; de Oliviera Santana, M. C.; Klaps, J.; Kostygov, A. Y.; Yurchenko, V.; Lemey, P.; Dujardin, J.-C.; Van den Broeck, F.; Cupolillo, E.

10.1101/2025.11.20.685321 — evolutionary biology — Posted on 2025-11-20

1655 Peculiar Pigment Pattern and Population Profile of a Poisonous Pufferfish

Miyazawa, S.; Doi, H.; Takahashi, H.; Nishiyama, T.; Shigenobu, S.; Misawa, K.; Kikuchi, K.; Sakai, H.

10.1101/2025.11.20.687103 — evolutionary biology — Posted on 2025-11-20

1656 Global warming drives the evolutionary rate of H1N1 and H3N2 influenza viruses

Vilain, M.; Mghabghab, R.; Aris-Brosou, S.

10.1101/2025.11.20.689475 — evolutionary biology — Posted on 2025-11-20

1657 Tracking morphological development in stony corals

Fundakowski, G. J.; Brambilla, V.; Zawada, K. J. A.; Chow, C. F. Y.; Croasdale, E.; Errington, A.; Fontoura, L.; Marais, W. J.; Woods, R. M.; Edelaar, P.; Lala, K.; Madin, J. S.; Dornelas, M.

10.1101/2025.11.20.689442 — ecology — Posted on 2025-11-20

1658 Political legacies shape bear use of anthropogenic spaces

Munteanu, C.; Nita, M. D.; Stritih, A.; Roverelli, S.; Kraemer, B. M.; Ionescu, O.; Storch, I.

10.1101/2025.11.20.689425 — ecology — Posted on 2025-11-20

1659 BirdAVES in the wild: individual recognition as a step toward zebra finch communication networks

Chauhan, A.; Loning, H.; ter Avest, E.; Botta, B.

10.1101/2025.11.20.689459 — ecology — Posted on 2025-11-20

1660 Phenological benchmarking with a land surface model: an in-silico experiment for temperate forests

Yajima, M.; Seitz, J. I.; Matthaeus, W. J.; Girish Nair, G.; Daly, L.; Caldararu, S.

10.1101/2025.11.20.689458 — ecology — Posted on 2025-11-20

1661 Tropicalisation of rocky shore gastropod communities along the Baja California Peninsula

Zarzyczny, K. M.; Paz-Garcia, D. A.; Williams, S. T.; Rius, M. V.; MacLean, M.; Fenberg, P. B.

10.1101/2025.11.20.689443 — ecology — Posted on 2025-11-20

1662 Resprouting sustains cork oak seedlings while recent grazing limits resprouting and survival

Wadud, A. I.; Craveiro, J.; Erroi, S.; Alcobia, S.; Branco, M.; Vaz, P. G.

10.1101/2025.11.20.689419 — ecology — Posted on 2025-11-20

1663 Force-responsive symmetric cell divisions orient stomata along global tissue axes

Hartman, K. S.; Lopez, B. Y.; Gonzalez, J. H.; Goetz, M. E.; Cleveland, A.; Muroyama, A.

10.1101/2025.11.19.689402 — developmental biology — Posted on 2025-11-20

1664 Csf1, a tunnel-like lipid-transfer protein, mediates lipid remodeling and underpins eukaryotic membrane resilience to high hydrostatic pressure and cold

Abe, F.; Mioka, T.; Suzuki, Y.; Ogasawara, A.; Mochizuki, D.; Imura, S.; Kato, Y.; Mochizuki, T.

10.1101/2025.11.20.689427 — cell biology — Posted on 2025-11-20

1665 RNA switch model for localization and translation of the myelin basic protein mRNA

Topkar, V. V.; Wu, V.; Ho, L. T.; Ambiel, N.; Valenzuela, A.; Yoshimura, K.; Zuchero, J. B.; Fu, M.-m.; Das, R.

10.1101/2025.11.19.689361 — cell biology — Posted on 2025-11-20

1666 Pathophysiological remodeling of the skeletal muscle microenvironment in patients with lung cancer

10.1101/2025.11.19.689342 — molecular biology — Posted on 2025-11-20

1667 The barley ear row-number allele ancestral to the six-row allele vrs1.a1 is found in wild barley from the Fertile Crescent

Bedford, J. A.; Jones, H.; the AEGIS Consortium, ; Cockram, J.

10.1101/2025.11.20.688930 — molecular biology — Posted on 2025-11-20

1668 Ku limits aberrant mRNA splicing promoted by intronic antisense Alu elements

Pascarella, G. C.; Mikhova, M.; Parkhi, G.; Godfrey, J.; Heyza, J.; Janovic, T.; Olive, A.; Carninci, P.; Schmidt, J. C.; Meek, K.

10.1101/2025.11.20.689478 — molecular biology — Posted on 2025-11-20

1669 Hantavirus stability and inactivation

Vandenabeele, L.; Ayanwale, A.; Pietschmann, T.; Nilsson-Payant, B. E.

10.1101/2025.11.20.689437 — microbiology — Posted on 2025-11-20

1670 Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ

Humolli, D.; Ransome, J.; Piel, D.; Veening, J.-W.; Harms, A.

10.1101/2025.11.20.689424 — microbiology — Posted on 2025-11-20

1671 In vitro Isolation and Identification of Metarhizium pinghaense Isolates and Assessment of Their Virulence against Whiteflies and Aphids

Hu, H.; Wang, Y.; Li, C.; Zhang, R.; Liu, F.; Sun, X.

10.1101/2025.11.19.689371 — microbiology — Posted on 2025-11-20

1672 Airway macrophage specific expression of a dense glycocalyx and its remodelling following viral infection

Zhang, Z.; Nabi, I.; Hussell, T.; Dyer, D. P.

10.1101/2025.11.20.689471 — immunology — Posted on 2025-11-20

1673 Transcutaneous auricular vagus nerve stimulation enhances emotional bias towards happiness in healthy young adults: A comparative study of electrical and ultrasound stimulation

Kang, J. C.; Ng, J. Y.; Kaiser, M.; Choi, H.; Song, J.-J.; Jung, J.

10.1101/2025.11.19.689293 — neuroscience — Posted on 2025-11-20

1674 Gut metabolite IPA alleviates white matter injury post-ICH by enhancing myelin debris phagocytosis via Stap1 inhibition

Peng, M.; Zeng, M.; Tian, H.; He, C.; Zhang, L.; Zhao, Z.; Luo, Y.; Li, X.; Xia, F.; Liu, S.; Cheng, X.; Sun, H.

10.1101/2025.11.19.689382 — neuroscience — Posted on 2025-11-20

1675 Independent Filter Analysis for Group Discrimination in fMRI

Souweidane, Z.; Llera, A.; Smith, S. M.; Beckmann, C. F.

10.1101/2025.11.20.689235 — neuroscience — Posted on 2025-11-20

1676 MExConn: A Mechanistically Interpretable Multi-Expert Framework for Multi-Organelle Segmentation in Connectomics

Abir, A. R.; Saha, A.; Sawmya, S.; Athey, T. L.; Shavit, N. N.; Bayzid, M. S.

10.1101/2025.11.19.689394 — neuroscience — Posted on 2025-11-20

1677 Impact of the pulse artifact on evoked activity in human wakefulness and sleep

Cataldi, J.; Pelentritou, A.; Schwartz, S.; De Lucia, M.

10.1101/2025.11.20.689416 — neuroscience — Posted on 2025-11-20

1678 Unveiling the Multifaceted Networks of the Left DLPFC for Precision TMS Targeting

Paas Oliveros, L. K.; Poeppl, T. B.; Reuter, N.; Patil, K. R.; Kreuzer, S.; Tse, N. Y.; Cash, R. F. H.; Hoffstaedter, F.; Eickhoff, S. B.; Mueller, V. I.

10.1101/2025.11.19.689337 — neuroscience — Posted on 2025-11-20

1679 Harmonized Protocol for Segmentation of the Hippocampal Tail on High-Resolution in vivo MRI from the Hippocampal Subfields Group (HSG)

de Flores, R.; Canada, K. L.; Brown, T.; Gervais, N. J.; Maass, A.; Radman, G.; Shine, J.; Tucker, H. L.; Molloy, E. N.; Adams, J. N.; Reinke, M. B.; Bakker, A.; Berron, D.; Dalton, M. A.; Kennedy, K. M.; La Joie, R.; Mueller, S. G.; Ofen, N.; Olsen, R. K.; Raz, N.; Riggins, T.; Rodrigue, K. M.; Stark, C.; Wang, L.; Wisse, L. E.; Yushkevich, P. A.; Carr, V. A.; Daugherty, A. M.; Alzheimer's Disease Neuroimaging Initiative, ; Hippocampal Subfields Group,

10.1101/2025.11.20.689476 — neuroscience — Posted on 2025-11-20

1680 Genomic insights into photosymbiosis in giant clams: Comparisons with coral strategies

Uchida, T.; Yamashita, H.; Shimada, G.; Kawamitsu, M.; Shoguchi, E.; Shinzato, C.

10.1101/2025.11.20.689417 — zoology — Posted on 2025-11-20

1681 Evaluating effects of elevated and accelerated NPQ relaxation on yield, physiology and transcription in soybean

Singh, D.; de Souza, A. P.; Doran, L.; Hansen, J.; Burgess, S. J.

10.1101/2025.11.19.689310 — plant biology — Posted on 2025-11-20

1682 Protein-free membrane fusion: a refined view of the delicate fusogenic properties of calcium

Accorsi, M.; Ni Earchai, R.; Yandrapalli, N.; Pramanik, S.; Dimova, R.

10.1101/2025.11.19.689405 — biophysics — Posted on 2025-11-20

1683 A Global Discovery of Antimicrobial Peptides in Deep-Sea Microbiomes Driven by an ESM-2 and Transformer-based Dual-Engine Framework

Chen, B.; Mou, X.; Song, Z.; Lin, H.; Zhang, Y.; Li, J.

10.1101/2025.11.20.689422 — bioinformatics — Posted on 2025-11-20

1684 IRCAS: a novel end-to-end approach to identify, rectify and classify comprehensive alternative splicing events in a transcriptome without genome reference

Shen, C.; Zhang, Q.; Cao, Q.; Liu, X.; Zhang, Z.; Li, B.; Zhang, R.

10.1101/2025.11.20.689457 — bioinformatics — Posted on 2025-11-20

1685 ybyra: Y-chromosome haplogroup calling using a tree-based scoring method

Pinotti, T.; McColl, H.; Sikora, M.; Czech, L.

10.1101/2025.11.20.689455 — bioinformatics — Posted on 2025-11-20

1686 An inherent T cell-activating mRNA delivery platform for in vivo CAR T generation

Cao, Q.; Yao, Y.; Zheng, W.; Liu, H.; Jiang, M.; Xie, D.; Zhang, S.; Su, P.; Yuan, H.; Chen, X.; Fang, H.; Tian, H.

10.1101/2025.11.19.688592 — bioengineering — Posted on 2025-11-20

1687 The trimeric Shu complex in C. elegans is an ATPase that remodels RAD51 filaments in the homologous recombination-associated DNA damage response.

Chu, S. S. H.; Xing, G.; Ling, H.

10.1101/2025.11.17.685403 — biochemistry — Posted on 2025-11-18

1688 Altered glr-1 expression is linked to EtOH cessation-mediated behavior deficits in C. elegans.

Brandel-Ankrapp, K. L.; Arey, R. N.

10.1101/2025.11.19.689356 — animal behavior and cognition — Posted on 2025-11-20

1689 Latent gene network expression underlies the reversion of a polyphenic trait in the worker caste of ants

Vasquez-Correa, A.; Arnet, J.; Chen, T.; Abouheif, E.

10.1101/2025.11.19.689334 — evolutionary biology — Posted on 2025-11-20

1690 Riparian Woody Species Composition, Diversity, and Structure in Kiliti Watershed, Northwestern Ethiopia

Asres, H. G.; Woldu, Z. W.; Tesefaye, G. T.; Haile, G. H.; Worku, G. B.

10.1101/2025.11.19.689373 — ecology — Posted on 2025-11-20

1691 Integrative analysis of GTEx data reveals that systemic transcriptomes correlate with human spermatogenic dysfunction

An, X.; Xie, F.-Y.; Chen, J.; Chen, Y.; Ma, J.-Y.

10.1101/2025.11.19.689370 — developmental biology — Posted on 2025-11-20

1692 Impact of Cell Size, Light Wavelengths, and Intensities on Growth, Oxygen Production, and Consumption Rates of Chromochloris zofingiensis and Haematococcus lacustris

Chigozie, U.; HASHIGUCHI, A.; NAGARE, H.

10.1101/2025.11.18.689143 — microbiology — Posted on 2025-11-20

1693 Targeting peptide-MHC complexes with designed T cell receptors and antibodies

Motmaen, A.; Jude, K. M.; Wang, N.; Minervina, A.; Feldman, D.; Lichtenstein, M. A.; Ebenezer, A.; Correnti, C.; Thomas, P. G.; Garcia, K. C.; Baker, D.; Bradley, P.

10.1101/2025.11.19.689381 — immunology — Posted on 2025-11-20

1694 Adult Drosophila aversion to caffeine requires a unique TrpA1 isoform and the PLC signaling cascade

MILLEVILLE, R.; GILLAS, J.; THUY LA, A.; MANIERE, G.; BERTHELOT-GROSJEAN, M.; GROSJEAN, Y.; ROYET, J.; Kurz, C.-L.

10.1101/2025.11.20.689420 — neuroscience — Posted on 2025-11-20

1695 COSTS AND BENEFITS OF ACTING TOGETHER: A NON-HUMAN PRIMATE MODEL OF COOPERATIVE DECISION-MAKING

Quarta, E.; Lacal, I.; Grasso, S.; Schito, A.; Papagni, V.; Battaglia Mayer, A.

10.1101/2025.11.20.689048 — neuroscience — Posted on 2025-11-20

1696 PlantCV v4: Image analysis software for high-throughput plant phenotyping

Schuhl, H.; Brown, K. E.; Sheng, H.; Bhatt, P. K.; Gutierrez, J.; Schneider, D.; Casto, A. L.; Acosta-Gamboa, L.; Ballenger, J. G.; Barbero, F.; Braley, J.; Brown, A. M.; Chavez, L.; Cunningham, S.; Dilhara, M.; Dimech, A. M.; Duenwald, J. G.; Fischer, A.; Gordon, J. M.; Hendrikse, C.; Hernandez, G. L.; Hodge, J. G.; Huber, M.; Hurr, B. M.; Jarolmasjed, S.; Medina Jimenez, K.; Kenney, S.; Konkel, G.; Kutschera, A.; Lama, S.; Lohbihler, M.; Lorence, A.; Luebbert, C.; Ly, N.; Manching, H. K.; Marrano, A.; Meerdink, S.; Miklave, N. M.; Mudrageda, P.; Murphy, K. M.; Peery, J. D.; Pierik, R.; Polyd

10.1101/2025.11.19.689271 — plant biology — Posted on 2025-11-20

1697 Anticancer potential of piericidin A1 and derivatives isolated from Streptomyces sp. associated with Palythoa variabilis from Brazilian Reefs

Sahm, B. D. B.; Florencio, K. G. D.; Pinto, F. C. L.; Maia, A. I. V.; Rocha, C. A. M.; Jimenez, P. C.; Pessoa, O. D. L.; Lotufo, T. M. C.; Costa-Lotufo, L. V.; Wilke, D. V.

10.1101/2025.11.19.689357 — pharmacology and toxicology — Posted on 2025-11-20

1698 EPHB2 promotes diet-induced MASH liver fibrosis

Mimche, P.; Yoshigi, M.; Kamdem, S. D.; Pellizzari, S.; Kameni, E.; Atiogue, E.; Sprouse, F.; Evason, K.; Helms, M. N.; Goodman, M.; Wang, S.; So, J.; Roh, H. C.; Boudina, S.; Henkemeyer, M.

10.1101/2025.11.19.688968 — pathology — Posted on 2025-11-20

1699 Diffusion Models vs. DCGANs for Class-Imbalanced Lung Cancer CT Classification: A Comparative Study

Tabibian, M.; Razmpour, T.; Saha, R.

10.1101/2025.11.19.689331 — cancer biology — Posted on 2025-11-20

1700 Dual RNA Polymerase I Inhibition with CX-5461 and BMH-21 Synergizes in Breast Cancer by Activating p53-Dependent Stress

Chung, J. Y.; Nguyen, K. N.; Knutson, B. A.

10.1101/2025.11.19.689351 — cancer biology — Posted on 2025-11-20

1701 Uncovering High-Resolution Organization of Genomic Loci using Experimentally Informed Polymer Model

Mittal, R.; Heermann, D.; Bhattarcharjee, A.

10.1101/2025.11.19.689404 — biophysics — Posted on 2025-11-20

1702 LABEL-FREE HEMODYNAMIC MAPPING VIA ULTRAFAST POWER DOPPLER-ENHANCED PHOTOACOUSTIC IMAGING REVEALS EARLY THERAPY-INDUCED FUNCTIONAL CHANGES IN THE TUMOR.

Sankepalle, D. M.; Wei, L.; Shethia, R. T.; Kruizinga, P.; Mallidi, S.

10.1101/2025.11.19.688289 — biophysics — Posted on 2025-11-20

1703 Targeted fluorescent lipid microparticles for quantitative measurement of phagosomal pH

Michelis, S.; Uhl, H.; Niedergang, F.; Fattaccioli, J.; Dumat, B.; Mallet, J.-M.

10.1101/2025.11.20.685382 — biophysics — Posted on 2025-11-20

1704 Zygosity-Aware DNA Language Modeling Improves Ancestry and Gene Expression Prediction

El Rashidy, H.; Varnosfaderanii, A. S.; Fellay, J.

10.1101/2025.11.19.689326 — bioinformatics — Posted on 2025-11-20

1705 Micro-CT Analysis of a Needle to Nerve Approach for Interfascicular Peripheral Nerve Stimulation in Porcine Nerves

Randolph, M. A.; Marcu, V. I.; Tsiptsis, C.; Shoffstall, A. J.; Baskin, J. Z.; Tyler, D. J.

10.1101/2025.11.19.687256 — bioengineering — Posted on 2025-11-20

1706 Incomplete functional divergence drives genetic synergy during floral development in tomato

Gaarslev, N.; Xu, Y.; Lize, E.; Julca, I.; Glover, N.; Soyk, S.

10.1101/2025.11.19.689068 — genetics — Posted on 2025-11-20

1707 Molecular Evolution under Macro-Perturbation Barrier and the Fixation Process of Polyploidization

Gu, X.

10.1101/2025.11.19.689354 — evolutionary biology — Posted on 2025-11-20

1708 No limit yet to phenological plasticity of reproductive timing in a high-elevation hibernator experiencing earlier springs

Wells, C. P.; Van Vuren, D. H.

10.1101/2025.11.19.688555 — ecology — Posted on 2025-11-20

1709 Cadmium toxicity to the human gut microbiome varies depending on composition

Perez-Donado, C.; Liu, S.; Seravalli, J.; Auchtung, J. M.; Rose, D.

10.1101/2025.11.19.689308 — microbiology — Posted on 2025-11-20

1710 Reproductive and Seasonal Impacts on Rock Iguana Health: A Cross-sectional Study of Microbiome Changes

Sobih, S. E.; Lewis, E. L.; Kapheim, K. M.; French, S. S.

10.1101/2025.11.19.689195 — microbiology — Posted on 2025-11-20

1711 Control of antigen presentation on MHC-I by a bacterial secretion system

Leddy, O.; McGinn, R.; Allsup, B.; Leone, M.; Timms, P.; Gutierrez-Gonzalez, M.; Fahad, A. S.; Milligan, R.; Garcia-Beltran, W. F.; DeKosky, B. J.; White, F. M.; Bryson, B. D.

10.1101/2025.11.19.689332 — immunology — Posted on 2025-11-20

1712 Comparing Methods for Mass Univariate Analyses of Human EEG: Empirical Data and Simulations

Tebbe, A.-L.; Panitz, C.; Keil, A.

10.1101/2025.11.19.689266 — neuroscience — Posted on 2025-11-20

1713 Silmitasertib, an FDA-designated orphan CK2 Inhibitor, ameliorates neuropathology and motor dysfunction in a Huntington's disease mouse model

Pelzel, R.; Herbst, M. A.; Rozema, N. B.; Solem, M. A.; Gomez-Pastor, R.

10.1101/2025.11.19.689275 — neuroscience — Posted on 2025-11-20

1714 A 4-pole Theory-Based Compensation Method using Multiple Loads for Impedance Spectroscopy of Porcine Brain Tissue

Gerber, M.; Symmank, M.; Possner, L.; Wallenta, M.; Pliquett, U.; Laukner, M.; Knoesche, T.; Gueresir, E.; Wilhelmy, F.; Weise, K.

10.1101/2025.11.19.689299 — neuroscience — Posted on 2025-11-20

1715 A New Method for Optimal Placement of Tumor Treating Fields Electrodes

Weise, K.; Mikic, N.; Cao, F.; Wong, E. T.; Knoesche, T.; Thielscher, A.; Korshoej, A. R.

10.1101/2025.11.19.689304 — neuroscience — Posted on 2025-11-20

1716 Longitudinal Exploration of Auditory Sensory-Perceptual Processing in CLN3 Disease (Juvenile Neuronal Ceroid Lipofuscinosis (Batten disease)): A High-Density Auditory Evoked Potential (AEP) Study.

Bojanek, E. K.; Lang, E. R.; Adams, H. R.; Vermilion, J.; Augustine, E. F.; Brima, T.; Nasimjonova, S.; Freedman, E. G.; Foxe, J. J.

10.1101/2025.11.19.689311 — neuroscience — Posted on 2025-11-20

1717 A validated panel of commercial antibodies for reliable detection of FET proteins.

Tacconelli, S.; Odemwingie, L.; Reber, S.; Di Pancrazio, S.; Zoller, T. I.; Biasetti, L.; Troakes, C.; Ruepp, M.-D.; Vance, C.

10.1101/2025.11.19.689317 — neuroscience — Posted on 2025-11-20

1718 DNA Methylation Dynamics Reveal Unique Plant Responses and Transcriptional Reprogramming to Combined Heat and Phosphate Deficiency Stress

Lozano-Enguita, A.; Victoria Baca-Gonzalez, V.; Morillas-Montaez, A.; Pascual, J.; Valledor, L.; del Pozo, J. C.; Caro, E.

10.1101/2025.11.19.689328 — plant biology — Posted on 2025-11-20

1719 Hundred-Picolitre Droplet on Demand Tape Drive and XES Prototypes for Time-Resolved Serial Crystallography at VMXi, Diamond Light Source

Aller, P.; Sanchez-Weatherby, J.; Bosman, R.; Devenish, N. E.; Hinchliffe, P.; Horrell, S.; Ip, J.; Littlewood, R.; Male, A.; Gimenez-Navarro, E.; Neuman, U.; Kamps, J. J. A. G.; Omar, D.; Parkinson, L.; Pandi, M.; Rubies, N.; Sandy, J.; Shilova, A.; Spencer, J.; Spiers, J.; Sutter, J. P.; Telfer, A.; Thompson, A. J.; Tooke, C. L.; Williams, B.; Zhou, T.; Hough, M.; Orville, A. M.

10.1101/2025.11.19.689295 — biophysics — Posted on 2025-11-20

1720 ApoE lipidation, not isoform, is the key modulator of Aβ interaction, uptake, and cytotoxicity

Nurmakova, K.; Gomes, G.-N. W.; Levine, Z. A.

10.1101/2025.11.19.685371 — biophysics — Posted on 2025-11-20

1721 Systematic evaluation of peptide property predictors with explainable AI technique SHAP

Lapin, J.; Iuzhaninov, M.; Hoelzlwimmer, A. J.; Wilhelm, M.

10.1101/2025.11.19.689259 — bioinformatics — Posted on 2025-11-20

1722 Semantic-Aware Graph Embedding Approach Uncovers LC-61, a Potent Anti-Leishmania infantum Compound

Costa, V. A. F.; Carvalho, A. M. d. S.; Chelucci, R. C.; Felizardo, G. S. S.; Bernardes, C. A. C.; Martin, H.-J.; Braga, R. d. C.; Charneau, S.; Muratov, E.; Andricopulo, A. D.; Bastos, I. M. D.; Neves, B. J.

10.1101/2025.11.19.687645 — bioinformatics — Posted on 2025-11-20

1723 Puget predicts gene expression across cell types using sequence and 3D chromatin organization data

Hang, S.; Wang, X.; Murtaza, G.; Jha, A.; Wen, B.; Fang, T.; Sanders, J.; Wang, S.; Noble, W. S.

10.1101/2025.11.19.689320 — bioinformatics — Posted on 2025-11-20

1724 Running with an exotendon reduces compressive knee contact force

Stingel, J.; Haralabidis, N.; Hicks, J.; Uhlrich, S.; Delp, S.

10.1101/2025.11.19.689319 — bioengineering — Posted on 2025-11-20

1725 A model-centered introduction to curiosity

Chartouny, A.; Girard, B.; Khamassi, M.

10.1101/2025.11.19.689250 — animal behavior and cognition — Posted on 2025-11-20

1726 Pathogens pull hardest in the coevolutionary arms-race to determine age-specific transmission biases

Hulse, S. V.; Bruns, E. L.

10.1101/2025.11.19.689276 — evolutionary biology — Posted on 2025-11-20

1727 Ancestral Sequences Cannot be Accurately Reconstructed via Interpolation in a Variational Autoencoder's Latent Space

Gorstein, E.; Tang, M.; Bruzzone, H.; Solis-Lemus, C.

10.1101/2025.11.19.689264 — evolutionary biology — Posted on 2025-11-20

1728 The double-edged sword of wildlife biodiversity in the agricultural matrix: a case study of reptiles in vineyards

Sagi, L.; Topper, A.; Keynan, O.; Bouskila, A.; Kolodny, O.

10.1101/2025.11.19.689282 — ecology — Posted on 2025-11-20

1729 Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR

Chavez-Abiega, S.; Bordes, L.; Postma, M.; Bruggeman, F. J.; Goedhart, J.

10.1101/2025.11.19.689196 — cell biology — Posted on 2025-11-20

1730 Consequences of dietary amino acid imbalance on growth and gas exchange in black soldier fly (Hermetia illucens) larvae

Schow-Madsen, M.; Jensen, K.; Marquez-Toribio, M.; Schon, M. L.; Schou, T. M.; Norgaard, J. V.; Overgaard, J.

10.1101/2025.09.05.674443 — physiology — Posted on 2025-11-20

1731 Impaired Chylomicron Secretion Results in Reduced Body Fat and Increased Intestinal Fatty Acid Oxidation by Activation of Autophagy

Neupane, K. R.; Karakashian, A.; Mobilia, M.; Hage, O.; Tso, P.; Liu, M.; Vergnes, L.; Reue, K.; Gordon, S. M.

10.1101/2025.11.19.689245 — physiology — Posted on 2025-11-20

1732 A unified genetic perturbation language for human cellular programming

Hartman, A.; Takacsi-Nagy, O.; Kernick, C.; Theberath, N. E.; Lu, J.; Wu, L.; Mantilla, M.; Mittra, S.; McClellan, A.; Johnson, N.; Mohamad, L.; Castillo-Colin, L.; Hoque, F.; Eapen, A.; Chen, A.; Moser, L. M.; Rogando, T.; Hernandez, A.; Santostefano, K.; Satpathy, A. T.; Roth, T. L.

10.1101/2025.11.20.689421 — genetics — Posted on 2025-11-20

1733 Whole Genome Assembly of the Atlantic Bluefin Tuna Thunnus thynnus, with Phased Haplotypes

Block, B. A.; Johri, S.; Machado, A.; Ciezerak, A.; Castro, F.; Del Rocio, L. J.; Eli-Zaquin, T.; Peluso, P.; Concepcion, G. T.

10.1101/2025.11.18.689121 — evolutionary biology — Posted on 2025-11-20

1734 CD8α+ cells suppress SIV replication without evidence of viral immune escape during post treatment control

Moriarty, R. V.; Harwood, O. E.; Johnson, E. P.; Gardner, W.; Valencia, C. C.; Conchas, A.; Immonen, T. T.; Reynolds, M. R.; Keele, B. F.; O'Connor, S. L.

10.1101/2025.11.18.689043 — microbiology — Posted on 2025-11-20

1735 A SARS-CoV-2 entry inhibitor trimerizes to lock the spike protein in a closed conformation

Mou, H.; Gao, B.; Ye, G.; Zhang, L.; Saxena, D.; Bu, F.; Vishwakarma, J.; Zhou, S.; Bayona, C. R.; Li, L.; Getmanenko, Y.; Bhandari, J.; Bailey, C. C.; Crynen, G. C.; Kitzmiller, C. E.; Li, H.; Otsuka, Y.; Wang, C.; Batra, L.; Weston, S.; Frieman, M. B.; Meyerholz, D. K.; Scampavia, L.; Spicer, T.; Harris, R. S.; Cameron, M.; Bannister, T.; Zheng, J.; Farzan, M.; Li, F.; Choe, H.

10.1101/2025.11.19.689107 — microbiology — Posted on 2025-11-20

1736 Iron acquisition strategies of the rock-inhabiting fungus Knufia petricola reveal vulnerability to chelator-based mitigation

Gerrits, R.; Schumacher, J.; Gorbushina, A.

10.1101/2025.11.18.689051 — microbiology — Posted on 2025-11-20

1737 Tissue macrophages stem sepsis induced altered organ repair

de ROQUETAILLADE, C.; Durand, M.; Beaucote, V.; Borouchaki, A.; BLOT, P.-L.; GUILLEMIN, J.; MANSOURI, S.; BROCIC, J.; CHERCHAME, E.; COUTELIER, M.; MEMMADI, M.; ZELCO, A.; Sadoune, M.; PICOD, A.; Chadjichristos, C. E.; Samuel, J.-L.; LAFONTAINE, R.; Tabibzadeh, N.; Gayat, E.; Mebazaa, A.; Chousterman, B. G.

10.1101/2025.11.18.689163 — immunology — Posted on 2025-11-20

1738 N6-methyladenosine RNA methylation is a novel epitranscriptomic regulator of excessive alcohol drinking and vulnerability to relapse

Maccioni, R.; Lorrai, I.; Torres, I.; Puliga, R.; Repunte-Canonigo, V.; Sanna, P. P.

10.1101/2025.11.16.688690 — neuroscience — Posted on 2025-11-20

1739 Hidden in Plain Sight. How Ks histogram dynamics can reveal and obscure ancient whole genome duplications.

Dunn, T.; Sethuraman, A.

10.1101/2025.11.19.689290 — genomics — Posted on 2025-11-19

1740 MeCP2 NID interaction with RNA: Implications for Rett Syndrome-Relevant Protein Regulation

Good, K. V.; Strickfaden, H.; Muhammad, T.; Vincent, J. B.; Hendzel, M.; Nelson, C. J.; Ausio, J.

10.1101/2025.11.19.689340 — molecular biology — Posted on 2025-11-19

1741 Assessing the diversity and functional profile of the microbial proteome in fermented foods

Winkler, L.; Awan, A.; Rideout, N.; Kleiner, M.

10.1101/2025.11.19.689333 — microbiology — Posted on 2025-11-19

1742 Expanding the scope of Mycobacterium abscessus reference strains to improve pulmonary disease modeling

Howe, R. A.; Tabor, C.; Panthi, C. M.; Cheng, G.; Rimal, B.; Chen, E.; Nguyen, N.; Lamichhane, G.

10.1101/2025.11.19.689313 — microbiology — Posted on 2025-11-19

1743 Optimization of fermentation conditions for Metarhizium robertsii and its effect on rice growth

Wang, D.; She, X.; Zhu, M.; Fu, J.; Han, D.; Bai, J.

10.1101/2025.11.19.689318 — microbiology — Posted on 2025-11-19

1744 Rapid neocortical network modifications via dendritic plateau potential induced plasticity

Xiao, K.; Li, Y.; Sullivan, B. J.; Li, G.; Magee, J. C.

10.1101/2025.11.19.689338 — neuroscience — Posted on 2025-11-19

1745 MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny

Alquaddoomi, F. S.; Burke, J. T.; Sosinski, L.; Mayer, D. A.; Brenner, E. P.; Chen, S. Z.; Krol, J. D.; Wolfe, E. P.; Rubinetti, V. P.; Amolitos, S.; Reason, K. M.; Johnston, J. B.; Ravi, J.

10.1101/2022.02.18.461833 — genomics — Posted on 2025-11-19

1746 A Multimodal Atlas Reveals the Anatomical Distribution of Medium Spiny Neuron Subtypes and a Novel RGS6+ Population in the Primate Striatum

Abdelhady, G.; Brull, O. R.; He, J.; Lin, M. K.; Galvan, A.; Pfenning, A. R.; Bostan, A. C.; Stauffer, W. R.

10.1101/2025.11.16.688724 — neuroscience — Posted on 2025-11-19

1747 Programmed Cell Death Modifies Neural Circuits and Tunes Intrinsic Behavior

Kochersberger, A.; Torkashvand, M. M.; Lee, D.; Baskoylu, S.; Sengupta, T.; Koonce, N.; Emerson, C.; Patel, N. V.; Colon-Ramos, D.; Flavell, S. W.; Horvitz, H. R.; Venkatachalam, V.; Hammarlund, M.

10.1101/2023.09.11.557249 — neuroscience — Posted on 2025-11-19

1748 Linking Electrophysiological Metrics to Oxidative Metabolism: Implications for EEG-fMRI Association

Zhong, X.; Van Lankveld, H.; Mathew, A.; Chen, J. J.

10.1101/2025.11.04.686568 — neuroscience — Posted on 2025-11-19

1749 Next-generation enhancer AAVs for selective interspecies targeting of midbrain dopaminergic neurons

Caplan, K. A.; Chen, K.; Wang, Y.; Wienisch, M.; Chai, R.; Kang, I.-H.; Chen, C. S.; del Rosario, R.; Krienen, F.; Wang, F.; Feng, G.

10.1101/2025.11.06.687071 — neuroscience — Posted on 2025-11-19

1750 Slow Electromechanical Interference Links Division Geometry, Differentiation Bias, and Senescence-like Arrest

Bueno, A. D. M.

10.1101/2025.10.28.684574 — biophysics — Posted on 2025-11-19

1751 The Rayleigh Quotient and Principal Component Analysis I

Carilli, M. T.; Jackson, K. C.; Pachter, L.

10.1101/2025.11.19.689125 — bioinformatics — Posted on 2025-11-19

1752 sc4D: spatio-temporal single-cell transcriptomics analysis through embedded optimal transport identifies joint glial response to Alzheimer's disease pathology

Rao, I.; Kellis, M.; Tanigawa, Y.

10.1101/2025.11.19.689166 — bioinformatics — Posted on 2025-11-19

1753 Adrenomedullin-RAMP2 enhances endothelial cell homeostasis synergistically with shear stress

Yoon, Y.; Duffy, R.; kirk, S.; Promnares, K.; Karki, P.; Birukova, A. A.; Birukov, K. G.; Yuan, Y.

10.1101/2025.09.21.677608 — bioengineering — Posted on 2025-11-19

1754 De novo Design of All-atom Biomolecular Interactions with RFdiffusion3

Butcher, J.; Krishna, R.; Mitra, R.; Brent, R. I.; Li, Y.; Corley, N.; Kim, P. T.; Funk, J.; Mathis, S. V.; Salike, S.; Muraishi, A.; Eisenach, H.; Thompson, T. R.; Chen, J.; Politanska, Y.; Sehgal, E.; Coventry, B.; Zhang, O.; Qiang, B.; Didi, K.; Kazman, M.; DiMaio, F.; Baker, D.

10.1101/2025.09.18.676967 — biochemistry — Posted on 2025-11-19

1755 De Novo Design of a Protein Binder to Probe Gas Channel and Enhance the Oxygen Tolerance of Hydrogenase

Sun, X.; Li, W.; Li, W.; Luo, H.; Xiao, Q.; Zhang, L.; Jiang, P.; Wu, G.; Zhang, L.

10.1101/2025.11.19.689374 — biochemistry — Posted on 2025-11-19

1756 Integrating morphology and gene expression of neural cells in unpaired single-cell data using GeoAdvAE

Du, J. T.; Lin, K. Z.

10.1101/2025.11.19.689368 — genomics — Posted on 2025-11-19

1757 Gene-Culture Coevolution Favours the Emergence of Traditions in Mate Choice through Conformist Social Learning

Federico, D.; Cosme, M.; Dechaume-Moncharmont, F.-X.; Ferdy, J.-B.; Pocheville, A.

10.1101/2025.09.05.674569 — evolutionary biology — Posted on 2025-11-19

1758 Long-read sequencing-based atlas of tissue-specific expression of Drp1 transcript variants

Yan, F.; Jabbari, J. S.; Ling, N. X.; Kong, A. M.; Truong, J. Q.; Rosdah, A. A.; Langendorf, C.; Zhang, L.; Lees, J. G.; Bass-Stringer, S.; Ann-Onda, D.; Loh, K.; Holien, J.; Lal, S.; Davidson, N. M.; Oakhill, J. S.; Lim, S. Y.

10.1101/2025.10.06.680828 — cell biology — Posted on 2025-11-19

1759 Mitotyping - An integrative framework to quantify mitochondrial specialization and plasticity

Monzel, A. S.; Devine, J.; Kapri, D.; Sturm, G.; Trumpff, C.; Menon, V.; De Jager, P.; Enriquez, J. A.; Picard, M.

10.1101/2025.02.03.635951 — cell biology — Posted on 2025-11-19

1760 Functional genomics reveals strain-specific genetic requirements conferring hypoxic growth in Mycobacterium intracellulare

Tateishi/Yoshitaka, Y.; Ozeki, Y.; Nishiyama, A.; Morishige, Y.; Minato, Y.; Baughn, A.; Matsumoto, S.

10.1101/2024.05.12.593797 — microbiology — Posted on 2025-11-19

1761 Innate-adaptive IFN cross-talk reprograms myeloid and T cells for antitumor immunity with a second-generation recombinant MVA

Liu, S.; Wang, Y.; Mazo, G.; Baseer Tariq, S.; Angulo-Lozano, J.; Yang, N.; Zhang, T.; Wang, Y.; Hirschhorn, D.; Ji, L.; Tan, A.; Wang, J.; Yan, W.; Choi, J.; Xiang, J. Z.; Li, M. O.; Merghoub, T.; Wolchok, J. D.; Rice, C. M.; Deng, L.

10.1101/2022.09.25.509429 — immunology — Posted on 2025-11-19

1762 Canopy1/Cnpy1 is required for proper V2R processing and transport; its loss impairs the function and circuit organization of basal/V2R vomeronasal sensory neurons

Mathias, N.; Dolphin, N.; Ruquet, A.; Forni, P. E.

10.1101/2025.11.19.689260 — neuroscience — Posted on 2025-11-19

1763 Dopamine reward transients calibrate movement timing via one-shot updates to behavioral vigor.

Hamilos, A. E.; Wijsman, I. C.; Ding, Q.; Assawaphadungsit, P.; Ozcan, Z.; Norri, E.; Reinhold, K.; Sabatini, B. L.; Assad, J. A.

10.1101/2025.04.04.647288 — neuroscience — Posted on 2025-11-19

1764 A Practical Resource for Multi-Omics Data Integration in Microbial Systems

Mujchariyakul, W.; Hachani, A.; Stinear, T. P.; Le Cao, K.-A.; Howden, B. P.; Walsh, C. J.; Guerillot, R.

10.1101/2025.11.19.689359 — systems biology — Posted on 2025-11-19

1765 EGFR suppression and drug-induced potentiation are widespread features of oncogenic RTK fusions

Gao, Y.; Gonzalez Martinez, D.; Wissert, S.; Bader, H.; Sahni, N.; Le, A.; Doebele, R.; Bugaj, L.

10.1101/2025.11.19.689362 — cancer biology — Posted on 2025-11-19

1766 Zα and Zβ domains of ADAR1 and ZBP1 bind to G-quadruplexes with low micromolar affinity

Kroft, C.; Krall, J. B.; Warchol, M.; Welty, R.; Herbert, A.; Henen, M. A.; Vögeli, B.

10.1101/2025.11.19.688355 — biophysics — Posted on 2025-11-19

1767 AI-HEAD: Auto-indexing for Helical assembles' diffraction and fast dynamic structure determination

Pei, T.; Yu, M.; Li, S.; Zhang, D.; Sun, F.; Zhang, Y.

10.1101/2025.11.17.688965 — biophysics — Posted on 2025-11-19

1768 SHEST: Single-cell-level artificial intelligence from haematoxylin and eosin morphology for cell type prediction and spatial transcriptomics reconstruction

Jeong, H.; Oh, J.; Lee, D.; Kang, J. H.; Choi, Y.-L.

10.1101/2025.11.19.689364 — bioinformatics — Posted on 2025-11-19

1769 Incorporating Large Language Model-Derived Information into Hypothesis Testing for Genomics

Bryan, J. G.; Niu, H.; Li, D.

10.1101/2025.04.30.651464 — bioinformatics — Posted on 2025-11-19

1770 Galectin-3 is a Nanotherapeutic Target in Graft-versus-Host Disease Mediated Kidney Injury

Panagiotakopoulou, M.; Sullivan, A. N.; Argyropoulos, K. V.; Kousa, A. I.; Nunez, J.; Pierpont, K.; Ruiz, S.; Grabarnik, E.; Gipson, B.; Ghale, R.; Seshan, S.; Muthukumar, T.; Hanash, A. M.; Van Den Brink, M. R. M.; Jaimes, E. A.; Heller, D. A.

10.1101/2025.11.19.688972 — bioengineering — Posted on 2025-11-19

1771 A simple library preparation modification significantly reduces barcode crosstalk in ONT multiplexed sequencing

Dai, Q.; Gunsch, C. K.; Granek, J. A.

10.1101/2025.11.19.689316 — genomics — Posted on 2025-11-19

1772 Spatially explicit forest mortality forecasts are driven by autocorrelation, not ecological context

Ganz, K.; van Wagtendonk, L.; Khatri-Chhetri, P.; Moskal, M.

10.1101/2025.11.19.689366 — ecology — Posted on 2025-11-19

1773 Cell-type-specific alternative splicing in the cerebral cortex and kidney of a Setbp1S858R Schinzel-Giedion Syndrome patient variant mouse

Soelter, T. M.; Jones, E. F.; Howton, T. C.; Crumley, A. B.; Wilk, E. J.; Lasseigne, B. N.

10.1101/2024.06.26.600823 — genomics — Posted on 2025-11-19

1774 Epistasis and background dependence in the evolution of Omicron variants of the SARS-CoV-2 Spike protein

Moulana, A.; Dupic, T.; Desai, M. M.

10.1101/2025.11.18.689118 — evolutionary biology — Posted on 2025-11-19

1775 RNA-guided nucleases enable a gene drive of insertion sequences in plasmids

Mears, K. S.; Rossine, F. W.; Quinones-Olvera, N.; Souque, C.; Wiesenfeld, S. S.; Jean, K. D. C.; Pai, S. V.; Baym, M.

10.1101/2025.02.20.638934 — microbiology — Posted on 2025-11-19

1776 A hierarchical framework for cortical and subcortical gray-matter parcellation across rodents, primates, and humans

Venkadesh, S.; Tian, Y.; Linn, W.-J.; Martinez, J. B.; Mansour, H.; Cook, J.; Schaeffer, D. J.; Szczupak, D.; Silva, A. C.; Johnson, G. A.; Yeh, F.-c.

10.1101/2025.09.08.675002 — neuroscience — Posted on 2025-11-19

1777 Root anatomical gradients and cultivar differences underlie variation in root hydraulic properties in German winter wheat

Baca Cabrera, J. C.; Jones, D. H.; Vanderborght, J.; Behrend, D.; Schneider, H. M.; Lobet, G.

10.1101/2025.11.19.689226 — plant biology — Posted on 2025-11-19

1778 Multimodal Cross-Attentive Graph-Based Framework for Predicting In Vivo Endocrine Disruptors

Santos, E. S. d. A.; Felizardo, G. S. S.; da Silva, A. C. G.; Martin, H.-J.; Muratov, E. N.; Braga, R. d. C.; Neves, B. J.

10.1101/2025.09.16.676584 — pharmacology and toxicology — Posted on 2025-11-19

1779 A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation

Rockenbach, K. C.; Zanini, S. F.; Tidy, A. C.; Morris, R. J.; Wells, R. J.; Golicz, A. A.

10.1101/2025.08.30.673246 — bioinformatics — Posted on 2025-11-19

1780 Shifting the PPARγ conformational ensemble towards a transcriptionally repressive state improves covalent inhibitor efficacy

Arifova, L.; MacTavish, B. S.; Laughlin, Z.; Karadi Girdhar, M. N.; Shang, J.; Li, M.-H.; Yu, X.; Zhu, D.; Kamenecka, T. M.; Kojetin, D. J.

10.1101/2025.03.04.640448 — biochemistry — Posted on 2025-11-19

1781 The AltR transcription factor responds to plant thiosulfinates to regulate gene expression in a bacterial pathogen of onion.

Jan, H.-H.; Kong, F.; MacLellan, M. P.; Yang, L.; Dutta, B.; Kvitko, B. H.

10.1101/2025.11.19.689302 — microbiology — Posted on 2025-11-19

1782 Generation of effector CD4+ T cells from Human iPSC

Amirault, J.; Heinze, D.; Yang, M.; Kerr, C. M.; Bawa, P. S.; Polanco, L.; Sgambettera, G. M.; Wang, F.; Belkina, A. C.; Snyder-Cappione, J. E.; Mostoslavsky, G.

10.1101/2025.08.01.667959 — immunology — Posted on 2025-11-19

1783 Analysis of cortical dysplasias using b-tensor encoding diffusion MRI in an animal model

Ortega-Fimbres, O.; Rios-Carrillo, R.; Gaspar-Martinez, E.; Ruiz-Acosta, P.; Regalado, M.; Luna-Munguia, H.; Ramirez-Manzanares, A.; Concha, L.

10.1101/2025.11.19.689314 — neuroscience — Posted on 2025-11-19

1784 Copper-Free Click Chemistry Enables High-Fidelity Engineering of Mitochondria Targeted Brain-Derived Exosomes

Yan, X.; Chen, X.; Hou, S.; Li, X.; Ju, J.; Shan, Z.; Bi, L.

10.1101/2025.11.19.689327 — neuroscience — Posted on 2025-11-19

1785 Reward-driven adaptation of movements requires strong recurrent basal ganglia-cortical loops

Leblois, A.; Boraud, T.; Hansel, D.

10.1101/2024.10.15.618421 — neuroscience — Posted on 2025-11-19

1786 Low rank adaptation of chemical foundation models generate effective odorant representations

McConachie, G. D.; Duniec, E.; Guerina, F.; Younger, M.; DePasquale, B.

10.1101/2025.11.04.686628 — neuroscience — Posted on 2025-11-19

1787 Selective distractor representations resolve multidimensional interference

Gheza, D.; Freund, M. C.; Zalabak, T. R.; Kool, W.

10.1101/2025.11.16.688701 — neuroscience — Posted on 2025-11-19

1788 Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation

Heyman, Y.; Erez, M.; Burnham, P.; Nitzan, M.; Raj, A.

10.1101/2025.11.14.688372 — systems biology — Posted on 2025-11-19

1789 Multi-lineage transcriptional and cell communication signatures define evolving personalized mechanisms that initiate and perpetuate rheumatoid arthritis

Liu, C.; Wang, Z. A.; Prideaux, E. B.; Boyle, D. L.; Westermann, A.; Nguyen, K.; Tsaltskan, V.; Ochoa, A.; Deane, K. D.; Feser, M. L.; Demouruelle, M. K.; Kuhn, K. A.; Holers, V. M.; Zhang, F.; Asamoah, A. G.; Okada, L.; Gillespie, M. A.; Genge, P.; Weiss, M.; Hernandez, V.; Reading, J.; Becker, L.; Buckner, J. H.; Speake, C.; Liu, J.; Wang, Z.; Hu, Z.; Bumol, T. F.; Skene, P.; Firestein, G. S.; Wang, W.

10.1101/2025.02.08.619913 — systems biology — Posted on 2025-11-19

1790 The Effects of Garlic Extract on Renal Histopathology and Function in a Cadmium Chloride-Induced Hypertension Model

Ojo, G. B.; Olorunnisola, A. A.; Adedayo, L. D.; Morakinyo, A. O.; Fakunle, R. R.; Dawodu, E. S.

10.1101/2025.11.19.689172 — pharmacology and toxicology — Posted on 2025-11-19

1791 Cardiac Hemorrhage Precedes Hypertension-induced Fibrosis inPlasminogen Activator Inhibitor-1 Deficient Mice

Pettey, A. C.; Ito, S.; Franklin, M. K.; Howatt, D. A.; Moorleghen, J. J.; Levitan, B. M.; Graf, D. B.; Guzman, V. Z.; Zhang, N.; Sawada, H.; Saffitz, J. E.; Lu, H. S.; Daugherty, A.

10.1101/2025.11.19.689269 — pathology — Posted on 2025-11-19

1792 Detecting Foldback Artifacts in Long-reads

Heinz, J. M.; Meyerson, M.; Li, H.

10.1101/2025.07.15.664946 — bioinformatics — Posted on 2025-11-19

1793 NK cell immunotherapy administered at the time of HIV recrudescence is associated with viral control.

Thron, L. K.; Pumtang-on, P.; Woong Chang, J.; Cantor, M. E.; Gorrell-Brown, I.; Becklin, K. L.; Quinn, Z. E.; Karim, A. F.; Rendahl, A. K.; Pampusch, M. S.; Casares, S. A.; Vezys, V.; Moriarity, B.; Skinner, P. J.

10.1101/2025.11.19.688897 — bioengineering — Posted on 2025-11-19

1794 Aromatic residues in mobile regions distal to the active site support the closed conformation of E. coli DXPS

Kramer, L. J.; Austin, S. L.; Majumdar, A.; Smith, N. D.; Woodcock, H. L.; Freel Meyers, C. L.

10.1101/2025.10.24.684457 — biochemistry — Posted on 2025-11-19

1795 Cycling Molecular Assemblies (CyMA) for Ultrasensitive Golgi Imaging

Tan, W.; Zhang, Q.; Dresselhaus, E. C.; Divyanshu, M.; Ashton-Rickardt, I.; Lu, L.; Rodal, A. A.; Xu, B.

10.1101/2025.11.19.689330 — biochemistry — Posted on 2025-11-19

1796 CiFi: Accurate long-read chromosome conformation capture with low-input requirements

McGinty, S. P.; Kaya, G.; Sim, S. B.; Makunin, A.; Corpuz, R. L.; Quail, M. A.; Abuelanin, M.; Lawniczak, M. K.; Geib, S. M.; Korlach, J.; Dennis, M. Y.

10.1101/2025.01.31.635566 — genomics — Posted on 2025-11-19

1797 Mutational divergence in local populations of the selfing nematode Caenorhabditis elegans

Wei, X.; Richaud, A.; Tanny, R. E.; Andersen, E. C.; Felix, M.-A.

10.1101/2025.11.19.689209 — evolutionary biology — Posted on 2025-11-19

1798 Transcriptional feedback of Erk signaling waves in zebrafish scale regeneration

Coudeville, C.; Guyomar, T.; Allamand, J.; Voigt, F.; De Simone, A.

10.1101/2025.11.19.689292 — developmental biology — Posted on 2025-11-19

1799 Dengue Virus NS1 Binds Ephrin B1 to Trigger Endothelial Dysfunction

Pahmeier, F.; Hammond, S. R.; Flory, C.; Feng, X.; Lee, S. E.; Jimenez-Posada, E. V.; Duarte, E. M.; Cardona-Ospina, J. A.; Ball, A. H.; Lee, N. E.; Leung, K.; Tjang, L. V.; Beatty, P. R.; Biering, S. B.; Scaturro, P.; Harris, E.

10.1101/2025.11.19.689067 — microbiology — Posted on 2025-11-19

1800 GABA-glutamate corelease is a mechanism for state-dependent neurotransmission

Warlow, S. M.; Dowlat, D. S.; Hollon, N. G.; Faget, L.; Oriol, L.; Zell, V.; Zweifel, L.; Hnasko, T. S.

10.1101/2025.11.19.689286 — neuroscience — Posted on 2025-11-19

1801 MatClassRSA v2 release: A MATLAB toolbox for M/EEG classification, proximity matrix construction, and visualization

Wang, B. C.; Gifford, R.; Kong, N. C.; Ruan, F.; Norcia, A. M.; Kaneshiro, B.

10.1101/2025.11.19.689115 — neuroscience — Posted on 2025-11-19

1802 Mecp2 deficiency induces dysphagia in a preclinical model of Rett Syndrome

Oliveira, L. M. M.; Aslam, M. S.; Ramirez, J. M.; Huff, A.

10.1101/2025.11.19.689305 — neuroscience — Posted on 2025-11-19

1803 Characterization of lymphoma models for the surface ROR1 expression

Tarantelli, C.; Civanelli, E.; Spriano, F.; Risi, G.; Cascione, L.; Kaufmann, G.; Bertoni, F.

10.1101/2025.11.19.684505 — cancer biology — Posted on 2025-11-19

1804 Predicting lead hotspots in urban stormwater ponds across the Twin Cities Metro

Pollack, L.; Zweifel, C.; Janke, B.; Ting, T.; Culshaw-Klein, Z.; Finlay, J.; Santelli, C.; Snell-Rood, E.

10.1101/2025.11.13.688297 — ecology — Posted on 2025-11-19

1805 A unique mechanism explaining the outstanding performance of a newly discovered doxycycline riboswitch

Hoetzel, J.; Walbrun, A.; Schaefer, M.; Wang, T.; Jorgensen, A. G.; Stamatakis, K.; Gunawan, V.; Becker, O.; Reichardt, L.; Boettger, L.; Bruckhoff, R. W.; Kjems, J.; Wachtveitl, J.; Rief, M.; Suess, B.

10.1101/2025.11.11.687352 — molecular biology — Posted on 2025-11-19

1806 Impact of Maternal Antibodies and Weaning Stress on the Replication and Transmission of Human H3N2 Influenza A in Piglets

Ciacci Zanella, G.; Cardenas Perez, M.; Hutter, C. R.; Snyder, C. A.; Wymore Brand, M.; (Wilberts) Arruda, B.; Perez, D. R.; Anderson, T.; Rajao, D. S.; Baker, A. L.

10.1101/2025.11.18.689042 — immunology — Posted on 2025-11-19

1807 Absence of Sensory Cooling Activity and Cooling Agents from California's New ''Non-Menthol'' Cigarettes Marketed in 2025

Jabba, S. V.; Erythropel, H. C.; Anastas, P. T.; Krishnan-Sarin, S.; O'Malley, S.; Zimmerman, J. B.; Jordt, S. E.

10.1101/2025.11.17.688932 — pharmacology and toxicology — Posted on 2025-11-19

1808 Curcumin Analogues Trigger HMOX1-Mediated Ferroptosis to Halt Endometrial Cancer Growth

wu, x.; Padilla, J. L.; Smith, L. E.; Goodla, L.; Leslie, K. K.; Xue, X.

10.1101/2025.11.18.689080 — cancer biology — Posted on 2025-11-19

1809 The patchy distribution of the photosynthetic gene cluster in Erythrobacteraceae

Walling, A. G.; DeSalle, R.; Perkins, S. L.

10.1101/2025.11.19.689285 — evolutionary biology — Posted on 2025-11-19

1810 T-regulatory cell protection of progenitor cells from CD4+ T-cell-mediated cytotoxicity is essential for endogenous mouse digit-tip regeneration.

Beal, Z.; Reeve, R. E.; Hammond, E.; Rosenthal, N.; Godwin, J. W.

10.1101/2025.11.19.689270 — developmental biology — Posted on 2025-11-19

1811 Long-Term Imprint of Prenatal War Trauma on Brain Structure: Evidence from Genetically Informed Neuroimaging

Aydogan, G.; Kollmorgen, S.; Mante, V.; Linner, R. K.; Kleim, B.; Nave, G.; Ruff, C. C.

10.1101/2025.11.05.686844 — neuroscience — Posted on 2025-11-19

1812 Single-cell Spatial Transcriptional Profiling Uncovers Heterogeneous Cellular Responses to Pathogenic Tau in a Mouse Model of Neurodegeneration

Sun, X.; Wu, L.; Orr, T. C.; Heck, A.; Young, K.; Dunaway, N.; Navarro, J. C.; Beechem, J. M.; Orr, M. E.

10.1101/2025.11.19.689127 — neuroscience — Posted on 2025-11-19

1813 Pericyte and Endothelial Primary Cilia and Centrioles have Disparate Organization Across the Brain Microvasculature

Grubb, S.; Chanddha, V.; Lippincott-Schwartz, J.; Ott, C.; Mughal, A.

10.1101/2025.11.19.689283 — neuroscience — Posted on 2025-11-19

1814 The Paradox of Unpredictability: Trying to Be Unpredictable Makes Sequences More Predictable

Yamada, K.; Tsutsui, K.; Kudo, K.

10.1101/2025.11.16.688665 — neuroscience — Posted on 2025-11-19

1815 Proximity-induced rewiring of oncogenic kinase triggers apoptosis

Merz, M. L.; Shoba, V. M.; Pergu, R.; Severance, Z. C.; Munkanatta Godage, D. N. P.; Deb, A.; Kwok, H. S.; Singh, P.; Singh, S.; Allen, J. B.; Tian, W.; Gosavi, P. M.; Chaudhary, S. K.; Anokhina, V.; Weisberg, E. L.; Payne, N. C.; He, Y.; Dhaliwal, R.; Osadchey, R.; Shekhar, M.; Mazitschek, R.; Rees, M. G.; Roth, J. A.; Cui, Q.; Griffin, J. D.; Liau, B. B.; Choudhary, A.

10.1101/2025.06.13.659082 — synthetic biology — Posted on 2025-11-19

1816 Mobility-enhanced virus vectors enable meristem genome editing in model and crop plants

Chiu, K. T.; Higgs, H.; Antunes, M. S.; Lin, Y. T.; McGarry, R. C.

10.1101/2025.11.19.689159 — plant biology — Posted on 2025-11-19

1817 Rapid hypothalamic-pituitary recovery after chronic glucocorticoid therapy enables strategies that prevent adrenal suppression

Gaston, L. S.; Jorgensen, B. C.; Friedman, H. R.; Sherman, M. S.; Majzoub, J. A.

10.1101/2025.04.30.651350 — physiology — Posted on 2025-11-19

1818 MicroSplit: Semantic Unmixing of Fluorescent Microscopy Data

Ashesh, A.; Carrara, F.; Zubarev, I.; Galinova, V.; Croft, M.; Pezzotti, M.; Gong, D.; Casagrande, F.; Colombo, E.; Giussani, S.; Restelli, E.; Cammarota, E.; Battagliotti, J. M.; Klena, N.; Di Sante, M.; Adhikari, R.; Feliciano, D.; Pigino, G.; Taverna, E.; Harschnitz, O.; Maghelli, N.; Scherer, N. F.; Dalle Nogare, D. E.; Dechamps, J.; Pasqualini, F.; Jug, F.

10.1101/2025.02.10.637323 — bioinformatics — Posted on 2025-11-19

1819 Fix or Freeze? Spectral Differences Arising from Tissue Preparation in Chemical Imaging

Zheng, T.; Adi, W.; Campagnola, P.; Yesilkoy, F.

10.1101/2025.11.19.689284 — biochemistry — Posted on 2025-11-19

1820 Density-dependent inhibition and higher-order interactions enable coexistence in phage-bacteria community dynamics

Dey, R.; Coenen, A. R.; Solonenko, N. E.; Burris, M. N.; Mackey, A. I.; Galasso, J.; Sun, C. L.; Demory, D.; Muratore, D.; Beckett, S. J.; Sullivan, M. B.; Weitz, J. S.

10.1101/2025.05.15.651590 — ecology — Posted on 2025-11-19

1821 MANY PATHS TO DESTRUCTION: FAMILY-SPECIFIC TURNOVER AND STRESS RESPONSES FOR TRNA INTRONS

Metcalf, S.; Nostramo, R. T.; Bao, A.; Clark, K.; Sinopoli, P. L.; Hopper, A. K.

10.1101/2025.11.19.689297 — molecular biology — Posted on 2025-11-19

1822 IFNγ-associated immune--metabolic remodeling drives serotonin-kynurenine imbalance with cortical vulnerability in lupus-prone mice

Matmat, K.; Gueant-Rodriguez, R.-M.; Darcq, E.; Baspinar, O.; Alberto, J.-M.; Gueant, J.-L.; Mensah-Nyagan, A. G.; Jeltsch-David, H.

10.1101/2025.11.19.689278 — immunology — Posted on 2025-11-19

1823 Highly Consistent Anatomical Asymmetry in a Small Primate Brain: Left is Always Larger in the Marmoset Monkey

Mundinano, I.-C.; Atapour, N.; Jiang, K.; Samandra, R.; Liu, C.; Mansouri, F. A.; Rosa, M. G. P.

10.1101/2025.11.19.689300 — neuroscience — Posted on 2025-11-19

1824 A glial cell derived pathway directs regenerating optic nerve axons toward the optic chiasm

Harvey, B. M.; Baxter, M.; Garcia, A. M.; Granato, M.

10.1101/2024.10.15.618346 — neuroscience — Posted on 2025-11-19

1825 LAMA5 deficiency disrupts ECM-WNT crosstalk in chondrogenesis and contributes to idiopathic short stature

Schulz, A.; Brockmann, E. M.; Uebe, S.; Ekici, A. B.; Thiel, C. T.

10.1101/2025.11.19.689218 — genetics — Posted on 2025-11-19

1826 Coastal winds are stronger and impact seabird behaviour and fitness in a warming Arctic

MARTIN, T. J. B.; Fort, J.; Grunst, A. S.; Grunst, M. L.; Amelineau, F.; Harding, A. M. A.; Perret, S.; Ardhuin, F.; Gremillet, D.

10.1101/2025.11.19.689241 — ecology — Posted on 2025-11-19

1827 Transcriptional Reprogramming Drives Cold Adaptation During Long-Term Starvation in S. eubayanus

Saona, L. A.; Mateluna-Caceres, T.; Villarreal, P.; Las Heras, M.; Zavaleta, V.; Cubillos, F. A.

10.1101/2025.11.19.689257 — microbiology — Posted on 2025-11-19

1828 The transcription factor BCL11A restores differentiation potential to aged oligodendrocyte progenitor cells

Ghosh, T.; Baror, R.; Zhao, C.; Sharma, A.; Goldman, N.; Franklin, R. J.

10.1101/2025.11.19.689239 — neuroscience — Posted on 2025-11-19

1829 Neuronal activity promotes repair by microglial reprogramming following demyelination

PERROT, C.; Ronzano, R.; Li, Z.; Aigrot, M.-S.; Pantazou, V.; Stheneur, P.; Lejeune, F. X.; Zalc, B.; Quintana, F.; Stankoff, B.; Lubetzki, C.; Desmazieres, A.

10.1101/2025.11.19.689194 — neuroscience — Posted on 2025-11-19

1830 Peri-operative pregabalin does not adversely impact experimentaloutcomes in rat models of chronic pain

Di Domenico, F.; Patel, R.; Bannister, K.

10.1101/2025.11.19.689268 — neuroscience — Posted on 2025-11-19

1831 Root anatomical gradients and cultivar differences underlie variation in root hydraulic properties in German winter wheat

Baca Cabrera, J. C.; Jones, D. H.; Vanderborght, J.; Behrend, D.; Schneider, H.; Lobet, G.

10.1101/2025.11.19.689226 — plant biology — Posted on 2025-11-19

1832 Spatiotemporal transcriptional networks control the plasticity of chickpea root exodermis

Jo, L.; Kluck, R. M. C.; Buti, S.; Razus, M.; Holbein, J.; Chhillar, H.; Ding, P.; Franke, R.; Kajala, K.

10.1101/2025.01.03.631192 — plant biology — Posted on 2025-11-19

1833 The Small Non-coding RNA miR-16-1-3p Hampers Cancer Stem Cell Self-renewal and Invasiveness, Boosting Chemosensitivity by Adjusting TGF-β1 Signaling via MDM2/p53 Axis in Human Osteosarcoma.

XUE, W.; WANG, Y.; Smirnova, A. V.; Malakhov, P. A.; Mochalova, E. N.; Pustovalova, M.; Kuzmin, D. V.; Leonov, S. V.

10.1101/2025.11.19.689220 — cancer biology — Posted on 2025-11-19

1834 PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms

Zhai, J.; Gokaslan, A.; Hsu, S.-K.; Chen, S.-P.; Liu, Z.-Y.; Marroquin, E.; Czech, E.; Cannon, B.; Berthel, A.; Romay, C.; Pennell, M.; Kuleshov, V.; Buckler, E. S.

10.1101/2025.08.27.672609 — bioinformatics — Posted on 2025-11-19

1835 XIST Drives X-Chromosome Inactivation and Safeguards Female Extraembryonic Cells in Humans

Panda, A.; Carrillo, L.; Balaton, B. P.; Brouillet, J.; Nshemereirwe, S.; Bonroy, J.; Alfeghaly, C.; Facchinello, R.; Khodeer, S.; Boers, R.; Castel, G.; London, C.; Cazottes, E.; Moscatelli, M.; Tchinda, R. S.; Pham, T. X. A.; To, S. K.; Allsop, R. N.; Wang, Y.; Staneva, D.; Rugg-Gunn, P.; Niakan, K.; Gribnau, J.; Ouimette, J.-F.; Rougeulle, C.; Pasque, V.

10.1101/2025.11.19.689206 — developmental biology — Posted on 2025-11-19

1836 A minimal tooth enhancer regulates dlx2b expression during zebrafish tooth formation: insights into cis-regulatory logic in organogenesis

Jackman, W. R.; Moon, Y.; Cox, C. K.; Anderson, D. R.; DeFusco, A. A.; Nguyen, V. M.; Liu, S. Y.; Carter, E. H.; Littleford, H. E.; Richards, E. K.; Jowdry, A. L.; Gibert, Y.

10.1101/2022.01.20.477116 — developmental biology — Posted on 2025-11-19

1837 LRRK2 integrates Rab and GABARAP interactions to sense and respond to distinct lysosomal stresses

Clegg, D.; Bentley-DeSousa, A.; Roczniak-Ferguson, A.; Ferguson, S. M.

10.1101/2025.11.19.689251 — cell biology — Posted on 2025-11-19

1838 Mycobacterium tuberculosis diversity and macrophage heterogeneity dictate phagosomal acidification

Chiacchiaretta, M.; Sorrentino, R.; Bresciani, N.; Aiello, A.; Vanini, V.; Zambrano, S.; Mazza, D.; Cugnata, F.; Cirillo, D. M.; Agresti, A.; Goletti, D.; Miotto, P.

10.1101/2025.11.19.689035 — microbiology — Posted on 2025-11-19

1839 Spore type-specific gene expression profiles underlying development and leaf infection processes of Colletotrichum graminicola

Rathi, D.; Andresen, K.; Daniel, R.; Guerreiro, M. A.; Kretschmer, M.; Kronstad, J. W.; Nowrousian, M.; Poeggeler, S.; Poehlein, A.; Voll, L. M.; Nordzieke, D. E.

10.1101/2025.11.19.689217 — microbiology — Posted on 2025-11-19

1840 Microbial Life Inside Posidonia Seeds: Beneficial En-dophytes and Implications for Marine Plant Health

Crucitti, D.; Sutera, A.; De Michele, R.; Carimi, F.; Barone, S.; Badalamenti, F.; Pacifico, D.

10.1101/2025.11.19.689238 — microbiology — Posted on 2025-11-19

1841 CDK7, CDK9, or CDK11 Inhibition Reduces Neutrophil-Driven Inflammation and Tissue Damage in Experimental Autoimmune Models

Schlotfeldt, M.; Dräger, S.; Voss, L.; Mansini, A. P.; Mehlberg, D.; Johannisson, S.; Radziewitz, M.; Schneider, A.-K.; Vahabi, S. M.; Wang, Y.; Gainer, H.; Li, J.; Osterloh, C.; Ernst, N.; Visser, R.; Vidarsson, G.; Petersen, F.; Yu, X.; Ludwig, R. J.; Vorobyev, A.; Amber, K. T.; Lux, A.; Bieber, K.

10.1101/2025.11.19.689221 — immunology — Posted on 2025-11-19

1842 Distinct spatial distribution of potentiated dendritic spines in encoding- and recall-activated hippocampal neurons

Gobbo, F.; Jacob, A.; Pinto, B.; Mainardi, M.; Cancedda, L.; Cattaneo, A.

10.1101/2025.11.19.689242 — neuroscience — Posted on 2025-11-19

1843 First record of Aedes albopictus in the department of Magdalena, North of Colombia: implications for arboviral disease transmission

Perdomo-Balaguera, E.; Ariza-Campo, K.; Atencio, L.; Usme-Ciro, J. A.; Parra Henao, G.

10.1101/2025.11.19.689261 — zoology — Posted on 2025-11-19

1844 PANCS-spec-Binders: A system for rapidly discovering isoform- or epitope-specific binders

Pixley, J. A.; Styles, M. J.; Aphicho, K.; Endres, M.; Gade, P.; Michalska, K.; Joachimiak, A.; Dickinson, B. C.

10.1101/2025.11.19.689279 — synthetic biology — Posted on 2025-11-19

1845 Caveolin-1 regulates context-dependent signaling and survival in Ewing Sarcoma.

Segal, D.; Wang, X.; Mazloom-Farsibaf, H.; Zhou, F. Y.; Rajendran, D.; Butler, E.; Chen, B.; Chang, B.-J.; Ahuja, K.; Perny, A.; Bhatt, K.; Reed, D. K.; Castrillon, D.; Lee, J.; Jeffery, E.; Wang, L.; Nguyen, K.; Williams, N. S.; Rajaram, S.; Fiolka, R. P.; Jaqaman, K.; Skapek, S. X.; Hon, G. C.; Amatruda, J.; Danuser, G.

10.1101/2024.09.23.614468 — cancer biology — Posted on 2025-11-19

1846 The impacts of shape in lateral migration of cancer cells in a microchannel

Ahmed, M.; Akerkouch, L.; Haage, A.; Le, T. B.

10.1101/2025.11.19.689215 — biophysics — Posted on 2025-11-19

1847 Pseudotimecascade visualizes gene expression cascade in pseudotime analysis

Wan, C.; Ji, B.; Ji, Z.

10.1101/2025.11.19.689263 — bioinformatics — Posted on 2025-11-19

1848 A Near Telomere-to-Telomere Reference Genome for Drakensberger Cattle Achieved Through Trio-Binned Long-Read Sequencing

Mapholi, N.; Tshilate, T.; Smith, R.; Hlongwane, N.; Nesengani, L. T.

10.1101/2025.11.19.689200 — genomics — Posted on 2025-11-19

1849 From deserts to forests: sequencing of the giant forest hog completes the genomic history of the African Suids

Ciucani, M. M.; Aninta, S. G.; Gomes Martins, N. F.; Duchene, D. A.; Wang, X.; Lazagabaster, I. A.; Liu, X.; Staeger, F. F.; Schubert, M.; Boeggild, T.; He, S.; Li, Z.; Reyna-Hurtado, R.; Meijaard, E.; Butynski, T. M.; Muwanika, V. B.; Masembe, C.; Dufour, S.; Gaubert, P.; Siegismund, H. R.; Moltke, I.; Albrechtsen, A.; Heller, R.

10.1101/2025.11.19.689022 — genomics — Posted on 2025-11-19

1850 Integrating Natural and Engineered Genetic Variation to Decode Regulatory Influence on Blood Traits

Tardaguila, M.; Von Schiller, D.; Colombo, M.; Gori, I.; Coomber, E. L.; Vanderstichele, T.; Benaglio, P.; Chiereghin, C.; Gerety, S. S.; Vuckovic, D.; Landini, A.; Clerici, G.; Casiraghi, A.; Albers, P. K.; Ray-Jones, H.; Burnham, K. L.; Tokolyi, A.; Persyn, E.; Spivakov, M.; Sankaran, V. G.; Walter, K.; Kundu, K.; Pirastu, N.; Inouye, M.; Paul, D. S.; Davenport, E.; Sahlen, P.; Watt, S.; Soranzo, N.

10.1101/2024.08.05.606572 — genetics — Posted on 2025-11-19

1851 Mutational divergence in local populations of the selfing nematode Caenorhabditis elegans

Felix, M.-A.; Wei, X.; Richaud, A.; Tanny, R. E.; Andersen, E. C.

10.1101/2025.11.19.689209 — evolutionary biology — Posted on 2025-11-19

1852 A rapid and accurate PCR-based method for mating-type determination in the heterothallic oomycete Plasmopara viticola, the causal agent of grapevine downy mildew

Couture, C.; Mazet, I. D.; Dussert, Y.; Guyomar, C.; Delmotte, F.

10.1101/2025.11.19.689015 — molecular biology — Posted on 2025-11-19

1853 Variations in cow milk and teat skin microbiota across the lactation cycle with intra-mammary cephalosporin use at dry-off

Van Beeck, W.; Lemos, M.; Niesen, A. M.; Finnegan, P.; Shih, T.; Ho, A.; Rossow, H. A.; Marco, M. L.

10.1101/2025.11.19.689190 — microbiology — Posted on 2025-11-19

1854 Cryo-FIB Lift-out and Electron Tomography Workflow for Bacteria-Nanopillar Interface Imaging Under Native Conditions: Investigating Dragonfly Inspired Bactericidal Titanium Surfaces

Bandara, C. D.; Pinkas, D.; Zanova, M.; Uher, M.; Mantell, J.; Su, B.; Nobbs, A. H.; Verkade, P.

10.1101/2025.11.19.688262 — microbiology — Posted on 2025-11-19

1855 The HosA histone deacetylase regulates stress resistance, host cell interactions, and virulence in Aspergillus fumigatus

Liu, H.; Lee, P.; Vo, A.; Paul, S.; Phan, Q. T.; Lin, J.; Bruno, V. M.; Stamnes, M. A.; Moye-Rowley, W. S.; Filler, S. G.

10.1101/2025.11.19.689210 — microbiology — Posted on 2025-11-19

1856 T-cell Multiomic Analysis Identifies Subsets and Mechanisms of Interaction with Epithelial Cells in Idiopathic Pulmonary Fibrosis

Serezani, A.; Bazzano, J. M.; Pascoalino, B. D.; da Silva, L.; Dietrich, A. J.; Taylor, C. J.; Sherrill, T.; Calvi, C. L.; Gonzalez-Ericsson, P. I.; Wilfong, E. M.; Bacchetta, M.; Shaver, C. M.; Ware, L. B.; Salisbury, M.; Van Kaer, L.; Banovich, N.; Kropski, J. A.; Blackwell, T. S.

10.1101/2025.11.19.689037 — immunology — Posted on 2025-11-19

1857 Independent Basal Ganglia Neural Populations Encode Speech Production and Ambient-Noise Levels

Bullock, L.; Vissani, M.; Bush, A.; Kim, J. S.; Holt, L. L.; Fiez, J.; Turner, R. S.; Herrington, T. M.; Schweitzer, J.; Guenther, F. H.; Richardson, R. M.

10.1101/2025.11.18.689157 — neuroscience — Posted on 2025-11-19

1858 Incentive Salience, not Psychomotor Sensitization or Tolerance, Drives Escalation of Cocaine Self-Administration in Heterogeneous Stock Rats

10.1101/2025.10.04.680105 — neuroscience — Posted on 2025-11-19

1859 The Virtual Brain Ontology: A Digital Knowledge Framework for Reproducible Brain Network Modeling

Martin, L.; Buelau, K.; Pille, M.; Schmitt, R. A.; Huettl, C.; Meier, J. M.; Taher, H.; Perdikis, D.; Schirner, M.; Ritter, P.

10.1101/2025.11.19.689211 — neuroscience — Posted on 2025-11-19

1860 Spatiotemporal-multimodal integration reveals BCG-induced skin-blood crosstalk

Singh, A.; Baek, O.; Schaltz-Buchholzer, F.; Campbell, J.; West, N.; Elgamoudi, B.; Campbell, A.; Ca, E.; Tebbutt, S.; Shannon, C.; Aaby, P.; Kollmann, T.; Benn, C.; Amenyogbe, N.

10.1101/2025.11.19.689184 — systems biology — Posted on 2025-11-19

1861 High-Quality Predicted Pathway Annotations Greatly Improve Pathway Enrichment Analysis of Metabolomics Datasets

Huckvale, E. D.; Thompson, P. T.; Flight, R. M.; Moseley, H. N. B.

10.1101/2025.11.18.689105 — systems biology — Posted on 2025-11-19

1862 Light-up nanostructures with allosteric DNA mimics of GFP

Zhang, T.; Qian, X.; Zhang, J.; Cui, H.; Bai, T.; Wang, W.; Wang, Y.; Gao, Z.; Han, D.; Zeng, W.; Wei, B.

10.1101/2025.07.10.664110 — synthetic biology — Posted on 2025-11-19

1863 Lymphotoxin-driven cancer cell eradication by tumoricidal CD8+ tumor-infiltrating lymphocytes

10.1101/2025.11.19.689204 — cancer biology — Posted on 2025-11-19

1864 Binding Paths: Describing Small Molecule Interactionswith Disordered Proteins via Markov State Models

Louet, A. A. B.; Hummer, G.; Vendruscolo, M.

10.1101/2025.11.19.688850 — biophysics — Posted on 2025-11-19

1865 Optimal bioelectric control accelerates collective wound healing

Yodh, J. S.; Lin, Y.; Sinha, S.; Krishnan, V.; Mahadevan, L.; Cohen, D. J.

10.1101/2025.11.19.689141 — biophysics — Posted on 2025-11-19

1866 Polarization MultiFocus Microscopy for volumetric super-resolution and orientation imaging of biofilaments

Regnier, L.; Rimoli, C. V.; Dey, S.; Tsai, F.-C.; Orsi, G.; Brasselet, S.; Hajj, B.

10.1101/2025.11.19.687997 — biophysics — Posted on 2025-11-19

1867 Inference and validation of a dynamic gene regulatory network influencing cell fate during Duchenne muscular dystrophy initiation

Guillot, E. G.; Fort, Q. G.; Mozin, E.; Robert, B.; Bouvier, M.; Fourgeux, C.; Simon, P.; Munoz, S.; Childers, M. C.; Poschmann, J.; Adjali, O.; Mack, D. L.; Bonnaffoux, A.; Dupont, J.-B.

10.1101/2025.11.19.689189 — bioinformatics — Posted on 2025-11-19

1868 Graph Neural Networks Model Based on Atomic Hybridization for Predicting Drug Targets

Mohamed, A. k.; Galal, N.; Brooks, B. R.; Amin, M.

10.1101/2025.11.19.689219 — bioinformatics — Posted on 2025-11-19

1869 Unconventional linkers facilitate potent stabilized coronavirus stem antibody responses following nanoparticle vaccination

Dzuvor, C. K. O.; Moak, S. P.; McManus, L. R.; Dzordzorme, A. E.; Evanson, L. R.; Kim, T.; Thomas, A.; Adeyemi, O.; Foley, V.; Limaye, A.; McNamara, R. P.; Corbett-Helaire, K. S.

10.1101/2025.11.19.689216 — bioengineering — Posted on 2025-11-19

1870 Scalable production of immune-silent circular RNAs for efficient protein expression

Liu, X.; Xiao, H.; Whitehead, M.; Varshney, D.; Du, Y.

10.1101/2025.11.19.689249 — bioengineering — Posted on 2025-11-19

1871 Single-nucleotide resolution mapping of m6A of zebrafish mRNAs in early embryonic development links m6A modifications to the maternal-to-zygotic transition

Wardale, A.; Peng, Y.; Ge, R.; Jorgensen, T. E.; Johansen, S. D.; He, C.; Babiak, I.

10.1101/2025.11.19.688951 — genomics — Posted on 2025-11-19

1872 Epigenomic and transcriptomic germ-free ageing atlas reveals sterile inflammation as an intrinsic ageing feature

Twilhaar, W. N.; Chang, J.-C.; Terooatea, T. W.; Yabukami, H.; Kato, S.; Satoh-Takayama, N.; Ahmadi, A.; Hetherington, N.; Jeyamohan, P.; Kageyama, T.; Kadono-Maekubo, N.; Maeda, S.; Mochizuki, M.; Nakanishi, Y.; Rother, N.; Tahara, U.; Takeno, N.; Tsutsui, K.; Barcelo, M. V.; Wang, H.; Motomura, Y.; Amagai, M.; Fujiwara, H.; Hon, C. C.; Matsui, T.; Moro, K.; Nourshargh, S.; Ohno, H.; Minoda, A.

10.1101/2025.11.19.689100 — genomics — Posted on 2025-11-19

1873 De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology

Nyarko, P.; Quenu, M.; Guery, M.-A.; Cohen, C.; Girgis, S. T.; Makunin, A.; McCarthy, S. A.; Hamilton, W. L.; Lawniczak, M.; Claessens, A.

10.1101/2025.11.19.689036 — genomics — Posted on 2025-11-19

1874 Linking sediment porosity to taxon-specific patterns of eDNA preservation in a temperate, semi-enclosed bay

Hoshino, T.; Toyama, S.; Tanikawa, W.; Murayama, M.

10.1101/2025.11.19.689188 — ecology — Posted on 2025-11-19

1875 Immune-Derived THBS1-CD47 Axis Induces Cellular Senescence and Suppresses Osteogenesis in Diabetic Periosteum

Shen, F.; Zhou, J.; Liu, M.; Ren, Q.; Cui, J.; Yang, P.; Zheng, T.; Wang, J.; Ye, L.; Shi, Y.

10.1101/2025.11.19.689158 — cell biology — Posted on 2025-11-19

1876 Extracellular ssDNA from P. tobira Exerts Strong Insecticidal Activity on C. hesperidum

Oberemok, V. V.; Laikova, K.; Gal'chinsky, N.; Ali, J.; Petrishina, N.; Yatskova, Y.; Chachoua, I.

10.1101/2025.11.18.689116 — molecular biology — Posted on 2025-11-19

1877 Copper deficiency disrupts OXPHOS and mitochondrial dynamics through MTCH2-dependent copper trafficking in skeletal muscle

Lee, Y.-S.; Kim, H. S.; Nguyen, P. L.; Lee, J.; Kim, D.-I.; Lee, J.; Moon, C.; Cho, K.-O.; Kim, B.-E.; Ahn, J.; Osborne, T. F.; Duysak, T.; Kim, J.-S.; Jung, C. H.; Jeon, T.-I.

10.1101/2025.11.19.688750 — molecular biology — Posted on 2025-11-19

1878 Equipositioning of Chromosomes in the Polyploid Archaeon Haloferax volcanii by HpaAB

Premrajka, K.; Johnsen, U.; Preidel, H.; Wienberg, J.; Corleis, C.; Ortjohann, M.; Giacomelli, G.; Bramkamp, M.

10.1101/2025.11.19.689047 — microbiology — Posted on 2025-11-19

1879 Minute-scale control of ubiquitin-mediated degradation reveals dynamics of bacterial secreted effector-functions

Zhang, H.; Guo, Y.; Adhikari, B.; Dudvarski-Stankovic, N.; Wolf, E.; Rudel, T.

10.1101/2025.11.19.688170 — microbiology — Posted on 2025-11-19

1880 Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific

Schön, M. E.; Schvarcz, C. R.; Malkewitz, S. V.; Hinner, F. C.; Koslova, A.; Mersdorf, U.; Schimm, F.; Rickert, S.; Pozhydaieva, N.; McBeain, K.; Hackl, T.; Schneider, A. C.; Barenhoff, K.; Höfer, K.; Edwards, K. F.; Steward, G. F.; Fischer, M. G.

10.1101/2025.11.19.688996 — microbiology — Posted on 2025-11-19

1881 Volatilized ammonia supports extremophilic cave ecosystems with unusual nitrogen isotopic signatures

Best, M. B. B.; Wankel, S. D.; Graham, H. V.; Stern, J. C.; Macalady, J. L.; Mainiero, M.; Recanatini, S.; Mariani, S.; D'Angeli, I.; Vaccarelli, I.; Jones, D. S.

10.1101/2025.11.19.689070 — microbiology — Posted on 2025-11-19

1882 Taste dysfunction in Long COVID

Morad, H.; Vanhala, T.; Kisiel, M. A.; Andreason, A.; Li, M.; Andersson, G.; Laurell, G.; Finger, T. E.; Hellekant, G.

10.1101/2025.07.17.661973 — neuroscience — Posted on 2025-11-19

1883 Convergent and divergent spatial topographies of individualized brain functional networks and their developmental origins

Zhao, J.; Zhai, Y.; Xu, Y.; Sun, L.; Zhao, T.

10.1101/2025.11.18.689167 — neuroscience — Posted on 2025-11-19

1884 Immature C. elegans motor neurons control early embryo behavior via both synaptic and non-synaptic GABA release

Marvel-Coen, J.; Ardiel, E. L.; Zhao, J.; Nurrish, S.; Kaplan, J. M.

10.1101/2025.11.19.689106 — neuroscience — Posted on 2025-11-19

1885 A novel method to sort and enrich sensory neurons

Kurtovic, Z.; Arvidsson, S. D.; Vazquez Mora, J. A.; Ye, S.; Bersellini Farinotti, A.; Simon, N.; Krock, E.; Haglund, L.; Hagemann-Jensen, M.; Lund, H.; Svensson, C. I.

10.1101/2025.11.19.688847 — neuroscience — Posted on 2025-11-19

1886 Identity Domains Reveal How Life Experiences and the Microbiome Shape Individuality and Uncover the Presence of Social Memory in Drosophila

Pozeilov, H.; Dayan, E.; Yehuda, R.; Levi, M.; Shohat-Ophir, G.; Forkosh, O.

10.1101/2025.11.19.689229 — neuroscience — Posted on 2025-11-19

1887 Epithelial FOXP3 Drives Pancreatic Fibrosis through O-glycosylated IL-6

Gong, R.; Ren, M.; Wang, J.; Zhang, W.; Ping, S.; Ke, L.; Qian, Y.; Ma, L.; Gao, C.; Zhao, C.; Fu, S.; Xue, J.; Wang, J.; Sun, H.; Chen, J.; Zhang, S.; Liu, M.; Zhao, T.; Saluja, A.; Yang, Z.; Ren, H.

10.1101/2025.11.19.689208 — cancer biology — Posted on 2025-11-19

1888 Dataset Documentation for Responsible AI: Analysis of Suitability and Usage for Health Datasets

Heinke, A.; Huang, L.; Simpkins, K. U.; Kalaw, F. G. P.; Karsolia, A.; Singh, K.; Soundarajan, S.; Nebeker, C.; Baxter, S. L.; Lee, C. S.; Lee, A. Y.; Patel, B.

10.1101/2025.11.18.689064 — bioinformatics — Posted on 2025-11-19

1889 Linker-rigidified VHL homodimerizers convert degraders into stabilizers of non-ubiquitinable ternary complexes

Crowe, C.; Salerno, A.; Sathe, G.; Marsh, G.; Maple, H.; Ciulli, A.

10.1101/2025.11.18.689129 — biochemistry — Posted on 2025-11-19

1890 Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs

Weilert, M.; Brennan, K.; Dalal, K.; Krueger, S.; Jiang, H.; Martinez-Corral, R.; Zeitlinger, J.

10.1101/2025.11.18.685822 — genomics — Posted on 2025-11-19

1891 A deep learning framework for building INDEL mutation rate maps

Deng, S.; Song, H.; Li, C.

10.1101/2025.11.18.689146 — genomics — Posted on 2025-11-19

1892 Mean fitness is maximized in small populations under stabilizing selection on highly polygenic traits

Ragsdale, A. P.

10.1101/2025.11.17.688329 — evolutionary biology — Posted on 2025-11-19

1893 Continuous chlorophyll fluorescence measurements trace sudden cold spell effects on photosynthetic efficiency in a temperate mixed forest

Stock, C.; Dumberger, S.; Kuehnhammer, K.; Sulzer, M.; Christen, A.; Haberstroh, S.; Werner, C.

10.1101/2025.11.18.688898 — ecology — Posted on 2025-11-19

1894 DNMT1 Coordinates PV Interneuron-Glia Coupling to Maintain Cortical Network Stability and Regulate Behavior

Linde, J.; Yildiz, C. B.; Voehringer, K.; Nabbefeld, G.; Graff, S.; Pensold, D.; Reichard, J.; Hermanns, M.; Weber-Hamacher, C.; Spehr, M.; Kampa, B.; Urbach, A.; Musall, S.; Zimmer-Bensch, G. M.

10.1101/2025.11.18.689032 — neuroscience — Posted on 2025-11-19

1895 Time-Resolved Neural Oscillations Across Sleep Stages: Associations with Sleep Quality and Aging

Passaro, A. D.; Poltorak, A.

10.1101/2024.12.16.628645 — neuroscience — Posted on 2025-11-19

1896 Limitations of Variational Laplace-based Dynamic Causal Modelling for Multistable Cortical Circuits

Asadpour, A.; Azimi, A.; Wong-Lin, K.

10.1101/2025.03.10.642327 — neuroscience — Posted on 2025-11-19

1897 REST/NRSF phosphorylation by CaMKIV regulates its transcriptional repressor activity and half-life

Tsushima, H.; Corradi, B.; Shmal, D.; Chiacchiaretta, M.; Liessi, N.; Di Fonzo, A.; Carminati, E.; Armirotti, A.; Fassio, A.; Matagliano, L.; Rocchi, A.; Benfenati, F.

10.1101/2025.09.04.674163 — neuroscience — Posted on 2025-11-19

1898 Designing optimal perturbation inputs for system identification in neuroscience

Ogino, M.; Sekizawa, D.; Kitazono, J.; Oizumi, M.

10.1101/2025.03.02.641008 — neuroscience — Posted on 2025-11-19

1899 A ventral hippocampus to nucleus accumbens pathway regulates impulsivity

Klug, M. E.; Decarie-Spain, L.; Tierno Lauer, L.; Kao, A. E.; Moody, O. P.; Morano, N. R.; Huang, H.; Arnold, D. B.; Noble, E. E.; Kanoski, S. E.

10.1101/2025.11.18.689154 — neuroscience — Posted on 2025-11-19

1900 Association between white-matter lesion volume and heart-rate variability: A comparison of T1, T1-T2 and T1-FLAIR-based segmentations using FreeSurfer SAMSEG

Robinson, T. D.; Cerri, S.; Zhang, F. E.; van Leemput, K.; Chen, J. J.

10.1101/2025.11.18.689161 — neuroscience — Posted on 2025-11-19

1901 Emergence of Individualized Functional Topography in the Neonatal Brain

Zhao, J.; Xu, Y.; Cui, Z.; Li, H.; Sun, L.; Liang, X.; Han, M.; Zeng, Z.; Li, Q.; Zhao, T.; He, Y.

10.1101/2025.11.18.689151 — neuroscience — Posted on 2025-11-19

1902 Supervised Deep Learning for Efficient Cryo-EM Image Alignment in Drug Discovery with cryoPARES

Sanchez-Garcia, R.; Berndt, A.; Apelbaum, A.; Reeks, J.; Williams, P. A.; Poelking, C.; Deane, C.; Saur, M.

10.1101/2025.03.04.641536 — bioinformatics — Posted on 2025-11-19

1903 KIAA1217/SKT and its paralog p140Cap are centrosomal proteins that regulate ciliogenesis through Src family signaling pathway.

GREIBILL, L.; Raimbourg, L.; Siegfried, H.; Bonaventure, J.; Defilippi, P.; Sago, L.; Redeker, V.; Etienne-Manneville, S.; Bouhouche, K.; Tassin, A.-M.

10.1101/2025.10.30.685566 — cell biology — Posted on 2025-11-19

1904 Early intermittent low-dose sclerostin antibody treatment promotes surface bone formation and reduces bone loss, but also decreases osteocyte apoptosis and mechanotransduction in ovariectomized rats: a pilot study

Naqvi, S. M.; Ali Rizvi, S. W.; Allison, H.; O'Sullivan, L.; Holdsworth, G.; Panadero-Perez, J. A.; Schiavi, J.; McNamara, L. M.

10.1101/2024.10.02.616263 — molecular biology — Posted on 2025-11-19

1905 Previously uncharacterized aliphatic amino acid positions modulate the apparent catalytic activity of the EAL domain of ZMO_1055 and other cyclic di-GMP specific EAL phosphodiesterases

Cao, L.-Y.; Zhang, X.; Bai, F.-W.; Romling, U.

10.1101/2024.06.21.600002 — microbiology — Posted on 2025-11-19

1906 A nucleic acid labeling chemistry reveals surface DNA on exosomes

Boskovic, F.; Dutta Gupta, P.; Zhang, J.; Krishnan, Y.; Szostak, J. W.

10.1101/2025.11.18.689134 — biochemistry — Posted on 2025-11-19

1907 Pan-cancer analysis reveals mtDNA copy number as a key determinant of mutational load and disease progression in cancer

Acharyya, A.; Dhar, R.

10.1101/2025.11.18.689019 — genomics — Posted on 2025-11-19

1908 Spectral theory of stochastic gene expression: a Hilbert space framework

Wu, B.; Grima, R.; Jia, C.

10.1101/2025.05.19.654994 — molecular biology — Posted on 2025-11-19

1909 Neural Entrainment in the Theta Band Predicts Groove Perception in Popular Music

Keller, D.; Rohe, T.; Raake, A.

10.1101/2025.11.11.687596 — neuroscience — Posted on 2025-11-19

1910 CDH3 as a Novel Therapeutic Target in Basal-like Double-Negative Prostate Cancer

Liu, G.; Wang, S.; Duong, L.; Zeng, Z.; Yang, J.; Zhao, Y.; Rahmy, S.; Feng, S.; Arce, A.; Jia, L.; Wan, J.; Cheng, L.; Lu, X.; Lu, X.

10.1101/2025.11.18.689150 — cancer biology — Posted on 2025-11-19

1911 In silico design and validation of high-affinity RNA aptamers for SARS-CoV-2 comparable to neutralizing antibodies

Yang, Y.; Qiao, L.; Jiang, Y.; Wang, Z.; Zhang, D.; Buratto, D.; Huang, L.; Zhou, R.

10.1101/2025.06.04.657802 — biophysics — Posted on 2025-11-19

1912 CBKMR: A Copula-based Bayesian Kernel Machine Regression Framework for Optimal Marker Detection in Omics Data

Chakraborty, A.; Mattila, C.; Ghosh, D.; Neelon, B.; Seal, S.

10.1101/2025.11.18.689140 — bioinformatics — Posted on 2025-11-19

1913 Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture

Fang, T.; Wang, X.; Xiao, Z.; Hang, S.; Murtaza, G.; Yang, J.; Xu, H.; Jha, A.; Noble, W. S.; Wang, S.

10.1101/2025.11.18.689171 — bioinformatics — Posted on 2025-11-19

1914 XChrom: a cross-cell chromatin accessibility prediction model integrating genomic sequence and cellular context

Miao, Y.; Liang, X.; Zhang, W.; Han, D.; Li, Y.; Wang, Z.

10.1101/2025.11.18.689149 — bioinformatics — Posted on 2025-11-19

1915 RegFormer: A Single-Cell Foundation Model Powered by Gene Regulatory Hierarchies

Hu, L.; Qin, H.; Zhang, Y.; Lu, Y.; Qiu, P.; Cao, L.; Jiang, W.; Feng, B.; Zhang, Y.; Chen, Q.; Shang, Y.; Xia, T.; Deng, Z.; Xu, X.; Fang, S.; Li, Y.; Zhang, Y.

10.1101/2025.01.24.634217 — bioinformatics — Posted on 2025-11-19

1916 Lipid Tail Length Determines Nano-Bio Interactions of Peptide Amphiphile Nanostructures

Bonic, K.; Stewart, M. R.; Xiang, L.; Mooney, K.; Armstrong, R.; Esener, S.; Fischer, J. M.; Yildirim, A.

10.1101/2025.11.18.689169 — bioengineering — Posted on 2025-11-19

1917 Dual-lineage human 3D bone niche model reveals osteoclast-driven osteomimicry in prostate cancer

Mazzoleni, A.; Dolgos, R.; Menter, T.; Dasen, B.; Scherberich, A.; Le Magnen, C.; Muraro, M. G.; Martin, I.

10.1101/2025.11.18.689049 — bioengineering — Posted on 2025-11-19

1918 intDesc-AbMut: Describing and understanding how antibody mutations impact their environmental interactions

Chiba, S.; Ohta, M.; Yamane, T.; Okuno, Y.; Ikeguchi, M.

10.1101/2025.11.18.688974 — bioengineering — Posted on 2025-11-19

1919 Charting the Undiscovered Metabolome with Synthetic Multiplexing

Patan, A.; Xing, S.; Charron-Lamoureux, V.; Hu, Z.; Deleray, V.; Agongo, J.; El Abiead, Y.; Mannochio-Russo, H.; Mohanty, I.; Gouda, H.; Zemlin, J.; Rajkumar, P.; Lee, C.; Leanos, D.; Weimann, N.; Tsuda, W.; Giddings, S.; Bui, T.; Kvitne, K. E.; Zhao, H. N.; Zuffa, S.; Nguyen, V.; Andrade, A.; Goncalves Nunes, W. D.; Caraballo-Rodriguez, A. M.; Caetano David, L.; Carver, J.; Bandeira, N.; Wang, M.; Burnett, L.; Siegel, D.; Dorrestein, P. C.

10.1101/2025.11.18.689170 — biochemistry — Posted on 2025-11-19

1920 Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells

Soltys, V.; Peters, M.; Su, D.; Kucka, M.; Chan, Y. F.

10.1101/2024.02.26.581705 — genomics — Posted on 2025-11-19

1921 Integrative Network Meta-Analysis Reveals Estrogen-Mediated RUNX2PDLIM3microRNA Crosstalk via ERG Signaling: Implications for Bone and Tissue Regeneration

Hassan, A.

10.1101/2025.11.18.688656 — genetics — Posted on 2025-11-19

1922 Insights on genomic profiles of drug resistance and virulence in a cohort of Leishmania infantum isolates from the Mediterranean area

Carrasco Martin, M.; Marti-Carreras, J.; Gomez Ponce, M.; Alcover, M. M.; Roura, X.; Ferrer, L.; Baneth, G.; Bruno, F.; Chicharro, C.; Cordeiro-da-Silva, A.; Cristovao, J.; Di Muccio, T.; Maia, C.; Moreno, J.; Priego, A.; Roca-Gerones, X.; Santarem, N.; Vila Soriano, A.; Vitale, F.; Yasur-Landau, D.; Francino, O.

10.1101/2025.01.23.634476 — genetics — Posted on 2025-11-19

1923 Functional Characterization of Hsp110 in Drosophila Reveals its Essential and Dosage-Sensitive Role in Nervous System Integrity

Rios, B.; Xu, S.; Farmer, S. M.; Ye, X.; Ye, L.; Morano, K. A.; Zhang, S. A.

10.1101/2025.11.18.687301 — developmental biology — Posted on 2025-11-19

1924 Genotype-phenotype correlations in Wilms tumor initiation.

Pop, N. S.; Koot, D.; Brouwers, C. M.; Linssen, M. M.; Claassens, J. W. C.; Catrlidge, C. W. J.; Ozdemir, D. D.; Dolt, K. S.; Hohenstein, P.

10.1101/2025.11.19.689177 — developmental biology — Posted on 2025-11-19

1925 An AmotL2 - Yap1 Module Integrates Flow and Junctional Mechanics to Specify Vascular Pruning Hotspots

Kotini, M. P.; Maggi, L.; Schmelzer, E.; Nakajima, H.; Belting, H.-G.; Affolter, M.

10.1101/2025.11.19.689183 — developmental biology — Posted on 2025-11-19

1926 Targeting Troponin I Phosphorylation for Precision Treatment of Diastolic Dysfunction

Chao, Y.-C.; McAndrew, D. J.; Revuelta, D.; Yadav, R.; Hong, W.-H.; Hu, J.; Folmanaite, M.; Valli, E.; Olmedilla, M. G.; Koscinski, A.; Surdo, N. C.; Tomek, J.; Edwards, H.; Blair, C.; Girdauskas, E.; Henderson, D.; Hurst, J.; Linekar, A.; Psaras, Y.; Gorelik, J.; Smart, N.; Toepfer, C. N.; Maddock, H.; Baillie, G. S.; Lygate, C.; Molina, C. E.; Zaccolo, M.

10.1101/2025.11.18.689162 — cell biology — Posted on 2025-11-19

1927 Multiheme selenoenzyme essential for elemental sulfur respiration

Mihara, H.; Yoshizawa, T.; Izu, Y.; Zhang, W.; Inoue, M.; Shimamoto, N.; Tobe, R.; Aono, R.; Kurihara, T.; Matsumura, H.

10.1101/2025.11.18.688581 — microbiology — Posted on 2025-11-19

1928 The orthobunyavirus Gc glycoprotein head and stalk drives an infectious virion assembly pathway that is specific for the insect host

Shaw, A. B.; Tse, H. N.; Durawa, M. V.; Byford, O. M.; Pearson, H. M.; Stapleford, K. A.; Fontana, J.; Barr, J. N.

10.1101/2025.11.18.689178 — microbiology — Posted on 2025-11-19

1929 Circular viral copy DNA of Dengue virus (DENV-2) isolated from infected mosquito cell cultures

Kanthong, N.; Flegel, T. W.; Gangnonngiw, W.; Thongda, W.; Bunnontae, M.

10.1101/2023.06.07.544120 — microbiology — Posted on 2025-11-19

1930 Identification and characterization of Porphyromonas gingivalis TonB

Rostami, S.; Belvin, B. R.; Lewis, J. P.

10.1101/2025.11.18.689179 — microbiology — Posted on 2025-11-19

1931 Soil trace gas oxidizers divergently respond to short- and long-term warming

Nguyen-Dinh, T.; Tlaskal, V.; Leung, P. M.; Wutkowska, M.; Nweze, J. A.; Yla-Soininmaki, K.; Kerttula, J.; Dahl, M. B.; Sollinger, A.; Schmider, T.; Kohl, L.; Biasi, C.; Richter, A.; Urich, T.; Tveit, A. T.; Greening, C.; Sigurdsson, B. D.; Daebeler, A.

10.1101/2025.11.18.689010 — microbiology — Posted on 2025-11-19

1932 Scalable Human Cellular Models of Parkinson Disease Reveal A Druggable Link Between the Angiotensin Receptor 1 and Alpha-Synuclein Pathology

Daynac, M.; Mouilleau, V.; Liu, Y.; Yang, X.; Shen, Y.; Guo, S.

10.1101/2025.11.18.689137 — neuroscience — Posted on 2025-11-19

1933 CNS Myelin Sheath Lengths Locally Scale to Axon Diameter via Piezo1

Young, A. R.; Lewis, R. W.; Cash, M.; Polis, B.; Zalusky, M.; Reyngoudt, J.; Datta, A.; Bechler, M. E.

10.1101/2025.11.18.689045 — neuroscience — Posted on 2025-11-19

1934 Human assembloid model of emergent neurotropic enteroviruses

Peters, C. E.; Andersen, J.; Li, M.-Y.; Varanese, L.; Thete, M. V.; Yoon, S.-J.; Pio, T.; Thom, N.; Chen, X.; Qiao, W.; Carette, J.; Pasca, S. P.

10.1101/2025.11.18.689148 — neuroscience — Posted on 2025-11-19

1935 Hedonic hotspot in rat olfactory tubercle: map for mu-opioid, orexin, and muscimol enhancement of sucrose 'liking'.

Murata, K.; Berridge, K. C.

10.1101/2025.11.18.689156 — neuroscience — Posted on 2025-11-19

1936 The Role of Pavlovian Bias in Smoking Cessation Success and Neurocognitive Alterations During Nicotine Withdrawal

Lee, E.; Park, H.; Lee, J.-H.; Kim, H.; Park, H. J.; Joh, H.-K.; Ahn, W.-Y.

10.1101/2025.11.18.688678 — neuroscience — Posted on 2025-11-19

1937 PLANT MICROTECHNIQUE WITH RESIN - TOWARDS PLANT HISTOLOMICS

Cerritos-Castro, I. T.; Patron-Soberano, O. A.; Barba de la Rosa, A. P.

10.1101/2025.11.18.689160 — plant biology — Posted on 2025-11-19

1938 Discovery of pseudobaptigenin synthase, completing the (-)-maackiain biosynthetic pathway

Raytek, L. M.; Liu, L.; Bayen, S.; Dastmalchi, M.

10.1101/2025.11.18.689130 — plant biology — Posted on 2025-11-19

1939 Predicting peptide aggregation with protein language model embeddings

Eschbach, E.; Deibler, K.; Korani, D.; Swanson, S. R.

10.1101/2025.09.26.678773 — bioinformatics — Posted on 2025-11-18

1940 Local adaptation in climate tolerance at a small geographic scale contrasts with broad latitudinal patterns

Walter, G. M.; Chakraborty, A.; Cockerell, F.; Kellermann, V.; Alton, L. A.; White, C. R.; Hall, M. D.; Sgro, C. M.

10.1101/2025.05.27.655235 — evolutionary biology — Posted on 2025-11-18

1941 Binary vector origin predictably determines Agrobacterium-mediated transformation outcome across eukaryotic kingdoms

Szarzanowicz, M.; Busche, M.; Dai, Z.; Lapp, N.; Geiselman, G.; Jia, J.; Waldburger, L.; Liang, Y.; Yuan, G.; Duong, R.; Hillson, N.; Brunkard, J. O.; Simmons, B. A.; Gladden, J.; Kim, J.; Thompson, M.; Shih, P.

10.1101/2025.11.18.688525 — plant biology — Posted on 2025-11-18

1942 Ovarian Hormones Moderate Hypertension in Female Eln Haploinsufficient Mice

Dixon, A. J.; MOHANTY, I.; Kaur, G.; McCormick, J. A.; Osei-Owusu, P.

10.1101/2025.11.18.689164 — physiology — Posted on 2025-11-18

1943 Beyond the dyad: higher-order structure within cohesive animal groups reveals the social pathway to leadership

Betti, L.; Musciotto, F.; Papageorgiou, D.; Battiston, F.; Farine, D. R.

10.1101/2022.05.30.494018 — animal behavior and cognition — Posted on 2025-11-18

1944 Taxonomic, geographic, and phylogenetic patterns in the conservation status of the squamate reptiles (Reptilia: Squamata) of Colombia

Vasquez-Restrepo, J. D.; Garcia-Cobos, D.

10.1101/2025.11.18.689145 — ecology — Posted on 2025-11-18

1945 Targeting Troponin I Phosphorylation for Precision Treatment of Diastolic Dysfunction

10.1101/2025.11.18.689162 — cell biology — Posted on 2025-11-18

1946 Microcompartments in archaeal ancestors of eukaryotes: a bioenergetic engine that could have fuelled eukaryogenesis

Du, H.; Xu, A.; Feng, X.; Huang, W.-C.; Li, H.; Liu, L.; Li, Y.; Zhang, S.; Song, N.; Appler, K. E.; Baker, B.; Koonin, E. V.; Li, M.; Liu, Y.

10.1101/2025.11.08.687404 — microbiology — Posted on 2025-11-18

1947 Active learning guides automated discovery of DNA delivery via electroporation for non-model microbes

Brumwell, S. L.; Lord, A.; Corts, A. D.; Harken, S.; Crits-Christoph, A.; Nguyen, M.-A.; Leung, J.; Mendler, K.; Esmurria, A.; Gilbert, C.; Ling, L.; Lee, H. H.; Ostrov, N.

10.1101/2025.11.18.689155 — microbiology — Posted on 2025-11-18

1948 Host reverse transcriptase likely required to maintain persistent dengue virus infections in C6/36 insect cells

Gangnonngiw, W.; Flegel, T. W.; Kanthong, N.

10.1101/2022.12.20.521226 — immunology — Posted on 2025-11-18

1949 Physical Network Constraints Define the Lognormal Architecture of the Brain's Connectome

Piazza, B.; Barabasi, D. L.; Ferreira Castro, A.; Menichetti, G.; Barabasi, A.-L.

10.1101/2025.02.27.640551 — neuroscience — Posted on 2025-11-18

1950 Parallel CLE peptide signaling pathways control nodulation in pea

Scott, T. E.; Wulf, K. E.; Correa-Lozano, A.; Velandia, K.; Reid, J. B.; Foo, E.

10.1101/2025.11.17.688984 — plant biology — Posted on 2025-11-18

1951 De Novo Hepatic Pyrimidine Synthesis Regulates Systemic Energy Homeostasis

Fu, L.; Patil, P. H.; Zhang, P.; Norambuena-Soto, I.; Xiong, Q.; Wang, Y.; Jang, C.; Wang, K.; Peng, Y.; Ding, L.; Fueger, P.; Jin, L.; Huang, W.; Lorenzi, P. L.; Tan, L.; Kalkum, M.; Scherer, P. E.; Wang, Z. V.; Deng, Y.

10.1101/2025.11.18.689117 — pathology — Posted on 2025-11-18

1952 Accurate Multiple Sequence Alignment of Ultramassive Genome Sets

Lai, X.; Luan, H.; Tian, P.

10.1101/2024.09.22.613454 — bioinformatics — Posted on 2025-11-18

1953 The Wnt/APC destruction complex targets SREBP2 in a β-catenin-independent pathway to control cholesterol metabolism

Rattani, A.; Anderson, C.; Trim, W. V.; Garita, E.; Imada, S.; Khawaled, S.; Shin, H.; Zhang, J.; Yilmaz, O. H.; Kirschner, M. W.

10.1101/2025.10.12.681896 — biochemistry — Posted on 2025-11-18

1954 Shifting the PPARγ conformational ensemble towards a transcriptionally repressive state improves covalent inhibitor efficacy

Arifova, L.; MacTavish, B. S.; Laughlin, Z.; Karadi Girdhar, M. N.; Shang, J.; Li, M.-H.; Yu, X.; Zhu, D.; Kamenecka, T. M.; Kojetin, D. J.

10.1101/2025.03.04.640448 — biochemistry — Posted on 2025-11-18

1955 Inference of clonal hematopoiesis using the collective behaviour of DNA methylation states

Crofts, S.; Grenko, C.; Robertson, N.; Kirschner, K.; Chandra, T.

10.1101/2025.11.18.689122 — genetics — Posted on 2025-11-18

1956 Comparative genomics indicate multiple genetic routes to the evolution of torpor in placental mammals

Kontopoulos, D. - G.; Ahmed, A.-W.; Bein, B.; Levesque, D. L.; Hiller, M.

10.1101/2025.11.18.689136 — evolutionary biology — Posted on 2025-11-18

1957 Recent horizontal transfer of transposable elements in Drosophila

Pritam, S.; Signor, S.

10.1101/2025.10.30.685650 — evolutionary biology — Posted on 2025-11-18

1958 The cloacal outgrowth orchestrates co-development of the bladder and umbilical arteries

Ye, X.; Xia, L.; Yang, X.; Tan, R.; Zhang, H.; Lei, L.; Huang, J.; Zhang, Y.; Morrisey, E.; Zhu, P.; Li, Z.; Jing, N.; Li, X.

10.1101/2025.11.18.689093 — developmental biology — Posted on 2025-11-18

1959 Reduced TBX5 dosage undermines developmental control of atrial cardiomyocyte identity in a model of human atrial disease

Kathiriya, I. S.; Rao, K. S.; Clark, A. P.; Hu, K. M.; Grant, Z. L.; Matthews, M. N.; Chen, Z.; Hota, S. K.; Saucerman, J. J.; Bruneau, B.

10.1101/2025.08.16.669546 — developmental biology — Posted on 2025-11-18

1960 Consensus Co-Expression Analysis Identifies A Common Set Of Co-Expressed Genes Associated With Diabetic Peripheral Neuropathy And Chemotherapy-Induced Peripheral Neuropathy

Kober, K.; Chavez-Iglesias, E.; Cho, N. W.; Yom, S.; Dixit, N.; Sirota, M.; Chan, A.; Olshen, A.

10.1101/2025.11.18.689101 — systems biology — Posted on 2025-11-18

1961 Fucoidan exerts anti-cancer activity in a 3D prostate spheroid cell culture model.

Vider, J.; Shelper, T. B.; Lee, K. T. W.; Fitton, J. H.; West, N.

10.1101/2025.11.18.689081 — cancer biology — Posted on 2025-11-18

1962 Dehydration Adaptation of the Adult Rat Modifies Brain Microtubule Electrical Activity of the Osmosensitive Supraoptic Nucleus

Cantiello, H. F.; Porcari, C.; Albarracin, V. H.; Murphy, D.; Mecawi, A. S.; Cantero, M. d. R.; Godino, A.

10.1101/2025.11.18.688944 — biophysics — Posted on 2025-11-18

1963 Biosynthesis of peptidic thiooxazole metallophores installed by multinuclear nonheme iron enzymes.

Gadgil, M. G.; Dommaraju, S. R.; Liu, X.; Battiste, A. J.; Bregman, M. H.; Mitchell, D. A.

10.1101/2025.11.18.689057 — biochemistry — Posted on 2025-11-18

1964 PETRA: Prime editing of transcribed regulatory elements to assay expression

Reyes, M. A.; Herger, M.; Cubitt, L.; Findlay, G. M.

10.1101/2025.11.18.689114 — genomics — Posted on 2025-11-18

1965 NFAT5 Confers Differential Expression in Innate Immune Cells vs. Renal Epithelial Cells in the Face of Osmotic Stress

Kraus, X.; Nnah, F.; Cowley, C.; Araos, P.; Wynne, B. M.

10.1101/2025.11.18.689108 — cell biology — Posted on 2025-11-18

1966 FRG1 Regulates Nonsense-Mediated mRNA Decay by Modulating UPF1 Levels

Palo, A.; Mohapatra, T.; Singh, A.; T, S.; Mohanty, S.; Swain, R. K.; Dixit, M.

10.1101/2025.11.18.689056 — molecular biology — Posted on 2025-11-18

1967 Broad-spectrum antiviral activity of the synthetic rocaglate zotatifin against multiple viruses

Valdes-Torres, P.; Campos, D.; Galan-Jurado, P. E.; Zegarra, D.; Tunon-Lorenzo, I.; Castillo-Gonzalez, F.; Blanquer, M.; Mewa, J. C.; Rivas, C.; Santamaria, J. G.

10.1101/2025.11.18.689102 — microbiology — Posted on 2025-11-18

1968 Neural mechanisms of handedness for precision drawing: hand-dependent engagement of cortical networks for bimanual control and tool use

Kapil, N.; Kim, T.; Gassass, S.; Zhou, R.; Carter, A. R.; Dobbins, I. G.; Liu, L.; McAvoy, M. P.; Wheelock, M. D.; Wang, Y.; Brogan, D. M.; Dy, C. J.; Susan, M. E.; Philip, B. A.

10.1101/2025.11.18.689091 — neuroscience — Posted on 2025-11-18

1969 Whole-Brain Millisecond-Scale Effective Connectivity Atlas of Auditory and Visual Naming

Kochi, R.; Kanno, A.; Uda, H.; Hatano, K.; Sonoda, M.; Endo, H.; Cools, M.; Rothermel, R.; Luat, A. F.; ASANO, E.

10.1101/2025.11.18.689014 — neuroscience — Posted on 2025-11-18

1970 Umbilical cord structure shapes feto-maternal heat exchange across mammals

Wan, T.; Laundon, D.; Saw, S. N.; Cheng, N.; Lee, H. K.; Johnstone, E. D.; Jensen, O. E.; Lewis, R. M.; Chernyavsky, I. L.

10.1101/2025.11.18.688874 — physiology — Posted on 2025-11-18

1971 Differences in Brain Microtubule Electrical Activity of the Hippocampus and Neocortex from the Adult Rat

Cantiello, H. F.; Porcari, C. Y.; Albarracin, V. H.; Murphy, D.; Mecawi, A. S.; Godino, A.; Cantero, M. d. R.

10.1101/2025.11.18.688943 — biophysics — Posted on 2025-11-18

1972 Maternal glucocorticoids and behavior shape offspring developmental trade-offs in wild baboons

Patterson, S. K.; Hinde, K.; Bowen Bond, A.; Trumble, B. C.; Lu, A.; Strum, S. C.; Silk, J. B.

10.1101/2025.11.18.689046 — animal behavior and cognition — Posted on 2025-11-18

1973 Climate-Driven Forest Reassembly Follows Divergent Functional Pathways in Cold- and Warm-Adapted Communities

Shabanov, I.; Tonkin, J. D.; Lensen, A.; Deslippe, J. R.

10.1101/2025.11.18.689113 — ecology — Posted on 2025-11-18

1974 Supracellular Mechanics and Counter-Rotational Bilateral Flows Orchestrate Posterior Morphogenesis

Geneva, M.; Davidson, L.

10.1101/2025.11.18.689090 — developmental biology — Posted on 2025-11-18

1975 Reconstructing the emergence of the human chorion via HIPPO-mediated trophoblast induction

Zhang, M.; Lim, R. L.; Reis, A. H.; Piszker, W.; Boyd, W. W.; Pagon, A.; Mahajan, A.; Wu, L.; Zhao, C.; Petropoulos, S.; Ronda, C.; Simunovic, M.

10.1101/2025.11.18.688276 — cell biology — Posted on 2025-11-18

1976 A hidden protamine PTM code in sperm generates heterogeneous chromatin states and finetunes reproductive fitness

Moritz, L.; Woodilla, C. J.; Agrawal, R.; Rabbani, M.; Schon, S. B.; Xie, W.; Tower, C. A.; Srinivasan, S.; Sheng, Y.; Baldwin, M. R.; O'Brien, P. J.; Hess, R. A.; Orwig, K. E.; Redding, S.; Hammoud, S.

10.1101/2025.11.18.688960 — molecular biology — Posted on 2025-11-18

1977 Large-scale culturing of the tree microbiome enables targeted disease suppression

Ordonez-Ordonez, A.; Cambon, M. C.; Downie, J.; Kajamuhan, A.; Hussain, U.; Crampton, B.; Richardson, M.; Jones, M.; Green, R.; Pettifor, B.; Pyne, E.; Finch, J.; Brady, C.; Denman, S.; McDonald, J. E.

10.1101/2025.11.18.689053 — microbiology — Posted on 2025-11-18

1978 Antibiotic-induced microbiota disruption impairs neutrophil-mediated immunity to Aspergillus fumigatus

Aufiero, M.; Hohl, T.

10.1101/2025.11.18.689104 — immunology — Posted on 2025-11-18

1979 Deoxyguanosine Kinase Deficiency Couples Purine Metabolism to Innate Immune Activation and Lipid Accumulation in Hepatocytes

Corey, M.; Rayadurgam, M.; Jung, J.; Gibbons, A.; Reddy, N.; Vatanmakanian, M.; Kakugawa, K.; Saminathan, P.; Sharma, S. Y.

10.1101/2025.11.18.688341 — immunology — Posted on 2025-11-18

1980 Non-selective beta blockers reduce bystander CD8+ T cell activation in decompensated liver cirrhosis

Lietzau, A.; Tapken, I.; Kim, S.-Y.; Souleiman, R.; Freyer, E.; Kraft, A. R.; Schuette, S.; Tergast, T. L.; Maasoumy, B.; Wedemeyer, H.; Drath, I.; Zurek, G.; Shin, E.-C.; Cornberg, M.; Niehaus, C.

10.1101/2025.11.18.688703 — immunology — Posted on 2025-11-18

1981 Deep Learning-Augmented Stimulated Raman Imaging for Cell-Type-Specific Metabolic Profiling in Live Neuronal Co-Cultures

Lin, L.-E.; Bi, X.; Colazo, A.; Wang, H.; Wei, L.

10.1101/2025.11.18.689078 — neuroscience — Posted on 2025-11-18

1982 Astrocytic RNA degradation suppresses calcium signaling to support synapse function and restrain anxiety

Lituma, P. J.; Deveci, A.; Barrio-Alonso, E.; Tan, K.; Wilkinson, M. F.; Castillo, P. E.; Colak, D.

10.1101/2025.11.18.689044 — neuroscience — Posted on 2025-11-18

1983 Auditory Cortical Gradients Integrate Bottom-Up and Top-Down Structure During Natural Sound Categorisation

Haydock, D.; Leech, R.; Kachlicka, M.; Dick, F.

10.1101/2025.11.18.689038 — neuroscience — Posted on 2025-11-18

1984 Perceiving Instability: How Expectations Bias Sensorimotor Processing in Balance Control

Parr, J. V. V.; Mills, R.; Kal, E. C.; Bronstein, A. M.; Ellmers, T. J.

10.1101/2025.11.18.688816 — neuroscience — Posted on 2025-11-18

1985 Machine-Learning Classification of Motor Unit Types in the Adult Mouse

Martinez-Silva, M. d. L.; Ahorklo, R. M.; Reedich, E. J.; Imhoff-Manuel, R. D.; Katenka, N.; Manuel, M.

10.1101/2025.11.18.689075 — neuroscience — Posted on 2025-11-18

1986 Sex Differences in B2 SINE RNA Expression and its Role in Hippocampal Development

Richter, T. A.; Bartlett, A. A.; Lapp, H. E.; O'Neil, E. T.; Pritchard, E. K.; Guffanti, G.; Zup, S. L.; Hunter, R. G.

10.1101/2025.11.18.689111 — neuroscience — Posted on 2025-11-18

1987 Separable neurocomputational mechanisms underlying multisensory learning

Bedi, S.; Casimiro, E.; de Hollander, G.; Raduner, N.; Helmchen, F.; Brem, S.; Konovalov, A.; Ruff, C.

10.1101/2025.11.18.688925 — neuroscience — Posted on 2025-11-18

1988 A dopamine circuit regulates locomotor initiation and persistence in Drosophila

Wen, X.; Connors, K. E.; Snell, C. C.; Mcgrath, R.; Mehta, A.; Hattori, D.

10.1101/2025.11.18.689052 — neuroscience — Posted on 2025-11-18

1989 CUSP: Complex Spike Sorting from Multi-electrode Array Recordings with U-net Sequence-to-Sequence Prediction

Bao, C.; Mildren, R.; Charles, A.; Cullen, K. E.

10.1101/2025.11.18.689109 — neuroscience — Posted on 2025-11-18

1990 Neural Dynamics of Multiattribute Decision Making Under Choice Overload

Stanley, J. M.; Wedell, D. H.

10.1101/2025.11.18.689103 — neuroscience — Posted on 2025-11-18

1991 A Reversible Mitochondrial ROS Probe for Monitoring Mitophagy Dynamics: Development and Application of MitoFlare

Hou, S.; Yan, X.; Li, X.; Ju, J.; Shan, Z.; Bi, L.

10.1101/2025.11.18.689025 — neuroscience — Posted on 2025-11-18

1992 Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss

Masid, M.; Rota, I. A.; Barras, D.; De Carlo, F.; Ginefra, P.; Desbuisson, M.; Ortiz-Miranda, Y.; Zamarin, D.; Shah, S. P.; Vannini, N.; Coukos, G.; Dangaj-Laniti, D.; Hatzimanikatis, V.

10.1101/2025.11.18.689039 — systems biology — Posted on 2025-11-18

1993 A three amino acid sequence gates protein stability control of bHLH104 and iron uptake in Arabidopsis thaliana

Baby, D.; Weldi, S.; Knopf, M.; Venkadasamy, V. L.; Erickson, J. L.; Bauer, P.

10.1101/2025.11.18.689088 — plant biology — Posted on 2025-11-18

1994 Binary vector origin predictably determines Agrobacterium-mediated transformation outcome across eukaryotic kingdom

10.1101/2025.11.18.688525 — plant biology — Posted on 2025-11-18

1995 TRIB2 supports a high glycolytic phenotype in melanoma cells

Mayoral, V.; Coelho, A. L. D. S.; Lopes, C.; Costa, O. M.; Oliveira, P. J.; Aragon, J.; Ferreira, B.; Link, W.

10.1101/2025.11.18.689112 — cancer biology — Posted on 2025-11-18

1996 Molecular mechanism by which SARS-CoV-2 Orf9b suppresses the Tom70-Hsp90 interaction to evade innate immunity

Sherer, N.; Bastiray, A.; Chen, X.-R.; Molugu, T.; Yadav, G. P.; Igumenova, T. I.; Cho, J.-H.

10.1101/2025.11.18.689095 — biophysics — Posted on 2025-11-18

1997 CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs

Kolodziej, A. R.; Abulnaga, S. M.; Ovchinnikov, S.

10.1101/2025.11.18.689110 — biophysics — Posted on 2025-11-18

1998 The electrophilic metabolite of kynurenine, kynurenine-CKA, targets C151 in Keap1 to derepress Nrf2.

Feng, J.; Carreno, M. A.; Jung, H.; Naidu, S. D.; Arroyo-Diaz, N.; Ang, A. D.; Kulkarni, B.; Kisielewski, D.; Suzuki, T.; Yamamoto, M.; Hayes, J. D.; Honda, T.; Leon-Ruiz, B.; Eggler, A. L.; Vitturi, D. A.; Dinkova-Kostova, A. T.

10.1101/2025.11.18.689077 — biochemistry — Posted on 2025-11-18

1999 Lighting and circadian cues shape locomotor strategies for balance and navigation in larval zebrafish

Liu, J.; Davis, S. N.; Gelnaw, H.; Schoppik, D.; Zhu, Y.

10.1101/2025.11.18.689084 — animal behavior and cognition — Posted on 2025-11-18

2000 The 9p21.3 Coronary Artery Disease Risk Locus Modulates Vascular Cell-State Transitions via Enhancer-Driven Regulation of MTAP

Audam, T. N.; Schmandt, B.; Huang, Y.; Cho, Y. B.; Murali, M.; Kaalia, R.; Agrawal, S.; Liu, J.; Shi, H.; Zhou, Y.; Cao, D.; Jiang, L.; Li, Y.; Wen, J.; Zhao, H.; Saadat, A.; Melanson, M.; Hall, A. W.; Laber, S.; Strobel, S.; Chen, S.; McGonagle, E. R.; Stefek, A.; Reeve, M. P.; Ham, A. M.; White, C. M.; Khera, A. V.; Epstein, C. B.; Chaffin, M.; Ellinor, P.; Wang, M.; Daly, M.; Karczewski, K. J.; Jones, T. R.; Dashti, H.; Claussnitzer, M.

10.1101/2025.11.18.689066 — genomics — Posted on 2025-11-18

2001 Epo and hypoxia accelerate a pattern of gradual cell cycle shortening in BFU-e and CFU-e erythroid progenitors in vivo

Winward, A.; Lalonde, L.; Nair, D.; Socolovsky, M.

10.1101/2025.11.18.688855 — cell biology — Posted on 2025-11-18

2002 Translatome and translation dynamics analysis of a RiboCancer cell line panel reveals that leukemia-associated Rps15 mutations rewire translation through codon-specific tRNA accommodation defects.

Astier, A.; Caruso, M.; Vereecke, S.; E. Santo, P.; Capron, C.; Froment, C.; Rinaldi, D.; Cabrerizo Granados, D.; Leclercq, M.; Royaert, J.; Verbeeck, J.; Pasau, N.; Plassart, L.; Pepe, D.; Verbruggen, S.; Paraqindes, H.; Lebaron, S.; Marcel, V.; Durand, S.; Chapat, C.; Menschaert, G.; Close, P.; Rapino, F.; Catez, F.; Marcoux, J.; Plisson-Chastang, C.; De Keersmaecker, K.

10.1101/2025.11.18.687986 — molecular biology — Posted on 2025-11-18

2003 Cell-autonomous mitochondrial calcium flux governs oligodendrocyte regeneration

Maas, D. A.; Bancel-Vega, R.; Baudouin, L. R.; Bun, P.; Manot-Saillet, B.; Habermacher, C.; Verburg, N.; Rusconi, F.; Angulo, M. C.

10.1101/2025.11.18.689087 — neuroscience — Posted on 2025-11-18

2004 Atypical endo-β-1,4-mannanases are necessary for normal glucomannan synthesis in Arabidopsis

Kikuchi, A.; Sato, E.; Yoshimi, Y.; Takasaki, H.; Nishigaki, N.; Atsuzawa, K.; Kaneko, Y.; Yamaguchi, M.; Takahashi, D.; Dupree, P.; Kotake, T.

10.1101/2025.02.21.639209 — plant biology — Posted on 2025-11-18

2005 Vimentin promotes actin assembly by stabilizing ATP-actin subunits at the barbed end

Paty, L.; Varela-Salgado, M.; Tran, Q. D.; Jegou, A.; Romet-Lemonne, G.; Leduc, C.

10.1101/2025.11.17.688760 — biophysics — Posted on 2025-11-18

2006 Computational characterization of the xanthan gum glycosyltransferase GumK

Luciano, D.; Thomasen, F. E.; Lindorff-Larsen, K.; Courtade, G.

10.1101/2025.08.28.672881 — biophysics — Posted on 2025-11-18

2007 SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets

Seal, S.; Neelon, B.

10.1101/2025.03.29.646124 — bioinformatics — Posted on 2025-11-18

2008 Benchmarking the impact of reference genome selection on taxonomic profiling accuracy

van Bemmelen, J.; Nika, I.; Baaijens, J. A.

10.1101/2025.02.07.637076 — bioinformatics — Posted on 2025-11-18

2009 Nona: A unifying multimodal masking framework for functional genomics

Nair, S.; Hajiramezanali, E.; Tseng, A.; Diamant, N.; Hingerl, J.; Lal, A.; Biancalani, T.; Bravo, H. C.; Scalia, G.; Eraslan, G.

10.1101/2025.11.06.687036 — genomics — Posted on 2025-11-18

2010 Selective chr21 homolog silencing reveals polymorphisms influence the epigenetic silencing and functional dosage of RWDD2B

Larsen, E. C.; Moon, J. E.; King, O. D.; Lawrence, J. B.

10.1101/2025.09.17.676855 — genetics — Posted on 2025-11-18

2011 araucan regulates butterfly wing iridescence by coordinating scale structure and pigmentation

Chatterjee, M.; Finet, C.; Siegel, K. J.; Tian, S.; Zhou, Y. J.; Loh, L. S.; Yu, X. Y.; Delgado, S.; McDonald, J. M. C.; Markenscoff-Papadimitriou, E.; Mazo-Vargas, A.; Monteiro, A.; Reed, R. D.

10.1101/2023.11.21.568172 — genetics — Posted on 2025-11-18

2012 Not So Mosaic After All? The Core Genomes of IncP-1 Plasmids Evolve Predominantly Through Vertical Transmission

Sneddon, D.; Elg, C. A.; Sullivan, J.; Top, E. M.

10.1101/2025.08.13.669769 — evolutionary biology — Posted on 2025-11-18

2013 CroCoNet: a novel framework for cross-species network analysis reveals POU5F1 (OCT4) rewiring

Termeg, A.; Storozhuk, V.; Kliesmete, Z.; Edenhofer, F. C.; Geuder, J.; Vieth, B.; Janssen, P.; Hellmann, I.

10.1101/2025.11.18.689002 — evolutionary biology — Posted on 2025-11-18

2014 A method for massively scalable phylogenetic network inference

Kolbow, N.; Kong, S.; Solis-Lemus, C.

10.1101/2025.05.05.652278 — evolutionary biology — Posted on 2025-11-18

2015 Global change factors reshape the links between litter properties, decomposers, and decomposition in mature oak forests

Meehan, M. L.; Chomel, M.; Vilkiji, Z.; Faulkner, K. J.; Caruso, T.; MacKenzie, A. R.; Baldy, V.; Bardgett, R. D.; Johnson, D.

10.1101/2025.07.18.665400 — ecology — Posted on 2025-11-18

2016 Evolutionary stasis and homogeneous selection structure microbial communities in the deep subseafloor sedimentary biosphere

Hoshino, T.; Sakuma, A.; Kajitani, R.; Doi, H.; Ito, T.; Inagaki, F.

10.1101/2025.11.18.689030 — ecology — Posted on 2025-11-18

2017 Density-dependent spatial patterns and habitat associations of a dominant desert ant

Cao, A. L.; Milesi, F. A.; Pol, R. G.; Vullo, L.; Miretti, M. F.; Pirk, G. I.; Lopez de Casenave, J.

10.1101/2025.06.10.658907 — ecology — Posted on 2025-11-18

2018 Identification and characterization of a dlx2b cis-regulatory element both sufficient and necessary for correct transcription during zebrafish tooth development

Jackman, W. R.; Moon, Y.; Cox, C. K.; Anderson, D. R.; DeFusco, A. A.; Nguyen, V. M.; Liu, S. Y.; Carter, E. H.; Littleford, H. E.; Richards, E. K.; Jowdry, A. L.; Gibert, Y.

10.1101/2022.01.20.477116 — developmental biology — Posted on 2025-11-18

2019 A Biophysical Model of Phagocytic Cup Dynamics: The Effect of Membrane Tension

Shadmani, P.; mehrafrooz, B.; Montazeri hedesh, A.; Richards, D.

10.1101/2025.11.18.688812 — cell biology — Posted on 2025-11-18

2020 DCLRE1A orchestrates CAG repeat contraction following Cas12a-induced DNA breaks

Dabrowska, M.; Siegner, S.; Misiukiewicz, A.; Bandaruk, Y.; Schroeder, M. S.; Muhar, M.; Kreutzer, S.; Corn, J. E.; Olejniczak, M.

10.1101/2025.11.18.689026 — cell biology — Posted on 2025-11-18

2021 Texas 2-Step: A new Model for YcgR::c-di-GMP Action at the Flagellar Motor

Bhattarai, N.; Guo, W.; Partridge, J. D.; Harshey, R. M.

10.1101/2025.08.21.671521 — microbiology — Posted on 2025-11-18

2022 Females with Obesity Exhibit Greater Influenza Vaccine-induced Immunity and Protection than Males in a Mouse Model

Wolfe, B.; Pantha, S.; Vijayakumar, S.; Budha Magar, S.; Aboellail, T.; Dhakal, S.

10.1101/2025.11.18.689040 — immunology — Posted on 2025-11-18

2023 Multilingual Computational Models Capture a Shared Meaning Component in Brain Responses across 21 Languages

de Varda, A. G.; Malik-Moraleda, S.; Tuckute, G.; Fedorenko, E.

10.1101/2025.02.01.636044 — neuroscience — Posted on 2025-11-18

2024 Dynamics of sensorimotor plasticity during exoskeletal finger augmentation

Radziun, D.; Geurts, S.; Peviani, V. C.; Miller, L. E.

10.1101/2025.07.01.662639 — neuroscience — Posted on 2025-11-18

2025 Injury-induced nuclear export of RNA-binding proteins drives mRNA stabilization and translation to promote dendrite regeneration

Qu, Z.; Yan, D.

10.1101/2025.11.18.688889 — neuroscience — Posted on 2025-11-18

2026 Prefrontal gamma oscillations and fear extinction learning require early postnatal interneuron-oligodendroglia communication

Plaisier, F.; Ibaceta-Gonzalez, C.; Khelfaoui, H.; Watson, A. E. S.; Poilbout, C.; Voronova, A.; Angulo, M. C.

10.1101/2024.12.19.629474 — neuroscience — Posted on 2025-11-18

2027 Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome

Bayer, F. P.; Mueller, J.; Kabella, N.; Abele, M.; Chang, Y.-C.; Estrada, L.; Jensen, C.; Hamood, F.; Lee, C.-Y.; Schneider, A.; The, M.; Kuster, B.

10.1101/2025.11.18.689017 — systems biology — Posted on 2025-11-18

2028 Adropin protects against cardiac remodeling and metabolic dysfunction in a mouse model of HFpEF

Mushala, B. A.; Stoner, M. W.; Sharifi-Sanjani, M.; Manning, J. R.; Bugga, P.; Bhattarai, N.; McMahon, B.; Vandevender, A.; Mullett, S. J.; Kaufman, B. A.; Shiva, S. S.; Zhang, C.; Goetzman, E. S.; Chan, S. Y.; Gelhaus, S. L.; Jurczak, M. J.; Scott, I.

10.1101/2025.05.03.652038 — physiology — Posted on 2025-11-18

2029 Decoding the pituitary gonadotrope regulatory architecture governing the preovulatory surge in vivo

Le Cicle, C.; Garrel-lazayres, G.; Chauvin, S.; Giton, F.; Taboureau, O.; Miralles, F.; Cohen Tannoudji, J.; David, L.

10.1101/2025.11.18.689023 — physiology — Posted on 2025-11-18

2030 Pulsed laser lensing for phase modulation in electron microscopy

Du, D. X.; Bartnik, A. C.; Duncan, C. J. R.; Choudhry, U.; Tabachnik, T.; Sallah, C.; Ogawa, Y.; Najafi, E.; Yang, D.-S.; Maxson, J. M.; Fitzpatrick, A. W. P.

10.1101/2025.06.12.659428 — biophysics — Posted on 2025-11-18

2031 Uncovering the genetic basis of fruit volatiles in Fragaria vesca through GWAS reveals FvJMT2 as a methyl benzoate biosynthesis gene with insect-repellent function

Jimenez-Munoz, R.; Urrutia, M.; Meco, V.; Rambla, J. L.; Toivainen, T.; Perez-Hedo, M.; Sanchez-Sevilla, J. F.; Urbaneja, A.; Salas, J. J.; Hytönen, T.; Granell, A.; Martin-Pizarro, C.; Pose, D.

10.1101/2025.11.18.689018 — genomics — Posted on 2025-11-18

2032 Embracing the power of genomics to inform evolutionary significant units

Bergman, J. C.; Taylor, R. S.; Manseau, M.

10.1101/2025.06.14.659582 — genomics — Posted on 2025-11-18

2033 HDAC1 has a role in double strand break repair by regulating γH2AX signalling

Marqueta-Gracia, J.; Bejarano-Franco, M.; Spaag, S.; Silva, S.; Aguilera, A.; Gomez-Gonzalez, B.

10.1101/2025.11.18.689006 — molecular biology — Posted on 2025-11-18

2034 Microfluidics based exploration for quorum quenching genes in Antarctic microbiomes

White, J. J.; Diaz-Rullo, J.; Morgante, V.; Gonzalez-Pastor, J. E.; Hidalgo, A.; Sanchez-Costa, M.

10.1101/2025.11.18.689007 — molecular biology — Posted on 2025-11-18

2035 Anopheles mosquitoes exposed to long-acting antimalarials via drug-spiked bloodmeal absorb drug but do not suffer fitness costs

Goheen, M. M.; Orfano, A.; Dah, S. R.; Foy, B. D.; Brackney, D. E.; Li, F.; Ouedraogo, J. B.; Da, D. F.; Dabire, R. K.; Some, A. F.; Bei, A. K.; Parikh, S.

10.1101/2025.11.13.688204 — microbiology — Posted on 2025-11-18

2036 Soil trace gas oxidizers divergently respond to short- and long-term warming

Nguyen-Dinh, T.; Tlaskal, V.; Leung, P. M.; Wutkowska, M.; Nweze, J. A.; Yla-Soininmaki, K.; Kerttula, J.; Dahl, M. B.; Sollinger, A.; Schmider, T.; Biasi, C.; Richter, A.; Urich, T.; Tveit, A. T.; Greening, C.; Sigurdsson, B. D.; Daebeler, A.

10.1101/2025.11.18.689010 — microbiology — Posted on 2025-11-18

2037 Biological Sex Differences after High and Low Doses of Influenza A Virus Infection in a Diet-induced Obesity Mouse Model

Pantha, S.; Wolfe, B.; Vijayakumar, S.; Budha Magar, S.; Aboellail, T.; Dhakal, S.

10.1101/2025.11.18.689021 — immunology — Posted on 2025-11-18

2038 Tau oligomers can occur in human brains within days of a single traumatic brain injury

Vuono, R.; Bhorla, S. K.; Steponenaite, A.; Allinson, K.; Coleman, M.

10.1101/2025.11.18.688238 — neuroscience — Posted on 2025-11-18

2039 Fast and Easy Whole-Brain Network Model Parameter Estimation with Automatic Differentiation

Pille, M.; Martin, L.; Richter, E.; Perdikis, D.; Schirner, M.; Ritter, P.

10.1101/2025.11.18.689003 — neuroscience — Posted on 2025-11-18

2040 Scopolamine induced learning deficit in marmosets

Harkins, H. E.; Christopher, K.; Matrov, D.; Ingram, I. D.; Saglio, E. B.; Dold, G. R.; Chudasama, Y.

10.1101/2025.11.18.688868 — neuroscience — Posted on 2025-11-18

2041 Opioid receptor distribution in the claustrum-dorsal endopiriform complex

Bolger, M.; Jackson, J.; Taylor, A. M. W.

10.1101/2025.11.18.687877 — neuroscience — Posted on 2025-11-18

2042 DNMT1 Coordinates PV Interneuron-Glia Coupling to Maintain Cortical Network Stability and Regulate Behavior

Linde, J.; Yildiz, C. B.; Voehringer, K.; Nabbefeld, G.; Graff, S.; Pensold, D.; Reichard, J.; Hermanns, M.; Weber-Hamacher, C.; Spehr, M.; Kampa, B.; Urbach, A.; Musall, S.; Zimmer-Bensch, G. M.

10.1101/2025.11.18.689032 — neuroscience — Posted on 2025-11-18

2043 CANVAS causing AAGGG repeat expansions cause tissue-specific reduction in RFC1 expression and increase sensitivity to DNA damage

Curro, R.; Dominik, N.; Facchini, S.; Schnekenberg, R. P.; Perini, C.; Ronco, R.; Rugginini, B.; Ghia, A.; Bione, S.; Tagliaferri, N.; Grupelli, G. P.; Lowe, S. A.; Hicks, A. R.; Vegezzi, E.; Simone, R.; Bertini, A.; Abati, E.; Velasco, R.; Sereno, M.; Gutierrez-Gutierrez, G.; Thomas, S.; Alberti, P.; Khurana, V.; Attems, J.; Troakes, C.; Gustavsson, E. K.; Lignani, G.; Qiu, Y.; Sleigh, J. N.; Tucci, A.; Fratta, P.; Isaacs, A.; Lim, Y. M.; Jaunmuktane, Z.; Brandner, S.; Bennett, D. L.; Przedborski, S.; Opal, P.; Hoke, A.; Kuo, S.-H.; Reilly, M. M.; Houlden, H.; Ryten, M.; Cavaletti, G.; Argyri

10.1101/2025.11.18.688292 — neuroscience — Posted on 2025-11-18

2044 SEXUAL DIMORPHISM IN FIN SIZE AND SHAPE IN BLUEFIN KILLIFISH

Brockelsby, K.; Davis, E. J.; Roden, O. A.; Shamsyna, V.; Fuller, R. C.

10.1101/2025.11.18.689072 — zoology — Posted on 2025-11-18

2045 TurboID-based proximity labeling enables in vivo mapping of Plasmodiophora brassicae secretome in Arabidopsis

Kalinger, K. S.; Gallipeau-Burns, E.; Hossain, M. M.; Nourimand, M.; Mietkiewska, E.; Talasila, M.; Uhrig, R. G.; Todd, C. D.; MacLean, A. M.

10.1101/2025.11.18.684874 — plant biology — Posted on 2025-11-18

2046 MAAD: Multidimensional Antiviral Antibody Database

Li, Y.; Wang, J.; Zhang, C.; Zhang, Y.; Deng, J.; Zhang, H.; Li, M.; Wang, F.; Wang, X.

10.1101/2025.11.18.688681 — bioinformatics — Posted on 2025-11-18

2047 Infarctsize-AI: an efficient infarct size image analysis tool for small rodent myocardial infarction studies

Kovacshazi, C.; Kapui, D.; Weber, B. Y.; Gergely, T. G.; Brenner, G. B.; Agg, B.; Tabajdi, C.; Racz, A.; Horvath, A.; Hernandez-Resendiz, S.; Hausenloy, D. J.; Vilskersts, R.; Okninska, M.; Waszkiewicz, M.; Maczewski, M.; Molnar, A.; Szabados, T.; Bencsik, P.; Krieg, T.; Inserter, J.; Schulz, R.; Zuurbier, C. J.; Andreadou, I.; Podesser, B. K.; Ferdinandy, P.; Giricz, Z.

10.1101/2025.11.18.688527 — bioinformatics — Posted on 2025-11-18

2048 A Plug-and-Play Platform for Automated Azapeptide Synthesis: Case study of Azapeptide-based GLP-1

He, M.; Cheng, K. F.; Al-Abed, Y.

10.1101/2025.03.03.641232 — biochemistry — Posted on 2025-11-18

2049 Unified Generation of Regionalized Neural Organoids from Single-Lumen Neuroepithelium

Rao, J.; He, Z.; Loskarn, S.; Bender, A.; Jo, Y.; Lueckel, J.; Curcio, M.; Cubela, I.; Camp, G.; Treutlein, B.; Lutolf, M. P.

10.1101/2025.11.18.689013 — developmental biology — Posted on 2025-11-18

2050 Human airway epithelia clear rhinovirus-infected cells using two waves of cell extrusion

Fore, F.; Bagley, D. C.; Martinez-Nunez, R. T.; Aniscenko, J.; Johnston, S.; Rosenblatt, J.

10.1101/2025.11.18.689008 — cell biology — Posted on 2025-11-18

2051 Methanobacterium nebraskense sp. nov., a hydrogenotrophic methanogen isolated from saline wetland soil

Fiore, N. A.; Zhou, Y.; Weber, K. A.

10.1101/2025.11.18.688885 — microbiology — Posted on 2025-11-18

2052 Linear ubiquitin chain assembly complex contributes to NLRP3-mediated pyroptotic cell death

Douanne, T.; Moreau, R.; Trapani, V.; Trillet, K.; Leloup, H.; Petrili, V.; Gavard, J.; Bidere, N.

10.1101/2025.11.18.689012 — immunology — Posted on 2025-11-18

2053 Nrg1 regulates cortical wiring and motor recovery upon traumatic injury

Gonzalez-Manteiga, A.; Navarro-Gonzalez, C.; Rodriguez-Prieto, A.; Zavaglia, M. V.; Fazzari, P.

10.1101/2025.11.18.689009 — neuroscience — Posted on 2025-11-18

2054 A painless nerve growth factor variant uncouples nociceptive and neurotrophic TrkA signaling

10.1101/2025.11.18.686377 — neuroscience — Posted on 2025-11-18

2055 Local differences in baseline sodium shape astrocytic potassium uptake by the NKA

Meyer, J.; Eitelmann, S.; Bhattarai, A.; Bornemann, V.; Unichenko, P.; Durry, S.; Kafitz, K. W.; Henneberger, C.; Ullah, G.; Rose, C. R.

10.1101/2025.11.18.687951 — neuroscience — Posted on 2025-11-18

2056 Deletion or Targeted Blockade of FcγRIIb (CD32b) Impairs α-Syn Propagation In-Vivo

Hennegan, J.; Teeling, J.; Roghanian, A.; Cragg, M.; Duriez, P.; Cox, K.; Oldham, R.; Douglas, L.; Frendeus, B.; Hurley, M.

10.1101/2025.11.18.687143 — neuroscience — Posted on 2025-11-18

2057 LCI9 is required for normal pyrenoid starch sheath formation and efficiency of the CO2-concentrating mechanism in Chlamydomonas reinhardtii

Adler, L.; Lau, J.; Esch, L.; Dao, O.; Barrett, J.; Grant, S.; Yates, G.; McCormick, A.; Mackinder, L.

10.1101/2025.11.18.689020 — plant biology — Posted on 2025-11-18

2058 In Vitro Dynamic and Quantitative Monitoring of Strigolactone-signaling Complex Formation by Time-resolved FRET

Suzuki, T.; Nishiyama, K.; Kato, Y.; Shinkai, C.; Ishikawa, T.; Robertlee, J.; Kuruma, M.; Hagihara, S.; Marco, B.; Fukui, K.; Asami, T.; Seto, Y.

10.1101/2025.11.18.688998 — plant biology — Posted on 2025-11-18

2059 Hepatocyte FGFR2 Mediates the Antifibrotic Effects of FGF10 in Advanced Liver Fibrosis.

Yang, X.; Yu, B.; Ma, J.; Yan, Y.; Wang, H.; Dong, Q.; Peng, S.; Wu, Q.; Zhang, T.; Zhang, P.; Jiang, Z.; Lu, C.; Li, L.; You, X.; Xu, Y.; Joshua, B.; Mu, Z.; Zheng, M.; Li, X.; Hui, Q.; Wang, X.

10.1101/2025.11.18.689001 — pharmacology and toxicology — Posted on 2025-11-18

2060 INVA8001, a Novel and Highly Selective Chymase Inhibitor, Ameliorates Liver Inflammation, Fibrosis, and Hyperplasia in Mdr2 Knockout Mice

Sharma, S.; Chen, L.; Zhou, T.; Chawla, M.; Ganjoo, A.; Okada, S.; Alesci, S.; Nandabalan, K.; Francis, H.

10.1101/2025.11.18.688305 — pathology — Posted on 2025-11-18

2061 High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences

Hertz, L. M.; Arce, A.; Rivas, E. B.; Lucks, J. B.

10.1101/2025.11.18.689055 — biochemistry — Posted on 2025-11-18

2062 PANK2-mediated de novo CoA synthesis is required for metabolic switching to fatty acid oxidation

Nordlie, S. M.; Schafer, R.; Rauckhorst, A.; Santos-Exposito, A. M.; Prieto-Rodriguez, A.; Wilson, B. A.; Evans, I. A.; Hadziamehtovic, U.; Nowlen, F.; Santos-Ocana, C.; Taylor, E. B.; Kruer, M. C.; Padilla Lopez, S.

10.1101/2025.10.07.680981 — biochemistry — Posted on 2025-11-18

2063 Systematic and proactive evaluation of AIRE missense variant effects

Axakova, A.; Berger, A. H.; van Loggerenberg, W.; Kishore, N.; Gebbia, M.; Ding, M. X.; Douville, S. V.; Tabet, D. R.; Cote, A. G.; Weile, J.; Johansson, S.; Bratland, E.; Roth, F. P.

10.1101/2025.11.18.688830 — genetics — Posted on 2025-11-18

2064 N6-Methyladenosine Safeguards Mouse and Human Germline Competence

Filipczyk, A.; Lerdrup, M.; Zuo, R.; Jin, K.-X.; Bai, B.; So/egaard, M. L. C.; Ilaslan, E.; Yao, Y.; Li, J.; Wyrozemski, L.; Wu, X.; Li, Y.; Klungland, A.; Wang, J.

10.1101/2025.11.18.688769 — developmental biology — Posted on 2025-11-18

2065 Ion-Pair-Free Nanoflow HILIC-MS With RNase Benchmarking for Native RNA

Qi, Y.; Li, C.; Yesiltac-Tosun, N.; Schicktanz, J.; Rusling, L.; Kaiser, S.; Wein, S. P.; Kaiser, S.

10.1101/2025.11.18.689004 — molecular biology — Posted on 2025-11-18

2066 The coloNISation: spatio-temporal metabarcoding surveys in ports reveal homogenised communities with high genetic diversity and connectivity of non-indigenous species

Zarcero, J.; Antich, A.; Palacin, C.; Fernandez, M.; Wangensteen, O. S.; Rius, M.; Turon, X.

10.1101/2025.11.18.688838 — molecular biology — Posted on 2025-11-18

2067 An altered cell-specific subcellular distribution of translesion synthesis DNA polymerase kappa (POLK) in aging neurons

Abdelmageed, M.; Palamisamy, P.; Vernail, V.; Silberman, Y.; Paul, S.; Paul, A.

10.1101/2023.09.27.559771 — neuroscience — Posted on 2025-11-18

2068 Data-driven identification of functional networks in artificial and biological neural networks

Ivankovic, K.; Dimou, A.; Montoya-Galvez, J.; Zucca, R.; Valero, M.; Principe, A.

10.1101/2025.11.18.688989 — neuroscience — Posted on 2025-11-18

2069 Partitioning Genotypic and Environmental Variance of Fresh Root Yield in Provitamin A Cassava Genotypes Using Mixed Models

Badewa, O. D.; Parkes, E. Y.; Gana, A.; Tsado, E. K.; Tolorunse, K. D.; Iluebbey, P.; Akpotuzor, P.; Ayankami, T.

10.1101/2025.11.18.688222 — plant biology — Posted on 2025-11-18

2070 Pantoea ananatis-triggered systemic resistance requires root sensing through the LORE receptor kinase in Arabidopsis

Duchateau, S.; Crouzet, J.; Cordelier, S.; Touchard, M.; Schellenberger, R.; Borrego, C.; Villaume, S.; Guise, J.-F.; Esmaeel, Q.; Groleau, M.-C.; Cloutier, M.; Gauthier, C.; Dhondt-Cordelier, S.; Mazeyrat-Gourbeyre, F.; Baillieul, F.; Ranf, S.; Deziel, E.; Aziz, A.; Dorey, S.

10.1101/2025.11.18.688997 — plant biology — Posted on 2025-11-18

2071 Conserved Gαq-PLCβ-PKC signaling mediates trametinib resistance in BRAFV600E melanoma

Ke, J.; Wang, Z.; Guo, Z.; Ou, G.; Li, W.

10.1101/2025.11.18.688995 — cancer biology — Posted on 2025-11-18

2072 Protease-Resistant Azapeptide GLP-1 Analogue Improves Metabolic Control in Diet-Induced Obesity

He, M.; Cheng, K. F.; VanPatten, S.; D.T. Torres, M.; Al Jabari, B.; Mughrabi, I. T.; Ballarin-Gonzalez, B.; Son, M.; de la Fuente-Nunez, C.; Al-Abed, Y.

10.1101/2025.05.09.653092 — biochemistry — Posted on 2025-11-18

2073 Pho-Tip: one-pot dephosphorylation for rapid and sensitive analysis of DIA phosphoproteomics data

Faisst, K. D.; Lau, K.; Sinn, L. R.; Szyrwiel, L.; Demichev, V.

10.1101/2025.11.17.687597 — biochemistry — Posted on 2025-11-18

2074 Impact of vitamin D deficiency on defective endometrial decidualization and the repressive role of vitamin D receptor (VDR) in the epigenomic network

Yi, M.; Montague Redecke, S. G.; Wang, T.; Bell-Hensley, A.; Li, S.; Massri, A. J.; Jukic, A. M. Z.; DeMayo, F. J.

10.1101/2025.11.14.688535 — molecular biology — Posted on 2025-11-18

2075 Insights on Skin Adherent Microbiota of the Danube sturgeon (Acipenser gueldenstaedtii)

Pop, C.-E.; Jawdhari, A.; Fendrihan, S.; Wolff, R.; Craciun, N.

10.1101/2024.03.13.584882 — microbiology — Posted on 2025-11-18

2076 CRISPR-Cas is beneficial in plasmid competition, but limited by competitor toxin-antitoxin activity when horizontally transferred

Sünderhauf, D.; Ringger, J. R.; Payne, L. J.; Pinilla-Redondo, R.; Gaze, W. H.; Brown, S. P.; van Houte, S.

10.1101/2025.05.09.653016 — microbiology — Posted on 2025-11-18

2077 Prenatal valproic acid-exposed autism marmosets increase mutual gaze and reduce inter-individual distance during dyadic social interactions

Nakamura, M.; Sato, T.; Kurotani, T.; Sakai, K.; Hadjiev, A. M.; Sasai, S.; Mimura, K.; Kawai, N.; Shimmura, T.; Ichinohe, N.

10.1101/2025.11.17.688777 — neuroscience — Posted on 2025-11-18

2078 Causal evidence for a domain-specific role of left superior frontal sulcus in human perceptual decision-making

Barretto Garcia, M.; Grueschow, M.; Moisa, M.; Polania, R.; Ruff, C. C.

10.1101/2021.10.04.462977 — neuroscience — Posted on 2025-11-18

2079 MitoEM 2.0: A Benchmark for Challenging 3D MitochondriaInstance Segmentation from EM Images

Liu, P.; Shen, B.; Liu, L.; Wang, Q.; Zhang, S.; Bhardwaj, A.; Arganda-Carreras, I.; Narayan, K.; Wei, D.

10.1101/2025.11.12.687478 — neuroscience — Posted on 2025-11-18

2080 Brain endothelial PRMT5-ANGPTL4 axis regulates cerebellar inhibitory synaptogenesis and motor coordination

Lu, J.; Zhang, Y.; Hao, Y.; Ning, H.; Fan, Z.; Hao, S.; Cui, Y.; Han, Y.; Cai, Y.; Liu, W.; Ao, H.; Xiu, S.; Wang, J.; Yang, X.

10.1101/2025.11.18.688985 — neuroscience — Posted on 2025-11-18

2081 A Syngeneic Immunocompetent Mouse Model of Gallbladder Cancer Reveals Tumorigenesis and Therapeutic Response

Qiu, W.; Ni, X.; Xiang, F.; Meng, W.; Qin, R.; Ma, J.; Zhang, D.; Li, B.; Xu, S.; Wang, C.; Nan, L.; Bo, X.; Liu, Y.; Wang, L.; Wang, Y.; Liu, H.

10.1101/2025.11.17.687512 — cancer biology — Posted on 2025-11-18

2082 Multidimensional Single-Cell Transcriptomic Profiling of Uterine Leiomyosarcomas Identifies Molecular Subtypes with Distinct Therapeutic Vulnerabilities

Korah, M.; Agolia, J. P.; Reddy, B.; Flojo, R. A. B.; Goncalves, A.; Wang, L.; Bobst, W.; Liang, B.; Yip, K. A.; Reveron-Thornton, R.; Guo, C.; Gruener, R.; Delitto, A.; Xie, P. Y.; Tabora, A.; Sun, B.; Daniel, S. K.; Litkouhi, B.; Dorigo, O.; Bui, N. Q.; Pan, M.; Moding, E. J.; Kalbasi, A.; Kirane, A. R.; Poultsides, G. A.; Norton, J. A.; Newman, A. M.; Charville, G.; Ganjoo, K. N.; Foster, D. S.; Huang, R. S.; Lee, B.; Longaker, M. T.; Delitto, D.

10.1101/2025.11.17.688894 — cancer biology — Posted on 2025-11-18

2083 Epstein-Barr viral product-containing exosome facilitates LIF-associated immunosuppressive polarization of macrophage in nasopharyngeal carcinoma

Liu, T.-T.; Sui, Y.-H.; Jiang, S.-S.; Tsai, F.-Y.; Chang, K.-P.; Tsang, N.-M.; Lee, M.-H.; Huang, C.-H.; Liu, S.-C.

10.1101/2024.11.25.625317 — cancer biology — Posted on 2025-11-18

2084 Targeting STING-ATM axis overcomes radiotherapy-induced immune suppression and restores anti-tumor immunity in nasopharyngeal carcinoma

Liu, T.-T.; Chang, K.-P.; Wang, Y.-N.; OuYang, C.-N.; Li, M.-H.; Tsang, N.-M.; Jiang, S. S.; Sui, Y.-H.; Hu, C.-M.; Chou, Y.-C.; Chen, H.-C.; Liu, S.-C.

10.1101/2025.11.12.687945 — cancer biology — Posted on 2025-11-18

2085 Atom-level backbone engineering preserves peptide function while enhancing stability

He, M.; Cheng, K. F.; Vu, A.; D.T. Torres, M.; Zanos, S.; Mughrabi, I.; de la Fuente-Nunez, C.; Al-Abed, Y.

10.1101/2025.10.06.678421 — biochemistry — Posted on 2025-11-18

2086 Short-term fluctuating and long-term divergent selection on sympatric Monkeyflowers: insights from repeated reciprocal transplants

Dong, C. M.; Aponte Rolon, B. A.; Sullivan, J. K.; Tataru, D.; Deleon, M.; Dennis, R.; Dutton, S.; Machado Perez, F. J.; Montano, L.; Ferris, K. G.

10.1101/2024.06.26.600870 — evolutionary biology — Posted on 2025-11-18

2087 The Drosophila ovary produces three follicle waves similar to those in mice

Fu, W. Y.; Spradling, A. C.

10.1101/2025.11.11.687893 — developmental biology — Posted on 2025-11-18

2088 Imp1 acts as a dosage- and stage-dependent temporal rheostat orchestrating radial glial fate transitions and cortical morphogenesis

Azur, R. A. G.; Feliciano, D.; Espinosa-Medina, I.; Adhikari, R.; Lilao-Garzon, J.; Jansen, E.; Yang, C.-P.; Lee, T.

10.1101/2025.11.18.688993 — developmental biology — Posted on 2025-11-18

2089 TGF-β drives the conversion of conventional NK cells into uterine tissue-resident NK cells to support murine pregnancy

Barahona, J. D.; Yang, L.; Nelson, D. M.; Yokoyama, W. M.

10.1101/2025.11.18.688992 — immunology — Posted on 2025-11-18

2090 Cognitive and brain function enhancement in Gen X group after personalized, AI supervised EEG-neurofeedback training

Rogala, J.; Malinowska, U.; Ociepka, M.; Wojciechowski, J.; Zych, J.; Tryc, P.; Kołodziejak, A.; Ogniewski, P.; Niedbalski, P.; Skorupski, J.; Chuderski, A.

10.1101/2025.11.17.688986 — neuroscience — Posted on 2025-11-18

2091 Parallel CLE peptide signaling pathways control nodulation in pea

Scott, T. E.; Wulf, K. E.; Correa-Lozano, A.; Velandia, K.; Reid, J. B.; Foo, E.

10.1101/2025.11.17.688984 — plant biology — Posted on 2025-11-18

2092 AI-HEAD: Auto-indexing for Helical assembles' diffraction and fast dynamic structure determination

Pei, T.; Yu, M.; Li, S.; Zhang, D.; Sun, F.; Zhang, Y.

10.1101/2025.11.17.688965 — biophysics — Posted on 2025-11-18

2093 TAF15 amyloids propagate via defined motifs in a prion-like fashion

Konstantoulea, K.; Gadhe, L.; Goodavish, F.; GUPTA, A.; Tagad, H.; Vaquer-Alicea, J.; Ghayal, N. B.; Roemer, S. F.; DeTure, M. A.; Nana, A. L.; Spina, S.; Grinberg, L. T.; Seeley, W. W.; Dickson, D. W.; White, C. L.; Diamond, M. I.; Louros, N. N.

10.1101/2025.11.17.688886 — biophysics — Posted on 2025-11-18

2094 Phosphatidylinositol Phospholipids Modulate Hepatitis C Virus Core Protein Assembly on Lipid Membranes

Mandal, T.; Albrecht, B.; Abdelwahed, S.; Ruickoldt, J.; Jones, P.; Wendler, P.; Chiantia, S.

10.1101/2025.05.13.653720 — biophysics — Posted on 2025-11-18

2095 Comparative study of Dog and Human Lipid Droplet-associated protein (PLIN2)

sahu, G.; Behera, A.; Pandey, V. K.; PS, F.; kumar, M.; Saini, M.; Irungbam, K.

10.1101/2025.11.17.688867 — bioinformatics — Posted on 2025-11-18

2096 Neighboring codon adjacent nucleotides have a conserved influence on mRNA decay

Sorenson, R. S.; Sieburth, L. E.

10.1101/2025.11.17.688958 — genomics — Posted on 2025-11-18

2097 Genome assembly and diagnostic DNA markers for sex of the largest freshwater fish in North America, the white sturgeon (Acipenser transmontanus).

Willis, S. C.; Smith, J.; Narum, S. R.

10.1101/2025.11.14.688503 — genomics — Posted on 2025-11-18

2098 Comparative genomic analyses shed light on the introduction routes of rice-pathogenic Burkholderia gladioli strains into Bangladesh

Protic, I. A.; Uddin, M. N.; Gorzalski, A.; Islam, M. R.; Alvarez-Ponce, D.

10.1101/2025.11.17.688954 — genomics — Posted on 2025-11-18

2099 Frequent Whole-Genome Duplication Events Drive the Genomic Evolution of Triple-Negative Breast Cancer During Neoadjuvant Chemotherapy

Bendixen, D. P.; Semple, F.; Ironside, A.; Özkaraca, M. I.; Wilson, N.; Meynert, A.; Ewing, A.; Semple, C. A.; OIkonomidou, O.

10.1101/2025.11.17.688693 — genomics — Posted on 2025-11-18

2100 Hybridization but minimal introgression: ecologically-based divergent selection maintains a steep hybrid zone in parapatric stickleback fish

Baebler, O.; Haenel, Q.; Oke, K.; Hendry, A.; Berner, D.

10.1101/2025.11.17.688987 — evolutionary biology — Posted on 2025-11-18

2101 Parallel and non-parallel features of adaptive radiation in Yucatan pupfishes

Kustra, M. C.; Tian, D.; Palominos, M. F.; Guo, F.; Chau, D.; Golwala, O.; Chan, H.; Alvarez Zapata, A.; Cetz Paredes, R. G.; Cortes Sanchez, F. X.; Hernandez, S. G.; Mar-Silva, A. F.; Mex, F.; Tralka, C.; Badillo-Aleman, M.; Schmitter-Soto, J. J.; Gracida-Juarez, C. A.; Martinez, C. M.; Arroyave, J.; Martin, C. H.

10.1101/2025.11.17.688971 — evolutionary biology — Posted on 2025-11-18

2102 Gene loss associated with plasticity-first evolution in Heliconius butterflies

Pinheiro de Castro, E. C.; Cicconardi, F.; Warren, I. A.; Rueda-M, N.; Salazar, C.; Bak, S.; Montgomery, S. H.; Jiggins, C. D.

10.1101/2025.06.22.660914 — evolutionary biology — Posted on 2025-11-18

2103 Diversity of vector-dispersed microbes peaks at a landscape-defined intermediate rate of dispersal

Nagano, Y.; Natsume, K.; Fukami, T.; Tsuji, K.

10.1101/2025.11.17.688957 — ecology — Posted on 2025-11-18

2104 TEAD4 regulates apical domain homeostasis and cell-positioning to maintain the trophectoderm lineage during preimplantation mouse embryo development.

Collier, R.; Bohuslavova (nee Stiborova), M.; Vaskovicova, M.; Mihajlovic, A. I.; Hauserova, A.; Zabelina, V.; Fluks, M.; Gahurova, L.; Drutovic, D.; Bruce, A. W.

10.1101/2025.11.18.689016 — developmental biology — Posted on 2025-11-18

2105 DMEM, or Opti-MEM, that is the Question: An Important Consideration for Extracellular Vesicle Isolation and their Downstream Applications.

Salmond, N.; Melamed, J.; Halvaei, S.; Williams, K. C.

10.1101/2025.11.17.683537 — cell biology — Posted on 2025-11-18

2106 Rice NH2 Functions as a Positive Regulator of Salicylic Acid Mediated Defense Responses Against Sheath Blight and Bacterial Blight

Ponnurangan, V.; Ashokkumar, S.; KK, K.; Eswaran, k.; Loganathan, A.; Duraialagara, S.; Chellappan, G.; Vaikuntavasan, P.; Maduraimuthu, D.; Shanmugam, V.

10.1101/2025.11.17.688593 — molecular biology — Posted on 2025-11-18

2107 Cultivation and genomic characterization of human gut-associated Bdellovibrio reveals natural predatory bacteria with specialized prey interactions

Romero-Rivera, M.; Diez-Fernandez-de-Bobadilla, M.; Beltran, M.; Avendano-Ortiz, J.; del Campo, R.; Herencias, C.

10.1101/2025.11.17.688821 — microbiology — Posted on 2025-11-18

2108 Soil pH as an external filter shaping insect-microbe gut symbiosis

Itoh, H.; Shimoji, H.; Nakane, D.; Jang, S.; Kikuchi, Y.

10.1101/2025.11.17.688959 — microbiology — Posted on 2025-11-18

2109 Exploratory Multi-Omics Profiling of Rheumatoid Arthritis Heterogeneity

Rajeevan, N.; Khan, Z.

10.1101/2025.11.17.688813 — immunology — Posted on 2025-11-18

2110 Interleukin-17A Mediates Cardiorenal Injury In Oxalate Nephropathy

Wimmer, M. I.; Reichel, M.; Thiele, A.; Yarritu, A.; Matz-Rauch, A.; Anandakumar, H.; Hernandez Goetz, L.; Lesker, T. R.; Potapenko, O.; Gebremedhin, N.; Anders, W.; Lievano Contreras, S. V.; Wang, R.; Nonn, O.; Schiattarella, G. G.; Schaefer, F.; Holle, J.; Strowig, T.; Zernecke, A.; Eckardt, K.-U.; Knauf, F.; Wilck, N.; Bartolomaeus, H.

10.1101/2025.11.17.687153 — immunology — Posted on 2025-11-18

2111 Explainable 3D CNNs link regional and network level disruption in early Parkinson's MRIs to symptom progression

Moroze, E.; Zikopoulos, B.; Yazdanbakhsh, A.

10.1101/2025.11.17.688918 — neuroscience — Posted on 2025-11-18

2112 A Neurodevelopment-Inspired Deep Spiking Neural Network for Auditory Spatial Attention Detection using Single Trial EEG

Faghihi, F.; Moustafa, A.

10.1101/2025.11.17.688781 — neuroscience — Posted on 2025-11-18

2113 Anxious vision: Trait-like visual cortical hyperactivity in trait anxiety

Wu, Z.; You, Y.; Brown, J. A.; Dolan, R. J.; Li, W.

10.1101/2025.11.17.688929 — neuroscience — Posted on 2025-11-18

2114 Modeling Psychophysical Data in R: A Comparative Study of Four Model Frameworks

Balestrucci, P.; Mezzetti, M.; La Scaleia, B.; Moscatelli, A.

10.1101/2025.11.17.688833 — neuroscience — Posted on 2025-11-18

2115 Effort choices are sensitive to prior learning

Guinea, C.; Xiao, B.; Lawson, R. P.

10.1101/2025.07.24.666522 — neuroscience — Posted on 2025-11-18

2116 Chronic cervical vibration ameliorates depression-like behavior in Wistar-Kyoto rats

Fujiwara, S.-e.; Narumi, S.; Kakehashi, C.; Fujioka, H.

10.1101/2025.11.17.688804 — neuroscience — Posted on 2025-11-18

2117 Optimizing Cancer Vaccinations Using a Physiologically Based Pharmacokinetic (PBPK) Model

Nikmaneshi, M.; Padera, T. P.; Munn, L. L.

10.1101/2025.11.17.688910 — systems biology — Posted on 2025-11-18

2118 Hemodynamic and Microvascular Adaptations to Aerobic Training Intensity Improve Maximal Oxygen Consumption

Maufroy, E.; Rigaut, C.; Maufroy, C.; Baeyens, N.; Deboeck, G.

10.1101/2025.11.17.688970 — physiology — Posted on 2025-11-18

2119 Sex- and ketogenesis-dependent effects of intermittent fasting against diet-induced obesity and fatty liver disease

Aslani, T.; Asif, S.; Oh, Y.; Lee, H.; Stocker, C.; Kwon, S.; Pan, J.; Dababneh, S.; Zhao, X.; Taylor, L.; Mullick, A. E.; Tibbits, G. F.; Kim, R. Y.; Fullerton, M. D.; Mulvihill, E. E.; Son, J. E.; Kim, K.-H.

10.1101/2025.11.17.688915 — physiology — Posted on 2025-11-18

2120 Post-treatment recovery of docetaxel-treated prostate cancer monolayer and spheroid culture

Swanson, S.; McKenna, C. B.; Cheraghi, E.; Osei, E.

10.1101/2025.11.17.688723 — cancer biology — Posted on 2025-11-18

2121 Identifying gene regulation modules associated with tumor metastasis using a network decomposition approach and combinatorial fusion analysis

Astuti, A.; Schweikert, C.; Hsu, D. F.; KALOK, N.

10.1101/2025.11.17.688950 — bioinformatics — Posted on 2025-11-18

2122 Performance of Information Theory Derived Semantic Similarity Algorithms for Differential Diagnosis and Clustering

COLEMAN, B. D.; Danis, D.; Reese, J.; Robinson, P. N.

10.1101/2025.11.17.688933 — bioinformatics — Posted on 2025-11-18

2123 Isotonic tartrazine is sufficient to improve transscleral penetration of optical coherence tomography

Dhodapkar, R. M.

10.1101/2025.11.17.688647 — bioengineering — Posted on 2025-11-18

2124 Structural framework for the assembly of the human tRNA ligase complex

Pfleiderer, M. M.; Leitner, M.; Nievergelt, A.; Kroupova, A.; Martinez, J.; Jinek, M.

10.1101/2025.08.01.668197 — biochemistry — Posted on 2025-11-18

2125 Importance of Apparatus Scaling in Novel Object Recognition for Juvenile and Adult Rats.

Baron, L.; Hetherington, S.; Poulos, A. M.

10.1101/2025.11.17.683970 — animal behavior and cognition — Posted on 2025-11-18

2126 Understanding epigenetic regulation in non-model plants: Transcriptomic responses to seed demethylation in leaves and roots of the annual herb Erodium cicutarium (Geraniaceae)

Martin-Blazquez, R.; Medrano, M.; Alonso, C.

10.1101/2025.11.17.688907 — genomics — Posted on 2025-11-18

2127 Using all available evidence to solve kinship cases

Egeland, T.; Marsico, F.

10.1101/2025.05.03.652046 — genetics — Posted on 2025-11-18

2128 On the influence of stratification and lake size on pelagic and benthic algal dynamics: A modelling study using 'Lake2D'

Harlin, H.; Larsson, K.; Brännström, A.; Diehl, S.

10.1101/2025.11.17.688809 — ecology — Posted on 2025-11-18

2129 Effects of a native, dominant tree, Colophospermum mopane, on diversity of plants, insects, and vertebrates in South African savannas

Gaona, F. P.; Albrecht, T.; Cuda, J.; Delabye, S.; Foxcroft, L. C.; Govorov, V.; Horacek, I.; MacFadyen, S.; Potocky, P.; Pyskova, K.; Remes, V.; Sedlacek, O.; Stankova, M.; Pysek, P.; Tropek, R.

10.1101/2025.11.17.688835 — ecology — Posted on 2025-11-18

2130 Dual origins for neural cells during development of the Clytia planula larva

Ruggiero, A.; Ferraioli, A.; Chevalier, S.; Lapebie, P.; Girard, R.; Momose, T.; Barreau, C.; Houliston, E.

10.1101/2025.11.17.688882 — developmental biology — Posted on 2025-11-18

2131 Inactivation of microtubule organizing center function of the centrosome is required for neuronal development and centriole elimination

Ng, R.; Magescas, J.; Feldman, J.

10.1101/2025.11.17.688953 — cell biology — Posted on 2025-11-18

2132 Condensate-Driven Triglyceride Depletion Links alpha-Synuclein to Mitochondrial Dysfunction

Zhang, T.; Goya, M. E.; Herron-Bedoya, A.; van der Weerd, J. C.; Tsagkari, D.; Couzijn, S.; Güngördü, L.; Seinstra, R. I.; Fokkema, M. R. H.; Chang, M.; Tavernarakis, N.; Kuipers, F.; Nollen, E.

10.1101/2025.10.22.682553 — cell biology — Posted on 2025-11-18

2133 Rab11B is required for binding and entry of recent H3N2, but not H1N1, influenza A isolates

Turner, A. H.; Jaffrani, S. A.; Kubinski, H. C.; Ajayi, D. P.; Owens, M. B.; Fanuele, C. D.; McTigue, M. P.; Appenzeller, C. L.; Bowling, A.; Despres, H. W.; Schmidt, M. M.; Shirley, D. J.; Crothers, J. W.; Barrantes-Reynolds, R.; Bruce, E. A.

10.1101/2025.04.23.650275 — microbiology — Posted on 2025-11-18

2134 The cold-inducible RNA-binding protein RBM3 stabilises viral mRNA at the cooler temperatures of the upper respiratory tract.

Coutts, H. L.; Sukumar, S.; Turkington, H. L.; Bonazza, S.; Peate, E.; Getty, E. M. P. E.; Power, U. F.; Courtney, D. G.

10.1101/2024.07.25.605104 — microbiology — Posted on 2025-11-18

2135 A Hybrid Multiscale Model for Predicting CAR-T Therapy Outcomes in SolidTumors

Nikmaneshi, M.; Munn, L. L.

10.1101/2025.11.17.688869 — immunology — Posted on 2025-11-18

2136 Mosaicism of BRAF V600E in Healthy Skin Predicts Neurodegeneration in Histiocytosis

Emile, J.-F.; Helias-Rodzewicz, Z.; Papo, M.; Ungureanu, I. A.; Baek, c.; Triboulet, f.; Wong, T. H.; Jannet, R. B.; Terrones, N.; Qalli, S. E.; Suret, p. m.; Reig, B.; Atallah, A.; Semenov, A.; DEGRAVE, R.; Nguyen, m.; Sutera, r.; Siliogka, E.; Cariou, P. L.; Prevost, g.; DE LA ROCHEFOUCAULD, J.; Biassette, H. A.; Plu, i.; Mathian, a.; CATELAIN, C.; Razanamahery, j.; Ewenczyk, c.; Heritier, s.; Aubart, F. C.; Hirsch, p.; Amoura, Z.; Donadieu, J.; Idbaih, A.; Haroche, J.

10.1101/2025.11.17.688335 — cancer biology — Posted on 2025-11-18

2137 Opposite and complementary roles of the two calcium thresholds for inducing LTP and LTD in models of striatal projection neurons

Trpevski, D.

10.1101/2025.11.17.688856 — neuroscience — Posted on 2025-11-18

2138 Methamphetamine Conditioned Place Preference in Adolescent Mice: Interaction Between Sex and Strain

Severino, L. N.; Toussaint, A. B.; Langa, R. M.; McKenna, G.; Bodziony, I.; Burghardt, N. S.

10.1101/2025.11.17.688853 — neuroscience — Posted on 2025-11-18

2139 Differential regulation of p62-ubiquitin conjugates in neurons versus astrocytes during cellular stress

Sidibe, D. K.; Smith, E. M.; Spivey, M. L.; Vogel, M. C.; Maday, S.

10.1101/2025.11.17.688722 — neuroscience — Posted on 2025-11-18

2140 Metric Selection Effects in Consciousness Measurement: Lessons from Sleep EEG Analysis

Dobbin, E.

10.1101/2025.11.10.687628 — neuroscience — Posted on 2025-11-18

2141 Chronic oral cannabidiol delays or prevents seizures in a mouse model of CLN2 disease

Dearborn, J. T.; Takahashi, K.; Rensing, N. R.; Wong, M.; Cooper, J. D.; Sands, M. S.

10.1101/2025.11.17.688949 — neuroscience — Posted on 2025-11-18

2142 Neuroimaging Correlates of Altered Sense of Agency in First-Episode Schizophrenia-Spectrum Patients: A Comparative Study Across Two Sites

Volfikova, K.; Tomecek, D.; Spaniel, F.; Tintera, J.; Rydlo, J.; Hlinka, J.

10.1101/2025.10.10.681418 — neuroscience — Posted on 2025-11-18

2143 From Tasks to Topology: Dorsal and Ventral Streams Emerge in Optimized Neural Networks

Reza, T.; Jordan, E.; Luo, S.; Patel, K.; Tang, J.; Niemeier, M.

10.1101/2025.11.16.688720 — neuroscience — Posted on 2025-11-18

2144 Flux modelling analysis reveals the metabolic impact of cryptic plasmids and environmental conditions in probiotic Escherichia coli Nissle 1917

Corbin-Agusti, P.; Arevalo-Lalanne, A.; Alvarez, P.; Ramon, D.; Pereto, J.; Tortajada, M.

10.1101/2025.11.17.688048 — systems biology — Posted on 2025-11-18

2145 Activity-dependent remodeling of muscle architecture during distinct locomotor behaviors in Caenorhabditis elegans

Fazyl, A.; Anbu, A.; Kollbaum, S.; Vidal-Gadea, A. G.

10.1101/2024.08.30.610496 — molecular biology — Posted on 2025-11-18

2146 Non-enzymatic error correction in self-replicators without extraneous energy supply

Ghosh, K.; Sahu, P.; Barik, S.; Subramanian, H.

10.1101/2025.06.26.661679 — biochemistry — Posted on 2025-11-18

2147 Myeloperoxidase impairs mucociliary transport on human airway epithelium

Boboltz, A.; Rathi, V.; Kumar, S.; Duncan, G. A.

10.1101/2025.11.17.688903 — cell biology — Posted on 2025-11-18

2148 A breath of fresh air: comparative evaluation of passive versus active airborne eDNA sampling strategies

Jager, H.; Trimbos, K.; Luursema, J.-M.; Speksnijder, A.; Stewart, K.

10.1101/2025.03.26.645491 — ecology — Posted on 2025-11-18

2149 Model of ocular surface ion and water transport predicts efficacy of dry eye therapeutics targeting epithelial transport and tear fluid dynamics

Verma, V.; Lindgren, E. S.; Levin, M. H.; Cil, O.; Tradtrantip, L.; Yan, R.; Pasricha, N. D.; Verkman, A. S.

10.1101/2025.11.17.688783 — systems biology — Posted on 2025-11-18

2150 Telomeric G-quadruplex Intermediates unveiled by Complex Markov Network Analysis.

Sainz-Agost, A.; Falo, F.; Fiasconaro, A.

10.1101/2025.01.16.633340 — biophysics — Posted on 2025-11-18

2151 Efficiency and localisation of AURKA degradation by PROTACs is modulated by deubiquitinases UCHL5 and target-selective OTUD6A

Cardno, A.; Roberts, K.; Lindon, C.

10.1101/2025.04.23.650020 — cell biology — Posted on 2025-11-18

2152 Hidden but discoverable diversity in the global microbiome

Prasoodanan P K, V.; Maistrenko, O. M.; Fullam, A.; Mende, D. R.; Kartal, E.; Coelho, L. P.; Spang, A.; Bork, P.; Schmidt, T. S. B.

10.1101/2025.06.26.661807 — microbiology — Posted on 2025-11-18

2153 Micro-/nano-plastics accentuate Parkinson's Disease-relevant phenotypes in a Drosophila model

Lowe, S. A.; Jepson, J. E.

10.1101/2025.11.17.688805 — neuroscience — Posted on 2025-11-18

2154 Bioinformatic Mining of Novel Lipopeptides Enabled by Dap-tomycin Cs Domain and Structural Modeling

Bai, W.; Zhu, H.; Ding, M.; Chen, N.; Zhu, D.; Wang, N.; Tan, R.

10.1101/2025.06.21.660876 — bioinformatics — Posted on 2025-11-18

2155 Male social dominance affects access to mates but not female mate choice in a livebearing fish

Goncalves, A.; Reuland, C.; Daupagne, L.; Wheatcroft, D.; Kolm, N.; Fitzpatrick, J. L.

10.1101/2025.10.16.682567 — animal behavior and cognition — Posted on 2025-11-18

2156 Genomic architecture of the self-incompatibility locus in apple provides insights into the evolution of collaborative non-self recognition

Mesnil, A.; Castric, V.; Lombardi, G.; Monniaux, M.; Saidi, S.; Chen, X.; Marande, W.; Confais, J.; Fuchs, A.-L.; Dapena, E.; Venon, A.; Tsuchimatsu, T.; Carbone, A.; Vekemans, X.; Cornille, A. M.

10.1101/2025.10.28.683340 — genomics — Posted on 2025-11-18

2157 SNaQ.jl: Improved Scalability for Phylogenetic Network Inference

Kolbow, N.; Kong, S.; Chafin, T.; Justison, J.; Ane, C.; Solis-Lemus, C.

10.1101/2025.11.17.688917 — evolutionary biology — Posted on 2025-11-18

2158 Divergent evolution of insecticidal protein families across bacteria and ferns

Endo, H.; Kazama, H.

10.1101/2025.11.17.688980 — molecular biology — Posted on 2025-11-18

2159 Functional Effects of CD33 SNP rs12459419 on Microglial Gene Regulation and Alzheimer's Disease Risk

Lu, Y.

10.1101/2025.11.07.684725 — molecular biology — Posted on 2025-11-18

2160 Power Pixels: a turnkey pipeline for processing of Neuropixel recordings

Meijer, G. T.; Battaglia, F. P.

10.1101/2025.06.27.661890 — neuroscience — Posted on 2025-11-18

2161 Effort choices are sensitive to prior learning

Guinea, C.; Xiao, B.; Lawson, R. P.

10.1101/2025.07.24.666522 — neuroscience — Posted on 2025-11-18

2162 Evolutionary rewiring of host metabolism and interferon signalling by SARS-CoV-2 variants

Somji, R.-A.; Brown, J. C.; Rowles-Khalid, S.; Abdullahi, T. B.; Luo, D.; Barthel, N.; Mulleder, M.; Ralser, M. S.; Barclay, W. S. S.; Rallis, C.; Giotis, E. S.

10.1101/2025.11.15.688605 — systems biology — Posted on 2025-11-18

2163 Engineering amino acid-derived malonyl-CoA pathways to boost polyketide production in Yarrowia lipolytica

Wang, J.; Hong, Y.; Wu, Z.; Fishman, A.; Xu, P.

10.1101/2025.08.03.668335 — synthetic biology — Posted on 2025-11-18

2164 Functional memory of drought affects leaf chemical defenses and microbial interactions in aspen

Hawks, A. M.; Fickle, J. C.; Kerr, K. L.; Perkins, A. M.; Forrister, D. L.; Symeonidi, E.; Allen, M.; Fehrenbach, C.; Hsiao-Nung, C.; Lindroth, R.; Anderegg, W. R. L.; Karasov, T.

10.1101/2025.11.17.688914 — plant biology — Posted on 2025-11-18

2165 Dynamic Tumor Immune Microenvironment Remodeling Predicts Response of Checkpoint Inhibitor Therapy

Lin, Z.; Chandra, M.; Srinivas, N.; Ugurel, S.; Becker, J.; Aran, D.

10.1101/2024.06.30.601413 — cancer biology — Posted on 2025-11-18

2166 Estimating Boltzmann Statistical Energy for Proteins from 3D Structure Using Pairwise Amino Acid Energy Matrix - GEM-X2120-N871

GURUPRASAD, K.

10.1101/2025.11.17.688978 — bioinformatics — Posted on 2025-11-18

2167 Comparative Molecular Docking and Toxicity Profiling of Buspirone and Tandospirone Targeting the HTR1A Receptor

Lu, Y.

10.1101/2025.11.17.688977 — bioinformatics — Posted on 2025-11-18

2168 PCLIPtools: A Robust Framework for Identifying RNA-Protein Interaction Sites from PAR-CLIP experiments.

Polash, A. H.; Hafner, M.

10.1101/2025.11.17.688892 — bioinformatics — Posted on 2025-11-18

2169 b3alien: A Python package to assess the introduction rate ofalien species in a FAIR and reproducible way

Trekels, M.; Groom, Q. J.

10.1101/2025.11.17.688820 — ecology — Posted on 2025-11-18

2170 Activity and retinoic acid drive hair cell spatial patterning in the zebrafish utricle

Baeza-Loya, S.; Bui, J. T.; Raible, D.

10.1101/2025.11.17.687290 — developmental biology — Posted on 2025-11-18

2171 Reduced TBX5 dosage undermines developmental control of atrial cardiomyocyte identity in a model of human atrial disease

Kathiriya, I. S.; Rao, K. S.; Clark, A. P.; Hu, K. M.; Grant, Z. L.; Matthews, M. N.; Chen, Z.; Hota, S. K.; Saucerman, J. J.; Bruneau, B.

10.1101/2025.08.16.669546 — developmental biology — Posted on 2025-11-18

2172 High-Fidelity Simulation of Cell Adhesion and Flow with Coarse Grain Modelling: A Numerical and Experimental Approach

Mishra, R.; Jaiswal, S.; Arora, A.; Majumder, A.

10.1101/2025.09.22.677682 — cell biology — Posted on 2025-11-18

2173 Different data analysis models for detecting miRNAs using nanopores

Koch, C.; Sakthimani, S.; Noakes, V.; Cretu, M.; Gutierrez, R.; Bruce, M.; Gorelik, J.; Guerra, N.; Edel, J.; Ivanov, A.

10.1101/2025.11.17.688909 — biophysics — Posted on 2025-11-17

2174 Dynamics of TFIIH and Spt5 during the transition from transcription initiation to elongation

Portman, J. R.; Torrens, K.; Chung, J.; Friedman, L. J.; Gelles, J.; Buratowski, S.

10.1101/2025.11.17.686592 — molecular biology — Posted on 2025-11-17

2175 Selective engagement of the primate orbitofrontal cortex during value-based but not perceptual decisions

Moll, M. G.; Read, R. K.; Wallis, J. D.; Elston, T. W.

10.1101/2025.11.17.688922 — neuroscience — Posted on 2025-11-17

2176 Nighttime sleep modulates mechanosensory habituation in Drosophila

Lowe, S. A.; Chen, K.-F.; Jepson, J. E.

10.1101/2025.11.17.688779 — neuroscience — Posted on 2025-11-17

2177 Ribosome-Associated Vesicles promote activity-dependent local translation in neurons

Martin-Solana, E.; Carter, S. D.; Krishnamurthy, K.; de Nola, G.; Ning, J.; Glausier, J. R.; Preisegger, M. A.; Hughes, L.; Meyer, L.; Eisenman, L.; Joseph, P. N.; Bouchet-Marquis, C.; Wu, K.; Mobini, C. L.; Frantz, A. N.; Puig, S.; Hampton, C. M.; Kabbani, N.; Mankus, D.; Donahue, E. K.; Burkewitz, K.; Jensen, G. J.; Watkins, S. C.; Deisseroth, K.; Fenno, L. E.; Gold, M. S.; Wills, Z. P.; Lytton-Jean, A. K.; Das, S.; Freyberg, Z.

10.1101/2024.06.07.598007 — neuroscience — Posted on 2025-11-17

2178 Multi-scale network topology analysis reveals metabolic reprogramming and therapeutic vulnerabilities in the tumor microenvironment

Cetin, H.; Bogdan, P. D.; Mumenthaler, S. M.; Finley, S. D.

10.1101/2025.11.16.688737 — systems biology — Posted on 2025-11-17

2179 Gut Microbiota-derived Adenosine Determines the Efficacy of Electroconvulsive Therapy for Depression

Wang, Y.; Dai, M.; Yang, D.; Fan, S.; Li, Y.; Zhao, H.; Ye, Z.; Xu, Q.; Dou, Y.; Han, Z.; Ji, Y.; Wu, Y.; Wang, K.; Zhu, S.; Huang, C.; Tian, Y.

10.1101/2025.11.13.688184 — systems biology — Posted on 2025-11-17

2180 Recurrent Breast Cancer Cells Depend on De novo Pyrimidine Biosynthesis to Suppress Ferroptosis

McCutcheon, K. R.; Wu, J.; Ozdemir, Y. C.; McKinney, B. J.; Srinivasan, S.; Itokawa, A.; Newsom, O. J.; Vigil, A.; Fox, D. B.; Sullivan, L. B.; Alvarez, J. V.

10.1101/2025.11.17.688927 — cancer biology — Posted on 2025-11-17

2181 Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation

Russell, K.; Chen, Y.; Espinosa, J. R.; Gil, D. F.; Zhou, H.; Maristany, M. J.; Lopez, J. I. P.; Huertas, J.; Orozco, M.; Rosen, M. K.; Collepardo-Guevara, R.

10.1101/2025.11.17.688899 — biophysics — Posted on 2025-11-17

2182 Deciphering DEL Pocket Patterns Through Contrastive Learning

Zhang, W.; Wang, Y.; Zhan, R.; Qian, R.; Hu, Q.; Huang, J.

10.1101/2025.06.12.659183 — biophysics — Posted on 2025-11-17

2183 Efficient near telomere-to-telomere assembly of Nanopore Simplex reads

Cheng, H.; Qu, H.; McKenzie, S.; Lawrence, K. R.; Windsor, R.; Vella, M.; Park, P. J.; Li, H.

10.1101/2025.04.14.648685 — bioinformatics — Posted on 2025-11-17

2184 Multi-strain Analysis of Pseudomonas putida Reveals the Metabolic and Genetic Diversity of the Species.

Mueller, J.; Krishnan, J.; Wei, Q.; Hefner, Y.; Monk, J. M.; Verkler, H.; Tibocha-Bonilla, J. D.; Ayala, A.; Palsson, B. O.; Feist, A. M.; Niu, W.

10.1101/2025.11.17.688870 — bioengineering — Posted on 2025-11-17

2185 A universal buffer system for native LC-MS analysis of antibody-based therapeutics

Vosper, K. R.; Davis, B. T. V.; Saraya, J.; O'Flaherty, D. K.; Velyvis, A.; Vahidi, S.

10.1101/2025.11.17.688837 — biochemistry — Posted on 2025-11-17

2186 Cellular turnover can increase or decrease the mutant burden in expanding cell population

Mondal, S. S.; Komarova, N. L.; Wodarz, D.

10.1101/2025.11.17.688895 — evolutionary biology — Posted on 2025-11-17

2187 Local extraction of predatory fish may initiate behaviourally mediated trophic cascades in coral reefs in the Andaman Islands.

Dsouza, S.; Joshi, A.; Ahuja, B.; Ahmad, S.; Shanker, K.

10.1101/2025.11.17.688842 — ecology — Posted on 2025-11-17

2188 Ecological niche modeling reveals habitat differentiation and climatic vulnerability in two imperiled, sympatric southern Appalachian carnivorous plants

Chang, N.; Eserman, L.; Carmichael, A.; Smith, A. B.; Loy, X.; Coffey, E. E. D.; Ojacastro, J.

10.1101/2025.10.30.685572 — ecology — Posted on 2025-11-17

2189 Probabilistic working memory representations in human cortex guide behavior

Zhou, Y.; Curtis, C. E.; Fougnie, D.; Sreenivasan, K. K.

10.1101/2025.11.17.688881 — neuroscience — Posted on 2025-11-17

2190 Real-time spatial evolution of the fMRI response to photobiomodulation in the healthy human brain

Chen, J. X.; Van Lankveld, H.; Zhong, X.; Chen, J. J.

10.1101/2025.11.17.688884 — physiology — Posted on 2025-11-17

2191 Rethinking the seven-day treatment-free interval in T-cell engager therapy using agent-based modeling

Obertopp, N.; Froid, M.; Pilon-Thomas, S.; Basanta, D.

10.1101/2025.11.17.688873 — cancer biology — Posted on 2025-11-17

2192 Model-based Standardization of Correlation Coefficients Improves Multi-Omic Clustering and Biological Signal Discovery

Robinson, M.; Noh, H.; Pflieger, L.; Rappoport, N.

10.1101/2025.11.17.688875 — bioinformatics — Posted on 2025-11-17

2193 DNA methylation landscapes in human cells and their chromatin determinants

Cui, W.; Huang, Z.; Pfeifer, G. P.

10.1101/2025.11.17.688913 — genomics — Posted on 2025-11-17

2194 Vascular Basement Membrane Laminins Modulate Functional Zonation of Cerebral Microvessels

Sorokin, L.; Deshpande, T.; Kapupara, K.; Hannocks, M.-J.; Huppert, J.; Samawar, S.-K.; Thulichery, D. R.; Budny, S.; Ghavampour, S.; Song, J.; Meng, L.; Adams, R. H.; Jeong, H.-W.; Wachsmuth, L.; Faber, C.; Soltwisch, J.; Hallmann, R.

10.1101/2025.11.17.688818 — cell biology — Posted on 2025-11-17

2195 Comparative Single-Cell Transcriptomics Uncovers Shared and Distinct Molecular Signatures in Cystic Fibrosis and Primary Ciliary Dyskinesia

Hadas, N.; Xu, H.; Twan, W. K.; Neupane, S.; Elgamal, A.; Koenitzer, J. R.; Horani, A.

10.1101/2025.11.17.688876 — cell biology — Posted on 2025-11-17

2196 ERK builds a population of short-lived nascent adhesions that produce persistent edge protrusion and cell migration

Shepherd, A. P.; Carney, K. R.; Elliott, A.; Han, S. J.; Mendoza, M. C.

10.1101/2025.11.17.688923 — cell biology — Posted on 2025-11-17

2197 Single-cell analysis reveals the cellular and transcriptional diversity of thyrocytes in the normal pediatric thyroid

Reichenberger, E. R.; Bambach, N. E.; Spangler, Z.; Ricarte-Filho, J. C.; Hinkle, K.; Isaza, A.; Bhatti, T.; Bauer, A. J.; Franco, A. T.

10.1101/2025.11.17.687863 — cell biology — Posted on 2025-11-17

2198 Autoencoder Denoising for Network-Based Spatial Transcriptomics Data with Applications for Cell Signaling Estimation

Javaid, A.; Frost, H. R.

10.1101/2025.11.17.688924 — systems biology — Posted on 2025-11-17

2199 A scalable screening platform for discovering predominant miRNA target genes and druggable siRNA sequences

Kong, J.; Leung, S. S. K.; Lau, C. F.; Mok, B. W.-Y.; Weng, M.; Jauch, R.; Chen, H.; Kwon, S. C.

10.1101/2025.11.17.688664 — molecular biology — Posted on 2025-11-17

2200 Discovery of an orally available potent ER aminopeptidase 1 (ERAP1) inhibitor that enhances anti-tumor responses and limits inflammatory autoimmunity in vivo.

Tinworth, C. P.; Wojno-Picon, J.; Adam, M.; Gade, S.; Hancock, A. P.; Hirst, D. J.; Hutchinson, J. P.; Kitchen, S. J.; Koumantou, D.; Lea, J. D.; Lehmann, S.; Liddle, J.; Lonsdale, R.; Neu, M.; Nickels, L.; Phillipou, A.; Rowedder, J. E.; Rowland, P.; Schneck, J. L.; Scott-Stevens, P. T.; Sheehan, H.; Steidel, M.; Tayler, C. L.; Temponeras, I.; Thang, K.; Tough, D. F.; Vitulli, G.; Wall, I. D.; Young, R. J.; Zinn, N.; Peace, S.; Stratikos, E.

10.1101/2025.11.17.686761 — immunology — Posted on 2025-11-17

2201 Overexpression of the sugar transporter VvHT5 turns grapevine into a better host for Botrytis cinerea

Monnereau, B.; Cuello, C.; Gaillard, C.; Lebeurre, V.; Videau, P.; Zekri, O.; Coutos-Thevenot, P.; La Camera, S.

10.1101/2025.11.17.687010 — plant biology — Posted on 2025-11-17

2202 Chewing phase - theta amplitude coupling facilitates working memory

Espinoza, S.; EL-DEREDY, W.; Moraga-Espinoza, D.; Monrreal-Ortega, L.

10.1101/2025.11.17.688859 — neuroscience — Posted on 2025-11-17

2203 Hemodynamic modelling improves population receptive field estimates

Schwarzkopf, D. S.; Altan, E.; Dakin, S. C.; Morgan, C. A.

10.1101/2025.11.17.688931 — neuroscience — Posted on 2025-11-17

2204 A Unified Neural Timecourse for Words, Phrases, and Sentences: MEG Evidence from Parallel Presentation

Flower, N.; Pylkkänen, L.

10.1101/2025.11.17.688866 — neuroscience — Posted on 2025-11-17

2205 Subliminal beauty engages the brain's valuation circuits

Fernandes, P.; Kable, J. W.; Almeida, J.; Tusche, A.; Ruff, C. C.; Bergström, F.

10.1101/2025.11.17.688735 — neuroscience — Posted on 2025-11-17

2206 Fresh Paraformaldehyde Preserves Thrombus Biochemistry - An ATR-FTIR and PCA Investigation of Pulmonary Artery Thrombi

Moyo, S.; Stepien, E.; Wrobel, A.; Moskal, P.; Skalska, M.; Leszczynski, B.; Stepniewski, J.; Kopec, G.

10.1101/2025.11.17.688840 — biophysics — Posted on 2025-11-17

2207 Crowding does not suppress the opening of a cryptic pocket

Mishra, P.; Bowman, G.

10.1101/2025.11.17.688865 — biophysics — Posted on 2025-11-17

2208 Frequency-dependent effects of hip abductor vibration and surface translation on mediolateral sway

Rock, S. M.; Alvarez, M. C.; Schonhaut, E. B.; Dean, J. C.

10.1101/2025.11.17.688857 — bioengineering — Posted on 2025-11-17

2209 Induced ubiquitination of the partially disordered Estrogen Receptor alpha protein via a 14-3-3-directed molecular glue-based PROTAC design

Verhoef, C. J. A.; Crowe, C.; Nakesone, M. A.; de la Cuadra Baste, A.; Harzing, T.; Span, N. A. S.; Sathe, G.; Iso, K.; Ottmann, C.; Brunsveld, L.; Ciulli, A.; Cossar, P. J.

10.1101/2025.11.17.688825 — biochemistry — Posted on 2025-11-17

2210 Fine-Tuning of Label-Free Single-Cell Proteomics Workflows

Perdu-Alloy, P.; Charline, K.; Seth, A.; CARAPITO, C.

10.1101/2025.11.17.688849 — biochemistry — Posted on 2025-11-17

2211 10,239 whole genomes with multiomic and clinical health information as the Korean population multiomic reference dataset

An, K.; Jeon, S.; Kwon, Y.; Yoon, C.; Choi, Y.; Jeon, Y.; Choi, H.-J.; Bhak, J.; Shin, D.-H.; Lee, H.; Kim, Y. J.; Shin, E.-S.; Ryu, H.; Blazyte, A.; Park, S.; Cho, J.; Bolser, D.; Jeon, J.; Joe, S.; Yang, J. O.; Kim, J.-H.; Kim, B.-C.; Kim, J.; Park, N.-H.; Lee, S.; Jin, H.-j.; Baek, Y.; Jung, D.; Cho, Y.; Ahn, Y. M.; Jung, H.-T.; Ham, B.; Choi, Y. Y.; Choi, S. A.; Kim, S.-K.; Phi, J. H.; Gee, H. Y.; Kim, B.; Myung, W.; Cheon, C. K.; Kim, D. U.; Jin, G.-N.; Lee, H.; Chae, K. S.; Kim, C. G.; Lee, B.; Lee, J.; Lee, S.; Church, G. M.; Jeong, H.; Bhak, J.

10.1101/2025.11.17.688763 — genomics — Posted on 2025-11-17

2212 Optimization of reference population for imputation of low-density SNPs panel for genomic prediction in Atlantic salmon.

Fraslin, C.; Gonen, S.; Boison, S.; Baranski, M.; Norris, A.; Robledo, D.

10.1101/2025.11.17.688860 — genetics — Posted on 2025-11-17

2213 Stressed Overwintering Bottleneck Hypothesis: Ocean warming and acidification synergistically disrupt Arctic zooplankton overwintering

Dijkstra, J.; Schott, L.; Thomsen, N.; Reinardy, H.; Lutier, M.; Soereide, J. E.; Dinh, K. V.

10.1101/2025.11.17.688696 — ecology — Posted on 2025-11-17

2214 Validation of Extracellular Vesicles in FACTORFIVEs EXOFECTA LyoBeads

Stachura, D. L.; Rueb, K. F.; Hadley, D.; Bozkurt, B.; Carney, R.; Aylworth, J.

10.1101/2025.11.17.688893 — molecular biology — Posted on 2025-11-17

2215 Dynamics of interactions between three major respiratory pathogens in reconstituted human epithelium

Gibeaud, A.; Terra, C.; Portier, E.; Lukas, P.; Le Gouellec, A.; Guedj, J.; Graw, F.; Pizzorno, A.; Terrier, O.

10.1101/2025.11.17.688795 — microbiology — Posted on 2025-11-17

2216 The repertoire of resistance mutations selected by a Pseudomonas aeruginosa type IV pilus-targeting lytic bacteriophage

Tran, V. N.; Harvey, H.; Lahane, T. S.; Burrows, L. L.

10.1101/2025.11.17.688846 — microbiology — Posted on 2025-11-17

2217 Inhibiting Glycan Degradation Prevents HIV-Induced Inflammaging and Cognitive Impairment

Giron, L. B.; Borjabad, A.; Hadas, E.; Granche, J.; de Menezes, E. G. M.; Premeaux, T. A.; He, H.; Yeung, S. T. T.; Singh, S.; Friday, C.; Glover, J.; Balboa, E.; Dopkin, D.; Burrows, M.; Secreto, A.; Skuli, N.; Tateno, H.; Denton, P. W.; Palella, F.; Corley, M. J. J.; Ndhlovu, L.; Norris, P. J.; Tassiopoulos, K.; Volsky, D. J.; Abdel-Mohsen, M.

10.1101/2025.11.17.688839 — microbiology — Posted on 2025-11-17

2218 Whole-body homogenates restore disrupted microbiota composition in a model insect better than feces or no restoration treatment

Romo, R.; Ricks, E.; Ogden, R.; Bonnette, P. E.; Olson, S. C.; Pearman, K.; Call, G. B.; Chaston, J. M.

10.1101/2025.11.17.688872 — microbiology — Posted on 2025-11-17

2219 Regulation of lipid metabolism is a primordial function of STING

Guha, S.; Re, J.; Chemarin, M.; Gregoire, S.; Messaoud-Nacer, Y.; Chamma, H.; Augereau, A.; Barrat, J.; Acar, N.; Vila, I. K.; Boudinot, P.; Laguette, N.

10.1101/2025.11.17.688879 — immunology — Posted on 2025-11-17

2220 Blinatumomab-driven T-cell activation in αβ and γδ T-cell subsets: Insights from in vitro assays

Kelm, M.; Nasr, N.; Bendig, S.; Kabelitz, D.; Lustig, M.; Trautmann, H.; Laqua, A.; Peters, C.; Wesch, D.; Oberg, H.; Janssen, O.; Valerius, T.; Baldus, C.; Scheffold, A.; Brueggemann, M.; Chitadze, G.

10.1101/2025.11.17.688178 — immunology — Posted on 2025-11-17

2221 Key determinants of T cell epitope recognition revealed by TCR specificity profiles

Liu, Y.; Croce, G.; Tadros, D.; Moreno, D.; Michel, A.; Thierry, A.-C.; Genolet, R.; Perez Gomes, M. A. S.; Lani, R.; Guillaume, P.; Hebeisen, M.; Teleman, M.; Lau, K.; Larabi, A.; Racle, J.; Speiser, D.; Pojer, F.; Dunn, S.; Baumgartner, P.; Zoete, V.; Harari, A.; Gfeller, D.

10.1101/2025.11.17.688817 — immunology — Posted on 2025-11-17

2222 Posterior Cortex Isolation Enhances Detection of Alpha Desynchronization During Sustained Attention

St. Clair, N. M.; Mahajan, S.; Leung, C.; Srinivas, C.; Oushana, L.; Zhou, F.; Dewan, N.

10.1101/2025.11.17.688558 — neuroscience — Posted on 2025-11-17

2223 Simultaneous Triple Modes of Cross-Frequency Coupling in Brainstem Nonlinear Oscillator Networks: Cooperative Rhythms of Respiration, Heartbeat, and Brainwaves

Kawai, Y.

10.1101/2025.11.15.688616 — neuroscience — Posted on 2025-11-17

2224 Degraded neural coding of temporal fine structure with age predicts effortful listening in multi-talker environments

Zhen, L.; Parida, S.; McHaney, J.; Zink, M.; Chandrasekaran, B.; Parthasarathy, A.

10.1101/2025.11.17.688858 — neuroscience — Posted on 2025-11-17

2225 Systematic Discovery of Pathogen Effector Functions across Human Pathogens and Pathways

Pachano, T.; Leng, H.; Dugied, G.; Tribble, T.; Loubiere, V.; Rauh, F.; Lee, Y.; Schleiffer, A.; Weller, B.; Lyons, E. A.; Hass, M. R.; Kottyan, L. C.; Weirauch, M. T.; Fuxman Bass, J.; Newton, H. J.; Ensminger, A. W.; Falter-Braun, P.; Schramek, D.; Stark, A.; Taipale, M.

10.1101/2025.11.17.687821 — systems biology — Posted on 2025-11-17

2226 Evolutionary rewiring of host metabolism and interferon signalling by SARS-CoV-2 variants

Giotis, E. S.; Somji, R.-A.; Brown, J. C.; Rowles-Khalid, S.; Abdullahi, T. B.; Luo, D.; Barthel, N.; Mulleder, M.; Ralser, M. S.; Barclay, W. S. S.; Rallis, C.

10.1101/2025.11.15.688605 — systems biology — Posted on 2025-11-17

2227 Pan-EphB tyrosine kinase inhibitor mitigates diabetic cardiomyopathy

Ewida, H. A.; Aziz, M. T.; Tareq, S.; Chelikani, P. K.; Ahmed, M. S.

10.1101/2025.11.17.688935 — pharmacology and toxicology — Posted on 2025-11-17

2228 RUNX2 promotes epigenetic WNT signaling in inflamed intestinal epithelial cells

Cabrera-Silva, R. I.; Wilson, Z. S.; Miranda, J.; Fan, S.; Dame, M. K.; Bishu, S.; Spence, J. R.; Brazil, J.; Colacino, J.; Nusrat, A.; Parkos, C. A.

10.1101/2025.11.17.688458 — pathology — Posted on 2025-11-17

2229 Liquid Crystalline Ordering of Banana-Shaped Gapped DNA Duplexes

Kodikara, S. G.; Gyawali, P.; Gleeson, J. T.; Jakli, A.; Sprunt, S.; Balci, H.

10.1101/2025.11.17.688902 — biophysics — Posted on 2025-11-17

2230 Structure and mechanism of microtubule stabilization and motor regulation by MAP9

Cetin, B.; Taheri, A.; Golcuk, M.; Monroy, B. Y.; Fernandes, J.; Ori-McKenney, K. M.; Gur, M.; Nogales, E.; Yildiz, A.

10.1101/2025.11.17.688911 — biophysics — Posted on 2025-11-17

2231 AFM-Fold: Rapid Reconstruction of Protein Conformations from AFM Images

Kawai, T.; Matsunaga, Y.

10.1101/2025.11.17.688836 — biophysics — Posted on 2025-11-17

2232 Spatial regulation of AMPK activity under oxidative stress requires LKB1

Parks, K.; Jhawar, A.; Andrikopoulos, A.; Winters, D. M.; Dean, T. S.; Kapelczak, E. D.; TeSlaa, T.; Bouhaddou, M.; Schmitt, D. L.

10.1101/2025.11.17.688926 — biochemistry — Posted on 2025-11-17

2233 PTPRJ-Targeting Peptide Agonist Induces Broad Cellular Signaling Perturbations and DNA Damage in Lung Cancer Cells

Rizzo, S.; Hart, W. S.; Fetter, R. L.; Song, B.; White, F. M.; Lazzara, M.; Thevenin, D.

10.1101/2025.11.17.688709 — biochemistry — Posted on 2025-11-17

2234 Structural Basis for Iterative Methylation by a Cobalamin-dependent Radical S-Adenosylmethionine Enzyme in Cystobactamids Biosynthesis

Cui, J.; Wang, B.; Maurya, R.; Booker, S. J.

10.1101/2025.11.17.688841 — biochemistry — Posted on 2025-11-17

2235 Telomere-to-Telomere Accurate and Gapless Korean Standard Reference Genome

Kwon, Y.; Bhak, J.; Jeon, S.; Park, S.; Yoon, C.; An, K.; Choi, Y.; Shin, D.-H.; Choi, H.; Lee, H.; Jeon, Y.; Jeon, J.; Joe, S.; Yang, J. O.; Kim, J.-H.; Cho, Y. S.; Kim, J.; Chae, K. S.; Kim, C. G.; Lee, S.; Jeong, H.; Bhak, J.

10.1101/2025.11.17.688257 — genomics — Posted on 2025-11-17

2236 Differential contribution of the RNA recognition motifs to SRSF1 protein interaction network

Mammi, P.; Pawellek, A.; Gaioli, N.; Bragado, L.; Pozzi, B.; Grecco, H. E.; Lamond, A. I.; Srebrow, A.

10.1101/2025.11.17.688470 — molecular biology — Posted on 2025-11-17

2237 Distinct Mechanisms for Inhibition of SARS-CoV-2 Main Protease: Dimerization Promoted by Peptidomimetic Inhibitors and Disrupted by Ebselen

Liu, C.; Jia, Q.; Zhao, C.; Zhongping, Y.

10.1101/2025.11.16.688752 — molecular biology — Posted on 2025-11-17

2238 The L-lactate dehydrogenase LldD contributes to oxidative stress resistance, survival from neutrophils, and host colonization in Neisseria gonorrhoeae

Lankford, J.; Barr, W.; Andersen, C.; Karuppiah, A.; Thomas, K. S.; Glomski, I.; Criss, A. K.; Potter, A. D.

10.1101/2025.11.17.688940 — microbiology — Posted on 2025-11-17

2239 Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli

Mäklin, T.; Calland, J. K.; Mallawaarachchi, S.; Thorpe, H. A.; Gladstone, R. A.; Corander, J.

10.1101/2025.11.17.686825 — microbiology — Posted on 2025-11-17

2240 Iron and peroxide regulation of the PrrF sRNAs and a conserved Dps-like protein in Pseudomonas aeruginosa and Pseudomonas fluorescens

Ouattara, K.; Oglesby, A. G.

10.1101/2025.11.17.688906 — microbiology — Posted on 2025-11-17

2241 Expelling of P. falciparum sporozoites by Anopheles stephensi mosquitoes during repeated feeding

Andolina, C.; van Gemert, G.-J.; Ramjith, J.; Evers, F.; Graumans, W.; Stoter, R.; Teelen, K.; Hol, F. J.; Lanke, K.; Bousema, T.

10.1101/2025.11.17.688877 — microbiology — Posted on 2025-11-17

2242 Determinant host differences in ZIKV sfRNA accumulation.

Ricciardi-Jorge, T.; Storrie, S.; Mansur, D. S.; Sweeney, T. R.

10.1101/2025.11.17.688941 — microbiology — Posted on 2025-11-17

2243 IFIT3 controls IFIT1 accumulation and specificity preventing self mRNA targeting during the innate immune response.

Fleith, R. C.; Leong, X. Y.; Ricciardi-Jorge, T.; Mears, H. V.; Emmott, E.; Mansur, D. S.; Sweeney, T. R.

10.1101/2025.11.17.688928 — immunology — Posted on 2025-11-17

2244 Connecting the dots - Recognition of artificial and natural shapes relies on representing points of high information

Schmidtmann, G.; Baker, N.; Lande, K. J.; Schmidt, F.

10.1101/2025.11.17.688832 — neuroscience — Posted on 2025-11-17

2245 Unmixing the Psychedelic Connectome: Brain Network Traits of Psilocybin

Bhavaraju, K. P.; Mason, N. L.; Mallaroni, P.; Heinke, D.; Toennes, S.; Ramaekers, J.; Amico, E.

10.1101/2025.11.17.688834 — neuroscience — Posted on 2025-11-17

2246 Combinatorial Cell-Adhesion and Activity Codes Instruct Cortical Modality Identity

Guillamon-Vivancos, T.; Puche-Aroca, L.; Wang, L.; Vandael, D.; Torres, D.; Anibal-Martinez, M.; Fuentes-Jurado, I.; Martini, F.; Lopez-Bendito, G.

10.1101/2025.11.17.688831 — neuroscience — Posted on 2025-11-17

2247 BiosInt: Biosensor-based smart design of pathway dynamic regulation for industrial biomanufacturing

Martin Lazaro, H.; Otero-Muras, I.; Carbonell, P.

10.1101/2025.11.17.688676 — synthetic biology — Posted on 2025-11-17

2248 UT-018, A Stem-Cell Chemoattractant Nutraceutical for intestinal Healing in DSS-Induced Colitis

Saxena, U.; Kambrath, S.; Kadiyala, G.; Gorantla, M.

10.1101/2025.11.17.688808 — pharmacology and toxicology — Posted on 2025-11-17

2249 FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models

Xu, C.; Pouyabahar, D.; Voisin, V.; Heydari, H.; Bader, G.

10.1101/2025.04.08.647860 — bioinformatics — Posted on 2025-11-17

2250 pH-induced structural changes in SARS-CoV-2 spike variants

Oliveira, A. S. F.; Tulli, L.; Kearns, K. L.; Casalino, L.; Rosenfeld, M. A.; Berger, I.; Schaffitzel, C.; Davidson, A. D.; Haddrell, A. E.; Reid, J. P.; Amaro, R. E.; Mulholland, A. J.

10.1101/2025.11.17.688702 — biochemistry — Posted on 2025-11-17

2251 Capturing Translation in Action with Protein Synthesis Profiling

Matta, C. A.; Ten, Z. Q.; Joseph, S.

10.1101/2025.11.17.688896 — biochemistry — Posted on 2025-11-17

2252 Unraveling Genomic Signatures of lncRNA Expression in Zebrafish Caudal Fin Regeneration: Bridging Regenerative Potential and Positional Memory.

Paul, S.; Hariharan, A.; Abhilash, D.; Kohli, S.; Minocha, S.; Gupta, I.

10.1101/2025.11.17.688827 — genomics — Posted on 2025-11-17

2253 Complementarity of ecosystem types drives landscape-wide productivity in North America

Landauer, S.; Altermatt, F.; Furrer, R.; Isbell, F.; Spehn, E. M.; Niklaus, P. A.

10.1101/2025.11.17.688810 — ecology — Posted on 2025-11-17

2254 Cardiac neurons expressing a glucagon-like receptor mediate cardiac arrhythmia induced by high-fat diet in Drosophila

Zhao, Y.; Duan, J.; van de Leemput, J.; Han, Z.

10.1101/2023.12.13.571403 — cell biology — Posted on 2025-11-17

2255 Condensin chromatin association is regulated by SMC head and hinge engagement and phosphorylation

Miles, C.; Yu, M.; Schalbetter, S.; Minchell, N.; Sweet, S.; Baxter, J.

10.1101/2025.11.17.688780 — molecular biology — Posted on 2025-11-17

2256 Optimized CART Cell Therapy for Metastatic Aggressive Thyroid Cancer

Manriquez-Roman, C.; Siegler, E. L.; Gleba, J. J.; Huynh, T. N.; DeFranco, G. E.; Alasonyalilar Demirer, A.; Pawlush, M. L.; Redig, M.; Klinge, S. M.; Mai, L. K.; Miller, J. L.; Miller, E. E.; Kimball, B. L.; Tapper, E. E.; Sakemura, R. L.; Stewart, C. M.; Can, I.; Sirpilla, O. L.; Feigin, J. M.; Yun, K.; Gutierrez-Ruiz, O. L.; Xia, H.; Hefazi, M.; Schick, K. J.; Ogbodo, E. J.; Olivier, G.; Qiu, Y.; Smallridge, R. C.; Zubair, A.; Tun, H. W.; Copland, J. A.; Kenderian, S. S.

10.1101/2024.03.15.585286 — immunology — Posted on 2025-11-17

2257 An inhibitory feedback circuit mediating sleep need and sensory gating in Drosophila

Brodersen, C. B.; Wibroe, J.; Shakespeare, L. M.; Owald, D.; Krohn, K.; Raccuglia, D.

10.1101/2025.11.17.688806 — neuroscience — Posted on 2025-11-17

2258 Insular error network enables self-correcting intracranial brain-computer interface

Weger, P.; Ottenhoff, M. C.; Verwoert, M.; Gimple, S. V.; Ostrowski, L.; Colon, A.; Wagner, L.; van Dijk, J. P.; Temel, Y.; Kubben, P.; Herff, C.

10.1101/2025.11.17.688824 — neuroscience — Posted on 2025-11-17

2259 Allosteric deimmunisation of a Salmonella phosphatase enhances catalytic function

Ko, S.; You, S.-H.; Moon, Y.; Ko, J.; Shin, W.-H.; Choi, Y.

10.1101/2025.11.17.688463 — biophysics — Posted on 2025-11-17

2260 Development of a metabolic signature of post-weaning diarrhoea in pigs

Wolthuis, J.; Magnusdottir, S.; Stigter, E.; Tang, Y. F.; Jans, J.; Gilbert, M.; van der Hee, B.; Langhout, P.; Gerrits, W.; Kies, A.; de Ridder, J.; van Mil, S.

10.1101/2025.11.17.688604 — bioinformatics — Posted on 2025-11-17

2261 Video-Based Cattle Behavior Detection for Digital Twin Development in Precision Dairy Systems

Rao, S.; Garcia, E.; Neethirajan, S.

10.1101/2025.11.13.688203 — animal behavior and cognition — Posted on 2025-11-17

2262 Sentinel-2 based estimates of rangeland fractional cover and canopy gap class for the western United States

Allred, B. W.; McCord, S. E.; Assal, T. J.; Bestelmeyer, B. T.; Boyd, C. S.; Brooks, A. C.; Cady, S. M.; Duniway, M. C.; Fuhlendorf, S. D.; Green, S. A.; Harrison, G. R.; Jensen, E. R.; Kachergis, E. J.; Knight, A. C.; Mattilio, C. M.; Mealor, B. A.; Naugle, D. E.; O'Leary, D.; Olsoy, P. J.; Peirce, E. S.; Reinhardt, J. R.; Shriver, R. K.; Smith, J. T.; Tack, J. D.; Tanner, A. M.; Tanner, E. P.; Twidwell, D.; Webb, N. P.; Morford, S. L.

10.1101/2025.03.13.643073 — ecology — Posted on 2025-11-17

2263 LRBA promotes drug-induced liver injury and MASLD by scaffolding MAPK activation

Tokunaga, F.; Oikawa, D.; Gi, M.; Okina, Y.; Minh, D. P.; Kosako, H.; Thuy, L. T. T.; Sato, Y.; Ikenaga, H.; Kosugi, M.; Matsubara, T.; Shimizu, K.; Shiota, M.; Ando, F.; Uchida, S.; Takahashi, H.; Horii, T.; Hatada, I.; Ikeda, K.; Sawasaki, T.; Kawada, N.

10.1101/2025.11.17.688803 — cell biology — Posted on 2025-11-17

2264 Heat shock alters the distribution and interaction of major nuclear proteins--Lamin B with DNA topoisomerase II and chromatin

Rowinska, M.; Tomczak, A.; Jablonska, J.; Zielinska, A.; Piekarowicz, K.; Machowska, M.; Rzepecki, R.

10.1101/2024.02.28.582469 — cell biology — Posted on 2025-11-17

2265 Establishment and application of a vesicle extraction method for clinical strains of Pseudomonas aeruginosa

Henriquez, T.; Santoro, F.; Medaglini, D.; Pallecchi, L.; Paccagnini, E.; Gentile, M.; Lupetti, P.; Falciani, C.

10.1101/2025.11.17.688223 — microbiology — Posted on 2025-11-17

2266 CD301b lectin expression in the breast tumor microenvironment augments tumor growth

Ozdilek, A.; Paschall, A. V.; Nawaz, Z.; Niyas, A. M. M.; Avci, F. Y.

10.1101/2024.03.13.584829 — immunology — Posted on 2025-11-17

2267 Super-resolution microscopy of nanoscopic alpha-synuclein aggregates in brain samples indicates a subset of cells have disrupted protein homeostasis prior to Lewy body formation in Parkinson's disease

Fertan, E.; Danial, J.; Neame, S.; Lam, J. Y. L.; Cotton, M. W.; Burke, M.; Xia, Z.; Wu, Y.; Powney, B.; Imaizumi, Y.; Quaegebeur, A.; Meisl, G.; Staddon, J.; Klenerman, D.

10.1101/2025.09.16.676632 — neuroscience — Posted on 2025-11-17

2268 Micro-/nano-plastics accentuate Parkinson's Disease-relevant phenotypes in a Drosophila model

Lowe, S. A.; jepson, j.

10.1101/2025.11.17.688805 — neuroscience — Posted on 2025-11-17

2269 Adrenomedullin restores human cortical interneurons migration defects induced by hypoxia

Puno, A.; Michno, W. M.; Li, L.; Everitt, A.; McCluskey, K.; Htun, S.; Nagar, D.; Choi, J. B.; Dai, Y.; Park, S.; Gurwitz, E.; Willsey, J.; Birey, F.; Pasca, A. M.

10.1101/2023.05.01.538334 — neuroscience — Posted on 2025-11-17

2270 Tatton-Brown-Rahman-Syndrome-associated DNMT3A mutations de-repress cortical interneuron differentiation to disrupt neuronal network function

Chapman, G.; Determan, J.; Edwards, J. R.; Batool, F.; Huettner, J. E.; Prakasam, R.; Crump, S.; Jetter, H.; Gabel, H. W.; Kroll, K. L.

10.1101/2025.06.24.661324 — neuroscience — Posted on 2025-11-17

2271 Statistically valid explainable black-box machine learning: applications in sex classification across species using brain imaging

Liu, T.; Dey, J.; Xu, B.; Bridgeford, E. W.; Alldritt, S. S.; Nenning, K.-H.; Byeon, K.; Xu, T.; Vogelstein, J. T.

10.1101/2025.07.09.664026 — neuroscience — Posted on 2025-11-17

2272 Intracellular Expression of a Fluorogenic DNA Aptamer Using Retron Eco2

Vibhute, M. A.; Machatzke, C.; Krumpel, S.; Dirks, M.; Bigler, K.; Summerer, D.; Mutschler, H.

10.1101/2024.05.21.595248 — synthetic biology — Posted on 2025-11-17

2273 MpNPR modulates lineage-specific oil body development and defence against gastropod herbivory in Marchantia polymorpha

Espinosa-Cores, L.; Michavila, S.; Gonzalez-Zuloaga, M.; Solano, R.; Gimenez-Ibanez, S.

10.1101/2025.11.17.688000 — plant biology — Posted on 2025-11-17

2274 DETERMINATION OF CYTOTOXICITY AND FUNCTIONAL GROUPS IN THE RIGHT-WING OF MUSCA DOMESTICA

Lumogdang, L. P.; Guroalim, J. F. R.; Domingo, P.; Osabel, R.

10.1101/2025.11.11.687935 — pharmacology and toxicology — Posted on 2025-11-17

2275 Large-scale synthetic data enable digital twins of human excitable cells

Yang, P.-C.; Jeng, M.-T.; Lieu, D. K.; Smithers, R. L.; Hernandez-Hernandez, G.; Santana, L. F.; Clancy, C. E.

10.1101/2025.09.03.674034 — pharmacology and toxicology — Posted on 2025-11-17

2276 Tau hyperphosphorylation impairs cooperative binding tomicrotubules and perturbs organelle trafficking in neurons

Beaudet, D.; Berger, C. L.; Hendricks, A. G.

10.1101/2025.07.31.667882 — biophysics — Posted on 2025-11-17

2277 Computational characterization of the xanthan gum glycosyltransferase GumK

Luciano, D.; Thomasen, F. E.; Lindorff-Larsen, K.; Courtade, G.

10.1101/2025.08.28.672881 — biophysics — Posted on 2025-11-17

2278 ProtAttn-QuadNet: An attention-based deep learning framework for protein-protein interaction prediction using ProtBERT embeddings

Islam, M. S.; Mim, M. M. R.; Kabir, M. R.

10.1101/2025.11.17.688786 — bioinformatics — Posted on 2025-11-17

2279 NaBC1 Acts as a Mechanosensitive Co-regulator of Fibronectin-binding Integrins Adhesion and Myoblast Polarization

Gonzalez-Valdivieso, J. G.-V.; Castillo, R.; Rodrigo-Navarro, A.; Rodriguez-Romano, A.; Mnatsakanyan, H.; Salmeron-Sanchez, M.; Rico, P.

10.1101/2025.11.17.688253 — bioengineering — Posted on 2025-11-17

2280 Social connections, group size and fine-scale manipulations of social stability shape learning, scrounging and foraging rate in mixed flocks of wild songbirds

Reichert, M. S.; Firth, J. A.; Troisi, C. A.; Quinn, J. L.

10.1101/2025.08.18.670876 — animal behavior and cognition — Posted on 2025-11-17

2281 New genomic resources for an invasive mite pest help guide the development of KASP markers for pesticide resistance screening

Thia, J. A.; Richardson, K. M.; Brown, C.; Arthur, A.; Micic, S.; Lord, A.; Young, N. D.; Sumanam, S.; Chang, B.; Wei, S.-J.; Gasser, R.; Umina, P.; Hoffmann, A.

10.1101/2025.11.17.688773 — genomics — Posted on 2025-11-17

2282 New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales

Freel, K. C.; Tucker, S. J.; Freel, E. B.; Stingl, U.; Giovannoni, S. J.; Eren, A. M.; Rappe, M. S.

10.1101/2024.12.24.630191 — microbiology — Posted on 2025-11-17

2283 Bioplastic Production Potential of Azospira suillum PS: Growth-Associated PHB Production Under Aerobic and Anaerobic Conditions

Meier, D. A. O.; Glazer, B.; Lanclos, V. C.; Carlson, H. K.; Coates, J. D.

10.1101/2025.11.12.688118 — microbiology — Posted on 2025-11-17

2284 Bacterial degradation of a plant toxin and nutrient competition with commensals trade off to constrain pathogen growth

Unger, K.; Mauri, M.; Gershenzon, J.; Allen, R.; Agler, M. T.

10.1101/2025.11.17.688815 — microbiology — Posted on 2025-11-17

2285 Emergence of mutHV76G among longitudinal carbapenem resistant Klebsiella pneumoniae causing long-term colonization and recurrent infection disrupts DNA mismatch repair and results in a hypermutator phenotype

Cheng, S.; Clancy, C. J.; Fleres, G.; Badrane, H.; Culyba, M. J.; Newbrough, A.; Chen, L.; Nguyen, M. H.

10.1101/2025.11.17.688822 — microbiology — Posted on 2025-11-17

2286 Disease-specific fibroblast-myeloid interactions in rheumatoid arthritis synovium

Khmelevskaya, A.; Apostolopoulou, K.; Calvo Cebrian, C.; Ezen, E.; Toitou, M.; Laphanuwat, P.; Mirrsahimi, M.; Geiss, C.; Lugar, M.; Kakale, A.; Malkewitz, S.; Laimbacher, A.; Konstantopoulos, D.; Rinotas, V.; Armaka, M.; Houtman, M.; Meier, E.; Bürki, K.; Leclerc, J.; Mohammadian, H.; Seiler, C.; Camarillo-Retamosa, E.; Pauli, C.; Ramming, A.; Fearon, U.; Zachariassen, K.; Rauer, T.; Ciurea, A.; Elhai, M.; Micheroli, R.; Ospelt, C.

10.1101/2025.11.17.688477 — immunology — Posted on 2025-11-17

2287 From Bird Viremia to Bird Surveillance: Identifiability in a Multiscale Vector-Borne Model of Usutu Virus Infection

Tuncer, N.; Liyanage, Y.; Murphy, Q.; Persinger, R.; Duggal, N.; Ciupe, S. M.

10.1101/2025.11.17.688793 — immunology — Posted on 2025-11-17

2288 Mislocalisation of TDP-43 to the cytoplasm of either neurons or oligodendrocytes causes axonopathy and dysmyelination

Keatinge, M.; Constantinou Juhasz, S.; Shaw-McGrath, T.; Albayrak, J.; Soong, D.; Marshall-Phelps, K.; Story, D.; Hoodless, L.; Cooper, J.; Almeida, R. G.; Czopka, T.; Hardingham, G.; Lyons, D. A.; Chandran, S.

10.1101/2025.11.17.688801 — neuroscience — Posted on 2025-11-17

2289 Peripheral anatomy and central connectivity of proprioceptive sensory neurons in the Drosophila wing

Lesser, E.; Moussa, A.; Tuthill, J. C.

10.1101/2025.05.29.656810 — neuroscience — Posted on 2025-11-17

2290 Critical neuronal avalanches emerge from excitation-inhibition balanced spontaneous activity

Janbon, M.; Amortegui, M.; Hansen, E. C. A.; Nourin, S.; Sumbre, G.; Ponce-Alvarez, A.

10.1101/2025.11.17.688775 — neuroscience — Posted on 2025-11-17

2291 Distinct prior expectations shape tactile and proprioceptive localization

Elmas, H.; Medendorp, W. P.; Miller, L. E.

10.1101/2025.11.17.688784 — neuroscience — Posted on 2025-11-17

2292 Engineering directional phosphoryl flow enables programmable signaling dynamics in bacteria

Nieves, M.; Valle, J. M.; Dalla Rizza, J.; Carrion, F.; Naranjo-Meneses, P.; Larrieux, N.; Bischofs, I.; Buschiazzo, A.; Trajtenberg, F.

10.1101/2025.11.17.688798 — systems biology — Posted on 2025-11-17

2293 Model of ocular surface ion and water transport predicts efficacy of dry eye therapeutics targeting epithelial transport and tear fluid dynamics

Verma, V.; Lindgren, E. S.; Levin, M. H.; Cil, O.; Tradtrantip, L.; Yan, R.; Pasricha, N. D.; Verkman, A. S.

10.1101/2025.11.17.688783 — systems biology — Posted on 2025-11-17

2294 Calibration-free molecular counting from a single DNA-PAINT intensity trace using cumulants

Huijben, T. A. P. M.; Marie, R.; Pedersen, J. N.

10.1101/2025.11.17.688450 — biophysics — Posted on 2025-11-17

2295 Vimentin promotes actin assembly by stabilizing ATP-actin subunits at the barbed end

Paty, L.; Varela-Salgado, M.; Tran, Q. D.; Jegou, A.; Romet-Lemonne, G.; Leduc, C.

10.1101/2025.11.17.688760 — biophysics — Posted on 2025-11-17

2296 Data-driven traction force microscopy in 3D collagen hydrogels

Barrasa-Fano, J.; Kimps, L.; Apolinar-Fernandez, A.; Nunez Ortega, E.; Muntz, I.; Koenderink, G.; Sanz-Herrera, J.; Van Oosterwyck, H.

10.1101/2025.11.17.688772 — biophysics — Posted on 2025-11-17

2297 AstroLogics: A simulation-based analysis framework for monotonous Boolean model ensemble

Pankaew, S.; Noel, V.; Pauleve, L.; Thieffry, D.; Barillot, E.; Calzone, L.

10.1101/2025.11.17.688236 — bioinformatics — Posted on 2025-11-17

2298 Primer Blind Spots: Underrepresentation of ESKAPE Pathogens from Developing Regions in 16S rRNA Targeted Sequencing

Chouhan, K.; Gawande, D.; Gupta, I.

10.1101/2025.11.17.688800 — bioinformatics — Posted on 2025-11-17

2299 Modeling synthetic serum marker kinetics for monitoring deep-tissue gene expression.

Buitrago, N.; Brau, J.; Szablowski, J. O.

10.1101/2025.11.17.688787 — bioengineering — Posted on 2025-11-17

2300 Recurrent neural network dynamics may not purely reflect cognitive strategies: A commentary on Ji-An et al. (Nature, 2025)

Katahira, K.

10.1101/2025.10.30.685524 — animal behavior and cognition — Posted on 2025-11-17

2301 Genomic Evidence for a Novel Introduction and Intra-host Diversity of DENV-2 in Dar es Salaam, Tanzania

Hälg, S.; Tenywa, F. S. C.; Liechti, N.; Beuret, C.; Moore, S. J.; Müller, P.

10.1101/2025.11.17.688789 — genomics — Posted on 2025-11-17

2302 Complete de novo assembly and re-annotation of the zebrafish genome

Okendo, J.; Koren, S.; Rhie, A.; Torrado-Tapias, A.; Pickett, B. D.; Brooks, S. Y.; Bouffard, G. G.; Crawford, J. K.; Sison, C.; Joardar, V. S.; Murphy, T. D.; Tierney, J. A. S.; Haggerty, L.; Martin, F. J.; Wilson, C.; Amores, A.; Postlethwait, J. H.; Murphy, J.; Sakai, N.; Varga, Z. M.; Phillippy, A. M.; Burgess, S. M.

10.1101/2025.11.17.688901 — genomics — Posted on 2025-11-17

2303 Genetic and Functional Characterization of AMH Signaling in Zebrafish - Evidence for Roles of Amh-Bmpr2a-Bmpr1bb Pathway in Controlling Gonadal Homeostasis

Ge, W.; Yue, Y.; Zeng, C.; Zhang, X.; Bian, C.; Zhang, Z.; Wu, K.; Chen, W.; Zhou, X.; Lu, L.; Ai, N.

10.1101/2025.11.17.688792 — genetics — Posted on 2025-11-17

2304 First growth, then information: the path to genetic heredity in protocells

Nunes Palmeira, R.; Colnaghi, M.; Pomiankowski, A.; Lane, N.

10.1101/2025.11.17.688785 — evolutionary biology — Posted on 2025-11-17

2305 Extracellular glutamine is essential in cell division and flagellar function in bloodstream forms of Trypanosoma brucei

Damasceno, F. S.; Marsiccobetre, S.; Souza, R. O. O.; Issa, M.; Thiemann, O. H.; Sorrentino, A.; Figarella, K.; Duszenko, M.; Silber, A. M.

10.1101/2025.11.17.688794 — cell biology — Posted on 2025-11-17

2306 Dietary sulfur amino acid restriction elicits a cold-like transcriptional response in inguinal but not epididymal white adipose tissue of male mice

Ruppert, P. M.; Gueller, A. S.; Rosendal, M.; Stanic, N.; Kornfeld, J.-W.

10.1101/2025.08.06.669020 — molecular biology — Posted on 2025-11-17

2307 The phenotypic landscape of the mycobacterial cell

Herrera, N.; Todor, H.; Kim, L. M.; Burkhart, H. N.; Billings, E.; Warner, T. C.; Lee, S. Y.; Sayegh, N. Y.; Bosch, B.; Kiessling, L. L.; Mancia, F.; Rock, J. M.; Gross, C. A.

10.1101/2025.11.14.688347 — microbiology — Posted on 2025-11-17

2308 Active vision modulates early cortical stages of visual processing: Evidence from MEG and eye-tracking

Huber-Huber, C.; De Lange, F. P.

10.1101/2025.11.17.688782 — neuroscience — Posted on 2025-11-17

2309 An integrative computational approach for obstacle avoidance during action selection

Zhong, S.; Pouratian, N.; Schrater, P.; Christopoulos, V.

10.1101/2025.11.17.688790 — neuroscience — Posted on 2025-11-17

2310 Vectorial boundary representation of 3D layout in human visual cortex

Wu, Y.; Li, S.

10.1101/2025.11.17.688791 — neuroscience — Posted on 2025-11-17

2311 Immunogenicity and Protective Efficacy of Toxoplasma gondii SRS67 and SRS20A Proteins in Mice

Yin, D.; Li, Q.; YI, T.

10.1101/2025.11.17.688744 — zoology — Posted on 2025-11-17

2312 Optimization of a T7 RNA polymerase expression system for high-yield protein production in Cupriavidus necator H16

Vajente, M.; Ballerstedt, H.; Blank, L. M.; Schmidt, S.

10.1101/2025.11.17.688765 — synthetic biology — Posted on 2025-11-17

2313 Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024

Isaac, K. J.; Cox, K. E. L.; Ho, K. Y.; Humphries, E. M.; Kucher, N.; Leek, J. T.; Mosher, S.; Schatz, M. C.; Tan, F. J.; Hoffman, A. M.

10.1101/2025.11.14.688517 — scientific communication and education — Posted on 2025-11-17

2314 SAMP1/TMEM201 Promotes Hepatic Gluconeogenesis by PKA/CREB Pathway

Schena, E.; Columbaro, M.

10.1101/2025.11.17.688768 — pathology — Posted on 2025-11-17

2315 A Druggable Tumor Suppressor and Leukemic Stem Cell Marker

Pan, Y.; Wang, C.; Meng, X.; Zhou, W.; Hammer, R.; Zheng, H.; Hildebrandt, G.; Kang, X.

10.1101/2025.10.16.682831 — cancer biology — Posted on 2025-11-17

2316 FLIM Playground: An interactive, end-to-end graphical user interface for analyzing single-cell fluorescence lifetime data

Zhao, W.; Samimi, K.; Skala, M. C.; Datta, R.

10.1101/2025.09.30.679625 — bioengineering — Posted on 2025-11-17

2317 Supporting the implementation of chemometrics models in bioprocess from development to commercial stage

Helleputte, T.; Cornet, T.; Kanfoud, A.; des Touches, T.; Gerkens, P.; Dumas, P.; Cardillo, A. G.; de Lannoy, G.

10.1101/2025.11.17.688770 — bioengineering — Posted on 2025-11-17

2318 Insights into the mechanism of succinimide formation in an archaeal glutaminase.

Chandrashekarmath, A.; Jash, O.; Singh, K.; Bellur, A.; Roy, C. S.; Dongre, A.; Chathoth, N. E.; Anjukandi, P.; Kumar, S.; Mukherjee, S.; Balaram, P.; Balasubramanian, S.; Balaram, H.

10.1101/2025.11.17.688757 — biochemistry — Posted on 2025-11-17

2319 Effects of Short-Term Breathwork on Respiration and Cognition

Hehemann, L.; Stetza, L.; Kayser, C.

10.1101/2025.11.17.688761 — animal behavior and cognition — Posted on 2025-11-17

2320 Contrasting genomic routes to domestication in Occidental and Oriental pears

NIE, Y.; Chen, X.; SAIDI, S.; Bourgeois, Y.; VENON, A.; CONFAIS, J.; Mesnil, A.; LIU, S.; GAO, Y.; NI, J.; BAI, S.; GAO, L.; LI, G.; HOEFER, M.; FRANCILLONE, N.; ROMAN, A.; LUKACS, L.; DENANCE, C.; AKAGI, T.; NERSESYAN, A.; PAPIKYAN, A.; GABRIELYAN, I. G.; ABDOLLAHI, H.; BASSIL, N. V.; STEFFENSMEIER, S.; ALIX, K.; TENG, Y.; CORNILLE, A.

10.1101/2025.11.17.687327 — genomics — Posted on 2025-11-17

2321 A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker)

Clark, R. C.; Manning, A. C.; Howard, J. M.; Barberan-Soler, S.; Kazakov, S. A.

10.1101/2025.11.12.688114 — molecular biology — Posted on 2025-11-17

2322 Dual Transcriptional Drivers of Immune Suppression in SACC: NOTCH1 for Cellular and MYB for Humoral Immunity

Yang, G.; Wang, X.; Ye, T.; Ma, T.; Chen, Y.; Nan, F.; Chen, Q.; KONG, L.; Chen, X.

10.1101/2025.11.17.688163 — immunology — Posted on 2025-11-17

2323 Order code in the olfactory system.

Samoilova, K.; Harvey, J. S.; Nakayama, H.; Rinberg, D.; Koulakov, A.

10.1101/2025.11.16.688691 — neuroscience — Posted on 2025-11-17

2324 Wormtrails: a python package for viewing C. elegans movement

Ashih, C. D.; Xu, Y.; Apfeld, J.

10.1101/2025.11.14.688522 — neuroscience — Posted on 2025-11-17

2325 Candling analysis of egg development in an endangered bird species Crested ibis (Nipponia nippon)

He, Y.; Xi, X.; Zeng, S.; Huang, H.; Zhan, X.; Wang, D.

10.1101/2025.11.17.688759 — zoology — Posted on 2025-11-17

2326 Cell-Based Immunization Combined with Single-Round Cell Panning Enables Discovery of PSMA-Targeting Nanobodies from Phage Display Libraries

Yang, T.; Veldhoven-Zweistra, J.; Ligtenberg, M.; Erkens, S.; Vredenbregt-van den Berg, M.; Jansen, R.; Chames, P.; Bindels, E. M. J.; Ahmadi, K.; Bangma, C. H.; Kalsbeek, A. M. F.; Leivo, J.; Lumen, N.; van de Werken, H. J. G.; van Weerden, W. M.; Kavousipour, S.; Tooyserkani, R.; Jenster, G.

10.1101/2025.11.17.688677 — cancer biology — Posted on 2025-11-17

2327 A disease mutation reveals a non-swapped pore and rewired gating cycle of the mechanically activated PIEZO1 channel

Wang, C.; Zhang, Z.; Yang, X.; Liu, S.; Yuan, J.; Lin, C.; Zhang, X.; Tian, B.; Li, X.; Xiao, B.

10.1101/2025.11.17.688653 — biophysics — Posted on 2025-11-17

2328 Vimentin promotes actin assembly by stabilizing ATP-actin subunits at the barbed end

Paty, L.; Varela-Salgado, M.; Romet-Lemonne, G.; Tran, Q. D.; Jegou, A.; Leduc, C.

10.1101/2025.11.17.688760 — biophysics — Posted on 2025-11-17

2329 Influence of anthropogenic environments on the activity patterns and vigilance of Cape chacma baboons (Papio ursinus ursinus) in the Garden Route, South Africa

Dany, S.; Lacomme, C.; Guionneau, A.; Ramaru, A.; Prugnolle, F.; Petit, O.; Rougeron, V.

10.1101/2025.11.17.688758 — animal behavior and cognition — Posted on 2025-11-17

2330 Selective Targeting of Kinesin on Lipid Droplets in the Liver Reduces Serum Lipids

Tripathy, S. K.; Mahapatra, A.; Saharan, O.; Chatterjee, H.; Sengupta, N.; Kamat, S. S.; Nair, S.; Mallik, R.

10.1101/2025.11.17.688766 — cell biology — Posted on 2025-11-17

2331 The influence of power-training and aging on endomysium content and fiber cross-sectional area in the human soleus muscle

Clemen, C. S.; Humbsch, S. W.; Berwanger, C.; Mill, L.; Schmidt, A.; Schröder, R.; Rittweger, J.

10.1101/2025.08.28.672902 — physiology — Posted on 2025-11-17

2332 Surface-by-temperature interactions shape the relationship between viral free-living survival and reproduction

Kabengele, K.; Seth, A.; Johnson, T.; Ogbunugafor, C. B.

10.1101/2025.11.16.688743 — ecology — Posted on 2025-11-17

2333 A ceramide synthase is important for filamentous fungal biofilm morphology and antifungal drug resistance

Puerner, C.; Wilkins, O. M.; Cramer, R. A.

10.1101/2025.11.16.688756 — microbiology — Posted on 2025-11-17

2334 Nuclear envelope dysfunction drives premature aging and modulates heterochromatic methylome drift in Arabidopsis

Juez, O.; Saze, H.

10.1101/2025.11.16.688749 — plant biology — Posted on 2025-11-17

2335 Human Stress Response Specificity through Biochemical Resonance Selectivity

Worcester, M.; Nejad, S.; Naeini, A. E.; Arian, S.; O'Donnell, D.; Mishra, P.; Li, S.; Yang, K.; Anbir, A.; Guevara, M.; Yuan, N. Y.; O'Leary, S.; Kaul, M.; Zandi, R.; Kuhlman, T. E.

10.1101/2025.03.05.641735 — biophysics — Posted on 2025-11-17

2336 Predicting the Dynamic Viscosity of High-Concentration Antibody Solutions with a Chemically Specific Coarse-Grained Model

Prass, T. M.; Garidel, P.; Blech, M.; Schäfer, L. V.

10.1101/2025.09.17.676805 — biophysics — Posted on 2025-11-17

2337 Hit or Miss: Understanding Emergence and Absence of Homo-oligomeric Contacts in Protein Language Models

Zhang, Z.; Akiyama, Y.; Cho, Y.; Jajoo, S.; Ovchinnikov, S.

10.1101/2025.11.16.688745 — biophysics — Posted on 2025-11-17

2338 BioPrediction-PPI: Simplifying the Prediction of Protein-Protein Interactions through Artificial Intelligence

Florentino, B. R.; Bonidia, R. P.; Nunes da Rocha, U.; Carlos Ponce de Leon Ferreira de Carvalho, A.

10.1101/2025.11.16.688401 — bioinformatics — Posted on 2025-11-17

2339 Toward Accurate RNA Non-Canonical Structure Prediction: The NC-Bench Benchmark and the NCfold Framework

Zhu, H.; Li, R.; Chang, A.; Li, M.; Chen, H.; Xiong, P.; Zhou, S. K.

10.1101/2025.11.16.688746 — bioinformatics — Posted on 2025-11-17

2340 A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

Thompsky, B.; Beraut, E.; Cooper, R. D.; Escalona, M.; Espinoza, R. E.; Fisher, R. N.; Miller, C.; Nguyen, O.; Sacco, S.; Sahasrabudhe, R.; Seligmann, W. E.; Tofflemier, E.; Wang, I. J.; Shaffer, H. B.

10.1101/2025.11.16.688715 — genomics — Posted on 2025-11-17

2341 Hypoxia-induced gene expression changes in N. vectensis embryos

Hadife, S.; Wang, H.; Hongo, Y.; Watanabe, H.

10.1101/2025.11.16.688652 — evolutionary biology — Posted on 2025-11-17

2342 CONSERVED LIFE HISTORY PHENOTYPES AMONG HISTORICALLY ISOLATED CLADES IN THE CHIRAL LIVEBEARER FISH OF LOWER CENTRAL AMERICA

Johnson, E. E.; Johnson, E. S.

10.1101/2025.11.16.688739 — ecology — Posted on 2025-11-17

2343 The biodiversity of plant-frugivore interactions: types, functions, and consequences

Jordano, P.

10.1101/2025.11.14.688423 — ecology — Posted on 2025-11-17

2344 A Novel 3D Visualization Method in Mice Identifies the Periportal Lamellar Complex (PLC) as a Key Regulator of Hepatic Ductal and Neuronal Branching Morphogenesis

Xu, T.; Cao, F.; Zhou, R.; Chen, Q.; Zhong, J.; Wang, Y.; Xiao, C.; Yin, B.; Chen, C.; Zhao, C.

10.1101/2025.08.29.673025 — developmental biology — Posted on 2025-11-17

2345 A two-component system signaling hub controls enterococcal membrane remodeling in response to daptomycin

Colomer-Winter, C.; Nair, Z. J.; Chua, J.; Jabli, S.; Roch, M.; Cazenave-Gassiot, A.; Sierra, R.; Andrey, D. O.; Chng, S.-S.; Kline, K. A.

10.1101/2025.11.16.688641 — microbiology — Posted on 2025-11-17

2346 CochleaNet: deep learning-based image analysis for cochlear connectomics and gene therapy

Roos, L.; Diniz, A. M.; Koert, E.; Schilling, M.; Uhl, M.; Thirumalai, A.; Aakhte, M.; Kusch, K.; Huisken, J.; Moser, T.; Pape, C.

10.1101/2025.11.16.688700 — neuroscience — Posted on 2025-11-17

2347 Eigenmode decomposition of asymmetries in whole-brain effective connectivity reveals multiscale hierarchical dynamics

Baron, G.; Baggio, G.; Facca, M.; Benozzo, D.; Chiuso, A.; Zampieri, S.; Bertoldo, A.

10.1101/2025.11.16.688716 — neuroscience — Posted on 2025-11-17

2348 Dynamic interactions in human amygdala subregions support hierarchical processing of fearful faces

Cao, D.; Cui, J.; Yan, X.; Zhang, X.; Dang, Y.; Zhao, H.; Li, J.; Zhang, J.; Zhang, Y.

10.1101/2025.11.16.688165 — neuroscience — Posted on 2025-11-17

2349 A Novel Cell-Type Specific Circadian Reporter Mouse Reveals Self-Sustained Food Entrainable Nature in Enteric Neurons

Magana, I.; Taufique, S. K. T.; Shan, Y.; Shen, M.; Ehichioya, D. E.; Takahashi, J. S.; Yamazaki, S.; Obata, Y.

10.1101/2025.11.16.688705 — neuroscience — Posted on 2025-11-17

2350 A Lightweight Deep Learning Architecture for Potato Leaf Disease Detection: A Comprehensive Survey

MANJHVAR, A. K.; Parmula, R.

10.1101/2025.11.16.688731 — neuroscience — Posted on 2025-11-17

2351 Functional organization of the human visual system at birth and across late gestation

Ayzenberg, V.; Arcaro, M.

10.1101/2025.09.22.677834 — neuroscience — Posted on 2025-11-17

2352 Multi-scale network topology analysis reveals metabolic reprogramming and therapeutic vulnerabilities in the tumor microenvironment

Cetin, H.; Bogdan, P. D.; Mumenthaler, S. M.; Finley, S. D.

10.1101/2025.11.16.688737 — systems biology — Posted on 2025-11-17

2353 Minute-scale single-cell transcriptomics enables dynamic modeling of cellular behavior

Asthana, K.; Jambor, A. N.; Wang, W.

10.1101/2025.11.15.688181 — bioinformatics — Posted on 2025-11-17

2354 Inferring binding specificities of human transcription factors with the wisdom of crowds

Gryzunov, N.; Penzar, D.; Kamenets, V.; Vyaltsev, V.; Kozin, I.; Eliseeva, I. A.; Nozdrin, V.; Vorontsov, I. E.; Bushuev, S.; Strekalovskikh, V.; Zinkevich, A.; Andrews, G.; Bedarew, M.; Blass, I.; Frolov, D.; Lariushina, I.; Moore, J.; Orenstein, Y.; Roev, G.; Salimov, D.; Shimshoviz, N.; Tziony, I.; Weng, Z.; IBIS Consortium, ; GRECO-BIT/Codebook Consortium, ; Bucher, P.; Deplancke, B.; Fornes, O.; Grau, J.; Grosse, I.; Jolma, A.; Kolpakov, F. A.; Makeev, V. J.; Hughes, T. R.; Kulakovskiy, I. V.

10.1101/2025.11.16.688692 — bioinformatics — Posted on 2025-11-17

2355 Engineering ATP Import in Yeast Uncovers a Synthetic Route to Extend Cellular Lifespan

Oz, N.; Su, H.; Sari, V.; Patnaik, P.; Hameed, R.; Song, J. H.; Prosser, D.; Labunskyy, V.; Gladyshev, V. N.; Hao, N.; Kaya, A.

10.1101/2025.04.14.648769 — molecular biology — Posted on 2025-11-17

2356 GPR15 and CD38 define a subset of peripheral blood pathogenic effector Th2 cells associated with active eosinophilic esophagitis

Burk, C. M.; Morgan, D. M.; Glickman, J. N.; Virkud, Y. V.; Liao, E.; Moseley, E. G.; Canziani, K. E.; Bhowmik, M.; Li, J. C.; Keswani, T.; Virk-Hundal, N. K.; Katz, A. J.; Yuan, Q.; Patil, S. U.; Love, J. C.; Shreffler, W. G.

10.1101/2025.11.16.688265 — immunology — Posted on 2025-11-17

2357 Order code in the olfactory system.

Samoilova, K.; Harvey, J. S.; Nakayama, H.; Rinberg, D.; Koulakov, A.

10.1101/2025.11.16.688691 — neuroscience — Posted on 2025-11-17

2358 Selective distractor representations resolve multidimensional interference

Gheza, D.; Freund, M. C.; Zalabak, T. R.; Kool, W.

10.1101/2025.11.16.688701 — neuroscience — Posted on 2025-11-17

2359 A Load-Induced Energetic Tipping Point Explains Selective Vulnerability of Substantia Nigra Neurons

Anfilofyev, M.

10.1101/2025.11.16.688654 — neuroscience — Posted on 2025-11-17

2360 The cost of dual-task walking: cognitive demands restrict visual search and gait planning

Russo, Y.; Ye, J. R.; Lamb, S. E.; Gear, A. E.; Lyon, W. R.; Qiu, J. R.; Banks, M. T.; Martin, E.; Wang, Z.; Alghamdi, M.; Leveridge, P. K.; Young, W. R.

10.1101/2025.11.16.688732 — neuroscience — Posted on 2025-11-17

2361 MORPH2DIAG: Automated Structural MRI Preprocessing and Tissue Segmentation for Interpretable Machine and Deep Learning-Based Neuroanatomical Classification

Bangera, S. C.; Pospisil, L.; Bengtsson, T.

10.1101/2025.11.16.688711 — neuroscience — Posted on 2025-11-17

2362 Delayed growth of Ewing sarcoma tumors associated with reduced expression and activity of Trk receptors, PI3K, and IGF1R

dos Santos, B. A.; Freire, N. H.; Fratini, L.; Dalmolin, M.; de Castro, J. M.; Fernandes, M. A. C.; Gregianin, L.; Brunetto, A. T.; Brunetto, A. L.; Rivero, L. F. d. R.; Jaeger, M. d. C.; Roesler, R.; de Farias, C. B.

10.1101/2025.10.23.684233 — cancer biology — Posted on 2025-11-17

2363 pH-dependent structural dynamics of the neuropeptide Y in aqueous solution

Nguyen, T. H.; Spehr, M.; Bondar, A.-N.; Carloni, P.

10.1101/2024.11.04.621936 — biophysics — Posted on 2025-11-17

2364 A Multi-Omic Atlas of Convergent and Divergent Metabolic Regulatory Circuitries in Cancer

Almeida Cordeiro Nogueira, H.; Rodrigues de Souza, E.; dos Santos Lopes, V.; Medina-Acosta, E.

10.1101/2025.11.15.688631 — bioinformatics — Posted on 2025-11-17

2365 Engineering patient-derived organotypic bone model to understand osteoanabolic therapy in skeletal disease

de Leeuw, A.; Steffi, C.; Schädli, G. N.; Singh, A.; Lim, P. J.; Rohrbach, M.; Giunta, C.; Rüger, M.; Müller, R.

10.1101/2025.04.17.649276 — bioengineering — Posted on 2025-11-17

2366 FERAL: A Video-Understanding System for Direct Video-to-Behavior Mapping

Skovorodnikov, P.; Zhao, J.; Buck, F.; Kay, T.; Frank, D. D.; Koger, B.; Costelloe, B. R.; Couzin, I. D.; Razzauti, J.

10.1101/2025.11.16.688666 — animal behavior and cognition — Posted on 2025-11-17

2367 Genome assembly and diagnostic DNA markers for sex of the largest freshwater fish in North America, the white sturgeon (Acipenser transmontanus).

Willis, S. C.; Smith, J.; Narum, S. R.

10.1101/2025.11.14.688503 — genomics — Posted on 2025-11-17

2368 Rice-Fish Co-Culturing for Sustainability, Food Security, and Disease and Poverty Reduction

Selland, E.; Jouanard, N.; Guisse, A.; Seck, M.; Lund, A. J.; Lopez-Carr, D.; Sack, A.; Dossou Magblenou, L.; De Leo, G. A.; Doruska, M. J.; Barrett, C. B.; Rohr, J. R.

10.1101/2025.11.14.688524 — ecology — Posted on 2025-11-17

2369 Experimental infections with a honeybee virus induce fitness costs in ant colonies

Lo, L. K.; Baruah, A.; Paxton, R. J.; Ulrich, Y.

10.1101/2025.10.22.683975 — ecology — Posted on 2025-11-17

2370 A JSDM with zero-inflation to increase the ecological relevance of analyses of species distribution data.

Tous, J.; Chiquet, J.; Deacon, A. E.; Fontrodona-Eslava, A.; Fraser, D. F.; Magurran, A. E.

10.1101/2025.07.24.666553 — ecology — Posted on 2025-11-17

2371 Quantitative comparison of PI(3,5)P2 biosensors reveals SnxA is the most sensitive and unbiased

Swayhoover, T.; Weckerly, C.; Hammond, G. R.

10.1101/2025.11.10.687688 — cell biology — Posted on 2025-11-17

2372 Multi-omics reveal critical differentiation target for Parkinsons' Disease-vulnerable midbrain dopaminergic neurons

Garcia Swinburn, R.; Lyu, G.; Kreutzmann, J. C.; Xiong, A.; Kojima, R.; Abaurre, C.; Tremolanti, C.; Gellhaar, S.; Uhlen, P.; Svenningsson, P.; Castelo Branco, G.; Dagliyan, O.; Salto, C.; Arenas, E.

10.1101/2025.06.18.660098 — cell biology — Posted on 2025-11-17

2373 MPKaDB: A pKa Database for Exploring pH Dependence in Membrane Proteins

He, J.; Chen, Y.; Wu, J.; Cai, Z.; Jia, W.; Yue, Q.; Huang, Y.

10.1101/2025.11.14.688495 — molecular biology — Posted on 2025-11-17

2374 Epithelial Reprogramming by OM-89 Enhances Antibiotic Clearance of Uropathogenic E. coli in a Bladder Organoid Model

Tomasek, K.; Skurvydaite, K.; Paduthol, G.; Burns, A. M.; Schlunke, L.; Pasquali, C.; Romani, M.; McKinney, J. D.

10.1101/2025.10.22.683857 — microbiology — Posted on 2025-11-17

2375 Neural dynamics in ventrolateral prefrontal cortex underlie learning from feedback

Lu, R.; Kadohisa, M.; Kusunoki, M.; Mitchell, D. J.; Woolgar, A.; Buckley, M.; Duncan, J.

10.1101/2025.11.16.688684 — neuroscience — Posted on 2025-11-17

2376 Sphingosine-1-phosphate (S1P) signaling as a novel therapeutic target for alcohol abuse.

Lorrai, I.; Maccioni, R.; Wu, C.; Shankula, C.; Marquez Gaytan, J.; Torres, I.; Puliga, R.; Repunte-Canonigo, V.; Sanna, P.

10.1101/2025.11.15.688635 — neuroscience — Posted on 2025-11-17

2377 Shared neural geometries for bilingual semantic representations

Yan, X.; Krishna, A.; Van Arsdel, K.; Gautam, I.; Kim, Y.; Shrivastava, A.; Belanger, J.; Chavez, A. G.; Chericoni, A.; Franch, M.; Ismail, T.; Katlowitz, K.; Mickiewicz, E.; Paulo, D.; Zhu, H.; Goldman, A. M.; Krishnan, V.; Maheshwari, A.; Bartoli, E.; Provenza, N.; Yoo, S. B. M.; Hayden, B. Y.; Sheth, S.

10.1101/2025.11.16.688726 — neuroscience — Posted on 2025-11-17

2378 Functional connectivity drifts during sleep as a marker of fluctuations in the level of consciousness

Patriota, J.; Moreni, G.; Mejias, J. F.; Talamini, L.; Olcese, U.

10.1101/2025.11.14.688400 — neuroscience — Posted on 2025-11-17

2379 Spatial Multi-Omics Workflow and Analytical Guidelines for Alzheimer's Neuropathology

Sun, X.; Hudson, H. R.; Orr, T. C.; Koutarapu, S.; Rosenbloom, A.; Ingalls, M.; Braubach, O.; Keene, C. D.; Beechem, J. M.; Orr, M. E.

10.1101/2025.11.16.688710 — neuroscience — Posted on 2025-11-17

2380 Mixture-models for stimulus-selective stopping

Jahansa, P.; Diederich, A.; Colonius, H.

10.1101/2025.11.14.688422 — neuroscience — Posted on 2025-11-17

2381 Simultaneous Triple Modes of Cross-Frequency Coupling in Brainstem Nonlinear Oscillator Networks: Cooperative Rhythms of Respiration, Heartbeat, and Brainwaves

Kawai, Y.

10.1101/2025.11.15.688616 — neuroscience — Posted on 2025-11-17

2382 Socio-emotional difficulties observed in alexithymia reflect altered interactions of the semantic and monoaminergic neuromodulatory brain networks

Montolio, M. I.; Visser, M.; Zareba, M. R.

10.1101/2025.05.23.655721 — neuroscience — Posted on 2025-11-17

2383 Peas on Mars: A study of garden pea, Lathyrus oleraceus (=Pisum sativum), growth in Martian regolith simulant treated with black soldier fly frass

Mendoza, J. E.; Lemke, N. B.; Tomberlin, J. K.

10.1101/2025.11.14.688485 — plant biology — Posted on 2025-11-17

2384 Reduced-order modeling of solute transport within physiologically realistic solid tumor microenvironment

Akash, M. M. H.; Yeasin, M.; Mahmoudirad, S.; Niloy, R. A.; Mohammad, J.; Reindl, K.; Pandey, A.; Basu, S.

10.1101/2025.11.15.688588 — physiology — Posted on 2025-11-17

2385 WITHDRAWN: Targeting BRAF kinase fusions with pan-RAF and vertical MAPK inhibition

Turner, J. A.; MacBeth, M. L.; Bagby, S. M.; Whitty, P.; Hartman, S. J.; Simmons, D.; Pitts, T. M.; Yacob, B.; Robinson, W. A.; Couts, K.

10.1101/2025.02.06.636895 — cancer biology — Posted on 2025-11-17

2386 Integrative Multi-Omic Profiling of the Human Phosphatome Identifies DUSP15 as a Tumour-Selective Regulator of Immune-Metabolic Reprogramming in Chromophobe Renal Cell Carcinoma

Sarhan, A. R.

10.1101/2025.11.15.688610 — cancer biology — Posted on 2025-11-17

2387 PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks

Holtgrefe, N.; van Iersel, L.; Meuwese, R.; Murakami, Y.; Schestag, J.

10.1101/2025.11.14.688467 — bioinformatics — Posted on 2025-11-17

2388 Distinct matrix viscoelasticity in bone fracture hematoma steers macrophage polarization

Knecht, R. S.; Morgan, D. M.; Kollert, M. R.; Noom, A.; Bucher, C. H.; Mooney, D. J.; Schmidt-Bleek, K.; Duda, G. N.

10.1101/2025.11.14.688455 — bioengineering — Posted on 2025-11-17

2389 Hunger, displacement, or play? Object manipulation behaviour in Asian small-clawed otters (Aonyx cinereus)

Evans, I.; Cooke, A. S.; Cooper, J.; Ventura, B.

10.1101/2025.11.14.688474 — animal behavior and cognition — Posted on 2025-11-17

2390 Positive Reinforcement Training Insight from Working Elephants in India

Kharkar, R.; Velho, N.; Rathod, S.; RathodC, P.; Boro, A.; Pratt, C.; Rambia, K.

10.1101/2025.11.15.688661 — animal behavior and cognition — Posted on 2025-11-17

2391 A zebrafish seizure model of cblX syndrome reveals a dose-dependent refractory response to mTor inhibition.

Gil, C. B.; Paz, D.; Pinales, B. E.; Castro, V. L.; Perucho, C. E.; Gonzales, A.; Francia, G.; Masenga, S. K.; Hinton, A.; Quintana, A. M.

10.1101/2025.11.14.688058 — developmental biology — Posted on 2025-11-17

2392 AT-hook-dependent DNA loop extrusion by STAG1 drives 3D genome folding

Sakata, R.; Gimenez, D.; Losada, A.; Nishiyama, T.

10.1101/2025.11.17.688764 — molecular biology — Posted on 2025-11-17

2393 Global Mapping of circRNA-Target RNA Interactions Reveals P-Body-Mediated Translational Repression

Li, P.; Zhang, H.; Cai, Z.; Zhang, Y.; Yang, R.; Ye, R.; Li, J.; Zhao, H.; Liu, B.; Yuan, Z.; Li, X.; Wang, X.; Zhu, P.; Xue, Y.

10.1101/2025.11.16.688748 — molecular biology — Posted on 2025-11-17

2394 abcFISH enables multiplexed, single-molecule visualization of circular RNA spatial heterogeneity

Liu, Y.-X.; Jiang, B.-W.; Liu, K.-M.; Yang, L.; Chen, L.-L.

10.1101/2025.11.16.688740 — molecular biology — Posted on 2025-11-17

2395 Anopheles mosquitoes exposed to long-acting antimalarials via drug-spiked bloodmeal absorb drug but do not suffer fitness costs

Goheen, M. M.; Orfano, A.; Dah, S. R.; Foy, B. D.; Brackney, D. E.; Li, F.; Ouedraogo, J. B.; Da, D. F.; Dabire, R. K.; Some, A. F.; Bei, A. K.; Parikh, S.

10.1101/2025.11.13.688204 — microbiology — Posted on 2025-11-17

2396 Fine-tuning of outer membrane-peptidoglycan tethering by the redox-active lipoprotein LppB from Salmonella enterica

Pierre Despas, E. S.; Cho, S.-H.; Iorga, B. I.; Collet, J.-F.

10.1101/2025.11.13.688167 — microbiology — Posted on 2025-11-17

2397 A single small RNA shapes multiple symbiotic traits in rhizobia

Garcia-Tomsig, N. I.; Guedes-Garcia, S. K.; Robledo, M.; Jimenez-Zurdo, J. I.

10.1101/2025.11.14.688489 — microbiology — Posted on 2025-11-17

2398 Aging alters tumor cell - T cell crosstalk to promote breast cancer progression

Yin, S.; Yeung, K. T.; Mamde, S.; Lin, K.; Gandhi, A.; Lei, X.; Davis, A.; Arnold, R.; Yang, J.; Adams, P. D.

10.1101/2025.11.17.688754 — cancer biology — Posted on 2025-11-17

2399 H pilin cyclisation and pilus biogenesis are promiscuous but electrostatic perturbations impair conjugation efficiency

He, S.; Ishimoto, N.; Wong, J. L. C.; David, S.; Sanchez-Garrido, J.; Bogdanov, M.; Beis, K.; Frankel, G.

10.1101/2025.07.15.664925 — microbiology — Posted on 2025-11-17

2400 Surgical Protocol for a Large, Resealable Cranial Window Enabling Longitudinal, Multi-Modal Electrophysiology Recordings of the Mouse Default Mode Network

Kiiso, T.; Partanen, P.; Jacobs, K.; Varga, B. A.; Palva, S.; Palva, M.; Castren, E.; Balin, R.

10.1101/2025.11.13.688186 — neuroscience — Posted on 2025-11-17

2401 A hidden network of gene relationships unifies behavioral and molecular research

Connell, D. R.; Gaiteri, C.; Tasaki, S.

10.1101/2025.11.14.688547 — systems biology — Posted on 2025-11-17

2402 A genome-scale metabolic model of a pathosystem sheds new light on bacterial wilt

Gerlin, L.; Genin, S.; Baroukh, C.

10.1101/2024.12.12.628148 — plant biology — Posted on 2025-11-17

2403 Molecular Insights into Species-Specific ACE2 Recognition of Coronavirus HKU5

Zhang, Y.; Li, Y.; Gao, W.; Li, d.; Xia, L.; Zhou, Q.

10.1101/2025.01.10.632062 — biophysics — Posted on 2025-11-17

2404 SELEX-HTCFQ Platform: Developing DNA Enhancers of ADAR1 to Suppress ZBP1-Dependent Immunopathology

Hu, Y.; Huang, R.; Wang, Y.-F.; Zhu, H.; Ye, Q.-Q.; Wang, J.-M.; Yao, Z.; Wang, Z.-G.; Pang, D.-W.; Liu, S.-L.

10.1101/2025.10.22.683608 — biochemistry — Posted on 2025-11-17

2405 The insulin / IGF axis is critically important controlling gene transcription in the podocyte.

Hurcombe, J. A.; Dayalan, L.; Barrington, F.; Burdet, F.; Ni, L.; Coward, J. T.; Ibberson, M.; Brinkkoetter, P.; Holzenberger, M.; Jeffries, A. R.; Oltean, S.; Welsh, G. I.; Coward, R. J.

10.1101/2024.05.20.594973 — cell biology — Posted on 2025-11-17

2406 Differential sensitivity to LINE 1-induced damage contributes to the expansion of Tet2-deficient HSCs upon chronic inflammatory stress

STOLZ, A.; XUAN, C.; FREITAS, C.; CHELBI, R.; AIT-OUGOURAM, H.; FANDREI, D.; YE, M.; NELSON, E.; MAILLARD, C.; BOHM, M.; EL-CHOUFANI, S.; ZHANG, W.; PORQUET, A.; ISSOULAIENE, K.; MUCHARDT, C.; ZUEVA, E.; GOODHARDT, M.; GARRICK, D.; PORTEU, F.; ELVIRA-MATELOT, E.

10.1101/2025.07.21.665900 — cell biology — Posted on 2025-11-17

2407 Orthogonal representational geometry in dACC underpins human hierarchical reasoning

Xu, C.; Mei, N.; Dong, W.; Hu, R.; Verguts, T.; Chen, Q.

10.1101/2025.11.16.688413 — neuroscience — Posted on 2025-11-17

2408 Multimodal profiling unveils a reversible breast basal-like cell state in AKT-inhibitor resistant tumours

Ratcliffe, C. D. H.; Sparks, H.; Boezio, G. L. M.; Alexandrov, Y.; Jenkins, R. P.; Le Marois, A.; Soro-Barrio, P.; Moughari, F. A.; Hulme, H.; Lee, R. J.; Strohbuecker, S.; Joshi, S.; Ellis, J. K.; Fabrini, G.; Flint, L.; Fortier, A.-M.; Gustafsson, N.; Cunha, A. C.; Tully, L.; Park, M.; Frohlich, F.; MacRae, J. I.; Natrajan, R.; Serio, A.; Briscoe, J.; Riddell, A.; Barry, S. T.; Dunsby, C.; Sahai, E.

10.1101/2025.06.06.658331 — cancer biology — Posted on 2025-11-17

2409 Scalable prediction of symmetric protein complex structures

Yu, V. S.; Demsko, P.; Castells-Graells, R.; Parker, H.; Huang, A.; Chen, C.; Huang, M.; Srinivasan, V.; Ajjarapu, K.; Tofighbakhsh, N.; Yu, R.; Lake, M.; Glanzman, D.; Warren, S.; Alzagatiti, J.

10.1101/2025.11.14.688531 — bioengineering — Posted on 2025-11-17

2410 Field performance of the cardenolide-producing crucifer Erysimum cheiranthoides under herbivore attack and heterospecific competition.

Wang, K.; van Bergen, E.; Zust, T.

10.1101/2023.11.27.568809 — ecology — Posted on 2025-11-17

2411 Reliable repurposing of the antibody interactome inside the cell

O'Shea, C. M.; Shahzad, R.; Aghasoleimani, K.; Newman, S.; Panmanee, J.; Schalkwyk, L. C.; Brooke, G. N.; Benson, F. E.; Trimmer, J. S.; Bosco, D.; Fujisawa, T.; Ichijo, H.; Cashman, N. R.; Engel, S.; Wright, G. S. A.

10.1101/2025.11.16.688718 — molecular biology — Posted on 2025-11-17

2412 Orthogonal representational geometry in dACC underpins human hierarchical reasoning

Xu, C.; Mei, N.; Dong, W.; Hu, R.; Verguts, T.; Chen, Q.

10.1101/2025.11.16.688413 — neuroscience — Posted on 2025-11-17

2413 Neural ensembles for music production recruit more language instruments as rhythmic complexity increases

Lei, U. M.; Tian, Y.; Wang, M.; Mu, Y.; Choi, C. U.; Ho Weatherly, K. I. C.; Sereno, M. I.; Li, D.; Lei, V. L. C.; Huang, R.-S.

10.1101/2025.11.16.688175 — neuroscience — Posted on 2025-11-17

2414 Comparative Cilia Analysis in the Cerebral Cortices of Turtles, Mice, and Macaques

Mirhosseiniardakani, S.; Qiu, L.; Sousounis, K.; Lyon, M.; Chen, X.

10.1101/2025.11.16.688725 — neuroscience — Posted on 2025-11-17

2415 From Tasks to Topology: Dorsal and Ventral Streams Emerge in Optimized Neural Networks

Reza, T.; Jordan, E.; Luo, S.; Patel, K.; Tang, J.; Niemeier, M.

10.1101/2025.11.16.688720 — neuroscience — Posted on 2025-11-17

2416 A Multimodal Atlas Reveals the Anatomical Distribution of Medium Spiny Neuron Subtypes and a Novel RGS6+ Population in the Primate Striatum

Abdelhady, G.; Brull, O. R.; He, J.; Lin, M. K.; Galvan, A.; Pfenning, A. R.; Bostan, A. C.; Stauffer, W. R.

10.1101/2025.11.16.688724 — neuroscience — Posted on 2025-11-17

2417 Associations between canine temperament and salivary levels of cortisol and serotonin

Jung, Y.; Song, Y.; Yang, K.; Yoo, K.; Heo, Y.; Yoon, M.

10.1101/2025.11.16.688729 — physiology — Posted on 2025-11-17

2418 Single-cell transcriptomics identifies altered neutrophil dynamics and accentuated T-cell cytotoxicity in tobacco flavored e-cigarette exposed mouse lungs

Kaur, G.; Lamb, T.; Tjitropranoto, A.; Rahman, I.

10.1101/2025.02.17.638715 — pharmacology and toxicology — Posted on 2025-11-17

2419 Evolution of sideways locomotion in crabs

Taniguchi, J.; Inoue, T.; Kohara, K.; Huang, J.-F.; Hirai, A.; Mizumoto, N.; Takeshita, F.; Kawabata, Y.

10.1101/2025.09.20.677458 — evolutionary biology — Posted on 2025-11-17

2420 SpaTranslator: A deep generative framework for universal spatial multi-omics cross-modality translation

Dong, H.; Mao, S.; Liu, Y.; Tian, T.; Zhang, L.; Wu, J.; Zhang, S.; Jiang, P.; Yin, D.; Xing, X.; Wang, P.; Li, H.

10.1101/2025.11.15.688644 — bioinformatics — Posted on 2025-11-16

2421 Constrained Open Chromatin Regions Reveal Functional Elements Shaping Human Traits

Tomizuka, K.; Koido, M.; Suzuki, A.; Yoshino, S.; Tanaka, N.; Ishikawa, Y.; Liu, X.; Koyama, S.; Ishigaki, K.; Murakawa, Y.; Immune transcript/enhancer consortium (ITEC), ; Yamamoto, K.; Terao, C.

10.1101/2024.10.31.621195 — genetics — Posted on 2025-11-16

2422 EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology

Monziani, A.; Unfried, J. P.; Cvetanovic, T.; Ulitsky, I.

10.1101/2025.04.08.647803 — molecular biology — Posted on 2025-11-16

2423 Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases

Sathe, A.; Zhang, M.; Bai, X.; Kang, J. I.; Meka, R.; Sun, H.; Grimes, S. M.; Khan, A.; Liu, M.; Luksik, A. S.; Lim, M.; Petrisch, C. K.; Jackson, C. M.; Vogel, H.; Shen, J.; Gephart, M.; Han, S.; Ji, H. P.

10.1101/2025.11.14.688538 — cancer biology — Posted on 2025-11-16

2424 Evaluating genetic-ancestry inference from single-cell transcriptomic datasets

Yao, J.; Gazal, S.

10.1101/2025.03.25.645175 — bioinformatics — Posted on 2025-11-16

2425 Heterozygote advantage cannot explain MHC diversity, but MHC diversity can explain heterozygote advantage

Cherry, J. L.

10.1101/2025.05.27.656382 — evolutionary biology — Posted on 2025-11-16

2426 Metal-Binding Ligands Rather Than Redox Active Metabolites Are Essential to Microbially-Induced Corrosion of Cobalt

DeJager, A.; Kirkland, A.; Hinz, A.; McMullin, D. R.; Gregoire, D. S.

10.1101/2025.06.04.657868 — microbiology — Posted on 2025-11-16

2427 T Cell Receptors for Antigen on Intraepitheial Cytolytic T Lymphocytes in Celiac Disease Engage Enterocyte HLA-E and HLA-B

Johnson, J. E.; Agrawal, K.; Al-Lamki, R. S.; Zhang, F.; Xi, W. D.; Liburd, S.; Tobiasova, Z.; Rodriguez, L.; Martins, A. J.; Flavell, R.; Robert, M. E.; Sefik, E.; Pober, J. S.

10.1101/2024.09.03.610908 — immunology — Posted on 2025-11-16

2428 Humans use a dual information-seeking policy to improve noisy inferences outside the explore-exploit tradeoff

Cao, Y.; Almeras, C.; Lee, J. K.; Wyart, V.

10.1101/2025.10.08.681186 — neuroscience — Posted on 2025-11-16

2429 Parallax indicates simple cue-anchoring in the head-direction system

Krausse, S.; Duszkiewicz, A. J.; Neftci, E.; Sommer, F. T.; Renner, A.

10.1101/2025.04.25.650191 — neuroscience — Posted on 2025-11-16

2430 A Druggable Tumor Suppressor and Leukemic Stem Cell Marker

Pan, Y.; Wang, C.; Meng, X.; Zhou, W.; Hammer, R.; Zheng, H.; Hildebrandt, G.; Kang, X.

10.1101/2025.10.16.682831 — cancer biology — Posted on 2025-11-16

2431 Self-supervised AI reveals a lethal discohesive phenotype in lung adenocarcinoma

Rakovic, K.; Pancheva, A.; Quiros, A. C.; Coelho-Lima, J.; He, Z.; Dorward, D. A.; Sereno, M.; Wilson, C.; Dick, C.; Moore, D. A.; Ballantyne, F.; Ficken, C.; Teodosio, A.; Martinelli, S.; Baird, R.; Officer-Jones, L.; Powley, I.; Chang, D.; Miller, C. J.; Yuan, K.; Le Quesne, J.

10.1101/2025.11.12.688049 — cancer biology — Posted on 2025-11-16

2432 Tau-Driven Coordination of Microtubule-Actin Crosstalk in Cell-Sized Vesicles

Akter, M.; Shivers, J. L.; Ding, L.; Dinner, A. R.; Liu, A. P.

10.1101/2025.08.12.669979 — biophysics — Posted on 2025-11-16

2433 MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements

Hera, M. R.; Koslicki, D.; Martinez, C.

10.1101/2025.11.11.687920 — bioinformatics — Posted on 2025-11-16

2434 ELITE: E3 Ligase Inference for Tissue specific Elimination: A LLM Based E3 Ligase Prediction System for Precise Targeted Protein Degradation

Patjoshi, S.; Froehlich, H.; Madan, S.

10.1101/2025.11.05.686884 — bioinformatics — Posted on 2025-11-16

2435 Memory CD4 T cells orchestrate neoadjuvant-responsive niches in colorectal cancer liver metastases

Mayoux, M.; Litscher, G.; Wiesmann, F.; Vermeer, M.; Jorba Adolff, P.; Guido Vinzoni, E.; Gonzalo Nunez, N.; Sparano, C.; Vetter, V. K.; Friebel, E.; Wertheimer, T.; Ficht, X.; Burr, S.; Karimi, A.; Dergun, S.; Schmid, J.; Krishnarajah, S.; Mair, F.; Moor, A.; Burkhard, B.; Sobottka, B.; Tugues, S.

10.1101/2025.08.22.671704 — immunology — Posted on 2025-11-16

2436 Analysis of SIV Spatiotemporal Dissemination Patterns in Rhesus Macaques During Early Rectal Transmission Demonstrates Systemic Infection Does Not Require Viral Local Amplification at the Entry Portal

Cheng, Y.; Chen, J.; Zhao, M.; Mandal, S.; Lewis, M. G.; Luo, M.; Gale, M.; Li, Q.

10.1101/2025.11.12.687929 — immunology — Posted on 2025-11-16

2437 Loss of endogenous tau suppresses APOE4-induced patterned behavioral decline and axon dysmorphia in a C. elegans model of Alzheimers disease

Cardona, E. A.; Wu, Z.; Sarinay Cenik, E.; Webber, C. J.; Bolton, B. M.; Pierce-Shimomura, J.

10.1101/2025.05.06.652574 — neuroscience — Posted on 2025-11-16

2438 Bat power-metabolic profiling of the Egyptian fruit bat Rousettus aegyptiacus reveals distinctive cardiac adaptations

Karlstaedt, A.; Cullen, F.; Drinkwater, R.; Kim, K.; Young, M.; Rossiter, S.; Aksentijevic, D.

10.1101/2025.04.16.649087 — physiology — Posted on 2025-11-16

2439 Spatially Mapping the Mechanical and Structural Properties of the Seedling Uterine Fibroid-Myometrium Interface

Fodera, D. M.; Sutcu, A.; Joasil, A. S.; Therien, A. M.; Jackson, J.; Advincula, A. P.; Chen, X.; Hendon, C. P.; Oyen, M. L.; Korem, T.; Myers, K. M.

10.1101/2025.11.14.687752 — bioengineering — Posted on 2025-11-16

2440 A single large restored patch has lower tree diversity than several smaller ones

GALAN ACEDO, C.; Riva, F.; Fahrig, L.; Holscher, D.; Martin, A. E.

10.1101/2025.11.15.688657 — ecology — Posted on 2025-11-16

2441 Growth-promoting rhizobacteria amend the defense of strawberry plants against sequentially attacking herbivores

Hosseini, A.; Hosseini, M.; Schausberger, P.

10.1101/2025.11.16.688721 — ecology — Posted on 2025-11-16

2442 Predicting current and future distribution of the common waxbill using a mechanistic modelling approach

Vila, M. S.; Pacioni, C.; Reino, L.; Lens, L.; Strubbe, D.

10.1101/2025.11.16.688699 — ecology — Posted on 2025-11-16

2443 Climate warming and urbanization may expand dengue transmission risk in California

Couper, L.; Sipin, T. J.; Sambado, S.; Rennie, Z.; Shanebeck, K. M.; Lyberger, K. P.; Collender, P. P. A.; Ngo, V.; Remais, J. V.; MacDonald, A. J.

10.1101/2025.11.14.688544 — ecology — Posted on 2025-11-16

2444 Approximating spatial processes with too many knots degrades the quality of probabilistic predictions

Ward, E. J.; Anderson, S. C.

10.1101/2025.11.14.688354 — ecology — Posted on 2025-11-16

2445 Interferon signaling promotes early neutrophil recruitment after zebrafish heart injury

Schmid, A. V.; Gagnon, J. A.

10.1101/2025.11.16.688717 — developmental biology — Posted on 2025-11-16

2446 Reliable repurposing of antibody interactome inside the cell

10.1101/2025.11.16.688718 — molecular biology — Posted on 2025-11-16

2447 Recurrent RNA-lipoplex vaccination is required to sustain functional tumor-infiltrating neoantigen-specific CD8 T cells and therapeutic efficacy

Gibson, J. T.; Hornburg, M.; Lehar, S.; Javinal, V.; Liao, L.; McCarron, M. J.; Jones, T. N.; Oei, Y.; Dunlap, D.; Marroquin, K. A.; Lo, A. A.; Bergman, J. H.; Tong, A.-J.; Nissenbaum, A.; Freund, E. C.; Capietto, A.-H.; de la Cruz, C. C.; Sahin, U.; Mellman, I.; Schartner, J. M.; Delamarre, L.

10.1101/2025.11.16.687774 — immunology — Posted on 2025-11-16

2448 Activation parameters, enthalpy-entropy compensation and the temperature-dependent activity of enzymes

McLeod, M. J.; Thorne, R. E.

10.1101/2025.11.16.688712 — biophysics — Posted on 2025-11-16

2449 Pathway and gates for ATG2A-mediated lipid transport in autophagy

Cabezudo, A. C.; Holzer, E.; Martens, S.; Hummer, G.

10.1101/2025.11.16.688672 — biophysics — Posted on 2025-11-16

2450 Predicting gene-specific regulation with transcriptomic andepigenetic single-cell data

Rumpf, L.; Behjati Ardakani, F.; Hecker, D.; Schulz, M. H.

10.1101/2025.11.16.688671 — bioinformatics — Posted on 2025-11-16

2451 Accelerated and High-Accuracy Variant Calling on Oxford Nanopore Technologies Sequencing Data with the Sentieon DNAscope LongRead and Hybrid Pipelines

Hu, J.; Freed, D. N.; Li, Z.; Feng, H.; Chen, H.; Chen, H.

10.1101/2025.11.14.688541 — bioinformatics — Posted on 2025-11-16

2452 mIDEA: An Interpretable Structure-Sequence Model for Methylation-Dependent Protein-DNA Binding Sensitivity

Zhang, Y.; Li, R.; Zhong, J.; Lin, X.

10.1101/2025.11.14.688575 — bioinformatics — Posted on 2025-11-16

2453 Sequence-aware Prediction of Point Mutation-induced Effects on Protein-Protein Binding Affinity using Deep Learning

Zhuang, J.; Li, Z.; Wang, S.; Zheng, R.; Zhang, G.

10.1101/2025.11.15.688659 — bioinformatics — Posted on 2025-11-16

2454 Rectal Transplantation of Fragmented Intestinal Organoids and Crypts Promotes Mucosal Regeneration in DSS-Induced Colitis

Wang, Y.; Xu, X.; Wang, D.

10.1101/2025.11.15.688663 — bioengineering — Posted on 2025-11-16

2455 Ultrafast tyrosine-based cell membrane modification via diazonium salts: a new frontier for biomedical applications

Bouzelha, M.; Pavageau, K.; Renault, S.; Ferron, E.; Jaulin, N.; Marchand, M.; Alvarez-Dorta, D.; Peumery, R.; Scalabrini, M.; Delepee, H.; Pereira, A.; Enouf, E.; Cinier, M.; Adjali, O.; Gouin, S. G.; Retiere, C.; Guilbaud, M.; Deniaud, D.; Mevel, M.

10.1101/2025.11.15.688583 — bioengineering — Posted on 2025-11-16

2456 Master of none: GPRC6A gene loss is more widespread than previously known

Gupta, S.; Patil, A. B.; Soman, A. S.; Vijay, N.

10.1101/2025.11.14.688574 — evolutionary biology — Posted on 2025-11-16

2457 Efficient Bayesian Phylogenetics under the Infinite Sites Model

Specht, I.; Palacios, J. A.

10.1101/2025.11.14.688551 — evolutionary biology — Posted on 2025-11-16

2458 Evolutionary diversity and function of odorant receptors in birds

Driver, R. J.; Marie, M. A.; Ko, V. J.; Meesa, P.; Sun, W.; Li, R. J.; Brewer, M. S.; Lu, H.-Y.; Bennett, K. F. P.; Ojiro, I.; Mantha, N. E.; Matsunami, H.; Balakrishnan, C. N.

10.1101/2025.11.14.688425 — evolutionary biology — Posted on 2025-11-16

2459 Sparse learning for scalable phylogenetic network inference

Rosas-Puchuri, U.; Kolbow, N.; Solis-Lemus, C.; Khanmohammadi, S.; Betancur, R.

10.1101/2025.11.16.688704 — evolutionary biology — Posted on 2025-11-16

2460 Persistent trade-offs balance competition and colonization across centuries

Backman, T.; Cui, J.; Caullireau, E.; Bleak, E.; Bezrukov, I.; Girardi, P.; Hawks, A.; Lasky, J. R.; Latorre, S. M.; Erberich, J. M.; Lopez, L.; Neumann, M.; Perkins, A. M.; Symeonidi, E.; Azadi, P.; Horvath, M. P.; Muszynski, A.; Lang, P. L. M.; Karasov, T. L.; Burbano, H. A.

10.1101/2025.11.16.688059 — evolutionary biology — Posted on 2025-11-16

2461 Temporal changes in macrofungal alpha diversity over four decades in Europe

Krah, F.-S.; Baessler, C.; Zibold, M.; Heilmann-Clausen, J.

10.1101/2025.11.16.688674 — ecology — Posted on 2025-11-16

2462 Butterfly host plant use driven by microclimate not nutritional quality

Langdon, W. B.; Fox, R.; Lewis, O. T.

10.1101/2025.11.15.688506 — ecology — Posted on 2025-11-16

2463 Fast Optimization of Robust Transcriptomics Embeddings using Probabilistic Inference Autoencoder Networks for multi-Omics

Wang, N.; Turner, D.; Feinberg, H.; Nieto Caballero, V. E.; Yuan, D.; Scott, N.; Cardenas, C.; DeBerardine, M.; Dan, S.; Caceres, L.; Schembri, J.; Yao, Z.; Lee, C.; Pillow, J. W.; Krienen, F. M.

10.1101/2025.11.16.686778 — neuroscience — Posted on 2025-11-16

2464 pH-responsive synthetic cells for controlled protein synthesis and release

Hwang, S.-W.; Li, Y.; Green, A. A.; Liu, A. P.

10.1101/2025.11.16.688650 — synthetic biology — Posted on 2025-11-16

2465 Using Large Language Models to Assemble, Audit, and Prioritize the Therapeutic Landscape

Thyagatur Kidigannappa, A.; Sonti, N.; Vijayan, R.; Parikh, A.; Faller, R.

10.1101/2025.11.14.688562 — bioinformatics — Posted on 2025-11-16

2466 Contrastive modelling of transcription and transcript abundance in legumes using PlanTT

Raymond, N.; Zhang, X.; Sheikh, J.; Daveouis, F.; Verma, R.; Cram, D.; Song, H.; Cao, Y.; Kirzinger, M.; Akaniru, D.; Ubbens, J.; Konkin, D.

10.1101/2025.11.15.685414 — bioinformatics — Posted on 2025-11-16

2467 Hybrid modeling framework for bioprocesses with minimal prior knowledge and limited data

Martinez, C.; Rocha Calvette, F.; Pere, M.; Barrientos, M.; Ossandon, S.

10.1101/2025.11.14.688550 — bioengineering — Posted on 2025-11-16

2468 Mechanochemical Energy Landscapes Under Force: Catch-Slip Bonds in T-Cell Activation

bali, y.; Rendall, A.; Quapp, W.

10.1101/2025.11.15.688643 — immunology — Posted on 2025-11-16

2469 Ephaptic coupling and power fluctuations in depression

Pinotsis, D.; Alagapan, S.; Sarikhani, P.; Nauvel, T.; Rozell, C.; Mayberg, H.

10.1101/2025.11.15.688471 — neuroscience — Posted on 2025-11-16

2470 SCAPE: An AI-Driven Platform for Comprehensive Single-Cell Data Analysis

Wu, M.; Wu, H.; Zhou, Y.; CHENG, S.

10.1101/2025.11.15.688526 — cancer biology — Posted on 2025-11-16

2471 ecDNA-driven oncogene super-expressors shape immunoevasive tumor microenvironment

Qiao, K.; Yang, Q.-L.; Li, T.; Chen, X.; Yazgan, Z.; Kim, Y. J.; Gilbreath, C.; Lim, J. Y. S.; Xie, Y.; Sun, X.; Liu, Y.; Jia, Y.; Chen, Z. J.; Huang, H.; Wu, S.

10.1101/2025.11.15.688565 — cancer biology — Posted on 2025-11-16

2472 Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases

10.1101/2025.11.14.688538 — cancer biology — Posted on 2025-11-16

2473 Remodeling of KRAS interactome induced by clinically relevant RAS inhibitors reveals convergent responses and a KRAS-mediated regulation of directional cell migration

Yang, Y.; Cho, C. Y.; Brock, A.; Quackenbush, D.; Chen, K.; Lo, F.; Benes, C. H.; Haling, J. R.

10.1101/2025.11.14.688534 — cancer biology — Posted on 2025-11-16

2474 Mechanism of Ribosome Stalling by the AMD1 C-terminal Tail Arrest Peptide

Maldosevic, E.; Boiocchi, F. S.; Swirski, M. I.; Meiklejohn, K. A.; Yordanova, M. M.; Baranov, P.; Jomaa, A.

10.1101/2025.11.16.688537 — biophysics — Posted on 2025-11-16

2475 Autolamellasomes: An Autophagy-Dependent Parallel Pathway for Bulk ER Degradation and Lysosome Biogenesis

Lu, D.; Zhang, R.; Shi, W.; Zhan, D.; Yang, Y.; Sun, X.; Zhang, H.; Li, Y.; Li, X.; Yu, L.

10.1101/2025.11.16.688694 — cell biology — Posted on 2025-11-16

2476 Immunomodulatory Functions of Intercalated Cells in Kidney Autoimmunity

Avenatti, M. C.; Elizagaray, M. L.; Purba, M. C.; Barachina, F.; Chen, A.; Bastepe, I.; Radavanovic, K.; Battistone, M. A.

10.1101/2025.11.14.688275 — immunology — Posted on 2025-11-16

2477 Autofluorescence imaging reveals the impact of cryopreservation on T cell metabolism and activation response

Pham, D. L.; Kalluri, M.; Weaver, C.; Hsu, A.; Gillette, A.; Zhao, W.; Kearl, T.; Hematti, P.; Shah, N.; Skala, M. C.

10.1101/2025.11.14.688556 — immunology — Posted on 2025-11-16

2478 Transcranial Static Magnetic Stimulation Dissociates the Causal Roles of the Parietal Cortex in Spatial and Temporal Processing

Sugimoto, M.; Kimura, I.; Hayashi, M. J.

10.1101/2025.11.16.688651 — neuroscience — Posted on 2025-11-16

2479 Inhibition governs stimulus preference encoding in mPFC pyramidal neurons during a social choice

Jabarin, R.; Wagner, S.; Netser, S.

10.1101/2025.11.16.688668 — neuroscience — Posted on 2025-11-16

2480 Live longitudinal imaging of meningeal cerebrovascular injury and its sequelae in adult zebrafish

Kraus, A.; Prosper-Santiago, J. S.; Potopova, A.; Prevedel, J.; Castranova, D.; Weinstein, B.

10.1101/2025.11.14.688311 — neuroscience — Posted on 2025-11-16

2481 Cortical response to balance perturbation is more sensitive in modern dancers than nondancers during biomechanically similar balance recovery

Kerr, K. G.; Boebinger, S. E.; Mirdamadi, J. L.; Protzak, J.; Borich, M. R.; Ting, L. H.

10.1101/2025.11.14.688528 — neuroscience — Posted on 2025-11-16

2482 Locus Coeruleus alpha-Synuclein Overexpression Induces Prodromal Parkinsonian Features in Mice

Razquin, J.; DeLasHeras-Garcia, L.; Vaquero-Rodriguez, A.; Gonzalez-Aseguinolaza, G.; Soria-Gomez, E.; Baufreton, J. M.; Bengoetxea, H.; Ortuzar, N.; Ortega, J. E.; Miguelez, C.

10.1101/2025.11.15.688542 — neuroscience — Posted on 2025-11-16

2483 Spontaneous otocoherence of the active ear

Peacock, S. N. S.; Vencovsky, V.; Whiley, R. E.; Mhatre, N.; Bergevin, C.

10.1101/2025.11.14.687084 — neuroscience — Posted on 2025-11-16

2484 No Evidence for Stronger Brain-Behavior Associations in the Bimanual Motor Network of Older Adults

Noven, M.; Lundbye-Jensen, J.; Lundell, H.; Siebner, H. R.; Karabanov, A. N.

10.1101/2025.11.15.688248 — neuroscience — Posted on 2025-11-16

2485 Deciphering the role of brainstem vestibular-related inhibitory networks in shaping postural reflexes in the Xenopus tadpole

Lavenu, L.; Pain, M.; Barrios, G.; Cardoit, L.; Boulain, M.; Duveau, A.; Tostivint, H.; Lambert, F. M.; Fossat, P.; Le Ray, D.

10.1101/2025.11.16.688675 — neuroscience — Posted on 2025-11-16

2486 Cochlear histopathology in macaques after noise-induced temporary threshold shifts

Mondul, J.; Mackey, C. A.; Conner, A. N.; Alek, C. A.; Pitchford, D.; Rausis, O.; Liberman, L.; Liberman, C.; Ramachandran, R.; Hackett, T. A.

10.1101/2025.11.14.688497 — neuroscience — Posted on 2025-11-16

2487 Adipocyte IL-22RA1 signaling promotes structural and functional remodeling of white adipose tissue following acute intestinal damage.

Singh, A.; Shiomitsu, K.; Gaudino, S. J.; Tariq, H.; Kumar, P.

10.1101/2025.11.14.688505 — pathology — Posted on 2025-11-16

2488 Analysis of the possible pathways of cancer cell repopulation after irradiation in vitro

Eidelman, Y.; Shevchenko, E.; Andreev, S.

10.1101/2025.11.12.688027 — cancer biology — Posted on 2025-11-16

2489 ProMPt: A modular preclinical platform for functional modelling of prostate cancer heterogeneity and therapeutic vulnerabilities

Pandell, N.; Househam, J.; Tartagni, M.; Thankamony, A.; Gabel, F.; Rota, R.; Flittner, E.; Gurel, B.; Figueiredo, I.; Seed, G.; Neeb, A. J.; Chol, M.; Yuan, W.; Clohessy, J. G.; Tape, C. J.; Sharp, A.; de Bono, J. S.; Bezzi, M.

10.1101/2025.11.16.688689 — cancer biology — Posted on 2025-11-16

2490 A Pan-Cancer Blueprint of Early Tumor Microenvironment Reprogramming

Bhavya, B.; Agrawal, S.; Pathak, E.; Mishra, R.

10.1101/2025.11.14.688523 — cancer biology — Posted on 2025-11-16

2491 Variable Schwann cell merlin inactivation is targetable with TEAD1 inhibition in schwannomas.

Laws, M. T.; Bhatt, D.; Mandal, D.; Ramavenkat, N.; Asuzu, D. T.; Stoica, S.; Rampalli, I.; Mullaney, D.; Laraba, L.; Odom, H. G.; Ravindra, N.; Varghese, S.; Tang, T.; Zhang, X.; Shern, J. F.; Elkahloun, A.; Sisay, B.; Maric, D.; Johnson, K.; Abdullaev, Z.; Aldape, K.; Hertzano, R. P.; Kim, H. J.; Parkinson, D.; Chittiboina, P.

10.1101/2025.11.15.688608 — cancer biology — Posted on 2025-11-16

2492 Mechanisms of Ub-independent ODC recognition and translocation by the 26S proteasome revealing proteasome's functional adaptability

Cong, Y.; Chen, K.; Wang, Y.; Ye, X.; Ding, Z.

10.1101/2025.11.15.688597 — biophysics — Posted on 2025-11-16

2493 Disordered activation domains enhance DNA target search rate of a bZIP transcription factor

Gaudez, J.; Shammas, S. L.

10.1101/2025.11.15.688632 — biophysics — Posted on 2025-11-16

2494 Deep learning reveals a microprotein atlas in maize and uncovers novel regulators of seed amino acid metabolism

Jia, A.; Yang, Y.; Jin, M.; Zhan, J.; Zhang, M.; Xu, S.; Li, Z.; Tao, K.; Yu, Y.; Feng, L.; Fu, J.; Li, W.; Zhang, P.; Liu, Y.; Xu, J.; Wang, S.; Zhang, Z.; Wang, H.; Yan, J.; Liu, H.

10.1101/2025.11.14.688563 — genomics — Posted on 2025-11-16

2495 SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation

Melendez, D.; Sapci, A. O. B.; Bafna, V.; Mirarab, S.

10.1101/2025.11.14.688492 — genomics — Posted on 2025-11-16

2496 Propagation of genotypic variation across phenotypic levels: a model based on concave relationships unifies disparate observations on phenotypic buffering, dominance, heritability, and inbreeding depression

de Vienne, D.; Coton, C.

10.1101/2025.11.15.688638 — genetics — Posted on 2025-11-16

2497 MLT-11 is necessary for C. elegans embryogenesis and conserved sequences play distinct roles in cuticle structure

Ragle, J. M.; Turzo, A.; Jackson, A.; Vo, A. A.; Pham, V. T.; Daly, K.; Clancy, J. C.; Levenson, M. T.; Lee, A. D.; Ward, J. D.

10.1101/2025.11.14.688552 — developmental biology — Posted on 2025-11-16

2498 Multiple glycoforms of TrkA interact with N-cadherin during trigeminal ganglion neurodevelopment

Halmi, C.; Taneyhill, L.

10.1101/2025.11.14.688512 — developmental biology — Posted on 2025-11-16

2499 CD4⁺ T cells confer transplantable rejuvenation via Rivers of telomeres

Lanna, A.; Valvo, S.; Dustin, M.; Rinaldi, F.

10.1101/2025.11.14.688504 — cell biology — Posted on 2025-11-16

2500 Mechanism of ERK-mediated Rho Activation and Stress Fiber Assembly for Cell Migration

Khan, A. M.; Shawon, J.; Bergman, J. P.; Carney, K. R.; Mendoza, M. C.

10.1101/2025.11.15.688645 — cell biology — Posted on 2025-11-16

2501 A multiplexed approach for genetic screening of human cells by electron microscopy uncovers a critical effector of mitochondrial cristae shape

Hassdenteufel, S.; Bykov, Y. S.; Dubreuil, B.; Noll, K.; Faust, O.; Kamyshinsky, R.; Itkin, M.; Cohen, N.; Malitsky, S.; Peleg, Y.; Albeck, S.; von der Malsburg, K.; Fass, D.; van der Laan, M.; Schuldiner, M.

10.1101/2025.11.15.688601 — cell biology — Posted on 2025-11-16

2502 Nonsense mutations can also increase mRNA levels

Owuamalam, P.; Hossain, M. N.; Brogna, S.

10.1101/2025.11.16.688500 — molecular biology — Posted on 2025-11-16

2503 Cryptococcus neoformans responds to presence of mycobacterium by diversifying its morphologies and remodelling its capsular material

Dambuza, I. M.; Ross, O.; Mukaremera, L.

10.1101/2025.11.16.687457 — microbiology — Posted on 2025-11-16

2504 Antigen presenting cells play a critical role in determining response to regulatory T cell therapy in type 1 diabetes

Dalton, M.; Asante-Asamani, E.; Greene, J. M.

10.1101/2025.11.15.688620 — immunology — Posted on 2025-11-16

2505 Short trains of transcutaneous vagus nerve stimulation increase online corticospinal excitability and pupil size in humans

Denyer, R.; Su, S.; Patnaik, M.; Duque, J.

10.1101/2025.11.14.688461 — neuroscience — Posted on 2025-11-16

2506 UCM-A86 is a selective positive allosteric modulator of GluN1/GluN3 NMDA receptors

Benton, A. J.; Johns, M. R.; Diamant, E.; Rouzbeh, N.; Sorensen, V. P.; Anderson, C. M.; Secci, D.; Zhang, Z.; Rau, A. R.; Clausen, R. P.; Hansen, K. B.

10.1101/2025.11.14.688378 — neuroscience — Posted on 2025-11-16

2507 Quantitative profiling of whole-brain connectomes at single-axon resolution using deep learning and high-resolution light sheet microscopy

Attarpour, A.; Raffiee, M.; Xu, T.; Osmann, J.; Patel, S.; Yu, F.; Au, B.; Clappison, A.; Biparva, M.; Zhu, R.; Crow, A.; Eshaghi Gharagoz, B.; Rozak, M. W.; Aubert, I.; McLaurin, J.; Deisseroth, K.; Stefanovic, B.; Goubran, M.

10.1101/2025.11.14.688340 — neuroscience — Posted on 2025-11-16

2508 Numerosity Is Directly Sensed and Dynamically Transformed in the Human Brain: Evidence from MEG-MRI Fusion

Karami, A.; Castaldi, E.; Eger, E.; Hebart, M.; Piazza, M.

10.1101/2025.11.15.687894 — neuroscience — Posted on 2025-11-16

2509 Deep Learning for Cognitive Task Presence Prediction from Dynamic Functional Connectivity

Chen, K.; Torabi, M.; Jian, J.; Yang, A.; Poline, J.-B.

10.1101/2025.11.14.688561 — neuroscience — Posted on 2025-11-16

2510 Gene network inference and master regulator analysis identifies the estrogen-related receptor gamma (ERRγ) as a therapeutic target for alcohol use disorder (AUD).

Lorrai, I.; Maccioni, R.; Torres, I.; Puliga, R.; Marquez Gaytan, J.; Giorgi, F. M.; Repunte-Canonigo, V.; Sanna, P.

10.1101/2025.11.15.688629 — neuroscience — Posted on 2025-11-16

2511 Delta Opioid Receptors on Parvalbumin Neurons are Necessary for the Convulsant and Anxiolytic Effects of the Delta Agonist SNC80

Walicki, M. C.; Mueller, M. R.; Raigosa Garza, A.; Traynor, J. R.; Levitt, E. S.; Jutkiewicz, E. M.; Birdsong, W. T.

10.1101/2025.11.14.688475 — neuroscience — Posted on 2025-11-16

2512 Microstructural functional coupling as a multimodal biomarker of emotional state transitions in bipolar disorder

Wei, L.; Wang, D.; Xue, S.; Wang, H.

10.1101/2025.11.14.688566 — neuroscience — Posted on 2025-11-16

2513 Population Morphology Implies a Common Developmental Blueprint for Drosophila Motion Detectors

Drummond, N.; Zhao, A.; Borst, A.

10.1101/2025.11.15.688637 — neuroscience — Posted on 2025-11-16

2514 The Turbulent Brain: a toolbox to compute the turbulent dynamical behaviour of whole-brain activity

Sanz Perl, Y.; Vohryzek, J.; Escrichs, A.; Kringelbach, M. L.; Deco, G.

10.1101/2025.11.14.688068 — neuroscience — Posted on 2025-11-16

2515 Consistent drought regulation in grapevine is driven by directional transcription factor activity

Vasquez-Marambio, G.; Moyano, T.; Navarro, D.; Sequeida, A.; Gainza-Cortes, F.; Matus, J. T.; Orellana, A.; Alvarez, J. M.

10.1101/2025.11.14.688560 — plant biology — Posted on 2025-11-16

2516 Local glucocorticoid signalling promotes pancreatic cancer

Veiga-Villauriz, C.; Hussein, H. A. M.; Ward, C. J.; Saji, S. K.; Chakraborty, S. C.; Pramanik, J.; Yamashita-Kanemaru, Y.; Simpson, J.; Laforest, S.; Diez, F.; Homer, N. Z. M.; Roychoudhuri, R.; Halim, T. Y. F.; Mahata, B.

10.1101/2025.11.14.688472 — cancer biology — Posted on 2025-11-16

2517 Characterizing the landscape of gene process dependencies in cancer

Curd, J. B.; Way, G. P.

10.1101/2025.11.14.688518 — cancer biology — Posted on 2025-11-16

2518 Phase-targeting rapid cryofixation of the beating heart and histological analysis unveil contractile state-dependent sarcomere dynamics

Tamura, S.; Mochizuki, K.; Kumamoto, Y.; Morishita, Y.; Yamanaka, M.; Ho, W. J.; Harada, Y.; Fujita, K.; Tanaka, H.

10.1101/2025.11.15.688585 — biophysics — Posted on 2025-11-16

2519 A membrane-driven biochemical oscillator tunable by the volume to surface area ratio

Fischer, J.; Greenberg, E.; Ying, Y. M.; Takeshita, S. S.; Foley, S. L.; Johnson, M. E.

10.1101/2025.11.14.688573 — biophysics — Posted on 2025-11-16

2520 pH-Sensitive Amino Lipid-Driven Pore Formation Enables Endosomal Escape of Lipid Nanoparticles

Singh, A. P.; Shibata, K.; Miyazaki, Y.; Shinoda, W.

10.1101/2025.11.15.688617 — biophysics — Posted on 2025-11-16

2521 Quantum-Coherent Identity Preservation and Substrate-Invariant Embodiment: A Theoretical Framework for Sustained Pure-State Dynamics in Complex Biological Systems

Petalcorin, M. I. R.; Vega, M. A. R.

10.1101/2025.11.15.688570 — biophysics — Posted on 2025-11-16

2522 Conformational dynamics of actin filaments crosslinked with alpha-actinin and their roles in suppressing cofilin-induced helical shortening and cluster formation

Ngo, K. X.; Sumikama, T.; Vuillemot, R.; Nguyen, H. G.; Le, N. T. P.; Grudinin, S.; Uyeda, T. Q.

10.1101/2025.11.16.688667 — biophysics — Posted on 2025-11-16

2523 Adaptive surface sensing enables mammalian sperm navigation in complex environments

Karimi, A.; Jiang, X.; Abbaspourrad, A.

10.1101/2025.11.16.688464 — biophysics — Posted on 2025-11-16

2524 Homogeneous antibody-DNA-conjugates using unmodified oligonucleotides and photo-crosslinkable protein G-HUH endonuclease fusion proteins

Swietlikwoska, A.; Hesen, F.; Graewe, A.; Merkx, M.

10.1101/2025.11.14.688079 — bioengineering — Posted on 2025-11-16

2525 RNMT is recruited to RNA by interaction with RNA G-quadraplexes

Hepburn, L. A.; Granneman, S.; Cowling, V. H.; Clara Silva, J.

10.1101/2025.11.16.688685 — biochemistry — Posted on 2025-11-16

2526 Overcoming the eIF2α Brake in Human Cell-Derived Translation Systems

Aleksashin, N. A.; Shelke, R. R.; Yin, T.; Cate, J. H. D.

10.1101/2025.11.16.688697 — biochemistry — Posted on 2025-11-16

2527 Persistent transcriptomic changes following repeated exposure to wood smoke in non-human primate airway epithelial cells

Holmes, E.; Brown, A. P.; Elston, S. P.; Royer, C. M.; Ji, H.

10.1101/2025.11.14.688533 — genomics — Posted on 2025-11-16

2528 Epigenomic Landscape of Oak (Quercus robur) across Seasons and Generations

Sanchez-Lucas, R.; He, J.; Chirico, M.; Bosanquet, J. L.; Lehner, A. A. B.; Oyesola, K. S.; Hart, K.; MacKenzie, R. A.; Luna, E.; Catoni, M.

10.1101/2025.11.14.688509 — genetics — Posted on 2025-11-16

2529 Defining and detecting global transcriptional amplitude in circadian gene expression

Saint-Antoine, M. M.; Anafi, R.

10.1101/2025.11.14.688559 — cell biology — Posted on 2025-11-16

2530 Prohibitin complexes associate with unique membrane microdomains in cells

Medina, M.; Rahmani, H.; Chang, Y.-T.; Barad, B. A.; Grotjahn, D. A.

10.1101/2025.11.14.688579 — cell biology — Posted on 2025-11-16

2531 DHA Increases Angptl4 Gene Expression and Reduces LPL Activity in a PPARγ-dependent manner in Adipocytes

McTavish, P. V.; Rajna, A.; Brown, L. H.; Elzaanoun, R.; Mutch, D. M.

10.1101/2025.11.15.685896 — cell biology — Posted on 2025-11-16

2532 Environmental and vector detection of African swine fever virus DNA in Vietnam: Evidence for potential transmission through wastewater and Amblyomma javanense ticks

Mai, T. N.; Duong, D. H.; Dong, V. H.; Tran, T. H. G.; Cao, T. B. P.; Huynh, T. M. L.; Bui, T. P.; Dao, V. K.; Nguyen, T. H.; Hoang, T. P.; Bui, T. A. D.; Nguyen, T. L.; Yamazaki, Y.; Yamazaki, W.

10.1101/2025.11.13.688377 — microbiology — Posted on 2025-11-16

2533 E2F1-3 activate polyomavirus early transcription and viral replication

Salisbury, N. J. H.; Amonkar, S.; Roman, A.; Galloway, D. A.

10.1101/2025.11.15.688648 — microbiology — Posted on 2025-11-16

2534 Repeat Opioid Use Modulates Microglia Activity and Amyloid Beta Clearance in a Mouse Model of Alzheimer's Disease

Gogola, J. V.; Wee, S. W. S.; Garcia, A. J.

10.1101/2025.11.14.688256 — neuroscience — Posted on 2025-11-16

2535 Ether lipids influence cancer cell fate by modulating iron uptake

Mansell, R. P.; Müller, S.; Yang, J.-S.; Innes-Gold, S.; Das, S.; Reinhardt, F.; Sigmund, K. J.; Phadnis, V. V.; Wan, Z.; Stark, J.; Hwang, D.; Sindikubwabo, F.; Syx, L.; Servant, N.; Eaton, E. N.; Sampaio, J. L.; Bell, G. W.; Thiru, P.; Viravalli, A.; Deik, A.; Clish, C. B.; Hammond, P. T.; Kamm, R. D.; Cohen, A. E.; Levental, I.; Boehnke, N.; Hsu, V. W.; Levental, K. R.; Rodriguez, R.; Weinberg, R. A.; Henry, W. S.

10.1101/2024.03.20.585922 — cancer biology — Posted on 2025-11-16

2536 Image-based profiling of healthy donor immune cells with Blood Cell Painting reveals novel genotype-phenotype associations

Hogel-Starck, C.; Timonen, V. A.; Atarsaikhan, G.; Mogollon, I.; Polso, M.; Hassinen, A.; Honkanen, J.; David Sarmento, C.; Koski, J.; Soini, J.; Urpa, L.; Ruokoranta, T.; Ahlnas, T.; Juvila, J.; Miettinen, J. J.; Rodosthenous, R.; FinnGen, ; Kilpivaara, O.; Arvas, M.; Heckman, C. A.; Partanen, J.; Daly, M.; Palotie, A.; Ollila, H. M.; Paavolainen, L.; Pietiainen, V.; Pitkanen, E.

10.1101/2024.05.17.594648 — cell biology — Posted on 2025-11-16

2537 Small molecule intervention of actin-binding protein profilin1 reduces tumor angiogenesis in renal cell carcinoma

Gau, D.; Chawla, P.; Xu, K.; Welling, N.; Antonello, J.; Consoli, C.; Wei, M.; Zdancewicz, S.; DaSilva, M.; Varghese, C.; Francoeur, P.; Shi, H.; Chen, X.; Paranjape, A.; Villanueva, F.; Smithgall, T. E.; VanDemark, A. P.; Koes, D. R.; Huryn, D.; Roy, P.

10.1101/2025.07.18.665115 — cell biology — Posted on 2025-11-16

2538 Native spike flexibility revealed by BSL3 Cryo-ET of active SARS-CoV-2 virions

Fukuhara, H.; Dokainish, H. M.; Kita, S.; Tabata, K.; Takasu, A.; Huiskonen, J. T.; Anraku, Y.; Nomai, T.; Someya, T.; Senda, T.; Stuart, D. I.; Sasaki, M.; Orba, Y.; Suzuki, Y.; Sawa, H.; Maenaka, K.

10.1101/2023.10.10.561643 — microbiology — Posted on 2025-11-16

2539 Non-classical NMDA receptor subunit GluN3A in a specialized hippocampal region regulates stress-coping strategies in mice

Zhang, W.; Zhao, M.; Dai, J.; Zhuo, L.; Ye, H.; Wang, J.; Wang, W.

10.1101/2024.04.24.590964 — neuroscience — Posted on 2025-11-16

2540 Reprogrammed SimCells for Antimicrobial Therapy

Dong, Y.; Ji, X.; Dong, T.; Wang, Y.; Bakkeren, E.; Foster, K. R.; Huang, W. E.

10.1101/2025.11.15.688600 — synthetic biology — Posted on 2025-11-16

2541 Distribution, Prevalence of Non-Tuberculous Mycobacteria in Hainan Island and Antibiotic Resistance of Mycobacterium abscessus

Xu, X.; Huang, J.; Wang, H.; Xiang, T.; Liu, J.; Zheng, L.

10.1101/2024.06.09.596927 — microbiology — Posted on 2025-11-16

2542 Deep cerebellar tFUS engages cortical circuits via convergent local and sensory-driven mechanisms

Sariev, A.; Baek, H.; Jung, D.; Kim, H.; Pak, A.

10.1101/2025.11.15.688639 — neuroscience — Posted on 2025-11-16

2543 Predicting stress response trajectories: Differential contributions of limbic and prefrontal regions to cortisol and affective responses

Lipka, R.; Baertl, C.; Kreuzpointner, L.; Giglberger, M.; Konzok, J.; Speicher, N.; Waller, L.; Kudielka, B. M.; Wuest, S.; Walter, H.; Henze, G.-I.

10.1101/2025.11.14.688580 — neuroscience — Posted on 2025-11-16

2544 Four phases and temporal threshold of population calcium response during locomotion in cortical astrocytes

Fedotova, A.; Brazhe, A.; Semyanov, A.

10.1101/2025.11.15.688660 — neuroscience — Posted on 2025-11-16

2545 Autism and Schizophrenia-Associated Pcdh8 Regulates Cortical Development in Mice

Calvo Parra, S.; Barredo Paniagua, G.; Carrillo-Barbera, P.; Garcia Deante, A.; Cwetsch, A. W.

10.1101/2025.11.15.688622 — neuroscience — Posted on 2025-11-16

2546 Improved Stability and Interpretability of Motor Modules Computed with an Autoencoder

Nathella, S. R.; Seamon, B. A.; Young, A. J.; Ting, L. H.

10.1101/2025.11.11.687901 — physiology — Posted on 2025-11-16

2547 Cell-Type-Resolved Isoform Atlas of Human Tissues Reveals Age and Alzheimer's Disease-Associated Splicing Changes

Yamamoto, R.; Fu, T.; Huang, E.; Fraser, A.; Nazim, M.; Xiao, X.; Zaitlen, N.

10.1101/2025.11.14.688520 — bioinformatics — Posted on 2025-11-16

2548 Vertical Transmission of Bovine H5N1 Influenza Virus during Pregnancy and Lactation in Mice

Seibert, B. A.; Parish, M. A.; Talukdar, S. N.; Zhang, T.; Chaulagain, S.; Liu, J. A.; Sachithanandham, J.; Hernandez, O.; Schneider, C.; Coughlan, L.; Bowman, A.; Webby, R. J.; Harkema, J. R.; Pekosz, A.; Klein, S. L.

10.1101/2025.07.07.663583 — microbiology — Posted on 2025-11-15

2549 Robust Deep Learning-based 3D Segmentation and Morphological Analysis of Mitochondria using Soft X-ray Tomography

Yadav, A.; Singh, A.; Deshmukh, A.; Bharadwaj, P.; Baliyan, A.; White, K. L.; Singla, J.

10.1101/2025.10.16.682919 — cell biology — Posted on 2025-11-15

2550 Enhanced reconstruction of Holocene bryophytes from sedimentary ancient DNA using bryophyte-specific primers

Timilsina, B.; Rijal, D. P.

10.1101/2025.11.15.688602 — ecology — Posted on 2025-11-15

2551 Elevated Plasmodium falciparum sexual conversion in HbAC and HbAS red blood cells without altered IgG/IgM levels to trophozoite and stage I gametocyte-specific antigens

Drissi-El Boukili, Y.; Kuehne, V. V.; Moris, P.; Tinto-Font, E.; Goovaerts, O.; Guetens, P.; Moreno-Murillo, A.; Valgaerts, Y.; Natama, M. H.; Cortes, A.; Caljon, G.; Rosanas-Urgell, A.

10.1101/2025.11.15.688532 — microbiology — Posted on 2025-11-15

2552 Bark-associated diazotroph communities are a cryptic source of nitrogen in forests

Gomez Alvarez, P.; Zhang, C.; Jeffrey, L. C.; Leung, P. M.; Cook, P. L. M.; Erler, D. V.; Kohtz, A. J.; Dittmann, J.; Wong, W. W.; Cramb, S.; Euler, S.; Hall, M.; Hopkins, B.; Lee, C.; Johnston, S. G.; Dong, X.; Greening, C.; Maher, D. T.

10.1101/2025.11.14.688567 — microbiology — Posted on 2025-11-15

2553 Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes

Noonan, A. J. C.; Moriniere, L. C.; Rivera-Lopez, E. O.; Patel, K.; Pena, M.; Svab, M.; Kazakov, A.; Deutschbauer, A.; Dudley, E. G.; Mutalik, V. K.; Arkin, A. P.

10.1101/2025.11.15.688630 — microbiology — Posted on 2025-11-15

2554 Predicting Real-life Drinking Scenarios through a Physiological Digital Twin Incorporating Secondary Alcohol Markers

Podeus, H.; Simonsson, C.; Jakobsson, G.; Kronstrand, R.; Nyman, E.; Lövfors, W.; Cedersund, G.

10.1101/2025.11.14.686953 — systems biology — Posted on 2025-11-15

2555 An optimized contact map for GoMartini 3 enabling conformational changes in protein assemblies

Ramirez-Olivos, G. E.; Cofas-Vargas, L. F.; Marrink, S.-J.; Poma, A.

10.1101/2025.11.14.688437 — biophysics — Posted on 2025-11-15

2556 PAF15 stabilizes PCNA on DNA and slows down its sliding dynamics

Kim, D.; Gonzalez-Magana, A.; Langlen Chanu, A.; Bu, G.; Tehseen, M.; Jeong, C.; Jeon, J.-H.; Hamdan, S. M.; De Biasio, A.; Blanco, F. J.; Lee, J.-B.

10.1101/2025.11.15.688598 — biophysics — Posted on 2025-11-15

2557 Multimodal AI Decodes Extreme Environment Functional Dark Matter Beyond Homology

Xu, M.; Wang, D.; Liu, Q.; Jiang, H.; Liu, X.; Li, Y.; Wang, D.; Dong, H.; Yan, X.; Liu, Y.; Xu, A.; Peng, H.; Zhang, Y.; Li, H.; Li, S.; Chen, J.; Wu, X.; Wang, Y.; Li, D.; Liu, S.; Meng, L.; Li, Y.; Xue, C.; Jiang, L.; Zhang, Y.; Song, J.; Wang, M.; Guo, Y.; Li, Z.; Shen, Y.; Fu, X.; Mock, T.; Zhuang, Y.; Xue, C.; Wang, J.; Yang, H.; Xu, X.; Lee, S. M. Y.; Fan, G.; Mao, X.

10.1101/2025.11.15.688615 — bioinformatics — Posted on 2025-11-15

2558 A structural solution to functional HGT: Gene chimerism bypasses mitochondrial expression barriers in parasitic plants

Roulet, M. E.; Ceriotti, L. F.; Gatica-Soria, L. M.; Tulle, W. D.; Sanchez Puerta, M. V.

10.1101/2025.11.14.688545 — genomics — Posted on 2025-11-15

2559 SigRescueR: A Pan-System Framework for Noise Correction and Mutational Signature Identification Across Sequencing Platforms

Nguyen, P.; Zhivagui, M.

10.1101/2025.11.14.688578 — genomics — Posted on 2025-11-15

2560 The challenges of single cell transcriptomics on difficult human tissue: the placenta

Xenakis, T.; Moreno Villena, J. J.; Hall, G. T.; Hillman, S. L.; Sanchez Corrales, Y. E.; Castellano, S.

10.1101/2025.11.14.688483 — genomics — Posted on 2025-11-15

2561 Hippo signaling regulates cuticle pigmentation and dopamine metabolism in Drosophila

Gibson, S. B.; Deal, S. L.; Park, Y.-J.; Sun, B.; Qi, Y.; Mok, J.-W.; Chung, H.-L.; Li, H.; Yamamoto, S.

10.1101/2025.11.13.688152 — genetics — Posted on 2025-11-15

2562 A cold-water coral garden with co-occurring Antipathella subpinnata and Dendrophyllia cornigera in the mesophotic zone of the northern Bay of Biscay

Marques, R.; Le Gal, A.; Boulay, A.; Fournier, S.; Wauters, L.; Patry, Y.; Pommier, T.; Bornens, P.

10.1101/2025.11.14.688465 — ecology — Posted on 2025-11-15

2563 MIRO1 controls energy production and proliferation of vascular smooth muscle cells

Qian, L.; Koval, O. M.; Endoni, B. T.; Juhr, D.; Stein, C. C.; Allamargot, C.; Lin, L.-H.; Guo, D.-F.; Rahmouni, K.; Hinton, A.; Abel, E. D.; Boudreau, R. L.; Streeter, J.; Thiel, W. H.; Grumbach, I. M.

10.1101/2024.08.13.607854 — cell biology — Posted on 2025-11-15

2564 Optimizing Tissue Lysis and DNA Extraction Protocols to Enhance Bacterial Diversity Profiling in the Drosophila melanogaster Gut Microbiome

Quinones-Sanchez, C. L.; Bilbao-Del Valle, J. L.; Urdaneta-Colon, M. A.; Santiago-Rodriguez, T. M.; Rodriguez-Fernandez, I. A.

10.1101/2025.11.15.688634 — microbiology — Posted on 2025-11-15

2565 Study on Dianthus superbus L. against Acute Liver Injury via the Gut-Liver Axis -- Regulation of Gut Microbiota and Tryptophan Metabolism to Activate AhR Signaling

Jiang, X.; Zhuang, Y.; Meng, T.; Meng, T.-w.; Liu, J. l.; Meng, H.; Chang, H.

10.1101/2025.11.14.688543 — microbiology — Posted on 2025-11-15

2566 Systems analysis reveals alternate metabolic states adopted by Mycobacterium tuberculosis across species

Padilla-Gomez, J.; McGinn, R.; Liang, Y.; Libby, K.; Ringel, A.; Evavold, C.; Bryson, B. D.

10.1101/2025.11.15.688116 — microbiology — Posted on 2025-11-15

2567 TraN variants mediate conjugation species specificity of IncA/C, IncH and Acinetobacter baumannii plasmids

He, S.; David, S.; Rattle, J.; Sanchez-Garrido, J.; Wong, J. L. C.; Beis, K.; Frankel, G.

10.1101/2025.11.14.688549 — microbiology — Posted on 2025-11-15

2568 Microbiota reduce Drosophila triacylglyceride density by providing pantothenate

Sannino, D. R.; Booth, J. R.; Blackburn, G.; Dobson, A. J.

10.1101/2025.11.15.688587 — physiology — Posted on 2025-11-15

2569 Joint Biophysical Modeling of Paired Single-Cell RNA and Protein Measurements

Felce, C.; Fang, M.; Pachter, L.

10.1101/2025.11.14.688548 — biophysics — Posted on 2025-11-15

2570 Scalable prediction of symmetric protein complex structures

Yu, V. S.; Demsko, P.; Castells-Graells, R.; Parker, H.; Huang, A.; Chen, C.; Huang, M.; Srinivasan, V.; Ajjarapu, K.; Tofighbakhsh, N.; Yu, R.; Lake, M.; Glanzman, D.; Warren, S.; Alzagatiti, J.

10.1101/2025.11.14.688531 — bioengineering — Posted on 2025-11-15

2571 Aromatic cage-directed azide-methyllysine photochemistry for profiling non-histone interacting partners of the MeCP2 methyl-CpG binding domain

Padhan, J.; Sudhamalla, B.

10.1101/2025.11.15.688584 — biochemistry — Posted on 2025-11-15

2572 Pervasive binding of the stem cell transcription factor SALL4 shapes the chromatin landscape

Chhatbar, K.; Giuliani, S.; Quante, T.; Alexander-Howden, B.; Selfridge, J.; Guy, J.; Auchynnikava, T.; Spanos, C.; Mathieson, T.; Sanguinetti, G.; Bird, A.; Pantier, R.

10.1101/2025.11.14.688441 — genomics — Posted on 2025-11-15

2573 Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells

Godden, A. M.; De Coriolis, J.-C.; Immler, S.

10.1101/2025.11.15.688619 — evolutionary biology — Posted on 2025-11-15

2574 Ancient balanced polymorphism underlies long-standing adaptation for seasonal camouflage in the least weasel

Miranda, I.; Ruivo, R.; Farelo, L.; Alvarenga, M.; Borowski, Z.; Elmeros, M.; Kalthoff, D. C.; Merilä, J.; Müller, J. P.; Schley, L.; Suchentrunk, F.; Sundell, J.; Rodrigues, M.; Santos-Reis, M.; Fernandes, C. R.; Zub, K.; Good, J. M.; Mills, L. S.; Castro, L. F. C.; Dalen, L.; Melo-Ferreira, J.

10.1101/2025.11.14.688436 — evolutionary biology — Posted on 2025-11-15

2575 Understanding Abundances and Behaviors of Shorebirds in Coastal Louisiana

Zenzal, T. J.; Anderson, A. N.; Enwright, N. M.; Thurman, H. R.; Cheney, W. C.; LeBlanc, D.; Dobbs, R. C.; Geary, B.; Waddle, J. H.

10.1101/2025.11.15.688530 — ecology — Posted on 2025-11-15

2576 The BMP ligand Gdf6a Regulates Development of the Zebrafish Craniofacial Skeleton in a Pharyngeal Arch-Specific Manner

Fox, S. C.; Hay, S. M.; Waskiewicz, A. J.; Hocking, J. C.

10.1101/2025.11.14.688493 — developmental biology — Posted on 2025-11-15

2577 Impact of vitamin D deficiency on defective endometrial decidualization and the repressive role of vitamin D receptor (VDR) in the epigenomic network

Yi, M.; Montague Redecke, S. G.; Wang, T.; Bell-Hensley, A.; Li, S.; Massri, A. J.; Jukic, A. M. Z.; DeMayo, F. J.

10.1101/2025.11.14.688535 — molecular biology — Posted on 2025-11-15

2578 ENGINEERING AND PRECLINICAL EVALUATION OF DRIED FOOD-FORMULATED YEAST-SECRETED ANTIBODIES AS PERI-EXPOSURE PROPHYLAXIS AGAINST CLOSTRIDIOIDES DIFFICILE DISEASE.

Roels, C.; Ballegeer, M.; Yilmaz, S.; Grootaert, H.; Meuris, L.; Wyseure, E.; Herman, T.; Haverbeke, P. V.; Vanmarcke, S.; Claes, K.; Roose, K.; Callewaert, N.

10.1101/2025.11.14.688569 — molecular biology — Posted on 2025-11-15

2579 The crystal structure of the activin B:Fst288 complex and computational insights into the broad antagonistic activity and specificity of follistatin

Hok, L.; Walker, R. G.; Howard, J. A.; Mast, J. F.; Kattamuri, C.; Goebel, E. J.; Thompson, T. B.

10.1101/2025.11.14.688564 — molecular biology — Posted on 2025-11-15

2580 Viral protease-Initiated Pyroptosis Activator mRNA therapy as a Universal Antiviral Strategy

Li, L.; Yan, X.-L.; Wang, H.-Y.; Zhou, H.-Y.; Li, Y.-Y.; Li, J.; Zhang, R.-R.; Lv, L.; Huang, X.-Y.; Du, H.; Cao, T.-S.; Ye, Q.; Zhao, H.; Fu, Y.; Wu, A.; Huang, Y.-J.; Qin, C.-F.

10.1101/2025.11.14.688189 — microbiology — Posted on 2025-11-15

2581 The phenotypic landscape of the mycobacterial cell

Herrera, N.; Todor, H.; Kim, L. M.; Burkhart, H. N.; Billings, E.; Warner, T. C.; Lee, S. Y.; Sayegh, N. Y.; Bosch, B.; Kiessling, L. L.; Mancia, F.; Rock, J. M.; Gross, C. A.

10.1101/2025.11.14.688347 — microbiology — Posted on 2025-11-15

2582 Dissecting the homeodomain MAT locus and engineering novel tripolar and bipolar mating systems in Cryptococcus amylolentus

Xiong, L.; Yadav, V.; Sun, S.; Heitman, J.

10.1101/2025.11.14.688536 — microbiology — Posted on 2025-11-15

2583 Clade C MERS-CoV camel strains vary in protease utilizationduring viral entry

Winstone, H. G.; Stillwell, H.; Tan, T.; Cohen, N. A.; Perera, R. A. P. M.; Weiss, S. R.

10.1101/2025.11.15.688481 — microbiology — Posted on 2025-11-15

2584 Architecture of an asymmetric mycobacterial short chain/long chain acyl-CoA carboxylase

Mullapudi, E.; Thai, H. M.; de Carvalho, L.; Wilmanns, M.

10.1101/2025.11.15.688623 — microbiology — Posted on 2025-11-15

2585 Expanding the toolbox for hypervirulent Klebsiella pneumoniae using the social amoeba Dictyostelium discoideum as a virulence biosensor

Perez, I.; Galvez-Silva, M.; Rojas, D.; Ramos, A.; Chen, Y.; Gan, Y.-H.; Chavez, F. P.; Marcoleta, A. E.

10.1101/2025.11.14.688115 — microbiology — Posted on 2025-11-15

2586 Reprogrammed SimCells for Antimicrobial Therapy

Dong, Y.; Ji, X.; Dong, T.; Wang, Y.; Bakkeren, E.; Foster, K. R.; Huang, W. E.

10.1101/2025.11.15.688600 — synthetic biology — Posted on 2025-11-15

2587 Predicting Future Development of Stress-Induced Anhedonia From Cortical Dynamics and Facial Expression

Coley, A.; Batra, K.; Delahanty, J.; Keyes, L.; Pamintuan, R.; Ramot, A.; Hagemann, J.; Lee, C.; Liu, V.; Adivikolanu, H.; Cressy, J.; Jia, C.; Massa, F.; LeDuke, D.; Gabir, M.; Durubeh, B.; linderhof, L.; Patel, R.; Wichmann, R.; Li, H.; Fischer, K.; Pereira, T.; Tye, K.

10.1101/2024.12.18.629202 — neuroscience — Posted on 2025-11-15

2588 Thermodynamically Explicit Kinetics with Potential for Genome-wide Application

Bodeit, O.; Sutthaphirom, C.; Ulas, E. C.; Linding, R.; Chaiyen, P.; Klipp, E.

10.1101/2025.03.02.641056 — biophysics — Posted on 2025-11-15

2589 Different learning algorithms achieve shared optimal outcomes in humans, rats, and mice

Menichini, E.; Pajot-moric, Q.; Low, R.; Pourdehghan, A.; Pedrosa, V.; Vincent, P.; Teachen, L.; Zhou, L.; Akrami, A.

10.1101/2023.01.30.526119 — animal behavior and cognition — Posted on 2025-11-15

2590 Genomic insights into Ceratobasidium sp. associated with vascular streak dieback of woody ornamentals in the United States using a metagenomic sequencing approach

Belay, K.; Abdelrazek, S.; Bily, D.; Gyatso, T.; Avin, F. A.; Bonkowski, J.; Liyanapathiranage, P.; Salamanca, L. R.; Heath, L. S.; Baysal-Gurel, F.; Vinatzer, B.; Mazloom, R.; Kaur, S.

10.1101/2025.08.11.669776 — genomics — Posted on 2025-11-15

2591 Smc5/6 - microtubules binding shapes pericentromeric chromatin

Carre-Simon, A.; Martuzzi, C.; Isler, S.; Batrin, R.; Dahl Pinholt, H.; Foldes, T.; Laflamme, G.; Barbi, M.; Mirny, L.; D'Amours, D.; Fabre, E.

10.1101/2024.11.13.623393 — cell biology — Posted on 2025-11-15

2592 A proteome-wide dependency map of protein interaction motifs

Ambjoern, S.; Meeusen, B.; Kliche, J.; Wang, J.; Garvanska, D.; Kruse, T.; Lopez-Mendez, B.; Mann, M.; Mailand, N.; Hertz, E.; Davey, N. E.; Nilsson, J.

10.1101/2024.09.11.612445 — cell biology — Posted on 2025-11-15

2593 Development of capsaicin-derived prohibitin ligands to modulate the Aurora kinase A/PHB2 interaction and mitophagy in cancer cells

Djehal, A.; Caron, C.; Giordano, D.; Pizza, V.; Farin, K.; Facchiano, A.; Desaubry, L.; Bertolin, G.

10.1101/2024.06.14.598962 — cell biology — Posted on 2025-11-15

2594 Single-cell transcriptomics uncover conserved molecular mechanisms and functional diversification in multilayered epithelia

Merle, C.; Huyghe, M.; Kimber, E.; Faraldo, M. M.; PANTALACCI, S.; Semon, M.; Fre, S.; Journot, R. P.

10.1101/2025.11.14.688286 — cell biology — Posted on 2025-11-15

2595 Causal role of the individual alpha phase in multisensory perception

Rohe, T.; Senkowski, D.

10.1101/2025.11.11.687884 — neuroscience — Posted on 2025-11-15

2596 CMV can spread through plant to plant contact: implications for experimental practices

Chateau, L.; Szadkowski, M.; Theodore, J.; Rimbaud, L.

10.1101/2025.07.30.667662 — plant biology — Posted on 2025-11-15

2597 Nuclear-import receptors remodel the dilute phase to suppress phase transitions of RNA-binding proteins with prion-like domains.

Linsenmeier, M.; Shinn, M. K.; Mumford, T. R.; Liu, V.; Bugaj, L.; Pappu, R. V.; Shorter, J.

10.1101/2025.11.14.688546 — biochemistry — Posted on 2025-11-15

2598 Preference-Based Fine-Tuning of Genomic Sequence Models for Personal Expression Prediction with Data Augmentation

Choi, M.; Cho, B.; Lee, S.

10.1101/2025.11.09.687505 — bioinformatics — Posted on 2025-11-15

2599 Dynamics of dN/dS within recombining bacterial populations

Liu, Z.; Good, B. H.

10.1101/2025.09.09.675256 — evolutionary biology — Posted on 2025-11-15

2600 Half as high for twice as long: male bias in the fertile-age sex ratio

Nitschke, M. C.; Hawkes, K.; Kim, P.

10.1101/2025.05.19.654849 — evolutionary biology — Posted on 2025-11-15

2601 Evolution and development of segmented body plan revealed by engrailed and wnt1 gene expression in the annelid Alitta virens

Kairov, A. I.; Kozin, V. V.

10.1101/2025.01.26.634940 — developmental biology — Posted on 2025-11-15

2602 Shared striatal neurons exhibit context-specific dynamics for internally and externally driven actions

Klee, J. L.; Fernando-Peiris, S.; Suresh, S.; Rodrigues-Vaz, I.; Peterka, D. S.; Costa, R. M.; Athalye, V. R.; Sippy, T.

10.1101/2025.09.18.677137 — neuroscience — Posted on 2025-11-15

2603 Validation of deep learning enabled web based and smartphone optimized application RadAnalyzer to measure vertebral heart size and vertebral left atrial size in dogs

Gordon, S.; Reyes, T.; Baibos-Reyes, T.; Sykes, K. T.; Watson, A.

10.1101/2025.11.13.688321 — physiology — Posted on 2025-11-15

2604 BIRC5 dependency defines a targetable vulnerability in TP53 mutant acute myeloid leukemia

Mamdouh, A. M.; Lim, F. Q.; Mi, Y.; Olesinski, E. A.; Jasdanwala, S.; Lin, X. X.; Ayoub, E.; Tan, J. Y. M.; Bhatia, K. S.; Wang, Y.; Garnaik, S.; Tomar, K.; Sapozhnikova, V.; Chan, C. G. T.; Wang, C.; Mahesh, A. N.; Mertins, P.; Brown, B. D.; Haferlach, T.; Ooi, M.; Lobry, C.; Puissant, A.; Taylor, J.; Abbas, H.; Kornblau, S. M.; Miller, P. G.; Das, S.; Krönke, J.; Itahana, K.; Andreeff, M.; Bhatt, S.

10.1101/2025.05.17.654633 — cancer biology — Posted on 2025-11-15

2605 Differential expression of mitochondria-associated genes in clinical samples of Plasmodium falciparum showing severe manifestations

Gujarati, S.; Singal, B. R.; Gupta, D.; Kochar, S. K.; Kochar, D. K.; Das, A.

10.1101/2025.05.24.655897 — genomics — Posted on 2025-11-15

2606 Genome-wide screen for deficiencies modifying Cyclin G-induced developmental instability in Drosophila melanogaster.

Ribeiro, V.; Da Costa, M.; Dardalhon-Cumenal, D.; Dupont, C. A.; Gibert, J.-M.; Mouchel-Vielh, E.; Thomassin, H.; Randsholt, N. B.; Debat, V.; Peronnet, F.

10.1101/2025.07.31.667991 — genetics — Posted on 2025-11-15

2607 A Novel 3D Visualization Method in Mice Identifies the Periportal Lamellar Complex (PLC) as a Key Regulator of Hepatic Ductal and Neuronal Branching Morphogenesis

Xu, T.; Cao, F.; Zhou, R.; Chen, Q.; Zhong, J.; Wang, Y.; Xiao, C.; Yin, B.; Chen, C.; Zhao, C.

10.1101/2025.08.29.673025 — developmental biology — Posted on 2025-11-15

2608 Tryptophan-Driven Metabolomic Shift in Acidobacteriaceae Reveals Phytohormones and Antifungal Metabolites

Zumkeller, C. M.; Hartwig, C.; Lanzalonga, W.; Patras, M. A.; Liu, Y.; Marner, M.; Mihajlovic, S.; Spohn, M. S.; Schaeberle, T. F.

10.1101/2025.10.02.680145 — microbiology — Posted on 2025-11-15

2609 Genetic Convergence Analysis of CRISPR Perturbations Deciphers Gene Functional Similarity

Zhang, T.; Shang, E.; Roeder, K.

10.1101/2025.11.13.688060 — genomics — Posted on 2025-11-15

2610 Loss of MGST1 during fibroblast differentiation enhances vulnerability to oxidative stress in human heart failure

Youness, M.; Ronda, O. A. H. O.; Pradhan, A.; Rega, F.; Sipido, K.; Roderick, L.

10.1101/2025.11.14.688417 — cell biology — Posted on 2025-11-15

2611 Learning in nonstationary environments with minimal neuralcircuitry

Raman, D. V.; Dunne, C. R.; Davyson, K.; O'Leary, T.

10.1101/2025.11.13.688216 — neuroscience — Posted on 2025-11-15

2612 Fixel-Based Analysis reveals microstructural visual pathway changes associated with retinal remodeling in retinitis pigmentosa

Righetti, G.; Cuevas Villanueva, V.; Reith, M.; Wolfram, L.; Merle, D. A.; Kühlewein, L.; Braun, C.; Stingl, K.; Stingl, K.

10.1101/2025.11.14.688435 — neuroscience — Posted on 2025-11-15

2613 Trial-Level Sequence Modeling Reveals Hidden Dynamics of Dual-Task Interference

den Otter, R.; Dame, A.; Stuit, S.; van Maanen, L.

10.1101/2025.11.14.688220 — neuroscience — Posted on 2025-11-15

2614 Degraded ecosystem soil and type 2 diabetes gut microbiomes share altered potential metabolism for sugars, lignin and branched-chain fatty acids: a blind spot for global health?

Liddicoat, C.; Eijkelkamp, B. A.; Cavagnaro, T. R.; Robinson, J. M.; Wallace, K. J.; Barnes, A. D.; Harmsworth, G.; Keating, D. J.; Edwards, R. A.; Breed, M. F.

10.1101/2025.03.11.642605 — genomics — Posted on 2025-11-15

2615 The balance between stability and plasticity of the Visual Word Form Area in dyslexia

Mitchell, J. L.; Yablonski, M.; Stone, H. L.; Jimenez, M.; Takada, M.; Tang, K. A.; Tran, J. E.; Chou, C.; Yeatman, J. D.

10.1101/2025.01.14.632854 — neuroscience — Posted on 2025-11-15

2616 Innate immune signaling in a sponge reveals ancient origin of host-symbiont recognition

Yang, B.; Yuen, B.; Yuan, H.; Degnan, B. M.; Degnan, S. M.

10.1101/2025.05.27.656460 — evolutionary biology — Posted on 2025-11-15

2617 Context-specific configuration of orthogonal integrator dynamics for flexible foraging decisions

Kingsbury, L.; Zhang, G.; Sanguinetti-Scheck, J. I.; Uchida, N.

10.1101/2025.11.14.688540 — neuroscience — Posted on 2025-11-14

2618 Relative phase of membrane potential theta oscillations between individual hippocampal neurons code space

Athif, M.; Malmberg, S.; Mount, R. A.; Patel, K.; Wang, Y.; Shaw, D.; Ravasio, C.; Xiao, S.; Rillosi, E.; Tseng, H.-a.; Plutkis, S. E.; Grimm, J. B.; Lavis, L.; Mertz, J.; Han, X.; Hasselmo, M. E.

10.1101/2025.11.14.688496 — neuroscience — Posted on 2025-11-14

2619 Dysregulation of transcription networks regulating oligodendrogenesis in age-related decline in CNS remyelination

Dimas, P.; Morabito, S.; Rawji, K. S.; Wang, Q.; Krause, F. N.; Cubillos, J.; Belaadi, N.; Assinck, P.; Shi, Z.; Cao, Z.; Heyn, H.; Kawaguchi, R.; Geschwind, D. H.; Swarup, V.; Franklin, R. J.

10.1101/2025.11.14.688494 — neuroscience — Posted on 2025-11-14

2620 Multimodal cell lineage reconstruction in the hindbrain reveals a link between progenitor origin and activity patterning

Blanc, M.; Meister, L.; Lemon, W. C.; Fiuza, U.-M.; Keller, P. J.; Espinosa Medina, I.; Pujades, C.

10.1101/2025.11.14.688499 — developmental biology — Posted on 2025-11-14

2621 The Role of TCF7L2 in Regulating Energy Metabolism in Thalamocortical Circuitry and its Broader Impact on Social Behavior

Nagalski, A.; Kozinski, K.; Baggio, S.; Szewczyk, L. M.; Lipiec, M. A.; Mussulini, B. H. M.; Gabriel, M. O.; Bem, J.; Meyza, K.; Goncerzewicz, A.; Kondrakiewicz, L.; Danielewski, K.; Golowicz, D.; Kiryk, A.; Wojda, U.; Kazimierczuk, K.; Knapska, E.; Chacinska, A.; Wisniewska, M. B.

10.1101/2025.11.14.684361 — neuroscience — Posted on 2025-11-14

2622 A Context-Sensitive Neural Hierarchy for Evaluating Temporal Structure in Primate Vocalizations

Cui, D.; Loewith, M.; Dureux, A.; Zanini, A.; Everling, S.

10.1101/2025.11.14.688454 — neuroscience — Posted on 2025-11-14

2623 Functional Genomic Profiling of Schizophrenia-Associated Genes Reveals Key Microglial Regulators

Horng, J. E.; McCrea, L. T.; Batorsky, R. E.; Bowen, J. J.; Boschian, C.; Song, Y.; Perlis, R. H.; Sheridan, S. D.

10.1101/2025.11.14.688490 — neuroscience — Posted on 2025-11-14

2624 The extracellular ATP/P2X7R signaling axis drives early neuroinflammation and neuronal hyperexcitability in an Alzheimer's disease mouse model

Arnst, N.; Bedetta, M.; Redolfi, N.; Falzoni, S.; Kachappilly, N.; Tarantini, M.; Basso, E.; Giuliani, A. L.; Sandona, D.; Di Virgilio, F.; Lia, A.; Greotti, E.; Pizzo, P.

10.1101/2025.11.14.688405 — neuroscience — Posted on 2025-11-14

2625 Dephosphorylation of YES kinase-mediated co-chaperone DNAJB6b phosphorylation attenuates tau protein aggregation

Lin, M.-C.; Chen, H.-Y.; Lin, T.-S.; Lin, S.-J.; Lin, P.-J.; Liao, C.-Y.; Chan, N.-L.; Lin, C.-H.; Teng, S.-C.

10.1101/2025.11.14.688390 — neuroscience — Posted on 2025-11-14

2626 Promotion of seed germination in Echinochloa crus-galli with atmospheric air plasma

Nakamura, Y.; Ohnishi, Y.; Oshimo, K.; Hiramatsu, R.; Shindo, M.; Tominaga, T.; Terabayashi, S.; Takagi, D.; Matsuo, M.

10.1101/2025.11.14.688452 — plant biology — Posted on 2025-11-14

2627 Clustering of Omic Data Using Semi-Supervised Transfer Learning for Gaussian Mixture Models via Natural-Gradient Variational Inference: Method and Applications to Bulk and Single-Cell Transcriptomics

Jia, Q.; Goodrich, J. A.; Conti, D. V.

10.1101/2025.11.13.688299 — bioinformatics — Posted on 2025-11-14

2628 A De Novo Algorithm for Allele Reconstruction from Oxford Nanopore Amplicon Reads, with Application to CYP2D6

Brown, S. D.; Dreolini, L.; Minor, A.; Mozel, M.; Wong, N.; Mar, S.; Lieu, A.; Khan, M.; Carlson, A.; Hrynchak, M.; Holt, R. A.; Missirlis, P. I.

10.1101/2025.11.06.687066 — bioinformatics — Posted on 2025-11-14

2629 Intestinal RICT-1/Rictor regulates larval germline progenitors via vitellogenins VIT-1 and VIT-3 in C. elegans

Kloock, A.; Hubbard, E. J. A.

10.1101/2025.01.08.632040 — developmental biology — Posted on 2025-11-14

2630 Polymorphic IGLV6-57 AL amyloid fibrils and features of a shared folding pathway

Bassett, P. T.; Nguyen, B. A.; Singh, V.; Garrett, P. T.; Moresco, J. J.; Eddy, J.; Afrin, S.; Pekala, M.; Lopez, C.; Evers, B. M.; Ahmed, Y.; Pedretti, R.; Grodin, J. L.; Roth, L. R.; Kaur, G.; Chung, S.; Morgan, G. J.; Yates, J. R.; Saelices, L.

10.1101/2024.12.04.626857 — molecular biology — Posted on 2025-11-14

2631 Inherited retinal degenerations: PARP regulates calpain activation via TRPM2 channels in rd1 mouse photoreceptors

Yan, J.; Lei, K.; zhao, Z.; Yang, Q.; Wang, L.; Yang, Q.; Jiao, K.; Hu, Z.; Paquet-Durand, F.

10.1101/2025.11.13.688383 — neuroscience — Posted on 2025-11-14

2632 Charting the Normal Development of Structural Brain Connectivity in Utero using Diffusion MRI

Karimi, D.; Li, B.; Taymourtash, A.; Jaimes, C.; Grant, E. P.; Warfield, S. K.

10.1101/2025.09.14.676101 — neuroscience — Posted on 2025-11-14

2633 Traces of parenthood but not pregnancy loss in UK Biobank structural brain MRI data

Fischer, J. L.; Skalkidou, A.; Derntl, B.; Kaufmann, T.

10.1101/2025.11.14.688235 — neuroscience — Posted on 2025-11-14

2634 Tanycyte-mediated synapse pruning shapes hypothalamic circuits controlling metabolism.

Dali, R.; Kolotuev, I.; Lopez-Rodriguez, D.; Gavini, C.; Deglise, T.; Langlet, F.

10.1101/2025.11.14.688419 — neuroscience — Posted on 2025-11-14

2635 An image-computable spatio-chromatic receptive field model of the midget retinal ganglion mosaic across the retina

Cottaris, N. P.; Wandell, B.; Brainard, D. H.

10.1101/2025.10.20.683437 — neuroscience — Posted on 2025-11-14

2636 Working Memory Selectively Modulates Subjective Perception: A Pilot Study

Che, W.; Nakamura, T.; Lau, H.

10.1101/2025.11.14.688399 — neuroscience — Posted on 2025-11-14

2637 Cis-Regulatory Editing of Peptide Signaling Rewires Plant Root Architecture

Liao, J. C.-Y.; Bagman, A.-M.; Liu, A. J.; Shim, Y.; Brady, S. M.; Ronald, P. C.

10.1101/2025.09.29.679155 — plant biology — Posted on 2025-11-14

2638 Panax notoginseng saponins protect the blood brain barrier against oxidative stress by activating the Akap12/PI3K/AKT/AQP1 signaling axis

Fan, L.; Qu, S.; Miao, C.; Wu, D.; Rao, Y.; Xu, W.; He, Y.; Ding, R.; Song, G.

10.1101/2025.11.14.688373 — pharmacology and toxicology — Posted on 2025-11-14

2639 NLRP12-mediated Glioblastoma-Astrocyte Cross-talk Promotes Tumor Growth

Rajkhowa, S.; Meena, D.; Sha, L.; Janu, V.; Garg, M.; Revanth, M.; Chakraborty, D. B.; Jha, D.; Jha, S.

10.1101/2025.11.13.688374 — cancer biology — Posted on 2025-11-14

2640 A Critical Re-evaluation of the Somatic Mutation Theory (SMT)Conceptual and Quantitative Limits of the Cell-Centric Paradigm

Liisberg, C.; Olsen, F. E.

10.1101/2025.10.17.683033 — cancer biology — Posted on 2025-11-14

2641 A Mass Spectrometry-Based Interactome Study on Anisomelic Acid and Its Effects on HPV16 E7

Santos Silva, M.; Coelho-Rato, L. S.; Delshad, N.; Tarkhova, T.; Edman, J.; Paul, P.; Meinander, A.; Eriksson, J. E.

10.1101/2025.11.14.688426 — cancer biology — Posted on 2025-11-14

2642 Spatial deconstruction of the plasma membrane

Mandala, V. S.; Zhao, C.; Chen, Q.; Gross, S.; Geri, J. B.; MacKinnon, R.

10.1101/2025.11.14.688519 — biophysics — Posted on 2025-11-14

2643 Mesoscopic viscous-to-elastic transition underlies aging of biomolecular condensates

Li, M.; Lin, J.

10.1101/2025.11.13.688393 — biophysics — Posted on 2025-11-14

2644 Genolator: A Multimodal Large Language Model Fusing Natural Language, Genomic, and Structural Tokens for Protein Function Interpretation

Danner, M.; Islam, T.; Begemann, M.; Kraft, F.; Elbracht, M.; Kurth, I.; Krause, J.

10.1101/2025.11.14.688396 — bioinformatics — Posted on 2025-11-14

2645 Denoising image-based spatial transcriptomics data with DenoIST

Kwok, A. W. C.; Vannan, A.; Banovich, N. E.; Kropski, J. A.; Shim, H.; McCarthy, D. J.

10.1101/2025.11.13.688387 — bioinformatics — Posted on 2025-11-14

2646 Batch-Harmonized Machine Learning Framework for Cross-Cohort RNA Biomarker Discovery in Pancreatic Adenocarcinoma

Markarian, M. B.; Houssigian, G. V.

10.1101/2025.11.14.688421 — bioinformatics — Posted on 2025-11-14

2647 PMGen: From Peptide-MHC Prediction to Neoantigen Generation

Asgary, A. H.; Aleyasin, A.; Mehl, J. A.; Ludewig, B.; Mishto, M.; Liepe, J.; Soeding, J.

10.1101/2025.11.14.688404 — bioinformatics — Posted on 2025-11-14

2648 Elucidating the conformational dynamics of the mitochondrial localization signal, M3, of TDP-43 and accessing potential inhibitors using molecular docking and simulation

Balaji, R.; Joshi, H.; Patel, B. K.

10.1101/2025.11.13.688389 — bioinformatics — Posted on 2025-11-14

2649 Integrating Genomics into Multimodal EHR Foundation Models

Amar, J.; Liu, E.; Breschi, A.; Zhang, L.; Kheradpour, P.; Li, S.; Soleymani Lehmann, L.; Giulianelli, A.; Edwards, M.; Jia, Y.; Nola, D.; Mani, R.; Vats, P.; Tetreault, J.; Chen, T. J.; McLean, C. Y.

10.1101/2025.10.26.684668 — bioinformatics — Posted on 2025-11-14

2650 Joint attention biases dogs' memory towards object identity

Sommese, A.; Thiele, M.; Völter, C.

10.1101/2025.11.14.687955 — animal behavior and cognition — Posted on 2025-11-14

2651 Systematic morphological profiling of human and mouse miRNAs in 24M single cells

Wagner, J.; Smillie, C. L.; Sirey, T. M.; Khamseh, A.; Ponting, C. P.; Beentjes, S. V.

10.1101/2025.11.14.687149 — genomics — Posted on 2025-11-14

2652 Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses

Ries, H. J.; Lalli, J.; Florek, K. R.; Barlow, S.; Goss, M.; Griesser, R.; Danz, T.; Uzicanin, A.; Temte, J.; Friedrich, T. C.

10.1101/2025.11.04.686470 — evolutionary biology — Posted on 2025-11-14

2653 Planar cell polarity-directed cell crawling drives polarized hair follicle morphogenesis

Sharan, R.; Du, X.; Leybova, L.; Sewavi, A.; Biswas, A.; Devenport, D.

10.1101/2025.11.13.688366 — developmental biology — Posted on 2025-11-14

2654 Paternal over- and under-nutrition program fetal and placental development in a sex-specific manner in mice

Morgan, H. L.; Eid, N.; Holmes, N.; Carlile, M.; Henson, S.; Sang, F.; Wright, V.; Castellanos-Uribe, M.; Khan, I.; Nazar, N.; May, S.; Mitchell, R.; Lopes, F.; Robinson, R. S.; Coppi, A. A.; Batra, V.; Watkins, A. J.

10.1101/2025.11.14.688439 — developmental biology — Posted on 2025-11-14

2655 Single-cell quantification of senescence burden reveals cell type-specific ageing dynamics across organs

Cherqui, U.; Sopher, I.-R.; Akiva, H.; Menahem, O.; Kopitman, E.; Blecher-Gonen, R.; Keren-Shaul, H.; Rachmian, N.; Mayo, A.; Alon, U.; Gal, H.; Krizhanovsky, V.

10.1101/2025.11.14.688272 — cell biology — Posted on 2025-11-14

2656 PIKfyve is an essential component of the endolysosomal pathway within photoreceptors and the retinal pigment epithelium

Attia, K.; Anjum, I.; Lingrell, S.; Benson, M.; Macdonald, I. M.; Hocking, J. C.

10.1101/2025.09.15.676399 — cell biology — Posted on 2025-11-14

2657 Single-cell transcriptomics uncover conserved molecular mechanisms and functional diversification in multilayered epithelia

Merle, C.; Huyghe, M.; Kimber, E.; Faraldo, M. M.; PANTALACCI, S.; Semon, M.; Fre, S.; Journot, R. P.

10.1101/2025.11.14.688286 — cell biology — Posted on 2025-11-14

2658 Yuanyang allele pairs enable engineered obligate co-inheritance for population replacement and suppression

Li, Y.; Qiao, Z.; Xian, C.; Hu, S.; Jia, J.; Li, W.; Tian, M.; Yang, R.; Zhang, Q.; Hua, H.; Champer, J.; Ma, W.; Zhu, Z.

10.1101/2025.11.14.688408 — molecular biology — Posted on 2025-11-14

2659 Disruption of the FGFR1-FGF23-Phosphate Axis and Targeted Therapy in a Murine Model of Osteoglophonic Dysplasia

Ascone, G.; Kaur, R.; Mehran, A.; Rivas, C.; Galisteo, R.; Ginty, I.; Cloud, S.; MacLarty, A.; Li, L.; Elliot, G.; Riminucci, M.; Corsi, A.; Watkins-Chow, D. E.; Garrett, L.; Hartley, I. R.; Fernandez de Castro Diaz, L.; Ferreira, C. R.

10.1101/2025.11.14.680268 — molecular biology — Posted on 2025-11-14

2660 Structure and functional analyses of Vaccinia virus entry- fusion complex component J5 protein

Chang, W.; Chiu, H.-J.; Tzou, D.-L.; Carillo, K. J.; Hsieh, L. T.-H.

10.1101/2025.11.13.688282 — microbiology — Posted on 2025-11-14

2661 A CRP-Mediated Coherent Type 4 Feed-Forward Loop Involving Glucose-Regulated LacI in Escherichia coli

Lin, Y.-C.-D.

10.1101/2025.11.14.688166 — microbiology — Posted on 2025-11-14

2662 Heightened empathic responses led by imbalanced cortico-amygdala circuit in Shank3 autism mouse model

Qiao, S.; Jiang, Y.-h.

10.1101/2025.11.14.688290 — neuroscience — Posted on 2025-11-14

2663 Exercise remodels hippocampal extracellular matrix to alleviate chondroitin-4-sulphate-induced memory impairment.

Doody, N. E.; Stevens, B.; Smith, N. J.; Lall, V. K.; Boxall, S. A.; Hughes, R. E.; Akam, E. C.; Askew, G. N.; Kwok, J. C. F.; Ichiyama, R. M.

10.1101/2025.11.14.688432 — neuroscience — Posted on 2025-11-14

2664 MyeliMAP: Studying Oligodendrocyte Function in Brain Networks

Ahuja, K.; Clement, B. F.; Amos, G.; Küchler, J.; Wierda, K.; Chin Chai, Y.; Moons, L.; Verfaillie, C.

10.1101/2025.11.14.688409 — neuroscience — Posted on 2025-11-14

2665 Context-dependent benefits of training and reminders in visual skill learning

Kolken, Y. J. T.; Roberts, M. J.; Naseri, P.; Martino, F. D.; Censor, N.; Weerd, P. D.

10.1101/2025.11.14.688438 — neuroscience — Posted on 2025-11-14

2666 Predictive Networks Generate Motion-Induced Color Illusions

Ueda, K.; Sinapayen, L.; Watanabe, E.

10.1101/2025.11.13.688160 — neuroscience — Posted on 2025-11-14

2667 DNA adduct and mutational profiles reveal a threshold of cellular defenses against N-nitrosodimethylamine administered to mice in drinking water

Gubina, N. E.; Volk, L. B.; Dormitzer, A. F.; Michelsen, E. M.; Pribyl, L. J.; Corrigan, J. J.; Dalvie, E. D.; Armijo, A. L.; Norales, M. M.; Bugher, N. A.; Schonvisky, K. M.; Plata, D. L.; Engelward, B. P.; Croy, R. G.; Essigmann, J. M.; Fedeles, B. I.

10.1101/2025.11.13.687536 — pharmacology and toxicology — Posted on 2025-11-14

2668 Morphological determinants of glycosylation efficiency in Golgi cisternae

Revell, C. K.; Stevenson, N. L.; Lowe, M.; Jensen, O. E.

10.1101/2025.11.14.688478 — biophysics — Posted on 2025-11-14

2669 Structural and Binding Properties of Dps: A Nucleoid Associated Protein

Gaines, M.; Parrell, D.; Rajek, K.; Garvis, S.; Sibert, B.; Wright, E. R.

10.1101/2025.11.14.688440 — biophysics — Posted on 2025-11-14

2670 Localized control of protein phase separation via membrane binding

LuValle-Burke, I.; Bartolucci, G.; Sun, D.; Zhao, X.; Weber, C. A.; Honigmann, A.

10.1101/2025.11.14.688424 — biophysics — Posted on 2025-11-14

2671 Reconstructing Ambient Temperature in Forensic Death Time Estimation

Shanmugam, J. S.; Hubig, M.; Schenkl, S.; Muggenthaler, H.; Springer, S.; Weiser, M.; Sudau, J.; Shah, F.; Mall, G.

10.1101/2025.11.14.688394 — biophysics — Posted on 2025-11-14

2672 Social Information Quality Determines Learned Collective Foraging Strategies

Chirkov, V.; Romanczuk, P.

10.1101/2025.11.14.688412 — biophysics — Posted on 2025-11-14

2673 Kinetic modeling of continuous meta-fermentation quantifies metabolic activity in a complex microbial system

Koga, T.; Kajimoto, K.; Ishizu, M.; Hamada, H.; Miyamoto, H.; Oshiro, M.; Sakai, K.; Tashiro, Y.

10.1101/2025.11.13.688382 — bioinformatics — Posted on 2025-11-14

2674 Mechanistically Interpretable Toxicity Prediction Through Multimodal Integration of Structure and Transcriptomics

Cattebeke, G.; Vermeersch, A.-S.; Cappoen, D.; Deforce, D.; Nieuwerburgh, F. V.

10.1101/2025.11.14.686754 — bioinformatics — Posted on 2025-11-14

2675 Modular mRNA lipid nanoparticle platform rescues diverse genetic male infertility

Jiang, Q. K.; Su, K.; Luo, H.; Wang, H.; Luo, J.; Zhong, Y. J.; Li, Q.; Zhang, Z.; Zhang, H.; He, B.; Zhang, L.; Li, Q.; Ma, L. X.; Cui, H.; Ma, J.; Yang, X.; Li, L.; Yuan, Z.; Liu, S.; Li, X. Z.

10.1101/2025.11.13.688269 — bioengineering — Posted on 2025-11-14

2676 An Engineered Living Material with pro-angiogenic activity inducible by near-infrared light

Chatterjee, A.; Meier, S.; Trujillo, S.; Moeglich, A.; Sankaran, S.

10.1101/2025.11.14.688407 — bioengineering — Posted on 2025-11-14

2677 Screening for residues in Atg11, a central organizer of selective autophagy in yeast, important for binding with Atg9

Sherpa, C. D.; Woghiren, P.; Leonello, E.; Abdel-Khalek, M.; Schuessler, B. J.; Vermaas, J. V.; Backues, S. K.

10.1101/2025.11.14.688473 — biochemistry — Posted on 2025-11-14

2678 Switching Metazoan Fatty Acid Synthase Between Reducing and Non-reducing Elongation Mode via Programming of the Ketoreductase Domain

Ludig, D. L.; Herber, A.; Grininger, M.

10.1101/2025.11.14.688466 — biochemistry — Posted on 2025-11-14

2679 Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1

Andree, G. A.; Stier, L.; Schmiederer, K.; Thielen, A.; Schmid, L.; Maiwald, S. A.; Du, J.; von Gronau, S.; Strasser, C.; Mueller, J.; Henneberg, L. T.; Guyot, C.; Kleiger, G.; Mann, M.; Murray, P. J.; Schulman, B. A.

10.1101/2025.11.14.688510 — biochemistry — Posted on 2025-11-14

2680 Development and validation of an exome-wide SNP genotyping array for genomic prediction, GWAS and assessment of introgressive hybridization between black and red spruces, and transferability to white and Norway spruces

Gerardi, S.; Gagnon, F.; Pavy, N.; Laroche, J.; Nadeau, S.; Boyle, B.; Soro, A.; Millican, S.; Thompson, I.; Thomson, A.; Perron, M.; Bockstette, S.; Beaulieu, J.; Lenz, P.; Bousquet, J.

10.1101/2025.11.14.688480 — genomics — Posted on 2025-11-14

2681 NF2 lacking exon 11 isoform induced by antisense gene therapy is able to recover partially merlin deficiency on NF2-related Schwannomatosis iPSC-derived spheroid model

Casals-Sendra, G.; Jarne-Sanz, I.; Catasus, N.; Boluda-Luis, I.; Quer, A.; Amilibia, E.; Lazaro, C.; Serra, E.; Blanco, I.; Castellanos, E.

10.1101/2025.11.14.688164 — genetics — Posted on 2025-11-14

2682 Somatic epigenetic mosaicism within Pistacia terebinthus (Anacardiaceae) trees leaves signature in reproductive cells

Herrera, C. M.; Medrano, M.; Alonso, C.

10.1101/2025.11.14.688420 — evolutionary biology — Posted on 2025-11-14

2683 Anopheles (Kerteszia) cruzii, the main malaria vector in the Brazilian Atlantic Forest, is a complex of at least five cryptic species

Voges, K.; Dias, G. d. R.; Dupim, E. G.; Pitaluga, A. N.; Vanderlinde, T.; Carvalho-Pinto, C. J. d.; Rezende, H. R.; Uno, F.; Forrester, S.; Chong, J.; Carvalho, A. B.; Rona, L. D.

10.1101/2025.11.14.688459 — evolutionary biology — Posted on 2025-11-14

2684 Priority effects drive fungal and nematode emergence from insect larvae

Payelleville, A.; Warren, M.; Golde, C.; Sasai, D.; Pan, B.; Cleary, P. J.; Gomez, A.; Shrestha, R.; Ogier, J.-C.; Gaudriault, S.; Jacobs-Wagner, C.; Fukami, T.

10.1101/2025.11.14.688296 — ecology — Posted on 2025-11-14

2685 The biodiversity of plant-frugivore interactions: types, functions, and consequences

Jordano, P.

10.1101/2025.11.14.688423 — ecology — Posted on 2025-11-14

2686 Morphometric analyses of shape: The analysis software toolbox for quantification of craniofacial shape

Stearsman, M. C.; Lahamer, J. A.; Gray, R.; Lovely, C. B.

10.1101/2025.11.14.688515 — developmental biology — Posted on 2025-11-14

2687 Polycomb Repressive Complexes 1 and 2 are recruited independently to pericentromeric heterochromatin in response to hypomethylation in mouse embryonic stem cells

Dimova-Vasileva, S.; Stepanova, O.; Hay, D.; Pickup, K. E.; Gautier, P.; Murphy, L. C.; Kumar, Y.; Adams, I. R.; Pennings, S.; Meehan, R. R.

10.1101/2025.11.14.688451 — molecular biology — Posted on 2025-11-14

2688 Proteolytic activation of diverse antiviral defense modules in prokaryotes

Evans, S. A.; Zhang, J.; Lam, Y.; Wang, K.; Lin, Y. T.; Herschlag, D.; Feng, L.; Gao, A.

10.1101/2025.11.14.688446 — molecular biology — Posted on 2025-11-14

2689 Bemnifosbuvir and remdesivir inhibit tick-borne encephalitis virus infection in complementary in vitro and ex vivo disease models

Leoni, S.; Schultz-Pernice, I.; Kratka, Z.; Eyer, L.; Freiholz, L.; Fahmi, A.; David, T.; Golomingi, A.; Blank, F.; Dejmek, M.; Grandgirard, D.; Dijkman, R.; Ruzek, D.; Alves, M. P.; Leib, S. L.

10.1101/2025.11.13.688315 — microbiology — Posted on 2025-11-14

2690 Tools for genetic manipulation of the endemic fungal pathogen, Emergomyces africanus, and the application of a fluorescent reporter strain in infection models

Duvenage, L.; Chetty, A.; Thomson, D. D.; Ballou, E. R.; Govender, N. P.; Rappleye, C. A.; Hoving, J. C.

10.1101/2025.11.14.688410 — microbiology — Posted on 2025-11-14

2691 Rapid and Complete Inactivation of Enveloped Viruses by Electrochemical Disinfection: Unraveling the Contribution of Reactive Chlorine Species

Xu, C.; Jiang, C.; Sun, S.-H.; Sang, P.; Shao, R.; zhou, x.; Zhang, X.; Liu, Y.; Wen, X.; Huang, X.

10.1101/2025.11.14.688411 — microbiology — Posted on 2025-11-14

2692 HIV-1 latency reversing agents converge on phosphoregulation of nuclear protein complexes

Ni, J. J.; Kaushal, P.; Sharma, S.; Makanani, S. K.; Delgado, Y.; Blanc, S. F.; Olwal, C. O.; Ashley, I. A.; Winters, D. M.; Yang, V.; Phung, C. N.; Alba, K.; Wynn, E.; Johnson, J. R.; Hultquist, J. F. R.; Fregoso, O. I.; Bouhaddou, M.

10.1101/2025.11.13.688376 — microbiology — Posted on 2025-11-14

2693 Endothelial protein C receptor CD201 is a better marker than SCA1 to identify mouse long-term reconstituting hematopoietic stem cells following septic challenge

Bisht, K.; Barbier, V.; Shatunova, S.; Winkler, I. G.; Levesque, J.-P.

10.1101/2025.11.13.688157 — immunology — Posted on 2025-11-14

2694 An IL-21R hypomorph circumvents functional redundancy to define STAT1 signaling in germinal center responses

Jandl, C.; Warren, J.; Owens, S.; Batten, M.; Wang, H.; King, C.

10.1101/2025.11.14.688418 — immunology — Posted on 2025-11-14

2695 Rho signaling promotes cell excitability and synaptic transmission

Jose, A.; Dhakal, P.; Signorelli, R.; Case, C.; Chaudhry, S.; Collins, K. M.

10.1101/2025.11.13.688363 — neuroscience — Posted on 2025-11-14

2696 Tuning a Genetic Circuit with Double Negative Feedforward Loops to Approximate Square Waves

Wu, J.; Johnson, C.; Yeung, E.

10.1101/2025.11.13.688370 — synthetic biology — Posted on 2025-11-14

2697 Somatostatin Receptors Shape Insulin and Glucagon Output within the Pancreatic Islet through Direct and Paracrine Effects

Hart, R. G.; Lee, J. J.; Zhai, K.; Lee, S.; Chauhan, R.; Hosseini, A.; Nguyen, A. D.; Huising, M. O.

10.1101/2025.11.13.688371 — physiology — Posted on 2025-11-14

2698 The cumulative impact of passenger mutations on cancer development

Nayak, A.; Chan, C.; Mouratidis, I.; Georgakopoulos-Soares, I.

10.1101/2025.11.13.688369 — cancer biology — Posted on 2025-11-14

2699 Unified modeling of cellular responses to diverse perturbation types

Li, C.; Wei, L.; Zhang, X.

10.1101/2025.11.13.688367 — bioinformatics — Posted on 2025-11-14

2700 Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history

Ni, Z.; Osborn, T.; Zhong, J.; Gonzalez, A.; Puzella, W.; Klos, A.; Le, B.; Leonetti, A.; Boden, J. S.; Stueeken, E. E.; Anderson, R. E.

10.1101/2025.11.13.688358 — bioinformatics — Posted on 2025-11-14

2701 Discovery and optimization of antimicrobial peptides from extreme environments on global scale

Kang, Z.; Zhang, H.; Zhou, Q.; Liu, J.; Zhou, K.; Chen, P.; Liu, B.-F.; Ning, K.

10.1101/2025.11.13.688364 — bioinformatics — Posted on 2025-11-14

2702 Bruch's Membrane Contributes to the Structural Integrity of the Human Eye

Tan, R. K. Y.; Sharma, S.; Chan, A.; Ho, C.; Braeu, F.; Jonas, J.; Han, L.; Wang, X.; Zhu, Y.; Leo, H. L.; Buist, M.; Aung, T.; Perera, S.; Girard, M. J. A.

10.1101/2025.11.13.688375 — bioengineering — Posted on 2025-11-14

2703 Challenging a role for ceramide channels and microdomains in apoptosis induction using a bottom-up approach

Wessing, M.; Klassen, S.; Fiedler, B.; Cosentino, K.; Holthuis, J. C. M.

10.1101/2025.11.14.688508 — biochemistry — Posted on 2025-11-14

2704 Emergence of Dual-Risk Klebsiella pneumoniae: Global Hotspots of Convergence Between Resistance and Hypervirulence

Selvam, P. K.; Mohan, S.; Vasudevan, K.

10.1101/2025.11.13.688379 — genomics — Posted on 2025-11-14

2705 Identification of gingipains in glioblastoma tumors and evidence that P. gingivalis infection drives IL-6 and PD-L1 expression in glioma cells

Moore, E. M.; Bekale, L. A.; Tun, Z. M. M.; Chen, J.; Ryder, M. I.; Ermini, F.; Dominy, S. S.; Barron, A. E.

10.1101/2025.11.13.686868 — neuroscience — Posted on 2025-11-14

2706 The retinal light response is modulated by an mGluR5-mediated retrograde signal from ON-bipolar cells to photoreceptors

Morgans, C. W.; Haley, T. L.; Ren, G.; Taylor, I. A. M.; Randall, K. L.; Duvoisin, R. M.

10.1101/2025.11.13.687902 — neuroscience — Posted on 2025-11-14

2707 Contrast and pattern adaptation in visual cortex share a common gain control mechanism

Moosavi, S. A.; Tring, E.; Ringach, D.

10.1101/2025.11.13.688361 — neuroscience — Posted on 2025-11-14

2708 Characterizing spatial functional microniches with SpaceTravLR

Ramjattun, K.; Wang, A.; Lee, H.; Giri, S.; Chen, Y.; MacDonald, W. A.; Lord, N.; Poholek, A. C.; Lee, Y.; Das, J.

10.1101/2025.11.13.688264 — systems biology — Posted on 2025-11-14

2709 Early persistence of recipient stem-cells and T-cell dysregulation are associated with relapse after transplant in AML/MDS

Sariipek, N. E.; Safina, K. R.; Lu, W. S.; Li, S.; Janes, J. T.; Van Orden, M.; Livak, K. J.; Heaton, H.; Ho, V. T.; Koreth, J.; Luskin, M. R.; Griffin, G. K.; Garcia, J. S.; Lindsley, R. C.; Cutler, C.; Soiffer, R. J.; Ritz, J.; Wu, C. J.; Antin, J. H.; Lane, A. A.; Gooptu, M.; Galen, P. v.

10.1101/2025.11.13.688350 — cancer biology — Posted on 2025-11-14

2710 A spatially-aware unsupervised pipeline to identify co-methylation regions in DNA methylation data

Meshram, S.; Fadikar, A.; Arunkumar, G.; Chatterjee, S.

10.1101/2025.11.13.688356 — bioinformatics — Posted on 2025-11-14

2711 Anti-CD38-Targeted Piperazine-Derived Lipid Nanoparticles Overcome Hepatic Clearance for mRNA Delivery to Multiple Myeloma Cells In Vivo

Figueroa-Espada, C. G.; Geisler, H. C.; Joseph, R. A.; Ricciardi, A. S.; Metzloff, A. E.; Acosta-Gonzalez, J. O.; Xue, L.; Yamagata, H. M.; Thatte, A. S.; MITCHELL, M. J.

10.1101/2025.11.12.687398 — bioengineering — Posted on 2025-11-14

2712 The genome of Doleromyrma darwiniana and annotations for five additional Dolichoderinae species

Keddell, P.; Guhlin, J. G.; Dearden, P. K.

10.1101/2025.11.13.688362 — genomics — Posted on 2025-11-14

2713 A default silencing mechanism restrains stress-induced genes in C. elegans

Ilbay, O.; Gama, A. R.; Jarosz, D. F.; Morimoto, R.; Fire, A.

10.1101/2025.10.22.683740 — genetics — Posted on 2025-11-14

2714 Evaluating rapid extraction methods for recovering ancient DNA from archaeological sediments

Dagtas, N. D.; Jabareen, A.; Cyrek, K.; Krajcarz, M. T.; Krajcarz, M.; Rojo-Guerra, M. A.; Sanchez-Yustos, P.; Sudoł-Procyk, M.; Safra, S.; Slon, V.

10.1101/2025.11.13.688359 — evolutionary biology — Posted on 2025-11-14

2715 Distinct Ire1-driven transcriptional responses control morphogenesis in Candida albicans

Stack-Couture, S.; Librais, G. M.; Lung, B.; Genereaux, J.; Halder, V.; Dumeaux, V.; Shapiro, R. S.; Lajoie, P.

10.1101/2025.11.13.688365 — cell biology — Posted on 2025-11-14

2716 Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses

Oshiro, R.; Dunham, D.; Gill, C.; Chouldjian, A.; Piya, D.; Mutalik, V. K.; Seed, K.

10.1101/2025.11.13.688357 — microbiology — Posted on 2025-11-14

2717 Inflammatory profiles of transdiagnostic symptom dimensions in healthy females

Smith, A. J.; Kigar, S.; Dercon, Q.; Lynall, M.-E.; Ioannidis, K.; Kaser, M.; Hitchcock, C.; Dalgleish, T.; Nord, C.

10.1101/2025.11.13.688353 — immunology — Posted on 2025-11-14

2718 Porosome reconstitution reverses Alzheimers in human brain organoids

Jena, B. P.; Cho, W. J.; Taatjes, D. J.; Patil, S. R.

10.1101/2025.11.13.688334 — neuroscience — Posted on 2025-11-14

2719 Patient-Specific Midbrain Organoids with CRISPR Correction Reveal Disease Mechanisms and Enable Therapeutic Evaluation in Neuronopathic Gaucher Disease

Lin, Y.; Liou, B.; Fannin, V.; Adler, S.; Mayhew, C. N.; Hammonds, J. E.; Hu, Y.-C.; Tchieu, J.; Zhang, W.; Zhao, X.; Beres, R. L.; Setchell, K. D.; Kaynak, A.; Qi, X.; Feldman, R. A.; Sun, Y.

10.1101/2025.11.06.686937 — neuroscience — Posted on 2025-11-14

2720 Simultaneous stomach-brain electrophysiology reveals dynamic coupling in human sleep

Rao, A. A.; Fredericks, M.; Dresler, M.; Rebollo, I.; Zeitzer, J. M.; Schoch, S. F.; Coleman, T. P.

10.1101/2025.11.13.686572 — neuroscience — Posted on 2025-11-14

2721 Decoding hidden goal-directed navigational states and their neuronal representations using a novel labyrinth paradigm and probabilistic modeling framework

Honma, P. S.; Bangera, S. C.; Thomas, R. R.; Kaliss, N.; Xia, D.; Palop, J. J.

10.1101/2025.11.13.688348 — neuroscience — Posted on 2025-11-14

2722 Infraslow histaminergic dynamics govern priming states to gate moment-to-moment memory accessibility

Morishita, Y.; Takamura, Y.; Nishimura, K.; Yokoi, Y.; Ishihama, Y.; Idutsu, R.; Ohno, M.; Matsumoto, R.; Hitora-Imamura, N.; Minami, M.; Nomura, H.

10.1101/2025.11.13.687922 — neuroscience — Posted on 2025-11-14

2723 Single-Cell Sequencing Reveals Extensive Genetic Diversity Underlying Pediatric ALL Treatment Complexity

Pang, Y.; Prieto, T.; Gonzalez-Pena, V.; Aragon, A.; Xia, Y.; Kao, S.; Rajagopalan, S.; Zinno, J.; Quentin, J.; Laval, J.; Yuan, D.; Shawn, S.; Omans, N.; Klein, D.; MacKay, M.; De Vlaminck, I.; Easton, J.; Evans, W.; Landau, D. A.; Gawad, C.

10.1101/2025.03.19.644196 — cancer biology — Posted on 2025-11-14

2724 Targeted analysis of chondrocyte central metabolites in response to cyclical compression and shear deformations

Myers, E. P.; Gallagher, A.; Welfley, A.; Battles, S.; Gregory, A.; Brahmachary, P.; Greenwood, M.; June, R.

10.1101/2025.08.04.668582 — bioengineering — Posted on 2025-11-14

2725 Massively parallel reporter assay for mapping gene-specific regulatory regions at single nucleotide resolution

Tulloch, A. J.; Delgado, R. N.; Catta-Preta, R.; Cepko, C. L.

10.1101/2025.05.13.653746 — developmental biology — Posted on 2025-11-14

2726 Phospholipase D3 regulates lysosomal morphology, biogenesis, and function in neurons.

Wang, Y.; Carvajal-Tapia, C.; Jain, S.; Wang, E.; Rieschick, P.; Hepowit, N.; Applebaum, N.; Prusky, A.; Anghelina, T.; Kulsomphob, A.; Janve, V.; Frank, S.; Kozunda, A.; Hohman, T.; Mobley, B.; MacGurn, J.; Fernandez, W. R.; Schrag, M.

10.1101/2024.09.26.615214 — cell biology — Posted on 2025-11-14

2727 Chronic pancreatitis patient-derived organoids reveal new paths to precision therapeutics

Osorio-Vasquez, V.; Zhu, J.; Lumibao, J. C.; Lande, K.; Peck, K. L.; Stamp, M.; Okhovat, S. R.; Song, H.; Ogawa, S.; Kubota, C.; Pantazopoulou, V.; Dai, Y.; Rock, A.; Bottomley, C.; Thomas, E.; Herrera Morales, A.; Hsu, J.; Fowler, A.; McGriff, T.; Evensen, K. G.; Larsen, S.; Abdulla, M.; Greer, P.; Gibson, J.; Downes, M.; Evans, R.; Lowy, A.; Whitcomb, D. C.; Zou, J.; Molinolo, A.; Oh, T. G.; White, R.; Bellin, M.; Tiriac, H.; Engle, D. D.

10.1101/2024.10.30.620903 — cell biology — Posted on 2025-11-14

2728 Autonomous division of the outer membranes in Gram-negative bacteria

Basurto De Santiago, C.; Ramirez Carbo, C. A.; Nan, B.

10.1101/2025.05.15.654258 — microbiology — Posted on 2025-11-14

2729 A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on Hyphomicrobiales dark matter

Leducq, J.-B.; St-Amand, L.-P.; Ross, D.; Kembel, S. W.

10.1101/2025.08.19.671110 — microbiology — Posted on 2025-11-14

2730 A high-throughput platform for biophysical antibody developability assessment to enable AI/ML model training

Arsiwala, A.; Bhatt, R.; van Niekerk, L.; Quintero Cadena, P.; Ao, X.; Rosenbaum, A.; Bhatt, A.; Smith, A.; Yang, Y.; Anderson, K.; Grippo, L.; Cao, X.; Cohen, R.; Patel, J.; Allen, O.; Faraj, A.; Nandy, A.; Hocking, J.; Tural, B.; Salvador, S.; Jacobowitz, J.; Schaven, K.; Sherman, M.; Shah, S.; Tessier, P. M.; Borhani, D.

10.1101/2025.05.01.651684 — biophysics — Posted on 2025-11-14

2731 Simulation and empirical evaluation of biologically-informed neural network performance

Miller, G. A.; Roman, A.; Glettig, M.; Elmarakeby, H. A.; AlDubayan, S. H.; Park, J.; Collins, R. L.; Van Allen, E.

10.1101/2025.11.13.687845 — bioinformatics — Posted on 2025-11-14

2732 SAM-based Automatic Workflow for Histology Cyst Segmentation in Autosomal Dominant Polycystic Kidney Disease

Delgado-Rodriguez, P.; Kinakh, R.; Aldabe, R.; Munoz-Barrutia, A.

10.1101/2024.09.02.610807 — bioinformatics — Posted on 2025-11-14

2733 Using Dynamic Bayesian Optimization to Induce Desired Effects in the Presence of Motor Learning: a Simulation Study

Kim, G.; Chishty, H. A.; Sergi, F.

10.1101/2024.08.13.607783 — bioengineering — Posted on 2025-11-14

2734 Temporal analysis of reproduction distributed in space illuminates the climate-change resiliency of toyon (Heteromeles arbutifolia)

Dakduk, D.; Yoder, J. B.

10.1101/2025.09.09.675207 — ecology — Posted on 2025-11-14

2735 DETERMINATION OF THE TRANSBILAYER DISTRIBUTION OF PLASMA MEMBRANE CHOLESTEROL

Steck, T. L.; Lange, Y.

10.1101/2025.11.13.687888 — cell biology — Posted on 2025-11-14

2736 Modulating MyoD1 dosage activates alternate cell fate beyond myogenic differentiation

Whitney, O. N.; Dailey, G. M.; McKenna, J. K.; Darzacq, X.; Tjian, R.

10.1101/2025.11.13.688391 — molecular biology — Posted on 2025-11-14

2737 Fiber Type and Stimulus Determine Progression of Skeletal Muscle Atrophy

Maas, G.; Mullen, M. P.; Shepard, B. D.; Gugel, J. F.; Hunt, D.; Calve, S.; Ferguson, V.; Martin, T. G.; Leinwand, L. A.

10.1101/2025.11.13.687882 — molecular biology — Posted on 2025-11-14

2738 Comparative Evaluation of Assumption Lean Community Detection Methods for Human Connectome Networks

Bhattacharya, A.; Chakraborty, N.; Wang, X.; Tu, J.; Dierker, D.; Eck, A.; Lahiri, S.; Eggebrecht, A.; Wheelock, M. D.

10.1101/2025.11.13.688333 — neuroscience — Posted on 2025-11-14

2739 Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation

Heyman, Y.; Erez, M.; Burnham, P.; Nitzan, M.; Raj, A.

10.1101/2025.11.14.688372 — systems biology — Posted on 2025-11-14

2740 Acute Myeloid Leukemia Relapse after Bromodomain Inhibitor Treatment or Chemotherapy is Characterized by Myc-Ras Transcriptional Remodeling

Huang, B. J.; D'Souza, J.; Batingana, A. R.; Harris, M. D.; Wang, X.; Hwang, E.; Wandler, A. M.; Burgess, M. R.; Li, Q.; Meshinchi, S.; Bollag, G.; Shannon, K.

10.1101/2025.11.13.688312 — cancer biology — Posted on 2025-11-14

2741 YAP1 Depletion Enhances TAZ and its Complexation with TEAD4 and AP-1 Heterodimer C-JUN/FOSB to Promote Gastric Cancer Progression and Metastases

Wu, J.; Athavale, D.; Balch, C.; Zhao, J.; Zou, G.; Fan, Y.; Zhang, Y.; Zhao, J.; Ghelfi, M.; Pompetti, A.; Calendo, G.; Scott, A.; Shao, S.; Yao, X.; Pizzi, M. P.; Vellano, C.; Khazak, V.; Zhang, S.; Yap, T. A.; Dhar, S. S.; Sundar, R.; Spitz, F.; Grana, G.; Ajani, J. A.; Song, S.

10.1101/2025.11.13.683933 — cancer biology — Posted on 2025-11-14

2742 Hydraulic Activation of the AsLOV2 Photoreceptor

Maity, S.; Sheppard, J.; Russell, H.; Han, C.-T.; Epstein, L.; Johnson, B. A.; Price, B. D.; Han, R.; Potnuru, L. R.; Cui, J.; Sherwin, M. S.; Shea, J.-E.; Lovett, J. E.; Gardner, K. H.; Han, S.

10.1101/2025.06.19.660617 — biophysics — Posted on 2025-11-14

2743 Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings

BRIERE, G.; STOSSKOPF, T.; LOIRE, B.; BAUDOT, A.

10.1101/2025.01.23.634511 — bioinformatics — Posted on 2025-11-14

2744 Tuning Histone Site Selectivity in the Nucleosome with Organometallic Agents

Levy, A.; Adhireksan, Z.; von Erlach, T.; Palermo, G.; Nazarov, A. A.; Hartinger, C. G.; Dyson, P. J.; Rothlisberger, U.; Davey, C. A.

10.1101/2025.11.13.688318 — biochemistry — Posted on 2025-11-14

2745 Including fitness and health proxies can alter our understanding of habitat selection

Auger-Methe, M.; Dupont, F.; Eby, A.; Elliott, K. H.; Hussey, N.; Lyons, D. A.; Marcoux, M.; Patterson, A.; Shadloo, S.; Shuert, C. R.

10.1101/2025.11.13.688337 — ecology — Posted on 2025-11-14

2746 Genotoxic formaldehyde and lipid aldehydes are sources of DNA damage in keratinocytes

Blobel, N. J.; Yao, Y.; Okondo, M. C.; Smogorzewska, A.

10.1101/2025.11.13.688345 — cell biology — Posted on 2025-11-14

2747 Thermal optimized PCR coupled to CRISPR-Cas12a for rapid detection of blaOXA-1 resistance gene

Quiroz-Huanca, A.; Vargas-Reyes, M.; Lopez, J. D.; Flores-Jimenez, K.; Saldarriaga-Moran, S.; Cifuentes, K.; Alcantara, R.

10.1101/2025.11.13.688324 — molecular biology — Posted on 2025-11-14

2748 A cytochrome P450 G subfamily member, CYP4G35, is highly expressed in antennae and modulates olfactory response in Aedes aegypti mosquitoes.

Sharma, A.; Nuss, A.; Cruz, O. G.; Arshad, F.; Reyes, J.; Mathew, M.; MacLean, M.; Young, S.; Hu, R.; Beniwal, S.; Tittiger, C.; Blomquist, G.; Pham, M.; Petereit, J.; Mathew, D.; Harrell, R.; Gulia-Nuss, M.

10.1101/2025.11.13.688110 — molecular biology — Posted on 2025-11-14

2749 In situ Architecture of the Tad Pilus Machine in Caulobacter crescentus

Iarocci, J.; Whitfield, G. B.; Williston, R. F.; Wozny, M. R.; Presley, J. F.; Ellison, C. K.; Brun, Y. V.; Guo, S.

10.1101/2025.11.05.686773 — microbiology — Posted on 2025-11-14

2750 Development of immortalized Callithrix jacchus kidney cell lines supporting infection with a panel of viruses

Gärtner, S.; Stomberg, P.; Pöhlmann, S.; Winkler, M.

10.1101/2025.11.13.688326 — microbiology — Posted on 2025-11-14

2751 Human resistin is critical to activation of the NLRP3 inflammasome in macrophages

Kariyawasam, U.; Skinner, J.; Lam, W.; Chakrabarti, R.; Cox, A.; Hassoun, P. M.; Lin, Q.; Johns, R.

10.1101/2025.11.13.688330 — immunology — Posted on 2025-11-14

2752 Antibody feedback establishes an affinity brake in the germinal center

Yan, Y.; Wang, X.; Xie, Z.; Bader, D. L. V.; Lim, R. H.; Ma, K. M.; Cottrell, C. A.; Steichen, J. M.; Xu, L.; Villavicencio, P. M.; Akauliya, M.; Koo, J.-H.; Shen, J. M.; Vernich, A.; Kalyuzhniy, O.; Allen, J. D.; Albowaidey, A. A.; Alicea, A.; Chen, B.; Georgeson, E.; Ellis-Pugh, J. R.; Alavi, N.; Esposito, A.; Naili, H.; Phelps, N.; Kelley, B.; Kubitz, M.; Phan, Q. A.; Liguori, A.; Prum, T.; Tingle, R.; Lu, D.; Eskandarzadeh, S.; Liu, X.; Warner, J. E.; Weldon, S. R.; Himansu, S.; Crispin, M.; Nair, U.; Liu, S.; Schief, W. R.; Batista, F. D.

10.1101/2025.11.13.688298 — immunology — Posted on 2025-11-14

2753 The DNA methylation enzymatic machinery in substance use disorders: a systematic review

Diringer, M.; Bruggeman, M.; Lutz, P.-E.

10.1101/2025.11.12.688056 — neuroscience — Posted on 2025-11-14

2754 FMRP regulates adult human cortical neuron excitability via cyclic-AMP signalling

Knops, M. J.; Meftah, S.; Wilson, M. A.; Taylor, L. W.; Bonthron, C.; Bilal, A.; Liaquat, I.; Brennan, P. M.; Durrant, C. S.; Booker, S. A.

10.1101/2025.10.14.682273 — neuroscience — Posted on 2025-11-14

2755 Toward Understanding the Role of Visual Hierarchy in Flicker-induced Time Dilation: A Preregistered Study

Houshmand Chatroudi, A.; Yotsumoto, Y.

10.1101/2025.11.10.687470 — neuroscience — Posted on 2025-11-14

2756 Human Medial Ganglionic Eminence Organoids Robustly Generate Parvalbumin Interneurons and Fast-Spiking Neurons and Reveal Migratory Deficits in SLC6A1 Deficient Interneurons

Varela, M. C.; Walker, M. P.; Bok, J.; Crespo, E. L.; Thenstedt, T.; Goldstein, L.; Tidball, A. M.; Yuan, Y.; Isom, L.; Fu, J.; Uhler, M.; Parent, J. M.

10.1101/2025.07.01.662594 — neuroscience — Posted on 2025-11-14

2757 Inhibitory circuits control leg movements during Drosophila grooming

Syed, D. S.; Ravbar, P.; Simpson, J. H.

10.1101/2024.06.05.597468 — neuroscience — Posted on 2025-11-14

2758 Grid to Place Cell Connectivity in Eleven Different Rooms

Aggarwal, A.

10.1101/2024.11.15.623794 — neuroscience — Posted on 2025-11-14

2759 Bright Light Exposure Reduces Negative Affect and Modulates EEG Activity in Sleep-Deprived and Well-Rested Adolescents

Koprivova, J.; Kankova, Z.; Vlcek, P.; Piorecky, M.; Maierova, L.; Bendova, Z.; Skalova, K.; Nekovarova, T.

10.1101/2025.07.16.664355 — neuroscience — Posted on 2025-11-14

2760 Misalignment between perceived and actual ability on a balance beam walking task

Beech, S.; Geisler, C.; Creer, S.; Monoli, C.; Render, A. C.; Fino, P. C.

10.1101/2025.11.10.687691 — physiology — Posted on 2025-11-14

2761 TrkC has distinct spatiotemporal dynamics compared to TrkA and TrkB

Duffy, R. T.; Hill, S. J.; Peach, C. J.

10.1101/2025.11.13.688325 — pharmacology and toxicology — Posted on 2025-11-14

2762 WITHDRAWN: Genome-wide association study reveals novel resistance loci to banana weevil (Cosmopolites sordidus) in Rwandan Musa cultivars

Erastus, D.; Edema, R.; Ebapu, D.; Nduwumuremyi, A.; Mukamuhirwa, A.

10.1101/2025.09.05.674467 — bioinformatics — Posted on 2025-11-14

2763 Deciphering the global genomic landscape of C. neoformans: Population dynamics, molecular epidemiology and genomic signatures of pathogenicity

Sathiyamoorthy, J.; Ramakrishnan, J.

10.1101/2025.11.11.687764 — bioinformatics — Posted on 2025-11-14

2764 S3R: Modeling spatially varying associations with Spatially Smooth Sparse Regression

zhou, x.; dang, p.; Wang, X.; Peng, L. X.; Yeh, J. J.; Sears, R. C.; Zhang, N.; Neelon, B.; Zimmers, T.; Zhang, C.; Cao, S.

10.1101/2025.09.06.674629 — bioinformatics — Posted on 2025-11-14

2765 An Enhanced Variant-Aware Deep Learning Model for Individual Gene Expression Prediction

Zhao, X.; Su, S.

10.1101/2025.11.12.688070 — bioinformatics — Posted on 2025-11-14

2766 WITHDRAWN: Comprehensive Error Profiling of NovaSeq6000, NovaSeqX, and Salus Pro Using Overlapping Paired-End Reads

Yao, T.

10.1101/2025.07.15.665004 — bioinformatics — Posted on 2025-11-14

2767 WITHDRAWN: Comparison of Three Next Generation Sequencers on Their Basecall Error Rates and Bias Patterns

Yao, T.

10.1101/2025.04.15.649007 — genomics — Posted on 2025-11-14

2768 Influence of cis-regulatory elements on expression divergence in human segmental duplications

Shew, C. J.; Kaya, G.; McGinty, S. P.; Dennis, M.

10.1101/2025.10.03.680410 — genomics — Posted on 2025-11-14

2769 Reproducibility of the evaluation of genetic variant pathogenicity based on the animal variant classification guidelines

Casselman, I.; Ferrari, C.; Abitbol, M.; Bannasch, D.; Bell, J.; Dufaure de Citres, C.; Finno, C. J.; Hayward, J. J.; Häggström, J.; Huff, J. T.; Leeb, T.; Ljungvall, I.; Longeri, M.; Lyons, L. A.; Martinez, M.; Mellersh, C.; Nicholas, F. W.; Ohlsson, A.; Smets, P.; Strillacci, M. G.; Tammen, I.; van Steenbeek, F.; Broeckx, B.

10.1101/2025.11.12.687631 — genetics — Posted on 2025-11-14

2770 Efficient Gibson Assembly of Ultra-Large cDNAs: Generation of Full-length Wild-Type and Mutated futsch transgenes in Drosophila

Wu, C.

10.1101/2025.11.11.687501 — genetics — Posted on 2025-11-14

2771 Shortcomings of shortcuts: common species cannot fully explain multiscale patterns of species richness

Schwenk, W. S.

10.1101/2025.11.11.687838 — ecology — Posted on 2025-11-14

2772 A self-limiting mechanotransduction feedback loop ensures robust organ formation

Mori, Y.; Robin, P.; Briggs, A. B.; Levic, D. S.; Wang, J.; Heikes, K. L.; Bagnat, M.; Hannezo, E.; Munjal, A.

10.1101/2025.09.25.678607 — developmental biology — Posted on 2025-11-14

2773 Disruption of ribosome dynamics and mRNA homeostasis triggers a cascading imbalance in protein synthesis in models of Amyotrophic Lateral Sclerosis

Lauria, F.; Maniscalco, F.; Perrucci, C.; Marchioretto, M.; Bruno, I.; Tome, G.; Cella, F.; Busarello, E.; Sevegnani, M.; Lunelli, L.; Donini, L.; Tebaldi, T.; D Antoni, M.; Pollini, D.; Peroni, D.; Pisciottani, A.; Croci, L.; Badaloni, A.; Arnese, R.; Provenzani, A.; Quattrone, A.; Consalez, G. G.; Clamer, M.; Siciliano, V.; Basso, M.; Viero, G.

10.1101/2025.05.15.654227 — molecular biology — Posted on 2025-11-14

2774 Beta bursts in SMA mediate anticipatory muscle inhibition

Manyukhina, V.; Abdoun, O.; Rienzo, F. D.; Barlaam, F.; Daligault, S.; Delpuech, C.; Szul, M. J.; Bonaiuto, J. J.; Bonnefond, M.; Schmitz, C.

10.1101/2025.01.24.634650 — neuroscience — Posted on 2025-11-14

2775 Uncertainty-aware genomic deep learning with knowledge distillation

Zhou, J.; Rizzo, K.; Christensen, T.; Tang, Z.; Koo, P. K.

10.1101/2024.11.13.623485 — genomics — Posted on 2025-11-14

2776 Evolutionary basis of intermale sexual behavior by multiple pheromone switches in Drosophila

Ouadah, Y.; Naragon, T. H.; Smihula, H.; Behrman, E. L.; Khallaf, M. A.; Ding, Y.; Stern, D. L.; Parker, J.; Anderson, D. J.

10.1101/2025.10.14.682417 — evolutionary biology — Posted on 2025-11-14

2777 Neural crest induction requires SALL4-mediated BAF recruitment to lineage specific enhancers

Demurtas, M.; Barnada, S. M.; Van Domselaar, E.; Mitchell, Z. H.; Deelen, L. L.; Trizzino, M.

10.1101/2025.06.10.658805 — developmental biology — Posted on 2025-11-14

2778 Defining the chromatin-associated protein landscapes on Trypanosoma brucei repetitive elements using synthetic TALE proteins

Carloni, R.; Devlin, T.; Tong, P.; Auchynnikava, T.; Spanos, C. R.; Rappsilber, J.; Matthews, K. R.; Allshire, R. C.

10.1101/2025.04.22.649942 — cell biology — Posted on 2025-11-14

2779 Disruption without diversity loss: how spreading thermotolerant Pilidium lythri infection perturbs plant-soil microbiome stability

Siegieda, D.; Panek, J.; Hannula, E. S.; Frac, M.

10.1101/2025.01.28.633866 — microbiology — Posted on 2025-11-14

2780 Novel tensor decomposition-based approach for cell type deconvolution in Visium datasets when reference scRNA-seqs include multiple minor cell types

Taguchi, Y.-h.; Turki, T.

10.1101/2025.04.18.649484 — bioinformatics — Posted on 2025-11-14

2781 Selective brain network stimulation by frequency entrainment

Otero, M.; Poo, E.; Torres, F.; Mendoza, C.; Lea-Carnall, C. A.; Weinstein, A.; Guevara, P.; Cortes, J.; Prado, P.; Cabral, J.; EL-DEREDY, W.

10.1101/2025.04.30.651283 — bioengineering — Posted on 2025-11-14

2782 Detection of zoonotic Cryptosporidium parvum in invasive beavers from southern Tierra del Fuego, Chile

Aguilar, P. A. L.; Contreras, G.; Cabrera, G.; Arredondo, C.; Federici, F.; Briceno, C.

10.1101/2025.11.13.688090 — bioengineering — Posted on 2025-11-14

2783 SMARCA2 is an essential and potent cofactor for a specific subset of the glucocorticoid response in A549 cells

Melore, S. M.; Kocak, D. D.; Siklenka, K.; Johnson, G. D.; Williams, C.; Bartelt, L. C.; Jones, A. G.; Barrera, A.; Venukuttan, R.; Gersbach, C. A.; Reddy, T. E.

10.1101/2025.11.13.688306 — genomics — Posted on 2025-11-14

2784 FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity

Ladewig, E.; Nazir, A.; Park, T.; Fan, V. B.; Cao, Z.; Hawk, J.; Kelly, L.; Tjian, R.; Leslie, C. S.; Sawyers, C.

10.1101/2025.11.13.688263 — genomics — Posted on 2025-11-14

2785 A patient derived missense mouse model of Kabuki syndrome 1

Halldorsdottir, S. T.; Vinod, M.; Gunnlaugsson, H. O.; Bjornsdottir, E. D.; Luperchio, T.; Fahrner, J. A.; Ulfig, A.; Bjornsson, H. T.

10.1101/2025.11.13.688040 — genetics — Posted on 2025-11-14

2786 A wild genome of the underutilized legume lablab (Lablab purpureus) reveals the genetic basis of domestication

Cheung, T.-Y.; Almerick Tan Boncan, D.; Yuan, Y.; Zhang, Y.; Somta, P.; Chapman, M. A.; Chan, T.-F.

10.1101/2025.11.13.688277 — evolutionary biology — Posted on 2025-11-14

2787 Oxidative-stress related increase in keratoconus tear MDA and GPX3 while NRF2-antioxidant functions decrease in stromal cells

Koduri, M. A.; Charter, M.; Sonar, R.; Deshmukh, R.; Prescott, C. R.; Mandel, R.; Sperber, L.; Lee, T.; Kahan, E. H.; Haberman, I. D.; Singh, V.; Blitzer, A. L.; Maiti, G.; Chakravarti, S.

10.1101/2025.11.13.688300 — cell biology — Posted on 2025-11-14

2788 A Novel Prognostic Metric Resolves the MYCN enigma in Silico and Points to a Biosynthetic Regulatory Shift Driven by MYCN Amplification in Neuroblastoma

Italia, M.; Parker, M.; Deignan, R.; Dercole, F.; Walker, D.; Wertheim, K. Y.

10.1101/2025.11.13.688307 — systems biology — Posted on 2025-11-14

2789 Phase Behavior of TDP-43 and hnRNP H1: From Soluble and Aggregated States to Liquid-Like Droplets

Wang, T. R.; Wang, J.

10.1101/2025.11.12.687994 — molecular biology — Posted on 2025-11-14

2790 WITHDRAWN: Defective HIV DNA genomes provide ancestralrelevance critical for phylogenetic inference of reservoir dynamics

Droske, L.; Ramirez-Mata, A. S.; Cash, M. N.; Estrada, J.; Shank, S. D.; Browning, A.; Rafiei, F.; Kosakovsky Pond, S.; Salemi, M.; Rife Magalis, B.

10.1101/2025.10.03.680205 — microbiology — Posted on 2025-11-14

2791 Contrasting behavioral and physiological effects of Gtf2i duplication and deletion in mouse models of the 7q11.23 Duplication and Williams-Beuren Syndromes

Peles, D.; Netser, S.; Ray, N.; Suliman, T.; Wagner, S.

10.1101/2025.11.13.688274 — neuroscience — Posted on 2025-11-14

2792 Validation of deep learning enabled web based and smartphone optimized application RadAnalyzer to measure vertebral heart size and vertebral left atrial size in dogs

Gordon, S.; Reyes, T.; Baibos-Reyes, T.; Sykes, K. T.; Watson, A.

10.1101/2025.11.13.688321 — physiology — Posted on 2025-11-14

2793 PROX1 loss in adult mouse Schlemm's canal causes permanent ocular hypertension

Ochoa, S. L.; Li, H. L.; Kim, H.; Yan, Z.; Mendonca, N. C.; Liu, P.; Lee, H. J.; Vincent, M. P.; Zhang, H. F.; Gong, H.; Scott, E. A.; Johnson, M.; Thomson, B. R.

10.1101/2025.11.13.688015 — physiology — Posted on 2025-11-14

2794 The Closed State of the Shaker Potassium Channel and the Mechanism of Voltage Activation

Agrawal, R.; Uriarte, R. M.; Anwandter, B. P.; Thomas, T.; Blachowicz, L.; Koh, Y.; Bezanila, F.; Perozo, E.; Roux, B.

10.1101/2025.11.13.687653 — biophysics — Posted on 2025-11-14

2795 TooTranslator: Zero-Shot Classification of Specific Substrates for Transport Proteins by Language Embedding Alignment of Proteins and Chemicals

Ataei, S.; Butler, G.

10.1101/2025.11.13.688294 — bioinformatics — Posted on 2025-11-14

2796 CryoSiam: self-supervised representation learning for automated analysis of cryo-electron tomograms

Stojanovska, F.; Sanchez, R. M.; Jensen, R. K.; Mahamid, J.; Kreshuk, A.; Zaugg, J. B.

10.1101/2025.11.11.687379 — bioinformatics — Posted on 2025-11-14

2797 Single-cell transcriptomics reveals spaceflight-induced accelerated aging and impaired recovery in the murine bone marrow

Zhao, Z.; Zhang, J.; Ji, G.; Zhou, Z.; Yang, Y.; Sun, F.; Lu, H.

10.1101/2025.11.12.688138 — bioinformatics — Posted on 2025-11-14

2798 Clustering of Omic Data Using Semi-Supervised Transfer Learning for Gaussian Mixture Models via Natural-Gradient Variational Inference: Method and Applications to Bulk and Single-Cell Transcriptomics

Jia, Q.; Conti, D. V.; Goodrich, J. A.

10.1101/2025.11.13.688299 — bioinformatics — Posted on 2025-11-14

2799 Defective HIV DNA genomes provide ancestral relevance critical for phylogenetic inference of reservoir dynamics

Droske, L. E.; Ramirez-Mata, A.; Cash, M. N.; Estrada, J.; Shank, S. D.; Browning, A.; Rafiei, F.; Pond, S. L. K.; Salemi, M.; Magalis, B. R.

10.1101/2022.05.04.490630 — genomics — Posted on 2025-11-14

2800 MCUR1-CCDC90B complex is a conserved mitochondrial scaffold regulating metabolic homeostasis

Ferreira, J.; Wettmarshausen, J.; Goh, V.; Lagerborg, K.; Watrous, J.; Feng, M.; de la Herran, H. D.; Walia, S.; Cheng, Y.; Leimpek, A.; Gorza, M.; Braun, S. J.; Nilsson, R.; Jain, M.; Mann, M.; Mokranjac, D.; Murgia, M.; Haack, T.; Deschauer, M.; Prokisch, H.; Filipp, F. V.; Perocchi, F.

10.1101/2025.10.14.682030 — cell biology — Posted on 2025-11-14

2801 Feeder-free generation of functional dendritic cells from human pluripotent stem cells

Jung, W.-H.; Khalil, A.; Binenbaum, Y.; Price, J. M.; Vining, K. H.; Lungjangwa, T.; Sobroal, M. C.; Jaenisch, R.; Mooney, D. J.

10.1101/2025.11.13.687739 — immunology — Posted on 2025-11-14

2802 Exclusive ipsilateral representation of sequential tactile differences challenges contralateral dominance

Yoon, H.; Park, S.; Kim, S.

10.1101/2025.11.13.688241 — neuroscience — Posted on 2025-11-14

2803 Development of Recombinant Anti-TLR2 Antibodies and PLGA Nanoparticle-based Gene Therapy for the Treatment of Neuropathic Pain

Lee, S.; Jeon, J.; Lee, H.; Barcelona, E. E.; Hong, J.; Lee, S. J.

10.1101/2025.11.13.688281 — neuroscience — Posted on 2025-11-14

2804 Inhibition of oxytocin neurons during key periods of development has long-term behavioural and body composition effects.

Schaller, F.; Alifrangis, M.-S.; BARELLE, P.-Y.; Santos, C.; Tyzio, R.; Bertoni, A.; Omnes, F.; belaidouni, Y.; Bader, F.; Pallesi, E.; Gaiarsa, J.-L.; Bouret, S.; Muscatelli, F.

10.1101/2025.11.13.688271 — neuroscience — Posted on 2025-11-14

2805 Single nuclear RNA sequencing shows altered microglial and astrocytic functions in post-mortem Parkinson's disease tissue

Roy, I.; Thomas, R.; Ambriz, G. J.; Farhan, S. M. K.; Piscopo, V. E. C.; Durcan, T. M.

10.1101/2025.11.13.687853 — neuroscience — Posted on 2025-11-14

2806 ADHD Medications and Preadolescent Brain Structure: Patterns of Cortical Attenuation from the ABCD Study

Overholtzer, L. N.; Bottenhorn, K. L.; Karalunas, S. L.; Peterson, B. S.; Herting, M.

10.1101/2025.11.13.687018 — neuroscience — Posted on 2025-11-14

2807 Cytogenetic constraints on hybridization: A meta-analysis investigating the role of chromosome number in monocot hybrid evolution using a newly developed tool, the ploidy deviation index (PDI).

Scholten, J.; Sprenger, A.; Perez, A.; Hullihen, O.; Specht, C. D.

10.1101/2025.11.13.688279 — plant biology — Posted on 2025-11-14

2808 Revisiting Humidity Ramp Protocols for Assessing Human Heat Tolerance

Wang, F.; Xu, Y.; Wang, H.; Cui, M.; Hou, X.; Wei, B.

10.1101/2025.11.09.686670 — physiology — Posted on 2025-11-14

2809 CONCLAVE: CONsensus CLustering with Annotation-Validation Extrapolation for cyclic multiplexed immunofluorescence data

Nazari, P.; Arnould, A.; Andhari, M. D.; Fontecha, M.; Hernandez, J. M.; De Moor, B.; Pey, J.; De Smet, F.; Bosisio, F. M.; Antoranz, A.

10.1101/2025.11.13.688190 — bioinformatics — Posted on 2025-11-14

2810 Covary: A translation-aware framework for alignment-free phylogenetics using machine learning

De los Santos, M.

10.1101/2025.11.13.687960 — bioinformatics — Posted on 2025-11-14

2811 A unified language model bridging de novo and fragment-based 3D molecule design delivers potent CBL-B inhibitors for cancer treatment

Wang, H.; Sun, G.; Zhang, B.; Wang, Y.; Xi, B.; Yang, M.; Liu, C.; Ge, Y.; Fan, F.; Feng, W.; Zhu, Y.; Xiao, Y.; Wang, Y.; Liu, Z.; Jiang, D.; Wang, H.; Zhou, W.; Huang, B.

10.1101/2025.11.13.688260 — bioinformatics — Posted on 2025-11-14

2812 Compound-specific DNA adduct profiling with nanopore sequencing and IonStats

Koski, Y.; Patel, D.; Kakko von Koch, N.; Jouhten, P.; Aaltonen, L.; Palin, K.; Sahu, B.; Pitkanen, E.

10.1101/2025.10.31.685820 — bioinformatics — Posted on 2025-11-14

2813 Biologically-constrained insect models enable realistic simulations and improve biomechanical predictions of locomotion

Yuval, O.; Amir, A.; Ozeri, E.; Ayali, A.

10.1101/2025.11.13.687989 — animal behavior and cognition — Posted on 2025-11-14

2814 Diversity and distribution of the subtelomeric Y' elements across Saccharomyces cerevisiae

Dudragne, L.; Bernardes, J. S.; Xu, Z.

10.1101/2025.11.13.688250 — genomics — Posted on 2025-11-14

2815 Telomere-to-telomere reference genome of the common five-lined skink, Plestiodon fasciatus (Squamata: Scincidae)

Hoffman, J. J.; Burbrink, F.; Pyron, R. A.; Raxworthy, C. J.

10.1101/2025.07.03.663019 — genomics — Posted on 2025-11-14

2816 Dissecting the Cellular Genetics of Cardiovascular Disease Through Endothelial and Immune Compartments Profiling

Watt, S. B.; Ozols, M.; Landini, A.; LIU, B.; Sharapov, S.; Zanotti, D.; Gabriela, I. D.; Solomon, C. U.; Yang, X. D.; Balogun, T.; Staudt, N.; Li, W.; Al-Janabi, F.; Webb, T. R.; McVey, D. G.; Morrell, N. W.; Bennett, M. R.; Samani, N. J.; Gräf, S.; Ye, S.; Pirastu, N.; Soranzo, N.; Frontini, M.

10.1101/2025.11.10.687750 — genomics — Posted on 2025-11-14

2817 Multi-dimensional regulation of LIN-28 temporal expression dynamics in the C. elegans heterochronic gene cascade

Nelson, C.; Ambros, V.

10.1101/2025.11.13.688268 — developmental biology — Posted on 2025-11-14

2818 METTL3-mediated SOCS3 m6A Modification in Preserving CD4+ T Cell Homeostasis in HIV Infected Long-term Non-progressors

Su, J.; Chen, R.; Tao, X.; An, S.; Chen, X.; Qin, T.; Li, J.; Chen, S.; Li, Y.; Lin, Y.; Liu, J.; Chu, J.; Ye, L.; Liang, H.; Jiang, J. j.

10.1101/2025.11.13.688240 — immunology — Posted on 2025-11-14

2819 Interdependent Dynamics of mRNA Expression and HIV-1 Viral Load: Insights from Transcriptomics and Mendelian Randomization

Oreshkov, S.; Thorball, C.; Meylan, J.; Muriset, M.; Calmy, A.; Ciuffi, A.; Elzi, L.; Nemeth, J.; Muhammad, A.; Baumann, L.; Schmid, P.; Stoeckle, M.; Alpern, D.; Fellay, J.; Santoni, F.

10.1101/2025.11.13.688267 — immunology — Posted on 2025-11-14

2820 Does Infarct Size Influence Gut Barrier Integrity and Bacterial Translocation after Experimental Stroke?

Granados-Martinez, C.; ALFAGEME-LOPEZ, N.; Fernandez-Bustelo, A.; Amarilla, M. A.; Navarro-Oviedo, M.; Sevillano-Fernandez, D.; Alou-Cervera, L.; Hurtado, O.; Moro, M. A.; Lizasoain, I.; PRADILLO, J. M.

10.1101/2025.11.13.688219 — neuroscience — Posted on 2025-11-14

2821 A Surgical Protocol for a Large, Resealable Cranial Window Enabling Longitudinal, Multi-Modal Electrophysiological Recordings of the Mouse Default Mode Network

Kiiso, T.; Partanen, P.; Jacobs, K.; Varga, B. A.; Palva, S.; Palva, M.; Castren, E.; Balin, R.

10.1101/2025.11.13.688186 — neuroscience — Posted on 2025-11-14

2822 Selective targeting of hippocampal fast-spiking basket cell interneurons via noninvasive enhancer-AAV delivery

Olah, V. J.; Rowan, M. J.

10.1101/2025.11.13.688234 — neuroscience — Posted on 2025-11-14

2823 cuBNM: GPU-Accelerated Brain Network Modeling

Saberi, A.; Wan, B.; Wischnewski, K. J.; Jung, K.; Sasse, L.; Hoffstaedter, F.; Bernhardt, B. C.; Eickhoff, S. B.; Popovych, O. V.; Valk, S. L.

10.1101/2025.11.13.688224 — neuroscience — Posted on 2025-11-14

2824 Disrupted Top-Down Modulation as a Mechanism of Impaired Multisensory Processing in Autistic Children

Vanneau, T.; Foxe, J. J.; Beker, S.; Molholm, S.

10.1101/2025.11.13.688243 — neuroscience — Posted on 2025-11-14

2825 Gut Microbiota-derived Adenosine Determines the Efficacy of Electroconvulsive Therapy for Depression

Wang, Y.; Dai, M.; Yang, D.; Fan, S.; Zhao, H.; Ye, Z.; Xu, Q.; Dou, Y.; Han, Z.; Li, Y.; Ji, Y.; Wu, Y.; Wang, K.; Zhu, S.; Huang, C.; Tian, Y.

10.1101/2025.11.13.688184 — systems biology — Posted on 2025-11-14

2826 Analytical Solutions for the Time-Dependent Dynamics of Stochastic Gene Expression with mRNA-sRNA Interactions

Yu, Z.; Wang, Y.; Wang, Z.; Shu, Z.; Cao, Z.

10.1101/2025.11.13.688103 — systems biology — Posted on 2025-11-14

2827 Integrated Bioinformatics analysis and Metabolomic Responses in finding novel therapeutic approach to treat viral myocarditis

Yao, L.; Zhou, Q.; Wang, Y.; Shen, A.; Zhou, X.; He, Y.; Wang, J.; Jiang, L.; Yao, J.; Gu, R.; Zhao, J.; Gao, X.; Mu, D.

10.1101/2025.11.13.688209 — pathology — Posted on 2025-11-14

2828 Complexity Begets Simplicity: Self-Supervised Learning for Palaeontological Images with Few or No Labels

Rodgers, N.

10.1101/2025.11.13.688022 — paleontology — Posted on 2025-11-14

2829 Brain-wide Genome Editing via STEP-RNPs for Treatment of Angelman Syndrome

Lu, X.; Xie, Y.; Bao, Y.; Yu, J.; Wang, Z.; Fan, J.; Sheu, W. C.; Long, G.; Tu, Z.; Tong, J.; Manquen, G.; Li, Y.; Katta, V.; Chow, R.; Chen, B.; Meng, Z.; Ma, Y.-h.; Qiu, C.; Chen, S.; Tsai, S.; Kumar, B. D.; Hendry, C. E.; Jiang, Y.-h.; Zhou, J.

10.1101/2025.11.13.684643 — genetics — Posted on 2025-11-14

2830 SignifiKANTE: Efficient P-value computation for gene regulatory networks

Woller, F.; Martini, P.; Sen, S.; Blumenthal, D. B.; Hartebrodt, A.

10.1101/2025.11.13.688227 — bioinformatics — Posted on 2025-11-14

2831 Resource scarcity increases foraging activity despite thermal risk in an arid-adapted bird

Christensen, C.; Sikenykeny, K.; Farine, D.

10.1101/2025.11.13.688088 — ecology — Posted on 2025-11-14

2832 LEM-3/ANKLE1 nuclease prevents the formation of syncytium between postmitotic sister cells and safeguards neuronal differentiation

Deng, S.; Zheng, C.

10.1101/2025.11.13.688214 — developmental biology — Posted on 2025-11-14

2833 Inhibition of lagging strand replication by G-rich telomeric DNA and the shelterin subunit POT1

Leonard-Booker, C.; Mazzucco, G.; Fisher, C. E. L.; Hussain, K.; Deegan, T. D.; Doksani, Y.; Douglas, M. E.

10.1101/2025.11.13.688213 — molecular biology — Posted on 2025-11-14

2834 Nuclear Irregularity as a Universal Diagnostic Tool in Solid Tumors

Hamilton, F.; Foster, K.

10.1101/2025.08.12.669986 — bioinformatics — Posted on 2025-11-14

2835 Depletion of rRNA Methyltranferase METTL5 Enhances Anti-Tumor Immune Response via Neoantigen Generated from Cryptic Translation

Zhang, Y.; Shi, X.; Wang, Y.; Wang, R.; Cao, Y.; Lin, F.; li, w.; Chen, H.

10.1101/2025.06.06.658288 — cancer biology — Posted on 2025-11-14

2836 A machine learning framework for supervised treatment response prediction from tumor transcriptomics: A large-scale pan-cancer study

Pal, L. R.; Gertz, E. M.; Ulhas Nair, N.; Mukherjee, S.; Patiyal, S.; Cantore, T.; Campagnolo, E. M.; Chang, T.; Dhruba, S. R.; Kim, Y.; Shulman, E. D.; Rajagopal, P. S.; Hoang, D.-T.; Schaffer, A. A.; Ruppin, E.

10.1101/2025.10.24.684491 — cancer biology — Posted on 2025-11-14

2837 Tardigrade cytoplasmic abundant heat-soluble proteins serve as membrane protectors during dehydration

Zhang, C.

10.1101/2025.04.14.648834 — cell biology — Posted on 2025-11-14

2838 USP-ddG: A Unified Structural Paradigm with Data Efficacy and Mixture-of-Experts for Predicting Mutational Effects on Protein-Protein Interactions

Yu, G.; Bi, X.; Zhao, Q.; Wang, J.

10.1101/2025.11.09.687124 — molecular biology — Posted on 2025-11-14

2839 Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib

Podszywalow-Bartnicka, P.; Shine, M.; Lin, J.; Neugebauer, K. M.

10.1101/2025.11.04.686193 — molecular biology — Posted on 2025-11-14

2840 Mycobacterial surface shedding drives bystander cells response during early intracellular infection

D'Amico, D.; Raykov, L.; Soldati, T.; Foulon, M.

10.1101/2025.11.13.687818 — microbiology — Posted on 2025-11-14

2841 The Primate Hippocampus Constructs a Temporal Scaffold Anchored to Behavioral Events

Rueckemann, J. W.; Browning, Y.; Mallory, A. J.; Kim, B.; Fairhall, A. L.; Buffalo, E. A.

10.1101/2025.11.12.687961 — neuroscience — Posted on 2025-11-14

2842 Dissecting surveying behavior of reactive microglia under chronic neurodegeneration

Subhramanian, S.; Bocharova, O.; Makarava, N.; Safadi, T.; Baskakov, I. V.

10.1101/2025.06.02.657382 — neuroscience — Posted on 2025-11-14

2843 Towards Modeling in Large-Scale Genetic and Metabolic Networks

Castillo-Villalba, M. P.

10.1101/2025.11.11.687908 — synthetic biology — Posted on 2025-11-14

2844 Single-cell transcriptomics reveals spaceflight-induced accelerated aging and impaired recovery in the murine bone marrow

Zhao, Z.; Zhang, J.; Ji, G.; Zhou, Z.; Yang, Y.; Sun, F.; Lv, H.

10.1101/2025.11.12.688138 — bioinformatics — Posted on 2025-11-14

2845 PRISM: ancestry-aware integration of tissue-specific genomic annotations enhances the transferability of polygenic scores

Tian, X.; Fabiha, T.; Li, W. F.; Dey, K. K.; Kellis, M.; Tanigawa, Y.

10.1101/2025.11.13.688144 — genetics — Posted on 2025-11-13

2846 Lifetime fitness and annual survival are heritable and highly genetically correlated in a wild primate population

Tuliozi, B.; Archie, E.; Tung, J.; Alberts, S.

10.1101/2025.11.13.688343 — evolutionary biology — Posted on 2025-11-13

2847 Disrupted Top-Down Modulation as a Mechanism of Impaired Multisensory Processing in Children with an Autism Spectrum Diagnosis.

Vanneau, T.; Foxe, J. J.; Beker, S.; Molholm, S.

10.1101/2025.11.13.688243 — neuroscience — Posted on 2025-11-13

2848 A Common Neural Signal of Evidence Accumulation for Perceptual and Mnemonic Decisions

Tsvinev, A.; Pilipenko, A.; Samaha, J.

10.1101/2025.11.13.688140 — neuroscience — Posted on 2025-11-13

2849 Processing of Emotional Faces Has Unique Functional and Cytoarchitectural Associations in those with an Autism Spectrum Diagnosis.

Christensen, Z.; Freedman, E. G.; Foxe, J. J.

10.1101/2025.11.13.688249 — neuroscience — Posted on 2025-11-13

2850 Expansion of Working Memory Capacity Supports Early Skill Learning

Iwane, F.; Hayward, W.; Karunathilake, D.; Buch, E. R.; Cohen, L.

10.1101/2025.11.13.686780 — neuroscience — Posted on 2025-11-13

2851 Inhibition of oxytocin neurons during key periods of development has long-term behavioural and body composition effects

Schaller, F.; Alifrangis, M.-S.; BARELLE, P.-Y.; Santos, C.; Tyzio, R.; Bertoni, A.; Omnes, F.; belaidouni, Y.; Bader, F.; Pallesi, E.; Gaiarsa, J.-L.; Bouret, S.; Muscatelli, F.

10.1101/2025.11.13.688271 — neuroscience — Posted on 2025-11-13

2852 Multivariate environmental exposures are reflected in whole-brain functional connectivity and cognition in youth

Lichenstein, S. D.; Weng, Y.; Robinson, H.; Rodriguez, L.; Babaeianjelodar, M.; Maynard, J.; Metayer, M.; Suneja, S.; Horien, C.; Greene, A. S.; Constable, R. T.; Moore, T. M.; Barzilay, R.; Yip, S. W.; Keller, A. S.

10.1101/2025.11.13.688261 — neuroscience — Posted on 2025-11-13

2853 Storing long-lived memories via molecular error correction: a minimal mathematical model of Crick's memory switch

Vastola, J. J.; Ramdas, T.; Gershman, S. J.

10.1101/2025.11.13.688304 — systems biology — Posted on 2025-11-13

2854 The Sikkim mouse (Mus pahari) exhibits distinct spatial, circadian, and social behaviors compared to laboratory mice

Vogt, C. C.; Sheehan, M. J.

10.1101/2025.11.13.688123 — animal behavior and cognition — Posted on 2025-11-13

2855 Mechanism of Phosphatidylserine Lipid Scrambling by Human SERINC3, an HIV-1Restriction Factor

Banerjee, P.; Yeager, M.; Voth, G. A.

10.1101/2025.11.13.688349 — biophysics — Posted on 2025-11-13

2856 TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity

Du, J.; Wijayaratna, U. N.; Wang, X.; Fung, J. P.; Huang, B.; Farzaneh, F.; Kohn, D. B.; Combes, A. J.; Gaensler, K. M. L.

10.1101/2025.11.07.687000 — cancer biology — Posted on 2025-11-13

2857 Activation and regulation of the dynein-dynactin-NuMA complex

Aslan, M.; d'Amico, E. A.; Cho, N. H.; Taheri, A.; Perez-Bertoldi, J. M.; Zhao, Y.; Zhong, X.; Blaauw, M.; Carter, A. P.; Dumont, S.; Yildiz, A.

10.1101/2024.11.26.625568 — biophysics — Posted on 2025-11-13

2858 Applying standardised methods to assess the potential risks of alien freshwater crayfish introductions to South Africa

Botha, L.-A.; Chimimba, C. T.; Zengeya, T. A.

10.1101/2025.11.12.687953 — ecology — Posted on 2025-11-13

2859 Late-Onset Preeclampsia is characterised by Accelerated Placental Aging

Arthurs, A. L.; Bhattacharjee, R.; Smith, M. D.; Medina, D.; Menkhorst, E.; Mora, G.; Williamson, J. M.; Harris, L.; Polo, J. M.; MacIntyre, D.; Roberts, C. T.

10.1101/2025.11.12.687933 — developmental biology — Posted on 2025-11-13

2860 A biological PROTAC for α-synuclein.

O'Shea, C. M.; Wright, G. S. A.

10.1101/2025.11.13.687972 — molecular biology — Posted on 2025-11-13

2861 The G3BP stress-granule proteins reinforce the integrated-stress-response translation program

Smith, J.; Bartel, D. P.

10.1101/2024.10.04.616305 — molecular biology — Posted on 2025-11-13

2862 A dynamic causal inference framework for perception-action loops

Cooke, J. R. H.; Medendorp, W. P.

10.1101/2025.11.13.688198 — neuroscience — Posted on 2025-11-13

2863 Aligning transformer circuit mechanisms to neural representations in relational reasoning

Hearne, L. J.; Robinson, C. N.; Cocchi, L.; Ito, T.

10.1101/2025.10.29.685457 — neuroscience — Posted on 2025-11-13

2864 Identifying Neuroimaging Biomarkers of Resilience and Vulnerability to Chronic Stress in An Animal Model: An Exploratory Analysis

Dai, T.; Algar, S. D.; Small, M.; Zalesky, A.; Rodger, J.

10.1101/2025.08.05.667822 — neuroscience — Posted on 2025-11-13

2865 Observing being touched enhances the neural processing and perception of digital gentle stroking

Gonzalez Sousa, B.; Senkowski, D.; Li, S.-C.

10.1101/2025.11.13.688063 — neuroscience — Posted on 2025-11-13

2866 Sub-strain-Dependent Differences in Gut Barrier Permeability, Bacterial Translocation and Post-Stroke Inflammation in Wistar Rats

Granados-Martinez, C.; Alfageme-Lopez, N.; Navarro-Oviedo, M.; Mora-Cuadrado, V.; Sevillano-Fernandez, D.; Alou-Cervera, L.; Fernandez-Valle, M. E.; Hurtado, O.; Moro, M. A.; Lizasoain, I.; PRADILLO, J. M.

10.1101/2025.11.13.688185 — neuroscience — Posted on 2025-11-13

2867 Microbial Cell-Adaptive Segmentation in Quantitative Phase Imaging

Tuson, S. J.; Nemati, S. J.; Alleman, A. B.; Marx, C. J.; Vasdekis, A. E.

10.1101/2025.11.13.688197 — systems biology — Posted on 2025-11-13

2868 Redistribution of excitation energy between two photosystems during light-shade adaptation in marine diatoms: State conversion of light-harvesting complexes

Inoue-Kashino, N.; Kumazawa, M.; Aikawa, S.; Fujimoto-Omori, K.; Ishihara-Masunaga, T.; Kudoh, S.; Satoh, K.; Takahashi, Y.; Ifuku, K.; Kashino, Y.

10.1101/2025.11.13.688172 — plant biology — Posted on 2025-11-13

2869 Systemic and local regulation of root growth by vascular trehalose 6-phosphate is correlated with re-allocation of primary metabolites between shoots and roots

Goebel, M.; Foster, J.; Westhoff, P.; Skorzinski, N.; Lepper, H.; Njo, M. F.; Schmid, M.; Beeckman, T.; Tanurdzic, M.; Amtmann, A.; Fichtner, F.

10.1101/2025.11.13.688188 — plant biology — Posted on 2025-11-13

2870 A PLM-Based Method for Predicting Protein Ion Channel Modulators for Drug Discovery and Safety Evaluation

Rathore, A. S.; Jain, S.; Mehta, N. K.; Raghava, G. P. S.

10.1101/2025.11.13.688159 — bioinformatics — Posted on 2025-11-13

2871 PocketMaster: a flexible, automated tool for analyzing, clustering, and visualizing protein pocket structural diversity

Abelyan, N.

10.1101/2025.10.30.685483 — bioinformatics — Posted on 2025-11-13

2872 Benchmarking Real-World Applicability of Molecular Generative Models from De novo Design to Lead Optimization with MolGenBench

Cao, D.; Fan, Z.; Yu, J.; Chen, M.; Jiang, X.; Wang, X.; Sheng, X.; Zeng, C.; Luo, X.; Teng, D.; Zheng, M.

10.1101/2025.11.03.686215 — bioinformatics — Posted on 2025-11-13

2873 A Single-Aliquot, Enrichment-Free Workflow for High-Throughput Plasma Proteome and N-Glycoproteome Profiling

Chang, K.-H.; Deyarmin, J.; Pradita, T.; Chen, Y.-J.; Samra, S.; Chang, G.-C.; Yu, C.-J.; Chuang, Y.-S.; Arrey, T.; Hsu, H.-E.; Xuan, Y.; Huang, P.-R.; Lin, K.-T.; Yen, K.-H.; Tsai, H.-j.; Hermanson, D.; Chang, Y.; Yu, S.-L.; Yang, P.-C.; Chen, Y.-J.

10.1101/2025.11.11.687106 — biochemistry — Posted on 2025-11-13

2874 A comprehensive AMR genotype-phenotype database (CABBAGE)

Dickens, E.; Derelle, R.; Beardmore, R. E.; Suresh, A.; Uplekar, S.; Yates, A. D.; Keatley, J.; Winterbottom, A.; Azov, A.; El Houdaigui, B.; Ochkalova, S.; Gurbich, T. A.; Shivalikanjli, A.; Yordanova, G.; Lees, J.; Chindelevitch, L.

10.1101/2025.11.12.688105 — genomics — Posted on 2025-11-13

2875 Sequence context and methylation interact to shape germline mutation rate variation at CpG sites

Chandra, S.; Gao, Z.

10.1101/2025.11.13.688199 — genetics — Posted on 2025-11-13

2876 Apoptosis reveals human evolutionary heritage sequestered in non-coding DNA

Joshi, R.; Roy, A.; Lopes, R.; Kata, L.; Selukar, R.; Markam, M.; Banerji, S.; Raghuram, G. V.; Shabrish, S.; Mittra, I.

10.1101/2025.11.13.688179 — evolutionary biology — Posted on 2025-11-13

2877 TRIM24 preserves cardiomyocyte immune quiescence by repressing interferon/STAT signaling

Neu, M.; Borlepawar, A.; Deshpande, A.; Neuberger, L.; Baral, T. K.; Senger, F.; Hammer, E.; Schmiedel, N.; Hausmann, M.; Frey, N.; Kumari, M.; Rangrez, A. Y.

10.1101/2025.11.13.688187 — molecular biology — Posted on 2025-11-13

2878 Regional adaptation to mosquito vectors shapes Plasmodium falciparum populations

Loesbanluechai, D.; Sollelis, L.; Armstrong, M.; Menezes, I.; Cox, A.; Divala, L. B. T.; Lawson, A.; Pradhan, S.; Ubiaru, P. C.; Pallikara, A.; Parker, G.; Pearson, R. D.; Lee, C.; Stokes, B. H.; Ranford-Cartwright, L. C.; Marti, M.; Howick, V. M.

10.1101/2025.11.13.688255 — microbiology — Posted on 2025-11-13

2879 Molecular insights into phycobilisome assembly pathway reveal crystalline bodies in cyanobacteria

Dahlgren, K.; Avramov, A.; Koke, E.; Iragavarapu, A. G.; Hren, A.; Acosta-Reyes, F. J.; Carl, A.; Herrmann, J.; Goldstein, L.; Spear, J.; Cameron, J. C.; Aydin, H.

10.1101/2025.11.13.688327 — microbiology — Posted on 2025-11-13

2880 Increased striatal coupling one week after ischemic stroke revealed by ultrafast functional MRI

Shemesh, N.; Alves, R.; Cabral, J.; Carvalho, T.

10.1101/2025.11.12.688149 — neuroscience — Posted on 2025-11-13

2881 Non-canonical, ligand-independent basal mGluR1 signaling tunes Kv1.2 surface expression through PKA

Madasu, S. C.; Morielli, A.

10.1101/2025.11.12.687507 — neuroscience — Posted on 2025-11-13

2882 Paw posture is a robust indicator for injury, pain, and age.

Pritz, C. O.; Dotta, S.; Freund, P. A.; Musso, G.; Bader, M.; Okladnikov, N.; Rother, F.; Marvaldi, L.

10.1101/2025.11.13.688005 — neuroscience — Posted on 2025-11-13

2883 Cross-task, explainable, and real-time decoding of human emotion states by integrating grey and white matter intracranial neural activity

Yang, Y.; Chen, W.; Chen, Y.; Ding, L.; Zhang, C.; Jiang, H.; Zhu, Z.; Guo, X.; Wang, S.; Pan, G.; Wei, N.; Hu, S.; Zhu, J.; Wang, Y.

10.1101/2025.11.12.687932 — neuroscience — Posted on 2025-11-13

2884 Interpretable and Brain-Inspired Recurrent Model of Hierarchical Decision-Making Capturing Trial-by-Trial Variability

Mousavi-Harris, A.; Zabbah, S.; Esmaily, J.; Ebrahimpour, R.

10.1101/2025.11.13.688200 — neuroscience — Posted on 2025-11-13

2885 Thalamofrontal synaptic weakening underlies short-term memory deficits from adolescent NMDAR hypofunction

Yu, J.; Choi, I. S.; Kim, G. H.; Bahn, S.; Bae, S.; Lee, T.; Choi, J. H.; Kwon, J. S.; Kim, M.; Lee, K. J.; Rah, J.-C.

10.1101/2025.11.11.687794 — neuroscience — Posted on 2025-11-13

2886 Single-component optogenetic control enables human portrait formation in cells

Yilmaz-Atay, F.; Kocoglu, M.; Cevik, B. N.; Eker, A. C.; Demirozcan-Kurun, E.; Ozturk, N.

10.1101/2025.11.13.688218 — synthetic biology — Posted on 2025-11-13

2887 Myosin VI orchestrates estrogen-driven gene expression in breast cancer cells.

Hari-Gupta, Y.; Lambert, D.; Shahid-Fuente, I.; Fili, N.; dos Santos, A.; Sprules, A.; Kim, H. R.; Cook, A.; Ellis, P. J.; Arron, J. J.; Chew, T. L.; Wang, L.; Toseland, C. P.

10.1101/2025.11.13.688007 — cancer biology — Posted on 2025-11-13

2888 Mechanism of Phosphatidylserine Lipid Scrambling by Human SERINC3, an HIV-1Restriction Factor

Banerjee, P.; Yeager, M. A.; Voth, G. A.

10.1101/2025.11.13.688349 — biophysics — Posted on 2025-11-13

2889 Benchmarking Framework to Catalyze Individual Human Genome Projects

Kalpande, M.; Ganesh, A.; Srinivasan, S.

10.1101/2025.11.12.688148 — bioinformatics — Posted on 2025-11-13

2890 In silico assessment of arrhythmic risk following the implantation of engineered heart tissues in porcine hearts with varying infarct locations

Rosales, R. M.; Rios-Munoz, G. R.; Sanchez de la Nava, A. M.; Fernandez-Santos, M. E.; Bermejo, J.; Doblare, M.; Minchole, A.; Pueyo, E.

10.1101/2025.11.13.688201 — bioengineering — Posted on 2025-11-13

2891 Opponent-flipping tactics in aggressive interactions of the cricket Gryllus bimaculatus

Murata, A.; Takemoto, K.; Aonuma, H.

10.1101/2025.11.13.688168 — animal behavior and cognition — Posted on 2025-11-13

2892 Plasmodium vivax genome evolution for erythrocyte invasion in Duffy-negative infections from East Africa

Ford, A. F.; Dieng, C. C.; Abagero, B. R.; Yan, G.; Yewhalaw, D.; Janies, D.; Lo, E.

10.1101/2025.11.13.688259 — genomics — Posted on 2025-11-13

2893 Expression of four mitochondrial tRNAs from only two loci

Warren, J. M.; Prasad, K. V. S. K.; Mendez, A. M.; Temnyk, S.; McCutcheon, J.

10.1101/2025.11.12.688142 — molecular biology — Posted on 2025-11-13

2894 Mutant p53 binds RNA to drive mitochondrial dysfunction

Zhou, W.; Long, A.; Douglas, C. J.; Gallegos, D.; Burke, J.; MacMillan, D.; Hacisuleyman, E.; Seath, C. P.

10.1101/2025.11.12.688127 — molecular biology — Posted on 2025-11-13

2895 Development of a Norway Rat Hepacivirus Reporter for High-Throughput Quantification of Neutralising Antibodies

Kennedy, M. J.; Wolfisberg, R.; Thorselius, C.; Collignon, L.; Lundsgaard, E. A.; Nielsen, L.; Holmbeck, K.; Bukh, J.; Scheel, T. K. H.

10.1101/2025.11.13.688247 — microbiology — Posted on 2025-11-13

2896 Compositional analysis of yellow fever virus induced stress granules reveals a functional connection to mitochondrial homeostasis

Jakob, C.; Streicher, F.; Lopez-Nieto, M.; Eke, L.; Lee, D.; Wu, J.; Taylor, J. P.; Matia-Gonzalez, A. M.; Jouvenet, N.; Locker, N.

10.1101/2025.11.13.688208 — microbiology — Posted on 2025-11-13

2897 An optimized flow cytometry sorting-sequencing workflow reduces storage, sorting and extraction bias in sorted microbial communities

Goethals, V.; Vanwinsen, N.; Mermans, F.; De Gand, S.; Boon, N.; van de Wiele, T.; De Paepe, K.

10.1101/2025.11.13.688239 — microbiology — Posted on 2025-11-13

2898 Niche partitioning by resource size in the gut microbiome

Moreno-Gamez, S.; Anderson, B. W.; Vercelli, G. T.; Altmann, F.; Goodman, A. L.; Cordero, O. X.

10.1101/2025.11.13.688124 — microbiology — Posted on 2025-11-13

2899 Phosphate Limitation Modulates Vibrio cholerae Outer Membrane Vesicle Formation, Composition and Toxicity

Luchetta da Fonseca, M.; Carvalho Barbosa, L.; Patricio, B. F. d. C.; Ferreira, W. d. S.; Keim, C. N.; Delporte, C.; van Antwerpen, P.; Ruysschaert, J.-M.; Mascarello Bisch, P.; Maria Almeida von Kruger, W.

10.1101/2025.11.13.688205 — microbiology — Posted on 2025-11-13

2900 When Brain Models Are not Universal: Benchmarking of Ethnic Bias in MRI-Based Cognitive Prediction Across Modalities

Lal Khakpoor, F.; van der Vliet, W.; Deng, J.; Pat, N.

10.1101/2025.11.12.688133 — neuroscience — Posted on 2025-11-13

2901 The antiviral Interferon pathway drives astrocyte aging and motor decline

Labarta-Bajo, L.; Thanawalla, A. R.; Gutierrez, I. L.; Lei Soe, S. M.; Chick, B. Y.; Andritsogianni, I.; Metanat, S.; Hargreaves, D. C.; Kaech, S. M.; Azim, E.; Allen, N. J.

10.1101/2025.11.12.688147 — neuroscience — Posted on 2025-11-13

2902 Head stabilization behavior and underlying circuit mechanisms in larval zebrafish

Sugioka, T.; Thiele, T. R.; Baier, H.; Tanimoto, M.; Higashijima, S.-i.

10.1101/2025.11.12.688155 — neuroscience — Posted on 2025-11-13

2903 MitoEM 2.0 - A Benchmark for Challenging 3D MitochondriaInstance Segmentation from EM Images

Liu, P.; Shen, B.; Liu, L.; Wang, Q.; Zhang, S.; Bhardwaj, A.; Arganda-Carreras, I.; Narayan, K.; Wei, D.

10.1101/2025.11.12.687478 — neuroscience — Posted on 2025-11-13

2904 Conjugation-mediated DNA delivery to the filamentous fungus Ustilago maydis

Jaafar, T.; Jaafar, A.; Nasrollahi, V.; Karas, B. J.

10.1101/2025.11.13.688287 — synthetic biology — Posted on 2025-11-13

2905 E1: Retrieval-Augmented Protein Encoder Models

Jain, S.; Beazer, J.; Ruffolo, J. A.; Bhatnagar, A.; Madani, A.

10.1101/2025.11.12.688125 — synthetic biology — Posted on 2025-11-13

2906 Genetic and preclinical evidence implicating chondroitin sulfate as a matritherapeutic target for the treatment of type 2 diabetes

Johansen, V. B. I.; Lund, J.; Romero-Lado, M. J.; Breum, A. W.; Svendsen, C.; Jorgensen, K. S.; Miller, R. L.; Fritzen, A. M.; Kilpeläinen, T. O.; Schjoldager, K. T.; Clemmensen, C.

10.1101/2025.11.12.688143 — physiology — Posted on 2025-11-13

2907 A dual-metric framework for quantifying the biological fidelity of scRNA-seq pipelines

Su, Q.; Long, Y.; Duan, F.; Lian, Q.

10.1101/2025.11.12.688141 — bioinformatics — Posted on 2025-11-13

2908 CycleGRN: Inferring Gene Regulatory Networks from Cyclic Flow Dynamics in Single-Cell RNA-seq

Zhao, W.; Fertig, E. J.; Stein-O'Brien, G. L.

10.1101/2025.11.12.688126 — bioinformatics — Posted on 2025-11-13

2909 MindSight: A Bio-Inspired Neural Architecture for Visual Restoration via Cortical Electrical Stimulation

Zou, Y.; Niu, H.; Zhao, B.; Yi, G.; Yang, M.; Ju, J.; Yin, J.; Li, C. T.

10.1101/2025.11.12.688136 — bioengineering — Posted on 2025-11-13

2910 Neuronal tRNA Modifications in Aplysia californica are Repatterned during Behavioral Habituation

Huang, H. X.; Floro, G. M.; Asare, E.; Huang, W.; Clark, K. D.

10.1101/2025.11.13.688303 — biochemistry — Posted on 2025-11-13

2911 The virulence gene ToxB is both amplified and disrupted by transposons in the wheat pathogen Pyrenophora tritici-repentis

Gourlie, R.; McDonald, M. C.; Hafez, M.; Aboukhaddour, R.

10.1101/2025.11.13.688278 — evolutionary biology — Posted on 2025-11-13

2912 Applying invasion criterion to cultural evolution

Shibasaki, S.; Yamamichi, M.

10.1101/2025.11.12.688139 — evolutionary biology — Posted on 2025-11-13

2913 Cytoplasmic roles of HSATIII RNAs in RNA granule assembly and production of actin cytoskeleton-associated repeat-containing proteins

Ninomiya, K.; Adachi, S.; Suzuki, T.; Souquere, S.; Pierron, G.; Inada, T.; Hirose, T.

10.1101/2025.11.12.688122 — molecular biology — Posted on 2025-11-13

2914 Peroxiredoxin 1 safeguards the nucleolar genome from oxidative damage

Furusawa, T.; Gujar, V.; Sharma, S.; Boateng, F.; Li, H.; Achour, C.; Taniyama, D.; Pommier, Y.; Oberdoerffer, S.; Stracker, T. H.; Weyemi, U.

10.1101/2025.11.12.685177 — molecular biology — Posted on 2025-11-13

2915 A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker)

Clark, R. C.; Manning, A. C.; Howard, J. M.; Barberan-Soler, S.; Kazakov, S. A.

10.1101/2025.11.12.688114 — molecular biology — Posted on 2025-11-13

2916 Cap1 forms a cyclic tetra-adenylate-induced membrane pore during the type III-A CRISPR-Cas immune response

Majumder, P.; Cahir, C. W.; Roberts, C. G.; Patel, D. J.; Marraffini, L. A.

10.1101/2025.11.13.688252 — microbiology — Posted on 2025-11-13

2917 Viral RNA persistence in sheep tissues following acute Crimean-Congo hemorrhagic fever virus infection

Li, H.; Moffat, E.; Handel, K.; Nebroski, M.; Sullivan, D.; Embury-Hyatt, C.; Lung, O.; Pickering, B. S.

10.1101/2025.11.13.688338 — microbiology — Posted on 2025-11-13

2918 Random barcode transposon-site sequencing in Mycobacterium tuberculosis reveals the functions of uncharacterized genes

Dinshaw, K.; Lien, K.; Knight, M.; Ounkap, S.; Liu, H.; Savage, D.; Carlson, H.; Deutschbauer, A.; Stanley, S. A.

10.1101/2025.11.13.688195 — microbiology — Posted on 2025-11-13

2919 Adaptation of Anaplasma phagocytophilum to the tick vector is controlled by the transcriptional regulator Tr1

Warwick, E.; Burt, R.; Badigian, J. T.; Howell, D.; Swallow, K. T.; Leach, C.; Falghoush, A. M.; Shaw, D. K.; Cadby, I. T.; Park, J. M.

10.1101/2025.11.12.688119 — microbiology — Posted on 2025-11-13

2920 Sugar ABC transporter repertoires predict ecological dynamics in gut microbiome communities

Maan, H.; Jogia, W.; Duan, C.; Matheis, F.; Nishimoto, E.; Zhang, C.; Sullivan, A.; Schluter, J.

10.1101/2025.11.12.686590 — microbiology — Posted on 2025-11-13

2921 Construction of a CMV promoter-driven Langat virus cDNA clone and reporter viruses

Hermacinski, A. I.; Richardson, R. B.; Bednarski, E.; Salim, M.; Garg, A.; Lim, J. K.; Evans, M. J.

10.1101/2025.11.13.688285 — microbiology — Posted on 2025-11-13

2922 Mycobacterial surface shedding drives bystander cells response during early intracellular infection

D'Amico, D.; Raykov, L.; Soldati, T.; Foulon, M.

10.1101/2025.11.13.687818 — microbiology — Posted on 2025-11-13

2923 M-Sec promotes the production of infectious HIV-1 virus through the exocyst complex

Mahmoud, R. M.; Hiyoshi, M.; Abdelnaser, R. A.; Monde, K.; Monde, N.; Koma, T.; Mizuno, H.; Habash, S. A.; Takahashi, N.; Maeda, Y.; Ono, A.; Suzu, S.

10.1101/2025.11.13.688207 — microbiology — Posted on 2025-11-13

2924 In situ profiling of bacterial growth activity during the early stages of Pseudomonas aeruginosa infection in airway epithelia

Fuglsang-Madsen, A.; Haagensen, J. A. J.; Colque, C. A.; Johansen, H. K.; Molin, S.

10.1101/2025.11.13.688211 — microbiology — Posted on 2025-11-13

2925 ISKNV-pORF71 hijacks outer mitochondrial membrane-localized VDAC2 to the nucleus, enhancing apoptosis by disrupting mitochondrial membrane permeability

Zhang, H.-t.; Fu, Y.; Dong, Y.; Qi, H.; Weng, S.; He, J.; Dong, C.

10.1101/2025.11.13.688210 — microbiology — Posted on 2025-11-13

2926 Antibiotic-resistance mutations in penicillin-binding protein 2 from the ceftriaxone-resistant Neisseria gonorrhoeae strain H041 strike a delicate balance between increasing resistance and maintaining transpeptidase activity

Bivins, M. M.; Tomberg, J.; Bagshaw, M.; Singh, A.; Bala, S.; Davies, C.; Nicholas, R. A.

10.1101/2025.11.13.688206 — microbiology — Posted on 2025-11-13

2927 Enrichment of a CD4-CD8- NK-like cytotoxic Vδ1/3 T cell subset in tuberculosis disease

Kearns, K.; Tippalagama, R.; Chawla, A.; Greenbaum, J.; De Silva, A. D.; Gunasinghe, W.; Perera, J.; Gunasekara, H.; Senevirathne, D. D.; Scriba, T.; Burel, J. G.; Lindestam Arlehamn, C. S.; Peters, B.

10.1101/2025.11.12.688134 — immunology — Posted on 2025-11-13

2928 Central role for fast nociceptors in mechanical nocifensive behavior and sensitization

Chen, J. C.-Y.; Le Moëne, O.; de-Faria, F. M.; Ahemaiti, A.; Thorell, O.; Kaczmarczyk, L.; Henriksson, K.; Cole, J.; Olausson, H.; Jackson, W. S.; Nagi, S. S.; Lagerström, M. C.; Szczot, M.; Larsson, M.

10.1101/2025.11.12.688120 — neuroscience — Posted on 2025-11-13

2929 Electrophysiological Brain Connectivity and Subjective States Evoked by Electrical Stimulation of the Human Mediodorsal Thalamus

Pantis, S.; Lyu, D.; Quabs, J.; Huang, W.; Togo, M.; Jung, H.; van Staalduinen, E.; Liu Yang, L.; Chan, A.; Fedor, M.; Fisher, R.; Buch, V.; Parvizi, J.

10.1101/2025.11.12.688132 — neuroscience — Posted on 2025-11-13

2930 Integrated microdroplet workflow for high-throughput cell-free transcription in double emulsion picoreactors

Totlani, K.; Khan, E. A.; Ahmed, H.; Lale, R.; Stokke, B. T.

10.1101/2025.11.13.688266 — synthetic biology — Posted on 2025-11-13

2931 A High-throughput Sequencing Screen to Identify Apomixis in Plants

Goeckeritz, C. Z.; Polcar, V.; Gutierrez, B.; Urfus, T.; Harkess, A.

10.1101/2025.11.12.688100 — plant biology — Posted on 2025-11-13

2932 DTI-ALPS PRIMARILY REFLECTS WHITE MATTER DIFFUSION DISPERSION AND MICROSTRUCTURAL HETEROGENEITY IN NEURODEGENERATION: INSIGHTS FROM MULTI-MODAL MRI

Sacchi, L.; Farruggio, G.; Bocca, G.; Carandini, T.; De Riz, M.; Ghezzi, L.; Pintus, M.; Pietroboni, A. M.; Boffa, G.; Scola, E.; Triulzi, F.; Bozzali, M.; Cercignani, M.; Galimberti, D.; Arighi, A.

10.1101/2025.11.12.688102 — neuroscience — Posted on 2025-11-13

2933 Crossing thermal limits: functional collapse of the surfgrass Phyllospadix scouleri under extreme marine heatwaves

Vivanco-Bercovich, M.; Bonet-Melia, P.; Schubert, N.; Marin-Guirao, L.; Muniz-Salazar, R.; Cabello-Pasini, A.; Ferreira-Arrieta, A.; Garcia-Pantoja, J. A.; Guzman-Calderon, J. M.; Procaccini, G.; Samperio-Ramos, G.; Sandoval-Gil, J. M.

10.1101/2025.11.12.688107 — plant biology — Posted on 2025-11-13

2934 Off-target mapping enhances selectivity of machine learning-predicted CK2 inhibitors

Ying, H.; Kong, W.; Schulman, A.; Panajotovikj, N.; Tanoli, Z.; Mestres, J.; Aittokallio, T.; Miihkinen, M.

10.1101/2025.11.12.688093 — pharmacology and toxicology — Posted on 2025-11-13

2935 Wasserstein Critics Outperform Discriminatorsin Adversarial Deconfounding of Gene Expression Data

Reid, K.; Guven, E.

10.1101/2025.11.12.688061 — bioinformatics — Posted on 2025-11-13

2936 Inferring cellular communication through mapping cells in space using Tangram 2

Huang, H.; Andersson, A.; Wu, S. Z.; Scalia, G.; Collier, J.; Hoi, K. H.; Muller, S.; Heimberg, G.; Corrada Bravo, H.; Gaddam, S.; Huetter, J.-C.; Turley, S.; Richmond, D.; BenTaieb, A.; Biancalani, T.

10.1101/2025.09.28.679077 — genomics — Posted on 2025-11-13

2937 Circulating chromatin reveals the effects of disease-associated variants on gene regulation

Zhang, Z.; Chhetri, S. B.; Semaan, K.; Zhang, Z.; Jin, Z.; Sotudian, S.; Liang, L.; Gusev, A.; Baca, S. C.

10.1101/2025.11.12.688010 — genomics — Posted on 2025-11-13

2938 Fantastic Antagonists and Where to Find Them: The Global Distribution of Nematode-Antagonistic Fungi

van Himbeeck, R.; Smant, G.; Geisen, S.; Helder, J.

10.1101/2025.11.12.688024 — ecology — Posted on 2025-11-13

2939 No rest for the rodent: energy management strategies in the naked mole-rat

Chan, P. V.; Turchyn, D. M.; Careau, V.; Pamenter, M. E.

10.1101/2025.11.12.688094 — ecology — Posted on 2025-11-13

2940 Mycobacterium tuberculosis suppresses protective Th17 responses during infection

Zilinskas, A.; Balakhmet, A.; Fox, D.; Ni, H. M.; Agudelo, C.; Samani, H.; Stanley, S. A.

10.1101/2025.05.08.652811 — immunology — Posted on 2025-11-13

2941 Inflammation increases the penetrance of behavioral impairment in Shank3 haploinsufficiency mice -- can it explain the behavioral regression in Autism?

Qiao, S.-N.; Wang, S. E.; Kim, K.-Y.; Jo, S.; Jiang, Y.-H.

10.1101/2025.08.07.669241 — neuroscience — Posted on 2025-11-13

2942 Single-cell transcriptome of developing inhibitory neurons reveals expanding and contracting modes of diversification.

Liu, M.; Ferrero Restelli, F.; Micoli, E.; Barbiera, G.; Moors, R.; Nouboers, E.; Reverendo, M.; Du, J. X.; Bertels, H.; Konstantopoulos, D.; Wierd, K.; Takeoka, A.; Lippi, G.; Lim, L.

10.1101/2025.02.19.636192 — neuroscience — Posted on 2025-11-13

2943 Hyperthermic Seizure Susceptibility and Focal Decreases in Parvalbumin-Expressing Cortical Interneurons in a Mouse Model of PCDH19-Clustering Epilepsy

Ziobro, J.; Huang, J.; Daddo, N.; Margolis, E.; Jonatzke, K.; Umemori, H.; Parent, J. M.

10.1101/2025.11.12.688097 — neuroscience — Posted on 2025-11-13

2944 Towards modeling in Large-Scale Genetic and Metabolic Networks

Villalba, M. P. C.

10.1101/2025.11.11.687908 — systems biology — Posted on 2025-11-13

2945 ER-located PIN5 transporter generates potent auxin sinks driven by the IAA decarboxylation pathway

Covanova, M.; Muller, K.; Klierova, N.; Abdollahi Sisi, N.; Skupa, P.; Smetana, O.; Dobrev, P. I.; Ruzicka, K.; Petrasek, J.

10.1101/2024.01.24.576992 — plant biology — Posted on 2025-11-13

2946 RHOA Deletion Downregulates CD19 and Promotes Dysfunctional Immune Microenvironments in CAR-T Resistant B-Cell Lymphoma

Newsam, A. D.; Ziccheddu, B.; Youssfi, A. A.; Gowda Saralamma, V. V.; Goretsky, Y. E.; Sheffield-Veney, I.; Manara, P.; Tsai, D. E.; Jeevan, A.; Foos-Russ, S.; Suissa, D. M.; Russo, M. V.; Fattakhov, N.; Carmona-Berrio, D.; Campos Gallego, N.; Coughlin, C. A.; Sondhi, A. K.; Roberts, E. R.; Spiegel, J. Y.; Alderuccio, J. P.; Amador, C.; Bilbao, D.; Coffey, D. G.; Jain, M. D.; Maura, F.; Locke, F. L.; Schatz, J. H.

10.1101/2025.02.27.640687 — cancer biology — Posted on 2025-11-13

2947 Ribosomal protein control of hematopoietic stem cell transformation through regulation of metabolism.

Harris, B.; Singh, D. K.; Truong, B.; Rhodes, M.; Price, R.; Shinton, S.; Verma, M.; Aylward, B.; Fahl, S. P.; Sprinkle, S. R.; Aminov, S.; Wang, M.; Zhang, Y.; Perrigoue, J.; Kessel, R.; Peri, S.; West, J.; Giricz, O.; Boultwood, J.; Pellagatti, A.; Ramesh, K.; Montangna, C.; Pradhan, K.; Tyner, J.; Kennedy, B. K.; Holinstat, M.; Steidl, U.; Sykes, S.; Verma, A.; Wiest, D. L.

10.1101/2023.05.31.543132 — cancer biology — Posted on 2025-11-13

2948 GABA-GABA_A Receptor Signaling Orchestrates Invasion and Metastasis in Triple Negative Breast Cancer

Afolayan, E.; Zhang, B.; Han, M.; White, C.; Emmanuel, M.; Velenosi, T. J.; Williams, K. C.

10.1101/2025.10.03.674636 — cancer biology — Posted on 2025-11-13

2949 Quantitative Analysis of Cytoplasmic Viscosity in Colorectal Cancer Cells by Differential Dynamic Microscopy of Genetically Encoded Nanoparticles

Huysecom, S.; Schouwstra, K.; Aytekin, S.; Neyrinck, N.; Heyvaert, Y.; Louis, B.; Rocha, S.; Solis Fernandez, G.

10.1101/2025.11.13.687967 — biophysics — Posted on 2025-11-13

2950 Axis-specific neuro-musculoskeletal contributions to postural stability and vibration avoidance in mice

Suzuki, M.; Saito, M.; Ueda, T.; Inaba, H.; Sasaki, K.; Hirai, H.; Hosoi, N.

10.1101/2025.11.12.687975 — biophysics — Posted on 2025-11-13

2951 Spatially Resolved Determination of Small Molecule Protein Affinities by Hydrogen Deuterium Exchange Mass Spectrometry

Lin, D.; Magalhaes, L. G.; McMillan, J.; Eadsforth, T. C.; Stewart, G.; Cartmill, K.; Postis, V.; Masson, G.

10.1101/2025.11.13.688232 — biophysics — Posted on 2025-11-13

2952 Machine-learning informs mitigation strategies for nitrous oxide emissions from wastewater operations

Augustine, G.; Chandran, K.

10.1101/2025.08.31.673305 — bioengineering — Posted on 2025-11-13

2953 Individual and social contributions to learning of mice in Intellicages: the general framework and mean field theory

Jura, B.; Lenarczyk, M.; Harda, Z.; Szumiec, Łukasz; Ziemianska, M.; Kłosowicz, R.; Parkitna, J. M. R.; Wojcik, D. K.

10.1101/2025.11.12.687796 — animal behavior and cognition — Posted on 2025-11-13

2954 Distinct D-Box Motifs in SPD-2 Mediate APC/CFZR-1-Dependent Degradation and Centrosomal Localization in Caenorhabditis elegans

Yim, R. N.; Rivera, P.; DiPanni, J.; Song, M. H.

10.1101/2025.10.14.682142 — genetics — Posted on 2025-11-13

2955 Ecological context shapes microbial contributions to nutrition and development in Drosophila melanogaster

Riedel, E. K.; Lender, L.; Kowallik, V.; Pollierer, M. M.; Rohlfs, M.

10.1101/2025.10.14.682149 — ecology — Posted on 2025-11-13

2956 A vascular origin for pulmonary smooth muscle in the avian lung

Griffing, A. H.; Goodwin, K.; Palmer, M. A.; Park, C. J.; Rothstein, M.; Brack, B. J.; Moreno, J. A.; Lemma, B.; Wang, W.; Mallarino, R.; Nelson, C. M.

10.1101/2022.07.13.499952 — developmental biology — Posted on 2025-11-13

2957 A Minimally Invasive, Scalable and Reproducible Neonatal Rat Model of Severe Focal Brain Injury

Mondal, V.; Ross-Munro, E.; Balasuriya, G. K.; Kumari, R.; Shearer, I. K.; Micic, A.; Sohag, A. A. M.; Shi, A.; Barresi, M.; Nisbet, D. R.; King, G. F.; Williams, R. J.; Gressens, P.; Wong, F. Y.-w.; Cheong, J.; Walker, D. W.; Tolcos, M.; Fleiss, B.

10.1101/2025.11.10.687751 — developmental biology — Posted on 2025-11-13

2958 Ganaxolone, an approved therapy for CDKL5-Deficiency Disorder, is an inhibitor of PTP1B

Zubiete-Franco, I.; Hu, Q.; Tonks, N. K.

10.1101/2025.10.31.685887 — molecular biology — Posted on 2025-11-13

2959 HENMT1 restricts endogenous retrovirus activity by methylation of 3'-tRNA fragments

Steinberg, J. I.; Sertznig, H.; Desmarais, J. J.; Wilken, J.; Rubio, D.; Peacey, M.; Kinney, J. B.; Schorn, A. J.

10.1101/2025.05.12.650695 — molecular biology — Posted on 2025-11-13

2960 Cryogenic Electron Tomography Redefines Herpesvirus Capsid Assembly Intermediates Inside the Cell Nucleus.

Oliver, S. L.; Chen, M.; Engel, L.; Hecksel, C. W.; Zhou, X.; Schmid, M. F.; Arvin, A. M.; Chiu, W.

10.1101/2025.06.27.661840 — microbiology — Posted on 2025-11-13

2961 A Novel Technique to Characterize Klebsiella pneumoniae Populations Indicates that Mono-Colonization is Associated with Risk of Infection

Unverdorben, L.; Mason, S.; Wu, W.; Noda, M.; Castaneda, S.; Vornhagen, J.; Snitkin, E. S.; Rao, K.; Bachman, M. A.

10.1101/2025.11.05.686704 — microbiology — Posted on 2025-11-13

2962 Localization of Mutant Huntingtin with HTT Exon1 P90 C-terminal Neoepitope Antibodies in Relation to Regional and Neuronal Vulnerability in Forebrain in Q175 Mice and Human Huntington's Disease

Deng, Y.; Joni, M.; Wang, H.; Cox, R.; Sapp, E.; DiFiglia, M.; Reiner, A.

10.1101/2025.08.06.668984 — neuroscience — Posted on 2025-11-13

2963 Hierarchical and Context-Dependent Encoding of Actions in Human Posterior Parietal and Motor Cortex

Bougou, V.; Gamez, J.; Rosario, E. R.; Liu, C.; Pejsa, K.; Bari, A.; Andersen, R. A.

10.1101/2025.11.10.687245 — neuroscience — Posted on 2025-11-13

2964 TEIP: A Compact, Open-Source Framework for Predicting Tumor Epitope Immunogenicity in Glioblastoma Cancer Using Deep Learning and Multi-Modal Biological Features

Mahapatra, R.; Sundar, A.; Shekhar, A.

10.1101/2025.11.09.687510 — cancer biology — Posted on 2025-11-13

2965 Biophysical Design Space for Cellular Self-assembly and Dynamics

Das, S.; Sreepadmanabh, M.; Parashar, D.; Bhattacharjee, T.; Dutta, S.

10.1101/2025.11.13.688226 — biophysics — Posted on 2025-11-13

2966 PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification

Foster, Z. S. L.; Sudermann, M. A.; Parada Rojas, C. H.; Blair, L. K.; Iruegas Bocardo, F.; Dhakal, U.; Alcala-Briseno, R. I.; Weisberg, A. J.; Phan, H.; Schummer, T. R.; Chang, J. H.; Grunwald, N. J.

10.1101/2025.10.31.685798 — bioinformatics — Posted on 2025-11-13

2967 Scalable flow synthesis of ultrasmall inorganic nanoparticles for biomedical applications via a confined impinging jet mixer

Kian, A. C.; Gupta, M.; Hong, H.; Rivera, K. L. L.; Pandey, N.; Mossburg, K. J.; Rosario-Berrios, D. N.; Maidment, P.; Hanna, A. R.; Singh, P.; Xiang, Z.; Issadore, D.; Maidment, A.; Koo, H.; Cormode, D.

10.1101/2025.11.12.688080 — bioengineering — Posted on 2025-11-13

2968 CGK733 binds to adenine nucleotide translocator 2 and modulates mitochondrial function and protein translation

Kaida, D.; Inagaki, Y.; Yaku, K.; Sasaki, K.; Ikeda, S. K.; Koike, S.; Shima, M.; Iwasaki, S.; Inobe, T.; Nakagawa, T.; Yoshida, M.; Ishigami, K.; Katsuta, R.

10.1101/2025.11.13.688169 — biochemistry — Posted on 2025-11-13

2969 STbayes: An R package for creating, fitting and understanding Bayesian models of social transmission

Chimento, M.; Hoppitt, W.

10.1101/2025.06.07.658152 — animal behavior and cognition — Posted on 2025-11-13

2970 Macrophages induce stromal differentiation and endothelialization in iPSC-derived kidney organoids.

Pecksen, E.; Vives Enrich, M.; Jang, M.-S.; Tkachuk, S.; Kapanadze, T.; Johnson, C. P.; Limbourg, F.; Lachmann, N.; Schmidt-Ott, K. M.; Haller, H.; Kiyan, Y.

10.1101/2025.11.13.688016 — cell biology — Posted on 2025-11-13

2971 Enteric viral infections promote systemic accelerated aging in Drosophila

Gonzalez, R.; Castello-Sanjuan, M.; Saleh, M.-C.

10.1101/2025.03.13.643076 — microbiology — Posted on 2025-11-13

2972 Pre-existing and emergent cortical neuronal assembly sequences during learning

Pemberton, L.; Jeong, H.; K Namboodiri, V. M.

10.1101/2025.11.12.688154 — neuroscience — Posted on 2025-11-13

2973 Inhibitory inputs to avian ITD circuits

Kuokkanen, P. T.; Faghani, Z. M.; Kraemer, I.; Kempter, R.; Carr, C. E.

10.1101/2025.11.13.688251 — neuroscience — Posted on 2025-11-13

2974 Characterizing neuronal population geometry with AI equation discovery

Tilbury, R.; Kwon, D.; Haydaroglu, A.; Ratliff, J.; Schmutz, V.; Carandini, M.; Miller, K. J.; Stachenfeld, K.; Harris, K. D.

10.1101/2025.11.12.688086 — neuroscience — Posted on 2025-11-13

2975 Stress resilience is associated with transcriptional remodeling in the VTA

Minerva, A. R.; McMannon, B.; Lin, R.; Zhukovskaya, A.; Witten, I. B.; Pena, C. J.

10.1101/2025.11.13.687606 — neuroscience — Posted on 2025-11-13

2976 Using AI-MIDD for Mechanistic Erythropoietin Modeling: A Digital-Twin Framework for Optimizing ESA Therapies

Goryanin, I.; Goryanin, I. V.

10.1101/2025.11.12.688044 — systems biology — Posted on 2025-11-13

2977 The role of muscle fascia in heterotopic ossification and maintenance of skeletal muscle integrity in fibrodysplasia ossificans progressiva

Hanson, L. R.; Scalise, K. L.; Esch, R. M.; Nevo, L.; Goldhamer, D. J.

10.1101/2025.11.12.688008 — pathology — Posted on 2025-11-13

2978 Inter-Instrument Quantification of Fluorescence Read-out Signal Using DNA Origami Calibrator Beads

Bohn, A. B.; Petersen, C. C.; Wood, J.; Selnihhin, D.; Pedersen, F. S.

10.1101/2025.11.13.683362 — biophysics — Posted on 2025-11-13

2979 Critical Assessment of a Structure-Based Pipeline for Targeting the Long Non-Coding RNA MALAT1

Aguti, R.; Bernetti, M.; Cavalli, A.; Masetti, M.

10.1101/2025.11.13.688270 — biophysics — Posted on 2025-11-13

2980 3D-printed toolkit for regulating epithelial unjamming

Lavi, Y.; Sandler, Y.; Saleem, A.; Daraf, L.; Nachum, S.; Atia, L.

10.1101/2025.11.13.688246 — biophysics — Posted on 2025-11-13

2981 SCOUT: Ornstein-Uhlenbeck modelling of gene expression evolution on single-cell lineage trees

Stuart, H.; McKenna, A.

10.1101/2025.11.12.688020 — bioinformatics — Posted on 2025-11-13

2982 An infusible decellularized extracellular matrix material binds to vasculature in infarcted myocardium and induces pro-reparative gene expression following acute myocardial infarction through inherent avidity and bioactive signaling

Nguyen, M. B.; Chen, A.; Ninh, V. K.; McCabe, M. C.; Lyons, Q. P.; Luo, C.; Bridgelal, B. D.; Uhre, C.; Reimold, K. E.; Cao, S.; Hansen, K. C.; King, K. R.; Christman, K. L.

10.1101/2025.11.12.687915 — bioengineering — Posted on 2025-11-13

2983 The ESCRT-0 protein HRS regulates hepatocellular lipid droplet catabolism

Willoughby, M. M.; Shroff, A.; Crossman, B. E.; Schott, M. B.

10.1101/2025.11.13.686840 — biochemistry — Posted on 2025-11-13

2984 HP1 dimerization but not LLPS drives the condensation and segregation of H3K9me-marked chromatin

Eswara, K.; Semple, J.; Rivas-Cuestas, F.; Ali, S.; El Mouridi, S.; Ostwal, Y.; Frokjaer-Jensen, C.; Mesiter, P.; Fischle, W.

10.1101/2025.11.13.687974 — biochemistry — Posted on 2025-11-13

2985 Symmetry and similarity in eco-evo: advective environments,dispersal, and climate change

Filin, I.

10.1101/2025.08.26.672437 — ecology — Posted on 2025-11-13

2986 Non-intrusive optical measurement of egg geometry and volume for macro- and microscopic ovoids

Moreno-Rodenas, A.; Le Hesran, S.

10.1101/2025.11.12.688065 — ecology — Posted on 2025-11-13

2987 Tankyrase inhibition demonstrates anti-fibrotic effects in preclinical pulmonary fibrosis models

Brinch, S. A.; Johnsen, I.; Willmer, L.; Vidhammer Bjornstad, O.; Lucifora, T.; Forbord, K. M.; Candamo-Lourido, M.; Tania Meling, M.; Lofthus Morken, I.; Strand, M. F.; Jonigk, D.; Zardo, P.; Fieguth, H. G.; Hesse, C.; Skarsfeldt, M. A.; Karsdal, M. A.; Ferrari, E.; Occhetta, P.; Visone, R.; Jordan, S.; Lee, J.; Holton, H.; Rayner, S.; Wegert, A.; Cruwys, S.; Krauss, S.; Waaler, J.

10.1101/2025.11.13.688191 — cell biology — Posted on 2025-11-13

2988 Structural basis for co-translational assembly of homo-oligomeric proteins

Koubek, J.; Filbeck, S.; Kopetschke, S.; Schmitt, J.; Pfeffer, S.; Kramer, G.; Bukau, B.

10.1101/2025.11.12.687954 — molecular biology — Posted on 2025-11-13

2989 Functional Activity of HIV-1 bNAbs Across Diverse Strains is Driven by Binding Site and Can be Enhanced Through Fc Engineering

Li, C. J.; Lim, E.; Phelps, M.; Brady, J. M.; Okonkwo, V.; McCarthy, C.; Alexander, C.; Ackerman, M. E.; Lingwood, D.; Balazs, A. B.

10.1101/2025.11.12.688078 — immunology — Posted on 2025-11-13

2990 Therapeutic Inducers of NK cell Killing (ThINKK)-induced NK cell cytotoxicity against childhood acute lymphoblastic leukemia: unraveling the dual role of TRAIL leads to the establishment of an efficacy biomarker

Ollame-Omvane, E.; Ben Khemis, L.; Cordeiro, P.; Fuchs, C.; Richard-Saint-Hilaire, A.; Beland, K.; Haddad, E.; Sinnett, D.; Herblot, S.; Duval, M.

10.1101/2025.11.12.687655 — immunology — Posted on 2025-11-13

2991 The neuroscience of highly stable, positive, and refined states of consciousness during jhana-type advanced concentration absorption meditation (ACAM-J)

Yang, W. F.; Potash, R.; Mackin, G.; Beslic, I.; Bianciardi, M.; Sprby, T.; Sacchet, M. D.

10.1101/2025.11.12.688050 — neuroscience — Posted on 2025-11-13

2992 Characterization of mechanical tissue properties in post-mortem human brain using magnetic resonance elastography

Mojumder, J.; Lu, Y.-C.; Diano, A. M.; Alshareef, A. A.; McGarry, M.; Bayly, P. V.; Johnson, C. L.; Butman, J. A.; Pham, D. L.

10.1101/2025.11.12.688069 — neuroscience — Posted on 2025-11-13

2993 Slow waves generation and propagation in a model of brain lesions

Gaglioti, G.; Dalla Porta, L.; Colombo, M. A.; Russo, S.; Nieus, T. R.; Deco, G.; Corbetta, M.; Sarasso, S.; Sanchez-Vives, M. V.; Massimini, M.

10.1101/2025.11.12.688042 — neuroscience — Posted on 2025-11-13

2994 Temporal dynamics of CNS cholesterol esters correlate with demyelination and remyelination

De Silva Mohotti, N.; Williams, J. M.; Binjawadagi, R.; Kobayashi, H.; Dedunupitiya, D.; Petersen, J. M.; Garcia, A.; Hartley, M. D.

10.1101/2025.09.06.674663 — neuroscience — Posted on 2025-11-13

2995 Endosomal MrGPRX1 signaling sensitizes TRPV1 to enhance itch

Duran, P.; Retamal, J. S.; de Amorim Ferreira, M.; Trevett, K.; Jensen, D. D.

10.1101/2025.11.12.688053 — neuroscience — Posted on 2025-11-13

2996 Efficient and reproducible pipelines for spike sorting large-scale electrophysiology data

Buccino, A. P.; Sridhar, A.; Feng, D.; Svoboda, K.; Siegle, J. H.

10.1101/2025.11.12.687966 — neuroscience — Posted on 2025-11-13

2997 Disrupting the Feed-Forward Cycle of RyR1 Calcium Leak and Oxidative Stress Mitigates Doxorubicin-Induced Skeletal Myopathy

Figueroa, L. C.; Tammineni, E. D.; Marco-Moreno, P. A.; Vallejo-Illarramendi, A.; Arregui, A. L. d. M.; Sagartzazu-Aizpurua, M.; Fill, M.; Manno, C. D.

10.1101/2025.11.12.688073 — physiology — Posted on 2025-11-13

2998 Learning from All Views: A Multiview Contrastive Framework for Metabolite Annotation

Zhou Chen, Y.; Hassoun, S.

10.1101/2025.11.12.688047 — bioinformatics — Posted on 2025-11-13

2999 Elucidating Neurodevelopmental Trajectories in Cancer with Topic Modeling: Revealing Persistent External Granule Layer Lineages in Medulloblastoma

Rajendran, A.; Haldipur, P.; Arora, S.; Grama, K.; Subramanian, S. S.; Galan, L. M.; Johnson, D.; Aldinger, K. A.; Shendure, J.; Millen, K. J.; Gennari, J. H.; Pattwell, S. S.

10.1101/2025.11.12.687706 — bioinformatics — Posted on 2025-11-13

3000 SAGA (Simplified Association Genomewide Analyses): a user-friendly Pipeline to Democratize Genome-Wide Association Studies

Cieza, B.; Pandey, N.; Ruhela, V.; Ali, S.; tosto, g.

10.1101/2025.08.25.672146 — bioinformatics — Posted on 2025-11-13

3001 Anti-CD38-Targeted Piperazine-Derived Lipid Nanoparticles Overcome Hepatic Clearance for mRNA Delivery to Multiple Myeloma Cells In Vivo

Figueroa-Espada, C. G.; Geisler, H. C.; Joseph, R. A.; Ricciardi, A. S.; Metzloff, A. E.; Acosta-Gonzalez, J. O.; Xue, L.; Yamagata, H. M.; Thatte, A. S.; MITCHELL, M. J.

10.1101/2025.11.12.687398 — bioengineering — Posted on 2025-11-13

3002 Structural promiscuity in the human circulatory IgA1 clonal repertoire

Rolland, A. D.; Kalaidopoulou Nteak, S.; Vidarsson, G.; Bondt, A.; Heck, A. J. R.

10.1101/2025.11.13.688237 — biochemistry — Posted on 2025-11-13

3003 The ABCs of Cyanobacterial Glycogen: In Vitro Modelling of Glycogen Synthesis and Functional Divergence of Glycogen Synthases in Synechocystis sp. PCC 6803

Lee, K.; Bekiari, D.; Doello, S.; Forchhammer, K.

10.1101/2025.11.13.688228 — biochemistry — Posted on 2025-11-13

3004 Breaking new ground into RAD51-BRC repeats interplay in Homologous Recombination

Rinaldi, F.; Franco, P.; Veronesi, M.; Romeo, E.; Bresciani, V.; Varignani, G.; Catalano, F.; Bernetti, M.; Masetti, M.; Langer, J.; Girotto, S.; Cavalli, A.

10.1101/2025.11.13.688182 — biochemistry — Posted on 2025-11-13

3005 Sodium Aurothiomalate Induces Ferroptosis by Targeting GPX4 via Gold-Dependent Thiomalate Covalent Modification

Hugo, M.; Gross, L. Z. F.; Messias, A.; Alcober-Boquet, L.; Vignane, T.; Ghosh, B.; Aroua, N.; Denson, L.; Delgado-Martin, S.; Kaushal, K.; Yildiz, U.; Müller, S.; Martinez-Ruiz, A.; Estrin, D. A.; Augustin, H. G.; Rodriguez, R.; Biondi, R. M.; Trumpp, A.; Jayavelu, A. K.; Cheng, Q.; Etzkorn, M.; Berndt, C.; Arner, E. S. J.; Filipovic, M. R.; Di Lella, S.; Pastor-Flores, D.; Alborzinia, H.

10.1101/2025.11.13.687868 — biochemistry — Posted on 2025-11-13

3006 MELODY: Mediation Analysis in Logistic Regression for High-Dimensional Mediators and a Binary Outcome

Chi, S.; Li, X.; Wei, P.; Huang, X.

10.1101/2025.11.12.688038 — genomics — Posted on 2025-11-13

3007 Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish

Kanchi, R.; Grimm, S. L.; Vella, D.; Saoud, R.; Gandhi, T.; Koirala, A.; Cervino, A.; MacGowan, J.; Coarfa, C.; Williams, M. K.

10.1101/2025.11.12.688039 — developmental biology — Posted on 2025-11-13

3008 Multifaceted fusion defects converge on altered mitochondrial distribution and increased mutant mitofusin level in CMT2A models

VARUK, O. O.; RUIZ, A.; ORENGO, C.; COZZOLINO, A.; DE BOISSIER, P.; AOUANE, A.; RIVAL, T.

10.1101/2025.03.14.642792 — cell biology — Posted on 2025-11-13

3009 A tale of two distinct actin networks underlies the entire life cycle of focal adhesion

Dong, R.; ishii, K.; Plotnikov, S. V.; Liu, J.

10.1101/2025.11.12.688129 — cell biology — Posted on 2025-11-13

3010 Eukaryotic translation initiation factor 3d regulates stress granule assembly via its RNA binding domain

Whitmarsh, A. J.; Lang, J.; Sfakianos, A. P.; Binder, P.; Zhang, W.; Tournier, C.; Ashe, M. P.; Poulin, G. B.

10.1101/2025.11.13.688230 — cell biology — Posted on 2025-11-13

3011 Dynamic interaction between stress hormones and neutrophils promotes neutrophil extracellular trap formation with behavioral consequences

Thangamani, K. B.; Prece, H.; Carter, J.; Douglas, O.; Brengel, E.; Ferris, C.; Okeke, E.

10.1101/2025.11.12.688017 — immunology — Posted on 2025-11-13

3012 Analysis of SIV Spatiotemporal Dissemination Patterns in Rhesus Macaques During Early Rectal Transmission Demonstrates Systemic Infection Does Not Require Viral Local Amplification at the Entry Portal

Cheng, Y.; Chen, J.; Zhao, M.; Mandal, S.; Lewis, M.; Luo, M.; Gale, M.; Li, Q.

10.1101/2025.11.12.687929 — immunology — Posted on 2025-11-13

3013 ERK5 is required for neutrophil-mediated ROS release and essential in epidermolysis bullosa acquisita

Draeger, S.; Schlotfeldt, M.; Voss, L.; Johannisson, S.; Radziewitz, M.; Osterloh, C.; Gross, N.; Kamaguchi, M.; Schneider, A.-K.; Vidarsson, G.; Visser, R.; Petersen, F.; Yu, X.; Recke, A.; Ernst, N.; Lux, A.; Bieber, K.

10.1101/2025.11.12.688045 — immunology — Posted on 2025-11-13

3014 Multiparametric MRI and imaging transcriptomics reveal molecular and cellular correlates of neurodegeneration in experimental multiple system atrophy

Kim, E.; Cash, D.; Martins, D.; Simmons, C.; Heras-Garvin, A.; Klippel, E.; Krismer, F.; Mantoan-Ritter, L.; Stefanova, N.

10.1101/2025.11.12.688033 — neuroscience — Posted on 2025-11-13

3015 A Parallelized, Automated System for Higher-Throughput Spatial Navigation Testing of Rats

Saathoff, V.; O'Leary, C. I.; Gillespie, A. K.

10.1101/2025.07.22.666070 — neuroscience — Posted on 2025-11-13

3016 Decoding brain-wide signatures of uninformed choices for BCI assisted decision-making

Gimple, S.; Verwoert, M.; Marras, L.; Weger, P.; Herff, S.; van Dijk, J. P.; Tousseyn, S.; Kubben, P. L.; Temel, Y.; Janssen, M. L. F.; Herff, C.

10.1101/2025.11.12.688013 — neuroscience — Posted on 2025-11-13

3017 Cornichon Homolog-3 (Cnih3) deletion impairs spatial memory, reward-cue association, and fentanyl self-administration behavior.

Lintz, T.; Liu, A.; Aal, T.; Park, A.; Dearman, J.; Agrawal, A.; Nelson, E. C.; Moron, J.

10.1101/2025.11.12.688051 — neuroscience — Posted on 2025-11-13

3018 Establishment of an in vitro Culture and Regeneration Protocol for the Native Grass Polypogon australis Brong.

Venegas Rioseco, J. F.; Hensel, G.; Ortiz Calderon, C.; Ginocchio Cea, R.

10.1101/2025.11.12.688029 — plant biology — Posted on 2025-11-13

3019 Leveraging FracMinHash Containment for Genomic dN/dS

Rodriguez, J. S.; Hera, M. R.; Koslicki, D.

10.1101/2025.11.12.688019 — bioinformatics — Posted on 2025-11-13

3020 Stratified Active Learning for Spatiotemporal Generalisation in Large-Scale Bioacoustic Monitoring

McEwen, B.; Bernard, C.; Stowell, D.

10.1101/2025.09.01.673472 — bioinformatics — Posted on 2025-11-13

3021 Extrinsic polarity cues control lamination versus cluster-based organisation in vertebrate retinal development

Schlagheck, C.; Podlipensky, X.; Afting, C.; Curticean, R.; Wacker, I.; Schroeder, R. R.; Weinhardt, V.; Zilova, L.; Wittbrodt, J.

10.1101/2025.11.12.688026 — developmental biology — Posted on 2025-11-13

3022 MetaXtract: Extracting Metadata from Raw Files for FAIR Data Practices and Workflow Optimisation

Lutfi, A.; Chen, Z. A.; Fischer, L.; Rappsilber, J.

10.1101/2025.11.12.687968 — bioinformatics — Posted on 2025-11-13

3023 Continuous Light-Induced Circadian Rhythm Disruption Impairs Intestinal Barrier Integrity in Male C57BL/6 Mice Through Gut Microbiota Dysbiosis and the Apoptosis-Inflammation-Oxidative Stress Cascade Animal Experimental Study)

Zhang, T.-W.; LI, C.-z.; Hao, N.-B.; Song, J.-C.; Qu, M.-Y.; Guo, B.-S.

10.1101/2025.11.11.687914 — animal behavior and cognition — Posted on 2025-11-13

3024 From form to function: Morphology as a proxy for life history and population performance in fish

Dixon, V.; Smallegange, I. M.

10.1101/2025.11.12.688009 — ecology — Posted on 2025-11-13

3025 Is there a fly in my soup? To what extent do metabarcoding and individual barcoding tell the same story?

Furneaux, B.; Roslin, T.; Hardwick, B.; Kerdraon, D.; Autto, H.; Banelyte, G.; deWaard, J. R.; deWaard, S.; Farrell, A.; Kalttopaa, O. M.; Kristensen, E.; Rogers, H. M. K.; Sones, J. E.; Zakharov, E. V.; Ovaskainen, O.

10.1101/2025.11.12.687976 — ecology — Posted on 2025-11-13

3026 Plant litter chemistry and associated changes in microbial decomposition under drought

Chung, B.; Wang, S.; Hao, Z.; Allison, S.; Malik, A. A.

10.1101/2025.11.12.688006 — ecology — Posted on 2025-11-13

3027 Effects and mechanisms of monoclonal and polyclonal human antibodies in protection of humanized mice from HIV-1 challenge

Khanwalkar, U. S.; Fields, J.; Weiner, J. A.; Lindman, M. L.; Balazs, A. B.; Seaman, M. S.; Baden, L. R.; Walsh, S. R.; Fiering, S. N.; Huang, Y. H.; Ackerman, M. E.

10.1101/2025.11.12.688003 — immunology — Posted on 2025-11-13

3028 Motor Cortical Output Integrates Distorted Proprioceptive Feedback

Li, Y.; Xu, X. H.; Pan, S.; An, X.; Mulcahey, P. J.; Qiu, Z.; Zhao, S.; Li, N.; Pearson, J.; Huang, Z. J.

10.1101/2025.11.11.687832 — neuroscience — Posted on 2025-11-13

3029 Temporal cueing improves audition with no evidence for attentional tradeoffs

Wang, J.; Conroy, C.; Denison, R. N.

10.1101/2025.11.11.687452 — neuroscience — Posted on 2025-11-13

3030 Mycophenolate mofetil reduces the branching of microglial processes

Teruya, R.-i.; Ueda, K.; Taketomi, T.; Yamamoto, T.; Yamashita, N.; Konno, H.; Tsuruta, F.

10.1101/2025.11.12.687812 — neuroscience — Posted on 2025-11-13

3031 CRISPR/Cas9-mediated generation of a de novo C9ORF72 knock-in isogenic iPSC cell bank to model ALS and FTD

O'Brien, N. L.; Hedges, E.; Nair, R. R.; Cammack, A. J.; Carcole, M.; Vaizoglu, D.; Tacconelli, S.; Sutherland, C.; Fisher-Ward, C. L.; Awan, A. R.; Topp, S.; Iacoangeli, A.; Isaacs, A. M.; Cunningham, T. J.; Ruepp, M.-D.; Mizielinska, S.

10.1101/2025.11.12.687564 — neuroscience — Posted on 2025-11-13

3032 FGF13 is not secreted from neurons

Malvezzi, M.; Zhang, H.; Towers, P.; Lyden, D. C.; Marx, S. O.; Pitt, G. S.

10.1101/2025.11.12.688075 — neuroscience — Posted on 2025-11-13

3033 Redefining Housekeeping Genes in the Context of Vertebrate Development

Lou, A.; Poyatos, J. F.; Chagoyen, M.

10.1101/2025.11.12.687949 — systems biology — Posted on 2025-11-13

3034 From plasmid sequence to process design: A computational analysis of metabolism in the context of plasmid DNA manufacturing

Stratis, N.; Morbidelli, M.; Kiparissides, A.

10.1101/2025.11.12.687962 — systems biology — Posted on 2025-11-13

3035 High-throughput PBK modelling for dermal exposure: a pragmatic approach to predict systemic pharmacokinetics

Edizcan, Z.; Schaller, S.; Kuepfer, L.; Geci, R.

10.1101/2025.11.12.687995 — pharmacology and toxicology — Posted on 2025-11-13

3036 An aerosolised dual-action Autotaxin inhibitor- PPARγ agonist for the treatment of pulmonary fibrosis

Matralis, A. N.; Stylianaki, E.-A.; Ladopoulou, E.; Kanellopoulou, P.; Smyrniotis, S.; Magkrioti, C.; Papavasileiou, K. D.; Willems, S.; Pabon, J. P. R.; Nastos, D.; Galaras, A.; Dedos, S. G.; Kaffe, E.; Hatzis, P.; Merk, D.; Politis, A.; Afantitis, A.; Tseti, I.; Antoniou, K. M.; Wells, A. U.; Aidinis, V.

10.1101/2025.11.12.687859 — pathology — Posted on 2025-11-13

3037 CDR Conformation Aware Antibody Sequence Design with ConformAb

Sinha, I.; Stanton, S.; Lillington, S.; Robinson, S. A.; Nerli, S.; Zadorozhny, K.; Kleinhenz, J.; MohammadiPeyhani, H.; Dillon, M.; Chen, Y.; Bevers, J.; Wu, Y.; Watkins, A. M.; Dwyer, H.; Bonneau, R.; Cho, K.; Seeger, F.; Gligorijevic, V.; Kelow, S.

10.1101/2025.11.12.688095 — biophysics — Posted on 2025-11-13

3038 Integrating Millions of Years of Evolutionary Information into Protein Structure Models for Function Prediction

Ma, R.; He, C.; Zhang, Z.; Zheng, H.; Duan, L.

10.1101/2025.11.11.687944 — bioinformatics — Posted on 2025-11-13

3039 Chemical Dice Integrator (CDI): A Scalable Framework for Multimodal Molecular Representation Learning

Ahuja, G.; Kumar, S.; Solanki, S.; Gupta, M.; Mohanty, S. K.; Satija, S.; Chauhan, S.; Duari, S.; Sharma, A.; Gautam, V.; Arora, S.; Shome, R.; Sinha, S.; Sharma, A. K.; Mittal, A.; Sengupta, D.; Murugan, N. A.

10.1101/2025.11.11.687860 — bioinformatics — Posted on 2025-11-13

3040 Agentic Lab: An Agentic-physical AI system for cell and organoid experimentation and manufacturing

Wang, W.; Swain, S.; Lee, J.; Lin, Z.; Canales, B.; Aljovic, A.; Liu, Y.; Li, Q.; Marin-Llobet, A.; Liu, M.; Gao, Z.; Liu, R.; Alvarez-Dominguez, J. R.; Liu, J.

10.1101/2025.11.11.686354 — bioengineering — Posted on 2025-11-13

3041 4D force patterning enables spatial control of angiogenesis

Kheiri, S.; Shah, J.; Venkatesh, S. A.; Kamm, R. D.; Raman, R.

10.1101/2025.11.11.687921 — bioengineering — Posted on 2025-11-13

3042 Perfusable 3D human urothelial model for real-time analysis of bacterial infection dynamics and therapeutic interventions

Kurmashev, A.; Sorg, I.; Boos, J. A.; Grassi, L.; Sellner, B.; Fino, C.; Girgin, M.; Mueller, A. L.; Klimke, S.; Tschudin-Sutter, S.; Hierlemann, A.; Dehio, C.

10.1101/2025.11.12.687885 — bioengineering — Posted on 2025-11-13

3043 Targeted and efficient AAV therapy for neuroblastoma via direct capsid-antibody coupling

Luoni, M.; Giannelli, S. G.; Parracino, S.; Morosi, F.; Ventura, E.; Di Pizio, A.; Muggeo, S.; Iannielli, A.; Canu, T.; Russo, T.; Antonio, E.; Pastorino, F.; Broccoli, V.

10.1101/2025.11.12.687993 — bioengineering — Posted on 2025-11-13

3044 Signaling by RasG12V depends on EGFR activity in vivo

Vega-Cuesta, P.; Lopez-Varea, A.; Ruiz-Gomez, A.; de Celis, J. F.

10.1101/2025.11.12.687982 — genetics — Posted on 2025-11-13

3045 The Mitochondrial Palindrome Scaffold and Architectural Domains

Stumpf, D. A.

10.1101/2025.11.11.687892 — evolutionary biology — Posted on 2025-11-13

3046 Genetic Fingerprinting of Herbarium Hop Specimens Reveals Genetic Diversity and Relationships with Modern Finnish Hops

Bitz, L.; Lempiainen-Avci, M.; Huttunen, S.; Tenhola-Roininen, T.; Hartikainen, M.; Luong, T.-T.

10.1101/2025.11.12.687964 — evolutionary biology — Posted on 2025-11-13

3047 The role of fecundity dynamics and time of injury for femalereproductive fitness

Michalak, P.; Ferdy, J.-B.; Duneau, D.

10.1101/2025.11.12.687561 — evolutionary biology — Posted on 2025-11-13

3048 Symbiotic versatility in action: Trebouxia diversity expands the niche of the lichen Xanthoria parietina

Chiva, S.; Pazos, T.; Montero-Pau, J.; Moya, P.; Garrido-Benavent, I.; Barreno, E.; Muggia, L.

10.1101/2025.11.12.687866 — ecology — Posted on 2025-11-13

3049 Dual human lung models reveal compartment-specific activity of anti-tuberculosis drugs and host-directed therapies

Barbosa Bomfim, C. C.; Faivre, N.; Benoist, T.; Popis, M.; Suire, B.; Pericat, D.; Sanchez-Lopez, J. M.; Aponte-Castillo, B. M.; Naser, E.; Viana, P.; Guibert, N.; Verge, R.; Mazieres, J.; Metais, A.; Poincloux, R.; Raynaud-Messina, B.; Dumas, F.; Neyrolles, O.; Verollet, C.; Meunier, E.; Lugo-Villarino, G.; Cougoule, C.

10.1101/2025.11.10.685269 — immunology — Posted on 2025-11-13

3050 Depletion and recovery of IgG following treatment with Rozanoliximab and Imlifidase in pigtail macaques

Rzasa, K. M.; Zikos, J.; Penney, T.; Schiro, F. R.; Doyle-Meyers, L. A.; Aye, P. P.; Veazey, R. S.; Hoxie, J. A.; Maness, N. J.; Magnani, D. M.; Ackerman, M. E.

10.1101/2025.11.11.687913 — immunology — Posted on 2025-11-13

3051 Sequence preparation is not always associated with a reaction time cost

Panjehpour, A.; Kashefi, M.; Diedrichsen, J.; Pruszynski, J. A.

10.1101/2025.11.11.687917 — neuroscience — Posted on 2025-11-13

3052 Investigating the Effects of APOE Genotype on Intracellular Cholesterol and the Endolysosomal System in the Aging Mouse Brain

de Leeuw, S.; Nuriel, T.

10.1101/2025.11.11.687891 — neuroscience — Posted on 2025-11-13

3053 AA-ending codon-based computational analyses uncover novel cytoplasmic effectors in the Magnaporthe oryzae secretome

Li, G.; Tiwari, S.; Dulal, N.; Wheeler, B.; Wilson, R. A.

10.1101/2025.11.10.687658 — plant biology — Posted on 2025-11-13

3054 MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements

Hera, M. R.; Koslicki, D.; Martinez, C.

10.1101/2025.11.11.687920 — bioinformatics — Posted on 2025-11-13

3055 A Minimally Invasive, Scalable and Reproducible Neonatal Rat Model of Severe Focal Brain Injury

10.1101/2025.11.10.687751 — developmental biology — Posted on 2025-11-13

3056 Loss of ErbB3 redirects Integrin β1 from early endosomal recycling to secretion in extracellular vesicles

Rodrigues-Junior, D. M.; Saez-Ibanez, A. R.; Terabayashi, T.; Daubel, N.; Makinen, T.; Idevall-Hagren, O.; Moustakas, A.; Ferby, I.

10.1101/575449 — cell biology — Posted on 2025-11-13

3057 Revisiting Cysteine Protease Function in Trypanosoma cruzi: Implications for Parasite Egress and Differentiation

De Grandis, S.; Niggli, A.; Bogenstatter, D.; Lentini, G.

10.1101/2025.11.11.687948 — microbiology — Posted on 2025-11-13

3058 Tissue-embedded CD4⁺ plasticity structures mucosal immunity in IBD-related inflammation

Jiang, Q.; Merkus, V. A.; Lindelauf, C.; Guo, N.; Ouboter, L. F.; Hollt, T.; Voorneveld, P. W.; Meijer- Boekel, C. R.; Koning, F.; van der Meulen-de Jong, A. E.; Pascutti, M. F.; van Unen, V.

10.1101/2025.10.31.685649 — immunology — Posted on 2025-11-13

3059 A Challenge To The Assumption That Short- versus Long-Access Groups of Opioid Users Represent Distinct Phenotypes

Giunta, M. A.; Madhuranthakam, I. M.; Job, M. O.

10.1101/2025.11.10.687622 — neuroscience — Posted on 2025-11-13

3060 Sleep arousals are associated with the polygenic risk for developing Alzheimer's disease and with cognitive decline in healthy late middle-aged individuals

Mortazavi, N.; Zubkov, M.; Chylinski, D.; Collette, F.; Bastin, C.; Maquet, P.; Vandewalle, G.; Talwar, P.

10.1101/2025.11.11.687823 — neuroscience — Posted on 2025-11-13

3061 Spinal electrophysiology reveals frequency-specific spatial patterns of neural activity and corticospinal coherence during pincer-grip

Mehra, P.; Bista, S.; Metzger, M.; Giglia, E.; Plaitano, S.; Nash, L.; Mac Domhnaill, E.; Bede, P.; Muthuraman, M.; Hardiman, O.; Lowery, M. M.; Nasseroleslami, B.

10.1101/2025.11.11.687864 — neuroscience — Posted on 2025-11-13

3062 Extracting task-relevant preserved dynamics from contrastive aligned neural recordings

Jiang, Y.; Sheng, K.; Gao, Y.; Buchanan, E. K.; Shikano, Y.; Kim, T. H.; Zhao, Y.; Woo, S. J.; Dinc, F.; Linderman, S. W.; Schnitzer, M. J.

10.1101/2025.11.11.686428 — neuroscience — Posted on 2025-11-13

3063 Evaluating Sample-Size Efficiency and Sensitivity of Tractometry in Alzheimer's Disease

Feng, Y.; Villalon-Reina, J. E.; Gari, I. B.; Alibrando, J. D.; Nir, T. M.; Jahanshad, N.; Chandio, B. Q.; Thompson, P. M.

10.1101/2025.11.11.687878 — neuroscience — Posted on 2025-11-13

3064 Assessing the Influence of Tractography Methods on White Matter Microstructure and Tractometry Analysis in Alzheimer's Disease

Shuai, Y.; Feng, Y.; Villalon-Reina, J. E.; Nir, T. M.; Thomopoulos, S. I.; Thompson, P. M.; Chandio, B. Q.

10.1101/2025.11.11.687747 — neuroscience — Posted on 2025-11-13

3065 Behavioral Thermoceptive Responses and Morphologic Correlates in Mouse Models of CMT1A, HNPP and Aging

Oberoi, V.; Campbell, J. O.; Akpabli-Tsigbe, N.; Imran, F.; Bond, S.; Tenlep, S. N.; Brennan, C.; Wang, M.; Saxena, S.; Moss, K. R.; Arnold, W. D.; Castoro, R.

10.1101/2025.11.11.686785 — neuroscience — Posted on 2025-11-13

3066 Tractography-based transcranial magnetic stimulation prediction using machine learning

Betioli, L. d. S.; Matsuda, R. H.; Marchetti, T. C.; Rondinoni, C.; Moraes, V. H.; Junior, M. A. d. C.; Salmon, C. E. G.; Tinos, R.; Baffa Filho, O.

10.1101/2025.11.11.685674 — neuroscience — Posted on 2025-11-13

3067 Binding Affinity Ranking at the Molecular Initiating Event (BARMIE): An open-source computational pipeline used to identify novel fish glucocorticoid receptor chemical agonists and antagonists

Calahorro, F.; Fouladi, P.; Pandini, A.; Khushi, M.; Gaihre, Y.; Bury, N. R.

10.1101/2025.02.05.636649 — pharmacology and toxicology — Posted on 2025-11-13

3068 Automated filtering of particle images in single particle cryoEM

Malhotra, S.; Hatton, D.; Jackson, S.; Iadanza, M.; Joseph, A. P.; Palmer, C.; Thiyagalingam, J.; Burnley, T.; Chaban, Y.

10.1101/2025.11.12.688030 — biophysics — Posted on 2025-11-13

3069 Suppressing the suppressor: Gallic acid induced asymmetric tetramerization of the pleotropic virulence factor SuhB from Pseudomonas aeruginosa abolishes its extragenic suppressor activities. A structure-based functional study

Yadav, V. K.; Jena, A. K.; Mukerji, M.; Bhattacharyya, S.

10.1101/2025.11.12.687946 — biophysics — Posted on 2025-11-13

3070 Snooping helices: The elastic path finding algorithm of growing hyphae

Rittaud, A.; Couttenier, E.; Bachellier-Bassi, S.; D'Enfert, C.; Kulic, I. M.; Villard, C.

10.1101/2025.11.12.685335 — biophysics — Posted on 2025-11-13

3071 Wood ants on the edge: how do the characteristics of linear edges affect the population dynamics of an edge specialist?

Podesta, J. A.; Parr, C. L.; Redeker, K. R.; Robinson, E. J. H.

10.1101/2025.02.12.637965 — ecology — Posted on 2025-11-13

3072 Photoclickable HaloTag Ligands for Spatiotemporal Multiplexed Protein Labeling on Living Cells

Walterspiel, F.; Ugarte-Uribe, B.; Cabrera, A.; Khan, A. U. M.; Terjung, S.; Deo, C.

10.1101/2025.11.13.686492 — biochemistry — Posted on 2025-11-13

3073 Shape, Strain, and Stability: Epithelia Under High Strain

Yang, J.; Dong, Y.; Jones, C.; Wang, Y.; Merino, C.; Stuckenholz, C.; Davidson, L.

10.1101/2025.11.12.687918 — cell biology — Posted on 2025-11-13

3074 Effects of biological fixation methods on stimulated Raman scattering microscopy signal

Ceconello, C.; Han, W.; Manifold, B.; Polli, D.; Streets, A. M.

10.1101/2025.11.11.687741 — cell biology — Posted on 2025-11-13

3075 Characterization of Endogenous and Epitope-Tagged Ubiquitin Expression and Ubiquitination Patterns at Drosophila Neuromuscular Junctions

Kala-Bhattacharjee, S.; Davis, S.; Sheline, B.; Schayot, C.; Tian, X.; Wu, C.

10.1101/2025.11.11.687520 — genetics — Posted on 2025-11-13

3076 Comparative ASCL1 interactome analysis reveals CDK2-Cyclin A2 as suppressors of differentiation in MYCN-amplified neuroblastoma

Mykhaylechko, L.; Woods, L. M.; Papachristou, E. K.; Gomez, R. L.; Ramachandran, R.; Lundie-Brown, J.; Marcos, D.; Drummond, R.; Ali, F. R.; Carroll, J.; Philpott, A.

10.1101/2025.11.11.687869 — cancer biology — Posted on 2025-11-13

3077 SC-Framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets

Schultheis, H.; Detleffsen, J.; Wiegandt, R.; Bentsen, M.; Alayoubi, Y.; Valente, G.; Kessler, M. F.; Bruns, B.; Mirza, D.; Usanayo, A.; Walter, J.; Goymann, P.; Hobein, M.; Kuenne, C.; Looso, M.

10.1101/2025.11.11.687874 — bioinformatics — Posted on 2025-11-13

3078 PI3K/mTOR activity sensitizes cancer cells to nucleolar stress

Barz, M.; Corman, A.; Haggblad, M.; Gonzalez-Serrano, A.; Lidemalm, L.; Murga, M.; Huhn, D.; Fernandez-Capetillo, O.

10.1101/2025.11.12.688066 — cell biology — Posted on 2025-11-13

3079 Environmental DNA monitoring of waterfowl reveals community changes during migration

Guimaraes de Andrade, L.; Bogdanowicz, S. M.; Klinck, H.; Lodge, D.; Andres, J.

10.1101/2025.11.11.687912 — genetics — Posted on 2025-11-13

3080 Harnessing protein-folding algorithms to drug intrinsically disordered epitopes

Lala, J.; Angioletti-Uberti, S.

10.1101/2025.11.11.687846 — bioinformatics — Posted on 2025-11-13

3081 Targeting of ibrutinib resistance driving pathways by miR-28 in ABC-DLBCL

Alvarez-Corrales, E.; Gomez-Escolar, C.; Moreno-Palomares, R.; Martinez, M.; Laguna-Herrero, M.; Fuertes, T.; Estrada, B. S.; Mur, S.; Martinez-Martin, N.; Somoza, A.; Ramiro, A. R.; de Yebenes, V. G.

10.1101/2025.11.12.687947 — cancer biology — Posted on 2025-11-13

3082 Redefining Ovarian Fibrosis Through Comparative Analysis of Collagen Architecture

Aitken, C. J.; Kadhim, L.; Murray, A.; Landry, D. A.

10.1101/2025.11.12.688021 — cell biology — Posted on 2025-11-13

3083 Reprogramming the Immune Suppressive Tumor Microenvironment in Glioma Enhances the Efficacy of Immune-Mediated Gene Therapy

McClellan, B. L.; Agudelo, J. A. P.; Mujeeb, A. A.; Dabaja, A. A.; Zhu, Z.; Raghuram, S.; Verela, M. L.; Tronrud, C.; Banerjee, K.; Wei, A.; Calatroni, C.; Zhang, L.; Romero, L. C.; Oh, P.; Alghamri, M. S.; Robbins, A.; Perricone, M. D.; Wang, Y.; Shay, B.; Sajjakulnukit, P.; Lyssiotis, C. A.; Welch, J. D.; Schwendeman, A.; Lowenstein, P. R.; Castro, M. G.

10.1101/2025.11.11.687828 — cancer biology — Posted on 2025-11-13

3084 Profiling Nucleotide Signalling Pathways and STING Agonist Activity with a Nucleotide Library

Bekere, I.; Oellinger, R.; Schrimpf, M. R.; Rad, R.; de Oliveira Mann, C. C.

10.1101/2025.11.11.687896 — immunology — Posted on 2025-11-13

3085 Simultaneous stabilizing feedback control of linear and angular momentum in human walking

van Dieen, J. H.; Bruijn, S. M.; Lemaire, K. K.; Kistemaker, D. A.

10.1101/2025.01.09.632072 — biophysics — Posted on 2025-11-13

3086 RHODOPSIN 7: An ancient non-retinal photoreceptor for contrast vision, darkness detection, and circadian regulation

Kirsch, V.; Reinhard, N.; Hartlieb, H.; Mohr, A.; Rieger, D.; Soba, P.; Helfrich-Förster, C.; Senthilan, P. R.

10.1101/2025.07.29.667052 — neuroscience — Posted on 2025-11-13

3087 WITHDRAWN: Production, Purification, and Crystallization of Recombinant Epidermal Growth Factor Receptor Tyrosine Kinase Domain (EGFR-TKD) for Drug Screening Applications

TOPALAN, E.; Ciftci, H.; Demirci, H.

10.1101/2025.06.02.657332 — biochemistry — Posted on 2025-11-13

3088 Novel tensor decomposition-based approach for cell type deconvolution in Visium datasets when reference scRNA-seqs include multiple minor cell types

Taguchi, Y.-h.; Turki,

10.1101/2025.04.18.649484 — bioinformatics — Posted on 2025-11-13

3089 One-Hot News: Drug Synergy Models Take a Shortcut

Candir, E. B.; Kuru, H. I.; Rattray, M.; Cicek, A. E.; Tastan, O.

10.1101/2025.04.18.649584 — bioinformatics — Posted on 2025-11-13

3090 The non-kinase function of CDK6 is a key driver of acquired resistance to CDK4/6 inhibitors in Estrogen Receptor-positive breast cancer

Udden, S. N.; Jiang, B.; Pandey, K.; Lewis, C.; Sahoo, S.; Williams, N.; Alluri, P. G.

10.1101/2025.11.11.687883 — cancer biology — Posted on 2025-11-13

3091 PRC2 Restricts Malignant Peripheral Nerve Sheath Tumorigenesis in a Genetically Engineered Mouse Model of MPNST

Cho, W. H.; Patel, A. J.; Khudoynazarova, M.; Warda, S.; Yan, J.; Li, D.; Schoeps, D.; Fishinevich, E.; Pachai, M. R.; Lee, C. J.; Jacobs, Z.; Kristoff, K.; Sher, J.; Antonescu, C. R.; Chen, Y.; Chi, P.

10.1101/2025.11.12.687881 — cancer biology — Posted on 2025-11-13

3092 Self-supervised AI reveals a lethal discohesive phenotype in lung adenocarcinoma

10.1101/2025.11.12.688049 — cancer biology — Posted on 2025-11-13

3093 Why early birds sing early: rebound singing from nighttime suppression can explain dawn chorus

dos Santos, E. B.; Mori, C.; Kim, Y.; Kim, J.; Tachibana, R. O.; Jeong, O.-Y.; Lee, J.; KOJIMA, S.

10.1101/2025.09.29.679172 — animal behavior and cognition — Posted on 2025-11-13

3094 Proximity proteomics reveals the molecular architecture of phytochrome B photobodies in Arabidopsis thaliana

Olson, K.; Lee, J.-H.; Dean, M.; Doan, T. M.; Manuel, A. M.; Yoo, C. Y.

10.1101/2025.11.09.687487 — plant biology — Posted on 2025-11-13

3095 NF-kappaB is a Central Regulator of Hypoxia-Induced Gene Expression

Shakir, D.; Batie, M.; Kwok, C.-S.; Cook, S. J.; Kenneth, N. S.; Rocha, S.

10.1101/2025.01.08.631917 — molecular biology — Posted on 2025-11-13

3096 Tumor cell-specific loss of GPX4 reprograms triacylglycerol metabolism to escape ferroptosis and impair antitumor immunity in NSCLC

Wang, P.; Zhang, S.; Chen, X.; Yang, X.-D.; Huang, S.; Yin, H.; Duan, H.-Y.; Zhou, F.; Yu, J.; Zhong, B.; Lin, D.

10.1101/2025.11.12.687999 — cell biology — Posted on 2025-11-13

3097 TGF-β Signalling Drives Chemotaxis of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes in Response to MI Stimulus

Deelen, L.; Kobayashi, K.; Gasim, A. H. A.; Lewis-McDougall, F.; Suzuki, K.

10.1101/2025.06.06.658033 — cell biology — Posted on 2025-11-13

3098 WITHDRAWN: Different functions for the lateral line in schooling behavior in three fish species

Tidswell, B. K.; Tytell, E. D.

10.1101/2025.01.24.634378 — animal behavior and cognition — Posted on 2025-11-13

3099 Convergent and lineage-specific genomic changes shape adaptations in sugar-consuming birds

Osipova, E.; Ko, M.-C.; Petricek, K. M.; Yung Wa Sin, S.; Brown, T.; Winkler, S.; PIppel, M.; Jarrells, J.; Weiche, S.; Mosbech, M.-B.; Taborsak-Lines, F.; Wang, C.; Contreras-Lopez, O.; Olsen, R.-A.; Ewels, P.; Mendez Aranda, D.; Gaede, A.; Sadanandan, K.; Weijie Low, G.; Monte, A.; Ballerstaedt, N.; Adreani, N. M.; Mentesana, L.; von Bayern, A.; Rico-Guevara, A.; Edwards, S.; Altshuler, D.; Buttemer, W. A.; Frankl-Vilches, C.; Kuhl, H.; Bakker, A.; Gahr, M.; Schupp, M.; Baldwin, M. W.; Hiller, M.; Sackton, T. B.

10.1101/2024.08.30.610474 — evolutionary biology — Posted on 2025-11-13

3100 Class-I myosin responds to change in membrane tension during clathrin-mediated endocytosis in human induced pluripotent stem cells

Smith, S. L.; Zhan, T.; Li, W.; De Belly, H.; Zhang, Q.; Xu, K.; Weiner, O.; Drubin, D. G.

10.1101/2025.11.12.688091 — cell biology — Posted on 2025-11-13

3101 Importin-β1 functions as a chromatin sensor to position the contractile ring for cytokinesis

Brancheriau, C. R.; Larocque, K.; Tountas, I.; Perlman, A.; Piekny, A.

10.1101/2025.11.12.688041 — cell biology — Posted on 2025-11-13

3102 CREG1 promotes autophagy and protects the heart against nutritional stress-induced injury and age-associated hypertrophy, fibrosis and diastolic dysfunction

Qi, Y.; Pepe, R. J.; Tejeda, G.; Joo, Y.; Yang, N. K.; Hayes, K. B.; rahimi, s.; Zhou, Z.; Li, S.; Lee, L.

10.1101/2025.11.11.687936 — cell biology — Posted on 2025-11-13

3103 Landscape context drives within-species variation in dispersal kernels and limits transferability

Wolff, J.; Fandos, G.; Albert, C. H.; Bocedi, G.; Travis, J. M. J.; Zurell, D.

10.1101/2025.11.09.687206 — ecology — Posted on 2025-11-13

3104 From expert opinion to empirical evidence: Data-driven parametrization of urban connectivity models using movement-proxy data

Merkens, L.; Mimet, A.; Bae, S.; Eberl, E.; Lauppe, E.; Mesarek, F.; Stauffer-Bescher, D.; Hauck, T. E.; Weisser, W. W.

10.1101/2023.12.22.571399 — ecology — Posted on 2025-11-13

3105 Tear fluid as noninvasive liquid biopsy reveals proteins associated with malignant transformation of oral lesions

Santos, E. S.; Granato, D. C.; Carnielli, C. M.; de Figueiredo, D.; Trino, L. D.; Patroni, F. M. S.; Pauletti, B. A.; Domingues, R. R.; Sa, J.; Normando, A. G. C.; Daher, N.; Kravchenko-Balasha, N.; Debasis, P.; Minghim, R.; Kowalski, L. P.; Santos-Silva, A. R.; Lopes, M. A.; Brandao, T. B.; Prado-Ribeiro, A. C.; Leme, A. F. P.

10.1101/2025.11.06.686738 — biochemistry — Posted on 2025-11-13

3106 Heat stress induces unreduced male gamete formation by targeting meiocyte translation

Schindfessel, C.; Cairo, A.; Mikulkova, P.; Jin, C.; Lamelas Penas, L.; Wigge, P. A.; Riha, K.; Geelen, D. N. V.

10.1101/2022.08.11.503651 — plant biology — Posted on 2025-11-13

3107 Polar localization of putative phospholipid transporters in Escherichia coli

Tan, W. B.; Chong, Z.-S.; Cheong, J. W. M.; Yeow, J.; Chng, S.-S.

10.1101/2025.04.17.649288 — microbiology — Posted on 2025-11-13

3108 Primary Cilia Dysfunction in Brown Fat Results in Fatal Thermogenesis Failure in Neonatal Mice

Lee, J.; Kim, Y. M.; Lee, H.; Kim, J. H.; Kang, J.; Han, S. Y.; Park, J. S.; Park, H.-W.; Shin, J.; Kim, J.-s.; Park, H. S.

10.1101/2025.11.12.687971 — cell biology — Posted on 2025-11-13

3109 mRNA isoform switching plays a crucial role in mural cumulus differentiation

Shila, S.; Pei, G. J.; Peramsetty, N.; Bahadursingh, E.; Dahiya, V.; Marsh, C. A.; Thiyagarajan, R.; Zhang, M.; Fields, P. E.; Rumi, M. A.

10.1101/2025.11.11.684658 — cell biology — Posted on 2025-11-13

3110 SPG11 models reveal lysosomal calcium as a regulator of neural progenitor proliferation

SAMAROO, D.; CAUHAPE, M.; BERNACHOT, L.; DARIOS, F.

10.1101/2025.07.21.665525 — cell biology — Posted on 2025-11-13

3111 Epigenetic silencing of transposable elements by IRF2BP2 is a selective dependency of myeloid leukemia

Xu, J.; Whittle, J.; Clayfield, L.; Lie-a-Ling, M.; Leddy, E. A.; Smith, D.; Sellers, R.; Deniz, O.; Lacaud, G.

10.1101/2025.11.12.688028 — cancer biology — Posted on 2025-11-13

3112 EMT activates ER-to-Golgi trafficking through upregulation of REEP2 to promote lung cancer progression

Fulp, K.; Obaleye, O.; Wang, S.; Liu, X.; Yu, J.; Kurie, J. M.; Xu, J.; Russell, W. K.; Tan, X.; Xiao, G.-Y.

10.1101/2025.11.12.688098 — cancer biology — Posted on 2025-11-13

3113 A Population-Specific PARP1 Gene Variation Modulates PARP Trapping

Cai, J.; Billur, R.; Cohen, M. S.; Ladurner, A. G.; Black, B. E.

10.1101/2025.11.11.687916 — cancer biology — Posted on 2025-11-13

3114 Co-Hyperpolarized Dehydroascorbate and Pyruvate MRI Predicts Radiation Response in Glioblastoma Models

Coffee, E.; Porcari, P.; Patel, S.; Figlioli, G.; Berishaj, M.; Rahimi-Keshari, K.

10.1101/2025.11.11.687898 — cancer biology — Posted on 2025-11-13

3115 Combined expression of FOXO and Tribbles proteins predicts survival of glioma patients

Santos, B. F.; Maia, A.-T.; Grenho, I.; Besouro-Duarte, A.; Sepulveda, J. M.; Ferreira, B. I.; Link, W.

10.1101/2025.01.20.633940 — cancer biology — Posted on 2025-11-13

3116 Weight distributions in the fruit-fly and the mouse connectomes

Cirunay, M. T.; Papp, I.; Odor, G.

10.1101/2025.11.10.687553 — neuroscience — Posted on 2025-11-13

3117 Disentangling Stimulus & Population Dynamics in Mouse V1: Orthogonal Subspace Decomposition for Neural Representation

Tzanakis, N.; Barberis, A.; Savaglio, M. A.; Chourdaki, I.; Smirnakis, S. M.; Papadopouli, M.

10.1101/2025.11.10.687558 — neuroscience — Posted on 2025-11-13

3118 Twelve phosphomimetic mutations induce the assembly of recombinant full-length human tau into paired helical filaments

Lövestam, S.; Wagstaff, J. L.; Katsinelos, T.; Shi, J.; Freund, S. M.; Goedert, M.; Scheres, S. H.

10.1101/2024.10.23.619846 — neuroscience — Posted on 2025-11-13

3119 Matrix Stiffness Dictates Doxorubicin-Induced Apoptosis by Modulating Cell-Cycle State in HeLa Cells

Calahan, N.; Burlingham, S.; Prasad, A.; Ghosh, S.

10.1101/2025.11.11.687886 — biophysics — Posted on 2025-11-13

3120 Feather aerodynamics suggest importance of lift and flow predictability over drag minimization

Alenius, F.; Revstedt, J.; Johansson, C.

10.1101/2024.05.27.596009 — zoology — Posted on 2025-11-13

3121 A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements

Yang, A.; Lee, G. G.; Chhetri, S.; El Hajj Chehade, R.; Gulati, G.; Fu, D.; Kim, Y.-N.; Pandey, M.; Sotudian, S.; Savignano, H.; Shahbazi, S. D.; Philpot, C.; Hoggood, T. A.; Gulhan, D. C.; Kellis, M.; Berchuck, J. E.; Baca, S. C.

10.1101/2025.11.06.686988 — genomics — Posted on 2025-11-13

3122 Organism-wide cellular dynamics and epigenomic remodeling in mammalian aging

Lu, Z.; Zhang, Z.; Xu, Z.; Abdulraouf, A.; Zhou, W.; Cao, J.

10.1101/2025.05.12.653376 — genomics — Posted on 2025-11-13

3123 Accelerating ligand discovery by combining Bayesian optimization with MMGBSA-based binding affinity calculations

Andersen, L.; Rausch-Dupont, M.; Martinez Leon, A.; Volkamer, A.; Hub, J.; Klakow, D.

10.1101/2025.06.22.660936 — bioinformatics — Posted on 2025-11-13

3124 Single-cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location

Cruz, J.; Sun, W. Y.; Verbeke, A.; Hariharan, I. K.

10.1101/2024.12.10.627868 — genomics — Posted on 2025-11-13

3125 A METHOD TO CALIBRATE CHEMICAL AGNOSTIC QUANTITATIVE ADVERSE OUTCOME PATHWAYS ON MULTIPLE CHEMICAL DATA

Zhou, Z.; Sahlin, U.

10.1101/2025.03.11.642550 — bioinformatics — Posted on 2025-11-13

3126 A higher load of deleterious mutations has a detrimental effect on tree growth in maritime pine

Pineiro, R.; Cahn, L.; Budde, K. B.; Hurel, A.; Theraroz, A.; Vendramin, G. G.; Pinosio, S.; Lesur, I.; de Miguel, M.; Plomion, C.; Heuertz, M.; Gonzalez-Martinez, S. C.

10.1101/2025.11.09.687477 — evolutionary biology — Posted on 2025-11-13

3127 Increased clonality, decreased allele diversity and high genetic structure in tetraploid sea anemone Aulactinia stella populations from North Pacific to Atlantic across the Arctic Ocean

Bocharova, E.; Volkov, A.; Stoeckel, S.

10.1101/2025.04.24.650399 — evolutionary biology — Posted on 2025-11-13

3128 Comprehensive pan-cancer characterization of cancer-testis genes at single-cell resolution

Fu, C.; Yin, S.; Li, L.; Liu, X.; Jin, X.; Liu, K.

10.1101/2025.08.25.672079 — cancer biology — Posted on 2025-11-13

3129 Topological data analysis identifies PURPL as a prognostic gene in breast cancer Luminal A patients

Ochoa Zavalza, S. J.; Pouokam, M.; Kruse, M.; Gonzalez-Isunza, G.; Sazdanovic, R.; Arsuaga, J.

10.1101/2025.11.11.687413 — cancer biology — Posted on 2025-11-13

3130 NUAK2 is a therapeutically tractable regulator of RNA splicing and tumor progression in neuroendocrine prostate cancer

Mehraj, U.; Maimekov, U.; Manzoor, S.; Cordova, E.; Patel, M.; Mancera-Ortiz, I. Y.; Howell, S.; Davis-Gilbert, Z. W.; Wang, M.-E.; Chen, M.; Park, J. W.; Wang, Y.; Armstrong, A. J.; Huang, J.; Drewry, D. H.; Mitrofanova, A.; Macias, E.

10.1101/2025.11.12.687734 — cancer biology — Posted on 2025-11-13

3131 Targeting STING-ATM axis overcomes radiotherapy-induced immune suppression and restores anti-tumor immunity in nasopharyngeal carcinoma

Liu, T.-T.; Chang, K.-P.; Wang, Y.-N.; OuYang, C.-N.; Li, M.-H.; Tsang, N.-M.; Jiang, S. S.; Sui, Y.-H.; Hu, C.-M.; Chou, Y.-C.; Chen, H.-C.; Liu, S.-C.

10.1101/2025.11.12.687945 — cancer biology — Posted on 2025-11-13

3132 Siglec-engaging immunosuppressive sialoglycans are upregulated in prostate cancer and are targetable to suppress bone metastasis

Peng, Z.; Hodgson, K.; Fisher, M.; Mei, S.; Orozco-Moreno, M.; Cao, L.; Kemp, M.; Gatlin, W.; Donald, L.; Zeng, F.; Lawson, M. A.; Ungar, D.; Sykes, D. B.; Elliott, D. J.; Peng, L.; Schumann, B.; Wang, N.; Munkley, J.

10.1101/2025.11.12.687981 — cancer biology — Posted on 2025-11-13

3133 Mitochondria redistribution organizes the immunosuppressive tumor ecosystem

Terasaki, A.; Weiner, A. T.; Tan, Y.; Szeifert, V.; Bhatnagar, K.; Rada, C. C.; Shankar, V.; Kernick, C.; Mahmood, M.; Wiggers, L.; Rodrigues, V. R.; Gammage, P. A.; Roth, T.; Axelrod, J. D.; Engleman, E.; Li, B.; Okwan-Duodu, D.

10.1101/2025.11.11.687895 — cancer biology — Posted on 2025-11-13

3134 Drought, thermal response and climate-patterning in cuticular conductance of the widespread C4 grass, Themeda triandra

Middha, A.; Jacob, V.; Choat, B.; Wright, I. J.; Blackman, C. J.

10.1101/2025.11.02.686155 — ecology — Posted on 2025-11-13

3135 Comparative risk-assessment of highly pathogenic avian influenza H5 viruses spread in French broiler and layer sectors

Hautefeuille, C.; Munoz, F.; Dauphin, G.; Paul, M.; Peyre, M.; Goutard, F.

10.1101/2024.09.11.612235 — ecology — Posted on 2025-11-13

3136 Uncovering the molecular basis of kinase activity and substrate recognition with phospho-PCA

Yu, C.; Pao, E.; Van Valen, D. A.

10.1101/2025.11.07.687244 — molecular biology — Posted on 2025-11-13

3137 Developing a Molecular Toolkit to ENABLE all to apply CRISPR/Cas9-based Gene Editing in planta

Abate, B. A.; Hahn, F.; Chirivi, D.; Betti, C.; Fornara, F.; Molloy, J. C.; Krainer, K. M. C.

10.1101/2025.11.09.687425 — plant biology — Posted on 2025-11-13

3138 Proteome-wide identification of metamorphic protein candidates using mass spectrometry

Quan, B.; Qiu, Y.; Carillo, K.; Liwang, A.; Orban, J.; Chou, T.-F.

10.1101/2025.11.12.688092 — biophysics — Posted on 2025-11-13

3139 Decorin promotes nascent proteoglycan retention in cartilage matrix by strengthening collagen II-aggrecan integration

Li, T.; Canziani, G.; Liu, Y.; Patel, N.; Han, B.; Fan, M.; Porter, A.; Kwok, B.; Wang, C.; Li, Q.; Birk, D. E.; Iozzo, R. V.; Chaiken, I. M.; Lu, X. L.; Mauck, R. L.; Han, L.

10.1101/2025.11.12.688145 — biophysics — Posted on 2025-11-13

3140 Helical charge distribution at the transmembrane-luminal interface determines subcellular localization

Saad, H.; Benyair, R.; Mazor, T.; Lederkremer, G. Z.

10.1101/2025.11.12.688035 — cell biology — Posted on 2025-11-13

3141 A nematic framework for sprouting angiogenesis

Barrasa-Ramos, S.; Blanch-Mercader, C.; Barakat, A. I.

10.1101/2025.11.12.688071 — biophysics — Posted on 2025-11-13

3142 Multi-step implementation of meiotic crossover patterning

Cavka, I.; Woglar, A.; Wu, Y.-L.; Durmus, E. B.; Sloat, L.; Gros, A.; Pineiro Lopez, C.; Hecht, F.; Villeneuve, A. M.; Ries, J.; Koehler, S.

10.1101/2025.11.12.687980 — cell biology — Posted on 2025-11-13

3143 Gene interaction enrichment analysis for transcriptomic data with GREA

Liu, X.; Jiang, A.; Lyu, C.; Chen, L.

10.1101/2025.04.15.649030 — bioinformatics — Posted on 2025-11-13

3144 GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments

Kruithoff, R.; Spendlove, M. D.; Sheppard, S. J.; Schweiger, M. C.; Pessoa, P.; Abbasi, M.; Presse, S.; Bartelle, B. B.; Shepherd, D. P.

10.1101/2025.10.10.681751 — bioinformatics — Posted on 2025-11-13

3145 SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design

Zhang, P.; Han, R.; Kong, X.; Chen, T.; Ma, J.

10.1101/2025.11.06.687093 — bioinformatics — Posted on 2025-11-13

3146 Transferring active inference to newly encountered prism-shifted environments

Yoshihara, M.; Isomura, T.

10.1101/2025.11.10.687533 — neuroscience — Posted on 2025-11-13

3147 Single-step in vitro ribosome reconstitution mediated by two GTPase factors, EngA and ObgE

Sato, A.; Lai, W. Y.; Sakai, Y.; Shimizu, Y.

10.1101/2024.10.17.618970 — biochemistry — Posted on 2025-11-13

3148 Anti-Kv1.2 Immunoprecipitation Identifies shared mGluR1-Associated Signalosome Complex proteins and PKC-Mediated Regulation of Kv1.2 in the Cerebellum

Madasu, S. C.; Morielli, A. D.

10.1101/2025.11.09.687499 — neuroscience — Posted on 2025-11-13

3149 Optimizing Language Model Embeddings to Voxel Activity Improves Brain Activity Predictions

Negi, A.; Tseng, C.; Nunez-Elizalde, A. O.; Gong, X. L.; Deniz, F.

10.1101/2025.09.18.676935 — neuroscience — Posted on 2025-11-13

3150 Molecular, anatomical, and functional organization of lung interoceptors

Liu, Y.; Kinsey, L.; Diaz de Arce, A. J.; Krasnow, M. A.

10.1101/2021.11.10.468116 — neuroscience — Posted on 2025-11-13

3151 Blockade of associative spine enlargement impairs awake cortical function

Zhou, S.; Sawada, T.; Arima, T.; Panezai, S. K.; Ohtsuka, M.; Okazaki, H.; Takaramoto, S.; Terada, S.-I.; Kondo, M.; Hashimoto, T.; Ohki, K.; Matsuzaki, M.; Yagishita, S.; Kasai, H.

10.1101/2025.11.06.686434 — neuroscience — Posted on 2025-11-13

3152 Geometry representations along visual pathways in human spatial navigation

Zeng, T.; Cai, M. B.

10.1101/2024.08.04.605402 — neuroscience — Posted on 2025-11-13

3153 Decoding the Valence of Developmental Social Behavior: Dopamine Governs Social Motivation Deficits in Autism

Chen, X.; Tao, X.; Zhong, Z.; Zhang, Y.; Li, Y.; Ouyang, Y.; Ding, Z.; An, M.; Wang, M.; Li, Y.

10.1101/2025.11.12.687985 — neuroscience — Posted on 2025-11-13

3154 A platform for standardized, online delivered, clinically applicable neurocognitive assessment: WebNeuro

Williams, L. M.

10.1101/2023.08.28.553107 — neuroscience — Posted on 2025-11-13

3155 Selection History Models in a Population under Ongoing Directional Selection

Jansen, A. C. M.; Calus, M. P. L.; Wientjes, Y. C. J.

10.1101/2025.11.11.687909 — genetics — Posted on 2025-11-12

3156 Causal role of the individual alpha phase in multisensory perception

Rohe, T.; Senkowski, D.

10.1101/2025.11.11.687884 — neuroscience — Posted on 2025-11-12

3157 Early impairment in dentate pattern separation in a rodent model of temporal lobe epilepsy.

Ewell, L. A.; Ramezani, A.; Suarez, G.; Piatti, V. C.; Lam, V.; Mills, T. G.; McGinness, A.; Kuk, R.; Ukai, M.; Schlenner, A.-L.; Leutgeb, S.; Leutgeb, J. K.

10.1101/2025.11.12.688087 — neuroscience — Posted on 2025-11-12

3158 FGF13 is not secreted from neurons

Malvezzi, M.; Zhang, H.; Towers, P.; Lyden, D. C.; Marx, S. O.; Pitt, G. S.

10.1101/2025.11.12.688075 — neuroscience — Posted on 2025-11-12

3159 Acetylcholine reflects uncertainty during hidden state inference

Svahn, E.; Wang, Y.; Knebelmann, H.; Pan, Y.; Shahab-Dehkordi, N.; Akrami, A.; MacAskill, A. F.

10.1101/2025.11.12.688036 — neuroscience — Posted on 2025-11-12

3160 An Autophagy-Inducing Compound Reduces Tau Pathology, Microglia Reactivity, and Rescues Working Memory in 3xTg AD Mice

Mayeri, Z.; Woods, G.; Rane, A.; Kifle, A.; Chamoli, M.; Shukla, S.; Walton, C. C.; Andersen, J. K.

10.1101/2025.11.09.687389 — neuroscience — Posted on 2025-11-12

3161 Bayesian Inference Framework to Identify Skin Material Properties \textit{in vivo} from Active Membranes

Wilkinson, M.; Goparaju, K.; Nunez-Alvarez, L.; Goergen, C. J.; Arrieta, A. F.; Tepole, A. B.

10.1101/2025.11.11.687900 — biophysics — Posted on 2025-11-12

3162 Discovery and evaluation of cadmium-adapted Daphnia pulex genotypes in a region of historical mining reveals adaptation protects the germline from cadmium-induced mutations

Keith, N.; Glaholt, S. P.; Jackson, C. E.; Young, K.; DeSchamphelaere, K.; Colbourne, J. K.; Shaw, J. R.

10.1101/2025.11.11.687873 — evolutionary biology — Posted on 2025-11-12

3163 Recovery of infectious Oz virus from cloned cDNA

Rakib, T. M.; Akter, L.; Shimoda, H.; Kuroda, Y.; Matsugo, H.; Urata, S.; Matsumoto, Y.

10.1101/2025.11.12.687958 — microbiology — Posted on 2025-11-12

3164 Strain-Level Adaptation of Pyrophilous Bacteria through Gene Fragmentation and Horizontal Gene Transfer

Sari, E.; Enright, D. J.; Ordonez, M.; Cordova-Ortiz, E.; Byrd, A.; Allison, S. D.; Homyak, P. M.; Wilkins, M. J.; Glassman, S. I.

10.1101/2025.11.11.687939 — microbiology — Posted on 2025-11-12

3165 The Rise and Fall of SARM1 Base-Exchange Inhibitors

Lundback, T.; Chandrasekar, V.; Gu, C.; Ju, H.; McAdam, R.; Palomero, M.; Sader, K.; Peter, B.; Wissler, L.; Nevin, P.; Foster, E.; Jamier, T.; Manjappa, P.; Johansson, C.; Sandmark, J.; Ding, M.; Persson-Kry, A.; Mitra, S.; Satir, T. M.; Bilican, B.; Messa, M.; Fraser, G.; Linley, J.; Plant, H.; Moore, R.; Seifert, T.; Lerche, M.; Raynochek, C.; Nilsson, E.; Majbour, N.; Lucey, R.; Maia de Oliveira, T.; Wang, Q.; Chessell, I.; Breccia, P.; Jarvis, R.

10.1101/2025.11.11.687870 — neuroscience — Posted on 2025-11-12

3166 A funnel-type pipeline for accelerating discovery of tailored designer xylanosomes for efficient arabinoxylan valorization

Fonseca, M. J.; Vanderstraeten, J.; De Coninck, T.; Vlyminck, S.; Briers, Y.

10.1101/2025.11.12.687223 — synthetic biology — Posted on 2025-11-12

3167 Terminal conjugation enables nanopore sequencing of peptides

Ritmejeris, J.; Chen, X.; Albada, B.; Dekker, C.

10.1101/2025.11.12.687956 — biophysics — Posted on 2025-11-12

3168 Phage-encoded factor stimulates DNA degradation by the Hna anti-phage defense system

Hooper, M. M.; Hoover, B. T.; Zhang, H.; Franco, A. S.; Finkelstein, I. J.; Taylor, D. W.

10.1101/2025.11.12.688083 — biochemistry — Posted on 2025-11-12

3169 Differential nucleosome organization in human interphase and metaphase chromosomes

Li, K.; Unlu, I.; Tu, Y.; Voong, L.; Lu, Y.; Kendall, B.; Ma, X.; Pui, S. L.; Tao, M.; Wang, J.-P.; Wang, X.

10.1101/2025.11.11.687715 — genomics — Posted on 2025-11-12

3170 Tick Genome Assemblies: Overcoming biological limitations through advances in sequencing and assembly

Dillon, K. C.; Frederick, J. C.; Sprong, H.; Glenn, T. C.; Ronai, I.

10.1101/2025.11.11.687924 — genomics — Posted on 2025-11-12

3171 Homoploid hybrid speciation between cryptic species of a hidden snout weevil

Noguerales, V.; Eisele, M. H.; Gray, S. L.; Stankowski, S.; Emerson, B. C.

10.1101/2025.11.12.688067 — evolutionary biology — Posted on 2025-11-12

3172 Mineral guided molecular enrichment: An interfacial driving force for protocell emergence on early Earth

Chen, W.; Zheng, R.; Luo, Z.; Wu, G.; Lei, J.; Gou, H.; Li, H.; Wang, Z.; Xiao, W.; Li, C.; Yu, G.

10.1101/2025.11.12.687952 — evolutionary biology — Posted on 2025-11-12

3173 Structural basis of lipid-mediated gating in a two-pore domain potassium channel

Sano, F. K.; Kasuya, G.; Yamaguchi, K.; Suzuki, T.; Yamanouchi, D.; Hashimoto, K. M.; Inoue, M.; Sawada, K.; Ishitani, R.; Yoshimura, K.; Hirano, H.; Itoh, Y.; Nakajo, K.; Dohmae, N.; Kise, Y.; Nureki, O.

10.1101/2025.11.12.688043 — molecular biology — Posted on 2025-11-12

3174 Bioplastic Production Potential of Azospira suillum PS: Growth-Associated PHB Production Under Aerobic and Anaerobic Conditions

Meier, D. A. O.; Glazer, B.; Lanclos, V. C.; Carlson, H. K.; Coates, J. D.

10.1101/2025.11.12.688118 — microbiology — Posted on 2025-11-12

3175 Human exposure to spirochete-infected Ornithodoros turicata collected from the home of an individual in the Austin, Texas Metropolitan Area

Filatov, S.; Mayes, B.; Gunter, S.; Kneubehl, A. R.; Lopez, J. E.

10.1101/2025.11.12.688062 — microbiology — Posted on 2025-11-12

3176 Clinical stringent response activation promotes conjugal transfer of staphylococcal resistance plasmids

Deventer, A. T.; Sutherland, A.; Biernacka, D.; Johnston, P. R.; Stevens, C. E.; Kaczorowska, A.-K.; Boraston, A.; Hobbs, J. K.

10.1101/2025.11.12.688057 — microbiology — Posted on 2025-11-12

3177 Environmental factors contribute to cancer therapy toxicity

Mehl, L. C.; Nunez, M. S.; Sanz, J. M.; Geraghty, A.; Dal Cengio, L.; Kaval, A.; Chen, Y.; Gibson, E. M.

10.1101/2025.11.11.687867 — neuroscience — Posted on 2025-11-12

3178 Modular in vivo engineering of the reductive methylaspartate cycles for synthetic CO2 fixation

Rainaldi, V.; Schulz-Mirbach, H.; Solomon, J. B.; Sloothaak, S. Q.; Paczia, N.; Erb, T. J.; D'Adamo, S.; Claassens, N. J.

10.1101/2025.11.12.688011 — synthetic biology — Posted on 2025-11-12

3179 Mutation and ACE2-induced Allosteric Network Rewiring in Delta and Omicron SARS-CoV-2 Spike Proteins

Dutta, M.; Voth, G. A.

10.1101/2025.11.12.688084 — biophysics — Posted on 2025-11-12

3180 Loop Plasticity Drives Paralog-Specific Recognition in BET ET Domains

Alvarez, G.; Sebastian, E.; Mondal, A.; Roth, M. J.; Montelione, G. T.; Perez, A.

10.1101/2025.11.11.687848 — biophysics — Posted on 2025-11-12

3181 Mechanistic Understanding of Protein-MOF Integration through Surfactant-Driven Interfacial Design

Rashidniyaghi, E.; Khavani, M.; Coerver, C.; Liang, R.; Ravanfar, R.

10.1101/2025.11.11.687871 — biophysics — Posted on 2025-11-12

3182 Biofuel-driven Adaptable n-type Supramolecular Wires: Mimicking Conducting Microbial Nano-filaments

Kumar, S.; Kapila, R.; Panda, A.; Singh, P.; Kaliginedi, V.; Rana, S.

10.1101/2025.11.12.687965 — bioengineering — Posted on 2025-11-12

3183 Structural basis for constitutive activation of oncogenic gp130 mutants in human inflammatory hepatocellular adenomas

Zhou, Y.; Cao, J.; Ramlall, T.; McGoldrick, L.; Jones, J.; Cook, A.; Leidich, R.; Sleeman, M.; Olson, W.; Stevis, P.; Franklin, M.

10.1101/2025.11.11.685192 — biochemistry — Posted on 2025-11-12

3184 Computational redesign of a thermostable T7 RNA polymerase

Baumer, Z. T.; Whitehead, T. A.

10.1101/2025.11.12.688101 — biochemistry — Posted on 2025-11-12

3185 Exploration of American Elderberry Bioactive Compounds for Inhibition of the Influenza Virus Polymerase Acidic Endonuclease

Dwikarina, A.; Hsieh, H.; Greenlief, M.; Thomas, A. L.; Lin, C.-H.

10.1101/2025.11.12.688002 — biochemistry — Posted on 2025-11-12

3186 Quantification of bioactive compounds in the juices of 21 American elderberry cultivars

Dwikarina, A.; Greenlief, M. C.; Andrew L. Thomas, A. L.; Lin, C.-H.

10.1101/2025.11.12.688025 — biochemistry — Posted on 2025-11-12

3187 Diverse expression and modification of tRNAs and tRNA-derived RNAs in 19 mouse tissues

Manning, A. C.; Chan, P. P.; Lowe, T. M.

10.1101/2025.11.11.685198 — genomics — Posted on 2025-11-12

3188 High-efficiency targeted integration of extrachromosomal arrays in C. elegans using PhiC31 integrase

Rich, M. S.; Pellow, R.; Hefel, A.; Rog, O.; Jorgensen, E. M.

10.1101/2025.11.11.687718 — genetics — Posted on 2025-11-12

3189 Export-biased, 3'UTR-preserving TDP-43 model links nuclear loss to cytoplasmic aggregation in ALS/FTLD

Toyama, G.; Koide, S.; Yamagishi, T.; Washida, A.; Hanyu, R.; Onodera, O.; Sugai, A.

10.1101/2025.11.12.687969 — molecular biology — Posted on 2025-11-12

3190 Phase Behavior of TDP-43 and hnRNP H1: From Soluble and Aggregated States to Liquid-Like Droplets

Wang, T. R.; Wang, J.

10.1101/2025.11.12.687994 — molecular biology — Posted on 2025-11-12

3191 SLC11A2 affects nutritional immunity in the gastrointestinal epithelium

Norberg, E. S.; Westerman, T. L.; Cruz, E.; Bushman, S. D.; Skaar, E. P.; Elfenbein, J. R.; Knodler, L. A.

10.1101/2025.11.12.688034 — microbiology — Posted on 2025-11-12

3192 Effect of human urinary microenvironment and fluid flow on antibiotic and phage therapy efficacy against uropathogenic Escherichia coli

Maset, R. G.; Crowther, A.; Chu, V.; De Grandi, D.; Jariah, R. O. A.; Yoon, J.; Blumgart, D.; Hodek, M. A. E.; Yuen, N.; Murray, B. O.; Pasquina-Lemonche, L.; Alghamdd, S. N. H.; Millard, A. D.; LuTheryn, G.; Haines, M. E. K.; Clokie, M. R. J.; Stride, E.; Carugo, D.; Rohn, J. L.

10.1101/2025.11.12.688052 — microbiology — Posted on 2025-11-12

3193 Multifaceted suppression of staphylococcal virulence: in vitro study of a cellular status with reduced Agr activity and impaired biofilm

Nguyen, N. B.; Ushijima, Y.; Morikawa, K.; Nguyen, T. T. L.

10.1101/2025.11.11.687926 — microbiology — Posted on 2025-11-12

3194 Tunneling nanotubes propagate a BMP-dependent preneoplastic state.

CUELLA MARTIN, C.; NGUYEN, T. T.; BERTIN, A.; GEISTLICH, K.; GUYOT, B.; LEFORT, S.; DELAY, E.; DALVERNY, C.; BOISSARD, A.; HENRY, C.; GUILLONNEAU, F.; PECHEUR, E. I.; MAGUER-SATTA, V.

10.1101/2025.11.11.687852 — cancer biology — Posted on 2025-11-12

3195 Global Analysis of Aggregation Determinants in Small Protein Domains

Martell, C. M.; Gebis, K. K.; Van, H. M.; Gutierrez, Y. M.; Jung, M. D.; Savas, J. N.; Rocklin, G. J.

10.1101/2025.11.11.687847 — biophysics — Posted on 2025-11-12

3196 metaboprep v2: Broadening the application of the metaboprep beyond metabolomics

Sunderland, N.; Hughes, D. A.; Lee, M. A.; McKinlay, A.; Timpson, N. J.; Corbin, L. J.

10.1101/2025.11.11.687831 — bioinformatics — Posted on 2025-11-12

3197 Anti-CD3 microporous annealed particle hydrogel protects stem cell derived beta cells from autoreactive T cells

Widener, A. E.; Manson, C. T.; Barra, J. M.; Spencer, C. P.; Grodman, A. D.; Ladd, A. M.; Russ, H. A.; Phelps, E. A.

10.1101/2025.11.11.687837 — bioengineering — Posted on 2025-11-12

3198 Weak evaporative cooling capacity and body size shape thermal limits in tropical montane forest birds

Pacioni, C.; Xu, R.; Apfelbeck, B.; Verbruggen, F.; Njoroge, P.; Githiru, M.; Strubbe, D.; Lens, L.

10.1101/2025.11.11.687810 — ecology — Posted on 2025-11-12

3199 A self-organizing single-cell morphology circuit optimizes Podophrya collini predatory trap structure

Xu, Z.; Mazurkiewicz, L. E.; Olivetta, M.; Morrissey, M.; Dudin, O.; Weeks, A. M.; Coyle, S. M.

10.1101/2025.11.12.688106 — cell biology — Posted on 2025-11-12

3200 Phage N4 uses a SAR endolysin-holin system for host cell lysis

Awuah, M. B.; Martin, C.; Chamblee, J. S.; Tomaszewski, A. J.; Sullivan, T. E.; Emilia, Q.; Tran, S.; Snowden, J. H.; Niemiec, K. A.; Zhu, J.; Ramsey, J.

10.1101/2025.11.12.688109 — microbiology — Posted on 2025-11-12

3201 Repurposing Nelfinavir: AIM2 Inflammasome-Driven Anti-tumor Effects in Glioblastoma

Meena, D.; Chhipa, S.; Solanki, P.; Sha, L.; Jha, S.

10.1101/2025.11.11.687819 — cancer biology — Posted on 2025-11-12

3202 An atlas of microtubule lattice parameters regulated through ligand binding to the microtubule stabilizing sites.

Lucena-Agell, D.; Fernandez, O.; Paris-Ogayar, R.; Estevez-Gallego, J.; Ondruskova, D.; Alvarez-Bernad, B.; Bonato, F.; Larraga, J.; Ortiz de Elguea, D.; Cano, G. J.; Scheers, M.; Imai, H.; Yagi, T.; Iwamoto, H.; Martinez-Guil, J. C.; Sing, J.; Keyzers, R.; Vanderwal, C.; Altmann, K.-H.; Van der Eyken, J.; Palomo, V.; Fang, W.-S.; Gago, F.; Lansky, Z.; Braun, M.; Kamimura, S.; Diaz, J. F.

10.1101/2025.11.11.687833 — biophysics — Posted on 2025-11-12

3203 SignalGen: A Protein Language Model Based AI Agent For Optimal Signal Peptide Prediction

McKenzie, J. H.; Do, H. N.; Shanker, A.; Kubicek-Sutherland, J. Z.; Gnanakaran, S.

10.1101/2025.11.12.688111 — bioinformatics — Posted on 2025-11-12

3204 Ecological stoichiometry and life history theory, not the identity of genomic variants, predict rapid adaptation

Rudman, S. M.; Faber-Hammond, J. J.; Sherman, R. E.; Shahmohamadloo, R. S.; Greenblum, S. I.; MacMillan, H. A.; Jeyasingh, P. D.; Schmidt, P. S.

10.1101/2025.11.11.687836 — evolutionary biology — Posted on 2025-11-12

3205 Different transcriptional responses to developmental versus short-term acclimation temperatures in Pieris rapae

Sturiale, S. L.; He, L. L. Y.; Malinski, K. H.; Willett, C. S.; Kingsolver, J. G.; Ries, L.; Armbruster, P. A.

10.1101/2025.11.11.686846 — ecology — Posted on 2025-11-12

3206 The Dishevelled C-terminus interacts with the centrosomal protein Kizuna to regulate microtubule organization during ciliogenesis.

Lines, M.; Murray, K.; Luo, A.; Yang, T.; Hwang, Y.-S.; Westlake, C. J.; Daar, I. O.; Yoon, J.

10.1101/2025.11.12.688108 — developmental biology — Posted on 2025-11-12

3207 Targeting C5aR1 Reveals Protective Macrophage Maturation States in Intestinal Injury

Clark, H.; Chai, I. J.; Melemenidis, S.; Nambiar, D. K.; Kim, R. K.; Jiang, Y.; Casey, K. M.; Zherka, I.; Majorova, D.; Woodruff, T. M.; Graves, E. E.; Le, Q.-T.; Buczacki, S. J.; Giaccia, A. J.; Olcina, M. M.

10.1101/2025.11.11.687632 — immunology — Posted on 2025-11-12

3208 Scalable spike sorting across thousands of neurons by modeling neural dynamics with NeuroSort

Liu, L.; Hu, Z.; Zhang, S.; Liu, Y.; Jia, H.; Sun, H.; Jia, S.; Sun, X.; Liu, J. K.; Duan, X.; Li, X.

10.1101/2025.11.11.687825 — neuroscience — Posted on 2025-11-12

3209 Multiple patterns of selectivity in superior colliculus control visual search

Leite, A.; Adeli, H.; McPeek, R. M.; Zelinsky, G. J.

10.1101/2025.11.11.687826 — neuroscience — Posted on 2025-11-12

3210 Thyrotropin-releasing hormone protects hippocampal neurons against glutamate toxicity via phosphatidylinositol 3-kinase/AKT pathway and new protein synthesis

Dong, Y.; Watson, D. J.

10.1101/2025.11.11.687668 — neuroscience — Posted on 2025-11-12

3211 Olfactory biopsy analysis of Alzheimer's pathobiology across disease stages

D'Anniballe, V.; Kim, S.; Finlay, J. B.; Wang, M.; Ko, T.; Luo, S.; Whitson, H.; Johnson, K. G.; Goldstein, B.

10.1101/2025.11.11.687356 — neuroscience — Posted on 2025-11-12

3212 Cell Type Specific Inference of Perturbations in Synaptic Communication with MultiNeuronChat

Volkmer, G.; Hjerling-Leffler, J.; Bast, L.

10.1101/2025.11.11.687822 — bioinformatics — Posted on 2025-11-12

3213 Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages

Huang, W.-C.; Dombrowski, N.; Mahendrarajah, T. A.; Wahl, N.; Stamatakis, A.; Szollosi, G. J.; Williams, T. A.; Spang, A.

10.1101/2025.11.11.687807 — evolutionary biology — Posted on 2025-11-12

3214 Effects of forest cover, temperature and flower abundance on cashew pollinators in the northern Western Ghats, India

Satish, A.; Sadekar, V.; Madhu, N.; Manimoole, S.; Narayanan, H. R.; Rege, A.; Naniwadekar, R.

10.1101/2025.11.11.686480 — ecology — Posted on 2025-11-12

3215 Pathogenic Keratinocyte States and Fibroblast Niches Define the Tissue Microenvironment in Severe Hidradenitis Suppurativa

Du-Harpur, X.; Ganier, C.; Mazin, P.; Cheshire, C.; Rashidghamat, E.; Luscombe, N. M.; Lynch, M. D.; Watt, F. M.

10.1101/2025.11.11.682326 — cell biology — Posted on 2025-11-12

3216 Endoplasmic reticulum-mitochondrion disconnection promotesmetabolic reprogramming and cystogenesis in polycystic kidneydisease

Padhy, B.; Xie, J.; Idrees, D.; Cheng, C.-J.; Huang, C.-L.

10.1101/2025.10.31.685870 — molecular biology — Posted on 2025-11-12

3217 Assessing the molecular and phenotypic contribution of a horizontally acquired region to yeast adaptation

Romero, A.; Bastias, C.; De Chiara, M.; Saayman, X.; Cherkaoui, H.; Barre, B. P.; Cubillos, F. A.; Martinez, C.; Kessi-Perez, E. I.; Liti, G.; Salinas, F.

10.1101/2025.11.11.687820 — molecular biology — Posted on 2025-11-12

3218 Autonomic reflex plasticity associates with time-dependent SUDEP susceptibility in a murine model with hyperactive stress circuits

Saunders, S. E.; Dow, K. E.; Bostic, G. E.; Boychuk, J. A.; Maguire, J. L.; Boychuk, C. R.

10.1101/2025.11.11.687816 — neuroscience — Posted on 2025-11-12

3219 Self-compassion is linked to positive affect and buffers declines in self-esteem in low performers

Weis, J. F.; Krach, S.; Paulus, F. M.; Stolz, D. S.

10.1101/2025.11.11.687618 — neuroscience — Posted on 2025-11-12

3220 Thalamofrontal synaptic weakening underlies short-term memory deficits from adolescent NMDAR hypofunction

Yu, J.; Choi, I. S.; Kim, G. H.; Bahn, S.; Bae, S.; Lee, T.; Choi, J. H.; Kwon, J. S.; Kim, M.; Lee, K. J.; Rah, J.-C.

10.1101/2025.11.11.687794 — neuroscience — Posted on 2025-11-12

3221 Response dynamics in macaque ventral stream recapitulate the visual hierarchy

Xiao, W.; Vinken, K.; Livingstone, M. S.

10.1101/2025.11.11.686115 — neuroscience — Posted on 2025-11-12

3222 The School Cafeteria Problem: Disrupted Visuospatial Attention During Multisensory Speech-in-Noise Perception in Children with ADHD

Dinesha, N. J.; Mehta, S.; Brown, Z.; Richardson, A. A.; Rivera, R. A.; Layton, C.; Foxe, J. J.; Knight, E. J.

10.1101/2025.11.11.687600 — neuroscience — Posted on 2025-11-12

3223 Defining the Growth Stages of Mungbean (Vigna radiata L.) using the BBCH Scale

Boddepalli, V. N.; Singh, A.

10.1101/2025.11.09.687504 — plant biology — Posted on 2025-11-12

3224 Employing RNA editing to engineer personalized tumor-specific neoantigens (editopes)

Pecori, R.; Casati, B.; Merdler-Rabinowicz, R.; Landesman, N.; Sanghvi, K.; Zens, S.; Kipfstuhl, K.; Pinamonti, V.; Arnold, A.; Lindner, J. M.; Platten, M.; Offringa, R.; Carretero, R.; Ruppin, E.; Levanon, E. Y.; Papavasiliou, F. N.

10.1101/2023.03.16.532918 — cancer biology — Posted on 2025-11-12

3225 Metabolic zonation and characterization of tissue slices with spatial transcriptomics

Etxezarreta Arrastoa, O.; Pirona, A.-C.; Wagner, A.; Yosef, N.

10.1101/2025.11.11.687271 — bioinformatics — Posted on 2025-11-12

3226 Putative azithromycin-resistance mutations in Chlamydia trachomatis are globally distributed but arose before azithromycin was discovered

Sharma, P.; Dean, D.; Read, T. D.

10.1101/2025.11.10.687758 — genomics — Posted on 2025-11-12

3227 Machine Learning Identifies Common Risk Variants and Implicates Abnormal Vision Physiology in ASD

Rabner, A.; Avrahami, A.; Meidan, A.; Vorobyov, I.; Mandel- Gutfreund, Y.; Horev, G.

10.1101/2025.11.11.687806 — genetics — Posted on 2025-11-12

3228 A critical look at directional random walk modeling of sparse fossil data

Ergon, R.

10.1101/2025.11.11.687792 — evolutionary biology — Posted on 2025-11-12

3229 Oligodendroglia as functional effectors of Multiple Sclerosis risk variants

Carlstrom, K.; Agirre, E.; Sun, T.; Dumral, O.; Kabbe, M.; Mahmud, N.; Kit Lor, Y.; Pahlevan Kakhki, M.; Khademi, M.; Jagodic, M.; Goldman, S. A.; Castelo-Branco, G.

10.1101/2025.11.11.687640 — cell biology — Posted on 2025-11-12

3230 Dynamical memory underlies prolonged plasmid persistence after transient antibiotic treatment

Zhou, Z.; Weiss, A.; Yao, Z.; Chen, X.; Lok, K.; Son, H.-i.; You, L.

10.1101/2025.10.31.685803 — microbiology — Posted on 2025-11-12

3231 Unraveling IGK Locus in Dog Breeds: IMGT(R) New Insights into Canine Immunogenetics.

Kustro Garnica, T.; Papadaki, A.; Georga, M.; Zeitoun, G.; Jabado-Michaloud, J.; Folch, G.; Giudicelli, V.; Gonzales, P.; Chagas Lesbon, J. C.; Alves, T. G. L.; Fukumasu, H.; Kossida, S.

10.1101/2025.11.10.687733 — immunology — Posted on 2025-11-12

3232 An AI-driven approach for nanobody affinity maturation

Yang, X.; Guo, Z.; Zhao, Q.

10.1101/2025.11.11.687768 — immunology — Posted on 2025-11-12

3233 Natural killers in pregnancy: servants of two masters

Krechetov, S. P.; Khoroshkeeva, O. V.; Jankevic, T. E.; Borovikov, P. I.; Shirokov, Y. V.; Krechetova, L. V.; Tetruashvili, N. K.; Trofimov, D. Y.; Sukhikh, G. T.

10.1101/2025.11.11.685990 — immunology — Posted on 2025-11-12

3234 Autonomic Indicators of Self-Transcendence: Insights from the Numadelic VR Paradigm

Bonnelle, V.; Parola, G.; Andreu, C.; Hardy, J. L.; Timmermann, C.; Cebolla, A.; Wrzesien, M.; Glowacki, D. R.

10.1101/2025.11.11.686736 — neuroscience — Posted on 2025-11-12

3235 Sex-dependent hypothalamic microinflammation and microglial polarization: The role of JNK in high-fat diet-induced insulin resistance

Rodriguez-Garcia, M.; Bolanos-Hurtado, M.; Redondo, A.; Caelles, C.; Gonzalez, M.; Sanz, E.; Quintana, A.; Zagmutt, S.; Rodriguez-Rodriguez, R.

10.1101/2025.11.11.687241 — neuroscience — Posted on 2025-11-12

3236 What is happening in Dorsal Root Ganglia? A computational analysis of cross-excitation phenomenon

Perevozniuk, D.; Gorskii, O.; Musienko, P.; Koshev, N.

10.1101/2025.11.11.687782 — neuroscience — Posted on 2025-11-12

3237 Unveiling early visual cortical mechanisms in perceptual filling-in: a parametric study of eccentricity and movement dependence

Koiso, K.; Razafindrahaba, A.; van de Ven, V.; De Martino, F.; Roberts, M. J.; De Weerd, P.

10.1101/2025.11.11.687787 — neuroscience — Posted on 2025-11-12

3238 Spatial Attention and Session Day Independently Modulate Human Visual Cortical Plasticity

Limon, P. N.; Norcia, A. M.; Ash, R. T.

10.1101/2025.10.31.685945 — neuroscience — Posted on 2025-11-12

3239 Mirror effect of genomic deletions and duplications on cognitive ability across the human cerebral cortex

Kumar, K.; Kazem, S.; Huguet, G.; Engchuan, W.; Kopal, J.; Renne, T.; Shanta, O.; Thiruvahindrapuram, B.; MacDonald, J. R.; Mollon, J.; Schultz, L. M.; Knowles, E. E. M.; Porteous, D.; Davies, G.; Redmond, P.; Harris, S. E.; Cox, S. R.; Schumann, G.; Pausova, Z.; Greenwood, C. M. T.; Paus, T.; Scherer, S. W.; Almasy, L.; Sebat, J.; Glahn, D.; Dumas, G.; Jacquemont, S.

10.1101/2025.01.06.631492 — neuroscience — Posted on 2025-11-12

3240 JPT2/HN1L functions as an NAADP-binding protein in a cell type-specific manner

Ottenheijm, R.; Winterberg, K.; Throm, V.; Bukva, M.; Tsvilovskyy, V.; Medert, R.; Guse, A.; Freichel, M.

10.1101/2025.11.11.687795 — pharmacology and toxicology — Posted on 2025-11-12

3241 Comparative analysis of morphological and acoustic correlates of bush-cricket tympanic membranes

Islam, M. N.; Holmes, L. B.; Rooke, D.; Sarria-S, F. A.; Montealegre-Z, F.

10.1101/2025.11.11.687687 — biophysics — Posted on 2025-11-12

3242 Improved marker detection for rare population in single-cell transcriptomics through text mining-inspired scoring approach

Chen, J.; Li, M.; Bhuva, D. D.; Davis, M. J.; Papenfuss, A. T.; Tan, C. W.

10.1101/2025.11.10.687759 — bioinformatics — Posted on 2025-11-12

3243 Discovery of Inverted Repeats and Palindromes in Viral Genomes

Sen, M.; Rivera, G. M.; Gao, J.; Shtrahman, M.; Ganapathiraju, M.

10.1101/2025.11.10.687097 — bioinformatics — Posted on 2025-11-12

3244 Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT

Yuan, C.; Patel, K.; Shi, H.; Wang, H.-L.; Wang, F.; Li, R.; Li, Y.; Corces, V.; Shi, H.; Das, S.; Yu, J.; Jin, P.; Yao, B.; Hu, J.

10.1101/2025.03.27.645744 — bioinformatics — Posted on 2025-11-12

3245 Predicting Toxicity and Bioactivity of the Chemical Exposome: A Case Study for the Blood Exposome Database

Dutta, A.; Barupal, D.

10.1101/2025.11.10.687755 — bioinformatics — Posted on 2025-11-12

3246 CryoSiam: self-supervised representation learning for automated analysis of cryo-electron tomograms

Stojanovska, F.; Sanchez, R. M.; Jensen, R. K.; Mahamid, J.; Kreshuk, A.; Zaugg, J. B.

10.1101/2025.11.11.687379 — bioinformatics — Posted on 2025-11-12

3247 Advancing DIA-based Limited Proteolysis Workflows: introducing DIA-LiPA

Van Leene, C.; Araftpoor, E.; Staes, A.; Argentini, A.; Bühler, M.; Gevaert, K.

10.1101/2025.11.11.687786 — bioinformatics — Posted on 2025-11-12

3248 Paracrine Factor Local Gradient-Generating System for Engineering Perfusable Vascularized Hepatocyte Tissues with Perfusion-Induced Proliferation

Huang, Y.-H.; Yamashita, T.; Sudo, R.

10.1101/2025.11.10.687539 — bioengineering — Posted on 2025-11-12

3249 Strong STMP-Crosslinked Lignin/Chitosan Hydrogel Films with Enhanced Aqueous Stability and Bioactivity for Active Food Packaging

Garg, S.; Althuri, A.

10.1101/2025.11.11.687780 — bioengineering — Posted on 2025-11-12

3250 A Single-Aliquot, Enrichment-Free Workflow for High-Throughput Plasma Proteome and N-Glycoproteome Profiling

10.1101/2025.11.11.687106 — biochemistry — Posted on 2025-11-12

3251 Dissecting the Cellular Genetics of Cardiovascular Disease Through Endothelial and Immune Compartments Profiling

10.1101/2025.11.10.687750 — genomics — Posted on 2025-11-12

3252 Structural and Functional Insights into HBx-Smc6 Targeting for HBV Inhibition

Cheng, T.; Zhou, J.; Huang, W.; Du, L.; He, P.; Yang, R.; Gao, Y.; Hao, M.; Hu, K.; Chen, J.; Wang, H.; Rao, Z.; Yuan, Z.; Wang, L.

10.1101/2025.11.11.685253 — cell biology — Posted on 2025-11-12

3253 GluTrooper: a novel reporter mouse line for whole-brain imaging of glutamate dynamics

Calandra, G. M.; Varga, D. P.; Feyen, P. L. C.; Gubinelli, F.; Wefers, B.; Makra, P.; Shrouder, J. J.; Cattaneo, A.; Gökce, S.; Wurst, W.; Liesz, A.; Herms, J.; Burbulla, L.; Filser, S.; Plesnila, N.

10.1101/2025.11.11.686940 — neuroscience — Posted on 2025-11-12

3254 Excessive activation of the RAS/MAPK pathway triggers adult-onset motor axonal degeneration

Been, M.; Lambert, E.; Serna, A.; Balvert, A. C.; Heisinger, S.; Kreshpani, M.; te Dorsthorst-Maas, C.; Paskeviciute, P.; Rodriguez Arias, H.; Beijer, D.; Astuti, G.; Kenna, K. P.; van Reijmersdal, B.; Gloudemans, S.; van Lith, P.; Sijlmans, C.; Verstreken, P.; Veldink, J.; Zuchner, S.; Gilissen, C.; Schenck, A.; Storkebaum, E.

10.1101/2025.11.11.687669 — neuroscience — Posted on 2025-11-12

3255 Graded regulation of microtubule-binding of Tau by the phosphorylation state of the proline-rich region in living neurons

Nakata, R.; Torii, T.; Miyasaka, T.; Misonou, H.

10.1101/2025.11.11.687775 — neuroscience — Posted on 2025-11-12

3256 Do twitching and twitch-spindle coupling differ between N2 and N3 sleep in 6-month-olds?

Christiansen, T. G.; Sokoloff, G.; Long, H. C.; Kopp, O. K.; Karr, L. K.; Blumberg, M. S.

10.1101/2025.07.23.666445 — neuroscience — Posted on 2025-11-12

3257 AutoMorphoTrack: A modular framework for quantitative analysis of organelle morphology, motility, and interactions at single-cell resolution

Bayati, A.; Schumacher, J. G.; Chen, X.

10.1101/2025.07.19.665650 — neuroscience — Posted on 2025-11-12

3258 Thermotolerant pollen tube growth is controlled by RALF signaling.

Althiab Almasaud, R.; Ouonkap Yimga, S. V.; Ingram, J.; Oseguera, Y.; Alkassem Alosman, M.; Travis, C.; Henry, A.; Medina, M.; Oulhen, N.; Wessel, G. M.; Delong, A.; Pease, J.; DaSilva, N.; Johnson, M.

10.1101/2025.10.25.684177 — plant biology — Posted on 2025-11-12

3259 Post-Inhibitory Rebound by δ-Cells Transforms Inhibition into Excitationand Redefines Islet Plasticity.

Tamayo, A. M.; Hakim-Rodriguez, D.; Pereira, E.; Camacho, S.; Mateus Goncalves, L.; Alcazar, O.; Rodriguez-Diaz, R.

10.1101/2025.11.10.687745 — physiology — Posted on 2025-11-12

3260 Menin inhibition impairs metastatic colonization of Ewing sarcoma

Braun, K. A.; Garcia, N. M.; Ahmed, M.; Tu, D. S.; Walter, S. I.; Wrenn, E. D.; Dean, M. E. B.; Lawlor, E. R.

10.1101/2025.11.10.687648 — cancer biology — Posted on 2025-11-12

3261 Cardiac myofibril networks induce shear stress

Murray, L.; Quinn, A.; Pinali, C.; Collins, D.; Rajagopal, V.

10.1101/2025.11.10.687713 — biophysics — Posted on 2025-11-12

3262 Single-cell Transcriptomic Profiling of Pancreatic Ductal Adenocarcinoma: Epithelial Reprogramming and Systemic Immune Exhaustion

Xu, Q.

10.1101/2025.11.10.687730 — bioinformatics — Posted on 2025-11-12

3263 Learning the Unseen: Data-Augmented Deep Learning for PTM Discovery with Prosit-PTM

Gabriel, W.; Zolg, D. P.; Giurcoiu, V.; Shouman, O.; Prokofeva, P.; Seefried, F.; Bayer, F. P.; Lautenbacher, L.; Soleymaniniya, A.; Schnatbaum, K.; Zerweck, J.; Knaute, T.; Delanghe, B.; Huhmer, A.; Wenschuh, H.; Reimer, U.; Medard, G.; Kuster, B.; Wilhelm, M.

10.1101/2025.11.07.687302 — bioinformatics — Posted on 2025-11-12

3264 GeneCAD: Plant Genome Annotation with a DNA Foundation Model

Liu, Z.-Y.; Berthel, A.; Czech, E.; Stitzer, M. C.; Hsu, S.-K.; Pennell, M.; Buckler, E. S.; Zhai, J.

10.1101/2025.10.31.685877 — bioinformatics — Posted on 2025-11-12

3265 Optimizing Bispecific Antibody Expression via Multi-Omics Analysis and Vector Redesign

Gam, J. J.; Chang, M. M.; Zheng, D.; Stevens, J.; Nielsen, A. A. K.; Smith, K. D.

10.1101/2025.11.10.687454 — bioengineering — Posted on 2025-11-12

3266 An epigenomic investigation of atrial fibrillation in a matched left and right atrial human cohort

Rodriguez-Gonzalez, A.; Frost, S.; Thomas, A. M.; Fernandez-Aroca, D. M.; Choudhury, J.; Tikkas, G.; Tinker, A. M.; Munroe, P. B.; Bell, C. G.; Villar, D.

10.1101/2025.08.29.673028 — genomics — Posted on 2025-11-12

3267 Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCF

Henikoff, S.; Henikoff, J. G.

10.1101/2025.11.10.687711 — genomics — Posted on 2025-11-12

3268 Phenotypic dominance emerges from activity-fitness functions and molecular interactions

Pal, T.; Dibyachintan, S.; Cisneros, A. F.; Landry, C.

10.1101/2025.03.21.644634 — genetics — Posted on 2025-11-12

3269 Data-driven symbolic regression reveals microbial growth laws

Sun, T. A.; Kiciatovas, D.; Aapalampi, I.-K.; Kuosmanen, T.; Hiltunen, T.; Mustonen, V.

10.1101/2025.06.02.657040 — ecology — Posted on 2025-11-12

3270 Seagrass Extent Expansion in the Gulf of Mexico and Northwestern Caribbean (1987-2021)

Lizcano-Sandoval, L.; Bell, S.; Cerdeira-Estrada, S.; Martinez-Daranas, B.; Montes, E.; van Tussenbroek, B.; Muller-Karger, F.

10.1101/2025.11.10.687714 — ecology — Posted on 2025-11-12

3271 Lactate dehydrogenase-induced DNA Topoisomerase 1 is a novel regulator of smooth muscle cell proliferation and remodeling in pulmonary arterial hypertension

Jiang, L.; Zhyvylo, I.; Goncharov, D.; Dey, T.; Kelly, N.; Teos, L.; Franzi, L.; Saiyed, A.; Kenyon, N. J.; Greenland, J. R.; Wolters, P. J.; Chen, S. Y.; Delisser, H.; Kudryashova, T. V.; Goncharova, E. A.

10.1101/2025.11.10.687749 — cell biology — Posted on 2025-11-12

3272 A Two-Component Regulatory System Mediates Quorum Sensing-Dependent Morphology and Motility Transitions in the Archaeon Haloferax volcanii

Cote, J.; Chatterjee, P.; Garcia, M.; Tao, R.; Mathijssen, A. J.; Pohlschroder, M.

10.1101/2025.11.10.687552 — microbiology — Posted on 2025-11-12

3273 Isolation of functional supramolecular attack particles (SMAPs)

Jainarayanan, A. K.; Chandrasekar, V.; Almeida, V. P.; Widdess, M. A.; Staton, C. C.; Bernand, A.; Pfannenstill, V.; Flannery, S.; Watson, H.; Wicki, A.; Onupom, O.; Elanchezhian, M.; Capera, J.; Chen, L.; Valvo, S.; Anand, N. M.; Mahla, R. S.; Kurz, E.; Franchet, C.; Dalenc, F.; Ysebaert, L.; Michelet, A.; Gupta, D.; Naismith, J. H.; Dustin, L. B.; Fritzsche, M.; Fischer, R.; Valitutti, S.; Leung, C. S.; Wood, M. J. A.; Dustin, M. L.

10.1101/2025.11.10.687675 — immunology — Posted on 2025-11-12

3274 Sensory neuronal mTORC1 signaling establishes neuroimmune memory that initiates allergic immunity

Zhu, X.; Yang, H.; Zhan, H.; Kernin, I. J.; Le, N.; Buttaci, D. R.; Han, C.; Naik, P.; Altenburger, L.; Wu, E.; Matatia, P. R.; Zaghouani, S.; Smith, N. P.; Londoner, R.; Flayer, C.; Sun, Z.; Villani, A.-C.; Rahimi, R. A.; Sokol, C. L.

10.1101/2025.11.10.687723 — immunology — Posted on 2025-11-12

3275 Multi-omics identification of activated T cells and spatial PD-1/PD-L1 signaling as biomarkers of diabetic foot ulcer healing

Bilik, S. M.; Dodson, C.; Rivas, K.; Balukoff, N.; Burgess, J. L.; Griswold, A. J.; Sawaya, A.; Pastar, I.; Strbo, N.; Morasso, M. I.; Tomic-Canic, M.; Stone, R. C.

10.1101/2025.11.10.687697 — immunology — Posted on 2025-11-12

3276 Eye-hand coordination beyond vision: preceding gaze history shapes reaching memories

Abekawa, N.; Gomi, H.

10.1101/2025.11.11.687771 — neuroscience — Posted on 2025-11-12

3277 Locally balanced inhibition allows for robust learning of input-output associations in feedforward networks with Hebbian plasticity

Cecchini, G.; Roxin, A.

10.1101/2025.11.11.687798 — neuroscience — Posted on 2025-11-12

3278 Minute- and second-scale hippocampal network dysfunctions in the 3xTgAD mouse model of Alzheimer's disease are prevented by TSPO knockout

Vidal, B.; Badina, A. M.; Dorogan, V.; Schirmbeck, G.; Sanches, E. F.; Ceyzeriat, K.; Knoop, M.; Abjean, L.; Tsartsalis, S.; Sizonenko, S.; Baud, O.; Millet, P.; Zerbi, V.; Tournier, B. B.

10.1101/2025.11.11.687784 — neuroscience — Posted on 2025-11-12

3279 Continuous theta-burst stimulation of the ventromedial prefrontal cortex reduces Pavlovian go-invigoration and enhances thalamo-striatal reward prediction error signals

Aster, H.-C.; Schmitt, J.; Herrmann, M.; Zeller, D.; Homola, G. A.; Kampf, T.; Pham, M.; Walther, S.; Romanos, M.; Scholz, V.; Deserno, L. J.

10.1101/2025.11.11.686520 — neuroscience — Posted on 2025-11-12

3280 Sample size critically shapes the reliability of EEG case-control findings in psychiatry

Ebadi, A.; Kaderi, S.; Rodriguez-Herreros, B.; Chabane, N.; Allouch, S.; Hassan, M.

10.1101/2025.11.10.687610 — neuroscience — Posted on 2025-11-12

3281 Neural dynamics of covert habit activation and control in humans

Buabang, E. K.; Suddell, S.; Grogan, J. P.; Cox, A.; St. Martin, N.; Donegan, K. R.; Rafei, P.; O'Connell, R. G.; Gillan, C. M.

10.1101/2025.11.12.687990 — neuroscience — Posted on 2025-11-12

3282 Fast-conducting mechanonociceptors uniquely engage reflexive and affective pain circuitry to drive protective responses

10.1101/2025.11.11.687663 — neuroscience — Posted on 2025-11-12

3283 Sex-specific trajectories of gait adaptation following partial dopaminergic lesions in a rat model of parkinsons disease

Lievano Parra, D.; Garavito Coronado, J. D.; Jensen, G.; Gonzalez Diaz, V.; Cardenas Parra, F.

10.1101/2025.11.10.687728 — neuroscience — Posted on 2025-11-12

3284 A deep convolutional neural network trained for lightness constancy is susceptible to lightness illusions

Patel, J.; Flachot, A.; Vazquez-Corral, J.; Brainard, D. H.; Wallis, T. S. A.; Brubaker, M. A.; Murray, R. F.

10.1101/2025.11.10.687742 — neuroscience — Posted on 2025-11-12

3285 Brain bases for navigating acoustic features

Billig, A. J.; Sedley, W.; Gander, P. E.; Kumar, S.; Lad, M. J.; Chait, M.; Mohammadi, Y.; Berger, J. I.; Griffiths, T.

10.1101/2025.02.10.636597 — neuroscience — Posted on 2025-11-12

3286 Genetic rescue of pathogenic O-GlcNAc dyshomeostasis associated with microcephaly and motor deficits

Authier, F.; Esperon-Abril, I.; Coquelin, K.-S.; Stald Skoven, C.; Fristed Eskildsen, S.; Ondruskova, N.; Ferenbach, A. T.; Thomsen, J. S.; Hansen, B.; van Aalten, D.

10.1101/2025.11.12.687959 — neuroscience — Posted on 2025-11-12

3287 Unilateral striatal deep brain stimulation improves cognitive control

Sachse, E. M.; Dastin-van Rijn, E. M.; Bennek, J. P.; Buccini, M. C.; Mensinger, M. E.; Iacobucci, F. A.; Reimer, A. E.; Widge, A. S.

10.1101/2025.11.10.686309 — neuroscience — Posted on 2025-11-12

3288 An Open, Fully-processed, Longitudinal Data Resource to Study Brain Development and Transdiagnostic Executive Function

Sevchik, B. L.; Shafiei, G.; Murtha, K.; Linguiti, S.; Brodrick, L.; Brook, J. B. H.; Cieslak, M.; Flook, E.; Mehta, K.; Meisler, S. L.; Ruparel, K.; Rush, S.; Salo, T.; Singleton, S. P.; Tong, T. T.; Salunke, M.; Bassett, D. S.; Calkins, M. E.; Elliott, M. A.; Gur, R. E.; Gur, R. C.; Moore, T. M.; Scott, J. C.; Shinohara, R. T.; Tisdall, M. D.; Wolf, D. H.; Roalf, D. R.; Satterthwaite, T. D.

10.1101/2025.11.10.687633 — neuroscience — Posted on 2025-11-12

3289 Brainstem enkephalinergic neural circuit underlying cold-induced pain relief in mice

Kim, H.; Lee, Y.; oh, S. B.

10.1101/2025.11.10.686886 — neuroscience — Posted on 2025-11-12

3290 Differential controls of forelimb versus whole-body movements by striatum

Cao, J.; Zhao, Y.; Yu, J.

10.1101/2025.11.10.687756 — neuroscience — Posted on 2025-11-12

3291 Metabarcoding and microtomography reveal new insights into the dietary niche of near-extinct amphibians

Plewnia, A.; Boistel, R.; Heine, C.; Hildwein, T.; Quezada-Riera, A. B.; Teran-Valdez, A.; Reyes-Puig, J. P.; Loetters, S.

10.1101/2025.11.10.687692 — zoology — Posted on 2025-11-12

3292 Single-Islet Proteomics Maps Pseudo-Temporal Islet Immune Responses and Dysfunction in Stage 1 Type 1 Diabetes

Kelly, S.; Sarkar, S.; Williams, S. M.; Fu, A. D.; Butterworth, E. A.; Sagendorf, T. J.; Nierves, L.; Kwon, Y.; Li, X.; Petyuk, V. A.; Chen, J.; Nakayasu, E. S.; Atkinson, M. A.; Kulkarni, R. N.; Mathews, C. E.; Zhu, Y.; Campbell-Thompson, M.; QIAN, W.-J.

10.1101/2025.11.10.687674 — systems biology — Posted on 2025-11-12

3293 Software System Design to Support Scale in Mammalian Cell Line Engineering.

McClymont, D. W.; McIlwraith, B.; Green, A.; Coulson, S.; Scott, E.

10.1101/2025.09.01.673445 — synthetic biology — Posted on 2025-11-12

3294 Postoperative Automated Platelet Count and Its Predictive Factors in Dogs Undergoing Mitral Valve Repair

Kurogochi, K.; Furusato, S.; Nii, Y.; Chen, A.; Ueda, Y.; Mizuno, M.; Uechi, M.

10.1101/2025.11.10.687737 — physiology — Posted on 2025-11-12

3295 Developmental exposure to a PFAS mixture impairs the anamnestic response to influenza A virus infection in mice

Post, C. M.; Agyemang, J. J.; McDonald, K. A.; McDonough, C. A.; Lawrence, B. P.

10.1101/2025.11.10.687657 — pharmacology and toxicology — Posted on 2025-11-12

3296 Fosl2 regulates the transition from parietal epithelial cells to myofibroblasts in the kidney

Bronstein, R.; Estrada, C. C.; Revelo, M. P.; Sheikh, F.; Haley, J. D.; D'Agati, V.; Salant, D. J.; He, J. C.; Guo, Y.; Mallipattu, S. K.

10.1101/2025.11.10.687667 — pathology — Posted on 2025-11-12

3297 New data on Quaternary lagomorphs from Lagoa Santa, State Of Minas Gerais, Brazil

Ramos, V. A. d. C.; Chahud, A.

10.1101/2025.11.10.687685 — paleontology — Posted on 2025-11-12

3298 Decoding the Circulating Proteome: Matrix and Immune Context Markers Shape Early Multi-Cancer Detection

Singh, V.; Kushwaha, R.

10.1101/2025.11.10.687473 — cancer biology — Posted on 2025-11-12

3299 eIF2B Selectively Anchors and Activates Mutant KRAS

Kim, H.; Diao, S.; Cho, K.-J.; Lee, H.-R.; Liu, J.; Egea, P.; Pantsar, T.; Kurki, M.; Ghaddar, N.; Wang, S.; Zou, J. Y.; Amiri, M.; Gannaban, R.; Hancock, J. F.; Rice, K. M.; Deng, Q.; Sasaki, A.; Asara, J. M.; Tripathi, B.; Lowy, D.; Lawrence, R.; Hatzoglou, M.; Azpilcueta-Nicolas, C. R.; Lumb, J.-P.; Columbus, J.; Turbyville, T. J.; Marshall, C. B.; Ikura, M.; Groves, J. T.; Sonenberg, N.; Walter, P.; Koromilas, A. E.

10.1101/2025.11.10.686860 — cancer biology — Posted on 2025-11-12

3300 Systems analysis uncovers early temozolomide responses and peptide antigens in glioblastoma

Choe, E. Y.; Leddy, O.; Riviere-Cazaux, C.; Burgenske, D. M.; Hu, Z.; Mladek, A. C.; Hu, S.; Fedeles, B. I.; Essigmann, J. M.; Prins, R. M.; Sarkaria, J. N.; Burns, T. C.; Vaubel, R. A.; White, F. M.

10.1101/2025.11.10.687735 — cancer biology — Posted on 2025-11-12

3301 NEUROG3 Is Sufficient to Drive Neuroendocrine Differentiation in Prostate Cancer Cells.

Daoud, A.; Han, L.; Christensen, R. K.; Munera, J. O.

10.1101/2025.11.10.687642 — cancer biology — Posted on 2025-11-12

3302 Automation of high-throughput workflow for arrayed CRISPR activation library screening

Yang, C.-C.; Deshpande, A. J.; Jackson, M.; Adams, P. D.; Pasquale, E. B.; Murad, R.; Yin, J.-A.; Wu, Y.; Beketova, A.; Huang, C.-T.

10.1101/2025.11.10.687722 — cancer biology — Posted on 2025-11-12

3303 Cross-Species Transcriptomic Integration Reveals a Conserved, MIRO1-Mediated Macrophage-to-T Cell Signaling Axis Driving Immunosuppression in Glioma

Du, Z.; Li, M.; Bergsneider, B. H.; Tsai, A. P.; Cho, K. B.; Kim, L. H.; Choi, J.; Li, G.; Wyss-Coray, T.; Lim, M.; Wang, X.

10.1101/2025.11.10.686781 — cancer biology — Posted on 2025-11-12

3304 DEER of Singly Labelled Proteins to Evaluate Supramolecular Packing of Amyloid Fibrils

Tsay, K.; Equbal, A.; Li, Y.; Tsui, T.; Han, S.; Fichou, Y.

10.1101/2025.11.10.687719 — biophysics — Posted on 2025-11-12

3305 Uncovering the flexibility of CDR loops in antibodies and TCRs through large-scale molecular dynamics

Cagiada, M.; Spoendlin, F. C.; Ifashe, K.; Deane, C. M.

10.1101/2025.11.10.687725 — biophysics — Posted on 2025-11-12

3306 Proteome-wide in silico screening for human protein-protein interactions

Schmid, E.; Zhu, H.; Ryu, E.; Lim, Y.; Smogorzewska, A.; Brown, A.; Walter, J.

10.1101/2025.11.10.687652 — bioinformatics — Posted on 2025-11-12

3307 Deep Learning links TP53 genotype to expression-defined transcriptional program in Acute Myeloid Leukemia

Tsesmelis, M.; Andersson, R.; Perez, A. F.; Vazquez, S. M.; Carolina Florian, M.; Mulaw, M. A.

10.1101/2025.11.10.687690 — bioinformatics — Posted on 2025-11-12

3308 MethylSeqR: An R package for efficient analysis of modified nucleotide data

Zimmerman, H. E.; Stirland, I.; Miller, R. H.; Jenkins, A.; Saito, E.; Jenkins, T.; Hill, J. T.

10.1101/2025.11.10.687705 — bioinformatics — Posted on 2025-11-12

3309 Robust design and validation of LAMP assays for in-field detection of three major bacterial vascular diseases of banana

ROBENE, I.; Arrieta-Salgado, M.; Rozsasi, S.; Mostert, D.; Maillot-Lebon, V.; Chilin-Charles, Y.; Jansen van Vuuren, J.; Nakato, G. V.; Kanaabi, R.; Magdama, F.; Paredes Salgado, E.; Hermanto, C.; Sutanto, A.; Conie, J.; Henry, D.; Le Roux, S.; Viljoen, A.; Jouen, E.; Poussier, S.; Wicker, E.; Pecrix, Y.

10.1101/2025.11.10.687727 — molecular biology — Posted on 2025-11-12

3310 Wake consolidates event memory, sleep binds it with context

Miao, X.; Dahmen, J.; Thoma, A. S.; Weber, A.-L.; Waszak, F.; Born, J.; Rauss, K.

10.1101/2025.11.12.687983 — neuroscience — Posted on 2025-11-12

3311 Cortex-Wide Substrates for Body Schema and Action Awareness

Severson, K. S.; Lu, J.; Xiao, W.; Jiang, H.; Lou, T.; Caplan, K. A.; Levy, M. S.; Li, T.; Dunn, T. W.; Wang, F.

10.1101/2025.09.23.678085 — neuroscience — Posted on 2025-11-12

3312 Reversible synaptic deficits in early-stage Batten disease

Wani, M. A.; Hall, C. M.; Mittmann, T.; Grünewald, B.; von Engelhardt, J.

10.1101/2025.11.12.687979 — neuroscience — Posted on 2025-11-12

3313 Protectin DX resolves fracture-induced postoperative pain in mice via neuronal signaling and GPR37-activated macrophage efferocytosis

Li, Y.; Bang, S.; Ji, J.; Xu, J.; Lee, M.; Chandra, S.; Serhan, C. N.; Ji, R.-R.

10.1101/2025.11.10.687700 — neuroscience — Posted on 2025-11-12

3314 PIAS1/PIAS4-Mediated SUMOylation of TDP-43 is Induced by Oxidative Stress

Pendlebury, D.; Truong, K.; Heath, M.; Reidling, J. C.; Sarkar, P.; Thompson, L. M.

10.1101/2025.11.10.687649 — neuroscience — Posted on 2025-11-12

3315 A Compound Enhancing Lysosomal Function Reduces Tau Pathology, Microglial Reactivity and Rescues Working Memory in 3xTg AD Mice

Mayeri, Z.; Woods, G.; Rane, A.; Kifle, A.; Chamoli, M.; Shukla, S.; Walton, C. C.; Andersen, J. K.

10.1101/2025.11.09.687389 — neuroscience — Posted on 2025-11-12

3316 Targeting the IRE1α/XBP1 Signaling Axis Suppresses Rhabdomyosarcoma Growth and Promotes Myogenic Differentiation

Vuong, A. T.; Joshi, A. S.; Ho, P. T.; Tomaz da Silva, M.; Guo, B.; Trivedi, M. V.; Kumar, A.

10.1101/2025.11.10.687677 — cancer biology — Posted on 2025-11-12

3317 BarlowTrack: A Self-Supervised Framework for Zero-Shot Multi-Object Cell Tracking

Fieseler, C.; Lev, I.; Madhusudhanan, J.; Zhai, Z.; Schwartz, S.; Zimmer, M.

10.1101/2025.11.10.687595 — bioinformatics — Posted on 2025-11-12

3318 Upwelling periodically disturbs the ecological assembly of microbial communities in Lake Ontario

Pendleton, A.; Wells, M. G.; Schmidt, M. L.

10.1101/2025.01.17.633667 — ecology — Posted on 2025-11-12

3319 Keratin 16 spatially inhibits type I interferon responses in stressed and diseased skin

Cohen, E.; Xu, Y.; Ghodke, S.; Orosco, A.; Wang, D.; Johnson, C. N.; Steen, K.; Sarkar, M. K.; Ozlu, N.; Tsoi, L. C.; Gudsonsson, J. E.; Marchal, L.; Hovnanian, A.; Parent, C.; Coulombe, P. A.

10.1101/2024.12.27.630544 — immunology — Posted on 2025-11-12

3320 Low-Dimensional and Optimised Representations of High-Level Information in the Expert Brain

Costantino, A. I.; Platonov, A.; Fontana Vieira, F.; Van Hove, E.; Bilalic, M.; Op de Beeck, H.

10.1101/2025.11.12.688012 — neuroscience — Posted on 2025-11-12

3321 The Primate Hippocampus Constructs a Temporal Scaffold Anchored to Behavioral Events

Rueckemann, J. W.; Browning, Y.; Mallory, A. J.; Kim, B.; Fairhall, A. L.; Buffalo, E. A.

10.1101/2025.11.12.687961 — neuroscience — Posted on 2025-11-12

3322 Systematic structural and functional analysis of metal-binding sites in native proteomes

Quast, J.-P.; Pagotto, A.; Separovich, R. J.; Duenebacke, M.; Gillet, L.; Luo, X.; Zueger, E.; Magnusson, G.; Correia, M. S. P.; Ciofalo, C.; Andreini, C.; Rosato, A.; Beltrao, P.; Zamboni, N.; de Souza, N.; Picotti, P.

10.1101/2025.11.10.687516 — systems biology — Posted on 2025-11-12

3323 Shared genetic basis for brain structure, insulin resistance and inflammation in schizophrenia: a colocalization study

Couch, A. C. M.; Perry, B. I.; Rosoff, D.; Palmer, E. R.; Rogers, J.; Ray, D.; Upthegrove, R.

10.1101/2025.07.23.666268 — neuroscience — Posted on 2025-11-12

3324 The effects of Alcohol Dependence on the CSF Proteome in Mice: Evidence for Blood-Brain Barrier Dysfunction and Neuroinflammation

Turner, N. P.; Bajo, M.; Roberts, A. J.; Roberto, M. P.; Yates, J. R.

10.1101/2025.11.10.687295 — neuroscience — Posted on 2025-11-12

3325 Divergent spatial codes in retrosplenial cortex and hippocampus support multi-scale representation of complex environments

Laurent, C.; El Mahmoudi, N.; Smith, D. M.; Sargolini, F.; Jacob, P.-Y.

10.1101/2024.08.22.609122 — neuroscience — Posted on 2025-11-12

3326 RRAS and RRAS2 mutations are recurrent oncogenic drivers in lung cancer and are sensitive to the pan-RAS inhibitor RMC-6236

Pfeil, A. J.; Zhang, T.; Cheng, R.; Mattar, M.; Gomez Marti, J. L.; Gili, L.; Lai, R.; Master, R. P.; Dix, J.-M.; Gazzo, A.; Arbour, K. C.; de Stanchina, E.; Febres-Aldana, C.; Ladanyi, M.; Yang, S.-R.; Somwar, R.

10.1101/2025.09.19.677259 — cancer biology — Posted on 2025-11-12

3327 Emergent collective alignment gives competitive advantage to longer cells during range expansion

van den Berg, N.; Thijssen, K.; Nguyen, T. T.; Cordero, M.; Vazquez, A. G.; Mitarai, N.; Doostmohammadi, A.; Jauffred, L.

10.1101/2024.01.26.577059 — biophysics — Posted on 2025-11-12

3328 SiSaNA: A Python-based command line interface for Single-Sample Network Analysis

Newman, N. K.; Belova, T.; Kuijjer, M. L.

10.1101/2025.11.06.680212 — bioinformatics — Posted on 2025-11-12

3329 SHORT DISORDERED PEPTIDES ARE SUFFICIENT TO CONVERT PROTEINS INTO MECHANOSENSORS THAT RESPOND TO PHYSIOLOGICAL CELLULAR FORCES

Callejas Marin, A.; Gonzalez, W.; Pleiner, T.; De la Cruz, A.; Pandey, A.; Sanchez Guardado, L.; Jafar-Nejad, H.; Voorhees, R.; Lois, C.

10.1101/2025.11.11.685779 — cell biology — Posted on 2025-11-12

3330 Making deep mutational scanning accessible: a cost-efficient approach to construct barcoded libraries for genes of any length

Jann, J.; Gagnon-Arsenault, I.; Pageau, A.; Dube, A. K.; Fijarczyk, A.; Durand, R.; Landry, C. R.

10.1101/2025.05.29.656836 — synthetic biology — Posted on 2025-11-12

3331 Discovery Stack Pilot: Feasibility and Outcomes of a Scientist-Designed Peer Review Model Separating Quality and Impact

McGargill, M. A.; Liu, B. C.; Kuhns, M. S.; Mucida, D.; Rauch, I.; Rodda, L. B.; Koch, M. A.; Gonzalez Velozo, H.; Cadwell, K.; Freedman, T. S.; Scharschmidt, T. C.; Sever, R.; Ordovas-Montanes, J.; Suliman, S.; Oberst, A.; Runnette, B.; Krummel, M. F.

10.1101/2025.10.31.685758 — scientific communication and education — Posted on 2025-11-12

3332 Effects of 7.83 Hz and 528 Hz Extremely Low-Frequency Electromagnetic Fields on Early Growth of Turnip Greens Brassica rapa var. rapa

Cruz, I. N.

10.1101/2025.11.11.687793 — plant biology — Posted on 2025-11-12

3333 Mechanisms of adaptive interlimb coordination to sudden ground loss: a neuromusculoskeletal modeling study

Shinohara, K.; Ambe, Y.; Kim, Y.; Mano, F.; Ramalingasetty, S. T.; Lockhart, A. B.; Markin, S. N.; Ausborn, J.; Rybak, I. A.; Danner, S. M.; Aoi, S.

10.1101/2025.11.11.687930 — neuroscience — Posted on 2025-11-12

3334 Advancing Human iPSC-Derived Motor Neuron Models Using Glutamatergic Modulators for Synaptic Function Studies

Rostami, I.; Leuenberger, J.; Ott, G.; Nevian, T.; Zuber, B.

10.1101/2025.11.11.687934 — neuroscience — Posted on 2025-11-12

3335 Remembering the "When": Hebbian Memory Models for the Time of Past Events

Brea, J.; Modirshanechi, A.; Iatropoulos, G.; Gerstner, W.

10.1101/2022.11.28.518209 — neuroscience — Posted on 2025-11-12

3336 Decoding the Valence of Developmental Social Behavior: Dopamine Governs Social Motivation Deficits in Autism

Chen, X.; Tao, X.; Zhong, Z.; Zhang, Y.; Li, Y.; Ouyang, Y.; Ding, Z.; An, M.; Wang, M.; Li, Y.

10.1101/2025.11.12.687985 — neuroscience — Posted on 2025-11-12

3337 Test-Retest Reliability of Dopaminergic fPET and fMRI Measures During Reward Processing

Schlosser, G. D.; Handschuh, P. A.; Murgas, M.; Graf, S.; Milz, C.; Klug, S.; Falb, P.; Schmidt, C.; Eggerstorfer, B.; Briem, E.; Mayerweg, A.; Artmeier, L.; Godbersen, G. M.; Nics, L.; Rasul, S.; Hacker, M.; Hahn, A.; Lanzenberger, R.; Reed, M. B.

10.1101/2025.11.03.686252 — neuroscience — Posted on 2025-11-12

3338 Single-Cell Resolution of Cellular Damage Illuminates Disease Progression

Padvitski, T.; Unger Avila, P.; Chen, H.; Oezel, C.; Braun, F.; Mueller, R.-U.; Westermark, P.; Brinkkoetter, P.; Schermer, B.; Benzing, T.; Wunderlich, T.; Kann, M.; Beyer, A.; Kroll, M.-K.; Vossen, C.; Wienand, P.; Butt, L.; Unnersjoe-Jess, D.; Goebel, H.; Kuppe, C.

10.1101/2025.02.20.639269 — bioinformatics — Posted on 2025-11-12

3339 Sex Dependent Effects of Minocycline on Contextual Fear Memory

Lin, T.-C. E.; Hall, J.; Thomas, K.

10.1101/2025.11.11.687783 — animal behavior and cognition — Posted on 2025-11-12

3340 Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Hamptons Road Sanitation District (HRSD) with High and Low Dissolved Oxygen Conditions

Enuh, B. M.; Myers, K. S.; Bott, C.; Klaus, S.; McCullough, K.; McIntosh, L.; Beach, N.; Young, M.; Donohue, T. J.; Noguera, D. R.

10.1101/2025.11.10.687637 — genomics — Posted on 2025-11-12

3341 WNT inhibition primes the transcriptional landscape of mesoderm to initiate a phased ventricular cardiomyocyte specification programme

Velecela, V.; Bassil, A.; Fawcett, E.; Smith, E.; Konstantopoulos, D.; Salmen, F.; Bernardo, A. S.; Hoppler, S. S.

10.1101/2025.11.11.687613 — developmental biology — Posted on 2025-11-12

3342 Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for Activation

Munakata, Y.; Hu, M.; Dani, R. G.; Inoue, N.; Schultz, R. M.; Namekawa, S. H.

10.1101/2025.11.10.687753 — developmental biology — Posted on 2025-11-12

3343 Acridine Orange dye for long-term staining and live imaging of cnidarian development and regeneration

Patel, V. N.; Dountcheva, V.; Rouhana, L.

10.1101/2025.11.10.687709 — developmental biology — Posted on 2025-11-12

3344 Simple Methods to Acutely Measure Multiple Timing Metrics among Sexual Repertoire of Male Drosophila

Song, Y.; Sun, D.; Liu, X.; Jiang, F.; Yang, X.; Kim, W. J.

10.1101/2025.11.11.687834 — developmental biology — Posted on 2025-11-12

3345 In Ovo Sexing and Genotyping using PCR techniques: A Contribution to the 3R Principles in Chicken Breeding

Dierks, C.; Foerster, A.; Meunier, D.; Preisinger, R.; Klein, C.; Weigend, S.; Altgilbers, S.

10.1101/2025.11.11.687802 — developmental biology — Posted on 2025-11-12

3346 N6-methyladenosine regulation of mRNA translation is essential for early human erythropoiesis

Kuppers, D.; Arora, S.; Wladyka, C.; Ge, R.; Liu, S.; Peng, Y.; Su, R.; Wilhite, A.; Chen, J.; He, C.; Hsieh, A.; Paddison, P.

10.1101/2025.11.10.687731 — developmental biology — Posted on 2025-11-12

3347 Absence of posterior commissure and sub-commissural organ precedes encephalocele development in a new mouse model

Chan, H. N.; Savery, D.; Chakraborty, S.; Wenzlitschke, N.; Rocha, P. P.; Copp, A.

10.1101/2025.11.10.687701 — developmental biology — Posted on 2025-11-12

3348 Stationary and germ layer-specific cellular flows shape the zebrafish gastrula

Wopat, S.; Derksen, P.; Jain-Sharma, V.; Han, G.; Claussen, N. H.; Streichan, S. J.

10.1101/2025.11.10.687746 — developmental biology — Posted on 2025-11-12

3349 Developmental control of DNA damage responses in α- and β-cells shapes the selective beta-cell susceptibility in diabetes

Varghese, S. S.; Hernandez-De La Pena, A. G.; Pandey, A.; Anchondo, L.; Wu, X.; Bhattacharya, S.; Dhawan, S.

10.1101/2025.11.10.687707 — developmental biology — Posted on 2025-11-12

3350 The Drosophila ovary produces three follicle waves similar to those in mice

Fu, W. Y.; Spradling, A. C.

10.1101/2025.11.11.687893 — developmental biology — Posted on 2025-11-12

3351 Reconstituting epiblast-extraembryonic endoderm interactions restores anterior-ventral patterning in mouse stem cell-based embryo models.

Smirnova, N. P.; Ponomartsev, S. V.; Ali, T. M. L.; Lycke, M.; Chung, B. K.; Ogaard, J.; Melum, E.; Veenvliet, J. V.; Krauss, S.

10.1101/2025.11.09.687163 — developmental biology — Posted on 2025-11-12

3352 Non-transcriptional gibberellin DELLA signalling for microtubule dynamics

Yuliya, S.; Sravankumar, T.; Alexander, J.; Han, T.; Lukas, H.; Friml, J.

10.1101/2025.11.11.687800 — cell biology — Posted on 2025-11-12

3353 A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing

Liu, H.; Huch, S.; Hull, R.; Romero Garcia, F.; Nersisyan, L.; Yin, X.; Chen, W.-H.; Chen, J.; Pelechano, V.

10.1101/2025.11.12.687992 — microbiology — Posted on 2025-11-12

3354 Disequilibrium between chloroplast proton motive force and ATP levels in Arabidopsis

Degen, G. E.; Schwarzlander, M.; Johnson, M. P.

10.1101/2025.11.12.687978 — plant biology — Posted on 2025-11-12

3355 pBOSC: A method for source-level identification of neural oscillations in electromagnetic brain signals

Stern, E.; Niso, G.; Capilla, A.

10.1101/2025.07.20.665618 — neuroscience — Posted on 2025-11-12

3356 Visual landmark coding and dynamic coupling with path integration circuits in area 29e of the rodent parahippocampal cortex

Secer, G.; Krishnan, B.; Cowan, N.; Knierim, J. J.

10.1101/2025.11.11.687899 — neuroscience — Posted on 2025-11-12

3357 Local and network neural activations and their associations with sleep parameters during threat conditioning and extinction in persons with Generalized Anxiety Disorder with and without Insomnia Disorder

Seo, J.; Yuksel, C.; Oliver, K. I.; Daffre, C.; Song, H.; Lasko, N. B.; McCoy, E. R.; Milad, M. R.; Min, B.-K.; Pace-Schott, E. F.

10.1101/2025.11.11.687905 — neuroscience — Posted on 2025-11-12

3358 Neurogenesis Leads Early Development in Zebrafish

Wang, Z.; Tian, L.; Li, B.

10.1101/2025.11.12.687769 — neuroscience — Posted on 2025-11-12

3359 The anticonvulsant and mood-stabilizing drug valproic acid attracts C. elegans and activates chemosensory neurons via a cGMP signaling pathway

Rogel-Hernandez, L. E.; Casademunt, H.; Samuel, A. D. T.; Goodman, M. B.

10.1101/2025.11.11.687732 — neuroscience — Posted on 2025-11-12

3360 Spinal cord regeneration deploys cell-type specific developmental and non-developmental strategies to restore neuron diversity

Angell Swearer, A.; Perkowski, S. B.; Husain, I.; Figueiredo, T. A.; McCartney, M.; Wills, A. E.

10.1101/2025.11.10.687703 — developmental biology — Posted on 2025-11-12

3361 Cell division during Xenopus gastrulation influences neuroectoderm patterning

Velloso, I.; Araujo, R.; Horb, M.; Abreu, J. G.

10.1101/2025.11.11.687238 — developmental biology — Posted on 2025-11-12

3362 Antigenic Mapping of H2 Influenza Viruses recognized by Ferret and Human Sera and Predicting Antigenically Significant Sites

Reneer, Z. B.; Ngyen, C.; Corn, M. R.; Paugh, J. L.; Reynolds, O. C.; O'Hara, E.; Ross, T. M.; Baric, R. S.

10.1101/2025.11.12.687988 — microbiology — Posted on 2025-11-12

3363 MycoMobilome: A community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom

Baril, T. J.; Croll, D.

10.1101/2025.10.28.685023 — genomics — Posted on 2025-11-12

3364 Activation of nuclear receptors correlates with tuberculosis severity and is a target for host directed therapy

Maceiras, A. R.; Silva, M. L.; Couto, J.; Goncalves, R.; Silva, M.; Macedo, S.; Machado, D.; Indafa, I.; Sifna, A.; Malaca, C.; Namara, N.; Sanca, L.; Rodrigues, P. N. S.; Viveiros, M.; Rudolf, F.; Wejse, C.; Ca, B.; Saraiva, M.

10.1101/2025.07.23.666296 — immunology — Posted on 2025-11-12

3365 HIF1α-dependent induction of the T-Type calcium channel CaV3.2 mediates hypoxia-induced neuronal hyperexcitability

Troescher, A. R.; Tsortouktzidis, D.; Ammer-Pickhardt, F.; Penzenleitner, M.; Aichholzer, M.; Rauch, P.-R.; Rossmann, T.; Stroh-Holly, N.; Alti, B.; Gruber, A.; Helbok, R.; Haubold, J.; Thome, C.; Engelhardt, M.; von Oertzen, T. J.; Schoch, S.; Becker, A.; van Loo, K. M. J.

10.1101/2025.10.13.682038 — neuroscience — Posted on 2025-11-12

3366 Mothers respond to biological pup calls with heart rate changes in Japanese house bats, Pipistrellus abramus

Yoshino-Hashizawa, K.; Hiragochi, M.; Kobayasi, K. I.; Hiryu, S.

10.1101/2025.07.21.666052 — animal behavior and cognition — Posted on 2025-11-12

3367 mAIcrobe: an open-source framework for high-throughput bacterial image analysis

Brito, A. D.; Alwardt, D.; Mariz, B. d. P.; Filipe, S. R.; Pinho, M. G.; Saraiva, B. M.; Henriques, R.

10.1101/2025.10.21.683709 — microbiology — Posted on 2025-11-12

3368 Parameterisation of epidemiological models from small field experiments: a case study of banana bunchy top virus transmission

Retkute, R.; Omondi, A. B.; Soko, M.; Staver, C.; Thomas, J. E.; Gilligan, C. A.

10.1101/2025.11.11.687876 — plant biology — Posted on 2025-11-12

3369 Effects of Extremely Low-Frequency Electromagnetic Fields on Early Growth of Brassica rapa var. rapa

Cruz, I. N.

10.1101/2025.11.11.687793 — plant biology — Posted on 2025-11-12

3370 Pathogenic Fusarium verticillioides and Ophiostoma clavatum Associated with Ips acuminatus in Ukraine

Yusypovych, Y. M.; Shalovylo, Y. I.; Kit, O. Y.; Kramarets, V. O.; Zaika, V. K.; Korol, M. K.; Lavnyy, V. V.; Krynytskyy, H. T.; Kovaleva, V. A.

10.1101/2025.11.11.687790 — plant biology — Posted on 2025-11-12

3371 Setting priorities for the acquisition of primary plant occurrence data

10.1101/2025.11.11.683036 — plant biology — Posted on 2025-11-12

3372 Key molecular and cellular events of table olive fruit abscission zone formation during natural maturation and after ethephon treatment

Wang, M.; Santos, E.; Eagle, S.; Chernikova, A.; Zhang, S.; Tran, P.; Marino, G.; Jernstedt, J.; Niederholzer, F.; Wheeler-Dykes, B.; Wilkop, T.; Ferguson, L.; Drakakaki, G.

10.1101/2025.11.10.687704 — plant biology — Posted on 2025-11-12

3373 Comparative pangenomics unveils distinct host adaptation levels and conserved biosynthetic potential in microbiome Clostridia

De Vrieze, L.; Aerts, J.; Masschelein, J.

10.1101/2025.02.12.637840 — bioinformatics — Posted on 2025-11-12

3374 Sticky salts: overbinding of monovalent cations to phosphorylations in all-atom forcefields

Marien, J.; Puyo-Fourtine, J.; Prevost, C.; Sacquin-Mora, S.; Duboue-Dijon, E.

10.1101/2025.08.28.672842 — biochemistry — Posted on 2025-11-12

3375 Population history shapes urban evolutionary dynamics: distinct genetic structure across urban and rural Europe in two lepidopterans

Kivela, S. M.; Lee, K. M.; Adamidis, G. C.; Bonelli, S.; Hendrickx, F.; Huemer, P.; Kadlec, T.; Kankaanpaa, T.; Minard, G.; Nielsen, M. E.; Piano, E.; Tammaru, T.; Zografou, K.; Merckx, T.

10.1101/2025.01.27.635009 — evolutionary biology — Posted on 2025-11-12

3376 In situ evidence that mast cells release mutant NLRP1 in keratoacanthomas from multiple self-healing palmoplantar carcinoma

Dobre, A.; Fertig, T. E.; Niculae, A. M.; Cohn, A. M.; Curici, A.; Andrei, R. T.; Marta, D. S.; Peteu, V. E.; Popescu, R. G.; Marinescu, G. C.; Turcu, G.; Forsea, A. M.; Ion, D. A.; Gherghiceanu, M.; Nedelcu, R. I.

10.1101/2025.09.12.675637 — immunology — Posted on 2025-11-12

3377 An abstract relational map emerges in the human medial prefrontal cortex with consolidation

Baram, A.; Nili, H.; Barreiros, I.; Samborska, V.; Behrens, T. E.; Garvert, M. M.

10.1101/2024.10.11.617652 — neuroscience — Posted on 2025-11-12

3378 Auxiliary data, quality assurance and quality control for wearable light loggers and optical radiation dosimeters

Zauner, J.; Stefani, O.; Abarca, G. B.; Guidolin, C.; Schrader, B.; Udovicic, L.; Spitschan, M.

10.1101/2025.09.11.675633 — neuroscience — Posted on 2025-11-12

3379 Hypoxia Promotes Early Tumorigenesis through Dynamical-Mechanical Balance and Genetic Instability

Wang, Z.; Tian, L.; Li, B.

10.1101/2024.12.31.630973 — cancer biology — Posted on 2025-11-12

3380 METRIN-KG: A knowledge graph integrating plant metabolites, traits and biotic interactions

Tandon, D.; Mendes de Farias, T.; Allard, P.-M.; Defossez, E.

10.1101/2025.08.20.671289 — bioinformatics — Posted on 2025-11-12

3381 Stem cell morphology defines functional heterogeneity and therapeutic vulnerabilities in glioblastoma

Barelli, C.; Bonfanti, M.; Mirabella, F.; Ricca, D.; Alizadehmohajer, N.; Bosotti, R.; Bertani, I.; Sokolova, V.; Campione, A.; Sicuri, G. M.; Peano, C.; Faletti, S.; Stefini, R.; Kalebic, N.

10.1101/2025.03.24.644884 — cell biology — Posted on 2025-11-12

3382 APOE4-Aβ synergy drives brain network dysfunction and neuronal lysosomal-ER proteostasis dysregulation in preclinical Alzheimer's disease

Shin, J.; Brady, E.; Chen, C.; Lauderdale, K.; Agrawal, A.; Zhang, Y.; Jiang, X.; Herbert, J.; Mallen, D. D.; Ly, K. K.; Honma, P. S.; Guo, Z.; Sant, C.; Thomas, R.; Miller, S. R.; Cobos, I.; Palop, J. J.

10.1101/2025.11.11.687887 — neuroscience — Posted on 2025-11-12

3383 Early life adversity increases striatal dopamine D1 receptor density and promotes social alcohol drinking in mice, especially males

Anderson, L. G.; Tischer, A.; Bock, R.; Michaelides, M.; Alvarez, V.

10.1101/2025.11.10.687736 — neuroscience — Posted on 2025-11-12

3384 Topological basal ganglia model with dopamine-modulated spike-timing-dependent plasticity reproduces reinforcement learning, discriminatory learning, and neuropsychiatric disorders

Gutierrez, C. E.; Lienard, J.; Girard, B.; Urakubo, H.; Doya, K.

10.1101/2025.11.10.687760 — neuroscience — Posted on 2025-11-12

3385 Modelling Auditory Enhancement: Efferent Control of Cochlear Gain can Explain Level Dependence and Effects of Hearing Loss

Agarwalla, S.; Farhadi, A.; Carney, L. H.

10.1101/2025.11.10.687695 — neuroscience — Posted on 2025-11-12

3386 Sex-specific regulation of social play in juvenile rats by oxytocin neurons in the hypothalamus and oxytocin signaling in the nucleus accumbens

Bowden, S. M.; Becker, K. D.; Grinevich, V.; Lee, J. D.; Veenema, A.

10.1101/2025.11.11.687699 — neuroscience — Posted on 2025-11-12

3387 Lower engagement of cognitive control, attention, modulation networks and lower creativity in children while using ChatGPT: an fMRI study

Horowitz-Kraus, T.; Kenett, Y. N.; Link, D.; Ashqar, E.; Farah, R.

10.1101/2025.11.07.687207 — neuroscience — Posted on 2025-11-12

3388 Time- and frequency-resolved decomposition of beta brain activity reveals two functionally distinct beta bands

Korkealaakso, S.; Ahrends, C.; Niemela, L.; Vidaurre, D.; Renvall, H.; Pauls, A.

10.1101/2025.11.10.682052 — neuroscience — Posted on 2025-11-12

3389 Differential Regulation of Hepatic Macrophage Fate by Chi3l1 in MASLD

He, J.; Chen, B.; Lu, W.; Wang, X.; Yang, R.; Deng, C.; Zhu, X.; Wang, K.; Wang, L.; Xie, C.; Li, R.; Lu, X.; Yang, R.; Peng, C.; Li, C.; Shan, Z.

10.1101/2025.05.06.652369 — physiology — Posted on 2025-11-12

3390 Housing environment bilaterally alters transcriptomic profile in the rat hippocampal CA1 region

Kubota, A.; Kojima, K.; Koketsu, S.; Kannon, T.; Sato, T.; Hosomichi, K.; Shinohara, Y.; Tajima, A.

10.1101/2025.04.29.651351 — neuroscience — Posted on 2025-11-11

3391 Cerebellin-2 neurons in the parafascicular thalamic nucleus regulate self-grooming behavior

Zhang, L.; Song, H.; Li, Y.; Zhang, H.; Diao, S.; Geng, D.; Zhao, Z.; Yang, B.; Zheng, R.; Li, Z.; Wang, L.; Zhang, T.; Jiang, Y.; Liu, Z.; Zhang, L.; Liu, Y.; Xie, Z.; Li, D.; Zhang, F.; Cao, P.

10.1101/2025.03.22.644777 — neuroscience — Posted on 2025-11-11

3392 The Cerebellum Implements an Oscillatory Forward Model for Accurate Motor Timing

West, T. O.; Spedden, M. E.; O'Neill, G. C.; Bestmann, S.; Barnes, G.; Farmer, S. F.; Cagnan, H.

10.1101/2025.11.11.687835 — neuroscience — Posted on 2025-11-12

3393 Cell-type-resolved NRXN1 isoforms across human brain tissues and hiPSC organoids

Cao, L.; Fan, Y.; Ghorbani, S.; Mariani, J.; Zhang, Y.; Fernando, M. B.; Bendl, J.; Fullard, J.; Ramos, S. I.; Mead, E. A.; Deikus, G.; Beaumont, K. G.; Sebra, R.; Tsankova, N.; Roussos, P.; Brennand, K. J.; Fang, G.

10.1101/2025.11.11.687875 — neuroscience — Posted on 2025-11-12

3394 Old-New Recognition Memory Revisited

Wei, X.; Buckner, R. L.

10.1101/2025.11.11.687844 — neuroscience — Posted on 2025-11-12

3395 Neural Entrainment in the Theta Band Predicts Groove Perception in Popular Music

Keller, D.; Rohe, T.; Raake, A.

10.1101/2025.11.11.687596 — neuroscience — Posted on 2025-11-12

3396 Evaluation of phantom doping materials in quantitative susceptibility mapping

Hooper, P.; Jin, J.; O'Brien, K.; Tourell, M.; Robinson, S. D.; Barth, M.

10.1101/2024.02.18.580843 — biophysics — Posted on 2025-11-11

3397 Refined Myocardium Segmentation from CT Using a Hybrid-Fusion Transformer

Qin, S.; Xing, F.; Cho, J.; Park, J.; Liu, X.; Rouhollahi, A.; Bou Farhat, E. J.; Javadikasgari, H.; Sabe, A.; Nezami, F. R.; Woo, J.; Aganj, I.

10.1101/2024.09.27.615510 — bioengineering — Posted on 2025-11-11

3398 Data-Driven Discovery of Mechanistic Ecosystem Models with LLMs

Spillias, S.; Rogers, J.; Boschetti, F.; Fulton, E. A.; Guglielmo, M.; Yong, S. Y.; Trebilco, R.

10.1101/2025.07.14.664628 — ecology — Posted on 2025-11-11

3399 Roles of MKI67, GNL2, and MDN1 in Chromosome Organization, Nucleolar Function, and Transcriptome Regulation

iuchi, s.; Paulo, J. A.

10.1101/2025.02.13.638155 — cell biology — Posted on 2025-11-11

3400 Heme's relevance genuine? Re-visiting the roles of TANGO2 homologs including HRG-9 and HRG-10 in C. elegans

Sandkuhler, S. E.; Youngs, K.; Gottipali, O.; Owlett, L.; Bandora, M.; Naaz, A.; Kim, E. S.; Wang, L.; Wojtovich, A. P.; Gupta, V. A.; Sacher, M.; Mackenzie, S. J.

10.1101/2023.11.29.569072 — cell biology — Posted on 2025-11-11

3401 The fungal peptide toxin candidalysin induces distinct membrane repair mechanisms compared to bacterial pore-forming toxins

Thapa, R.; Kayejo, V. G.; Lyon, C. M.; Naglik, J. R.; Hube, B.; Keyel, P. A.

10.1101/2025.05.09.653080 — cell biology — Posted on 2025-11-11

3402 Blocking Nonspecific Primer Amplification in Loop-Mediated Isothermal Amplification with TrueLAMP

Chen, Z.

10.1101/2025.10.23.684253 — molecular biology — Posted on 2025-11-11

3403 An AI-Guided Framework Reveals Conserved Features Governing microRNA Strand Selection

Meadows, D.; Hargis, H. L.; Ellis, A.; Lee, H.; Mangone, M.

10.1101/2025.04.30.651563 — molecular biology — Posted on 2025-11-11

3404 Adult patients with autoinflammation of unknown origin partially phenocopy the immune presentation of Still's disease

Veiga, R.; De Vuyst, L.; Poulet, C.; Neumann, J.; Bucken, L.; Prezzemolo, T.; Willemsen, M.; Vanderschueren, S.; Matthys, P.; Chabaane, E.; Fleron, M.; Cobraiville, G.; Baiwir, D.; Mazzucchelli, G.; Immunome Project Consortium for Autoinflammatory Disorders (ImmunAID), ; Fautrel, B.; Wouters, C.; De Seny, D.; Humblet-Baron, S.; Liston, A.

10.1101/2024.11.27.625689 — immunology — Posted on 2025-11-11

3405 Deterministic versus Probabilistic Tractography: Impact on White Matter Bundle Shape

SHUAI, Y.; Chandio, B. Q.; Feng, Y.; Villalon-Reina, J. E.; Nir, T. M.; Ching, C. M.; Ba Gari, I.; Thomopoulos, S. I.; Alibrando, J. D.; John, J. P.; Venkatasubramanian, G.; Jahanshad, N.; Thompson, P. M.

10.1101/2025.08.19.669949 — neuroscience — Posted on 2025-11-11

3406 Phenotypic heterogeneity in lag reflects an evolutionarily stable bet-hedging strategy

George, A. V.; Wingreen, N. S.; Reddy, G.

10.1101/2025.11.02.686100 — systems biology — Posted on 2025-11-11

3407 HapBridge: A Methylation-Guided Approach for Correcting Switch Errors and Bridging Phased Blocks in Long-Read Phasing

Chen, H.; Nie, F.; Luo, F.; Wang, J.

10.1101/2025.11.07.687303 — bioinformatics — Posted on 2025-11-11

3408 Functional dissection of metabolic trait-associated gene regulation in steady state and stimulated human skeletal muscle cells

Nishino, K.; Bloss, G.; Kitzman, J. O.; Parker, S. C. J.; Tovar, A.

10.1101/2024.11.28.625886 — genomics — Posted on 2025-11-11

3409 AI-Driven Knowledge Synthesis for Food WebParameterisation

Spillias, S.; Fulton, E. A.; Boschetti, F.; Bulman, C.; Strzelecki, J.; Trebilco, R.

10.1101/2025.05.18.654761 — ecology — Posted on 2025-11-11

3410 Drivers of thermal tolerance breadth of plants across contrasting biomes

Briceno, V. F.; Arnold, P. A.; Cook, A. M.; Courtney Jones, S. K.; Gallagher, R. V.; French, K.; Bravo, L. A.; Nicotra, A. B.; Leigh, A.

10.1101/2023.10.02.560437 — ecology — Posted on 2025-11-11

3411 A system for functional studies of the major virulence factor of malaria parasites

Cronshagen, J.; Allweier, J.; Mesen-Ramirez, J. P.; Staecker, J.; Vaaben, A. V.; Ramon-Zamorano, G.; Naranjo, I.; Graser, M.; Lopez-Barona, P.; Ofori, S.; Jansen, P. W.; Hornebeck, J.; Kieferle, F.; Murk, A.; Martin, E.; Castro-Pena, C.; Bartfai, R.; Lavstsen, T.; Bruchhaus, I.; Spielmann, T.

10.1101/2024.04.30.591946 — microbiology — Posted on 2025-11-11

3412 Atypical developmental remodeling of dopamine neurons involves AKT-GSK3β signaling and glia activity

Zhang, X.; Chen, W.; Wang, Y.; Tu, X.; Zhang, X.; Davis, R. L.; Jan, L. Y.; Jan, Y. N.

10.1101/2025.08.29.673168 — neuroscience — Posted on 2025-11-11

3413 Neural Synchrony Links Sensorimotor Cortices in a Network for Facial Motor Control

Vazquez, Y.; Ianni, G. R.; Rassi, E.; Rouse, A. G.; Schieber, M. H.; Yazdani, F.; Prut, Y.; Freiwald, W. A.

10.1101/2025.03.04.641458 — neuroscience — Posted on 2025-11-11

3414 Brain-wide connectivity patterns of feedforward and feedback cortico-cortical neurons in the mouse secondary visual cortex

Dickson, R. G.; Jacobs, M. W.; Ratliff, J. M.; Soronow, A. L. R.; An, F.; Yuqob, W. A.; Kim, E. J.

10.1101/2025.07.08.663552 — neuroscience — Posted on 2025-11-11

3415 A spatial representation of information underlies probabilistic computation in cells

Wang, Z.; Thomson, M.

10.1101/2025.02.12.637580 — systems biology — Posted on 2025-11-11

3416 In vivo models for rustrela virus (RusV) infection in potential reservoir and spill-over hosts

Klein, A.; Michaely, L. M.; Geers, J.; Weinert, S.-C.; Wylezich, C.; Aebischer, A.; Ulrich, L.; Beer, M.; Schlottau, K.; Breithaupt, A.; Rubbenstroth, D.

10.1101/2025.11.10.687696 — microbiology — Posted on 2025-11-11

3417 Phylum-wide propionate degradation and its potential connection to poly- γ-glutamate biosynthesis in Candidatus Cloacimonadota

Calusinska, M.; Herold, M.; Klimek, D.; Bertucci, M.; Lemaigre, S.; Cambier, S.; Zorzan, S.; Leclercq, C.; Dolfing, J.; Westerholm, M.; Mueller, B.; Nasirzadeh, L.; Schnuerer, A.; Wilmes, P.; Delfosse, P.; Goux, X.

10.1101/2025.11.11.687785 — microbiology — Posted on 2025-11-11

3418 Harnessing Plasmid Crosstalk in Transcription Factor Mediated Cell-Free Biosensors

Patterson, A. T.; Piorino, F.; Bronovitskiy, S. S.; Godavarti, D. R.; Styczynski, M. P.

10.1101/2025.11.11.687754 — synthetic biology — Posted on 2025-11-11

3419 Discovery and Functional Characterization of Salinity-Responsive Promoters in Pseudomonas putida KT2440

de Simone, C. M.; de Siqueira, G. M. V.; Guazzaroni, M.-E.

10.1101/2025.11.11.687801 — synthetic biology — Posted on 2025-11-11

3420 Cryo-EM structures of Mycobacterium tuberculosis pyruvate carboxylase reveal allosteric activation and domain dynamics during catalysis

Singh, A.; Singh, S.; Das, U.

10.1101/2025.11.11.687647 — biophysics — Posted on 2025-11-11

3421 Targeting ligand binding sites in Plasmodium falciparum NCR1 enables antimalarial drug discovery

Kohling, A.; Boulet, C.; Al Makhlouf, M.; Khanppnavar, B.; Chen, Y.; Ganga, E.; Kirchmair, J.; Stockner, T.; Brochet, M.; Korkhov, V. M.

10.1101/2025.11.11.687791 — biochemistry — Posted on 2025-11-11

3422 Molecular Evolutionary Analysis for Estimating the Strength of Fluctuating Selection among Individuals (FSI)

Gu, X.

10.1101/2025.11.10.687654 — evolutionary biology — Posted on 2025-11-11

3423 The long-standing relationship between replication timing, gene expression, and chromatin accessibility is maintained in early mouse embryogenesis

Rivera-Mulia, J. C.

10.1101/2025.11.10.687227 — developmental biology — Posted on 2025-11-11

3424 Widespread DNA off-targeting confounds studies of RNA chromatin occupancy

Goldrich, M. J.; Delhaye, L.; Bekaert, S.-L.; Decaesteker, B.; Van Nieuwerburgh, F.; Speleman, F.; Eyckerman, S.; Mestdagh, P.; Ulitsky, I.

10.1101/2025.11.11.687850 — molecular biology — Posted on 2025-11-11

3425 Mechanistic insights into Phage SSB-activated bacterial Retron-Eco8 immunity

Ji, C.-G.; Li, Z.; Wei, X.-Y.; Li, Y.; Zhang, J.-T.; Liu, X.; Jia, N.

10.1101/2025.11.11.687766 — microbiology — Posted on 2025-11-11

3426 Strain-level translocation and enrichment mechanisms of oral bacteria in the lower gastrointestinal tract of stunted children

Yersin, S.; Gody, J.-C.; Mazel, F.; Djmbele, E.; Nigateloum, C.; Gondje, B. P.; Vondo, S. S.; Kandou, K.; Raub, A.; Teo, Y.; Djorie, S.; Kapel, N.; Sansonetti, P.; Vonaesch, P.; Afribiota Investigators,

10.1101/2025.11.11.687814 — microbiology — Posted on 2025-11-11

3427 The in vitro bacterial viability and microbial composition of commercially available canine and feline fecal microbial transplantation products

Randolph, N. K.; Wetzel, L.; Diaz-Campos, D.; van Balen, J. C.; Winston, J. A.

10.1101/2025.11.10.687729 — microbiology — Posted on 2025-11-11

3428 Dual resistance to cold and ethanol in Penicillium species persistently contaminating donated cadavers

Yoshinouchi, T.; Nakamura, T.; Manabe, M.; Mori, D.; Yasunaga, J.-i.; Tanaka, Y.; Iwanaga, J.; Kitagawa, N.

10.1101/2025.11.10.687738 — microbiology — Posted on 2025-11-11

3429 Enhanced Zika Virus Suppression by Coupling Ribavirin with Biodegradable Drug Delivery

Rodriguez, J.; Waterman, A.; Blahove, M. R.; Saviskas, J.; Santos-Villalobos, B.; Wallace, M.; Carter, J.

10.1101/2025.11.10.687694 — microbiology — Posted on 2025-11-11

3430 Gene-centric analysis of Raskinella chloraquaticus reveals a functionally conserved taxonomic group in global drinking water distribution systems

Sudarshan, A. S.; Konstantinidis, K. T.; Pinto, A. J.

10.1101/2025.11.10.687676 — microbiology — Posted on 2025-11-11

3431 The histone variant H2A.Z and its chaperone SRCAP are required for RNA polymerase II to access HBV chromatin

Jay, B.; Lopez, O.; Gerossier, L.; Sarica, N.; Pozo, G.; Gerbal-Chaloin, S.; Daujat-Chavanieu, M.; Hantz, O.; Neuveut, C.; Diogo Dias, J.

10.1101/2025.11.10.687638 — microbiology — Posted on 2025-11-11

3432 Synergies on many levels: Microbially driven redoxgradients as drivers of greenhouse gas emissions in a pH neutral fen

Kujala, K.; Berezovska, V.; Cunow, J.; Hegazy, S.; Heilmann, E.; Horn, M. A.; Hoyhtya, I.; Korhonen, P.; Lyytinen, E.; Martinez Quimbayo, J.; Prieto-Fernandez, F.; Pakkila, L.; Poykio, V.; Solastie, S.; Tarvainen, L.

10.1101/2025.11.10.687636 — microbiology — Posted on 2025-11-11

3433 pGGTOX: a versatile plasmid platform for recombination-based genome editing across Enterobacteriaceae

Liu, M.; Tian, E.; Cui, X.; Liu, K.; Feng, L.; Liu, Y.; Wang, Y.; Shi, X.; Chen, L.; Hao, M.

10.1101/2025.11.11.687829 — microbiology — Posted on 2025-11-11

3434 Accurate interpretation of within-host dissemination using barcoded bacteria

Giorgio, R. T.; Zhang, T.; Holmes, C. L.; Hullahalli, K.

10.1101/2025.11.11.687827 — microbiology — Posted on 2025-11-11

3435 Functional genomics in a microbe that degrades and metabolizes PET plastic

Crits-Christoph, A.; Leung, J.; Piedra, F.-A.; Brumwell, S. L.; Sajtovich, V. A.; Abrams, M. B.; Esmurria, A.; Kang, S. C.; Mendler, K.; Gilbert, C.; Lee, H. H.; Ostrov, N.

10.1101/2025.11.11.687616 — microbiology — Posted on 2025-11-11

3436 A conserved sRNA regulates mucin adhesion and gut colonization across the Enterococcaceae

Bowden, S.; Jennings, K. C.; Zlitni, S.; Brooks, E. F.; Davin, M. E.; Natarajan, A.; Asare, L.; Fremin, B. J.; Wilmes, P.; Hettich, R. L.; Salzman, N. H.; Bhatt, A. S.

10.1101/2025.11.10.687296 — microbiology — Posted on 2025-11-11

3437 Ribosomal Architecture and rRNA Modification Landscape in the Tick-Borne Parasite Babesia divergens

Gutierrez-Vargas, C.; Izhaki-Tavor, L. S.; Calvopina-Chavez, D.; Keroack, C. D.; Copello, P.; Duraisingh, M. T.; Leger-Abraham, M.

10.1101/2025.11.11.687446 — microbiology — Posted on 2025-11-11

3438 Nanoplasmonic SERS reveals previously uncharacterised indole derivative in E. coli metabolism

Vali, M.; Wyatt, E.; Abbott, K.; Lio, P.; Croft, C.; Krauss, T.; Khan, M.; Zarkan, A.; Baumberg, J.; Fusco, D.

10.1101/2025.11.10.687708 — microbiology — Posted on 2025-11-11

3439 Mosquito Viromes in England and Wales Reveal Hidden Arbovirus Signals and Limited Ecological Structuring

Pilgrim, J.; Widlake, E.; Wilson, R.; Vaux, A. G.; Medlock, J. M.; Darby, A. C.; Baylis, M.; Blagrove, M. S.

10.1101/2025.11.11.687861 — microbiology — Posted on 2025-11-11

3440 Efficient elimination of microbial infections in wounds using plasma activated water hydrogel

Mukherjee, D.; Ghosh, P.; Rajmani, R. S.; Verma, K.; Gowda, A.; Birua, A.; Rao, L.; Chakravortty, D.

10.1101/2025.11.10.687761 — microbiology — Posted on 2025-11-11

3441 The Lysis Cassette of Jumbophage phiKZ

Manohar, P.; Wan, J.; Ganser, G.; Sharp, K.; Young, R.

10.1101/2025.11.11.687635 — microbiology — Posted on 2025-11-11

3442 Streptavidins play a multifunctional role within a biotin-pathway antibiotic network encoded in a biosynthetic supercluster

Kurosawa, S.; Mo, J.; Diao, X.; Xie, F.; Wang, T.; Zhao, H.; Wu, D.; Müller, R.; Fu, C.

10.1101/2025.11.10.687665 — microbiology — Posted on 2025-11-11

3443 Hydroxychloroquine decouples reactogenicity from efficacy in mRNA and viral-vector gene delivery

Jerala, R.; Lainscek, D.; Malensek, S.; Golob-Urbanc, A.; Orehek, S.; Bohinc, J.; Mancek Keber, M.; Sotosek, T.; Esih, H.; Fortsneric, V.; Pecan, P.; Pantovic Zalig, J.; Bencina, M.; Bester, R.; Protzer, U.

10.1101/2025.11.10.687670 — immunology — Posted on 2025-11-11

3444 Intrathymic progenitor cell transplantation restores T cell development through ILC3-TEC crosstalk

Machado, A.; Houques, C.; Pouzolles, M.; Evain, E.; Dardalhon, V.; Harly, C.; Taylor, N.; Zimmermann, V. S.

10.1101/2025.11.10.687563 — immunology — Posted on 2025-11-11

3445 An Ehrlich-inspired retrobiosynthesis of pharmaceutical scaffolds

Rumpl, A. E. C.; Kowalski, D.; Goodhew, J. R.; Hirano, M.; Bogucki, L.; Rosa, C. A.; Lachance, M.-A.; Pyne, M. E.

10.1101/2025.11.10.687684 — synthetic biology — Posted on 2025-11-11

3446 Oncogenic mutations convert MET from a pro-apoptotic tumor suppressor to an oncogenic driver

Tellier, R.; Fernandes, M.; Vinchent, A.; Paget, S.; Laratte, A.; Vuillier, C.; Werkmeister, E.; Villenet, C.; Meneboo, J.-P.; Chotteau-Lelievre, A.; Wasielewski, E.; Kherrouche, Z.; Truong, M.-J.; Descarpentries, C.; Grumolato, L.; Figeac, M.; Cortot, A. B.; Poulain, L.; Paradisi, A.; Tulasne, D.

10.1101/2025.11.10.687614 — cancer biology — Posted on 2025-11-11

3447 Automated Annotation of Plant Gene Regions Using Supervised Machine Learning

Simoes, B. M.; Pinho, A. J.; Pratas, D.

10.1101/2025.11.10.687603 — bioinformatics — Posted on 2025-11-11

3448 Ancestral neuronal receptors are bacterial accessory toxins

Raoelijaona, F.; Szczepaniak, J.; Schahl, A.; Bray, J.; Zhou, J.; Baker, L.; El Omari, K.; Lowe, E.; Low, Y. S.; Rodriguez, C. M.; Landsberg, M. J.; Lott, J. S.; Kleanthous, C.; Chavent, M.; Maiden, M. C.; Seiradake, E.

10.1101/2025.11.11.687626 — biochemistry — Posted on 2025-11-11

3449 Cell Numbers Contribute to Cell Fate During Ciona Cardiopharyngeal Mesoderm Specification

Singer, E.; Kim, H.; Levine, M.; Treen, N.

10.1101/2025.11.10.687625 — developmental biology — Posted on 2025-11-11

3450 Phytic Acid (InsP6) Activates HDAC3 Epigenetic Axis to Maintain Intestinal Barrier Function

Chatterjee, S.; Sin, Z.; Tran, N.; Preval, L. V.; Shukla, A.; Tran, T.; Koshkaryan, G.; Ritter, K.; Su, X. B.; Ragsac, S. J.; Park, S.; Liu, Q.; Van, R.; Han, M.; Saiardi, A.; Huang, K.; Huff-Hardy, K.; Rood, R.; Gremida, A.; Gregory, M.; Chen, C.-H.; Deepak, P.; Centlivre, J. P.; Hedlund, B. P.; Jessen, H.; Guha, P.

10.1101/2024.09.15.613154 — cell biology — Posted on 2025-11-11

3451 Intramammary infection of bovine H5N1 influenza virus in ferrets leads to transmission in suckling neonates

Baker, P. H.; Moyer, M.; Bai, Y.; Stafford, L. S.; Kelvin, A. A.; Lee, C.; Langel, S. N.

10.1101/2024.11.15.623885 — microbiology — Posted on 2025-11-11

3452 Phosphorus stress and spatial confinement lower the threshold for quorum-sensing activation of redox-active metabolite production in Pseudomonas synxantha

Alcade, R. E.; Jeckel, H.; Zhang, O.; Avila, R. L.; Dalleska, N.; Mavrodi, D.; Yang, C.; Newman, D. K.

10.1101/2025.11.11.687776 — microbiology — Posted on 2025-11-11

3453 Inhibition of systemic mammalian metabolism by carnitine mimics from the gut microbiota

Thuemmler, K.; Basak, S.; Hulme, H.; Dritsa, C.; Foreman, R.; Naseer, H.; Salah, E.; Tumber, A.; Worboys, S.; Douce, G.; Haggarty, J. H.; Williams, R.; Taylor, V.; Ormsby, M. J.; Whitfield, P.; McCullagh, J.; Salt, I.; Burchmore, R. J.; Goodwin, R. J.; Schofield, C. J.; Wall, D. M.

10.1101/2025.11.11.687811 — microbiology — Posted on 2025-11-11

3454 Phenotypic Heterogeneity Shapes Phage Resistance and Cocktail Efficacy in Klebsiella pneumoniae

Mora-Quilis, L.; Sanjuan, R.; Domingo-Calap, P.

10.1101/2025.11.11.687788 — microbiology — Posted on 2025-11-11

3455 Decoupling badger and sett distributions for improved bovine tuberculosis management

Morera-Pujol, V.; Byrne, A. W.; Barret, D.; Breslin, P.; McGrath, G.; Quinn, D. J.; Ciuti, S.

10.1101/2025.11.10.687598 — zoology — Posted on 2025-11-11

3456 Missense Mutation ADNP p.C687R Disrupts Chromatin Regulation and GABAergic Differentiation in HVDAS

Chen, Q.; Liu, X.; Wu, M.; Sun, D.; Ding, X.; Zhou, M.; Peng, W.; Chen, Y.; Xue, B.; Tang, N.; Gang, X.; Tai, Y.; Xu, Q.; Xiong, M.; Jiang, Y.

10.1101/2025.11.10.687585 — neuroscience — Posted on 2025-11-11

3457 Disentangling Stimulus & Population Dynamics in Mouse V1: Orthogonal Subspace Decomposition for Neural Representation

TZANAKIS, N.; Barberis, A.; Savaglio, M. A.; Chourdaki, I.; Smirnakis, S. M.; Papadopouli, M.

10.1101/2025.11.10.687558 — neuroscience — Posted on 2025-11-11

3458 White Matter Tract Vulnerability to Amyloid Pathology on the Alzheimer's Disease Continuum

Chandio, B. Q.; Nir, T. M.; Villalon-Reina, J. E.; Thomopoulos, S. I.; Feng, Y.; Reid, R. I.; Jack, C. R.; Weiner, M. W.; Garyfallidis, E.; Jahanshad, N.; Braskie, M. N.; O'Bryant, S.; Thompson, P. M.

10.1101/2025.08.18.670970 — neuroscience — Posted on 2025-11-11

3459 Dual Architecture of Consciousness Transitions: Evidence from Sleep EEG Analysis

Dobbin, E.

10.1101/2025.11.10.687628 — neuroscience — Posted on 2025-11-11

3460 Revisiting the explicit-implicit additivity assumption in visuomotor adaptation

Chen, Y.; Taylor, J. A.

10.1101/2025.10.20.683435 — neuroscience — Posted on 2025-11-11

3461 Counterconditioning Alcohol Cues: Neural and Behavioral Modulation of Automatic Tendencies and Pavlovian-to-Instrumental Transfer in Male Alcohol Users

Verma, A. K.; Chivukula, U.; Garbusow, M.; Kumar, N.

10.1101/2025.11.10.687519 — neuroscience — Posted on 2025-11-11

3462 Transferring active inference to newly encountered prism-shifted environments

Yoshihara, M.; Isomura, T.

10.1101/2025.11.10.687533 — neuroscience — Posted on 2025-11-11

3463 Skull Bone Marrow Drainage and Its Associations with Inflammation, Sleep Quality, and Cognitive Performance

zhou, y.; Jin, H.; Zhu, X.; Li, Y.; Zhou, Z.; Huang, X.; Ke, H.; Fang, M.; Sun, J.; Lou, M.

10.1101/2025.11.10.687593 — neuroscience — Posted on 2025-11-11

3464 Colibactin-producing E. coli promote carcinogenesis of gastroesophageal adenocarcinoma and simultaneously induce autophagy and differentiation

Proano Vasco, A. I.; Obwegs, D.; Bruder, K.; Ritzkowski, C.; Eichner, S.; Houle, L.; Sun, Y.; Tanes, C.; Klaas, L.; Schoemig, L. R.; Mohammad-Shahi, D. S.; Bittinger, K.; Wang, K. K.; Rustgi, A. K.; Falk, G. W.; Thimme, R.; Wang, T. C.; Wang, H. H.; Stecher, B.; Dobrindt, U.; Abrams, J. A.; Sagar, S.; Quante, M.

10.1101/2025.11.10.687579 — cancer biology — Posted on 2025-11-11

3465 Anoikis resistance and metastasis of ovarian cancer can be overcome by CDK8/19 Mediator kinase inhibition.

Monavarian, M.; Rajkarnikar, R.; Page, E. F.; Kumari, A.; Macias, L. Q.; Massicano, F.; Lee, N. Y.; Sahoo, S.; Hempel, N.; Jolly, M. K.; Ianov, L.; Worthey, E.; Singh, A.; Roninson, I.; Broude, E. V.; Chen, M.; Mythreye, K.

10.1101/2023.12.04.569970 — cancer biology — Posted on 2025-11-11

3466 Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers

Tourneur, A.; Rodrigues Vitoria, J.; Saiselet, M.; Craciun, L.; Larsimont, D.; Lefort, A.; Libert, F.; Maenhaut, C.; Costagliola, S.; Tarabichi, M.; Romitti, M.; Detours, V.

10.1101/2024.02.15.580495 — cancer biology — Posted on 2025-11-11

3467 Large Language Models for Accessible Reporting of Bioinformatics Analyses in Interdisciplinary Contexts

Yu, L.; Kim, D.; Cao, Y.; Shu, M. W. S.; Shen, M.; Liang, X.; Gu, J.; Jayakumar, R.; Ding, W.; Yang, F.; Zhang, X.; Kim, J.; Yang, P.; Yang, J. Y. H.

10.1101/2025.11.09.687479 — bioinformatics — Posted on 2025-11-11

3468 Simulating Tandem Mass Spectra for Small Molecules using a General-Purpose Large-Language Model

Nguyen, T.; Barupal, D.

10.1101/2025.11.10.687298 — bioinformatics — Posted on 2025-11-11

3469 Overcoming Extrapolation Challenges of Deep Learning by Incorporating Physics in Protein Sequence-Function Modeling

Barethiya, S.; Huang, J.; Liu, X.; Guan, H.; Chen, J.

10.1101/2025.11.09.687530 — bioinformatics — Posted on 2025-11-11

3470 Causal network perturbation analysis identifies known and novel type-2 diabetes driver genes

Zhao, Y.; Taha, H. B.; Aman, A.; Qian, K.; Kumar, P.; Mahoney, J. M.; He, H.; George, J.; Li, S.

10.1101/2024.05.22.595431 — bioinformatics — Posted on 2025-11-11

3471 MODERATE 3D ORBITAL SHAKING MITIGATES MATERNAL SEPARATION-INDUCED NEURODEVELOPMENTAL IMPAIRMENTS IN RATS

Keskin, U.; KARA, M. K.; Ozel, O.; Kuragi, C. C.; Akyol, S.; Ozbayer, C.; Senem-Ari, N.; Tunc, Y.; Bayir, E.

10.1101/2025.11.10.687583 — animal behavior and cognition — Posted on 2025-11-11

3472 Chromosome-level genome assemblies of Nicotiana attenuata and Nicotiana obtusifolia

Chakraborty, A.; Xu, S.

10.1101/2025.11.10.687602 — genomics — Posted on 2025-11-11

3473 Transcriptomic analysis of cells following decreased mitochondrial DNA-copy number reveals compensatory mechanisms in mitochondrial DNA replication and cellular energetics

Xie, J.; Win, P. W.; Newcomb, C. E.; Zeng, S.; Castellani, C. A.; Arking, D.

10.1101/2025.11.10.687605 — genetics — Posted on 2025-11-11

3474 On the variation of structural divergence among residues in enzyme evolution

Echave, J.; Carpentier, M.

10.1101/2024.12.23.629899 — evolutionary biology — Posted on 2025-11-11

3475 Can evolutionary potential help plants survive climate change? High variability in evolvability and G-matrix structure of Hypericum populations

Mattila, A. L. K.; Hyvaerinen, M.-T.; Haellfors, M. H.; Koivusaari, S. H. M.; Moeller, C.; Pietikaeinen, L.; Opedal, O. H.

10.1101/2025.11.10.687560 — evolutionary biology — Posted on 2025-11-11

3476 Normative assembly rule reveals fairness in microbial communities

Kuosmanen, T.; Rantanen, J.; Kiciatovas, D.; Pausio, S.; Friman, V. P.; Hiltunen, T.; Mustonen, V.

10.1101/2025.11.10.687608 — ecology — Posted on 2025-11-11

3477 TGFβ-dependent upregulation of OCIAD2 is essential for epithelial-to-mesenchymal transition during mesendoderm differentiation

Kamat, K.; Inamdar, M. S.

10.1101/2025.11.10.687537 — developmental biology — Posted on 2025-11-11

3478 Enabling regiospecific di-halogenation in one-pot reactions using an engineered single-component flavin-dependent tryptophan halogenase

Li, H.; Huang, J.-W.; Dai, S.; Feng, D.; Liu, J.; Zhang, N.; Guo, Y.; Chen, C.-C.; Guo, R.-T.

10.1101/2025.11.10.687318 — molecular biology — Posted on 2025-11-11

3479 Modulation of Neutrophil Function by Foetal Bovine Serum and Type I Collagen

Bektas, E. I.; Fan, J.; Miklosic, G.; Wychowaniec, J. K.; Jahed, V.; Klavins, K.; D'Este, M.

10.1101/2025.11.10.687474 — immunology — Posted on 2025-11-11

3480 Dual human lung models reveal compartment-specific activity of anti-tuberculosis drugs and host-directed therapies

10.1101/2025.11.10.685269 — immunology — Posted on 2025-11-11

3481 High Precision Peptide-MHC Class I CARs Enhance In Vivo Killing ofTargeted CD8 T Cells to Prevent Type 1 Diabetes in Novel RIP-mOVA Model

Francis, M. P.; Hibler, W.; Yarnell, M.; Singh, N.; Kedl, R. P.; Burchill, M. A.; Fry, T.; Nakayama, M.

10.1101/2025.11.10.687586 — immunology — Posted on 2025-11-11

3482 The cerebellar components of the human language network

Casto, C.; Poliak, M.; Tuckute, G.; Small, H.; Sherlock, P.; Wolna, A.; Lipkin, B.; D'Mello, A. M.; Fedorenko, E.

10.1101/2025.04.14.645351 — neuroscience — Posted on 2025-11-11

3483 Anticipatory modulation as a unifying principle of sensory coding during locomotion

Gant, J. M.; Mlynarski, W. F.

10.1101/2025.06.29.662230 — neuroscience — Posted on 2025-11-11

3484 Quantum Holographic Dynamics in the Brain's Proton Spin Ensemble

Kerskens, C.

10.1101/2025.11.10.687594 — neuroscience — Posted on 2025-11-11

3485 On Temporal Robustness & Brain-State Stability of Functional Connectivity in Mouse Primary Visual Area V1 compared to Higher Visual Area AL

Savaglio, M. A.; Brozi, C.; Smirnakis, S. M.; Papadopouli, M.

10.1101/2025.11.10.687557 — neuroscience — Posted on 2025-11-11

3486 Circadian timing does not modulate human chromatic temporal contrast sensitivity

Heinrichs, H. S.; Spitschan, M.

10.1101/2025.11.10.687546 — neuroscience — Posted on 2025-11-11

3487 Photoreceptor-specific scene statistics reveal melanopic structure in natural environments

Tabandeh, N.; Spitschan, M.

10.1101/2025.11.10.687567 — neuroscience — Posted on 2025-11-11

3488 Transcranial ultrasound stimulation induces white matter plasticity in the human corticospinal tract

Curtin, D.; Walinjkar, J.; Fouragnan, E. F.; Hendrikse, J. J.; Coxon, J. P.

10.1101/2025.11.10.687582 — neuroscience — Posted on 2025-11-11

3489 Scalable imaging-based profiling of CRISPR perturbations with protein barcodes

Choudhary, K.; McManus, M. T.

10.1101/2025.11.11.687767 — systems biology — Posted on 2025-11-11

3490 Adenosine-specific transcriptional programs in murine connective tissue type mast cells

Liang, Q.; Tsvilovskyy, V.; Belkacemi, A.; Bukva, M.; Richter, C.; Ludwig, N.; Keller, A.; Freichel, M.

10.1101/2025.11.10.687562 — pharmacology and toxicology — Posted on 2025-11-11

3491 Image Analysis for Non-Neoplastic Kidney Disease: Utilizing Morphological Segmentation to Improve Quantification of Interstitial Fibrosis

Mola, N.; Maya Barbosa Silva, M.; Leh, S.; Weishaupt, H.

10.1101/2025.11.10.686700 — pathology — Posted on 2025-11-11

3492 Deep single-cell immune and signaling profiles predict long term therapy response in chronic myeloid leukemia within hours

Gullaksen, S.-E.; Brevik, M.; Sefland, O.; Craig, E.; Hellesoy, M.; Olsson-Strömberg, U.; Stentoft, J.; Richter, J.; Gedde-Dahl, T.; Tibshirani, R.; Plevritis, S.; Wolf, D.; Mustjoki, S.; Hjorth-Hansen, H.; Gjertsen, B. T.

10.1101/2025.11.10.687542 — cancer biology — Posted on 2025-11-11

3493 Prior to Undergoing Epithelial to Mesenchymal Transition, Premalignant Cells Transiently Increase Tensile Forces at Cell-Cell and Cell-Matrix Adhesions

Faria, L.; Goncalves, C. M.; Fidalgo, I.; Lopes, C. S.; Rodrigues, V.; Azevedo, M. M.; Sampaio, P.; Tavares, S.; Mahajan, V.; Taubenberger, A.; Janody, F.

10.1101/2025.07.05.663275 — cancer biology — Posted on 2025-11-11

3494 Coupling of Lipid Phase Behavior and Protein Oligomerization in a Lattice Model of Raft Membranes

Basu, S.; Farago, O.

10.1101/2025.11.10.687571 — biophysics — Posted on 2025-11-11

3495 Two-Step Mechanism of Bruton's Tyrosine Kinase MembraneRecruitment and Activation

McAllister, R.; Stiegler, A.; Chari, K.; Chari, M.; Bhattacharyya, M.; Gupta, K.

10.1101/2025.10.28.685231 — biophysics — Posted on 2025-11-11

3496 LSTM-Attention-Guided Graph Neural Networks for Integrated Genotype-Environment Modeling in Maize Yield Prediction

Morshedian, A.; Domaratzki, M.

10.1101/2025.11.09.687529 — bioinformatics — Posted on 2025-11-11

3497 Cellohood: multi-granular discovery of cellular neighborhoods with a permutation-invariant set transformer auto-encoder

Mozejko, M.; Schulz, D.; Gogolewski, K.; Eling, N.; Krawczyk, J.; Bogatyrova, O.; Golab, J.; Nowis, D.; Liechti, R.; Morfouace, M.; Hong, H.; Bodenmiller, B.; Staub, E.; Szczurek, E.

10.1101/2025.11.10.687184 — bioinformatics — Posted on 2025-11-11

3498 A Rapid and High-Sensitivity Non-radioactive Screening Assay for Insulin Receptor Ligands

Stanurova, J.; Cermakova, K.; Just, D.; Jahn, U.; Fabre, B.; Rozkovec, E.; Zakova, L.; Sacha, P.; Jiracek, J.; Konvalinka, J.

10.1101/2025.03.20.644157 — biochemistry — Posted on 2025-11-11

3499 CODABEILLES: A Reliable Reference Library of COI DNA Barcodes for French Wild Bees Monitoring (Apoidea: Anthophila)

Ollivier, M.; Marquisseau, A.; Dufrene, E.; Rudelle, R.; The CODABEILLES Consortium, ; Rougerie, R.; Perrard, A.; Pichon, M.

10.1101/2025.11.10.687545 — ecology — Posted on 2025-11-11

3500 A Conserved Mechanism in Eye Optical Development: Lens Nucleus Centralization in Xenopus laevis

Garcia, K. A.; Tseng, K.; Vorontsova, I.

10.1101/2025.11.09.687506 — developmental biology — Posted on 2025-11-11

3501 Dosage-sensitive RBFOX2 autoregulation promotes cardiomyocyte differentiation by maturing the transcriptome

Huang, M.; Ladha, F. A.; Wang, Y.; Trembley, M. A.; Yin, H.-M.; Zheng, R.; Prondzynski, M.; Tharani, Y.; Akerberg, A. A.; Aigner, S.; Yee, B. A.; Mayourian, J.; Morton, S. U.; Bezzerides, V. J.; Pu, W. T.; Yeo, G. W.; Chen, K.; Burns, C. G.; Burns, C. E.

10.1101/2025.10.28.685214 — developmental biology — Posted on 2025-11-11

3502 Pre-cheliceral region patterning in a spider provides new insights into the development and evolution of arthropod neurosecretory centres

Harper, A.; Sumner-Rooney, L.; Janssen, R.; McGregor, A. P.

10.1101/2025.11.10.687188 — developmental biology — Posted on 2025-11-11

3503 Phylo-MIP: Phylogeny-based Molecular Identification Pipeline for DNA metabarcoding, and assessment of insect communities in subalpine river ecosystems

Yoshida, T.; Shigeta, S.; Hasebe, Y.; Takenaka, M.

10.1101/2025.11.10.687572 — molecular biology — Posted on 2025-11-11

3504 Mycobacterium tuberculosis growth arrest on propionate at acidic pH is suppressed by mutations in phoPR and pyrazinamide treatment

Murdoch, H. M.; Dechow, S. J.; Abdalla, B. J.; Abramovitch, R. B.

10.1101/2025.09.24.678100 — microbiology — Posted on 2025-11-11

3505 How to Improve the Reliability of Aperiodic Parameter Estimates in M/EEG: A Method Comparison and Recommendations for Best Practices

Kalamala, P.; Clements, G. M.; Gyurkovics, M.; Chen, T.; Low, K.; Fabiani, M.; Gratton, G.

10.1101/2025.11.10.687541 — neuroscience — Posted on 2025-11-11

3506 Physical determinants of perceived vibration intensity: Insights from haptic feedback given at the wrist

Bonnet, S.; Watkins, R.; Ericsson, R.; Daumas, H.; Ackerley, R.

10.1101/2025.11.10.687548 — neuroscience — Posted on 2025-11-11

3507 Toward precision EEG: Assessing the reliability of individual-level ERPs across EEG Systems

Korisky, A.; Rabinovitch, E.; Har-shai Yahav, P.; McCandliss, B.; Zion Golumbic, E.

10.1101/2025.11.10.687573 — neuroscience — Posted on 2025-11-11

3508 Crosstalk of noradrenergic Ca2+ and cAMP signaling in astrocytes of the murine olfactory bulb

Sauer, J.; Beiersdorfer, A.; Schmidt, F. L.; Nordbeck, M.; Constantin, O.; Hirnet, D.; Gee, C. E.; Lohr, C.

10.1101/2025.11.10.687535 — neuroscience — Posted on 2025-11-11

3509 The role of the glutamate-glutamine cycle in synaptic transmission during ischemia and recovery

van Susteren, H.; Rose, C. R.; van Putten, M. J. A. M.; Meijer, H. G. E.

10.1101/2025.11.10.687543 — neuroscience — Posted on 2025-11-11

3510 Hippocampal indexing alters the stability landscape of synaptic weight space allowing life-long learning

Gonzalez, O. C.; Golden, R.; Delanois, J. E.; McNaughton, B. L.; Bazhenov, M.

10.1101/2025.11.10.687549 — neuroscience — Posted on 2025-11-11

3511 Predatory orienting is jointly controlled by optic tectum and pretectum.

Antinucci, P.; Colinas-Fischer, S.; Bianco, I. H.

10.1101/2025.11.10.687578 — neuroscience — Posted on 2025-11-11

3512 A neural circuit for rapid control of hunger by arousal.

Kosar, S.; Bracey, E.; Du, Y.; Peleg-Raibstein, D.; Burdakov, D.

10.1101/2025.03.07.642010 — neuroscience — Posted on 2025-11-11

3513 QuNex Recipes: Executable, Human-Readable Workflows for Reproducible Neuroimaging Research

Demsar, J.; Kraljic, A.; Matkovic, A.; Brege, S.; Pan, L.; Tamayo, Z.; Fonteneau, C.; Helmer, M.; Ji, J. L.; Anticevic, A.; Korponay, C.; Salavrakos, M.; Glasser, M. F.; Nickerson, L. D.; Cho, Y. T.; Repovs, G.

10.1101/2025.11.08.687330 — neuroscience — Posted on 2025-11-11

3514 High protein diets early in life improve survival, reduce cannibalism, and increase growth and yield in farmed yellow mealworms

Dobrowolski, N.; Perl, C. D.; Brumfield, J.; Christie, J.; Rodriguez-Guevara, R.; Durosaro, S. O.; Barrett, M.

10.1101/2025.11.09.687235 — zoology — Posted on 2025-11-11

3515 TEIP: A Compact, Open-Source Framework for Predicting Tumor Epitope Immunogenicity in Glioblastoma Cancer Using Deep Learning and Multi-Modal Biological Features

Shekhar, A.

10.1101/2025.11.09.687510 — cancer biology — Posted on 2025-11-11

3516 Pseudogene co-expression networks reveal a robust prognostic signature of survival in pediatric B-ALL

Nakamura-Garcia, A. K.; Kuijjer, M. L.; Espinal-Enriquez, J.

10.1101/2025.03.14.643224 — cancer biology — Posted on 2025-11-11

3517 Pharmacological Modulation of TRIB2 Stability in Melanoma Reveals CDK12/13 as Dominant Regulators and Potential Therapeutic Targets

Mayoral-Varo, V.; Orea-Soufi, A.; Jimenez, L.; Santos, B.; Amenabar, C.; Kyriakou, P.; Serrao, G.; Jociles, M.; Obeso, S.; Garnes-Garcia, C.; Fernandez-Aroca, P.; Sanchez-Prieto, R. s.; Ferreira, B.; Link, W.

10.1101/2024.07.17.603886 — cancer biology — Posted on 2025-11-11

3518 Prediction of lncRNA-protein interacting pairs using LLM embeddings based on evolutionary information

Choudhury, S.; Bajiya, N.; Raghava, G. P. S.

10.1101/2025.11.10.687101 — bioinformatics — Posted on 2025-11-11

3519 AstraBIND: Graph Attention Network for Predicting Ligand Binding Sites

Goteti, A.; Bozkurt, C.; Vasilyeva, A.

10.1101/2025.11.10.687555 — bioinformatics — Posted on 2025-11-11

3520 GeneSNAKE: a Python package for benchmarking and simulation of gene regulatory networks and perturbation-induced expression data

Hillerton, T.; Bjork, A.; Lundqvist, N.; Zhivkoplias, E.; Garbulowski, M.; Sonnhammer, E. L. L.

10.1101/2025.11.10.685583 — bioinformatics — Posted on 2025-11-11

3521 Overcoming Extrapolation Challenges of Deep Learning by Incorporating Physics in Protein Sequence-Function Modeling

Barethiya, S.; Huang, J.; Liu, X.; Guan, H.; Chen, J.

10.1101/2025.11.09.687530 — bioinformatics — Posted on 2025-11-11

3522 OpEnHiMR: Optimization based Ensemble Model for Prediction of Histone Modification in Rice

Sinha, D.; Murmu, S.; Sarkar, A.; Yeasin, M.; Bhattacharjee, S.; Chaurasia, H.; Mishra, D. C.; Budhlakoti, N.; Srivastava, S.; Archak, S.; Kumari, A.; Jha, G. K.

10.1101/2025.11.10.687509 — bioinformatics — Posted on 2025-11-11

3523 Biocompatibility assessment of SilkMA-Gelatin ink tuned for 3D extrusion bioprinting

Agarwal, P.; Singh Sandhu, J.; Bhatt, H. K.; Das, P.; Seetharam, R. N.; S Vasanathan, K.

10.1101/2025.11.09.687334 — bioengineering — Posted on 2025-11-11

3524 Differential Tissue Coupled Powering for Battery-Free Injectable Electroceuticals

Wu, H.; Mahmud, S.; Halac, M.; Baez, D.; Dados, J.; Cheng, C.; Omi, A. I.; Jiang, A.; Wallace, C.; Singh, A.; Patrick, E.; Chatterjee, B.; Srinivasan, S.; Khalifa, A.

10.1101/2025.11.09.687502 — bioengineering — Posted on 2025-11-11

3525 Pan-cancer analysis reveals context-dependent roles of LINE-1 ORF1p in immune regulation and copy number alterations

Kaparos, E. I.; Zhang, W.; Miyanaga, R.; McKerrow, W.; Boeke, J. D.; Davoli, T.; Mita, P.; Ruggles, K. V.; Fenyo, D.

10.1101/2025.10.03.680361 — genomics — Posted on 2025-11-11

3526 jsdmstan: An R package for fitting joint species distribution models in Stan

Seaton, F. M.

10.1101/2025.11.10.687559 — ecology — Posted on 2025-11-11

3527 Hox - Meis-relayed topographical genetic switch underlies cardiopharyngeal neural crest diversification, revealed by multimodal analysis

Iwase, A.; Uchijima, Y.; Seya, D.; Kida, M.; Higashiyama, H.; Matsui, K.; Taguchi, A.; Harada, Y.; Yunce, W.; Yamamoto, S.; Fukuda, S.; Nomura, S.; Kohro, T.; Shukunami, C.; Akiyama, H.; Seki, M.; Kanai, A.; Suzuki, Y.; Kawamura, T.; Nakagawa, O.; Katoh, H.; Ishikawa, S.; Wada, Y.; Aburatani, H.; Kurihara, Y.; Miyagawa-Tomita, S.; Kurihara, H.

10.1101/2025.11.09.687497 — developmental biology — Posted on 2025-11-11

3528 Anticipatory Capture of Circulating Peptidergic Vesicles in a Clock Neuron

Klose, M. K.; Kim, J.; Schmidt, B. F.; Deitcher, D. L.; Levitan, E.

10.1101/2025.10.22.684038 — cell biology — Posted on 2025-11-11

3529 USP-ddG: A Unified Structural Paradigm with Data Efficacy and Mixture-of-Experts for Predicting Mutational Effects on Protein-Protein Interactions

Yu, G.; bi, x.; zhao, q.; Wang, J.

10.1101/2025.11.09.687124 — molecular biology — Posted on 2025-11-11

3530 A Quantitative Design Guideline for Biomolecular Positive Feedback Systems

KUMAR, V.; Sen, S.

10.1101/2025.11.09.687517 — systems biology — Posted on 2025-11-11

3531 Computational Cellular Programming: In Silico Modeling of Direct and Reprogrammed Hepatic Lineage Induction via Gene Regulatory and Functional Dynamics

Panchagnula, S. D. K.; Jonnala, P.

10.1101/2025.11.09.687523 — systems biology — Posted on 2025-11-11

3532 A common cross-species atlas of cortical gray matter

Venkadesh, S.; Tian, Y.; Linn, W.-J.; Martinez, J. B.; Mansour, H.; Cook, J.; Schaeffer, D. J.; Szczupak, D.; Silva, A. C.; Johnson, G. A.; Yeh, F.-c.

10.1101/2025.09.08.675002 — neuroscience — Posted on 2025-11-11

3533 Powerful read processing with matchbox

Schuster, J.; Zeglinski, K.; Xiao, L. C.; Voulgaris, O.; Rivera, S. M.; Vervoort, S. J.; Ritchie, M. E.; Gouil, Q.; Clark, M. B.

10.1101/2025.11.09.685711 — bioinformatics — Posted on 2025-11-11

3534 Parsing auditory neural code into maximum-entropy packets

Zhang, H.; Nelken, I.; Sharpee, T.

10.1101/2025.11.09.687481 — neuroscience — Posted on 2025-11-11

3535 Variability in the effects of transcranial direct current stimulation on free choice behaviour

Caie, B.; Blohm, G.

10.1101/2024.08.23.609379 — neuroscience — Posted on 2025-11-11

3536 Optimizing cytochrome P450 activity for quillaic acid biosynthesis in Saccharomyces cerevisiae

Han, Y.; Coe, L.; Voss, J. D.; Ebert, B. E.

10.1101/2025.11.09.685466 — synthetic biology — Posted on 2025-11-11

3537 Impact of Slow Wave Abnormalities and Impaired Coordination of Pyloric Closure and Antral Contraction on Gastric Emptying: A Compartmental Modeling Study

Fernandes, S. Q.; Kothare, M. V.; Sclocco, R.; Mahmoudi, B.

10.1101/2025.11.09.687391 — biophysics — Posted on 2025-11-11

3538 OS2CR-Diff: A Self-Refining Diffusion Framework for CD8 Imputation from One-Step Inference to Conditional Representation

Li, X.; Rana, P.; Gide, T. N.; Adegoke, N.; Mao, Y.; Wilmott, J.; Liu, S.

10.1101/2025.11.09.687488 — bioinformatics — Posted on 2025-11-11

3539 AutoMorphoTrack: A modular framework for quantitative analysis of organelle morphology, motility, and interactions at single-cell resolution

Bayati, A.; Schumacher, J. G.; Chen, X.

10.1101/2025.07.19.665650 — neuroscience — Posted on 2025-11-11

3540 Biophysical Basis of the in vivo ERG of the Mouse: Rod, RPE and Müller glial Cell Contributions To Dark and to Light-driven Changes in Sub-Retinal Space o

Peinado Allina, G.; Alexander, P. C.; Ronning, K.; Burns, M. E.; Pugh, E. N.

10.1101/2025.11.09.687427 — biophysics — Posted on 2025-11-11

3541 A Computational Pipeline for Stratifying Autoimmune Patients Using Binary Antibody Data

Zhuang, N. Z.; Howells, J. M.

10.1101/2025.09.11.670596 — bioinformatics — Posted on 2025-11-11

3542 Looking for Details: Fine-Grained Visual Search at the Foveal Scale

Poletti, M.; Kapisthalam, S.

10.1101/2025.11.09.687480 — neuroscience — Posted on 2025-11-11

3543 HyperBind2: Multi-Shot Learning Enables Progressive Improvement in Computational Antibody Discovery

Dell'uomo, D.; Satz, A.; Averso, B.

10.1101/2025.11.06.687005 — bioengineering — Posted on 2025-11-11

3544 Neutral pH Plasma-Activated Water eliminates ESKAPE pathogens via reactive nitrogen species with dual potential for surface sanitation and wound cleansing

Mukherjee, D.; Roy Chowdhury, A.; Ghosh, P.; Vishwa, N.; Rao, L.; Chakravortty, D.

10.1101/2024.10.06.616848 — bioengineering — Posted on 2025-11-11

3545 Synthesis of Cyclopropene-Modified Fatty Acids Allows Single Cell Quantification of Uptake By Immune Cells

Reinalda, L.; Heieis, G.; Torres-Garcia, D.; el Boujadayni, M.; Steuten, K.; Bertheussen, K.; Bogue, L. I.; Punt, J. M.; Driever, W. P. F.; Corrigan, C.; Wang, X.; Everts, B.; Finlay, D. K.; van der Stelt, M.; Van Kasteren, S. I.

10.1101/2025.07.11.664320 — biochemistry — Posted on 2025-11-11

3546 Emergent self-inhibition governs the landscape of stable states in complex ecosystems

Patro, N. K.; Taylor, W.; Goyal, A.

10.1101/2025.11.09.687513 — ecology — Posted on 2025-11-11

3547 Consistent covariation of dispersal, life history and thermal niches across terrestrial arthropods

Logghe, G.; Batsleer, F.; Fandos, G.; Maes, D.; Bonte, D.

10.1101/2025.01.10.632369 — ecology — Posted on 2025-11-11

3548 Spreading alpha-Synuclein Oligomers Trigger Astrocyte Changes and Astrocyte-Glutamatergic Neuron system dysfunction in an Age-related Manner

LeeBae, J.; Bopp, V.; Goreth, A.; Grozdanov, V.; Kuehlwein, J. K.; Gazzola, E.; Rombach, D.; Meier, L.; Dimou, L.; Danzer, K. M.

10.1101/2025.08.08.669249 — neuroscience — Posted on 2025-11-11

3549 Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications

Cieslak, M.; Irfanoglu, M. O.; Meisler, S. L.; Salo, T.; Raikes, A. C.; Cook, P. A.; Chung, A. W.; Lee, E. G.; Li, R.; Li, X.; Pecheva, D.; Fair, D. A.; Smyser, C. D.; Harms, M. P.; Landman, B. A.; Wisnowski, J. L.; Huang, H.; Alexander, A. L.; Satterthwaite, T. D.

10.1101/2025.11.10.687672 — neuroscience — Posted on 2025-11-11

3550 Peripheral modulation of Pumilio in intestinal stem cells and the corpus allatum affects sleep latency in Drosophila

Rodriguez-Cordero, J. A.; Dorta-Aviles, M.; Rodriguez-Fernandez, I. A.; Ghezzi, A.; Lizardi-Ortiz, J. E.; Agosto-Rivera, J. L.

10.1101/2025.11.09.687465 — neuroscience — Posted on 2025-11-11

3551 High protein diets early in life improve survival, reduce cannibalism, and increase growth and yield in farmed yellow mealworms

Dobrowlowski, N.; Perl, C. D.; Brumfield, J.; Christie, J.; Rodriguez-Guevara, R.; Durosaro, S. O.; Barrett, M.

10.1101/2025.11.09.687235 — zoology — Posted on 2025-11-11

3552 Scalable imaging-based profiling of CRISPR perturbations with protein barcodes

Choudhary, K.; McManus, M.

10.1101/2025.11.11.687767 — systems biology — Posted on 2025-11-11

3553 Inhibition of bladder cancer cell proliferation by 2-deoxy-D-glucose: A potential therapeutic approach

Taoka, R.

10.1101/2025.11.09.687468 — cancer biology — Posted on 2025-11-11

3554 An evolutionary approach to predict the orientation of CRISPR arrays

Fehrenbach, A.; Mitrofanov, A.; Alkhnbashi, O.; Backofen, R.; Baumdicker, F.

10.1101/2025.05.09.653049 — bioinformatics — Posted on 2025-11-11

3555 Spillover of H5 influenza viruses to vampire bats at the marine-terrestrial interface

Tu, I.-T.; Lynggaard, C.; Adams, L.; Walsh, S. K.; Chen, H.; Raveendran, S.; Turnbull, M. L.; Griffiths, M. E.; Ribeiro, R.; Perez, J. G.; Bazan, W. V.; Tello, C.; Zariquiey, C.; Rodriguez, K. P.; Risco, M.; Mamani, I. Q.; Chavez, W.; Villafuerte, R. Z.; Manuttupa, J. C.; Castro Namuche, J. P.; Moreira-Soto, A.; Drexler, J. F.; Delhon, G.; Faust, C.; Cardenas-Alayza, S.; Hutchinson, E.; Murcia, P. R.; Palmarini, M.; Bohmann, K.; Harvey, R.; Streicker, D. G.

10.1101/2025.11.09.686930 — ecology — Posted on 2025-11-11

3556 High co-occurrence of invasive wetland plants and species at risk in Canada's biodiverse Carolinian

Watkinson, A. D.; Carscadden, C.; Rooney, R. C.

10.1101/2025.11.09.687476 — ecology — Posted on 2025-11-11

3557 Inflammatory Agonists Modulate the Host Response to Type 2 ECM scaffold Immune Environment and Long-Term Remodeling After Severe Traumatic Injury

Li, W.; Baurceanu, I.; Pal, S.; Chaudhari, R.; Kimmel, A. E.; Wolf, M.

10.1101/2025.11.09.687444 — immunology — Posted on 2025-11-11

3558 Hidden Literacy in Minimally Verbal Autistic Individuals Revealed by Eye Gaze

Ellert, K.; Sykes-Haas, H. S.; Shefer-Kaufmann, N.; Bonneh, Y. S.

10.1101/2025.11.09.687411 — neuroscience — Posted on 2025-11-11

3559 Phase-Dependent EEG Decoding of Continuous Visual Stimuli

Deodato, M.; Melcher, D.

10.1101/2025.11.10.687532 — neuroscience — Posted on 2025-11-11

3560 Antirrhinum flower shape: unravelling gene expression across developmental axes and boundaries

Cunha, A. M.; Raimundo, J.; Verweij, A.; Bradley, D.; Coen, E.; Costa, M. M. R.

10.1101/2025.11.10.687484 — plant biology — Posted on 2025-11-11

3561 Epigenetic gene regulation is controlled by distinct regulatory complexes utilizing specialized paralogs of TELOMERE REPEAT BINDING FACTORS

Mendler, M.; Krause, K.; Zuendorf, S.; Sannak, P.; Taenzler, P.; Stolze, S. C.; Nakagami, H.; Turck, F. K.

10.1101/2025.11.10.687574 — plant biology — Posted on 2025-11-11

3562 Introduction of regioselective bacterial heme oxygenases into Arabidopsis hy1-1 supports the retrograde heme signaling hypothesis

Takenoya, M.; Shimizu, T.; Miyake, K.; Masuda, T.

10.1101/2025.11.09.686882 — plant biology — Posted on 2025-11-11

3563 The EGY1-SGR1 module controls chloroplast development and senescence by modulating photosynthetic functions

Shapiguzov, A.; Trotta, A.; Mancini, I.; Hani, U.; Sultana, N.; Vahisalu, T.; Waszczak, C.; Aro, E.-M.; Brosche, M.

10.1101/2025.11.10.687641 — plant biology — Posted on 2025-11-11

3564 Glassy dynamics in active epithelia emerge from an interplay of mechanochemical feedback and crowding.

Muthukrishnan, S.; Dewan, P.; Tejaswi, T.; Sebastian, M. B.; Chhabra, T.; Mondal, S.; Kolya, S.; Sarkar, S.; Vishwakarma, M.

10.1101/2025.11.08.687351 — biophysics — Posted on 2025-11-11

3565 Leveraging Disease Association Degree for High-Accuracy MicroRNA Target Prediction

Chen, B.

10.1101/2025.11.06.686936 — bioinformatics — Posted on 2025-11-11

3566 Predicting microbial transcriptome using annotated genome sequence

FU, G.; YAN, Y.; ZHAO, Z.; CHEN, Y.; SHAO, B.

10.1101/2024.12.30.630741 — bioinformatics — Posted on 2025-11-11

3567 Methyl-CpG Binding Protein 2 Reads Histone Methylation via an Aromatic Cage to Regulate Gene Expression and Chromatin Association

Padhan, J.; Sudhamalla, B.

10.1101/2025.05.10.653294 — biochemistry — Posted on 2025-11-11

3568 The deubiquitinating enzyme Otu1 releases substrates from the conserved initiation complex of the Cdc48/p97 ATPase for proteasomal degradation

Li, H.; Guan, H.; Rapoport, T.

10.1101/2025.11.08.687396 — biochemistry — Posted on 2025-11-11

3569 PyMSQ: a python package for fast Mendelian sampling (co)variance and haplotype-based similarity in genomic selection

Musa, A. A.; Reinsch, N.

10.1101/2025.10.14.682303 — genetics — Posted on 2025-11-11

3570 Activation of latent programs for maternal behavior

Streit Morsch, E.; Amadei, E. A.; Boehringer, R.; Grewe, B. F.; Vilimelis Aceituno, P.

10.1101/2025.11.05.686743 — animal behavior and cognition — Posted on 2025-11-11

3571 DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage

Angeloni, A.; Hammond, J. M.; Peters, T. J.; Reis, A. L. M.; Kemp, L.; Amos, T.; Gamaarachchi, H.; Humphries, S.; Wilmott, L. A.; Pal, S.; Masamsetti, V. P.; Weatherstone, M.; Ip, K. C. K.; Pazaky, K.; Steel, A.; Lyons, R.; Walters, E. D.; Liu, N.; Tam, P.; Polo, J. M.; Waters, P. D.; Clark, S. J.; Richards, L. J.; Smith, A. D.; Lee, H.; Deveson, I. W.; Griffith, O. W.; Skvortsova, K.

10.1101/2025.11.09.686659 — developmental biology — Posted on 2025-11-11

3572 Learning-dependent cholinergic plasticity reconfigures cortical circuit dynamics.

Moberly, A.; Cardin, J. A.; Higley, M.

10.1101/2025.11.10.687664 — neuroscience — Posted on 2025-11-11

3573 Deviation from typical brain activity during naturalistic stimulation is related to personality traits

Jajcay, L.; Tomecek, D.; Androvicova, R.; Fajnerova, I.; Dechterenko, F.; Rydlo, J.; Tintera, J.; Lukavsky, J.; Horacek, J.; Hlinka, J.

10.1101/2024.04.23.586759 — neuroscience — Posted on 2025-11-11

3574 Insertion of an invading retrovirus regulates a novel color trait in swordtail fish

Haghani, N.; Dodge, T. O.; Baczenas, J. J.; Gunn, T.; He, Q.; Pangburn, W.; Sood, R.; Du, K.; Fascinetto-Zago, P.; Kaatmann, A.; Ou, Z.; Dougan, S.; Olmos-Santiago, N. S.; Preising, G. A.; Payne, C. Y.; Haase Cox, S. K.; Hunnicutt, K. E.; Madrzyk, M.; Moran, B. M.; Stigloher, C.; Powell, D. L.; Schartl, M.; Gifford, C.; Han, G. z.; Schumer, M.

10.1101/2025.11.07.687308 — evolutionary biology — Posted on 2025-11-11

3575 Structure-informed evolutionary analysis of the meiotic recombination machinery

Arter, M.; Vedanayagam, J.; Lu, M.; Diop, M.; Liu, K.; Lai, E. C.; Keeney, S.

10.1101/2025.11.07.687317 — evolutionary biology — Posted on 2025-11-11

3576 Twist and Scout: Analysis and Curation of Particles in Cryo-Electron Tomography Using TANGO

Schreiber, M.; Turonova, B.

10.1101/2025.07.17.665296 — molecular biology — Posted on 2025-11-11

3577 Fern and gymnosperm SPCH/MUTE and FAMA can regulate multiple cell fate transitions during stomatal development

Iida, M.; Elhazzime, K.; Vaten, A.

10.1101/2025.11.10.687565 — plant biology — Posted on 2025-11-11

3578 Nodal analysis of the human brain networks - a new way to couple function and structure

Sairanen, V.

10.1101/2024.03.03.583186 — neuroscience — Posted on 2025-11-11

3579 Clustering of Direct and Indirect DNA Binding Motifs of Human and Mouse Transcription Factors: X-TFBS Compendium from ChIP-seq

Sharov, A. A.

10.1101/2025.11.09.687492 — bioinformatics — Posted on 2025-11-11

3580 A lettuce receptor-like kinase recognizes the highly conserved heptapeptide motif within microbial NEP1-like proteins

Banales, I.; Mehrem, S. L.; Almeida Landman, S.; Alderkamp, M.; Pijfers, L. C. P. M.; Baijens, S.; von Bredow, A.; Schutte, P.; Prevoo, S.; Hans van Asselt, G.; Sagayaradj, S.; Snoek, B. L.; Michelmore, R.; Lapin, D.; Van den Ackerveken, G.

10.1101/2025.11.10.687460 — plant biology — Posted on 2025-11-11

3581 Antagonism between blue and red light-signalling controls thallus flatness in Marchantia polymorpha

Roetzer, J.; Asper, B.; Meir, Z.; Edelbacher, N.; Merai, Z.; Datta, S.; Dolan, L.

10.1101/2025.11.10.687525 — plant biology — Posted on 2025-11-11

3582 Polyclonal origins of human premalignant colorectal lesions

Van Egeren, D.; Schenck, R. O.; Khan, A.; Horning, A. M.; Mo, S.; Weiss, C. L.; Esplin, E. D.; Becker, W. R.; Wu, S.; Hanson, C.; Barapour, N.; Jiang, L.; Contrepois, K.; Lee, H.; Nevins, S. A.; Guha, T. K.; Zhang, H.; He, Z.; Ma, Z.; Monte, E.; Karathanos, T. V.; Laquindanum, R.; Mills, M. A.; Chaib, H.; Chiu, R.; Jiang, R.; Chan, J.; Ellenberger, M.; Bahmani, B.; Michael, B.; Weimer, A. K.; Esplin, D. G.; Lancaster, S.; Shen, J.; Ladabaum, U.; Longacre, T. A.; Kundaje, A.; Greenleaf, W. J.; Hu, Z.; Ford, J. M.; Snyder, M. P.; Curtis, C.

10.1101/2025.09.08.674484 — cancer biology — Posted on 2025-11-11

3583 Combinatorial inhibition of LSD1 and Menin induces therapeutic differentiation in AML

Carrera Rodriguez, M. F.; Rico, J.; Vijayaraghavan, M.; Yang, F.; King, A.; Petroni, R.; Leu, N. A.; Goodrow, H.; Bernt, K.; McGeehan, G.; Blanco, M. A.

10.1101/2025.11.09.687496 — cancer biology — Posted on 2025-11-11

3584 Extrinsic biological stochasticity and technical noise normalization of single-cell RNA sequencing data

Fang, M.; Pachter, L.

10.1101/2025.05.11.653373 — bioinformatics — Posted on 2025-11-11

3585 Revisiting the evidence for long-lived balancing selection in humans.

Munby, H.; Przeworski, M.

10.1101/2025.11.10.687682 — evolutionary biology — Posted on 2025-11-11

3586 Trehalose-mediated activation of Mitf corrects autophagy defects and ameliorates neurodegeneration in MPS VII

Das, A.; Datta, R.

10.1101/2025.11.10.687576 — cell biology — Posted on 2025-11-11

3587 Lgr5+ Stem Cells Maintain Apex Position in Cell Hierarchy of the Intestinal Epithelium During Homeostasis and Injury

Chua, J.; Driver, L.; Narimatsu, M.; Fink, M.; Luo, L.; Tran, J.; Kaur, A.; Habib, R.; Roper, J.; G. Kirsch, D.; L. Wrana, J.; Lee, C.-L.; Ayyaz, A.

10.1101/2025.11.09.687498 — cell biology — Posted on 2025-11-11

3588 The anti-retroviral therapy emtricitabine affects skeletal muscle DNA methylation and transcriptome patterns in a male HIV mouse model

Tripathi, A.; Sultana, S.; Bensreti, H.; Chen, J.; Paul, A.; Shi, H.; Anand, A.; Mendhe, B.; Yu, K.; Long, W.; MacArthur, R.; Belin de Chantemele, E.; Hamrick, M. W.; McGee-Lawrence, M. E.

10.1101/2025.11.10.686758 — cell biology — Posted on 2025-11-11

3589 Independent validation of the SnxA biosensor as a sensitive reporter of PI(3,5)P2 dynamics

Swayhoover, T.; Weckerly, C.; Hammond, G. R.

10.1101/2025.11.10.687688 — cell biology — Posted on 2025-11-11

3590 Biological sex affects human islet gene expression and mitochondrial function in type 2 diabetes

Chen, S.-Y.; Cen, H. H.; Johnson, J. D.; Rideout, E. J.

10.1101/2025.11.10.687716 — cell biology — Posted on 2025-11-11

3591 Bioengineered 3D hPSC-cholangiocyte ducts with physiological signals for biliary disease modelling

Tian, B.; Ogawa, M.; Kondo, M.; Langeveld, G.; Huan, L. J.; Zhang, F.; Hollinger, A.; Deir, S.; Bear, C.; Zhang, B.; Ogawa, S.

10.1101/2025.11.10.686855 — cell biology — Posted on 2025-11-11

3592 Inhibiting epithelial cell extrusion and inflammation synergistically reverses asthmatic airway remodelling

Bagley, D. C.; Russell, T.; Martinez-Nunez, R. T.; Marcotti, S.; Rosenblatt, J.

10.1101/2025.11.10.687569 — cell biology — Posted on 2025-11-11

3593 Insights into the regulation of VPS13 family bridge-like lipid transfer proteins from the structure of VPS13C.

Li, D.; Wang, X.; Hu, B.; Hao, H.; Hamill, S.; Li, Y.; Chen, G.; De Camilli, P.; Reinisch, K.

10.1101/2025.11.10.687702 — cell biology — Posted on 2025-11-11

3594 From HeLa to human blood: extending single-cell proteomics to the smallest immune cells

Hendriks, I. A.; Buch-larsen, S. C.; Rykaer, M.; Lechner, M. Y.; Kverneland, A. H.; Arrey, T. N.; Hermanson, D.; Damoc, E.; Olsen, J. V.

10.1101/2025.11.10.687556 — cell biology — Posted on 2025-11-11

3595 Paradoxic enhancement of mitochondrial capacity in aging-specific megakaryopoiesis from hematopoietic stem cells

Chattopadhyaya, S.; Smith-Berdan, S.; Huerta, S.; Forsberg, C.

10.1101/2025.11.10.687744 — cell biology — Posted on 2025-11-11

3596 Control of mitotic spindle disassembly through SUMO-targeted ubiquitylation of yeast kinesin-5

Gaven, F.; Panigada, D.; Portran, D.; Liakopoulos, D.

10.1101/2025.11.10.687237 — cell biology — Posted on 2025-11-11

3597 RNA splicing is required for timely completion of abscission and is modulated by the abscission checkpoint

Couldwell, G. C.; Vincent-Mueller, J. N.; Mackay, D. R.; Jensen, C. C.; Stubben, C. J.; Li, L.; Tan, A. C.; Sundquist, W. I.; Ullman, K. S.

10.1101/2025.11.09.687034 — cell biology — Posted on 2025-11-11

3598 The blood proteome predicts the impact of circulating factors on age-related mitochondrial health

Heimler, S. R.; Bergstrom, J.; Sun, N. S.; Tanaka, T.; Moore, A. Z.; Candia, J.; Chen, B. H.; Tian, Q.; Bektas, A.; Fantoni, G.; Dunn, C.; Kaileh, M.; Sen, R.; Ferrucci, L.; Molina, A. J. A.

10.1101/2025.11.09.687483 — cell biology — Posted on 2025-11-11

3599 Syntaxin11 Deficiency Inhibits CRAC Channel Priming To Suppress Cytotoxicity And Gene Expression In FHLH4 Patient T Lymphocytes.

Datta, S.; Gupta, A.; Jagetiya, K. M.; Yande, A. R.; Tiwari, V. R.; Yamashita, M.; Bera, R.; Ammann, S.; Shahrooei, M.; Sowdhamini, R.; Prakriya, M.; Dani, A.; Vig, M.

10.1101/2024.10.25.620144 — cell biology — Posted on 2025-11-11

3600 Sea-ice microbial community succession and the potential role of parasitoids in the maintenance of diversity during the spring bloom

Dilliplaine, K.; Whitmore, L.; Aguilar-Islas, A.; Bolt, C.; Dumack, K.; Jin, M.; Kaufman, M.; Oggier, M.; Hennon, G.

10.1101/2025.05.18.654361 — microbiology — Posted on 2025-11-11

3601 A lobule-specific neuronal representation of song temporal structure in the songbird cerebellum

Ursu, R.; Centeno, E. G. Z.; Leblois, A.

10.1101/2025.11.10.687662 — neuroscience — Posted on 2025-11-11

3602 Proteomic profile of hippocampal growth cones through early postnatal development

Krause, M.; Kronberg, K. A.; Girao, P. J. B.; Strohmeier, L. S.; Quattrocolo, G.

10.1101/2025.11.10.687591 — neuroscience — Posted on 2025-11-11

3603 Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications

10.1101/2025.11.10.687672 — neuroscience — Posted on 2025-11-11

3604 Method of loci training yields unique prefrontal representations that support effective memory encoding

Ren, J.; Konrad, B. N.; Zhu, Y.; Li, F.; Czisch, M.; Dresler, M.; Wagner, I. C.

10.1101/2025.02.24.639840 — neuroscience — Posted on 2025-11-11

3605 Prefrontal cortex and striatum dissociate modality and learning order in cross-modal sensorimotor learning

Song, D.; Peters, A. J.

10.1101/2025.11.10.687671 — neuroscience — Posted on 2025-11-11

3606 Hierarchical and Context-Dependent Encoding of Actions in Human Posterior Parietal and Motor Cortex

Bougou, V.; Gamez, J.; Rosario, E. R.; Liu, C.; Pejsa, K.; Bari, A.; Andersen, R. A.

10.1101/2025.11.10.687245 — neuroscience — Posted on 2025-11-11

3607 Improving DNA Modeling with WaveDNA: Enhancing Speed, Generalizability, and Interpretability through Wavelet Transformation

Ruggeri, L.; Tognon, M.; Giugno, R.

10.1101/2025.11.07.687194 — bioinformatics — Posted on 2025-11-11

3608 Local trade-offs shape flower size evolution across Arabidopsis thaliana distribution.

Sartori, K. F.; Fernandez Mestre, C.; Hossain, M. J.; Estarague, A. F.; Gaignon, E.; Lasky, J. R.; Vile, D.; Vasseur, F.; Violle, C.; Sicard, A.

10.1101/2025.04.19.649637 — evolutionary biology — Posted on 2025-11-11

3609 Transcranial direct current stimulation of the supplementary motor area modulates behavioral and peripheral electrophysiological measures of motor preparation.

Kumar, A.; Murthy, A.

10.1101/2025.10.31.685710 — neuroscience — Posted on 2025-11-11

3610 Contact networks of small mammals highlight potential transmission foci of Mammarenavirus lassaense

Simons, D.; Goyal, R.; Bangura, U.; Gibb, R.; Rushton, B.; Sondufu, D.; Lamin, J.; Koninga, J.; Foday, M.; Dawson, M.; Lahai, J.; Ansumana, R.; Fichet-Calvet, E.; Watson-Jones, D.; Kock, R.; Jones, K. E.

10.1101/2025.02.25.639449 — ecology — Posted on 2025-11-11

3611 Draft genome sequences for Enterococcus mundtii isolates from soil in Minnesota

Karic, E.; Haeberle, A. L.; Willett, J.

10.1101/2025.11.06.687061 — microbiology — Posted on 2025-11-11

3612 ZFT is the major iron and zinc transporter in Toxoplasma gondii

Aghabi, D.; Gallego Rubio, C.; Cortijo Martinez, M.; Pouzache, A.; Gibson, E. J.; Pagura, L.; Fairweather, S. J.; van Dooren, G. G.; Harding, C. R.

10.1101/2025.04.17.649150 — microbiology — Posted on 2025-11-11

3613 A Triple-Hit Alcoholic Liver Disease Model Linking High-Fat Diet, Endotoxins, and Neo-Antigen Formation

Arora, S.; Katyal, A.

10.1101/2025.11.10.687007 — immunology — Posted on 2025-11-11

3614 A BCG toxic effector induces mitochondrial DNA compaction to refrain protective immunity

Ge, B.; Wang, L.; Peng, C.; Chen, Q.; Huang, J.; Bu, W.; Wu, X.; Duan, Y.; Liu, S.; Cheng, H.; Ma, M.; Cheng, Y.; Wang, J.; Yang, H.; Zheng, R.; Wang, J.; Huang, X.

10.1101/2025.11.09.687409 — immunology — Posted on 2025-11-11

3615 Anti-Kv1.2 Immunoprecipitation Identifies shared mGluR1-Associated Signalosome Complex proteins and PKC-Mediated Regulation of Kv1.2 in the Cerebellum

Madasu, S. C.; Morielli, A. D.

10.1101/2025.11.09.687499 — neuroscience — Posted on 2025-11-10

3616 Spared Nav1.8-Positive Nociceptors Drive Persistent Tactile Hypersensitivity After Sciatic Nerve Crush Injury in Mice

Shim, S. W.; Lee, Y. K.; Roh, D.; Lee, K.; Kim, H. W.; Oh, S. B.

10.1101/2025.11.09.687306 — neuroscience — Posted on 2025-11-11

3617 QuNex Recipes: Executable, Human-Readable Workflows for Reproducible Neuroimaging Research

10.1101/2025.11.08.687330 — neuroscience — Posted on 2025-11-11

3618 No neurobehavioral evidence for reduced motivational potential of social rewards in alcohol use disorder

Schwarze, Y.; Stierand, J.; Voges, J.; Zillikens, E.; Junghanns, K.; Voss, O.; Paulus, F. M.; Krach, S.; Cabanis, M.; Rademacher, L.

10.1101/2025.07.17.665126 — neuroscience — Posted on 2025-11-11

3619 Defining the Growth Stages of Mungbean (Vigna radiata L.) using the BBCH Scale

Singh, A.; Boddepalli, V. N.

10.1101/2025.11.09.687504 — plant biology — Posted on 2025-11-11

3620 Generation of an in vitro 3D multicellular culture model of ovarian high-grade serous carcinoma

Wennerberg, K.; Bulanova, D.; Gall-Mas, L.; Senkowski, W.; Moyano-Galceran, L.

10.1101/2025.11.07.686515 — cancer biology — Posted on 2025-11-11

3621 A Study on the Pharmacokinetic/Pharmacodynamic Profiles of the Novel PPAR Pan Agonist Chiglitazar Sodium in Rats with Hypoalbuminemia

Liu, X.; He, W.; Zhang, X.; Li, M.; Chen, B.; Tian, Y.; Sun, Q.; Zhao, X.; Zhao, Y.; Li, D.

10.1101/2025.11.09.687466 — pharmacology and toxicology — Posted on 2025-11-11

3622 T cell costimulatory and inhibitory signals differentially modulate LAT condensate nucleation propensity after TCR ligation

Choi, S.; Kim, S.; Tijam, J. R.; Eisen, T. J.; Morita, S.; McAffee, D. B.; Groves, J. T.

10.1101/2025.11.01.685673 — biophysics — Posted on 2025-11-11

3623 Towards Human Inverse Dynamics from Real Images: A Dataset and Benchmark for Joint Torque Estimation

Chen, C.; Su, W.

10.1101/2025.10.03.679772 — bioinformatics — Posted on 2025-11-11

3624 Preference-Based Fine-Tuning of Genomic Sequence Models for Personal Expression Prediction with Data Augmentation

Choi, M.; Cho, B.; Lee, S.

10.1101/2025.11.09.687505 — bioinformatics — Posted on 2025-11-11

3625 A large language model for predicting pancreatic ductal adenocarcinoma patients from blood-derived exosomal transcriptomics data

Choudhury, S.; Mehta, N. K.; Raghava, G. P. S.

10.1101/2025.03.06.641795 — bioinformatics — Posted on 2025-11-11

3626 Time- and frequency-resolved decomposition of beta brain activity reveals two functionally distinct beta bands

Korkealaakso, S.; Ahdends, C.; Niemela, L.; Vidaurre, D.; Renvall, H.; Pauls, A.

10.1101/2025.11.10.682052 — neuroscience — Posted on 2025-11-11

3627 Brain-wide single-neuron bases of working memory for sounds in humans

Berger, J. I.; Billig, A. J.; Gander, P. E.; Kovach, C. K.; Rhone, A. E.; Calmus, R. M.; Garcia, C. M.; Kumar, S.; Kawasaki, H.; Howard, M. A.; Griffiths, T. D.

10.1101/2025.11.10.687666 — neuroscience — Posted on 2025-11-11

3628 PKMζ-PKC{iota}/{lambda} double-knockout reveals the atypical PKCs are crucial for hippocampal late-LTP and spatial long-term memory

Tsokas, P.; Hsieh, C.; Grau-Perales, A.; Kwok, L.; Rodriguez-Valencia, L. M.; Cano, D. A.; Allen, K. D.; Smith, H. J. H.; Kubayeva, S.; Wei, B. J.; Sabzanov, S.; Flores-Obando, R. E.; Ghosh, S.; Bergold, P. J.; Cottrell, J. E.; Fenton, A. A.; Sacktor, T. C.

10.1101/2025.11.10.687514 — neuroscience — Posted on 2025-11-11

3629 Brain function in language and associated networks in non- or minimally verbal children

Montana-Valverde, G.; Linke, A.; Slusna, D.; Muchart-Lopez, J.; Rodriguez-Fornells, A.; Deco, G.; Hinzen, W.

10.1101/2025.11.10.686908 — neuroscience — Posted on 2025-11-11

3630 Deep learning the cis-regulatory code of chromatin dynamics during cellular reprogramming

Nair, S.; Ameen, M.; Sundaram, L.; Pampari, A.; Schreiber, J.; Balsubramani, A.; Wang, Y. X.; Burns, D.; Blau, H. M.; Karakikes, I.; Wang, K. C.; Kundaje, A.

10.1101/2023.10.04.560808 — genetics — Posted on 2025-11-11

3631 Annotation-Free Prediction of Cancer Cells and Glands and Spatial Analysis of Immune Cells.

Jung, K. J.; Ghose, S.; Cho, S.; McDonough, E.; Chadwick, C.; West, R.; Brooks, J. D.; Chung, D.; Ginty, F.; Machiraju, R.; Mallick, P.

10.1101/2025.11.09.687528 — cancer biology — Posted on 2025-11-10

3632 Slow Electromechanical Interference Links Division Geometry, Differentiation Bias, and Senescence-like Arrest

Bueno, A. D. M.

10.1101/2025.10.28.684574 — biophysics — Posted on 2025-11-10

3633 ELITE: E3 Ligase Inference for Tissue specific Elimination: A LLM Based E3 Ligase Prediction System for Precise Targeted Protein Degradation

Patjoshi, S.; Froehlich, H.; Madan, S.

10.1101/2025.11.05.686884 — bioinformatics — Posted on 2025-11-10

3634 hmde: Hierarchical Methods for Differential Equations

O'Brien, T. A.; Kar, F.; Warton, D.; Falster, D. S.

10.1101/2025.01.15.633280 — bioinformatics — Posted on 2025-11-10

3635 Caudata macrogenetics: Geographic attributes and lineage age predict global patterns of mitochondrial genetic variation in salamanders

Amador, L.; Wiley, D. L. F.; Arroyo-Torres, I.; McDaniels, C. X.; Rosario-Sanchez, E. O.; Farmer, H.; Bradley, H.; Erdmann, J.; Pelletier, T. A.; Barrow, L. N.

10.1101/2025.01.24.634750 — evolutionary biology — Posted on 2025-11-10

3636 The assembly of microbial communities on red sandstone surfaces was shaped by dispersal limitation and heterogeneous selection

Wang, B.; Zhu, C.; Wang, X.; Yang, T.; Zhang, B.; Hu, Y.

10.1101/2024.10.02.616369 — ecology — Posted on 2025-11-10

3637 CtBP restricts DUX-dependent and -independent genetic program for the 2-cell-like state in murine embryonic stem cells

Yoshioka, K.; Sugiyama, K.; Ichisakino, M.; Abadi, S. A.; Hayakawa, N.; Marutani, M.; Masuda, R.; Takahashi, K.; Seki, Y.

10.1101/2024.01.12.575352 — cell biology — Posted on 2025-11-10

3638 Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography

Peck, A.; Hutchings, J.; Schwartz, J.; Yu, Y.; Ermel, U. H.; Kandel, S.; Kimanius, D.; Zhao, Z.; Zheng, S.; Artley, B.; List, D.; Silva, S. A.; Reade, W.; Asuncion, J.; Evans, K.; Gadling, J.; Khandwala, K.; McCanny, S.; McCarthy, D. G.; Ni, J. X.; Pourroy, J.; Venkatakrishnan, M.; Wang, Z. S.; Agard, D. A.; Potter, C. S.; Carragher, B.; Harrington, K.; Paraan, M.

10.1101/2025.11.03.686153 — cell biology — Posted on 2025-11-10

3639 Genomic analysis of the probiotic candidate Bifidobacterium bifidum strain 900791 in the context of the B. bifidum pangenome

Cardenas, J. P.; Vidal-Veuthey, B.; Meza, K.; Almonacid, D. E.; Gutkevich, A.

10.1101/2025.11.10.687612 — microbiology — Posted on 2025-11-10

3640 A mathematical kinetic model of memory in Bacillus subtilis spore germination

de Koster, C. G.; Lin, X.; Lee, Y.-Q.; Brul, S.; Koning, L. d.; Setlow, P.

10.1101/2025.10.14.682329 — microbiology — Posted on 2025-11-10

3641 Shigella OspF blocks rapid p38-dependent priming of the NAIP-NLRC4 inflammasome

Turcotte, E. A.; Kim, K.; Eislmayr, K. D.; Goers, L.; Mitchell, P. S.; Lesser, C. F.; Vance, R. E.

10.1101/2025.02.01.636075 — immunology — Posted on 2025-11-10

3642 Top-down feedback matters: Functional impact of brainlike connectivity motifs on audiovisual integration

Tugsbayar, M.; Li, M.; Muller, E.; Richards, B. A.

10.1101/2024.10.01.615270 — neuroscience — Posted on 2025-11-10

3643 Dopaminergic processes predict temporal distortions in event memory

Morrow, E.; Huang, R.; Clewett, D.

10.1101/2025.05.14.654133 — neuroscience — Posted on 2025-11-10

3644 Revisiting Humidity Ramp Protocols for Assessing Human Heat Tolerance

Wang, F.; Xu, Y.; Wang, H.; Cui, M.; Hou, X.; Wei, B.

10.1101/2025.11.09.686670 — physiology — Posted on 2025-11-10

3645 Quantification of Cholesterol Incorporation in Giant Unilamellar Vesicles Produced by a Modified cDICE Method

Arribas Perez, M.; Koenderink, G. H.

10.1101/2025.11.10.687550 — biophysics — Posted on 2025-11-10

3646 A mathematical model of osteocyte network control of bone mechanical adaptation

Mehrpooya, A.; Challis, V. J.; Buenzli, P. R.

10.1101/2025.10.10.681578 — bioengineering — Posted on 2025-11-10

3647 Flux organizations and control modes in antagonistically combined negative feedback loops

Ruoff, H. P.

10.1101/2025.11.09.687434 — biochemistry — Posted on 2025-11-10

3648 Seipin mediates Perilipin-1 recruitment to lipid droplets to preserve human adipocyte identity

Zhong, D.; Stavrakaki, I.; Desai, A.; DeSouza, T.; Linskey, S.; Joyce, S.; Hatton, C. L.; Garcia, D.; Kassam, R.; Hendricks, G.; Reddig, K.; Gao, G.; Xie, J.; Gonzalez-Perez, M. P.; Vieira, A. F. C.; Chidley, C. L.; Haley, J. A.; Corvera, S.

10.1101/2025.11.09.687445 — cell biology — Posted on 2025-11-10

3649 Distinct and Shared Impacts of Virulence Plasmids on the Phenotype and Transcriptome in Convergent Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae

Hao, M.; Cui, X.; Feng, L.; Liu, K.; Shi, X.; Long, T.; Rowe, S. E.; Lin, Y.-T.; Chen, L.

10.1101/2025.11.10.687661 — microbiology — Posted on 2025-11-10

3650 A Two-Component Regulatory System Mediates Quorum Sensing-Dependent Morphology and Motility Transitions in the Archaeon Haloferax volcanii

Cote, J.; Chatterjee, P.; Garcia, M.; Tao, R.; Mathijssen, A. J.; Pohlschroder, M.

10.1101/2025.11.10.687552 — microbiology — Posted on 2025-11-10

3651 Alternative Splicing And Global Transcriptome Changes Associated With LPS Stimulation In Human Peripheral Blood Mononuclear Cells

Chavez-Iglesias, E.; Sucher, A.; Thati, N.; Trudeau, J.; Yom, S.; Sirota, M.; Olshen, A.; Cho, N. W.; Kober, K.

10.1101/2025.11.09.687437 — immunology — Posted on 2025-11-10

3652 BUB1B MITOTIC KINASE DRIVES THERAPY RESISTANT PROSTATE CANCER

Martinez, M. J.; Blanco, C.; Peinetti, N.; Lyles, R.; Revuelta, M. V.; Burnstein, K. L.

10.1101/2025.11.09.687448 — cancer biology — Posted on 2025-11-10

3653 CASPULE: A computational tool to study sticker spacer polymer condensates

Chattaraj, A.; Kanovich, D. S.; Ranganathan, S.; Shakhnovich, E. I.

10.1101/2025.11.09.687447 — biophysics — Posted on 2025-11-10

3654 Validating folding energy estimates as a method for variant interpretation

Elwes, C.; Alcraft, R.; Lister, H.; Smith, P. A.; Shorthouse, D.; Hall, B. A.

10.1101/2025.11.09.687451 — biophysics — Posted on 2025-11-10

3655 From Peaks to Patterns

Fathollahian, H.; Salahshour, M.

10.1101/2025.11.09.687456 — bioinformatics — Posted on 2025-11-10

3656 Additive Manufacturing of real-scale carotid artery models: The content-container interaction in sickle cell disease-related cerebral vasculopathy

Eckert, S.; Kassasseya, C.; Garreau, M.; Kakpovi, C. J.; Vignon-Clementel, I.; Verlhac, S.; Bapst, B.; Scarcia, L.; Guillet, H.; Dremont, K.; Kouidri, S.; Segonds, F.; Nguyen-Peyre, K.-A.; Bartolucci, P.

10.1101/2025.11.09.687432 — bioengineering — Posted on 2025-11-10

3657 Untargeted Metabolomics of Plant Samples using HPLC-DAD and Gaussian Mixture Models

Gambill, J. T.; Mason, C. M.; Dowell, J. A.

10.1101/2025.11.10.687686 — biochemistry — Posted on 2025-11-10

3658 Activation of oligonucleotide polyanions using collisions, electrons and photons in a timsOmni platform

Rosu, F.; Chiba, R.; Mani Mallika, A.; Smyrnakis, A.; Greisch, J.-F.; Papanastasiou, D.; Gabelica, V.

10.1101/2025.11.10.687689 — biochemistry — Posted on 2025-11-10

3659 Prebiotically Plausible Peptides can Self-assemble into β-rich Nanostructures

Makarov, M.; Krystufek, R.; Fricek, M.; Manriquez-Sandoval, E.; Dutta, S.; Kormanik, J. M.; Kalvoda, T.; Verner, V.; Bednarova, L.; Charnavets, T.; Lebl, M.; Brown, S. M.; Hadravova, R.; Konvalinka, J.; Singharoy, A.; Fried, S. D.; Hlouchova, K.

10.1101/2025.11.09.687475 — biochemistry — Posted on 2025-11-10

3660 Tobacco twin and single spots result from genome instability, chromosome breaks, and translocations

Demarco, I. J.; Amundson, K. R.; Phan, A.; Henry, I. M.; Comai, L.

10.1101/2025.11.09.687472 — genetics — Posted on 2025-11-10

3661 Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Los Angeles County Sanitation District (LACSD) with High and Low Dissolved Oxygen Conditions

Enuh, B. M.; Myers, K. S.; Ackman, P.; Weiland, T.; Beach, N.; Young, M.; Donohue, T. J.; Noguera, D. R.

10.1101/2025.11.10.687646 — genetics — Posted on 2025-11-10

3662 Sea urchin consumption of kelp controlled by the density of drift algae

Randell, Z.; Sheridan, C.; Frey, J.; Carr, M.; Novak, M.

10.1101/2025.11.09.687392 — ecology — Posted on 2025-11-10

3663 Reconstituting epiblast-extraembryonic endoderm interactions restores anterior-ventral patterning in stem cell-based embryo models.

Smirnova, N. P.; Ponomartsev, S. V.; Ali, T. M. L.; Lycke, M.; Chung, B. K.; Ogaard, J.; Melum, E.; Veenvliet, J.; Krauss, S.

10.1101/2025.11.09.687163 — developmental biology — Posted on 2025-11-10

3664 Plasmodium falciparum Myosin F with a Rab-like tail domain localises to perinuclear membranes and associates with trafficking proteins

Holmes, A. J.; Ilani, P.; Batters, C.; Kemp, A.; Rayner, J. C.; Buss, F.

10.1101/2025.11.10.687607 — molecular biology — Posted on 2025-11-10

3665 Mus Musculus papillomavirus MmuPV1 resists restriction by human APOBEC3B

Liu, X.; Bilger, A.; Lee, D.; Argyris, P.; Chen, J.; Ward-Shaw, E.; Barreto Duran, E.; Lin, Y.-H.; Durfee, C.; Chun, S. H.; Ibrahim, M.; Proehl, J.; Allen, Y.; Lambert, P. F.; Harris, R. S.

10.1101/2025.11.10.687577 — microbiology — Posted on 2025-11-10

3666 Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria

Cascino, J. A.; Dierksheide, K. J.; Vishwakarma, R. K.; Yuzenkova, Y.; Babitzke, P.; Murakami, K.; Li, G.-W.

10.1101/2025.11.10.687660 — microbiology — Posted on 2025-11-10

3667 Coriander leaf essential oil as an immunomodulator: enhancing NF-κB-driven RAW246.7 murine macrophages response to Candida albicans

Hiengrach, P.; Sangsiwarit, P.; Kuwatjanakul, W.; Samerpitak, K.; Luksanawilas, P.

10.1101/2025.11.09.687462 — microbiology — Posted on 2025-11-10

3668 Increased levels of HAPLN2, which anchors dense extracellular matrix, in the hippocampus of APOE4 targeted replacement mice

Deasy, S.; Amontree, M.; Colon, Z. A.; Thorland, E.; Modi, K.; Hummel, K. A.; Blanco, I.; Greco, G. A.; Maguire-Zeiss, K.; Conant, K.

10.1101/2025.11.09.687435 — neuroscience — Posted on 2025-11-10

3669 Brain lipidomics identifies mitochondrial redox dysfunction and metabolic trade-offs associated with Parkinsons disease-like pathology induced by Nanoplastics exposure

Rathor, P.; Tiwari, A.; Patel, R. P.; Singh, S. P.; CH, R.

10.1101/2025.11.09.687439 — neuroscience — Posted on 2025-11-10

3670 Impact of early locus coeruleus lesions in the TgF344 Alzheimer's disease rat model

Marriott, A. E.; Schroeder, J. P.; Korukonda, A.; Pate, B. S.; McCann, K. E.; Weinshenker, D.; Kelberman, M. A.

10.1101/2025.11.09.687363 — neuroscience — Posted on 2025-11-10

3671 Billion-Scale Deciphering of Human Gene Regulatory Grammar

Mayne, J.; Exposito Rodriguez, M.; Burrell, M.; Ceroni, F.; Goldrick, S.

10.1101/2025.11.10.687627 — synthetic biology — Posted on 2025-11-10

3672 Identification and Development of Functional Markers Associated with Triple Pistil Phenotype in Wheat

Raza, Q.; Song, Q.; Rehman, S. u.; Ali, Z.

10.1101/2025.11.09.687415 — plant biology — Posted on 2025-11-10

3673 Alternate VEGFA isoform expression in fibrosarcoma leads to plasticity in cellular migration and differences in sensitivity to inhibition with anti-VEGFA antibodies

Lee, Y.-C.; L Aguero Burgos, B.; Green, N. H.; Claeyssens, F.; English, W. R.

10.1101/2025.11.09.687017 — cancer biology — Posted on 2025-11-10

3674 Optical tweezers combined with FRET tension sensor reveal force-dependent vinculin dynamics

Dubois, C.; Cohen, R. I.; Boustany, N. N.; Westbrook, N.

10.1101/2025.11.10.687568 — biophysics — Posted on 2025-11-10

3675 Microstructure evolution of multivalent ion-complexed polyelectrolyte gels

Jie, Y. S.; Jia, D.

10.1101/2025.11.10.687581 — biophysics — Posted on 2025-11-10

3676 Structural dynamics in the CENP-A nucleosome impacted by protein-protein interactions with centromere protein N

Ghosh Moulick, A.; Erhardt, S.; Wenzel, W.; Kozlowska, M.

10.1101/2025.11.10.686994 — biophysics — Posted on 2025-11-10

3677 ALC1 Finds a New Foothold on the Nucleosome's Super-Groove

Bridges, H. R.; Bacic, L.; Deindl, S.; Gaullier, G.

10.1101/2025.11.10.687450 — biophysics — Posted on 2025-11-10

3678 Assessing the feasibility of machine learning for ancient DNA age prediction: limitations and insights

Kazanskii, M. A.; Golikova, M.; Kasianov, A.; Ivanova, A.; Suraganov, A.; Uroshlev, L.

10.1101/2025.11.09.687346 — bioinformatics — Posted on 2025-11-10

3679 Design, synthesis, and pharmacological evaluation of novel PROTAC degraders targeting 11β-HSD1 for metabolic disease intervention

Wang, L.; Tao, X.; He, M.; Lu, Y.; Wang, Y.; Zhu, J.

10.1101/2025.11.09.687522 — biochemistry — Posted on 2025-11-10

3680 Structural basis of substrate recognition and membrane association by the bacterial lysyl-phosphatidylglycerol hydrolase AcvB

Hoshi, M.; Watanabe, Y.

10.1101/2025.11.10.687609 — biochemistry — Posted on 2025-11-10

3681 Graph attention with structural features improves the generalizability of identifying functional sequences at a protein interface

Ash, J. E.; Francino-Urdaniz, I. M.; Kells, S. P.; Davis, C. N.; Whitehead, T. A.; Khare, S. D.

10.1101/2025.11.04.686550 — biochemistry — Posted on 2025-11-10

3682 Hidden Markov Models Detect Recombination and Ancestry of SARS-CoV-2

Masaki, N.; Bedford, T.

10.1101/2025.11.08.687354 — genomics — Posted on 2025-11-10

3683 Drosophila melanogaster model of RVCL-S demonstrates age dependent disease progression

Gracheva, E.; Matt, A.; Wang, F.; Hsin, R.; Liang, H.; Ouyang, X.; Ding, J.; Miner, J. J.; Zhou, C.

10.1101/2025.11.10.687584 — genetics — Posted on 2025-11-10

3684 Horizontal Gene Transfers Underpin Ribose Heterotrophy and Central Carbon Metabolism Remodeling in Gloeobacteraceae

Sudianto, E.; Baurain, D.; Cornet, L.

10.1101/2025.11.10.686926 — evolutionary biology — Posted on 2025-11-10

3685 Susceptibility of Human Neural Stem Cells to SARS-CoV-2: Entry Mechanisms and Glycocalyx Influence

Song, A.; Zuvia, C.; Talbot, P.

10.1101/2025.11.10.687698 — developmental biology — Posted on 2025-11-10

3686 Integrated Antibody and DIA Based Plasma Proteomics Uncover Temporal Host Responses to SARS CoV 2 Infection

Fukuda, T.; Nakayama, A.; Chikaoka, Y.; Bando, Y.; Kawamura, T.

10.1101/2025.11.06.687090 — molecular biology — Posted on 2025-11-10

3687 Co-occurrence of Antibiotic Residues and Antimicrobial Resistance Genes in Animal Manure and Agricultural Soils from Machakos, Kiambu, and Kajiado Counties, Kenya

Machoka, R.; Ngonga, F.; Muhonja, C.; Tindih, H.; Getenga, Z.; Sören, T.-B.

10.1101/2025.11.09.687469 — molecular biology — Posted on 2025-11-10

3688 Cryo-EM structures of the BAM-P2-visible SurA complex reveal dynamic and cooperative interactions in outer membrane protein assembly

Miyazaki, R.; Kohga, H.; Matsuoka, N.; Maruno, Y.; Yoshimoto, W.; Takahashi, Y. S.; Yanto, D. H. Y.; Nugraha, Y.; Shigematsu, H.; Shiota, T.; Tsukazaki, T.

10.1101/2025.11.10.687524 — molecular biology — Posted on 2025-11-10

3689 The Divergent 3D Genome Landscapes of Aging and Neurodegenerative mouse models

Kashuk, E.; Smirnov, D.; Eremenko, E.; Tsitrina, A.; Kriukov, D.; Golova, A.; Kalusk-Kopatch, S.; Khrameeva, E. E.; Toiber, D.

10.1101/2025.11.10.687599 — molecular biology — Posted on 2025-11-10

3690 Development and pilot application of a point-of-need molecular xenomonitoring protocol for tsetse (Glossina sp.) in a low-resource setting

Saldanha, I.; Aziku, E.; Trima, A. T.; Drapari, V.; Garrod, G.; Ombanya, H.; Tirados, I.; Betson, M.; Mugenyi, A.; Dunkley, S.; Torr, S. J.; Hope, A.; Cunningham, L. J.

10.1101/2025.11.10.685795 — molecular biology — Posted on 2025-11-10

3691 Magnetosome organelles are organized through interactions between McaA and McaB that alter the dynamics of the bacterial actin-like protein MamK

Ra, Y.; Pan, Y.; Chen, T. Y.; Dixon, K.; Taoka, A.; Komeili, A.

10.1101/2025.11.10.687720 — microbiology — Posted on 2025-11-10

3692 Structural insights into cobalamin loading and reactivation of human methionine synthase

Ferreira, D. S. M.; McLennan, K.; Diamond, C.; Vollmar, M.; Kiyani, W.; Froese, D. S.; Bailey, H. J.; Chalk, R.; Basle, A.; Elkins, J. M.; Coker, J. A.; Yue, W.; McCorvie, T. J.

10.1101/2025.11.10.687659 — biochemistry — Posted on 2025-11-10

3693 Benchmarking gene embeddings from sequence, expression, network, and text models for functional prediction tasks

Zhong, J.; Li, L.; Dannenfelser, R.; Yao, V.

10.1101/2025.01.29.635607 — bioinformatics — Posted on 2025-11-10

3694 The Evidence Aggregator: AI reasoning applied to rare disease diagnostics

Twede, H.; Pais, L.; Bryen, S.; O'Heir, E.; Smith, G.; Paulsen, R.; Austin-Tse, C. A.; Bloemendal, A.; Simons, C.; Hall, A. K.; Saponas, S.; Wander, J. D.; MacArthur, D. G.; Rehm, H. L.; Conard, A. M.

10.1101/2025.03.10.642480 — genomics — Posted on 2025-11-10

3695 Postnatal Abrogation of VEGFR2 Blocks Terminal Cap2 Differentiation by Preventing the Developmental Progression from a Capillary Intermediate Cell State

Zhang, D.; Knutsen, C.; Stroud, D. J.; Che, X.; Cornfield, D. N.; Zanini, F.; Alvira, C. M.

10.1101/2025.07.23.666389 — developmental biology — Posted on 2025-11-10

3696 Predicting individual incubation of opioid craving by whole-brain functional connectivity

Duan, Y.; Tsai, P.-J.; Ma, Z.; fredriksson, I.; Wang, D.; Lu, H.; Shaham, Y.; Yang, Y.

10.1101/2025.11.08.687395 — neuroscience — Posted on 2025-11-10

3697 PHA-4/FoxA controls the function of pharyngeal and extrapharyngeal enteric neurons of C. elegans

Walker, Z.; Cao, W. X.; Leyva-Diaz, E.; Rahman, M.; Sural, S.; Attner, M. A.; Hobert, O.

10.1101/2025.08.13.670029 — neuroscience — Posted on 2025-11-10

3698 Ulk1(S555) inhibition alters nutrient stress response by prioritizing amino acid metabolism

Willoughby, O. S.; Nichenko, A. S.; Brisendine, M. H.; Amiri, N.; Henry, S. N.; Braxton, D. S.; Brown, J. R.; Kraft, B. J.; Jenkins, K. S.; Addington, A. K.; Zaitsev, A. V.; Burrows, S. T.; McMillan, R. P.; Zhang, H.; Tye, S. A.; Najt, C. P.; Craige, S. E.; Rhoads, T. W.; Warren, J. S.; Drake, J. C.

10.1101/2025.06.30.662412 — physiology — Posted on 2025-11-10

3699 igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review

Robinson, J. T.; Thorvaldsdottir, H.; Mesirov, J. P.

10.1101/2025.10.29.685397 — bioinformatics — Posted on 2025-11-10

3700 HEIMDALL: A Modular Framework for Tokenization in Single-Cell Foundation Models

Haber, E.; Alam, S.; Ho, N.; Liu, R.; Trop, E.; Liang, S.; Yang, M.; Krieger, S.; Ma, J.

10.1101/2025.11.09.687403 — bioinformatics — Posted on 2025-11-10

3701 Longitudinal multimodal characterization of radiation dermatitis in the C57BL/6J mouse model

Wong, J. H.; Rivas, S.; Liu, L.; Koba, W.; Brodin, N. P.; Guha, C.; Deutsch, A.; Mir, A.; McLellan, B. N.; Shinoda, K.

10.1101/2025.11.08.687376 — genomics — Posted on 2025-11-10

3702 Can Lightweight LLM Agents Improve Spatial TranscriptomicsAnnotation?

Dip, S. A.; Zhang, L.

10.1101/2025.11.08.687410 — genomics — Posted on 2025-11-10

3703 A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements

10.1101/2025.11.06.686988 — genomics — Posted on 2025-11-10

3704 Causes and consequences of sex-chromosome turnovers in Diptera

Layana, L.; Toups, M. A.; Vicoso, B.

10.1101/2025.10.24.684443 — evolutionary biology — Posted on 2025-11-10

3705 Characterization of RNA interference in the model cnidarian Nematostella vectensis reveals partial target silencing but lack of small RNA amplification

Admoni, Y.; Lewandowska, M.; Aharoni, R.; Shi, J.; Zhang, X.; Chen, Q.; Moran, Y.

10.1101/2025.01.03.631050 — evolutionary biology — Posted on 2025-11-10

3706 Genomes from 117 vertebrate species reveal rapidly evolving segmental duplication landscapes

Aqil, A.; Islam, S.; Hach, F.; Numanagic, I.; Masuda, N.; Gokcumen, O.

10.1101/2024.11.22.624925 — evolutionary biology — Posted on 2025-11-10

3707 Wood ants on the edge: how do the characteristics of linear edges affect the population dynamics of an edge specialist?

Podesta, J. A.; Parr, C. L.; Redeker, K. R.; Robinson, E. J. H.

10.1101/2025.02.12.637965 — ecology — Posted on 2025-11-10

3708 Lightweight open-source fine-tuning of SAM2 enables domain-specific microscopy segmentation

Bhat, E.; Selvan, S.; Okekenwa, S.; Dechkounian, Z.; Lin, V.; Nakano, M.; Saha, M.; Song, Y.

10.1101/2025.11.08.687405 — cell biology — Posted on 2025-11-10

3709 Multiple broadly neutralizing antibody lineages can co-exist and mature in the same germinal centres

Garg, A. K.; Binder, S. C.; Meyer-Hermann, M.

10.1101/2025.11.09.687328 — immunology — Posted on 2025-11-10

3710 T-Cell Synaptosomes Orchestrate Long-Term Anti-Tumor Immunity via Proliferative and Metabolic Reprogramming

Kang, S.-K.; Kim, N.-Y.; Lee, S.; Lee, H.; Soh, W.-C.; Park, J.-S.; Kang, H.-T.; Park, J.; Lee, S.; Shim, Y.; Kwon, J.; Kim, H.-R.; Jun, C.-D.

10.1101/2025.11.06.687075 — immunology — Posted on 2025-11-10

3711 Dissociable neural substrates of integration and segregation in exogenous attention

Chen, Y.; Li, A.-S.; Yu, Y.; Hu, S.; He, X.; Zhang, Y.

10.1101/2025.11.08.687384 — neuroscience — Posted on 2025-11-10

3712 A human forebrain organoid model phenocopies dysregulated RNA and protein homeostasis in ALS/FTD-associated TDP-43 proteinopathies

Zhang, Q.; Liu, M.; Fan, X.; Chin, N.; Xu, Y.; Suh, J.; Amniouel, S.; Linask, K.; Zou, J.; Hafner, M.; Ma, L.; Zheng, W.; Ye, Y.

10.1101/2025.11.09.687455 — neuroscience — Posted on 2025-11-10

3713 Brain-wide coordination of internal signals during decision-making

Bondy, A. G.; Charlton, J. A.; Luo, T. Z.; Kopec, C. D.; Stagnaro, W. M.; Venditto, S. J. C.; Lynch, L.; Janarthanan, S.; Oline, S. N.; Harris, T. D.; Brody, C. D.

10.1101/2024.08.21.609044 — neuroscience — Posted on 2025-11-10

3714 Androgen receptor activation stabilizes a hybrid epithelial/mesenchymal phenotype in presence of Notch-Jagged signaling

Guha, S.; R, S.; Tikader, B.; Jolly, M. K.

10.1101/2025.11.09.687414 — systems biology — Posted on 2025-11-10

3715 Ecological and Stochastic Determinants of the Growth and Persistence of the Oral Pathogen Porphyromonas gingivalis

Hussein, M.; Barua, A.; Qasaimeh, M.; Smardz, M.; Diaz, P. I.; Hatzikirou, H.

10.1101/2025.11.08.687400 — systems biology — Posted on 2025-11-10

3716 An extensive forward genetic screen identifies the HWS-AGO1 axis as pivotal for target mimicry-mediated miRNA degradation in Arabidopsis

Yang, L.; Liu, M.; Guo, M.; Fan, Y.; Wang, Y.; Kang, G.; Li, N.; Fang, Y.; Mei, J.; Zhang, X.; Yang, J.; Ren, G.

10.1101/2025.11.08.687406 — plant biology — Posted on 2025-11-10

3717 Effect of PAPE Induced by Different Squat Loads on Jump Performance in Collegiate Female Basketball Players

Si, X.; Liu, Y. H.; Zhou, X. R.; Ning, S. J.; Li, Q. B.

10.1101/2025.11.06.687070 — physiology — Posted on 2025-11-10

3718 Detection of a novel Puccinia coronata f. sp. avenae genotypic lineage in Australia during the 2024 oat growing season

Su, Z.; Lewis, D.; Henningsen, E.; Nguyen, D. T.; Sperschneider, J.; Dodds, P.; Figueroa, M.

10.1101/2025.11.08.687394 — pathology — Posted on 2025-11-10

3719 Comparison of volumetric dynamic optical coherence tomography with biological methods for evaluation of radiation effects in prostate tumor spheroids

Swanson, S.; Chen, K.; Cheraghi, E.; Osei, E.; Bizheva, K.

10.1101/2025.11.08.687368 — cancer biology — Posted on 2025-11-10

3720 Glassy dynamics in active epithelia emerge from an interplay of mechanochemical feedback and crowding.

Muthukrishnan, S.; Dewan, P.; Tejaswi, T.; Sebastian, M. B.; Chhabra, T.; Mondal, S.; Kolya, S.; Nandi, S. K.; Sarkar, S.; Vishwakarma, M.

10.1101/2025.11.08.687351 — biophysics — Posted on 2025-11-10

3721 Infusible Extracellular Matrix Biomaterial Enhances Cell-Specific Pro-Repair Responses Following Acute Myocardial Infarction

Mesfin, J. M.; Chen, A.; Lyons, Q. P.; Nguyen, M. B.; Karkanitsa, M. L.; Yu, J.; Ninh, V. K.; Gardner, E.; Wong, E. G.; Paleti, S. N.; Cheng, J.; Bridgelal, B. D.; Reimold, K. E.; Cao, S.; Uhre, C.; Luo, C. G.; Fu, Z.; King, K. R.; Christman, K. L.

10.1101/2025.11.08.687255 — bioengineering — Posted on 2025-11-10

3722 First study of an aye-aye (Daubentonia madagascariensis) mother's anxiety behaviors peripartum

Olson, R. V.; Watts, D.; Paciulli, L. M.

10.1101/2025.11.08.686247 — animal behavior and cognition — Posted on 2025-11-10

3723 Enhancing Intra-Continental Biogeographical Ancestry Prediction Through a Machine Learning Marker Selection Method

Maurer, T.; Purucker, L.; Hutter, F.; Pfaffelhuber, P.; Heinzel, C. S.

10.1101/2025.11.08.687358 — genetics — Posted on 2025-11-10

3724 Staphylococcus haemolyticus Population Genomics Provides Insights into Pathogenicity and Commensalism

Felgate, H. M.; Lamberte, L.; de Oliveira Martins, L.; Acuna-Gonzalez, A.; Berrington, J. E.; Chapman, J. A.; Sethi, D. K.; Stewart, C. J.; Fluit, A.; O'Shea, M.; Cavanagh, P.; Hall, L.; van Schaik, W.; Webber, M. A.

10.1101/2025.11.08.687178 — genetics — Posted on 2025-11-10

3725 Recapitulating the length polymorphism of RS3, a composite microsatellite implicated in human social behavior, via recombination in Saccharomyces cerevisiae

Kean, C. E.; Radchenko, E. A.; Lindenbaum, N. M.; Materne, G.; Mirkin, S. M.

10.1101/2025.11.09.687482 — genetics — Posted on 2025-11-10

3726 Phylogenomics and Fossilized Birth-Death Dating Reveals Gondawanan Origin and Extensive Post-Cretaceous Diversification of Worldwide Cicadidae.

Stukel, M.; Matzke, N. J.; Douglas, J.; Ruschel, T. P.; Puissant, S.; Price, B. W.; Villet, M.; Lemmon, A. R.; Lemmon, E.; Simon, C.

10.1101/2025.11.08.687401 — evolutionary biology — Posted on 2025-11-10

3727 Fragmentation reduces vesper bat abundance and evenness in a southern Appalachian forest

Ramey, E. J.; McRae, T. R.

10.1101/2025.11.08.687270 — ecology — Posted on 2025-11-10

3728 Flexible parental care in a songbird correlates with sex-specific responses to seasonal phenology, mating opportunity and reproductive success

Zheng, J.; Jiang, W.; Wang, H.; Chen, D.; Zhang, Z.; Komdeur, J.

10.1101/2025.11.08.687196 — ecology — Posted on 2025-11-10

3729 Evaluating a structured expert elicitation approach for adaptive conservation: Lessons from five years in practice

Mayfield, H. J.; Brazill-Boast, J.; Andren, M.; Bowen, M.; Fawcett, A.; Forge, T.; Foster, L.; Goldingay, R.; Hillier, P.; Hinds, M.; Lee, S.; Mahon, E.; Maron, M.; Mills, D.; Rowell, T.; Stuart, S.; Taylor, C.; Webster, G.; Hansen, N.

10.1101/2025.11.08.687399 — ecology — Posted on 2025-11-10

3730 Post-translational Tuning of Human Cortical Progenitor Neuronal Output

Pigeon, J.; Dietl, T.; Abou Mrad, M.; Rizzuti, L.; Silva, M. V.; Danda, N.; Marie, C.; Avalos, C. B.; Mokrani, H.; El Khattabi, L.; Baffet, A.; Castro, D. S.; Parras, C.; Hassan, B. A.

10.1101/2025.10.27.684791 — developmental biology — Posted on 2025-11-10

3731 Physical, chemical, and structural properties of human gastric organoid-derived mucus

Lyon, K. N.; Sidar, B.; Dudiak, C.; Vermulm, C.; Jordan, G.; Sebrell, T. A.; Burcham, A.; Domanico, L. F.; Helm, R. F.; Liao, W.; Davis, B.; Brown, J.; McCalla, S. G.; Wilking, J. N.; Bansil, R.; Bimczok, D.

10.1101/2025.11.08.687257 — cell biology — Posted on 2025-11-10

3732 Spatial transcriptomics reveals distinct inflammatory and adaptive immune properties of rheumatoid arthritis synovial fibroblasts

Machado, C. R. L.; Yao, M.; Boyle, D. L.; Benschop, R. J.; Parker, J. T.; Wang, W.; Firestein, G. S.

10.1101/2025.11.08.687060 — immunology — Posted on 2025-11-10

3733 Truncating RELA variants drive autoinflammation and autoimmunity by impairing the negative feedback control of NF-kB

Lucas, N.; Weidler, S.; Eicher, A.; Keller, B.; Satirer, O.; Desrochers, A.; Ramnarine, T.; Mokhtari, M.; Elstner, S.; Strauss, T.; Mages, S.; Kendirli, A.; Buzoianu, O.; Igel, L.; Niehues, T.; von Hardenberg, S.; Fasshauer, M.; Abou Jamra, R.; Ott, H.; Huffmeier, U.; Schuetz, C.; Bijwaard, M.; Wagner, S.; Switala, P.; Koss, S.; Schultz, J.; Kretschmer, S.; Kummerle-Deschner, J.; Wolf, C.; Klughammer, J.; Lee-Kirsch, M. A.

10.1101/2025.11.09.687461 — immunology — Posted on 2025-11-10

3734 Activation of IRF7/ISG15 axis in microglia inhibits NLRP3 Expression and Improves the Prognosis of Ischemia/Reperfusion in Mice

Yan, H.; Cao, X.; Ma, M.; He, Q.; Li, F.; Xu, R.; Wang, Y.; Zheng, Y.; Yang, J.; Xiao, Y.

10.1101/2025.11.08.687338 — neuroscience — Posted on 2025-11-10

3735 Mediodorsal thalamus of alcohol-dependent mice shows genetic and physiological adaptations and alcohol-biased calcium signaling

Martin, J. C.; Reeves, K. C.; Carter, K. A.; Davis, M.; Schneider, A.; Meade, E.; Lebonville, C. L.; Nimitvilai-Roberts, S.; Hoffman, M.; Woodward, J. J.; Loewinger, G.; Smith, R. J.; Lopez, M. F.; Becker, H. C.; Mulholland, P. J.; Rinker, J. A.

10.1101/2024.10.28.620696 — neuroscience — Posted on 2025-11-10

3736 QuNex Recipes: Executable, Human-Readable Workflows for Reproducible Neuroimaging Research

10.1101/2025.11.08.687330 — neuroscience — Posted on 2025-11-10

3737 Astrocytic FABP5 drives non-cell-autonomous oligodendrocyte injury in multiple system atrophy by promoting TNF signaling and ferroptotic stress

Wu, C.; Lin, J.; Chen, Y.; Takahashi, N.; Chen, Q.; Liu, B.; Dai, F.; Zhao, W.; Finkelstein, D. I.; Kawahata, I.; Fukunaga, K.; Cheng, A.

10.1101/2025.11.08.687320 — neuroscience — Posted on 2025-11-10

3738 The Earlier You Know, the Smoother You Act

Chowdhury, A.; Maurer, H.; Kshirsagar, A.; Ploeger, K.; Peters, J.; Müller, H.; Maurer, L. K.

10.1101/2025.11.08.687371 — neuroscience — Posted on 2025-11-10

3739 Beyond synthetic lethality in large-scale metabolic and regulatory network models via genetic minimal intervention sets

Barrena, N.; Rodriguez, C. J.; Valcarcel, L. V.; Olaverri-Mendizabal, D.; Agirre, X.; Prosper, F.; Planes, F. J.

10.1101/2025.11.07.687323 — systems biology — Posted on 2025-11-10

3740 Highly polygenic control of photosynthetic responses to nighttime temperature in Arabidopsis studied by genomic prediction

dos Santos Sa, A. C.; Bazarova, A.; Fischbach, A.; Kesselheim, S.; Stich, B.; Matsubara, S.

10.1101/2025.11.08.687332 — plant biology — Posted on 2025-11-10

3741 Effects of true to life polyethylene terephthalate and polycaprolactone nanoparticles on macrophages under a repeated exposure mode.

Collin, V.; Villacorta, A.; Diemer, H.; CIANFERANI, S.; Marcos, R.; Hernandez, A.; Carriere, M.; Darrouzet, E.; Rabilloud, T.

10.1101/2025.11.08.687361 — pharmacology and toxicology — Posted on 2025-11-10

3742 Inferring the regulation dynamics of oscillatory networks from scRNA-seq data

Zhao, W.; Plaza-Rodriguez, A.; Luanpaisanon, P.; Wang, E. X.; Gyllingberg, L.; Singh, R.; Fertig, E.; Stein-O'Brien, G. L.

10.1101/2025.11.08.687360 — bioinformatics — Posted on 2025-11-10

3743 Fast Probabilistic Whitening Transformation for Ultra-High Dimensional Genetic Data

Hoffman, G. E.; Dillard, C. P.; Girdhar, K.; Roussos, P.

10.1101/2025.09.01.673591 — genetics — Posted on 2025-11-10

3744 A human supergene: BRCA1, CCDC200, and U2 snRNAs

Scholten, P.; Segel, M.; Haig, D.

10.1101/2025.11.08.687349 — evolutionary biology — Posted on 2025-11-10

3745 Stress granules and protein aggregates reveal intracellular resource competition

Buchholz, H. E.; Martin, S. A.; Dorweiler, J. E.; Prosser, D. C.; Sontag, E. M.; Manogaran, A. L.

10.1101/2025.11.08.687377 — cell biology — Posted on 2025-11-10

3746 Dissecting mammalian cortical circuit development at single-cell resolution using inducible barcoded rabies virus

Zhang, Z.; D'Arcy, B.; He, L.; Arroyo, D.; Deasy, S.; Matthews, E.; Yan, Z.; Rastogi, N.; Mancia Leon, W.; Kaur, K. S.; Southwell, D. G.; Huang, Z. J.; Silver, D.; Velmeshev, D.

10.1101/2025.11.07.687321 — neuroscience — Posted on 2025-11-10

3747 Recurrent neural network models reveal unified mechanisms generating event-related potentials from MMN to P300

Strock, A.; Nghiem, T.-A. E.; Trouvain, N.; Mistry, P. K.; Menon, V.

10.1101/2025.11.06.687057 — neuroscience — Posted on 2025-11-10

3748 Electrostatics Govern Protein Orientation on Citrate-Capped Gold Nanoparticles

Tiwari, S.; jha, a. k.; arora, s.; Das, D.; Ainavarapu, S. r. K.

10.1101/2025.11.07.687172 — biophysics — Posted on 2025-11-10

3749 Learning the Unseen: Data-Augmented Deep Learning for PTM Discovery with Prosit-PTM

10.1101/2025.11.07.687302 — bioinformatics — Posted on 2025-11-10

3750 SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics

Cheng, J.; Chow, P. K. H.; Liu, N.

10.1101/2025.11.07.687304 — bioinformatics — Posted on 2025-11-10

3751 MetaboliteChat: A Unified Multimodal Large Language Model for Interactive Metabolite Analysis and Functional Insights

Guo, Z.; Duan, D.; Liang, Y.; Patil, A.; Xie, P.

10.1101/2025.11.07.687008 — bioinformatics — Posted on 2025-11-10

3752 Language may be all omics needs: Harmonizing multimodal data for omics understanding with CellHermes

Gao, Y.; Wang, W.; Zhao, Y.; Dong, K.; Shan, C.; Zheng, W.; Richter, T.; Li, Z.; Chen, S.; Theis, F. J.; Liu, Q.

10.1101/2025.11.07.687322 — bioinformatics — Posted on 2025-11-10

3753 Extracellular matrix remodeling supports Hydra vulgaris head regeneration and stem cell invasion

Cox, B.; Mah, J.; Perez, A.; Juliano, C.

10.1101/2025.11.07.687297 — developmental biology — Posted on 2025-11-10

3754 Coronavirus NSP14 Drives Internal m7G Modification to Rewire Host Splicing and Promote Viral Replication

Saenz Altamirano, E. E.; Huang, C.-H.; Tsai, Y.-L.; Tzeng, T. J.; Borges Teruel, N. F.; Pandey, I.; Oswal, N.; Chen, Y. G.; Chang, C.-W.; Rajsbaum, R.; Wong, L. Y. R.; Correa, I. R.; Hsu, J. C.-C.

10.1101/2025.09.03.673802 — microbiology — Posted on 2025-11-10

3755 FOODEEG: An open dataset of human electroencephalographic and behavioural responses to food images

Chae, V. J.; Grootswagers, T.; Bode, S.; Feuerriegel, D.

10.1101/2025.11.07.687287 — neuroscience — Posted on 2025-11-10

3756 Morphogenesis and morphometry of brain folding patterns across species

Yin, S.; Liu, C.; Choi, G. P. T.; Jung, Y.; Heuer, K.; Toro, R.; Mahadevan, L.

10.1101/2025.03.05.641692 — neuroscience — Posted on 2025-11-10

3757 A Distinct Subpopulation of Extended Amygdala Neurons Drives Food Intake

Kandil, I. F.; Rogers, E. T.; Morningstar, A. R.; Giardino, W. J.

10.1101/2025.11.07.685941 — neuroscience — Posted on 2025-11-10

3758 Investigating the Role of Exosome-associated Human Endogenous Retroviruses as Biomarkers in Motor Neuron Disease

Roy, T.; Ramesh, M.; Nizam, N. A. A.; Al-Chalabi, A.; Iacoangeli, A.; Al Kheifat, A.

10.1101/2025.11.07.686090 — neuroscience — Posted on 2025-11-10

3759 Peripheral Nerve Transection Predominantly Drives Sympathetic Nerve Sprouting in Mouse Dorsal Root Ganglia

Shim, S. W.; Kim, H. W.; Lee, Y. K.; Woolf, C. J.; Lee, K.; Oh, S. B.

10.1101/2025.11.07.687300 — neuroscience — Posted on 2025-11-10

3760 Short-term microglia depletion via CSF-1R inhibition promotes functional network reorganization and motor recovery after cortical ischemia

Isla Cainzos, S.; Quandt, F.; Borggrewe, M.; Altjohann, H.-M.; Magnus, T.; Biskamp, J.

10.1101/2025.11.07.687313 — neuroscience — Posted on 2025-11-10

3761 The Cortical Temporal Axis: MEG-Based Cross-Frequency Gradients with Biological Anchors

Liu, X.; Wu, X.; Long, S.; Power, L.; Boutet, D.; Liu, L.; Liu, Z.; Ge, R.; Wang, S.; Feng, Z.; Dong, L.; Yan, T.; Yang, G.

10.1101/2025.11.07.687284 — neuroscience — Posted on 2025-11-10

3762 Trade-offs between surviving and thriving: A careful balance of physiological limitations and reproductive effort under thermal stress

Hubert, D. L.; Bentz, E. J.; Mason, R. T.

10.1101/2025.11.07.687289 — zoology — Posted on 2025-11-10

3763 Fish diversity in a human-impacted coastal lagoon in Central Peru

Aramayo, V.

10.1101/2025.11.07.687100 — zoology — Posted on 2025-11-10

3764 Impact of Voluntary Wheel Running on Gene Expression of Histone 3 Lysine 27-Modifying Enzymes in Mouse Skeletal Muscle

Gamu, D.; Cameron, M.; Jalil, Y.; Zouaoui, I.; Sangha, J.; Kim, J.

10.1101/2025.11.07.687293 — physiology — Posted on 2025-11-10

3765 A dimerization-activated proximity labeling system for direct characterization of cadherin cis interactions

Davis, C. M. O.; Pagay, S. S.; Khatiwada, P.; Wu, Y.; Sivasankar, S.

10.1101/2025.11.07.687288 — biophysics — Posted on 2025-11-10

3766 Improving DNA Modeling with WaveDNA: Enhancing Speed, Generalizability, and Interpretability through Wavelet Transformation

Ruggeri, L.; Tognon, M.; Giugno, R.

10.1101/2025.11.07.687194 — bioinformatics — Posted on 2025-11-10

3767 RiboZAP: Custom probe design for rRNA depletion in complex metatranscriptomes

Bunga, S.; Tan, A.; Roos, M.; Kuersten, S.

10.1101/2025.11.07.687087 — bioinformatics — Posted on 2025-11-10

3768 HapBridge: A Methylation-Guided Approach for Correcting Switch Errors and Bridging Phased Blocks in Long-Read Phasing

Chen, H.; Nie, F.; Long, F.; Wang, J.

10.1101/2025.11.07.687303 — bioinformatics — Posted on 2025-11-10

3769 Eyes wide open: Frogs with reduction of auditory communication ability show lower eye, but higher corneal, investment

Ortega, J. A.; Thomas, K. N.; Ron, S. R.; Bell, R. C.; Fujita, M. K.; Gower, D. J.; Streicher, J. W.; Schott, R. K.

10.1101/2025.11.07.687275 — evolutionary biology — Posted on 2025-11-10

3770 PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development

Raulino Lima, J.; Ungvijanpunya, N.; Chen, Q.; Hai Pham, H. Q.; Rosen, T.; Park, G.; Vatankhah, M.; Chai, Y.; Yen, S.; Merrill, A. E.; Liu, Z.; Chen, J.-F.; Yang, Y.; Peng, W.; Xu, J.

10.1101/2024.07.09.598733 — developmental biology — Posted on 2025-11-10

3771 The inner membrane complex protein, IMC55, is dispensable for intra-erythrocytic development of Plasmodium falciparum

Vick, G. W.; Fierro, M. A.; Park, L.; Brooks, C.; Muralidharan, V.

10.1101/2025.11.07.687246 — cell biology — Posted on 2025-11-10

3772 Ribosomal modification by BUD23 drives selective translational control over energy state and metabolic health

Martinez-Sanchez, N.; Brümmer, A.; Barron, N. J.; Voronkov, M.; Rosoff, D. B.; Liechti, A.; Hayter, E. A.; Chamois, S.; Dreos, R.; Guex, N.; Johnson, E.; Baxter, M.; Smith, K.; Northeast, R. C.; Galli, G.; Hodson, L.; Gatfield, D.; Ray, D.; Bechtold, D.

10.1101/2025.05.16.654455 — cell biology — Posted on 2025-11-10

3773 Inhibitory Motifs Quench Synchrony Induced by Excitatory Motifs in Biological Neuronal Networks

Biswas, A.; Kumar, A.

10.1101/2025.11.07.687261 — neuroscience — Posted on 2025-11-10

3774 Restoring signatures of consciousness by thalamic stimulation in a whole-brain model of an anesthetized nonhuman primate

Perez-Ordoyo, E.; Tasserie, J.; Uhrig, L.; Gomez, C.; Grigis, A.; Stikvoort, W.; Geli, S. M.; Tagliazucchi, E.; Kringelbach, M. L.; Luppi, A. I.; Deco, G.; Jarraya, B.; Sanz Perl, Y.

10.1101/2025.11.07.686535 — neuroscience — Posted on 2025-11-10

3775 Restraint Stress Prolongs Diestrus Phase of Mouse Estrous Cycle

Urbain, G. R.; Chapman, A. D.; Van Loh, B.; Folger, J. K.; Laumet, G.

10.1101/2025.11.07.687283 — neuroscience — Posted on 2025-11-10

3776 Distinct Effects of Aging and Klotho Deletion on the Choroid Plexus

Fanaei-Kahrani, Z.; Patel, T.; Valkova, C.; Gloria, A.; Wagner, J.; Heuer, H.; Schwaninger, M.; Hoffmann, S.; Bauer, R.; Kaether, C.

10.1101/2025.11.07.686549 — neuroscience — Posted on 2025-11-10

3777 Electrophysiological profiling of exocytosis during early-stage development of the zebrafish lateral line

Wang, J.; Karatekin, E.; Zenisek, D.

10.1101/2025.11.07.686968 — neuroscience — Posted on 2025-11-10

3778 Lower engagement of cognitive control, attention, modulation networks and lower creativity in children while using ChatGPT: an fMRI study

Horowitz-Kraus, T.; Kenett, Y. N.; Link, D.; Ashqar, E.; Farah, R.

10.1101/2025.11.07.687207 — neuroscience — Posted on 2025-11-10

3779 Designing Convergent Overlapping Genes with Transformer Encoder Models and Lightweight Structural Proxies

Morgan, J. K.

10.1101/2025.11.07.687268 — synthetic biology — Posted on 2025-11-10

3780 FLOWERING LOCUS T1 is a pleiotropic regulator of reproductive development, plant longevity, and source-sink relations in barley

Helmsorig, G.; Lan, T.; Haraldsson, E. B.; Ruetjes, T.; Westhoff, P.; Weber, K.; Kumlehn, J.; Hensel, G.; Simon, R.; von Korff, M.

10.1101/2025.11.07.687273 — plant biology — Posted on 2025-11-10

3781 Combining the alpha-2 adrenergic agonist clonidine with naloxone rescues fentanyl-induced physiologic dysfunction and increases survival

Rivera, A.; Schutzer, W. E.; Sonneborn, A.; Shotwell, S. L.; Janowsky, A.; Abbas, A.; Torralva, R.

10.1101/2025.11.07.687263 — pharmacology and toxicology — Posted on 2025-11-10

3782 Star-Motifs: Revealing Single-Cell Spatiotypes from Routine Histology Using Star-Convex Neighborhoods

Gunesli, G. N.; Dawood, M.; Young, L. S.; Minhas, F.; Raza, S. E. A.; Rajpoot, N. M.

10.1101/2025.11.07.687248 — cancer biology — Posted on 2025-11-10

3783 Reversible and reusable compartmentalized microfluidic chip for coculture of dorsal root ganglion neurons

Moreau, S.; Berdines, R. F.; El Jalkh, T.; Simon, A.; Taret, G.; Fomina, A.; Becker, C.; Estevez-Torres, A.; Bernard, S.; Salmon, H.

10.1101/2024.12.10.627139 — biophysics — Posted on 2025-11-10

3784 CONCERT predicts niche-aware perturbation responses in spatial transcriptomics

Lin, X.; Kong, Z.; Ghosh, S.; Kellis, M.; Zitnik, M.

10.1101/2025.11.08.686890 — bioinformatics — Posted on 2025-11-10

3785 HEIMDALL: A Modular Framework for Tokenization in Single-Cell Foundation Models

Haber, E.; Alam, S.; Ho, N.; Liu, R.; Trop, E.; Liang, S.; Yang, M.; Krieger, S.; Ma, J.

10.1101/2025.11.09.687403 — bioinformatics — Posted on 2025-11-10

3786 An Explainable AI Framework for Identifying Universal Aging Signatures in Cell Embeddings

Qiu, W.; Arian, C.; Weinberger, E.; Yun, S. R.; Mendenhall, A. R.; Young, J. E.; Brbic, M.; Lee, S.-I.

10.1101/2025.11.07.687286 — bioinformatics — Posted on 2025-11-10

3787 A Precisely Controlled Long-Acting Immunosuppression Platform Enables Prolonged Survival of Vascularized Composite Allografts

Lee, S.; Zor, F.; Kulahci, Y.; Joseph, J.; Karagoz, H.; Barooj, S.; Malik, G.; Park, D.; Luo, J. N.; Zhu, L.; Wang, A.; Chung, K.; Li, N.; Shah, P.; Agus, E.; Janarthanan, G.; Vijayavenkataraman, S.; Baby, H. M.; Snapper, O.; Chen, X.; Slaughter, K.; Dang, M.; Sam, E.; Gorantla, A.; Zhang, W.; Karp, J. M.; Joshi, N.; Gorantla, V.

10.1101/2025.11.07.687240 — bioengineering — Posted on 2025-11-10

3788 CapuchinAI: Leveraging AI to study wild primate cognition

Sanchez Vargas, F.; Potluri, S. R.; Abernethy, J.; Benitez, M. E.

10.1101/2025.11.07.687266 — animal behavior and cognition — Posted on 2025-11-10

3789 The phylogenetic Janzen-Connell effect can explain multiple macroecological and macroevolutionary patterns

Xu, L.; Hildenbrandt, H.; Etienne, R.

10.1101/2025.11.07.687215 — evolutionary biology — Posted on 2025-11-10

3790 Intercellular mitochondrial transfer and transmitophagy in response to protein import dysfunction

Glover, E.; Wiseman, B.; Dugdale, C.; Hodgson, L.; Wilkinson, K.; Collinson, I.

10.1101/2025.11.10.687620 — cell biology — Posted on 2025-11-10

3791 Neat1 alleviates ischemic injury in skeletal muscles

Kim, K.; Yu, T.; Mun, H.; Oh, D. G.; Lee, S.; Kim, M.; Kim, J.; Kang, Y.; Li, J.; Jang, Y. C.; Yoon, J.-H.; Hansen, L.; Choo, H. J.

10.1101/2025.11.08.687205 — cell biology — Posted on 2025-11-10

3792 Synergy mediates Long-Range Correlations in the Visual Cortex Near Criticality

Rajpal, H.; Stefens, C.; Saeedian, M.; Canzano, J. S.; Kareithi, M. G.; Barahona, M.; Smith, S. L.; Schultz, S. R.; Jensen, H. J.

10.1101/2025.11.07.687179 — neuroscience — Posted on 2025-11-10

3793 Movement Effort does not alter the Planning Horizon of Sequential Reaching Movements

Bellmann, A.; Oostwoud Wijdenes, L.; Medendorp, W. P.

10.1101/2025.11.07.686755 — neuroscience — Posted on 2025-11-10

3794 iPSC derived MSC secretome activates distinct neuroprotective pathways in a preclinical model of Parkinsons disease

Salgado, A. J.; Ferreira-Antunes, F.; Marote, A.; Sampaio-Marques, B.; Mendes-Pinheiro, B.; Soares-Cunha, C.; Domingues, A. V.; Oliveira, S.; Anjo, S. I.; Monteiro, D.; Patricio, P.; Manadas, B.; Teixeira-Castro, A.; Pinto, L.

10.1101/2025.11.07.687231 — neuroscience — Posted on 2025-11-10

3795 The Effect of Musical Groove on Sensorimotor Network Cortical Dynamics during Active Tapping and Passive Listening

Zampini, T.; Ross, J. M.; Janata, P.; Balasubramaniam, R.

10.1101/2025.11.07.687225 — neuroscience — Posted on 2025-11-10

3796 Timing Is Everything: Temporal Dynamics of BOLD Responses to Naturalistic Features in Movie Watching

Di, X.; Hanna, G. B.; Biswal, B. B.

10.1101/2025.11.07.687226 — neuroscience — Posted on 2025-11-10

3797 Pupil dilation indexes - but does not causally influence - conscious error detection: a double-blind, placebo-controlled investigation of performance-monitoring using atomoxetine.

Choo, Y.; Segal, A. E.; Carnahan, R. M.; Chalkley, N.; Potter, R.; Dolan, K.; Nickl-Jockschat, T.; Wessel, J. R.

10.1101/2025.11.07.687236 — neuroscience — Posted on 2025-11-10

3798 Interval Timing Shows Selective Enhancement Under Psychosocial Stress: A Cortisol-Mediated Dissociation From Spatial Processing

Gumus-Akay, G.; Vatansever, G.; Cetinkaya, F.; Varol, N.; Cicek, M.

10.1101/2025.11.07.686532 — neuroscience — Posted on 2025-11-10

3799 High-throughput imaging of GABA fluorescence as a functional assay for variants in the neurodevelopmental gene, SLC6A1

McGraw, C. M.; Zhang, G.; Prinzing, G.; Wiltrout, K.; Poduri, A.

10.1101/2025.11.06.687003 — neuroscience — Posted on 2025-11-10

3800 Distinct hippocampal mechanisms support concept formation and updating

Mack, M. L.; Love, B. C.; Preston, A. R.

10.1101/2024.02.14.580181 — neuroscience — Posted on 2025-11-10

3801 ICAM-5: A Novel Marker for Neuronally Derived Extracellular Vesicles.

Deleon, P.; Hattenberger, R.; Knollmann-Ritschel, B.; Bhomia, M.

10.1101/2025.11.07.686794 — neuroscience — Posted on 2025-11-10

3802 Structured Neural Variability from Repeated Naturalistic Video Watching Experiences

Yang, M.; Chen, P.-h. A.; Brandt, A. M.; Sadhukha, S.; Farrens, M.; Jolly, E.; Chang, L. J.

10.1101/2025.11.07.687258 — neuroscience — Posted on 2025-11-10

3803 Bayesian multilevel modeling of group and participant level effect sizes: Stronger inter-individual differences in pupil dilation compared to EEG alpha power during aversive conditioning

Gardy, S. M.; Pouliot, J. J.; Gilbert, F.; Ward, R. T.; Traiser, C.; Chiasson, P.; Keil, A.; Farkas, A.

10.1101/2025.11.07.687228 — neuroscience — Posted on 2025-11-10

3804 Ketogenesis is dispensable for the metabolic adaptations to caloric restriction

Yeh, C.-Y.; Borgelt, A. L.; Vogt, B. J.; Clark, A. A.; Wong, T. T.; Grunow, I.; Sonsalla, M. M.; Babygirija, R.; Liu, Y.; Trautman, M. E.; Calubag, M. F.; Knopf, B. A.; Xiao, F.; Lamming, D.

10.1101/2025.05.29.656153 — physiology — Posted on 2025-11-10

3805 Dual mechanism of kinetochore microtubule detachment

Conway, W.; Qiu, L.; Ha, G.; Amir, A.; Needleman, D. J.

10.1101/2023.06.05.543640 — biophysics — Posted on 2025-11-10

3806 Dynamics-enhanced Molecular Property Prediction Guided by Deep Learning

Liu, Q.; Wang, D. D.; Guo, W.; Huang, Y.; Wang, X.

10.1101/2025.11.07.687115 — bioinformatics — Posted on 2025-11-10

3807 Cold Atmospheric Plasma for Alzheimer's disease

Chen, X.; Yu, Z.; Du, C.; Huang, Y.; Chen, Z.; Xu, Z.; Chen, Z.

10.1101/2025.11.07.687156 — bioengineering — Posted on 2025-11-10

3808 Decoupling synaptic weight and connection sparsity reveals asymmetriccontrol of network dynamics

Tompos, T.; Zeldenrust, F.; Celikel, T.

10.1101/2025.04.02.646896 — neuroscience — Posted on 2025-11-10

3809 Modelling the effect of V1a receptor antagonism and its potential therapeutic effect in circadian disorders

Boareto, M.; Mendoza, J.; Holst, S.; Kalsbeek, A.; Prinssen, E.; Grundschober, C.

10.1101/2025.11.07.687173 — neuroscience — Posted on 2025-11-10

3810 Alcohol dependence-induced neuroadaptations in prelimbic KV7 channels contribute to working memory deficits in mice

Lindquist, K. L.; Rinker, J. A.; Mulholland, P. J.

10.1101/2025.11.07.687180 — neuroscience — Posted on 2025-11-10

3811 Ventromedial prefrontal cortex shields value computations from bodily arousal in decision making

Christian, P.; Kaiser, J.; Kapetaniou, G. E.; Schutz-Bosbach, S.; Soutschek, A.

10.1101/2025.11.07.687164 — neuroscience — Posted on 2025-11-10

3812 Biophysical basis for brain folding and misfolding patterns in ferrets and humans

Choi, G. P. T.; Yin, S.; Liu, C.; Sejourne, G.; Smith, R.; Walsh, C. A.; Mahadevan, L.

10.1101/2025.03.05.641682 — neuroscience — Posted on 2025-11-10

3813 Effort choices are sensitive to prior learning

Guinea, C.; Xiao, B.; Lawson, R. P.

10.1101/2025.07.24.666522 — neuroscience — Posted on 2025-11-10

3814 Region-specific proteomic analysis of aging rhesus macaques following chronic glutamate-carboxypeptidase-II (GCPII) inhibition elucidates potential treatment strategies for sporadic Alzheimer's disease

Steigmeyer, A. D.; Battison, A. S.; Liebman, I. R.; van Dyck, C. H.; Slusher, B. S.; Arnsten, A. F.; Malaker, S. A.; Datta, D.

10.1101/2025.11.07.687004 — neuroscience — Posted on 2025-11-10

3815 Pharmacological and Physiological Characteristics of Synaptic Transmissions from the Medial Prefrontal Cortex onto Noradrenergic Neurons and Their Presynaptic Neurons in the Mouse Locus Coeruleus

Lai, P.-H.; Hung, W.-C.; Min, M.-Y.; Yang, H.-W.

10.1101/2025.11.07.687181 — neuroscience — Posted on 2025-11-10

3816 GPCR-MAPS: high-resolution functional and allosteric mapping of G protein-coupled receptor activation and bias

Mighell, T.; Lehner, B.

10.1101/2025.05.30.656974 — systems biology — Posted on 2025-11-10

3817 Single recipient cell tracking of tellurium-labeled extracellular vesicle proteomes (TeLEV) identifies EV-driven immunomodulation

Bachurski, D.; Gholamipoorfard, R.; Bu, Y.-J.; Hoelker, P.; Wessendorf, L.; Jestrabek, H.; Schreurs, L. D.; Stahl, D.; Mokhlesi, A.; Goedel, P.; Gaedke, F.; Ranjbari, E.; Seyhan, S.; Resch, U.; Schmidt, L. M.; Tertel, T.; Rose, F.; Pinheiro, C.; Corona, M. L.; von Lom, A.; vom Stein, A. F.; Nguyen, P.-H.; Reiners, K. S.; Hendrix, A.; van Niel, G.; Krueger, M.; Bozek, K.; Meder, L.; Malmberg, P.; Cramer, P.; Eichhorst, B.; Peifer, M.; Ullrich, R. T.; Schauss, A.; Pallasch, C.; Broeckelmann, P. J.; Jachimowicz, R. D.; Preusser, C.; Giebel, B.; Pogge von Strandmann, E.; Nitz, M.; Hallek, M.; Abed

10.1101/2025.11.01.685872 — cancer biology — Posted on 2025-11-10

3818 Indocyanine green excitation-emission matrix characterization: excitation-dependent emission shifts and application-specific spectra

Ruiz, A. J.; Lyon, S. A.; LaRochelle, E. P. M.; Samkoe, K. S.

10.1101/2025.08.12.667954 — biochemistry — Posted on 2025-11-10

3819 Assessment of Visual Function in Mice Using Light/Dark Box and Multi-Feature Machine Learning

Wang, T.; Chang, K.; Tomasi, M.; Lee, C.-Y.; Shi, C.; Chen, D. F.; Luo, G.

10.1101/2025.11.07.687135 — animal behavior and cognition — Posted on 2025-11-10

3820 PyrMol: A Knowledge-Structured Pyramid Graph Framework forGeneralizable Molecular Property Prediction

Li, Y.; Zhao, Q.; Wang, J.

10.1101/2025.11.09.686426 — bioinformatics — Posted on 2025-11-10

3821 Revealing the Paper Mill Iceberg: AI-Based Screening of Cancer Research Publications.

Scancar, B.; Byrne, J. A.; Causeur, D.; Barnett, A. G.

10.1101/2025.08.29.673016 — cancer biology — Posted on 2025-11-10

3822 The impact of patient biology on racial disparities in breast cancer outcome

DeWitt, J. T.; Jimenez-Tovar, D.; Nguyen, C.; Oropeza, E.; Raghunathan, M.; Karabay, E. T.; Lamichhane, A.; Kirk, E.; Raghavan, S.; Katira, P.; Luna Lopez, C.; Troester, M.; Freedland, S.; Haricharan, S.

10.1101/2025.11.05.685148 — cancer biology — Posted on 2025-11-10

3823 SiSaNA: A Python-based command line interface for Single-Sample Network Analysis

Newman, N. K.; Kuijjer, M. L.; Belova, T.

10.1101/2025.11.06.680212 — bioinformatics — Posted on 2025-11-10

3824 HiC-SCA: A Spectral Clustering Method for Reliable A/B Compartment Assignment From Hi-C Data

Chan, J.; Kono, H.

10.1101/2025.09.22.677711 — genomics — Posted on 2025-11-10

3825 A chromosome-scale genome assembly for Clark's Nutcracker (Nucifraga columbiana)

Innes, P.; Carling, M. D.; Linck, E.

10.1101/2025.11.06.687043 — genomics — Posted on 2025-11-10

3826 Gene expression profiling for forensic age assessment of porcine skin wounds

Baekgaard, C.; Skovgaard, K.; Hansen, M. H.; Jensen, H. E.; Barington, K.

10.1101/2025.11.06.686914 — genetics — Posted on 2025-11-10

3827 Assessing the potential of ancient protein sequences in the study of hominid evolution

Patramanis, I.; Skov, L.; Cappellini, E.; Racimo, F.

10.1101/2025.04.08.647730 — evolutionary biology — Posted on 2025-11-10

3828 Oxygen-adaptive plasticity of Asgard archaea dependent on terminal oxidase and globin

Lu, Z.; Xia, R.; Xu, A.; Gu, J.; Cai, H.; Liu, Y.; Koonin, E. V.; Li, M.

10.1101/2025.11.07.685452 — evolutionary biology — Posted on 2025-11-10

3829 Coevolution of phenological traits shapes plant-pollinator coexistence

Duchenne, F.; Dominguez-Garcia, V.; Molina, F.; Bartomeus, I.

10.1101/2024.08.08.607160 — ecology — Posted on 2025-11-10

3830 Phylogenetic patterns over sixty-five years of vegetation change across a montane elevation gradient

Veldhuisen, L. N.; Zorio, S. D.; Williams, C. F.; Dlugosch, K. M.

10.1101/2025.11.07.687265 — ecology — Posted on 2025-11-10

3831 Prognosis prediction using autophagy gene expression in osteosarcoma

Bi, Y.; Liu, Q.; Zhou, C.; xu, k.; zhu, Q.; Lu, J.; zhang, C.; Xie, W.; Fang, G.; chen, X.; Tian, D.; Jing, J.; Li, Y.; Wang, H.; Duan, W.

10.1101/2025.11.05.685081 — cell biology — Posted on 2025-11-10

3832 Ribosome-binding protein 1, RRBP1, maintains peroxisomal biogenesis

Fatima, K.; Vihinen, H.; Akpinar, B. A.; Somborac, T.; Jokitalo, E.; Katajisto, P.; Konovalova, S.

10.1101/2024.04.10.588905 — cell biology — Posted on 2025-11-10

3833 Engineered bacterial M1GS ribozyme efficiently cleaves the most abundant ribosomal RNA in a human cancer cell line

Priyadarshini, N.; Puppala, N. V.; Poiyamozhi, H.; Biswas, S.; Mohannath, G.

10.1101/2025.11.07.687305 — molecular biology — Posted on 2025-11-10

3834 Alpine peatlands: spatially and temporally complex ecosystems with year-round methane cycling activity

van Grinsven, S.; Kunz, S.; Jueterbock, F.; Kappler, A.

10.1101/2025.11.07.687222 — microbiology — Posted on 2025-11-10

3835 Synergy unleashed: Leishmania donovani GP63 paralogues cooperatively function to drive parasite infectivity at various pathogenic stages and regulate host survival mechanisms

Manna, D.; Nandi, S.; Jana, S.; Zahanova, K.; Bhattacharya, S.; S, D.; Pradhan, N.; Pandey, N.; Biswas, D.; Mandal, M.; Mukherjee, G.; Yurchenko, V.; Mukherjee, B.

10.1101/2025.11.09.687440 — microbiology — Posted on 2025-11-10

3836 Neuropathological Correlates of Apathy Progression in Alzheimer's Disease and Related Dementias: A Longitudinal NACC Cohort Study

Qi, Y.; Goldberg, T. E.; Kim, H.; Devanand, D. P.; Lee, S.

10.1101/2025.11.06.686966 — neuroscience — Posted on 2025-11-10

3837 Psychiatric risk implications of adolescent exposure to environmental insecticides: a systematic review of rodent studies

Chen, M. X.; Hing, B.; Taylor, R. J.; Stevens, H. E.

10.1101/2025.11.06.687006 — neuroscience — Posted on 2025-11-10

3838 Nose-to-Brain Administration of Cannabidiol-Loaded Polymeric Micelles Improves the Core Behavioral Symptoms of Autism Spectrum Disorder

Awad, R.; Aga-Mizrachi, S.; Maoz, I.; Simchi, L.; Avital, A.; Sosnik, A.

10.1101/2025.11.05.686695 — neuroscience — Posted on 2025-11-10

3839 The Research Mind: A Multi-Dimensional Framework for Evaluating Research Quality, Productivity, and Integrity by Mitigating Citation Bias

Rathee, S.; Chaudhary, C.

10.1101/2025.11.08.687364 — scientific communication and education — Posted on 2025-11-10

3840 Repeated Disuse Atrophy Imprints a Molecular Memory in Skeletal Muscle: Transcriptional Resilience in Young Adults and Susceptibility in Aged Muscle

Turner, D. C.; Raastad, T.; Ullrich, M.; Christiansen, S. F.; Sutherland, H.; Boot, J.; Wozniak, E.; Mein, C.; Dalbram, E.; Treebak, J. T.; Owens, D. J.; Hughes, D. C.; Bodine, S. C.; Jarvis, J. C.; Sharples, A. P.

10.1101/2025.10.16.681134 — physiology — Posted on 2025-11-10

3841 MADRe: Strain-Level Metagenomic Classification Through Assembly-Driven Database Reduction

Lipovac, J.; Sikic, M.; Vicedomini, R.; Krizanovic, K.

10.1101/2025.05.12.653324 — bioinformatics — Posted on 2025-11-10

3842 Challenges in predicting chromatin accessibility differences between species

Stephen, A. Z. M.; Raje, A.; Sestili, H. H.; Wirthlin, M. E.; Lawler, A. J.; Brown, A. R.; Stauffer, W. R.; Pfenning, A. R.; Kaplow, I. M.

10.1101/2025.11.09.687449 — genomics — Posted on 2025-11-10

3843 Neural recordings of continuous speech reveal robust signatures of prediction in second language learners of English

Thorburn, C. A.; Karunathilake, I. M. D.; Dixon, L. N.; Lau, E.; Simon, J. Z.

10.1101/2025.11.10.684289 — neuroscience — Posted on 2025-11-10

3844 Head movements integrate with brain signals to guide attention

Woestmann, M.; Obleser, J.

10.1101/2025.11.10.687554 — neuroscience — Posted on 2025-11-10

3845 Reading ability in both deaf and hearing adults is linked to neural representations of abstract phonology derived from visual speech

Evans, S.; Price, C. J.; Diedrichsen, J.; Twomey, T.; Beedie, I.; Fraser, M.; MacSweeney, M.

10.1101/2025.11.09.684749 — neuroscience — Posted on 2025-11-10

3846 The Road Not Taken: Unsaid Word Alternatives are Represented in the Brain

Liobashevski, D.; Friedman, D.; Flinker, A.; Goldstein, A.

10.1101/2025.11.09.687421 — neuroscience — Posted on 2025-11-10

3847 Inter- and intra-individual differences in temporal modulation patterns of the β-band sensorimotor rhythm and its relationship to corticomuscular coherence during intermittent voluntary contraction

Zhou, J.; Ushiyama, J.

10.1101/2025.11.10.687531 — neuroscience — Posted on 2025-11-10

3848 Precision functional imaging in infants using multi-echo fMRI at 7T

Moser, J.; Sadeghi-Tarakameh, A.; Ramirez, J. S. B.; Madison, T. J.; Hantzsch, L.; Weldon, K. B.; Pham, H. H. N.; Lundquist, J. T.; Sung, S.; Ukpong, I.; Drexler, E.; Labonte, A. K.; Auerbach, E. J.; Adriany, G.; Sylvester, C. M.; Nelson, S. M.; Eryaman, Y.; Elison, J. T.; Fair, D. A.; Yacoub, E.

10.1101/2025.11.09.687453 — neuroscience — Posted on 2025-11-10

3849 XomicsToModel: Multiomics data integration and generation of thermodynamically consistent metabolic models

Preciat, G.; Wegrzyn, A. B.; Thiele, I.; Hankemeier, T.; Fleming, R. M.

10.1101/2021.11.08.467803 — systems biology — Posted on 2025-11-10

3850 Inferring the regulation dynamics of oscillatorynetworks from scRNA-seq data

Zhao, W.; Plaza-Rodriguez, A.; Luanpaisanon, P.; Wang, E. X.; Gyllingberg, L.; Fertig, E.; Stein-O'Brien, G. L.

10.1101/2025.11.08.687360 — bioinformatics — Posted on 2025-11-10

3851 Analysis of coding gene expression from small RNA sequencing

Azadova, A.; Ekperuoh, A.; Brooke, G. N.; Marco, A.

10.1101/2024.06.21.600062 — genomics — Posted on 2025-11-10

3852 Spatial Partitioning of Core Glycolysis Enables Tissue-Specific Metabolic Programs In Vivo

Gonzalez, I. J.; Wolfe, A. D.; Clark, B.; Hanna, M.; Sun, Q.; Ravikumar, S.; Tsives, A.; Emerson, S. E.; Siebel, S.; Kibbey, R.; Colon-Ramos, D.

10.1101/2025.11.09.687253 — cell biology — Posted on 2025-11-10

3853 igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review

Robinson, J. T.; Thorvaldsdottir, H.; Mesirov, J. P.

10.1101/2025.10.29.685397 — bioinformatics — Posted on 2025-11-10

3854 ELITE: E3 Ligase Inference for Tissue specific Elimination: A LLM Based E3 Ligase Prediction System for Precise Targeted Protein Degradation

Froehlich, H.; Patjoshi, S.; Madan, S.

10.1101/2025.11.05.686884 — bioinformatics — Posted on 2025-11-10

3855 Deep learning challenge to generate apo RNA conformations with cryptic binding site

Kurisaki, I.; Hamada, M.

10.1101/2025.01.07.631832 — bioinformatics — Posted on 2025-11-10

3856 A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2

Zhan, S. H.; Wong, Y.; Ignatieva, A.; Eaton, K.; Guthrie, I.; Jeffery, B.; Palmer, D. S.; Murall, C. L.; Otto, S.; Kelleher, J.

10.1101/2023.06.08.544212 — evolutionary biology — Posted on 2025-11-10

3857 Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps

Han, Y.; Liao, J.; Li, C.; Xing, F.; Peng, J.; Liu, X.; Xie, W.; Wu, F.; Jian, H.; Cheng, R.; Dong, X.

10.1101/2024.09.26.614923 — microbiology — Posted on 2025-11-10

3858 GFAP Degradation in TBI: Linking Novel Modified Products to Astrocyte Pathology and Patient Outcome

Wanner, I. B.; Halford, J.; Lopez, J.; Shen, S.; Chen, Y.; Zhao, H.; Salas, C. I.; Loo, R. R.; Robicsek, S.; Ellingson, B. M.; Gornbein, J.; Van Meter, T. E.; Shaw, G.; Loo, J. A.; Vespa, P. M.

10.1101/2025.08.01.668181 — neuroscience — Posted on 2025-11-10

3859 Integrated multi-omics reveals coordinated Staphylococcus aureus metabolic, iron transport and stress responses to human serum

Mujchariyakul, W.; Walsh, C.; Giulieri, S.; Cramond, C.; Le Cao, K.-A.; Stinear, T. P.; Howden, B. P.; Guerillot, R.; Hachani, A.

10.1101/2025.08.11.669730 — microbiology — Posted on 2025-11-09

3860 Physics-Diffusion-Driven Multiscale Aggregation for Drug-Target Interaction Prediction

Liu, J.; Le, J.; Wei, C.; Liu, M.; Yin, Z.; Luo, Y.; Qin, H.; Yu, G.

10.1101/2025.11.03.686185 — bioinformatics — Posted on 2025-11-09

3861 Tertiary and quaternary structure remodeling by occupancy of the substrate binding pocket in a large glutamate dehydrogenase

Lazaro, M.; Chamorro, N.; Lopez-Alonso, J. P.; Charro, D.; Rasia, R. M.; Jimenez-Oses, G.; Valle, M.; Lisa, M.-N.

10.1101/2024.12.26.630402 — molecular biology — Posted on 2025-11-09

3862 Unreal? A Behavioral, Physiological, and Computational Model of the Sense of Reality

Drori, G.; Bar-Tal, P.; Hirsh, O.; Berlinger, A.; Goldberg, N.; Zvilichovsky, Y.; Hertz, U.; Zaidel, A.; Salomon, R.

10.1101/2025.04.07.647542 — neuroscience — Posted on 2025-11-09

3863 HalluDesign: Protein Optimization and de novo Design via Iterative Structure Hallucination and Sequence design

Fang, M.; Wang, C.; Shi, J.; Lian, F.; JIn, Q.; Wang, Z.; Zhang, Y.; Cui, Z.; Wang, Y.; Ke, Y.; Han, Q.; Cao, L.

10.1101/2025.11.08.686881 — bioinformatics — Posted on 2025-11-09

3864 BayesCurveFit: Enhancing Curve Fitting for Early-Stage Compound Screening Using Bayesian Inference

Du, N.; Chen, Y.; Qian, Y.

10.1101/2025.02.23.639769 — bioinformatics — Posted on 2025-11-09

3865 Evaluating the impact of two different diets on the protein profile expression of the brain, liver, and intestine of barramundi

Shatouri, M. M.; Pirozzi, I.; Soker, P. D.; Ali, Z.; Amirkhani, A.; Haynes, P. A.

10.1101/2025.11.03.686387 — biochemistry — Posted on 2025-11-09

3866 A microvolume method for measuring catalase activity

Rocha, B. C.; Rosa, M. T.; Rocha, J. B. T.; Loreto, E. L. S.

10.1101/2025.11.07.687299 — biochemistry — Posted on 2025-11-09

3867 Seasonal variation in wind speed and oceanic salt spray favors delayed reproduction in coastal yellow monkeyflowers

Toll, K.; Crockett, C.; Tocci, L.; Lowry, D.

10.1101/2025.11.07.687229 — ecology — Posted on 2025-11-09

3868 Exercise training improves sarcopenic muscle function via restoration of mitochondrial quality control

Alldritt, I.; Sligar, J.; Campelj, D.; Padilha, C. S.; Ritenis, E.; Mantamadiotis, T.; Widodo, S.; Dinevska, M.; Nielsen, J.; Philp, A. M.; Philp, A.

10.1101/2025.11.03.686168 — cell biology — Posted on 2025-11-09

3869 Rapamycin reverts cavernoma endothelial cell phenotype and when combined with lapatinib ameliorates chronic lesions

Garcia-Colomer, M.; Martinez, J. E.; Diaz-Gomez, L.; Sartages, M.; Esquinas-Roman, E. M.; Riobello, C.; Martinez-Dalgado, D.; Gonzalez-Perez, D.; Gomez-Duran, A.; Fidalgo, M.; Varela-Rey, M.; Pombo, C. M.; Zalvide, J.

10.1101/2025.11.03.686432 — cell biology — Posted on 2025-11-09

3870 PPAR-delta rather than PPAR-gamma is likely to be the key modulator of central carbon metabolism in human adipocytes

Sun, L.; Wabitsch, M.; Yang, J.; Sakharkar, M.

10.1101/2025.11.08.687092 — molecular biology — Posted on 2025-11-09

3871 Single-Molecule Imaging Reveals Transcription-Driven Supercoiling in Unconstrained DNA

Yang, L.; Wang, Y.; Lyu, W.; Egbert, R.; Yeung, E.

10.1101/2025.11.08.687369 — molecular biology — Posted on 2025-11-09

3872 Epithelial and stromal remodeling in murine Crohn's disease-like ileitis

Letai, K. C.; Islam, B. N.; Menghini, P.; De Salvo, C.; Khandekar, N.; Armstrong, B. W.; Tomar, A.; Curry, K.; Pizarro, T. T.; Tesar, P. J.; Scavuzzo, M. A.; Cominelli, F.

10.1101/2025.11.08.684908 — molecular biology — Posted on 2025-11-09

3873 Distinct regulation of AEBP2 isoforms on PRC2 activity

Lee, C.-H.; Li, Y.; Kim, H.

10.1101/2025.11.09.687442 — molecular biology — Posted on 2025-11-09

3874 Examining Selection Dynamics and Limitations in Multi-round Protein Selection of High Diversity Libraries

Chen, J. Z.; Gall, B.; Lu, T. Y.; Heslop, I.; Hesselson, D.; Nitsche, C.; Tham, W.-H.; Payne, R. J.; Jackson, C. J.

10.1101/2025.11.09.687419 — molecular biology — Posted on 2025-11-09

3875 Passaging Human Tauopathy Patient Samples in Cells Generates Heterogeneous Fibrils with a Subpopulation Adopting Disease Folds

Zeng, Z.; Tsay, K.; Vijayan, V.; Frost, M.; Prakash, S.; Quddus, A.; Albert, A.; Vigers, M.; Srivastava, M.; Woerman, A.; Han, S.

10.1101/2023.07.19.549721 — molecular biology — Posted on 2025-11-09

3876 Phylogenetic Insights into Antifungal Susceptibility: Comparing Environmental and Clinical Scedosporium and Lomentospora Isolates from Taiwan

Lin, S.-Y.; Tseng, Y.-T.; Abdrabo, K. A. E.-S.; Wu, H.-M.; Sun, P.-L.; Wu, C.-J.; Sukphopetch, P.; Chen, S. C.- A.; Huang, Y.-T.

10.1101/2025.11.08.687386 — microbiology — Posted on 2025-11-09

3877 Functional and genomic insights into landfill-isolated Brucella intermedia strains capable of degrading Linear Low-Density Polyethylene (LLDPE)

Zaman, I.; Moosa, M. M.; Hossain, M. M.

10.1101/2025.11.09.687417 — microbiology — Posted on 2025-11-09

3878 Host EV derived lipids promote malaria parasite development via mosquito fatty acid oxidation

Song, X.; Cai, W.; Wu, J.; Liu, L.; Gu, X.; Zhou, H.; Zhao, H.; Tian, P.; Xu, Q.; Qian, K.; Huang, W.; Wang, J.

10.1101/2025.11.09.687433 — microbiology — Posted on 2025-11-09

3879 Synergy unleashed: Leishmania donovani GP63 paralogues cooperatively function to drive parasite infectivity at various pathogenic stages and regulate host survival mechanisms

Manna, D.; Nandi, S.; Jana, S.; Zahanova, K.; Bhattacharya, S.; S, D.; Pradhan, N.; Pandey, N.; Biswas, D.; Mandal, M.; Mukherjee, G.; Yurchenko, V.; Mukherjee, B.

10.1101/2025.11.09.687440 — microbiology — Posted on 2025-11-09

3880 Microcompartments in Hodarchaeales: a bioenergetic engine that could have fuelled eukaryogenesis

Du, H.; Xu, A.; Feng, X.; Huang, W.-C.; Li, H.; Liu, L.; Li, Y.; Zhang, S.; Song, N.; Appler, K. E.; Baker, B.; Koonin, E. V.; Li, M.; Liu, Y.

10.1101/2025.11.08.687404 — microbiology — Posted on 2025-11-09

3881 Quantitative evaluation of growth rate and survival of planktonic yeast under dual-parameter photodynamic treatment

Maldonado-Carmona, N.; Insero, G.; Fusi, F.; Romano, G.

10.1101/2025.11.09.687416 — microbiology — Posted on 2025-11-09

3882 Proteomic characterization of extracellular vesicles from 12 commensal bacterial species

Makunja, R. N.; Maltseva, A.; Pessa-Morikawa, T.; Khatun, M.; Stensland, M.; Kaisanlahti, A.; Muhandiram, S.; Ruuska-Loewald, T.; Nyman, T. A.; Niku, M.

10.1101/2025.11.06.686325 — microbiology — Posted on 2025-11-09

3883 HIV broadly neutralizing antibody escape dynamics drive the outcome of AAV vectored immunotherapy in humanized mice

Galvez, N. M. S.; Nitido, A. D.; Yoo, S. B.; Cao, Y.; Deal, C. E.; Boutros, C. L.; MacDonald, S. W.; Soto Albrecht, Y. E.; Lam, E. C.; Sheehan, M. L.; Parsons, D.; Lin, A. Z.; Deymier, M. J.; Brady, J. M.; Moon, B.; Bullock, C. B.; Tanno, S.; Pegu, A.; Chen, X.; Liu, C.; Koup, R. A.; Mascola, J. R.; Vrbanac, V. D.; Lingwood, D.; Balazs, A. B.

10.1101/2024.07.11.603156 — microbiology — Posted on 2025-11-09

3884 Confidence-based Prediction of Antibiotic Resistance at the Patient Level

Inda-Diaz, J. S.; Johnning, A.; Hessel, M.; Sjoberg, A.; Lokrantz, A.; Helldal, L.; Jirstrand, M.; Svensson, L.; Kristiansson, E.

10.1101/2023.05.09.539832 — microbiology — Posted on 2025-11-09

3885 Meningeal γδ T cells facilitate bacterial entry into the brain in neonatal meningitis and trigger long-term behavioural sequelae

Lorga, I.; Soares, J.; Bravo, J.; Mesquita, P.; Ribeiro, N.; Rodrigues, J.; Hassan, A.; Mesquita, M.; Cavadas, B.; Georgiev, H.; Magalhaes, A.; Summavielle, T.; Vilanova, M.; Ribot, J. C.; Bonifacio Andrade, E.

10.1101/2025.11.07.686929 — immunology — Posted on 2025-11-09

3886 Coordinated circulating and tissue-based T cell responses precede xenograft rejection

Novikova, E.; Severa, E.; Chen, H.; Doepke, E.; Chacon, F.; Fathi, F.; Suek, N.; Vermette, B.; Bombardi, R.; Schmauch, E.; Williams, S. H.; Kim, J. I.; Aljabban, I.; Eitan, T.; Jaffe, I. S.; Hammond, G.; Khalil, K.; Mattoo, A.; Tatapudi, V.; Skolnik, E.; Weldon, E. P.; Ayares, D.; Nellore, A.; Sykes, M.; Griesemer, A. D.; Stern, J. M.; Keating, B. J.; Montgomery, R. A.; Herati, R. S.

10.1101/2025.11.07.687259 — immunology — Posted on 2025-11-09

3887 Escherichia coli-induced gut IL-33 release inhibits lung type 2 allergic responses

Salgado, C. L.; Ayupe, M. C.; Rodrigues, J. F.; Mandu-Goncalves, L.; Silva, L. M.; Pizzolante, B. C.; Oliveira, B. d. C.; Silva, G. W.; Moreira, F.; de Oliveira, E. E.; Araujo, M. V. d.; Rodrigues, G. M. B.; Zamame, J. A.; Brammer, K.; Santiago-Carvalho, I.; Macedo, B. d. G.; Alves-Filho, J. C.; Kita, H.; Norton, E.; D Imperio-Lima, M. R.; de Souza Ferreira, L. C.; Borges da Silva, H.; Fonseca, D. M. d.

10.1101/2025.11.07.687219 — immunology — Posted on 2025-11-09

3888 Neurophysiology of mismatch negativity generation: a biophysical modeling study

Fernandez Pujol, C.; Bruce, J.; Thorpe, R. V.; Jones, S. R.; Dykstra, A. R.

10.1101/2025.11.08.687373 — neuroscience — Posted on 2025-11-09

3889 Two classes of amine/glutamate multi-transmitter neurons innervate Drosophila internal male reproductive organs

Chaverra, M.; Toney, J. P.; Dardenne-Ankringa, L. D.; Knee, J. T.; Morris, A. R.; Wadhams, J. B.; Certel, S. J.; Stowers, R. S.

10.1101/2025.07.23.666348 — neuroscience — Posted on 2025-11-09

3890 Blockade of associative spine enlargement impairs awake cortical function

Zhou, S.; Sawada, T.; Arima, T.; Panezai, S. K.; Ohtsuka, M.; Okazaki, H.; Takaramoto, S.; Terada, S.-I.; Kondo, M.; Hashimoto, T.; Ohki, K.; Matsuzaki, M.; Yagishita, S.; Kasai, H.

10.1101/2025.11.06.686434 — neuroscience — Posted on 2025-11-09

3891 Integrated Cross-Organ Transcriptomic Analysis Uncovers Conserved Gene Signatures Predictive of Allograft Rejection

Poorvi, H. C.; Vinod, P. K.

10.1101/2025.11.07.687316 — systems biology — Posted on 2025-11-09

3892 A minimal activator-inhibitor-repressor model of the hepatic circadian clock

Delpierre, P.; Lefranc, M.

10.1101/2025.08.08.669290 — systems biology — Posted on 2025-11-09

3893 A Deep Learning Framework for Quantifying Dynamic Self-Organization in Myxococcus xanthus

Zhang, J.; Caro, E. A.; Chen, P.; Khan, T. T.; Murphy, P. A.; Shimkets, L. J.; Patel, A. B.; Welch, R. D.; Igoshin, O. A.

10.1101/2025.11.07.686839 — systems biology — Posted on 2025-11-09

3894 Engineering butyrate-producing Lachnospiraceae to treat metabolic disease

Arnold, J.; McClure, S.; Glazier, J.; Ahan, R. E.; Shakya, S.; Villegas, D.; Chen, T. L.; Fuerte-Stone, J.; McGann, R.; Mimee, M.

10.1101/2025.11.08.687059 — synthetic biology — Posted on 2025-11-09

3895 Virus induced transgene- and tissue-culture free heritable genome editing in tomato

Jacobsen, S. E.; Liu, Y.; Weiss, T.; Lee, J.; Powell, J.; Choo, S. Y. C.; Roshannai, E.; Kamalu, M.; Amerasekera, J.; Feng, S.

10.1101/2025.11.08.687402 — plant biology — Posted on 2025-11-09

3896 Developing a Molecular Toolkit to ENABLE all to apply CRISPR/Cas9-based Gene Editing in planta

Abate, B. A.; Hahn, F.; Chirivi, D.; Betti, C.; Fornara, F.; Molloy, J. C.; Krainer, K. M. C.

10.1101/2025.11.09.687425 — plant biology — Posted on 2025-11-09

3897 Risk Factors and Patterns of Treponema Infection Affecting Olive Baboons in Gombe National Park

Mwacha, D.; Collins, D. A.; Raphael, J.; Wambura, P.; Hoza, A.

10.1101/2025.11.07.687138 — pathology — Posted on 2025-11-09

3898 Two-photon volumetric study of cleared, invasive ductal carcinoma breast tissue samples and associated axillary lymph nodes

Pisarovic, U.; van Nijnatten, T. J. A.; Kooreman, L. F. S.; Hildebrand, S.; Schueth, A. A.

10.1101/2025.11.07.687157 — cancer biology — Posted on 2025-11-09

3899 TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity

Du, J.; Wijayaratna, U. N.; Wang, X.; Fung, J. P.; Huang, B.; Farzaneh, F.; Kohn, D. B.; Combes, A. J.; Gaensler, K. M. L.

10.1101/2025.11.07.687000 — cancer biology — Posted on 2025-11-09

3900 A Sequential Triple-Drug Strategy for Selective Targeting of p53-Mutant Cancers

Bakin, A. V.; Alruwaili, M.; Guo, Y.; Zonneville, J.; Melendy, T.; Straubinger, R. M.; Foster, B. A.; Rajan, P.; Withers, H.; Chatley, S.; Iyer, R.; Fountzilas, C.

10.1101/2025.11.06.687028 — cancer biology — Posted on 2025-11-09

3901 Active bacterial pattern formation in evaporating droplets

Wilting, T. J.; Reijnier, A. W.; Brebels, M. H.; Villie, A.; Colin, R.; Gelderblom, H.

10.1101/2025.11.07.687264 — biophysics — Posted on 2025-11-09

3902 Seqwin: Ultrafast Identification of Signature Sequences in Microbial Genomes

Wang, M. X.; Kille, B.; Nute, M. G.; Zhou, S.; Stadler, L. B.; Treangen, T. J.

10.1101/2025.11.07.687294 — bioinformatics — Posted on 2025-11-09

3903 Identifying differential effects from eleven mixing techniques on mRNA lipid nanoparticle physicochemistry and biological performance

Bethiana, T.; Aljabbari, A.; Li, Y.; Mitra, H.; Baghbanbashi, M.; Harris, G.; Dasaro, S.; Masoomi, F.; Vago, F.; Hartzler, S.; Figueiredo, M.; Metskas, L. A.; Vlachos, P.; Ardekani, A.; Yeo, Y.; Ristroph, K.

10.1101/2025.11.07.687311 — bioengineering — Posted on 2025-11-09

3904 Cryo-EM reveals multiple mechanisms of ribosome inhibition by doxycycline

Stuart, W. S.; Isupov, M. N.; McLaren, M.; Jenkins, C. H.; Monier, A.; Daum, B.; Norville, I. H.; Gold, V. A. M.; Harmer, N. J.

10.1101/2025.11.08.686982 — biochemistry — Posted on 2025-11-09

3905 Overglycosylation introduces local changes in triple helix alignment in collagen type I fibril structure

Rutten, L.; Schaart, J. M.; Fermin, L. A. S.; Xu, J.; de Beer, M.; Van der Meijden, R. H. M.; Reiding, K. R.; Akiva, A.; Sommerdijk, N.; Macias-Sanchez, E.

10.1101/2025.11.09.687185 — biochemistry — Posted on 2025-11-09

3906 Control of gene output by intron RNA structure

Schärfen, L.; Bech, P.; Podszywałow-Bartnicka, P.; Neugebauer, K. M.

10.1101/2025.11.08.687378 — biochemistry — Posted on 2025-11-09

3907 The deubiquitinating enzyme Otu1 releases substrates from the conserved initiation complex of the Cdc48/p97 ATPase for proteasomal degradation

Li, H.; Guan, H.; Rapoport, T.

10.1101/2025.11.08.687396 — biochemistry — Posted on 2025-11-09

3908 Integrated analysis of multimodal long-read epigenetic assays

Marcus, J.; Dixon-Luinenburg, O.; Gamarra, N.; Schwartz, J. P.; Rozenwald, M.; Maslan, A.; Urnov, F.; Straight, A. F.; Altemose, N.; Ioannidis, N. M.; Streets, A.

10.1101/2025.11.09.687458 — genomics — Posted on 2025-11-09

3909 Continental diversification and insular speciation in a widespread passerine (Troglodytes musculus) in southern South America

Recuerda, M.; Kopuchian, C.; Fracas, P. A.; Tubaro, P. L.; Campagna, L.; Lijtmaer, D. A.

10.1101/2025.11.07.687267 — evolutionary biology — Posted on 2025-11-09

3910 Long-term population monitoring reveals an alarming decline in the endangered endemic Reunion Harrier Circus maillardi

Villers, A.; Cornulier, T.; Eraud, C.; Couturier, T.; Ferret, P.; Chiron, D.; Laurent, N.; Besnard, A.; Bretagnolle, V.; Salamolard, M.; Grondin, V.; Couzi, F.-X.; Fay, R.; Augiron, S.

10.1101/2025.11.07.687144 — ecology — Posted on 2025-11-09

3911 Three-dimensional correlated random walks for animal movement and habitat selection

Klappstein, N. J.; Michelot, T.; Togunov, R. R.; Mills Flemming, J.

10.1101/2025.11.07.687274 — ecology — Posted on 2025-11-09

3912 Sonic hedgehog signaling promotes basal epidermal fibrillin 3 expression for zebrafish fin ray branching

Horst, S. G.; Yette, G. A.; Henner, A. L.; Stewart, S.; Stankunas, K.

10.1101/2025.11.07.687116 — developmental biology — Posted on 2025-11-09

3913 Targeted recruitment of USP15 enhances CTLA4 surface levels and restricts its degradation.

Querques, F.; Ciampani, V.; Tey, P. Y.; Kutilek, V. D.; Kadic, E.; Clague, M. J.; Urbe, S.

10.1101/2025.11.07.687309 — cell biology — Posted on 2025-11-09

3914 The CENP-A chaperone complex spatially organizes centromeres

Gupta, H.; Haase, J.; Wu, Y.; Chen, J.; Karadimov, G.; Shroff, H.; Kelly, A. E.

10.1101/2025.11.07.687291 — cell biology — Posted on 2025-11-09

3915 Depletion of microenvironmental syndecan-2 impairs hematopoietic stem cell self-renewal and cytokine responses

Hagen, M. W.; Setiawan, N. J.; Wellington, R.; Woodruff, K. A.; Newman, C.; Billings, T. M.; Nazzaro, M. N.; Hadland, B.; Termini, C. M.

10.1101/2025.11.07.687077 — cell biology — Posted on 2025-11-09

3916 Viscoelasticity driven deformation dynamics of the substrate affect mechanically induced Ca2+ signals

Peussa, H.; Peltola, S.; Tervonen, A.; Lehtimäki, S.; Kauppila, M.; Bhati, R.; Fedele, C.; Tran, H.; Mäntylä, E.; Priimägi, A.; Nymark, S.; Ihalainen, T. O.

10.1101/2025.11.07.687272 — cell biology — Posted on 2025-11-09

3917 Reconstitution of multistep recruitment of ULK1 to membranes in autophagy

Duan, Y.; Lu, Y.; Paul, S.; Betz, J.; Wilhelm, L. P.; Cook, A. S. I.; Ren, X.; Adriaenssens, E.; Martens, S.; Ganley, I.; Hummer, G.; Hurley, J. H.

10.1101/2025.11.07.687251 — cell biology — Posted on 2025-11-09

3918 Antiphospholipid syndrome (APS) is a platelet factor 4 (PF4)-centric immunothrombotic disorder

Field, C. O.; Sarka, A.; Bdeir, K.; Kim, H.; Yadav, S. K.; Oberg, J.; Zhao, G.; Jiang, S.; Gumedeli, M.; McCrae, K. R.; Arepally, G. M.; Rollin, J.; Gruel, Y.; Ortel, T.; Kowalska, M. A.; Cines, D. B.; Gollomp, K.; Rauova, L.; Poncz, M.

10.1101/2025.11.07.687095 — cell biology — Posted on 2025-11-09

3919 Drosophila HS dendrites are resilient to adult-onset deficits in mitochondrial dynamics

Wang, H. Q.; Fortson, D. G.; Burton, E. D.; Whitbeck, H. S.; Robles, B. M.; Bortey, L.; Adler, A. J.; Kalai, J. I.; Napoleone, G.; Barnhart, E. L.

10.1101/2025.11.07.687201 — cell biology — Posted on 2025-11-09

3920 Gene editing in "cell villages" enables exploring disease-relevant mutations in many genetic backgrounds

Battaglia, R. A.; Bolshakova, S.; Mazureac, I.; Liyanage, D.; Pettinari, N.; Johnson, A.; Crouse, E.; Habib, S.; Flessas, I.; Nadig, A.; Hawes, D.; Tegtmeyer, M.; Becker, C.; Ghosh, S.; Genovese, G.; Hogan, M.; Maglieri, A.; Barrett, L. E.; Daheron, L.; McCarroll, S. A.; Nehme, R.

10.1101/2025.11.08.687374 — cell biology — Posted on 2025-11-09

3921 CRK2 modulates flowering in Arabidopsis together with GLYCINE- RICH RNA BINDING PROTEIN 7 (GRP7)

Colina, F. J.; Krasensky-Wrzaczek, J.; Perez Guillen, A.; Wrzaczek, M.

10.1101/2025.08.05.668606 — plant biology — Posted on 2025-11-09

3922 Polysialic acid is a versatile marker for retinal Müller glia in common vertebrate model organisms and systems

San Juan, A. N.; Tran, A. D. N. N.; Kriese, L. M.; Van Engelen, N. H. N.; Hore, D.; Sharkova, M.; Noel, N. C. L.; Hunter, C.; Spencer Carreira, O.; Hocking, J. C.; Willis, L. M.; Carr, B. J.

10.1101/2025.09.04.672712 — cell biology — Posted on 2025-11-09

3923 Coiling in gastropods: a lead to synthesis

Filin, I.

10.1101/2025.06.24.659690 — evolutionary biology — Posted on 2025-11-09

3924 Keratin 15 promotes a progenitor cell state in basal keratinocytes of skin epidermis

Redmond, C. J.; Steiner, S. N.; Cohen, E.; Johnson, C. N.; Ozlu, N.; Coulombe, P. A.

10.1101/2025.02.27.640633 — developmental biology — Posted on 2025-11-09

3925 Distinct cis-acting elements combinatorically mediate co-localization of mRNAs encoding for co-translational interactors in cytoplasmic clusters in S. cerevisiae

Shhade, Q.; Estrada, M.; Hanna, R.; Makhzumy, M.; Bar-Yosef, H.; Kramer, G.; Bukau, B.; Shiber, A.

10.1101/2025.02.19.639054 — cell biology — Posted on 2025-11-09

3926 Pre-exposure to time-restricted feeding reduces tissue CD4+ T cells with a limited effect on Mycobacterium tuberculosis clearance at the early time point

Gupta, A.; Yadav, N.; Das, S.; Rajendra Kumar Reddy, R.; Sharma, N.; Suryawanshi, A. R.; Maras, J. S.; Nanda, R.

10.1101/2025.04.18.649546 — immunology — Posted on 2025-11-09

3927 LRP8 is a Receptor for Yellow Fever Virus

Mei, M.; Yang, Y.; Zhang, Z.; Yin, Y.; Tan, J.; Jiang, C.; Gao, Y.; Wang, Z.; Wang, D.; Li, Y.; Cong, Y.; Zhang, Z.; Peng, Y.; Tan, W.; Li, J.; Li, L.; Wang, H.; Lang, R.; He, Q.; Deng, Z.; Shan, C.; Zhang, Y.; Cheng, G.; Tan, X.; Huang, X.

10.1101/2025.10.28.685229 — microbiology — Posted on 2025-11-09

3928 Researchers' perspectives on preregistration in animal research

Priboi, C.; Mayer, B.; Vergauwe, E.; Elger, B. S.; Würbel, H.

10.1101/2025.11.07.687141 — scientific communication and education — Posted on 2025-11-09

3929 Stacking of anthocyanin related QTLs in the chromosome 10 and postulation of SmNac-like gene to be involve in anthocyanin biodhynthesis

Gomis-Cebolla, J.; Manrique, S.; Arrones, A.; Toledo-Tolgar, M. D.; Luna, J.; Baraja-Fonseca, V.; Sanchez-Pascual, J.; Gimeno-Paez, E.; Plazas, M.; Gramazio, P.; Vilanova, S.; Prohens, J.

10.1101/2025.09.19.677371 — plant biology — Posted on 2025-11-09

3930 BAP1 modulates endoplasmic reticulum stress signaling and balances liver homeostasis and malignant progression

Gege, O. O.; Seretny, A.; Butthof, L.; Pan, L.; Wendler-Link, L.; Traini, L.; Boese, L.; Neuhaeuser, S.; Scheiter, A.; Heide, D.; Luechtenborg, C.; Bruegger, B.; Calvisi, D.; Heikenwaelder, M.; Zucman-Rossi, J.; Breining, M.; Tschaharganeh, D. F.

10.1101/2025.11.06.686752 — cancer biology — Posted on 2025-11-09

3931 Cryo-electron microscopy structures of a zinc uptake ABC transporter

Pang, C.; Nguygen, H.; Zhang, Q.; Bahar, I.; Liu, Q.

10.1101/2025.07.03.663024 — biochemistry — Posted on 2025-11-09

3932 Cell-cycle-dependent cues regulate temporal patterning of the Drosophila central brain neural stem cells

Syed, M. H.; Chaya, G. M.

10.1101/2025.01.16.629716 — developmental biology — Posted on 2025-11-09

3933 Structural basis and physiological significance of non-canonical Gs coupling to the prototypical Gi-coupled melatonin MT1 receptor

Oishi, A.; Okamoto, H.; Ikegami, K.; McHugh, R.; Masri, B.; Kusakizako, T.; Kobayashi, K.; Karamitri, A.; Cecon, E.; Dam, J.; Nagase, M.; Tikhonova, I.; Nureki, O.; Jockers, R.

10.1101/2025.11.08.687348 — molecular biology — Posted on 2025-11-09

3934 Generative cerebral vasculature visualization using spatialtranscriptomic data

Berg, I.; Wu, J.; Koelzer, V. H.

10.1101/2025.07.10.664153 — neuroscience — Posted on 2025-11-09

3935 Inferring the causes of animal social network structure from time-series data

Kawam, B.; McElreath, R.; Ostner, J.; Redhead, D.; Schuelke, O.

10.1101/2025.11.08.687336 — animal behavior and cognition — Posted on 2025-11-09

3936 Competition between memories for reactivation as a mechanism for long-delay credit assignment

Mokashe, S.; Miller, P.

10.1101/2025.11.08.687292 — neuroscience — Posted on 2025-11-09

3937 Synaptic Synchronization-Based Learning of Pattern Separation in Self-Organizing Probabilistic Spiking Neural Networks

Faghihi, F.; Moustafa, A.; Neymotin, S. A.

10.1101/2025.11.08.687345 — neuroscience — Posted on 2025-11-09

3938 Parvalbumin interneurons gate and shape striatal sequences

Duhne, M.; Gonzalez Montalvo, I.; Zheng, C. S.; Pelattini, L.; Berke, J. D.

10.1101/2025.11.08.687375 — neuroscience — Posted on 2025-11-09

3939 Neural manifolds that orchestrate walking and stopping

Komi, S. A.; Kaur, J.; Winther, A.; Bonfils, M. C. A.; Houser, G. A.; Sorensen, R. J. F.; Li, G.; Sobriel, K.; Berg, R. W.

10.1101/2025.11.08.687367 — neuroscience — Posted on 2025-11-09

3940 Intrinsic ion dynamics underlies the temporal nature of resting-state functional connectivity

Gonzalez, O. C.; Sanda, P.; Hlinka, J.; Bazhenov, M.; Krishnan, G.

10.1101/2025.11.08.687387 — neuroscience — Posted on 2025-11-09

3941 Sensory processing reformats odor coding around valence and dynamics

Lizbinski, K.; Ellison, K. J.; Sancer, G.; Mao, H. X.; Jeanne, J. M.

10.1101/2025.11.08.687380 — neuroscience — Posted on 2025-11-09

3942 Cell surface markers identify astrocyte subpopulations in the adult hippocampus with a heterogeneous response to aging

Casares-Crespo, L.; Cano-Jaimez, M.; Anta, R.; Ripolles-Boix, A.; Robledo-Yague, F.; Zuniga-Trejos, S.; Mira, H.

10.1101/2025.11.07.685575 — neuroscience — Posted on 2025-11-09

3943 Population-level temporal decoding and dynamical structure in frontostriatal circuits during decision making

Goldring, A. B.; De, A.; Stevenson, T.; Stewart, K.; Akhmetzhanova, A.; Chaudhuri, R.; Hanks, T. D.

10.1101/2025.11.07.687310 — neuroscience — Posted on 2025-11-09

3944 Self-multimerization of mRNA LNP-derived antigen improves antibody responses

Despins, C. A.; Round, J.; Dreolini, L.; Lee, T. S.; Brown, S. D.; Holt, R.

10.1101/2025.09.09.675153 — immunology — Posted on 2025-11-08

3945 Identifying the exposure of taxonomic, functional, and phylogenetic diversity of steppe birds to renewable energy developments

Medrano Vizcaino, P.; Mougeot, F.; Arroyo, B.; Bota, G.; Giralt, D.; Maeso-Pueyo, L.; Martin, C. A.; Morales, M. B.; Olea, P. P.; Traba, J.; Benitez-Lopez, A.

10.1101/2025.11.07.687200 — ecology — Posted on 2025-11-08

3946 GRAS salts and eastern hemlock extract: a dual approach to sustainable plant disease management‎‎

Soltaniband, V.; Barrada, A.; Delisle-Houde, M.; Dorais, M.; Tweddell, R. J.; Michaud, D.

10.1101/2025.11.07.687209 — plant biology — Posted on 2025-11-08

3947 Transcriptomic Profiling of scWAT Reveals Reduced Lipid-Associated Macrophage Signatures in Long-Term Endurance- and Resistance-Trained Athletes

Emanuelsson, E. B.; Reitzner, S. M.; Quizon, A.; Burrows, J. T.; Elmastas, M.; Jalkanen, J.; Perez, S.; Gilljam, H.; Lindholm, M. E.; Norrbom, J.; Palsson, B.; Zielinski, D. C.; Ryden, M.; Chapman, M. A.; Sundberg, C. J.

10.1101/2025.11.07.687158 — physiology — Posted on 2025-11-08

3948 NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations

Riveros, I.; Zhang, B.

10.1101/2025.11.07.687145 — biophysics — Posted on 2025-11-08

3949 MEDUSA: Maintaining Entire DNA Duplexes for Utmost Sequencing Accuracy

Xiong, K.; Li, R.; Li, N.; Liu, R.; Narayan, A.; Rhoades, J.; Song, C.; Lindsley, R. C.; Parsons, H. A.; Makrigiorgos, G. M.; Adalsteinsson, V. A.

10.1101/2025.11.07.687202 — genomics — Posted on 2025-11-08

3950 LRMD: Reference-Free Misassembly Detection Based on Multiple Features from Long-Read Alignments

Wang, J.; Nie, F.; Shi, X.

10.1101/2025.11.07.686952 — genomics — Posted on 2025-11-08

3951 Spatiotemporal data integration for marine megafauna SDMs in dynamic environments: A point process approach

Klaassen, M.; Fernandez, M.; Lindgren, F.; Morera-Pujol, V.; Thomas, L.; Oliveira, N.; Castro, J.; Martinho, F.; Magalhaes, S.; Rodrigues, A.; Martins, M.; Alves, F.; Marques, T. A.

10.1101/2025.11.07.687170 — ecology — Posted on 2025-11-08

3952 Human pluripotent stem cell-derived macrophages modify development of human kidney organoids

Lopes, F. M.; Bantounas, I.; Sarov, A.; Woolf, A. S.; Kimber, S. J.

10.1101/2025.11.07.687192 — developmental biology — Posted on 2025-11-08

3953 Development of long-term oyster tissue cultures reveals cellular plasticity, regenerative potential, and sustained physiological activity

Sullivan, K. R.; Steketee, P. C.; Maxwell, S.; Morrison, L.; Regan, T.; Bean, T. P.

10.1101/2025.11.07.687009 — cell biology — Posted on 2025-11-08

3954 Suppression of hepatic amino acid catabolism by the human-specific lncRNA hLMR1

Jaso-Vera, M. E.; Takaoka, S.; Faccioli, L.; Hu, Z.; Soto-Gutierrez, A.; Ruan, X.

10.1101/2025.11.08.686969 — molecular biology — Posted on 2025-11-08

3955 The EXS domain of rice PHOSPHATE1 (OsPHO1;2) reduces the low phosphate response through jasmonate signaling

Mani, B.; Maurya, K.; Verma, L.; Gupta, P.; Kohli, P. S.; Gupta, G.; Jaskolowski, A.; Poirier, Y.; Giri, J.

10.1101/2025.11.07.687324 — molecular biology — Posted on 2025-11-08

3956 Outbreak of leaf spot disease of Cavendish banana caused by Nigrospora spp. in Mindanao Island, Philippines

Nozawa, S.; Harada, Y.; Takata, Y.; Uchida, K.; Malonzo, M. A.; Valle, R.; Chavez, S. M.; Penalosa, A. F.; Watanabe, K.

10.1101/2025.11.07.685480 — molecular biology — Posted on 2025-11-08

3957 Decreased substrate stiffness leads to mitochondrial dysfunctions and Endothelial to Mesenchymal transition through Focal Adhesion Kinase activity in corneal endothelial cells

Ghag, S. A.; de Campos, V. S.; Murugan, S.; Herberg, S.; Shyam, R.

10.1101/2025.11.08.687366 — molecular biology — Posted on 2025-11-08

3958 Formation of DNA duplexes in the presence of urea as a chaotropic agent.

Gottschalk, M.; Jacobi, R.; Rosencrantz, S.; Rosencrantz, R. R.; Fedorych, O.

10.1101/2025.11.07.686900 — molecular biology — Posted on 2025-11-08

3959 Two-Year Field Trial of Genetically Engineered American Chestnut Reveals Greater Fungal Blight Tolerance Compared to Wild-Type Full-Sibling Trees

Klak, T.; Travis, S.; May, V. G.; Tan, E. H.; Chatfield, M. W.; Wheeler, M.

10.1101/2025.11.07.687213 — synthetic biology — Posted on 2025-11-08

3960 Effects of mixing technique and ethanol removal on lipidnanoparticle physicochemical properties

Mitra, H.; Bethiana, T.; Jia, D.; Majidi, M.; Mota-Santiago, P.; Milogrodzka, I.; Manni, L. S.; Ristroph, K. D.; Ardekani, A. M.

10.1101/2025.11.07.686408 — biophysics — Posted on 2025-11-08

3961 Structural Integrity of RyR2 Clusters Controls Cardiac Calcium Leak

Noren, A.; Shiferaw, Y.

10.1101/2025.11.07.687312 — biophysics — Posted on 2025-11-08

3962 Estimating haplotype values and mutation effects in the context of a local DNA tree

Mafra Fortuna, G.; Obsteter, J.; Moskric, A.; Gorjanc, G.

10.1101/2025.11.08.687335 — genomics — Posted on 2025-11-08

3963 Scale dependent temporal and spatial patterns of population change in anadromous sea trout (Salmo trutta) in Scotland over seven decades

Dodd, J. A.; Moore, I. E.; Bowman, A. W.; Bean, C. W.; Rodger, J. R.; Adams, C. E.

10.1101/2025.11.07.687197 — ecology — Posted on 2025-11-08

3964 FAM19A4 Enhances Neutrophil Respiratory Burst via p38 MAPK in Lethal Sepsis

Li, S.; Zhu, F.; Jiang, L.; Xue, H.; Li, T.; Wang, T.; Wang, W.; Zhang, K.

10.1101/2025.11.07.687190 — molecular biology — Posted on 2025-11-08

3965 A TaqMan Assay That Knows Its Mite: Specific Detection of Tropilaelaps mercedesae Clade I

van Gent- Pelzer, M.; Hendriks, M.; Disayathanoowat, T.; Phokasem, P.; Graham, H.; Panziera, D.

10.1101/2025.11.07.686760 — molecular biology — Posted on 2025-11-08

3966 Researchers' perspectives on preregistration in animal research

Priboi, C.; Würbel, H.; Mayer, B.; Vergauwe, E.; Elger, B. S.

10.1101/2025.11.07.687141 — scientific communication and education — Posted on 2025-11-08

3967 Assessing fish diversity in the Amazon: The impact of primers and reference libraries in eDNA surveys

Hashimoto, S.; Carvalho, S. V.; Miranda, S. d. S. C.; Machado, V. N.; Carvalho, L. N.; Deus, C. P. d.; Farias, I. P.; Hrbek, T.

10.1101/2025.11.07.686145 — genetics — Posted on 2025-11-08

3968 Microprotein miP-PSTPIP2 affects cytoskeleton dynamics to modulate endothelial cell endocytosis, barrier function and migration

Gueven, B.; Bezuneh, B.; Raheja, M.; Szymanski, W.; Brandes, R. P.; Graumann, J.; Fleming, I.; Siragusa, M.

10.1101/2025.11.07.687176 — cell biology — Posted on 2025-11-08

3969 Low concentrations of tetrasodium EDTA cause significant killing of biofilm-associated P. aeruginosa in high validity models of chronic wound and CF lung infections but not in a model of endotracheal tube colonisation

Orababa, O. Q.; Cornbill, C.; Kade, A.; Reddy, N.; Gulati, R.; Harrison, F.

10.1101/2025.11.08.687333 — microbiology — Posted on 2025-11-08

3970 Structural basis and physiological significance of non-canonical Gs coupling to the prototypical Gi-coupled melatonin MT1 receptor

Okamoto, H.; Oishi, A.; Ikegami, K.; McHugh, R.; Masri, B.; Kusakizako, T.; Kobayashi, K.; Karamitri, A.; Cecon, E.; Dam, J.; Nagase, M.; Tikhonova, I.; Nureki, O.; Jockers, R.

10.1101/2025.11.08.687348 — molecular biology — Posted on 2025-11-08

3971 Impact of N6-methyladenosine (m6A) machinery on HIV-1 replication in primary CD4+ T cells

Jackson-Jones, K. A.; Simons, L. M.; Huang, S.; Joseph, T.; Sawyer, A.; Wu, L.; Hultquist, J. F.

10.1101/2025.11.07.686373 — microbiology — Posted on 2025-11-08

3972 Impact of gestational antibiotics on maternal and offspring gut microbiota and growth in pigs

Mahmud, M. R.; Orro, T.; Munsterhjelm, C.; Pessa-Morikawa, T.; Ahlqvist, K.; Junnikkala, S.; Konig, E.; Pujolassos, M.; Calle, M. L.; Kwon, H. N.; Oliviero, C.; Heinonen, M.; Niku, M.

10.1101/2025.11.08.687112 — microbiology — Posted on 2025-11-08

3973 Genomic insights into antiviral defense systems in haloarchaea and their impact on virus susceptibility

Aguirre-Sourrouille, Z.; Hackl, T.; Oksanen, H. M.; Quax, T. E. F.

10.1101/2025.11.08.687337 — microbiology — Posted on 2025-11-08

3974 Influence of ploidy and genetic background on stress tolerance of intraspecific yeast hybrids

Rinta-Harri, K.; Koponen, T.; Mojzita, D.; Jouhten, P.; Liti, G.; Krogerus, K.

10.1101/2025.11.08.686703 — microbiology — Posted on 2025-11-08

3975 Predation limits the abundance of {triangleup}gacA cheaters in Pseudomonas protegens populations

Steele, M. I.; Oxender, E. E.; Ge, C.; Queller, D. C.; Strassmann, J. E.

10.1101/2025.11.08.687362 — microbiology — Posted on 2025-11-08

3976 Cross-Fostering with control dams rescues Gut Dysbiosis and Chromatin-associated Transcriptional Changes in Offspring of Opioid-Exposed Dams

Pandey, S.; Abu, Y. F.; Singh, P. K.; Roy, S.

10.1101/2025.11.07.687278 — microbiology — Posted on 2025-11-08

3977 Nurture over nature in new Micromonospora spp. strains metabolism: multi-omics analyses reveal fermentation conditions as the dominant driver over phylogeny

Han, J.-R.; Li, S.; Lian, W.-H.; Xu, L.; Duan, L.; Li, J.; Shi, G.-Y.; Wei, Q.-C.; Ali, M.; Li, W.-J.; Dong, L.

10.1101/2025.11.08.687343 — microbiology — Posted on 2025-11-08

3978 Breaking the ''one nucleus, one whole genome'' rule: Neurospora crassa separates its haploid chromosomes into different nuclei

Tan, J.; Xu, Y.; Tian, L.; Chen, X.; Fischer, M.; Zhang, Y.; Li, X.

10.1101/2025.11.08.687325 — microbiology — Posted on 2025-11-08

3979 Translatable electrophysiological and behavioral abnormalities in a humanized model of SYNGAP1-disorder

Felix, A. J.; Brown, B. L.; Marotta, N.; Gessner, M. J.; Houserova, M.; Huerta-Ocampo, I.; Wilson, T.; Randell, R.; Dawicki-McKenna, J.; Reinhardt, D.; Uchida, K.; McSalley, I.; McKee, J. L.; Helbig, I.; Boland, M. J.; Davidson, B. L.; Prosser, B. L.

10.1101/2024.08.22.609238 — neuroscience — Posted on 2025-11-08

3980 A unifying account of replay as context-driven memory reactivation

Zhou, Z.; Kahana, M. J.; Schapiro, A. C.

10.1101/2023.03.22.533833 — neuroscience — Posted on 2025-11-08

3981 Rubisco is slow across the tree of life

de Pins, B.; Malbranke, C.; Jablonska, J.; Shmuel, A.; Sharon, I.; Bitbol, A.-F.; Mueller-Cajar, O.; Noor, E.; Milo, R.

10.1101/2025.01.19.633714 — systems biology — Posted on 2025-11-08

3982 Mitochondrial G4 DNA Cleavage by EndoG Activates a Flexible, Stress-Dependent Repair Response via Double strand break repair pathways

Rathore, D.; Raghavan, S. C.

10.1101/2025.08.26.672151 — molecular biology — Posted on 2025-11-08

3983 Functional Effects of CD33 SNP rs12459419 on Microglial Gene Regulation and Alzheimer's Disease Risk

Lu, Y.

10.1101/2025.11.07.684725 — molecular biology — Posted on 2025-11-08

3984 Investigation of Powassan virus lineage II pathogenesis and neurotropism in mice

Courtney, S. J.; Gallichotte, E.; Nilsson, E.; Trammell, C.; Kimball, K.; Fagre, A.; Vilander, A.; Overby, A. K.; Ebel, G. D.

10.1101/2025.11.07.687151 — microbiology — Posted on 2025-11-08

3985 Influence of iron uptake systems on cefiderocol activity in Escherichia coli: at the crossroads of antibiotic resistance and virulence

Mallecot, E.; Berti, V.; Petitjean, M.; MEYER, J.; Gueye, S.; Morel-Journel, T.; Clermont, O.; Poirel, L.; Denamur, E.; Royer, G.; Armand, L.

10.1101/2025.11.06.687119 — microbiology — Posted on 2025-11-08

3986 Modeling Phage Therapy

De Boer, R. j.; Schooley, R.; Perelson, A. S.

10.1101/2025.11.08.687339 — microbiology — Posted on 2025-11-08

3987 The Bone Morphogenetic Pathway Controls the Uptake of Infectious Prions

De Cecco, E.; Mariutti, G.; Oueslati Morales, C. O.; Caredio, D.; Erana, H.; Appleton, C.; Sellitto, S.; Hornemann, S.; Scialo, C.; Yin, J.-A.; Vidal, E.; Polymenidou, M.; Castilla, J.; Aguzzi, A.

10.1101/2025.11.08.687161 — neuroscience — Posted on 2025-11-08

3988 Drosophila ryanodine receptor gene triggers functional and developmental muscle properties and could be used to assess the impact of human RYR1 mutations

Jagla, K.; Zmojdzian, M.; Teresa, J.; Cherik, F.; Dubinska-Magiera, M.; Migocka-Patrzalek, M.; Daczewska, M.; Rendu, J.; Sarret, C.

10.1101/2025.11.06.686948 — developmental biology — Posted on 2025-11-08

3989 Secondary bile acid lithocholic acid ameliorates colitis-like inflammation in a human intestine-on-chip system

Kaden, T.; Allwang, M.; Stallhofer, J.; Graf, K.; Raasch, M.; Mosig, A. S.

10.1101/2025.11.07.686950 — cell biology — Posted on 2025-11-08

3990 Conjugates of α-d-Galp-(1->3)-β-d-Galp for the serological diagnosis of Chagas disease.

Balouz, V.; Lopez, R.; Conte, N.; Abal, M.; Ducrey, I.; Giorgi, M. E.; de Lederkremer, R. M.; Altcheh, J.; Ciocchini, A. E.; Melli, L. J.; Marino, C.; Buscaglia, C. A.

10.1101/2025.11.07.687140 — microbiology — Posted on 2025-11-08

3991 Daily Heat Stress Induces Accumulation of Non-functional PSII-LHCII and Donor-side Limitation of PSI via Downregulation of the Cyt bf Complex in Arabidopsis thaliana

Laihonen, L.; Tomberg, T.; Vuorijoki, L.; Mulo, P.; Rantala, M.

10.1101/2025.11.06.687104 — plant biology — Posted on 2025-11-08

3992 Characterization of an Open-Channel Structure and Lateral Conduction Pathway in the Cation-Selective Pentameric Ligand-Gated Ion Channel, ELIC

Arcario, M. J.; Wu-Chen, E. J.; Henin, J.; Brannigan, G.; Cheng, W. W.-L.

10.1101/2025.11.06.686614 — biophysics — Posted on 2025-11-08

3993 Multi-Dimensional Spatiotemporal Attention Neural Network for Next Generation Sequencing Basecalling

Peng, K.; Chen, W.; Yao, T.; Xia, H.; Fu, G.; Li, G.; Bao, Y.; Liu, E.; Zhao, L.; Wang, G.

10.1101/2025.11.06.686985 — bioinformatics — Posted on 2025-11-08

3994 High dynamic range shortwave infrared (SWIR) imaging of mice with an InGaAs camera

Patel, A.; Zhong, X.; Moffett, M. A.; Sun, Y.; Dennis, A. M.

10.1101/2025.11.06.687088 — bioengineering — Posted on 2025-11-08

3995 Common marmosets (Callithrix jacchus) do not differentiate between familiar and unfamiliar conspecifics based on pitch contour information

Grabner, J. V.; Pigmans, E.; Mircheva, M.; Knoester, J. M.; Baumgartner, R.; Pomper, U.; Bugnyar, T.; Spierings, M. J.

10.1101/2025.10.27.684793 — animal behavior and cognition — Posted on 2025-11-08

3996 Postnatal developmental temperature affects the ontogeny of heat- and cold tolerance

Persson, E.; Correia, M.; Nord, A.

10.1101/2025.11.07.686921 — ecology — Posted on 2025-11-08

3997 Proteomic characterisation of matrix vesicles from primary osteoblasts indicates a mixed population with both exosomal and ectosomal routes of biogenesis.

Dillon, S.; Clews, C.; Kurian, D.; Nudelman, F.; Farquharson, C.; Stephen, L. A.

10.1101/2025.11.07.687130 — cell biology — Posted on 2025-11-08

3998 tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations

Tsui, H.-C. T.; Chan, C.-K.; Yuan, Y.; Elias, R.; Sun, J.; Marchand, V.; Jaroch, M.; Sun, G.; Manzoor, I.; Kutchuashvili, A.; Leszczynska, G.; Seaton, K.; Motorin, Y.; Rice, K. C.; Swairjo, M.; Dedon, P. C.; Winkler, M. E.; de Crecy-Lagard, V.

10.1101/2025.10.13.681863 — microbiology — Posted on 2025-11-08

3999 Structure basis for distinct protective mechanisms of IGHV3-23 antibodies targeting influenza hemagglutinin stem

Lv, H.; Huan, Y. W.; Pholcharee, T.; Teo, Q. W.; Liu, W.; Gopal, A. B.; Choi, D.; Ardagh, M. R.; Tan, T. J. C.; Sun, Y.; Mehta, A.; Li, J.; Szlembarski, M.; Huang, J. J.; Ma, E. X.; Wittenborn, L. E.; Kasture, P.; Mok, C. K. P.; Wu, N. C.

10.1101/2025.11.06.687086 — immunology — Posted on 2025-11-08

4000 Antibodies, Memory B Cells, and Antigen Valency Reshape B Cell Responses to Drifted Influenza Virus Vaccination

Reusch, L.; Mathew, N. R.; Schön, K.; Kosik, I.; Gibbs, J. S.; Mankowski, M. C.; Besavilla, D. F.; yewdell, j.; Bemark, M.; Angeletti, D.

10.1101/2025.11.07.687210 — immunology — Posted on 2025-11-08

4001 Repeated fentanyl abstinence intensifies opioid withdrawal and induces a proinflammatory state in striatal microglia

Bergkamp, D. J.; Coffey, K. R.; Dawkins, A. J.; Rice, M. T.; Peden-Asarch, A. M.; Neumaier, J. F.

10.1101/2025.11.06.687032 — neuroscience — Posted on 2025-11-08

4002 Patient-Specific Midbrain Organoids with CRISPR Correction Reveal Disease Mechanisms and Enable Therapeutic Evaluation in Neuronopathic Gaucher Disease

Lin, Y.; Liou, B.; Fannin, V.; Adler, S.; Mayhew, C. N.; Hammonds, J. E.; Hu, Y.-C.; Tchieu, J.; Zhang, W.; Zhao, X.; Beres, R. L.; Setchell, K. D.; Kaynak, A.; Qi, X.; Feldman, R. A.; Sun, Y.

10.1101/2025.11.06.686937 — neuroscience — Posted on 2025-11-08

4003 Morphological Identification of Ticks in district Swabi, Mardan, and Charsadda

Mohammad, A.; Hongsu, H.; Ali, A.; Zhao, J.; Wu, Y.; Alam, U.; Dai, J.; Zhao, C.; Zhao, T.; Hui, Z.; Zhihua, S.

10.1101/2025.11.07.687134 — zoology — Posted on 2025-11-08

4004 Barley (Hordeum vulgare) maintains tricarboxylic acid cycle activity without invoking the GABA shunt under salt stress

Bandehagh, A.; Taylor, N. L.

10.1101/2025.11.06.687118 — plant biology — Posted on 2025-11-08

4005 A 5'-end based Molecular Marker Enables Identification and Deployment of a Functional Rpi-vnt1.1 Allele for Durable Late Blight Resistance in Potato

Wang, S.; Wang, L.; Feng, S.; Hu, C.; Meng, X.; Chang, S.; Feng, Y.; Kong, L.; Zhao, X.

10.1101/2025.11.06.687089 — plant biology — Posted on 2025-11-08

4006 Permeabilization with fenchone enhances cryopreservation of Drosophila embryos

Zimmerman, D. M.; Yin, R.; Vaca, M.; Samuel, A. D. T.; de Bivort, B. L.

10.1101/2025.11.06.687078 — physiology — Posted on 2025-11-08

4007 Automated spermatogenic staging in PAS-stained testes of Sprague-Dawley rats using a deep learning model for nomal and atrophied tissues

Kim, D.-M.; Rho, J.-H.; Wee, S.-Y.; Son, H.-Y.

10.1101/2025.11.06.687107 — pathology — Posted on 2025-11-08

4008 Characterization of calcifications in posterior horn of human meniscus using micro-computed tomography

Karjalainen, V.-P.; Hellberg, I.; Turkiewicz, A.; Shakya, B. R.; Khoshimova, N.; Nevanranta, E. A.; Das Gupta, S.; Elkhouly, K.; Sjogren, A.; Finnila, M. A. J.; Onnerfjord, P.; Hughes, V.; Tjornstrand, J.; Englund, M.; Saarakkala, S.

10.1101/2025.11.07.686933 — bioengineering — Posted on 2025-11-08

4009 SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments

Calvo-Roitberg, E.; Lehman, J. W.; Tam, E.; Elhajjajy, S.; Engelhardt, B. E.; Pai, A. A.

10.1101/2025.11.06.687082 — genomics — Posted on 2025-11-08

4010 Extracellular matrix and cytoskeletal reverse remodeling pathways are key drivers of myocardial recovery following left ventricular assist device therapy

SHANKAR, T. S.; Marchetti, M.; Srinivasan, H.; Visker, J. R.; Hamouche, R.; Johnson, E.; Jeong, J.; Kyriakoulis, I.; Ling, J.; Sideris, K.; Selzman, C. H.; Hernandez, E. J.; Tristani-Firouzi, M.; Tseliou, E.; Drakos, S. G.; Wever-Pinzon, O.

10.1101/2025.11.06.687098 — genomics — Posted on 2025-11-08

4011 HeartMap: An Integrated Cell Atlas of 2.4 million cells across 209 Individuals in Health and Disease

Datar, Y.; Chaffin, M.; Simonson, B.; Mandia, A.; Ellinor, P. T.

10.1101/2025.11.06.686995 — cell biology — Posted on 2025-11-08

4012 3D Mapping of Intact Ovaries Reveals the Aging Dynamics of the Ovarian Reserve

D'Angelo, A.; Franco-Barranco, D.; Musy, M.; Sharpe, J.; Arganda-Carreras, I.; Boke, E.

10.1101/2025.11.07.686728 — cell biology — Posted on 2025-11-08

4013 Splicing of a core clock gene regulates seasonal adaptations by a winter gating mechanism

Hidalgo, S.; Del Rio, R.; Tabuloc, C. A.; Perez Hernandez, L. A.; Berry, A. L.; Cai, Y. D.; Lewald, K. M.; Chiu, J. C.

10.1101/2025.11.06.687099 — neuroscience — Posted on 2025-11-08

4014 How tp1, an indirect wing steering muscle, stabilizes Drosophila's flight

Teoh, H. K.; Biswas, D.; Leung, A.; Ludlow, B. K.; Whitehead, S. C.; Ehrhard, E.; Dickinson, M. H.; Beatus, T.; Cowan, N.; Cohen, I.

10.1101/2025.11.02.686144 — neuroscience — Posted on 2025-11-08

4015 Task-similarity dependent reconfiguration of compositional modules and geometry in frontal cortex

Chen, X.; Yao, X.; Yin, X.; Guo, Z. V.

10.1101/2025.11.06.687080 — neuroscience — Posted on 2025-11-08

4016 SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design

Zhang, P.; Han, R.; Kong, X.; Chen, T.; Ma, J.

10.1101/2025.11.06.687093 — bioinformatics — Posted on 2025-11-08

4017 Engineering a Multilayer Microfluidic Airway-On-A-Chip with Tunable GelMA Hydrogel for Physiologically Relevant Aerosol Exposure Studies

Bennet, T. J.; Randhawa, A.; Caffrey, T. M.; Solomon, T.; Lyall, E.; Huff, R. D.; Schwartz, C.; Xi, Y.; Carlsten, C.; Cheung, K. J.

10.1101/2025.11.06.687056 — bioengineering — Posted on 2025-11-08

4018 ALKBH1 activity in vitro and human cell lines by isotope dilution mass spectrometry

Henzeler, B.; Hofmeister, O.; Kögel, K.; Qi, Y.; Hagelskamp, F.; Heiss, M.; Schelter, F.; Xu, F.; Daumann, L. J.; Carell, T.; Kaiser, S.; Schneider, S.

10.1101/2025.11.06.687068 — biochemistry — Posted on 2025-11-08

4019 Modeling social influence as a reinforcer reveals varying individual learning strategies and the group's structure

Lenarczyk, M.; Jura, B.; Harda, Z.; Szumiec, Łukasz; Ziemianska, M.; Parkitna, J. R.; Wojcik, D. K.

10.1101/2025.11.06.686867 — animal behavior and cognition — Posted on 2025-11-08

4020 Mutations in legume genes that influence symbiosis create a complex selective landscape for rhizobial symbionts

Guha, S.; Bledsoe, R. B.; Sutherland, J.; Epstein, B.; Fry, G. M.; Venugopal, V.; Sankari, S.; Polo, A. G.; Levin, G.; Geddes, B.; Young, N. D.; Tiffin, P.; Burghardt, L. T.

10.1101/2024.09.11.612462 — evolutionary biology — Posted on 2025-11-08

4021 Metabolic fluctuations explain allometric scaling diversity

Tabi, A.; Merbis, W.; Santos, F.; Sole, R.

10.1101/2025.11.06.686202 — ecology — Posted on 2025-11-08

4022 Spatial variability of shade and its effects on cocoa trees productivity in agroforestry systems

GUEI, S. H.; Sanogo, S.; Mbo, A. A. K.; Wibaux, T.; Cherif, M.; Jagoret, P.

10.1101/2025.11.06.687074 — ecology — Posted on 2025-11-08

4023 Preservation of vision after chemically induced retinal ganglion-like-cell transplantation.

SHOAIB, R. M.; Tripathi, P.; Medvidovic, S.; Lin, R.; Sandrosyan, A.; Mahato, B.

10.1101/2025.11.06.686630 — cell biology — Posted on 2025-11-08

4024 Structure-based engineering of a nutrient acquisition protein enhances neutralizing antibodies and protection for the development of a gonococcal vaccine

Au, N. Y. T.; Zhong-Johnson, L. E. Z.; Fegan, J.; Islam, E.; Xu, S.; Ng, D.; Shah, M.; Caruso, L.-L.; Lai, C. C. L.; Schryvers, A. B.; Gray-Owen, S.; Moraes, T. F.

10.1101/2025.11.06.685839 — immunology — Posted on 2025-11-08

4025 Recurrent neural network models reveal unified mechanisms generating event-related potentials from MMN to P300

Strock, A.; Nghiem, T.-A. E.; Trouvain, N.; Mistry, P. K.; Menon, V.

10.1101/2025.11.06.687057 — neuroscience — Posted on 2025-11-08

4026 Retinal ganglion cell input to superior colliculus encodes salient information

Borges, K.; Xian, Q.; Lu, R.; Liang, Y.; Haley, S.; Nigam, S.; Ji, N.

10.1101/2025.11.06.687035 — neuroscience — Posted on 2025-11-08

4027 Lack of Reproducibility of Gulf War Illness-like Behavioral Effects in War-related Chemical Agents and Stressor Exposure Rat Models

Lin, C.-l. G.; Lashley, R.; Foster, J. B.; Wang, X.; Muhleman, A. J.; Weaver, S.; Lin, E.; Lai, L.

10.1101/2025.11.06.687069 — neuroscience — Posted on 2025-11-08

4028 Blockade of associative spine enlargement impairs awake cortical function

Zhou, S.; Sawada, T.; Arima, T.; Panezai, S. K.; Ohtsuka, M.; Okazaki, H.; Takaramoto, S.; Terada, S.-I.; Kondo, M.; Hashimoto, T.; Ohki, K.; Matsuzaki, M.; Yagishita, S.; Kasai, H.

10.1101/2025.11.06.686434 — neuroscience — Posted on 2025-11-08

4029 Attractors are less stable than their basins: Canalization creates a coherence gap in gene regulatory networks

Bavisetty, V. S. N.; Wheeler, M.; Kadelka, C.

10.1101/2025.11.06.687062 — systems biology — Posted on 2025-11-08

4030 Na+/H+ Exchanger Isoform 1 Regulates Apoptosis Susceptibility in Pulmonary Arterial Smooth Muscle from the Sugen/Hypoxia model of Pulmonary Hypertension

Andrade, M. R.; Yun, X.; Croglio, M.; Niedermeyer, S.; Jiang, H.; Philip, N.; Murray, S.; Munson, M.; Suresh, K.; Damarla, M.; Huetsch, J.; Shimoda, L.

10.1101/2025.11.06.687041 — physiology — Posted on 2025-11-08

4031 Serotonin 5-HT2C receptor as a cellular target of PI3K inhibitor LY294002 and its analog LY303511

Kotova, P. D.; Dymova, E. A.; Lyamin, O. O.; Rogachevskaja, O. A.; Voronova, E. A.; Kolesnikov, S. S.

10.1101/2025.11.06.687025 — pharmacology and toxicology — Posted on 2025-11-08

4032 Omnidirectional 3D Printing of Anisotropic Nanofibrous Peptide Hydrogels

Farsheed, A. C.; Makhoul, J. T.; Chew-Martinez, D.; Maldonado, E.; Liu, J.; Yu, L. T.; Gorostieta-Salas, E.; Jones, J. R.; Gage, F. H.; Hartgerink, J. D.

10.1101/2025.11.06.687046 — bioengineering — Posted on 2025-11-08

4033 Parkinsons disease modeling in regenerative spiny mice (Acomys dimidiatus) captures key disease-relevant behavioral, histological, and molecular signatures

Dutta, S.; Pang, M.; Donahue, R. R.; Chou, T.-F.; Seifert, A. W.; Gradinaru, V.

10.1101/2025.11.06.687049 — neuroscience — Posted on 2025-11-08

4034 Ketamine disrupts consciousness in healthy participants in relation with psychotic-like symptoms

Berkovitch, L.; Salvador, A.; Andrillon, T.; Dehaene, S.; Gaillard, R.

10.1101/2025.11.06.687042 — neuroscience — Posted on 2025-11-08

4035 AI-assisted Image-Based Phenotyping Reveals Genetic Architecture of Pod Traits in Mungbean (Vigna radiata L.)

Boddepalli, V. N.; Jubery, T. Z.; Dutta, S.; Ganapathysubramanian, B.; Singh, A.

10.1101/2025.11.06.687031 — genomics — Posted on 2025-11-08

4036 Nona: A unifying multimodal masking framework for functional genomics

Nair, S.; Hajiramezanali, E.; Tseng, A.; Diamant, N.; Hingerl, J.; Lal, A.; Biancalani, T.; Bravo, H. C.; Scalia, G.; Eraslan, G.

10.1101/2025.11.06.687036 — genomics — Posted on 2025-11-08

4037 A nutrient-sensitive enterokine coordinates developmental plasticity through inter-organ signalling

Bai, L.; Ramos, C. I.; Leulier, F.

10.1101/2025.11.06.687047 — developmental biology — Posted on 2025-11-08

4038 Electron transport chain disruption leads to failure of glucose derepression via the Snf1/AMPK pathway

Lewis, A. G.; Smith, J. R.; Smardz, M. C.; Sandoval, C. M.; Suzuki, S. W.; Bennett, B. D.; Gibney, P. A.

10.1101/2025.11.06.687039 — cell biology — Posted on 2025-11-08

4039 OptoLoop: An optogenetic tool to probe the functional role of genome organization

Stortz, M.; Keikhosravi, A.; Pegoraro, G.; Misteli, T.

10.1101/2025.11.06.686574 — molecular biology — Posted on 2025-11-08

4040 T cell fate is dictated by different antigen presenting cells in response to dietary versus gut epithelial self-antigen

Zhou, Y. D.; Brown, H.; Schaffer, E.; Taylor, G. M.; Fiske, K. L.; Komnick, M. R.; Lopez, S.; Dermody, T. S.; Esterhazy, D.

10.1101/2025.11.06.687030 — immunology — Posted on 2025-11-08

4041 Efficacy of Minnelide in a Next-Generation Dual-Recombinase Regulated Genetically Engineered Mouse Model of CIC::DUX4 Sarcoma

Browne, M. R.; Silver, A. V.; Banerjee, R.; Oristian, K. M.; Himes, J. E.; Hendrickson, P. G.; Kirsch, D. G.

10.1101/2025.11.06.687065 — cancer biology — Posted on 2025-11-08

4042 A De Novo Algorithm for Allele Reconstruction from Oxford Nanopore Amplicon Reads, with Application to CYP2D6

Brown, S. D.; Dreolini, L.; Minor, A.; Mozel, M.; Wong, N.; Mar, S.; Lieu, A.; Khan, M.; Carlson, A.; Hrynchak, M.; Holt, R. A.; Missirlis, P. I.

10.1101/2025.11.06.687066 — bioinformatics — Posted on 2025-11-08

4043 Integrating Longitudinal Metabolite Profiles Improves Trait Prediction in Pigs in a Trait- and Timepoint-Dependent Manner

Roddur, Q. A. H.; Qu, J.; Liang, D.; Carrara, E. R.; Lourenco, D.; Valente, B.; Chen, C.-Y.; Holl, J.; Cheng, H.

10.1101/2025.11.06.687040 — genetics — Posted on 2025-11-08

4044 Ecological drift in the flour beetle microbiome and associated instability in host benefits

Sanjenbam, P.; Guruswamy, H. K.; Deb, R.; Singhal, S.; Garge, S.; Buddh, S.; Dhanush, A.; Haque, A. M.; Govindarajan, S.; Agashe, D.

10.1101/2025.09.16.676705 — ecology — Posted on 2025-11-08

4045 Human non-canonical inflammasomes activate CASP3 to limit intracellular Salmonella replication in macrophages.

Kulkarni, M.; Bourne, C. M.; Mahale, A. B.; Exconde, P. M.; Murphy, C.; Cervantes, S.; Kardhashi, M.; Kambayashi, M.; Yoo, W.; Wrong, T. J.; Patio, R. C.; Discher, B. M.; Taabazuing, C. Y.

10.1101/2025.10.31.685927 — cell biology — Posted on 2025-11-08

4046 Maltose attenuates the virulence of Salmonella Typhimurium by impairing its entry into epithelial cells

Parmar, K.; Selvaraj, J.; Chakravortty, D.

10.1101/2025.05.06.652415 — microbiology — Posted on 2025-11-08

4047 Microglia attenuate regenerative neurogenesis via sema4ab after spinal cord injury in zebrafish

Docampo Seara, A.; Cosacak, M. I.; Heilemann, K.; Kessel, F.; Oprisoreanu, A. M.; Westphal, M.; Cark, O.; Zoeller, D.; Arnold, J.; Bretschneider, A.; Hnatiuk, A.; Ninov, N.; Becker, C. G.; Becker, T.

10.1101/2024.10.16.618445 — neuroscience — Posted on 2025-11-08

4048 The potential to breed for genetic legacy effects in sustainable farming systems

Van Haeften, S.; Brunner, S.; Dinglasan, E.; Fabreag, E.; Eyre, J.; Mens, C.; Hayes, B. J.; Udvardi, M.; Alahmad, S.; Eglinton, M.; McQuinn, R.; Ryan, M.; van der Meer, S.; Smith, M. R.; Hickey, L.

10.1101/2025.11.03.686422 — plant biology — Posted on 2025-11-08

4049 S-Alk(en)yl-Cysteine Sulfoxides in Allium Species Are Excellent Acrolein Scavengers: Implications for Secondary Antioxidants in Plants

Hada, A.; Nozaki, C.; Tamura, N.; Matsui, K.; Matsuoka, Y.; Shibata, D.; Mano, J.

10.1101/2025.08.18.670978 — plant biology — Posted on 2025-11-08

4050 Lab-in-the-loop therapeutic antibody design with deep learning

Frey, N. C.; Hotzel, I.; Stanton, S. D.; Kelly, R. L.; Alberstein, R. G.; Makowski, E. K.; Martinkus, K.; Berenberg, D.; Bevers, J.; Bryson, T.; Chan, P.; Chen, Y.; Czubaty, A.; D'Souza, T. A.; Dwyer, H.; Dziewulska, A.; Fairman, J. W.; Goodman, A.; Hofmann, J. L.; Isaacson, H. H.; Ismail, A. A.; James, S.; Joren, T.; Kelow, S. P.; Kiefer, J. R.; Kirchmeyer, M.; Kleinhenz, J.; Koerber, J. T.; Lafrance-Vanasse, J.; Leaver-Fay, A.; Lee, J. H.; Lee, E.; Lee, D. W.; Liang, W.-C.; Lin, J. Y.-Y.; Lisanza, S.; Loukas, A.; Ludwiczak, J.; Mahajan, S. P.; Mahmood, O.; MohammadiPeyhani, H.; Nerli, S.; Pa

10.1101/2025.02.19.639050 — bioengineering — Posted on 2025-11-08

4051 ELITE: E3 Ligase Inference for Tissue specific Elimination: A LLM Based E3 Ligase Prediction System for Precise Targeted Protein Degradation

Froehlich, H.; Patajoshi, S.; Madan, S.

10.1101/2025.11.05.686884 — bioinformatics — Posted on 2025-11-08

4052 Profiling of Burkholderia pseudomallei variants derived from Queensland clinical isolates

Coulon, P. M. L.; Ramsay, K. A.; Lee, A.; Ritmejeryte, E.; Pitt, M. E.; To, J.; Mediati, D. G.; Gassiep, I.; Reed, S.; Harris, P. N. A.; Myers, G. S. A.

10.1101/2025.08.10.669548 — microbiology — Posted on 2025-11-08

4053 Distinctive Functionality of Semantic Hubs: Evidence from Semantic Dementia

Cui, Z.; Liu, D.; Dai, Z.; Zhang, X.; Zeng, J.; Guo, Q.; Han, Z.; Huang, L.

10.1101/2025.11.06.686766 — neuroscience — Posted on 2025-11-08

4054 Fronto-Hippocampal Synchronization in Rapid Spatial Learning in Humans

Geva-Sagiv, M.; Jun, S.; Kryven, M.; Tenenbaum, J. B.; Boorman, E. D.; O'Reilly, R. C.; Lin, J. J.; Ranganath, C.; Saez, I.

10.1101/2025.11.07.685935 — neuroscience — Posted on 2025-11-07

4055 Plateau potentials are instructive signals for behavioral timescale synaptic plasticity in the neocortex

Yaeger, C. E.; Mojica Soto-Albors, R.; Liu, W.; Beltramini, A.; Harnett, M. T.

10.1101/2025.11.07.687250 — neuroscience — Posted on 2025-11-07

4056 Computational mechanisms for temporal integration in the anterior claustrum

Sohn, K.; Yoon, D.; Lee, J.; Choi, S.

10.1101/2025.11.07.687167 — neuroscience — Posted on 2025-11-07

4057 Basolateral Amygdala Projections to the Prelimbic Cortex Suppress the Motivational Value of Reward-Associated Cues

LeCocq, M. R.; Tue, A.; Casale, D.; Laplante, I.; Elrakhawy, K.; Samaha, A.-N.

10.1101/2025.11.06.687050 — neuroscience — Posted on 2025-11-07

4058 Distributed Population Coding and Memory Consolidation in the Cerebellar Cortex and Dentate Nucleus

Ipata, A. E.; Soni, V.; Shah, D. S.; Goldberg, M. E.

10.1101/2025.11.07.687239 — neuroscience — Posted on 2025-11-07

4059 Next-generation enhancer AAVs for selective interspecies targeting of midbrain dopaminergic neurons

Caplan, K. A.; Chen, K.; Wang, Y.; Wienisch, M.; Chai, R.; Kang, I.-H.; Chen, C. S.; del Rosario, R.; Krienen, F.; Wang, F.; Feng, G.

10.1101/2025.11.06.687071 — neuroscience — Posted on 2025-11-07

4060 A unified model of short- and long-term plasticity: Effects on network connectivity and information capacity

Ahokainen, I.; Linne, M.-L.

10.1101/2025.11.07.687160 — neuroscience — Posted on 2025-11-07

4061 Exploring the importance and preference of sugar feeding behaviour of malaria vectors in sugar plantations of southern Malawi

Zembere, K.; Coleman, S.; Chirombo, J.; Mbewe, R.; Tangena, J.-A.

10.1101/2025.11.06.687027 — ecology — Posted on 2025-11-07

4062 Harnessing artificial intelligence to automate environmental predictions

Malhotra, A.; Forbes, B.; Gary, S. F.; Goldman, A. E.; Waterman, B. R.; Garayburu-Caruso, V.; Fluet-Chouinard, E.; Mehan, S.; Bruen, M.; Taylor, M.; Ardon, M.; Cardenas, M. B.; Dodds, W. K.; Lonborg, C.; McDowell, W. H.; Moustapha, M.; Myers-Pigg, A. N.; Regier, P.; Rubin, T.; Song, H.; Stewart, R. D.; Villa, J.; Ward, N. D.; Scheibe, T. D.; Stegen, J. C.

10.1101/2025.11.06.684583 — ecology — Posted on 2025-11-07

4063 HDAC2 inhibition restores H4K16 Acetylation and Rescues Cellular Senescence in Hutchinson-Gilford progeria syndrome

Karimpour, R.; Ngubo, M.; Stanford, W. L.; Hendzel, M.

10.1101/2025.11.07.687234 — molecular biology — Posted on 2025-11-07

4064 Cryptic multicellularity in wild yeast brings selective advantages under stress

Sexton, W. K.; Schmidt, K.; Dickinson, Q.; Childress, J.; Rosenzweig, F.; Kroll, E.

10.1101/2025.11.06.687064 — microbiology — Posted on 2025-11-07

4065 Emotional Semantic Meaning Enhances Neural Tracking of Conversations Through Context-Sensitive Modulation of Auditory - Language Areas

Heikkinen, P.; Lepistö, S.; Wikman, P.; Koskinen, E.; Peräkylä, A.; Ravaja, N.; Harjunen, V.

10.1101/2025.11.06.686308 — neuroscience — Posted on 2025-11-07

4066 Disruption in Patterning in the Whisker-to-Barrel Cortex Pathway Alters Behavior

Lutchman, J. M.; Lutchman, S. A.; Brumberg, J. C.

10.1101/2025.11.06.687024 — neuroscience — Posted on 2025-11-07

4067 Cell state plasticity emerging from co-regulated, competitive, and configurable interactions within the AP-1 network

Degefu, Y. N.; Bujnowska, M.; Baumann, D. G.; Fallahi-Sichani, M.

10.1101/2025.11.06.686987 — systems biology — Posted on 2025-11-07

4068 High-salt diet disturbs the physiological uterine endothelial junction remodeling during pregnancy

Wang, H.; Huang, L.; Kong, S.; Chen, Q.; Huang, Z.; Li, M.; Guo, N.; Yu, X.; Huang, M.; Chen, D.; Chen, J.

10.1101/2025.11.06.687038 — physiology — Posted on 2025-11-07

4069 A Sequential Triple-Drug Strategy for Selective Targeting of p53-Mutant Cancers

Bakin, A. V.; Alruwaili, M.; Guo, Y.; Zonneville, J.; Melendy, T.; Straubinger, R. M.; Foster, B. A.; Rajan, P.; Withers, H.; Chatley, S.; Iyer, R.; Fountzilas, C.

10.1101/2025.11.06.687028 — cancer biology — Posted on 2025-11-07

4070 Hot and Bothered, Bees Gut Microbiome Shifts Under Thermal Stress and Pathogen Infection.

Van Wyk, J.; Beirne, L.; Bowder, S.; Campbell, E.; Disharoon, M.; Dreyer, M.; Frolichstein-Appel, N.; Gill, A.; Jones-Ducharme, A.; Kinkaid, A.; Broussard Korr, G.; McCabe, M.; McDowell, E.; Perez, F.; Villarreal-Mentz, R.; Johnston, J.

10.1101/2025.11.06.687019 — ecology — Posted on 2025-11-07

4071 A functional amyloid matrix underpins the PDIM-architected corded superstructure of the Mycobacterium tuberculosis biofilm

Lee, B. S.; Godejohann, M.; Gürtler, F.; Deloria, A. J.; Liu, M.; Leitgeb, R.; Drexler, W.; Berney, M.; Haindl, R.

10.1101/2025.11.07.687260 — microbiology — Posted on 2025-11-07

4072 Comparative genomics and pathogenicity of Pantoea stewartii subsp. stewartii reveal multiple introductions and limited distribution in Europe

Bencic, A.; Pothier, J. F.; Dreo, T.

10.1101/2025.11.07.687269 — microbiology — Posted on 2025-11-07

4073 T cell fate is dictated by different antigen presenting cells in response to dietary versus gut epithelial self-antigen

Zhou, Y. D.; Brown, H.; Schaffer, E.; Taylor, G. M.; Fiske, K. L.; Komnick, M. R.; Lopez, S.; Dermody, T. S.; Esterhazy, D.

10.1101/2025.11.06.687030 — immunology — Posted on 2025-11-07

4074 NF-kB-Dependent Transcriptional Regulation of Piezo1 Mediates Bacterial Clearance on Stiffened Lung

Orsini, E. M.; Boulton, A. M.; Abraham, S.; Brown, A.; Ricci, H.; Ahuja, A.; Pant, B.; Snyder, C. M.; Reinhardt, A.; Attaway, A. H.; Musich, R.; Grove, L. M.; Olman, M. A.; Vachharajani, V.; Scheraga, R. G.

10.1101/2025.11.06.687026 — immunology — Posted on 2025-11-07

4075 Ketamine and Psilocybin Differentially Impact Sensory Learning During the Mismatch Negativity

Allohverdi, G.; Soltanzadeh, M.; Schmidt, A.; Charlton, C.; Hauke, D. J.; Karvelis, P.; Vollenweider, F. X.; Diaconescu, A.

10.1101/2025.11.06.687023 — neuroscience — Posted on 2025-11-07

4076 On the mechanism of calcium permeability and magnesium block in NMDA receptors - a central molecular paradigm in neuroplasticity

Steigerwald, R.; Epstein, M.; Chou, T.-H.; Furukawa, H.

10.1101/2025.11.06.686637 — neuroscience — Posted on 2025-11-07

4077 Distinct Mechanisms of Surround Modulation for Dynamic Natural Scenes in Motion- and Scene-Selective Cortex

Kiniklioglu, M.; Pitcher, D.; Kaiser, D.

10.1101/2025.11.06.686956 — neuroscience — Posted on 2025-11-07

4078 Biological nitrification inhibition (BNI) in wheat for climate adaptation in acidic and alkaline soils

Bozal-Leorri, A.; Gonzalez-Murua, C.; Zarraonaindia, I.; Marino, D.; Arrese-Igor, C.; Gonzalez-Moro, M. B.

10.1101/2025.11.06.686715 — plant biology — Posted on 2025-11-07

4079 From Blue to Pink: Resazurin as a High-Throughput Proxy for Metabolic Rate in Oysters

Huffmyer, A. S.; Ozguner, N.; Baird, M.; Elvrum, C.; Kounellas, C.; Dicksion, D.; White, S. J.; Plough, L.; Gavery, M. R.; Krebs, N.; Walton, W.; Small, J.; Pitsenbarger, M.; Ealy-Whitfield, H.; Roberts, S.

10.1101/2025.11.06.686367 — physiology — Posted on 2025-11-07

4080 On the Mechanism of Ezrin Activation

Vasiliauskas, D.; Beiter, J.; Iyer, S. S.; Lombardo, A. T.; Mendoza, M. C.; Voth, G. A.

10.1101/2025.11.07.687285 — biophysics — Posted on 2025-11-07

4081 Epithelial convergent extension as a tuning process

Arzash, S.; Liu, A. J.; Manning, M. L.

10.1101/2025.11.06.687029 — biophysics — Posted on 2025-11-07

4082 Axonemal dynein contributions to flagellar beat types and waveforms

Fochler, S.; Doran, M. H.; Beneke, T.; Smith, J.; Fort, C.; Walker, B. J.; Brown, A.; Gluenz, E.; Wheeler, R. J.

10.1101/2025.11.06.687033 — biophysics — Posted on 2025-11-07

4083 Active geometrodynamics predicts the emergence of cytokinesis

Rajput, A. S.; Kumar, K.; Nishikawa, M.; Kumar, K. V.

10.1101/2025.11.07.683232 — biophysics — Posted on 2025-11-07

4084 GONNECT: A Gene Ontology-guided Neural Network for Explainable Cancer Typing

Lieftinck, M.; Verlaan, T.; Reinders, M.

10.1101/2025.11.06.686983 — bioinformatics — Posted on 2025-11-07

4085 RiboZAP: Custom Probe Design for rRNA Depletion in complex Metatranscriptomes

Bunga, S.; Tan, A.; Roos, M.; Kuersten, S.

10.1101/2025.11.07.687087 — bioinformatics — Posted on 2025-11-07

4086 Detection of five viruses commonly implicated with Bovine Respiratory Disease using loop-mediated isothermal amplification

Davidson, J. L.; Maruthumuthu, M. K.; Kamel, M.; Mohan, S.; Pascual-Garrigos, A.; Dextre, A.; Centeno-Delphia, R. E.; Boerman, J.; Pillai, D.; Koziol, J.; Ault, A.; Schoonmaker, J. P.; Johnson, T. A.; Verma, M. S.

10.1101/2025.11.06.687045 — bioengineering — Posted on 2025-11-07

4087 The Role of Linker Length and Composition in Actin Binding and Bundling by Palladin

Sargent, R. A.; Bradford, C.; Hughes, L. M.; Ta, N.; Limpiado, M. A.; Vattepu, R.; Brungardt, J. G.; Beck, M. R.

10.1101/2025.11.06.687016 — biochemistry — Posted on 2025-11-07

4088 Sample-multiplexed FACS-preprocessing of PBMCs enables scalable scRNA-seq without compromising transcriptomic or cellular integrity

Mokhtari, M.; Ramnarine, T. J. S.; Eicher, A.; Braunsperger, A.; Baumert, P.; Wolf, C.; Durmaz, G.; Pfaffenstaller, V.; Kendirli, A.; Kerschensteiner, M.; Schoenfelder, M.; Lee-Kirsch, M. A.; Wackerhage, H.; Mages, S. W.; Klughammer, J.

10.1101/2025.11.06.687014 — genomics — Posted on 2025-11-07

4089 Dici: a novel DNA transposon reshaping the genome of the opportunistic yeast Diutina catenulata

BIGEY, F.; WESSNER, M.; PRADAL, M.; CRUAUD, C.; AURY, J.-M.; NEUVEGLISE, C.

10.1101/2025.11.06.686975 — genomics — Posted on 2025-11-07

4090 Post-admixture selection favours Duffy negativity in the Lower Okavango Basin

Kasianov, A.; Fehn, A.-M.; Bolaane, M.; Masunga, G.; Fabiano, E. C.; Rocha, J.

10.1101/2025.11.06.687002 — genetics — Posted on 2025-11-07

4091 Phage-Plasmids Are Rare in Bacteria, May Exhibit Pseudolysogeny and Lack Antibiotic Resistance Genes

Sankaranarayanan, G.; Kodiveri Muthukaliannan, G.

10.1101/2025.11.07.687105 — genetics — Posted on 2025-11-07

4092 Systematic comparison of colocalization methods using protein quantitative trait loci

Hwang, S.; Pullin, J. M.; Wallace, C.; Whittaker, J.; Burgess, S.

10.1101/2025.11.07.686776 — genetics — Posted on 2025-11-07

4093 The effect of spontaneous mutations on CUP1 copy number and copper tolerance in Saccharomyces cerevisiae

Sohoni, R.; Schatz, G. G.; Sharp, N. P.

10.1101/2025.11.06.687044 — evolutionary biology — Posted on 2025-11-07

4094 Tree-Cover Gradients Modulate the Taxonomic and Functional Diversity of Birds in Amazonian Cattle-Ranching Landscapes

Velasquez-Valencia, A.; Diaz-Chaux, J. T.; Bonilla Gomez, M. A.; Navarro-Morales, A.; Giraldo, L. P.; Casanoves, F.

10.1101/2025.11.07.687096 — ecology — Posted on 2025-11-07

4095 Electron Cryo-Tomography Reveals the Caulobacter vibrioidesTight Adherence Pilus Architecture

Maggi, S.; Rosenzweig, R.; Panis, G.; Viollier, P. H.; Jensen, G. J.

10.1101/2025.11.06.686991 — cell biology — Posted on 2025-11-07

4096 Allosteric Gain-of-Function and Off-Mechanism Effects of ATP-Competitive Kinase Inhibitors Revealed by Multimodal Proteomics

Reber, V.; Keller, S.; Loosli, S. A.; Arima, Y.; Kleele, T.; Picotti, P.; Gstaiger, M.

10.1101/2025.11.06.687012 — molecular biology — Posted on 2025-11-07

4097 Uncovering the molecular basis of kinase activity and substrate recognition with phospho-PCA

Yu, C.; Pao, E.; Van Valen, D. A.

10.1101/2025.11.07.687244 — molecular biology — Posted on 2025-11-07

4098 The mRNA architecture of the termination site primes programmed stop codon readthrough events in Drosophila

Kansara, L.; Wolfstetter, G.; Wintermayr, D.; Alexopoulos, I.; Escos, A.; Friedländer, M. R.; Engström, Y.

10.1101/2025.11.07.685291 — molecular biology — Posted on 2025-11-07

4099 Molecular architecture and diversity of StopGo/2A translational recoding

Li, X.; Zuber, P. K.; Loughran, G.; Bhatt, P. R.; Alquraish, F.; Ramakrishnan, V.; Firth, A. E.; Atkins, J. F.

10.1101/2025.11.07.687186 — molecular biology — Posted on 2025-11-07

4100 Mapping unsolved lipidomes accelerates lipid discovery in major bacterial pathogens

Nair, Y. M.; Menon, A. R.; Lin, Z.; Vossenberg, M. R. L.; Munsamy-Govender, V.; Young, D. C.; Xet-Mull, A. M.; Babunovic, G. H.; Cheng, T.-Y.; Raman, S.; Rhee, K. Y.; Rock, J. M.; de Jong, A.; Minnaard, A. J.; Mayfield, J. A.; Tobin, D. M.; Moody, D. B.

10.1101/2025.11.06.685907 — microbiology — Posted on 2025-11-07

4101 Facilitation-competition tradeoffs structure microbial niches and nitrogen cycling

Xu, L.; Sun, X.; Zakem, E.

10.1101/2025.11.07.687282 — microbiology — Posted on 2025-11-07

4102 Dairy manure analysis reveals significant risk of Antibiotic resistance from Extracellular DNA in Manure storage Pit

Sakib, N.; Andersen, D. S.; Jarboe, L. R.; Howe, A.

10.1101/2025.11.07.687174 — microbiology — Posted on 2025-11-07

4103 Carbon monoxide-driven proton respiration enables facultative anaerobes to survive electron acceptor limitation

Katayama, Y. A.; Inoue, M.; Okamoto, S.; Sako, Y.; Kamikawa, R.; Greening, C.; Yoshida, T.

10.1101/2025.11.06.687094 — microbiology — Posted on 2025-11-07

4104 Genetic evidence for a periplasmic protein as a component for a subset of NtrYX two-component systems

Wolber, A. R.; McKay, L.; Johnson, R. M.; Hameed, Z.; Mote, K. B.; Julio, S.; Cotter, P. A.

10.1101/2025.11.07.687182 — microbiology — Posted on 2025-11-07

4105 Histone H1 Promotes Silencing of Unintegrated HIV-1 DNA

Zhu, J.; Wang, G. Z.; Pinto, H. D.; Hilton, S. E.; Skoultchi, A. I.; Goff, S. P.

10.1101/2025.11.07.687224 — microbiology — Posted on 2025-11-07

4106 Antibody-mediated feedback modulates interclonal competition in the germinal center

Barbulescu, A.; Bilanovic, J.; Langelaar, T.; Teetz, A. K.; Urnavicius, L.; Hobbs, A.; Shen, J.-J.; Abrahamse, N. H.; de Carvalho, R. V.; Mesin, L.; Ferreira, C. L.; Bortolatto, J.; Victora, G. D.

10.1101/2025.11.06.686519 — immunology — Posted on 2025-11-07

4107 Immune transcriptomic differences in paediatric patients with SARS-CoV-2 compared to other lower respiratory tract infections

Kitaba, N. T.; Workman, L.; Cohen, C.; Baralle, D.; Kong, E.; Botha, M.; Johnson, M.; Goldblatt, D.; Nicol, M. P.; Holloway, J. W.; Zar, H. J.

10.1101/2025.11.07.687132 — immunology — Posted on 2025-11-07

4108 From Atoms to Neuronal Spikes: A Multi-Scale Simulation Framework

Damjanovic, A.; Carnevale, V.; Hater, T.; Sultan, N.; Rossetti, G.; Diaz, S.; Carloni, P.

10.1101/2025.11.06.686996 — neuroscience — Posted on 2025-11-07

4109 Hybrid Ornstein-Uhlenbeck-Branching Modeling of Pediatric Leukemia Evolution: A Computational Extension and Cohort-Level Application

Kim, S.-H.

10.1101/2025.11.07.686044 — cancer biology — Posted on 2025-11-07

4110 Integrative single-cell and spatial mapping of oxidative stress response uncovers GCLC+ mesenchymal tumor cell state linked with favorable outcomes in triple negative breast cancer

Girnius, N.; Vallius, T.; Chen, W.; Launonen, I.-M.; Palomino-Echeverria, S.; Lin, J.-R.; Mills, C. E.; Kauppila, S.; Kronqvist, P.; Ellonen, A.; Perala, M.; Withnell, E.; Chen, Y.-A.; Secrier, M.; Santagata, S.; Sorger, P. K.; Farkkila, A.

10.1101/2025.11.06.686771 — cancer biology — Posted on 2025-11-07

4111 Topological defects drive influenza glycoprotein lattice assembly on spherical membranes

Liu, Z. B.; Halldorsson, S.; Calcraft, T.; Calder, L. J.; Rosenthal, P. B.

10.1101/2025.11.06.686978 — biophysics — Posted on 2025-11-07

4112 Metagenomic Classification of Ancient Viruses

Marques, L. L.; Pinho, A. J.; Pratas, D.

10.1101/2025.11.07.687203 — bioinformatics — Posted on 2025-11-07

4113 Discovery and characterization of bacterial unspecific peroxygenase-like heme-thiolate enzymes

Lopez-Tavera, E.; Stepnov, A. A.; Ersdal, N. S.; Barros-Reguera, M.; Sandholm, R. M.; La Rosa, S. L.; Sorlie, M.; Eijsink, V. G. H.; Vaaje-Kolstad, G.

10.1101/2025.11.07.687166 — biochemistry — Posted on 2025-11-07

4114 The SPATA5-SPATA5L1-CINP-C1ORF109 complex is essential for cytoplasmic pre-60S ribosome maturation

Choudhary, C.; Walter, J.; Weisser, M.; Masternak, M.; WIld, T.; Garcia-Martin, R.; Liebner, T.; Bragado-Nilsson, E.; Narita, T.; Zavogianni, N.; Montoya, G.

10.1101/2025.11.07.687187 — biochemistry — Posted on 2025-11-07

4115 The tiny germline chromosomes of Paramecium aurelia have anexceptionally high recombination rate and are capped by a new class of Helitrons

Arnaiz, O.; Guerin, F.; Couloux, A.; Miro-Pina, C.; Pellerin, G.; Nekrasova, I.; Amselem, J.; Aury, J.-M.; Bhullar, S.; Frapporti, A.; Lerat, E.; Luyten, I.; Malinsky, S.; Mathy, N.; Potekhin, A.; Regnier, V.; Sawka-Gadek, N.; Touzeau, A.; de Vanssay, A.; Zangarelli, C.; Quesneville, H.; Betermier, M.; Labadie, K.; Duret, L.; Meyer, E.; Duharcourt, S.; Sperling, L.

10.1101/2025.11.06.686955 — genomics — Posted on 2025-11-07

4116 A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements

Yang, A.; Lee, G. G.; Chhetri, S.; El Hajj Chehade, R.; Gulati, G.; Fu, D.; Kim, Y.-N.; Sotudian, S.; Savignano, H.; Shahbazi, S. D.; Philpot, C.; Hoggood, T. A.; Gulhan, D. C.; Kellis, M.; Berchuck, J. E.; Baca, S. C.

10.1101/2025.11.06.686988 — genomics — Posted on 2025-11-07

4117 Evolutionary dynamics of a lethal recessive allele in reintroduced fragmented lynx populations

Niehaus, J.; Imlau, M.; Keller, S.; Marti, I.; Breitenmoser, C.; Letko, A.; Jagannathan, V.; Grossen, C.; Leeb, T.; Pewsner, M.

10.1101/2025.11.06.686959 — evolutionary biology — Posted on 2025-11-07

4118 Sexual selection driven by direct benefits leads to the erosion of direct benefits

Riederer, J. M.; Cordeschi, G.; Mosna, M.; Weissing, F. J.

10.1101/2025.11.07.687154 — evolutionary biology — Posted on 2025-11-07

4119 When morphology stands still: constrained floral evolution in a mega diverse legume genus

Maianne, M.; Barros-Souza, Y.; Machado, F. A.; Borges, L. M.

10.1101/2025.11.07.687212 — evolutionary biology — Posted on 2025-11-07

4120 Evidence for Early Evolution of Sulfated Peptide Signaling in Plant Development

Tulio, D. V.; Shigenaga, A. M.; Wu, S.-Z.; Ronald, P. C.; Bezanilla, M.

10.1101/2025.11.07.687175 — developmental biology — Posted on 2025-11-07

4121 Blood originates in hypoblasts during embryonic development

Chao, Y.; Li, H.; Liu, L.; Tay, Z.; Zhang, S.; Xu, X.; Xu, S.; Xiang, Y.; Ruan, D.; Huang, Y.; Lan, G.; Liu, P.; Sugimura, R.

10.1101/2025.11.07.687183 — developmental biology — Posted on 2025-11-07

4122 The Unique Efg1 Fungal Virulence Regulon in the Catheterized Bladder Environment

La Bella, A. A.; Gervais, N. C.; Kohler, K. N.; Obernuefemann, C. L. P.; Jacobsen, I. D.; Shapiro, R. S.; Caparon, M.; Hultgren, S. J.; Flores-Mireles, A. L. H.; Santiago-Tirado, F. H.

10.1101/2025.11.06.686417 — microbiology — Posted on 2025-11-07

4123 The halophilic archaeon Halogranum roseipondis sp. nov. is susceptible to a virus carrying an exceptionally high number of viral tRNA genes

Lampi, M. J.; Nordman, E. M.; Gregorova, P.; Ravantti, J. J.; Sarin, P.

10.1101/2025.11.07.687168 — microbiology — Posted on 2025-11-07

4124 Development and Genome-level Microevolution of Oral Microbiome during Surface Colonization

Zhang, Y.; Yang, Y.; Liu, Y.; Lu, E. M.-C.; Moyes, D.; Niazi, S. A.; Zhou, Q.

10.1101/2025.11.07.685765 — microbiology — Posted on 2025-11-07

4125 Cross-Molecular Active Learning for the Discovery of Antimicrobial Polyacrylamides

Williams, S. C.; Greenstein, G.; Liu, X.; Fragasso, A.; Eckman, N.; Prossnitz, A.; Dong, C.; Makar-Limanov, A.; Jacobs-Wagner, C.; Cegelski, L.; Lopez Hernandez, H.; Appel, E.

10.1101/2025.11.07.687243 — microbiology — Posted on 2025-11-07

4126 The pupal stage is a developmental window for RNA virus persistence in Drosophila

Castello-Sanjuan, M.; Gonzalez, R.; Bergman, A.; Blanc, H.; Frangeul, L.; Nigg, J.; Saleh, M.-C.

10.1101/2025.11.07.687216 — microbiology — Posted on 2025-11-07

4127 Human Norovirus NS7 Protein Activates Canonical Inflammasome Pathways via NLRP6 in Intestinal Epithelial Cells

Park, S.; Cho, S.-G.; Chung, H. W.; Hwang, S. J.; Kim, T.; Lee, J. M.

10.1101/2025.11.07.687139 — immunology — Posted on 2025-11-07

4128 Non-Enzymatic Structural Modifications Reshape Peptide Presentation and Antigen Recognition

Kelly, J.; Newkirk, S.; Singh, S.; Ocius, K.; Zhang, T.; Pires, M.

10.1101/2025.11.06.687013 — immunology — Posted on 2025-11-07

4129 Retargeted adenoviruses for local IgA and CD47 blocker production as a novel cancer therapy

Chernyavska, M.; Hartmann, K. P.; Jansen, M.; Baumann, N.; Kolibius, J.; Bruecher, D.; Kristoforus, T.; Peters, R. H. W.; Huijs, L.; Laarveld, D.; Weiss, F.; Burger, R.; Lustig, M.; Gimenez de Assis, N.; Schmid, M.; Leusen, J. H. W.; Valerius, T.; Plueckthun, A.; Verdurmen, W. P. R.

10.1101/2025.11.07.686998 — immunology — Posted on 2025-11-07

4130 Offline Reconstruction of Diffusion MRI Acquisitions for Comparison Between Complex PCA-based and AI-based Denoising

D'Antonio, F.; Warrington, S.; Manzano-Patron, J.-P.; Morgan, P. S.; Sotiropoulos, S. N.

10.1101/2025.11.07.682283 — neuroscience — Posted on 2025-11-07

4131 Complex environmental cycles reveal evolution of circadian activity waveform and thermosensitive timeless splicing

Sharma, P. N.; Sheeba, V.

10.1101/2025.11.06.687109 — neuroscience — Posted on 2025-11-07

4132 High-throughput imaging of GABA fluorescence as a functional assay for variants in the neurodevelopmental gene, SLC6A1

McGraw, C. M.; Poduri, A.; Wiltrout, K.; Prinzing, G.; Zhang, G.

10.1101/2025.11.06.687003 — neuroscience — Posted on 2025-11-07

4133 A silent Kv channel subunit shapes PV neuron action potential waveform and short-term synaptic plasticity during high-frequency firing

Ganesh, S.; Canty, T. M.; Sabatini, B. L.

10.1101/2025.11.06.686832 — neuroscience — Posted on 2025-11-07

4134 The Median Preoptic Nucleus is a Key Site for Estradiol Regulation of Sleep-Wake Behaviors in Females Rats

MONG, J. A.; Kruk, K.; Viechweg, S. S.; Smith, P. C.; Byrd, C.

10.1101/2025.11.06.687021 — neuroscience — Posted on 2025-11-07

4135 The TEAIV model: Extending the standard TEIV model to account for viral budding ramp up

Gholami, S.; Korosec, C.; Su, Q.; Betti, M.; Conway, J. M.; Moyles, I.; Watmough, J.; Heffernan, J. M.

10.1101/2025.11.07.687137 — systems biology — Posted on 2025-11-07

4136 Collective parameter estimation of related models with an initial stability constraint

Clark, P.; Timpen, L. E.; Heberle, A.; Prugger, M.; van Eunen, K.; Rehbein, U.; Thedieck, K.; Shanley, D. P.

10.1101/2025.11.07.684636 — systems biology — Posted on 2025-11-07

4137 Multi-agent AI enables evidence-based cell annotation in single-cell transcriptomics

Ahuja, G.; Antill, A.; Su, Y.; Dall'Olio, G. M.; Basnayake, S.; Karlsson, G.; Dhapola, P.

10.1101/2025.11.06.686964 — bioinformatics — Posted on 2025-11-07

4138 RNApdbee 3.0: A unified web server for comprehensive RNA secondary structure annotation from 3D coordinates

Pielesiak, J.; Niznik, K.; Snioszek, P.; Wachowski, G.; Zurawski, M.; Antczak, M.; Szachniuk, M.; Zok, T.

10.1101/2025.11.07.687208 — bioinformatics — Posted on 2025-11-07

4139 Development and Evaluation of Novel Quantitative PCR (qPCR) and Loop-Mediated Isothermal Amplification (LAMP) Assays for Bovine Adenovirus Type 7

Kamel, M.; Davidson, J. L.; Dextre, A.; Ault, A.; Pillai, D.; Koziol, J.; Schoonmaker, J. P.; Johnson, T. A.; Verma, M. S.

10.1101/2025.11.06.687058 — bioengineering — Posted on 2025-11-07

4140 3D Hybrid Bioprinting for Complex Multi-Tissue Engineering

Alizadeh, H. V.; Flores Perez, A. S.; Uno, T.; Muniz, R. S.; Kwon, S. H.; Balachandar, A.; Riley, N.; Le, C. A.; Li, J.; Zhao, P.; Lui, E.; Kim, C.; Moeinzadeh, S.; Pan, C.-C.; Bhutani, N.; Chu, C.; Kim, S.; Yang, Y. P.

10.1101/2025.11.06.682452 — bioengineering — Posted on 2025-11-07

4141 CYP46A1 Activation Improves Retinal Neovascularization in a Mouse Model of Retinopathy of Prematurity

Bailey, B.; Manis, J. R. Z.; Seth, G.; Rajpurohit, S.; Oxenrider, A.; Martin, P. M.; Jadeja, R. N.; Thounaojam, M.

10.1101/2025.10.14.682405 — biochemistry — Posted on 2025-11-07

4142 End-to-end genomic prediction: direct prediction of images and text from genome-wide molecular markers

Watson, M. T.; Feldmann, M.; Yu, H.; Cheng, H.

10.1101/2025.11.03.686395 — genomics — Posted on 2025-11-07

4143 Anthropogenic factors explain wing colour variation in Colias (Lepidoptera: Pieridae) across the Toronto urbanization gradient

Sabatino, A.; Jahner, J. P.; McFarlane, S. E.

10.1101/2025.11.06.686962 — evolutionary biology — Posted on 2025-11-07

4144 Community coalescence reveals strong selection and coexistence within species in complex microbial communities

Walton, S. J.; Xu, Q.; Sharma, R.; Gellert, H. R.; Yeh, C.-F.; Cremer, J.; Xue, K. S.; Petrov, D. A.; Good, B. H.

10.1101/2025.11.06.687011 — evolutionary biology — Posted on 2025-11-07

4145 The response of Allolobophora chlorotica to drought stress in four soils

Bray, R. V. A.; Hodson, M. E.; Watt, P. J.

10.1101/2025.11.06.686976 — ecology — Posted on 2025-11-07

4146 Dysregulation of U12-Type Splicing in Lupus Neutrophils

Blanco, L.; Regmi, B.; Carmona-Rivera, C.; Liu, Y.; Wang, X.; Carlucci, P.; Jackson, M.; Manna, Z.; Hasni, S.; Hafner, M.; Sun, H.-W.; Kaplan, M. J.

10.1101/2025.11.06.686965 — immunology — Posted on 2025-11-07

4147 Connecting a P300 speller to a large language model

Lebedev, M.; Makarova, A. V.; Kleeva, D. F.; Maysuradze, A. I.

10.1101/2025.11.06.686984 — neuroscience — Posted on 2025-11-07

4148 Acoustic parameter combinations underlying mapping of pseudoword sounds to multiple domains of meaning: representational similarity analyses and machine-learning models

Kumar, G. V.; Lacey, S.; Dorsi, J.; Nygaard, L. C.; Sathian, K.

10.1101/2024.09.27.615393 — neuroscience — Posted on 2025-11-07

4149 Phantom Forms in Amblyopic Vision and what they reveal about the Generative Brain

Maruya, A.; Ramakrishnan, B.; Olianezhad, F.; Wang, J.; Alonso, J. M.; Zaidi, Q.

10.1101/2025.06.24.661078 — neuroscience — Posted on 2025-11-07

4150 Pupillometry Reveals Autonomic Adjustments During Diving Reflex in Face Immersion Apnea

Rizzuto, V.; Montanari, R.; Mesin, L.; Bortolozzo-Gleich, H.; Laurino, M.; Bonneh, Y.; Yellin, D.; Laganovska, G.; Vanags, J.; Borroni, D.; Giuliano, G.; Moccia, E.; Uthaug, M. V.; Gemignani, A.

10.1101/2025.01.31.635967 — physiology — Posted on 2025-11-07

4151 Taxonomy-free fecal microbiome profiles enable robust prediction of immunotherapy response and toxicity in melanoma

Lucas, A.; Reale, M.; Wolf, Y. I.; Duong, B.; Zhang, Y.; Wickramasinghe, J.; Behlman, L.; Jones, S. M.; Higgins, S.; Moustafa, A. M.; Elbasir, A.; Amaravadi, R.; Mitchell, T.; Huang, A.; Auslander, N.

10.1101/2025.11.06.686285 — cancer biology — Posted on 2025-11-07

4152 Unlocking Scalable Ligand Residence Time Predictions with Koffee Unbinding Kinetics Simulations

Madsen, N. K.; Ziolek, R. M.; Kongsgaard, D.; Nielsen, C. F.; Norlov, A. D.; Dolciami, D.; Sacher, J. R.; Michelsen, K.; Acker, M. G.; Berglund, N. A.; Christensen, M. H.; Gronlund, A.; Husted, L.; Gloriam, D. E.; Kooistra, A. J.; Zinner, N. T.

10.1101/2025.11.06.686759 — biophysics — Posted on 2025-11-07

4153 Svirlpool: structural variant detection from long read sequencing by local assembly

May, V.; Hartmann, T.; Beule, D.; Holtgrewe, M.

10.1101/2025.11.03.686231 — bioinformatics — Posted on 2025-11-07

4154 Towards light responsive hydrogel-based valves for flow regulation

Mittelholzer, A.; Hickl, V.; Maniura-Weber, K.; Boesel, L. F.; Rossi, R. M.; Rottmar, M.; Chandorkar, Y.

10.1101/2025.11.06.686031 — bioengineering — Posted on 2025-11-07

4155 Discovery and chemical biology of CDK8 inhibitors reveals insights for kinase inhibitor development.

Le Bihan, Y. V.; Foll-Josselin, B.; Robert, T.; Duez, J.; Angevin, L.; Simboeck, E.; Prieto, S.; Hodimont, E.; Ferrer, J.-L.; Krasinska, L.; Ruchaud, S.; Fisher, D.

10.1101/2025.11.06.686927 — biochemistry — Posted on 2025-11-07

4156 Experimental evidence of male-male interaction in laboratory swarms of Anopheles gambiae mosquitoes

Iacomelli, G.; Lombardi, M.; Parisi, L.; Fiorini, M.; Grucci, F.; Lavorgna, A.; Ligato, M.; Zarcone, G.; Peirce, M. J.; Melillo, S.; Spaccapelo, R.

10.1101/2025.11.06.686941 — animal behavior and cognition — Posted on 2025-11-07

4157 Phylogenomics supports monophyly of marsupial crustaceans: a journey to direct development

Barta, A.-C.; Grams, M.; Bracken-Grissom, H.; Brix, S.; Cordeiro, L. M.; Cummings, B.; Collins, S.; Farris, W. J.; Gerken, S.; Höpel, C. G.; Lörz, A.-N.; McKim, S.; Meland, K.; Kruckenhauser, L.; Olesen, J.; Peres, P. A.; Richter, S.; Wetzer, R.; Williams, J.; Kocot, K. M.; Schwentner, M.

10.1101/2025.11.06.686749 — evolutionary biology — Posted on 2025-11-07

4158 Inhibitory cell type heterogeneity in a spatially structured mean-field model of V1

Kim, S. H.; Choi, H.

10.1101/2025.03.13.643046 — neuroscience — Posted on 2025-11-07

4159 Center-surround inhibition in expectation and its underlying computational and artificial neural network models

Huang, L.; Shen, S.; Sun, Y.; Ou, S.; Zhang, R.; de Lange, F. P.; ZHANG, X.

10.1101/2024.08.26.609781 — neuroscience — Posted on 2025-11-07

4160 Attentional reconfiguration during acute and sustained fear

Seppälä, K.; Rantala, N.; Hudson, M.; Putkinen, V. J.; Santavirta, S.; Hyönä, J.; Nummenmaa, L.

10.1101/2025.11.06.686932 — neuroscience — Posted on 2025-11-07

4161 Metabolic Dysfunction Underlying Fatigue in Multiple Sclerosis: Elevated Lactate and Impaired Post-Exercise Creatine Response in the Anterior Cingulate Cortex

Brownbill, G.; Dekerle, J.; Cercignani, M.; Ronen, I.; Stone, J.

10.1101/2025.11.06.686949 — neuroscience — Posted on 2025-11-07

4162 Distinctive Functionality of Semantic Hubs: Evidence from Semantic Dementia

Cui, Z.; Liu, D.; Dai, Z.; Zhang, X.; Zeng, J.; Guo, Q.; Han, Z.; Huang, L.

10.1101/2025.11.06.686766 — neuroscience — Posted on 2025-11-07

4163 Hippocampal ERK2 dimerization is critical for memory reconsolidation and synaptic plasticity

Ojea Ramos, S.; Medina, C.; Krawczyk, M. d. C.; Millan, J.; Acutain, M. F.; Romano, A.; Baez, M. V.; Urbano, F.; Boccia, M. M.; Feld, M.

10.1101/2024.09.06.611755 — neuroscience — Posted on 2025-11-07

4164 Genomic Perception Fusion: A Lightweight, Interpretable Kernel for Protein Functional Tuning

Qurashi, S. U.

10.1101/2025.11.06.686961 — synthetic biology — Posted on 2025-11-07

4165 Guanosine tetraphosphate (ppGpp) signalling promotes high-light tolerance in Arabidopsis thaliana.

Romand, S.; Hu, C.; Crepin, A.; NAWROCKI, W.; Lecampion, C.; Ksas, B.; Citerne, S.; Terese, M.; Sugliani, M.; Caffarri, S.; Croce, R.; Havaux, M.; Field, B.

10.1101/2025.11.06.686924 — plant biology — Posted on 2025-11-07

4166 Sphingolipid-driven interleaflet coupling orchestrates Rho-GTPase recruitment to nanodomains for signal activation in plants

Montrazi, M.; Poitout, A.; Depenveiller, C.; Bayle, V.; Nagano, M.; Mamode Cassim, A.; Jolivet, M.-D.; Fiche, J.-B.; Sarazin, C.; Fouillen, L.; Simon-Plas, F.; Crowet, J.-M.; Jaillais, Y.; MONGRAND, S.; Martiniere, A.; BOUTTE, Y.

10.1101/2025.11.06.686946 — plant biology — Posted on 2025-11-07

4167 Targeting immunometabolic pathways with AZD1656 alleviates inflammation and metabolic dysfunction in type 2 diabetic cardiomyopathy

Anderson, S.; Karlstaedt, A.; Young, M.; Karatzia, L.; Cullen, F.; Chen, J.; O'Riordan, C.; Barnes, M.; Staka, Z.; Albee, L.; Garrod-Ketchley, C.; Dambure, S.; Prag, H.; Cvetko, F.; Miller, J.; Thiemermann, C.; Lewis, A. J.; Murphy, M. P.; Smith, D. M.; Henson, S.; Tyler, D.; Aksentijevic, D.

10.1101/2025.04.10.648128 — physiology — Posted on 2025-11-07

4168 Tear fluid as noninvasive liquid biopsy reveals proteins associated with malignant transformation of oral lesions

10.1101/2025.11.06.686738 — biochemistry — Posted on 2025-11-07

4169 Safeguarding Genome Integrity: Polo-like kinase Cdc5 and phosphatase Cdc14 Orchestrate Topoisomerase II-Mediated Catenane Resolution in Mitosis

Massari, L. F.; Finardi, A.; Visintin, C.; Calabrese, E.; Dondi, A.; Visintin, R.

10.1101/2025.11.06.686928 — genetics — Posted on 2025-11-07

4170 Seasonal and diel environment effects on host-seeking behaviour in the European tick vector, Ixodes ricinus

Noll, M.; Wall, R.; Makepeace, B. L.; Rose Vineer, H.

10.1101/2025.11.06.685884 — ecology — Posted on 2025-11-07

4171 An actomyosin-mediated mechanical mechanism for brain neural tube elevation

De La O, J.; Okeke, C.; Galea, G. L.; Martin, A.

10.1101/2025.05.15.654327 — developmental biology — Posted on 2025-11-07

4172 Effects of ΔmotY mutations on motility behavior of Pseudomonas aeruginosa chimeric periplasmic stator variants

Ferguson, N.; Desai, M.; Silva, J. F.; Nguyen, H.; Rodenborn, B.; Shindell, O.; Healy, F.

10.1101/2025.11.06.686970 — microbiology — Posted on 2025-11-07

4173 Regulation of miR-219 and its target RalGPS dictates acute synaptic plasticity at the Drosophila neuromuscular junction

Aavula, K.; Heggeness, H.; Yokokura, T.; Van Vactor, D.

10.1101/2025.11.06.686960 — neuroscience — Posted on 2025-11-07

4174 Phase-Specific Hippocampal and Cortical Medial Temporal Lobe Involvement in Allocentric Working Memory

Orvik, E. A.; Fjell, A. M.; Overbye, K.; Walhovd, K. B.; Sneve, M. H.; Grydeland, H.

10.1101/2025.11.06.686935 — neuroscience — Posted on 2025-11-07

4175 Motor Imagery Affects both Cortical and Spinal Circuitry: A Transcranial and Transspinal Magnetic Stimulation Study.

Benachour, A.; Nikolay, S.; Lebedev, M.

10.1101/2025.11.06.686943 — neuroscience — Posted on 2025-11-07

4176 Quantitative manipulation of the photoperiodic flowering by a small-molecule clock modulator

Maeda, A. E.; Ito, S.; Oyama, T.; Sato, A.; Nakamichi, N.; Muranaka, T.

10.1101/2025.11.06.686944 — plant biology — Posted on 2025-11-07

4177 Non-uniform filament turnover and mechanically-driven contractility and bundle formation in disordered actomyosin networks

Tam, A. K. Y.; Mogilner, A.; Oelz, D. B.

10.1101/2025.11.05.686892 — biophysics — Posted on 2025-11-07

4178 Deep-Learning Cortical Registration Guided by Structural and Diffusion MRI and Connectivity

ZHOU, Z.; Li, J.; Williams, J.; Fischl, B.; Aganj, I.

10.1101/2025.10.31.685908 — bioinformatics — Posted on 2025-11-07

4179 Deep learning methods for automated bone segmentation and biomechanical modelling in zebrafish

Bowers, F. C.; Lane, R.; Kawafi, W.; Rayfield, E.; Paul, D.; Pollock, T.; Berks, H.; Hammond, C. L.

10.1101/2025.11.06.686240 — bioengineering — Posted on 2025-11-07

4180 High-Throughput Spatial Proteomics at Cellular and Subcellular Resolution via a Hanging Droplet Workflow

Chen, H.; Guzman, U.; Olsen, J. V.

10.1101/2025.11.06.686925 — biochemistry — Posted on 2025-11-07

4181 Genotype-level quality control substantially reduces error rates in population-scale whole-genome sequencing

Chundru, V. K.; Wright, H. I. W.; Frayling, T. M.; Wood, A. R.; Weedon, M. N.; Wright, C. F.; Beaumont, R. N.; Hawkes, G.

10.1101/2025.11.06.686913 — genetics — Posted on 2025-11-07

4182 Dystonia-associated Torsins sustain CLCC1 function to promote membrane fusion of the nuclear envelope for NPC biogenesis

Maslennikova, D.; Baird, H.; Loffreda, A.; Ramachandran, K.; Kumar, A.; uit de Bos, J.; Ashiono, C.; Frischer-Ordu, K.; Luithle, N.; Uliana, F.; Dey, G.; Vanni, S.; Jagannathan, M.; Kutay, U.

10.1101/2025.11.07.687155 — cell biology — Posted on 2025-11-07

4183 Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes

Gomez-Gil, E.; Guerra, P.; Gu, Y.; Foo, S.; Billard, B.; Balogh, G.; Peter, M.; Oliferenko, S.

10.1101/2025.11.06.686945 — cell biology — Posted on 2025-11-07

4184 ORP5 controls the partitioning of phosphatidic acid between triacylglycerol and cardiolipin synthesis at mitochondria-ER-lipid droplet contact sites

Monteiro-Cardoso, V. F.; Guyard, V.; Trager, J.; Sauvanet, C.; Elhan, H.; Zouiouich, M.; El Khalloki, N.; Botte Yamaryo, Y.; Tareste, D.; Botte, C. Y.; Thiam, A. R.; Giordano, F.

10.1101/2025.11.06.685814 — cell biology — Posted on 2025-11-07

4185 The genetic driver of Acute Necrotizing Encephalopathy, RANBP2, regulates the inflammatory response to Influenza A virus infection

Desgraupes, S.; Decorsiere, A.; Perrin, S.; Gouy, B.; Wang, Y. E.; Palazzo, A. F.; Munier, S.; Arhel, N. J.

10.1101/2025.03.23.644734 — immunology — Posted on 2025-11-07

4186 Flagellin-mediated TLR5 activation enhances innate immune responses in healthy and diseased human airway epithelium

Li, X.; Cayet, D.; Zeroual, Y.; Sanjuan-Garcia, I.; Bonnefond, A.; Derhourhi, M.; Caul-Futy, M.; Caul-Futy, C.; van der Poll, T.; Carnoy, C.; Baldry, M.; Constant, S.; Sirard, J.-C.

10.1101/2025.11.06.686934 — immunology — Posted on 2025-11-07

4187 Adaptation to transient and local electrical muscle stimulation elicits persistent and global changes in walking kinematics

Murai, R.; Nozaki, D.

10.1101/2025.11.05.686889 — neuroscience — Posted on 2025-11-07

4188 Top-down feedback matters: Functional impact of brainlike connectivity motifs on audiovisual integration

Tugsbayar, M.; Li, M.; Muller, E.; Richards, B. A.

10.1101/2024.10.01.615270 — neuroscience — Posted on 2025-11-07

4189 A Pilot Study on Assessing Auditory Masking Using Auditory Steady-State Responses

Sergeeva, A.; Kidmose, P.

10.1101/2025.11.06.686909 — neuroscience — Posted on 2025-11-07

4190 Spinal interneuronal populations encode static hindlimb posture in the cat

Soga, Y.; Maeda, K.; Egawa, S.; Contreras, E. H.; Fukuyama, S.; Takahashi, M.; Takakusaki, K.; Funato, T.; Seki, K.

10.1101/2025.11.06.686917 — neuroscience — Posted on 2025-11-07

4191 Parkinsonian striatal acetylcholine dynamics are refractory to L-DOPA treatment

Potjer, E. V.; Wu, X.; Kane, A. N.; Parker, J. G.

10.1101/2025.11.06.686401 — neuroscience — Posted on 2025-11-07

4192 Multi-cohort, cross-species urinary proteomics reveals signatures of LRRK2 dysfunction in Parkinsons disease

Vu, D. T.; Sibran, W.; Metousis, A.; Vandewynckel, L.; Eraslan, B.; Goveas, L.; Itang, E. C.; Deldycke, C.; Figueroa Garcia, A.; Lefebvre, R.; Mueller Reif, J. B.; Virreira Winter, S.; Chartier-Harlin, M.-C.; Taymans, J.-M.; Mann, M.; Karayel, O.

10.1101/2025.11.06.686787 — systems biology — Posted on 2025-11-07

4193 BAP1 modulates endoplasmic reticulum stress signaling and balances liver homeostasis and malignant progression

Tschaharganeh, D. F.; Seretny, A.

10.1101/2025.11.06.686752 — cancer biology — Posted on 2025-11-07

4194 Hypoxia-inducible factors drive miRNA-mediated downregulation of L2HGDH and HIF1A in clear cell renal cancer independent of 14q deletion

Seal, S.; Luchtel, R. A.; Akram, T.; Isaila, B.; Perry, K. T.; Procissi, D.; Hafizi, S.; Shenoy, N. K.

10.1101/2024.12.01.625494 — cancer biology — Posted on 2025-11-07

4195 Structure and Function of Lens Suture Examined by 2-photon Fluorescence Microscopic Imaging

Zhang, Q.; Zhu, J.; Painter, T.; Xia, C.-h.; Ji, N.; Gong, X.

10.1101/2025.09.08.675023 — biophysics — Posted on 2025-11-07

4196 The 3D nuclear position and compartmentalization of genes prime their response to mechano-confinement

Oshagi, S.; Hovet, O.; Halaburkova, A.; Progida, C.; Paulsen, J.

10.1101/2025.11.06.686901 — genomics — Posted on 2025-11-07

4197 Genomic resources of Ascidiella aspersa and comparative analysis across tunicates reveal conserved class-level features and evolutionary diversification

Shito, T. T.; Jayakumar, V.; Nishitsuji, K.; Nishitsuji, Y.; Shimon, K.; Miyasaka, S. O.; Oka, K.; Sakakibara, Y.; Hotta, K.

10.1101/2025.11.06.686920 — genomics — Posted on 2025-11-07

4198 Coevolution in a warming world: an experimental test of the geographic mosaic of coevolution

Rusman, Q.; Figueira, T.; Traine, J.; Schiestl, F.

10.1101/2025.11.06.686912 — evolutionary biology — Posted on 2025-11-07

4199 Provenance Legacies Override Species Effects in Shaping Oak Rhizosphere Microbiomes and Metabolomes

Bibinger, S.; Nosenko, T.; Sivaprakasam Padmanaban, P. B.; Schulz, S.; Schroeder, H.; Kersten, B.; Zimmer, I.; Buegger, F.; Schloter, M.; Schnitzler, J.-P.

10.1101/2025.11.06.686906 — ecology — Posted on 2025-11-07

4200 Earthworm invasion reduces above-belowground biodiversity and ecosystem multifunctionality

Ferlian, O.; Eisenhauer, N.; Bonkowski, M.; Ciobanu, M.; Dumack, K.; Frelich, L. E.; Johnson, E. A.; Klarner, B.; Rosenbaum, B.; Salamon, J.-A.; Thakur, M. P.; Thouvenot, L.; Wubet, T.; Jochum, M.

10.1101/2025.11.05.686452 — ecology — Posted on 2025-11-07

4201 Avian elevational migration patterns in the Western Ghats, as revealed by participatory science and systematic surveys.

Faizee, A. K.; Ramesh, V.; Robin, V. V.

10.1101/2025.11.05.684726 — ecology — Posted on 2025-11-07

4202 Transcriptomic and functional comparison of cells isolated from healthy and degenerated ovine intervertebral discs

Humbert, P.; Danet, L.; Carrot, E.; Etienne, F.; Halgand, B.; Blanchard, F.; Vinatier, C.; Guicheux, J.; Fusellier, M.; Le Visage, C.; Guiho, R.

10.1101/2025.11.06.686904 — cell biology — Posted on 2025-11-07

4203 Naturally occurring CodY variants alter ligand binding, DNA target affinity, and virulence in Clostridioides difficile

Hasan, M. K.; Roy, S.; Govind, R.

10.1101/2025.11.06.687015 — microbiology — Posted on 2025-11-07

4204 LACK OF OXYGEN AND/OR GLUCOSE DIFFERENTIALLY POTENTIATES Aβ40E22Q- AND Aβ42-INDUCED CEREBRAL ENDOTHELIAL CELL DEATH, BARRIER DYSFUNCTION AND ANGIOGENESIS IMPAIRMENT

Carey, A. M.; Buzhdygan, T.; Fossati, S.

10.1101/2025.10.05.680546 — neuroscience — Posted on 2025-11-07

4205 An EEG-based Multi-Scale Hybrid Attention and Squeeze Network for objective taste assessment

Yang, T.; Xiao, Y.; Li, Z.; Chen, C.; Ye, F.; Cao, M.; Liu, R.; Zhu, Y.; Qian, Z.; Rajapakse, J. C.

10.1101/2025.11.06.686898 — neuroscience — Posted on 2025-11-07

4206 Context-Dependent Effects of Midkine on Plexiform Neurofibroma Growth and Drug Response in 3D Coculture Models

Rain, A. Z.; Sundararaghavan, H. G.; Ji, K.

10.1101/2025.10.20.683475 — cancer biology — Posted on 2025-11-07

4207 Novel small-molecule inhibitors of the protein kinase DYRK: Potential Therapeutic candidates in cancer

Venkataramani, P.; Elkayam, E.; Garg, A.; Cheng, K. F.; Altiti, A.; He, M.; Thakur, K.; Michalopoulou, E.; Gonzalez, C.; Felice, C.; Van Aelst, L.; Pappin, D.; Joshua-Tor, L.; Al-Abed, Y.; Tonks, N. K.

10.1101/2025.11.05.686653 — cancer biology — Posted on 2025-11-07

4208 Explainable Machine Learning for Preoperative Relapse Prediction in Molecularly Stratified Endometrial Cancer: A Single-Center Finnish Cohort Study

Moreno, S. V.; Khatun, M.; Pasanen, A.; Butzow, R.; Salumets, A.; Loukovaara, M.; Modhukur, V.

10.1101/2025.11.06.686680 — cancer biology — Posted on 2025-11-07

4209 Random crosslinks generate anomalous scaling of dynamic modulus of biomolecular condensates

Lyu, B.; Lin, J.

10.1101/2025.11.05.686888 — biophysics — Posted on 2025-11-07

4210 A metaproteomics-based meta study of samples from patients with inflammatory bowel disease identifies potential markers for diagnosis and therapy monitoring

Wolf, M.; Knipper, L.; Schallert, K.; Groba, A.-C.; Hellwig, P.; Bang, C.; Rausch, P.; Franke, A.; Benndorf, D.; Aden, K.; Sczyrba, A.; Heyer, R.

10.1101/2025.11.06.684320 — bioinformatics — Posted on 2025-11-07

4211 ELITE: E3 Ligase Inference for Tissue specific Elimination: A LLM Based E3 Ligase Prediction System for Precise Targeted Protein Degradation

Froehlich, H.; Patajoshi, S.; Madan, S.

10.1101/2025.11.05.686884 — bioinformatics — Posted on 2025-11-07

4212 ECLIPSE: Exploration of Complex Ligand-Protein Interactions through Learning from Systems-level Heterogeneous Biomedical Knowledge Graphs

Atas Guvenilir, H.; Dogan, T.

10.1101/2025.11.05.686382 — bioinformatics — Posted on 2025-11-07

4213 An InDel Genomic Variant within a Bifunctional Super-Enhancer for LINC00636 and CD47 Regulation in Breast Cancer

Di Benedetto, C.; Tsark, A.; Acenas, D. D.; Thach, A.; Singal, A.; Opazo-Medallo, V.; Rodriguez, A.; El Zeini, M.; Zhang, H.; Park, C.; Gonzales-Velozo, H.; Weissman, I. L.; Betancur, P.

10.1101/2025.11.05.684493 — genomics — Posted on 2025-11-07

4214 The conserved bridging domain on HCV E1E2 glycoprotein complex is targeted by neutralizing antibodies from diverse lineages

Chen, F.; Nguyen, Y. T. K.; Lee, Y.-Z.; Giang, E.; Lau, S. C.; Koide, Y.; Hung, S.-H.; Ueno, L.; He, L.; Fuerst, T. R.; Lauer, G. M.; Stanfield, R. L.; Zhu, J.; Wilson, I. A.; Law, M.

10.1101/2025.11.05.686883 — immunology — Posted on 2025-11-07

4215 Trial-by-trial learning of successor representations in human behavior

Kahn, A. E.; Bassett, D. S.; Daw, N. D.

10.1101/2024.11.07.622528 — neuroscience — Posted on 2025-11-07

4216 Visual experience shapes functional connectome gradients

Koba, C.; Falco-Roget, J.; Collignon, O.; Raczy, K.; Bedny, M.; Tian, M.; Szwed, M.; Stroh, A.-L.

10.1101/2025.02.28.640746 — neuroscience — Posted on 2025-11-07

4217 Representational drift shows same-class acceleration in visual cortex and artificial neural networks

Liu, J.; Farahat, A.; Vinck, M.

10.1101/2025.11.05.686897 — neuroscience — Posted on 2025-11-07

4218 Targeting RARβ With a Stable Retinoic Acid Mimic Promotes Neurite Outgrowth, Neurogenesis, and Behavioral Recovery

Sanyal, K.; Haque, S. R.; Pendharkar, R.; Chermakani, P.; Kumaran, M.; Acharya, P.; Maity, D.; Venkatesh, I.

10.1101/2025.11.05.686894 — neuroscience — Posted on 2025-11-07

4219 Stable Somatotopy in Chronic Low Back Pain: Is Cortical Map Reorganization a Myth?

Doerig, M.; Cole, D.; Guekos, A.; Staempfli, P.; Schuetz, P.; Schweinhardt, P.; Meier, M. L.

10.1101/2025.11.05.686896 — neuroscience — Posted on 2025-11-07

4220 Endothelial-targeted CD39 prevents Toxin-induced Pulmonary Hypertension Mice.

Willcox, A.; Savvidou, I.; Lee, N. T.; Selan, C.; Calvello, I.; Robson, S.; Bongcaron, V.; Walsh, A.; Song, Y.; Wang, X.; Williams, T.; Peter, K.; Nandurkar, H. H.; Sashindranath, M.

10.1101/2025.11.05.686887 — physiology — Posted on 2025-11-07

4221 High-Concordance Validation of Droplet Digital PCR and Next-Generation Sequencing for EGFR Mutation Detection Across Diverse Biospecimens in a Large-scale NSCLC Cohort Study

Liu, M.; Lu, L.; Zhu, L.; Zhang, X.; Liu, Y.; Ren, X.; Liu, S.; Cheng, S.; Xu, M.; lu, C.; Peng, Y.; Su, W.; Guo, Y.; Chen, S.

10.1101/2025.11.05.686693 — cancer biology — Posted on 2025-11-07

4222 MEX3A control of mitochondrial fitness is essential for ovarian clear cell carcinoma tumorigenesis and liver metastasis

Vinothkumar, P.; Lin, P.-Y.; Cheng, L.-T.; Yu, C.-H.; Hsu, P.-H.; Chou, Y.-C.; Hwang-Verslues, W. W.

10.1101/2025.11.05.686880 — cancer biology — Posted on 2025-11-07

4223 mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories

Woody Santos, J. B.; Chen, L.; Miranda Quintana, R. A.

10.1101/2025.11.05.686879 — biophysics — Posted on 2025-11-07

4224 Task-dependent pupillary responses to glossiness and attractiveness judgments

Tamura, H.; Nakauchi, S.; Minami, T.

10.1101/2025.11.05.686874 — neuroscience — Posted on 2025-11-07

4225 From Cytoplasmic Membrane to Thylakoids: Evolution of Membrane Biogenesis and Photosystem II assembly in early diverging Cyanobacteria

Hambucken, L.; BAURAIN, D.; Cornet, L.

10.1101/2025.11.06.686923 — evolutionary biology — Posted on 2025-11-07

4226 Tumors Located in the Brain Impair the Frequency and Phenotype of Dendritic Cells in Blood and Tumor

Gardam, B.; Gargett, T.; Nam, E.; Khan, S.; Ormsby, R. J.; Poonnoose, S. I.; Bracken, J. M.; Pasam, A.; Lenin, S.; Gliddon, B. L.; Tea, M. N.; Shard, C. L.; Pitson, S. M.; Gomez, G. A.; Pillman, K. A.; Sandhu, S.; Brown, M. P.; Ebert, L. M.

10.1101/2025.11.05.686441 — immunology — Posted on 2025-11-07

4227 muSim: A goal-driven framework for elucidating the neural control of movement through musculoskeletal modeling

Almani, M. N.; Lazzari, J.; Saxena, S.

10.1101/2024.02.02.578628 — neuroscience — Posted on 2025-11-07

4228 A transient neural code for feedback-driven motor corrections during reaching

Kudryashova, N.; Hurwitz, C.; Perich, M. G.; Hennig, M. H.

10.1101/2025.03.21.644350 — neuroscience — Posted on 2025-11-07

4229 Geographic distribution of the Birmingham Darter Etheostoma birminghamense

Brownstein, C. D.; Andriotis, K.; Haynes, C. B.; Sturm, N. D.; Kuhajda, B. R.; Near, T. J.

10.1101/2025.11.05.686853 — zoology — Posted on 2025-11-07

4230 MicroRNA156 and its targeted SPL genes interact with the photoperiod, vernalization, and gibberellin pathways to regulate wheat heading time

Liu, Q.; Zhang, L.; Zhou, Z.; Zhang, C.; Li, C.; Debernardi, J. M.; Dubcovsky, J.

10.1101/2025.11.05.686864 — plant biology — Posted on 2025-11-07

4231 Synergistic therapeutic effects of endolysin BNT331 and a Lactobacillus crispatus consortium in a human vagina chip model of bacterial vaginosis

Gulati, A.; Jorgenson, A. C.; Williams, A.; Rhbiny, H.; Tisakova, L. P.; Corsini, L.; Fazel-Zarandi, M.; Xu, J.; Elsherbini, J.; Gutzeit, O.; Stejskalova, A.; LoGrande, N. T.; Demidkina, B. C.; Man, Y.; Goyal, G.; Kwon, D. S.; Mitchell, C. M.; Junaid, A.; Ingber, D. E.

10.1101/2025.11.05.686849 — pathology — Posted on 2025-11-07

4232 Machine Learning-Driven Discovery of Synergistic Protein Interactions Identifies ATL3 as a Putative Biomarker for Cancer Drug Response

Ramarao-Milne, P.; Kaphle, A.; Reguant, R.; Klein, A.; Kuiper, M.; Hosking, B.; Wenzel, J.; Al-Mamun, H.; Elazab, L.; Zhong, Q.; Reddel, R.; Wilson, L.; Jain, Y.; Twine, N.; Bauer, D.

10.1101/2025.11.05.686871 — cancer biology — Posted on 2025-11-07

4233 SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets

Seal, S.; Neelon, B.

10.1101/2025.03.29.646124 — bioinformatics — Posted on 2025-11-07

4234 Pro4S: prediction of protein solubility by fusing sequence, structure, and surface

Qian, J.; Yang, L.; Wang, R.; Qi, Y.

10.1101/2025.11.05.686869 — bioinformatics — Posted on 2025-11-07

4235 Fast and interpretable quantification of biological shape heterogeneity via stratified Wasserstein kernel

Zhao, W.; Sutherland, D. J.; Dao Duc, K.

10.1101/2025.11.05.686865 — bioinformatics — Posted on 2025-11-07

4236 Insect Identification with ESEM Imaging and DNA Barcoding for Forensic Use

Hoffman, R. B.; Miller, N. J.; Hall, A.

10.1101/2025.11.05.686861 — genetics — Posted on 2025-11-07

4237 Increased clonality, decreased allele diversity and high genetic structure in tetraploid sea anemone Aulactinia stella populations from North Pacific to Atlantic across the Arctic Ocean

Bocharova, E.; Volkov, A.; Stoeckel, S.

10.1101/2025.04.24.650399 — evolutionary biology — Posted on 2025-11-07

4238 A sub-set of guanine- and cytosine-rich genes are actively transcribed at the nuclear Lamin B1 region

Balasooriya, G. I.; Naik, P.; Wee, T. L.; Spector, D.

10.1101/2023.10.28.564411 — cell biology — Posted on 2025-11-07

4239 Human coronavirus HKU1 neutralization by glycan receptor mimicry

Feng, Z.; Kose, N.; Moreira, F. R.; Kimpel, A. L. M.; Copps, J.; Suryadevara, N.; Jackson, D. J.; Gern, J. E.; Wilson, I. A.; Li, S.; de Vries, R. P.; Baric, R. S.; Bangaru, S.; Crowe, J. E.; Ward, A. B.

10.1101/2025.11.05.686863 — immunology — Posted on 2025-11-07

4240 Circuit-specific gene editing for precision modulation of neuronal activity with CRISPR-rabies virus

Zhang, Z.; Xu, J.; Matthews, E. A.; Deasy, S.; He, L.; Arroyo, D.; Pan, E.; Deshmukh, A.; Kaur, K. S.; McNamara, J. O.; Southwell, D. G.; Gersbach, C. A.; Ji, R. R. A.; Velmeshev, D.

10.1101/2025.11.03.686433 — neuroscience — Posted on 2025-11-07

4241 Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism

Yuan, G.; Suresh, V.; Wigdor, E.; Hao, Y.; Leonard, R.; Steyert, M.; Griffiths, M.; Evans, C.; Rohani, N.; Weiss, J.; Lassen, F. H.; Schafer, N.; Dong, S.; Palmer, D. S.; Sanders, S. J.; Nowakowski, T. J.

10.1101/2025.11.05.686845 — neuroscience — Posted on 2025-11-07

4242 A segment of Triticum timopheevii chromosome 3G confers type II Fusarium head blight resistance and reduces DON accumulation in wheat.

Steed, A.; Grewal, S.; Badgami, R.; King, J.; King, I. P.; Nicholson, P.

10.1101/2025.10.27.684833 — plant biology — Posted on 2025-11-07

4243 Beyond Traditional Poincare Analysis: Second-Order Plots Reveal Respiratory Effects in Heart Rate Variability

Lebedev, M. A.; Medvedeva, A. S.; Solovieva, K. P.; Starodubtseva, N. M.; Makarova, A. V.; Kleeva, D. F.

10.1101/2025.08.13.670042 — physiology — Posted on 2025-11-07

4244 Altair-LSFM: A High-Resolution, Easy-to-Build Light-Sheet Microscope for Sub-Cellular Imaging

Haug, J.; Gałecki, S.; Lin, H.-Y.; Wang, X.; Dean, K. M.

10.1101/2025.04.08.647739 — biophysics — Posted on 2025-11-07

4245 Alternating Angle Milling Suppresses Streaking Artifacts in FIB-SEM Imaging

Shtengel, G.; Qiu, W.; Arron, J. S.; Crowe, A. S.; Polilov, A. A.; Karkali, K.; Bleck, C. K. E.; Hess, H. F.

10.1101/2025.09.25.678572 — biophysics — Posted on 2025-11-07

4246 Exploring the Potential of AlphaFold Distograms for Predicting Binding-induced Hinge Motions

Savas, B.; Barlas, A. B.; Karaca, E.

10.1101/2025.07.25.666757 — bioinformatics — Posted on 2025-11-07

4247 Prevalence and mechanisms of high-level carbapenem antibiotic tolerance in clinical isolates of Klebsiella pneumoniae

Cross, T.; Torres, F. V.; Nikulin, N.; McGee, A.; Jalees, L.; Balakrishnan, R.; Aliyu, T.; Westblade, L. F.; Singh, A.; Doerr, T.

10.1101/2025.02.19.639047 — microbiology — Posted on 2025-11-07

4248 RATS: Unsupervised manifold learning using low-distortion alignment of tangent spaces

Kohli, D.; Nieuwenhuis, J. S.; Zegwaard, K.; Cloninger, A.; Mishne, G.; Narain, D.

10.1101/2024.10.31.621292 — neuroscience — Posted on 2025-11-07

4249 Integrated tissue proteomics and lipidomics from ovine organs suggests novel functional implications for fatty acids and lipid mediators.

Hagn, G.; Jenner, F.; Bileck, A.; Gueltekin, S.; Hamberg, M.; Mohr, T.; Gerner, C.; Gerner, I.

10.1101/2025.10.28.685055 — systems biology — Posted on 2025-11-07

4250 Measuring serotonin binding to its receptors in vitro via charge transfer to ANAP

Brado, O. G.; Hawkins, A. T.; Hill, A. D.; Puljung, M. C.

10.1101/2025.10.01.679840 — biophysics — Posted on 2025-11-07

4251 From Transporter to Motor: Evolutionary and Structural Insights into the Emergence of Prestin's Area-Motor Activity in Mammals

Fuentes-Ugarte, N.; Ruiz-Rojas, T.; Garcia-Olave, F.; Ruiz-Fernandez, A.; Garate, J. A.; Castro-Fernandez, V.; Araya-Secchi, R.

10.1101/2025.04.11.648445 — evolutionary biology — Posted on 2025-11-07

4252 Recombination shapes the diversification of the wtf meiotic drivers

Wang, Y.; Xu, H.; He, Q.; Wu, Z.; Gong, Z.; Han, G.-Z.

10.1101/2024.09.04.611149 — evolutionary biology — Posted on 2025-11-07

4253 Extra-ciliary role for polycystins in regulation of Ezrin and renal tubular morphology

Dixon, E. E.; Zapf, A. M.; Halperin Kuhns, V. L.; Basquin, D.; Park, R. M.; Coleman, R.; Franklin, L.; Lane-Harris, A. C.; Hofherr, A.; Kottgen, M.; Qian, F.; Welling, P. A.; Watnick, T. J.; Woodward, O. M.

10.1101/2025.11.05.684799 — cell biology — Posted on 2025-11-07

4254 Adaptive radiation during long-term experimental evolution of the multicellular bacterium, Streptomyces

Munnoch, J. T.; Vahtokari, S.; Kerr, l.; Hoskisson, P. A.

10.1101/2025.08.20.671327 — microbiology — Posted on 2025-11-07

4255 Uncertainty-Aware Deep Learning for Multi-Metric and Dose-Specific Prediction of Drug Synergy

Heydari, M. J.; Lye, B.; Masouri, P.; Marsland, T.; Lock, J.; McKenna, J.; Vafaee, F. G.

10.1101/2025.11.05.686895 — bioinformatics — Posted on 2025-11-07

4256 Endothelial CLK2 as a therapeutic target for acute radiation syndrome

Posey, R. R.; Ozkan, A.; Man, Y.; Feitor, J. F.; Jiang, A.; Ji, J.; LoGrande, N. T.; Kyprianou, C.; Howley, A. M.; Budnik, B.; Lee, J. D.; Chou, D. B.; Ingber, D. E.

10.1101/2025.11.05.686891 — molecular biology — Posted on 2025-11-07

4257 Neural correlates of pure presence

Boly, M.; Smith, R.; Vigueras Borrego, G.; Pozuelos, J. P.; Allaudin, T.; Malinowski, P.; Tononi, G.

10.1101/2024.04.18.590081 — neuroscience — Posted on 2025-11-07

4258 The Christchurch point mutation in mouse APOE reduces Aβ-induced tau and α-synuclein pathologies

Soto-Faguas, C. M.; O'Niel, A.; Mueller, P. A.; Sanchez-Molina, P.; Woltjer, R. L.; Raber, J.; Unni, V. K.

10.1101/2025.11.05.686857 — neuroscience — Posted on 2025-11-07

4259 Individuals born with congenital cataracts exhibit both persisting impairment and considerable recovery of white matter microstructure after sight restoration

Hassett, J.; Hoelig, C.; Lingareddy, S.; Kekunnaya, R.; Roeder, B.

10.1101/2025.09.09.675092 — neuroscience — Posted on 2025-11-07

4260 Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature

Unitt, A.; Krisna, M. A.; Parfitt, K. M.; Jolley, K. A.; Maiden, M. C. J.; Harrison, O. B.

10.1101/2025.03.28.646058 — genomics — Posted on 2025-11-07

4261 Quantitative genetics of lifetime growth curves in a lizard

Aragon, A.; Rutschmann, A.; Richard, M.; Bestion, E.; Pellerin, F.; Winandy, L.; San Jose, L.-M.; Di Gesu, L.; Darnet, E.; Cribellier, J.; Massot, M.; Clobert, J.; Cote, J.; de Villemereuil, P.

10.1101/2025.10.14.682310 — evolutionary biology — Posted on 2025-11-07

4262 Phospholipid-independent biogenesis of a functional RP4 conjugation pilus

Ishimoto, N.; He, S.; Bogdanov, M. V.; Smith, T. K.; Frankel, G.; Beis, K.

10.1101/2025.06.27.661960 — microbiology — Posted on 2025-11-07

4263 Characterising the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse testset of 2,663 Mycobacterium tuberculosis samples

Westhead, J.; Baker, C. S.; Brouard, M.; Colpus, M.; Constantinides, B.; Hall, A.; Knaggs, J.; Lopes Alves, M.; Spies, R.; Thai, H.; Surrall, S.; Govender, K.; Peto, T. E.; Crook, D. W.; Omar, S. V.; Turner, R.; Fowler, P. W.

10.1101/2024.11.08.622466 — microbiology — Posted on 2025-11-07

4264 Sex-peptide targets distinct higher order processing neurons in the brain to induce the female post-mating response

Nallasivan, M. P.; Singh, D. N.; Sahir, M. S. R.; Soller, M.

10.1101/2024.04.24.590874 — neuroscience — Posted on 2025-11-07

4265 Prior cocaine use disrupts identification of hidden states by single units and neural ensembles in orbitofrontal cortex

Zong, W.; Mueller, L.; Zhang, Z.; Zhou, J.; Schoenbaum, G.

10.1101/2025.03.28.645972 — neuroscience — Posted on 2025-11-07

4266 Symbiont diversity and light-organ morphology in Sepiola affinis

Bongrand, C.; Lami, R.; Suzuki, M. T.; Koch, E. J.

10.1101/2025.11.06.686942 — microbiology — Posted on 2025-11-07

4267 Semaglutide Alters Behaviour and Nucleus Accumbens Oscillatory Activity in Healthy Mice

Mosqueira, A.; Ansarifar, S.; Nabavi, S.; Moreno, A.

10.1101/2024.09.06.611514 — neuroscience — Posted on 2025-11-07

4268 A BIOPOLYMER LAMINARIN ELICITS ANTIOXIDANT DEFENSE IN DIFFERENT CULTIVARS OF SOLANUM LYCOPERSICUM AGAINST EARLY BLIGHT DISEASE CAUSED BY ALTERNARIA SOLANI

Muthukumar, G.; Mohana Prasad, J.; Arulvasu, C.; Godhantaraman, N.; Muthamilarasan, M.; Radhakrishnan, N.

10.1101/2025.10.05.680597 — plant biology — Posted on 2025-11-07

4269 Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework

Rieger, W. J.; Boden, M.; Arnold, F. H.; Mora, A.

10.1101/2025.06.13.659624 — bioinformatics — Posted on 2025-11-07

4270 Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods

Szikszai, M.; Wang, T.-Y.; Krueger, R.; Mathews, D. H.; Ward, M.; Aviran, S.

10.1101/2025.11.04.686644 — bioinformatics — Posted on 2025-11-07

4271 An open-source platform for reference data-driven analysis of untargeted metabolomics

Mendoza Cantu, A.; Gauglitz, J.; Bittremieux, W.

10.1101/2025.11.05.686710 — bioinformatics — Posted on 2025-11-07

4272 Ultrasensitive graphene FET aptasensor for direct attomolar detection of glutamate in human clinical samples

Abrantes, M.; Blanco, Y.; Giacomazzi, R. P.; Moreira, I. P.; Monteiro, P.; Borme, J.; Vieira-Coelho, M.; Sousa, S. F.; Briones, C.; Jacinto, L.; Alpuim, P.

10.1101/2025.11.05.686731 — bioengineering — Posted on 2025-11-07

4273 Ultrahigh throughput screening to train generative protein models for engineering specificity into unspecific peroxygenases

Nair, P. M.; Steinberg, D. M.; Resende, T.; Suarez, A. F.; Power, H.; Ong, C. S.; Sairam, V.; Cheng, S. H.-Y.; Fragata, L.; Serafini, A.; Oh, V.; Tan, S. H.; Speight, R. E.; Vahidi, A. K.

10.1101/2025.11.02.685536 — bioengineering — Posted on 2025-11-07

4274 Across (conformational) space and (relaxation) time: using coarse-grain simulations to probe the intra- and interdomain dynamics of the Tau protein

Marien, J.; Prevost, C.; Sacquin-Mora, S.

10.1101/2025.07.21.665865 — biochemistry — Posted on 2025-11-07

4275 Putting BASIL in a BLT: A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations

Kuo, H.-Y.; Kryazhimskiy, S.

10.1101/2025.03.29.646120 — evolutionary biology — Posted on 2025-11-07

4276 Dorsoventral-mediated Shh induction is required for axolotl limb regeneration

Yamamoto, S.; Furukawa, S.; Ohashi, A.; Hamada, M.; Satoh, A.

10.1101/2025.04.07.647593 — developmental biology — Posted on 2025-11-07

4277 An Asgard archaeon with internal membrane compartments

MacLeod, F. I.; von Kuegelgen, A.; Lechowska, M. K.; Parham, J.; Richard, I. A.; Aguilar-Pine, E. J.; Baker, B. J.; Bharat, T.; Baum, B.

10.1101/2025.11.06.686947 — cell biology — Posted on 2025-11-07

4278 Pharmaceuticals residues lead to enrichment of Human, Animal, and Plant Pathogens in Wastewater

Suleiman, M.; Jiang, G.; Jousset, A.

10.1101/2025.11.05.686723 — microbiology — Posted on 2025-11-07

4279 MHC Class I-like Gene in Squirrel Monkey Cytomegalovirus and the Evolution of the Virus

Hondo, E.; Mizutani, T.; Shimoda, H.; Iida, A.

10.1101/2025.04.10.648282 — microbiology — Posted on 2025-11-07

4280 Human gloss perception reproduced by tiny neural networks

Morimoto, T.; Akbarinia, A.; Storrs, K. R.; Cheeseman, J. R.; Smithson, H. E.; Gegenfurtner, K. R.; Fleming, R. W.

10.1101/2025.05.09.653112 — neuroscience — Posted on 2025-11-07

4281 Examining the Effect of Social Determinants of Health on Human Trait Heritability

Liquori, J. L.; Risse-Adams, O. S.; Bharadwaj, R.; Ong, D.; Sinnott-Armstrong, N.; Musharoff, S. A.

10.1101/2025.06.12.659317 — genetics — Posted on 2025-11-06

4282 Chemically induced in vivo retinal neuron regeneration rescues vision in mice

Shoaib, R. M.; Medvidovic, S.; Korobkova, L.; Tripathi, P.; Lin, R. P.; Sandrosyan, A.; Hariharan, S.; Mahato, B.

10.1101/2023.12.27.572921 — cell biology — Posted on 2025-11-06

4283 Antibiotic-induced Recombination in Escherichia coli Requires the Formation of DNA Double-Strand Breaks

Nath, A.; Roizman, D.; Amin, I.; Pachaimuthu, N.; Blazquez, J.; Makarova, O.; Rolff, J.; Rodriguez Rojas, A.

10.1101/2022.03.08.483535 — molecular biology — Posted on 2025-11-06

4284 B cell expression of the enzyme PexRAP, an intermediary in ether lipid biosynthesis, promotes antibody responses and germinal center size

Cho, S. H.; Jones, M. A.; Meyer, K.; Anderson, D. M.; Chetyrkin, S.; Calcutt, M. W.; Caprioli, R. M.; Semenkovich, C. F.; Boothby, M. R.

10.1101/2024.10.17.618760 — immunology — Posted on 2025-11-06

4285 Sleep deprivation constrains dynamic configurations of integrated and segregated brain states impacting cognitive performance

Cross, N.; Borgetto, F.; Uji, M.; Jegou, A.; Nguyen, A.; Lee, K.; Aydin, U.; Perrault, A.; Dang-Vu, T. T.; Grova, C.

10.1101/2025.10.21.683658 — neuroscience — Posted on 2025-11-06

4286 Biophysical validation of explainable AI for functional brain imaging: bridging cellular mechanisms and network dynamics

Strock, A.; Nghiem, T.-A. E.; De Lecea, A.; Hassan, A.; Ryali, S.; Menon, V.

10.1101/2025.02.24.639808 — neuroscience — Posted on 2025-11-06

4287 NRT1.1s and NRT2.1 affect rhizosphere and apoplastic pHduring plant nitrate uptake

Murray, J. D.; Xiao, Q.; Wang, J.; Chen, Y.; Li, F.; Jiwu, W.; Miller, A. J.

10.1101/2025.10.30.685715 — plant biology — Posted on 2025-11-06

4288 SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets

Seal, S.; Neelon, B.

10.1101/2025.03.29.646124 — bioinformatics — Posted on 2025-11-06

4289 Dual DNA-binding capability of Cdc13 coordinates with Ku to safeguard telomere integrity

Feng, Z.; Shen, J.; Li, Y.; Gonzalez-Gutierrez,, G.; Wang, Q.; Niu, H.

10.1101/2025.09.02.671137 — biochemistry — Posted on 2025-11-06

4290 War Trauma Impairs Prenatal Brain Development: Evidence from Genetically-Informed Brain Imaging

Aydogan, G.; Kollmorgen, S.; Mante, V.; Linner, R. K.; Kleim, B.; Nave, G.; Ruff, C. C.

10.1101/2025.11.05.686844 — neuroscience — Posted on 2025-11-06

4291 Fast and accurate tree of blobs reconstruction under the network multispecies coalescent

Dai, J.; Han, Y.; Molloy, E.

10.1101/2025.11.05.686850 — bioinformatics — Posted on 2025-11-06

4292 Programmable DNA-Silk fibroin hydrogel scaffold with temporal mechanical reinforcement for mesenchymal stem cells differentiation and accelerated wound healing in a full-thickness skin defect mice model

Singh, N.; Parmar, B.; Joshi, A.; Gajjar, D.; Kashyap, V.; Solanki, R.; Singh, A.; Seshadri, S.; Bhatia, D. D.

10.1101/2025.11.06.686972 — bioengineering — Posted on 2025-11-06

4293 An amplicon panel for high-throughput and low-cost genotyping of Yesso scallop Mizuhopecten yessoensis

Sutherland, B. J. G.; Walker, C. Y. V.; Moody, D.; Bennett, C.; Wright-LaGreca, M.; Shamash-McLaughlin, C.; Leask, K.; Roth, D.; Lebeuf, M.; Green, T. J.

10.1101/2025.11.05.686843 — genomics — Posted on 2025-11-06

4294 aPKC and F-actin Dynamics Promote Hippo Pathway Polarity in Asymmetrically Dividing Neuroblasts

Joshi, N. S.; Sullivan, V. M.; Tokamov, S. A.; Fehon, R. G.

10.1101/2025.11.05.686779 — developmental biology — Posted on 2025-11-06

4295 Macrophage chemotaxis steered by complex self-generated gradients of complement C5a

Kiran, A.; Thomason, P. A.; Versluis, D. M.; Paschke, P. I.; Donnelly, H.; Tweedy, L.; Lilla, S.; Bravo-Ferrer, I.; Shergold, A.; Devlin, R.; Roberts, E. W.; Insall, R. H.

10.1101/2025.11.05.686842 — immunology — Posted on 2025-11-06

4296 Display of clustered antigen by follicular dendritic cells tunes B-cell receptor activation

Shahrokhtash, A.; Ogasawara, H.; Kastberg, K. S.; Salaita, K.; Degn, S. E.; Sutherland, D. S.

10.1101/2025.11.05.686827 — immunology — Posted on 2025-11-06

4297 Mini-Pcdh15b Gene Therapy Rescues Visual Deficits in a Zebrafish Model of Usher Syndrome Type 1F

Chen, X.; Hathaway, D. M.; Klein, A. J.; Phillips, J. B.; Booth, K. T.; Heitsch, M.; Lytvyn, A.; Derfler, B. H.; Wegner, J.; Goldstein, C.; Murphy, A.; Megason, S. G.; Westerfield, M.; Corey, D. P.; Ivanchenko, M. V.

10.1101/2025.11.05.686814 — neuroscience — Posted on 2025-11-06

4298 S-Equol: A Novel Therapeutic For HIV-1-Associated Gastrointestinal Dysbiosis

Rodriguez, M. T.; Olmstead, S. J.; McLaurin, K. A.; Mactutus, C. F.; Booze, R. M.

10.1101/2025.11.05.686823 — neuroscience — Posted on 2025-11-06

4299 A Reference Atlas of the Human Dorsal Root Ganglion

Bhuiyan, S. A.; Nagi, S. S.; Sankaranarayanan, I.; Semizoglou, E.; Usoskin, D.; Yang, L.; Yu, H.; Arendt-Tranholm, A.; Bertels, Z.; Bhatia, P.; Bouchatta, O.; Boyer, K.; Cervantes, A.; Chalif, J.; Chintalapudi, H.; Cicalo, A.; Copits, B.; Cronin, C.; Curatolo, M.; Dong, X.; Dougherty, P. M.; Dourson, A.; Funk, G.; Gabriel, K.; Griesemer, D. S.; Guo, H.; Gupta, P.; Hofstetter, C.; Horton, P.; Hsieh, A.; Inturi, N. N.; Jain, A.; Jayakar, S.; Johnston, B.; Kim, R.; Krauter, D.; Kupari, J.; Lemen, J.; Lesnak, J. B.; Liu, W.; Lopez, I.; Lu, Y.; MacMillan, H. J.; Mazhar, K.; Meriau, P.; Moffitt, J.

10.1101/2025.11.05.686654 — neuroscience — Posted on 2025-11-06

4300 Rewiring protein function through genetically encoded oxidative chemistry

Li, H.; Pavlic, A.; Ibrahim, N. E.; Wu, D.; Shapiro, M. G.

10.1101/2025.11.06.686050 — synthetic biology — Posted on 2025-11-06

4301 Ambient mass spectrometry imaging enables spatial metabolomics of optimal cutting temperature compound (OCT)-embedded tumors

Monaghan, J.; Woytowich, N.; Zhao, T.; Nguyen, K.; Mahony, E.; Lum, J. J.; Duncan, K. D.

10.1101/2025.11.05.686836 — cancer biology — Posted on 2025-11-06

4302 Iron addicted colorectal cancers exploit Heme-Complex II axis to resist oxidative cell death

Jain, C.; Essani, M.; Kumar, R.; Das, N. k.; Singhal, R.; Rossiter, N. J.; Chen, B.; Huang, W.; Lee, Z. H.; Solanki, S.; Zhang, Y.; Sajjakulnukit, P.; Zhang, L.; Dalal, P. J.; Hanna, D. A.; McCollum, S.; Stoffel, E. M.; Greenson, J. K.; Maher, L. J.; Lyssiotis, C. A.; Banerjee, R.; Shah, Y. M.

10.1101/2025.11.05.686813 — cancer biology — Posted on 2025-11-06

4303 Identification of Therapeutic Gene Targets in Triple-Negative Breast Cancer: A Hybrid Approach Integrating Semidefinite Programming, Boolean Simulation, and Druggability Analysis

MONTEIRO, S. A.; de Carvalho, L. A. V.; da Silva, F. A. B.

10.1101/2025.11.05.686831 — bioinformatics — Posted on 2025-11-06

4304 A structural and regulatory framework for Atg9-containing vesicle formation and their Atg1-dependent remodelling during autophagy initiation

Oeo-Santos, C.; Knüpling, E.; Davis, C.; Meng, X.; Maslen, S.; Kunzelmann, S.; D'Antuono, R.; Olerinyova, A.; Auchynnikava, T.; Skehel, M.; Schreiber, A.

10.1101/2025.11.06.685569 — biochemistry — Posted on 2025-11-06

4305 Generalizing Drift Diffusion Models with a State-Dependent Framework

Cely-Acosta, J. S.; Trimmer, P. C.

10.1101/2025.11.05.686838 — animal behavior and cognition — Posted on 2025-11-06

4306 Two cortical mechanisms of audiovisual processing in the human brain

Pushpita, S. N.; Wehbe, L.

10.1101/2025.11.05.686819 — neuroscience — Posted on 2025-11-06

4307 Cargo-directed assembly of nonviral nucleocapsid with controlled size

Tajima, K.; Sakai, Y.; Terasaka, N.

10.1101/2025.11.06.684264 — synthetic biology — Posted on 2025-11-06

4308 When Animals Turn Inside Out: The Eversion of Bloodworms

Kim, S.; Tuma, A.; Qin, D.; Ryu, Y. J.; Kim, D.; Abhilash, A.; Chintawar, S.; Thomas-Holness, C.; Fladger, A.; Behravesh, E.; Zhen, Y.; Zhou, Y.; Thompson, J. T.; Hu, D. L.

10.1101/2025.11.05.686822 — biophysics — Posted on 2025-11-06

4309 Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution

Wang, J.; Maldifassi, M.; Bratus-Neuenschwander, A.; Zhang, Q.; Beuschlein, F.; Penton, D.; Robinson, M. D.

10.1101/2025.11.06.686971 — bioinformatics — Posted on 2025-11-06

4310 Scalable and systematic hierarchical virus taxonomy with vConTACT3

Bolduc, B.; Zablocki, O.; Turner, D.; Jang, H. B.; Guo, J.; Adriaenssens, E. M.; Dutilh, B. E.; Sullivan, M. B.

10.1101/2025.11.06.686974 — bioinformatics — Posted on 2025-11-06

4311 HyperBind2: Multi-Shot Learning Enables Progressive Improvement in Computational Antibody Discovery

Dell'uomo, D.; Satz, A.; Averso, B.

10.1101/2025.11.06.687005 — bioengineering — Posted on 2025-11-06

4312 Culmorin inhibits detoxification of the mycotoxin deoxynivalenol by plant UDP-glucosyltransferases

Michlmayr, H.; Wiesenberger, G.; Rehak, K.; Funtak, K.; Sopel, M.; Malachova, A.; Fruhmann, P.; Weber, J.; Krska, R.; Dufresne, M.; Berthiller, F.; Adam, G.

10.1101/2025.11.06.686973 — biochemistry — Posted on 2025-11-06

4313 RNA-Focused DNA-Encoded Library Construction, Screening, and Integration of Docking Identify Bioactive Ligands of Pathogenic r(G4C2)exp RNA

Yang, X.; Taghavi, A.; Akahori, Y.; Pedrini, M.; Ishii, T.; Disney, M. D.

10.1101/2025.11.06.686979 — biochemistry — Posted on 2025-11-06

4314 Environmental Contributions to Proton Sharing in Protein Low-Barrier Hydrogen Bonds

Lin, J.; Gerlits, O.; Kneller, D. W.; Weiss, K. L.; Coates, L.; Hix, M. A.; Effah, S. Y.; Kovalevsky, A.; Walker, A. R.; Wilson, M. A.

10.1101/2025.11.05.686872 — biochemistry — Posted on 2025-11-06

4315 Base editing and nanoparticle transfection of airway cell types essential for treatment of cystic fibrosis

Kavanagh, E. W.; Joynt, A. T.; Pion, A. R.; Eastman, A. C.; Parr, A. I.; Starego, K. L.; Jain, M.; Shannon, S. R.; Yoo, E.; Newby, G. A.; Tzeng, S. Y.; Sharma, N.; Green, J. J.; Cutting, G. R.

10.1101/2025.11.06.687048 — genetics — Posted on 2025-11-06

4316 CARP Protects Against Doxorubicin-induced Cardiotoxicity through NRF1-driven Mitochondrial Homeostasis

Zhong, D.; Xu, X.; Feng, T.; Zhang, W.; Luo, F.; Guo, J.; Luo, Z.; Chen, R.; Wang, Y.; Ma, G.

10.1101/2025.11.06.683842 — molecular biology — Posted on 2025-11-06

4317 Genetic and Epigenetic Factors Influencing Methamphetamine Addiction and Aggressive Behavior among Iraqi Adult men

Al-Rubai, H. K.; Tejada, Y. L.

10.1101/2025.11.05.686833 — molecular biology — Posted on 2025-11-06

4318 Oxidative stress triggers RNAPII arrest through PARylation and DNA damage

Thomas, Q. A.; Wu, L.; Lesage, E.; Iversen, H. K. M.; Lopez Martinez, D.; Kompocholi, S.; Liu, H.; Nieto Moreno, N.; Gregersen, L. H.

10.1101/2025.11.06.686939 — molecular biology — Posted on 2025-11-06

4319 mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth

Lin, D. H.; Elcavage, L. E.; Khalizeva, E.; Bartel, D. P.

10.1101/2025.11.06.686990 — molecular biology — Posted on 2025-11-06

4320 Multi-omic characterization of the sow colostrum and milk microbiome and proteome

Holman, D. B.; Gzyl, K. E.; Kommadath, A.; Maattanen, P.

10.1101/2025.11.05.686862 — microbiology — Posted on 2025-11-06

4321 Proton stress adaptation in acidophilic sulfate-reducing bacteria: insights from Acididesulfobacillus acetoxydans for acid mine drainage bioremediation

Egas, R. A.; Bale, N. J.; Koenen, M.; Villanueva, L.; Sousa, D. Z.; Welte, C. U.; Sanchez-Andrea, I.

10.1101/2025.11.06.686915 — microbiology — Posted on 2025-11-06

4322 Mosquito NF-κB-mediated innate immunity exerts arbovirus-specific antiviral effects at multiple stages of the viral life cycle

Hollinghurst, P.; Cheung, Y. P.; Alexander, R.; Russell, T. A.; Fredericks, A. C.; Kumar, V.; Wallace, L. E.; Dietrich, I.; Mendum, T. A.; Davidson, A. D.; Fernandez-Sesma, A.; Maringer, K.

10.1101/2025.11.06.687020 — microbiology — Posted on 2025-11-06

4323 Increased mutation rates and diversity are dominant features of Geobacter multiheme cytochromes

Starwalt-Lee, R.; Gralnick, J. A.; Bond, D. R.

10.1101/2025.11.06.686851 — microbiology — Posted on 2025-11-06

4324 Proteomic characterization of extracellular vesicles from 12 commensal bacterial species

Makunja, R. N.; Maltseva, A.; Pessa-Morikawa, T.; Khatun, M.; Stensland, M.; Kaisanlahti, A.; Muhandiram, S.; Ruuska-Loewald, T.; Nyman, T. A.; Niku, M.

10.1101/2025.11.06.686325 — microbiology — Posted on 2025-11-06

4325 Naturally occurring CodY variants alter ligand binding, DNA target affinity, and virulence in Clostridioides difficile

Hasan, M. K.; Ray, S.; Garcia, B.; Govind, R.

10.1101/2025.11.06.687015 — microbiology — Posted on 2025-11-06

4326 A phage-derived reconfigurable effector associated with an actinobacterial contractile nanomachine tailors bacterial responses to competition

Nagakubo, T.; Nishiyama, T.; Asamizu, S.; Onaka, H.; NOMURA, N.; Toyofuku, M.

10.1101/2025.11.06.686954 — microbiology — Posted on 2025-11-06

4327 Surveillance of migratory shorebirds and seabirds in 2024 in Australia reveals incursions of a diversity of low pathogenicity avian influenza viruses, but not high pathogenicity avian influenza H5N1

Wille, M.; Atkinson, R.; Barr, I. G.; Bond, A. L.; Boyle, D.; Christie, M.; Deng, Y.-M.; Dewar, M.; Douglas, T.; He, M.; Jessop, R.; Kidd, L.; Klaassen, H.; Lavers, J. L.; Lau, H.; Marks, I.; Miller, E.; Neave, M. J.; Ross, T. A.; Stevens, V.; Sutherland, D. R.; Klaassen, M.

10.1101/2025.11.06.687052 — microbiology — Posted on 2025-11-06

4328 Miniature inverted-repeat transposable elements mobilize diverse antibiotic resistance genes in Enterobacteriaceae

Gomi, R.; Yano, H.

10.1101/2025.11.05.686661 — microbiology — Posted on 2025-11-06

4329 Symbiont diversity and light-organ morphology in Sepiola affinis

Suzuki, M. T.; Lami, R.; Bongrand, C.; Koch, E. J.

10.1101/2025.11.06.686942 — microbiology — Posted on 2025-11-06

4330 Human Papillomavirus Infection Blunts STING Signaling and Alters Downstream Response

Tobey, I. G.; Kosanke, D. P.; King, K. M.; Uhlorn, B. L.; Jeevanandam, A.; Campos, S. K.; Van Doorslaer, K. K.

10.1101/2025.11.06.686957 — microbiology — Posted on 2025-11-06

4331 Streptococcus pneumoniae fratricide-induced cell lysis does not require the type IV competence pilus.

Borowska, A. K.; Eddington, D.; Morrison, D.

10.1101/2025.11.06.685197 — microbiology — Posted on 2025-11-06

4332 De novo Cyclic Peptides Allow Visualisation of the Monomeric and Functional Amyloid Conformations of the Kinase RIPK3

Buchanan, J. A.; Lavidis, O.; Shields, N.; Harrison, K.; Nguyen, H. T.; Payne, R. J.; Passioura, T.; Steain, M.; Sunde, M.

10.1101/2025.11.05.686663 — biochemistry — Posted on 2025-11-06

4333 Hypoxia-induced mitoROS triggers M1 linear ubiquitin chains and activates NF-κB signaling

Kiri, T.; Ram, J.; Reis, N.; Maniv, I.; Ordureau, A.; Glickman, M. H.; Sulkshane, P.

10.1101/2025.11.06.686916 — biochemistry — Posted on 2025-11-06

4334 A Quantitative Review of Biodiversity Trends during the Great Ordovician Biodiversification Event

Richards, J.; Nanglu, K.; Ortega-Hernandez, J.

10.1101/2025.11.05.686803 — paleontology — Posted on 2025-11-06

4335 Massively parallel evolution reveals a biophysical scaling law between cell size and internal cell density

Sastokas, A.; Ho, W.-C.; Schmidlin, K.; Brown, P. T.; Crossland, P.; Shepherd, D. P.; Lynch, M. P.; Geiler-Samerotte, K.

10.1101/2025.11.05.686806 — biophysics — Posted on 2025-11-06

4336 Deep Learning Enables Automated Segmentation and Quantification of Ultrastructure from Transmission Electron Microscopy Images

Zou, A.; Tan, W.; Ji, J.; Rojas-Miguez, F.; Dodd, L.; Oei, E.; Chen, H.; Henderson, J. M.; Fan, X.; Lu, W.; Zhang, C.

10.1101/2025.11.05.686793 — bioinformatics — Posted on 2025-11-06

4337 Strain-dependent variation in maternal care and early behavioral development in laboratory rats

Pardo, G. E.; Pary, A. C.; Ccori, M. E. G.; Aguilar, M. C.; Cuevas, L. B.; Oruro, E. M.; Pacheco, L. F.

10.1101/2025.11.05.686817 — animal behavior and cognition — Posted on 2025-11-06

4338 The eukaryotic horizontal gene transfer dataset a compendium

Spaulding, J. A.; Fierst, J. L.

10.1101/2025.11.05.686818 — genomics — Posted on 2025-11-06

4339 Evaluating Field Trial Designs for Genetically Modified Mosquito Interventions: An In-Silico Simulation Approach

Chitturi, J.; Ventura, P. C.; Kummer, A. G.; Vasquez, C.; SeRine, E.; Hill, M. D.; Manica, M.; Poletti, P.; Beier, J. C.; Ejima, K.; Johansson, M.; Merler, S.; Yu, H.; Mutebi, J.-P.; Litvinova, M.; Wilke, A. B. B.; Ajelli, M.

10.1101/2025.11.05.686816 — ecology — Posted on 2025-11-06

4340 Lateral plate mesoderm directs human amnion and ventral skin organoid formation

Le, A. P.; Kim, J.; Ma, Q.; Gim, K. Y.; Serdy, S. A.; Lee, E. H.; Shaila, S. T.; Nakajima, T.; Nist-Lund, C.; Glass, I. A.; Mai, Y.; Nuzzi, L. C.; McNamara, C. T.; Labow, B. I.; Sun, L.; Lee, J.; Pourquie, O.; Koehler, K. R.

10.1101/2025.11.05.685987 — developmental biology — Posted on 2025-11-06

4341 Unraveling yeast diversity in food fermentation using ITS1-2 amplicon-based metabarcoding

Pradal, I.; Gettemans, T.; Weckx, S.

10.1101/2025.11.05.686804 — microbiology — Posted on 2025-11-06

4342 Atomistic TCR-ligand interactions instruct memory T-cell differentiation

Akitsu, A.; Tan, K.; Mallis, R. J.; Booker, M. A.; Duke-Cohan, J. S.; Brazin, K. N.; Kirkpatrick, E. H.; Parkins, A. N.; Aryal, S.; Cinella, V.; Lee, J. J.; Uberoy, K. I.; Koenig, J. K.; Biddle, M.; Messier, C. M.; Lizotte, P. H.; Tolstorukov, M. Y.; Hwang, W.; Lang, M. J.; Reinherz, E. L.

10.1101/2025.11.05.686789 — immunology — Posted on 2025-11-06

4343 Persistent Activation of Monocytes/Macrophages and Cell Senescence in SIV-Infected Macaques on ART

Chen, Y.; Ding, X.; Ray, S.; Thirugnanam, S.; Blair, R.; Saied, A.; Sukhanov, S.; Kolls, J.; Kim, W.-K.; Delafontaine, P.; Rappaport, J.; Qin, X.; Rout, N.

10.1101/2025.11.05.686810 — immunology — Posted on 2025-11-06

4344 Maternal care modulates chloride cotransporter development during inhibitory circuit maturation in the piriform cortex

Becerra-Flores, C.; Oruro, E. M.; Medina-Saldivar, C.; Pardo, G. E.; Pacheco, L. F.

10.1101/2025.11.05.686805 — neuroscience — Posted on 2025-11-06

4345 Coupling mathematical modeling with a novel human intestinal stem cell system to understand feedback regulation during planar cell polarity

Breau, K. A.; Dunahey, E. G.; Fosnocht, H. V.; Magness, S. T.; Elston, T. C.

10.1101/2025.11.05.686808 — systems biology — Posted on 2025-11-06

4346 Predator-prey scaling laws support a suspension-feeding lifestyle in Cambrian lobopodians

Richards, J.; Ortega-Hernandez, J.

10.1101/2025.11.05.686786 — paleontology — Posted on 2025-11-06

4347 Integrated Proteomic and Epigenomic Analysis Reveals IGF2 as a Vulnerability in PRC2-Deficient Malignant Peripheral Nerve Sheath Tumors

Lempiainen, J. K.; Miachin, K.; Liu, X.; Yang, K.; Horth, C.; Bareke, E.; Grinwald, M. F.; Saintilnord, W. N.; Wang, T.; Majewski, J.; Hirbe, A. C.; Garcia, B. A.

10.1101/2025.11.05.686792 — cancer biology — Posted on 2025-11-06

4348 phylobar: an R package for multiresolution compositional barplots in omics studies

Kuo, M.; Le Cao, K.-A.; Kodikara, S.; Mao, J.; Sankaran, K.

10.1101/2025.11.05.686662 — bioinformatics — Posted on 2025-11-06

4349 Alterations in protein N-glycosylation confer vanadate resistance in Ogataea polymorpha mutants defective in phosphomannosylation

Pakhomova, M.; Karginov, A.; Kulakova, M.; Vladimirova, P.; Mitkevich, O.; Agaphonov, M.

10.1101/2025.11.05.686784 — bioengineering — Posted on 2025-11-06

4350 A novel allele of Sh1 underlines the conversion of waxy corn to wx-sweet corn

Zhou, L.; Ning, L.; Liang, S.; Hu, Q.; Zhang, W.; Pan, Y.; Gao, Z.; Hong, J.; Wang, Y.; Zhao, W.; Chen, Y.; Dai, H.; Zhao, H.

10.1101/2025.11.05.686684 — genetics — Posted on 2025-11-06

4351 Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes

Kerdoncuff, E.; Marohn, M.; Cramer, N.; Dey, S.; Kardia, S.; Thangaraj, K.; Segurel, L.; Dey, A. B.; Lee, J.; Moorjani, P.

10.1101/2025.11.05.686799 — evolutionary biology — Posted on 2025-11-06

4352 Neo-sex chromosomes are not correlated with ecology or environment in eutherian mammals

Choi, J.; Hughes, J. J.; Campbell, P.

10.1101/2025.11.05.686331 — evolutionary biology — Posted on 2025-11-06

4353 Carbohydrate adaptation drives liver-brain axis maturation

Cui, H.; Wu, Z.; Zhang, Y.; Vu, H. S.; Chen, H.; Gao, X.; Jin, Y.; Cai, D.; Achyutuni, S.; Nguyen, P.; Pan, C.; Cao, H.; Robinson, C. G.; Steinberg, J. D.; Janke, L. J.; Nowinski, S. M.; Xu, J.; DeBerardinis, R. J.; Ni, M.

10.1101/2025.11.05.685548 — developmental biology — Posted on 2025-11-06

4354 IGF-1 from bone marrow Adipoq-lineage cells stimulates endocortical bone formation in mature female mice

Bertels, J. C.; Koehnken Sawall, J.; Dulmovits, B.; Liu, X.; Phan, A.; Ji, X.; Song, F.; Thom, C.; Long, F.

10.1101/2025.11.05.686616 — developmental biology — Posted on 2025-11-06

4355 Identification of Protein Cargo in Extracellular Vesicles from Macrophages in Progressing and Regressing Tumors

Zhu, Y.; Cai, J.; Suhandynata, R. T.; Bui, J. D.

10.1101/2025.11.05.685429 — immunology — Posted on 2025-11-06

4356 Stenocytosis: a mechanism for supramolecular attack particle transfer at the CTL lytic synapse

Demeersseman, L.; Schirra, C.; Becherer, U.; Puissegur-Lay, M.-P.; McKenzie, B.; Dustin, M. L.; Muller, S.; Valitutti, S.

10.1101/2025.11.05.686769 — immunology — Posted on 2025-11-06

4357 A spatial transcriptomic atlas of autism-associated genes identifies convergence in the developing human thalamus

Aivazidis, A.; Memi, F.; Rademaker, K.; Koko, M.; Roberts, K.; Trinh, A.; Petryszak, R.; Kleshchevnikov, V.; Tuck, E.; Lisgo, S.; Li, T.; Makarchuk, S.; Prete, M.; Nowakowski, T. J.; Martin, H. C.; Bayraktar, O. A.

10.1101/2025.11.05.685843 — neuroscience — Posted on 2025-11-06

4358 The Icelandic mutation APPA673T on amyloid-β plaque burden in the 5xFAD Alzheimer model

Anschuetz, A.; Listyono, R.; Vorley, T.; Platt, B.; Harrington, C. R.; Riedel, G.; Schwab, K.

10.1101/2025.11.05.686739 — neuroscience — Posted on 2025-11-06

4359 Continuous Flash Suppression responses in mouse visual cortex: stimulus laterality and anesthesia effects

Bassler, M.; Emming, L.; Whyte, C. J.; Huis in 't Veld, G.; Suzuki, M.; Pennartz, C.

10.1101/2025.11.05.686768 — neuroscience — Posted on 2025-11-06

4360 Resolving Heterogeneity in Major Depression: Overcoupling and Undercoupling Subtypes Exhibit Differential Treatment Response and Molecular Pathways

Gao, H.; Ma, Y.; Qian, R.; Jin, T.; Gu, B.; Qiu, B.; Ye, S.; Huang, M.; Wu, D.; zhao, z.

10.1101/2025.11.05.686774 — neuroscience — Posted on 2025-11-06

4361 Estrogen Dependent Variation in the Contributions of TRPM4 and TRPM5 to Fat Taste

Masterson, E.; Dahir, N. S.; Calder, A. N.; Liu, Y.; Lin, F.; Gilbertson, T. A.

10.1101/2025.11.05.686796 — neuroscience — Posted on 2025-11-06

4362 Dynamic epigenetic and transcriptional regulatory network in pepper fruit development and ripening

Liu, Q.; Tan, J. J.; Yang, R.; Li, X.; Jiang, D.

10.1101/2025.11.05.686000 — plant biology — Posted on 2025-11-06

4363 Hydrogen sulfide modulates plant hypoxic responses through the persulfidation of Plant Cysteine Oxidases

Telara, Y.; Akter, S.; Aroca, A.; Piccigallo, L.; Zhang, D.; Novi, G.; Lavilla, M.; Gunawardana, D.; La Monaca, N.; Lichtenauer, S.; Gotor, C.; Schwarzlaender, M.; Perata, P.; Flashman, E.; Giuntoli, B.

10.1101/2025.11.05.686772 — plant biology — Posted on 2025-11-06

4364 Nanoclustering of a plant transcription factor enables strong yet specific DNA binding

Arfman, K.; Janssen, B. P. J.; Romein, R.; van den Boom, S.; van der Woude, M.; Jansen, L.; Rademaker, M.; Hernandez-Garcia, J.; Ramalho, J. J.; Dipp-Alvarez, M.; Borst, J. W.; Weijers, D.; van Mierlo, C. P. M.; Sprakel, J.

10.1101/2025.11.05.686732 — plant biology — Posted on 2025-11-06

4365 NOVEL SMALL-MOLECULE INHIBITORS OF THE PROTEIN KINASE DYRK: POTENTIAL THERAPEUTIC CANDIDATES IN CANCER

Venkataramani, P.; Elkayam, E.; Garg, A.; Cheng, K. F.; Altiti, A.; He, M.; Thakur, K.; Michalopoulou, E.; Gonzalez, C.; Van Aelst, L.; Pappin, D.; Joshua-Tor, L.; Al-Abed, Y.; Tonks, N. K.

10.1101/2025.11.05.686653 — cancer biology — Posted on 2025-11-06

4366 Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data

Gorin, G.; Chari, T.; Carilli, M.; Vastola, J. J.; Pachter, L.

10.1101/2022.06.11.495771 — bioinformatics — Posted on 2025-11-06

4367 Network-Based Analysis of Human Astrocytes Links Aging to Neurodegenerative and Cardiovascular Diseases

Bota, P. M.; Picon-Pages, P.; Fanlo-Ucar, H.; Almabhouh, S.; Bagudanch, O.; Zeylan, M. E.; Senyuz, S.; Gohl, P.; Molina-Fernandez, R.; Fernandez-Fuentes, N.; Barbu, E.; Vicente, R.; Nattel, S.; Ois, A.; Puig-Pijoan, A.; Garcia-Ojalvo, J.; Keskin, O.; Gursoy, A.; Munoz, F. J.; Oliva, B.

10.1101/2025.11.05.686746 — bioinformatics — Posted on 2025-11-06

4368 Bridging Language Markers and Pathology: Correlations Between Digital Speech Measures and Surrogate CSF Biomarkers in Alzheimer's Disease

Pang, Y.; Chen, L.; Dodge, H. H.; Zhou, J.

10.1101/2025.11.05.686472 — bioinformatics — Posted on 2025-11-06

4369 Pilot-scale production of leucine from CO2

Fink, C.; Steger, F.; Schmidt, S.; Hilts, E.; Unger, F.; Ruddyard, A.; Klein, M.; Akerboom, B.-J.; Stehrer- Polasek, T.; Driessler, S.; Gurav, S.; Fennessy, R. T.; Smith, J.; Bochmann, G.; Rittmann, S. K.- M. R.

10.1101/2025.11.05.686735 — bioengineering — Posted on 2025-11-06

4370 A simple technique to create pre-vascularised delivery scaffolds for organoid therapies

Cao, K. X.; Owji, N.; Kaizer, A.; Pomeranz, G.; Price, K.; Johal, N.; Long, D. A.

10.1101/2025.11.05.686546 — bioengineering — Posted on 2025-11-06

4371 Targeting dendritic cells with RNA-loaded nanoparticles grafted with short peptides

Stamenkovic, V.; Brajkovic, M.; Garcia-Fernandez, C.; Borros, S.; Biarnes, X.; Fornaguera, C.

10.1101/2025.11.05.686747 — bioengineering — Posted on 2025-11-06

4372 Ubiquitin-dependent signal amplification in lipid saturation sensing

Causemann, J.; Schmidt, B.; Granz, D.; Mosler, T.; Jung, M.; Dikic, I.; Rieger, H.; Ernst, R.

10.1101/2025.11.05.686737 — biochemistry — Posted on 2025-11-06

4373 Activation of latent programs for maternal behavior

Streit Morsch, E.; Amadei, E. A.; Boehringer, R.; Grewe, B. F.; Vilimelis Aceituno, P.

10.1101/2025.11.05.686743 — animal behavior and cognition — Posted on 2025-11-06

4374 Chicken IRF10 suppresses the cGAS-STING-IFN antiviral signaling pathway by targeting IRF7

Jiang, S.; He, J.; Wang, K.; Lv, M.; Han, H.; Sun, B.; Chen, N.; Zheng, W.; Zhu, J.

10.1101/2025.11.05.686717 — immunology — Posted on 2025-11-06

4375 Exploring the neuroimmune cellular landscape in the skin of subjects with fibromyalgia.

Morado-Urbina, C.; Agashkov, K.; Hunt, M.; Tejos-Bravo, M.; af Ekenstam, K.; Fanton, S.; Venckute-Larsson, S.; Sandor, K.; Linderoth, E.; Kuliszkiewicz, A.; Arlestig, T.; Lofgren, M.; Kosek, E.; Svensson, C.

10.1101/2025.11.05.686713 — immunology — Posted on 2025-11-06

4376 The individual brain: mapping variability in hemispheric functional organization across cognitive domains in a representative sample

Karlsson, E. M.; Gerrits, R.; Vingerhoets, G.

10.1101/2025.11.05.686697 — neuroscience — Posted on 2025-11-06

4377 Eye Movement-Related Eardrum Oscillations (EMREOs) Do Not Have a Direct Impact on Auditory Spatial Discrimination

Sotero Silva, N.; Bröhl, F.; Kayser, C.

10.1101/2025.11.05.686724 — neuroscience — Posted on 2025-11-06

4378 A system for 3D reconstruction of mouse behaviour

Storchi, R.

10.1101/2025.11.05.686730 — neuroscience — Posted on 2025-11-06

4379 Fibrin-containing Hydrogels Regulate Human Astrocyte State and Neuronal Reprogramming

Distler, T.; Konrad Daga, K.; Bürkle, M.; Vasquez Sepulveda, S.; Franze, K.; Götz, M.; Masserdotti, G.

10.1101/2025.11.05.686711 — neuroscience — Posted on 2025-11-06

4380 Immature olfactory sensory neurons provide complementary input in the healthy olfactory system

Gregory, J. D.; Herzog, R. S.; Curtis, K. A.; Marar, M. I.; Cheetham, C. E. J.

10.1101/2025.11.05.686656 — neuroscience — Posted on 2025-11-06

4381 Circadian rhythms in sexual behavior and their influence on reproductive outcomes in mice

Aten, S.; Blake, C.; Keister, E.; Veith, A.; Fishbein, E.; Ramirez-Plascencia, O.; Thompson, M.; Howe, S.; Pereira, S.; Sela, Y.; Navarro, V.; Saper, C.

10.1101/2025.11.05.686629 — physiology — Posted on 2025-11-06

4382 Engineered Extracellular Vesicles Enriched with the miR-214/199a Cluster Enhance the Efficacy of Chemotherapy for Ovarian Cancer

Wang, W.; Alvero, A.; Qin, Y.; Wang, M.; Fox, A.; Li, Y.; Millman, M.; Kemper, A.; Gil, M.; Liu, X. S.; Chopp, M.; Zhang, Z. G.; Zhang, Y.

10.1101/2025.07.18.665422 — cancer biology — Posted on 2025-11-06

4383 A Minimal Plasma Proteome-Based Biomarker Panel for Accurate Prostate Cancer Diagnosis

Shahid, S. A.; Al-Harrasi, A.; Alsiyabi, A.

10.1101/2025.11.05.686712 — cancer biology — Posted on 2025-11-06

4384 Synthesis and Preclinical Development of a Novel 68Ga/89Zr-Labelled α{nu}β6-Integrin Targeting Trimer

Gariglio, G.; Patino, F. A.; Zierke, M. A.; Stangl, S.; Rheinfrank, T.; Holzleitner, N.; Kossatz, S.; DECRISTOFORO, C.

10.1101/2025.11.05.686720 — cancer biology — Posted on 2025-11-06

4385 Geometry-Constrained Prediction of Catalytically Competent Kinase Domains Across the Human Kinome

Wang, Y.; Hu, Q.; Huang, J.

10.1101/2025.11.03.686188 — biophysics — Posted on 2025-11-06

4386 The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge

Astore, M. A.; Woollard, G.; Silva-Sanchez, D.; Zhou, W.; Kopylov, M.; Dao Duc, K.; Lederman, R. R.; Li, Y.; Zhou, Y.; Yuan, J.; Ye, F.; Gu, Q.; Vuillemot, R.; Jonic, S.; Dang, L.; Ludtke, S. J.; Bridges, H.; Liu, S.; McLean, M.; Peretroukhin, V.; Schwab, J.; Cruz-Chu, E. R.; Schwander, P.; Gilles, M. A.; Singer, A.; Herreros, D.; Carazo, J. M.; Sorzano, C. O. S.; Feathers, J. R.; Zhong, E. D.; Grigorieff, N.; Cossio, P.; Hanson, S. M.

10.1101/2025.07.18.665582 — biophysics — Posted on 2025-11-06

4387 Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing

Ohnezeit, D.; Loliashvili, E.; Putzel, G.; Verstraten, R.; Liu, J.; Nicholson, L. S.; Pironti, A.; Jaffrey, S. R.; Depledge, D. P.; Wilson, A. C.

10.1101/2025.11.02.686099 — bioinformatics — Posted on 2025-11-06

4388 A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons

Blacksmith, M. S.; Nguyen, A.; Moran, J.; Kidd, J. M.

10.1101/2025.09.10.675418 — genomics — Posted on 2025-11-06

4389 The impact of incomplete taxon sampling on inference of gene flow by Bayesian and summary methods using genomic sequence data

Cheng, S.; Flouri, T.; Zhu, T.; Yang, Z.

10.1101/2025.11.05.686701 — genomics — Posted on 2025-11-06

4390 The Duality of Insect Macroevolution: Pulsed Genomes and Gradual Morphology Shape Lineage Diversification

Ajay, A.; M, S.; K, A.; K, Y.

10.1101/2025.11.05.686547 — evolutionary biology — Posted on 2025-11-06

4391 The APOL1 variant p.N264K blocks ion flow by occluding a pore at the cell surface

Hoeffken, V.; Console, L.; Nelde, N.; Pavenstadt, H.; INDIVERI, C.; Weide, T.

10.1101/2025.11.05.686714 — cell biology — Posted on 2025-11-06

4392 Derivation, Characterizations, and Applications of Rabbit Haploid Embryonic Stem Cells

Zhuang, Z.; Yu, M.; Cui, T.; Qiu, T.; Yang, Y.; Quan, L.; Li, L.; Zhang, Q.; Ye, Y.; Ouyang, Z.; Tang, C.; Wang, J.; Mao, J.; Lai, L.

10.1101/2025.11.05.686447 — cell biology — Posted on 2025-11-06

4393 Brain defence by the extracellular matrix protein Cochlin

Ghosh, R.; Jeong, I.; Jurisch-Yaksi, N.; Lee, B. T. K.; Jesuthasan, S.

10.1101/2025.11.05.686104 — immunology — Posted on 2025-11-06

4394 GFAP Degradation in TBI: Linking Novel Modified Products to Astrocyte Pathology and Patient Outcome

Wanner, I. B.; Halford, J.; Lopez, J.; Shen, S.; Chen, Y.; Zhao, H.; Salas, C. I.; Loo, R. R.; Robicsek, S.; Ellingson, B. M.; Gornbein, J.; Van Meter, T. E.; Shaw, G.; Loo, J. A.; Vespa, P. M.

10.1101/2025.08.01.668181 — neuroscience — Posted on 2025-11-06

4395 Ionic Direct Current Enables Millimeter- and Millisecond-Scale Cortical Gain Control in vivo

Wang, R.; Fridman, G. Y.

10.1101/2025.06.19.660597 — neuroscience — Posted on 2025-11-06

4396 Rhythmic light stimulation elicits multiple concurrent neural responses that separably shape human perception

Griffiths, B. J.; Duecker, K.; Fakche, C.; Dugue, L.; Quinn, A.; Jensen, O.

10.1101/2025.11.05.686709 — neuroscience — Posted on 2025-11-06

4397 Modes of action and in planta antifungal activity of Olea europaea defensin OefDef1.1-derived peptide variant

Tiwari, R.; Sekar, H.; James, G.; Tetorya, M.; Usher, E.; Shah, D. M.

10.1101/2025.11.05.686674 — plant biology — Posted on 2025-11-06

4398 A simple method of mechanical scarification to break seed dormancy in Viola odorata

Kim, J. Y.; Idiyatullina, K.; Colquhoun, T. A.

10.1101/2025.11.05.686783 — plant biology — Posted on 2025-11-06

4399 Spatial Conformation of Pancreatic Cancer Is Associated with Disease Recurrence after Curative-Intent Total Neoadjuvant Therapy

Cisneros, L. H.; Toruner, M. D.; siddiqui, Z.; Maraone, A. V.; Lin, M.; Xiao, A.; Thiels, C.; Truty, M. J.; George, B.; Jazieh, K.; McWilliams, R.; Maley, C. C.; Hartley, C.; Elhalaby, R.; Dizona, P.; Shi, Q.; Fernandez-Zapico, M. E.; Carr, R. M.

10.1101/2025.11.03.686383 — cancer biology — Posted on 2025-11-06

4400 Phospho 394Y LCK flow-cytometry readout predicts dasatinib sensitivity in paediatric T-cell acute lymphoblastic leukaemia

POLL, A. A.; Shi, Y.; Rauwolf, K. K.; Bornhauser, B.; Kulozik, A.; Bourquin, J.-P.; Irving, J. A.; van Delft, F.

10.1101/2025.11.04.684929 — cancer biology — Posted on 2025-11-06

4401 A hydrophobic cluster controls long-range allostery in the TRMT2A RNA recognition motif

Khaled, M.; Johannknecht, L.; Palomino-Hernandez, O.

10.1101/2025.11.05.686750 — biophysics — Posted on 2025-11-06

4402 Hepatitis B virus HBx protein masks epigenetic reader Spindlin1 via an inter-molecular zinc finger to subvert transcriptional control

Clavier, A.; Shida, T.; Gomez-Evain, S.; Droemer, M. A.; von Hammerstein, F.; Holzinger, J.; Leuthold, M. M.; Schuetz, A.

10.1101/2025.11.05.686744 — biophysics — Posted on 2025-11-06

4403 PRISM-G: an interpretable privacy scoring method for assessing risk in synthetic human genome data

Correa Rojo, A.; Moreau, Y.; Ertaylan, G.

10.1101/2025.10.17.682995 — bioinformatics — Posted on 2025-11-06

4404 When should adaptation arise from a polygenic response versus few large effect changes?

Milligan, W. R.; Hayward, L. K.; Sella, G.

10.1101/2025.05.15.654234 — evolutionary biology — Posted on 2025-11-06

4405 Diverse gene ancestries reveal multiple microbial associations during eukaryogenesis

Bernabeu, M.; Manzano-Morales, S.; Marcet-Houben, M.; Gabaldon, T.

10.1101/2024.10.14.618062 — evolutionary biology — Posted on 2025-11-06

4406 Nutrient fluctuation alters effects of litter diversity of invasive species on native communities

Wang, X.; Van Kleunen, M.; Zheng, W.-L.; Han, J.-J.; Wu, C.-L.; Yang, S.; Yu, F.-H.

10.1101/2025.11.05.686688 — ecology — Posted on 2025-11-06

4407 BMP-Smad1/9 signaling is required for PGC proliferation in zebrafish

Zheng, T.; Li, Y.; Li, G.; Wei, Z.; Jiang, Z.; Shah, R.; Zhang, W.; Xing, C.; Meng, A.; Wu, X.

10.1101/2025.11.04.686672 — developmental biology — Posted on 2025-11-06

4408 Isolation of region-specific factors assembled on the Immunoglobulin heavy chain locus during antibody class switch recombination

Gothwal, S. K.

10.1101/2025.11.04.677290 — molecular biology — Posted on 2025-11-06

4409 From Biofilms to Biocontrol: Aquaculture Biofilms as a Reservoir of Pseudomonas spp. with Activity Against Fish and Human Pathogens

Nguyen, J. N.; Testerman, T.; McBride, K.; Donohue, H.; Marden, J.; Balunas, M.; Graf, J.

10.1101/2025.11.05.686791 — microbiology — Posted on 2025-11-06

4410 Sox4 in Treg Cells Suppresses IL-10 Production via c-Maf Degradation and Exacerbates Type 2 Inflammation

Hayashi, Y.; Suga, K.; Suto, A.; Iwata, A.; Ishikawa, J.; Abe, K.; Kageyama, T.; Ito, T.; Tanaka, S.; Suzuki, K.; Yamashita, M.; Lefebvre, V.; Nakajima, H.

10.1101/2025.11.04.686669 — immunology — Posted on 2025-11-06

4411 Early Sleep-Dependent Sensory Gating in the Olfactory System

Serantes, D.; Gallo, D.; Garcia, A.; Gonzalez, J.; Mendoza, M.; Lagos, P.; Torterolo, P.; Cavelli, M. L.

10.1101/2025.11.04.686664 — neuroscience — Posted on 2025-11-06

4412 Embodied Navigation: whole-body movement drives path integration in large-scale free-walking virtual reality

Scherer, J.; Kroehnert, A.; Egelhaaf, M.; Boeddeker, N.

10.1101/2025.11.05.686699 — neuroscience — Posted on 2025-11-06

4413 A switch in arousal circuit architecture shapes sleep across the lifespan

Szuperak, M.; Selcho, M. S.; Eichler, K.; McClanahan, P. D.; Asahina, K.; Rosa, J.; Fang-Yen, C.; Thum, A. S.; Kayser, M. S.

10.1101/2025.11.05.686742 — neuroscience — Posted on 2025-11-06

4414 Global distribution patterns of an ocean-surface dwelling animal are associated with organismal mirror asymmetry

Iwanicki, T.; Maximenko, N.; Dunn, C.; Church, S. H.; Goodwin, D. S.; Helm, R. R.

10.1101/2025.11.04.686608 — zoology — Posted on 2025-11-06

4415 Throwing dice, but not always: bet-hedging strategy of parthenogenesis

Chai, Y.

10.1101/2025.11.05.686691 — zoology — Posted on 2025-11-06

4416 Integration of Hematopoietic and Thymus-like Niches in a Human iPSC-derived Bone Marrow Organoid

Lee, J.; Kawasaki, T.; Tabata, L.; Chen, J.; Uchiyama, T.; Yamazaki, S.; Umezawa, A.; Akutsu, H.

10.1101/2025.11.04.686649 — systems biology — Posted on 2025-11-06

4417 Bootstrap-based criteria for identifying differences between learned Bayesian networks

Berners-Lee, R.; Smith, V. A.

10.1101/2025.11.04.686685 — systems biology — Posted on 2025-11-06

4418 Periductal Fibroblast Density Defines Lymphocyte Exclusion via a CD44-Dependent Stromal Checkpoint in Pancreatic Cancer

Malchiodi, Z. X.; Lekan, A. A.; Suter, R. K.; Deshpande, A.; Peran, I.; Harris, B. T.; Duttargi, A.; Chien, M.-J.; Hariharan, S.; Wetherill, L.; Arslan, S.; Jablonski, S. A.; Ho, W. J.; Afifi, M.; Fertig, E. J.; Weiner, L. M.

10.1101/2024.05.23.593868 — cancer biology — Posted on 2025-11-06

4419 Cascade-Targeting Nanoparticles for Reversing Chemoresistance in Osteosarcoma

Li, X.; Xu, S.; Peng, Y.; Su, Z.; Wang, S.; Li, A.; Huang, X.; Shao, Z.; Du, Y.

10.1101/2025.11.04.686585 — cancer biology — Posted on 2025-11-06

4420 A switch from histone methyltransferase-EZH2 to demethylase KDM6A activity marks reinitiation of proliferation of drug treated colorectal cancer cells

Chatterjee, S.; Jaiswal, R.; Roy, A.; Chowdhury, S.; Mukherjee, S.; Chowdhury, R.

10.1101/2025.11.04.686665 — cancer biology — Posted on 2025-11-06

4421 Direct Optical Quantification of Chain Collapse, Reduced Dielectric, and Water Release Driving Protein Phase Separation

Perets, E. A.; Spies, J. A.; Cheong, J. H.; Shi, L.; Asamoto, D. K.; Holehouse, A. S.; Kim, J. E.; Min, W.; Neu, J.; Yan, E. C. Y.

10.1101/2025.11.04.686660 — biophysics — Posted on 2025-11-06

4422 Identification of a First-In-Class Small Molecule CAPON Binder Using Affinity Selection-Mass Spectrometry Screening

Abdo, A.; Nada, H.; Gabr, M.

10.1101/2025.11.05.686689 — biophysics — Posted on 2025-11-06

4423 SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets

Seal, S.; Neelon, B.

10.1101/2025.03.29.646124 — bioinformatics — Posted on 2025-11-06

4424 Development and Validation of a Continuous Real-Time Optical Sensor for Indocyanine Green Clearance Measurement During Ex-Vivo Perfusion of Human Livers

Derwent, E. N. J.; Risbey, C. W. G.; Niu, A.; Yousif, P.; Fonseka, N.; Curry, S.; Seow, C.; Ng, I.; McCaughan, G. W.; Crawford, M.; Pulitano, C.; Babekuhl, D.

10.1101/2025.11.05.686646 — bioengineering — Posted on 2025-11-06

4425 Nematode infections induce distinct chemical signatures and provoke aggression in ants

Bhat, B. A.; Jiang, N.-J.; Haltischke, R.; Ulrich, Y.

10.1101/2025.11.05.686619 — animal behavior and cognition — Posted on 2025-11-06

4426 Tracking community change via network coherence

Fuster-Calvo, A.; Higino, G. T.; Parent, C.; Caron, D.; Banville, F.; Massol, F.; Blanchet, F. G.; Hebert, K.; Pollock, L.; Maiorano, L.; Guimaraes, P. R.; Silva, P.; Thuiller, W.; Gravel, D.

10.1101/2025.11.04.686602 — ecology — Posted on 2025-11-06

4427 Sparse delivery of Synaptobrevin-2 to neurons using extracellular vesicles

Hannett, V.; Vilcaes, A. A.; Hugelier, S.; Tang, Q.; Lakadamyali, M.; Chanaday, N. L.

10.1101/2025.11.04.686638 — cell biology — Posted on 2025-11-06

4428 The scaffold protein PRR14L links the PP2A-TACC3 axis to mitotic fidelity and sensitivity to MPS1 inhibition

Liu, A. Z.; Narkar, A.; Li, K.; Bertomeu, T.; Johnson, B. A.; Coulombe-Huntington, J.; Dong, Y.; Zhu, J.; Tyers, M.; Li, R.

10.1101/2025.11.04.686150 — cell biology — Posted on 2025-11-06

4429 BCHS acts as a stress transducer connecting autophagic quality control with DNA damage repair

Lu, K.-H.; Yu, B.-H.; Sang, T.-K.

10.1101/2025.11.04.685471 — cell biology — Posted on 2025-11-06

4430 Bispecific CD20xCD40 Antibodies Achieve Multi-Lineage Modulation of Humoral and Cellular Immunity

McLaughlin, B.; de Boer, M.; Cowden, J.; Choudhry, M.

10.1101/2025.11.04.686640 — immunology — Posted on 2025-11-06

4431 VTA dopamine neuron activity produces spatially organized value representations

Pan-Vazquez, A.; Zimmerman, C. A.; McMannon, B.; Fabre, J. M. J.; Louka, M.; Jia, T.; Sagiv, Y.; West, S. J.; Faulkner, M.; Brain Laboratory, I.; Dayan, P.; Witten, I. B.

10.1101/2025.11.04.685995 — neuroscience — Posted on 2025-11-06

4432 Comparing electromyography, accelerometry, and visual inspection to assess the resting motor threshold for transcranial magnetic stimulation

Hamoline, G.; Lunardi, A. E.; Moreno-Verdu, M.; Waltzing, B. M.; Van Caenegem, E. E.; MacAteer, S.; Hardwick, R. M.

10.1101/2025.06.04.657787 — neuroscience — Posted on 2025-11-06

4433 KiF1a-regulated neuronal infrastructures in sensory and prefrontal cortices essential for fear memory and anxiety

Li, J.-y.; Chen, B.-c.; Zhang, Y.; Xu, Y.; Wang, L.; Wang, J.-H.

10.1101/2025.07.29.667346 — neuroscience — Posted on 2025-11-06

4434 Distinct neural routes for evaluative and informational social influence

Manivasagam, S.; Schultze, T.; Schacht, A.; Fischer, A.

10.1101/2025.10.30.685641 — neuroscience — Posted on 2025-11-06

4435 Unconscious switching of dorsal and medial pathways for plasticity and stability during NREM and REM sleep

Yamada, T.; Labonte-Clark, T.; Censor, N.; Watanabe, T.; Sasaki, Y.

10.1101/2025.11.04.686485 — neuroscience — Posted on 2025-11-06

4436 Mitochondrial bioenergetic signatures differentiate asymptomatic from symptomatic Alzheimer's disease

Mandal, P.; Trushina, E.; Arnold, M.; Kaddurah-Daouk, R.; Baloni, P.

10.1101/2025.11.04.686626 — neuroscience — Posted on 2025-11-06

4437 Methodological choices strongly modulate the sensitivity and specificity of lesion-symptom mapping analyses

Moore, M. J.; Rorden, C.; Robinson, G. A.; Mattingley, J. B.; Demeyere, N.

10.1101/2025.11.04.686650 — neuroscience — Posted on 2025-11-06

4438 Bayesian causal inference unifies perceptual and neuronal processing of center-surround motion in area MT

Lengyel, G.; Shivkumar, S.; DeAngelis, G.; Haefner, R. M.

10.1101/2025.09.17.676722 — neuroscience — Posted on 2025-11-06

4439 Environmental Noise Alters Neural Regulation Without Behavioral Impairment: A Pilot EEG Study

Morina, E.

10.1101/2025.11.04.685163 — neuroscience — Posted on 2025-11-06

4440 Mechanistic insight into the oligomerisation of Arabidopsis CRY1 and its inhibition by BIC1

Just, A.; Niemann, N.; Gnau, P.; Kock, D.; Heimerl, T.; Essen, L.-O.; Batschauer, A.; Morgner, N.

10.1101/2025.10.06.680677 — plant biology — Posted on 2025-11-06

4441 Bronsted-basic small molecules activate GTP hydrolysis in Ras Q61 mutants

Wang, Y.; Chen, S.; Wu, Y.; Cao, Y.; Shi, Z.; Norinskiy, M. A.; Wang, C.; Celik, H.; Zhang, Z.

10.1101/2025.11.04.686643 — cancer biology — Posted on 2025-11-06

4442 Disrupting Akt-Wnt/β-catenin signaling suppresses glioblastoma stem cell growth and tumor progression in immunocompetent mice

Sarkar, M. M.; Gonsalves, N.; Davarzani, A.; Mitchell, E.; Singh, A. M.; Karumbaiah, L.; Stice, S. L.

10.1101/2025.07.25.666376 — cancer biology — Posted on 2025-11-06

4443 Structural rationalization of IPMK inhibitor potency.

Wang, H.; Shears, S. B.; Blind, R. D.

10.1101/2025.08.16.670669 — biochemistry — Posted on 2025-11-06

4444 Integrating Biological and Machine Learning Models for Rainbow Trout Growth: Balancing Accuracy and Interpretability

Fulton, L.; Lyu, P.

10.1101/2025.11.04.686633 — ecology — Posted on 2025-11-06

4445 Single-cell morphodynamics predict cell fate decisions during mucociliary epithelial differentiation.

Tolonen, M.; Xu, Z.; Beker, O.; Kapoor, V.; Dumitrascu, B.; Sedzinski, J.

10.1101/2025.09.17.676780 — developmental biology — Posted on 2025-11-06

4446 Cryptococcus neoformans employs both PP1 and PP2A phosphatases to silence the spindle checkpoint

Suresh, A. P.; Cheng, H.; Davies, T.; Clark, I.; Spanos, C.; Hardwick, K.

10.1101/2025.11.04.686612 — cell biology — Posted on 2025-11-06

4447 Iterative immunogen optimization to focus elicited responses on a conserved, subdominant influenza hemagglutinin epitope

Marston, D. J.; Watanabe, A.; Kapingidza, A. B.; Harris, C.; Van Itallie, E.; Devkota, K.; Christopher, J.; Liu, P.; Pun, B.; Rhodes, B.; Frazier, M.; Winters, K.; Burre, H.; Kannan, P.; Liang, X.; Kelsoe, G.; Wiehe, K.; Singh, R.; Wrapp, D.; Kuraoka, M.; Azoitei, M. L.

10.1101/2025.11.04.686334 — immunology — Posted on 2025-11-06

4448 Low rank adaptation of chemical foundation models generate effective odorant representations

McConachie, G. D.; Duniec, E.; Guerina, F.; Younger, M.; DePasquale, B.

10.1101/2025.11.04.686628 — neuroscience — Posted on 2025-11-06

4449 Distinct involvements of the subthalamic nucleus subpopulations in reward-biased decision-making in monkeys

Branam, K.; Gold, J. I.; Ding, L.

10.1101/2025.11.04.686631 — neuroscience — Posted on 2025-11-06

4450 Mapping brain volume changes in the zQ175DN mouse model of Huntington's disease: a longitudinal MRI study

Vidas-Guscic, N. D.; Vasilkovska, T.; Pluym, S.; van Rijswijk, J.; Van Audekerke, J.; Tang, H.; Munoz-Sanjuan, I.; Pustina, D.; Cachope, R.; Van der Linden, A.; Bertoglio, D.; Verhoye, M.

10.1101/2025.11.04.686560 — neuroscience — Posted on 2025-11-06

4451 Octopamine and Tyramine Modulate Motor Program Competition in Drosophila larvae

Smith, W. V.; Pulver, S. R.

10.1101/2025.08.17.670699 — neuroscience — Posted on 2025-11-06

4452 Integrated control of redox and energy metabolism by the membrane-bound and soluble transhydrogenases of Pseudomonas putida across metabolic regimes

Partipilo, M.; Favoino, G.; Puiggene, O.; Rocha, C.; Meiners, C.; Gurdo, N.; Donati, S.; Volke, D. C.; Nikel, P. I.

10.1101/2025.11.04.686620 — systems biology — Posted on 2025-11-06

4453 Synthetic blood-based infrared molecular fingerprints: artificial cohorts for methodological research

Leopold-Kerschbaumer, N.; Feiler, N.; Kepesidis, K.

10.1101/2025.10.27.684739 — bioinformatics — Posted on 2025-11-06

4454 Automated Seizure Detection in Animal EEG Signals

Ganguly, S.; Jiang, Z.; Massey, N.; Rao, N. S.; Thippeswamy, T.; Sarkar, S.

10.1101/2025.11.04.686618 — animal behavior and cognition — Posted on 2025-11-06

4455 Disruption of the insulin signaling pathway in C. elegans dramatically increases male longevity and enhances reproductive health late in life

Al-Saadi, R. S.; Lewack, H. B.; Phillips, P. C.

10.1101/2025.11.04.686639 — genetics — Posted on 2025-11-06

4456 Tracking changes in birds' interaction milieu

Rigal, S.; Devictor, V.; Dakos, V.

10.1101/2025.02.14.638220 — ecology — Posted on 2025-11-06

4457 Molecular mechanisms underlying p62-dependent secretion of the Alzheimer-associated ubiquitin variant, UBB+1

Wagh, A. R.; Glickman, M. H.

10.1101/2024.12.31.630908 — cell biology — Posted on 2025-11-06

4458 Biased inter-columnar communication and short-term plasticity in mouse barrel cortex

Judge, J. M.; Jackson, M. B.

10.1101/2025.11.04.686617 — neuroscience — Posted on 2025-11-06

4459 DESpace2: detection of differential spatial patterns in spatial omics data

Cai, P.; Robinson, M. D.; Tiberi, S.

10.1101/2025.06.30.662268 — bioinformatics — Posted on 2025-11-06

4460 A plug-and-play transepithelial/transendothelial electric resistance (TEER)-upgraded organ-on-chip system to measure barrier dynamics in real-time

Kaden, T.; Besser, S.; Abdo, N.; Mosig, A. S.; Rennert, K.; Nietzsche, S.

10.1101/2025.04.10.648170 — bioengineering — Posted on 2025-11-06

4461 Evolution of a fuzzy ribonucleoprotein complex in viral assembly

Zhao, H.; Li, T.; Hassan, S. A.; Nguyen, A.; Datta, S. A.; Zhang, G.; Trent, C.; Czaja, A. M.; Wu, D.; Aronova, M. A.; Lai, K. K.; Piszczek, G.; Leapman, R. D.; Yewdell, J. W.; Schuck, P.

10.1101/2025.04.26.650775 — biophysics — Posted on 2025-11-06

4462 Ultra-long-range Polycomb-coupled interactions underlie subtype identity of human cortical neurons

Pletenev, I. A.; Vaulin, N.; Molodova, M. N.; Kuznechenkova, E.; Soldatenkova, A.; Efimova, O. I.; Tvorogova, A. V.; Khaitovich, P.; Razin, S. V.; Ulianov, S. V.; Khrameeva, E. E.

10.1101/2025.11.05.686502 — genomics — Posted on 2025-11-06

4463 Pachytene piRNAs define a conserved program of meiotic gene regulation

Loubalova, Z.; Ahrend, F.; Stoyko, D.; Cosby, R.; Ralls, S.; Meister, G.; Macfarlan, T.; Haase, A. D.

10.1101/2025.11.05.686807 — developmental biology — Posted on 2025-11-06

4464 Growth of Corynebacterium glutamicum on 5-oxo-L-proline (pyroglutamate) as carbon and nitrogen source requires the PxpR-controlled pxpTABC genes

Sundermeyer, L.; Mack, C.; Bott, M.

10.1101/2025.10.30.685629 — microbiology — Posted on 2025-11-06

4465 Whole Metagenome Sequencing: not Deep Enough for Complete Microbial Function Recovery

Liu, J.; Coker, M. O.; Osazuwa-Peters, N.; Peter, O.; Idemudia, N. L.; Schlecht, N. F.; Obuekwe, O.; Eki-Udoko, F. E.; Bromberg, Y.

10.1101/2025.11.04.685665 — bioinformatics — Posted on 2025-11-06

4466 Development and characterization of a scalable calcium imaging assay using human iPSC-derived neurons

Haustein, M. D.; Deymier, C.; Schlienger, S.; Lexcellent-Bissler, L.; Mawet, J.; Gutknecht, E.; Thenoz, L.; Brazauskas, P.; Renault, B.; Brun, S.; Winnistörfer, S.; Portmann, T.

10.1101/2025.09.05.674208 — neuroscience — Posted on 2025-11-06

4467 Time-series RNA-Seq and data-driven network inference unveil dynamics of cell activation, survival and crosstalk in Chronic Lymphocytic Leukaemia in vitro models

Marku, M.; Chenel, H.; Bordenave, J.; Hurtado, M.; Domagala, M.; Raynal, F.; Poupot, M.; Ysebaert, L.; Zinovyev, A.; Pancaldi, V.

10.1101/2025.04.20.649300 — systems biology — Posted on 2025-11-06

4468 NRT1.1s and NRT2.1 affect rhizosphere and apoplastic pHduring plant nitrate uptake

Murray, J. D.; Xiao, Q.; Wang, J.; Chen, Y.; Li, F.; Jiwu, W.; Miller, A. J.

10.1101/2025.10.30.685715 — plant biology — Posted on 2025-11-06

4469 SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets

Seal, S.; Neelon, B.

10.1101/2025.03.29.646124 — bioinformatics — Posted on 2025-11-06

4470 Wearable sweat nicotine biosensor based on a nicotineoxidoreductase and its natural electron acceptor

Zhang, Z.; Addokhi, A.; Hughes, K. A.; Zang, H.; Piqueras, M. D. C.; Kuzmanovic, U.; Charles, R.; Leung, L.; Klapperich, C. M.; Allen, K. N.; Grinstaff, M. W.; Galagan, J. E.

10.1101/2025.10.31.685570 — bioengineering — Posted on 2025-11-06

4471 When splicing is not all or none: Challenges for variant classification

Lin, J.-H.; Wu, H.; Tang, X.-Y.; Masson, E.; Cooper, D. N.; Ferec, C.; Liao, Z.; Zou, W.-B.; Chen, J.-M.

10.1101/2025.10.30.685113 — genetics — Posted on 2025-11-06

4472 Assessing the potential of ancient protein sequences in the study of hominid evolution

Patramanis, I.; Skov, L.; Cappellini, E.; Racimo, F.

10.1101/2025.04.08.647730 — evolutionary biology — Posted on 2025-11-06

4473 Major cell type differences between larval and adult hemichordate body plans

Bump, P.; Brewster, C.; Formery, L.; Lubeck, L.; Campbell, C.; Morri, M.; Sit, R.; Rokhsar, D.; Benham-Pyle, B.; Sanchez Alvarado, A.; Lowe, C.

10.1101/2025.10.31.685866 — developmental biology — Posted on 2025-11-06

4474 Aeschynomene americana induces terminal bacteroid differentiation in Bradyrhizobium sp. USDA3516, a novel model for Dalbergioid-rhizobia symbiosis

Carlew, T. S.; Atherton, A. A.; Shim, A.; Rojas, C. P.; Buchanan, R. A.; Chang, J. H.; Sachs, J. R.; Belin, B. J.

10.1101/2025.11.05.682141 — plant biology — Posted on 2025-11-05

4475 Algae-specific Immune Modulation Influences Responses to Heat and Pathogen Challenge in a Symbiotic Coral

Da-Anoy, J.; Chen, M.-H.; Bouchie, A.; Dougherty, J.; Lapadula, A.; Skena, A.; Wang, W.; Abraham, T.; Thompson, K.; Jasnos, O.; Toyama, K. S.; Ayivor, J.; Diya, O.; Gilmore, T. D.; Davies, S. W.

10.1101/2025.11.05.684850 — genomics — Posted on 2025-11-05

4476 West Nile virus dissemination among individual wild mosquito vectors in Northern Colorado, 2023

DeCook, J. R.; Ring, M. E.; Stewart, C.; Pavelko, H. M.; Burton, T. A.; Ebel, G. D.; Fauver, J. R.; Foy, B. D.

10.1101/2025.11.05.686815 — ecology — Posted on 2025-11-05

4477 Aberrant 5-Methylcytosine tRNA Modification Disrupts Proteostasis and Exacerbates Age-Related Osteoporosis

Peng, Z.; Peng, N.; Yuan, M.; Yan, F.; Jiang, T.; Ye, M.; Xiao, Y.

10.1101/2025.11.04.686482 — cell biology — Posted on 2025-11-05

4478 Pitavastatin counteracts venetoclax resistance mechanisms in acute myeloid leukemia by depleting geranylgeranyl pyrophosphate

Fruman, D.; Buono, R.; Juarez, D.; Paul, M.; Skuli, S. J.; Wong, I. B.; Tarnekar, I.; Ying, Z.; Le, I.; Wertheim, G.; Bakayoko, A.; Kruidenier, M.; Sebti, S.; Konopleva, M.; Fleischman, A. G.; Jang, C.; Carroll, M.

10.1101/2025.10.27.684888 — cancer biology — Posted on 2025-11-05

4479 Triple-helical ligands selectively targeting the closed αI domain of integrin α2β1

Shibata, S. S.; Oki, H.; Kawahara, K.; Masuda, R.; Fujii, K. K.; Koide, T.

10.1101/2025.07.28.667101 — biochemistry — Posted on 2025-11-05

4480 Modeling and Inferring Metacommunity Dynamics with Maximum Caliber

Jackson, Z. L.; Leibold, M. A.; Holt, R. D.; Xue, B.

10.1101/2025.06.20.660802 — ecology — Posted on 2025-11-05

4481 The mammalian rapid tRNA decay pathway is critical for N⁷-methylguanosine-hypomodified tRNA degradation under physiological conditions

Miyoshi, K.; Otsubo, K.; Kaneko, S.; Terauchi, M.; Hatoyama, Y.; Noguchi, H.; Kanemaki, M. T.; Saito, K.

10.1101/2025.11.05.686800 — molecular biology — Posted on 2025-11-05

4482 Complement C3 recognition by C3 convertases

Changhao, J.; Xiaoke, Y.; Minghui, Z.; Ying, T.; Xiao, J.

10.1101/2025.08.09.669456 — molecular biology — Posted on 2025-11-05

4483 Loss of essential outer membrane functions causes drug hypersensitization in Acinetobacter baumannii overexpressing multidrug efflux pumps

Hamami, E.; Huo, W.; Neal, K.; Neisewander, I.; Geisinger, E.; Isberg, R. R.

10.1101/2024.01.04.574119 — microbiology — Posted on 2025-11-05

4484 Resistance and heteroresistance as a consequence of colistin therapy during Acinetobacter baumannii murine pneumonia

Hernandez-Bird, J.; He, B.; VanOtterloo, L. M.; Billings, E. B.; Huo, W.; Teodoro, G. I. C.; Echlin, H.; Rosch, J. M.; Trent, M. S.; Isberg, R. R.

10.1101/2025.07.24.666669 — microbiology — Posted on 2025-11-05

4485 From perception to valence: a pair of interneurons that assign positive valence to sweet sensation in Drosophila

Christie, K. W.; Dadyala, T. S.; Chung, P.; Ito, M.; Shao, L.

10.1101/2025.10.31.685871 — neuroscience — Posted on 2025-11-05

4486 A three-dimensional immunofluorescence atlas of the brain of the hackled-orb weaver spider, Uloborus diversus.

Artiushin, G.; Corver, A.; Gordus, A. G.

10.1101/2024.09.05.611298 — neuroscience — Posted on 2025-11-05

4487 Prior cocaine use disrupts identification of hidden states by single units and neural ensembles in orbitofrontal cortex

Zong, W.; Mueller, L.; Zhang, Z.; Zhou, J.; Schoenbaum, G.

10.1101/2025.03.28.645972 — neuroscience — Posted on 2025-11-05

4488 Cellular and molecular associations with intrinsic brain organization

Feng, G.; Chen, J.; Sui, J.; Calhoun, V. D.

10.1101/2025.04.28.651051 — neuroscience — Posted on 2025-11-05

4489 The proteomic landscape and temporal dynamics of mammalian gastruloid development

Garge, R. K.; Lynch, V.; Fields, R.; Casadei, S.; Best, S.; Stone, J.; Snyder, M.; Kubo, C.; Wakimoto, A.; Liu, Z.; McGann, C. D.; Shendure, J.; Starita, L. M.; Hamazaki, N.; Schweppe, D. K.

10.1101/2024.09.05.609098 — systems biology — Posted on 2025-11-05

4490 Thermogenetics for cardiac pacing

Balatskiy, A. V.; Nesterenko, A. M.; Ovechkina, V. S.; Lanin, A. A.; Jappy, D.; Sokolov, R. A.; Dzhabrailov, V. D.; Turchaninova, E. A.; Slotvitsky, M. M.; Fetisova, E. S.; Moshchenko, A. A.; Andrianova, S. K.; Karpov, R. M.; Sabinin, S. S.; Biglova, D. Z.; Zakharov, A.; Solius, G. M.; Solyus, E. M.; Korolev, S. V.; Podgorny, O. V.; Tsvelaya, V. A.; Agladze, K. I.; Kelmanson, I. V.; Fedotov, A. B.; Rozov, A. V.; Bruegmann, T.; Zheltikov, A. M.; Mozhaev, A. A.; Belousov, V. V.

10.1101/2024.01.02.573885 — synthetic biology — Posted on 2025-11-05

4491 Functional characterisation of bicarbonate transporters from the cyanobacterial SbtA2 family and subsequent expression in tobacco

Rourke, L. M.; Byrt, C. S.; Long, B. M.; Price, G. D.

10.1101/2025.11.03.686429 — plant biology — Posted on 2025-11-05

4492 Epithelial HO-1 regulates iron availability and promotes colonic tumorigenesis in a context-dependent manner

Callahan, R. C.; Curry, J. C.; Bhagavatula, G.; Staley, A. W.; Schaefer, R. E. M.; Minhajuddin, F.; Zhou, L.; Neuhart, R. M.; Atif, S. M.; Orlicky, D. J.; Cartwright, I. M.; Gerich, M. E.; Steiner, C. A.; Theiss, A. L.; Hall, C. H. T.; Colgan, S. P.; Onyiah, J. C.

10.1101/2024.03.06.583112 — cancer biology — Posted on 2025-11-05

4493 Elastohydrodynamic mechanisms govern beat pattern transitions in eukaryotic flagella

Veeraragavan, S.; Parast, F. Y.; Nosrati, R.; Ranganathan, P.

10.1101/2024.02.04.578806 — biophysics — Posted on 2025-11-05

4494 scFPC-DE: Robust Differential Expression Analysis Along Single Cell Trajectories via Functional Principal Component Analysis

Lopez Candelaria, R. J.; Qian, Y.; Law, M.; Chen, F.; Zhang, Y.; Qiu, X.

10.1101/2025.11.03.686374 — bioinformatics — Posted on 2025-11-05

4495 Conkazal-M1 from the MKAVA family of conotoxins - a dual-function protease inhibitor and neuroactive peptide

Hackney, C. M.; Koch, T. L.; Ryding, N. L.; Rogalski, A.; Chase, K.; Giglio, M. L.; Espino, S. S.; Acyatan, Z. G.; Watkins, M.; Olivera, B. M.; Safavi-Hemami, H.; Teilum, K.; Ellgaard, L.

10.1101/2025.11.05.686841 — biochemistry — Posted on 2025-11-05

4496 Live-Cell Covalent Profiling Reveals Principles of RNA-Small Molecule Recognition across the Human Transcriptome

Tong, Y.; Taghavi, A.; Su, X.; Yang, X.; Rouse, W.; Kovachka, S.; Childs-Disney, J. L.; Sekioka, R.; Zavala, R.; Li, Y.; Moss, W.; Disney, M. D.

10.1101/2025.11.05.686775 — biochemistry — Posted on 2025-11-05

4497 A Comprehensive Structural and Functional Analysis of Saccharomyces Killer Toxins.

Creagh, J. W.; Reetz, D. C.; Givens, L. L.; Coss, S. A.; Bizarria, R.; Patel, J. S.; Rodrigues, A.; Ytreberg, F. M.; Rowley, P. A.

10.1101/2025.11.04.686668 — molecular biology — Posted on 2025-11-05

4498 Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation

Chen, X. D.; Jim, M.; Vallurupalli, M.; Cao, K.; Torres, A. N.; Leong, J. W.; Zhang, Y.; Wollensak, D.; Gong, Q.; Sun, J.; Borji, M.; Schor, G.; Mrowka, S.; Hu, M.; Laumas, A.; Roth, J. A.; Golub, T.; Chen, F.

10.1101/2025.11.05.686847 — molecular biology — Posted on 2025-11-05

4499 RNA polymerase II-TFIIE-TFIIH interface functions in transcription start site selection in Saccharomyces cerevisiae

Basnet, P.; Zhu, Y.; Vvendenskaya, I. O.; Arora, P.; Hammer, S. E.; McVicar, B. R.; Alex, S. A.; Nickels, B. E.; Kaplan, C. D.

10.1101/2025.11.05.686797 — molecular biology — Posted on 2025-11-05

4500 Dual apical methyltransferases orchestrate motility initiation in apicomplexan parasites

Qin, P.; Kumar, T.; Koczy, O.; Li, W.; Forne, I.; Mattei, S.; Jimenez Ruiz, E.

10.1101/2025.11.05.686696 — microbiology — Posted on 2025-11-05

4501 HCMV promotes viral reactivation through the coordinated regulation of Notch signaling by UL8 and miR-UL36

Dirck, A.; Diggins, N.; Perez, W.; Parkins, C.; Daily, M. A.; Turner, R.; Slind, L. E.; Nguyen, L. K.; Malouli, D.; Wu, G.; Hancock, M. H.; Caposio, P.

10.1101/2025.11.05.686718 — microbiology — Posted on 2025-11-05

4502 In situ Architecture of the Tad Pilus Machine in Caulobacter crescentus

Iarocci, J.; Whitfield, G. B.; Williston, R. F.; Wozny, M. R.; Presley, J. F.; Ellison, C. K.; Brun, Y. V.; Guo, S.

10.1101/2025.11.05.686773 — microbiology — Posted on 2025-11-05

4503 Inverse stable isotope labeling (InverSIL) links predicted catecholate siderophore gene clusters to their products in diverse bacteria

Robes, J. M. D.; Liebergesell, T. C. E.; Medvedeva, V. P.; Puri, A. W.

10.1101/2025.11.05.686764 — microbiology — Posted on 2025-11-05

4504 Modeling and minimization of dCas9-induced competition in CRISPRi-based genetic circuits

Jatkar, D. D.; Al-Radhawi, M. A.; Voigt, C. A.; Sontag, E. D.

10.1101/2025.11.05.686856 — synthetic biology — Posted on 2025-11-05

4505 In vitro pharmacokinetics and pharmacodynamics of the diarylquinoline TBAJ-587 and its metabolites against Mycobacterium tuberculosis

Aguilar Ayala, D. A.; Rabodoarivelo, M. S.; Eveque-Mourroux, M. R.; Leding, A. A.; Sonnekalb, L.; Pico Marco, A.; Willand, N.; Serbina, N.; Simonsson, U. S.; Lucia, A.; Ramon-Garcia, S.; ERA4TB consortium,

10.1101/2025.11.05.686716 — pharmacology and toxicology — Posted on 2025-11-05

4506 Molecular Dynamics-Guided All-Atom Reconstruction of Cryo-ET Maps Reveals Mechanisms of Histone Tail-Mediated Chromatin Compaction

Li, S.; Aristizabal, M. J.; Grigoryev, S. A.; Panchenko, A. R.

10.1101/2025.11.05.686627 — biophysics — Posted on 2025-11-05

4507 Diversity-driven biochemical survey reveals dimeric structural origin of rubisco

Kehl, A. J.; Taylor-Kearney, L.; Jaffe, A. L.; Pereira, J. H.; Lee, J.; Hammel, M.; Waldburger, L.; Yeow, C.; Alvarado, L. V.; Adams, P. D.; Banfield, J.; Siegel, J. B.; Prywes, N.; Shih, P. M.

10.1101/2025.11.05.686826 — biochemistry — Posted on 2025-11-05

4508 Ecological coherence in abundance dynamics across terrestrial and marine assemblages

Fuster-Calvo, A.; Hebert, K.; Dolezal, A. J.; Parent, C.; Massol, F.; Waters, M. T.; Gravel, D.

10.1101/2025.11.05.686795 — ecology — Posted on 2025-11-05

4509 A Grapholita molesta (Lepidoptera: Tortricidae) cadherin in the 99C cadherin clade binds to Bacillus thuringiensis Cry1A proteins

Toledo, D.; Crava, C. M.; Escriche, B.; Bel, Y.

10.1101/2025.11.05.686530 — molecular biology — Posted on 2025-11-05

4510 Proteomic profiling of skeletal muscle ribosomes from higher versus lower responders to 10 weeks of resistance training

Michel, J. M.; Norton, S. C.; Bergamasco, J.; Scarpelli, M.; Chaves, T.; da Silva, D.; Bittencourt, D.; Ugochukwu, C.; Boersma, M.; Mobley, C. B.; Godwin, J.; Nader, G.; Libardi, C.; Roberts, M.

10.1101/2025.11.04.686603 — molecular biology — Posted on 2025-11-05

4511 Non-Optimal Codon Usage Shapes Cell Cycle Regulators: Codon Optimization Studies on CDK1 and NUF2

Bhattacharya, M.; Sivan, A.; Baum, G.; Mukherjee, S.; Morgenstern, M.

10.1101/2025.11.05.681855 — molecular biology — Posted on 2025-11-05

4512 Functional divergence of Capicua isoforms explains differential tissue vulnerability in neurological disease

Lee, H.; Gonzalez, E. V.; Rivera, E. M.; Durham, M. A.; Richman, R.; Chu, E. H.- Y.; Xia, K.; Chen, H.; Liu, Z.; Veeraragavan, S.; Shivanna, B.; Zoghbi, H. Y.

10.1101/2025.11.05.686788 — molecular biology — Posted on 2025-11-05

4513 Phenotypic assessment and genetic validation of Plasmodium falciparum molecular markers associated with malaria chemoprevention in Senegal

Brenneman, K. V.; Wong, W.; Ndiaye, Y. D.; Schaffner, S.; Ngom, B.; Bellavia, K.; Ullah, I.; Gaye, A.; Sow, D.; Ndiaye, M. F.; Toure, M.; Gadiaga, N.; Sene, A.; Deme, A. B.; Dieye, B.; Yade, M. S.; Diongue, K.; Diedhiou, Y.; Gomis, J. F.; Ndiaye, M.; Diallo, M. A.; Ndiaye, I. M.; MacInnis, B. L.; Wirth, D.; Ndiaye, D.; Volkman, S. K.

10.1101/2025.11.05.686777 — molecular biology — Posted on 2025-11-05

4514 PaRXLR40, a broad cell death suppressor of the kauri dieback pathogen Phytophthora agathidicida, targets a plant ARM/BTB domain-containing protein

Tarallo, M.; Guo, Y.; McLellan, H.; Bradley, E.; Bradshaw, R.; Boevink, P.; Birch, P. R.; Mesarich, C. H.

10.1101/2025.11.05.686655 — molecular biology — Posted on 2025-11-05

4515 Nitric oxide tunes secreted metabolite bioactivity

Lonergan, Z. R.; Weisflog, S. L.; Scurria, M.; Li, J.; Thalhammer, K.; Gutierrez, O.; Conway, S. J.; Newman, D. K.

10.1101/2025.11.05.686753 — microbiology — Posted on 2025-11-05

4516 A Novel Technique to Characterize Klebsiella pneumoniae Populations Indicates that Mono-Colonization is Associated with Risk of Infection

Unverdorben, L.; Mason, S.; Wu, W.; Noda, M.; Castaneda, S.; Vornhagen, J.; Snitkin, E. S.; Rao, K.; Bachman, M. A.

10.1101/2025.11.05.686704 — microbiology — Posted on 2025-11-05

4517 SET-M33 peptide as a selective in vitro antimicrobial agent against the porcine respiratory pathogen Glaesserella parasuis

Pereira Lourenco, A. L.; Rouam el Khatab, O.; Falciani, C.; Pini, A.; Aragon, V.; Cerda-Cuellar, M.; Kochanowski, K.

10.1101/2025.11.05.686722 — microbiology — Posted on 2025-11-05

4518 Bacteria sense virus-induced genome degradation via methylated mononucleotides

Osterman, I.; Hurieve, B.; Moses, S.; Falkovich, A. H.; Itkin, M.; Malitsky, S.; Yirmiya, E.; Sorek, R.

10.1101/2025.11.05.686725 — microbiology — Posted on 2025-11-05

4519 Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of a generalist macro-algivorous fish

Plominsky, A. M.; Allen, E. E.; Sims, N. A.; Minich, J. J.; Podell, S.; Oliver, A.; Henriquez-Castillo, C.; Augyte, S.; Lowell-Hawkins, J.

10.1101/2025.11.04.686673 — microbiology — Posted on 2025-11-05

4520 Genetic incorporation of diverse non-canonical amino acids for histidine substitution

Natter Perdiguero, A.; Fischer, S.; Lischke, A. R.; Manser, B. P.; Deliz Liang, A.

10.1101/2025.11.04.686677 — synthetic biology — Posted on 2025-11-05

4521 Temporal Dynamics of Antigen-Specific T Cell Expansion in Primary SARS-CoV-2 Infection

Pyo, A. G. T.; Chan, A.; Rosenheim, J.; Thakker, C.; Bell, L.; Nageswaran, G.; Byrne, S.; Killingley, B.; Scobie, D.; Kalinova, M.; Boyers, A.; Catchpole, A.; Mann, A.; Lindeboom, R. G. H.; Nikolic, M. Z.; Teichmann, S.; Wagstaffe, H.; Noursadeghi, M.; Chiu, C.; Callan, C.; Mayer, A.; Wingreen, N. S.; Chain, B.

10.1101/2025.11.04.686558 — biophysics — Posted on 2025-11-05

4522 Comprehensive and accelerated mapping of driver mutations through single-nucleotide random mutagenesis of target genes

Yoshida, K.; Solovieva, E.; Miura, N.; Shichino, S.; Hamada, M.; Muratani, M.; Amano, T.; Honda, K.

10.1101/2025.11.05.686667 — bioengineering — Posted on 2025-11-05

4523 The Structural Basis of Pacs1-Wdr37 Complex Assembly and Stability

Xiao, L.; Grzemska, M.; Pi, X.; Chen, L.; Turner, M.; Peddada, N.; Calvache, S.; Jia, J.; Beutler, B.; Wu, H.; Nair-Gill, E.

10.1101/2025.11.05.686565 — biochemistry — Posted on 2025-11-05

4524 Staying in the loop to make ends meet: roles and regulation of GlmR in Bacillus subtilis

Suits, L.; Khan, S.; Bhattacharya, D.; Dimitrova, S.; Eswara, P. J.

10.1101/2025.11.05.686802 — microbiology — Posted on 2025-11-05

4525 Distinct patterns of de novo coding variants contribute to Tourette Syndrome etiology

Zhan, L.; Yu, D.; Ivankovic, F.; Niarchou, M.; Domenech-Salgado, L.; Barr, C. L.; Benarroch, F.; Budman, C. L.; Cath, D. C.; Freimer, N. B.; Garrido, H.; Grados, M. A.; Gross-Tsur, V.; Herrera-Amighetti, L.; King, R. A.; Kurlan, R.; Leckman, J. F.; Lyon, G. J.; McMahon, W. M.; Pauls, D. L.; Pollak, Y.; Robertson, M. M.; Romero, R.; Rouleau, G. A.; Sandor, P.; Singer, H. S.; Giusti-Rodriguez, P.; Davis, L. K.; Mathews, C. A.; Scharf, J. M.; Ophoff, R. A.

10.1101/2025.11.04.686570 — neuroscience — Posted on 2025-11-05

4526 Selective loss of Y chromosomes in lung adenocarcinoma modulates the tumor immune environment through cancer/testis antigens

Fischer, J.; Shutta, K. H.; Chen, C.; Fanfani, V.; Saha, E.; Mandros, P.; Ben Guebila, M.; Xiu, J.; Nieva, J.; Liu, S.; Uprety, D.; Spetzler, D.; Lopes-Ramos, C.; DeMeo, D. L.; Quackenbush, J.

10.1101/2024.09.19.613876 — cancer biology — Posted on 2025-11-05

4527 Cell-line specific role of Cathepsin B in triple-negative breast cancer growth, invasion and response to chemotherapy

Kelley, C.; Guarin, J. R.; Henrich, E.; Fatherree, J. P.; Dunn, C. M.; Yui, A.; Oudin, M. J.

10.1101/2025.11.04.686610 — cancer biology — Posted on 2025-11-05

4528 Human Strategy Adaptation in Reinforcement Learning Resembles Policy Gradient Ascent

Xiong, H.-D.; Ji-An, L.; Wilson, R. C.; Mattar, M. G.

10.1101/2025.07.28.667308 — animal behavior and cognition — Posted on 2025-11-05

4529 Umbilical Cord Blood Cell Transcriptional and Methylation Signatures at Birth Are Associated with BPD Development.

Liu, Q.; Helmin, K. A.; Bailey, J.; Perez-Leonor, X. G.; Phan, D.; Abdala-Valencia, H.; Mithal, L. B.; Singer, B. D.; Robbins, M. E.; Perez, M.

10.1101/2025.11.04.686323 — genomics — Posted on 2025-11-05

4530 RainBar: Optical Barcoding for Pooled Live-Cell Imaging with Single-Cell Resolution

Mosadeghi, R.; Foyt, D.; Sharp, L.; Taylor, C. A.; Tay, N.; Oberlin, S.; Fan, J.; Bourke, S.; Kattah, M. G.; Huang, B. Q.; McManus, M. T.

10.1101/2025.11.04.686676 — genomics — Posted on 2025-11-05

4531 CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis

Samelson, A. J.; Ariqat, N.; McKetney, J.; Rohanitazangi, G.; Parra Bravo, C.; Bose, R.; Travaglini, K. J.; Lam, V. L.; Goodness, D.; Dixon, G.; Marzette, E.; Jin, J.; Tian, R.; Tse, E.; Abskharon, R.; Pan, H.; Carroll, E. C.; Lawrence, R. E.; Gestwicki, J. E.; Rexach, J.; Eisenberg, D.; Kanaan, N. M.; Southworth, D. R.; Gross, J. D.; Gan, L.; Swaney, D. L.; Kampmann, M.

10.1101/2023.06.16.545386 — cell biology — Posted on 2025-11-05

4532 Gram-positive bacterial cell wall components inhibit herpes simplex virus infection.

Adams, A. N.; Griffin, L. E.; Burnie, J.; Powers, J.; Causey, A.; Glick, V. J.; Gavitt, M.; Richmond-Buccola, D.; Kim, C. H.; Ahmad, M.; Jackson, M.; Keiser, G.; Cheng, J. L.; Kumar, A.; Fernando, L. D.; Vlach, J.; Orzalli, M. H.; Corbett-Helaire, K. S.; Decout, A.; Azadi, P.; Gopinath, S.

10.1101/2025.11.02.686169 — microbiology — Posted on 2025-11-05

4533 A Caveat Regarding the Unfolding Argument: Implications of Plasticity for Computational Theories of Consciousness

O'Reilly-Shah, V. N.; Selvitella, A.; Schurger, A.

10.1101/2025.11.04.686457 — neuroscience — Posted on 2025-11-05

4534 Conspecific attraction in songbirds during spring migration

Desrochers, A.; Desbordes, L.

10.1101/2025.10.20.683507 — zoology — Posted on 2025-11-05

4535 Optimized quantitative bacterial two-hybrid (qB2H) for protein-protein interaction assessment

Guyot, A.; Maillard, E.; Ferreira-Pinto, K.; Plancon-Arnould, L.; Nadaradjane, A. A.; Ochsenbein, F.; Guerois, R.; Martin, L.; Ramos, O. H. P.

10.1101/2025.10.29.680610 — synthetic biology — Posted on 2025-11-05

4536 Nuclear auxin signalling induces autophagy for developmental reprogramming

Giannini, C.; Loefke, C.; Brunoud, G.; Bertran Garcia de Ollala, E.; Guan, B.; Riegler, S.; Teplova, A.; Perez Gonzalez, A.; Nava Garcia, M. M.; Benkova, E.; VERNOUX, T.; Dagdas, Y.; Friml, J.

10.1101/2025.11.04.686542 — plant biology — Posted on 2025-11-05

4537 Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance

DenAdel, A.; Hughes, M.; Thoutam, A.; Gupta, A.; Navia, A. W.; Fusi, N.; Raghavan, S.; Winter, P. S.; Amini, A. P.; Crawford, L.

10.1101/2024.12.13.628448 — bioinformatics — Posted on 2025-11-05

4538 Identification of the Regulatory Elements and Protein Substrates of Lysine Acetoacetylation

Fu, Q.; Nguyen, T.; Kumar, B.; Azadi, P.; Zheng, Y. G.

10.1101/2024.10.31.621296 — biochemistry — Posted on 2025-11-05

4539 Preclinical evaluation of antisense oligonucleotide therapy in a mouse model of HNRNPH2-related neurodevelopmental disorder

Korff, A.; Yang, X.; Ozdemir, O.; Samanta, A.; Wang, Y.-D.; Patni, T.; Lavado, A. J.; Kavirayani, A. M.; Ochaba, J.; Powers, B.; Bennett, C. F.; Kim, H. J.; Taylor, J. P.

10.1101/2025.11.04.686541 — animal behavior and cognition — Posted on 2025-11-05

4540 Hybridization Reveals Cell Type-Specific Regulatory Variation Driving Brain Transcriptomic Divergence

Soria, E.; X, M.; Boswell, W.; Carroll, R. A.; Weldon, K. S.; Lai, Z.; Warren, W. C.; Schartl, M.; Lu, Y.

10.1101/2025.11.04.686555 — genetics — Posted on 2025-11-05

4541 Characterization of Phytoplankton-Excreted Metabolites Mediating Carbon Flux through the Surface Ocean

Zhu, Y.; Anderson, H. S.; Salcedo, E.; Miller, S. E.; Longnecker, K.; Soule, M. C. K.; Haley, S. T.; Swarr, G. J.; Braakman, R.; Dyhrman, S. T.; Kujawinski, E. B.

10.1101/2025.11.04.686593 — ecology — Posted on 2025-11-05

4542 Fission yeast cells use distinct cell size control mechanisms for size adaptation to osmotic, oxidative, or low glucose conditions

Cabral, E. J.; Andres, P.; Argandona, G.; Duggan, P.; Kuran, B. M.; Miller, K. E.

10.1101/2025.11.04.686600 — cell biology — Posted on 2025-11-05

4543 Anti-resonance in developmental signaling regulates cell fate decisions

Rosen, S. J.; Witteveen, O.; Baxter, N.; Lach, R. S.; Hopkins, E.; Bauer, M.; Wilson, M. Z.

10.1101/2025.02.04.636331 — cell biology — Posted on 2025-11-05

4544 GNL3 SUMOylation is essential for DNA double-strand break repair by homologous recombination

Yang, Y.; Li, Y.; Dai, R. S.; Chen, C.; Zientek, K.; Reddy, A.; Xia, Z.; Sears, R. C.; Sun, X.-X.; Dai, M.-S.

10.1101/2025.11.04.686352 — cell biology — Posted on 2025-11-05

4545 Development of Loop Mediated Isothermal Amplification for Rapid and Sensitive Detection of Enteroaggregative Escherichia coli (EAEC).

Amare Amdiyee, A.; Sisay Tessema, T.

10.1101/2025.11.04.686462 — molecular biology — Posted on 2025-11-05

4546 Early Pregnancy Marks Significant Shifts in the Oral Microbiome

Finkelstein, S.; Frishman, S.; Turjeman, S.; Shtossel, O.; Tikhonov, E.; Ohayon, M. N.; Pinto, Y.; Popova, P.; Tkachuk, A.; Vasukova, E.; Anopova, A.; Pustozerov, E.; Pervunina, T.; Grineva, E.; Hod, M.; Schwartz, B.; Hadar, E.; Koren, O.; Louzoun, Y.

10.1101/2025.09.29.679276 — microbiology — Posted on 2025-11-05

4547 The 1000+ mouse project: large-scale spatiotemporal parametrization and modeling of preclinical cancer immunotherapies

Kenet, A. L.; Achar, S.; Dwivedi, A.; Buckley, J.; Pouzolles, M.; Qin, H.; Chien, C.; Taylor, N.; Altan-Bonnet, G. Y.

10.1101/2025.03.17.643712 — immunology — Posted on 2025-11-05

4548 Lipid lowering alone fails to limit atherosclerosis progression and neutrophilic inflammation in middle-aged mice

Gannon, O. J.; Rahtes, A.; Bonin, J.; Salfate del Rio, I.; Partridge, J.; Khan, S.; Nobles, A.; Covert, G.; Bahr, A.; Ramos, R. B.; MacNamara, K. C.; Fredman, G.

10.1101/2025.11.04.686598 — immunology — Posted on 2025-11-05

4549 Hemocyte Viability Assay as an Alternative Method for Testing Bacterial Pathogenicity in Bivalves

Samson, J. S.; Rowley, D.; Gomez-Chiarri, M.

10.1101/2025.11.04.686564 — immunology — Posted on 2025-11-05

4550 Inducible Calling Cards: Developing Mouse Reagents for Experimentally Controlled Transposon Insertion in vivo.

Sarafinovska, S.; Venkatesan, A.; Akinwe, T. M.; Chamessian, A.; Chen, X.; Payne, M.; Creed, M. C.; Mitra, R. D.; Dougherty, J. D.

10.1101/2025.11.04.685928 — neuroscience — Posted on 2025-11-05

4551 Harnessing Interpretable Deep Learning to Predict Meropenem Resistance in Klebsiella pneumoniae

Araujo, N. d. M. F.; Santos, M. F.; Pereira, R. F. A.; Brum, R. C.; Pinheiro, F. R.; Silveira, M. C.; Dure, F. M.; Muller, B. d. L. A.; de Souza, A. A. A.; Souza, A. B. S. R.; de Souza, A. F.; Carvalho-Assef, A. P.; Moreira, A. d. S.; de Melo, A. C. M. A.; dos Santos, M. T.; Cortes, A. M. d. A.; Penna, B.; Chagas, T.; Aguiar-Alves, F.; Silva, F. A. B. d.

10.1101/2025.11.04.686393 — systems biology — Posted on 2025-11-05

4552 Brown Adipose Tissue Dysfunction Links Obesogen Exposure to Reduced Energy Expenditure and Transgenerational Obesity

Huang, Y.; Chang, R. C.; Nguyen, K. U.; To, K. T.; Deeprompt, K. G.; Gibbs, M.; Shioda, T.; Blumberg, B.

10.1101/2025.11.04.686561 — pharmacology and toxicology — Posted on 2025-11-05

4553 Differential Wnt/β-Catenin Signaling via TCF7L2/LEF1 Binding Specificity Shapes Cellular and Tumor Phenotypes

Kluiver, T. A.; Nordin, A.; Lu, Y.; Zhang, C.; Schubert, S. A.; Duan, X.; Savur, R.; van den Heuvel, M. C.; de Meijer, V. E.; de Kleine, R. H.; Kraal, K.; de Krijger, R. R.; Zsiros, J.; Cantu, C.; Peng, W. C.

10.1101/2025.11.04.686471 — cancer biology — Posted on 2025-11-05

4554 Longitudinal investigation of prostate tumor spheroid proliferation with dynamic line-field optical coherence tomography

Swanson, S.; Chen, K.; Cheraghi, E.; Osei, E.; Bizheva, K.

10.1101/2025.11.04.686594 — cancer biology — Posted on 2025-11-05

4555 EVOSYNTH: Enabling Multi-Target Drug Discovery through Latent Evolutionary Optimization and Synthesis-Aware Prioritization

Nguyen, V. T. D.; Pham, P.; Hy, T.-S.

10.1101/2025.11.04.686584 — bioinformatics — Posted on 2025-11-05

4556 3D bone printing via primed differentiation of stem cells with ultrasound (3DBonUS)

Marcotulli, M.; Patuto, C.; Scognamiglio, C.; Serpe, F.; Iafrate, L.; Senturk, E.; Keller, S.; De Grandi, D.; Palmisano, B.; Corsi, A.; Riminucci, M.; Ruocco, G.; Carugo, D.; Cidonio, G.

10.1101/2025.11.04.686554 — bioengineering — Posted on 2025-11-05

4557 Elevated Na+/K+ Ratio in Alzheimers Disease: A Potential Biomarker for Braak Stage

Mizuno, Y.; Pan, S.; Zhou, T.; Kehoe, P. G.; Feng Earley, Y.

10.1101/2025.11.04.686539 — biochemistry — Posted on 2025-11-05

4558 The shared genomic history of Middle to Late Holocene Southern Cone populations

Krettek, K.-L.; Postillone, M. B.; Spangenberg, L.; Lopez, J. M.; Migliore, N. R.; Osorio, A. M. C.; Naya, H.; Reiter, E.; Tondini, T.; Bonomo, M.; Bernal, V.; Gonzalez, M. E.; Scheifler, N.; Messineo, P. G.; Flensborg, G.; Dejean, C.; Achilli, A.; Reich, D.; Mazz, J. L.; Perez, S. I.; Politis, G.; Martinez, G.; Posth, C.

10.1101/2025.11.04.686483 — genetics — Posted on 2025-11-05

4559 Modeling the effect of temperature on species coexistence

Saavedra, S.; Yang, Y.; Arroyo, J. I.; Kempes, C. A.

10.1101/2025.11.04.686381 — ecology — Posted on 2025-11-05

4560 Multimerin1, not Galectin-8, Promotes Gastric Chief Cell Differentiation by Tempering WNT Signaling

Lin, X.; Nicolazzi, G. A.; Liu, X.; Nwokolo, C.; Zick, Y.; Saenz, J.; Brown, J. W.

10.1101/2025.11.04.685347 — developmental biology — Posted on 2025-11-05

4561 A role for the Stentor syntaxin protein in post-wound cell survival

Nadkarni, A. V.; Diaz, U.; Zhang, K. F.; Tang, S. K. Y.; Marshall, W. F.

10.1101/2025.11.04.686591 — cell biology — Posted on 2025-11-05

4562 Immunoglobulin sub-class levels define inter-donor plasma variability: a longitudinal dual-lab study

Michalik, S.; Kalaidopoulou Nteak, S.; Drouin, N.; Salazar, M. G.; Hammer, E.; Dhople, V.; Holtfreter, S.; Weiss, S.; van den Toorn, H.; Broker, B.; Domanska, G.; Volker, U.; Heck, A. J. R.

10.1101/2025.11.04.686385 — molecular biology — Posted on 2025-11-05

4563 Unipolar polysaccharide-mediated attachment of the N2O-reducing bacterium Bradyrhizobium ottawaense SG09 to plant roots.

Takeguchi, Y.; Shibuya, R.; Kondo, M.; Betsuyaku, E.; Itakura, M.; Minamisawa, K.; Sugawara, M.; Betsuyaku, S.

10.1101/2025.06.05.658015 — microbiology — Posted on 2025-11-05

4564 Identification of distinct cDC2 subpopulations that direct microbiota-specific T cell differentiation

Carroll, S. L.; Ly, A.; Liu, A. K.; Canesso, M. C. C.; Victora, G. D.; Mucida, D.; Barton, G. M.

10.1101/2025.11.04.686414 — immunology — Posted on 2025-11-05

4565 Cerebral small vessel disease due to Col4a1 mutations include cognitive impairment and white matter defects that can be modulated by targeting protein folding.

Brezzo, G.; Pokhilko, A.; Moss, J.; Koudelka, J.; Jansen, M. A.; Lennen, R.; Thompson, G.; Fialova, N.; Konstantinidou, S. M.; Yau, J.; Boland, E.; Williams, A.; Allan, S. M.; Granata, A.; Sinha, S.; Wang, T.; Markus, H. S.; Fisher, R.; Cader, M. Z.; Van Agtmael, T.; Horsburgh, K.

10.1101/2025.04.04.647207 — neuroscience — Posted on 2025-11-05

4566 Methodological approaches to derive the heartbeat-evoked potential: pastpractices and future recommendations

Virjee, R.-I.; Kandasamy, R.; Garfinkel, S.; Carmichael, D.; Yogarajah, M.

10.1101/2024.07.23.604405 — neuroscience — Posted on 2025-11-05

4567 Limited Effects of Isolated Congenital Anosmia on Cerebral White Matter Morphology

Winter, A. L.; Peter, M.; Thunell, E.; Lundstrom, J. N.; Darki, F.

10.1101/2025.11.04.686499 — neuroscience — Posted on 2025-11-05

4568 Unreal? A Behavioral, Physiological, and Computational Model of the Sense of Reality

Drori, G.; Bar-Tal, P.; Hirsh, O.; Berlinger, A.; Goldberg, N.; Zvilichovsky, Y.; Hertz, U.; Zaidel, A.; Salomon, R.

10.1101/2025.04.07.647542 — neuroscience — Posted on 2025-11-05

4569 Feedforward representation of face information in the fusiform face area revealed by VASO 7T layer fMRI

Koiso, K.; Akamatsu, K.; Huber, R.; Miyawaki, Y.

10.1101/2025.11.04.686314 — neuroscience — Posted on 2025-11-05

4570 Linking Electrophysiological Metrics to Oxidative Metabolism: Implications for EEG-fMRI Association

Zhong, X.; Van Lankveld, H.; Mathew, A.; Chen, J. J.

10.1101/2025.11.04.686568 — neuroscience — Posted on 2025-11-05

4571 Neural Dynamics Underlying Repeated Learning of Visual Image Sequences

Zhao, C.; Kim, A.; Campos, L.; Vogel, E. K.

10.1101/2025.11.04.686589 — neuroscience — Posted on 2025-11-05

4572 Inferring absolute counts from proportions by constraining multivariate normal distributions

Hage, J.; Koestler, D.; Christensen, B.

10.1101/2025.11.04.686543 — systems biology — Posted on 2025-11-05

4573 The Maculalactone Biosynthetic Gene Cluster, a Cryptic Furanolide Pathway Revealed in Nodularia sp. NIES-3585

D'Agostino, P. M.; de Castro, R. R.; Uka, V.; Saurav, K.; Kriukova, Y.; Milzarek, T. M.; Sester, A.; Schneider, M. P.; Gulder, T. A.

10.1101/2025.02.26.640319 — synthetic biology — Posted on 2025-11-05

4574 Identification and validation of liquid biopsy-based methylation biomarkers: a germ cell tumor subtype-specific study

Janssen, F. W.; Gillis, A. J. M.; Kester, L. A.; Takami, H.; Ichimura, K.; Eleveld, T. F.; Looijenga, L. H. J.

10.1101/2025.11.04.686501 — cancer biology — Posted on 2025-11-05

4575 Molecular insights on the mechanism of α1-antitrypsin condensate formation and maturation

Sanchez-Burgos, I.; Tejedor, A. R.; Collepardo-Guevara, R.; de la Serna, J. B.; Espinosa, J. R.

10.1101/2025.03.11.642656 — biophysics — Posted on 2025-11-05

4576 The Tissue Engineering Grail: Seamless Biofabrication of Scaffold-free Hollow Constructs

Shahin-Shamsabadi, A.; Cappuccitti, J.

10.1101/2025.11.04.685834 — bioengineering — Posted on 2025-11-05

4577 The Role of Fetuin-A on the Attachment and Proliferation of Osteoblast-like Cells on Model Gold Surfaces

Merlo, A.; Medin, J.; Scott, S.; Dahlin, A.; Grandfield, K.; Sask, K. N.

10.1101/2025.11.04.686303 — bioengineering — Posted on 2025-11-05

4578 Structure of the human CTF18-RFC clamp loader bound to PCNA

Briola, G.; Tehseen, M.; Al-Amodi, A.; Young, G.; Danazumi, A. U.; Nguyen, P. Q.; Savva, C. G.; Hedglin, M.; Hamdan, S. M.; De Biasio, A.

10.1101/2024.05.08.593111 — biochemistry — Posted on 2025-11-05

4579 Physical-Chemical Approach to Identify Local Structural Determinants of Molecular Mechanisms: Case Study of Antimalarial Drug Pyronaridine and Crystal-Growth Inhibition

Medvedeva, A.; Kolomeisky, K.; Kolomeisky, A. B.

10.1101/2025.11.04.686507 — biochemistry — Posted on 2025-11-05

4580 PanSpace: Fast and Scalable Indexing for Massive Bacterial Databases

Avila Cartes, J. E.; Ciccolella, S.; Denti, L.; Dandinasivara, R.; Della Vedova, G.; Bonizzoni, P.; Schonhuth, A.

10.1101/2025.03.19.644115 — genomics — Posted on 2025-11-05

4581 A Benchmark of Modern Statistical Phasing Methods

Beck, A. T.; Kang, H. M.; Zoellner, S.

10.1101/2025.06.24.660794 — genomics — Posted on 2025-11-05

4582 Variants in Cas9 and nanos regulatory elements modulate activity and reduce resistance allele formation in homing gene drive

Zhou, R.; Du, J.; Faber, N. R.; Champer, J.

10.1101/2025.11.04.686506 — genetics — Posted on 2025-11-05

4583 Daily and Weekly Fluctuations in the Microbiome of the Urinary Tract of Postmenopausal Women with No History of Urinary Tract Infections

Hogins, J.; Mekala, S.; Resendiz, J. A.; Nelapolu, A.; Papp, S.; Zimmern, P. E.; Reitzer, L.

10.1101/2025.11.04.686513 — genetics — Posted on 2025-11-05

4584 DYRK1A ortholog mbk-1 knockout in Caenorhabditis elegans as a tool for genetics research of developmental disorders

Roper, R. J.; Otte, E.; Bratch, E.; Robbins, A.; Goodlett, C. R.

10.1101/2025.11.04.686526 — genetics — Posted on 2025-11-05

4585 Flexibly Modeling Rare Variant Pathogenicity Improves Gene Discovery for Complex Traits

Schwartzentruber, J.; Fiziev, P.; McRae, J.; Ulirsch, J. C.; Farh, K. K.-H.

10.1101/2025.11.04.686320 — genetics — Posted on 2025-11-05

4586 Early-life temperature drives recruitment success in Eurasian perch (Perca fluviatilis) populations

Cavoy, V.; Guillard, J.; Barouillet, C.; Anneville, O.; Sharaf, N.; Gillet, C.; Goulon, C.

10.1101/2025.11.04.686284 — ecology — Posted on 2025-11-05

4587 The effect of repeated periods of drought and aestivation on Allolobophora chlorotica reproductive output

Bray, R. V. A.; Hodson, M. E.; Watt, P. J.

10.1101/2025.11.04.686498 — ecology — Posted on 2025-11-05

4588 BehaveAI: a framework for rapidly detecting and classifying objects and behaviour from motion

Troscianko, J.; OShea-Wheller, T. A.; Galloway, J.; Gaston, K. J.

10.1101/2025.11.04.686536 — ecology — Posted on 2025-11-05

4589 Phylogenetic signal dynamics during niche filling in food webs

Fuster-Calvo, A.; Proulx, M.; Parent, C.; Massol, F.; Besson, M.; Guimaraes, P. R.; Gravel, D.

10.1101/2025.11.04.686537 — ecology — Posted on 2025-11-05

4590 Multimodal profiling reveals a Notch-responsive regenerative subpopulation of cochlear supporting cells

Khalaily, L.; Kasirer, S.; Domb, K.; Zhou, M.; Shao, B.; Taiber, S.; Elkon, R.; Tao, L.; Sprinzak, D.; Avraham, K. B.

10.1101/2025.11.04.686551 — developmental biology — Posted on 2025-11-05

4591 Superoxide dismutase impacts extracellular vesicle biogenesis and uptake

Prova, N. S.; Elsayyid, M.; Tanis, J. E.

10.1101/2025.11.04.686557 — cell biology — Posted on 2025-11-05

4592 Loss of SETDB1-mediated H3K9me3 in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons

Karlsson, O.; Pandiloski, N.; Horvath, V.; Adami, A.; Garza, R.; Johansson, P. A.; Johansson, J. G.; Douse, C. H.; Jakobsson, J.

10.1101/2025.03.28.645885 — molecular biology — Posted on 2025-11-05

4593 Glutamine-Dependent Biosynthetic Pathways Fuel Autoreactive T and B Cells in Foxp3 Deficiency-mediated Disease

Zafar, M. A.; Machado, C. N. H.; Bahera, J.; Zhong, Y.; Li, X.; Joshi, S.; El Fazaa, Y.; Camacho, V.; Georgiev, P.; Kurmi, K.; Haigis, M. C.; Charbonnier, L.-M.

10.1101/2025.11.04.686569 — immunology — Posted on 2025-11-05

4594 A Caveat Regarding the Unfolding Argument: Implications of Plasticity for Computational Theories of Consciousness

O'Reilly-Shah, V. N.; Selvitella, A.; Schurger, A.

10.1101/2025.11.04.686457 — neuroscience — Posted on 2025-11-05

4595 Structural and functional brain asymmetry in relation to heterogeneous causes of situs inversus totalis

Wang, M.-Y.; Ng, N.; Eising, E.; Fisher, S. E.; Vingerhoets, G.; Francks, C.

10.1101/2025.11.04.686509 — neuroscience — Posted on 2025-11-05

4596 Choosing the best or avoiding the worst: complementary and opponent value signals in the human brain

Baratin, C.; Lopez-Persem, A.; Kahane, P.; Minotti, L.; Hammer, J.; Marusic, P.; Nica, A.; Rheims, S.; Maillard, L.; Denuelle, M.; Barbeau, E.; Chanteloup-Foret, B.; Pessiglione, M.; Becq, G.; Bastin, J.

10.1101/2025.11.04.686111 — neuroscience — Posted on 2025-11-05

4597 Fully Automated EEG Source Imaging Using Structured Sparsity for Single and Multiple Synchronous Epileptic Activities

Aud'hui, M.; Kachenoura, A.; Albera, L.; Merlet Paquin, I.; Yochum, M.; Van Bogaert, P.; Kuchenbuch, M.; Benquet, P.

10.1101/2025.11.04.686464 — neuroscience — Posted on 2025-11-05

4598 Human-specific fast synaptic kinetics enable rapid detection of predictive features

Obi-Nagata, K.; Suzuki, N.; Kosugi, K.; Ozawa, K.; Sasaguri, H.; Niimi, K.; Miyamoto, K.; Takao, M.; Toda, M.; Asabuki, T.; Hayashi-Takagi, A.

10.1101/2025.11.03.686448 — neuroscience — Posted on 2025-11-05

4599 The brains lipid landscapes uncovered by mass spectrometry imaging and explainable machine learning

Gildenblat, J.; Stamnaes, J.; Pahnke, J.

10.1101/2025.09.12.675752 — neuroscience — Posted on 2025-11-05

4600 Functionally Relevant and Reliable Brain Stimulation Targets for Enhancement of Novel Word-Learning

Kocatas, H.; Abdelmotaleb, M.; Caisachana Guevara, L. M.; Niemann, F.; Shahbabaie, A.; Malinowski, R.; Riemann, S.; Hayek, D.; Antonenko, D.; Rodriguez-Fornells, A.; Floeel, A.; Meinzer, M.

10.1101/2025.11.04.686295 — neuroscience — Posted on 2025-11-05

4601 HDA19-mediated deacetylation of histone H3.3 lysine 27 and 36 regulates plant sensitivity to salt stress

Kotnik, F.; Ueda, M.; Ito, A.; Ishida, J.; Sakai, K.; Takagi, H.; Seidel, J.; Abe, T.; Eirich, J.; Takahashi, S.; Schwarzer, D.; Seki, M.; Finkemeier, I.

10.1101/2025.11.04.686508 — plant biology — Posted on 2025-11-05

4602 Functional Characterization of Target of Rapamycin (TOR) Signalling in Physcomitrella

Saliba, E.; Hoernstein, S. N. W.; van Gessel, N.; Sentimenti, A.; Hoess, K. M. V.; Parsons, J.; Decker, E. L.; Huesgen, P. F.; Simonsen, H. T.; Reski, R.

10.1101/2025.11.04.686496 — plant biology — Posted on 2025-11-05

4603 Muscle Fiber- and Cell Type-Specificity of Training Adaptation in Male Mice

Dilbaz, S.; Skrinjar, P.; Furrer, R.; Adak, V.; Stein, A.; Steurer, S. A.; Santos, G.; Handschin, C.

10.1101/2025.11.04.686534 — physiology — Posted on 2025-11-05

4604 IgM hyposialylation drives podocyte injury in pediatric and young adult patients with podocytopathies.

Spinelli, S.; Garbarino, A.; Lugani, F.; La Porta, E.; Petretto, A.; Bartolucci, M.; Lavarello, C.; Grinovero, N.; Gaudiano, S.; Musante, I.; Scudieri, P.; trivelli, A.; Piaggio, G.; Magnasco, A.; Degl'Innocenti, M. L.; Granata, S.; Zaza, G.; VERRINA, E. E.; Candiano, G.; Bruschi, M.

10.1101/2025.11.04.686538 — pathology — Posted on 2025-11-05

4605 Immune infiltration is linked to increased transcriptional activity and distinct metabolic profiles in chordomas

van Oost, S.; Ursem, R.; Erdem, Z. B.; Cardoso, S.; Venneker, S.; van der Breggen, R.; Briaire-de Bruijn, I. H.; Kruisselbrink, A. B.; Peul, W. C.; Szuhai, K.; van der Wal, R. J. P.; van Zeijl, R.; Heijs, B.; de Miranda, N. F. C. C.; Bovee, J. V. M. G.

10.1101/2025.11.04.686078 — cancer biology — Posted on 2025-11-05

4606 An agent-based model of Trypanosoma brucei social motility to explore determinants of colony pattern formation

Kuhn, A.; Krüger, T.; Engstler, M.; Fischer, S. C.

10.1101/2025.11.04.686461 — biophysics — Posted on 2025-11-05

4607 Understanding the Mechanisms Behind the Annuloplasty Effect in Tricuspid Valve TEER: A Computational Study

Haese, C. E.; Dubey, V.; Mathur, M.; Kreidel, F.; Fuhg, J. N.; Moussa, I.; Timek, T.; Rausch, M. K.

10.1101/2025.11.04.686540 — bioengineering — Posted on 2025-11-05

4608 Evaluating the impact of two different diets on the protein profile expression of the brain, liver, and intestine of barramundi

Shatouri, M. M.; Pirozzi, I.; Soker, P. D.; Ali, Z.; Amirkhani, A.; Haynes, P. A.

10.1101/2025.11.03.686387 — biochemistry — Posted on 2025-11-05

4609 A multi-tissue atlas of genetic regulatory effects in sheep

Gong, M.; Zhuang, Z.; Sun, X.; Xu, Y.; Zhang, H.; Wang, Y.; Guan, D.; Li, R.; Lu, X.; Bai, Z.; Feng, P.; Song, M.; Tian, M.; Lu, J.; Wang, M.; Lu, X.; Wu, D.; Su, P.; Liu, P.; Zhang, G.; Shi, J.; Shan, M.; Zhang, Y.; Meng, Z.; Li, H.; He, X.; Yang, J.; Song, Y.; Li, X.; Du, X.; Zhang, X.; Yang, H.; Teng, J.; Li, H.; Zhu, X.; Zhang, H.; Lin, Q.; Zhu, D.; Lin, B.; Liu, X.; Liu, J.; Zheng, W.; Gong, W.; An, B.; Zhang, Q.; Sahana, G.; Lund, M. S.; Li, C.; Guo, J.; Wang, X.; Liu, Y.; Zhao, B.; Yao, X.; Zhang, Y.; Wang, F.; Zheng, W.; Huang, J.; Wang, S.; Di, J.; Tulafu, H.; Liu, Z.; Fu, S.; Liu, Y.

10.1101/2025.11.03.686346 — genomics — Posted on 2025-11-05

4610 WITHDRAWN: A New Aneurysm Rupture-Prone Marfan Mouse Model with FBN1Q2467X Nonsense Mutation Reveals Adventitial Inflammation

Wu, S.; Zhao, J.; Ponce, A.; Pham, L.; Xie, D.; Ju, D.; Hernandez, F.; Jones, S.; Li, C.; Chung, C. S.; Komnenov, D.; Rossi, N. F.; Yang, Z.; Yang, M.; Li, H.; Xie, Y.; Chen, K.; Zhang, K.; Li, L.

10.1101/2025.09.23.678101 — genetics — Posted on 2025-11-05

4611 Transmission of an environmental modification in quails across three generations: changes in phenotypic variance components

Rousse, S.; Leroux, S.; Gourichon, D.; Calandreau, L.; David, I.; Rau, A.; lagarrigue, S.; Zerjal, T.; Pitel, F.; Eynard, S. E.

10.1101/2025.07.04.663137 — genetics — Posted on 2025-11-05

4612 Shedding dynamics of the Ross seal (Ommatophoca rossii) whiskers investigated through carbon and nitrogen bulk stable isotope composition

Seon, N.; McIntyre, T.; Connan, M.; Bester, M. N.; Bornemann, H.; Bury, S.; Geldenhuys, M. B.; Lewis, C. B.; Wege, M.

10.1101/2025.11.04.685852 — ecology — Posted on 2025-11-05

4613 R-loops orchestrate the maternal-to-zygotic transition by harnessing RNA polymerase II pause release

Li, Y.; Li, Q.; Wang, X.; Di, C.; Sheng, Y.; Cai, Q.; Huang, S.; Chen, J.; Wu, G.; Gao, S.; Yao, H.

10.1101/2025.11.03.686253 — developmental biology — Posted on 2025-11-05

4614 Environmental sex determination in the cyst nematode Globodera pallida defaults to male development

Schaveling, A. S.; van de Ruitenbeek, S. J. S.; Smant, G.; Sterken, M. G.

10.1101/2025.11.04.686318 — developmental biology — Posted on 2025-11-05

4615 Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib

Podszywalow-Bartnicka, P.; Shine, M.; Lin, J.; Neugebauer, K. M.

10.1101/2025.11.04.686193 — molecular biology — Posted on 2025-11-05

4616 Acute AMPK activation does not adequately stimulate insulin signaling in skeletal muscle models of Myotonic Dystrophy Type 1

Adjei-Afriyie, O.; Spendiff, S.; Carmona-Martinez, R.; Manta, A.; Hentschel, A.; Ho, K.; O'Neil, D.; Dawe, L.; Roos, A.; Ljubicic, V.; MacKenzie, A.; Ravel-Chapuis, A.; Lochmuller, H.

10.1101/2025.11.04.686135 — molecular biology — Posted on 2025-11-05

4617 The evolution lifecycle of ribosome hibernation factors

Chan, L. I.; Omae, K.; Brown, C. R.; Amikura, K. I.; Ekemezie, C. L.; Clark, J.; Nishide, K.; Helena-Bueno, K.; Palmowski, P.; Porter, A.; Suzuki, S.; Melnikov, S. V.

10.1101/2025.11.04.686544 — microbiology — Posted on 2025-11-05

4618 Single Cell Analysis of pBMCs of Psoriasis patients reveals distinct CD4+ T cell phenotypes associated with response to IL-23 blockade.

Marks, K. E.; Sun, A. Y.; Adejoorin, I.; Chada, L. P.; Perillo, A.; Barrett, L.; Garshick, M.; Krueger, J.; Merola, J.; DiCarli, M.; Rao, D. A.; Weber, B. N.

10.1101/2025.11.04.686122 — immunology — Posted on 2025-11-05

4619 Individuality across environmental context in Drosophila melanogaster

Mathejczyk, T.; Knief, C.; Haidar, M. A.; Freitag, F.; McClary, T.; Wernet, M. F.; Linneweber, G. A.

10.1101/2023.11.26.568741 — neuroscience — Posted on 2025-11-05

4620 Functional specialization of mPFC-BLA and mPFC-NAc pathways in affective state representation

Lai, C.-H.; Park, G.; Xu, P.; Sun, X.; Ge, Q.; Jin, Z.; Betts, S.; Liu, X.; Liu, Q.-s.; Simha, R.; Zeng, C.; Lu, H.; Du, J.

10.1101/2024.05.28.596238 — neuroscience — Posted on 2025-11-05

4621 Functional architecture for speed tuning in primary visual cortex of carnivores

Suarez Casanova, V. M.; Lasky-Nielson, N. K.; Ye, L.; Touboul, J. D.; Ribot, J.; Van Hooser, S.

10.1101/2025.11.04.686504 — neuroscience — Posted on 2025-11-05

4622 An induced pluripotent stem cell-based chemical genetic approach for studying spinal muscular atrophy

Giadone, R. M.; Holton, K. M.; Hu, X.; Natoli, T.; Ghosh, S.; Gill, S. P.; Subramanian, A.; Rubin, L. L.

10.1101/2025.11.04.686319 — neuroscience — Posted on 2025-11-05

4623 BudFinder: A Masked Auto-Encoder Vision Transformer Framework for Yeast Budding Detection

Nguyen, P.; Mousavi Karimi, Z.; Layer, A.; Wan, M.; Su, H.; Hasty, J.; Hao, N.

10.1101/2025.11.04.686463 — systems biology — Posted on 2025-11-05

4624 Predicting strain-specific metabolic capabilities in the Genus Pseudomonas using a Flux-to-AI approach unravels hidden cell envelope properties.

Focil, C.; Dalldorf, C.; Martinez, D.; Zepeda, A.; Zuniga, C.

10.1101/2025.11.04.686459 — systems biology — Posted on 2025-11-05

4625 CycleVI: Isolating cell cycle variation with an interpretable deep generative model

Mozdzanowski, P.; Tarbier, M.; S. Jeuken, G.

10.1101/2025.11.04.686009 — systems biology — Posted on 2025-11-05

4626 Temperate grasslands facing heatwaves: species diversity buffers effects on shoot growth but not on leaf parameters

Cera, A.; Brunel-Muguet, S.; Lemauviel-Lavenant, S.

10.1101/2025.11.04.686479 — plant biology — Posted on 2025-11-05

4627 Estrogen-Mediated Suppression of IL-11 as a Hormonal Mechanism Underlying Female Longevity Advantage

Lakshmanane, B.

10.1101/2025.11.03.686437 — physiology — Posted on 2025-11-05

4628 Therapeutic Eradication of Cancer-associated Fibroblasts Inhibits in vivo progression of Pancreatic Cancer

Roos-Mattila, M.; Mustonen, H.; Vaha-Koskela, M.; Boyd, S.; Vainionpaa, S.; Hwang, R. F.; Puolakkainen, P.; Le Joncour, V.; Laakkonen, P.; Seppanen, H.

10.1101/2025.11.04.686484 — cancer biology — Posted on 2025-11-05

4629 Mid-Infrared Photothermal Mesoscopy with Millimeter Field of View and Sub-micron Spatial Resolution

Tang, R.; Yin, J.; Weinberg, B.; Lin, H.; Lu, J.; Gate, D.; Klementieva, O.; Cheng, J.-X.

10.1101/2025.11.03.686410 — bioengineering — Posted on 2025-11-05

4630 Misspecified models create the appearance of adaptive control during value-based choice

Ritz, H.; Frömer, R.; Shenhav, A.

10.1101/2023.01.18.524640 — animal behavior and cognition — Posted on 2025-11-05

4631 A Chromatin-Structure-Guided Framework for Predictive and Interpretable Regulatory Genomics

Ye, B.; Du, L.; Chen, M.; Dai, Y.; Ma, A.; Liang, J.

10.1101/2025.11.03.686435 — genomics — Posted on 2025-11-05

4632 Genetic interaction of Specc1l and Thm1 reveals cytoskeletal - ciliary crosstalk

Hufft-Martinez, B. M.; Thalman, D. N.; Tran, A. J.; Goering, J. P.; Stetsiv, M.; Moedritzer, M.; Wilson, S. C.; Wang, H. H.; Tran, P. V.; Saadi, I.

10.1101/2025.11.03.686369 — cell biology — Posted on 2025-11-05

4633 Cisplatin and Copper Induce Distinct Endocytic Pathways of Copper Transporter-1 and Elicits Unique Response on Copper Homeostasis Proteins

Chakraborty, M.; Pal, A.; Kar, S.; Gupta, A.

10.1101/2025.11.03.686439 — cell biology — Posted on 2025-11-05

4634 In vitro reconstitution defines the mechanistic basis of HSET motor activity regulation by IntraFlagellar Transport proteins

Guesdon, A.; Simon, V.; Siaden Ortega, R.; van Dijk, J.; Marcoux, J.; Delaval, B.; Vitre, B.

10.1101/2025.01.13.632783 — cell biology — Posted on 2025-11-05

4635 A multidisciplinary approach for the study of age-dependent expression patterns in porcine experimental wounds

Baekgaard, C.; Andresen, L.; Hansen, M. H.; Jensen, H. E.; Freude, K.; Barington, K.

10.1101/2025.11.04.686454 — cell biology — Posted on 2025-11-05

4636 Natural variation in the oxytocin receptor gene predicts social observation in female prairie voles

Lee, S. L. T.; Cao, X. M.; Agezo, S.; Boender, A. J.; Bowen, C.; Johnson, Z. V.; Young, L. J.; Berman, G. J.; Liu, R. C.

10.1101/2025.11.03.686389 — neuroscience — Posted on 2025-11-05

4637 Reduced cerebrovascular reactivity is more pronounced in female than male youth with complex congenital heart defects

Gauthier, C.; Potvin-Jutras, Z.; Sanami, S.; Easson, K.; Gilbert, G.; Saint-Martin, C.; Brossard-Racine, M.

10.1101/2025.11.03.686431 — neuroscience — Posted on 2025-11-05

4638 No sex differences in predictive processing

Botia, I.; Brezoczki, B.; Holczer, A.; Nemeth, D.; Vekony, T.

10.1101/2025.11.04.686317 — neuroscience — Posted on 2025-11-05

4639 End-to-end high-throughput single-cell proteomics via SPRINT and dual-spray LC-MS

Liu, Z.; Dong, W.; Gu, L.; Ge, R.; Zeng, X.; Deng, J.; Zhang, H.; Ye, Z.

10.1101/2025.11.03.686420 — systems biology — Posted on 2025-11-05

4640 Integrating image-based phenotyping and GWAS to map tolerance to Spittlebug nymphs in interspecific Urochloa grasses

Espitia-Buitrago, P.; Perea, C.; Mejia-Medina, J. C.; Hernandez, L. M.; Castiblanco, V.; Ryan, C.; De Vega, J. J.; Jauregui, R. N.

10.1101/2025.11.03.686394 — plant biology — Posted on 2025-11-05

4641 Scaling up orphan crop research: A global genetic perspective of cowpea (Vigna unguiculata) diversity from 10,617 accessions

Pearson, S. M.; Hathorn, A.; Sun, S.; Cruickshank, A.; Shatte, T. L.; Munisse, P.; Macharia, M.; Conner, J.; Koltunow, A. M. G.; Vielle-Calzada, J. P.; Ozias-Akins, P.; Ishii, T.; Dell Acqua, M.; Norton, S.; Tao, Y.; Jordan, D.; Mace, E.

10.1101/2025.11.03.686174 — plant biology — Posted on 2025-11-05

4642 The potential to breed for genetic legacy effects in sustainable farming systems

Van Haeften, S.; Brunner, S.; Dinglasan, E.; Fabreag, E.; Eyre, J.; Mens, C.; Hayes, B. J.; Udvardi, M.; Alahmad, S.; Eglinton, M.; McQuinn, R.; Ryan, M.; van der Meer, S.; Smith, M. R.; Hickey, L.

10.1101/2025.11.03.686422 — plant biology — Posted on 2025-11-05

4643 Functional characterisation of bicarbonate transporters from the cyanobacterial SbtA2 family and subsequent expression in tobacco

Rourke, L. M.; Byrt, C. S.; Long, B.; Price, G. D.

10.1101/2025.11.03.686429 — plant biology — Posted on 2025-11-05

4644 High-throughput heterospheroid-based screening identifies drugs that reprogram tumor-associated macrophages

Tsuchiya, H.; Hanaki, T.; Obora, M.; Yoshida, J.; Fujiwara, Y.; Nanba, D.

10.1101/2025.11.04.686451 — pharmacology and toxicology — Posted on 2025-11-05

4645 In vivo effects of Cisplatin and titanium dioxide nanoparticles combined treatment

Costa, C. N.; Ciapina, L. P.; Bahia, A. C.; Neto, V. B. d. S.; da Silva, F. A. B.; Lopes, F. J. P.

10.1101/2025.11.03.685613 — pharmacology and toxicology — Posted on 2025-11-05

4646 TAK1 is a key regulator of oncogenic signaling and differentiation blockade in rhabdomyosarcoma

Vuong, A. T.; Joshi, A. S.; Roy, A.; Mathukumalli, K.; Ho, P. T.; Bhat, R.; Tomaz da Silva, M.; Samanta, T.; Trivedi, M. V.; Guo, B.; Kiapparettu, B. A.; Kumar, A.

10.1101/2025.11.03.686399 — cancer biology — Posted on 2025-11-05

4647 Integrative transcriptomic analysis identifies miR-642a-5p as a regulator of POFUT1 expression in colon cancer

Mazour, O.; Ababou, M.; Badaoui, B.; Germot, A.

10.1101/2025.11.03.686298 — cancer biology — Posted on 2025-11-05

4648 Exploring the Conformational Landscape of Adenylate Kinase and Beyond: A Benchmark of Protein Folding Models

Bhasin, A.; Delaunay, A. P.; Saccon, F.; Fu, Y.

10.1101/2025.11.04.686486 — bioinformatics — Posted on 2025-11-05

4649 GNAT: An Interactive Web Tool for Gene Neighbourhood Analysis

Timmerman, N. J.; Thakurdeen, M.; Wilson, R. E. J.; Fung, B.; Trost, B.; Davidson, A. R.; Trost, C. N.; Jin, L.

10.1101/2025.11.03.686425 — bioinformatics — Posted on 2025-11-05

4650 Phylogeny-Informed Random Forests for Human Microbiome Studies

Koh, H.

10.1101/2025.11.04.686494 — bioinformatics — Posted on 2025-11-05

4651 Quantifying predictability of gene expression from histology image

Xia, C.-R.; Yao, J.-W.; Gao, G.

10.1101/2025.11.04.686651 — bioinformatics — Posted on 2025-11-05

4652 On the Thermodynamic Consequences of Oscillatory Dynamics in Image Processing: Application of Gas Molecule Models and Hierarchical Meta-Information Data Structures in Life Sciences Image Analysis

Sachikonye, K.

10.1101/2025.11.03.686363 — bioinformatics — Posted on 2025-11-05

4653 Metabolically driven differentiation of human pluripotent stem cells to generate robust and functional lymphatic endothelial cells

Jeong, D. P.; Saha, S.; Montes-Pinzon, D.; Taglione, A.; Lightsey, N. K.; Gamage, R. S.; Stein, B.; Dixon, J. B.; Hanjaya-Putra, D.

10.1101/2025.11.03.686405 — bioengineering — Posted on 2025-11-05

4654 End-to-end genomic prediction: direct prediction of images and text from genome-wide molecular markers

Watson, M. T.; Feldmann, M.; Yu, H.; Cheng, H.

10.1101/2025.11.03.686395 — genomics — Posted on 2025-11-05

4655 Using insects for sustainable waste management of superabundant animals.

Lopez-Manzano, C.; Mahdjoub, H.; Arce-Valdes, L. R.; Khelifa, R.

10.1101/2025.11.03.686388 — ecology — Posted on 2025-11-05

4656 Sequestration of clock proteins into repressive nuclear condensates orchestrates circadian gene repression

Chen, Q.; Yuan, Y.; Clark, D.; Yadlapalli, S.

10.1101/2025.11.03.686412 — cell biology — Posted on 2025-11-05

4657 Rapamycin can revert CCM phenotype in brain endothelial cells and ameliorates chronic cavernoma development in combination with lapatinib

10.1101/2025.11.03.686432 — cell biology — Posted on 2025-11-05

4658 VISTA-FISH: Video Imaging with Spatial-Temporal Analysis by Fluorescent In Situ Hybridization

Lee, K. H.; Yao, M.; Ghaemmanghami, J.; DeLong, C.; Zhao, N.; Moline, J.; Sexton, J. Z.; Barmada, S. J.; Welch, J. D.

10.1101/2025.11.03.686351 — molecular biology — Posted on 2025-11-05

4659 Spatial transcriptomic profiling identifies lacrimal gland epithelial cell-driven mechanisms underlying autoimmunity in Sjogrens disease.

Gupta, S.; Ploumakis, A.; Kalavros, N.; Masli, S.

10.1101/2025.11.03.686353 — immunology — Posted on 2025-11-05

4660 Lymphatic constraint of germinal centers optimizes protective antibody responses

Mudianto, T.; Berman, G. R.; Zaldana, K.; Firmino-Cruz, L.; Schips, M.; Schwan, N.; Ibrahim, O.; Cristaldi, V.; Foster, W. S.; Fikri, L.; Solis, S.; Chen, H.; Cammer, M.; Herati, R. S.; Koralov, S. B.; Miller, A. D.; Meyer-Hermann, M.; Nowosad, C. R.; Lund, A. W.

10.1101/2025.11.03.686378 — immunology — Posted on 2025-11-05

4661 Ephaptic-Axonal Interactions Shape Radial Biases DuringNeural Self-Organization

Rebbin, D.; Hesp, C.; Pinotsis, D.; Levin, M.; Clawson, W.

10.1101/2025.11.03.686361 — neuroscience — Posted on 2025-11-05

4662 Similar processing of novelty in rat dorsal and intermediate CA1 despite differences in spatial tuning

Lee, S. L. T.; Troha, R.; Yoon, J.; Anam, A.; Citrin, K.-A.; Hu, Q.; Katz, M.; Kuperstein, M.; Subramanian, D.; Katz, D.; Katugam, K.; Pattoli, M.; Vu, S.; Stevenson, I. H.; Markus, E. J.

10.1101/2025.11.03.686060 — neuroscience — Posted on 2025-11-05

4663 Transcriptional Profiling of D1-MSNs Reveals SIRT1-Dependent and -Independent Responses to Chronic Social Defeat Stress

Kim, H.-D.; Cho, H. J.; Nguyen, A.; Barney, A.; Qiu, S.; Ferguson, D.

10.1101/2025.11.03.686384 — neuroscience — Posted on 2025-11-05

4664 A chemogenetic ligand-receptor pair for voltage-gated sodium channel subtype-selective inhibition

Park, E. R.; Denomme, N.; Hajare, H. S.; Du Bois, J.

10.1101/2025.11.03.686046 — neuroscience — Posted on 2025-11-05

4665 Assessing molecular, cellular and transcriptomic bases of laminar perfusion and cytoarchitecture coupling in the human cortex

Guo, F.; Zhao, C.; Bhatt, R. R.; Liu, Z.; Kim, A. J.; Yang, Z.; Xu, S.; Jann, K.; Mather, M.; Jahanshad, N.; Wang, D. J.

10.1101/2025.11.03.686411 — neuroscience — Posted on 2025-11-05

4666 Sickness engrams modulate anticipatory immune responses

Douglas, A.; Munoz Zamora, A.; Conway, P.; Urrieta, E.; Lynch, L.; Ryan, T.

10.1101/2025.11.03.686140 — neuroscience — Posted on 2025-11-05

4667 The emerging contaminant Cl-PFESA/F-53B is toxic to meiotic cell division and reproduction in Arabidopsis thaliana

Chen, Y.; Cui, X.; Ren, Z.; Fu, H.; Luo, Y.; Xu, L.; Song, Z.; Qin, Y.; Yu, G.; Lei, X.; Liu, B.

10.1101/2025.11.03.686200 — plant biology — Posted on 2025-11-05

4668 Xanthomonas type III effector XopN targets scaffold protein OsRACK1B to suppress rice immunity

Wang, J.; Ni, Z.; Chen, X.; Zhang, Y.; Qin, H.; Wang, H.; He, Y.; Tang, J.; Huang, S.

10.1101/2025.11.03.686189 — plant biology — Posted on 2025-11-05

4669 Lrrc55 modulates beta-cell resilience and calcium transporter expression under metabolic and physiologic stress

Pretorius, M.; Kahlon, R.; Xie, Q.; Huang, C.

10.1101/2025.11.03.686179 — physiology — Posted on 2025-11-05

4670 Molecular and Functional Analysis of Calcium Binding by a Cancer-linked Calreticulin Mutant

Tagoe, I. N. A.; Kaur, A.; Quaye, O.; Tagoe, E. A.; Koropatkin, N. M.; Satin, L. S.; Raghavan, M.

10.1101/2025.06.25.661618 — cancer biology — Posted on 2025-11-05

4671 Viral transport in evaporating sessile model respiratory droplets

Martinez-Puig, J.; de la Torre Luque, C.; Arbesu Nieto, C.; Hoekstra, P. I.; Usera, F.; Martin Jouve, B.; de la Encina, A.; Bartolome, T.; Sanz, M.; Almazan, F.; Ona, A.; Marin, A.; Rodriguez Rodriguez, J.

10.1101/2025.09.30.679206 — biophysics — Posted on 2025-11-05

4672 Direction-Driven Feature Engineering for Low-Data BiologicalClassification

Qurashi, S. U.

10.1101/2025.11.05.686264 — bioinformatics — Posted on 2025-11-05

4673 MotifAE Reveals Functional Motifs from Protein Language Model: Unsupervised Discovery and Interpretability Analysis

Hou, C.; Liu, D.; Shen, Y.

10.1101/2025.11.04.686576 — bioinformatics — Posted on 2025-11-05

4674 ConsensusMetaDA: an R Package for consensus-based differential abundance analysis of metagenomic data.

KUMAR, M.; Field, M. A.

10.1101/2025.11.03.686403 — bioinformatics — Posted on 2025-11-05

4675 Curating 16S rRNA databases enhances taxonomic accuracy and computational efficiency in microbial profiling

Baghbanzadeh, M.; Mahangade, V.; Crandall, K. A.; Rahnavard, A.

10.1101/2025.11.04.686545 — bioinformatics — Posted on 2025-11-05

4676 AutoLead: An LLM-Guided Bayesian Optimization Framework for Multi-Objective Lead Optimization

Zhang, Y.; Choong, J. j.; Madhawa, K.; Ozawa, K.

10.1101/2025.08.19.671029 — bioinformatics — Posted on 2025-11-05

4677 Integrative genomic insights into parallel local adaptation to Danxia and Karst edaphic islands in the endangered tree Firmiana danxiaensis

Li, Y.; Luo, J.; Duan, L.; Zhou, R.; Wen, J.; Chen, H.

10.1101/2025.11.05.686652 — evolutionary biology — Posted on 2025-11-05

4678 Sexually antagonistic co-evolution at the molecular level predicts phenotypic outcomes of mating interactions.

Thorson, A.; Snook, R.; Wiberg, R. A. W.

10.1101/2025.11.04.686516 — evolutionary biology — Posted on 2025-11-05

4679 Migration load, competition, and metabolic trade-offs shape spatial divergence through eco-evolutionary dynamics

Ekkers, D. M.; Tusso, S.; Rillo, M. C.; Kuipers, O.; van Doorn, G. S.

10.1101/2025.11.04.686607 — ecology — Posted on 2025-11-05

4680 Differential Control of HIV-1 Replication by IFN-α14 Compared to IFN-α2 Relates to Differences in the Modulation of Host Antiretroviral Restriction Factors

Rout, S. S.; Stewart, M. T. H.; Seidel, N. B.; Dittmer, U.; Sutter, K.; Lavender, K. J.

10.1101/2025.11.01.685890 — immunology — Posted on 2025-11-05

4681 Introducing PIGMO, a novel PIGmented MOuse model of Parkinson's disease

Chocarro, J.; Marana, S.; Espelosin, M.; Rico, A. J.; Ariznabarreta, G.; Lorenzo-Ramos, E.; Ilarduya, M. M.; Hernandez-Alcoceba, R.; Chillon, M.; Vila, M.; Kordower, J.; Schapira, A. H. V.; Garcia-Osta, A.; Cuadrado-Tejedor, M.; Lanciego, J. L.

10.1101/2025.05.09.653000 — neuroscience — Posted on 2025-11-05

4682 Arm dominance emerges through asymmetric practice of complex trajectory shapes inherent to tool use

Arac, A.; Jeong Lee, N. Y.; Krakauer, J. W.

10.1101/2025.10.08.680998 — neuroscience — Posted on 2025-11-05

4683 Advancing Protein Ensemble Predictions Across the Order-Disorder Continuum

Invernizzi, M.; Bottaro, S.; Streit, J. O.; Trentini, B.; Venanzi, N. A.; Reidenbach, D.; Lee, Y.; Dallago, C.; Sirelkhatim, H.; Jing, B.; Airoldi, F.; Lindorff-Larsen, K.; Fisicaro, C.; Tamiola, K.

10.1101/2025.10.18.680935 — biophysics — Posted on 2025-11-05

4684 The Open Constellation of Nutritional Values: Mapping the Health Star Rating System

Lafargue, V.; Suguem, F. N.

10.1101/2025.11.05.686692 — bioinformatics — Posted on 2025-11-05

4685 BASSL-MI: Batch-Agnostic Self-Supervised Learning Uncovers Clinically Relevant Tumor Niches in Multiplexed Imaging

Lin, A. L.; Bao, S.; Lau, K.; Vandekar, S.; Moyer, D.; Liu, Q.; Ma, S.

10.1101/2025.11.04.686632 — bioinformatics — Posted on 2025-11-05

4686 Adaptive resampling for improved machine learning in imbalanced single-cell datasets

Navidi, Z.; Thoutam, A.; Hughes, M.; Raghavan, S.; Winter, P. S.; Crawford, L.; Amini, A. P.

10.1101/2025.11.04.686583 — bioinformatics — Posted on 2025-11-05

4687 Uncovering biological patterns across studies through automated large-scale reanalyses of public transcriptomic data

Chen, K. G.; Lassmann, T.

10.1101/2025.11.04.686647 — bioinformatics — Posted on 2025-11-05

4688 Assessing Scale and Predictive Diversity in Models for Single-Cell Transcriptomics based on Geneformer

Chen, J.; Schmidt, F.; Henao, R.

10.1101/2025.11.04.686458 — bioinformatics — Posted on 2025-11-05

4689 Structural Basis of Glycoform Selectivity in Prion Strains

Peccati, F.

10.1101/2025.11.04.686259 — bioinformatics — Posted on 2025-11-05

4690 OligoN-design: A simple and versatile tool to design specific probes and primers from large heterogeneous datasets

Mendez Sandin, M.; Walde, M.; Henry, N.; Forn, I.; Simon, N.; Berney, C.; Massana, R.; Richter, D. J.

10.1101/2025.11.04.685038 — bioinformatics — Posted on 2025-11-05

4691 Using artificial intelligence to optimize ecological restoration for climate and biodiversity

Silvestro, D.; Goria, S.; Rau, E.-P.; Ferreira de Lima, R. A.; Groom, B.; Jacobsson, P.; Sterner, T.; Antonelli, A.

10.1101/2025.01.31.635975 — bioinformatics — Posted on 2025-11-05

4692 Functional Lipid Analysis via Index-Based Lipidomics Profile: A New Computational Module in LipidOne

Alabed, H. B. R.; Frongia Mancini, D.; Pergola, M.; Romani, L.; Martino, S.; Koulman, A.; Pellegrino, R.

10.1101/2025.11.04.686489 — bioinformatics — Posted on 2025-11-05

4693 scFPC-DE: Robust Differential Expression Analysis Along Single Cell Trajectories via Functional Principal Component Analysis

Lopez Candelaria, R. J.; Qian, Y. J.; Law, M.; Chen, F.; Zhang, Y.; Qiu, X.

10.1101/2025.11.03.686374 — bioinformatics — Posted on 2025-11-05

4694 Synthetic Biology Driven Melanin Deposition for Wood Coating

Das, A.; Tiwari, T.; Pushpavanam, K. S.

10.1101/2025.11.02.684288 — bioengineering — Posted on 2025-11-05

4695 A Comprehensive Catalog of Telomere Content Variation Across Human Populations

Shah, P.; Sethuraman, A.

10.1101/2025.11.03.686324 — genomics — Posted on 2025-11-05

4696 Large-scale discovery of neural enhancers for cis-regulation therapies

McDiarmid, T. A.; Page, N. F.; Chardon, F. M.; Daza, R. M.; Chen, G. T.; Kosicki, M.; James, L. M.; Nourie, H. C.; Laboy-Cintron, D.; Lee, A. S.; Vij, P.; Calderon, D.; Lalanne, J.-B.; Martin, B. K.; Fink, K.; Talkowski, M. E.; Muotri, A. R.; Philpot, B. D.; Pennacchio, L. A.; Geschwind, D. H.; Sanders, S. J.; Ahituv, N.; Shendure, J.

10.1101/2025.11.04.686611 — genomics — Posted on 2025-11-05

4697 Simulated sample splitting approach to address biases due to instrument selection and participant overlap in two-sample Mendelian Randomization studies

Forde, A.; Hemani, G.; Ferguson, J.

10.1101/2025.11.04.686460 — genetics — Posted on 2025-11-05

4698 Mammalian longevity is associated with restricted epithelial plasticity

Zheng, Z. N.

10.1101/2025.10.22.683248 — evolutionary biology — Posted on 2025-11-05

4699 Temperature effects on reproductive and life-history traits in Drosophila (Diptera: Drosophilidae): a systematic map

Stazione, L.

10.1101/2025.11.03.686415 — evolutionary biology — Posted on 2025-11-05

4700 Emergent metabolic parasitism driven by organelle sequestration

Lasek-Nesselquist, E.; Moeller, H. V.; Paight, C.; Seah, B. K. B.; Shaikhutdinov, N.; Swart, E.; Johnson, M. D.

10.1101/2025.11.03.686365 — evolutionary biology — Posted on 2025-11-05

4701 Hypoxia adaptation shapes genomic architecture and vertical niche transitions in copepods

Sugier, K.; Laso-Jadart, R.; Dorval, L.; Meng, A.; Kiko, R.; Blanco-Bercial, L.; Maas, A. E.; Cornils, A.; Maps, F.; Ayata, S.-D.; Madoui, M.-A.

10.1101/2025.11.05.686523 — evolutionary biology — Posted on 2025-11-05

4702 Does wearable neurofeedback training improve memory aptitudes in healthy adults?--A systematic review and meta-analysis

HAGIHARA, M.; Ohkuma, R.; Fujimaki, T.; Tamaki, M.; Takemi, M.; Machizawa, M. G.

10.1101/2025.11.03.685283 — neuroscience — Posted on 2025-11-05

4703 Reports of Lipoptena fortisetosa on dogs and in the environment, and evidence of its widespread establishment in Hungary

Toth, A. G.; Bende, A.; Hornok, S.; Wagenhoffer, Z.; Szulyovszky, B.; Galla, V.; Voroskoi, P.; Keve, G.

10.1101/2025.11.03.686229 — zoology — Posted on 2025-11-05

4704 MDMR: Balancing Diversity and Redundancy for Annotation-Efficient Fine-Tuning of Pretrained Cell Segmentation Models

Sheikh, E. M.; Tharwat, A.; Schwan, C.; Schenck, W.

10.1101/2025.11.04.686267 — bioengineering — Posted on 2025-11-05

4705 Coupling of habitat-preference barriers leads to reproductive isolation in sympatric speciation

Sultana, Z.; Heyda, C.; How, K.; Lin, J.

10.1101/2025.07.03.662681 — evolutionary biology — Posted on 2025-11-05

4706 Phylodynamics of Somatic Evolution: A Likelihood-Based Approach for Cellular Reproduction

Dieselhorst, T.; Berg, J.

10.1101/2024.12.05.627005 — evolutionary biology — Posted on 2025-11-05

4707 CRITICAL ROLE OF ADULT-BORN DENTATE GRANULE NEURONS IN PATTERN COMPLETION

Roullet, P.; Koehl, M.; Delage, P.; Guillemot, F.; Abrous, N.

10.1101/2025.05.15.654267 — neuroscience — Posted on 2025-11-05

4708 The Drosophila EGF domain protein Uninflatable sets the switch between wrapping glia growth and axon wrapping instructed by Notch

Baldenius, M.; Kautzmann, S.; Kottmeier, R.; Zipfel, J.; Klämbt, C.

10.1101/2025.01.02.631076 — neuroscience — Posted on 2025-11-05

4709 Maternal antibody-mediated elimination of a Puumala hantavirus outbreak in a bank vole colony

Drewes, S.; Wyszkowska, J.; Jaromin, E.; Hajduk, J.; Onik, I.; Konczal, M.; Lach, K.; Bober-Sowa, B.; Baliga-Klimczyk, K.; Sadowska, E. T.; Ulrich, R. G.; Koteja, P.

10.1101/2025.11.04.686465 — zoology — Posted on 2025-11-05

4710 De novo design of light-regulated dynamic proteins using deep learning

Scutteri, L.; Abriata, L.; Zhang, S.; Hacisuleyman, A.; Lau, K.; Pojer, F.; Rahi, S. J.; Barth, P.

10.1101/2025.08.12.669910 — biophysics — Posted on 2025-11-05

4711 Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae

Moore-Pollard, E. R.; Ellestad, P. A.; Cliver, B. R.; Baczynski, J.; Pollard, M. D.; Meharg, Z.; Willoughby, A. C.; Drewry, S.; Harkess, A.; Bonifacino, J. M.; Nimchuk, Z. L.; Burke, J. M.; Jones, D. S.; Mandel, J. R.

10.1101/2025.10.29.685401 — genomics — Posted on 2025-11-05

4712 Multi-ancestry Transcriptome-Wide Association Study Reveals Shared and Population-Specific Genetic Effects in Alzheimer's Disease

Sun, X.; Mews, M.; Wheeler, N. R.; Benchek, P.; Gu, T.; Gomez, L.; Ray, N.; Reitz, C.; Naj, A. C.; Below, J. E.; Tosto, G.; Cornejo-Olivas, M.; Byrd, G. S.; Feliciano-Astacio, B. E.; Celis, K.; Rajabli, F.; Kunkle, B. W.; Pericak-Vance, M. A.; Haines, J. L.; Griswold, A. J.; Bush, W. S.

10.1101/2025.11.03.686160 — genomics — Posted on 2025-11-05

4713 The dominance of gene expression controlled by trans-eQTL hotspots contributes to phenotypic heterosis in maize

Xu, G.; Yang, X.; Zhang, M.; Kang, C.; Tian, Z.; Qi, Y.; Luo, M.; Liu, P.; Ross-Ibarra, J.; Yang, J.; Liu, H.

10.1101/2025.11.03.686376 — genetics — Posted on 2025-11-05

4714 Neutrophil Transcriptomics in SLE: Exploring Intrinsic, Ex Vivo Adaptation, and CAR T-Cell Therapy-Induced Changes

Dehdashtian, E.; Hu, G.; Whiteman, L.; Islam, M. T.; Gallucci, S.; Garber, M.; Borie, D.; Schett, G.; Caricchio, R.

10.1101/2025.11.03.686294 — immunology — Posted on 2025-11-05

4715 Phospotyrosine proteomics reveals novel Zap70 and Itk pathway targets downstream of TCR and CAR in Jurkat T cells

Callahan, A.; Trychanh, S. S.; Ro, T.; Mojumdar, A.; Salomon, A.

10.1101/2025.11.03.686362 — immunology — Posted on 2025-11-05

4716 Influence of exoskeleton stiffness on primary afferent feedback during stretch perturbations of isolated muscle-tendon unit

Alshareef, A. A.; Nardelli, P. J.; Simha, S. N.; Cope, T. C.; Ting, L. H.; Sawicki, G. S.

10.1101/2025.11.03.686366 — neuroscience — Posted on 2025-11-05

4717 Efficient mixed representation of active and passive motion in the mouse visual thalamus during natural behaviour

Ebrahimi, A. S.; Hogan, M. P.; Jin, F.; Martial, F. P.; Huang, Q.; Joshi, R.; Shirvanian, K.; Burgess, M.; Montazeri, Z.; Petersen, R. S.; Storchi, R.

10.1101/2025.11.03.686375 — neuroscience — Posted on 2025-11-05

4718 Structured and Target-Specific Development of Cortico-Cortical Connectivity in the Mouse Visual Cortex

Jacobs, M. W.; Ratliff, J. M.; Soronow, A. L. R.; Nichols, J. A.; James, H. T.; Eddy, J. A. G.; Murray, A. M.; Kim, E. J.

10.1101/2025.11.03.686379 — neuroscience — Posted on 2025-11-05

4719 M4 drug discovery: human drug predictions from integrated pre-clinical insights exemplified with a GLP1-R agonist

Silfvergren, O.; Rigal, S.; Schimek, K.; Simonsson, C.; Kanebratt, K. P.; Forschler, F.; Yesildag, B.; Marx, U.; Vilen, L.; Gennemark, P.; Cedersund, G.

10.1101/2025.11.03.686224 — systems biology — Posted on 2025-11-05

4720 The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs

Park, J.; De Gregorio, R.; Hissong, E.; Ozcelik, E.; Bartelo, N.; Dezem, F. S.; Zhang, L.; Marcao, M.; DuBose, H.; Zheng, Y.; Abila, E.; Kim, J.; Proszynski, J.; Agyemang, A. A.; Arikatla, M. R.; Wani, A.; Liu, Y.; Metzger, E.; Rogers, S.; Divakar, P.; Dulai, P. S.; Reeves, J. W.; Liang, Y.; Pan, L.; Bhattacharjee, S.; Patrick, M.; Young, K.; Heck, A.; Korukonda, M.; McGuire, D.; Wu, L.; Wardhani, A.; Beechem, J.; Church, G.; Lipkin, S. M.; Patel, S.; Socciarelli, F.; Chandwani, R.; Monette, S.; Robinson, B.; Loda, M.; Elemento, O.; Martelotto, L.; Plummer, J. T.; Rendeiro, A. F.; Alonso, A.;

10.1101/2025.06.16.658716 — systems biology — Posted on 2025-11-05

4721 The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution

Berg, L. S.; Duarte, P. R.; Prados, I. H.; Lacombe, N. T.; Tandon, R.; Vardanega, I.; Maika, J. E.; Spiegelhalder, R. P.; Gore, A.; Lindner, H.; Simon, R.; Raissig, M. T.

10.1101/2025.11.03.686118 — plant biology — Posted on 2025-11-05

4722 Mineralocorticoid and glucocorticoid receptor interaction drives TGFB1-induced triple-negative breast cancer progression to metastasis

Posani, S. H.; Diep, C. H.; Krutilina, R. I.; Smith, H.; Seagroves, T. N.; Blenis, J.; Lange, C. A.

10.1101/2025.11.03.686330 — cancer biology — Posted on 2025-11-05

4723 DORSSAA: Drug-target interactOmics Resource based on Stability/Solubility Alteration Assay

Zangene, E.; Gholizadeh, E.; Schwammle, v.; Saei, A. A.; Wilhelm, M.; Kall, L.; Jafari, M.

10.1101/2023.12.29.573639 — bioinformatics — Posted on 2025-11-05

4724 mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing

Suzuki, H.; Sugawa, M.; Sakamoto, Y.; Shiraishi, Y.

10.1101/2025.07.11.664273 — bioinformatics — Posted on 2025-11-05

4725 MARTS-DB: A Database of Mechanisms And Reactions of Terpene Synthases

Engst, M.; Brokes, M.; Calounova, T.; Samusevich, R.; Bushuiev, R.; Bushuiev, A.; Chatpatanasiri, R.; Akmese, S. M.; Tajovska, A.; Perkovic, M.; Soldat, M.; Sivic, J.; Pluskal, T.

10.1101/2025.05.11.653183 — bioinformatics — Posted on 2025-11-05

4726 SOORENA: Self-lOOp containing or autoREgulatory Nodes in biological network Analysis

Arar, H.; Aldahdooh, J.; Nickchi, P.; JAFARI, M.

10.1101/2025.11.03.685842 — bioinformatics — Posted on 2025-11-05

4727 SKiM-GPT: Combining Biomedical Literature-Based Discovery with Large Language Model Hypothesis Evaluation

Freeman, J.; Millikin, R. J.; Xu, L.; Sharma, I.; Moore, B. M.; Lock, C.; George, K. S.; Bal, A.; Mohanty, C.; Stewart, R.

10.1101/2025.07.28.664797 — bioinformatics — Posted on 2025-11-05

4728 Conformational Dynamics and Catalytic Backups in a Hyper-Thermostable Engineered Archaeal Protein Tyrosine Phosphatase

Yehorova, D.; Alansson, N.; Shen, R.; Denson, J. M.; Robinson, M.; Risso, V. A.; Molina, N. R.; Loria, J. P.; Gaucher, E.; Sanchez-Ruiz, J. M.; Hengge, A. C.; Johnson, S.; Kamerlin, S. C. L.

10.1101/2025.03.26.645524 — biochemistry — Posted on 2025-11-05

4729 Spatially heterogeneous gene flow may hinder linking phylogeographic data to macroevolutionary patterns

Gyllenhaal, E. F.; Musher, L. J.

10.1101/2025.11.04.686599 — evolutionary biology — Posted on 2025-11-05

4730 Additivity of the genetic load is a product of both synergistic and antagonistic epistasis in Drosophila

Sayyed, I.; McNamara, H.; Day, T.; Chippindale, A. K.

10.1101/2025.11.04.686015 — evolutionary biology — Posted on 2025-11-05

4731 Hidden hematological, biochemical and immune costs of asymptomatic malaria infections in semi-wild chimpanzees

Nowakowski, A.; Elguero, E.; Patterson, K.; Boissiere, A.; Degrugillier, F.; Sidobre, C.; Arnathau, C.; Grentzinger, P.; Willaume, E.; Talman, A. M.; Malleret, B.; Boundenga, L.; Ngoubangoye, B.; Prugnolle, F.; Wassmer, S. C.; Rougeron, V.

10.1101/2025.11.04.686503 — evolutionary biology — Posted on 2025-11-05

4732 Timing the initiation of sex: Delay mechanisms alter fitness outcomes in a rotifer population model

Stevens, B. L. F.; van Daalen, S. F.; Blomquist, T. J.; Gribble, K. E.; Neubert, M. G.

10.1101/2025.04.25.650506 — evolutionary biology — Posted on 2025-11-05

4733 Shell-bound archives: uncovering nematode encapsulations in the Galapagos' largest radiation

Fuster-Calvo, A.; Oiler, I. M.; MacDonald, A.; Parent, C.; Massol, F.; Burin, G.; Phillips, J. G.; Rae, R.; Gravel, D.

10.1101/2025.11.03.686299 — ecology — Posted on 2025-11-05

4734 Junctional Heterogeneity Shapes Epithelial Morphospace

Prakash, A.; Kaushik, R.; Singh, N.; Walvekar, A.; Saji, S.; Ladher, R. K.

10.1101/2025.11.03.686357 — developmental biology — Posted on 2025-11-05

4735 Bruce suppresses autophagy-regulated caspase activity and wing tissue growth in Drosophila

Shinoda, N.; Hama, Y.; Hanawa, N.; Miura, M.

10.1101/2025.08.24.672027 — developmental biology — Posted on 2025-11-05

4736 Extracellular vesicle-mediated release of bis(monoacylglycerol)phosphate is regulated by LRRK2 and Glucocerebrosidase activity

Meneses-Salas, E.; Castella, M.; Arnold, M.; Hsieh, F.; Fernandez-Santiago, R.; Ezquerra, M.; Garrido, A.; Marti, M. J.; Enrich, C.; Pfeffer, S. R.; Merchant, K. M.; Lu, A.

10.1101/2023.07.12.548710 — cell biology — Posted on 2025-11-05

4737 Derivation of functional early gestation decidual natural killer cell subtypes from induced pluripotent stem cells

Cheung, V. C.; DaCosta, C.; Jaimez, J.; Arora, H.; Caron, C.; Slamecka, J.; Fierro, M.; Meads, M.; Fisch, K.; Morey, R. E.; Pant, D.; Kaufman, D. S.; Horii, M.; Bui, J. D.; Parast, M. M.

10.1101/2025.11.03.685424 — cell biology — Posted on 2025-11-05

4738 The Function of Efhd1+ Telocytes in the Synovial Lymphatic System and Inflammatory-Erosive Arthritis

Peng, Y.; Kenney, H. M.; Lydon, S.; de Mesy Bentley, K. L.; Xing, L.; Korman, B.; Ritchlin, C.; Schwarz, E.

10.1101/2025.11.03.685859 — cell biology — Posted on 2025-11-05

4739 Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography

10.1101/2025.11.03.686153 — cell biology — Posted on 2025-11-05

4740 Developmental senescence profiling reveals Eda2r as a common mediator in the core senescence program

Klein, A.; Sampaio Goncalves, D.; Dulac, L.; Knauer-Meyer, T.; Durik, M.; Chan, A. S. L.; Birling, M.-C.; Rhinn, M.; Narita, M.; Keyes, W. M.

10.1101/2025.10.30.685553 — cell biology — Posted on 2025-11-05

4741 Exercise training improves sarcopenic muscle function via restoration of mitochondrial quality control

Alldritt, I.; Sligar, J.; Campelj, D.; Padilha, C. S.; Ritenis, E.; Mantamadiotis, T.; Widodo, S.; Dinevska, M.; Nielsen, J.; Philp, A. M.; Philp, A.

10.1101/2025.11.03.686168 — cell biology — Posted on 2025-11-05

4742 Senescent cells exhibit features of developmental signaling centres

Sampaio Goncalves, D.; Dulac, L.; Ritschka, B.; Rhinn, M.; Klein, A.; Wyatt, C. D. R.; Irimia, M.; Keyes, W. M.

10.1101/2025.10.30.685565 — cell biology — Posted on 2025-11-05

4743 Intrinsic mechanotransduction during apical constriction licenses lineage competence in pluripotent stem cells

Hamouda, M. S.; Labouesse, C.; Wylde, G. W.; Yamamoto, D.; Miroshnikova, Y. A.; Basu, S.; Clare, W. M.; Chalut, K. J.

10.1101/2025.11.03.686286 — cell biology — Posted on 2025-11-05

4744 Poultry Litter Microbiome Shifts in Commercial Broiler Houses Following a Biotic-Based Litter Treatment

Olson, E. G.; Hale, B.; Ricke, S. C.

10.1101/2025.10.31.685678 — microbiology — Posted on 2025-11-05

4745 Interpreting UniFrac with Absolute Abundance: A Conceptual and Practical Guide

Pendleton, A. R.; Schmidt, M. L.

10.1101/2025.07.18.665540 — microbiology — Posted on 2025-11-05

4746 Data-optimal scaling of paired antibody language models

Neyestanak, M. S.; Burbach, S. M.; Ng, K.; Gangavarapu, P.; Hurtado, J.; Magura, J.; Ismail, N.; Muema, D.; Ndung'u, T.; Ward, A.; Briney, B.

10.1101/2025.09.02.673765 — immunology — Posted on 2025-11-05

4747 Labile iron overload reprograms microglia and neurons for lipid droplet synthesis in the aging brain

Cunha e Rocha, K.; Xiang, Q.; Qian, C.; Wang, L.; Yuan, W.; Beldona, V.; Duan, Y.; Veras, L.; Abolmaali, D.; An, G.; Park, J.; Lim, W.; Chen, X.; Ying, W.

10.1101/2025.11.03.686315 — immunology — Posted on 2025-11-05

4748 H3BERTa: A CDR-H3 specific language model for antibody repertoire analysis

Rodella, C.; Lemmin, T.

10.1101/2025.11.03.686198 — immunology — Posted on 2025-11-05

4749 Behaviorally-relevant features of observed actions dominate cortical representational geometry in natural vision

Han, J.; Chauhan, V.; Philip, R.; Taylor, M. K.; Jung, H.; Halchenko, Y. O.; Gobbini, M. I.; Haxby, J. V.; Nastase, S. A.

10.1101/2024.11.26.624178 — neuroscience — Posted on 2025-11-05

4750 Multimodal Imaging and Logistic Weighted Cognitive Scores for Classification of MCI, AD, and FTD Subtypes

Khokhar, S. K.; Misra, R.; Kumar, M.; Arshad, F.; Thanissery, N.; Kumar, S.; Manae, T.; Ramakrishnan, S.; Mangalore, S.; Alladi, S.; Gandhi, T. K.; Bharath, R. D.

10.1101/2025.09.27.678895 — neuroscience — Posted on 2025-11-05

4751 Distinct System-Level Computations Underlie Perceptual Variation Across the Visual Field

Xue, S.; Barbot, A.; Abrams, J.; Chen, Q.; Carrasco, M.

10.1101/2025.09.19.677418 — neuroscience — Posted on 2025-11-05

4752 RetINaBox: A hands-on learning tool for experimental neuroscience

Bettler, B.; Armas, F. A.; Cianfarano, E.; Bordonaro, V.; Liu, M.; Loukine, M.; Wan, M.; Villemain, A.; Richards, B.; Trenholm, S.

10.1101/2025.09.11.673547 — neuroscience — Posted on 2025-11-05

4753 How the Brain Predicts Timing: Distinct Network Hubs for Predicting and Evaluating Auditory Sensory Events

Nagy, P.; Kovacs, P.; Boncz, A.; Szalardy, O.; Baumgartner, R.; Ignatiadis, K.; Winkler, I.; Toth, B.

10.1101/2024.11.19.624242 — neuroscience — Posted on 2025-11-05

4754 Oscillatory Multi-Timescale Mechanisms Underlying Audiovisual Sequence Prediction

Wang, P.; Maÿe, A.; Daume, J.; Xue, G.; Engel, A. K.

10.1101/778969 — neuroscience — Posted on 2025-11-05

4755 Dynamic respiration-neural coupling in substantia nigra across sleep and anesthesia

Dehdar, K.; Neuberg, E.; Gu, B.-M.

10.1101/2025.06.11.659127 — neuroscience — Posted on 2025-11-05

4756 The Intermediate CA1 and CA3 Subfields of the Hippocampus Differentially Encode Social Recognition

Dykstra, B.; Kim, P.; Lin, A.; Berman, G. J.; Murugan, M.

10.1101/2025.10.27.684580 — neuroscience — Posted on 2025-11-05

4757 Dual-feature selectivity enables bidirectional coding in visual cortical neurons

Franke, K.; Karantzas, N.; Willeke, K.; Diamantaki, M.; Ramakrishnan, K.; Bedel, H. A.; Elumalai, P.; Restivo, K.; Fahey, P.; Nealley, C.; Shinn, T.; Garcia, G.; Patel, S.; Ecker, A.; Walker, E. Y.; Froudarakis, E.; Sanborn, S.; Sinz, F. H.; Tolias, A.

10.1101/2025.07.16.665209 — neuroscience — Posted on 2025-11-05

4758 Oscillatory Control of Cortical Space as a Computational Dimension

Chen, Z.; Brincat, S. L.; Lundqvist, M.; Loonis, R. F.; Warden, M. R.; Miller, E. K.

10.1101/2025.06.24.661361 — neuroscience — Posted on 2025-11-05

4759 Ablation of microglial estrogen receptor alpha predisposes to diet-induced obesity in male mice

Velasco, I.; Frey, J. M.; Baglaev, V.; Jafari, T.; Huang, T.; Schwie, S.; Santiago, O. D.; Fasnacht, R. D.; Thaler, J. P.; Dorfman, M. D.

10.1101/2025.11.03.685977 — neuroscience — Posted on 2025-11-05

4760 Emotional Responses to Naturalistic and AI-generated Affective Pictures: A Systematic Comparison

Gilbert, F.; Yang, F.; Smith, E.; Gardy, S. M.; Farkas, A.; Ding, M.; Fang, R.; Keil, A.

10.1101/2025.11.03.686276 — neuroscience — Posted on 2025-11-05

4761 Cortical markers of PAS-induced long-term potentiation and depression in the motor system: A TMS-EEG Registered Report

Arrigoni, E.; Bolognini, N.; Pisoni, A.; Guidali, G.

10.1101/2025.04.03.647045 — neuroscience — Posted on 2025-11-05

4762 miRNA modules for precise, tunable control of gene expression

Du, R.; Flynn, M. J.; Mahe, K.; Honsa, M.; Gu, B.; Li, D.; McGeary, S. E.; Gradinaru, V.; Jungmann, R.; Elowitz, M. B.

10.1101/2024.03.12.583048 — synthetic biology — Posted on 2025-11-05

4763 Nitrate restricts the expression of non-symbiotic leghemoglobin through inhibition of nodule inception protein in nodules of peanut (Arachis hypogaea)

Kuiry, R.; Roy Choudhury, S.

10.1101/2025.11.03.684091 — plant biology — Posted on 2025-11-05

4764 Bacterial metabolism of tryptophan causes toxicity in Caenorhabditis elegans that is alleviated by sugar supplementation

Gahlot, S.; Subodh, S.; Singh, J.

10.1101/2025.06.09.658597 — physiology — Posted on 2025-11-05

4765 The Role of Supraoptic Hypothalamic Arginine Vasopressin Neurons in Aging-Associated Water Balance and Thermoregulatory Deficits

Morones, N.; Jovanovic, P.; Sanetra, A.; Jang, K.; Keshishian, N.; Cui, Z.; Novinbakht, E.; Breunig, J.; Berg, A. H.; Pirtskhalava, T.; Chaib, S.; Karumanchi, S. A.; Tchkonia, T.; Silm, K.; Kirkland, j. L.; Riera, C.

10.1101/2025.11.03.686336 — physiology — Posted on 2025-11-05

4766 Jumonji-C demethylase 2 interacts with a nucleosome component to modulate chromatin state in Plasmodium falciparum

Macedo-Silva, T.; Beatriz Duque Araujo, R.; Fernanda Ortega Sepulveda, L.; Cristina Ribeiro Fernandes, J.; Wunderlich, G.

10.1101/2025.11.03.686342 — pathology — Posted on 2025-11-05

4767 Agent-based simulations of lung tumour evolution suggest that ongoing cell competition drives realistic clonal expansions

Coggan, H.; Black, J. R.; Martinez-Ruiz, C.; Grigoriadis, K.; Fisher, J.; McGranahan, N.

10.1101/2025.11.04.686578 — cancer biology — Posted on 2025-11-05

4768 Context-aware geometric deep learning for RNA sequence design

Bibekar, P.; Krapp, L. F.; Dal Peraro, M.

10.1101/2025.06.21.660801 — bioinformatics — Posted on 2025-11-05

4769 Harnessing Contextual Embeddings: A Deep Learning Framework for Predicting PCR Amplification Using BERT Tokenization

Latifian, N.; Nazer, N.; Jafarpisheh, A. M.; Hossein Khalaj, B.

10.1101/2024.11.23.624986 — bioinformatics — Posted on 2025-11-05

4770 Himito: a Graph-based Toolkit for Mitochondrial Genome Analysis using Long Reads

Su, H.; Huang, Y.; Durham, T.; Kong, N.; Casey,, E.; Benjamin, D.; Jin, S. C.; Garimella, K. V.

10.1101/2025.11.03.686348 — bioinformatics — Posted on 2025-11-05

4771 Reversing transgene silencing via targeted chromatin editing

Palacios, S.; Salibi, E.; Lu, E. J.; Weiss, R.; SCHLAEGER, T. M.; Collins, J. J.; Del Vecchio, D.

10.1101/2025.10.28.685244 — bioengineering — Posted on 2025-11-05

4772 Evolution under Stochastic Transmission: Mutation-Rate Modifiers

Feldman, M. W.; Heinrich-Mora, E.

10.1101/2025.11.04.686407 — evolutionary biology — Posted on 2025-11-04

4773 Independent colonisations of serpentine habitats highlight species-specific evolutionary histories of lineage diversification

Arrufat, P.; Hidalgo-Triana, N.; Keen, N.; Perena-Ortiz, J. F.; Perez-Latorre, A. V.; Leunda-Esnaola, A.; Garcia-Florez, A.; Kaberdin, V. R.; Kolar, F.; Lopez-Idiaquez, D.; Pearman, P. B.

10.1101/2025.11.04.686350 — evolutionary biology — Posted on 2025-11-04

4774 High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation

Smiley-Rhodes, J. A.; Bitter, M. C.; Berardi, S.; Oken, H.; Beltz, J. K.; Petrov, D. A.; Schmidt, P.

10.1101/2025.11.04.686622 — evolutionary biology — Posted on 2025-11-04

4775 Evolutionary trade-offs between intergenerational and transgenerational fitness effects

Harris, I.; Duxbury, E. M. L.; Chapman, T.; Immler, S.; Maklakov, A. A.

10.1101/2025.11.04.686475 — evolutionary biology — Posted on 2025-11-05

4776 Combined interventions are required to reverse biodiversity and carbon losses in tropical forest frontiers

Miranda, L. D. S.; Thomson, J. R.; Ferreira, J.; Gardner, T. A.; Berenguer, E.; Lees, A. C.; Mac Nally, R.; Aragao, L. E. O. C.; Brancalion, P. H. S.; Ferraz, S. F. B.; Garrett, R. D.; Molin, P. G.; Moura, N. G.; Nunes, S. S.; Parry, L.; Silveira, J. M.; Vieira, I. C. G.; Viana, C.; Barlow, J.

10.1101/2025.11.04.686271 — ecology — Posted on 2025-11-04

4777 Trapped in the web: network architectures spread coevolution and shape adaptation

Fuster-Calvo, A.; Andreazzi, C. S.; Parent, C.; Massol, F.; Guimaraes, P. R.; Gravel, D.

10.1101/2025.11.04.686579 — ecology — Posted on 2025-11-05

4778 Environmental conditions modulate constitutive and induced host immunity contributing to spatial patterns of coral disease susceptibility

Jones, N. P.; Dutton, S. E.; Shilling, E. N.; Nowlin, W. H.; Fuess, L. E.

10.1101/2025.11.04.686625 — ecology — Posted on 2025-11-05

4779 When and how leachate toxicity of tire wear particles peaks: quantifying its dynamics using dose-response analysis

Chai, Y.; Wang, X.; Wang, H.; Zhang, Y.; Yang, J.

10.1101/2024.03.30.587449 — ecology — Posted on 2025-11-05

4780 Trained ILC2 prevent IL-17-associated lung injury during helminth infection through a serotonin-dependent mechanism

Femoe, U. M.; Musaigwa, F.; Nicolis, I.; Hung, L.-Y.; Napuri, C.; Uzoije, C.; Rossi, H. L.; Lin, C.; Winters, H.; Reed, D. R.; Herbert, D. R.; Inclan-Rico, J. M.

10.1101/2025.11.03.683154 — immunology — Posted on 2025-11-04

4781 Differences in neutralization susceptibility between clade C HIV viruses from breastmilk versus contemporaneous circulating viruses from sexually acquired infections

Giorgi, E.; Gillespie, K.; Domin, E.; Fouda, G.; Permar, S. R.; Montefiori, D.; Janes, H.

10.1101/2025.11.04.686466 — immunology — Posted on 2025-11-04

4782 Vulnerability in the breadth evolution of an influenza broadly neutralizing antibody

Dailey, K.; Wang, Y.; Teo, Q. W.; Wang, C.; Lei, R.; Tong, M.; Rodriguez, L. A.; Wang, L.; Wu, N. C.

10.1101/2025.11.03.686356 — immunology — Posted on 2025-11-04

4783 CeDNe: A multi-scale computational framework for modeling structure-function relationships in the C. elegans nervous system

Moza, S.; Zhang, Y.

10.1101/2025.11.03.683805 — neuroscience — Posted on 2025-11-04

4784 Deep learning-driven characterization of single cell tuning in primate visual area V4 supports topological organization

Willeke, K. F.; Restivo, K.; Franke, K.; Nix, A. F.; Cadena, S. A.; Shinn, T.; Nealley, C.; Rodriguez, G.; Patel, S.; Ecker, A. S.; Sinz, F. H.; Tolias, A. S.

10.1101/2023.05.12.540591 — neuroscience — Posted on 2025-11-05

4785 Maternal antibody-mediated elimination of a Puumala hantavirus outbreak in a bank vole colony

Drewes, S.; Wyszkowska, J.; Jaromin, E.; Hajduk, J.; Onik, I.; Konczal, M.; Lach, K.; Bober-Sowa, B.; Baliga-Klimczyk, K.; Sadowska, E. T.; Ulrich, R. G.; Koteja, P.

10.1101/2025.11.04.686465 — zoology — Posted on 2025-11-04

4786 VirTarget: Virus-Informed Pharmacogenomics Framework Identifies Immunotherapies That Mitigate Epstein-Barr Virus-Driven Dysregulation in Multiple Sclerosis

Altas, B.; Georgiou, P.; Onisiforou, M.; Zanos, P.; Onisiforou, A.

10.1101/2025.11.03.686445 — bioinformatics — Posted on 2025-11-04

4787 Svirlpool: structural variant detection from long read sequencing by local assembly

Holtgrewe, M.; Beule, D.; Hartmann, T.; May, V.

10.1101/2025.11.03.686231 — bioinformatics — Posted on 2025-11-04

4788 Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes

Sieg, J.; Zeng, H.; Palova, H.; Smeds, L.; Mohanty, S.; Lahnsteiner, A.; Chiaromonte, F.; Makova, K.

10.1101/2025.11.03.686349 — genomics — Posted on 2025-11-04

4789 Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses

Ries, H. J.; Lalli, J.; Florek, K. R.; Barlow, S.; Goss, M.; Griesser, R.; Danz, T.; Uzicanin, A.; Temte, J.; Friedrich, T. C.

10.1101/2025.11.04.686470 — evolutionary biology — Posted on 2025-11-04

4790 Environmental exosomes: Evidence of extracellular RNA release by aquatic organisms

Yonezawa, R.; Meng, L.; Hashimoto, N.; Igarashi, I.; Kimura, S.; Yasuda, N.; Mitsuyama, S.; Kobayashi, T.; Yoshitake, K.; Kinoshita, S.; Bailey-Kobayashi, N.; Maeyama, K.; Nagai, K.; Watabe, S.; Yoshida, T.; Asakawa, S.

10.1101/2025.11.04.686478 — ecology — Posted on 2025-11-04

4791 Non-cytolytic re-engineering of a viral vaccine vector enables durable effector-memory T cell immunity by reinforcing type I IFN induction

Ciancaglini, M.; Avanthay, R.; Friederike Marx, A.; Abreu-Mota, T.; Finozzi, D.; Fixemer, J.; Geier, F.; Burri, D.; Wagner, I.; Vincenti, I.; Kreuzfeldt, M.; Merkler, D.; Zimmer, G.; Pinschewer, D.

10.1101/2025.11.04.685127 — immunology — Posted on 2025-11-04

4792 Characterize Oral-to-Blood Microbial DNA Translocation in Individuals with Cocaine Use Disorder

10.1101/2025.11.03.686400 — microbiology — Posted on 2025-11-04

4793 Evolutionary responses to increased opportunity for sexual selection in yeast

Sandell, L.; Bazzicalupo, A.; Otto, S.; Sharp, N. P.

10.1101/2025.11.03.686343 — evolutionary biology — Posted on 2025-11-04

4794 Models for the architecture of the human inner kinetochore CCAN complex on centromeric α-satellite CENP-A nucleosome arrays

Yu, C.; Muir, K. W.; Yang, J.; Zhang, Z.; McLaughlin, S. H.; Barford, D.

10.1101/2025.11.04.686567 — molecular biology — Posted on 2025-11-04

4795 Engineering of Pseudomonas putida KT2440 for Broad-Chain-Length 3-Hydroxy Fatty Acid Biosynthesis

Meng, H.; Schwanemann, T.; Lipa, M. K.; Michel, C. V.; Xia, J.; Blank, L. M.

10.1101/2025.11.04.686531 — synthetic biology — Posted on 2025-11-04

4796 Key determinants of VDAC-hexokinase I complex assembly revealed by a minimal vesicle-based interaction assay

Wessing, M.; Watrinet, I.; Timme, M.; Fiedler, B.; Melo, M. N.; Piehler, J.; Holthuis, J. C. M.

10.1101/2025.11.03.686449 — biophysics — Posted on 2025-11-04

4797 The C-terminal intrinsically disordered region of a fungal LPMO binds copper and displays anti-fungal properties

Tamburrini, K. C.; Chorozian, K.; Roblin, C.; Labourel, A.; Haon, M.; Grisel, S.; Topakas, E.; Lafond, M.; Guigliarelli, B.; Courtade, G.; Longhi, S.; Berrin, J.-G.

10.1101/2025.11.04.686606 — biochemistry — Posted on 2025-11-04

4798 Bio-synthesis of 15N-Labeled G-Quadruplexes to Investigate the Structure and Interactions in the Cell Lysate using Nuclear Magnetic Resonance

Zou, M.; Tian, F.; Zheng, W.; Jiang, M.; Zhang, S.; Liu, X.; Ma, C.; Zhao, M.; Dai, L.; Li, C.; Wang, S.

10.1101/2025.11.03.685478 — biochemistry — Posted on 2025-11-04

4799 Discovery of Host-Directed Small Molecules with Broad Anti-Leishmanial Efficacy

Gurysh, E. G.; Zahid, M. S. H.; Johnson, M. M.; Landavazo, A.; Namjoshi, O. A.; Wilson, J. W.; Varma, D. M.; Woodring, R. N.; Hendricksen, A. T.; Vath, J. F.; Quan, B.; Pino, E. N.; Fitzgerald, M. C.; Bachelder, E. M.; Blough, B. E.; Ainslie, K.

10.1101/2025.11.04.686469 — biochemistry — Posted on 2025-11-04

4800 Structural and functional insights into QueC-family protein in QatABCD anti-phage system

Gao, Z.; Li, F.; Wang, H.; Liu, X.; Li, N.; Xiong, W.; Ma, W.; Sun, D.; Yan, D.; Ma, Q.; Xu, L.; Zhang, Y.

10.1101/2025.11.03.686418 — biochemistry — Posted on 2025-11-04

4801 Genomic prediction for general combining ability in hybrid canola (Brassica napa L.)

Tessema, B. B.; Andrahennadi, C. P.; Poff, K.; Yao, K.; Ehlert, Z.; Kubik, T.; Anton, T.; Light, K.; Burton, W.; Robbins, K. R.

10.1101/2025.11.03.686416 — genetics — Posted on 2025-11-04

4802 Amphibious Transitions Drive Lineage-Specific Diversification of Olfactory Receptors in Vertebrates

Panda, B.; Nath, R.; Dey, A.; Krishnan, A.

10.1101/2025.11.03.686341 — evolutionary biology — Posted on 2025-11-04

4803 MeRIP-seq detects temperature related variation in methylated environmental RNA in fish

Ahi, E. P.; Papakostas, S.; Moulistanos, A.; Schenekar, T.

10.1101/2025.11.03.686443 — molecular biology — Posted on 2025-11-04

4804 An Electromechanical Relay-like Multi-enzymatic System Gates c-di-GMP-Dependent Cell Fate in a Cyanobacterium

Sun, Q.-X.; Huang, M.; Zeng, X.; Zhang, C.-C.

10.1101/2025.11.04.686522 — microbiology — Posted on 2025-11-04

4805 Host range and zoonotic potential linked to P-like fimbrial adhesin specificity in avian pathogenic Escherichia coli

Akrami, f.; Jamali, H.; Houle, S.; Armoa Ortiz, P.; Calmettes, C.; Dozois, C. M.

10.1101/2025.11.04.686467 — microbiology — Posted on 2025-11-04

4806 Evaluating the potential of cross-species neutralization of anti-PfCyRPA and anti-PfRIPR Monoclonal Antibodies

Guerra, N.; Hagadorn, K. A.; Nair, M.; Thiam, L. G.; Williams, B. G.; McHugh, K.; Pipini, D.; Healer, J.; Masendycz, P.; Cowman, A. F.; Draper, S. J.; Bei, A. K.

10.1101/2025.11.03.682341 — immunology — Posted on 2025-11-04

4807 Enhanced liver regeneration via targeted mRNA delivery for partial in vivo reprogramming

Jo, B.-K.; Song, Y. S.; Song, W.; Eom, H.-J.; Lee, Y. J.; Kim, J.; Hong, S.; Cho, S.-W.; Cha, H.-J.

10.1101/2025.11.03.686120 — physiology — Posted on 2025-11-04

4808 Time-Series RNA Sequencing Reveals Temperature-Specific and Temperature-Compensated Circadian Genes in Drosophila

Ito, F.; Zhang, F.; Li, W.

10.1101/2025.11.04.686609 — molecular biology — Posted on 2025-11-04

4809 Development of a viability real time PCR assay for Bordetella pertussis, B parapertussis and B holmesii

Alagarasu, K.; Katendra, S.; Prabhakar, M.; Viswanathan, R.

10.1101/2025.11.04.686548 — microbiology — Posted on 2025-11-04

4810 Distinct modes of redox-mediated DegP activation govern its role as a general protease

Roy, D.; Nandakumar, A.; Chaba, R.

10.1101/2025.11.03.686187 — microbiology — Posted on 2025-11-04

4811 Symbiotic State Affects Microbiome Recovery in a Facultatively Symbiotic Cnidarian

Valadez-Ingersoll, M.; Bodnar, C. A.; Feng, E. X.; Wong, A.; Gilmore, T. D.; Davies, S.

10.1101/2025.11.04.686571 — microbiology — Posted on 2025-11-04

4812 Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils

Peng, Y.; Woods, L. C.; Perlaza-Jimenez, L.; Lappan, R.; Jespersen, M.; Dong, X.; Holland, S. I. R.; Chown, S. L.; Leung, P. M.; Greening, C.

10.1101/2025.11.03.686391 — microbiology — Posted on 2025-11-04

4813 Skin lipid chemistry influences host-microbiome-pathogen interactions in snake fungal disease (ophidiomycosis)

Murphy, K. M.; Dallas, J. W.; Ghotbi, M.; Vargas-Gastelum, L.; Van Moorleghem, C.; Phillips, J. L.; Ludwig, D.; Sun, T.; Mason, R. T.; Niedzwiecki, J. H.; Parker, M. R.; Leblond, J. D.; Miller, J. M.; Stalzer, C.; Bergman, O.; Donahey, M. S. C.; Chevrette, M. G.; Walker, D. W.

10.1101/2025.11.04.686605 — microbiology — Posted on 2025-11-04

4814 On Copiotrophy and Temperature: Controls on Microbial Maximum Growth Rate Versus Translation Rate Optimization

Weissman, J.; Walling, A.; Zakem, E.

10.1101/2025.11.04.686613 — microbiology — Posted on 2025-11-04

4815 Signal peptidase complex mediates rotavirus VP7 processing and virion assembly

Zhu, X.; Sanchez-Tacuba, L.; Beatty, W.; Li, B.; Ding, S.

10.1101/2025.11.04.686468 — microbiology — Posted on 2025-11-04

4816 Sugar Import Suppresses Klebsiella pneumoniae Mucoidy in cAMP-CRP-dependent Manner

Khadka, S.; Gates, G.; Stark, D. J.; Allison, B. A.; Mike, L. A.

10.1101/2025.11.04.686645 — microbiology — Posted on 2025-11-04

4817 Deciphering the pangenome of the shellfish pathogen Vibrio europaeus: Evolutionary history and functional impact of core and accessory genes in aquaculture.

Rodriguez, S.; Rey-Varela, D.; Blanco-Hortas, A.; Martinez, C.; Martinez, P.; Travers, M.-A.; Dubert, J.; Barja, J. L.

10.1101/2025.11.04.686615 — microbiology — Posted on 2025-11-04

4818 NINJ1 is activated by Mycobacterium tuberculosis ESX-1 secreted effector EsxA and mediates necrosis of infected human macrophages

Saetra, R. S. R.; Hansen, M.; Kappelhoff, S.; Bugge, M.; Marstad, A.; Ryan, L.; Devant, P.; Kagan, J. C.; Freude, K. K.; Beckwith, K. S.; FLO, T. H.

10.1101/2025.11.04.685750 — microbiology — Posted on 2025-11-04

4819 Genome-wide screen identifies novel factors for surface protein cross-wall trafficking and cell envelope homeostasis in Staphylococcus aureus

Scaffidi, S. J.; Zhang, R.; Jia, Y.; Yu, W.

10.1101/2025.11.03.686427 — microbiology — Posted on 2025-11-04

4820 The evolution lifecycle of ribosome hibernation factors

Chan, L. I.; Omae, K.; Brown, C. R.; Amikura, K. I.; Ekemezie, C. L.; Clark, J.; Nishide, K.; Helena-Bueno, K.; Palmowski, P.; Porter, A.; Suzuki, S.; Melnikov, S. V.

10.1101/2025.11.04.686544 — microbiology — Posted on 2025-11-04

4821 Microbial mechanisms responsible for diurnal dynamics of N2O fluxes in a nutrient-poor subarctic permafrost environment

paul, D.; Hashmi, W.; Triches, N. Y.; Znaminko, M.; Siljanen, H. M. P.; Mammarella, I.; Gockede, M.; Biasi, C.; Marushchak, M. E.

10.1101/2025.11.04.686510 — microbiology — Posted on 2025-11-04

4822 Associations Between Gut Microbiome and 24-Hour Blood Pressure Variability: A Cross-sectional Study Highlighting Sex Differences and Potential Therapeutic Targets

Virwani, P. D.; Qian, G.; Cheung, C. N.-M.; Pijarnvanit, T. K. K. T. S.; Hsu, M. S. S.; Chow, Y. H.; Tang, L. K.; Tse, Y.-H.; Xian, J.-W.; Lam, S. S.-W.; Lee, C. P. I.; Lo, C. C. W.; Liu, R. K. C.; Ho, T. L.; Chow, B. Y.; Leung, K. S.; Lo, E. K. K.; Yuen, M.-F.; Leung, S. Y.; Hung, I. F.-N.; Louie, J. C. Y.; Teo, K.-C.; El-Nezami, H.; Ho, J. W. K.; Lau, K. K.

10.1101/2025.11.03.685706 — microbiology — Posted on 2025-11-04

4823 Lipid Droplets mediated Japanese Encephalitis Virus small Extracellular Vesicle Release

Ghosh, S.

10.1101/2025.11.04.686473 — microbiology — Posted on 2025-11-04

4824 Cell recovery and DNA extraction methods skew relative abundance estimations of foodborne pathogens and spoilage organisms on stainless steel surfaces

Feng, J.; Daly, S. E.; Roth, K.; Snyder, A. B.

10.1101/2025.11.03.686371 — microbiology — Posted on 2025-11-04

4825 Transcriptomic and proteomic analysis show minimal role formast cell ST2 in primary Heligmosomoides polygyrus bakeriinfection

Ong, N. W. P.; Hodge, S. H.; Baker, C. P.; Smyth, D. J.; Frangova, T.; McSorley, H. J.

10.1101/2025.11.03.686316 — immunology — Posted on 2025-11-04

4826 Persistent Classical and Atypical Memory B Cells Underlie Heterogeneous Vaccine Responses in Ocrelizumab-Treated Multiple Sclerosis

Curtin, R.; Velmurugu, Y.; Dibba, F.; Hao, Y.; Sreenivasaiah, C.; Khodadadi-Jamayran, A.; Nyovanie, S. T.; Kim, A.; Samanovic-Golden, M.; Mulligan, M. J.; Priest, J.; Cabatingan, M.; Winger, R.; Patskovsky, Y.; Kister, I.; Silverman, G. J.; Krogsgaard, M.

10.1101/2025.11.03.686372 — immunology — Posted on 2025-11-04

4827 Impact of air pollution on Neurite Orientation Dispersion and Density metrics (NODDI) in 10-13-year-old children with and without ADHD diagnosis

Lewandowska, P.; Bajada, C. J.; Compa, M.; Mysak, Y.; Domagalik, A.; Kossowski, B.; Baumbach, C.; Kaczmarek-Majer, K.; Degorska, A.; Skotak, K.; Sitnik-Warchulska, K.; Lipowska, M.; Izydorczyk, B.; Grellier, J.; Markevych, I.; Szwed, M.

10.1101/2025.11.03.686321 — neuroscience — Posted on 2025-11-04

4828 Design and Development of DNA Damage Chemical Inducers of Proximity (DD-CIP) for Targeted Cancer Therapy

Qiu, T.; Lee, Y. T.; Dwyer, B. G.; Tan, Y. J.; Chen, T.; Romero, B. A.; Wang, Y.; Deng, J.; Zhang, T.; Crabtree, G. R.; Hinshaw, S. M.; Wong, K.-K.; Gray, N. S.

10.1101/2025.11.03.686423 — cancer biology — Posted on 2025-11-04

4829 Generating long deletions across the genome with pooled paired prime editing screens

Weller, J.; Girling, G.; Peets, E. M.; Koeppel, J.; Kitada, S.; Murat, P.; Liberante, F. G.; Belattar, Y.; Iwama, S.; Ellis, T.; Parts, L.

10.1101/2025.11.03.686307 — genomics — Posted on 2025-11-04

4830 Shadow competition and the evolution of sensory capability in sit-and-wait predators

Ali, S.; Mehta, R. S.

10.1101/2025.11.03.686329 — ecology — Posted on 2025-11-04

4831 TMEM9 and SEC22B interact with ClC-5 to shape renal proximal tubule function and Dent's Disease type I pathogenesis

Duran, M.; Casal-Pardo, A.; Sarro, E.; Stein, F.; Cases-Palau, S.; Garcia, C.; Ariceta, G.; Meseguer, A.; Cantero, G.

10.1101/2025.11.03.686312 — cell biology — Posted on 2025-11-04

4832 Neural Encoding through Hierarchical Amplitude Modulation

Ruffini, G.

10.1101/2025.11.03.686310 — neuroscience — Posted on 2025-11-04

4833 Reactivating aversive memories in humans: An EEG and Microstates study of post-retrieval processes

Cavallino, L.; Bavassi, L.; Pedreira, M. E.

10.1101/2025.11.03.686328 — neuroscience — Posted on 2025-11-04

4834 The hidden phase of memory: EEG signatures of reactivation during post-retrieval rest

Bavassi, L.; Campos-Arteaga, G.; Palacios-Garcia, I.; Villena-Gonzalez, M.; Campassi, L.; Marachlian, E.; Balboa, E. R.; Forcato, C.; Pedreira, M. E.

10.1101/2025.11.03.685924 — neuroscience — Posted on 2025-11-04

4835 Neural oscillatory dynamics reveal altered top-down and integrative mechanisms during face processing in autistic children and unaffected siblings of autistic children

Vanneau, T.; Brittenham, C.; Darrell, M.; Foxe, J. J.; Molholm, S.

10.1101/2025.11.03.684159 — neuroscience — Posted on 2025-11-04

4836 Circuit-specific gene editing for precision modulation of neuronal activity with CRISPR-rabies virus

Zhang, Z.; Xu, J.; Matthews, E. A.; Deasy, S.; He, L.; Arroyo, D.; Pan, E.; Deshmukh, A.; Kaur, K. S.; McNamara, J. O.; Southwell, D. G.; Gersbach, C. A.; Ji, R. R. A.; Velmeshev, D.

10.1101/2025.11.03.686433 — neuroscience — Posted on 2025-11-04

4837 INTERACT: Interactome Network Targeting via Enzyme Reactivity and Activity-based Chemoproteomic Tools

Porta, E. O. J.; Koutsogiannis, Z.; Kalesh, K.; Denny, P. W.; Steel, P. G.

10.1101/2025.11.03.686322 — pharmacology and toxicology — Posted on 2025-11-04

4838 AXL mediates mast cell survival and resistance to tyrosine kinase inhibitors in mastocytosis

Kangboonruang, K.; Drabent, P.; Heintze, M.; Maksut, F.; Lepelletier, Y.; Lhermitte, L.; Feroul, M.; Letard, S.; Kabore, C.; Brenet, F.; Meni, C.; Cagnard, N.; Bondet, V.; Lefevre, G.; Bruneau, J.; Dussiot, M.; Halse, H.; Bigorgne, A.; Collange, A.-F.; Bouktit, H.; Retornaz, F.; Megret, J.; Barete, S.; Droin, N.; Bulai Livideanu, C.; Lebouvier, A.; Duffy, D.; Solary, E.; Arock, M.; Gandhi, D.; Bodemer, C.; Rossignol, J.; Polivka, L.; Molina, T.; Hermine, O.; Maouche-Chretien, L.

10.1101/2025.11.03.686205 — cancer biology — Posted on 2025-11-04

4839 Spontaneous Emergence of Symmetry in a Generative Model of Protein Structure

Oresten, A.; Sato, K.; Stalmarck, A.; Billera, L.; Nordlinder, H. N.; Ryder, J. C.; Kaduk, M.; Murrell, B.

10.1101/2025.11.03.686219 — bioinformatics — Posted on 2025-11-04

4840 The genome of Istocheta aldrichi (Diptera: Tachinidae), a parasitoid of the Japanese beetle, Popillia japonica (Coleoptera: Scarabaeidae)

Stilwell, P. A.; Culotta, J. A.; Hutchison, W. D.; Lindsey, A. R. I.

10.1101/2025.11.02.686142 — genomics — Posted on 2025-11-04

4841 Genomic editors for localised population suppression

Willis, K.; Burt, A.

10.1101/2025.11.03.686305 — evolutionary biology — Posted on 2025-11-04

4842 A memory-driven model of phenotypic adaptation for anticipating the emergence of enzalutamide resistance in prostate cancer

Ghoreyshi, Z.; Debnath, S.; Olawuni, P.; Armstrong, A.; Somarelli, J.; George, J. T.

10.1101/2025.11.03.686133 — evolutionary biology — Posted on 2025-11-04

4843 Shedding light on Amazonian phylogeographic patterns and evolutionary history of night monkeys (Genus: Aotus) using reconstructed fecal metagenomic shotgun sequencing

Helenbrook, W. D.

10.1101/2025.11.03.686292 — evolutionary biology — Posted on 2025-11-04

4844 Echosounders for fish detection disturb harbour porpoises

Hubert, J.; Berges, B.; Parcerisas, C.; Debusschere, E.; de Bruijn, J. A. C.; Demuynck, J. M.; Muniz, C.; Slabbekoorn, H.

10.1101/2025.11.03.686290 — ecology — Posted on 2025-11-04

4845 River biofilm bacteria as sentinels of national-scale freshwater ecosystems

Thorpe, A. C.; Busi, S. B.; Warren, J.; Newbold, L. K.; Taylor, J. D.; Walsh, K.; Read, D. S.

10.1101/2025.11.03.686311 — ecology — Posted on 2025-11-04

4846 IRF4 is a master regulator of multinucleated giant cell formation

Hofmann, M.; Heller, G.; Kieler, M.; Musiejovsky, L.; Kremp, L.; Kerndl, M.; Ettel, P.; Niederreiter, B.; Quemada Garrido, L.; Sedighi, A.; Krausgruber, T.; Heinz, L. X.; Dietschmann, A.; Voehringer, D.; Everts, B.; Weichhart, T.; Sharif, O.; Blueml, S.; Schabbauer, G.

10.1101/2025.11.03.686191 — immunology — Posted on 2025-11-04

4847 Timing of immune checkpoint blockade shapes anti-tumor immunity via a clock-dependent chemokine axis

Lichterman, J. N.; Srinivasan, T.; Wang, R.; Dende, C.; Zarek, C.; Ramirez, J. I.; Park, N.; Wang, H.; Li, W.; Kim, J.; Coughlin, L.; Poulides, N.; Sabaeifard, P.; Palmer, S. N.; Morrill, A. C.; Hassell, B.; Shelton, J. M.; Li, X. V.; Evers, B. M. M.; Zhan, X.; Takahashi, J. S.; Hooper, L. V.; Koh, A. Y.

10.1101/2025.11.03.686293 — immunology — Posted on 2025-11-04

4848 A novel role of circCPSF6 regulating antiviral innate immunity via miR-665 and PCBP2-IPS-1 axis

Meher, A.; Chaudhary, R.; Kumar, H.

10.1101/2025.11.03.686289 — immunology — Posted on 2025-11-04

4849 Inverse Neural-Kinematic Dynamics Revealed by RQA During Motor Skill Learning

Entezari, N.; Hassanzadeh, Z.; Bahrami, F.; Kalhor, A.

10.1101/2025.11.03.685985 — neuroscience — Posted on 2025-11-04

4850 All Memories Are Equal at Night: Sleep Protects Without Preference for Strength

Schabus, M.; Ameen, M. S.; Heib, D. P.

10.1101/2025.11.03.686279 — neuroscience — Posted on 2025-11-04

4851 A Human Hippocampal Organoid Model with Sustained Neural Stem Cells Reveals State Shifts Under Glucocorticoid Stress

Soper, O.; Assir, M. Z. K.; Ramirez, D.; Crawford, G.; Gyuris, R.; Valkila, S. S. M.; Lecante, L. L.; Liu, P.; Fowler, P. A.; Gonzalez, J. A.; Berg, D. A.; Kang, E.

10.1101/2025.11.03.686207 — neuroscience — Posted on 2025-11-04

4852 Uric acid accumulation in cockroach wings

Noda, T.; Moriyama, M.; Harumoto, T.; Katsuno, T.; Fukatsu, T.

10.1101/2025.11.03.686272 — physiology — Posted on 2025-11-04

4853 Benchmarking Real-World Applicability of Molecular Generative Models from De novo Design to Lead Optimization with MolGenBench

Cao, D.; Fan, Z.; Yu, J.; Chen, M.; Jiang, X.; Wang, X.; Sheng, X.; Luo, X.; Teng, D.; Zheng, M.

10.1101/2025.11.03.686215 — bioinformatics — Posted on 2025-11-04

4854 FADVI: disentangled representation learning for robust integration of single-cell and spatial omics data

Liu, W.; Qu, G.; Simon, L.; Theis, F. J.; Zhao, Z.

10.1101/2025.11.03.683998 — bioinformatics — Posted on 2025-11-04

4855 Ultrahigh throughput screening to train generative protein models for engineering specificity into unspecific peroxygenases

Nair, P. M.; Steinberg, D. M.; Resende, T.; Suarez, A. F.; Power, H.; Ong, C. S.; Sairam, V.; Cheng, S. H.-Y.; Fragata, L.; Serafini, A.; Oh, V.; Tan, S. H.; Speight, R. E.; Vahidi, A. K.

10.1101/2025.11.02.685536 — bioengineering — Posted on 2025-11-04

4856 Microfluidics-Enabled Simultaneous Imaging of Neural Activity and Behavior in Chemically Stimulated, Head-Fixed C. elegans

Lee, H. J.; Vallier, J.; Lu, H.

10.1101/2025.11.03.686171 — bioengineering — Posted on 2025-11-04

4857 Macrophage-to-Myofibroblast Transition (MMT)- an adverse response to polypropylene mesh implanted for pelvic organ prolapse repair surgery in a non-human primate model

Therriault, M.; Knight, K.; Kottapalli, S.; Obisesan, T.; Harinath, M.; Brown, B.; Moalli, P.

10.1101/2025.11.03.686251 — bioengineering — Posted on 2025-11-04

4858 Measuring Perfusion Pressure and Flow Resistance in a Microfluidic Device Using an External Optical System

Coughlin, M. C.; Floryan, M.; Offeddu, G.; Coughlin, M. F.

10.1101/2025.11.03.686291 — bioengineering — Posted on 2025-11-04

4859 Experimentally assessing the role of foraging encounters on social partner choice in a kin-biased bird society

Fourie, B.; Doutrelant, C.; Depalle, Y.; Ferreira, A.; Covas, R.

10.1101/2025.11.03.686260 — animal behavior and cognition — Posted on 2025-11-04

4860 Genetic insights into Iron Age Saka culture: Ancient DNA analysis of the Boz-Barmak burial ground, Kyrgyzstan

Rymbekova, A.; Gelabert, P.; Llanos-Lizcano, A.; Balakrishnan, K.; Hämmerle, M.; Cheronet, O.; Abdykanova, A.; Kasymkulov, K.; Hrivnyak, M.; T. Eng, J.; Pinhasi, R.; Kuhlwilm, M.

10.1101/2025.11.03.686206 — genomics — Posted on 2025-11-04

4861 Disruption of ADAMTSL4 Causes Ectopia Pupillae in Zebrafish via COL8A1-Driven Cell Migration

Chen, Z.; Huang, X.; Jia, W.; Shen, X.; Chen, X.; Wang, Y.; Huo, Q.; Chen, T.; Zhang, M.; Jiang, K.; Xuqing, G.; A, G.; Yang, F.; Pi, Y.; Jiang, Y.

10.1101/2025.11.03.686242 — genetics — Posted on 2025-11-04

4862 Additive effects of environmental and demographic variation shape the repeatability of evolution across replicated experiments

Bisschop, K.; Wortel, M. T.; Kraaijeveld, K.; Marien, J.; Rathmann, I.; Bonte, D.; Declerck, S.; de Vos, M. G.; Etienne, R.; Goossens, S.; Kammenga, J.; Mortier, F.; Riksen, J.; van der Zee, M.; Verhoeven, K.; Wiezer, S.; Zandbergen, L. E.; Egas, M.; Ellers, J.; Groot, A. T.; Visser, M.; Blankers, T.

10.1101/2025.11.03.686244 — evolutionary biology — Posted on 2025-11-04

4863 Two routes to land: Genomic underpinnings of parallel aerial egg deposition in aquatic Old-World Pila and New-World Pomacea (Ampullariidae)

Zhou, Y.; Mu, H.; Nie, X.; Gao, Y.; Wang, H.; Fang, L.; Luan, T.; Ganmanee, M.; Qiu, J.-W.; Sun, J.; Ip, J. C.-H.

10.1101/2025.11.03.686255 — evolutionary biology — Posted on 2025-11-04

4864 Deep Blueprint: A Literature Review and Guide to Automated Image Classification for Ecologists

Game, C. A.; Piechaud, N.; Howell, K.

10.1101/2025.11.03.686223 — ecology — Posted on 2025-11-04

4865 Cdh-2 modulates tissue stiffness and cortical F-actin distribution in neuroepithelial cells to drive forebrain roof plate invagination.

Sachdeva, M.; Sharma, P.; Gupta, P.; Kushwaha, S.; Sen, J.

10.1101/2025.11.03.686203 — developmental biology — Posted on 2025-11-04

4866 Deciphering cytokine-driven ADP-ribosylation signaling networks via Af1521-based mass spectrometry analysis of labile Glu/Asp-linkages

Buch-Larsen, S. C.; Hendriks, I. A.; Tashiro, K.; Elsborg, J. D.; Vakhrushev, S. Y.; Olsen, J. V.; Luescher, B.; Liszczak, G.; Ahel, I.; Nielsen, M. L.

10.1101/2025.11.03.686237 — cell biology — Posted on 2025-11-04

4867 Isolation of rat and human hepatic cholangiocytes using a peptide derived from a conserved domain of enterobacteria BamA/TamA-like proteins

METLEJ, P.; RIBAULT, C.; DAVID-LE GALL, S.; NAHAS, H.; LEROYER, P.; MAUNAND, K.; SOLER, N.; COPPENS-EXANDIER, H.; VLACH, M.; OSMAN, D.; BOUSARGHIN, L.; CORLU, A.; LOYER, P.

10.1101/2025.11.03.686257 — cell biology — Posted on 2025-11-04

4868 Identification of short peptides that correlate with cytoplasmic retention of human proteins

Brown, J. C.; Wang, B.

10.1101/2025.11.03.686273 — cell biology — Posted on 2025-11-04

4869 Evolutionary Remodelling of a Remnant GET-Pathway Factor into PEX38, a Novel and Essential Peroxin in Euglenozoa

Krishna, C. K.; Gaussmann, S.; Das, H.; Jung, M.; Oeljeklaus, S.; Sattler, M.; Warscheid, B.; Kalel, V.; Erdmann, R.

10.1101/2025.11.03.686288 — cell biology — Posted on 2025-11-04

4870 During an inflammatory response, zebrafish tnfa and tnfb are expressed by different cell types and have distinct expression kinetics

van Dijk, K. S. E.; Begon-Pescia, C.; de Bruin, B.; Resul Özbilgic, R.; Elks, P. M.; Nguyen Chi, M. E.; Forlenza, M.

10.1101/2025.11.04.686030 — immunology — Posted on 2025-11-04

4871 CD8 T lymphocytes infiltrate the kidneys and correlate with disease progression in B6.NZMSle1/Sle2/Sle3 lupus mice

Montigny, P.; Aydin, S.; Maudoux, A.-L.; van Baren, N.; Brusa, D.; Dauguet, N.; Houssiau, F.; Lauwerys, B.; Coulie, P. G.

10.1101/2025.11.03.685164 — immunology — Posted on 2025-11-04

4872 The two groups of zebrafish type I interferons target different tissues, paralleling the mammalian type I: type III IFN functional division

Wiggett, H.; Porter, D.; Briolat, V.; Balaboi, T.; Abi Younes, M.; Colin, I.; Lutfalla, G.; Levraud, J.-P.

10.1101/2025.11.03.686239 — immunology — Posted on 2025-11-04

4873 Hidden Spirals Reveal Neurocomputational Mechanisms of Traveling Waves in Human Memory

Das, A.; Zhang, J.; Zabeh, E.; Ermentrout, B.; Jacobs, J.

10.1101/2025.11.03.686225 — neuroscience — Posted on 2025-11-04

4874 Elevated urea levels in human frontotemporal dementia and amyotrophic lateral sclerosis post-mortem brain tissue: Evidence of a multi-dementia pathogenic mechanism

Philbert, S.; Church, S.; Unwin, R.; Cooper, G.

10.1101/2025.11.03.686199 — neuroscience — Posted on 2025-11-04

4875 Dopamine D1Aa and D2a Receptor Expression in the Auditory System of a Vocal Fish

Kobi, K.; Forlano, P. M.

10.1101/2025.11.03.686280 — neuroscience — Posted on 2025-11-04

4876 Epigenetic control of microglial developmental milestones from proliferative progenitors to efficient phagocytes

Pereira-Iglesias, M.; Martinson, D.; Falco, C.; Maldonado-Teixido, J.; Gonzalez-Rodriguez, M.; Senovilla-Ganzo, R.; Benito, E.; Beccari, S.; Valero, J.; Mora-Romero, B.; Ballasch, I.; Viguier, S.; Haene, P.; Boettiger, M.; Reisz, J. A.; Manso, Y.; Parkkinen, L.; Aransay, A. M.; Soria, F. N.; D'Alessandro, A.; Soriano, E.; Thion, M.; Garel, S.; Greter, M.; Giralt, A.; Pascual, A.; Garcia-Moreno, F.; Menassa, D. A.; Carrillo, J. A.; Sierra, A.

10.1101/2025.11.03.685577 — neuroscience — Posted on 2025-11-04

4877 Mechanistic Link between Executive Functions and Higher Cognition: Evidence from Psychometric Modeling and Brain Stimulation

Zivanovic, M.; Bjekic, J.; Filipovic, S. R.

10.1101/2025.11.03.686235 — neuroscience — Posted on 2025-11-04

4878 Beyond retinotopy: exploiting native visual representations in cortical neuroprostheses for vision loss remediation

Baroni, L.; Picek, M.; Patel, S.; Tolias, A. S.; Antolik, J.

10.1101/2025.11.03.684808 — neuroscience — Posted on 2025-11-04

4879 AHA1 regulates Aβ production via modulation of APP expression and γ-secretase assembly

Noorani, A. A.; Islam, S.; Catalfano, K.; Wilkins, H. M.; Blagg, B. S. J.; Zou, K.; Wolfe, M. S.

10.1101/2025.11.03.686106 — neuroscience — Posted on 2025-11-04

4880 Pitch selectivity in ferret auditory cortex

Tarka, V. M.; Gaucher, Q.; Walker, K. M. M.

10.1101/2025.11.03.686220 — neuroscience — Posted on 2025-11-04

4881 Test-Retest Reliability of Dopaminergic fPET and fMRI Measures During Reward Processing

Schlosser, G. D.; Handschuh, P. A.; Murgas, M.; Graf, S.; Milz, C.; Klug, S.; Falb, P.; Schmidt, C.; Eggerstorfer, B.; Briem, E.; Mayerweg, A.; Artmeier, L.; Godbersen, G. M.; Nics, L.; Razul, S.; Hacker, M.; Hahn, A.; Lanzenberger, R.; Reed, M. B.

10.1101/2025.11.03.686252 — neuroscience — Posted on 2025-11-04

4882 Predictive vision-language integration in the human visual cortex

Li, S.; Jin, Z.; Zhang, R.-Y.; Gu, S.; Li, Y.

10.1101/2025.11.03.686222 — neuroscience — Posted on 2025-11-04

4883 Neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases predicted via a systems biology-based approach

Jiang, B.; Wang, S.; Xie, J.; Kim, H.; Tukker, A. M.; Wang, J.; Bowman, A. B.; Yuan, C.; Baloni, P.

10.1101/2025.11.03.686281 — systems biology — Posted on 2025-11-04

4884 Systems-level Plant Responses Reveal Pseudomonas-Mediated Growth Promotion in Brachypodium Under Nitrogen Limitation

Sanow, S.; Mantz, M.; Wissel, H.; Bhatnagar, A.; Sturm, E.; Kelm, J. M.; Walker, R.; Luecke, A.; Schaaf, G.; Huesgen, P.; Roessner, U.; Watt, M.; Arsova, B.

10.1101/2025.11.03.686263 — plant biology — Posted on 2025-11-04

4885 Decoupling of stomatal conductance from net assimilation at high temperature as a mechanism to increase transpiration

Schuler, P.; Didion-Gency, M.; Bortolami, G.; Juillard, T.; Hoch, G.; Bachofen, C.; Kahmen, A.

10.1101/2025.11.03.686201 — plant biology — Posted on 2025-11-04

4886 Administration of short-chain fatty acids reduces bacterial translocation to peripheral organs and the brain, preserves gut barrier integrity, and mitigates brain injury following stroke

Castillo Gonzalez, J.; Mousavi, M.; Buscemi, L.; Price, M.; Hirt, L.

10.1101/2025.11.03.686233 — physiology — Posted on 2025-11-04

4887 Cytoskeleton remodeling caused by keratin dysregulation triggers tumor aggressiveness via promoting genomic instability and cellular adaption

Chuang, H.-H.; Kuo, B. Y.-T.; Sriramadasu, K.; Lai, M.-T.; Lin, L. Y.-T.; Boominathan, P. K.; Hwang, T.; Chen, Y.-C.; Chen, C.-M.; Chang, C. Y.-Y.; Sheu, J. J.-C.

10.1101/2025.11.03.686269 — cancer biology — Posted on 2025-11-04

4888 Rule-based mitigation of charge asymmetry-triggered monoclonal antibody self-assembly

Brakti, I.; Henriksen, A.; Tomczak, M. L.; Godsk, S. L.; Lenton, S.; Fodera, V.; Groenning, M.

10.1101/2025.11.03.686261 — biophysics — Posted on 2025-11-04

4889 SOORENA: Self-lOOp containing or autoREgulatory Nodes in biological network Analysis

Arar, H.; Aldahdooh, J.; Nickchi, P.; JAFARI, M.

10.1101/2025.11.03.685842 — bioinformatics — Posted on 2025-11-04

4890 Physics-Diffusion-Driven Multiscale Aggregation for Drug-Target Interaction Prediction

Liu, J.; Le, J.; Wei, C.; Liu, M.; Yin, Z.; Luo, Y.; Qin, H.; Yu, G.

10.1101/2025.11.03.686185 — bioinformatics — Posted on 2025-11-04

4891 annoSnake: a Snakemake workflow for taxonomic and functional annotation of metagenomes and metagenome-assembled genomes (MAGs)

Heimburger, B.; Clement, R.; Hartke, T.

10.1101/2025.11.03.686227 — bioinformatics — Posted on 2025-11-04

4892 Exploring the Structural Lexicon of the Proteome via Metric Geometry

Gunther, E.; Camara, P. G.

10.1101/2025.11.03.686256 — bioinformatics — Posted on 2025-11-04

4893 High-accuracy structure modeling for antibody-antigen complexes

Wang, S.; Zhuang, J.; Cui, X.; Lv, Z.; Hou, D.; Zhang, G.

10.1101/2025.11.03.686275 — bioinformatics — Posted on 2025-11-04

4894 ProteoCast: a web server to predict, validate, and interpret missense variant effects

Abakarova, M.; Freiberger, M. I.; Liehrmann, A.; Rera, M.; Laine, E.

10.1101/2025.11.03.686214 — bioinformatics — Posted on 2025-11-04

4895 MOFA-FLEX: A Factor Model Framework for Integrating Omics Data with Prior Knowledge

Qoku, A.; Rohbeck, M.; Walter, F. C.; Kats, I.; Stegle, O.; Buettner, F.

10.1101/2025.11.03.686250 — bioinformatics — Posted on 2025-11-04

4896 EvoPRAISE: computationally guided directed evolution for rational AAV capsid engineering

Ono, H.; Fujino, S.; Sunagawa, G. A.

10.1101/2025.11.02.686002 — bioengineering — Posted on 2025-11-04

4897 Highly Efficient Coreactant-Free Electrochemiluminescence Sensing Platform Using Novel Microfabricated Multiplexed Entwined Spiral Microelectrodes for Point-of-Care Applications

Bozorgzadeh, S.; Murray, R.; Hamidi, H.; Seymour, I.; Iacopino, D.; O'Riordan, A.

10.1101/2025.11.03.686208 — bioengineering — Posted on 2025-11-04

4898 Effects of basalt amendment and mycorrhizal inoculation on soil chemical properties and maize growth

Boito, L.; Rijnders, J.; Steinwidder, L.; Frings, P. J.; Vienne, A.; Maes, M.; Verbruggen, E.; Vicca, S.

10.1101/2025.11.03.686277 — bioengineering — Posted on 2025-11-04

4899 A Low-Cost Markerless motion capture system to automate Functional Gait Assessment: Feasibility Study

Darici, O.; Cabak, C.; Wong, J. D.

10.1101/2024.12.17.628985 — bioengineering — Posted on 2025-11-04

4900 Aggressive nitrogen assimilation during exponential growth in Chlamydomonas reinhardtii

Tibule, M.; Mallawarachchi, W.; Oyateru, O.; Ziaeian, M.; Kim, M.; Dharmasiri, H. N.; Lee, J.-H.

10.1101/2025.11.02.686124 — plant biology — Posted on 2025-11-04

4901 Functionally-Coupled Ion Channels Begin Co-assembling at the Start of Their Synthesis

Pournejati, R.; Huang, J. M.; Ma, M.; Moreno, C. M.; Vivas, O.

10.1101/2025.04.08.647703 — biophysics — Posted on 2025-11-04

4902 RNAcentral in 2026: Genes and literature integration

Green, A. F.; Ribas, C. E.; Jandalala, I.; Muston, P.; O'Cathail, C.; Cochrane, G.; Ernst, C.; Zhao, L.; Madrigal, P.; Attrill, H.; Marygold, S.; Lancet, D.; Dobzinski, N.; Chan, P. P.; Lowe, T. M.; Bruford, E. A.; Seal, R. L.; Hermjakob, H.; Panneerselvam, K.; Finn, R. D.; Gurbich, T. A.; Griffiths-Jones, S.; Fromm, B.; Peterson, K. J.; Sordyl, D.; Bujnicki, J. M.; Velankar, S.; Appasamy, S. D.; Ganguly, S.; Zhang, P.; He, S.; Rutherford, K. M.; Wood, V.; Lovering, R. C.; Picardi, E.; Ontiveros, N.; Huang, L.; Miao, Z.; Petrov, A. S.; McCann, H.; Cavalleri, E.; Mesiti, M.; Rivas, E.; Szikszai

10.1101/2025.09.19.677274 — bioinformatics — Posted on 2025-11-04

4903 Optimizing stability in dynamic small-molecule binding proteins

Scherer, M.; Kriegel, M.; Höcker, B.; Fleishman, S.

10.1101/2025.07.07.663574 — biochemistry — Posted on 2025-11-04

4904 Fibril Paint: a class of amyloid-targeting peptides

Pedrola, J. A.; Dekker, F. A.; Guttmann, K.; van Leeuwen, L. M.; Singh, S.; Mayer, G.; Garfagnini, T.; Friedler, A.; Rudiger, S. G. D.

10.1101/2024.08.25.609586 — biochemistry — Posted on 2025-11-04

4905 Sex differentiation, divergence, and introgression in the leishmaniasis vector Lutzomyia longipalpis

Stuckert, A. M.; Turissini, D.; DAgostino, E. R.; Peede, D.; Parvathaneni, M.; Rader, J. A.; Muskus, C.; Bejarano, E.; Wang, J. R.; Vivero, R.; Matute, D. R.

10.1101/2025.04.08.647763 — genomics — Posted on 2025-11-04

4906 Distinct System-Level Computations Underlie Perceptual Variation Across the Visual Field

Xue, S.; Barbot, A.; Abrams, J.; Chen, Q.; Carrasco, M.

10.1101/2025.09.19.677418 — neuroscience — Posted on 2025-11-04

4907 FibrilPaint20 directs the ubiquitin-proteasome system to Tau amyloid fibrils

Dekker, F. A.; Aragnones Pedrola, J.; van Weert, E.; den Breejen, A.; Peters, L.; Poza-Rodriguez, A.; Mayer, G.; Singh, S.; Vertegaal, A. C. O.; Friedler, A.; Rudiger, S. G. D.

10.1101/2024.08.27.609886 — biochemistry — Posted on 2025-11-04

4908 Development and social dynamics of stone tool use in wild white-faced capuchin monkeys

Goldsborough, Z.; Carlson, M. K. W.; Reetz, L. S.; Crofoot, M. C.; Barrett, B. J.

10.1101/2025.04.08.647785 — animal behavior and cognition — Posted on 2025-11-04

4909 Divergent patterns of richness and density in the global soil seed bank

Auffret, A. G.; Ladouceur, E.; Haussmann, N. S.; Keil, P.; Daouti, E.; Elumeeva, T. G.; Kacergyte, I.; Knape, J.; Kotowska, D.; Low, M.; Onipchenko, V. G.; Paquet, M.; Rubene, D.; Plue, J.

10.1101/2023.11.08.566230 — ecology — Posted on 2025-11-04

4910 The cortical microenvironment drives early immune organization and controls early osteoclastogenesis in bone healing

Noom, A.; Oktay, H. Z.; Morgan, D. M.; Kroh, S.; Ellinghaus, A.; Kochan, M.; Bolaji, O. A.; Uecker, R.; Guenther, R.; Bucher, C. H.; Triantafyllopoulou, A.; Haas, S.; Schmidt-Bleek, K.; Hauser, A. E.; Sawitzki, B.; Duda, G. N.

10.1101/2025.11.03.684298 — immunology — Posted on 2025-11-04

4911 Acute stress reduces risk-aversion by changing magnitude perception

Renkert, M. F.; de Hollander, G.; Aydogan, G.; Bedi, S.; Forbes, P.; Lamm, C.; Ruff, C. C.

10.1101/2025.11.03.685504 — neuroscience — Posted on 2025-11-04

4912 Functional and morphological alterations of the light perception circuits in postmortem retina from donors at different stages of Alzheimer's disease

Sanda, N.; Milea, D.; Kovari, E.; Tong, Y.; Bruegger, T.; Hannibal, J.; Egervari, K. L.; Lobrinus, J. A.; Carrera, E.; Thumann, G.; Kleinlogel, S.; Adamantidis, A.; Mure, L. S.

10.1101/2025.02.18.638646 — neuroscience — Posted on 2025-11-04

4913 Xanthomonas type III effector XopN targets scaffold protein OsRACK1B to suppress rice immunity

Wang, J.; Ni, Z.; Chen, X.; Zhang, Y.; Qin, H.; Wang, H.; He, Y.; Tang, J.; Huang, S.

10.1101/2025.11.03.686189 — plant biology — Posted on 2025-11-04

4914 Structure-Based Calculation of Excipient Effects on the Viscosity ofConcentrated Antibody Solutions

Shelley, J.; Chai, Q.; Wu, L.; Vafaei, S.; Shelley, M. Y.; Feyfant, E.; Feng, J.; Woldeyes, M.; Babin, V.; Jou, J.

10.1101/2025.11.02.686170 — pharmacology and toxicology — Posted on 2025-11-04

4915 qcGEM: a graph-based molecular representation with quantum chemistry awareness

Wang, H.; Gong, H.

10.1101/2025.11.02.686183 — biophysics — Posted on 2025-11-04

4916 Geometry-Constrained Prediction of Catalytically Competent Kinase Domains Across the Human Kinome

Wang, Y.; Hu, Q.; Huang, J.

10.1101/2025.11.03.686188 — biophysics — Posted on 2025-11-04

4917 Decoding Diabetes: Harnessing AI to Accurately Predict Real-Time and Future Blood Glucose Levels for Diabetes Management Using Diet, Exercise, Insulin Intake, and Heart Rate Variability

Singhvi, R. P.; Singhvi, S.

10.1101/2025.11.02.686165 — bioinformatics — Posted on 2025-11-04

4918 MkAtt-SDN2GO: Multi-kernel Attentive-SDN2GO Network for Protein Function Prediction in Humans

Jhawar, K.; Bhatt, T.; Sunil, R.; Lipo, W.

10.1101/2025.11.02.686093 — bioinformatics — Posted on 2025-11-04

4919 Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data

LeRoy, N. J.; Zheng, G.; Khoroshevskyi, O.; Campbell, D. R.; Zhang, A.; Sheffield, N. C.

10.1101/2025.11.03.685753 — bioinformatics — Posted on 2025-11-04

4920 Recapitulation of clinical and molecular hallmarks of lipid-induced hepatic insulin resistance in a zonated, vascularized human liver acinus microphysiological system during metabolic dysfunction-associated steatotic liver disease (MASLD) progression

Aleman, J.; Vernetti, L.; Schurdak, M. E.; DeBiasio, R.; LaRocca, G.; Yechoor, V. K.; Taylor, D. L.; Stern, A. M.; Miedel, M. T.

10.1101/2025.11.02.686163 — bioengineering — Posted on 2025-11-04

4921 Delivery of collagen-encoding mRNA to the skin for cosmetic applications

Wen, J.; Pang, B.; Han, J.; Wang, S.; Xu, L.; Wu, Y.; Zhang, H.; Luo, F.; Jin, Z.; Hu, Y.

10.1101/2025.11.02.686162 — bioengineering — Posted on 2025-11-04

4922 StrainOptimizer empowers rational cell factory design through multi-scale metabolic models with expression and proteome constraints

Wang, H.; Zhang, M.; Zhang, C.; He, S.; Liao, W.; Zhu, R.; Zhou, Y.; Lu, H.

10.1101/2025.11.03.685948 — bioengineering — Posted on 2025-11-04

4923 A Novel Approach to Fabricating Sustainable Enzymatic Lactate Biofuel Cells Using Direct Laser Writing Technology for Wearable Real-Time Monitoring Applications

Hamidi, H.; Bozorgzadeh, S.; Setti, M.; Pontiroli, D.; O`Riordan, A.; Quinn, A. J.; Iacopino, D.

10.1101/2025.11.03.686210 — bioengineering — Posted on 2025-11-04

4924 Captamer: A Novel Quantitative Protein Detecting Method Depending on Aptamer-activated Molecular Switches and RPA Signal Amplification

Cao, Y.; Li, M.; Xu, G.; Xia, S.; Wu, X.; Shi, K.; Xue, R.; Wang, H.; Ye, R.; Han, Z.; Xu, J.; Hong, J.

10.1101/2025.11.02.686180 — biochemistry — Posted on 2025-11-04

4925 Century-old ethanol-preserved Vega Collection reveal the unexpected phylogeography of Slender bitterling Tanakia lanceolata in Japan

Tsuchiyama, K.; Kawase, S.; Takigawa, Y.; Fujita, T.; Hosoya, K.; Kitamura, J.-i.; Mishina, T.

10.1101/2025.11.02.686072 — evolutionary biology — Posted on 2025-11-04

4926 Uncovering Fusarium species diversity, distribution and pathogenicity associated with cotton-corn rotation fields in recently expanded cotton-growing areas of the Northern High Plains of Texas

Khaliq, I.; Anderson, N.

10.1101/2025.07.02.662791 — ecology — Posted on 2025-11-04

4927 What kind of birds are more susceptible to avian malaria? A global analysis based on interpretable machine learning approach

Wang, X.; Mishra, S.; Dong, L.

10.1101/2025.11.02.686156 — ecology — Posted on 2025-11-04

4928 High-throughput functional characterization of enhancers in totipotent-like cells

Yang, L.; Peng, T.; Zhu, Y.; Zhai, X.; Huang, B.; Li, L.; Zhang, T.; Chen, J.; Liang, D.; He, J.; Zhang, M.

10.1101/2025.11.03.686172 — developmental biology — Posted on 2025-11-04

4929 Mitotic bypass and endocycling promote cancer cell survival after genotoxic chemotherapy

Truskowski, K.; Rolle, L.; Butler, G.; Yang, M. E.; Pienta, K. J.; Amend, S. R.

10.1101/2025.11.03.686258 — cell biology — Posted on 2025-11-04

4930 Infant gut microbiota in multi-child families converges with adults without a sibling-specific signature

Hanski, E.; Ponsero, A. J.; Kolho, K.-L.; de Vos, W. M.; Salonen, A.

10.1101/2025.10.31.685886 — microbiology — Posted on 2025-11-04

4931 Synergistic short-term synaptic plasticity mechanisms for working memory

Fiebig, F.; Chrysanthidis, N.; Lansner, A.; Herman, P. A.

10.1101/2025.05.07.652583 — neuroscience — Posted on 2025-11-04

4932 Population genomic structure of sorghum landraces across landscape, environment and culture

Vasquez Cerda, E. E.; Bellis, E. S.; Das, A.; Slayton, E. R.; Morris, G. P.; Lasky, J. R.

10.1101/2025.11.02.686151 — plant biology — Posted on 2025-11-04

4933 Adeno-associated virus (AAV)-TBX18 does not generate biological pacemaker activity, unlike AAV-Hcn2

Wang, J.; Rivaud, M. R.; Klerk, M.; Boender, A. R.; Visser, R. N.; Sparrius, R.; Lee, H. Y.; van Duijvenboden, K.; Yang, Y.; Kramer, E. J. M.; Park, K. H.; Park, L. C.; Schrödel, S.; Thirion, C.; Ehrke-Schulz, E.; Ehrhardt, A.; Kirzner, O. F.; Neef, K.; Tan, H. L.; Verkerk, A. O.; Christoffels, V. M.; Boink, G. J. J.

10.1101/2025.09.11.672351 — physiology — Posted on 2025-11-04

4934 Possible Synergistic Modulation of Hormonal Balance and Ovarian Structure by Clomiphene Letrozole Co-Administration in a Rodent Model of Hyperandrogenism

Onaolapo, O.; Aworinde, O.; Olufemi-Aworinde, K. J.; Onaolapo, A. Y.

10.1101/2025.11.02.686116 — pharmacology and toxicology — Posted on 2025-11-04

4935 A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales

Gros, A.; Vanaret, J.; Dunsing-Eichenauer, V.; Rostan, A.; Roudot, P.; Lenne, P.-F.; Guignard, L.; Tlili, S.

10.1101/2024.08.13.607832 — biophysics — Posted on 2025-11-04

4936 Integrative analysis of genomic and transcriptomic data informs precancer progression in the pancreas

Noller, K.; Lai, J.; Lesperance, D.; Adkins, R. S.; Elhossiny, A.; Guerrero, P. A.; Rajapakshe, K. I.; Maitra, A.; Giglio, M.; Mahurkar, A.; White, O.; Pasca di Magliano, M.; Ochs, M. F.; Kagohara, L. T.; Wood, L. D.; Karchin, R.; Fertig, E. J.

10.1101/2025.11.03.686234 — bioinformatics — Posted on 2025-11-04

4937 Structure-Based Pharmacophore Modeling, High-throughput Screening, and Molecular Dynamics Identify a Novel DrugBank-Derived HIV-1 Protease Inhibitor

Khazaal Nazal, A. S.; Rashid Alrashedi, A. M.; Risan Al-Iessa, L. A.; Ali Rabeea, M. A. H.

10.1101/2025.11.02.686148 — bioinformatics — Posted on 2025-11-04

4938 Machine Learning Driven Simulations of the SARS-CoV-2 Fitness Landscape from Deep Mutational Scanning Experiments

Durumeric, A. E. P.; McCarty, S.; Smith, J.; Koehler, J.; Elez, K.; Raich, L.; Suriana, P. A.; Sztain, T.

10.1101/2024.09.20.614179 — bioinformatics — Posted on 2025-11-04

4939 Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy

Gong, C.; Affatato, P.; Fay, M.; Guttikonda, S. R.; O'Connor, N. J.; Noble, E.; Heal, M.; Haydock, B.; Mapa, R.; De La Cruz, E. D.; Kowalko, J. E.; Tosches, M. A.; Gerfen, C. R.; Hen, R.; Makinson, C. D.; Hibshoosh, H.; Glaser, J.; Tomer, R.

10.1101/2025.11.02.685475 — bioengineering — Posted on 2025-11-04

4940 WITHDRAWN: α-SMA/VCAM-1 Dual-Targeted Nanoplatform Improves Drug Release and Therapeutic Efficacy in Liver Fibrosis

Bennett, O. J.; Hughes, C. M.; Anderson, L. R.; Foster, A. K.; Clarke, H. T.

10.1101/2025.09.01.673607 — bioengineering — Posted on 2025-11-04

4941 Evolutionary remodeling of the ventral retina enables aerial vision in the four-eyed fish Anableps anableps

Perez, L.; Shi, L.; Daspit, A.; Pruett, K.; Smith, C.; Prideaux, A.; Sousa, J. F.; Schneider, P.

10.1101/2025.11.02.686143 — evolutionary biology — Posted on 2025-11-04

4942 Accessing Meaning During Encoding Shapes Subsequent Memory Reactivation in the Brain

Qi, X.; Coutanche, M. N.

10.1101/2025.11.02.686134 — neuroscience — Posted on 2025-11-04

4943 Network modularity reveals context and state-dependent reorganization of time-varying functional connectivity in single-cell resolved neural activity recordings

Moon, S.; Liang, J.; Lee, H. J.; Maalouf, A.; Yu, Z.; Moza, S.; Zhang, Y.; Lu, H.

10.1101/2025.11.02.686048 — neuroscience — Posted on 2025-11-04

4944 Dormant viral pathways underlie space-induced neural senescence: a neuroprotective strategy for spaceflight and neurological diseases

Martins, A. M.; Nakashima, H.; Macia, A.; Umeyama, T.; Miyashita, S.; Nascimento, L. L.; Coelho, L. B.; Mesci, P.; Viirre, E.; Suarez, N.; Saleh, A.; Savchenko, A.; Freitas, B.; Leite, A. L.; Assis, D. M.; Ishizu, M.; Owa, T.; Hoshino, M.; Yates, J. R.; Nakashiima, K.; Muotri, A. R.

10.1101/2025.11.02.686043 — neuroscience — Posted on 2025-11-04

4945 A proteomic analysis of the PHF-forming tau fragment (tau297-391) following uptake into differentiated human neuronal SHSY5Y cells

Copsey, A.; Oakley, S.; Maina, M. B.; Marshall, K. E.; Harrington, C.; Storey, J.; WISCHIK, C. M.; Serpell, L.

10.1101/2025.11.03.684805 — cell biology — Posted on 2025-11-04

4946 RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcription

Budinich, K. A.; Yao, X.; Gong, C.; Song, L.; Wang, X.; Lee, M. C.; Mathias, K. M.; Li, Q.; Tang, S.; Liu, Y.; Nguyen, S. C.; Joyce, E. F.; Li, Y.; Li, H.; Wan, L.

10.1101/2025.07.29.665963 — molecular biology — Posted on 2025-11-04

4947 Trypanosomes Modulation of Motility from Swimming to Threading Propulsion in Confined Environments

Jamshidi Khameneh, N.; Krüger, T.; Nienaltowski, P.; Emery, Y.; Fedosov, D.; Polin, M.; Engstler, M.

10.1101/2025.11.03.686241 — microbiology — Posted on 2025-11-04

4948 Dual Preconditioned Mesenchymal Stem Cells-Derived Culture Conditioned Media Augment Immunomodulation and Drive Metabolic Reprogramming in Acute Graft-versus-Host Disease

Mendiratta, M.; Mendiratta, M.; Rai, S.; Gupta, R.; Bakhshi, S.; Dadhwal, V.; Pushpam, D.; Malik, P. S.; Pramanik, R.; Aggarwal, M.; Gupta, A. K.; Dhawan, R.; Seth, T.; Mahapatra, M.; Nayak, B.; Singh, T. D.; Singla, S. K.; Mir, R. A.; Malhotra, L.; Bandyopadhyay, S.; Hariprasad, G.; Prakash, H.; Mohanty, S.; Sahoo, R. K.

10.1101/2025.11.02.686182 — immunology — Posted on 2025-11-04

4949 Visual Field Inhomogeneities and the Architectonics of Early Visual Cortex shape Visual Working Memory

Papiernik-Kłodzinska, J.; Del Pin, S. H.; Sandberg, K.; Wierzchon, M.; Carrasco, M.; Rutiku, R.

10.1101/2025.05.13.653695 — neuroscience — Posted on 2025-11-04

4950 How tp1, an indirect wing steering muscle, stabilizes Drosophila's flight

Teoh, H. K.; Biswas, D.; Leung, A.; Ludlow, B. K.; Whitehead, S. C.; Ehrhard, E.; Dickinson, M. H.; Beatus, T.; Cowan, N.; Cohen, I.

10.1101/2025.11.02.686144 — neuroscience — Posted on 2025-11-04

4951 mTOR pathway gene knockout results in mTOR-dependent cellular aggregation

Roark, K. M.; Crino, P. B.; Iffland, P. H.

10.1101/2025.11.02.685388 — neuroscience — Posted on 2025-11-04

4952 Phospho-eIF2B-epsilon links stress response-driven translation to amyloidogenesis in Alzheimer's disease

Fanlo-Ucar, H.; Planas-Clopes, C.; Bagudanch, O.; Pardo, C.; Troncoso, S.; Alvarez, A.; Oliva, B.; Munoz, F. J.

10.1101/2025.11.03.686297 — neuroscience — Posted on 2025-11-04

4953 Investigating the Influence of Anti-Seizure Medications on Aperiodic EEG Activity

Holden, M. M.; Premoli, I.; Clark, S. R.; Richardson, M. P.; Goldsworthy, M. R.; Rogasch, N. C.

10.1101/2025.11.02.686141 — neuroscience — Posted on 2025-11-04

4954 Hypoxia-induced regulation of zDHHC23 opens avenues for new biomarkers for NON MYCN-amplified neuroblastoma

Oswald, S. O.; Daly, L. A.; Clarke, K.; Brownridge, P. J.; Pizer, B.; Prior, I.; See, V.; Eyers, C. E.

10.1101/2025.11.03.686197 — neuroscience — Posted on 2025-11-04

4955 Activity drives local CaMKII synthesis and subcellular localization via autophosphorylation-dependent pathways

Clements, K. J.; Chen, N.; Gonzalez, K. M. D. L.; Zhang, Y.; Rodal, A. A.; Griffith, L.

10.1101/2025.11.03.686364 — neuroscience — Posted on 2025-11-04

4956 Conservation and divergence of UVR8-COP1/SPA-HY5 signaling in UV-B responses of Marchantia polymorpha

Liang, Y.; Podolec, R.; Chappuis, R.; Defossez, E.; Glauser, G.; Rötzer, J.; Stolze, S. C.; Dolan, L.; Nakagami, H.; Demarsy, E.; Ulm, R.

10.1101/2025.07.16.665153 — plant biology — Posted on 2025-11-04

4957 AAV6-HCN4t-mediated biological pacing as a potential life-saving therapy for congenital complete heart block

Wang, J.; Birza, E. E.; Meijborg, V. M. F.; Verkerk, A. O.; Cervera-Barea, A.; Jonker, T.; Visser, R. N.; Sparrius, R.; Klerk, M.; Boender, A. R.; Yang, Y.; Kramer, E. J. M.; Kwak, G.; Park, K. H.; Park, L. C.; Visser, J.; Jansen, M. S.; Schrödel, S.; Mishra, M.; Thirion, C.; Sluijter, J. P. G.; de Jager, S. C. A.; Neef, K.; Blom, N. A.; Haak, M. C.; Kirzner, O. F.; Tan, H. L.; Christoffels, V. M.; Boink, G. J. J.

10.1101/2025.07.31.666254 — physiology — Posted on 2025-11-04

4958 Model-based EEG phenotyping uncovers distinct neurocomputational mechanisms underlying learning impairments across psychopathologies

Ging-Jehli, N. R.; Rac-Lubashevsky, R.; Bera, K.; Roberts, A.; Loder, A.; Boudewyn, M. A.; Carter, C. S.; Erickson, M. A.; Gold, J. M.; Luck, S. J.; Ragland, J. D.; Yonelinas, A. P.; MacDonald, A. W.; Barch, D. M.; Frank, M. J.

10.1101/2025.11.01.685815 — pathology — Posted on 2025-11-04

4959 Suppression of Glucosylceramide Synthase Reverses Drug Resistance in Cancer Cells Harbor Homozygous p53 Mutants

Mostaq, M. S.; Amin, M. N.; Raphael, A.; Asbury, C.; Gupta, A.; Gu, X.; Han, X.; Sekulic, D.; Michchalak, P.; Kang, L.; Liu, Y.-Y.

10.1101/2025.11.02.686136 — cancer biology — Posted on 2025-11-04

4960 IMMUNIA: A Multi-LLM Reasoning Agent for Immunoregulatory Surfaceome Discovery

Park, N.; Lee, J. H.

10.1101/2025.11.02.686138 — cancer biology — Posted on 2025-11-04

4961 The transcriptional regulatory circuit as a driver and therapeutic target in CML blast crisis

Jiang, L.; Lou, E.; Fang, J.; Jiang, L.; Peng, G.; Chen, J.; Liu, B.; Lu, B.; Meng, Y.; Zhang, H.; Liu, A.; Mao, Q.; Lai, P.; Zheng, Y.; Liu, J.; Shi, X.

10.1101/2025.11.02.686161 — cancer biology — Posted on 2025-11-04

4962 Lamin B1 Safeguards the B Cell Genome and Shapes Lymphoma Outcome

Filipsky, F.; Chapman, K. B.; Bloehdorn, J.; Wang, J.; Gribben, J.; Hausmann, M.; Cremer, C.; Braun, A.; Crespi Sallan, M.; Klymenko, T.

10.1101/2025.11.03.686246 — cancer biology — Posted on 2025-11-04

4963 p53-induced RNA-binding protein ZMAT3 inhibits transcription of a hexokinase to suppress mitochondrial respiration

Kumar, R.; Couly, S.; Muys, B. R.; Li, X. L.; Grammatikakis, I.; Singh, R.; Guest, M.; Wen, X.; Tang, W.; Ambs, S.; Jenkins, L. M.; Pehrsson, E. C.; Chari, R.; Su, T.-P.; Lal, A.

10.1101/2025.05.12.653341 — cancer biology — Posted on 2025-11-04

4964 AutoLead: An LLM-Guided Bayesian Optimization Framework for Multi-Objective Lead Optimization

Zhang, Y.; Choong, J. j.; Madhawa, K.; Ozawa, K.

10.1101/2025.08.19.671029 — bioinformatics — Posted on 2025-11-04

4965 Machine Learning Analysis of Cilia-Driven Particle Transport Distinguishes Primary Ciliary Dyskinesia Cilia from Normal Cilia

Hadas, N.; Xu, H.; Neupane, S.; Twan, W. K.; Elgamal, A.; Horani, A.

10.1101/2025.11.02.686130 — bioinformatics — Posted on 2025-11-04

4966 Chemical mechanism of allosteric and asymmetric dark reversion in a bacterial phytochrome uncovered by cryo-EM.

Bodizs, S. A.; Fischer, A.-L. M.; Cervenak, M.; Prodhan, S.; Maj, M.; Westenhoff, S.

10.1101/2025.08.21.671592 — biochemistry — Posted on 2025-11-04

4967 Combinatorial multiomic analysis from a pedigree of Sox10Dom Hirschsprung mice implicates Dach1 as a modifier of Enteric Nervous System development

Benthal, J. T.; Avila, J. A.; Smith, J. R.; Southard-Smith, E. M.

10.1101/2025.11.02.686123 — genomics — Posted on 2025-11-04

4968 Single Nucleus MultiOmics and In Vivo Massively Parallel Reporter Assays Identify Functional Sex-Biased Enhancers Linked to Liver Metabolism and Disease

Chang, T.-y.; Waxman, D. J.

10.1101/2025.11.02.686175 — genomics — Posted on 2025-11-04

4969 MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart

Kern, C.; Zhang, Q.; Lu, Y.; Eschbach, J.; Zeng, Z.; Farah, E. N.; Tai, C.-Y.; Yang, K.; Jenie, I.; Yao, F.; Zhao, Z.; Ma, Q.; Padilla, C. G.; Monell, A.; Moghadami, S.; Zhu, F.; Li, B.; Hou, A.; Tucker, G.; Ellison, D.; Chi, N. C.; Qiu, X.; Zhu, Q.; Bintu, B.

10.1101/2025.11.02.686137 — genomics — Posted on 2025-11-04

4970 BAP1 deletion in hepatocytes primes an inflammatory transcriptional response

Nenad, W. C.; Kuhlers, P.; Sturgill, I. R.; Biju, I.; Bucklan, M.; Hernandez, L.; Zhu, L.-C.; Hoadley, K.; Raab, J.

10.1101/2025.10.31.685807 — genetics — Posted on 2025-11-04

4971 Environmental filtering shapes patch dynamics across isolated mesophotic reefs

Pittoors, N. C.; Tweedt, S. M.; McCartin, L. J.; Vohsen, S. A.; Lopera, L.; Mihalek, S.; Lai, J.; Durkin, K. M.; Weigt, L.; Nuttall, M. F.; Bracco, A.; Meyer, C. P.; Herrera, S.

10.1101/2025.11.02.686126 — ecology — Posted on 2025-11-04

4972 INDITEK-2.0: A Bayesian inverse eco-evolutionary modelling framework for reconstructing Phanerozoic biodiversity

Cermeno, P.; Garcia-Comas, C.; Herrero Gascon, G.; Benton, M. J.; Bodin, T.; Gurung, K.; Mills, B.; Pohl, A.

10.1101/2025.08.22.671786 — ecology — Posted on 2025-11-04

4973 Spatiotemporal control of PIWI compartmentalization by mitochondrial scaffolds defines pachytene piRNA pathway organization

Wei, C.; Yan, X.; Mann, J. M.; Shang, G.; Wang, Q.; Xie, H.; Demireva, E. Y.; Sun, L.; Ding, D.; Chen, C.

10.1101/2025.11.02.684826 — developmental biology — Posted on 2025-11-04

4974 Redistribution of sidechain-sidechain interactions govern ligand-specific binding affinity changes in missense Shank1 PDZ mutants

Santa, A.; Kalman, Z. E. E.; Nagy-Kanta, E.; Gaspari, Z.; Peterfia, B.

10.1101/2025.07.03.662971 — molecular biology — Posted on 2025-11-04

4975 Quorum sensing antiactivators constrain Pseudomonas aeruginosa RhlR activity

Sridhar, V.; Smalley, N. E.; Dandekar, A. A.; Asfahl, K. L.

10.1101/2025.10.31.685934 — microbiology — Posted on 2025-11-04

4976 E3 ubiquitin ligase SKP2 limits autophagy during S. aureus infection

Singh, A. K.; Baglanova, M.; Topfstedt, E.; Surmann, K.; Holtfreter, S.; Lammers, M.; Bröker, B. M.; Becker, K.; Cammann, C.; Seifert, U.

10.1101/2025.11.03.686196 — microbiology — Posted on 2025-11-04

4977 Growth of Corynebacterium glutamicum on 5-oxo-L-proline (pyroglutamate) as carbon and nitrogen source requires the PxpR-controlled pxpTABC genes

Sundermeyer, L.; Mack, C.; Bott, M.

10.1101/2025.10.30.685629 — microbiology — Posted on 2025-11-04

4978 Post-infection pig and ferret antisera show similar antigenic profiles for human influenza A(H1N1pdm09) viruses

Harvey, R.; Cayol, T.; Paudyal, B.; Lilley, A.; Carr, C.; Hatton, C.; Briggs, E.; Daniels, R. S.; Richardson, S.; Peacock, T. P.; Lewis, N. S.; Brown, I.; Mccauley, J.; Tchilian, E.

10.1101/2025.10.30.685573 — immunology — Posted on 2025-11-04

4979 Perceptual Decoys Do Not Reliably Bias Choice: Boundary-Condition Evidence

Ibarra, D.; Suri, G.

10.1101/2025.11.02.686051 — neuroscience — Posted on 2025-11-04

4980 Maternal n-3 PUFA deficiency alters brain fatty acid and oxylipin profiles across perinatal development in offspring

Marchaland, F.; Martinat, M.; Di Miceli, M.; Gregoire, S.; Rossitto, M.; Morel, L.; Aubert, A.; Sere, A.; Delpech, J.-C.; Joffre, C.; Acar, N.; Bazinet, R. P.; Laye, S.

10.1101/2025.11.02.686109 — neuroscience — Posted on 2025-11-04

4981 Non-invasive in vivo acoustoelectric neuromodulation and its contribution to ultrasound stimulation

Rintoul, J. L.; Butler, C.; Cleveland, R. O.; Grossman, N.

10.1101/2025.11.02.685597 — neuroscience — Posted on 2025-11-04

4982 Robust dual dynamics of ictogenesis in temporal lobe seizures in vivo

Mashiel, A.; Achvat, S.; Schiller, Y.

10.1101/2025.11.02.686119 — neuroscience — Posted on 2025-11-04

4983 Alzheimer's Disease Risk Variants Interact with Amyloid-beta to Modulate Monocyte Function

Chatila, Z. K.; Bradshaw, E. M.

10.1101/2025.11.02.686117 — neuroscience — Posted on 2025-11-04

4984 Investigation of Neurons and Microglia from APOE3 Induced Pluripotent Stem Cells using Data-Independent Acquisitions on a ZenoTOF 7600

Burton, J. B.; McHugh, T.; Schurman, C. A.; Bons, J.; Ellerby, L.; Schilling, B.

10.1101/2025.11.02.686128 — neuroscience — Posted on 2025-11-04

4985 New topologies in the unfolding of the Doubly DegenerateTakens-Bogdanov singularity

Saggio, M.

10.1101/2025.11.02.686129 — neuroscience — Posted on 2025-11-04

4986 Phenotypic heterogeneity in lag reflects an evolutionarily stable bet-hedging strategy

George, A. V.; Wingreen, N. S.; Reddy, G.

10.1101/2025.11.02.686100 — systems biology — Posted on 2025-11-04

4987 Aggressive nitrogen assimilation during exponential growth in Chlamydomonas reinhardtii

Tibule, M.; Mallawarachchi, W.; Oyateru, O.; Ziaeian, M.; Kim, M.; Dharmasiri, H. N.; Lee, J.-H.

10.1101/2025.11.02.686124 — plant biology — Posted on 2025-11-04

4988 Pre-implantation non-steroidal anti-inflammatory drug treatment disrupts mouse embryo spacing and post-implantation chamber morphogenesis

Massri, N.; LaBuda, S. E.; Oltean, M.; Arora, R.

10.1101/2025.11.02.686054 — physiology — Posted on 2025-11-04

4989 Longitudinal Imaging of the Premalignant Tumor Microenvironment Reveals Transient Myeloid States Predictive of Tumor Fate

Madsen, T. D.; Chen, D.; Maria, H.; Hammoudeh, S.; Heydecker, M.; Chen, E.; Abu-Elnaj, S.; Kedei, N.; Wang, W.; Weigert, R.

10.1101/2025.11.02.686127 — cancer biology — Posted on 2025-11-04

4990 Spatio-temporal Patterns of T Cell Traction Forces Depend on Stimulation and Cell Subtype

Mustapha, F.; Biarnes-Pelicot, M.; Torro, R.; El Husseiny, J.; Sengupta, K.; Puech, P.-H.

10.1101/2022.02.11.480084 — biophysics — Posted on 2025-11-04

4991 Single-cell analysis of the human retina reveals stage-linked microglial states and neural-immune circuit rewiring in diabetic retinopathy

Yang, L.; Lin, S.; Tao, Y.; Pan, Q.; Cai, T.; Ye, Y.; Liu, J.; Zhou, Y.; Yi, Q.; Lu, Z. H.; Chen, L.; McKay, G.; Rankin, R.; Shao, Y.; Meng, W.

10.1101/2025.02.07.637193 — bioinformatics — Posted on 2025-11-04

4992 GeneScanner: profiling genetic variation across bacterial populations

Kobras, C. M.; Ko, S.; Raikwar, P. S.; Sanjuan, B. A.; Jolley, K. A.; Sheppard, S. K.

10.1101/2025.11.02.685864 — bioinformatics — Posted on 2025-11-04

4993 Maternal-fetal inflammation affects Cdh1/E-cadherin epigenetic regulation and craniofacial development

Nani, D.; Alvizi, L.; Bueno, H. M. S.; Lacerda, E. C. M.; Passos-Bueno, M. R.

10.1101/2025.09.27.676141 — developmental biology — Posted on 2025-11-04

4994 A non-human primate model of Amyotrophic Lateral Sclerosis

Jones, R. H. A.; Saieva, L.; Balezeau, F.; Schofield, I.; McCardle, C.; Baker, M. R.; Baker, S. N.

10.1101/2025.10.27.684759 — neuroscience — Posted on 2025-11-04

4995 Precision cutaneous stimulation in freely moving mice

Parkes, I.; Schorscher-Petcu, A.; Gan, Q.; Browne, L. E.

10.1101/2024.08.06.606618 — neuroscience — Posted on 2025-11-04

4996 Comprehensive Atlas of Cancer-Type-Specific Molecular Features from Comparative Analysis of TCGA Data

Tung, Y.-G.

10.1101/2025.10.26.684620 — cancer biology — Posted on 2025-11-04

4997 CD38hiCD19dim cells in lymph nodes predict favorable prognosis in patients with stage III melanoma receiving adjuvant PD-1-blockade

Ailte, I.; Chauhan, S. K.; Prasmickaite, L.; Bassarova, A. V.; Poissonnier, A.; Feenstra, M.; Nyakas, M.; Johannessen, B.; Ryder, T.; Hermann, R.; Frich, L.; Holth, A.; Inderberg, E. M.; Jespersen, H.; Florenes, V. A.; Kyte, J. A.; Maelandsmo, G. M.; Egeland, E. V.

10.1101/2025.11.03.685725 — cancer biology — Posted on 2025-11-04

4998 Quantitative Calibration of a Spatial QSP Model Identifies Fibroblast Impact on HCC Immunotherapy

Zhang, S.; Wang, H.; Cho, Y.; Wong, W.; Yarchoan, M.; Jaffee, E. M.; Ho, W. J.; Kagohara, L. T.; Fertig, E. J.; Popel, A. S.; Deshpande, A.

10.1101/2025.10.31.685939 — bioinformatics — Posted on 2025-11-04

4999 Data-Driven Symbolic Higher-Order Epistasis Discovery with Kolmogorov-Arnold Networks

Patil, O. R.; Shazand, K.; Marteau, B.; Shen, Y.; Wang, M. D.

10.1101/2025.10.31.685894 — genomics — Posted on 2025-11-04

5000 Thresholds of drought and terrain complexity shape biomasspatterns in South America's Caatinga

Lozado, B. S.; de Oliveira, C. P.; de Paula, A.; Barreto-Garcia, P. A. B.; Lemos, O. L.; Pereira, A. L. L.; Silva, E. A.; Ferreira, R. L. C.; da Silva, J. A. A.; Pareyn, F.; Moonlight, P. W.; Cardoso, D.; Veenendaal, E.; de Queiroz, L. P.; Rodrigues, P. M. S.; dos Santos, R. M.; Sarkinen, T.; Pennington, T.; Phillips, O. L.; de Lima, R. B.

10.1101/2025.11.02.684225 — ecology — Posted on 2025-11-04

5001 Transcranial direct current stimulation of the supplementary motor area modulates behavioral and peripheral electrophysiological measures of motor preparation.

Kumar, A.; Murthy, A.

10.1101/2025.10.31.685710 — neuroscience — Posted on 2025-11-04

5002 Distractor suppression operates exclusively in retinotopic coordinates

Ilksoy, Y. A.; van Moorselaar, D.; Wang, B.; Los, S. A.; Theeuwes, J.

10.1101/2024.02.01.578407 — neuroscience — Posted on 2025-11-04

5003 Human parainfluenza virus infection remodels the host cell glycome

Das, P. K.; Dirr, L.; Bailly, B.; Guillon, P.; Everest-Dass, A.; von Itzstein, M.

10.1101/2025.06.15.659808 — microbiology — Posted on 2025-11-03

5004 Cross-dataset evaluation of deep learning models for plant pest and disease diagnosis

Sun, J.

10.1101/2024.10.07.617111 — plant biology — Posted on 2025-11-03

5005 Chronic delivery of buprenorphine during abstinence decreases incubation of heroin seeking and neuronal activation in medial prefrontal cortex and striatum in male and female rats

Bossert, J.; Caldwell, K.; Bonbrest, H.; Pishgar, M.; Patil, R.; Madangopal,, R.; Wang, H.; Shaham, Y.

10.1101/2025.09.20.677438 — neuroscience — Posted on 2025-11-03

5006 Temporal and cell-type specific SPAK-NKCC1 disruption following severe TBI in the developing gyrencephalic brain.

Hochstetler, A. E.; Courtney, Y.; Oloko, P.; Baskin, B.; Ding-Su, A.; Stinson, T.; McGuone, D.; Haynes, R.; Lehtinen, M. K.; Costine-Bartell, B. A.

10.1101/2025.01.20.633889 — neuroscience — Posted on 2025-11-03

5007 Mitochondrial uncoupler BAM15 improves skeletal muscle function and mitochondrial respiration in Sarcopenia

Campelj, D. G.; Philp, A. M.; Ritenis, E. J.; Padilha, C. S.; Alldritt, I.; Sligar, J.; Cree, T.; Alexopoulos, S. J.; Santos, W. L.; Joanisse, S.; Coen, P. M.; Hoehn, K. L.; Philp, A.

10.1101/2025.10.30.685477 — physiology — Posted on 2025-11-03

5008 ProCyon: A multimodal foundation model for protein phenotypes

Queen, O.; Huang, Y.; Calef, R.; Giunchiglia, V.; Chen, T.; Dasoulas, G.; Tai, L.; Abbadessa, G.; Howell, O.; Ektefaie, Y.; Noori, A.; Farkas, I.; Brown, J.; Cobley, T.; Hrovatin, K.; Hartvigsen, T.; Theis, F.; Pentelute, B. L.; Zou, J.; Khurana, V.; Owen, D. R.; Nicholas, R.; Kellis, M.; Zitnik, M.

10.1101/2024.12.10.627665 — bioinformatics — Posted on 2025-11-03

5009 EpiBlot: Joint Mapping of Chromatin Accessibility and Targeted Proteomics in HER2-expressing Breast Cancer Systems

Fomitcheva Khartchenko, A.; Lam, T.; Goldhammer, N.; Bont, M.; Warhadpande, S.; Rosenbluth, J.; Herr, A.

10.1101/2025.09.25.678463 — bioengineering — Posted on 2025-11-03

5010 Decode-gLM: Tools to Interpret, Audit, and Steer GenomicLanguage Models

Maiwald, A.; Jedryszek, P.; Draye, F.; Morris, G. M.; Crook, O. M.

10.1101/2025.10.31.685860 — genomics — Posted on 2025-11-03

5011 Small phytoplankton community composition cycles annually with a coastal bloom

Stevens, B. L. F.; Gast, R. J.; Peacock, E. E.; Girdhar, Y. A.; Neubert, M. G.; Sosik, H. M.

10.1101/2025.09.15.675855 — ecology — Posted on 2025-11-03

5012 ANTIPODE Provides a Global View of Cell Type Homology and Transcriptomic Divergence in the Developing Mammalian Brain

Schmitz, M. T.; Ding, J. W.; Nolbrant, S.; McMullen, R.; Kim, C. N.; Pavlovic, B. J.; Nowakowski, T. J.; Bakken, T. E.; Ye, C. J.; Pollen, A. A.

10.1101/2025.10.18.683238 — developmental biology — Posted on 2025-11-03

5013 Dynamic profiling of the aggresome processing pathway

Ghosh, S.; Wang, L.; Hess, D.; lesmantavicius, V.; Englinger, J.; Cao, C.; Matthias, G.; Seebacher, J.; Matthias, P.

10.1101/2025.10.30.684516 — molecular biology — Posted on 2025-11-03

5014 Kidney-specific Wdr72 deletion leads to incomplete distal renal tubular acidosis through impaired V-ATPase B1 subunit localization

Al-Shebel, A.; Mossmann, P.; Wendlinge, S.; Breiderhof, T.; Kaminski, M. M.; Müller, D.; Bufler, P.; Klämbt, V.

10.1101/2025.10.29.684588 — molecular biology — Posted on 2025-11-03

5015 Precision Prediction of Microbial Ecosystem Impact on Host Metabolism Using Genome-Resolved Metagenomics

Mohssen, M.; Zayed, A. A.; Kigerl, K. A.; Du, J.; Smith, G. J.; Schwab, J. M.; Sullivan, M. B.; Popovich, P. G.

10.1101/2025.06.27.661827 — microbiology — Posted on 2025-11-03

5016 The Stenotrophomonas maltophilia MntR miniregulon includes novel extracytoplasmic components and affects replication in Acanthamoeba castellanii phagosomes

Argueta-Zepeda, F.-S.; Rivera, J.; Valerdi-Negreros, J. C.; Rensing, C.; Vinuesa, P.

10.1101/2025.10.14.682371 — microbiology — Posted on 2025-11-03

5017 Global Landscape of Human Kinase Motifs in Viral Proteomes

Alba, K.; Winters, D. M.; Makanani, S. K.; Kaushal, P.; Delgado, Y.; Ashley, I. A.; Sharma, S.; Blanc, S. F.; Kim, E.; Yaron, T.; Johnson, J. L.; Selby, J.; Hur, M.; Ni, J.; Nguyen, J.; Lawson, M.; Wynn, E.; Lin, S.; Brent, M. H.; Yip, E.; Kassem, A.; Olwal, C. O.; Wohlschlegel, J.; Fregoso, O. I.; Wu, T.-T.; Li, M. M.; Bouhaddou, M.

10.1101/2025.06.02.657064 — microbiology — Posted on 2025-11-03

5018 Impaired IFNγ responsiveness of monocyte-derived lung cells limits immunity to Mycobacterium tuberculosis

Zheng, W.; Limberis, J. D.; Howard, Z. P.; Mohapatra, A.; Takagi, E.; Ernst, J. D.

10.1101/2025.10.06.680719 — immunology — Posted on 2025-11-03

5019 Multiarrangement: A Plug & Play Geometric Data CollectionPackage For Video Stimuli

Yıldız, U.; Ürgen, B. A.

10.1101/2025.10.17.683124 — neuroscience — Posted on 2025-11-03

5020 Potentiation of active locomotor state by spinal-projecting serotonergic neurons

Fenstermacher, S.; Vonasek, A.; Cavanagh, A.; Gattuso, H.; Chaimowitz, C.; Dymecki, S.; Jessell, T.; Dasen, J.

10.1101/2024.09.26.615260 — neuroscience — Posted on 2025-11-03

5021 Blue Light Promotes Root Iron Acquisition via a Shoot CRY-HY5 Signaling Module in Arabidopsis.

Jakhar, P.; Mankotia, S.; Ladhwal, S.; Bodh, N.; Dhanawat, K.; Pandey, A. K.; Satbhai, S. B.

10.1101/2025.11.02.686065 — plant biology — Posted on 2025-11-03

5022 Development alters genotype-environment interactions and shapes adaptation in Arabidopsis

Lawrence-Paul, E. H.; Janakiraman, J.; Lawrence-Paul, M. R.; Ben-Zeev, R.; Xu, Y.; Penn, A.; Lasky, J. R.

10.1101/2025.05.13.653704 — plant biology — Posted on 2025-11-03

5023 AnnotateAnyCell: Open-Source AI Framework for Efficient Annotation in Digital Pathology

Verma, S.; Malusare, A.; Wang, M.; Wang, L.; Mahapatra, A.; English, A. L.; Cox, A. D.; Broman, M.; de Brot, S.; Burcham, G.; Knapp, D.; Dhawan, D.; Sola, M.; Aggarwal, V.; Grama, A.; Lanman, N. A.

10.1101/2025.11.02.686114 — pathology — Posted on 2025-11-03

5024 GlomExtractor: a versatile tool for extracting glomerular patches from whole slide kidney biopsy images

Silva, M. B.; Besusparis, J.; Laurinavicius, A.; Leh, S.; Weishaupt, H.

10.1101/2025.11.02.686103 — pathology — Posted on 2025-11-03

5025 Slow spatial migration can help eradicate cooperative antimicrobial resistance in time-varying environments

Hernandez-Navarro, L.; Distefano, K.; Täuber, U. C.; Mobilia, M.

10.1101/2024.12.30.630406 — biophysics — Posted on 2025-11-03

5026 Slow Electromechanical Interference Links Division Geometry, Differentiation Bias, and Senescence-like Arrest

Bueno, A. D. M.

10.1101/2025.10.28.684574 — biophysics — Posted on 2025-11-03

5027 Cation-Cation Photosensitization for Protein Ligation and Intracellular Catalysis

Agarwal, V.; Pham, H.; Bartko, S. G.; Taylor, M. T.

10.1101/2025.11.03.686045 — biochemistry — Posted on 2025-11-03

5028 Regioselective biosynthesis of oligoamides as precursors for sequence-controlled co-polyamides

Qian, L.; Dishner, I.; Capra, N.; Carper, D.; Ogbonna, N.; Kertesz, V.; Cahill, J.; Foster, J.; Michener, J. K.

10.1101/2025.11.03.685623 — biochemistry — Posted on 2025-11-03

5029 Choice history biases evidence accumulation: a cross-species comparison from humans to mice

Fernandez, K.; Fengler, A.; Urai, A. E.

10.1101/2025.08.22.671879 — animal behavior and cognition — Posted on 2025-11-03

5030 Correlated Gene Copy Number Changes in a Seminal Fluid Protein Network in Drosophila

Carlisle, J. A.; McCormick, B. K.; Verbakel, L.; von Philipsborn, A. C.; Wolfner, M. F.; Clark, A. G.

10.1101/2025.10.27.684572 — evolutionary biology — Posted on 2025-11-03

5031 AXIS: A Lab-in-the-Loop Machine Learning approach for generalized detection of macromolecular crystals.

Personnaz, A.; Sung, S.; Bourgeas, R.; Sunni, S.; Dupeux, F.; Adediran, B.; Barbosa, R.; Humm, A.-S.; Colaco-Osorio, E.; Marquez, J. A.

10.1101/2025.11.03.685844 — molecular biology — Posted on 2025-11-03

5032 Coordination of membrane synthesis with cell growth: localization of the Escherichia coli phospholipid synthesis enzyme PlsB responds to membrane abundance in a manner consistent with filamentation-mediated inhibition

Beije, J.; Fierlier, D.; Guurink, M.; Stapert, A.; Zoumaru-Djayoon, A.; Bokinsky, G.

10.1101/2025.11.03.685888 — microbiology — Posted on 2025-11-03

5033 The coronavirus envelope is conserved, contains bioactive lipids needed for replication, and is modulated in response to host inflammation

Tyrrell, V.; Zaragkoulias, A.; Powell, W.; Elfar, M.; Grossoni, V.; Monaco, F.; Protty, M.; Stenhouse, E.; Heyman, J.; Costa, D.; Roche, L.; Lynch, C.-A. B.; Ghazal, P.; Jones, S. A.; Lambeau, G. A.; Benatzy, Y.; Kandler, J.; Bojkova, D.; Snodgrass, R.; Brune, B.; Thomas, D.; Stanton, R.; O'Donnell, V.

10.1101/2025.11.03.686211 — immunology — Posted on 2025-11-03

5034 Ultra-High Field 31P functional Magnetic Resonance Spectroscopy Reveals NAD+ Dynamics in Brain Energy Metabolism during Visual Stimulation.

Kaiser, A.; Anvari Vind, F.; Duarte, J. M. N.; Jelescu, I. O.; Lin, Y.; Yu, X.; Widmaier, M.; Wenz, D.; Xin, L.

10.1101/2025.11.02.686085 — neuroscience — Posted on 2025-11-03

5035 Loss of the Parkinson's disease-associated protein DJ-1 impacts dopamine metabolism in astrocytes

Wagener, A.; Mayeen, N.; Mueller, S. A.; Tschirner, S. K.; Nuscher, B.; Mencke, P.; Lichtenthaler, S. F.; Boussaad, I.; Krueger, R.; Burbulla, L. F.

10.1101/2025.11.02.685006 — neuroscience — Posted on 2025-11-03

5036 Methionine Triggers Metabolic, Transcriptional, and Epigenetic Reprogramming in Arabidopsis Leaves

Yerushalmy, Y.; Dafni, M.; Rabach, N.; Hacham, Y.; Amir, R.

10.1101/2025.11.02.686087 — plant biology — Posted on 2025-11-03

5037 A functional map of CDK-drug interactions at single amino acid resolution

Gould, S. I.; Acosta, J.; Bielo, L. B.; Jaboldinov, A.; Johnson, G. A.; Contreras, M. E.; Wuest, A. N.; Bremont, E.; Toure, M. A.; Xiang, Y.; Kozicka, Z.; Hemann, M. T.; Koehler, A. N.; Chandarlapaty, S.; Rivera, F. J. S.

10.1101/2025.11.02.685764 — cancer biology — Posted on 2025-11-03

5038 Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Kretsch, R. C.; Posani, E.; Baulin, E. F.; Bujnicki, J. M.; Bussi, G.; Cheatham, T. E.; Chen, S.-J.; Elofsson, A.; Farsani, M. A.; Fisher, O. N.; Gromiha, M. M.; Gupta, A.; Hamada, M.; Harini, K.; Hu, G.; Huang, D.; Iwakiri, J.; Jain, A.; Kagaya, Y.; Kihara, D.; Kmiecik, S.; Krishnan, S. R.; Kurisaki, I.; Languin-Cattoen, O.; Li, J.; Li, S.; Malekzadeh, K.; Nakamura, T.; Ni, W.; Nithin, C.; Palo, M. Z.; Park, J. H.; Pilla, S. P.; Poblete, S.; Pucci, F.; Punuru, P.; Saha, A.; Sato, K.; Srivastava, A.; Terashi, G.; Tugolukova, E.; Verburgt, J.; Wuyun, Q.; Zerze, G. H.; Zhang, K.; Zhang, S.; Zhen

10.1101/2025.11.03.685595 — biophysics — Posted on 2025-11-03

5039 Transforming a Fragile Protein Helix into an Ultrastable Scaffold via a Hierarchical AI and Chemistry Framework

Qiu, J.; Tang, G.; Feng, T.; Zheng, B.; Liu, Y.; Zheng, P.

10.1101/2025.11.03.686355 — biophysics — Posted on 2025-11-03

5040 Ultraflexible, Biodegradable ECoG Arrays via Rapid Fabrication Enables High-Resolution Cortical Mapping and Seizure Network Classification In Vivo

Saleh, S.; Bakri, N.; Issa, K.; Badawi, H.; Al-Sadek, T.; El Jammal, R.; Awad, M.; Obeid, M.; Khraiche, M.

10.1101/2025.11.02.686028 — bioengineering — Posted on 2025-11-03

5041 MBOAT2 limits the amounts of PUFA in phosphatidylcholine of neonatal and dystrophic skeletal muscle and promotes muscle regeneration

Valentine, W. J.; Tokuoka, S. M.; Hashidate-Yoshida, T.; Yanagida, K.; Suzuki, T.; Inagaki, N. F.; Motohashi, N.; Nakano, K.; Okamura, T.; Kita, Y.; Shindou, H.; Aoki, Y.; Shimizu, T.

10.1101/2025.11.02.686003 — biochemistry — Posted on 2025-11-03

5042 Benchmarking enrichment and depletion methods for quantitative plasma proteomics in different plasma types and the correlation to clinical routine assays.

Kverneland, A.; Ostergaard, O.; Schmidt, L. M.; Johansen, M. O.; Thorsen, S. U.; Schmidt, R. F.; Christoffersen, C.; Olsen, J. V.

10.1101/2025.11.03.686186 — biochemistry — Posted on 2025-11-03

5043 Adaptive introgression from Pacific herring to Atlantic herring in the brackish Baltic Sea

Ferreira, M. S.; Felkel, S.; Fuentes-Pardo, A. P.; Goodall, J.; Wang, D.; Cocco, A.; Pettersson, M.; Andersson, L.

10.1101/2025.11.02.685776 — evolutionary biology — Posted on 2025-11-03

5044 Challenges and opportunities in detecting leaf water and carotenoid content across biomes from satellite multispectral indices

Montes-Bojorquez, M. G.; Robles-Zazueta, C. A.; Tinoco-Ojanguren, C.; Enquist, B. J.; Frazier, A. E.; Maitner, B. S.; Massaine Moulatlet, G.; Romo-Leon, J. R.; Song, L.; Hinojo-Hinojo, C.

10.1101/2025.11.01.686024 — ecology — Posted on 2025-11-03

5045 Niche dimensionality drives microbial community structure

Srinivasan, K.; Plata, G.; Dixit, P. D.

10.1101/2025.11.02.686095 — ecology — Posted on 2025-11-03

5046 Drought, thermal response and climate-patterning in cuticular conductance of the widespread C4 grass, Themeda triandra

Middha, A.; Jacob, V.; Lozano, A. C.; Warren, C.; Foo, E.; Choat, B.; Wright, I. J.

10.1101/2025.11.02.686155 — ecology — Posted on 2025-11-03

5047 Tracking the opening of spike crowns on the surface of coronaviruses

Wu, D.

10.1101/2025.11.02.686173 — microbiology — Posted on 2025-11-03

5048 Gram-positive bacterial cell wall components inhibit herpes simplex virus infection.

10.1101/2025.11.02.686169 — microbiology — Posted on 2025-11-03

5049 Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence

Chitale, P.; Ocke, E.; Odom, A. R.; Fan, H.; Henoch, A.; Vasco, K.; Fogarty, E. C.; Grady, C.; Lemenze, A. D.; Kumar, P.; Manning, S.; Eren, A. M.; Johnson, W. E.; Alland, D.

10.1101/2025.11.03.686283 — microbiology — Posted on 2025-11-03

5050 Longitudinal analysis of influenza A virus deletion-containing viral genomes reveals key determinants of co-evolutionary dynamics and interference

Alnaji, F. G.; Farjo, M.; Guo, S. L.; Aw, D. Z. H.; Lorenzini, P. A.; Liu, T.; Lin-Zhen, R. C.; Lee, C.; Vignuzzi, M.; Brooke, C. B.

10.1101/2025.11.03.686333 — microbiology — Posted on 2025-11-03

5051 Viral lineage and mode of exposure modulate within host spatial dynamics of influenza A viruses

Leyson, C.; Vargas-Maldonado, N.; Gaddy, M.; Raghunathan, V.; Matias-Ferreri, L.; Sethi, M.; Patatanian, K.; Carnaccini, S.; Ganti, K.; VanInsberghe, D.; Lowen, A. C.

10.1101/2025.11.03.686270 — microbiology — Posted on 2025-11-03

5052 Development of an efficient PEG-Mediated protoplast transformation system for the medicinal fungus Ophiocordyceps xuefengensis

Feng, X.; Sheng, X.; Liu, J.; Zhou, R.; Yang, Z.; Tang, X.; Zhang, S.

10.1101/2025.11.03.686195 — microbiology — Posted on 2025-11-03

5053 Metabolic diversity of the Ferrovales and potential contributions to iron oxidation

Grettenberger, C. L.; Macalady, J.; Hamilton, T. L.

10.1101/2025.11.03.686282 — microbiology — Posted on 2025-11-03

5054 Engineering and evaluation of Sinorhizobium meliloti nodulation (nod) gene reporter systems in rhizobia and non-rhizobia

Luu, C. X.; Geddes, B. A.

10.1101/2025.11.03.686230 — microbiology — Posted on 2025-11-03

5055 Cdc25-mediated activation of the small GTPase RasB is essential for hyphal fusion and symbiotic infection of Epichloë festucae

Inagaki, M.; Kamiya, S.; Okamura, A.; Miura, A.; Kayano, Y.; Tanaka, A.; Takemoto, D.

10.1101/2025.11.03.686139 — microbiology — Posted on 2025-11-03

5056 Caspase-11 Mediated Hyperinflammation Impairs CD8⁺ T Cell Immunity and Viral Clearance in Severe SARS-CoV-2 Infection

ELTOBGY, M.; Shamseldin, M.; Whitham, O.; Amer, H.; Atkinson, J.; Badr, A.; Hall, J.; Omran, J.; Gupta, G.; Hassan, Y.; Abdelaleem, R.; Perez, R.; Faber, S.; Pietrzak, M.; Webb, A.; Zhang, X.; Kenney, A.; Bissel, D.; Estfanous, S.; Daily, K.; Mcnamara, A.; KC, M.; Peeples, M.; Hemann, E.; Nimjee, S.; Cormet-Boyaka, E.; Li, J.; Boyaka, P.; Yount, J.; Segal, B.; Dubey, P.; Amer, A.

10.1101/2025.11.01.684729 — microbiology — Posted on 2025-11-03

5057 Neutral Frustration Landscape Architecture of SARS-CoV-2 Spike -Antibody Interfaces Shapes Immune Evasion Mechanisms for Ultrapotent Neutralizing Antibodies and Determines Pathways of Viral Adaptation: Insights from Integrative Computational Approach

Alshahrani, M.; Parikh, V.; Foley, B.; Verkhivker, G.

10.1101/2025.10.31.685956 — biophysics — Posted on 2025-11-03

5058 Changes in peripheral blood leukocyte composition precede development of heart-reactive autoantibodies in patients hospitalised for acute heart failure

Boshra, A.; Bauser, M.; Pelin, D.; Shemshadi, S.; Hollmann, C.; Hepp, H.; Al Hassan, W.; Heil, M.; Goepfert, D.; Schmidbauer, L.; Kaiser, E.; Gellermann, N.; Paetkau, J.; Kerwagen, F.; Heuschmann, P.; Gasteiger, G.; Kastenmueller, W.; Ramos, G.; Kerkau, T.; Hofmann, U.; Frantz, S.; Stoerk, S.; Morbach, C.; Beyersdorf, N.

10.1101/2025.11.01.685879 — immunology — Posted on 2025-11-03

5059 Modelling cognitive outcomes in the UK Biobank: education, noradrenaline and frontoparietal networks

Bravo-Merodio, L.; Williams, J. A.; Russ, D. R.; Gkoutos, G.; Brosnan, M.; Bellgrove, M. A.; Chechlacz, M.

10.1101/2023.08.31.555645 — neuroscience — Posted on 2025-11-03

5060 Discrete cytokine signaling networks instruct distinctsynovial pathotypes in inflammatory arthritis

Derrac Soria, A.; Hill, D.; Hughes, S. T.; Scott, R. N.; Cardus Figueras, A.; Dimonte, S.; Costa, D.; Vinh, N.-N.; Monaco, F.; Jenkins, R. H.; Liu, X.; Lewis, M. J.; Twohig, J.; Guy, C.; Cossins, B. C.; Morrin, A. S.; Andrews, R.; Szomolay, B.; Fossati, L.; Nowell, M. A.; Williams, A. S.; Choy, E. H.; Jenkins, B. J.; Williams, N. M.; Yu, H.; Kortylewski, M.; Turner, S. J.; Tiganis, T.; Pitzalis, C.; Jones, G. W.; Jones, S. A.

10.1101/2025.11.01.686006 — pathology — Posted on 2025-11-03

5061 High-throughput bacterial aggregation analysis in droplets

Saar-Abroi, M.; Lindpere, K.; Kacsor, D.; Olman, T.; Gonzalez, D.; Sulp, F. L.; Kiir, K.; Sanka, I.; Bartkova, S.; Scheler, O.

10.1101/2024.09.24.613170 — bioinformatics — Posted on 2025-11-03

5062 When Firing Rate Falls Short: Spike Synchrony Reliably Disentangles Stimulus Saliency and Familiarity

Zemliak, V.; Pipa, G.; Nieters, P.

10.1101/2025.08.09.669457 — neuroscience — Posted on 2025-11-03

5063 A Comprehensive Genetic Toolkit for Rapid and High-Resolution Engineering of Metabolic Pathways in Zymomonas mobilis.

Poma, M.; Marchetti, M.; Burns, C.; Zannetou, A.; Riley, E. M.; Sargent, F. L.; Azimov, U.; Munoz-Munoz, J. L.; Kelly, C. L.

10.1101/2025.10.29.685439 — synthetic biology — Posted on 2025-11-03

5064 Mechanistic Links Between Metabolic Dysfunction-Associated Steatotic Liver Disease and Heart Failure with Preserved Ejection Fraction in a Mouse Model

Rweished, N.; Rokach, Y.; Parnassa, E.; Abedat, S. M.; Bsoul, A.; Nachman, D.; Amir, O.; Safadi, R.; Asleh, R.

10.1101/2025.11.02.686066 — physiology — Posted on 2025-11-03

5065 An integrated model of population growth saturation and basal ROS levels predicts cellular ferroptosis sensitivity

Seidel, E.; Itak, E. Y.; Mueller, F.; Yapici, F. I.; Braegelmann, J.; Berg, J.; von Karstedt, S.

10.1101/2025.09.15.676259 — cancer biology — Posted on 2025-11-03

5066 Aducanumab Binding to Aβ1-42 Fibrils Alters Dynamics of the N-Terminal Tail While Preserving the Fibril Core

Palani, R. S.; Williams, C. G.; Thacker, D.; Silvers, R.; Qian, F.; Weinreb, P. H.; Mueller, L. J.; Linse, S.; Griffin, R. G.

10.1101/2025.11.01.686027 — biophysics — Posted on 2025-11-03

5067 Phase Separation Tunes the Stability and Dynamics of G-quadruplex and i-Motif DNA in the Nuclei of Living Cells

Patel, B.; Hoang, C.; Yoo, H.; Davis, C.

10.1101/2025.06.30.661982 — biophysics — Posted on 2025-11-03

5068 Privacy-Preserving Genomic Data Sharing via Hybrid AES/ECC and Blockchain-Based Dynamic Consent

Soundararajan, J.; Zhuang, Y.; Xu, D.

10.1101/2025.11.01.686038 — bioinformatics — Posted on 2025-11-03

5069 Inference with Viral Quasispecies. Methods for Individual Samples Comparative Analysis.

Gregori, J.

10.1101/2024.12.30.630765 — bioinformatics — Posted on 2025-11-03

5070 Rapid-Response, High-Gain Inkjet-Printed Organic Electrochemical Transistors with Geometry-Optimized Design for Neural Recording and Biosensing

Khoury, F.; Habli, Z.; Daorah, J.; Xu, Y.; Obeid, M.; Cauwenberghs, G.; Khraiche, M.

10.1101/2025.11.01.686019 — bioengineering — Posted on 2025-11-03

5071 Calibration-free single-frame super-resolution fluorescence microscopy

Dostalova, A.; Vasinka, D.; Starek, R.; Jezek, M.

10.1101/2025.05.20.655080 — molecular biology — Posted on 2025-11-03

5072 Comprehensive OrgDb Packages for Fungal Comparative Genomics: MycoCosm-Derived Standardized GO and InterPro Annotations Across Five Major Phyla

Sista Kameshwar, A. K.

10.1101/2025.11.01.681922 — microbiology — Posted on 2025-11-03

5073 Targeting Macrophage Folate Receptor-β for Diagnosis and Treatment of Autoimmune Myocarditis

Jahandideh, A.; Atencio Herre, E.; Nammas, W.; Virta, J.; Liljenback, H.; Ponkamo, J.; Putri, A.; Zhuang, X.; Rajander, J.; Srinivasarao, M.; Low, P. S.; Lu, Y.; Li, X.-G.; Knuuti, J.; Roivainen, A.; Saraste, A.

10.1101/2025.11.02.686077 — immunology — Posted on 2025-11-03

5074 Differential Control of HIV-1 Replication by IFN-α14 Compared to IFN-α2 Relates to Differences in the Modulation of Host Antiretroviral Restriction Factors

Rout, S. S.; Stewart, M. T. E.; Seidel, N. B.; Dittmer, U.; Sutter, K.; Lavender, K. J.

10.1101/2025.11.01.685890 — immunology — Posted on 2025-11-03

5075 Antigen-scaffolds drive preferential expansion of functional genetically engineered CAR and TCR T cells

Johansen, K. H.; Ramanathan, K.; Rodriguez-Pardo, C.; Gjelstrup, A. K.; Halldorsdottir, H. R.; Voss, L. F.; Tvingsholm, S.; Grand, L. S.; Dionisio, E.; Skriver, A. H.; Frederiksen, L. P.; Bjornson, M.; Svensson-Frej, M.; Ormhoj, M.; Hadrup, S. R.

10.1101/2025.11.01.686037 — immunology — Posted on 2025-11-03

5076 Functional clusters for shape, texture, and motion encoding in macaque V2

Kim, T.; Kamath, R.; Hatanaka, G.; Namima, T.; Dylla, C.; Bair, W.; Pasupathy, A.

10.1101/2025.11.01.686029 — neuroscience — Posted on 2025-11-03

5077 Simultaneous detection and estimation in olfactory sensing

Jiang, C.; He, M. Y.; Murthy, V. N.; Pehlevan, C.; Zavatone-Veth, J. A.; Masset, P.

10.1101/2025.11.01.686013 — neuroscience — Posted on 2025-11-03

5078 Cortical Excitability is Affected by Light Exposure - Distinct Effects in Adolescents and Young Adults

Sharifpour, R.; Balda Aizpurua, F.; Paparella, I.; Read, J.; Leysens, Z.; Letot, S.; Campbell, I.; Beckers, E.; Collette, F.; Phillips, C.; Zubkov, M.; Vandewalle, G.

10.1101/2024.08.21.608922 — neuroscience — Posted on 2025-11-03

5079 Spectral features of heart rate variability in Williams syndrome during sleep

Schneider, B.; Gombos, F.; Kovacs, I.; Bodizs, R.

10.1101/2025.11.01.685999 — physiology — Posted on 2025-11-03

5080 Macrophage-secreted Pyrimidine Metabolites Confer Chemotherapy Resistance in Acute Myeloid Leukemia (AML)

Wang, C.; Wang, Y.; Benetti, C.; Lin, X. X.; Dasdemir, E.; Hyrossov, P.; Tan, J. Y. M.; Ayoub, E.; Bhatia, K. S.; Lim, F. Q.; Li, Y.; Zhao, Z.; Mohamed, A. M. M.; Lee, S. Y.; Rohlena, J.; Pecot, C. V.; Andreeff, M.; Rohlenova, K.; Abbas, H. A.; Bhatt, S.

10.1101/2025.11.01.686055 — cancer biology — Posted on 2025-11-03

5081 A novel 18F-labeled brain penetrant PET ligand for imaging poly(ADP-ribose) polymerase-1

Patel, J. S.; Zhou, X.; Chen, J.; Gao, Y.; Zhao, C.; Song, Z.; Zhao, T.; Hu, Q.; Li, X.; Li, C.; Wu, S.; Schuster, D. M.; Yang, L.; Li, Y.; Yu, D. S.; Liang, S. H.

10.1101/2025.11.01.686021 — cancer biology — Posted on 2025-11-03

5082 Single recipient cell tracking of tellurium-labeled extracellular vesicle proteomes (TeLEV) identifies EV-driven immunomodulation

10.1101/2025.11.01.685872 — cancer biology — Posted on 2025-11-03

5083 Contribution of Mesenchymal-like and Epithelial Cellular Subsets to Chemotherapy Resistance in Triple-Negative Breast Cancer

Vuong, N. B.; korolkova, O. Y.; Izban, M.; SAKWE, N. I.; McIntosh, A. R.; Ball, D.; Black, P. J.; Edwards, A.; Ballard, B. R.; Adunyah, S. E.; Sakwe, A. M.

10.1101/2025.11.01.685128 — cancer biology — Posted on 2025-11-03

5084 Probing the energy landscape of α-Synuclein amyloid fibril formation by systematic K-to-Q mutagenesis

Kunka, A.; Farzadfard, A.; Larsen, J. A.; Saraceno, F.; Norrild, R. K.; Fricke, C.; Mohammad-Beigi, H.; Sadek, A.; Folke, J.; Aznar, S.; Buell, A. K.

10.1101/2025.11.01.685997 — biophysics — Posted on 2025-11-03

5085 Dangling Ends of Third Strand and Duplex Drive Nucleic Acid Triplex Stabilization through Bimodal Association

Zhou, F.; Liu, Y.; Shu, Z.; Wang, Y.; Chen, G.

10.1101/2025.11.02.686076 — biophysics — Posted on 2025-11-03

5086 Do 5' regions of human protein-coding genes contain the blueprints for alternative splicing?

Thomas, W.; Moulinier, L.; Scalzitti, N.; Thompson, J.; Chennen, K.; Poch, O.

10.1101/2025.11.01.686005 — bioinformatics — Posted on 2025-11-03

5087 pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics

Yue, Q.-X.; Dai, C.; Kamatchinathan, S.; Bandla, C.; Webel, H.; Larrea, A.; Bittremieux, W.; Uszkoreit, J.; Muller, T. D.; Xiao, J.; Cox, J.; Ewels, P.; Demichev, V.; Kohlbacher, O.; Sachsenberg, T.; Bielow, C.; Bai, M.; Perez-Riverol, Y.

10.1101/2025.11.02.685980 — bioinformatics — Posted on 2025-11-03

5088 KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles

Selvanayagam, S.; Quiroz-Chavez, J.; Ramirez Gonzalez, R. H.; Uauy, C.; Smit, S.; Schranz, M. E.

10.1101/2025.11.01.685998 — bioinformatics — Posted on 2025-11-03

5089 deCYPher: Star Allele-Resolution Computational Framework of Pharmacogenes for Haplotype-Resolved Long-Read Assemblies

Chang, T.-Y.; Liu, Y.-S.; Lai, H.-S.; Hung, T.-K.; Lin, H.-F.; Lin, Y.-H.; Hsu, C.-L.; Yang, Y.-C.; Chen, C.-Y.; Chen, P.-L.; Hsu, J. S.

10.1101/2025.10.13.681303 — bioinformatics — Posted on 2025-11-03

5090 Detection dog performance state estimation from pre-stimulus video and physiological signals using deep learning and Bayesian inference

Schultz, J.; Rothkoff, L.; Aviles-Rosa, E.; Hall, N. J.; Maughan, M. N.

10.1101/2025.10.31.685787 — animal behavior and cognition — Posted on 2025-11-03

5091 Chromosome-scale genome assembly and annotation of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae)

Kataoka, K.; Sanno, R.; Gaczorek, T.; Bhattarai, U. R.; Ito, Y.; Inoue, S.; Yura, K.; Asahi, T.; Ylla, G.; Mito, T.; Extavour, C. G.

10.1101/2025.10.31.685973 — genomics — Posted on 2025-11-03

5092 Plasticity promotes persistence across novel environments in experimental microcosms

Harmon, E. A.; Malum, C.; Siddapureddy, S.; Pfennig, D. W.

10.1101/2025.11.01.686023 — ecology — Posted on 2025-11-03

5093 Beyond Coral Cover: A framework for assessing the condition of coral reef habitats and informing conservation targets

Gonzalez-Rivero, M.; Crossman, K.; Thompson, A.; Ortiz, J. C.; Kim, S. W.; Emslie, M.; Hoey, A. S.; Hoogenboom, M.; Bairos-Novak, K.; McClure, E.; Pandolfi, J. M.; Mumby, P. J.; Logan, M.; Schaffelke, B.; Staples, T.; Fabricius, K. E.

10.1101/2025.11.01.686047 — ecology — Posted on 2025-11-03

5094 On the energetic boundaries of trophic systems

Saavedra, S.; Long, C.; Kefi, S.; Levin, S.; Marquet, P.; Rohr, R. P.; Angulo, M. T.

10.1101/2025.10.20.683547 — ecology — Posted on 2025-11-03

5095 Heat shock-mediated transformation is possible in several Gram-negative bacteria

Giri, S. J.; Sharma, P. L.; Dutta, L.; Begum, S.; Bhuyan, S.; Jain, M.; Agarwala, N.; Ray, S. K.

10.1101/2025.10.30.685485 — microbiology — Posted on 2025-11-03

5096 Integrating Mathematical and Mouse Models Identifies T regulatory Cell Influx as a Key Determinant of Acquired Resistance to PD-1 Immunotherapy

Sousa, R. S.; Geels, S. N.; Murat, C.; Moshensky, A.; Villalta, S. A.; Lowengrub, J. S.; Marangoni, F.

10.1101/2025.10.31.685923 — immunology — Posted on 2025-11-03

5097 Macrophage PIM1 Drives Atherosclerosis by Enhancing Foam Cell Formation Via CD36

Chen, Y.; Beg, M. A.; Luu, Q. Q.; Chen, V.; Wang, Y.; Xin, G.; Cui, W.; Silverstein, R. L.

10.1101/2025.10.31.685966 — immunology — Posted on 2025-11-03

5098 Functional Connectivity Localizes a Distributed Supramodal Core for Naturalistic Viewing

Fokin, V.; Sherafati, A.

10.1101/2025.11.01.685026 — neuroscience — Posted on 2025-11-03

5099 Dynamic Causal Modelling for Functional Near-Infrared Spectroscopy Using Spatial Priors Derived from Diffuse Optical Tomography

Chu, T.; Niioka, K.; Dan, I.; Tak, S.

10.1101/2025.10.31.685970 — neuroscience — Posted on 2025-11-03

5100 Argon inhibits autophagy and improves cerebral ischemia-reperfusion injury via PI3K/Akt/mTOR pathway

yang, L.; Wang, M.; Luo, Z.; Ma, S.; Petersen, P.; Wang, E.; Xia, Y.-X.

10.1101/2025.10.31.685964 — neuroscience — Posted on 2025-11-03

5101 Intrinsic electrophysiological activity maps a latent dimension of poor sleep quality and reduced cognitive performance: a magnetoencephalography study using Cam-CAN data.

Hardy, S.; Roberts, G.; O'Neill, G.; Bhat, V.; Pan, Y.; Reichelt, A.; Seymour, R. A.; Dunkley, B. T.

10.1101/2025.11.01.686036 — neuroscience — Posted on 2025-11-03

5102 Tau seeding in neurons enabled by transient endolysosomal perforations are confined within endolysosomes

Sanyal, A.; Scanavachi, G.; Somerville, E.; Aylan, B.; Costa-Filho, J. I.; Brooks, F.; Dickson, J. R.; Hyman, B.; Kirchhausen, T.

10.1101/2025.11.02.686178 — neuroscience — Posted on 2025-11-03

5103 Modified self-amplifying RNA mediates robust and prolonged gene expression in the mammalian brain

Freire, J.; McGee, J. E.; Shaw, D.; Zhou, Y.; Porter, C.; Dang, L.; San Antonio, E.; Yu, Z.; Li, K.; Wong, W.; Grinstaff, M.; Han, X.

10.1101/2025.10.30.685635 — neuroscience — Posted on 2025-11-03

5104 Chloroplast- and Mitochondrion-Specific Random C-to-T Mutagenesis for Forward Genetics of Organelle Genomes

Kosaka, N.; Harada, Y.; Nakazato, I.; Okuno, M.; Itoh, T.; Tsutsumi, N.; Arimura, S.-i.

10.1101/2025.11.01.685978 — plant biology — Posted on 2025-11-03

5105 Delineating Mutation Bias and Selection during Plant Development

Monroe, G.; Lensink, M.; Ahn, V.; Davis, M. W.; Oya, S.; Zhao, K.

10.1101/2025.11.01.686053 — plant biology — Posted on 2025-11-03

5106 Characterization of a dominant SmNac-like gene as a candidate for photosensitivity in the fruit peel of eggplant

Gomis-Cebolla, J.; Manrique, S.; Arrones, A.; Toledo-Tolgar, M. D.; Luna, J.; Baraja-Fonseca, V.; Sanchez-Pascual, J.; Gimeno-Paez, E.; Plazas, M.; Gramazio, P.; Vilanova, S.; Prohens, J.

10.1101/2025.09.19.677371 — plant biology — Posted on 2025-11-03

5107 A broken power-law model of heart rate variability spectra in sleep

Schneider, B.; Dresler, M.; Gombos, F.; Kovacs, I.; Bodizs, R.

10.1101/2025.11.01.685631 — physiology — Posted on 2025-11-03

5108 DIfferential Branched-Chain Amino Acid Metabolism in Tissues of Tumour-Bearing Mice

Zerrouk, M.; Delfinis, L. J.; Perry, C. A. J.; Adegoke, O. A. J.

10.1101/2025.11.01.685925 — physiology — Posted on 2025-11-03

5109 IRIS PIGMENTATION IRREGULARITIES FOLLOWING AN AVIAN INFLUENZA OUTBREAK: IMPLICATIONS FOR DISEASE SURVEILLANCE AND POPULATION MONITORING IN A COLONIAL SEABIRD

Petalas, C.; Giacinti, J. A.; Provencher, J. F.; Rail, J.-F.; Avery-Gomm, S.; Lavoie, R.; Elliott, K. H.; Seyer, Y.

10.1101/2025.10.31.685885 — physiology — Posted on 2025-11-03

5110 Long-term Locus Coeruleus Stimulation Exacerbates Tau Pathology in PS19 Mice

Nong, Y.; Wellman, S.; Zhang, H.; Liu, Y. A.; Argyrousi, E. K.; Arancio, O.; Wang, Q.

10.1101/2025.11.01.686018 — pathology — Posted on 2025-11-03

5111 Scaffold-free 3D-Cell Co-Culture Model System for the Study of Metastatic Cancer Cell Behavior in the Brain TME

Lazar, I. M.; Sarkar, P.; Ahuja, S.

10.1101/2025.10.31.685975 — cancer biology — Posted on 2025-11-03

5112 GeneCAD: Plant Genome Annotation with a DNA Foundation Model

Liu, Z.-Y.; Berthel, A.; Czech, E.; Stitzer, M. C.; Hsu, S.-K.; Pennell, M.; Buckler, E. S.; Zhai, J.

10.1101/2025.10.31.685877 — bioinformatics — Posted on 2025-11-03

5113 TimeFlow 2: an unsupervised cell lineage detection method for flow cytometry data

Liarou, M.; Matthes, T.; Marchand-Maillet, S.

10.1101/2025.11.01.685988 — bioinformatics — Posted on 2025-11-03

5114 Initial Condition Decision to Ensure Reliable Circadian Phase Estimation with Shorter-Term Wearable Data

Lim, D.; Kim, J.; Kim, J. H.; Kim, J. K.

10.1101/2025.11.01.686004 — bioinformatics — Posted on 2025-11-03

5115 Zwitterionic hydrogel designs for conducting polymers enable bioelectronics with suppressed foreign body response

Wai, S.; Kang, S.; Li, N.; Dai, Y.; Lavoie, T.; Strzalka, J.; Sutyak, S.; Weires, M.; Fu, T.; Wang, J.; Stevens, K. C.; Li, R.; Hubbell, J. A.; Tirrell, M. V.; Wang, S.

10.1101/2025.10.31.683260 — bioengineering — Posted on 2025-11-03

5116 FE-DOE: Finite element informed design of experiments to optimise bioinspired melt electrowritten (MEW) polymeric heart valves

Hughes, C.; Johnston, R. D.; McCarthy, D.; Klusak, E.; Growney, E.; Campbell, E.; Lally, C.

10.1101/2025.11.01.684363 — bioengineering — Posted on 2025-11-03

5117 Redeployment of Archaeal ESCRT Systems Reveals Conserved Mechanisms Underlying Eukaryotic Complexity

Naripogu, K. B.; Tee, Y. H.; Senju, Y.; Li, H.; Bershadsky, A.; Honda, T.; Robinson, R. C.

10.1101/2025.11.01.685982 — evolutionary biology — Posted on 2025-11-03

5118 Live visualization of extracellular matrix dynamics during development and regeneration in zebrafish

Shen, J.; Jayadev, R.; Ou, J.; Rich, A.; Ando, K.; Di Talia, S.; Sherwood, D. R.; Poss, K. D.

10.1101/2025.11.02.686082 — developmental biology — Posted on 2025-11-03

5119 Dynamics of local B cell migration during affinity maturation in the human tonsil

McEnany, J. D.; Good, B. H.; Cvijovic, I.

10.1101/2025.10.31.685876 — immunology — Posted on 2025-11-03

5120 Contextual Scaling of Representational Uncertainty for Size and Number

Sakamoto, Y.; Hayashi, M. J.

10.1101/2025.10.31.685954 — neuroscience — Posted on 2025-11-03

5121 Absence of cortical reorganization following an internal capsule stroke in rodents

Cettina, P. E.; Guggenmos, D. J.; Sivakumar, S. S.; Murphy, M. D.; Barbay, H. S.; Nudo, R. J.; Bundy, D. T.

10.1101/2025.10.31.685962 — neuroscience — Posted on 2025-11-03

5122 SIMAIS: A swarm intelligence inspired biosensor for rapid protein detection

Zheng, J.; Bayinqiaoge, ; Schiff, H.; Wang, X.; Wu, T.; Lu, X.; Zhang, Y.; Wang, Y.; Tang, S.; Zhang, C.

10.1101/2025.10.31.685929 — biophysics — Posted on 2025-11-03

5123 Integrating Artificial Intelligence and Machine Learning to Forecast Air Pollution Impacts on Climate Variability and Public Health

Shafaghat, A.

10.1101/2025.10.31.685968 — bioinformatics — Posted on 2025-11-03

5124 cfOncoXpress: Tumor gene expression prediction from cell-free DNA whole-genome sequences

Li, W.; Roskes, M.; Martinez-Fundichely, A.; Khurana, E.

10.1101/2025.10.31.685915 — genomics — Posted on 2025-11-03

5125 Third-nucleotide codon bias and synonymous codon bias define functional translational programs that shape human tissue and cancer proteomes.

Rashad, S.; Niizuma, K.

10.1101/2025.10.31.685942 — genomics — Posted on 2025-11-03

5126 The origins and molecular evolution of sperm

Matte, A.; Skerrett-Byrne, D.; Manica, A.; LeBoeuf, A. C.

10.1101/2025.11.03.685759 — evolutionary biology — Posted on 2025-11-03

5127 Thinking past owl vs owl: The barred owl invasion threatens ecological communities in the western United States

Arenas-Viveros, D.; Fehlker Campbell, E.; Munes, A. L.; Howe, H.; Gonzales, H. M.; Higley, J. M.; Hofstadter, D. F.; Hobart, B. K.; Wengert, G.; Rex, A.; Dotters, B. P.; Roberts, K. N.; Varian, C. P.; Peery, M. Z.; Fountain, E.

10.1101/2025.10.31.685899 — ecology — Posted on 2025-11-03

5128 Integrating nekton communities, salt pool dynamics, and fish foraging patterns to assess salt marsh restoration success in Maritime Canada

Endresz, K. C.; McLellan, N. R.; Barbeau, M. A.

10.1101/2025.10.31.685895 — ecology — Posted on 2025-11-03

5129 Clonal overlap and convergent clustering of T-cell receptor signatures in Crohn's disease in monozygotic twins

Brand, E. C.; Vandoren, R. C.; Lutter, L.; Van Deuren, V. M. L.; Servaas, N.; Pandit, A.; Meysman, P.; Oldenburg, B.; van Wijk, F.

10.1101/2025.10.31.685913 — immunology — Posted on 2025-11-03

5130 B Cell-Induced Lymph Node Stromal Remodeling Compromises Neutrophil Response to Secondary Staphylococcus aureus Infection

Xue, J.; Oo, D.; Rosin, N.; Biernaskie, J.; Huang, P.; Liao, S.

10.1101/2025.10.31.681727 — immunology — Posted on 2025-11-03

5131 Spatial Attention and Session Day Independently Modulate Human Visual Cortical Plasticity

Limon, P. N.; Norcia, A. M.; Ash, R. T.

10.1101/2025.10.31.685945 — neuroscience — Posted on 2025-11-03

5132 A subset of world barley collection was used in the identification of sources of resistance and marker-trait association for resistance for bacterial leaf streak

Velasco, D. D. P.; Shi, G.; Brueggeman, R. S.; Horsley, R. D.; Liu, Z.; Baldwin, T. T.

10.1101/2025.10.31.685662 — plant biology — Posted on 2025-11-03

5133 Empirical Evaluation of Single-Cell Foundation Models for Predicting Cancer Outcomes

Elmarakeby, H.; Roman, A.; Johri, S.; Van Allen, E.

10.1101/2025.10.31.685892 — cancer biology — Posted on 2025-11-03

5134 Rete Ovarii Epithelial Cells as an Unappreciated Cell of Origin for Pelvic and Ovarian High-Grade Serous Carcinoma

Wang, C.; Chen, P.; Zhao, X.; Ruan, J.; Lv, X.; Liu, J.; Xu, R.; Islam, K.; Wang, H.; Shi, D.; Moness, M. L.; Carbajal, B.; Kumar, G.; Abioye, O. A.; McKey, J.; Davis, J. S.

10.1101/2025.10.31.685873 — cancer biology — Posted on 2025-11-03

5135 Deep-Learning Cortical Registration Guided by Structural and Diffusion MRI and Connectivity

ZHOU, Z.; Li, J.; Williams, J.; Fischl, B.; Aganj, I.

10.1101/2025.10.31.685908 — bioinformatics — Posted on 2025-11-03

5136 A comprehensive view of somatic mosaicism by single-cell DNA analysis

Luquette, L. J.; Coorens, T. H. H.; Natu, A.; Suvakov, M.; Caplin, A.; Jun, M. S.; Mo, A.; Pelt, J.; Anderson, L.; Berselli, M.; Bhamidipati, S.; Blanchard, T.; Brew, J.; Chun, H.-J. E.; Chun, H.; Dehankar, M. K.; Feng, W. C.; Furatero, R.; Grochowski, C. M.; Ho, E.; Jang, Y.; Kottapalli, K.; Leonard, M. K.; Lim, N. S.; Lindsay, T.; Nicholson, S.; Raimondi, I.; Runnels, A.; Scharlee, C.; Shin, J.; Veit, A. D.; VonDran, M.; Wang, Y.; Yuan, D. J.; Zhao, Y.; Bell, T. J.; Ardlie, K.; Doddapaneni, H.; Fulton, R.; Germer, S.; Landau, D.; Oh, J. W.; Park, P. J.; Vaccarino, F. M.; Walsh, C. A.; Abyzov

10.1101/2025.10.31.685648 — genomics — Posted on 2025-11-03

5137 Distance to future climate analogues reveals refugia for agricultural adaptation

Geldbach Jones, A.; Pironon, S.; Friis, G.; Geldbach, D.; Borrell, J. S.

10.1101/2025.10.31.685848 — ecology — Posted on 2025-11-03

5138 A catastrophic marine mortality event caused by a complex algal bloom including the novel brevetoxin producer, Karenia cristata (Dinophyceae)

Murray, S.; Bolch, C. J. S.; Brett, S.; Chan, C. X.; Doubell, M.; Farrell, H.; Gaiani, G.; Greenhough, H.; Hallegraeff, G.; Smith Harding, T.; Harwood, D. T.; Hatfield, R. G.; Moody, I.; Rhodes, L.; Selwood, A.; Seymour, J.; Siboni, N.; Snigirova, A.; Rolton, A.; Wilkinson, C.; Bastos de Oliveira, H.; Streiber, N.; MacDonald, N.; Smith, K. S.

10.1101/2025.10.31.685766 — ecology — Posted on 2025-11-03

5139 Major cell type differences between larval and adult hemichordate body plans

Bump, P.; Brewster, C.; Formery, L.; Lubeck, L.; Campbell, C.; Morri, M.; Sit, R.; Rokhsar, D.; Benham-Pyle, B.; Lowe, C.

10.1101/2025.10.31.685866 — developmental biology — Posted on 2025-11-03

5140 Effects of Social Status on Reproductive Success, Physiology and Maternal Care in Socially housed Female Rhesus Macaques

Bailey, K. L.; Jonesteller, T.; Kovacs-Balint, Z. A.; Bachevalier, J.; Alvarado, M. C.; Wilson, M. E.; Raper, J.; Sanchez, M. M.

10.1101/2025.10.31.685853 — developmental biology — Posted on 2025-11-03

5141 Contextual control of CD8+ T cell priming by dendritic cell subsets in tumor and inflammatory microenvironments

Schuster, V. P.; Brown, K.; Unsworth, J. R.; Berkowitz, N.; Ruhland, M. K.

10.1101/2025.10.31.685861 — immunology — Posted on 2025-11-03

5142 SNNs Are Not Transformers (Yet): The Architectural Problems for SNNs in Modeling Long-Range Dependencies

Fishell, W.; Honnuraiah, S.

10.1101/2025.10.31.685901 — neuroscience — Posted on 2025-11-03

5143 Probabilistic Cognitive State Modeling (PCSM): Decoding Latent Spatiotemporal Dynamics to Reveal Serial-Parallel Processing, Cognitive Demand, and Serial Bottleneck in Task-Based fMRI

Winters, D. E.

10.1101/2025.10.31.685855 — neuroscience — Posted on 2025-11-03

5144 Biophysical model for predicting muscle short-range stiffness during movement

van der Zee, T. J.; Simha, S. N.; Milburn, G. N.; Campbell, K. S.; Ting, L. H.; De Groote, F.

10.1101/2025.10.31.685881 — physiology — Posted on 2025-11-03

5145 NSeqVerify: An Easy-to-Use Desktop Suite for Integrated NGS Data Analysis, from Raw Reads to Taxonomic Assignment

Reinosa, R.

10.1101/2025.10.31.685854 — bioinformatics — Posted on 2025-11-03

5146 Characterizing Variants of Uncertain Drug Resistance (VUDRs) Using Quantitative Measurements at Clinical Exposures

Inam, H.; Tomaszkiewicz, M.; Reynolds, J.; Yang, Z.; Leighow, S.; Pritchard, J. R.

10.1101/2025.10.31.685392 — bioengineering — Posted on 2025-11-03

5147 Computational Stabilization of the Human VH Germline Repertoire to Enable Conditional Multi-Specific Therapeutic Development

Thieker, D. F.; Hanna, J.; White, P.; Capodagli, G.; Buetz-Duncan, C.; Carnevale, C. D.; Sereno, A.; Chai, F.; Lin, A.; Pigott, C. R.; Sharma, R. K.; Del Cid, N.; Nicely, N. I.; Kuhlman, B.; Demarest, S. J.

10.1101/2025.10.31.685826 — bioengineering — Posted on 2025-11-03

5148 Decode-gLM: Tools to Interpret, Audit, and Steer GenomicLanguage Models

Maiwald, A.; Crook, O. M.; Jedryszek, P.; Draye, F.; Morris, G. M.

10.1101/2025.10.31.685860 — genomics — Posted on 2025-11-03

5149 A chromosome-level assembly and functional genomic resources for the model annelid Capitella teleta

Davies, B. E.; Gonzalez, P.; Sur, A.; Wei, J.; Frankish, T.; Montagne, J.; Carrillo-Baltodano, A. M.; Guynes, K.; Liang, Y.; Donnellan, R. D.; Moreland, R. T.; Singh, S.; Zhang, S.; Wolfsberg, T. G.; Meyer, N. P.; Seaver, E. C.; Baxevanis, A. D.; Martin-Duran, J. M.

10.1101/2025.10.31.685816 — genomics — Posted on 2025-11-03

5150 Consequences of cannibalism: induced defense and kin discrimination in a rotifer

Harmon, E.; Bimagambetov, A. K.; Lee, H. T.; Pfennig, D. W.

10.1101/2025.10.31.685857 — evolutionary biology — Posted on 2025-11-03

5151 Variation of multiple plant defenses and herbivory reveal different patterns of adaptation across a productivity gradient.

Herschberger, J. E.; Calixto, E. S.; Campbell, V. R.; Maron, J. L.; Hahn, P. G.

10.1101/2025.10.31.684923 — ecology — Posted on 2025-11-03

5152 HLH-30/TFEB is necessary for chromatin reorganization and maintenance of cell quiescence during starvation in C. elegans

Munoz-Barrera, M.; Mata-Cabana, A.; Moreno-Rivero, A.; Piubeli, F. A.; Ren-Barroso, B.; Al-Refaie, N.; Gutierrez, G.; Cabianca, D. S.; Olmedo, M.

10.1101/2025.10.31.685810 — developmental biology — Posted on 2025-11-03

5153 Fusobacterium nucleatum outer membrane vesicles activate the TNFR1/NF-κB signaling pathway to promote OSCC proliferation

Li, Z.; Liu, J.; Fu, R.; Wen, X.; Huang, X.; Gopinath, D.; Zhang, L.

10.1101/2025.10.31.685796 — microbiology — Posted on 2025-11-03

5154 Dynamical memory underlies prolonged plasmid persistence after transient antibiotic treatment

Zhou, Z.; Weiss, A.; Yao, Z.; Chen, X.; Lok, K.; Son, H.-i.; You, L.

10.1101/2025.10.31.685803 — microbiology — Posted on 2025-11-03

5155 Regulatory effects of beta-2-microglobulin on reactive oxygen species generation in polymorphonuclear cells

Poulsen, S. E.; Staudinger, E. M.; Steffensen, M. A.; Jensen, P. O.; Vilhardt, F.; Nissen, M. H.

10.1101/2025.10.31.685808 — immunology — Posted on 2025-11-03

5156 Spatial Transcriptomics Identify T Cell-Driven Mechanisms of Kidney Damage in Immune Checkpoint Inhibitor-Associated Acute Interstitial Nephritis

Qin, Q. A.; Ostendorf, L.; Wells, S. L.; Gao, C.; Tran, M.; Alikhan, F. M.; Zhang, X.; Chewcharat, A.; Rider, R. S.; Prell, S. A.; Chowdhury, R. B.; Weins, A.; Shah, S. I.; Mistry, K.; Bowman, T.; Villani, A.-C.; LeBoeuf, N.; Selamet, U.; Ravi, K. S.; Sharon, E.; Leaf, D. E.; Moledina, D. G.; Sise, M. E.; De Vlaminck, I.; Rao, D. A.; Wei, K.; Gupta, S.

10.1101/2025.10.31.685702 — immunology — Posted on 2025-11-03

5157 Integrated 3D Light-Sheet and 2D Multiplex Imaging for Deep Histological Profiling of a Somatic Mouse Glioblastoma Model

Marie-Catherine, T.; Core, N.; Bigott, K.; Hurriaux Fontana, Y.; Caccavalle, M.; Vilvandre, L.; El Yassouri, F.; Schoppel, V.; Ruberg, S.; Jungblut, M.; Figarella-Branger, D.; Tchoghandjian, a.; Bosio, A.; Cremer, H.

10.1101/2025.10.31.685751 — cancer biology — Posted on 2025-11-03

5158 Whole-genome sequencing of CRFK and PG-4 cells to infer the phenotype of the original donors

Tanaka, G.; Goto, R.; Komoto, T.; Kubota, A.; Hayashi, R.; Igawa, T.; Sakamoto, N.; Awazu, A.

10.1101/2025.10.31.685720 — genomics — Posted on 2025-11-03

5159 Genetic background and transient prenatal disruption of vitamin A signaling determine susceptibility to airway hyperresponsiveness in mice

Otoshi, T.; Kameshwar, A. K. S.; Kotton, B. D.; Seki, Y.; Cardell, Z.; Xiangyi, K.; Matsuno, Y.; Rajaram, P.; Kim, Y.-K.; Sharpton, S. M.; Quadro, L.; Cardoso, W. V.; Suzuki, M.

10.1101/2025.10.31.685835 — developmental biology — Posted on 2025-11-03

5160 Spatiotemporal dynamics of DNA repair proteins between the Golgi and nucleus maintain genomic stability.

Galea, G.; Kuodyte, K.; Khan, M. M.; Thul, P. J.; Neumann, B.; Lundberg, E.; Pepperkok, R.

10.1101/2022.10.17.512236 — cell biology — Posted on 2025-11-03

5161 Dynamic cytokine interplay governing implantation and immune tolerance in pregnant pigs

Borah, S.

10.1101/2025.10.30.685716 — immunology — Posted on 2025-11-03

5162 TOM: Transformer Optimization of mRNA initiation

Gupta, R.

10.1101/2025.10.30.685412 — bioinformatics — Posted on 2025-11-03

5163 Design of Tissue-Selective PROTACs Through Recruiting E3 Ligase Scaffolding Protein MAGEA11

Jacobsen, I. E.; Shi, R.; Scholtz, C. R.; Pomerantz, W. C. K.; Georg, G. I.

10.1101/2025.11.03.686228 — biochemistry — Posted on 2025-11-03

5164 A membrane-bound nuclease directly cleaves phage DNA during genome injection

Saxton, D. S.; Deweirdt, P. C.; Doering, C. R.; Roney, I. J.; Laub, M. T.

10.1101/2025.11.03.685801 — microbiology — Posted on 2025-11-03

5165 A Data-Driven Closed-Loop Control Approach to Drive Neural State Transitions for Mechanistic Insight

Emonds, N.; Herberg, E.; Gerchen, M. F.; Pritsch, M.; Rocha, J.; Zamoscik, V.; Kirsch, P.; Herzog, R.; Koppe, G.

10.1101/2025.07.21.665992 — neuroscience — Posted on 2025-11-03

5166 A dynamical systems model of arousal-driven behavioural state transitions

Johnson, P.; Nieuwenhuis, S.; Mejias, J. F.; Urai, A. E.

10.1101/2025.10.31.685593 — animal behavior and cognition — Posted on 2025-11-03

5167 Disentangling urbanisation, climate effects and their interaction on ornamental colourations

Sandmeyer, L.; Lopez-Idiaquez, D.; Fargevieille, A.; Giovannini, P.; Perret, S.; Del Rey, M.; Charmantier, A.; Doutrelant, C.; Gregoire, A.

10.1101/2025.02.19.639098 — ecology — Posted on 2025-11-03

5168 Alpine marmot (Marmota marmota) pups emerge increasingly earlier with the ongoing climate change

Bonenfant, C.; Cohas, A.; Quittet, P.-A.; Cavailhes, J.; Garcia, R.; Blache, N.; Gaillard, J.-M.; Douhard, M.

10.1101/2025.03.28.645887 — ecology — Posted on 2025-11-03

5169 Supercentenarian and remarkable age records exhibit patterns indicative of clerical errors and pension fraud

Newman, S. J.

10.1101/704080 — developmental biology — Posted on 2025-11-03

5170 Symbiotic diversification relies on an ancestral gene network in plants

Castanedo, L.; Melkonian, K.; Vernie, T.; Chauderon, L.; Pellen, T.; Bianconi, M.; Lefort, C.; Libourel, C.; Le Ru, A.; Aziz, S.; Latorre, C.; Thiercelin, O.; Rodde, N.; Cauet, S.; Callot, C.; Forrest, L.; Nishiyama, T.; Wickell, D.; Li, F.-W.; Keller, J.; Delaux, P.-M.

10.1101/2025.04.01.646537 — plant biology — Posted on 2025-11-03

5171 Host-Specific Fluorescence Dynamics in Legume-Rhizobia Symbiosis During Nodulation

Gautam, C. K.; Senanayake, G.; Pease, A. B.; Salem, M. A.; Rabia, A. H.; Pruess, B. M.; Geddes, B. A.

10.1101/2025.10.11.681774 — bioengineering — Posted on 2025-11-03

5172 Conserved gene- and network-level thermal memory intervals in two divergent perennial crucifers in nature

Endo, Y.; Nishio, H.; Oguchi, T.; Yamane, K.; Eseese, V. F.; Frederica, C. F.; Kudoh, H.; Buzas, D. M. M.

10.1101/2025.10.31.685746 — molecular biology — Posted on 2025-11-03

5173 Real-time volatilomics reveals microbiota and pathogen fingerprints in the honey bee

Fido, M.; Moriano-Gutierrez, S.; Lan, J.; Pirat, A.; Zufferey, L.; Cappio Barazzone, E.; Zenobi, R.; Engel, P.; Slack, E.

10.1101/2025.10.30.685588 — microbiology — Posted on 2025-11-03

5174 Telomeric assemblies of Paracoccidioides genomes

Grinevich, D.; Kompathoum, O.; Li, J.; Turissini, D. A.; Kelly, P.; Sutherland, M.; Marin, S.; Gomez, O. M.; Benard, G.; Shikanai-yasuda, M. A.; Cocio, T. A.; Vicentini, A. P.; Pires de Camargo, Z.; Messias Rodrigues, A.; Hahn, R.; Mota, B.; Marques de Macedo, P.; Almeida-Paes, R.; Alvarado, P.; Zancope-Oliveira, R. M.; McEwen, J. G.; Sepulveda, V. E.; Teixeira, M. d. M.; Matute, D. R.

10.1101/2025.10.30.685552 — microbiology — Posted on 2025-11-03

5175 In vitro Characterization of Peptidomimetic Proteolysis Targeting Chimera (PROTAC) as a Degrader of 3-Chymotrypsin-Like Protease (Mpro/3CLpro) against SARS-CoV-2

Liturri, M. G.; Bergna, A.; Lai, A.; Della Ventura, C.; Gabrieli, A.; Seravalli, I.; Ciofi-Baffoni, S.; Lenci, E.; Trabocchi, A.; Rusconi, S.

10.1101/2025.10.30.685646 — microbiology — Posted on 2025-11-03

5176 Biotope-dependent High Level Resistance to Reactive Oxygen Species, Antibiotic Tolerance, and Virulence of Staphylococcus aureus

Leguillier, V.; Gloux, K.; Khalife, M.; D'Mello, R.; Minic, Z.; Sentic, M.; Catto, M.; Manzano, M.; Pechoux, C.; Truchet, S.; Gaudu, P.; Nielsen-Leroux, C.; Heddi, B.; Gruss, A.; Vidic, J.

10.1101/2025.10.31.685911 — microbiology — Posted on 2025-11-03

5177 Frontal Vulnerability vs. Temporal Resilience within the core Language Network : Neuro-compensatory mechanisms underline differential language aging trajectories

Jain, P.; Akhter, A.; Banerjee, A.

10.1101/2025.04.29.651293 — neuroscience — Posted on 2025-11-03

5178 Retrosplenial cortex enables context-dependent goal-directed sensorimotor transformation

Bech, P.; Dard, R.; Lebert, J.; Smith, L.; Bisi, A.; Renard, A.; Crochet, S.; Petersen, C. C.

10.1101/2025.10.31.685738 — neuroscience — Posted on 2025-11-03

5179 Negative affective traits moderate transcranial direct current stimulation (tDCS) effects on memory

Zivanovic, M.; Bjekic, J.; Miniussi, C.; Paulus, W.; Filipovic, S. R.

10.1101/2025.08.15.670509 — neuroscience — Posted on 2025-11-03

5180 Estimating resource acquisition and water-use traits in wine grapes using reflectance spectroscopy

Mariani, R. O.; Isaac, M. E.; Cathline, K.; Robertson, G.; Martin, A. R.

10.1101/2025.10.29.685438 — plant biology — Posted on 2025-11-03

5181 NRT1.1s and NRT2.1 affect rhizosphere and apoplastic pH during nitrate uptake in Medicago truncatula

Murray, J. D.; Xiao, Q.; Wang, J.; Chen, Y.; Li, F.; Jiwu, W.; Miller, A. J.

10.1101/2025.10.30.685715 — plant biology — Posted on 2025-11-03

5182 Effects of residue substitutions on the cellular abundance of proteins

Schulze, T. K.; Lindorff-Larsen, K.

10.1101/2024.09.23.614650 — biophysics — Posted on 2025-11-03

5183 Beyond reference bias: Making pangenomes accessible with PangyPlot

Mastromatteo, S.; Chirmade, S.; Roshandel, D.; Thiruvahindrapuram, B.; Wang, Z.; Patel, R. V.; Sung, W. W.; Hajianpour, A.; Wang, C.; Lin, F.; Keenan, K.; Avolio, J.; Eckford, P.; Ratjen, F.; Canadian Cystic Fibrosis Gene Modifier Consortium, ; Strug, L.

10.1101/2025.10.31.684064 — genomics — Posted on 2025-11-03

5184 Selection inference in a complex genomic landscape: the impact of polymorphic inversions

Morales-Garcia, J.; Babik, W.; Zielinski, P.; Nadachowska-Brzyska, K.

10.1101/2025.07.01.662526 — evolutionary biology — Posted on 2025-11-03

5185 SARS-CoV-2 Variant-Dependent Alterations in Nasopharyngeal Microbiota and Host Inflammatory Response

Maulen, M.; Pezoa-Soto, I.; Leon, D.; Dominguez, E. M.; Martin, A. J.; Diaz-Vasquez, W. A.

10.1101/2025.10.30.685528 — microbiology — Posted on 2025-11-03

5186 Spanning spatial scales with functional imaging in the human brain; initial experiences at 10.5 Tesla

Vizioli, L.; Moeller, S.; Dowdle, L.; Grant, A.; Sadeghi-Tarakameh, A.; Eryaman, Y.; Lagore, R.; Auerbach, E.; Adriany, G.; Knudsen, L.; De Martino, F.; Faes, L.; Yacoub, E.; Ugurbil, K.

10.1101/2024.12.20.629800 — neuroscience — Posted on 2025-11-03

5187 Epithelial-mesenchymal transition couples with cell cycle arrest at various stages

Hu, S.; Lu, Y.; Yu, G.; Zheng, Z.; Ni, K.; Giri, A.; Zhang, J.; Zhang, Y.; Yao, G.; Xing, J.

10.1101/2025.02.24.639880 — systems biology — Posted on 2025-11-03

5188 BioToken and BioFM - Biologically-Informed Tokenization Enables Accurate and Efficient Genomic Foundation Models

Medvedev, A.; Viswanathan, K.; Kanithi, P.; Vishniakov, K.; Munjal, P.; Christophe, C.; Magalhaes, T. R.; Pimentel, M. A.; Rajan, R.; Khan, S.

10.1101/2025.03.27.645711 — genomics — Posted on 2025-11-03

5189 T cell costimulatory and inhibitory signals differentially modulate LAT condensate nucleation propensity after TCR ligation

Choi, S.; Kim, S.; Tijam, J. R.; Eisen, T. J.; Morita, S.; McAffee, D. B.; Groves, J. T.

10.1101/2025.11.01.685673 — biophysics — Posted on 2025-11-03

5190 A Python framework for magnetic tweezers real-time image processing and microscope control

London, J. A.; Singh, A. K.; Svendsen, T. C.; Tirtom, N. E.; Root, Z. A.; Fishel, R.

10.1101/2025.10.31.685671 — biophysics — Posted on 2025-11-03

5191 ProAffinity++

Xu, K.; Di, Z.; Zhao, J.; Zhang, H.; Bu, D.

10.1101/2025.10.31.685718 — bioinformatics — Posted on 2025-11-03

5192 Permissive and instructive Hox codes govern limb positioning

Wang, Y.; Hintze, M.; Wang, J.; Tao, H.; Petzsch, P.; Kohrer, K.; Cheng, L.; Zhou, P.; Wang, J.; Liao, Z.; Qi, X.-F.; Cai, D.; Bartolomaeus, T.; Schilling, K.; Wilting, J.; Kuerten, S.; Koentges, G.; Patel, K.; Pu, Q.; Huang, R.

10.1101/2024.07.15.603511 — developmental biology — Posted on 2025-11-03

5193 Signaling bias of the protease-activated receptor-1 is dictated by distinct GRK5 and β-arrestin-2 determinants

Gonzalez Ramirez, M. L.; Orduna-Castillo, L. B.; Bardeleben, C.; Qin, H.; Lin, Y.; Birch, C. A.; Kufareva, I.; Trejo, J.

10.1101/2025.11.02.686167 — cell biology — Posted on 2025-11-03

5194 Human non-canonical inflammasomes activate CASP3 to limit intracellular Salmonella replication in macrophages.

Kulkarni, M.; Bourne, C. M.; Mahale, A. B.; Exconde, P. M.; Murphy, C.; Cervantes, S.; Kardhashi, M.; Kambayashi, M.; Yoo, W.; Wrong, T. J.; Patio, R. C.; Discher, B. M.; Taabazuing, C. Y.

10.1101/2025.10.31.685927 — cell biology — Posted on 2025-11-03

5195 Germline-limited transposon remnants foster somatic genome diversification

Stefanov, B.-A.; Nowacki, M.

10.1101/2025.11.02.686105 — cell biology — Posted on 2025-11-03

5196 Activated protein C promotes beta-arrestin-2- and c-Src-dependent caveolin-1 (Cav1) phosphorylation and alters Cav1 association with PAR1 and GRK5

Qin, H.; Orduna-Castillo, L.; Molinar-Inglis, O.; Gonzalez Ramirez, M.; Lopez-Ramirez, M. A.; Bardeleben, C.; Trejo, J.

10.1101/2025.11.02.686166 — cell biology — Posted on 2025-11-03

5197 ER-liquid condensate contacts sequester FAM134B/C and RhoA to govern cell morphology

Jimenez-Moreno, N.; Karageorgiou, A.; Winnington-Ingram, K.; Wills, J.; Pednekar, C.; Pearson, M.; Gerasimavicius, L.; Wheeler, A.; Marsh, J. A.; Verkade, P.; von Kriegsheim, A.; Lane, J. D.; Wilkinson, S.

10.1101/2025.11.01.685922 — cell biology — Posted on 2025-11-03

5198 Transcriptional control of meiotic recombination by the DREAM complex

Tuncay, H.; Ma, X.; Lang, L.; Boewer, F.; Latrasse, D.; Benhamed, M.; Schnittger, A.

10.1101/2025.11.02.686075 — cell biology — Posted on 2025-11-03

5199 Deficient Cardiolipin Remodeling Alters Muscle Fiber Composition and Neuromuscular Connectivity in Barth Syndrome

Matias, C.; Snider, P. L.; Potchanant, E. A. S.; Huot, J. R.; Raghav, R.; Chin, M. T.; Conway, S. J.; Brault, J. J.

10.1101/2025.10.31.685856 — cell biology — Posted on 2025-11-03

5200 Novel high-resolution ion mobility mass spectrometry for site-specific quantification of the sirtuin-5 regulated kidney succinylome

Schilling, B.; Rorrer, L.; Royer, L.; Silva-Barbosa, A.; Pfister, K.; Goetzman, E. S.; Sims-Lucas, S.; DeBord, D.; Bons, J.

10.1101/2025.11.01.686011 — cell biology — Posted on 2025-11-03

5201 Regulation of Muscle Stem Cell Dynamics and Quiescence by Netrin-1 Cytoskeletal Signaling

Lo, H.-F.; Lu, Y.; Sachs, D.; Cloutier, J.-F.; Chen, E.; Krauss, R.

10.1101/2025.11.01.686042 — cell biology — Posted on 2025-11-03

5202 A single-component optogenetic toolkit for programmable control of microtubule

Ma, G.; Liu, X.; Lan, T.-H.; Duong, T.; Chiu, M.; Du, D.; Reiner, D.; Huang, Y.; Zhou, Y.

10.1101/2025.10.31.685931 — cell biology — Posted on 2025-11-03

5203 Glucagon-like peptide-1 receptor C-terminal tail phosphorylation determines signalling responses from pancreatic β-cells

Manchanda, Y.; Wong, N.; Milner, A.; Tomas, A.

10.1101/2025.11.01.686001 — cell biology — Posted on 2025-11-03

5204 Generation of cloned sheep lacking galactose-α1,3-galactose and Nglycolylneuraminic acid antigens

Appleby, S. J.; Fermin, L. M.; McLean, Z.; Delaney, S.; Wagner, S.; Di Genova, C.; Wei, J.; Meng, F.; Wells, D. N.; Oback, B.

10.1101/2025.10.31.684537 — cell biology — Posted on 2025-11-03

5205 CD133 shapes extracellular vesicle cargo and angiogenic function in basal-like triple-negative breast cancer

D'ANGELO, G.; Gomez-Duro, M.; BERGAM, P.; Martin-Jaular, L.; Sanchez-Redondo, S.; Hergueta-Redondo, M.; Dingli, F.; Loew, D.; Peinado, H.; Dubois, T.; raposo, G.

10.1101/2025.10.31.685601 — cell biology — Posted on 2025-11-03

5206 Steroid hormone production by coral-associated Endozoicomonasduring thermal stress

Mohamed, A. R.; Ochsenkuhn, M.; Haydon, T. D.; Abdelrazig, S.; Coe, L. S.; Mochales-Riano, G.; Raina, J.-B.; Abrego, D.; Amin, S. A.

10.1101/2023.09.19.558257 — microbiology — Posted on 2025-11-03

5207 Tracing the neural trajectories of evidence accumulation and motor preparation processes during voluntary decisions

Fong, L. C.; Garrett, P. M.; Smith, P. L.; Hester, R.; Bode, S.; Feuerriegel, D.

10.1101/2025.10.30.685712 — neuroscience — Posted on 2025-11-03

5208 Distinct, asynchronous processes underlie cultural and genetic variation in a bird species with a complex song repertoire

Arvind, C.; Sawant, S. G.; Srinivasan, R.; GP, A.; Goyal, N.; Warudkar, A.; VV, R.

10.1101/2025.11.02.684965 — evolutionary biology — Posted on 2025-11-02

5209 Structural changes in autism reflect atypical brain network organization and phenotypical heterogeneity: a hybrid deep network approach

Lokray, S.; Zikopoulos, B.; Yazdanbakhsh, A.

10.1101/2025.11.02.686152 — neuroscience — Posted on 2025-11-02

5210 Modelling Predictive Coding in the Primary Visual Cortex (V1): Layer 2/3 Circuits for Prediction Error Computation through Compartmentalized Spiking Neurons

Nemati, E.; Davey, C. E.; Meffin, H.; Burkitt, A. N.

10.1101/2025.11.01.686040 — neuroscience — Posted on 2025-11-02

5211 Striatal Pathways for Action Counting and Steering

Fallon, I. P.; Roshchina, M.; Hong, F.; Fernandez, S.; Ruan, S.; Yin, H.

10.1101/2025.11.02.686102 — neuroscience — Posted on 2025-11-02

5212 An intron-based timer for circadian rhythms

Yuan, Y.; Linskens, A.; Gouvea, R. D.; Liu, H.; Xiao, Y.; Suresh, S.; Hu, I.; Yadlapalli, S.

10.1101/2025.10.27.684876 — molecular biology — Posted on 2025-11-02

5213 Atlas-Guided Discovery of Transcription Factors for T Cell Programming

Chung, H. K.; Liu, C.; Battu, A.; Jambor, A. N.; Pratt, B. M.; Xie, F.; Riesenberg, B. P.; Casillas, E.; Sun, M.; Landoni, E.; Li, Y.; Ye, Q.; Joo, D.; Green, J.; Syed, Z.; Brown, N. J.; Smith, M.; Ma, S.; Chick, B.; Tripple, V.; Tan, S.; Wang, Z. A.; Wang, J.; Mcdonald, B.; He, P.; Yang, Q.; Chen, T.; Varanasi, S. K.; LaPorte, M.; Mann, T. H.; Chen, D.; Hoffmann, F.; Ho, J.; Modliszewski, J.; Williams, A.; Liu, Y.; Wang, Z.; Liu, J.; Gao, Y.; Hu, Z.; Cho, U. H.; Liu, L.; Wang, Y.; Hargreaves, D. C.; Dotti, G.; Savoldo, B.; Thaxton, J. E.; Milner, J. J.; Wang, W.; Kaech, S. M.

10.1101/2023.01.03.522354 — immunology — Posted on 2025-11-02

5214 The tree cricket ear is a highly phase sensitive biomechanical interferometer.

Celiker, E.; Sutton, G. P.; Mhatre, N. P.

10.1101/2025.10.28.684507 — physiology — Posted on 2025-11-02

5215 Epithelium Stratifies via Nucleation and Growth Induced by Foam-Geometric Instability

Fukamachi, S.; Datta, R.; Wuergezhen, D.; Ichikawa, T.; Yagasaki, R.; Leeaw, P.; Arai, M.; Teranihsi, A.; Horiguchi, S. A.; Omachi, K.; Sada, A.; Imayoshi, I.; Kajiwara, K.; Hiraiwa, T.; Fukuma, T.; Fujiwara, H.; Okuda, S.

10.1101/2024.12.26.630435 — biophysics — Posted on 2025-11-02

5216 Deviation Error: assessing machine learning predictions for replicate measurements in genomics and beyond

Abdulnabi, H.; Westwood, J. T.

10.1101/2025.05.29.656931 — bioinformatics — Posted on 2025-11-02

5217 scBaseCount: an AI agent-curated, uniformly processed, and autonomously updated single cell data repository

Youngblut, N. D.; Carpenter, C.; Nayebnazar, A.; Adduri, A.; Shah, R.; Ricci-Tam, C.; Prashar, J.; Ilango, R.; Teyssier, N.; Konermann, S.; Hsu, P.; Dobin, A.; Burke, D. P.; Goodarzi, H.; Roohani, Y. H.

10.1101/2025.02.27.640494 — bioinformatics — Posted on 2025-11-02

5218 Unveiling the evolutionary code of NOTCH3: mammalian bioinformatics sheds light on human pathogenicity.

Siddiqui, K. S.; Ertan, H.; Ren, Y.; Plojak, A.; Jayasena, T.; Sachdev, P. S.

10.1101/2025.09.28.678708 — bioinformatics — Posted on 2025-11-02

5219 ARCLID: Accurate and Robust Characterization of Long Insertions and Deletions in Genome

Tavakoli, S.; Frandsen, R. J. N.; Mansourvar, M.

10.1101/2025.10.10.681591 — bioinformatics — Posted on 2025-11-02

5220 Secretory Autophagy via VMP1-Containing Extracellular Vesicles in Pancreatic Stress Responses

Tadic, M. S.; Renna, F. J.; Lopez, M. H.; Mingorance, F. L.; Orquera, T.; Chiappetta, D.; Ropolo, A. J.; Vaccaro, M. I.

10.1101/2024.10.31.615473 — biochemistry — Posted on 2025-11-02

5221 Dosage compensation and meiotic sex chromosome inactivation are maintained in the absence of selection

Parker, D. J.; Dumas, Z.; Lencero, R. G.; Aury, J.-M.; Labedan, M.; Tran Van, P.; Istace, B.; Cruaud, C.; Labadie, K.; Noel, B.; Freitas, S.; Djordjevic, J.; Schwander, T.

10.1101/2025.07.27.667025 — evolutionary biology — Posted on 2025-11-02

5222 C. elegans pre-dauer starvation arrests germ cell proliferation and ligand presentation by the germline stem cell niche via a rapidly reversible, protein-based mechanism

Koitz, F. A.; Miller, C. P.; Kinney, B.; Gordon, K. L.

10.1101/2025.05.23.655783 — developmental biology — Posted on 2025-11-02

5223 Modelling cognitive outcomes in the UK Biobank: education, noradrenaline and frontoparietal networks

Bravo-Merodio, L.; Williams, J. A.; Russ, D. R.; Gkoutos, G.; Brosnan, M.; Bellgrove, M. A.; Chechlacz, M.

10.1101/2023.08.31.555645 — neuroscience — Posted on 2025-11-02

5224 Age-related microbiome metabolites alter RNA splicing and chromatin accessibility in the brain

Chakraborty, M.; Shi, S. M.; Porter, I. E.; Richard, D. J.; Marinov, G. K.; Moore, A. A.; Blum, J. L. E.; Natarajan, A.; Jahng, J. W.; Wu, J. C.; Lu, S. X.; Davidson, S. M.; Greenleaf, W. J.; Saw, N. L.; Shamloo, M.; Brunet, A.; Wyss-Coray, T.; Bhatt, A. S.

10.1101/2025.10.03.680371 — neuroscience — Posted on 2025-11-02

5225 Cue-Invariant Geometric Structure of the Population Codes in Macaque V1 and V2

Massot, C.; Zhang, X.; Wang, Z.; Rockwell, H.; Papandreou, G.; Yuille, A.; Lee, T.-S.

10.1101/2023.12.05.570110 — neuroscience — Posted on 2025-11-02

5226 Adolescent social profiles predict adult social behaviour, monoamine brain content and regional gene expression

Mirofle, N.; Jamain, S.; Chauveau, F.; Penot, M.; Chater, D.; Latapie, V.; Deneux, T.; Faure, A.; Granon, S.

10.1101/2025.10.23.684125 — neuroscience — Posted on 2025-11-02

5227 Backward Conditioning Reveals Flexibility in Infralimbic Cortex Inhibitory Memories

Lingawi, N. W.; Chieng, B.; Westbrook, R. F.; Holmes, N. M.; Bouton, M. E.; Laurent, V.

10.1101/2025.08.02.668258 — neuroscience — Posted on 2025-11-02

5228 Cerebellar climbing fibers impact experience-dependent plasticity in the mouse primary somatosensory cortex

Silbaugh, A.; Koster, K. P.; Hansel, C.

10.1101/2025.04.18.649578 — neuroscience — Posted on 2025-11-02

5229 Impact of dopaminergic modulation on the state transitions of striatal medium spiny neuron sub-types - a computational study

Anisetty, N.; Manchanda, R.

10.1101/2024.12.22.629989 — neuroscience — Posted on 2025-11-02

5230 The basolateral amygdala complex and perirhinal cortex represent focal and peripheral states of information processing in rats

Wong, F. S.; Killcross, S.; Westbrook, R. F.; Holmes, N. M.

10.1101/2025.06.25.661598 — neuroscience — Posted on 2025-11-02

5231 Transient dopamine response on medium spiny neuron subtypes in switching approach-avoidance outcomes against action bias - A framework for exploration in action selection

Anisetty, N.; Manchanda, R.

10.1101/2024.12.24.630270 — neuroscience — Posted on 2025-11-02

5232 Dissociating internal representations underlying knowing and experiencing

Tian, S.; Mao, X.; Wang, D.-H.; Wang, X.; Bi, Y.

10.1101/2025.08.01.668040 — neuroscience — Posted on 2025-11-02

5233 Brain-like neural dynamics for behavioral control develop through reinforcement learning

Codol, O.; Krishna, N. H.; Lajoie, G.; Perich, M. G.

10.1101/2024.10.04.616712 — neuroscience — Posted on 2025-11-02

5234 From Lab to Industry: Awareness of the translational potential of Extracellular Vesicles by the ISEV Translation, Regulation and Advocacy Committee (ISEV-TRA).

Gurriaran, U.; Bussolati, B.; Gimona, M.; Glebov, K.; Fujita, Y.; Marcilla, A.; Neri, C.; Fu, Q.-l.; Das, S.; Pluchino, S.; Zarovni, N.; Salomon, C.; Witver, K.; Falcon-Perez, J. M.

10.1101/2025.10.31.685739 — scientific communication and education — Posted on 2025-11-02

5235 Characterization of genetically novel chimeric plasmids from Salmonella Heidelberg conferring multi-drug resistance and increased pathogenicity

Betts, J.; Liaropoulos, A.; Buffoni, M.; Brouwer, M. S. M.; Veldman, K. T.; Salguero, F. J.; La Ragione, R.; Ceccarelli, D.; Liakopoulos, A.

10.1101/2025.10.27.684768 — microbiology — Posted on 2025-11-02

5236 Press Releases Shape Online Attention for Neuroscience Articles

Bastida-Barau, R.; Giner-Miguelez, J.; Barcia, C.; Ferre, S.

10.1101/2025.10.31.685745 — scientific communication and education — Posted on 2025-11-02

5237 Discovery Stack Pilot: Feasibility and Outcomes of a Scientist-Designed Peer Review Model Separating Quality and Impact

10.1101/2025.10.31.685758 — scientific communication and education — Posted on 2025-11-02

5238 Mapping Allosteric Rewiring in Viral RNA: Sequence-Encoded Control of Protein Binding Mechanisms

Samant, D.; Chakraborty, A.; Sinha, A.; Sarkar, R.; Roy, S.

10.1101/2025.11.01.685830 — biophysics — Posted on 2025-11-02

5239 Structural basis for lipid binding by the blood protein vitronectin, a component of HDL

Shin, K.; Brown, W.; Tian, Y.; Gopinath, T.; Bobkov, A. A.; Marinelli, F.; Marassi, F. M.

10.1101/2025.11.01.685992 — biophysics — Posted on 2025-11-02

5240 Studying macromolecular composition in cell-cell interfaces using 3D membrane reconstitution systems

Ragaller, F.; Schneider, A. M.; Sjule, E.; Sun, R.; Han, X.; Jenkins, E.; Dustin, M.; Achour, A.; Sezgin, E.

10.1101/2025.11.01.686034 — biophysics — Posted on 2025-11-02

5241 Singletrack: An Algorithm for Improving Memory Consumption and Performance of Gap-Affine Sequence Alignment

Lopez-Villellas, L.; Iniguez, C.; Jimenez-Blanco, A.; Aguado-Puig, Q.; Moreto, M.; Alastruey-Benede, J.; Ibanez, P.; Marco-Sola, S.

10.1101/2025.10.31.685625 — bioinformatics — Posted on 2025-11-02

5242 An Application for Automated Drosophila Locomotor Assay with Integrated Device Design and Computer Vision Tracking

Melkani, D.; Harnwal, N.; Desai, S.; Patel, D.; Melkani, G. C.

10.1101/2025.10.31.685789 — bioinformatics — Posted on 2025-11-02

5243 Detection dog performance state estimation from pre-stimulus video and physiological signals using deep learning and Bayesian inference

Schultz, J.; Rothkoff, L.; Aviles-Rosa, E.; Hall, N. J.; Maughan, M. N.

10.1101/2025.10.31.685787 — animal behavior and cognition — Posted on 2025-11-02

5244 A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions

Camargo, A. P.; Baltoumas, F. A.; Ndela, E. O.; Fiamenghi, M. B.; Merrill, B. D.; Carter, M. M.; Pinto, Y.; Chakraborty, M.; Andreeva, A.; Ghiotto, G.; Shaw, J.; Proal, A. D.; Sonnenburg, J. L.; Bhatt, A. S.; Roux, S.; Pavlopoulos, G. A.; Nayfach, S.; Kyrpides, N. C.

10.1101/2025.11.01.686033 — genomics — Posted on 2025-11-02

5245 Fission yeast histone chaperone Rtt106 regulates histone levels, prevents early division, and promotes genome stability

Sanayhie, S. A.; Da Pra, V. A.; Khodabakhshian, N.; Karam, E.; Chhipa, M. A.; Kang, S.; Ahmed, A.; Fillingham, J.; Sabatinos, S. A.

10.1101/2025.11.01.686071 — genetics — Posted on 2025-11-02

5246 Split-luciferin Assay for Real-time Measurement of Cytosolic Drug Accumulation in Live Mycobacteria

Dash, R.; Spira, A.; Lucas, N.; Bhandari, S.; Chordia, M.; Pires, M.

10.1101/2025.11.02.686125 — microbiology — Posted on 2025-11-02

5247 Spatiotemporal regulation of arbuscular mycorrhizal symbiosis at cellular resolution

Chancellor, T.; Ferreras-Garrucho, G.; Akmakjian, G. Z.; Montero, H.; Bowden, S. L.; Hope, M.; Wallington, E.; Bhattacharya, S.; Korfhage, C.; Bailey-Serres, J.; Paszkowski, U.

10.1101/2025.10.31.685811 — plant biology — Posted on 2025-11-02

5248 Physical mechanisms of nanoparticle-membrane interactions: A coarse-grained study

Paesani, M.; Ilie, I. M.

10.1101/2025.10.31.685850 — biophysics — Posted on 2025-11-02

5249 Clair-Mosaic: A deep-learning method for long-read mosaic small variant calling

Chen, L.; Zheng, Z.; He, M.; Wong, A. O. K.; Yu, X.; Li, J.; Zhang, J.; Zhou, Y.; Luo, R.

10.1101/2025.10.31.685831 — bioinformatics — Posted on 2025-11-02

5250 InCytokine, an open-source software, reveals a TREM2 variant specific cytokine signature

Jha, D.; Ancona, M.; Oplt, F.; Farmer, S. L.; Vagenknecht, M.; Vazquez-Otero, A.; Pradznyk, I.; Soukup, J.; Mathew, R. S.; Peterson, V.; Bitton, D. A.

10.1101/2025.10.31.685741 — bioinformatics — Posted on 2025-11-02

5251 iDeepLC: chemical structure information yields improved retention time prediction of peptides with unseen modifications

Nameni, A.; Declercq, A.; Gabriels, R.; Devreese, R.; Degroeve, S.; Martens, L.; Bouwmeester, R.

10.1101/2025.10.31.685771 — bioinformatics — Posted on 2025-11-02

5252 Deep learning assessment of nativeness and pairing likelihood for antibody and nanobody design with AbNatiV2

Ramon, A.; Frassetto, N.; Zhao, H.; Xu, X.; Greenig, M.; Onuoha, S.; Sormanni, P.

10.1101/2025.10.31.685806 — bioengineering — Posted on 2025-11-02

5253 Integrated multi-modal data analysis for computational modeling of healthy and location-dependent myocardial infarction conditions in porcine hearts

Rosales, R. M.; Wu, M.; Claus, P.; Janssens, S.; Rios-Munoz, G. R.; Fernandez-Santos, M. E.; Martinez-Legazpi, P.; Bermejo, J.; Flanagan, A.; Doblare, M.; Minchole, A.; Pueyo, E.

10.1101/2025.10.31.685788 — bioengineering — Posted on 2025-11-02

5254 Oral delivery of mesenchymal stem cell-derived extracellular vesicles to treat intestinal inflammation

Belaid, M.; Chng, W. H.; Muthuramalingam, R. P. K.; Lim, Y. W.; Javorovic, J.; Zhang, Y.; Luo, X.; Czarny, B.; Vllasaliu, D.

10.1101/2025.10.31.685898 — bioengineering — Posted on 2025-11-02

5255 VariantFormer: A hierarchical transformer integrating DNA sequences with genetic variations and regulatory landscapes for personalized gene expression prediction

Ghosal, S.; Barhomi, Y.; Ganapathi, T.; Krystosik, A.; Krishnan, L.; Guntury, S.; Li, D.; Casale, F. P.; Karaletsos, T.

10.1101/2025.10.31.685862 — genomics — Posted on 2025-11-02

5256 Oyster: a neural network for modelling genomic sequences that enables exact position-specific k-mer contributions

Abdulnabi, H.; Westwood, J. T.

10.1101/2025.11.01.686014 — genomics — Posted on 2025-11-02

5257 Forecasting bryozoan assemblage dynamics under simulated climate change

Baer, M.; Allhoff, K. T.; Barnes, D. K. A.; Koch, F.

10.1101/2025.10.31.685734 — ecology — Posted on 2025-11-02

5258 Decoding pathogen ecological memory from chemical-stress phenotypes

Baek, I.; Lim, S.; Lovelace, A.; Oh, S.; Kazem-Rostami, M.; Ngo, H.; Kim, M.; Meinhardt, L.; Kandpal, L.; Cha, M.; Hwang, C.; Ashby, R.; Ahn, E.

10.1101/2025.11.01.686032 — microbiology — Posted on 2025-11-02

5259 Development of a stable transformation method for Saprolegnia parasitica

Trusch, F.; Tumpa, I.; McLaggan, D.; van der Giezen,, M.; van West, P.

10.1101/2025.11.02.686010 — microbiology — Posted on 2025-11-02

5260 An Eligibility-Aware Pipeline for Robust ITS Diagnostics in Fungi: A Cacao Case Study with Generalizable Rules

Lim, S.; Baek, I.; Bhatt, J.; Upadhyay, R.; Oh, S.; Cha, M.; Kim, M. S.; Meinhardt, L.; Ahn, E.

10.1101/2025.11.01.686068 — microbiology — Posted on 2025-11-02

5261 Entomopathogenic fungi as dual-function biocontrol agents: persistence and microbiome modulation in date palm soils

Matveev, S.; Reingold, V.; Doron-Faigenboim, A.; Livne, Y.; Davidovitz, M.; Ment, D.

10.1101/2025.11.02.686131 — microbiology — Posted on 2025-11-02

5262 A cattle-derived human H5N1 isolate suppresses innate immunity despite efficient replication in human respiratory organoids

Shichinohe, S.; Sugimoto, H.; Yamasaki, M.; Hashimoto, R.; Morita, T.; Kobayashi, D.; Hiono, T.; Motooka, D.; Shimooka, M.; Isoda, N.; Le, M. T. Q.; Takada, A.; Sakoda, Y.; Kawakami, E.; Takayama, K.; Watanabe, T.

10.1101/2025.11.02.684669 — microbiology — Posted on 2025-11-02

5263 Phosphorylation of a conserved intrinsically disordered region is necessary for activation of a bacterial Hanks-type Ser/Thr kinase signaling pathway

Grunfeld, N.; Levine, E.; Libby, E. A.

10.1101/2025.11.01.686061 — microbiology — Posted on 2025-11-02

5264 Open and closed forms of assembled henipavirus nucleoprotein suggest structural basis of genome access

Jayachandran, R. B.; Quignon, E.; Renner, M.

10.1101/2025.11.02.686081 — microbiology — Posted on 2025-11-02

5265 A Specialized CD107a+ Macrophage Subset Drives Selective Mycobacterial Phagocytosis

Eto, C.; Luiz, G.; Silva, H. M.; Munari, E. L.; Mendes, D. A. G. B.; Beck, B. K.; Mascarin, L. Z.; Starick, M.; Canesso, M. C. C.; Reis, B. S.; Silveira, G.; Bordignon, J.; de Menezes, Y. K. T.; Mansur, D. S.; Lummertz da Rocha, E.; Bafica, A. L. B.

10.1101/2025.10.31.685620 — immunology — Posted on 2025-11-02

5266 Tissue-embedded CD4⁺ plasticity structures mucosal immunity in IBD-related inflammation

Jiang, Q.; Merkus, V.; Lindelauf, C.; Guo, N.; Ouboter, L. F.; Hollt, T.; Meijer- Boekel, C. R.; Koning, F.; van der Meulen-de Jong, A. E.; Pascutti, M. F.; van Unen, V.

10.1101/2025.10.31.685649 — immunology — Posted on 2025-11-02

5267 CryoWriter: A Robotic Solution for Improved Cryo-EM Grid Preparation

K.V., C.; Ekundayo, B.; di Fabrizio, M.; Mohammed, I.; Radecke, J.; Stahlberg, H.; Kube, M.

10.1101/2025.11.01.686008 — biophysics — Posted on 2025-11-02

5268 Mitochondrial genome microhomology-mediated editing by donor DNA delivery into mitochondria in human cells.

Maximov, V. V.; Shebanov, N.; Nikitchina, N.; Rapoport, R.; Maor, Y.; Tarassov, I.; Pines, O.; Entelis, N.

10.1101/2025.11.02.686110 — molecular biology — Posted on 2025-11-02

5269 Mitochondrial Dysfunction Rewires Macrophage Metabolism, Driving Pro-inflammatory Priming and Immune System Remodeling

Markov, N.; Hosseini, A.; Fettrelet, T.; Oberson, K.; Brichkina, A.; Yousefi, S.; Bourquin, C.; Simon, H.-U.

10.1101/2025.11.01.686039 — immunology — Posted on 2025-11-02

5270 Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing

Ohnezeit, D.; Loliashvili, E.; Putzel, G.; Verstraten, R.; Liu, J.; Nicholson, L. S.; Pironti, A.; Jaffrey, S. R.; Depledge, D. P.; Wilson, A. C.

10.1101/2025.11.02.686099 — bioinformatics — Posted on 2025-11-02

5271 Large mRNA language foundation modeling with NUWA for unified sequence perception and generation

Zhong, Y.; Yan, W.; Zhang, Y.; Tan, K.; Bian, B.

10.1101/2025.11.01.686058 — bioinformatics — Posted on 2025-11-02

5272 Detection of environmental DNA of the Indo-Pacific humpback dolphins in Hong Kong waters using quantitative PCR

Kisero, R. O.; Tsuji, S.; Ohigashi, T.; Porter, L.; Matrai, E.; Ushio, M.

10.1101/2025.10.30.685690 — ecology — Posted on 2025-11-02

5273 Cost of altered translation accuracy shapes adaptation to antibiotics in E. coli

Samhita, L.; Tamhankar, S.; Miranda, J.; Basu, A. K.; Agashe, D.

10.1101/2025.06.28.662112 — evolutionary biology — Posted on 2025-11-02

5274 Modelling DNA replication fork stability and collapse using chromatin fiber analysis and the R-ODD-BLOBS program

Cheng, K.; Aliar, K.; Manshaei, R.; Forsburg, S. L.; Mazalek, A.; Sabatinos, S. A.

10.1101/2024.11.01.621594 — cell biology — Posted on 2025-11-02

5275 Tryptophan-Driven Metabolomic Shift in Acidobacteriaceae Reveals Phytohormones and Antifungal Metabolites

Zumkeller, C. M.; Hartwig, C.; Lanzalonga, W.; Patras, M. A.; Liu, Y.; Marner, M.; Mihajlovic, S.; Spohn, M. S.; Schaeberle, T. F.

10.1101/2025.10.02.680145 — microbiology — Posted on 2025-11-02

5276 KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS

Le, P.; Lal, N.; Xu, S.; Mumford, S.; Huang, M.; Yang, D.; Mizrahi, O.; Hoover, B.; Mei, Y.; Rothamel, K.; Her, H.-L.; Blue, S.; Shneider, N.; Yeo, G. W.

10.1101/2025.10.31.685813 — neuroscience — Posted on 2025-11-02

5277 Predictive learning enables compositional representations

Boeshertz, G.; Clopath, C.

10.1101/2025.09.26.678731 — neuroscience — Posted on 2025-11-02

5278 Enhanced Tactile Coding in Rat Neocortex Under Darkness

Yamashiro, K.; Shiyori, T.; Matsumoto, N.; Ikegaya, Y.

10.1101/2025.04.11.648316 — neuroscience — Posted on 2025-11-02

5279 Non-cell-autonomous mechanisms of tumor initiation and relapse by chromosomal instability

Lafirenze, S. J. A.; Kops, G. J.; van Gerwen, B.; Quirindongo, A. I.; Janssen, A.; Etemad, B.; Toonen, P.; Hoevenaar, W. H. M.; Costermans, N.; Youssef, S.; de Bruin, A.; Brosens, L. A. A.; Jelluma, N.

10.1101/2025.10.31.685838 — cancer biology — Posted on 2025-11-02

5280 Biophysical modeling identifies an optimal hybrid amoeboid-mesenchymal mechanism for maximal T cell migration speeds

Alonso Matilla, R.; Pedro, D. I.; Pepe, A.; Serrano-Velez, J.; Dunne, M.; Nguyen, D. T.; Sawyer, W. G.; Provenzano, P. P.; Odde, D. J.

10.1101/2023.10.29.564655 — biophysics — Posted on 2025-11-02

5281 Probing circuit mechanisms of feature selectivity in mouse visual cortex through synaptic-resolution connectomics

Buendia, V.; Biggiogera, J.; Sanzeni, A.

10.1101/2024.11.18.624135 — neuroscience — Posted on 2025-11-02

5282 A small cationic probe for accurate, punctate discovery of RNA tertiary structure

Ehrhardt, J. E.; Qiu, D. Y.; Jin, S.; Boerneke, M. A.; Aufgebauer, C. J.; Horner, S. M.; Weeks, K. M.

10.1101/2025.08.29.672938 — biochemistry — Posted on 2025-11-02

5283 Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape

Springstein, B. L.; Javoor, M. G.; Megrian, D.; Hajdu, R.; Hanke, D. M.; Zens, B.; Weiss, G. L.; Schur, F. K.; Loose, M.

10.1101/2025.06.27.661541 — microbiology — Posted on 2025-11-02

5284 Tuned to explore: Increased phasic responses to auditory targets and novelty in children regardless of induced tonic arousal

Mathieu, A.; Schöllkopf, U.; Chen, S.; Widmann, A.; Wetzel, N.; Bidet-Caulet, A.

10.1101/2025.11.01.684607 — neuroscience — Posted on 2025-11-02

5285 Deletion of Cacna1c (CaV1.2) in D1-expressing cells elicits divergent sex-specific effects on aversive and spatial memories

Walsh, J. D.; Scala Chavez, D.; Lee, A. S.; Martinez-Rivera, A.; Rajadhyaksha, A. M.

10.1101/2025.10.31.684545 — neuroscience — Posted on 2025-11-02

5286 Senescent astrocytic deposits drive cognitive decline by disrupting tripartite synapse in the aging brain

Wang, E.-J.; Ming, C.; Wang, Y.-T.; Wang, S.-J.; Song, Z.-H.; Yang, K.; Li, J.-T.; Zhuang, X.-X.; Wang, W.; Wu, M.-Y.; Xie, L.-M.; Ren, Z.-Y.; Liu, C.-P.; Wang, L.; Yao, Y.-G.; Li, M.; Cheung, K.-H.; Wu, A. J.; Shen, H.-M.; Su, H.; Yue, Z.; Lu, j.

10.1101/2025.10.31.685958 — neuroscience — Posted on 2025-11-02

5287 Rapid generation of ventral A9-like dopaminergic neurons from patterned iPSCs

Chaplot, K.; Zhang, L.; Wessman, J.; Rivera, M.; Wang, Z.; Wang, F.; Duan, X.; England, P. M.; Clark, I. C.; Ullian, E. M.

10.1101/2025.10.31.685897 — neuroscience — Posted on 2025-11-02

5288 Oligodendrocytes support functional development of subcortical premotor neurons and navigation

Auer, F.; Zhang, Y.; Schoppik, D.

10.1101/2025.11.01.686017 — neuroscience — Posted on 2025-11-02

5289 Behavioral age-detection in individuals reconstructs minute-scale developmental transcriptomics

Ganem, N. S.; Scher-Arazi, D.; Inberg, S.; Zeisel, A.; Stern, S.

10.1101/2025.11.01.686022 — developmental biology — Posted on 2025-11-02

5290 A semantotopic map in human hippocampus

Mickiewicz, E.; Franch, M.; Katlowitz, K.; Chavez, A. G.; Zhu, H.; Chericoni, A.; Yan, X.; Belanger, J.; Ismail, T.; Paulo, D.; Goldman, A.; Krishnan, V.; Maheshwari, A.; Bartoli, E.; Heilbronner, S.; Provenza, N.; Sheth, S.; Hayden, B.

10.1101/2025.10.31.685959 — neuroscience — Posted on 2025-11-02

5291 Task-optimized models of sensory uncertainty reproduce human confidence judgments

Govindarajan, L. N.; Alavilli, S.; McDermott, J. H.

10.1101/2025.10.31.685933 — neuroscience — Posted on 2025-11-02

5292 From perception to valence: a pair of interneurons that assign positive valence to sweet sensation in Drosophila

Christie, K. W.; Dadyala, T. S.; Sinakevitch, I. T.; Chung, P.; Ito, M.; Shao, L.

10.1101/2025.10.31.685871 — neuroscience — Posted on 2025-11-02

5293 Neonatal brain volumes and birth characteristics predict behavioural outcomes in toddlerhood

Khan, Y. T.; Tsompanidis, A.; Allison, C.; Bethlehem, R. A. I.; Baron-Cohen, S.

10.1101/2025.11.01.686012 — neuroscience — Posted on 2025-11-02

5294 A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects

Kathiriya, I. S.; Dominguez, M. H.; Rao, K. S.; Muncie-Vasic, J. M.; Devine, W. P.; Hu, K. M.; Hota, S. K.; Garay, B. I.; Quintero, D.; Goyal, P.; Matthews, M. N.; Thomas, R.; Sukonnik, T.; Miguel-Perez, D.; Winchester, S.; Brower, E. F.; Forjaz, A.; Wu, P.-H.; Wirtz, D.; Kiemen, A. L.; Bruneau, B. G.

10.1101/2024.02.05.578995 — developmental biology — Posted on 2025-11-01

5295 Dual recognition of structurally unrelated mildew effectors underlies the broad-spectrum resistance of Pm3e in wheat

Kunz, L.; Bernasconi, Z.; Heuberger, M.; Isaksson, J.; Sotiropoulos, A. G.; Stirnemann, U.; Jigisha, J.; Menardo, F.; Wicker, T.; Mueller, M. C.; Keller, B.

10.1101/2025.10.26.683672 — plant biology — Posted on 2025-11-01

5296 Classification models distinguish functional and trafficking effects of KCNQ1 variants to enhance variant interpretation

Chang-Gonzalez, A. C.; Bell, E. W.; Vanoye, C. G.; Guadarrama, E.; Desai, R. R.; DeKeyser, J.-M.; Butcher, K. R.; Scott, T.; Sanders, C. R.; George, A. L.; Ledwitch, K. V.; Meiler, J.

10.1101/2025.10.31.685955 — biophysics — Posted on 2025-11-01

5297 Co-opting the bacterial lipoprotein pathway in the biosynthesis of a lipidated macrocyclic peptide

Chen, J. Y.; Zhu, L.; Zhang, K. Y.; Berthold, D. A.; van der Donk, W. A.

10.1101/2025.10.31.685832 — biochemistry — Posted on 2025-11-01

5298 Molecular evolution of octopamine receptors in Drosophila

Yang, M.; Carlisle, J. A.; Hopkins, B. R.; Wolfner, M. F.

10.1101/2025.10.30.685676 — evolutionary biology — Posted on 2025-11-01

5299 Neural Progenitors as a Novel Pathogenic Mechanism in Microcephaly

Tshuva, R. Y.; Bok, J.; Nonaka, M.; Xue, X.; Bhattacharya, B.; Kshirsagar, A.; Olender, T.; Danan-Gotthold, M.; Fu, J.; Sapir, T.; Reiner, O.

10.1101/2025.08.12.669854 — developmental biology — Posted on 2025-11-01

5300 Ganaxolone, an approved therapy for CDKL5-Deficiency Disorder, is an inhibitor of PTP1B

Zubiete-Franco, I.; Hu, Q.; Tonks, N. K.

10.1101/2025.10.31.685887 — molecular biology — Posted on 2025-11-01

5301 The Phosphate-Specific Transport System Gene pstA1 Contributes to Rifampin Tolerance in Mycobacterium tuberculosis

Danchik, C.; Chinmayi, G. V. A.; Lee, G. Y.; Bader, J. S.; Eoh, H.; Karakousis, P.

10.1101/2025.10.31.685634 — microbiology — Posted on 2025-11-01

5302 Evolutionary landscape of oral microbiome over 100,000 years

Zhong, L.; Li, H.; Xia, S.; Xie, S.; Bianucci, R.; Li, S.; Supa-Amornkul, S.; Speller, C.; Shi, Q.; Cui, Y.; Yang, H.; Achtman, M.; Zhou, Z.

10.1101/2025.11.01.685986 — microbiology — Posted on 2025-11-01

5303 Human gaze behaviors track abstract stimulus categories

Caron, A.; Ester, E.

10.1101/2025.08.08.669367 — neuroscience — Posted on 2025-11-01

5304 Rhodo-Box: a Synthetic Biology Toolbox to Facilitate Metabolic Engineering of Rhodobacter sphaeroides

Kostanjsek, M.; Raynal, A.; Dimopoulos, G.; Behrendt, G.; Martins dos Santos, V. A. P.; Beekwilder, J.; Batianis, C.; Weusthuis, R. A.; Asin-Garcia, E.; Bisschops, M. M. M.

10.1101/2025.10.31.685836 — synthetic biology — Posted on 2025-11-01

5305 Novel binning-based methods for model fitting and data splitting improved machine learning imbalanced data

Abdulnabi, H.; Westwood, J. T.

10.1101/2025.06.26.661884 — bioinformatics — Posted on 2025-11-01

5306 CoxMDS: Multiple Data Splitting for High-dimensional Mediation Analysis with Survival Outcomes in Epigenome-wide Studies

Yao, M.; Tian, P.; Li, X.; Bian, S.; Wang, G.; Gu, Y.; Navas-Acien, A.; Vardarajan, B. N.; Belsky, D. W.; Miller, G. W.; Baccarelli, A. A.; Liu, Z.

10.1101/2025.10.11.681836 — bioinformatics — Posted on 2025-11-01

5307 Dual-Channel Event Microscopy for Ultrafast Biological Imaging

Guo, R.; Pan, X.; Deng, Q.; Ahmed, A.; Yang, Q.; Greene, J.; Li, T.; Chan, S. Y.; Chen, Z.; Hu, G.; Feng, H.; Tian, L.

10.1101/2025.11.01.685972 — bioengineering — Posted on 2025-11-01

5308 Unfolded protein response signaling promotes myeloid cell production and cooperates with oncogenic mutation

Choi, H.; Jung, S.-E.; Paik, H.; Earth, Y.; Yi, J.; Cox, M. J.; Oh, S. T.; Kang, Y.-A.

10.1101/2025.09.07.674755 — cell biology — Posted on 2025-11-01

5309 EVOH Hollow Fiber Encapsulation of Individual Caenorhabditis elegans for Transmission Electron Microscopy

Liou, W.; Belnap, D. M.

10.1101/2025.10.08.681240 — cell biology — Posted on 2025-11-01

5310 Endoplasmic reticulum-mitochondrion disconnection promotesmetabolic reprogramming and cystogenesis in polycystic kidneydisease

Padhy, B.; Xie, J.; Idrees, D.; Cheng, C.-J.; Huang, C.-L.

10.1101/2025.10.31.685870 — molecular biology — Posted on 2025-11-01

5311 A single-cell atlas of Toxoplasma sexual development identifies regulators of gametogenesis

Alrubaye, H. S.; Reilly, S. M.; da Silva, R. J.; Washington, N.; Boyle, J. P.

10.1101/2025.10.31.685900 — microbiology — Posted on 2025-11-01

5312 Twin-arginine transport complex plays an essential role in Caulobacter cell shape and viability

Chong, T. N.; Christensen, K.; Whitfield, D. L.; Panjalingam, M.; Pendar, N.; Myat, P. P.; Chen, J. C.

10.1101/2025.10.31.685914 — microbiology — Posted on 2025-11-01

5313 Tracing the neural trajectories of evidence accumulation and motor preparation processes during voluntary decisions

Fong, L. C.; Garrett, P. M.; Smith, P. L.; Hester, R.; Bode, S.; Feuerriegel, D.

10.1101/2025.10.30.685712 — neuroscience — Posted on 2025-11-01

5314 Specialized parallel pathways for adaptive control of visual object pursuit

Collie, M. F.; Jin, C.; Rockwell, V.; Kellogg, E.; Vanerbeck, Q. X.; Hartman, A. K.; Holtz, S. L.; Wilson, R. I.

10.1101/2025.04.23.650240 — neuroscience — Posted on 2025-11-01

5315 Data-driven model reveals increased stability of CAG-expanded huntingtin RNA due to MID1 binding

Liu, Y.; Reisbitzer, A.; Doresic, D.; Hasenauer, J.; Krauss, S.; Tchumatchenko, T.

10.1101/2025.10.31.685889 — systems biology — Posted on 2025-11-01

5316 De novo design of metal-oxide templating proteins

Saragovi, A.; Pyles, H.; Huddy, T. F.; Li, X.; Borst, A. J.; Hanikel, N.; Courbet, A.; Kwon, P.; Davila-Hernandez, F. A.; Kibler, R. D.; Vafeados, D. K.; Allen, A.; Carr, K. D.; Bera, A.; Kang, A.; Brackenbrough, E.; Schmid, S.; Bae, Y.; Stewart, L.; Zhang, S.; De Yoreo, J.; Baker, D.

10.1101/2024.06.24.600095 — synthetic biology — Posted on 2025-11-01

5317 Structural Mechanism of Prestin-Membrane Mechanotransduction

Bavi, N.; Haller, P.; Homma, K.; Lin, X.; Milewski, W.; Zhao, M.; Sosnick, T.; Perozo, E.

10.1101/2025.10.31.685930 — biophysics — Posted on 2025-11-01

5318 Beyond the 1:1 Ligand-Protein Paradigm: An In Silico Assay for Competitive Ligand Binding

Cardenas, V. B.; Raniolo, S.; Conflitti, P.; Limongelli, V.

10.1101/2025.10.31.685849 — biochemistry — Posted on 2025-11-01

5319 RNA G-Quadruplexes Function as a Tunable Switch of FUS Phase Separation

Carey, J. L.; Hayashi, M.; Welebob, E.; Ganser, L. R.; Wang, H.; Buckhaults, K.; DePierro, J. A.; Shi, Z.; Shorter, J.; Myong, S.; Haeusler, A.; Guo, L.

10.1101/2025.10.31.685846 — biochemistry — Posted on 2025-11-01

5320 Mechanistic dissection of a dopamine-gated cation channel from Daphnia reveals key determinants of ligand selectivity and sensitivity

McRunnel, T. M.; Reynoldson, T. E.; Hardege, I.

10.1101/2025.10.31.685654 — biochemistry — Posted on 2025-11-01

5321 Evolutionary convergence of a Pyroptosis-Apoptosis crosstalk drives non-canonical inflammasome signalling.

Grant, S.; Nicholson, E.; Chen, Z. H. X.; Robson, C.; Viswanathan, B.; Chang, Y.; Sung, A. W.; Patel, P.; Kleppen, J.; Ozdenya, T.; Chen, K.; Spicer, C. D.; Boucher, D.

10.1101/2025.11.01.685735 — biochemistry — Posted on 2025-11-01

5322 Molecular mechanism of naturally-encoded signaling-bias at the complement anaphylatoxin receptors

Tiwari, D.; Sawada, K.; Dalal, A.; Mishra, S.; Li, X. X.; Dent, J.; Kim, K.; Yadav, M. K.; Roy, N.; Ganguly, M.; Banerjee, N.; Stepniewski, T. M.; Ahn, D.; Yamaguchi, K.; Oshima, H. S.; Hashimoto, K.; Fung, J. N.; Lerskiatiphanich, T.; Cui, C. S.; Lee, J.; Selent, J.; Inoue, A.; Clark, R. J.; Chung, K. Y.; Banerjee, R.; Sano, F. K.; Woodruff, T.; Nureki, O. M.; SHUKLA, A. K.

10.1101/2025.11.01.685996 — biochemistry — Posted on 2025-11-01

5323 Analysis of glutamine synthetase target-site mutations and their role in endowing glufosinate-ammonium resistance

Porri, A.; Sudhakar, S.; Noguera, M.; Betz, M.; Lerchl, J.; Dayan, F.; Norsworthy, J. K. E.

10.1101/2025.11.01.685562 — biochemistry — Posted on 2025-11-01

5324 Genomic Prediction and SNP Importance Analysis for Agronomic Traits in Two Coffea canephora Populations

Ahn, E.; Park, S.; Bhatt, J.; Lim, S.; Meinhardt, L. W.

10.1101/2025.10.31.685932 — genetics — Posted on 2025-11-01

5325 Elevated mutation near crossovers inhibits the evolution of recombination

Payseur, B. A.; Otto, S. P.

10.1101/2025.11.01.685904 — evolutionary biology — Posted on 2025-11-01

5326 The contribution of transposable element insertions to genetic diversity in Aedes aegypti populations

Valente-Almeida, G.; Daigle, A. T.; Matute, D. R.; Schrider, D. R.

10.1101/2025.10.31.685655 — evolutionary biology — Posted on 2025-11-01

5327 DCBK: A Fragment-Based Hybrid Simulation and Machine Learning Framework for Predicting Ligand Dissociation Kinetics

Li, Y.; Wang, Y.; Zheng, X.; Guo, J.; Zhang, R.

10.1101/2025.11.01.685950 — molecular biology — Posted on 2025-11-01

5328 Generation of broad-spectrum vaccine platforms against tick-borne flaviviruses using ancestral sequence reconstruction

Trammell, C. E.; Enney, B. M.; Savran, M. J.; Geiss, B. J.; Ebel, G. D.

10.1101/2025.10.31.685878 — microbiology — Posted on 2025-11-01

5329 Infant gut microbiota in multi-child families converges with adults without a sibling-specific signature

Hanski, E.; Ponsero, A. J.; Kolho, K.-L.; de Vos, W. M.; Salonen, A.

10.1101/2025.10.31.685886 — microbiology — Posted on 2025-11-01

5330 Adapting CRISPR-associated transposons for rapid and high-throughput reverse genetics

Basta, D. W.; Zingl, F. G.; Yang, Y.; Nguyen, K. T.; Liu, Y.-Y.; Waldor, M. K.

10.1101/2025.10.31.685825 — microbiology — Posted on 2025-11-01

5331 Poultry Litter Microbiome Shifts in Commercial Broiler Houses Following a Biotic-Based Litter Treatment

Olson, E. G.; Hale, B.; Ricke, S. C.

10.1101/2025.10.31.685678 — microbiology — Posted on 2025-11-01

5332 In vivo genome-wide CRISPRi-Seq in Streptococcus pneumoniae reveals host-adaptive pathways essential for meningitis and identifies new therapeutic targets

Jim, K. K.; Quinn, A.; de Bakker, V.; Willemin, G.; Engel, P.; Vastenhouw, N.; Veening, J.-W.

10.1101/2025.10.31.685840 — microbiology — Posted on 2025-11-01

5333 Shared Binding Site but Divergent Resistance Profiles Uncover Novel Resistance Mechanisms in Plasmodium HSP90 Inhibitors

Ko, F.-H.; Lukens, A.; de Souza, M. L.; Foy, A.; Hsiao, J.; Ndiaye, T.; Okombo, J.; Yeo, T.; Park, H.; Uhlemann, A.-C.; Boonyalai, N.; Kumpornsin, K.; Girling, G.; Pasaje, C.; Godoy, L.; Ottilie, S.; Durst, G. L.; Chatterjee, A.; Niles, J.; Lee, M.; Fidock, D. A.; Wirth, D. F.; Winzeler, E.

10.1101/2025.10.30.684657 — microbiology — Posted on 2025-11-01

5334 Rolling out plaque-2-sequence: a single plaque sequencing approach enabling rapid, low-cost sequencing of phages directly from plaques

Michniewski, S.; Glenny, R. L.; Kinsella, A.; Porter, K.; Wright, K.; Harrison, S.; Ugokwe, N. I.; Alrashidi, A.; Lee, J. C.; Patel, F.; Josephs, T.; Pedramfar, A.; Coleman, M.; Sampson, H.; Misol, G. N.; Rihtman, B.; Eke, C.; Smith, E.; Sabuholo, G.; Roemer, N.; Puxty, R.; Scanlan, D.; Schaik, W. V.; Stafford, G.; Galyov, E.; Clokie, M.; Megremis, S.; Millard, A. D.; Rashid, S. J.

10.1101/2025.11.01.684647 — microbiology — Posted on 2025-11-01

5335 The magnitude and durability of neutralizing antibody responses to human papillomavirus vaccine do not depend on DNA sensing pathways

Patel, J.; Yang, Z.; Ping, S.; Simon, T. W.; Waggoner, J. J.; Scherer, E. M.

10.1101/2025.10.31.685858 — immunology — Posted on 2025-11-01

5336 Marker effect p-values for single-step SNP-BLUP genomic models

Adekale, D. J.; Liu, Z.; Alkhoder, H.; Segelke, D.; Thaller, G.; Tetens, J.

10.1101/2025.10.30.685527 — genomics — Posted on 2025-11-01

5337 Modular evolution and strain-specific partnerships: how Hamiltonella defensa shapes defense and symbiont communities in aphids

Lynn-Bell, N.; Patel, V.; Weldon, S. R.; Peng, L.; Carpenter, M.; Kim, K.; Russell, J. A.; Oliver, K.

10.1101/2025.10.31.685823 — evolutionary biology — Posted on 2025-11-01

5338 An RNA replicon vaccine encoding HA and NA prevents shedding of antigen-drifted 2009 pandemic H1N1 influenza virus in the pig model

Garcia-Nicolas, O.; Butticaz, L.; Avanthay, R.; Ruggli, N.; Summerfield, A.; Zimmer, G.

10.1101/2025.11.01.685547 — microbiology — Posted on 2025-11-01

5339 Altitudin S from Bacillus altitudinis ECC22 defines a new subgroup of circular bacteriocins

Sevillano, E.; Lafuente, I.; Pena, N.; Cintas, L. M.; Munoz-Atienza, E.; Hernandez, P. E.; Borrero, J.

10.1101/2025.10.31.685828 — microbiology — Posted on 2025-11-01

5340 TOMM40 suppression promotes neuronal cholesterol imbalance and molecular and behavioral phenotypes of Alzheimer's disease

Yang, N. V.; Wang, S.; Li, B.; Simms, J.; Dinh, L.; Huang, A.; Oei, J. H.; Yassine, H. N.; Krauss, R. M.

10.1101/2025.10.31.685963 — molecular biology — Posted on 2025-11-01

5341 Compound-specific DNA adduct profiling with nanopore sequencing and IonStats

Koski, Y.; Patel, D.; Kakko von Koch, N.; Jouhten, P.; Aaltonen, L.; Palin, K.; Sahu, B.; Pitkanen, E.

10.1101/2025.10.31.685820 — bioinformatics — Posted on 2025-11-01

5342 B lymphocytes that enter the germinal center late preferentially differentiate into memory cells that recognize subdominant epitopes

Zhou, P.; Hartweger, H.; MacLean, A. J.; Ramos, V.; Yao, K.-h.; Hernandez, B.; Wang, Z.; Gazumyan, A.; Nussenzweig, M. C.

10.1101/2025.10.30.685663 — immunology — Posted on 2025-11-01

5343 CD4+ T cells fuel the Duchenne cardiomyopathy

Gladow, N.; Rizzo, G.; Michel, T.; Krammer, T.; Saliba, A.-E.; Frantz, S.; Ramos, G. C.; Cochain, C.; Hofmann, U.

10.1101/2025.10.30.684828 — immunology — Posted on 2025-11-01

5344 ER-to-Golgi Trafficking is a Nutrient-Sensitive Checkpoint Linking Glucose Starvation to Cell Surface Remodeling

Joo, J. H.; Kasberg, W.; Douglas, S.; Udoh, U.; Carisey, A.; Messing, J.; Wang, Y.-D.; Narina, S.; Pruett-Miller, S. M.; Labelle, M.; Lippincott-Schwartz, J.; Chang, C.-L.; Kundu, M.

10.1101/2025.10.31.685804 — cell biology — Posted on 2025-11-01

5345 Lipid bilayer thinning near a ubiquitin ligase selects ER membrane proteins for degradation

Pisa, R.; Rapoport, T. A.

10.1101/2025.10.31.685944 — cell biology — Posted on 2025-11-01

5346 A chromatin-associated pool of Aurora A controls kinetochore-microtubule attachments to ensure chromosome biorientation

Meaders, J. L.; Rodriguez, A. A.; Variyar, S.; Park, S.; Cirulli, A. E.; Oegema, K.; Corbett, K. D.; Desai, A.

10.1101/2025.10.31.685952 — cell biology — Posted on 2025-11-01

5347 Is poor dose selection undermining the translational validity of antidepressant research involving animal models?

Anderson, D.; Hinchcliffe, J.; Jackson, M. G.; Robinson, E.

10.1101/2025.10.25.684561 — neuroscience — Posted on 2025-11-01

5348 Individual-level contextual alignment and aperiodic slope reveal improved comprehension of unexpected language

Platt, A. L. M.

10.1101/2025.10.28.685236 — neuroscience — Posted on 2025-11-01

5349 The W-index: a novel tool to evaluate gender equity in STEM research

Holland, E. P.; LaMontagne, J. M.; Chaudry, V. B.; Charman-Anderson, S.; Gillson, L.; Helgason, T.; Lipscombe, A.; Robinson, E. J. H.; James, A.

10.1101/2025.10.29.685415 — scientific communication and education — Posted on 2025-11-01

5350 LINKER-Pred: A Public Web Server for Accurate Prediction of Disordered Flexible Linkers in Proteins

Meng, D.; Glavina, J.; Pollastri, G.; Chemes, L. B.

10.1101/2025.10.29.685455 — bioinformatics — Posted on 2025-11-01

5351 Confocal-Compatible Workflow for Sectioning, Staining, and Imaging Serial Vibratome Sections for 3D Anatomical Reconstruction of the Lymph Node

Kibler, M. A.; Miller, M. D.; Donzanti, M. J.; Gleghorn, J. P.

10.1101/2025.10.29.685350 — bioengineering — Posted on 2025-11-01

5352 Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking

Mandros, P.; Gallagher, I.; Fanfani, V.; Chen, C.; Fischer, J.; Ismail, A.; Hsu, L.; Saha, E.; DeConti, D. K.; Quackenbush, J.

10.1101/2024.06.16.599201 — bioinformatics — Posted on 2025-11-01

5353 Serial Dependence Predicts Generalization in Perceptual Learning

Pinchuk Yacobi, N.; Sagi, D.; Bonneh, Y.

10.1101/2025.02.06.636846 — neuroscience — Posted on 2025-11-01

5354 Predicting Future SARS-CoV-2 Mutations using Deep Learning

Ayaz, H.; Ibrahimzada, A. R.; Armani, A.; Baysan, M.; Buyukbingol, M. E.; Demir, G.; Karlik, E.; Ozpolat, B.; CAKMAK, A.

10.1101/2025.07.12.664533 — bioinformatics — Posted on 2025-11-01

5355 Optogenetic tripwires resolve models of how cells count DNA breaks

Labagnara, M.; Gligorovski, V.; Rahi, S. J.

10.1101/2025.10.31.685943 — molecular biology — Posted on 2025-11-01

5356 Alzheimer's Disease-Related Mutations in APP Influence Colorectal Tumor Formation in a Sex-Dependent Manner

Ishida-Takaku, T.; Sohrabi, M.; Pecoraro, H. L.; Combs, C. K.

10.1101/2025.10.31.685949 — neuroscience — Posted on 2025-11-01

5357 Exploring Proteomic Differences in PBMCs for Sex-Specific Insights into Alzheimer's Disease

Ishida-Takaku, T.; Combs, C. K.

10.1101/2025.10.31.685960 — neuroscience — Posted on 2025-11-01

5358 An artifact-robust framework for measuring tCS effects during stimulation

Noury, N.; Damiani, F.; Siegel, M.

10.1101/2025.10.31.685770 — neuroscience — Posted on 2025-11-01

5359 Aversive Learning Induces Context-Gated Global Reorganization of Neural Dynamics in Caenorhabditis elegans

Liang, J.; Moon, S.; Moza, S.; Lee, H. J.; Eleftheriadis, P. E.; Chen, J.; Ge, M.; Chen, M.; Lu, H.; Zhang, Y.

10.1101/2025.10.31.685731 — neuroscience — Posted on 2025-11-01

5360 Morphological variations in external genitalia do not explain the interspecific reproductive isolation in Nasonia species complex (Hymenoptera: Pteromalidae)

Baisla, B. R.; Verma, T.; Rana, A.; Sen, R.; Raychoudhury, R.

10.1101/2025.10.31.685729 — zoology — Posted on 2025-11-01

5361 A novel genetic strategy to interrogate an unknown phenotypic modifier: an Sdhc KO-Robertsonian mouse with a semi-homologous chromosome develops papillary thyroid carcinoma-like tumours

Bayley, J.-P.; Rebel, H. G.; Devilee, P.

10.1101/2025.10.31.685748 — cancer biology — Posted on 2025-11-01

5362 Mathematical modeling of light chain aggregation and cardiac damage in AL amyloidosis

Kuznetsov, A. V.

10.1101/2025.10.30.685705 — biophysics — Posted on 2025-11-01

5363 A unifying model of LAT condensates in reconstitution experiments

Omar, Y. A. D.; Sun, S.; Kardar, M.; Groves, J. T.; Chakraborty, A. K.

10.1101/2025.10.31.685772 — biophysics — Posted on 2025-11-01

5364 ProAffinity++

Xu, K.; Di, Z.; Zhao, J.; Zhang, H.; Bu, D.

10.1101/2025.10.31.685718 — bioinformatics — Posted on 2025-11-01

5365 Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research

Hak, F.; MARCHET, C.; Gautheret, D.; Gallopin, M.

10.1101/2025.10.31.685769 — bioinformatics — Posted on 2025-11-01

5366 From bench assays to bedside: context-embedding transformer predicts monoclonal antibody viscosity, clearance, and regulatory success

Virk, S. S.; Virk, A. S.

10.1101/2025.10.31.685722 — bioinformatics — Posted on 2025-11-01

5367 Automatic measurement of temporalis muscle thickness from CT head scans using deep learning

Hernandez, A. N.; Korhonen, T. K.; Pesonen, E. K.; Tetri, S.; Pikkarainen, L.; Pertuz, S.; Arponen, O.

10.1101/2025.10.31.685721 — bioengineering — Posted on 2025-11-01

5368 Mechanisms and Safety of Ultrasound Phacoemulsification

Graf, T.; Gisler, T.; Emmenegger, S.; Tanner, S.; Menapace, R.; Di Nardo, S.

10.1101/2025.10.31.685733 — bioengineering — Posted on 2025-11-01

5369 Motivational trade-offs in a cockroach: impact of conditions, injury, and development

Jenkinson, J.; Logan, J.; Robertson, C.; Lockhart, K.; Fisher, D. N.

10.1101/2025.10.31.685749 — animal behavior and cognition — Posted on 2025-11-01

5370 The ID93 + GLA-3M-052-LS vaccine candidate elicits mucosal and systemic immunogenicity and protective efficacy against Mycobacterium tuberculosis challenge in BCG-primed Collaborative Cross inbred mice

Voigt, E. A.; Alsharaydeh, A.; Kasal, D. N.; Jennewein, M. F.; Brandt, D. S.; Lin, S.; Singh, J.; Bakken, J.; Mohamath, R.; Fusco, P.; Torrelles, J. B.; Beamer, G.; Fox, C. B.

10.1101/2025.10.31.685426 — immunology — Posted on 2025-11-01

5371 Competition Between Memory Updating and Differentiation Emerges from Intrinsic Network Dynamics

Pronoza, J.; Liedtke, N.; Boeltzig, M.; Schubotz, R. I.; Cheng, S.

10.1101/2025.10.31.685486 — neuroscience — Posted on 2025-11-01

5372 lncRNA 3222401L13Rik/ENSG00000272070 modulates microglial inflammatory programs in association with PU.1

Pradhan, R.; Sakib, M. S.; Kaurani, L.; Krueger, D. M.; Pena, T.; Burckhardt, S.; Schuetz, A.-L.; Kronenberg-Verstee, D.; Delalle, I.; Sananbenesi, F.; Fischer, A.

10.1101/2025.10.31.685723 — neuroscience — Posted on 2025-11-01

5373 From Perception to Appraisal: Hierarchical Brain Responses to Natural and Built Features in Urban Environments

Zaehme, C.; Sander, I.; Koselevs, A.; Kuehn, S.; Gramann, K.

10.1101/2025.10.31.685763 — neuroscience — Posted on 2025-11-01

5374 Pre-stimulus pupil-linked arousal enhances initial stimulus availability and accelerates decay in iconic memory.

Smith, P. J. C.; Busch, N. A.

10.1101/2025.10.31.685757 — neuroscience — Posted on 2025-11-01

5375 Effects of carbon dioxide enrichment and environmental factors on photosynthesis, growth and yield and their interaction in cucumber: a meta-analysis

Liu, X.; Liu, X.; Xu, Y.; Wang, Z.; Sun, Q.; Liu, S.; Liu, B.; Li, Q.

10.1101/2025.10.31.685732 — plant biology — Posted on 2025-11-01

5376 Stretchable thin-film metal electronics enabled by multilayered nanomembranes

Jung, D.; Cunin, C. E.; Mondal, R.; Pang, K. K. L.; kim, Y.; Frey, E.; Winther, S.; Beckham, J.; Cannon, T. M.; Cea, C.; Gumyusenge, A.; Anikeeva, P.

10.1101/2025.10.30.685700 — physiology — Posted on 2025-11-01

5377 Novel therapy for gastric cancer peritoneal dissemination using genetically modified dental pulp cells and astatine-211

Kuge, K.; Du, W.-Y.; Masuda, H.; Yasuda, T.; Tatsumi, T.; Yin, X.; Yoshino, M.; Sugiyama, A.; Numata, R.; Yokoyama, W.; Shibahara, H.; Tanaka, T.; Kobayashi, M.; Taguchi, A.; Kohro, T.; Takubo, N.; Nakamura, M.; Jang, J.; Kumakura, Y.; Yoshida, H.; Yoshikawa, A.; Haba, H.; Wada, Y.; Imagawa, K.; Nomura, S.

10.1101/2025.10.15.682497 — cancer biology — Posted on 2025-11-01

5378 Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications

Giniunaite, R.; Sharma, R.; Maddocks, J. H.; Kriaucionis, S.; Petkeviciute-Gerlach, D.

10.1101/2024.04.06.588401 — biophysics — Posted on 2025-11-01

5379 Deep learning challenge to generate apo RNA conformations with cryptic binding site

Kurisaki, I.; Hamada, M.

10.1101/2025.01.07.631832 — bioinformatics — Posted on 2025-11-01

5380 Oriented Hydrogels with Wireless Electromagnetic Cues Direct Neural Morphogenesis Across Central and Peripheral Systems

Jensen, B. N.; Tong, T.; Tang, Y.; Skovborg, G.; Zhang, Y.; Klompmaker, K. K.; Matthiesen, C. L.; Eschen, J. T.; Elbaek, K. J.; Wang, Y.; Pallesen, L. T.; Seliktar, D.; Sun, D.; Dong, M.; Vaegter, C. B.; Korshoej, A. R.; Chen, M.

10.1101/2024.09.29.615659 — bioengineering — Posted on 2025-11-01

5381 Graphene nanoedge electronics for monolithic and chronic recording of local microcircuits at neuronal density

Jin, Y.; Tsai, C.-W.; Achavananthadith, S.; Nguyen, D. T.; Xiong, Z.; Liang, Z.; Herikstad, R.; Chuan, Y.; Kurt, S. A.; Ali, H. P. A.; Tee, B. C. K.; Kong, Y. L.; Libedinsky, C.; Tan, A. Y. Y.; Lim, C. T.; Ho, J. S.; Liu, Y.

10.1101/2025.10.30.685707 — bioengineering — Posted on 2025-11-01

5382 Gaps in archaeological metadata reporting: a meta-analysis of humanpaleogenomic studies in Western Eurasia

Staniuk, R.; Lee, V. Y. K.; Timpson, A.; Kristiansen, K.; Shennan, S.; Racimo, F.; Thomas, M. G.

10.1101/2025.07.16.665041 — genomics — Posted on 2025-11-01

5383 SMURF: soft-segmentation for single-cell reconstruction and topological analysis of spatial transcriptomic data

Guo, J.; Sarafinovska, S.; Hagenson, R.; Valentine, M.; Chen, D. Y.; McCoy, W. H.; Dougherty, J.; Mitra, R. D.; Muegge, B. D.

10.1101/2025.05.28.656357 — genomics — Posted on 2025-11-01

5384 Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster

Patel, P. H.; Eicholt, L. A.; Lange, A.; McDermott, K. L.; Bornberg-Bauer, E.; Findlay, G. D.

10.1101/2025.05.01.651694 — genetics — Posted on 2025-11-01

5385 Genomic analyses in Drosophila do not support the classic allopatric model of speciation.

Yusuf, L.; Lohse, K.; Laetsch, D. R.; Ritchie, M.

10.1101/2024.05.20.595063 — evolutionary biology — Posted on 2025-11-01

5386 Genetic variation in host selectivity and adaptive strain enrichment within legume-rhizobia symbiosis: processes are host-dependent, far from perfect, and correlate with nodule morphology

Burghardt, L. T.; Sydow, P.; Sutherland, J.; Epstein, B.; Tiffin, P.

10.1101/2025.06.16.659998 — evolutionary biology — Posted on 2025-11-01

5387 Phylogeny, morphology, and behavior of the new ciliate species Stentor stipatus

Rajan, D. H.; Lee, B.; Albright, A.; Tang, E. J.; Ressler, K.; Maravillas, A.; Vargas, C.; Marshall, W. F.; Cortes, D.

10.1101/2024.08.03.606273 — cell biology — Posted on 2025-11-01

5388 Unexpected Detection of Highly Pathogenic Avian Influenza (HPAI) H5N1 virus in bovine semen from a bull used for natural breeding on an affected dairy farm

Lim, A.; Poulsen, K.; Caserta, L. C.; Guan, L.; Opgernorth, E.; Beal, M.; Eisfeld, A. J.; Kawaoka, Y.; Diel, D.

10.1101/2025.10.16.682947 — molecular biology — Posted on 2025-11-01

5389 Acetoacetate suppresses colon cancer via an MR1-MAIT axis

Clay, S. L.; El Tekle, G.; Rashan, E. H.; Fonseca-Pereira, D.; Shin, Y.-H.; Andreeva, N.; Nakatsu, G.; Lobo, A. F.; Chen, S. P.; Bae, S.; Michaud, M.; Glickman, J. N.; Clardy, J.; Vander Heiden, M. G.; Garrett, W. S.

10.1101/2025.10.29.685375 — immunology — Posted on 2025-11-01

5390 Integrative multiomic analysis links TDP-43-driven splicing defects to cascading proteomic disruption of ALS/FTD pathways

Kozareva, V.; Liu, Z.; Blake, K.; Qi, Y. A.; Rollinson, S.; Seddighi, S.; Alsaidi, M.; Tsitkov, S.; Prudencio, M.; Petrucelli, L.; Dickson, D. W.; Brown, A.-L.; Fratta, P.; Kim, H. J.; Taylor, J. P.; Ward, M. E.; Fraenkel, E.; Kargbo-Hill, S. E.

10.1101/2025.09.29.679403 — neuroscience — Posted on 2025-11-01

5391 Modulation of metastable ensemble dynamics explains the inverted-U relationship between tone discriminability and arousal in auditory cortex

Papadopoulos, L.; Jo, S.; Zumwalt, K.; Wehr, M.; Jaramillo, S.; McCormick, D. A.; Mazzucato, L.

10.1101/2024.04.04.588209 — neuroscience — Posted on 2025-11-01

5392 Transcriptional and synaptic regulation of NMDA glutamate receptor-mediated hippocampal plasticity and memory

Parra-Damas, A.; del Ser-Badia, A.; Fernandez-Olalla, X.; Deprada-Fernandez, A.; Enriquez-Barreto, L.; Mengual, J. P.; Catala-Solsona, J.; Brito, V.; Rodriguez-Alvarez, J.; Gines, S.; Rodriguez-Moreno, A.; Saura, C. A.

10.1101/2025.01.19.633774 — neuroscience — Posted on 2025-11-01

5393 Spontaneous emergence and evolution of neuronal sequences inrecurrent networks

Shao, S.; Riquelme, J. L.; Gjorgjieva, J.

10.1101/2024.09.27.615499 — neuroscience — Posted on 2025-11-01

5394 Degeneracy in neuronal bifurcation landscapes: equivalent bifurcation sequences across distinct parameter sets

Cafaro, G.; Bernard, C.; Hashemi, M.; Depannemaecker, D.

10.1101/2025.08.04.668451 — neuroscience — Posted on 2025-11-01

5395 BOGO: A Proteome-Wide Gene Overexpression Platform for Discovering Rational Cancer Combination Therapies

Jo, K. B.; Alruwaili, M. M.; Kim, D.-E.; Koh, Y.; Kim, H.; You, K.; Kim, J.-S.; Sane, S.; Guo, Y.; Wright, J. P.; Naranjo, M. N.; Cote, A. G.; Roth, F. P.; Hill, D. E.; Choi, J.-H.; Lee, H.; Matreyek, K. A.; Farh, K. K.- H.; Park, J.-E.; Kim, H.; Bakin, A. V.; Kim, D.-K.

10.1101/2025.09.02.673780 — systems biology — Posted on 2025-11-01

5396 PIONEER: A Periplasmic Display Platform for Synthetic Biology-Based Screening of Genetically Encoded Protein Regulators

Rowe, J. B.; Lee, K.; Isom, D. G.

10.1101/2025.10.26.684622 — synthetic biology — Posted on 2025-11-01

5397 Single molecule studies of the bacterial curli protein CsgA reveal a structurally dynamic monomeric structure

Foster, D. A. N.; Dee, D. R.

10.1101/2025.09.08.674806 — biophysics — Posted on 2025-11-01

5398 The transitional kinetics between open and closed Rep structures can be tuned by salt via two intermediate states

Howard, J. A. L.; Ambrose, B.; Abdelhamid, M. A. S.; Frame, L.; Alevropoulos-Borrill, A.; Ejaz, A.; Dresser, L.; Dienerowitz, M.; Quinn, S. D.; Squires, A. H.; Noy, A.; Craggs, T. D.; Leake, M. C.

10.1101/2024.07.12.603287 — biophysics — Posted on 2025-11-01

5399 Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets

Luo, R. S.; Kille, B.; Vaughan, E. E.; Clark, J. R.; Maresso, A. W.; Nute, M. G.; Treangen, T. J.

10.1101/2025.10.10.681738 — bioinformatics — Posted on 2025-11-01

5400 LMI4Boltz: Optimising VRAM utilisation to predict large macromolecular complexes with consumer grade hardware

Litfin, T.; Caley, J. S.; Michie, K. A.

10.1101/2025.10.29.684571 — bioinformatics — Posted on 2025-11-01

5401 Highly Conserved Core Residues Define Old-World Alphaviruses and Trace Early Evolutionary Divergence

Pin-Ruiz, W. C.; Jaime Rocha, L. R.; Castorena Robles, A.; Castells-Graells, R.; Zandi, R.; Munoz-Escalante, J. C.; Comas-Garcia, M.

10.1101/2025.09.25.678619 — evolutionary biology — Posted on 2025-11-01

5402 Simplifying species-interaction models by grouping parameters: optimal groupings differ between effects and responses

Brown, C. R. P.; Stouffer, D. B.

10.1101/2025.01.18.633749 — ecology — Posted on 2025-11-01

5403 Linking power, efficiency, and bifurcations in consumer-resource systems

Saavedra, S.; Yang, Y.; Kempes, C.; Long, C.; Sole, R.; Yoshino, T.; Angulo, M. T.

10.1101/2025.07.14.664758 — ecology — Posted on 2025-11-01

5404 From leaves to defenders: how the amount and dispersion of leaf damage affect extrafloral nectar production and ant-mediated protection in wild cotton

Ramirez-Delgado, V. H.; Briones-May, Y.; Garnica-Cabrera, A.; Sanchez-Duran, J.; Martin-Cacheda, L.; Moreira, X.; Turlings, T. C. J.; Vasquez-Bolanos, M.; Abdala-Roberts, L.

10.1101/2025.07.31.667819 — ecology — Posted on 2025-11-01

5405 Janzen-Connell effects and habitat-induced aggregation synergistically promote species coexistence

Smith, D. J. B.

10.1101/2022.04.11.487940 — ecology — Posted on 2025-11-01

5406 Regenerative Grazing as a Climate Change Mitigation Strategy: A Systematic Review

Clark, D.; McClelland, S. C.; Dillon, J. A.; Hayek, M. N.

10.1101/2025.10.11.677897 — ecology — Posted on 2025-11-01

5407 Coordinated regulation of Citron kinase by CDK1 and Aurora B regulates midbody formation and stability

Capalbo, L.; Halcrow, E.; Bassi, Z.; D'Avino, P. P.

10.1101/2025.08.25.672096 — cell biology — Posted on 2025-11-01

5408 Distinct Non-occluding Functions of Septate Junction Components in Signaling Pathway Regulation and Cell Polarity During Epithelial Development

Holtwick, V.; Mueller, H.; Schubert, A.; Rust, K.

10.1101/2024.09.06.611635 — cell biology — Posted on 2025-11-01

5409 XPF mediates 3' flap processing for FEN1-independent Okazaki fragment maturation

Li, K.; Yang, F.; Wang, Y.; Shi, G.; Yan, Y.; Lei, Y.; Wang, Y.; Sun, H.; Zhou, M.; Zheng, L.; Shen, B.

10.1101/2025.10.24.684453 — cell biology — Posted on 2025-11-01

5410 Rank- and Threat-Dependent Social Modulation of Innate Defensive Behaviors

Li, L.-y.; Gao, X.; Li, Y.-t.

10.1101/2025.10.31.685719 — neuroscience — Posted on 2025-11-01

5411 Sensorimotor confidence during explicit motor adaptation

Evans, M. H.; Landy, M. S.

10.1101/2025.10.31.685783 — neuroscience — Posted on 2025-11-01

5412 Reward-induced endogenous pain inhibition scales with action-outcome certainty in humans

Hubschmid, F.; Desch, S.; Florin, E.; Becker, S.

10.1101/2025.10.31.685818 — neuroscience — Posted on 2025-11-01

5413 Syntactic Processing Engages the Semantic Control Network

Chang, Q.; Jefferies, E.; Jackson, R. L.

10.1101/2025.10.31.685882 — neuroscience — Posted on 2025-11-01

5414 Can you feel what I am saying? Speech-based vibrotactile stimulation enhances the cortical tracking of attended speech in a multi-talker background

Rautu, I. S.; Bourguignon, M.; Wens, V.; Jousmäki, V.; Bertels, J.; De Tiege, X.

10.1101/2025.10.31.685484 — neuroscience — Posted on 2025-11-01

5415 Hypothalamic CRH neurons gate rapid social appraisal of conspecifics

Akinrinade, I. D.; Pardasani, M.; Sterley, T.-L.; Fuzesi, T.; Bains, J. S.

10.1101/2025.10.31.685874 — neuroscience — Posted on 2025-11-01

5416 Independent Markers of Attentional Shifts

Arora, K.; Van der Stigchel, S.; Kenemans, J. L.; Chota, S.; Gayet, S.

10.1101/2025.10.31.685868 — neuroscience — Posted on 2025-11-01

5417 The hippocampus as an epistemic forager: When curiosity and reward jointly steer exploration and hippocampal replay

Nemeth, E.; Chartouny, A.; Jedlovszky, K.; Freire, I. T.; Khamassi, M.

10.1101/2025.10.31.685837 — neuroscience — Posted on 2025-11-01

5418 A molecular map of the human spinal dorsal and ventral horn defines arrangement of neuronal types and glial sex differences

Gabriel, K. A.; Davis, O. C.; Palomino, S. M.; Ishishita, S.; Poldsam, H.; Brandon, J. M.; Inturi, N. N.; Mydugolam, H.; Khan, I. O.; Selvakumaran, N.; Shiers, S.; Yousuf, M. S.; Vines, E.; Horton, P.; Khan, T.; Cervantes, A.; Reese, J. C.; Patwardhan, A.; Dussor, G.; Meyers, E.; Tavares-Ferreira, D.; Pool, A.-H.; Price, T. J.

10.1101/2025.10.31.685953 — neuroscience — Posted on 2025-11-01

5419 Single-cell, multi-region profiling of the macaque brain across the lifespan

Yang, W.; Watkins, K. L.; DeCasien, A. R.; O'Neill, M. B.; Bohlen, M. O.; O'Day, D. R.; Duran, M.; Qiu, C.; Meleshko, A.; Vo, A.; Menke, M.; Calderon, D.; Cayo Biobank Research Unit, ; Sallet, J.; Higham, J. P.; Martinez, M. I.; Trapnell, C.; Starita, L. M.; Montague, M. J.; Platt, M.; Chiou, K. L.; Shendure, J.; Snyder-Mackler, N.

10.1101/2025.10.31.685880 — neuroscience — Posted on 2025-11-01

5420 The neural orchestra of aggression: neurogenetic network mapping of human aggressiveness

Dugre, J. R.; Buades-Rotger, M.; De Brito, S. A.

10.1101/2025.10.31.685919 — neuroscience — Posted on 2025-11-01

5421 SLAy-ing oversplitting errors in high-density electrophysiology spike sorting

Koukuntla, S.; DeWeese, T.; Cheng, A.; Mildren, R.; Lawrence, A.; Graves, A. R.; Cullen, K. E.; Colonell, J.; Harris, T. D.; Charles, A. S.

10.1101/2025.06.20.660590 — neuroscience — Posted on 2025-11-01

5422 Native community resistance modulates the spread of non-native species along Mediterranean mountain roads under global change

La Bella, G.; Santoianni, L. A.; Marzialetti, F.; De Toma, A.; Zitarelli, C.; Cao Pinna, L.; Stanisci, A.; Acosta, A. T.; Bartolucci, F.; Conti, F.; Carboni, M.

10.1101/2025.10.31.685799 — ecology — Posted on 2025-11-01

5423 Neuronal SET1/COMPASS-mediated epigenetic regulation of de novo transcription drives accelerated forgetting with age

Sengupta, T.; Kaletsky, R.; Morillo, K.; Zhou, S.; Brown, A. K.; Novak, K.; Weng, Y.; Murphy, C.

10.1101/2025.10.31.685883 — neuroscience — Posted on 2025-11-01

5424 Neural heterogeneity shapes the temporal structure of human working memory

Kussovska, D.; Kim, R.; Rungratsameetaweemana, N.

10.1101/2025.10.31.684900 — neuroscience — Posted on 2025-11-01

5425 Spontaneous thought orientation tracked by fMRI networks and EEG alpha power dynamics

Hampejs, T.; Tomecek, D.; Jiricek, S.; Kondelka, V.; Jajcay, L.; Mantini, D.; Hlinka, J.

10.1101/2025.10.31.684884 — neuroscience — Posted on 2025-11-01

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