bioRxiv Channel: The Howard Hughes Medical Institute (HHMI)
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https://biorxiv.org
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Regulation of replication origin licensing by ORC phosphorylation reveals a two-step mechanism for Mcm2-7 ring closing
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https://biorxiv.org/cgi/content/short/2023.01.02.522488v1?rss=1"
Amasino, A.Gupta, S.Friedman, L. J.Gelles, J.Bell, S. P.2023-01-02doi:10.1101/2023.01.02.522488Cold Spring Harbor Laboratory Press2023-01-02
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Dimensional Reduction for Single Molecule Imaging of DNA and Nucleosome Condensation by Polyamines, HP1α and Ki-67
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https://biorxiv.org/cgi/content/short/2023.01.04.522433v1?rss=1"
View larger version (35K):
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]]>Benning, N. A.Kaestel-Hansen, J.Rashid, F.Park, S.Urteaga, R. M.Liao, T.-W.Hao, J.Berger, J. M.Hatzakis, N. S.Ha, T.2023-01-04doi:10.1101/2023.01.04.522433Cold Spring Harbor Laboratory Press2023-01-04
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An entorhinal-like region in food-caching birds
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https://biorxiv.org/cgi/content/short/2023.01.05.522940v1?rss=1"
Applegate, M. C.Gutnichenko, K. S.Mackevicius, E. L.Aronov, D.2023-01-06doi:10.1101/2023.01.05.522940Cold Spring Harbor Laboratory Press2023-01-06
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Wheat plant height locus RHT25 encodes a PLATZ transcription factor that interacts with DELLA (RHT1)
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https://biorxiv.org/cgi/content/short/2023.01.05.522836v1?rss=1"
Zhang, J.Li, C.Zhang, W.Zhang, X.Mo, Y.Tranquilli, G. E.Vanzetti, L. S.Dubcovsky, J.2023-01-06doi:10.1101/2023.01.05.522836Cold Spring Harbor Laboratory Press2023-01-06
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Solving the spike sorting problem with Kilosort
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https://biorxiv.org/cgi/content/short/2023.01.07.523036v1?rss=1"
Pachitariu, M.Sridhar, S.Stringer, C.2023-01-07doi:10.1101/2023.01.07.523036Cold Spring Harbor Laboratory Press2023-01-07
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Massively parallel single molecule tracking of sequence-dependent DNA mismatch repair in vivo
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https://biorxiv.org/cgi/content/short/2023.01.08.523062v1?rss=1"
Kayikcioglu, T.Zarb, J. S.Lin, C.-T.Mohapatra, S.London, J. A.Hansen, K. D.Rishel, R.Ha, T.2023-01-08doi:10.1101/2023.01.08.523062Cold Spring Harbor Laboratory Press2023-01-08
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Genetics of Latin American Diversity (GLAD) Project: insights into population genetics and association studies in recently admixed groups in the Americas
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https://biorxiv.org/cgi/content/short/2023.01.07.522490v1?rss=1"
Borda, V.Loesch, D. P.Guo, B.Laboulaye, R.Veliz-Otani, D.French-Kwawu, J. N.Peixoto Leal, T.Gogarten, S. M.Ikpe, S.Gouveia, M. H.Mendes, M.Abecasis, G. R.Alvim, I.Arboleda-Bustos, C. E.Arboleda, G.Arboleda, H.Barreto, M. L.Barwick, L.Bezzera, M. A.Blangero, J.Borges, V.Caceres, O.Cai, J.Chana-Cuevas, P.Chen, Z.Custer, B.Dean, M.Dinardo, C.Domingos, I.Duggirala, R.Dieguez, E.Fernandez, W.Ferraz, H. B.Gilliland, F. D.Guio, H.Horta, B.Curran, J. E.Johnsen, J. M.Kaplan, R. C.Kelly, S.Kenny, E. E.Kittner, S.Konkle,2023-01-09doi:10.1101/2023.01.07.522490Cold Spring Harbor Laboratory Press2023-01-09
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Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters
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https://biorxiv.org/cgi/content/short/2023.01.09.523323v1?rss=1"
Wooten, M.Takushi, B.Ahmad, K.Henikoff, S.2023-01-10doi:10.1101/2023.01.09.523323Cold Spring Harbor Laboratory Press2023-01-10
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Bacterial meningitis in the early postnatal mouse studied at single-cell resolution
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https://biorxiv.org/cgi/content/short/2023.01.11.523597v1?rss=1"
Wang, J.Rattner, A.Nathans, J.2023-01-11doi:10.1101/2023.01.11.523597Cold Spring Harbor Laboratory Press2023-01-11
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Two RNA-binding proteins mediate the sorting of miR223 from mitochondria into exosomes
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https://biorxiv.org/cgi/content/short/2023.01.11.523558v1?rss=1"
Ma, L.Singh, J.Schekman, R.2023-01-11doi:10.1101/2023.01.11.523558Cold Spring Harbor Laboratory Press2023-01-11
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Design of amyloidogenic peptide traps
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https://biorxiv.org/cgi/content/short/2023.01.13.523785v1?rss=1"
Sahtoe, D. D.Andrzejewska, E. A.Han, H. L.Rennella, E.Schneider, M. M.Meisl, G.Ahlrichs, M.Decarreau, J.Nguyen, H.Kang, A.Levine, P. M.Lamb, M.Li, X.Bera, A. K.Kay, L. E.Knowles, T.Baker, D.2023-01-13doi:10.1101/2023.01.13.523785Cold Spring Harbor Laboratory Press2023-01-13
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A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
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https://biorxiv.org/cgi/content/short/2023.01.13.524003v1?rss=1"
Martin Alonso, C.Tabrizi, S.Xiong, K.Blewett, T.Patel, S.An, Z.Sridhar, S.Bekdemir, A.Shea, D.Amini, A. P.Wang, S.-T.Kirkpatrick, J.Rhoades, J.Golub, T.Love, J. C.Adalsteinsson, V.Bhatia, S.2023-01-14doi:10.1101/2023.01.13.524003Cold Spring Harbor Laboratory Press2023-01-14
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Transplantation-based screen uncovers inducers of muscle progenitor cell engraftment across vertebrate species
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https://biorxiv.org/cgi/content/short/2023.01.13.523942v1?rss=1"
Tavakoli, S.Garcia, V.Gahwiler, E.Adatto, I.Rangan, A.Messemer, K.Ashrafi Kakhki, S.Yang, S.Chan, V.Manning, M.Fotowat, H.Wagers, A.Zon, L.2023-01-14doi:10.1101/2023.01.13.523942Cold Spring Harbor Laboratory Press2023-01-14
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Contrasting patterns of somatic mutations in neurons and glia reveal differential predisposition to disease in the aging human brain
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https://biorxiv.org/cgi/content/short/2023.01.14.523958v1?rss=1"
67,000 somatic single nucleotide variants (sSNVs) and small insertions and deletions (indels). While both cell types accumulate mutations with age, oligodendrocytes accumulate sSNVs 69% faster than neurons (27/year versus 16/year) whereas indels accumulate 42% slower (1.8/year versus 3.1/year). Correlation with single-cell RNA and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These patterns highlight differences in the mutagenic processes in glia and neurons and suggest cell type-specific, age-related contributions to neurodegeneration and oncogenesis.
]]>Ganz, J.Luquette, L. J.Bizzotto, S.Bohrson, C.Jin, H.Miller, M. B.Zhou, Z.Galor, A.Park, P. J.Walsh, C. A.2023-01-14doi:10.1101/2023.01.14.523958Cold Spring Harbor Laboratory Press2023-01-14
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Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome
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https://biorxiv.org/cgi/content/short/2023.01.16.524325v1?rss=1"
Feng, X.Cui, X.Zhang, L.-S.Ye, C.Wang, P.Zhong, Y.Zheng, Z.He, C.2023-01-17doi:10.1101/2023.01.16.524325Cold Spring Harbor Laboratory Press2023-01-17
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Structure and DNA bridging activity of the essential Rec114-Mei4 trimer interface
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https://biorxiv.org/cgi/content/short/2023.01.18.524603v1?rss=1"
Liu, K.Grasso, E. M.Pu, S.Eliezer, D.Liu, S.Keeney, S.2023-01-18doi:10.1101/2023.01.18.524603Cold Spring Harbor Laboratory Press2023-01-18
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Experimental Tests of the Virtual Circular Genome Model for Non-enzymatic RNA Replication
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https://biorxiv.org/cgi/content/short/2023.01.16.524303v1?rss=1"
Ding, D.Zhou, L.Mittal, S.Szostak, J. W.2023-01-18doi:10.1101/2023.01.16.524303Cold Spring Harbor Laboratory Press2023-01-18
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GEARBOCS: An Adeno Associated Virus Tool for In Vivo Gene Editing in Astrocytes
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https://biorxiv.org/cgi/content/short/2023.01.17.524433v1?rss=1"
Sivadasan Bindu, D.Tan, C. X.Savage, J. T.Eroglu, C.2023-01-19doi:10.1101/2023.01.17.524433Cold Spring Harbor Laboratory Press2023-01-19
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Apparent simplicity and emergent robustness in bacterial cell cycle control
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https://biorxiv.org/cgi/content/short/2023.01.16.524295v1?rss=1"
800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often found to be nutrient-dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ-ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length). Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a systems-level understanding of the design principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability.
]]>Govers, S. K.Campos, M.Tyagi, B.Laloux, G.Jacobs-Wagner, C.2023-01-19doi:10.1101/2023.01.16.524295Cold Spring Harbor Laboratory Press2023-01-19
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Cas9-induced nonhomologous recombination in C. elegans
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https://biorxiv.org/cgi/content/short/2023.01.19.524763v1?rss=1"
Zdraljevic, S.Walter-McNeill, L.Marquez, H.Kruglyak, L.2023-01-20doi:10.1101/2023.01.19.524763Cold Spring Harbor Laboratory Press2023-01-20
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Woronin bodies move dynamically and bidirectionally by hitchhiking on early endosomes in Aspergillus nidulans
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https://biorxiv.org/cgi/content/short/2023.01.20.524968v1?rss=1"
Songster, L. D.Bhuyan, D.Christensen, J. R.Reck-Peterson, S. L.2023-01-21doi:10.1101/2023.01.20.524968Cold Spring Harbor Laboratory Press2023-01-21
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Single molecule visualization of native centromeric nucleosome formation reveals coordinated deposition by kinetochore proteins and centromere DNA sequence
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https://biorxiv.org/cgi/content/short/2023.01.20.524981v1?rss=1"
Popchock, A.Larson, J.Dubrulle, J.Asbury, C. L.Biggins, S.2023-01-21doi:10.1101/2023.01.20.524981Cold Spring Harbor Laboratory Press2023-01-21
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Modeling of African population history using f-statistics can be highly biased and is not addressed by previously suggested SNP ascertainment schemes
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https://biorxiv.org/cgi/content/short/2023.01.22.525077v1?rss=1"
Flegontov, P.Isıldak, U.Maier, R.Yüncü, E.Changmai, P.Reich, D.2023-01-22doi:10.1101/2023.01.22.525077Cold Spring Harbor Laboratory Press2023-01-22
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RNA Polymerase II, the BAF remodeler and transcription factors synergize to evict nucleosomes
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https://biorxiv.org/cgi/content/short/2023.01.22.525083v1?rss=1"
Brahma, S.Henikoff, S.2023-01-22doi:10.1101/2023.01.22.525083Cold Spring Harbor Laboratory Press2023-01-22
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Genome expansion by a CRISPR trimmer-integrase
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https://biorxiv.org/cgi/content/short/2023.01.23.522648v1?rss=1"
Wang, J. Y.Tuck, O. T.Skopintsev, P.Soczek, K. M.Li, G.Al-Shayeb, B.Zhou, J.Doudna, J. A.2023-01-24doi:10.1101/2023.01.23.522648Cold Spring Harbor Laboratory Press2023-01-24
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Hacking brain development to test models of sensory coding
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https://biorxiv.org/cgi/content/short/2023.01.25.525425v1?rss=1"
Ahmed, M.Rajagopalan, A. E.Pan, Y.Li, Y.Williams, D. L.Pedersen, E. A.Thakral, M.Previero, A.Close, K. C.Christoforou, C. P.Cai, D.Turner, G. C.Clowney, E. J.2023-01-26doi:10.1101/2023.01.25.525425Cold Spring Harbor Laboratory Press2023-01-26
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Design of stimulus-responsive two-state hinge proteins
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https://biorxiv.org/cgi/content/short/2023.01.27.525968v1?rss=1"
Praetorius, F.Leung, P. J. Y.Tessmer, M. H.Broerman, A.Demakis, C.Dishman, A. F.Pillai, A.Idris, A.Juergens, D.Dauparas, J.Li, X.Levine, P. M.Lamb, M.Ballard, R. K.Gerben, S. R.Nguyen, H.Kang, A.Sankaran, B.Bera, A. K.Volkman, B. F.Nivala, J.Stoll, S.Baker, D.2023-01-28doi:10.1101/2023.01.27.525968Cold Spring Harbor Laboratory Press2023-01-28
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Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages
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https://biorxiv.org/cgi/content/short/2023.01.30.526059v1?rss=1"
Chen, H. I.Turakhia, Y.Bejerano, G.Kingsley, D. M.2023-01-31doi:10.1101/2023.01.30.526059Cold Spring Harbor Laboratory Press2023-01-31
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Fitness effects of mutations to SARS-CoV-2 proteins
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https://biorxiv.org/cgi/content/short/2023.01.30.526314v1?rss=1"
Bloom, J. D.Neher, R. A.2023-01-31doi:10.1101/2023.01.30.526314Cold Spring Harbor Laboratory Press2023-01-31
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Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism
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https://biorxiv.org/cgi/content/short/2023.01.30.526383v1?rss=1"
Harris, R. S.Fanunza, E.Cheng, A.Auerbach, A.Stefanovska, B.Moraes, S. N.Lokensgard, J.Biolatti, M.Dell'Oste, V.Bierle, C. J.Bresnahan, W. A.2023-01-31doi:10.1101/2023.01.30.526383Cold Spring Harbor Laboratory Press2023-01-31
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The viral packaging motor potentiates late gene expression in Kaposi's sarcoma-associated herpesvirus
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https://biorxiv.org/cgi/content/short/2023.01.29.526158v1?rss=1"
McCollum, C. O.Didychuk, A. L.Liu, D.Murray-Nerger, L. A.Christea, I. M.Glaunsinger, B. A.2023-01-31doi:10.1101/2023.01.29.526158Cold Spring Harbor Laboratory Press2023-01-31
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The formation of an expanding memory representation in the hippocampus
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https://biorxiv.org/cgi/content/short/2023.02.01.526663v1?rss=1"
Vaidya, S. P.Chitwood, R. A.Magee, J. C.2023-02-02doi:10.1101/2023.02.01.526663Cold Spring Harbor Laboratory Press2023-02-02
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Discovery of a unique pathway for glutathione utilization in Francisella
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https://biorxiv.org/cgi/content/short/2023.02.02.526638v1?rss=1"
Wang, Y.Ledvina, H. E.Tower, C. A.Kambarev, S.Liu, E.Charity, J. C.Kreuk, L. S. M.Chen, Q.Gallagher, L. A.Radey, M. C.Rerolle, G. F.Li, Y.Penewit, K. M.Turkarslan, S.Skerrett, S. J.Salipante, S. J.Baliga, N. S.Woodward, J. J.Dove, S. L.Peterson, S. B.Celli, J.Mougous, J. D.2023-02-02doi:10.1101/2023.02.02.526638Cold Spring Harbor Laboratory Press2023-02-02
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RNA conformation and metal ion coordination in the nonenzymatic primer extension reaction center
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https://biorxiv.org/cgi/content/short/2023.02.03.527041v1?rss=1"
Mittal, S.Nisler, C.Szostak, J. W.2023-02-04doi:10.1101/2023.02.03.527041Cold Spring Harbor Laboratory Press2023-02-04
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A role for the Gram-negative outer membrane in bacterial shape determination
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https://biorxiv.org/cgi/content/short/2023.02.03.527047v1?rss=1"
Fivenson, E. M.Rohs, P. D.Vettiger, A.Sardis, M. F.Torres, G.Forchoh, A.Bernhardt, T. G.2023-02-04doi:10.1101/2023.02.03.527047Cold Spring Harbor Laboratory Press2023-02-04
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Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells
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https://biorxiv.org/cgi/content/short/2023.02.03.527025v1?rss=1"
Abruzzi, K. C.Ratner, C.Rosbash, M.2023-02-04doi:10.1101/2023.02.03.527025Cold Spring Harbor Laboratory Press2023-02-04
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Ketamine evoked disruption of entorhinal and hippocampal spatial maps
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https://biorxiv.org/cgi/content/short/2023.02.05.527227v1?rss=1"
Masuda, F. K.Sun, Y.Aery Jones, E. A.Giocomo, L. M.2023-02-06doi:10.1101/2023.02.05.527227Cold Spring Harbor Laboratory Press2023-02-06
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Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8
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https://biorxiv.org/cgi/content/short/2023.02.07.527505v1?rss=1"
Verma, P.Kwansa, A. L.Ho, R.Yingling, Y. G.Zimmer, J.2023-02-07doi:10.1101/2023.02.07.527505Cold Spring Harbor Laboratory Press2023-02-07
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A remarkable transformation catalyzed by a domain-of-unknown-function 692 during the biosynthesis of a new RiPP natural product
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https://biorxiv.org/cgi/content/short/2023.02.06.527370v1?rss=1"
Ayikpoe, R. S.Zhu, L.Chen, J. Y.Ting, C. P.van der Donk, W. A.2023-02-07doi:10.1101/2023.02.06.527370Cold Spring Harbor Laboratory Press2023-02-07
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Mitochondrial metabolism in primary and metastatic human kidney cancers
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https://biorxiv.org/cgi/content/short/2023.02.06.527285v1?rss=1"
Bezwada, D.DeBerardinis, R. J.Lesner, N. P.Brooks, B.Vu, H. S.Wu, Z.Cai, L.Kasitinon, S.Kelekar, S.Cai, F.Aurora, A. B.Patrick, M.Leach, A.Ghandour, R.Zhang, Y.Do, D.Sudderth, J.Dumesnil, D.House, S.Rosales, T.Poole, A. M.Lotan, Y.Woldu, S.Bagrodia, A.Meng, X.Cadeddu, J. A.Mishra, P.Pedrosa, I.Kapur, P.Courtney, K. D.Malloy, C. R.Margulis, V.2023-02-07doi:10.1101/2023.02.06.527285Cold Spring Harbor Laboratory Press2023-02-07
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Selection of a de novo gene that can promote survival of E. coli by modulating protein homeostasis pathways
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https://biorxiv.org/cgi/content/short/2023.02.07.527531v1?rss=1"
Frumkin, I.Laub, M. T.2023-02-07doi:10.1101/2023.02.07.527531Cold Spring Harbor Laboratory Press2023-02-07
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Multiplicity of Agrobacterium infection of Nicotiana benthamiana for transient DNA delivery
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https://biorxiv.org/cgi/content/short/2023.02.07.527564v1?rss=1"
1 event/cell). Here, we analyze the Poisson probability distribution of T-DNA transfer in leaf pavement cells to determine the MOI for the widely used model system Agrobacterium GV3101/Nicotiana benthamiana. These data delineate the relationship between an individual Agrobacterium strain infiltration OD600, plant cell perimeter and leaf age, as well as plant cell co-infection rates. Our analysis also establishes experimental regimes where the probability of near-simultaneous delivery of >20 unique T-DNAs to a given plant cell remains high throughout the leaf. We anticipate that these data will enable users to develop new approaches to in-leaf library development using Agrobacterium transient expression and the reliable combinatorial assaying of multiple heterologous proteins in a single plant cell.
]]>Carlson, E.Rajniak, J.Sattely, E.2023-02-08doi:10.1101/2023.02.07.527564Cold Spring Harbor Laboratory Press2023-02-08
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RNA-catalyzed RNA Ligation within Prebiotically Plausible Model Protocells
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https://biorxiv.org/cgi/content/short/2023.02.09.527907v1?rss=1"
DasGupta, S.Zhang, S. J.Smela, M. P.Szostak, J. W.2023-02-09doi:10.1101/2023.02.09.527907Cold Spring Harbor Laboratory Press2023-02-09
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Unified bursting strategies in ectopic and endogenous even-skipped expression patterns
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https://biorxiv.org/cgi/content/short/2023.02.09.527927v1?rss=1"
Berrocal, A.Lammers, N. C.Garcia, H. G.Eisen, M. B.2023-02-10doi:10.1101/2023.02.09.527927Cold Spring Harbor Laboratory Press2023-02-10
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Ormdl3 regulation of specific ceramides is dispensable for β-cell function and glucose homeostasis under obesogenic conditions
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https://biorxiv.org/cgi/content/short/2023.02.11.528130v1?rss=1"
Hurley, L. D.Lee, H.Wade, G.Simcox, J.Engin, F.2023-02-11doi:10.1101/2023.02.11.528130Cold Spring Harbor Laboratory Press2023-02-11
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Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders
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https://biorxiv.org/cgi/content/short/2023.02.14.528208v1?rss=1"
Li, Y.-D.Ma, M. W.Hassan, M. M.Hunkeler, M.Teng, M.Puvar, K.Lumpkin, R.Sandoval, B.Jin, C. Y.Ficarro, S. B.Wang, M. Y.Xu, S.Groendyke, B. J.Sigua, L. H.Tavares, I.Zou, C.Tsai, J. M.Park, P. M. C.Yoon, H.Majewski, F. C.Marto, J. A.Qi, J.Nowak, R. P.Donovan, K. A.Slabicki, M.Gray, N. S.Fischer, E. S.Ebert, B. L.2023-02-15doi:10.1101/2023.02.14.528208Cold Spring Harbor Laboratory Press2023-02-15
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Regulated assembly and neurosteroid modulation constrain GABAA receptor pharmacology in vivo
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https://biorxiv.org/cgi/content/short/2023.02.16.528867v1?rss=1"
Sun, C.Zhu, H.Clark, S. A.Gouaux, E.2023-02-16doi:10.1101/2023.02.16.528867Cold Spring Harbor Laboratory Press2023-02-16
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Marginal specificity in protein interactions constrains evolution
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https://biorxiv.org/cgi/content/short/2023.02.18.529082v1?rss=1"
Ghose, D. A.Przydzial, K. E.Mahoney, E. M.Keating, A. E.Laub, M. T.2023-02-19doi:10.1101/2023.02.18.529082Cold Spring Harbor Laboratory Press2023-02-19
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OME-Zarr: a cloud-optimized bioimaging file format with international community support
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https://biorxiv.org/cgi/content/short/2023.02.17.528834v1?rss=1"
Moore, J.Basurto-Lozada, D.Besson, S.Bogovic, J.Brown, E. M.Burel, J.-M.de Medeiros, G.Diel, E. E.Gault, D.Ghosh, S. S.Gold, I.Halchenko, Y. O.Hartley, M.Horsfall, D.Keller, M. S.Kittisopikul, M. S.Kovacs, G.Kuepcue Yoldas, A.le Tournoulx de la Villegeorges, A.Li, T.Liberali, P.Linkert, M.Lindner, D.Luethi, J.Maitin-Shepard, J.Manz, T.McCormick, M.Mohamed, K.Moore, W.oezdemir, B.Pape, C.Pelkmans, L.Prete, M.Pietzsch, T.Preibisch, S.Rzepka, N.Stirling, D. R.Striebel, J.Tischer, C.Toloudis, D.Walczysko, P.Watson, A2023-02-21doi:10.1101/2023.02.17.528834Cold Spring Harbor Laboratory Press2023-02-21
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O-GlcNAcylation regulates neurofilament-light assembly and function and is perturbed by Charcot-Marie-Tooth disease mutations
]]>
https://biorxiv.org/cgi/content/short/2023.02.22.529563v1?rss=1"
Huynh, D. T.Hu, J.Schneider, J. R.Tsolova, K. N.Soderblom, E. J.Watson, A. J.Chi, J.-T. A.Evans, C. S.Boyce, M.2023-02-22doi:10.1101/2023.02.22.529563Cold Spring Harbor Laboratory Press2023-02-22
<![CDATA[
Dissecting cell-specific functions of circadian genes using modified cell-specific CRISPR approaches
]]>
https://biorxiv.org/cgi/content/short/2023.02.23.529279v1?rss=1"
Richhariya, S.Shin, D.Le, J. Q.Rosbash, M.2023-02-23doi:10.1101/2023.02.23.529279Cold Spring Harbor Laboratory Press2023-02-23
<![CDATA[
Human APOBEC3B promotes tumor heterogeneity in vivo including signature mutations and metastases
]]>
https://biorxiv.org/cgi/content/short/2023.02.24.529970v1?rss=1"
Durfee, C.Temiz, N. A.Levin-Klein, R.Argyris, P.Alsoe, L.Carracedo, S.Alonso, A.Proehl, J.Holzhauer, A.Seeman, Z.Lin, Y.-H. T.Vogel, R. I.Sotillo, R.Nilsen, H.Harris, R.2023-02-25doi:10.1101/2023.02.24.529970Cold Spring Harbor Laboratory Press2023-02-25
<![CDATA[
Chromosome-specific maturation of the epigenome in the Drosophila male germline
]]>
https://biorxiv.org/cgi/content/short/2023.02.24.529909v1?rss=1"
Anderson, J.Henikoff, S.Ahmad, K.2023-02-25doi:10.1101/2023.02.24.529909Cold Spring Harbor Laboratory Press2023-02-25
<![CDATA[
Drought Recovery Induced Immunity Confers Pathogen Resistance
]]>
https://biorxiv.org/cgi/content/short/2023.02.27.530256v1?rss=1"
Illouz-Eliaz, N.Lande, K.Yu, J.Jow, B.Swift, J.Lee, T.Nobori, T.Castanon, R. G.Nery, J. R.Ecker, J. R.2023-02-27doi:10.1101/2023.02.27.530256Cold Spring Harbor Laboratory Press2023-02-27
<![CDATA[
Rapid resistance profiling of SARS-CoV-2 protease inhibitors
]]>
https://biorxiv.org/cgi/content/short/2023.02.25.530000v1?rss=1"
Moghadasi, S. A.Biswas, R.Harki, D. A.Harris, R.2023-02-27doi:10.1101/2023.02.25.530000Cold Spring Harbor Laboratory Press2023-02-27
<![CDATA[
Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses
]]>
https://biorxiv.org/cgi/content/short/2023.02.26.529821v1?rss=1"
Boys, I. N.Johnson, A. G.Quinlan, M.Kranzusch, P. J.Elde, N. C.2023-02-27doi:10.1101/2023.02.26.529821Cold Spring Harbor Laboratory Press2023-02-27
<![CDATA[
Requirements for establishment and epigenetic stability of mammalian heterochromatin
]]>
https://biorxiv.org/cgi/content/short/2023.02.27.530221v1?rss=1"
Tatarakis, A.Saini, H.Moazed, D.2023-02-28doi:10.1101/2023.02.27.530221Cold Spring Harbor Laboratory Press2023-02-28
<![CDATA[
Three rules for epigenetic inheritance of human Polycomb silencing
]]>
https://biorxiv.org/cgi/content/short/2023.02.27.530239v1?rss=1"
Shafiq, T.Moazed, D.2023-02-28doi:10.1101/2023.02.27.530239Cold Spring Harbor Laboratory Press2023-02-28
<![CDATA[
A molecularly distinct accumbal-to-lateral hypothalamic circuit modulates food seeking and consumption
]]>
https://biorxiv.org/cgi/content/short/2023.02.27.530275v1?rss=1"
Liu, Y.Zhao, Z.Xie, G.Chen, R.Zhang, Y.2023-02-28doi:10.1101/2023.02.27.530275Cold Spring Harbor Laboratory Press2023-02-28
<![CDATA[
Pptc7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy
]]>
https://biorxiv.org/cgi/content/short/2023.02.28.530351v1?rss=1"
Niemi, N. M.Serrano, L. R.Muehlbauer, L. K.Balnis, C.Kozul, K.-L.Rashan, E. H.Shishkova, E.Schueler, K. L.Keller, M. P.Attie, A. D.Pagan, J.Coon, J. J.Pagliarini, D. J.2023-03-01doi:10.1101/2023.02.28.530351Cold Spring Harbor Laboratory Press2023-03-01
<![CDATA[
Condensate-driven interfacial forces reposition DNA loci and measure chromatin viscoelasticity
]]>
https://biorxiv.org/cgi/content/short/2023.02.27.530281v1?rss=1"
Strom, A. R.Kim, Y.Zhao, H.Orlovsky, N. D.Chang, Y.-C.Kosmirlj, A.Storm, C.brangwynne, C. P.2023-03-01doi:10.1101/2023.02.27.530281Cold Spring Harbor Laboratory Press2023-03-01
<![CDATA[
Monocarboxylate transporters facilitate succinate uptake into brown adipocytes
]]>
https://biorxiv.org/cgi/content/short/2023.03.01.530625v1?rss=1"
Reddy, A.Winther, S.Tran, N.Xiao, H.Jakob, J.Garrity, R.Smith, A.Mills, E.Chouchani, E.2023-03-02doi:10.1101/2023.03.01.530625Cold Spring Harbor Laboratory Press2023-03-02
<![CDATA[
A critical role of a eubiotic microbiota in gating proper immunocompetence in Arabidopsis
]]>
https://biorxiv.org/cgi/content/short/2023.03.02.527037v1?rss=1"
Paasch, B. C.Sohrabi, R.Kremer, J. M.Nomura, K.Martz, J.Kvitko, B.Tiedje, J. M.He, S. Y.2023-03-02doi:10.1101/2023.03.02.527037Cold Spring Harbor Laboratory Press2023-03-02
<![CDATA[
Brain-wide neural activity underlying memory-guided movement
]]>
https://biorxiv.org/cgi/content/short/2023.03.01.530520v1?rss=1"
Chen, S.Liu, Y.Wang, Z.Colonell, J.Liu, L. D.Hou, H.Tien, N.-W.Wang, T.Harris, T.Druckmann, S.Li, N.Svoboda, K.2023-03-02doi:10.1101/2023.03.01.530520Cold Spring Harbor Laboratory Press2023-03-02
<![CDATA[
BuTT-Seq: a new method for facile profiling of transcription
]]>
https://biorxiv.org/cgi/content/short/2023.03.04.531084v1?rss=1"
Yu, A. D.Rosbash, M.2023-03-04doi:10.1101/2023.03.04.531084Cold Spring Harbor Laboratory Press2023-03-04
<![CDATA[
A bile metabolite atlas reveals infection-triggered interorgan mediators of intestinal homeostasis and defense
]]>
https://biorxiv.org/cgi/content/short/2023.03.04.531105v1?rss=1"
Zhang, T.Hasegawa, Y.Waldor, M. K.2023-03-05doi:10.1101/2023.03.04.531105Cold Spring Harbor Laboratory Press2023-03-05
<![CDATA[
Structurally divergent and recurrently mutated regions of primate genomes
]]>
https://biorxiv.org/cgi/content/short/2023.03.07.531415v1?rss=1"
Mao, Y.Harvey, W. T.Porubsky, D.Munson, K. M.Hoekzema, K.Lewis, A. P.Audano, P. A.Rozanski, A.Yang, X.Zhang, S.Gordon, D. S.Wei, X.Logsdon, G. A.Haukness, M.Dishuck, P. C.Jeong, H.del Rosario, R.Bauer, V. L.Fattor, W. T.Wilkerson, G. K.Lu, Q.Paten, B.Feng, G.Sawyer, S. L.Warren, W. C.Carbone, L.Eichler, E. E.2023-03-07doi:10.1101/2023.03.07.531415Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
A molecularly defined and spatially resolved cell atlas of the whole mouse brain
]]>
https://biorxiv.org/cgi/content/short/2023.03.06.531348v1?rss=1"
1,100 genes in [~]8 million cells across the entire adult mouse brain using multiplexed error-robust fluorescence in situ hybridization (MERFISH)12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating MERFISH and single-cell RNA-sequencing (scRNA-seq) data. Using this approach, we generated a comprehensive cell atlas of >5,000 transcriptionally distinct cell clusters, belonging to [~]300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of the MERFISH images to the common coordinate framework (CCF) of the mouse brain further allowed systematic quantifications of the cell composition and organization in individual brain regions defined in the CCF. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes in the gene-expression profiles of cells. Finally, this high-resolution spatial map of cells, with a transcriptome-wide expression profile associated with each cell, allowed us to infer cell-type-specific interactions between several hundred pairs of molecularly defined cell types and predict potential molecular (ligand-receptor) basis and functional implications of these cell-cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a valuable resource for future functional investigations of neural circuits and their dysfunction in diseases.
]]>Zhang, M.Pan, X.Jung, W.Halpern, A.Eichhorn, S. W.Lei, Z.Cohen, L.Smith, K. A.Tasic, B.Yao, Z.Zeng, H.Zhuang, X.2023-03-07doi:10.1101/2023.03.06.531348Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
Loss of kinase Atg1 increases yeast maintenance energy requirement
]]>
https://biorxiv.org/cgi/content/short/2023.03.06.531285v1?rss=1"
Chen, X.van Aalst, A. C. A.Petranovic, D.Bisschops, M. M. M.2023-03-07doi:10.1101/2023.03.06.531285Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
Bacterial cGAS senses a viral RNA to initiate immunity
]]>
https://biorxiv.org/cgi/content/short/2023.03.07.531596v1?rss=1"
Banh, D. V.Roberts, C. G.Amador, A. M.Brady, S. F.Marraffini, L. A.2023-03-07doi:10.1101/2023.03.07.531596Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
A nanobody-based strategy for rapid and scalable purification of native human protein complexes
]]>
https://biorxiv.org/cgi/content/short/2023.03.09.531980v1?rss=1"
Stevens, T. A.Tomaleri, G. P.Hazu, M.Wei, S.Nguyen, V. N.DeKalb, C.Voorhees, R. M.Pleiner, T.2023-03-10doi:10.1101/2023.03.09.531980Cold Spring Harbor Laboratory Press2023-03-10
<![CDATA[
Drosophila antennae are dispensable for gravity orientation
]]>
https://biorxiv.org/cgi/content/short/2023.03.08.531317v1?rss=1"
Kladt, N.Reiser, M. B.2023-03-10doi:10.1101/2023.03.08.531317Cold Spring Harbor Laboratory Press2023-03-10
<![CDATA[
Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level
]]>
https://biorxiv.org/cgi/content/short/2023.03.08.531827v1?rss=1"
Liao, T.-W.Huang, L.Wilson, T. J.Ganser, L.Lilley, D. M. J.Ha, T.2023-03-11doi:10.1101/2023.03.08.531827Cold Spring Harbor Laboratory Press2023-03-11
<![CDATA[
Self-regulating living material with temperature-dependent light absorption
]]>
https://biorxiv.org/cgi/content/short/2023.03.11.532239v1?rss=1"
Xiong, L. L.Garrett, M. A.Kornfield, J. A.Shapiro, M. G.2023-03-12doi:10.1101/2023.03.11.532239Cold Spring Harbor Laboratory Press2023-03-12
<![CDATA[
Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility
]]>
https://biorxiv.org/cgi/content/short/2023.03.11.532188v1?rss=1"
Rana, U.Xu, K.Narayanan, A.Walls, M. T.Panagiotopoulos, A. Z.Avalos, J. L.Brangwynne, C. P.2023-03-12doi:10.1101/2023.03.11.532188Cold Spring Harbor Laboratory Press2023-03-12
<![CDATA[
A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis
]]>
https://biorxiv.org/cgi/content/short/2023.03.12.532304v1?rss=1"
103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features, each with mild contributions. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.
]]>Taggart, J.Lalanne, J.-B.Durand, S.Braun, F.Condon, C.Li, G.-W.2023-03-13doi:10.1101/2023.03.12.532304Cold Spring Harbor Laboratory Press2023-03-13
<![CDATA[
Connectome-constrained deep mechanistic networks predict neural responses across the fly visual system at single-neuron resolution
]]>
https://biorxiv.org/cgi/content/short/2023.03.11.532232v1?rss=1"
Lappalainen, J. K.Tschopp, F. D.Prakhya, S.McGill, M.Nern, A.Shinomiya, K.Takemura, S.-y.Gruntman, E.Macke, J. H.Turaga, S. C.2023-03-13doi:10.1101/2023.03.11.532232Cold Spring Harbor Laboratory Press2023-03-13
<![CDATA[
Hem25p is a mitochondrial IPP transporter
]]>
https://biorxiv.org/cgi/content/short/2023.03.14.532620v1?rss=1"
Tai, J.Guerra, R. M.Rogers, S. W.Fang, Z.Muehlbauer, L. K.Shishkova, E.Overmyer, K. A.Coon, J. J.Pagliarini, D. J.2023-03-14doi:10.1101/2023.03.14.532620Cold Spring Harbor Laboratory Press2023-03-14
<![CDATA[
Phosphorylation of pyruvate dehydrogenase marks the inhibition of in vivo neuronal activity
]]>
https://biorxiv.org/cgi/content/short/2023.03.13.532494v1?rss=1"
Dong, Y.Wang, Y.Qi, T.Zhang, X.Shen, L.Ma, J.Pang, Z.McClatchy, D. B.Lal, N.Wang, K.Xie, Y.Polli, F.Maximov, A.Augustine, V.Cline, H. T.Yates, J. R.Ye, L.2023-03-14doi:10.1101/2023.03.13.532494Cold Spring Harbor Laboratory Press2023-03-14
<![CDATA[
Topography of inputs into the hippocampal formation of a food-caching bird
]]>
https://biorxiv.org/cgi/content/short/2023.03.14.532572v1?rss=1"
Applegate, M. C.Gutnichenko, K. S.Aronov, D.2023-03-15doi:10.1101/2023.03.14.532572Cold Spring Harbor Laboratory Press2023-03-15
<![CDATA[
Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies
]]>
https://biorxiv.org/cgi/content/short/2023.03.14.532666v1?rss=1"
View larger version (35K):
org.highwire.dtl.DTLVardef@151f6eforg.highwire.dtl.DTLVardef@2ae877org.highwire.dtl.DTLVardef@103e0d1org.highwire.dtl.DTLVardef@19cd695_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Edman, N. I.Redler, R. L.Phal, A.Schlichthaerle, T.Srivatsan, S. R.Etemadi, A.An, S.Favor, A.Ehnes, D.Li, Z.Praetorius, F.Gordon, M.Yang, W.Coventry, B.Hicks, D. R.Cao, L.Bethel, N.Heine, P.Murray, A. N.Gerben, S.Carter, L.Miranda, M.Negahdari, B.Lee, S.Trapnell, C.Stewart, L.Ekiert, D. C.Schlessinger, J.Shendure, J.Bhabha, G.Ruohola-Baker, H.Baker, D.2023-03-15doi:10.1101/2023.03.14.532666Cold Spring Harbor Laboratory Press2023-03-15
<![CDATA[
Social association predicts immunological similarity in rewilded mice
]]>
https://biorxiv.org/cgi/content/short/2023.03.15.532825v1?rss=1"
Downie, A. E.Oyesola, O.Barre, R. S.Caudron, Q.Chen, Y.- H.Dennis, E. J.Garnier, R.Kiwanuka, K.Menezes, A.Navarrete, D. J.Mondragon-Palomino, O.Saunders, J. B.Tokita, C. K.Zaldana, K.Cadwell, K.Loke, P.Graham, A. L.2023-03-16doi:10.1101/2023.03.15.532825Cold Spring Harbor Laboratory Press2023-03-16
<![CDATA[
Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch
]]>
https://biorxiv.org/cgi/content/short/2023.03.17.533188v1?rss=1"
Handler, A.Zhang, Q.Pang, S.Nguyen, T. M.Iskols, M.Nolan-Tamariz, M.Cattel, S.Plumb, R.Sanchez, B.Ashjian, K.Shotland, A.Brown, B.Kabeer, M.Turecek, J.Rankin, G.Xiang, W.Pavarino, E. C.Africawala, N.Santiago, C.Lee, W.-C. A.Xu, C. S.Ginty, D. D.2023-03-18doi:10.1101/2023.03.17.533188Cold Spring Harbor Laboratory Press2023-03-18
<![CDATA[
Xiphoid nucleus of the midline thalamus controls cold-induced food seeking
]]>
https://biorxiv.org/cgi/content/short/2023.03.16.533067v1?rss=1"
Lal, N. K.Le, P.Aggarwal, S.Zhang, A.Wang, K.Qi, T.Pang, Z.Yang, D.Nudell, V.Yeo, G. W.Banks, A. S.Ye, L.2023-03-18doi:10.1101/2023.03.16.533067Cold Spring Harbor Laboratory Press2023-03-18
<![CDATA[
A biophysical framework for double-drugging kinases
]]>
https://biorxiv.org/cgi/content/short/2023.03.17.533217v1?rss=1"
Kim, C.Ludewig, H.Hadzipasic, A.Kutter, S.Nguyen, V.Kern, D.2023-03-18doi:10.1101/2023.03.17.533217Cold Spring Harbor Laboratory Press2023-03-18
<![CDATA[
Comparative landscape of genetic dependencies in human and chimpanzee stem cells
]]>
https://biorxiv.org/cgi/content/short/2023.03.19.533346v1?rss=1"
She, R.Fair, T.Schaefer, N. K.Saunders, R. A.Pavlovic, B. J.Weissman, J. S.Pollen, A. A.2023-03-20doi:10.1101/2023.03.19.533346Cold Spring Harbor Laboratory Press2023-03-20
<![CDATA[
Universal recording of cell-cell contacts in vivo for interaction-based transcriptomics
]]>
https://biorxiv.org/cgi/content/short/2023.03.16.533003v1?rss=1"
Nakandakari-Higa, S.Canesso, M. C. C.Walker, S.Chudnovskiy, A.Jacobsen, J. T.Parigi, S. M.Fiedorczuk, K.Fuchs, E.Bilate, A. M.Pasqual, G.Mucida, D.Pritykin, Y.Victora, G. D.2023-03-20doi:10.1101/2023.03.16.533003Cold Spring Harbor Laboratory Press2023-03-20
<![CDATA[
Nerve injury disrupts temporal processing in the spinal cord dorsal horn through alterations in PV+ interneurons
]]>
https://biorxiv.org/cgi/content/short/2023.03.20.533541v1?rss=1"
Rankin, G.Chirila, A. M.Emanuel, A. J.Zhang, Z.Woolf, C. J.Drugowitsch, J.Ginty, D. D.2023-03-21doi:10.1101/2023.03.20.533541Cold Spring Harbor Laboratory Press2023-03-21
<![CDATA[
Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells
]]>
https://biorxiv.org/cgi/content/short/2023.03.22.533709v1?rss=1"
Tsuchida, C. A.Brandes, N.Bueno, R.Trinidad, M.Mazumder, T.Yu, B.Hwang, B.Chang, C.Liu, J.Sun, Y.Hopkins, C. R.Parker, K. R.Qi, Y.Satpathy, A.Stadtmauer, E.Cate, J. H. D.Eyquem, J.Fraietta, J. A.June, C. H.Chang, H. Y.Ye, C. J.Doudna, J. A.2023-03-22doi:10.1101/2023.03.22.533709Cold Spring Harbor Laboratory Press2023-03-22
<![CDATA[
A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis
]]>
https://biorxiv.org/cgi/content/short/2023.03.23.533992v1?rss=1"
Lee, T. A.Nobori, T.Illouz-Eliaz, N.Xu, J.Jow, B.Nery, J. R.Ecker, J. R.2023-03-24doi:10.1101/2023.03.23.533992Cold Spring Harbor Laboratory Press2023-03-24
<![CDATA[
Split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80
]]>
https://biorxiv.org/cgi/content/short/2023.03.24.534001v1?rss=1"
Ewen-Campen, B.Luan, H.Xu, J.Singh, R.Joshi, N.Thakkar, T.Berger, B.White, B.Perrimon, N.2023-03-24doi:10.1101/2023.03.24.534001Cold Spring Harbor Laboratory Press2023-03-24
<![CDATA[
Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning
]]>
https://biorxiv.org/cgi/content/short/2023.03.23.533993v1?rss=1"
Radford, C. E.Schommers, P.Gieselmann, L.Crawford, K. H.Dadonaite, B.Yu, T. C.Dingens, A. S.Overbaugh, J.Klein, F.Bloom, J. D.2023-03-24doi:10.1101/2023.03.23.533993Cold Spring Harbor Laboratory Press2023-03-24
<![CDATA[
Capturing Spatiotemporal Signaling Patterns in Cellular Data with Geometric Scattering Trajectory Homology
]]>
https://biorxiv.org/cgi/content/short/2023.03.22.533807v1?rss=1"
Bhaskar, D.Moore, J. L.Gao, F.Rieck, B.Khasawneh, F.Munch, E.Greco, V.Krishnaswamy, S.2023-03-24doi:10.1101/2023.03.22.533807Cold Spring Harbor Laboratory Press2023-03-24
<![CDATA[
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements
]]>
https://biorxiv.org/cgi/content/short/2023.03.28.534017v1?rss=1"
Chardon, F. M.McDiarmid, T. A.Page, N. F.Martin, B. K.Domcke, S.Regalado, S. G.Lalanne, J.-B.Calderon, D.Starita, L. M.Sanders, S. J.Ahituv, N.Shendure, J.2023-03-28doi:10.1101/2023.03.28.534017Cold Spring Harbor Laboratory Press2023-03-28
<![CDATA[
Design and implementation of suspended drop crystallization
]]>
https://biorxiv.org/cgi/content/short/2023.03.28.534639v1?rss=1"
Gonen, T.Gillman, C.Martynowycz, M.Nicolas, W. J.2023-03-28doi:10.1101/2023.03.28.534639Cold Spring Harbor Laboratory Press2023-03-28
<![CDATA[
Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities
]]>
https://biorxiv.org/cgi/content/short/2023.03.28.534648v1?rss=1"
Garg, V.Yang, Y.Nowotschin, S.Setty, M.Kuo, Y.-Y.Sharma, R.Polyzos, A.Salataj, E.Murphy, D.Jang, A.Pe'er, D.Apostolou, E.Hadjantonakis, A.-K.2023-03-29doi:10.1101/2023.03.28.534648Cold Spring Harbor Laboratory Press2023-03-29
<![CDATA[
Matrin3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and YY1 mediated enhancer-promoter interactions
]]>
https://biorxiv.org/cgi/content/short/2023.03.30.534959v1?rss=1"
Orkin, S. H.Liu, T.Zhu, Q.Kai, Y.Bingham, T.Cha, H.Mehta, S.Schlaeger, T. M.Yuan, G.-C.2023-03-31doi:10.1101/2023.03.30.534959Cold Spring Harbor Laboratory Press2023-03-31
<![CDATA[
Multiple repeat regions within mouse DUX recruit chromatin regulators to facilitate an embryonic gene expression program
]]>
https://biorxiv.org/cgi/content/short/2023.03.29.534786v1?rss=1"
Smith, C. M.Grow, E. J.Shadle, S. C.Cairns, B. R.2023-04-01doi:10.1101/2023.03.29.534786Cold Spring Harbor Laboratory Press2023-04-01
<![CDATA[
The structure of the neurotoxin palytoxin determined by MicroED
]]>
https://biorxiv.org/cgi/content/short/2023.03.31.535166v1?rss=1"
Gillman, C.Patel, K.Unge, J.Gonen, T.2023-04-02doi:10.1101/2023.03.31.535166Cold Spring Harbor Laboratory Press2023-04-02
<![CDATA[
Astrocyte-Secreted Neurocan Controls Inhibitory Synapse Formation and Function
]]>
https://biorxiv.org/cgi/content/short/2023.04.03.535448v1?rss=1"
Irala, D.Wang, S.Sakers, K.Nagendren, L.Ulloa-Severino, F. P.Bindu, D. S.Eroglu, C.2023-04-03doi:10.1101/2023.04.03.535448Cold Spring Harbor Laboratory Press2023-04-03
<![CDATA[
No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas
]]>
https://biorxiv.org/cgi/content/short/2023.04.02.535232v1?rss=1"
Spencer, N.Łukasik, P.Meyer, M.Veloso, C.McCutcheon, J.2023-04-04doi:10.1101/2023.04.02.535232Cold Spring Harbor Laboratory Press2023-04-04
<![CDATA[
A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup
]]>
https://biorxiv.org/cgi/content/short/2023.04.05.535726v1?rss=1"
500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.
]]>Qiu, C.Martin, B. K.Welsh, I. C.Daza, R. M.Le, T.-M.Huang, X.Nichols, E. K.Taylor, M. L.Fulton, O.O'Day, D. R.Gomes, A. R.Ilcisin, S.Srivatsan, S.Deng, X.Disteche, C. M.Noble, W. S.Hamazaki, N.Moens, C. B.Kimelman, D.Cao, J.Schier, A. F.Spielmann, M.Murray, S. A.Trapnell, C.Shendure, J.2023-04-05doi:10.1101/2023.04.05.535726Cold Spring Harbor Laboratory Press2023-04-05
<![CDATA[
Secondary Structure Detection Through Direct Nanopore RNA Sequencing
]]>
https://biorxiv.org/cgi/content/short/2023.04.05.535757v1?rss=1"
Shaw, A.Craig, J. M.Amiri, H.Kim, J.Upton, H. E.Pimentel, S. C.Huang, J. R.Marqusee, S.Gundlach, J. H.Collins, K.Bustamante, C. J.2023-04-05doi:10.1101/2023.04.05.535757Cold Spring Harbor Laboratory Press2023-04-05
<![CDATA[
Identification of LMAN1 and SURF4 dependent secretory cargoes
]]>
https://biorxiv.org/cgi/content/short/2023.04.06.535922v1?rss=1"
Tang, V. T.Abbineni, P. S.da Veiga Leprevost, F.Basrur, V.Emmer, B. T.Nesvizhskii, A.Ginsburg, D.2023-04-06doi:10.1101/2023.04.06.535922Cold Spring Harbor Laboratory Press2023-04-06
<![CDATA[
Fluorescence lifetime analysis of smFRET with contribution of PIFE on donor and acceptor
]]>
https://biorxiv.org/cgi/content/short/2023.04.03.535482v1?rss=1"
Jazani, S.Ha, T.2023-04-06doi:10.1101/2023.04.03.535482Cold Spring Harbor Laboratory Press2023-04-06
<![CDATA[
The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes
]]>
https://biorxiv.org/cgi/content/short/2023.04.06.535797v1?rss=1"
10,000 ancient individuals with genome-wide data at the end of 2022. This note is intended as a citable description of the AADR.
]]>Mallick, S.Micco, A.Mah, M.Ringbauer, H.Lazaridis, I.Olalde, I.Patterson, N. J.Reich, D. E.2023-04-06doi:10.1101/2023.04.06.535797Cold Spring Harbor Laboratory Press2023-04-06
<![CDATA[
Stepwise design of pseudosymmetric protein hetero-oligomers
]]>
https://biorxiv.org/cgi/content/short/2023.04.07.535760v1?rss=1"
Kibler, R. D.Lee, S.Kennedy, M. A.Wicky, B. I. M.Lai, S. M.Kostelic, M. M.Li, X.Chow, C. M.Carter, L.Wysocki, V. H.Stoddard, B. L.Baker, D.2023-04-07doi:10.1101/2023.04.07.535760Cold Spring Harbor Laboratory Press2023-04-07
<![CDATA[
Astrocytic LRRK2 Controls Synaptic Connectivity through ERM Phosphorylation
]]>
https://biorxiv.org/cgi/content/short/2023.04.09.536178v1?rss=1"
Wang, S.Sivadasan Bindu, D.Tan, C. X.Sakers, K.Takano, T.Rodriguez Salazar, M. P.Dimond, K.Soderling, S. H.La Spada, A. R.Eroglu, C.2023-04-10doi:10.1101/2023.04.09.536178Cold Spring Harbor Laboratory Press2023-04-10
<![CDATA[
Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack
]]>
https://biorxiv.org/cgi/content/short/2023.04.10.536170v1?rss=1"
Nobori, T.Monell, A.Lee, T. A.Zhou, J.Nery, J. R.Ecker, J. R.2023-04-10doi:10.1101/2023.04.10.536170Cold Spring Harbor Laboratory Press2023-04-10
<![CDATA[
Mental navigation and telekinesis with a hippocampal map-based brain-machine interface
]]>
https://biorxiv.org/cgi/content/short/2023.04.07.536077v1?rss=1"
Lai, C.Tanaka, S.Harris, T. D.Lee, A. K.2023-04-10doi:10.1101/2023.04.07.536077Cold Spring Harbor Laboratory Press2023-04-10
<![CDATA[
Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides
]]>
https://biorxiv.org/cgi/content/short/2023.04.12.536642v1?rss=1"
Ding, D.Zhang, S. J.Szostak, J. W.2023-04-12doi:10.1101/2023.04.12.536642Cold Spring Harbor Laboratory Press2023-04-12
<![CDATA[
Dietary protein shapes the profile and repertoire of intestinal CD4+ T cells
]]>
https://biorxiv.org/cgi/content/short/2023.04.11.536475v1?rss=1"
Lockhart, A.Reed, A.de Castro, T. B. R.Herman, C.Canesso, M. C. C.Mucida, D.2023-04-13doi:10.1101/2023.04.11.536475Cold Spring Harbor Laboratory Press2023-04-13
<![CDATA[
Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs
]]>
https://biorxiv.org/cgi/content/short/2023.04.13.536294v1?rss=1"
Stahl, E. C.Sabo, J. K.Kang, M. H.Allen, R.Applegate, E.Kim, S. E.Kwon, M.Seth, A.Lemus, N.Salinas-Rios, V.Soczek, K.Trinidad, M.Vo, L. T.Jeans, C.Wozniak, A.Morris, T.Kimberlin, A.Foti, T.Savage, D. F.Doudna, J. A.2023-04-13doi:10.1101/2023.04.13.536294Cold Spring Harbor Laboratory Press2023-04-13
<![CDATA[
A critical role for CaMKII in behavioral timescale synaptic plasticity in hippocampal CA1 pyramidal neurons.
]]>
https://biorxiv.org/cgi/content/short/2023.04.18.537377v1?rss=1"
Xiao, K.Li, Y.Chitwood, R. A.Magee, J. C.2023-04-18doi:10.1101/2023.04.18.537377Cold Spring Harbor Laboratory Press2023-04-18
<![CDATA[
Computational design of non-porous, pH-responsive antibody nanoparticles
]]>
https://biorxiv.org/cgi/content/short/2023.04.17.537263v1?rss=1"
Yang, E. C.Divine, R.Miranda, M. C.Borst, A. J.Sheffler, W.Zhang, J. Z.Decarreau, J.Sarajovi, A.Abedi, M.Goldbach, N.Ahlrichs, M.Dobbins, C.Hand, A.Cheng, S.Lamb, M.Levine, P. M.Chan, S.Skotheim, R.Fallas, J.Ueda, G.Lubner, J.Somiya, M.Khmelinskaia, A.King, N. P.Baker, D.2023-04-18doi:10.1101/2023.04.17.537263Cold Spring Harbor Laboratory Press2023-04-18
<![CDATA[
Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain
]]>
https://biorxiv.org/cgi/content/short/2023.04.16.536509v1?rss=1"
Liu, H.Zeng, Q.Zhou, J.Bartlett, A.Wang, B.-A.Berube, P.Tian, W.Kenworthy, M.Altshul, J.Nery, J. R.Chen, H.Castanon, R. G.Zu, S.Li, Y. E.Lucero, J.Osteen, J. K.Pinto-Duarte, A.Lee, J.Rink, J.Cho, S.Emerson, N.Nunn, M.O'Connor, C.Yao, Z.Tasic, B.Smith, K. A.Zeng, H.Luo, C.Dixon, J. R.Ren, B.Behrens, M. M.Ecker, J. R.2023-04-18doi:10.1101/2023.04.16.536509Cold Spring Harbor Laboratory Press2023-04-18
<![CDATA[
The covariance environment defines cellular niches for spatial inference
]]>
https://biorxiv.org/cgi/content/short/2023.04.18.537375v1?rss=1"
Haviv, D.Gatie, M.Hadjantonakis, A.-K.Nawy, T.Pe'er, D.2023-04-20doi:10.1101/2023.04.18.537375Cold Spring Harbor Laboratory Press2023-04-20
<![CDATA[
Conservation of chromatin organization within human and primate centromeres
]]>
https://biorxiv.org/cgi/content/short/2023.04.20.537689v1?rss=1"
Dubocanin, D.Cortes, A. E. S.Hartley, G. A.Ranchalis, J. E.Agarwal, A.Logsdon, G.Munson, K. M.Real, T. D.Mallory, B. J.Eichler, E. E.O'Neill, R. J.Stergachis, A. B.2023-04-20doi:10.1101/2023.04.20.537689Cold Spring Harbor Laboratory Press2023-04-20
<![CDATA[
Circadian redox rhythm gates immune-induced cell death distinctly from the genetic clock
]]>
https://biorxiv.org/cgi/content/short/2023.04.21.535069v1?rss=1"
Karapetyan, S.Mwimba, M.Dong, X.2023-04-21doi:10.1101/2023.04.21.535069Cold Spring Harbor Laboratory Press2023-04-21
<![CDATA[
A DRG genetic toolkit reveals molecular, morphological, and functional diversity of somatosensory neuron subtypes
]]>
https://biorxiv.org/cgi/content/short/2023.04.22.537932v1?rss=1"
Qi, L.Iskols, M.Shi, D.Reddy, P.Walker, C.Lezgiyeva, K.Voisin, T.Pawlak, M.Kuchroo, V. K.Chiu, I.Ginty, D. D.Sharma, N.2023-04-23doi:10.1101/2023.04.22.537932Cold Spring Harbor Laboratory Press2023-04-23
<![CDATA[
Evidence for a role of human blood-borne factors in mediating age-associated changes in molecular circadian rhythms
]]>
https://biorxiv.org/cgi/content/short/2023.04.19.537477v1?rss=1"
Schwarz, J. E.Mrcela, A.Lahens, N. F.Li, Y.Hsu, C.Grant, G.Skarke, C.Zhang, S. L.Sehgal, A.2023-04-24doi:10.1101/2023.04.19.537477Cold Spring Harbor Laboratory Press2023-04-24
<![CDATA[
Isoform-specific C-terminal phosphorylation drives autoinhibition of Casein Kinase 1
]]>
https://biorxiv.org/cgi/content/short/2023.04.24.538174v1?rss=1"
Harold, R. L.Tulsian, N. K.Narasimamurthy, R.Yaitanes, N.Hernandez, M. G. A.Lee, H.-W.Virshup, D. M.Partch, C. L.2023-04-24doi:10.1101/2023.04.24.538174Cold Spring Harbor Laboratory Press2023-04-24
<![CDATA[
Turicibacterales protect mice from severe Citrobacter rodentium infection
]]>
https://biorxiv.org/cgi/content/short/2023.04.25.538270v1?rss=1"
Hoek, K. L.McClanahan, K. G.Latour, Y. L.Shealy, N.Piazuelo, M. B.Vallance, B. A.Byndloss, M. X.Olivares-Villagomez, D.Wilson, K. T.2023-04-25doi:10.1101/2023.04.25.538270Cold Spring Harbor Laboratory Press2023-04-25
<![CDATA[
Novel Chromatin Insulating Activities Uncovered upon Eliminating KnownInsulators in vivo
]]>
https://biorxiv.org/cgi/content/short/2023.04.25.538167v1?rss=1"
Ortabozkoyun, H.Huang, P.-Y.Cho, H.Mazzoni, E.Tsirigos, A.Reinberg, D.2023-04-25doi:10.1101/2023.04.25.538167Cold Spring Harbor Laboratory Press2023-04-25
<![CDATA[
Contribution of the IGCR1 regulatory element and the 3'Igh CBEs to Regulation of Igh V(D)J Recombination
]]>
https://biorxiv.org/cgi/content/short/2023.04.21.537836v1?rss=1"
Liang, Z.Zhao, L.Ye, A. Y.Lin, S. G.Zhang, Y.Guo, C.Dai, H.-Q.Ba, Z.Alt, F. W.2023-04-25doi:10.1101/2023.04.21.537836Cold Spring Harbor Laboratory Press2023-04-25
<![CDATA[
ORFeus: A Computational Method to Detect Programmed Ribosomal Frameshifts and Other Non-Canonical Translation Events
]]>
https://biorxiv.org/cgi/content/short/2023.04.24.538127v1?rss=1"
Richardson, M. O.Eddy, S. R.2023-04-25doi:10.1101/2023.04.24.538127Cold Spring Harbor Laboratory Press2023-04-25
<![CDATA[
PEELing: an integrated and user-centric platform for cell-surface proteomics analysis
]]>
https://biorxiv.org/cgi/content/short/2023.04.21.537871v1?rss=1"
Peng, X.Clements, J.Jiang, Z.Preibisch, S.Li, J.2023-04-25doi:10.1101/2023.04.21.537871Cold Spring Harbor Laboratory Press2023-04-25
<![CDATA[
Assessment of three-dimensional RNA structure prediction in CASP15
]]>
https://biorxiv.org/cgi/content/short/2023.04.25.538330v1?rss=1"
Das, R.Kretsch, R. C.Simpkin, A. J.Mulvaney, T.Pham, P.Rangan, R.Bu, F.Keegan, R.Topf, M.Rigden, D.Miao, Z.Westhof, E.2023-04-26doi:10.1101/2023.04.25.538330Cold Spring Harbor Laboratory Press2023-04-26
<![CDATA[
Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market
]]>
https://biorxiv.org/cgi/content/short/2023.04.25.538336v1?rss=1"
20% of their chordate mitochondrial material from raccoon dogs, but only one of these samples contains any SARS-CoV-2 reads, and that sample only has 1 of[~] 200,000,000 reads mapping to SARS-CoV-2. Instead, SARS-CoV-2 reads are most correlated with reads mapping to various fish, such as catfish and largemouth bass. These results suggest that while metagenomic analysis of the environmental samples is useful for identifying animals or animal products sold at the market, co-mingling of animal and viral genetic material is unlikely to reliably indicate whether any animals were infected by SARS-CoV-2.
]]>Bloom, J. D.2023-04-26doi:10.1101/2023.04.25.538336Cold Spring Harbor Laboratory Press2023-04-26
<![CDATA[
Essential roles of the ANKRD31-REC114 interaction in meiotic recombination and mouse spermatogenesis
]]>
https://biorxiv.org/cgi/content/short/2023.04.27.538541v1?rss=1"
Xu, J.Li, T.Kim, S.Boekhout, M.Keeney, S.2023-04-28doi:10.1101/2023.04.27.538541Cold Spring Harbor Laboratory Press2023-04-28
<![CDATA[
A Narrow Range of Transcript-error Rates Across the Tree of Life
]]>
https://biorxiv.org/cgi/content/short/2023.05.02.538944v1?rss=1"
Li, W.Baehr, S.Marasco, M.Reyes, L.Brister, D.Pikaard, C.Gout, J.-F.Vermulst, M.Lynch, M.2023-05-02doi:10.1101/2023.05.02.538944Cold Spring Harbor Laboratory Press2023-05-02
<![CDATA[
Molecular choreography of primer synthesis by the eukaryotic Pol α-primase
]]>
https://biorxiv.org/cgi/content/short/2023.05.03.539257v1?rss=1"
Yuan, Z.Georgescu, R.Li, H.O'Donnell, M. E.2023-05-03doi:10.1101/2023.05.03.539257Cold Spring Harbor Laboratory Press2023-05-03
<![CDATA[
Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall
]]>
https://biorxiv.org/cgi/content/short/2023.05.04.539448v1?rss=1"
Harvey, W. T.Ebert, P.Ebler, J.Audano, P. A.Munson, K. M.Hoekzema, K.Porubsky, D. E.Beck, C. R.Marschall, T. R.Garimella, K. V.Eichler, E. E.2023-05-04doi:10.1101/2023.05.04.539448Cold Spring Harbor Laboratory Press2023-05-04
<![CDATA[
ZBTB7A regulates MDD-specific chromatin signatures and astrocyte-mediated stress vulnerability in orbitofrontal cortex
]]>
https://biorxiv.org/cgi/content/short/2023.05.04.539425v1?rss=1"
Fulton, S. L.Bendl, J.Gameiro-Ros, I.Fullard, J. F.Al-Kachak, A.Lepack, A. E.Stewart, A. F.Singh, S.Poller, W. C.Bastle, R. M.Hauberg, M. E.Fakira, A. K.Chen, M.Durand-de Cuttoli, R.Cathomas, F.Ramakrishnan, A.Gleason, K.Shen, L.Tamminga, C. A.Milosevic, A.Russo, S. J.Swirski, F.Blitzer, R. D.Slesinger, P. A.Roussos, P.Maze, I.2023-05-04doi:10.1101/2023.05.04.539425Cold Spring Harbor Laboratory Press2023-05-04
<![CDATA[
Histone H3 serotonylation dynamics in dorsal raphe nucleus contribute to stress-induced gene expression and behavior
]]>
https://biorxiv.org/cgi/content/short/2023.05.04.539464v1?rss=1"
Al-Kachak, A.Fulton, S. L.Farrelly, L. A.Lepack, A. E.Bastle, R. M.Kong, L.Cathomas, F.Newman, E. L.Menard, C.Ramakrishnan, A.Chan, J. C.Safovich, P.Lyu, Y.Covington, H. E.Shen, L.Gleason, K.Tamminga, C. A.Russo, S. J.Maze, I.2023-05-04doi:10.1101/2023.05.04.539464Cold Spring Harbor Laboratory Press2023-05-04
<![CDATA[
The subiculum encodes environmental geometry
]]>
https://biorxiv.org/cgi/content/short/2023.05.07.539721v1?rss=1"
Sun, Y.Nitz, D. A.Xu, X.Giocomo, L. M.2023-05-07doi:10.1101/2023.05.07.539721Cold Spring Harbor Laboratory Press2023-05-07
<![CDATA[
Jumbo phages are active against extensively-drug-resistant eyedrop-associated Pseudomonas aeruginosa infections.
]]>
https://biorxiv.org/cgi/content/short/2023.05.08.539869v1?rss=1"
200kb in genome size) and non-jumbo phages that were active against these isolates, the former killing more efficiently. Jumbo phages effectively killed the 3 separate XDR P. aeruginosa isolates both on solid and liquid medium. Given the ongoing nature of the XDR P. aeruginosa eyedrop outbreak, the identification of phages active against them provides physicians with several novel potential alternatives for treatment.
]]>Cobian-Guemes, A. G.Ghatbale, P.Blanc, A. N.Morgan, C. J.Garcia, A.Leonard, J.Huang, L.Kovalick, G.Proost, M.Chiu, M.Kuo, P.Oh, J.Karthikeyan, S.Knight, R.Pogliano, J.Schooley, R.Pride, D.2023-05-08doi:10.1101/2023.05.08.539869Cold Spring Harbor Laboratory Press2023-05-08
<![CDATA[
IL-10 constrains sphingolipid metabolism via fatty acid desaturation to limit inflammation
]]>
https://biorxiv.org/cgi/content/short/2023.05.07.539780v1?rss=1"
York, A. G.Skadow, M. H.Qu, R. G.Oh, J.Mowel, W. K.Brewer, J. R.Kaffe, E.Williams, K. J.Kluger, Y.Crawford, J. M.Smale, S. M.Bensinger, S. J.Flavell, R. A.2023-05-08doi:10.1101/2023.05.07.539780Cold Spring Harbor Laboratory Press2023-05-08
<![CDATA[
The developmental timing of spinal touch processing alterations and its relation to ASD-associated behaviors in mouse models
]]>
https://biorxiv.org/cgi/content/short/2023.05.09.539589v1?rss=1"
Tasnim, A.Alkislar, I.Hakim, R.Turecek, J.Abdelaziz, A.Orefice, L. L.Ginty, D. D.2023-05-09doi:10.1101/2023.05.09.539589Cold Spring Harbor Laboratory Press2023-05-09
<![CDATA[
Joint Generation of Protein Sequence and Structure with RoseTTAFold Sequence Space Diffusion
]]>
https://biorxiv.org/cgi/content/short/2023.05.08.539766v1?rss=1"
Lisanza, S. L.Gershon, J. M.Tipps, S. W. K.Arnoldt, L.Hendel, S.Sims, J. N.Li, X.Baker, D.2023-05-10doi:10.1101/2023.05.08.539766Cold Spring Harbor Laboratory Press2023-05-10
<![CDATA[
Electron transport inhibition increases cellular dependence on purine transport and salvage
]]>
https://biorxiv.org/cgi/content/short/2023.05.11.540429v1?rss=1"
Wu, Z.Bezwada, D.Harris, R. C.Pan, C.Nguyen, P. T.Faubert, B.Cai, L.Cai, F.Vu, H. S.Chen, H.Martin-Sandoval, M.Do, D.Gu, W.Zhang, Y.Ko, B.Brooks, B.Kelekar, S.Zhang, Y.Zacharias, L. G.Oaxaca, K. C.Mathews, T. P.Garcia-Bermudez, J.Ni, M.DeBerardinis, R. J.2023-05-11doi:10.1101/2023.05.11.540429Cold Spring Harbor Laboratory Press2023-05-11
<![CDATA[
Immune-induced remodelling of mRNA structurome regulates uORF-mediated translation
]]>
https://biorxiv.org/cgi/content/short/2023.05.09.540021v1?rss=1"
Xiang, Y.Chen, T.Irving, P. S.Weeks, K.Dong, X.2023-05-11doi:10.1101/2023.05.09.540021Cold Spring Harbor Laboratory Press2023-05-11
<![CDATA[
Allosteric regulation of TRPV1 by the inflammatory lipid, LPA
]]>
https://biorxiv.org/cgi/content/short/2023.05.11.540281v1?rss=1"
Arnold, W. R.Julius, D.Cheng, Y.2023-05-11doi:10.1101/2023.05.11.540281Cold Spring Harbor Laboratory Press2023-05-11
<![CDATA[
Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct
]]>
https://biorxiv.org/cgi/content/short/2023.05.11.540414v1?rss=1"
Kosno, M.Currie, S. L.Kumar, A.Xing, C.Rosen, M. K.2023-05-12doi:10.1101/2023.05.11.540414Cold Spring Harbor Laboratory Press2023-05-12
<![CDATA[
A developmental gradient reveals biosynthetic pathways to eukaryotic toxins in monocot geophytes
]]>
https://biorxiv.org/cgi/content/short/2023.05.12.540595v1?rss=1"
150 Amaryllidaceae alkaloids (AmAs) including galantamine, an FDA-approved treatment for Alzheimers disease. We show that while AmAs accumulate to high levels in many tissues in daffodils, biosynthesis is localized to nascent, growing tissue at the base of leaves. A similar trend is found for the production of steroidal alkaloids (e.g. cyclopamine) in corn lily. This model of active biosynthesis enabled elucidation of a complete set of biosynthetic genes for the production of AmAs. Taken together, our work sheds light on the developmental and enzymatic logic of diverse alkaloid biosynthesis in daffodil. More broadly, it suggests a paradigm for biosynthesis regulation in monocot geophytes where plants are protected from herbivory through active charging of newly formed cells with eukaryotic toxins that persist as aboveground tissue develops.
]]>Mehta, N.Meng, Y.Zare, R. N.Kamenetsky, R.Sattely, E.2023-05-12doi:10.1101/2023.05.12.540595Cold Spring Harbor Laboratory Press2023-05-12
<![CDATA[
Structural snapshots of hyaluronan formation reveal principles of length control and secretion
]]>
https://biorxiv.org/cgi/content/short/2023.05.11.540447v1?rss=1"
Gorniak, I.Stephens, Z.Erramilli, S.Gawda, T.Kossiakoff, A.Zimmer, J.2023-05-12doi:10.1101/2023.05.11.540447Cold Spring Harbor Laboratory Press2023-05-12
<![CDATA[
Recurrent Viral Capture of a Host-Derived Immune Antagonist
]]>
https://biorxiv.org/cgi/content/short/2023.05.12.540623v1?rss=1"
Goldstein, S. A.Elde, N. C.2023-05-14doi:10.1101/2023.05.12.540623Cold Spring Harbor Laboratory Press2023-05-14
<![CDATA[
Overlapping representations of food and social stimuli in VTA dopamine neurons
]]>
https://biorxiv.org/cgi/content/short/2023.05.17.541104v1?rss=1"
Willmore, L.Minerva, A.Engelhard, B.McMannon, B.Oak, N.Thiberge, S.Murugan, M.Pena, C. J.Witten, I.2023-05-17doi:10.1101/2023.05.17.541104Cold Spring Harbor Laboratory Press2023-05-17
<![CDATA[
Recovery of a learned behavior despite partial restoration of neuronal dynamics after chronic inactivation of inhibitory neurons
]]>
https://biorxiv.org/cgi/content/short/2023.05.17.541057v1?rss=1"
Torok, Z.Luebbert, L.Feldman, J.Duffy, A.Nevue, A.Wongso, S.Mello, C.Fairhall, A.Pachter, L.Gonzalez, W.Lois, C.2023-05-18doi:10.1101/2023.05.17.541057Cold Spring Harbor Laboratory Press2023-05-18
<![CDATA[
ERG-driven prostate cancer emerges from basal-luminal hybrid cells
]]>
https://biorxiv.org/cgi/content/short/2023.05.15.540839v1?rss=1"
Feng, W.Ladewig, E.Salsabeel, N.Zhao, H.Lee, Y. S.Gopalan, A.Luo, H.Kang, W.Fan, N.Rosiek, E.Masilionis, I.Chaligne, R.De Stanchina, E.Chen, Y.Carver, B. S.Leslie, C. S.Sawyers, C.2023-05-18doi:10.1101/2023.05.15.540839Cold Spring Harbor Laboratory Press2023-05-18
<![CDATA[
A Hypothalamic Circuit Underlying the Dynamic Control of Social Homeostasis
]]>
https://biorxiv.org/cgi/content/short/2023.05.19.540391v1?rss=1"
Liu, D.Rahman, M.Johnson, A.Tsutsui-Kimura, I.Pena, N.Talay, M.Logeman, B. L.Finkbeiner, S.Choi, S.Capo-Battaglia, A.Abdus-Saboor, I.Ginty, D. D.Uchida, N.Watabe-Uchida, M.Dulac, C.2023-05-19doi:10.1101/2023.05.19.540391Cold Spring Harbor Laboratory Press2023-05-19
<![CDATA[
Periodic hypothalamic attractor-like dynamics during the estrus cycle
]]>
https://biorxiv.org/cgi/content/short/2023.05.22.541741v1?rss=1"
Liu, M.Nair, A.Linderman, S. W.Anderson, D. J.2023-05-22doi:10.1101/2023.05.22.541741Cold Spring Harbor Laboratory Press2023-05-22
<![CDATA[
Stem cells tightly regulate dead cell clearance to maintain tissue fitness
]]>
https://biorxiv.org/cgi/content/short/2023.05.22.541773v1?rss=1"
Stewart, K. S.Gonzales, K. A.Yuan, S.Tierney, M. T.Bonny, A. R.Yang, Y.Infarinato, N. R.Cowley, C. J.Levorse, J. M.Pasolli, H. A.Ghosh, S.Rothlin, C. V.Fuchs, E.2023-05-22doi:10.1101/2023.05.22.541773Cold Spring Harbor Laboratory Press2023-05-22
<![CDATA[
Cancer initiation is influenced by sex-biased tissue environment or imbalanced hormones
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https://biorxiv.org/cgi/content/short/2023.05.20.541565v1?rss=1"
Zhang, F.Deng, M.2023-05-22doi:10.1101/2023.05.20.541565Cold Spring Harbor Laboratory Press2023-05-22
<![CDATA[
Effects of focused ultrasound in a "clean" mouse model of ultrasonic neuromodulation
]]>
https://biorxiv.org/cgi/content/short/2023.05.22.541780v1?rss=1"
Guo, H.Salahshoor, H.Wu, D.Yoo, S.Sato, T.Tsao, D.Shapiro, M.2023-05-24doi:10.1101/2023.05.22.541780Cold Spring Harbor Laboratory Press2023-05-24
<![CDATA[
MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT
]]>
https://biorxiv.org/cgi/content/short/2023.05.25.542276v1?rss=1"
Araujo Tavares, R. d. C.Mahadeshwar, G.Wan, H.Pyle, A. M.2023-05-25doi:10.1101/2023.05.25.542276Cold Spring Harbor Laboratory Press2023-05-25
<![CDATA[
Rapid intracellular acidification is a novel plant defense response countered by the brown planthopper
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https://biorxiv.org/cgi/content/short/2023.05.24.542203v1?rss=1"
Jiang, Y.Zhang, X.-Y.Li, S.Xie, Y.-C.Li, Z.Jin, D.Yang, Y.Pu, Z.Zhang, L.Lu, J.-B.Huang, H.-J.Zhang, C.-X.He, S. Y.2023-05-25doi:10.1101/2023.05.24.542203Cold Spring Harbor Laboratory Press2023-05-25
<![CDATA[
Mapping memories: pulse-chase labeling reveals AMPA receptor dynamics during memory formation
]]>
https://biorxiv.org/cgi/content/short/2023.05.26.541296v1?rss=1"
Kim, D.Park, P.Li, X. T.Wong-Campos, J. D.Tian, H.Grimm, J. B.Lavis, L.Cohen, A. E.2023-05-26doi:10.1101/2023.05.26.541296Cold Spring Harbor Laboratory Press2023-05-26
<![CDATA[
Stoichiometric expression of messenger polycistrons by eukaryotic ribosomes (SEMPER) for compact, ratio-tunable multi-gene expression from single mRNAs
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https://biorxiv.org/cgi/content/short/2023.05.26.541240v1?rss=1"
Duan, M.Dev, I.Lu, A.You, M. Y.Shapiro, M. G.2023-05-26doi:10.1101/2023.05.26.541240Cold Spring Harbor Laboratory Press2023-05-26
<![CDATA[
Voltage dynamics of dendritic integration and back-propagation in vivo
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https://biorxiv.org/cgi/content/short/2023.05.25.542363v1?rss=1"
Wong-Campos, J. D.Park, P.Davis, H. C.Qi, Y.Tian, H.Itkis, D. G.Kim, D.Grimm, J. B.Plutkis, S. E.Lavis, L.Cohen, A. E.2023-05-26doi:10.1101/2023.05.25.542363Cold Spring Harbor Laboratory Press2023-05-26
<![CDATA[
Barcoding of episodic memories in the hippocampus of a food-caching bird
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https://biorxiv.org/cgi/content/short/2023.05.27.542597v1?rss=1"
Chettih, S. N.Mackevicius, E. L.Hale, S.Aronov, D.2023-05-28doi:10.1101/2023.05.27.542597Cold Spring Harbor Laboratory Press2023-05-28
<![CDATA[
DNA-guided transcription factor cooperativity shapes face and limb mesenchyme
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https://biorxiv.org/cgi/content/short/2023.05.29.541540v1?rss=1"
Kim, S.Morgunova, E.Naqvi, S.Bader, M.Koska, M.Popov, A.Luong, C.Pogson, A.Claes, P.Taipale, J.Wysocka, J.2023-05-29doi:10.1101/2023.05.29.541540Cold Spring Harbor Laboratory Press2023-05-29
<![CDATA[
Mechanisms of memory storage and retrieval in hippocampal area CA3
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https://biorxiv.org/cgi/content/short/2023.05.30.542781v1?rss=1"
Li, Y.Briguglio, J.Romani, S.Magee, J. C.2023-05-30doi:10.1101/2023.05.30.542781Cold Spring Harbor Laboratory Press2023-05-30
<![CDATA[
Pseudouridine guides germline small RNA transport and epigenetic inheritance
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https://biorxiv.org/cgi/content/short/2023.05.27.542553v1?rss=1"
Herridge, R. P.Dolata, J.Migliori, V.de Santis Alves, C.Borges, F.Van Ex, F.Lin, A.Bajczyk, M.Leonardi, T.Hendrick, A.Schorn, A. J.Kouzarides, T.Martienssen, R. A.2023-05-30doi:10.1101/2023.05.27.542553Cold Spring Harbor Laboratory Press2023-05-30
<![CDATA[
The variation and evolution of complete human centromeres
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https://biorxiv.org/cgi/content/short/2023.05.30.542849v1?rss=1"
Logsdon, G. A.Rozanski, A. N.Ryabov, F.Potapova, T.Shepelev, V. A.Mao, Y.Rautiainen, M.Koren, S.Nurk, S.Porubsky, D.Lucas, J. K.Hoekzema, K.Munson, K. M.Gerton, J. L.Phillippy, A. M.Alexandrov, I. A.Eichler, E. E.2023-05-31doi:10.1101/2023.05.30.542849Cold Spring Harbor Laboratory Press2023-05-31
<![CDATA[
Single-cell type analysis of wing premotor circuits in the ventral nerve cord of Drosophila melanogaster
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https://biorxiv.org/cgi/content/short/2023.05.31.542897v1?rss=1"
Ehrhardt, E.Whitehead, S. C.Namiki, S.Minegishi, R.Siwanowicz, I.Feng, K.Otsuna, H.FlyLight Project Team,Meissner, G. W.Stern, D.Truman, J.Shepherd, D.Dickinson, M. H.Dickson, B. J.Cohen, I.Card, G. M.Korff, W.2023-06-01doi:10.1101/2023.05.31.542897Cold Spring Harbor Laboratory Press2023-06-01
<![CDATA[
Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells
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https://biorxiv.org/cgi/content/short/2023.05.31.543160v1?rss=1"
Pang, L.-Y.DeLuca, S.Zhu, H.Urban, J.Spradling, A. C.2023-06-01doi:10.1101/2023.05.31.543160Cold Spring Harbor Laboratory Press2023-06-01
<![CDATA[
Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density
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https://biorxiv.org/cgi/content/short/2023.05.30.542205v1?rss=1"
Ma, Y.Budde, M. W.Zhu, J.Elowitz, M.2023-06-01doi:10.1101/2023.05.30.542205Cold Spring Harbor Laboratory Press2023-06-01
<![CDATA[
Sleep and memory consolidation are linked by RNA processing genes in the Drosophila mushroom body
]]>
https://biorxiv.org/cgi/content/short/2023.05.31.543136v1?rss=1"
Li, Y.Chouhan, N. S.Zhang, S. L.Moore, R. S.Shon, J.Yue, Z.Sehgal, A.2023-06-01doi:10.1101/2023.05.31.543136Cold Spring Harbor Laboratory Press2023-06-01
<![CDATA[
Dendritic voltage imaging reveals biophysical basis of associative plasticity rules
]]>
https://biorxiv.org/cgi/content/short/2023.06.02.543490v1?rss=1"
Park, P.Wong-Campos, J. D.Itkis, D.Qi, Y.Davis, H. C.Grimm, J. B.Plutkis, S. E.Lavis, L.Cohen, A. E.2023-06-02doi:10.1101/2023.06.02.543490Cold Spring Harbor Laboratory Press2023-06-02
<![CDATA[
Interplay between nutrient transporters ensures fertility in the malaria mosquito Anopheles gambiae
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https://biorxiv.org/cgi/content/short/2023.06.02.543516v1?rss=1"
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org.highwire.dtl.DTLVardef@1c9b326org.highwire.dtl.DTLVardef@1109e59org.highwire.dtl.DTLVardef@c263borg.highwire.dtl.DTLVardef@1a1f9df_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Stryapunina, I.Itoe, M.Trinh, Q.Vidoudez, C.Du, E.Mendoza, L.Hulai, O.Kauffman, J.Carew, J.Shaw, W. R.Catteruccia, F.2023-06-03doi:10.1101/2023.06.02.543516Cold Spring Harbor Laboratory Press2023-06-03
<![CDATA[
Natural Silencing of Quorum-Sensing Activity Protects Vibrio parahaemolyticus from Lysis by an Autoinducer-Detecting Phage
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https://biorxiv.org/cgi/content/short/2023.06.05.543668v1?rss=1"
Duddy, O.Silpe, J.Fei, C.Bassler, B. L.2023-06-05doi:10.1101/2023.06.05.543668Cold Spring Harbor Laboratory Press2023-06-05
<![CDATA[
Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation
]]>
https://biorxiv.org/cgi/content/short/2023.06.05.543407v1?rss=1"
Marin, E. C.Morris, B. J.Stuerner, T.Champion, A. S.Krzeminski, D.Badalamente, G.Gkantia, M.Dunne, C. R.Eichler, K.Takemura, S.-y.Tamimi, I. F. M.Fang, S.Moon, S. S.Cheong, H. S. J.Li, F.Schlegel, P.Berg, S.FlyEM Project Team,Card, G. M.Costa, M.Shepherd, D.Jefferis, G. S. X. E.2023-06-06doi:10.1101/2023.06.05.543407Cold Spring Harbor Laboratory Press2023-06-06
<![CDATA[
A Connectome of the Male Drosophila Ventral Nerve Cord
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https://biorxiv.org/cgi/content/short/2023.06.05.543757v1?rss=1"
Takemura, S.-y.Hayworth, K. J.Huang, G. B.Januszewski, M.Lu, Z.Marin, E. C.Preibisch, S.Xu, C. S.Bogovic, J.Champion, A. S.Cheong, H. S. J.Costa, M.Eichler, K.Katz, W.Knecht, C.Li, F.Morris, B. J.Ordish, C.Rivlin, P. K.Schlegel, P.Shinomiya, K.Sturner, T.Zhao, T.Badalamente, G.Bailey, D.Brooks, P.Canino, B. S.Clements, J.Cook, M.Duclos, O.Dunne, C. R.Fairbanks, K.Fang, S.Finley-May, S.Francis, A.George, R.Gkantia, M.Harrington, K.Hopkins, G. P.Hsu, J.Hubbard, P. M.Javier, A.Kainmueller, D.Korff, W.Kovalyak,2023-06-06doi:10.1101/2023.06.05.543757Cold Spring Harbor Laboratory Press2023-06-06
<![CDATA[
A Spatiotemporal Compartmentalization of Glucose Metabolism Guides Mammalian Gastrulation Progression
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https://biorxiv.org/cgi/content/short/2023.06.06.543780v1?rss=1"
Cao, D.Zhong, L.Hemalatha, A.Bergmann, J.Cox, A. L.Greco, V.Sozen, B.2023-06-07doi:10.1101/2023.06.06.543780Cold Spring Harbor Laboratory Press2023-06-07
<![CDATA[
The human Y and inactive X chromosomes similarly modulate autosomal gene expression
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https://biorxiv.org/cgi/content/short/2023.06.05.543763v1?rss=1"
San Roman, A. K.Skaletsky, H.Godfrey, A. K.Bokil, N. V.Teitz, L.Singh, I.Blanton, L. V.Bellott, D. W.Pyntikova, T.Lange, J.Koutseva, N.Hughes, J. F.Brown, L.Phou, S.Buscetta, A.Kruszka, P.Banks, N.Dutra, A.Pak, E.Lasutschinkow, P. C.Keen, C.Davis, S. M.Lin, A. E.Tartaglia, N. R.Samango-Sprouse, C.Muenke, M.Page, D. C.2023-06-07doi:10.1101/2023.06.05.543763Cold Spring Harbor Laboratory Press2023-06-07
<![CDATA[
Sequence and epigenetic landscapes of active and silenced nucleolus organizers in Arabidopsis
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https://biorxiv.org/cgi/content/short/2023.06.07.544131v1?rss=1"
Fultz, D.McKinlay, A.Enganti, R.Pikaard, C.2023-06-07doi:10.1101/2023.06.07.544131Cold Spring Harbor Laboratory Press2023-06-07
<![CDATA[
Lineage motifs: developmental modules for control of cell type proportions
]]>
https://biorxiv.org/cgi/content/short/2023.06.06.543925v1?rss=1"
Tran, M.Askary, A.Elowitz, M.2023-06-07doi:10.1101/2023.06.06.543925Cold Spring Harbor Laboratory Press2023-06-07
<![CDATA[
HNF4a regulates acyl chain remodeling and ether lipid accumulation in hepatic steatosis
]]>
https://biorxiv.org/cgi/content/short/2023.06.08.544272v1?rss=1"
Von Bank, H.Geoghegan, G.Jain, R.Kotulkar, M.Hurtado-Thiele, M.Gonzalez, P.Kirsh, C.Chevalier, A.Schueler, K. L.Attie, A. D.Keller, M. P.Apte, U.Simcox, J.2023-06-09doi:10.1101/2023.06.08.544272Cold Spring Harbor Laboratory Press2023-06-09
<![CDATA[
Blueprinting expandable nanomaterials with standardized protein building blocks
]]>
https://biorxiv.org/cgi/content/short/2023.06.09.544258v1?rss=1"
Huddy, T. F.Hsia, Y.Kibler, R. D.Xu, J.Bethel, N.Nagarajan, D.Redler, R.Leung, P. J. Y.Courbet, A.Yang, E. C.Bera, A. K.Coudray, N.Calise, S. J.Davila-Hernandez, F. A.Weidle, C.Han, H. L.Li, Z.McHugh, R.Reggiano, G.Kang, A.Sankaran, B.Dickinson, M. S.Coventry, B.Brunette, T.Liu, Y.Dauparas, J.Borst, A. J.Ekiert, D.Kollman, J. M.Bhabha, G.Baker, D.2023-06-09doi:10.1101/2023.06.09.544258Cold Spring Harbor Laboratory Press2023-06-09
<![CDATA[
Directing polymorph specific calcium carbonate formation with de novo protein templates
]]>
https://biorxiv.org/cgi/content/short/2023.06.09.544362v1?rss=1"
Davila Hernandez, F. A.Jin, B.Pyles, H.Zhang, S.Wang, Z.Huddy, T. F.Chen, C.-L.De Yoreo, J. J.Baker, D.2023-06-09doi:10.1101/2023.06.09.544362Cold Spring Harbor Laboratory Press2023-06-09
<![CDATA[
Genetic and immune determinants of E. coli liver abscess formation
]]>
https://biorxiv.org/cgi/content/short/2023.06.11.543319v1?rss=1"
Hullahalli, K.Dailey, K. G.Hasegawa, Y.Suzuki, M.Zhang, H.Threadgill, D. W.Waldor, M. K.2023-06-12doi:10.1101/2023.06.11.543319Cold Spring Harbor Laboratory Press2023-06-12
<![CDATA[
SAD-1 kinase controls presynaptic phase separation by relieving SYD-2/Liprin-α autoinhibition
]]>
https://biorxiv.org/cgi/content/short/2023.06.12.544643v1?rss=1"
McDonald, N. A.Tao, L.Dong, M.-Q.Shen, K.2023-06-12doi:10.1101/2023.06.12.544643Cold Spring Harbor Laboratory Press2023-06-12
<![CDATA[
Transforming descending input into behavior: The organization of premotor circuits in the Drosophila Male Adult Nerve Cord connectome
]]>
https://biorxiv.org/cgi/content/short/2023.06.07.543976v1?rss=1"
Cheong, H. S. J.Eichler, K.Stuerner, T.Asinof, S. K.Champion, A. S.Marin, E. C.Oram, T. B.Sumathipala, M.Venkatasubramanian, L.Namiki, S.Siwanowicz, I.Costa, M.Berg, S.Janelia FlyEM Project Team,Jefferis, G. S. X. E.Card, G. M.2023-06-12doi:10.1101/2023.06.07.543976Cold Spring Harbor Laboratory Press2023-06-12
<![CDATA[
CRISPR-mediated germline mutagenesis for genetic sterilization of Anopheles gambiae males.
]]>
https://biorxiv.org/cgi/content/short/2023.06.13.544841v1?rss=1"
Smidler, A. L.Paton, D. G.Church, G. M.Shaw, W. R.Catteruccia, F.2023-06-13doi:10.1101/2023.06.13.544841Cold Spring Harbor Laboratory Press2023-06-13
<![CDATA[
Dissociating the Contributions of Frontal Eye Field Activity to Spatial Working Memory and Motor Preparation
]]>
https://biorxiv.org/cgi/content/short/2023.06.12.544653v1?rss=1"
Jonikaitis, D.Noudoost, B.Moore, T.2023-06-13doi:10.1101/2023.06.12.544653Cold Spring Harbor Laboratory Press2023-06-13
<![CDATA[
Organization of an Ascending Circuit that Conveys Flight Motor State
]]>
https://biorxiv.org/cgi/content/short/2023.06.07.544074v1?rss=1"
Cheong, H. S. J.Boone, K. N.Bennett, M. M.Salman, F.Ralston, J. D.Hatch, K.Allen, R. F.Phelps, A. M.Cook, A. P.Phelps, J. S.Erginkaya, M.Lee, W.-C. A.Card, G. M.Daly, K. C.Dacks, A. M.2023-06-13doi:10.1101/2023.06.07.544074Cold Spring Harbor Laboratory Press2023-06-13
<![CDATA[
Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers
]]>
https://biorxiv.org/cgi/content/short/2023.06.13.544671v1?rss=1"
Kim, J. M.Carcamo, C. C.Jazani, S.Xie, Z.Feng, X. A.Poyton, M. F.Holland, K. L.Grimm, J. B.Lavis, L. D.Ha, T.Wu, C.2023-06-13doi:10.1101/2023.06.13.544671Cold Spring Harbor Laboratory Press2023-06-13
<![CDATA[
A window to the brain: ultrasound imaging of human neural activity through a permanent acoustic window
]]>
https://biorxiv.org/cgi/content/short/2023.06.14.544094v1?rss=1"
Rabut, C.Norman, S. L.Griggs, W. S.Russin, J. J.Jann, K.Christopoulos, V.Liu, C.Andersen, R. A.Shapiro, M. G.2023-06-15doi:10.1101/2023.06.14.544094Cold Spring Harbor Laboratory Press2023-06-15
<![CDATA[
Notch signaling and Bsh homeodomain activity are integrated to diversify Drosophila lamina neuron types
]]>
https://biorxiv.org/cgi/content/short/2023.06.15.545141v1?rss=1"
Xu, C.Ramos, T. B.Marshall, O.Doe, C. Q.2023-06-15doi:10.1101/2023.06.15.545141Cold Spring Harbor Laboratory Press2023-06-15
<![CDATA[
Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing.
]]>
https://biorxiv.org/cgi/content/short/2023.06.16.545300v1?rss=1"
Zhang, A.Friedman, L. J.Gelles, J.Bell, S. P.2023-06-16doi:10.1101/2023.06.16.545300Cold Spring Harbor Laboratory Press2023-06-16
<![CDATA[
Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking
]]>
https://biorxiv.org/cgi/content/short/2023.06.16.545341v1?rss=1"
Lee, S.Kibler, R. D.Hsia, Y.Borst, A. J.Philomin, A.Kennedy, M. A.Stoddard, B. L.Baker, D.2023-06-17doi:10.1101/2023.06.16.545341Cold Spring Harbor Laboratory Press2023-06-17
<![CDATA[
The Janelia Atalanta plasmids provide a simple and efficient CRISPR/Cas9-mediated homology directed repair platform for Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.06.17.545412v1?rss=1"
Stern, D. L.Kim, E.Berhman, E. L.2023-06-17doi:10.1101/2023.06.17.545412Cold Spring Harbor Laboratory Press2023-06-17
<![CDATA[
The principles of peptide selection by the transporter associated with antigen processing
]]>
https://biorxiv.org/cgi/content/short/2023.06.16.545308v1?rss=1"
Lee, J.Oldham, M. L.Manon, V.Chen, J.2023-06-17doi:10.1101/2023.06.16.545308Cold Spring Harbor Laboratory Press2023-06-17
<![CDATA[
Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications
]]>
https://biorxiv.org/cgi/content/short/2023.06.18.545436v1?rss=1"
Wang, Y.Zhang, L.Zhang, W.Gao, B.Ye, C.Dai, Q.Wang, K.Luo, M.Pan, T.He, C.2023-06-18doi:10.1101/2023.06.18.545436Cold Spring Harbor Laboratory Press2023-06-18
<![CDATA[
Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking
]]>
https://biorxiv.org/cgi/content/short/2023.06.20.545796v1?rss=1"
Chio, U. S.Palovcak, E.Autzen, A. A. A.Autzen, H. E.Munoz, E. N.Yu, Z.Wang, F.Agard, D. A.Armache, J.-P.Narlikar, G.Cheng, Y.2023-06-20doi:10.1101/2023.06.20.545796Cold Spring Harbor Laboratory Press2023-06-20
<![CDATA[
Epigenomic analysis of Formalin-Fixed Paraffin-Embedded samples by CUT&Tag
]]>
https://biorxiv.org/cgi/content/short/2023.06.20.545743v1?rss=1"
Henikoff, S.Henikoff, J. G.Ahmad, K.Paranal, R. M.Janssens, D. H.Russell, Z. R.Szulzewsky, F.Kugel, S.Holland, E. C.2023-06-22doi:10.1101/2023.06.20.545743Cold Spring Harbor Laboratory Press2023-06-22
<![CDATA[
Small-field visual projection neurons detect translational optic flow and support walking control
]]>
https://biorxiv.org/cgi/content/short/2023.06.21.546024v1?rss=1"
Isaacson, M. D.Eliason, J. L.Nern, A.Rogers, E. M.Lott, G. K.Tabachnik, T.Rowell, W. J.Edwards, A. W.Korff, W. L.Rubin, G. M.Branson, K.Reiser, M. B.2023-06-22doi:10.1101/2023.06.21.546024Cold Spring Harbor Laboratory Press2023-06-22
<![CDATA[
The widespread influence of ZSWIM8 on microRNAs during mouse embryonic development
]]>
https://biorxiv.org/cgi/content/short/2023.06.21.545803v1?rss=1"
50 miRNAs observed across 12 tissues, which often led to enhanced repression of their mRNA targets. These ZSWIM8-sensitive miRNAs were preferentially produced from genomic miRNA clusters, and in some cases, ZSWIM8 caused a switch in the dominant strand that accumulated from a miRNA hairpin--observations suggesting that TDMD provides a mechanism to uncouple co-produced miRNAs from each other. Overall, our findings indicate that the regulatory influence of TDMD in mammalian biology is widespread and posit the existence of many yet-unidentified transcripts that trigger miRNA degradation.
]]>Shi, C.Elcavage, L.Chivukula, R.Stefano, J.Kleaveland, B.Bartel, D.2023-06-22doi:10.1101/2023.06.21.545803Cold Spring Harbor Laboratory Press2023-06-22
<![CDATA[
Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans
]]>
https://biorxiv.org/cgi/content/short/2023.06.22.546003v1?rss=1"
Ratnasiri, K.Zheng, H.Toh, J.Yao, Z.Duran, V.Donato, M.Roederer, M.Kamath, M.Todd, J.-P. M.Gagne, M.Foulds, K. E.Francica, J. R.Corbett, K. S.Douek, D. C.Seder, R. A.Einav, S.Blish, C. A.Khatri, P.2023-06-25doi:10.1101/2023.06.22.546003Cold Spring Harbor Laboratory Press2023-06-25
<![CDATA[
TOMM40 and TOMM22 of the Translocase Outer Mitochondrial Membrane Complex rescue statin-impaired mitochondrial dynamics, morphology, and mitophagy in skeletal myotubes
]]>
https://biorxiv.org/cgi/content/short/2023.06.24.546411v1?rss=1"
View larger version (27K):
org.highwire.dtl.DTLVardef@1845842org.highwire.dtl.DTLVardef@1be8a26org.highwire.dtl.DTLVardef@5fd618org.highwire.dtl.DTLVardef@1e0f523_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Yang, N. V.Rogers, S.Guerra, R.Pagliarini, D. J.Theusch, E.Krauss, R. M.2023-06-26doi:10.1101/2023.06.24.546411Cold Spring Harbor Laboratory Press2023-06-26
<![CDATA[
Target-directed microRNA degradation regulates developmental microRNA expression and embryonic growth in mammals
]]>
https://biorxiv.org/cgi/content/short/2023.06.26.546601v1?rss=1"
Jones, B. T.Han, J.Zhang, H.Hammer, R. E.Evers, B. M.Rakheja, D.Acharya, A.Mendell, J. T.2023-06-26doi:10.1101/2023.06.26.546601Cold Spring Harbor Laboratory Press2023-06-26
<![CDATA[
Distinct Conformations of Mirabegron Determined by MicroED
]]>
https://biorxiv.org/cgi/content/short/2023.06.28.546957v1?rss=1"
Lin, J.Unge, J.Gonen, T.2023-06-28doi:10.1101/2023.06.28.546957Cold Spring Harbor Laboratory Press2023-06-28
<![CDATA[
SynBot: An open-source image analysis software for automated quantification of synapses
]]>
https://biorxiv.org/cgi/content/short/2023.06.26.546578v1?rss=1"
Savage, J. T.Ramirez, J.Risher, W. C.Irala, D.Eroglu, C.2023-06-28doi:10.1101/2023.06.26.546578Cold Spring Harbor Laboratory Press2023-06-28
<![CDATA[
Truly tiny acoustic biomolecules for ultrasound imaging and therapy
]]>
https://biorxiv.org/cgi/content/short/2023.06.27.546773v1?rss=1"
Ling, B.Gungoren, B.Yao, Y.Dutka, P.Smith, C. A. B.Lee, J.Swift, M. B.Shapiro, M. G.2023-06-28doi:10.1101/2023.06.27.546773Cold Spring Harbor Laboratory Press2023-06-28
<![CDATA[
Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures
]]>
https://biorxiv.org/cgi/content/short/2023.06.29.546792v1?rss=1"
Wang, W.Hariharan, M.Bartlett, A.Barragan, C.Castanon, R.Rothenberg, V.Song, H.Nery, J.Aldridge, A.Altshul, J.Kenworthy, M.Ding, W.Liu, H.Tian, W.Zhou, J.Chen, H.Wei, B.Gunduz, I. B.Norell, T.Broderick, T. J.McClain, M.Satterwhite, L.Burke, T.Petzold, E.Shen, X.Woods, C.Fowler, V. G.Ruffin, F.Panuwet, P.Barr, D. B.Beare, J. L.Smith, A. K.Spurbeck, R. R.Vangeti, S.Ramos, I.Nudelman, G.Sealfon, S. C.Castellino, F.Walley, A. M.Evans, T.Muller, F.Greenleaf, W. J.Ecker, J. R.2023-06-30doi:10.1101/2023.06.29.546792Cold Spring Harbor Laboratory Press2023-06-30
<![CDATA[
Neuronal wiring diagram of an adult brain
]]>
https://biorxiv.org/cgi/content/short/2023.06.27.546656v1?rss=1"
Dorkenwald, S.Matsliah, A.Sterling, A. R.Schlegel, P.Yu, S.-c.McKellar, C. E.Lin, A.Costa, M.Eichler, K.Yin, Y.Silversmith, W.Schneider-Mizell, C.Jordan, C. S.Brittain, D.Halageri, A.Kuehner, K.Ogedengbe, O.Morey, R.Gager, J.Kruk, K.Perlman, E.Yang, R.Deutsch, D.Bland, D.Sorek, M.Lu, R.Macrina, T.Lee, K.Bae, J. A.Mu, S.Nehoran, B.Mitchell, E.Popovych, S.Wu, J.Jia, Z.Castro, M.Kemnitz, N.Ih, D.Bates, A. S.Eckstein, N.Funke, J.Collman, F.Bock, D. D.Jefferis, G. S. X. E.Seung, H. S.Murthy, M.the FlyWire Co2023-06-30doi:10.1101/2023.06.27.546656Cold Spring Harbor Laboratory Press2023-06-30
<![CDATA[
Electron-counting in MicroED
]]>
https://biorxiv.org/cgi/content/short/2023.06.29.547123v1?rss=1"
Hattne, J.Martynowycz, M.Clabbers, M.Gonen, T.2023-06-30doi:10.1101/2023.06.29.547123Cold Spring Harbor Laboratory Press2023-06-30
<![CDATA[
SARS-CoV-2 spike glycosylation affects function and neutralization sensitivity
]]>
https://biorxiv.org/cgi/content/short/2023.06.30.547241v1?rss=1"
Zhang, F.Schmidt, F.Muecksch, F.Wang, Z.Gazumyan, A.Nussenzweig, M. C.Gaebler, C.Caskey, M.Hatziioannou, T.Bieniasz, P. D.2023-06-30doi:10.1101/2023.06.30.547241Cold Spring Harbor Laboratory Press2023-06-30
<![CDATA[
Macrophages sense ECM mechanics and growth factor availability through cytoskeletal remodeling to regulate their tissue repair program
]]>
https://biorxiv.org/cgi/content/short/2023.06.28.545586v1?rss=1"
Meizlish, M. L.Kimura, Y.Pope, S. D.Matta, R.Kim, C.Philip, N.Meyaard, L.Gonzalez, A.Medzhitov, R.2023-06-30doi:10.1101/2023.06.28.545586Cold Spring Harbor Laboratory Press2023-06-30
<![CDATA[
Chemical alkylation of Asp12 enables mutant selective targeting of K-Ras(G12D)
]]>
https://biorxiv.org/cgi/content/short/2023.07.01.547359v1?rss=1"
Zhang, Z.Zheng, Q.Guiley, K. Z.Shokat, K.2023-07-02doi:10.1101/2023.07.01.547359Cold Spring Harbor Laboratory Press2023-07-02
<![CDATA[
A single genetic locus lengthens deer mouse burrows via motor pattern evolution
]]>
https://biorxiv.org/cgi/content/short/2023.07.03.547545v1?rss=1"
Harringmeyer, O. S.Hu, C. K.Metz, H. C.Mihelic, E. L.Rosher, C.Hoekstra, H. E.2023-07-03doi:10.1101/2023.07.03.547545Cold Spring Harbor Laboratory Press2023-07-03
<![CDATA[
Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias
]]>
https://biorxiv.org/cgi/content/short/2023.07.03.547552v1?rss=1"
Lucas, B. A.Himes, B. A.Grigorieff, N.2023-07-03doi:10.1101/2023.07.03.547552Cold Spring Harbor Laboratory Press2023-07-03
<![CDATA[
Modeling the Correlation between Z and B in an X-ray Crystal Structure Refinement
]]>
https://biorxiv.org/cgi/content/short/2023.07.04.547724v1?rss=1"
Buscagan, T. M.Rees, D. C.2023-07-04doi:10.1101/2023.07.04.547724Cold Spring Harbor Laboratory Press2023-07-04
<![CDATA[
The neural basis of defensive behaviour evolution in Peromyscus mice
]]>
https://biorxiv.org/cgi/content/short/2023.07.04.547734v1?rss=1"
Baier, F.Reinhard, K.Tong, V.Murman, J.Farrow, K.Hoekstra, H.2023-07-05doi:10.1101/2023.07.04.547734Cold Spring Harbor Laboratory Press2023-07-05
<![CDATA[
MicroED structure of the human vasopressin 1B receptor
]]>
https://biorxiv.org/cgi/content/short/2023.07.05.547888v1?rss=1"
Shiriaeva, A.Martynowycz, M. W.Nicolas, W. J.Cherezov, V.Gonen, T.2023-07-06doi:10.1101/2023.07.05.547888Cold Spring Harbor Laboratory Press2023-07-06
<![CDATA[
α-carboxysome size is controlled by the disordered scaffold protein CsoS2
]]>
https://biorxiv.org/cgi/content/short/2023.07.07.548173v1?rss=1"
100 nm and >300 megadaltons. Although many of the protein interactions driving the assembly process have been determined, it remains unknown how size and composition are precisely controlled. Here we show that the size of -carboxysomes is controlled by the disordered scaffolding protein CsoS2. CsoS2 contains two classes of related peptide repeats which bind to the shell in a distinct fashion, and our data indicate that size is controlled by the relative number of these interactions. We propose an energetic and structural model wherein the two repeat classes bind at the junction of shell hexamers but differ in their preferences for the shell contact angles, and thus the local curvature. In total, this model suggests that a set of specific and repeated interactions between CsoS2 and shell proteins collectively achieve the large size and monodispersity of -carboxysomes.
]]>Oltrogge, L. M.Chen, A. W.Chaijarasphong, T.Turnsek, J. B.Savage, D. F.2023-07-08doi:10.1101/2023.07.07.548173Cold Spring Harbor Laboratory Press2023-07-08
<![CDATA[
Conserved and repetitive motifs in an intrinsically disordered protein drive α-carboxysome assembly
]]>
https://biorxiv.org/cgi/content/short/2023.07.08.548221v1?rss=1"
Turnsek, J. B.Oltrogge, L. M.Savage, D. F.2023-07-08doi:10.1101/2023.07.08.548221Cold Spring Harbor Laboratory Press2023-07-08
<![CDATA[
GIGANTEA accelerates wheat heading time through gene interactions converging on FLOWERING LOCUS T1
]]>
https://biorxiv.org/cgi/content/short/2023.07.11.548614v1?rss=1"
Li, C.Lin, H.Debernardi, J. M.Zhang, C.Dubcovsky, J.2023-07-12doi:10.1101/2023.07.11.548614Cold Spring Harbor Laboratory Press2023-07-12
<![CDATA[
Ladder-like multimerization of FoxP3 enables microsatellite recognition and DNA bridging
]]>
https://biorxiv.org/cgi/content/short/2023.07.12.548762v1?rss=1"
Zhang, W.Leng, F.Wang, X.Ramirez, R. N.Park, J.Benoist, C.Hur, S.2023-07-12doi:10.1101/2023.07.12.548762Cold Spring Harbor Laboratory Press2023-07-12
<![CDATA[
A simple mechanism for epigenetic inheritance of silent chromatin.
]]>
https://biorxiv.org/cgi/content/short/2023.07.18.549577v1?rss=1"
Yuan, A. H.Moazed, D.2023-07-18doi:10.1101/2023.07.18.549577Cold Spring Harbor Laboratory Press2023-07-18
<![CDATA[
Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at ribosomal large-subunit genes
]]>
https://biorxiv.org/cgi/content/short/2023.07.18.549406v1?rss=1"
Simon, N. M.Kim, Y.Bautista, D. M.Dutton, J. R.Brem, R. B.2023-07-18doi:10.1101/2023.07.18.549406Cold Spring Harbor Laboratory Press2023-07-18
<![CDATA[
A modular chemigenetic calcium indicator enables in vivo functional imaging with near-infrared light
]]>
https://biorxiv.org/cgi/content/short/2023.07.18.549527v1?rss=1"
Farrants, H.Shuai, Y.Lemon, W. C.Hernandez, C. M.Yang, S.Patel, R.Qiao, G.Frei, M. S.Grimm, J. B.Hanson, T. L.Tomaska, F.Turner, G. C.Stringer, C.Keller, P. J.Beyene, A. G.Chen, Y.Liang, Y.Lavis, L. D.Schreiter, E. R.2023-07-19doi:10.1101/2023.07.18.549527Cold Spring Harbor Laboratory Press2023-07-19
<![CDATA[
Coordinated inheritance of extrachromosomal DNA species in human cancer cells
]]>
https://biorxiv.org/cgi/content/short/2023.07.18.549597v1?rss=1"
Hung, K. L.Jones, M. G.Wong, I. T.-L.Lange, J. T.Luebeck, J.Scanu, E.He, B. J.Brückner, L.Li, R.Gonzalez, R. C.Schmargon, R.Dörr, J. R.Belk, J. A.Bafna, V.Werner, B.Huang, W.Henssen, A. G.Mischel, P. S.Chang, H. Y.2023-07-19doi:10.1101/2023.07.18.549597Cold Spring Harbor Laboratory Press2023-07-19
<![CDATA[
Nonlinear manifolds underlie neural population activity during behaviour
]]>
https://biorxiv.org/cgi/content/short/2023.07.18.549575v1?rss=1"
Fortunato, C.Bennasar-Vazquez, J.Park, J.Chang, J. C.Miller, L. E.Dudman, J. T.Perich, M. G.Gallego, J. A.2023-07-19doi:10.1101/2023.07.18.549575Cold Spring Harbor Laboratory Press2023-07-19
<![CDATA[
A neuronal substrate for translating nutrient state and resource density estimations into foraging decisions
]]>
https://biorxiv.org/cgi/content/short/2023.07.19.549514v1?rss=1"
Goldschmidt, D.Tastekin, I.Munch, D.Park, J.-Y.Haberkern, H.Serra, L.Baltazar, C.Jayaraman, V.Rubin, G. M.Ribeiro, C.2023-07-19doi:10.1101/2023.07.19.549514Cold Spring Harbor Laboratory Press2023-07-19
<![CDATA[
Coenyzme Q4 is a functional substitute for coenyzme Q10 and can be targeted to the mitochondria
]]>
https://biorxiv.org/cgi/content/short/2023.07.20.549963v1?rss=1"
Steenberge, L. H.Sung, A. Y.Fan, J.Pagliarini, D. J.2023-07-20doi:10.1101/2023.07.20.549963Cold Spring Harbor Laboratory Press2023-07-20
<![CDATA[
Unified fate mapping in multiview single-cell data
]]>
https://biorxiv.org/cgi/content/short/2023.07.19.549685v1?rss=1"
Weiler, P.Lange, M.Klein, M.Pe'er, D.Theis, F.2023-07-20doi:10.1101/2023.07.19.549685Cold Spring Harbor Laboratory Press2023-07-20
<![CDATA[
Calcium-permeable AMPA receptors govern PV neuron feature selectivity
]]>
https://biorxiv.org/cgi/content/short/2023.07.20.549908v1?rss=1"
Hong, I.Kim, J.Hainmueller, T.Kim, D. W.Johnson, R. C.Park, S. H.Limjunyawong, N.Yang, Z.Cheon, D.Hwang, T.Agarwal, A.Cholvin, T.Krienen, F. M.McCarroll, S. A.Dong, X.Leopold, D. A.Blackshaw, S.Bergles, D. E.Bartos, M.Brown, S. P.Huganir, R. L.2023-07-20doi:10.1101/2023.07.20.549908Cold Spring Harbor Laboratory Press2023-07-20
<![CDATA[
Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression
]]>
https://biorxiv.org/cgi/content/short/2023.07.21.550110v1?rss=1"
Zhang, J.Xiong, H.Burguener, G. F.Vasquez-Gross, H.Liu, Q.Debernardi, J. M.Akhunova, A.Campbell-Garland, K.Kianian, S.Brown-Guedira, G.Pozniak, C.Faris, J.Akhunov, E.Dubcovsky, J.2023-07-22doi:10.1101/2023.07.21.550110Cold Spring Harbor Laboratory Press2023-07-22
<![CDATA[
The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.07.21.550043v1?rss=1"
Sabaris, G.Ortiz, D. M.Laiker, I.Mayansky, I.Naik, S.Cavalli, G.Stern, D. L.Preger-Ben Noon, E.Frankel, N.2023-07-22doi:10.1101/2023.07.21.550043Cold Spring Harbor Laboratory Press2023-07-22
<![CDATA[
Glial-derived mitochondrial signals impact neuronal proteostasis and aging.
]]>
https://biorxiv.org/cgi/content/short/2023.07.20.549924v1?rss=1"
Bar-Ziv, R.Dutta, N.Hruby, A.Sukarto, E.Henderson, H. R.Durieux, J.Tronnes, S. U.Averbukh, M.Alcala, A.Ahmad, Q.Bolas, T.Perez, J.Dishart, J. G.Vega, M.Garcia, G.Higuchi-Sanabria, R.Dillin, A.2023-07-23doi:10.1101/2023.07.20.549924Cold Spring Harbor Laboratory Press2023-07-23
<![CDATA[
The Hippo kinase cascade regulates a contractile cell behavior and cell density in a close unicellular relative of animals
]]>
https://biorxiv.org/cgi/content/short/2023.07.25.550562v1?rss=1"
Phillips, J. E.Pan, D.2023-07-25doi:10.1101/2023.07.25.550562Cold Spring Harbor Laboratory Press2023-07-25
<![CDATA[
Gas vesicle-blood interactions enhance ultrasound imaging contrast
]]>
https://biorxiv.org/cgi/content/short/2023.07.24.550434v1?rss=1"
Ling, B.Ko, J. H.Stordy, B.Zhang, Y.Didden, T. F.Malounda, D.Swift, M. B.Chan, W. C. W.Shapiro, M. G.2023-07-25doi:10.1101/2023.07.24.550434Cold Spring Harbor Laboratory Press2023-07-25
<![CDATA[
Three-dimensional single-cell transcriptome imaging of thick tissues
]]>
https://biorxiv.org/cgi/content/short/2023.07.21.550124v1?rss=1"
Fang, R.Halpern, A. R.Rahman, M. M.Huang, Z.Lei, Z.Hell, S. J.Dulac, C.Zhuang, X.2023-07-25doi:10.1101/2023.07.21.550124Cold Spring Harbor Laboratory Press2023-07-25
<![CDATA[
Microglia Regulate Sleep via Calcium-Dependent Modulation of Norepinephrine Transmission
]]>
https://biorxiv.org/cgi/content/short/2023.07.24.550176v1?rss=1"
Ma, C.Li, B.Silverman, D.Ding, X.Li, A.Xiao, C.Huang, G.Worden, K.Muroy, S.Chen, W.Xu, Z.Tso, C. F.Huang, Y.Zhang, Y.Luo, Q.Saijo, K.Dan, Y.2023-07-26doi:10.1101/2023.07.24.550176Cold Spring Harbor Laboratory Press2023-07-26
<![CDATA[
Human Plasma Proteomic Profile of Clonal Hematopoiesis
]]>
https://biorxiv.org/cgi/content/short/2023.07.25.550557v1?rss=1"
Yu, Z.Vromman, A.Nguyen, N. Q. H.Vellarikkal, S. K.Uddin, M. M.Niroula, A.Griffin, G.Honigberg, M. C.Lin, A. E.Gibson, C. J.Katz, D. H.Tahir, U.Haidermota, S.Ganesh, S.Antoine, T.Weinstock, J.Austin, T. R.Vasan, R. S.peloso, G. M.Hornsby, W.Ganz, P.Manson, J. E.Haring, B.Kooperberg, C. L.Reiner, A. P.Bis, J. C.Psaty, B. M.Min, Y.-I.Correa, A.Lange, L. A.Post, W.Rotter, J. I.Rich, S. S.Wilson, J. G.Ebert, B. L.Yu, B.Ballantyne, C. M.Coresh, J.Sankaran, V. G.Bick, A. G.Jaiswal, S.Libby, P.Gerszten, R. E.NHLBI T2023-07-27doi:10.1101/2023.07.25.550557Cold Spring Harbor Laboratory Press2023-07-27
<![CDATA[
H2O2 sulfenylates CHE linking local infection to establishment of systemic acquired resistance
]]>
https://biorxiv.org/cgi/content/short/2023.07.27.550865v1?rss=1"
Cao, L.Yoo, H.Chen, T.Mwimba, M.Zhang, X.Dong, X.2023-07-28doi:10.1101/2023.07.27.550865Cold Spring Harbor Laboratory Press2023-07-28
<![CDATA[
Rastermap: a discovery method for neural population recordings
]]>
https://biorxiv.org/cgi/content/short/2023.07.25.550571v1?rss=1"
Stringer, C.Zhong, L.Syeda, A.Du, F.Pachitariu, M.2023-07-28doi:10.1101/2023.07.25.550571Cold Spring Harbor Laboratory Press2023-07-28
<![CDATA[
Network Statistics of the Whole-Brain Connectome of Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.07.29.551086v1?rss=1"
Lin, A.Yang, R.Dorkenwald, S.Matsliah, A.Sterling, A. R.Schlegel, P.Yu, S.-c.McKellar, C. E.Costa, M.Eichler, K.Bates, A. S.Eckstein, N.Funke, J.Jefferis, G. S. X. E.Murthy, M.2023-07-29doi:10.1101/2023.07.29.551086Cold Spring Harbor Laboratory Press2023-07-29
<![CDATA[
Bacterial pathogens deliver water/solute-permeable channels as a virulence strategy
]]>
https://biorxiv.org/cgi/content/short/2023.07.29.547699v1?rss=1"
Nomura, K.Andreazza, F.Cheng, J.Dong, K.Zhou, P.He, S. Y.2023-07-29doi:10.1101/2023.07.29.547699Cold Spring Harbor Laboratory Press2023-07-29
<![CDATA[
A diversified, widespread microbial gene cluster encodes homologs of methyltransferases involved in methanogenesis.
]]>
https://biorxiv.org/cgi/content/short/2023.07.31.551370v1?rss=1"
Kountz, D. J.Balskus, E. P.2023-07-31doi:10.1101/2023.07.31.551370Cold Spring Harbor Laboratory Press2023-07-31
<![CDATA[
MicroED as a powerful tool for structure determination of macrocyclic drug compounds directly from their powder formulations
]]>
https://biorxiv.org/cgi/content/short/2023.07.31.551405v1?rss=1"
Danelius, E.Bu, G.Wieske, L.Gonen, T.2023-08-01doi:10.1101/2023.07.31.551405Cold Spring Harbor Laboratory Press2023-08-01
<![CDATA[
A feedback control mechanism governs the synthesis of lipid-linked precursors of the bacterial cell wall
]]>
https://biorxiv.org/cgi/content/short/2023.08.01.551478v1?rss=1"
Marmont, L. S.Orta, A. K.Corey, R. A.Sychantha, D.Fernandez-Galliano, A.Li, Y. E.Baileeves, B. W.Greene, N. G.Stansfeld, P. J.Clemons, W. M.Bernhardt, T. G.2023-08-01doi:10.1101/2023.08.01.551478Cold Spring Harbor Laboratory Press2023-08-01
<![CDATA[
Multiple host targets of Pseudomonas effector protein HopM1 form a protein complex regulating apoplastic immunity and water homeostasis
]]>
https://biorxiv.org/cgi/content/short/2023.07.31.551310v1?rss=1"
He, S. Y.2023-08-01doi:10.1101/2023.07.31.551310Cold Spring Harbor Laboratory Press2023-08-01
<![CDATA[
Protein Ensemble Generation through VariationalAutoencoder Latent Space Sampling
]]>
https://biorxiv.org/cgi/content/short/2023.08.01.551540v1?rss=1"
Mansoor, S.Baek, M.Park, H.Lee, G. R.Baker, D.2023-08-01doi:10.1101/2023.08.01.551540Cold Spring Harbor Laboratory Press2023-08-01
<![CDATA[
Wheat bZIPC1 interacts with FT2 and contributes to the regulation of spikelet number per spike
]]>
https://biorxiv.org/cgi/content/short/2023.08.01.551548v1?rss=1"
Glenn, P.Woods, D. P.Zhang, J.Odle, N.Dubcovsky, J.2023-08-02doi:10.1101/2023.08.01.551548Cold Spring Harbor Laboratory Press2023-08-02
<![CDATA[
Oxidative rearrangement of tryptophan to indole nitrile by a single diiron enzyme
]]>
https://biorxiv.org/cgi/content/short/2023.08.03.551874v1?rss=1"
Adak, S.Ye, N.Calderone, L. A.Schafer, R. J. B.Lukowski, A. L.Pandelia, M.-E.Drennan, C. L.Moore, B. S.2023-08-03doi:10.1101/2023.08.03.551874Cold Spring Harbor Laboratory Press2023-08-03
<![CDATA[
Lysosomal release of amino acids at ER three-way junctions regulates transmembrane and secretory protein mRNA translation
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https://biorxiv.org/cgi/content/short/2023.08.01.551382v1?rss=1"
Choi, H.Liao, Y.-C.Yoon, Y. J.Grimm, J. B.Lavis, L.Singer, R. H.Lippincott-Schwartz, J.2023-08-03doi:10.1101/2023.08.01.551382Cold Spring Harbor Laboratory Press2023-08-03
<![CDATA[
Structure of the complete S. cerevisiae Rpd3S-nucleosome complex
]]>
https://biorxiv.org/cgi/content/short/2023.08.03.551877v1?rss=1"
Markert, J. W.Vos, S. M.Farnung, L.2023-08-03doi:10.1101/2023.08.03.551877Cold Spring Harbor Laboratory Press2023-08-03
<![CDATA[
Sulfolobus acidocaldarius adhesion pili power twitching motility in the absence of a dedicated retraction ATPase
]]>
https://biorxiv.org/cgi/content/short/2023.08.04.552066v1?rss=1"
Charles-Orszag, A.van Wolferen, M.Lord, S. J.Albers, S.-V.Mullins, D.2023-08-04doi:10.1101/2023.08.04.552066Cold Spring Harbor Laboratory Press2023-08-04
<![CDATA[
The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction
]]>
https://biorxiv.org/cgi/content/short/2023.08.02.551673v1?rss=1"
Ernst, E.Abramson, B.Acosta, K.Hoang, P. T.Mateo-Elizalde, C.Schubert, V.Pasaribu, B.Hartwick, N.Colt, K.Aylward, A. J.Ramu, U.Birchler, J. A.Schubert, I.Lam, E.Michael, T. P.Martienssen, R. A.2023-08-05doi:10.1101/2023.08.02.551673Cold Spring Harbor Laboratory Press2023-08-05
<![CDATA[
Txnip deletions and missense alleles prolong the survival of cones in a retinitis pigmentosa mouse model
]]>
https://biorxiv.org/cgi/content/short/2023.08.03.551766v1?rss=1"
Xue, Y.Cepko, C. L.2023-08-05doi:10.1101/2023.08.03.551766Cold Spring Harbor Laboratory Press2023-08-05
<![CDATA[
Learning produces a hippocampal cognitive map in the form of an orthogonalized state machine
]]>
https://biorxiv.org/cgi/content/short/2023.08.03.551900v1?rss=1"
Sun, W.Winnubst, J.Natrajan, M.Lai, C.Kajikawa, K.Michaelos, M.Gattoni, R.Fitzgerald, J. E.Spruston, N.2023-08-06doi:10.1101/2023.08.03.551900Cold Spring Harbor Laboratory Press2023-08-06
<![CDATA[
A competitive disinhibitory network for robust optic flow processing in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.08.06.552150v1?rss=1"
Erginkaya, M.Cruz, T. L.Brotas, M.Steck, K.Nern, A.Torrao, F.Varela, N.Bock, D.Reiser, M. B.Chiappe, M. E.2023-08-07doi:10.1101/2023.08.06.552150Cold Spring Harbor Laboratory Press2023-08-07
<![CDATA[
Cell-type-specific plasticity shapes neocortical dynamics for motor learning
]]>
https://biorxiv.org/cgi/content/short/2023.08.09.552699v1?rss=1"
Majumder, S.Hirokawa, K.Yang, Z.Gerfen, C. R.Fontolan, L.Romani, S.Jain, A.Yasuda, R.Inagaki, H. K.2023-08-09doi:10.1101/2023.08.09.552699Cold Spring Harbor Laboratory Press2023-08-09
<![CDATA[
Erythroid differentiation dependent interaction of VPS13A with XK at the plasma membrane of K562 cells
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https://biorxiv.org/cgi/content/short/2023.08.09.552634v1?rss=1"
Amos, C.Xu, P.De Camilli, P.2023-08-10doi:10.1101/2023.08.09.552634Cold Spring Harbor Laboratory Press2023-08-10
<![CDATA[
Casein kinase II promotes piRNA production through direct phosphorylation of USTC component TOFU-4
]]>
https://biorxiv.org/cgi/content/short/2023.08.09.552615v1?rss=1"
Mello, C.ZHANG, G.Zheng, C.ding, y.-h.2023-08-10doi:10.1101/2023.08.09.552615Cold Spring Harbor Laboratory Press2023-08-10
<![CDATA[
The juxtamembrane linker of synaptotagmin 1 regulates Ca2+ binding via liquid-liquid phase separation
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https://biorxiv.org/cgi/content/short/2023.08.11.551903v1?rss=1"
Mehta, N.Mondal, S.Watson, E. T.Cui, Q.Chapman, E. R.2023-08-12doi:10.1101/2023.08.11.551903Cold Spring Harbor Laboratory Press2023-08-12
<![CDATA[
A molecular proximity sensor based on an engineered, dual-component guide RNA
]]>
https://biorxiv.org/cgi/content/short/2023.08.14.553235v1?rss=1"
Choi, J.Chen, W.Liao, H.Li, X.Shendure, J.2023-08-14doi:10.1101/2023.08.14.553235Cold Spring Harbor Laboratory Press2023-08-14
<![CDATA[
Developmental transcriptomes predict adult social behaviors in the socially flexible sweat bee, Lasioglossum baleicum
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https://biorxiv.org/cgi/content/short/2023.08.14.553238v1?rss=1"
Omufwoko, K. S.Cronin, A. L.Nguyen, T. T. H.Webb, A. E.Traniello, I. M.Kocher, S. D.2023-08-15doi:10.1101/2023.08.14.553238Cold Spring Harbor Laboratory Press2023-08-15
<![CDATA[
Epithelial Ca2+ waves triggered by enteric neurons heal the gut
]]>
https://biorxiv.org/cgi/content/short/2023.08.14.553227v1?rss=1"
Petsakou, A.Liu, Y.Liu, Y.Comjean, A.Hu, Y.Perrimon, N.2023-08-15doi:10.1101/2023.08.14.553227Cold Spring Harbor Laboratory Press2023-08-15
<![CDATA[
Triaging of -helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology
]]>
https://biorxiv.org/cgi/content/short/2023.08.16.553624v1?rss=1"
Muthukumar, G.Stevens, T. A.Inglis, A. J.Esantsi, T. K.Saunders, R. A.Schulte, F.Voorhees, R. M.Guna, A.Weissman, J. S.2023-08-17doi:10.1101/2023.08.16.553624Cold Spring Harbor Laboratory Press2023-08-17
<![CDATA[
Structure of C. elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction
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https://biorxiv.org/cgi/content/short/2023.08.16.553618v1?rss=1"
Clark, S.Jeong, H.Posert, R.Goehring, A.Gouaux, E.2023-08-17doi:10.1101/2023.08.16.553618Cold Spring Harbor Laboratory Press2023-08-17
<![CDATA[
Molecular blueprints of the Langya virus attachment and fusion glycoproteins
]]>
https://biorxiv.org/cgi/content/short/2023.08.20.554025v1?rss=1"
Wang, Z.McCallum, M.Yan, L.Sharkey, W.Park, Y.-J.Dang, H. V.Amaya, M.Person, A.Broder, C. C.Veesler, D. J.2023-08-20doi:10.1101/2023.08.20.554025Cold Spring Harbor Laboratory Press2023-08-20
<![CDATA[
Microglia mediate contact-independent neuronal pruning via secreted Neuraminidase-3 associated with extracellular vesicles
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https://biorxiv.org/cgi/content/short/2023.08.21.554214v1?rss=1"
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]]>Delaveris, C. S.Wang, C. L.Riley, N. M.Kulkarni, R. U.Bertozzi, C. R.2023-08-21doi:10.1101/2023.08.21.554214Cold Spring Harbor Laboratory Press2023-08-21
<![CDATA[
Designed Endocytosis-Triggering Proteins mediate Targeted Degradation and amplify signaling
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https://biorxiv.org/cgi/content/short/2023.08.19.553321v1?rss=1"
Huang, B.Abedi, M.Ahn, G.Coventry, B.Sappington, I.Wang, R.Schlichthaerle, T.Zhang, J. Z.Wang, Y.Goreshnik, I.Chiu, C. W.Chazin-Gray, A.Chan, S.Gerben, S.Murray, A.Wang, S.O'Neill, J.Yeh, R.Misquith, A.Wolf, A.Tomasovic, L. M.Piraner, D. I.Gonzalez, M. J. D.Bennett, N. R.Venkatesh, P.Ahlrichs, M.Dobbins, C.Yang, W.Wang, X.Vafeados, D.Mout, R.Shivaei, S.Cao, L.Carter, L.Stewart, L.Spangler, J. B.Bernardes, G. J. L.Roybal, K. T.Greisen, P. J.Li, X.Bertozzi, C.Baker, D.2023-08-21doi:10.1101/2023.08.19.553321Cold Spring Harbor Laboratory Press2023-08-21
<![CDATA[
Olfaction regulates peripheral mitophagy and mitochondrial function
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https://biorxiv.org/cgi/content/short/2023.08.21.554156v1?rss=1"
Dishart, J. G.Pender, C.Shen, K.Zhang, H.Ly, M.Webb, M.Dillin, A. G.2023-08-22doi:10.1101/2023.08.21.554156Cold Spring Harbor Laboratory Press2023-08-22
<![CDATA[
Germline mitochondria integrate neuronal cell nonautonomous signaling for the mitochondrial unfolded protein response
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https://biorxiv.org/cgi/content/short/2023.08.21.554217v1?rss=1"
Shen, K.Durieux, J.Mena, C. G.Webster, B. M.Berendzen, K.Dillin, A.2023-08-22doi:10.1101/2023.08.21.554217Cold Spring Harbor Laboratory Press2023-08-22
<![CDATA[
De novo design of buttressed loops for sculpting protein functions
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https://biorxiv.org/cgi/content/short/2023.08.22.554384v1?rss=1"
Jiang, H.Jude, K. M.Wu, K.Fallas, J.Ueda, G.Brunette, T.Hicks, D.Pyles, H.Yang, A.Carter, L.Lamb, M.Li, X.Levine, P. M.Stewart, L. J.Garcia, K. C.Baker, D.2023-08-23doi:10.1101/2023.08.22.554384Cold Spring Harbor Laboratory Press2023-08-23
<![CDATA[
Cell Fate Programming by Transcription Factors and Epigenetic Machinery in Stomatal Development
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https://biorxiv.org/cgi/content/short/2023.08.23.554515v1?rss=1"
Liu, A.Mair, A.Matos, J.Vollbrecht, M.Xu, S.-L.Bergmann, D.2023-08-24doi:10.1101/2023.08.23.554515Cold Spring Harbor Laboratory Press2023-08-24
<![CDATA[
The genome of the Wollemi pine, a critically endangered living fossil unchanged since the Cretaceous, reveals extensive ancient transposon activity.
]]>
https://biorxiv.org/cgi/content/short/2023.08.24.554647v1?rss=1"
Stevenson, D. W.Ramakrishnan, S.Alves, C. d. S.Coelho, L. A.Kramer, M.Goodwin, S.Ramos, O. M.Eshel, G.Sondervan, V. M.Frangos, S.Zumajo-Cardona, C.Jenike, K.Ou, S.Wang, X.Lee, Y. P.Loke, S.Rossetto, M.McPherson, H.Nigris, S.Moschin, S.Little, D. P.Katari, M. S.Varala, K.Kolokotronis, S.-O.Ambrose, B.Croft, L. J.Coruzzi, G. M.Schatz, M.McCombie, W. R.Martienssen, R. A.2023-08-24doi:10.1101/2023.08.24.554647Cold Spring Harbor Laboratory Press2023-08-24
<![CDATA[
Integrated high-confidence and high-throughput approaches for quantifying synapse engulfment by oligodendrocyte precursor cells
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https://biorxiv.org/cgi/content/short/2023.08.24.554663v1?rss=1"
Kahng, J. A.Xavier, A. M.Ferro, A.Auguste, Y. S. S.Cheadle, L.2023-08-25doi:10.1101/2023.08.24.554663Cold Spring Harbor Laboratory Press2023-08-25
<![CDATA[
Diversity in Notch ligand-receptor signaling interactions
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https://biorxiv.org/cgi/content/short/2023.08.24.554677v1?rss=1"
Kuintzle, R.Santat, L. A.Elowitz, M. B.2023-08-25doi:10.1101/2023.08.24.554677Cold Spring Harbor Laboratory Press2023-08-25
<![CDATA[
PTPN2 copper-sensing rapidly relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression
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https://biorxiv.org/cgi/content/short/2023.08.29.555401v1?rss=1"
Ross, M. O.Xie, Y.Owyang, R. C.Ye, C.Zbihley, O. N. P.Lyu, R.Wu, T.Wang, P.Karginova, O.Olopade, O. I.Zhao, M.He, C.2023-08-29doi:10.1101/2023.08.29.555401Cold Spring Harbor Laboratory Press2023-08-29
<![CDATA[
The Neural Basis of Drosophila Courtship Song
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https://biorxiv.org/cgi/content/short/2023.08.30.555537v1?rss=1"
Lillvis, J. L.Wang, K.Shiozaki, H. M.Xu, M.Stern, D. L.Dickson, B. J.2023-09-01doi:10.1101/2023.08.30.555537Cold Spring Harbor Laboratory Press2023-09-01
<![CDATA[
A unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior
]]>
https://biorxiv.org/cgi/content/short/2023.08.30.554672v1?rss=1"
Newman, J. P.Zhang, J.Cuevas-Lopez, A.Miller, N. J.Honda, T.van der Goes, M.-S. H.Leighton, A. H.Carvalho, F.Lopes, G.Lakunina, A.Siegle, J. H.Harnett, M. T.Wilson, M. A.Voigts, J.2023-09-01doi:10.1101/2023.08.30.554672Cold Spring Harbor Laboratory Press2023-09-01
<![CDATA[
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning
]]>
https://biorxiv.org/cgi/content/short/2023.09.03.556122v1?rss=1"
Laubscher, E.Wang, X.Razin, N.Dougherty, T.Xu, R.Ombelets, L.Pao, E.Moffitt, J.Yue, Y.Van Valen, D. A.2023-09-05doi:10.1101/2023.09.03.556122Cold Spring Harbor Laboratory Press2023-09-05
<![CDATA[
Gene protein sequence evolution can predict the rapid divergence of ovariole numbers in Drosophila
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https://biorxiv.org/cgi/content/short/2023.09.03.556080v1?rss=1"
Whittle, C.Extavour, C. G.2023-09-06doi:10.1101/2023.09.03.556080Cold Spring Harbor Laboratory Press2023-09-06
<![CDATA[
Unraveling the Structure of Meclizine Dihydrochloride with MicroED
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https://biorxiv.org/cgi/content/short/2023.09.05.556418v1?rss=1"
Lin, J.Unge, J.Gonen, T.2023-09-06doi:10.1101/2023.09.05.556418Cold Spring Harbor Laboratory Press2023-09-06
<![CDATA[
A potential space making role for a lytic transglycosylase in cell wall biogenesis revealed by a beta-lactamase induction phenotype in Pseudomonas aeruginosa
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https://biorxiv.org/cgi/content/short/2023.09.05.556436v1?rss=1"
Fumeaux, C.Bernhardt, T. G.2023-09-07doi:10.1101/2023.09.05.556436Cold Spring Harbor Laboratory Press2023-09-07
<![CDATA[
One-shot entorhinal maps enable flexible navigation in novel environments
]]>
https://biorxiv.org/cgi/content/short/2023.09.07.556744v1?rss=1"
Wen, J. H.Sorscher, B.Ganguli, S.Giocomo, L.2023-09-08doi:10.1101/2023.09.07.556744Cold Spring Harbor Laboratory Press2023-09-08
<![CDATA[
Polymorphic Structure Determination of the Macrocyclic Drug Paritaprevir by MicroED
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https://biorxiv.org/cgi/content/short/2023.09.09.556999v1?rss=1"
Bu, G.Danelius, E.Wieske, L.Gonen, T.2023-09-10doi:10.1101/2023.09.09.556999Cold Spring Harbor Laboratory Press2023-09-10
<![CDATA[
Structure-based discovery of CFTR potentiators and inhibitors
]]>
https://biorxiv.org/cgi/content/short/2023.09.09.557002v1?rss=1"
Liu, F.Kaplan, A. L.Levring, J.Einsiedel, J.Tiedt, S.Distler, K.Omattage, N.Kondratov, I. S.Moroz, Y. S.Pietz, H. L.Irwin, J. J.Gmeiner, P.Shoichet, B. K.Chen, J.2023-09-12doi:10.1101/2023.09.09.557002Cold Spring Harbor Laboratory Press2023-09-12
<![CDATA[
Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus
]]>
https://biorxiv.org/cgi/content/short/2023.09.12.557371v1?rss=1"
Lee, J.Zepeda, S.Park, Y.-J.Taylor, A. L.Quispe, J.Stewart, C.Leaf, E. M.Treichel, C.Corti, D.King, N. P.Starr, T. N.Veesler, D.2023-09-13doi:10.1101/2023.09.12.557371Cold Spring Harbor Laboratory Press2023-09-13
<![CDATA[
Toolkits for detailed and high-throughput interrogation of synapses in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2023.09.12.557402v1?rss=1"
Majeed, M.Han, H.Zhang, K.Liao, C.-P.Hobert, O.Lu, H.2023-09-13doi:10.1101/2023.09.12.557402Cold Spring Harbor Laboratory Press2023-09-13
<![CDATA[
Wnt signaling and contact-mediated repulsion shape sensory dendritic fields
]]>
https://biorxiv.org/cgi/content/short/2023.09.14.557812v1?rss=1"
Tzeng, C. P.Shen, K.2023-09-15doi:10.1101/2023.09.14.557812Cold Spring Harbor Laboratory Press2023-09-15
<![CDATA[
Sensory neuron population expansion enhances odour tracking through relaxed projection neuron adaptation
]]>
https://biorxiv.org/cgi/content/short/2023.09.15.556782v1?rss=1"
Takagi, S.Abuin, L.Stupski, S. D.Arguello, J. R.Prieto-Godino, L. L.Stern, D. L.Cruchet, S.Alvarez-Ocana, R.Wienecke, C. F. R.van Breugel, F.Auer, T. O.Benton, R.2023-09-15doi:10.1101/2023.09.15.556782Cold Spring Harbor Laboratory Press2023-09-15
<![CDATA[
Driver lines for studying associative learning in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.09.15.557808v1?rss=1"
Shuai, Y.Sammons, M.Sterne, G. R.Hibbard, K.Yang, H.Yang, C.-P.Managan, C.Siwanowicz, I.Lee, T.Rubin, G. M.Turner, G. C.Aso, Y.2023-09-16doi:10.1101/2023.09.15.557808Cold Spring Harbor Laboratory Press2023-09-16
<![CDATA[
The diverse evolutionary histories of domesticated metaviral capsid genes in mammals
]]>
https://biorxiv.org/cgi/content/short/2023.09.17.558119v1?rss=1"
Henriques, W. S.Young, J. M.Nemudryi, A.Nemudraia, A.Wiedenheft, B.Malik, H. S.2023-09-17doi:10.1101/2023.09.17.558119Cold Spring Harbor Laboratory Press2023-09-17
<![CDATA[
A modular circuit architecture coordinates the diversification of courtship strategies in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.09.16.558080v1?rss=1"
Coleman, R. T.Morantte, I.Koreman, G. T.Cheng, M. L.Ding, Y.Ruta, V.2023-09-17doi:10.1101/2023.09.16.558080Cold Spring Harbor Laboratory Press2023-09-17
<![CDATA[
Structure-Activity Relationship Studies of Novel Gut-derived Lantibiotics Against Human Gut Commensals
]]>
https://biorxiv.org/cgi/content/short/2023.09.15.557961v1?rss=1"
Zhang, Z. J.Wu, C.Dorantes, D.Pappas, T.Sundararajan, A.Lin, H.Pamer, E. G.van der Donk, W. A.2023-09-17doi:10.1101/2023.09.15.557961Cold Spring Harbor Laboratory Press2023-09-17
<![CDATA[
General Transcription Factor from E. coli with a Distinct Mechanism of Action
]]>
https://biorxiv.org/cgi/content/short/2023.09.17.558134v1?rss=1"
Nudler, E.Vasilyev, N.Liu, M.Epshtein, V.Shamovsky, I.2023-09-17doi:10.1101/2023.09.17.558134Cold Spring Harbor Laboratory Press2023-09-17
<![CDATA[
Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi
]]>
https://biorxiv.org/cgi/content/short/2023.09.18.558157v1?rss=1"
Adler, B. A.Al-Shimary, M. J.Patel, J. R.Ambruster, E.Colognori, D.Charles, E. J.Miller, K. V.Lahiri, A.Trinidad, M.Boger, R.Nomburg, J.Beurnier, S.Cui, M. L.Barrangou, R.Mutalik, V. K.Schoeniger, J. S.Pogliano, J. A.Savage, D. F.Doudna, J. A.Cress, B. F.2023-09-18doi:10.1101/2023.09.18.558157Cold Spring Harbor Laboratory Press2023-09-18
<![CDATA[
Model-directed generation of CRISPR-Cas13a guide RNAs designs artificial sequences that improve nucleic acid detection
]]>
https://biorxiv.org/cgi/content/short/2023.09.20.557569v1?rss=1"
Mantena, S.Pillai, P. P.Petros, B. A.Welch, N. L.Myhrvold, C.Sabeti, P. C.Metsky, H. C.2023-09-20doi:10.1101/2023.09.20.557569Cold Spring Harbor Laboratory Press2023-09-20
<![CDATA[
Identification and targeting of microbial putrescine acetylation in bloodstream infections
]]>
https://biorxiv.org/cgi/content/short/2023.09.21.558834v1?rss=1"
Mayers, J. R.Varon, J.Zhou, R. R.Daniel-Ivad, M.Beaulieu, C.Bholse, A.Glasser, N. R.Lichtenauer, F. M.Ng, J.Pinilla Vera, M.Huttenhower, C.Perrella, M. A.Clish, C. B.Zhao, S. D.Baron, R. M.Balskus, E. P.2023-09-21doi:10.1101/2023.09.21.558834Cold Spring Harbor Laboratory Press2023-09-21
<![CDATA[
Effects of protein G-quadruplex interactions on phase transitions and protein aggregation
]]>
https://biorxiv.org/cgi/content/short/2023.09.21.558871v1?rss=1"
Sahoo, B.Kocman, V.Clark, N.Myers, N.Deng, X.Wong, E. L.Yang, H. J.Kotar, A.Guzman, B. B.Dominguez, D. C.Plavec, J.Bardwell, J. C.2023-09-21doi:10.1101/2023.09.21.558871Cold Spring Harbor Laboratory Press2023-09-21
<![CDATA[
High-resolution dissection of human cell type-specific enhancers in cis and trans activities
]]>
https://biorxiv.org/cgi/content/short/2023.09.23.559140v1?rss=1"
Wang, M.Yang, X.Wu, Q.2023-09-24doi:10.1101/2023.09.23.559140Cold Spring Harbor Laboratory Press2023-09-24
<![CDATA[
Activity-dependent development of the body's touch receptors
]]>
https://biorxiv.org/cgi/content/short/2023.09.23.559109v1?rss=1"
Santiago, C.Sharma, N.Africawala, N.Siegrist, J.Handler, A.Tasnim, A.Anjum, R.Turecek, J.Lehnert, B. P.Renauld, S.Nolan-Tamariz, M.Iskols, M.Magee, A. R.Paradis, S.Ginty, D. D.2023-09-24doi:10.1101/2023.09.23.559109Cold Spring Harbor Laboratory Press2023-09-24
<![CDATA[
A rotational velocity estimate constructed through visuomotor competition updates the fly's neural compass
]]>
https://biorxiv.org/cgi/content/short/2023.09.25.559373v1?rss=1"
Hulse, B. K.Stanoev, A.Turner-Evans, D. B.Seelig, J.Jayaraman, V.2023-09-26doi:10.1101/2023.09.25.559373Cold Spring Harbor Laboratory Press2023-09-26
<![CDATA[
Membrane Bound O-Acyltransferase 7 (MBOAT7) Shapes Lysosomal Lipid Homeostasis and Function to Control Alcohol-Associated Liver Injury
]]>
https://biorxiv.org/cgi/content/short/2023.09.26.559533v1?rss=1"
Varadharajan, V.Ramachandiran, I.Massey, W. J.Jain, R.Banerjee, R.Horak, A. J.McMullen, M. R.Huang, E.Bellar, A.Lorkowski, S. W.Gulshan, K.Helsley, R. N.James, I.Pathak, V.Dasarathy, J.Welch, N.Dasarathy, S.Streem, D.Reizes, O.Allende, D. S.Smith, J. D.Simcox, J.Nagy, L. E.Brown, J. M.2023-09-27doi:10.1101/2023.09.26.559533Cold Spring Harbor Laboratory Press2023-09-27
<![CDATA[
Mapping the biochemical landscape of rubisco
]]>
https://biorxiv.org/cgi/content/short/2023.09.27.559826v1?rss=1"
99% of single amino acid mutants across CO2 concentrations, we inferred enzyme velocity and CO2 affinity for thousands of substitutions. We identified many highly conserved positions that tolerate mutation and rare mutations that improve CO2 affinity. These data suggest that non-trivial kinetic improvements are readily accessible and provide a comprehensive sequence-to-function mapping for enzyme engineering efforts.
]]>Prywes, N.Phillips, N. R.Oltrogge, L. M.de Pins, B.Cowan, A. E.Taylor-Kearney, L. J.Chang, H. A.Hall, L. N.Bhatt, A.Shih, P.Milo, R.Savage, D. F.2023-09-27doi:10.1101/2023.09.27.559826Cold Spring Harbor Laboratory Press2023-09-27
<![CDATA[
Exonuclease Xrn1 regulates TORC1 signaling in response to SAM availability
]]>
https://biorxiv.org/cgi/content/short/2023.09.28.559955v1?rss=1"
McGinnis, M. M.Sutter, B. M.Jahangiri, S.Tu, B. P.2023-09-28doi:10.1101/2023.09.28.559955Cold Spring Harbor Laboratory Press2023-09-28
<![CDATA[
Evolution of gene expression across brain regions in behaviorally divergent deer mice
]]>
https://biorxiv.org/cgi/content/short/2023.09.28.559844v1?rss=1"
Kautt, A.Chen, J.Lewarch, C. L.Hu, C.Turner, K.Lassance, J.-M.Baier, F.Bedford, N. L.Bendesky, A.Hoekstra, H. E.2023-09-28doi:10.1101/2023.09.28.559844Cold Spring Harbor Laboratory Press2023-09-28
<![CDATA[
Transient States During Oligonucleotides Hybridization: Insights from Annealing Kinetics of Mismatches and Bulges
]]>
https://biorxiv.org/cgi/content/short/2023.09.27.559754v1?rss=1"
Todisco, M.Ding, D.Szostak, J. W.2023-09-28doi:10.1101/2023.09.27.559754Cold Spring Harbor Laboratory Press2023-09-28
<![CDATA[
HI-FISH: WHOLE BRAIN IN SITU MAPPING OF NEURONAL ACTIVATION IN DROSOPHILA DURING SOCIAL BEHAVIORS AND OPTOGENETIC STIMULATION
]]>
https://biorxiv.org/cgi/content/short/2023.09.28.560045v1?rss=1"
Anderson, D. J.Chiu, H. V.Watanabe, K.2023-09-29doi:10.1101/2023.09.28.560045Cold Spring Harbor Laboratory Press2023-09-29
<![CDATA[
Sleepiness, not total sleep amount, increases seizure risk
]]>
https://biorxiv.org/cgi/content/short/2023.09.30.560325v1?rss=1"
Cuddapah, V. A.Hsu, C. T.Li, Y.Shah, H. M.Saul, C.Killiany, S.Shon, J.Yue, Z.Gionet, G.Putt, M. E.Sehgal, A.2023-10-02doi:10.1101/2023.09.30.560325Cold Spring Harbor Laboratory Press2023-10-02
<![CDATA[
CRWN nuclear lamina components maintain the H3K27me3 landscape and promote successful reproduction in Arabidopsis
]]>
https://biorxiv.org/cgi/content/short/2023.10.03.560721v1?rss=1"
Choi, J.Gehring, M.2023-10-03doi:10.1101/2023.10.03.560721Cold Spring Harbor Laboratory Press2023-10-03
<![CDATA[
Improving protein expression, stability, and function with ProteinMPNN
]]>
https://biorxiv.org/cgi/content/short/2023.10.03.560713v1?rss=1"
Sumida, K. H.Nunez Franco, R.Kalvet, I.Pellock, S. J.Wicky, B. I. M.Milles, L. F.Dauparas, J.Wang, J.Kipnis, Y.Jameson, N.Kang, A.De La Cruz, J.Sankaran, B.Bera, A. K.Jimenez Oses, G.Baker, D.2023-10-03doi:10.1101/2023.10.03.560713Cold Spring Harbor Laboratory Press2023-10-03
<![CDATA[
Chromatinization Modulates Topoisomerase II Processivity
]]>
https://biorxiv.org/cgi/content/short/2023.10.03.560726v1?rss=1"
6000 turns. We further discovered that topo II could relax supercoiled DNA prior to plectoneme formation, but with a [~]100-fold reduction in processivity; strikingly, the relaxation rate in this regime decreased with diminishing torsion in a manner consistent with the capture of transient DNA loops by topo II. Chromatinization preserved the high processivity of the enzyme under high torsional stress. Interestingly, topo II was still highly processive ([~] 1000 turns) even under low torsional stress, consistent with the predisposition of chromatin to readily form DNA crossings. This work establishes that chromatin is a major stimulant of topo II function, capable of enhancing function even under low torsional stress.
]]>Lee, J.Wu, M.Inman, J.Singh, G.Park, S. h.Lee, J. H.Fulbright, R. M.Hong, Y.Jeong, J. D.Berger, J. M.Wang, M. D.2023-10-04doi:10.1101/2023.10.03.560726Cold Spring Harbor Laboratory Press2023-10-04
<![CDATA[
Wide Transition-State Ensemble as Key Component for Enzyme Catalysis
]]>
https://biorxiv.org/cgi/content/short/2023.10.03.560706v1?rss=1"
Jara, G.Pontiggia, F.Otten, R.Agafonov, R. V.Marti, M. A.Kern, D.2023-10-05doi:10.1101/2023.10.03.560706Cold Spring Harbor Laboratory Press2023-10-05
<![CDATA[
Conjoint specification of action by neocortex and striatum
]]>
https://biorxiv.org/cgi/content/short/2023.10.04.560957v1?rss=1"
Park, J.Polidoro, P.Fortunato, C.Arnold, J. A.Mensh, B. D.Gallego, J. A.Dudman, J. T.2023-10-05doi:10.1101/2023.10.04.560957Cold Spring Harbor Laboratory Press2023-10-05
<![CDATA[
Cue-specific neuronal ensembles span intermittent rate coding of working memory
]]>
https://biorxiv.org/cgi/content/short/2023.10.06.561121v1?rss=1"
Panichello, M. F.Jonikaitis, D.Oh, J.Zhu, S.Trepka, E. B.Moore, T.2023-10-06doi:10.1101/2023.10.06.561121Cold Spring Harbor Laboratory Press2023-10-06
<![CDATA[
A Flat Protein Complex Shapes Rough ER Membrane Sheets
]]>
https://biorxiv.org/cgi/content/short/2023.10.06.559866v1?rss=1"
Sawyer, E. M.Jensen, L. E.Meehl, J. B.Larsen, K. P.Petito, D. A.Hurley, J. H.Voeltz, G. K.2023-10-06doi:10.1101/2023.10.06.559866Cold Spring Harbor Laboratory Press2023-10-06
<![CDATA[
Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom
]]>
https://biorxiv.org/cgi/content/short/2023.10.09.561603v1?rss=1"
Krishna, R.Wang, J.Ahern, W.Sturmfels, P.Venkatesh, P.Kalvet, I.Lee, G. R.Morey-Burrows, F. S.Anishchenko, I.Humphreys, I. R.McHugh, R.Vafeados, D.Li, X.Sutherland, G. A.Hitchcock, A.Hunter, C. N.Baek, M.DiMaio, F.Baker, D.2023-10-09doi:10.1101/2023.10.09.561603Cold Spring Harbor Laboratory Press2023-10-09
<![CDATA[
A neural mechanism for learning from delayed postingestive feedback
]]>
https://biorxiv.org/cgi/content/short/2023.10.06.561214v1?rss=1"
Zimmerman, C. A.Pan-Vazquez, A.Wu, B.Keppler, E. F.Guthman, E. M.Fetcho, R. N.Bolkan, S. S.McMannon, B.Lee, J.Hoag, A. T.Lynch, L. A.Janarthanan, S. N.Lopez Luna, J. F.Bondy, A. G.Falkner, A. L.Wang, S. S.-H.Witten, I. B.2023-10-10doi:10.1101/2023.10.06.561214Cold Spring Harbor Laboratory Press2023-10-10
<![CDATA[
Suppression of epithelial proliferation and tumorigenesis by immunoglobulin A
]]>
https://biorxiv.org/cgi/content/short/2023.10.06.561290v1?rss=1"
Donaldson, G. P.Reis, G. L.Saad, M.Mamede, I.Chen, G.DelGaudio, N. L.Zhang, D.Aydin, B.Harrer, C. E.Castro, T. B. R.Grivennikov, S.Reis, B. S.Stadtmueller, B. M.Victora, G. D.Mucida, D.2023-10-10doi:10.1101/2023.10.06.561290Cold Spring Harbor Laboratory Press2023-10-10
<![CDATA[
A feasibility study of smartphone sensors to assess the effect of acute high altitude (3,800 m) exposure on cognition and motor function in healthy participants
]]>
https://biorxiv.org/cgi/content/short/2023.10.09.561578v1?rss=1"
Goldman, O. G.Dubowitz, G.Anderson, D.2023-10-10doi:10.1101/2023.10.09.561578Cold Spring Harbor Laboratory Press2023-10-10
<![CDATA[
SERF2, an RNA G-quadruplex Binding Protein, promotes stress granule formation
]]>
https://biorxiv.org/cgi/content/short/2023.10.09.561572v1?rss=1"
Sahoo, B. R.Deng, X.Wong, E. L.Clark, N.Yang, H.Subramanian, V.Guzman, B. B.Harris, S. E.Dehury, B.Miyashita, E.Saito, H.Dominguez, D.Bardwell, J. C.2023-10-10doi:10.1101/2023.10.09.561572Cold Spring Harbor Laboratory Press2023-10-10
<![CDATA[
A Simple Subcortical Feeding Circuit Linking Interoceptive Inputs to Consummatory Behavior
]]>
https://biorxiv.org/cgi/content/short/2023.10.11.561735v1?rss=1"
Kosse, C.Ivanov, J.Knight, Z.Pellegrino, K.Friedman, J.2023-10-11doi:10.1101/2023.10.11.561735Cold Spring Harbor Laboratory Press2023-10-11
<![CDATA[
Cross-modal sensory compensation increases mosquito attraction to humans
]]>
https://biorxiv.org/cgi/content/short/2023.10.10.561721v1?rss=1"
Morita, T.Lyn, N. G.von Heynitz, R. K.Goldman, O. V.Sorrells, T. R.DeGennaro, M.Matthews, B. J.Houri-Zeevi, L.Vosshall, L. B.2023-10-11doi:10.1101/2023.10.10.561721Cold Spring Harbor Laboratory Press2023-10-11
<![CDATA[
Structural basis for CFTR inhibition by CFTRinh-172
]]>
https://biorxiv.org/cgi/content/short/2023.10.11.561899v1?rss=1"
Young, P.Levring, J.Fiedorczuk, K.Blanchard, S. C.Chen, J.2023-10-12doi:10.1101/2023.10.11.561899Cold Spring Harbor Laboratory Press2023-10-12
<![CDATA[
Structural identification of a selectivity filter in CFTR
]]>
https://biorxiv.org/cgi/content/short/2023.10.11.561906v1?rss=1"
Levring, J.Chen, J.2023-10-12doi:10.1101/2023.10.11.561906Cold Spring Harbor Laboratory Press2023-10-12
<![CDATA[
Representations of information value in mouse orbitofrontal cortex during information seeking
]]>
https://biorxiv.org/cgi/content/short/2023.10.13.562291v1?rss=1"
Bussell, J. J.Badman, R. P.Marton, C. D.Bromberg-Martin, E. S.Abbott, L.Rajan, K.Axel, R.2023-10-13doi:10.1101/2023.10.13.562291Cold Spring Harbor Laboratory Press2023-10-13
<![CDATA[
Parkinsonism Sac domain mutation in Synaptojanin-1 affects ciliary properties in iPSC-derived dopaminergic neurons
]]>
https://biorxiv.org/cgi/content/short/2023.10.12.562142v1?rss=1"
Mohd Rafiq, N.Fujise, K.Rosenfeld, M.Xu, P.Wu, Y.De Camilli, P.2023-10-13doi:10.1101/2023.10.12.562142Cold Spring Harbor Laboratory Press2023-10-13
<![CDATA[
Hidden evolutionary constraints dictate the retention of coronavirus accessory genes
]]>
https://biorxiv.org/cgi/content/short/2023.10.12.561935v1?rss=1"
Goldstein, S. A.Feeley, T. M.Babler, K. M.Hilbert, Z. A.Downhour, D. M.Moshiri, N.Elde, N. C.2023-10-14doi:10.1101/2023.10.12.561935Cold Spring Harbor Laboratory Press2023-10-14
<![CDATA[
The genetic basis of novel trait gain in walking fish
]]>
https://biorxiv.org/cgi/content/short/2023.10.14.562356v1?rss=1"
Herbert, A. L.Allard, C. A.McCoy, M. J.Wucherpfennig, J. I.Krueger, S. P.Chen, H. I.Gourlay, A. N.Jackson, K. D.Abbo, L. A.Bennett, S. H.Sears, J. D.Rhyne, A. L.Bellono, N. W.Kingsley, D. M.2023-10-14doi:10.1101/2023.10.14.562356Cold Spring Harbor Laboratory Press2023-10-14
<![CDATA[
Liver size is predetermined in the neonate by adding lobules at the periphery
]]>
https://biorxiv.org/cgi/content/short/2023.10.12.562109v1?rss=1"
Azizoglu, D. B.Perez, K.Zheng, S. L.Rahman, S.Rim, E. Y.Anbarchian, T.Fish, M.Loh, K. M.Red-Horse, K.Nusse, R.2023-10-14doi:10.1101/2023.10.12.562109Cold Spring Harbor Laboratory Press2023-10-14
<![CDATA[
Molecular Time Capsules Enable Transcriptomic Recording in Living Cells
]]>
https://biorxiv.org/cgi/content/short/2023.10.12.562053v1?rss=1"
Parker, M. L.Rubien, J.McCormick, D.Li, G.-W.2023-10-16doi:10.1101/2023.10.12.562053Cold Spring Harbor Laboratory Press2023-10-16
<![CDATA[
Influence of myosin regulatory light chain and myosin light chain kinase on hair cells of the inner ear
]]>
https://biorxiv.org/cgi/content/short/2023.10.14.562357v1?rss=1"
Oya, R.Woo, K. M.Fabella, B.Alonso, R. G.Hudspeth, A. J.2023-10-16doi:10.1101/2023.10.14.562357Cold Spring Harbor Laboratory Press2023-10-16
<![CDATA[
The rotavirus VP5*/VP8* conformational transition permeabilizes membranes to Ca2+
]]>
https://biorxiv.org/cgi/content/short/2023.10.15.562449v1?rss=1"
de Sautu, M.Herrmann, T.Jenni, S.Harrison, S. C.2023-10-16doi:10.1101/2023.10.15.562449Cold Spring Harbor Laboratory Press2023-10-16
<![CDATA[
The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex
]]>
https://biorxiv.org/cgi/content/short/2023.10.15.562437v1?rss=1"
250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.
HIGHLIGHTSO_LISequence of guide RNA can alter slicing rate of fully paired substrate by 250-fold
C_LIO_LISequences that cause more rapid slicing direct more efficient RNAi in cells
C_LIO_LIStrong central pairing imparts tolerance for mismatches to the guide 3' region
C_LIO_LIThis tolerance is attributable to more fully populating the slicing conformation
C_LI
]]>Wang, P. Y.Bartel, D. P.2023-10-16doi:10.1101/2023.10.15.562437Cold Spring Harbor Laboratory Press2023-10-16
<![CDATA[
Fine-grained descending control of steering in walking Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.10.15.562426v1?rss=1"
Yang, H. H.Brezovec, L. E.Serratosa Capdevila, L.Vanderbeck, Q. X.Rayshubskiy, S.Wilson, R. I.2023-10-17doi:10.1101/2023.10.15.562426Cold Spring Harbor Laboratory Press2023-10-17
<![CDATA[
A comprehensive neuroanatomical survey of the Drosophila Lobula Plate Tangential Neurons with predictions for their optic flow sensitivity
]]>
https://biorxiv.org/cgi/content/short/2023.10.16.562634v1?rss=1"
Zhao, A.Nern, A.Koskela, S.Dreher, M.Erginkaya, M.Laughland, C. W.Ludwig, H. D.Thomson, A. G.Hoeller, J.Parekh, R.Romani, S.Bock, D. D.Chiappe, E.Reiser, M. B.2023-10-17doi:10.1101/2023.10.16.562634Cold Spring Harbor Laboratory Press2023-10-17
<![CDATA[
Epigenome erosion in Alzheimer's disease brain cells and induced neurons
]]>
https://biorxiv.org/cgi/content/short/2023.10.15.562394v1?rss=1"
Ecker, J. R.Gage, F. H.Wang, B.Jones, J.Zhou, J.Tian, W.Wu, Y.Wang, W.Berube, P.Bartlett, A.Castanon, R. G.Nery, J. R.Chen, H.Kenworthy, M.Altshul, J.Valadon, C.Wang, Y.Kang, A.Goodman, R.Liem, M.Claffey, N.O'Connor, C.Metcalf, J.Luo, C.2023-10-18doi:10.1101/2023.10.15.562394Cold Spring Harbor Laboratory Press2023-10-18
<![CDATA[
Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos
]]>
https://biorxiv.org/cgi/content/short/2023.10.18.562922v1?rss=1"
Xiang, K.Ly, J.Bartel, D.2023-10-19doi:10.1101/2023.10.18.562922Cold Spring Harbor Laboratory Press2023-10-19
<![CDATA[
Conflicts in natural selection constrain adaptation to climate change in Arabidopsis thaliana
]]>
https://biorxiv.org/cgi/content/short/2023.10.16.562583v1?rss=1"
Ruffley, M. R.Levanthal, L.Hateley, S.Rhee, S. Y.Exposito-Alonso, M.2023-10-19doi:10.1101/2023.10.16.562583Cold Spring Harbor Laboratory Press2023-10-19
<![CDATA[
Long-Term In Vivo Molecular Monitoring Using Aptamer-Graphene Microtransistors
]]>
https://biorxiv.org/cgi/content/short/2023.10.18.562080v1?rss=1"
Wu, G.Zhang, E. T.Qiang, Y.Esmonde, C.Chen, X.Wei, Z.Song, Y.Zhang, X.Schneider, M. J.Li, H.Sun, H.Weng, Z.Santaniello, S.He, J.Lai, R. Y.Li, Y.Bruchas, M. R.Zhang, Y.2023-10-20doi:10.1101/2023.10.18.562080Cold Spring Harbor Laboratory Press2023-10-20
<![CDATA[
Multiplexed CRISPR/Cas9 mutagenesis of rice PSBS1 non-coding sequences for transgene-free overexpression
]]>
https://biorxiv.org/cgi/content/short/2023.10.20.563333v1?rss=1"
Patel-Tupper, D.Kelikian, A.Leipertz, A.Maryn, N.Tjahjadi, M.Karavolias, N. G.Cho, M.-J.Niyogi, K. K.2023-10-21doi:10.1101/2023.10.20.563333Cold Spring Harbor Laboratory Press2023-10-21
<![CDATA[
A Markovian dynamics for C. elegans behavior across scales
]]>
https://biorxiv.org/cgi/content/short/2023.10.19.563098v1?rss=1"
Costa, A. C.Ahamed, T.Jordan, D.Stephens, G. J.2023-10-22doi:10.1101/2023.10.19.563098Cold Spring Harbor Laboratory Press2023-10-22
<![CDATA[
Low-cost camera-based estrous tracking enables transgenesis in Peromyscus leucopus, the primary reservoir for Lyme disease
]]>
https://biorxiv.org/cgi/content/short/2023.10.20.563285v1?rss=1"
View larger version (45K):
org.highwire.dtl.DTLVardef@19a3fb2org.highwire.dtl.DTLVardef@1cbce4corg.highwire.dtl.DTLVardef@1551e0corg.highwire.dtl.DTLVardef@127c028_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Buchthal, J.Chory, E. J.Hill, Z.Dennison, C.Tu, B.Wierenga, R. P.Cevrim, C.Golas, S.Telford, S. R.McKinley, K. L.Jaenisch, R.Markoulaki, S.Esvelt, K. M.2023-10-22doi:10.1101/2023.10.20.563285Cold Spring Harbor Laboratory Press2023-10-22
<![CDATA[
Expression of Lanthipeptides in Human Cells
]]>
https://biorxiv.org/cgi/content/short/2023.10.19.563208v1?rss=1"
View larger version (19K):
org.highwire.dtl.DTLVardef@aafac8org.highwire.dtl.DTLVardef@13687caorg.highwire.dtl.DTLVardef@10d16caorg.highwire.dtl.DTLVardef@533398_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Eslami, S.Rahman, I. R.van der Donk, W.2023-10-23doi:10.1101/2023.10.19.563208Cold Spring Harbor Laboratory Press2023-10-23
<![CDATA[
Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair
]]>
https://biorxiv.org/cgi/content/short/2023.10.22.563489v1?rss=1"
Rose, J. C.Wang, I. T.-L.Daniel, B.Jones, M. G.Yost, K. E.Hung, K. L.Curtis, E. J.Mischel, P. S.Chang, H.2023-10-23doi:10.1101/2023.10.22.563489Cold Spring Harbor Laboratory Press2023-10-23
<![CDATA[
Combinatorial CRISPR screens and lectin microarrays identify novel glycosylation regulators
]]>
https://biorxiv.org/cgi/content/short/2023.10.23.563662v1?rss=1"
Tsui, C. K.Twells, N.Doan, E.Brooks, J.Kulepa, A.Webster, B.Mahal, L. K.Dillin, A.2023-10-24doi:10.1101/2023.10.23.563662Cold Spring Harbor Laboratory Press2023-10-24
<![CDATA[
A new mode of transcriptional hub assembly by autoimmune regulator Aire
]]>
https://biorxiv.org/cgi/content/short/2023.10.23.563603v1?rss=1"
Huoh, Y.-S.Zhang, Q.Torner, R.Baca, S. C.Arthanari, H.Hur, S.2023-10-25doi:10.1101/2023.10.23.563603Cold Spring Harbor Laboratory Press2023-10-25
<![CDATA[
A Facile Method for Determining Lanthipeptide Stereochemistry
]]>
https://biorxiv.org/cgi/content/short/2023.10.26.564210v1?rss=1"
Luo, Y.Xu, S.van der Donk, W.2023-10-26doi:10.1101/2023.10.26.564210Cold Spring Harbor Laboratory Press2023-10-26
<![CDATA[
Neural-circuit basis of song preference learning in fruit flies
]]>
https://biorxiv.org/cgi/content/short/2023.10.24.563693v1?rss=1"
Imoto, K.Ishikawa, Y.Aso, Y.Funke, J.Tanaka, R.Kamikouchi, A.2023-10-26doi:10.1101/2023.10.24.563693Cold Spring Harbor Laboratory Press2023-10-26
<![CDATA[
Nanoscale imaging reveals the mechanisms of ER-to-Golgi transport via a dynamic tubular-vesicular network
]]>
https://biorxiv.org/cgi/content/short/2023.10.27.563951v1?rss=1"
Wong-Dilworth, L.Bregu, G.Restel, S.Rodilla-Ramirez, C.Ebeling, S.Harel, S.Leupold, P.Grimm, J.Lavis, L.Bottanelli, F.Angulo-Capel, J.Campelo, F.2023-10-27doi:10.1101/2023.10.27.563951Cold Spring Harbor Laboratory Press2023-10-27
<![CDATA[
Chemically induced proximity reveals mechanotransduction of a meiotic checkpoint at the nuclear envelope
]]>
https://biorxiv.org/cgi/content/short/2023.10.28.564506v1?rss=1"
Liu, C.Dernburg, A. F.2023-10-28doi:10.1101/2023.10.28.564506Cold Spring Harbor Laboratory Press2023-10-28
<![CDATA[
Discovery of biaryl macrocyclic peptides with C-terminal beta-keto acid groups
]]>
https://biorxiv.org/cgi/content/short/2023.10.30.564719v1?rss=1"
Nguyen, D.Zhu, L.Mitchell, D. A.van der Donk, W.2023-10-30doi:10.1101/2023.10.30.564719Cold Spring Harbor Laboratory Press2023-10-30
<![CDATA[
Parabrachial Calca neurons drive nociplasticity
]]>
https://biorxiv.org/cgi/content/short/2023.10.26.564223v1?rss=1"
Condon, L. F.Yu, Y.Park, S.Cao, F.Pauli, J. L.Nelson, T. S.Palmiter, R. D.2023-10-31doi:10.1101/2023.10.26.564223Cold Spring Harbor Laboratory Press2023-10-31
<![CDATA[
dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets
]]>
https://biorxiv.org/cgi/content/short/2023.10.29.564578v1?rss=1"
View larger version (31K):
org.highwire.dtl.DTLVardef@6c623forg.highwire.dtl.DTLVardef@1a62199org.highwire.dtl.DTLVardef@1e7d71eorg.highwire.dtl.DTLVardef@1dc1252_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Large mutation-associated datasets are used in a variety of experimental contexts. They can be used to map antibody footprints on viral glycoproteins, assess the impact of mutations on protein function in a laboratory setting, and identify patterns of selection from natural mutation frequencies.
C_FIG The mutation-based data generated by these approaches is often best understood in the context of a proteins 3D structure; for instance, to assess questions like how mutations that affect antibody escape relate to the physical antibody binding epitope on the protein. However, current approaches for visualizing mutation data in the context of a proteins structure are often cumbersome and require multiple steps and softwares. To streamline the visualization of mutation-associated data in the context of a protein structure, we developed a web-based tool, dms-viz. With dms-viz, users can straightforwardly visualize mutation-based data such as those from DMS experiments in the context of a 3D protein model in an interactive format. See https://dms-viz.github.io/ to use dms-viz.
]]>Hannon, W. W.Bloom, J. D.2023-11-01doi:10.1101/2023.10.29.564578Cold Spring Harbor Laboratory Press2023-11-01
<![CDATA[
Nanometer-scale views of visual cortex reveal anatomical features of primary cilia poised to detect synaptic spillover
]]>
https://biorxiv.org/cgi/content/short/2023.10.31.564838v1?rss=1"
Ott, C. M.Torres, R.Kuan, T.-S.Kuan, A. T.Buchanan, J.Elabbady, L.Seshamani, S.Bodor, A. L.Collman, F. C.Bock, D. D.Lee, W.-C. A.Macarico da Costa, N.Lippincott-Schwartz, J.2023-11-01doi:10.1101/2023.10.31.564838Cold Spring Harbor Laboratory Press2023-11-01
<![CDATA[
Cryo-EM structure of the Spo11 core complex bound to DNA
]]>
https://biorxiv.org/cgi/content/short/2023.10.31.564985v1?rss=1"
Yu, Y.Wang, J.Liu, K.Zheng, Z.Arter, M.Bouuaert, C. C.Pu, S.Patel, D. J.Keeney, S.2023-11-01doi:10.1101/2023.10.31.564985Cold Spring Harbor Laboratory Press2023-11-01
<![CDATA[
Immunosuppression is a conserved driver of tuberculosis susceptibility
]]>
https://biorxiv.org/cgi/content/short/2023.10.27.564420v1?rss=1"
Kotov, D. I.Lee, O. V.Ji, D. X.Jaye, D. L.Suliman, S.Gabay, C.Vance, R. E.2023-11-01doi:10.1101/2023.10.27.564420Cold Spring Harbor Laboratory Press2023-11-01
<![CDATA[
Principles of Computation by Competitive Protein Dimerization Networks
]]>
https://biorxiv.org/cgi/content/short/2023.10.30.564854v1?rss=1"
View larger version (36K):
org.highwire.dtl.DTLVardef@1917f39org.highwire.dtl.DTLVardef@13795bcorg.highwire.dtl.DTLVardef@47913eorg.highwire.dtl.DTLVardef@90bd30_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Parres-Gold, J.Levine, M.Emert, B.Stuart, A.Elowitz, M.2023-11-02doi:10.1101/2023.10.30.564854Cold Spring Harbor Laboratory Press2023-11-02
<![CDATA[
Neuropeptide Signaling Is Required To Implement A Line Attractor Encoding A Persistent Internal Behavioral State
]]>
https://biorxiv.org/cgi/content/short/2023.11.01.565073v1?rss=1"
Mountoufaris, G.Nair, A.Yang, B.Kim, D.-W.Anderson, D. J.2023-11-02doi:10.1101/2023.11.01.565073Cold Spring Harbor Laboratory Press2023-11-02
<![CDATA[
Small-molecule binding and sensing with a designed protein family
]]>
https://biorxiv.org/cgi/content/short/2023.11.01.565201v1?rss=1"
Lee, G. R.Pellock, S. J.Norn, C.Tischer, D.Dauparas, J.Anishchenko, I.Mercer, J. A. M.Kang, A.Bera, A.Nguyen, H.Goreshnik, I.Vafeados, D.Roullier, N.Han, H. L.Coventry, B.Haddox, H. K.Liu, D. R.Yeh, A. H.-W.Baker, D.2023-11-02doi:10.1101/2023.11.01.565201Cold Spring Harbor Laboratory Press2023-11-02
<![CDATA[
Targeting editing of tomato SPEECHLESS cis-regulatory regions generates plants with altered stomatal density in response to changing climate conditions
]]>
https://biorxiv.org/cgi/content/short/2023.11.02.564550v1?rss=1"
Nir, I.Budrys, A.Smoot, N. K.Erberich, J.Bergmann, D.2023-11-02doi:10.1101/2023.11.02.564550Cold Spring Harbor Laboratory Press2023-11-02
<![CDATA[
Modulation of hepatic transcription factor EB activity during cold exposure uncovers direct regulation of bis(monoacylglycerol)phosphate lipids by Pla2g15
]]>
https://biorxiv.org/cgi/content/short/2023.11.03.565498v1?rss=1"
Jain, R.Geoghegan, G.Davidson, J.Nesbitt, D. J.Abe, A.Chao, X.James, I.Cavanagh, A. T.Michorowska, S.Verma, R.Schueler, K. L.Hinkoka-Galcheva, V.Shishkova, E.Ding, W.-X.Coon, J. J.Shayman, J.Simcox, J.2023-11-03doi:10.1101/2023.11.03.565498Cold Spring Harbor Laboratory Press2023-11-03
<![CDATA[
Nitrate-mediated luminal expansion of Salmonella Typhimurium is dependent on the ER stress protein CHOP
]]>
https://biorxiv.org/cgi/content/short/2023.11.03.565559v1?rss=1"
Sweet, L. A.Kuss-Duerkop, S. K.Byndloss, M. X.Keestra-Gounder, A. M.2023-11-03doi:10.1101/2023.11.03.565559Cold Spring Harbor Laboratory Press2023-11-03
<![CDATA[
Seven-up acts in neuroblasts to specify adult central complex neuron identity and initiate neuroblast decommissioning
]]>
https://biorxiv.org/cgi/content/short/2023.11.02.565340v1?rss=1"
Dillon, N.Manning, L.Hirono, K.Doe, C. Q.2023-11-03doi:10.1101/2023.11.02.565340Cold Spring Harbor Laboratory Press2023-11-03
<![CDATA[
Spatially resolved proteomics of the stomatal lineage: polarity complexes for cell divisions and stomatal pores
]]>
https://biorxiv.org/cgi/content/short/2023.11.03.564551v1?rss=1"
Wallner, E.-S.Mair, A.Handler, D.McWhite, C. D.Xu, S.-L.Dolan, L.Bergmann, D.2023-11-03doi:10.1101/2023.11.03.564551Cold Spring Harbor Laboratory Press2023-11-03
<![CDATA[
LEAFY interacts with WHEAT ORTHOLOG OF APO1 to regulate spikelet number per spike in wheat
]]>
https://biorxiv.org/cgi/content/short/2023.11.02.565263v1?rss=1"
Paraiso, F.Zhang, J.Lin, H.Li, C.Woods, D. P.Lan, T.Debernardi, J. M.Joe, A.Dubcovsky, J.2023-11-04doi:10.1101/2023.11.02.565263Cold Spring Harbor Laboratory Press2023-11-04
<![CDATA[
Chemical inhibition of stomatal differentiation by perturbation of the master-regulatory bHLH heterodimer via an ACT-Like domain
]]>
https://biorxiv.org/cgi/content/short/2023.11.02.565226v1?rss=1"
Nakagawa, A.Sepuru, K. M.Yip, S. J. A.Seo, H.Coffin, C. M.Segawa, Y.Iwasaki, R.Kato, H.Kim, S.Aihara, Y.Kinoshita, T.Itami, K.Han, S.-K.Murakami, K.Torii, K. U.2023-11-04doi:10.1101/2023.11.02.565226Cold Spring Harbor Laboratory Press2023-11-04
<![CDATA[
High temporal frequency light response in mouse retina is mediated by ON and OFF bipolar cells and requires FAT3 signaling
]]>
https://biorxiv.org/cgi/content/short/2023.11.02.565326v1?rss=1"
Aviles, E. C.Wang, S. K.Patel, S.Shi, S.Lin, L.Kefalov, V.Goodrich, L.Cepko, C.Xue, Y.2023-11-04doi:10.1101/2023.11.02.565326Cold Spring Harbor Laboratory Press2023-11-04
<![CDATA[
Male-male interactions shape mate selection in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.11.03.565582v1?rss=1"
Hindmarsh Sten, T.Li, R.Hollunder, F.Eleazer, S.Ruta, V.2023-11-05doi:10.1101/2023.11.03.565582Cold Spring Harbor Laboratory Press2023-11-05
<![CDATA[
Renal mechanotransduction is an essential regulator of renin
]]>
https://biorxiv.org/cgi/content/short/2023.11.04.565646v1?rss=1"
Hill, R. Z.Shirvan, S.Burquez, S.Dubin, A. E.Servin Vences, M. R.Miner, J. H.Patapoutian, A.2023-11-05doi:10.1101/2023.11.04.565646Cold Spring Harbor Laboratory Press2023-11-05
<![CDATA[
Differences in an aversive teaching signal produce brainwide and behavioral substrates of susceptibility
]]>
https://biorxiv.org/cgi/content/short/2023.11.06.565681v1?rss=1"
Zhukovskaya, A.Christopher, Z.Willmore, L.Janarthanan, S.Falkner, A.Witten, I.2023-11-06doi:10.1101/2023.11.06.565681Cold Spring Harbor Laboratory Press2023-11-06
<![CDATA[
Cell lineage analysis with somatic mutations reveals late divergence of neuronal cell types and cortical areas in human cerebral cortex
]]>
https://biorxiv.org/cgi/content/short/2023.11.06.565899v1?rss=1"
Kim, S. N.Viswanadham, V. V.Doan, R. N.Dou, Y.Bizzotto, S.Khoshkoo, S.Huang, A. Y.Yeh, R.Chhouk, B.Truong, A.Chappell, K. M.Beaudin, M.Barton, A. R.Akula, S. K.Rento, L.Lodato, M.Ganz, J.Szeto, R. A.Li, P.Tsai, J. W.Hill, R. S.Park, P. J.Walsh, C. A.2023-11-07doi:10.1101/2023.11.06.565899Cold Spring Harbor Laboratory Press2023-11-07
<![CDATA[
NLRP3 Cys126 palmitoylation by ZDHHC7 Promotes Inflammasome Activation
]]>
https://biorxiv.org/cgi/content/short/2023.11.07.566005v1?rss=1"
Yu, T.Hou, D.Zhao, J.Lu, X.Greentree, W. K.Zhao, Q.Conde, D.-G.Linder, M. E.Lin, H.2023-11-08doi:10.1101/2023.11.07.566005Cold Spring Harbor Laboratory Press2023-11-08
<![CDATA[
Striatum supports fast learning but not memory recall
]]>
https://biorxiv.org/cgi/content/short/2023.11.08.566333v1?rss=1"
Reinhold, K.Iadarola, M.Tang, S.Kuwamoto, W.Sun, S.Hakim, R.Zimmer, J.Wang, W.Sabatini, B. L.2023-11-10doi:10.1101/2023.11.08.566333Cold Spring Harbor Laboratory Press2023-11-10
<![CDATA[
Social isolation recruits amygdala-cortical circuitry to escalate alcohol drinking
]]>
https://biorxiv.org/cgi/content/short/2023.11.09.566421v1?rss=1"
Patel, R.Patarino, M.Kim, K.Pamintuan, R.Taschbach, F.Li, H.Lee, C.van Hoek, A.Castro, R.Cazares, C.Miranda, R.Jia, C.Delahanty, J.Batra, K.Keyes, L.Libster, A.Wichmann, R. W.Pereira, T.Benna, M.Tye, K. M.2023-11-10doi:10.1101/2023.11.09.566421Cold Spring Harbor Laboratory Press2023-11-10
<![CDATA[
Distinct and interdependent functions of three RING proteins regulate recombination during mammalian meiosis
]]>
https://biorxiv.org/cgi/content/short/2023.11.07.566091v1?rss=1"
Ito, M.Yun, Y.Kulkarni, D. S.Sandhu, S.Nunez, B.Hu, L.Lee, K.Lim, N.Hirota, R.Prendergast, R.Huang, C.Huang, I.Hunter, N.2023-11-10doi:10.1101/2023.11.07.566091Cold Spring Harbor Laboratory Press2023-11-10
<![CDATA[
Ultrasonic reporters of calcium for deep tissue imaging of cellular signals
]]>
https://biorxiv.org/cgi/content/short/2023.11.09.566364v1?rss=1"
Jin, Z.Lakshmanan, A.Zhang, R.Tran, T. A.Rabut, C.Dutka, P.Duan, M.Hurt, R. C.Malounda, D.Yao, Y.Shapiro, M. G.2023-11-12doi:10.1101/2023.11.09.566364Cold Spring Harbor Laboratory Press2023-11-12
<![CDATA[
Hypermetabolic state is associated with circadian rhythm disruption in mouse and human cancer cells
]]>
https://biorxiv.org/cgi/content/short/2023.11.08.566310v1?rss=1"
Iascone, D. M.Zhang, X.Bafford, P.Mesaros, C.Sela, Y.Hofbauer, S.Zhang, S. L.Cook, K.Pivarshev, P.Stanger, B.Anderson, S. A.Dang, C. V.Sehgal, A.2023-11-13doi:10.1101/2023.11.08.566310Cold Spring Harbor Laboratory Press2023-11-13
<![CDATA[
Serotonin transporter-dependent histone serotonylation in placenta contributes to the neurodevelopmental transcriptome
]]>
https://biorxiv.org/cgi/content/short/2023.11.14.567020v1?rss=1"
Chan, J. C.Alenina, N.Cunningham, A. M.Ramakrishnan, A.Shen, L.Bader, M.Maze, I.2023-11-14doi:10.1101/2023.11.14.567020Cold Spring Harbor Laboratory Press2023-11-14
<![CDATA[
Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades
]]>
https://biorxiv.org/cgi/content/short/2023.11.13.566961v1?rss=1"
9,000 mutations across the full XBB.1.5 and BA.2 spikes affect ACE2 binding, cell entry, or escape from human sera. We find that mutations outside the receptor-binding domain (RBD) have meaningfully impacted ACE2 binding during SARS-CoV-2 evolution. We also measure how mutations to the XBB.1.5 spike affect neutralization by serum from individuals who recently had SARS-CoV-2 infections. The strongest serum escape mutations are in the RBD at sites 357, 420, 440, 456, and 473--however, the antigenic impacts of these mutations vary across individuals. We also identify strong escape mutations outside the RBD; however many of them decrease ACE2 binding, suggesting they act by modulating RBD conformation. Notably, the growth rates of human SARS-CoV-2 clades can be explained in substantial part by the measured effects of mutations on spike phenotypes, suggesting our data could enable better prediction of viral evolution.
]]>Dadonaite, B.Brown, J.McMahon, T. E.Farrell, A. G.Asarnow, D.Stewart, C.Logue, J.Murrell, B.Chu, H. Y.Veesler, D.Bloom, J. D.2023-11-14doi:10.1101/2023.11.13.566961Cold Spring Harbor Laboratory Press2023-11-14
<![CDATA[
Structural basis for VLDLR recognition by eastern equine encephalitis virus
]]>
https://biorxiv.org/cgi/content/short/2023.11.14.567065v1?rss=1"
Yang, P.Li, W.Fan, X.Pan, J.Mann, C. J.Varnum, H.Clark, L. E.Clark, S. A.Coscia, A.Smith, K. N.Brusic, V.Abraham, J.2023-11-14doi:10.1101/2023.11.14.567065Cold Spring Harbor Laboratory Press2023-11-14
<![CDATA[
Lung and liver editing by lipid nanoparticle delivery of a stable CRISPR-Cas9 RNP
]]>
https://biorxiv.org/cgi/content/short/2023.11.15.566339v1?rss=1"
100X greater than those induced by the native GeoCas9 enzyme. Furthermore, iGeoCas9 RNP:LNP complexes edited a variety of cell lines and induced homology-directed repair (HDR) in cells receiving co-delivered single-stranded DNA (ssDNA) templates. Using tissue-selective LNP formulations, we observed genome editing of 35-56% efficiency in the liver or lungs of mice that received intravenous injections of iGeoCas9 RNP:LNPs. In particular, iGeoCas9 complexed to acid-degradable LNPs edited lung tissue in vivo with an average of 35% efficiency, a significant improvement over editing efficiencies observed previously using viral or non-viral delivery strategies. These results show that thermostable Cas9 RNP:LNP complexes are a powerful alternative to mRNA:LNP delivery vehicles, expanding the therapeutic potential of genome editing.
]]>Chen, K.Han, H.Zhao, S.Xu, B.Yin, B.Trinidad, M.Burgstone, B. W.Murthy, N.Doudna, J. A.2023-11-15doi:10.1101/2023.11.15.566339Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
Directed Evolution of Genetically Encoded LYTACs for Cell-Mediated Delivery
]]>
https://biorxiv.org/cgi/content/short/2023.11.14.567117v1?rss=1"
Yang, J. L.Yamada-Hunter, S. A.Labanieh, L.Sotillo, E.Cheah, J. S.Roberts, D. S.Mackall, C.Ting, A. Y.Bertozzi, C.2023-11-15doi:10.1101/2023.11.14.567117Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
Engineering self-deliverable ribonucleoproteins for genome editing in the brain
]]>
https://biorxiv.org/cgi/content/short/2023.11.15.567251v1?rss=1"
Chen, K.Stahl, E. C.Kang, M. H.Xu, B.Allen, R.Trinidad, M.Doudna, J. A.2023-11-15doi:10.1101/2023.11.15.567251Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
Expansion of human centromeric arrays in cells undergoing break-induced replication
]]>
https://biorxiv.org/cgi/content/short/2023.11.11.566714v1?rss=1"
Showman, S.Talbert, P. B.Xu, Y.Adeyemi, R. O.Henikoff, S.2023-11-15doi:10.1101/2023.11.11.566714Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
A Foundation Model for Cell Segmentation
]]>
https://biorxiv.org/cgi/content/short/2023.11.17.567630v1?rss=1"
Israel, U.Marks, M.Dilip, R.Li, Q.Schwartz, M. S.Pradhan, E.Pao, E.Li, S.Pearson-Goulart, A.Perona, P.Gkioxari, G.Barnowski, R.Yue, Y.Van Valen, D. A.2023-11-20doi:10.1101/2023.11.17.567630Cold Spring Harbor Laboratory Press2023-11-20
<![CDATA[
Distributed representations of innate behaviors in the hypothalamus do not predict specialized functional centers
]]>
https://biorxiv.org/cgi/content/short/2023.11.21.568163v1?rss=1"
Stagkourakis, S.Spigolon, G.Marks, M.Feyder, M.Kim, J.Perona, P.Pachitariu, M.Anderson, D. J.2023-11-21doi:10.1101/2023.11.21.568163Cold Spring Harbor Laboratory Press2023-11-21
<![CDATA[
Hippocampal place code plasticity in CA1 requires postsynaptic membrane fusion
]]>
https://biorxiv.org/cgi/content/short/2023.11.20.567978v1?rss=1"
Plitt, M. H.Kaganovsky, K.Südhof, T. C.Giocomo, L. M.2023-11-21doi:10.1101/2023.11.20.567978Cold Spring Harbor Laboratory Press2023-11-21
<![CDATA[
One-Hour Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer
]]>
https://biorxiv.org/cgi/content/short/2023.11.21.568149v1?rss=1"
Lancaster, N. M.Sinitcyn, P.Forny, P.Peters-Clarke, T. M.Fecher, C.Smith, A. J.Shishkova, E.Arrey, T. N.Pashkova, A.Robinson, M. L.Arp, N.Fan, J.Hansen, J.Galmozzi, A.Serrano, L. R.Westphall, M. S.Stewart, H.Hock, C.Damoc, E.Pagliarini, D. J.Zabrouskov, V.Coon, J. J.2023-11-21doi:10.1101/2023.11.21.568149Cold Spring Harbor Laboratory Press2023-11-21
<![CDATA[
Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses
]]>
https://biorxiv.org/cgi/content/short/2023.11.22.567964v1?rss=1"
Kretsch, R. C.Xu, L.Zheludev, I. N.Zhou, X.Huang, R.Nye, G.Li, S.Zhang, K.Chiu, W.Das, R.2023-11-22doi:10.1101/2023.11.22.567964Cold Spring Harbor Laboratory Press2023-11-22
<![CDATA[
Asgard archaea modulate potential methanogenesis substrates in wetland soil
]]>
https://biorxiv.org/cgi/content/short/2023.11.21.568159v1?rss=1"
Valentin-Alvarado, L. E.Appler, K. E.De Anda, V.Schoelmerich, M. C.West-Roberts, J.Kivenson, V.Crits-Christoph, A.Ly, L.Sachdeva, R.Savage, D. F.Baker, B. J.Banfield, J. F.2023-11-22doi:10.1101/2023.11.21.568159Cold Spring Harbor Laboratory Press2023-11-22
<![CDATA[
A communication hub for phosphoregulation of kinetochore-microtubule attachment
]]>
https://biorxiv.org/cgi/content/short/2023.11.22.568383v1?rss=1"
Zahm, J. A.Harrison, S. C.2023-11-23doi:10.1101/2023.11.22.568383Cold Spring Harbor Laboratory Press2023-11-23
<![CDATA[
Experience-dependent place-cell referencing in hippocampal area CA1
]]>
https://biorxiv.org/cgi/content/short/2023.11.23.568469v1?rss=1"
Qian, F. K.Li, Y.Magee, J. C.2023-11-23doi:10.1101/2023.11.23.568469Cold Spring Harbor Laboratory Press2023-11-23
<![CDATA[
Neuronal calcium spikes enable vector inversion in the Drosophila brain
]]>
https://biorxiv.org/cgi/content/short/2023.11.24.568537v1?rss=1"
Ishida, I. G.Sethi, S.Mohren, T. L.Abbott, L.Maimon, G.2023-11-24doi:10.1101/2023.11.24.568537Cold Spring Harbor Laboratory Press2023-11-24
<![CDATA[
Bioorthogonal metabolic labeling of the virulence factor phenolic glycolipid in mycobacteria
]]>
https://biorxiv.org/cgi/content/short/2023.11.28.569059v1?rss=1"
Guzman, L. E.Cambier, C.Cheng, T.-Y.Naqvi, K. F.Shiloh, M. U.Moody, D. B.Bertozzi, C.2023-11-28doi:10.1101/2023.11.28.569059Cold Spring Harbor Laboratory Press2023-11-28
<![CDATA[
Role of a holo-insertase complex in the biogenesis of biophysically diverse ER membrane proteins
]]>
https://biorxiv.org/cgi/content/short/2023.11.28.569054v1?rss=1"
Page, K. R.Nguyen, V. N.Pleiner, T.Tomaleri, G. P.Wang, M. L.Guna, A.Wang, T.-Y.Chou, T.-F.Voorhees, R. M.2023-11-29doi:10.1101/2023.11.28.569054Cold Spring Harbor Laboratory Press2023-11-29
<![CDATA[
Connectomic reconstruction predicts the functional organization of visual inputs to the navigation center of the Drosophila brain
]]>
https://biorxiv.org/cgi/content/short/2023.11.29.569241v1?rss=1"
Garner, D.Kind, E.Nern, A.Houghton, L.Zhao, A.Sancer, G.Rubin, G. M.Wernet, M. F.Kim, S. S.2023-11-30doi:10.1101/2023.11.29.569241Cold Spring Harbor Laboratory Press2023-11-30
<![CDATA[
Persistent immune imprinting after XBB.1.5 COVID vaccination in humans
]]>
https://biorxiv.org/cgi/content/short/2023.11.28.569129v1?rss=1"
Tortorici, M. A.Addetia, A.Seo, A. J.Brown, J.Sprouse, K.Logue, J.Clarke, E.Franko, N.Chu, H.Veesler, D.2023-11-30doi:10.1101/2023.11.28.569129Cold Spring Harbor Laboratory Press2023-11-30
<![CDATA[
Somatic Mosaicism in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Reveals Widespread Degeneration from Focal Mutations
]]>
https://biorxiv.org/cgi/content/short/2023.11.30.569436v1?rss=1"
Zhou, Z.Kim, J.Huang, A. Y.Nolan, M.Park, J.Doan, R.Shin, T.Miller, M. B.Chhouk, B.Morillo, K.Yeh, R. C.Kenny, C.Neil, J. E.Lee, C.-Z.Ohkubo, T.Ravits, J.Ansorge, O.Ostrow, L. W.Lagier-Tourenne, C.Lee, E. A.Walsh, C. A.2023-12-01doi:10.1101/2023.11.30.569436Cold Spring Harbor Laboratory Press2023-12-01
<![CDATA[
Bioorthogonal labeling enables in situ fluorescence imaging of expressed gas vesicle nanostructures
]]>
https://biorxiv.org/cgi/content/short/2023.11.30.569486v1?rss=1"
Schrunk, E.Dutka, P.Hurt, R. C.Wu, D.Shapiro, M. G.2023-12-01doi:10.1101/2023.11.30.569486Cold Spring Harbor Laboratory Press2023-12-01
<![CDATA[
Structure, interaction, and nervous connectivity of beta cell primary cilia
]]>
https://biorxiv.org/cgi/content/short/2023.12.01.568979v1?rss=1"
Müller, A.Klena, N.Pang, S.Garcia, L. E. G.Sulaymankhil, D.Topcheva, O.Seliskar, M.Mziaut, H.Schöniger, E.Friedland, D.Kipke, N.Kretschmar, S.Münster, C.Weitz, J.Distler, M.Kurth, T.Schmidt, D.Hess, H. F.Xu, C. S.Pigino, G.Solimena, M.2023-12-01doi:10.1101/2023.12.01.568979Cold Spring Harbor Laboratory Press2023-12-01
<![CDATA[
Negative feedback control of hunger circuits by the taste of food
]]>
https://biorxiv.org/cgi/content/short/2023.11.30.569492v1?rss=1"
Aitken, T. J.Ly, T.Shehata, S.Sivakumar, N.La Santa Medina, N.Gray, L. A.Dundar, N.Barnes, C.Knight, Z. A.2023-12-03doi:10.1101/2023.11.30.569492Cold Spring Harbor Laboratory Press2023-12-03
<![CDATA[
Uncoupled substrate binding underlies the evolutionary switch between Na+ and H+-coupled prokaryotic aspartate transporters
]]>
https://biorxiv.org/cgi/content/short/2023.12.03.569786v1?rss=1"
Reddy, K. D.Rasool, B.Akher, F. B.Kutlesic, N.Pant, S.Boudker, O.2023-12-04doi:10.1101/2023.12.03.569786Cold Spring Harbor Laboratory Press2023-12-04
<![CDATA[
Cell-type-specific 3D-genome organization and transcription regulation in the brain
]]>
https://biorxiv.org/cgi/content/short/2023.12.04.570024v1?rss=1"
Liu, S.Zheng, P.Wang, C. Y.Jia, B. B.Zemke, N. R.Ren, B.Zhuang, X.2023-12-05doi:10.1101/2023.12.04.570024Cold Spring Harbor Laboratory Press2023-12-05
<![CDATA[
Imaging neuronal voltage beyond the scattering limit
]]>
https://biorxiv.org/cgi/content/short/2023.12.03.568403v1?rss=1"
Chen, T.-W.Huang, X.-B.Plutkis, S. E.Holland, K. L.Lavis, L. D.Lin, B.-J.2023-12-05doi:10.1101/2023.12.03.568403Cold Spring Harbor Laboratory Press2023-12-05
<![CDATA[
Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation
]]>
https://biorxiv.org/cgi/content/short/2023.12.05.570292v1?rss=1"
Gaudinier, A.Van den Broeck, L.Moreno-Risueno, M.Rodriguez-Mendina, J.Sozzani, R.Brady, S.2023-12-06doi:10.1101/2023.12.05.570292Cold Spring Harbor Laboratory Press2023-12-06
<![CDATA[
A complex of the lipid transport ER proteins TMEM24 and C2CD2 with band 4.1 at cell-cell contacts
]]>
https://biorxiv.org/cgi/content/short/2023.12.06.570396v1?rss=1"
Johnson, B.Iuliano, M.Lam, T.Biederer, T.De Camilli, P.2023-12-06doi:10.1101/2023.12.06.570396Cold Spring Harbor Laboratory Press2023-12-06
<![CDATA[
Rapid, concerted switching of the neural code in inferotemporal cortex
]]>
https://biorxiv.org/cgi/content/short/2023.12.06.570341v1?rss=1"
Shi, Y.Bi, D.Hesse, J. K.Lanfranchi, F. F.Chen, S.Tsao, D. Y.2023-12-06doi:10.1101/2023.12.06.570341Cold Spring Harbor Laboratory Press2023-12-06
<![CDATA[
A niche-derived non-ribosomal peptide triggers planarian sexual development
]]>
https://biorxiv.org/cgi/content/short/2023.12.06.570471v1?rss=1"
Issigonis, M.Browder, K. L.Chen, R.Collins, J. J.Newmark, P. A.2023-12-07doi:10.1101/2023.12.06.570471Cold Spring Harbor Laboratory Press2023-12-07
<![CDATA[
Permanent deconstruction of intracellular primary cilia in differentiating granule cell neurons
]]>
https://biorxiv.org/cgi/content/short/2023.12.07.565988v1?rss=1"
Ott, C. M.Constable, S.White, K.Nguyen, T.Lee, W.-C. A.Lippincott-Schwartz, J.Mukhopadhyay, S.2023-12-08doi:10.1101/2023.12.07.565988Cold Spring Harbor Laboratory Press2023-12-08
<![CDATA[
Electrostatic encoding of genome organization principles within single native nucleosomes
]]>
https://biorxiv.org/cgi/content/short/2023.12.08.570828v1?rss=1"
Park, S.Athreya, A.Carrizo, G.Benning, N.Mitchener, M.Bhanu, N.Garcia, B.Zhang, B.Muir, T. W.Pearce, E.Ha, T.2023-12-09doi:10.1101/2023.12.08.570828Cold Spring Harbor Laboratory Press2023-12-09
<![CDATA[
Mitotic chromosomes harbor cell type and species-specific structural features within a universal looping architecture
]]>
https://biorxiv.org/cgi/content/short/2023.12.08.570796v1?rss=1"
Oomen, M. E.Fox, A. N.Gonzalez, I.Molliex, A.Papadopoulou, T.Navarro, P.Dekker, J.2023-12-09doi:10.1101/2023.12.08.570796Cold Spring Harbor Laboratory Press2023-12-09
<![CDATA[
Umbrella toxin particles produced by Streptomyces block mycelial growth of competing species
]]>
https://biorxiv.org/cgi/content/short/2023.12.09.570830v1?rss=1"
Zhao, Q.Bertolli, S.Park, Y.-J.Tan, Y.Cutler, K. J.Srinivas, P.Asfahl, K. L.Fonseca Garcia, C.Gallagher, L. A.Li, Y.Wang, Y.Coleman-Derr, D.DiMaio, F.Zhang, D.Peterson, S. B.Veesler, D.Mougous, J. D.2023-12-10doi:10.1101/2023.12.09.570830Cold Spring Harbor Laboratory Press2023-12-10
<![CDATA[
Rapid long-distance migration of RPA on single stranded DNA occurs through intersegmental transfer utilizing multivalent interactions
]]>
https://biorxiv.org/cgi/content/short/2023.12.09.570606v1?rss=1"
Pangeni, S.Biswas, G.Kaushik, V.Kuppa, S.Yang, O.Lin, C.-T.Mishra, G.Levy, Y.Antony, E.Ha, T.2023-12-10doi:10.1101/2023.12.09.570606Cold Spring Harbor Laboratory Press2023-12-10
<![CDATA[
Programmed withdrawal of cilia maintenance followed by centriole capping leads to permanent cilia loss during cerebellar granule cell neurogenesis
]]>
https://biorxiv.org/cgi/content/short/2023.12.07.565993v1?rss=1"
Constable, S.Ott, C. M.Lemire, A. L.White, K.Lim, A.Lippincott-Schwartz, J.Mukhopadhyay, S.2023-12-11doi:10.1101/2023.12.07.565993Cold Spring Harbor Laboratory Press2023-12-11
<![CDATA[
Transcriptional complexity in the insect central complex: single nuclei RNA sequencing of adult brain neurons derived from type 2 neuroblasts
]]>
https://biorxiv.org/cgi/content/short/2023.12.10.571022v1?rss=1"
Epiney, D.Chaya, G. M.Dillon, N.Lai, S.-L.doe, c.2023-12-11doi:10.1101/2023.12.10.571022Cold Spring Harbor Laboratory Press2023-12-11
<![CDATA[
RluA is the major mRNA pseudouridine synthase in Escherichia coli
]]>
https://biorxiv.org/cgi/content/short/2023.12.08.570740v1?rss=1"
Schaening Burgos, C.Li, G.-W.Gilbert, W. V.2023-12-12doi:10.1101/2023.12.08.570740Cold Spring Harbor Laboratory Press2023-12-12
<![CDATA[
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin
]]>
https://biorxiv.org/cgi/content/short/2023.12.12.571235v1?rss=1"
Welsh, F. C.Eguia, R. T.Lee, J. M.Haddox, H. K.Galloway, J.Vinh, N. V.Loes, A. N.Huddleston, J.Yu, T. C.Le, M. Q.Nhat, N. T.Thanh, N. T. L.Greninger, A. L.Chu, H. Y.Englund, J. A.Bedford, T.Matsen, F. A.Boni, M. F.Bloom, J. D.2023-12-12doi:10.1101/2023.12.12.571235Cold Spring Harbor Laboratory Press2023-12-12
<![CDATA[
Single molecule studies of the native hair cell mechanosensory transduction complex
]]>
https://biorxiv.org/cgi/content/short/2023.12.11.571162v1?rss=1"
Clark, S.Mitra, J.Elferich, J.Goehring, A.Ge, J.Ha, T.Gouaux, E.2023-12-12doi:10.1101/2023.12.11.571162Cold Spring Harbor Laboratory Press2023-12-12
<![CDATA[
Model Based Inference of Synaptic Plasticity Rules
]]>
https://biorxiv.org/cgi/content/short/2023.12.11.571103v1?rss=1"
Mehta, Y.Tyulmankov, D.Rajagopalan, A. E.Turner, G. C.Fitzgerald, J. E.Funke, J.2023-12-12doi:10.1101/2023.12.11.571103Cold Spring Harbor Laboratory Press2023-12-12
<![CDATA[
A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines
]]>
https://biorxiv.org/cgi/content/short/2023.12.12.571160v1?rss=1"
Lee, J.Stewart, C.Schaefer, A.Leaf, E. M.Park, Y.-J.Asarnow, D.Powers, J. M.Treichel, C.Corti, D.Baric, R.King, N. P.Veesler, D.2023-12-13doi:10.1101/2023.12.12.571160Cold Spring Harbor Laboratory Press2023-12-13
<![CDATA[
Persistence of backtracking by human RNA polymerase II
]]>
https://biorxiv.org/cgi/content/short/2023.12.13.571520v1?rss=1"
Yang, K. B.Rasouly, A.Epshtein, V.Martinez, C.Nguyen, T.Shamovsky, I.Nudler, E.2023-12-14doi:10.1101/2023.12.13.571520Cold Spring Harbor Laboratory Press2023-12-14
<![CDATA[
A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases
]]>
https://biorxiv.org/cgi/content/short/2023.12.13.571473v1?rss=1"
Soni, C.Prywes, N.Hall, M.Savage, D. F.Schepartz, A.Chatterjee, A.2023-12-14doi:10.1101/2023.12.13.571473Cold Spring Harbor Laboratory Press2023-12-14
<![CDATA[
Recent evolution of large offspring size and post-fertilization nutrient provisioning in swordtails
]]>
https://biorxiv.org/cgi/content/short/2023.12.15.571831v1?rss=1"
Payne, C. Y.Ly, D.Rodriguez-Soto, R. A.Powell, D. L.Robles, N. D.Gunn, T. R.Baczenas, J. J.Bergman, A. J.Pollock, A. C.Moran, B. M.Baker, J. C.Reznick, D.Schumer, M.2023-12-15doi:10.1101/2023.12.15.571831Cold Spring Harbor Laboratory Press2023-12-15
<![CDATA[
Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome
]]>
https://biorxiv.org/cgi/content/short/2023.12.14.571752v1?rss=1"
Martin, A.Lopez-Alfonzo, E. M.Saurabh, A.Zarafshan, S.Presse, S.2023-12-15doi:10.1101/2023.12.14.571752Cold Spring Harbor Laboratory Press2023-12-15
<![CDATA[
Opposing effects of pre-existing antibody and memory T cell help on the dynamics of recall germinal centers
]]>
https://biorxiv.org/cgi/content/short/2023.12.15.571936v1?rss=1"
Schiepers, A.van 't Wout, M. F. L.Hobbs, A.Mesin, L.Victora, G. D.2023-12-15doi:10.1101/2023.12.15.571936Cold Spring Harbor Laboratory Press2023-12-15
<![CDATA[
Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9
]]>
https://biorxiv.org/cgi/content/short/2023.12.14.571777v1?rss=1"
100-fold higher genome editing levels. Cryo-EM structures of the wildtype and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome editing activity.
]]>Eggers, A. R.Chen, K.Soczek, K. M.Tuck, O. T.Doherty, E. E.Thornton, B. W.Xu, B.Trinidad, M. I.Doudna, J. A.2023-12-15doi:10.1101/2023.12.14.571777Cold Spring Harbor Laboratory Press2023-12-15
<![CDATA[
Imaging the voltage of neurons distributed across entire brains of larval zebrafish
]]>
https://biorxiv.org/cgi/content/short/2023.12.15.571964v1?rss=1"
Wang, Z.Zhang, J.Symvoulidis, P.Guo, W.Zhang, L.Wilson, M. A.Boyden, E. S.2023-12-16doi:10.1101/2023.12.15.571964Cold Spring Harbor Laboratory Press2023-12-16
<![CDATA[
VPS13B is localized at the cis-trans Golgi complex interface and is a functional partner of FAM177A1
]]>
https://biorxiv.org/cgi/content/short/2023.12.18.572081v1?rss=1"
Ugur, B.Schueder, F.Shin, J.Hanna, M. G.Wu, Y.Leonzino, M.Su, M.McAdow, A. R.Wilson, C. A.Postlethwait, J.Solnica-Krezel, L.Bewersdorf, J.De Camilli, P.2023-12-18doi:10.1101/2023.12.18.572081Cold Spring Harbor Laboratory Press2023-12-18
<![CDATA[
The membrane curvature inducing REEP1 proteins generate a novel ER-derived vesicular compartment
]]>
https://biorxiv.org/cgi/content/short/2023.12.19.572386v1?rss=1"
Shibata, Y.Mazur, E. E.Pan, B.Hernandez, S. V.Zhang, J.Rapoport, T. A.2023-12-19doi:10.1101/2023.12.19.572386Cold Spring Harbor Laboratory Press2023-12-19
<![CDATA[
Phase diversity-based wavefront sensing for fluorescence microscopy
]]>
https://biorxiv.org/cgi/content/short/2023.12.19.572369v1?rss=1"
100-fold faster than comparable methods (corresponding to wavefront sensing on the ~100 ms scale), and sensing and subsequent correction of severe aberrations (RMS wavefront distortion exceeding {lambda}/2), restoring diffraction-limited imaging on extended biological samples.
]]>Johnson, C.Guo, M.Schneider, M. C.Su, Y.Khuon, S. C.Reiser, N.Wu, Y.La Riviere, P. J.Shroff, H.2023-12-19doi:10.1101/2023.12.19.572369Cold Spring Harbor Laboratory Press2023-12-19
<![CDATA[
Bidirectional substrate shuttling between the 26S proteasome and the Cdc48 ATPase promotes protein degradation
]]>
https://biorxiv.org/cgi/content/short/2023.12.20.572403v1?rss=1"
Li, H.Ji, Z.Paulo, J. A.Gygi, S. P.Rapoport, T. A.2023-12-20doi:10.1101/2023.12.20.572403Cold Spring Harbor Laboratory Press2023-12-20
<![CDATA[
Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator
]]>
https://biorxiv.org/cgi/content/short/2023.12.20.572550v1?rss=1"
Ciren, D.Zebell, S.Lippman, Z.2023-12-20doi:10.1101/2023.12.20.572550Cold Spring Harbor Laboratory Press2023-12-20
<![CDATA[
High-throughput computational discovery of inhibitory protein fragments with AlphaFold
]]>
https://biorxiv.org/cgi/content/short/2023.12.19.572389v1?rss=1"
Savinov, A.Swanson, S.Keating, A. E.Li, G.-W.2023-12-20doi:10.1101/2023.12.19.572389Cold Spring Harbor Laboratory Press2023-12-20
<![CDATA[
Identification of a short, single site matriglycan that maintains neuromuscular function in the mouse
]]>
https://biorxiv.org/cgi/content/short/2023.12.20.572361v1?rss=1"
Yang, T.Chandel, I.Gonzales, M.Okuma, H.Prouty, S. J.Zarei, S.Joseph, S.Garringer, K. W.Ocampo Landa, S.Yonekawa, T.Walimbe, A. S.Venzke, D. P.Anderson, M. E.Hord, J. M.Campbell, K. P.2023-12-21doi:10.1101/2023.12.20.572361Cold Spring Harbor Laboratory Press2023-12-21
<![CDATA[
De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles
]]>
https://biorxiv.org/cgi/content/short/2023.12.20.572602v1?rss=1"
An, L.Said, M.Tran, L.Majumder, S.Goreshnik, I.Lee, G. R.Juergens, D.Dauparas, J.Anishchenko, I.Coventry, B.Bera, A. K.Kang, A.Levine, P. M.Alvarez, V.Pillai, A.Norn, C.Feldman, D.Zorine, D.Hicks, D. R.Li, X.Sanchez, M. G.Vafeados, D. K.Salveson, P. J.Vorobieva, A. A.Baker, D.2023-12-21doi:10.1101/2023.12.20.572602Cold Spring Harbor Laboratory Press2023-12-21
<![CDATA[
Atomic context-conditioned protein sequence design using LigandMPNN
]]>
https://biorxiv.org/cgi/content/short/2023.12.22.573103v1?rss=1"
Dauparas, J.Lee, G. R.Pecoraro, R.An, L.Anishchenko, I.Glasscock, C.Baker, D.2023-12-23doi:10.1101/2023.12.22.573103Cold Spring Harbor Laboratory Press2023-12-23
<![CDATA[
Genome evolution is surprisingly predictable after initial hybridization
]]>
https://biorxiv.org/cgi/content/short/2023.12.21.572897v1?rss=1"
Langdon, Q. K.Groh, J. S.Aguillon, S.Powell, D. L.Gunn, T. R.Payne, C. Y.Baczenas, J. J.Donny, A.Dodge, T. O.Du, K.Schartl, M.Rios-Cardenas, O.Gutierrez-Rodriguez, C.Morris, M.Schumer, M.2023-12-23doi:10.1101/2023.12.21.572897Cold Spring Harbor Laboratory Press2023-12-23
<![CDATA[
PEARL-catalyzed peptide bond formation after chain reversal during the biosynthesis of non-ribosomal peptides
]]>
https://biorxiv.org/cgi/content/short/2023.12.23.573212v1?rss=1"
Yu, Y.van der Donk, W.2023-12-23doi:10.1101/2023.12.23.573212Cold Spring Harbor Laboratory Press2023-12-23
<![CDATA[
A neurotransmitter atlas of the nervous system of C.elegans males and hermaphrodites
]]>
https://biorxiv.org/cgi/content/short/2023.12.24.573258v1?rss=1"
Wang, C.Vidal, B.Sural, S.Merritt, D. M.Toker, I. A.Vogt, M. C.Cros, C. C.Hobert, O.2023-12-25doi:10.1101/2023.12.24.573258Cold Spring Harbor Laboratory Press2023-12-25
<![CDATA[
KMT2A oncoproteins induce epigenetic resistance to targeted therapies
]]>
https://biorxiv.org/cgi/content/short/2023.12.29.573681v1?rss=1"
Janssens, D. H.Duran, M.Otto, D. J.Kirkey, D.Yi, J. S.Meshinchi, S.Sarthy, J. F.Ahmad, K.Henikoff, S.2023-12-30doi:10.1101/2023.12.29.573681Cold Spring Harbor Laboratory Press2023-12-30
<![CDATA[
Mitochondrial choline import regulates purine nucleotide pools via SLC25A48
]]>
https://biorxiv.org/cgi/content/short/2023.12.31.573776v1?rss=1"
Verkerke, A. R. P.Shi, X.Abe, I.Gerszten, R. E.Kajimura, S.2024-01-01doi:10.1101/2023.12.31.573776Cold Spring Harbor Laboratory Press2024-01-01
<![CDATA[
A Genome-Wide CRISPR Screen Identifies Sortilin as the Receptor Responsible for Galectin-1 Lysosomal Trafficking
]]>
https://biorxiv.org/cgi/content/short/2024.01.03.574113v1?rss=1"
Donnelly, J.Kamber, R. A.Wisnovsky, S.Roberts, D. S.Peltan, E. L.Bassik, M. C.Bertozzi, C. R.2024-01-03doi:10.1101/2024.01.03.574113Cold Spring Harbor Laboratory Press2024-01-03
<![CDATA[
Compact RNA sensors for increasingly complex functions of multiple inputs
]]>
https://biorxiv.org/cgi/content/short/2024.01.04.572289v1?rss=1"
Choe, C. A.Andreasson, J. O. L.Melaine, F.Kladwang, W.Wu, M. J.Portela, F.Wellington-Oguri, R.Nicol, J. J.Wayment-Steele, H. K.Gotrik, M.Eterna Participants,Kahtri, P.Greenleaf, W. J.Das, R.2024-01-04doi:10.1101/2024.01.04.572289Cold Spring Harbor Laboratory Press2024-01-04
<![CDATA[
Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer's disease microglia
]]>
https://biorxiv.org/cgi/content/short/2024.01.03.574078v1?rss=1"
1000X) gene panel sequencing of 311 prefrontal cortex samples showed enrichment of sSNVs and somatic insertions and deletions (sIndels) in cancer driver genes in AD brain compared to control, with recurrent, and often multiple, mutations in genes implicated in clonal hematopoiesis (CH)8,9. Pathogenic sSNVs were enriched in CSF1R+ microglia of AD brains, and the high proportion of microglia (up to 40%) carrying some sSNVs in cancer driver genes suggests mutation-driven microglial clonal expansion (MiCE). Analysis of single-nucleus RNA sequencing (snRNAseq) from temporal neocortex of 62 additional AD cases and controls exhibited nominally increased mosaic chromosomal alterations (mCAs) associated with CH10,11. Microglia carrying mCA showed upregulated pro-inflammatory genes, resembling the transcriptomic features of disease-associated microglia (DAM) in AD. Our results suggest that somatic driver mutations in microglia are common with normal aging but further enriched in AD brain, driving MiCE with inflammatory and DAM signatures. Our findings provide the first insights into microglial clonal dynamics in AD and identify potential new approaches to AD diagnosis and therapy.
]]>Huang, A. Y.Zhou, Z.Talukdar, M.Miller, M. B.Chhouk, B.Enyenihi, L.Rosen, I.Stronge, E.Zhao, B.Kim, D.Choi, J.Khoshkhoo, S.Kim, J.Ganz, J.Travaglini, K. J.Gabitto, M.Hodge, R. D.Kaplan, E.Lein, E.De Jager, P.Bennett, D. A.Lee, E. A.Walsh, C. A.2024-01-04doi:10.1101/2024.01.03.574078Cold Spring Harbor Laboratory Press2024-01-04
<![CDATA[
Next-generation mapping of the salicylic acid signaling hub and transcriptional cascade
]]>
https://biorxiv.org/cgi/content/short/2024.01.03.574047v1?rss=1"
Powers, J.Zhang, X.Reyes, A. V.Zavaliev, R.Xu, S.-L.Dong, X.2024-01-04doi:10.1101/2024.01.03.574047Cold Spring Harbor Laboratory Press2024-01-04
<![CDATA[
Reconstructing cell histories in space with image-readable base editor recording
]]>
https://biorxiv.org/cgi/content/short/2024.01.03.573434v1?rss=1"
Chadly, D. M.Frieda, K. L.Gui, C.Klock, L.Tran, M.Sui, M. Y.Takei, Y.Bouckaert, R.Lois, C.Cai, L.Elowitz, M. B.2024-01-04doi:10.1101/2024.01.03.573434Cold Spring Harbor Laboratory Press2024-01-04
<![CDATA[
MicroED structure of the C11 cysteine protease Clostripain
]]>
https://biorxiv.org/cgi/content/short/2024.01.04.574240v1?rss=1"
Ruma, Y. N.Bu, G.Gonen, T.2024-01-05doi:10.1101/2024.01.04.574240Cold Spring Harbor Laboratory Press2024-01-05
<![CDATA[
Uncovering the Elusive Structures and Mechanisms of Prevalent Antidepressants
]]>
https://biorxiv.org/cgi/content/short/2024.01.04.574265v1?rss=1"
Lin, J.Bu, G.Unge, J.Gonen, T.2024-01-05doi:10.1101/2024.01.04.574265Cold Spring Harbor Laboratory Press2024-01-05
<![CDATA[
A comprehensive landscape of the zinc-regulated human proteome
]]>
https://biorxiv.org/cgi/content/short/2024.01.04.574225v1?rss=1"
Burger, N.Mittenbuhler, M.Xiao, H.Shin, S.Bozi, L.Wei, S.Sprenger, H.-G.Sun, Y.Zhu, Y.Darabedian, N.Petrocelli, J.Latorre Muro, P.Che, J.Chouchani, E. T.2024-01-05doi:10.1101/2024.01.04.574225Cold Spring Harbor Laboratory Press2024-01-05
<![CDATA[
Retention of an endosymbiont for the production of a single molecule
]]>
https://biorxiv.org/cgi/content/short/2024.01.04.574232v1?rss=1"
Garber, A.Garcia de la Filia Molina, A.Vea, I. M.Mongue, A. J.Ross, L.McCutcheon, J. P.2024-01-05doi:10.1101/2024.01.04.574232Cold Spring Harbor Laboratory Press2024-01-05
<![CDATA[
A historical sequence deletion in a commonly used Bacillus subtilis chromosome integration vector generates undetected loss-of-function mutations
]]>
https://biorxiv.org/cgi/content/short/2024.01.04.574214v1?rss=1"
Dierksheide, K. J.Li, G.-W.2024-01-06doi:10.1101/2024.01.04.574214Cold Spring Harbor Laboratory Press2024-01-06
<![CDATA[
Concerted neuron-astrocyte gene expression declines in aging and schizophrenia
]]>
https://biorxiv.org/cgi/content/short/2024.01.07.574148v1?rss=1"
Ling, E.Nemesh, J.Goldman, M.Kamitaki, N.Reed, N.Handsaker, R. E.Genovese, G.Vogelgsang, J. S.Gerges, S.Kashin, S.Ghosh, S.Esposito, J. M.French, K.Meyer, D.Lutservitz, A.Mullally, C. D.Wysoker, A.Spina, L.Neumann, A.Hogan, M.Ichihara, K.Berretta, S.McCarroll, S. A.2024-01-08doi:10.1101/2024.01.07.574148Cold Spring Harbor Laboratory Press2024-01-08
<![CDATA[
ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism
]]>
https://biorxiv.org/cgi/content/short/2024.01.09.574893v1?rss=1"
Rashan, E. H.Bartlett, A. K.Khana, D. B.Zhang, J.Jain, R.Smith, A. J.Baker, Z. N.Cook, T.Caldwell, A.Chevalier, A. R.Pfleger, B. F.Yuan, P.Amador-Noguez, D.Simcox, J. A.Pagliarini, D. J.2024-01-09doi:10.1101/2024.01.09.574893Cold Spring Harbor Laboratory Press2024-01-09
<![CDATA[
Human coronavirus HKU1 recognition of the TMPRSS2 host receptor
]]>
https://biorxiv.org/cgi/content/short/2024.01.09.574565v1?rss=1"
McCallum, M.Park, Y.-J.Stewart, C.Sprouse, K. R.Brown, J.Tortorici, M. A.Gibson, C.Wong, E.Ieven, M.Telenti, A.Veesler, D.2024-01-09doi:10.1101/2024.01.09.574565Cold Spring Harbor Laboratory Press2024-01-09
<![CDATA[
Prevotella are major contributors of sialidases in the human vaginal microbiome.
]]>
https://biorxiv.org/cgi/content/short/2024.01.09.574895v1?rss=1"
Pelayo, P.Hussain, F. A.Werlang, C. A.Wu, C.Woolston, B. M.Ribbeck, K.Kwon, D. S.Balskus, E. P.2024-01-09doi:10.1101/2024.01.09.574895Cold Spring Harbor Laboratory Press2024-01-09
<![CDATA[
Song Torrent: A modular, open-source 96-chamber audio and video recording apparatus with optogenetic activation and inactivation capabilities for Drosophila
]]>
https://biorxiv.org/cgi/content/short/2024.01.09.574712v1?rss=1"
Sawtelle, S.Narayan, L.Ding, Y.Kim, E.Berhman, E. L.Lillvis, J. L.Kawase, T.Stern, D. L.2024-01-10doi:10.1101/2024.01.09.574712Cold Spring Harbor Laboratory Press2024-01-10
<![CDATA[
A split-GAL4 driver line resource for Drosophila CNS cell types
]]>
https://biorxiv.org/cgi/content/short/2024.01.09.574419v1?rss=1"
Meissner, G. W.Vannan, A.Jeter, J.Atkins, M.Bowers, S.Close, K.DePasquale, G. M.Dorman, Z.Forster, K.Beringer, J. A.Gibney, T. V.Gulati, A.Hausenfluck, J. H.He, Y.Henderson, K.Johnson, L.Johnston, R. M.Ihrke, G.Iyer, N.Lazarus, R.Lee, K.Li, H.-H.Liaw, H.-P.Melton, B.Miller, S.Motaher, R.Novak, A.Ogundeyi, O.Petruncio, A.Price, J.Protopapas, S.Tae, S.Tata, A.Taylor, J.Vorimo, R.Yarbrough, B.Zeng, K. X.Zugates, C. T.Dionne, H.Angstadt, C.Ashley, K.Cavallaro, A.Dang, T.Gonzalez, G. A.Hibbard, K. L.Huang, C.2024-01-10doi:10.1101/2024.01.09.574419Cold Spring Harbor Laboratory Press2024-01-10
<![CDATA[
SARS-CoV-2 papain-like protease activates nociceptors to drive sneeze and pain
]]>
https://biorxiv.org/cgi/content/short/2024.01.10.575114v1?rss=1"
Mali, S. S.Silva, R.Gong, Z.Cronce, M.Vo, U.Vuong, C.Moayedi, Y.Cox, J. S.Bautista, D. M.2024-01-11doi:10.1101/2024.01.10.575114Cold Spring Harbor Laboratory Press2024-01-11
<![CDATA[
Epigenetic priming of embryonic lineages in the mammalian epiblast
]]>
https://biorxiv.org/cgi/content/short/2024.01.11.575188v1?rss=1"
Sendra, M.McDole, K.Jimenez-Carretero, D.de Dios-Hourcade, J.Temino Valbuena, S.Raiola, M.Guignard, L.Keller, P. J.Sanchez-Cabo, F.Dominguez, J. N.Torres, M.2024-01-11doi:10.1101/2024.01.11.575188Cold Spring Harbor Laboratory Press2024-01-11
<![CDATA[
RNA polymerase II-mediated rDNA transcription mediates rDNA copy number expansion in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2024.01.11.575146v1?rss=1"
Watase, G. J.Yamashita, Y. M.2024-01-11doi:10.1101/2024.01.11.575146Cold Spring Harbor Laboratory Press2024-01-11
<![CDATA[
D-type cyclins regulate DNA mismatch repair in the G1 and S phases of the cell cycle, maintaining genome stability
]]>
https://biorxiv.org/cgi/content/short/2024.01.12.575420v1?rss=1"
Rona, G.Miwatani-Minter, B.Zhang, Q.Goldberg, H. V.Kerzhnerman, M. A.Howard, J. B.Simoneschi, D.Lane, E.Hobbs, J. W.Sassani, E.Wang, A. A.Keegan, S.Laverty, D. J.Piett, C. G.Pongor, L. S.Xu, M. L.Andrade, J.Thomas, A.Sicinski, P.Askenazi, M.Ueberheide, B.Fenyo, D.Nagel, Z. D.Pagano, M.2024-01-13doi:10.1101/2024.01.12.575420Cold Spring Harbor Laboratory Press2024-01-13
<![CDATA[
Eliminating the missing cone challenge through innovative approaches
]]>
https://biorxiv.org/cgi/content/short/2024.01.11.575283v1?rss=1"
Gillman, C.Bu, G.Danelius, E.Hattne, J.Nannenga, B.Gonen, T.2024-01-14doi:10.1101/2024.01.11.575283Cold Spring Harbor Laboratory Press2024-01-14
<![CDATA[
The RNA polymerase II general transcription factor TFIIB is a target for transcriptome control during cellular stress and viral infection
]]>
https://biorxiv.org/cgi/content/short/2024.01.16.575933v1?rss=1"
View larger version (22K):
org.highwire.dtl.DTLVardef@8c8db7org.highwire.dtl.DTLVardef@1ac2421org.highwire.dtl.DTLVardef@7828baorg.highwire.dtl.DTLVardef@b9de0a_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementTranscription by RNA polymerase II (RNAPII) synthesizes all cellular protein-coding mRNA. Many cellular stressors and viral infections dampen RNAPII activity, though the processes underlying this are not fully understood. Here we describe a two-pronged degradation strategy by which cells respond to stress by depleting the abundance of the key RNAPII general transcription factor, TFIIB. We further demonstrate that an oncogenic human gammaherpesvirus antagonizes this process, retaining enough TFIIB to support its own robust viral transcription. Thus, modulation of RNAPII machinery plays a crucial role in dictating the outcome of cellular perturbation.
]]>Gulyas, L.Glaunsinger, B.2024-01-17doi:10.1101/2024.01.16.575933Cold Spring Harbor Laboratory Press2024-01-17
<![CDATA[
Structural Insights into the DNA-Binding Mechanism of BCL11A: The Integral Role of ZnF6
]]>
https://biorxiv.org/cgi/content/short/2024.01.17.576058v1?rss=1"
Viennet, T.Yin, M.Jayaraj, A.Kim, W.Sun, Z.-Y. J.Fujiwara, Y.Zhang, K.Seruggia, D.Seo, H.-S.Dhe-Paganon, S.Orkin, S. H.Arthanari, H.2024-01-20doi:10.1101/2024.01.17.576058Cold Spring Harbor Laboratory Press2024-01-20
<![CDATA[
Integrated cancer cell-specific single-cell RNA-seq datasets of immune checkpoint blockade-treated patients
]]>
https://biorxiv.org/cgi/content/short/2024.01.17.576110v1?rss=1"
Gondal, M. N.Cieslik, M.Chinnaiyan, A. M.2024-01-22doi:10.1101/2024.01.17.576110Cold Spring Harbor Laboratory Press2024-01-22
<![CDATA[
Constraints on the Emergence of RNA through Non-Templated Primer Extension with Mixtures of Potentially Prebiotic Nucleotides
]]>
https://biorxiv.org/cgi/content/short/2024.01.21.576316v1?rss=1"
Jia, X.Zhang, S. J.Zhou, L.Szostak, J. W.2024-01-22doi:10.1101/2024.01.21.576316Cold Spring Harbor Laboratory Press2024-01-22
<![CDATA[
Multiplex generation and single cell analysis of structural variants in a mammalian genome
]]>
https://biorxiv.org/cgi/content/short/2024.01.22.576756v1?rss=1"
Pinglay, S.Lalanne, J.-B.Daza, R. M.Koeppel, J.Li, X.Lee, D. S.Shendure, J.2024-01-23doi:10.1101/2024.01.22.576756Cold Spring Harbor Laboratory Press2024-01-23
<![CDATA[
Birth of new protein folds and functions in the virome
]]>
https://biorxiv.org/cgi/content/short/2024.01.22.576744v1?rss=1"
25% of unannotated viral proteins, including those with roles in the evasion of innate immunity. In particular, RNA ligase T- (ligT) like phosphodiesterases were found to resemble phage-encoded proteins that hydrolyze the host immune-activating cyclic dinucleotides 33 and 23 cyclic G-A monophosphate (cGAMP). Experimental analysis showed that ligT homologs encoded by avian poxviruses likewise hydrolyze 23 cGAMP, showing that ligT-mediated targeting of cGAMP is an evolutionarily conserved mechanism of immune evasion present in both bacteriophage and eukaryotic viruses. Together, the viral protein structural database and analytics presented here afford new opportunities to identify mechanisms of virus-host interactions that are common across the virome.
]]>Nomburg, J.Price, N.Doudna, J. A.2024-01-23doi:10.1101/2024.01.22.576744Cold Spring Harbor Laboratory Press2024-01-23
<![CDATA[
FicD Sensitizes Cellular Response to Glucose Fluctuations in Mouse Embryonic Fibroblasts
]]>
https://biorxiv.org/cgi/content/short/2024.01.22.576705v1?rss=1"
Gulen, B.Kinch, L. N.Servage, K. A.Blevins, A.Stewart, N. M.Gray, H. F.Casey, A. K.Orth, K.2024-01-23doi:10.1101/2024.01.22.576705Cold Spring Harbor Laboratory Press2024-01-23
<![CDATA[
Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development
]]>
https://biorxiv.org/cgi/content/short/2024.01.23.576835v1?rss=1"
Kaplan, H. S.Logeman, B. L.Zhang, K.Santiago, C.Sohail, N.Naumenko, S.Ho Sui, S. J.Ginty, D. D.Ren, B.Dulac, C.2024-01-23doi:10.1101/2024.01.23.576835Cold Spring Harbor Laboratory Press2024-01-23
<![CDATA[
Phenotypic screening of covalent compound libraries identifies chloromethyl ketone antibiotics and MiaA as a new target
]]>
https://biorxiv.org/cgi/content/short/2024.01.22.576576v1?rss=1"
View larger version (21K):
org.highwire.dtl.DTLVardef@8d6420org.highwire.dtl.DTLVardef@a89d44org.highwire.dtl.DTLVardef@1ed0ae2org.highwire.dtl.DTLVardef@1659d3e_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Jin, Y.Jana, S.Abbasov, M.Lin, H.2024-01-23doi:10.1101/2024.01.22.576576Cold Spring Harbor Laboratory Press2024-01-23
<![CDATA[
Targeting the mSWI/SNF Complex in POU2F-POU2AF Transcription Factor-Driven Malignancies
]]>
https://biorxiv.org/cgi/content/short/2024.01.22.576669v1?rss=1"
He, T.Xiao, L.Qiao, Y.Klingbeil, O.Young, E.Wu, X. S.Mannan, R.Mahapatra, S.Eyunni, S.Tien, J. C.-Y.Wang, X.Zheng, Y.Kim, N.Zheng, H.Hou, S.Su, F.Miner, S. J.Mehra, R.Cao, X.Abbineni, C.Samajdar, S.Ramachandra, M.Parolia, A.Vakoc, C. R.Chinnaiyan, A. M.2024-01-25doi:10.1101/2024.01.22.576669Cold Spring Harbor Laboratory Press2024-01-25
<![CDATA[
Elucidation of chalkophomycin biosynthesis reveals N-hydroxypyrrole-forming enzymes
]]>
https://biorxiv.org/cgi/content/short/2024.01.24.577118v1?rss=1"
Crooke, A. M.Chand, A. K.Balskus, E. P.2024-01-25doi:10.1101/2024.01.24.577118Cold Spring Harbor Laboratory Press2024-01-25
<![CDATA[
Spyglass: a data analysis framework for reproducible and shareable neuroscience research
]]>
https://biorxiv.org/cgi/content/short/2024.01.25.577295v1?rss=1"
Lee, K. H.Denovellis, E. L.Ly, R.Magland, J.Soules, J.Comrie, A. E.Gramling, D. P.Guidera, J. A.Nevers, R.Adenekan, P.Brozdowski, C.Bray, S.Monroe, E.Bak, J. H.Coulter, M.Sun, X.Tritt, A.Oliver Ruebel, O.Nguyen, T.Yatsenko, D.Chu, J.Kemere, C.Garcia, S.Buccino, A.Frank, L. M.2024-01-26doi:10.1101/2024.01.25.577295Cold Spring Harbor Laboratory Press2024-01-26
<![CDATA[
Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake
]]>
https://biorxiv.org/cgi/content/short/2024.01.25.577315v1?rss=1"
Tan, H. L.Yin, L.Tan, Y.Ivanov, J.Plucinska, K.Ilanges, A.Herb, B. R.Wang, P.Kosse, C.Cohen, P.Lin, D.Friedman, J. M.2024-01-26doi:10.1101/2024.01.25.577315Cold Spring Harbor Laboratory Press2024-01-26
<![CDATA[
Highly specific intracellular ubiquitination of a small molecule
]]>
https://biorxiv.org/cgi/content/short/2024.01.26.577493v1?rss=1"
Li, W.Garcia-Rivera, E. M.Mitchell, D. C.Chick, J. M.Maetani, M.Knapp, J. M.Matthews, G. M.Shirasaki, R.de Matos Simoes, R.Viswanathan, V.Pulice, J. L.Rees, M. G.Roth, J. A.Gygi, S. P.Mitsiades, C. S.Kadoch, C.Schreiber, S. L.Ostrem, J. M. L.2024-01-28doi:10.1101/2024.01.26.577493Cold Spring Harbor Laboratory Press2024-01-28
<![CDATA[
Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)
]]>
https://biorxiv.org/cgi/content/short/2024.01.26.577275v1?rss=1"
90% of individuals, leading to the species designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species recovery.
]]>Wooldridge, B.Orland, C.Enbody, E.Escalona, M.Mirchandani, C. D.Corbett-Detig, R.Kapp, J. D.Fletcher, N.Ammann, K.Raimondi, P.Shapiro, B.2024-01-29doi:10.1101/2024.01.26.577275Cold Spring Harbor Laboratory Press2024-01-29
<![CDATA[
Distributed fMRI dynamics predict distinct EEG rhythms across sleep and wakefulness
]]>
https://biorxiv.org/cgi/content/short/2024.01.29.577429v1?rss=1"
Jacob, L. P. L.Bailes, S. M.Williams, S. D.Stringer, C.Lewis, L. D.2024-01-30doi:10.1101/2024.01.29.577429Cold Spring Harbor Laboratory Press2024-01-30
<![CDATA[
Computational basis of hierarchical and counterfactual information processing
]]>
https://biorxiv.org/cgi/content/short/2024.01.30.578076v1?rss=1"
Ramadan, M.Tang, C.Watters, N.Jazayeri, M.2024-02-01doi:10.1101/2024.01.30.578076Cold Spring Harbor Laboratory Press2024-02-01
<![CDATA[
BRD4-mediated epigenetic regulation of endoplasmic reticulum-mitochondria contact sites is governed by the mitochondrial complex III
]]>
https://biorxiv.org/cgi/content/short/2024.02.02.578646v1?rss=1"
Chen, B.Lynn-Nguyen, T. M.Jadhav, P.Halligan, B. S.Rossiter, N. J.Guerra, R. M.Koshkin, S.Koo, I.Morlacchi, P.Hanna, D. A.Lin, J.Banerjee, R.Pagliarini, D.Patterson, A. D.Mosalaganti, S.Sexton, J.Cali, T.Lyssiotis, C. A.Shah, Y. M.2024-02-04doi:10.1101/2024.02.02.578646Cold Spring Harbor Laboratory Press2024-02-04
<![CDATA[
Enhancing mitochondrial pyruvate metabolism ameliorates myocardial ischemic reperfusion injury.
]]>
https://biorxiv.org/cgi/content/short/2024.02.01.577463v1?rss=1"
View larger version (38K):
org.highwire.dtl.DTLVardef@1a7a9b8org.highwire.dtl.DTLVardef@779e0aorg.highwire.dtl.DTLVardef@128d1f3org.highwire.dtl.DTLVardef@efc1bb_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Visker, J. R.Cluntun, A. A.Velasco-Silva, J. N.Eberhardt, D. R.Shankar, T. S.Hamouche, R.Ling, J.Kwak, H.Hillas, Y.Aist, I.Tseliou, E.Navankasattusas, S.Chaudhuri, D.Ducker, G. S.Drakos, S. G.Rutter, J.2024-02-04doi:10.1101/2024.02.01.577463Cold Spring Harbor Laboratory Press2024-02-04
<![CDATA[
Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex
]]>
https://biorxiv.org/cgi/content/short/2024.02.05.579020v1?rss=1"
Carr, C. R.Crawford, K. H.Murphy, M.Galloway, J. G.Haddox, H. K.Matsen, F. A.Andersen, K. G.King, N. P.Bloom, J. D.2024-02-06doi:10.1101/2024.02.05.579020Cold Spring Harbor Laboratory Press2024-02-06
<![CDATA[
A Functional and Non-Homuncular Representation of the Larynx in the Primary Motor Cortex of Mice, a Vocal Non-Learner
]]>
https://biorxiv.org/cgi/content/short/2024.02.05.579004v1?rss=1"
Vargas, C. D. M.Agravat, R. K.Waidmann, E. N.Bochalis, C.Bermudez, H.Giannakopoulos, T.Jarvis, E. D.2024-02-06doi:10.1101/2024.02.05.579004Cold Spring Harbor Laboratory Press2024-02-06
<![CDATA[
Interplay of condensation and chromatin binding underlies BRD4 targeting
]]>
https://biorxiv.org/cgi/content/short/2024.02.07.579384v1?rss=1"
Strom, A. R.Eeftens, J. M.Polyachenko, Y.Weaver, C. J.Watanabe, H.-F.Bracha, D.Orlovsky, N. D.Jumper, C. C.Jacobs, W. M.Brangwynne, C. P.2024-02-07doi:10.1101/2024.02.07.579384Cold Spring Harbor Laboratory Press2024-02-07
<![CDATA[
Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications
]]>
https://biorxiv.org/cgi/content/short/2024.02.09.579730v1?rss=1"
Cookis, T.Lydecker, A.Sauer, P. V.Kasinath, V.Nogales, E.2024-02-10doi:10.1101/2024.02.09.579730Cold Spring Harbor Laboratory Press2024-02-10
<![CDATA[
Unselfish meiotic drive maintains heterozygosity in a parthenogenetic ant
]]>
https://biorxiv.org/cgi/content/short/2024.02.09.579553v1?rss=1"
Lacy, K. D.Hart, T.Kronauer, D. J. C.2024-02-12doi:10.1101/2024.02.09.579553Cold Spring Harbor Laboratory Press2024-02-12
<![CDATA[
Cellpose3: one-click image restoration for improved cellular segmentation
]]>
https://biorxiv.org/cgi/content/short/2024.02.10.579780v1?rss=1"
Stringer, C.Pachitariu, M.2024-02-12doi:10.1101/2024.02.10.579780Cold Spring Harbor Laboratory Press2024-02-12
<![CDATA[
The Cas10 nuclease activity relieves host dormancy to facilitate spacer acquisition and retention during type III-A CRISPR immunity
]]>
https://biorxiv.org/cgi/content/short/2024.02.11.579731v1?rss=1"
Aviram, N.Shilton, A.Lyn, N.Reis, B. S.Brivanlou, A.Marraffini, L. A.2024-02-12doi:10.1101/2024.02.11.579731Cold Spring Harbor Laboratory Press2024-02-12
<![CDATA[
Induction and in silico staging of human gastruloids with neural tube, segmented somites & advanced cell types
]]>
https://biorxiv.org/cgi/content/short/2024.02.10.579769v1?rss=1"
Hamazaki, N.Yang, W.Kubo, C.Qiu, C.Martin, B. K.Garge, R. K.Regalado, S. G.Nichols, E.Lee, C.Daza, R. M.Srivatsan, S.Shendure, J.2024-02-12doi:10.1101/2024.02.10.579769Cold Spring Harbor Laboratory Press2024-02-12
<![CDATA[
Wnt signaling modulates the response to DNA damage in the Drosophila wing imaginal disc by regulating the EGFR pathway
]]>
https://biorxiv.org/cgi/content/short/2024.02.13.580041v1?rss=1"
Ewen-Campen, B.Perrimon, N.2024-02-13doi:10.1101/2024.02.13.580041Cold Spring Harbor Laboratory Press2024-02-13
<![CDATA[
Advanced Surface Passivation for High-Sensitivity Studies of Biomolecular Condensates
]]>
https://biorxiv.org/cgi/content/short/2024.02.12.580000v1?rss=1"
Yao, R.-W.Rosen, M. K.2024-02-13doi:10.1101/2024.02.12.580000Cold Spring Harbor Laboratory Press2024-02-13
<![CDATA[
The Drosophila histone methyl-transferase SET1 coordinates multiple signaling pathways in regulating male germline stem cell maintenance and differentiation
]]>
https://biorxiv.org/cgi/content/short/2024.02.14.580277v1?rss=1"
Vidaurre, V.Song, A.Li, T.Ku, W. L.Zhao, K.Qian, J.Chen, X.2024-02-14doi:10.1101/2024.02.14.580277Cold Spring Harbor Laboratory Press2024-02-14
<![CDATA[
Postdoctoral Scholar Recruitment and Hiring Practices in STEM: A Pilot Study
]]>
https://biorxiv.org/cgi/content/short/2024.02.12.580018v1?rss=1"
Heirwegh, M.Rees, D. C.Malcom-Piqueux, L.2024-02-14doi:10.1101/2024.02.12.580018Cold Spring Harbor Laboratory Press2024-02-14
<![CDATA[
Pheromone representation in the ant antennal lobe changes with age
]]>
https://biorxiv.org/cgi/content/short/2024.02.13.580193v1?rss=1"
Hart, T.Lopes, L. E.Frank, D. D.Kronauer, D. J. C.2024-02-14doi:10.1101/2024.02.13.580193Cold Spring Harbor Laboratory Press2024-02-14
<![CDATA[
In vitro function, assembly, and interaction of primary cell wall cellulose synthase homotrimers
]]>
https://biorxiv.org/cgi/content/short/2024.02.13.580128v1?rss=1"
Pallinti, P.Ho, R.Zimmer, J.2024-02-15doi:10.1101/2024.02.13.580128Cold Spring Harbor Laboratory Press2024-02-15
<![CDATA[
Epigenetic repression of cFos supports sequential formation of distinct spatial memories
]]>
https://biorxiv.org/cgi/content/short/2024.02.16.580703v1?rss=1"
Franzelin, A.Lamothe-Molina, P. J.Gee, C. E.Formozov, A.Schreiter, E. R.Morellini, F.Oertner, T. G.2024-02-21doi:10.1101/2024.02.16.580703Cold Spring Harbor Laboratory Press2024-02-21
<![CDATA[
TFEB controls syncytiotrophoblast differentiation
]]>
https://biorxiv.org/cgi/content/short/2024.02.20.581304v1?rss=1"
Esbin, M. N.Dahal, L.Fan, V. B.McKenna, J. K.Yin, E.Darzacq, X.Tjian, R.2024-02-21doi:10.1101/2024.02.20.581304Cold Spring Harbor Laboratory Press2024-02-21
<![CDATA[
Behavioral fingerprinting of the naked mole-rat uncovers signatures of eusociality and social touch
]]>
https://biorxiv.org/cgi/content/short/2024.02.21.581483v1?rss=1"
Schwark, R.Ogundare, S.Weinreb, C.Sheng, P.Foster, W.Toussaint, A.Chang, P.Tsai, Y.-Y.Comfere, M.Arnold, A.Guadagnino, A.McCloskey, D.Schaffer, E.Rajan, K.Datta, S. R.Abdus-Saboor, I.2024-02-22doi:10.1101/2024.02.21.581483Cold Spring Harbor Laboratory Press2024-02-22
<![CDATA[
Nanobody-targeted conditional antimicrobial therapeutics
]]>
https://biorxiv.org/cgi/content/short/2024.02.20.580917v1?rss=1"
Ngambenjawong, C.Ko, H.Pishesha, N.Ploegh, H. L.Bhatia, S. N.2024-02-22doi:10.1101/2024.02.20.580917Cold Spring Harbor Laboratory Press2024-02-22
<![CDATA[
Diaminopurine in Nonenzymatic RNA Template Copying
]]>
https://biorxiv.org/cgi/content/short/2024.02.20.581310v1?rss=1"
Jia, X.Fang, Z.Kim, S. C.Ding, D.Zhou, L.Szostak, J. W.2024-02-22doi:10.1101/2024.02.20.581310Cold Spring Harbor Laboratory Press2024-02-22
<![CDATA[
Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time
]]>
https://biorxiv.org/cgi/content/short/2024.02.21.581474v1?rss=1"
Satterlee, J. W.Alonso, D.Gramazio, P.Jenike, K. M.He, J.Arrones, A.Villanueva, G.Plazas, M.Ramakrishnan, S.Benoit, M.Gentile, I.Hendelman, A.Shohat, H.Fitzgerald, B.Robitaille, G. M.Green, Y.Swartwood, K.Passalacqua, M. J.Gagnon, E.Hilgenhof, R.Huggins, T. D.Eizenga, G. C.Gur, A.Rutten, T.Stein, N.Yao, S.Bellot, C.Bendahmane, M.Frary, A.Knapp, S.Sarkinen, T.Gillis, J.Van Eck, J.Schatz, M. C.Eshed, Y.Prohens, J.Vilanova, S.Lippman, Z. B.2024-02-22doi:10.1101/2024.02.21.581474Cold Spring Harbor Laboratory Press2024-02-22
<![CDATA[
Molecular and Cellular Mechanisms of Teneurin Signaling in Synaptic Partner Matching
]]>
https://biorxiv.org/cgi/content/short/2024.02.23.581689v1?rss=1"
Xu, C.Li, Z.Lyu, C.Hu, Y.McLaughlin, C.Wong, K. K. L.Xie, Q.Luginbuhl, D. J.Li, H.Udeshi, N.Svinkina, T.Mani, D. R.Carr, S. A.Han, S.Li, T.Li, Y.Guajardo, R.Ting, A. Y.Li, J.Luo, L.2024-02-23doi:10.1101/2024.02.23.581689Cold Spring Harbor Laboratory Press2024-02-23
<![CDATA[
The Dorsal Column Nuclei Scales Mechanical Allodynia During Neuropathic Pain
]]>
https://biorxiv.org/cgi/content/short/2024.02.20.581208v1?rss=1"
Upadhyay, A.Gradwell, M. A.Vajtay, T. J.Conner, J.Sayal, A. A.Azadegan, C.Patel, K. R.Thackray, J. K.Bohic, M.Imai, F.Ogundare, S. O.Yoshida, Y.Abdus-Saboor, I.Azim, E.Abraira, V. E. G.2024-02-23doi:10.1101/2024.02.20.581208Cold Spring Harbor Laboratory Press2024-02-23
<![CDATA[
A series of spontaneously blinking dyes for super-resolution microscopy
]]>
https://biorxiv.org/cgi/content/short/2024.02.23.581625v1?rss=1"
Holland, K. L.Plutkis, S. E.Daugird, T. A.Sau, A.Grimm, J. B.English, B. P.Zheng, Q.Dave, S.Rahman, F.Xie, L.Dong, P.Tkachuk, A. N.Brown, T. A.Singer, R. H.Liu, Z. J.Galbraith, C. G.Musser, S. M.Legant, W. R.Lavis, L. D.2024-02-24doi:10.1101/2024.02.23.581625Cold Spring Harbor Laboratory Press2024-02-24
<![CDATA[
Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation
]]>
https://biorxiv.org/cgi/content/short/2024.02.24.581662v1?rss=1"
Vassallo, C. N.Doering, C. R.Laub, M. T.2024-02-24doi:10.1101/2024.02.24.581662Cold Spring Harbor Laboratory Press2024-02-24
<![CDATA[
Complete chromosome 21 centromere sequences from a Down syndrome family reveal size asymmetry and differences in kinetochore attachment
]]>
https://biorxiv.org/cgi/content/short/2024.02.25.581464v1?rss=1"
10-fold) is unique of T21 (p-value=0.003), suggesting that this feature may represent a genetic risk factor for a subset of families with free T21. Additionally, phylogenetic reconstruction reveals that human chr21 has been particularly prone to such variation with some of the biggest size differences occurring over the last [~]17 thousand years of human evolution.
]]>Mastrorosa, F. K.Rozanski, A. N.Harvey, W. T.Knuth, J.Garcia, G.Munson, K. M.Hoekzema, K.Logsdon, G. A.Eichler, E. E.2024-02-26doi:10.1101/2024.02.25.581464Cold Spring Harbor Laboratory Press2024-02-26
<![CDATA[
Ribonanza: deep learning of RNA structure through dual crowdsourcing
]]>
https://biorxiv.org/cgi/content/short/2024.02.24.581671v1?rss=1"
He, S.Huang, R.Townley, J.Kretsch, R. C.Karagianes, T. G.Cox, D. B. T.Blair, H.Penzar, D.Vyaltsev, V.Aristova, E.Zinkevich, A.Bakulin, A.Sohn, H.Krstevski, D.Fukui, T.Tatematsu, F.Uchida, Y.Jang, D.Lee, J. S.Shieh, R.Ma, T.Martynov, E.Shugaev, M. V.Bukhari, H. S. T.Fujikawa, K.Onodera, K.Henkel, C.Ron, S.Romano, J.Nicol, J. J.Nye, G. P.Wu, Y.Choe, C.Reade, W.Eterna participants,Das, R.2024-02-27doi:10.1101/2024.02.24.581671Cold Spring Harbor Laboratory Press2024-02-27
<![CDATA[
Distinct streams for supervised and unsupervised learning in the visual cortex
]]>
https://biorxiv.org/cgi/content/short/2024.02.25.581990v1?rss=1"
Zhong, L.Baptista, S.Gattoni, R.Arnold, J.Flickinger, D.Stringer, C.Pachitariu, M.2024-02-27doi:10.1101/2024.02.25.581990Cold Spring Harbor Laboratory Press2024-02-27
<![CDATA[
NSD2 is a requisite subunit of the AR/FOXA1 neo-enhanceosome in promoting prostate tumorigenesis
]]>
https://biorxiv.org/cgi/content/short/2024.02.22.581560v1?rss=1"
Parolia, A.Eyunni, S.Verma, B. K.Young, E.Liu, L.George, J.Aras, S.Das, C. K.Mannan, R.ur Rasool, R.Luo, J.Carson, S. E.Mitchell-Velasquez, E.Liu, Y.Xiao, L.Gajjala, P. R.Jaber, M.He, T.Qiao, Y.Pang, M.Zhang, Y.Alhusayan, M.Cao, X.Tavana, O.Hou, C.Wang, Z.Ding, K.Chinnaiyan, A. M.Asangani, I. A.2024-02-27doi:10.1101/2024.02.22.581560Cold Spring Harbor Laboratory Press2024-02-27
<![CDATA[
Pre-existing visual responses in a projection-defined dopamine population explain individual learning trajectories
]]>
https://biorxiv.org/cgi/content/short/2024.02.26.582199v1?rss=1"
Pan Vazquez, A.Sanchez Araujo, Y.McMannon, B.Louka, M.Bandi, A.Haetzel, L.International Brain Laboratory, n.Pillow, J. W.Daw, N. D.Witten, I.2024-02-28doi:10.1101/2024.02.26.582199Cold Spring Harbor Laboratory Press2024-02-28
<![CDATA[
The microbiome interacts with the circadian clock and dietary composition to regulate metabolite cycling in the gut
]]>
https://biorxiv.org/cgi/content/short/2024.02.29.582770v1?rss=1"
Zhang, Y.Li, Y.Noya, S. B.Sehgal, A.2024-02-29doi:10.1101/2024.02.29.582770Cold Spring Harbor Laboratory Press2024-02-29
<![CDATA[
SIRT2-Mediated ACSS2 K271 Deacetylation Suppresses Lipogenesis Under Nutrient Stress
]]>
https://biorxiv.org/cgi/content/short/2024.02.27.582293v1?rss=1"
Karim, R.Teng, W.Lin, H.2024-02-29doi:10.1101/2024.02.27.582293Cold Spring Harbor Laboratory Press2024-02-29
<![CDATA[
Hachiman is a genome integrity sensor
]]>
https://biorxiv.org/cgi/content/short/2024.02.29.582594v1?rss=1"
Tuck, O. T.Adler, B. A.Armbruster, E. G.Lahiri, A.Hu, J. J.Zhou, J.Pogliano, J.Doudna, J. A.2024-02-29doi:10.1101/2024.02.29.582594Cold Spring Harbor Laboratory Press2024-02-29
<![CDATA[
Functional overlap between the mammalian SAR1A and SAR1B paralogs in vivo
]]>
https://biorxiv.org/cgi/content/short/2024.02.27.582310v1?rss=1"
Tang, V. T.Xiang, J.Chen, Z.McCormick, J.Abbineni, P.Chen, X.-W.Hoenerhoff, M.Emmer, B. T.Khoriaty, R.Lin, J. D.Ginsburg, D.2024-02-29doi:10.1101/2024.02.27.582310Cold Spring Harbor Laboratory Press2024-02-29
<![CDATA[
Genome concentration limits cell growth and modulates proteome composition in Escherichia coli
]]>
https://biorxiv.org/cgi/content/short/2024.02.26.582181v1?rss=1"
Makela, J.Papagiannakis, A.Lin, W.-H.Lanz, M. C.Glenn, S.Swaffer, M.Marinov, G. K.Skotheim, J. M.Jacobs-Wagner, C.2024-02-29doi:10.1101/2024.02.26.582181Cold Spring Harbor Laboratory Press2024-02-29
<![CDATA[
Architecture and flexibility of native kinetochores revealed by structural studies utilizing a thermophilic yeast
]]>
https://biorxiv.org/cgi/content/short/2024.02.28.582571v1?rss=1"
Barrero, D. J.Wijeratne, S. S.Zhao, X.Cunningham, G. F.Yan, R.Nelson, C. R.Arimura, Y.Funabiki, H.Asbury, C. L.Yu, Z.Subramanian, R.Biggins, S.2024-03-01doi:10.1101/2024.02.28.582571Cold Spring Harbor Laboratory Press2024-03-01
<![CDATA[
PIKfyve controls dendritic cell function and tumor immunity
]]>
https://biorxiv.org/cgi/content/short/2024.02.28.582543v1?rss=1"
Choi, J. E.Qiao, Y.Kryczek, I.Yu, J.Gurkan, J.Bao, Y.Gondal, M.Tien, J. C.-Y.Maj, T.Yazdani, S.Parolia, A.Xia, H.Zhou, J.Wei, S.Grove, S.Vatan, L.Lin, H.Li, G.Zheng, Y.Zhang, Y.Cao, X.Su, F.Wang, R.He, T.Cieslik, M.Green, M. D.Zou, W.Chinnaiyan, A. M.2024-03-02doi:10.1101/2024.02.28.582543Cold Spring Harbor Laboratory Press2024-03-02
<![CDATA[
Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq
]]>
https://biorxiv.org/cgi/content/short/2024.02.29.582869v1?rss=1"
Lyu, R.Gao, Y.Wu, T.Ye, C.Wang, P.He, C.2024-03-02doi:10.1101/2024.02.29.582869Cold Spring Harbor Laboratory Press2024-03-02
<![CDATA[
Development of an orally bioavailable mSWI/SNF ATPase degrader and acquired mechanisms of resistance in prostate cancer
]]>
https://biorxiv.org/cgi/content/short/2024.02.29.582768v1?rss=1"
He, T.Cheng, C.Qiao, Y.Cho, H.Young, E.Mannan, R.Mahapatra, S.Miner, S. J.Zheng, Y.Kim, N.Zeng, V. Z.Wisniewski, J. P.Hou, S.Jackson, B.Cao, X.Su, F.Wang, R.Chang, Y.Kuila, B.Mukherjee, S.Dukare, S.Aithal, K. B.D.S., S.Abbineni, C.Lyssiotis, C. A.Parolia, A.Xiao, L.Chinnaiyan, A. M.2024-03-03doi:10.1101/2024.02.29.582768Cold Spring Harbor Laboratory Press2024-03-03
<![CDATA[
Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples
]]>
https://biorxiv.org/cgi/content/short/2024.02.28.582647v1?rss=1"
Henikoff, S.Henikoff, J. G.Paranal, R. M.Greene, J. E.Russell, Z. R.Szulzewsky, F.Kugel, S.Holland, E. C.Ahmad, K.2024-03-03doi:10.1101/2024.02.28.582647Cold Spring Harbor Laboratory Press2024-03-03
<![CDATA[
Kruppel-like Factor (KLF) family members control expression of genes required for serous cavity and alveolar macrophage identities
]]>
https://biorxiv.org/cgi/content/short/2024.02.28.582578v1?rss=1"
Pestal, K.Slayden, L.Barton, G.2024-03-03doi:10.1101/2024.02.28.582578Cold Spring Harbor Laboratory Press2024-03-03
<![CDATA[
Structure-guided aminoacylation and assembly of chimeric RNAs
]]>
https://biorxiv.org/cgi/content/short/2024.03.02.583109v1?rss=1"
Radakovic, A.Lewicka, A.Todisco, M.Aitken, H. R. M.Weiss, Z.Kim, S.Bannan, A.Piccirilli, J. A.Szostak, J. W.2024-03-03doi:10.1101/2024.03.02.583109Cold Spring Harbor Laboratory Press2024-03-03
<![CDATA[
Activation of locus coeruleus noradrenergic neuronsrapidly drives homeostatic sleep pressure
]]>
https://biorxiv.org/cgi/content/short/2024.02.29.582852v1?rss=1"
Silverman, D.Chen, C.Chang, S.Bui, L.Zhang, Y.Raghavan, R.Jiang, A.Darmohray, D.Sima, J.Ding, X.Li, B.Ma, C.Dan, Y.2024-03-04doi:10.1101/2024.02.29.582852Cold Spring Harbor Laboratory Press2024-03-04
<![CDATA[
Prioritizing replay when future goals are unknown
]]>
https://biorxiv.org/cgi/content/short/2024.02.29.582822v1?rss=1"
Sagiv, Y.Akam, T.Witten, I.Daw, N. D.2024-03-04doi:10.1101/2024.02.29.582822Cold Spring Harbor Laboratory Press2024-03-04
<![CDATA[
Astrocytic thrombospondins 1 and 2 are required for cortical synapse development controlling instrumental performance
]]>
https://biorxiv.org/cgi/content/short/2024.03.01.582935v1?rss=1"
Lawal, O. O.Ulloa Severino, F. P.Wang, S.Bindu, D. S.Sakers, K.Johnson, S. A.Yin, H. H.Eroglu, C.2024-03-04doi:10.1101/2024.03.01.582935Cold Spring Harbor Laboratory Press2024-03-04
<![CDATA[
Assessing the impact of Brd2 depletion on chromatin compartmentalization
]]>
https://biorxiv.org/cgi/content/short/2024.03.02.583085v1?rss=1"
Athreya, A.Xie, L.Tjian, R.Zhang, B.Liu, Z. J.2024-03-06doi:10.1101/2024.03.02.583085Cold Spring Harbor Laboratory Press2024-03-06
<![CDATA[
Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues
]]>
https://biorxiv.org/cgi/content/short/2024.03.07.583776v1?rss=1"
Shin, T. W.Wang, H.Zhang, C.An, B.Lu, Y.Zhang, E.Lu, X.Karagiannis, E.Kang, J. S.Emenari, A.Symvoulidis, P.Asano, S.Lin, L.Costa, E.IMAXT Grand Challenge Consortium,Marblestone, A. H.Kasthuri, N.Tsai, L.-H.Boyden, E.2024-03-08doi:10.1101/2024.03.07.583776Cold Spring Harbor Laboratory Press2024-03-08
<![CDATA[
The auditory midbrain mediates tactile vibration sensing
]]>
https://biorxiv.org/cgi/content/short/2024.03.08.584077v1?rss=1"
Huey, E. L.Turecek, J.Delisle, M. M.Mazor, O.Romero, G. E.Dua, M.Sarafis, Z. K.Hobble, A.Booth, K. T.Goodrich, L. V.Corey, D. P.Ginty, D. D.2024-03-08doi:10.1101/2024.03.08.584077Cold Spring Harbor Laboratory Press2024-03-08
<![CDATA[
Light and dopamine impact two circadian neurons to promote morning wakefulness
]]>
https://biorxiv.org/cgi/content/short/2024.03.04.583333v1?rss=1"
Le, J. Q.Ma, D.Dai, X.Rosbash, M.2024-03-08doi:10.1101/2024.03.04.583333Cold Spring Harbor Laboratory Press2024-03-08
<![CDATA[
High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains
]]>
https://biorxiv.org/cgi/content/short/2024.03.08.584176v1?rss=1"
Loes, A. N.Tarabi, R. A. L.Huddleston, J.Touyon, L.Wong, S. S.Cheng, S. M.Leung, N. H.Hannon, W. W.Bedford, T.Cobey, S.Cowling, B. J.Bloom, J. D.2024-03-09doi:10.1101/2024.03.08.584176Cold Spring Harbor Laboratory Press2024-03-09
<![CDATA[
Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM)
]]>
https://biorxiv.org/cgi/content/short/2024.03.09.584243v1?rss=1"
Chandler, T.Guo, M.Su, Y.Chen, J.Wu, Y.Liu, J.Agashe, A.Fischer, R. S.Mehta, S. B.Kumar, A.Baskin, T. I.Jamouille, V.Liu, H.Swaminathan, V.Nain, A.Oldenbourg, R.La Riviere, P.Shroff, H.2024-03-12doi:10.1101/2024.03.09.584243Cold Spring Harbor Laboratory Press2024-03-12
<![CDATA[
miRNA circuit modules for precise, tunable control of gene expression
]]>
https://biorxiv.org/cgi/content/short/2024.03.12.583048v1?rss=1"
Du, R.Flynn, M. J.Honsa, M.Jungmann, R.Elowitz, M. B.2024-03-12doi:10.1101/2024.03.12.583048Cold Spring Harbor Laboratory Press2024-03-12
<![CDATA[
Analysis of meiotic recombination in Drosophila simulans shows heterozygous inversions do not cause an interchromosomal effect
]]>
https://biorxiv.org/cgi/content/short/2024.03.09.584235v1?rss=1"
Man, B.Kim, E.Vadlakonda, A.Stern, D. L.Crown, N.2024-03-12doi:10.1101/2024.03.09.584235Cold Spring Harbor Laboratory Press2024-03-12
<![CDATA[
Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans
]]>
https://biorxiv.org/cgi/content/short/2024.03.12.584650v1?rss=1"
Eichler, E.Guitart, X.Porubsky, D.Yoo, D.Dougherty, M. L.Dishuck, P. C.Munson, K. M.Lewis, A. P.Hoekzema, K.Knuth, J.Chang, S.Pastinen, T.2024-03-13doi:10.1101/2024.03.12.584650Cold Spring Harbor Laboratory Press2024-03-13
<![CDATA[
Enhanced mucosal mitochondrial function corrects dysbiosis and OXPHOS metabolism in IBD
]]>
https://biorxiv.org/cgi/content/short/2024.03.14.584471v1?rss=1"
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org.highwire.dtl.DTLVardef@41e437org.highwire.dtl.DTLVardef@1eddf37org.highwire.dtl.DTLVardef@1d9bff3org.highwire.dtl.DTLVardef@c925f0_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Kapur, N.Alam, A.Hassan, S. A.Patel, P. H.Wempe, L.Bhogoju, S.Goretsky, T.Kim, J. H.Herzog, J.Ge, Y.Awuah, S.Byndloss, M.Baumler, A. J.Zadeh, M.Sator, R. B.Barrett, T. A.2024-03-14doi:10.1101/2024.03.14.584471Cold Spring Harbor Laboratory Press2024-03-14
<![CDATA[
Synthetic dosage-compensating miRNA circuits for quantitative gene therapy
]]>
https://biorxiv.org/cgi/content/short/2024.03.13.584179v1?rss=1"
Flynn, M. J.Mayfield, A. M.Du, R.Gradinaru, V.Elowitz, M. B.2024-03-14doi:10.1101/2024.03.13.584179Cold Spring Harbor Laboratory Press2024-03-14
<![CDATA[
Unexpected transformations during pyrroloiminoquinone biosynthesis
]]>
https://biorxiv.org/cgi/content/short/2024.03.12.584671v1?rss=1"
Figueroa, J. R.Zhu, L.van der Donk, W.2024-03-14doi:10.1101/2024.03.12.584671Cold Spring Harbor Laboratory Press2024-03-14
<![CDATA[
Tumor cell-based liquid biopsy using high-throughput microfluidic enrichment of entire leukapheresis product
]]>
https://biorxiv.org/cgi/content/short/2024.03.13.583573v1?rss=1"
Mishra, A.Huang, S.-B.Dubash, T.Burr, R.Wittner, B. S.Cunneely, Q. E.Putaturo, V. R.Deshpande, A.Antmen, E.Gopinathan, K. A.Otani, K.Miyazawa, Y.Kwak, J. E.Guay, S. Y.Kelly, J.Walsh, J.Nieman, L.Galler, I.Chan, P.Lawrence, M. S.Sullivan, R. J.Bardia, A.Micalizzi, D. S.Sequist, L. V.Lee, R. J.Franses, J. W.Ting, D. T.Brunker, P. A. R.Maheswaran, S.Miyamoto, D. T.Haber, D. A.Toner, M.2024-03-14doi:10.1101/2024.03.13.583573Cold Spring Harbor Laboratory Press2024-03-14
<![CDATA[
Whole-body simulation of realistic fruit fly locomotion with deep reinforcement learning
]]>
https://biorxiv.org/cgi/content/short/2024.03.11.584515v1?rss=1"
Vaxenburg, R.Siwanowicz, I.Merel, J.Robie, A. A.Morrow, C.Novati, G.Stefanidi, Z.Card, G. M.Reiser, M. B.Botvinick, M. M.Branson, K. M.Tassa, Y.Turaga, S. C.2024-03-14doi:10.1101/2024.03.11.584515Cold Spring Harbor Laboratory Press2024-03-14
<![CDATA[
Social state gates vision using three circuit mechanisms in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2024.03.15.585289v1?rss=1"
Schretter, C. E.Hindmarsh Sten, T.Klapoetke, N.Shao, M.Nern, A.Dreher, M.Bushey, D.Robie, A. A.Taylor, A. L.Branson, K. M.Otopalik, A.Ruta, V.Rubin, G. M.2024-03-17doi:10.1101/2024.03.15.585289Cold Spring Harbor Laboratory Press2024-03-17
<![CDATA[
Live imaging of Alu elements reveals non-uniform euchromatin dynamics coupled to transcription
]]>
https://biorxiv.org/cgi/content/short/2024.03.15.585287v1?rss=1"
Chang, Y.-C.Quinodoz, S. A.Brangwynne, C. P.2024-03-17doi:10.1101/2024.03.15.585287Cold Spring Harbor Laboratory Press2024-03-17
<![CDATA[
Imprinting and DNA methylation in water lily endosperm: implications for seed evolution
]]>
https://biorxiv.org/cgi/content/short/2024.03.15.585284v1?rss=1"
Povilus, R. A.Martin, C. A.Gehring, M.2024-03-17doi:10.1101/2024.03.15.585284Cold Spring Harbor Laboratory Press2024-03-17
<![CDATA[
Metastatic site influences driver gene function in pancreatic cancer
]]>
https://biorxiv.org/cgi/content/short/2024.03.17.585402v1?rss=1"
Tsanov, K. M.Barriga, F. M.Ho, Y.-J.Alonso-Curbelo, D.Livshits, G.Koche, R. P.Baslan, T.Simon, J.Tian, S.Wuest, A. N.Luan, W.Wilkinson, J. E.Masilionis, I.Dimitrova, N.Iacobuzio-Donahue, C. A.Chaligne, R.Pe'er, D.Massague, J.Lowe, S. W.2024-03-18doi:10.1101/2024.03.17.585402Cold Spring Harbor Laboratory Press2024-03-18
<![CDATA[
Atomically accurate de novo design of single-domain antibodies
]]>
https://biorxiv.org/cgi/content/short/2024.03.14.585103v1?rss=1"
Bennett, N. R.Watson, J. L.Ragotte, R. J.Borst, A. J.See, D. L.Weidle, C.Biswas, R.Shrock, E. L.Leung, P. J. Y.Huang, B.Goreshnik, I.Ault, R.Carr, K. D.Singer, B.Criswell, C.Vafeados, D.Garcia Sanchez, M.Kim, H. M.Vazquez Torres, S.Chan, S.Baker, D.2024-03-18doi:10.1101/2024.03.14.585103Cold Spring Harbor Laboratory Press2024-03-18
<![CDATA[
Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types
]]>
https://biorxiv.org/cgi/content/short/2024.03.18.585578v1?rss=1"
Blanton, L. V.San Roman, A. K.Wood, G.Buscetta, A.Banks, N.Skaletsky, H.Godfrey, A. K.Pham, T. T.Hughes, J. F.Brown, L. G.Kruszka, P.Lin, A. E.Kastner, D. L.Muenke, M.Page, D. C.2024-03-19doi:10.1101/2024.03.18.585578Cold Spring Harbor Laboratory Press2024-03-19
<![CDATA[
Gut microbiota gate host exposure to metabolites from dietary Solanums
]]>
https://biorxiv.org/cgi/content/short/2024.03.20.584512v1?rss=1"
Liou, C. S.Iakiviak, M.Rajniak, J.Murugkar, P. P.Higginbottom, S. K.Jasper, M.Fischbach, M. A.Sattely, E. S.2024-03-20doi:10.1101/2024.03.20.584512Cold Spring Harbor Laboratory Press2024-03-20
<![CDATA[
Targeting PIKfyve-driven lipid homeostasis as a metabolic vulnerability in pancreatic cancer
]]>
https://biorxiv.org/cgi/content/short/2024.03.18.585580v1?rss=1"
Cheng, C.Hu, J.Mannan, R.Bhattacharyya, R.Rossiter, N. J.Magnuson, B.Wisniewski, J. P.Zheng, Y.Xiao, L.Li, C.Awad, D.He, T.Bao, Y.Zhang, Y.Cao, X.Wang, Z.Mehra, R.Morlacchi, P.Sahai, V.Pasca di Magliano, M.Shah, Y. M.Ding, K.Qiao, Y.Lyssiotis, C. A.Chinnaiyan, A. M.2024-03-20doi:10.1101/2024.03.18.585580Cold Spring Harbor Laboratory Press2024-03-20
<![CDATA[
Structural and genetic diversity in the secreted mucins, MUC5AC and MUC5B
]]>
https://biorxiv.org/cgi/content/short/2024.03.18.585560v1?rss=1"
Plender, E. G.Prodanov, T.Hsieh, P.Nizamis, E.Harvey, W. T.Sulovari, A.Munson, K. M.Kaufman, E.O'Neal, W. K.Valdmanis, P. N.Marschall, T.Eichler, E. E.2024-03-20doi:10.1101/2024.03.18.585560Cold Spring Harbor Laboratory Press2024-03-20
<![CDATA[
Timing of treatment shapes the path to androgen receptor signaling inhibitor resistance in prostate cancer
]]>
https://biorxiv.org/cgi/content/short/2024.03.18.585532v1?rss=1"
Lee, E.Zhang, Z.Chen, C.-C.Choi, D.Rivera, A. C. A.Linton, E.Ho, Y.-j.Love, J.LaClair, J.Wongvipat, J.Sawyers, C.2024-03-20doi:10.1101/2024.03.18.585532Cold Spring Harbor Laboratory Press2024-03-20
<![CDATA[
PLD3 and PLD4 synthesize S,S-BMP, a key phospholipid enabling lipid degradation in lysosomes
]]>
https://biorxiv.org/cgi/content/short/2024.03.21.586175v1?rss=1"
Singh, S.Dransfeld, U.Ambaw, Y.Lopez-Scarim, J.Farese, R. V.Walther, T. C.2024-03-21doi:10.1101/2024.03.21.586175Cold Spring Harbor Laboratory Press2024-03-21
<![CDATA[
CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality
]]>
https://biorxiv.org/cgi/content/short/2024.03.20.585990v1?rss=1"
Tien, J. C.-Y.Chang, Y.Zhang, Y.Chou, J.Cheng, Y.Wang, X.Yang, J.Mannan, R.Shah, P.Wang, X.-M.Todd, A. J.Eyunni, S.Cheng, C.Rebernick, R. J.Xiao, L.Bao, Y.Neiswender, J.Brough, R.Pettitt, S. J.Cao, X.Miner, S. J.Zhou, L.Wu, Y.-M.Labanca, E.Wang, Y.Parolia, A.Cieslik, M.Robinson, D. R.Wang, Z.Feng, F. Y.Lord, C. J.Ding, K.Chinnaiyan, A. M.2024-03-21doi:10.1101/2024.03.20.585990Cold Spring Harbor Laboratory Press2024-03-21
<![CDATA[
A torpor-like state (TLS) in mice slows blood epigenetic aging and prolongs healthspan
]]>
https://biorxiv.org/cgi/content/short/2024.03.20.585828v1?rss=1"
Jayne, L.Lavin-Peter, A.Roessler, J.Tyshkovskiy, A.Antoszewski, M.Ren, E.Markovski, A.Sun, S.Yao, H.Sankaran, V. G.Gladyshev, V. N.Brooke, R. T.Horvath, S.Griffith, E. C.Hrvatin, S.2024-03-25doi:10.1101/2024.03.20.585828Cold Spring Harbor Laboratory Press2024-03-25
<![CDATA[
Global coral genomic vulnerability explains recent reef losses
]]>
https://biorxiv.org/cgi/content/short/2024.03.25.586253v1?rss=1"
Selmoni, O.Cleves, P. A.Exposito-Alonso, M.2024-03-25doi:10.1101/2024.03.25.586253Cold Spring Harbor Laboratory Press2024-03-25
<![CDATA[
Parabrachial Calca neurons mediate second-order conditioning
]]>
https://biorxiv.org/cgi/content/short/2024.03.21.586150v1?rss=1"
Palmiter, R.Park, S.Zhu, A.Cao, F.2024-03-25doi:10.1101/2024.03.21.586150Cold Spring Harbor Laboratory Press2024-03-25
<![CDATA[
The Molecular Architecture of the Nuclear Basket
]]>
https://biorxiv.org/cgi/content/short/2024.03.27.587068v1?rss=1"
Singh, D.Soni, N.Hutchings, J.Echeverria, I.Shaikh, F.Duquette, M.Suslov, S.Li, Z.van Eeuwen, T.Molloy, K.Shi, Y.Wang, J.Guo, Q.Chait, B. T.Fernandez-Martinez, J.Rout, M. P.Sali, A.Villa, E.2024-03-28doi:10.1101/2024.03.27.587068Cold Spring Harbor Laboratory Press2024-03-28
<![CDATA[
How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimers disease brain by a strain-relief mechanism
]]>
https://biorxiv.org/cgi/content/short/2024.03.25.586668v1?rss=1"
Hou, K.Ge, P.Sawaya, M. R.Dolinsky, J. L.Yang, Y.Jiang, Y. X.Lutter, L.Boyer, D. R.Cheng, X.Pi, J.Zhang, J.Lu, J.Yang, S.Yu, Z.Feigon, J.Eisenberg, D. S.2024-03-29doi:10.1101/2024.03.25.586668Cold Spring Harbor Laboratory Press2024-03-29
<![CDATA[
Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers
]]>
https://biorxiv.org/cgi/content/short/2024.03.29.586681v1?rss=1"
Tang, J.Weiser, N. E.Wang, G.Chowdhry, S.Curtis, E. J.Zhao, Y.Wong, I. T.-L.Marinov, G. K.Li, R.Hanoian, P.Tse, E.Hansen, R.Plum, J.Steffy, A.Milutinovic, S.Meyer, S. T.Altemose, N.Curtis, C.Greenleaf, W. J.Bafna, V.Benkovic, S. J.Pinkerton, A. B.Kasibhatla, S.Hassig, C. A.Mischel, P. S.Chang, H. Y.2024-03-29doi:10.1101/2024.03.29.586681Cold Spring Harbor Laboratory Press2024-03-29
<![CDATA[
p300/CBP degradation is required to disable the active AR enhanceosome in prostate cancer
]]>
https://biorxiv.org/cgi/content/short/2024.03.29.587346v1?rss=1"
Luo, J.Chen, Z.Qiao, Y.Tien, J. C.-Y.Young, E.Mannan, R.Mahapatra, S.He, T.Eyunni, S.Zhang, Y.Zheng, Y.Su, F.Cao, X.Wang, R.Cheng, Y.Seri, R.George, J.Shahine, M.Miner, S. J.Vaishampayan, U.Wang, M.Wang, S.Parolia, A.Chinnaiyan, A. M.2024-03-30doi:10.1101/2024.03.29.587346Cold Spring Harbor Laboratory Press2024-03-30
<![CDATA[
Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses
]]>
https://biorxiv.org/cgi/content/short/2024.04.01.587595v1?rss=1"
Matsui, A.Spangler, C.Elferich, J.Shiozaki, M.Jean, N.Zhao, X.Qin, M.Zhong, H.Yu, Z.Gouaux, E.2024-04-01doi:10.1101/2024.04.01.587595Cold Spring Harbor Laboratory Press2024-04-01
<![CDATA[
Broadly neutralizing antibodies against emerging delta-coronaviruses
]]>
https://biorxiv.org/cgi/content/short/2024.03.27.586411v1?rss=1"
Rexhepaj, M.Park, Y.-J.Perruzza, L.Asarnow, D.McCallum, M.Culap, K.Saliba, C.Leoni, G.Balmeli, A.Yoshiyama, C.Dickinson, M. S.Quispe, J.Brown, J. T.Tortorici, M. A.Sprouse, K. R.Taylor, A. L.Starr, T. N.Corti, D.Begnini, F.Veesler, D.2024-04-01doi:10.1101/2024.03.27.586411Cold Spring Harbor Laboratory Press2024-04-01
<![CDATA[
Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening
]]>
https://biorxiv.org/cgi/content/short/2024.03.30.587094v1?rss=1"
Hurt, R. C.Jin, Z.Soufi, M.Wong, K. K.Sawyer, D. P.Shen, H. K.Dutka, P.Deshpande, R.Zhang, R.Mittelstein, D. R.Shapiro, M. G.2024-04-01doi:10.1101/2024.03.30.587094Cold Spring Harbor Laboratory Press2024-04-01
<![CDATA[
Co-transcriptional splicing facilitates transcription of gigantic genes
]]>
https://biorxiv.org/cgi/content/short/2024.04.02.587678v1?rss=1"
Yamashita, Y. M.Fingerhut, J. M.Lannes, R.Whitfield, T. W.Thiru, P.2024-04-02doi:10.1101/2024.04.02.587678Cold Spring Harbor Laboratory Press2024-04-02
<![CDATA[
The LuxO-OpaR quorum-sensing cascade differentially controls Vibriophage VP882 lysis-lysogeny decision making in liquid and on surfaces
]]>
https://biorxiv.org/cgi/content/short/2024.04.02.587679v1?rss=1"
Santoriello, F.Bassler, B. L.2024-04-02doi:10.1101/2024.04.02.587679Cold Spring Harbor Laboratory Press2024-04-02
<![CDATA[
The cytokine receptor Fn14 is a molecular brake on neuronal activity that mediates circadian function in vivo
]]>
https://biorxiv.org/cgi/content/short/2024.04.02.587786v1?rss=1"
Ferro, A.Arshad, A.Boyd, L.Stanley, T.Berisha, A.Vrudhula, U.Gomez, A. M.Borniger, J. C.Cheadle, L. M.2024-04-02doi:10.1101/2024.04.02.587786Cold Spring Harbor Laboratory Press2024-04-02
<![CDATA[
Small molecule telomerase inhibitors are also potent inhibitors of telomeric C-strand synthesis
]]>
https://biorxiv.org/cgi/content/short/2024.04.01.587626v1?rss=1"
Johnson, K.Seidel, J. M.Cech, T. R.2024-04-02doi:10.1101/2024.04.01.587626Cold Spring Harbor Laboratory Press2024-04-02
<![CDATA[
Ascorbate depletion increases quiescence and self-renewal potential in hematopoietic stem cells and multipotent progenitors
]]>
https://biorxiv.org/cgi/content/short/2024.04.01.587574v1?rss=1"
Comazzetto, S.Cassidy, D.DeVilbiss, A. W.Jeffery, E. C.Ottesen, B. R.Reyes, A. R.Muh, S.Mathews, T. P.Chen, B.Zhao, Z. P.Morrison, S. J.2024-04-02doi:10.1101/2024.04.01.587574Cold Spring Harbor Laboratory Press2024-04-02
<![CDATA[
Mapping immunodominant sites on the MERS-CoV spike glycoprotein targeted by infection-elicited antibodies in humans
]]>
https://biorxiv.org/cgi/content/short/2024.03.31.586409v1?rss=1"
Addetia, A.Stewart, C.Seo, A. J.Sprouse, K. R.Asiri, A. Y.Al-Mozaini, M.Memish, Z. A.Alshukairi, A.Veesler, D.2024-04-02doi:10.1101/2024.03.31.586409Cold Spring Harbor Laboratory Press2024-04-02
<![CDATA[
Structure and function of an intermediate GPCR-G protein complex
]]>
https://biorxiv.org/cgi/content/short/2024.04.02.587841v1?rss=1"
Bi, M.Wang, X.Wang, J.xu, J.Sun, W.Adediwrua, V. A.Miao, Y.Cheng, Y.Ye, L.2024-04-03doi:10.1101/2024.04.02.587841Cold Spring Harbor Laboratory Press2024-04-03
<![CDATA[
A tunable and versatile chemogenetic near infrared fluorescent reporter
]]>
https://biorxiv.org/cgi/content/short/2024.04.05.588310v1?rss=1"
El Hajji, L.Bunel, B.Joliot, O.Li, C.Tebo, A. G.Rampon, C.Volovitch, M.Fischer, E.Pietrancosta, N.Perez, F.Morin, X.VRIZ, S.Gautier, A.2024-04-06doi:10.1101/2024.04.05.588310Cold Spring Harbor Laboratory Press2024-04-06
<![CDATA[
Transformers do not outperform Cellpose
]]>
https://biorxiv.org/cgi/content/short/2024.04.06.587952v1?rss=1"
Stringer, C.Pachitariu, M.2024-04-07doi:10.1101/2024.04.06.587952Cold Spring Harbor Laboratory Press2024-04-07
<![CDATA[
Molecular insights into phosphoethanolamine cellulose formation and secretion
]]>
https://biorxiv.org/cgi/content/short/2024.04.04.588173v1?rss=1"
Verma, P.Ho, R.Chambers, S. A.Cegelski, L.Zimmer, J.2024-04-08doi:10.1101/2024.04.04.588173Cold Spring Harbor Laboratory Press2024-04-08
<![CDATA[
Coupling of cell growth modulation to asymmetric division and cell cycle regulation in Caulobacter crescentus
]]>
https://biorxiv.org/cgi/content/short/2024.04.10.587378v1?rss=1"
Glenn, S.Lin, W.-H.Papagiannakis, A.Kato, S.Jacobs-Wagner, C.2024-04-10doi:10.1101/2024.04.10.587378Cold Spring Harbor Laboratory Press2024-04-10
<![CDATA[
Evolution of the substrate specificity of an RNA ligase ribozyme from phosphorimidazole- to triphosphate-activation
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https://biorxiv.org/cgi/content/short/2024.04.11.588910v1?rss=1"
DasGupta, S.Weiss, Z.Nisler, C.Szostak, J. W.2024-04-11doi:10.1101/2024.04.11.588910Cold Spring Harbor Laboratory Press2024-04-11
<![CDATA[
Molecular interplay between HURP and Kif18A in mitotic spindle regulation
]]>
https://biorxiv.org/cgi/content/short/2024.04.11.589088v1?rss=1"
Perez-Bertoldi, J. M.Zhao, Y.Thawani, A.Yildiz, A.Nogales, E.2024-04-11doi:10.1101/2024.04.11.589088Cold Spring Harbor Laboratory Press2024-04-11
<![CDATA[
The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1
]]>
https://biorxiv.org/cgi/content/short/2024.04.09.588557v1?rss=1"
Romero, R.Chu, T.Gonzalez-Robles, T. J.Smith, P.Xie, Y.Kaur, H.Yoder, S.Zhao, H.Mao, C.Kang, W.Pulina, M.Lawrence, K. E.Gopalan, A.Zaidi, S.Yoo, K.Choi, J.Fan, N.Gerstner, O.Karthaus, W. R.De Stanchina, E.Ruggles, K.Westcott, P. M. K.Chaligne, R.Pe'er, D. D.Sawyers, C.2024-04-11doi:10.1101/2024.04.09.588557Cold Spring Harbor Laboratory Press2024-04-11
<![CDATA[
Single Cell Analysis of Treatment-Resistant Prostate Cancer: Implications of Cell State Changes for Cell Surface Antigen Targeted Therapies
]]>
https://biorxiv.org/cgi/content/short/2024.04.09.588340v1?rss=1"
Zaidi, S.Park, J.Chan, J. M.Roudier, M.Zhao, J. L.Gopalan, A.Wadosky, K. M.Patel, R. A.Sayar, E.Karthaus, W. R.Kates, D. H.Chaudhary, O.Xu, T.Masilionis, I.Mazutis, L.Chaligne, R.Obradovic, A.Linkov, I.Barlas, A.Jungbluth, A.Rekhtman, N.Silber, J.Manova-Todorova, K.Watson, P. A.True, L. D.Morrissey, C. M.Scher, H. I.Rathkopf, D.Morris, M. J.Goodrich, D. W.Choi, J.Nelson, P. S.Haffner, M.Sawyers, C.2024-04-12doi:10.1101/2024.04.09.588340Cold Spring Harbor Laboratory Press2024-04-12
<![CDATA[
Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions
]]>
https://biorxiv.org/cgi/content/short/2024.04.09.588596v1?rss=1"
Schmid, E. W.Walter, J. C.2024-04-12doi:10.1101/2024.04.09.588596Cold Spring Harbor Laboratory Press2024-04-12
<![CDATA[
On the critical concentration for net assembly of dynamically unstable polymers
]]>
https://biorxiv.org/cgi/content/short/2024.04.12.589322v1?rss=1"
Mullins, R. D.2024-04-13doi:10.1101/2024.04.12.589322Cold Spring Harbor Laboratory Press2024-04-13
<![CDATA[
RNA complexes with nicks and gaps: thermodynamic and kinetic effects of coaxial stacking and dangling ends
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https://biorxiv.org/cgi/content/short/2024.04.13.589350v1?rss=1"
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]]>Todisco, M.Radakovic, A.Szostak, J.2024-04-13doi:10.1101/2024.04.13.589350Cold Spring Harbor Laboratory Press2024-04-13
<![CDATA[
Characterization of Medusavirus encoded histones reveals nucleosome-like structures and a unique linker histone
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https://biorxiv.org/cgi/content/short/2024.04.13.589364v1?rss=1"
Toner, C. M.Hoitsma, N. M.Luger, K.2024-04-14doi:10.1101/2024.04.13.589364Cold Spring Harbor Laboratory Press2024-04-14
<![CDATA[
Spatial Coding Dysfunction and Network Instability in the Aging Medial Entorhinal Cortex
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https://biorxiv.org/cgi/content/short/2024.04.12.588890v1?rss=1"
Herber, C. S.Pratt, K. J. B.Shea, J. M.Villeda, S. A.Giocomo, L. M.2024-04-15doi:10.1101/2024.04.12.588890Cold Spring Harbor Laboratory Press2024-04-15
<![CDATA[
Ectopic Reconstitution of a Spine-Apparatus Like Structure Provides Insight into Mechanisms Underlying Its Formation
]]>
https://biorxiv.org/cgi/content/short/2024.04.16.589782v1?rss=1"
Falahati, H.Wu, Y.De Camilli, P.2024-04-16doi:10.1101/2024.04.16.589782Cold Spring Harbor Laboratory Press2024-04-16
<![CDATA[
A fine kinetic balance of interactions directs transcription factor hubs to genes
]]>
https://biorxiv.org/cgi/content/short/2024.04.16.589811v1?rss=1"
Mukherjee, A.Fallacaro, S.Ratchasanmuang, P.Zinski, J.Boka, A.Shankta, K.Mir, M.2024-04-16doi:10.1101/2024.04.16.589811Cold Spring Harbor Laboratory Press2024-04-16
<![CDATA[
Directed evolution-based discovery of ligands for in vivo restimulation of CAR-T cells
]]>
https://biorxiv.org/cgi/content/short/2024.04.16.589780v1?rss=1"
Ma, L.Ramasubramanian, R.Mehta, N.Cossette, B.Morgan, D.Sukaj, I.Bergaggio, E.Kadauke, S.Myers, R.Paruzzo, L.Ghilardi, G.Grzywa, T.Cozzone, A.Schuster, S.Frey, N.Zhang, L.Yousefpour, P.Abraham, W.Suh, H.Ruella, M.Grupp, S.Chiarle, R.Wittrup, K. D.Irvine, D. J.2024-04-17doi:10.1101/2024.04.16.589780Cold Spring Harbor Laboratory Press2024-04-17
<![CDATA[
FicD regulates adaptation to the unfolded protein response in the murine liver.
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https://biorxiv.org/cgi/content/short/2024.04.15.589620v1?rss=1"
Casey, A. K.Stewart, N. M.Zaidi, N.Gray, H. A.Cox, A.Fields, H. A.Orth, K.2024-04-17doi:10.1101/2024.04.15.589620Cold Spring Harbor Laboratory Press2024-04-17
<![CDATA[
Meiotic DNA break resection and recombination rely on chromatin remodeler Fun30
]]>
https://biorxiv.org/cgi/content/short/2024.04.17.589955v1?rss=1"
Huang, P.-C.Hong, S.Mimitou, E. P.Kim, K. P.Murakami, H.Keeney, S.2024-04-18doi:10.1101/2024.04.17.589955Cold Spring Harbor Laboratory Press2024-04-18
<![CDATA[
Connectome-driven neural inventory of a complete visual system
]]>
https://biorxiv.org/cgi/content/short/2024.04.16.589741v1?rss=1"
Nern, A.Loesche, F.Takemura, S.-y.Burnett, L. E.Dreher, M.Gruntman, E.Hoeller, J.Huang, G. B.Januszewski, M.Klapoetke, N. C.Koskela, S.Longden, K. D.Lu, Z.Preibisch, S.Qiu, W.Rogers, E. M.Seenivasan, P.Zhao, A.Bogovic, J.Canino, B. S.Clements, J.Cook, M.Finley-May, S.Flynn, M. A.Hameed, I.Hayworth, K. J.Hopkins, G. P.Hubbard, P. M.Katz, W. T.Kovalyak, J.Lauchie, S. A.Leonard, M.Lohff, A.Maldonado, C. A.Mooney, C.Okeoma, N.Olbris, D. J.Ordish, C.Paterson, T.Phillips, E. M.Pietzsch, T.Rivas Salinas, J.Rivlin, P.2024-04-18doi:10.1101/2024.04.16.589741Cold Spring Harbor Laboratory Press2024-04-18
<![CDATA[
Functional and antigenic landscape of the Nipah virus receptor binding protein
]]>
https://biorxiv.org/cgi/content/short/2024.04.17.589977v1?rss=1"
Larsen, B. B.McMahon, T.Brown, J. T.Wang, Z.Radford, C. E.Crowe, J. E.Veesler, D.Bloom, J. D.2024-04-19doi:10.1101/2024.04.17.589977Cold Spring Harbor Laboratory Press2024-04-19
<![CDATA[
Pervasive gene flow despite strong and varied reproductive barriers in swordtails
]]>
https://biorxiv.org/cgi/content/short/2024.04.16.589374v1?rss=1"
Aguillon, S. M.Haase Cox, S. K.Langdon, Q. K.Gunn, T. R.Baczenas, J. J.Banerjee, S. M.Donny, A. E.Moran, B. M.Gutierrez-Rodriguez, C.Rios-Cardenas, O.Morris, M. R.Powell, D. L.Schumer, M.2024-04-20doi:10.1101/2024.04.16.589374Cold Spring Harbor Laboratory Press2024-04-20
<![CDATA[
Glycogen phase separation drives macromolecular rearrangement and asymmetric division in E. coli
]]>
https://biorxiv.org/cgi/content/short/2024.04.19.590186v1?rss=1"
Thappeta, Y.Canas-Duarte, S. J.Kallem, T.Fragasso, A.Xiang, Y.Gray, W.Lee, C.Cegelski, L.Jacobs-Wagner, C.2024-04-20doi:10.1101/2024.04.19.590186Cold Spring Harbor Laboratory Press2024-04-20
<![CDATA[
Dependence of Contextual Modulation in Macaque V1 on Interlaminar Signal Flow
]]>
https://biorxiv.org/cgi/content/short/2024.04.18.590176v1?rss=1"
Zhu, S.Oh, Y. J.Trepka, E. B.Chen, X.Moore, T.2024-04-21doi:10.1101/2024.04.18.590176Cold Spring Harbor Laboratory Press2024-04-21
<![CDATA[
A Bayesian Solution to Count the Number of Molecules within a Diffraction Limited Spot
]]>
https://biorxiv.org/cgi/content/short/2024.04.18.590066v1?rss=1"
Hillsley, A.Stein, J.Tillberg, P. W.Stern, D. L.Funke, J.2024-04-22doi:10.1101/2024.04.18.590066Cold Spring Harbor Laboratory Press2024-04-22
<![CDATA[
Expansion of in vitro Toxoplasma gondii cysts using enzymatically enhanced ultrastructure expansion microscopy
]]>
https://biorxiv.org/cgi/content/short/2024.04.24.590991v1?rss=1"
Bondarenko, K.Limoge, F.Pedram, K.Gissot, M.Young, J. C.2024-04-25doi:10.1101/2024.04.24.590991Cold Spring Harbor Laboratory Press2024-04-25
<![CDATA[
Identification of MYC synthetic lethal genes and networks
]]>
https://biorxiv.org/cgi/content/short/2024.04.25.590465v1?rss=1"
Martin, T. D.Choi, M. Y.Patel, R. S.Liang, A. C.Li, M. Z.Elledge, S. J.2024-04-25doi:10.1101/2024.04.25.590465Cold Spring Harbor Laboratory Press2024-04-25
<![CDATA[
A maternal-effect toxin-antidote element causes larval arrest in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2024.04.26.591160v1?rss=1"
Zdraljevic, S.Walter-McNeill, L.Bruni, G.Marquez, H.Leighton, D. H. W.Bloom, J. S.Kruglyak, L.2024-04-26doi:10.1101/2024.04.26.591160Cold Spring Harbor Laboratory Press2024-04-26
<![CDATA[
Microglial MyD88-dependent pathways are regulated in a sex specific manner in the context of HMGB1-induced anxiety
]]>
https://biorxiv.org/cgi/content/short/2024.04.22.590482v1?rss=1"
Rawls, A.Nguyen, D.Dziabis, J.Clark, M.Anbarci, D.Bilbo, S. D.2024-04-26doi:10.1101/2024.04.22.590482Cold Spring Harbor Laboratory Press2024-04-26
<![CDATA[
Transcription of HIV-1 at sites of intact latent provirus integration
]]>
https://biorxiv.org/cgi/content/short/2024.04.26.591331v1?rss=1"
Teixeira, A. R.Bittar, C.Silva Santos, G. S.Oliveira, T. Y.Huang, A. S.Linden, N.Ferreira, I. A. T. M.Murdza, T.Muecksch, F.Jones, R. B.Caskey, M.Jankovic, M.Nussenzweig, M. C.2024-04-29doi:10.1101/2024.04.26.591331Cold Spring Harbor Laboratory Press2024-04-29
<![CDATA[
Reduced Levels of Lagging Strand Polymerases Shape Stem Cell Chromatin
]]>
https://biorxiv.org/cgi/content/short/2024.04.26.591383v1?rss=1"
Snedeker, J.Davis, B. E. M.Ranjan, R.Wooten, M. I.Blundon, J.Chen, X.2024-04-29doi:10.1101/2024.04.26.591383Cold Spring Harbor Laboratory Press2024-04-29
<![CDATA[
A survival-critical role for Drosophila giant interneurons during predation
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https://biorxiv.org/cgi/content/short/2024.04.30.591368v1?rss=1"
Chai, C. M.Morrow, C.Parikh, D. D.von Reyn, C. R.Leonardo, A.Card, G. M.2024-05-01doi:10.1101/2024.04.30.591368Cold Spring Harbor Laboratory Press2024-05-01
<![CDATA[
Design of High Affinity Binders to Convex Protein Target Sites
]]>
https://biorxiv.org/cgi/content/short/2024.05.01.592114v1?rss=1"
Baker, D.Yang, W.Hicks, D. R.Ghosh, A.Schwartze, T. A.Coventry, B.Goreshnik, I.Allen, A.Halabiya, S.Kim, C.Hinck, C. S.Lee, D. S.Bera, A.Li, Z.Wang, Y.Schlichthaerle, T.Cao, L.Huang, B.Garrett, S.Gerben, S. R.Rettie, S.Heine, P.Edman, N.Murray, A. N.Carter, L. P.Stewart, L.Almo, S.Hinck, A. P.2024-05-03doi:10.1101/2024.05.01.592114Cold Spring Harbor Laboratory Press2024-05-03
<![CDATA[
Oxidative Stress is a shared characteristic of ME/CFS and Long COVID
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https://biorxiv.org/cgi/content/short/2024.05.04.592477v1?rss=1"
Shankar, V.Wilhelmy, J.Michael, B.Cervantes, L.Mallajosyula, V.Davis, R.Snyder, M.Younis, S.Robinson, W. H.Shankar, S.Mischel, P.Bonilla, H.Davis, M.2024-05-05doi:10.1101/2024.05.04.592477Cold Spring Harbor Laboratory Press2024-05-05
<![CDATA[
Novel clock neuron subtypes regulate temporal aspects of sleep
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https://biorxiv.org/cgi/content/short/2024.05.03.592478v1?rss=1"
Ma, D.Le, J. Q.Dai, X.Diaz, M.Abruzzi, K.Rosbash, M.2024-05-06doi:10.1101/2024.05.03.592478Cold Spring Harbor Laboratory Press2024-05-06
<![CDATA[
Remote automated delivery of mechanical stimuli coupled to brain recordings in behaving mice
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https://biorxiv.org/cgi/content/short/2024.05.06.592101v1?rss=1"
Burdge, J.Jhumka, A.Ogundare, S.Baer, N.Fulton, S.Bistis, B.Foster, W.Toussaint, A.Li, M.Morizawa, Y. M.Yadessa, L.Khan, A.Delinois, A.Mayiseni, W.Loran, N.Yang, G.Abdus-Saboor, I.2024-05-07doi:10.1101/2024.05.06.592101Cold Spring Harbor Laboratory Press2024-05-07
<![CDATA[
Experience-dependent, sexually dimorphic synaptic connectivity defined by sex-specific cadherin expression
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https://biorxiv.org/cgi/content/short/2024.05.08.593207v1?rss=1"
Liao, C.-P.Majeed, M.Hobert, O.2024-05-08doi:10.1101/2024.05.08.593207Cold Spring Harbor Laboratory Press2024-05-08
<![CDATA[
Stochastic growth and selective stabilization generate stereotyped dendritic arbors
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https://biorxiv.org/cgi/content/short/2024.05.08.591205v1?rss=1"
Shi, R.Ho, X. Y.Tao, L.Taylor, C. A.Zhao, T.Zou, W.Lizzappi, M.Eichel, K.Shen, K.2024-05-08doi:10.1101/2024.05.08.591205Cold Spring Harbor Laboratory Press2024-05-08
<![CDATA[
Closed-loop modulation of remote hippocampal representations with neurofeedback
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https://biorxiv.org/cgi/content/short/2024.05.08.593085v1?rss=1"
Coulter, M. E.Gillespie, A. K.Chu, J. P.Denovellis, E. L.Nguyen, T. T. K.Liu, D.Wadhwani, K.Sharma, B.Wang, K.Deng, X.Eden, U.Kemere, C.Frank, L. M.2024-05-08doi:10.1101/2024.05.08.593085Cold Spring Harbor Laboratory Press2024-05-08
<![CDATA[
A conserved chronobiological complex times C. elegans development
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https://biorxiv.org/cgi/content/short/2024.05.09.593322v1?rss=1"
Spangler, R. K.Ashley, G. E.Braun, K.Wruck, D.Ramos-Coronado, A.Ragle, J. M.Iesmantavicius, V.Hess, D.Partch, C. L.Grosshans, H.Ward, J. D.2024-05-09doi:10.1101/2024.05.09.593322Cold Spring Harbor Laboratory Press2024-05-09
<![CDATA[
Embryonically Active Piriform Cortex Neurons Promote Intracortical Recurrent Connectivity during Development
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https://biorxiv.org/cgi/content/short/2024.05.08.593265v1?rss=1"
Wang, D. C.Santos Valencia, F. G.Song, J. H.Franks, K.Luo, L.2024-05-09doi:10.1101/2024.05.08.593265Cold Spring Harbor Laboratory Press2024-05-09
<![CDATA[
The structural landscape of Microprocessor Mediated pri-let-7 miRNAs processing
]]>
https://biorxiv.org/cgi/content/short/2024.05.09.593372v1?rss=1"
Garg, A.Shang, R.Cvetanovic, T.Lai, E. C.Joshua-Tor, L.2024-05-09doi:10.1101/2024.05.09.593372Cold Spring Harbor Laboratory Press2024-05-09
<![CDATA[
Imaging the extracellular matrix in live tissues and organisms with a glycan-binding fluorophore
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https://biorxiv.org/cgi/content/short/2024.05.09.593460v1?rss=1"
Fiore, A.Yu, G.Northey, J. J.Patel, R.Ravenscroft, T. A.Ikegami, R.Kolkman, W.Kumar, P.Grimm, J. B.Dilan, T. L.Ruetten, V. M. S.Ahrens, M. B.Shroff, H.Lavis, L. D.Wang, S.Weaver, V. M.Pedram, K.2024-05-10doi:10.1101/2024.05.09.593460Cold Spring Harbor Laboratory Press2024-05-10
<![CDATA[
A versatile bacterial innate immunity protein directly senses two disparate phage proteins
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https://biorxiv.org/cgi/content/short/2024.05.10.593582v1?rss=1"
Zhang, T.Cepauskas, A.Nadieina, A.Thureau, A.Coppieters 't Wallant, K.Martens, C.Lim, D. C.Garcia-Pino, A.Laub, M. T.2024-05-10doi:10.1101/2024.05.10.593582Cold Spring Harbor Laboratory Press2024-05-10
<![CDATA[
Coumarin as a general switching auxiliary to prepare photochromic and spontaneously blinking fluorophores
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https://biorxiv.org/cgi/content/short/2024.05.12.593749v1?rss=1"
Jradi, F.English, B. P.Brown, T. A.Arron, J.Khuon, S.Galbraith, J. A.Galbraith, C. G.Lavis, L. D.2024-05-12doi:10.1101/2024.05.12.593749Cold Spring Harbor Laboratory Press2024-05-12
<![CDATA[
Proteasomal control of anti-CRISPRs for the regulation of CRISPR/Cas9 activity using Cas9-ACROBAT
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https://biorxiv.org/cgi/content/short/2024.05.13.593596v1?rss=1"
Martin, T. D.Watson, E. V.Choi, M. Y.Nabet, B.Gray, N. S.Xu, Q.Elledge, S.2024-05-13doi:10.1101/2024.05.13.593596Cold Spring Harbor Laboratory Press2024-05-13
<![CDATA[
Complex structural variation and behavioral interactions underpin a balanced sexual mimicry polymorphism
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https://biorxiv.org/cgi/content/short/2024.05.13.594052v1?rss=1"
Dodge, T. O.Kim, B. Y.Baczenas, J. J.Banerjee, S. M.Gunn, T. R.Donny, A. E.Given, L. A.Rice, A. R.Haase Cox, S. K.Weinstein, M. L.Cross, R.Moran, B. M.Haber, K.Haghani, N. B.Machin Kairuz, J. A.Gellert, H. R.Du, K.Aguillon, S. M.Tudor, M. S.Gutierrez-Rodriguez, C.Rios-Cardenas, O.Morris, M. R.Schartl, M.Powell, D. L.Schumer, M.2024-05-14doi:10.1101/2024.05.13.594052Cold Spring Harbor Laboratory Press2024-05-14
<![CDATA[
Asymmetric Engagement of Dimeric CRL3KBTBD4 by the Molecular Glue UM171 Licenses Degradation of HDAC1/2 Complexes
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https://biorxiv.org/cgi/content/short/2024.05.14.593897v1?rss=1"
Yeo, M. J.Zhang, O.Xie, X.Nam, E.Payne, N. C.Gosavi, P. M.Kwok, H. S.Iram, I.Lee, C.Li, J.Chen, N. J.Jiang, H.Wang, Z. A.Lee, K.Mao, H.Harry, S. A.Barakat, I. A.Takahashi, M.Waterbury, A. L.Barone, M.Mattevi, A.Bar-Peled, L.Cole, P. A.Mazitschek, R.Liau, B. B.Zheng, N.2024-05-14doi:10.1101/2024.05.14.593897Cold Spring Harbor Laboratory Press2024-05-14
<![CDATA[
Immunotherapy-related cognitive impairment after CAR T cell therapy in mice
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https://biorxiv.org/cgi/content/short/2024.05.14.594163v1?rss=1"
Geraghty, A. C.Acosta-Alvarez, L.Rotiroti, M. C.Dutton, S.O'Dea, M.Woo, P.Xu, H.Shamardani, K.Mancusi, R.Ni, L.Mulinyawe, S. B.Kim, W. J.Liddelow, S.Majzner, R. G.Monje, M.2024-05-14doi:10.1101/2024.05.14.594163Cold Spring Harbor Laboratory Press2024-05-14
<![CDATA[
Structure of the lens MP20 mediated adhesive junction
]]>
https://biorxiv.org/cgi/content/short/2024.05.13.594022v1?rss=1"
Nicolas, W. J.Shiriaeva, A.Martynowycz, M. W.Grey, A. C.Ruma, Y.Donaldson, P. J.Gonen, T.2024-05-14doi:10.1101/2024.05.13.594022Cold Spring Harbor Laboratory Press2024-05-14
<![CDATA[
Ultrasound-actuated drug delivery with acoustic percolation switches
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https://biorxiv.org/cgi/content/short/2024.05.10.593654v1?rss=1"
Abundo, M. P.Tifrea, A. T.Buss, M. T.Barturen-Larrea, P.Jin, Z.Malounda, D.Shapiro, M. G.2024-05-14doi:10.1101/2024.05.10.593654Cold Spring Harbor Laboratory Press2024-05-14
<![CDATA[
IL-4 Licenses B Cell Activation Through Cholesterol Synthesis
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https://biorxiv.org/cgi/content/short/2024.05.13.593964v1?rss=1"
Steach, H. R.York, A. G.Skadow, M. H.Chen, S.Zhao, J.Williams, K. J.Zhou, Q.Hsieh, W.-Y.Brewer, J. R.Qu, R.Shyer, J. A.Harman, C.Sefik, E.Mowell, W. K.Bailis, W.Cui, C.Kluger, Y.Bensinger, S. J.Craft, J.Flavell, R.2024-05-15doi:10.1101/2024.05.13.593964Cold Spring Harbor Laboratory Press2024-05-15
<![CDATA[
Regulatory T cells restrain skin inflammation by modulating peripheral neuron activation
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https://biorxiv.org/cgi/content/short/2024.05.14.594055v1?rss=1"
Mendoza, A.Bou-Puerto, R.Giovanelli, P.Dikiy, S.Andretta, E.Rudensky, A.2024-05-15doi:10.1101/2024.05.14.594055Cold Spring Harbor Laboratory Press2024-05-15
<![CDATA[
FlyBox: A Flexible Open-Source Behavior Monitoring System
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https://biorxiv.org/cgi/content/short/2024.05.15.594443v1?rss=1"
Yu, A. D.Le, J. Q.Dai, X.Rosbash, M.2024-05-16doi:10.1101/2024.05.15.594443Cold Spring Harbor Laboratory Press2024-05-16
<![CDATA[
Courtship song differs between African and European populations of Drosophila melanogaster and involves a strong effect locus
]]>
https://biorxiv.org/cgi/content/short/2024.05.14.594231v1?rss=1"
Lollar, M. J.Kim, E.Stern, D. L.Pool, J. E.2024-05-17doi:10.1101/2024.05.14.594231Cold Spring Harbor Laboratory Press2024-05-17
<![CDATA[
Kinetic Analysis of Cyclization Reactions Performed by Substrate-Tolerant ProcM
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https://biorxiv.org/cgi/content/short/2024.05.16.594612v1?rss=1"
Desormeaux, E. K.van der Donk, W. A.2024-05-17doi:10.1101/2024.05.16.594612Cold Spring Harbor Laboratory Press2024-05-17
<![CDATA[
Deep-Tissue Spatial Omics: Imaging Whole-Embryo Transcriptomics and Subcellular Structures at High Spatial Resolution
]]>
https://biorxiv.org/cgi/content/short/2024.05.17.594641v1?rss=1"
Gandin, V.Kim, J.Yang, L.-Z.Lian, Y.Kawase, T.Hu, A.Rokicki, K.Fleishman, G.Tillberg, P.Aguilera Castrejon, A.Stringer, C.Preibisch, S.Liu, Z. J.2024-05-17doi:10.1101/2024.05.17.594641Cold Spring Harbor Laboratory Press2024-05-17
<![CDATA[
Sympathetic neuron-derived NPY protects from obesity by sustaining the mural progenitors of thermogenic adipocytes.
]]>
https://biorxiv.org/cgi/content/short/2024.05.18.594804v1?rss=1"
Zhu, Y.Yao, L.Gallo-Ferraz, A. L.Bombassaro, B.Simoes, M. R.Abe, I.Chen, J.Sarker, G.Ciccarelli, A.Zhou, L.Lee, C.Martinez-Sanchez, N.Dustin, M.Anderson, K.Zhan, C.Horvath, T.Velloso, L.Kajimura, S.Domingos, A. I.2024-05-21doi:10.1101/2024.05.18.594804Cold Spring Harbor Laboratory Press2024-05-21
<![CDATA[
Cell-type-specific effects of autism-associated chromosome 15q11.2-13.1 duplications in human brain
]]>
https://biorxiv.org/cgi/content/short/2024.05.22.595175v1?rss=1"
Dias, C.Mo, A.Cai, C.Sun, L.Cabral, K.Brownstein, C. A.Rockowitz, S.Walsh, C. A.2024-05-22doi:10.1101/2024.05.22.595175Cold Spring Harbor Laboratory Press2024-05-22
<![CDATA[
Intrinsic dynamics and neural implementation of a hypothalamic line attractor encoding an internal behavioral state
]]>
https://biorxiv.org/cgi/content/short/2024.05.21.595051v1?rss=1"
Vinograd, A.Nair, A.Linderman, S. W.Anderson, D. J.2024-05-22doi:10.1101/2024.05.21.595051Cold Spring Harbor Laboratory Press2024-05-22
<![CDATA[
Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance
]]>
https://biorxiv.org/cgi/content/short/2024.05.23.595634v1?rss=1"
Dadonaite, B.Ahn, J. J.Ort, J. T.Yu, J.Furey, C.Dosey, A.Hannon, W. W.Baker, A. V.Webby, R. J.King, N. P.Liu, Y.Hensley, S. E.Peacock, T. P.Moncla, L. H.Bloom, J. D.2024-05-24doi:10.1101/2024.05.23.595634Cold Spring Harbor Laboratory Press2024-05-24
<![CDATA[
Discovery and characterization of dietary antigens in oral tolerance
]]>
https://biorxiv.org/cgi/content/short/2024.05.26.593976v1?rss=1"
Blum, J. E.Kong, R.Schulman, E. A.Chen, F. M.Upadhyay, R.Romero-Meza, G.Littman, D. R.Fischbach, M.Nagashima, K.Sattely, E. S.2024-05-29doi:10.1101/2024.05.26.593976Cold Spring Harbor Laboratory Press2024-05-29
<![CDATA[
Structural and functional analysis of the Nipah virus polymerase complex
]]>
https://biorxiv.org/cgi/content/short/2024.05.29.596445v1?rss=1"
Hu, S.Kim, H.Yang, P.Yu, Z.Ludeke, B.Mobilia, S.Pan, J.Stratton, M.Bian, Y.Fearns, R.Abraham, J.2024-05-29doi:10.1101/2024.05.29.596445Cold Spring Harbor Laboratory Press2024-05-29
<![CDATA[
Overlapping role of synaptophysin and synaptogyrin family proteins in determining the small size of synaptic vesicles
]]>
https://biorxiv.org/cgi/content/short/2024.05.29.596401v1?rss=1"
Park, D.Fujise, K.Wu, Y.Lujan, R.Del Olmo-Cabrera, S.Wesseling, J.De Camilli, P.2024-05-31doi:10.1101/2024.05.29.596401Cold Spring Harbor Laboratory Press2024-05-31
<![CDATA[
Early mouse ovarian follicles develop into a thecal cell network that generates androgens during peri-puberty
]]>
https://biorxiv.org/cgi/content/short/2024.05.30.596686v1?rss=1"
Yin, Q.Spradling, A. C.2024-05-31doi:10.1101/2024.05.30.596686Cold Spring Harbor Laboratory Press2024-05-31
<![CDATA[
Periodic ER-plasma membrane junctions support long-range Ca2+ signal integration in dendrites
]]>
https://biorxiv.org/cgi/content/short/2024.05.27.596121v1?rss=1"
Benedetti, L.Fan, R.Weigel, A. V.Moore, A. S.Houlihan, P. R.Kittisopikul, M.Park, G.Petruncio, A.Hubbard, P. M.Pang, S.Xu, C. S.Hess, H.Saalfeld, S.Rangaraju, V.Clapham, D. E.De Camilli, P.Ryan, T. A.Lippincott-Schwartz, J.2024-05-31doi:10.1101/2024.05.27.596121Cold Spring Harbor Laboratory Press2024-05-31
<![CDATA[
Optical Torque Calculations and Measurements for DNA Torsional Studies
]]>
https://biorxiv.org/cgi/content/short/2024.05.29.596477v1?rss=1"
Hong, Y.Ye, F.Qian, J.Gao, X.Inman, J.Wang, M. D.2024-06-01doi:10.1101/2024.05.29.596477Cold Spring Harbor Laboratory Press2024-06-01
<![CDATA[
The structures of protein kinase A in complex with CFTR: mechanisms of phosphorylation and reversible activation
]]>
https://biorxiv.org/cgi/content/short/2024.05.28.596263v1?rss=1"
Fiedorczuk, K.Iordanov, I.Mihalyi, C.Szollosi, A.Csanady, L.Chen, J.2024-06-01doi:10.1101/2024.05.28.596263Cold Spring Harbor Laboratory Press2024-06-01
<![CDATA[
CRMP/UNC-33 maintains neuronal microtubule arrays by promoting individual microtubule rescue
]]>
https://biorxiv.org/cgi/content/short/2024.05.31.596870v1?rss=1"
Liang, X.Agulto, R.Eichel, K.Taylor, C. A.Paat, V. A.Deng, H.Ori-McKenney, K. M.Shen, K.2024-06-01doi:10.1101/2024.05.31.596870Cold Spring Harbor Laboratory Press2024-06-01
<![CDATA[
Genes of the fatty acid oxidation pathway are upregulated in female as compared to male cardiomyocytes
]]>
https://biorxiv.org/cgi/content/short/2024.05.29.594850v1?rss=1"
Talukdar, M.Chmatal, L.Mao, L.Reichart, D.Murashige, D.Skaletsky, Y.DeLaughter, D. M.Arany, Z.Seidman, J.Seidman, C.Page, D. C.2024-06-02doi:10.1101/2024.05.29.594850Cold Spring Harbor Laboratory Press2024-06-02
<![CDATA[
The conformational landscape of fold-switcher KaiB is tuned to the circadian rhythm timescale
]]>
https://biorxiv.org/cgi/content/short/2024.06.03.597139v1?rss=1"
Wayment-Steele, H. K.Otten, R.Pitsawong, W.Ojoawo, A. M.Glaser, A.Calderone, L. A.Kern, D.2024-06-03doi:10.1101/2024.06.03.597139Cold Spring Harbor Laboratory Press2024-06-03
<![CDATA[
Distinct Perception Mechanisms of BACH1 Quaternary Structure Degrons by Two F-box Proteins under Oxidative Stress
]]>
https://biorxiv.org/cgi/content/short/2024.06.03.594717v1?rss=1"
Cao, S.Shi, H.Garcia, S. F.Kito, Y.Shi, H.Goldberg, H. V.Ponce, J.Ueberheide, B.Lignitto, L.Pagano, M.Zheng, N.2024-06-03doi:10.1101/2024.06.03.594717Cold Spring Harbor Laboratory Press2024-06-03
<![CDATA[
Dietary isoleucine content defines the metabolic and molecular response to a Western diet
]]>
https://biorxiv.org/cgi/content/short/2024.05.30.596340v1?rss=1"
Trautman, M. E.Green, C. L.MacArthur, M. R.Chaiyakul, K.Alam, Y. H.Yeh, C.-Y.Babygirija, R.James, I.Gilpin, M.Zelenovskiy, E.Green, M.Marshall, R. N.Sonsalla, M. M.Flores, V.Simcox, J.Ong, I. M.Malecki, K.Jang, C.Lamming, D.2024-06-03doi:10.1101/2024.05.30.596340Cold Spring Harbor Laboratory Press2024-06-03
<![CDATA[
Protein Sequence Domain Annotation using Language Models
]]>
https://biorxiv.org/cgi/content/short/2024.06.04.596712v1?rss=1"
Sarkar, A.Krishnan, K.Eddy, S. R.2024-06-05doi:10.1101/2024.06.04.596712Cold Spring Harbor Laboratory Press2024-06-05
<![CDATA[
Spatial Single-cell Analysis Decodes Cortical Layer and Area Specification
]]>
https://biorxiv.org/cgi/content/short/2024.06.05.597673v1?rss=1"
Qian, X.Coleman, K.Jiang, S.Kriz, A. J.Marciano, J. H.Luo, C.Cai, C.Manam, M. D.Caglayan, E.Otani, A.Ghosh, U.Shao, D. D.Andersen, R. E.Neil, J. E.Johnson, R.LeFevre, A.Hecht, J. L.Miller, M. B.Sun, L.Stringer, C.Li, M.Walsh, C. A.2024-06-05doi:10.1101/2024.06.05.597673Cold Spring Harbor Laboratory Press2024-06-05
<![CDATA[
Multiplexed optical barcoding and sequencing for spatial omics
]]>
https://biorxiv.org/cgi/content/short/2024.06.04.597495v1?rss=1"
Venkatramani, A. V.Ciftci, D.Cohen, L.Li, C.Pham, K.Zhuang, X.2024-06-05doi:10.1101/2024.06.04.597495Cold Spring Harbor Laboratory Press2024-06-05
<![CDATA[
The inactive X chromosome drives sex differences in microglial inflammatory activity in human glioblastoma
]]>
https://biorxiv.org/cgi/content/short/2024.06.06.597433v1?rss=1"
Tharp, M. E.Han, C. Z.Balak, C. D.Fitzpatrick, C.O'Connor, C.Preissl, S.Buchanan, J.Nott, A.Escoubet, L.Mavrommatis, K.Gupta, M.Schwartz, M. S.U, H. S.Jones, P. S.Levy, M. L.Gonda, D. D.Ben-Haim, S.Ciacci, J.Barba, D.Khalessi, A.Coufal, N. G.Chen, C. C.Glass, C. K.Page, D. C.2024-06-06doi:10.1101/2024.06.06.597433Cold Spring Harbor Laboratory Press2024-06-06
<![CDATA[
An Updated Structure of Oxybutynin Hydrochloride
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https://biorxiv.org/cgi/content/short/2024.06.05.597682v1?rss=1"
Lin, J.Bu, G.Unge, J.Gonen, T.2024-06-06doi:10.1101/2024.06.05.597682Cold Spring Harbor Laboratory Press2024-06-06
<![CDATA[
Structural polymorphism and diversity of human segmental duplications
]]>
https://biorxiv.org/cgi/content/short/2024.06.04.597452v1?rss=1"
Jeong, H.Dishuck, P. C.Yoo, D.Harvey, W. T.Munson, K. M.Lewis, A. P.Kordosky, J.Garcia, G. H.Human Genome Structural Variation Consortium (HGSVC),Yilmaz, F.Hallast, P.Lee, C.Pastinen, T.Eichler, E. E.2024-06-06doi:10.1101/2024.06.04.597452Cold Spring Harbor Laboratory Press2024-06-06
<![CDATA[
Comparative connectomics of the descending and ascending neurons of the Drosophila nervous system: stereotypy and sexual dimorphism
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https://biorxiv.org/cgi/content/short/2024.06.04.596633v1?rss=1"
Stuerner, T.Brooks, P.Serratosa Capdevila, L.Morris, B. J.Javier, A.Fang, S.Gkantia, M.Cachero, S.Beckett, I. R.Champion, A. S.Moitra, I.Richards, A.Klemm, F.Kugel, L.Namiki, S.Cheong, H. S.Kovalyak, J.Tenshaw, E.Parekh, R.Schlegel, P.Phelps, J. S.Mark, B.Dorkenwald, S.Bates, A. S.Matsliah, A.Yu, S.-c.McKellar, C. E.Sterling, A.Seung, S.Murthy, M.Tuthill, J.Lee, W.-C. A.Card, G. M.Costa, M.Jefferis, G. S. X. E.Eichler, K.2024-06-06doi:10.1101/2024.06.04.596633Cold Spring Harbor Laboratory Press2024-06-06
<![CDATA[
UNC-6/Netrin promotes both adhesion and directed growth within a single axon
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https://biorxiv.org/cgi/content/short/2024.06.05.597665v1?rss=1"
Nichols, E. L.Lee, J.Shen, K.2024-06-06doi:10.1101/2024.06.05.597665Cold Spring Harbor Laboratory Press2024-06-06
<![CDATA[
Identification and characterization of a human MORC2 DNA binding region that is required for gene silencing
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https://biorxiv.org/cgi/content/short/2024.06.05.597643v1?rss=1"
Fendler, N. L.Ly, J.Welp, L.Urlaub, H.Vos, S. M.2024-06-06doi:10.1101/2024.06.05.597643Cold Spring Harbor Laboratory Press2024-06-06
<![CDATA[
Hematopoietic stem cell division is governed by distinct RUNX1 binding partners.
]]>
https://biorxiv.org/cgi/content/short/2024.06.07.596542v1?rss=1"
Robertson, A. L.Yue, L.Choudhuri, A.Kubaczka, C.Wattrus, S. J.Mandelbaum, J.Avagyan, S.Yang, S.Freeman, R. J.Chan, V.Blair, M. C.Daley, G. Q.Zon, L. I.2024-06-08doi:10.1101/2024.06.07.596542Cold Spring Harbor Laboratory Press2024-06-08
<![CDATA[
Lysosome damage triggers acute formation of ER to lysosomes membrane tethers mediated by the bridge-like lipid transport protein VPS13C
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https://biorxiv.org/cgi/content/short/2024.06.08.598070v1?rss=1"
Wang, X.Xu, P.Bentley-DeSousa, A.Hancock-Cerutti, W.Cai, S.Johnson, B. T.Tonelli, F.Talaia, G.Alessi, D. R.Ferguson, S. M.De Camilli, P.2024-06-08doi:10.1101/2024.06.08.598070Cold Spring Harbor Laboratory Press2024-06-08
<![CDATA[
Targeted mutagenesis of specific genomic DNA sequences in animals for the in vivo generation of variant libraries
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https://biorxiv.org/cgi/content/short/2024.06.10.598328v1?rss=1"
20 gRNAs that can efficiently introduce mutations along a 200bp sequence, making it a promising tool to test enhancer function in vivo in a high throughput manner.
]]>Falo-Sanjuan, J.Diaz-Tirado, Y.Turner, M. A.Davis, J.Medrano, C.Haines, J.McKenna, J.Eisen, M. B.Garcia, H. G.2024-06-10doi:10.1101/2024.06.10.598328Cold Spring Harbor Laboratory Press2024-06-10
<![CDATA[
C-LTMRs mediate wet dog shakes via the spinoparabrachial pathway
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https://biorxiv.org/cgi/content/short/2024.06.10.597395v1?rss=1"
Zhang, D.Turecek, J.Choi, S.Delisle, M.Pamplona, C. L.Meltzer, S.Ginty, D. D.2024-06-11doi:10.1101/2024.06.10.597395Cold Spring Harbor Laboratory Press2024-06-11
<![CDATA[
Where is the boundary of the human pseudoautosomal region?
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https://biorxiv.org/cgi/content/short/2024.06.10.598234v1?rss=1"
Bellott, D. W.Hughes, J. W.Skaletsky, H.Owen, E. C.Page, D. C.2024-06-11doi:10.1101/2024.06.10.598234Cold Spring Harbor Laboratory Press2024-06-11
<![CDATA[
Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome
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https://biorxiv.org/cgi/content/short/2024.06.12.598715v1?rss=1"
Arkinson, C.Dong, K. C.Gee, C. L.Costello, S. M.Marqusee, S.Martin, A.2024-06-12doi:10.1101/2024.06.12.598715Cold Spring Harbor Laboratory Press2024-06-12
<![CDATA[
Molecular insights into the interaction between a disordered protein and a folded RNA
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https://biorxiv.org/cgi/content/short/2024.06.12.598678v1?rss=1"
Mitra, R.Usher, E. T.Dedeoglu, S.Crotteau, M. J.Fraser, O. A.Yannawar, N. H.Gadkari, V. V.Ruotolo, B. T.Holehouse, A. S.Salmon, L.Showalter, S. A.Bardwell, J. C.2024-06-12doi:10.1101/2024.06.12.598678Cold Spring Harbor Laboratory Press2024-06-12
<![CDATA[
Comparative connectomics of two distantly related nematode species reveals patterns of nervous system evolution
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https://biorxiv.org/cgi/content/short/2024.06.13.598904v1?rss=1"
Cook, S. J.Kalinski, C. A.Loer, C. M.Memar, N.Majeed, M.Stephen, S. R.Bumbarger, D. J.Riebesell, M.Schnabel, R.Sommer, R. J.Hobert, O.2024-06-13doi:10.1101/2024.06.13.598904Cold Spring Harbor Laboratory Press2024-06-13
<![CDATA[
Comparative analysis of new, mScarlet-based red fluorescent tags in Caenorhabditis elegans
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https://biorxiv.org/cgi/content/short/2024.06.11.598534v1?rss=1"
Cao, W. X.Merritt, D.Pe, K.Cesar, M.Hobert, O.2024-06-13doi:10.1101/2024.06.11.598534Cold Spring Harbor Laboratory Press2024-06-13
<![CDATA[
Zinc-starved Brassicaceae Plants Secrete Peptides thatInduce Root Expansion
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https://biorxiv.org/cgi/content/short/2024.06.11.598559v1?rss=1"
Niehs, S.Rajniak, J.Johnson, A.Wengier, D. L.Sattely, E.2024-06-14doi:10.1101/2024.06.11.598559Cold Spring Harbor Laboratory Press2024-06-14
<![CDATA[
Design of Repeat Alpha-Beta Proteins with Capping Helices
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https://biorxiv.org/cgi/content/short/2024.06.15.590358v1?rss=1"
Baker, D.Zorine, D.2024-06-16doi:10.1101/2024.06.15.590358Cold Spring Harbor Laboratory Press2024-06-16
<![CDATA[
Cryo-electron tomography reveals the microtubule-bound form of inactive LRRK2
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https://biorxiv.org/cgi/content/short/2024.06.18.599606v1?rss=1"
Chen, S.Basiashvili, T.Hutchings, J.Murillo, M. S.Suarez, A. V.Louro, J. A.Leschziner, A. E.Villa, E.2024-06-20doi:10.1101/2024.06.18.599606Cold Spring Harbor Laboratory Press2024-06-20
<![CDATA[
Harmonic imaging for nonlinear detection of acoustic biomolecules
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https://biorxiv.org/cgi/content/short/2024.06.18.599141v1?rss=1"
Nayak, R.Duan, M.Ling, B.Jin, Z.Malounda, D.Shapiro, M. G.2024-06-22doi:10.1101/2024.06.18.599141Cold Spring Harbor Laboratory Press2024-06-22
<![CDATA[
Variation in season length and development time is sufficient to drive the emergence and coexistence of social and solitary behavioral strategies
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https://biorxiv.org/cgi/content/short/2024.06.18.599518v1?rss=1"
Ruttenberg, D. M.Levin, S. A.Wingreen, N. S.Kocher, S. D.2024-06-22doi:10.1101/2024.06.18.599518Cold Spring Harbor Laboratory Press2024-06-22
<![CDATA[
Single-molecule live imaging of subunit interactions and exchange within cellular regulatory complexes
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https://biorxiv.org/cgi/content/short/2024.06.25.600644v1?rss=1"
Graham, T. G. W.Dugast-Darzacq, C.Dailey, G. M.Weng, B.Darzacq, X.Tjian, R.2024-06-25doi:10.1101/2024.06.25.600644Cold Spring Harbor Laboratory Press2024-06-25
<![CDATA[
STHD: probabilistic cell typing of single Spots in whole Transcriptome spatial data with High Definition
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https://biorxiv.org/cgi/content/short/2024.06.20.599803v1?rss=1"
Sun, C.Zhang, Y.2024-06-25doi:10.1101/2024.06.20.599803Cold Spring Harbor Laboratory Press2024-06-25
<![CDATA[
Structural basis for the transport and regulation mechanism of the Multidrug resistance-associated protein 2
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https://biorxiv.org/cgi/content/short/2024.06.24.600277v1?rss=1"
Koide, E.Pietz, H. L.Beltran, J.Chen, J.2024-06-25doi:10.1101/2024.06.24.600277Cold Spring Harbor Laboratory Press2024-06-25
<![CDATA[
De Novo Design of Integrin α5β1 Modulating Proteins for Regenerative Medicine
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https://biorxiv.org/cgi/content/short/2024.06.21.600123v1?rss=1"
Wang, X.Guillem-Marti, J.Kumar, S.Lee, D.Werther, R.Alamo, K. A. E.Zhao, Y.-T.Nguyen, A.Kopyeva, I.Huang, B.Li, J.Hao, Y.Li, X.Cabrerizo-Aguado, D.Brizuela-Velasco, A.Murray, A. N.Gerben, S.Roy, A.DeForest, C. A.Springer, T.Ruohola-Baker, H.Cooper, J.Campbell, M. G.Manero, J. M.Ginebra, M.-P.Baker, D.2024-06-25doi:10.1101/2024.06.21.600123Cold Spring Harbor Laboratory Press2024-06-25
<![CDATA[
A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex
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https://biorxiv.org/cgi/content/short/2024.06.25.600673v1?rss=1"
Xavier, A. M.Lin, Q.Kang, C. J.Cheadle, L.2024-06-26doi:10.1101/2024.06.25.600673Cold Spring Harbor Laboratory Press2024-06-26
<![CDATA[
Chromosome-scale genome assembly and gene annotation of the hydrothermal vent annelid Alvinella pompejana yield insight into animal evolution in extreme environments
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https://biorxiv.org/cgi/content/short/2024.06.25.600561v1?rss=1"
El Hilali, S.Dru, P.Le Moan, A.Li, Y. I.Huynen, M.Hoelz, A.Robinson, R. C.Martin-Duran, J. M.Jollivet, D.Claridge-Chang, A.Copley, R. R.2024-06-27doi:10.1101/2024.06.25.600561Cold Spring Harbor Laboratory Press2024-06-27
<![CDATA[
Diversification of gene expression across extremophytes and stress-sensitive species in the Brassicaceae
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https://biorxiv.org/cgi/content/short/2024.06.21.599952v1?rss=1"
Wang, G.Ryu, K. H.Dinneny, A.Carlson, J.Goodstein, D. M.Lee, J.Oh, D.-H.Oliva, M.Lister, R.Dinneny, J. R.Schiefelbein, J.Dassanayake, M.2024-06-27doi:10.1101/2024.06.21.599952Cold Spring Harbor Laboratory Press2024-06-27
<![CDATA[
Exploration and exploitation are flexibly balanced during local search in flies
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https://biorxiv.org/cgi/content/short/2024.06.26.600764v1?rss=1"
Goldschmidt, D.Guo, Y.Chitnis, S. S.Christoforou, C.Turner-Evans, D.Ribeiro, C.Hermundstad, A.Jayaraman, V.Haberkern, H.2024-06-28doi:10.1101/2024.06.26.600764Cold Spring Harbor Laboratory Press2024-06-28
<![CDATA[
Widespread destabilization of C. elegans microRNAs by the E3 ubiquitin ligase EBAX-1
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https://biorxiv.org/cgi/content/short/2024.06.28.601170v1?rss=1"
Stubna, M. W.Shukla, A.Bartel, D. P.2024-06-29doi:10.1101/2024.06.28.601170Cold Spring Harbor Laboratory Press2024-06-29
<![CDATA[
Quantification of Salmonella enterica serovar Typhimurium Population Dynamics in Murine Infection Using a Highly Diverse Barcoded Library
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https://biorxiv.org/cgi/content/short/2024.06.28.601246v1?rss=1"
Hotinger, J. A.Campbell, I. W.Hullahali, K.Osaki, A.Waldor, M. K.2024-06-29doi:10.1101/2024.06.28.601246Cold Spring Harbor Laboratory Press2024-06-29
<![CDATA[
A widespread electrical brain network encodes anxiety in health and depressive states
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https://biorxiv.org/cgi/content/short/2024.06.26.600900v1?rss=1"
Hughes, D. N.Klein, M. H.Walder-Christensen, K. K.Thomas, G. E.Grossman, Y.Waters, D.Matthews, A. E.Carson, W. E.Filali, Y.Tsyglakova, M.Fink, A.Gallagher, N. M.Perez-Balaguer, M.McClung, C. A.Zarate, J. M.Hultman, R. C.Mague, S. D.Carlson, D.Dzirasa, K.2024-06-30doi:10.1101/2024.06.26.600900Cold Spring Harbor Laboratory Press2024-06-30
<![CDATA[
Towards a simplified model of primary visual cortex
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https://biorxiv.org/cgi/content/short/2024.06.30.601394v1?rss=1"
Du, F.Nunez-Ochoa, M. A.Pachitariu, M.Stringer, C.2024-07-02doi:10.1101/2024.06.30.601394Cold Spring Harbor Laboratory Press2024-07-02
<![CDATA[
Functional ultrasound neuroimaging reveals mesoscopic organization of saccades in the lateral intraparietal area of posterior parietal cortex
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https://biorxiv.org/cgi/content/short/2024.06.28.600796v1?rss=1"
Griggs, W. S.Norman, S. L.Tanter, M.Liu, C.Christopoulos, V.Shapiro, M. G.Andersen, R. A.2024-07-02doi:10.1101/2024.06.28.600796Cold Spring Harbor Laboratory Press2024-07-02
<![CDATA[
Cytosolic N6AMT1-dependent translation supports mitochondrial RNA processing
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https://biorxiv.org/cgi/content/short/2024.07.02.601698v1?rss=1"
Foged, M. M.Recazens, E.Chollet, S.Lisci, M.Allen, G. E.Zinshteyn, B.Boutguetait, D.Munch, C. A.Mootha, V. K.Jourdain, A. A.2024-07-02doi:10.1101/2024.07.02.601698Cold Spring Harbor Laboratory Press2024-07-02
<![CDATA[
iTome Volumetric Serial Sectioning Apparatus for TEM
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https://biorxiv.org/cgi/content/short/2024.07.02.601671v1?rss=1"
Peale, D. R.Hess, H.Lee, P. R.Cardona, A.Bock, D.Schneider-Mizell, C. M.Fetter, R. D.Lee, W.-P.Robinson, C. G.Iyer, N.Managan, C.2024-07-04doi:10.1101/2024.07.02.601671Cold Spring Harbor Laboratory Press2024-07-04
<![CDATA[
ZIP13 regulates lipid metabolism by changing intracellular iron and zinc balance
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https://biorxiv.org/cgi/content/short/2024.07.03.601606v1?rss=1"
Fukunaka, A.Tanaka, G.Kimura, T.Hengphasatporn, K.Saito, D.Shigeta, M.Shibata, H.Ichinose, T.Abe, I.Shimura, M.Sato, T.Nakagawa, Y.Horii, T.Hatada, I.Kajimura, S.Kiyonari, H.Sakurai, H.Shigeta, Y.Watada, H.Fukada, T.Fujitani, Y.2024-07-05doi:10.1101/2024.07.03.601606Cold Spring Harbor Laboratory Press2024-07-05
<![CDATA[
Restoration of locus coeruleus noradrenergic transmission during sleep
]]>
https://biorxiv.org/cgi/content/short/2024.07.03.601820v1?rss=1"
Sima, J.Zhang, Y.Farriday, D.Ahn, A. Y.-E.Lopez, E. R.Jin, C.Harrell, J.Darmohray, D.Silverman, D.Dan, Y.2024-07-05doi:10.1101/2024.07.03.601820Cold Spring Harbor Laboratory Press2024-07-05
<![CDATA[
TRPML1 gating modulation by allosteric mutations and lipids
]]>
https://biorxiv.org/cgi/content/short/2024.07.04.602033v1?rss=1"
Gan, N.Han, Y.Zeng, W.Jiang, Y.2024-07-07doi:10.1101/2024.07.04.602033Cold Spring Harbor Laboratory Press2024-07-07
<![CDATA[
'Target-and-release' nanoparticles for effective immunotherapy of metastatic ovarian cancer
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https://biorxiv.org/cgi/content/short/2024.07.05.602135v1?rss=1"
Pires, I. S.Covarrubias, G.Gomerdinger, V. F.Backlund, C. M.Shanker, A.Gordon, E.Wu, S.Pickering, A. J.Melo, M. B.Suh, H.Irvine, D. J.Hammond, P. T.2024-07-07doi:10.1101/2024.07.05.602135Cold Spring Harbor Laboratory Press2024-07-07
<![CDATA[
Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
]]>
https://biorxiv.org/cgi/content/short/2024.07.08.602613v1?rss=1"
Rengarajan, S.Derks, J.Bellott, D. W.Slavov, N.Page, D. C.2024-07-10doi:10.1101/2024.07.08.602613Cold Spring Harbor Laboratory Press2024-07-10
<![CDATA[
Rapid evolution of gene expression patterns in flowering plants
]]>
https://biorxiv.org/cgi/content/short/2024.07.08.602577v1?rss=1"
Schuster, C.Gabel, A.Drost, H.-G.Grosse, I.Leyser, O.Meyerowitz, E. M.2024-07-10doi:10.1101/2024.07.08.602577Cold Spring Harbor Laboratory Press2024-07-10
<![CDATA[
Acute rapamycin treatment reveals novel mechanisms of behavioral, physiological, and functional dysfunction in a maternal inflammation mouse model of autism and sensory over-responsivity
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https://biorxiv.org/cgi/content/short/2024.07.08.602602v1?rss=1"
Le Belle, J. E.Condro, M.Cepeda, C.Oikonomou, K. D.Tessema, K.Dudley, L.Schoenfield, J.Kawaguchi, R.Geschwind, D.Silva, A. J.Zhang, Z.Shokat, K.Harris, N. G.Kornblum, H. I.2024-07-11doi:10.1101/2024.07.08.602602Cold Spring Harbor Laboratory Press2024-07-11
<![CDATA[
Chromosomal fusion drives sex chromosome evolution in treehoppers despite long-term X chromosome conservation
]]>
https://biorxiv.org/cgi/content/short/2024.07.12.603334v1?rss=1"
Palmer Droguett, D. H.Fletcher, M.Kocher, S. D.Cabral-de-Mello, D. C.Wright, A.2024-07-15doi:10.1101/2024.07.12.603334Cold Spring Harbor Laboratory Press2024-07-15
<![CDATA[
Diffusing protein binders to intrinsically disordered proteins
]]>
https://biorxiv.org/cgi/content/short/2024.07.16.603789v1?rss=1"
Liu, C.Wu, K.Choi, H.Han, H.Zhang, X.Watson, J. L.Shijo, S.Bera, A. K.Kang, A.Brackenbrough, E.Coventry, B.Hick, D. R.Hoofnagle, A. N.Zhu, P.Li, X.Decarreau, J.Gerben, S. R.Yang, W.Wang, X.Lamp, M.Murray, A.Bauer, M.Baker, D.2024-07-16doi:10.1101/2024.07.16.603789Cold Spring Harbor Laboratory Press2024-07-16
<![CDATA[
Single-molecule live-cell RNA imaging with CRISPR-Csm
]]>
https://biorxiv.org/cgi/content/short/2024.07.14.603457v1?rss=1"
Xia, C.Colognori, D.Jiang, X.Xu, K.Doudna, J. A.2024-07-16doi:10.1101/2024.07.14.603457Cold Spring Harbor Laboratory Press2024-07-16
<![CDATA[
Functional analysis of conserved C. elegans bHLH family members uncovers lifespan control by a peptidergic hub neuron
]]>
https://biorxiv.org/cgi/content/short/2024.07.12.603289v1?rss=1"
Aguilar, G. R.Vidal, B.Ji, H.Evenblij, J.Ji, H.Valperga, G.Liao, C.-P.Fang-Yen, C.Hobert, O.2024-07-16doi:10.1101/2024.07.12.603289Cold Spring Harbor Laboratory Press2024-07-16
<![CDATA[
Local keratinocyte-nociceptor interactions enhance obesity-mediated small fiber neuropathy via NGF-TrkA-PI3K signaling axis
]]>
https://biorxiv.org/cgi/content/short/2024.07.12.603316v1?rss=1"
Koui, Y.Song, S.Dong, X.Mukouyama, Y.-S.2024-07-16doi:10.1101/2024.07.12.603316Cold Spring Harbor Laboratory Press2024-07-16
<![CDATA[
Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile
]]>
https://biorxiv.org/cgi/content/short/2024.07.15.603560v1?rss=1"
Sulaiman, J. E.Thompson, J.Cheung, P. L. K.Qian, Y.Mill, J.James, I.Vivas, E.Simcox, J.Venturelli, O. S.2024-07-17doi:10.1101/2024.07.15.603560Cold Spring Harbor Laboratory Press2024-07-17
<![CDATA[
Single-cell gene-expression measurements in Vibrio cholerae biofilms reveal spatiotemporal patterns underlying development
]]>
https://biorxiv.org/cgi/content/short/2024.07.17.603784v1?rss=1"
Johnson, G. E.Fei, C.Wingreen, N. S.Bassler, B. L.2024-07-17doi:10.1101/2024.07.17.603784Cold Spring Harbor Laboratory Press2024-07-17
<![CDATA[
Long range regulation of transcription scales with genomic distance in a gene specific manner
]]>
https://biorxiv.org/cgi/content/short/2024.07.19.604327v1?rss=1"
Jensen, C. L.Chen, L.-F.Swigut, T.Crocker, O. J.Yao, D.Bassik, M. C.Ferrell, J.Boettiger, A.Wysocka, J.2024-07-19doi:10.1101/2024.07.19.604327Cold Spring Harbor Laboratory Press2024-07-19
<![CDATA[
Alternative splicing controls pan-neuronal homeobox gene expression
]]>
https://biorxiv.org/cgi/content/short/2024.07.16.603806v1?rss=1"
Leyva-Diaz, E.Cesar, M.Pe, K.Jorda-Llorens, J. I.Valdivia, J.Hobert, O.2024-07-19doi:10.1101/2024.07.16.603806Cold Spring Harbor Laboratory Press2024-07-19
<![CDATA[
The temporal refinement of Dach1 is a key step in the functional maturation of primary somatosensory neurons
]]>
https://biorxiv.org/cgi/content/short/2024.07.18.604081v1?rss=1"
Szemes, T.Sabate San Jose, A.Azouz, A.Sitte, M.Salinas, G.Achouri, Y.Kricha, S.Ris, L.Red-Horse, K.Bellefroid, E. J.Desiderio, S.2024-07-20doi:10.1101/2024.07.18.604081Cold Spring Harbor Laboratory Press2024-07-20
<![CDATA[
Encoding of cerebellar dentate neuronal activity during visual attention in rhesus macaques
]]>
https://biorxiv.org/cgi/content/short/2024.07.18.604119v1?rss=1"
Flierman, N. A.Koay, S. A.van Hoogstraten, W. S.Ruigrok, T. J. H.Roelfsema, P.Badura, A.De Zeeuw, C. I.2024-07-20doi:10.1101/2024.07.18.604119Cold Spring Harbor Laboratory Press2024-07-20
<![CDATA[
Deletion of wheat alpha-gliadins from chromosome 6D improves gluten strength and reduces immunodominant celiac disease epitopes
]]>
https://biorxiv.org/cgi/content/short/2024.07.19.604379v1?rss=1"
Rottersman, M. G.Zhang, W.Zhang, J.Grigorian, G.Burguener, G.Carter, C.Vang, T.Hegarty, J.Zhang, X.Dubcovsky, J.2024-07-23doi:10.1101/2024.07.19.604379Cold Spring Harbor Laboratory Press2024-07-23
<![CDATA[
STK19 positions TFIIH for cell-free transcription-coupled DNA repair
]]>
https://biorxiv.org/cgi/content/short/2024.07.22.604623v1?rss=1"
Mevissen, T. E. T.Kuemmecke, M.Schmid, E. W.Farnung, L.Walter, J. C.2024-07-23doi:10.1101/2024.07.22.604623Cold Spring Harbor Laboratory Press2024-07-23
<![CDATA[
Synapse protein signatures in cerebrospinal fluid and plasma predict cognitive maintenance versus decline in Alzheimers disease
]]>
https://biorxiv.org/cgi/content/short/2024.07.22.604680v1?rss=1"
Oh, H. S.-H.Urey, D. Y.Karlsson, L.Zhu, Z.Shen, Y.Farinas, A.Timsina, J.Guldner, I. H.Morshed, N.Yang, C.Western, D.Ali, M.Le Guen, Y.Trelle, A.Herukka, S.-K.Rauramaa, T.Hiltunen, M.Lipponen, A.Luikku, A. J.Poston, K. L.Mormino, E.Wagner, A. D.Wilson, E. N.Channappa, D.Leinonen, V.Stevens, B.Ehrenberg, A. J.Zetterberg, H.Bennett, D. A.Franzmeier, N.Hansson, O.Cruchaga, C.Wyss-Coray, T.2024-07-23doi:10.1101/2024.07.22.604680Cold Spring Harbor Laboratory Press2024-07-23
<![CDATA[
Parametrically guided design of beta barrels and transmembrane nanopores using deep learning
]]>
https://biorxiv.org/cgi/content/short/2024.07.22.604663v1?rss=1"
Kim, D. E.Watson, J. L.Juergens, D.Majumder, S.Gerben, S. R.Kang, A.Bera, A. K.Li, X.Baker, D.2024-07-23doi:10.1101/2024.07.22.604663Cold Spring Harbor Laboratory Press2024-07-23
<![CDATA[
Amortized template-matching of molecular conformations from cryo-electron microscopy images using simulation-based inference
]]>
https://biorxiv.org/cgi/content/short/2024.07.23.604154v1?rss=1"
Dingeldein, L.Silva-Sanchez, D.Evans, L.D'Imprima, E.Grigorieff, N.Covino, R.Cossio, P.2024-07-24doi:10.1101/2024.07.23.604154Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation
]]>
https://biorxiv.org/cgi/content/short/2024.07.23.604857v1?rss=1"
Lee, J.-S.Dan, T.Zhang, H.Cheng, Y.Rehfeld, F.Brugarolas, J.Mendell, J. T.2024-07-24doi:10.1101/2024.07.23.604857Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
RORγt-dependent antigen-presenting cells direct regulatory T cell-mediated tolerance to food antigen
]]>
https://biorxiv.org/cgi/content/short/2024.07.23.604803v1?rss=1"
Fu, L.Upadhyay, R.Pokrovskii, M.Romero-Meza, G.Griesemer, A.Littman, D. R.2024-07-24doi:10.1101/2024.07.23.604803Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
Stable centromere association of the yeast histone variant Cse4 requires its essential N-terminal domain
]]>
https://biorxiv.org/cgi/content/short/2024.07.24.604937v1?rss=1"
Popchock, A. R.Hedouin, S.Mao, Y.Asbury, C. L.Stergachis, A. B.Biggins, S.2024-07-24doi:10.1101/2024.07.24.604937Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
Mechanism-guided engineering of a minimal biological particle for genome editing
]]>
https://biorxiv.org/cgi/content/short/2024.07.23.604809v1?rss=1"
Ngo, W.Peukes, J. T.Baldwin, A.Xue, Z. W.Hwang, S.Stickels, R. R.Lin, Z.Satpathy, A.Wells, J. A.Schekman, R.Nogales, E.Doudna, J. A.2024-07-24doi:10.1101/2024.07.23.604809Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
Entorhinal cortex represents task-relevant remote locations independent of CA1
]]>
https://biorxiv.org/cgi/content/short/2024.07.23.604815v1?rss=1"
Aery Jones, E. A.Low, I. I. C.Cho, F. S.Giocomo, L. M.2024-07-24doi:10.1101/2024.07.23.604815Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds
]]>
https://biorxiv.org/cgi/content/short/2024.07.25.605164v1?rss=1"
Vasan, R.Ferrante, A.Borensztejn, A.Frick, C. L.Gaudreault, N.Mogre, S. S.Morris, B.Pires, G. G.Rafelski, S. M.Theriot, J. A.Viana, M. P.2024-07-26doi:10.1101/2024.07.25.605164Cold Spring Harbor Laboratory Press2024-07-26
<![CDATA[
In vivo analysis of the relationship between CP26 and qE-type NPQ via higher-order Arabidopsis cp26 mutants
]]>
https://biorxiv.org/cgi/content/short/2024.07.26.605339v1?rss=1"
Kromdijk, J.Walter, J.Patel-Tupper, D.Lam, L.Ma, A.Taylor, G.Fleming, G.Niyogi, K. K.2024-07-26doi:10.1101/2024.07.26.605339Cold Spring Harbor Laboratory Press2024-07-26
<![CDATA[
Environmentally-mediated selection parallels population divergence across a chimpanzee subspecies contact zone
]]>
https://biorxiv.org/cgi/content/short/2024.07.26.605171v1?rss=1"
Mitchell, M. W.Alexander, W.Mitchell, D. V.Freedman, A. H.Dordel, J.Harrigan, R. J.Sacan, A.Kentatchime, F.Featherstone, B. S.Abwe, E. E.Sesink Clee, P. R.Abwe, A. E.Locatelli, S.Morgan, B. J.Fosso, B.Fotso, R.Tishkoff, S. A.Eichler, E. E.Anthony, N. M.Smith, T. B.Gonder, M. K.2024-07-26doi:10.1101/2024.07.26.605171Cold Spring Harbor Laboratory Press2024-07-26
<![CDATA[
Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference
]]>
https://biorxiv.org/cgi/content/short/2024.07.28.605517v1?rss=1"
Lareau, C. A.Chapman, M. S.Penter, L.Nawy, T.Pe'er, D.Ludwig, L. S.2024-07-29doi:10.1101/2024.07.28.605517Cold Spring Harbor Laboratory Press2024-07-29
<![CDATA[
A bacterial TIR-based immune system senses viral capsids to initiate defense
]]>
https://biorxiv.org/cgi/content/short/2024.07.29.605636v1?rss=1"
Roberts, C.Fishman, C.Banh, D.Marraffini, L. A.2024-07-29doi:10.1101/2024.07.29.605636Cold Spring Harbor Laboratory Press2024-07-29
<![CDATA[
Chemical genetics reveals cross-activation of plant developmental signaling by the immune peptide-receptor pathway
]]>
https://biorxiv.org/cgi/content/short/2024.07.29.605519v1?rss=1"
Herrmann, A.Sepuru, K. M.Endo, H.Nakagawa, A.Kusao, S.Bai, P.Ziadi, A.Kato, H.Sato, A.Liu, J.Shan, L.Kimura, S.Itami, K.Uchida, N.Hagihara, S.Torii, K. U.2024-07-30doi:10.1101/2024.07.29.605519Cold Spring Harbor Laboratory Press2024-07-30
<![CDATA[
Paternal genome elimination creates contrasting evolutionary trajectories in male and female citrus mealybugs
]]>
https://biorxiv.org/cgi/content/short/2024.07.28.604693v1?rss=1"
Mongue, A. J.Woodman, T.Marshall, H.Garber, A. J.Franco, J. C.McCutcheon, J. P.Ross, L.2024-07-30doi:10.1101/2024.07.28.604693Cold Spring Harbor Laboratory Press2024-07-30
<![CDATA[
Complete sequencing of ape genomes
]]>
https://biorxiv.org/cgi/content/short/2024.07.31.605654v1?rss=1"
Yoo, D.Rhie, A.Hebbar, P.Antonacci, F.Logsdon, G. A.Solar, S. J.Antipov, D.Pickett, B. D.Safonova, Y.Montinaro, F.Luo, Y.Malukiewicz, J.Storer, J. M.Lin, J.Sequeira, A. N.Mangan, R. J.Hickey, G.Anez, G. M.Balachandran, P.Bankevich, A.Beck, C. R.Biddanda, A.Borchers, M.Bouffard, G. G.Brannan, E.Brooks, S. Y.Carbone, L.Carrel, L.Chan, A. P.Crawford, J.Diekhans, M.Engelbrecht, E.Feschotte, C.Formenti, G.Garcia, G. H.Gennaro, L. d.Gilbert, D.Green, R. E.Guarracino, A.Gupta, I.Haddad, D.Han, J.Harris, R. S.Hartley2024-07-31doi:10.1101/2024.07.31.605654Cold Spring Harbor Laboratory Press2024-07-31
<![CDATA[
The big tau splice isoform resists Alzheimer's-related pathological changes
]]>
https://biorxiv.org/cgi/content/short/2024.07.30.605685v1?rss=1"
Chung, D.-e. C.Deng, X.Yalamanchili, H. K.Revelli, J.-P.Han, A. L.Tadros, B.Richman, R.Dias, M.Alavi Naini, F.Boeynaems, S.Hyman, B. T.Zoghbi, H. Y.2024-07-31doi:10.1101/2024.07.30.605685Cold Spring Harbor Laboratory Press2024-07-31
<![CDATA[
Beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy
]]>
https://biorxiv.org/cgi/content/short/2024.07.31.605623v1?rss=1"
Pakharukova, N.Thomas, B. N.Bansia, H.Li, L.Abzalimov, R. R.Kim, J.Kahsai, A. W.Pani, B.Bassford, D. K.Liu, S.Zhang, X.des Georges, A.Lefkowitz, R. J.2024-07-31doi:10.1101/2024.07.31.605623Cold Spring Harbor Laboratory Press2024-07-31
<![CDATA[
Nonlinear sound-sheet microscopy: imaging opaque organs at the capillary and cellular scale
]]>
https://biorxiv.org/cgi/content/short/2024.07.31.605825v1?rss=1"
Heiles, B.Nelissen, F.Terwiel, D.Park, B. M.Munoz Ibarra, E.Matalliotakis, A.Waasdorp, R.Ara, T.Barturen-Larrea, P.Duan, M.Shapiro, M. G.Gazzola, V.Maresca, D.2024-07-31doi:10.1101/2024.07.31.605825Cold Spring Harbor Laboratory Press2024-07-31
<![CDATA[
CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation
]]>
https://biorxiv.org/cgi/content/short/2024.07.31.606079v1?rss=1"
Soczek, K. M.Cofsky, J. C.Tuck, O. T.Shi, H.Doudna, J. A.2024-07-31doi:10.1101/2024.07.31.606079Cold Spring Harbor Laboratory Press2024-07-31
<![CDATA[
Concerted modulation of spontaneous behavior and time-integrated whole-brain neuronal activity by serotonin receptors
]]>
https://biorxiv.org/cgi/content/short/2024.08.02.606282v1?rss=1"
Friedmann, D.Gonzalez, X.Moses, A.Watts, T.Degleris, A.Ticea, N.Song, J. H.Datta, S. R.Linderman, S. W.Luo, L.2024-08-03doi:10.1101/2024.08.02.606282Cold Spring Harbor Laboratory Press2024-08-03
<![CDATA[
PNPLA3(148M) Promotes Hepatic Steatosis by Interfering with Triglyceride Hydrolysis Through a Gain-of-Function Mechanism
]]>
https://biorxiv.org/cgi/content/short/2024.08.02.606015v1?rss=1"
View larger version (19K):
org.highwire.dtl.DTLVardef@1dd7acaorg.highwire.dtl.DTLVardef@1a869dborg.highwire.dtl.DTLVardef@1bde743org.highwire.dtl.DTLVardef@99effc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIABHD5 binds preferentially to PNPLA3 relative to ATGL.
C_LIO_LIPNPLA3(WT) and PNPLA3(148M) compete similarly for binding and inhibition of ATGL.
C_LIO_LIABHD5 activates the triglyceride lipase activity of PNPLA3, as well as ATGL.
C_LIO_LIThe steatotic effect of PNPLA3(148M) requires expression of ATGL.
C_LIO_LIOverexpression of ABHD5 can rescue the steatosis associated with PNPLA3(148M).
C_LI
]]>Wang, Y.Hong, S.Hudson, H.Kory, N.Kinch, L. N.Kozlitina, J.Cohen, J. C.Hobbs, H. H.2024-08-04doi:10.1101/2024.08.02.606015Cold Spring Harbor Laboratory Press2024-08-04
<![CDATA[
A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree
]]>
https://biorxiv.org/cgi/content/short/2024.08.05.606142v1?rss=1"
95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to systematically assess de novo mutations (DNMs) and recombination. From this family, we estimate an average of 192 DNMs per generation, including 75.5 de novo single-nucleotide variants (SNVs), 7.4 non-tandem repeat indels, 79.6 de novo indels or structural variants (SVs) originating from tandem repeats, 7.7 centromeric de novo SVs and SNVs, and 12.4 de novo Y chromosome events per generation. STRs and VNTRs are the most mutable with 32 loci exhibiting recurrent mutation through the generations. We accurately assemble 288 centromeres and six Y chromosomes across the generations, documenting de novo SVs, and demonstrate that the DNM rate varies by an order of magnitude depending on repeat content, length, and sequence identity. We show a strong paternal bias (75-81%) for all forms of germline DNM, yet we estimate that 17% of de novo SNVs are postzygotic in origin with no paternal bias. We place all this variation in the context of a high-resolution recombination map ([~]3.5 kbp breakpoint resolution). We observe a strong maternal recombination bias (1.36 maternal:paternal ratio) with a consistent reduction in the number of crossovers with increasing paternal (r=0.85) and maternal (r=0.65) age. However, we observe no correlation between meiotic crossover locations and de novo SVs, arguing against non-allelic homologous recombination as a predominant mechanism. The use of multiple orthogonal technologies, near-telomere-to-telomere phased genome assemblies, and a multi-generation family to assess transmission has created the most comprehensive, publicly available "truth set" of all classes of genomic variants. The resource can be used to test and benchmark new algorithms and technologies to understand the most fundamental processes underlying human genetic variation.
]]>Porubsky, D.Dashnow, H.Sasani, T. A.Logsdon, G. A.Hallast, P.Noyes, M. D.Kronenberg, Z. N.Mokveld, T.Koundinya, N.Nolan, C.Steely, C. J.Guarracino, A.Dolzhenko, E.Harvey, W. T.Rowell, W. J.Grigorev, K.Nicholas, T. J.Oshima, K. K.Lin, J.Ebert, P.Watkins, W. S.Leung, T. Y.Hanlon, V. C. T.McGee, S.Pedersen, B. S.Goldberg, M. E.Happ, H. C.Jeong, H.Munson, K. M.Hoekzema, K.Chan, D. D.Wang, Y.Knuth, J.Garcia, G. H.Fanslow, C.Lambert, C.Lee, C.Smith, J. D.Levy, S. E.Mason, C. E.Garrison, E.Lansdorp, P. M.Neklason, D.2024-08-05doi:10.1101/2024.08.05.606142Cold Spring Harbor Laboratory Press2024-08-05
<![CDATA[
The molecular basis of Human FN3K mediated phosphorylation of glycated substrate
]]>
https://biorxiv.org/cgi/content/short/2024.08.05.606604v1?rss=1"
Garg, A.On, K. F.Xiao, Y.Elkayam, E.Cifani, P.David, Y.Joshua-Tor, L.2024-08-05doi:10.1101/2024.08.05.606604Cold Spring Harbor Laboratory Press2024-08-05
<![CDATA[
Nanoscale volumetric fluorescence imaging via photochemical sectioning
]]>
https://biorxiv.org/cgi/content/short/2024.08.01.605857v1?rss=1"
Wang, W.Ruan, X.Liu, G.Milkie, D. E.Li, W.Betzig, E.Upadhyayula, S.Gao, R.2024-08-05doi:10.1101/2024.08.01.605857Cold Spring Harbor Laboratory Press2024-08-05
<![CDATA[
Antiviral Mx proteins have an ancient origin and widespread distribution among eukaryotes
]]>
https://biorxiv.org/cgi/content/short/2024.08.06.606855v1?rss=1"
Langley, C. A.Dietzen, P. A.Emerman, M.Tenthorey, J. L.Malik, H. S.2024-08-06doi:10.1101/2024.08.06.606855Cold Spring Harbor Laboratory Press2024-08-06
<![CDATA[
Bridging tuning and invariance with equivariant neuronal representations
]]>
https://biorxiv.org/cgi/content/short/2024.08.02.606398v1?rss=1"
Hoeller, J.Zhong, L.Pachitariu, M.Romani, S.2024-08-06doi:10.1101/2024.08.02.606398Cold Spring Harbor Laboratory Press2024-08-06
<![CDATA[
Manipulation of the microRNA172 - AP2L2 interaction provides precise control of wheat and triticale plant height
]]>
https://biorxiv.org/cgi/content/short/2024.08.05.606718v1?rss=1"
Zhang, C.Hegarty, J.Padilla, M.Tricoli, D. M.Dubcovsky, J.Debernardi, J. M.2024-08-07doi:10.1101/2024.08.05.606718Cold Spring Harbor Laboratory Press2024-08-07
<![CDATA[
Nervous system-wide analysis of all C. elegans cadherins reveals neuron-specific functions across multiple anatomical scales
]]>
https://biorxiv.org/cgi/content/short/2024.08.06.606874v1?rss=1"
Majeed, M.Liao, C.-P.Hobert, O.2024-08-08doi:10.1101/2024.08.06.606874Cold Spring Harbor Laboratory Press2024-08-08
<![CDATA[
Mechanism of ASF1 Inhibition by CDAN1
]]>
https://biorxiv.org/cgi/content/short/2024.08.08.607204v1?rss=1"
Sedor, S. F.Shao, S.2024-08-08doi:10.1101/2024.08.08.607204Cold Spring Harbor Laboratory Press2024-08-08
<![CDATA[
A pan-variant miniprotein inhibitor protects against SARS-CoV-2 variants
]]>
https://biorxiv.org/cgi/content/short/2024.08.08.606885v1?rss=1"
Lee, J.Case, J. B.Ravichandran, R.Asarnow, D.Tortorici, M. A.Brown, J. T.Sanapala, S.Carter, L.Baker, D.Diamond, M. S.Veesler, D.2024-08-10doi:10.1101/2024.08.08.606885Cold Spring Harbor Laboratory Press2024-08-10
<![CDATA[
Optimized methods for mapping DNA double-strand-break ends and resection tracts and application to meiotic recombination in mouse spermatocytes
]]>
https://biorxiv.org/cgi/content/short/2024.08.10.606181v1?rss=1"
Kim, S.Yamada, S.Maekawa, K.Keeney, S.2024-08-10doi:10.1101/2024.08.10.606181Cold Spring Harbor Laboratory Press2024-08-10
<![CDATA[
Population coding of predator imminence in the hypothalamus
]]>
https://biorxiv.org/cgi/content/short/2024.08.12.607651v1?rss=1"
Cheung, K. Y. M.Nair, A.Li, L.-y.Shapiro, M. G.Anderson, D. J.2024-08-13doi:10.1101/2024.08.12.607651Cold Spring Harbor Laboratory Press2024-08-13
<![CDATA[
Opto-CLIP reveals dynamic FMRP regulation of mRNAs upon CA1 neuronal activation
]]>
https://biorxiv.org/cgi/content/short/2024.08.13.607210v1?rss=1"
Singer, R. A.Rajchin, V.Park, K.Heintz, N.Darnell, R. B.2024-08-14doi:10.1101/2024.08.13.607210Cold Spring Harbor Laboratory Press2024-08-14
<![CDATA[
Bibacillin 1: A two-component lantibiotic from Bacillus thuringiensis
]]>
https://biorxiv.org/cgi/content/short/2024.08.13.607848v1?rss=1"
Moreira, R.Yang, Y.Luo, Y.Gilmore, M. S.van der Donk, W.2024-08-14doi:10.1101/2024.08.13.607848Cold Spring Harbor Laboratory Press2024-08-14
<![CDATA[
Microbiota-induced plastic T cells enhance immune control of antigen-sharing tumors
]]>
https://biorxiv.org/cgi/content/short/2024.08.12.607605v1?rss=1"
Najar, T. A.Hao, Y.Hao, Y.Romero-Meza, G.Dolynuk, A.Littman, D. R.2024-08-15doi:10.1101/2024.08.12.607605Cold Spring Harbor Laboratory Press2024-08-15
<![CDATA[
Repeated shifts in sociality are associated with fine-tuning of highly conserved and lineage-specific enhancers in a socially flexible bee
]]>
https://biorxiv.org/cgi/content/short/2024.08.15.608154v1?rss=1"
Jones, B. M.Webb, A. E.Geib, S. M.Sim, S.Schweizer, R. M.Branstetter, M. G.Evans, J. D.Kocher, S. D.2024-08-16doi:10.1101/2024.08.15.608154Cold Spring Harbor Laboratory Press2024-08-16
<![CDATA[
Imaging high-frequency voltage dynamics in multiple neuron classes of behaving mammals
]]>
https://biorxiv.org/cgi/content/short/2024.08.15.607428v1?rss=1"
Haziza, S.Chrapkiewicz, R.Zhang, Y.Kruzhilin, V.Li, J.Li, J.Delamare, G.Swanson, R.Buzsaki, G.Kannan, M.Vasan, G.Lin, M. Z.Zeng, H.Daigle, T. L.Schnitzer, M. J.2024-08-16doi:10.1101/2024.08.15.607428Cold Spring Harbor Laboratory Press2024-08-16
<![CDATA[
The brain simulates actions and their consequences during REM sleep
]]>
https://biorxiv.org/cgi/content/short/2024.08.13.607810v1?rss=1"
Senzai, Y.Scanziani, M.2024-08-16doi:10.1101/2024.08.13.607810Cold Spring Harbor Laboratory Press2024-08-16
<![CDATA[
The MRE11-RAD50-NBS1 complex both starts and extends DNA end resection in mouse meiosis
]]>
https://biorxiv.org/cgi/content/short/2024.08.17.608390v1?rss=1"
Kim, S.Yamada, S.Li, T.Canasto-Chibuque, C.Kim, J. H.Marcet-Ortega, M.Xu, J.Eng, D. Y.Feeney, L.Petrini, J. H. J.Keeney, S.2024-08-17doi:10.1101/2024.08.17.608390Cold Spring Harbor Laboratory Press2024-08-17
<![CDATA[
Vaccines combining slow delivery and follicle targeting of antigens increase germinal center B cell clonal diversity and clonal expansion
]]>
https://biorxiv.org/cgi/content/short/2024.08.19.608655v1?rss=1"
Rodrigues, K. A.Zhang, Y.Aung, A.Morgan, D. M.Maiorino, L.Yousefpour, P.Gibson, G.Ozorowski, G.Gregory, J. R.Amlashi, P.Buckley, M.Ward, A. B.Schief, W. R.Love, J. C.Irvine, D. J.2024-08-19doi:10.1101/2024.08.19.608655Cold Spring Harbor Laboratory Press2024-08-19
<![CDATA[
Population Representation of the Confidence in a Decision in the Lateral Intraparietal Area of the Macaque
]]>
https://biorxiv.org/cgi/content/short/2024.08.15.608159v1?rss=1"
Zylberberg, A.Shadlen, M. N.2024-08-19doi:10.1101/2024.08.15.608159Cold Spring Harbor Laboratory Press2024-08-19
<![CDATA[
Natural alleles of LEAFY and WAPO1 interact to regulate spikelet number per spike in wheat
]]>
https://biorxiv.org/cgi/content/short/2024.08.17.608376v1?rss=1"
Zhang, J.Burguener, G. F.Paraiso, F.Dubcovsky, J.2024-08-19doi:10.1101/2024.08.17.608376Cold Spring Harbor Laboratory Press2024-08-19
<![CDATA[
The structural basis for RNA slicing by human Argonaute2
]]>
https://biorxiv.org/cgi/content/short/2024.08.19.608718v1?rss=1"
Mohamed, A. A.Wang, P. Y.Bartel, D. P.Vos, S. M.2024-08-20doi:10.1101/2024.08.19.608718Cold Spring Harbor Laboratory Press2024-08-20
<![CDATA[
Multi-Modal Large Language Model Enables Protein Function Prediction
]]>
https://biorxiv.org/cgi/content/short/2024.08.19.608729v1?rss=1"
Huo, M.Guo, H.Cheng, X.Singh, D.Rahmani, H.Li, S.Gerlof, P.Ideker, T.Grotjahn, D. A.Villa, E.Song, L.Xie, P.2024-08-20doi:10.1101/2024.08.19.608729Cold Spring Harbor Laboratory Press2024-08-20
<![CDATA[
Pseudomonas aeruginosa population dynamics in a vancomycin-induced murine model of gastrointestinal carriage
]]>
https://biorxiv.org/cgi/content/short/2024.08.19.608679v1?rss=1"
Lebrun-Corbin, M.Cheung, B.Hullahalli, K.dailey, k.Bailey, K.Waldor, M. K.Wunderlink, R.Bachta, K. E. R.Hauser, A. R.2024-08-20doi:10.1101/2024.08.19.608679Cold Spring Harbor Laboratory Press2024-08-20
<![CDATA[
Learning reshapes the hippocampal representation hierarchy
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.608911v1?rss=1"
Chiossi, H. S. C.Nardin, M.Tkacik, G.Csicsvari, J. L.2024-08-21doi:10.1101/2024.08.21.608911Cold Spring Harbor Laboratory Press2024-08-21
<![CDATA[
Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.609075v1?rss=1"
Johansen, N. J.Kempynck, N.Zemke, N. R.Somasundaram, S.Winter, S. D.Hooper, M.Dwivedi, D.Lohia, R.Wehbe, F.Li, B.Abaffyova, D.Armand, E. J.Man, J. D.Eksi, E. C.Hecker, N.Hulselmans, G.Konstantakos, V.Mauduit, D.Mich, J. K.Partel, G.Daigle, T. L.Levi, B. P.Zhang, K.Tanaka, Y.Gillis, J.Ting, J. T.Ben-Simon, Y.Miller, J.Ecker, J. R.Ren, B.Aerts, S.Lein, E. S.Tasic, B.Bakken, T. E.2024-08-21doi:10.1101/2024.08.21.609075Cold Spring Harbor Laboratory Press2024-08-21
<![CDATA[
ActSort: An active-learning accelerated cell sorting algorithm for large-scale calcium imaging datasets
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.609011v1?rss=1"
Jiang, Y.Akengin, H. O.Zhou, J.Aslihak, M. A.Li, Y.Hernandez, O.Ebrahimi, S.Zhang, Y.Inan, H.Jaidar, O.Miranda, C.Dinc, F.Blanco-Pozo, M.Schnitzer, M. J.2024-08-22doi:10.1101/2024.08.21.609011Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
CARD8 inflammasome activation during HIV-1 cell-to-cell transmission
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.608981v1?rss=1"
Kulsuptrakul, J.Emerman, M.Mitchell, P. S.2024-08-22doi:10.1101/2024.08.21.608981Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
Castor is a temporal transcription factor that specifies early born central complex neuron identity
]]>
https://biorxiv.org/cgi/content/short/2024.08.22.609207v1?rss=1"
Dillon, N. R.Doe, C. Q.2024-08-22doi:10.1101/2024.08.22.609207Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
Genetically encoded fluorescent sensors for visualizing polyamine levels, uptake, and distribution
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.609037v1?rss=1"
Tamura, R.Chen, J.De Jaeger, M.Morris, J. F.Scott, D. A.Vangheluwe, P.Looger, L. L.2024-08-22doi:10.1101/2024.08.21.609037Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
Histone deacetylase inhibition expands cellular proteostasis repertoires to enhance neuronal stress resilience
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.608176v1?rss=1"
Taylor, C. A.Maor-Nof, M.Metzl-Raz, E.Hidalgo, A.Yee, C.Gitler, A. D.Shen, K.2024-08-22doi:10.1101/2024.08.21.608176Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
Coordinated cross-brain activity during accumulation of sensory evidence and decision commitment
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.609044v1?rss=1"
Bondy, A. G.Charlton, J. A.Luo, T. Z.Kopec, C. D.Stagnaro, W. M.Venditto, S. J. C.Lynch, L.Janarthanan, S.Oline, S. N.Harris, T. D.Brody, C. D.2024-08-22doi:10.1101/2024.08.21.609044Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
An autonomous robotic system for high-throughput phenotyping and behavioral studies of individual fruit flies
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.607451v1?rss=1"
1,000 flies per day for high-throughput inspection and characterization assays. Robotic handling had no detectable adverse effects on fly longevity or our assessments of fly health. Moreover, the behavioral performance of flies, especially of males, was better and less variable than of flies handled manually. Our system employs deep learning-based machine vision for real-time assessments of picking quality and fly phenotypes. This enables fully pipelined, autonomous experimentation for behavioral assays with individual flies in controlled environments, which was previously infeasible. Overall, FlyMAX constitutes a promising technology to enhance the efficiency and reproducibility of research with flies and other insects in fields such as genetics, neuroscience, and drug screening.
]]>Woo, S. J.Huang, C.Savall, J.Conrad, B. L.Luo, J.Schnitzer, M. J.2024-08-22doi:10.1101/2024.08.21.607451Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
Multi-scale dynamics influence the division potential of stomatal lineage ground cells in Arabidopsis
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.609020v1?rss=1"
Fung, H. F.Amador, G. O.Dale, R.Gong, Y.Vollbrecht, M.Erberich, J. M.Mair, A.Bergmann, D. C.2024-08-22doi:10.1101/2024.08.21.609020Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling
]]>
https://biorxiv.org/cgi/content/short/2024.08.23.609473v1?rss=1"
Weng, C.Weissman, J. S.Sankaran, V. G.2024-08-24doi:10.1101/2024.08.23.609473Cold Spring Harbor Laboratory Press2024-08-24
<![CDATA[
De novo designed inhibitor confers protection against lethal toxic shock
]]>
https://biorxiv.org/cgi/content/short/2024.08.23.608890v1?rss=1"
Ragotte, R. J.Liang, H.Berman, J. M.Gloegl, M.Schramek, D.Melnyk, R.Baker, D.2024-08-24doi:10.1101/2024.08.23.608890Cold Spring Harbor Laboratory Press2024-08-24
<![CDATA[
Evolutionary adaptation under climate change: Aedes sp. demonstrates potential to adapt to warming
]]>
https://biorxiv.org/cgi/content/short/2024.08.23.609454v1?rss=1"
Couper, L. I.Dodge, T. O.Hemker, J. A.Kim, B. Y.Exposito-Alonso, M.Brem, R. B.Mordecai, E. A.Bitter, M. C.2024-08-24doi:10.1101/2024.08.23.609454Cold Spring Harbor Laboratory Press2024-08-24
<![CDATA[
Molecular basis of pathogenicity of the recently emerged FCoV-23 coronavirus
]]>
https://biorxiv.org/cgi/content/short/2024.08.25.607996v1?rss=1"
Tortorici, M. A.Choi, A.Gibson, C.Lee, J.Brown, J. T.Stewart, C.Joshi, A.Harari, S.Willoughby, I.Treichel, C.Leif, E.Bloom, J. D.King, N. P.Tait-Burkard, C.Whittaker, G. R.Veesler, D.2024-08-26doi:10.1101/2024.08.25.607996Cold Spring Harbor Laboratory Press2024-08-26
<![CDATA[
Cellular and molecular networks of intercellular signaling in bone marrow hematopoiesis
]]>
https://biorxiv.org/cgi/content/short/2024.08.25.609544v1?rss=1"
Thomas, Z.Wang, B.Boohar, W.Vergel, M.Eerdeng, J.Shon, D.Elowitz, M. B.Lu, R.2024-08-26doi:10.1101/2024.08.25.609544Cold Spring Harbor Laboratory Press2024-08-26
<![CDATA[
De novo design of potent inhibitors of Clostridioides difficile toxin B
]]>
https://biorxiv.org/cgi/content/short/2024.08.26.609740v1?rss=1"
Ragotte, R. J.Tam, J.Miletic, S.Palou, R.Weidle, C.Li, Z.Gloegl, M.Beilhartz, G. L.Liang, H.Carr, K. D.Borst, A. J.Coventry, B.Wang, X.Rubinstein, J. L.Tyers, M.Melnyk, R. A.Baker, D.2024-08-26doi:10.1101/2024.08.26.609740Cold Spring Harbor Laboratory Press2024-08-26
<![CDATA[
Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice
]]>
https://biorxiv.org/cgi/content/short/2024.08.22.608850v1?rss=1"
Chen, J.Richardson, P. R.Kirby, C.Eddy, S. R.Hoekstra, H.2024-08-26doi:10.1101/2024.08.22.608850Cold Spring Harbor Laboratory Press2024-08-26
<![CDATA[
Maize genetic diversity identifies moisture-dependent root-branch signaling pathways
]]>
https://biorxiv.org/cgi/content/short/2024.08.26.609741v1?rss=1"
Scharwies, J. D.Clarke, T.Zheng, Z.Dinneny, A.Birkeland, S.Veltman, M. A.Sturrock, C. J.Torres-Martinez, H. H.Viana, W. G.Khare, R.Kieber, J.Pandey, B. K. K.Bennett, M. J.Schnable, P. S.Dinneny, J. R.2024-08-27doi:10.1101/2024.08.26.609741Cold Spring Harbor Laboratory Press2024-08-27
<![CDATA[
A theory of rapid behavioral inferences under the pressure of time
]]>
https://biorxiv.org/cgi/content/short/2024.08.26.609738v1?rss=1"
Hermundstad, A. M.Młynarski, W. F.2024-08-27doi:10.1101/2024.08.26.609738Cold Spring Harbor Laboratory Press2024-08-27
<![CDATA[
Dimensionality reduction simplifies synaptic partner matching in an olfactory circuit
]]>
https://biorxiv.org/cgi/content/short/2024.08.27.609939v1?rss=1"
Lyu, C.Li, Z.Xu, C.Wong, K. K. L.Luginbuhl, D. J.McLaughlin, C. N.Xie, Q.Li, T.Li, H.Luo, L.2024-08-27doi:10.1101/2024.08.27.609939Cold Spring Harbor Laboratory Press2024-08-27
<![CDATA[
Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses
]]>
https://biorxiv.org/cgi/content/short/2024.08.28.608351v1?rss=1"
Park, Y.-J.Liu, C.Lee, J.Brown, J. T.Ma, C.-B.Liu, P.Xiong, Q.Stewart, C.Addetia, A.Craig, C. J.Tortorici, M. A.Alshukari, A.Starr, T.Yan, H.Veesler, D.2024-08-28doi:10.1101/2024.08.28.608351Cold Spring Harbor Laboratory Press2024-08-28
<![CDATA[
Modulation of antigen delivery and lymph node activation in non-human primates by saponin adjuvant SMNP
]]>
https://biorxiv.org/cgi/content/short/2024.08.28.608716v1?rss=1"
Yousefpour, P.J. Zhang, Y.Maiorino, L.Melo, M. B.Arainga Ramirez, M. A.Kumarapperuma, S. C.Xiao, P.Silva, M.Li, N.Michaels, K. K.Georgeson, E.Eskandarzadeh, S.Kubitz, M.Groschel, B.Qureshi, K.Fontenot, J.Hangartner, L.Nedellec, R.Love, J. C.Burton, D. R.Schief, W. R.Villinger, F. J.Irvine, D. J.2024-08-28doi:10.1101/2024.08.28.608716Cold Spring Harbor Laboratory Press2024-08-28
<![CDATA[
Single-molecule analysis of protein targeting from the endoplasmic reticulum to lipid droplets
]]>
https://biorxiv.org/cgi/content/short/2024.08.27.610018v1?rss=1"
Mizrak, A.Kaestel-Hansen, J.Matthias, J.Harper, J. W.Hatzakis, N. S.Walther, T. C.Farese, R. V.2024-08-28doi:10.1101/2024.08.27.610018Cold Spring Harbor Laboratory Press2024-08-28
<![CDATA[
The SP140-RESIST pathway regulates interferon mRNA stability and antiviral immunity
]]>
https://biorxiv.org/cgi/content/short/2024.08.28.610186v1?rss=1"
Witt, K. C.Dziulko, A.An, J.Lee, O. V.Liu, G.Lari, A. C.Chavez, R.Turner, D. J.Cheng, A.Kotov, D. I.Abraham, P.Lee, A. Y.Dhaliwal, H.Coscoy, L.Glaunsinger, B.Chuong, E.Vance, R.2024-08-29doi:10.1101/2024.08.28.610186Cold Spring Harbor Laboratory Press2024-08-29
<![CDATA[
Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry
]]>
https://biorxiv.org/cgi/content/short/2024.08.29.610268v1?rss=1"
Welp, L. M.Sachsenberg, T.Wulf, A.Chernev, A.Horokhovskyi, Y.Neumann, P.Pasen, M.Siraj, A.Raabe, M.Johannsson, S.Schmitzova, J.Netz, E.Pfeuffer, J.He, Y.Fritzemeier, K.Delanghe, B.Viner, R.Vos, S.Cramer, P.Ficner, R.Liepe, J.Kohlbacher, O.Urlaub, H.2024-08-29doi:10.1101/2024.08.29.610268Cold Spring Harbor Laboratory Press2024-08-29
<![CDATA[
Diverse RNA Structures Induce PRC2 Dimerization and Inhibit Histone Methyltransferase Activity
]]>
https://biorxiv.org/cgi/content/short/2024.08.29.610323v1?rss=1"
Song, J.Yao, L.Gooding, A. R.Thron, V.Kasinath, V.Cech, T. R.2024-08-29doi:10.1101/2024.08.29.610323Cold Spring Harbor Laboratory Press2024-08-29
<![CDATA[
Energy filtering enables macromolecular MicroED data at sub-atomic resolution
]]>
https://biorxiv.org/cgi/content/short/2024.08.29.610380v1?rss=1"
Clabbers, M. T. B.Hattne, J.Martynowycz, M. W.Gonen, T.2024-08-29doi:10.1101/2024.08.29.610380Cold Spring Harbor Laboratory Press2024-08-29
<![CDATA[
Phospho-regulated tuning of viscoelastic properties balances centrosome growth and strength
]]>
https://biorxiv.org/cgi/content/short/2024.08.29.610374v1?rss=1"
Amato, M.Hwang, J. H.Rios, M. U.Familiari, N. E.Rosen, M. K.Woodruff, J. B.2024-08-30doi:10.1101/2024.08.29.610374Cold Spring Harbor Laboratory Press2024-08-30
<![CDATA[
De novo design of Ras isoform selective binders
]]>
https://biorxiv.org/cgi/content/short/2024.08.29.610300v1?rss=1"
Zhang, J. Z.Li, X.Liu, C.Jiang, H.Wu, K.Baker, D.2024-08-30doi:10.1101/2024.08.29.610300Cold Spring Harbor Laboratory Press2024-08-30
<![CDATA[
Computational design of serine hydrolases
]]>
https://biorxiv.org/cgi/content/short/2024.08.29.610411v1?rss=1"
Lauko, A.Pellock, S. J.Anischanka, I.Sumida, K. H.Juergens, D.Ahern, W.Shida, A.Hunt, A.Kalvet, I.Norn, C.Humphreys, I. R.Jamieson, C. S.Kang, A.Brackenbrough, E.Sankaran, B.Houk, K. N.Baker, D.2024-08-30doi:10.1101/2024.08.29.610411Cold Spring Harbor Laboratory Press2024-08-30
<![CDATA[
Sec18 side-loading is essential for universal SNARE recycling across cellular contexts
]]>
https://biorxiv.org/cgi/content/short/2024.08.30.610324v1?rss=1"
Khan, Y. A.White, K. I.Pfuetzner, R. A.Singal, B.Esquivies, L.Mckenzie, G.Liu, F.DeLong, K.Choi, U.Montabana, E.Mclaughlin, T.Wickner, W.Brunger, A. T.2024-09-01doi:10.1101/2024.08.30.610324Cold Spring Harbor Laboratory Press2024-09-01
<![CDATA[
Chronic mitochondrial fragmentation elicits a neuroprotective Warburg-like effect in Drosophila neurons
]]>
https://biorxiv.org/cgi/content/short/2024.08.30.610549v1?rss=1"
Richhariya, S.Shin, D.Schlichting, M.Rosbash, M.2024-09-01doi:10.1101/2024.08.30.610549Cold Spring Harbor Laboratory Press2024-09-01
<![CDATA[
Evolution of lateralized gustation in nematodes
]]>
https://biorxiv.org/cgi/content/short/2024.08.31.610597v1?rss=1"
Mackie, M.Le, V. V.Carstensen, H. R.Kushnir, N. R.Castro, D. L.Dimov, I. M.Quach, K. T.Cook, S. J.Hobert, O.Chalasani, S. H.Hong, R. L.2024-09-02doi:10.1101/2024.08.31.610597Cold Spring Harbor Laboratory Press2024-09-02
<![CDATA[
Four SpsP neurons are an integrating sleep regulation hub in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2024.09.02.610881v1?rss=1"
Dai, X.Le, J. Q.Ma, D.Rosbash, M.2024-09-03doi:10.1101/2024.09.02.610881Cold Spring Harbor Laboratory Press2024-09-03
<![CDATA[
Overcoming nucleotide bias in the nonenzymatic copying of RNA templates.
]]>
https://biorxiv.org/cgi/content/short/2024.09.03.610991v1?rss=1"
Duzdevich, D.Carr, C. E.Colville, B.Aitken, H. R. M.Szostak, J. W.2024-09-03doi:10.1101/2024.09.03.610991Cold Spring Harbor Laboratory Press2024-09-03
<![CDATA[
USP37 prevents premature disassembly of stressed replisomes by TRAIP
]]>
https://biorxiv.org/cgi/content/short/2024.09.03.611025v1?rss=1"
Kochenova, O. V.D'Alessandro, G.Pilger, D.Schmid, E.Richards, S. L.Garcia, M. R.Jhujh, S. S.Voigt, A.Gupta, V.Carnie, C. J.Wu, R. A.Gueorguieva, N.Stewart, G. S.Walter, J. C.Jackson, S. P.2024-09-04doi:10.1101/2024.09.03.611025Cold Spring Harbor Laboratory Press2024-09-04
<![CDATA[
RTN4IP1 is essential for the final stages of mitochondrial complex I assembly and coenzyme Q biosynthesis
]]>
https://biorxiv.org/cgi/content/short/2024.09.04.610987v1?rss=1"
Olahova, M.Guerra, R. M.Collier, J. J.Heidler, J.Thompson, K.White, C. R.Castaneda-Tamez, P.Cabrera-Orefice, A.Lightowlers, R. N.Chrzanowska-Lightowlers, Z. M. A.Wittig, I.Pagliarini, D. J.Taylor, R. W.2024-09-05doi:10.1101/2024.09.04.610987Cold Spring Harbor Laboratory Press2024-09-05
<![CDATA[
Gradients of Recognition Molecules Shape Synaptic Specificity of a Visuomotor Transformation
]]>
https://biorxiv.org/cgi/content/short/2024.09.04.610846v1?rss=1"
Dombrovski, M.Zang, Y.Frighetto, G.Vaccari, A.Jang, H.Mirshahidi, P. S.Xie, F.Sanfilippo, P.Hina, B. W.Rehan, A.Hussein, R. H.Mirshahidi, P. S.Lee, C.Frye, M. A.von Reyn, C. R.Kurmangaliyev, Y. Z.Card, G. M.Zipursky, S. L.2024-09-07doi:10.1101/2024.09.04.610846Cold Spring Harbor Laboratory Press2024-09-07
<![CDATA[
The proteomic landscape and temporal dynamics of mammalian gastruloid development
]]>
https://biorxiv.org/cgi/content/short/2024.09.05.609098v1?rss=1"
Garge, R. K.Lynch, V.Fields, R.Casadei, S.Best, S.Stone, J.Snyder, M.McGann, C. D.Shendure, J.Starita, L. M.Hamazaki, N.Schweppe, D. K.2024-09-07doi:10.1101/2024.09.05.609098Cold Spring Harbor Laboratory Press2024-09-07
<![CDATA[
Data Release: High-Resolution Imaging and Segmentation of P7 Mouse Tissue Microarchitecture Using FIB-SEM and Machine Learning
]]>
https://biorxiv.org/cgi/content/short/2024.09.05.611438v1?rss=1"
Ackerman, D.Avetissian, E.Bleck, C. K. E.Bogovic, J. A.Innerberger, M.Korff, W.Li, W.-P.Lu, Z.Petruncio, A.Preibisch, S.Qiu, W.Rhoades, J.Saalfeld, S.Silva, M.Trautman, E. T.Vorimo, R.Weigel, A. V.Yu, Z.Zubov, Y.CellMap Project Team,2024-09-07doi:10.1101/2024.09.05.611438Cold Spring Harbor Laboratory Press2024-09-07
<![CDATA[
Calpains Orchestrate Secretion of Annexin-containing Microvesicles during Membrane Repair
]]>
https://biorxiv.org/cgi/content/short/2024.09.05.611512v1?rss=1"
Williams, J. K.Ngo, J. M.Murugupandiyan, A.Croall, D. E.Hartzell, H. C.Schekman, R.2024-09-07doi:10.1101/2024.09.05.611512Cold Spring Harbor Laboratory Press2024-09-07
<![CDATA[
Pentose Phosphate Pathway Protects E. coli from Antibiotic Lethality
]]>
https://biorxiv.org/cgi/content/short/2024.09.07.611820v1?rss=1"
Seregina, T.Shakulov, R.Shatalin, K.Petrushanko, I.Mitkevich, V.Makarov, A.Mironov, A.Nudler, E.2024-09-07doi:10.1101/2024.09.07.611820Cold Spring Harbor Laboratory Press2024-09-07
<![CDATA[
Structural basis of the excitatory amino acid transporter 3 substrate recognition
]]>
https://biorxiv.org/cgi/content/short/2024.09.05.611541v1?rss=1"
Qiu, B.Boudker, O.2024-09-08doi:10.1101/2024.09.05.611541Cold Spring Harbor Laboratory Press2024-09-08
<![CDATA[
Structural basis for sequence context-independent single-stranded DNA cytosine deamination by the bacterial toxin SsdA
]]>
https://biorxiv.org/cgi/content/short/2024.09.08.611884v1?rss=1"
Yin, L.Shi, K.Chen, Y.Harris, R. S.Aihara, H.2024-09-08doi:10.1101/2024.09.08.611884Cold Spring Harbor Laboratory Press2024-09-08
<![CDATA[
Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes
]]>
https://biorxiv.org/cgi/content/short/2024.09.09.611392v1?rss=1"
Martin-Rufino, J. D.Caulier, A.Lee, S.Castano, N.King, E.Joubran, S.Jones, M.Goldman, S. R.Arora, U. P.Wahlster, L.Lander, E. S.Sankaran, V. G.2024-09-09doi:10.1101/2024.09.09.611392Cold Spring Harbor Laboratory Press2024-09-09
<![CDATA[
High-quality peptide evidence for annotating non-canonical open reading frames as human proteins
]]>
https://biorxiv.org/cgi/content/short/2024.09.09.612016v1?rss=1"
Deutsch, E. W.Kok, L. W.Mudge, J. M.Ruiz-Orera, J.Fierro-Monti, I.Sun, Z.Abelin, J. G.Alba, M. M.Aspden, J. L.Bazzini, A. A.Bruford, E.Brunet, M. A.Calviello, L.Carr, S. A.Carvunis, A.-R.Chothani, S.Clauwaert, J.Dean, K.Faridi, P.Frankish, A.Hubner, N.Ingolia, N.Magrane, M.Martin, M. J.Martinez, T. F.Menschaert, G.Ohler, U.Orchard, S.Rackham, O.Roucou, X.Slavoff, S. A.Valen, E.Wacholder, A. C.Weissman, J. S.Wu, W.Xie, Z.Choudhary, J.Bassani-Sternberg, M.Vizcaino, J. A.Ternette, N.Moritz, R. L.Prensner, J.van He2024-09-09doi:10.1101/2024.09.09.612016Cold Spring Harbor Laboratory Press2024-09-09
<![CDATA[
Identification of Proteins Influencing CRISPR-Associated Transposases for Enhanced Genome Editing
]]>
https://biorxiv.org/cgi/content/short/2024.09.11.612086v1?rss=1"
View larger version (13K):
org.highwire.dtl.DTLVardef@12609e5org.highwire.dtl.DTLVardef@53a128org.highwire.dtl.DTLVardef@794e63org.highwire.dtl.DTLVardef@9835f_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Song, L.Alker, A. T. P.Oromi-Bosch, A.Swartz, S. E.Martinson, J. N. V.Arora, J.Wang, A. M.Rovinsky, R.Smith, S. J.Pierce, E. C.Deutschbauer, A. M.Doudna, J. A.Cress, B. F.Rubin, B. E.2024-09-11doi:10.1101/2024.09.11.612086Cold Spring Harbor Laboratory Press2024-09-11
<![CDATA[
Leukemia-derived apelin selects endothelial niche clones to promote tumorigenesis
]]>
https://biorxiv.org/cgi/content/short/2024.09.09.612077v1?rss=1"
Baron, C. S.Mitchell, O.Avagyan, S.Menard, R.Yang, S.Robertson, A. L.Potluri, R.Shendure, J.Madelaine, R.McKenna, A.Zon, L. I.2024-09-13doi:10.1101/2024.09.09.612077Cold Spring Harbor Laboratory Press2024-09-13
<![CDATA[
Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists
]]>
https://biorxiv.org/cgi/content/short/2024.09.13.612773v1?rss=1"
Gloegl, M.Krishnakumar, A.Ragotte, R.Goreshnik, I.Coventry, B.Bera, A. K.Kang, A.Joyce, E.Ahn, G.Huang, B.Yang, W.Chen, W.Sanchez, M. G.Koepnick, B.Baker, D.2024-09-13doi:10.1101/2024.09.13.612773Cold Spring Harbor Laboratory Press2024-09-13
<![CDATA[
Effects of Nf1 on sleep behavior are mediated through starvation caused by deficits in SARM1 dependent NAD+ metabolism.
]]>
https://biorxiv.org/cgi/content/short/2024.09.14.612058v1?rss=1"
Sofela, F. A.Lopez Valencia, M.Jongens, T. A.Sehgal, A.2024-09-14doi:10.1101/2024.09.14.612058Cold Spring Harbor Laboratory Press2024-09-14
<![CDATA[
SVbyEye: A visual tool to characterize structural variation among whole genome assemblies
]]>
https://biorxiv.org/cgi/content/short/2024.09.11.612418v1?rss=1"
Porubsky, D.Guitart, X.Yoo, D.Dishuck, P. C.Harvey, W. T.Eichler, E. E.2024-09-14doi:10.1101/2024.09.11.612418Cold Spring Harbor Laboratory Press2024-09-14
<![CDATA[
Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering
]]>
https://biorxiv.org/cgi/content/short/2024.09.10.612244v1?rss=1"
Benoit, M.Jenike, K. M.Satterlee, J. W.Ramakrishnan, S.Gentile, I.Hendelman, A.Passalacqua, M. J.Suresh, H.Shohat, H.Robitaille, G. M.Fitzgerald, B.Alonge, M. M.Wang, X.Santos, R.He, J.Ou, S.Golan, H.Green, Y.Swartwood, K.Sierra, G. P.Orejuela, A.Fornaguera, F.Goodwin, S.McCombie, W. R.Kizito, E. B.Gagnon, E.Knapp, S.Sarkinen, T.Frary, A.Gillis, J.Van Eck, J.Schatz, M. C.Lippman, Z. B.2024-09-14doi:10.1101/2024.09.10.612244Cold Spring Harbor Laboratory Press2024-09-14
<![CDATA[
Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation
]]>
https://biorxiv.org/cgi/content/short/2024.09.14.613021v1?rss=1"
99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from [~]0% to [~]20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1; a rise from [~]0% to [~]8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from [~]2% to [~]9% from [~]5500 to [~]3000 years ago before dropping to [~]3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the "Thrifty Gene" hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.
]]>Akbari, A.Barton, A. R.Gazal, S.Li, Z.Kariminejad, M.Perry, A.Zeng, Y.Mittnik, A.Patterson, N.Mah, M.Zhou, X.Price, A. L.Lander, E. S.Pinhasi, R.Rohland, N.Mallick, S.Reich, D.2024-09-15doi:10.1101/2024.09.14.613021Cold Spring Harbor Laboratory Press2024-09-15
<![CDATA[
Synaptonemal complex protects double-Holliday junctions during meiosis
]]>
https://biorxiv.org/cgi/content/short/2024.09.14.613089v1?rss=1"
Tang, S. M.Koo, J.Pourhosseinzadeh, M.Nguyen, E.Liu, N.Ma, C.Lu, H.Lee, M.Hunter, N.2024-09-15doi:10.1101/2024.09.14.613089Cold Spring Harbor Laboratory Press2024-09-15
<![CDATA[
Gene identification for ocular congenital cranial motor neuron disorders using human sequencing, zebrafish screening, and protein binding microarrays
]]>
https://biorxiv.org/cgi/content/short/2024.09.12.612713v1?rss=1"
Jurgens, J. A.Ruiz, P. M. M.King, J.Foster, E. E.Berube, L.Chan, W.-M.Barry, B. J.Jeong, R.Rothman, E.Whitman, M. C.MacKinnon, S.Rivera-Quiles, C.Pratt, B. M.Easterbrooks, T.Mensching, F. M.Di Gioia, S. A.Pais, L.England, E. M.de Berardinis, T.Magli, A.Koc, F.Asakawa, K.Kawakami, K.O'Donnell-Luria, A.Hunter, D. G.Robson, C. D.Bulyk, M. L.Engle, E. C.2024-09-15doi:10.1101/2024.09.12.612713Cold Spring Harbor Laboratory Press2024-09-15
<![CDATA[
Sleep-wake states are encoded across emotion-regulation regions of the mouse brain
]]>
https://biorxiv.org/cgi/content/short/2024.09.15.613104v1?rss=1"
Walder-Christensen, K.Goffinet, J.Bey, A.Syed, R.Benton, J.Mague, S.Adamson, E.Vera, D.Soliman, H.Kansagr, S.Carlson, D.Dzirasa, K.2024-09-15doi:10.1101/2024.09.15.613104Cold Spring Harbor Laboratory Press2024-09-15
<![CDATA[
Carboxy-terminal blockade of sortilin binding enhances progranulin gene therapy, a potential treatment for frontotemporal dementia
]]>
https://biorxiv.org/cgi/content/short/2024.09.15.613118v1?rss=1"
Kashyap, S. N.Fox, S. N.Wilson, K. I.Murchison, C. F.Ambaw, Y. A.Walther, T. C.Farese, R. V.Arrant, A. E.Roberson, E. D.2024-09-16doi:10.1101/2024.09.15.613118Cold Spring Harbor Laboratory Press2024-09-16
<![CDATA[
Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm
]]>
https://biorxiv.org/cgi/content/short/2024.09.16.613305v1?rss=1"
Schooley, A.Venev, S. V.Aksenova, V.Navarrete, E.Dasso, M.Dekker, J.2024-09-16doi:10.1101/2024.09.16.613305Cold Spring Harbor Laboratory Press2024-09-16
<![CDATA[
Cross-Tissue Coordination between SLC Nucleoside Transporters Regulates Reproduction in Caenorhabditis elegans
]]>
https://biorxiv.org/cgi/content/short/2024.09.12.612591v1?rss=1"
Guan, Y.Yu, Y.Gao, S. M.Ding, L.Zhao, Q.Wang, M.2024-09-16doi:10.1101/2024.09.12.612591Cold Spring Harbor Laboratory Press2024-09-16
<![CDATA[
Voltage imaging reveals circuit computations in the raphe underlying serotonin-mediated motor vigor learning
]]>
https://biorxiv.org/cgi/content/short/2024.09.15.613083v1?rss=1"
Kawashima, T.Wei, Z.Haruvi, R.Shainer, I.Narayan, S.Baier, H.Ahrens, M. B.2024-09-16doi:10.1101/2024.09.15.613083Cold Spring Harbor Laboratory Press2024-09-16
<![CDATA[
The tilt illusion arises from an efficient reallocation of neural coding resources at the contextual boundary
]]>
https://biorxiv.org/cgi/content/short/2024.09.17.613538v1?rss=1"
Zhang, L.-Q.Mao, J.Aguirre, G. K.Stocker, A. A.2024-09-17doi:10.1101/2024.09.17.613538Cold Spring Harbor Laboratory Press2024-09-17
<![CDATA[
Type-II kinase inhibitors that target Parkinson's Disease-associated LRRK2
]]>
https://biorxiv.org/cgi/content/short/2024.09.17.613365v1?rss=1"
Raig, N. D.Surridge, K. J.Sanz-Murillo, M.Dederer, V.Kramer, A.Schwalm, M. P.Elson, L.Chatterjee, D.Mathea, S.Hanke, T.Leschziner, A. E.Reck-Peterson, S. L.Knapp, S.2024-09-18doi:10.1101/2024.09.17.613365Cold Spring Harbor Laboratory Press2024-09-18
<![CDATA[
The Drosophila maternal-effect gene abnormal oocyte (ao) does not repress histone gene expression
]]>
https://biorxiv.org/cgi/content/short/2024.09.17.613536v1?rss=1"
Takenaka, R.Simmerman, S. M.Schmidt, C. A.Albanese, E. H.Rieder, L. E.Malik, H. S.2024-09-18doi:10.1101/2024.09.17.613536Cold Spring Harbor Laboratory Press2024-09-18
<![CDATA[
Higher resolution pooled genome-wide CRISPR knockout screening in Drosophila cells using integration and anti-CRISPR (IntAC)
]]>
https://biorxiv.org/cgi/content/short/2024.09.19.613976v1?rss=1"
Viswanatha, R.Entwisle, S.Hu, Y.Mohr, S. E.Perrimon, N.2024-09-19doi:10.1101/2024.09.19.613976Cold Spring Harbor Laboratory Press2024-09-19
<![CDATA[
An integrated view of the structure and function of the human 4D nucleome
]]>
https://biorxiv.org/cgi/content/short/2024.09.17.613111v1?rss=1"
The 4D Nucleome Consortium,Dekker, J.Oksuz, B. A.Zhang, Y.Wang, Y.Minsk, M. K.Kuang, S.Yang, L.Gibcus, J. H.Krietenstein, N.Rando, O.Xu, J.Janssens, D. H.Henikoff, S.Kukalev, A.Willemin, A.Winick-Ng, W.Kempfer, R.Pombo, A.Yu, M.Kumar, P.Zhang, L.Belmont, A. S.Sasaki, T.van Schaik, T.Brueckner, L.Peric-Hupkes, D.van Steensel, B.Wang, P.Chai, H.Kim, M.Ruan, Y.Zhang, R.Quinodoz, S. A.Bhat, P.Guttman, M.Zhao, W.Chien, S.Liu, Y.Venev, S. V.Plewczynski, D.Irastorza Azcarate, I.Szabo, D.Thieme, C. J.Szczepinska,2024-09-19doi:10.1101/2024.09.17.613111Cold Spring Harbor Laboratory Press2024-09-19
<![CDATA[
Most Beefalo cattle have no detectable bison genetic ancestry
]]>
https://biorxiv.org/cgi/content/short/2024.09.16.613218v1?rss=1"
Shapiro, B.Oppenheimer, J.Heaton, M. P.Kuhn, K. L.Green, E.Blackburn, H. D.Smith, T. P. L.2024-09-19doi:10.1101/2024.09.16.613218Cold Spring Harbor Laboratory Press2024-09-19
<![CDATA[
MicroED Structures of Fluticasone Furoate and Fluticasone Propionate Provide New Insights to Their Function
]]>
https://biorxiv.org/cgi/content/short/2024.09.18.613782v1?rss=1"
Lin, J.Unge, J.Gonen, T.2024-09-19doi:10.1101/2024.09.18.613782Cold Spring Harbor Laboratory Press2024-09-19
<![CDATA[
Modulating DNA Polα Enhances Cell Reprogramming Across Species
]]>
https://biorxiv.org/cgi/content/short/2024.09.19.613993v1?rss=1"
Ranjan, R.Ma, B.Gleason, R. J.Liao, Y.Bi, Y.Davis, B. E. M.Yang, G.Clark, M.Mahajan, V.Condon, M.Broderick, N. A.Chen, X.2024-09-20doi:10.1101/2024.09.19.613993Cold Spring Harbor Laboratory Press2024-09-20
<![CDATA[
High-throughput amino acid-level characterization of the interactions of plasminogen activator inhibitor-1 with variably divergent proteases
]]>
https://biorxiv.org/cgi/content/short/2024.09.16.612699v1?rss=1"
Haynes, L. M.Holding, M. L.DiGiovanni, H.Siemieniak, D.Ginsburg, D.2024-09-20doi:10.1101/2024.09.16.612699Cold Spring Harbor Laboratory Press2024-09-20
<![CDATA[
Hippocampal γCaMKII dopaminylation promotes synaptic-to-nuclear signaling and memory formation
]]>
https://biorxiv.org/cgi/content/short/2024.09.19.613951v1?rss=1"
Stewart, A. F.Fulton, S. L.Durand-de Cuttoli, R.Thompson, R. E.Chen, P.-J.Brindley, E.Cetin, B.Farrelly, L. A.Futamura, R.Claypool, S.Bastle, R. M.Di Salvo, G.Peralta, C.Molina, H.Baljinnyam, E.Marro, S. G.Russo, S. J.Devita, R. J.Muir, T. W.Maze, I.2024-09-20doi:10.1101/2024.09.19.613951Cold Spring Harbor Laboratory Press2024-09-20
<![CDATA[
Nucleation limited assembly and polarized growth of a de novo-designed allosterically modulatable protein filament
]]>
https://biorxiv.org/cgi/content/short/2024.09.20.613980v1?rss=1"
Shen, H.Lynch, E. M.Watson, J. L.Wu, K.Bai, H.Sheffler, W.Derivery, E.Kollman, J. M.Baker, D.2024-09-21doi:10.1101/2024.09.20.613980Cold Spring Harbor Laboratory Press2024-09-21
<![CDATA[
Preventing Inappropriate Signals Pre- and Post-Ligand Perception by a Toggle-Switch Mechanism of ERECTA
]]>
https://biorxiv.org/cgi/content/short/2024.09.20.612365v1?rss=1"
Chen, L.Maes, M.Cochran, A. M.Avila, J. R.Derbyshire, P.Sklenar, J.Haas, K. M.Villen, J.Menke, F.Torii, K. U.2024-09-21doi:10.1101/2024.09.20.612365Cold Spring Harbor Laboratory Press2024-09-21
<![CDATA[
The HIV-1 Nuclear Export Complex Reveals the Role of RNA in Crm1 Cargo Recognition
]]>
https://biorxiv.org/cgi/content/short/2024.09.22.614349v1?rss=1"
1000 human proteins including ribonucleoprotein (RNP) complexes. The interface between Crm1 and RNP cargos is unknown. The HIV regulatory protein, Rev, was one of the first identified cargos for Crm1 and contains a prototypic nuclear export sequence (NES). We present the cryo-electron microscopy structure of the HIV-1 nuclear export complex (Crm1/Ran-GTP and the Rev/RRE RNP). Rev binds at a previously unseen protein-protein binding site that stabilizes a unique Crm1 dimer and positions two NESs within the Crm1 dimer. The orientation of Rev binding positions the RRE within a charged pocket on the inside of the Crm1 toroid, mediating direct RNA-Ran-GTP contacts, highlighting the significant role of the RRE in the interaction. Structure based mutations, combined with cell-based assays, show that Crm1 has multiple distinct cargo recognition sites and explains how Crm1 can recognize a diverse range of protein and RNP cargos.
]]>Smith, A. M.Li, Y.Velarde, A.Cheng, Y.Frankel, A. D.2024-09-22doi:10.1101/2024.09.22.614349Cold Spring Harbor Laboratory Press2024-09-22
<![CDATA[
Hippocampal representations of alternative possibilities are flexibly generated to meet cognitive demands
]]>
https://biorxiv.org/cgi/content/short/2024.09.23.613567v1?rss=1"
Comrie, A. E.Monroe, E. J.Kahn, A. E.Denovellis, E. L.Joshi, A.Guidera, J. A.Krausz, T. A.Berke, J. D.Daw, N. D.Frank, L. M.2024-09-23doi:10.1101/2024.09.23.613567Cold Spring Harbor Laboratory Press2024-09-23
<![CDATA[
Quorum sensing orchestrates parallel cell death pathways in Vibrio cholerae via Type 6 secretion dependent and independent mechanisms
]]>
https://biorxiv.org/cgi/content/short/2024.09.23.614608v1?rss=1"
Mashruwala, A. A.Bassler, B. L.2024-09-23doi:10.1101/2024.09.23.614608Cold Spring Harbor Laboratory Press2024-09-23
<![CDATA[
Distinct Neural Representations of Hunger and Thirst in Neonatal Mice before the Emergence of Food- and Water-seeking Behaviors
]]>
https://biorxiv.org/cgi/content/short/2024.09.22.614378v1?rss=1"
Wang, D. C.Wu, Y.Mehaffey, C.Espinoza-Campomanes, L. A.Luo, L.2024-09-23doi:10.1101/2024.09.22.614378Cold Spring Harbor Laboratory Press2024-09-23
<![CDATA[
Cholinergic Neuronal Activity Promotes Diffuse Midline Glioma Growth through Muscarinic Signaling
]]>
https://biorxiv.org/cgi/content/short/2024.09.21.614235v1?rss=1"
Monje, M.Deisseroth, K.Drinnenberg, A.Drexler, R.Gavish, A.Yalcin, B.Shamardani, K.Rogers, A.Mancusi, R.Taylor, K. R.Kim, Y. S.Woo, P. J.Ravel, A.Tatlock, E.Ayala-Sarmiento, A. E.Rincon Fernandez Pacheco, D.Ramakrishnan, C.Daigle, T. L.Siverts, L.Tasic, B.Zeng, H.2024-09-23doi:10.1101/2024.09.21.614235Cold Spring Harbor Laboratory Press2024-09-23
<![CDATA[
Galvanin is an electric-field sensor for directed cell migration
]]>
https://biorxiv.org/cgi/content/short/2024.09.23.614580v1?rss=1"
Belliveau, N. M.Footer, M. J.Platenkamp, A.Kim, H.Eustis, T. E.Theriot, J. A.2024-09-24doi:10.1101/2024.09.23.614580Cold Spring Harbor Laboratory Press2024-09-24
<![CDATA[
A genome-wide CRISPR screen in Anopheles mosquito cells identifies essential genes and required components of clodronate liposome function
]]>
https://biorxiv.org/cgi/content/short/2024.09.24.614595v1?rss=1"
Mameli, E.Samantsidis, G.-R.Viswanatha, R.Kwon, H.Hall, D. R.Butnaru, M.Hu, Y.Mohr, S. E.Perrimon, N.Smith, R. C.2024-09-24doi:10.1101/2024.09.24.614595Cold Spring Harbor Laboratory Press2024-09-24
<![CDATA[
The fate of pyruvate dictates cell growth by modulating cellular redox potential
]]>
https://biorxiv.org/cgi/content/short/2024.09.23.614588v1?rss=1"
Toshniwal, A. G.Lam, G.Bott, A. J.Cluntun, A.Nam, H.-J.Skabelund, R.Wisidagama, D. R.Thummel, C. S.Rutter, J.2024-09-24doi:10.1101/2024.09.23.614588Cold Spring Harbor Laboratory Press2024-09-24
<![CDATA[
Achieving Single Cell Acoustic Localisation with Deactivation Super Resolution
]]>
https://biorxiv.org/cgi/content/short/2024.09.20.614052v1?rss=1"
Smith, C. A. B.Duan, M.Yan, J.Taylor, L.Shapiro, M. G.Tang, M.-X.2024-09-24doi:10.1101/2024.09.20.614052Cold Spring Harbor Laboratory Press2024-09-24
<![CDATA[
Modeling protein-small molecule conformational ensembles with ChemNet
]]>
https://biorxiv.org/cgi/content/short/2024.09.25.614868v1?rss=1"
Anishchenko, I.Kipnis, Y.Kalvet, I.Zhou, G.Krishna, R.Pellock, S. J.Lauko, A.Lee, G. R.An, L.Dauparas, J.DiMaio, F.Baker, D.2024-09-25doi:10.1101/2024.09.25.614868Cold Spring Harbor Laboratory Press2024-09-25
<![CDATA[
Probiotic acoustic biosensors for noninvasive imaging of gut inflammation
]]>
https://biorxiv.org/cgi/content/short/2024.09.23.614598v1?rss=1"
Buss, M. T.Zhu, L.Kwon, J. H.Tabor, J. J.Shapiro, M. G.2024-09-25doi:10.1101/2024.09.23.614598Cold Spring Harbor Laboratory Press2024-09-25
<![CDATA[
Complex genetic variation in nearly complete human genomes
]]>
https://biorxiv.org/cgi/content/short/2024.09.24.614721v1?rss=1"
Logsdon, G. A.Ebert, P.Audano, P. A.Loftus, M.Porubsky, D.Ebler, J.Yilmaz, F.Hallast, P.Prodanov, T.Yoo, D.Paisie, C. A.Harvey, W. T.Zhao, X.Martino, G. V.Henglin, M.Munson, K. M.Rabbani, K.Chin, C.-S.Gu, B.Ashraf, H.Austine-Orimoloye, O.Balachandran, P.Bonder, M. J.Cheng, H.Chong, Z.Crabtree, J.Gerstein, M.Guethlein, L. A.Hasenfeld, P.Hickey, G.Hoekzema, K.Hunt, S. E.Jensen, M.Jiang, Y.Koren, S.Kwon, Y.Li, C.Li, H.Li, J.Norman, P. J.Oshima, K. K.Paten, B.Phillippy, A. M.Pollock, N. R.Rausch, T.Rautiainen2024-09-25doi:10.1101/2024.09.24.614721Cold Spring Harbor Laboratory Press2024-09-25
<![CDATA[
An Effective Surface Passivation Assay for Single-Molecule Studies of Chromatin and Topoisomerase II
]]>
https://biorxiv.org/cgi/content/short/2024.09.25.614989v1?rss=1"
View larger version (32K):
org.highwire.dtl.DTLVardef@d52b73org.highwire.dtl.DTLVardef@117bfc3org.highwire.dtl.DTLVardef@2eb670org.highwire.dtl.DTLVardef@cb88b2_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Le, T. T.Gao, X.Park, S. h.Lee, J.Inman, J. T.Wang, M. D.2024-09-26doi:10.1101/2024.09.25.614989Cold Spring Harbor Laboratory Press2024-09-26
<![CDATA[
Tunable Elliptical Cylinders for Rotational Mechanical Studies of Single DNA Molecules
]]>
https://biorxiv.org/cgi/content/short/2024.09.25.614944v1?rss=1"
Hong, Y.Ye, F.Gao, X.Inman, J. T.Wang, M. D.2024-09-27doi:10.1101/2024.09.25.614944Cold Spring Harbor Laboratory Press2024-09-27
<![CDATA[
Dysregulation of the fluid homeostasis system by aging
]]>
https://biorxiv.org/cgi/content/short/2024.09.26.615271v1?rss=1"
Jang, H.Behne Sharma, A.Dan, U.Wong, J. H.Knight, Z. A.Garrison, J. L.2024-09-27doi:10.1101/2024.09.26.615271Cold Spring Harbor Laboratory Press2024-09-27
<![CDATA[
Bridge-like lipid transfer protein 3A (BLTP3A) is associated with membranes of the late endocytic pathway and is an effector of CASM
]]>
https://biorxiv.org/cgi/content/short/2024.09.28.615015v1?rss=1"
Hanna, M. G.Rodriguez Cruz, H. O.Fujise, K.Zhuoning, L.Monetti, M.De Camilli, P.2024-09-28doi:10.1101/2024.09.28.615015Cold Spring Harbor Laboratory Press2024-09-28
<![CDATA[
Mapping and engineering RNA-controlled architecture of the multiphase nucleolus
]]>
https://biorxiv.org/cgi/content/short/2024.09.28.615444v1?rss=1"
Quinodoz, S. A.Jiang, L.Abu-Alfa, A. A.Comi, T. J.Zhao, H.Yu, Q.Wiesner, L. W.Botello, J. F.Donlic, A.Soehalim, E.Zorbas, C.Wacheul, L.Kosmrlj, A.Lafontaine, D. L.Klinge, S.Brangwynne, C. P.2024-09-29doi:10.1101/2024.09.28.615444Cold Spring Harbor Laboratory Press2024-09-29
<![CDATA[
Cryo-EM visualizes multiple steps of dynein activation pathway
]]>
https://biorxiv.org/cgi/content/short/2024.09.28.615567v1?rss=1"
Kendrick, A.Nguyen, K.MA, W.Karasmanis, E.Amaro, R. E.Reck-Peterson, S.Leschziner, A.2024-09-30doi:10.1101/2024.09.28.615567Cold Spring Harbor Laboratory Press2024-09-30
<![CDATA[
Latent-TGF-β has a domain swapped architecture
]]>
https://biorxiv.org/cgi/content/short/2024.09.27.615443v1?rss=1"
Jin, M.Seed, R.Shing, T.Cheng, Y.Nishimura, S.2024-09-30doi:10.1101/2024.09.27.615443Cold Spring Harbor Laboratory Press2024-09-30
<![CDATA[
The first complete 3D reconstruction and morphofunctional mapping of an insect eye
]]>
https://biorxiv.org/cgi/content/short/2024.09.30.615804v1?rss=1"
Makarova, A. A.Chua, N. J.Diakova, A. V.Desyatirkina, I. A.Gunn, P.Pang, S.Xu, C. S.Hess, H. F.Chklovskii, D. B.Polilov, A. A.2024-10-01doi:10.1101/2024.09.30.615804Cold Spring Harbor Laboratory Press2024-10-01
<![CDATA[
Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording
]]>
https://biorxiv.org/cgi/content/short/2024.09.30.615957v1?rss=1"
McDiarmid, T. A.Taylor, M. L.Chen, W.Chardon, F. M.Choi, J.Liao, H.Li, X.Kim, H.Lalanne, J.-B.Li, T.Nathans, J. F.Martin, B. K.Knuth, J.Coradini, A. L. V.Gray, J. M.Pinglay, S.Shendure, J.2024-10-01doi:10.1101/2024.09.30.615957Cold Spring Harbor Laboratory Press2024-10-01
<![CDATA[
An aneuploidy epistasis map reveals metabolic vulnerabilities associated with supernumerary chromosomes in cancer
]]>
https://biorxiv.org/cgi/content/short/2024.09.30.615609v1?rss=1"
90% of solid tumors carry an imbalanced karyotype. Regardless of this existing paradox, our understanding of the molecular responses to aneuploidy remains limited. Here, we explore these cellular stresses and unique vulnerabilities in aneuploid human mammary epithelial cells (HMECs) enriched for breast cancer-associated copy number alterations (CNAs). To uncover the genetic dependencies specific to aneuploid cells, we conducted a comprehensive, genome-wide CRISPR knockout screen targeting isogenic diploid and aneuploid HMEC lines. Our study reveals that aneuploid HMECs exhibit an increased reliance on pyrimidine biosynthesis and mitochondrial oxidative phosphorylation genes, and demonstrate heightened fitness advantages upon loss of tumor suppressor genes. Using an integrative multi-omic analysis, we confirm nucleotide pool insufficiency as a key contributor to widespread cellular dysfunction in aneuploid HMECs with net copy number gain. While diploid cells can switch seamlessly between pyrimidine synthesis and salvage, cells with increased chromosomal content exhibit p53 activation and S-phase arrest when relying on salvage alone, and exhibit increased sensitivity to DNA-damaging chemotherapeutics. This work advances our understanding of the consequences of aneuploidy and uncovers potential avenues for patient stratification and therapeutic intervention based on tumor ploidy.
]]>Magesh, R. Y.Kaur, A. N.Keller, F. N.Frederick, A.Tseyang, T.Haley, J. A.Rivera Nieves, A. M.Liang, A. C.Guertin, D.Spinelli, J.Elledge, S. J.Watson, E. V.2024-10-01doi:10.1101/2024.09.30.615609Cold Spring Harbor Laboratory Press2024-10-01
<![CDATA[
Remote activation of place codes by gaze in a highly visual animal
]]>
https://biorxiv.org/cgi/content/short/2024.09.30.615982v1?rss=1"
Payne, H. L.Aronov, D.2024-10-02doi:10.1101/2024.09.30.615982Cold Spring Harbor Laboratory Press2024-10-02
<![CDATA[
Posterior Parietal Cortex Regulates Intrinsic Neural Timescales and Attentional Processing in Frontal Eye Field
]]>
https://biorxiv.org/cgi/content/short/2024.09.30.615928v1?rss=1"
Soyuhos, O.Moore, T.Chaudhuri, R.Chen, X.2024-10-02doi:10.1101/2024.09.30.615928Cold Spring Harbor Laboratory Press2024-10-02
<![CDATA[
Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing
]]>
https://biorxiv.org/cgi/content/short/2024.10.01.616117v1?rss=1"
Shi, H.Al-Sayyad, N.Wasko, K.Trinidad, M. I.Doherty, E. E.Vohra, K.Boger, R. S.Colognori, D.Cofsky, J. C.Skopintsev, P.Bryant, Z.Doudna, J. A.2024-10-02doi:10.1101/2024.10.01.616117Cold Spring Harbor Laboratory Press2024-10-02
<![CDATA[
Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems
]]>
https://biorxiv.org/cgi/content/short/2024.10.02.615924v1?rss=1"
Novak, V.Andeer, P. F.King, E.Calabria, J.Fitzpatrick, C.Kelm, J. M.Wippel, K.Kosina, S. M.Daum, C.Zane, M.Yadav, A.Chen, M.Russ, D.Adams, C. A.Owens, T. K.Lee, B.Ding, Y.Sordo, Z.Chakraborty, R.Roux, S.Deutschbauer, A. M.Ushizima, D.Zengler, K.Arsova, B.Dangl, J.Schulze-Lefert, P.Watt, M.Vogel, J.Northen, T. R.2024-10-03doi:10.1101/2024.10.02.615924Cold Spring Harbor Laboratory Press2024-10-03
<![CDATA[
The Platinum Pedigree: A long-read benchmark for genetic variants
]]>
https://biorxiv.org/cgi/content/short/2024.10.02.616333v1?rss=1"
Kronenberg, Z.Nolan, C.Mokveld, T.Rowell, W. J.Lee, S.Dolzhenko, E.Chang, P.-C.Holt, J. M.Saunders, C. T.Olson, N. D.McGee, S.Guarracino, A.Koundinya, N.Harvey, W. T.Watkins, W. S.Munson, K. M.Hoekzema, K.Chua, K. P.Fanslow, C.Lambert, C.Dashnow, H.Garrison, E.Smith, J.Lansdorp, P.Zook, J. M.Carroll, A.Jorde, L. B.Neklason, D. W.Quinlan, A.Eichler, E.Eberle, M. A.2024-10-03doi:10.1101/2024.10.02.616333Cold Spring Harbor Laboratory Press2024-10-03
<![CDATA[
New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM
]]>
https://biorxiv.org/cgi/content/short/2024.10.01.616095v1?rss=1"
Zhang, K.Cossio, P.Rangan, A. V.Lucas, B. A.Grigorieff, N.2024-10-03doi:10.1101/2024.10.01.616095Cold Spring Harbor Laboratory Press2024-10-03
<![CDATA[
Dietary lipid is largely deposited in skin and rapidly affects insulating properties
]]>
https://biorxiv.org/cgi/content/short/2024.10.03.615679v1?rss=1"
Riley, N.Kasza, I.Hermsmeyer, I. D.Trautman, M.Barrett-Wilt, G.Jain, R.Simcox, J. A.Yen, C.-L. E.MacDougald, O. A.Lamming, D. W.Alexander, C. M.2024-10-03doi:10.1101/2024.10.03.615679Cold Spring Harbor Laboratory Press2024-10-03
<![CDATA[
Sciphy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.
]]>
https://biorxiv.org/cgi/content/short/2024.10.01.615771v1?rss=1"
Seidel, S.Zwaans, A.Regalado, S.Choi, J.Shendure, J.Stadler, T.2024-10-03doi:10.1101/2024.10.01.615771Cold Spring Harbor Laboratory Press2024-10-03
<![CDATA[
Engineered Whole Lungs for Tissue Biology
]]>
https://biorxiv.org/cgi/content/short/2024.10.02.616240v1?rss=1"
Greaney, A. M.Raredon, M. S. B.Obata, T.Wang, J.Adams, T. S.Schupp, J. C.Mizoguchi, S.Edelstein, S.Yuan, Y.Baevova, P.Wang, N.Engler, A.Leiby, K.Tsuchiya, T.Homer, R.Kaminski, N.Langer, R.Niklason, L.Medzhitov, R.2024-10-03doi:10.1101/2024.10.02.616240Cold Spring Harbor Laboratory Press2024-10-03
<![CDATA[
Structural basis for a nucleoporin exportin complex between RanBP2, SUMO1-RanGAP1, the E2 Ubc9, Crm1 and the Ran GTPase
]]>
https://biorxiv.org/cgi/content/short/2024.10.04.616749v1?rss=1"
Baytshtok, V.DiMattia, M. A.Lima, C. D.2024-10-05doi:10.1101/2024.10.04.616749Cold Spring Harbor Laboratory Press2024-10-05
<![CDATA[
The G3BP Stress-Granule Proteins Reinforce the Translation Program of the Integrated Stress Response
]]>
https://biorxiv.org/cgi/content/short/2024.10.04.616305v1?rss=1"
Smith, J.Bartel, D. P.2024-10-05doi:10.1101/2024.10.04.616305Cold Spring Harbor Laboratory Press2024-10-05
<![CDATA[
ProteinAligner: A Multi-modal Pretraining Framework for Protein Foundation Models
]]>
https://biorxiv.org/cgi/content/short/2024.10.06.616870v1?rss=1"
Zhang, L.Guo, H.Schaffer, L. V.Ko, Y. S.Singh, D.Rahmani, H.Grotjahn, D.Villa, E.Gilson, M.Wang, W.Ideker, T.Xing, E.Xie, P.2024-10-06doi:10.1101/2024.10.06.616870Cold Spring Harbor Laboratory Press2024-10-06
<![CDATA[
A shared code for perceiving and imagining objects in human ventral temporal cortex
]]>
https://biorxiv.org/cgi/content/short/2024.10.05.616828v1?rss=1"
Wadia, V. S.Reed, C. M.Chung, J. M.Bateman, L. M.Mamelak, A. N.Rutishauser, U.Tsao, D. Y.2024-10-06doi:10.1101/2024.10.05.616828Cold Spring Harbor Laboratory Press2024-10-06
<![CDATA[
Transcriptomic Insights into Hypothalamic Aging During Menopause: A Comparative Analysis of Human and Mouse Models
]]>
https://biorxiv.org/cgi/content/short/2024.10.05.616758v1?rss=1"
Bloom, J. C. B.Torres, E.Pereira, S. A.Arvizu-Sanchez, L.Fontes, A. N.Joffe, H.Page, D. C.Navarro, V. M.2024-10-06doi:10.1101/2024.10.05.616758Cold Spring Harbor Laboratory Press2024-10-06
<![CDATA[
The Hunchback temporal transcription factor determines interneuron molecular identity, morphology, and presynapse targeting in the Drosophila NB5-2 lineage
]]>
https://biorxiv.org/cgi/content/short/2024.10.07.616945v1?rss=1"
Pollington, H. Q.Doe, C. Q.2024-10-07doi:10.1101/2024.10.07.616945Cold Spring Harbor Laboratory Press2024-10-07
<![CDATA[
Direct mitochondrial import of lactate supports resilient carbohydrate oxidation
]]>
https://biorxiv.org/cgi/content/short/2024.10.07.617073v1?rss=1"
Cluntun, A. A.Visker, J. R.Velasco-Silva, J. N.Lang, M. J.Cedeno-Rosario, L.Shankar, T. S.Hamouche, R.Ling, J.Kim, J. E.Toshniwal, A. G.Low, H.Cunningham, C. N.Carrington, J.Catrow, J. L.Pearce, Q.Wells, C. E.Jeong, M.-Y.Bott, A. J.Narbona-Perez, A. J.Stanley, C.Li, Q.Morgan, J. T.Yadav, T.Swiatek, W. I.Ramadurai, D. K. A.Eberhardt, D. R.Chaudhuri, D.Rothstein, J. D.Muoio, D. M.Paulo, J. A.Gygi, S. P.Cox, J. E.Funai, K.Navankasattusas, S.Baker, S. A.Drakos, S. G.Rutter, J.Ducker, G. S.2024-10-08doi:10.1101/2024.10.07.617073Cold Spring Harbor Laboratory Press2024-10-08
<![CDATA[
Perinatal Reduction of Genetically Aberrant Neurons from Human Cerebral Cortex
]]>
https://biorxiv.org/cgi/content/short/2024.10.08.617159v1?rss=1"
1,200 single neurons from human postmortem brain of 16 neurotypical individuals, ranging in age from gestational week 14 to 90 years old using Tn5-transposase-based single-cell whole-genome amplification. We surveyed CNVs in another 44,861 nuclei with 10X Multiome analysis. Up to 45% of postmitotic neurons in the prenatal cortex showed aberrant genomes, characterized by widespread CNVs of multiple chromosomes, but this reduces sharply after birth (p<0.01). We identified micronuclei in the developing cortex in situ, reflecting chromosomal material missegregated during neurodevelopment [4-6]. The size of CNV appeared to define the trajectory of neuronal elimination, since cells with widespread CNVs were eliminated earlier and faster than cells with smaller CNVs. CNVs in surviving neurons were depleted for genes that are dosage-sensitive or involved in neurodevelopmental disorders (p<0.05), suggesting selective elimination of neurons with CNVs involving these critical genes. Neurons with high CNV burdens also showed abnormal expression of synaptic gene sets, indicating that abnormal synaptic gene regulation may contribute to neuronal elimination. Elimination of defective neuronal genomes during during synaptogenesis may represent a critical process of genome quality control and a vulnerable target of factors that contribute to neurodevelopmental disease.
]]>Shao, D. D.Zhao, Y.Ghosh, U.Brew, J.Zhao, S.Qian, X.Tran, J.Taketomi, T.Tsuruta, F.Park, P. J.Walsh, C. A.2024-10-09doi:10.1101/2024.10.08.617159Cold Spring Harbor Laboratory Press2024-10-09
<![CDATA[
Independent effects of testosterone, estradiol, and sex chromosomes on gene expression in immune cells of trans- and cisgender individuals
]]>
https://biorxiv.org/cgi/content/short/2024.10.08.617275v1?rss=1"
Harris, R. M.Whitfield, T.Blanton, L. V.Skaletsky, H.Blumen, K.Hyland, P.McDermott, E.Summers, K.Hughes, J. F.Jackson, E.Teglas, P.Liu, B.Chan, Y.-M.Page, D. C.2024-10-09doi:10.1101/2024.10.08.617275Cold Spring Harbor Laboratory Press2024-10-09
<![CDATA[
Heterozygous and generalist MxA super-restrictors overcome breadth-specificity tradeoffs in antiviral restriction
]]>
https://biorxiv.org/cgi/content/short/2024.10.10.617484v1?rss=1"
Geiger, R. A.Khera, D.Tenthorey, J.Kochs, G.Graf, L.Emerman, M.Malik, H. S.2024-10-10doi:10.1101/2024.10.10.617484Cold Spring Harbor Laboratory Press2024-10-10
<![CDATA[
Torsional Mechanics of Circular DNA
]]>
https://biorxiv.org/cgi/content/short/2024.10.08.617281v1?rss=1"
Singh, G.Hong, Y.Inman, J. T.Sethna, J. P.Wang, M. D.2024-10-10doi:10.1101/2024.10.08.617281Cold Spring Harbor Laboratory Press2024-10-10
<![CDATA[
Deep mutational scanning identifies variants of Cas1 and Cas2 that increase spacer acquisition in type II-A CRISPR-Cas systems
]]>
https://biorxiv.org/cgi/content/short/2024.10.10.617623v1?rss=1"
Hofmann, R.Herman, C.Mo, C.Mathai, J.Marraffini, L. A.2024-10-10doi:10.1101/2024.10.10.617623Cold Spring Harbor Laboratory Press2024-10-10
<![CDATA[
DNA Polymerase Locks Replication Fork Under Stress
]]>
https://biorxiv.org/cgi/content/short/2024.10.09.617451v1?rss=1"
Jia, X.Inman, J. T.Singh, A.Patel, S. S.Wang, M. D.2024-10-10doi:10.1101/2024.10.09.617451Cold Spring Harbor Laboratory Press2024-10-10
<![CDATA[
2.6-A resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor N3CDP
]]>
https://biorxiv.org/cgi/content/short/2024.10.09.617422v1?rss=1"
Westmoreland, D. E.Feliciano, P. R.Kang, G.Cui, C.Kim, A.Stubbe, J.Nocera, D. G.Drennan, C. L.2024-10-10doi:10.1101/2024.10.09.617422Cold Spring Harbor Laboratory Press2024-10-10
<![CDATA[
A collection of split-Gal4 drivers targeting conserved signaling ligands in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2024.10.10.617664v1?rss=1"
Ewen-Campen, B.Joshi, N.Herman, A. S.Thakkar, T.Zirin, J.Perrimon, N.2024-10-11doi:10.1101/2024.10.10.617664Cold Spring Harbor Laboratory Press2024-10-11
<![CDATA[
Tuning Insulin Receptor Signaling Using De Novo Designed Agonists
]]>
https://biorxiv.org/cgi/content/short/2024.10.07.617068v1?rss=1"
Wang, X.Cardoso, S.Cai, K.Venkatesh, P.Hung, A.Ng, M.Hall, C.Coventry, B.Lee, D.Chowhan, R.Gerben, S.Li, J.An, W.Hon, M.Accili, D.Bai, X.Choi, E.Baker, D.2024-10-11doi:10.1101/2024.10.07.617068Cold Spring Harbor Laboratory Press2024-10-11
<![CDATA[
Geometry of Braided DNA Dictates Supercoiling Partition
]]>
https://biorxiv.org/cgi/content/short/2024.10.08.617221v1?rss=1"
Hong, Y.Park, S. h.Wang, H.Wang, M. D.2024-10-11doi:10.1101/2024.10.08.617221Cold Spring Harbor Laboratory Press2024-10-11
<![CDATA[
Structural and functional evidence supports re-defining mouse higher order visual areas into a single area V2
]]>
https://biorxiv.org/cgi/content/short/2024.10.10.617533v1?rss=1"
Rowley, D. P.Sedigh-Sarvestani, M.2024-10-12doi:10.1101/2024.10.10.617533Cold Spring Harbor Laboratory Press2024-10-12
<![CDATA[
Intranasal hemagglutinin protein boosters induce robust mucosal immunity and cross-protection against influenza A viral challenge
]]>
https://biorxiv.org/cgi/content/short/2024.10.10.616291v1?rss=1"
Moriyama, M.Rodrigues, G.Wang, J.Hudak, A.Dong, H.Homer, R. J.Weissman, D.Ma, S.Iwasaki, A.2024-10-12doi:10.1101/2024.10.10.616291Cold Spring Harbor Laboratory Press2024-10-12
<![CDATA[
Polyserine peptides are toxic and exacerbate tau pathology in mice
]]>
https://biorxiv.org/cgi/content/short/2024.10.10.616100v1?rss=1"
Van Alstyne, M.Nguyen, V. L.Hoeffer, C. A.Parker, R.2024-10-12doi:10.1101/2024.10.10.616100Cold Spring Harbor Laboratory Press2024-10-12
<![CDATA[
Improved protein binder design using -pairing targeted RFdiffusion
]]>
https://biorxiv.org/cgi/content/short/2024.10.11.617496v1?rss=1"
Sappington, I.Toul, M.Lee, D. S.Robinson, S. A.Goreshnik, I.McCurdy, C.Chan, T. C.Buchholz, N.Huang, B.Vafeados, D.Roullier, N.Garcia-Sanchez, M.Glögl, M.Kim, C.Watson, J. L.Torres, S. V.Verschueren, K. H. G.Verstraete, K.Hinck, C. S.Bernard-Valle, M.Coventry, B.Sims, J. N.Ahn, G.Wang, X.Hinck, A. P.Jenkins, T. P.Ruohola-Baker, H.Banik, S.Savvides, S. N.Baker, D.2024-10-12doi:10.1101/2024.10.11.617496Cold Spring Harbor Laboratory Press2024-10-12
<![CDATA[
Pre-fusion AAA+ remodeling of target-SNARE protein complexes enables synaptic transmission
]]>
https://biorxiv.org/cgi/content/short/2024.10.11.617886v1?rss=1"
White, K. I.Khan, Y. A.Qiu, K.Balaji, A.Couoh-Cardel, S.Esquivies, L.Pfuetzner, R. A.Diao, J.Brunger, A. T.2024-10-12doi:10.1101/2024.10.11.617886Cold Spring Harbor Laboratory Press2024-10-12
<![CDATA[
High-Resolution Genome-Wide Mapping of Chromatin Accessibility and Torsional Stress
]]>
https://biorxiv.org/cgi/content/short/2024.10.11.617876v1?rss=1"
Hall, P. M.Mayse, L. M.Bai, L.Smolka, M. B.Pugh, B. F.Wang, M. D.2024-10-13doi:10.1101/2024.10.11.617876Cold Spring Harbor Laboratory Press2024-10-13
<![CDATA[
RNA Polymerase II is a Polar Roadblock to a Progressing DNA Fork
]]>
https://biorxiv.org/cgi/content/short/2024.10.11.617674v1?rss=1"
Kay, T. M.Inman, J. T.Lubkowska, L.Le, T. T.Qian, J.Hall, P. M.Wang, D.Kashlev, M.Wang, M. D.2024-10-13doi:10.1101/2024.10.11.617674Cold Spring Harbor Laboratory Press2024-10-13
<![CDATA[
An in vitro platform for the enzymatic characterization of the rhomboid protease RHBDL4
]]>
https://biorxiv.org/cgi/content/short/2024.10.13.618094v1?rss=1"
Bhaduri, S. E.Braza, M. K. E.Stanchev, S.Bach, K.Tauber, M.Al-Bawab, R.Liu, L. J.Trujillo, D. F.Solorio-Kirpichyan, K.Srivastava, A.Sanlley-Hernandez, J.O'Donoghue, A. J.Lemberg, M. K.Amaro, R. E.Strisovsky, K.Neal, S. E.2024-10-13doi:10.1101/2024.10.13.618094Cold Spring Harbor Laboratory Press2024-10-13
<![CDATA[
ExoSloNano: Multi-Modal Nanogold Tags for identi-fication of Macromolecules in Live Cells & Cryo-Electron Tomograms
]]>
https://biorxiv.org/cgi/content/short/2024.10.12.617288v1?rss=1"
Young, L. N.Sherrard, A.Zhou, H.Shaikh, F.Hutchings, J.Riggi, M.Rosen, M. K.Giraldez, A.Villa, E.2024-10-13doi:10.1101/2024.10.12.617288Cold Spring Harbor Laboratory Press2024-10-13
<![CDATA[
Enhancing cortico-motoneuronal projections for vocalization in mice
]]>
https://biorxiv.org/cgi/content/short/2024.10.14.618267v1?rss=1"
Boyd, J. L.Kuper, L.Waidmann, E.Yang, V.Jarvis, E. D.2024-10-16doi:10.1101/2024.10.14.618267Cold Spring Harbor Laboratory Press2024-10-16
<![CDATA[
Torsion is a Dynamic Regulator of DNA Replication Stalling and Reactivation
]]>
https://biorxiv.org/cgi/content/short/2024.10.14.618227v1?rss=1"
Jia, X.Gao, X.Zhang, S.Inman, J. T.Hong, Y. T.Singh, A.Patel, S. S.Wang, M. D.2024-10-17doi:10.1101/2024.10.14.618227Cold Spring Harbor Laboratory Press2024-10-17
<![CDATA[
OpenASO: RNA Rescue--designing splice-modulating antisense oligonucleotides through community science
]]>
https://biorxiv.org/cgi/content/short/2024.10.15.618608v1?rss=1"
Tse, V.Guiterrez, M.Townley, J.Romano, J.Pearl, J.Chacaltana, G.Players, E.Das, R.Sanford, J.Stone, M.2024-10-17doi:10.1101/2024.10.15.618608Cold Spring Harbor Laboratory Press2024-10-17
<![CDATA[
Initiation of ERAD by the bifunctional complex of Mnl1 mannosidase and protein disulfide isomerase
]]>
https://biorxiv.org/cgi/content/short/2024.10.17.618908v1?rss=1"
Zhao, D.Wu, X.Rapoport, T.2024-10-17doi:10.1101/2024.10.17.618908Cold Spring Harbor Laboratory Press2024-10-17
<![CDATA[
Octahedral small virus-like particles of dengue virus type 2
]]>
https://biorxiv.org/cgi/content/short/2024.10.17.618815v1?rss=1"
Johnson, A.Dodes Traian, M.Walsh, R. M.Jenni, S.Harrison, S. C.2024-10-18doi:10.1101/2024.10.17.618815Cold Spring Harbor Laboratory Press2024-10-18
<![CDATA[
ybx1 acts upstream of atoh1a to promote the rapid regeneration of hair cells in zebrafish lateral-line neuromasts
]]>
https://biorxiv.org/cgi/content/short/2024.10.15.618534v1?rss=1"
Reagor, C. C.Hudspeth, A. J.2024-10-18doi:10.1101/2024.10.15.618534Cold Spring Harbor Laboratory Press2024-10-18
<![CDATA[
Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryo-electron tomography
]]>
https://biorxiv.org/cgi/content/short/2024.10.15.618557v1?rss=1"
Huang, Q. Y.Kim, R.Song, K.Grigorieff, N.Munro, J.Schiffer, C. A.Somasundaran, M.2024-10-18doi:10.1101/2024.10.15.618557Cold Spring Harbor Laboratory Press2024-10-18
<![CDATA[
Chromatin Buffers Torsional Stress During Transcription
]]>
https://biorxiv.org/cgi/content/short/2024.10.15.618270v1?rss=1"
Qian, J.Lubkowska, L.Zhang, S.Tan, C.Hong, Y.Fulbright, R. M.Inman, J. T.Kay, T. M.Jeong, J.Gotte, D.Berger, J. M.Kashlev, M.Wang, M. D.2024-10-18doi:10.1101/2024.10.15.618270Cold Spring Harbor Laboratory Press2024-10-18
<![CDATA[
Statistical analysis of repertoire data demonstrates the influence of microhomology in V(D)J recombination
]]>
https://biorxiv.org/cgi/content/short/2024.10.16.618753v1?rss=1"
Russell, M. L.Trofimov, A.Bradley, P.Matsen, F. A.2024-10-18doi:10.1101/2024.10.16.618753Cold Spring Harbor Laboratory Press2024-10-18
<![CDATA[
Gut bacteria-derived succinate induces enteric nervous system regeneration
]]>
https://biorxiv.org/cgi/content/short/2024.10.15.618589v1?rss=1"
Aydin, B.Mamede, I.Cardoso, J.Deere, J.Alvarez, Y.Qiao, S.Sharma, V. P.Scavuzzo, M. A.Donaldson, G. P.Guo, C.-J.Mucida, D.2024-10-18doi:10.1101/2024.10.15.618589Cold Spring Harbor Laboratory Press2024-10-18
<![CDATA[
Human Topoisomerase IIα Promotes Chromatin Condensation Via a Phase Transition
]]>
https://biorxiv.org/cgi/content/short/2024.10.15.618281v1?rss=1"
Wu, M.Beck, C.Lee, J. H.Fulbright, R. M.Jeong, J.Inman, J. T.Woodhouse, M. V.Berger, J. M.Wang, M. D.2024-10-18doi:10.1101/2024.10.15.618281Cold Spring Harbor Laboratory Press2024-10-18
<![CDATA[
Packaged delivery of CRISPR-Cas9 ribonucleoproteins accelerates genome editing
]]>
https://biorxiv.org/cgi/content/short/2024.10.18.619117v1?rss=1"
1300 Cas9 RNPs per nucleus are typically required for productive genome editing. EDV-mediated editing was >30-fold more efficient than electroporation, and editing occurs at least two-fold faster for EDV delivery at comparable total Cas9 RNP doses. We hypothesize that differences in efficacy between these methods result in part from the increased duration of RNP nuclear residence resulting from EDV delivery. Our results directly compare RNP delivery strategies, showing that packaged delivery could dramatically reduce the amount of CRISPR-Cas9 RNPs required for experimental or clinical genome editing.
Graphical Abstract
O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/619117v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@11a1f94org.highwire.dtl.DTLVardef@f3130org.highwire.dtl.DTLVardef@1666938org.highwire.dtl.DTLVardef@85fd13_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Karp, H.Zoltek, M.Wasko, K.Vazquez, A. L.Brim, J.Ngo, W.Schepartz, A.Doudna, J. A.2024-10-19doi:10.1101/2024.10.18.619117Cold Spring Harbor Laboratory Press2024-10-19
<![CDATA[
In-Situ Structure and Topography of AMPA Receptor Scaffolding Complexes Visualized by CryoET
]]>
https://biorxiv.org/cgi/content/short/2024.10.19.619226v1?rss=1"
Held, R. G.Liang, J.Esquivies, L.Khan, Y. A.Wang, C.Azubel, M.Brunger, A. T.2024-10-20doi:10.1101/2024.10.19.619226Cold Spring Harbor Laboratory Press2024-10-20
<![CDATA[
Resolving an unconventional non-photochemical quenching signature at the light-to-dark transition
]]>
https://biorxiv.org/cgi/content/short/2024.10.17.618902v1?rss=1"
Lam, L.Patel-Tupper, D.Lam, H. E.Steen, C. J.Ma, A.Ma, S. A.Leipertz, A.Lee, T.-Y.Fleming, G.Niyogi, K. K.2024-10-21doi:10.1101/2024.10.17.618902Cold Spring Harbor Laboratory Press2024-10-21
<![CDATA[
Harnessing GPT-4 for Automated Curation of E3-Substrate Relationships in the Ubiquitin-Proteasome System
]]>
https://biorxiv.org/cgi/content/short/2024.10.20.619305v1?rss=1"
Zhang, Z.Elledge, S.2024-10-21doi:10.1101/2024.10.20.619305Cold Spring Harbor Laboratory Press2024-10-21
<![CDATA[
Computational design of bifaceted protein nanomaterials with tailorable properties
]]>
https://biorxiv.org/cgi/content/short/2024.10.18.619149v1?rss=1"
Rankovic, S.Carr, K. D.Decarreau, J.Skotheim, R.Kibler, R. D.Ols, S.Lee, S.Chun, J.-H.Tooley, M.Dauparas, J.Eisenach, H. E.Gloegl, M.Weidle, C.Borst, A. J.Baker, D.King, N. P.2024-10-22doi:10.1101/2024.10.18.619149Cold Spring Harbor Laboratory Press2024-10-22
<![CDATA[
Genetic diversity loss in the Anthropocene will continue long after habitat destruction ends
]]>
https://biorxiv.org/cgi/content/short/2024.10.21.619096v1?rss=1"
Mualim, K. S.Spence, J. P.Weiss, C. L.Selmoni, O.Lin, M.Exposito-Alonso, M.2024-10-22doi:10.1101/2024.10.21.619096Cold Spring Harbor Laboratory Press2024-10-22
<![CDATA[
Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation
]]>
https://biorxiv.org/cgi/content/short/2024.10.21.619448v1?rss=1"
Wolff, T.Eddison, M.Chen, N.Nern, A.Sundaramurthi, P.Sitaraman, D.Rubin, G. M.2024-10-22doi:10.1101/2024.10.21.619448Cold Spring Harbor Laboratory Press2024-10-22
<![CDATA[
Mitochondrial fission controls astrocyte morphogenesis and organization in the cortex
]]>
https://biorxiv.org/cgi/content/short/2024.10.22.619706v1?rss=1"
Salazar, M. P. R.Kolanukuduru, S.Ramirez, V.Lyu, B.Sejourne, G.Sesaki, H.Yu, G.Eroglu, C.2024-10-23doi:10.1101/2024.10.22.619706Cold Spring Harbor Laboratory Press2024-10-23
<![CDATA[
RPE-specific MCT2 expression promotes cone survival in models of retinitis pigmentosa
]]>
https://biorxiv.org/cgi/content/short/2024.10.23.619878v1?rss=1"
Chandler, L. C.Gardner, A.Cepko, C. L.2024-10-23doi:10.1101/2024.10.23.619878Cold Spring Harbor Laboratory Press2024-10-23
<![CDATA[
Endogenous neuronal DNA double-strand breaks are not sufficient to drive brain aging and neurodegeneration
]]>
https://biorxiv.org/cgi/content/short/2024.10.22.619740v1?rss=1"
Cohen, S.Cheradame, L.Pratt, K.Collins, S.Barillas, A.Carlson, A.Ramani, V.Legube, G.Villeda, S.Mullins, D.Schwer, B.2024-10-23doi:10.1101/2024.10.22.619740Cold Spring Harbor Laboratory Press2024-10-23
<![CDATA[
Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis
]]>
https://biorxiv.org/cgi/content/short/2024.10.21.619529v1?rss=1"
Jones, M. G.Sun, D.Min, K. H.Colgan, W. N.Tian, L.Weir, J. A.Chen, V. Z.Koblan, L. W.Yost, K. E.Mathey-Andrews, N.Russell, A. J. C.Stickels, R. R.Balderrama, K. S.Rideout, W. M.Chang, H. Y.Jacks, T.Chen, F.Weissman, J. S.Yosef, N.Yang, D.2024-10-24doi:10.1101/2024.10.21.619529Cold Spring Harbor Laboratory Press2024-10-24
<![CDATA[
Computational design of prefusion-stabilized Herpesvirus gB trimers
]]>
https://biorxiv.org/cgi/content/short/2024.10.23.619923v1?rss=1"
McCallum, M.Veesler, D.2024-10-24doi:10.1101/2024.10.23.619923Cold Spring Harbor Laboratory Press2024-10-24
<![CDATA[
The deubiquitinase Rpn11 functions as an allosteric ubiquitin sensor to promote substrate engagement by the 26S proteasome
]]>
https://biorxiv.org/cgi/content/short/2024.10.24.620116v1?rss=1"
Htet, Z. M.Dong, K. C.Martin, A.2024-10-24doi:10.1101/2024.10.24.620116Cold Spring Harbor Laboratory Press2024-10-24
<![CDATA[
Duplex PCR assay to determine sex and mating status of Ixodes scapularis (Acari: Ixodidae), vector of the Lyme disease pathogen
]]>
https://biorxiv.org/cgi/content/short/2024.10.23.619921v1?rss=1"
Ronai, I.Frederick, J. C.Thompson, A. T.Sharma, P.Yabsley, M. J.Pal, U.Extavour, C. G.Glenn, T. C.2024-10-24doi:10.1101/2024.10.23.619921Cold Spring Harbor Laboratory Press2024-10-24
<![CDATA[
PACT prevents aberrant activation of PKR by endogenous dsRNA without sequestration
]]>
https://biorxiv.org/cgi/content/short/2024.10.23.619951v1?rss=1"
Ahmad, S.Zou, T.Zhao, L.Wang, X.Hwang, J.Davydenko, A.Buchumenski, I.Zhuang, P.Fishbein, A. R.Capcha-Rodriguez, D.Orgel, A.Levanon, E. Y.Myong, S.Chou, J.Meyerson, M.Hur, S.2024-10-24doi:10.1101/2024.10.23.619951Cold Spring Harbor Laboratory Press2024-10-24
<![CDATA[
The fourspine stickleback (Apeltes quadracus) has an XY sex chromosome system with polymorphic inversions on both X and Y chromosomes
]]>
https://biorxiv.org/cgi/content/short/2024.10.21.619356v1?rss=1"
Liu, Z.Herbert, A. L.Chan, Y. F.Kucka, M.Kingsley, D. M.Peichel, C. L.2024-10-24doi:10.1101/2024.10.21.619356Cold Spring Harbor Laboratory Press2024-10-24
<![CDATA[
An attractor state zone precedes neural crest fate in melanoma initiation
]]>
https://biorxiv.org/cgi/content/short/2024.10.22.618007v1?rss=1"
McConnell, A. M.Chasse, M. H.Noonan, H. R.Mito, J. K.Barbano, J.Weiskopf, E.Gosselink, I. F.Prasad, M.Yang, S.Abarzua, P.Lian, C. G.Murphy, G. F.Trapnell, C.Zon, L. I.2024-10-25doi:10.1101/2024.10.22.618007Cold Spring Harbor Laboratory Press2024-10-25
<![CDATA[
Too dim, too bright, and just right: Systems analysis of the Chlamydomonas diurnal program upon acclimation to light stress and limitation
]]>
https://biorxiv.org/cgi/content/short/2024.10.22.618525v1?rss=1"
Dupuis, S.Ojeda, V.Gallaher, S. D.Purvine, S. O.Glaesener, A. G.Ponce, R.Nicora, C. D.Bloodsworth, K.Lipton, M. S.Niyogi, K. K.Iwai, M.Merchant, S. S.2024-10-25doi:10.1101/2024.10.22.618525Cold Spring Harbor Laboratory Press2024-10-25
<![CDATA[
A high throughput single molecule platform to study DNA supercoiling effect on protein-DNA interactions
]]>
https://biorxiv.org/cgi/content/short/2024.10.24.620099v1?rss=1"
Lee, H.Hwang, J.Rashid, F.London, J. A.Fishel, R.Berger, J. M.Myong, S.Ha, T.2024-10-25doi:10.1101/2024.10.24.620099Cold Spring Harbor Laboratory Press2024-10-25
<![CDATA[
Dysregulation of FicD AMPylation causes diabetes by disrupting pancreatic endocrine homeostasis
]]>
https://biorxiv.org/cgi/content/short/2024.10.25.620287v1?rss=1"
Casey, A. K.Stewart, N. M. S.Zaidi, N.Gray, H. F.Fields, H. A.Sakurai, M.Pinzon-Arteaga, C. A.Evers, B. M.Wu, J.Orth, K.2024-10-26doi:10.1101/2024.10.25.620287Cold Spring Harbor Laboratory Press2024-10-26
<![CDATA[
Borrelia burgdorferi loses essential genetic elements and cell proliferative potential during stationary phase in culture but not in the tick vector.
]]>
https://biorxiv.org/cgi/content/short/2024.10.28.620338v1?rss=1"
Zhang, J.Takacs, C. N.McCausland, J. W.Mueller, E.Buron, J.Thappeta, Y.Wachter, J.Rosa, P. A.Jacobs-Wagner, C.2024-10-28doi:10.1101/2024.10.28.620338Cold Spring Harbor Laboratory Press2024-10-28
<![CDATA[
TreeFormer: A transformer-based tree rearrangement operation for phylogenetic reconstruction
]]>
https://biorxiv.org/cgi/content/short/2024.10.28.620561v1?rss=1"
Ly-Trong, N.Albert Matsen, F.Minh, B. Q.2024-10-29doi:10.1101/2024.10.28.620561Cold Spring Harbor Laboratory Press2024-10-29
<![CDATA[
Stratified analysis identifies HIF-2α as a therapeutic target for highly immune-infiltrated melanomas
]]>
https://biorxiv.org/cgi/content/short/2024.10.29.620300v1?rss=1"
Huang, A. Y.Burke, K. P.Porter, R.Meiger, L.Fatouros, P.Yang, J.Robitschek, E.Vokes, N. I.Ricker, C.Rosado, V.Tarantino, G.Chen, J.Aprati, T. J.Glettig, M. C.He, Y.Wang, C.Fu, D.Ho, L.-l.Galani, K.Freeman, G. J.Buchbinder, E. I.Hodi, F. S.Kellis, M.Boland, G. M.Sharpe, A. H.Liu, D.2024-10-30doi:10.1101/2024.10.29.620300Cold Spring Harbor Laboratory Press2024-10-30
<![CDATA[
A near telomere-to-telomere phased reference assembly for the male mountain gorilla
]]>
https://biorxiv.org/cgi/content/short/2024.10.28.620258v1?rss=1"
Nelson, D. R.Muvunyi, R.Hazzouri, K. M.Tumushime, J.-C.Nzayisenga, G.Nziza, J.Meert, W.Karim, L.Coppieters, W.Munson, K. M.Yoo, D.Eichler, E.Salehi-Ashtiani, K.Twizere, J.-C.2024-10-31doi:10.1101/2024.10.28.620258Cold Spring Harbor Laboratory Press2024-10-31
<![CDATA[
Neural mechanisms underlying robust target selection in response to microstimulation of the oculomotor system
]]>
https://biorxiv.org/cgi/content/short/2024.10.29.620929v1?rss=1"
Rakhshan, M.Schafer, R.Moore, T.Soltani, A.2024-10-31doi:10.1101/2024.10.29.620929Cold Spring Harbor Laboratory Press2024-10-31
<![CDATA[
Proteomic analysis of the pyrenoid-traversing membranes of Chlamydomonas reinhardtii reveals novel components
]]>
https://biorxiv.org/cgi/content/short/2024.10.28.620638v1?rss=1"
Franklin, E.Wang, L.Cruz, E. R.Duggal, K.Ergun, S. L.Garde, A.Jonikas, M. C.2024-10-31doi:10.1101/2024.10.28.620638Cold Spring Harbor Laboratory Press2024-10-31
<![CDATA[
GESIAP3.0: Sensor-based Image Analysis Program for Transmission Visualization In Vivo
]]>
https://biorxiv.org/cgi/content/short/2024.10.28.620522v1?rss=1"
Zhu, R. E.Diao, X.Liu, X.Ru, Q.Wu, Z.Zhang, Z.Looger, L.Zhu, J.2024-10-31doi:10.1101/2024.10.28.620522Cold Spring Harbor Laboratory Press2024-10-31
<![CDATA[
From the fly connectome to exact ring attractor dynamics
]]>
https://biorxiv.org/cgi/content/short/2024.11.01.621596v1?rss=1"
Biswas, T.Stanoev, A.Romani, S.Fitzgerald, J. E.2024-11-01doi:10.1101/2024.11.01.621596Cold Spring Harbor Laboratory Press2024-11-01
<![CDATA[
Genetic architecture of a light-temperature coincidence detector
]]>
https://biorxiv.org/cgi/content/short/2024.10.30.621125v1?rss=1"
Seluzicki, A.Chory, J.2024-11-02doi:10.1101/2024.10.30.621125Cold Spring Harbor Laboratory Press2024-11-02
<![CDATA[
PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation with relevance to human fertility
]]>
https://biorxiv.org/cgi/content/short/2024.10.29.620940v1?rss=1"
Xiang, K.Bartel, D.2024-11-02doi:10.1101/2024.10.29.620940Cold Spring Harbor Laboratory Press2024-11-02
<![CDATA[
SOQ1 functions as a methionine sulfoxide reductase in the chloroplast lumen for regulation of photoprotective qH in Arabidopsis
]]>
https://biorxiv.org/cgi/content/short/2024.11.01.621559v1?rss=1"
Hao, J.Johansson, A.Svensson Fall, J.Duan, J.Hertle, A. P.Brooks, M. D.Niyogi, K. K.Yoshida, K.Hisabori, T.Malnoe, A.2024-11-02doi:10.1101/2024.11.01.621559Cold Spring Harbor Laboratory Press2024-11-02
<![CDATA[
Multiplexed ultrasound imaging of gene expression
]]>
https://biorxiv.org/cgi/content/short/2024.10.30.621148v1?rss=1"
Nystrom, N. N.Jin, Z.Bennett, M. E.Zhang, R.Swift, M. B.Shapiro, M. G.2024-11-03doi:10.1101/2024.10.30.621148Cold Spring Harbor Laboratory Press2024-11-03
<![CDATA[
Non-invasive imaging of cell-based therapies using acoustic reporter genes
]]>
https://biorxiv.org/cgi/content/short/2024.11.01.621111v1?rss=1"
Shivaei, S.Liu, A.Abedi, M. H.Revilla, J.Hurvitz, I. U.Swift, M. B.Shapiro, M. G.2024-11-03doi:10.1101/2024.11.01.621111Cold Spring Harbor Laboratory Press2024-11-03
<![CDATA[
ImmunoStruct: Integration of protein sequence, structure, and biochemical properties for immunogenicity prediction and interpretation
]]>
https://biorxiv.org/cgi/content/short/2024.11.01.621580v1?rss=1"
Givechian, K. B.Rocha, J. F.Yang, E.Liu, C.Greene, K.Ying, R.Caron, E.Iwasaki, A.Krishnaswamy, S.2024-11-03doi:10.1101/2024.11.01.621580Cold Spring Harbor Laboratory Press2024-11-03
<![CDATA[
Spatial Transcriptomics of IPMN Reveals Divergent Indolent and Malignant Lineages
]]>
https://biorxiv.org/cgi/content/short/2024.10.29.620810v1?rss=1"
Iyer, M. K.Fletcher, A.Shi, C.Chen, F.Kanu, E.Eckhoff, A.Bao, M.Frankel, T. L.Chinnaiyan, A. M.Nussbaum, D. P.Allen, P. J.2024-11-03doi:10.1101/2024.10.29.620810Cold Spring Harbor Laboratory Press2024-11-03
<![CDATA[
Generalized cell phenotyping for spatial proteomics with language-informed vision models
]]>
https://biorxiv.org/cgi/content/short/2024.11.02.621624v1?rss=1"
Wang, X.Dilip, R.Bussi, Y.Brown, C.Pradhan, E.Jain, Y.Yu, K.Li, S.Abt, M.Borner, K.Keren, L.Yue, Y.Barnowski, R.Van Valen, D. A.2024-11-03doi:10.1101/2024.11.02.621624Cold Spring Harbor Laboratory Press2024-11-03
<![CDATA[
Mouse Pachytene piRNAs Cleave Hundreds of Transcripts,But Alter the Steady-State Abundance of Only a Minority of Targets
]]>
https://biorxiv.org/cgi/content/short/2024.11.02.621675v1?rss=1"
Cecchini, K.Ajaykumar, N.Bagci, A.Zamore, P.Gainetdinov, I.2024-11-03doi:10.1101/2024.11.02.621675Cold Spring Harbor Laboratory Press2024-11-03
<![CDATA[
A global dopaminergic learning rate enables adaptive foraging across many options
]]>
https://biorxiv.org/cgi/content/short/2024.11.04.621923v1?rss=1"
Grima, L. L.Guo, Y.Narayan, L.Hermundstad, A. M.Dudman, J. T.2024-11-04doi:10.1101/2024.11.04.621923Cold Spring Harbor Laboratory Press2024-11-04
<![CDATA[
The Fly Disco: Hardware and software for optogenetics and fine-grained fly behavior analysis
]]>
https://biorxiv.org/cgi/content/short/2024.11.04.621948v1?rss=1"
Robie, A. A.Taylor, A. L.Schretter, C. E.Kabra, M.Branson, K.2024-11-04doi:10.1101/2024.11.04.621948Cold Spring Harbor Laboratory Press2024-11-04
<![CDATA[
Designed miniproteins potently inhibit and protect against MERS-CoV
]]>
https://biorxiv.org/cgi/content/short/2024.11.03.621760v1?rss=1"
Ragotte, R. J.Tortorici, M. A.Cantazaro, N. J.Addetia, A.Coventry, B.Froggatt, H. M.Lee, J.Stewart, C.Brown, J. T.Goreshnik, I.Sims, J. N.Milles, L. F.Wicky, B. I.Gloegl, M.Gerben, S.Kang, A.Bera, A. K.Sharkey, W.Schaefer, A.Baric, R. S.Baker, D.Veesler, D.2024-11-04doi:10.1101/2024.11.03.621760Cold Spring Harbor Laboratory Press2024-11-04
<![CDATA[
Identification and annotation of centromeric hypomethylated regions with Centromere Dip Region (CDR)-Finder
]]>
https://biorxiv.org/cgi/content/short/2024.11.01.621587v1?rss=1"
Mastrorosa, F. K.Oshima, K. K.Rozanski, A. N.Harvey, W. T.Eichler, E. E.Logsdon, G. A.2024-11-04doi:10.1101/2024.11.01.621587Cold Spring Harbor Laboratory Press2024-11-04
<![CDATA[
The 5-methylcytosine DNA glycosylase ROS1 antagonizes parent-of-origin specific DNA methylation in Arabidopsis endosperm
]]>
https://biorxiv.org/cgi/content/short/2024.11.05.622036v1?rss=1"
Hemenway, E. A.Gehring, M.2024-11-05doi:10.1101/2024.11.05.622036Cold Spring Harbor Laboratory Press2024-11-05
<![CDATA[
Antagonizing cis-regulatory elements of a conserved flowering gene mediate developmental robustness
]]>
https://biorxiv.org/cgi/content/short/2024.11.03.621740v1?rss=1"
Lanctot, A.Hendelman, A.Udilovich, P.Robitaille, G. M.Lippman, Z.2024-11-05doi:10.1101/2024.11.03.621740Cold Spring Harbor Laboratory Press2024-11-05
<![CDATA[
A green lifetime biosensor for calcium that remains bright over its full dynamic range
]]>
https://biorxiv.org/cgi/content/short/2024.11.05.622032v1?rss=1"
1 nanosecond. This sensor, named G-Ca-FLITS, is comparable in brightness to the bright state of GCaMP3 and jGCaMP7c in mammalian cells. The calcium induced loss in fluorescence intensity is only around 30% and therefore we observe little variation in the SNR when calcium levels change. G-Ca-FLITS shows negligible sensitivity to pH in the physiological range, like its turquoise parent. Using fluorescence lifetime imaging (FLIM), we measured the calcium concentration with G-Ca-FLITS in various organelles and observed in HeLa cells transient and spatially heterogeneous calcium elevations in mitochondria. Finally, we evaluated the use of G-Ca-FLITS and its turquoise predecessor for two-photon FLIM in Drosophila brains.
O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/622032v2_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@1caf016org.highwire.dtl.DTLVardef@586996org.highwire.dtl.DTLVardef@7c15cdorg.highwire.dtl.DTLVardef@7b6f03_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>van der Linden, F. H.Thornquist, S. C.ter Beek, R. M.Huijts, J. Y.Hink, M. A.Gadella, T. W. J.Maimon, G.Goedhart, J.2024-11-06doi:10.1101/2024.11.05.622032Cold Spring Harbor Laboratory Press2024-11-06
<![CDATA[
The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase
]]>
https://biorxiv.org/cgi/content/short/2024.11.07.622497v1?rss=1"
Leitner, D. R.Zingl, F. G.Morano, A. A.Zhang, H.Waldor, M. K.2024-11-07doi:10.1101/2024.11.07.622497Cold Spring Harbor Laboratory Press2024-11-07
<![CDATA[
Rad52 sorts and stacks Rad51 at the DNA junction to promote homologous recombination
]]>
https://biorxiv.org/cgi/content/short/2024.11.07.622519v1?rss=1"
Deveryshetty, J.Mistry, A.Pangeni, S.Ghoneim, M.Tokmina, M.Kaushik, V.Taddei, A.Ha, T.Bothner, B.Antony, E.2024-11-07doi:10.1101/2024.11.07.622519Cold Spring Harbor Laboratory Press2024-11-07
<![CDATA[
Multiplexed perturbation of yew reveals cryptic proteins that enable a total biosynthesis of baccatin III and Taxol precursors
]]>
https://biorxiv.org/cgi/content/short/2024.11.06.622305v1?rss=1"
McClune, C. J.Liu, J. C.-T.Wick, C.De La Pena, R.Lange, B. M.Fordyce, P. M.Sattely, E. S.2024-11-08doi:10.1101/2024.11.06.622305Cold Spring Harbor Laboratory Press2024-11-08
<![CDATA[
RNA methylation controls stress granule formation and function during erythropoiesis
]]>
https://biorxiv.org/cgi/content/short/2024.11.07.622459v1?rss=1"
GUNAGE, R. D.Lin, S.Wiley, D.Choudhuri, A.Smith, M.Han, T.Shah, A.Coyne, S.Koczirka, K.Zhi Ming Chen, K.Yu, C.Drake, K.Yang, X.Yang, S.Zhou, Y.Bauer, D.Qian, Z.Calo, E.Gregory, R.Zon, L.2024-11-08doi:10.1101/2024.11.07.622459Cold Spring Harbor Laboratory Press2024-11-08
<![CDATA[
Phenotypic high-throughput screening identifies modulators of gut microbial choline metabolism
]]>
https://biorxiv.org/cgi/content/short/2024.11.08.621386v1?rss=1"
Woo, A. Y. M.Sandoval-Espinola, W. J.Bollenbach, M.Wong, A.Sakanaka-Yokoyama, M.Zhang, Q.Nieto, V.Rey, F. E.Balskus, E. P.2024-11-09doi:10.1101/2024.11.08.621386Cold Spring Harbor Laboratory Press2024-11-09
<![CDATA[
Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1
]]>
https://biorxiv.org/cgi/content/short/2024.11.08.622731v1?rss=1"
Martin, A.Arkinson, C.Gee, C. L.Zhang, Z.Dong, K.2024-11-09doi:10.1101/2024.11.08.622731Cold Spring Harbor Laboratory Press2024-11-09
<![CDATA[
Structure of the TXNL1-bound proteasome
]]>
https://biorxiv.org/cgi/content/short/2024.11.08.622741v1?rss=1"
Gao, J.Nardone, C.Yip, M. C.Chino, H.Gu, X.Mirman, Z.Rale, M. J.Paulo, J. A.Elledge, S. J.Shao, S.2024-11-10doi:10.1101/2024.11.08.622741Cold Spring Harbor Laboratory Press2024-11-10
<![CDATA[
Reducing functionally defective HSCs alleviates aging-related phenotypes in old mice
]]>
https://biorxiv.org/cgi/content/short/2024.11.09.622774v1?rss=1"
Zhang, Y.Wang, Y.Zhang, W.Van, H. T.Seino, T.Zhang, C.2024-11-10doi:10.1101/2024.11.09.622774Cold Spring Harbor Laboratory Press2024-11-10
<![CDATA[
The transcription factor GABPA is a master regulator of naive pluripotency
]]>
https://biorxiv.org/cgi/content/short/2024.11.11.623003v1?rss=1"
Zhou, C.Wang, M.Zhang, C.Zhang, Y.2024-11-12doi:10.1101/2024.11.11.623003Cold Spring Harbor Laboratory Press2024-11-12
<![CDATA[
Mapping Plasmodium transitions and interactions in the Anopheles female
]]>
https://biorxiv.org/cgi/content/short/2024.11.12.623125v1?rss=1"
Yan, Y.Cheung, E.Verzier, L. H.Appetecchia, F.March, S.Craven, A. R.Du, E.Probst, A. S.Rinvee, T. A.de Vries, L. E.Kauffman, J.Bhatia, S. N.Nelson, E.Singh, N.Peng, D.Shaw, W. R.Catteruccia, F.2024-11-13doi:10.1101/2024.11.12.623125Cold Spring Harbor Laboratory Press2024-11-13
<![CDATA[
Computational Design of Metallohydrolases
]]>
https://biorxiv.org/cgi/content/short/2024.11.13.623507v1?rss=1"
Kim, D.Woodbury, S. M.Ahern, W.Kalvet, I.Hanikel, N.Salike, S.Pellock, S. J.Lauko, A.Hilvert, D.Baker, D.2024-11-14doi:10.1101/2024.11.13.623507Cold Spring Harbor Laboratory Press2024-11-14
<![CDATA[
Mechanisms driving epigenetic and transcriptional responses of microglia in a neurodegenerative lysosomal storage disorder model
]]>
https://biorxiv.org/cgi/content/short/2024.11.12.623296v1?rss=1"
Balak, C. D.Schlachetzki, J. C. M.Lana, A. J.West, E.Hong, C.DuGal, J.Zhou, Y.Li, B.Saisan, P.Spann, N. J.Sarsani, V.Pasillas, M. P.O'Brien, S.Gordts, P.Stevens, B.Kamme, F.Glass, C. K.2024-11-14doi:10.1101/2024.11.12.623296Cold Spring Harbor Laboratory Press2024-11-14
<![CDATA[
Self-restrained sex chromosome drive through sequential asymmetric meiosis
]]>
https://biorxiv.org/cgi/content/short/2024.11.14.623699v1?rss=1"
Meng, X.Yamashita, Y. M. M.2024-11-15doi:10.1101/2024.11.14.623699Cold Spring Harbor Laboratory Press2024-11-15
<![CDATA[
Real-time volumetric imaging of cells and molecules in deep tissues with Takoyaki ultrasound
]]>
https://biorxiv.org/cgi/content/short/2024.11.14.623368v1?rss=1"
Lee, S.Wu, D.Malounda, D.Rabut, C.Shapiro, M. G.2024-11-15doi:10.1101/2024.11.14.623368Cold Spring Harbor Laboratory Press2024-11-15
<![CDATA[
Biochemical principles of miRNA targeting in flies
]]>
https://biorxiv.org/cgi/content/short/2024.11.16.623948v1?rss=1"
Vega-Badillo, J.Zamore, P.Jouravleva, K.2024-11-16doi:10.1101/2024.11.16.623948Cold Spring Harbor Laboratory Press2024-11-16
<![CDATA[
Design of facilitated dissociation enables control over cytokine signaling duration
]]>
https://biorxiv.org/cgi/content/short/2024.11.15.623900v1?rss=1"
Broerman, A. J.Pollmann, C.Lichtenstein, M. A.Jackson, M. D.Tessmer, M. H.Ryu, W. H.Abedi, M. H.Sahtoe, D. D.Allen, A.Kang, A.De La Cruz, J.Brackenbrough, E.Sankaran, B.Bera, A. K.Zuckerman, D. M.Stoll, S.Praetorius, F.Piehler, J.Baker, D.2024-11-16doi:10.1101/2024.11.15.623900Cold Spring Harbor Laboratory Press2024-11-16
<![CDATA[
A novel rhodopsin-based voltage indicator for simultaneous two-photon optical recording with GCaMP in vivo
]]>
https://biorxiv.org/cgi/content/short/2024.11.15.623698v1?rss=1"
Villette, V.Yang, S.Valenti, R.Macklin, J. J.Bradley, J.Mathieu, B.Lombardini, A.Podgorski, K.Dieudonne, S.Schreiter, E. R.Abdelfattah, A. S.2024-11-17doi:10.1101/2024.11.15.623698Cold Spring Harbor Laboratory Press2024-11-17
<![CDATA[
Dynamic cytoplasmic fluidity during morphogenesis in a human fungal pathogen
]]>
https://biorxiv.org/cgi/content/short/2024.11.16.623909v1?rss=1"
Serrano, A.Puerner, C.Plumb, E.Chevalier, L.Elferich, J.Sinn, L. R.Grigorieff, N.Ralser, M.Delarue, M.Bassilana, M.Arkowitz, R. A.2024-11-17doi:10.1101/2024.11.16.623909Cold Spring Harbor Laboratory Press2024-11-17
<![CDATA[
Accurate de novo design of high-affinity protein binding macrocycles using deep learning
]]>
https://biorxiv.org/cgi/content/short/2024.11.18.622547v1?rss=1"
Rettie, S.Juergens, D.Adebomi, V.Bueso, Y. F.Zhao, Q.Leveille, A.Liu, A.Bera, A.Wilms, J.Üffing, A.Kang, A.Brackenbrough, E.Lamb, M.Gerben, S.Murray, A.Levine, P.Schneider, M.Vasireddy, V.Ovchinnikov, S.Weiergräber, O.Willbold, D.Kritzer, J.Mougous, J.Baker, D.DiMaio, F.Bhardwaj, G.2024-11-18doi:10.1101/2024.11.18.622547Cold Spring Harbor Laboratory Press2024-11-18
<![CDATA[
Sensory History Drives Adaptive Neural Geometry in LP/Pulvinar-Prefrontal Cortex Circuits
]]>
https://biorxiv.org/cgi/content/short/2024.11.16.623977v1?rss=1"
Leow, Y. N.Barlowe, A.Luo, C. T.Osako, Y.Jazayeri, M.Sur, M.2024-11-18doi:10.1101/2024.11.16.623977Cold Spring Harbor Laboratory Press2024-11-18
<![CDATA[
ELAVL3 regulates splicing of RNAs encoding synaptic signaling proteins in D1 and D2 striatal medium spiny neurons.
]]>
https://biorxiv.org/cgi/content/short/2024.11.18.622571v1?rss=1"
Irmady, K.Scheckel, C.Singer, R. A.Carroll, T.Darnell, R. B.2024-11-19doi:10.1101/2024.11.18.622571Cold Spring Harbor Laboratory Press2024-11-19
<![CDATA[
A key role of PIEZO2 mechanosensitive ion channel in adipose sensory innervation
]]>
https://biorxiv.org/cgi/content/short/2024.11.18.624210v1?rss=1"
Wang, Y.Zhang, Y.Leung, V.Heydari-Seradj, S.Sonmez, U.Servin-Vences, R.Lipomi, D. J.Ye, L.Patapoutian, A.2024-11-19doi:10.1101/2024.11.18.624210Cold Spring Harbor Laboratory Press2024-11-19
<![CDATA[
Recurrent hyper-motif circuits in developmental programs
]]>
https://biorxiv.org/cgi/content/short/2024.11.20.624466v1?rss=1"
Adler, M.Medzhitov, R.2024-11-20doi:10.1101/2024.11.20.624466Cold Spring Harbor Laboratory Press2024-11-20
<![CDATA[
Cellular behavior analysis from live-cell imaging of TCR T cell-cancer cell interactions
]]>
https://biorxiv.org/cgi/content/short/2024.11.19.624390v1?rss=1"
Verma, A.Yu, C.Bachl, S.Lopez, I.Schwartz, M. S.Moen, E.Kale, N.Ching, C.Miller, G.Dougherty, T.Pao, E.Graf, W.Ward, C.Jena, S. G.Marson, A.Carnevale, J.Van Valen, D. A.Engelhardt, B. E.2024-11-21doi:10.1101/2024.11.19.624390Cold Spring Harbor Laboratory Press2024-11-21
<![CDATA[
Reconstitution of SPO11-dependent double-strand break formation
]]>
https://biorxiv.org/cgi/content/short/2024.11.20.624382v1?rss=1"
Zheng, Z.Zheng, L.Arter, M.Liu, K.Yamada, S.Ontoso, D.Kim, S.Keeney, S.2024-11-21doi:10.1101/2024.11.20.624382Cold Spring Harbor Laboratory Press2024-11-21
<![CDATA[
Genomes of two invasive Adelges species (hemlock woolly adelgid and pineapple gall adelgid) enable characterization of nicotinic acetylcholine receptors
]]>
https://biorxiv.org/cgi/content/short/2024.11.21.624573v1?rss=1"
Glendening, A. M.Stephens, C.Vuruputoor, V. S.Stern, D. L.Hogenhout, S. A.Mathers, T. C.Chaganti, T.Pauloski, N.Cernack, T. A.Wegrzyn, J. L.Fetter, K. C.2024-11-22doi:10.1101/2024.11.21.624573Cold Spring Harbor Laboratory Press2024-11-22
<![CDATA[
Global Neuron Shape Reasoning with Point Affinity Transformers
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https://biorxiv.org/cgi/content/short/2024.11.24.625067v1?rss=1"
Troidl, J.Knittel, J.Li, W.Zhan, F.Pfister, H.Turaga, S. C.2024-11-24doi:10.1101/2024.11.24.625067Cold Spring Harbor Laboratory Press2024-11-24
<![CDATA[
Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine
]]>
https://biorxiv.org/cgi/content/short/2024.11.22.624893v1?rss=1"
Hernandez, G.Osinski, A.Majumdar, A.Eitson, J. L.Antczak, M.Pawlowski, K.Niederstrasser, H.Servage, K. A.Posner, B.Schoggins, J. W.Ready, J. A.Tagliabracci, V. S.2024-11-25doi:10.1101/2024.11.22.624893Cold Spring Harbor Laboratory Press2024-11-25
<![CDATA[
Evidence for non-optimal codon choice in highly transcribed sex-biased genes of Drosophila melanogaster
]]>
https://biorxiv.org/cgi/content/short/2024.11.24.625100v1?rss=1"
Whittle, C. A.Extavour, C. G.2024-11-25doi:10.1101/2024.11.24.625100Cold Spring Harbor Laboratory Press2024-11-25
<![CDATA[
Molecular patterns of evolutionary changes throughout the whole nervous system of multiple nematode species
]]>
https://biorxiv.org/cgi/content/short/2024.11.23.624988v1?rss=1"
Toker, I. A.Ripoll-Sanchez, L.Geiger, L. T.Saini, K. S.Beets, I.Vertes, P. E.Schafer, W. R.Ben-David, E.Hobert, O.2024-11-25doi:10.1101/2024.11.23.624988Cold Spring Harbor Laboratory Press2024-11-25
<![CDATA[
Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping
]]>
https://biorxiv.org/cgi/content/short/2024.11.22.624784v1?rss=1"
Wang, K.Nie, Y.Maguire, C.Syphurs, C.Sheen, H.Karoly, M.Lapp, L.Gygi, J. P.Jayavelu, N. D.Patel, R. K.Hoch, A.IMPACC Network,Corry, D.Kheradmand, F.McComsey, G. A.Fernandez-Sesma, A.Simon, V.Metcalf, J. P.Agudelo Higuita, N. I.Messer, W. B.David, M. M.Nadeau, K. C.Kraft, M.Bime, C.Schaenman, J.Erle, D.Calfee, C. S.Atkinson, M. A.Brackenridge, S. C.Hafler, D. A.Shaw, A. C.Rahman, A.Hough, C. L.Geng, L. N.Ozonoff, A.Haddad, E. K.Reed, E. F.Bakel, H. v.Kim-Schulze, S. H.Krammer, F.Wilson, M.Eckalbar, W.Bosinger,2024-11-25doi:10.1101/2024.11.22.624784Cold Spring Harbor Laboratory Press2024-11-25
<![CDATA[
Dynamic regulation of the oxidative stress response by the E3 ligase TRIP12
]]>
https://biorxiv.org/cgi/content/short/2024.11.25.625235v1?rss=1"
Ingersoll, A. J.McCloud, D. M.Hu, J. Y.Rape, M.2024-11-25doi:10.1101/2024.11.25.625235Cold Spring Harbor Laboratory Press2024-11-25
<![CDATA[
Stereoselectivity of Aminoacyl-RNA Loop-closing Ligation
]]>
https://biorxiv.org/cgi/content/short/2024.11.26.625528v1?rss=1"
Kim, S.Todisco, M.Radakovic, A.Szostak, J. W.2024-11-27doi:10.1101/2024.11.26.625528Cold Spring Harbor Laboratory Press2024-11-27
<![CDATA[
An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology
]]>
https://biorxiv.org/cgi/content/short/2024.11.26.625329v1?rss=1"
Sokolowski, D. J.Miclaus, M.Nater, A.Faykoo-Martinez, M.Hoekzema, K.Zuzarte, P.Monis, S.Alvi, S. A.Erdmann, J.Erdmann, A. L.Kumaragurubaran, R.Bayerl, J.Yoo, D.Karimpour, N.Ungerleider, K.Hou, H.Fergal, M.Hourlier, T.Clarke, Z. A.Lischer, H. E.Leordean, D. V.Jiang, Y.Pugh, T. J.Smith, E. S. J.Haggerty, L.Laird, D. J.Lilue, J.Holmes, M. M.Eichler, E. E.Bruggmann, R.Simpson, J. T.Balmus, G.Wilson, M. D.2024-11-28doi:10.1101/2024.11.26.625329Cold Spring Harbor Laboratory Press2024-11-28
<![CDATA[
Actin filament assembly driven by distributive polymerases clustered on membrane surfaces
]]>
https://biorxiv.org/cgi/content/short/2024.11.26.625540v1?rss=1"
200 {micro}M). The finite time required for profilin dissociation decreases the advantage conferred by surface-associated polymerases, but only in the absence of force. Load forces enhance the effect of surface polymerases, which can both accelerate elongation and increase the force required to stall filament assembly.
]]>Mullins, D.Skruber, K.2024-11-28doi:10.1101/2024.11.26.625540Cold Spring Harbor Laboratory Press2024-11-28
<![CDATA[
Reliable amplification of highly repetitive or low complexity sequence DNA enabled by superhelicase-mediated isothermal amplification
]]>
https://biorxiv.org/cgi/content/short/2024.11.27.625726v1?rss=1"
Kang, J.Rashid, F.Murray, P. J.Merino-Urteaga, R.Gavrilov, M.Shang, T.Jo, W.Ahmed, A.Aksel, T.Barrick, D.Berger, J. M.Ha, T.2024-11-29doi:10.1101/2024.11.27.625726Cold Spring Harbor Laboratory Press2024-11-29
<![CDATA[
Immunofocusing on the conserved fusion peptide of HIV envelope glycoprotein in rhesus macaques
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https://biorxiv.org/cgi/content/short/2024.11.27.625755v1?rss=1"
Pratap, P. P.Cottrell, C. A.Quinn, J.Carnathan, D. G.Bader, D. L. V.Tran, A. S.Enemuo, C. A.Ngo, J. T.Richey, S. T.Gao, H.Shen, X.Greene, K. M.Hurtado, J.Ben-Akiva, E.Michaels, K. K.Allen, J. D.Ozorowski, G.Crispin, M.Briney, B.Montefiori, D.Silvestri, G.Irvine, D. J.Crotty, S.Ward, A. B.2024-11-29doi:10.1101/2024.11.27.625755Cold Spring Harbor Laboratory Press2024-11-29
<![CDATA[
TTF2 promotes replisome eviction from stalled forks in mitosis
]]>
https://biorxiv.org/cgi/content/short/2024.11.30.626186v1?rss=1"
Can, G.Shyian, M.Krishnamoorthy, A.Lim, Y.Wu, A.Zaher, M.Raeschle, M.Walter, J.Pellman, D.2024-11-30doi:10.1101/2024.11.30.626186Cold Spring Harbor Laboratory Press2024-11-30
<![CDATA[
Thrifty wide-context models of B cell receptor somatic hypermutation
]]>
https://biorxiv.org/cgi/content/short/2024.11.26.625407v1?rss=1"
Sung, K.Johnson, M. M.Dumm, W.Simon, N.Haddox, H.Fukuyama, J.Matsen, F. A.2024-12-01doi:10.1101/2024.11.26.625407Cold Spring Harbor Laboratory Press2024-12-01
<![CDATA[
The molecular basis of integrated stress response silencing
]]>
https://biorxiv.org/cgi/content/short/2024.12.02.626349v1?rss=1"
Yang, Z.Haakonsen, D.Heider, M.Witus, S. R.Zelter, A.Beschauner, T.MacCoss, M. J.Rape, M.2024-12-02doi:10.1101/2024.12.02.626349Cold Spring Harbor Laboratory Press2024-12-02
<![CDATA[
Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography
]]>
https://biorxiv.org/cgi/content/short/2024.12.01.626131v1?rss=1"
Zhou, H.Hutchings, J.Shiozaki, M.Zhao, X.Doolittle, L. K.Yang, S.Yan, R.Jean, N.Riggi, M.Yu, Z.Villa, E.Rosen, M. K.2024-12-02doi:10.1101/2024.12.01.626131Cold Spring Harbor Laboratory Press2024-12-02
<![CDATA[
Quantitative Attributions with Counterfactuals
]]>
https://biorxiv.org/cgi/content/short/2024.11.26.625505v1?rss=1"
Adjavon, D.-Y.Eckstein, N.Bates, A. S.Jefferis, G. S. X. E.Funke, J.2024-12-02doi:10.1101/2024.11.26.625505Cold Spring Harbor Laboratory Press2024-12-02
<![CDATA[
PITHD1: An Endogenous Inhibitor of the 26S Proteasome During Cellular Dormancy
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https://biorxiv.org/cgi/content/short/2024.12.04.626795v1?rss=1"
Amann, S. J.Dong, K.Roehsner, J.Krall, D.Grishkovskaya, I.Kotisch, H.Schleiffer, A.Roitinger, E.Pauli, A.Martin, A.Haselbach, D.2024-12-04doi:10.1101/2024.12.04.626795Cold Spring Harbor Laboratory Press2024-12-04
<![CDATA[
Induced B-Cell Receptor Diversity Predicts PD-1 Blockade Immunotherapy Response.
]]>
https://biorxiv.org/cgi/content/short/2024.12.03.626669v1?rss=1"
Che, Y.Lee, J.Abou-Taleb, F.Rieger, K. E.Satpathy, A.Chang, A. L. S.Chang, H.2024-12-04doi:10.1101/2024.12.03.626669Cold Spring Harbor Laboratory Press2024-12-04
<![CDATA[
Structural mechanisms of PIP2 activation and SEA0400 inhibition in human cardiac sodium-calcium exchanger NCX1
]]>
https://biorxiv.org/cgi/content/short/2024.12.05.627058v1?rss=1"
Xue, J.Zeng, W.John, S.Attiq, N.Ottolia, M.Jiang, Y.2024-12-06doi:10.1101/2024.12.05.627058Cold Spring Harbor Laboratory Press2024-12-06
<![CDATA[
Potent antitumor activity of a designed interleukin-21 mimic
]]>
https://biorxiv.org/cgi/content/short/2024.12.06.626481v1?rss=1"
Chun, J.-H.Lim, B. S.Roy, S.Walsh, M. J.Abhiraman, G. C.Zhangxu, K.Atajanova, T.Revach, O.-Y.Clark, E. C.Li, P.Palin, C. A.Khanna, A.Tower, S.Kureshi, R.Hoffman, M. T.Sharova, T.Lawless, A.Cohen, S.Boland, G. M.Nguyen, T.Peprah, F.Tello, J. G.Liu, S. Y.Kim, C. J.Shin, H.Quijano-Rubio, A.Jude, K. M.Ulge, U. Y.Gerben, S.Murray, A.Heine, P.DeWitt, M.Carter, L.King, N. P.Silva, D.-A.Kueh, H. Y.Kalia, V.Sarkar, S.Jenkins, R. W.Garcia, K. C.Leonard, W. J.Dougan, M.Dougan, S. K.Baker, D.2024-12-07doi:10.1101/2024.12.06.626481Cold Spring Harbor Laboratory Press2024-12-07
<![CDATA[
Spatial single-cell Organellomics reveals nutrient dependent hepatocyteheterogeneity and predicts pathophysiological status in vivo
]]>
https://biorxiv.org/cgi/content/short/2024.12.06.627285v1?rss=1"
Hillsley, A.Adhikari, R.Johnson, A. D.Espinosa-Medina, I.Funke, J.Feliciano, D.2024-12-08doi:10.1101/2024.12.06.627285Cold Spring Harbor Laboratory Press2024-12-08
<![CDATA[
Defining a highly conserved B cell epitope in the receptor binding motif of SARS-CoV-2 spike glycoprotein
]]>
https://biorxiv.org/cgi/content/short/2024.12.06.625234v1?rss=1"
Malladi, S. K.Jaiswal, D.Ying, B.Alsoussi, W.Darling, T.Dadonaite, B.Civljak, A.Horvath, S.Zhou, J.Kim, W.Turner, J.Schmitz, A.Han, F.Scheaffer, S.Farnsworth, C.Nachbagauer, R.Nestorova, B.Chalkias, S.Klebert, M.Edwards, D.Paris, R.Strnad, B.Middleton, W.OHalloran, J.Presti, R.Bloom, J. D.Boon, A. C. M.Diamond, M. S.Bajic, G.Ellebedy, A. H.2024-12-09doi:10.1101/2024.12.06.625234Cold Spring Harbor Laboratory Press2024-12-09
<![CDATA[
Naturally ornate RNA-only complexes revealed by cryo-EM
]]>
https://biorxiv.org/cgi/content/short/2024.12.08.627333v1?rss=1"
Kretsch, R. C.Wu, Y.Shabalina, S. A.Lee, H.Nye, G. P.Koonin, E. V.Gao, A.Chiu, W.Das, R.2024-12-09doi:10.1101/2024.12.08.627333Cold Spring Harbor Laboratory Press2024-12-09
<![CDATA[
Fe starvation induces a second LHCI tetramer to photosystem I in green algae
]]>
https://biorxiv.org/cgi/content/short/2024.12.11.624522v1?rss=1"
Liu, H. W.Khera, R.Grob, P.Gallaher, S. D.Purvine, S. O.Nicora, C. D.Lipton, M.Niyogi, K. K.Nogales, E.Iwai, M.Merchant, S.2024-12-12doi:10.1101/2024.12.11.624522Cold Spring Harbor Laboratory Press2024-12-12
<![CDATA[
Regulatory interactions between APOBEC3B N- and C-terminal domains
]]>
https://biorxiv.org/cgi/content/short/2024.12.11.628032v1?rss=1"
Braza, K.Demir, O.Ahn, S.-H.Morris, C.Calvo-Tusell, C.McGuire, K.Carpenter, M.Chen, Y.de la Pena Avalos, B.Casalino, L.Aihara, H.Harris, R. S.Amaro, R. E.2024-12-12doi:10.1101/2024.12.11.628032Cold Spring Harbor Laboratory Press2024-12-12
<![CDATA[
Ultrastable and Versatile FoxP3 Ensembles on Microsatellites
]]>
https://biorxiv.org/cgi/content/short/2024.12.12.628245v1?rss=1"
Leng, F.Merino, R.Wang, X.zhang, w.Ha, T.Hur, S.2024-12-12doi:10.1101/2024.12.12.628245Cold Spring Harbor Laboratory Press2024-12-12
<![CDATA[
The human RAD52 complex undergoes phase separation and facilitates bundling and end-to-end tethering of RAD51 presynaptic filaments
]]>
https://biorxiv.org/cgi/content/short/2024.12.09.627445v1?rss=1"
Alshareedah, I.Pangeni, S.Dewan, P. A.Honda, M.Liao, T.-W.Spies, M.Ha, T.2024-12-12doi:10.1101/2024.12.09.627445Cold Spring Harbor Laboratory Press2024-12-12
<![CDATA[
OrthoHMM: Improved Inference of Ortholog Groups using Hidden Markov Models
]]>
https://biorxiv.org/cgi/content/short/2024.12.07.627370v1?rss=1"
Steenwyk, J. L.Buida, T. J.Rokas, A.King, N.2024-12-12doi:10.1101/2024.12.07.627370Cold Spring Harbor Laboratory Press2024-12-12
<![CDATA[
Structural serology of polyclonal antibody responses to mRNA-1273 and NVX-CoV2373 COVID-19 vaccines
]]>
https://biorxiv.org/cgi/content/short/2024.12.11.628030v1?rss=1"
Bangaru, S.Jackson, A. M.Copps, J.Fernandez-Quintero, M. L.Torres, J. L.Richey, S. T.Nogal, B.Sewall, L. M.Torrents de la Pena, A.Rehman, A.Guebre-Xabier, M.Girard, B.Das, R.Corbett-Helaire, K. S.Seder, R. A.Graham, B. S.Edwards, D. K.Patel, N.Smith, G.Ward, A. B.2024-12-12doi:10.1101/2024.12.11.628030Cold Spring Harbor Laboratory Press2024-12-12
<![CDATA[
Food-Derived Compounds Extend the Shelf-Life of Frozen Human Milk
]]>
https://biorxiv.org/cgi/content/short/2024.12.11.627965v1?rss=1"
90% of lactating mothers reported using breast pumps to express milk.1 We conducted a survey of n = 1,049 lactating or recently lactating individuals from a US nationally representative population to explore breastmilk storage practices among this group. The data revealed that 83% of respondents store breastmilk in their homes, with 68% using freezers to do so for >1 month. The lowest available temperature in most household freezers is -20 {degrees}C, a temperature that is inadequate to maintain human milks emulsified structure, leading to separation, degradation of fats, loss of key vitamins, and changes in palatability. We developed a first-of-its-kind high-throughput screening platform to identify food-derived compounds and combinations of compounds that, when added to human breastmilk, preserve fat content, retain antioxidant capacity, and reduce production of rancid-associated free fatty acids during extended freezer storage. These formulations represent leads for the development of safe and affordable frozen breastmilk shelf-life extenders for easy at-home use to increase the longevity of stored breastmilk.
]]>Silpe, J. E.Damian-Medina, K.Bassler, B. L.2024-12-12doi:10.1101/2024.12.11.627965Cold Spring Harbor Laboratory Press2024-12-12
<![CDATA[
The Chlamydomonas reinhardtii CLiP2 mutant collection expands genome coverage with high-confidence disrupting alleles
]]>
https://biorxiv.org/cgi/content/short/2024.12.16.626622v1?rss=1"
Lunardon, A.Patena, W.Pacini, C.Warren-Williams, M.Zubak, Y.Laudon, M.Silflow, C.Lefebvre, P.Jonikas, M. C.2024-12-16doi:10.1101/2024.12.16.626622Cold Spring Harbor Laboratory Press2024-12-16
<![CDATA[
Recombinant Expression of Photo-crosslinkable 26S Proteasome Base Subcomplex
]]>
https://biorxiv.org/cgi/content/short/2024.12.16.628829v1?rss=1"
Yori Restrepo, S.Martin, A.2024-12-17doi:10.1101/2024.12.16.628829Cold Spring Harbor Laboratory Press2024-12-17
<![CDATA[
Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations
]]>
https://biorxiv.org/cgi/content/short/2024.12.17.628970v1?rss=1"
Aditham, A. K.Radford, C. E.Carr, C. R.Jasti, N.King, N. P.Bloom, J. D.2024-12-17doi:10.1101/2024.12.17.628970Cold Spring Harbor Laboratory Press2024-12-17
<![CDATA[
Persistent genomic erosion in whooping cranes despite demographic recovery
]]>
https://biorxiv.org/cgi/content/short/2024.12.12.628160v1?rss=1"
Fontsere, C.Speak, S. S.Caven, A. J.Rodriguez, J. A.Wang, X.Pacheco, C.Cassatt-Johnstone, M.Femerling, G.Maloney, B.Balacco, J.Collins, J.Sims, Y.Abueg, L.Fedrigo, O.Jarvis, E. D.Hartup, B. K.Shapiro, B.Gilbert, M. T. P.van Oosterhout, C.Morales, H. E.2024-12-17doi:10.1101/2024.12.12.628160Cold Spring Harbor Laboratory Press2024-12-17
<![CDATA[
Coupling CRISPR Scanning with Targeted Chromatin Accessibility Profiling using a Double-Stranded DNA Deaminase
]]>
https://biorxiv.org/cgi/content/short/2024.12.17.628791v1?rss=1"
Roh, H.Shen, S. P.Hu, Y.Kwok, H. S.Siegenfeld, A. P.Lee, C.Zepeda, M.Guo, C.-J.Roseman, S. A.Sankaran, V. G.Buenrostro, J. D.Liau, B. B.2024-12-18doi:10.1101/2024.12.17.628791Cold Spring Harbor Laboratory Press2024-12-18
<![CDATA[
Bottom-up design of calcium channels from defined selectivity filter geometry
]]>
https://biorxiv.org/cgi/content/short/2024.12.19.629320v1?rss=1"
Liu, Y.Weidle, C.Mihaljevic, L.Watson, J. L.Li, Z.Yu, L. T.Majumder, S.Borst, A. J.Carr, K. D.Kibler, R. D.Gamal El-Din, T. M.Catterall, W. A.Baker, D.2024-12-20doi:10.1101/2024.12.19.629320Cold Spring Harbor Laboratory Press2024-12-20
<![CDATA[
De novo design and structure of a peptide-centric TCR mimic binding module
]]>
https://biorxiv.org/cgi/content/short/2024.12.16.628822v1?rss=1"
Householder, K. D.Xiang, X.Jude, K. M.Deng, A.Obenaus, M.Wilson, S. C.Chen, X.Wang, N.Garcia, K. C.2024-12-20doi:10.1101/2024.12.16.628822Cold Spring Harbor Laboratory Press2024-12-20
<![CDATA[
Phage-displayed synthetic library and screening platform for nanobody discovery
]]>
https://biorxiv.org/cgi/content/short/2024.12.20.629765v1?rss=1"
Xia, B.Kim, A.-R.Liu, F.Han, M.Stoneburner, E.Makdissi, S.Di Cara, F.Mohr, S.Ring, A.Perrimon, N.2024-12-21doi:10.1101/2024.12.20.629765Cold Spring Harbor Laboratory Press2024-12-21
<![CDATA[
A simple method to efficiently generate structural variation in plants
]]>
https://biorxiv.org/cgi/content/short/2024.12.20.629831v1?rss=1"
Bechen, L. L.Ahsan, N.Bahrainwala, A.Gehring, M.Rajavasireddy, S.2024-12-21doi:10.1101/2024.12.20.629831Cold Spring Harbor Laboratory Press2024-12-21
<![CDATA[
Acoustic tumor paint for real-time imaging, surgical guidance and recurrence monitoring of brain tumors with ultrasound
]]>
https://biorxiv.org/cgi/content/short/2024.12.22.629782v1?rss=1"
Rabut, C.Daghlian, G. H.Barturen-Larrea, P.Li, H. R.Vorder Bruegge, R.Jones, R. M.Malounda, D.Pinton, G. F.Shapiro, M. G.2024-12-22doi:10.1101/2024.12.22.629782Cold Spring Harbor Laboratory Press2024-12-22
<![CDATA[
Pearling Drives Mitochondrial DNA Nucleoid Distribution
]]>
https://biorxiv.org/cgi/content/short/2024.12.21.629917v1?rss=1"
Landoni, J. C.Lycas, M. D.Macuada, J.Jaccard, R.Obara, C. J.Moore, A. S.Ben Nejma, S.Hoffman, D.Lippincott-Schwartz, J.Marshall, W.Sturm, G.Manley, S.2024-12-22doi:10.1101/2024.12.21.629917Cold Spring Harbor Laboratory Press2024-12-22
<![CDATA[
CESA: Cross-species Epitope Sequence Analysis for discovery of existing antibodies useful for phospho-specific protein detection in model species
]]>
https://biorxiv.org/cgi/content/short/2024.12.20.629730v1?rss=1"
Hu, Y.Gao, C.McKenna, W.Xia, B.Ariss, M.Mohr, S.Perrimon, N.2024-12-22doi:10.1101/2024.12.20.629730Cold Spring Harbor Laboratory Press2024-12-22
<![CDATA[
In vivo multiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors
]]>
https://biorxiv.org/cgi/content/short/2024.12.22.629999v1?rss=1"
Zheng, Y.Cai, R.Wang, K.Zhang, J.Zhuo, Y.Dong, H.Zhang, Y.Wang, Y.Deng, F.Ji, E.Cui, Y.Fang, S.Zhang, X.zhang, k.Wang, J.Li, G.Miao, X.Wang, Z.Yang, Y.Li, S.Grimm, J.Johnsson, K.Schreiter, E. R.Lavis, L.Chen, Z.Mu, Y.Li, Y.2024-12-23doi:10.1101/2024.12.22.629999Cold Spring Harbor Laboratory Press2024-12-23
<![CDATA[
Mammalian ZAP and KHNYN independently restrict CpG-enriched avian viruses
]]>
https://biorxiv.org/cgi/content/short/2024.12.23.629495v1?rss=1"
Becker, J. T.Mickelson, C. K.Pross, L. M.Sanders, A. E.Vogt, E. R.Shepherd, F. K.Wick, C.Barkhymer, A. J.Aron, S. L.Fay, E. J.Harris, R. S.Langlois, R. A.2024-12-23doi:10.1101/2024.12.23.629495Cold Spring Harbor Laboratory Press2024-12-23
<![CDATA[
Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics
]]>
https://biorxiv.org/cgi/content/short/2024.12.22.629997v1?rss=1"
600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties.
]]>Park, J.Prokopchuk, G.Popchock, A. R.Hao, J.Liao, T.-W.Yan, S.Hedman, D. J.Larson, J. D.Walther, B.Becker, N. A.Basu, A.Maher, L. J.Wheeler, R. J.Asbury, C. L.Biggins, S.Lukes, J.Ha, T.2024-12-23doi:10.1101/2024.12.22.629997Cold Spring Harbor Laboratory Press2024-12-23
<![CDATA[
Nucleosome Spacing Can Fine-Tune Higher Order Chromatin Assembly
]]>
https://biorxiv.org/cgi/content/short/2024.12.23.627571v1?rss=1"
Chen, L.Maristany, M. J.Farr, S. E.Luo, J.Gibson, B. A.Doolittle, L. K.Rene Espinosa, J.Huertas, J.Redding, S.Collepardo-Guevara, R.Rosen, M. K.2024-12-23doi:10.1101/2024.12.23.627571Cold Spring Harbor Laboratory Press2024-12-23
<![CDATA[
The cytosolic cysteinyl-tRNA synthetase is capable of regulating ATF4 translation independent of eIF2α phosphorylation state
]]>
https://biorxiv.org/cgi/content/short/2024.12.23.630120v1?rss=1"
Xu, A. E.Weissman, J. S.2024-12-23doi:10.1101/2024.12.23.630120Cold Spring Harbor Laboratory Press2024-12-23
<![CDATA[
Histone H4 limits transcription of the histone locus in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2024.12.23.630206v1?rss=1"
Ahmad, K.Wooten, M.Takushi, B. N.Vidaurre, V.Chen, X.Henikoff, S.2024-12-24doi:10.1101/2024.12.23.630206Cold Spring Harbor Laboratory Press2024-12-24
<![CDATA[
pipemake: A pipeline creation tool using Snakemake for reproducible analysis of biological datasets
]]>
https://biorxiv.org/cgi/content/short/2024.12.20.629758v1?rss=1"
Webb, A. E.Wolf, S. W.Traniello, I. M.Kocher, S. D.2024-12-24doi:10.1101/2024.12.20.629758Cold Spring Harbor Laboratory Press2024-12-24
<![CDATA[
Conditional fusogenic lipid nanocarriers for cytosolic delivery of macromolecular therapeutics
]]>
https://biorxiv.org/cgi/content/short/2024.12.27.630514v1?rss=1"
Zhong, Q.Tan, E. K. W.Shyamal, A.Ngambenjawong, C.Parisi, T.Ko, H.Flemming, H.Jacks, T.Bhatia, S.2024-12-27doi:10.1101/2024.12.27.630514Cold Spring Harbor Laboratory Press2024-12-27
<![CDATA[
Small Molecule Modulators of Beta-arrestins
]]>
https://biorxiv.org/cgi/content/short/2024.12.27.630464v1?rss=1"
Kahsai, A. W.Pakharukova, N.Kwon, H. Y.Shah, K. S.Liang-Lin, J. G.del Real, C. T.Shim, P. J.Lee, M. A.Ngo, V. A.Shreiber, B. N.Liu, S.Schwalb, A. M.Espinoza, E. F.Thomas, B. N.Kunzle, C. A.Smith, J. S.Wang, J.Kim, J.Zhang, X.Rockman, H. A.Thomsen, A. R. B.Rein, L. A. M.Shi, L.Ahn, S.Masoudi, A.Lefkowitz, R. J.2024-12-27doi:10.1101/2024.12.27.630464Cold Spring Harbor Laboratory Press2024-12-27
<![CDATA[
Expandable, Functional Hepatocytes Derived from Primary Cells Enable Liver Therapeutics
]]>
https://biorxiv.org/cgi/content/short/2024.12.28.630269v1?rss=1"
Mallanna, S. K.Karanth, S. S.Marturano, J. E.Kudva, A. K.Lehmann, M.Morse, J. K.Jamiel, M.Norman, T.Wilson, C. G.Munarin, F.Broderick, D.Van Buskirk, M.Uddin, E.Ret, M.Steele, C. A.Cheema, M. K.Black, J.Vanderploeg, E. J.Chen, C. S.Bhatia, S.Rezania, A.Lowery, T. J.Cazanave, S. C.Chhabra, A.2024-12-28doi:10.1101/2024.12.28.630269Cold Spring Harbor Laboratory Press2024-12-28
<![CDATA[
Layilin Regulates Treg Motility and Suppressive Capacity in Skin
]]>
https://biorxiv.org/cgi/content/short/2024.12.30.630730v1?rss=1"
Gouirand, V.Clancy, S.Macon, C.Valle, J.Pauli, M.Truong, H.-A.Cohen, J.Kinet, M.Lowe, M. M.Lord, S. J.Skruber, K.Harris, H.Kim, E.Neuhaus, I.Reif, K.Zarrin, A. A.Mullins, R. D.Rosenblum, M.2024-12-30doi:10.1101/2024.12.30.630730Cold Spring Harbor Laboratory Press2024-12-30
<![CDATA[
CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias
]]>
https://biorxiv.org/cgi/content/short/2024.12.30.630680v1?rss=1"
Fleming, T. J.Antoszewski, M.Lambo, S.Gundry, M. C.Piussi, R.Wahlster, L.Shah, S.Reed, F. E.Dong, K. D.Paulo, J. A.Gygi, S. P.Mimoso, C.Goldman, S. R.Adelman, K.Perry, J. A.Pikman, Y.Stegmaier, K.Barrachina, M. N.Machlus, K. R.Hovestadt, V.Arruda, A.Minden, M. D.Voit, R. A.Sankaran, V. G.2024-12-30doi:10.1101/2024.12.30.630680Cold Spring Harbor Laboratory Press2024-12-30
<![CDATA[
Gut bacterial sphingolipid production modulates dysregulated skin lipid homeostasis
]]>
https://biorxiv.org/cgi/content/short/2024.12.29.629238v1?rss=1"
Lee, M.-T.Tan, X.Le, H.Besler, K.Thompson, S.Harris-Tryon, T. A.Johnson, E.2024-12-30doi:10.1101/2024.12.29.629238Cold Spring Harbor Laboratory Press2024-12-30
<![CDATA[
Discovery of neuronal cell types by pairing whole cell reconstructions with RNA expression profiles
]]>
https://biorxiv.org/cgi/content/short/2024.12.30.630829v1?rss=1"
Ferreira, T. A.Eddison, M.Copeland, M.Lay, M.Tenshaw, E.Weldon, M.Schauder, D.Olbris, D. J.Rokicki, K.Spruston, N.Tillberg, P. W.Korff, W.Dudman, J. T.The MouseLight Project Team,2024-12-31doi:10.1101/2024.12.30.630829Cold Spring Harbor Laboratory Press2024-12-31
<![CDATA[
Engineering Multiplexed Synthetic Breath Biomarkers as Diagnostic Probes
]]>
https://biorxiv.org/cgi/content/short/2024.12.30.630769v1?rss=1"
Wang, S.-T.Anahtar, M.Kim, D. M.Samad, T. S.Zhang, C. M.Patel, S.Ko, H.Ngambenjawong, C.Wang, C. S.Kirkpatrick, J. D.Kumar, V.Fleming, H. E.Bhatia, S. N.2024-12-31doi:10.1101/2024.12.30.630769Cold Spring Harbor Laboratory Press2024-12-31
<![CDATA[
An in planta single-cell screen to accelerate functional genetics
]]>
https://biorxiv.org/cgi/content/short/2025.08.06.668818v1?rss=1"
Lowensohn, T. N.Cody, W. B.Tsai, C.Vlahos, A. E.Call, C. C.Gao, X. J.Sattely, E. S.2025-08-07doi:10.1101/2025.08.06.668818Cold Spring Harbor Laboratory Press2025-08-07
<![CDATA[
Exploring the deletion landscape of S. aureus Cas9 with SABER
]]>
https://biorxiv.org/cgi/content/short/2025.08.12.669962v1?rss=1"
Plebanek, A. J.Oltrogge, L. M.Terrace, C. I.Lukarska, M.Khoury, M.Savage, D.2025-08-12doi:10.1101/2025.08.12.669962Cold Spring Harbor Laboratory Press2025-08-12
<![CDATA[
A non-catalytic role for RFC in PCNA-mediated processive DNA synthesis
]]>
https://biorxiv.org/cgi/content/short/2025.08.08.669392v1?rss=1"
Chua, G. N. L.Beckwitt, E. C.Miller-Browne, V.Yurieva, O.Zhang, D.Katch, B. J.Watters, J. W.Abrantes, K.Funabiki, R.Zhao, X.O'Donnell, M. E.Liu, S.2025-08-12doi:10.1101/2025.08.08.669392Cold Spring Harbor Laboratory Press2025-08-12
<![CDATA[
Translational control of innate barrier defense by the gut microbiota
]]>
https://biorxiv.org/cgi/content/short/2025.08.11.668728v1?rss=1"
Li, Y.Wu, R.Ma, X.Zhang, J.Ma, J.Duan, Y.Hassell, B.Ruhn, K.Behrendt, C. L.Dende, C.Wang, L.Lemoff, A.Raj, P.Kuang, Z.Hooper, L. N.2025-08-11doi:10.1101/2025.08.11.668728Cold Spring Harbor Laboratory Press2025-08-11
<![CDATA[
Renal Coenzyme A (CoA) Production Fuels Stem Cell Proliferation and Tumor Growth
]]>
https://biorxiv.org/cgi/content/short/2025.08.08.669325v1?rss=1"
Miao, T.Liu, Y.Qadiri, M.Asara, J. M.Hu, Y.Sun, X.Dibble, C.Perrimon, N.2025-08-11doi:10.1101/2025.08.08.669325Cold Spring Harbor Laboratory Press2025-08-11
<![CDATA[
HIV-1 expression is heterogeneous among clones of CD4+ T cells carrying authentic intact latent proviruses
]]>
https://biorxiv.org/cgi/content/short/2025.08.05.668730v1?rss=1"
Bittar, C.Teixeira, A. R.Oliveira, T. Y.Santos, G. S. S.Lenart, K.Fumagalli, M. J.Linden, N. L.Ferreira, I. A. T. M.Caskey, M.Jones, R. B.Jankovic, M.Nussenzweig, M. C.2025-08-07doi:10.1101/2025.08.05.668730Cold Spring Harbor Laboratory Press2025-08-07
<![CDATA[
Accelerating protein design by scaling experimental characterization
]]>
https://biorxiv.org/cgi/content/short/2025.08.05.668824v1?rss=1"
1000 designs to be purified and characterized in arrayed, clonal format at a cost of $5 per construct. By reframing standard molecular biology practices and orchestrating wetlab workflows with partial automation instead of complex end-to-end robotics, these protocols should be widely adoptable, accelerating protein design.
]]>Qian, J.Milles, L. F.Wicky, B. I. M.Motmaen, A.Li, X.Kibler, R. D.Stewart, L.Baker, D.2025-08-06doi:10.1101/2025.08.05.668824Cold Spring Harbor Laboratory Press2025-08-06
<![CDATA[
There and back again: the dynamic evolution of panarthropod germ cell specification mechanisms
]]>
https://biorxiv.org/cgi/content/short/2025.08.05.668520v1?rss=1"
Kao, J. A.Rivard, E. L.Kapoor, R. R.Extavour, C. G.2025-08-06doi:10.1101/2025.08.05.668520Cold Spring Harbor Laboratory Press2025-08-06
<![CDATA[
A Genome-wide CRISPR Screen Reveals ZDHHC8-Dependent Gαq Palmitoylation as a Key Regulator of GPCR Signaling
]]>
https://biorxiv.org/cgi/content/short/2025.08.06.668953v1?rss=1"
Ahmad, M.Perrimon, N.Viswanatha, R.Kim, A.-R.2025-08-06doi:10.1101/2025.08.06.668953Cold Spring Harbor Laboratory Press2025-08-06
<![CDATA[
Genome-wide chromatin recording resolves dynamic cell state changes
]]>
https://biorxiv.org/cgi/content/short/2025.08.05.668773v1?rss=1"
Takei, Y.Lay, J. A.Linton, J. M.Chadly, D. M.Ochiai, Y.Hadas, R.Perez, A. A.Blanco, M. R.Laurino, P.Guttman, M.Elowitz, M. B.2025-08-06doi:10.1101/2025.08.05.668773Cold Spring Harbor Laboratory Press2025-08-06
<![CDATA[
Design of Orthogonal Far-Red, Orange and Green Fluorophore-binding Proteins for Multiplex Imaging
]]>
https://biorxiv.org/cgi/content/short/2025.08.03.668343v1?rss=1"
Tran, L.Sharma, S.Klein, S.Jurgens, D.Decarreau, J.Liu, B.Wang, Y.Bera, A. K.Kang, A.Woods, J.Joyce, E.Vafeados, D. K.Roullier, N.Chen, W.Lee, G. R.Mahamid, J.Lavis, L. D.An, L.Baker, D.2025-08-03doi:10.1101/2025.08.03.668343Cold Spring Harbor Laboratory Press2025-08-03
<![CDATA[
Cellulose Synthase Complex and Remorin Nanodomains Mediate Stress Resilience Through Cell Wall-Plasma Membrane Attachments
]]>
https://biorxiv.org/cgi/content/short/2025.08.01.664786v1?rss=1"
Rui, Y.Reyes, A. V.Grismer, T. S.Abel, N. B.Dwyer, W. P.Ott, T.Kieber, J. J.Xu, S.-L.Dinneny, J. R.2025-08-02doi:10.1101/2025.08.01.664786Cold Spring Harbor Laboratory Press2025-08-02
<![CDATA[
Protein sequence evolution underlies interspecies incompatibility of a cell fate determinant
]]>
https://biorxiv.org/cgi/content/short/2025.08.02.668269v1?rss=1"
Rivard, E. L.Srouji, J.Repouliou, A.Extavour, C. G.2025-08-02doi:10.1101/2025.08.02.668269Cold Spring Harbor Laboratory Press2025-08-02
<![CDATA[
Bioactive Enhanced Adjuvant Chemokine Oligonucleotide Nanoparticles (BEACONs) for Mucosal Vaccination Against Genital Herpes
]]>
https://biorxiv.org/cgi/content/short/2025.07.31.667899v1?rss=1"
Bhagchandani, S. H.Ehrenzeller, S.Pires, I. S.Chaudhary, N.Booth, C. J.Guedes de Sa, K. S.Kwon, D.-i.Li, S.Olszowka, A.Hudak, A.Fischer, S.Bayarri-Olmos, R.Iwasaki, A.2025-08-02doi:10.1101/2025.07.31.667899Cold Spring Harbor Laboratory Press2025-08-02
<![CDATA[
Hunchback functions in the post-mitotic larval MDN to restrict axon outgrowth, synapse formation, and backward locomotion
]]>
https://biorxiv.org/cgi/content/short/2025.07.31.667971v1?rss=1"
Lee, K. M.Rico Carvajal, N.Graciani, J.Doe, C. Q.2025-08-01doi:10.1101/2025.07.31.667971Cold Spring Harbor Laboratory Press2025-08-01
<![CDATA[
A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform
]]>
https://biorxiv.org/cgi/content/short/2025.08.01.667725v1?rss=1"
Jain, S.Williamson, K. E.Ying, A. W.Jiang, R. J.Turner, A. M.So, K.Allison, M. P.Sankar, A.Same Guerra, D. D.Mashtalir, N.Rohrs, H. W.Lichti, C. F.Paulo, J. A.Gygi, S. P.Gross, M. L.Kadoch, C.2025-08-01doi:10.1101/2025.08.01.667725Cold Spring Harbor Laboratory Press2025-08-01
<![CDATA[
Fibroblast depletion reveals mammalian epithelial resilience across neonatal and adult stages
]]>
https://biorxiv.org/cgi/content/short/2025.07.29.667423v1?rss=1"
Gaeta, I. M.Du, S.Villeneuve, C.Gonzalez, D. G.Matte-Martone, C.Ganesan, S.Simpson, D.Moore, J. L.Kam, C. Y.Gallini, S.Wei, H.Bertillot, F.Zeuschner, D.Gonzalez, L. E.Sumigray, K.Wickstrom, S. A.Greco, V.2025-07-31doi:10.1101/2025.07.29.667423Cold Spring Harbor Laboratory Press2025-07-31
<![CDATA[
The Drosophila ovarian terminal filament imports molecules needed to produce lipid droplets, the fusome, and functional germ cells
]]>
https://biorxiv.org/cgi/content/short/2025.07.30.667757v1?rss=1"
Maurya, B.Spradling, A. C.2025-07-31doi:10.1101/2025.07.30.667757Cold Spring Harbor Laboratory Press2025-07-31
<![CDATA[
A family of linear plasmid phages that detect a quorum-sensing autoinducer exists in multiple bacterial species
]]>
https://biorxiv.org/cgi/content/short/2025.07.30.667625v1?rss=1"
Santoriello, F. J.Bassler, B.2025-07-30doi:10.1101/2025.07.30.667625Cold Spring Harbor Laboratory Press2025-07-30
<![CDATA[
SPEECHLESS duplication in grasses expands potential for environmentalregulation of stomatal development
]]>
https://biorxiv.org/cgi/content/short/2025.07.29.667563v1?rss=1"
Erberich, J. M.Bennett, B.Bergmann, D.2025-07-30doi:10.1101/2025.07.29.667563Cold Spring Harbor Laboratory Press2025-07-30
<![CDATA[
Early female germline development in Xenopus laevis: stem cells, nurse cells and germline cysts
]]>
https://biorxiv.org/cgi/content/short/2025.07.29.667541v1?rss=1"
Davidian, A.Spradling, A. C.2025-07-30doi:10.1101/2025.07.29.667541Cold Spring Harbor Laboratory Press2025-07-30
<![CDATA[
Striatal pathways oppositely shift cortical activity along the decision axis
]]>
https://biorxiv.org/cgi/content/short/2025.07.29.667406v1?rss=1"
Cho, J. R.Bolkan, S. S.Brown, L. S.Skuza, M.El-Jayyousi, Y.Midler, B.Fetcho, R. N.Zimmerman, C. A.Pan-Vazquez, A.Schottdorf, M.Bondy, A. G.Sanchez, M. A.Lopez Luna, J. F.Luna, A.Eilers, T.Kalmbach, A. S.Lu, Y.Lynch, L. A.Witten, I.2025-07-30doi:10.1101/2025.07.29.667406Cold Spring Harbor Laboratory Press2025-07-30
<![CDATA[
A SNP panel for co-analysis of capture and shotgun ancient DNA data
]]>
https://biorxiv.org/cgi/content/short/2025.07.30.667733v1?rss=1"
Fournier, R.Pearson Fulton, A.Reich, D. E.2025-07-30doi:10.1101/2025.07.30.667733Cold Spring Harbor Laboratory Press2025-07-30
<![CDATA[
Mouse pre-meiotic germline cysts contain fusome-like structure dependent on Dazl that mediates cyst fragmentation and oocyte development
]]>
https://biorxiv.org/cgi/content/short/2025.07.25.666884v1?rss=1"
Pathak, M.Spradling, A. C.2025-07-29doi:10.1101/2025.07.25.666884Cold Spring Harbor Laboratory Press2025-07-29
<![CDATA[
Recurrent acquisition of nuclease-protease pairs in antiviral immunity
]]>
https://biorxiv.org/cgi/content/short/2025.07.28.667249v1?rss=1"
Tuck, O. T.Hu, J. J.Adler, B. A.O'Brien, C. E.Lopez, S. C.Hsieh, K.Meredith, C.Lahiri, A.Doherty, E. E.Doudna, J. A.2025-07-28doi:10.1101/2025.07.28.667249Cold Spring Harbor Laboratory Press2025-07-28
<![CDATA[
Cleavage of the RNA polymerase II general transcription factor TFIIB tunes transcription during stress
]]>
https://biorxiv.org/cgi/content/short/2025.07.28.667251v1?rss=1"
Gulyas, L.Lari, A.Shah, S. B.Glaunsinger, B.2025-07-28doi:10.1101/2025.07.28.667251Cold Spring Harbor Laboratory Press2025-07-28
<![CDATA[
Axonal defasciculation is restricted to specific branching points during regeneration of the lateral line nerve in zebrafish
]]>
https://biorxiv.org/cgi/content/short/2025.07.23.666336v1?rss=1"
Roy, R. S.Hudspeth, A. J.2025-07-25doi:10.1101/2025.07.23.666336Cold Spring Harbor Laboratory Press2025-07-25
<![CDATA[
Synaptic sign switching mediates online dopamine updates
]]>
https://biorxiv.org/cgi/content/short/2025.07.23.666367v1?rss=1"
Li, S.Wang, W.Knipe, G.Jerng, E.Capelli, P.Zhou, C.Bilsel, E.Sabatini, B. L.2025-07-24doi:10.1101/2025.07.23.666367Cold Spring Harbor Laboratory Press2025-07-24
<![CDATA[
Comparative Proteomic Profiling of Receptor Kinase Signaling Reveals Key Trafficking Components Enforcing Plant Stomatal Development
]]>
https://biorxiv.org/cgi/content/short/2025.07.20.665823v1?rss=1"
Bai, P.Vu, M. H.Komatsu, C.Papoulas, O.Ebine, K.Nozawa, A.Sawasaki, T.Ueda, T.Marcotte, E. M.Torii, K. U.2025-07-23doi:10.1101/2025.07.20.665823Cold Spring Harbor Laboratory Press2025-07-23
<![CDATA[
Mouse pups lacking a cerebral cortex develop abnormal vocal behavior
]]>
https://biorxiv.org/cgi/content/short/2025.07.17.665371v1?rss=1"
Boyd, J. L.Vargas, C.Jarvis, E. D.2025-07-22doi:10.1101/2025.07.17.665371Cold Spring Harbor Laboratory Press2025-07-22
<![CDATA[
Temperate phages enhance host fitness via RNA-guided flagellar remodeling
]]>
https://biorxiv.org/cgi/content/short/2025.07.22.666180v1?rss=1"
Walker, M. W. G.Richard, E.Wiegand, T.Wang, J.Yang, Z.Casas-Ciniglio, A. A.Hoffmann, F. T.Shahnawaz, H.Gaudet, R. G.Arpaia, N.Fernandez, I. S.Sternberg, S. H.2025-07-22doi:10.1101/2025.07.22.666180Cold Spring Harbor Laboratory Press2025-07-22
<![CDATA[
Long-read sequencing of trios reveals increased germline and postzygotic mutation rates in repetitive DNA
]]>
https://biorxiv.org/cgi/content/short/2025.07.18.665621v1?rss=1"
Noyes, M. D.Sui, Y.Kwon, Y.Koundinya, N.Wong, I.Munson, K. M.Hoekzema, K.Kordosky, J.Garcia, G. H.Knuth, J.Lewis, A. P.Eichler, E. E.2025-07-19doi:10.1101/2025.07.18.665621Cold Spring Harbor Laboratory Press2025-07-19
<![CDATA[
Neuroligin-3 interaction with CSPG4 regulates normal and malignant glial precursors through PIEZO1
]]>
https://biorxiv.org/cgi/content/short/2025.07.12.664340v1?rss=1"
Gillespie, S. M.Kim, Y. S.Geraghty, A. C.Yalcin, B.Mancusi, R.Hysinger, J.Ivec, A. E.Reed, J.Drexler, R.Quezada, M.Malacon, K.Woo, P. J.Yang, A.Lam, M.Pan, Y.Zuchero, J. B.Trotter, J.Monje, M.2025-07-17doi:10.1101/2025.07.12.664340Cold Spring Harbor Laboratory Press2025-07-17
<![CDATA[
Genetic variation reveals a homeotic long noncoding RNA that modulates human hematopoietic stem cells
]]>
https://biorxiv.org/cgi/content/short/2025.07.16.664824v1?rss=1"
Lyu, P.Agarwal, G.Guo, C.-J.Ye, T.Weng, C.Antoszewski, M.Joubran, S.Caulier, A.Poeschla, M.Sankaran, V. G.2025-07-16doi:10.1101/2025.07.16.664824Cold Spring Harbor Laboratory Press2025-07-16
<![CDATA[
Programmable translational inhibition by a molecular glue-oligonucleotide conjugate
]]>
https://biorxiv.org/cgi/content/short/2025.07.15.664547v1?rss=1"
Wang, S.Kovalski, J. R.Zapatero-Belinchon, F. J.Bennett, M.Kuzuoglu-Öztürk, D.Li, Q.Stevenson, E.Liu, J.Krogan, N. J.Ott, M.Swaney, D. L.Ruggero, D.Lou, K.Shokat, K.2025-07-16doi:10.1101/2025.07.15.664547Cold Spring Harbor Laboratory Press2025-07-16
<![CDATA[
A 3D in vitro model of the human hepatobiliary junction
]]>
https://biorxiv.org/cgi/content/short/2025.07.11.664464v1?rss=1"
Westerfield, A. D.Grzelak, K. A.Katsuyama, K.Kumar, V.Miller, B. M.Yun, J.Kirkpatrick, J.Mankus, D.Bisher, M. E.Lytton-Jean, A. K.Jiang, Z. G.Lee, D. D.Chen, C. S.Bhatia, S. N.2025-07-14doi:10.1101/2025.07.11.664464Cold Spring Harbor Laboratory Press2025-07-14
<![CDATA[
AAV NRF2 Gene Therapy Preserves Retinal Structure and Function in Rodent Models of Oxidative Damage
]]>
https://biorxiv.org/cgi/content/short/2025.07.09.663952v1?rss=1"
View larger version (67K):
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]]>Gardner, A.Wang, S.Daniels, A.Li, D.Wu, C.Lin, L.Hong, C.Zhao, S.Kruczek, K.Weist, G.Real, L. B.Haurigot, V.Born, R.Cepko, C.2025-07-14doi:10.1101/2025.07.09.663952Cold Spring Harbor Laboratory Press2025-07-14
<![CDATA[
Potentially Prebiotic Isocyanide Activation Chemistry Drives RNA Assembly via both Nonenzymatic and Ribozyme-catalyzed Ligation
]]>
https://biorxiv.org/cgi/content/short/2025.07.11.664453v1?rss=1"
Zhang, S. J.Jia, X.DasGupta, S.Szostak, J. W.2025-07-12doi:10.1101/2025.07.11.664453Cold Spring Harbor Laboratory Press2025-07-12
<![CDATA[
Multi-omic mapping of Drosophila protein secretomes reveals tissue-specific origins and inter-organ trafficking
]]>
https://biorxiv.org/cgi/content/short/2025.07.09.659702v1?rss=1"
Bosch, J. A.Beltran, P. M. J.Cavers, C.LaGraff, J. T.Melanson, R.Singh, A.Chen, W.Hu, Y.Tattikota, S. G.Liu, Y.Hashmi, Y.Asara, J. M.Branon, T.Ting, A. Y.Carr, S. A.Perrimon, N.2025-07-11doi:10.1101/2025.07.09.659702Cold Spring Harbor Laboratory Press2025-07-11
<![CDATA[
A Congenic C57BL/6 rd1 Mouse Model for Retinal Degeneration Research
]]>
https://biorxiv.org/cgi/content/short/2025.07.09.663548v1?rss=1"
Chandler, L. C.Gardner, A.Cepko, C. L.2025-07-09doi:10.1101/2025.07.09.663548Cold Spring Harbor Laboratory Press2025-07-09
<![CDATA[
Cytoplasmic mRNA decay by the anti-viral nuclease RNase L promotes transcriptional repression
]]>
https://biorxiv.org/cgi/content/short/2025.07.08.663778v1?rss=1"
Mao, X.Tokamov, S.Pahmeier, F.Lari, A.Xu, J.Harris, E.Glaunsinger, B.2025-07-08doi:10.1101/2025.07.08.663778Cold Spring Harbor Laboratory Press2025-07-08
<![CDATA[
Ultrasound imaging of in situ transcriptional activity in opaque tissue
]]>
https://biorxiv.org/cgi/content/short/2025.07.06.663365v1?rss=1"
Shivaei, S.Cheung, K. Y. M.Yadav, A.Hurvitz, I. U.Lee, S.Revilla, J.Rabut, C.Criado-Hidalgo, E.Zhang, R. J.Shapiro, M. G.2025-07-07doi:10.1101/2025.07.06.663365Cold Spring Harbor Laboratory Press2025-07-07
<![CDATA[
Population differences of chromosome 22q11.2 duplication structure predisposes differentially to microdeletion and inversion.
]]>
https://biorxiv.org/cgi/content/short/2025.07.04.662981v1?rss=1"
Porubsky, D.Yoo, D.Dishuck, P. C.Koundinya, N.Souche, E.Harvey, W. T.Munson, K. M.Hoekzema, K.Chan, D. D.Leung, T. Y.Santos, M. S.Meynants, S.Swillen, A.Breckpot, J.Tsapalou, V.Hasenfeld, P.Korbel, J. O.Lansdorp, P. M.Vermeesch, J. R.Eichler, E. E.2025-07-05doi:10.1101/2025.07.04.662981Cold Spring Harbor Laboratory Press2025-07-05
<![CDATA[
Cholinergic Signaling Modulates Intestinal Pathophysiology in a Drosophila Model of Cystic Fibrosis
]]>
https://biorxiv.org/cgi/content/short/2025.07.02.662792v1?rss=1"
Lane, E.Petsakou, A.Liu, Y.Chen, W.Qadiri, M.Hu, Y.Perrimon, N.2025-07-05doi:10.1101/2025.07.02.662792Cold Spring Harbor Laboratory Press2025-07-05
<![CDATA[
Multimodal profiling of proinflammatory protease activity identifies caspase-1 as a target for lung cancer interception
]]>
https://biorxiv.org/cgi/content/short/2025.07.01.662195v1?rss=1"
Wang, C. S.Zhong, Q.Wang, S.-T.Alonso, M. C. M.Neaher, S.Patel, S.Parisi, T.Kirkpatrick, J. D.Sequist, L. V.Jacks, T. E.Bhatia, S.2025-07-02doi:10.1101/2025.07.01.662195Cold Spring Harbor Laboratory Press2025-07-02
<![CDATA[
DNA polymerase α-primase can function as a translesion DNA polymerase
]]>
https://biorxiv.org/cgi/content/short/2025.07.02.662785v1?rss=1"
20 base hybrid RNA-DNA primer. Interestingly, the DNA Pol1 subunit of Pol lacks a 3-5 proofreading exonuclease, contrary to the high fidelity normally associated with DNA replication. However, Polo and Pol{delta} synthesize the majority of the eukaryotic genome and both contain 3-5 exonuclease activity for high fidelity. None the less, even the small amount of DNA produced by Pol1 in each of the many RNA/DNA primers during chromosome replication adds up to tens of millions of nucleotides in a human genome. Thus it has been a longstanding question why Pol1 lacks a proofreading exonuclease. We show here that Pol is uniquely capable of traversing common oxidized or hydrolyzed template nucleotides and propose that Pol evolved to bypass these common template lesions when they are encountered during chromosome replication.
Significance statementEukaryotic Pol-primase contains DNA polymerase (Pol1) and RNA primase subunits that together synthesize a >20 nucleotide hybrid RNA-DNA primer. Bacteria and archaea only require a dozen or less RNA residues to prime DNA synthesis. Therefore, why do eukaryotes require the additional DNA? We propose, and demonstrate here that Pol1, which lacks a proofreading 3-5 exonuclease, is capable of traversing some common template lesions produced in the normal hydrolytic and metabolic oxidative environment of cells. Thus, we hypothesize that Pol1 activity within the eukaryotic primase evolved to help replisomes bypass template damage. Bypassed damaged sites can be dealt with by repair processes after replication has occurred.
]]>Mayle, R.Georgescu, R.O'Donnell, M. E.2025-07-02doi:10.1101/2025.07.02.662785Cold Spring Harbor Laboratory Press2025-07-02
<![CDATA[
The Drosophila proventriculus lacks stem cells but compensates for age-related cell loss via endoreplication-mediated cell growth
]]>
https://biorxiv.org/cgi/content/short/2025.06.27.662004v1?rss=1"
Ewen-Campen, B.Chen, W.Gopal Tattikota, S.Liu, Y.Hu, Y.Perrimon, N.2025-07-02doi:10.1101/2025.06.27.662004Cold Spring Harbor Laboratory Press2025-07-02
<![CDATA[
Plagl1 and Lrrc58 control mammalian body size by triggering target-directed microRNA degradation of miR-322 and miR-503
]]>
https://biorxiv.org/cgi/content/short/2025.06.30.662380v1?rss=1"
LaVigne, C. A.Han, J.Zhang, H.Cho, S.Kim, M.Sethia, K.Evers, B. M.Acharya, A.Chang, T.-C.Mendell, J. T.2025-07-01doi:10.1101/2025.06.30.662380Cold Spring Harbor Laboratory Press2025-07-01
<![CDATA[
Ligand-induced ubiquitination regulates endocytosis and homeostasis of the ERECTA receptor kinase for stomatal development
]]>
https://biorxiv.org/cgi/content/short/2025.06.29.662054v1?rss=1"
Chen, L.Vu, M. H.Cochran, A. M.Ying, C. F.Torii, K. U.2025-07-01doi:10.1101/2025.06.29.662054Cold Spring Harbor Laboratory Press2025-07-01
<![CDATA[
OocystMeter, a machine-learning algorithm to count and measure Plasmodium oocysts, reveals clustering patterns in the Anopheles midgut
]]>
https://biorxiv.org/cgi/content/short/2025.06.28.662088v1?rss=1"
Peng, D.Marrogi, E.Nelson, E.Liu, Q.Rinvee, T. A.de Vries, L. E.Thornburg, K.Singh, N.Shaw, W. R.Catteruccia, F.2025-06-29doi:10.1101/2025.06.28.662088Cold Spring Harbor Laboratory Press2025-06-29
<![CDATA[
A cell-based scrambling assay reveals phospholipid headgroup preference of TMEM16F on the plasma membrane
]]>
https://biorxiv.org/cgi/content/short/2025.06.25.661602v1?rss=1"
Teo, C. F.Tuomivaara, S. T.van Hilten, N.Crottes, D.Jan, Y. N.Grabe, M.Jan, L. Y.2025-06-27doi:10.1101/2025.06.25.661602Cold Spring Harbor Laboratory Press2025-06-27
<![CDATA[
Histone diversity in the archaeal domain of life
]]>
https://biorxiv.org/cgi/content/short/2025.06.26.661778v1?rss=1"
Laursen, S. p.Luger, K.2025-06-27doi:10.1101/2025.06.26.661778Cold Spring Harbor Laboratory Press2025-06-27
<![CDATA[
Direct observation of interdependent and hierarchical kinetochore assembly on individual centromeres
]]>
https://biorxiv.org/cgi/content/short/2025.06.25.661565v1?rss=1"
View larger version (14K):
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]]>Hu, C.Popchock, A. R.Latino, A. A.Asbury, C. L.Biggins, S.2025-06-26doi:10.1101/2025.06.25.661565Cold Spring Harbor Laboratory Press2025-06-26
<![CDATA[
Early transcriptional signatures of MeCP2 positive and negative cells in Rett syndrome
]]>
https://biorxiv.org/cgi/content/short/2025.06.26.661761v1?rss=1"
Li, Y.Anderson, A. G.Qi, G.Wu, S.-R.Revelli, J.-P.Liu, Z.Zoghbi, H. Y.2025-06-26doi:10.1101/2025.06.26.661761Cold Spring Harbor Laboratory Press2025-06-26
<![CDATA[
A trove of antiviral TRIM family E3 ligases in reptiles
]]>
https://biorxiv.org/cgi/content/short/2025.06.23.661133v1?rss=1"
Boys, I. N.Quinlan, M. R.Elde, N. C.2025-06-25doi:10.1101/2025.06.23.661133Cold Spring Harbor Laboratory Press2025-06-25
<![CDATA[
Bacteriophages target membrane-anchored glycopolymers to promote host cell lysis and progeny release
]]>
https://biorxiv.org/cgi/content/short/2025.06.24.661397v1?rss=1"
McKitterick, A. C.Lyerly, E. W.Bernhardt, T. G.2025-06-24doi:10.1101/2025.06.24.661397Cold Spring Harbor Laboratory Press2025-06-24
<![CDATA[
A global map for introgressed structural variation and selection in humans
]]>
https://biorxiv.org/cgi/content/short/2025.06.24.661368v1?rss=1"
Hsieh, P.Soisangwan, N.Gordon, D.Athef Javidh, A.Harvey, W.Porubsky, D.Hoekzema, K.Baker, C.Munson, K.Kinipi, C.Leavesley, M.Brucato, N.Cox, M.RICAUT, F.-X.Gallego Romero, I.Eichler, E.2025-06-24doi:10.1101/2025.06.24.661368Cold Spring Harbor Laboratory Press2025-06-24
<![CDATA[
Phase separation of PGL-3 driven by structured domains that oligomerize and interact with terminal RGG motifs.
]]>
https://biorxiv.org/cgi/content/short/2025.06.23.660947v1?rss=1"
Kuroiwa, R.Sharma, P.Putnam, A.Fried, S. D.Seydoux, G.2025-06-24doi:10.1101/2025.06.23.660947Cold Spring Harbor Laboratory Press2025-06-24
<![CDATA[
Vocal convergence during formation of social relationships in vampire bats
]]>
https://biorxiv.org/cgi/content/short/2025.06.21.660856v1?rss=1"
Vrtilek, J.Smith-Vidaurre, G.Fosler-Lussier, E.Page, R. A.Carter, G. G.2025-06-23doi:10.1101/2025.06.21.660856Cold Spring Harbor Laboratory Press2025-06-23
<![CDATA[
Protein folding stress transcriptionally reprograms muscle metabolism
]]>
https://biorxiv.org/cgi/content/short/2025.06.20.660805v1?rss=1"
Paiano, J.Qadiri, M.Sharma, S.Hu, Y.Perrimon, N.2025-06-23doi:10.1101/2025.06.20.660805Cold Spring Harbor Laboratory Press2025-06-23
<![CDATA[
Correction: Replication of BRIT1/MCPH1 G2/M Checkpoint Function Confirms Original Conclusions
]]>
https://biorxiv.org/cgi/content/short/2025.06.19.660578v1?rss=1"
Lin, S.-Y.Dai, H.Elledge, S.2025-06-22doi:10.1101/2025.06.19.660578Cold Spring Harbor Laboratory Press2025-06-22
<![CDATA[
A Structural Atlas of TAP Inhibition by Herpesviruses and Poxviruses
]]>
https://biorxiv.org/cgi/content/short/2025.06.19.660632v1?rss=1"
Lee, J.Manon, V.Chen, J.2025-06-20doi:10.1101/2025.06.19.660632Cold Spring Harbor Laboratory Press2025-06-20
<![CDATA[
Salicylic Acid Engages Central Metabolic Regulators SnRK1 and TOR to Govern Immunity by Differential Phosphorylation of NPR1
]]>
https://biorxiv.org/cgi/content/short/2025.06.17.660129v1?rss=1"
Chen, Y.Withers, J.Chen, T.Karapetyan, S.Draken, J.Xiang, Y.Droege-Laser, W.Dong, X.2025-06-18doi:10.1101/2025.06.17.660129Cold Spring Harbor Laboratory Press2025-06-18
<![CDATA[
Nucleotide context models outperform protein language models for predicting antibody affinity maturation
]]>
https://biorxiv.org/cgi/content/short/2025.06.16.659977v1?rss=1"
Johnson, M. M.Sung, K.Haddox, H. K.Vora, A. A.Araki, T.Victora, G. D.Song, Y. S.Fukuyama, J.Matsen, F. A.2025-06-18doi:10.1101/2025.06.16.659977Cold Spring Harbor Laboratory Press2025-06-18
<![CDATA[
Seasonal influenza viruses show distinct adaptive dynamics during growth in chicken eggs
]]>
https://biorxiv.org/cgi/content/short/2025.06.12.659400v1?rss=1"
Kistler, K.Bedford, T.2025-06-17doi:10.1101/2025.06.12.659400Cold Spring Harbor Laboratory Press2025-06-17
<![CDATA[
Nucleotide-dependent conformational changes direct peptide export by the transporter associated with antigen processing
]]>
https://biorxiv.org/cgi/content/short/2025.06.12.659373v1?rss=1"
Lee, J.Manon, V.Chen, J.2025-06-17doi:10.1101/2025.06.12.659373Cold Spring Harbor Laboratory Press2025-06-17
<![CDATA[
Sono-uncaging for Spatiotemporal Control of Chemical Reactivity
]]>
https://biorxiv.org/cgi/content/short/2025.06.11.659141v1?rss=1"
Schrunk, E.Lee, S.Dutka, P.Wu, D.Shapiro, M. G.2025-06-17doi:10.1101/2025.06.11.659141Cold Spring Harbor Laboratory Press2025-06-17
<![CDATA[
Pathway Sculptor for Compact and Versatile Combinatorial Genetic Perturbation
]]>
https://biorxiv.org/cgi/content/short/2025.06.15.659618v1?rss=1"
Gu, B.Linton, J.Hendrickson, B. G.Li, H.Hadas, R.Manella, G.Gregrowicz, J.Elowitz, M. B.2025-06-16doi:10.1101/2025.06.15.659618Cold Spring Harbor Laboratory Press2025-06-16
<![CDATA[
Condensate-driven chromatin organization via elastocapillary interactions
]]>
https://biorxiv.org/cgi/content/short/2025.06.12.659369v1?rss=1"
Zhao, H.Strom, A. R.Eeftens, J. M.Haataja, M.Kosmrlj, A.Brangwynne, C. P.2025-06-15doi:10.1101/2025.06.12.659369Cold Spring Harbor Laboratory Press2025-06-15
<![CDATA[
Polygenic and monogenic adaptation drive evolutionary rescue at different magnitudes of environmental change
]]>
https://biorxiv.org/cgi/content/short/2025.06.13.659553v1?rss=1"
Bellagio, T.Exposito-Alonso, M.2025-06-15doi:10.1101/2025.06.13.659553Cold Spring Harbor Laboratory Press2025-06-15
<![CDATA[
High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer
]]>
https://biorxiv.org/cgi/content/short/2025.06.15.659774v1?rss=1"
Koblan, L. W.Yost, K. E.Zheng, P.Colgan, W. N.Jones, M. G.Yang, D.Kumar, A.Sandhu, J.Schnell, A.Sun, D.Ergen, C.Saunders, R. A.Zhuang, X.Allen, W. E.Yosef, N.Weissman, J. S.2025-06-15doi:10.1101/2025.06.15.659774Cold Spring Harbor Laboratory Press2025-06-15
<![CDATA[
Thermally controlled state switches for macrophage immunotherapy
]]>
https://biorxiv.org/cgi/content/short/2025.06.09.658763v1?rss=1"
Liu, A.Farooq, A. S.Abedi, M. H.Smith, C. A. B.Wu, D.Shapiro, M. G.2025-06-13doi:10.1101/2025.06.09.658763Cold Spring Harbor Laboratory Press2025-06-13
<![CDATA[
Biological causes and impacts of rugged tree landscapes in phylodynamic inference
]]>
https://biorxiv.org/cgi/content/short/2025.06.10.657742v1?rss=1"
Gao, J.Brusselmans, M.Carvalho, L. M.Suchard, M. A.Baele, G.Matsen, F. A.2025-06-12doi:10.1101/2025.06.10.657742Cold Spring Harbor Laboratory Press2025-06-12
<![CDATA[
Exapted CRISPR-Cas12f homologs drive RNA-guided transcription
]]>
https://biorxiv.org/cgi/content/short/2025.06.10.658865v1?rss=1"
Hoffmann, F. T.Wiegand, T.Palmieri, A. I.Glass-Klaiber, J.Xiao, R.Tang, S.Le, H.Meers, C.Lampe, G. D.Chang, L.Sternberg, S. H.2025-06-10doi:10.1101/2025.06.10.658865Cold Spring Harbor Laboratory Press2025-06-10
<![CDATA[
Pan-angiosperm analysis of the CLE signaling peptide family unveils paths, patterns, and predictions of paralog diversification
]]>
https://biorxiv.org/cgi/content/short/2025.06.04.657892v1?rss=1"
Gentile, I.Santo Domingo, M.Zebell, S. G.Fitzgerald, B.Lippman, Z.2025-06-08doi:10.1101/2025.06.04.657892Cold Spring Harbor Laboratory Press2025-06-08
<![CDATA[
Constant light impairs memory processing transgenerationally in D. melanogaster
]]>
https://biorxiv.org/cgi/content/short/2025.06.04.657854v1?rss=1"
Moore, R. S.Sehgal, A.2025-06-08doi:10.1101/2025.06.04.657854Cold Spring Harbor Laboratory Press2025-06-08
<![CDATA[
A covalent recognition strategy enables conspecific mate identification
]]>
https://biorxiv.org/cgi/content/short/2025.05.30.657074v1?rss=1"
Jang, S. S.Mandala, S.Jiang, H.Zhang, X.Cole, P. A.del Marmol, J. I.2025-06-03doi:10.1101/2025.05.30.657074Cold Spring Harbor Laboratory Press2025-06-03
<![CDATA[
A primate model organism for cardiac arrhythmias identifies a magnesium transporter in pacemaker function
]]>
https://biorxiv.org/cgi/content/short/2025.05.28.655959v1?rss=1"
Chang, S.Karanewsky, C. J.Pendleton, J. L.Ren, L.Anzeraey, A.Froelicher, V.Liang, D.Razafindrakoto, A.Ravelonjanahary, H. N.Albertelli, M. A.Quertermous, T.Wright, P. C.Perret, M.Terrien, J.Aujard, F.Wu, J. C.Krasnow, M. A.2025-06-01doi:10.1101/2025.05.28.655959Cold Spring Harbor Laboratory Press2025-06-01
<![CDATA[
Epigenetic and evolutionary features of ape subterminal heterochromatin
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https://biorxiv.org/cgi/content/short/2025.05.29.656835v1?rss=1"
Yoo, D.Munson, K. M.Eichler, E. E.2025-05-30doi:10.1101/2025.05.29.656835Cold Spring Harbor Laboratory Press2025-05-30
<![CDATA[
Chemical capture of diazo metabolites reveals biosynthetic hydrazone oxidation
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https://biorxiv.org/cgi/content/short/2025.05.24.655970v1?rss=1"
Pfeifer, K.Van Cura, D.Wu, K. J. Y.Balskus, E. P.2025-05-28doi:10.1101/2025.05.24.655970Cold Spring Harbor Laboratory Press2025-05-28
<![CDATA[
Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana
]]>
https://biorxiv.org/cgi/content/short/2025.05.28.654549v1?rss=1"
Wu, X.Bellagio, T.Peng, Y.Czech, L.Lin, M.Lang, P.Epstein, R.Abdelaziz, M.Alexander, J.Caton-Darby, M.Alonso-Blanco, C.Andersen, H. L.Berbel, M.Bergelson, J.Burghardt, L.Delker, C.Dimitrakopoulos, P. G.Donohue, K.Durka, W.Escribano-Avila, G.Franks, S. J.Fritschi, F. B.Galanidis, A.Garcia-Fernandez, A.Garcia-Munoz, A.Hamann, E.Herber, M.Hutt, A.Iriondo, J. M.Juenger, T. E.Keller, S.Koehl, K.Korte, A.Korte, P.Kuschera, A.Lara-Romero, C.Leventhal, L.Maag, D.Marcer, A.March-Salas, M.Meaux, J. d.Mendez-Vigo, B.Moren2025-05-28doi:10.1101/2025.05.28.654549Cold Spring Harbor Laboratory Press2025-05-28
<![CDATA[
Mechanism of age-related accumulation of mitochondrial DNA mutations in human blood
]]>
https://biorxiv.org/cgi/content/short/2025.05.25.655566v1?rss=1"
Gupta, R.Durham, T. J.Chau, G.Uddin, M. M.Lu, W.Karczewski, K. J.Howrigan, D.Natarajan, P.Zhou, W.Neale, B. M.Mootha, V. K.2025-05-28doi:10.1101/2025.05.25.655566Cold Spring Harbor Laboratory Press2025-05-28
<![CDATA[
The specificity and structure of DNA crosslinking by the gut bacterial genotoxin colibactin
]]>
https://biorxiv.org/cgi/content/short/2025.05.26.655968v1?rss=1"
Carlson, E. S.Haslecker, R.Lecchi, C.Ramos, M. A.Vennelakanti, V.Honaker, L.Stornetta, A.Millan, E. S.Johnson, B. A.Kulik, H. J.Balbo, S.Villalta, P. W.D'Souza, V.Balskus, E. P.2025-05-27doi:10.1101/2025.05.26.655968Cold Spring Harbor Laboratory Press2025-05-27
<![CDATA[
A new heme enzyme family forms hydrazine groups in diverse biosynthetic pathways
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https://biorxiv.org/cgi/content/short/2025.05.27.656397v1?rss=1"
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C_FIG
]]>Kenney, G. E.Wang, K.-K. A.Ng, T.van der Donk, W.Balskus, E. P.2025-05-27doi:10.1101/2025.05.27.656397Cold Spring Harbor Laboratory Press2025-05-27
<![CDATA[
Defective splicing of Y-chromosome-linked gigantic genes underlies hybrid male sterility in Drosophila
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https://biorxiv.org/cgi/content/short/2025.05.22.655455v1?rss=1"
Fontan, A.Lannes, R.Fingerhut, J.Flynn, J.Yamashita, Y. M.2025-05-27doi:10.1101/2025.05.22.655455Cold Spring Harbor Laboratory Press2025-05-27
<![CDATA[
Pleiotropic mutational effects on function and stability constrain the antigenic evolution of influenza hemagglutinin
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https://biorxiv.org/cgi/content/short/2025.05.24.655919v1?rss=1"
Yu, T. C.Kikawa, C.Dadonaite, B.Loes, A. N.Englund, J. A.Bloom, J. D.2025-05-24doi:10.1101/2025.05.24.655919Cold Spring Harbor Laboratory Press2025-05-24
<![CDATA[
Lineage recording in monoclonal gastruloids reveals heritable modes of early development
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https://biorxiv.org/cgi/content/short/2025.05.23.655664v1?rss=1"
Regalado, S. G.Qiu, C.Kottapalli, S.Martin, B. K.Chen, W.Liao, H.Kim, H.Li, X.Lalanne, J.-B.Hamazaki, N.Domcke, S.Choi, J.Shendure, J.2025-05-24doi:10.1101/2025.05.23.655664Cold Spring Harbor Laboratory Press2025-05-24
<![CDATA[
Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens
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https://biorxiv.org/cgi/content/short/2025.05.23.655669v1?rss=1"
Regalado, S. G.Qiu, C.Lalanne, J.-B.Martin, B. K.Duran, M.Trapnell, C.Keith, A.Domcke, S.Shendure, J.2025-05-24doi:10.1101/2025.05.23.655669Cold Spring Harbor Laboratory Press2025-05-24
<![CDATA[
Prevalence of Group II Introns in Phage Genomes
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https://biorxiv.org/cgi/content/short/2025.05.22.655115v1?rss=1"
Merk, L. N.Jones, T. A.Eddy, S. R.2025-05-23doi:10.1101/2025.05.22.655115Cold Spring Harbor Laboratory Press2025-05-23
<![CDATA[
Endosome transcriptomics reveal trafficking of Cajal bodies into multivesicular bodies
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https://biorxiv.org/cgi/content/short/2025.05.22.655499v1?rss=1"
Singh, J.Williams, J. K.Elliott, Q.Jhawar, R.Ferguson, L.Collins, K.Schekman, R.2025-05-22doi:10.1101/2025.05.22.655499Cold Spring Harbor Laboratory Press2025-05-22
<![CDATA[
Characterization of a novel glycocin from a thermophile
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https://biorxiv.org/cgi/content/short/2025.05.19.655019v1?rss=1"
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org.highwire.dtl.DTLVardef@17c74bforg.highwire.dtl.DTLVardef@1d4ddb3org.highwire.dtl.DTLVardef@27490dorg.highwire.dtl.DTLVardef@12cffd7_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Martini, R. M.van der Donk, W.2025-05-20doi:10.1101/2025.05.19.655019Cold Spring Harbor Laboratory Press2025-05-20
<![CDATA[
Potent neutralization of Marburg virus by a vaccine-elicited monoclonal antibody
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https://biorxiv.org/cgi/content/short/2025.05.14.654121v1?rss=1"
Addetia, A.Perruzza, L.Park, Y.-J.McCallum, M.Stewart, C.Brown, J. T.Donati, A.Culap, K.Balmelli, A.Gazi, M.Carrion, R.Corti, D.Benigni, F.Veesler, D.2025-05-18doi:10.1101/2025.05.14.654121Cold Spring Harbor Laboratory Press2025-05-18
<![CDATA[
Pervasive homeobox gene function in the male-specific nervous system of Caenorhabditis elegans
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https://biorxiv.org/cgi/content/short/2025.05.13.653874v1?rss=1"
Fernandez, R. W.Digirolamo, A. J.Valperga, G.Aguilar, G. R.Molina-Garcia, L.Kersh, R. M.Wang, C.Pe, K.Ramadan, Y. H.Loer, C.Barrios, A.Hobert, O.2025-05-17doi:10.1101/2025.05.13.653874Cold Spring Harbor Laboratory Press2025-05-17
<![CDATA[
The sensitising effect of IgG in fibromyalgia syndrome is mediated by Mrgprb2 in mast cells
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https://biorxiv.org/cgi/content/short/2025.05.15.652596v1?rss=1"
Sanchez, K. R.Burgess, J. G.Zheng, Q.Alam, U.Neiland, H.Berwick, R.Andersson, D.Korver, S.Marshall, A.Goebel, A.Dong, X.2025-05-16doi:10.1101/2025.05.15.652596Cold Spring Harbor Laboratory Press2025-05-16
<![CDATA[
RNA polymerase III transcription-associated polyadenylation promotes the accumulation of noncoding retrotransposons during infection
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https://biorxiv.org/cgi/content/short/2025.05.14.654096v1?rss=1"
Lari, A.Shah, S. B.Mao, X.Sanghrajka, P.Karijolich, J.Lareau, L. F.Glaunsinger, B. A.2025-05-16doi:10.1101/2025.05.14.654096Cold Spring Harbor Laboratory Press2025-05-16
<![CDATA[
Control of myogenesis by the E3 ubiquitin ligase CUL3-BTBD9
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https://biorxiv.org/cgi/content/short/2025.05.15.654347v1?rss=1"
Padovani, C.Perez, F. R.Tsai, M.Xiong, J.Pogson, A.Martinez, B.Rape, M.2025-05-15doi:10.1101/2025.05.15.654347Cold Spring Harbor Laboratory Press2025-05-15
<![CDATA[
Frog-killing chytrid fungi deploy different strategies to regulate intracellular pressure in cell types that have or lack a cell wall
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https://biorxiv.org/cgi/content/short/2025.05.13.653819v1?rss=1"
Prostak, S. M.Velle, K. B.Fritz-Laylin, L.2025-05-14doi:10.1101/2025.05.13.653819Cold Spring Harbor Laboratory Press2025-05-14
<![CDATA[
An Orc6 tether mediates ORC binding site switching during replication origin licensing
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https://biorxiv.org/cgi/content/short/2025.05.09.652650v1?rss=1"
Driscoll, D.Friedman, L. J.Gelles, J.Bell, S. P.2025-05-13doi:10.1101/2025.05.09.652650Cold Spring Harbor Laboratory Press2025-05-13
<![CDATA[
Massively parallel reporter assay for mapping gene-specific regulatory regions at single nucleotide resolution
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https://biorxiv.org/cgi/content/short/2025.05.13.653746v1?rss=1"
Tulloch, A. J.Delgado, R. N.Catta-Preta, R.Cepko, C. L.2025-05-13doi:10.1101/2025.05.13.653746Cold Spring Harbor Laboratory Press2025-05-13
<![CDATA[
Defect in hematopoiesis and embryonic lethality at midgestation of Vps13a/Vps13c double knockout mice
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https://biorxiv.org/cgi/content/short/2025.05.09.653147v1?rss=1"
Xu, P.Mancuso, R. I.Leonzino, M.Zeiss, C. J.Krause, D. S.De Camilli, P.2025-05-13doi:10.1101/2025.05.09.653147Cold Spring Harbor Laboratory Press2025-05-13
<![CDATA[
Metabolic immunity to infection is driven by mitochondrial one-carbon metabolism
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https://biorxiv.org/cgi/content/short/2025.05.07.652698v1?rss=1"
Medeiros, T. C. D.Reato, S.Li, X.Garcia, B. M.Rais, I.Allmeroth, K.Hartman, M.Denzel, M.Purrio, M.Mesaros, A.Leung, K.-y.Greene, N.Giavalisco, P.Pernas, L.2025-05-13doi:10.1101/2025.05.07.652698Cold Spring Harbor Laboratory Press2025-05-13
<![CDATA[
Phylogeny-driven design of broadly protective sarbecovirus receptor-binding domain nanoparticle vaccines
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https://biorxiv.org/cgi/content/short/2025.05.11.652904v1?rss=1"
Addetia, A.Schaefer, A.Sprouse, K.Valdez, A.Taylor, A.Navarro, M.-J.Brown, J. T.Leaf, E.Miranda, M.Walls, A. C.Lee, J.Catanzaro, N. J.Treichel, C.Willoughby, I.Powers, J.Martinez, D. R.Vesari, B.Ravichandran, R.Seo, A. J.Stewart, C.Merz, B.Beirne, E.Zepeda, S.Cook, A.Pessaint, L.Sharma, A.Edwards, D.Lee, K.Smith, K.Starr, T. N.Baric, R.King, N. P.Veesler, D.2025-05-13doi:10.1101/2025.05.11.652904Cold Spring Harbor Laboratory Press2025-05-13
<![CDATA[
Social Exclusion Amplifies Behavioral Responses to Physical Pain via Insular Neuromodulation
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https://biorxiv.org/cgi/content/short/2025.05.09.653162v1?rss=1"
Jia, C.Tran, A.Aloboudi, F.Say, E.Thao, N.Lee, C. R.Batra, K.Nguyen, A.Bal, A.Nono, N. N.Delahanty, J.Chan, M. G.Keyes, L. R.Patel, R. R.Wichmann, R.Taschbach, F.Li, Y.Benna, M. K.Pereira, T. D.Li, H.Tye, K. M.2025-05-13doi:10.1101/2025.05.09.653162Cold Spring Harbor Laboratory Press2025-05-13
<![CDATA[
A human-specific regulatory mechanism revealed in a preimplantation model
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https://biorxiv.org/cgi/content/short/2025.05.10.653263v1?rss=1"
Fueyo, R.Wang, S.Crocker, O. J.Swigut, T.Nakauchi, H.Wysocka, J.2025-05-12doi:10.1101/2025.05.10.653263Cold Spring Harbor Laboratory Press2025-05-12
<![CDATA[
Assessment of nucleic acid structure prediction in CASP16
]]>
https://biorxiv.org/cgi/content/short/2025.05.06.652459v1?rss=1"
Kretsch, R. C.Hummer, A. M.He, S.Yuan, R.Zhang, J.Karagianes, T.Cong, Q.Kryshtafovych, A.Das, R.2025-05-10doi:10.1101/2025.05.06.652459Cold Spring Harbor Laboratory Press2025-05-10
<![CDATA[
Promoter strength and position govern promoter competition
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https://biorxiv.org/cgi/content/short/2025.05.06.652547v1?rss=1"
Koska, M.Swigut, T.Boettiger, A. N.Wysocka, J.2025-05-07doi:10.1101/2025.05.06.652547Cold Spring Harbor Laboratory Press2025-05-07
<![CDATA[
Chinmo is a novel regulator of differential Hippo signaling response within a single developing organ.
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https://biorxiv.org/cgi/content/short/2025.05.02.651944v1?rss=1"
Tarikere, S.Kumar, T.Ylla, G.Extavour, C. G.2025-05-06doi:10.1101/2025.05.02.651944Cold Spring Harbor Laboratory Press2025-05-06
<![CDATA[
The LOTUS domain of Oskar promotes localisation of both protein and mRNA components of Drosophila germ plasm
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https://biorxiv.org/cgi/content/short/2025.05.02.651258v1?rss=1"
Repouliou, A.Srouji, J. R.Rivard, E. L.Leschziner, A.Extavour, C. G.2025-05-06doi:10.1101/2025.05.02.651258Cold Spring Harbor Laboratory Press2025-05-06
<![CDATA[
Effect of plant tissue culture parameters on the ploidy level of Physalis grisea, Solanum lycopersicum, and Solanum prinophyllum regenerants
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https://biorxiv.org/cgi/content/short/2025.05.01.651681v1?rss=1"
Van Eck, J.Swartwood, K.Green, Y.Gentile, I.Lippman, Z. B.2025-05-03doi:10.1101/2025.05.01.651681Cold Spring Harbor Laboratory Press2025-05-03
<![CDATA[
Molecular and Spatial Organization of the Primary Olfactory System and its Responses to Social Odors
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https://biorxiv.org/cgi/content/short/2025.05.02.651832v1?rss=1"
Bintu, B.Isogai, Y.Zhuang, X.Dulac, C.2025-05-02doi:10.1101/2025.05.02.651832Cold Spring Harbor Laboratory Press2025-05-02
<![CDATA[
Fmp30 is a phosphatidylinositol hydrolase that regulates CoQ biosynthesis
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https://biorxiv.org/cgi/content/short/2025.05.01.651778v1?rss=1"
Baker, Z. N.Guerra, R. M.Rogers, S. W.Pagliarini, D. J.2025-05-02doi:10.1101/2025.05.01.651778Cold Spring Harbor Laboratory Press2025-05-02
<![CDATA[
LipidCruncher: An open-source web application for processing, visualizing, and analyzing lipidomic data
]]>
https://biorxiv.org/cgi/content/short/2025.04.28.650893v1?rss=1"
Abdi, H.Ambaw, Y.Chitraju, C.Singh, S.Zon, W. L.Farese, R.Walther, T. C.2025-05-01doi:10.1101/2025.04.28.650893Cold Spring Harbor Laboratory Press2025-05-01
<![CDATA[
A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination
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https://biorxiv.org/cgi/content/short/2025.04.29.651360v1?rss=1"
Martin, C. A.Cogdill, K. R.Pusey, A. L.Gehring, M.2025-04-30doi:10.1101/2025.04.29.651360Cold Spring Harbor Laboratory Press2025-04-30
<![CDATA[
A CARF-HAD phosphatase effector provides immunity during the type III-A CRISPR-Cas response
]]>
https://biorxiv.org/cgi/content/short/2025.04.30.651354v1?rss=1"
Stella, G.Ye, L.Brady, S. F.Marraffini, L. A.2025-04-30doi:10.1101/2025.04.30.651354Cold Spring Harbor Laboratory Press2025-04-30
<![CDATA[
Anoxia activates CRISPR-Cas immunity in the intestine
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https://biorxiv.org/cgi/content/short/2025.04.30.651551v1?rss=1"
Campbell, I. W.Basta, D. W.Zingl, F. G.Sullivan, E. J.Doranga, S.Waldor, M. K.2025-04-30doi:10.1101/2025.04.30.651551Cold Spring Harbor Laboratory Press2025-04-30
<![CDATA[
Short-term gonadal cultures are sufficient for germline transmission in a songbird
]]>
https://biorxiv.org/cgi/content/short/2025.04.25.650428v1?rss=1"
Biegler, M. T.Harter, E.Sidhu, A. V.Szialta, C.Durham, G.Tchernichovski, L.Collier, P.Luo, J.-D.Wang, W.MacIsaac, R.Belay, K.Carroll, T.Keyte, A. L.Jarvis, E. D.2025-04-29doi:10.1101/2025.04.25.650428Cold Spring Harbor Laboratory Press2025-04-29
<![CDATA[
Specialized parallel pathways for adaptive control of visual object pursuit
]]>
https://biorxiv.org/cgi/content/short/2025.04.23.650240v1?rss=1"
Collie, M. F.Jin, C.Kellogg, E.Vanderbeck, Q. X.Hartman, A. K.Holtz, S. L.Wilson, R. I.2025-04-29doi:10.1101/2025.04.23.650240Cold Spring Harbor Laboratory Press2025-04-29
<![CDATA[
DNA Methylation Dynamics of Dose-dependent Acute Exercise, Training Adaptation, and Detraining
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https://biorxiv.org/cgi/content/short/2025.04.22.650067v1?rss=1"
Hariharan, M.Patel, S.Song, H.Rehman, A.Barragan, C.Bartlett, A.Castanon, R.Nery, J.Rothenberg, V.Chen, H.Tian, W.Ding, W.Wang, W.McAdam, J.Graham, Z.Lavin, K.Bamman, M.Broderick, T.Ecker, J.2025-04-25doi:10.1101/2025.04.22.650067Cold Spring Harbor Laboratory Press2025-04-25
<![CDATA[
Tanycyte Bmal1 sex-specifically regulates weight gain and hypothalamic neurogenesis in female mice
]]>
https://biorxiv.org/cgi/content/short/2025.04.21.649851v1?rss=1"
Iascone, D. M.Pivarshev, P.Yang, J.Lopez Valencia, M.Noya, S. B.Lin, H.Anafi, R. C.Bedont, J. L.Sehgal, A.2025-04-28doi:10.1101/2025.04.21.649851Cold Spring Harbor Laboratory Press2025-04-28
<![CDATA[
Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testicular stem cells
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https://biorxiv.org/cgi/content/short/2025.04.19.649648v1?rss=1"
Urban, J.Ringwalt, D.Urban, J.Xue, W.Gleason, R.Zhao, K.Chen, X.2025-04-24doi:10.1101/2025.04.19.649648Cold Spring Harbor Laboratory Press2025-04-24
<![CDATA[
BRCA2 reversion mutation-independent resistance to PARP inhibition in prostate cancer through loss of function perturbations in the DNA pre-replication complex
]]>
https://biorxiv.org/cgi/content/short/2025.04.20.649668v1?rss=1"
Pappas, K. J.Ferrari, M.Smith, P.Nandakumar, S.Khan, Z.Young, S. B.LaClair, J.Russo, M. V.Huang-Hobbs, E.Schultz, N.Abida, W.Karthaus, W.Jasin, M.Sawyers, C.2025-04-24doi:10.1101/2025.04.20.649668Cold Spring Harbor Laboratory Press2025-04-24
<![CDATA[
Structures of human organellar SPFH protein complexes
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https://biorxiv.org/cgi/content/short/2025.04.21.649849v1?rss=1"
Gao, J.Sherpa, D.Kupko, N.Shao, S.2025-04-22doi:10.1101/2025.04.21.649849Cold Spring Harbor Laboratory Press2025-04-22
<![CDATA[
Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain
]]>
https://biorxiv.org/cgi/content/short/2025.04.21.648266v1?rss=1"
Zeng, Q.Tian, W.Klein, A.Bartlett, A.Liu, H.Nery, J. R.Castanon, R. G.Osteen, J.Johnson, N.Wang, W.Ding, W.Chen, H.Altshul, J.Kenworthy, M.Valadon, C.Owens, W.Wu, Z.Amaral, M. L.Song, Y.Baez-Becerra, C. T.Cho, S.Chen, C.Willier, J.Cao, S.Rink, J.Lee, J.Barcoma, A.Arzavala, J.Emerson, N.Lu, Y. R.Ren, B.Behrens, M. M.Ecker, J. R.2025-04-21doi:10.1101/2025.04.21.648266Cold Spring Harbor Laboratory Press2025-04-21
<![CDATA[
Nuclear 2'-O-methylation regulates RNA splicing through its binding protein FUBP1
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https://biorxiv.org/cgi/content/short/2025.04.20.649728v1?rss=1"
Gao, B.Jiang, B.Zou, Z.Liu, B.Liu, W.Chen, L.Zhang, L.He, C.2025-04-21doi:10.1101/2025.04.20.649728Cold Spring Harbor Laboratory Press2025-04-21
<![CDATA[
Nuclear envelope budding is a non-canonical mechanism to export large transcripts in muscle cells
]]>
https://biorxiv.org/cgi/content/short/2025.04.18.649598v1?rss=1"
Zaganelli, S.Meehl, J.Abrisch, R. G.Voeltz, G. K.2025-04-21doi:10.1101/2025.04.18.649598Cold Spring Harbor Laboratory Press2025-04-21
<![CDATA[
Genome-wide mapping of mesoscale neuronal RNA organization and condensation
]]>
https://biorxiv.org/cgi/content/short/2025.04.19.649570v1?rss=1"
Becker, L. A.Quinodoz, S. A.Comi, T. J.Kimchi, O.Knowles, D. A.Brangwynne, C. P.2025-04-20doi:10.1101/2025.04.19.649570Cold Spring Harbor Laboratory Press2025-04-20
<![CDATA[
L-2-hydroxyglutarate impairs neuronal differentiation through epigenetic activation of MYC expression
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https://biorxiv.org/cgi/content/short/2025.04.16.649033v1?rss=1"
Gu, W.Wang, X.Solmonson, A.Cai, L.Tasdogan, A.Franklin, J.Zhang, Y.Zhang, H.Westfall, A. K.Rowe, A.Trivedi, H.Faubert, B.Wu, Z.Sudderth, J.Zacharias, L. G.Afroze, B.Bezprozvanny, I.Sudarshan, S.Cai, F.McBrayer, S. K.Mathews, T. P.DeBerardinis, R. J.2025-04-19doi:10.1101/2025.04.16.649033Cold Spring Harbor Laboratory Press2025-04-19
<![CDATA[
G protein-coupled receptor diversity and evolution in the closest living relatives of Metazoa
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https://biorxiv.org/cgi/content/short/2025.04.15.649019v1?rss=1"
Garcia De Las Bayonas, A.King, N.2025-04-17doi:10.1101/2025.04.15.649019Cold Spring Harbor Laboratory Press2025-04-17
<![CDATA[
Engineered protein circuits for cancer therapy
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https://biorxiv.org/cgi/content/short/2025.04.16.647665v1?rss=1"
Lu, A. C.Moeller, L.Moore, S.Xia, S.Ho, K.Zhang, E.Budde, M. W.Larson, H.Ahmed Diaz, A.Gu, B.Linton, J. M.Klock, L.Flynn, M. J.Gao, X. J.Siegwart, D. J.Zhu, H.Elowitz, M. B.2025-04-16doi:10.1101/2025.04.16.647665Cold Spring Harbor Laboratory Press2025-04-16
<![CDATA[
Archaeal SegAB forms a bipolar structure that promotes chromosome segregation in spherical cells
]]>
https://biorxiv.org/cgi/content/short/2025.04.15.649018v1?rss=1"
Charles-Orszag, A.Lord, S. J.Herrera, N.Strauskulage, L.Bhowmick, A.Goddard, T.Wassmer, B.van Wolferen, M.Asper, G.Flis, A.Rodriguez, J.Redding, S.Rosenberg, O.Albers, S.-V.Mullins, D.2025-04-16doi:10.1101/2025.04.15.649018Cold Spring Harbor Laboratory Press2025-04-16
<![CDATA[
Mosquito sex under lock and key
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https://biorxiv.org/cgi/content/short/2025.04.11.648401v1?rss=1"
Houri-Zeevi, L.Walker, M. M.Razzauti, J.Sharma, A.Pasolli, H. A.Vosshall, L. B.2025-04-16doi:10.1101/2025.04.11.648401Cold Spring Harbor Laboratory Press2025-04-16
<![CDATA[
Distinct satellite DNA composition between core and germline restricted chromosomes in Bradysia (Sciara) coprophila
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https://biorxiv.org/cgi/content/short/2025.04.15.648937v1?rss=1"
Kerrebrock, A.Flynn, J. M.Baird, R. B.Hodson, C. N.Ross, L.Yamashita, Y. M. M.2025-04-16doi:10.1101/2025.04.15.648937Cold Spring Harbor Laboratory Press2025-04-16
<![CDATA[
The E3 ligase HECTD4 regulates COX-2 dependent tumor progression and metastasis
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https://biorxiv.org/cgi/content/short/2025.04.09.647907v1?rss=1"
Vuille, J. A.Tanriover, C.Micalizzi, D. S.Ebright, R. Y.Animesh, S.Morris, R.Hajizadeh, S.Nicholson, Z. J.Russell, H. C.Zaniewski, E. F.Wittner, B. S.Wesley, B. K.Grunewald, J.Szalay, R. N.Antmen, E.Fox, D. B.Yang, M.Joung, J. K.Gulhan, D. C.Elia, A. E. H.Haas, W.Oh, E.Maheswaran, S.Haber, D. A.2025-04-15doi:10.1101/2025.04.09.647907Cold Spring Harbor Laboratory Press2025-04-15
<![CDATA[
Super Recombinator (SuRe): An in vivo recombination system for scalable and efficient transgene assembly at a single genomic locus
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https://biorxiv.org/cgi/content/short/2025.04.15.646138v1?rss=1"
Luo, J.Huang, C.Taylor, C. A.Li, J.Woo, S. J.Yu, C.Shen, K.Schnitzer, M. J.2025-04-15doi:10.1101/2025.04.15.646138Cold Spring Harbor Laboratory Press2025-04-15
<![CDATA[
Designed NGF mimetics with reduced nociceptive signatures in neurons
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https://biorxiv.org/cgi/content/short/2025.04.14.648806v1?rss=1"
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org.highwire.dtl.DTLVardef@c48066org.highwire.dtl.DTLVardef@c9c5a7org.highwire.dtl.DTLVardef@cf8ebdorg.highwire.dtl.DTLVardef@a4345a_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Schlichthaerle, T.Yang, A.Detraux, D.Johnson, D. E.Peach, C. J.Edman, N. I.Sniezek, C.Williams, C. A.Arora, S.Katiyar, N.Chen, I.Etemadi, A.Favor, A.Lee, D.Kubo, C.Coventry, B.Huang, B.Gerben, S.Ennist, N. M.Milles, L.Sankaran, B.Kang, A.Nguyen, H.Bera, A. K.Negahdari, B.Hamazaki, N.Schweppe, D. K.Stewart, L.Young, J. E.Bunnett, N. W.Ruohola-Baker, H.Mathieu, J.Pattwell, S.Garcia, K. C.Baker, D.2025-04-14doi:10.1101/2025.04.14.648806Cold Spring Harbor Laboratory Press2025-04-14
<![CDATA[
Modular regulation of the stem cell transcriptome defines self-renewal, differentiation, and dedifferentiation
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https://biorxiv.org/cgi/content/short/2025.04.10.648217v1?rss=1"
Raz, A. A.Hassan, H.Yamashita, Y. M.2025-04-14doi:10.1101/2025.04.10.648217Cold Spring Harbor Laboratory Press2025-04-14
<![CDATA[
Vascular endothelial-specific loss of TGF-beta signaling as a model for choroidal neovascularization and central nervous system vascular inflammation
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https://biorxiv.org/cgi/content/short/2025.04.11.648449v1?rss=1"
Wang, Y.Rattner, A.Li, Z.Smallwood, P. M.Nathans, J.2025-04-11doi:10.1101/2025.04.11.648449Cold Spring Harbor Laboratory Press2025-04-11
<![CDATA[
Atom level enzyme active site scaffolding using RFdiffusion2
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https://biorxiv.org/cgi/content/short/2025.04.09.648075v1?rss=1"
Ahern, W.Yim, J.Tischer, D.Salike, S.Woodbury, S.Kim, D.Kalvet, I.Kipnis, Y.Coventry, B.Altae-Tran, H.Bauer, M.Barzilay, R.Jaakkola, T.Krishna, R.Baker, D. A.2025-04-10doi:10.1101/2025.04.09.648075Cold Spring Harbor Laboratory Press2025-04-10
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Time-resolved phenotyping at subcellular resolution reveals shared principles and key trade-offs across antimicrobial peptide activities
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https://biorxiv.org/cgi/content/short/2025.04.10.648262v1?rss=1"
Fragasso, A.Schlechtweg, T.Lin, W.-H.Barron, A. E.Jacobs-Wagner, C.2025-04-10doi:10.1101/2025.04.10.648262Cold Spring Harbor Laboratory Press2025-04-10
<![CDATA[
Transcription factor hubs exhibit gene-specific properties that tune expression
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https://biorxiv.org/cgi/content/short/2025.04.07.647578v1?rss=1"
Fallacaro, S.Mukherjee, A.Turner, M. A.Garcia, H. G.Mir, M.2025-04-08doi:10.1101/2025.04.07.647578Cold Spring Harbor Laboratory Press2025-04-08
<![CDATA[
Biosynthesis of Macrocyclic Peptides by Formation and Crosslinking of ortho-Tyrosines
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https://biorxiv.org/cgi/content/short/2025.04.04.647296v1?rss=1"
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org.highwire.dtl.DTLVardef@37d9c8org.highwire.dtl.DTLVardef@baf547org.highwire.dtl.DTLVardef@3d0ed8org.highwire.dtl.DTLVardef@99aaee_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Padhi, C.Zhu, L.Chen, J. Y.Moreira, R.van der Donk, W. A.2025-04-08doi:10.1101/2025.04.04.647296Cold Spring Harbor Laboratory Press2025-04-08
<![CDATA[
OmniSplice: a framework-free splicing event reporter
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https://biorxiv.org/cgi/content/short/2025.04.06.647416v1?rss=1"
Lannes, R.Fingerhut, J. M.Yamashita, Y. M. M.2025-04-08doi:10.1101/2025.04.06.647416Cold Spring Harbor Laboratory Press2025-04-08
<![CDATA[
Lipid metabolism of hepatocyte-like cells supports intestinal tumor growth by promoting tracheogenesis
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https://biorxiv.org/cgi/content/short/2025.04.04.647255v1?rss=1"
Huang, K.Miao, T.Dantas, E.Han, M.Hu, Y.Wang, K.Sanford, J.Goncalves, M.Perrimon, N.2025-04-05doi:10.1101/2025.04.04.647255Cold Spring Harbor Laboratory Press2025-04-05
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Superinfection with intact HIV-1 results in conditional replication of defective proviruses and nonsuppressible viremia in people living with HIV-1
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https://biorxiv.org/cgi/content/short/2025.04.04.647291v1?rss=1"
1, enabling in vivo spread. Despite this, clinical outcomes show no evidence of a beneficial effect of these DIPs.
]]>Hariharan, V.White, J. A.Dragoni, F.Fray, E. J.Pathoulas, N.Moskovljevic, M.Zhang, H.Singhal, A.Lai, J.Beg, S. A.Scully, E. P.Gilliams, E. A.Block, D. S.Keruly, J.Moore, R. D.Siliciano, J. D.Simonetti, F. R.Siliciano, R. F.2025-04-04doi:10.1101/2025.04.04.647291Cold Spring Harbor Laboratory Press2025-04-04
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The aPBP-type cell wall synthase PBP1b plays a specialized role in fortifying the Escherichia coli division site against osmotic rupture
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https://biorxiv.org/cgi/content/short/2025.04.02.646830v1?rss=1"
Navarro, P. P.Vettiger, A.Hajdu, R.Ananda, V. Y.Lopez-Tavares, A.Schmid, E.Walter, J.Loose, M.Chao, L. H.Bernhardt, T. G.2025-04-02doi:10.1101/2025.04.02.646830Cold Spring Harbor Laboratory Press2025-04-02
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Striatal neural ensemble codes for voluntary locomotor and involuntary dyskinetic movements
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https://biorxiv.org/cgi/content/short/2025.04.01.646527v1?rss=1"
Chattree, G.Chrapkiewicz, R.Zhang, Y.Li, J.Schnitzer, M. J.2025-04-02doi:10.1101/2025.04.01.646527Cold Spring Harbor Laboratory Press2025-04-02
<![CDATA[
Mapping cellular targets of covalent cancer drugs in the entire mammalian body
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https://biorxiv.org/cgi/content/short/2025.03.28.645991v1?rss=1"
Pang, Z.Leung, V. H.Wang, C. C.Attarpour, A.Rinaldi, A.Shen, H.Glynn, C.Sigua, L. H.Yender, M.Selke, A.Xu, S.Wu, P.Goubran, M.Cravatt, B. F.Ye, L.2025-04-02doi:10.1101/2025.03.28.645991Cold Spring Harbor Laboratory Press2025-04-02
<![CDATA[
Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA
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https://biorxiv.org/cgi/content/short/2025.04.01.643995v1?rss=1"
Paul, T.Lee, I.-R.Pangeni, S.Rashid, F.Yang, O.Antony, E.Berger, J. M.Myong, S.Ha, T.2025-04-01doi:10.1101/2025.04.01.643995Cold Spring Harbor Laboratory Press2025-04-01
<![CDATA[
In-Situ High-Resolution Cryo-EM Reconstructions from CEMOVIS
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https://biorxiv.org/cgi/content/short/2025.03.29.646093v1?rss=1"
Elferich, J.Kaminek, M.Kong, L.Odriozola, A.Kukulski, W.Zuber, B.Grigorieff, N.2025-03-31doi:10.1101/2025.03.29.646093Cold Spring Harbor Laboratory Press2025-03-31
<![CDATA[
Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks
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https://biorxiv.org/cgi/content/short/2025.03.25.645253v1?rss=1"
Varilly, P.Schifferli, M.Yang, K.Burcham, T.Cronan, P.Glennon, O.Jacks, O.Laning, E.Marrs, L.Oba, K.Yeung, S.Parker, E.Omah, I.Pekar, J. E.Luebbert, L.Andersen, K. G.Park, D. J.Schaffner, S. F.MacInnis, B. L.Happi, C.Lemieux, J. E.Ozonoff, A.Mitzenmacher, M. D.Fry, B.Sabeti, P. C.2025-03-26doi:10.1101/2025.03.25.645253Cold Spring Harbor Laboratory Press2025-03-26
<![CDATA[
Population and adaptation history of 739 Thlaspi arvense natural accessions
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https://biorxiv.org/cgi/content/short/2025.03.21.644658v1?rss=1"
Wu, X.Epstein, R.Esfahanian, M.Gautam, B.Griffiths, M.Perez, J.Barry, K.Lipzen, A.Daum, C.Yoshinaga, Y.Abeyratne, C. R.Akhmetov, Z.Arana, S. T.Bayliss, R.Borphukan, B.Brusa, A.Chhetri, H.Combs-Giroir, R.Czech, L.Dyderski, M. K.Gjesvold, E. S.Grzejszczak, G.Hateley, S.Heller, N.Hoffmann, D.Jaikumar, N.Jarvis, B. A.Jawahir, V.Klisz, M.Kruse, P.Lane, M.Lima, A.Liu, A.Madrid, G.Marlino, M.McGinn, M.Pavicic, M.Perry, W.Shah, M.Thomas, J.Townsend, A.Wanigarathna, T. L.Wesley, T.Connolly, B.Lim, Y. P.Puchałka, R2025-03-25doi:10.1101/2025.03.21.644658Cold Spring Harbor Laboratory Press2025-03-25
<![CDATA[
Long-term hunter-gatherer continuity in the Rhine-Meuse region was disrupted by local formation of expansive Bell Beaker groups
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https://biorxiv.org/cgi/content/short/2025.03.24.644985v1?rss=1"
Olalde, I.Altena, E.Bourgeois, Q.Fokkens, H.Amkreutz, L.Deguilloux, M.-F.Fichera, A.Flas, D.Gandini, F.Kegler, J. F.Kootker, L. M.Leijnse, K.Kooijmans, L. L.Lauwerier, R.Miller, R.Molthof, H.Noiret, P.Raemaekers, D. C. M.Rivollat, M.Smits, L.Stewart, J. R.ten Anscher, T.Toussaint, M.Callan, K.Cheronet, O.Frost, T.Iliev, L.Mah, M.Micco, A.Oppenheimer, J.Patterson, I.Qiu, L.Soos, G.Workman, J. N.Edwards, C. J.Lazaridis, I.Mallick, S.Patterson, N.Rohland, N.Richards, M. B.Pinhasi, R.Haak, W.Pala, M.Reich, D.2025-03-25doi:10.1101/2025.03.24.644985Cold Spring Harbor Laboratory Press2025-03-25
<![CDATA[
Nonenzymatic RNA copying with a potentially primordial genetic alphabet
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https://biorxiv.org/cgi/content/short/2025.03.19.644114v1?rss=1"
Fang, Z.Jia, X.Xing, Y.Szostak, J. W.2025-03-19doi:10.1101/2025.03.19.644114Cold Spring Harbor Laboratory Press2025-03-19
<![CDATA[
HortaCloud: An Open and Collaborative Platform for Whole Brain Neuronal Reconstructions
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https://biorxiv.org/cgi/content/short/2025.03.13.642887v1?rss=1"
Rokicki, K.Schauder, D.Olbris, D. J.Goina, C.Clements, J.Edson, P.Kawase, T.Svirskas, R.Arshadi, C.Feng, D.Chandrashekar, J.Ferreira, T. A.MouseLight Project Team,2025-03-14doi:10.1101/2025.03.13.642887Cold Spring Harbor Laboratory Press2025-03-14
<![CDATA[
Loss of the Integrator and Nuclear Exosome Targeting complexes disrupts oogenesis and causes the emergenceof atypical transcripts in Drosophila
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https://biorxiv.org/cgi/content/short/2025.03.05.641556v1?rss=1"
Lee, Y.Biasini, A.Tipping, C.Hong, S. H.Zamore, P.2025-03-11doi:10.1101/2025.03.05.641556Cold Spring Harbor Laboratory Press2025-03-11
<![CDATA[
Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer
]]>
https://biorxiv.org/cgi/content/short/2025.02.28.640922v1?rss=1"
Jimenez-Sanchez, A.Persad, S.Hayashi, A.Umeda, S.Sharma, R.Xie, Y.Mehta, A.Park, W.Masilionis, I.Chu, T.Zhu, F.Hong, J.Chaligne, R.O'Reilly, E. M.Mazutis, L.Nawy, T.Pe'er, I.Iacobuzio-Donahue, C. A.Pe'er, D.2025-03-06doi:10.1101/2025.02.28.640922Cold Spring Harbor Laboratory Press2025-03-06
<![CDATA[
Recurrent patterns of widespread neuronal genomic damage shared by major neurodegenerative disorders
]]>
https://biorxiv.org/cgi/content/short/2025.03.03.641186v1?rss=1"
Zhou, Z.Luquette, L. J.Dong, G.Kim, J.Ku, J.Kim, K.Bae, M.Shao, D. D.Sahile, B.Miller, M. B.Huang, A. Y.Park, P. J.Lagier-Tourenne, C.Lee, E. A.Walsh, C. A.2025-03-05doi:10.1101/2025.03.03.641186Cold Spring Harbor Laboratory Press2025-03-05
<![CDATA[
Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells
]]>
https://biorxiv.org/cgi/content/short/2025.03.02.641101v1?rss=1"
Ma, B.Yang, G.Yao, J.Wu, C.Vega, J. P.Manske, G.Sue, H.Sinha, S.Singh, A.Zhao, H.Chen, X.2025-03-04doi:10.1101/2025.03.02.641101Cold Spring Harbor Laboratory Press2025-03-04
<![CDATA[
Evidence accumulation from experience and observation in the cingulate cortex
]]>
https://biorxiv.org/cgi/content/short/2025.02.13.638172v1?rss=1"
Chen, R.Radkani, S.Valluru, N.Yoo, S. B.Jazayeri, M.2025-02-14doi:10.1101/2025.02.13.638172Cold Spring Harbor Laboratory Press2025-02-14
<![CDATA[
A lateralized pathway for associating nutrients with flavors
]]>
https://biorxiv.org/cgi/content/short/2025.02.09.637334v1?rss=1"
Grove, J. C. R.Li, Q.Backes, H.Kuzmanovic, B.Choi, J.Ubadiah, V.Qiu, L.Zhang, J.Liu, Z.Small, D. M.Tittgemeyer, M.Knight, Z. A.2025-02-10doi:10.1101/2025.02.09.637334Cold Spring Harbor Laboratory Press2025-02-10
<![CDATA[
Cutaneous lupus features specialized stromal niches and altered retroelement expression
]]>
https://biorxiv.org/cgi/content/short/2025.02.01.636053v1?rss=1"
Gehlhausen, J. R.Kong, Y.Baker, E.Ramachandran, S.Koumpouras, F.Ko, C.Vesely, M.Little, A.Damsky, W.King, B.Iwasaki, A.2025-02-06doi:10.1101/2025.02.01.636053Cold Spring Harbor Laboratory Press2025-02-06
<![CDATA[
Separable Dorsal Raphe Dopamine Projections mediate the Facets of Loneliness-like state
]]>
https://biorxiv.org/cgi/content/short/2025.02.03.636224v1?rss=1"
Lee, C. R.Matthews, G. A.Lemieux, M. E.Wasserlein, E. M.Borio, M.Miranda, R. L.Keyes, L. R.Schneider, G. P.Jia, C.Tran, A.Aloboudi, F.Chan, M. G.Peroni, E.Pereira, G.Lopez-Moraga, A.Pall e, A.Kimchi, E. Y.Padilla-Coreano, N.Wichmann, R.Tye, K. M.2025-02-04doi:10.1101/2025.02.03.636224Cold Spring Harbor Laboratory Press2025-02-04
<![CDATA[
Evaluation of sequencing reads at scale using rdeval
]]>
https://biorxiv.org/cgi/content/short/2025.02.01.636073v1?rss=1"
Formenti, G.Koo, B.Sollitto, M.Balacco, J.Brajuka, N.Burhans, R.Duarte, E.Giani, A. M.McCaffrey, K.Medico, J. A.Myers, E. W.Jarvis, E. D.2025-02-01doi:10.1101/2025.02.01.636073Cold Spring Harbor Laboratory Press2025-02-01
<![CDATA[
Multi-scale structure of chromatin condensates rationalizes phase separation and material properties
]]>
https://biorxiv.org/cgi/content/short/2025.01.17.633609v1?rss=1"
Zhou, H.Huertas, J.Maristany, M. J.Russell, K.Hwang, J. H.Yao, R.Hutchings, J.Shiozaki, M.Zhao, X.Doolittle, L. K.Gibson, B. A.Riggi, M.Rene Espinosa, J.Yu, Z.Villa, E.Collepardo-Guevara, R.Rosen, M. K.2025-01-22doi:10.1101/2025.01.17.633609Cold Spring Harbor Laboratory Press2025-01-22
<![CDATA[
The epigenetic factor Zrf1 regulates intestinal stem cell proliferation during midgut regeneration
]]>
https://biorxiv.org/cgi/content/short/2025.01.16.633419v1?rss=1"
Li, J. S. S.Liu, Y.Kim, A.-R.Qadiri, M.Xu, J.Xia, B.Binari, R.Asara, J. M.Hu, Y.Perrimon, N.2025-01-21doi:10.1101/2025.01.16.633419Cold Spring Harbor Laboratory Press2025-01-21
<![CDATA[
The bile acid-sensitive ion channel is gated by Ca2+-dependent conformational changes in the transmembrane domain
]]>
https://biorxiv.org/cgi/content/short/2025.01.10.632481v1?rss=1"
Freitas, M. M.Gouaux, E.2025-01-12doi:10.1101/2025.01.10.632481Cold Spring Harbor Laboratory Press2025-01-12
<![CDATA[
Queen loss unmasks cryptic worker influence and decentralizes the bumble bee social network
]]>
https://biorxiv.org/cgi/content/short/2025.01.07.630106v1?rss=1"
Ruttenberg, D. M.Wolf, S. W.Webb, A. E.Wyman, E. S.White, M.Melo, D.Traniello, I. M.Kocher, S. D.2025-01-07doi:10.1101/2025.01.07.630106Cold Spring Harbor Laboratory Press2025-01-07
<![CDATA[
Molecular basis for shifted receptor recognition by an encephalitic arbovirus
]]>
https://biorxiv.org/cgi/content/short/2025.01.01.631009v1?rss=1"
Fan, X.Li, W.Oros, J.Plung, J. S.Plante, J. A.Basu, H.Nagappan-Chettiar, S.Boeckers, J. M.Tjang, L. V.Mann, C. J.Brusic, V.Buck, T. K.Varnum, H.Yang, P.Malcolm, L. M.Choi, S. Y.de Souza, W. M.Chiu, I. M.Umemori, H.Weaver, S. M.Plante, K. S.Abraham, J.2025-01-02doi:10.1101/2025.01.01.631009Cold Spring Harbor Laboratory Press2025-01-02
<![CDATA[
Cellular cartography reveals mouse prostate organization and determinants of castration resistance
]]>
https://biorxiv.org/cgi/content/short/2024.12.27.630532v1?rss=1"
Cho, H.Zhang, Y.Tien, J. C.-Y.Mannan, R.Luo, J.Narayanan, S. P.Mahapatra, S.Hu, J.Shelley, G.Cruz, G.Shahine, M.Wang, L.Su, F.Wang, R.Cao, X.Dhanasekaran, S. M.Keller, E. T.Pitchiaya, S.Chinnaiyan, A. M.2024-12-28doi:10.1101/2024.12.27.630532Cold Spring Harbor Laboratory Press2024-12-28
<![CDATA[
Predicting Future Development of Stress-Induced Anhedonia From Cortical Dynamics and Facial Expression
]]>
https://biorxiv.org/cgi/content/short/2024.12.18.629202v1?rss=1"
Coley, A.Batra, K.Delahanty, J.Keyes, L.Pamintuan, R.Ramot, A.Hagemann, J.Lee, C.Liu, V.Adivikolanu, H.Cressy, J.Jia, C.Massa, F.LeDuke, D.Gabir, M.Durubeh, B.linderhof, L.Patel, R.Wichmann, R.Li, H.Fischer, K.Pereira, T.Tye, K.2024-12-20doi:10.1101/2024.12.18.629202Cold Spring Harbor Laboratory Press2024-12-20
<![CDATA[
MEDiCINe: Motion Correction for Neural Electrophysiology Recordings
]]>
https://biorxiv.org/cgi/content/short/2024.11.06.622160v1?rss=1"
Watters, N.Buccino, A. P.Jazayeri, M.2024-11-07doi:10.1101/2024.11.06.622160Cold Spring Harbor Laboratory Press2024-11-07
<![CDATA[
Autocatalytic assembly of a chimeric aminoacyl-RNA synthetase ribozyme
]]>
https://biorxiv.org/cgi/content/short/2024.10.26.620442v1?rss=1"
Radakovic, A.Todisco, M.Mishra, A.Szostak, J. W.2024-10-28doi:10.1101/2024.10.26.620442Cold Spring Harbor Laboratory Press2024-10-28
<![CDATA[
A novel PhoPQ-potentiated mechanism of colistin resistance impairs membrane integrity in Pseudomonas aeruginosa
]]>
https://biorxiv.org/cgi/content/short/2024.10.15.618514v1?rss=1"
Hsieh, Y.-Y. P.O'Keefe, I. P.Sun, W.Wang, Z.Yang, H.Vu, L. M.Ernst, R. K.Dandekar, A. A.Malik, H. S.2024-10-16doi:10.1101/2024.10.15.618514Cold Spring Harbor Laboratory Press2024-10-16
<![CDATA[
Bond-centric modular design of protein assemblies
]]>
https://biorxiv.org/cgi/content/short/2024.10.11.617872v1?rss=1"
Wang, S.Favor, A.Kibler, R. D.Lubner, J. M.Borst, A. J.Coudray, N.Redler, R.Chiang, H. T.Sheffler, W.Hsia, Y.Li, Z.Ekiert, D. C.Bhabha, G.Pozzo, L. D.Baker, D.2024-10-12doi:10.1101/2024.10.11.617872Cold Spring Harbor Laboratory Press2024-10-12
<![CDATA[
Cell-type-informed genotyping of mosaic focal epilepsies reveals cell-autonomous and non-cell-autonomous disease-associated transcriptional programs
]]>
https://biorxiv.org/cgi/content/short/2024.10.01.615793v1?rss=1"
Bizzotto, S.Stronge, E. A.Talukdar, M.Hu, Q.Zhou, Z.Huang, A. Y.Chhouk, B. H.D'Gama, A. M.Yang, E.Green, T. E.Reutens, D. C.Mullen, S. A.Hildebrand, M. S.Buono, R. J.Poduri, A. H.Khoshkhoo, S.Walsh, C. A.2024-10-02doi:10.1101/2024.10.01.615793Cold Spring Harbor Laboratory Press2024-10-02
<![CDATA[
Homeodomain protein codes specify neuronal diversity in the first ganglion of the Drosophila visual system
]]>
https://biorxiv.org/cgi/content/short/2024.09.27.615552v1?rss=1"
Xu, C.Newstein, P.Sastry, R.Doe, C.2024-09-29doi:10.1101/2024.09.27.615552Cold Spring Harbor Laboratory Press2024-09-29
<![CDATA[
DNA polymerase Zeta is a robust reverse transcriptase
]]>
https://biorxiv.org/cgi/content/short/2024.09.27.615452v1?rss=1"
Mayle, R.Holloman, W. K.O'Donnell, M. E.2024-09-28doi:10.1101/2024.09.27.615452Cold Spring Harbor Laboratory Press2024-09-28
<![CDATA[
Analysis of genetic requirements and nutrient availability for Staphylococcus aureus growth in cystic fibrosis sputum
]]>
https://biorxiv.org/cgi/content/short/2024.09.24.614743v1?rss=1"
Shull, L. M.Wolter, D. J.Kunkle, D. E.Legg, K. A.Giedroc, D. P.Skaar, E. P.Hoffman, L. R.Reniere, M. L.2024-09-25doi:10.1101/2024.09.24.614743Cold Spring Harbor Laboratory Press2024-09-25
<![CDATA[
Disparate demographic impacts of the Roman Colonization and the Migration Period in the Iberian Peninsula.
]]>
https://biorxiv.org/cgi/content/short/2024.09.23.614606v1?rss=1"
Carrion, P.Olalde, I.Jimenez-Arenas, J. M.Coromina, N.Vivo, D.Verges, J. M.Costa, A.Botella, D.Bustamante-Alvarez, M.Heras-Mora, J.Ortega-Ruiz, R.Chaves, C.Garcia-Collado, M. I.Quiros-Castillo, J.Roig, J.Suarez-Padilla, J.Navarro-Luengo, I.Cuadrado, M. A.Aguilera, I.Morera, J.Catalan, R.Cerdeno, M. L.Roig-Perez, J. F.Diaz-Garcia, M.Chirosa-Canavate, P.Piza-Ruiz, T.Vallejo-Casas, E.Vidal-Alvarez, S.Burch, J.Sagrera, J.Vivo, J.Cubo-Cordoba, A.Martinez-Enamorado, V.Rengel-Castro, F.Garcia-Entero, V.Rodero, A.Viguera, E.Rohl2024-09-23doi:10.1101/2024.09.23.614606Cold Spring Harbor Laboratory Press2024-09-23
<![CDATA[
Structure-guided engineering of type I-F CASTs for targeted gene insertion in human cells
]]>
https://biorxiv.org/cgi/content/short/2024.09.19.613948v1?rss=1"
Lampe, G. D.Liang, A. R.Zhang, D. J.Fernandez, I. S.Sternberg, S. H.2024-09-19doi:10.1101/2024.09.19.613948Cold Spring Harbor Laboratory Press2024-09-19
<![CDATA[
Craters on the melanoma surface facilitate tumor-immune interactions and demonstrate pathologic response to checkpoint blockade in humans
]]>
https://biorxiv.org/cgi/content/short/2024.09.18.613595v1?rss=1"
Ludin, A.Stirtz, G. L.Tal, A.Nirmal, A. J.Besson, N.Jones, S. M.Pfaff, K. L.Manos, M.Liu, S.Barrera, I.Gong, Q.Rodrigues, C. P.Sahu, A.Jerison, E.Alessi, J. V.Ricciuti, B.Richardson, D. S.Weiss, J. D.Moreau, H. M.Stanhope, M. E.Afeyan, A. B.Sefton, J.McCall, W. D.Formato, E.Yang, S.Zhou, Y.Hoytema van Konijnenburg, D. P.Cole, H. L.Cordova, M.Deng, L.Rajadhyaksha, M.Quake, S. R.Awad, M. M.Chen, F.Sorger, P. K.Hodi, F. S.Rodig, S. J.Murphy, G. F.Zon, L. I.2024-09-19doi:10.1101/2024.09.18.613595Cold Spring Harbor Laboratory Press2024-09-19
<![CDATA[
Engineered Receptors for Soluble Cell-to-Cell Communication
]]>
https://biorxiv.org/cgi/content/short/2024.09.17.613377v1?rss=1"
Piraner, D. I.Abedi, M. H.Duran Gonzalez, M. J.Chazin-Gray, A.Zhu, I.Ravindran, P. T.Schlichthaerle, T.Huang, B.Lee, D.Baker, D.Roybal, K. T.2024-09-18doi:10.1101/2024.09.17.613377Cold Spring Harbor Laboratory Press2024-09-18
<![CDATA[
MtvS Regulates the Francisella Type V-A CRISPR-Cas System
]]>
https://biorxiv.org/cgi/content/short/2024.09.12.612765v1?rss=1"
Brodmann, M.Marraffini, L. A.2024-09-12doi:10.1101/2024.09.12.612765Cold Spring Harbor Laboratory Press2024-09-12
<![CDATA[
Chromosome breakage-replication/fusion enables rapid DNA amplification
]]>
https://biorxiv.org/cgi/content/short/2024.08.17.608415v1?rss=1"
Zhang, C.-Z.Pellman, D.2024-08-19doi:10.1101/2024.08.17.608415Cold Spring Harbor Laboratory Press2024-08-19
<![CDATA[
Functional protein mining with conformal guarantees
]]>
https://biorxiv.org/cgi/content/short/2024.06.27.601042v1?rss=1"
Boger, R. S.Chithrananda, S.Angelopoulos, A. N.Yoon, P. H.Jordan, M. H.Doudna, J. A.2024-06-28doi:10.1101/2024.06.27.601042Cold Spring Harbor Laboratory Press2024-06-28
<![CDATA[
Visualizing lipid nanoparticle trafficking for mRNA vaccine delivery in non-human primates
]]>
https://biorxiv.org/cgi/content/short/2024.06.21.600088v1?rss=1"
Buckley, M.Arainga, M.Maiorino, L.Pires, I. S.Kim, B. J.Kaczmarek Michaels, K.Dye, J.Qureshi, K.Zhang, Y.Mak, H.Steichen, J. M.Schief, W. R.Villinger, F.Irvine, D. J.2024-06-27doi:10.1101/2024.06.21.600088Cold Spring Harbor Laboratory Press2024-06-27
<![CDATA[
Controlling semiconductor growth with structured de novo protein interfaces
]]>
https://biorxiv.org/cgi/content/short/2024.06.24.600095v1?rss=1"
Saragovi, A.Pyles, H.Kwon, P.Hanikel, N.Davila-Hernandez, F. A.Bera, A.Kang, A.Brackenbrough, E.Vafeados, D. K.Allen, A.Stewart, L.Baker, D.2024-06-25doi:10.1101/2024.06.24.600095Cold Spring Harbor Laboratory Press2024-06-25
<![CDATA[
Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage
]]>
https://biorxiv.org/cgi/content/short/2024.05.28.596078v1?rss=1"
Naqvi, S.Kim, S.Tabatabaee, S.Pampari, A.Kundaje, A.Pritchard, J. K.Wysocka, J.2024-05-29doi:10.1101/2024.05.28.596078Cold Spring Harbor Laboratory Press2024-05-29
<![CDATA[
Structure of the Flotillin Complex in a Native Membrane Environment
]]>
https://biorxiv.org/cgi/content/short/2024.05.09.593390v1?rss=1"
Fu, Z.MacKinnon, R.2024-05-09doi:10.1101/2024.05.09.593390Cold Spring Harbor Laboratory Press2024-05-09
<![CDATA[
Empowering STEM Students: A University-wide Mentorship Program Fostering Retention and Belonging
]]>
https://biorxiv.org/cgi/content/short/2024.04.02.587784v1?rss=1"
Ravishankar, S.Spencer-Drakes, T. C. J.Fernandes, I. H.Hayes, M. I.Coopwood, S.Spencers, I.Neal, S. E.2024-04-02doi:10.1101/2024.04.02.587784Cold Spring Harbor Laboratory Press2024-04-02
<![CDATA[
MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions
]]>
https://biorxiv.org/cgi/content/short/2024.03.06.583734v1?rss=1"
Müller, N. F.Bouckaert, R. R.Wu, C.-H.Bedford, T. F.2024-03-09doi:10.1101/2024.03.06.583734Cold Spring Harbor Laboratory Press2024-03-09
<![CDATA[
Kinetochores grip microtubules with directionally asymmetric strength
]]>
https://biorxiv.org/cgi/content/short/2024.02.22.581622v1?rss=1"
Larson, J. D.Heitkamp, N. A.Murray, L. E.Popchock, A. R.Biggins, S.Asbury, C. L.2024-02-24doi:10.1101/2024.02.22.581622Cold Spring Harbor Laboratory Press2024-02-24
<![CDATA[
Evolutionary analyses of IDRs reveal widespread signals of conservation
]]>
https://biorxiv.org/cgi/content/short/2023.12.05.570250v1?rss=1"
Singleton, M.Eisen, M.2023-12-07doi:10.1101/2023.12.05.570250Cold Spring Harbor Laboratory Press2023-12-07
<![CDATA[
A proposed function for the red body of Nannochloropsis in the formation of the recalcitrant cell wall polymer, algaenan
]]>
https://biorxiv.org/cgi/content/short/2023.09.17.558137v1?rss=1"
Gee, C. W.Andersen-Ranberg, J.Rosen, R. Z.Jorgens, D.Grob, P.Holman, H.-Y.Niyogi, K. K.2023-09-17doi:10.1101/2023.09.17.558137Cold Spring Harbor Laboratory Press2023-09-17
<![CDATA[
Progressive plasticity during colorectal cancer metastasis
]]>
https://biorxiv.org/cgi/content/short/2023.08.18.553925v1?rss=1"
Moorman, A.Cambuli, F.Benitez, E.Jiang, Q.Xie, Y.Mahmoud, A.Lumish, M.Hartner, S.Balkaran, S.Bermeo, J.Asawa, S.Firat, C.Saxena, A.Luthra, A.Sgambati, V.Luckett, K.Wu, F.Li, Y.Yi, Z.Masilionis, I.Soares, K.Pappou, E.Yaeger, R.Kingham, P.Jarnagin, W.Paty, P.Weiser, M. R.Mazutis, L.D'Angelica, M.Shia, J.Garcia-Aguilar, J.Nawy, T.Hollman, T.Chaligne, R.Sanchez-Vega, F.Sharma, R.Pe'er, D.Ganesh, K.2023-08-21doi:10.1101/2023.08.18.553925Cold Spring Harbor Laboratory Press2023-08-21
<![CDATA[
Thermodynamic Coupling of the tandem RRM domains of hnRNP A1 underlie its Pleiotropic RNA Binding Functions
]]>
https://biorxiv.org/cgi/content/short/2023.08.17.553700v1?rss=1"
Levengood, J. D.Potoyan, D.Penumutchu, S.Kumar, A.Wang, Y.Hansen, A. L.Kutluay, S.Roche, J.Tolbert, B. S.2023-08-17doi:10.1101/2023.08.17.553700Cold Spring Harbor Laboratory Press2023-08-17
<![CDATA[
Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs
]]>
https://biorxiv.org/cgi/content/short/2023.07.31.551037v1?rss=1"
1,000-fold in the impact of the same mutation on spike-mediated viral infection across spikes from different SARS-CoV-2 variants. Overall, our work establishes a general approach for comparing sets of DMS experiments to identify biologically important shifts in mutational effects.
Significance StatementAmino-acid mutations to a protein have effects that can shift as the protein evolves or is put under new selective pressure. The effects of amino-acid mutations to a specific protein under a defined selective pressure can be measured by deep mutational scanning experiments. Here, we devise an approach to quantify shifts in mutational effects between experiments performed on different homologs (i.e. variants) of the same protein, or on the same protein selected under different conditions. We use this approach to compare experiments performed on three homologs of SARS-CoV-2 spike, identifying mutations that have shifted in their effect on spike-mediated viral infection by >1,000 fold across SARS-CoV-2 variants.
]]>Haddox, H. K.Galloway, J. G.Dadonaite, B.Bloom, J. D.Matsen, F. A.DeWitt, W. S.2023-08-02doi:10.1101/2023.07.31.551037Cold Spring Harbor Laboratory Press2023-08-02
<![CDATA[
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
]]>
https://biorxiv.org/cgi/content/short/2023.06.28.546576v1?rss=1"
Lariviere, D.Abueg, L.Brajuka, N.Gallardo-Alba, C.Gruning, B.Ko, B. J.Ostrovsky, A.Palmada-Flores, M.Pickett, B. D.Rabbani, K.Balacco, J. R.Chaisson, M.Cheng, H.Collins, J.Denisova, A.Fedrigo, O.Gallo, G. R.Giani, A. M.Gooder, G. M.Jain, N.Johnson, C.Kim, H.Lee, C.Marques-Bonet, T.O'Toole, B.Rhie, A.Secomandi, S.Sozzoni, M.Tilley, T.Uliano-Silva, M.van den Beek, M.Waterhouse, R. M.Phillippy, A. M.Jarvis, E. D.Schatz, M.Nekrutenko, A.Formenti, G.2023-06-30doi:10.1101/2023.06.28.546576Cold Spring Harbor Laboratory Press2023-06-30
<![CDATA[
Magnetogenetic cell activation using endogenous ferritin
]]>
https://biorxiv.org/cgi/content/short/2023.06.20.545120v1?rss=1"
Stanley, S. A.Pomeranz, L. E.Li, R.Yu, X. A.Kelly, L.Hassanzadeh, G.Molina, H.Gross, D.Brier, M. I.Vaisey, G.Jimenez-Gonzalez, M.Garcia-Ocana, A.Dordick, J.Friedman, J. M.2023-06-20doi:10.1101/2023.06.20.545120Cold Spring Harbor Laboratory Press2023-06-20
<![CDATA[
Innate immune responses yield tissue-specific bottlenecks that scale with pathogen dose
]]>
https://biorxiv.org/cgi/content/short/2023.06.09.543079v1?rss=1"
Hullahalli, K.Dailey, K. G.Waldor, M. K.2023-06-09doi:10.1101/2023.06.09.543079Cold Spring Harbor Laboratory Press2023-06-09
<![CDATA[
Matters Arising: FBXO38 does not control PD-1 stability
]]>
https://biorxiv.org/cgi/content/short/2023.03.19.531556v1?rss=1"
Dibus, N.Salyova, E.Kolarova, K.Pagano, M.Stepanek, O.Cermak, L.2023-03-21doi:10.1101/2023.03.19.531556Cold Spring Harbor Laboratory Press2023-03-21
<![CDATA[
Flexible and site-specific manipulation of histones in live animals
]]>
https://biorxiv.org/cgi/content/short/2023.03.19.533378v1?rss=1"
Finkin-Groner, E.Al-Kachak, A.Agustinus, A. S.Bastle, R.Lepack, A.Lyu, Y.Maze, I.David, Y.2023-03-20doi:10.1101/2023.03.19.533378Cold Spring Harbor Laboratory Press2023-03-20
<![CDATA[
Enterovirus Evolution Reveals the Mechanism of an RNA-Targeted Antiviral and Determinants of Viral Replication
]]>
https://biorxiv.org/cgi/content/short/2023.02.20.529064v1?rss=1"
Davila-Calderon, J.Li, M.-L.Penumutchu, S.Haddad, C.Malcolm, L.Hargrove, A. E.Brewer, G.Tolbert, B. S.2023-02-20doi:10.1101/2023.02.20.529064Cold Spring Harbor Laboratory Press2023-02-20
<![CDATA[
Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening
]]>
https://biorxiv.org/cgi/content/short/2023.02.02.525347v1?rss=1"
Fiorin, G.Forrest, L. R.Faraldo-Gomez, J. D.2023-02-03doi:10.1101/2023.02.02.525347Cold Spring Harbor Laboratory Press2023-02-03
<![CDATA[
Dimerization mechanism of an inverted-topology ion channel in membranes
]]>
https://biorxiv.org/cgi/content/short/2023.01.27.525942v1?rss=1"
Ernst, M.Orabi, E. A.Stockbridge, R. B.Faraldo-Gomez, J. D.Robertson, J. L.2023-01-28doi:10.1101/2023.01.27.525942Cold Spring Harbor Laboratory Press2023-01-28
<![CDATA[
The molecular mechanism of selective and active transport in a Na+/Ca2+ exchanger
]]>
https://biorxiv.org/cgi/content/short/2023.01.20.524959v1?rss=1"
Marinelli, F.Faraldo-Gomez, J. D.2023-01-21doi:10.1101/2023.01.20.524959Cold Spring Harbor Laboratory Press2023-01-21
<![CDATA[
Continuous muscle, glial, epithelial, neuronal, and hemocyte cell lines for Drosophila research
]]>
https://biorxiv.org/cgi/content/short/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.2023-01-19doi:10.1101/2023.01.18.524445Cold Spring Harbor Laboratory Press2023-01-19
<![CDATA[
De Novo Design of Miniprotein Inhibitors of Bacterial Adhesins
]]>
https://biorxiv.org/cgi/content/short/2025.08.18.670751v1?rss=1"
Chazin-Gray, A. M.Thompson, T. R.Lopatto, E. D. B.Magala, P.Erickson, P. W.Hunt, A. C.Manchenko, A.Aprikian, P.Tchesnokova, V.Basova, I.Sanick, D. A.Tamadonfar, K. O.Timm, M. R.Pinkner, J. S.Dodson, K. W.Kang, A.Joyce, E.Bera, A. K.Schmitz, A. J.Ellebedy, A. H.Hvorecny, K. L.Cartwright, M. J.Vernet, A.Bardales, S.White, D.Klevit, R. E.Sokurenko, E. V.Hultgren, S. J.Baker, D.2025-08-18doi:10.1101/2025.08.18.670751Cold Spring Harbor Laboratory Press2025-08-18
<![CDATA[
Inverse expression of Ten3 and Lphn2 across the developing mouse brain reveals a global strategy for circuit assembly
]]>
https://biorxiv.org/cgi/content/short/2025.08.13.670004v1?rss=1"
Chon, U.Pederick, D. T.Song, J. H.Zhang, Y.Rana, I.Luo, L.2025-08-15doi:10.1101/2025.08.13.670004Cold Spring Harbor Laboratory Press2025-08-15
<![CDATA[
Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits
]]>
https://biorxiv.org/cgi/content/short/2025.08.20.670374v1?rss=1"
Ruetten, V. M.Zheng, W.Siwanowicz, I. R.Mensh, B. D.Eddison, M.Hu, A.Chi, Y.Lemire, A. L.Guo, C.Kadobianskyi, M.Renz, M.Lelek-Greskovic, S.He, Y.Close, K.Ihrke, G.Dev, A.Petruncio, A.Wan, Y.Engert, F.Fishman, M. C.Judkewitz, B.Rubinov, M.Keller, P. J.Satou, C.Yu, G.Tillberg, P. W.Sahani, M.Ahrens, M. B.2025-08-21doi:10.1101/2025.08.20.670374Cold Spring Harbor Laboratory Press2025-08-21
<![CDATA[
Augment rice ANNEXIN expression to counter planthopper NlAnnexin-like5 as an anti-virulence strategy against a major crop pest
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https://biorxiv.org/cgi/content/short/2025.08.18.670976v1?rss=1"
Zhang, X.-Y.Li, S.Opachaloemphan, C.Zhang, C.-X.Jiang, Y.he, s. y.2025-08-22doi:10.1101/2025.08.18.670976Cold Spring Harbor Laboratory Press2025-08-22
<![CDATA[
Divergent viral phosphodiesterases for immune signaling evasion
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https://biorxiv.org/cgi/content/short/2025.08.21.671373v1?rss=1"
Doherty, E. E.Nomburg, J. E.Adler, B. A.Lopez, S.Hsieh, K.Price, N.Blount, N.Doudna, J. A.2025-08-21doi:10.1101/2025.08.21.671373Cold Spring Harbor Laboratory Press2025-08-21
<![CDATA[
Transcriptional Interference Gates Monogenic Odorant Receptor Expression in Ants
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https://biorxiv.org/cgi/content/short/2025.08.21.671318v1?rss=1"
Glotzer, G. L.H. Pastor, P. D.Kronauer, D. J. C.2025-08-21doi:10.1101/2025.08.21.671318Cold Spring Harbor Laboratory Press2025-08-21
<![CDATA[
Skin capillary endothelial cells form a network of spatiotemporally conserved Ca2+ activity
]]>
https://biorxiv.org/cgi/content/short/2025.08.15.669933v1?rss=1"
Swaminathan, A.Gonzalez, D. G.Matte-Martone, C.Xu, F.Simpson, D.Monedero-Alonso, D.Moore, J. L.Mack, J. J.Kam, C. Y.Greco, V.2025-08-20doi:10.1101/2025.08.15.669933Cold Spring Harbor Laboratory Press2025-08-20
<![CDATA[
Strain variation identifies a neural substrate for behavioral evolution in Drosophila
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https://biorxiv.org/cgi/content/short/2025.08.15.670615v1?rss=1"
Ryba, A.Brand, P.Coleman, R. T.Greenfeld, Y.Tsitohay, Y. N.Hollunder, F.Keller, K.Hathiyari, M.Wei, T.Barbano, P. E.Ruta, V.2025-08-19doi:10.1101/2025.08.15.670615Cold Spring Harbor Laboratory Press2025-08-19
<![CDATA[
Deep Learning of Functional Perturbations from Condensate Morphology
]]>
https://biorxiv.org/cgi/content/short/2025.08.18.670955v1?rss=1"
Donlic, A.Comi, T. J.Quinodoz, S. A.Jaberi-Lashkari, N.Fernandes, K. A.Jiang, L.Wiesner, L. W.Lim, A. I.Brangwynne, C. P.2025-08-19doi:10.1101/2025.08.18.670955Cold Spring Harbor Laboratory Press2025-08-19
<![CDATA[
Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants
]]>
https://biorxiv.org/cgi/content/short/2025.08.18.671001v1?rss=1"
Dadonaite, B.Harari, S.Larsen, B. B.Kampman, L.Harteloo, A.Elias-Warren, A.Chu, H. Y.Bloom, J. D.2025-08-19doi:10.1101/2025.08.18.671001Cold Spring Harbor Laboratory Press2025-08-19
<![CDATA[
Engineering compact Physalis peruviana (goldenberry) to promote its potential as a global crop
]]>
https://biorxiv.org/cgi/content/short/2025.08.15.670557v1?rss=1"
Santo Domingo, M.Fitzgerald, B.Robitaille, G. M.Ramakrishnan, S.Swartwood, K.Karavolias, N.Schatz, M.Van Eck, J.Lippman, Z.2025-08-19doi:10.1101/2025.08.15.670557Cold Spring Harbor Laboratory Press2025-08-19
<![CDATA[
Ten3-Lphn2-mediated target selection across the extended hippocampal network demonstrates a repeated strategy for circuit assembly
]]>
https://biorxiv.org/cgi/content/short/2025.08.13.670207v1?rss=1"
Gingrich, E. C.Pederick, D. T.Zhang, Y.Luo, L.2025-08-15doi:10.1101/2025.08.13.670207Cold Spring Harbor Laboratory Press2025-08-15
<![CDATA[
Inference of germinal center evolutionary dynamics via simulation-based deep learning
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https://biorxiv.org/cgi/content/short/2025.08.12.669950v1?rss=1"
Ralph, D. K.Bakis, A. G.Galloway, J.Vora, A. A.Araki, T.Song, Y. S.DeWitt, W. S.Matsen, F. A.2025-08-15doi:10.1101/2025.08.12.669950Cold Spring Harbor Laboratory Press2025-08-15
<![CDATA[
PHA-4/FoxA controls the function of pharyngeal and extrapharyngeal enteric neurons of C. elegans
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https://biorxiv.org/cgi/content/short/2025.08.13.670029v1?rss=1"
Walker, Z.Cao, W. X.Leyva-Diaz, E.Rahman, M.Sural, S.Attner, M. A.Hobert, O.2025-08-15doi:10.1101/2025.08.13.670029Cold Spring Harbor Laboratory Press2025-08-15
<![CDATA[
Accelerating Biomolecular Modeling with AtomWorks andRF3
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https://biorxiv.org/cgi/content/short/2025.08.14.670328v1?rss=1"
Corley, N.Mathis, S.Krishna, R.Bauer, M. S.Thompson, T. R.Ahern, W.Kazman, M. W.Brent, R. I.Didi, K.Kubaney, A.McHugh, L.Nagle, A.Favor, A.Kshirsagar, M.Sturmfels, P.Li, Y.Butcher, J.Qiang, B.Schaaf, L. L.Mitra, R.Campbell, K.Zhang, O.Weissman, R.Humphreys, I. R.Cong, Q.Funk, J.Sonthalia, S.Lio, P.Baker, D.DiMaio, F.2025-08-14doi:10.1101/2025.08.14.670328Cold Spring Harbor Laboratory Press2025-08-14
<![CDATA[
Determinants of human versus mosquito cell entry by the Chikungunya virus envelope proteins
]]>
https://biorxiv.org/cgi/content/short/2025.08.25.672233v1?rss=1"
Ju, X.Hannon, W. W.Kaszuba, T.Radford, C. E.Larsen, B. B.Nelson, S. S.Nelson, C. A.Baltazar-Perez, I.Zimmerman, O.Fremont, D. H.Diamond, M. S.Bloom, J. D.2025-08-25doi:10.1101/2025.08.25.672233Cold Spring Harbor Laboratory Press2025-08-25
<![CDATA[
Widespread purine bias in bacterial genes driven by runaway transcription
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https://biorxiv.org/cgi/content/short/2025.08.25.672197v1?rss=1"
Dierksheide, K. J.Taggart, J. C.Johnson, G. E.Li, G.-W.2025-08-25doi:10.1101/2025.08.25.672197Cold Spring Harbor Laboratory Press2025-08-25
<![CDATA[
Engineering Synthetic Phase Variation for Control of Microbial consortium
]]>
https://biorxiv.org/cgi/content/short/2025.08.25.672192v1?rss=1"
Kratz, M. F.Murray, R. M.Elowitz, M. B.2025-08-25doi:10.1101/2025.08.25.672192Cold Spring Harbor Laboratory Press2025-08-25
<![CDATA[
A transcription factor-sRNA-mediated double-negative feedback loop confers pathogen-specific control of quorum-sensing genes
]]>
https://biorxiv.org/cgi/content/short/2025.08.22.671807v1?rss=1"
Mashruwala, A. A.Decker, K.Fei, C.Valastyan, J. S.Bassler, B.2025-08-22doi:10.1101/2025.08.22.671807Cold Spring Harbor Laboratory Press2025-08-22
<![CDATA[
An interneuronal CRH and CRHBP circuit stabilizes birdsong performance
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https://biorxiv.org/cgi/content/short/2025.08.16.670679v1?rss=1"
Colquitt, B. M.Brainard, M.2025-08-17doi:10.1101/2025.08.16.670679Cold Spring Harbor Laboratory Press2025-08-17
<![CDATA[
Positive Selection Screen for Natural Product β-Catenin Inactivators
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https://biorxiv.org/cgi/content/short/2025.08.27.671140v1?rss=1"
Boudreau, M. W.Freire, V. F.Corbett, S. C.Martinez-Fructuoso, L.Kumar, R.Thornburg, C. C.Akee, R. K.Peyser, B. D.Jiang, Q.Splaine, J.Pfaff, J. L.Chandler, B. C.Abeja, D. M.Donovan, K. A.Che, J.Lampson, B. L.Szajner, P.Smith, J. A.Koduri, V.Grkovic, T.OKeefe, B. R.Kaelin, W. G.2025-08-27doi:10.1101/2025.08.27.671140Cold Spring Harbor Laboratory Press2025-08-27
<![CDATA[
Evolutionary innovation through fusion of sequences from across the tree of life
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https://biorxiv.org/cgi/content/short/2025.08.30.672725v1?rss=1"
Kapoor, R.Schwager, E. E.Phuangphong, S.Rivard, E. L.Kuyyamudi, C.Ghosh, S.Ronai, I.Extavour, C. G.2025-08-31doi:10.1101/2025.08.30.672725Cold Spring Harbor Laboratory Press2025-08-31
<![CDATA[
Homology-mediated transformation of frog-killing fungus Batrachochytrium dendrobatidis illuminates chytrid development and pathogenesis
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https://biorxiv.org/cgi/content/short/2025.08.29.673073v1?rss=1"
Brody, S. M.Kalinka, E.Prostak, S. M.Carvalho, T.Man, J.James, T.Fritz-Laylin, L.2025-08-31doi:10.1101/2025.08.29.673073Cold Spring Harbor Laboratory Press2025-08-31
<![CDATA[
Heterotypic intercellular adhesion tunes efficiency of cell-on-cell migration
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https://biorxiv.org/cgi/content/short/2025.08.29.673192v1?rss=1"
Kuyyamudi, C.Ghosh, S.Extavour, C. G.2025-08-31doi:10.1101/2025.08.29.673192Cold Spring Harbor Laboratory Press2025-08-31
<![CDATA[
CUT&TIME captures the history of open chromatin indeveloping neurons
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https://biorxiv.org/cgi/content/short/2025.08.29.673195v1?rss=1"
Eldred, K. C.Wooten, M.Janssens, D. H.Hahn, J.Neph, S. J.Edgerton, S. J.Wyatt-Draher, G.Sherman, S. M.Ranchalis, J. E.Stergachis, A.Reh, T. A.Henikoff, S.2025-08-31doi:10.1101/2025.08.29.673195Cold Spring Harbor Laboratory Press2025-08-31
<![CDATA[
Whole-transcriptome-scale and isoform-resolved spatial imaging of single cells in complex tissues
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https://biorxiv.org/cgi/content/short/2025.08.27.672533v1?rss=1"
Cohen, L.Halpern, A.Blosser, T. R.Che, P.Pan, X.Zhuang, X.2025-08-30doi:10.1101/2025.08.27.672533Cold Spring Harbor Laboratory Press2025-08-30
<![CDATA[
Catalytic pocket of Clr4 (Suv39h) methyltransfer-ase serves as a substrate receptor for Cullin 4-dependent histone H3 ubiquitination
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https://biorxiv.org/cgi/content/short/2025.08.28.672867v1?rss=1"
Psenakova, K.Parhard, S. S.Paulo, J. A.Liu, X.Patterson, E. F.Watson, R.Cheek, M. A.Keogh, M.Kalocsay, M.Gygi, S.Farnung, L.Moazed, D.2025-08-30doi:10.1101/2025.08.28.672867Cold Spring Harbor Laboratory Press2025-08-30
<![CDATA[
Endocytome profiling uncovers cell-surface protein dynamics underlying neuronal connectivity
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https://biorxiv.org/cgi/content/short/2025.08.28.672852v1?rss=1"
McLaughlin, C.Ji, H.Dong, K.Xu, C.Wong, K. K. L.Li, Z.Luginbuhl, D. J.Xu, C.Lyu, C.Qin, W.Li, J.Udeshi, N.Carr, S. A.Ting, A. Y.Luo, L.2025-08-29doi:10.1101/2025.08.28.672852Cold Spring Harbor Laboratory Press2025-08-29
<![CDATA[
Impact of 2'-deoxyribo-purine substrates on nonenzymatic RNA template-directed primer extension
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https://biorxiv.org/cgi/content/short/2025.08.29.673048v1?rss=1"
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]]>Fang, Z.Acikgoz, O.Jia, X.Essex, J.Wen, R.Szostak, J. W.2025-08-29doi:10.1101/2025.08.29.673048Cold Spring Harbor Laboratory Press2025-08-29
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Discovery of homoharringtonine pathway enzymes reveals a whole plant model for coordinated biosynthesis
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https://biorxiv.org/cgi/content/short/2025.08.26.672243v1?rss=1"
Dho, Y.Smith, K.Sattely, E. S.2025-08-29doi:10.1101/2025.08.26.672243Cold Spring Harbor Laboratory Press2025-08-29
<![CDATA[
The Kaposi's sarcoma-associated herpesvirus TBP mimic uses a non-canonical DNA binding mode to promote viral late gene transcription
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https://biorxiv.org/cgi/content/short/2025.08.25.672222v1?rss=1"
Llacsahuanga Allcca, L. E.Didychuk, A. L.Rodriguez-Vargas, A.Glaunsinger, B.2025-08-29doi:10.1101/2025.08.25.672222Cold Spring Harbor Laboratory Press2025-08-29
<![CDATA[
A conserved electron transport chain sensitizes Bacteroides to a pore-forming type VI secretion toxin
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https://biorxiv.org/cgi/content/short/2025.08.29.672963v1?rss=1"
Ratner, H. K.Duong, B. D.Miao, P.Bertolli, S.Shen, B. A.Mitchell, U.Gallagher, L. A.Radey, M.Peterson, S. B.Mougous, J.2025-08-29doi:10.1101/2025.08.29.672963Cold Spring Harbor Laboratory Press2025-08-29
<![CDATA[
The Eukaryotic homology search complex distorts donor DNA structure to probe for homology
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https://biorxiv.org/cgi/content/short/2025.08.28.672940v1?rss=1"
Woodhouse, M. V.Hu, J.Wu, M.Qian, J.Inman, J. T.Wang, M. D.Crickard, J. B.2025-08-28doi:10.1101/2025.08.28.672940Cold Spring Harbor Laboratory Press2025-08-28
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Tissue-specific clonal selection and differentiation of CD4+ T cells during infection
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https://biorxiv.org/cgi/content/short/2025.08.25.672130v1?rss=1"
Parsa, R.Carvalho de Assis, H.B.R. de Castro, T.Lima dos Reis, G.Hartweger, H.Bilate, A.Mucida, D.2025-08-28doi:10.1101/2025.08.25.672130Cold Spring Harbor Laboratory Press2025-08-28
<![CDATA[
A molecularly defined basalo-prefrontal-thalamic circuit regulates sensory and affective dimensions of pain
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https://biorxiv.org/cgi/content/short/2025.08.22.671771v1?rss=1"
Xie, G.Liu, Y.Qi, X.Bhattacherjee, A.Zhang, C.Zhang, Y.2025-08-26doi:10.1101/2025.08.22.671771Cold Spring Harbor Laboratory Press2025-08-26
<![CDATA[
Reprogramming Factors Activate a Non-Canonical Oxidative Resilience Pathway That Can Rejuvenate RPEs and Restore Vision
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https://biorxiv.org/cgi/content/short/2025.08.30.673239v1?rss=1"
Lu, Y. R.Cameron, J. C.Hu, Y.Shen, H.Shirahama, S.Tyshkovskiy, A.Chen, Z.Ai, J.Zhu, D. Y.Karg, M. M.Chew, L. A.Bell, G. W.Jena, S. G.He, Y.Seifert, P.Shu, D. Y.El-Brolosy, M. A.Lou, Q.Zhang, B.Puszynska, A. M.Qiu, X.Tian, X.Gregory-Ksander, M.Gladyshev, V. N.Sinclair, D. A.Saint-Geniez, M.Buenrostro, J. D.Rickman, C. B.Ksander, B. R.Weissman, J. S.2025-09-01doi:10.1101/2025.08.30.673239Cold Spring Harbor Laboratory Press2025-09-01
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Affinity maturation of antibody responses is mediated by differential plasma cell proliferation
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https://biorxiv.org/cgi/content/short/2024.11.26.625430v1?rss=1"
MacLean, A. J.Deimel, L. P.Zhou, P.ElTanbouly, M. A.Merkenschlager, J.Ramos, V.Santos, G. S.Hagglof, T.Mayer, C. T.Hernandez, B.Gazumyan, A.Nussenzweig, M. C.2024-11-29doi:10.1101/2024.11.26.625430Cold Spring Harbor Laboratory Press2024-11-29
<![CDATA[
Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in dedifferentiated endometrial carcinomas
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https://biorxiv.org/cgi/content/short/2025.10.13.681937v1?rss=1"
St. Laurent, J. D.Xu, G. D.Ying, A. W.Gokbayrak, B.Patil, A.Paulo, J. A.Cervantes, K. S.Chen, S.Feng, W. W.Sankar, A.Same Guerra, D. D.Qi, J.Neel, D. S.Hornick, J. L.Kolin, D. L.Gygi, S.Huntsman, D. G.Wang, Y.Kadoch, C.2025-10-14doi:10.1101/2025.10.13.681937Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
Imp1 acts as a dosage- and stage-dependent temporal rheostat orchestrating radial glial fate transitions and cortical morphogenesis
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https://biorxiv.org/cgi/content/short/2025.11.18.688993v1?rss=1"
Azur, R. A. G.Feliciano, D.Espinosa-Medina, I.Adhikari, R.Lilao-Garzon, J.Jansen, E.Yang, C.-P.Lee, T.2025-11-18doi:10.1101/2025.11.18.688993Cold Spring Harbor Laboratory Press2025-11-18
<![CDATA[
Parkinsons disease modeling in regenerative spiny mice (Acomys dimidiatus) captures key disease-relevant behavioral, histological, and molecular signatures
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https://biorxiv.org/cgi/content/short/2025.11.06.687049v1?rss=1"
Dutta, S.Pang, M.Donahue, R. R.Chou, T.-F.Seifert, A. W.Gradinaru, V.2025-11-08doi:10.1101/2025.11.06.687049Cold Spring Harbor Laboratory Press2025-11-08
<![CDATA[
Uncovering the molecular basis of kinase activity and substrate recognition with phospho-PCA
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https://biorxiv.org/cgi/content/short/2025.11.07.687244v1?rss=1"
Yu, C.Pao, E.Van Valen, D. A.2025-11-07doi:10.1101/2025.11.07.687244Cold Spring Harbor Laboratory Press2025-11-07
<![CDATA[
Antibody-mediated feedback modulates interclonal competition in the germinal center
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https://biorxiv.org/cgi/content/short/2025.11.06.686519v1?rss=1"
Barbulescu, A.Bilanovic, J.Langelaar, T.Teetz, A. K.Urnavicius, L.Hobbs, A.Shen, J.-J.Abrahamse, N. H.de Carvalho, R. V.Mesin, L.Ferreira, C. L.Bortolatto, J.Victora, G. D.2025-11-07doi:10.1101/2025.11.06.686519Cold Spring Harbor Laboratory Press2025-11-07
<![CDATA[
MicroRNA156 and its targeted SPL genes interact with the photoperiod, vernalization, and gibberellin pathways to regulate wheat heading time
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https://biorxiv.org/cgi/content/short/2025.11.05.686864v1?rss=1"
Liu, Q.Zhang, L.Zhou, Z.Zhang, C.Li, C.Debernardi, J. M.Dubcovsky, J.2025-11-07doi:10.1101/2025.11.05.686864Cold Spring Harbor Laboratory Press2025-11-07
<![CDATA[
A silent Kv channel subunit shapes PV neuron action potential waveform and short-term synaptic plasticity during high-frequency firing
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https://biorxiv.org/cgi/content/short/2025.11.06.686832v1?rss=1"
Ganesh, S.Canty, T. M.Sabatini, B. L.2025-11-07doi:10.1101/2025.11.06.686832Cold Spring Harbor Laboratory Press2025-11-07
<![CDATA[
mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth
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https://biorxiv.org/cgi/content/short/2025.11.06.686990v1?rss=1"
Lin, D. H.Elcavage, L. E.Khalizeva, E.Bartel, D. P.2025-11-06doi:10.1101/2025.11.06.686990Cold Spring Harbor Laboratory Press2025-11-06
<![CDATA[
VTA dopamine neuron activity produces spatially organized value representations
]]>
https://biorxiv.org/cgi/content/short/2025.11.04.685995v1?rss=1"
Pan-Vazquez, A.Zimmerman, C. A.McMannon, B.Fabre, J. M. J.Louka, M.Jia, T.Sagiv, Y.West, S. J.Faulkner, M.Brain Laboratory, I.Dayan, P.Witten, I. B.2025-11-06doi:10.1101/2025.11.04.685995Cold Spring Harbor Laboratory Press2025-11-06
<![CDATA[
Rewiring protein function through genetically encoded oxidative chemistry
]]>
https://biorxiv.org/cgi/content/short/2025.11.06.686050v1?rss=1"
Li, H.Pavlic, A.Ibrahim, N. E.Wu, D.Shapiro, M. G.2025-11-06doi:10.1101/2025.11.06.686050Cold Spring Harbor Laboratory Press2025-11-06
<![CDATA[
Identification of distinct cDC2 subpopulations that direct microbiota-specific T cell differentiation
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https://biorxiv.org/cgi/content/short/2025.11.04.686414v1?rss=1"
Carroll, S. L.Ly, A.Liu, A. K.Canesso, M. C. C.Victora, G. D.Mucida, D.Barton, G. M.2025-11-05doi:10.1101/2025.11.04.686414Cold Spring Harbor Laboratory Press2025-11-05
<![CDATA[
Functional divergence of Capicua isoforms explains differential tissue vulnerability in neurological disease
]]>
https://biorxiv.org/cgi/content/short/2025.11.05.686788v1?rss=1"
Lee, H.Gonzalez, E. V.Rivera, E. M.Durham, M. A.Richman, R.Chu, E. H.- Y.Xia, K.Chen, H.Liu, Z.Veeraragavan, S.Shivanna, B.Zoghbi, H. Y.2025-11-05doi:10.1101/2025.11.05.686788Cold Spring Harbor Laboratory Press2025-11-05
<![CDATA[
Large-scale discovery of neural enhancers for cis-regulation therapies
]]>
https://biorxiv.org/cgi/content/short/2025.11.04.686611v1?rss=1"
McDiarmid, T. A.Page, N. F.Chardon, F. M.Daza, R. M.Chen, G. T.Kosicki, M.James, L. M.Nourie, H. C.Laboy-Cintron, D.Lee, A. S.Vij, P.Calderon, D.Lalanne, J.-B.Martin, B. K.Fink, K.Talkowski, M. E.Muotri, A. R.Philpot, B. D.Pennacchio, L. A.Geschwind, D. H.Sanders, S. J.Ahituv, N.Shendure, J.2025-11-05doi:10.1101/2025.11.04.686611Cold Spring Harbor Laboratory Press2025-11-05
<![CDATA[
A membrane-bound nuclease directly cleaves phage DNA during genome injection
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https://biorxiv.org/cgi/content/short/2025.11.03.685801v1?rss=1"
Saxton, D. S.Deweirdt, P. C.Doering, C. R.Roney, I. J.Laub, M. T.2025-11-03doi:10.1101/2025.11.03.685801Cold Spring Harbor Laboratory Press2025-11-03
<![CDATA[
Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16
]]>
https://biorxiv.org/cgi/content/short/2025.11.03.685595v1?rss=1"
Kretsch, R. C.Posani, E.Baulin, E. F.Bujnicki, J. M.Bussi, G.Cheatham, T. E.Chen, S.-J.Elofsson, A.Farsani, M. A.Fisher, O. N.Gromiha, M. M.Gupta, A.Hamada, M.Harini, K.Hu, G.Huang, D.Iwakiri, J.Jain, A.Kagaya, Y.Kihara, D.Kmiecik, S.Krishnan, S. R.Kurisaki, I.Languin-Cattoen, O.Li, J.Li, S.Malekzadeh, K.Nakamura, T.Ni, W.Nithin, C.Palo, M. Z.Park, J. H.Pilla, S. P.Poblete, S.Pucci, F.Punuru, P.Saha, A.Sato, K.Srivastava, A.Terashi, G.Tugolukova, E.Verburgt, J.Wuyun, Q.Zerze, G. H.Zhang, K.Zhang, S.Zhen2025-11-03doi:10.1101/2025.11.03.685595Cold Spring Harbor Laboratory Press2025-11-03
<![CDATA[
Chromosome-scale genome assembly and annotation of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae)
]]>
https://biorxiv.org/cgi/content/short/2025.10.31.685973v1?rss=1"
Kataoka, K.Sanno, R.Gaczorek, T.Bhattarai, U. R.Ito, Y.Inoue, S.Yura, K.Asahi, T.Ylla, G.Mito, T.Extavour, C. G.2025-11-03doi:10.1101/2025.10.31.685973Cold Spring Harbor Laboratory Press2025-11-03
<![CDATA[
Adapting CRISPR-associated transposons for rapid and high-throughput reverse genetics
]]>
https://biorxiv.org/cgi/content/short/2025.10.31.685825v1?rss=1"
5,200 guides targeting 88 genes in E. coli across twelve nutrient conditions, accurately identifying genes with condition-specific fitness effects. The simplicity, speed, and throughput of MultiCAST make genome-scale functional screens more accessible across a wide range of bacterial species.
SignificanceEfficient gene disruption is essential for understanding bacterial gene function, but traditional genetic approaches are labor-intensive and generally not well-suited for high-throughput studies. We developed MultiCAST, a simple and scalable method that harnesses guide RNA-directed CRISPR-associated transposons for targeted bacterial gene disruption. MultiCAST enables single and pooled transposon mutagenesis in a single step and eliminates the need for complex sequencing library preparation protocols by using the guide sequence as a quantifiable surrogate for mutant abundance. This approach allows thousands of mutants to be generated and screened simultaneously across multiple conditions using only amplicon sequencing. By dramatically reducing the time, cost, and complexity of reverse genetics, MultiCAST opens new possibilities for genome-scale functional studies, accelerating the discovery of bacterial gene functions.
]]>Basta, D. W.Zingl, F. G.Yang, Y.Nguyen, K. T.Liu, Y.-Y.Waldor, M. K.2025-11-01doi:10.1101/2025.10.31.685825Cold Spring Harbor Laboratory Press2025-11-01
<![CDATA[
B lymphocytes that enter the germinal center late preferentially differentiate into memory cells that recognize subdominant epitopes
]]>
https://biorxiv.org/cgi/content/short/2025.10.30.685663v1?rss=1"
Zhou, P.Hartweger, H.MacLean, A. J.Ramos, V.Yao, K.-h.Hernandez, B.Wang, Z.Gazumyan, A.Nussenzweig, M. C.2025-11-01doi:10.1101/2025.10.30.685663Cold Spring Harbor Laboratory Press2025-11-01
<![CDATA[
Co-opting the bacterial lipoprotein pathway in the biosynthesis of a lipidated macrocyclic peptide
]]>
https://biorxiv.org/cgi/content/short/2025.10.31.685832v1?rss=1"
Chen, J. Y.Zhu, L.Zhang, K. Y.Berthold, D. A.van der Donk, W. A.2025-11-01doi:10.1101/2025.10.31.685832Cold Spring Harbor Laboratory Press2025-11-01
<![CDATA[
Lipid bilayer thinning near a ubiquitin ligase selects ER membrane proteins for degradation
]]>
https://biorxiv.org/cgi/content/short/2025.10.31.685944v1?rss=1"
Pisa, R.Rapoport, T. A.2025-11-01doi:10.1101/2025.10.31.685944Cold Spring Harbor Laboratory Press2025-11-01
<![CDATA[
Oxidative Peptide Backbone Cleavage by a HEXXH Enzyme During RiPP Biosynthesis
]]>
https://biorxiv.org/cgi/content/short/2025.10.30.685615v1?rss=1"
Ouyang, Y.Yu, Y.Zhu, L.van der Donk, W.2025-10-31doi:10.1101/2025.10.30.685615Cold Spring Harbor Laboratory Press2025-10-31
<![CDATA[
Trimodal brain-wide ultrasound imaging of brain-tumor interaction
]]>
https://biorxiv.org/cgi/content/short/2025.10.29.685462v1?rss=1"
Rabut, C.Shivaei, S.Heiles, B.Shapiro, M. G.2025-10-31doi:10.1101/2025.10.29.685462Cold Spring Harbor Laboratory Press2025-10-31
<![CDATA[
Sleep-dependent clearance of brain lipids by peripheral blood cells
]]>
https://biorxiv.org/cgi/content/short/2025.10.30.685668v1?rss=1"
Cho, B.Youngstrom, D. E.Killiany, S.Guevara, C.Randolph, C. E.Beveridge, C. H.Saklani, P.Chopra, G.Sehgal, A.2025-10-31doi:10.1101/2025.10.30.685668Cold Spring Harbor Laboratory Press2025-10-31
<![CDATA[
HaloTrace: A spatiotemporally precise fluorescent readout of blood-brain barrier permeability in mice
]]>
https://biorxiv.org/cgi/content/short/2025.10.30.685531v1?rss=1"
Zucker, H. L.Konshina, E.Mitchell, P.Gu, C.2025-10-31doi:10.1101/2025.10.30.685531Cold Spring Harbor Laboratory Press2025-10-31
<![CDATA[
Microbial-inspired antidotes to repurpose toxic compounds as antibiotics
]]>
https://biorxiv.org/cgi/content/short/2025.10.31.685078v1?rss=1"
Samad, T. S.Ngambenjawong, C.Ko, H.Patel, S.DeAgazio, C.Fleming, H. E.Bhatia, S. N.2025-10-31doi:10.1101/2025.10.31.685078Cold Spring Harbor Laboratory Press2025-10-31
<![CDATA[
larch: mapping the parsimony-optimal landscape of trees for directed exploration
]]>
https://biorxiv.org/cgi/content/short/2025.10.29.685337v1?rss=1"
Barker, M.Milanov, O.Dumm, W.Rich, D.Turakhia, Y.Matsen, F. A.2025-10-31doi:10.1101/2025.10.29.685337Cold Spring Harbor Laboratory Press2025-10-31
<![CDATA[
Phage display-mediated immuno-PCR to detect low-abundance secreted proteins in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2025.10.31.685841v1?rss=1"
Han, M.Xia, B.Kim, A.-R.Filine, E.Stoneburner, E.Miao, T.Liu, Y.Zirin, J.Perrimon, N.2025-10-31doi:10.1101/2025.10.31.685841Cold Spring Harbor Laboratory Press2025-10-31
<![CDATA[
Human Coronavirus HKU1 Neutralizing Monoclonal Antibodies Target Diverse Epitopes Within and Around the TMPRSS2 Receptor Binding Site
]]>
https://biorxiv.org/cgi/content/short/2025.10.29.685445v1?rss=1"
Wang, L.Joseph, J.Vasquez, S.Wrapp, D.Sheahan, T. P.Dzuvor, C. K. O.Rosen, O.Kirchdoerfer, R.Abiona, O. M.Hammond, C.Shi, W.Moak, S. P.Kong, W.-P.Zhang, Y.Eso, M. R.Brown, A. J.Ward, A.Baric, R. S.McLellan, J. S.Pierson, T. C.Mascola, J.Graham, B. S.Yassine, H.Barnes, C. O.Corbett-Helaire, K. S.2025-10-30doi:10.1101/2025.10.29.685445Cold Spring Harbor Laboratory Press2025-10-30
<![CDATA[
An unusual ring pattern in the Rosβ lanthipeptide of the two-component lantibiotic roseocin
]]>
https://biorxiv.org/cgi/content/short/2025.10.27.684949v1?rss=1"
View larger version (20K):
org.highwire.dtl.DTLVardef@125226borg.highwire.dtl.DTLVardef@f6a170org.highwire.dtl.DTLVardef@1e0e57corg.highwire.dtl.DTLVardef@1fa4c8d_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Desormeaux, E. K.Zhu, L.Luo, Y.Sareen, D.van der Donk, W. A.2025-10-28doi:10.1101/2025.10.27.684949Cold Spring Harbor Laboratory Press2025-10-28
<![CDATA[
Alternative splicing of synaptotagmin 7 regulates oligomerization and short-term synaptic plasticity
]]>
https://biorxiv.org/cgi/content/short/2025.10.27.684894v1?rss=1"
Mehta, N.Larson, D. T.Salaka, R. J.Wozney, M.Subramani, S.Mishra, S.Kaur, S.Jain, A.Chapman, E. R.2025-10-28doi:10.1101/2025.10.27.684894Cold Spring Harbor Laboratory Press2025-10-28
<![CDATA[
Faf1 accelerates p97-mediated protein unfolding by promoting ubiquitin engagement
]]>
https://biorxiv.org/cgi/content/short/2025.10.27.684972v1?rss=1"
Liao, Z.Arkinson, C.Martin, A.2025-10-28doi:10.1101/2025.10.27.684972Cold Spring Harbor Laboratory Press2025-10-28
<![CDATA[
Tissue-specific regulation of PNPLA3 promotes lipid remodeling in response to dietary and temperature stress
]]>
https://biorxiv.org/cgi/content/short/2025.10.27.684800v1?rss=1"
19-fold in brown adipose tissue (BAT), despite causing a >75% reduction in Pnpla3 mRNA, indicating robust post-translational regulation. In BAT, adrenergic signaling via cAMP/PKA and PI3K/AKT elevated PNPLA3 by reducing proteasomal degradation. PNPLA3 expression correlated with depletion of TG-long-chain polyunsaturated fatty acids (TG-LCPUFAs) in both liver and BAT, consistent with a role in lipid remodeling.
ConclusionsThese findings reveal striking tissue- and context-specific regulation of PNPLA3, but a conserved association between its expression and TG-LCPUFAs levels, suggesting that PNPLA3 modulates lipid remodeling in response to metabolic stress and that disrupting this function may contribute to SLD susceptibility.
Impact and implicationsDespite being the strongest genetic risk factor for SLD, PNPLA3s physiological role remains unclear. Using mouse models, this study reveals that PNPLA3 is regulated in a tissue-specific manner in response to feeding and cold exposure, thereby promoting remodeling of cellular lipids to adapt to dietary and environmental challenges. The localization of PNPLA3 action and its tissue-specific regulation are directly relevant to hepatologists and metabolic researchers aiming to understand its influence on intracellular lipid composition and its effects on disease susceptibility. Moreover, modulation of PNPLA3 turnover--and its impact on LCPUFAs remodeling--emerges as a potential therapeutic strategy for regulating lipid homeostasis in SLD.
Graphical Abstract
O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/684800v2_ufig1.gif" ALT="Figure 1">
View larger version (42K):
org.highwire.dtl.DTLVardef@ee6ac7org.highwire.dtl.DTLVardef@a45d74org.highwire.dtl.DTLVardef@f39929org.highwire.dtl.DTLVardef@cc826b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPNPLA3 is regulated in a highly tissue-specific manner in mice.
C_LIO_LIIn liver, feeding-but not cold exposure-induces PNPLA3 primarily through transcriptional mechanisms.
C_LIO_LIIn adipose tissue, cold exposure-but not feeding-induces PNPLA3 through post-transcriptional mechanisms.
C_LIO_LIIn adipose tissue, cold exposure increases PNPLA3 despite a reduction in Pnpla3 mRNA.
C_LIO_LIPNPLA3 remodels lipids in liver and adipose tissue to maintain lipid homeostasis, a process disrupted in SLD.
C_LI
]]>Wu, P.Wang, Y.Cohen, J. C.Hobbs, H. H.2025-10-27doi:10.1101/2025.10.27.684800Cold Spring Harbor Laboratory Press2025-10-27
<![CDATA[
The proton motive force maintains mtDNA euploidy by balancing mtDNA replication with cell proliferation
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https://biorxiv.org/cgi/content/short/2025.10.27.684790v1?rss=1"
Rath, S. P.Mootha, V. K.2025-10-27doi:10.1101/2025.10.27.684790Cold Spring Harbor Laboratory Press2025-10-27
<![CDATA[
Neural control of coordinated wing and leg movements during a terrestrial threat display
]]>
https://biorxiv.org/cgi/content/short/2025.10.25.684556v1?rss=1"
Cao, S.Anderson, D. J.2025-10-26doi:10.1101/2025.10.25.684556Cold Spring Harbor Laboratory Press2025-10-26
<![CDATA[
pH-dependent regulation in SLC38A9
]]>
https://biorxiv.org/cgi/content/short/2025.10.24.684471v1?rss=1"
Mu, X.Sae Her, A.Gonen, T.2025-10-25doi:10.1101/2025.10.24.684471Cold Spring Harbor Laboratory Press2025-10-25
<![CDATA[
Lipid composition and mechanical force underlie multi-modal regulation of Piezo1 gating
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https://biorxiv.org/cgi/content/short/2025.10.24.684433v1?rss=1"
Vaisey, G.MacKinnon, R.2025-10-25doi:10.1101/2025.10.24.684433Cold Spring Harbor Laboratory Press2025-10-25
<![CDATA[
Environmental Novelty Modulates Rapid Cortical Plasticity During Navigation
]]>
https://biorxiv.org/cgi/content/short/2025.10.21.683723v1?rss=1"
Attinger, A.Drinnenberg, A.Dong, C.Ramakrishnan, C.Tasic, B.Daigle, T. L.Siverts, L.Quirin, S.Zeng, H.Deisseroth, K.Giocomo, L. M.2025-10-22doi:10.1101/2025.10.21.683723Cold Spring Harbor Laboratory Press2025-10-22
<![CDATA[
Separating selection from mutation in antibody language models
]]>
https://biorxiv.org/cgi/content/short/2025.10.21.683652v1?rss=1"
Matsen, F. A.Dumm, W.Sung, K.Johnson, M. M.Rich, D.Starr, T.Song, Y. S.Fukuyama, J.Haddox, H. K.2025-10-22doi:10.1101/2025.10.21.683652Cold Spring Harbor Laboratory Press2025-10-22
<![CDATA[
Large-scale cellular-resolution read/write of activity enables discovery of cell types defined by complex circuit properties
]]>
https://biorxiv.org/cgi/content/short/2025.10.21.683734v1?rss=1"
Drinnenberg, A.Attinger, A.Raventos, A.Ramakrishnan, C.Gharagoz, B. E.Cordero, A.Jo, Y.Siverts, L.Daigle, T. L.Tasic, B.Zeng, H.Giocomo, L. M.Quirin, S.Ganguli, S.Deisseroth, K.2025-10-22doi:10.1101/2025.10.21.683734Cold Spring Harbor Laboratory Press2025-10-22
<![CDATA[
Networks of sexually dimorphic neurons that regulate social behaviors in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2025.10.21.683766v1?rss=1"
Rubin, G. M.Managan, C.Dreher, M.Kim, E.Miller, S.Boone, K.Robie, A.Taylor, A. L.Branson, K.Schretter, C. E.Otopalik, A. G.2025-10-22doi:10.1101/2025.10.21.683766Cold Spring Harbor Laboratory Press2025-10-22
<![CDATA[
Repeated COVID-19 vaccine boosters elicit variant-specific memory B cells in humans
]]>
https://biorxiv.org/cgi/content/short/2025.10.16.682893v1?rss=1"
Tortorici, M. A.Sprouse, K. R.Addetia, A.Brown, J. T.Harteloo, A.Elias-Warren, A.Chiu, H. Y.Veesler, D.2025-10-20doi:10.1101/2025.10.16.682893Cold Spring Harbor Laboratory Press2025-10-20
<![CDATA[
A genetically-defined population of amygdalofugal neurons promotes suckling and early postnatal growth
]]>
https://biorxiv.org/cgi/content/short/2025.10.18.683193v1?rss=1"
Moore, J.Bachmann, L.McElvain, L.Pfaff, S.Dulac, C.2025-10-18doi:10.1101/2025.10.18.683193Cold Spring Harbor Laboratory Press2025-10-18
<![CDATA[
Tbx genes influence early gene expression and photoreceptor patterning in the chick retina
]]>
https://biorxiv.org/cgi/content/short/2025.10.18.683251v1?rss=1"
Ayten, M.Joisher, H. N. V.Cepko, C.2025-10-18doi:10.1101/2025.10.18.683251Cold Spring Harbor Laboratory Press2025-10-18
<![CDATA[
Insights into substrate binding and utilization by hyaluronan synthase
]]>
https://biorxiv.org/cgi/content/short/2025.10.17.683186v1?rss=1"
Stephens, Z.Karasinska, J.Zimmer, J.2025-10-18doi:10.1101/2025.10.17.683186Cold Spring Harbor Laboratory Press2025-10-18
<![CDATA[
Structures of folding intermediates on BAM show diverse substrates fold by a uniform mechanism
]]>
https://biorxiv.org/cgi/content/short/2025.10.16.682720v1?rss=1"
Thomson, B. D.Marquez, M. D.Rawson, S.dos Santos, T. M. A.Harrison, S. C.Kahne, D.2025-10-17doi:10.1101/2025.10.16.682720Cold Spring Harbor Laboratory Press2025-10-17
<![CDATA[
A line attractor maintains aggressiveness during feeding in hangry mice
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https://biorxiv.org/cgi/content/short/2025.10.16.682711v1?rss=1"
Kim, J. J.Nair, A.Coria, N.Huynh, S.Vinograd, A.Xu, J.Liu, M.Anderson, D. J.2025-10-17doi:10.1101/2025.10.16.682711Cold Spring Harbor Laboratory Press2025-10-17
<![CDATA[
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
]]>
https://biorxiv.org/cgi/content/short/2025.10.16.682844v1?rss=1"
Tang, S.Ramirez, J. L.Mestre, M. R.Zhang, D. J.Wang, M.Wiegand, T.Ma, Y.Jovanovic, M.Pinilla-Redondo, R.Sternberg, S. H.2025-10-16doi:10.1101/2025.10.16.682844Cold Spring Harbor Laboratory Press2025-10-16
<![CDATA[
Functional and antigenic constraints on the Nipah virus fusion protein
]]>
https://biorxiv.org/cgi/content/short/2025.10.15.682664v1?rss=1"
Larsen, B. B.Harari, S.Gen, R.Stewart, C.Veesler, D.Bloom, J. D.2025-10-15doi:10.1101/2025.10.15.682664Cold Spring Harbor Laboratory Press2025-10-15
<![CDATA[
An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics
]]>
https://biorxiv.org/cgi/content/short/2025.10.13.682236v1?rss=1"
Picard, C. L.Ichino, L.Buckley, T. J.Boone, B. A.Abuhanna, K. D.Zhang, Y.Behrendt, N. J.May Lei Soe, S.Luo, C.Jacobsen, S. E.2025-10-15doi:10.1101/2025.10.13.682236Cold Spring Harbor Laboratory Press2025-10-15
<![CDATA[
Nascent CUT&Tag captures transcription factor binding after chromatin duplication
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https://biorxiv.org/cgi/content/short/2025.10.13.682212v1?rss=1"
Wooten, M.Nguyen, K.Takushi, B. N.Ahmad, K.Henikoff, S.2025-10-15doi:10.1101/2025.10.13.682212Cold Spring Harbor Laboratory Press2025-10-15
<![CDATA[
Natural evolution of intermale sexual behavior by multiple pheromone switches among Drosophila species
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https://biorxiv.org/cgi/content/short/2025.10.14.682417v1?rss=1"
Ouadah, Y.Naragon, T. H.Smihula, H.Behrman, E. L.Khallaf, M. A.Ding, Y.Stern, D. L.Parker, J.Anderson, D. J.2025-10-15doi:10.1101/2025.10.14.682417Cold Spring Harbor Laboratory Press2025-10-15
<![CDATA[
Ecological cues orchestrate concerted courtship in a Drosophila host specialist
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https://biorxiv.org/cgi/content/short/2025.10.13.681913v1?rss=1"
Brand, P.Keller, K.Coleman, R. T.Eghbali, N. B.Zylka, S.Prieto-Godino, L. L.Ruta, V.2025-10-14doi:10.1101/2025.10.13.681913Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
The mycomembrane proteins PorH and ProtX are inserted at polar growth zones and linked to the cell wall
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https://biorxiv.org/cgi/content/short/2025.10.14.682376v1?rss=1"
Hart, E. M.de Bruin, D. A.Marando, V. M.Alemany, M. A.Snow, E. D.Schultz, B. J.Kuru, E.Walker, S.Vettiger, A.Bernhardt, T. G.2025-10-14doi:10.1101/2025.10.14.682376Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
Transcriptional targets of SPEECHLESS and FAMA control guard cell division and expansion in the late stomatal lineage
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https://biorxiv.org/cgi/content/short/2025.10.12.681868v1?rss=1"
Gonzalez-Suarez, P.Hilbers, Y.Budrys, A.Liu, A.Richter, S.Bergmann, D. C.Smit, M. E.2025-10-14doi:10.1101/2025.10.12.681868Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
A reference brain for the clonal raider ant
]]>
https://biorxiv.org/cgi/content/short/2025.10.13.679875v1?rss=1"
Frank, D. D.Lopes, L. E.Mohanta, R.Seckler, I.Lacroix, I.Kronauer, D. J. C.2025-10-14doi:10.1101/2025.10.13.679875Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
The complete genome of a songbird
]]>
https://biorxiv.org/cgi/content/short/2025.10.14.682431v1?rss=1"
Formenti, G.Jain, N.Medico, J. A.Sollitto, M.Antipov, D.Balacco, J.Barcellos, S.Biegler, M. T.Borges, I.Chang, J. K.Chen, Y.Cheng, H.Conceicao, H. B.Davenport, M.De Oliveira, L. C.Duarte, E.Durham, G. P.Fenn, J.Forde, N.Kim, J.Komissarov, A.Koo, B.Koren, S.Galante, P. A. F.Gerhardt, K.Giani, A. M.Giunta, S.Larkin, D.Lee, C.Li, H.Makova, K.Masterson, P.Murphy, T.McCaffrey, K.Mercuri, R. L. V.Na, Y.O Connell, M. J.Ou, S.Phillippy, A. M.Popova, M.Rhie, A.Ruiz-Ruano, F. J.Secomandi, S.Smeds, L.Suh, A.Tilley,2025-10-14doi:10.1101/2025.10.14.682431Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
Primary metabolism determines the outcome of salicylic acid-mediated immune induction
]]>
https://biorxiv.org/cgi/content/short/2025.10.13.682132v1?rss=1"
Zhang, Q.Xie, Y.Karapetyan, S.Wang, J.Mwimba, M.Yoo, H.Dong, X.2025-10-14doi:10.1101/2025.10.13.682132Cold Spring Harbor Laboratory Press2025-10-14
<![CDATA[
Oxidative stress sensing by the translation elongation machinery promotes production of detoxifying selenoproteins
]]>
https://biorxiv.org/cgi/content/short/2025.10.13.682107v1?rss=1"
Rehfeld, F.Lundstrom, C.Zhang, H.Mendell, J. T.2025-10-13doi:10.1101/2025.10.13.682107Cold Spring Harbor Laboratory Press2025-10-13
<![CDATA[
Multiplex design and discovery of proximity handles for programmable proteome editing
]]>
https://biorxiv.org/cgi/content/short/2025.10.13.681693v1?rss=1"
Suiter, C. C.Ahn, G.Chiu, M.Fu, Y.Sadre, S.Simon, J. J.Lee, D. S.Fowler, D. M.Maly, D. J.Baker, D.Shendure, J.2025-10-13doi:10.1101/2025.10.13.681693Cold Spring Harbor Laboratory Press2025-10-13
<![CDATA[
Direct cell reprogramming by a designed agonist inducing HER2-FGFR proximity
]]>
https://biorxiv.org/cgi/content/short/2025.10.12.681903v1?rss=1"
Keshri, R.Exposit, M.Abedi, M.R Hicks, D.Foreman, Z.Phal, A.Lim, Y. C.Barrett, P.Sniezek, C.Lin, J.Schlichthaerle, T.J Robinson, A.Detraux, D.Ching, T. C.Wu, K.Coventry, B.Chang, L.S.T. Smith, A.L Mack, D.K Schweppe, D.Martin, B. E.Hristova, K.Mathieu, J.Baker, D.Ruohola-Baker, H.2025-10-13doi:10.1101/2025.10.12.681903Cold Spring Harbor Laboratory Press2025-10-13
<![CDATA[
Geometric Tuning of Cytokine Receptor Association Modulates Synthetic Agonist Signaling
]]>
https://biorxiv.org/cgi/content/short/2025.10.12.681819v1?rss=1"
Exposit, M.Abedi, M.Krishnakumar, A.Jain, S.Yu, T.-Y.Hercus, T. R.Mathew, D.Gray-Gaillard, S.Chen, Z.Grubbe, W. S.Favor, A.Kan, W. L.Schlichthaerle, T.Chen, W.Parker, M. W.Mendoza, J. L.Lopez, A. F.Wherry, E. J.Baker, D.2025-10-13doi:10.1101/2025.10.12.681819Cold Spring Harbor Laboratory Press2025-10-13
<![CDATA[
High-Throughput De Novo Protein Design Yields Novel Immunomodulatory Agonists
]]>
https://biorxiv.org/cgi/content/short/2025.10.12.681920v1?rss=1"
Abedi, M.Exposit, M.Coventry, B.Mathew, D.Jain, S.Krishnakumar, A.Goreshnik, I.Gray-Gaillard, S.Lunn-Halbert, M.Yu, T.-Y.Glögl, M.Mitchell, U.Keshri, R.Chun, J. H.Ruohola-Baker, H.Wherry, E. J.Baker, D.2025-10-13doi:10.1101/2025.10.12.681920Cold Spring Harbor Laboratory Press2025-10-13
<![CDATA[
A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome
]]>
https://biorxiv.org/cgi/content/short/2025.10.10.681672v1?rss=1"
Kim, A.-R.Huang, K.Johnson, J. L.Yaron-Barir, T. M.Wang, K.Cantley, L. C.Hu, Y.Perrimon, N.2025-10-12doi:10.1101/2025.10.10.681672Cold Spring Harbor Laboratory Press2025-10-12
<![CDATA[
A human arteriovenous differentiation roadmap reveals vein developmental mechanisms and vascular effects of viruses
]]>
https://biorxiv.org/cgi/content/short/2025.10.11.681838v1?rss=1"
Ang, L. T.Zheng, S. L.Liu, K. J.Masaltseva, A.Winters, J.von Creytz, I.Jha, S. K.Yin, Q.Qian, C.Xiong, X.Dailamy, A.Xi, E.Alcocer, J. C.Sorensen, D. W.She, R.Smolyar, K.Szumska, D.Nornes, S.Martin, R. M.Lesch, B. J.Restrepo, N. K.Sun, W.Weissman, J. S.Lickert, H.Porteus, M. P.Skylar-Scott, M. A.Mosimann, C.Sumanas, S.De Val, S.Prescott, J. B.Red-Horse, K.Loh, K. M.2025-10-12doi:10.1101/2025.10.11.681838Cold Spring Harbor Laboratory Press2025-10-12
<![CDATA[
Ultra-mild bisulfite outperforms EM-seq for 5-methylcytosine detection with low input DNA
]]>
https://biorxiv.org/cgi/content/short/2025.10.09.681456v1?rss=1"
He, C.Dai, Q.Baldwin, T.Lyu, R.Daniels, B.Ye, C.Cao, C.Zhu, C.Fan, D.Lin, L.Liu, Y.Wang, Y.2025-10-10doi:10.1101/2025.10.09.681456Cold Spring Harbor Laboratory Press2025-10-10
<![CDATA[
mRNA poly(A)-tail length is a battleground for coronavirus-host competition
]]>
https://biorxiv.org/cgi/content/short/2025.10.09.680815v1?rss=1"
Latifkar, A.Levdansky, Y.Balabaki, A.Nyeo, S.Valkov, E.Bartel, D.2025-10-10doi:10.1101/2025.10.09.680815Cold Spring Harbor Laboratory Press2025-10-10
<![CDATA[
Kinase KEY1 controls pyrenoid condensate size throughout the cell cycle by disrupting phase separation interactions
]]>
https://biorxiv.org/cgi/content/short/2025.10.09.681382v1?rss=1"
He, S.Lemma, L. M.Martinez-Calvo, A.He, G.Hennacy, J. H.Wang, L.Ergun, S. L.Rai, A. K.Wang, C.Bunday, L.Kayser-Browne, A.Wang, Q.Brangwynne, C. P.Wingreen, N. S.Jonikas, M. C.2025-10-10doi:10.1101/2025.10.09.681382Cold Spring Harbor Laboratory Press2025-10-10
<![CDATA[
Endosome-associated Rab GTPases control distinct aspects of neural circuit assembly
]]>
https://biorxiv.org/cgi/content/short/2025.10.09.681358v1?rss=1"
Dong, K. X.Ji, H.Luginbuhl, D. J.Luo, L.McLaughlin, C.2025-10-10doi:10.1101/2025.10.09.681358Cold Spring Harbor Laboratory Press2025-10-10
<![CDATA[
Sexual dimorphism in the complete connectome of the Drosophila male central nervous system
]]>
https://biorxiv.org/cgi/content/short/2025.10.09.680999v1?rss=1"
Berg, S.Beckett, I. R.Costa, M.Schlegel, P.Januszewski, M.Marin, E. C.Nern, A.Preibisch, S.Qiu, W.Takemura, S.-y.Fragniere, A. M. C.Champion, A. S.Adjavon, D.-Y.Cook, M.Gkantia, M.Hayworth, K. J.Huang, G. B.Kampf, F.Katz, W. T.Lu, Z.Ordish, C.Paterson, T.Stuerner, T.Trautman, E. T.Whittle, C. R.Burnett, L. E.Hoeller, J.Li, F.Loesche, F.Morris, B. J.Pietzsch, T.Pleijzier, M. W.Silva, V.Yin, Y.Ali, I.Badalamente, G.Bates, A. S.Bogovic, J.Brooks, P.Cachero, S.Canino, B. S.Chaisrisawatsuk, B.Clements, J.Crowe, A.2025-10-09doi:10.1101/2025.10.09.680999Cold Spring Harbor Laboratory Press2025-10-09
<![CDATA[
Induction of menstruation in mice reveals the regulation of menstrual shedding
]]>
https://biorxiv.org/cgi/content/short/2025.10.08.681007v1?rss=1"
Cevrim, C.Hilgert, N. J.Kaage, A. M.Russell, A. J. C.Goldstein, A. E.Ang, C. J.Gable, J. L. R.Bagamery, L. E.Breznik, A.Di Bella, D. J.Talay, M.Peng, J.O'Neill, K. E.Chen, F.Eddy, S. R.McKinley, K. L.2025-10-09doi:10.1101/2025.10.08.681007Cold Spring Harbor Laboratory Press2025-10-09
<![CDATA[
Ingestion-activated CGRP neurons control learning but not satiety
]]>
https://biorxiv.org/cgi/content/short/2025.10.08.681275v1?rss=1"
Jarvie, B. C.Ravi, A.Nanavati, R.Qui, L.Ly, T.Oh, J. Y.Barnhill, O. K.Knight, Z. A.2025-10-09doi:10.1101/2025.10.08.681275Cold Spring Harbor Laboratory Press2025-10-09
<![CDATA[
A family of lethal exotoxins defined by cell entry via the Attractin receptor
]]>
https://biorxiv.org/cgi/content/short/2025.10.08.681221v1?rss=1"
Viswanatha, R.Lee, D.Robins, W. P.Mameli, E.Hu, Y.Kim, A.-R.Hashmi, Y.Nishida, H.Prakash, G.Butnaru, M.Churchman, L. S.Mohr, S.Mekalanos, J.Perrimon, N.2025-10-08doi:10.1101/2025.10.08.681221Cold Spring Harbor Laboratory Press2025-10-08
<![CDATA[
A TCR-mimic bispecific antibody reduces HIV-1 provirus and delays viral rebound in HLA-matched humanized mice
]]>
https://biorxiv.org/cgi/content/short/2025.10.06.680344v1?rss=1"
Yuan, Z.Board, N. L.Zhao, M.Zu, G.Sengupta, S.Li, Q.Siliciano, J. D.Siliciano, R. F.Montaner, L. J.2025-10-06doi:10.1101/2025.10.06.680344Cold Spring Harbor Laboratory Press2025-10-06
<![CDATA[
RNA sequence design and protein-DNA specificity prediction with NA-MPNN
]]>
https://biorxiv.org/cgi/content/short/2025.10.03.679414v1?rss=1"
Kubaney, A.Favor, A. H.McHugh, L.Mitra, R.Pecoraro, R.Dauparas, J.Glasscock, C.Baker, D.2025-10-04doi:10.1101/2025.10.03.679414Cold Spring Harbor Laboratory Press2025-10-04
<![CDATA[
Disentangling the importance of microbiological and physicochemical properties of Ethiopian field soils for the Striga seed bank and sorghum infestations
]]>
https://biorxiv.org/cgi/content/short/2025.10.03.680328v1?rss=1"
Taylor, T.Benti, G.Fernandes Alves Leite, M.Etalo, D.Lombard, L.AriasGiraldo, L.-M.Ryba, D.Sanow, S.Mostert, T.Martinez de la Parte, E.Macia-Vicente, J.Yimer, D.Tsega, U.Daska, J.van Doorn, R.Rosa Leite, R.Tessema, T.Crous, P. W.Kuramae, E.Raajimakers, J.Brady, S.2025-10-04doi:10.1101/2025.10.03.680328Cold Spring Harbor Laboratory Press2025-10-04
<![CDATA[
Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer
]]>
https://biorxiv.org/cgi/content/short/2025.10.01.679814v1?rss=1"
Liu, Y.Miao, T.Wang, A.Ezequiel, D.Kim, A.-R.Zhang, Z.Sun, X.Binari, R.Asara, J. M.Hu, Y.Goncalves, M.Janowitz, T.Perrimon, N.2025-10-03doi:10.1101/2025.10.01.679814Cold Spring Harbor Laboratory Press2025-10-03
<![CDATA[
Flow Autoencoders are Effective Protein Tokenizers
]]>
https://biorxiv.org/cgi/content/short/2025.10.01.679645v1?rss=1"
Dilip, R.Varshney, A.Zhang, E.Van Valen, D. A.2025-10-03doi:10.1101/2025.10.01.679645Cold Spring Harbor Laboratory Press2025-10-03
<![CDATA[
A regulatory region that controls Wnt gene expression following tissue injury is required for proper muscle regeneration
]]>
https://biorxiv.org/cgi/content/short/2025.10.01.679323v1?rss=1"
Logan, C. Y.Lim, X.Fish, M.Mizutani, M.Swain, B.Nusse, R.2025-10-03doi:10.1101/2025.10.01.679323Cold Spring Harbor Laboratory Press2025-10-03
<![CDATA[
De novo design of RNA and nucleoprotein complexes
]]>
https://biorxiv.org/cgi/content/short/2025.10.01.679929v1?rss=1"
Favor, A. H.Quijano, R.Chernova, E.Kubaney, A.Weidle, C.Esler, M. A.McHugh, L.Carr, A.Hsia, Y.Juergens, D.Carr, K. D.Kim, P. T.Politanska, Y.Sehgal, E.Kwon, P. S.Pecoraro, R. J.Glasscock, C.Borst, A. J.DiMaio, F.Stoddard, B. L.Baker, D.2025-10-02doi:10.1101/2025.10.01.679929Cold Spring Harbor Laboratory Press2025-10-02
<![CDATA[
Memory B cell Development in Response to mRNA SARS-CoV-2 and Nanoparticle Immunization in Mice
]]>
https://biorxiv.org/cgi/content/short/2025.10.01.679787v1?rss=1"
Wiatr, m.wang, z.Canis, M.Gazumyan, A.hernandez, B.Santos, G. S.Shawraz, S.lee, S.Bieniasz, P. D.Hatziioannou, T.Muecksch, F.Nussenzweig, M. C.2025-10-02doi:10.1101/2025.10.01.679787Cold Spring Harbor Laboratory Press2025-10-02
<![CDATA[
D. melanogaster meiotic driver Stellate compromises sperm development by impeding nuclear envelope remodeling
]]>
https://biorxiv.org/cgi/content/short/2025.09.29.679412v1?rss=1"
Meng, X. M.Yamashita, Y. M.2025-10-01doi:10.1101/2025.09.29.679412Cold Spring Harbor Laboratory Press2025-10-01
<![CDATA[
Rational Design of Multiclade Coronavirus Spike Immunodominant Domain Nanoparticles Elicit Broad Antibody Responses
]]>
https://biorxiv.org/cgi/content/short/2025.10.01.679649v1?rss=1"
Dzuvor, C. K. O.Moak, S.McManus, L. R.Thomas, A.Dzordzorme, A. E.Kim, T.Joseph, J.Foley, V.Gordon, I. J.Novik, L.Holman, L. A.Dropulic, L. K.McNamara, R. P.Corbett-Helaire, K. S.2025-10-01doi:10.1101/2025.10.01.679649Cold Spring Harbor Laboratory Press2025-10-01
<![CDATA[
De novo design of phospho-tyrosine peptide binders
]]>
https://biorxiv.org/cgi/content/short/2025.09.29.678898v1?rss=1"
Bauer, M. S.Zhang, J. Z.Wu, K.Lee, G. R.Coventry, B.Klupt, K. A.Shi, J.Brent, R. I.Li, X.Moller, C.Roullier, N.Vafeados, D. K.Kalvet, I.Skotheim, R. K.Zhu, S.Motmaen, A.Herrmann, L. C.Sturmfels, P.Tischer, D.Altae-Tran, H. R.Juergens, D.Krishna, R.Ahern, W.Yim, J.Bera, A. K.Kang, A.Joyce, E.Lu, A.Stewart, L.DiMaio, F.Baker, D.2025-09-30doi:10.1101/2025.09.29.678898Cold Spring Harbor Laboratory Press2025-09-30
<![CDATA[
Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer's Disease
]]>
https://biorxiv.org/cgi/content/short/2025.09.29.678849v1?rss=1"
Wang, W.Berube, P.Yang, B.Castanon, R.Bartlett, A.Komandur, K.Nery, J. R.Barragan, C.Kenworthy, M.Valadon, C.Altshul, J.Petrella, A.Chan, D.Chen, C.Acerbo, A. S.Luo, J.Jain, M.Soma, E.Chen, H.Liem, M.Marrin, M.O'Connor, C.Zemke, N.Oakley, D. H.Ren, B.Hyman, B. T.Ecker, J. R.2025-09-30doi:10.1101/2025.09.29.678849Cold Spring Harbor Laboratory Press2025-09-30
<![CDATA[
Computational design of pH-sensitive binders
]]>
https://biorxiv.org/cgi/content/short/2025.09.29.678932v1?rss=1"
Ahn, G.Coventry, B.Sadre, S.Haefner, E.Hu, J.Van, M.Huang, B.Sappington, I. W.Broerman, A. J.Lichtenstein, M.Glögl, M.Goreshnik, I.Vafeados, D.Baker, D.2025-09-29doi:10.1101/2025.09.29.678932Cold Spring Harbor Laboratory Press2025-09-29
<![CDATA[
The Sindbis virus nsP3 opal codon protects viral RNA and fitness by maintaining replication spherule integrity
]]>
https://biorxiv.org/cgi/content/short/2025.09.27.679005v1?rss=1"
Bhattacharya, T.Freeman, T. S.Alleman, E. M.Wang, F.Chechik, L.Emerman, M.Myles, K. M.Malik, H. S.2025-09-28doi:10.1101/2025.09.27.679005Cold Spring Harbor Laboratory Press2025-09-28
<![CDATA[
Atlas of Lysosomal Aging Reveals a Molecular Clock of Storage Disorder-Associated Metabolites
]]>
https://biorxiv.org/cgi/content/short/2025.09.25.678303v1?rss=1"
Puszynska, A. M.Nguyen, T. P.Cangelosi, A. L.Armani, A.Roberts, J. M.Singh, K. A.Cameron, J. C.Tseyang, T.Liu, G. Y.Lai, S.Sprenger, H.-G.Yang, J.Colgan, W. N.Kedir, J. F.Kajderowicz, K. M.Esantsi, T. K.Lu, Y. R.Waite, M.Kunchok, T.Lewis, C. A.Schulte, F.Bell, G. W.Sabatini, D. M.Weissman, J. S.2025-09-26doi:10.1101/2025.09.25.678303Cold Spring Harbor Laboratory Press2025-09-26
<![CDATA[
The Fd4 transcription factor translates transient spatial cues in progenitors into long-term lineage identity
]]>
https://biorxiv.org/cgi/content/short/2025.09.26.678798v1?rss=1"
Lai, S.-L.Doe, C. Q.2025-09-26doi:10.1101/2025.09.26.678798Cold Spring Harbor Laboratory Press2025-09-26
<![CDATA[
Alternating Angle Milling Suppresses Streaking Artifacts in FIB-SEM Imaging
]]>
https://biorxiv.org/cgi/content/short/2025.09.25.678572v1?rss=1"
Shtengel, G.Qiu, W.Arron, J. S.Crowe, A. S.Polilov, A. A.Karkali, K.Bleck, C. K. E.Hess, H. F.2025-09-26doi:10.1101/2025.09.25.678572Cold Spring Harbor Laboratory Press2025-09-26
<![CDATA[
Regulation of Glypican 6-mediated Wnt activation maintains TDP-43 nuclear localization in neurons
]]>
https://biorxiv.org/cgi/content/short/2025.09.24.678385v1?rss=1"
Zhang, N.Sockanathan, S.2025-09-25doi:10.1101/2025.09.24.678385Cold Spring Harbor Laboratory Press2025-09-25
<![CDATA[
EPOP and MTF2 Activate PRC2 Activity through DNA-sequence specificity
]]>
https://biorxiv.org/cgi/content/short/2025.09.25.678634v1?rss=1"
Granat, J.Liu, S.Popoca, L.Oksuz, O.Reinberg, D.2025-09-25doi:10.1101/2025.09.25.678634Cold Spring Harbor Laboratory Press2025-09-25
<![CDATA[
Simulated climate change magnifies genetic vulnerabilities from mutation load and maladaptation
]]>
https://biorxiv.org/cgi/content/short/2025.09.25.677362v1?rss=1"
Leventhal, L.Ruffley, M. R.Carnegie Field Consortium,Exposito-Alonso, M.2025-09-25doi:10.1101/2025.09.25.677362Cold Spring Harbor Laboratory Press2025-09-25
<![CDATA[
Dual-patterned pluripotent stem cells self-organize into a human embryo model with extended anterior-posterior patterning
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https://biorxiv.org/cgi/content/short/2025.09.25.678678v1?rss=1"
Shendure, J.Hamazaki, N.Liu, Z.Qiu, C.Kubo, C. A.Xu, S.Daza, R. M.Nichols, E.Yang, W.Vo, A.O'Neill, M. B.Lee, C.2025-09-25doi:10.1101/2025.09.25.678678Cold Spring Harbor Laboratory Press2025-09-25
<![CDATA[
Combining brainwide activity imaging and electron microscopy reveals novel nociceptive circuits
]]>
https://biorxiv.org/cgi/content/short/2025.09.25.678485v1?rss=1"
Randel, N.Wang, C.Clayton, M. S.Wang, K.Pang, S.Xu, S. C.Champion, A.Hess, H. F.Cardona, A.Keller, P. J.Zlatic, M.2025-09-25doi:10.1101/2025.09.25.678485Cold Spring Harbor Laboratory Press2025-09-25
<![CDATA[
Observing biological spatio-angular structures and dynamics with statistical image reconstruction and polarized fluorescence microscopy
]]>
https://biorxiv.org/cgi/content/short/2025.09.23.678164v1?rss=1"
Liu, J.Chandler, T.Li, Y.Agashe, A.Wei, M.Su, Y.Wu, Y.Baskin, T. I.Jaumouille, V.Chen, J.Xu, P.Ye, H.Zhu, W.Fischer, R. S.Swaminathan, V.Nain, A. S.Mehta, S. B.La Riviere, P. J.Shroff, H.Liu, H.Guo, M.2025-09-25doi:10.1101/2025.09.23.678164Cold Spring Harbor Laboratory Press2025-09-25
<![CDATA[
Composing trajectories for rapid inference of navigational goals
]]>
https://biorxiv.org/cgi/content/short/2025.09.24.678123v1?rss=1"
AbdelRahman, N. Y.Jiang, W.Coddington, L. T.Gong, S.Dudman, J. T.Hermundstad, A. M.2025-09-24doi:10.1101/2025.09.24.678123Cold Spring Harbor Laboratory Press2025-09-24
<![CDATA[
CDCA7 facilitates MET1-mediated CG DNA methylation maintenance in centromeric heterochromatin via histone H1
]]>
https://biorxiv.org/cgi/content/short/2025.09.22.677529v1?rss=1"
Wang, S.Li, T.Naish, M.Chuang, R.Lin, E. K.Fonkalsrud, C.Yan, H.Feng, S.Henderson, I. R.Jacobsen, S. E.2025-09-22doi:10.1101/2025.09.22.677529Cold Spring Harbor Laboratory Press2025-09-22
<![CDATA[
Dynamic changes in chromosome and nuclear architecture during maturation of normal and ALS C9orf72 motor neurons
]]>
https://biorxiv.org/cgi/content/short/2025.09.22.677835v1?rss=1"
Dekker, J.Uyan, O.Sambare, S.Oomen, M. E.Wightman, N.Schooley, A.Klim, J. R.Belaghzal, H.Aydemir, O.Akgol-Oksuz, B.Uslu, Z. S. A.Eggan, K.Brown, R. H.2025-09-22doi:10.1101/2025.09.22.677835Cold Spring Harbor Laboratory Press2025-09-22
<![CDATA[
Single-sequence deep learning delivers crystal-quality models of covalent K-Ras G12 hotspot complexes
]]>
https://biorxiv.org/cgi/content/short/2025.09.16.676163v1?rss=1"
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<![CDATA[
Murine models for triple-negative breast cancer with differential responsiveness to immunotherapy
]]>
https://biorxiv.org/cgi/content/short/2025.09.18.677171v1?rss=1"
Kalantzakos, T.Zhou, Y.Liu, X.Proehl, J.Durfee, C.Tamayo, I.Temiz, N. A.Troness, B.Soni, A.Gupta, H.Harris, R.2025-09-21doi:10.1101/2025.09.18.677171Cold Spring Harbor Laboratory Press2025-09-21
<![CDATA[
Spatial predictive coding in visual cortical neurons
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https://biorxiv.org/cgi/content/short/2025.09.17.676794v1?rss=1"
Zhang, Q.Grodem, S.Gracias, A.Lensjo, K. K.Fyhn, M.Stringer, C.Pachitariu, M.2025-09-19doi:10.1101/2025.09.17.676794Cold Spring Harbor Laboratory Press2025-09-19
<![CDATA[
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3
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https://biorxiv.org/cgi/content/short/2025.09.18.676967v1?rss=1"
Butcher, J. K. V.Krishna, R.Mitra, R.Brent, R. I.Li, Y.Corley, N.Kim, P.Funk, J.Mathis, S. V.Salike, S.Muraishi, A.Eisenach, H.Thompson, T. R.Chen, J.Politanska, Y.Sehgal, E.Coventry, B.Zhang, O.Qiang, B.Didi, K.Kazman, M.DiMaio, F.Baker, D.2025-09-18doi:10.1101/2025.09.18.676967Cold Spring Harbor Laboratory Press2025-09-18
<![CDATA[
PIEZO channels link mechanical forces to uterine contractions in parturition
]]>
https://biorxiv.org/cgi/content/short/2025.09.17.676899v1?rss=1"
Zhang, Y.Kini, S. A.Mishkanian, S. A.Luo, R.Seradj, S. H.Leung, V.Wang, Y.Rocio, S.-V. M.Keenan, W. T.Sonmez, U.Yarishkin, O.Sanchez-Alavez, M.Liu, Y.Jin, X.Lipomi, D. J.Li, Y.Petrascheck, M.Frolova, A. I.England, S. K.Patapoutian, A.2025-09-18doi:10.1101/2025.09.17.676899Cold Spring Harbor Laboratory Press2025-09-18
<![CDATA[
RiboCop surveils pre-rRNA processing by Dicer in cellular quiescence
]]>
https://biorxiv.org/cgi/content/short/2025.09.16.676644v1?rss=1"
Roche, B.Martienssen, R. A.2025-09-18doi:10.1101/2025.09.16.676644Cold Spring Harbor Laboratory Press2025-09-18
<![CDATA[
FoxP3 forms a head-to-head dimer in vivo and stabilizes its multimerization on adjacent microsatellites
]]>
https://biorxiv.org/cgi/content/short/2025.09.16.676304v1?rss=1"
Leng, F.Clark, R.Zhang, W.Viennet, T.Arthanari, H.Wang, X.Hur, s.2025-09-18doi:10.1101/2025.09.16.676304Cold Spring Harbor Laboratory Press2025-09-18
<![CDATA[
FixGrower: An efficient and robust curriculum for shaping fixation behavior in rodents
]]>
https://biorxiv.org/cgi/content/short/2025.09.12.675850v1?rss=1"
Breda, J. R.Charlton, J. A.Willock, J. M.Kopec, C. D.Brody, C. D.2025-09-17doi:10.1101/2025.09.12.675850Cold Spring Harbor Laboratory Press2025-09-17
<![CDATA[
Disruption of theta-timescale spiking impairs learning but spares hippocampal replay
]]>
https://biorxiv.org/cgi/content/short/2025.09.15.675587v1?rss=1"
Joshi, A.Comrie, A. E.Bray, S.Mankili, A.Guidera, J. A.Nevers, R.Sun, X.Monroe, E.Kharazia, V.Ly, R.Maya, D. A.Morales-Rodriguez, D.Yu, J.Kiseleva, A.Perez, V.Frank, L. M.2025-09-17doi:10.1101/2025.09.15.675587Cold Spring Harbor Laboratory Press2025-09-17
<![CDATA[
Human-specific tandem repeat in CACNA1C modulates responses to neuronal stimulation
]]>
https://biorxiv.org/cgi/content/short/2025.09.15.676436v1?rss=1"
Song, J. H.Birey, F.Hung, T.-C.Hall, N. A.Guenther, C. A.Chen, X.Alkuraya, I. F.Tunbridge, E. M.Haerty, W. `Pasca, S. P.Kingsley, D. M.2025-09-16doi:10.1101/2025.09.15.676436Cold Spring Harbor Laboratory Press2025-09-16
<![CDATA[
ALM enables contextual decision-making via dynamic reconfiguration of local circuits
]]>
https://biorxiv.org/cgi/content/short/2025.09.11.675319v1?rss=1"
Shen, J.Rungratsameetaweemana, N.Sharma, P.Peterka, D. S.Wu, H. Z.Shadlen, M. N.2025-09-16doi:10.1101/2025.09.11.675319Cold Spring Harbor Laboratory Press2025-09-16
<![CDATA[
Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching
]]>
https://biorxiv.org/cgi/content/short/2025.09.11.675606v1?rss=1"
Zhang, K.Grant, T.Grigorieff, N.2025-09-16doi:10.1101/2025.09.11.675606Cold Spring Harbor Laboratory Press2025-09-16
<![CDATA[
marApp: An R package and web portal to calculate mutations- and genetic diversity-area relationship for conservation
]]>
https://biorxiv.org/cgi/content/short/2025.09.09.675155v1?rss=1"
Lin, M.Mualim, K.Selmoni, O.Exposito-Alonso, M.2025-09-14doi:10.1101/2025.09.09.675155Cold Spring Harbor Laboratory Press2025-09-14
<![CDATA[
Aminoacyl-tRNA specificity of a ligase catalyzing non-ribosomal peptide extension
]]>
https://biorxiv.org/cgi/content/short/2025.09.13.676032v1?rss=1"
Nguyen, D. T.Ramos-Figueroa, J. S.Vinogradov, A. A.Goto, Y.Gadgil, M. G.Splain, R. A.Suga, H.van der Donk, W. A.Mitchell, D. A.2025-09-14doi:10.1101/2025.09.13.676032Cold Spring Harbor Laboratory Press2025-09-14
<![CDATA[
ACAD10 encodes two orphan enzymes in the ether lipid biosynthetic and salvage pathways
]]>
https://biorxiv.org/cgi/content/short/2025.09.10.675409v1?rss=1"
Ye, J.Purlyte, E.Lopez, V. A.Kizzar, T.Tatge, L.Mill, J.Baldwin, D.Rashan, E.Kim, J.Pagliarini, D. A.Tomchick, D. R.Pawlowski, K.Douglas, P.Simcox, J.Tagliabracci, V. S.2025-09-13doi:10.1101/2025.09.10.675409Cold Spring Harbor Laboratory Press2025-09-13
<![CDATA[
Neutral lipid processing in glia is sexually dimorphic and promotes sleep through diacylglycerol catabolism
]]>
https://biorxiv.org/cgi/content/short/2025.09.10.674993v1?rss=1"
Pyfrom, E. S.Beveridge, C.Haynes, P. R.Kanigicherla, V. A.Randolph, C. E.Carvalho Costa, P.Negatu, S. G.Iyer, S.Killiany, S. L.Yue, Z.Astacio, E. N.Walker, K. A.Luu, K. N.Pivarshev, P. A.Jurado, K. A.Chopra, G.Sehgal, A.2025-09-12doi:10.1101/2025.09.10.674993Cold Spring Harbor Laboratory Press2025-09-12
<![CDATA[
Atlas of innate immune responses to experimental cholera and IL22 treatment demonstrates protection by mucus-secreting cells
]]>
https://biorxiv.org/cgi/content/short/2025.09.12.675873v1?rss=1"
Suzuki, M.Hasegawa, Y.Zhang, H.Waldor, M. K.2025-09-12doi:10.1101/2025.09.12.675873Cold Spring Harbor Laboratory Press2025-09-12
<![CDATA[
Spectral envelopes of rhythmic facial movements predict intention and motor cortical representations
]]>
https://biorxiv.org/cgi/content/short/2025.09.10.675423v1?rss=1"
Hakim, R.Heo, G.Jaggi, A.Musall, S.Datta, S. R.Sabatini, B. L.2025-09-11doi:10.1101/2025.09.10.675423Cold Spring Harbor Laboratory Press2025-09-11
<![CDATA[
HIF2-driven PTHrP Causes Cachexia and Hypercalcemia in Kidney Cancer: Treatment with HIF2 Inhibitors
]]>
https://biorxiv.org/cgi/content/short/2025.09.09.675147v1?rss=1"
Abu-Remaileh, M.Stransky, L. A.Bhalerao, N.Shirole, N. H.Jiang, Q.Saad, E.Machaalani, M.Vigeant, S. H.Woldemichael, H.Xu, C.Lu, J.Wei, H.Liu, Z.Sun, W.Enomoto, K.Choueiri, T. K.Pitarresi, J. R.Carr, S. A.Udeshi, N. D.Kaelin, W. G.2025-09-11doi:10.1101/2025.09.09.675147Cold Spring Harbor Laboratory Press2025-09-11
<![CDATA[
The gut microbiota directs vitamin A flux to regulate intestinal T cell development
]]>
https://biorxiv.org/cgi/content/short/2025.09.08.674524v1?rss=1"
View larger version (53K):
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]]>Srinivasan, T.Dende, C.Ruhn, K. A.Moye, S. L.Johnson, A.Behrendt, C. L.Hassell, B.Vale, G.Kim, J.Lichterman, J. N.Liang, C.Arana, C.Raj, P.Zhan, X.McDonald, J. G.Koh, A. Y.Hooper, L. V.2025-09-10doi:10.1101/2025.09.08.674524Cold Spring Harbor Laboratory Press2025-09-10
<![CDATA[
Lysosomal RNA profiling reveals targeting of specific types of RNAs for degradation
]]>
https://biorxiv.org/cgi/content/short/2025.09.09.674968v1?rss=1"
Ray, G. J.Nardini, E.Keys, H. R.Lin, D. H.Sabatini, D. M.Bartel, D.2025-09-09doi:10.1101/2025.09.09.674968Cold Spring Harbor Laboratory Press2025-09-09
<![CDATA[
Vnd and En are expressed in orthogonal stripes and act in a brief competence window to combinatorially specify NB7-1 and its early lineage
]]>
https://biorxiv.org/cgi/content/short/2025.09.04.674256v1?rss=1"
Anderson, N.Lai, S.-L.Doe, C. Q.2025-09-08doi:10.1101/2025.09.04.674256Cold Spring Harbor Laboratory Press2025-09-08
<![CDATA[
Tandem association of CLOCK:BMAL1 complexes on DNA enables recruitment of CBP/p300 through multivalent interactions
]]>
https://biorxiv.org/cgi/content/short/2025.09.04.674342v1?rss=1"
Sharma, D.Stoos, L.Torgrimson, M. R.Crosby, P.Franks, K. M.Parsley, N. C.Membreno, M.Kempf, G.Kater, L.Gustafson, C. L.Lee, H.-W.Rubin, S.Michael, A. K.Thoma, N. H.Partch, C. L.2025-09-07doi:10.1101/2025.09.04.674342Cold Spring Harbor Laboratory Press2025-09-07
<![CDATA[
Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025
]]>
https://biorxiv.org/cgi/content/short/2025.09.06.674661v1?rss=1"
Kikawa, C.Huddleston, J.Loes, A. N.Turner, S. A.Lee, J.Barr, I. G.Cowling, B. J.Englund, J. A.Greninger, A. L.Harvey, R.Hasegawa, H.Ho, F.Lacombe, K.Leung, N. H.Lewis, N. S.Peck, H.Watanabe, S.Smith, D. J.Bedford, T.Bloom, J. D.2025-09-06doi:10.1101/2025.09.06.674661Cold Spring Harbor Laboratory Press2025-09-06
<![CDATA[
The Biosynthetic Pathway to the Pyrroloiminoquinone Marine Natural Product Ammosamide C
]]>
https://biorxiv.org/cgi/content/short/2025.09.03.674030v1?rss=1"
Figueroa, J. S. R.Zhu, L.Halliman, M.van der Donk, W. A.2025-09-06doi:10.1101/2025.09.03.674030Cold Spring Harbor Laboratory Press2025-09-06
<![CDATA[
Early postpartum development of pup urine preference in mothers
]]>
https://biorxiv.org/cgi/content/short/2025.09.01.673527v1?rss=1"
Andreu, V.Sen, R.Mimouni, N. E. H.Lee, E. J.Ferguson, D.-L.Stutzman, A.Marlin, B. J.2025-09-05doi:10.1101/2025.09.01.673527Cold Spring Harbor Laboratory Press2025-09-05
<![CDATA[
Rapid protamine evolution suppresses meiotic drive in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2025.09.03.674087v1?rss=1"
Chang, C.-H.de la Cruz, A. F.Natividad, I. M.Noyola, A.Malik, H. S.2025-09-05doi:10.1101/2025.09.03.674087Cold Spring Harbor Laboratory Press2025-09-05
<![CDATA[
Identification of bacterial signals that modulate enteric sensory neurons to influence behavior in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2025.09.03.674032v1?rss=1"
Estrem, C.Dua, M.Fees, C.Hoeprich, G.Au, M.Goode, B. W.Deng, L.Flavell, S. W.2025-09-03doi:10.1101/2025.09.03.674032Cold Spring Harbor Laboratory Press2025-09-03
<![CDATA[
Electrical stimulation directs formation of perfused vasculature in engineered tissues
]]>
https://biorxiv.org/cgi/content/short/2025.08.28.672965v1?rss=1"
Grzelak, K. A.Westerfield, A. D.Kumar, V.Chakraborty, K.Pandian, N. K. R.Chen, C. S.Bhatia, S. N.2025-09-03doi:10.1101/2025.08.28.672965Cold Spring Harbor Laboratory Press2025-09-03
<![CDATA[
Lineage domains and cytoskeletal cables organize a cellular square grid in a crustacean
]]>
https://biorxiv.org/cgi/content/short/2025.08.31.673345v1?rss=1"
Steinert, B. L.Blondel, L.Kuyyamudi, C.Stamatakis, E.Pavlopoulos, A.Extavour, C. G.2025-09-02doi:10.1101/2025.08.31.673345Cold Spring Harbor Laboratory Press2025-09-02
<![CDATA[
Signals of consistent genetic diversity decline are not yet measurable in global meta-analysis
]]>
https://biorxiv.org/cgi/content/short/2025.08.01.663988v1?rss=1"
Exposito-Alonso, M.2025-08-04doi:10.1101/2025.08.01.663988Cold Spring Harbor Laboratory Press2025-08-04
<![CDATA[
Concerted actions of distinct serotonin neurons orchestrate female pup care behavior
]]>
https://biorxiv.org/cgi/content/short/2025.07.31.667987v1?rss=1"
Xiao, S. A.Chen, C. C.Horvath, P.Tsai, V.Cardenas, V. M.Biderman, D.Deng, F.Li, Y.Linderman, S.Dulac, C.Luo, L.2025-08-01doi:10.1101/2025.07.31.667987Cold Spring Harbor Laboratory Press2025-08-01
<![CDATA[
Mechanism and Structure-Guided Optimization of SLC1A1/EAAT3-Selective Inhibitors in Kidney Cancer
]]>
https://biorxiv.org/cgi/content/short/2025.07.03.663021v1?rss=1"
Koochaki, P.Qiu, B.Coker, J. A.Earsley, A.Wang, N. S.Romigh, T.Goins, C. M.Stauffer, S. R.Boudker, O.Chakraborty, A. A.2025-07-07doi:10.1101/2025.07.03.663021Cold Spring Harbor Laboratory Press2025-07-07
<![CDATA[
Engineering gene expression dynamics via self-amplifying RNA with drug-responsive non-structural proteins
]]>
https://biorxiv.org/cgi/content/short/2025.06.08.658495v1?rss=1"
Yousefpour, P.Gregory, J. R.Si, K.Lonzaric, J.Li, Y.Wang, J.Qureshi, K.Ledbetter, A.Melo, M. B.Lemnios, A. A.Dye, J.Remba, T. K.Yeung, R.Rodriguez, L.Guereca, M.Wu, S.Zhang, Y.Dong, Y.Weiss, R.Irvine, D. J.2025-06-08doi:10.1101/2025.06.08.658495Cold Spring Harbor Laboratory Press2025-06-08
<![CDATA[
Cell-type-specific patterns and consequences of somatic mutation in development and aging brain
]]>
https://biorxiv.org/cgi/content/short/2025.05.30.656844v1?rss=1"
10,000-fold while eliminating artifactual mutational signatures. When applied to 98%/2% mixed cell lines, Duplex-Multiome identified sSNVs present in 2% of cells with 92% precision and accurately captured known sSNV mutational spectra, while revealing unexpected subclonal lineages. Duplex-Multiome of > 51,400 nuclei from postmortem brain tissue captured sSNV burdens and spectra across all major brain cell types and subtypes, including those difficult to assay by single-cell whole-genome sequencing (scWGS). This revealed for the first time that diverse neuronal and glial cell types show distinct rates and patterns of age-related mutation, while also directly discovering developmental cell lineage relationships. Duplex-Multiome identified clonal sSNVs occurring at increased rates in glia of certain aged brains, as well as clonal sSNVs that correlated with changes in expression of nearby genes, in both neurotypical and autism spectrum disorder (ASD) individuals, directly demonstrating that somatic mutagenesis can contribute to gene expression phenotypes. Duplex-Multiome can be easily adopted into the 10X Multiome protocol and will bridge somatic mosaicism to a wide range of phenotypic readouts across cell types and tissues.
]]>Kriz, A. J.Mao, S.Shao, D. D.Snellings, D. A.Andersen, R.Dong, G.Ma, C. C.Cline, H. E.Huang, A. Y.Lee, E. A.Walsh, C. A.2025-06-01doi:10.1101/2025.05.30.656844Cold Spring Harbor Laboratory Press2025-06-01
<![CDATA[
Myosin 2 drives actin contractility in fast-crawling species outside of the amorphean lineage
]]>
https://biorxiv.org/cgi/content/short/2025.05.16.654244v1?rss=1"
Guest, S. L.Velle, K. B.Jacques, S. M.Park, Y.Man, J.Titus, M. A.Fritz-Laylin, L.2025-05-19doi:10.1101/2025.05.16.654244Cold Spring Harbor Laboratory Press2025-05-19
<![CDATA[
Spatiotemporal Analysis of Remyelination Reveals a Concerted Interferon-Responsive Glial State That Coordinates Immune Infiltration
]]>
https://biorxiv.org/cgi/content/short/2025.04.22.649486v1?rss=1"
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]]>Dolan, M.-J.Rakosi-Schmidt, R.Garcia, E.Lin, Y.Nadaf, N. M.Dixon, J.Guo, S.Morshed, N.Depp, C.Doman, J.Xia, J.Jäntti, H.Stevens, B.Macosko, E. Z.2025-04-29doi:10.1101/2025.04.22.649486Cold Spring Harbor Laboratory Press2025-04-29
<![CDATA[
NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT
]]>
https://biorxiv.org/cgi/content/short/2025.03.29.646096v1?rss=1"
Wu, Z.Nguyen, P. T.Sondhi, V.Yao, R.-W.Dai, T.Chiang, J.-C.Shang, Z.Cai, F.Zhang, J.Moore, M. D.Alshamleh, I.Li, X.Ogu, T.Zacharias, L. G.Winston, R.Patricio, J. S.Johnson, X.Chen, W.-M.Cong, Q.Mathews, T. P.Zhang, Y.DeBerardinis, R. J.2025-04-01doi:10.1101/2025.03.29.646096Cold Spring Harbor Laboratory Press2025-04-01
<![CDATA[
SIRT2 Mediates Integrated Stress Response by Deacetylating and Stabilizing 4EBP1 to Suppress Translation
]]>
https://biorxiv.org/cgi/content/short/2025.03.31.646365v1?rss=1"
Zi, Y.Wang, M.Hou, D.Cerione, R. A.Lin, H.2025-04-01doi:10.1101/2025.03.31.646365Cold Spring Harbor Laboratory Press2025-04-01
<![CDATA[
A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway
]]>
https://biorxiv.org/cgi/content/short/2025.03.28.646030v1?rss=1"
Doherty, E. E.Adler, B. A.Yoon, P. H.Hsieh, K.Loi, K.Armbuster, E. G.Lahiri, A.Bolling, C. S.Wilcox, X. E.Akkati, A.Iavarone, A. T.Pogliano, J.Doudna, J. A.2025-03-30doi:10.1101/2025.03.28.646030Cold Spring Harbor Laboratory Press2025-03-30
<![CDATA[
Synaptic editing of frontostriatal circuitry prevents excessive grooming in SAPAP3-deficient mice
]]>
https://biorxiv.org/cgi/content/short/2025.03.27.645613v1?rss=1"
Walder-Christensen, K. K.Soliman, H. A.Calakos, N.Dzirasa, K.2025-03-29doi:10.1101/2025.03.27.645613Cold Spring Harbor Laboratory Press2025-03-29
<![CDATA[
IL-25-induced memory ILC2s mediate long-term small intestinal adaptation
]]>
https://biorxiv.org/cgi/content/short/2025.03.25.645270v1?rss=1"
Cortez, V. S.Viragova, S.Koga, S.Liu, M.O'Leary, C.Ricardo-Gonzalez, R. R.Schroeder, A. W.Kochhar, N.Klein, O.Diamond, M.Liang, H.-E.Locksley, R. M.2025-03-29doi:10.1101/2025.03.25.645270Cold Spring Harbor Laboratory Press2025-03-29
<![CDATA[
Divergence of germ cell-less roles in germ line development across insect species
]]>
https://biorxiv.org/cgi/content/short/2025.03.26.645619v1?rss=1"
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]]>Kao, J.Ewen-Campen, B.Extavour, C. G.2025-03-28doi:10.1101/2025.03.26.645619Cold Spring Harbor Laboratory Press2025-03-28
<![CDATA[
De novo design of inducibly assembling multi-component filaments
]]>
https://biorxiv.org/cgi/content/short/2025.03.26.645066v1?rss=1"
Shen, H.Lynch, E. M.Jameson, N.Decarreau, J.Shi, C.Chen, Z.Sheffler, W.Xu, M.De Yoreo, J. J.Zalatan, J. G.Kollman, J. M.Baker, D.2025-03-26doi:10.1101/2025.03.26.645066Cold Spring Harbor Laboratory Press2025-03-26
<![CDATA[
Directed evolution expands CRISPR-Cas12a genome editing capacity
]]>
https://biorxiv.org/cgi/content/short/2025.03.26.645588v1?rss=1"
Ma, E.Chen, K.Shi, H.Wasko, K. M.Esain-Garcia, I.Trinidad, M. I.Zhou, K.Ye, J.Doudna, J. A.2025-03-26doi:10.1101/2025.03.26.645588Cold Spring Harbor Laboratory Press2025-03-26
<![CDATA[
Long-term editing of brain circuits in mice using an engineered electrical synapse
]]>
https://biorxiv.org/cgi/content/short/2025.03.25.645291v1?rss=1"
Ransey, E.Thomas, G.Wisdom, E.Almoril-Porras, A.Bowman, R.Adamson, E.Walder-Christensen, K. K.White, J. A.Hughes, D. N.Schwennesen, H.Ferguson, C.Tye, K.Mague, S. D.Niu, L.-G.Wang, Z.-W.Colon-Ramos, D.Hultman, R.Bursac, N.Dzirasa, K.2025-03-26doi:10.1101/2025.03.25.645291Cold Spring Harbor Laboratory Press2025-03-26
<![CDATA[
Addendum to Ancient DNA data from Mengzi Ren, a Late Pleistocene individual from Southeast Asia, cannot be reliably used in population genetic analysis
]]>
https://biorxiv.org/cgi/content/short/2025.03.24.645126v1?rss=1"
Tabin, D. R.Patterson, N. J.Mah, M.Reich, D. E.2025-03-26doi:10.1101/2025.03.24.645126Cold Spring Harbor Laboratory Press2025-03-26
<![CDATA[
Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation
]]>
https://biorxiv.org/cgi/content/short/2025.03.24.645017v1?rss=1"
Agarwal, G.Antoszewski, M.Xie, X.Pershad, Y.Arora, U. P.Poon, C.-L.Lyu, P.Lee, A. J.Guo, C.-J.Ye, T.Norford, L. B.Neehus, A.-L.della Volpe, L.Wahlster, L.Ranasinghe, D.Ho, T.-C.Barlowe, T. S.Chow, A.Schurer, A.Taggart, J.Durham, B. H.Abdel-Wahab, O.McGraw, K. L.Allan, J. M.Soldatov, R.Bick, A. G.Kharas, M. G.Sankaran, V. G.2025-03-26doi:10.1101/2025.03.24.645017Cold Spring Harbor Laboratory Press2025-03-26
<![CDATA[
Short-term alterations in dietary amino acids override host genetic susceptibility and reveal mechanisms of Salmonella Typhimurium small intestine colonization
]]>
https://biorxiv.org/cgi/content/short/2025.03.25.645332v1?rss=1"
Shealy, N.Baltagulov, M.de Brito, C.McGovern, A.Castro, P.Schrimpe-Rutledge, A. C.Malekshahi, C.Condreanu, S. G.Sherrod, S. D.Jana, S.Jones, K.Machado Ribeiro, T. R.McLean, J.Beiting, D. P.Byndloss, M. X.2025-03-25doi:10.1101/2025.03.25.645332Cold Spring Harbor Laboratory Press2025-03-25
<![CDATA[
Membrane-associated polymerases deliver most of the actin subunits to a lamellipodial network
]]>
https://biorxiv.org/cgi/content/short/2025.03.24.645090v1?rss=1"
Skruber, K.Sept, D.Mullins, D.2025-03-25doi:10.1101/2025.03.24.645090Cold Spring Harbor Laboratory Press2025-03-25
<![CDATA[
Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation
]]>
https://biorxiv.org/cgi/content/short/2025.03.23.644697v1?rss=1"
Zhou, J.Wu, Y.Liu, H.Tian, W.Castanon, R. G.Bartlett, A.Zhang, Z.Yao, G.Shi, D.Clock, B.Marcotte, S.Nery, J. R.Liem, M.Claffey, N.Boggeman, L.Barragan, C.eDrigo, R. A.Weimer, A. K.Shi, M.Cooper-Knock, J.Zhang, S.Snyder, M. P.Preissl, S.Ren, B.O'Connor, C.Chen, S.Luo, C.Dixon, J. R.Ecker, J. R.2025-03-24doi:10.1101/2025.03.23.644697Cold Spring Harbor Laboratory Press2025-03-24
<![CDATA[
Glutamate indicators with increased sensitivity and tailored deactivation rates
]]>
https://biorxiv.org/cgi/content/short/2025.03.20.643984v1?rss=1"
Aggarwal, A.Negrean, A.Chen, Y.Iyer, R.Reep, D.Liu, A.Palutla, A.Xie, M. E.MacLennan, B.Hagihara, K. M.Kinsey, L. W.Sun, J. L.Yao, P.Zheng, J.Tsang, A.Tsegaye, G.Zhang, Y.Patel, R. H.Arthur, B. J.Hiblot, J.Leippe, P.Tarnawski, M.Marvin, J. S.Vevea, J. D.Turaga, S. C.Tebo, A. G.Carandini, M.Rossi, L. F.Kleinfeld, D.Konnerth, A.Svoboda, K.Turner, G. C.Hasseman, J.Podgorski, K.2025-03-24doi:10.1101/2025.03.20.643984Cold Spring Harbor Laboratory Press2025-03-24
<![CDATA[
De novo design of miniprotein agonists and antagonists targeting G protein-coupled receptors
]]>
https://biorxiv.org/cgi/content/short/2025.03.23.644666v1?rss=1"
Muratspahic, E.Feldman, D.Kim, D. E.Qu, X.Bratovianu, A.-M.Rivera-Sanchez, P.Dimitri, F.Cao, J.Cary, B. P.Belousoff, M. J.Keov, P.Chen, Q.Ren, Y.Fine, J.Sappington, I.Schlichthaerle, T.Zhang, J. Z.Pillai, A.Mihaljevic, L.Bauer, M.Torres, S. V.Motmaen, A.Lee, G. R.Tran, L.Wang, X.Goreshnik, I.Vafeados, D. K.Svendsen, J. E.Hosseinzadeh, P.Lindegaard, N.Brandt, M.Waltenspühl, Y.Deibler, K.Oostdyk, L.Cao, W.Anantharaman, L.Stewart, L.Halloran, L.Spangler, J. B.Sexton, P. M.Roth, B. L.Krumm, B. E.Wootten, D.Tate,2025-03-23doi:10.1101/2025.03.23.644666Cold Spring Harbor Laboratory Press2025-03-23
<![CDATA[
Bacterial ubiquitin ligase engineered for small molecule and protein target identification
]]>
https://biorxiv.org/cgi/content/short/2025.03.20.644192v1?rss=1"
Ye, J. S.Majumdar, A.Park, B. C.Black, M. H.Hsieh, T.-S.Osinski, A.Servage, K. A.Kulkarni, K.Naidoo, J.Alto, N. M.Stratton, M. M.Alfandari, D.Ready, J. M.Pawłowski, K.Tomchick, D. R.Tagliabracci, V. S.2025-03-22doi:10.1101/2025.03.20.644192Cold Spring Harbor Laboratory Press2025-03-22
<![CDATA[
p62 sorts Lupus La and selected microRNAs into breast cancer-derived exosomes
]]>
https://biorxiv.org/cgi/content/short/2025.03.20.644464v1?rss=1"
Ngo, J. M.Williams, J. K.Temoche-Diaz, M. M.Murugupandiyan, A.Schekman, R.2025-03-20doi:10.1101/2025.03.20.644464Cold Spring Harbor Laboratory Press2025-03-20
<![CDATA[
GMCL1 Controls 53BP1 Stability and Modulates Paclitaxel Sensitivity in Cancer
]]>
https://biorxiv.org/cgi/content/short/2025.03.18.643855v1?rss=1"
KITO, Y.Gonzalez-Robles, T. J.Kaisari, S.Pae, J.Garcia, S. F.Ortiz-Pacheco, J.Ueberheide, B.Lehmann, R.Marzio, A.Rona, G.Pagano, M.2025-03-20doi:10.1101/2025.03.18.643855Cold Spring Harbor Laboratory Press2025-03-20
<![CDATA[
Learning millisecond protein dynamics from what is missing in NMR spectra
]]>
https://biorxiv.org/cgi/content/short/2025.03.19.642801v1?rss=1"
100 Nuclear Magnetic Resonance (NMR) relaxation datasets, we realized an observable for {micro}s-ms dynamics might be hiding in plain sight. Millisecond dynamics can cause NMR signals to broaden beyond detection, leaving some residues not assigned in the chemical shift datasets of [~]10,000 proteins deposited in the Biological Magnetic Resonance Data Bank (BMRB)1. We made the bold assumption that residues missing assignments are exchange-broadened due to {micro}s-ms motions and trained various deep learning models to predict missing assignments. Strikingly, these models also predict exchange measured via NMR relaxation experiments, indicative of {micro}s-ms dynamics. The best of these models, which we named Dyna-1, leverages an intermediate layer of the multimodal language model ESM-32. Notably, dynamics directly linked to biological function -- including enzyme catalysis and ligand binding -- are particularly well predicted by Dyna-1, which parallels our findings that residues experiencing {micro}s-ms exchange are more conserved. We anticipate the datasets and models presented here will be transformative in unlocking the common language of dynamics and function.
]]>Wayment-Steele, H. K.El Nesr, G.Hettiarachchi, R.Kariyawasam, H.Ovchinnikov, S.Kern, D.2025-03-19doi:10.1101/2025.03.19.642801Cold Spring Harbor Laboratory Press2025-03-19
<![CDATA[
CTCF-RNA interactions orchestrate cell-specific chromatin loop organization
]]>
https://biorxiv.org/cgi/content/short/2025.03.19.643339v1?rss=1"
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]]>Lucero, K.Han, S.Huang, P.-Y.Qiu, X.Mazzoni, E. O.Reinberg, D.2025-03-19doi:10.1101/2025.03.19.643339Cold Spring Harbor Laboratory Press2025-03-19
<![CDATA[
Genetic diversity and regulatory features of human-specific NOTCH2NL duplications
]]>
https://biorxiv.org/cgi/content/short/2025.03.14.643395v1?rss=1"
Real, T. D.Hebbar, P.Yoo, D.Antonacci, F.Pacar, I.Diekhans, M.Mikol, G. J.Popoola, O. G.Mallory, B.Vollger, M. R.Dishuck, P. C.Guitart, X.Rozanski, A. N.Munson, K. M.Hoekzema, K.Ranchalis, J. E.Neph, S. J.Sedeno-Cortes, A. E.Paten, B.Salama, S.Stergachis, A.Eichler, E. E.2025-03-16doi:10.1101/2025.03.14.643395Cold Spring Harbor Laboratory Press2025-03-16
<![CDATA[
A genome-scale drug discovery pipeline uncovers new therapeutic targets and a unique p97 allosteric binding site in Schistosoma mansoni
]]>
https://biorxiv.org/cgi/content/short/2025.03.14.643303v1?rss=1"
Stephens, D. R.Fung, H. Y. J.Han, Y.Liang, J.Chen, Z.Ready, J.Collins, J.2025-03-15doi:10.1101/2025.03.14.643303Cold Spring Harbor Laboratory Press2025-03-15
<![CDATA[
Design of solubly expressed miniaturized SMART MHCs
]]>
https://biorxiv.org/cgi/content/short/2025.03.14.643101v1?rss=1"
White, W. L.Bai, H.Kim, C. J.Jude, K. M.Sun, R.Guerrero, L.Han, X.Chen, X. T.Chaudhuri, A.Bonzanini, J. E.Sun, Y.Onwuka, A. E.Wang, N.Wang, C.Li, X.Goreshnik, I.Allen, A.Levine, P. M.Kueh, H. Y.Jewett, M. C.Sgourakis, N.Achour, A.Garcia, K. C.Baker, D.2025-03-14doi:10.1101/2025.03.14.643101Cold Spring Harbor Laboratory Press2025-03-14
<![CDATA[
Canonical Wnt Signaling Suppresses Brain Endothelial Cell Transcytosis to Maintain Blood-Brain Barrier Integrity
]]>
https://biorxiv.org/cgi/content/short/2025.03.10.642437v1?rss=1"
du Maine, X.Gu, C.2025-03-13doi:10.1101/2025.03.10.642437Cold Spring Harbor Laboratory Press2025-03-13
<![CDATA[
High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
]]>
https://biorxiv.org/cgi/content/short/2025.03.04.641544v1?rss=1"
Kikawa, C.Loes, A. N.Huddleston, J.Figgins, M. D.Steinberg, P.Griffiths, T.Drapeau, E. M.Peck, H.Barr, I. G.Englund, J. A.Hensley, S. E.Bedford, T.Bloom, J. D.2025-03-12doi:10.1101/2025.03.04.641544Cold Spring Harbor Laboratory Press2025-03-12
<![CDATA[
Functional microRNA targeting without seed pairing
]]>
https://biorxiv.org/cgi/content/short/2025.03.03.641270v1?rss=1"
View larger version (21K):
org.highwire.dtl.DTLVardef@1e6045corg.highwire.dtl.DTLVardef@2859eborg.highwire.dtl.DTLVardef@12761beorg.highwire.dtl.DTLVardef@820fe6_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Hall, M. H.Wang, P. Y.Pham, T. M.Bartel, D. P.2025-03-11doi:10.1101/2025.03.03.641270Cold Spring Harbor Laboratory Press2025-03-11
<![CDATA[
Targeted suppression of type 1 interferon signaling during RNA delivery enhances vaccine-elicited immunity
]]>
https://biorxiv.org/cgi/content/short/2025.03.09.642244v1?rss=1"
10-fold, increased immune cell infiltration, and increased antigen presenting cell activation in the injection site and draining lymph nodes. Compared to repRNA alone, siRNA/repRNA co-delivery increased serum antibody titers >10-fold, dramatically augmented antigen-specific germinal center (GC) B cell responses, and primed 4.4-fold more antigen-specific T cells. Ifnar1 silencing by siRNA co-delivery similarly enhanced mRNA vaccines. Thus, siRNA co-delivery is a readily translatable approach to substantially enhance the immunogenicity of RNA vaccines.
]]>Kim, B. J.Hosn, R. R.Remba, T. K.Dye, J.Mak, H. H.Jeong, J. Y.Cornwall-Brady, M.Abraham, W.Maiorino, L.Melo, M. B.Li, B.Zhang, Y.Dong, Y.Irvine, D. J.2025-03-10doi:10.1101/2025.03.09.642244Cold Spring Harbor Laboratory Press2025-03-10
<![CDATA[
Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy
]]>
https://biorxiv.org/cgi/content/short/2025.03.03.641217v1?rss=1"
Dong, G.Ma, C. C.Mao, S.Naik, S. M.Brown, K. S.-M.McDonough, G. A.Kim, J.Kirkham, S. L.Cherry, J.Uretsky, M.Spurlock, E.McKee, A.Huang, A. Y.Miller, M. B.Lee, E. A.Walsh, C. A.2025-03-04doi:10.1101/2025.03.03.641217Cold Spring Harbor Laboratory Press2025-03-04
<![CDATA[
Repulsive interactions instruct synaptic partner matching in an olfactory circuit
]]>
https://biorxiv.org/cgi/content/short/2025.03.01.640985v1?rss=1"
Li, Z.Lyu, C.Xu, C.Hu, Y.Luginbuhl, D. J.Caspi-Lebovic, A. B.Priest, J. M.Özkan, E.Luo, L.2025-03-02doi:10.1101/2025.03.01.640985Cold Spring Harbor Laboratory Press2025-03-02
<![CDATA[
Rewiring an olfactory circuit by altering the combinatorial code of cell-surface proteins
]]>
https://biorxiv.org/cgi/content/short/2025.03.01.640986v1?rss=1"
Lyu, C.Li, Z.Xu, C.Kalai, J.Luo, L.2025-03-02doi:10.1101/2025.03.01.640986Cold Spring Harbor Laboratory Press2025-03-02
<![CDATA[
Deep learning guided design of protease substrates
]]>
https://biorxiv.org/cgi/content/short/2025.02.27.640681v1?rss=1"
Martin Alonso, M. C.Alamdari, S.Samad, T. S.Yang, K. K.Bhatia, S. N.Amini, A. P.2025-03-02doi:10.1101/2025.02.27.640681Cold Spring Harbor Laboratory Press2025-03-02
<![CDATA[
Deconvolution to restore cryo-EM maps with anisotropic resolution
]]>
https://biorxiv.org/cgi/content/short/2025.02.23.639707v1?rss=1"
Li, J.chen, Y.Zheng, S.McDonald, A.Sedat, J. W.Agard, D. A.Cheng, Y.2025-03-01doi:10.1101/2025.02.23.639707Cold Spring Harbor Laboratory Press2025-03-01
<![CDATA[
Characterization of energy filtering slit widths for MicroED data collection
]]>
https://biorxiv.org/cgi/content/short/2025.02.24.639939v1?rss=1"
Clabbers, M. T. B.Hattne, J.Martynowycz, M. W.Gonen, T.2025-02-27doi:10.1101/2025.02.24.639939Cold Spring Harbor Laboratory Press2025-02-27
<![CDATA[
DNA origami vaccines program antigen-focused germinal centers
]]>
https://biorxiv.org/cgi/content/short/2025.02.21.639354v1?rss=1"
Romanov, A.Knappe, G. A.Ronsard, L.Suh, H.Omer, M.Chapman, A. P.Lewis, V.Spivakovsky, K.Canales, J.Reizis, B.Tingle, R.Cottrell, C.Schiffner, T.Lingwood, D.Bathe, M.Irvine, D. J.2025-02-27doi:10.1101/2025.02.21.639354Cold Spring Harbor Laboratory Press2025-02-27
<![CDATA[
Pseudomonads coordinate innate defense against viruses and bacteria with a single regulatory system
]]>
https://biorxiv.org/cgi/content/short/2025.02.26.640152v1?rss=1"
Brinkley, D. M.Bertolli, S. K.Gallagher, L. A.Tan, Y.Motha de Silva, M.Brockman, A.Zhang, D.Peterson, S. B.Mougous, J. D.2025-02-27doi:10.1101/2025.02.26.640152Cold Spring Harbor Laboratory Press2025-02-27
<![CDATA[
Combining Sampling Methods with Attractor Dynamics in Spiking Models of Head-Direction Systems
]]>
https://biorxiv.org/cgi/content/short/2025.02.25.640158v1?rss=1"
Pjanovic, V.Zavatone-Veth, J. A.Masset, P.Keemink, S. W.Nardin, M.2025-02-26doi:10.1101/2025.02.25.640158Cold Spring Harbor Laboratory Press2025-02-26
<![CDATA[
Mosquito Cell Atlas: A single-nucleus transcriptomic atlas of the adult Aedes aegypti mosquito
]]>
https://biorxiv.org/cgi/content/short/2025.02.25.639765v1?rss=1"
Goldman, O. V.DeFoe, A. E.Qi, Y.Jiao, Y.Weng, S.-C.Houri-Zeevi, L.Lakhiani, P.Morita, T.Razzauti, J.Rosas-Villegas, A.Tsitohay, Y. N.Walker, M.Hopkins, B. R.Mosquito Cell Atlas Consortium,Joshua X D Ang,Igor Antoshechkin,Yu Cai,Fangying Chen,Yen-Chung Chen,Julien Devilliers,Linhan Dong,Roberto Feuda,Paolo Gabrieli,Artyom Kopp,Hyeogsun Kwon,Hsing-Han Li,Tzu-Chiao Lu,Thalita Lucio,Joao T Marques,Marcus F Oliveira,Roenick P Olmo,Umberto Palatini,Zeaan M Pithawala,Julien Pompon,Yan Reis,2025-02-25doi:10.1101/2025.02.25.639765Cold Spring Harbor Laboratory Press2025-02-25
<![CDATA[
Cryptic variation fuels plant phenotypic change through hierarchical epistasis
]]>
https://biorxiv.org/cgi/content/short/2025.02.23.639722v1?rss=1"
Zebell, S. G.Martl-Gomez, C.Fitzgerald, B.Pinto Da Cunha, C.Lach, M.Seman, B. M.Hendelman, A.Sretenovic, S.Qi, Y.Eshed, Y.McCandlish, D. M.Lippman, Z.2025-02-25doi:10.1101/2025.02.23.639722Cold Spring Harbor Laboratory Press2025-02-25
<![CDATA[
Stress drives plasticity in leaf maturation transcriptional dynamics
]]>
https://biorxiv.org/cgi/content/short/2025.02.24.639183v1?rss=1"
Swift, J.Wu, X.Xu, J.Jain, T.Illouz-Eliaz, N.Nery, J. R.Chory, J.Ecker, J. R.2025-02-25doi:10.1101/2025.02.24.639183Cold Spring Harbor Laboratory Press2025-02-25
<![CDATA[
Persistent dopamine-dependent remodeling of the neural transcriptome in response to pregnancy and postpartum
]]>
https://biorxiv.org/cgi/content/short/2025.02.20.639313v1?rss=1"
Chan, J. C.Di Salvo, G.Cunningham, A. M.Dutta, S.Brindley, E. A.Wan, E.Zhang, C.Maze, I.2025-02-25doi:10.1101/2025.02.20.639313Cold Spring Harbor Laboratory Press2025-02-25
<![CDATA[
Actin crosslinking is required for force sensing at tricellular junctions
]]>
https://biorxiv.org/cgi/content/short/2025.02.21.639590v1?rss=1"
Taneja, N.Moubarak, M. F.McGovern, M. J.Yeoh, K.Zallen, J. A.2025-02-24doi:10.1101/2025.02.21.639590Cold Spring Harbor Laboratory Press2025-02-24
<![CDATA[
High-throughput MicroED for probing ion channel dynamics
]]>
https://biorxiv.org/cgi/content/short/2025.02.19.639122v1?rss=1"
Gallenito, M. J.Clabbers, M. T. B.Lin, J.Hattne, J.Gonen, T.2025-02-23doi:10.1101/2025.02.19.639122Cold Spring Harbor Laboratory Press2025-02-23
<![CDATA[
Arabidopsis REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA Polymerase IV transcription complexes.
]]>
https://biorxiv.org/cgi/content/short/2025.02.21.639493v1?rss=1"
Wu, Z.Xue, Y.Wang, S.Shih, Y.-H.Zhong, Z.Feng, S.Draper, J.Lu, A.Sha, J.Li, L.Wohlschlegel, J.Wu, K.Jacobsen, S. E.2025-02-23doi:10.1101/2025.02.21.639493Cold Spring Harbor Laboratory Press2025-02-23
<![CDATA[
Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development
]]>
https://biorxiv.org/cgi/content/short/2025.02.15.638402v1?rss=1"
Xu, X.Lin, H.Zhang, J.Burguener, G.Paraiso, F.Tumelty, C.Li, C.Liu, Y.Dubcovsky, J.2025-02-19doi:10.1101/2025.02.15.638402Cold Spring Harbor Laboratory Press2025-02-19
<![CDATA[
Mapping the nanoscale organization of the human cell surface proteome reveals new functional associations and surface antigen clusters
]]>
https://biorxiv.org/cgi/content/short/2025.02.12.637979v1?rss=1"
Floyd, B. M.Schmidt, E. L.Till, N. A.Yang, J. L.Liao, P.George, B. M.Flynn, R. A.Bertozzi, C. R.2025-02-17doi:10.1101/2025.02.12.637979Cold Spring Harbor Laboratory Press2025-02-17
<![CDATA[
A vector-based strategy for olfactory navigation in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2025.02.15.638426v1?rss=1"
Siliciano, A. F.Minni, S.Morton, C.Dowell, C. K.Eghbali, N. B.Rhee, J. Y.Abbott, L. F.Ruta, V.2025-02-16doi:10.1101/2025.02.15.638426Cold Spring Harbor Laboratory Press2025-02-16
<![CDATA[
TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2025.02.13.638157v1?rss=1"
Hu, Y.Rodiger, J.Liu, Y.Gao, C.Liu, Y.Qadiri, M.Veal, A.Bulyk, M. L.Perrimon, N.2025-02-14doi:10.1101/2025.02.13.638157Cold Spring Harbor Laboratory Press2025-02-14
<![CDATA[
A connection between Vibrio cholerae motility and inter-animal transmission
]]>
https://biorxiv.org/cgi/content/short/2025.02.12.637895v1?rss=1"
Campbell, I. W.Dehinwal, R.Morano, A. A.Dailey, K. G.Zingl, F. G.Waldor, M. K.2025-02-13doi:10.1101/2025.02.12.637895Cold Spring Harbor Laboratory Press2025-02-13
<![CDATA[
A dendritic guidance receptor functions in both ligand dependent and independent modes
]]>
https://biorxiv.org/cgi/content/short/2025.02.11.637350v1?rss=1"
Reddy, A. R.Machera, S. J.Cook, Z. T.Ozkan, E.Shen, K.2025-02-12doi:10.1101/2025.02.11.637350Cold Spring Harbor Laboratory Press2025-02-12
<![CDATA[
Cohesin drives chromatin scanning during the RAD51-mediated homology search.
]]>
https://biorxiv.org/cgi/content/short/2025.02.10.637451v1?rss=1"
Marin-Gonzalez, A.Rybczynski, A. T.Nilavar, N. M.Nguyen, D.Karwacki- Neisius, V.Li, A. G.Zou, R. S.Aviles-Vazquez, F. J.Kanemaki, M. T.Scully, R.Ha, T.2025-02-11doi:10.1101/2025.02.10.637451Cold Spring Harbor Laboratory Press2025-02-11
<![CDATA[
Inhibitors of the PqsR Quorum-Sensing Receptor Reveal Differential Roles for PqsE and RhlI in Control of Phenazine Production
]]>
https://biorxiv.org/cgi/content/short/2025.02.10.637488v1?rss=1"
100,000 compounds with the aim of identifying inhibitors of either or both the PqsR and RhlR quorum-sensing receptors. We report results for 30 PqsR inhibitors from this screen. All of the identified compounds inhibit PqsR with IC50 values in the nanomolar to low micromolar range and they are readily docked into the autoinducer binding site of the PqsR crystal structure, suggesting they function competitively. The majority of hits identified are not structurally related to previously reported PqsR inhibitors. Recently, RhlR was shown to rely on the accessory protein PqsE for full function. Specifically, RhlR controls different subsets of genes depending on whether it is bound to PqsE or to C4-HSL, however, the consequences of differential regulation on the quorum-sensing output response have not been defined. PqsR regulates pqsE. That feature of the system enabled us to exploit our new set of PqsR inhibitors to show that RhlR requires PqsE to activate the biosynthetic genes for pyocyanin, a key P. aeruginosa virulence factor, while C4-HSL is dispensable. These results highlight the promise of inhibition of PqsR as a possible P. aeruginosa therapeutic to suppress production of factors under RhlR-PqsE control.
]]>Valastyan, J. S.Shine, E. E.Mook, R. A.Bassler, B. L.2025-02-11doi:10.1101/2025.02.10.637488Cold Spring Harbor Laboratory Press2025-02-11
<![CDATA[
A cluster of RNA Polymerase II molecules is stably associated with an active gene
]]>
https://biorxiv.org/cgi/content/short/2025.02.10.637507v1?rss=1"
Mukherjee, A.Kapoor, M.Shankta, K.Fallacaro, S.Carter, R. D.Ratchasanmuang, P.Haloush, Y. I.Mir, M.2025-02-11doi:10.1101/2025.02.10.637507Cold Spring Harbor Laboratory Press2025-02-11
<![CDATA[
Multiple interactions mediate the localization of BLTP2 at ER-PM contacts to control plasma membrane dynamics
]]>
https://biorxiv.org/cgi/content/short/2025.02.07.637094v1?rss=1"
Dai, A.Xu, P.Amos, C.Fujise, K.Wu, Y.Yang, H.Eisen, J. N.Guillen-Samander, A.De Camilli, P.2025-02-08doi:10.1101/2025.02.07.637094Cold Spring Harbor Laboratory Press2025-02-08
<![CDATA[
Optogenetic interrogation of the lateral-line sensory system reveals mechanisms of pattern separation in the zebrafish brain
]]>
https://biorxiv.org/cgi/content/short/2025.02.07.637118v1?rss=1"
Velez, N.Lu, S.Fabella, B.Reagor, C. C.Brown, H. R.Vazquez, Y.Jacobo, A.Hudspeth, A. J.2025-02-08doi:10.1101/2025.02.07.637118Cold Spring Harbor Laboratory Press2025-02-08
<![CDATA[
Natural Variation in Photoprotection: Rapid NPQ Kinetics in Ferns
]]>
https://biorxiv.org/cgi/content/short/2025.02.07.637181v1?rss=1"
Maryn, N.Chaparro, A.Short, A.Fleming, G. R.Niyogi, K. K.2025-02-08doi:10.1101/2025.02.07.637181Cold Spring Harbor Laboratory Press2025-02-08
<![CDATA[
Flavoaffinins, elusive cellulose-binding natural products from an anaerobic bacterium
]]>
https://biorxiv.org/cgi/content/short/2025.02.08.637243v1?rss=1"
Kountz, D. J.Yu, R.Lee, J. H.Maloney, K. N.Balskus, E. P.2025-02-08doi:10.1101/2025.02.08.637243Cold Spring Harbor Laboratory Press2025-02-08
<![CDATA[
Anti- and Pro-tumor Functions of Distinct Regulatory T Cell Subsets in Colorectal Cancer
]]>
https://biorxiv.org/cgi/content/short/2025.02.07.637083v1?rss=1"
Huang, X.Feng, D.Mitra, S.Andretta, E. S.Hooshdaran, N. B.Ghelani, A. p.Wang, E. Y.Frost, J. N.Lawless, V. R.Vancheswaran, A.Jiang, Q.Leslie, C. S.Rudensky, A.2025-02-08doi:10.1101/2025.02.07.637083Cold Spring Harbor Laboratory Press2025-02-08
<![CDATA[
Pleomorphic effects of three small-molecule inhibitors on transcription elongation by Mycobacterium tuberculosis RNA polymerase
]]>
https://biorxiv.org/cgi/content/short/2025.02.07.637008v1?rss=1"
Herrera-Asmat, O.Tong, A. B.Lin, W.Kong, T.Del Valle, J. R.Guerra, D. G.Ebright, Y. W.Ebridght, R.Bustamante, C.2025-02-07doi:10.1101/2025.02.07.637008Cold Spring Harbor Laboratory Press2025-02-07
<![CDATA[
Structural variation, selection, and diversification of the NPIP gene family from the human pangenome
]]>
https://biorxiv.org/cgi/content/short/2025.02.04.636496v1?rss=1"
Dishuck, P. C.Munson, K. M.Lewis, A. P.Dougherty, M. L.Underwood, J. G.Harvey, W. T.Hsieh, P.Pastinen, T.Eichler, E. E.2025-02-05doi:10.1101/2025.02.04.636496Cold Spring Harbor Laboratory Press2025-02-05
<![CDATA[
Solubilization of Membrane Proteins using designed protein WRAPS
]]>
https://biorxiv.org/cgi/content/short/2025.02.04.636539v1?rss=1"
Mihaljevic, L.Kim, D. E.Eisenach, H. E.Bandawane, P. D.Borst, A. J.Courbet, A.Bettin, E.Liu, Q.Weidle, C.Majumder, S.Li, X.Lamb, M.Azcarraga Murray, A. N.Ravichandran, R.Williams, E. C.Hu, S.Stuart, L.Grillova, L.Thomson, N. R.Chang, P.Caimano, M. J.Hawley, K. L.King, N. P.Baker, D.2025-02-05doi:10.1101/2025.02.04.636539Cold Spring Harbor Laboratory Press2025-02-05
<![CDATA[
Listeria monocytogenes cell-to-cell spread bypasses nutrient limitation for replicating intracellular bacteria
]]>
https://biorxiv.org/cgi/content/short/2025.01.31.635960v1?rss=1"
Radhakrishnan, P.Theriot, J. A.2025-02-01doi:10.1101/2025.01.31.635960Cold Spring Harbor Laboratory Press2025-02-01
<![CDATA[
Admixture mapping reveals evidence for multiple mitonuclear incompatibilities in swordtail fish hybrids
]]>
https://biorxiv.org/cgi/content/short/2025.01.30.635158v1?rss=1"
Robles, N. V.Moran, B. M.Rodriguez Barrera, M. J.Jofre, G. I.Gunn, T.Iverson, E. N. K.Beskid, S.Baczenas, J.Sedghifar, A.Andolfatto, P.Brandvain, Y.Havird, J. C.Rosenthal, G. G.Schumer, M.2025-01-31doi:10.1101/2025.01.30.635158Cold Spring Harbor Laboratory Press2025-01-31
<![CDATA[
Three-dimensional cellularization in chytrid fungi uses distinct mechanisms from those driving one- and two-dimensional cytokinesis in animals and yeast
]]>
https://biorxiv.org/cgi/content/short/2025.01.30.635136v1?rss=1"
Medina, E. M.Elting, M. W.Fritz-Laylin, L. K.2025-01-30doi:10.1101/2025.01.30.635136Cold Spring Harbor Laboratory Press2025-01-30
<![CDATA[
Structural insights into transcriptional regulation by the helicase RECQL5
]]>
https://biorxiv.org/cgi/content/short/2025.01.29.634372v1?rss=1"
Ariza, A. J. F.Lue, N. Z.Grob, P.Kaeser, B.Fang, J.Kassube, S. A.Nogales, E.2025-01-29doi:10.1101/2025.01.29.634372Cold Spring Harbor Laboratory Press2025-01-29
<![CDATA[
Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant
]]>
https://biorxiv.org/cgi/content/short/2025.01.24.634795v1?rss=1"
Lacy, K. D.Lee, J.Rozen-Gagnon, K.Wang, W.Carroll, T. S.Kronauer, D. J. C.2025-01-27doi:10.1101/2025.01.24.634795Cold Spring Harbor Laboratory Press2025-01-27
<![CDATA[
Centromeres in the thermotolerant yeast K. marxianusmediate attachment to a single microtubule
]]>
https://biorxiv.org/cgi/content/short/2025.01.24.634737v1?rss=1"
Barrero, D. J.Hedouin, S.Mao, Y.Asbury, C. L.Stergachis, A.O'Toole, E.Biggins, S.2025-01-27doi:10.1101/2025.01.24.634737Cold Spring Harbor Laboratory Press2025-01-27
<![CDATA[
Tobacco smoke carcinogens exacerbate APOBEC mutagenesis and carcinogenesis
]]>
https://biorxiv.org/cgi/content/short/2025.01.18.633716v1?rss=1"
Durfee, C.Bergstrom, E. N.Diaz-Gay, M.Zhou, Y.Temiz, N. A.Ibrahim, M. A.Nandi, S. P.Wang, Y.Liu, X.Steele, C. D.Proehl, J.Vogel, R. I.Argyris, P. P.Alexandrov, L. B.Harris, R.2025-01-22doi:10.1101/2025.01.18.633716Cold Spring Harbor Laboratory Press2025-01-22
<![CDATA[
Markovian State Models uncover Casein Kinase 1 dynamics that govern circadian period
]]>
https://biorxiv.org/cgi/content/short/2025.01.17.633651v1?rss=1"
Gravina Ricci, C.Philpott, J. M.Torgrimson, M. R.Freeberg, A. M.Narasimamurthy,, R.Pecora de Barros, E.Amaro, R. E.Virshup, D. M.McCammon, J. A.Partch, C. L.2025-01-22doi:10.1101/2025.01.17.633651Cold Spring Harbor Laboratory Press2025-01-22
<![CDATA[
Autism-Associated Genes and Neighboring lncRNAs Converge on Key Gene Regulatory Networks
]]>
https://biorxiv.org/cgi/content/short/2025.01.20.634000v1?rss=1"
Andersen, R.Talukdar, M.Sakamoto, T.Song, J. H.Qian, X.Lee, S.Delgado, R. N.Zhao, S.Eichfeld, G.Harms, J.Walsh, C. A.2025-01-22doi:10.1101/2025.01.20.634000Cold Spring Harbor Laboratory Press2025-01-22
<![CDATA[
Distinct Classes of Gut Bacterial Molybdenum-Dependent Enzymes Produce Urolithins
]]>
https://biorxiv.org/cgi/content/short/2025.01.17.632430v1?rss=1"
Bae, M.Dong, X.Avila-Pacheco, J.Inyama, F.Hill-Maini, V.Clish, C.Balskus, E. P.2025-01-18doi:10.1101/2025.01.17.632430Cold Spring Harbor Laboratory Press2025-01-18
<![CDATA[
Melbournevirus encodes a shorter H2B-H2A doublet histone variant that forms structurally distinct nucleosome structures.
]]>
https://biorxiv.org/cgi/content/short/2025.01.15.633200v1?rss=1"
Villalta, A.Bisio, H.Toner, C. M.Abergel, C.Luger, K.2025-01-16doi:10.1101/2025.01.15.633200Cold Spring Harbor Laboratory Press2025-01-16
<![CDATA[
Extensive length and homology dependent chimerism in pool-packaged AAV libraries
]]>
https://biorxiv.org/cgi/content/short/2025.01.14.632594v1?rss=1"
Lalanne, J.-B.Mich, J. K.Huynh, C.Hunker, A.McDiarmid, T. A.Levi, B. P.Ting, J. T.Shendure, J.2025-01-15doi:10.1101/2025.01.14.632594Cold Spring Harbor Laboratory Press2025-01-15
<![CDATA[
Squid primary cell culture as a model system and experimental tool
]]>
https://biorxiv.org/cgi/content/short/2025.01.12.632648v1?rss=1"
Kim, Y.Tanner, H. M.Rosenthal, J. J.Brangwynne, C. P.2025-01-13doi:10.1101/2025.01.12.632648Cold Spring Harbor Laboratory Press2025-01-13
<![CDATA[
Absolute measurement of fast and slow neuronal signals with fluorescence lifetime photometry at high temporal resolution
]]>
https://biorxiv.org/cgi/content/short/2025.01.10.632162v1?rss=1"
Lodder, B.Kamath, T.Savenco, E.Roring, B.Siegel, M.Chouinard, J.Lee, S. J.Zagoren, C.Rosen, P. C.Tian, L.Adan, R.Sabatini, B. L.2025-01-12doi:10.1101/2025.01.10.632162Cold Spring Harbor Laboratory Press2025-01-12
<![CDATA[
Testing the function of widespread transcription of the testis
]]>
https://biorxiv.org/cgi/content/short/2025.01.10.632443v1?rss=1"
Kumon, T.Raz, A. A.Fingerhut, J. M.Yamashita, Y. M.2025-01-11doi:10.1101/2025.01.10.632443Cold Spring Harbor Laboratory Press2025-01-11
<![CDATA[
A critical initialization for biological neural networks
]]>
https://biorxiv.org/cgi/content/short/2025.01.10.632397v1?rss=1"
Pachitariu, M.Zhong, L.Gracias, A.Minisi, A.Lopez, C.Stringer, C.2025-01-10doi:10.1101/2025.01.10.632397Cold Spring Harbor Laboratory Press2025-01-10
<![CDATA[
Bacterial and host enzymes modulate the inflammatory response produced by the peptidoglycan of the Lyme disease agent
]]>
https://biorxiv.org/cgi/content/short/2025.01.08.631998v1?rss=1"
McCausland, J. W.Kloos, Z. A.Irnov, I.Sonnert, N. D.Zhou, J.Putnick, R.Mueller, E. A.Steere, A. C.Palm, N. W.Grimes, C. L.Jacobs-Wagner, C.2025-01-08doi:10.1101/2025.01.08.631998Cold Spring Harbor Laboratory Press2025-01-08
<![CDATA[
DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems
]]>
https://biorxiv.org/cgi/content/short/2025.01.08.631726v1?rss=1"
750 additional unique proteins receiving high confidence predictions. Our model, provided as open-source software, will help comprehensively map the anti-phage defense landscape of bacteria, further reveal connections between prokaryotic and eukaryotic immunity, and accelerate biotechnology development.
]]>DeWeirdt, P. C.Mahoney, E. M.Laub, M. T.2025-01-08doi:10.1101/2025.01.08.631726Cold Spring Harbor Laboratory Press2025-01-08
<![CDATA[
Cell-death induced immune response and coagulopathy promote cachexia in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2025.01.07.631515v1?rss=1"
Singh, A.Hu, Y.Lopes, R. F.Lane, L.Woldemichael, H.Xu, C.Udeshi, N.Carr, S. A.Perrimon, N.2025-01-08doi:10.1101/2025.01.07.631515Cold Spring Harbor Laboratory Press2025-01-08
<![CDATA[
Gut epithelium modifies enteric behaviors during nutritional adversity via distinct peptidergic signaling axes
]]>
https://biorxiv.org/cgi/content/short/2025.01.06.631508v1?rss=1"
Sural, S.Walker, Z.Hobert, O.2025-01-06doi:10.1101/2025.01.06.631508Cold Spring Harbor Laboratory Press2025-01-06
<![CDATA[
Colorectal tumor-induced orexigenic imbalance lowers protein appetite and drives early organ wasting symptoms
]]>
https://biorxiv.org/cgi/content/short/2025.01.02.631110v1?rss=1"
Petsakou, A.Filine, E.Li, M.Zheng, A.Perrimon, N.2025-01-03doi:10.1101/2025.01.02.631110Cold Spring Harbor Laboratory Press2025-01-03
<![CDATA[
Stability through plasticity: Finding robust memories through representational drift
]]>
https://biorxiv.org/cgi/content/short/2024.12.19.629245v1?rss=1"
Natrajan, M.Fitzgerald, J. E.2024-12-20doi:10.1101/2024.12.19.629245Cold Spring Harbor Laboratory Press2024-12-20
<![CDATA[
Electric field-induced pore constriction in the human Kv2.1 channel
]]>
https://biorxiv.org/cgi/content/short/2024.12.18.629208v1?rss=1"
Mandala, V. S.MacKinnon, R.2024-12-20doi:10.1101/2024.12.18.629208Cold Spring Harbor Laboratory Press2024-12-20
<![CDATA[
Age-related remodeling of the glycocalyx drives T cell exhaustion
]]>
https://biorxiv.org/cgi/content/short/2024.12.06.627213v1?rss=1"
Zhang, H.Tsui, C. K.Castillo, J. G.Evangelista, A. C.Kim, E. J. Y.Joe, L. K.Twells, N.Robey, E. A.Mahal, L. K.DuPage, M. J.Dillin, A.2024-12-09doi:10.1101/2024.12.06.627213Cold Spring Harbor Laboratory Press2024-12-09
<![CDATA[
The sparse driver system for in vivo single-cell labeling and manipulation in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2024.12.02.626507v1?rss=1"
View larger version (77K):
org.highwire.dtl.DTLVardef@1a53b9org.highwire.dtl.DTLVardef@6eaa3aorg.highwire.dtl.DTLVardef@169cb2forg.highwire.dtl.DTLVardef@9aafb3_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Xu, C.Luo, L.2024-12-04doi:10.1101/2024.12.02.626507Cold Spring Harbor Laboratory Press2024-12-04
<![CDATA[
RCVT: a novel diagnostic to quantify compositional biases among taxa for phylogenomics
]]>
https://biorxiv.org/cgi/content/short/2024.11.28.625917v1?rss=1"
Steenwyk, J. L.Buida, T. J.2024-12-03doi:10.1101/2024.11.28.625917Cold Spring Harbor Laboratory Press2024-12-03
<![CDATA[
Design of high specificity binders for peptide-MHC-I complexes
]]>
https://biorxiv.org/cgi/content/short/2024.11.28.625793v1?rss=1"
Liu, B.Greenwood, N. F.Bonzanini, J. E.Motmaen, A.Sharp, J.Wang, C.Visani, G. M.Vafeados, D. K.Roullier, N.Nourmohammad, A.Garcia, K. C.Baker, D.2024-11-28doi:10.1101/2024.11.28.625793Cold Spring Harbor Laboratory Press2024-11-28
<![CDATA[
A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function
]]>
https://biorxiv.org/cgi/content/short/2024.11.18.624217v1?rss=1"
Saunders, R. A.Allen, W. E.Pan, X.Sandhu, J.Lu, J.Lau, T. K.Smolyar, K.Sullivan, Z.Dulac, C.Weissman, J. S.Zhuang, X.2024-11-21doi:10.1101/2024.11.18.624217Cold Spring Harbor Laboratory Press2024-11-21
<![CDATA[
Inter- and Intrahemispheric Sources of Vestibular Signals to V1
]]>
https://biorxiv.org/cgi/content/short/2024.11.18.624137v1?rss=1"
Bouvier, G.Sanzeni, A.Hamada, E.Brunel, N.Scanziani, M.2024-11-19doi:10.1101/2024.11.18.624137Cold Spring Harbor Laboratory Press2024-11-19
<![CDATA[
Wireless recordings from dragonfly target detecting neurons during prey interception flight
]]>
https://biorxiv.org/cgi/content/short/2024.11.12.622977v1?rss=1"
Lin, H.-T.Siwanowicz, I.Leonardo, A.2024-11-13doi:10.1101/2024.11.12.622977Cold Spring Harbor Laboratory Press2024-11-13
<![CDATA[
Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second strand nicking
]]>
https://biorxiv.org/cgi/content/short/2024.11.11.623112v1?rss=1"
Thawani, A.Rodriguez-Vargas, A.Treeck, B. V.Hassan, N. T.Adelson, D. L.Nogales, E.Collins, K.2024-11-12doi:10.1101/2024.11.11.623112Cold Spring Harbor Laboratory Press2024-11-12
<![CDATA[
Hunger modulates exploration through suppression of dopamine signaling in the tail of striatum
]]>
https://biorxiv.org/cgi/content/short/2024.11.11.622990v1?rss=1"
Kamath, T.Lodder, B.Bilsel, E.Green, I.Dalangin, R.Capelli, P.Raghubardayal, M.Legister, J.Hulshof, L. G.Wallace, J. B.Tian, L.Uchida, N.Watabe-Uchida, M.Sabatini, B. L.2024-11-11doi:10.1101/2024.11.11.622990Cold Spring Harbor Laboratory Press2024-11-11
<![CDATA[
Projections between the globus pallidus externa and cortex span motor and non-motor regions
]]>
https://biorxiv.org/cgi/content/short/2024.11.08.622712v1?rss=1"
Ferenczi, E. A.Wang, W.Biswas, A.Pottala, T.Dong, Y.Chan, A. K.Albanese, M. A.Sohur, R. S.Jia, T.Mastro, K. J.Sabatini, B. L.2024-11-09doi:10.1101/2024.11.08.622712Cold Spring Harbor Laboratory Press2024-11-09
<![CDATA[
Type IV pili-associated secretion of a biofilm matrix protein from Clostridium perfringens that forms intermolecular isopeptide bonds
]]>
https://biorxiv.org/cgi/content/short/2024.11.04.621531v1?rss=1"
25 kD. To determine if the T4P-associated genes comprise a Gram-positive TTSS, the secretome of mutants lacking type IV pilins were examined and a single protein, a von Willebrand A domain containing protein, BsaC (CPE0517), was identified as being dependent on pilin PilA3 for secretion. The bsaC gene is in an operon with genes encoding a SipW signal peptidase and two putative biofilm matrix proteins BsaA and BsaB, both of which have remote homology to Bacillus subtilis biofilm protein TasA. Since BsaA forms long oligomers that are secreted, we analyzed BsaA monomer interactions with de novo modeling. These models projected that the monomers formed isopeptide bonds as part of a donor strand exchange process, in which an N-terminal disordered loop of one monomer intercalates into a beta sheet structure of an adjacent monomer and reforms into a beta sheet with subsequent isopeptide bond formation. Mutations in residues predicted to form the isopeptide bonds led to loss of oligomerization, supporting an exchange and lock mechanism. Phylogenetic analysis showed the BsaA family of proteins are widespread among bacteria and archaea but only a subset is predicted to form isopeptide bonds.
ImportanceFor bacteria to secrete folded proteins to the environment, they have to overcome the physical barriers of an outer membrane in Gram-negative bacteria and the thick peptidoglycan layer in Gram-positive bacteria. One mechanism to do this is the use of a Type II secretion system in Gram-negative bacteria, which has a structure similar to type IV pili and is modeled to act as a piston that pumps folded proteins through the outer membrane to the environment. Clostridium perfringens, like all or most all of the clostridia, has type IV pili and, in fact, has two sets of pilus-associated genes. Here we present evidence that C. perfringens uses one set of pilus genes to secrete a biofilm associated protein and may be responsible for secreting the main biofilm protein, BsaA. We show that BsaA monomers are, unlike most other biofilm matrix proteins, linked by intermolecular isopeptide bonds, enhancing the physical strength of BsaA fibers.
]]>Kivimaki, S. E.Dempsey, S.Tani, J. M.Camper, C.Hicklin, I. K.Blaby-Haas, C. E.Brown, A. M.Melville, S.2024-11-04doi:10.1101/2024.11.04.621531Cold Spring Harbor Laboratory Press2024-11-04
<![CDATA[
Telocytes link epithelial nutrient sensing with amplification of the ILC2-tuft cell circuit
]]>
https://biorxiv.org/cgi/content/short/2024.10.14.618111v1?rss=1"
Liao, C.Ji, M.Wang, Z.-E.Drucker, D. J.Liang, H.-E.Locksley, R. M.2024-10-17doi:10.1101/2024.10.14.618111Cold Spring Harbor Laboratory Press2024-10-17
<![CDATA[
DNA/polysome phase separation and cell width confinement couple nucleoid segregation to cell growth in Escherichia coli
]]>
https://biorxiv.org/cgi/content/short/2024.10.08.617237v1?rss=1"
Papagiannakis, A.Yu, Q.Govers, S. K.Lin, W.-H.Wingreen, N. S.Jacobs-Wagner, C.2024-10-08doi:10.1101/2024.10.08.617237Cold Spring Harbor Laboratory Press2024-10-08
<![CDATA[
Enhancer activation from transposable elements in extrachromosomal DNA
]]>
https://biorxiv.org/cgi/content/short/2024.09.04.611262v1?rss=1"
Kraft, K.Murphy, S. E.Jones, M. G.Shi, Q.Bhargava-Shah, A.Luong, C.Hung, K. L.He, B. J.Li, R.Park, S. K.Weiser, N. E.Luebeck, J.Bafna, V.Boeke, J. D.Mischel, P. S.Boettiger, A. N.Chang, H. Y.2024-09-08doi:10.1101/2024.09.04.611262Cold Spring Harbor Laboratory Press2024-09-08
<![CDATA[
In Vivo Optical Clearing of Mammalian Brain
]]>
https://biorxiv.org/cgi/content/short/2024.09.05.611421v1?rss=1"
Talei Franzesi, G.Gupta, I.Hu, M.Piatkveich, K.Yildirim, M.Zhao, J.-P.Eom, M.Han, S.Park, D.Andaraarachchi, H.Li, Z.Greenhagen, J.Islam, A. M.Vashishtha, P.Yaqoob, Z.Pak, N.Wissner-Gross, A. D.Martin-Alarcon, D.Veinot, J.So, P. T.Kortshagen, U.Yoon, Y.-G.Sur, M.Boyden, E. S.2024-09-07doi:10.1101/2024.09.05.611421Cold Spring Harbor Laboratory Press2024-09-07
<![CDATA[
Widespread Neuroanatomical Integration and Distinct Electrophysiological Properties of Glioma-Innervating Neurons
]]>
https://biorxiv.org/cgi/content/short/2024.08.25.609573v1?rss=1"
Hsieh, A. L.Ganesh, S.Kula, T.Irshad, M.Ferenczi, E. A.Wang, W.Chen, Y.-C.Hu, S.-H.Li, Z.Joshi, S.Haigis, M. C.Sabatini, B. L.2024-08-26doi:10.1101/2024.08.25.609573Cold Spring Harbor Laboratory Press2024-08-26
<![CDATA[
To integrate or not to integrate: Testing degenerate strategies for solving an accumulation of perceptual evidence decision-making task
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.609064v1?rss=1"
Kopec, C. D.Luo, T. Z.Bondy, A. G.Gupta, D.Elliott, V. A.Charlton, J. A.Breda, J. R.Stagnaro, W. M.Reyes, E. J.Sirko, A. I.Bustos, A. F.Willock, J. M.Morrison, J. M.Osorio, K. L.Brody, C. D.2024-08-22doi:10.1101/2024.08.21.609064Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses
]]>
https://biorxiv.org/cgi/content/short/2024.08.21.609082v1?rss=1"
Bhattacharya, T.Alleman, E. M.Noyola, A. C.Emerman, M.Malik, H. S.2024-08-22doi:10.1101/2024.08.21.609082Cold Spring Harbor Laboratory Press2024-08-22
<![CDATA[
Insect size responses to climate changes vary across elevations according to seasonal timing
]]>
https://biorxiv.org/cgi/content/short/2024.08.15.608059v1?rss=1"
Nufio, C.Sheffer, M.Smith, J.Troutman, M.Bawa, S.Taylor, E.Schoville, S.Williams, C.Buckley, L.2024-08-19doi:10.1101/2024.08.15.608059Cold Spring Harbor Laboratory Press2024-08-19
<![CDATA[
Genome-wide screen overexpressing mycobacteriophage Amelie genes identifies multiple inhibitors of mycobacterial growth
]]>
https://biorxiv.org/cgi/content/short/2024.08.14.607960v1?rss=1"
Tafoya, C.Ching, B.Garcia, E. P.Lee, A.Acevedo, M.Bass, K.Chau, E.Lin, H.Mamora, K.Reeves, M.Vaca, M.van Iderstein, W.Velasco, L.Williams, V.Yonemoto, G.Yonemoto, T.Heller, D. M.Diaz, A.2024-08-14doi:10.1101/2024.08.14.607960Cold Spring Harbor Laboratory Press2024-08-14
<![CDATA[
Examining NFκB Genomic Interactions by ChIP-seq and CUT&Tag
]]>
https://biorxiv.org/cgi/content/short/2024.08.11.607521v1?rss=1"
Daly, A. E.Schiffman, A.Hoffmann, A.Smale, S.2024-08-12doi:10.1101/2024.08.11.607521Cold Spring Harbor Laboratory Press2024-08-12
<![CDATA[
A genome-wide screen in ex vivo gallbladders identifies Listeria monocytogenes factors required for virulence in vivo
]]>
https://biorxiv.org/cgi/content/short/2024.08.12.607554v1?rss=1"
Schwardt, N. H.Halsey, C. R.Sanchez, M. E.Reniere, M. L.2024-08-12doi:10.1101/2024.08.12.607554Cold Spring Harbor Laboratory Press2024-08-12
<![CDATA[
Biogenesis, engineering and function of membranes in the CO2-fixing pyrenoid
]]>
https://biorxiv.org/cgi/content/short/2024.08.08.603944v1?rss=1"
Hennacy, J. H.Atkinson, N.Kayser-Browne, A.Ergun, S. L.Franklin, E.Wang, L.Kafri, M.Fauser, F.Vilarrasa-Blasi, J.Jinkerson, R. E.McCormick, A. J.Jonikas, M. C.2024-08-09doi:10.1101/2024.08.08.603944Cold Spring Harbor Laboratory Press2024-08-09
<![CDATA[
Optics-free reconstruction of 2D images via DNA barcode proximity graphs
]]>
https://biorxiv.org/cgi/content/short/2024.08.06.606834v1?rss=1"
Liao, H.Kottapalli, S.Huang, Y.Chaw, M.Gehring, J.Waltner, O.Phung-Rojas, M.Daza, R. M.Matsen, F. A.Trapnell, C.Shendure, J.Srivatsan, S. R.2024-08-08doi:10.1101/2024.08.06.606834Cold Spring Harbor Laboratory Press2024-08-08
<![CDATA[
Single-nucleus transcriptomics resolves differentiation dynamics between shoot stem cells and primary stem.
]]>
https://biorxiv.org/cgi/content/short/2024.08.06.606781v1?rss=1"
Moreno, S. R.Lenz, M. O.Meyerowitz, E. M.Locke, J. C.Jonsson, H.2024-08-08doi:10.1101/2024.08.06.606781Cold Spring Harbor Laboratory Press2024-08-08
<![CDATA[
Synapse weakening-induced caspase-3 activity confers specificity to microglia-mediated synapse elimination
]]>
https://biorxiv.org/cgi/content/short/2024.08.02.606316v1?rss=1"
Yu, Z.Gutu, A.Kim, N.O'Shea, E. K.2024-08-05doi:10.1101/2024.08.02.606316Cold Spring Harbor Laboratory Press2024-08-05
<![CDATA[
Dose-dependent regulation of immune memory responses against HIV by saponin monophosphoryl lipid A nanoparticle adjuvant
]]>
https://biorxiv.org/cgi/content/short/2024.07.31.604373v1?rss=1"
Ramezani-Rad, P.Marina-Zarate, E.Maiorino, L.Myers, A.Michaels, K. K.Pires, I. S.Bloom, N. I.Lopez, P. G.Cottrell, C. A.Burton, I.Groschel, B.Pradhan, A.Stiegler, G.Budai, M.Kumar, D.Pallerla, S.Sayeed, E.Sagar, S. L.Kasturi, S. P.Van Rompay, K. K. A.Hangartner, L.Wagner, A.Burton, D. R.Schief, W. R.Crotty, S.Irvine, D. J.2024-08-03doi:10.1101/2024.07.31.604373Cold Spring Harbor Laboratory Press2024-08-03
<![CDATA[
Unraveling cysteine deficiency-associated rapid weight loss
]]>
https://biorxiv.org/cgi/content/short/2024.07.30.605703v1?rss=1"
Varghese, A.Gusarov, I.Gamallo-Lana, B.Dolgonos, D.Mankan, Y.Shamovsky, I.Phan, M.Jones, R.Gomez-Jenkins, M.White, E.Wang, R.Jones, D.Papagiannakopoulos, T.Pacold, M. E.Mar, A. C.Littman, D. R.Nudler, E.2024-07-31doi:10.1101/2024.07.30.605703Cold Spring Harbor Laboratory Press2024-07-31
<![CDATA[
A resource for comparing AF-Cluster and other AlphaFold2 sampling methods
]]>
https://biorxiv.org/cgi/content/short/2024.07.29.605333v1?rss=1"
Wayment-Steele, H. K.Ovchinnikov, S.Colwell, L.Kern, D.2024-07-30doi:10.1101/2024.07.29.605333Cold Spring Harbor Laboratory Press2024-07-30
<![CDATA[
Gustatory Thalamic Neurons Mediate Aversive Behaviors
]]>
https://biorxiv.org/cgi/content/short/2024.07.29.605702v1?rss=1"
Cao, F.Park, S.Pauli, J. L.Seo, E. Y.Palmiter, R. D.2024-07-30doi:10.1101/2024.07.29.605702Cold Spring Harbor Laboratory Press2024-07-30
<![CDATA[
Distinct mechanisms of inhibition of Kv2 potassium channels by tetraethylammonium and RY785
]]>
https://biorxiv.org/cgi/content/short/2024.07.25.605170v1?rss=1"
Zhang, S.Stix, R.Orabi, E. A.Bernhardt, N.Faraldo-Gomez, J. D.2024-07-25doi:10.1101/2024.07.25.605170Cold Spring Harbor Laboratory Press2024-07-25
<![CDATA[
Chemical Induction of Longevity-Promoting Colanic Acid in the Host's Microbiota
]]>
https://biorxiv.org/cgi/content/short/2024.07.23.604802v1?rss=1"
Hu, G.Cooke, M. B.Wen, A. X.Yu, X.Wang, J.Herman, C.Wang, M. C.2024-07-24doi:10.1101/2024.07.23.604802Cold Spring Harbor Laboratory Press2024-07-24
<![CDATA[
A multi-region recurrent circuit for evidence accumulation in rats
]]>
https://biorxiv.org/cgi/content/short/2024.07.08.602544v1?rss=1"
Gupta, D.Kopec, C. D.Bondy, A. G.Luo, T. Z.Elliott, V. A.Brody, C. D.2024-07-11doi:10.1101/2024.07.08.602544Cold Spring Harbor Laboratory Press2024-07-11
<![CDATA[
Transcriptional landscape of a hypoxia response identifies cell-specific pathways for adaptation
]]>
https://biorxiv.org/cgi/content/short/2024.07.02.601765v1?rss=1"
Kong, J. N.Ghosh, D. D.Savvidis, A.Sando, S. R.Droste, R.Horvitz, H. R.2024-07-04doi:10.1101/2024.07.02.601765Cold Spring Harbor Laboratory Press2024-07-04
<![CDATA[
MeCP2 Interacts with the Super Elongation Complex to Regulate Transcription
]]>
https://biorxiv.org/cgi/content/short/2024.06.30.601446v1?rss=1"
Sonn, J. Y.Kim, W.Iwanaszko, M.Aoi, Y.Li, Y.Parkitny, L.Brissette, J. L.Weiner, L.Al-Ramahi, I.Botas, J.Shilatifard, A.Zoghbi, H. Y.2024-07-01doi:10.1101/2024.06.30.601446Cold Spring Harbor Laboratory Press2024-07-01
<![CDATA[
In silico screening identifies SHPRH as a novel nucleosome acidic patch interactor
]]>
https://biorxiv.org/cgi/content/short/2024.06.26.600687v1?rss=1"
James, A. M.Schmid, E. W.Walter, J. C.Farnung, L.2024-06-27doi:10.1101/2024.06.26.600687Cold Spring Harbor Laboratory Press2024-06-27
<![CDATA[
A cognitive process model captures near-optimal confidence-guided waiting in rats
]]>
https://biorxiv.org/cgi/content/short/2024.06.07.597954v1?rss=1"
Boyd-Meredith, J. T.Piet, A. T.Kopec, C. D.Brody, C. D.2024-06-08doi:10.1101/2024.06.07.597954Cold Spring Harbor Laboratory Press2024-06-08
<![CDATA[
Emergence of activation or repression in transcriptional control under a fixed molecular context
]]>
https://biorxiv.org/cgi/content/short/2024.05.29.596388v1?rss=1"
Martinez-Corral, R.Friedrich, D.Fromel, R.Velten, L.Gunawardena, J.DePace, A.2024-06-02doi:10.1101/2024.05.29.596388Cold Spring Harbor Laboratory Press2024-06-02
<![CDATA[
How repeats rearrange chromosomes in deer mice
]]>
https://biorxiv.org/cgi/content/short/2024.05.29.596518v1?rss=1"
1 Mb) inversions are primarily associated with segmental duplications (SDs). Large inversion breakpoints frequently occur near centromeres, which may be explained by an accumulation of transposable elements in pericentromeric regions driving SD formation. Additionally, multiple large inversions likely arose from ectopic recombination between near-identical centromeric satellite arrays located megabases apart, a previously uncharacterized mechanism of inversion formation. Together, our results illuminate how repeats give rise to massive shifts in chromosome architecture.
]]>Gozashti, L.Harringmeyer, O. S.Hoekstra, H. E.2024-05-29doi:10.1101/2024.05.29.596518Cold Spring Harbor Laboratory Press2024-05-29
<![CDATA[
Developmental maturation of frontal cortical circuits impacts decision-making
]]>
https://biorxiv.org/cgi/content/short/2024.05.24.595609v1?rss=1"
Mastro, K. J.Lee, W.-C.Wang, W.Stevens, B.Sabatini, B. L.2024-05-24doi:10.1101/2024.05.24.595609Cold Spring Harbor Laboratory Press2024-05-24
<![CDATA[
Norepinephrine changes behavioral state via astroglial purinergic signaling
]]>
https://biorxiv.org/cgi/content/short/2024.05.23.595576v1?rss=1"
Chen, A. B.Duque, M.Wang, V. M.Dhanasekar, M.Mi, X.Rymbek, A.Tocquer, L.Narayan, S.Prober, D. A.Yu, G.Wyart, C.Engert, F.Ahrens, M. B.2024-05-23doi:10.1101/2024.05.23.595576Cold Spring Harbor Laboratory Press2024-05-23
<![CDATA[
Inducible transposon mutagenesis for genome-scale forward genetics
]]>
https://biorxiv.org/cgi/content/short/2024.05.21.595064v1?rss=1"
Basta, D. W.Campbell, I. W.Sullivan, E. J.Hotinger, J. A.Hullahalli, K.Waldor, M. K.2024-05-21doi:10.1101/2024.05.21.595064Cold Spring Harbor Laboratory Press2024-05-21
<![CDATA[
KBTBD4 Cancer Hotspot Mutations Drive Neomorphic Degradation of HDAC1/2 Corepressor Complexes
]]>
https://biorxiv.org/cgi/content/short/2024.05.14.593970v1?rss=1"
Xie, X.Zhang, O.Yeo, M. J.Lee, C.Harry, S. A.Paul, L.Li, Y.Payne, N. C.Nam, E.Kwok, H. S.Jiang, H.Mao, H.Hadley, J. L.Lin, H.Batts, M.Gosavi, P. M.D'Angiolella, V.Cole, P. A.Mazitschek, R.Northcott, P. A.Zheng, N.Liau, B. B.2024-05-14doi:10.1101/2024.05.14.593970Cold Spring Harbor Laboratory Press2024-05-14
<![CDATA[
Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations
]]>
https://biorxiv.org/cgi/content/short/2024.05.07.592993v1?rss=1"
Tenthorey, J.del Banco, S.Ramzan, I.Klingenberg, H.Liu, C.Emerman, M.Malik, H. S.2024-05-10doi:10.1101/2024.05.07.592993Cold Spring Harbor Laboratory Press2024-05-10
<![CDATA[
RealtimeDecoder: A fast software module for online clusterless decoding
]]>
https://biorxiv.org/cgi/content/short/2024.05.03.592417v1?rss=1"
Chu, J. P.Coulter, M. E.Denovellis, E. L.Nguyen, T. T.Liu, D. F.Deng, X.Eden, U. T.Kemere, C. T.Frank, L. M.2024-05-06doi:10.1101/2024.05.03.592417Cold Spring Harbor Laboratory Press2024-05-06
<![CDATA[
Identification of high sugar diet-induced dysregulated metabolic pathways in muscle using tissue-specific metabolic models in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2024.04.24.591006v1?rss=1"
Moon, S. J.Hu, Y.Dzieciatkowska, M.Kim, A.-R.Chen, P.-L.Asara, J. M.D'Alessandro, A.Perrimon, N.2024-04-28doi:10.1101/2024.04.24.591006Cold Spring Harbor Laboratory Press2024-04-28
<![CDATA[
The Genetic Origin of the Indo-Europeans
]]>
https://biorxiv.org/cgi/content/short/2024.04.17.589597v1?rss=1"
View larger version (91K):
org.highwire.dtl.DTLVardef@127de98org.highwire.dtl.DTLVardef@87010aorg.highwire.dtl.DTLVardef@1554627org.highwire.dtl.DTLVardef@170dd63_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSummary Figure:C_FLOATNO The origin of Indo-Anatolian and Indo-European languages.
Genetic reconstruction of the ancestry of Pontic-Caspian steppe and West Asian populations points to the North Caucasus-Lower Volga area as the homeland of Indo-Anatolian languages and to the Serednii Stih archaeological culture of the Dnipro-Don area as the homeland of Indo-European languages. The Caucasus-Lower Volga people had diverse distal roots, estimated using the qpAdm software on the left barplot, as Caucasus hunter-gatherer (purple), Central Asian (red), Eastern hunter-gatherer (pink), and West Asian Neolithic (green). Caucasus-Lower Volga expansions, estimated using qpAdm on the right barplot as disseminated Caucasus Neolithic (blue)-Lower Volga Eneolithic (orange) proximal ancestries, mixing with the inhabitants of the North Pontic region (yellow), Volga region (yellow), and West Asia (green).
C_FIG
]]>Lazaridis, I.Patterson, N.Anthony, D.Vyazov, L.Fournier, R.Ringbauer, H.Olalde, I.Khokhlov, A. A.Kitov, E. P.Shishlina, N. I.Ailincai, S. C.Agapov, D. S.Agapov, S. A.Batieva, E.Bauyrzhan, B.Bereczki, Z.Buzhilova, A.Changmai, P.Chizhevsky, A. A.Ciobanu, I.Constantinescu, M.Csanyi, M.Dani, J.Dashkovskiy, P. K.Evinger, S.Faifert, A.Flegontov, P. N.Frinculeasa, A.Frinculeasa, M. N.Hajdu, T.Higham, T.Jarosz, P.Jelinek, P.Khartanovich, V. I.Kirginekov, E. N.Kiss, V.Kitova, A.Kiyashko, A. V.Koledin, J.Korolev, A.Kosintsev2024-04-18doi:10.1101/2024.04.17.589597Cold Spring Harbor Laboratory Press2024-04-18
<![CDATA[
A genomic history of the North Pontic Region from the Neolithic to the Bronze Age
]]>
https://biorxiv.org/cgi/content/short/2024.04.17.589600v1?rss=1"
Nikitin, A. G.Lazaridis, I.Patterson, N.Ivanova, S.Videiko, M.Dergachev, V.Kotova, N.Lillie, M.Potekhina, I.Krenz-Niedbała, M.Łukasik, S.Makhortykh, S.Renson, V.Shephard, H.Sirbu, G.Svyryd, S.Tkachuk, T.Włodarczak, P.Callan, K.Curtis, E.Harney, E.Iliev, L.Kearns, A.Lawson, A. M.Michel, M.Mah, M.Micco, A.Oppenheimer, J.Qiu, L.Workman, J. N.Zalzala, F.Mallick, S.Rohland, N.Reich, D.2024-04-18doi:10.1101/2024.04.17.589600Cold Spring Harbor Laboratory Press2024-04-18
<![CDATA[
Essential and virulence-related protein interactions of pathogens revealed through deep learning
]]>
https://biorxiv.org/cgi/content/short/2024.04.12.589144v1?rss=1"
Humphreys, I. R.Zhang, J.Baek, M.Wang, Y.Krishnakumar, A.Pei, J.Anishchenko, I.Tower, C. A.Jackson, B. A.Warrier, T.Hung, D. T.Peterson, S. B.Mougous, J. D.Cong, Q.Baker, D.2024-04-12doi:10.1101/2024.04.12.589144Cold Spring Harbor Laboratory Press2024-04-12
<![CDATA[
Automated live-cell single-molecule tracking in enteroid monolayers reveals transcription factor dynamics probing lineage-determining function
]]>
https://biorxiv.org/cgi/content/short/2024.04.04.587889v1?rss=1"
Walther, N.Anantakrishnan, S.Dailey, G. M.Tjian, R.Darzacq, X.2024-04-06doi:10.1101/2024.04.04.587889Cold Spring Harbor Laboratory Press2024-04-06
<![CDATA[
Transcription factors ERα and Sox2 have differing multiphasic DNA and RNA binding mechanisms
]]>
https://biorxiv.org/cgi/content/short/2024.03.18.585577v1?rss=1"
Hemphill, W. O.Steiner, H. R.Kominsky, J. R.Wuttke, D. S.Cech, T. R.2024-03-19doi:10.1101/2024.03.18.585577Cold Spring Harbor Laboratory Press2024-03-19
<![CDATA[
Next Generation Neuropeptide Y Receptor Small Molecule Agonists Inhibit Mosquito Biting Behavior
]]>
https://biorxiv.org/cgi/content/short/2024.02.28.582529v1?rss=1"
Zeledon, E. V.Baxt, L. A.Khan, T. A.Michino, M.Miller, M.Huggins, D. J.Jiang, C. S.Vosshall, L. B.Duvall, L. B.2024-03-02doi:10.1101/2024.02.28.582529Cold Spring Harbor Laboratory Press2024-03-02
<![CDATA[
Cognate Antigen Engagement Induces HIV-1 Expression In CD4+ T Cells From People On Long-Term ART
]]>
https://biorxiv.org/cgi/content/short/2024.02.27.582096v1?rss=1"
Moskovjlevic, M.Dragoni, F.Board, N. L.Wu, F.Lai, J.Zhang, H.White, J. R.Ho, R.Lynn, K.Tebas, P.Mounzer, K.Deeks, S. G.Montaner, L. J.Siliciano, J. D.Simonetti, F. R.Siliciano, R. F.2024-03-01doi:10.1101/2024.02.27.582096Cold Spring Harbor Laboratory Press2024-03-01
<![CDATA[
Insulin signaling regulates R2 retrotransposon expression to orchestrate transgenerational rDNA copy number maintenance
]]>
https://biorxiv.org/cgi/content/short/2024.02.28.582629v1?rss=1"
Nelson, J. O.Slicko, A.Raz, A. A.Yamashita, Y. M.2024-02-29doi:10.1101/2024.02.28.582629Cold Spring Harbor Laboratory Press2024-02-29
<![CDATA[
Dynamic reinforcement learning reveals time-dependent shifts in strategy during reward learning.
]]>
https://biorxiv.org/cgi/content/short/2024.02.28.582617v1?rss=1"
Venditto, S. J. C.Miller, K. J.Brody, C. D.Daw, N. D.2024-02-28doi:10.1101/2024.02.28.582617Cold Spring Harbor Laboratory Press2024-02-28
<![CDATA[
CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples
]]>
https://biorxiv.org/cgi/content/short/2024.02.26.582023v1?rss=1"
Elferich, J.Kong, L.Zottig, X.Grigorieff, N.2024-02-28doi:10.1101/2024.02.26.582023Cold Spring Harbor Laboratory Press2024-02-28
<![CDATA[
TASOR expression in naive embryonic stem cells safeguards their developmental potential
]]>
https://biorxiv.org/cgi/content/short/2024.02.25.581951v1?rss=1"
Pinzon-Arteaga, C. A.O'Hara, R.Mazzagati, A.Ballard, E.Hu, Y.Pan, A.Schmitz, D. A.Wei, Y.Sakurai, M.Ly, P.Banaszynski, L.Wu, J.2024-02-26doi:10.1101/2024.02.25.581951Cold Spring Harbor Laboratory Press2024-02-26
<![CDATA[
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.
]]>
https://biorxiv.org/cgi/content/short/2024.02.22.581585v1?rss=1"
Cahn, J.Regulski, M.Lynn, J.Ernst, E.de Santis Alves, C.Ramakrishnan, S.Chougule, K.Wei, S.Lu, Z.Xu, X.Drenkow, J.Kramer, M.Seetharam, A.Hufford, M. B.McCombie, W. R.Ware, D.Jackson, D.Schatz, M. C.Gingeras, T. R.Martienssen, R. A.2024-02-23doi:10.1101/2024.02.22.581585Cold Spring Harbor Laboratory Press2024-02-23
<![CDATA[
CDKN1B (p27kip1) enhances drug tolerant persister CTCs by restricting polyploidy following mitotic inhibitors.
]]>
https://biorxiv.org/cgi/content/short/2024.02.20.581202v1?rss=1"
Horwitz, E.Dubash, T. D.Szabolcs, A.Wittner, B. S.Kreuzer, J.Morris, R.Bardia, A.Chirn, B.Wiley, D.Che, D.Russel, H. C.Lopez, X. I. H.Fox, D. B.Antmen, E.Ting, D. T.Haas, W.Sade-Feldman, M.Maheswaran, S.Haber, D. A.2024-02-22doi:10.1101/2024.02.20.581202Cold Spring Harbor Laboratory Press2024-02-22
<![CDATA[
Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer
]]>
https://biorxiv.org/cgi/content/short/2024.02.19.580970v1?rss=1"
Kim, A.-R.Hu, Y.Comjean, A.Rodiger, J.Mohr, S. E.Perrimon, N.2024-02-21doi:10.1101/2024.02.19.580970Cold Spring Harbor Laboratory Press2024-02-21
<![CDATA[
CoRAL accurately resolves extrachromosomal DNA genomestructures with long-read sequencing
]]>
https://biorxiv.org/cgi/content/short/2024.02.15.580594v1?rss=1"
Zhu, K.Jones, M. G.Luebeck, J.Bu, X.Yi, H.Hung, K. L.Wong, I. T.-L.Zhang, S.Mischel, P. S.Chang, H. Y.Bafna, V.2024-02-16doi:10.1101/2024.02.15.580594Cold Spring Harbor Laboratory Press2024-02-16
<![CDATA[
Mountable miniature microphones to identify and assign mouse ultrasonic vocalizations
]]>
https://biorxiv.org/cgi/content/short/2024.02.05.579003v1?rss=1"
Waidmann, E. N.Yang, V. H.Doyle, W. C.Jarvis, E. D.2024-02-06doi:10.1101/2024.02.05.579003Cold Spring Harbor Laboratory Press2024-02-06
<![CDATA[
Incorporation of a cost of deliberation time in perceptual decision making
]]>
https://biorxiv.org/cgi/content/short/2024.01.31.578067v1?rss=1"
Kira, S.Zylberberg, A.Shadlen, M. N.2024-01-31doi:10.1101/2024.01.31.578067Cold Spring Harbor Laboratory Press2024-01-31
<![CDATA[
Depot-Specific mRNA Expression Programs in Human Adipocytes Suggest Physiological Specialization via Distinct Developmental Programs
]]>
https://biorxiv.org/cgi/content/short/2024.01.28.577632v1?rss=1"
Clemons, H. J.Hogan, D. J.Brown, P. O.2024-01-28doi:10.1101/2024.01.28.577632Cold Spring Harbor Laboratory Press2024-01-28
<![CDATA[
FBM: Freestanding bilayer microscope for single-molecule imaging of membrane proteins
]]>
https://biorxiv.org/cgi/content/short/2024.01.26.577465v1?rss=1"
Perez-Mitta, G.Sezgin, Y.Wang, W.MacKinnon, R.2024-01-27doi:10.1101/2024.01.26.577465Cold Spring Harbor Laboratory Press2024-01-27
<![CDATA[
Regional specialization manifests in the reliability of neural population codes
]]>
https://biorxiv.org/cgi/content/short/2024.01.25.576941v1?rss=1"
Guidera, J. A.Gramling, D. P.Comrie, A. E.Joshi, A.Denovellis, E. L.Lee, K. H.Zhou, J.Thompson, P.Hernandez, J.Yorita, A.Haque, R.Kirst, C.Frank, L. M.2024-01-26doi:10.1101/2024.01.25.576941Cold Spring Harbor Laboratory Press2024-01-26
<![CDATA[
Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer
]]>
https://biorxiv.org/cgi/content/short/2024.01.21.576304v1?rss=1"
Duplaquet, L.So, K.Ying, A. W.Li, X.Li, Y.Qiu, X.Li, R.Singh, S.Wu, X. S.Liu, Q.Qi, J.Somerville, T. D. D.Heiling, H.Mazzola, E.Lee, Y.Zoller, T.Vakoc, C. R.Doench, J. G.Forrester, W. C.Abrams, T.Long, H. W.Niederst, M. J.Kadoch, C.Oser, M. G.2024-01-24doi:10.1101/2024.01.21.576304Cold Spring Harbor Laboratory Press2024-01-24
<![CDATA[
Stepwise neofunctionalization of the NF-κB family member c-Rel during vertebrate evolution
]]>
https://biorxiv.org/cgi/content/short/2024.01.23.575293v1?rss=1"
Daly, A. E.Chang, A. B.Purbey, P.Williams, K. J.Yeh, G.Li, S.Pope, S. D.Venkatesh, B.Redelings, B. D.Li, S.Nguyen, K.Rodriguez, J.Jorgensen, K.Siggers, T.Chen, L.Smale, S. T.2024-01-23doi:10.1101/2024.01.23.575293Cold Spring Harbor Laboratory Press2024-01-23
<![CDATA[
Accurate inference of population history in the presence of background selection
]]>
https://biorxiv.org/cgi/content/short/2024.01.18.576291v1?rss=1"
Cousins, T.Tabin, D.Patterson, N.Reich, D.Durvasula, A.2024-01-20doi:10.1101/2024.01.18.576291Cold Spring Harbor Laboratory Press2024-01-20
<![CDATA[
Value construction through sequential sampling explains serial dependencies in decision making
]]>
https://biorxiv.org/cgi/content/short/2024.01.13.575363v1?rss=1"
Zylberberg, A.Bakkour, A.Shohamy, D.Shadlen, M. N.2024-01-15doi:10.1101/2024.01.13.575363Cold Spring Harbor Laboratory Press2024-01-15
<![CDATA[
The conserved σD envelope stress response monitors multiple aspects of envelope integrity in corynebacteria
]]>
https://biorxiv.org/cgi/content/short/2024.01.07.574573v1?rss=1"
Hart, E.Lyerly, E.BERNHARDT, T.2024-01-08doi:10.1101/2024.01.07.574573Cold Spring Harbor Laboratory Press2024-01-08
<![CDATA[
Local delivery of cell surface-targeted immunocytokines programs systemic anti-tumor immunity
]]>
https://biorxiv.org/cgi/content/short/2024.01.03.573641v1?rss=1"
Santollani, L.Zhang, Y. J.Maiorino, L.Palmeri, J. R.Stinson, J. A.Duhamel, L. R.Qureshi, K.Suggs, J. R.Porth, O. T.Pinney, W.Al Msari, R.Wittrup, K. D.Irvine, D. J.2024-01-03doi:10.1101/2024.01.03.573641Cold Spring Harbor Laboratory Press2024-01-03
<![CDATA[
Image processing tools for petabyte-scale light sheet microscopy data
]]>
https://biorxiv.org/cgi/content/short/2023.12.31.573734v1?rss=1"
Ruan, X.Mueller, M.Liu, G.Görlitz, F.Fu, T.-M.Milkie, D. E.Lillvis, J.Killilea, A.Betzig, E.Upadhyayula, S.2024-01-01doi:10.1101/2023.12.31.573734Cold Spring Harbor Laboratory Press2024-01-01
<![CDATA[
Transforming chemigenetic bimolecular fluorescence complementation systems into chemical dimerizers using chemistry
]]>
https://biorxiv.org/cgi/content/short/2023.12.30.573644v1?rss=1"
Kumar, P.Gutu, A.Waring, A.Brown, T. A.Lavis, L. D.Tebo, A. G.2024-01-01doi:10.1101/2023.12.30.573644Cold Spring Harbor Laboratory Press2024-01-01
<![CDATA[
Precise 3D Localization of Intracerebral Implants with a simple Brain Clearing Method
]]>
https://biorxiv.org/cgi/content/short/2023.12.22.573088v1?rss=1"
Catanese, J.Murakami, T.Ibanez-Tallon, I.2023-12-23doi:10.1101/2023.12.22.573088Cold Spring Harbor Laboratory Press2023-12-23
<![CDATA[
Cell type specific enrichment of somatic aneuploidy in the mammalian brain
]]>
https://biorxiv.org/cgi/content/short/2023.12.18.572285v1?rss=1"
Mukamel, E. A.Liu, H.Behrens, M. M.Ecker, J. R.2023-12-19doi:10.1101/2023.12.18.572285Cold Spring Harbor Laboratory Press2023-12-19
<![CDATA[
The activated plant NRC4 immune receptor forms a hexameric resistosome
]]>
https://biorxiv.org/cgi/content/short/2023.12.18.571367v1?rss=1"
Liu, F.Yang, Z.Wang, C.Martin, R.Qiao, W.Carette, J. E.Luan, S.Nogales, E.Staskawicz, B.2023-12-18doi:10.1101/2023.12.18.571367Cold Spring Harbor Laboratory Press2023-12-18
<![CDATA[
Vision sculpts a continuum of L2/3 cell types in the visual cortex during the critical period
]]>
https://biorxiv.org/cgi/content/short/2023.12.18.572244v1?rss=1"
Xie, F.Jain, S.Butrus, S.Shekhar, K.Zipursky, L. L.2023-12-18doi:10.1101/2023.12.18.572244Cold Spring Harbor Laboratory Press2023-12-18
<![CDATA[
MBD2 couples DNA methylation to Transposable Elements silencing during male gametogenesis.
]]>
https://biorxiv.org/cgi/content/short/2023.12.12.571353v1?rss=1"
Wang, S.Wang, M.Ichino, L.Boone, B. A.Zhong, Z.Papareddy, R. K.Lin, E. K.Yun, J.Feng, S.Jacobsen, S. E.2023-12-13doi:10.1101/2023.12.12.571353Cold Spring Harbor Laboratory Press2023-12-13
<![CDATA[
An interactive web application for exploring human plasma and fibroblast metabolomics data from patients with inborn errors of metabolism
]]>
https://biorxiv.org/cgi/content/short/2023.12.11.571124v1?rss=1"
Cai, L.Hieu, V.Gu, W.Chen, H.Franklin, J.Abou Haidar, L.Wu, Z.Pan, C.Cai, F.Nguyen, P.Ko, B.Yang, C.Zacharias, L. G.Sudderth, J.Montgomery, S.Uhles, C.Fisher, H.Hudnall, J.Hornbuckle, C.Quinn, C.Michel, D.Umana, L.Scheuerle, A.McNutt, M.Gotway, G.Afroze, B.Ni, M.DeBerardinis, R. J.2023-12-12doi:10.1101/2023.12.11.571124Cold Spring Harbor Laboratory Press2023-12-12
<![CDATA[
Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction
]]>
https://biorxiv.org/cgi/content/short/2023.12.07.570640v1?rss=1"
Boocock, J.Alexander, N.Tapia, L. A.Walter-McNeill, L.Munugala, C.Bloom, J. S.Kruglyak, L.2023-12-08doi:10.1101/2023.12.07.570640Cold Spring Harbor Laboratory Press2023-12-08
<![CDATA[
Tumor Immune Cell Targeting Chimeras (TICTACs) For Targeted Depletion of Macrophage-Associated Checkpoint Receptors
]]>
https://biorxiv.org/cgi/content/short/2023.12.06.570444v1?rss=1"
Morimoto, M.Till, N. A.Bertozzi, C. R.2023-12-06doi:10.1101/2023.12.06.570444Cold Spring Harbor Laboratory Press2023-12-06
<![CDATA[
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes
]]>
https://biorxiv.org/cgi/content/short/2023.11.30.569198v1?rss=1"
100 great ape individuals. These reference assemblies are expected to inform human evolution and conservation genetics of nonhuman apes, all of which are endangered species.
]]>Makova, K. D.Pickett, B. D.Harris, R. S.Hartley, G. A.Cechova, M.Pal, K.Nurk, S.Yoo, D.Li, Q.Hebbar, P.McGrath, B. C.Antonacci, F.Aubel, M.Biddanda, A.Borchers, M.Bornberg, E.Bouffard, G. G.Brooks, S. Y.Carbone, L.Carrel, L.Carroll, A.Chang, P.-C.Chin, C.-S.Cook, D. E.Craig, S. J. C.de Gennaro, L.Diekhans, M.Dutra, A.Garcia, G. H.Grady, P. G. S.Green, R. E.Haddad, D.Hallast, P.Harvey, W. T.Hickey, G.Hillis, D. A.Hoyt, S. J.Jeong, H.Kamali, K.Pond, S. L. K.LaPolice, T. M.Lee, C.Lewis, A. P.Loh, Y.-H. E.Maste2023-12-01doi:10.1101/2023.11.30.569198Cold Spring Harbor Laboratory Press2023-12-01
<![CDATA[
Connectivity underlying motor cortex activity during naturalistic goal-directed behavior
]]>
https://biorxiv.org/cgi/content/short/2023.11.25.568673v1?rss=1"
20,000,000 excitatory neuronal pairs revealed fine-scale columnar architecture in layer 2/3 of the motor cortex. Neurons displayed local (< 100 {micro}m) like-to-like connectivity according to target-location tuning, and inhibition over longer spatial scales. Connectivity patterns comprised a continuum, with abundant weakly connected neurons and sparse strongly connected neurons that function as network hubs. Hub neurons were weakly tuned to target-location and reward-outcome but strongly influenced neighboring neurons. This network of neurons, encoding location and outcome of movements to different motor goals, may be a general substrate for rapid learning of complex, goal-directed behaviors.
]]>Finkelstein, A.Daie, K.Rozsa, M.Darshan, R.Svoboda, K.2023-11-26doi:10.1101/2023.11.25.568673Cold Spring Harbor Laboratory Press2023-11-26
<![CDATA[
Two-dose "extended priming" immunization amplifies humoral immune responses by synchronizing vaccine delivery with the germinal center response
]]>
https://biorxiv.org/cgi/content/short/2023.11.20.563479v1?rss=1"
Bhagchandani, S.Yang, L.Maiorino, L.Ben-Akiva, E.Rodrigues, K. A.Romanov, A.Suh, H.Aung, A.Wu, S.Wadhera, A.Chakraborty, A. K.Irvine, D. J.2023-11-21doi:10.1101/2023.11.20.563479Cold Spring Harbor Laboratory Press2023-11-21
<![CDATA[
Flow-field inference from neural data using deep recurrent networks
]]>
https://biorxiv.org/cgi/content/short/2023.11.14.567136v1?rss=1"
Kim, T. D.Luo, T. Z.Can, T.Krishnamurthy, K.Pillow, J. W.Brody, C. D.2023-11-16doi:10.1101/2023.11.14.567136Cold Spring Harbor Laboratory Press2023-11-16
<![CDATA[
Deep generative model deciphers derailed trajectories in acute myeloid leukemia
]]>
https://biorxiv.org/cgi/content/short/2023.11.11.566719v1?rss=1"
Nazaret, A.Fan, J. L.Lavallee, V.-P.Cornish, A. E.Kiseliovas, V.Masilionis, I.Chun, J.Bowman, R. L.Eisman, S. E.Wang, J.Shi, L.Levine, R. L.Mazutis, L.Blei, D.Pe'er, D.Azizi, E.2023-11-15doi:10.1101/2023.11.11.566719Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
Development of LRRK2 designed ankyrin-repeat proteins
]]>
https://biorxiv.org/cgi/content/short/2023.11.14.567123v1?rss=1"
Dederer, V.Sanz Murillo, M.Karasmanis, E. P.Hatch, K. S.Chatterjee, D.Preuss, F.Abdul Azeez, K. R.Nguyen, L. V.Galicia, C.Dreier, B.Pluckthun, A.Versees, W.Mathea, S.Leschziner, A. E.Reck-Peterson, S. L.Knapp, S.2023-11-15doi:10.1101/2023.11.14.567123Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
Cell type-specific effects of age and sex on human cortical neurons
]]>
https://biorxiv.org/cgi/content/short/2023.11.11.566717v1?rss=1"
Chien, J.-F.Liu, H.Wang, B.-A.Luo, C.Bartlett, A.Castanon, R.Johnson, N. D.Nery, J. R.Osteen, J.Li, J.Altshul, J.Kenworthy, M.Valadon, C.Liem, M.Claffey, N.O'Connor, C.Seeker, L. A.Ecker, J. R.Behrens, M. M.Mukamel, E. A.2023-11-15doi:10.1101/2023.11.11.566717Cold Spring Harbor Laboratory Press2023-11-15
<![CDATA[
Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment
]]>
https://biorxiv.org/cgi/content/short/2023.11.09.566470v1?rss=1"
Daugird, T. A.Shi, Y.Holland, K. L.Rostamian, H.Liu, Z.Lavis, L. D.Rodriguez, J.Strahl, B. D.Legant, W. R.2023-11-13doi:10.1101/2023.11.09.566470Cold Spring Harbor Laboratory Press2023-11-13
<![CDATA[
LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins
]]>
https://biorxiv.org/cgi/content/short/2023.11.01.565189v1?rss=1"
Saba, J. A.Huang, Z.Schole, K. L.Ye, X.Bhatt, S. D.Li, Y.Timp, W.Cheng, J.Green, R.2023-11-02doi:10.1101/2023.11.01.565189Cold Spring Harbor Laboratory Press2023-11-02
<![CDATA[
Critical capillary waves of biomolecular condensates
]]>
https://biorxiv.org/cgi/content/short/2023.10.29.564316v1?rss=1"
Shimobayashi, S. F.Konishi, K.Ackerman, P. J.Taniguchi, T.brangwynne, C. P.2023-11-01doi:10.1101/2023.10.29.564316Cold Spring Harbor Laboratory Press2023-11-01
<![CDATA[
Multi-modal skin atlas associates a multicellular immune-stromal community with altered cornification and T cell expansion in atopic dermatitis
]]>
https://biorxiv.org/cgi/content/short/2023.10.29.563503v1?rss=1"
Fiskin, E.Eraslan, G.Alora-Palli, M. B.Leyva-Castillo, J. M.Kim, S.Choe, H.Lareau, C. A.Lau, H.Finan, E. P.Teixeira-Soldano, I.LaBere, B.Chu, A.Woods, B.Chou, J.Slyper, M.Waldman, J.Islam, S.Schneider, L.Phipatanakul, W.Platt, C.Rozenblatt-Rosen, O.Delorey, T. M.Deguine, J.Smith, G. P.Geha, R. S.Regev, A.Xavier, R. J.2023-10-30doi:10.1101/2023.10.29.563503Cold Spring Harbor Laboratory Press2023-10-30
<![CDATA[
Single nuclei sequencing reveals C4 photosynthesis is based on rewiring of ancestral cell identity networks
]]>
https://biorxiv.org/cgi/content/short/2023.10.26.562893v1?rss=1"
Swift, J.Luginbuehl, L. H.Schreier, T.Donald, R. M.Lee, T.Nery, J.Ecker, J. R.Hibberd, J. M.2023-10-27doi:10.1101/2023.10.26.562893Cold Spring Harbor Laboratory Press2023-10-27
<![CDATA[
Widespread fungal-bacterial competition for magnesium enhances antibiotic resistance
]]>
https://biorxiv.org/cgi/content/short/2023.10.25.563990v1?rss=1"
Hsieh, Y.-Y. P.Sun, W. W.Young, J. M.Cheung, R.Hogan, D. A.Dandekar, A. A.Malik, H. S.2023-10-26doi:10.1101/2023.10.25.563990Cold Spring Harbor Laboratory Press2023-10-26
<![CDATA[
Enhancer-driven local 3D chromatin domain folding modulates transcription in human mammary tumor cells
]]>
https://biorxiv.org/cgi/content/short/2023.10.17.562690v1?rss=1"
Kocanova, S.Raynal, F.Goiffon, I.Oksuz, B. A.Bau, D.Kamgoue, A.Cantaloube, S.Zhan, Y.Lajoie, B.Marti-Renom, M. A.Dekker, J.Bystricky, K.2023-10-19doi:10.1101/2023.10.17.562690Cold Spring Harbor Laboratory Press2023-10-19
<![CDATA[
Nanomechanics of wild-type and mutant dimers of the tip-link protein protocadherin 15
]]>
https://biorxiv.org/cgi/content/short/2023.10.17.562769v1?rss=1"
Villasante, C. M.Deng, X.Cohen, J. E.Hudspeth, A. J.2023-10-19doi:10.1101/2023.10.17.562769Cold Spring Harbor Laboratory Press2023-10-19
<![CDATA[
Evolution of novel sensory organs in fish with legs
]]>
https://biorxiv.org/cgi/content/short/2023.10.14.562285v1?rss=1"
Allard, C. A.Herbert, A. L.Krueger, S. P.Liang, Q.Walsh, B. L.Rhyne, A.Gourlay, A.Seminara, A.Baldwin, M. W.Kingsley, D. M.Bellono, N.2023-10-18doi:10.1101/2023.10.14.562285Cold Spring Harbor Laboratory Press2023-10-18
<![CDATA[
A blue-shifted genetically encoded Ca2+ indicator with enhanced two-photon absorption
]]>
https://biorxiv.org/cgi/content/short/2023.10.12.562058v1?rss=1"
Aggarwal, A.Sunil, S.Bendifallah, I.Moon, M.Drobizhev, M.Zarowny, L.Zheng, J.Wu, S.-Y.Lohman, A.Tebo, A.EMILIANI, V.Podgorski, K.Shen, Y.Campbell, R.2023-10-18doi:10.1101/2023.10.12.562058Cold Spring Harbor Laboratory Press2023-10-18
<![CDATA[
Non-canonical attractor dynamics underlie perceptual decision-making
]]>
https://biorxiv.org/cgi/content/short/2023.10.15.562427v1?rss=1"
Luo, T. Z.Kim, T. D.Gupta, D.Bondy, A. G.Kopec, C. D.Elliott, V. A.DePasquale, B.Brody, C.2023-10-17doi:10.1101/2023.10.15.562427Cold Spring Harbor Laboratory Press2023-10-17
<![CDATA[
Methylphenidate modulates motor cortical dynamics and behavior
]]>
https://biorxiv.org/cgi/content/short/2023.10.15.562405v1?rss=1"
Verhein, J. R.Vyas, S.Shenoy, K. V.2023-10-17doi:10.1101/2023.10.15.562405Cold Spring Harbor Laboratory Press2023-10-17
<![CDATA[
hkb is required for DIP-α expression and target recognition in the Drosophila neuromuscular circuit
]]>
https://biorxiv.org/cgi/content/short/2023.10.15.562341v1?rss=1"
Carrillo, R. A.Wang, Y.Salazar, R.Simonetta, L.Sorrentino, V.Gatton, T. J.Wu, B.Vecsey, C. G.2023-10-17doi:10.1101/2023.10.15.562341Cold Spring Harbor Laboratory Press2023-10-17
<![CDATA[
Chlorophyll to Zeaxanthin Energy Transfer in Non-Photochemical Quenching: An Exciton Annihilation-free Transient Absorption Study
]]>
https://biorxiv.org/cgi/content/short/2023.10.11.561813v1?rss=1"
Lee, T.-Y.Lam, L.Patel-Tupper, D.Roy, P. P.Ma, S. A.Lucas-DeMott, A.Karavolias, N. G.Niyogi, K. K.Fleming, G. R.2023-10-14doi:10.1101/2023.10.11.561813Cold Spring Harbor Laboratory Press2023-10-14
<![CDATA[
Activation of automethylated PRC2 by dimerization on chromatin
]]>
https://biorxiv.org/cgi/content/short/2023.10.12.562141v1?rss=1"
Sauer, P. V.Pavlenko, E.Cookis, T.Zirden, L. C.Renn, J.Singhal, A.Hunold, P.Hoehne, M. N.van Ray, O.Haensel-Hertsch, R.Sanbonmatsu, K. Y.Nogales, E.Poepsel, S.2023-10-13doi:10.1101/2023.10.12.562141Cold Spring Harbor Laboratory Press2023-10-13
<![CDATA[
Exploration of the Tunability of BRD4 Degradation by DCAF16 Trans-labelling Covalent Glues
]]>
https://biorxiv.org/cgi/content/short/2023.10.07.561308v1?rss=1"
Hassan, M. M.Li, Y.-D.Ma, M. W.Teng, M.Byun, W. S.Puvar, K.Lumpkin, R.Sandoval, B.Rutter, J. C.Jin, C. Y.Wang, M. Y.Xu, S.Schmoker, A. M.Cheong, H.Groendyke, B. J.Qi, J.Fischer, E. S.Ebert, B. L.Gray, N.2023-10-10doi:10.1101/2023.10.07.561308Cold Spring Harbor Laboratory Press2023-10-10
<![CDATA[
Post-transcriptional control contributes to hypoxia induced tumorigenic phenotypes in macrophages
]]>
https://biorxiv.org/cgi/content/short/2023.10.09.561558v1?rss=1"
Courvan, E. M. C.Parker, R.2023-10-10doi:10.1101/2023.10.09.561558Cold Spring Harbor Laboratory Press2023-10-10
<![CDATA[
The Essential Role of Latrophilin-1 Adhesion GPCR Nanoclusters in Inhibitory Synapses
]]>
https://biorxiv.org/cgi/content/short/2023.10.08.561368v1?rss=1"
Matus, D.Lopez, J. M.Sando, R. C.Südhof, T. C.2023-10-08doi:10.1101/2023.10.08.561368Cold Spring Harbor Laboratory Press2023-10-08
<![CDATA[
Dissecting telomerase RNA structural heterogeneity in living human cells with DMS-MaPseq
]]>
https://biorxiv.org/cgi/content/short/2023.10.04.560962v1?rss=1"
Forino, N. M.Woo, J. Z.Zaug, A. J.Jimenez, A. G.Cech, T. R.Rouskin, S.Stone, M.2023-10-05doi:10.1101/2023.10.04.560962Cold Spring Harbor Laboratory Press2023-10-05
<![CDATA[
A Modular Design for Synthetic Membraneless Organelles Enables Compositional and Functional Control
]]>
https://biorxiv.org/cgi/content/short/2023.10.03.560789v1?rss=1"
Walls, M. T.Xu, K.Brangwynne, C. P.Avalos, J. L.2023-10-04doi:10.1101/2023.10.03.560789Cold Spring Harbor Laboratory Press2023-10-04
<![CDATA[
Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance
]]>
https://biorxiv.org/cgi/content/short/2023.10.02.560617v1?rss=1"
Zhang, J. Z.Ong, S.-E.Baker, D.Maly, D. J.2023-10-04doi:10.1101/2023.10.02.560617Cold Spring Harbor Laboratory Press2023-10-04
<![CDATA[
Alternative Splicing of Latrophilin-3 Controls Synapse Formation
]]>
https://biorxiv.org/cgi/content/short/2023.10.02.560463v1?rss=1"
Wang, S.Sudhof, T. C.Sun, W.Quake, S. R.Roth, B. L.DeLeon, C.2023-10-03doi:10.1101/2023.10.02.560463Cold Spring Harbor Laboratory Press2023-10-03
<![CDATA[
Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility associated with the spread of the Uralic and Yeniseian languages
]]>
https://biorxiv.org/cgi/content/short/2023.10.01.560332v1?rss=1"
Zeng, T. C.Vyazov, L. M.Kim, A.Flegontov, P. N.Sirak, K.Maier, R.Lazaridis, I.Akbari, A.Frachetti, M.Tishkin, A. A.Ryabogina, N. E.Agapov, S. A.Agapov, D. S.Alekseev, A. N.Boeskorov, G. G.Chizhevsky, A. A.Derevianko, A. P.Dyakonov, V. M.Enshin, D. N.Fribus, A. V.Frolov, Y. V.Grushin, S. P.Khokhlov, A. A.Kitov, E. P.Kosintsev, P.Kovtun, I. V.Kiryushin, K. Y.Kiryushin, Y. F.Makarov, N. P.Morozov, V. V.Nikolaev, E. N.Rykun, M. P.Savenkova, T. M.Shchelchkova, M. V.Skochina, S. N.Shirokov, V.Sherstobitova, O. S.Slepchenko, S.2023-10-02doi:10.1101/2023.10.01.560332Cold Spring Harbor Laboratory Press2023-10-02
<![CDATA[
Mapping of multiple neurotransmitter receptor subtypes and distinct protein complexes to the connectome
]]>
https://biorxiv.org/cgi/content/short/2023.10.02.560011v1?rss=1"
Sanfilippo, P.Kim, A. J.Bhukel, A.Yoo, J.Mirshahidi, P. S.Pandey, V.Bevir, H.Yuen, A.Mirshahidi, P. S.Guo, P.Li, H.-S.Wohlschlegel, J. A.Aso, Y.Zipursky, S. L.2023-10-02doi:10.1101/2023.10.02.560011Cold Spring Harbor Laboratory Press2023-10-02
<![CDATA[
Inhalable point-of-care urinary diagnostic platform
]]>
https://biorxiv.org/cgi/content/short/2023.09.30.560328v1?rss=1"
Zhong, Q.Tan, E. K. W.Martin-Alonso, C.Parisi, T.Hao, L.Kirkpatrick, J. D.Fadel, T.Fleming, H.Jacks, T.Bhatia, S. N.2023-10-02doi:10.1101/2023.09.30.560328Cold Spring Harbor Laboratory Press2023-10-02
<![CDATA[
Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes
]]>
https://biorxiv.org/cgi/content/short/2023.09.30.560311v1?rss=1"
Sauer, P. V.Cupellini, L.Sutter, M.Bondanza, M.Dominguez Martin, M. A.Kirst, H.Bina, D.Koh, A. F.Kotecha, A.Greber, B. J.Nogales, E.Polivka, T.Mennucci, B.Kerfeld, C. A.2023-09-30doi:10.1101/2023.09.30.560311Cold Spring Harbor Laboratory Press2023-09-30
<![CDATA[
Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling
]]>
https://biorxiv.org/cgi/content/short/2023.09.26.559641v1?rss=1"
Weingarten-Gabbay, S.Bauer, M. R.Stanton, A. C.Klaeger, S.Verzani, E. K.Lopez, D.Clauser, K. R.Carr, S. A.Abelin, J. G.Rice, C. M.Sabeti, P. C.2023-09-28doi:10.1101/2023.09.26.559641Cold Spring Harbor Laboratory Press2023-09-28
<![CDATA[
Advancement in Cellular Topographic and Nanoparticle Capture Imaging by High Resolution Microscopy Incorporating a Freeze-Drying and Gaseous Nitrogen-based Approach
]]>
https://biorxiv.org/cgi/content/short/2023.09.28.559906v1?rss=1"
Uryu, K.Soplop, N.Sheahan, T. P.Catanese, M.-T.Huynh, C.Pena, J.Boudreau, N.Matei, I.Kenific, C.Hashimoto, A.Hoshino, A.Rice, C. M.Lyden, D.2023-09-28doi:10.1101/2023.09.28.559906Cold Spring Harbor Laboratory Press2023-09-28
<![CDATA[
Reconstitution of Early Paclitaxel Biosynthetic Network
]]>
https://biorxiv.org/cgi/content/short/2023.09.27.559859v1?rss=1"
Liu, J. C.-T.De La Pena, R.Tocol, C.Sattely, E. S.2023-09-28doi:10.1101/2023.09.27.559859Cold Spring Harbor Laboratory Press2023-09-28
<![CDATA[
Nucleolar dynamics are determined by the ordered assembly of the ribosome
]]>
https://biorxiv.org/cgi/content/short/2023.09.26.559432v1?rss=1"
Sheu-Gruttadauria, J.Yan, X.Stuurman, N.Floor, S. N.Vale, R. D.2023-09-27doi:10.1101/2023.09.26.559432Cold Spring Harbor Laboratory Press2023-09-27
<![CDATA[
BAllC and BAllCools: Efficient Formatting and Operating for Single-Cell DNA Methylation Data
]]>
https://biorxiv.org/cgi/content/short/2023.09.22.559047v1?rss=1"
Tian, W.Ding, W.Ecker, J. R.2023-09-25doi:10.1101/2023.09.22.559047Cold Spring Harbor Laboratory Press2023-09-25
<![CDATA[
Graph-Dynamo: Learning stochastic cellular state transition dynamics from single cell data
]]>
https://biorxiv.org/cgi/content/short/2023.09.24.559170v1?rss=1"
Zhang, Y.Qiu, X.Weissman, J. S.Bahar, I.Xing, J.2023-09-24doi:10.1101/2023.09.24.559170Cold Spring Harbor Laboratory Press2023-09-24
<![CDATA[
De novo designed Hsp70 activator dissolves intracellular condensates
]]>
https://biorxiv.org/cgi/content/short/2023.09.18.558356v1?rss=1"
Zhang, J. Z.Greenwood, N.Hernandez, J.Cuperus, J. T.Huang, B.Ryder, B. D.Queitsch, C.Gestwicki, J. E.Baker, D.2023-09-19doi:10.1101/2023.09.18.558356Cold Spring Harbor Laboratory Press2023-09-19
<![CDATA[
Double-Strand Break Repair Pathways Differentially Affect Processing and Transduction by Dual AAV Vectors
]]>
https://biorxiv.org/cgi/content/short/2023.09.19.558438v1?rss=1"
Maurer, A. C.Benyamini, B.Fan, V. B.Whitney, O. N.Dailey, G. M.Darzacq, X.Weitzman, M. D.Tjian, R.2023-09-19doi:10.1101/2023.09.19.558438Cold Spring Harbor Laboratory Press2023-09-19
<![CDATA[
Surprising Features of Nuclear Receptor Interaction Networks Revealed by Live Cell Single Molecule Imaging
]]>
https://biorxiv.org/cgi/content/short/2023.09.16.558083v1?rss=1"
Dahal, L.Graham, T. G. W.Dailey, G. M.Heckert, A. B.Tjian, R.Darzacq, X.2023-09-17doi:10.1101/2023.09.16.558083Cold Spring Harbor Laboratory Press2023-09-17
<![CDATA[
Low-latency extracellular spike assignment for high-density electrodes at single-neuron resolution
]]>
https://biorxiv.org/cgi/content/short/2023.09.14.557854v1?rss=1"
Lai, C.Kim, D.Lustig, B.Tanaka, S.Barbartis, B.Narayan, L.Colonell, J.Paulsen, O.Lee, A. K.Harris, T. D.2023-09-15doi:10.1101/2023.09.14.557854Cold Spring Harbor Laboratory Press2023-09-15
<![CDATA[
Coding of self and environment by Pacinian neurons in freely moving animals
]]>
https://biorxiv.org/cgi/content/short/2023.09.11.557225v1?rss=1"
Turecek, J.Ginty, D. D.2023-09-13doi:10.1101/2023.09.11.557225Cold Spring Harbor Laboratory Press2023-09-13
<![CDATA[
Plasma membrane abundance dictates phagocytic capacity and functional crosstalk in myeloid cells
]]>
https://biorxiv.org/cgi/content/short/2023.09.12.556572v1?rss=1"
Winer, B. Y.Settle, A. H.Yakimov, A. M.Jeronimo, C.Lazarovt, T.Tipping, M.Saoi, M.Sawh, A.Sepp, A.-L. L.Galiano, M.Perry, J. S. A.Wong, Y. Y.Geissmann, F.Cross, J.Zhou, T.Kam, L. C.Pasoli, H. A.Hohl, T.Cyster, J. G.Weiner, O.Huse, M.2023-09-13doi:10.1101/2023.09.12.556572Cold Spring Harbor Laboratory Press2023-09-13
<![CDATA[
A cell atlas of the larval Aedes aegypti ventral nerve cord
]]>
https://biorxiv.org/cgi/content/short/2023.09.08.556941v1?rss=1"
Yin, C.Morita, T.Parrish, J. Z.2023-09-09doi:10.1101/2023.09.08.556941Cold Spring Harbor Laboratory Press2023-09-09
<![CDATA[
Drugs of abuse hijack a mesolimbic pathway that processes homeostatic need
]]>
https://biorxiv.org/cgi/content/short/2023.09.03.556059v1?rss=1"
Tan, B.Browne, C. J.Nobauer, T.Vaziri, A.Friedman, J. M.Nestler, E. J.2023-09-05doi:10.1101/2023.09.03.556059Cold Spring Harbor Laboratory Press2023-09-05
<![CDATA[
The mechanism of Gαq regulation of PLCβ3-catalyzed PIP2 hydrolysis.
]]>
https://biorxiv.org/cgi/content/short/2023.08.29.555394v1?rss=1"
Falzone, M. E.MacKinnon, R.2023-08-30doi:10.1101/2023.08.29.555394Cold Spring Harbor Laboratory Press2023-08-30
<![CDATA[
Niche-specific macrophage loss promotes skin capillary aging
]]>
https://biorxiv.org/cgi/content/short/2023.08.25.554832v1?rss=1"
Mesa, K. R.O'Connor, K. A.Ng, C.Salvatore, S.Littman, D. R.2023-08-27doi:10.1101/2023.08.25.554832Cold Spring Harbor Laboratory Press2023-08-27
<![CDATA[
Cellular and Molecular Basis of Leptin Resistance
]]>
https://biorxiv.org/cgi/content/short/2023.08.24.554526v1?rss=1"
Tan, B.Hedbacker, K.Kelly, L.Zhang, Z.Luo, J.-D.Rabinowitz, J. D.Friedman, J. M.2023-08-26doi:10.1101/2023.08.24.554526Cold Spring Harbor Laboratory Press2023-08-26
<![CDATA[
iATPSnFR2: a high dynamic range fluorescent sensor for monitoring intracellular ATP
]]>
https://biorxiv.org/cgi/content/short/2023.08.24.554624v1?rss=1"
Marvin, J. S.Kokotos, A. C.Kumar, M.Pulido, C.Tkachuk, A. N.Yao, J. S.Brown, T. A.Ryan, T. A.2023-08-24doi:10.1101/2023.08.24.554624Cold Spring Harbor Laboratory Press2023-08-24
<![CDATA[
ACD15, ACD21, and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements.
]]>
https://biorxiv.org/cgi/content/short/2023.08.23.554494v1?rss=1"
Boone, B. A.Ichino, L.Wang, S.Gardiner, J.Yun, J.Jami-Alahmadi, Y.Sha, J.Mendoza, C. P.Steelman, B. J.Aardenne, A. v.Kira-Lucas, S.Trentchev, I.Wohlschlegel, J.Jacobsen, S. E.2023-08-24doi:10.1101/2023.08.23.554494Cold Spring Harbor Laboratory Press2023-08-24
<![CDATA[
NMR measurements of transient low-populated tautomeric and anionic Watson-Crick-like G·T/U in RNA:DNA hybrids: Implications for the fidelity of transcription and CRISPR/Cas9 gene editing
]]>
https://biorxiv.org/cgi/content/short/2023.08.24.554670v1?rss=1"
Szekely, O.Rangadurai, A. K.Gu, S.Manghrani, A.Guseva, S.Al-Hashimi, H.2023-08-24doi:10.1101/2023.08.24.554670Cold Spring Harbor Laboratory Press2023-08-24
<![CDATA[
Evaluation of the RNA-dependence of PRC2 binding to chromatin in human pluripotent stem cells
]]>
https://biorxiv.org/cgi/content/short/2023.08.17.553776v1?rss=1"
Long, Y.Hwang, T.Gooding, A. R.Goodrich, K. J.Vallery, T. K.Rinn, J. L.Cech, T. R.2023-08-18doi:10.1101/2023.08.17.553776Cold Spring Harbor Laboratory Press2023-08-18
<![CDATA[
Expanding the Drosophila toolkit for dual control of gene expression
]]>
https://biorxiv.org/cgi/content/short/2023.08.15.553399v1?rss=1"
Zirin, J.Jusiak, B.Lopes, R.Ewen-Campen, B.Bosch, J.Villalta, C.Forman, C.Hu, Y.Mohr, S.Perrimon, N.2023-08-16doi:10.1101/2023.08.15.553399Cold Spring Harbor Laboratory Press2023-08-16
<![CDATA[
Action space restructures visual working memory in prefrontal cortex
]]>
https://biorxiv.org/cgi/content/short/2023.08.13.553135v1?rss=1"
Jonikaitis, D.Zhu, S.2023-08-15doi:10.1101/2023.08.13.553135Cold Spring Harbor Laboratory Press2023-08-15
<![CDATA[
Thyroid hormone rewires cortical circuits to coordinate body-wide metabolism and exploratory drive
]]>
https://biorxiv.org/cgi/content/short/2023.08.10.552874v1?rss=1"
Hochbaum, D. R.Dubinsky, A. C.Farnsworth, H. C.Hulshof, L.Kleinberg, G.Urke, A.Wang, W.Hakim, R.Robertson, K.Park, C.Solberg, A.Yang, Y.Baynard, C.Nadaf, N. M.Beron, C.Girasole, A.Chantranupong, L.Cortopassi, M.Prouty, S.Geistlinger, L.Banks, A.Scanlan, T.Greenberg, M.Boulting, G. L.Macosko, E.Sabatini, B. L.2023-08-10doi:10.1101/2023.08.10.552874Cold Spring Harbor Laboratory Press2023-08-10
<![CDATA[
Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes
]]>
https://biorxiv.org/cgi/content/short/2023.08.09.552727v1?rss=1"
Yoon, P. H.Skopintsev, P.Shi, H.Chen, L.-X.Adler, B. A.Al-Shimary, M.Craig, R. J.Li, Z.Amerasekera, J.Trinidad, M.Nisonoff, H.Chen, K.Lahiri, A.Boger, R.Jacobsen, S.Banfield, J. F.Doudna, J. A.2023-08-10doi:10.1101/2023.08.09.552727Cold Spring Harbor Laboratory Press2023-08-10
<![CDATA[
Machine-guided design of synthetic cell type-specific cis-regulatory elements
]]>
https://biorxiv.org/cgi/content/short/2023.08.08.552077v1?rss=1"
Gosai, S. J.Castro, R. I.Fuentes, N.Butts, J. C.Kales, S.Noche, R. R.Mouri, K.Sabeti, P. C.Reilly, S. K.Tewhey, R.2023-08-09doi:10.1101/2023.08.08.552077Cold Spring Harbor Laboratory Press2023-08-09
<![CDATA[
Discovery of a Well-Folded Protein Interaction Hub Within the Human Long Non-Coding RNA NORAD
]]>
https://biorxiv.org/cgi/content/short/2023.08.07.552337v1?rss=1"
Kumar, A.Wan, H.Perry, Z.Patel, S.Araujo Tavares, R. d. C.Pyle, A. M.2023-08-07doi:10.1101/2023.08.07.552337Cold Spring Harbor Laboratory Press2023-08-07
<![CDATA[
Feedforward amplification in recurrent networks underliesparadoxical neural coding
]]>
https://biorxiv.org/cgi/content/short/2023.08.04.552026v1?rss=1"
Daie, K.Fontolan, L.Druckmann, S.Svoboda, K.2023-08-06doi:10.1101/2023.08.04.552026Cold Spring Harbor Laboratory Press2023-08-06
<![CDATA[
Multi-day Neuron Tracking in High Density Electrophysiology Recordings using EMD
]]>
https://biorxiv.org/cgi/content/short/2023.08.03.551724v1?rss=1"
Harris, T. D.Yuan, A. X.Colonell, J. I.Lebedeva, A.Charles, A.2023-08-05doi:10.1101/2023.08.03.551724Cold Spring Harbor Laboratory Press2023-08-05
<![CDATA[
A genome-wide cytotoxicity screen of Cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth
]]>
https://biorxiv.org/cgi/content/short/2023.08.04.552056v1?rss=1"
65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes of interest like inhibition of host growth. This study describes the results of a screen evaluating the effects of overexpressing each gene encoded by the temperate Cluster F1 mycobacteriophage Girr on the growth of the host bacterium Mycobacterium smegmatis. Overexpression of 29 of the 102 Girr genes ([~]28% of the genome) resulted in mild to severe cytotoxicity. Of the 29 toxic genes described, 12 have no known function (NKF) and are predominately small proteins of <125 amino acids. Overexpression of the majority of these 12 cytotoxic NKF proteins resulted in moderate to severe growth reduction and represent novel antimicrobial products. The remaining 17 toxic genes have predicted functions, encoding products involved in phage structure, DNA replication/modification, DNA binding/gene regulation, or other enzymatic activity. Comparison of this dataset with prior genome-wide cytotoxicity screens of mycobacteriophages Waterfoul and Hammy reveals some common functional themes, though several of the predicted Girr functions associated with cytotoxicity in our report, including genes involved in lysogeny, have not been described previously. This study, completed as part of the HHMI-supported SEA-GENES project, highlights the power of parallel, genome-wide overexpression screens to identify novel interactions between phages and their hosts.
]]>Pollenz, R. S.Barhnhill, K.Biggs, A.Bland, J.Carter, V.Chase, M.Clark, H.Coleman, C.Daffner, M.Deam, C.Finocchiaro, A.Franco, V.Fuller, T.Pinera, J. G.Horne, M.Howard, Z.Kanahan, O.Miklaszewski, C.Miller, S.Morgan, R.Onalaja, O.Otero, L.Padhye, S.Rainey, E.Rasul, F.Robichaux, K.Rodier, A.Schlosser, S.Sciacchitano, A.Stewart, E.Thakkar, R.Heller, D.2023-08-05doi:10.1101/2023.08.04.552056Cold Spring Harbor Laboratory Press2023-08-05
<![CDATA[
Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs
]]>
https://biorxiv.org/cgi/content/short/2023.08.02.551486v1?rss=1"
Shimada, A.Cahn, J.Ernst, E.Lynn, J.Grimanelli, D.Henderson, I. R.Kakutani, T.Martienssen, R. A.2023-08-02doi:10.1101/2023.08.02.551486Cold Spring Harbor Laboratory Press2023-08-02
<![CDATA[
A multiplex, prime editing framework for identifying drug resistance variants at scale
]]>
https://biorxiv.org/cgi/content/short/2023.07.27.550902v1?rss=1"
Chardon, F. M.Suiter, C.Daza, R.Smith, N. T.Parrish, P.McDiarmid, T.Lalanne, J.-B.Martin, B. K.Calderon, D.Ellison, A.Berger, A.Shendure, J.Starita, L. M.2023-07-30doi:10.1101/2023.07.27.550902Cold Spring Harbor Laboratory Press2023-07-30
<![CDATA[
ME3BP-7 is a targeted cytotoxic agent that rapidly kills pancreatic cancer cells expressing high levels of monocarboxylate transporter MCT1
]]>
https://biorxiv.org/cgi/content/short/2023.07.23.550207v1?rss=1"
Rincon-Torroella, J.Dal Molin, M.Mog, B.Han, G.Watson, E.Wyhs, N.Ishiyama, S.Ahmedna, T.Minn, I.Azad, N. S.Bettegowda, C.Papadopoulos, N.Kinzler, K. W.Zhou, S.Vogelstein, B.Gabrielson, K. L.Sur, S.2023-07-25doi:10.1101/2023.07.23.550207Cold Spring Harbor Laboratory Press2023-07-25
<![CDATA[
GAGA Factor Overcomes 1D Diffusion Barrier by 3D Diffusion in Search of Nucleosomal Targets
]]>
https://biorxiv.org/cgi/content/short/2023.07.14.549009v1?rss=1"
Feng, X. A.Ness, K. M.Liu, C.Ahmed, I.Bowman, G. D.Ha, T.Wu, C.2023-07-15doi:10.1101/2023.07.14.549009Cold Spring Harbor Laboratory Press2023-07-15
<![CDATA[
Teosinte Pollen Drive guides maize domestication and evolution by RNAi
]]>
https://biorxiv.org/cgi/content/short/2023.07.12.548689v1?rss=1"
Berube, B.Ernst, E.Cahn, J.Roche, B.de Santis Alves, C.Lynn, J.Scheben, A.Siepel, A.Ross-Ibarra, J.Kermicle, J.Martienssen, R. A.2023-07-13doi:10.1101/2023.07.12.548689Cold Spring Harbor Laboratory Press2023-07-13
<![CDATA[
Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features
]]>
https://biorxiv.org/cgi/content/short/2023.07.11.548536v1?rss=1"
Hoge, C. R.de Manuel, M.Mahgoub, M.Okami, N.Fuller, Z. L.Banerjee, S.Baker, Z.Mcnulty, M.Andolfatto, P.Macfarlan, T. S.Schumer, M.Tzika, A. C.Przeworski, M.2023-07-11doi:10.1101/2023.07.11.548536Cold Spring Harbor Laboratory Press2023-07-11
<![CDATA[
Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation
]]>
https://biorxiv.org/cgi/content/short/2023.07.11.548598v1?rss=1"
Lee, S. C.Adams, D. W.Ipsaro, J. J.Cahn, J.Lynn, J.Kim, H.-S.Berube, B.Major, V.Calarco, J. P.LeBlanc, C.Bhattacharjee, S.Ramu, U.Grimanelli, D.Jacob, Y.Voigt, P.Joshua-Tor, L.Martienssen, R. A.2023-07-11doi:10.1101/2023.07.11.548598Cold Spring Harbor Laboratory Press2023-07-11
<![CDATA[
Social and genetic diversity in first farmers of central Europe
]]>
https://biorxiv.org/cgi/content/short/2023.07.07.548126v1?rss=1"
Gelabert, P.Bickle, P.Hofmann, D.Teschler-Nicola, M.Anders, A.Huang, X.Olalde, I.Fournier, R.Ringbauer, H.Akbari, A.Cheronet, O.Lazaridis, I.Broomandkhoshbacht, N.Fernandes, D. M.Buttinger, K.Callan, K.Candilio, F.Bravo, G.Curtis, E.Ferry, M.Keating, D.Freilich, S.Kearns, A.Harney, E.Lawson, A. M.Mandl, K.Michel, M.Oberreiter, V.Oppenheimer, J.Sawyer, S.Schattke, C.Ozdogan, K. T. T.Qiu, L.Workman, N.Zalzala, F.Mallick, S.Mah, M.Micco, A.Pieler, F.Pavuk, J.Lazar, C.Skrivanko, M. K.Slaus, M.Bedic, Z.Novotny,2023-07-09doi:10.1101/2023.07.07.548126Cold Spring Harbor Laboratory Press2023-07-09
<![CDATA[
Coding and non-coding elements comprise a regulatory network controlling transcription in Kaposi's sarcoma-associated herpesvirus
]]>
https://biorxiv.org/cgi/content/short/2023.07.08.548212v1?rss=1"
Morgens, D. W.Gulyas, L.Souza, A. S.Glaunsinger, B. A.2023-07-08doi:10.1101/2023.07.08.548212Cold Spring Harbor Laboratory Press2023-07-08
<![CDATA[
Cryo-EM structure of TMEM63C suggests it functions as a monomer
]]>
https://biorxiv.org/cgi/content/short/2023.07.04.547736v1?rss=1"
Qin, Y.Yu, D.Wu, D.Dong, J.Li, W. T.Ye, C.Cheung, K. C.Zhang, Y.Xu, Y.Wang, Y.Shi, Y. S.Dang, S.2023-07-04doi:10.1101/2023.07.04.547736Cold Spring Harbor Laboratory Press2023-07-04
<![CDATA[
Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen
]]>
https://biorxiv.org/cgi/content/short/2023.07.03.547508v1?rss=1"
Steenwyk, J. L.Knowles, S. L.Bastos, R.Balamurugan, C.Rinker, D.Mead, M. E.Roberts, C. D.Raja, H. A.Li, Y.Colabardini, A. C.Castro, P. A.Reis, T. F.Canovas, D.Sanchez, R. L.Lagrou, K.Torrado, E.Rodrigues, F.Oberlies, N. H.Zhou, X.Goldman, G.Rokas, A.2023-07-03doi:10.1101/2023.07.03.547508Cold Spring Harbor Laboratory Press2023-07-03
<![CDATA[
An engineered biosensor enables dynamic aspartate measurements in living cells
]]>
https://biorxiv.org/cgi/content/short/2023.06.27.546775v1?rss=1"
Davidsen, K.Marvin, J. S.Aggarwal, A.Brown, T. A.Sullivan, L. B.2023-06-27doi:10.1101/2023.06.27.546775Cold Spring Harbor Laboratory Press2023-06-27
<![CDATA[
New genetic tools for mushroom body output neurons in Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.06.23.546330v1?rss=1"
Rubin, G. M.Aso, Y.2023-06-26doi:10.1101/2023.06.23.546330Cold Spring Harbor Laboratory Press2023-06-26
<![CDATA[
A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy
]]>
https://biorxiv.org/cgi/content/short/2023.06.21.545952v1?rss=1"
Amaya, I.Edwards, K.Wise, B. M.Bhattacharyya, A.Pablo, C. H. D.Mushrush, E.Coats, A. N.Dao, S.Dittmar, G.Gore, T.Jarva, T. M.Kenkebashvili, G.Rathan-Kumar, S.Reyes, G. M.Watts, G. L.Watts, V. K.Dubrow, D.Lewis, G. S.Stone, B. H.Xue, B.Cresawn, S. G.Mavrodi, D.Sivanathan, V.Heller, D.2023-06-21doi:10.1101/2023.06.21.545952Cold Spring Harbor Laboratory Press2023-06-21
<![CDATA[
Metal Ions and their Effects on Antimicrobial Resistance Development in Wastewater
]]>
https://biorxiv.org/cgi/content/short/2023.06.16.545339v1?rss=1"
Sutradhar, I.Kalyan, P.Chukwu, K.Abia, A. L. K.Mbanga, J.Hamer, D. H.Essack, S.Zaman, M. H.2023-06-17doi:10.1101/2023.06.16.545339Cold Spring Harbor Laboratory Press2023-06-17
<![CDATA[
Krause corpuscles of the genitalia are vibrotactile sensors required for normal sexual behavior
]]>
https://biorxiv.org/cgi/content/short/2023.06.14.545006v1?rss=1"
Qi, L.Iskols, M.Handler, A.Ginty, D. D.2023-06-15doi:10.1101/2023.06.14.545006Cold Spring Harbor Laboratory Press2023-06-15
<![CDATA[
De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8
]]>
https://biorxiv.org/cgi/content/short/2023.06.12.544624v1?rss=1"
1000-fold selectivity over other RGD integrins. CryoEM structures are within 0.6-0.7[A] root-mean-square deviation (RMSD) to the computational design models; the designed v{beta}6 inhibitor and native ligand stabilize the open conformation in contrast to the therapeutic anti-v{beta}6 antibody BG00011 that stabilizes the bent-closed conformation and caused on-target toxicity in patients with lung fibrosis, and the v{beta}8 inhibitor maintains the constitutively fixed extended-closed v{beta}8 conformation. In a mouse model of bleomycin-induced lung fibrosis, the v{beta}6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics when delivered via oropharyngeal administration mimicking inhalation, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity.
]]>Roy, A.Shi, L.Chang, A.Dong, X.Fernandez, A.Kraft, J. C.Li, J.Le, V. Q.Winegar, R. V.Cherf, G. M.Slocum, D.Poulson, P. D.casper, G. E.Vallecillo-Zuniga, M. L.Valdoz, J. C.Miranda, M. C.Bai, H.Kipnis, Y.Olshefsky, A.Priya, T.Carter, L.Ravichandran, R.Chow, C.Johnson, M. R.Chang, S.Roy, A.Overed-Sayer, C.Finch, D. K.Lowe, D.Bera, A. K.Matute-Bello, G.Birkland, T. P.DiMaio, F.Raghu, G.Cochran, J. R.Stewart, L.Campbell, M. G.Van Ry, P. M.Springer, T. A.Baker, D.2023-06-12doi:10.1101/2023.06.12.544624Cold Spring Harbor Laboratory Press2023-06-12
<![CDATA[
Cholangiocytic differentiation drives cell proliferation in hepatoblastoma through Wnt-dependent FGF19 signaling
]]>
https://biorxiv.org/cgi/content/short/2023.06.08.544267v1?rss=1"
Wu, P. V.Fish, M.Hazard, F. K.Zhu, C.Vennam, S.Walton, H. E.Morri, M.Neff, N.West, R. B.Nusse, R.2023-06-08doi:10.1101/2023.06.08.544267Cold Spring Harbor Laboratory Press2023-06-08
<![CDATA[
Recognition of centromere-specific histone Cse4 by the inner kinetochore Okp1-Ame1 complex
]]>
https://biorxiv.org/cgi/content/short/2023.06.06.543957v1?rss=1"
Deng, S.Cai, J.Harrison, S.Zhou, H.Hinshaw, S. M.2023-06-07doi:10.1101/2023.06.06.543957Cold Spring Harbor Laboratory Press2023-06-07
<![CDATA[
Cell type-specific contributions to a persistent aggressive internal state in female Drosophila
]]>
https://biorxiv.org/cgi/content/short/2023.06.07.543722v1?rss=1"
Chiu, H.Robie, A. A.Branson, K. M.Vippa, T.Epstein, S.Rubin, G. M.Anderson, D. J.Schretter, C. E.2023-06-07doi:10.1101/2023.06.07.543722Cold Spring Harbor Laboratory Press2023-06-07
<![CDATA[
A NanoDam toolkit for tissue-specific transcription factor profiling in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2023.05.31.543105v1?rss=1"
Yee, C.Xiao, Y.Katsanos, D.Medwig-Kinney, T. N.Zhang, W.Shen, K.Matus, D. Q.Barkoulas, M.2023-06-04doi:10.1101/2023.05.31.543105Cold Spring Harbor Laboratory Press2023-06-04
<![CDATA[
De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity
]]>
https://biorxiv.org/cgi/content/short/2023.06.02.543449v1?rss=1"
Mout, R.Bretherton, R. C.Decarreau, J.Lee, S.Edman, N. I.Ahlrichs, M.Hsia, Y.Sahtoe, D. D.Ueda, G.Gregorio, N.Sharma, A.Schulman, R.DeForest, C. A.Baker, D.2023-06-03doi:10.1101/2023.06.02.543449Cold Spring Harbor Laboratory Press2023-06-03
<![CDATA[
The HLA-II immunopeptidome of SARS-CoV-2
]]>
https://biorxiv.org/cgi/content/short/2023.05.26.542482v1?rss=1"
Weingarten-Gabbay, S.Chen, D.-Y.Sarkizova, S.Taylor, H. B.Gentili, M.Pearlman, L. R.Bauer, M. R.Rice, C. M.Clauser, K. R.Hacohen, N.Carr, S. A.Abelin, J. G.Saeed, M.Sabeti, P. C.2023-06-01doi:10.1101/2023.05.26.542482Cold Spring Harbor Laboratory Press2023-06-01
<![CDATA[
An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway
]]>
https://biorxiv.org/cgi/content/short/2023.05.25.541239v1?rss=1"
Liu, G. Y.Jouandin, P.Bahng, R. E.Perrimon, N.Sabatini, D. M.2023-05-26doi:10.1101/2023.05.25.541239Cold Spring Harbor Laboratory Press2023-05-26
<![CDATA[
An Atlas of Adaptive Evolution in Endemic Human Viruses
]]>
https://biorxiv.org/cgi/content/short/2023.05.19.541367v1?rss=1"
Kistler, K.Bedford, T.2023-05-22doi:10.1101/2023.05.19.541367Cold Spring Harbor Laboratory Press2023-05-22
<![CDATA[
Computational modeling of methylation impact of AML drivers reveals new pathways and refines AML risk-stratification
]]>
https://biorxiv.org/cgi/content/short/2023.05.17.541249v1?rss=1"
Gurun, B.Tyner, J. W.Demir, E.Druker, B. J.Spellman, P. T.2023-05-21doi:10.1101/2023.05.17.541249Cold Spring Harbor Laboratory Press2023-05-21
<![CDATA[
Tumor Cytokine-Induced Hepatic Gluconeogenesis Contributes to Cancer Cachexia: Insights from Full Body Single Nuclei Sequencing
]]>
https://biorxiv.org/cgi/content/short/2023.05.15.540823v1?rss=1"
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]]>Liu, Y.Dantas, E.Ferrer, M.Liu, Y.Comjean, A.Davidson, E. E.Hu, Y.Goncalves, M. D.Janowitz, T.Perrimon, N.2023-05-18doi:10.1101/2023.05.15.540823Cold Spring Harbor Laboratory Press2023-05-18
<![CDATA[
p300 Is an Obligate Integrator of Combinatorial Transcription Factor Inputs
]]>
https://biorxiv.org/cgi/content/short/2023.05.18.541220v1?rss=1"
Ferrie, J. J.Karr, J. P.Graham, T. G.Dailey, G. M.Zhang, G.Tjian, R.Darzacq, X.2023-05-18doi:10.1101/2023.05.18.541220Cold Spring Harbor Laboratory Press2023-05-18
<![CDATA[
Peripheral serotonergic neurons regulate anxiety-like behavior and intestinal barrier immunity
]]>
https://biorxiv.org/cgi/content/short/2023.05.12.540588v1?rss=1"
Waldor, M. K.Zhang, H.Hasegawa, Y.Leitner, D.Zhang, T.Suzuki, M.Jackson, R.2023-05-14doi:10.1101/2023.05.12.540588Cold Spring Harbor Laboratory Press2023-05-14
<![CDATA[
H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment
]]>
https://biorxiv.org/cgi/content/short/2023.05.10.539968v1?rss=1"
Harris, C. J.Zhong, Z.Ichino, L.Feng, S.Jacobsen, S. E.2023-05-11doi:10.1101/2023.05.10.539968Cold Spring Harbor Laboratory Press2023-05-11
<![CDATA[
High-resolution molecular atlas of a lung tumor in 3D
]]>
https://biorxiv.org/cgi/content/short/2023.05.10.539644v1?rss=1"
Pentimalli, T. M.Schallenberg, S.Leon-Perinan, D.Legnini, I.Theurillat, I.Thomas, G.Boltengagen, A.Fritzsche, S.Nimo, J.Ruff, L.Dernbach, G.Jurmeister, P.Murphy, S.Gregory, M.Liang, Y.Cordenonsi, M.Piccolo, S.Coscia, F.Woehler, A.Karaiskos, N.Klauschen, F.Rajewsky, N.2023-05-10doi:10.1101/2023.05.10.539644Cold Spring Harbor Laboratory Press2023-05-10
<![CDATA[
Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter
]]>
https://biorxiv.org/cgi/content/short/2023.05.02.539146v1?rss=1"
Wang, Y.Gallagher, L. A.Andrade, P. A.Liu, A.Humphreys, I. R.Turkarslan, S.Cutler, K. J.Arrieta-Ortiz, M. L.Li, Y.Radey, M. C.Cong, Q.Baker, D.Baliga, N. S.Peterson, S. B.Mougous, J. D.2023-05-03doi:10.1101/2023.05.02.539146Cold Spring Harbor Laboratory Press2023-05-03
<![CDATA[
Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology
]]>
https://biorxiv.org/cgi/content/short/2023.05.03.539266v1?rss=1"
Zheng, F.Georgescu, R. E.Yao, N. Y.O'Donnell, M. E.Li, H.2023-05-03doi:10.1101/2023.05.03.539266Cold Spring Harbor Laboratory Press2023-05-03
<![CDATA[
Meta-learning in head fixed mice navigating in virtual reality: A Behavioral Analysis
]]>
https://biorxiv.org/cgi/content/short/2023.05.01.538936v1?rss=1"
Zhao, X.Gattoni, R.Kozlosky, A.Jacobs, A.Morrow, C.Lindo, S.Spruston, N.2023-05-02doi:10.1101/2023.05.01.538936Cold Spring Harbor Laboratory Press2023-05-02
<![CDATA[
Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections
]]>
https://biorxiv.org/cgi/content/short/2023.05.01.538832v1?rss=1"
Zhou, J.Zhang, Z.Wu, M.Liu, H.Pang, Y.Bartlett, A.Rivkin, A. C.Lagos, W. N.Williams, E.Lee, C.-T.Miyazaki, P. A.Aldridge, A. I.Zeng, Q.Salinda, J. L. A.Claffey, N.Liem, M.Fitzpatrick, C.Boggeman, L.Yao, Z.Smith, K. A.Tasic, B.Altshul, J.Kenworthy, M. A.Valadon, C.Nery, J. R.Castanon, R. G.Patne, N. S.Vu, M.Rashid, M.Jacobs, M. W.Ito-Cole, T.Osteen, J.Emerson, N.Lee, J.Cho, S.Rink, J.Huang, H.-H.Pinto-Duartec, A.Dominguez, B.Smith, J. B.O'Connor, C.Zeng, H.Lee, K.-F.Mukamel, E. A.Jin, X.Behrens, M. M.Eck2023-05-01doi:10.1101/2023.05.01.538832Cold Spring Harbor Laboratory Press2023-05-01
<![CDATA[
Molecular crowding facilitates ribozyme-catalyzed RNA assembly
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https://biorxiv.org/cgi/content/short/2023.04.30.538884v1?rss=1"
View larger version (19K):
org.highwire.dtl.DTLVardef@17d282borg.highwire.dtl.DTLVardef@1d8531aorg.highwire.dtl.DTLVardef@1380f7borg.highwire.dtl.DTLVardef@180708f_HPS_FORMAT_FIGEXP M_FIG C_FIG SYNOPSISMolecular crowding enables ribozyme-catalyzed RNA assembly under low Mg2+ conditions, and consequently may have played an essential role in the origin and evolution of RNA-based primordial life.
]]>DasGupta, S.Zhang, S. J.Szostak, J. W.2023-04-30doi:10.1101/2023.04.30.538884Cold Spring Harbor Laboratory Press2023-04-30
<![CDATA[
A Zika virus protein expression screen in Drosophila to investigate targeted host pathways during development
]]>
https://biorxiv.org/cgi/content/short/2023.04.28.538736v1?rss=1"
Link, N.Harnish, J. M.Hull, B.Gibson, S.Dietze, M.Mgbike, U. E.Medina-Balcazar, S.Shah, P. S.Yamamoto, S.2023-04-29doi:10.1101/2023.04.28.538736Cold Spring Harbor Laboratory Press2023-04-29
<![CDATA[
Mechanistic characterization of a Drosophila model of paraneoplastic nephrotic syndrome
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https://biorxiv.org/cgi/content/short/2023.04.23.538006v1?rss=1"
Xu, J.Liu, Y.Chen, W.Li, J. S. S.Comjean, A.Hu, Y.Perrimon, N.2023-04-25doi:10.1101/2023.04.23.538006Cold Spring Harbor Laboratory Press2023-04-25
<![CDATA[
Identification of FacZ as a division site placement factor in Staphylococcus aureus
]]>
https://biorxiv.org/cgi/content/short/2023.04.24.538170v1?rss=1"
Bartlett, T. M.Sisley, T. A.Mychack, A.Walker, S.Baker, R. W.Rudner, D. Z.Bernhardt, T. G.2023-04-24doi:10.1101/2023.04.24.538170Cold Spring Harbor Laboratory Press2023-04-24
<![CDATA[
Translating deep learning to neuroprosthetic control
]]>
https://biorxiv.org/cgi/content/short/2023.04.21.537581v1?rss=1"
Deo, D. R.Willett, F. R.Avansino, D. T.Hochberg, L. R.Henderson, J. M.Shenoy, K. V.2023-04-21doi:10.1101/2023.04.21.537581Cold Spring Harbor Laboratory Press2023-04-21
<![CDATA[
Chromatin context-dependent regulation and epigenetic manipulation of prime editing
]]>
https://biorxiv.org/cgi/content/short/2023.04.12.536587v1?rss=1"
Li, X.Chen, W.Martin, B. K.Calderon, D.Lee, C.Choi, J.Chardon, F. M.McDiarmid, T.Kim, H.Lalanne, J.-B.Nathans, J. F.Shendure, J.2023-04-12doi:10.1101/2023.04.12.536587Cold Spring Harbor Laboratory Press2023-04-12
<![CDATA[
Astrocytic Neuroligins Are Not Required for Synapse Formation or a Normal Astrocyte Cytoarchitecture
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https://biorxiv.org/cgi/content/short/2023.04.10.536254v1?rss=1"
Golf, S. R.Trotter, J.Nakahara, G.Südhof, T.2023-04-12doi:10.1101/2023.04.10.536254Cold Spring Harbor Laboratory Press2023-04-12
<![CDATA[
Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation
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https://biorxiv.org/cgi/content/short/2023.04.10.536281v1?rss=1"
Grow, E. J.Liu, Y.Fan, Z.Perisse, I.Patrick, T.Regouski, M.Shadle, S.Polejaeva, I.Cairns, B.White, K.2023-04-11doi:10.1101/2023.04.10.536281Cold Spring Harbor Laboratory Press2023-04-11
<![CDATA[
Impact of Zinc Pre-exposure on de novo Antibiotic Resistance Development
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https://biorxiv.org/cgi/content/short/2023.04.10.536219v1?rss=1"
Suprenant, M. P.Ching, C.Sutradhar, I.Gross, N.Anderson, J. E.El Sherif, N.Zaman, M. H.2023-04-10doi:10.1101/2023.04.10.536219Cold Spring Harbor Laboratory Press2023-04-10
<![CDATA[
Glial Draper signaling triggers cross-neuron plasticity in bystander neurons after neuronal cell death
]]>
https://biorxiv.org/cgi/content/short/2023.04.09.536190v1?rss=1"
Wang, Y.Zhang, R.Huang, S.Valverde, P. T.-T.Lobb-Rabe, M.Ashley, J.Venkatasubramanian, L.Carrillo, R. A.2023-04-10doi:10.1101/2023.04.09.536190Cold Spring Harbor Laboratory Press2023-04-10
<![CDATA[
Do perineuronal nets stabilize the engram of a synaptic circuit?
]]>
https://biorxiv.org/cgi/content/short/2023.04.09.536164v1?rss=1"
Lev-Ram, V.Palida, S.Deerinck, T. J.Bushong, E. A.Toyoma, B. H.Perez, A.McClatchy, D. B.Prichard, D. R.Savas, J. N.Ellisman, M. H.Yates, J. R.Tsien, R. Y.2023-04-09doi:10.1101/2023.04.09.536164Cold Spring Harbor Laboratory Press2023-04-09
<![CDATA[
Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex
]]>
https://biorxiv.org/cgi/content/short/2023.04.08.536119v1?rss=1"
Zemke, N. R.Armand, E. J.Wang, W.Lee, S.Zhou, J.Li, Y. E.Liu, H.Tian, W.Nery, J. R.Castanon, R. G.Bartlett, A.Osteen, J. K.Li, D.Zhuo, X.Xu, V.Miller, M.Krienen, F. M.Zhang, Q.Taskin, N.Ting, J.Feng, G.McCarroll, S. A.Callaway, E. M.Wang, T.Behrens, M.Lein, E. S.Ecker, J. R.Ren, B.2023-04-08doi:10.1101/2023.04.08.536119Cold Spring Harbor Laboratory Press2023-04-08
<![CDATA[
Rapid-kinetics degron benchmarking reveals off-target activities and mixed agonism-antagonism of MYB inhibitors
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https://biorxiv.org/cgi/content/short/2023.04.07.536032v1?rss=1"
Harada, T.Perez, M. W.Kalfon, J.Dievenich Braes, F.Batley, R.Eagle, K.Nabet, B.Leifer, B.Kruell, J.Paralkar, V. R.Stegmaier, K.Koehler, A. N.Orkin, S. H.Pimkin, M.2023-04-07doi:10.1101/2023.04.07.536032Cold Spring Harbor Laboratory Press2023-04-07
<![CDATA[
Identifying determinants of synaptic specificity by integrating connectomes and transcriptomes
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https://biorxiv.org/cgi/content/short/2023.04.03.534791v1?rss=1"
Yoo, J.Dombrovski, M.Mirshahidi, P.Nern, A.LoCascio, S. A.Zipursky, S. L.Kurmangaliyev, Y. Z.2023-04-04doi:10.1101/2023.04.03.534791Cold Spring Harbor Laboratory Press2023-04-04
<![CDATA[
Mitochondrial GTP Metabolism Regulates Reproductive Aging
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https://biorxiv.org/cgi/content/short/2023.04.02.535296v1?rss=1"
Lee, Y.-T.Savini, M.Chen, T.Yang, J.Zhao, Q.Ding, L.Gao, S. M.Senturk, M.Sowa, J.Wang, J. D.Wang, M. C.2023-04-03doi:10.1101/2023.04.02.535296Cold Spring Harbor Laboratory Press2023-04-03
<![CDATA[
APOBEC3 degradation is the primary function of HIV-1 Vif for virus replication in the myeloid cell line THP-1
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https://biorxiv.org/cgi/content/short/2023.03.28.534666v1?rss=1"
Ikeda, T.Shimizu, R.Nasser, H.Carpenter, M. A.Cheng, A. Z.Brown, W. L.Sauter, D.Harris, R. S.2023-03-30doi:10.1101/2023.03.28.534666Cold Spring Harbor Laboratory Press2023-03-30
<![CDATA[
Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors
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https://biorxiv.org/cgi/content/short/2023.03.27.534457v1?rss=1"
Hannon, C. E.Eisen, M. B.2023-03-27doi:10.1101/2023.03.27.534457Cold Spring Harbor Laboratory Press2023-03-27
<![CDATA[
SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling
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https://biorxiv.org/cgi/content/short/2023.03.26.534250v1?rss=1"
Tuomivaara, S. T.Teo, C. F.Jan, Y. N.Jan, L. Y.Wiita, A. P.2023-03-26doi:10.1101/2023.03.26.534250Cold Spring Harbor Laboratory Press2023-03-26
<![CDATA[
Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)
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https://biorxiv.org/cgi/content/short/2023.03.21.533680v1?rss=1"
Comiter, C.Vaishnav, E. D.Ciapmricotti, M.Li, B.Yang, Y.Rodig, S. J.Turner, M.Pfaff, K. L.Jane-Valbuena, J.Slyper, M.Waldman, J.Vigneau, S.Wu, J.Blosser, T. R.Segerstolpe, A.Abravanel, D.Wagle, N.Zhuang, X.Rudin, C. M.Klughammer, J.Rozenblatt-Rosen, O.Kobayash-Kirschvink, K. J.Shu, J.Regev, A.2023-03-23doi:10.1101/2023.03.21.533680Cold Spring Harbor Laboratory Press2023-03-23
<![CDATA[
A spinal synergy of excitatory and inhibitory neurons coordinates ipsilateral body movements
]]>
https://biorxiv.org/cgi/content/short/2023.03.21.533603v1?rss=1"
Hayashi, M.Gullo, M.Senturk, G.Di Costanzo, S.Nagasaki, S. C.Kageyama, R.Imayoshi, I.Goulding, M.Pfaff, S. L.Gatto, G.2023-03-21doi:10.1101/2023.03.21.533603Cold Spring Harbor Laboratory Press2023-03-21
<![CDATA[
Spatial and single-cell transcriptomics reveal neuron-astrocyte interplay in long-term memory
]]>
https://biorxiv.org/cgi/content/short/2023.03.20.533566v1?rss=1"
Sun, W.Liu, Z.Jiang, X.Chen, M. B.Dong, H.Liu, J.Sudhof, T. C.Quake, S. R.2023-03-21doi:10.1101/2023.03.20.533566Cold Spring Harbor Laboratory Press2023-03-21
<![CDATA[
Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi
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https://biorxiv.org/cgi/content/short/2023.03.19.532819v1?rss=1"
Ren, Z.Takacs, C. N.Brandao, H. B.Jacobs-Wagner, C.Wang, X.2023-03-20doi:10.1101/2023.03.19.532819Cold Spring Harbor Laboratory Press2023-03-20
<![CDATA[
Mitigation of membrane morphology defects explain stability and orientational specificity of CLC dimers
]]>
https://biorxiv.org/cgi/content/short/2023.03.16.533024v1?rss=1"
Ozturk, T. N.Bernhardt, N.Schwartz, N.Chadda, R.Robertson, J. L.Faraldo-Gomez, J.2023-03-20doi:10.1101/2023.03.16.533024Cold Spring Harbor Laboratory Press2023-03-20
<![CDATA[
Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops
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https://biorxiv.org/cgi/content/short/2023.03.13.532438v1?rss=1"
Harada, T.Kalfon, J.Perez, M. W.Eagle, K.Braes, F. D.Batley, R.Heshmati, Y.Ferrucio, J. X.Ewers, J.Mehta, S.Kossenkov, A.Ellegast, J. M.Bowker, A.Wickramasinghe, J.Nabet, B.Paralkar, V. R.Dharia, N. V.Stegmaier, K.Orkin, S. H.Pimkin, M.2023-03-15doi:10.1101/2023.03.13.532438Cold Spring Harbor Laboratory Press2023-03-15
<![CDATA[
An extra-circadian function for human CLOCK in the neocortex
]]>
https://biorxiv.org/cgi/content/short/2023.03.13.531623v1?rss=1"
Liu, Y.Fontenot, M. R.Kulkarni, A.Khandelwal, N.Park, S.-H. E.Douglas, C.Harper, M.Xu, P.Gupta, N.Gibson, J. R.Takahashi, J. S.Konopka, G.2023-03-14doi:10.1101/2023.03.13.531623Cold Spring Harbor Laboratory Press2023-03-14
<![CDATA[
The Role of Terminal Uridyl Transferases in the Circadian Rhythm
]]>
https://biorxiv.org/cgi/content/short/2023.03.13.516290v1?rss=1"
Song, W.Wang, J.Piao, W.Yang, Y.Son, A.Chang, H.Wen, X.Zhang, H.Li, C.Na, D.Lu, Y.Menet, J.Kim, V. N.Jin, H.2023-03-14doi:10.1101/2023.03.13.516290Cold Spring Harbor Laboratory Press2023-03-14
<![CDATA[
ancIBD - Screening for identity by descent segments in human ancient DNA
]]>
https://biorxiv.org/cgi/content/short/2023.03.08.531671v1?rss=1"
Ringbauer, H.Huang, Y.Akbari, A.Mallick, S.Patterson, N.Reich, D. E.2023-03-09doi:10.1101/2023.03.08.531671Cold Spring Harbor Laboratory Press2023-03-09
<![CDATA[
Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways
]]>
https://biorxiv.org/cgi/content/short/2023.03.07.531630v1?rss=1"
Yin, L.Zander, M.Huang, S.-s. C.Xie, M.Song, L.Saldierna Guzman, J. P.Hann, E.Shanbhag, B. K.Ng, S.Jain, S.Janssen, B. J.Clark, N. M.Walley, J.Beddoe, T.Bar-Joseph, Z.Lewsey, M. G.Ecker, J. R.2023-03-09doi:10.1101/2023.03.07.531630Cold Spring Harbor Laboratory Press2023-03-09
<![CDATA[
Roles of microbiota in autoimmunity in Arabidopsis
]]>
https://biorxiv.org/cgi/content/short/2023.03.06.531303v1?rss=1"
Cheng, Y. T.Thireault, C. A.Paasch, B. C.Zhang, L.He, S. Y.2023-03-07doi:10.1101/2023.03.06.531303Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types
]]>
https://biorxiv.org/cgi/content/short/2023.03.05.531189v1?rss=1"
Agarwal, V.Inoue, F.Schubach, M.Martin, B.Dash, P.Zhang, Z.Sohota, A.Noble, W.Yardimci, G.Kircher, M.Shendure, J.Ahituv, N.2023-03-06doi:10.1101/2023.03.05.531189Cold Spring Harbor Laboratory Press2023-03-06
<![CDATA[
Aging Atlas Reveals Cell-Type-Specific Regulation of Pro-longevity Strategies
]]>
https://biorxiv.org/cgi/content/short/2023.02.28.530490v1?rss=1"
Gao, S. M.Qi, Y.Zhang, Q.Mohammed, A. S.Lee, Y.-T.Guan, Y.Li, H.Fu, Y.Wang, M. C.2023-03-01doi:10.1101/2023.02.28.530490Cold Spring Harbor Laboratory Press2023-03-01
<![CDATA[
Cerebellar Granule Cells Develop Non-neuronal 3D Genome Architecture over the Lifespan
]]>
https://biorxiv.org/cgi/content/short/2023.02.25.530020v1?rss=1"
Tan, L.Shi, J.Moghadami, S.Wright, C. P.Parasar, B.Seo, Y.Vallejo, K.Cobos, I.Duncan, L.Chen, R.Deisseroth, K.2023-02-25doi:10.1101/2023.02.25.530020Cold Spring Harbor Laboratory Press2023-02-25
<![CDATA[
A compact regulatory RNA element in human Hsp70 mRNA
]]>
https://biorxiv.org/cgi/content/short/2023.02.22.529618v1?rss=1"
Wang, W.Liu, F.Pyle, A. M.2023-02-23doi:10.1101/2023.02.22.529618Cold Spring Harbor Laboratory Press2023-02-23
<![CDATA[
Dynamical states of self-organized waves in a giant single-celled organism feeding on light
]]>
https://biorxiv.org/cgi/content/short/2023.02.22.529174v1?rss=1"
Afik, E.Liu, T. J.Meyerowitz, E. M.2023-02-22doi:10.1101/2023.02.22.529174Cold Spring Harbor Laboratory Press2023-02-22
<![CDATA[
PANGEA: A New Gene Set Enrichment Tool for Drosophila and Common Research Organisms
]]>
https://biorxiv.org/cgi/content/short/2023.02.20.529262v1?rss=1"
Hu, Y.Comjean, A.Attrill, H.Antonazzo, G.Thurmond, J.Li, F.Chao, T.Mohr, S.Brown, N. H.Perrimon, N.2023-02-21doi:10.1101/2023.02.20.529262Cold Spring Harbor Laboratory Press2023-02-21
<![CDATA[
A tRNA modification in Mycobacterium tuberculosis facilitates optimal intracellular growth
]]>
https://biorxiv.org/cgi/content/short/2023.02.20.529267v1?rss=1"
Tomasi, F. G.Kimura, S.Rubin, E. J.Waldor, M. K.2023-02-20doi:10.1101/2023.02.20.529267Cold Spring Harbor Laboratory Press2023-02-20
<![CDATA[
Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A
]]>
https://biorxiv.org/cgi/content/short/2023.02.17.528918v1?rss=1"
Harjes, S.Kurup, H. M.Rieffer, A. E.Bayarjagal, M.Filitcheva, J.Su, Y.Hale, T. K.Filichev, V. V.Harjes, E.Harris, R. S.Jameson, G. B.2023-02-17doi:10.1101/2023.02.17.528918Cold Spring Harbor Laboratory Press2023-02-17
<![CDATA[
Redox Regulation of m6A Methyltransferase METTL3 in Human β-cells Controls the Innate Immune Response in Type 1 Diabetes
]]>
https://biorxiv.org/cgi/content/short/2023.02.16.528701v1?rss=1"
De Jesus, D. F.Zhang, Z.Brown, N. K.Li, X.Gaffrey, M. J.Kahraman, S.Wei, J.Hu, J.Basile, G.Xiao, L.Rana, T. M.Mathews, C. E.Powers, A. C.Atkinson, M. A.Eizirik, D. L.Dhe-Paganon, S.Parent, A. V.Qian, W.-J.He, C.Kulkarni, R. N.2023-02-16doi:10.1101/2023.02.16.528701Cold Spring Harbor Laboratory Press2023-02-16
<![CDATA[
Transmembrane protein CD69 acts as an S1PR1 agonist
]]>
https://biorxiv.org/cgi/content/short/2023.02.13.528406v1?rss=1"
Chen, H.Qin, Y.Chou, M.Cyster, J. G.Li, X.2023-02-15doi:10.1101/2023.02.13.528406Cold Spring Harbor Laboratory Press2023-02-15
<![CDATA[
Structural insight into guanylyl cyclase receptor hijacking of the kinase-Hsp90 regulatory mechanism
]]>
https://biorxiv.org/cgi/content/short/2023.02.14.528495v1?rss=1"
Caveney, N. A.Tsutsumi, N.Garcia, K. C.2023-02-14doi:10.1101/2023.02.14.528495Cold Spring Harbor Laboratory Press2023-02-14
<![CDATA[
Effects of Antibiotic Interaction on Antimicrobial Resistance Development in Wastewater
]]>
https://biorxiv.org/cgi/content/short/2023.02.10.528009v1?rss=1"
Sutradhar, I.Ching, C.Desai, D.Heins, Z.Khalil, A. S.Zaman, M. H.2023-02-10doi:10.1101/2023.02.10.528009Cold Spring Harbor Laboratory Press2023-02-10
<![CDATA[
Structural basis for inactivation of PRC2 by G-quadruplex RNA
]]>
https://biorxiv.org/cgi/content/short/2023.02.06.527314v1?rss=1"
Song, J.Gooding, A. R.Hemphill, W. O.Kasinath, V.Cech, T. R.2023-02-06doi:10.1101/2023.02.06.527314Cold Spring Harbor Laboratory Press2023-02-06
<![CDATA[
Large-scale brain-wide neural recording in nonhuman primates
]]>
https://biorxiv.org/cgi/content/short/2023.02.01.526664v1?rss=1"
Trautmann, E. M.Hesse, J. K.Stine, G.Xia, R.Shude Zhu, S.O'Shea, D. J.Karsh, B.Colonell, J.Lanfranchi, F.Vyas, S.Zimnik, A.Steinemann, N. A.Wagenaar, D. A.Andrei, A.Mora Lopez, C.OCallaghan, J. M.Putzeys, J.Raducanu, B. C.Welkenhuysen, M.Churchland, M.Moore, T.Shadlen, M. N.Shenoy, K. V.Tsao, D.Dutta, B.Harris, T.2023-02-03doi:10.1101/2023.02.01.526664Cold Spring Harbor Laboratory Press2023-02-03
<![CDATA[
Quantification of gallium cryo-FIB milling damage in biological lamella
]]>
https://biorxiv.org/cgi/content/short/2023.02.01.526705v1?rss=1"
Lucas, B. A.Grigorieff, N.2023-02-03doi:10.1101/2023.02.01.526705Cold Spring Harbor Laboratory Press2023-02-03
<![CDATA[
Histone-organized chromatin in bacteria
]]>
https://biorxiv.org/cgi/content/short/2023.01.26.525422v1?rss=1"
Hocher, A.Laursen, S.Radford, P.Tyson, J.Lambert, C.Stevens, K. M.Picardeau, M.Sockett, R. E.Luger, K.Warnecke, T.2023-01-26doi:10.1101/2023.01.26.525422Cold Spring Harbor Laboratory Press2023-01-26
<![CDATA[
Leveraging genomic redundancy to improve inference and alignment of orthologous proteins
]]>
https://biorxiv.org/cgi/content/short/2023.01.24.525427v1?rss=1"
Singleton, M.Eisen, M.2023-01-25doi:10.1101/2023.01.24.525427Cold Spring Harbor Laboratory Press2023-01-25
<![CDATA[
A fundamental law underlying predictive remapping
]]>
https://biorxiv.org/cgi/content/short/2023.01.24.525276v1?rss=1"
Adeyefa-Olasupo, I.-E.2023-01-25doi:10.1101/2023.01.24.525276Cold Spring Harbor Laboratory Press2023-01-25
<![CDATA[
Multimodal characterization of antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection.
]]>
https://biorxiv.org/cgi/content/short/2023.01.24.525203v1?rss=1"
Zhang, B.Upadhyay, R.Hao, Y.Samanovic, M. I.Herati, R. S.Blair, J.Axelrad, J.Mulligan, M. J.Littman, D. R.Satija, R.2023-01-24doi:10.1101/2023.01.24.525203Cold Spring Harbor Laboratory Press2023-01-24
<![CDATA[
A high-performance speech neuroprosthesis
]]>
https://biorxiv.org/cgi/content/short/2023.01.21.524489v1?rss=1"
Willett, F. R.Kunz, E.Fan, C.Avansino, D.Wilson, G.Choi, E. Y.Kamdar, F.Hochberg, L. R. H.Druckmann, S.Shenoy, K.Henderson, J.2023-01-21doi:10.1101/2023.01.21.524489Cold Spring Harbor Laboratory Press2023-01-21
<![CDATA[
Immune sensing of food allergens promotes aversive behaviour
]]>
https://biorxiv.org/cgi/content/short/2023.01.19.524823v1?rss=1"
Florsheim, E. B.Bachtel, N. D.Cullen, J.Costa Lima, B. G.Godazgar, M.Zhang, C.Carvalho, F.Gautier, G.Launay, P.Wang, A.Dietrich, M. O.Medzhitov, R.2023-01-21doi:10.1101/2023.01.19.524823Cold Spring Harbor Laboratory Press2023-01-21
<![CDATA[
Neuronal Activity-Dependent Mechanisms of Small Cell Lung Cancer Progression
]]>
https://biorxiv.org/cgi/content/short/2023.01.19.524430v1?rss=1"
Savchuk, S.Gentry, K.Wang, W.Carleton, E.Yalcin, B.Liu, Y.Pavarino, E. C.LaBelle, J.Toland, A. M.Woo, P. J.Qu, F.Filbin, M. G.Krasnow, M. A.Sabatini, B. L.Sage, J.Monje, M.Venkatesh, H. S.2023-01-20doi:10.1101/2023.01.19.524430Cold Spring Harbor Laboratory Press2023-01-20
<![CDATA[
Trial-history biases in evidence accumulation can give rise to apparent lapses
]]>
https://biorxiv.org/cgi/content/short/2023.01.18.524599v1?rss=1"
Gupta, D.DePasquale, B.Kopec, C. D.Brody, C.2023-01-20doi:10.1101/2023.01.18.524599Cold Spring Harbor Laboratory Press2023-01-20
<![CDATA[
The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi
]]>
https://biorxiv.org/cgi/content/short/2023.01.17.524442v1?rss=1"
Balamurugan, C.Steenwyk, J. L.Goldman, G. H.Rokas, A.2023-01-20doi:10.1101/2023.01.17.524442Cold Spring Harbor Laboratory Press2023-01-20
<![CDATA[
Functional specialization and structured representations for space and time in prefrontal cortex
]]>
https://biorxiv.org/cgi/content/short/2023.01.16.524214v1?rss=1"
Bohm, C.Lee, A. K.2023-01-18doi:10.1101/2023.01.16.524214Cold Spring Harbor Laboratory Press2023-01-18
<![CDATA[
Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants
]]>
https://biorxiv.org/cgi/content/short/2023.01.17.523798v1?rss=1"
Addetia, A.Piccoli, L.Case, J. B.Park, Y.-J.Beltramello, M.Guarino, B.Dang, H.Pinto, D.Scheaffer, S.Sprouse, K.Bassi, J.Silacci-Fregni, C.Muoio, F.Dini, M.Vincenzetti, L.Acosta, R.Johnson, D.Subramanian, S.Saliba, C.Giurdanella, M.Lombardo, G.Leoni, G.Culap, K.McAlister, C.Rajesh, A.Dellota, E.Cameroni, E.Whitener, B.Giannini, O.Ceschi, A.Ferrari, P.Franzetti-Pellanda, A.Biggiogero, M.Garzoni, C.Zappi, S.Bernasconi, L.Kim, M. J.Schnell, G.Czudnochowski, N.Franko, N.Logue, J. K.Yoshiyama, C.Stewart, C.Chu, H.2023-01-17doi:10.1101/2023.01.17.523798Cold Spring Harbor Laboratory Press2023-01-17
<![CDATA[
An intravenous DNA-binding priming agent protects cell-free DNA and improves the sensitivity of liquid biopsies
]]>
https://biorxiv.org/cgi/content/short/2023.01.13.523947v1?rss=1"
Tabrizi, S.Martin-Alonso, C.Xiong, K.Blewett, T.Sridhar, S.An, Z.Patel, S.Rodriguez-Aponte, S. A.Naranjo, C. A.Wang, S.-T.Shea, D.Golub, T.Bhatia, S.Adalsteinsson, V.Love, J. C.2023-01-14doi:10.1101/2023.01.13.523947Cold Spring Harbor Laboratory Press2023-01-14
<![CDATA[
Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14
]]>
https://biorxiv.org/cgi/content/short/2023.01.10.523456v1?rss=1"
Wang, M.Zhong, Z.Gallego-Bartolome, J.Feng, S.Shih, Y.-H.Liu, M.Zhou, J.Richey, J. C.Ng, C.Jami-Alahmadi, Y.Wohlschlegel, J.Wu, K.Jacobsen, S. E.2023-01-10doi:10.1101/2023.01.10.523456Cold Spring Harbor Laboratory Press2023-01-10
<![CDATA[
The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation.
]]>
https://biorxiv.org/cgi/content/short/2023.01.10.523455v1?rss=1"
Li, Z.Wang, M.Zhong, Z.Gallego-Bartolome, J.Feng, S.Jami-Alahmadi, Y.Wang, X.Wohlschlegel, J.Bischof, S.Long, J. A.Jacobsen, S. E.2023-01-10doi:10.1101/2023.01.10.523455Cold Spring Harbor Laboratory Press2023-01-10
<![CDATA[
Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis
]]>
https://biorxiv.org/cgi/content/short/2023.01.09.523347v1?rss=1"
He, S.Shao, W.Chen, S.Wang, T.Gibson, M.2023-01-10doi:10.1101/2023.01.09.523347Cold Spring Harbor Laboratory Press2023-01-10
<![CDATA[
Passive endocytosis in protocells enables nutrient transport bypassing permeability limits
]]>
https://biorxiv.org/cgi/content/short/2023.01.07.522792v1?rss=1"
Zhang, S. J.Anees, P.Krishnan, Y.Fai, T. G.Szostak, J. W.Wang, A.2023-01-07doi:10.1101/2023.01.07.522792Cold Spring Harbor Laboratory Press2023-01-07
<![CDATA[
Discovery of oxyacanthine dihydrochloride monohydrate polymorphs from obfuscated samples by MicroED
]]>
https://biorxiv.org/cgi/content/short/2025.07.03.663078v1?rss=1"
Lin, J.Paz, O.Unge, J.Gonen, T.2025-07-05doi:10.1101/2025.07.03.663078Cold Spring Harbor Laboratory Press2025-07-05
<![CDATA[
Memory traces bias new learning for hippocampal generalization
]]>
https://biorxiv.org/cgi/content/short/2025.11.24.690297v1?rss=1"
Qian, F. K.Li, G.Lipshutz, D.Romani, S.Magee, J. C.2025-11-25doi:10.1101/2025.11.24.690297Cold Spring Harbor Laboratory Press2025-11-25
<![CDATA[
Multimodal cell lineage reconstruction in the hindbrain reveals a link between progenitor origin and activity patterning
]]>
https://biorxiv.org/cgi/content/short/2025.11.14.688499v1?rss=1"
Blanc, M.Meister, L.Lemon, W. C.Fiuza, U.-M.Keller, P. J.Espinosa Medina, I.Pujades, C.2025-11-14doi:10.1101/2025.11.14.688499Cold Spring Harbor Laboratory Press2025-11-14
<![CDATA[
Hidden Markov Models Detect Recombination and Ancestry of SARS-CoV-2
]]>
https://biorxiv.org/cgi/content/short/2025.11.08.687354v1?rss=1"
Masaki, N.Bedford, T.2025-11-10doi:10.1101/2025.11.08.687354Cold Spring Harbor Laboratory Press2025-11-10
<![CDATA[
Mus Musculus papillomavirus MmuPV1 resists restriction by human APOBEC3B
]]>
https://biorxiv.org/cgi/content/short/2025.11.10.687577v1?rss=1"
Liu, X.Bilger, A.Lee, D.Argyris, P.Chen, J.Ward-Shaw, E.Barreto Duran, E.Lin, Y.-H.Durfee, C.Chun, S. H.Ibrahim, M.Proehl, J.Allen, Y.Lambert, P. F.Harris, R. S.2025-11-10doi:10.1101/2025.11.10.687577Cold Spring Harbor Laboratory Press2025-11-10
<![CDATA[
Virus induced transgene- and tissue-culture free heritable genome editing in tomato
]]>
https://biorxiv.org/cgi/content/short/2025.11.08.687402v1?rss=1"
Jacobsen, S. E.Liu, Y.Weiss, T.Lee, J.Powell, J.Choo, S. Y. C.Roshannai, E.Kamalu, M.Amerasekera, J.Feng, S.2025-11-09doi:10.1101/2025.11.08.687402Cold Spring Harbor Laboratory Press2025-11-09
<![CDATA[
5-azacytosine induces cytotoxicity via 5-methylcytosine depletion on chromatin-associated RNA in leukemia
]]>
https://biorxiv.org/cgi/content/short/2025.06.24.661348v1?rss=1"
Gao, B.Li, Y.Zhao, L.Zou, Z.Ma, X.Hong, J.Xiang, J.Dou, X.Yang, F.-C.Xu, M.He, C.2025-06-27doi:10.1101/2025.06.24.661348Cold Spring Harbor Laboratory Press2025-06-27
<![CDATA[
ERM proteins regulate the shape and number of Endoplasmic Reticulum-Plasma Membrane Junctions in neurons
]]>
https://biorxiv.org/cgi/content/short/2025.06.18.660273v1?rss=1"
Deng, H.Cheng, J.Fetter, R. D.Qin, G.Zhang, J.Liang, X.Taylor, C.Zhang, M.Wu, X.Shen, K.2025-06-18doi:10.1101/2025.06.18.660273Cold Spring Harbor Laboratory Press2025-06-18
<![CDATA[
Modulating MyoD1 dosage activates alternate cell fate beyond myogenic differentiation
]]>
https://biorxiv.org/cgi/content/short/2025.11.13.688391v1?rss=1"
Whitney, O. N.Dailey, G. M.McKenna, J. K.Darzacq, X.Tjian, R.2025-11-14doi:10.1101/2025.11.13.688391Cold Spring Harbor Laboratory Press2025-11-14
<![CDATA[
The Drosophila ovary produces three follicle waves similar to those in mice
]]>
https://biorxiv.org/cgi/content/short/2025.11.11.687893v1?rss=1"
Fu, W. Y.Spradling, A. C.2025-11-12doi:10.1101/2025.11.11.687893Cold Spring Harbor Laboratory Press2025-11-12
<![CDATA[
map3k1 is required for spatial restriction of progenitor differentiation in planarians
]]>
https://biorxiv.org/cgi/content/short/2025.03.04.641450v1?rss=1"
Canales, B.King, H. O.Reddien, P. W.2025-03-04doi:10.1101/2025.03.04.641450Cold Spring Harbor Laboratory Press2025-03-04
<![CDATA[
Sleep controls peroxisomal abundance to reduce wake-induced brain oxidation
]]>
https://biorxiv.org/cgi/content/short/2025.11.28.691144v1?rss=1"
Guevara, C.Li, Y.Pyfrom, E. S.Killiany, S.Yue, Z.Sehgal, A.2025-12-01doi:10.1101/2025.11.28.691144Cold Spring Harbor Laboratory Press2025-12-01
<![CDATA[
Naegleria amoebae seek confinement and crawl persistently through narrow spaces
]]>
https://biorxiv.org/cgi/content/short/2025.11.30.691445v1?rss=1"
50 m/min) and unidirectionally over long distances (>1 mm) using only bleb-based motility. We also introduced Naegleria to granular hydrogel matrices that mimic pond sediments and found that cells readily enter and migrate through these three-dimensional matrices using both blebs and lamellar protrusions. Although cells in matrices showed lower persistence at short timescales, longer time scales correlate with increased persistence, suggesting Naegleria cells may retain memory of past orientation. We propose that pond life may select for three behaviors that prime Naegleria for pathogenesis: memory-guided motility that would facilitate exploration of sinus cavities, confinement-seeking ("claustrophilia") that would promote entry into narrow passages along olfactory axons, and fast bleb-based migration that would allow rapid transit along axons to the brain.
SIGNIFICANCE STATEMENTThe "brain-eating amoeba" Naegleria fowleri causes a devastating brain infection with a [~]95% fatality rate, yet how these normally harmless pond-dwellers invade the human brain remains mysterious. Using the model species N. gruberi, we show that Naegleria amoebae exhibit three key behaviors: they retain directional memory during exploration, actively enter confined spaces, and crawl rapidly and persistently through narrow channels for millimeter-scale distances. We propose these behaviors are adaptations for hunting bacteria in pond sediments that inadvertently enable pathogenesis--directional memory facilitates sinus exploration, confinement-seeking draws amoebae into spaces between olfactory axons, and persistent channel migration enables rapid transit to the brain.
]]>Velle, K.Ramaswamy, M.Hokmabad, B. V.Martin-Perez, T.Carrasco, T. T.Callahan, W. S.Kim, H. S.Datta, S. S.Edwards, M.Fritz-Laylin, L.2025-12-01doi:10.1101/2025.11.30.691445Cold Spring Harbor Laboratory Press2025-12-01
<![CDATA[
The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome
]]>
https://biorxiv.org/cgi/content/short/2025.11.29.690828v1?rss=1"
Shen, B. A.Asfahl, K. L.Lim, B.Bertolli, S. K.Minot, S. S.Radey, M. C.Penewit, K.Ngo, B.Salipante, S. J.Johnston, C. D.Peterson, S. B.Goodman, A. D.Mougous, J. D.2025-11-30doi:10.1101/2025.11.29.690828Cold Spring Harbor Laboratory Press2025-11-30
<![CDATA[
Molecular interplay between the DNA damage checkpoint kinase Mec1-Ddc2 and its activator Dpb11 on gapped DNA
]]>
https://biorxiv.org/cgi/content/short/2025.11.28.691181v1?rss=1"
Beckwitt, E. C.Chua, G. N. L.Liu, S.O'Donnell, M. E.2025-11-30doi:10.1101/2025.11.28.691181Cold Spring Harbor Laboratory Press2025-11-30
<![CDATA[
Long-range mRNA folding shapes expression and sequence of bacterial genes
]]>
https://biorxiv.org/cgi/content/short/2025.11.27.690947v1?rss=1"
Gill, M. S.Kim, I. A.Xue, J. R.Thappeta, Y.Taggart, J. C.Li, G.-W.2025-11-27doi:10.1101/2025.11.27.690947Cold Spring Harbor Laboratory Press2025-11-27
<![CDATA[
In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles
]]>
https://biorxiv.org/cgi/content/short/2025.11.25.690450v1?rss=1"
95% of ribosomes and, unexpectedly, to 60S subunits. eEF2*GDP is stabilized by interactions with the sarcin-ricin loop and protein uL14. Hibernating ribosomes also feature LARP1 involved in initiation and mTOR signaling; eIF5A implicated in elongation and termination; and other factors, exposing the variety of hibernation scenarios. Our work underscores the efficiency and potential of in extracto cryo-EM to discover native cellular complexes and mechanisms at near-atomic resolution.
]]>Seraj, Z.Zottig, X.Huang, C.Loveland, A. B.Diggs, S.Sholi, E.Grigorieff, N.Korostelev, A. A.2025-11-25doi:10.1101/2025.11.25.690450Cold Spring Harbor Laboratory Press2025-11-25
<![CDATA[
A gene expression atlas of a juvenile nervous system
]]>
https://biorxiv.org/cgi/content/short/2025.11.21.689793v1?rss=1"
Taylor, S. R.Olson, C.Ripoll-Sanchez, L.Valperga, G.McWhirter, R.Barney, S. T.Atkinson, A.Goel, S.Weinreb, A.Hardin, A.Rolfson, A.Pattee, J.Aguilar, G. R.Merritt, D. M.Eroglu, M.Majeed, M.Grundvig, E.Child, E.Vertes, P. E.Schafer, W.Varol, E.Hammarlund, M.Hobert, O.Miller, D. M.2025-11-22doi:10.1101/2025.11.21.689793Cold Spring Harbor Laboratory Press2025-11-22
<![CDATA[
Computational design of metalloproteases
]]>
https://biorxiv.org/cgi/content/short/2025.11.20.689622v1?rss=1"
Chen, A.Wu, K.Choi, H.Venkatesh, P.Pellock, S. J.Hanikel, N.Coventry, B.Kim, D.Woodbury, S. M.Ji, P.Honda, S.Li, X.Gerben, S.Chang, L.Yan, X.Hyman, A. A.Hilvert, D.Baker, D.2025-11-21doi:10.1101/2025.11.20.689622Cold Spring Harbor Laboratory Press2025-11-21
<![CDATA[
RNA switch model for localization and translation of the myelin basic protein mRNA
]]>
https://biorxiv.org/cgi/content/short/2025.11.19.689361v1?rss=1"
Topkar, V. V.Wu, V.Ho, L. T.Ambiel, N.Valenzuela, A.Yoshimura, K.Zuchero, J. B.Fu, M.-m.Das, R.2025-11-20doi:10.1101/2025.11.19.689361Cold Spring Harbor Laboratory Press2025-11-20
<![CDATA[
A nucleic acid labeling chemistry reveals surface DNA on exosomes
]]>
https://biorxiv.org/cgi/content/short/2025.11.18.689134v1?rss=1"
Boskovic, F.Dutta Gupta, P.Zhang, J.Krishnan, Y.Szostak, J. W.2025-11-19doi:10.1101/2025.11.18.689134Cold Spring Harbor Laboratory Press2025-11-19
<![CDATA[
Rapid neocortical network modifications via dendritic plateau potential induced plasticity
]]>
https://biorxiv.org/cgi/content/short/2025.11.19.689338v1?rss=1"
Xiao, K.Li, Y.Sullivan, B. J.Li, G.Magee, J. C.2025-11-19doi:10.1101/2025.11.19.689338Cold Spring Harbor Laboratory Press2025-11-19
<![CDATA[
Structure and mechanism of microtubule stabilization and motor regulation by MAP9
]]>
https://biorxiv.org/cgi/content/short/2025.11.17.688911v1?rss=1"
Cetin, B.Taheri, A.Golcuk, M.Monroy, B. Y.Fernandes, J.Ori-McKenney, K. M.Gur, M.Nogales, E.Yildiz, A.2025-11-17doi:10.1101/2025.11.17.688911Cold Spring Harbor Laboratory Press2025-11-17
<![CDATA[
Structural Basis for Iterative Methylation by a Cobalamin-dependent Radical S-Adenosylmethionine Enzyme in Cystobactamids Biosynthesis
]]>
https://biorxiv.org/cgi/content/short/2025.11.17.688841v1?rss=1"
Cui, J.Wang, B.Maurya, R.Booker, S. J.2025-11-17doi:10.1101/2025.11.17.688841Cold Spring Harbor Laboratory Press2025-11-17
<![CDATA[
FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity
]]>
https://biorxiv.org/cgi/content/short/2025.11.13.688263v1?rss=1"
Ladewig, E.Nazir, A.Park, T.Fan, V. B.Cao, Z.Hawk, J.Kelly, L.Tjian, R.Leslie, C. S.Sawyers, C.2025-11-14doi:10.1101/2025.11.13.688263Cold Spring Harbor Laboratory Press2025-11-14
<![CDATA[
Expression of four mitochondrial tRNAs from only two loci
]]>
https://biorxiv.org/cgi/content/short/2025.11.12.688142v1?rss=1"
Warren, J. M.Prasad, K. V. S. K.Mendez, A. M.Temnyk, S.McCutcheon, J.2025-11-13doi:10.1101/2025.11.12.688142Cold Spring Harbor Laboratory Press2025-11-13
<![CDATA[
Cap1 forms a cyclic tetra-adenylate-induced membrane pore during the type III-A CRISPR-Cas immune response
]]>
https://biorxiv.org/cgi/content/short/2025.11.13.688252v1?rss=1"
Majumder, P.Cahir, C. W.Roberts, C. G.Patel, D. J.Marraffini, L. A.2025-11-13doi:10.1101/2025.11.13.688252Cold Spring Harbor Laboratory Press2025-11-13
<![CDATA[
High-efficiency targeted integration of extrachromosomal arrays in C. elegans using PhiC31 integrase
]]>
https://biorxiv.org/cgi/content/short/2025.11.11.687718v1?rss=1"
Rich, M. S.Pellow, R.Hefel, A.Rog, O.Jorgensen, E. M.2025-11-12doi:10.1101/2025.11.11.687718Cold Spring Harbor Laboratory Press2025-11-12
<![CDATA[
Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCF
]]>
https://biorxiv.org/cgi/content/short/2025.11.10.687711v1?rss=1"
Henikoff, S.Henikoff, J. G.2025-11-12doi:10.1101/2025.11.10.687711Cold Spring Harbor Laboratory Press2025-11-12
<![CDATA[
Fast-conducting mechanonociceptors uniquely engage reflexive and affective pain circuitry to drive protective responses
]]>
https://biorxiv.org/cgi/content/short/2025.11.11.687663v1?rss=1"
Lezgiyeva, K.Liu, J.Nguyen, K.DeLisle, M. M.Ko, F. C.Fullam, S.Obeidat, A. M.Turecek, J.Alkislar, I.Lehnert, B. P.Martinez-Garcia, R. I.Sivakumar, R.Choi, J.Mazor, O.Garibyan, L.Sharma, N.Emanuel, A. J.Malfait, A.-M.Miller, R. E.Ginty, D. D.2025-11-12doi:10.1101/2025.11.11.687663Cold Spring Harbor Laboratory Press2025-11-12
<![CDATA[
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
]]>
https://biorxiv.org/cgi/content/short/2025.11.07.687308v1?rss=1"
Haghani, N.Dodge, T. O.Baczenas, J. J.Gunn, T.He, Q.Pangburn, W.Sood, R.Du, K.Fascinetto-Zago, P.Kaatmann, A.Ou, Z.Dougan, S.Olmos-Santiago, N. S.Preising, G. A.Payne, C. Y.Haase Cox, S. K.Hunnicutt, K. E.Madrzyk, M.Moran, B. M.Stigloher, C.Powell, D. L.Schartl, M.Gifford, C.Han, G. z.Schumer, M.2025-11-11doi:10.1101/2025.11.07.687308Cold Spring Harbor Laboratory Press2025-11-11
<![CDATA[
Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria
]]>
https://biorxiv.org/cgi/content/short/2025.11.10.687660v1?rss=1"
Cascino, J. A.Dierksheide, K. J.Vishwakarma, R. K.Yuzenkova, Y.Babitzke, P.Murakami, K.Li, G.-W.2025-11-10doi:10.1101/2025.11.10.687660Cold Spring Harbor Laboratory Press2025-11-10
<![CDATA[
The deubiquitinating enzyme Otu1 releases substrates from the conserved initiation complex of the Cdc48/p97 ATPase for proteasomal degradation
]]>
https://biorxiv.org/cgi/content/short/2025.11.08.687396v1?rss=1"
Li, H.Guan, H.Rapoport, T.2025-11-09doi:10.1101/2025.11.08.687396Cold Spring Harbor Laboratory Press2025-11-09
<![CDATA[
Social interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback
]]>
https://biorxiv.org/cgi/content/short/2025.05.20.655113v1?rss=1"
Robertson, A. J.Kerr, B.Feder, A. F.2025-05-26doi:10.1101/2025.05.20.655113Cold Spring Harbor Laboratory Press2025-05-26
<![CDATA[
Signatures of remote planning in hippocampal replay
]]>
https://biorxiv.org/cgi/content/short/2025.12.02.691753v1?rss=1"
Lustig, B.Wang, Y.Romani, S.Pastalkova, E.Lee, A. K.2025-12-04doi:10.64898/2025.12.02.691753Cold Spring Harbor Laboratory Press2025-12-04
<![CDATA[
Replaying germinal center evolution on a quantified affinity landscape
]]>
https://biorxiv.org/cgi/content/short/2025.06.02.656870v1?rss=1"
DeWitt, W. S. S.Vora, A. A.Araki, T.Galloway, J. G.Alkutkar, T.Bortolatto, J.Castro, T. B.Dumm, W.Jennings-Schaffer, C.Jia, T.Mesin, L.Ozorowski, G.Pae, J.Ralph, D. K.Bloom, J. D.Nourmohammad, A.Song, Y. S.Ward, A.Starr, T. N.Matsen, F. A.Victora, G. D.2025-06-05doi:10.1101/2025.06.02.656870Cold Spring Harbor Laboratory Press2025-06-05
<![CDATA[
Conserved phenotype and function of human brain border-associated macrophages in iPSC-derived models
]]>
https://biorxiv.org/cgi/content/short/2025.12.11.693582v1?rss=1"
Barr, H. J.Depp, C.Hingerl, M.Nguyen, T.Reimertz, J. M.Connolly, E.Patel, J.Doman, J. L.Marsh, S. E.Stevens, B.2025-12-14doi:10.64898/2025.12.11.693582Cold Spring Harbor Laboratory Press2025-12-14
<![CDATA[
Synthetic Control of Implanted Engineered Liver Tissue Growth
]]>
https://biorxiv.org/cgi/content/short/2025.12.10.693527v1?rss=1"
Stoddard, A. E.Kumar, V.Tzouanas, C. N.Hui, V.Li, J.Jain, A.Farrell, A.Bhatia, S.Chen, C. S.2025-12-12doi:10.64898/2025.12.10.693527Cold Spring Harbor Laboratory Press2025-12-12
<![CDATA[
Serotonergic neuron-glioma interactions drive high-grade glioma pathophysiology
]]>
https://biorxiv.org/cgi/content/short/2025.12.10.693579v1?rss=1"
Drexler, R.Yalcin, B.Mancusi, R.Rogers, A.Shamardani, K.Woo, P. J.Ravel, A.Wu, S.Yabo, Y.Oliveira de Biagi-Junior, C. A.Lo Cascio, C.Malenka, R. C.Heifets, B. D.Filbin, M. G.Heiland, D. H.Deisseroth, K.Monje, M.2025-12-12doi:10.64898/2025.12.10.693579Cold Spring Harbor Laboratory Press2025-12-12
<![CDATA[
The circadian clock regulates scavenging of fluid-borne substrates by brain border-associated macrophages
]]>
https://biorxiv.org/cgi/content/short/2025.12.08.693074v1?rss=1"
Barr, H. J.Caldwell, S. K.Reimertz, J. M.Depp, C.Walker, A. J.Marsh, S. E.Gupte, A. S.Hingerl, M.Patel, J.Park, S.-O.Ferraro, S.Lipton, J.Stevens, B.2025-12-11doi:10.64898/2025.12.08.693074Cold Spring Harbor Laboratory Press2025-12-11
<![CDATA[
Engineering immunotoxin-equipped effector cells and evaluation in primary human immune cells
]]>
https://biorxiv.org/cgi/content/short/2025.12.09.691975v1?rss=1"
Pearlman, A. H.Mog, B. J.Hwang, M. S.Rincon-Torroella, J.DiNapoli, S. R.Paul, S.Douglass, J.Hsiue, E. H.-C.Glavaris, S. A.Pardoll, D. M.Papadopoulos, N.Kinzler, K. W.Bettegowda, C.Zhou, S.Vogelstein, B.Konig, M. F.2025-12-11doi:10.64898/2025.12.09.691975Cold Spring Harbor Laboratory Press2025-12-11
<![CDATA[
A shared DNA-repeat toxicity threshold, reached somatically at cell-type-specific rates, unites cortical and striatal neurodegeneration in Huntingtons disease
]]>
https://biorxiv.org/cgi/content/short/2025.12.09.688862v1?rss=1"
Kashin, S.Lee, W.-S.McDonald, T. M.Morris, K.Handsaker, R. E.Mello, C.Spina, L.Reed, N. M.de Rivera, H.Jana, S. H.Hogan, M.Berretta, S.McCarroll, S. A.2025-12-11doi:10.64898/2025.12.09.688862Cold Spring Harbor Laboratory Press2025-12-11
<![CDATA[
Structural basis of stepwise G protein activation by a viral chemokine receptor
]]>
https://biorxiv.org/cgi/content/short/2025.12.10.692789v1?rss=1"
Jude, K. M.Suomivuori, C.-M.Waghray, D.Maeda, S.Fujiyoshi, Y.Inoue, A.Garcia, K. C.Tsutsumi, N.2025-12-10doi:10.64898/2025.12.10.692789Cold Spring Harbor Laboratory Press2025-12-10
<![CDATA[
Preoptic Neurons that Regulate Hibernation Entry
]]>
https://biorxiv.org/cgi/content/short/2025.12.05.692394v1?rss=1"
Martinez, A. J.Reid, C. M.Lavin-Peter, A. J.Li, W.Lee, A. S.Griffith, E. C.Hrvatin, S.2025-12-09doi:10.64898/2025.12.05.692394Cold Spring Harbor Laboratory Press2025-12-09
<![CDATA[
Structure and evolution-guided design of minimal RNA-guided nucleases
]]>
https://biorxiv.org/cgi/content/short/2025.12.08.692503v1?rss=1"
Skopintsev, P.Esain-Garcia, I.DeTurk, E. C.Yoon, P. H.Zhou, Z.Weiss, T.Kamalu, M.Chamraj, A.Loi, K. J.Langeberg, C. J.Boger, R.Nisonoff, H.Karp, H. M.Chen, L.Shi, H.Vohra, K.Banfield, J. F.Cate, J. H. D.Jacobsen, S. E.Doudna, J. A.2025-12-08doi:10.64898/2025.12.08.692503Cold Spring Harbor Laboratory Press2025-12-08
<![CDATA[
Brain-immune interactions generate pathogen-specific sickness states
]]>
https://biorxiv.org/cgi/content/short/2025.12.06.692770v1?rss=1"
Sullivan, Z. A.Wong, B. J.Kapoor, V.Vincze, P. K.Kaplan, H. S.Giraudet, P.Watson, B. R.Misherghi, A.Lourido, S.Moffitt, J. R.Dulac, C.2025-12-08doi:10.64898/2025.12.06.692770Cold Spring Harbor Laboratory Press2025-12-08
<![CDATA[
Inhibition of FicD-mediated AMPylation and deAMPylation by Isoprenoid Diphosphates
]]>
https://biorxiv.org/cgi/content/short/2025.12.08.693056v1?rss=1"
Blevins, A. M.Peng, W.Kinch, L.Monshad, Z.Paredes, A. G.Volz, C.Rutter, J.Casey, A.Hicks, K.Orth, K.2025-12-08doi:10.64898/2025.12.08.693056Cold Spring Harbor Laboratory Press2025-12-08
<![CDATA[
Structural Basis of Human Kinetochore-Microtubule Coupling by the Ndc80 and Ska Complexes
]]>
https://biorxiv.org/cgi/content/short/2025.12.06.692780v1?rss=1"
Zhou, J.Zhao, Y.Yildiz, A.Nogales, E.2025-12-07doi:10.64898/2025.12.06.692780Cold Spring Harbor Laboratory Press2025-12-07
<![CDATA[
Bispecific T cell engagers control solid tumors through clonal replacement and IL2-driven effector differentiation of CD8 T-cells
]]>
https://biorxiv.org/cgi/content/short/2025.12.04.692214v1?rss=1"
Obenaus, M.Poupault, C. L.McGinnis, C. S.Prange, C.Jiang, H.Su, L. L.Chen, X.Miao, Z.Muldoon, J. J.Yao, W.Waghray, D.Sun, Q.Eyquem, J.Hernandez-Lopez, R. A.Satpathy, A. T.Sage, J.Garcia, K. C.2025-12-06doi:10.64898/2025.12.04.692214Cold Spring Harbor Laboratory Press2025-12-06
<![CDATA[
Vagal volume receptors in the heart compensate for blood loss and posture change
]]>
https://biorxiv.org/cgi/content/short/2025.12.05.692432v1?rss=1"
Liu, Z.Lu, S.Haskell, I. A.Min, S.Josipovic, M.Alabi, A. A.Chi, J.Kim, M.Liberles, S. D.2025-12-05doi:10.64898/2025.12.05.692432Cold Spring Harbor Laboratory Press2025-12-05
<![CDATA[
A paradoxical impact of alcohol on sleep-memory coupling
]]>
https://biorxiv.org/cgi/content/short/2025.12.03.692036v1?rss=1"
Chouhan, N. S.Mitra, W.Singh, K.Sehgal, A.2025-12-04doi:10.64898/2025.12.03.692036Cold Spring Harbor Laboratory Press2025-12-04
<![CDATA[
Elucidating an anterior cingulate circuit for self-initiated actions and rescue of Parkinsonian akinesia
]]>
https://biorxiv.org/cgi/content/short/2025.12.01.691607v1?rss=1"
Ulloa Severino, F.Lu, B.Kim, J.Friedman, A.Roshchina, M.Johnson, S.Bakhurin, K.Eroglu, C.Yin, H.2025-12-03doi:10.64898/2025.12.01.691607Cold Spring Harbor Laboratory Press2025-12-03
<![CDATA[
Ultrasonic Reporter of Kinase Activity
]]>
https://biorxiv.org/cgi/content/short/2025.11.30.691048v1?rss=1"
Yang, J. W.Jin, Z.Wang, T. Y.Shapiro, M. G.2025-12-02doi:10.64898/2025.11.30.691048Cold Spring Harbor Laboratory Press2025-12-02
<![CDATA[
Need-selective gating of dopamine neuron cue responses by real and virtual hunger
]]>
https://biorxiv.org/cgi/content/short/2025.11.29.691326v1?rss=1"
Mamaligas, A. A.Berke, J.Kreitzer, A. C.Knight, Z. A.2025-12-02doi:10.64898/2025.11.29.691326Cold Spring Harbor Laboratory Press2025-12-02
<![CDATA[
Cellular coding of ingestion in the caudal brainstem
]]>
https://biorxiv.org/cgi/content/short/2025.11.30.691333v1?rss=1"
Ly, T.Yi, X.Lee, G. R.Grove, J. C.Sibih, Y. E.Oh, Y. Y.Qiu, L.Sivakumar, N.Knight, Z. A.2025-12-02doi:10.64898/2025.11.30.691333Cold Spring Harbor Laboratory Press2025-12-02
<![CDATA[
A genetic screen in enteroendocrine cells reveals mechanisms that control protein sensing and GLP-1 release
]]>
https://biorxiv.org/cgi/content/short/2025.11.30.691441v1?rss=1"
20,000 sgRNAs identified numerous genes associated with mitochondrial respiration as being necessary for this process. We showed through secondary assays that impairing oxidative phosphorylation (OXPHOS) reduced EEC activation and GLP-1 release in response to nutrients but not in response to a non-nutritive stimulus. On the other hand, boosting OXPHOS increased EEC activation and GLP-1 release. These data reveal that intracellular metabolism within EECs controls the detection of dietary protein, possibly by monitoring the entry of ingested amino acids into the TCA cycle. More broadly, these findings suggest a general strategy to screen for genes and pathways that might be used to boost the nutrient-regulated release of gut peptides such as GLP-1.
]]>Yu, S.Lee, Y.Boggess, S. C.Klein, N. R.Teyssier, N.Kampmann, M.Knight, Z. A.2025-12-02doi:10.64898/2025.11.30.691441Cold Spring Harbor Laboratory Press2025-12-02
<![CDATA[
An orthogonal TRAP enables intersectional genetic access to activated neurons in the mouse brain
]]>
https://biorxiv.org/cgi/content/short/2025.11.30.691330v1?rss=1"
Chatziris, N.Jarvie, B. C.Liu, C.Knight, Z. A.2025-12-02doi:10.64898/2025.11.30.691330Cold Spring Harbor Laboratory Press2025-12-02
<![CDATA[
Orthosteric Molecular Glue Inhibits COP9 Signalosome with Substrate-Dependent Potency
]]>
https://biorxiv.org/cgi/content/short/2025.11.26.690573v1?rss=1"
Shi, H.Wang, X.Yu, C.Mao, H.Jiao, F.Braitbard, M.Shor, B.Zhang, Z.Hinds, T. R.Cao, S.Fan, E.Schneidman-Duhovny, D.Huang, L.Zheng, N.2025-11-30doi:10.1101/2025.11.26.690573Cold Spring Harbor Laboratory Press2025-11-30
<![CDATA[
Early-life stromal niches orchestrate B lymphopoiesis at the brain's borders
]]>
https://biorxiv.org/cgi/content/short/2025.11.27.690844v1?rss=1"
Walker, A. J.Fisher, T. M.Caldwell, S. K.Gupte, A. S.Colville-Reimertz, J. M.Sabikunnahar, B.Marsh, S. E.de Soysa, Y.Gazestani, V. H.Walker, A. C.Huang, Y.Mavinkurve, A. V.Barr, H. J.Lanser, T. B.Murphy, S.Bowling, S.Dissing-Olesen, L.Camargo, F. D.Stevens, B.2025-11-29doi:10.1101/2025.11.27.690844Cold Spring Harbor Laboratory Press2025-11-29
<![CDATA[
Ultrafast CTCF dynamics control cohesin barrier function
]]>
https://biorxiv.org/cgi/content/short/2025.11.25.690553v1?rss=1"
Rudnizky, S.Murray, P. J.Sorensen, E. W.Koenig, T. J. R.Pangeni, S.Merino-Urteaga, R.Chhabra, H.Caccianini, L.Davidson, I. F.Osorio-Valeriano, M.Hook, P. W.Meneses, P.Hao, J.Zarb, J. S.Hatzakis, N. S.Timp, W.Farnung, L.Vos, S. M.Peters, J.-M.Aksimentiev, A.Ha, T.2025-11-29doi:10.1101/2025.11.25.690553Cold Spring Harbor Laboratory Press2025-11-29
<![CDATA[
Life-long behavioral screen reveals an architecture of vertebrate aging
]]>
https://biorxiv.org/cgi/content/short/2025.11.21.688112v1?rss=1"
Bedbrook, C. N.Nath, R. D.Zhang, L.Linderman, S. W.Brunet, A.Deisseroth, K.2025-11-24doi:10.1101/2025.11.21.688112Cold Spring Harbor Laboratory Press2025-11-24
<![CDATA[
Computational design of cysteine proteases
]]>
https://biorxiv.org/cgi/content/short/2025.11.21.689808v1?rss=1"
Choi, H.Coventry, B.Bauer, M. S.Venkatesh, P.Chen, A.Kim, D.Bera, A. K.Kang, A.Nguyen, H.Joyce, E.Shankaran, B.Thompson, T. R.Gershon, J.Shida, A. F.Lee, G. R.Hilvert, D.Pellock, S. J.Baker, D.2025-11-22doi:10.1101/2025.11.21.689808Cold Spring Harbor Laboratory Press2025-11-22
<![CDATA[
Targeting peptide-MHC complexes with designed T cell receptors and antibodies
]]>
https://biorxiv.org/cgi/content/short/2025.11.19.689381v1?rss=1"
Motmaen, A.Jude, K. M.Wang, N.Minervina, A.Feldman, D.Lichtenstein, M. A.Ebenezer, A.Correnti, C.Thomas, P. G.Garcia, K. C.Baker, D.Bradley, P.2025-11-20doi:10.1101/2025.11.19.689381Cold Spring Harbor Laboratory Press2025-11-20
<![CDATA[
Unconventional linkers facilitate potent stabilized coronavirus stem antibody responses following nanoparticle vaccination
]]>
https://biorxiv.org/cgi/content/short/2025.11.19.689216v1?rss=1"
Dzuvor, C. K. O.Moak, S. P.McManus, L. R.Dzordzorme, A. E.Evanson, L. R.Kim, T.Thomas, A.Adeyemi, O.Foley, V.Limaye, A.McNamara, R. P.Corbett-Helaire, K. S.2025-11-19doi:10.1101/2025.11.19.689216Cold Spring Harbor Laboratory Press2025-11-19
<![CDATA[
Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation
]]>
https://biorxiv.org/cgi/content/short/2025.11.17.688899v1?rss=1"
Russell, K.Chen, Y.Espinosa, J. R.Gil, D. F.Zhou, H.Maristany, M. J.Lopez, J. I. P.Huertas, J.Orozco, M.Rosen, M. K.Collepardo-Guevara, R.2025-11-17doi:10.1101/2025.11.17.688899Cold Spring Harbor Laboratory Press2025-11-17
<![CDATA[
ecDNA-driven oncogene super-expressors shape immunoevasive tumor microenvironment
]]>
https://biorxiv.org/cgi/content/short/2025.11.15.688565v1?rss=1"
Qiao, K.Yang, Q.-L.Li, T.Chen, X.Yazgan, Z.Kim, Y. J.Gilbreath, C.Lim, J. Y. S.Xie, Y.Sun, X.Liu, Y.Jia, Y.Chen, Z. J.Huang, H.Wu, S.2025-11-16doi:10.1101/2025.11.15.688565Cold Spring Harbor Laboratory Press2025-11-16
<![CDATA[
Extracting task-relevant preserved dynamics from contrastive aligned neural recordings
]]>
https://biorxiv.org/cgi/content/short/2025.11.11.686428v1?rss=1"
Jiang, Y.Sheng, K.Gao, Y.Buchanan, E. K.Shikano, Y.Kim, T. H.Zhao, Y.Woo, S. J.Dinc, F.Linderman, S. W.Schnitzer, M. J.2025-11-13doi:10.1101/2025.11.11.686428Cold Spring Harbor Laboratory Press2025-11-13
<![CDATA[
Proteome-wide in silico screening for human protein-protein interactions
]]>
https://biorxiv.org/cgi/content/short/2025.11.10.687652v1?rss=1"
Schmid, E.Zhu, H.Ryu, E.Lim, Y.Smogorzewska, A.Brown, A.Walter, J.2025-11-12doi:10.1101/2025.11.10.687652Cold Spring Harbor Laboratory Press2025-11-12
<![CDATA[
Structure-informed evolutionary analysis of the meiotic recombination machinery
]]>
https://biorxiv.org/cgi/content/short/2025.11.07.687317v1?rss=1"
Arter, M.Vedanayagam, J.Lu, M.Diop, M.Liu, K.Lai, E. C.Keeney, S.2025-11-11doi:10.1101/2025.11.07.687317Cold Spring Harbor Laboratory Press2025-11-11
<![CDATA[
Insights into the regulation of VPS13 family bridge-like lipid transfer proteins from the structure of VPS13C.
]]>
https://biorxiv.org/cgi/content/short/2025.11.10.687702v1?rss=1"
Li, D.Wang, X.Hu, B.Hao, H.Hamill, S.Li, Y.Chen, G.De Camilli, P.Reinisch, K.2025-11-11doi:10.1101/2025.11.10.687702Cold Spring Harbor Laboratory Press2025-11-11
<![CDATA[
Polyserine-tau interactions modulate tau fibrilization
]]>
https://biorxiv.org/cgi/content/short/2025.06.03.657713v1?rss=1"
Pratt, J.McCann, K.Kuo, J.Parker, R.2025-06-03doi:10.1101/2025.06.03.657713Cold Spring Harbor Laboratory Press2025-06-03
<![CDATA[
The SHR/Akr Y chromosome reveals repeated turnover of the rat pseudoautosomal region
]]>
https://biorxiv.org/cgi/content/short/2025.05.28.656580v1?rss=1"
Bellott, D. W.Skaletsky, H.Hughes, J.Brown, L. G.Pyntikova, T.Cho, T.-J.Koutseva, N.Zaghlul, S.Kizghin, D.Mendoza, M.Raudsepp, T.Dugan, S.Khan, Z.Wang, Q.Watt, J.Worley, K. C.Scherer, S.Muzny, D. M.Gibbs, R. A.Page, D. C.2025-06-01doi:10.1101/2025.05.28.656580Cold Spring Harbor Laboratory Press2025-06-01
<![CDATA[
Reconstructing a physiological state space via chronic jugular microdialysis in freely moving mice
]]>
https://biorxiv.org/cgi/content/short/2025.12.08.692974v1?rss=1"
Nardin, M.Wang, N.Elziny, S.Boyer, C.Pjanovic, V.Schuster, L.Boklund, P.Lindo, S.Morris, K.Ilanges, A.Voigts, J.Dennis, E. J.2025-12-11doi:10.64898/2025.12.08.692974Cold Spring Harbor Laboratory Press2025-12-11
<![CDATA[
Spatial gene expression maps in vertebrate limbs display conserved and regenerative species-specific features within connective tissue
]]>
https://biorxiv.org/cgi/content/short/2025.12.15.694399v1?rss=1"
McMann, C. L.Park, C.Cloutier, J. K.Reddien, P.2025-12-17doi:10.64898/2025.12.15.694399Cold Spring Harbor Laboratory Press2025-12-17
<![CDATA[
Mitochondria-derived PEP licenses glycerolipid synthesis via SLC25A35
]]>
https://biorxiv.org/cgi/content/short/2025.12.12.693842v1?rss=1"
Yamamuro, T.Katoh, D.Silva, G. M.Nishida, H.Oikawa, S.Higuchi, Y.Wang, D.Fujimoto, M.Yoshida, N.Li, M.Shin, J.Zhao, Z.Yook, J.-S.Sun, L.Kajimura, S.2025-12-16doi:10.64898/2025.12.12.693842Cold Spring Harbor Laboratory Press2025-12-16
<![CDATA[
Neuroligin-2 is ubiquitinated by Nedd4l to control developmental astrocyte morphogenesis.
]]>
https://biorxiv.org/cgi/content/short/2025.12.15.694023v1?rss=1"
Eroglu, C.Sakers, K.Ramirez, J. J.Elazar, N.Nagendren, L.Soderblom, E. J.2025-12-16doi:10.64898/2025.12.15.694023Cold Spring Harbor Laboratory Press2025-12-16
<![CDATA[
Nanopore-based profiling of PEGylation in nucleic acid therapeutics
]]>
https://biorxiv.org/cgi/content/short/2025.12.15.694309v1?rss=1"
Patino Guillen, G.Schmidt, T. T.Baumberg, J. J.Szostak, J. W.Keyser, U. F.Boskovic, F.2025-12-17doi:10.64898/2025.12.15.694309Cold Spring Harbor Laboratory Press2025-12-17
<![CDATA[
Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry
]]>
https://biorxiv.org/cgi/content/short/2025.12.19.695558v1?rss=1"
Martin, A.MacRae, N. S.Dong, K. C.Harimoto, H.2025-12-20doi:10.64898/2025.12.19.695558Cold Spring Harbor Laboratory Press2025-12-20
<![CDATA[
In-cell cryo-electron tomography reveals differential effects of type I and type II kinase inhibitors on LRRK2 filament formation and microtubule association
]]>
https://biorxiv.org/cgi/content/short/2025.12.18.694444v1?rss=1"
Basiashvili, T.Hutchings, J.Chen, S.Karasmanis, E. P.Flaherty, W. A.Leschziner, A. E.Villa, E.2025-12-19doi:10.64898/2025.12.18.694444Cold Spring Harbor Laboratory Press2025-12-19
<![CDATA[
VEGF/ERK activation and PI3K inhibition together drive a vein-to-artery transition in an in vitro model of human angiogenesis
]]>
https://biorxiv.org/cgi/content/short/2025.12.17.694993v1?rss=1"
Amir-Ugokwe, Z.Red-Horse, K.Loh, K. M.Ang, L. T.Pyke, A.Trimm, E.Chakraborty, M.Fan, X.2025-12-19doi:10.64898/2025.12.17.694993Cold Spring Harbor Laboratory Press2025-12-19
<![CDATA[
Ectopic engraftment of nociceptive neurons derived from hPSCs for pain relief and joint homeostasis
]]>
https://biorxiv.org/cgi/content/short/2025.12.16.694733v1?rss=1"
View larger version (70K):
org.highwire.dtl.DTLVardef@15f0948org.highwire.dtl.DTLVardef@5a59bforg.highwire.dtl.DTLVardef@1ba4439org.highwire.dtl.DTLVardef@1d518d1_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIhPSC-derived nociceptors (hPSC-NNs) as Decoy Engraftment for Cellular Interception and Repair (DECIR) when transplanted into the knee joint, extending beyond conventional regenerative strategies
C_LIO_LICD200 serves as a clinically actionable surface marker for the purification of hPSC-NNs
C_LIO_LIEctopic grafting of CD200high hPSC-NNs delivers dual benefits, alleviating pain and modulating the neuro-immune environment within joint tissues
C_LIO_LIProteomic analyses reveal that CD200highhPSC-NNs sequester inflammatory mediators and secrete reparative factors to support joint homeostasis
C_LI
]]>Dong, X.Lee, G.Wang, Z. P.Zhang, W.Cao, X.Peng, J.Wang, J.Wu, Z.2025-12-19doi:10.64898/2025.12.16.694733Cold Spring Harbor Laboratory Press2025-12-19
<![CDATA[
Mitochondrial control of fuel switching via carnitine biosynthesis
]]>
https://biorxiv.org/cgi/content/short/2025.12.16.694762v1?rss=1"
Auger, C.Nishida, H.Yuan, B.Silva, G. M.Fujimoto, M.Li, M.Katoh, D.Wang, D.Granath-Panelo, M.Shin, J.Verkerke, A.Banks, A.Hui, S. T.Sun, L.Yook, J.-S.Witte, R.Kajimura, S.2025-12-18doi:10.64898/2025.12.16.694762Cold Spring Harbor Laboratory Press2025-12-18
<![CDATA[
Humanized Extracellular Vesicles for Efficient RNA Delivery
]]>
https://biorxiv.org/cgi/content/short/2025.12.15.694436v1?rss=1"
Ma, X.Zhao, S. R.Cepko, C. L.2025-12-17doi:10.64898/2025.12.15.694436Cold Spring Harbor Laboratory Press2025-12-17
<![CDATA[
Human acrocentric chromosome short arm de novo mutation and recombination
]]>
https://biorxiv.org/cgi/content/short/2025.12.16.694519v1?rss=1"
T but increased C>G and A>C mutations. We hypothesize that acrocentric sequence composition biases and the dearth of allelic recombination contribute to an elevated mutation rate and unique mutational signatures suggestive of mismatch repair defects and oxidative stress-induced DNA lesions.
]]>Lin, J.Mastrorosa, F. K.Noyes, M. D.Yoo, D.Rhie, A.Porubsky, D.Hoekzema, K.Munson, K. M.Koundinya, N.Watkins, W. S.Jorde, L. B.Quinlan, A. R.Neklason, D. W.Phillippy, A. M.Eichler, E. E.2025-12-17doi:10.64898/2025.12.16.694519Cold Spring Harbor Laboratory Press2025-12-17
<![CDATA[
Antibody Mediated Diversification of Primary and Secondary Immune Responses
]]>
https://biorxiv.org/cgi/content/short/2025.12.15.694384v1?rss=1"
Schaefer-Babajew, D.Binet, L.Santos, G. S. S.Ruprecht, C.Deimel, L. P.ElTanbouly, M. A.Gharrassi, D.Uhe, C.Yao, K.-H.Hernandez, B.Agrawal, P.Gazumyan, A.Stamatatos, L.Hartweger, H.Nussenzweig, M. C.2025-12-17doi:10.64898/2025.12.15.694384Cold Spring Harbor Laboratory Press2025-12-17
<![CDATA[
Phosphatase SHP2 pathogenic mutations enhance activity by altering conformational sampling
]]>
https://biorxiv.org/cgi/content/short/2025.12.12.694068v1?rss=1"
Glaser, A.Padua, R.Ojoawo, A.Sullivan, C.Kern, D.2025-12-14doi:10.64898/2025.12.12.694068Cold Spring Harbor Laboratory Press2025-12-14
<![CDATA[
Cell Type-Specific Hormonal Signaling Configures Hypothalamic Circuits for Parenting
]]>
https://biorxiv.org/cgi/content/short/2025.12.11.693766v1?rss=1"
Logeman, B. L.Horvath, P. M.Talay, M.Kapoor, V.Kaplan, H. S.Dulac, C.2025-12-12doi:10.64898/2025.12.11.693766Cold Spring Harbor Laboratory Press2025-12-12
<![CDATA[
Drosophila maintain a consistent navigational goal angle for days to weeks
]]>
https://biorxiv.org/cgi/content/short/2025.12.09.693277v1?rss=1"
Weisman, J. L.Mohren, T. L.Ryu, J. D.Wyse, M. Z.Dias-Ferreira, E.Maimon, G.2025-12-11doi:10.64898/2025.12.09.693277Cold Spring Harbor Laboratory Press2025-12-11
<![CDATA[
Distributed control circuits across a brain-and-cord connectome
]]>
https://biorxiv.org/cgi/content/short/2025.07.31.667571v1?rss=1"
Bates, A. S.Phelps, J. S.Kim, M.Yang, H. H.Matsliah, A.Ajabi, Z.Perlman, E.Delgado, K. M.Osman, M. A. M.Salmon, C. K.Gager, J.Silverman, B.Renauld, S.Collie, M. F.Fan, J.Pacheco, D. A.Zhao, Y.Patel, J.Zhang, W.Serratosa Capdevilla, L.Roberts, R. J.Munnelly, E. J.Griggs, N.Langley, H.Moya-Llamas, B.Maloney, R. T.Yu, S.-c.Sterling, A. R.Sorek, M.Kruk, K.Serafetinidis, N.Dhawan, S.Stuerner, T.Klemm, F.Brooks, P.Lesser, E.Jones, J. M.Pierce-Lundgren, S. E.Lee, S.-Y.Luo, Y.Cook, A. P.McKim, T. H.Kophs, E. C.Falt,2025-08-01doi:10.1101/2025.07.31.667571Cold Spring Harbor Laboratory Press2025-08-01
<![CDATA[
Sequence-specific targeting of intrinsically disordered protein regions
]]>
https://biorxiv.org/cgi/content/short/2024.07.15.603480v1?rss=1"
Wu, K.Jiang, H.Hicks, D. R.Liu, C.Muratspahic, E.Ramelot, T. A.Liu, Y.McNally, K.Gaur, A.Coventry, B.Chen, W.Bera, A. K.Kang, A.Gerben, S.Lamb, M. Y.-L.Murray, A.Li, X.Kennedy, M. A.Yang, W.Schober, G.Brierley, S. M.Gelb, M. H.Montelione, G. T.Derivery, E.Baker, D.2024-07-16doi:10.1101/2024.07.15.603480Cold Spring Harbor Laboratory Press2024-07-16
<![CDATA[
Discovery of the metalloenzyme IsmB revises a pathway for coprostanol formation by the human gut microbiome
]]>
https://biorxiv.org/cgi/content/short/2025.12.29.696961v1?rss=1"
Tinoco, A.Li, C.Khurana, J.Banuelos Jara, B.Plichta, D. R.Kenny, D.Xavier, R. J.Balskus, E. P.2025-12-30doi:10.64898/2025.12.29.696961Cold Spring Harbor Laboratory Press2025-12-30
<![CDATA[
Template-based RNA structure prediction advanced through a blind code competition
]]>
https://biorxiv.org/cgi/content/short/2025.12.30.696949v1?rss=1"
Lee, Y.He, S.Oda, T.Rao, G. J.Kim, Y.Kim, R.Kim, H.Heng, C. K.Kowerko, D.Li, H.Nguyen, H.Sampathkumar, A.Enrique Gomez, R.Chen, M.Yoshizawa, A.Kuraishi, S.Ogawa, K.Zou, S.Paullier, A.Zhao, B.Chen, H.-L.Hsu, T.-A.Hirano, T.Gezelle, J. G.Haack, D.Hong, Y.Jadhav, S.Koirala, D.Kretsch, R. C.Lewicka, A.Li, S.Marcia, M.Piccirilli, J.Rudolfs, B.Srivastava, Y.Steckelberg, A.-L.Su, Z.Toor, N.Wang, L.Yang, Z.Zhang, K.Zou, J.Baker, D.Chen, S.-J.Chiu, W.Demkin, M.Favor, A.Hummer, A. M.Joshi, C. K.Kryshtafovyc2025-12-30doi:10.64898/2025.12.30.696949Cold Spring Harbor Laboratory Press2025-12-30
<![CDATA[
Ensemble Coding of Hidden Objects in Visual Cortex
]]>
https://biorxiv.org/cgi/content/short/2025.12.29.696959v1?rss=1"
Zhu, S.Lopes, D. A.Cital, S. N.Moore, T.2025-12-30doi:10.64898/2025.12.29.696959Cold Spring Harbor Laboratory Press2025-12-30
<![CDATA[
Structural basis for non-AUG translation regulation by 5MPs
]]>
https://biorxiv.org/cgi/content/short/2025.12.28.696766v1?rss=1"
Zottig, X.Huang, C.-Y.Seraj, Z.Grigorieff, N.Korostelev, A. A.2025-12-29doi:10.64898/2025.12.28.696766Cold Spring Harbor Laboratory Press2025-12-29
<![CDATA[
Transcriptomic and functional characterization indicate sexual dimorphism of discrete circadian neuron subtypes
]]>
https://biorxiv.org/cgi/content/short/2025.12.26.696620v1?rss=1"
Perez Torres, M.Jiang, R.Ma, D.Kurmangaliyev, Y.Guo, F.Rosbash, M.2025-12-27doi:10.64898/2025.12.26.696620Cold Spring Harbor Laboratory Press2025-12-27
<![CDATA[
HIV-1 Integration Site Determines the Transcriptional Fate and Persistence of Integrated Proviruses
]]>
https://biorxiv.org/cgi/content/short/2025.12.26.696579v1?rss=1"
Pal, V.Danesh, A.Canis, M.Dilling, T.Miller, I.Huynh, T. T.Copertino, D.Barrows, D.Carroll, T.Hatziioannou, T.Jones, R. B.Lee, G. Q.Muecksch, F.Bieniasz, P. D.2025-12-26doi:10.64898/2025.12.26.696579Cold Spring Harbor Laboratory Press2025-12-26
<![CDATA[
Chromatin profiling for everyone: FFPE-CUTAC for the theory and practice of modern molecular biology
]]>
https://biorxiv.org/cgi/content/short/2025.12.24.696395v1?rss=1"
Xu, Y.Henikoff, S.Ahmad, K.2025-12-26doi:10.64898/2025.12.24.696395Cold Spring Harbor Laboratory Press2025-12-26
<![CDATA[
A System for Live Sorting of Neuronal Spiking Activity from Large-scale Recordings
]]>
https://biorxiv.org/cgi/content/short/2025.12.29.696938v1?rss=1"
Muralidharan, S.Leng, C.Orts, L.Trepka, E.Zhu, S.Panichello, M.Jonikaitis, D.Pennington, J.Pachitariu, M.Moore, T.2026-01-02doi:10.64898/2025.12.29.696938Cold Spring Harbor Laboratory Press2026-01-02
<![CDATA[
Endothelial TLR4 signaling drives tissue inflammation, Claudin-5 internalization, and vascular barrier breakdown in a mouse model of neonatal meningitis
]]>
https://biorxiv.org/cgi/content/short/2025.12.31.697193v1?rss=1"
Seegren, P. V.Rattner, A.Smallwood, P. M.Nathans, J.2026-01-02doi:10.64898/2025.12.31.697193Cold Spring Harbor Laboratory Press2026-01-02
<![CDATA[
Meta-learning is expressed through altered prefrontal cortical dynamics
]]>
https://biorxiv.org/cgi/content/short/2026.01.01.697272v1?rss=1"
Sun, X.Comrie, A. E.Kahn, A. E.Monroe, E. J.Joshi, A.Guidera, J. A.Denovellis, E. L.Krausz, T. A.Zhou, J.Thompson, P.Hernandez, J.Yorita, A.Haque, R.Berke, J. D.Daw, N. D.Frank, L. M.2026-01-02doi:10.64898/2026.01.01.697272Cold Spring Harbor Laboratory Press2026-01-02
<![CDATA[
Memory from variability: Heritable short-term cellular memory emerges from stochastic biochemical reaction networks
]]>
https://biorxiv.org/cgi/content/short/2025.12.31.694479v1?rss=1"
Aronson, M. S.Zhou, B. Y.Fitzgerald, J. E.Sgro, A. E.2026-01-01doi:10.64898/2025.12.31.694479Cold Spring Harbor Laboratory Press2026-01-01
<![CDATA[
PtdIns(3,5)P2 Is an Endogenous Ligand of STING in Innate Immune Signaling
]]>
https://biorxiv.org/cgi/content/short/2025.12.29.696917v1?rss=1"
Tan, J. X.Lv, B.Li, J.Li, T.Du, F.Chen, X.Zhang, X.Bai, X.-c.Chen, Z. J.2025-12-29doi:10.64898/2025.12.29.696917Cold Spring Harbor Laboratory Press2025-12-29
<![CDATA[
mRNAbow: A versatile gene expression system for multiplexed fluorescent imaging using optimized in vitro transcribed mRNA
]]>
https://biorxiv.org/cgi/content/short/2026.01.02.697412v1?rss=1"
Choi, H.Halanych, C.Kasberg, W.Testa, M. D.Rubin-Elgressy, S.Nguyen, P.Walpita, D.Tsang, A.Cortes, D.Song, E. Y.Wu, H.Weissman, I. L.Espinosa-Medina, I.Satou, C.Song, J. L.Matus, D. Q.Lippincott-Schwartz, J.2026-01-02doi:10.64898/2026.01.02.697412Cold Spring Harbor Laboratory Press2026-01-02
<![CDATA[
ABCC1 protects skin dendritic cells from FITC-induced toxicity by efflux and extracellular glutathione buffering
]]>
https://biorxiv.org/cgi/content/short/2026.01.02.697391v1?rss=1"
Knopper, K.Rao, A.An, J.Cyster, J. G.2026-01-02doi:10.64898/2026.01.02.697391Cold Spring Harbor Laboratory Press2026-01-02
<![CDATA[
Mitochondrial depolarization stabilizes the vitamin B12 chaperone MMADHC in the cytosol to increase MTR activity
]]>
https://biorxiv.org/cgi/content/short/2025.12.31.697091v1?rss=1"
Rath, S. P.Li, Z.Guha, A.Dong, F.Banerjee, R.Mootha, V. K.2025-12-31doi:10.64898/2025.12.31.697091Cold Spring Harbor Laboratory Press2025-12-31
<![CDATA[
Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD
]]>
https://biorxiv.org/cgi/content/short/2025.12.30.697072v1?rss=1"
Han, T.Sun, Z.Lange, M.Cho, Y. Z.Mcgillivray, P.Buttner, M.Kastan, N. R.Nandakumar, S.Zhao, H.Oak, S.Fong, L.Kang, W.Fan, N.Zhao, J.Salsabeel, N.Kaur, H.Mao, N.Chang, Q.Rosiek, E.Chan, E.Tipping, M.Schultz, N.Hamard, P.-J.De Stanchina, E.Pe'er, D.Koche, R. P.Chen, Z.Hudspeth, A.Sawyers, C.2025-12-31doi:10.64898/2025.12.30.697072Cold Spring Harbor Laboratory Press2025-12-31
<![CDATA[
The organization of visual pathways in the Drosophila brain
]]>
https://biorxiv.org/cgi/content/short/2025.12.22.696097v1?rss=1"
Hoeller, J.Zhao, A.Nern, A.Rogers, E. M.Romani, S.Reiser, M. B.2025-12-25doi:10.64898/2025.12.22.696097Cold Spring Harbor Laboratory Press2025-12-25
<![CDATA[
Innate immune sensing via the cGAS-STING pathway restricts extrachromosomal DNA-driven tumorigenesis
]]>
https://biorxiv.org/cgi/content/short/2025.12.31.697191v1?rss=1"
Li, T.Yang, Q.-L.Qiao, K.Zhang, A.Sun, C.Huang, H.Mischel, P. S.Wu, S.Chen, Z. J.2026-01-01doi:10.64898/2025.12.31.697191Cold Spring Harbor Laboratory Press2026-01-01
<![CDATA[
The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation
]]>
https://biorxiv.org/cgi/content/short/2026.01.05.697729v1?rss=1"
Farnung, J.Slobodyanyuk, E.Wang, P. Y.Blodgett, L. W.Lin, D. H.von Gronau, S.Schulman, B. A.Bartel, D. P.2026-01-05doi:10.64898/2026.01.05.697729Cold Spring Harbor Laboratory Press2026-01-05
<![CDATA[
A panoramic view of the expression and function of the Doublesex/DMRT gene family in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2026.01.01.697290v1?rss=1"
Wang, C.Salzberg, Y.Oren-Suissa, M.Hobert, O.2026-01-05doi:10.64898/2026.01.01.697290Cold Spring Harbor Laboratory Press2026-01-05
<![CDATA[
Integration of in situ hybridization and scRNA-seq data provides a 2D topographical map of the developing retina across species
]]>
https://biorxiv.org/cgi/content/short/2026.01.04.697548v1?rss=1"
View larger version (44K):
org.highwire.dtl.DTLVardef@e9b84aorg.highwire.dtl.DTLVardef@4207deorg.highwire.dtl.DTLVardef@112bc79org.highwire.dtl.DTLVardef@113e1d3_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIQuantification of multiplexed RNA-FISH signals generated reproducible spatial expression maps in the developing chicken retina.
C_LIO_LIResolution of relative boundaries for early patterning genes revealed nested expression domains marking the boundaries of the developing HAA.
C_LIO_LIRNA-FISH experimental data using genes with axis-specific expression allowed the generation of DV and NT scores which enabled the localization of each cell in a scRNA-seq dataset onto a 2D topographical map of the developing retina.
C_LIO_LI2D topographic maps derived from scRNA-seq data revealed novel HAA-enriched genes in the developing chicken retina.
C_LIO_LICross-species comparisons showed conserved DV/NT programs but divergent fine-scale organization in retinal development.
C_LIO_LICyp26c1 expression pattern was validated in human retina correlating with the location of the future HAA.
C_LI
]]>Joisher, H. N.Lee, C.Prabhakara, C.van der Weide, I.Si, Y.Lonfat, N.Cepko, C.2026-01-04doi:10.64898/2026.01.04.697548Cold Spring Harbor Laboratory Press2026-01-04
<![CDATA[
Chemiluminescent probes allow for the rapid identification of colibactin-producing bacteria
]]>
https://biorxiv.org/cgi/content/short/2026.01.02.697419v1?rss=1"
Aguilar Ramos, M.Gutkin, S.David, M.Shabat, D.Balskus, E. P.2026-01-02doi:10.64898/2026.01.02.697419Cold Spring Harbor Laboratory Press2026-01-02
<![CDATA[
Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures
]]>
https://biorxiv.org/cgi/content/short/2026.01.05.697808v1?rss=1"
Ahn, J. J.Yu, T. C.Dadonaite, B.Radford, C. E.Bloom, J. D.2026-01-06doi:10.64898/2026.01.05.697808Cold Spring Harbor Laboratory Press2026-01-06
<![CDATA[
SCREWx: A Screwless, Chronic, Recoverable, and Lightweight Neuropixels fixture for freely-moving rodents
]]>
https://biorxiv.org/cgi/content/short/2026.01.06.697790v1?rss=1"
Cheng, A.DeWeese, T.Zhou, Y.Sueoka, Y.Koukuntla, S.Green, M.Cullen, K.Knierim, J.Graves, A.Harris, T.2026-01-06doi:10.64898/2026.01.06.697790Cold Spring Harbor Laboratory Press2026-01-06
<![CDATA[
Architecting cis-regulation to quantitatively tune gene expression in cereals
]]>
https://biorxiv.org/cgi/content/short/2026.01.08.698005v1?rss=1"
30,000 CRISPR-like mutations-deletions, substitutions, and motif insertions-across entire native promoters and 5' untranslated regions (UTRs) of three photosynthesis genes: PsbS, Raf1, and SBPase. We find that gene expression is most tunable within a [~]500 base pair core promoter region, where mutational effects are reproducible across biological replicates and predictive of protein output. Within these regions, we identify compact deletions and motif insertions that strongly increase protein production (>30-fold relative to wild type), exceeding the performance of transgenic enhancer elements. Mutation-effect relationships are gene-specific, highlighting the need for tailored regulatory maps. Our results establish a high-throughput strategy for cis-regulatory fine-mapping that enables crop improvements via minimal, precise, and non-transgenic gene edits.
]]>Groover, E. D.Ding, D.Wang, F. Z.Benegas, G.Rivera, J.Schwartz, S.Chen, S.Moubarak, M. F.Georgieva, V.Lemaux, P. G.Staskawicz, B.Niyogi, K. K.Song, Y. S.Savage, D.2026-01-08doi:10.64898/2026.01.08.698005Cold Spring Harbor Laboratory Press2026-01-08
<![CDATA[
A signature-agnostic test for differences between tumor mutation spectra reveals carcinogen and ancestry effects
]]>
https://biorxiv.org/cgi/content/short/2025.05.15.654154v1?rss=1"
Hart, S. F. M.Alcala, N.Feder, A. F.Harris, K.2025-05-19doi:10.1101/2025.05.15.654154Cold Spring Harbor Laboratory Press2025-05-19
<![CDATA[
An efflux pump family distributed across plant commensal bacteria conditions host- and organ-specific detoxfication of a host-specific glucosinolate
]]>
https://biorxiv.org/cgi/content/short/2024.10.18.619176v1?rss=1"
Russ, D.Fitzpatrick, C. R.Saha, C.Law, T. F.Jones, C. D.Kliebenstein, D. J.Dangl, J. L.2024-10-19doi:10.1101/2024.10.18.619176Cold Spring Harbor Laboratory Press2024-10-19
<![CDATA[
Ultrafast Frame-Free Imaging of Neural Activity with Event Cameras
]]>
https://biorxiv.org/cgi/content/short/2026.01.08.698496v1?rss=1"
Forli, A.Kasuba, K. C.Henn, K.Lee, D.Hernandez-Morales, M.Liu, C.Miller, E. W.Yartsev, M.2026-01-09doi:10.64898/2026.01.08.698496Cold Spring Harbor Laboratory Press2026-01-09
<![CDATA[
A commensally regulated immune rheostat fine-tunes skin barrier fitness
]]>
https://biorxiv.org/cgi/content/short/2026.01.07.698149v1?rss=1"
Gola, A.Srinivas, R.Rodig, E. G.Schernthanner, M.Abdusselamoglu, M. D.Tierney, M. T.Alexander, N. J.Gonzales, K. A. U.Sajjath, S. M.Soto-Ugaldi, L. F.Bonny, A. R.Fuchs, E.2026-01-08doi:10.64898/2026.01.07.698149Cold Spring Harbor Laboratory Press2026-01-08
<![CDATA[
Regulation of spikelet number during wheat spike development
]]>
https://biorxiv.org/cgi/content/short/2026.01.07.698073v1?rss=1"
Li, C.Li, K.Zhang, C.Dubcovsky, J.2026-01-08doi:10.64898/2026.01.07.698073Cold Spring Harbor Laboratory Press2026-01-08
<![CDATA[
Stepwise DNA unwinding gates TnpB genome-editing activity
]]>
https://biorxiv.org/cgi/content/short/2026.01.09.698545v1?rss=1"
Zhou, Z.Saffarian-Deemyad, I.Shi, H.Weiss, T.ur-Rehman, M. M.Vohra, K.Skopintsev, P.Yoon, P. H.Trinidad, M. I.Langeberg, C. J.Kamalu, M.Amerasekera, J.Doherty, E. E.Aris, K. D. P.Al-Sayyad, N.Thornton, B. W.Weissman, R. F.Wasko, K. M.Esain-Garcia, I.DeTurk, E. C.Savage, D. F.Jacobsen, S. E.Bryant, Z.Doudna, J. A.2026-01-09doi:10.64898/2026.01.09.698545Cold Spring Harbor Laboratory Press2026-01-09
<![CDATA[
Pannexin-1 channel activity regulates neurogenesis and cell survival in the developing cortex
]]>
https://biorxiv.org/cgi/content/short/2026.01.09.697058v1?rss=1"
Hylton, N. K.Kang, D. J.Decker, S. C.Exposito-Alonso, D.Cambridge, C. N.Golinski, S. R.Soriano, K. I.Neil, J. E.Talukdar, M.Andersen, R. E.Buckner, T. M.Qian, X.Doddi, A. D.Braddock, S. R.DeGennaro, E. M.Akula, S. K.Simo, S.Smith, R. S.Walsh, C. A.2026-01-09doi:10.64898/2026.01.09.697058Cold Spring Harbor Laboratory Press2026-01-09
<![CDATA[
Amplified genome editing by in vivo editor production
]]>
https://biorxiv.org/cgi/content/short/2026.01.13.699115v1?rss=1"
Ngo, W.Rosas-Rivera, D.Wasko, K. M.Qiu, L.Kang, M. H.Gogna, S.Zeng, J.Hooks, M. T.Wu, J. L. Y.Li, Z.Doudna, J. A.2026-01-13doi:10.64898/2026.01.13.699115Cold Spring Harbor Laboratory Press2026-01-13
<![CDATA[
Behavioral Signatures of Post-Decisional Attention in Preferential Choice
]]>
https://biorxiv.org/cgi/content/short/2026.01.10.698805v1?rss=1"
Zylberberg, A.Krajbich, I.Shadlen, M. N.2026-01-12doi:10.64898/2026.01.10.698805Cold Spring Harbor Laboratory Press2026-01-12
<![CDATA[
Peaceful Queen Succession in the Naked Mole Rat
]]>
https://biorxiv.org/cgi/content/short/2026.01.09.698689v1?rss=1"
Abeywardena, S. C.Schraibman, A. M.Delgado Cuevas, V.Ayres, J. S.2026-01-12doi:10.64898/2026.01.09.698689Cold Spring Harbor Laboratory Press2026-01-12
<![CDATA[
Modular gene tagging in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2026.01.15.699741v1?rss=1"
Hefel, A.Kruse, K.Wall, K.Jorgensen, S. B.Ng, K. H.Stolley, R.Rich, M. S.Jorgensen, E. M.2026-01-15doi:10.64898/2026.01.15.699741Cold Spring Harbor Laboratory Press2026-01-15
<![CDATA[
Dysregulated Microglial Synaptic Engulfment in Diffuse Midline Glioma
]]>
https://biorxiv.org/cgi/content/short/2025.12.22.696064v1?rss=1"
Mancusi, R.Tatlock, E.Shamardani, K.Acosta-Alvarez, L.Drexler, R.Trivedi, V.Gavish, A.Niizuma, K.Soni, N.Woo, P. J.Mulinyawe, S.Jahan, S.Logan, N.Malacon, K.Byun, Y. G.Geraghty, A. C.Barron, T.Taylor, K. R.Monje, M.2025-12-25doi:10.64898/2025.12.22.696064Cold Spring Harbor Laboratory Press2025-12-25
<![CDATA[
Rapid fluorescence lifetime sensor development of LifeCamp enables transient and baseline absolute calcium measurements
]]>
https://biorxiv.org/cgi/content/short/2025.12.23.696288v1?rss=1"
Lodder, B.Raghubardayal, M.Ganesh, S.Cai, X.Stern, J.Sherman, M.Rosen, P.Kamath, T.Hartman, I.Siegel, M.Timmins, J.Adan, R.Andermann, M. L.Sabatini, B. L.2025-12-25doi:10.64898/2025.12.23.696288Cold Spring Harbor Laboratory Press2025-12-25
<![CDATA[
Stomatal setpoints and environmental responsiveness are sculpted by developmental trajectories
]]>
https://biorxiv.org/cgi/content/short/2025.12.22.696041v1?rss=1"
Rath, M.Sharma, N.Mani, M.Bergmann, D.2025-12-25doi:10.64898/2025.12.22.696041Cold Spring Harbor Laboratory Press2025-12-25
<![CDATA[
Influence of phosphate activation chemistry on the selection of the primordial genetic alphabet
]]>
https://biorxiv.org/cgi/content/short/2025.12.23.696203v1?rss=1"
Boskovic, F.Zhang, J.Swatiputra, A. A.Szostak, J. W.2025-12-25doi:10.64898/2025.12.23.696203Cold Spring Harbor Laboratory Press2025-12-25
<![CDATA[
Vibrio cholerae serotype impacts pathogenicity
]]>
https://biorxiv.org/cgi/content/short/2025.12.23.696279v1?rss=1"
Zingl, F. G.Leitner, D. R.Fakoya, B.Morano, A. A.Waldor, M. K.2025-12-24doi:10.64898/2025.12.23.696279Cold Spring Harbor Laboratory Press2025-12-24
<![CDATA[
Cooperative Interaction Between IL-4 Signaling and FLT3 in Multipotent Progenitors Restore Lymphopoiesis in Inflammation and Aging
]]>
https://biorxiv.org/cgi/content/short/2025.12.19.695491v1?rss=1"
Yao, J.Wang, Y.Zhang, Y.2025-12-22doi:10.64898/2025.12.19.695491Cold Spring Harbor Laboratory Press2025-12-22
<![CDATA[
Comparing the evolvability of an ancestrally reconstructed and modern adenylate kinase
]]>
https://biorxiv.org/cgi/content/short/2025.12.12.693990v1?rss=1"
Patterson, M.Ludewig, H.Wilson, C.Woldring, D. R.Kim, C.Using, A.Irvin, J.Theobald, D. L.Kern, D.2025-12-14doi:10.64898/2025.12.12.693990Cold Spring Harbor Laboratory Press2025-12-14
<![CDATA[
Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals
]]>
https://biorxiv.org/cgi/content/short/2025.12.12.693809v1?rss=1"
Raman, P.Khan, H.Young, J. M.Tsukiyama, T.Malik, H. S.2025-12-13doi:10.64898/2025.12.12.693809Cold Spring Harbor Laboratory Press2025-12-13
<![CDATA[
Ultra-deep duplex sequencing reveals unique features of somatic evolution in the normal tissues of a family with Li-Fraumeni syndrome
]]>
https://biorxiv.org/cgi/content/short/2026.01.12.699071v1?rss=1"
Colegrove, H. L.Dubard-Gault, M. E.Marshall, H.Kohrn, B. F.Smith, T. H.Norgaard, Z. K.Lo, F. Y.Schmidt, E. K.Higgins, J. E.Valentine, C. C.Marshall, D. A.Clark, J. I.Konnick, E. Q.Salk, J. J.Horwitz, M. S.Rahbari, R.Feder, A. F.Risques, R. A.2026-01-13doi:10.64898/2026.01.12.699071Cold Spring Harbor Laboratory Press2026-01-13
<![CDATA[
Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding
]]>
https://biorxiv.org/cgi/content/short/2025.02.24.639402v1?rss=1"
5,000 proteins. We use these barcodes together with mass spectrometry to assay the solution behavior of libraries of de novo-designed monomeric scaffolds, oligomers, binding proteins and nanocages, rapidly identifying design failure modes and successes.
]]>Feldman, D.Sims, J. N.Li, X.Johnson, R.Gerben, S.Kim, D. E.Richardson, C.Koepnik, B.Eisenach, H.Hicks, D. R.Yang, E.Wicky, B. I. M.Milles, L. F.Bera, A.Brackenbrough, E.Joyce, E.Sankaran, B.Lubner, J. M.Goreshnik, I.Vafeados, D.Allen, A.Stewart, L.MacCoss, M. J.Baker, D.2025-02-28doi:10.1101/2025.02.24.639402Cold Spring Harbor Laboratory Press2025-02-28
<![CDATA[
Adaptive optical third-harmonic generation microscopy for in vivo imaging of tissues
]]>
https://biorxiv.org/cgi/content/short/2024.05.02.592275v1?rss=1"
Rodriguez, C.Pan, D.Natan, R. G.Mohr, M. A.Miao, M.Chen, X.Northen, T. R.Vogel, J. P.Ji, N.2024-05-05doi:10.1101/2024.05.02.592275Cold Spring Harbor Laboratory Press2024-05-05
<![CDATA[
Sibling chimerism among microglia in marmosets
]]>
https://biorxiv.org/cgi/content/short/2023.10.16.562516v1?rss=1"
del Rosario, R. C. H.Krienen, F. M.Zhang, Q.Goldman, M.Mello, C.Lutservitz, A.Ichihara, K.Wysoker, A.Nemesh, J.Feng, G.McCarroll, S. A.2023-10-17doi:10.1101/2023.10.16.562516Cold Spring Harbor Laboratory Press2023-10-17
<![CDATA[
Discovery of a Human Metabolite that Mimics the Bacterial Quorum-Sensing Autoinducer AI-2
]]>
https://biorxiv.org/cgi/content/short/2026.01.16.699917v1?rss=1"
Shine, E.Valastyan, J. S.Ying, V. Y.Huang, J. Z.Seyedsayamdost, M. R.Bassler, B. L.2026-01-17doi:10.64898/2026.01.16.699917Cold Spring Harbor Laboratory Press2026-01-17
<![CDATA[
A conserved C. elegans zinc finger-homeodomain protein, ZFH-2, continuously required for structural integrity and function of alimentary tract and gonad
]]>
https://biorxiv.org/cgi/content/short/2026.01.13.699069v1?rss=1"
Sussfeld, A.Vidal, B.Sural, S.Merritt, D. M.Aguilar, G. R.Ramadan, Y.Hobert, O.2026-01-14doi:10.64898/2026.01.13.699069Cold Spring Harbor Laboratory Press2026-01-14
<![CDATA[
Unifying phylogenetic traversal and deep learning to guide tree exploration
]]>
https://biorxiv.org/cgi/content/short/2026.01.14.699358v1?rss=1"
Collienne, L.Richman, H.Rich, D. H.Barker, M.Jennings-Shaffer, C.Matsen, F. A.2026-01-14doi:10.64898/2026.01.14.699358Cold Spring Harbor Laboratory Press2026-01-14
<![CDATA[
Modular mRNA LNP design integrates RNA, lipid, and antigen engineering for protective vaccination
]]>
https://biorxiv.org/cgi/content/short/2026.01.17.699915v1?rss=1"
Farzani, T.Espinoza, N.M. Manafi, M.R. Welch, S.D. Coleman-McCray, J.Aida-Ficken, V.R. Spengler, J.Bergeron, E.F. Spiropoulou, C.Borges, C.Bielecki, K.Li, L.Shah, D.Paye, M.Rojas, E.N. Spector, S.Samani, P.E. Hensley, L.Ozonoff, A.Sabeti, P.2026-01-18doi:10.64898/2026.01.17.699915Cold Spring Harbor Laboratory Press2026-01-18
<![CDATA[
A Preoptic Neurocircuit That Modulates Metabolic Flexibility
]]>
https://biorxiv.org/cgi/content/short/2026.01.15.699760v1?rss=1"
Roessler, J. M.Alkire, M.Nigrin, N.Wang, H.Reid, C. M.Cortopassi, M. D.Waite, M.Linnehan, B.Griffith, E. C.Madigan, M.Kunchok, T.Banks, A. S.Schulte, F.Kim, B.Kim, B.-Y.Kim, J. K.Hrvatin, S.2026-01-16doi:10.64898/2026.01.15.699760Cold Spring Harbor Laboratory Press2026-01-16
<![CDATA[
NPEPPS segmental duplication drives position effect expression of TBC1D3 in the human brain
]]>
https://biorxiv.org/cgi/content/short/2026.01.14.699559v1?rss=1"
3-fold higher expression relative to other copies is driven by a 110 kbp segmental duplication that occurred [~]8.9 million years ago, relocating a partial duplication of the puromycin-sensitive aminopeptidase gene (NPEPPS), including its promoter, adjacent to this TBC1D3 locus. Using neurospheres and comparative transcriptomics of iPSC-derived cultures, we show that expression of NPEPPSP1-TBC1D3 increases as neurons differentiate as a result of alternative splicing and differential polyadenylation usage. While the fusion exists in other ape lineages, we show subsequent deletion of the NPEPPSP1 promoter in Gorilla and a separate, lineage-specific duplication in the Pan lineage ablated the production of this fusion product, rendering this position effect of TBC1D3 specific to humans.
]]>Guitart, X.Brunner, J. W.Ren, L.Jeong, H.Yoo, D.Porubsky, D.Vollger, M. R.Hoekzema, K.Munson, K. M.Sun, K.Ayllon, M.Hoglin, K.McMullen, R.Pavlovic, B.Pollen, A. A.Eichler, E. E.2026-01-15doi:10.64898/2026.01.14.699559Cold Spring Harbor Laboratory Press2026-01-15
<![CDATA[
Diverse infection models demonstrate robust resistance of Mycobacterium tuberculosis to innate immunity
]]>
https://biorxiv.org/cgi/content/short/2025.11.20.687493v1?rss=1"
100,000 CFU) of Lp from the lung within a few days. However, pre-infection with Lp only modestly reduced Mtb CFU compared to mice infected with only Mtb, indicating that Mtb can robustly replicate even in the presence of a strong innate inflammatory response. We performed single-cell RNA-sequencing on myeloid cells from mice either infected with Mtb alone or mice primed with Lp. We found that Lp priming before Mtb infection induced measurable changes in myeloid cells responding to Mtb, but these changes had little effect on innate control of Mtb. Together, these data demonstrate the robust resistance of Mtb to innate immune clearance under diverse experimental conditions.
]]>Fairgrieve, M. R.Brydon, E. C.Chavez, R. A.Kotov, D. I.Vance, R.2025-11-20doi:10.1101/2025.11.20.687493Cold Spring Harbor Laboratory Press2025-11-20
<![CDATA[
Human-chimpanzee tetraploid system defines mechanisms of species-specific neural gene regulation
]]>
https://biorxiv.org/cgi/content/short/2025.03.31.646367v1?rss=1"
Song, J. H.Carter, A. C.Bushinsky, E. M.Beck, S. G.Petrocelli, J. E.Koreman, G. T.Babu, J.Kingsley, D. M.Greenberg, M. E.Walsh, C. A.2025-03-31doi:10.1101/2025.03.31.646367Cold Spring Harbor Laboratory Press2025-03-31
<![CDATA[
Discovery of widespread activating mutations in a compact RNA-guided endonuclease
]]>
https://biorxiv.org/cgi/content/short/2025.02.11.637750v1?rss=1"
Thornton, B. W.-L.Weissman, R. F.Tran, R. V.Duong, B. T.Rodriguez, J. E.Terrace, C. I.Groover, E. D.Park, J.-U.Tartaglia, J.Doudna, J. A.Savage, D.2025-02-12doi:10.1101/2025.02.11.637750Cold Spring Harbor Laboratory Press2025-02-12
<![CDATA[
Deep Neural Networks to Register and Annotate the Cells of the C. elegans Nervous System
]]>
https://biorxiv.org/cgi/content/short/2024.07.18.601886v1?rss=1"
100 neuronal cell types in the C. elegans head based on multi-spectral fluorescence of genetic markers. This network labels >100 different cell types per animal with 98% accuracy, exceeding individual human labeler performance by aggregating knowledge across manually labeled datasets. Finally, we trained a third network (CellDiscoveryNet) to perform unsupervised discovery of >100 cell types in the C. elegans nervous system: by comparing multi-spectral imaging data from many animals, it can automatically identify and annotate cell types without using any human labels. The performance of CellDiscoveryNet matched that of trained human labelers. These tools should be immediately useful for a wide range of biological applications and should be straightforward to generalize to many other contexts requiring alignment and annotation of dense heterogeneous cell types in complex tissues.
]]>Atanas, A. A.Lu, A. K.-Y.Kim, J.Baskoylu, S.Kang, D.Kramer, T. S.Bueno, E.Wan, F. K.Flavell, S. W.2024-07-22doi:10.1101/2024.07.18.601886Cold Spring Harbor Laboratory Press2024-07-22
<![CDATA[
Establishing the molecular basis for MDA5 mutation-linked autoimmunity
]]>
https://biorxiv.org/cgi/content/short/2026.01.20.700587v1?rss=1"
Xu, L.Chung, K.Guo, R.Pan, A.Pyle, A.2026-01-20doi:10.64898/2026.01.20.700587Cold Spring Harbor Laboratory Press2026-01-20
<![CDATA[
Structural and Spectroscopic Basis for Catalysis by a Class C Radical S-adenosylmethionine Methylase Involved in Nosiheptide/Nocathiacin Biosynthesis
]]>
https://biorxiv.org/cgi/content/short/2026.01.19.700444v1?rss=1"
Wang, B.Knox, H. L.York, N. J.Radle, M. I.Silakov, A.Booker, S. J.2026-01-20doi:10.64898/2026.01.19.700444Cold Spring Harbor Laboratory Press2026-01-20
<![CDATA[
Inefficient autophagosome formation limits the temporal dynamics of OPTN-mediated mitophagy in neurons
]]>
https://biorxiv.org/cgi/content/short/2026.01.16.700014v1?rss=1"
Green, J. R.Gooden, M. K.Ojo, A. E.Kalejaiye, T. D.Evans, C. S.2026-01-20doi:10.64898/2026.01.16.700014Cold Spring Harbor Laboratory Press2026-01-20
<![CDATA[
Discovery of the Phosphonate Flavophos Produced by Burkholderia
]]>
https://biorxiv.org/cgi/content/short/2026.01.15.699783v1?rss=1"
Simon, M. A.Ramos-Figueroa, J. S.Reyes Lopez, V.Ongpipattanakul, C.Zhu, L.Giurgiu, C.Hoffpauir, Z. A.Lamb, A. L.Nair, S. K.van der Donk, W. A.2026-01-16doi:10.64898/2026.01.15.699783Cold Spring Harbor Laboratory Press2026-01-16
<![CDATA[
B Lymphocyte Protein Factories produced by Hematopoietic Stem Cell Gene Editing
]]>
https://biorxiv.org/cgi/content/short/2026.01.16.699998v1?rss=1"
Hartweger, H.Ruprecht, C.Yao, K.-H.Laffont, P.Lima dos Reis, G.Zhou, P.Hägglöf, T.Binet, L.Loewe, M.Hong, J. P.Xiao, T.Sefik, E.Hernandez, B.Gazumyan, A.Jankovic, M.Seaman, M. S.Costa, G.Nelson, S. A.Clark, J.Kanatani, S.Wilson, P. C.Krammer, F.Levashina, E. A.Julien, J.-P.Wardemann, H.Sinnis, P.Stamatatos, L.Flavell, R. A.Nussenzweig, M. C.2026-01-18doi:10.64898/2026.01.16.699998Cold Spring Harbor Laboratory Press2026-01-18
<![CDATA[
PfApiAT2 is a proline transporter essential for the transmission of Plasmodium falciparum by the mosquito vector.
]]>
https://biorxiv.org/cgi/content/short/2026.01.20.700404v1?rss=1"
Khushu, M.Kissel, R. C.Kauffman, J.Taccheri, C.Singh, N.Summers, R. L.Plant, L. D.Wirth, D.Catteruccia, F.Bopp, S.2026-01-20doi:10.64898/2026.01.20.700404Cold Spring Harbor Laboratory Press2026-01-20
<![CDATA[
Selective Immune Silencing by Targeted TGF-β Agonists
]]>
https://biorxiv.org/cgi/content/short/2026.01.19.700410v1?rss=1"
Sun, Q.Ogishi, M.Jiang, H.Barrett, A. K.Yan, H.Sola, E.Zhang, J.Xiao, P.Lyu, H.Salehi, A.Tang, Q.Lanz, T. V.Davis, M. M.Negrin, R. S.Garcia, K. C.2026-01-20doi:10.64898/2026.01.19.700410Cold Spring Harbor Laboratory Press2026-01-20
<![CDATA[
UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity
]]>
https://biorxiv.org/cgi/content/short/2026.01.19.700311v1?rss=1"
Liu, J.Gibcus, J. H.Dekker, J.2026-01-20doi:10.64898/2026.01.19.700311Cold Spring Harbor Laboratory Press2026-01-20
<![CDATA[
Decoding the cell intrinsic and extrinsic roles of PRC2 in early embryogenesis
]]>
https://biorxiv.org/cgi/content/short/2026.01.20.700679v1?rss=1"
Zhou, C.Wang, M.Chen, Z.Zhang, Y.2026-01-20doi:10.64898/2026.01.20.700679Cold Spring Harbor Laboratory Press2026-01-20
<![CDATA[
Efficient transgene-free multiplexed genome editing via viral delivery of an engineered TnpB.
]]>
https://biorxiv.org/cgi/content/short/2026.01.23.700382v1?rss=1"
Weiss, T.Kamalu, M.Shi, H.Wirnowski, G.Ingelsson, A.Amerasekera, J.Vohra, K.Trinidad, M. I.Li, Z.Freitas, E.Steinmetz, N.Ambrose, C.Chen, K.Doudna, J. A.Jacobsen, S. E.2026-01-23doi:10.64898/2026.01.23.700382Cold Spring Harbor Laboratory Press2026-01-23
<![CDATA[
New methods for epigenetic characterization and manipulation of rare fly brain neurons
]]>
https://biorxiv.org/cgi/content/short/2026.01.21.700891v1?rss=1"
Ojha, P.Berglund, G.Yu, A. D.Rosbash, M.2026-01-23doi:10.64898/2026.01.21.700891Cold Spring Harbor Laboratory Press2026-01-23
<![CDATA[
Mechanism of membrane perforation in rotavirus cell entry
]]>
https://biorxiv.org/cgi/content/short/2026.01.21.700916v1?rss=1"
de Sautu, M.Leistner, C.Kirchhausen, T.Jenni, S.Harrison, S. C.2026-01-23doi:10.64898/2026.01.21.700916Cold Spring Harbor Laboratory Press2026-01-23
<![CDATA[
Strong sustained type I IFN signaling acts cell intrinsically to impair IFNγ responses and cause tuberculosis susceptibility
]]>
https://biorxiv.org/cgi/content/short/2026.01.19.700487v1?rss=1"
Fattinger, S. A.Chavez, R. A.Witt, K. C.Parisi, B.Rodriguez, J. J.Turcotte, E. A.Brydon, E. C.Fairgrieve, M. R.Dhaliwal, H.Lee, A. Y.Kotov, D. I.Vance, R. E.2026-01-22doi:10.64898/2026.01.19.700487Cold Spring Harbor Laboratory Press2026-01-22
<![CDATA[
The spliceosome assembles on excised linear introns to protect them from degradation
]]>
https://biorxiv.org/cgi/content/short/2026.01.21.700889v1?rss=1"
Li, G. W.Wilkinson, M. E.Bartel, D. P.2026-01-22doi:10.64898/2026.01.21.700889Cold Spring Harbor Laboratory Press2026-01-22
<![CDATA[
Live dynamics of induced cell-cell fusion between mitotic and interphasic cells
]]>
https://biorxiv.org/cgi/content/short/2026.01.27.700572v1?rss=1"
Afonso, O.Feliciano, D.Lippincott-Schwartz, J.2026-01-27doi:10.64898/2026.01.27.700572Cold Spring Harbor Laboratory Press2026-01-27
<![CDATA[
Engaging Unstabilized Alkyl Radicals with Pyridoxal Radical Biocatalysis: Enantiodivergent Synthesis of Aliphatic Non-Canonical Amino Acids
]]>
https://biorxiv.org/cgi/content/short/2026.01.21.700944v1?rss=1"
Cheng, L.Chen, J.Bo, Z.Zhang, X.Liu, P.Yang, Y.2026-01-23doi:10.64898/2026.01.21.700944Cold Spring Harbor Laboratory Press2026-01-23
<![CDATA[
Leptin Receptor+ cells create a perisinusoidal niche for thrombopoiesis in the bone marrow by synthesizing CXCL14
]]>
https://biorxiv.org/cgi/content/short/2026.01.27.702029v1?rss=1"
Xue, y.Merchant, S.Reyes, A.Luo, M.Zhang, R.Tippetts, T.Grabowski, G.Ngo, T.Zhang, Y.Shang, Z.Jiang, N.Jeffery, E.Li, Y.Wei, T.Gu, W.Du, L.DeBerardinis, R. J.Dean, K. M.Mathews, T. P.Lucas, D. P.Zhao, Z.Morrison, S. J.2026-01-28doi:10.64898/2026.01.27.702029Cold Spring Harbor Laboratory Press2026-01-28
<![CDATA[
TAK1 integrates the NLRP1 inflammasome into the innate immune response to double-stranded RNA
]]>
https://biorxiv.org/cgi/content/short/2026.01.23.701331v1?rss=1"
Corley, M. R.Hyodo, A.Toyoda, H. C.Yonemitsu, M. A.Chantharath, A.Hyde, J. L.Mitchell, P. S.2026-01-25doi:10.64898/2026.01.23.701331Cold Spring Harbor Laboratory Press2026-01-25
<![CDATA[
Kinetochore clustering is mediated by Mps1 phosphorylation of conserved MELT motifs in Stu1
]]>
https://biorxiv.org/cgi/content/short/2026.01.23.701336v1?rss=1"
Mallet, D. R.Jiang, M.Minnuto, G. M.Biggins, S.2026-01-25doi:10.64898/2026.01.23.701336Cold Spring Harbor Laboratory Press2026-01-25
<![CDATA[
A single-cell atlas of intestinal immune cells across the day-night cycle reveals dynamic populations
]]>
https://biorxiv.org/cgi/content/short/2026.01.24.701519v1?rss=1"
View larger version (34K):
org.highwire.dtl.DTLVardef@162f451org.highwire.dtl.DTLVardef@1960711org.highwire.dtl.DTLVardef@a9fd4aorg.highwire.dtl.DTLVardef@341f42_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Maples, R. W.Quinn, G.Srinivasan, T.Dende, C.Hooper, L. V.Pfeiffer, J. K.2026-01-26doi:10.64898/2026.01.24.701519Cold Spring Harbor Laboratory Press2026-01-26
<![CDATA[
Library transgenesis in zebrafish through delayed site-specific mosaic integration for in vivo pooled screening of transgenes
]]>
https://biorxiv.org/cgi/content/short/2026.01.30.702415v1?rss=1"
Bracha, S.Amsterdam, A.Xu, Y.Chitayat, L.Sinha, A.Boyden, E.2026-01-31doi:10.64898/2026.01.30.702415Cold Spring Harbor Laboratory Press2026-01-31
<![CDATA[
Principles of in situ protein sequencing: expansion microscopy-adapted Edman degradation and amino acid recognition
]]>
https://biorxiv.org/cgi/content/short/2026.01.29.702630v1?rss=1"
Mitchell, C. M.Tavana, S. Z.Peng, J.Wang, H.Shi, J.Zhang, C.Evgeniou, L.Domecillo, M.Wang, S.Estandian, D. M.Choueiri, A. G.Wong, E.Dohadwala, S.Polizzi, N.Kiessling, L. L.Boyden, E. S.2026-01-30doi:10.64898/2026.01.29.702630Cold Spring Harbor Laboratory Press2026-01-30
<![CDATA[
Unconstrained Plasticity Disrupts Memory Consolidation in a Mouse Model of Rett Syndrome
]]>
https://biorxiv.org/cgi/content/short/2026.01.29.702595v1?rss=1"
Zhang, T. R.Li, G.Magee, J. C.Zoghbi, H. Y.Vaidya, S. P.2026-01-30doi:10.64898/2026.01.29.702595Cold Spring Harbor Laboratory Press2026-01-30
<![CDATA[
Structural mechanism of Necrocide 1 activation of human TRPM4 that triggers necrosis by sodium overload
]]>
https://biorxiv.org/cgi/content/short/2026.01.28.702369v1?rss=1"
Teixeira-Duarte, C. M.Fu, W.Zeng, W. M.Wang, J.Jiang, X.Zhao, Z.Zhong, Q.Jiang, Y.2026-01-30doi:10.64898/2026.01.28.702369Cold Spring Harbor Laboratory Press2026-01-30
<![CDATA[
Social sensing of infection reprograms peripheral immunity in healthy mice
]]>
https://biorxiv.org/cgi/content/short/2026.01.28.702380v1?rss=1"
Ademolue, T. W.Pernas, L. F.2026-01-29doi:10.64898/2026.01.28.702380Cold Spring Harbor Laboratory Press2026-01-29
<![CDATA[
MDA5 multimerization on LINE RNA drives pathogenic extracellular immune complexes in autoimmunity
]]>
https://biorxiv.org/cgi/content/short/2026.01.27.702129v1?rss=1"
Hsu, T. Y.-T.Wang, X.Isayama, Y.Jung, V.Zhang, J.van Gompel, E.Maadadi, H.Torres, C.Shimazaki-Takahashi, A.Kurihara, N.Kondo, M.Galesic, M.Notarnicola, A.Sultana, S.Maeda, A.Vleugels, R. A.Dellaripa, P. F.Yamashita, T.Ito, Y.Awaji, K.Kotani, H.Matsuda, K. M.Horuluogu, B.Grönwall, C.Joshua, V.Ukai, Y.Hosomi, N.Wagner, D. D.Lundberg, I. E.Kato, K.Hur, S.2026-01-28doi:10.64898/2026.01.27.702129Cold Spring Harbor Laboratory Press2026-01-28
<![CDATA[
Activating Ras-MAPK pathway variants drive hippocampal clonal competition in human epilepsy
]]>
https://biorxiv.org/cgi/content/short/2026.01.26.701822v1?rss=1"
40% of MTLE specimens harboring activating Ras-MAPK variants in PTPN11, NF1, BRAF, KRAS, and twelve genes not previously associated with focal epilepsy. Eight Ras-MAPK genes showed positive clonal selection in MTLE. Increased somatic variant burden predicted worse surgical outcome. Somatic Ras-MAPK variants at ultra-low (<0.5%) variant allele fractions were associated with older seizure onset and HS pathology, supporting a late prenatal or postnatal origin. Ras-MAPK variants in MTLE were enriched in cells derived from hippocampal progenitors--neurons, astrocytes, oligodendrocytes--in line with the known neuronal hyperexcitability and seizures induced by Ras-MAPK overactivation9,10; in contrast, Alzheimer disease hippocampi exhibited microglial enrichment of Ras-MAPK variants, consistent with prior reports11. Single-nucleus RNA sequencing showed increased expression of Ras-MAPK genes in neurons and upregulation of pathways mediating neurogenesis and neural development in MTLE. Functional validation of novel, recurrent PTPN11 variants confirmed gain-of-function, while cellular modeling in induced pluripotent stem cells demonstrated proliferative/survival advantages for mutant cells in mosaic culture. Overall, our data suggest that somatic Ras-MAPK variants and acquired risk factors may converge on clonal competition in the hippocampus to modulate epilepsy risk.
]]>Khoshkhoo, S.Bae, M.Wang, Y.Tillett, A.Ramirez, R. B.Finander, B.Egan, E. D.Marx, L.Patel, D.Zhou, Z.Chahine, Y.Chhouk, B.Zoullas, S. M.Lai, A.Coras, R.Bielle, F.Navarro, V.Mathon, B.Valiante, T. A.Chameh, H. M.Gao, A.Krings, T.Gooley, S.Hildebrand, M. S.Bulluss, K.Clark, J.Morokoff, A. P.King, J. A.Todaro, M.Kwan, P.O'Brien, T. J.Berkovic, S. F.Scheffer, I. E.Perucca, P.Lapinskas, E.Rolston, J. D.Cosgrove, G. R.Sarkis, R. A.D'Gama, A. M.Alexadrescu, S.Yang, E.Poduri, A.Richardson, R. M.Erson-Omay, E. Z.DeL2026-01-27doi:10.64898/2026.01.26.701822Cold Spring Harbor Laboratory Press2026-01-27
<![CDATA[
Molecular mechanisms of mitochondrial Ca2+ exchanger NCLX
]]>
https://biorxiv.org/cgi/content/short/2026.01.28.702368v1?rss=1"
Zhang, L.Han, Y.Zeng, W.Xue, J.Wang, Y.Jiang, Y.2026-02-01doi:10.64898/2026.01.28.702368Cold Spring Harbor Laboratory Press2026-02-01
<![CDATA[
Ancient genomes from Ladakh reveal 2800-year-old mixture between Tibetans and South Asians
]]>
https://biorxiv.org/cgi/content/short/2026.01.30.702804v1?rss=1"
Patterson, N. J.Mushrif-Tripathy, V.Devers, Q.Qiu, L.Dolma, S.Soos, G.Mallick, S.Rohland, N.Reich, D. E.2026-01-30doi:10.64898/2026.01.30.702804Cold Spring Harbor Laboratory Press2026-01-30
<![CDATA[
Molecular determinants of antibody-mediated priming to enhance detection of ctDNA
]]>
https://biorxiv.org/cgi/content/short/2026.01.27.701975v1?rss=1"
Tabrizi, S.Sullivan, C.Chakraborty, K.Martin-Alonso, C.An, Z.Gao, L.Kim, D. M.Patel, S. K.Blewett, T.Rhoades, J.Liu, R.Patel, S.Xiong, K.Crnjac, A.Bhatia, S. N.Adalsteinsson, V. A.Love, J. C.2026-01-29doi:10.64898/2026.01.27.701975Cold Spring Harbor Laboratory Press2026-01-29
<![CDATA[
SAGA1 and SAGA2 localize the starch sheath to the pyrenoid in Chlamydomonas reinhardtii
]]>
https://biorxiv.org/cgi/content/short/2026.01.27.702031v1?rss=1"
Crans, V. L.Burton, M. I.Garde, A.Wang, L.Jonikas, M. C.2026-01-29doi:10.64898/2026.01.27.702031Cold Spring Harbor Laboratory Press2026-01-29
<![CDATA[
Maternal-fetal immune conflict contributes to male-specific impairments in a mouse model of neurodevelopmental disorders
]]>
https://biorxiv.org/cgi/content/short/2026.02.02.703351v1?rss=1"
Sanchez-Martin, I.Kukreja, B.Henderson, P.Lin, Q.DiMartino, D.Bagan, V.Park, J.Kalish, B. T.Cheadle, L.2026-02-03doi:10.64898/2026.02.02.703351Cold Spring Harbor Laboratory Press2026-02-03
<![CDATA[
Structure, biosynthesis, and bioactivity of nostolysamides
]]>
https://biorxiv.org/cgi/content/short/2026.01.31.703028v1?rss=1"
Weir, E.Anterola, I.van der Donk, W. A.2026-01-31doi:10.64898/2026.01.31.703028Cold Spring Harbor Laboratory Press2026-01-31
<![CDATA[
Native yeast kinetochore structures identify an essential inner kinetochore interaction
]]>
https://biorxiv.org/cgi/content/short/2026.01.30.702844v1?rss=1"
Jiang, M.Hu, C.Hedouin, S.Andrade Latino, A.Arimura, Y.Stergachis, A.Biggins, S.2026-01-31doi:10.64898/2026.01.30.702844Cold Spring Harbor Laboratory Press2026-01-31
<![CDATA[
Immune cells adapt to distinct stem cell niches to govern tissue homeostasis
]]>
https://biorxiv.org/cgi/content/short/2026.01.28.701831v1?rss=1"
Parigi, S. M.Sajjath, S. M.Bell, C. J.Yuan, S.Olyntho, V. M.Bonny, A. R.Nakandakari-Higa, S.Lira, S.Mucida, D.Victora, G. D.Fuchs, E.2026-01-31doi:10.64898/2026.01.28.701831Cold Spring Harbor Laboratory Press2026-01-31
<![CDATA[
PLCβs are recruited to the plasma membrane in macrophages by both Gβγ and Gαq
]]>
https://biorxiv.org/cgi/content/short/2026.01.28.702352v1?rss=1"
Falzone, M.Banerjee, P.MacKinnon, R.2026-01-31doi:10.64898/2026.01.28.702352Cold Spring Harbor Laboratory Press2026-01-31
<![CDATA[
Stem cell control and cancer initiation by an autocrine, injury-activated Igf complex
]]>
https://biorxiv.org/cgi/content/short/2026.02.02.703150v1?rss=1"
Zhang, Y.Ouadah, Y.Liu, Y.Kumar, M.Morck, M.Krasnow, M. A.2026-02-04doi:10.64898/2026.02.02.703150Cold Spring Harbor Laboratory Press2026-02-04
<![CDATA[
Orofacial behaviors, not eye movements, govern neural activity in mouse visual cortex
]]>
https://biorxiv.org/cgi/content/short/2026.02.04.703800v1?rss=1"
Syeda, A.Nunez-Ochoa, M. A.Zhong, L.Pachitariu, M.Stringer, C.2026-02-05doi:10.64898/2026.02.04.703800Cold Spring Harbor Laboratory Press2026-02-05
<![CDATA[
Components of an ESCRT-independent nuclear envelope assembly pathway
]]>
https://biorxiv.org/cgi/content/short/2026.02.01.703137v1?rss=1"
Sydir, E. M.Farra, M. H.Whitford, A. L.Hinojosa, S.Kao, P.-Y.Paulo, J. A.Swarup, S.Lusk, C. P.Harper, J. W.Lee, I.-J.Pellman, D.2026-02-03doi:10.64898/2026.02.01.703137Cold Spring Harbor Laboratory Press2026-02-03
<![CDATA[
Duration of Initial Viremia Modulates Functional Properties of HIV-specific T Cell Receptors
]]>
https://biorxiv.org/cgi/content/short/2026.01.29.702605v1?rss=1"
View larger version (17K):
org.highwire.dtl.DTLVardef@9a5a6dorg.highwire.dtl.DTLVardef@1a6bbdaorg.highwire.dtl.DTLVardef@17707e8org.highwire.dtl.DTLVardef@1a84d9e_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Ogunshola, F. J.Singh, N. K.Butty, V.Mishra, A. R.Habte, Z.Vecchiarello, L.Fahad, A.Juergens, K. B.Cheever, S.Allombert, M.Webber, A.Piechocka-Trocha, A.Ismail, N.Nathan, A.Li, X.Reddy, K.Gounder, K.Baiyegunhi, O. O.Collins, D. R.Ghebremichael, M.Gaiha, G.Dong, K. L.Dekosky, B. J.Ndung'u, T.Birnbaum, M. E.Walker, B. D.2026-02-02doi:10.64898/2026.01.29.702605Cold Spring Harbor Laboratory Press2026-02-02
<![CDATA[
Astrocyte-induced internal state transitions reshape brainwide sensory, integrative, and motor computations
]]>
https://biorxiv.org/cgi/content/short/2026.02.05.704034v1?rss=1"
Lim, J.-X.Wei, Z.Narayan, S.Zhang, Y.Hasseman, J. P.Kolb, I.Zheng, J.Sheikhattar, A.Mi, X.Zheng, W.Yang, X.Beriashvili, M.Fleishman, G.Wee, C.de Zeeuw, C.Yu, G.Babadi, B.Rubinov, M.Looger, L. L.Bergles, D. E.Fitzgerald, J. E.Ahrens, M. B.2026-02-05doi:10.64898/2026.02.05.704034Cold Spring Harbor Laboratory Press2026-02-05
<![CDATA[
m6A-dependent microRNA binding to chromatin-associated RNA for transcriptional activation
]]>
https://biorxiv.org/cgi/content/short/2026.02.02.703428v1?rss=1"
Zhong, Y.Zheng, L.Li, J.Liu, C.Wei, J.Ye, C.Dou, X.Liu, B.Barbosa, E.Yang, F.Pitroda, S.Chen, M.Weichselbaum, R.He, C.2026-02-03doi:10.64898/2026.02.02.703428Cold Spring Harbor Laboratory Press2026-02-03
<![CDATA[
Extracting large-scale neural activity with Suite2p
]]>
https://biorxiv.org/cgi/content/short/2026.02.04.703741v1?rss=1"
Stringer, C.Ki, C.Del Grosso, N.LaFosse, P.Zhang, Q.Pachitariu, M.2026-02-06doi:10.64898/2026.02.04.703741Cold Spring Harbor Laboratory Press2026-02-06
<![CDATA[
Regenerative base editing enables deep lineage recording
]]>
https://biorxiv.org/cgi/content/short/2026.02.06.703857v1?rss=1"
Chadly, D. M.Hadas, R.Klock, L.Yue, J.Horns, F.Askary, A.Granados, A. A.Bouckaert, R.Lois, C.Cai, L.Elowitz, M. B.2026-02-07doi:10.64898/2026.02.06.703857Cold Spring Harbor Laboratory Press2026-02-07
<![CDATA[
The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts
]]>
https://biorxiv.org/cgi/content/short/2026.02.04.703838v1?rss=1"
Garber, A.Nwachukwu, J.Stikeleather, R.York, C.McCutcheon, J.2026-02-06doi:10.64898/2026.02.04.703838Cold Spring Harbor Laboratory Press2026-02-06
<![CDATA[
Gaussian Process Inference Reveals Non-separability of Positionand Velocity Tuning in Grid Cells
]]>
https://biorxiv.org/cgi/content/short/2026.02.02.703269v1?rss=1"
Warton, L.Ganguli, S.Giocomo, L.2026-02-04doi:10.64898/2026.02.02.703269Cold Spring Harbor Laboratory Press2026-02-04
<![CDATA[
Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration
]]>
https://biorxiv.org/cgi/content/short/2026.02.03.703562v1?rss=1"
Atabay, K. D.Aoude, P.Park, C.Kadobianskyi, M.Paugois, O. H.Judkewitz, B.Reddien, P.2026-02-05doi:10.64898/2026.02.03.703562Cold Spring Harbor Laboratory Press2026-02-05
<![CDATA[
Whole-Brain Co-Mapping of Gene Expression and NeuronalActivity at Cellular Resolution in Behaving Zebrafish
]]>
https://biorxiv.org/cgi/content/short/2026.02.07.704095v1?rss=1"
Marquez Legorreta, E.Fleishman, G. M.Hesselink, L. W.Eddison, M.Smeets, K.Stringer, C.Keller, P. J.Narayan, S.Chen, A. B.Mensh, B. D.Sternson, S. M.Englitz, B.Tillberg, P. W.Ahrens, M. B.2026-02-10doi:10.64898/2026.02.07.704095Cold Spring Harbor Laboratory Press2026-02-10
<![CDATA[
A pilot study for whole proteome tagging in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2026.02.09.704846v1?rss=1"
Eroglu, M.Hobert, O.2026-02-10doi:10.64898/2026.02.09.704846Cold Spring Harbor Laboratory Press2026-02-10
<![CDATA[
Multiple redundant mechanisms account for the majority of gene silencing downstream of DNA methylation
]]>
https://biorxiv.org/cgi/content/short/2026.02.08.704674v1?rss=1"
Wang, S.Wu, Z.Li, Z.Movilli, A.He, L.Zhou, Y.Lin, E. K.Chuang, R.Thiri, W. W.Convery, S.Feng, S.Weigel, D.Jacobsen, S. E.2026-02-10doi:10.64898/2026.02.08.704674Cold Spring Harbor Laboratory Press2026-02-10
<![CDATA[
Structural basis for CTCF-mediated chromatin organization
]]>
https://biorxiv.org/cgi/content/short/2026.02.06.704447v1?rss=1"
Osorio Valeriano, M.Stone, A. C.Nagano, M.Su, B.Caccianini, L.Hansen, A. S.Farnung, L.Vos, S. M.2026-02-08doi:10.64898/2026.02.06.704447Cold Spring Harbor Laboratory Press2026-02-08
<![CDATA[
Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures
]]>
https://biorxiv.org/cgi/content/short/2026.02.12.705598v1?rss=1"
Lian, Y.Adjavon, D.Kawase, T.Kim, J.Fleishman, G.Preibisch, S.Funke, J.Liu, Z. J.2026-02-13doi:10.64898/2026.02.12.705598Cold Spring Harbor Laboratory Press2026-02-13
<![CDATA[
4,5-dihydroxyhexanoic acid is a robust circulating and urine marker of mitochondrial disease and its severity
]]>
https://biorxiv.org/cgi/content/short/2026.02.10.705117v1?rss=1"
90% of detected features in modern metabolomics experiments and hold immense untapped promise for new basic and biomedical research. We recently used mass spectrometry-based metabolomics to identify and validate 19 circulating blood-based biomarkers for patients with the mitochondrial DNA (mtDNA) m.3243A>G pathogenic variant, which is the most frequent cause of the mitochondrial disorder MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). However, the most significantly changing biomarker corresponded to an "unknown" metabolite. Here, we combine cheminformatics with analytical chemistry and identify that feature as 4,5-dihydroxyhexanoic acid (4,5-DHHA), a metabolite previously associated with inherited defects of gamma-aminobutyric acid (GABA) catabolism, but with no prior links to mitochondrial respiratory chain disorders. We validate this finding in an independent MELAS cohort and further show that 4,5-DHHA levels correlate with disease severity and are elevated in patients with other forms of mitochondrial disease and sepsis. Furthermore, brain 4,5-DHHA levels were elevated in two genetic mouse models of mitochondrial disease. In vitro and tissue culture experiments indicate that 4,5-DHHA is generated when the GABA catabolite succinic semialdehyde reacts with an intermediate of the pyruvate dehydrogenase reaction and is sensitive to mitochondrial complex I function. Our work identifies 4,5-DHHA as a robust plasma and urine marker of mitochondrial dysfunction in humans and reveals new connections between the respiratory chain and GABA metabolism.
Significance StatementInborn errors of the mitochondrial respiratory chain cause severe, progressive diseases, yet effective treatments and biomarkers remain limited. Modern metabolomics detects thousands of molecules in biofluids, but the vast majority are unidentified. In this study, we investigate the most significantly altered blood metabolite in patients with the most common mitochondrial disease - MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) - and identify it as an 4,5-dihydroxyhexanoic acid (4,5-DHHA). We show that 4,5-DHHA is reproducibly elevated and correlates with severity. Levels are increased across multiple mitochondrial disorders as well as in sepsis and rise when respiratory chain function is impaired. These findings establish 4,5-DHHA as a promising biomarker of mitochondrial dysfunction and reveal a link to dysregulated GABA metabolism.
]]>Skinner, O. S.Miranda, M.Dong, F.Struhl, T.Walker, M. A.Schleifer, G.Henke, M. T.Clardy, J.Hirano, M.De Vivo, D. C.Schon, E. A.Engelstad, K.Siegmund, S. E.Laprise, C.Des Rosiers, C.Sharma, R.Mootha, V. K.2026-02-12doi:10.64898/2026.02.10.705117Cold Spring Harbor Laboratory Press2026-02-12
<![CDATA[
A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia
]]>
https://biorxiv.org/cgi/content/short/2026.02.12.705594v1?rss=1"
Ding, W.Klein, A.Baez-Becerra, C. T.Rink, J. A.Bartlett, A.Zeng, Q.Wang, R.Castanon, R. G.Nery, J. R.Osgood, E.Owens, W.Petrella, A.Chen, C.Acerbo, A. S.Barcoma, A. S.Liu, J.Russo, K. G.Knutson, K. W.Young, C. K.Willier, J. K.Barragan, C.Arzavala, J.Cho, S.Altshul, J.Chan, D.Soma, E.Luo, J.Jain, M.Velazquez, S.Schenker-Ahmed, N.Sundaram, G. V.Manning, A. C.Sanchez, Y.Bikkina, A.Fu, S.OConnor, C.Liem, M.Marrin, M. V.Rose, C.Alt, S. N.Berry, J.Kern, C.Boone, E.Tian, W.Wu, Y.Hariharan, M.Fu, Y.Xie, Y.L2026-02-14doi:10.64898/2026.02.12.705594Cold Spring Harbor Laboratory Press2026-02-14
<![CDATA[
Cellpose-SAM: superhuman generalization for cellular segmentation
]]>
https://biorxiv.org/cgi/content/short/2025.04.28.651001v1?rss=1"
Pachitariu, M.Rariden, M.Stringer, C.2025-05-01doi:10.1101/2025.04.28.651001Cold Spring Harbor Laboratory Press2025-05-01
<![CDATA[
Cortical control of innate behavior from subcortical demonstration
]]>
https://biorxiv.org/cgi/content/short/2025.02.12.637930v1?rss=1"
Keller, J. A.Kwak, I. S.Stark, A. K.Pachitariu, M.Branson, K.Dudman, J. T.2025-02-13doi:10.1101/2025.02.12.637930Cold Spring Harbor Laboratory Press2025-02-13
<![CDATA[
Nuclear tau aggregates inhibit RNA export and form by secondary seeding from cytosolic tau aggregates.
]]>
https://biorxiv.org/cgi/content/short/2026.02.17.706203v1?rss=1"
Decker, C.McCann, K.Lester, E.Pratt, J.Van Alstyne, M.Wang, Y.Parker, R.2026-02-18doi:10.64898/2026.02.17.706203Cold Spring Harbor Laboratory Press2026-02-18
<![CDATA[
Rhomboid protease Rhbdl2 regulates macrophage recruitment and wound regeneration in zebrafish
]]>
https://biorxiv.org/cgi/content/short/2026.02.13.705804v1?rss=1"
Gourkanti, S.Ramakrishnan, G.Munoz, Y.Chavez, R. M.Cheung, J.Dohnalek, J.Schoen, T. J.Martin, K.Lovett-Barron, M. E.Whisenant, T.Strisovsky, K.Neal, S. E.2026-02-15doi:10.64898/2026.02.13.705804Cold Spring Harbor Laboratory Press2026-02-15
<![CDATA[
Viral delivery of an RNA-guided genome editor for transgene-free plant germline editing
]]>
https://biorxiv.org/cgi/content/short/2024.07.17.603964v1?rss=1"
Weiss, T.Kamalu, M.Shi, H.Li, Z.Amerasekera, J.Adler, B. A.Song, M.Vohra, K.Wirnowski, G.Chitkara, S.Ambrose, C.Steinmetz, N.Sridharan, A.Sahagun, D.Banfield, J.Doudna, J.Jacobsen, S. E.2024-07-19doi:10.1101/2024.07.17.603964Cold Spring Harbor Laboratory Press2024-07-19
<![CDATA[
Deciphering epileptogenic and activity-dependent gene programs in the human brain
]]>
https://biorxiv.org/cgi/content/short/2026.02.18.706645v1?rss=1"
Lin, Q.Kang, C.Xavier, A. M.Sanchez-Martin, I.Mehta, A. D.Cheadle, L. M.2026-02-18doi:10.64898/2026.02.18.706645Cold Spring Harbor Laboratory Press2026-02-18
<![CDATA[
A druggable redox switch on SHP1 controls macrophage inflammation
]]>
https://biorxiv.org/cgi/content/short/2026.02.19.706790v1?rss=1"
Ng, M. Y.Nix, M. N.Du, G.Davidek, I.Burger, N.Shin, S.Toenjes, S.Xiao, H.Wei, S.Seo, H.-S.Dhe-Paganon, S.Wales, T. E.Engen, J.Mills, E.Che, J.Zhang, T.Gray, N.Chouchani, E.2026-02-20doi:10.64898/2026.02.19.706790Cold Spring Harbor Laboratory Press2026-02-20
<![CDATA[
Structural evolution of the MTCH family of mitochondrial insertases
]]>
https://biorxiv.org/cgi/content/short/2026.02.17.705849v1?rss=1"
Stevens, T. A.Luo, Z.Lee, C.Hazu, M.Galatis, E. G.Inglis, A. J.Guna, A.Voorhees, R. M.2026-02-18doi:10.64898/2026.02.17.705849Cold Spring Harbor Laboratory Press2026-02-18
<![CDATA[
A sequence-encoded promoter proximal super pause stabilizes an offline RNA polymerase II state
]]>
https://biorxiv.org/cgi/content/short/2026.02.18.706689v1?rss=1"
Vazquez Nunez, R. J.Kesha, S.Vos, S. M.2026-02-18doi:10.64898/2026.02.18.706689Cold Spring Harbor Laboratory Press2026-02-18
<![CDATA[
High-efficiency, transgene-free plant genome editing by viral delivery of an engineered TnpB
]]>
https://biorxiv.org/cgi/content/short/2025.12.05.692691v1?rss=1"
Nagalakshmi, U.Rodriguez, J. E.Nguyen, T.Weissman, R. F.Thornton, B. W.Savage, D. F.Dinesh-Kumar, S. P.2025-12-09doi:10.64898/2025.12.05.692691Cold Spring Harbor Laboratory Press2025-12-09
<![CDATA[
Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection
]]>
https://biorxiv.org/cgi/content/short/2026.02.18.706711v1?rss=1"
Kikawa, C.Huddleston, J.Turner, S. A.Loes, A. N.Liu, J.Gang, S.Griffiths, T.Drapeau, E. M.Cowling, B. J.Ho, F.Leung, N. H.Englund, J. A.Lacombe, K.Watanabe, S.Hasegawa, H.Busch, M.Lanteri, M.Stone, M.Spencer, B.Neher, R. A.Smith, D. J.Bedford, T.Hensley, S. E.Bloom, J. D.2026-02-19doi:10.64898/2026.02.18.706711Cold Spring Harbor Laboratory Press2026-02-19
<![CDATA[
The Zelda interactome reveals diverse co-factors essential for the Drosophila zygotic genome activation
]]>
https://biorxiv.org/cgi/content/short/2026.02.23.707495v1?rss=1"
Li, X.-y.Eisen, M.2026-02-23doi:10.64898/2026.02.23.707495Cold Spring Harbor Laboratory Press2026-02-23
<![CDATA[
Lack of specificity of progenitor responses to injury in regeneration
]]>
https://biorxiv.org/cgi/content/short/2026.02.19.706786v1?rss=1"
Pellegrini, C. E.Reddien, P. W.2026-02-20doi:10.64898/2026.02.19.706786Cold Spring Harbor Laboratory Press2026-02-20
<![CDATA[
Husbandry and Maintenance of Carausius morosus Laboratory Populations
]]>
https://biorxiv.org/cgi/content/short/2026.02.19.706905v1?rss=1"
Ingersoll, M.Kovacikova, P.Hashmi, Y.Extavour, C. G.2026-02-20doi:10.64898/2026.02.19.706905Cold Spring Harbor Laboratory Press2026-02-20
<![CDATA[
Mechanistic machine learning enables interpretable and generalizable prediction of prime editing outcomes
]]>
https://biorxiv.org/cgi/content/short/2026.02.20.706353v1?rss=1"
Hsu, A.Chen, P. J.Li, A. H.Hemez, C. F.Gao, X. D.Terrey, M.Nelson, C.Selvam, V.Cristian, A.McElroy, A. N.Steinbeck, B. J.Mahadeshwar, G. K.Pandey, S.Barsdale, Z.Chen, P. Z.Sousa, A. A.Sakai, H. A.Silverstein, R. A.Morad, I.Krueger, R. K.Shen, M. W.Kleinstiver, B. P.Lutz, C. M.Tolar, J.Blazar, B. R.Osborne, M.Liu, D.2026-02-20doi:10.64898/2026.02.20.706353Cold Spring Harbor Laboratory Press2026-02-20
<![CDATA[
Reprogramming CAR T-Cells with designed bioPROTACs
]]>
https://biorxiv.org/cgi/content/short/2026.02.21.706835v1?rss=1"
Peche, V. S.Kenny, S.Kang, T. G.Coventry, B.Mi, T.Goreshnik, I.Garcia Sanchez, M.Martin, R.Smith, M.Vafeados, D.Kathayat, R.Kaiwen, Y.Yuan, Z.-F.Wu, L.High, A.Nemecek, A.Wickmann, E.Adeshakin, A.Ferrara, F.Throm, R.Chen, T.Youngblood, B.Baker, D.Gottschalk, S.2026-02-22doi:10.64898/2026.02.21.706835Cold Spring Harbor Laboratory Press2026-02-22
<![CDATA[
Viral SSB-bound ssDNA activates the bacterial anti-phage defense system DARNA
]]>
https://biorxiv.org/cgi/content/short/2026.02.22.705581v1?rss=1"
Puteikiene, R.Vassallo, C.Silanskas, A.Juozapaitis, J.Songailiene, I.Laub, M. T.Sasnauskas, G.2026-02-23doi:10.64898/2026.02.22.705581Cold Spring Harbor Laboratory Press2026-02-23
<![CDATA[
Targeted knockout of CYP79A1 reduces cyanogenic potential in grain sorghum
]]>
https://biorxiv.org/cgi/content/short/2026.02.23.707491v1?rss=1"
Groover, E. D.Shen, J.Aregawi, K.Li, S.Schwartz, S.Staskawicz, B.Lemaux, P. G.Savage, D. F.2026-02-24doi:10.64898/2026.02.23.707491Cold Spring Harbor Laboratory Press2026-02-24
<![CDATA[
Metabolic stress reveals widespread accumulation of cap-unmethylated RNAs
]]>
https://biorxiv.org/cgi/content/short/2026.02.23.707474v1?rss=1"
Xing, Z.Freitas, A. V.Sutter, B. M.Dang, N. K.Ingolia, N. T.Tu, B. P.2026-02-24doi:10.64898/2026.02.23.707474Cold Spring Harbor Laboratory Press2026-02-24
<![CDATA[
Automated localization of calling birds with small passive acoustic arrays in complex soundscapes
]]>
https://biorxiv.org/cgi/content/short/2026.02.23.707497v1?rss=1"
Eisen, M. B.Brown, P. O.Sanz-Matias, A.2026-02-24doi:10.64898/2026.02.23.707497Cold Spring Harbor Laboratory Press2026-02-24
<![CDATA[
Benzoxaboroles are structurally unique binders of eukaryotic translation initiation factor 4E
]]>
https://biorxiv.org/cgi/content/short/2026.02.24.707563v1?rss=1"
Combs, J. B.Peacock, D. M.Craven, G. B.Jung, S.Chen, Y.Le, S. M.Taunton, J.Shokat, K.2026-02-25doi:10.64898/2026.02.24.707563Cold Spring Harbor Laboratory Press2026-02-25
<![CDATA[
A 5-hydroxymethylcytosine DNA glycosylase provides defense against T-even bacteriophages
]]>
https://biorxiv.org/cgi/content/short/2026.02.25.707755v1?rss=1"
Mejia-Pitta, A.Zhang, Z.Hossain, A.Bartosik, K.Baca, C.Peralta, C.Molina, H.Teplova, M.Brady, S. F.Micura, R.Patel, D. J.Marraffini, L. A.2026-02-25doi:10.64898/2026.02.25.707755Cold Spring Harbor Laboratory Press2026-02-25
<![CDATA[
Aspartate aminotransferase is required for Salmonella expansion in the inflamed gut via TCA anaplerosis
]]>
https://biorxiv.org/cgi/content/short/2026.02.24.707732v1?rss=1"
Shealy, N. G.Baltagulov, M.Avalos, H. F.Olivas, J.Jones, K. M.Byndloss, M. X.2026-02-25doi:10.64898/2026.02.24.707732Cold Spring Harbor Laboratory Press2026-02-25
<![CDATA[
Cell body clustering drives gap junction-mediated synchronous activity in command neurons
]]>
https://biorxiv.org/cgi/content/short/2026.02.26.708359v1?rss=1"
Lee, K.Graciani, J.Rico Carvajal, N.Zhu, Z.Clark, M.Doe, C.2026-03-02doi:10.64898/2026.02.26.708359Cold Spring Harbor Laboratory Press2026-03-02
<![CDATA[
Molecular grammars of intrinsically disordered regions that span the human proteome
]]>
https://biorxiv.org/cgi/content/short/2025.02.27.640591v1?rss=1"
Ruff, K. M.King, M. R.Ying, A. W.Liu, V.Pant, A.Lieberman, W. E.Shinn, M. K.su, x.Kadoch, C.Pappu, R. V.2025-02-28doi:10.1101/2025.02.27.640591Cold Spring Harbor Laboratory Press2025-02-28
<![CDATA[
Structural Basis for C8 methylation of 23S ribosomal RNA by Cfr
]]>
https://biorxiv.org/cgi/content/short/2026.02.27.707579v1?rss=1"
Esakova, O. A.Jung, J.Lee, H.Cho, S. H.Alumasa, J. N.Schwalm, E.Grove, T. L.Bauerle, M.Hafenstein, S.Yu, Z.Booker, S.2026-03-02doi:10.64898/2026.02.27.707579Cold Spring Harbor Laboratory Press2026-03-02
<![CDATA[
Vampire bats target their social grooming to hard-to-reach body parts
]]>
https://biorxiv.org/cgi/content/short/2026.02.25.707567v1?rss=1"
Chen, C.Nguyen, T. I.Meyer, M.Hashem, E.Carter, G. G.2026-02-27doi:10.64898/2026.02.25.707567Cold Spring Harbor Laboratory Press2026-02-27
<![CDATA[
Intestinal intraepithelial lymphocyte migration and tissue homeostasis are dictated by Gα13
]]>
https://biorxiv.org/cgi/content/short/2026.03.01.708910v1?rss=1"
Earley, Z. M.Rao, A.Knopper, K.Peng, F.Qiu, L.Jo, N.Lisicka, W.Taglinao, H.An, J.Xu, Y.Yang, L. V.Liu, D.Looney, M. R.Cyster, J. G.2026-03-03doi:10.64898/2026.03.01.708910Cold Spring Harbor Laboratory Press2026-03-03
<![CDATA[
Somatic mutation in human cerebellum illustrates neuron type-specific patterns of age-related mutation
]]>
https://biorxiv.org/cgi/content/short/2026.02.27.708647v1?rss=1"
Essuman, K.Yang, Y.Goodman, E.Cambridge, C.Cai, C.An, Z.Mao, S.Manam, M. D.Finander, B.Khoshkhoo, S.Sun, L.Huang, A. Y.Walsh, C. A.2026-03-02doi:10.64898/2026.02.27.708647Cold Spring Harbor Laboratory Press2026-03-02
<![CDATA[
mSWI/SNF complex inhibition sensitizes KRAS-mutant lung cancers to targeted therapies via epithelial-mesenchymal subversion
]]>
https://biorxiv.org/cgi/content/short/2026.02.27.708377v1?rss=1"
Gentile, C.Feng, W. W.Lenahan, S. M.Ying, A. W.Card, D. C.Wu, F. T. H.Pham, N.-A.Radulovich, N.Cao, P. M.Hueniken, K.Li, Q.Tsao, M.-S.Kulesza, J.Hinkley, M. M.Liao, L.Tsai, J. A. < A.Kohler, J.Facchinetti, F.Li, J.Weston, C.Locquet, M.-A.Ngo, K.Gokhale, P. C.Sacher, A. G.Janne, P. A.Kadoch, C.2026-03-01doi:10.64898/2026.02.27.708377Cold Spring Harbor Laboratory Press2026-03-01
<![CDATA[
Endosome motility controls light-responsive reproductive development and secondary metabolite production in Aspergillus
]]>
https://biorxiv.org/cgi/content/short/2026.03.03.708097v1?rss=1"
Kumar, G.Allen, J. L.Oster, L. D.Amir Rawa, M. S.Ramirez, E. A.Bok, J. W.Suen, P. H.Driscoll, B. E.Salogiannis, J.Keller, N. P.Reck-Peterson, S. L.2026-03-04doi:10.64898/2026.03.03.708097Cold Spring Harbor Laboratory Press2026-03-04
<![CDATA[
Derlin-mediated ERAD of lipid regulator ORMDL3 safeguards mitochondrial function
]]>
https://biorxiv.org/cgi/content/short/2026.02.27.708653v1?rss=1"
Scott, N. A.Afolabi, J.Marshall, A. G.Schafer, J. C.Baskerville, V. R.Prasad, P.Kadam, A. A.Som de Cerff, C.Whisenant, T.Phillips, M. A.Tomar, D.McReynolds, M.Hinton, A.Neal, S. E.2026-03-03doi:10.64898/2026.02.27.708653Cold Spring Harbor Laboratory Press2026-03-03
<![CDATA[
Structural basis of RNA-guided transcription by a dCas12f-σE-RNAP complex
]]>
https://biorxiv.org/cgi/content/short/2025.06.10.658880v1?rss=1"
Xiao, R.Hoffmann, F. T.Xie, D.Wiegand, T.Palmieri, A. I.Sternberg, S. H.Chang, L.2025-06-10doi:10.1101/2025.06.10.658880Cold Spring Harbor Laboratory Press2025-06-10
<![CDATA[
Parabrachial Ntsr1 neurons modulate food intake and anxiety through a projection to the ventromedial hypothalamus
]]>
https://biorxiv.org/cgi/content/short/2026.03.03.709382v1?rss=1"
Pauli, J. L.Park, S.Felix, R. R.Palmiter, R.2026-03-05doi:10.64898/2026.03.03.709382Cold Spring Harbor Laboratory Press2026-03-05
<![CDATA[
Gothic Identity as Cultural Practice: Paleogenomic Evidence for Multi - Ethnic Assemblages Under Gothic Material Culture in Late Antique Bulgaria (4th - 6th centuries CE)
]]>
https://biorxiv.org/cgi/content/short/2026.03.03.709317v1?rss=1"
Stamov, S.Chobanov, T.Wang, T.Stoeva, K.Momchilov, D.Aladzhov, A.Chobanov, K.Nikolov, M.Nesheva, D.Heather, P.Toncheva, D. I.Zamfirov, M.Lazaridis, I.Reich, D. E.2026-03-05doi:10.64898/2026.03.03.709317Cold Spring Harbor Laboratory Press2026-03-05
<![CDATA[
Medulloblastoma-Associated KBTBD4 Mutations Disrupt PP2A-A Orphan Quality Control
]]>
https://biorxiv.org/cgi/content/short/2026.03.02.709011v1?rss=1"
Baur, R.Schneider, L. A.Sathe, G.Lunardi, T.Schneider, J.Krebs, A.-S.Silva, J. C.Haakonsen, D. L.Waszak, S. M.Lingner, J.Ciulli, A.Rape, M.Thoma, N. H.2026-03-03doi:10.64898/2026.03.02.709011Cold Spring Harbor Laboratory Press2026-03-03
<![CDATA[
Spligation enables programmable chimeric RNA generation in living cells
]]>
https://biorxiv.org/cgi/content/short/2026.03.06.709984v1?rss=1"
Colognori, D.Wasko, K. M.Trinidad, M. I.Zhou, Z.Doudna, J. A.2026-03-06doi:10.64898/2026.03.06.709984Cold Spring Harbor Laboratory Press2026-03-06
<![CDATA[
Ligand-guided Sequence-structure Co-design of De Novo Functional Enzymes
]]>
https://biorxiv.org/cgi/content/short/2026.03.02.709205v1?rss=1"
Song, Z.Liu, H.Zhao, Y.Yang, Y.Li, L.2026-03-04doi:10.64898/2026.03.02.709205Cold Spring Harbor Laboratory Press2026-03-04
<![CDATA[
Senescence-directed nanotherapy ameliorates fibrosis and overcomes immune exclusion in cancer
]]>
https://biorxiv.org/cgi/content/short/2026.03.02.706451v1?rss=1"
Hinterleitner, C.Barthet, V. J. A.Goldberg, H. V.Vogt, K. C.Perea, A. M.Ruiz, S.Hillger, L. R.McHugh, D.Ho, Y.-J.Chaves-Perez, A.Skamagki, M.Flowers, S.Rekhtman, N.Zhuang, X.Barretto, G. D.Li, X.Watson, J. T.Luan, W.Simon, J.Tammela, T.Gardner, R.Rudin, C. M.Romesser, P. B.Bott, M. J.Filliol, A.Heller, D. A.Lowe, S. W.2026-03-04doi:10.64898/2026.03.02.706451Cold Spring Harbor Laboratory Press2026-03-04
<![CDATA[
Miniprotein inhibitors of the Staphylococcus aureus efflux transporter NorA
]]>
https://biorxiv.org/cgi/content/short/2026.03.05.709893v1?rss=1"
Mishra, P.Chazin-Gray, A. M.Lamon, G.Kim, D. E.Baker, D.Traaseth, N. J.2026-03-05doi:10.64898/2026.03.05.709893Cold Spring Harbor Laboratory Press2026-03-05
<![CDATA[
Measuring Amorphous Motion: Application of Optical Flow to Three-Dimensional Fluorescence Microscopy Images
]]>
https://biorxiv.org/cgi/content/short/2026.03.06.710169v1?rss=1"
Lee, R. M.Eisenman, L. R.Hobson, C.Aaron, J. S.Chew, T.-L.2026-03-10doi:10.64898/2026.03.06.710169Cold Spring Harbor Laboratory Press2026-03-10
<![CDATA[
A Modular Framework for Automated Segmentation and Analysis of AFM Imaging of Chromatin Organization
]]>
https://biorxiv.org/cgi/content/short/2026.03.06.708946v1?rss=1"
Sorensen, E. W.Pangeni, S.Merino-Urteaga, R.Murray, P. J.Rudnizky, S.Liao, T.-W.Rashid, F.Hwang, J.Yamadi, M.Feng, X. A.Zähringer, J.Gu, S.Davidson, I. F.Caccianini, L.Osorio-Valeriano, M.Farnung, L.Vos, S.Peters, J.-M.Berger, J. M.Wu, C.Hatzakis, N. S.Kirkegaard, J. B.Ha, T.2026-03-07doi:10.64898/2026.03.06.708946Cold Spring Harbor Laboratory Press2026-03-07
<![CDATA[
Remote homology and functional genetics unmask deeply preserved Scm3/HJURP orthologs in metazoans
]]>
https://biorxiv.org/cgi/content/short/2026.03.04.709615v1?rss=1"
Hollis, J. A.Stonick, J. A.Topalidou, I.Young, J. M.Moens, C. B.Lehrbach, N. J.Campbell, M. G.Malik, H. S.2026-03-06doi:10.64898/2026.03.04.709615Cold Spring Harbor Laboratory Press2026-03-06
<![CDATA[
Elucidating genes sufficient for viral entry into cells through sequential genome-wide CRISPR activation screens
]]>
https://biorxiv.org/cgi/content/short/2026.03.06.710083v1?rss=1"
Chai, T.Wong, A.Yin, Q.von Creytz, I.Weissman, J. S.Saunders, R. A.Prescott, J. B.Loh, K. M.2026-03-06doi:10.64898/2026.03.06.710083Cold Spring Harbor Laboratory Press2026-03-06
<![CDATA[
Ribosome Molecular Aging Shapes Translation Dynamics
]]>
https://biorxiv.org/cgi/content/short/2026.03.08.710403v1?rss=1"
Botello, J. F.Jiang, L.Metzger, P. J.Comi, T. J.Abu-Alfa, A. A.Yu, Q.Ebert, M. S.Lee, M.Wiesner, L. W.Butani, M.Weaver, C. J.Kosmrlj, A.Cristea, I. M.Brangwynne, C. P.2026-03-09doi:10.64898/2026.03.08.710403Cold Spring Harbor Laboratory Press2026-03-09
<![CDATA[
Streptomyces enrichment in roots during drought is uncoupled from plant benefit and is driven by host suppression of iron uptake and immunity
]]>
https://biorxiv.org/cgi/content/short/2026.03.06.710171v1?rss=1"
Fitzpatrick, C.Smith, R.Hige, J.Law, T.Russ, D.Ajayi, O.Eida, A.Jacob, P.Jowers, M.Kumar, N.Lai, C.Anguita-Maeso, M.Peterson, B.Saha, C.Skelly, T.Zhao, Q.Zhou, W.Grant, S.Mougous, J.Jones, C.Dangl, J.2026-03-06doi:10.64898/2026.03.06.710171Cold Spring Harbor Laboratory Press2026-03-06
<![CDATA[
Optogenetic Analysis of Behavior in the Mosquito Aedes aegypti
]]>
https://biorxiv.org/cgi/content/short/2026.03.15.711871v1?rss=1"
Rami, S.So, M.Travis, C.Jiao, Y.Shamble, P.Sorrells, T. R.2026-03-18doi:10.64898/2026.03.15.711871Cold Spring Harbor Laboratory Press2026-03-18
<![CDATA[
Quinone reductase 2 reads H3 serotonylation to support neuronal maturation
]]>
https://biorxiv.org/cgi/content/short/2026.03.17.712426v1?rss=1"
Chen, M.Yang, C.Li, X.Kong, L.Weekley, B. H.Wei, X.O'Chan, J. C.Vinson, D. A.Cetin, B.Ramakrishnan, A.Shen, L.Zeng, R.Liu, Z.Zhang, J.Cappuccio, K. M.Sokol, J. R.Baljinnyam, E.Hu, R.Rosenblum, K.Molina, H.Zheng, Q.David, Y.Marro, S. G.Muir, T. W.Li, X. D.Li, H.Maze, I.2026-03-18doi:10.64898/2026.03.17.712426Cold Spring Harbor Laboratory Press2026-03-18
<![CDATA[
Midgestation metabolic constraint in purine metabolism drives distinct strategies for placenta and fetal growth
]]>
https://biorxiv.org/cgi/content/short/2026.03.18.712680v1?rss=1"
Xu, W.De La Cruz, N.Woods, A.Lokshtanov, D.Gao, S.Khan, N. A.Wright, S.Florian-Rodriguez, M.McIntire, D. D.Duryea, E. L.Nelson, D. B.Spong, C. Y.Herrera, C. L.Hanna, J. H.Srivatsan, S. R.Aguilera Castrejon, A.Solmonson, A.2026-03-18doi:10.64898/2026.03.18.712680Cold Spring Harbor Laboratory Press2026-03-18
<![CDATA[
UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism
]]>
https://biorxiv.org/cgi/content/short/2026.03.18.712693v1?rss=1"
Nguyen, P. T.Wu, Z.Kim, D.Ogu, T.Yin, S.Sondhi, V.Cai, F.Tippetts, T. S.Jen, A.Shishkova, E. J.Cai, L.Dumesnil, D.Cervantes, M.Chen, H.Mishra, P.Coon, J.Hoxhaj, G.Ni, M.DeBerardinis, R. J.2026-03-18doi:10.64898/2026.03.18.712693Cold Spring Harbor Laboratory Press2026-03-18
<![CDATA[
Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq
]]>
https://biorxiv.org/cgi/content/short/2026.03.16.711480v1?rss=1"
Shi, T.Korshunova, M.Kim, S.DeTomaso, D.Zheng, X.Vishvanath, L.Nyasulu, T.Huynh, N.Sun, A.Thompson, P. C.Zhang, Y.Wigdor, E. M.Rohani, N.Ali, S.Qiu, H.Geralt, M.Zhao, Z.Rabhi, S.Yao, Z.van Velthoven, C. T.Nery, J. R.Castanon, R. G.Dicks, S.Chen, T. J.Ecker, J. R.Zeng, H.Zheng, G. X.Sanders, S. J.Sundaram, L.Jin, X.2026-03-18doi:10.64898/2026.03.16.711480Cold Spring Harbor Laboratory Press2026-03-18
<![CDATA[
In vivo multiomic Perturb-seq with enhanced nuclear gRNA capture
]]>
https://biorxiv.org/cgi/content/short/2026.03.15.711739v1?rss=1"
Zheng, X.Li, J.Kim, K.Simmons, S. K.Zhao, Z.Tastemel, M.Huynh, N.Qiu, H.Ye, J.Whte, C. M.Levin, J. Z.Jin, X.2026-03-17doi:10.64898/2026.03.15.711739Cold Spring Harbor Laboratory Press2026-03-17
<![CDATA[
Statistical BURST imaging for high-fidelity biomolecular ultrasound
]]>
https://biorxiv.org/cgi/content/short/2026.03.13.711726v1?rss=1"
Lee, S.Shivaei, S.Shapiro, M. G.2026-03-17doi:10.64898/2026.03.13.711726Cold Spring Harbor Laboratory Press2026-03-17
<![CDATA[
A stress-function tradeoff organizes epithelial heterogeneity across spatial scales in the human thyroid
]]>
https://biorxiv.org/cgi/content/short/2026.03.12.711294v1?rss=1"
Korem Kohanim, Y.Barkai, T.Novoselsky, R.Shir, S.Bahar Halpern, K.Reich-Zeliger, S.Elkahal, J.Tessler, I.Shivatzki, S.Schwartz, I.Remer, E.Avior, G.Hoefllin, R.Kedmi, M.Keren-Shaul, H.Goliand, I.Addadi, Y.Golani, O.Alon, E.Itzkovitz, S.Medzhitov, R.2026-03-16doi:10.64898/2026.03.12.711294Cold Spring Harbor Laboratory Press2026-03-16
<![CDATA[
Vibrio parahaemolyticus quorum sensing controls phage VP882 transmission
]]>
https://biorxiv.org/cgi/content/short/2026.03.16.712183v1?rss=1"
Sargen, M. R.Bassler, B. L.2026-03-16doi:10.64898/2026.03.16.712183Cold Spring Harbor Laboratory Press2026-03-16
<![CDATA[
ESPeR-seq: Extremely Sensitive and Pure, End-to-end, RNA-seq library preparation
]]>
https://biorxiv.org/cgi/content/short/2026.03.12.711386v1?rss=1"
Chen, H.-M.Kao, J.-C.Yang, C.-P.Tan, C.Lee, T.Sugino, K.2026-03-15doi:10.64898/2026.03.12.711386Cold Spring Harbor Laboratory Press2026-03-15
<![CDATA[
Transcriptomic data and biomedical literature synergize in finding pharmacologic gene regulators
]]>
https://biorxiv.org/cgi/content/short/2026.03.13.708862v1?rss=1"
Deisseroth, C. A.Brazelton, B.Shaik, Z.Liu, Z.Zoghbi, H. Y.2026-03-15doi:10.64898/2026.03.13.708862Cold Spring Harbor Laboratory Press2026-03-15
<![CDATA[
Proteomics reveals extensive phosphoregulation of outer kinetochore protein KNL1
]]>
https://biorxiv.org/cgi/content/short/2026.03.13.711714v1?rss=1"
Jurasin, A. C.Frank, A. R.Biggins, S.2026-03-15doi:10.64898/2026.03.13.711714Cold Spring Harbor Laboratory Press2026-03-15
<![CDATA[
Image Analysis Tools for Electron Microscopy
]]>
https://biorxiv.org/cgi/content/short/2026.03.11.711125v1?rss=1"
Shtengel, D.Shtengel, G.Xu, C. S.Hess, H. F.2026-03-14doi:10.64898/2026.03.11.711125Cold Spring Harbor Laboratory Press2026-03-14
<![CDATA[
Discovery and Biosynthesis of Nitrilobacillins by Post-translational Introduction of C-Terminal Nitrile Groups
]]>
https://biorxiv.org/cgi/content/short/2026.03.11.711119v1?rss=1"
Cha, L.Qian, C.Padhi, C.Zhu, L.van der Donk, W.2026-03-14doi:10.64898/2026.03.11.711119Cold Spring Harbor Laboratory Press2026-03-14
<![CDATA[
A potential role for acyl-phosphate in the coordination of phospholipid and lipopolysaccharide synthesis in Escherichia coli
]]>
https://biorxiv.org/cgi/content/short/2026.03.13.711678v1?rss=1"
DeHart, T. G.Fivenson, E. M.de Bakker, V.Sakenova, N.Bernhardt, T. G.2026-03-14doi:10.64898/2026.03.13.711678Cold Spring Harbor Laboratory Press2026-03-14
<![CDATA[
Hypothesis: A modern human range expansion ~300,000 years ago explains Neandertal origins
]]>
https://biorxiv.org/cgi/content/short/2026.03.11.711219v1?rss=1"
Reich, D.2026-03-13doi:10.64898/2026.03.11.711219Cold Spring Harbor Laboratory Press2026-03-13
<![CDATA[
GAP mimetic activity of pan-Ras TCI daraxonrasib synergizes with K-Ras Switch-II pocket inhibition
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https://biorxiv.org/cgi/content/short/2026.03.11.711097v1?rss=1"
Pfaff, P.Shokat, K.2026-03-13doi:10.64898/2026.03.11.711097Cold Spring Harbor Laboratory Press2026-03-13
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Large-scale mutational analysis uncovers molecular mechanisms governing dual RNA functions in transposons
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https://biorxiv.org/cgi/content/short/2026.03.11.711047v1?rss=1"
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Interdependent RNA structural motifs at the 3'-terminus of the West Nile virus genome regulate viral growth
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https://biorxiv.org/cgi/content/short/2026.03.11.711107v1?rss=1"
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]]>Tsao, L. H.Brackney, D. E.Pyle, A. M.2026-03-11doi:10.64898/2026.03.11.711107Cold Spring Harbor Laboratory Press2026-03-11
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SUMO mediates the coordinate regulation of meiotic chromosome length and crossover rate
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https://biorxiv.org/cgi/content/short/2026.03.10.710713v1?rss=1"
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]]>Yun, Y.Qiao, H.White, M.Sandhu, S.Qiu, W.Bourne, S.Deshpande, A.Bhatt, S.Sharma, A.Bailey, L.Tran, H.Prasada Rao, H.Hunter, N.2026-03-11doi:10.64898/2026.03.10.710713Cold Spring Harbor Laboratory Press2026-03-11
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A Dimeric Rocaglate Promotes Multivalent eIF4A-RNA Assembly
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]]>Shokat, K.Liu, J.Moore, M. K.Lou, K.Wassarman, D. R.Arab, A.Ojeda, S.Karakyriakou, B.Koglin, A.-S.Ott, C. J.Gilbert, L.2026-03-10doi:10.64898/2026.03.09.710667Cold Spring Harbor Laboratory Press2026-03-10
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Evaluating the Utility of a Nanoscale Flow Cytometer for Detection of Surface Proteins on HIV and Extracellular Vesicles
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https://biorxiv.org/cgi/content/short/2026.03.09.710614v1?rss=1"
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Epithelial sensing of vitamin A shapes intestinal antimicrobial defense
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https://biorxiv.org/cgi/content/short/2026.03.08.710399v1?rss=1"
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C_LIO_LIRetinoic acid receptors (RARs) directly activate mouse Reg3g and human REG3G transcription
C_LIO_LIRARs bind the Reg3g promoter adjacent to STAT3, integrating nutritional and microbial signals
C_LIO_LIVitamin A-RAR signaling broadly regulates epithelial antimicrobial programs, including -defensins
C_LI
]]>Quinn, G.Propheter, D. C.Kulkarni, K.Johnson, M.Vale, G.McDonald, J. G.Johnson, A.Hassell, B.Behrendt, C. L.Munshi, N. V.Hooper, L. V.2026-03-10doi:10.64898/2026.03.08.710399Cold Spring Harbor Laboratory Press2026-03-10
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Luminal epithelium remodeling underlies endometrial regeneration during menstruation and pregnancy
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https://biorxiv.org/cgi/content/short/2026.03.08.710375v1?rss=1"
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]]>Ang, C. J.Gable, J. J. R.Lyons, K. C.Miguel Whelan, E.Cevrim, C.Skokan, T. D.Bennetts, S. G.Manetta, B. D.Kaage, A. M.Mopure, D.Breznik, A.Murphy, P. L.Goldstein, A. E.Sanchis-Calleja, F.Spencer, T. E.Kelleher, A. M.McKinley, K. L.2026-03-10doi:10.64898/2026.03.08.710375Cold Spring Harbor Laboratory Press2026-03-10
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A deep-time landscape of plant cis-regulatory sequence evolution
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https://biorxiv.org/cgi/content/short/2025.09.17.676453v1?rss=1"
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Inter-individual variation of cellular and gene-expression properties of the human striatum
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https://biorxiv.org/cgi/content/short/2026.03.20.713160v1?rss=1"
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Rapid and repeated evolution of myosin copy number in threespine stickleback
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Topographic CA1 input shapes subicular spatial coding
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https://biorxiv.org/cgi/content/short/2026.03.24.714092v1?rss=1"
Sun, Y.Pederick, D. T.Xu, X.Luo, L.Giocomo, L. M.2026-03-26doi:10.64898/2026.03.24.714092Cold Spring Harbor Laboratory Press2026-03-26
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Subsistence transition preceded population turnover in the eastern Colombian Andes
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https://biorxiv.org/cgi/content/short/2026.03.23.713713v1?rss=1"
Sirak, K.Delgado, M.Triana, A.Rivas, S.Argüello, P.Boada, A. M.Rivera-Sandoval, J.Pena, G.Langebaek, C.Ospina, J. P.Archila, S.Torres Orjuela, S. A.Mejia Cano, M. B.Rodriguez Saza, F.Barton, A.Callan, K.Curtis, E.Frost, T.Iliev, L.Kearns, A.Kellogg, J.Lawson, A. M.Qiu, L.Workman, J. N.Mah, M.Nawaz, M.Soos, G.Cherkinsky, A.Hadden, C. S.Prufer, K. M.Mallick, S.Rohland, N.Fehren-Schmitz, L.Reich, D.2026-03-25doi:10.64898/2026.03.23.713713Cold Spring Harbor Laboratory Press2026-03-25
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FoTO1 orchestrates Taxol biosynthesis through catalytic and non-catalytic mechanisms
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https://biorxiv.org/cgi/content/short/2026.03.21.713420v1?rss=1"
Wick, C.Somani, A.Liu, J.Karunadasa, S. S.Xu, S.-L.Fordyce, P. M.McClune, C. J.Sattely, E.2026-03-24doi:10.64898/2026.03.21.713420Cold Spring Harbor Laboratory Press2026-03-24
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Specialization of independently acquired flagellar FliC proteins in plant-associated Sphingomonas balances swimming and immunogenicity
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https://biorxiv.org/cgi/content/short/2026.02.23.707200v1?rss=1"
Russ, D.Saha, C.Paul, K.Zheng, Z.Law, T. F.Anguita-Maeso, M.Lundberg, D. S.Fitzpatrick, C. R.Dangl, J. L.2026-02-24doi:10.64898/2026.02.23.707200Cold Spring Harbor Laboratory Press2026-02-24
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Cell-specific Na+ accumulation is linked to symplastic transport in tomato leaves
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https://biorxiv.org/cgi/content/short/2026.03.26.714552v1?rss=1"
Shaar-Moshe, L.Runcie, D. E.Brady, S. M.2026-03-29doi:10.64898/2026.03.26.714552Cold Spring Harbor Laboratory Press2026-03-29
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Epigenome editing of human hematopoietic stem cells enables sustained and reversible thrombosis prevention
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https://biorxiv.org/cgi/content/short/2026.03.27.714536v1?rss=1"
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Rapidly evolving aphid gall effector proteins exhibit saposin-like folds
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https://biorxiv.org/cgi/content/short/2026.03.27.712717v1?rss=1"
Bhoinderwala, F.Korgaonkar, A.Gopalakrishna, K.Mathers, T. C.Shigenobu, S.Bazan, F. J.Hogenhout, S. A.Gronenborn, A.Stern, D.2026-03-28doi:10.64898/2026.03.27.712717Cold Spring Harbor Laboratory Press2026-03-28
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An interdependent Cbf1-CCAN interaction stabilizes the budding yeast kinetochore
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https://biorxiv.org/cgi/content/short/2026.03.25.714319v1?rss=1"
Hedouin, S.Hu, C.Biggins, S.2026-03-27doi:10.64898/2026.03.25.714319Cold Spring Harbor Laboratory Press2026-03-27
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Apical Localization of RNA Polymerases Modulate Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET
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https://biorxiv.org/cgi/content/short/2026.03.25.714350v1?rss=1"
Zhang, M.Canari-Chumpitaz, C.Liu, J.Onoa, B.de Cleir, S.Cheng, E.Requejo, K. I.Bustamante, C.2026-03-26doi:10.64898/2026.03.25.714350Cold Spring Harbor Laboratory Press2026-03-26
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Structural dynamics between Argonaute-2 and CK1α promote target RNA release in microRNA-mediated silencing
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https://biorxiv.org/cgi/content/short/2026.03.23.713669v1?rss=1"
Garg, A.Braviner, L.Axhemi, A.Bibel, B.Joshua-Tor, L.2026-03-25doi:10.64898/2026.03.23.713669Cold Spring Harbor Laboratory Press2026-03-25
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Mucin-binding protein shuttles enable delivery of brain-targeted therapeutics
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https://biorxiv.org/cgi/content/short/2026.03.22.713512v1?rss=1"
Shi, S. M.Tender, G. S.Xiong, J.Buff, J. K.Park, H. I.Mendiola, J. H.Wilson, E. N.Abu-Remaileh, M.Bertozzi, C. R.Wyss-Coray, T.2026-03-25doi:10.64898/2026.03.22.713512Cold Spring Harbor Laboratory Press2026-03-25
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Motor Cortical Computations Underlying Natural Dexterous Movement in Freely Flying Bats
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Styr, B.Qi, K.Chen, X.Liberti, W.Yartsev, M.2026-03-25doi:10.64898/2026.03.25.714017Cold Spring Harbor Laboratory Press2026-03-25
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HIV-1 infection does not confer intrinsic resistance to cell death induced by cytotoxic T lymphocytes
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https://biorxiv.org/cgi/content/short/2026.03.23.713717v1?rss=1"
Bachmann, N.Kim, B.Simonetti, F. R.Kovacs, C. M.Hoh, R.Deeks, S. G.Siliciano, J. D.Siliciano, R. F.2026-03-25doi:10.64898/2026.03.23.713717Cold Spring Harbor Laboratory Press2026-03-25
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Homozygosity for rare or common hypomorphic IL23R variants confers a predisposition to tuberculosis in humans
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https://biorxiv.org/cgi/content/short/2026.03.23.713554v1?rss=1"
Olguin Calderon, D.Kilpatrick, L. E.Conil, C.Philippot, Q.Ogishi, M.Vellutini, J.Eun Han, J.Keating, N.Li, H.Rao, G.Bohlen, J.Lay, C. S.Platt, S.Kerner, G.Feredj, E.Peel, J.Momenilandi, M.Seeleuthner, Y.Laine, C.soudee, c.Leloup, C.Debuisson, C.Lanternier, F.Bitoun, S. B.Pavy, S.Mariette, X.Rafik, A.Skhoun, H.EL Ouazzani, H.Abderahmani-Ghorfi, I.EL Baghdadi, J.Baena, A.Tejada-Giraldo, M.Barrera, L. F.Arias, A. A.Fabio, G.Carrabba, M.Emiroglu, M.Bezrodnik, L.EL Zein, L.Hammoud, H.Gregersen, P.Terrier, B.Leon L2026-03-25doi:10.64898/2026.03.23.713554Cold Spring Harbor Laboratory Press2026-03-25
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Structural basis of liver de-targeting and neuronal tropism of CNS-targeted AAV capsids
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https://biorxiv.org/cgi/content/short/2025.06.02.655683v1?rss=1"
Brittain, T. J.Jang, S.Coughlin, G. M.Barcelona, B. H.Giriat, I.Ristic, F.Appling, N.Chossis, C. P.Shay, T. F.Gradinaru, V.2025-06-03doi:10.1101/2025.06.02.655683Cold Spring Harbor Laboratory Press2025-06-03
<![CDATA[
Genetic encoding of climate-responsive stomatal developmental plasticity in tomato
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https://biorxiv.org/cgi/content/short/2026.03.27.714625v1?rss=1"
Nir, I.Budrys, A.Suraev, D.PRODJINOTO, H.Erberich, J.Tirnover, J.Zafrir, E.Kutcher, Y.Smoot, N. K.Bergmann, D.2026-03-30doi:10.64898/2026.03.27.714625Cold Spring Harbor Laboratory Press2026-03-30
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Epigenomic methylome landscape of promoters in vertebrate genomes
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https://biorxiv.org/cgi/content/short/2026.03.29.715150v1?rss=1"
Lee, Y. H.Lee, C.Jarvis, E.Kim, H.2026-03-30doi:10.64898/2026.03.29.715150Cold Spring Harbor Laboratory Press2026-03-30
<![CDATA[
Nextstrain automates real-time phylodynamic analysis of open data for endemic and emerging pathogens
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https://biorxiv.org/cgi/content/short/2026.03.23.713807v1?rss=1"
Andrews, K. R.Chang, J.Roemer, C.Hadfield, J.Lin, V.Brito, A. F.Daodu, R.Joia, I. A.Kistler, K.Li, A. W.Moncla, L. H.Paredes, M. I.Kuhnert, D.Torres, L. M.Voitl, L.Aksamentov, I.Hodcroft, E. B.Huddleston, J.McCrone, J. T.Anderson, J. S.Sibley, T. R.Lee, J.Neher, R. A.Bedford, T.2026-03-26doi:10.64898/2026.03.23.713807Cold Spring Harbor Laboratory Press2026-03-26
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Biophysical trade-offs in antibody evolution are resolved by conformation-mediated epistasis
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Tharp, C. R.Catalano, C.Khalifeh, A.Ghaffari-Kashani, S.Huang, R.Kang, G.Scapin, G.Phillips, A. M.2026-03-13doi:10.64898/2026.03.12.711465Cold Spring Harbor Laboratory Press2026-03-13
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Evolution of Origin Sequence and Recognition for Licensing of Eukaryotic DNA Replication
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Bauer, J.Zali, N.Chouhan, O. P.Demerdash, O. E.Loell, K.Kinney, J. B.Joshua-Tor, L. W.Stillman, B.2026-03-10doi:10.64898/2026.03.10.710760Cold Spring Harbor Laboratory Press2026-03-10
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Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines
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Loes, A. N.Tarabi, R. A.Li, S. H.Atkinson, R. K.Huddleston, J.Kikawa, C.Griffths, T.Drapeau, E. M.Wong, S.-S.Cheng, S. M.Leung, N. H.Cobey, S.Cowling, B. J.Bedford, T.Hensley, S. E.Bloom, J. D.2026-02-23doi:10.64898/2026.02.23.707528Cold Spring Harbor Laboratory Press2026-02-23
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The promoter-poised Rpd3 HDAC complex orchestrates global chromatin reprogramming upon nutrient transition
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Bhattacharya, S.Sutter, B. M.Tu, B.2026-02-20doi:10.64898/2026.02.19.706824Cold Spring Harbor Laboratory Press2026-02-20
<![CDATA[
Modeling mitochondrial inheritance enables high-precision single-cell lineage tracing in humans
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Gao, T.Weng, C.Johnson, I.Poeschla, M.Gudera, J.King, E.Rouya, C.Donovan, A.Bourke, L.Shao, Y.Marquez, E.Tyag, R.Zon, L. I.Weissman, J. S.Sankaran, V. G.2026-02-13doi:10.64898/2026.02.12.705660Cold Spring Harbor Laboratory Press2026-02-13
<![CDATA[
Complete definition of how mutations affect antibodies used to prevent RSV
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Simonich, C. A.McMahon, T. E.Kampman, L.Chu, H. Y.Bloom, J. D.2026-02-12doi:10.64898/2026.02.12.705519Cold Spring Harbor Laboratory Press2026-02-12
<![CDATA[
Working Memory of Multi-Object Scenes in Primate Frontal Cortex
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<![CDATA[
Single-molecule dissection of CFTR folding defects and pharmacological rescue
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<![CDATA[
Genetically engineered ESC-derived embryos reveal Vinculin-dependent force responses required for mammalian neural tube closure
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Prudhomme, I. S.Brooks, E. R.Taneja, N.Bhattacharya, B.LaFleche, B. J.Furuta, Y.Zallen, J. A.2025-12-25doi:10.64898/2025.12.22.696028Cold Spring Harbor Laboratory Press2025-12-25
<![CDATA[
HAMMER: Hairpin-based APOBEC3A-mediated mRNA editing reporter
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]]>Chen, Y.Mullally, C.Stefanovska, B.Harris, R. S.2025-12-24doi:10.64898/2025.12.22.695965Cold Spring Harbor Laboratory Press2025-12-24
<![CDATA[
Mechanisms of HSV-1 helicase-primase inhibition and replication fork complex assembly
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Yu, Z.Sathyanarayana, P.Lui, C.Yang, P.Weller, S. K.Shekhar, M.Coen, D. M.Loparo, J.Abraham, J.2025-12-24doi:10.64898/2025.12.23.696259Cold Spring Harbor Laboratory Press2025-12-24
<![CDATA[
Dendrite-targeting OLM interneurons regulate the formation of learning-related CA1 place cell representations
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Campbell, E. P.Martin, L.Magee, J. C.Grienberger, C.2025-12-23doi:10.64898/2025.12.21.695825Cold Spring Harbor Laboratory Press2025-12-23
<![CDATA[
Tolerance toward foreigners in ants requires chronic exposure for establishment but only sporadic exposure for maintenance
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Bailly, T. P. M.Rossi, M.Valdes-Rodriguez, S.Schmitt, T.Frank, E. T.Kronauer, D.2025-12-13doi:10.64898/2025.12.10.693507Cold Spring Harbor Laboratory Press2025-12-13
<![CDATA[
Acute in vivo proximity labeling for membrane targeted proteomics in neuronal circuits
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Anguiano, M.Zhang, R.Robles, M.Salemi, M. R.Phinney, B. S.Fenton, E. M.Leung, C. S.Lewis, E.Lin, S.Whistler, J. L.Nord, A. S.Kim, C. K.2025-12-09doi:10.64898/2025.12.04.691871Cold Spring Harbor Laboratory Press2025-12-09
<![CDATA[
Discovering Glycosylation-Dependent Protein Function by Thermal Proteome Profiling
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Hevler, J. F.Sojitra, M.Caval, T.Schoof, M. L.Mateus, A.Bertozzi, C.2025-12-07doi:10.64898/2025.12.06.692499Cold Spring Harbor Laboratory Press2025-12-07
<![CDATA[
A Conserved Metabolic Oxidative Axis Underlies Immune Cell Cryo-vulnerability
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https://biorxiv.org/cgi/content/short/2026.03.26.714376v1?rss=1"
Mo, Z.Yang, H.Zhang, M.Cao, H.Wang, L.Tao, K.Chen, X.Tian, C.Han, C.Bustamante, C.Liu, Z.Wang, J.2026-03-29doi:10.64898/2026.03.26.714376Cold Spring Harbor Laboratory Press2026-03-29
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Single-Molecule Methods to Investigate Mechanisms of Transcription by RNA Polymerase of Mycobacterium tuberculosis
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https://biorxiv.org/cgi/content/short/2026.03.27.714832v1?rss=1"
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Reconstituting Mouse Embryogenesis Ex Utero from Gastrulation to Fetal Development Reveals Maternally Independent Metabolic Programs
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https://biorxiv.org/cgi/content/short/2026.03.17.710314v1?rss=1"
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DHHC7 palmitoylates KRAS4A and promotes mutant KRAS-driven pancreatic cancers
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https://biorxiv.org/cgi/content/short/2026.03.31.715686v1?rss=1"
Chen, W.Maio, G.Chen, X.Lu, X.Zhao, J.Arora, N.Liu, Y.Ziolkowski, L. M.Macleod, K. F.Zhou, Y.Lin, H.2026-04-02doi:10.64898/2026.03.31.715686Cold Spring Harbor Laboratory Press2026-04-02
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Dual Control of LDL-cholesterol Levels by ANGPTL3 and ANGPTL8
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https://biorxiv.org/cgi/content/short/2026.03.30.715445v1?rss=1"
Xu, Y.Luo, F.Fletcher, J.Inigo, M. M.Burgess, S.Liang, G.Kinch, L. N.Cohen, J. C.Hobbs, H.2026-04-01doi:10.64898/2026.03.30.715445Cold Spring Harbor Laboratory Press2026-04-01
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Fc receptor dependent and independent mechanisms of antibody-mediatedenhancement of immune responses
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https://biorxiv.org/cgi/content/short/2026.03.27.714269v1?rss=1"
Cipolla, M.MacLean, A. J.Hernandez, B.Silva Santos, G. S.Stamatatos, L.Gazumyan, A.Hartweger, H.Merkenschlager, J.Bournazos, S.Ravetch, J.Nussenzweig, M.2026-03-31doi:10.64898/2026.03.27.714269Cold Spring Harbor Laboratory Press2026-03-31