bioRxiv Channel: University of New South Wales https://biorxiv.org This feed contains articles for bioRxiv Channel "University of New South Wales" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Model adequacy and the macroevolution of angiosperm functional traits ]]> https://biorxiv.org/content/10.1101/004002v1?rss=1 Matthew Pennell Richard G FitzJohn William K Cornwell Luke J Harmon 2014-04-07 doi:10.1101/004002 Cold Spring Harbor Laboratory Press 2014-04-07 <![CDATA[ A simple approach for maximizing the overlap of phylogenetic and comparative data ]]> https://biorxiv.org/content/10.1101/024992v1?rss=1 Matthew W. Pennell Richard G. FitzJohn William K. Cornwell 2015-08-20 doi:10.1101/024992 Cold Spring Harbor Laboratory Press 2015-08-20 <![CDATA[ General methods for evolutionary quantitative genetic inference from generalised mixed models. ]]> https://biorxiv.org/content/10.1101/026377v1?rss=1 Pierre de Villemereuil Holger Schielzeth Shinichi Nakagawa Michael Morrissey 2015-09-08 doi:10.1101/026377 Cold Spring Harbor Laboratory Press 2015-09-08 <![CDATA[ Modelling the role of immunity in reversion of viral antigenic sites ]]> https://biorxiv.org/content/10.1101/027995v1?rss=1 Carmen H. S. Chan Lloyd P. Sanders Mark M. Tanaka 2015-09-30 doi:10.1101/027995 Cold Spring Harbor Laboratory Press 2015-09-30 <![CDATA[ A universal model for carbon dioxide uptake by plants ]]> https://biorxiv.org/content/10.1101/040246v1?rss=1 3500 stable carbon isotope measurements. A single global equation embodying these relationships then unifies the empirical light use efficiency model with the standard model of C3 photosynthesis1, and successfully predicts gross primary production as measured at flux sites. This achievement is notable because of the equation's simplicity (with just two parameters, both independently estimated) and applicability across biomes and plant functional types. Thereby it provides a theoretical underpinning, grounded in eco-evolutionary principles, for large-scale analysis of the CO2 and water exchanges between atmosphere and land. ]]> Han Wang Iain Colin Prentice William Cornwell Trevor Keenan Tyler Davis Ian Wright Bradley Evans Changhui Peng 2016-02-19 doi:10.1101/040246 Cold Spring Harbor Laboratory Press 2016-02-19 <![CDATA[ Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder ]]> https://biorxiv.org/content/10.1101/044412v1?rss=1 9 million genetic variants in 9,784 bipolar disorder patients and 30,471 controls, the largest GWAS of BD to date. In this study, to increase power we used ~2,000 lithium-treated cases with a long-term diagnosis of BD from the Consortium on Lithium Genetics, excess controls, and analytic methods optimized for markers on the X-chromosome. In addition to four known loci, results revealed genome-wide significant associations at two novel loci: an intergenic region on 9p21.3 (rs12553324, p = 5.87x10-9; odds ratio = 1.12) and markers within ERBB2 (rs2517959, p = 4.53x10-9; odds ratio = 1.13). No significant X-chromosome associations were detected and X-linked markers explained very little BD heritability. The results add to a growing list of common autosomal variants involved in BD and illustrate the power of comparing well-characterized cases to an excess of controls in GWAS. ]]> Liping Hou Sarah E Bergen Nirmala Akula Jie Song Christina M Hultman Mikael Landen Mazda Adli Martin Alda Raffaella Ardau Barbara Arias Jean-Michel Aubry Lena Backlund Judith A Badner Thomas B Barrett Michael Bauer Bernhard T Baune Frank Bellivier Antonio Benabarre Susanne Bengesser Wade H Berrettini Abesh Kumar Bhattacharjee Joanna M Biernacka Armin Birner Cinnamon S Bloss Clara Brichant-Petitjean Elise T Bui William Byerley Pablo Cervantes Caterina Chillotti Sven Cichon Francesc Colom William Coryell David W Craig Cristiana Cruceanu Piotr M Czerski Tony Davis Alexandre Dayer Franziska Degenh 2016-03-22 doi:10.1101/044412 Cold Spring Harbor Laboratory Press 2016-03-22 <![CDATA[ Functional connectivity in neuromuscular system underlying bimanual muscle synergies ]]> https://biorxiv.org/content/10.1101/056671v1?rss=1 Ingmar E. J. de Vries Andreas Daffertshofer Dick F. Stegeman Tjeerd W. Boonstra 2016-06-02 doi:10.1101/056671 Cold Spring Harbor Laboratory Press 2016-06-02 <![CDATA[ Putting bandits into context: How function learning supports decision making ]]> https://biorxiv.org/content/10.1101/081091v1?rss=1 Schulz, E. Konstantinidis, E. Speekenbrink, M. 2016-10-14 doi:10.1101/081091 Cold Spring Harbor Laboratory Press 2016-10-14 <![CDATA[ Hierarchical Frequency Tagging reveals neural markers of predictive coding under varying uncertainty ]]> https://biorxiv.org/content/10.1101/081349v1?rss=1 Gordon, N. Koenig-Robert, R. Tsuchiya, N. vanBoxtel, J. Hohwy, J. 2016-10-17 doi:10.1101/081349 Cold Spring Harbor Laboratory Press 2016-10-17 <![CDATA[ RECONSTRUCTION OF THE CORTICAL MAPS OF THE TASMANIAN TIGER AND COMPARISON TO THE TASMANIAN DEVIL ]]> https://biorxiv.org/content/10.1101/083592v1?rss=1 Berns, G. S. Ashwell, K. W. S. 2016-10-26 doi:10.1101/083592 Cold Spring Harbor Laboratory Press 2016-10-26 <![CDATA[ Perfluorooctane sulfonate affects proliferation and differentiation of pluripotent human teratocarcinoma cells ]]> https://biorxiv.org/content/10.1101/089698v1?rss=1 Popovic, M. Neilan, B. A. Pomati, F. 2016-12-08 doi:10.1101/089698 Cold Spring Harbor Laboratory Press 2016-12-08 <![CDATA[ The E3 ubiquitin ligase UBR5 regulates centriolar satellite stability and primary cilia formation via ubiquitylation of CSPP-L. ]]> https://biorxiv.org/content/10.1101/090100v1?rss=1 Shearer, R. F. Frikstad, K.-A. M. McKenna, J. McCloy, R. Deng, N. Burgess, A. Stokke, T. Patzke, S. Saunders, D. N. 2016-12-22 doi:10.1101/090100 Cold Spring Harbor Laboratory Press 2016-12-22 <![CDATA[ Decoding the nonconscious dynamics of thought generation ]]> https://biorxiv.org/content/10.1101/090712v1?rss=1 Koenig-Robert, R. Pearson, J. 2016-12-08 doi:10.1101/090712 Cold Spring Harbor Laboratory Press 2016-12-08 <![CDATA[ A meta-analysis of bioinformatics softwarebenchmarks reveals that publication-bias undulyinfluences software accuracy ]]> https://biorxiv.org/content/10.1101/092205v1?rss=1 Gardner, P. Paterson, J. M. Ashari Ghomi, F. Umu, S. U. U. McGimpsey, S. Pawlik, A. 2016-12-07 doi:10.1101/092205 Cold Spring Harbor Laboratory Press 2016-12-07 <![CDATA[ Cortical excitability controls the strength of mental imagery ]]> https://biorxiv.org/content/10.1101/093690v1?rss=1 Keogh, R. Bergmann, J. Pearson, J. 2016-12-14 doi:10.1101/093690 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Coefficient of determination R2 and intra-class correlation coefficient ICC from generalized linear mixed-effects models revisited and expanded ]]> https://biorxiv.org/content/10.1101/095851v1?rss=1 Nakagawa, S. Schielzeth, H. 2016-12-21 doi:10.1101/095851 Cold Spring Harbor Laboratory Press 2016-12-21 <![CDATA[ Associative Learning from Replayed Experience ]]> https://biorxiv.org/content/10.1101/100800v1?rss=1 Ludvig, E. A. Mirian, M. S. Kehoe, E. J. Sutton, R. S. 2017-01-16 doi:10.1101/100800 Cold Spring Harbor Laboratory Press 2017-01-16 <![CDATA[ Sexual reproduction as bet-hedging ]]> https://biorxiv.org/content/10.1101/103390v1?rss=1 Li, X.-Y. Lehtonen, J. Kokko, H. 2017-01-26 doi:10.1101/103390 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ Bird interactions with drones, from individuals to large colonies ]]> https://biorxiv.org/content/10.1101/109926v1?rss=1 Lyons, M. Brandis, K. Callaghan, C. McCann, J. Mills, C. Ryall, S. Kingsford, R. 2017-02-20 doi:10.1101/109926 Cold Spring Harbor Laboratory Press 2017-02-20 <![CDATA[ The functional anatomy of self-generated and predictable speech ]]> https://biorxiv.org/content/10.1101/119644v1?rss=1 Oestreich, L. K. L. Whitford, T. J. Garrido, M. I. 2017-03-22 doi:10.1101/119644 Cold Spring Harbor Laboratory Press 2017-03-22 <![CDATA[ Response Of Microbial Community Function To Fluctuating Geochemical Conditions Within A Legacy Radioactive Waste Trench Environment ]]> https://biorxiv.org/content/10.1101/121376v1?rss=1 Vazquez-Campos, X. Kinsela, A. S. Bligh, M. W. Harrison, J. J. Payne, T. E. Waite, T. D. 2017-03-28 doi:10.1101/121376 Cold Spring Harbor Laboratory Press 2017-03-28 <![CDATA[ Coordinated Shifts In Allocation Among Reproductive Tissues Across 14 Coexisting Plant Species ]]> https://biorxiv.org/content/10.1101/141473v1?rss=1 Wenk, E. H. Abramowicz, K. Westoby, M. Falster, D. S. 2017-05-24 doi:10.1101/141473 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Male coercion, female resistance, and the evolutionary trap of sexual reproduction ]]> https://biorxiv.org/content/10.1101/146076v1?rss=1 Burke, N. W. Bonduriansky, R. 2017-06-05 doi:10.1101/146076 Cold Spring Harbor Laboratory Press 2017-06-05 <![CDATA[ More Highly Myelinated White Matter Tracts are Associated with Faster Processing Speed in Healthy Adults ]]> https://biorxiv.org/content/10.1101/152546v1?rss=1 Chopra, S. Shaw, M. Shaw, T. Sachdev, P. S. Anstey, K. J. Cherbuin, N. 2017-06-27 doi:10.1101/152546 Cold Spring Harbor Laboratory Press 2017-06-27 <![CDATA[ Facultative adjustment of paternal care in the face of female infidelity in dunnocks ]]> https://biorxiv.org/content/10.1101/158816v1?rss=1 Santos, E. S. A. Nakagawa, S. 2017-07-03 doi:10.1101/158816 Cold Spring Harbor Laboratory Press 2017-07-03 <![CDATA[ Harmonic brain modes: a unifying framework for linking space and time in brain dynamics ]]> https://biorxiv.org/content/10.1101/162040v1?rss=1 Atasoy, S. Deco, G. Kringelbach, M. L. Pearson, J. 2017-07-23 doi:10.1101/162040 Cold Spring Harbor Laboratory Press 2017-07-23 <![CDATA[ Population and conservation genomics of the world's rarest hyena species, the brown hyena (Parahyena brunnea) ]]> https://biorxiv.org/content/10.1101/170621v1?rss=1 Westbury, M. Hartmann, S. Barlow, A. Wiesel, I. Leo, V. Welch, R. Parker, D. M. Sicks, F. Ludwig, A. Dalen, L. Hofreiter, M. 2017-07-31 doi:10.1101/170621 Cold Spring Harbor Laboratory Press 2017-07-31 <![CDATA[ Genetic Architecture of Subcortical Brain Structures in Over 40,000 Individuals Worldwide ]]> https://biorxiv.org/content/10.1101/173831v1?rss=1 Satizabal, C. L. Adams, H. H. H. Hibar, D. P. White, C. C. Stein, J. L. Scholz, M. Sargurupremraj, M. Jahanshad, N. Smith, A. V. Bis, J. C. Jian, X. Luciano, M. Hofer, E. Teumer, A. van der Lee, S. J. Yang, J. Yanek, L. R. Lee, T. V. Li, S. Hu, Y. Koh, J. Y. Eicher, J. D. Desrivieres, S. Arias-Vasquez, A. Chauhan, G. Athanasiu, L. Renteria, M. E. Kim, S. Hohn, D. Armstrong, N. J. Chen, Q. Holmes, A. J. den Braber, A. Kloszewska, I. Andersson, M. Espeseth, T. Grimm, O. Abramovic, L. Alhusaini, S. Milaneschi, Y. Papmeyer, M. Axelsson, T. Ehrlich, S. Roi 2017-08-28 doi:10.1101/173831 Cold Spring Harbor Laboratory Press 2017-08-28 <![CDATA[ Ninety-nine independent genetic loci influencing general cognitive function include genes associated with brain health and structure (N = 280,360) ]]> https://biorxiv.org/content/10.1101/176511v1?rss=1 Davies, G. Lam, M. Harris, S. E. Trampush, J. Luciano, M. Hill, W. D. Hagenaars, S. P. Ritchie, S. J. Marioni, R. E. Fawns-Ritchie, C. Liewald, D. C. Okely, J. Ahola-Olli, A. Barnes, C. L. K. Bertram, L. Bis, J. C. Burdick, K. E. Christoforou, A. DeRosse, P. Djurovic, S. Espeseth, T. Giakoumaki, S. Giddaluru, S. Gustavson, D. E. Hayward, C. Hofer, E. Ikram, M. A. Karlsson, R. Knowles, E. Lahti, J. Leber, M. Li, S. Mather, K. A. Melle, I. Morris, D. Oldmeadow, C. Palviainen, T. Payton, A. Pazoki, R. Petrovic, K. Reynolds, C. A. Sargurupremraj, M. Scholz 2017-08-17 doi:10.1101/176511 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Dynamics of corticospinal motor control during overground and treadmill walking in humans ]]> https://biorxiv.org/content/10.1101/177915v1?rss=1 Roeder, L. Boonstra, T. W. Kerr, G. K. 2017-08-18 doi:10.1101/177915 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Prevalence of Mycoplasma genitalium in different population groups: systematic review and meta-analysis ]]> https://biorxiv.org/content/10.1101/180422v1?rss=1 Baumann, L. Cina, M. Egli-Gany, D. Goutaki, M. Halbeisen, F. Lohrer, G.-R. Ali, H. Scott, P. Low, N. 2017-08-25 doi:10.1101/180422 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ Network structure of the human musculoskeletal system shapes neural interactions on multiple timescales ]]> https://biorxiv.org/content/10.1101/181818v1?rss=1 Kerkman, J. N. Daffertshofer, A. Gollo, L. Breakspear, M. Boonstra, T. W. 2017-08-29 doi:10.1101/181818 Cold Spring Harbor Laboratory Press 2017-08-29 <![CDATA[ Catch-slip behavior observed upon rupturing membrane-cytoskeleton bonds ]]> https://biorxiv.org/content/10.1101/184069v1?rss=1 Rajasekharan, V. Sreenivasan, V. K. A. Pereira, F. A. Farrell, B. 2017-09-04 doi:10.1101/184069 Cold Spring Harbor Laboratory Press 2017-09-04 <![CDATA[ Association between alcohol consumption and Alzheimer’s disease: A Mendelian Randomization Study ]]> https://biorxiv.org/content/10.1101/190165v1?rss=1 Andrews, S. J. Anstey, K. J. 2017-09-18 doi:10.1101/190165 Cold Spring Harbor Laboratory Press 2017-09-18 <![CDATA[ Effects of tDCS Dosage on Working Memory in Healthy Participants ]]> https://biorxiv.org/content/10.1101/192419v1?rss=1 Nikolin, S. Martin, D. Loo, C. K. Boonstra, T. W. 2017-09-22 doi:10.1101/192419 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ Mapping Cortical Brain Asymmetry in 17,141 Healthy Individuals Worldwide via the ENIGMA Consortium ]]> https://biorxiv.org/content/10.1101/196634v1?rss=1 Kong, X.-Z. Mathias, S. Guadalupe, T. Abe, C. Agartz, I. Akudjedu, T. N. Aleman, A. Alhusaini, S. Allen, N. B. Ames, D. Andreassen, O. A. Armstrong, N. J. Bergo, F. Bastin, M. E. Batalla, A. Bauer, J. Baune, B. Baur, R. Biederman, J. Blaine, S. K. Boedhoe, P. Boen, E. Bose, A. Bralten, J. Brandeis, D. Brem, S. Brodaty, H. Bröhl, H. Buitelaar, J. Bürger, C. Bülow, R. Calhoun, V. Calvo, A. Canales-Rodriguez, E. J. Canive, J. M. Cannon, D. M. Caparelli, E. C. Castellanos, F. X. Cavalleri, G. L. Cendes, F. Chaim-Avancini, T. M. Chant 2017-10-01 doi:10.1101/196634 Cold Spring Harbor Laboratory Press 2017-10-01 <![CDATA[ Neural signatures of dynamic emotion constructs in the human brain ]]> https://biorxiv.org/content/10.1101/200873v1?rss=1 Grootswagers, T. Kennedy, B. L. Most, S. B. Carlson, T. A. 2017-10-10 doi:10.1101/200873 Cold Spring Harbor Laboratory Press 2017-10-10 <![CDATA[ Age-related changes of Peak width Skeletonized Mean Diffusivity (PSMD) across the adult life span: a multi-cohort study ]]> https://biorxiv.org/content/10.1101/2020.01.07.896951v1?rss=1 Beaudet, G. Tsuchida, A. Petit, L. Tzourio, C. Caspers, S. Schreiber, J. Pausova, Z. Patel, Y. Paus, T. Schmidt, R. Pirpamer, L. Sachdev, P. S. Brodathy, H. Kochan, N. Trollor, J. Wen, W. Armstrong, N. Deary, I. J. Bastin, M. E. Warlaw, J. M. Maniega, S. M. Witte, V. A. Villringer, A. During, M. Stephanie, D. Mazoyer, B. 2020-01-08 doi:10.1101/2020.01.07.896951 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Tissue engineered model of hepatic breast cancer micrometastasis shows host-dependent colonization patterns and drug responses ]]> https://biorxiv.org/content/10.1101/2020.01.08.898163v1?rss=1 Guller, A. E. Rozova, V. S. Kuschnerus, I. Khabir, Z. Nadort, A. Garcia-Bennett, A. E. Liang, L. Qian, Y. Goldys, E. M. Zvyagin, A. V. 2020-01-09 doi:10.1101/2020.01.08.898163 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ A silent disco: Persistent entrainment of low-frequency neural oscillations underlies beat-based, but not memory-based temporal expectations ]]> https://biorxiv.org/content/10.1101/2020.01.08.899278v1?rss=1 Bouwer, F. L. Fahrenfort, J. J. Millard, S. K. Slagter, H. A. 2020-01-08 doi:10.1101/2020.01.08.899278 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Structural Analysis of a Filamentous Chaperonin from Sulfolobus solfataricus ]]> https://biorxiv.org/content/10.1101/2020.01.13.905216v1?rss=1 Zeng, Y. C. Sobti, M. Stewart, A. G. 2020-01-14 doi:10.1101/2020.01.13.905216 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Dissecting the nanoscale lipid profile of caveolae ]]> https://biorxiv.org/content/10.1101/2020.01.16.909408v1?rss=1 Zhou, Y. Ariotti, N. Rae, J. Liang, H. Tillu, V. Tee, S. Bastiani, M. Bademosi, A. T. Collins, B. Meunier, F. A. Hancock, J. F. Parton, R. G. 2020-01-16 doi:10.1101/2020.01.16.909408 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Decoding non-conscious thought representations during successful thought suppression ]]> https://biorxiv.org/content/10.1101/2020.02.02.931352v1?rss=1 Koenig-Robert, R. Pearson, J. 2020-02-03 doi:10.1101/2020.02.02.931352 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Form and function: diverse homeostatic and immunomodulatory roles of immune cells in the developing lung revealed at single cell resolution ]]> https://biorxiv.org/content/10.1101/2020.02.10.942359v1?rss=1 Domingo-Gonzalez, R. Zanini, F. Che, X. Liu, M. Jones, R. C. Swift, M. A. Quake, S. R. Cornfield, D. N. Alvira, C. M. 2020-02-11 doi:10.1101/2020.02.10.942359 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Regulated unbinding of ZAP70 at the T cell receptor by kinetic avidity ]]> https://biorxiv.org/content/10.1101/2020.02.12.945170v1?rss=1 Goyette, J. Depoil, D. Yang, Z. Isaacson, S. A. Allard, J. van der Merwe, P. A. Gaus, K. Dustin, M. Dushek, O. 2020-02-13 doi:10.1101/2020.02.12.945170 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Causal dynamical modelling predicts novel regulatory genes of FOXP3 in human regulatory T cells ]]> https://biorxiv.org/content/10.1101/2020.02.13.943688v1?rss=1 Sawlekar, R. Magni, S. Capelle, C. Baron, A. Zeng, N. Mombaerts, L. Yue, Z. Yuan, Y. He, F. Q. Goncalves, J. 2020-02-14 doi:10.1101/2020.02.13.943688 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Greater male than female variability in regional brain structure across the lifespan ]]> https://biorxiv.org/content/10.1101/2020.02.17.952010v1?rss=1 Wierenga, L. M. Doucet, G. Dima, D. Agartz, I. Aghajani, M. Akudjedu, T. Albajes-Eizagirre, A. Alnaes, D. Alpert, K. Andreassen, O. A. Anticevic, A. Asherson, P. Banaschewski, T. Bargallo, N. Baumeister, S. Baur-Streubel, R. Bertolino, A. Bonvino, A. Boomsma, D. Borgwardt, S. Bourque, J. den Braber, A. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. Busatto, G. Calhoun, V. Canales-Rodriguez, E. Cannon, D. Caseras, X. Chaim-Avancini, T. Ching, C. Conrod, P. Conzelmann, A. Crivello, F. Davey, C. Dickie, E. Ehrlich, S. van 't Ent, D. Fouche, J.-P. Fuentes- 2020-02-17 doi:10.1101/2020.02.17.952010 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Clustering of CD3ζ is sufficient to initiate T cell receptor signaling ]]> https://biorxiv.org/content/10.1101/2020.02.17.953463v1?rss=1 Ma, Y. Lim, Y. J. Benda, A. Goyette, J. Gaus, K. 2020-02-19 doi:10.1101/2020.02.17.953463 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Non-invasive real-time imaging of reactive oxygen species (ROS) using multispectral auto-fluorescence imaging technique: a novel tool for redox biology ]]> https://biorxiv.org/content/10.1101/2020.02.18.955112v1?rss=1 400 nm); the latter being suitable for UV-sensitive systems such as the eye. Data were analyzed by linear regression combined with an optimization method of swarm intelligence. This allowed the calibration of AFMI signals to the level of ROS with excellent correlation (R= 0.84, p=0.00) in the entire spectral range and very good correlation (R= 0.78, p=0.00) in the limited, UV-free spectral range. We also developed a strong classifier which allowed us to distinguish moderate and high levels of ROS in these two regimes (AUC= 0.91 in the entire spectral range and AUC = 0.78 for UV-free imaging). These results indicate that ROS in cells and tissues can be imaged non-invasively, which opens the way to future clinical applications in conditions where reactive oxygen species are known to contribute to progressive disease such as in ophthalmology, diabetes, kidney disease, cancer and neurodegenerative diseases. ]]> Habibalahi, A. Dashtbani Moghari, M. Campbell, J. Anwer, A. Mahbub, S. Gosnell, M. saad, s. Pollock, C. Goldys, E. 2020-02-19 doi:10.1101/2020.02.18.955112 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ The transcriptional landscape of Venezuelan equine encephalitis virus infection ]]> https://biorxiv.org/content/10.1101/2020.02.18.955393v1?rss=1 Yao, Z. Zanini, F. Kumar, S. Panpradist, N. Muniz, A. Quake, S. R. Einav, S. 2020-02-19 doi:10.1101/2020.02.18.955393 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ A ventral striatal-orexin/hypocretin circuit modulates approach but not consumption of food. ]]> https://biorxiv.org/content/10.1101/2020.03.05.979468v1?rss=1 Mitchell, C. S. Fisher, S. D. Yeoh, J. W. Pearl, A. J. Burton, N. J. Bains, J. S. McNally, G. P. Andrews, Z. A. Graham, B. A. Dayas, C. V. 2020-03-06 doi:10.1101/2020.03.05.979468 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ An Endocytic Capture Model for Skeletal Muscle T-tubule Formation ]]> https://biorxiv.org/content/10.1101/2020.03.05.979666v1?rss=1 Hall, T. E. Martel, N. Ariotti, N. Xiong, Z. Lo, H. P. Ferguson, C. E. Rae, J. Lim, Y.-W. Parton, R. G. 2020-03-06 doi:10.1101/2020.03.05.979666 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Conditional repeatability and the variance explained by reaction norm variation in random slope models ]]> https://biorxiv.org/content/10.1101/2020.03.11.987073v1?rss=1 Schielzeth, H. Nakagawa, S. 2020-03-11 doi:10.1101/2020.03.11.987073 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Global shortfalls in extinction risk assessments for endemic flora ]]> https://biorxiv.org/content/10.1101/2020.03.12.984559v1?rss=1 Gallagher, R. V. Allen, S. Rivers, M. Allen, A. Butt, N. Keith, D. Auld, T. D. Enquist, B. J. Wright, I. J. Possingham, H. P. Espinosa-Ruiz, S. Dimitrova, N. Mifsud, J. C. Adams, V. M. 2020-03-14 doi:10.1101/2020.03.12.984559 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Varicella zoster virus encodes a viral decoy RHIM to inhibit cell death ]]> https://biorxiv.org/content/10.1101/2020.03.12.988659v1?rss=1 Steain, M. Baker, M. O. D. G. Pham, C. L. L. Gambin, Y. Sierecki, E. McSharry, B. P. Avdic, S. Slobedman, B. Sunde, M. Abendroth, A. 2020-03-12 doi:10.1101/2020.03.12.988659 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ A comparison of ThinPrep-PreservCyt against four non-volatile transport media for HPV testing at or near the point of care. ]]> https://biorxiv.org/content/10.1101/2020.03.18.998104v1?rss=1 Badman, S. G. Vallely, A. J. Pardo, C. Mhango, L. P. Cornall, A. M. Kaldor, J. Whiley, D. 2020-03-22 doi:10.1101/2020.03.18.998104 Cold Spring Harbor Laboratory Press 2020-03-22 <![CDATA[ An inverted Caveolin-1 topology defines a novel exosome secreted from prostate cancer cells ]]> https://biorxiv.org/content/10.1101/2020.03.19.999441v1?rss=1 Ariotti, N. Wu, Y. Okano, S. Gambin, Y. Follett, J. Rae, J. Ferguson, C. Teasdale, R. D. Alexandrov, K. Meunier, F. A. Hill, M. M. Parton, R. G. 2020-03-20 doi:10.1101/2020.03.19.999441 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Are there Physical Linkages between Genes that have Synergistic Fitness Effects? ]]> https://biorxiv.org/content/10.1101/2020.03.23.004630v1?rss=1 Byrnes, J. F. Sherwin, W. Goldys, B. Murray, J. Tanaka, M. Bellanto, A. Cayetano, L. 2020-03-25 doi:10.1101/2020.03.23.004630 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Ecology and molecular targets of hypermutation in the global microbiome. ]]> https://biorxiv.org/content/10.1101/2020.04.01.020958v1?rss=1 30,000 metagenome-derived DGRs, and determine that DGRs have a single evolutionary origin and a universal bias towards adenine mutations. We further identified six major lineages of DGRs, each associated with a specific ecological niche defined as a genome type, i.e. whether the DGR is encoded on a viral or cellular genome, a limited set of taxa and environments, and a distinct type of target. Finally, we leverage read mapping and metagenomic time series to demonstrate that DGRs are consistently and broadly active, and responsible for >10% of all amino acid changes in some organisms at a conservative estimate. Overall, these results highlight the strong constraints under which DGRs diversify and expand, and elucidate several distinct roles these elements play in natural communities and in shaping microbial community structure and function in our environment. ]]> Roux, S. Paul, B. G. Bagby, S. C. Allen, M. A. Attwood, G. Cavicchioli, R. Chistoserdova, L. Hallam, S. Hernandez, M. E. Hess, M. Liu, W.-T. O'Malley, M. A. Peng, X. Rich, V. I. Saleska, S. Eloe-Fadrosh, E. A. 2020-04-02 doi:10.1101/2020.04.01.020958 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ Ancient human genomes reveal a hidden history of strong selection in Eurasia ]]> https://biorxiv.org/content/10.1101/2020.04.01.021006v1?rss=1 Souilmi, Y. Tobler, R. Johar, A. Williams, M. Grey, S. T. Schmidt, J. Teixeira, J. C. Rohrlach, A. Tuke, J. Johnson, O. L. Gower, G. R. Turney, C. Cox, M. Huber, C. D. Cooper, A. 2020-04-03 doi:10.1101/2020.04.01.021006 Cold Spring Harbor Laboratory Press 2020-04-03 <![CDATA[ An oscillating MinD protein determines the cellular positioning of the motility machinery in archaea ]]> https://biorxiv.org/content/10.1101/2020.04.03.021790v1?rss=1 Nussbaum, P. Ithurbide, S. Walsh, J. C. Patro, M. Delpech, F. Rodriguez-Franco, M. Curmi, P. M. G. Duggin, I. G. Quax, T. E. F. Albers, S.-V. 2020-04-04 doi:10.1101/2020.04.03.021790 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ Changes to the resistome of Pseudomonas aeruginosa clone ST308 associated with corneal infection over time ]]> https://biorxiv.org/content/10.1101/2020.04.10.036673v1?rss=1 Khan, M. Willcox, M. D. P. Rice, S. A. Sharma, S. Stapleton, F. 2020-04-11 doi:10.1101/2020.04.10.036673 Cold Spring Harbor Laboratory Press 2020-04-11 <![CDATA[ Temporal ordering of omics and multiomic events inferred from time series data ]]> https://biorxiv.org/content/10.1101/2020.04.14.040527v1?rss=1 Kaur, S. Peters, T. J. Yang, P. Luu, L. D. W. Vuong, J. Krycer, J. R. O'Donoghue, S. I. 2020-04-14 doi:10.1101/2020.04.14.040527 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Pleiotropy-guided transcriptome imputation from normal and tumor tissues identifies new candidate susceptibility genes for breast and ovarian cancer ]]> https://biorxiv.org/content/10.1101/2020.04.23.043653v1?rss=1 1 Mb away from known breast and/or ovarian cancer susceptibility loci. We also identified 38 candidate breast cancer susceptibility genes and 17 candidate ovarian cancer susceptibility genes at conjunction FDR < 0.05 at known breast and/or ovarian susceptibility loci. Overlaying candidate causal risk variants identified by GWAS fine mapping onto expression prediction models for genes at known loci suggested that the association for 55% of these genes was driven by the underlying GWAS signal. SignificanceThe 22 new genes identified by our cross-cancer analysis represent promising candidates that further elucidate the role of the transcriptome in mediating germline breast and ovarian cancer risk. ]]> Kar, S. Considine, D. Tyrer, J. Plummer, J. Chen, S. Dezem, F. Barbeira, A. Rajagopal, P. Rosenow, W. Anton, F. Bodelon, C. Chang-Claude, J. Chenevix-Trench, G. deFazio, A. Doerk, T. Ekici, A. Ewing, A. Fountzilas, G. Goode, E. Hartman, M. Heitz, F. Hillemanns, P. Hogdall, E. Hogdall, C. Huzarski, T. Jensen, A. Karlan, B. Khusnutdinova, E. Kiemeney, L. Kjaer, S. Klapdor, R. Kobel, M. Li, J. Liebrich, C. May, T. Olsson, H. Permuth, J. Peterlongo, P. Radice, P. Ramus, S. Riggan, M. Saloustros, E. Simard, J. Szafron, L. Thompson, C. Vierkant, R. Winha 2020-04-24 doi:10.1101/2020.04.23.043653 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Dynamics of Brain Structure and its Genetic Architecture over the Lifespan ]]> https://biorxiv.org/content/10.1101/2020.04.24.031138v1?rss=1 Brouwer, R. M. Klein, M. Grasby, K. L. Schnack, H. G. Jahanshad, N. Teeuw, J. Thomopoulos, S. I. Sprooten, E. Franz, C. E. Gogtay, N. Kremen, W. Panizzon, M. S. Olde Loohuis, L. M. Whelan, C. D. Aghajani, M. Alloza, C. Alnaes, D. Artiges, E. Ayesa-Arriola, R. Barker, G. J. Blok, E. Boen, E. Breukelaar, I. A. Bright, J. K. Buimer, E. E. Bülow, R. Cannon, D. M. Ciufolini, S. Crossley, N. A. Damatac, C. G. Dazzan, P. de Mol, C. L. de Zwarte, S. M. Desrivieres, S. Diaz-Caneja, C. M. Doan, N. T. Dohm, K. Fröhner, J. H. Goltermann, J. Grigis, A. Grotegerd, D 2020-04-27 doi:10.1101/2020.04.24.031138 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ The case for formal methodology in scientific reform ]]> https://biorxiv.org/content/10.1101/2020.04.26.048306v1?rss=1 Devezer, B. Navarro, D. J. Vandekerckhove, J. Buzbas, E. O. 2020-04-28 doi:10.1101/2020.04.26.048306 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Genetic and environmental determinants of variation in the plasma lipidome of older Australian twins ]]> https://biorxiv.org/content/10.1101/2020.05.05.075606v1?rss=1 Wong, M. W. K. Thalamuthu, A. Braidy, N. Mather, K. A. Liu, Y. Ciobanu, L. Baune, B. T. Armstrong, N. J. Kwok, J. Schofield, P. R. Wright, M. J. Ames, D. Pickford, R. Lee, T. Poljak, A. Sachdev, P. S. 2020-05-07 doi:10.1101/2020.05.05.075606 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Cortical Thickness Trajectories across the Lifespan: Data from 17,075 healthy individuals aged 3-90 years ]]> https://biorxiv.org/content/10.1101/2020.05.05.077834v1?rss=1 Frangou, S. Modabbernia, A. Doucet, G. E. Papachristou, E. Williams, S. C. Agartz, I. Aghajani, M. Akudjedu, T. N. Albajes-Eizagirre, A. Alnaes, D. Alpert, K. I. Andersson, M. Andreasen, N. Andreassen, O. A. Asherson, P. Banaschewski, T. Bargallo, N. Baumeister, S. Baur-Streubel, R. Bertolino, A. Bonvino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buitelaar, J. K. Busatto, G. F. Buckner, R. L. Calhoun, V. Canales-Rodriguez, E. J. Cannon, D. M. Caseras, X. Castellanos, F. X. Cervenka, S. Chaim-Avancini, T. 2020-05-07 doi:10.1101/2020.05.05.077834 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Subcortical Volume Trajectories across the Lifespan: Data from 18,605 healthy individuals aged 3-90 years ]]> https://biorxiv.org/content/10.1101/2020.05.05.079475v1?rss=1 Dima, D. Papachristou, E. Modabbernia, A. Doucet, G. E. Agartz, I. Aghajani, M. Akudjedu, T. N. Albajes-Eizagirre, A. Alnaes, D. Alpert, K. I. Andersson, M. Andreasen, N. Andreassen, O. A. Asherson, P. Banaschewski, T. Bargallo, N. Baumeister, S. Baur-Streubel, R. Bertolino, A. Bonvino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buitelaar, J. K. Busatto, G. F. Buckner, R. L. Calhoun, V. Canales-Rodriguez, E. J. Cannon, D. M. Caseras, X. Castellanos, F. X. Cervenka, S. Chaim-Avancini, T. M. Ching, C. R. Cl 2020-05-07 doi:10.1101/2020.05.05.079475 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ A Method to sort heterogenous cell populations based on migration in 2D and 3D environments ]]> https://biorxiv.org/content/10.1101/2020.05.06.080234v1?rss=1 Arora, A. Galeano, J. L. Myaing, M. Z. Arasi, B. Huang, R. Y.-J. DasGupta, R. Biro, M. Viasnoff, V. 2020-05-07 doi:10.1101/2020.05.06.080234 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Host evolutionary history and ecology shape virome composition in fishes ]]> https://biorxiv.org/content/10.1101/2020.05.06.081505v1?rss=1 Geoghegan, J. L. Di Giallonardo, F. Wille, M. Ortiz-Baez, A. S. Costa, V. A. Ghaly, T. Mifsud, J. C. Turnbull, O. M. Bellwood, D. R. Williamson, J. E. Holmes, E. C. 2020-05-08 doi:10.1101/2020.05.06.081505 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ A comparison of two methods for estimating measurement repeatability in morphometric studies ]]> https://biorxiv.org/content/10.1101/2020.05.07.083428v1?rss=1 Wylde, Z. Bonduriansky, R. 2020-05-09 doi:10.1101/2020.05.07.083428 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ Skin protective effects of RM191A, a novel superoxide dismutase mimetic ]]> https://biorxiv.org/content/10.1101/2020.05.10.086694v1?rss=1 Shariev, A. Laos, A. J. Lai, D. Hua, S. Zinger, A. Mcrae, C. R. Casbolt, L. S. Combes, V. Hung, T.-t. Dixon, K. M. Thordarson, P. Mason, R. S. Das, A. 2020-05-11 doi:10.1101/2020.05.10.086694 Cold Spring Harbor Laboratory Press 2020-05-11 <![CDATA[ Medial Orbitofrontal Cortex Regulates Instrumental Conditioned Punishment, but not Pavlovian Conditioned Fear ]]> https://biorxiv.org/content/10.1101/2020.05.12.092205v1?rss=1 Ma, C. Jean-Richard-dit-Bressel, P. Roughley, S. Vissel, B. Balleine, B. Killcross, S. Bradfield, L. A. 2020-05-14 doi:10.1101/2020.05.12.092205 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Profiling of small non-coding RNAs across cellular and biofluid compartments: implications for multiple sclerosis immunopathology ]]> https://biorxiv.org/content/10.1101/2020.05.15.097519v1?rss=1 Zheleznyakova, G. Y. Piket, E. Needhamsen, M. Hagemann-Jensen, M. Ekman, D. Khademi, M. Al Nimer, F. Scicluna, P. Faridani, O. R. Olsson, T. Piehl, F. Jagodic, M. 2020-05-16 doi:10.1101/2020.05.15.097519 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Acquired fluoroquinolone resistance genes in corneal isolates of Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2020.05.17.100396v1?rss=1 Khan, M. Summers, S. Rice, S. A. Stapleton, F. Willcox, M. D. P. Subedi, D. 2020-05-21 doi:10.1101/2020.05.17.100396 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ High burden of Mycoplasma genitalium and other reproductive tract infections among pregnant women in Papua New Guinea ]]> https://biorxiv.org/content/10.1101/2020.05.22.109983v1?rss=1 Scoullar, M. J. L. Boeuf, P. Peach, E. Fidelis, R. Tokmun, K. Melepia, P. Elijah, A. Bradshaw, C. S. Fehler, G. Siba, P. M. Erskine, S. Mokany, E. Kennedy, E. Umbers, A. J. Luchters, S. Robinson, L. J. Wong, N. C. Vallely, A. Badman, S. G. Vallely, L. M. Fowkes, F. J. I. Morgan, C. Pomat, W. Crabb, B. S. Beeson, J. G. 2020-05-23 doi:10.1101/2020.05.22.109983 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Sex and Power: sexual dimorphism in trait variability and its eco-evolutionary and statistical implications ]]> https://biorxiv.org/content/10.1101/2020.05.23.106146v1?rss=1 26,900 mice, using meta-analysis methods. Neither hypothesis could universally explain patterns in trait variability. Sex-bias in variability was trait-dependent. While greater male variability was found in morphological traits, females were much more variable in immunological traits. Sex-specific variability has eco-evolutionary ramifications including sex-dependent responses to climate change, as well as statistical implications including power analysis considering sex difference in variance. ]]> Zajitschek, S. R. K. Zajitschek, F. Bonduriansky, R. Brooks, R. C. Cornwell, W. K. Falster, D. S. Lagisz, M. Mason, J. Senior, A. Noble, D. Nakagawa, S. 2020-05-26 doi:10.1101/2020.05.23.106146 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Novel antioxidant therapy with the immediate precursor to glutathione, γ-glutamylcysteine (GGC), ameliorates LPS-induced cellular stress in an in vitro cystic fibrosis model ]]> https://biorxiv.org/content/10.1101/2020.05.27.119990v1?rss=1 Hewson, C. K. Capraro, A. Wong, S. L. Pandzic, E. Fernando, B. S. M. Awatade, N. T. Zhong, L. Hart-Smith, G. Whan, R. M. Thomas, S. R. Jaffe, A. Bridge, W. J. Waters, S. A. 2020-05-28 doi:10.1101/2020.05.27.119990 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Atypical B cells are a normal component of immune responses to vaccination and infection in humans ]]> https://biorxiv.org/content/10.1101/2020.05.28.120808v1?rss=1 Sutton, H. J. Aye, R. Idris, A. H. Vistein, R. Nduati, E. Kai, O. Mwacharo, J. Xi, L. Gao, X. Andrews, D. Koutsakos, M. Nguyen, T. H. O. Nekrasov, M. Milburn, P. Ethala, A. Berry, A. A. KC, N. Chakravarty, S. Sim, B. K. L. Wheatley, A. K. Kent, S. J. Hoffman, S. L. Lyke, K. E. Bejon, P. Luciani, F. Kedzierska, K. Seder, R. A. Ndungu, F. M. Cockburn, I. A. 2020-05-28 doi:10.1101/2020.05.28.120808 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Significant functional differences despite morphological and molecular similarity in fully differentiated matched Conditionally Reprogrammed (CRC) and Feeder free dual SMAD inhibited expanded human nasal epithelial cells ]]> https://biorxiv.org/content/10.1101/2020.05.29.120006v1?rss=1 Awatade, N. T. Wong, S. L. Pandzic, E. Slapetova, I. Capraro, A. Zhong, L. Turgutoglu, N. Fawcett, L. K. Whan, R. Jaffe, A. Waters, S. 2020-05-31 doi:10.1101/2020.05.29.120006 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Optimised assembly of DNA-lipid nanostructures ]]> https://biorxiv.org/content/10.1101/2020.06.01.128686v1?rss=1 Darley, E. Ridone, P. Singh, J. K. D. Wickham, S. F. Baker, M. A. 2020-06-02 doi:10.1101/2020.06.01.128686 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts. ]]> https://biorxiv.org/content/10.1101/2020.06.05.135699v1?rss=1 Moustaqil, M. Ollivier, E. Chiu, H.-P. Rudolffi-Soto, P. Van Tol, S. Stevens, C. Bhumkar, A. Hunter, D. J. B. Freiberg, A. N. Jacques, D. Lee, B. Sierecki, E. Gambin, Y. 2020-06-05 doi:10.1101/2020.06.05.135699 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests. ]]> https://biorxiv.org/content/10.1101/2020.06.09.143412v1?rss=1 Madala, B. S. Reis, A. L. M. Deveson, I. W. Rawlinson, W. Mercer, T. R. 2020-06-11 doi:10.1101/2020.06.09.143412 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Genome modularization reveals overlapped gene topology is necessary for efficient viral reproduction ]]> https://biorxiv.org/content/10.1101/2020.06.10.143693v1?rss=1 Wright, B. W. Ruan, J. Molloy, M. P. Jaschke, P. R. 2020-06-12 doi:10.1101/2020.06.10.143693 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Red fox viromes across an urban-rural gradient ]]> https://biorxiv.org/content/10.1101/2020.06.15.153858v1?rss=1 Campbell, S. J. Ashley, W. Gil-Fernandez, M. Newsome, T. M. Di Giallonardo, F. Ortiz-Baez, A. S. Mahar, J. E. Towerton, A. L. Gillings, M. Holmes, E. C. Carthey, A. J. Geoghegan, J. L. 2020-06-16 doi:10.1101/2020.06.15.153858 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Combining genome-wide studies of breast, prostate, ovarian and endometrial cancers maps cross-cancer susceptibility loci and identifies new genetic associations ]]> https://biorxiv.org/content/10.1101/2020.06.16.146803v1?rss=1 1Mb from previously identified risk loci for the four cancers and an additional 23 lead variant-cancer associations were novel for one of the cancers. Bayesian models supported pleiotropic effects involving at least two cancers at 222/465 lead variants in 118/192 regions. Gene-level association analysis identified 13 shared susceptibility genes (P<2.6x10-6) in 13 regions not previously implicated in any of the four cancers and not uncovered by our variant-level meta-analysis. Several lead variants had opposite effects across cancers, including a cluster of such variants in the TP53 pathway. Fifty-four lead variants were associated with blood cell traits and suggested genetic overlaps with clonal hematopoiesis. Our study highlights the remarkable pervasiveness of pleiotropy across hormone-related cancers, further illuminating their shared genetic and mechanistic origins at variant- and gene-level resolution. ]]> Kar, S. P. Lindstroem, S. Hung, R. Lawrenson, K. Schmidt, M. O'Mara, T. Glubb, D. Tyrer, J. Schildkraut, J. Chang-Claude, J. Alsulimani, A. Anton, F. Beeghly-Fadiel, A. Bjorge, L. Bodelon, C. Brauch, H. Burghaus, S. Campa, D. Carney, M. Chen, Z. Daly, M. du Bois, A. Ekici, A. Ewing, A. Fasching, P. Flanagan, J. M. Gawelko, J. Giles, G. Hamilton, R. Harris, H. Heitz, F. Hildebrandt, M. Hillemanns, P. Huang, R.-Y. Imaz, L. Irmejs, A. Jakubowska, A. Jensen, A. John, E. Kannisto, P. Karlan, B. Khusnutdinova, E. Kiemeney, L. Kjaer, S. Klapdor, R. Kleiblo 2020-06-19 doi:10.1101/2020.06.16.146803 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data ]]> https://biorxiv.org/content/10.1101/2020.06.16.154377v1?rss=1 Shorten, D. Spinney, R. Lizier, J. 2020-06-16 doi:10.1101/2020.06.16.154377 Cold Spring Harbor Laboratory Press 2020-06-16 <![CDATA[ Optimised cell systems for the investigation ofhepatitis C virus E1E2 glycoproteins ]]> https://biorxiv.org/content/10.1101/2020.06.18.159442v1?rss=1 Kalemera, M. D. Capella-Pujol, J. Chumbe, A. Underwood, A. Bull, R. A. Schinkel, J. Sliepen, K. Grove, J. 2020-06-19 doi:10.1101/2020.06.18.159442 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Microbial dark matter filling the niche in hypersaline microbial mats ]]> https://biorxiv.org/content/10.1101/2020.06.18.160598v1?rss=1 Wong, H. L. MacLeod, F. I. White, R. A. Visscher, P. T. Burns, B. P. 2020-06-20 doi:10.1101/2020.06.18.160598 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ The N-terminus of GPR37L1 is proteolytically processed by matrix metalloproteases ]]> https://biorxiv.org/content/10.1101/2020.06.27.174847v1?rss=1 Coleman, J. L. J. Ngo, T. Smythe, R. E. Cleave, A. J. Jones, N. M. Graham, R. M. Smith, N. J. 2020-06-28 doi:10.1101/2020.06.27.174847 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Elucidation of global and local epidemiology of Salmonella Enteritidis through multilevel genome typing ]]> https://biorxiv.org/content/10.1101/2020.06.30.169953v1?rss=1 Luo, L. Payne, M. Kaur, S. Hu, D. Cheney, L. Octavia, S. Wang, Q. Tanaka, M. M. Sintchenko, V. Lan, R. 2020-07-01 doi:10.1101/2020.06.30.169953 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Decoding ribosomal RNA modification dynamics at single molecule resolution ]]> https://biorxiv.org/content/10.1101/2020.07.06.189969v1?rss=1 Begik, O. Lucas, M. C. Ramirez, J. M. Cruciani, S. Novoa, E. M. Cruciani, S. Vieira, H. G. S. Medina, R. Liu, H. Sas-Chen, A. Mattick, J. S. Schwartz, S. 2020-07-06 doi:10.1101/2020.07.06.189969 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Examining the boundary sharpness coefficient as an index of cortical microstructure and its relationship to age and sex in autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/2020.07.09.196212v1?rss=1 Emily Olafson Saashi A Bedford Gabriel A Devenyi Raihaan Patel Stephanie Tullo Min Tae M Park Evdokia Anagnostou Simon Baron-Cohen Edward T. Bullmore Lindsay R. Chura Michael C. Craig Christine Ecker Dorothea L. Floris Rosemary J. Holt Rhoshel Lenroot Jason P. Lerch Michael V. Lombardo Declan G. M. Murphy Armin Raznahan Amber N. V. Ruigrok Michael D. Spencer John Suckling Margot Taylor The Medical Research Council Autism Imaging Multicentre Study Consortium Meng-Chuan Lai M. Mallar Chakravarty 2020-07-10 doi:10.1101/2020.07.09.196212 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Genetic variants for head size share genes and pathways with cancer ]]> https://biorxiv.org/content/10.1101/2020.07.15.191114v1?rss=1 Knol, M. J. Poot, R. A. Evans, T. E. Satizabal, C. L. Mishra, A. van der Auwera, S. Duperron, M.-G. Jian, X. Hostettler, I. C. van Dam-Nolen, D. H. K. Lamballais, S. Pawlak, M. A. Lewis, C. E. Carrion-Castillo, A. van Erp, T. G. M. Reinbold, C. S. Shin, J. Scholz, M. Haberg, A. K. Kämpe, A. Li, G. H. Y. Avinun, R. Atkins, J. R. Hsu, F.-C. Amod, A. R. Lam, M. Tsuchida, A. Teunissen, M. W. A. Beiser, A. S. Beyer, F. Bis, J. C. Bos, D. Bryan, R. N. Bülow, R. Caspers, S. Catheline, G. Cecil, C. A. M. Dalvie, S. Dartigues, J.-F. DeCarli, C. Enlund-Cerullo, 2020-07-16 doi:10.1101/2020.07.15.191114 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ Drone-derived canopy height predicts biomass across non-forest ecosystems globally ]]> https://biorxiv.org/content/10.1101/2020.07.16.206011v1?rss=1 Cunliffe, A. M. Anderson, K. Boschetti, F. Graham, H. A. Brazier, R. E. Myers-Smith, I. H. Astor, T. Boer, M. M. Calvo, L. Clark, P. E. Cramer, M. D. Encinas-Lara, M. S. Escarzaga, S. M. Fernandez-Guisuraga, J. M. Fisher, A. G. Gdulov, K. Gillespie, B. M. Griebel, A. Hanan, N. P. Hanggito, M. S. Haselberger, S. Havrilla, C. A. Heilman, P. Ji, W. Karl, J. W. Kirchhoff, M. Kraushaar, S. Lyons, M. B. Marzolff, I. Mauritz, M. E. McIntire, C. D. Metzen, D. Mendez-Barroso, L. A. Power, S. C. Prosek, J. Sanz-Ablanedo, E. Sauer, K. J. Schulze-Bruninghoff, D. Simov 2020-07-17 doi:10.1101/2020.07.16.206011 Cold Spring Harbor Laboratory Press 2020-07-17 <![CDATA[ Ether lipid and sphingolipid expression patterns are G-protein coupled estrogen receptor 1-dependently altered in breast cancer cells ]]> https://biorxiv.org/content/10.1101/2020.07.20.212894v1?rss=1 Hahnefeld, L. Gruber, L. Schoemel, N. Fischer, C. Mattjus, P. Gurke, R. Beretta, M. Ferreiros Bouzas, N. Geisslinger, G. Wegner, M.-S. 2020-07-21 doi:10.1101/2020.07.20.212894 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America ]]> https://biorxiv.org/content/10.1101/2020.07.22.216119v1?rss=1 Earl, C. Belitz, M. W. Laffan, S. W. Barve, V. Barve, N. Soltis, D. E. Allen, J. M. Soltis, P. S. Mishler, B. D. Kawahara, A. Y. Guralnick, R. P. 2020-07-24 doi:10.1101/2020.07.22.216119 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia ]]> https://biorxiv.org/content/10.1101/2020.07.24.219048v1?rss=1 50,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA - a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre-H. sapiens hominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory. ]]> Teixeira, J. C. Jacobs, G. S. Stringer, C. Tuke, J. Hudjashov, G. Purnomo, G. A. Sudoyo, H. Cox, M. P. Tobler, R. Turney, C. S. Cooper, A. Helgen, K. M. 2020-07-24 doi:10.1101/2020.07.24.219048 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Surface-bound antigen induces B-cell permeabilization and lysosome exocytosis facilitating antigen uptake and presentation to T-cells ]]> https://biorxiv.org/content/10.1101/2020.07.24.220418v1?rss=1 Maeda, F. Y. van Haaren, J. J. H. Langley, D. B. Christ, D. Andrews, N. W. Song, W. 2020-07-25 doi:10.1101/2020.07.24.220418 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Cavin3 released from caveolae interacts with BRCA1to regulate the cellular stress response ]]> https://biorxiv.org/content/10.1101/2020.07.26.222158v1?rss=1 Parton, R. G. McMahon, K.-A. Stroud, D. A. Gambin, Y. Tillu, V. Bastiani, M. Sierecki, E. Polinkovsky, M. Hall, T. E. Gomez, G. A. Wu, Y. Parat, M.-O. Martel, N. Lo, H. P. Khanna, K. k. Alexandrov, K. Daly, R. Yap, A. S. Ryan, M. 2020-07-26 doi:10.1101/2020.07.26.222158 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Proteomic and Transcriptomic Analyses of the Hippocampus and Cortex in SUDEP and High-Risk SUDEP Cases ]]> https://biorxiv.org/content/10.1101/2020.07.27.223446v1?rss=1 Leitner, D. F. Mills, J. D. Pires, G. Faustin, A. Drummond, E. Kanshin, E. Nayak, S. Askenazi, M. Verducci, C. Chen, B. J. Janitz, M. Anink, J. J. Baayen, J. C. Idema, S. van Vliet, E. A. Devore, S. Friedman, D. Diehl, B. V. Scott, C. Thijs, R. Wisniewski, T. Ueberheide, B. Thom, M. Aronica, E. Devinsky, O. 2020-07-28 doi:10.1101/2020.07.27.223446 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Lipidome profiles of plasma microvesicles differ in experimental cerebral malaria, compared to malaria without neurological complications ]]> https://biorxiv.org/content/10.1101/2020.07.28.224170v1?rss=1 Batarseh, A. M. Vafaee, F. Hosseini-Beheshti, E. Chen, A. Cohen, A. Juillard, A. Hunt, N. H. Mariani, M. Mitchell, T. Grau, G. E. R. 2020-07-29 doi:10.1101/2020.07.28.224170 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Substrate-induced clustering activates Trim-Away of pathogens and proteins ]]> https://biorxiv.org/content/10.1101/2020.07.28.225359v1?rss=1 Zeng, J. Santos, A. F. Mukadam, A. Osswald, M. Luptak, J. Jacques, D. Dickson, C. Renner, N. Johnson, C. Vaysburd, M. McEwan, W. A. Morais-de-Sa, E. Clift, D. James, L. C. 2020-07-29 doi:10.1101/2020.07.28.225359 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Estimation of Three-Dimensional Chromatin Morphology for Nuclear Classification and Characterisation ]]> https://biorxiv.org/content/10.1101/2020.07.29.226498v1?rss=1 Rana, P. Sowmya, A. Meijering, E. Song, Y. 2020-07-29 doi:10.1101/2020.07.29.226498 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Insecticide resistance status of Aedes aegypti in Bangladesh ]]> https://biorxiv.org/content/10.1101/2020.07.31.231076v1?rss=1 Al-Amin, H. M. Johora, F. T. Irish, S. R. Hossainey, M. R. H. Vizcaino, L. Paul, K. K. Khan, W. A. Haque, R. Alam, M. S. Lenhar, A. 2020-07-31 doi:10.1101/2020.07.31.231076 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis ]]> https://biorxiv.org/content/10.1101/2020.08.04.236893v1?rss=1 99% sensitivity and >99% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives. ]]> Bull, R. A. Adikari, T. Hammond, J. M. Stevanovski, I. Ferguson, J. M. Beukers, A. G. Naing, Z. Yeang, M. Verich, A. Gamaarachichi, H. Kim, K. W. Luciani, F. Stelzer-Braid, S. Eden, J.-S. Rawlinson, W. D. van Hal, S. J. Deveson, I. W. 2020-08-04 doi:10.1101/2020.08.04.236893 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ A novel, dichloromethane-fermenting bacterium in the Peptococcaceae family, 'Candidatus Formamonas warabiya', gen. nov. sp. nov. ]]> https://biorxiv.org/content/10.1101/2020.08.09.233494v1?rss=1 Holland, S. I. Ertan, H. Manefield, M. J. Lee, M. 2020-08-10 doi:10.1101/2020.08.09.233494 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Sex-Dependent Shared and Non-Shared Genetic Architecture Across Mood and Psychotic Disorders ]]> https://biorxiv.org/content/10.1101/2020.08.13.249813v1?rss=1 Blokland, G. A. Grove, J. Chen, C.-Y. Cotsapas, C. Tobet, S. Handa, R. Schizophrenia Working Group of the Psychiatric Genomics Consortium, St Clair, D. Lencz, T. Mowry, B. J. Periyasamy, S. Cairns, M. J. Tooney, P. A. Wu, J. Q. Kelly, B. Kirov, G. Sullivan, P. F. Corvin, A. Riley, B. P. Esko, T. Milani, L. Jönsson, E. G. Palotie, A. Ehrenreich, H. Begemann, M. Steixner-Kumar, A. Sham, P. C. Iwata, N. Weinberger, D. R. Gejman, P. V. Sanders, A. R. Buxbaum, J. D. Rujescu, D. Giegling, I. Konte, B. Hartmann, A. M. Bramon, E. Murray, R. M. Pato, M. T. Lee, 2020-08-17 doi:10.1101/2020.08.13.249813 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Myanmar's terrestrial ecosystems: status, threats and conservation opportunities ]]> https://biorxiv.org/content/10.1101/2020.08.18.256750v1?rss=1 Murray, N. J. Keith, D. A. Duncan, A. Tizard, R. Ferrer-Paris, J. R. Worthington, T. A. Armstrong, K. Hlaing, N. Htut, W. T. Oo, A. H. Ya, K. Z. Grantham, H. 2020-08-20 doi:10.1101/2020.08.18.256750 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Freeform printing of heterotypic tumor models within cell-laden microgel matrices ]]> https://biorxiv.org/content/10.1101/2020.08.30.274654v1?rss=1 Molley, T. G. Jalandhra, G. K. Nemec, S. R. Tiffany, A. S. Harley, B. A. C. Hung, T.-t. Kilian, K. A. 2020-08-31 doi:10.1101/2020.08.30.274654 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ ZNF410 uniquely activates the NuRD component CHD4 to silence fetal hemoglobin expression ]]> https://biorxiv.org/content/10.1101/2020.08.31.274324v1?rss=1 Lan, X. Ren, R. Feng, R. Ly, L. C. Lan, Y. Zhang, Z. Aboreden, N. Qin, K. Horton, J. R. Grevet, J. D. Mayuranathan, T. Abdulmalik, O. Keller, C. A. Giardine, B. Hardison, R. C. Crossley, M. Weiss, M. J. Cheng, X. Shi, J. Blobel, G. A. 2020-08-31 doi:10.1101/2020.08.31.274324 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Combination of photoactivation with lattice light-sheet imaging allows visualizing complex dorsal ruffling dynamics ]]> https://biorxiv.org/content/10.1101/2020.09.01.276824v1?rss=1 Leyden, F. Uthistran, S. Moorthi, U. K. York, H. M. Patil, A. Gandhi, H. Petrov, E. P. Arumugam, S. 2020-09-01 doi:10.1101/2020.09.01.276824 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ BonA from Acinetobacter baumannii forms a divisome-localized decamer that supports outer envelope function ]]> https://biorxiv.org/content/10.1101/2020.09.01.278697v1?rss=1 Grinter, R. Morris, F. C. Dunstan, R. A. Leung, P. M. Belousoff, M. Gunasinghe, S. D. Beckham, S. Peleg, A. Y. Greening, C. Li, J. Heinz, E. Lithgow, T. 2020-09-02 doi:10.1101/2020.09.01.278697 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ A feedback loop between the androgen receptor and 6-phosphogluoconate dehydrogenase (6PGD) drives prostate cancer growth ]]> https://biorxiv.org/content/10.1101/2020.09.02.279356v1?rss=1 Gillis, J. L. Hinneh, J. A. Ryan, N. K. Irani, S. Moldovan, M. Shrestha, R. K. Quek, L.-E. Hoy, A. J. Holst, J. Centenera, M. M. Mills, I. G. Lynn, D. J. Selth, L. A. Butler, L. M. 2020-09-03 doi:10.1101/2020.09.02.279356 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Determination of the molecular reach of the protein tyrosine phosphatase SHP-1 ]]> https://biorxiv.org/content/10.1101/2020.09.04.283341v1?rss=1 Clemens, L. Kutuzov, M. Bayer, K. V. Goyette, J. Allard, J. Dushek, O. 2020-09-05 doi:10.1101/2020.09.04.283341 Cold Spring Harbor Laboratory Press 2020-09-05 <![CDATA[ In vitro study of BromAc on SARS-CoV-2 spike and envelope proteins shows synergy and disintegration at modest concentrations ]]> https://biorxiv.org/content/10.1101/2020.09.07.286906v1?rss=1 Akhter, J. Pillai, K. Badar, S. Mekkawy, A. Valle, S. Morris, D. L. 2020-09-08 doi:10.1101/2020.09.07.286906 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Inhibition of guanosine monophosphate synthetase (GMPS) blocks glutamine metabolism and prostate cancer growth in vitro and in vivo ]]> https://biorxiv.org/content/10.1101/2020.09.07.286997v1?rss=1 Wang, Q. Guan, Y. F. Hancock, S. E. Wahi, K. van Geldermalsen, M. Zhang, B. K. Pang, A. Nagarajah, R. Mak, B. Horvath, L. G. Turner, N. Holst, J. 2020-09-09 doi:10.1101/2020.09.07.286997 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Subcortical Atlas of the Rhesus Macaque (SARM) for Magnetic Resonance Imaging ]]> https://biorxiv.org/content/10.1101/2020.09.16.300053v1?rss=1 Hartig, R. Glen, D. Jung, B. Logothetis, N. K. Paxinos, G. Garza-Villarreal, E. A. Messinger, A. Evrard, H. C. 2020-09-18 doi:10.1101/2020.09.16.300053 Cold Spring Harbor Laboratory Press 2020-09-18 <![CDATA[ Novel genetic variants associated with brain functional networks in 18,445 adults from the UK Biobank ]]> https://biorxiv.org/content/10.1101/2020.09.17.268029v1?rss=1 Foo, H. Thalamuthu, A. Jiang, J. Koch, F. Mather, K. Wen, W. Sachdev, P. 2020-09-17 doi:10.1101/2020.09.17.268029 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ Metagenomic insights into ecosystem function in the microbial mats of Blue Holes, Shark Bay ]]> https://biorxiv.org/content/10.1101/2020.09.18.304444v1?rss=1 Kindler, G. S. Burns, B. P. Wong, H. L. L. Larkum, A. W. D. Johnson, M. MacLeod, F. I. 2020-09-19 doi:10.1101/2020.09.18.304444 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Integrative systems approach reveals dynamics of microbiome-metal-ion axis in mesocosms representing tropical urban freshwater canal ecosystem ]]> https://biorxiv.org/content/10.1101/2020.09.21.306803v1?rss=1 Saxena, G. Hill, E. D. Marzinelli, E. M. Umashankar, S. Wei, T. J. Yissue, W. W. Steinberg, P. D. Rajal, V. B. Kjelleberg, S. Williams, R. Wuertz, S. Swarup, S. 2020-09-21 doi:10.1101/2020.09.21.306803 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Hippocampal silent infarct leads to subtle cognitive decline that is associated with inflammation and gliosis at twenty-four hours after injury in a rat model ]]> https://biorxiv.org/content/10.1101/2020.09.29.318204v1?rss=1 Finney, C. A. Morris, M. J. Westbrook, R. F. Jones, N. M. 2020-09-30 doi:10.1101/2020.09.29.318204 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ RESCRIPt: Reproducible sequence taxonomy reference database management for the masses ]]> https://biorxiv.org/content/10.1101/2020.10.05.326504v1?rss=1 Robeson, M. S. O'Rourke, D. R. Kaehler, B. D. Ziemski, M. Dillon, M. R. Foster, J. T. Bokulich, N. A. 2020-10-05 doi:10.1101/2020.10.05.326504 Cold Spring Harbor Laboratory Press 2020-10-05 <![CDATA[ APEX-Gold: A genetically-encoded particulate marker for robust 3D electron microscopy ]]> https://biorxiv.org/content/10.1101/2020.10.06.328831v1?rss=1 Rae, J. Ferguson, C. Ariotti, N. Webb, R. Cheng, H.-H. Mead, J. Riches, J. Hunter, D. Martel, N. Baltos, J. Christopoulos, A. Bryce, N. Cagigas, M. Fonseka, S. Hardeman, E. Gunning, P. Gambin, Y. Hall, T. E. Parton, R. G. 2020-10-06 doi:10.1101/2020.10.06.328831 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Ancestral dietary change alters development of Drosophila larvae through MAPK signalling ]]> https://biorxiv.org/content/10.1101/2020.10.07.327478v1?rss=1 Towarnicki, S. G. Youngson, N. A. Corley, S. M. St John, J. C. Turner, N. Morris, M. J. Ballard, J. W. O. 2020-10-08 doi:10.1101/2020.10.07.327478 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Nanoscape, a data-driven 3D real-time interactive virtual cell environment ]]> https://biorxiv.org/content/10.1101/2020.10.15.340778v1?rss=1 Kadir, S. R. Lilja, A. Gunn, N. Strong, C. Hughes, R. T. Bailey, B. J. Rae, J. Parton, R. G. McGhee, J. 2020-10-15 doi:10.1101/2020.10.15.340778 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ The role of the rodent lateral orbitofrontal cortex in simple Pavlovian cue-outcome learning depends on training experience ]]> https://biorxiv.org/content/10.1101/2020.10.16.342832v1?rss=1 Panayi, M. C. Killcross, S. 2020-10-16 doi:10.1101/2020.10.16.342832 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Strain population structure varies widely across bacterial species and predicts strain colonization in unrelated individuals ]]> https://biorxiv.org/content/10.1101/2020.10.17.343640v1?rss=1 1000 sequenced bacterial strains from the fecal microbiota of 47 individuals from two countries and combined them with >150,000 bacterial genomes from NCBI to quantify the strain population size of different bacterial species, as well as the frequency of finding the same strain colonized in unrelated individuals who had no opportunities for direct microbial strain transmission. Strain population sizes ranged from tens to over one-hundred thousand per species. Prevalent strains in common gut microbiota species with small population sizes were the most likely to be harbored in two or more unrelated individuals. The finite strain population size of certain species creates the opportunity to comprehensively sequence the entirety of these species prevalent strains and associate their presence in different individuals with health outcomes. ]]> Faith, J. J. Chen Liaw, A. Aggarwala, V. Kaakoush, N. O. Borody, T. Mitchell, H. Kamm, M. A. Paramsothy, S. Snitkin, E. S. Mogno, I. 2020-10-17 doi:10.1101/2020.10.17.343640 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation ]]> https://biorxiv.org/content/10.1101/2020.10.17.343772v1?rss=1 Jonkhout, N. Cruciani, S. Vieira, H. G. S. Tran, J. Liu, H. Liu, G. Pickford, R. Kaczorowski, D. Franco, G. R. Vauti, F. Camacho, N. Abedini, S. S. Najmabadi, H. Ribas de Pouplana, L. Christ, D. Schonrock, N. Mattick, J. S. Novoa, E. M. 2020-10-17 doi:10.1101/2020.10.17.343772 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Embrace heterogeneity to improve reproducibility: A perspective from meta-analysis of variation in preclinical research ]]> https://biorxiv.org/content/10.1101/2020.10.26.354274v1?rss=1 Usui, T. Macleod, M. R. McCann, S. K. Senior, A. M. Nakagawa, S. 2020-10-27 doi:10.1101/2020.10.26.354274 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Brunner syndrome associated MAOA dysfunction in human dopaminergic neurons results in NMDAR hyperfunction and increased network activity. ]]> https://biorxiv.org/content/10.1101/2020.10.28.359224v1?rss=1 Shi, Y. van Rhijn, J.-R. Bormann, M. Mossink, B. Frega, M. Recaioglu, H. Hakobjan, M. Klein Gunnewiek, T. M. Schoenmaker, C. Palmer, E. Faivre, L. Kittel-Schneider, S. Schubert, D. Brunner, H. Franke, B. Nadif Kasri, N. 2020-10-29 doi:10.1101/2020.10.28.359224 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Supervised Application of Internal Validation Measures to Benchmark Dimensionality Reduction Methods in scRNA-seq Data ]]> https://biorxiv.org/content/10.1101/2020.10.29.361451v1?rss=1 Koch, F. C. Sutton, G. J. Voineagu, I. Vafaee, F. C. 2020-10-30 doi:10.1101/2020.10.29.361451 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Non-invasive, label-free optical analysis to detect aneuploidy within the inner cell mass of the preimplantation embryo ]]> https://biorxiv.org/content/10.1101/2020.11.01.364133v1?rss=1 Tan, C. Y. Mahbub, S. B. Campugan, C. A. Campbell, J. M. Habibalahi, A. Chow, D. J. X. Mustafa, S. Goldys, E. M. Dunning, K. R. 2020-11-02 doi:10.1101/2020.11.01.364133 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Metabolomics shows the Australian dingo has a unique plasma profile ]]> https://biorxiv.org/content/10.1101/2020.11.02.364307v1?rss=1 Yadav, S. Pickford, R. Zammit, R. A. Ballard, J. W. O. 2020-11-03 doi:10.1101/2020.11.02.364307 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Short-Beaked Echidna (Tachyglossus aculeatus) Home Range at Fowlers Gap Arid Zone Research Station, NSW. ]]> https://biorxiv.org/content/10.1101/2020.11.02.364687v1?rss=1 0.65 km2) suggesting that echidnas exhibit larger home ranges in arid zones. This study provides insight into the movement and home range of echidnas in arid zones, revealing that desert echidnas have large home ranges, dependent on the availability of resources. ]]> Badgery, G. J. Leggett, K. Lawes, J. 2020-11-02 doi:10.1101/2020.11.02.364687 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity. ]]> https://biorxiv.org/content/10.1101/2020.11.11.378968v1?rss=1 McCann, A. J. Lou, J. Moustaqil, M. Blum, A. Fontaine, F. Liu, H. Luu, W. Koopman, P. Sierecki, E. Gambin, Y. Meunier, F. A. Liu, Z. Hinde, E. Francois, M. 2020-11-12 doi:10.1101/2020.11.11.378968 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome ]]> https://biorxiv.org/content/10.1101/2020.11.11.379073v1?rss=1 Edwards, R. J. Field, M. A. J. Ferguson, J. M. Dudchenko, O. Keilwagen, J. Rosen, B. D. Johnson, G. S. Rice, E. Hillier, L. Hammond, J. M. Tomwarnicki, S. G. Omer, A. Skvortsova, K. Bogdanovic, O. Zammit, R. A. Aiden, E. L. Warren, W. C. Ballard, J. W. O. 2020-11-11 doi:10.1101/2020.11.11.379073 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Rapid HIV-1 capsid interaction screening using fluorescence fluctuationspectroscopy ]]> https://biorxiv.org/content/10.1101/2020.11.13.382242v1?rss=1 Lau, D. Walsh, J. C. Dickson, C. F. Tuckwell, A. Stear, J. H. Hunter, D. J. B. Bhumkar, A. Shah, V. Turville, S. G. Sierecki, E. Gambin, Y. Jacques, D. A. Böcking, T. 2020-11-16 doi:10.1101/2020.11.13.382242 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Inherent population structure determines the importance of filtering parameters for reduced representation sequencing analyses ]]> https://biorxiv.org/content/10.1101/2020.11.14.383240v1?rss=1 Selechnik, D. Richardson, M. F. Hess, M. Hess, A. S. Dodds, K. G. Martin, M. Chan, T. C. Cardilini, A. P. A. Sherman, C. Shine, R. Rollins, L. A. 2020-11-16 doi:10.1101/2020.11.14.383240 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ The selective estrogen receptor modulator tamoxifen protects against subtle cognitive decline and early markers of injury twenty-four hours after hippocampal silent infarct ]]> https://biorxiv.org/content/10.1101/2020.11.15.383737v1?rss=1 Finney, C. A. Shvetcov, A. Westbrook, R. F. Morris, M. J. Jones, N. 2020-11-17 doi:10.1101/2020.11.15.383737 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem. ]]> https://biorxiv.org/content/10.1101/2020.11.15.384057v1?rss=1 Yadav, S. Dudchenko, O. Esvaran, M. Rosen, B. D. Field, M. D. Skvortsova, K. Edwards, R. J. Gopalakrishnan, S. Keilwagen, J. Cochran, B. J. Manandhar, B. Bucknall, M. Bustamante, S. Rasmussen, J. A. Melvin, R. G. Omer, A. Colaric, Z. Chan, E. K. F. Minoche, A. E. Smith, T. P. Gilbert, M. T. P. Bogdanovic, O. Zammit, R. A. Thomas, T. Aiden, E. L. Ballard, J. W. O. 2020-11-16 doi:10.1101/2020.11.15.384057 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ Microbial function is related to behavior of an invasive anuran ]]> https://biorxiv.org/content/10.1101/2020.11.16.385690v1?rss=1 Zhou, J. Nelson, T. M. Rodriguez Lopez, C. Zhou, S. J. Ward-Fear, G. Stuart, K. C. Rollins, L. A. 2020-11-17 doi:10.1101/2020.11.16.385690 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ Low Repeatability of Aversive Learning in Zebrafish (Danio rerio) ]]> https://biorxiv.org/content/10.1101/2020.11.16.385930v1?rss=1 Mason, D. Zajitschek, S. Anwer, H. O'Dea, R. Hesselson, D. Nakagawa, S. 2020-11-17 doi:10.1101/2020.11.16.385930 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ A newly identified prophage-encoded gene, ymfM, causes SOS-inducible filamentation in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.11.19.390815v1?rss=1 Ansari, S. Walsh, J. C. Bottomley, A. L. Duggin, I. G. Burke, C. Harry, E. J. 2020-11-20 doi:10.1101/2020.11.19.390815 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ ACTN3 genotype influences skeletal muscle mass regulation and response to dexamethasone ]]> https://biorxiv.org/content/10.1101/2020.11.20.392282v1?rss=1 Seto, J. T. Roeszler, K. N. Meehan, L. R. Wood, H. D. Tiong, C. Bek, L. Lee, S. F. Shah, M. Quinlan, K. G. Gregorevic, P. Houweling, P. J. North, K. N. 2020-11-23 doi:10.1101/2020.11.20.392282 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Improve Concentration Of Frequency And Time (ConceFT) By Novel Complex Spherical Designs ]]> https://biorxiv.org/content/10.1101/2020.11.23.394007v1?rss=1 Sourisseau, M. Wang, Y. Womersley, R. S. Wu, H.-t. Yu, W.-H. 2020-11-23 doi:10.1101/2020.11.23.394007 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Seeing the forest through the trees: Identifying functional interactions from Hi-C ]]> https://biorxiv.org/content/10.1101/2020.11.29.402420v1?rss=1 Liu, N. low, w. y. Alinejad-Rokny, H. Sadlon, T. Pederson, S. M. Barry, S. C. Breen, J. 2020-11-29 doi:10.1101/2020.11.29.402420 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Quantitatively Monitoring in situ Mitochondrial Thermal Dynamics by Upconversion Nanoparticles ]]> https://biorxiv.org/content/10.1101/2020.11.29.402818v1?rss=1 Di, X. Wang, D. Zhou, J. Zhang, L. Stenzel, M. Jin, D. Su, Q. P. 2020-11-29 doi:10.1101/2020.11.29.402818 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Human major infections: tuberculosis, treponematoses, leprosy - a paleopathological perspective of their evolution ]]> https://biorxiv.org/content/10.1101/2020.11.30.403675v1?rss=1 Henneberg, M. Holloway-Kew, K. Lucas, T. 2020-11-30 doi:10.1101/2020.11.30.403675 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ The pan-cancer lncRNA PLANE regulates an alternative splicing program to promote cancer pathogenesis ]]> https://biorxiv.org/content/10.1101/2020.12.04.412536v1?rss=1 Teng, L. Feng, Y. C. Guo, S. T. Wang, P. L. Wang, S. X. Zhang, S. N. Qi, T. F. La, T. Zhang, Y. Y. Zhao, X. H. Zhang, D. Wang, J. Y. Shi, Y. Li, J. M. Cao, H. Liu, T. Thorne, R. F. Jin, L. Shao, F.-M. Zhang, X. D. 2020-12-06 doi:10.1101/2020.12.04.412536 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Global elongation and high shape flexibility as an evolutionary hypothesis of accommodating mammalian brains into skulls ]]> https://biorxiv.org/content/10.1101/2020.12.06.410928v1?rss=1 Weisbecker, V. Rowe, T. Wroe, S. Macrini, T. E. Garland, K. L. S. Travouillon, K. J. Black, K. Archer, M. Hand, S. J. Berlin, J. Beck, R. M. D. Ladeveze, S. Sharp, A. C. Mardon, K. Sherratt, E. 2020-12-07 doi:10.1101/2020.12.06.410928 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Evaluation of optically tailored fluorescent silicon quantum dots for bioimaging of the tear film ]]> https://biorxiv.org/content/10.1101/2020.12.09.411876v1?rss=1 Sarwat, S. Stapleton, F. Willcox, M. D. P. O'Mara, P. Tilley, R. Gooding, J. Roy, M. 2020-12-09 doi:10.1101/2020.12.09.411876 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Dietary and body mass reconstruction of the Miocene neotropical bat Notonycteris magdalenensis (Phyllostomidae) from La Venta, Colombia ]]> https://biorxiv.org/content/10.1101/2020.12.09.418491v1?rss=1 Lopez-Aguirre, C. Czaplewski, N. J. Link, A. Takai, M. Hand, S. J. 2020-12-10 doi:10.1101/2020.12.09.418491 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ The Ca2+-activated cation channel TRPM4 is a positive regulator of pressure overload-induced cardiac hypertrophy ]]> https://biorxiv.org/content/10.1101/2020.12.21.423727v1?rss=1 Guo, Y. Yu, J. Wu, Y. Gong, H. Kesteven, S. Iismaa, S. E. Chan, A. Holman, S. Pinto, S. Pironet, A. Cox, C. Vennekens, R. Graham, R. M. Feneley, M. P. Martinac, B. 2020-12-21 doi:10.1101/2020.12.21.423727 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses ]]> https://biorxiv.org/content/10.1101/2020.12.22.423111v1?rss=1 Kaminow, B. Ballouz, S. Gillis, J. Dobin, A. 2020-12-22 doi:10.1101/2020.12.22.423111 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Homology between the flagellar export apparatus and ATP synthetase: evidence from synteny predating the Last Universal Common Ancestor ]]> https://biorxiv.org/content/10.1101/2021.01.01.425057v1?rss=1 Matzke, N. J. Lin, A. Stone, M. Baker, M. A. B. 2021-01-02 doi:10.1101/2021.01.01.425057 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ The repertoire of testicular extracellular vesicles cargoes and their involvement in inter-compartmental communication required for spermatogenesis ]]> https://biorxiv.org/content/10.1101/2021.01.08.426002v1?rss=1 Choy, K. H. K. Chan, S. Y. Lam, W. Jin, J. Zheng, T. Yu, S. S. Wang, W. Li, L. Xie, G. Yim, H. C. H. Chen, H. FOK, E. K. L. 2021-01-09 doi:10.1101/2021.01.08.426002 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Anterior insula-associated social novelty recognition: orchestrated regulation by a local retinoic acid cascade and oxytocin signaling ]]> https://biorxiv.org/content/10.1101/2021.01.15.426848v1?rss=1 Kim, S.-H. An, K. Namkung, H. Rannals, M. D. Moore, J. R. Cash-Padgett, T. Mihaljevic, M. Saha, S. Oh, L. S. Kondo, M. A. Yang, K. Maher, B. J. Niwa, M. Sawa, A. 2021-01-15 doi:10.1101/2021.01.15.426848 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Universal DNA methylation age across mammalian tissues ]]> https://biorxiv.org/content/10.1101/2021.01.18.426733v1?rss=1 0.96) of any mammalian tissue. Deviations between epigenetic age and chronological age relate to mortality risk in humans, mutations that affect the somatotropic axis in mice, and caloric restriction. We characterized specific cytosines, whose methylation levels change with age across most mammalian species. These cytosines are greatly enriched in polycomb repressive complex 2-binding sites, are located in regions that gradually lose chromatin accessibility with age and are proximal to genes that play a role in mammalian development, cancer, human obesity, and human longevity. Collectively, these results support the notion that aging is indeed evolutionarily conserved and coupled to developmental processes across all mammalian species - a notion that was long-debated without the benefit of this new compelling evidence. SUMMARYThis study identifies and characterizes evolutionarily conserved cytosines implicated in the aging process across mammals and establishes pan mammalian epigenetic clocks. ]]> Lu, A. T. Fei, Z. Haghani, A. Robeck, T. R. Zoller, J. A. Li, C. Z. Zhang, J. Ablaeva, J. Adams, D. M. Almunia, J. Ardehali, R. Arneson, A. Baker, C. S. Belov, K. Black, P. Blumstein, D. T. Bors, E. K. Breeze, C. E. Brooke, R. T. Brown, J. L. Caulton, A. Cavin, J. M. Chatzistamou, I. Chen, H. Chiavellini, P. Choi, O.-W. Clarke, S. DeYoung, J. Dold, C. Emmons, C. K. Emmrich, S. Faulkes, C. G. Ferguson, S. H. Finno, C. J. Gaillard, J.-M. Garde, E. Gladyshev, V. N. Gorbunova, V. Goya, R. G. Grant, M. J. Hales, E. N. Hanson, M. B. Haulena, M. Hogan, A. N. 2021-01-19 doi:10.1101/2021.01.18.426733 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Spontaneous adaptation of ion selectivity in a bacterial flagellar motor ]]> https://biorxiv.org/content/10.1101/2021.01.26.427765v1?rss=1 Ridone, P. Sowa, Y. Baker, M. A. 2021-01-27 doi:10.1101/2021.01.26.427765 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Selectivity of Protein Interactions along the Aggregation Pathway of a-Synuclein ]]> https://biorxiv.org/content/10.1101/2021.01.29.428744v1?rss=1 Leitao, A. Rudolffi Soto, P. Chappard, A. Bhumkar, A. Hunter, D. J. B. Sierecki, E. Gambin, Y. 2021-01-29 doi:10.1101/2021.01.29.428744 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Cluster-specific gene marker enhance Shigella and Enteroinvasive Escherichia coli in silico serotyping ]]> https://biorxiv.org/content/10.1101/2021.01.30.428723v1?rss=1 Zhang, X. Payne, M. Nguyen, T. Kaur, S. Lan, R. 2021-01-30 doi:10.1101/2021.01.30.428723 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Manipulation of stimulus waveform and frequency permits targeted fiber activation during vagus nerve stimulation in 2 rodent species ]]> https://biorxiv.org/content/10.1101/2021.01.30.428827v1?rss=1 5KHz frequency and 7-10 times engagement threshold (xT) intensity in rats, 15-25xT in mice. These effects can be explained in computational models by how sodium channel responses to KES are shaped by axonal size and myelin. Our results indicate that selective engagement of vagal C-afferents is attainable by intermittent KES. ]]> Chang, Y.-C. Ahmed, U. Jayaprakash, N. Abbas, A. Lin, Q. Mughrabi, I. Guo, T. Wu, Y.-C. Gabalski, A. H. Daytz, A. Ashville, J. Dokos, S. Al-Abed, Y. Zanos, S. 2021-02-01 doi:10.1101/2021.01.30.428827 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance ]]> https://biorxiv.org/content/10.1101/2021.02.01.429068v1?rss=1 Luo, L. Wang, H. Payne, M. J. Liang, C. Bai, L. Zheng, H. Zhang, Z. Zhang, L. Zhang, X. Yan, G. Zou, N. Chen, X. Wan, Z. Xiong, Y. Lan, R. Li, Q. 2021-02-02 doi:10.1101/2021.02.01.429068 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Unravelling the Physiological Correlates of Mental Workload Variations in Tracking and Collision Prediction Tasks: Implications for Air Traffic Controllers ]]> https://biorxiv.org/content/10.1101/2021.02.02.428702v1?rss=1 John, A. R. Singh, A. K. Do, T.-T. N. Eidels, A. Nalivaiko, E. Gavgani, A. M. Brown, S. Bennett, M. Lal, S. Simpson, A. M. Gustin, S. M. Double, K. Walker, F. R. Kleitman, S. Morley, J. Lin, C.-T. 2021-02-03 doi:10.1101/2021.02.02.428702 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Niche-guided tissue patterning by chemomechanical flow lithography ]]> https://biorxiv.org/content/10.1101/2021.02.10.430691v1?rss=1 Newman, P. L. H. Osteil, P. Anderson, T. A. Sun, J. Q. J. Kempe, D. Biro, M. Tam, P. P. L. Shin, J.-W. Zreiqat, H. 2021-02-11 doi:10.1101/2021.02.10.430691 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ A covalently crosslinked bioink for multi-materials drop-on-demand 3D bioprinting of three-dimensional cell cultures ]]> https://biorxiv.org/content/10.1101/2021.02.18.431759v1?rss=1 Utama, R. H. Tan, V. Tjandra, K. C. Sexton, A. Nguyen, D. O'Mahony, A. P. Ribeiro, J. C. C. Kavallaris, M. Gooding, J. J. 2021-02-18 doi:10.1101/2021.02.18.431759 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Rare genera differentiate urban green space soil bacterial communities in three cities across the world ]]> https://biorxiv.org/content/10.1101/2021.02.21.432167v1?rss=1 Mills, J. G. Selway, C. A. Weyrich, L. S. Skelly, C. Weinstein, P. Thomas, T. Young, J. M. Marczylo, E. Yadav, S. Yadav, V. Lowe, A. J. Breed, M. F. 2021-02-22 doi:10.1101/2021.02.21.432167 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ A Machine Learning Approach to Unmask Novel Gene Signatures and Prediction of Alzheimers Disease Within Different Brain Regions. ]]> https://biorxiv.org/content/10.1101/2021.03.03.433689v1?rss=1 Sharma, A. Dey, P. 2021-03-03 doi:10.1101/2021.03.03.433689 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Recovery of high-qualitied Genomes from a deep-inland Salt Lake Using BASALT ]]> https://biorxiv.org/content/10.1101/2021.03.05.434042v1?rss=1 Yu, K. Qiu, Z. Mu, R. Qiao, X. Zhang, L. Lian, C.-A. Deng, C. Wu, Y. Xu, Z. Li, B. Pan, B. Zhang, Y. Fan, L. Liu, Y. Cao, H. Jin, T. Chen, B. Wang, F. Yan, Y. Xie, L. Zhou, L. Yi, S. Chi, S. Zhang, T. Zhuang, W. 2021-03-05 doi:10.1101/2021.03.05.434042 Cold Spring Harbor Laboratory Press 2021-03-05 <![CDATA[ Structural Covariance Networks in Post-Traumatic Stress Disorder: A Multisite ENIGMA-PGC Study ]]> https://biorxiv.org/content/10.1101/2021.03.13.432212v1?rss=1 Rakesh, G. Sun, D. Logue, M. Clarke-Rubright, E. O Leary, B. M. Haswell, C. Xie, H. Thompson, P. Dennis, E. Jahanshad, N. Koch, S. Frijling, J. Nawijn, L. Olff, M. van Zuiden, M. Rashid, F. Zhu, X. De Bellis, M. Daniels, J. K. Sierk, A. Manthey, A. Stevens, J. S. Jovanovic, T. Stein, M. B. Shenton, M. van der Werff, S. J. A. van der Wee, N. J. A. Vermeiren, R. R. J. M. Schmahl, C. Herzog, J. Kaufman, M. L. O'Connor, L. Lebois, L. A. M. Baker, J. T. Gruber, S. A. Wolff, J. D. Wolf, E. J. Winternitz, S. Gonenc, A. Ressler, K. J. Hofmann, D. Bryant, R. A. 2021-03-16 doi:10.1101/2021.03.13.432212 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Machine learning prediction of Antibody-Antigen binding: dataset, method and testing ]]> https://biorxiv.org/content/10.1101/2021.03.19.435772v1?rss=1 Ye, C. Hu, W. Gaeta, B. 2021-03-20 doi:10.1101/2021.03.19.435772 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Single dose of amphetamine induces delayed subregional attenuation of striatal cholinergic interneuron activity ]]> https://biorxiv.org/content/10.1101/2021.03.22.436417v1?rss=1 Ztaou, S. Oh, S. J. Tepler, S. Fleury, S. Matamales, M. Bertran-Gonzalez, J. Chuhma, N. Rayport, S. 2021-03-22 doi:10.1101/2021.03.22.436417 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Antidepressants are complex regulators of lipoprotein(a) macropinocytosis ]]> https://biorxiv.org/content/10.1101/2021.03.26.437114v1?rss=1 Redpath, G. M. I. Deo, N. Siddiqui, H. Madani, G. Kapoor-Kaushik, N. Ariotti, N. Rutledge, M. Williams, M. McCormick, S. P. 2021-03-27 doi:10.1101/2021.03.26.437114 Cold Spring Harbor Laboratory Press 2021-03-27 <![CDATA[ Thermal oscillations enable reshuffling of genetic material in a primitive cell cycle ]]> https://biorxiv.org/content/10.1101/2021.04.01.438038v1?rss=1 Rubio Sanchez, R. O'Flaherty, D. Wang, A. Coscia, F. Di Michele, L. Cicuta, P. Bonfio, C. 2021-04-02 doi:10.1101/2021.04.01.438038 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Single-molecule imaging of cytoplasmic dynein reveals the mechanism of motor activation and cargo capture ]]> https://biorxiv.org/content/10.1101/2021.04.05.438428v1?rss=1 Tirumala, N. A. Ananthanarayanan, V. 2021-04-05 doi:10.1101/2021.04.05.438428 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Transcript- and annotation-guided genome assembly of the European starling ]]> https://biorxiv.org/content/10.1101/2021.04.07.438753v1?rss=1 Stuart, K. C. Edwards, R. J. Cheng, Y. Warren, W. C. Burt, D. W. Sherwin, W. B. Hofmeister, N. R. Werner, S. J. Ball, G. F. Bateson, M. Brandley, M. C. Buchanan, K. L. Cassey, P. Clayton, D. F. De Meyer, T. Meddle, S. L. Rollins, L. A. 2021-04-08 doi:10.1101/2021.04.07.438753 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Rapid appetitive transitions are sculpted by amygdala to accumbens pathways ]]> https://biorxiv.org/content/10.1101/2021.04.11.435530v1?rss=1 Millan, E. Z. Lim, J. H. Power, J. McNally, G. 2021-04-11 doi:10.1101/2021.04.11.435530 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Novel amiloride derivatives that inhibit bacterial motility across multiple strains and stator types ]]> https://biorxiv.org/content/10.1101/2021.04.13.439105v1?rss=1 Islam, M. I. Bae, J. Ishida, T. Ridone, P. Lin, J. Kelso, M. J. Sowa, Y. Buckley, B. J. Baker, M. A. 2021-04-13 doi:10.1101/2021.04.13.439105 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ Opposing roles of the dorsolateral and dorsomedial striatum in the acquisition of skilled action sequencing ]]> https://biorxiv.org/content/10.1101/2021.04.15.439935v1?rss=1 Turner, K. M. Svegborn, A. Langguth, M. McKenzie, C. Robbins, T. 2021-04-15 doi:10.1101/2021.04.15.439935 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Translational Proteomics for Transfusion Medicine: Resolution of the IVIG Proteomes of Different Geographically Sourced and Prepared IVIG Immunotherapies. ]]> https://biorxiv.org/content/10.1101/2021.04.21.440739v1?rss=1 98% and the overseas-derived preparations at [≥] 95%. Because of these differences it was predicted that the formulations might individually vary in composition and that together with obvious genetic and geographic antigenic (Ag) environment differences may result in notable variability between formulations. Hence a focussed comparative proteomic profiling of IVIG formulations was undertaken to identify notable similarities and differences across products. Comparisons between formulations did reveal marked qualitative differences in 2D-gel Antibody profiling that included parameters of isoelectric charge (pI), as well as immunoglobulin (Ig) monomer to dimer ratio variability between products, including high molecular weight (MW) immunoglobulin multimers for some. These notable differences were in part quite likely a product of the respective purification methods used, and capacity to select (or de-select) for antibodies of such different properties. Furthermore, for identification of non-Ig proteins carried over from plasma through purifications Mass spectrometry was performed. This identified a few such ancillary proteins, and their identities, in general, differed between formulations. Proteins detected included the most abundant protein of plasma, albumin, as well as other mostly large and abundant proteins; RAG1 - V(D)J recombination activating protein1, gelsolin, complement Factor-B, serotransferrin, tetranectin, NADH ubiquinone oxidoreductase, caspase 3 and VEGFR1. An alternate strategy used commercial Multiplex xMAP assay to detect cytokines, which are small and present in plasma at trace but highly active quantities. This revealed various different cytokine profiles across the formulations studied. The identification of additional proteins, and especially cytokines in IVIGs, is particularly notable, and the positive, negative or null biological relevance for clinical use, needs resolution. Collectively these findings reveal marked differences between Australian and overseas-derived (non-Australian) IVIGs in immunoglobulin composition and biochemical characteristics, and presence of additional carry-over proteins from plasma. These findings prompt the need for further evaluation of the micro-compositions of individual formulations. Perhaps detailed mining and improved comparative understanding of each IVIG formulation, may enable highly tailored and strategic clinical use of certain formulations that are personalised best-fit treatments for particular conditions. Such as in treatment of a neuropathy, as compared to another formulation, more suited for treating a particular infectious disease. The most salient and overarching study conclusion is need for caution in attributing equivalence across IVIGs. ]]> Lynch, G. W. Fitzgerald, A. M. Walsh, B. J. Kapitza, N. Sullivan, J. S. 2021-04-21 doi:10.1101/2021.04.21.440739 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Punishment insensitivity in humans is due to failures in instrumental contingency learning ]]> https://biorxiv.org/content/10.1101/2021.04.23.441174v1?rss=1 Jean-Richard-dit-Bressel, P. Lee, J. C. Liew, S. X. Weidemann, G. Lovibond, P. F. McNally, G. P. 2021-04-27 doi:10.1101/2021.04.23.441174 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Phenotypic diversity and sensitivity to injury of the pulmonary endothelium during a period of rapid postnatal growth ]]> https://biorxiv.org/content/10.1101/2021.04.27.441649v1?rss=1 Zanini, F. Che, X. Knutsen, C. Liu, M. Suresh, N. Domingo-Gonzalez, R. Dou, S. H. Jones, R. C. Cornfield, D. N. Quake, S. R. Alvira, C. M. 2021-04-28 doi:10.1101/2021.04.27.441649 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Bromelain and Acetylcysteine (BromAc) alone and in combination with Gemcitabine inhibits subcutaneous deposits of pancreatic cancer after intraperitoneal injection ]]> https://biorxiv.org/content/10.1101/2021.05.05.442745v1?rss=1 Mekkawy, A. H. Pillai, K. Badar, S. Akhter, J. Kepenekian, V. Ke, K. Valle, S. Morris, D. L. 2021-05-05 doi:10.1101/2021.05.05.442745 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ T Cell Receptor Beta (TRB) Germline Variability is Revealed by Inference From Repertoire Data ]]> https://biorxiv.org/content/10.1101/2021.05.17.444409v1?rss=1 Omer, A. Peres, A. Rodrigues, O. L. Watson, C. T. Lees, W. Polak, P. Collins, A. M. Yaari, G. 2021-05-17 doi:10.1101/2021.05.17.444409 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Progressive Increases in Mesenchymal Cell Diversity Modulate Lung Development and are Attenuated by Hyperoxia ]]> https://biorxiv.org/content/10.1101/2021.05.19.444776v1?rss=1 Zanini, F. Che, X. Suresh, N. Knutsen, C. Klavina, P. Xie, Y. Domingo-Gonzales, R. Jones, R. C. Quake, S. R. Alvira, C. M. Cornfield, D. N. 2021-05-20 doi:10.1101/2021.05.19.444776 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. ]]> https://biorxiv.org/content/10.1101/2021.05.23.445341v1?rss=1 AAC, CC>TT, TG>CA, and AT>TA have come up in our analysis which are in the top 20 mutational cohort. Future mutation rate analysis predicts a 17%, 7%, and 3% increment of C>T, A>G, and A>T, respectively in the future. Conversely, 7%, 7%, and 6% decrement is estimated for T>C, G>A, and G>T mutations, respectively. T>GA, C>GA, and A>TC are not anticipated in the future. Since SARS-CoV-2 is evolving continuously, our findings will facilitate the tracking of mutations and help to map the progression of the COVID-19 intensity worldwide. ]]> Hossain, M. S. Pathan, A. Q. M. S. U. Islam, M. N. Tonmoy, M. I. Q. Rakib, M. I. Munim, M. A. Saha, O. Fariha, A. Al Reza, H. Roy, M. Bahadur, N. M. Rahaman, M. M. 2021-05-24 doi:10.1101/2021.05.23.445341 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ Single-cell transcriptome profiling reveals multicellular ecosystem of nucleus pulposus during degeneration progression ]]> https://biorxiv.org/content/10.1101/2021.05.25.445620v1?rss=1 Tu, J. Li, W. Yang, S. Yang, P. Yan, Q. Wang, S. Lai, K. Bai, X. Wu, C. Ding, W. Cooper-White, J. Diwan, A. Yang, C. Yang, H. Zou, J. 2021-05-26 doi:10.1101/2021.05.25.445620 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Neural coding of visual objects rapidly reconfigures to reflect sub-trial shifts in attentional focus ]]> https://biorxiv.org/content/10.1101/2021.05.25.445712v1?rss=1 Barnes, L. Goddard, E. Woolgar, A. 2021-05-26 doi:10.1101/2021.05.25.445712 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Sex-specific transcriptome of spinal microglia in neuropathic pain due to peripheral nerve injury ]]> https://biorxiv.org/content/10.1101/2021.05.27.446082v1?rss=1 Fiore, N. T. Yin, Z. Guneykaya, D. Gauthier, C. D. Hayes, J. DHary, A. Butovsky, O. Moalem-Taylor, G. 2021-05-29 doi:10.1101/2021.05.27.446082 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C ]]> https://biorxiv.org/content/10.1101/2021.06.02.444084v1?rss=1 Chen, S. H. Rossetto, M. van der Merwe, M. Lu-Irving, P. Yap, J.-Y. S. Sauquet, H. Bourke, G. Bragg, J. G. Edwards, R. J. 2021-06-02 doi:10.1101/2021.06.02.444084 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Multi-omics profiling of Earth's biomes reveals that microbial and metabolite composition are shaped by the environment ]]> https://biorxiv.org/content/10.1101/2021.06.04.446988v1?rss=1 Shaffer, J. P. Nothias, L.-F. Thompson, L. R. Jon, S. G. Salido, R. A. Couvillion, S. P. Brejnrod, A. D. Huang, S. Lejzerowicz, F. Lutz, H. L. Zhu, Q. Martino, C. Morton, J. T. Karthikeyan, S. Nothias-Esposito, M. Dührkop, K. Böcker, S. Kim, H. Aksenov, A. A. Bittremieux, W. Minich, J. J. Marotz, C. Bryant, M. M. Sanders, K. Schwartz, T. Humphrey, G. Vasquez-Baeza, Y. Tripathi, A. Parida, L. Carrieri, A. P. Haiminen, N. Beck, K. L. Das, P. Gonzalez, A. McDonald, D. Karst, S. M. Albertsen, M. Ackermann, G. DeReus, J. Thomas, T. Petras, D. Shade, A. St 2021-06-06 doi:10.1101/2021.06.04.446988 Cold Spring Harbor Laboratory Press 2021-06-06 <![CDATA[ School yard biodiversity determines short-term recovery of disturbed skin microbiota in children ]]> https://biorxiv.org/content/10.1101/2021.06.18.448749v1?rss=1 Mills, J. G. Selway, C. A. Thomas, T. Weyrich, L. S. Lowe, A. J. 2021-06-18 doi:10.1101/2021.06.18.448749 Cold Spring Harbor Laboratory Press 2021-06-18 <![CDATA[ Assessing neuromodulation effects of theta burst stimulation to the prefrontal cortex using TMS-evoked potentials ]]> https://biorxiv.org/content/10.1101/2021.06.21.449219v1?rss=1 .05). The largest effect size (Cohens d = -0.5) comparing iTBS and sham was obtained for the N100 component at 15 minutes post-stimulation. This result was in the same direction but smaller than found in previous studies, suggesting that the true effect size may be lower than previously reported. Accurate estimates of the effects sizes and inter-individual heterogeneity will critically inform clinical applications using TEPs to assess the neuromodulatory effects of TBS. ]]> Moffa, A. H. d. M. Nikolin, S. Martin, D. Loo, C. Boonstra, T. W. 2021-06-22 doi:10.1101/2021.06.21.449219 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Horizontal transfer and southern migration: the tale of Hydrophiinae's marine journey. ]]> https://biorxiv.org/content/10.1101/2021.06.22.449521v1?rss=1 Galbraith, J. D. Ludington, A. J. Edwards, R. J. Sanders, K. L. Suh, A. Adelson, D. L. 2021-06-23 doi:10.1101/2021.06.22.449521 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis ]]> https://biorxiv.org/content/10.1101/2021.06.29.450255v1?rss=1 Gamaarachchi, H. Samarakoon, H. Jenner, S. P. Ferguson, J. M. Amos, T. G. Hammond, J. M. Saadat, H. Smith, M. A. Parameswaran, S. Deveson, I. W. 2021-06-30 doi:10.1101/2021.06.29.450255 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ The blood vasculature instructs lymphatics patterning in a SOX7-dependent manner ]]> https://biorxiv.org/content/10.1101/2021.07.02.450967v1?rss=1 Chiang, I. K. N. Luu, W. Jiang, K. Kirschnick, N. Moustaqil, M. Davidson, T. L. Lesieur, E. Skoczylas, R. Kouskoff, V. Kazenwadel, J. Arriola-Martinez, L. Sierecki, E. Gambin, Y. Alitalo, K. Kiefer, F. Harvey, N. L. Francois, M. 2021-07-03 doi:10.1101/2021.07.02.450967 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ Genetic similarity enhances the strength of the relationship between gut bacteria and host DNA methylation ]]> https://biorxiv.org/content/10.1101/2021.07.10.451923v1?rss=1 Zhou, J. Tesfamicael, K. Zhou, S. J. Rollins, L. A. Rodriguez Lopez, C. M. 2021-07-11 doi:10.1101/2021.07.10.451923 Cold Spring Harbor Laboratory Press 2021-07-11 <![CDATA[ Untangling the ecological signal in the dental morphology in the bat superfamily Noctilionoidea ]]> https://biorxiv.org/content/10.1101/2021.07.21.453269v1?rss=1 Lopez-Aguirre, C. Hand, S. Simmons, N. B. Silcox, M. 2021-07-23 doi:10.1101/2021.07.21.453269 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Differential mitochondrial protein interaction profile between human translocator protein and its A147T polymorphism variant ]]> https://biorxiv.org/content/10.1101/2021.07.23.453531v1?rss=1 Asih, P. R. Plojak, A. Kassiou, M. Ke, Y. Ittner, L. M. 2021-07-23 doi:10.1101/2021.07.23.453531 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ A distinct CD115- erythro-myeloid precursor present at the maternal-embryonic interface and in the bone marrow of adult mice ]]> https://biorxiv.org/content/10.1101/2021.07.24.453629v1?rss=1 Tikoo, S. Jain, R. Martinez, B. Song, R. Wielscher, M. Rizzetto, S. Shaw, L. E. Mitchell, A. J. Torres-Pacheco, M. E. Luciani, F. Farlik, M. Wong, J. Jung, S. Fraser, S. T. Weninger, W. 2021-07-25 doi:10.1101/2021.07.24.453629 Cold Spring Harbor Laboratory Press 2021-07-25 <![CDATA[ Age- and sex-related topological organisation of human brain functional networks and their relationship to cognition ]]> https://biorxiv.org/content/10.1101/2021.07.25.453293v1?rss=1 Foo, H. Thalamuthu, A. Jiang, J. Koch, F. C. Mather, K. Wen, W. Sachdev, P. 2021-07-26 doi:10.1101/2021.07.25.453293 Cold Spring Harbor Laboratory Press 2021-07-26 <![CDATA[ Unravelling the effects of disease-associated mutations in TDP-43 protein via molecular dynamics simulation and machine learning ]]> https://biorxiv.org/content/10.1101/2021.07.28.454112v1?rss=1 Sharma, A. Dey, P. 2021-07-28 doi:10.1101/2021.07.28.454112 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ Cortical actin flow activates an alpha-catenin clutch to assemble adherens junctions ]]> https://biorxiv.org/content/10.1101/2021.07.28.454239v1?rss=1 Noordstra, I. Diez Hermoso, M. Schimmel, L. Bonfim-Melo, A. Kalappurakkal, J. M. Mayor, S. Gordon, E. Roca-Cusachs, P. Yap, A. S. 2021-07-28 doi:10.1101/2021.07.28.454239 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ Mesoderm-Derived PDGFRA+ Cells Regulate the Emergence of Hematopoietic Stem Cells in the Dorsal Aorta ]]> https://biorxiv.org/content/10.1101/2021.08.08.455592v1?rss=1 Chandrakanthan, V. Rorimpandey, P. Zanini, F. Chacon, D. Kang, Y. C. Knezevic, K. Huang, Y. Qiao, Q. Oliver, R. A. Unnikrishnan, A. Carter, D. R. Lee, B. Brownlee, C. Power, C. Mendez-Ferrer, S. Enikolopov, G. Walsh, W. Gottgens, B. Taoudi, S. Beck, D. Pimanda, J. 2021-08-09 doi:10.1101/2021.08.08.455592 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Single molecule fingerprinting reveals different amplification properties of α-synuclein oligomers and preformed fibrils in seeding assay. ]]> https://biorxiv.org/content/10.1101/2021.08.09.455607v1?rss=1 Lau, D. Magnan, C. Hill, K. Cooper, A. Gambin, Y. Sierecki, E. 2021-08-09 doi:10.1101/2021.08.09.455607 Cold Spring Harbor Laboratory Press 2021-08-09 <![CDATA[ Micromechanical Characterisation of 3D Bioprinted neural cell models using Brillouin Microscopy ]]> https://biorxiv.org/content/10.1101/2021.08.17.456575v1?rss=1 Rad, M. A. Mahmodi, H. Filipe, E. C. Cox, T. R. Kabakova, I. Tipper, J. L. 2021-08-18 doi:10.1101/2021.08.17.456575 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Ecological conditions experienced by bat reservoir hosts predict the intensity of Hendra virus excretion over space and time ]]> https://biorxiv.org/content/10.1101/2021.08.19.457011v1?rss=1 Becker, D. Eby, P. Madden, W. Peel, A. Plowright, R. 2021-08-19 doi:10.1101/2021.08.19.457011 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Using historical museum samples to examine divergent and parallel evolution in the invasive starling ]]> https://biorxiv.org/content/10.1101/2021.08.22.457241v1?rss=1 Stuart, K. C. Sherwin, W. B. Austin, J. J. Bateson, M. Eens, M. Brandley, M. C. Rollins, L. A. 2021-08-23 doi:10.1101/2021.08.22.457241 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ mRNA Vaccination Induces Durable Immune Memory to SARS-CoV-2 with Continued Evolution to Variants of Concern ]]> https://biorxiv.org/content/10.1101/2021.08.23.457229v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@16c64b1org.highwire.dtl.DTLVardef@146ca3aorg.highwire.dtl.DTLVardef@86b7edorg.highwire.dtl.DTLVardef@956879_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Goel, R. R. Painter, M. M. Apostolidis, S. A. Mathew, D. Meng, W. Rosenfeld, A. M. Lundgreen, K. A. Reynaldi, A. Khoury, D. S. Pattekar, A. Gouma, S. Kuri-Cervantes, L. Hicks, P. Dysinger, S. Hicks, A. Sharma, H. Herring, S. Korte, S. Baxter, A. E. Oldridge, D. A. Giles, J. R. Weirick, M. E. McAllister, C. M. Awofolaju, M. Tanenbaum, N. Drapeau, E. M. Dougherty, J. Long, S. D'Andrea, K. Hamilton, J. T. McLaughlin, M. Williams, J. C. Adamski, S. The UPenn COVID Processing Unit, Kuthuru, O. Frank, I. Betts, M. R. Vella, L. A. Grifoni, A. Weiskopf, D. Set 2021-08-23 doi:10.1101/2021.08.23.457229 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Isolation and Genomics of multidrug-resistant Brevundimonas diminuta collected from patients with pertussis-like symptoms ]]> https://biorxiv.org/content/10.1101/2021.08.23.457371v1?rss=1 Safarchi, A. Nikbin, V. S. Nakhost Lotfi, M. Saedi, S. Sedaghatpour, M. Lamichhane, B. Dinarvand, M. Tay, C. Y. Shahcheraghi, F. 2021-08-24 doi:10.1101/2021.08.23.457371 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Discovery of Antiviral Cyclic Peptides Targeting the Main Protease of SARS-CoV-2 via mRNA Display ]]> https://biorxiv.org/content/10.1101/2021.08.23.457419v1?rss=1 Johansen-Leete, J. Ullrich, S. Fry, S. Frkic, R. Bedding, M. Aggarwal, A. Ashhurst, A. Ekanayake, K. Mahawaththa, M. Sasi, V. Passioura, T. Larance, M. Otting, G. Turville, S. G. Jackson, C. J. Nitsche, C. Payne, R. J. 2021-08-24 doi:10.1101/2021.08.23.457419 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Enterohaemorrhagic E. coli utilizes an AND-OR logic gate to regulate expression of an outer membrane haem receptor ]]> https://biorxiv.org/content/10.1101/2021.08.24.457593v1?rss=1 Sy, B. M. Tree, J. J. 2021-08-25 doi:10.1101/2021.08.24.457593 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ High temporal resolution RNA-seq time course data reveals mammalian lncRNA activationmirrors neighbouring protein-coding genes ]]> https://biorxiv.org/content/10.1101/2021.08.25.457323v1?rss=1 Muskovic, W. Slavich, E. Maslen, B. Kaczorowski, D. Cursons, J. Crampin, E. Kavallaris, M. 2021-08-26 doi:10.1101/2021.08.25.457323 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ The eyes have it: The pupillary light response as a physiological index of aphantasia, sensory and phenomenological imagery strength ]]> https://biorxiv.org/content/10.1101/2021.09.02.457617v1?rss=1 Kay, L. Keogh, R. Andrillon, T. Pearson, J. 2021-09-03 doi:10.1101/2021.09.02.457617 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Initial contact shapes the perception of friction ]]> https://biorxiv.org/content/10.1101/2021.09.20.461039v1?rss=1 Willemet, L. Kanzari, K. Monnoyer, J. Birznieks, I. Wiertlewski, M. 2021-09-22 doi:10.1101/2021.09.20.461039 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ A Comparison of Methods to Harmonize Cortical Thickness Measurements Across Scanners and Sites ]]> https://biorxiv.org/content/10.1101/2021.09.22.461242v1?rss=1 Sun, D. Rakesh, G. Clarke-Rubright, E. K. Haswell, C. C. Logue, M. O'Leary, B. M. Cotton, A. S. Xie, H. Dennis, E. L. Jahanshad, N. Salminen, L. E. Thomopolous, S. I. Rashid, F. Ching, C. R. K. Koch, S. B. J. Frijling, J. L. Nawijn, L. van Zuiden, M. Zhu, X. Suarez-Jimenez, B. Sierk, A. Walter, H. Manthey, A. Stevens, J. S. Fani, N. van Rooij, S. J. H. Stein, M. Bomyea, J. Koerte, I. K. Choi, K. van der Werff, S. J. A. Vermeiren, R. R. J. M. Herzog, J. Lebois, L. A. M. Baker, J. T. Ressler, K. J. Olson, E. A. Straube, T. Korgaonkar, M. S. Andrew, E. Zhu, 2021-09-24 doi:10.1101/2021.09.22.461242 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Brain transcriptome analysis reveals gene expression differences associated with dispersal behaviour between range-front and range-core populations of invasive cane toads in Australia ]]> https://biorxiv.org/content/10.1101/2021.09.27.462079v1?rss=1 Yagound, B. West, A. J. Richardson, M. F. Selechnik, D. Shine, R. Rollins, L. A. 2021-09-28 doi:10.1101/2021.09.27.462079 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ LOTVS: a global collection of permanent vegetation plots ]]> https://biorxiv.org/content/10.1101/2021.09.29.462383v1?rss=1 Sperandii, M. G. de Bello, F. Valencia, E. Goetzenberger, L. Bazzichetto, M. Galland, T. E-Vojtko, A. Conti, L. Adler, P. Buckley, H. Danihelka, J. Day, N. J. Dengler, J. Eldridge, D. J. Estiarte, M. Garcia-Gonzalez, R. Garnier, E. Gomez-Garcia, D. Hallett, L. Harrison, S. P. Herben, T. Ibanez, R. Jentsch, A. Juergens, N. Kertesz, M. Kimuyu, D. M. Klumpp, K. Le Duc, M. Louault, F. Marrs, R. H. Onodi, G. Pakeman, R. J. Paertel, M. Peco, B. Penuelas, J. Rueda, M. Schmidt, W. Schmiedel, U. Schuetz, M. Skalova, H. Smilauer, P. Smilauerova, M. Smit, C. Son 2021-10-01 doi:10.1101/2021.09.29.462383 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ A standardized method to purify cardiomyocytes from individual mouse hearts of any age ]]> https://biorxiv.org/content/10.1101/2021.09.30.462562v1?rss=1 Nicks, A. M. Holman, S. R. Chan, A. Y. Tsang, M. Young, P. E. Humphreys, D. T. Naqvi, N. Husain, A. Li, M. Smith, N. J. Iismaa, S. E. Graham, R. M. 2021-09-30 doi:10.1101/2021.09.30.462562 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Climate shapes flowering periods across plant communities ]]> https://biorxiv.org/content/10.1101/2021.10.10.463841v1?rss=1 Stephens, R. E. Sauquet, H. Guerin, G. R. Jiang, M. Falster, D. S. Gallagher, R. V. 2021-10-12 doi:10.1101/2021.10.10.463841 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ Self-renewing tissue-resident endothelial-macrophage progenitor cells originate from yolk sac and are a local source of inflammation and neovascularization in postnatal aorta ]]> https://biorxiv.org/content/10.1101/2021.10.18.464001v1?rss=1 Williamson, A. Toledo-Flores, D. Liyanage, S. Hassanshahi, M. Dimasi, C. Schwarz, N. Fernando, S. Salagaras, T. Long, A. Di Bartolo, B. A. Kazenwadel, J. Harvey, N. L. Drummond, G. R. Vinh, A. Chandrakanthan, V. Misra, A. Tan, J. T. M. Bonder, C. S. Nicholls, S. J. Bursill, C. A. Psaltis, P. J. 2021-10-18 doi:10.1101/2021.10.18.464001 Cold Spring Harbor Laboratory Press 2021-10-18 <![CDATA[ In an arms race between host and parasite, a lungworm's ability to infect a toad is determined by host susceptibility, not parasite preference ]]> https://biorxiv.org/content/10.1101/2021.10.19.464902v1?rss=1 Eyck, H. J. F. Brown, G. P. Rollins, L. A. Shine, R. 2021-10-19 doi:10.1101/2021.10.19.464902 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Single-molecule analysis of the entire perfringolysin O poreformation pathway ]]> https://biorxiv.org/content/10.1101/2021.10.19.464937v1?rss=1 Mc Guinness, C. Walsh, J. Bayly-Jones, C. Dunstone, M. Morton, C. Christie, M. Parker, M. W. Boecking, T. 2021-10-19 doi:10.1101/2021.10.19.464937 Cold Spring Harbor Laboratory Press 2021-10-19 <![CDATA[ Microtubule dynamics and the evolution of mitochondrial populations in fission yeast cells: A kinetic Monte Carlo study ]]> https://biorxiv.org/content/10.1101/2021.10.20.465075v1?rss=1 15 minutes). Our study illustrates the critical role of microtubules in mitochondrial dynamics and that coupling their growth and shrinkage dynamics is critical to predicting the evolution of mitochondrial populations within the cell. Author summaryMitochondria are semi-autonomous organelles that undergo fission and fusion to facilitate quality control and exchange of mitochondrial mass within the cell. Impaired mitochondrial fusion and fission dynamics are associated with disease states such as cancer and neurodegeneration. Recent experiments in fission yeast cells revealed a reduction in mitochondrial fission events when mitochondria were bound to the microtubules and longer microtubules shifted the mitochondrial population to longer lengths. In a distinct departure from earlier reports [2-16], we develop a generic framework to study the evolution of the mitochondrial population in fission yeast cells to predict the observed mitochondrial population by coupling the microtubule and mitochondrial dynamics. Using kinetic Monte Carlo (KMC) simulations we predict the temporal evolution of mitochondria in both the mutated and wild-type states of microtubules in fission yeast cells. The mitochondrial population evolves due to multiple fission and fusion reactions occurring between mitochondrial species of various lengths. Several models with varying complexity have been developed to study mitochondrial evolution, and predictions of the mitochondrial populations agree well with experimental data on fission yeast cells without microtubules and cells with short, wild-type and long microtubules. These set of microtubule states are consistent with not only the microtubule dynamics typically observed in cells under different physiological stimuli such as mitosis and disease states but also the stable microtubule states obtained through post-translational modification of and {beta} tubulin subunits of microtubules. Our study reveals that the temporal evolution of mitochondrial populations is an intrinsic function of the state of microtubules which modulates the fission and fusion frequencies to maintain mitochondrial homeostasis within cells. ]]> Choudhury, S. Ananthanarayanan, V. Ayappa, K. G. 2021-10-20 doi:10.1101/2021.10.20.465075 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Disentangling single-cell omics representation with a power spectral density-based feature extraction ]]> https://biorxiv.org/content/10.1101/2021.10.25.465657v1?rss=1 Zandavi, S. M. Koch, F. Vijayan, A. Zanini, F. Mora, F. V. Ortega, D. G. Vafaee, F. 2021-10-26 doi:10.1101/2021.10.25.465657 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Hepatitis C Virus Infects and Perturbs Liver Stem Cells ]]> https://biorxiv.org/content/10.1101/2021.10.26.465357v1?rss=1 Meyers, N. L. Ashuach, T. Lyons, D. E. Simoneau, C. R. Erickson, A. L. Nguyen, T. T. Bouhaddou, M. Khalid, M. M. Taha, T. Y. Natarajan, V. Baron, J. L. Neff, N. Zanini, F. Mahmoudi, T. Quake, S. R. Krogan, N. J. Cooper, S. L. McDevitt, T. C. Yosef, N. Ott, M. 2021-10-26 doi:10.1101/2021.10.26.465357 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Spatial-temporal analysis of nanoparticles in live tumor spheroids impacted by cell origin and density ]]> https://biorxiv.org/content/10.1101/2021.10.26.465839v1?rss=1 Ahmed-Cox, A. Pandzic, E. Johnston, S. T. Heu, C. McGhee, J. B. Mansfeld, F. M. Crampin, E. J. Davis, T. P. Whan, R. M. Kavallaris, M. 2021-10-28 doi:10.1101/2021.10.26.465839 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Efficacy of anti-microbial gel vapours against aerosolised coronavirus, bacteria, and fungi ]]> https://biorxiv.org/content/10.1101/2021.10.27.466182v1?rss=1 Kalaiselvan, P. Yasir, M. Willcox, M. D. P. Vijay, A. K. 2021-10-29 doi:10.1101/2021.10.27.466182 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Defined microenvironments trigger in vitro gastrulation in human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2021.10.28.466327v1?rss=1 Srivastava, P. Romanazzo, S. Ireland, J. Nemec, S. Molley, T. G. Jayathilaka, P. Pandzic, E. Yeola, A. Chandrakanthan, V. Pimanda, J. Kilian, K. 2021-10-28 doi:10.1101/2021.10.28.466327 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Platelet generation from circulating megakaryocytes is triggered in the lung vasculature ]]> https://biorxiv.org/content/10.1101/2021.11.01.466743v1?rss=1 Zhao, X. Alibhai, D. Walsh, T. G. Tarassova, N. Birol, S. Z. Williams, C. M. Neil, C. R. Aitken, E. W. Waller, A. K. Ballester-Beltran, J. Gunning, P. W. Hardeman, E. C. Agbani, E. O. Hers, I. Ghevaert, C. Poole, A. W. 2021-11-03 doi:10.1101/2021.11.01.466743 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Volatility in coral cover erodes niche structure, but not diversity, in reef fish assemblages ]]> https://biorxiv.org/content/10.1101/2021.11.03.467170v1?rss=1 Tsai, C.-H. Sweatman, H. P. Thibaut, L. M. Connolly, S. R. 2021-11-04 doi:10.1101/2021.11.03.467170 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Closely-related tree species with overlapping ranges exhibit divergent adaptation to climate ]]> https://biorxiv.org/content/10.1101/2021.11.08.467758v1?rss=1 Whale, J. W. Ahrens, C. W. Tissue, D. T. Rymer, P. D. 2021-11-10 doi:10.1101/2021.11.08.467758 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ LRRC15 suppresses SARS-CoV-2 infection and controls collagen production ]]> https://biorxiv.org/content/10.1101/2021.11.09.467981v1?rss=1 Loo, L. Waller, M. A. Cole, A. J. Stella, A. O. Moreno, C. L. Denes, C. E. Hamoudi, Z. Chung, F. Aggarwal, A. Low, J. K. K. Patel, K. Siddique, R. Mackay, J. Turville, S. Hesselson, D. Neely, G. G. 2021-11-10 doi:10.1101/2021.11.09.467981 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Pan-tissue and -cancer analysis of ROR1 and ROR2 transcript variants identify novel functional significance for an alternative splice variant of ROR1 ]]> https://biorxiv.org/content/10.1101/2021.11.24.469652v1?rss=1 John, M. Ford, C. 2021-11-25 doi:10.1101/2021.11.24.469652 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Role of anterior insula cortex in context-induced relapse of nicotine-seeking ]]> https://biorxiv.org/content/10.1101/2021.12.08.471717v1?rss=1 Ghareh, H. Alonso-Lozares, I. Schetters, D. Herman, R. J. Heistek, T. S. Van Mourik, Y. Jean-Richard-dit-Bressel, P. Zernig, G. Mansvelder, H. D. De Vries, T. J. Marchant, N. J. 2021-12-09 doi:10.1101/2021.12.08.471717 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Reliability of transcranial magnetic stimulation evoked potentials to detect the effects of theta-burst stimulation of the prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2021.12.11.472198v1?rss=1 0.8) and moderate concordance between sessions (CCCmax{approx}0.7). Both N40 and P60 TEP amplitudes showed little concordance between sessions. Changes in TEP amplitudes after iTBS were marginally reliable for N100 (CCCmax=0.52), P200 (CCCmax=0.47) and P60 (CCCmax=0.40), presenting only fair levels of concordance at specific time points. ConclusionsThe present findings show that only the N100 and P200 components had good concordance between sessions. The reliability of earlier components may have been affected by TMS-evoked artefacts. The poor reliability to detect changes in neural excitability induced by TBS indicates that TEPs do not provide a precise estimate of the changes in excitability in the DLPFC or, alternatively, that TBS did not induce consistent changes in neural excitability. ]]> Moffa, A. H. d. M. Nikolin, S. Martin, D. Loo, C. Boonstra, T. W. 2021-12-13 doi:10.1101/2021.12.11.472198 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Stressed out underground?: Transcriptomics illuminates the genome-wide response to heat stress in surface and subterranean diving beetles ]]> https://biorxiv.org/content/10.1101/2021.12.12.470823v1?rss=1 Beasley-Hall, P. G. Bertozzi, T. Bradford, T. M. Foster, C. S. P. Jones, K. Tierney, S. M. Humphreys, W. F. Austin, A. D. Cooper, S. J. B. 2021-12-13 doi:10.1101/2021.12.12.470823 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Dehalobium species implicated in 2,3,7,8-tetrachloro-p-dioxin dechlorination in the contaminated sediments of Sydney Harbour Estuary ]]> https://biorxiv.org/content/10.1101/2021.12.12.472303v1?rss=1 50% of the toxicity attributed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) the most toxic and concerning of the PCDD/F congeners. Comparison of congener profiles at the contamination source with surrounding bays and historical data provided evidence for the attenuation of 2,3,7,8-TCDD and other congeners at the source. This finding was supported by the detection of di-, mono- and unchlorinated dibenzo-p-dioxin. Microbial community analysis of sediments by 16S amplicon sequencing revealed an abundance of lineages from the class Dehalococcoidia (up to 15% of the community), including the genus Dehalobium (up to 0.5%). Anaerobic seawater enrichment cultures using perchloroethene as a more amenable growth substrate enriched only the Dehalobium population by more than six-fold. The enrichment culture then proved capable of reductively dechlorinating 2,3,7,8-TCDD to 2,3,7-TCDD and octachlorodibenzo-p-dibenzodioxin to hepta and hexa congeners. This work is the first to show microbial reductive dehalogenation of 2,3,7,8-TCDD with a bacterium from outside the Dehalococcoides genus, and one of only a few that demonstrates PCDD/F degradation in a marine environment. ]]> Lee, M. Liang, G. Holland, S. I. O'Farrell, C. Osborne, K. Manefield, M. 2021-12-13 doi:10.1101/2021.12.12.472303 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Mechanisms underlying sequence-dependent DNA hybridisation rates in the absence of secondary structure ]]> https://biorxiv.org/content/10.1101/2021.12.17.473246v1?rss=1 Hertel, S. Spinney, R. Xu, S. Ouldridge, T. E. Morris, R. Lee, L. 2021-12-18 doi:10.1101/2021.12.17.473246 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ Parental provisioning drives brain size in birds ]]> https://biorxiv.org/content/10.1101/2021.12.19.470191v1?rss=1 Griesser, M. Drobniak, S. M. Graber, S. M. van Schaik, C. 2021-12-21 doi:10.1101/2021.12.19.470191 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Microtubule-mitochondrial attachment determines cell division symmetry and polarity in fission yeast ]]> https://biorxiv.org/content/10.1101/2021.12.19.473396v1?rss=1 Chacko, L. A. Ananthanarayanan, V. 2021-12-20 doi:10.1101/2021.12.19.473396 Cold Spring Harbor Laboratory Press 2021-12-20 <![CDATA[ Molecular and morphological analyses support recognition of Prostanthera volucris (Lamiaceae), a new species from the Central Tablelands of New South Wales ]]> https://biorxiv.org/content/10.1101/2021.12.21.473648v1?rss=1 O'Donnell, R. P. Bruhl, J. J. Telford, I. R. H. Wilson, T. C. Zimmer, H. C. Taseski, G. M. Andrew, R. L. 2021-12-22 doi:10.1101/2021.12.21.473648 Cold Spring Harbor Laboratory Press 2021-12-22 <![CDATA[ Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicans ]]> https://biorxiv.org/content/10.1101/2021.12.21.473717v1?rss=1 Ricci, L. Mackie, J. Donachie, G. E. Chapuis, A. Mezerova, K. Lenardon, M. D. Brown, A. J. Duncan, S. H. Walker, A. W. 2021-12-21 doi:10.1101/2021.12.21.473717 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Longitudinal characterisation of phagocytic and neutralisation functions of anti-Spike antibodies in plasma of patients after SARS-CoV-2 infection. ]]> https://biorxiv.org/content/10.1101/2021.12.21.473774v1?rss=1 Adhikari, A. Abayasingam, A. Rodrigo, C. Agapiou, D. Pandzic, E. Brasher, N. A. Fernando, B. S. M. Keoshkerian, E. Li, H. Kim, H. N. Lord, M. Popovic, G. Rawlinson, W. Mina, M. Post, J. J. Hudson, B. Gilroy, N. Bartlett, A. W. Ahlenstiel, G. Grubor-Bauk, B. Dwyer, D. Konecny, P. Lloyd, A. R. Martinello, M. Bull, R. A. Tedla, N. 2021-12-22 doi:10.1101/2021.12.21.473774 Cold Spring Harbor Laboratory Press 2021-12-22 <![CDATA[ Effect of nebulised BromAc(R) on rheology of artificial sputum: relevance to muco-obstructive respiratory diseases including COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.12.28.474344v1?rss=1 Pillai, K. Mekkawy, A. H. Valle, S. Akhter, J. Morris, D. L. 2021-12-28 doi:10.1101/2021.12.28.474344 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ A high-throughput 3D bioprinted cancer cell migration and invasion model with versatile and broad biological applicability ]]> https://biorxiv.org/content/10.1101/2021.12.28.474387v1?rss=1 Jung, M. Skhinas, J. Du, E. Y. Tolentino, M. K. Utama, R. Engel, M. Volkerling, A. Sexton, A. O'Mahony, A. Ribeiro, J. Gooding, J. J. Kavallaris, M. 2021-12-29 doi:10.1101/2021.12.28.474387 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis ]]> https://biorxiv.org/content/10.1101/2022.01.05.475016v1?rss=1 XU, Z. Hu, D. Luu, L. D. W. Octavia, S. Keil, A. D. Sintchenko, V. Tanaka, M. M. Mooi, F. R. Robson, J. Lan, R. 2022-01-05 doi:10.1101/2022.01.05.475016 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Genome characteristic of Bordetella parapertussis isolated from Iran ]]> https://biorxiv.org/content/10.1101/2022.01.05.475152v1?rss=1 Safarchi, A. Saedi, S. Tay, C. Y. Lamichhan, B. Nakhost Lotfi, M. Shahgheraghi, F. 2022-01-06 doi:10.1101/2022.01.05.475152 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ Recognition of HIV-1 capsid licenses innate immune response to viral infection ]]> https://biorxiv.org/content/10.1101/2022.01.10.472699v1?rss=1 yoh, s. M. Mamede, J. Lau, D. Ahn, N. Sanchez, M. T. Temple, J. Tuckwell, A. Fuchs, N. V. Cianci, G. Riva, L. Curry, H. Yin, X. Gambut, S. Simons, L. M. Hultquist, J. F. Koenig, R. Xiong, Y. Garcia-Sastre, A. BÖcking, T. Hope, T. J. Chanda, S. 2022-01-10 doi:10.1101/2022.01.10.472699 Cold Spring Harbor Laboratory Press 2022-01-10 <![CDATA[ Building programmable multicompartment artificial cells incorporating remotely activated protein channels using microfluidics and acoustic levitation ]]> https://biorxiv.org/content/10.1101/2022.01.13.476178v1?rss=1 Li, J. Jamieson, W. D. Dimitriou, P. Xu, W. Rohde, P. Martinac, B. Baker, M. A. Drinkwater, B. Castell, O. Barrow, D. 2022-01-14 doi:10.1101/2022.01.13.476178 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ Rapid exchange of stably bound protein and DNA cargo on a DNA origami receptor ]]> https://biorxiv.org/content/10.1101/2022.01.16.476526v1?rss=1 Brown, J. W. P. Alford, R. G. Walsh, J. C. Spinney, R. E. Xu, S. Y. Hertel, S. Berengut, J. F. Spenkelink, L. M. van Oijen, A. M. Boecking, T. Morris, R. G. Lee, L. K. 2022-01-17 doi:10.1101/2022.01.16.476526 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ XPD protects CTCF-Cohesin binding sites from somatic mutagenesis ]]> https://biorxiv.org/content/10.1101/2022.01.21.477237v1?rss=1 T]N mutations (SBS2) with altered correlation with replication timing. At a locoregional genomic level, mutant XPD BLCA had striking T>G mutation hotspots at CTCF-cohesin binding sites (CBS) with evidence linking XPD to genomic uracil repair. Leveraging differential distribution of somatic mutations, we developed a machine-learning model for predicting pathogenic XPD mutations, which we validated in an independent TCGA cohort with 100% accuracy. Our model enabled the discovery of missed XPD mutation calls and uncovered pathogenic non-hotspot XPD mutations in bladder cancer. Our study reveals how XPD mutations redistribute somatic mutations in cancer genomes and provides a genome sequencing approach to differentiate driver and passenger XPD mutations. ]]> Barbour, J. A. Ou, T. Fang, H. Yue, N. C. Zhu, X. Wong-Brown, M. Yang, H. Wong, Y. T. Wu, S. Wong, J. W. H. 2022-01-21 doi:10.1101/2022.01.21.477237 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ Macrophage activation of cGAS and TRIM5 distinguish pandemic and non-pandemic HIV ]]> https://biorxiv.org/content/10.1101/2022.01.21.477263v1?rss=1 Zuliani-Alvarez, L. Larsen, M. Rasaiyaah, J. Monit, C. Perry, S. O. Sumner, R. McAlpine-Scott, S. Dickson, C. Rifat Faysal, K. M. Hilditch, L. Miles, R. Bibollet-Ruche, F. Hahn, B. H. Bocking, T. Pinotsis, N. James, L. C. Jacques, D. Towers, G. J. 2022-01-22 doi:10.1101/2022.01.21.477263 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ ACCURATE DECODING OF THE SPINAL CORD OUTPUT IN HUMANS WITH IMPLANTED HIGH-DENSITY ELECTRODE ARRAYS ]]> https://biorxiv.org/content/10.1101/2022.01.29.478247v1?rss=1 Muceli, S. Poppendieck, W. Holobar, A. Gandevia, S. Liebetanz, D. Farina, D. 2022-01-30 doi:10.1101/2022.01.29.478247 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ Impact of APOE e3 and e4 genotypes on plasma proteome signatures in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2022.01.29.478291v1?rss=1 Kaur, G. Poljak, A. Masters, C. L. Fowler, C. Sachdev, P. 2022-01-31 doi:10.1101/2022.01.29.478291 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Deep proteome analysis of plasma reveals novel biomarkers of mild cognitive impairment and Alzheimer's disease: A longitudinal study ]]> https://biorxiv.org/content/10.1101/2022.01.30.478370v1?rss=1 Kaur, G. Poljak, A. Sachdev, P. 2022-02-01 doi:10.1101/2022.01.30.478370 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Striatal dopamine encodes the relationship between actions and reward ]]> https://biorxiv.org/content/10.1101/2022.01.31.478585v1?rss=1 Hart, G. Burton, T. J. Balleine, B. 2022-02-01 doi:10.1101/2022.01.31.478585 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Neuronal growth regulator 1 (NEGR1) promotes synaptic targeting of glutamic acid decarboxylase 65 (GAD65) ]]> https://biorxiv.org/content/10.1101/2022.02.08.479601v1?rss=1 Tan, R. P. A. Kozlova, I. Su, F. Sah, S. Keable, R. Hagan, D. W. Bustamante, S. Du, X. Osborne, B. Turner, N. Clemens, K. Begg, D. Phelps, E. A. Yang, H. Leshchyns'ka, I. Sytnyk, V. 2022-02-08 doi:10.1101/2022.02.08.479601 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ Lin28b specifies an innate-like lineage of CD8+ T cells in early life ]]> https://biorxiv.org/content/10.1101/2022.02.14.480406v1?rss=1 Watson, N. Patel, R. Oyesola, O. Laniewski, N. Grenier, J. Wang, J. Tabilas, C. Mon, K. J. Y. Peng, S. Wesnak, S. Nzingha, K. Smith, N. Davenport, M. Wojno, E. T. Scheible, K. Grimson, A. Rudd, B. 2022-02-16 doi:10.1101/2022.02.14.480406 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ High-throughput detection and quantification of phosphatidylcholines and sphingomyelins from single cells by chip-based nanoelectrospray ionisation ]]> https://biorxiv.org/content/10.1101/2022.02.15.479799v1?rss=1 Hancock, S. E. Ding, E. Johansson Beves, E. Mitchell, T. W. Turner, N. 2022-02-16 doi:10.1101/2022.02.15.479799 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Efficient recall of Omicron-reactive B cell memory after a third dose of SARS-CoV-2 mRNA vaccine ]]> https://biorxiv.org/content/10.1101/2022.02.20.481163v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@123d2d9org.highwire.dtl.DTLVardef@e7db82org.highwire.dtl.DTLVardef@1fc73deorg.highwire.dtl.DTLVardef@11b21f9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Goel, R. R. Painter, M. M. Lundgreen, K. A. Apostolidis, S. A. Baxter, A. E. Giles, J. R. Mathew, D. Pattekar, A. Reynaldi, A. Khoury, D. S. Gouma, S. Hicks, P. Dysinger, S. Hicks, A. Sharma, H. Herring, S. Korte, S. KC, W. Oldridge, D. A. Erickson, R. I. Weirick, M. E. McAllister, C. M. Awofolaju, M. Tanenbaum, N. Dougherty, J. Long, S. D'Andrea, K. Hamilton, J. T. McLaughlin, M. Williams, J. C. Adamski, S. Kuthuru, O. Drapeau, E. M. Davenport, M. P. Hensley, S. E. Bates, P. Greenplate, A. R. Wherry, E. J. 2022-02-22 doi:10.1101/2022.02.20.481163 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice ]]> https://biorxiv.org/content/10.1101/2022.02.28.482396v1?rss=1 Jackson, K. J. Kos, J. T. Lees, W. Gibson, W. S. Smith, M. L. Peres, A. Yaari, G. Corcoran, M. Busse, C. E. Ohlin, M. Watson, C. T. Collins, A. M. 2022-03-01 doi:10.1101/2022.02.28.482396 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ dSeqSb: A systems biology approach to decipher dynamics of 1 host-pathogen interactions using temporal dual RNA-seq data ]]> https://biorxiv.org/content/10.1101/2022.02.28.482417v1?rss=1 Dinarvand, M. Koch, F. Mouiee, D. A. Vuong, K. Vijayan, A. Tanzim, A. F. Azad, A. Penesyan, A. Castano-Rodriguez, N. Vafaee, F. 2022-03-01 doi:10.1101/2022.02.28.482417 Cold Spring Harbor Laboratory Press 2022-03-01 <![CDATA[ Global ecological and biogeochemical impacts of pelagic tunicates ]]> https://biorxiv.org/content/10.1101/2022.03.01.482560v1?rss=1 Luo, J. Y. Stock, C. A. Henschke, N. Dunne, J. P. O'Brien, T. D. 2022-03-04 doi:10.1101/2022.03.01.482560 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Blood-based transcriptomic signature panel identification for cancer diagnosis: Benchmarking of feature extraction methods ]]> https://biorxiv.org/content/10.1101/2022.03.13.483368v1?rss=1 Vijayan, A. Fatima, S. Sowmya, A. Vafaee, F. 2022-03-14 doi:10.1101/2022.03.13.483368 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Beyond inappropriate fire regimes: a synthesis of fire-driven declines of threatened mammals in Australia ]]> https://biorxiv.org/content/10.1101/2022.03.15.483873v1?rss=1 Santos, J. L. Hradsky, B. A. Keith, D. A. Rowe, K. Senior, K. L. Sitters, H. Kelly, L. T. 2022-03-18 doi:10.1101/2022.03.15.483873 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Humans trade-off energetic cost with fatigue avoidance while walking ]]> https://biorxiv.org/content/10.1101/2022.03.16.484670v1?rss=1 McDonald, K. A. Cusumano, J. P. Hieronymi, A. Rubenson, J. 2022-03-18 doi:10.1101/2022.03.16.484670 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Environmental and genetic disease modifiers of haploinsuffciency of A20 ]]> https://biorxiv.org/content/10.1101/2022.03.19.485004v1?rss=1 Zammit, N. N. Gray, P. Siggs, O. M. Yap, J. Y. Russell, A. Cultrone, D. Warren, J. Walters, S. N. Brink, R. T. Zahra, D. Burnett, D. L. Gayevskiy, V. Minoche, A. E. Ziegler, J. B. Craig, M. E. Wong, M. Benitez-Aguirre, P. Teo, J. Cowley, M. J. Dinger, M. E. Tangye, S. G. Burk, C. Phan, T. G. Goodnow, C. J. Grey, S. T. 2022-03-20 doi:10.1101/2022.03.19.485004 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ Dissociable Cellular and Genetic Mechanisms of Cortical Thinning at Different Life Stages ]]> https://biorxiv.org/content/10.1101/2022.03.21.484899v1?rss=1 60 years) in the patterns of association between inter-regional profiles of cortical thickness and expression profiles of marker genes for CA1 and S1 pyramidal cells, astrocytes, and microglia. Gene ontology and enrichment analyses indicated that each of the three life-stages was associated with different biological processes and cellular components: synaptic modeling in early life, neurotransmission in mid-life, and neurodegeneration in late-life. These findings provide mechanistic insights into age-related cortical thinning during typical development and aging. ]]> Modabbernia, A. Vidal-Pineiro, D. Agartz, I. Andreassen, O. A. Ayesa-Arriola, R. Bertolino, A. Boomsma, D. I. Bourque, J. Breier, A. Brouwer, R. M. Buitelaar, J. K. Canales-Rodriguez, E. J. Caseras, X. Conrod, P. J. Crespo-Facorro, B. Crivello, F. Crone, E. A. de Zubicaray, G. I. Dickie, E. W. Dima, D. Frenzel, S. Fisher, S. E. Franke, B. Glahn, D. C. Grabe, H.-J. Grotegerd, D. Gruber, O. Guerrero-Pedraza, A. Gur, R. E. Gur, R. C. Hartman, C. A. Hoekstra, P. J. Hulshoff Pol, H. E. Jahanshad, N. Jernigan, T. L. Jiang, J. Kalnin, A. J. Kochan, N. A. Mazoyer, 2022-03-22 doi:10.1101/2022.03.21.484899 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation ]]> https://biorxiv.org/content/10.1101/2022.04.07.487490v1?rss=1 Laine, R. F. Heil, H. S. Coelho, S. Nixon-Abell, J. Jimenez, A. Galgani, T. Stubb, A. Follain, G. Culley, S. Jacquemet, G. Hajj, B. Leterrier, C. Henriques, R. 2022-04-08 doi:10.1101/2022.04.07.487490 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Human genomic DNA is widely interspersed with i-motif structures ]]> https://biorxiv.org/content/10.1101/2022.04.14.488274v1?rss=1 Pena Martinez, C. D. Zeraati, M. Rouet, R. Mazigi, O. Gloss, B. Chan, C.-L. Bryan, T. M. Smith, N. M. Dinger, M. E. Kummerfeld, S. K. Christ, D. 2022-04-14 doi:10.1101/2022.04.14.488274 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ moRphology - dEep Learning Imaging Cells (RELIC) - to Differentiate Between Normal and Pathological Kidney Exfoliated Cells ]]> https://biorxiv.org/content/10.1101/2022.04.19.488847v1?rss=1 Habibalahi, A. Campbell, J. Mahbub, S. Anwer, A. Nguyen, L. Gill, A. Wong, M. chou, A. Pollock, C. Saad, S. Goldys, E. 2022-04-20 doi:10.1101/2022.04.19.488847 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii ]]> https://biorxiv.org/content/10.1101/2022.04.22.489119v1?rss=1 Edwards, R. J. Dong, C. Park, R. F. Tobias, P. A. 2022-04-22 doi:10.1101/2022.04.22.489119 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Characterization of Extensive Diversity In Immunoglobulin Light Chain Variable Germline Genes Across Biomedically Important Mouse Strains ]]> https://biorxiv.org/content/10.1101/2022.05.01.489089v1?rss=1 Kos, J. T. Safonova, Y. Shields, K. M. Silver, C. A. Lees, W. D. Collins, A. M. Watson, C. T. 2022-05-01 doi:10.1101/2022.05.01.489089 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions ]]> https://biorxiv.org/content/10.1101/2022.05.02.490371v1?rss=1 Doane, M. Ostrowski, M. Brown, M. V. Bramucci, A. Bodrossy, L. van de Kamp, J. Bissett, A. Steinberg, P. D. Doblin, M. A. Seymour, J. R. 2022-05-04 doi:10.1101/2022.05.02.490371 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps ]]> https://biorxiv.org/content/10.1101/2022.05.07.490900v1?rss=1 Spitzer, H. Berry, S. Donoghoe, M. Pelkmans, L. Theis, F. J. 2022-05-08 doi:10.1101/2022.05.07.490900 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Quantifying dynamic facial expressions under naturalistic conditions ]]> https://biorxiv.org/content/10.1101/2022.05.08.490793v1?rss=1 Jeganathan, J. Campbell, M. Hyett, M. Parker, G. Breakspear, M. 2022-05-10 doi:10.1101/2022.05.08.490793 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology ]]> https://biorxiv.org/content/10.1101/2022.05.10.491406v1?rss=1 Manubens-Gil, L. Zhou, Z. Chen, H. Ramanathan, A. Liu, X. Liu, Y. Bria, A. Gillette, T. Ruan, Z. Yang, J. Radojevic, M. Zhao, T. Cheng, L. Qu, L. Liu, S. Bouchard, K. E. Gu, L. Cai, W. Ji, S. Roysam, B. Wang, C.-W. Yu, H. Sironi, A. Iascone, D. M. Zhou, J. Bas, E. Conde-Sousa, E. Aguiar, P. Li, X. Li, Y. Nanda, S. Wang, Y. Muresan, L. Fua, P. Ye, B. He, H.-y. Staiger, J. F. Peter, M. Cox, D. N. Simonneau, M. Oberlaender, M. Jefferis, G. Ito, K. Gonzalez-Bellido, P. Kim, J. Rubel, E. Cline, H. T. Zeng, H. Nern, A. Chiang, A.-S. Yao, J. Roskams, 2022-05-11 doi:10.1101/2022.05.10.491406 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Computer-aided diagnosis of reflectance confocal images to differentiate between lentigo maligna (LM) and atypical intraepidermal melanocytic proliferation (AIMP) ]]> https://biorxiv.org/content/10.1101/2022.05.10.491423v1?rss=1 Mandal, A. Priyam, S. Chan, H. H. Gouveia, B. M. Guitera, P. Song, Y. Baker, M. A. Vafaee, F. 2022-05-11 doi:10.1101/2022.05.10.491423 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Genomic epidemiology and multilevel genome typing of Australian Salmonella enterica serovar Enteritidis ]]> https://biorxiv.org/content/10.1101/2022.05.18.492204v1?rss=1 Luo, L. Payne, M. Wang, Q. Kaur, S. Rathnayake, I. U. Graham, R. Gall, M. Draper, J. Martinez, E. Octavia, S. Tanaka, M. M. Jennison, A. V. Sintchenko, V. Lan, R. 2022-05-18 doi:10.1101/2022.05.18.492204 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Insulin sensitivity is preserved in mice made obese by feeding a high starch diet ]]> https://biorxiv.org/content/10.1101/2022.05.25.493410v1?rss=1 Brandon, A. E. Small, L. Nguyen, T.-V. Suryana, E. Gong, H. Yassmin, C. Hancock, S. E. Pulpitel, T. Stonehouse, S. Prescott, L. Kebede, M. A. Yau, B. Quek, L.-E. Kowalski, G. M. Bruce, C. Turner, N. Cooney, G. J. 2022-05-26 doi:10.1101/2022.05.25.493410 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Integrating proteomic data with metabolic modelling provides insight into key pathways of Bordetella pertussis biofilms ]]> https://biorxiv.org/content/10.1101/2022.05.27.493021v1?rss=1 Suyama, H. Luu, L. D. W. Zhong, L. Raftery, M. J. Lan, R. 2022-05-27 doi:10.1101/2022.05.27.493021 Cold Spring Harbor Laboratory Press 2022-05-27 <![CDATA[ MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens ]]> https://biorxiv.org/content/10.1101/2022.06.14.496187v1?rss=1 Kaur, S. Payne, M. Luo, L. Octavia, S. Tanaka, M. Sintchenko, V. Lan, R. 2022-06-16 doi:10.1101/2022.06.14.496187 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Effects of hydrological change in fire-prone wetland vegetation: an empirical simulation ]]> https://biorxiv.org/content/10.1101/2022.06.17.496658v1?rss=1 Mason, T. Popovic, G. McGillycuddy, M. Keith, D. 2022-06-20 doi:10.1101/2022.06.17.496658 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Flexible and efficient handling of nanopore sequencing signal data with slow5tools ]]> https://biorxiv.org/content/10.1101/2022.06.19.496732v1?rss=1 Samarakoon, H. Ferguson, J. M. Jenner, S. P. Amos, T. G. Parameswaran, S. Gamaarachchi, H. Deveson, I. W. 2022-06-20 doi:10.1101/2022.06.19.496732 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Functional traits trade-offs define plant population stability worldwide ]]> https://biorxiv.org/content/10.1101/2022.06.24.497476v1?rss=1 7000 plots from 78 datasets) from a wide range of habitats and combined this with existing trait databases. We tested whether the observed inter-annual variability in species abundance (coefficient of variation) was related to multiple individual traits and multivariate axes of trait variations (PCoA axes). C_LIO_LIWe found that species with greater leaf dry matter content and seed mass were consistently more stable over time (lower variability in species abundance) although other leaf traits played a significant role as well, albeit weaker. Using multivariate axes did not improve predictions by specific traits. C_LIO_LIOur results confirm existing theory, providing compelling empirical evidence on the importance of specific traits, which point at ecological trade-offs in different resource use and dispersal strategies, on the stability of plant populations worldwide. C_LI ]]> Conti, L. Valencia, E. Galland, T. Götzenberger, L. Leps, J. E-Vojtko, A. P. Carmona, C. Majekova, M. Danihelka, J. Dengler, J. Eldridge, D. J. Estiarte, M. Garcia-Gonzalez, R. Garnier, E. Gomez, D. Hadincova, V. Harrison, S. P. Herben, T. Ibanez, R. Jentsch, A. Juergens, N. Kertesz, M. Klumpp, K. Krahulec, F. Louault, F. Marrs, R. H. Onodi, G. Pakeman, R. J. Pärtel, M. Peco, B. Penuelas, J. Rueda, M. Schmidt, W. Schmiedel, U. Schuetz, M. Skalova, H. Smilauer, P. Smilauerova, M. Smit, C. Song, M. Stock, M. Val, J. Vandvik, V. Ward, D. Wesche, K. W 2022-06-27 doi:10.1101/2022.06.24.497476 Cold Spring Harbor Laboratory Press 2022-06-27 <![CDATA[ Spatial and temporal origin of the third SARS-CoV-2 Outbreak in Taiwan ]]> https://biorxiv.org/content/10.1101/2022.07.04.498645v1?rss=1 Tai, J.-H. Low, Y. K. Lin, H.-F. Wang, T.-Y. Lin, Y.-Y. Foster, C. Lai, Y.-Y. Yeh, S.-H. Chen, P.-J. Wang, H.-Y. 2022-07-05 doi:10.1101/2022.07.04.498645 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Contrasting patterns of single nucleotide polymorphisms and structural variations across multiple invasions ]]> https://biorxiv.org/content/10.1101/2022.07.04.498653v1?rss=1 Stuart, K. C. Edwards, R. J. Sherwin, W. B. Rollins, L. A. 2022-07-04 doi:10.1101/2022.07.04.498653 Cold Spring Harbor Laboratory Press 2022-07-04 <![CDATA[ IDENTIFICATION AND QUANTIFICATION OF MATRISOME PROTEINS OF MOUSE KIDNEYS ]]> https://biorxiv.org/content/10.1101/2022.07.06.499068v1?rss=1 Rende, U. Ahn, S. B. Adhikari, S. Guller, A. E. 2022-07-06 doi:10.1101/2022.07.06.499068 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ Omics Imagification: Transforming High-throughput Molecular Representation of a Cell into an Image ]]> https://biorxiv.org/content/10.1101/2022.07.08.499309v1?rss=1 Liu, D. Zandavi, S. M. Chung, V. Anaissi, A. Vafaee, F. 2022-07-10 doi:10.1101/2022.07.08.499309 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ How tactile afferents in the human fingerpad encode tangential torques associated with manipulation: are we better than monkeys? ]]> https://biorxiv.org/content/10.1101/2022.07.11.499647v1?rss=1 Loutit, A. J. Wheat, H. E. Khamis, H. Vickery, R. M. Macefield, V. Birznieks, I. 2022-07-13 doi:10.1101/2022.07.11.499647 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Goal-directed action is transiently impaired in an hAPP-J20 mouse model of Alzheimer's disease, and in aging male mice regardless of genotype ]]> https://biorxiv.org/content/10.1101/2022.07.25.501480v1?rss=1 Devalued). Goal-directed action was impaired (Valued = Devalued) for J20 mice of both sexes, and for 52-week-old male mice regardless of genotype. Following an additional 4 days of lever press training (i.e., 8 days lever pressing in total), outcome devaluation was intact for all mice regardless of age or genotype. Immunohistochemical analysis revealed that increased microglial expression in the dorsal CA1 region of the hippocampus was associated with poorer outcome devaluation performance on initial tests, but not with tests performed after 8 days of lever pressing. Together, these data demonstrate that goal-directed action is transiently impaired in J20 mice of both sexes and in aging male mice regardless of genotype, and that this impairment is related to neuroinflammation in the dorsal CA1 region of the hippocampus. ]]> Dhungana, A. Becchi, S. Leake, J. Morris, G. Avgan, N. Balleine, B. Vissel, B. Bradfield, L. A. 2022-07-25 doi:10.1101/2022.07.25.501480 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Brain structural covariances in the ageing brain in the UK Biobank ]]> https://biorxiv.org/content/10.1101/2022.07.26.501635v1?rss=1 Dong, C. Thalamuthu, A. Jiang, J. Mather, K. A. Sachdev, P. S. Wen, W. 2022-07-28 doi:10.1101/2022.07.26.501635 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Electricity-free nucleic acid extraction method from dried blood spots on filter paper for point-of-care diagnostics ]]> https://biorxiv.org/content/10.1101/2022.07.28.501845v1?rss=1 Malpartida-Cardenas, K. Baum, J. Cunnington, A. Georgiou, P. Rodriguez-Manzano, J. 2022-07-29 doi:10.1101/2022.07.28.501845 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix ]]> https://biorxiv.org/content/10.1101/2022.07.29.502101v1?rss=1 Tobias, P. A. Edwards, R. J. Surana, P. Mangelson, H. Inacio, V. do Ceu Silva, M. Varzea, V. Park, R. F. Batista, D. 2022-08-01 doi:10.1101/2022.07.29.502101 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Measurement error associated with gait cycle selection in treadmill running at various speeds ]]> https://biorxiv.org/content/10.1101/2022.08.11.503696v1?rss=1 Fox, A. S. Bonacci, J. Warmenhoven, J. Keast, M. F. 2022-08-14 doi:10.1101/2022.08.11.503696 Cold Spring Harbor Laboratory Press 2022-08-14 <![CDATA[ Single-step purification of functionalized protein nanostructures using multimodal chromatography ]]> https://biorxiv.org/content/10.1101/2022.08.21.504681v1?rss=1 Winter, D. L. Lebhar, H. McCluskey, J. B. Glover, D. J. 2022-08-21 doi:10.1101/2022.08.21.504681 Cold Spring Harbor Laboratory Press 2022-08-21 <![CDATA[ DeepGenePrior: A deep learning model to prioritize genes affected by copy number variants ]]> https://biorxiv.org/content/10.1101/2022.08.22.504862v1?rss=1 Rahaie, Z. Rabiee, H. R. Alinejad-Rokny, H. 2022-08-23 doi:10.1101/2022.08.22.504862 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Data augmentation for imbalanced blood cell image classification ]]> https://biorxiv.org/content/10.1101/2022.08.30.505762v1?rss=1 Rana, P. Sowmya, A. Meijering, E. Song, Y. 2022-09-02 doi:10.1101/2022.08.30.505762 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ ZEB2 regulates the development of CD11c+ atypical B cells ]]> https://biorxiv.org/content/10.1101/2022.09.01.506173v1?rss=1 Gao, X. Shen, Q. Roco, J. A. Frith, K. Munier, C. M. L. Nekrasov, M. Dalton, B. He, J.-S. Jaeger, R. Cook, M. C. Zaunders, J. J. Cockburn, I. A. 2022-09-02 doi:10.1101/2022.09.01.506173 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Gas modulating microcapsules for spatiotemporal control of hypoxia ]]> https://biorxiv.org/content/10.1101/2022.09.02.506302v1?rss=1 molley, t. G. Jiang, S. Kopecky, C. Ranaweera, C. D. Jalandhra, G. K. Rnjak-Kovacina, J. Kilian, K. A. 2022-09-04 doi:10.1101/2022.09.02.506302 Cold Spring Harbor Laboratory Press 2022-09-04 <![CDATA[ Oocyte and cumulus cell cooperativity and metabolic plasticity under the direction of oocyte paracrine factors ]]> https://biorxiv.org/content/10.1101/2022.09.05.506599v1?rss=1 Richani, D. Poljak, A. Wang, B. Mahbub, S. B. Biazik, J. Campbell, J. M. Habibalahi, A. Stocker, W. A. Marinova, M. B. Nixon, B. Bustamante, S. Skerrett-Byrne, D. A. Harrison, C. A. Goldys, E. Gilchrist, R. B. 2022-09-05 doi:10.1101/2022.09.05.506599 Cold Spring Harbor Laboratory Press 2022-09-05 <![CDATA[ Automated identification of aneuploid cells within the inner cell mass of an embryo using a numerical extraction of morphological signatures ]]> https://biorxiv.org/content/10.1101/2022.09.06.506861v1?rss=1 Habibalahi, A. Campbell, J. M. Tan, T. Mahbub, S. B. Rose, R. Mustafa, S. Dunning, K. Goldys, E. 2022-09-07 doi:10.1101/2022.09.06.506861 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ Imbalanced classification for protein subcellularlocalisation with multilabel oversampling ]]> https://biorxiv.org/content/10.1101/2022.09.12.507675v1?rss=1 Rana, P. Sowmya, A. Meijering, E. Song, Y. 2022-09-15 doi:10.1101/2022.09.12.507675 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ External validation and further exploration of fall prediction models based on questionnaires and daily-life trunk accelerometry ]]> https://biorxiv.org/content/10.1101/2022.09.26.509506v1?rss=1 Zhang, Y. Weijer, R. Schooten, K. v. Bruijn, S. M. Pijnappels, M. 2022-09-27 doi:10.1101/2022.09.26.509506 Cold Spring Harbor Laboratory Press 2022-09-27 <![CDATA[ Orbitofrontal Cortex is necessary for the behavioural expression, but not learning, of Pavlovian conditioned inhibition ]]> https://biorxiv.org/content/10.1101/2022.09.29.510151v1?rss=1 Panayi, M. C. Killcross, S. C. 2022-10-02 doi:10.1101/2022.09.29.510151 Cold Spring Harbor Laboratory Press 2022-10-02 <![CDATA[ Copper chelation inhibits TGF-β pathways and suppresses epithelial-mesenchymal transition in cancer ]]> https://biorxiv.org/content/10.1101/2022.10.03.510707v1?rss=1 Poursani, E. M. Mercatelli, D. Raninga, P. Bell, J. L. Saletta, F. Kohane, F. V. Zheng, Y. Rouaen, J. Jue, T. R. Michniewicz, F. T. Kasiou, E. Tsoli, M. Cirillo, G. Waters, S. Shai-Hee, T. Valli, E. Brettle, M. Whan, R. Vahdat, L. Ziegler, D. Lock, J. G. Giorgi, F. M. Khanna, K. k. VITTORIO, O. 2022-10-06 doi:10.1101/2022.10.03.510707 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ canaper: Categorical analysis of neo- and paleo-endemism in R ]]> https://biorxiv.org/content/10.1101/2022.10.06.511072v1?rss=1 Nitta, J. Laffan, S. W. Mishler, B. D. Iwasaki, W. 2022-10-07 doi:10.1101/2022.10.06.511072 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ A 3D bioprintable hydrogel with tuneable stiffness for exploring cells encapsulated in matrices of differing stiffnesses ]]> https://biorxiv.org/content/10.1101/2022.10.06.511222v1?rss=1 Du, E. Y. Jung, M. Skhinas, J. Tolentino, M. K. Jamshidi, N. Houng, J. Tjandra, K. C. Engel, M. Utama, R. Tilley, R. Kavallaris, M. Gooding, J. J. 2022-10-07 doi:10.1101/2022.10.06.511222 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Single-cell DNA methylation sequencing by combinatorial indexing and enzymatic DNA methylation conversion. ]]> https://biorxiv.org/content/10.1101/2022.10.09.511389v1?rss=1 0.99) whilst improving sequencing alignment rates, reducing adapter contamination and over-estimation of DNA methylation levels (CpG and non-CpG). As proof-of-concept we perform sciEM analysis of the temporal lobe, motor cortex, hippocampus and cerebellum of the human brain to resolve single-cell DNA methylation of all major cell-types. ]]> Chatterton, Z. Lamichhane, P. Rastegar, D. A. Fitzpatrick, L. Lebhar, H. Marquis, C. Halliday, G. Kwok, J. 2022-10-09 doi:10.1101/2022.10.09.511389 Cold Spring Harbor Laboratory Press 2022-10-09 <![CDATA[ An integrated cell barcoding and computational analysis pipeline for scalable analysis of differentiation at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2022.10.12.511862v1?rss=1 Shen, S. Werner, T. Sun, Y. Shim, W. J. Lukowski, S. Andersen, S. Chiu, H. S. Xia, D. Chen, X. Pham, D. Su, Z. Powell, J. E. Tam, P. P. L. Boden, M. Ho, J. W. K. Nguyen, Q. Palpant, N. J. 2022-10-14 doi:10.1101/2022.10.12.511862 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Smaller total and subregional cerebellar volumes in posttraumatic stress disorder: a mega-analysis by the ENIGMA-PGC PTSD workgroup ]]> https://biorxiv.org/content/10.1101/2022.10.13.512111v1?rss=1 Huggins, A. A. Baird, C. L. Briggs, M. Laskowitz, S. Fouda, S. Haswell, C. C. Sun, D. Salminen, L. E. Jahanshad, N. Thomopoulos, S. I. Veltman, D. J. Frijling, J. L. Olff, M. van Zuiden, M. Koch, S. B. J. Nawijn, L. Wang, L. Zhu, Y. Li, G. Stein, D. J. Ipser, J. Seedat, S. du Plessis, S. van den Heuvel, L. L. Suarez-Jimenez, B. Zhu, X. Kim, Y. He, X. Zilcha-Mano, S. Lazarov, A. Neria, Y. Stevens, J. S. Ressler, K. J. Jovanovic, T. van Rooij, S. J. H. Fani, N. Hudson, A. R. Mueller, S. C. Sierk, A. Manthey, A. Walter, H. Daniels, J. K. Schmahl, C. Herz 2022-10-17 doi:10.1101/2022.10.13.512111 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Hill-type computational models of muscle-tendon actuators: a systematic review ]]> https://biorxiv.org/content/10.1101/2022.10.14.512218v1?rss=1 Caillet, A. H. Phillips, A. T. Carty, C. Farina, D. Modenese, L. 2022-10-18 doi:10.1101/2022.10.14.512218 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ HumanBrainAtlas: an in vivo MRI dataset for detailed segmentations ]]> https://biorxiv.org/content/10.1101/2022.10.16.511844v1?rss=1 Schira, M. M. Isherwood, Z. J. Kassem, M. S. Barth, M. Shaw, T. B. Roberts, M. M. Paxinos, G. 2022-10-18 doi:10.1101/2022.10.16.511844 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Dietary restriction fails to extend life in stressful environments ]]> https://biorxiv.org/content/10.1101/2022.10.17.512576v1?rss=1 Zajitschek, F. Zajitschek, S. R. K. Vasconcelos, A. C. O. Bonduriansky, R. 2022-10-21 doi:10.1101/2022.10.17.512576 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Macaque Brainnetome Atlas with Fine-grained Parcellations and Reliable Connections ]]> https://biorxiv.org/content/10.1101/2022.10.18.512488v1?rss=1 Lu, Y. Cui, Y. Cao, L. Cheng, L. Wang, C. Liu, Y. Zhang, B. Wang, H. Li, K. Ma, L. Shi, W. Li, W. Dong, Z. Ma, Y. Du, Z. Xiong, H. Luo, N. Liu, Y. Hou, X. Liu, X. Sun, H. Wang, J. Paxinos, G. Yang, Z. Fan, L. Jiang, T. 2022-10-21 doi:10.1101/2022.10.18.512488 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ In depth characterization of an archaeal virus-host system reveals numerous virus exclusion mechanisms ]]> https://biorxiv.org/content/10.1101/2022.10.18.512658v1?rss=1 Mercier, C. Thies, D. Zhong, L. Raftery, M. J. Cavicchioli, R. Erdmann, S. 2022-10-18 doi:10.1101/2022.10.18.512658 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ CRF receptor type 1 modulates the nigrostriatal dopamine projection and facilitates cognitive flexibility after acute and chronic stress ]]> https://biorxiv.org/content/10.1101/2022.10.26.513963v1?rss=1 Becchi, S. Burton, C. L. Tsoukalas, M. Bowring, J. Balleine, B. W. mor, d. 2022-10-28 doi:10.1101/2022.10.26.513963 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment ]]> https://biorxiv.org/content/10.1101/2022.11.01.514782v1?rss=1 Chen-Liaw, A. Aggarwala, V. Mogno, I. Haifer, C. Eggers, J. Li, Z. Helmus, D. Hart, A. Wehkamp, J. Lamouse-Smith, E. Kerby, R. L. Rey, F. E. Colombel, J. F. Kamm, M. Borody, T. J. Grinspan, A. Paramsothy, S. Kaakoush, N. Dubinsky, M. C. Faith, J. J. 2022-11-02 doi:10.1101/2022.11.01.514782 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Genetic and phenotypic consequences of local transitions between sexual and parthenogenetic reproduction in the wild ]]> https://biorxiv.org/content/10.1101/2022.11.02.514965v1?rss=1 Miller, S. M. Stuart, K. C. Burke, N. W. Rollins, L. A. Bonduriansky, R. 2022-11-03 doi:10.1101/2022.11.02.514965 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Optopharmacological tools for precise spatiotemporal control of oxytocin signaling in the central nervous system and periphery ]]> https://biorxiv.org/content/10.1101/2022.11.10.516001v1?rss=1 Ahmed, I. Liu, J. Gieniec, K. Bair-Marshall, C. Adewakun, A. Hetzler, B. Arp, C. Khatri, L. Vanwalleghem, G. Seidenberg, A. Cowin, P. Trauner, D. Chao, M. Davis, F. Tsien, R. Froemke, R. 2022-11-13 doi:10.1101/2022.11.10.516001 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Evidence for a putative isoprene reductase in Acetobacterium wieringae ]]> https://biorxiv.org/content/10.1101/2022.11.16.516518v1?rss=1 Kronen, M. Vazquez-Campos, X. Wilkins, M. R. Lee, M. Manefield, M. J. 2022-11-17 doi:10.1101/2022.11.16.516518 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Cross-linking mass spectrometry discovers, evaluates, and validates the experimental and predicted structural proteome ]]> https://biorxiv.org/content/10.1101/2022.11.16.516813v1?rss=1 Bartolec, T. K. Vazquez-Campos, X. Norman, A. Luong, C. Payne, R. J. Wilkins, M. R. Mackay, J. P. Low, J. K. K. 2022-11-16 doi:10.1101/2022.11.16.516813 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Precision super-resolution cryo-correlative light and electron microscopy for rapid in situ structural analyses of optogenetically-positioned organelles ]]> https://biorxiv.org/content/10.1101/2022.11.22.516823v1?rss=1 Redpath, G. M. I. Rae, J. A. Yao, Y. Ruan, J. Cagigas, M. L. Whan, R. Hardeman, E. C. Gunning, P. W. Ananthanarayanan, V. Parton, R. G. Ariotti, N. 2022-11-23 doi:10.1101/2022.11.22.516823 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ TDCS modulates working memory maintenance processes in healthy individuals ]]> https://biorxiv.org/content/10.1101/2022.11.23.517774v1?rss=1 Nikolin, S. Martin, D. Loo, C. Boonstra, T. W. 2022-11-24 doi:10.1101/2022.11.23.517774 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ Visualization of Incrementally Learned Projection Trajectories for Longitudinal Data ]]> https://biorxiv.org/content/10.1101/2022.11.25.515889v1?rss=1 Malepathirana, T. A. Senanayake, D. Gautam, V. Engel, M. Balez, R. Lovelace, M. Sundaram, G. Heng, B. Chow, S. Marquis, C. Guillemin, G. Brew, B. Jagadish, C. Ooi, L. Halgamuge, S. 2022-11-25 doi:10.1101/2022.11.25.515889 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Danger changes the way the brain consolidates neutral information; and does so by interacting with processes involved in the encoding of that information. ]]> https://biorxiv.org/content/10.1101/2022.12.02.518124v1?rss=1 Qureshi, O. A. Leake, J. Delaney, A. J. Killcross, S. Westbrook, R. F. Holmes, N. M. 2022-12-03 doi:10.1101/2022.12.02.518124 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Contextual and temporal regulation of fear memory consolidation in the basolateral amygdala complex ]]> https://biorxiv.org/content/10.1101/2022.12.03.518947v1?rss=1 Leake, J. Saavedra Cardona, L. Westbrook, R. F. Holmes, N. M. 2022-12-03 doi:10.1101/2022.12.03.518947 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ What is learned determines how Pavlovian conditioned fear is consolidated in the brain. ]]> https://biorxiv.org/content/10.1101/2022.12.05.519226v1?rss=1 Leake, J. Leidl, D. M. Lay, B. P. P. Fam, J. P. Giles, M. C. Qureshi, O. A. Westbrook, R. F. Holmes, N. M. 2022-12-06 doi:10.1101/2022.12.05.519226 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments ]]> https://biorxiv.org/content/10.1101/2022.12.09.519815v1?rss=1 Wolfe, J. M. Ballou, L. Luque, J. Watson-Zink, V. M. Ahyong, S. T. Barido-Sottani, J. Chan, T.-Y. Chu, K. H. Crandall, K. A. Daniels, S. R. Felder, D. L. Mancke, H. Martin, J. W. Ng, P. K. L. Ortega-Hernandez, J. Palacios Theil, E. Pentcheff, N. D. Robles, R. Thoma, B. P. Tsang, L. M. Wetzer, R. Windsor, A. M. Bracken-Grissom, H. D. 2022-12-12 doi:10.1101/2022.12.09.519815 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Global and cell type-specific immunological hallmarks of severe dengue progression ]]> https://biorxiv.org/content/10.1101/2022.12.11.519930v1?rss=1 Ghita, L. Yao, Z. Xie, Y. Duran, V. Cagirici, B. H. Samir, J. Osman, I. Agudelo, O. L. Sanz, A. M. Sahoo, M. K. Robinson, M. Gelvez, R. M. Bueno, N. Luciani, F. Pinsky, B. A. Montoya, J. G. Estupinan Cardenas, M. I. Villar, L. A. Rojas Garrido, E. M. Rosso, F. Quake, S. R. Zanini, F. Einav, S. 2022-12-14 doi:10.1101/2022.12.11.519930 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Multimodal Imaging-Based Classification of PTSD Using Data-Driven Computational Approaches: A Multisite Big Data Study from the ENIGMA-PGC PTSD Consortium ]]> https://biorxiv.org/content/10.1101/2022.12.12.519838v1?rss=1 Zhu, X. Kim, Y. Ravid, O. He, X. Suarez-Jimenez, B. Zilcha-Mano, S. Lazarov, A. Lee, S. Abdallah, C. G. Angstadt, M. Averill, C. L. Baird, C. L. Baugh, L. A. Blackford, J. U. Bomyea, J. Bruce, S. E. Bryant, R. A. Cao, Z. Choi, K. Cisler, J. Cotton, A. S. Daniels, J. K. Davenport, N. D. Davidson, R. J. DeBellis, M. D. Dennis, E. L. Densmore, M. deRoon-Cassini, T. Disner, S. G. El Hage, W. Etkin, A. Fani, N. Fercho, K. A. Fitzgerald, J. Forster, G. L. Frijling, J. L. Geuze, E. Gonenc, A. Gordon, E. M. Gruber, S. Grupe, D. W. Guenette, J. P. Haswell, C. C 2022-12-13 doi:10.1101/2022.12.12.519838 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data ]]> https://biorxiv.org/content/10.1101/2022.12.26.521922v1?rss=1 Peres, A. Lees, W. D. Rodriguez, O. L. Lee, N. Y. Polak, P. Hope, R. Kedmi, M. Collins, A. M. Ohlin, M. Kleinstein, S. H. Watson, C. Yaari, G. 2022-12-27 doi:10.1101/2022.12.26.521922 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ Continuous muscle, glial, epithelial, neuronal, and hemocyte cell lines for Drosophila research ]]> https://biorxiv.org/content/10.1101/2023.01.18.524445v1?rss=1 Coleman-Gosser, N. Raghuvanshi, S. Stitzinger, S. Hu, Y. Chen, W. Luhur, A. Mariyappa, D. Josifov, M. Zelhof, A. Mohr, S. E. Perrimon, N. Simcox, A. 2023-01-19 doi:10.1101/2023.01.18.524445 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology ]]> https://biorxiv.org/content/10.1101/2023.01.26.525801v1?rss=1 Ballard, J. W. O. Field, M. A. Edwards, R. J. Wilson, L. A. B. Koungoulos, L. G. Rosen, B. R. Chernoff, B. Dudchenko, O. Omer, A. Keilwagen, J. Skvortsova, K. Bogdanovic, O. Chan, E. Zammit, R. Hayes, V. Aiden, E. L. 2023-01-27 doi:10.1101/2023.01.26.525801 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ The Effect of Electrical Resonance in Neurons upon the Instability of Electrical Nerve Stimulations ]]> https://biorxiv.org/content/10.1101/2023.01.26.525813v1?rss=1 Yu, S. Yue, W. Guo, T. Liu, Y. Zhang, Y. Khademi, S. Zhou, T. Xu, Z. Song, B. Wu, T. Liu, F. Tai, Y. Yu, X. Wang, M. 2023-01-27 doi:10.1101/2023.01.26.525813 Cold Spring Harbor Laboratory Press 2023-01-27 <![CDATA[ Normative Modeling of Brain Morphometry Across the Lifespan using CentileBrain: Algorithm Benchmarking and Model Optimization ]]> https://biorxiv.org/content/10.1101/2023.01.30.523509v1?rss=1 Ge, R. Yu, Y. Qi, Y. X. Fan, Y. V. Chen, S. Gao, C. Haas, S. S. Modabbernia, A. New, F. Agartz, I. Asherson, P. Ayesa-Arriola, R. Banaj, N. Banaschewski, T. Baumeister, S. Bertolino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buckner, R. Buitelaar, J. K. Cannon, D. M. Caseras, X. Cervenka, S. Conrod, P. J. Crespo-Facorro, B. Crivello, F. Crone, E. A. de Haan, L. de Zubicaray, G. I. Di Giorgio, A. Erk, S. Fisher, S. E. Franke, B. Frodl, T. Glahn, D. C. Grotegerd, D. Gruber, O. Gruner, P. Gur, R. E. G 2023-01-31 doi:10.1101/2023.01.30.523509 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Insects pollinated flowering plants for most of angiosperm evolutionary history ]]> https://biorxiv.org/content/10.1101/2023.01.31.526530v1?rss=1 Stephens, R. E. Gallagher, R. Dun, L. Cornwell, W. Sauquet, H. 2023-02-01 doi:10.1101/2023.01.31.526530 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ SaLTy: a novel Staphylococcus aureus Lineage Typer ]]> https://biorxiv.org/content/10.1101/2023.02.03.527095v1?rss=1 Cheney, L. Payne, M. Kaur, S. Lan, R. 2023-02-07 doi:10.1101/2023.02.03.527095 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Genomic signatures of bottleneck and founder effects in dingoes ]]> https://biorxiv.org/content/10.1101/2023.02.05.527211v1?rss=1 Kumar, M. Conroy, G. Ogbourne, S. Cairns, K. Borburgh, L. Subramanian, S. 2023-02-05 doi:10.1101/2023.02.05.527211 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ Assessing changes in global fire regimes ]]> https://biorxiv.org/content/10.1101/2023.02.07.527551v1?rss=1 Sayedi, S. S. Global group of fire experts, 2023-02-08 doi:10.1101/2023.02.07.527551 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Immp2l knockdown increases stimulus-driven instrumental behaviour but does not alter goal-directed learning or neuron density in cortico-striatal circuits in a mouse model of Tourette syndrome and autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/2023.02.12.528225v1?rss=1 Leung, B. K. Merlin, S. Walker, A. K. Lawther, A. J. Paxinos, G. Eapen, V. Clarke, R. Balleine, B. W. Furlong, T. M. 2023-02-13 doi:10.1101/2023.02.12.528225 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ Divergent patterns of meiotic double strand breaks and synapsis initiation dynamics suggest an evolutionary shift in the meiosis program between American and Australian marsupials ]]> https://biorxiv.org/content/10.1101/2023.02.13.527877v1?rss=1 Valero-Regalon, F. J. Sole, M. Lopez-Jimenez, P. Valerio-de Arana, M. Martin-Ruiz, M. de la Fuente, R. Marin-Gual, L. Renfree, M. B. Shaw, G. Berris, S. Fernandez-Donoso, R. Waters, P. D. Ruiz-Herrera, A. Gomez, R. Page, J. 2023-02-13 doi:10.1101/2023.02.13.527877 Cold Spring Harbor Laboratory Press 2023-02-13 <![CDATA[ P-Selectin promotes SARS-CoV-2 interactions with platelets and the endothelium ]]> https://biorxiv.org/content/10.1101/2023.02.13.528235v1?rss=1 Moreno, C. L. Castanheira, F. V. S. Stella, A. O. Chung, F. Aggarwal, A. Cole, A. J. Loo, L. Dupuy, A. Kong, Y. Hagimola, L. Fenwick, J. Coleman, P. Wilson, M. Bui-Marinos, M. Hesselson, D. Gamble, J. Passam, F. Turville, S. Kubes, P. Neely, G. G. 2023-02-14 doi:10.1101/2023.02.13.528235 Cold Spring Harbor Laboratory Press 2023-02-14 <![CDATA[ Larger and denser: an optimal design for surface grids of EMG electrodes to identify greater and more representative samples of motor units ]]> https://biorxiv.org/content/10.1101/2023.02.18.529050v1?rss=1 Caillet, A. H. Avrillon, S. Kundu, A. Yu, T. Phillips, A. T. M. Modenese, L. Farina, D. 2023-02-18 doi:10.1101/2023.02.18.529050 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Human Dermal Fibroblast Subpopulations and Epithelial Mesenchymal Transition Signals in Hidradenitis Suppurativa Tunnels are Normalized by Spleen Tyrosine Kinase Antagonism in Vivo ]]> https://biorxiv.org/content/10.1101/2023.02.23.529664v1?rss=1 Flora, A. Jepsen, R. Kozera, E. Woods, J. Cains, G. Razieta, M. Jensen, S. Malone, M. Frew, J. W. 2023-02-23 doi:10.1101/2023.02.23.529664 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ The intracellular lifestyle of an archaeal symbiont ]]> https://biorxiv.org/content/10.1101/2023.02.24.529834v1?rss=1 Hamm, J. N. Liao, Y. von Kügelgen, A. Dombrowski, N. Landers, E. Brownlee, C. Johansson, E. M. V. Whan, R. M. Baker, M. A. B. Baum, B. Bharat, T. A. M. Duggin, I. G. Spang, A. Cavicchioli, R. 2023-02-24 doi:10.1101/2023.02.24.529834 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Heat stress conditions affect the social network structure of free-ranging sheep ]]> https://biorxiv.org/content/10.1101/2023.02.26.530064v1?rss=1 Borthwick, Z. Quiring, K. Griffith, S. C. Leu, S. T. 2023-02-26 doi:10.1101/2023.02.26.530064 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ REMAP: An online remote sensing application for land cover classification and monitoring ]]> https://biorxiv.org/content/10.1101/212464v1?rss=1 Murray, N. J. Keith, D. A. Simpson, D. Wilshire, J. H. Lucas, R. M. 2017-11-01 doi:10.1101/212464 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Metagenomics for chronic meningitis: clarifying interpretation and diagnosis ]]> https://biorxiv.org/content/10.1101/213561v1?rss=1 Wilson, M. R. O'Donovan, B. D. Gelfand, J. M. Sample, H. A. Chow, F. C. Betjemann, J. P. Shah, M. P. Richie, M. B. Gorman, M. P. Hajj-Ali, R. A. Calabrese, L. H. Zorn, K. C. Greenlee, J. E. Blum, J. H. Green, G. Khan, L. M. Banerji, D. Langelier, C. Bryson-Cahn, C. Harrington, W. Lingappa, J. R. Shanbhag, N. M. Green, A. J. Brew, B. J. Soldatos, A. Strnad, L. Doernberg, S. B. Jay, C. A. Douglas, V. Josephson, S. A. DeRisi, J. L. 2017-11-07 doi:10.1101/213561 Cold Spring Harbor Laboratory Press 2017-11-07 <![CDATA[ The application of zeta diversity as a continuous measure of compositional change in ecology ]]> https://biorxiv.org/content/10.1101/216580v1?rss=1 McGeoch, M. A. Latombe, G. Andrew, N. R. Nakagawa, S. Nipperess, D. A. Roige, M. Marzinelli, E. M. Campbell, A. H. Verges, A. Thomas, T. Steinberg, P. D. Selwood, K. E. Hui, C. 2017-11-09 doi:10.1101/216580 Cold Spring Harbor Laboratory Press 2017-11-09 <![CDATA[ Insights into platypus population structure and history from whole-genome sequencing ]]> https://biorxiv.org/content/10.1101/221481v1?rss=1 Martin, H. C. Batty, E. M. Hussin, J. Westall, P. Daish, T. Kolomyjec, S. Piazza, P. Bowden, R. Hawkins, M. Grant, T. Moritz, C. Grutzner, F. Gongora, J. Donnelly, P. 2017-11-17 doi:10.1101/221481 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics ]]> https://biorxiv.org/content/10.1101/221564v1?rss=1 Aliota, M. T. Dudley, D. M. Newman, C. M. Weger-Lucarelli, J. Stewart, L. M. Koenig, M. R. Breitbach, M. E. Weiler, A. M. Semler, M. R. Barry, G. L. Zarbock, K. R. Mohns, M. S. Mohr, E. L. Venturi, V. Schultz-Darken, N. Peterson, E. Newton, W. Schotzko, M. L. Simmons, H. A. Mejia, A. Hayes, J. M. Capuano, S. Davenport, M. P. Friedrich, T. C. Ebel, G. D. O'Connor, S. L. O'Connor, D. H. 2017-11-17 doi:10.1101/221564 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ PDGFRα signaling in cardiac stem and stromal cells modulates quiescence, metabolism and self-renewal, and promotes anatomical and functional repair ]]> https://biorxiv.org/content/10.1101/225979v1?rss=1 Harvey, R. P. Asili, N. Xaymardan, M. Forte, E. Waardenberg, A. J. Cornwell, J. Janbandhu, V. Kesteven, S. Chandrakanthan, V. Malinowska, H. Reinhard, H. Yang, S. Pickett, H. Schofield, P. Christ, D. Ahmed, I. Chong, J. Heffernan, C. Li, J. Simonian, M. Bouveret, R. Srivastava, S. Mishra, R. Dhawan, J. Nordon, R. Macdonald, P. Graham, R. Feneley, M. 2017-11-28 doi:10.1101/225979 Cold Spring Harbor Laboratory Press 2017-11-28 <![CDATA[ Unifying intra- and inter-specific variation in tropical tree mortality ]]> https://biorxiv.org/content/10.1101/228361v1?rss=1 Camac, J. S. Condit, R. FitzJohn, R. G. McCalman, L. Steinberg, D. Westoby, M. Wright, S. J. Falster, D. S. 2017-12-04 doi:10.1101/228361 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Reticular adhesions: A new class of adhesion complex that mediates cell-matrix attachment during mitosis ]]> https://biorxiv.org/content/10.1101/234237v1?rss=1 Lock, J. G. Jones, M. C. Askari, J. A. Gong, X. Oddone, A. Olofsson, H. Goransson, S. Lakadamyali, M. Humphries, M. J. Stromblad, S. 2017-12-14 doi:10.1101/234237 Cold Spring Harbor Laboratory Press 2017-12-14 <![CDATA[ Planned missing data design: stronger inferences, increased research efficiency and improved animal welfare in ecology and evolution ]]> https://biorxiv.org/content/10.1101/247064v1?rss=1 Noble, D. W. A. Nakagawa, S. 2018-01-11 doi:10.1101/247064 Cold Spring Harbor Laboratory Press 2018-01-11 <![CDATA[ Reproducible, flexible and high throughput data extraction from primary literature: The metaDigitise R package ]]> https://biorxiv.org/content/10.1101/247775v1?rss=1 Pick, J. L. Nakagawa, S. W. Noble, D. W. 2018-01-15 doi:10.1101/247775 Cold Spring Harbor Laboratory Press 2018-01-15 <![CDATA[ Trans-ancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders ]]> https://biorxiv.org/content/10.1101/257311v1?rss=1 Walters, R. K. Adams, M. J. Adkins, A. E. Aliev, F. Bacanu, S.-A. Batzler, A. Bertelsen, S. Biernacka, J. Bigdeli, T. B. Chen, L.-S. Clarke, T.-K. Chou, Y.-L. Degenhardt, F. Docherty, A. R. Fontanillas, P. Foo, J. Fox, L. Frank, J. Giegling, I. Gordon, S. Hack, L. -, Hartz, S. M. Heilmann-Heimbach, S. Herms, S. Hodgkinson, C. Hoffmann, P. Hottenga, J.-J. Kennedy, M. A. Alanne-Kinnunen, M. Konte, B. Lahti, J. Lahti-Pulkkinen, M. Ligthart, L. Loukola, A.-M. Maher, B. S. Mbarek, H. McIntosh, A. M. McQueen, M. B. Milaneschi, Y. Palviainen, T. Pearson, J. 2018-03-10 doi:10.1101/257311 Cold Spring Harbor Laboratory Press 2018-03-10 <![CDATA[ Electromechanics and Volume Dynamics in Non-excitable Tissue Cells ]]> https://biorxiv.org/content/10.1101/275339v1?rss=1 Yellin, F. Li, Y. Sreenivasan, V. K. A. Farrell, B. Johny, M. Yu, D. Sun, S. X. 2018-03-08 doi:10.1101/275339 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Near-Infrared Spectroscopy for metabolite quantification and species identification ]]> https://biorxiv.org/content/10.1101/277053v1?rss=1 Aw, W. C. Ballard, J. W. O. 2018-03-06 doi:10.1101/277053 Cold Spring Harbor Laboratory Press 2018-03-06 <![CDATA[ Differentiation of Alzheimer’s disease based on local and global parameters in personalized Virtual Brain models ]]> https://biorxiv.org/content/10.1101/277624v1?rss=1 Zimmermann, J. Perry, A. Breakspear, M. Schirner, M. Sachdev, P. Wen, W. Kochan, N. Mapstone, M. Ritter, P. McIntosh, A. R. Solodkin, A. 2018-03-08 doi:10.1101/277624 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Telomere-loop dynamics in chromosome end protection ]]> https://biorxiv.org/content/10.1101/279877v1?rss=1 Van Ly, D. Low, R. R. J. Frölich, S. Bartolec, T. K. Kafer, G. R. Pickett, H. A. Gaus, K. Cesare, A. J. 2018-03-09 doi:10.1101/279877 Cold Spring Harbor Laboratory Press 2018-03-09 <![CDATA[ Meta-analysis challenges a textbook example of status signalling: evidence for publication bias ]]> https://biorxiv.org/content/10.1101/283150v1?rss=1 Sanchez-Tojar, A. Nakagawa, S. Sanchez-Fortun, M. Martin, D. A. Ramani, S. Girndt, A. Bokony, V. Kempenaers, B. Liker, A. Westneat, D. Burke, T. Schroeder, J. 2018-03-16 doi:10.1101/283150 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ The Functional effects of voluntary and involuntary visual phantom color on conscious awareness ]]> https://biorxiv.org/content/10.1101/286716v1?rss=1 Chang, S. Pearson, J. 2018-03-22 doi:10.1101/286716 Cold Spring Harbor Laboratory Press 2018-03-22 <![CDATA[ Thought Control Failure: Sensory Determinants and Functional Effects ]]> https://biorxiv.org/content/10.1101/293761v1?rss=1 Kwok, E. L. Leys, G. Koenig-Robert, R. Pearson, J. 2018-04-03 doi:10.1101/293761 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ Deleterious genetic variants in NOTCH1 are a major contributor to the incidence of non-syndromic Tetralogy of Fallot ]]> https://biorxiv.org/content/10.1101/300905v1?rss=1 Page, D. J. Miossec, M. J. Williams, S. G. Fotiou, E. Monaghan, R. M. Cordell, H. J. Sutcliffe, L. Topf, A. Bourgey, M. Bourque, G. Eveleigh, R. Dunwoodie, S. L. Winlaw, D. S. Bhattacharya, S. Breckpot, J. Devriendt, K. Gewillig, M. Brook, D. Setchfield, K. Bu'Lock, F. A. O'Sullivan, J. Stuart, G. Bezzina, C. Mulder, B. J. M. Postma, A. V. Bentham, J. R. Baron, M. Bhaskar, S. S. Black, G. C. Newman, W. G. Hentges, K. G. Lathrop, M. Santibanez-Koref, M. Keavney, B. D. 2018-04-13 doi:10.1101/300905 Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced de-novo mutation in survival outliers of glioblastoma ]]> https://biorxiv.org/content/10.1101/302042v1?rss=1 Hwang, T. Mathios, D. McDonald, K. L. Daris, I. Park, S.-H. Burger, P. C. Kim, S. Dho, Y.-S. Carolyn, H. Bettegowda, C. Shin, J. H. Lim, M. Park, C.-K. 2018-04-16 doi:10.1101/302042 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ The rodent lateral orbitofrontal cortex represents expected Pavlovian outcome value but not identity ]]> https://biorxiv.org/content/10.1101/303800v1?rss=1 Panayi, M. C. Killcross, S. 2018-04-18 doi:10.1101/303800 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ The RHIM within the M45 protein from murine cytomegalovirus forms heteromeric functional amyloid fibrils with RIPK1 and RIPK3 ]]> https://biorxiv.org/content/10.1101/324590v1?rss=1 Pham, C. L. L. Strange, M. O' Carroll, A. Shanmugam, N. Sierecki, E. Gambin, Y. Steain, M. Sunde, M. 2018-05-17 doi:10.1101/324590 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Marine sponges as Chloroflexi hot-spots: Genomic insights and high resolution visualization of an abundant and diverse symbiotic clade ]]> https://biorxiv.org/content/10.1101/328013v1?rss=1 Bayer, K. Jahn, M. T. Slaby, B. M. Moitinho-Silva, L. Hentschel, U. 2018-05-22 doi:10.1101/328013 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Metastable brain waves ]]> https://biorxiv.org/content/10.1101/347054v1?rss=1 Roberts, J. A. Gollo, L. L. Abeysuriya, R. Roberts, G. Mitchell, P. B. Woolrich, M. W. Breakspear, M. 2018-06-14 doi:10.1101/347054 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Effects of Pathological Mutations on the Prion-Like Polymerisation of MyD88 ]]> https://biorxiv.org/content/10.1101/351726v1?rss=1 O'Carroll, A. Chauvin, B. Brown, J. Meagher, A. Coyle, J. Hunter, D. Bhumkar, A. Kobe, B. Ve, T. Sierecki, E. Gambin, Y. 2018-06-20 doi:10.1101/351726 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Learned predictiveness acquired through experience prevails over the influence of conflicting verbal instructions in rapid selective attention ]]> https://biorxiv.org/content/10.1101/351908v1?rss=1 Cobos Cano, P. L. Vadillo, M. A. Luque, D. Le Pelley, M. E. 2018-06-20 doi:10.1101/351908 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Comprehensive cross-disorder analyses of CNTNAP2 suggest it is unlikely to be a primary risk gene for psychiatric disorders. ]]> https://biorxiv.org/content/10.1101/363846v1?rss=1 Toma, C. Pierce, K. D. Shaw, A. D. Heath, A. Mitchell, P. B. Schofield, P. R. Fullerton, J. M. 2018-07-06 doi:10.1101/363846 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Oral iron exacerbates colitis and influences the intestinal microbiome ]]> https://biorxiv.org/content/10.1101/385997v1?rss=1 Mahalhal, A. Williams, J. M. Johnson, S. Ellaby, N. Duckworth, C. A. Burkitt, M. D. Liu, X. Hold, G. L. Campbell, B. J. Pritchard, D. M. P. Probert, C. S. 2018-08-06 doi:10.1101/385997 Cold Spring Harbor Laboratory Press 2018-08-06 <![CDATA[ Propionic acid enhances the virulence of Crohn’s disease-associated adherent-invasive Escherichia coli ]]> https://biorxiv.org/content/10.1101/387647v1?rss=1 Ormsby, M. J. Johnson, S. A. Meikle, L. M. Goldstone, R. J. McIntosh, A. Wessel, H. M. Hulme, H. E. McConnachie, C. C. Connolly, J. P. Roe, A. J. Fitzgerald, E. Gerasimidis, K. Morrison, D. Smith, D. G. Wall, D. M. 2018-08-09 doi:10.1101/387647 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Hierarchical Bayesian inference for concurrent model fitting and comparison for group studies ]]> https://biorxiv.org/content/10.1101/393561v1?rss=1 Piray, P. Dezfouli, A. Heskes, T. Frank, M. J. Daw, N. 2018-08-16 doi:10.1101/393561 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ The genetic architecture of the human cerebral cortex ]]> https://biorxiv.org/content/10.1101/399402v1?rss=1 Grasby, K. L. Jahanshad, N. Painter, J. N. Colodro-Conde, L. Bralten, J. Hibar, D. P. Lind, P. A. Pizzagalli, F. Ching, C. R. McMahon, M. A. Shatokhina, N. Zsembik, L. C. P. Agartz, I. Alhusaini, S. Almeida, M. A. Alnaes, D. Amlien, I. K. Andersson, M. Ard, T. Armstrong, N. J. Ashley-Koch, A. Bernard, M. Brouwer, R. M. Buimer, E. E. Bülow, R. Bürger, C. Cannon, D. M. Chakravarty, M. Chen, Q. Cheung, J. W. Couvy-Duchesne, B. Dale, A. M. Dalvie, S. de Araujo, T. K. de Zubicaray, G. I. de Zwarte, S. M. den Braber, A. Doan, N. T. Dohm, K. Ehrlich, S. Engel 2018-09-03 doi:10.1101/399402 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Mycoplasma genitalium incidence, persistence, concordance between partners and progression: systematic review and meta-analysis ]]> https://biorxiv.org/content/10.1101/400713v1?rss=1 Cina, M. Baumann, L. Egli-Gany, D. Halbeisen, F. S. Ali, H. Scott, P. Low, N. 2018-08-29 doi:10.1101/400713 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Preserved cortical maps of the body in Complex Regional Pain Syndrome ]]> https://biorxiv.org/content/10.1101/409094v1?rss=1 Mancini, F. Wang, A. P. Shira, M. M. Isherwood, Z. J. McAuley, J. H. Iannetti, G. Sereno, M. I. Moseley, L. Rae, C. D. 2018-09-08 doi:10.1101/409094 Cold Spring Harbor Laboratory Press 2018-09-08 <![CDATA[ Genetic Determinants of Cortical Structure (Thickness, Surface Area and Volumes) among Disease Free Adults in the CHARGE Consortium ]]> https://biorxiv.org/content/10.1101/409649v1?rss=1 Hofer, E. Roshchupkin, G. V. Adams, H. Knol, M. Lin, H. Li, S. Zare, H. Ahmad, S. Armstrong, N. Satizabal, C. Bernard, M. Bis, J. Gillespie, N. Luciano, M. Mishra, A. Scholz, M. Teumer, A. Xia, R. Jian, X. Mosley, T. Saba, Y. Pirpamer, L. Seiler, S. Becker, J. Carmichael, O. Rotter, J. Psaty, B. Lopez, O. Amin, N. Lee, S. Yang, Q. Himali, J. Maillard, P. Beiser, A. DeCarli, C. Karama, S. Lewis, L. Bastin, M. Harris, M. Deary, I. Witte, V. Beyer, F. Loeffler, M. Mather, K. Schofield, P. Thalamuthu, A. Kwok, J. Wright, M. Ames, D. Trollor, J. Jia 2018-09-09 doi:10.1101/409649 Cold Spring Harbor Laboratory Press 2018-09-09 <![CDATA[ Temperate grass allergy season defined by spatio-temporal shifts in airborne pollen communities ]]> https://biorxiv.org/content/10.1101/410829v1?rss=1 Brennan, G. L. Potter, C. de Vere, N. Griffith, G. W. Skjoth, C. A. Osborne, N. J. Wheeler, B. W. McInnes, R. N. Clewlow, Y. Barber, A. Hanlon, H. M. Hegarty, M. Jones, L. Kurganskiy, A. Rowney, F. M. Armitage, C. Adams-Groom, B. Ford, C. R. Petch, G. M. Elliot, A. Frisk, C. A. Neilson, R. Potter, S. Rafiq, A. M. Roy, D. B. Selby, K. Steinberg, N. Creer, S. 2018-09-06 doi:10.1101/410829 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ A decision-support framework to optimize border control for global outbreak mitigation ]]> https://biorxiv.org/content/10.1101/414185v1?rss=1 Gardner, L. Rey, D. Zlojutro, A. 2018-09-12 doi:10.1101/414185 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ BNMCMC: a software for learning and visualizing Bayesian networks using MCMC methods ]]> https://biorxiv.org/content/10.1101/414953v1?rss=1 Azad, A. K. M. Alyami, S. A. Keith, J. M. 2018-09-12 doi:10.1101/414953 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ KPGminer: A tool for retrieving pathway genes from KEGG pathway database ]]> https://biorxiv.org/content/10.1101/416131v1?rss=1 Azad, A. K. M. 2018-09-13 doi:10.1101/416131 Cold Spring Harbor Laboratory Press 2018-09-13 <![CDATA[ Phasor histone FLIM-FRET microscopy quantifies spatiotemporal rearrangement of chromatin architecture during the DNA damage response. ]]> https://biorxiv.org/content/10.1101/419523v1?rss=1 Lou, J. Scipioni, L. Wright, B. K. Bartolec, T. K. Zhang, J. Masamsetti, V. P. Gaus, K. Gratton, E. Cesare, A. J. Hinde, E. 2018-09-17 doi:10.1101/419523 Cold Spring Harbor Laboratory Press 2018-09-17 <![CDATA[ CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes ]]> https://biorxiv.org/content/10.1101/424960v1?rss=1 Bayati, M. Rabiee, H. R. Mehrbod, M. Vafaee, F. Ebrahimi, D. Forrest, A. Alinejad-Rokny, H. 2018-09-29 doi:10.1101/424960 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ XTalkiiS: a tool for finding data-driven cross-talks between intra-/inter-species pathways ]]> https://biorxiv.org/content/10.1101/437541v1?rss=1 Azad, A. K. M. 2018-10-13 doi:10.1101/437541 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ The Influence of Molecular Reach and Diffusivity on the Efficacy of Membrane-Confined Reactions ]]> https://biorxiv.org/content/10.1101/439430v1?rss=1 Zhang, Y. Clemens, L. Goyette, J. Allard, J. Dushek, O. Isaacson, S. A. 2018-10-10 doi:10.1101/439430 Cold Spring Harbor Laboratory Press 2018-10-10 <![CDATA[ Expectation and attention increase the integration of top-down and bottom-up signals in perception through different pathways ]]> https://biorxiv.org/content/10.1101/446948v1?rss=1 Gordon, N. Tsuchiya, N. Koenig-Robert, R. Hohwy, J. 2018-10-18 doi:10.1101/446948 Cold Spring Harbor Laboratory Press 2018-10-18 <![CDATA[ Comparative mode of action of antimicrobial peptide melimine and its derivative Mel4 against Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/450577v1?rss=1 YASIR, M. Dutta, D. Willcox, M. D. P. 2018-10-23 doi:10.1101/450577 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ Nuclear filamentous actin functions in the replication stress response ]]> https://biorxiv.org/content/10.1101/451708v1?rss=1 Lamm, N. Masamsetti, V. P. Read, M. N. Biro, M. Cesare, A. 2018-10-24 doi:10.1101/451708 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Largest genome-wide association study for PTSD identifies genetic risk loci in European and African ancestries and implicates novel biological pathways ]]> https://biorxiv.org/content/10.1101/458562v1?rss=1 Nievergelt, C. M. Maihofer, A. X. Klengel, T. Atkinson, E. G. Chen, C.-Y. Choi, K. W. Coleman, J. R. I. Dalvie, S. Duncan, L. E. Logue, M. W. Provost, A. Ratanatharathorn, A. Stein, M. B. Torres, K. Aiello, A. E. Almli, L. M. Amstadter, A. B. Andersen, S. B. Andreassen, O. A. Arbisi, P. A. Ashley-Koch, A. E. Austin, S. B. Avdibegovic, E. Babic, D. Baekvad-Hansen, M. Baker, D. G. Beckham, J. C. Bierut, L. J. Bisson, J. I. Boks, M. P. Bolger, E. A. Borglum, A. D. Bradley, B. Brashear, M. Breen, G. Bryant, R. A. Bustamante, A. C. Bybjerg-Grauholm, J. Calabres 2018-11-01 doi:10.1101/458562 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ Fibroblast activation protein enzyme deficiency prevents liver steatosis, insulin resistance and glucose intolerance and increases fibroblast growth factor-21 in diet induced obese mice ]]> https://biorxiv.org/content/10.1101/460279v1?rss=1 Chowdhury, S. Song, S. Zhang, H. E. Wang, X. M. Gall, M. G. Yu, D. M.-T. Lay, A. J. Xiang, M. S.-W. Evans, K. A. Wetzel, S. Liu, Y. Yau, B. Coppage, A. L. Lo, L. Stokes, R. A. Hawthorne, W. J. Cooney, G. J. McLennan, S. V. Gunton, J. E. Bachovchin, W. W. Turner, N. Kebede, M. A. McCaughan, G. W. Twigg, S. M. Gorrell, M. D. 2018-11-04 doi:10.1101/460279 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group ]]> https://biorxiv.org/content/10.1101/460444v1?rss=1 Jia, T. Chu, C. Liu, Y. van Dongen, J. Armstrong, N. J. Bastin, M. E. Carrillo-Roa, T. den Braber, A. Harris, M. Jansen, R. Liu, J. Luciano, M. Ori, A. P. S. Roiz Santianez, R. Ruggeri, B. Sarkisyan, D. Shin, J. Sungeun, K. Tordesillas Gutierrez, D. van't Ent, D. Ames, D. Artiges, E. Bakalkin, G. Banaschewski, T. Bokde, A. L. W. Brodaty, H. Bromberg, U. Brouwer, R. Buchel, C. Burke Quinlan, E. Cahn, W. de Zubicaray, G. I. Ekstrom, T. J. Flor, H. Frohner, J. H. Frouin, V. Garavan, H. Gowland, P. Heinz, A. Ittermann, B. Jahanshad, N. Jiang, J. Kwok, J. 2018-11-05 doi:10.1101/460444 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Modeling the relative role of human mobility, land-use and climate factors on dengue outbreak emergence in Sri Lanka ]]> https://biorxiv.org/content/10.1101/462150v1?rss=1 Zhang, Y. Riera, J. Ostrow, K. Siddiqui, S. de Silva, H. Sarkar, S. Fernando, L. Gardner, L. 2018-11-09 doi:10.1101/462150 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia ]]> https://biorxiv.org/content/10.1101/465583v1?rss=1 Kerr, P. J. Eden, J.-S. Di Giallonardo, F. Peacock, D. Liu, J. Strive, T. Read, A. F. Holmes, E. C. 2018-11-08 doi:10.1101/465583 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ A dynamic neural network model for real-time prediction of the Zika epidemic in the Americas ]]> https://biorxiv.org/content/10.1101/466581v1?rss=1 Akhtar, M. Kraemer, M. U. Gardner, L. 2018-11-09 doi:10.1101/466581 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Untangling direct species associations from mediator species effects with graphical models ]]> https://biorxiv.org/content/10.1101/470161v1?rss=1 Popovic, G. Warton, D. I. Thomson, F. Hui, F. K. Moles, A. T. 2018-11-19 doi:10.1101/470161 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ The Medical Genome Reference Bank: Whole genomes and phenotype of 2,570 healthy elderly ]]> https://biorxiv.org/content/10.1101/473348v1?rss=1 Pinese, M. Lacaze, P. Rath, E. M. Stone, A. Brion, M.-J. Ameur, A. Nagpal, S. Puttick, C. Husson, S. Degrave, D. Navin Cristina, T. Silva Kahl, V. F. Statham, A. L. Woods, R. L. McNeil, J. J. Riaz, M. Barr, M. Nelson, M. R. Reid, C. M. Murray, A. M. Shah, R. C. Wolfe, R. Atkins, J. R. Fitzsimmons, C. Cairns, H. M. Green, M. J. Carr, V. J. Cowley, M. J. Pickett, H. A. James, P. A. Powell, J. E. Kaplan, W. Gibson, G. Gyllensten, U. Cairns, M. J. McNamara, M. Dinger, M. E. Thomas, D. M. 2018-11-18 doi:10.1101/473348 Cold Spring Harbor Laboratory Press 2018-11-18 <![CDATA[ Women in neotropical science: Gender parity in the 21st century and prospects for a post-war Colombia ]]> https://biorxiv.org/content/10.1101/477422v1?rss=1 Lopez Aguirre, C. 2018-11-27 doi:10.1101/477422 Cold Spring Harbor Laboratory Press 2018-11-27 <![CDATA[ The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation ]]> https://biorxiv.org/content/10.1101/477646v1?rss=1 Choudhury, R. Singh, S. Arumugam, S. Roguev, A. Stewart, A. F. 2018-11-24 doi:10.1101/477646 Cold Spring Harbor Laboratory Press 2018-11-24 <![CDATA[ Beyond a ribosomal RNA methyltransferase, the wider role of MraW in DNA methylation, motility and colonization in Escherichia coli O157:H7 ]]> https://biorxiv.org/content/10.1101/480244v1?rss=1 Xu, X. Zhang, H. Huang, Y. Zhang, Y. Wang, X. Wang, D. Pu, J. Zhao, H. Lu, X. Lu, S. Xiong, Y. Ye, C. Dong, Y. Lan, R. Xu, J. 2018-11-29 doi:10.1101/480244 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Hfq CLASH uncovers sRNA-target interaction networks enhancing adaptation to nutrient availability ]]> https://biorxiv.org/content/10.1101/481986v1?rss=1 Iosub, I. A. Marchioretto, M. Sy, B. McKellar, S. Nieken, K. J. van Nues, R. W. Tree, J. J. Viero, G. Granneman, S. 2018-11-29 doi:10.1101/481986 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ Structural venomics: evolution of a complex chemical arsenal by massive duplication and neofunctionalization of a single ancestral fold ]]> https://biorxiv.org/content/10.1101/485722v1?rss=1 Pineda, S. S. Chin, Y. K.-Y. Undheim, E. A. B. Senff, S. Mobli, M. Dauly, C. Escoubas, P. Nicholson, G. M. Kaas, Q. Mattick, J. S. King, G. F. 2018-12-03 doi:10.1101/485722 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Single molecule localization microscopy with autonomous feedback loops for ultrahigh precision ]]> https://biorxiv.org/content/10.1101/487728v1?rss=1 Coelho, S. baek, J. Graus, M. S. Halstead, J. M. Nicovich, P. R. Feher, K. Gandhi, H. Gaus, K. 2018-12-05 doi:10.1101/487728 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ Tax4Fun2: a R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences ]]> https://biorxiv.org/content/10.1101/490037v1?rss=1 Wemheuer, F. Taylor, J. A. Daniel, R. Johnston, E. Meinicke, P. Thomas, T. Wemheuer, B. 2018-12-09 doi:10.1101/490037 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ A qualitative exploration of eyecare professional perspectives on Age-Related Macular Degeneration (AMD) care ]]> https://biorxiv.org/content/10.1101/490383v1?rss=1 Jalbert, I. Rahardjo, D. Yashadhana, A. Liew, G. Gopinath, B. 2018-12-07 doi:10.1101/490383 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Reading eye movements in traumatic brain injury ]]> https://biorxiv.org/content/10.1101/496752v1?rss=1 Reddy, A. V. C. Mani, R. Selvakumar, A. Husaindeen, J. R. 2018-12-14 doi:10.1101/496752 Cold Spring Harbor Laboratory Press 2018-12-14 <![CDATA[ International travelers and genomics uncover a ‘hidden’ Zika outbreak ]]> https://biorxiv.org/content/10.1101/496901v1?rss=1 Grubaugh, N. Saraf, S. Gangavarapu, K. Watts, A. Tan, A. L. Roidtman, R. Ladner, J. T. Oliveira, G. Matteson, N. L. Kraemer, M. U. Vogels, C. B. Hentoff, A. Bhatia, D. Stanek, D. Scott, B. Landis, V. Stryker, I. Cone, M. Kopp, E. Cannons, A. Heberlein-Larson, L. White, S. Gillis, L. Ricciardi, M. Kwai, J. Lichtenberger, P. Magnani, D. Watkins, D. Palacios, G. Hamer, D. H. GeoSentinel Surveillance Network, Gardner, L. Perkins, T. A. Baele, G. Khan, K. Morrison, A. Isern, S. Michael, S. F. Andersen, K. G. 2018-12-14 doi:10.1101/496901 Cold Spring Harbor Laboratory Press 2018-12-14 <![CDATA[ Accessory genome contributes to the virulence and resistance of the ocular isolate of Pseudomonas aeruginosa: A complete genome analysis ]]> https://biorxiv.org/content/10.1101/497974v1?rss=1 Subedi, D. Kohli, G. S. Vijay, A. K. Willcox, M. D. P. Rice, S. A. 2018-12-17 doi:10.1101/497974 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ The Landscape Of Circular RNA Expression In The Human Brain ]]> https://biorxiv.org/content/10.1101/500991v1?rss=1 Gokoolparsadh, A. Anwar, F. Voineagu, I. 2018-12-19 doi:10.1101/500991 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Opsin gene evolution in amphibious and terrestrial combtooth blennies (Blenniidae) ]]> https://biorxiv.org/content/10.1101/503516v1?rss=1 Cortesi, F. Cheney, K. M. Cooke, G. M. Ord, T. 2018-12-21 doi:10.1101/503516 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ Mutations close to the peptidoglycan-binding region of the stators of the bacterial flagellar motor influence phenamil resistance ]]> https://biorxiv.org/content/10.1101/507533v1?rss=1 Ishida, T. Ito, R. Matzke, N. J. Sowa, Y. Baker, M. A. 2018-12-31 doi:10.1101/507533 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Fluorescence Microscopy of Piezo1 in Droplet Hydrogel Bilayers ]]> https://biorxiv.org/content/10.1101/508176v1?rss=1 Jaggers, O. B. Ridone, P. Martinac, B. Baker, M. A. 2018-12-30 doi:10.1101/508176 Cold Spring Harbor Laboratory Press 2018-12-30 <![CDATA[ Impairments in contractility and cytoskeletal organisation cause nuclear defects in nemaline myopathy ]]> https://biorxiv.org/content/10.1101/518522v1?rss=1 Ross, J. A. Levy, Y. Kolb, J. S. Turmaine, M. Holt, M. Ripolone, M. Moggio, M. Fiorillo, C. Lindqvist, J. Figeac, N. Zammit, P. Jungbluth, H. Vissing, J. Witting, N. Granzier, H. Zanoteli, E. Hardeman, E. C. Wallgren-Pettersson, C. Ochala, J. 2019-01-14 doi:10.1101/518522 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ C-terminal HSP90 Inhibitors Block the HSP90:HIF-1a Interaction and Inhibit the Cellular Hypoxic Response ]]> https://biorxiv.org/content/10.1101/521989v1?rss=1 Kataria, N. Kerr, B. Zaiter, S. McAlpine, S. R. Cook, K. M. 2019-01-24 doi:10.1101/521989 Cold Spring Harbor Laboratory Press 2019-01-24 <![CDATA[ Microbial predictors of environmental perturbations in coral reef ecosystems ]]> https://biorxiv.org/content/10.1101/524173v1?rss=1 Glasl, B. Bourne, D. G. Frade, P. Thomas, T. Schaffelke, B. Webster, N. S. 2019-01-18 doi:10.1101/524173 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ Stoichiometric quantification of spatially dense assemblies with qPAINT ]]> https://biorxiv.org/content/10.1101/525345v1?rss=1 Baker, M. Nieves, D. J. Hilzenrat, G. Berengut, J. F. Gaus, K. Lee, L. K. 2019-01-21 doi:10.1101/525345 Cold Spring Harbor Laboratory Press 2019-01-21 <![CDATA[ Ecological niche differentiation in soil cyanobacterial communities across the globe ]]> https://biorxiv.org/content/10.1101/531145v1?rss=1 Cano-Diaz, C. Maestre, F. T. Eldridge, D. J. Singh, B. K. Bardgett, R. D. Fierer, N. Delgado-Baquerizo, M. 2019-01-26 doi:10.1101/531145 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Sample preparation protocol enabling nano-to-mesoscopic mapping of cellular connectomes and their habitats in human tissues and organs ]]> https://biorxiv.org/content/10.1101/533448v1?rss=1 Ngo, L. Nathanson, A. Garbowski, T. Knothe, U. Zeidler, D. Tate, M. L. K. 2019-01-29 doi:10.1101/533448 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Design and Synthesis of Pleated DNA Origami Nanotubes with Adjustable Diameters ]]> https://biorxiv.org/content/10.1101/534792v1?rss=1 Berengut, J. F. Ruan, J. Kawamoto, A. Lee, L. K. 2019-01-30 doi:10.1101/534792 Cold Spring Harbor Laboratory Press 2019-01-30 <![CDATA[ Mouse Norovirus infection arrests host cell translation uncoupled from the stress granule-PKR-eIF2α axis ]]> https://biorxiv.org/content/10.1101/536052v1?rss=1 Fritzlar, S. Aktepe, T. Chao, Y.-W. McAllaster, M. Wilen, C. White, P. Mackenzie, J. 2019-01-31 doi:10.1101/536052 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ A generic cell surface ligand system for studying cell-cell recognition ]]> https://biorxiv.org/content/10.1101/546846v1?rss=1 Denham, E. M. Barton, M. I. Black, S. M. Bridge, M. J. de Wet, B. Paterson, R. L. van der Merwe, P. A. Goyette, J. 2019-02-11 doi:10.1101/546846 Cold Spring Harbor Laboratory Press 2019-02-11 <![CDATA[ Work Flows for Cellular Epidemiology, From Conception to Translation ]]> https://biorxiv.org/content/10.1101/548412v1?rss=1 Nathanson, A. D. Ngo, L. Garbowski, T. Srikantha, A. Wojek, C. Zeidler, D. Knothe Tate, M. 2019-02-13 doi:10.1101/548412 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Invaders weather the weather: rapid adaptation to a novel environment occurs despite reduced genetic diversity ]]> https://biorxiv.org/content/10.1101/557868v1?rss=1 Selechnik, D. Richardson, M. F. Shine, R. DeVore, J. Ducatez, S. Rollins, L. A. 2019-02-22 doi:10.1101/557868 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ Extreme niche partitioning promotes a remarkably high diversity of soil microbiomes across eastern Antarctica. ]]> https://biorxiv.org/content/10.1101/559666v1?rss=1 Zhang, E. Thibaut, L. M. Terauds, A. Wong, S. van Dorst, J. Tanaka, M. M. Ferrari, B. C. 2019-02-24 doi:10.1101/559666 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Brain Aging in Major Depressive Disorder: Results from the ENIGMA Major Depressive Disorder working group ]]> https://biorxiv.org/content/10.1101/560623v1?rss=1 Han, L. K. Dinga, R. Hahn, T. Ching, C. Eyler, L. Aftanas, L. Aghajani, M. Aleman, A. Baune, B. Berger, K. Brak, I. Busatto Filho, G. Carballedo, A. Connolly, C. Couvy-Duchesne, B. Cullen, K. Dannlowski, U. Davey, C. Dima, D. Duran, F. Enneking, V. Filimonova, E. Frenzel, S. Frodl, T. Fu, C. Godlewska, B. Gotlib, I. Grabe, H. Groenewold, N. Grotegerd, D. Gruber, O. Hall, G. Harrison, B. Hatton, S. Hermesdorf, M. Hickie, I. Ho, T. Hosten, N. Jansen, A. Kahler, C. Kircher, T. Klimes-Dougan, B. Kramer, B. Krug, A. Lagopoulos, J. Leenings, R. MacMaster 2019-02-26 doi:10.1101/560623 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ No evidence for kin recognition in a passerine bird. ]]> https://biorxiv.org/content/10.1101/560870v1?rss=1 Lattore, M. Plaza, M. Nakagawa, S. Burke, T. Schroeder, J. 2019-02-25 doi:10.1101/560870 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Tactile sensory channels over-ruled by frequency decoding system that utilizes spike pattern regardless of receptor type ]]> https://biorxiv.org/content/10.1101/570929v1?rss=1 60 Hz), subserved by two distinct receptor types (Meissners and Pacinian corpuscle, respectively) which may engage different neural processing pathways or channels and fulfill quite different biological roles. In psychological and physiological literature those two systems have been labelled as Pacinian and non-Pacinian channels. However, we present evidence that low-frequency spike trains in Pacinian afferents can readily induce a vibratory percept with the same low frequency attributes as sinusoidal stimuli of the same frequency thus demonstrating a universal frequency decoding system. We achieved this using brief low-amplitude pulsatile mechanical stimuli to selectively activate Pacinian afferents. This indicates that spiking pattern, regardless of receptor type, determines vibrotactile frequency perception. This mechanism may underlie the constancy of vibrotactile frequency perception across different skin regions innervated by distinct afferent types. ]]> Birznieks, I. McIntyre, S. Nilsson, H. M. Nagi, S. S. Macefield, V. G. Mahns, D. A. Vickery, R. M. 2019-03-09 doi:10.1101/570929 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ Characterization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus ]]> https://biorxiv.org/content/10.1101/576488v1?rss=1 Wada, N. Ishimochi, M. Matsui, T. Pollock, F. J. Tang, S.-L. Ainsworth, T. D. Willis, B. L. Mano, N. Bourne, D. G. 2019-03-14 doi:10.1101/576488 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ The structure of Macrophage Expressed Gene-1, a phagolysosome immune effector that is activated upon acidification. ]]> https://biorxiv.org/content/10.1101/580712v1?rss=1 Pang, S. S. Bayly-Jones, C. Radjainia, M. Spicer, B. A. Law, R. H. P. Hodel, A. W. Ekkel, S. M. Conroy, P. J. Ramm, G. Venugopal, H. Bird, P. I. Hoogenboom, B. W. Voskoboinik, I. Gambin, Y. Sierecki, E. Dunstone, M. A. Whisstock, J. C. 2019-03-17 doi:10.1101/580712 Cold Spring Harbor Laboratory Press 2019-03-17 <![CDATA[ Modular actin nano-architecture enables podosome protrusion and mechanosensing ]]> https://biorxiv.org/content/10.1101/583492v1?rss=1 van den Dries, K. Nahidiazar, L. Slotman, J. A. Meddens, M. B. M. Pandzic, E. Joosten, B. Ansems, M. Schouwstra, J. Meijer, A. Steen, R. Wijers, M. Fransen, J. Houtsmuller, A. B. Wiseman, P. W. Jalink, K. Cambi, A. 2019-03-20 doi:10.1101/583492 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Immune and environment-driven gene expression during invasion: An eco-immunological application of RNA-Seq ]]> https://biorxiv.org/content/10.1101/583617v1?rss=1 Selechnik, D. Richardson, M. F. Shine, R. Brown, G. P. Rollins, L. A. 2019-03-21 doi:10.1101/583617 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Long-term iron deficiency and iron supplementation exacerbate acute DSS-induced colitis and are associated with significant dysbiosis ]]> https://biorxiv.org/content/10.1101/585174v1?rss=1 Mahalhal, A. Burkitt, M. D. Duckworth, C. A. Hold, G. L. Campbell, B. J. Pritchard, D. M. Probert, C. S. 2019-03-21 doi:10.1101/585174 Cold Spring Harbor Laboratory Press 2019-03-21 <![CDATA[ Rapidly increasing prevalence of overweight and obesity in older Ghanaian adults from 2007-2015: evidence from WHO-SAGE Waves 1 & 2 ]]> https://biorxiv.org/content/10.1101/591222v1?rss=1 Lartey, S. T. Magnussen, C. G. Si, L. Boateng, G. O. de Graaff, B. Biritwum, R. B. Minicuci, N. Kowal, P. Blizzard, L. Palmer, A. J. 2019-03-27 doi:10.1101/591222 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Inferring infectious disease phylodynamics with notification data ]]> https://biorxiv.org/content/10.1101/596700v1?rss=1 Duchene, S. Di Giallonardo, F. Holmes, E. C. Vaughan, T. 2019-04-08 doi:10.1101/596700 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ Ageing in house sparrows is insensitive to environmental effects ]]> https://biorxiv.org/content/10.1101/598284v1?rss=1 Simons, M. Winney, I. Girndt, A. Rees, M. Nakagawa, S. Schroeder, J. Burke, T. 2019-04-04 doi:10.1101/598284 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Mode of action of the antimicrobial peptide Mel4 is independent of Staphylococcus aureus cell membrane permeability ]]> https://biorxiv.org/content/10.1101/603712v1?rss=1 Yasir, M. Dutta, D. Willcox, M. D. P. 2019-04-09 doi:10.1101/603712 Cold Spring Harbor Laboratory Press 2019-04-09 <![CDATA[ tagPAINT: Stoichiometric and covalent labelling of protein tags for multiplexed and quantitative DNA-PAINT imaging ]]> https://biorxiv.org/content/10.1101/604462v1?rss=1 Nieves, D. J. Hilzenrat, G. Tran, J. Yang, Z. MacRae, H. H. Baker, M. A. B. Gooding, J. J. Gaus, K. 2019-04-10 doi:10.1101/604462 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ Disruption of membrane cholesterol organization impairs the concerted activity of PIEZO1 channel clusters ]]> https://biorxiv.org/content/10.1101/604488v1?rss=1 Ridone, P. Pandzic, E. Vassalli, M. Cox, C. D. Macmillan, A. Gottlieb, P. A. Martinac, B. 2019-04-11 doi:10.1101/604488 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Fluorescent biosensor for real-time interaction dynamics of host proteins with HIV-1 capsid tubes ]]> https://biorxiv.org/content/10.1101/619841v1?rss=1 Lau, D. Walsh, J. Peng, W. Shah, V. Turville, S. Jacques, D. Böcking, T. 2019-04-30 doi:10.1101/619841 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Meta-analysis reveals that the provision of multiple ecosystem services requires a diversity of land covers ]]> https://biorxiv.org/content/10.1101/621706v1?rss=1 Gómez-Creutzberg, C. Tylianakis, J. M. Lagisz, M. Nakagawa, S. Brockerhoff, E. G. 2019-04-29 doi:10.1101/621706 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Matryoshka RNA virus 1: a novel RNA virus associated with Plasmodium parasites in human malaria ]]> https://biorxiv.org/content/10.1101/624403v1?rss=1 Charon, J. Grigg, M. J. Eden, J.-S. Piera, K. A. William, T. Rose, K. Davenport, M. P. Anstey, N. M. Holmes, E. C. 2019-05-01 doi:10.1101/624403 Cold Spring Harbor Laboratory Press 2019-05-01 <![CDATA[ Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains ]]> https://biorxiv.org/content/10.1101/630475v1?rss=1 Sprague, D. Waters, S. A. Kirk, J. M. Wang, J. R. Samollow, P. B. Waters, P. D. Calabrese, J. M. 2019-05-07 doi:10.1101/630475 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Germline murine immunoglobulin IGHV genes in wild-derived and classical inbred strains: a comparison ]]> https://biorxiv.org/content/10.1101/631754v1?rss=1 Watson, C. T. Kos, J. T. Gibson, W. S. Busse, C. E. Newman, L. Deikus, G. Smith, M. L. Jackson, K. J. Colins, A. M. 2019-05-08 doi:10.1101/631754 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Patterned substrates modulate growth and dynamics of 3D cellular systems ]]> https://biorxiv.org/content/10.1101/632034v1?rss=1 Fanous, M. Li, Y. Kandel, M. Kilian, K. Popescu, G. 2019-05-08 doi:10.1101/632034 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Estimating MIC distributions and cutoffs through mixture models: an application to establish M. Tuberculosis resistance. ]]> https://biorxiv.org/content/10.1101/643429v1?rss=1 GRAZIAN, C. 2019-05-20 doi:10.1101/643429 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Local signatures of founding populations confound examination of adaptive divergence in invasive populations ]]> https://biorxiv.org/content/10.1101/643569v1?rss=1 Stuart, K. C. Cardilini, A. P. A. Cassey, P. Richardson, M. F. Sherwin, W. Rollins, L. A. Sherman, C. D. H. 2019-05-21 doi:10.1101/643569 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Costs and benefits of giant sperm and sperm storage organs in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/652248v1?rss=1 Zajitschek, S. R. K. Zajitschek, F. Josway, S. Shabeeb, R. Manier, M. 2019-05-29 doi:10.1101/652248 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Pharmacological enrichment of polygenic risk for precision medicine in complex disorders ]]> https://biorxiv.org/content/10.1101/655001v1?rss=1 Reay, W. R. Atkins, J. R. Carr, V. J. Green, M. J. Cairns, M. J. 2019-06-03 doi:10.1101/655001 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ SiaABCD - A threonine phosphorylation pathway that controls biofilm formation in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/674879v1?rss=1 Poh, W.-H. Lin, J. Colley, B. Müller, N. Goh, B. C. Schleheck, D. Marquardt, A. Liang, Y. Kjelleberg, S. Lescar, J. Rice, S. A. Klebensberger, J. 2019-06-19 doi:10.1101/674879 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Transcriptome Dynamics Reveals Progressive Transition from Effector to Memory in CD4+ T cells. ]]> https://biorxiv.org/content/10.1101/675967v1?rss=1 Soon, M. S. F. Lee, H. J. Engel, J. A. Straube, J. Thomas, B. S. Clarke, L. S. Laohamonthonkul, P. Pernold, C. P. S. Haldar, R. N. Williams, C. G. Lansink, L. I. M. Koufariotis, R. Lakis, V. Wood, S. Chen, X. James, K. R. Lönnberg, T. Lane, S. W. Davenport, M. P. Khoury, D. S. Svensson, V. Teichmann, S. A. Haque, A. 2019-06-19 doi:10.1101/675967 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Altered White Matter Microstructural Organization in Post-Traumatic Stress Disorder across 3,049 Adults: Results from the PGC-ENIGMA PTSD Consortium ]]> https://biorxiv.org/content/10.1101/677153v1?rss=1 Dennis, E. Disner, S. E. Fani, N. Salminen, L. E. Logue, M. Clarke-Rubright, E. K. Haswell, C. C. Averill, C. Baugh, L. A. Bomyea, J. Bruce, S. E. Cha, J. Choi, K. Davenport, N. D. Densmore, M. du Plessis, S. Forster, G. L. Frijling, J. L. Gonenc, A. Gruber, S. Grupe, D. W. Guenette, J. P. Hayes, J. Hofmann, D. Ipser, J. Jovanovic, T. Kelly, S. Kennis, M. Kinzel, P. Koch, S. B. Koerte, I. Koopowitz, S. Korgaonkar, M. Krystal, J. Lebois, L. A. Li, G. Magnotta, V. A. Manthey, A. May, G. J. Menefee, D. S. Nawijn, L. Nelson, S. M. Neufeld, R. W. Nitschke, 2019-06-20 doi:10.1101/677153 Cold Spring Harbor Laboratory Press 2019-06-20 <![CDATA[ Common genetic variation indicates separate etiologies for periventricular and deep white matter hyperintensities ]]> https://biorxiv.org/content/10.1101/683367v1?rss=1 Armstrong, N. J. Mather, K. A. Sargurupremraj, M. Knol, M. J. Malik, R. Satizabal, C. L. Yanek, L. R. Wen, W. Gudnason, V. Dueker, N. D. Elliott, L. T. Hofer, E. Jahanshad, N. Li, S. Logue, M. A. Luciano, M. Scholz, M. Smith, A. V. Trompet, S. S. Vojinovic, D. Xia, R. Alfaro-Almagro, F. Ames, D. Amin, N. Amouyel, P. Beiser, A. S. Brodaty, H. Deary, I. J. Fennema-Notestine, C. Gampawar, P. G. Gottesman, R. F. Griffanti, L. Jack, C. R. Jenkinson, M. Jiang, J. Kral, B. G. Kwok, J. B. Lampe, L. Liewald, D. C. Maillard, P. Marchini, J. Bastin, M. E. Mazoyer 2019-06-27 doi:10.1101/683367 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Neurophysiological changes associated with combined transcranial direct current stimulation and cognitive emotional training for treatment-resistant depression ]]> https://biorxiv.org/content/10.1101/688317v1?rss=1 Nikolin, S. Martin, D. Loo, C. Iacoviello, B. Boonstra, T. 2019-07-05 doi:10.1101/688317 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ Hepatitis E as a cause of adult hospitalization in Bangladesh: Results from an acute jaundice surveillance study in six tertiary hospitals, 2014-2017 ]]> https://biorxiv.org/content/10.1101/688721v1?rss=1 Paul, R. Nazneen, A. Banik, K. C. Sumon, S. A. Paul, K. K. Akram, A. Uzzaman, M. S. Iqbal, T. Tejada-Strop, A. Kamili, S. Luby, S. P. Gidding, H. F. Hayen, A. Gurley, E. S. 2019-07-02 doi:10.1101/688721 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Drone-based effective counting and ageing of hippopotamus (Hippopotamus amphibius) in the Okavango Delta in Botswana ]]> https://biorxiv.org/content/10.1101/689059v1?rss=1 Inman, V. Kingsford, R. T. Leggett, K. E. Chase, M. J. 2019-07-01 doi:10.1101/689059 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ The fate of carbon in a mature forest under carbon dioxide enrichment ]]> https://biorxiv.org/content/10.1101/696898v1?rss=1 Jiang, M. Medlyn, B. E. Drake, J. E. Duursma, R. A. Anderson, I. C. Barton, C. V. M. Boer, M. M. Carrillo, Y. Castaneda-Gomez, L. Collins, L. Crous, K. Y. De Kauwe, M. G. Emmerson, K. M. Facey, S. L. Gherlenda, A. N. Gimeno, T. E. Hasegawa, S. Johnson, S. N. Macdonald, C. A. Mahmud, K. Moore, B. D. Nazaries, L. Nielsen, U. N. Noh, N. J. Ochoa-Hueso, R. Pathare, V. S. Pendall, E. Pineiro, J. Powell, J. R. Power, S. A. Reich, P. B. Renchon, A. A. Riegler, M. Rymer, P. Salomon, R. L. Singh, B. K. Smith, B. Tjoelker, M. G. Walker, J. K. M. Wujeska-Klause, A. 2019-07-11 doi:10.1101/696898 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ SiZer Map to investigate significant features of body-weight profile changes in HIV infected patients in the IeDEA Collaboration ]]> https://biorxiv.org/content/10.1101/699546v1?rss=1 Harezlak, J. Wools-Kaloustian, K. Sarwat, S. Balestre, E. Schomaker, M. Law, M. Kiertiburanakul, S. Fox, M. Huis in t Veld, D. Musick, B. S. Yiannoutsos, C. T. International Epidemiology Databases to Evaluate A, 2019-07-12 doi:10.1101/699546 Cold Spring Harbor Laboratory Press 2019-07-12 <![CDATA[ Functional harmonics reveal multi-dimensional basis functions underlying cortical organization ]]> https://biorxiv.org/content/10.1101/699678v1?rss=1 Glomb, K. Kringelbach, M. Deco, G. Hagmann, P. Pearson, J. Atasoy, S. 2019-07-11 doi:10.1101/699678 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Resolving genetic linkage reveals patterns of selection in HIV-1 evolution ]]> https://biorxiv.org/content/10.1101/711861v1?rss=1 Sohail, M. S. Louie, R. H. Y. McKay, M. R. Barton, J. P. 2019-07-23 doi:10.1101/711861 Cold Spring Harbor Laboratory Press 2019-07-23 <![CDATA[ Genomic Influences on Self-Reported Childhood Maltreatment ]]> https://biorxiv.org/content/10.1101/717314v1?rss=1 Dalvie, S. Maihofer, A. X. Coleman, J. R. Bradley, B. Breen, G. Brick, L. A. Chen, C.-Y. Choi, K. W. Duncan, L. E. Guffanti, G. Haas, M. Harnal, S. Liberzon, I. Nugent, N. R. Provost, A. C. Ressler, K. J. Torres, K. Amstadter, A. B. Austin, S. B. Baker, D. G. Bolger, E. A. Bryant, R. A. Calabrese, J. R. Delahanty, D. L. Farrer, L. A. Feeny, N. C. Flory, J. D. Forbes, D. Galea, S. Gautam, A. Gelernter, J. Hammamieh, R. Jett, M. Junglen, A. G. Kaufman, M. L. Kessler, R. C. Khan, A. Kranzler, H. R. Lebois, L. A. Marmar, C. Mavissakalian, M. R. McFarlane, A 2019-07-28 doi:10.1101/717314 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ Smaller limbic structures are associated with greater immunosuppression in over 1000 HIV-infected adults across five continents: Findings from the ENIGMA-HIV Working Group ]]> https://biorxiv.org/content/10.1101/724583v1?rss=1 Nir, T. M. Fouche, J.-P. Ananworanich, J. Ances, B. M. Boban, J. Brew, B. J. Chang, L. Chaganti, J. R. Ching, C. R. Cysique, L. A. Ernst, T. Faskowitz, J. Gupta, V. Harezlak, J. Heaps-Woodruff, J. M. Hinkin, C. H. Hoare, J. Joska, J. A. Kallianpur, K. J. Kuhn, T. Lam, H. Y. Law, M. Lebrun-Frenay, C. Levine, A. J. Mondot, L. Nakamoto, B. K. Navia, B. A. Pennec, X. Porges, E. C. Shikuma, C. M. Thames, A. D. Valcour, V. Vassallo, M. Woods, A. J. Thompson, P. M. Cohen, R. A. Paul, R. Stein, D. J. Jahanshad, N. 2019-08-05 doi:10.1101/724583 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ The critical role of mental imagery in human emotion: insights from Aphantasia. ]]> https://biorxiv.org/content/10.1101/726844v1?rss=1 Wicken, M. Keogh, R. Pearson, J. 2019-08-06 doi:10.1101/726844 Cold Spring Harbor Laboratory Press 2019-08-06 <![CDATA[ Genomic insights into the Archaea inhabiting an Australian radioactive legacy site ]]> https://biorxiv.org/content/10.1101/728089v1?rss=1 Vazquez-Campos, X. Kinsela, A. Bligh, M. Payne, T. Wilkins, M. Waite, T. D. 2019-08-13 doi:10.1101/728089 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ PGRMC1 phosphorylation status and cell plasticity 1: glucose metabolism, mitochondria, and mouse xenograft tumorigenesis ]]> https://biorxiv.org/content/10.1101/737718v1?rss=1 Thejer, B. M. Adhikary, P. P. Kaur, A. Teakel, S. L. Van Oosterum, A. Seth, I. Pajic, M. Hannan, K. M. Pavy, M. Poh, P. Jazayeri, J. A. Zaw, T. Pascovici, D. Ludescher, M. Pawlak, M. Cassano, J. C. Turnbull, L. Jazayeri, M. James, A. C. Coorey, C. P. Roberts, T. L. Kinder, S. J. Hannan, R. D. Patrick, E. Molloy, M. P. New, E. J. Fehm, T. N. Neubauer, H. Goldys, E. M. Weston, L. A. Cahill, M. A. 2019-08-24 doi:10.1101/737718 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ PGRMC1 phosphorylation status and cell plasticity 2: genomic integrity and CpG methylation ]]> https://biorxiv.org/content/10.1101/737783v1?rss=1 Thejer, B. M. Adhikary, P. P. Teakel, S. L. Fang, J. Weston, P. A. Gurusinghe, S. Anwer, A. G. Gosnell, M. Jazayeri, J. A. Ludescher, M. Gray, L.-A. Pawlak, M. Wallace, R. H. Pant, S. D. Wong, M. Fischer, T. New, E. J. Fehm, T. N. Neubauer, H. Goldys, E. M. Quinn, J. C. Weston, L. A. Cahill, M. A. 2019-08-23 doi:10.1101/737783 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Hippocampal subfield volumes are uniquely affected in PTSD and depression: International analysis of 31 cohorts from the PGC-ENIGMA PTSD Working Group ]]> https://biorxiv.org/content/10.1101/739094v1?rss=1 Salminen, L. E. Sämann, P. G. Zheng, Y. Dennis, E. L. Clarke, E. K. Jahanshad, N. Iglesias, J. E. Whelan, C. D. Bruce, S. E. Hayes, J. P. Seedat, S. Averill, C. L. Baugh, L. A. Bomyea, J. Bright, J. Buckle, C. J. Choi, K. Davenport, N. D. Davidson, R. J. Densmore, M. Disner, S. G. du Plessis, S. Elman, J. A. Fani, N. Forster, G. L. Franz, C. E. Frijling, J. L. Gonenc, A. Gruber, S. A. Grupe, D. W. Guenette, J. P. Haswell, C. C. Hofmann, D. Hollifield, M. Hosseini, B. Hudson, A. R. Ipser, J. Jovanovic, T. Kennedy-Krage, A. Kennis, M. King, A. Kinzel, P. 2019-08-21 doi:10.1101/739094 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Shared Genetic Risk between Eating Disorder- and Substance-Use-Related Phenotypes: Evidence from Genome-Wide Association Studies ]]> https://biorxiv.org/content/10.1101/741512v1?rss=1 Munn-Chernoff, M. Johnson, E. C. Chou, Y.-L. Coleman, J. R. Thornton, L. M. Walters, R. K. Yilmaz, Z. Baker, J. Hubel, C. Gordon, S. Medland, S. Watson, H. Gaspar, H. A. Bryois, J. Hinney, A. Leppa, V. Mattheisen, M. Ripke, S. Yao, S. Giusti-Rodriguez, P. Hanscombe, K. B. Adan, R. Alredsson, L. Ando, T. Andreassen, O. A. Berrettini, W. Boehm, I. Boni, C. Boraska Perica, V. Buehren, K. Burghardt, R. Cassina, M. Cichon, S. Clementi, M. Cone, R. Courtet, P. Crow, S. Crowley, J. J. Danner, U. Davis, O. de Zwaan, M. Dedoussis, G. Degortes, D. DeSocio, J. 2019-08-23 doi:10.1101/741512 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ The effect of blue-blocking lenses on photostress recovery times for low and high contrast chromatic and achromatic stimuli ]]> https://biorxiv.org/content/10.1101/745000v1?rss=1 Alzahrani, H. S. Khuu, S. K. Ali, A. Roy, M. 2019-08-22 doi:10.1101/745000 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Novel Quorum Sensing Activity in East Antarctic Soil Bacteria ]]> https://biorxiv.org/content/10.1101/749861v1?rss=1 Wong, S. Y. Charlesworth, J. C. Benaud, N. Burns, B. P. Ferrari, B. C. 2019-08-29 doi:10.1101/749861 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis ]]> https://biorxiv.org/content/10.1101/756122v1?rss=1 Gamaarachchi, H. Lam, C. W. Jayatilaka, G. Samarakoon, H. Simpson, J. T. Smith, M. A. Parameswaran, S. 2019-09-05 doi:10.1101/756122 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Cross-disorder GWAS meta-analysis for Attention Deficit/Hyperactivity Disorder, Autism Spectrum Disorder, Obsessive Compulsive Disorder, and Tourette Syndrome ]]> https://biorxiv.org/content/10.1101/770222v1?rss=1 0.9). Gene-based GWAS meta-analysis across ADHD, ASD, OCD, and TS identified 21 genes significantly associated under Bonferroni correction. Out of those, 15 could not be identified as significantly associated based on the individual disorder GWAS dataset, indicating increased power in the cross-disorder comparisons. Cross-disorder tissue-specificity analysis implicates the Hypothalamus-Pituitary-Adrenal axis (stress response) as possibly underlying shared pathophysiology across ADHD, ASD, OCD, and TS. Our work highlights genetic variants and genes that may contribute to overlapping neurobiology across the four studied disorders and highlights the value of re-defining the framework for the study across this spectrum of highly comorbid disorders, by using transdiagnostic approaches. ]]> Yang, Z. Wu, H. Lee, P. H. Tsetsos, F. Davis, L. K. Yu, D. Lee, S. H. Dalsgaard, S. D. Haavik, J. Barta, C. Zayats, T. Eapen, V. Wray, N. R. Devlin, B. Daly, M. Neale, B. Borglum, A. Crowley, J. J. Scharf, J. Mathews, C. A. Faraone, S. V. Franke, B. Mattheisen, M. Smoller, J. W. Paschou, P. 2019-09-16 doi:10.1101/770222 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ D1 and D2 systems converge in the striatum to update goal-directed learning ]]> https://biorxiv.org/content/10.1101/780346v1?rss=1 Matamales, M. McGovern, A. E. Mi, J. D. Mazzone, S. B. Balleine, B. W. Bertran-Gonzalez, J. 2019-09-26 doi:10.1101/780346 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Goal-directed action transiently depends on action space ]]> https://biorxiv.org/content/10.1101/783308v1?rss=1 Balleine, B. W. Bradfield, L. A. Boldt, S. Leung, B. K. 2019-09-27 doi:10.1101/783308 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ DNA Break-Induced Epigenetic Drift as a Cause of Mammalian Aging ]]> https://biorxiv.org/content/10.1101/808659v1?rss=1 Hayano, M. Yang, J.-H. Bonkowski, M. S. Amorim, J. A. Ross, J. M. Coppotelli, G. Griffin, P. T. Chew, Y. C. Guo, W. Yang, X. Vera, D. L. Salfati, E. L. Das, A. Thakur, S. Kane, A. E. Mitchell, S. J. Mohri, Y. Nishimura, E. K. Schaevitz, L. Garg, N. Balta, A.-M. Rego, M. A. Gregory-Ksander, M. Jakobs, T. C. Zhong, L. Wakimoto, H. Mostoslavsky, R. Wagers, A. J. Tsubota, K. Bonasera, S. J. Palmeira, C. M. Seidman, J. G. Seidman, C. E. Wolf, N. S. Kreiling, J. A. Sedivy, J. M. Murphy, G. F. Oberdoerffer, P. Ksander, B. R. Rajman, L. A. Sinclair, D. A. 2019-10-21 doi:10.1101/808659 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ Punishment insensitivity emerges from impaired contingency detection, not aversion insensitivity or reward dominance ]]> https://biorxiv.org/content/10.1101/808873v1?rss=1 Jean-Richard-dit-Bressel, P. Ma, C. Bradfield, L. Killcross, S. McNally, G. 2019-10-17 doi:10.1101/808873 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ northstar: leveraging cell atlases to identify healthy and neoplastic cells in transcriptomes from human tumors ]]> https://biorxiv.org/content/10.1101/820928v1?rss=1 Zanini, F. Berghuis, B. A. Jones, R. C. Nicolis di Robilant, B. Nong, R. Y. Norton, J. Clarke, M. F. Quake, S. R. 2019-10-27 doi:10.1101/820928 Cold Spring Harbor Laboratory Press 2019-10-27 <![CDATA[ Revisiting Australian Ectocarpus subulatus (Phaeophyceae) from the Hopkins River: distribution, abiotic environment, and associated microbiota ]]> https://biorxiv.org/content/10.1101/821579v1?rss=1 Dittami, S. M. Peters, A. F. West, J. Cariou, T. KleinJan, H. Burgunter-Delamare, B. Prechoux, A. Egan, S. Boyen, C. 2019-10-30 doi:10.1101/821579 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures ]]> https://biorxiv.org/content/10.1101/830968v1?rss=1 Begik, O. Lucas, M. C. Ramirez, J. M. Liu, H. Mattick, J. S. Novoa, E. 2019-11-05 doi:10.1101/830968 Cold Spring Harbor Laboratory Press 2019-11-05 <![CDATA[ Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation ]]> https://biorxiv.org/content/10.1101/831149v1?rss=1 Tillu, V. Rae, J. Gao, Y. Ariotti, N. Floetenmeyer, M. Kovtun, O. McMahon, K.-A. Parton, R. G. Collins, B. M. 2019-11-12 doi:10.1101/831149 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Detection of somatic structural variants from short-read next-generation sequencing data ]]> https://biorxiv.org/content/10.1101/840751v1?rss=1 Gong, T. Hayes, V. M. Chan, E. K. 2019-11-13 doi:10.1101/840751 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Defined microbiota transplant restores Th17/RORtγ+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas ]]> https://biorxiv.org/content/10.1101/844662v1?rss=1 Britton, G. J. Contijoch, E. J. Spindler, M. P. Aggarwala, V. Bongers, G. San Mateo, L. Baltus, A. Das, A. Gevers, D. Borody, T. J. Kaakoush, N. O. Kamm, M. A. Mitchell, H. Paramsothy, S. Clemente, J. C. Colombel, J.-F. Dubinsky, M. C. Grinspan, A. Faith, J. J. 2019-11-16 doi:10.1101/844662 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Sexual conflict explains diverse patterns of transgenerational plasticity ]]> https://biorxiv.org/content/10.1101/846287v1?rss=1 Burke, N. W. Bonduriansky, R. Nakagawa, S. 2019-11-20 doi:10.1101/846287 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ A natural antisense to brain-derived neurotrophic factor impairs extinction of drug seeking ]]> https://biorxiv.org/content/10.1101/851949v1?rss=1 Youngson, N. A. Castino, M. R. Stuart, A. Kershaw, K. A. Holmes, N. M. Waters, P. D. Morris, K. V. Clemens, K. J. 2019-11-23 doi:10.1101/851949 Cold Spring Harbor Laboratory Press 2019-11-23 <![CDATA[ Geometric regulation of histone state directs melanoma reprogramming ]]> https://biorxiv.org/content/10.1101/872226v1?rss=1 Lee, J. Molley, T. G. Seward, C. H. Abdeen, A. A. Zhang, H. Wang, X. Gandhi, H. Yang, J.-L. Gaus, K. Kilian, K. A. 2019-12-11 doi:10.1101/872226 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Melanotransferrin Functions as a Pro-Oncogenic WNT Agonist: A Yin-Yang Relationship in Melanoma with the WNT Antagonist and Metastasis Suppressor, NDRG1 ]]> https://biorxiv.org/content/10.1101/2023.02.27.530353v1?rss=1 Richardson, D. R. Paluncic, J. Gholam Azad, M. Lanbe, D. Skoda, J. Park, K. Chiang, S. Bae, D.-H. Scolyer, R. Afroz, R. Babu, G. Wilmott, J. Loh, K. Jansson, P. Dharmasivam, M. Huang, M. Zhao, X. Kovacevic, Z. 2023-03-03 doi:10.1101/2023.02.27.530353 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Replisome loading reduces chromatin motion independent of DNA synthesis ]]> https://biorxiv.org/content/10.1101/2023.03.07.531331v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@ed9743org.highwire.dtl.DTLVardef@65c9d4org.highwire.dtl.DTLVardef@a583a7org.highwire.dtl.DTLVardef@6681b1_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Direct and sequence unbiased labeling of DNA genome-wide - DNA labeled chromatin is more mobile in G1/G2 relative to the S-phase - Restriction of chromatin motion occurs proximal to sites of DNA replication - Loading of replisomes, even in the absence of processive DNA synthesis, restricts chromatin motion ]]> Pabba, M. K. Ritter, C. Chagin, V. O. Stear, J. H. Loerke, D. Kolobynina, K. Prorok, P. Schmid, A. K. Leonhardt, H. Rohr, K. Cardoso, M. C. 2023-03-07 doi:10.1101/2023.03.07.531331 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ Mitochondrial electron transport chain, ceramide and Coenzyme Q are linked in a pathway that drives insulin resistance in skeletal muscle ]]> https://biorxiv.org/content/10.1101/2023.03.10.532020v1?rss=1 Vegas, A. D. Madsen, S. Cooke, K. C. Carroll, L. Khor, J. X. Y. Turner, N. Lim, X. Y. Astore, M. A. Morris, J. Don, A. S. Garfield, A. Zarini, S. Zemski Berry, K. A. Ryan, A. P. Bergman, B. C. Brozinick, J. T. James, D. E. Burchfield, J. G. 2023-03-12 doi:10.1101/2023.03.10.532020 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Behavioral and neuroimaging correlates of attentional biases to angry faces in individuals in remission from depression: a population-derived study ]]> https://biorxiv.org/content/10.1101/2023.03.13.532400v1?rss=1 Nagrodzki, J. Passamonti, L. Schweizer, S. Stretton, J. Knights, E. Henson, R. N. Cam-CAN, Wolpe, N. 2023-03-14 doi:10.1101/2023.03.13.532400 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ Movement trajectories as a window into the dynamics of emerging neural representations. ]]> https://biorxiv.org/content/10.1101/2023.03.15.532848v1?rss=1 Koenig-Robert, R. Quek, G. Grootswagers, T. Varlet, M. 2023-03-16 doi:10.1101/2023.03.15.532848 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Karyopherin mimicry explains how the HIV capsid penetrates nuclear pores ]]> https://biorxiv.org/content/10.1101/2023.03.23.534032v1?rss=1 Dickson, C. F. Hertel, S. Ruan, J. Ariotti, N. Tuckwell, A. Li, N. Al-Izzi, S. Sierecki, E. Gambin, Y. Morris, R. G. Towers, G. J. Boecking, T. Jacques, D. A. 2023-03-24 doi:10.1101/2023.03.23.534032 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Learning transcriptional and regulatory dynamics driving cancer cell plasticity using neural ODE-based optimal transport ]]> https://biorxiv.org/content/10.1101/2023.03.28.534644v1?rss=1 Tong, A. Kuchroo, M. Gupta, S. Venkat, A. Perez San Juan, B. Rangel, L. Zhu, B. Lock, J. G. Chaffer, C. Krishnaswamy, S. 2023-03-29 doi:10.1101/2023.03.28.534644 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ High fat diet allows food-predictive stimuli to energize action performance in the absence of hunger, without distorting insulin signaling on accumbal cholinergic interneurons. ]]> https://biorxiv.org/content/10.1101/2023.03.29.534845v1?rss=1 Gladding, J. M. Lingawi, N. W. Leung, B. Kendig, M. D. Chieng, B. C. Laurent, V. 2023-03-31 doi:10.1101/2023.03.29.534845 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ Cell Type-Specific Regulation by a Heptad of Transcription Factors in Human Hematopoietic Stem and Progenitor Cells ]]> https://biorxiv.org/content/10.1101/2023.04.18.537282v1?rss=1 Subramanian, S. Thoms, J. Huang, Y. Cornejo, P. Koch, F. C. Jacquelin, S. Shen, S. Song, E. Joshi, S. Brownlee, C. Woll, P. S. Fajardo, D. C. Beck, D. Curtis, D. J. Yehson, K. Antonenas, V. O'Brien, T. Trickett, A. Powell, J. A. Lewis, I. D. Pitson, S. M. Gandhi, M. K. Lane, S. W. Vafaee, F. Wong, E. Gottgens, B. Rokny, H. A. Wong, J. W. H. Pimanda, J. E. 2023-04-18 doi:10.1101/2023.04.18.537282 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Norovirus NS3 protein induces apoptosis through translation repression and dysregulation of BCL-2 pro-survival proteins ]]> https://biorxiv.org/content/10.1101/2023.04.23.537759v1?rss=1 Aktepe, T. Deerain, J. Fritzlar, S. Hyde, J. L. Pearson, J. White, P. Mackenzie, J. M. 2023-04-24 doi:10.1101/2023.04.23.537759 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ The delayed bloodstream clearance of Plasmodium falciparum parasites after M5717 treatment is attributable to the inability to modify their red blood cell hosts. ]]> https://biorxiv.org/content/10.1101/2023.04.24.538013v1?rss=1 Schneider, M. P. Looker, O. Rebelo, M. Khoury, D. S. Dixon, M. W. Oeuvray, C. Crabb, B. S. McCarthy, J. Gilson, P. R. 2023-04-24 doi:10.1101/2023.04.24.538013 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Dysregulated expression of Hoxa1 isoforms in hematopoietic stem and progenitor cells causes myelodysplastic syndromes. ]]> https://biorxiv.org/content/10.1101/2023.04.24.538176v1?rss=1 Tan, S. Y. Joseph, C. Chalk, A. Hendy, J. Fabb, S. Schleibs, K. Lee, S. Tjin, G. Grace, C. Madugalle, V. Smeets, M. F. Maluenda, A. Rice, K. Baker, E. Nandurkar, H. Slape, C. Parker, M. Unnikrishnan, A. Mufti, G. Tobiasson, M. Hellstrom-Lindberg, E. Pimanda, J. Gudas, L. Holien, J. Walkley, C. Wall, M. Purton, L. 2023-04-24 doi:10.1101/2023.04.24.538176 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Genomic epidemiology and multilevel genome typing of Bordetella pertussis ]]> https://biorxiv.org/content/10.1101/2023.04.26.538362v1?rss=1 Payne, M. Xu, Z. Hu, D. Kaur, S. Octavia, S. Sintchenko, V. Lan, R. 2023-04-26 doi:10.1101/2023.04.26.538362 Cold Spring Harbor Laboratory Press 2023-04-26 <![CDATA[ An operational methodology to identify Critical Ecosystem Areas to help nations achieve the Kunming-Montreal Global Biodiversity Framework ]]> https://biorxiv.org/content/10.1101/2023.05.03.539215v1?rss=1 Venegas Li, R. Grantham, H. Rainey, H. Diment, A. Tizard, R. Watson, J. E. 2023-05-04 doi:10.1101/2023.05.03.539215 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters ]]> https://biorxiv.org/content/10.1101/2023.05.09.539953v1?rss=1 Gamaarachchi, H. Ferguson, J. M. Samarakoon, H. Liyanage, K. Deveson, I. W. 2023-05-10 doi:10.1101/2023.05.09.539953 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ DDHD2 interacts with STXBP1 to mediate long-term memory via the generation of myristic acid ]]> https://biorxiv.org/content/10.1101/2023.05.11.540316v1?rss=1 Akefe, I. O. Matthews, B. Saber, S. H. Venkatesh, B. G. Gormal, R. Blackmore, D. G. Sierecki, E. Gambin, Y. Bertran-Gonzalez, J. Michaels, A. A. Xue, M. Cravatt, B. F. Joensuu, M. Wallis, T. Meunier, F. A. 2023-05-11 doi:10.1101/2023.05.11.540316 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Model Parameter identification using 2D vs 3D experimental data: a comparative analysis ]]> https://biorxiv.org/content/10.1101/2023.05.17.541071v1?rss=1 Cortesi, M. Liu, D. Yee, C. Marsh, D. J. Ford, C. E. 2023-05-18 doi:10.1101/2023.05.17.541071 Cold Spring Harbor Laboratory Press 2023-05-18 <![CDATA[ The 3'UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions ]]> https://biorxiv.org/content/10.1101/2023.05.16.541063v1?rss=1 Mediati, D. G. Dan, W. Lalaouna, D. Dinh, H. Pokhrel, A. Stinear, T. P. Cain, A. Tree, J. J. 2023-05-19 doi:10.1101/2023.05.16.541063 Cold Spring Harbor Laboratory Press 2023-05-19 <![CDATA[ Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species ]]> https://biorxiv.org/content/10.1101/2023.05.24.542066v1?rss=1 Ross, S. E. Vazquez-Marin, J. Gert, K. R. B. Gonzalez-Rajal, A. Dinger, M. E. Pauli, A. Martinez-Morales, J. R. Bogdanovic, O. 2023-05-24 doi:10.1101/2023.05.24.542066 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Extensive DNA methylome rearrangement during early lamprey embryogenesis ]]> https://biorxiv.org/content/10.1101/2023.05.25.542242v1?rss=1 30% of the embryonic genome and is predominantly associated with partially methylated domains (PMDs). We further demonstrate that sequences eliminated during programmed genome rearrangement (PGR), a hallmark of lamprey embryogenesis, are hypermethylated in sperm prior to the onset of PGR. Our study thus unveils important insights into the evolutionary origins of vertebrate 5mC reprogramming, and how this process might participate in diverse developmental strategies. ]]> Angeloni, A. Fissette, S. Kaya, D. Hammond, J. M. Gamaarachchi, H. Deveson, I. W. Klose, R. J. Li, W. Zhang, X. Bogdanovic, O. 2023-05-25 doi:10.1101/2023.05.25.542242 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping ]]> https://biorxiv.org/content/10.1101/2023.05.30.542681v1?rss=1 Liyanage, K. Samarakoon, H. Parameswaran, S. Gamaarachchi, H. 2023-06-02 doi:10.1101/2023.05.30.542681 Cold Spring Harbor Laboratory Press 2023-06-02 <![CDATA[ A novel motoneuron-driven computational muscle model with motor unit resolution for subject-specific simulations of human voluntary muscle contraction ]]> https://biorxiv.org/content/10.1101/2023.06.03.543552v1?rss=1 Caillet, A. H. Phillips, A. T. Farina, D. Modenese, L. 2023-06-06 doi:10.1101/2023.06.03.543552 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Peripheral direct current for suppression of physiologically evoked nociceptive responses at the spinal cord ]]> https://biorxiv.org/content/10.1101/2023.06.07.544048v1?rss=1 Su, T. F. Hamilton, J. D. Guo, Y. Potas, J. R. Shivdasani, M. N. Moalem-Taylor, G. Fridman, G. Y. Aplin, F. P. 2023-06-11 doi:10.1101/2023.06.07.544048 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ The AusTraits Plant Dictionary ]]> https://biorxiv.org/content/10.1101/2023.06.16.545047v1?rss=1 Wenk, E. H. Sauquet, H. Gallagher, R. V. Brownlee, R. Boettiger, C. Coleman, D. Yang, S. Auld, T. Barrett, R. L. Brodribb, T. Choat, B. Dun, L. Ellsworth, D. Gosper, C. Guja, L. Jordan, G. J. Breton, T. Leigh, A. Irving, P. Medlyn, B. Nolan, R. Ooi, M. Sommerville, K. D. Vesk, P. White, M. Wright, I. J. Falster, D. S. 2023-06-18 doi:10.1101/2023.06.16.545047 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Infection by the lungworm Rhabdias pseudosphaerocephala affects the expression of immune-related microRNAs by its co-evolved host, the cane toad Rhinella marina. ]]> https://biorxiv.org/content/10.1101/2023.06.19.545515v1?rss=1 Chan, T. C. L. Yagound, B. Brown, G. P. Eyck, H. J. F. Shine, R. Rollins, L. A. 2023-06-22 doi:10.1101/2023.06.19.545515 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ The retinal RNA editome is concentrated in photoreceptor-specific genes and genetically linked to vision loss ]]> https://biorxiv.org/content/10.1101/2023.06.22.543349v1?rss=1 500 donor retinae and identified [~]153,000 high-confidence RNA editing sites. Some 80% of editing sites occurred within protein-coding RNA, with the majority in intronic Alu repeats, and 3 UTR sequence. Novel retina-specific sites were concentrated in genes related to photoreceptor function and which cause retinitis pigmentosa, most notably in PDE6A. Exonic, protein recoding sites were enriched in zinc-finger domains. AMD subjects exhibit relatively few differences in RNA editing compared to controls, consistent with limited gene expression differences. We identified [~]10,000 editing QTLs. The genetic architecture of editing in the retina resembles the brain, whereas editing and expression QTLs in the retina show modest genetic overlap. We report colocalization between edQTLs and retinal disease GWAS peaks for age-related macular degeneration, glaucoma and macular telangiectasia. These findings provide new insights into epi-transcriptomic regulation of genes critical for vision, and elaborate putative genetic disease driver mechanisms that appear to be independent of changes in gene expression. ]]> Ansell, B. R. E. Bonelli, R. Thomas, S. N. Manda, A. Ratnapriya, R. Pinelli, M. Swaroop, A. diBernardo, D. Banfi, S. Bahlo, M. 2023-06-24 doi:10.1101/2023.06.22.543349 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ The speed and phase of locomotion dictate saccade probability and simultaneous low-frequency power spectra ]]> https://biorxiv.org/content/10.1101/2023.06.22.546202v1?rss=1 Davidson, M. J. Barnes, L. Alais, D. J. 2023-06-26 doi:10.1101/2023.06.22.546202 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Revisiting the role of mean annual precipitation in shaping functional trait distributions at a continental scale ]]> https://biorxiv.org/content/10.1101/2023.06.29.546983v1?rss=1 Towers, I. R. Vesk, P. A. Wenk, E. Gallagher, R. V. Windecker, S. Wright, I. J. Falster, D. 2023-07-01 doi:10.1101/2023.06.29.546983 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Modulation of alpha oscillations by attention is predicted by hemispheric asymmetries of subcortical regions. ]]> https://biorxiv.org/content/10.1101/2023.07.03.547019v1?rss=1 Ghafari, T. Mazzetti, C. Garner, K. Gutteling, T. Jensen, O. 2023-07-03 doi:10.1101/2023.07.03.547019 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Functional variations in gamma-secretase activity are critical determinants of the clinical, biomarker, and cognitive progression of autosomal dominant Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2023.07.04.547688v1?rss=1 Schultz, S. Liu, L. Schultz, A. Fitzpatrick, C. Levin, R. Bellier, J.-P. Shirzadi, Z. Mathurin, N. Chen, C. Benzinger, T. Day, G. Farlow, M. Gordon, B. Hassenstab, J. Jack, C. Jucker, M. Karch, C. Lee, J. Levin, J. Perrin, R. Schofield, P. Xiong, C. Johnson, K. McDade, E. Bateman, R. Sperling, R. Selkoe, D. Chhatwal, J. the Dominantly Inherited Alzheimer's Network Investigators, 2023-07-05 doi:10.1101/2023.07.04.547688 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Pathogenic aggregates alter actin organization and cellular viscosity resulting in stalled clathrin mediated endocytosis ]]> https://biorxiv.org/content/10.1101/2023.07.10.548473v1?rss=1 Singh, S. B. Rajput, S. S. Sharma, A. Ananthanarayanan, V. Nandi, A. Patil, S. P. V. majumdar, a. Subramanyam, D. 2023-07-11 doi:10.1101/2023.07.10.548473 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ In vivo fate of systemically administered encapsulin protein nanocages and implications for their use in targeted drug delivery ]]> https://biorxiv.org/content/10.1101/2023.07.16.549228v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1691ecaorg.highwire.dtl.DTLVardef@647c31org.highwire.dtl.DTLVardef@115a146org.highwire.dtl.DTLVardef@10f2b6f_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rennie, C. Sives, C. Boyton, I. Diaz, D. Gorrie, C. A. Vittorio, O. Collins-Praino, L. Care, A. 2023-07-18 doi:10.1101/2023.07.16.549228 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ Comprehensive multi-platform tyrosine kinase profiling reveals novel actionable FGFR aberrations across pediatric and AYA sarcomas ]]> https://biorxiv.org/content/10.1101/2023.07.19.548825v1?rss=1 Fordham, A. M. Brown, L. M. Mayoh, C. Salib, A. Barger, Z. A. Wong, M. Sian, T. C. C. L. K. Xie, J. Gunther, K. Trebilcock, P. Terry, R. L. Barahona, P. Ajuyah, P. Sherstyuk, A. Avila, A. Cadiz, R. Perkins, C. M. Gifford, A. J. Mao, J. Zhao, A. O'Regan, L. P. Gorgels, D. Lau, L. M. Ziegler, D. S. Haber, M. Tyrrell, V. Lock, R. B. Cowley, M. Nicholls, W. Daly, R. J. Ekert, P. G. Fleuren, E. D. 2023-07-21 doi:10.1101/2023.07.19.548825 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ CRUX, a platform for visualising, exploring and analysing cancer genome cohort data ]]> https://biorxiv.org/content/10.1101/2023.07.25.550585v1?rss=1 El-Kamand, S. Quinn, J. M. Sareen, H. Becker, T. M. Wong-Erasmus, M. Cowley, M. J. 2023-07-25 doi:10.1101/2023.07.25.550585 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Disease-associated gut microbiome and metabolome changes in chronic low back pain patients with bone marrow lesions ]]> https://biorxiv.org/content/10.1101/2023.07.26.550629v1?rss=1 Li, W. Tu, J. Zheng, J. Das, A. Yan, Q. Jiang, X. Ding, W. Bai, X. Lai, K. Yang, S. Yang, C. Zou, J. Diwan, A. D. Zheng, Z. 2023-07-27 doi:10.1101/2023.07.26.550629 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Metagenomics untangles metabolic adaptations of Antarctic endolithic 1 bacteria at the fringe of habitability ]]> https://biorxiv.org/content/10.1101/2023.07.30.551190v1?rss=1 COLEINE, C. Albanese, D. Ray, A. DELGADO BAQUERIZO, M. Stajich, J. E. Williams, T. Larsen, S. Tringe, S. Pennacchio, C. Ferrari, B. C. Donati, C. Selbmann, L. 2023-07-30 doi:10.1101/2023.07.30.551190 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Inhibition of CERS1 in skeletal muscle exacerbates age-related muscle dysfunction ]]> https://biorxiv.org/content/10.1101/2023.08.05.552113v1?rss=1 Wohlwend, M. Laurila, P.-P. Goeminne, L. Lima, T. Lalou, A. Li, X. von Alvensleben, G. Crisol, B. Mangione, R. Gallart-Ayala, H. Burri, O. Butler, S. Morris, J. Turner, N. Ivanisevic, J. Auwerx, J. 2023-08-06 doi:10.1101/2023.08.05.552113 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Molecular dissection of the soluble photosynthetic antenna from a cryptophyte alga ]]> https://biorxiv.org/content/10.1101/2023.08.08.552318v1?rss=1 Rathbone, H. W. Laos, A. J. Michie, K. A. Iranmanesh, H. Biazik, J. Goodchild, S. Thordarson, P. Green, B. R. Curmi, P. M. 2023-08-09 doi:10.1101/2023.08.08.552318 Cold Spring Harbor Laboratory Press 2023-08-09 <![CDATA[ Environmental Uncertainty Affects Movement and Space-use in Sheep ]]> https://biorxiv.org/content/10.1101/2023.08.10.552758v1?rss=1 Bartsch, S. T. van Wettere, W. H. Griffith, S. C. Leu, S. T. 2023-08-14 doi:10.1101/2023.08.10.552758 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Conditional Protein Denoising Diffusion Generates Programmable Endonucleases ]]> https://biorxiv.org/content/10.1101/2023.08.10.552783v1?rss=1 Zhou, B. Zheng, L. Wu, B. Yi, K. Zhong, B. Lio, P. Hong, L. 2023-08-14 doi:10.1101/2023.08.10.552783 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Effects of nicotine compared to placebo gum on sensitivity to pain and mediating effects of peak alpha frequency ]]> https://biorxiv.org/content/10.1101/2023.08.11.552723v1?rss=1 Millard, S. K. Chiang, A. K. Humburg, P. Chowdhury, N. Rehan, R. Furman, A. J. Mazaheri, A. Schabrun, S. M. Seminowicz, D. A. 2023-08-14 doi:10.1101/2023.08.11.552723 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Does urbanization lead to parallel demographic shifts across the world in a cosmopolitan plant? ]]> https://biorxiv.org/content/10.1101/2023.08.14.552623v1?rss=1 Caizergues, A. E. Santangelo, J. S. Ness, R. W. Angeoletto, F. Anstett, D. N. Anstett, J. Baena-Diaz, F. Carlen, E. J. Chaves, J. A. Comerford, M. S. Dyson, K. Falahati-Anbaran, M. Fellowes, M. D. E. Hodgins, K. A. Hood, G. R. Iniguez-Armijos, C. Kooyers, N. J. Lazaro-Lobo, A. Moles, A. T. Munshi-South, J. Paule, J. Porth, I. M. Santiago-Rosario, L. Y. Stack Whitney, K. Tack, A. J. M. Johnson, M. T. J. 2023-08-14 doi:10.1101/2023.08.14.552623 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Evolutionary conservation of secondary structures in the lncRNAs of plants ]]> https://biorxiv.org/content/10.1101/2023.08.13.553158v1?rss=1 Corona-Gomez, J. A. Stadler, P. F. Fernandez-Valverde, S. L. 2023-08-15 doi:10.1101/2023.08.13.553158 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Multi-Site Statistical Mapping of Along-Tract Microstructural Abnormalities in Bipolar Disorder with Diffusion MRI Tractometry ]]> https://biorxiv.org/content/10.1101/2023.08.17.553762v1?rss=1 Nabulsi, L. Qamar, B. McPhilemy, G. Martyn, F. M. Roberts, G. Hallahan, B. Dannlowski, U. Kircher, T. Haarman, B. Mitchell, P. B. McDonald, C. Cannon, D. M. Andreassen, O. A. Ching, C. R. K. Thompson, P. M. 2023-08-21 doi:10.1101/2023.08.17.553762 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Both phenotypic and genotypic sex influence sex chromosome dosage compensation in a sex reversing lizard ]]> https://biorxiv.org/content/10.1101/2023.08.24.554710v1?rss=1 Hanrahan, B. J. Chang, J. K. Lister, N. C. Dissanayake, D. S. B. Hammond, J. M. Reis, A. L. M. Deveson, I. W. Ruiz-Herrera, A. Patel, H. R. Marshall Graves, J. A. Georges, A. Waters, P. D. 2023-08-26 doi:10.1101/2023.08.24.554710 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ Dysregulated actin dynamics and cofilin correlate with TDP-43 pathology in sporadic amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/2023.08.28.555209v1?rss=1 Jagaraj, C. J. Mehta, P. Parakh, S. Shadfar, S. Jamalli, M. S. Suchowerska, A. K. Ragagnin, A. Vidal, M. Sultana, J. Fath, T. Atkin, J. 2023-08-29 doi:10.1101/2023.08.28.555209 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ HIV-1 binds dynein directly to hijack microtubule transport machinery ]]> https://biorxiv.org/content/10.1101/2023.08.29.555335v1?rss=1 Badieyan, S. Lichon, D. Andreas, M. P. Gillies, J. P. Peng, W. Shi, J. DeSantis, M. E. Aiken, C. R. Böcking, T. Giessen, T. W. Campbell, E. M. Cianfrocco, M. A. 2023-08-29 doi:10.1101/2023.08.29.555335 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Vgamma9Vdelta2 T cells recognize butyrophilin 2A1 and 3A1 heteromers ]]> https://biorxiv.org/content/10.1101/2023.08.30.555639v1?rss=1 Fulford, T. S. Soliman, C. Castle, R. G. Rigau, M. Ruan, Z. Dolezal, O. Seneviratna, R. Brown, H. G. Hanssen, E. Hammet, A. Li, S. Redmond, S. J. Chung, A. Gorman, M. A. Parker, M. W. Patel, O. Peat, T. S. Newman, J. Behren, A. Gherardin, N. A. Godfrey, D. I. Uldrich, A. P. 2023-09-01 doi:10.1101/2023.08.30.555639 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Pre-existing tissue mechanical hypertension at adherens junctions disrupts apoptotic extrusion in epithelia ]]> https://biorxiv.org/content/10.1101/2023.08.31.555652v1?rss=1 Mann, Z. Lim, F. Verma, S. Nanavati, B. N. Davis, J. M. Begun, J. Hardeman, E. C. Gunning, P. W. Subramanyam, D. Yap, A. S. Duszyc, K. 2023-09-01 doi:10.1101/2023.08.31.555652 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes ]]> https://biorxiv.org/content/10.1101/2023.09.01.555348v1?rss=1 Collins, A. M. Ohlin, M. Corcoran, M. Heather, J. M. Ralph, D. Law, M. Martinez-Barnetche, J. Ye, J. Richardson, E. Gibson, W. S. Rodriguez, O. L. Peres, A. Yaari, G. Watson, C. T. Lees, W. D. 2023-09-01 doi:10.1101/2023.09.01.555348 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Passivating blunt-ended helices to control monodispersity and multi-subunit assembly of DNA origami structures ]]> https://biorxiv.org/content/10.1101/2023.09.09.557003v1?rss=1 Berengut, J. F. Rizzuto, F. J. Berg, W. R. Lee, L. K. 2023-09-11 doi:10.1101/2023.09.09.557003 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Electrochemically controlled blinking of fluorophores to enable quantitative stochastic optical reconstruction microscopy (STORM) imaging ]]> https://biorxiv.org/content/10.1101/2023.09.13.557504v1?rss=1 Yang, Y. Ma, Y. Tilley, R. Gaus, K. Gooding, J. J. 2023-09-13 doi:10.1101/2023.09.13.557504 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life ]]> https://biorxiv.org/content/10.1101/2023.09.11.557272v1?rss=1 Beasley-Hall, P. G. Kinjo, Y. Rose, H. A. Walker, J. Foster, C. S. P. Kovacs, T. G. L. Bourguignon, T. Ho, S. Y. W. Lo, N. 2023-09-14 doi:10.1101/2023.09.11.557272 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Ligand requirements for immunoreceptor triggering ]]> https://biorxiv.org/content/10.1101/2023.09.11.557203v1?rss=1 Barton, M. I. Paterson, R. L. Denham, E. M. Goyette, J. van der Merwe, P. A. 2023-09-15 doi:10.1101/2023.09.11.557203 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Genomic consequences of isolation and inbreeding in an island dingo population ]]> https://biorxiv.org/content/10.1101/2023.09.15.557950v1?rss=1 1 Mb) runs of homozygosity (ROH) -- indicators of inbreeding -- are elevated in all sampled dingoes. However, Kgari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the Kgari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs. SIGNIFICANCEA long-standing question in conservation genetics is whether long-term isolation and elevated levels of inbreeding always leads to inevitable population extinction. Here we conduct the first-ever whole-genome analysis of a population of dingoes living in long-term isolation on an island off the coast of Australia (Kgari). We show that these animals are beset by very low genetic diversity, likely the result of extensive inbreeding, and an elevated number of deleterious homozygotes. However, our results suggest that these dingoes are likely purging highly deleterious alleles, which may have allowed them to persist long term despite their extremely small population (<200 individuals). ]]> Leon-Apodaca, A. V. Kumar, M. del Castillo, A. Conroy, G. C. Lamont, R. W. Ogbourne, S. Cairns, K. M. Borburgh, L. Behrendorff, L. Subramanian, S. Szpiech, Z. A. 2023-09-15 doi:10.1101/2023.09.15.557950 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Mitochondrial genome analyses uncover intriguing population structure across the invasive trajectory of an iconic invader ]]> https://biorxiv.org/content/10.1101/2023.09.17.558141v1?rss=1 Cheung, K. Amos, T. G. Shine, R. Edwards, R. J. Rollins, L. A. 2023-09-17 doi:10.1101/2023.09.17.558141 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ TMPRSS2 activation of Omicron lineage Spike glycoproteins is regulated by TMPRSS2 cleavage of ACE2 ]]> https://biorxiv.org/content/10.1101/2023.09.22.558930v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@1c86cf0org.highwire.dtl.DTLVardef@16815feorg.highwire.dtl.DTLVardef@7be9e1org.highwire.dtl.DTLVardef@137de1c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO ACE2-TMPRSS2 pool model and evolution of SARS-CoV-2 tropism.A. &-B. ACE2-TMPRSS2 pool model to reconcile the evolving entry requirements of SARS-CoV-2 and changes in viral tropism in vivo. A. Both SARS-CoV-1 and early SARS-CoV-2 (pre-Omicron) lineages have molecular dual tropism, with efficient entry when ACE2 (blue protein) can form complexes with TMPRSS2 (green protein) and in settings where TMPRSS2 is excluded from ACE2 (C4-ACE2 CLD). In both settings ACE2 initially engages SARS-CoV-2 spike and fusion is then triggered through TMPRSS2 cleavage of the Spike S2 domain B. Over time, the dual tropism for two distinct pools of ACE2 (with and without TMPRSS2) has been lost, with consolidation towards ACE2 where TMPRSS2 is no longer in a complex. With the arrival of Omicron lineages, ACE2-TMPRSS2 complexes could no longer enable efficient Spike S2 cleavage and fusogenic activation (TMPRSS2 "off" confirmation"). Rather, only TMPRSS2 uncoupled from ACE2 could facilitate the latter cleavage of S2. C. Over time this has further consolidated over generations of omicron lineages from 2022 lineages (BA.1, BA.2 and BA.5) through to 2023 lineages (XBB.1.5) and now in 2024 JN.1 lineages such as KP.3. Overall, this supports the initial molecular tropism of early SARS-CoV-2 clades to be similar to that observed for SARS-CoV-1, with dual tropism across both ACE2 pools and replication proceeding in tissues where ACE2-TMPRSS2 complexes would be prevalent (e.g. Lung). The evolution away from ACE2-TMPRSS2 complexes towards ACE2 where TMPRSS2 is structurally uncoupled (e.g. ACE2 as a chaperone for solute carriers SLCA619 or SLCA620) is consistent selection of this ACE2 pool in a manner that has sustained transmission fitness within the human population. C_FIG ]]> Aggarwal, A. Fichter, C. Milogiannakis, V. Akerman, A. Ison, T. Ruiz Silva, M. Esneau, C. Bartlett, N. Burrell, L. Patel, S. Churchill, M. Angelovich, T. Parry, R. Sng, J. D. Neely, G. G. Moreno, C. L. Loo, L. Kelleher, A. D. Brilot, F. Khromykh, A. Turville, S. G. 2023-09-22 doi:10.1101/2023.09.22.558930 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Estimating multimodal brain variability in schizophreniaspectrum disorders: A worldwide ENIGMA study ]]> https://biorxiv.org/content/10.1101/2023.09.22.559032v1?rss=1 Omlor, W. Rabe, F. Fuchs, S. Cecere, G. Homan, S. Surbeck, W. Kallen, N. Georgiadis, F. Seifritz, E. Weickert, T. Bruggemann, J. Weickert, C. Potkin, S. Hashimoto, R. Sim, K. Rootes-Murdy, K. Quide, Y. Houenou, J. Banaj, N. Vecchio, D. Piras, F. Spalletta, G. Salvador, R. Rodrigue, A. Pearlson, G. Glahn, D. Tomecek, D. Kirschner, M. Kochunov, P. Fan, F.-M. Andreassen, O. Westlye, L. T. A. Berthet, P. Calhoun, V. Howells, F. M. Uhlmann, A. Stein, D. Iasevoli, F. van Erp, T. Turner, J. Homan, P. 2023-09-23 doi:10.1101/2023.09.22.559032 Cold Spring Harbor Laboratory Press 2023-09-23 <![CDATA[ A synthetic peptide mimic kills Candida albicans and synergistically prevents infection ]]> https://biorxiv.org/content/10.1101/2023.09.25.559234v1?rss=1 Schaefer, S. Vij, R. Sprague, J. L. Austermeier, S. Dinh, H. Judzewitsch, P. R. Seemann, E. Qualmann, B. Cain, A. K. Corrigan, N. Gresnigt, M. S. Boyer, C. Lenardon, M. D. Brunke, S. 2023-09-25 doi:10.1101/2023.09.25.559234 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Towards label-free non-invasive autofluorescence multispectral imaging for melanoma diagnosis ]]> https://biorxiv.org/content/10.1101/2023.09.25.559240v1?rss=1 Knab, A. Anwer, A. G. Pedersen, B. Handley, S. Marupally, A. G. Habibalahi, A. Goldys, E. M. 2023-09-25 doi:10.1101/2023.09.25.559240 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Metabolic and mitochondria alterations induced by SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10 ]]> https://biorxiv.org/content/10.1101/2023.09.26.559506v1?rss=1 Lopez-Ayllon, B. D. Marin, S. Farinas Fernandez, M. Garcia-Garcia, T. Fernandez-Rodriguez, R. de Lucas-Rius, A. Redondo, N. Mendoza-Garcia, L. Foguet, C. Grigas, J. Calvet, A. Villalba, J. M. Rodriguez Gomez, M. J. Megias, D. Mandracchia, B. Luque, D. Lozano, J. J. Calvo, C. Thomson, T. M. Garrido, J. J. Cascante, M. Montoya, M. 2023-09-26 doi:10.1101/2023.09.26.559506 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Bacterial Decellularization: Non-Chemical Production of Effective Plant Tissue Bio-Scaffolds ]]> https://biorxiv.org/content/10.1101/2023.09.27.559696v1?rss=1 Rybchyn, M. S. Biazik, J. Nunez, A. le Coutre, J. 2023-09-29 doi:10.1101/2023.09.27.559696 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Multi-modal transcriptomic analysis unravels enrichment of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer ]]> https://biorxiv.org/content/10.1101/2023.09.30.558960v1?rss=1 Sahoo, S. Ramu, S. Nair, M. G. Pillai, M. Perez San Juan, B. Milioli, H. Z. Mandal, S. Naidu, C. M. Mavatkar, A. D. Subramaniam, H. Neogi, A. G. Chaffer, C. L. Prabhu, J. S. Somarelli, J. A. Jolly, M. K. 2023-10-02 doi:10.1101/2023.09.30.558960 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Keywords to success: a practical guide to maximise the visibility and impact of academic papers ]]> https://biorxiv.org/content/10.1101/2023.10.02.559861v1?rss=1 Pottier, P. Lagisz, M. Burke, S. Drobniak, S. M. Downing, P. A. Macartney, E. L. Martinig, A. R. Mizuno, A. Morrison, K. Pollo, P. Ricolfi, L. Tam, J. Williams, C. Yang, Y. Nakagawa, S. 2023-10-03 doi:10.1101/2023.10.02.559861 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Colchicine promotes atherosclerotic plaque stability independently of inflammation ]]> https://biorxiv.org/content/10.1101/2023.10.03.560632v1?rss=1 Li, W. Lin, A. Hutton, M. Dhaliwal, H. Nadel, J. Rodor, J. Tumanov, S. Örd, T. Hadden, M. Mokry, M. Mol, B. M. Pasterkamp, G. Padula, M. P. Geczy, C. L. Ramaswamy, Y. Sluimer, J. C. Kaikkonen, M. U. Stocker, R. Baker, A. Fisher, E. Patel, S. Misra, A. 2023-10-03 doi:10.1101/2023.10.03.560632 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Modelling termites tunnelling and decision-making behaviors ]]> https://biorxiv.org/content/10.1101/2023.10.05.561127v1?rss=1 Mandal, S. Oberst, S. Lai, J. C. S. 2023-10-08 doi:10.1101/2023.10.05.561127 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ Functional coherence of the Xist and RSX protein interactomes: X chromosome inactivation marsupials ]]> https://biorxiv.org/content/10.1101/2023.10.08.560959v1?rss=1 McIntyre, K. L. Waters, S. Zhong, L. Hart-Smith, G. Raftery, M. Graves, J. A. M. Waters, P. D. 2023-10-08 doi:10.1101/2023.10.08.560959 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ Myeloperoxidase activity predicts atherosclerotic plaque disruption and atherothrombosis ]]> https://biorxiv.org/content/10.1101/2023.10.08.561454v1?rss=1 Nadel, J. Wang, X. Saha, P. Bongers, A. Tumanov, S. Giannotti, N. Chen, W. Vidger, N. Chowdhury, M. M. Lima da Cruz, G. J. Velasco, C. Prieto, C. Jabbour, A. Botnar, R. M. Stocker, R. Phinikaridou, A. 2023-10-13 doi:10.1101/2023.10.08.561454 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Accurate identification of cancer cells in complex pre-clinical models using deep-learning: a transfection free approach. ]]> https://biorxiv.org/content/10.1101/2023.10.15.562411v1?rss=1 Cortesi, M. Liu, D. Powell, E. Barlow, E. Warton, K. Ford, C. E. 2023-10-18 doi:10.1101/2023.10.15.562411 Cold Spring Harbor Laboratory Press 2023-10-18 <![CDATA[ Fecal microbial transfer and complex carbohydrates mediate protection against COPD ]]> https://biorxiv.org/content/10.1101/2023.10.16.562613v1?rss=1 Budden, K. F. Shukla, S. Bowerman, K. L. Gellatly, S. L. Wood, D. L. A. Lachner, N. Idrees, S. Patel, V. Faiz, A. F. Rehman, S. F. Donovan, C. Alemao, C. Shen, S. Vanka, K. S. Mason, J. Haw, T. J. Fricker, M. Keely, S. Hansbro, N. G. Belz, G. Horvat, J. C. Ashhurst, T. M. van Vreden, C. Mcguire, H. Fazekas de St Groth, B. F. King, N. J. C. Crossett, B. Cordwell, S. J. Bonaguro, L. Schultze, J. L. Forster, S. C. Cooper, M. A. Segal, L. Vaughan, A. Collins, P. Bowman, R. Fong, K. Yang, I. Wark, P. A. Dennis, P. G. Hugenholtz, P. Hansbro, P. M. 2023-10-19 doi:10.1101/2023.10.16.562613 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ The landscape of genomic structural variation in Indigenous Australians ]]> https://biorxiv.org/content/10.1101/2023.10.17.562810v1?rss=1 30%) and the majority of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short-tandem repeats (STRs) throughout the genome to characterise allelic diversity at 50 known disease loci, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among STR sequences. Our study sheds new light on the dimensions, diversity and evolutionary trajectories of genomic structural variation within and beyond Australia. ]]> Reis, A. M. Rapadas, M. Hammond, J. M. Gamaarachchi, H. Stevanovski, I. Kumaheri, M. Chintalaphani, S. Dissanayake, D. Brown, A. Llamas, B. Hewitt, A. Brown, A. Baynam, G. Mann, G. Hermes, A. Patel, H. R. Deveson, I. W. 2023-10-19 doi:10.1101/2023.10.17.562810 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad (Rhinella marina)? ]]> https://biorxiv.org/content/10.1101/2023.10.26.564158v1?rss=1 Yagound, B. Sarma, R. R. Edwards, R. J. Richardson, M. F. Lopez, C. M. R. Crossland, M. R. Brown, G. P. DeVore, J. L. Shine, R. Rollins, L. A. 2023-10-26 doi:10.1101/2023.10.26.564158 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ Women's representation in Indian academia and conferences ]]> https://biorxiv.org/content/10.1101/2023.10.26.564078v1?rss=1 Muralidhar, S. Ananthanarayanan, V. 2023-10-27 doi:10.1101/2023.10.26.564078 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Role of finger movement kinematics in friction perception at initial contact with smooth surfaces ]]> https://biorxiv.org/content/10.1101/2023.10.29.564644v1?rss=1 Afzal, H. M. N. Dullinac, S. d. B. d. Loutit, A. Shea, H. O. Martinez Ulloa, P. M. U. Khamis, H. Vickery, R. M. Wiertlewski, M. Redmond, S. J. Birznieks, I. 2023-11-01 doi:10.1101/2023.10.29.564644 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Opportunity nest egg: insights on the nutritional ecology, life history and captive management of three species of kiwi (Apteryx spp.) chick from Operation Nest Egg zoo hand-rearing records. ]]> https://biorxiv.org/content/10.1101/2023.10.31.564897v1?rss=1 Gray, L. J. Mitchell, B. A. Milner-Bradford, I. L. Bell, G. Revelly, K. Keller, L. Travers, C. 2023-11-02 doi:10.1101/2023.10.31.564897 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ The mechanistic basis of evolutionary transitions between grey, slate, and blue colour in Tanagers (Thraupidae) ]]> https://biorxiv.org/content/10.1101/2023.10.31.564904v1?rss=1 Babarovic, F. Cooney, C. R. Zinn, T. Drobniak, S. M. Janas, K. Kennedy, J. D. Nadeau, N. J. Parnell, A. J. Thomas, G. H. Burg, S. 2023-11-02 doi:10.1101/2023.10.31.564904 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Protein Engineering with Lightweight Graph Denoising Neural Networks ]]> https://biorxiv.org/content/10.1101/2023.11.05.565665v1?rss=1 Zhou, B. Zheng, L. Wu, B. Tan, Y. Lv, O. Yi, K. Fan, G. Hong, L. 2023-11-05 doi:10.1101/2023.11.05.565665 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Long-term serial passaging of SARS-CoV-2 reveals signatures of convergent evolution ]]> https://biorxiv.org/content/10.1101/2023.11.02.565396v1?rss=1 Foster, C. S. P. Walker, G. J. Jean, T. Wong, M. Brassil, L. Isaacs, S. Lu, Y. Turville, S. G. Kelleher, A. Rawlinson, W. D. 2023-11-06 doi:10.1101/2023.11.02.565396 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Transcriptomics and chromatin accessibility in multiple African population samples ]]> https://biorxiv.org/content/10.1101/2023.11.04.564839v1?rss=1 DeGorter, M. K. Goddard, P. C. Karakoc, E. Kundu, S. Yan, S. M. Nachun, D. C. Abell, N. Aguirre, M. Carstensen, T. Chen, Z. Durrant, M. G. Dwaracherla, V. Feng, K. Gloudemans, M. J. Hunter, N. Sathya Moorthy, M. P. Pomilla, C. Rodrigues, K. B. Smith, C. J. Smith, K. S. Ungar, R. A. Balliu, B. Fellay, J. Flicek, P. McLaren, P. J. Henn, B. M. McCoy, R. C. Sugden, L. A. Kundaje, A. Sandhu, M. S. Gurdasani, D. Montgomery, S. B. 2023-11-06 doi:10.1101/2023.11.04.564839 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Protein interaction kinetics delimit the performance of phosphorylation-driven protein switches. ]]> https://biorxiv.org/content/10.1101/2023.11.06.565761v1?rss=1 Winter, D. L. Wairara, A. R. Bennett, J. L. Donald, W. A. Glover, D. J. 2023-11-06 doi:10.1101/2023.11.06.565761 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Stimulating prefrontal cortex facilitates training transfer by increasing representational overlap ]]> https://biorxiv.org/content/10.1101/2023.11.23.568508v1?rss=1 Wards, Y. Ehrhardt, S. E. Filmer, H. L. Mattingley, J. B. Garner, K. G. Dux, P. E. 2023-11-24 doi:10.1101/2023.11.23.568508 Cold Spring Harbor Laboratory Press 2023-11-24 <![CDATA[ How strong is enemy release? A systematic compilation across taxa and approaches. ]]> https://biorxiv.org/content/10.1101/2023.11.24.568498v1?rss=1 Zeng, K. Schembri, J. Slavich, E. Moles, A. T. 2023-11-25 doi:10.1101/2023.11.24.568498 Cold Spring Harbor Laboratory Press 2023-11-25 <![CDATA[ Spatial niche separation of an invasive and a native mesopredator ]]> https://biorxiv.org/content/10.1101/2023.12.03.569481v1?rss=1 Jansen, J. Moseby, K. Comte, S. Dean, A. T. Axford, G. Peacock, D. E. Brandle, R. Jones, M. E. 2023-12-05 doi:10.1101/2023.12.03.569481 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ The effects of alternative rabbit control methods on feral cat activity in an open, semi-arid landscape ]]> https://biorxiv.org/content/10.1101/2023.12.03.569789v1?rss=1 Jansen, J. Comte, S. Dean, A. T. Axford, G. Moseby, K. E. Peacock, D. E. Brandle, R. Jones, M. E. 2023-12-05 doi:10.1101/2023.12.03.569789 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Spatial and Temporal Coordination of Force-generating Actin-based Modules Drives Membrane Remodeling In Vivo ]]> https://biorxiv.org/content/10.1101/2023.12.04.569944v1?rss=1 Heydecker, M. Shitara, A. Chen, D. Tran, D. Masedunskas, A. Tora, M. Ebrahim, S. Appaduray, M. A. Galeano Nino, J. L. Bhardwaj, A. Narayan, K. Hardeman, E. C. Gunning, P. Weigert, R. 2023-12-05 doi:10.1101/2023.12.04.569944 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Mutational and transcriptional landscape of pediatric B-cell precursor lymphoblastic lymphoma ]]> https://biorxiv.org/content/10.1101/2023.12.27.573433v1?rss=1 Kroeze, E. Iaccarino, I. Kleisman, M. M. Mondal, M. Beder, T. Khouja, M. Hoeppner, M. P. Scheijde-Vermeulen, M. Kester, L. A. Brueggemann, M. Baldus, C. D. Cario, G. Bladergroen, R. S. Garnier, N. Attarbaschi, A. Verdu-Amoros, J. J. Sutton, R. MacIntyre, E. Scholten, K. Padilla, L. A. Burkhardt, B. Beishuizen, A. den Boer, M. L. Kuiper, R. P. Loeffen, J. L. Boer, J. M. Klapper, W. 2023-12-27 doi:10.1101/2023.12.27.573433 Cold Spring Harbor Laboratory Press 2023-12-27 <![CDATA[ Impact of maternal obesogenic diet on maternal and offspring microbiome development ]]> https://biorxiv.org/content/10.1101/2024.01.21.576569v1?rss=1 Hasebe, K. Kendig, M. D. Kaakoush, N. O. Tajaddini, A. S. Westbrook, F. Morris, M. J. 2024-01-22 doi:10.1101/2024.01.21.576569 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Explaining plant trait variation in response to soil water availability using an optimal height-growth model ]]> https://biorxiv.org/content/10.1101/2024.01.23.576942v1?rss=1 Towers, I. R. O'Reilly Nugent, A. Sabot, M. E. B. Vesk, P. A. Falster, D. S. 2024-01-26 doi:10.1101/2024.01.23.576942 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ DIB-BOT: An open-source hardware approach for high throughput droplet interface bilayer deposition ]]> https://biorxiv.org/content/10.1101/2024.01.26.577347v1?rss=1 Mason, A. F. Wickham, S. F. Baker, M. A. 2024-01-26 doi:10.1101/2024.01.26.577347 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Modern Insights into Muscle Glycogen Phosphorylase Activity ]]> https://biorxiv.org/content/10.1101/2024.02.22.581477v1?rss=1 Kiriaev, L. Oakhill, J. S. Tiong, C. F. Seto, J. T. Crossman, V. G. Quinlan, K. G. R. North, K. N. Houweling, P. J. Ling, N. X. Y. 2024-02-23 doi:10.1101/2024.02.22.581477 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Roles of TYRO3 Family Receptors in Germ Cell Development During Mouse Testis Formation ]]> https://biorxiv.org/content/10.1101/2024.03.05.583252v1?rss=1 Ming, Z. Bagheri-Fam, S. Frost, E. R. Ryan, J. M. Binder, M. D. Harley, V. R. 2024-03-06 doi:10.1101/2024.03.05.583252 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Single molecule fingerprinting reveals different growth mechanisms in seed amplification assays for different polymorphs of alpha Synuclein fibrils. ]]> https://biorxiv.org/content/10.1101/2024.03.05.583619v1?rss=1 Lau, D. Tang, Y. Kenche, V. Copie, T. Kempe, D. Jary, E. Graves, N. J. Biro, M. Masters, C. L. Dzamko, N. Gambin, Y. Sierecki, E. 2024-03-11 doi:10.1101/2024.03.05.583619 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ A truncation mutant of adenomatous polyposis coli (APC) impairs apical cell extrusion through elevated epithelial tissue tension ]]> https://biorxiv.org/content/10.1101/2024.03.06.583801v1?rss=1 Gan, W. J. Giri, R. Begun, J. Abud, H. Hardeman, E. C. Gunning, P. W. Yap, A. S. Noordstra, I. 2024-03-10 doi:10.1101/2024.03.06.583801 Cold Spring Harbor Laboratory Press 2024-03-10 <![CDATA[ Multifaceted Representation of Genes via Deep Learning of Gene Expression Networks ]]> https://biorxiv.org/content/10.1101/2024.03.07.583777v1?rss=1 Su, Z. Fang, M. Smolnikov, A. Dinger, M. E. Oates, E. C. Vafaee, F. 2024-03-09 doi:10.1101/2024.03.07.583777 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ Reconfigurable multi-component nanostructures built from DNA origami voxels ]]> https://biorxiv.org/content/10.1101/2024.03.10.584331v1?rss=1 Luu, M. T. Berengut, J. Daljit Singh, J. K. Coffi Dit Glieze, K. Turner, M. Skipper, K. Meppat, S. Abbas, A. Fowler, H. Close, W. Doye, J. P. K. Wickham, S. F. J. 2024-03-11 doi:10.1101/2024.03.10.584331 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Allosteric adaptation in the stator complex rescues bacterial motility in Exb/Mot chimeras. ]]> https://biorxiv.org/content/10.1101/2024.03.12.584617v1?rss=1 Ridone, P. Baker, M. A. 2024-03-12 doi:10.1101/2024.03.12.584617 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Cycle-frequency content EEG analysis improves the assessment of respiratory-related cortical activity ]]> https://biorxiv.org/content/10.1101/2024.03.15.585182v1?rss=1 Navarro-Sune, X. Raux, M. Hudson, A. L. Similowski, T. Chavez, M. 2024-03-17 doi:10.1101/2024.03.15.585182 Cold Spring Harbor Laboratory Press 2024-03-17 <![CDATA[ Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2024.03.21.586080v1?rss=1 Sagniez, M. Budhraja, A. Pare, B. Simpson, S. M. Vinet-Ouellette, C. Rozendaal, M. Smith, M. A. 2024-03-23 doi:10.1101/2024.03.21.586080 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ Alzheimer's disease induced neurons bearing PSEN1 mutations exhibit reduced excitability ]]> https://biorxiv.org/content/10.1101/2024.03.22.586207v1?rss=1 Maksour, S. Finol-Urdaneta, R. K. Hulme, A. J. Cabral-da-Silva, M. C. Targa Dias Anastacio, H. Balez, R. Berg, T. Turner, C. Sanz Munoz, S. Engel, M. Kalajdzic, P. Lisowski, L. Sidhu, K. Sachdev, P. S. Dottori, M. Ooi, L. 2024-03-23 doi:10.1101/2024.03.22.586207 Cold Spring Harbor Laboratory Press 2024-03-23 <![CDATA[ Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells ]]> https://biorxiv.org/content/10.1101/2024.03.24.586475v1?rss=1 Tarbier, M. Mackowiak, S. D. Sekar, V. Bonath, F. Yapar, E. Fromm, B. Faridani, O. R. Biryukova, I. Friedländer, M. R. 2024-03-27 doi:10.1101/2024.03.24.586475 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Molecular basis for the assembly of the Vps5-Vps17 SNX-BAR proteins with Retromer ]]> https://biorxiv.org/content/10.1101/2024.03.24.586500v1?rss=1 Chen, K.-E. Tillu, V. A. Gopaldass, N. Chowdhury, S. R. Leneva, N. Kovtun, O. Ruan, J. Guo, Q. Ariotti, N. Mayer, A. Collins, B. M. 2024-03-26 doi:10.1101/2024.03.24.586500 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ Inferring gene regulatory networks by hypergraph variational autoencoder ]]> https://biorxiv.org/content/10.1101/2024.04.01.586509v1?rss=1 su, g. wang, h. zhang, y. Coster, A. C. Wilkins, M. Canete, P. F. Yu, D. Yang, Y. zhang, w. 2024-04-02 doi:10.1101/2024.04.01.586509 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Genes in Humans and Mice: Insights from Deep learning of 777K Bulk Transcriptomes ]]> https://biorxiv.org/content/10.1101/2024.04.01.587517v1?rss=1 Su, Z. Fang, M. Smolnikov, A. Vafaee, F. Dinger, M. E. Oates, E. 2024-04-02 doi:10.1101/2024.04.01.587517 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Does ecology shape geographical parthenogenesis? Evidence from the facultatively parthenogenetic stick insect Megacrania batesii ]]> https://biorxiv.org/content/10.1101/2024.04.02.587815v1?rss=1 Miller, S. M. Wilner, D. Boldbaatar, J. Bonduriansky, R. 2024-04-03 doi:10.1101/2024.04.02.587815 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in MDS/AML ]]> https://biorxiv.org/content/10.1101/2024.04.17.589858v1?rss=1 Truong, P. Shen, S. Joshi, S. Islam, M. I. Zhong, L. Raftery, M. Afrasiabi, A. Alinejad-Rokny, H. Nguyen, M. Zou, X. Bhuyan, G. S. Chowdhury, S. Ghoudousi, E. Stonehouse, O. Mohamed, S. Toscan, C. Connerty, P. Kakadia, P. M. Bohlander, S. K. Michie, K. Larsson, J. Lock, R. B. Walkley, C. Thoms, J. A. I. Jolly, C. J. Pimanda, J. E. 2024-04-18 doi:10.1101/2024.04.17.589858 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ The splicing factor kinase SRPK1 is a therapeutic target for Peripheral Vascular Disease ]]> https://biorxiv.org/content/10.1101/2024.04.17.589996v1?rss=1 Bhalla, S. R. Wahid, M. Amartey, J. Riu, F. Gao, Y. Agrawal, J. Lynch, A. P. Hawtrey, T. Kikuchi, R. Green, K. R. Teboul, L. Allen, C. Blackley, Z. Rajaji, K. Marsden, D. Batson, J. Harper, S. J. Oltean, S. Amoaku, W. Benest, A. V. Morris, J. C. Braithwaite, B. Bates, D. O. 2024-04-22 doi:10.1101/2024.04.17.589996 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Cerebrospinal fluid proteome profiling using machine learning shows a unique protein signature associated with APOE4 genotype ]]> https://biorxiv.org/content/10.1101/2024.04.18.590160v1?rss=1 Shvetcov, A. Thomson, S. Cho, A.-N. Wilkins, H. M. Reed, J. H. Swerdlow, R. H. Brown, D. A. Alzheimer's Disease Neuroimaging Initiative, Finney, C. A. 2024-04-22 doi:10.1101/2024.04.18.590160 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Antithrombotic Efficacy and Bleeding Risks of Vaccine-Induced Immune Thrombotic Thrombocytopenia Treatments ]]> https://biorxiv.org/content/10.1101/2024.04.21.589853v1?rss=1 Leung, H. Ahmadi, Z. Casey, J. Ratnasingam, S. McKenzie, S. Perdomo, J. Chong, B. 2024-04-26 doi:10.1101/2024.04.21.589853 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein ]]> https://biorxiv.org/content/10.1101/2024.04.22.590477v1?rss=1 Marzano, N. R. Johnston, B. Paudel, B. P. Schmidberger, J. Jergic, S. Bocking, T. Agostino, M. Small, I. van Oijen, A. M. Bond, C. S. 2024-04-22 doi:10.1101/2024.04.22.590477 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ CetZ1-dependent assembly and positioning of the motility machinery in haloarchaea ]]> https://biorxiv.org/content/10.1101/2024.05.02.592137v1?rss=1 Brown, H. J. Islam, M. I. Ruan, J. Baker, M. A. Ithurbide, S. Duggin, I. G. 2024-05-02 doi:10.1101/2024.05.02.592137 Cold Spring Harbor Laboratory Press 2024-05-02 <![CDATA[ Quantification of nanocondensates formation at the single molecule level ]]> https://biorxiv.org/content/10.1101/2024.05.05.592604v1?rss=1 Houx, J. Copie, T. Gambin, Y. Sierecki, E. 2024-05-06 doi:10.1101/2024.05.05.592604 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ State- and circuit-dependent opponent-processing of fear ]]> https://biorxiv.org/content/10.1101/2024.05.06.592282v1?rss=1 Yau, J. O.-Y. Li, A. Abdallah, L. Lisowski, L. McNally, G. P. 2024-05-07 doi:10.1101/2024.05.06.592282 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ Characterising Staphylococcus aureus genomic epidemiology with Multilevel Genome Typing. ]]> https://biorxiv.org/content/10.1101/2024.05.09.593273v1?rss=1 Cheney, L. Payne, M. Kaur, S. Mckew, G. Lan, R. 2024-05-09 doi:10.1101/2024.05.09.593273 Cold Spring Harbor Laboratory Press 2024-05-09 <![CDATA[ AAnet resolves a continuum of spatially-localized cell states to unveil tumor complexity ]]> https://biorxiv.org/content/10.1101/2024.05.11.593705v1?rss=1 Venkat, A. Youlten, S. E. Perez San Juan, B. Purcell, C. Amodio, M. Burkhardt, D. B. Benz, A. Holst, J. McCool, C. Mollbrink, A. Lundeberg, J. van Dijk, D. Goldstein, L. D. Kummerfeld, S. Krishnaswamy, S. Chaffer, C. L. 2024-05-14 doi:10.1101/2024.05.11.593705 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Global genomic dissection of antimicrobial resistance in Salmonella Typhimurium ]]> https://biorxiv.org/content/10.1101/2024.05.12.593721v1?rss=1 Kaur, S. Payne, M. Patridge, S. Sintchenko, V. Lan, R. 2024-05-12 doi:10.1101/2024.05.12.593721 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Bivariate multilevel meta-analysis of log response ratio and standardized mean difference for robust and reproducible environmental and biological sciences ]]> https://biorxiv.org/content/10.1101/2024.05.13.594019v1?rss=1 Yang, Y. Williams, C. Senior, A. Morrison, K. Ricolfi, L. Pan, J. Lagisz, M. Nakagawa, S. 2024-05-16 doi:10.1101/2024.05.13.594019 Cold Spring Harbor Laboratory Press 2024-05-16 <![CDATA[ Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data ]]> https://biorxiv.org/content/10.1101/2024.05.17.594625v1?rss=1 Chen, S. H. Jones, A. Lu-Irving, P. Yap, J.-Y. S. van der Merwe, M. Bragg, J. G. Edwards, R. J. 2024-05-20 doi:10.1101/2024.05.17.594625 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Hippocampal neuroinflammation causes sex-specific disruptions in instrumental conditioning, Pavlovian approach, and neuronal excitation ]]> https://biorxiv.org/content/10.1101/2024.05.19.594460v1?rss=1 Ganesan, K. Ghorbanpour, S. Kendall, W. Broome, S. T. Gladding, J. M. Dhungana, A. Abiero, A. R. Mahmoudi, M. Castorina, A. Kendig, M. D. Becchi, S. Valova, V. Cole, L. Bradfield, L. A. 2024-05-20 doi:10.1101/2024.05.19.594460 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation ]]> https://biorxiv.org/content/10.1101/2024.05.28.596153v1?rss=1 Grass Phylogeny Working Group 3, Arthan, W. Baker, W. J. Barrett, M. D. Barrett, R. L. Bennetzen, J. Besnard, G. Bianconi, M. E. Birch, J. L. Catalan, P. Chen, W. Christenhusz, M. Christin, P.-A. Clark, L. G. Couch, C. A. Columbus, J. T. Crayn, D. M. Davidse, G. Dunning, L. T. Duvall, M. R. Dransfield, S. Ficinski, S. Z. Fisher, A. E. Fjellheim, S. Forest, F. Gillespie, L. J. Hackel, J. Haevermans, T. Hodkinson, T. R. Huang, C.-H. Huang, W. Humphreys, A. M. Jobson, R. W. Kayombo, C. J. Kellogg, E. A. Kimeu, J. M. Larridon, I. Letsara, R. Li, D.-Z. Liu, 2024-06-02 doi:10.1101/2024.05.28.596153 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Electrochemically controlled switching of dyes for enhanced super-resolution optical fluctuation imaging (SOFI) ]]> https://biorxiv.org/content/10.1101/2024.06.02.597055v1?rss=1 Yang, Y. Ma, Y. Tilley, R. D. Gooding, J. 2024-06-03 doi:10.1101/2024.06.02.597055 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Chromatin remodeling with combined FACT and BET inhibition disrupts oncogenic transcription in Diffuse Midline Glioma ]]> https://biorxiv.org/content/10.1101/2024.06.06.597703v1?rss=1 Holliday, H. Khan, A. Ehteda, A. Ross, S. E. Jayatilleke, N. Gopalakrishnan, A. Guo, X. Liu, J. Nguyen, H. Lee, A. Colino Sanguino, Y. Dinger, M. E. Mayoh, C. Rayner, B. S. Tsoli, M. Ziegler, D. S. 2024-06-09 doi:10.1101/2024.06.06.597703 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Peak alpha frequency is not significantly altered by five days of experimental pain and repetitive transcranial stimulation of the left dorsolateral prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2024.06.14.599003v1?rss=1 Millard, S. K. Chiang, A. K. Chowdhury, N. Chang, W.-J. Furman, A. J. De Martino, E. Graven-Nielsen, T. Schabrun, S. M. Seminowicz, D. A. 2024-06-14 doi:10.1101/2024.06.14.599003 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Long-term NMN treatment increases lifespan and healthspan in mice in a sex dependent manner ]]> https://biorxiv.org/content/10.1101/2024.06.21.599604v1?rss=1 Kane, A. E. Chellappa, K. Schultz, M. B. Arnold, M. Li, J. Amorim, J. Diener, C. Zhu, D. Mitchell, S. J. Griffin, P. T. Tian, X. Petty, C. Conway, R. Walsh, K. Shelerud, L. Duesing, C. Mueller, A. Li, K. McNamara, M. Shima, R. T. deCabo, R. Gibbons, S. M. Wu, L. E. Ikeno, Y. Baur, J. A. Rajman, L. Sinclair, D. A. 2024-06-27 doi:10.1101/2024.06.21.599604 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Bird brains fit the bill: morphological diversification and the evolution of avian brain size ]]> https://biorxiv.org/content/10.1101/2024.07.02.601652v1?rss=1 Song, Z. Drobniak, S. M. Liu, Y. van Schaik, C. P. Griesser, M. 2024-07-03 doi:10.1101/2024.07.02.601652 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ A Systematic Review of the Neuroprotective Role and Biomarker Potential of GDF15 in Neurodegeneration ]]> https://biorxiv.org/content/10.1101/2024.07.07.600156v1?rss=1 Isik, F. I. Thomson, S. Cueto, J. F. Spathos, J. Breit, S. N. Tsai, V. W. W. Brown, D. A. Finney, C. A. 2024-07-09 doi:10.1101/2024.07.07.600156 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ Global genomics of the man-o'-war (Physalia) reveal biodiversity at the ocean surface ]]> https://biorxiv.org/content/10.1101/2024.07.10.602499v1?rss=1 Church, S. H. Abedon, R. B. Ahuja, N. Anthony, C. J. Ramirez, D. A. Rojas, L. M. Albinsson, M. E. Alvarez Trasobares, I. Bergemann, R. E. Bogdanovic, O. Burdick, D. R. Cunha, T. J. Damian-Serrano, A. D'Elia, G. Dion, K. Doyle, T. K. Goncalves, J. M. Gonzalez Rajal, A. Haddock, S. H. D. Helm, R. R. Le Gouvello, D. Lewis, Z. R. Magalhaes, B. I. M. M. Manko, M. K. de Mendoza, A. Moura, C. J. Nel, R. Perelman, J. N. Prieto, L. Munro, C. Oguchi, K. Pitt, K. A. Schaeffer, A. Schmidt, A. L. Sellanes, J. Wilson, N. G. Yamamoto, G. Lazo-Wasem, E. Simon, C. Decker, 2024-07-10 doi:10.1101/2024.07.10.602499 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication ]]> https://biorxiv.org/content/10.1101/2024.07.10.602835v1?rss=1 Yin, X. Pu, Y. Yuan, S. Pache, L. Churas, C. Weston, S. Riva, L. Simons, L. M. Cisneros, W. Clausen, T. de Jesus, P. Kim, H. N. Fuentes, D. Whitelock, J. Esko, J. Lord, M. Mena, I. Garcia-Sastre, A. Hultquist, J. Frieman, M. Ideker, T. Pratt, D. Martin-Sancho, L. Chanda, S. 2024-07-10 doi:10.1101/2024.07.10.602835 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Molecular and structural innovations of the stator motor complex at the dawn of flagellar motility ]]> https://biorxiv.org/content/10.1101/2024.07.22.604496v1?rss=1 Puente-Lelievre, C. Ridone, P. Douglas, J. Amritkar, K. Kacar, B. Baker, M. A. Matzke, N. J. 2024-07-23 doi:10.1101/2024.07.22.604496 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Weathering the storm for love: Mate searching behaviour of wild males of the Sydney funnel-web spider (Atrax robustus) ]]> https://biorxiv.org/content/10.1101/2024.07.23.604707v1?rss=1 Creak, C. N. Muirhead, H. Bonduriansky, R. Kasumovic, M. Buzatto, B. 2024-07-26 doi:10.1101/2024.07.23.604707 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Stem cell mechanoadaptation - Part A - Effect of microtubule stabilization and volume changing stresses on cytoskeletal remodeling ]]> https://biorxiv.org/content/10.1101/2024.07.28.605421v1?rss=1 Putra, V. L. Kilian, K. A. Knothe Tate, M. L. 2024-07-29 doi:10.1101/2024.07.28.605421 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Stem cell mechanoadaptation Part B - Microtubule stabilization and substrate compliance effects on cytoskeletal remodeling ]]> https://biorxiv.org/content/10.1101/2024.07.28.605537v1?rss=1 Putra, V. D. Kilian, K. A. Knothe Tate, M. L. 2024-07-29 doi:10.1101/2024.07.28.605537 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Single-molecule tracking reveals the dynamics of Ipl1 recruitment to the kinetochores and spindles in S. cerevisiae ]]> https://biorxiv.org/content/10.1101/2024.08.01.606162v1?rss=1 Podh, N. K. Das, A. Kumari, A. Garg, K. Yadav, R. Kashyap, K. Islam, S. Gupta, A. Mehta, G. 2024-08-01 doi:10.1101/2024.08.01.606162 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ The primary sclerosing cholangitis and ulcerative colitis colonic mucosa defined through paired microbial and single-cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2024.08.12.607536v1?rss=1 Tearle, J. L. E. Zhang, F. Jackson, K. J. L. Malhotra, P. Tavakoli, P. Koentgen, S. Warren, J. Williams, C. Haque, A. Arzivian, A. Tedla, N. Kim, A. King, H. W. Hold, G. L. Ghaly, S. James, K. R. 2024-08-12 doi:10.1101/2024.08.12.607536 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ PI(4)P recruits CIDE proteins to promote the formation of unilocular lipids droplets ]]> https://biorxiv.org/content/10.1101/2024.08.22.609036v1?rss=1 Wu, J. Gao, M. Wu, X. Liu, Y. Du, X. Liang, Y. Ma, C. Li, P. Chen, F.-J. Yang, H. 2024-08-23 doi:10.1101/2024.08.22.609036 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Integrating microscopy and transcriptomics from individual uncultured eukaryotic plankton ]]> https://biorxiv.org/content/10.1101/2024.08.25.609620v1?rss=1 Gatt, C. R. Xie, Y. Wahi, K. Johansson Beves, E. Zanini, F. 2024-08-26 doi:10.1101/2024.08.25.609620 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Yes, they're all individuals: Hierarchical models for repeat survey data improve estimates of tree growth and size ]]> https://biorxiv.org/content/10.1101/2024.08.27.609830v1?rss=1 O'Brien, T. Warton, D. Falster, D. S. 2024-08-28 doi:10.1101/2024.08.27.609830 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ A-Islands: A plant dataset for biodiversity research and species monitoring on Australian islands ]]> https://biorxiv.org/content/10.1101/2024.08.29.609992v1?rss=1 6,500 plant species from 844 islands ranging in size from 18 m2 to 4,400 km2, exhibiting different degrees of isolation from the mainland, and spanning all major Australian climate zones. Of these, 251 islands have been repeatedly sampled up to 11 times making it possible to investigate temporal compositional change. A-Islands is open access and will be continuously updated. Its simple data structure consisting of three comma separated files allows easy integration with other Australian and global plant-occurrence databases and can serve as a repository for island research in Australia. Knowing which species occur on Australia's islands will provide opportunities for future research, including studying changes in biodiversity and species-turnover within and among archipelagos, tests of classical island biogeography theory and as a baseline for ecological monitoring and conservation. ]]> Schrader, J. Coleman, D. Abbott, I. Bryant, S. Buckley, R. Crayn, D. Gallagher, R. V. Harris, S. Heatwole, H. Jackes, B. Kreft, H. Mills, K. Kirkpatrick, J. Latz, P. K. Neldner, J. Sattler, C. Visoiu, M. Wenk, E. H. Woinarski, J. C. Z. Wright, I. J. Zorn, I. Westoby, M. 2024-08-30 doi:10.1101/2024.08.29.609992 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Optimisation of a multiplexed, high throughput assay to measure neutralising antibodies against SARS-CoV-2 variants. ]]> https://biorxiv.org/content/10.1101/2024.09.01.610733v1?rss=1 Ashley, C. L. Bloul, M. Alca, S. Smith, L. Jin, W. Khoury, D. Counoupas, C. Davenport, M. P. Triccas, J. A. Steain, M. 2024-09-04 doi:10.1101/2024.09.01.610733 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies ]]> https://biorxiv.org/content/10.1101/2024.09.05.611471v1?rss=1 1 Mbp) were identified using Y-specific contigs generated by genome subtraction. We identified two novel alpha-satellite repeats of 187 bp and 199 bp in the putative centromeres that did not form higher order repeats. The genome assembly exceeds the standard recommended by the Earth Biogenome Project; 0.02% false expansions, 99.63% kmer completeness, 94.66% complete single copy BUSCO genes and an average 98.42% of transcriptome data mappable to the genome assembly. The mitochondrial genome (17,506 bp) and the model rDNA repeat unit (15,154 bp) were assembled. The B. duperreyi genome assembly has one of the highest completeness levels for a skink and will provide a resource for research focused on sex determination and thermolabile sex reversal, as an oviparous foundation species for studies of the evolution of viviparity, and for other comparative genomics studies of the Scincidae. Species TaxonomyEukaryota; Animalia; Chordata; Reptilia; Squamata; Scincidae; Lygosominae; Eugongylini; Bassiana (=Acritoscincus); Bassiana duperreyi (Gray, 1838) (NCBI: txid316450). ]]> Hanrahan, B. J. Alreja, K. Reis, A. L. M. Chang, J. K. Dissanayake, D. S. B. Edwards, R. J. Bertozzi, T. Hammond, J. M. O'Meally, D. Deveson, I. W. Georges, A. Waters, P. D. Patel, H. R. 2024-09-05 doi:10.1101/2024.09.05.611471 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Anti-phase clustering of regulatory factors shapes gene bursting ]]> https://biorxiv.org/content/10.1101/2024.09.10.612363v1?rss=1 Li, B. Wong, Y. Y. Flores-Rodriguez, N. Davidson, T. Graus, M. S. Smialkovska, V. Ohishi, H. Feldmann, A. Ochiai, H. Francois, M. 2024-09-11 doi:10.1101/2024.09.10.612363 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Temporal dynamics of viral fitness and the adaptive immune response in HCV infection ]]> https://biorxiv.org/content/10.1101/2024.09.07.611784v1?rss=1 Walker, M. R. Leung, P. Keoshkerian, E. Pirozyan, M. R. Lloyd, A. Luciani, F. Bull, R. A. 2024-09-13 doi:10.1101/2024.09.07.611784 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Unveiling multi-scale architectural features in single-cell Hi-C data using scCAFE ]]> https://biorxiv.org/content/10.1101/2024.09.10.611762v1?rss=1 Wang, F. Lin, J. Alinejad-Rokny, H. Ma, W. Meng, L. Huang, L. Yu, J. Chen, N. Wang, Y. Yao, Z. Xie, W. Li, X. Wong, K.-C. 2024-09-14 doi:10.1101/2024.09.10.611762 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ The level of endothelial glycocalyx maturity modulates interactions with charged nano-materials ]]> https://biorxiv.org/content/10.1101/2024.09.10.611831v1?rss=1 Bridges, C. Fu, L. Yeow, J. Huang, X. Jackson, M. Kuchel, R. Sterling, J. Baker, S. Lord, M. 2024-09-14 doi:10.1101/2024.09.10.611831 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ The global spectrum of tree crown architecture ]]> https://biorxiv.org/content/10.1101/2024.09.14.613032v1?rss=1 500,000 globally distributed trees, we explored how climate, disturbance, competition, functional traits, and evolutionary history constrain the height, crown size and shape of the worlds tree species. We found that variation in height scaling relationships was primarily controlled by water availability and light competition. Conversely, crown width was predominantly shaped by exposure to wind and fire, while also covarying with other functional traits related to mechanical stability and photosynthesis. Additionally, several plant lineages had crown architectures that defy their environments, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legumes in African savannas. Our study charts the global spectrum of tree crown architectural types. It provides a roadmap for integrating crown architecture with vegetation models and remote sensing observations, so that we may better understand the processes that shape the 3D structure of woody ecosystems. ]]> Jucker, T. Fischer, F. Chave, J. Coomes, D. Caspersen, J. Ali, A. Panzou, G. Feldpausch, T. Falster, D. Usoltsev, V. Jackson, T. Adu-Bredu, S. Alves, L. Aminpour, M. Angoboy, I. Anten, N. Antin, C. Askari, Y. Munoz, R. Ayyappan, N. Banin, L. Barbier, N. Battles, J. Beeckman, H. Bocko, Y. Bond-Lamberty, B. Bongers, F. Bowers, S. Breugel, M. Chantrain, A. Chaudhary, R. Dai, J. Dalponte, M. Dimobe, K. Domec, J.-C. Doucet, J.-L. Dupuy-Rada, J. Duursma, R. Enriquez, M. Ewijk, K. Farfan-Rios, W. Fayolle, A. Ferretti, M. Forni, E. Forrester, D. Gilani, H. 2024-09-17 doi:10.1101/2024.09.14.613032 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ ECSFinder: Optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences ]]> https://biorxiv.org/content/10.1101/2024.09.14.612549v1?rss=1 Gaonac'h-Lovejoy, V. A. Sauvageau, M. Mattick, J. S. Smith, M. A. 2024-09-19 doi:10.1101/2024.09.14.612549 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi ]]> https://biorxiv.org/content/10.1101/2024.09.30.613582v1?rss=1 99% agreement within one doubling dilution). We show strong concordance (>96% for genotype and >98% for AMR and plasmid) between calls made from ONT reads and those made from Illumina reads for isolates sequenced on both platforms (n =93 genomes). Typhi Mykrobe takes less than a minute per sample and is available at https://github.com/typhoidgenomics/genotyphi. ConclusionsTyphi Mykrobe provides rapid and sensitive genotyping of Typhi genomes direct from Illumina and ONT reads, although lower accuracy was observed for R9 ONT data. It demonstrated accurate assignment of GenoTyphi lineage, detection of AMR determinants and prediction of corresponding AMR phenotypes, and identification of plasmid replicons. ]]> Ingle, D. J. Hawkey, J. J. Hunt, M. Iqbal, Z. Keane, J. Afolayan, A. O. Ahmed, N. Andleeb, S. Ashton, P. M. Bogoch, I. I. Carey, M. E. Chattaway, M. A. Crump, J. A. Guevara, P. D. Howden, B. Izumiya, H. Jacob, J. J. Judd, L. M. Kapil, A. Keddy, K. H. Kim, J. Levine, M. M. Morita, M. Nair, S. Octavia, S. Okeke, I. N. Osadebamwen, P. Rahman, S. I. A. Rokney, A. Rasko, D. Shamanna, V. Sikorski, M. J. Smith, A. M. Sunmonu, G. T. Tagg, K. A. Wick, R. R. Dyson, Z. A. Holt, K. Global Typhoid Genomics Consortium, 2024-09-30 doi:10.1101/2024.09.30.613582 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Long-read metagenomics empowers precise tracking of bacterial strains and their genomic changes after fecal microbiota transplantation ]]> https://biorxiv.org/content/10.1101/2024.09.30.615906v1?rss=1 Fan, Y. Ni, M. Aggarwala, V. Mead, E. A. Ksiezarek, M. Kamm, M. A. Borody, T. Paramsothy, S. Kaakoush, N. O. Grinspan, A. Faith, J. J. Fang, G. 2024-09-30 doi:10.1101/2024.09.30.615906 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Development and validation of a computational tool to predict treatment outcomes in cells from High-Grade Serous Ovarian Cancer patients ]]> https://biorxiv.org/content/10.1101/2024.10.02.616212v1?rss=1 Cortesi, M. Liu, D. Powell, E. Barlow, E. Warton, K. Giordano, E. Ford, C. E. 2024-10-03 doi:10.1101/2024.10.02.616212 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Nanoscale biodegradable printing for designed tuneability of vaccine delivery kinetics ]]> https://biorxiv.org/content/10.1101/2024.10.02.616252v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@a2e8c0org.highwire.dtl.DTLVardef@15ecbf1org.highwire.dtl.DTLVardef@9f734forg.highwire.dtl.DTLVardef@4b7e39_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Peeler, D. J. Sun, R. Kütahya, C. Peschke, P. Zhou, K. Brachi, G. Yeow, J. Graham, O. R. Wojciechowski, J. P. Debets, T. F. Lalone, V. Song, X. Polra, K. Tregoning, J. S. Shattock, R. J. Stevens, M. M. 2024-10-03 doi:10.1101/2024.10.02.616252 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ A new compression strategy to reduce the size of nanopore sequencing data ]]> https://biorxiv.org/content/10.1101/2024.10.02.616377v1?rss=1 Jayasooriya, K. Jenner, S. P. Marasinghe, P. Senanayake, U. Saadat, H. Taubman, D. Ragel, R. Gamaarachchi, H. Deveson, I. W. 2024-10-03 doi:10.1101/2024.10.02.616377 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Single-Cell Data Integration and Cell Type Annotation through Contrastive Adversarial Open-set Domain Adaptation ]]> https://biorxiv.org/content/10.1101/2024.10.04.616599v1?rss=1 Aminzadeh, F. Wu, J. He, J. Saberi, M. Vafaee, F. 2024-10-04 doi:10.1101/2024.10.04.616599 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Dopamine and cortical iPSC-derived neurons with different Parkinsonian mutations show variation in lysosomal and mitochondrial dysfunction: implications for protein deposition versus selective cell loss ]]> https://biorxiv.org/content/10.1101/2024.10.07.617117v1?rss=1 Chedid, J. Li, Y. Labrador-Garrido, A. Abu-Bonsrah, D. Pavan, C. Fraser, T. Zhong, M. Johnston, J. A. Thompson, L. H. Kirik, D. Parish, C. Halliday, G. Sue, C. Wali, G. Dzamko, N. 2024-10-11 doi:10.1101/2024.10.07.617117 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ SMYD5 is a ribosomal methyltransferase which trimethylates RPL40 lysine 22 through recognition of a KXY motif ]]> https://biorxiv.org/content/10.1101/2024.10.10.616381v1?rss=1 Hamey, J. J. Shah, M. Wade, J. D. Bartolec, T. K. Wettenhall, R. E. Quinlan, K. G. Williamson, N. A. Wilkins, M. R. 2024-10-11 doi:10.1101/2024.10.10.616381 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Single Cell Integration Characterises Metaplasia in Inflammatory Intestinal Diseases ]]> https://biorxiv.org/content/10.1101/2024.10.11.614415v1?rss=1 Oliver, A. J. Huang, N. Li, R. Bartolome-Casado, R. Nilsen, H. R. Gudino, V. Melon-Ardanaz, C. d. I. B. e. R. d. E. Fitzpatrick, M. E. B. Provine, N. M. Polanski, K. Koplev, S. Milchsack, L. M. Dann, E. Predeus, A. V. Cakir, B. To, K. Prete, M. Chapman, J. A. Masi, A. C. Stephenson, E. Engelbert, J. Lobentanzer, S. Perera, S. Richardson, L. Kapuge, R. Wilbrey-Clark, A. Semprich, C. I. Moy, M. Ellams, S. Tudor, C. L. Joseph, P. Garrido-Trigo, A. Corraliza, C. d. I. B. e. R. d. E. M. Oliver, T. R. W. Hook, C. E. Saez-Rodriguez, J. James, K. R. Meyer, K. B. M 2024-10-12 doi:10.1101/2024.10.11.614415 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Assessing the Validity of Leucine Zipper Constructs Predicted in AlphaFold2. ]]> https://biorxiv.org/content/10.1101/2024.10.14.618350v1?rss=1 Mitic, I. Michie, K. A. Jacques, D. A. 2024-10-17 doi:10.1101/2024.10.14.618350 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Federated deep learning enables cancer subtyping by proteomics ]]> https://biorxiv.org/content/10.1101/2024.10.16.618763v1?rss=1 Cai, Z. Boys, E. L. Noor, Z. Aref, A. Xavier, D. Lucas, N. Williams, S. G. Koh, J. M. S. Poulos, R. C. Wu, Y. Dausmann, M. MacKenzie, K. L. Aguilar-Mahecha, A. Armengol, C. Barranco, M. M. Basik, M. Bowman, E. D. Clifton-Bligh, R. J. Connolly, E. A. Cooper, W. A. Dalal, B. DeFazio, A. Filipits, M. Flynn, P. J. Graham, J. D. George, J. Gill, A. J. Gnant, M. Habib, R. Harris, C. C. Harvey, K. Horvath, L. G. Jackson, C. Kohonen-Corish, M. R. J. Lim, E. Liu, J. Long, G. Lord, R. V. Mann, G. J. McCaughan, G. W. Morgan, L. Murphy, L. C. Nagabushan, S. Nagri 2024-10-18 doi:10.1101/2024.10.16.618763 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Comparative proteomics of biofilm development in Pseudoalteromonas tunicata discovers a distinct family of Ca2+-dependent adhesins ]]> https://biorxiv.org/content/10.1101/2024.10.22.619756v1?rss=1 Ali, S. Stavropoulos, A. Jenkins, B. Graves, S. Che, G. Cheng, J. Tan, H. Wei, X. Egan, S. Neufeld, J. D. Eckhard, U. Charles, T. C. Doxey, A. C. 2024-10-23 doi:10.1101/2024.10.22.619756 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Integrating predictors of host condition into spatiotemporal multi-scale models of virus shedding ]]> https://biorxiv.org/content/10.1101/2024.10.24.616488v1?rss=1 Kramer, A. M. Faust, C. L. Castellanos, A. A. Fischhoff, I. R. Peel, A. J. Eby, P. Ruiz-Aravena, M. Borremans, B. Plowright, R. K. Han, B. A. 2024-10-25 doi:10.1101/2024.10.24.616488 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Dorsomedial striatal neuroinflammation causes excessive goal-directed action control by disrupting homeostatic astrocyte function ]]> https://biorxiv.org/content/10.1101/2024.10.24.620154v1?rss=1 Abiero, A. R. Gladding, J. M. Iredale, J. Drury, H. R. Manning, E. E. Dayas, C. V. Dhungana, A. Ganesan, K. Turner, K. Becchi, S. Kendig, M. D. Nolan, C. Balleine, B. W. Castorina, A. Cole, L. Clemens, K. Bradfield, L. 2024-10-26 doi:10.1101/2024.10.24.620154 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Bacterial inoculation manipulates the coral epigenome ]]> https://biorxiv.org/content/10.1101/2024.10.27.620496v1?rss=1 Barno, A. R. Villela, H. D. Cardoso, P. M. Garcia, F. C. Cui, G. Delgadillo-Ordonez, N. Rosado, A. S. Thomas, T. Aranda, M. Voolstra, C. R. Peixoto, R. 2024-10-27 doi:10.1101/2024.10.27.620496 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence ]]> https://biorxiv.org/content/10.1101/2024.11.06.622096v1?rss=1 1 million PBMCs from 982 donors uncovers sex-specific immune aging trajectories. - Aging females show greater cellular remodeling and stronger transcriptional shifts than males. - Female-specific expansions with age of cytotoxic CD8+ T effector memory cells, inflammatory monocytes, and CD4+ T helper 22 cells reflect a systemic shift toward a pro-inflammatory, self-reactive immune state. - Male-specific B cell shifts reveal expansion of CD5+ clonal subpopulations linked to leukemic precursor states. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/622096v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@161b6b1org.highwire.dtl.DTLVardef@214d55org.highwire.dtl.DTLVardef@5c3ee8org.highwire.dtl.DTLVardef@263227_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Rios, M. S. Ripoll-Cladellas, A. Omidi, F. Ballouz, S. Alquicira-Hernandez, J. Oelen, R. Franke, L. van der Wijst, M. G. P. Powell, J. E. Mele, M. 2024-11-08 doi:10.1101/2024.11.06.622096 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Long lived liver-resident memory T cells of biased specificities for abundant sporozoite antigens drive malaria protection by radiation-attenuated sporozoite vaccination ]]> https://biorxiv.org/content/10.1101/2024.11.08.622604v1?rss=1 de Menezes, M. N. Ge, Z. Cozijnsen, A. Gras, S. Bertolino, P. Caminschi, I. Lahoud, M. H. Yui, K. McFadden, G. I. Beattie, L. Heath, W. R. Fernandez-Ruiz, D. 2024-11-11 doi:10.1101/2024.11.08.622604 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Insect-specific Alphamesonivirus-1 (Mesoniviridae) in lymph node and lung tissues from two horses with acute respiratory syndrome ]]> https://biorxiv.org/content/10.1101/2024.11.10.622896v1?rss=1 Jurisic, L. Auerswald, H. Marcacci, M. Di Giallonardo, F. Coetzee, L. M. Curini, V. Averaimo, D. Di Teodoro, G. Ortiz-Baez, A. S. Camma, C. Richt, J. A. Holmes, E. C. Lorusso, A. 2024-11-11 doi:10.1101/2024.11.10.622896 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ scPrediXcan integrates advances in deep learning and single-cell data into a powerful cell-type-specific transcriptome-wide association study framework ]]> https://biorxiv.org/content/10.1101/2024.11.11.623049v1?rss=1 Zhou, Y. Adeluwa, T. Zhu, L. Salazar, S. Sumner, S. Kim, H. Gona, S. Nyasimi, F. Kulkarni, R. Powell, J. Madduri, R. Liu, B. Chen, M. Im, H. K. 2024-11-14 doi:10.1101/2024.11.11.623049 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ Reintroduction of wild song culture to a critically endangered songbird ]]> https://biorxiv.org/content/10.1101/2024.11.19.624418v1?rss=1 Appleby, D. L. Langmore, N. E. Pitcher, B. Heinsohn, R. Tripovich, J. Matkovics, R. Crates, R. A. 2024-11-21 doi:10.1101/2024.11.19.624418 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ The conserved landscape of RNA modifications and transcript diversity across mammalian evolution ]]> https://biorxiv.org/content/10.1101/2024.11.24.624934v1?rss=1 Rodriguez, G. S. Akanksha, S. Ravindran, A. Oyelami, F. Ip, C. K. Gupta, P. Villanueva, J. King, H. E. Grootveld, A. Blackburn, J. Gupta, I. Viera, H. G. S. Shirokikh, N. Eyras, E. Weatheritt, R. J. 2024-11-24 doi:10.1101/2024.11.24.624934 Cold Spring Harbor Laboratory Press 2024-11-24 <![CDATA[ An operational framework to map Essential Life Support Areas (ELSAs) for biodiversity, climate, and sustainable development ]]> https://biorxiv.org/content/10.1101/2024.11.25.625159v1?rss=1 Venter, O. Ervin, J. Stilger Virnig, A. L. Consaul Atkinson, S. Marigo, M. Zhang, D. Supples, C. Paniagua, E. Phillips, L. Schuster, R. Llano, X. Pence, G. Arcese, P. de Assis Barros, L. Belgubayeva, A. Borja, D. Brumby, S. Burgess, N. D. Cardozo, L. Cordero Vega, C. Cordova, M. V. Corzo, L. Delgado, E. Fonseca, C. Game, E. Georges, Y. Grantham, H. Guerra, D. Hansen, A. Hawley-McMaster, G. Hout, N. Jallah, B. S. KC, D. Llactayo Leon, W. Leslie, J. Lihong, D. Llosa, C. Mahmood, A. R. J. Makholela, T. Mathis, M. Miller Granados, C. McGowan, J. Monge, R. 2024-11-26 doi:10.1101/2024.11.25.625159 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Spatial and feature-selective attention interact to drive selective coding in frontoparietal cortex ]]> https://biorxiv.org/content/10.1101/2024.12.03.626620v1?rss=1 Dermody, N. Lorenz, R. Goddard, E. Villringer, A. Woolgar, A. 2024-12-06 doi:10.1101/2024.12.03.626620 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ Easy come, easier go: mapping the loss of flagellar motility across the tree of life ]]> https://biorxiv.org/content/10.1101/2024.12.05.626484v1?rss=1 Philip, J. S. Grewal, S. Scadden, J. Puente Lelievre, C. Matzke, N. J. McNally, L. Baker, M. A. 2024-12-06 doi:10.1101/2024.12.05.626484 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ Vgamma1+ gammadelta T cell-derived IL-4 initiates CD8 T cell immunity ]]> https://biorxiv.org/content/10.1101/2024.12.06.627130v1?rss=1 Le, S. Murphy, D. Liu, S. Ge, Z. May, R. Cozijnsen, A. Burn, T. Jennison, C. Bachem, A. Xu, C. Koay, H.-F. Schroeder, J. Gras, S. Cockburn, I. A. Bedoui, S. Mackay, L. K. Mcfadden, G. I. Fernandez-Ruiz, D. Heath, W. R. Beattie, L. 2024-12-06 doi:10.1101/2024.12.06.627130 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ Tuning mechanical milieux of tissue templates and their cellular inhabitants to guide mechanoadaptation ]]> https://biorxiv.org/content/10.1101/2024.12.03.626678v1?rss=1 Putra, V. L. Sansalone, V. Kilian, K. A. Tate, M. L. K. 2024-12-07 doi:10.1101/2024.12.03.626678 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Detection of exotic biosecurity threat ribgrass mosaic virus and novel tobamoviruses through metatranscriptomic sequencing of animal gut content ]]> https://biorxiv.org/content/10.1101/2024.12.10.627875v1?rss=1 Mahar, J. Mifsud, J. C. Van Brussel, K. Lachenauer, A. E. Harvey, E. Turnbull, O. M. Bonat, S. Newsome, T. M. Olsson, A. Chiu-Werner, A. Jones, M. E. Holmes, E. C. Maina, S. 2024-12-11 doi:10.1101/2024.12.10.627875 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Tunicate metatranscriptomes reveal ancient virus-host co-divergence and inter-order recombination in the evolutionary history of disease-causing viruses ]]> https://biorxiv.org/content/10.1101/2024.12.15.628590v1?rss=1 Petrone, M. E. Grove, J. Parry, R. Van Brussel, K. Mifsud, J. C. Dindar, Z. Mei, S.-q. Shi, M. Turnbull, O. M. Marzinelli, E. M. Holmes, E. C. 2024-12-16 doi:10.1101/2024.12.15.628590 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Targeting de novo lipogenesis improves gemcitabine efficacy in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2024.12.18.628624v1?rss=1 Hancock, S. E. Garthwaite, L. Harellis, K. Susetio, M. Ding, E. Choong, L. Contreras, O. Nguyen, A. Lising, J. Hansen, F. K. Wongsomboon, P. Menzel, J. P. Poad, B. L. Mitchell, T. W. Blanksby, S. J. Turner, N. 2024-12-20 doi:10.1101/2024.12.18.628624 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Temporal evolution of color representations measured with MEG reveals a 'coarse to fine' dynamic ]]> https://biorxiv.org/content/10.1101/2024.12.19.629529v1?rss=1 Goddard, E. Mullen, K. T. 2024-12-20 doi:10.1101/2024.12.19.629529 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Temporally overlapping mechanisms diversify clonal B cell responses in vivo. ]]> https://biorxiv.org/content/10.1101/2024.12.17.628863v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@c57890org.highwire.dtl.DTLVardef@6e5936org.highwire.dtl.DTLVardef@a2e872org.highwire.dtl.DTLVardef@14abbac_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPartial temporal overlap of CSR with clonal expansion leads to isotype variegation in clones. C_LIO_LIClones seeding GCs bifurcate into plasmablasts and exhibit isotype variegation. C_LIO_LIGC B cells accrue [~]4 mutations/week, a rate unaffected by anti-malarials. C_LIO_LIPlasmodium infection triggers antigen-independent Type I IFN-mediated bystander activation. C_LIO_LIB cell development is preserved in malaria by shifting from bone marrow to spleen. C_LI ]]> Skinner, O. P. Asad, S. Moreira, M. L. Lee, H. J. Williams, C. G. Li, S. Jin, W. Steiner, T. M. Asatsuma, T. Lim, J. Ruan, Z. Soon, M. S. F. Engel, J. A. Khoury, D. S. Tuong, Z. K. King, H. W. Haque, A. 2024-12-21 doi:10.1101/2024.12.17.628863 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ FGF21 Analogue PF-05231023 on Alcohol Consumption and Neuronal Activity in the Nucleus Accumbens ]]> https://biorxiv.org/content/10.1101/2024.12.22.629996v1?rss=1 Cooley, B. J. Occelli Hanbury-Brown, C. V. Choi, E. A. Heller, W. A. Lim, A. W. Lawrence, A. J. Haber, P. S. McNally, G. P. Millan, E. Z. 2024-12-23 doi:10.1101/2024.12.22.629996 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Higher-order EEG microstate syntax and surrogate testing ]]> https://biorxiv.org/content/10.1101/2025.01.07.631820v1?rss=1 von Wegner, F. Hermann, G. Tödt, I. Todtenhaupt, I. K. Laufs, H. 2025-01-09 doi:10.1101/2025.01.07.631820 Cold Spring Harbor Laboratory Press 2025-01-09 <![CDATA[ hmde: Hierarchical Methods for Differential Equations ]]> https://biorxiv.org/content/10.1101/2025.01.15.633280v1?rss=1 O'Brien, T. A. Kar, F. Warton, D. Falster, D. S. 2025-01-20 doi:10.1101/2025.01.15.633280 Cold Spring Harbor Laboratory Press 2025-01-20 <![CDATA[ The Distribution of Elastin and Collagen Underpinning the Smart Properties of the Interosseous Membrane ]]> https://biorxiv.org/content/10.1101/2025.01.19.633808v1?rss=1 Anastopolous, S. Knothe Tate, M. L. 2025-01-22 doi:10.1101/2025.01.19.633808 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ De novo expression of neuropeptide Y in sensory neurons does not contribute to peripheral neuropathic pain ]]> https://biorxiv.org/content/10.1101/2025.01.25.634591v1?rss=1 Cooper, A. H. Nie, A. Hedden, N. Herzog, H. Taylor, B. K. 2025-01-27 doi:10.1101/2025.01.25.634591 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Clinical relevance of zebrafish for gene variants testing. Proof-of-principle with SMN1/SMA. ]]> https://biorxiv.org/content/10.1101/2025.01.30.632288v1?rss=1 US$2 million per child were avoided. Beyond SMA, this study provides robust proof-of-principle that the zebrafish represents a powerful translational tool for VUS-analysis, and that such approaches should be considered in clinical settings for supporting diagnosis and treatment decisions. ]]> Stringer, B. W. Zhang, Y. Taghipour-Sheshdeh, A. Goh, S. Kolbel, H. Farrar, M. A. Wirth, B. Giacomotto, J. 2025-01-31 doi:10.1101/2025.01.30.632288 Cold Spring Harbor Laboratory Press 2025-01-31 <![CDATA[ Recent thymic emigrants are preferentially recruited into the memory pool during persistent infection ]]> https://biorxiv.org/content/10.1101/2025.02.06.636722v1?rss=1 Hilt, Z. T. Reynaldi, A. Steinhilber, M. Zhang, S. Wesnak, S. P. Smith, N. L. Davenport, M. P. Rudd, B. D. 2025-02-08 doi:10.1101/2025.02.06.636722 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Diverse Viral Pathogens in Australian Canines: Limited Geographic Structure and the First Detection of an RNA Virus in Dingoes ]]> https://biorxiv.org/content/10.1101/2025.02.16.638538v1?rss=1 Mifsud, J. C. Harvey, E. Van Brussel, K. Olsson, A. Pitcher, B. J. Hall, J. Fenton, H. Alting, B. F. Sadiq, S. Holmes, E. C. 2025-02-17 doi:10.1101/2025.02.16.638538 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ The architecture, assembly, and evolution of a complex flagellar motor ]]> https://biorxiv.org/content/10.1101/2025.02.19.638559v1?rss=1 Feng, X. Tachiyama, S. He, J. Zhu, S. Zhao, H. Botting, J. M. Liu, Y. Chen, Y. Hua, C. Lara-Tejero, M. Baker, M. A. Gao, X. Liu, J. Gao, B. 2025-02-19 doi:10.1101/2025.02.19.638559 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ Unusual Ecofunctional Traits of Endozoicomonas: A Pan-Genomic Perspective ]]> https://biorxiv.org/content/10.1101/2025.03.06.641946v1?rss=1 Lim, S. L. Chin, C.-H. Chiou, Y.-J. Hsu, M.-T. Chiang, P.-W. Chen, H.-J. Tu, Y.-C. Tang, S.-L. 2025-03-11 doi:10.1101/2025.03.06.641946 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Blastocoel fluid RNA predicts pregnancy outcome in assisted reproduction ]]> https://biorxiv.org/content/10.1101/2025.03.09.641486v1?rss=1 Frisendahl, C. Gemzell-Danielsson, K. Nair, K. Koch, F. Menezes, J. Sheiki, M. Dahlgren, K. Alnahal, W. Lindgren, K. Bohlin, T. Olofsson, J. Tohonen, V. Vafaee, F. Grace, L. P. Boggavarapu, N. R. Faridani, O. R. 2025-03-11 doi:10.1101/2025.03.09.641486 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Region-specific variations in the cerebrovasculature underlie disease progression in Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2025.03.09.641541v1?rss=1 0.05) control cases (n=7). Analysis was carried out in brain regions variably affected by cell loss (substantia nigra) and protein deposition (substantia nigra and medial temporal cortex). The occipital cortex was included, as this region is not affected by cell loss or protein deposition. Group differences were analysed and the relationship with protein deposition (Lewy body stage, amyloid score, neurofibrillary tangle score) was assessed. Although total astrocyte density did not change (P >0.05), Parkinsons disease cases exhibited reduced aquaporin-4 in astrocytic endfeet and enlargement of the arteriolar and venular perivascular space. Significant changes in the capillary network were also observed with increased string vessel formation (P <0.001) and pericyte loss (P <0.001), changes likely to impact blood flow and its regulation. The formation of string vessels significantly correlated with disease duration (P <0.05), especially in the occipital cortex. The occipital cortex demonstrated the greatest decreases in pericytes (P <0.001) and aquaporin-4 mislocalisation (P <0.05), while changes in pericyte density were also significant in the substantia nigra. In contrast, these changes were not significant in the medial temporal cortex despite protein deposition in this region. Although no Lewy pathology was detected in the occipital cortex, there was a positive relationship between Lewy body stage and perivascular space size (Rho =0.6, P <0.05). These findings reveal progressive, region-specific alterations in the cellular components of the glymphatic system and vascular integrity in Parkinsons disease. Notably, the correlation between string vessel formation and disease duration, even in a region unaffected by protein deposition, suggests that vascular changes may play an important role in disease progression. These results emphasize the need for further investigation into the interplay between regional vascular changes and Parkinsons disease progression, which may offer novel insights for therapeutic strategies. ]]> Dik, D. Halliday, G. Sytnyk, V. Shepherd, C. E. 2025-03-11 doi:10.1101/2025.03.09.641541 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Tumbleweed: an artificial motor protein that walks along a DNA track ]]> https://biorxiv.org/content/10.1101/2025.03.07.641123v1?rss=1 Nilsson, P. Robertson, N. O. Gustafsson, N. Davies, R. Liew, C. Lyons, A. Eichhorn, R. Niman, C. Blab, G. Bromley, E. Whitten, A. E. Duff, A. Beech, J. Jönsson, P. Böcking, T. Höcker, B. Woolfson, D. Forde, N. R. Linke, h. Curmi, P. 2025-03-12 doi:10.1101/2025.03.07.641123 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Structural determinants of rotavirus proteolytic activation ]]> https://biorxiv.org/content/10.1101/2025.03.24.644915v1?rss=1 Asensio-Cob, D. Mata, C. P. Gomez-Blanco, J. Vargas, J. Rodriguez, J. M. Luque, D. 2025-03-24 doi:10.1101/2025.03.24.644915 Cold Spring Harbor Laboratory Press 2025-03-24 <![CDATA[ Dissecting the steps in early Simian Immunodeficiency Virus dissemination following mucosal and intravenous infection of rhesus macaques ]]> https://biorxiv.org/content/10.1101/2025.03.24.644849v1?rss=1 Docken, S. S. Macairan, A. Schlub, T. E. Fennessey, C. M. Varco-Merth, B. Picker, L. J. Okoye, A. A. Immonen, T. T. Cromer, D. Keele, B. F. Davenport, M. P. 2025-03-28 doi:10.1101/2025.03.24.644849 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ Structural Studies of an Anti-necroptosis Viral:Human Functional Hetero-amyloid M45:RIPK3 using SSNMR ]]> https://biorxiv.org/content/10.1101/2025.03.26.644761v1?rss=1 He, C. Varghese, N. R. Keeler, E. G. Pham, C. L. L. Williams, B. Tetter, S. Semaan, C. Wilde, K. L. Brown, S. H. J. Bouwer, J. C. Gambin, Y. Sierecki, E. Steain, M. Sunde, M. McDermott, A. E. 2025-03-29 doi:10.1101/2025.03.26.644761 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Mitochondrial function regulates cell growth kinetics to actively maintain mitochondrial homeostasis ]]> https://biorxiv.org/content/10.1101/2025.03.31.646474v1?rss=1 Chacko, L. A. Nakaoka, H. Morris, R. G. Marshall, W. Ananthanarayanan, V. 2025-04-01 doi:10.1101/2025.03.31.646474 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Adaptively integrated sequencing and assembly of near-complete genomes ]]> https://biorxiv.org/content/10.1101/2025.03.31.646505v1?rss=1 Gamaarachchi, H. Stevanovski, I. Hammond, J. M. Reis, A. L. M. Rapadas, M. Jayasooriya, K. Russell, T. Yeow, D. Hort, Y. Mallett, A. J. Stackpoole, E. Roman, L. Silver, L. W. Hogg, C. J. Streeting, L. Bogdanovic, O. Rodrigues, R. Nascimento, L. Cardoso, A. L. Georges, A. Cheng, H. Patel, H. R. Kumar, K. R. Mallawaarachchi, A. C. Deveson, I. W. 2025-04-04 doi:10.1101/2025.03.31.646505 Cold Spring Harbor Laboratory Press 2025-04-04 <![CDATA[ A selective inhibitor of oncogenic JNK signalling perturbs metastatic outgrowth of triple-negative breast cancer through metabolic blockade ]]> https://biorxiv.org/content/10.1101/2025.04.16.649243v1?rss=1 Latham, S. L. O'Donnell, Y. E. Girgis-Cook, O. Clearwater, M. S. Bryce, N. S. Mok, E. Lynn, S. A. Ni, J. Alfred, S. Leong, K. H. Quek, L.-e. Murphy, K. Pantarelli, C. Dragutinovic, I. Naeini, M. Thiel, C. Cadell, A. Phimmachanh, M. Sharma, R. Millar, E. Han, J. Z. Hastings, J. F. Koehler, M. Brummer, T. Young, A. O'Toole, S. Oakes, S. Hardeman, E. Lock, J. Kolch, W. Taft, M. H. Nobis, M. Goldstein, L. Timpson, P. Parker, B. L. Holst, J. Gunning, P. W. Cox, T. R. Morris, J. C. Croucher, D. R. 2025-04-17 doi:10.1101/2025.04.16.649243 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ Dysregulated Proline Metabolism Contributes to Subretinal Fibrosis in Neovascular AMD: Therapeutic Potential of Prolyl-4-Hydroxylase Inhibition ]]> https://biorxiv.org/content/10.1101/2025.04.13.648057v1?rss=1 Zeng, Y. Zhang, T. Cornish, E. Lee, S.-R. Yam, M. Eminhizer, M. Zeng, J. Zhang, J. Zeng, S. Wei, X. Yang, J. Zhu, M. Chang, A. Zhang, M. Du, J. Zhu, L. Gillies, M. C. 2025-04-19 doi:10.1101/2025.04.13.648057 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Impacts of high pathogenicity avian influenza H5N1 2.3.4.4b south of the Antarctic Circle ]]> https://biorxiv.org/content/10.1101/2025.04.13.648652v1?rss=1 Gorta, S. B. Z. Neira, V. Wille, M. Gajardo, D. Yılmaz, A. Oktar, O. Özsoy, B. Sekercioglu, C. H. 2025-04-19 doi:10.1101/2025.04.13.648652 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ Arcuate Fasciculus: Evolutionary Convergence in Marmosets and Humans ]]> https://biorxiv.org/content/10.1101/2025.04.21.649746v1?rss=1 Wang, Y. Cheng, L. Li, D. Lu, Y. Hopkins, W. Sherwood, C. Xu, T. Liu, C. Paxinos, G. Jiang, T. Chu, C. Fan, L. 2025-04-21 doi:10.1101/2025.04.21.649746 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Long-read transcriptome-wide RNA structure maps using DMS-FIRST-seq ]]> https://biorxiv.org/content/10.1101/2025.04.22.649934v1?rss=1 Begik, O. Diensthuber, G. Borovska, I. Mattick, J. S. Incarnato, D. Novoa, E. M. 2025-04-22 doi:10.1101/2025.04.22.649934 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ Medlib: A Feature-Rich C/C++ Library for Exact Alignment of Nanopore Sequences Using Multiple Edit Distance ]]> https://biorxiv.org/content/10.1101/2025.05.01.651420v1?rss=1 Rafeie, M. Vafaee, F. Faridani, O. R. 2025-05-07 doi:10.1101/2025.05.01.651420 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ An approach to differentiating biological from chemical sulfide oxidation on corroded concrete sewer surfaces ]]> https://biorxiv.org/content/10.1101/2025.05.13.653906v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@1cfd16aorg.highwire.dtl.DTLVardef@bd9677org.highwire.dtl.DTLVardef@e1610forg.highwire.dtl.DTLVardef@ab3dfc_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Huang, X. Yin, Y. Zuo, Z. Shi, T. Kuen, T. Zheng, M. 2025-05-14 doi:10.1101/2025.05.13.653906 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ The influence of nucleus accumbens shell D1 and D2 neurons on outcome-specific Pavlovian instrumental transfer ]]> https://biorxiv.org/content/10.1101/2025.05.26.656228v1?rss=1 Soegyono, O. Pepin, E. Leung, B. K. Chieng, B. Balleine, B. W. Laurent, V. 2025-05-27 doi:10.1101/2025.05.26.656228 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Rampant transitions between dispersal syndromes duringangiosperm evolution ]]> https://biorxiv.org/content/10.1101/2025.05.26.656093v1?rss=1 1200 species representing all extant angiosperm families. We used phylogenetic comparative methods to infer ancestral states of major angiosperm clades, trends in the evolution of dispersal syndromes, and evolutionary correlations between dispersal syndromes, biomes and pollination modes. C_LIO_LIWe show that angiosperms were ancestrally most likely animal-dispersed (zoochory) and had fleshy, indehiscent fruits. Over macroevolutionary time, frequent transitions between dispersal syndromes occurred, often with non-specialised (autonomous) dispersal as an intermediate state. Finally, we found that dispersal syndrome evolution affected transition rates among biomes and among pollination modes. C_LIO_LIThe number of dispersal syndrome transitions exceeded pollination mode transitions by a factor of five, emphasizing lability in dispersal syndrome evolution. The progressive evolution of diaspore complexity led to frequent and repeated evolution of dispersal syndromes, critical for the colonization of angiosperms across modern biomes. C_LI ]]> de Frens, D. Bakker, F. T. Sauquet, H. Stephens, R. E. Onstein, R. E. 2025-05-29 doi:10.1101/2025.05.26.656093 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ Host adaptation and genome evolution of the broad host range fungal rust pathogen, Austropuccinia psidii ]]> https://biorxiv.org/content/10.1101/2025.05.29.656941v1?rss=1 Luo, Z. Tobias, P. Singh, L. Dong, C. Martino, A. M. Quecine, M. Massola Junior, N. S. Silva, L. C. A. Li, J. Singh, S. Zhang, Z. Jones, A. Park, R. F. Schwessinger, B. Edwards, R. Boufleur, T. 2025-06-01 doi:10.1101/2025.05.29.656941 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Underappreciated role of environmental enrichment in alleviating depression and anxiety: Quantitative evidence synthesis of rodent models ]]> https://biorxiv.org/content/10.1101/2025.06.02.657339v1?rss=1 Yang, Y. Liu, M. Morrison, K. Lagisz, M. Nakagawa, S. 2025-06-04 doi:10.1101/2025.06.02.657339 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ Multifaceted evolution of dental morphology during the diversification of the bat superfamily Noctilionoidea ]]> https://biorxiv.org/content/10.1101/2025.06.10.658888v1?rss=1 Lopez Aguirre, C. Ballen, G. Hand, s. J. Silcox, M. T. 2025-06-15 doi:10.1101/2025.06.10.658888 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Predicting continuous outcomes: Some new tests of associative approaches to contingency learning. ]]> https://biorxiv.org/content/10.1101/2025.06.12.659290v1?rss=1 Chow, J. Don, H. J. Colagiuri, B. Livesey, E. J. 2025-06-15 doi:10.1101/2025.06.12.659290 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ FiPhoPHA - A fiber photometry python package for post-hoc analysis ]]> https://biorxiv.org/content/10.1101/2025.06.12.659422v1?rss=1 Drakopoulos, V. Reichenbach, A. Stark, R. Foldi, C. J. Jean-Richard-dit-Bressel, P. Andrews, Z. B. 2025-06-15 doi:10.1101/2025.06.12.659422 Cold Spring Harbor Laboratory Press 2025-06-15 <![CDATA[ Foot placement coordination is impaired in people with Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2025.06.11.659042v1?rss=1 Lang, C. Hausdorff, J. M. Bruijn, S. M. Brodie, M. A. Okubo, Y. Maetzler, W. van Leeuwen, A. M. Singh, N. B. van Dieen, J. H. Ravi, D. K. 2025-06-17 doi:10.1101/2025.06.11.659042 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis ]]> https://biorxiv.org/content/10.1101/2025.06.16.657725v1?rss=1 Steele, N. Morey, R. Hussain, A. Russell, C. Suarez-Jimenez, B. Pozzi, E. Jameei, H. Schmaal, L. Veer, I. Waller, L. Jahanshad, N. Thomopoulos, S. Salminen, L. Olff, M. Frijling, J. Veltman, D. Koch, S. Nawijn, L. van Zuiden, M. Wang, L. Zhu, Y. Li, G. Stein, D. Ipser, J. Neria, Y. Zhu, X. Ravid, O. Zilcha-Mano, S. Lazarov, A. Huggins, A. Stevens, J. Ressler, K. Jovanovic, T. van Rooij, S. Fani, N. Mueller, S. Hudson, A. Daniels, J. Sierk, A. Manthey, A. Walter, H. van der Wee, N. van der Werff, S. Vermeiren, R. Schmahl, C. Herzog, J. Rektor, I. i 2025-06-17 doi:10.1101/2025.06.16.657725 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Non-cell autonomous control of presynaptic remodeling by the hypothalamic autophagy/NPY axis ]]> https://biorxiv.org/content/10.1101/2025.06.20.660653v1?rss=1 Cazzolla, G. Toppe, D. Krause, G. Kochlamazashvili, G. Luetzkendorf, J. Schedina, I. M. Kerkhoff, Y. Reifenstein, E. von Kleist, M. Herzog, H. Albrecht, A. Schmitz, D. Haucke, V. Sigrist, S. J. Maglione, M. 2025-06-22 doi:10.1101/2025.06.20.660653 Cold Spring Harbor Laboratory Press 2025-06-22 <![CDATA[ Genomic analysis identifies Campylobacter concisus genomospecies 2 as a novel species and proposes the name Campylobacter oralis ]]> https://biorxiv.org/content/10.1101/2025.06.24.661227v1?rss=1 Liu, F. Chen, S. Biazik, J. M. Luk, C. Ravipati, A. Lan, R. Riordan, S. M. Zhang, L. 2025-06-26 doi:10.1101/2025.06.24.661227 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Expanding the utility of transcriptome analysis for mutation detection in high-risk childhood precision oncology ]]> https://biorxiv.org/content/10.1101/2025.06.25.661445v1?rss=1 Mayoh, C. Barahona, P. Lin, A. Cui, L. Ajuyah, P. Altekoester, A. Lau, L. M. Khuong-Quang, D.-A. Sullivan, P. Senapati, A. Nagabushan, S. Sullivan, A. Omer, N. Moore, A. S. Nicholls, W. Endersby, R. Gottardo, N. G. McCowage, G. B. Dalla Pozza, L. Hansford, J. R. Khaw, S.-L. Wood, P. J. Trahair, T. N. Marshall, G. M. Ziegler, D. S. Tyrrell, V. Haber, M. Wong, M. Ekert, P. G. Cowley, M. J. 2025-06-26 doi:10.1101/2025.06.25.661445 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Sodium Butyrate Rescues Neurodevelopmental Deficits Following Perinatal Methadone Exposure ]]> https://biorxiv.org/content/10.1101/2025.06.26.661851v1?rss=1 Williams, I. A. R. van Dorst, J. Leigh, S.-J. Baracz, S. J. Marcus, A. McCaffrey, D. Walker, A. Ooi, C. Y. Ward, M. C. Oei, J.-L. Clemens, K. 2025-06-28 doi:10.1101/2025.06.26.661851 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ The enduring advantages of the SLOW5 file format for raw nanopore sequencing data ]]> https://biorxiv.org/content/10.1101/2025.06.30.662478v1?rss=1 Gamaarachchi, H. Jenner, S. Samarakoon, H. Ferguson, J. M. Deveson, I. W. 2025-07-04 doi:10.1101/2025.06.30.662478 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Replication of SARS-CoV-2 Omicron lineages is defined by TMPRSS2 use in environments where ACE2 is complexed with solute carriers SLC6A19 and SLC6A20. ]]> https://biorxiv.org/content/10.1101/2025.07.07.663433v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@172aa47org.highwire.dtl.DTLVardef@109285eorg.highwire.dtl.DTLVardef@394f8corg.highwire.dtl.DTLVardef@958e31_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Aggarwal, A. Ognenovska, S. Ison, T. Fichter, C. Milogiannakis, V. Afzal, M. Ospina Stella, A. Waters, S. Esneau, C. Bartlett, N. Pöhlmann, S. Hoffmann, M. Burrell, L. M. Patel, S. Ellis, S. Wehrhahn, M. Ginn, A. Martinez, E. Churchill, M. Angelovich, T. Rawlinson, W. D. Yeang, M. Kok, J. Sintchenkov, V. Parry, R. Sng, J. D. Neely, G. G. Moreno, C. L. Loo, L. Kelleher, A. D. Brilot, F. Khromykh, A. Turville, S. G. 2025-07-08 doi:10.1101/2025.07.07.663433 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Navigating parasite antigen genetic diversity in the design of Plasmodium vivax serological exposure markers for malaria ]]> https://biorxiv.org/content/10.1101/2025.07.07.663616v1?rss=1 Bareng, P. Wu, K. W. Takashima, E. Argyropoulos, D. Smith, L. Naung, M. Mazhari, R. Schoffer, K. Kiernan-Walker, N. Abraham, A. Lamont, M. Mehra, S. Lim, P. Sattabongkot, J. Monteiro, W. M. Lacerda, M. V. G. d. Healer, J. Chitnis, C. E. Tham, W.-H. Tsuboi, T. Mueller, I. Barry, A. E. Longley, R. J. 2025-07-08 doi:10.1101/2025.07.07.663616 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Epithelial-mesenchymal cell state heterogeneity predetermines differential phospho-signaling responses to epidermal growth factor stimulation ]]> https://biorxiv.org/content/10.1101/2025.07.05.658545v1?rss=1 64,000 A549 NSCLC cells labeled for DNA, F-actin and alternate signaling markers (p-AKT-S473, p-AKT-T308, p-ERK or p-S6) after acute stimulation. Quantitative single-cell morphological and spatial profiling defined a stimulus-invariant E/M state landscape over which EGF signaling responses were compared. This revealed state-dependent differences in signal-activation magnitudes, dynamics and subcellular routing. AKT responses exhibited phosphosite- and compartment-specific dynamics across states, with epithelial cells showing strong, transient membrane-localized S473 and higher internalized T308, whereas mesenchymal cells displayed weaker but sustained nuclear and ruffle-localized S473. Regression-based computational multiplexing concurrently inferred all signaling responses per cell, mapping state-dependent divergence in multi-molecular signaling trajectories. E/M state thus pre-determines distinctive spatiotemporal profiles of EGF-induced signaling, with implications for signaling functions and anti-signaling therapy responses across E/M state-diverse tumors. ]]> Kohane, F. V. Johnstone, C. Neumann, D. P. Gunawan, I. Huang, T. Vafaee, F. Chaffer, C. L. Lock, J. G. 2025-07-09 doi:10.1101/2025.07.05.658545 Cold Spring Harbor Laboratory Press 2025-07-09 <![CDATA[ The effect of PEGylation on surface tethering of liposomes via DNA nanotechnology. ]]> https://biorxiv.org/content/10.1101/2025.07.07.663613v1?rss=1 View larger version (55K): org.highwire.dtl.DTLVardef@183b215org.highwire.dtl.DTLVardef@1208fd6org.highwire.dtl.DTLVardef@c343ccorg.highwire.dtl.DTLVardef@1982f80_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gaston, J. Meepat, S. Islam, M. S. Daljit Singh, J. K. Booth, M. J. Wickham, S. F. J. Baker, M. A. 2025-07-09 doi:10.1101/2025.07.07.663613 Cold Spring Harbor Laboratory Press 2025-07-09 <![CDATA[ Tracking breast cancer progression using Methylscape ]]> https://biorxiv.org/content/10.1101/2025.07.09.664004v1?rss=1 Zhang, Z. Ahmed, E. Constantin, N. Lu, J. Korbie, D. Wuethrich, A. Sina, A. Trau, M. 2025-07-15 doi:10.1101/2025.07.09.664004 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ Identifying the Minimal Number of Protein Markers for Cell Type Annotation Using MiniMarS ]]> https://biorxiv.org/content/10.1101/2025.07.14.664825v1?rss=1 0.9). Additionally, we showed that by appropriately combining clusters, MiniMarS improves the F1 score of a rare population identification (<1% of total cells) by 28.7%. Together, these findings highlight the broad applicability of MiniMarS in identifying appropriate markers for distinguishing cell populations. ]]> Parikh, D. Xue, A. Liao, H.-C. Wishart, C. Ashhurst, T. M. Putri, G. Luciani, F. Naik, S. Salim, A. Marsh-Wakefield, F. Louie, R. 2025-07-18 doi:10.1101/2025.07.14.664825 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Base modification analysis in long read sequencing data using Minimod ]]> https://biorxiv.org/content/10.1101/2025.07.16.665072v1?rss=1 Samarasinghe, S. Deveson, I. W. Gamaarachchi, H. 2025-07-21 doi:10.1101/2025.07.16.665072 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Volumetric Differences of Thalamic Nuclei are Associated with Post-Trauma Psychopathology ]]> https://biorxiv.org/content/10.1101/2025.07.24.666644v1?rss=1 Steele, N. Hussain, A. Baird, C. L. Haswell, C. C. Sun, D. Rangel-Jimenez, L. Abdallah, C. G. Angstadt, M. August, G. Berg, H. Blackford, J. U. Cisler, J. Daniels, J. K. Davenport, N. D. Davidson, R. J. Densmore, M. Disner, S. G. El-Hage, W. Etkin, A. Fani, N. Frijling, J. L. Gordon, E. M. Grupe, D. W. Herringa, R. J. Hudson, A. R. Jahanshad, N. Jovanovic, T. King, A. Koch, S. B. J. Lanius, R. Lazarov, A. Li, G. Liberzon, I. Lissek, S. Lu, G. M. Manthey, A. Maron-Katz, A. Nawijn, L. Nelson, S. M. Neria, Y. Neufeld, R. W. J. Nitschke, J. B. Olatunji, B. 2025-07-25 doi:10.1101/2025.07.24.666644 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Capillary constrictions prime cancer cell tumorigenicity through PIEZO1 ]]> https://biorxiv.org/content/10.1101/2025.07.22.666218v1?rss=1 Kilian, K. Silvani, G. Romanazzo, S. Das, A. Kopecky, C. Rodriguez, V. Chaffer, C. L. Lock, J. G. Poole, K. 2025-07-26 doi:10.1101/2025.07.22.666218 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ The impact of sex on the immune system explored at the single-cell level ]]> https://biorxiv.org/content/10.1101/2025.07.27.667062v1?rss=1 Yazar, S. Alquicira-Hernandez, J. Wing, K. Senabouth, A. Andersen, S. Fairfax, K. A. Hewitt, A. W. Powell, J. E. Ballouz, S. 2025-07-31 doi:10.1101/2025.07.27.667062 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Image quality metrics fail to accurately represent biological information in fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/2025.08.05.668508v1?rss=1 Gunawan, I. Marsh, R. Aggarwal, N. Meijering, E. Cox, S. Lock, J. G. Culley, S. 2025-08-07 doi:10.1101/2025.08.05.668508 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ A Scalable Toolkit for Modeling 3D Surface-based Brain Geometry ]]> https://biorxiv.org/content/10.1101/2025.08.06.668521v1?rss=1 Im, Y. Nabulsi, L. Kang, M. J. Y. Thomopoulos, S. I. Zuluaga, A. M. D. Dale, A. M. Karuk, A. Giorgio, A. D. Mwangi, B. Gutman, B. Overs, B. Jaramillo, C. L. McDonald, C. Stein, D. Cannon, D. M. Glahn, D. Hidalgo-Mazzei, D. Pecheva, D. Grotegerd, D. Pomarol-Clotet, E. Vieta, E. Olie, E. Cherto, E. V. Sambataro, F. Howells, F. Scheffler, F. Busatto, G. Anmella, G. Zunta-Soares, G. B. Roberts, G. Temmingh, H. Gotlib, I. Agartz, I. Soares, J. C. Karantonis, J. A. Prisciandaro, J. Fullerton, J. M. Radua, J. Savitz, J. Houenou, J. Sim, K. Harada, K. Berger, 2025-08-09 doi:10.1101/2025.08.06.668521 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Mechanistic Insights into Lenacapavir-Induced Off-Pathway HIV-1 Capsid Assembly ]]> https://biorxiv.org/content/10.1101/2025.08.13.670175v1?rss=1 Gupta, M. Waltmann, C. Renner, N. Wang, Y. James, L. Jacques, D. A. Bocking, T. Voth, G. A. 2025-08-13 doi:10.1101/2025.08.13.670175 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ 10 recommendations for strengthening citizen science for improved societal and ecological outcomes: A co-produced analysis of challenges and opportunities in the 21st century ]]> https://biorxiv.org/content/10.1101/2025.08.13.670232v1?rss=1 Nunn, J. S. da Silva Hyldmo, H. McKnight, L. McCulloch, H. Lavers, J. Old, J. Smith, L. Grobler, N. Tan Kay Yin, C. Chan, W. Y. Raeburn, C. Simard, N. S. M. Kingsley Smith, A. Van Holsbeeck, S. Drinkwater, E. Prendergast, K. Burrows, E. Lawson, C. L. 2025-08-17 doi:10.1101/2025.08.13.670232 Cold Spring Harbor Laboratory Press 2025-08-17 <![CDATA[ Multi-nucleation in two-cell human embryos stems from spindle and metaphase plate incoherence in the first mitosis ]]> https://biorxiv.org/content/10.1101/2025.08.20.671312v1?rss=1 Pieper, G. H. Aboelenain, M. Munro, L. Mihalas, B. P. Currie, C. E. Taylor, D. Collins, D. M. Hartshorne, G. M. McAinsh, A. D. Anderson, R. A. Marston, A. L. 2025-08-21 doi:10.1101/2025.08.20.671312 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ Endothelial Colony-Forming Cell Transcriptomic Profiling in CT-defined Coronary Artery Disease from the BioHEART-CT Study Implicate CCBE1 in Mitochondrial Dysfunction-associated Atherosclerosis ]]> https://biorxiv.org/content/10.1101/2025.08.18.670989v1?rss=1 10 had a 2.8-fold increase in the log-odds ratio of CT-defined CAD. CAD ECFCs displayed elevated mROS and mitochondrial mass. CCBE1 knockdown in HUVECs reduced mROS and mitochondrial mass without affecting proliferation or permeability, but shifted cells into a metabolically elevated state, marked by increased ATP production, respiration and glycolysis. CCBE1 cis-eQTLs were associated with increased odds of CAD in the BioHEART-CT cohort. ConclusionsCCBE1 expression in ECFCs was higher in patients with CT-defined CAD versus non-CAD. Quantitative assessment of transcript levels supported a causal relationship between greater CCBE1 expression and CAD burden and risk, and functional experiments on CCBE1 knockdown demonstrated improved mitochondrial function in human endothelial cells. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/670989v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@4e609aorg.highwire.dtl.DTLVardef@1a85810org.highwire.dtl.DTLVardef@12d97cdorg.highwire.dtl.DTLVardef@494ab3_HPS_FORMAT_FIGEXP M_FIG C_FIG Novelty and SignificanceO_ST_ABSWhat is Known?C_ST_ABSO_LIThe endothelium plays a critical role in vascular health and susceptibility to atherosclerosis. C_LIO_LIMitochondrial dysfunction has been implicated in atherosclerosis, but its role and mechanism in individual susceptibility to CAD in humans is not known. C_LI What New Information Does This Article Contribute?O_LINovel approach integrating CT imaging with ECFC functional data to link vascular structure with endothelial biology ex vivo. C_LIO_LIPatients with CT-defined CAD had 3.6-fold higher CCBE1 expression compared to non-CAD within the Validation Cohort. C_LIO_LICis-eQTL-association analysis revealed increased odds of CAD. C_LIO_LICCBE1 knockdown improved mitochondrial function in human endothelial cells. C_LIO_LITogether, these 4 lines of evidence point to a novel and causal role for CCBE1 in human CAD. C_LI ]]> Lee, W. E. Cook, S. L. Purvis, G. S. D. Henry, A. Schnitzler, K. Genetzakis, E. Besnier, M. Chandrakanthan, M. Tran, A. Strbenac, D. Mifsud, C. Bate, K. Vernon, S. T. Nguyen, T. V. Gray, M. P. Grieve, S. Yang, J. MacArthur, D. G. Powell, J. E. Channon, K. M. Douglas, G. Figtree, G. A. 2025-08-22 doi:10.1101/2025.08.18.670989 Cold Spring Harbor Laboratory Press 2025-08-22 <![CDATA[ Beyond species means - the intraspecific contribution to global wood density variation ]]> https://biorxiv.org/content/10.1101/2025.08.25.671896v1?rss=1 0.08 g cm-3; single-measurement R2 = 0.59). We recommend (i) systematic within-species sampling for local applications, and (ii) expanded taxonomic coverage combined with integrative models for robust estimates across ecological scales. ]]> Fischer, F. J. Chave, J. Zanne, A. Jucker, T. Fajardo, A. Fayolle, A. de Lima, R. A. F. Vieilledent, G. Beeckman, H. Hubau, W. De Mil, T. Wallenus, D. Aldana, A. M. Alvarez-Davila, E. Alves, L. F. Apgaua, D. M. G. Arcanjo, F. Bastin, J.-F. Bilous, A. Birnbaum, P. Blyshchyk, V. Borah, J. Boukili, V. Camarero, J. J. Casas, L. Gatti, R. C. Chambers, J. Q. Fabiano, E. C. Choat, B. Conti, G. Cornwell, W. Dar, J. A. Das, A. K. Dobler, M. Dougabka, D. Edwards, D. P. Evans, R. Falster, D. Fearnside, P. Flores, O. Fyllas, N. Gerard, J. Goodman, R. C. Guibal, D 2025-08-28 doi:10.1101/2025.08.25.671896 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ A global map of wood density ]]> https://biorxiv.org/content/10.1101/2025.08.25.671920v1?rss=1 Fischer, F. J. Chave, J. Zanne, A. Jucker, T. Fajardo, A. Fayolle, A. de Lima, R. A. F. Vieilledent, G. Beeckman, H. Hubau, W. De Mil, T. Wallenus, D. Aldana, A. M. Alvarez-Davila, E. Alves, L. F. Apgaua, D. M. G. Arcanjo, F. Bastin, J.-F. Bilous, A. Birnbaum, P. Blyshchyk, V. Borah, J. Boukili, V. Camarero, J. J. Casas, L. Cazzolla Gatti, R. Chambers, J. Q. Chimbioputo Fabiano, E. Choat, B. Cifuentes, E. Conti, G. Coomes, D. Cornwell, W. Dar, J. A. Das, A. K. Dobler, M. Dougabka, D. Edwards, D. P. Eggli, U. Evans, R. Falster, D. Fearnside, P. Flores, 2025-08-28 doi:10.1101/2025.08.25.671920 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Transdiagnostic symptomatology amidst real-world environmental uncertainty: a cross-sectional and cross-lagged panel network analysis ]]> https://biorxiv.org/content/10.1101/2025.08.25.672142v1?rss=1 Hedley, F. E. Lage, C. Hertz-Palmor, N. Sandhu, T. R. Schweizer, S. Lawson, R. P. 2025-08-30 doi:10.1101/2025.08.25.672142 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ A microbiome meta-transcriptomics pipeline identifies a novel human neutrophil elastase inhibitor that protects the colonic epithelial barrier ]]> https://biorxiv.org/content/10.1101/2025.09.11.675725v1?rss=1 Stojkovic, B. Bekkers, M. Violi, J. Neilan, B. Keely, S. Donald, W. A. Riveros, C. Kaiko, G. 2025-09-12 doi:10.1101/2025.09.11.675725 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ High-stability, clamp-free soluble Sarbecovirus spike trimers and their potential for pan-Sarbecovirus vaccine development. ]]> https://biorxiv.org/content/10.1101/2025.09.14.676173v1?rss=1 10-fold higher neutralizing antibody (NAb) titres than parental unlinked trimers and protected the mice against viral challenge. A trivalent vaccine formulation comprised of covalently stabilized spikes derived from 3 divergent ACE2-using Sarbecovirus clades elicited broad and potent neutralizing activity in mice. The covalently linked S trimers were stable at 37{degrees}C for 112 days and remained intact following lyophilization and storage at ambient temperature for 6 months. This study establishes a framework for producing simple and stable highly immunogenic pan-Sarbecovirus S subunit vaccines that can be stored and distributed in the absence of a cold chain. ]]> Langer, C. Boo, I. Zakir, T. Mackenzie-Kludas, C. Samuel, J. Fabb, S. A. Lee, C. Center, R. J. Aggarwal, A. Turville, S. G. Pouton, C. W. Subbarao, K. Coulibaly, F. Drummer, H. E. Poumbourios, P. 2025-09-15 doi:10.1101/2025.09.14.676173 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Generative semantic multiplexing (SemaPlex) for accessible and scalable multiplexed fluorescence imaging ]]> https://biorxiv.org/content/10.1101/2025.09.15.676186v1?rss=1 Gunawan, I. Dey, M. Neumann, D. P. Kohane, F. V. He, Y. Meijering, E. Lock, J. G. 2025-09-18 doi:10.1101/2025.09.15.676186 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Local translation of circular RNAs is required for synaptic activity and memory ]]> https://biorxiv.org/content/10.1101/2025.09.18.676988v1?rss=1 Gong, H. Ren, H. Liau, W.-S. Zhao, Q. Walsh, A. D. Musgrove, M. R. B. Davies, J. W. A. Zajackowski, E. L. Madugalle, S. U. Marshall, P. R. Xu, Z. Lan, T. Shi, J. Jiang, J. Wei, W. Li, X. Voineagu, I. U. Wang, J. Sultana, S. Chen, C.-k. Zhang, L. Banerjee, S. Anggono, V. Chang, H. Y. Bredy, T. W. 2025-09-19 doi:10.1101/2025.09.18.676988 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Selective degradation of oncogenic extrachromosomal DNA by type I-E CRISPR ]]> https://biorxiv.org/content/10.1101/2025.09.21.677573v1?rss=1 Poursani, E. Pham, V. V. Ehteda, A. Vittorio, O. 2025-09-21 doi:10.1101/2025.09.21.677573 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Neuroanatomical Correlates of Negative Symptoms in Schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.09.22.677864v1?rss=1 Kamalakannan, S. M. V. Male, A. G. Yilanli, M. Lella, A. Lee, J. Quide, Y. Green, M. J. Cairns, M. J. Carr, V. J. Catts, S. Henskens, F. A. Jablensky, A. Loughland, C. Michie, P. Mowry, B. Pantelis, C. Shall, U. Scott, R. J. Belger, A. Bustillo, J. Lim, K. Ford, J. M. Mathalon, D. H. Preda, A. Mueller, B. Potkin, S. G. Satterhwaite, T. D. Gur, R. C. Gur, R. E. Banaj, N. Vecchio, D. Piras, F. Piras, F. Ehrlich, S. Bernardoni, F. Borgwardt, S. Cobia, D. Alpert, K. Wang, L. Agartz, I. Jonsson, E. G. Kaiser, S. Clotet, E. P. Salvador, R. Jaramillo, C. L. 2025-09-23 doi:10.1101/2025.09.22.677864 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Fluorescently Labeled Gradient Hydrogels Reveal Matrix-Dependent Cell Responses to Substrate Stiffness ]]> https://biorxiv.org/content/10.1101/2025.09.23.677581v1?rss=1 Chong, S. W. Liu, L. Kempe, D. Zhang, Y. Kalantar-Zadeh, K. Bilek, M. Ju, L. A. Biro, M. Vigolo, D. 2025-09-25 doi:10.1101/2025.09.23.677581 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Study of Sex Differences in the Whole Brain White Matter Using Diffusion MRI Tractography and Suprathreshold Fiber Cluster Statistics ]]> https://biorxiv.org/content/10.1101/2025.09.27.679006v1?rss=1 Zhang, F. Rushmore, R. J. Li, Y. Cetin Karayumak, S. Song, Y. Cai, W. Westin, C.-F. Levitt, J. J. Makris, N. Rathi, Y. O'Donnell, L. J. 2025-09-28 doi:10.1101/2025.09.27.679006 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ OpenGRF: Predicting Ground Reaction Forces and Moments During Daily Living Activities in OpenSim ]]> https://biorxiv.org/content/10.1101/2025.09.27.678739v1?rss=1 Di Pietro, A. Di Puccio, F. Modenese, L. 2025-09-29 doi:10.1101/2025.09.27.678739 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Unveiling the evolutionary code of NOTCH3: mammalian bioinformatics sheds light on human pathogenicity. ]]> https://biorxiv.org/content/10.1101/2025.09.28.678708v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@5b54cforg.highwire.dtl.DTLVardef@1d0725org.highwire.dtl.DTLVardef@1c0417corg.highwire.dtl.DTLVardef@10b4b5b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Siddiqui, K. S. Ertan, H. Ren, Y. Plojak, A. Jayasena, T. Sachdev, P. S. 2025-09-29 doi:10.1101/2025.09.28.678708 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ High-content imaging reveals the ability of microexons to shape protein localisation ]]> https://biorxiv.org/content/10.1101/2025.09.30.679652v1?rss=1 Kjer-Hansen, P. Pazaky, K. Kavanagh, D. King, H. E. O'Connell, S. Santos-Rodriguez, G. Grootveld, A. K. Vieira, H. G. S. Berry, S. Fernandez-Chamorro, J. Weatheritt, R. J. 2025-10-01 doi:10.1101/2025.09.30.679652 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Mapping EGFR1 sorting domains in endosomes with a calibrated 3D expansion microscopy toolkit ]]> https://biorxiv.org/content/10.1101/2025.10.01.678490v1?rss=1 Shakespeare, T. Seehra, R. S. Rodriguez, N. F. Atuanya, N. Sheard, T. M. D. Koehler, R. Bose, D. Woodman, P. G. Ciani, B. Jayasinghe, I. 2025-10-02 doi:10.1101/2025.10.01.678490 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Between- and within-host mutation of dengue virus ]]> https://biorxiv.org/content/10.1101/2025.10.12.680595v1?rss=1 Maduranga, S. Valencia, B. M. Sigera, C. Weeratunga, P. Fernando, D. Rajapakse, S. Rapadas, M. Deveson, I. W. Lloyd, A. R. Bull, R. Rodrigo, C. 2025-10-14 doi:10.1101/2025.10.12.680595 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Chemotherapy accelerated bone ageing is reversed by NMN ]]> https://biorxiv.org/content/10.1101/2025.10.13.679926v1?rss=1 Marinova, M. B. Madawala, R. Ho, W.-H. J. Lovric, V. Bertoldo, M. J. Oliver, R. A. Maniam, J. Morris, M. J. Sinclair, D. A. Homer, H. A. Walters, K. A. Erlich, J. H. Walsh, W. R. Gilchrist, R. B. Wu, L. E. 2025-10-14 doi:10.1101/2025.10.13.679926 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ The illusion of infinity: Acoustic black holes in wood deceive termites ]]> https://biorxiv.org/content/10.1101/2025.10.13.681988v1?rss=1 Nerse, C. Sepehrirahnama, S. Lai, J. C. S. Evans, T. Oberst, S. 2025-10-14 doi:10.1101/2025.10.13.681988 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ The tuberculosis-associated microenvironment promotes HIV-1 persistence by impairing CD8+ T cell-mediated viral control ]]> https://biorxiv.org/content/10.1101/2025.10.14.682453v1?rss=1 Cronin, S. Simpson, J. Pereyra Casanova, A. Li, Y. Marin Rojas, J. Warner van Dijk, F. Fisher, K. Vahlas, Z. ONeil, T. Bertram, K. Lee, E. Turk, G. Quiroga, M. F. Kelleher, A. Verollet, C. Balboa, L. Palmer, S. Duette, G. A. 2025-10-15 doi:10.1101/2025.10.14.682453 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Perceiving surface colour requires attention ]]> https://biorxiv.org/content/10.1101/2025.10.14.682481v1?rss=1 Goddard, E. Paul Remician, K. 2025-10-16 doi:10.1101/2025.10.14.682481 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Silencing the signal: The metastasis suppressor NDRG1 disrupts exosome-mediated crosstalk in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2025.10.15.682724v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@154b908org.highwire.dtl.DTLVardef@13fe6f5org.highwire.dtl.DTLVardef@540fadorg.highwire.dtl.DTLVardef@d15636_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chang, J. Alenizi, S. Zaccaron Milioli, H. Lay, W. Pounraj, S. Li, Y. Shiferaw, M. S. Hosseini Beheshti, E. Kovacevic, Z. 2025-10-16 doi:10.1101/2025.10.15.682724 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Associations between volumes of grey matter regions and white matter hyperintensities with cognitive empathy in oldest-old adults ]]> https://biorxiv.org/content/10.1101/2025.10.16.682959v1?rss=1 Chander, R. J. Grainger, S. A. Crawford, J. D. Jiang, J. Kochan, N. A. Numbers, K. Brodaty, H. Henry, J. D. Wen, W. Sachdev, P. S. 2025-10-17 doi:10.1101/2025.10.16.682959 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ An efficient eukaryotic cell-free expression and correlative cryo-electron tomography platform for structural biology of macromolecular complexes ]]> https://biorxiv.org/content/10.1101/2025.10.18.683253v1?rss=1 Tillu, V. Hunter, D. Chen, K.-E. Smith, J. Rae, J. Sierecki, E. Kobe, B. Gambin, Y. Collins, B. Parton, R. G. Ariotti, N. 2025-10-20 doi:10.1101/2025.10.18.683253 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Specificity of the stabilising interaction between intrinsically disordered protein sequences and G-quadruplexes in RNA ]]> https://biorxiv.org/content/10.1101/2025.10.19.683336v1?rss=1 View larger version (13K): org.highwire.dtl.DTLVardef@71fdeborg.highwire.dtl.DTLVardef@1d55ff1org.highwire.dtl.DTLVardef@18dd57dorg.highwire.dtl.DTLVardef@bb2d6c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cox, L. B. Mattick, J. S. Middleton, I. A. Rizzuto, F. J. Thordarson, P. 2025-10-20 doi:10.1101/2025.10.19.683336 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Autoantibody origins in lupus and in relapse post CAR-T therapy ]]> https://biorxiv.org/content/10.1101/2025.10.20.683393v1?rss=1 Grenov, A. Yoon, J. Snell, D. M. Mikolajczak, A. Wang, H. Gurel, E. Rodriguez-Ronchel, A. Yegen, G. Lee, L. Artim Esen, B. Rahman, A. Maciocia, P. Vinuesa, C. 2025-10-20 doi:10.1101/2025.10.20.683393 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Stromal subsets modulate T-cell infiltration in early breast cancer ]]> https://biorxiv.org/content/10.1101/2025.10.20.683407v1?rss=1 Chen, J. Zhang, H. Ruan, T. Wu, S. Slapetova, I. Millar, E. Graham, P. Lynch, J. Browne, L. Lim, E. Swarbrick, A. 2025-10-21 doi:10.1101/2025.10.20.683407 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Towards key principles of host-associated microbiome assembly ]]> https://biorxiv.org/content/10.1101/2025.10.23.684190v1?rss=1 Araujo, G. Thomas, T. Montoya, J. M. Webster, N. S. Lurgi, M. 2025-10-23 doi:10.1101/2025.10.23.684190 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Deep multiplexed 50-marker imaging of circulating tumor cells expands actionable biomarker profiling for precision oncology ]]> https://biorxiv.org/content/10.1101/2025.10.23.684075v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@a36ff4org.highwire.dtl.DTLVardef@b06c1org.highwire.dtl.DTLVardef@1e8a572org.highwire.dtl.DTLVardef@c60753_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG ]]> Mann, T. J. Zheng, Y. Khan, T. Huang, T. Nindra, U. Ma, Y. James, A. Neumann, D. P. Kohane, F. V. Gunawan, I. Vafaee, F. Chua, W. de Souza, P. Roberts, T. L. Becker, T. M. Lock, J. G. 2025-10-24 doi:10.1101/2025.10.23.684075 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Anillin-dependent actin assembly at PML NBs protects genome stability ]]> https://biorxiv.org/content/10.1101/2025.10.26.679380v1?rss=1 Putra, V. D. L. Lay, H. W. Walker, C. Lane, B. J. E. Willett, V. J. Gao, J. Marshall, L. L. Nelson, C. B. Vora, S. Sharma, M. French, L. Jordan, D. Rogers, S. Graham, M. E. Lewis, J. S. Biro, M. Pickett, H. A. Stachowiak, J. C. Cesare, A. J. Lamm, N. 2025-10-27 doi:10.1101/2025.10.26.679380 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Positive joint work redistribution in running: the role of plantar flexor fatigue and the effect of advanced footwear technology ]]> https://biorxiv.org/content/10.1101/2025.10.26.684644v1?rss=1 0.05). ConclusionPlantar flexor fatigue contributes to the proximal redistribution of positive joint work during running. However, the adoption of a suboptimal gait strategy appears to occur regardless of whether a runner wears a traditional shoe or advanced running footwear technology. ]]> Nahan, K. Y. Willwacher, S. Kerr, J. Heroux, M. McDonald, K. A. 2025-10-28 doi:10.1101/2025.10.26.684644 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ NPM1 mislocalization mediated by RNA Pol I inhibition alters chromatin landscape ]]> https://biorxiv.org/content/10.1101/2025.10.28.684736v1?rss=1 Esteve, P. O. Sen, S. Raman, K. Unnikrishnan, A. Pradhan, S. 2025-10-28 doi:10.1101/2025.10.28.684736 Cold Spring Harbor Laboratory Press 2025-10-28 <![CDATA[ LMI4Boltz: Optimizing VRAM utilization to predict large macromolecular complexes with consumer grade hardware ]]> https://biorxiv.org/content/10.1101/2025.10.29.684571v1?rss=1 Litfin, T. Caley, J. S. Michie, K. A. 2025-10-31 doi:10.1101/2025.10.29.684571 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Mitochondrial uncoupler BAM15 improves skeletal muscle function and mitochondrial respiration in Sarcopenia ]]> https://biorxiv.org/content/10.1101/2025.10.30.685477v1?rss=1 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. 2025-10-31 doi:10.1101/2025.10.30.685477 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Detecting Somatic Mutations in Rare Clones using Single Cell Multi-Omics ]]> https://biorxiv.org/content/10.1101/2025.10.30.685685v1?rss=1 Gillman, R. Dukda, S. Sadir, J. Goodnow, C. Luciani, F. Singh, M. Field, M. A. 2025-10-31 doi:10.1101/2025.10.30.685685 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Paediatric MRI: High-Resolution in vivo 3T Methods ]]> https://biorxiv.org/content/10.1101/2025.10.30.685686v1?rss=1 Wright, B. R. Schira, M. M. Paxinos, G. Kassem, M. S. 2025-10-31 doi:10.1101/2025.10.30.685686 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ SIMAIS: A swarm intelligence inspired biosensor for rapid protein detection ]]> https://biorxiv.org/content/10.1101/2025.10.31.685929v1?rss=1 Zheng, J. Bayinqiaoge, Schiff, H. Wang, X. Wu, T. Lu, X. Zhang, Y. Wang, Y. Tang, S. Zhang, C. 2025-11-03 doi:10.1101/2025.10.31.685929 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Exercise training improves sarcopenic muscle function via restoration of mitochondrial quality control ]]> https://biorxiv.org/content/10.1101/2025.11.03.686168v1?rss=1 Alldritt, I. Sligar, J. Campelj, D. Padilha, C. S. Ritenis, E. Mantamadiotis, T. Widodo, S. Dinevska, M. Nielsen, J. Philp, A. M. Philp, A. 2025-11-05 doi:10.1101/2025.11.03.686168 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Uncertainty-Aware Deep Learning for Multi-Metric and Dose-Specific Prediction of Drug Synergy ]]> https://biorxiv.org/content/10.1101/2025.11.05.686895v1?rss=1 Heydari, M. J. Lye, B. Masouri, P. Marsland, T. Lock, J. McKenna, J. Vafaee, F. G. 2025-11-07 doi:10.1101/2025.11.05.686895 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage ]]> https://biorxiv.org/content/10.1101/2025.11.09.686659v1?rss=1 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. 2025-11-11 doi:10.1101/2025.11.09.686659 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ An IL-21R hypomorph circumvents functional redundancy to define STAT1 signaling in germinal center responses ]]> https://biorxiv.org/content/10.1101/2025.11.14.688418v1?rss=1 Jandl, C. Warren, J. Owens, S. Batten, M. Wang, H. King, C. 2025-11-14 doi:10.1101/2025.11.14.688418 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ The brain architecture of punishment learning ]]> https://biorxiv.org/content/10.1101/2025.11.24.690287v1?rss=1 Gregory, A. V. Jean-Richard-dit-Bressel, P. Huang, N. Diefenbach, J. Choi, E. Soo, J. Chen, J. Killcross, S. McNally, G. 2025-11-25 doi:10.1101/2025.11.24.690287 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Shear Difference: Flow Type Dictates Endothelial Flow-Responsive Gene Programs in a 3D-Printed in vitro Model ]]> https://biorxiv.org/content/10.1101/2025.11.24.690338v1?rss=1 Shah, N. A. Rye, K.-A. Endre, Z. H. Barber, T. J. Erlich, J. H. Cochran, B. J. 2025-11-26 doi:10.1101/2025.11.24.690338 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli ]]> https://biorxiv.org/content/10.1101/2025.11.27.690950v1?rss=1 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. 2025-11-27 doi:10.1101/2025.11.27.690950 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Developing a nuclear transplantation model for Australian amphibian conservation using a common species of Australian Frog (Limnodynastes peronii) ]]> https://biorxiv.org/content/10.1101/2025.11.25.690599v1?rss=1 Patel, R. Upton, R. Clulow, S. Nixon, B. Gruber, B. Archer, M. Mahony, M. Clulow, J. 2025-11-29 doi:10.1101/2025.11.25.690599 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ GatorSC: Multi-Scale Cell and Gene Graphs with Mixture-of-Experts Fusion for Single-Cell Transcriptomics ]]> https://biorxiv.org/content/10.64898/2025.12.03.691688v1?rss=1 Liu, Y. Zhang, Z. Qiu, M. Wang, S. Salim, F. Shen, J. Chen, T. Razzak, I. Bian, J. 2025-12-07 doi:10.64898/2025.12.03.691688 Cold Spring Harbor Laboratory Press 2025-12-07 <![CDATA[ SWARM: A Single-Molecule Workflow for High-Precision Profiling of RNA Modifications ]]> https://biorxiv.org/content/10.64898/2025.12.18.695332v1?rss=1 Prodic, S. Cleynen, A. Mahmud, S. Srivastava, A. Ravindran, A. Kanchi, M. Sethi, A. J. Corovic, M. Jain, R. Santos-Rodriguez, G. Vieira, G. Weatheritt, R. J. Hayashi, R. Martinez, N. M. Shirokikh, N. E. Eyras, E. 2025-12-20 doi:10.64898/2025.12.18.695332 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ Single-cell RNA-sequencing of cerebral spinal fluid identifies circulating tumour cells in children with brain cancer ]]> https://biorxiv.org/content/10.64898/2025.12.18.694991v1?rss=1 Mayoh, C. Li, W. Toumari, M. Razavi Bazaz, S. Gerard, A.-L. Lowe, A. Barahona, P. Lau, L. M. Staunton, J. Jacobson, E. Nagabushan, S. Manoharan, N. Mitchell, R. Ong, F. Wong-Erasmus, M. Ekert, P. G. Tyrrell, V. Haber, M. Ziegler, D. S. Cowley, M. J. Mateos, M. K. Salomon, R. 2025-12-22 doi:10.64898/2025.12.18.694991 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Fast phylogenetic generalised linear mixed-effects modelling using the glmmTMB R package ]]> https://biorxiv.org/content/10.64898/2025.12.20.695312v1?rss=1 Williams, C. McGillycuddy, M. Drobniak, S. M. Bolker, B. M. Warton, D. I. Nakagawa, S. 2025-12-23 doi:10.64898/2025.12.20.695312 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ A multilevel hierarchical framework for quantification of experimental heterogeneity ]]> https://biorxiv.org/content/10.64898/2025.12.21.695338v1?rss=1 Warne, D. J. Zhu, X. Steele, T. P. Johnston, S. T. Sisson, S. A. Faria, M. Murphy, R. J. Browning, A. P. 2025-12-23 doi:10.64898/2025.12.21.695338 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Gene expression profiling of dendritic cell tolerance dysfunction in women with Systemic lupus erythematosus ]]> https://biorxiv.org/content/10.64898/2025.12.21.695630v1?rss=1 Hernandez-Ledesma, A. L. Coss-Navarrete, E. L. Salazar-Magana, S. Ramirez-Espinosa, D. Tinajero-Nieto, L. Torres-Valdez, E. Pena-Ayala, A. Felix-Rodriguez, G. Frontana-Vazquez, G. Garcia-Sotelo, J. S. Trynka, G. Rosetti, F. Fernandez-Valverde, S. L. Gutierrez-Arcelus, M. Alpizar-Rodriguez, D. Medina-Rivera, A. 2025-12-23 doi:10.64898/2025.12.21.695630 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Attention biases the appearance of rapidly alternating stimuli ]]> https://biorxiv.org/content/10.64898/2025.12.21.695868v1?rss=1 Ishaq, A. N. Goddard, E. 2025-12-23 doi:10.64898/2025.12.21.695868 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Hierarchical buffering of cellular RNA polymerase II pools maintains transcriptional homeostasis ]]> https://biorxiv.org/content/10.64898/2025.12.22.695869v1?rss=1 Gillis, A. Cacioppo, R. Ng, P. Q. Li, H. Hiles-Murison, B. Tufegdzic Vidakovic, A. Berry, S. 2025-12-23 doi:10.64898/2025.12.22.695869 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ To FRET or Not to FRET: Bioinformatics and Fluorescence Spectroscopy suggest that Reduced Tryptophan to Heme Energy Transfer Facilitates Lignin Degradation in Class II Peroxidases ]]> https://biorxiv.org/content/10.64898/2025.12.31.697144v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@f8b3a8org.highwire.dtl.DTLVardef@1db18a4org.highwire.dtl.DTLVardef@12ebf1dorg.highwire.dtl.DTLVardef@54712_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ren, Y. Ang, D. Ertan, H. Plojak, A. Aldrich-Wright, J. Bridge, W. J. Siddiqui, K. S. 2025-12-31 doi:10.64898/2025.12.31.697144 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Threading the needle: Spatial constraints sharpen visual sensitivity in honeybees ]]> https://biorxiv.org/content/10.64898/2026.01.02.696520v1?rss=1 Jakobi, T. R. Garratt, M. Srinivasan, M. V. Ravi, S. 2026-01-02 doi:10.64898/2026.01.02.696520 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Linkage-aware inference of fitness from short-read time-series genomic data ]]> https://biorxiv.org/content/10.64898/2026.01.08.698347v1?rss=1 Abdullah, S. M. U. Sohail, M. S. Louie, R. H. Y. Sun, Y. Barton, J. P. McKay, M. R. 2026-01-08 doi:10.64898/2026.01.08.698347 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Proteo-transcriptomics and morphometrics of teleost cardiac cells define regulatory networks and exercise-induced cardiomyocyte hypertrophy and hyperplasia ]]> https://biorxiv.org/content/10.64898/2026.01.11.698907v1?rss=1 Contreras, O. Smith, G. Santiago, C. F. Dey, M. Thekkedam, C. Chand, R. Gonzalez-Rajal, A. Zhong, L. Wong, E. Fatkin, D. Harvey, R. P. 2026-01-12 doi:10.64898/2026.01.11.698907 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ First inhibitor of a bacterial two-partner secretion system. ]]> https://biorxiv.org/content/10.64898/2026.01.11.698920v1?rss=1 Hartojo, A. Luu, L. D. W. Adamson, L. Majors, K. Paparella, A. S. Cotter, P. A. Johnson, R. M. Doyle, M. T. 2026-01-12 doi:10.64898/2026.01.11.698920 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Disrupting astrocyte signalling in the nucleus accumbens impairs incentive-driven instrumental actions ]]> https://biorxiv.org/content/10.64898/2026.01.12.699167v1?rss=1 Gladding, J. Soegyono, O. abiero, a. Turner, K. kendig, m. Bradfield, L. 2026-01-13 doi:10.64898/2026.01.12.699167 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ Submaximal running energetics are maintained despite local muscle fatigue ]]> https://biorxiv.org/content/10.64898/2026.01.16.699896v1?rss=1 Nahan, K. Finn, H. Nahan, K. Heroux, M. McDonald, K. 2026-01-20 doi:10.64898/2026.01.16.699896 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ A proteomic signature of oocyte quality from models of varying oocyte developmental competence ]]> https://biorxiv.org/content/10.64898/2026.01.20.700687v1?rss=1 Frost, E. R. Richani, D. Poljak, A. Vuyyuru, A. Liao, X. Georgiou, E. Gunesekara, J. M. B. Mihalas, B. P. Sucquart, I. E. Kadam, K. Wu, L. E. Gilchrist, R. B. 2026-01-21 doi:10.64898/2026.01.20.700687 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Machine learning-based image analysis of Parkinson's disease iPS-derived neurons predicts genotype and reveals mitochondria-lysosome abnormalities ]]> https://biorxiv.org/content/10.64898/2026.01.28.702423v1?rss=1 Li, Y. Powell, M. Chedid, J. Sutharsan, R. Garrido, A. L. Abu-Bonsrah, D. Pavan, C. Fraser, T. Ovchinnikov, D. Zhong, M. Davis, R. Strbenac, D. Johnston, J. A. Thompson, L. H. Kirik, D. Parish, C. L. Halliday, G. M. Sue, C. M. Dzamko, N. Wali, G. 2026-01-29 doi:10.64898/2026.01.28.702423 Cold Spring Harbor Laboratory Press 2026-01-29 <![CDATA[ A Comprehensive epidemiological and molecular study of gastrointestinal helminths of Companion Animals in Northeastern Bangladesh: A neglected zoonotic threat ]]> https://biorxiv.org/content/10.64898/2026.02.05.704122v1?rss=1 Nath, T. C. Nyema, J. Raquib, R. Siddiki, T. Tasnim, J. Prity, Z. S. Tarek, M. Mukutmoni, M. Islam, K. M. Ahmed, S. 2026-02-06 doi:10.64898/2026.02.05.704122 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Dual transcriptomics reveal commensal interactions between microalgae and phycosphere bacteria ]]> https://biorxiv.org/content/10.64898/2026.02.09.704904v1?rss=1 Roager, L. Schostag, M. Garritano, A. Gram, L. Egan, S. 2026-02-09 doi:10.64898/2026.02.09.704904 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ An eco-evolutionary theory of host-associated microbiomes ]]> https://biorxiv.org/content/10.64898/2026.02.10.705025v1?rss=1 Araujo, G. D. Thomas, T. Webster, N. S. Montoya, J. M. Lurgi, M. 2026-02-11 doi:10.64898/2026.02.10.705025 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Designing High-Affinity Progesterone Binders: Pocket Analysis and Scaffold Selection ]]> https://biorxiv.org/content/10.64898/2026.02.12.704737v1?rss=1 Pourhassan-Moghaddam, M. Cornell, B. A. Valenzuela, S. M. 2026-02-14 doi:10.64898/2026.02.12.704737 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Functional Characterisation of Recombinant Proteins Using Ion Channel Switch Technology: A Label-Free, Wash-Free Platform for Biotechnological Applications ]]> https://biorxiv.org/content/10.64898/2026.02.13.705684v1?rss=1 Pourhassan Moghaddam, M. Jayasundera, K. Jiang, L. Cornell, B. A. Valenzuela, S. M. 2026-02-14 doi:10.64898/2026.02.13.705684 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Asgard archaeal origin of microtubules ]]> https://biorxiv.org/content/10.64898/2026.02.15.705738v1?rss=1 Löwe, J. von Kügelgen, A. Planelles-Herrero, V. J. McAndrew, M. B. L. Oliva, M. A. Vosseberg, J. Köstlbacher, S. Dharamshi, J. E. Appler, K. E. MacLeod, F. I. Nobs, S.-J. Jorgensen, S. L. Burns, B. P. Baker, B. J. Bharat, T. A. M. Derivery, E. Tamarit, D. Ettema, T. J. G. 2026-02-16 doi:10.64898/2026.02.15.705738 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Trace gas oxidation supports sub-surface microbial communities across Namib Desert fog and aridity gradients ]]> https://biorxiv.org/content/10.64898/2026.02.19.706496v1?rss=1 Tribbia, D. Z. Lebre, P. H. Vazquez-Campos, X. Ray, A. E. Laird, T. Machado de Lima, N. Maggs-Kölling, G. Cowan, D. A. Ferrari, B. C. 2026-02-20 doi:10.64898/2026.02.19.706496 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ The control of goal-directed actions by nutrient-specific appetites and rewards ]]> https://biorxiv.org/content/10.64898/2026.02.19.706921v1?rss=1 Roy, D. J. Burton, T. J. Balleine, B. W. 2026-02-20 doi:10.64898/2026.02.19.706921 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Divergence in skeletal muscle growth by differential spatial hyperplastic patterning in teleost fishes ]]> https://biorxiv.org/content/10.64898/2026.02.23.707519v1?rss=1 Lu, Y. Podobnik, M. Ando, K. Pan, M. Locop, J. Guo, A. Mourrain, P. Kikuchi, K. Ruparelia, A. A. Currie, P. D. 2026-02-25 doi:10.64898/2026.02.23.707519 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ DENcode: A model for haplotype-informed transmission probability of dengue virus ]]> https://biorxiv.org/content/10.64898/2026.02.26.708194v1?rss=1 Maduranga, S. Arroyo, B. M. V. Sigera, C. Weeratunga, P. Fernando, D. Rajapakse, S. Lloyd, A. R. Bull, R. A. Stone, H. Rodrigo, C. 2026-02-27 doi:10.64898/2026.02.26.708194 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Comparing the transmission blocking efficacy of Primaquine and Tafenoquine with in vivo pre-clinical models ]]> https://biorxiv.org/content/10.64898/2026.03.03.709295v1?rss=1 Duffey, M. Zakutansky, S. E. Gumpp, C. Delves, M. J. Sala, K. A. Sherrard-Smith, E. Baum, J. Leroy, D. J. Rottmann, M. Blagborough, A. M. 2026-03-03 doi:10.64898/2026.03.03.709295 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Unified Multi-Cohort Harmonisation and Normative Modelling of Neuroimaging Data via Hierarchical GAMLSS ]]> https://biorxiv.org/content/10.64898/2026.03.08.710422v1?rss=1 Ho, M. P. Husein, N. K. Fan, L. Visontay, R. Byrne, H. Devine, E. K. Squeglia, L. M. Sachdev, P. S. Jiang, J. Wen, W. Mewton, L. 2026-03-11 doi:10.64898/2026.03.08.710422 Cold Spring Harbor Laboratory Press 2026-03-11 <![CDATA[ Single cell multiomics reveal clonal and functional dynamics of MDS stem/progenitor cells during hypomethylating therapy ]]> https://biorxiv.org/content/10.64898/2026.03.13.711488v1?rss=1 Thoms, J. A. I. Hampton, H. R. Boon, P. L. S. Stonehouse, O. Zou, X. Chung, H. M. Koch, F. C. Yan, F. Joshi, S. Nguyen, M. N. T. Hung, D. Wright, D. C. Vafaee, F. Polizzotto, M. N. Swarbrick, A. Huang, Y. Jolly, C. J. Zanini, F. Pimanda, J. E. 2026-03-13 doi:10.64898/2026.03.13.711488 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Vibrational signatures and mimicry in ant-termite and termite-termite interactions ]]> https://biorxiv.org/content/10.64898/2026.03.15.711937v1?rss=1 Oberst, S. Lai, J. C. Evans, T. 2026-03-18 doi:10.64898/2026.03.15.711937 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Intranasal oxytocin mRNA-LNP can promote social behaviour and reduce pain ]]> https://biorxiv.org/content/10.64898/2026.03.18.711938v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@131252aorg.highwire.dtl.DTLVardef@17efb79org.highwire.dtl.DTLVardef@1afe479org.highwire.dtl.DTLVardef@c0f2f5_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryIntranasal administration of mRNA-LNP enables local transfection in nasal epithelium and subsequent secretion of therapeutic oxytocin peptides into the brain, promoting social interactions and reducing pain. ]]> Loo, L. Fujikake, K. Bergamasco, M. I. Carr, R. O'Shea, R. Du, T. Cohen, S. B. Sandra, F. Thordarson, P. Martin, L. Fong, C. Neely, G. G. 2026-03-20 doi:10.64898/2026.03.18.711938 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Domestic dog introgression in Australian dingoes: environmental drivers and evolutionary consequences ]]> https://biorxiv.org/content/10.64898/2026.03.22.713106v1?rss=1 Osuna-Mascaro, C. Cairns, K. Doan, K. Flores-Manzanero, A. Nesbitt, B. J. Newsome, T. M. Pilot, M. 2026-03-24 doi:10.64898/2026.03.22.713106 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Inactivation of Microorganisms in the Complex Regions of Transvaginal Ultrasound Probes By a UVC-LED Light Based Disinfection System ]]> https://biorxiv.org/content/10.64898/2026.03.23.713795v1?rss=1 6.7 log reduction of B. subtilis spores across all tested regions. These findings demonstrate that UV-C LED technology provides rapid, effective, and consistent high-level disinfection of complex TVUS probe surfaces, supporting its potential as a rapid and reliable disinfection modality in clinical setting. ]]> Yasir, M. Willcox, M. 2026-03-27 doi:10.64898/2026.03.23.713795 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Open-source, Hardware-Independent GPU Acceleration for Scalable Nanopore Basecalling with Slorado and Openfish ]]> https://biorxiv.org/content/10.64898/2026.03.25.714356v1?rss=1 Wong, B. Singh, G. Javaid, H. Denolf, K. Liyanage, K. Samarakoon, H. Deveson, I. W. Gamaarachchi, H. 2026-03-28 doi:10.64898/2026.03.25.714356 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ Towards the definition and measurement of routines and the cognitive processes that underpin their maintenance ]]> https://biorxiv.org/content/10.64898/2026.03.26.714585v1?rss=1 Nolan, C. R. Le Pelley, M. E. Garner, K. G. 2026-03-28 doi:10.64898/2026.03.26.714585 Cold Spring Harbor Laboratory Press 2026-03-28 <![CDATA[ fishROI: A specialized workflow for semi-automated muscle morphometry analysis in teleosts ]]> https://biorxiv.org/content/10.64898/2026.03.27.714781v1?rss=1 Lu, Y. Pan, M. Jamwal, V. Locop, J. Ruparelia, A. A. Currie, P. D. 2026-03-30 doi:10.64898/2026.03.27.714781 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Coral Probiotics Buffer Adjacent Ecosystem-Level Responses to Extreme Marine Heatwave ]]> https://biorxiv.org/content/10.64898/2026.03.30.715272v1?rss=1 El-Khaled, Y. C. Garcia, F. C. Santoro, E. P. Garcias-Bonet, N. Monti, M. Teixeira, M. A. L. Justo, M. S. S. Gil-Ramos, G. Sempere-Valverde, J. Kolbasova, G. Beenham, L. Duarte, G. Martins, D. Antony, C. P. Thomas, T. Carvalho, S. Peixoto, R. S. 2026-03-30 doi:10.64898/2026.03.30.715272 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Structural Brain Network Alterations in Relation to Treatment and Illness Severity in Bipolar Disorder ]]> https://biorxiv.org/content/10.64898/2026.03.28.714565v1?rss=1 Nabulsi, L. Kang, M. J. Y. Jahanshad, N. McPhilemy, G. Martyn, F. M. Haarman, B. McDonald, C. Hallahan, B. O'Donoghue, S. Stein, D. J. Howells, F. M. Scheffler, F. Temmingh, H. S. Glahn, D. C. Rodrigue, A. Pomarol-Clotet, E. Vieta, E. Radua, J. Salvador, R. Karuk, A. Canales-Rodriguez, E. J. Houenou, J. Favre, P. Polosan, M. Pouchon, A. Brambilla, P. Bellani, M. Mitchell, P. B. Roberts, G. Dannlowski, U. Borgers, T. Meinert, S. Flinkenflugel, K. Repple, J. Lehr, E. J. Grotegerd, D. Hahn, T. Wessa, M. Phillips, M. L. Teutenberg, L. Kircher, T. Straube, B 2026-03-31 doi:10.64898/2026.03.28.714565 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Monocyte Lineage Expansion Drives Transcriptomic Individuality in Genetically Identical Armadillo Quadruplets ]]> https://biorxiv.org/content/10.64898/2026.03.30.715171v1?rss=1 Kawaguchi, R. K. Ballouz, S. Pena, M. T. French, L. Knight, F. M. Adams, L. B. Gillis, J. 2026-04-01 doi:10.64898/2026.03.30.715171 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ When Tagging Frequency Matters to Attention: Effects on SSVEPs, ERPs, and Cognitive Processing ]]> https://biorxiv.org/content/10.64898/2026.03.30.715193v1?rss=1 Yang, J. Carter, O. Shivdasani, M. N. Grayden, D. B. Hester, R. Barutchu, A. 2026-04-01 doi:10.64898/2026.03.30.715193 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Flexible Asexuality: Naturally occurring variation in mechanisms of parthenogenesis within lineages and individuals of a facultative parthenogen, Megacrania batesii ]]> https://biorxiv.org/content/10.64898/2026.03.30.715418v1?rss=1 Miller, S. M. Wilner, D. Boldbaatar, J. Bonduriansky, R. 2026-04-01 doi:10.64898/2026.03.30.715418 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ The genome of the Delisea pulchra: a resource for the study of chemical host-microbe interactions in red algae ]]> https://biorxiv.org/content/10.64898/2026.03.31.715562v1?rss=1 Dittami, S. M. Hudson, J. Brillet-Gueguen, L. Ficko-Blean, E. Tanguy, G. Rousvoal, S. Legeay, E. Markov, G. V. Delage, L. Godfroy, O. Corre, E. Collen, J. Leblanc, C. Egan, S. 2026-04-02 doi:10.64898/2026.03.31.715562 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ The long noncoding RNA Dory is required for female but not male spatial learning and memory ]]> https://biorxiv.org/content/10.64898/2026.04.01.715990v1?rss=1 Jung, S. Cummins, M. J. Altaf, S. Heggen, R. Poljak, A. Delerue, F. Ittner, L. M. Mattick, J. S. 2026-04-06 doi:10.64898/2026.04.01.715990 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Energetic analysis of Na+/K+-ATPase using bond graphs ]]> https://biorxiv.org/content/10.64898/2026.04.05.716446v1?rss=1 Ai, W. Hunter, P. J. Pan, M. Nickerson, D. P. 2026-04-08 doi:10.64898/2026.04.05.716446 Cold Spring Harbor Laboratory Press 2026-04-08