bioRxiv Channel: University of Massachusetts Chan Medical School https://biorxiv.org This feed contains articles for bioRxiv Channel "University of Massachusetts Chan Medical School " bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Simultaneous optogenetic manipulation and calcium imaging in freely moving C. elegans ]]> https://biorxiv.org/content/10.1101/000943v1?rss=1 Frederick B. Shipley Christopher M. Clark Mark J. Alkema Andrew M. Leifer 2013-11-27 doi:10.1101/000943 Cold Spring Harbor Laboratory Press 2013-11-27 <![CDATA[ Human Cytomegalovirus Intrahost Evolution--A New Avenue for Understanding and Controlling Herpesvirus Infections ]]> https://biorxiv.org/content/10.1101/009571v1?rss=1 Nicholas Renzette Laura Gibson Jeffrey D. Jensen Timothy F. Kowalik 2014-09-25 doi:10.1101/009571 Cold Spring Harbor Laboratory Press 2014-09-25 <![CDATA[ DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome ]]> https://biorxiv.org/content/10.1101/013250v1?rss=1 Leslie Y Beh Noam Kaplan Manuel M Muller Tom W Muir Laura F Landweber 2014-12-26 doi:10.1101/013250 Cold Spring Harbor Laboratory Press 2014-12-26 <![CDATA[ Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs ]]> https://biorxiv.org/content/10.1101/031385v1?rss=1 Jenny Chen Alexander A. Shishkin Xiaopeng Zhu Sabah Kadri Itay Maza Jacob H Hanna Aviv Regev Manuel Garber 2015-11-11 doi:10.1101/031385 Cold Spring Harbor Laboratory Press 2015-11-11 <![CDATA[ Genome-wide histone modification patterns in Kluyveromyces Lactis reveal evolutionary adaptation of a heterochromatin-associated mark ]]> https://biorxiv.org/content/10.1101/039776v1?rss=1 Angela Bean Assaf Weiner Amanda Hughes Eyal Itskovits Nir Friedman Oliver Rando 2016-02-15 doi:10.1101/039776 Cold Spring Harbor Laboratory Press 2016-02-15 <![CDATA[ Prevalent Presence of Periodic Actin-spectrin-based Membrane Skeleton in a Broad Range of Neuronal Cell Types and Animal Species ]]> https://biorxiv.org/content/10.1101/045856v1?rss=1 Jiang He Ruobo Zhou Zhuhao Wu Monica Carrasco Peri Kurshan Jonathan Farley David Simon Guiping Wang Boran Han Junjie Hao Evan Heller Marc Freeman Kang Shen Tom Maniatis Marc Tessier-Lavigne Xiaowei Zhuang 2016-04-08 doi:10.1101/045856 Cold Spring Harbor Laboratory Press 2016-04-08 <![CDATA[ The genetic basis of natural variation in C. elegans telomere length ]]> https://biorxiv.org/content/10.1101/051276v1?rss=1 Daniel E Cook Stefan Zdraljevic Robyn E Tanny Beomseok Seo David Riccardi Luke M Noble Matthew V Rockman Mark Alkema Christian Braendle Jan Kammenga John Wang Leonid Kruglyak Marie-Anne Felix Junho Lee Erik Andersen 2016-05-02 doi:10.1101/051276 Cold Spring Harbor Laboratory Press 2016-05-02 <![CDATA[ A Common Class of Transcripts with 5’-Intron Depletion, Distinct Early Coding Sequence Features, and N1-Methyladenosine Modification ]]> https://biorxiv.org/content/10.1101/057455v1?rss=1 80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5 proximal-intron-minus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5 cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the Exon Junction Complex (EJC) at non-canonical 5 proximal positions. Finally, N1-methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising [~]20% of human transcripts. This class is defined by depletion of 5 proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N1-methyladenosines in the early coding region, and enrichment for non-canonical binding by the Exon Junction Complex. ]]> Can Cenik Hon Nian Chua Guramrit Singh Abdalla Akef Michael P Snyder Alexander F Palazzo Melissa J Moore Frederick P Roth 2016-06-07 doi:10.1101/057455 Cold Spring Harbor Laboratory Press 2016-06-07 <![CDATA[ Tuberculosis susceptibility and vaccine protection are independently controlled by host genotype ]]> https://biorxiv.org/content/10.1101/064253v1?rss=1 Clare M Smith Megan Proulx Andrew J Olive Dominick Laddy Bibhuti Mishra Caitlin Moss Nuria Martinez Gutierrez Michelle M Bellerose Palmira Barreira-Silva Jia Yao Phuah Richard E Baker Samuel M Behar Hardy Kornfeld Thomas G Evans Gillian Beamer Christopher M Sassetti 2016-08-18 doi:10.1101/064253 Cold Spring Harbor Laboratory Press 2016-08-18 <![CDATA[ Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome ]]> https://biorxiv.org/content/10.1101/071357v1?rss=1 Tsung-Han Hsieh Geoffrey Fudenberg Anton Goloborodko Oliver Rando 2016-08-24 doi:10.1101/071357 Cold Spring Harbor Laboratory Press 2016-08-24 <![CDATA[ PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions ]]> https://biorxiv.org/content/10.1101/074823v1?rss=1 Alex M Tamburino Ebru Kaymak Shaleen Shrestha Amy D Holdorf Sean P Ryder Marian (Albertha) Walhout 2016-09-12 doi:10.1101/074823 Cold Spring Harbor Laboratory Press 2016-09-12 <![CDATA[ Size-Dependent Accumulation of the Mitotic Activator Cdc25 as a Mechanism of Size Control in Fission Yeast ]]> https://biorxiv.org/content/10.1101/078592v1?rss=1 Daniel Keifenheim Xi-Ming Sun Edridge D'Souza Makoto Ohira Mira Magner Michael Mayhew Samuel Marguerat Nicholas Rhind 2016-10-05 doi:10.1101/078592 Cold Spring Harbor Laboratory Press 2016-10-05 <![CDATA[ The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain ]]> https://biorxiv.org/content/10.1101/080440v1?rss=1 Hilbert, B. J. Hayes, J. A. Stone, N. P. Xu, R.-G. Kelch, B. A. 2016-10-17 doi:10.1101/080440 Cold Spring Harbor Laboratory Press 2016-10-17 <![CDATA[ The p150N domain of Chromatin Assembly Factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer ]]> https://biorxiv.org/content/10.1101/082339v1?rss=1 Matheson, T. Kaufman, P. 2016-10-21 doi:10.1101/082339 Cold Spring Harbor Laboratory Press 2016-10-21 <![CDATA[ LR-DNase: Predicting TF binding from DNase-seq data ]]> https://biorxiv.org/content/10.1101/082594v1?rss=1 van der Velde, A. G. Purcaro, M. Noble, W. S. Weng, Z. 2016-10-24 doi:10.1101/082594 Cold Spring Harbor Laboratory Press 2016-10-24 <![CDATA[ A microRNA family exerts maternal control on sex determination in C. elegans ]]> https://biorxiv.org/content/10.1101/083949v1?rss=1 McJunkin, K. Ambros, V. 2016-10-28 doi:10.1101/083949 Cold Spring Harbor Laboratory Press 2016-10-28 <![CDATA[ A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types ]]> https://biorxiv.org/content/10.1101/086025v1?rss=1 Libbrecht, M. W. Rodriguez, O. Weng, Z. Hoffman, M. Bilmes, J. A. Noble, W. S. 2016-11-07 doi:10.1101/086025 Cold Spring Harbor Laboratory Press 2016-11-07 <![CDATA[ HI-C 2.0: AN OPTIMIZED HI-C PROCEDURE FOR HIGH-RESOLUTION GENOME-WIDE MAPPING OF CHROMOSOME CONFORMATION ]]> https://biorxiv.org/content/10.1101/090001v1?rss=1 Belaghzal, H. Dekker, J. Gibcus, J. H. 2016-11-27 doi:10.1101/090001 Cold Spring Harbor Laboratory Press 2016-11-27 <![CDATA[ Mechanism of ribosome rescue by ArfA and RF2 ]]> https://biorxiv.org/content/10.1101/091256v1?rss=1 Demo, G. Svidritskiy, E. Madireddy, R. Diaz-Avalos, R. Grant, T. Grigorieff, N. Sousa, D. Korostelev, A. 2016-12-02 doi:10.1101/091256 Cold Spring Harbor Laboratory Press 2016-12-02 <![CDATA[ An Estradiol-Inducible Promoter Enables Fast, Graduated Control of Gene Expression in Fission Yeast ]]> https://biorxiv.org/content/10.1101/092338v1?rss=1 Ohira, M. Hendrickson, D. G. McIsaac, R. S. Rhind, N. 2016-12-07 doi:10.1101/092338 Cold Spring Harbor Laboratory Press 2016-12-07 <![CDATA[ Cohesin dependent compaction of mitotic chromosomes ]]> https://biorxiv.org/content/10.1101/094946v1?rss=1 Schalbetter, S. A. Goloborodko, A. Fudenberg, G. Belton, J. M. Miles, C. Yu, M. Dekker, J. Mirny, L. Baxter, J. 2016-12-17 doi:10.1101/094946 Cold Spring Harbor Laboratory Press 2016-12-17 <![CDATA[ Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization ]]> https://biorxiv.org/content/10.1101/095802v1?rss=1 nView larger version (49K):norg.highwire.dtl.DTLVardef@79c6c5org.highwire.dtl.DTLVardef@e8e61forg.highwire.dtl.DTLVardef@5c2eedorg.highwire.dtl.DTLVardef@cf7f3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Nora, E. P. Goloborodko, A. Valton, A.-L. Gibcus, J. Uebsersohn, A. Abdennur, N. Dekker, J. Mirny, L. Bruneau, B. 2016-12-21 doi:10.1101/095802 Cold Spring Harbor Laboratory Press 2016-12-21 <![CDATA[ The 4D Nucleome Project ]]> https://biorxiv.org/content/10.1101/103499v1?rss=1 Dekker, J. Belmont, A. S. Guttman, M. Leshyk, V. O. Lis, J. T. Lomvardas, S. Mirny, L. A. O'Shea, C. C. Park, P. J. Ren, B. Ritland, J. C. Shendure, J. Zhong, S. The 4D Nucleome Network, 2017-01-26 doi:10.1101/103499 Cold Spring Harbor Laboratory Press 2017-01-26 <![CDATA[ Accuracy, Reproducibility And Bias Of Next Generation Sequencing For Quantitative Small RNA Profiling: A Multiple Protocol Study Across Multiple Laboratories ]]> https://biorxiv.org/content/10.1101/113050v1?rss=1 Giraldez, M. D. Spengler, R. M. Etheridge, A. Godoy, P. M. Barczak, A. J. Srinivasan, S. De Hoff, P. L. Tanriverdi, K. Courtright, A. Lu, S. Khoory, J. Rubio, R. Baxter, D. Driedonks, T. A. P. Buermans, H. P. J. Nolte-'t Hoen, E. N. M. Jiang, H. Wang, K. Ghiran, I. Wang, Y. Van Keuren-Jensen, K. Freedman, J. E. Woodruff, P. G. Laurent, L. C. Erle, D. J. Galas, D. J. Tewari, M. 2017-05-17 doi:10.1101/113050 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ An Integrative Framework For Detecting Structural Variations In Cancer Genomes ]]> https://biorxiv.org/content/10.1101/119651v1?rss=1 Dixon, J. Xu, J. Dileep, V. Zhan, Y. Song, F. Le, V. T. Yardimci, G. G. Chakraborty, A. Bann, D. V. Wang, Y. Clark, R. Zhang, L. Yang, H. Liu, T. Iyyanki, S. An, L. Pool, C. Sasaki, T. Mulia, J. C. R. Ozadam, H. Lajoie, B. R. Kaul, R. Buckley, M. Lee, K. Diegel, M. Pezic, D. Ernst, C. Hadjur, S. Odom, D. T. Stamatoyannopoulos, J. A. Broach, J. R. Hardison, R. Ay, F. Noble, W. S. Dekker, J. Gilbert, D. M. Yue, F. 2017-03-28 doi:10.1101/119651 Cold Spring Harbor Laboratory Press 2017-03-28 <![CDATA[ Replication Fork Slowing And Stalling are Distinct, Checkpoint-Independent Consequences of Replicating Damaged DNA ]]> https://biorxiv.org/content/10.1101/122895v1?rss=1 Iyer, D. R. Rhind, N. 2017-03-31 doi:10.1101/122895 Cold Spring Harbor Laboratory Press 2017-03-31 <![CDATA[ Intron-containing RNA from the HIV-1 provirus activates type I interferon and inflammatory cytokines ]]> https://biorxiv.org/content/10.1101/128447v1?rss=1 McCauley, S. M. Kim, K. Nowosielska, A. Dauphin, A. Diehl, W. E. Luban, J. 2017-08-07 doi:10.1101/128447 Cold Spring Harbor Laboratory Press 2017-08-07 <![CDATA[ c-Maf-dependent regulatory T cells mediate immunological tolerance to intestinal microbiota ]]> https://biorxiv.org/content/10.1101/129601v1?rss=1 Xu, M. Pokrovskii, M. Ding, Y. Yi, R. Au, C. Galan, C. Bonneau, R. Littman, D. R. 2017-04-22 doi:10.1101/129601 Cold Spring Harbor Laboratory Press 2017-04-22 <![CDATA[ Ki-67 Contributes To Normal Cell Cycle Progression And Inactive X Heterochromatin In p21 Checkpoint-Proficient Human Cells ]]> https://biorxiv.org/content/10.1101/134767v1?rss=1 Sun, X. Bizhanova, A. Matheson, T. D. Yu, J. Zhu, J. L. Kaufman, P. D. 2017-05-05 doi:10.1101/134767 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting ]]> https://biorxiv.org/content/10.1101/139352v1?rss=1 Mavor, D. Barlow, K. Asarnow, D. Birman, Y. Britain, D. Chen, W. Green, E. M. Kenner, L. R. Mensa, B. Morinishi, L. S. Nelson, C. A. Poss, E. M. Suresh, P. Tian, R. Arhar, T. Ary, B. E. Bauer, D. P. Bergman, I. D. Brunetti, R. M. Chio, C. M. Dai, S. A. Dickinson, M. S. Elledge, S. Hendel, N. L. Helsell, C. V. M. Kang, E. Kern, N. Khoroshkin, M. S. Kirkemo, L. L. Lewis, G. R. Lou, K. Marin, W. M. Maxwell, A. M. McTigue, P. F. Meyers-Turnbull, D. Nagy, T. L. Natale, A. M. Oltion, K. Pourmal, S. Reder, G. K. Rettko, N. J. Rohweder, P. J. Schwarz, D. M. C. 2017-05-17 doi:10.1101/139352 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Deconvolution Of Subcellular Protrusion Heterogeneity And The Underlying Actin Regulator Dynamics From Live Cell Imaging ]]> https://biorxiv.org/content/10.1101/144238v1?rss=1 Wang, C. Choi, H. J. Kim, S.-J. Bae, Y. Lee, K. 2017-05-31 doi:10.1101/144238 Cold Spring Harbor Laboratory Press 2017-05-31 <![CDATA[ Reconstructing Spatial Transport Distributions In The Nuclear Pore Complex From 2D Images -- How Reliable Is It? ]]> https://biorxiv.org/content/10.1101/145110v1?rss=1 Tu, L.-C. Huisman, M. Chung, Y.-C. Smith, C. Grunwald, D. 2017-06-02 doi:10.1101/145110 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ Project MinE: study design and pilot analyses of a large-scale whole-genome sequencing study in amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/152553v1?rss=1 - Project MinE Consortium, Van Rheenen, W. Pulit, S. L. Dekker, A. M. Al Khleifat, A. Brands, W. J. Iacoangeli, A. Kenna, K. P. Kavak, E. Kooyman, M. McLaughlin, R. L. Middelkoop, B. Moisse, M. Schellevis, R. D. Shatunov, A. Sproviero, W. Tazelaar, G. H. Van der Spek, R. A. Van Doormal, P. T. Van Eijk, K. R. Van Vugt, J. Basak, A. N. Glass, J. D. Hardiman, O. Hide, W. Landers, J. E. Mora, J. S. Morrison, K. E. Newhouse, S. Robberecht, W. Shaw, C. E. Shaw, P. J. Van Damme, P. Van Es, M. A. Al-Chalabi, A. Van den Berg, L. H. Veldink, J. H. 2017-06-20 doi:10.1101/152553 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Transcriptome-wide analysis of roles for tRNA modifications in translational regulation ]]> https://biorxiv.org/content/10.1101/154096v1?rss=1 Chou, H.-J. Donnar, E. Gustafsson, H. T. Garber, M. Rando, O. 2017-06-22 doi:10.1101/154096 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis ]]> https://biorxiv.org/content/10.1101/155036v1?rss=1 Rigano, A. Strambio De Castillia, C. 2017-07-13 doi:10.1101/155036 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Single-molecule FISH in Drosophila muscle reveals location dependent mRNA composition of megaRNPs ]]> https://biorxiv.org/content/10.1101/156091v1?rss=1 Noma, A. Smith, C. S. Huisman, M. Martin, R. M. Moore, M. J. Grunwald, D. 2017-06-26 doi:10.1101/156091 Cold Spring Harbor Laboratory Press 2017-06-26 <![CDATA[ Rapid isolation of functionally intact nuclei from the yeast Saccharomyces ]]> https://biorxiv.org/content/10.1101/162388v1?rss=1 Niepel, M. Farr, J. Rout, M. P. Strambio De Castillia, C. 2017-07-12 doi:10.1101/162388 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Fundamental limits on dynamic inference from single cell snapshots ]]> https://biorxiv.org/content/10.1101/170118v1?rss=1 Weinreb, C. Wolock, S. Tusi, B. K. Socolovsky, M. Klein, A. M. 2017-07-30 doi:10.1101/170118 Cold Spring Harbor Laboratory Press 2017-07-30 <![CDATA[ A synthetic biology approach to probing nucleosome symmetry ]]> https://biorxiv.org/content/10.1101/170811v1?rss=1 Ichikawa, Y. Connelly, C. F. Appleboim, A. Jacobi, H. Abshiru, N. A. Chou, H.-J. Chen, Y. Sharma, U. Zheng, Y. Thomas, P. M. Chen, H. V. Bajaj, V. Kelleher, N. L. Friedman, N. Bolon, D. N. Rando, O. J. Kaufman, P. D. 2017-07-31 doi:10.1101/170811 Cold Spring Harbor Laboratory Press 2017-07-31 <![CDATA[ Heterogeneity and Intrinsic Variation in Spatial Genome Organization ]]> https://biorxiv.org/content/10.1101/171801v1?rss=1 Finn, E. Pegoraro, G. Brandao, H. B. Valton, A.-L. Oomen, M. E. Dekker, J. Mirny, L. Misteli, T. 2017-08-02 doi:10.1101/171801 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2 ]]> https://biorxiv.org/content/10.1101/171819v1?rss=1 Gao, X. D. Tu, L.-C. Mir, A. Dekker, J. Shaffer, S. A. Zhu, L. J. Wolfe, S. A. Sontheimer, E. J. 2017-08-02 doi:10.1101/171819 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ NmeCas9 is an intrinsically high-fidelity genome editing platform ]]> https://biorxiv.org/content/10.1101/172650v1?rss=1 Amrani, N. Gao, X. D. Liu, P. Gupta, A. Edraki, A. Ibraheim, R. Sasaki, K. E. Zhu, L. J. Wolfe, S. A. Sontheimer, E. J. 2017-08-04 doi:10.1101/172650 Cold Spring Harbor Laboratory Press 2017-08-04 <![CDATA[ Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays ]]> https://biorxiv.org/content/10.1101/174649v1?rss=1 Gibcus, J. H. Samejima, K. Goloborodko, A. Samejima, I. Naumova, N. Kanemaki, M. Xie, L. Paulson, J. R. Earnshaw, W. C. Mirny, L. A. Dekker, J. 2017-08-10 doi:10.1101/174649 Cold Spring Harbor Laboratory Press 2017-08-10 <![CDATA[ Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions ]]> https://biorxiv.org/content/10.1101/176297v1?rss=1 Silvas, T. V. Hou, S. Myint, W. Somasundaran, M. Kelch, B. A. Matsuo, H. Kurt Yilmaz, N. Schiffer, C. A. 2017-08-17 doi:10.1101/176297 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Zinc detoxification: a functional genomics and transcriptomics analysis in Drosophila melanogaster cultured cells ]]> https://biorxiv.org/content/10.1101/179598v1?rss=1 Mohr, S. Rudd, K. Hu, Y. Song, W. R. Gilly, Q. Buckner, M. Housden, B. E. Kelley, C. Zirin, J. Tao, R. Amador, G. Sierzputowska, K. Comjean, A. Perrimon, N. 2017-08-22 doi:10.1101/179598 Cold Spring Harbor Laboratory Press 2017-08-22 <![CDATA[ TRIP6 inhibits the Hippo signaling pathway in response to tension at adherens junctions ]]> https://biorxiv.org/content/10.1101/182204v1?rss=1 Dutta, S. Mana-Capelli, S. Paramasivam, M. Dasgupta, I. Cirka, H. Billiar, K. McCollum, D. 2017-08-30 doi:10.1101/182204 Cold Spring Harbor Laboratory Press 2017-08-30 <![CDATA[ The genome of Trichoplusia ni, an agricultural pest and novel model for small RNA biology ]]> https://biorxiv.org/content/10.1101/183921v1?rss=1 393 piRNA-producing loci, as well as 39 genes encoding core small RNA pathway proteins. siRNAs target both endogenous transposons and the exogenous TNCL virus. Surprisingly, T. ni siRNAs are not 2{acute}-O-methylated. Five piRNA-producing loci account for 34.9% piRNAs in the ovary, 49.3% piRNAs in the testis, and 44.0% piRNAs in Hi5 cells. Nearly all of the W chromosome is devoted to piRNA production: >76.0% of bases in the assembled W produce piRNAs in ovary. To enable use of the T. ni germline-derived Hi5 cell line as a model system, we have established efficient genome editing and single-cell cloning protocols. Taken together, the T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo. ]]> Fu, Y. Yang, Y. Zhang, H. Farley, G. Wang, J. Quarles, K. A. Weng, Z. Zamore, P. D. 2017-09-04 doi:10.1101/183921 Cold Spring Harbor Laboratory Press 2017-09-04 <![CDATA[ Measuring the reproducibility and quality of Hi-C data ]]> https://biorxiv.org/content/10.1101/188755v1?rss=1 Yardimci, G. Ozadam, H. Sauria, M. E. G. Ursu, O. Yan, K.-K. Yang, T. Chakraborty, A. Kaul, A. Lajoie, B. R. Song, F. Zhan, Y. Ay, F. Gerstein, M. Kundaje, A. Li, Q. Taylor, J. Yue, F. Dekker, J. Noble, W. S. 2017-09-14 doi:10.1101/188755 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Pervasive contingency and entrenchment in a billion years of Hsp90 evolution ]]> https://biorxiv.org/content/10.1101/189803v1?rss=1 Starr, T. N. Flynn, J. M. Mishra, P. Bolon, D. N. A. Thornton, J. W. 2017-09-18 doi:10.1101/189803 Cold Spring Harbor Laboratory Press 2017-09-18 <![CDATA[ The HoxD Cluster is a Dynamic and Resilient TAD Boundary Controling the Segregation of Antagonistic Regulatory Landscapes ]]> https://biorxiv.org/content/10.1101/193706v1?rss=1 Rodriguez-Carballo, E. Lopez-Delisle, L. Zhan, Y. Fabre, P. Beccari, L. El-Idrissi, I. Nguyen Huynh, T. H. Ozadam, H. Dekker, J. Duboule, D. 2017-09-28 doi:10.1101/193706 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ Small RNAs are trafficked from the epididymis to developing mammalian sperm ]]> https://biorxiv.org/content/10.1101/194522v1?rss=1 Sharma, U. Sun, F. Reichholf, B. Herzog, V. Ameres, S. Rando, O. 2017-09-27 doi:10.1101/194522 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics ]]> https://biorxiv.org/content/10.1101/195966v1?rss=1 Ma, H. Tu, L.-C. Naseri, A. Chung, Y.-C. Grunwald, D. Zhang, S. Pederson, T. 2017-09-29 doi:10.1101/195966 Cold Spring Harbor Laboratory Press 2017-09-29 <![CDATA[ Fibroblasts from metastatic sites induce broad-spectrum drug desensitization via modulation of mitochondrial priming ]]> https://biorxiv.org/content/10.1101/197376v1?rss=1 Landry, B. D. Leete, T. Richards, R. Cruz-Gordillo, P. Ren, G. Schwartz, A. D. Peyton, S. R. Lee, M. J. 2017-10-02 doi:10.1101/197376 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Combining multi-omics and drug perturbation profiles to identify novel treatments that improve disease phenotypes in spinal muscular atrophy ]]> https://biorxiv.org/content/10.1101/2019.12.17.879353v1?rss=1 Meijboom, K. E. Volpato, V. Monzon-Sandoval, J. Hoolachan, J. M. Hammond, S. M. Abendroth, F. de Jong, O. G. Hazell, G. Ahlskog, N. Wood, M. J. Webber, C. Bowerman, M. 2019-12-18 doi:10.1101/2019.12.17.879353 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Ubiquitin Links Smoothened to Intraflagellar Transport to Regulate Hedgehog Signaling ]]> https://biorxiv.org/content/10.1101/2019.12.18.880799v1?rss=1 Desai, P. B. Stuck, M. W. Lv, B. Pazour, G. J. 2019-12-19 doi:10.1101/2019.12.18.880799 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Loss of prdm1a accelerates melanoma onset and progression ]]> https://biorxiv.org/content/10.1101/2019.12.20.884767v1?rss=1 Iwanaga, R. Truong, B. Lambert, K. Vyas, R. Orlicky, D. Shellman, Y. Tan, A.-C. Ceol, C. Artinger, K. 2019-12-22 doi:10.1101/2019.12.20.884767 Cold Spring Harbor Laboratory Press 2019-12-22 <![CDATA[ Biophysical basis of cellular multi-specificity encoded in a model molecular switch ]]> https://biorxiv.org/content/10.1101/2020.01.04.893909v1?rss=1 Perica, T. Mathy, C. J. P. Xu, J. Jang, G. M. Zhang, Y. Kaake, R. Ollikainen, N. Braberg, H. Swaney, D. L. Kelly, M. J. S. Krogan, N. J. Kortemme, T. 2020-01-06 doi:10.1101/2020.01.04.893909 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ RIP1 kinase activity promotes steatohepatitis through mediating cell death and inflammation in macrophages ]]> https://biorxiv.org/content/10.1101/2020.01.07.895516v1?rss=1 Tao, L. Yi, Y. Chen, Y. Zhang, H. Jie, J. Zhang, W. Xu, Q. Li, Y. Orning, P. Lien, E. Zhao, M. Gao, P. Ling, L. Ding, Z. Wu, C. Ding, Q. Wang, J. Zhang, J. Weng, D. 2020-01-08 doi:10.1101/2020.01.07.895516 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ SREBP1 regulates mitochondrial metabolism in oncogenic KRAS expressing NSCLC ]]> https://biorxiv.org/content/10.1101/2020.01.15.896373v1?rss=1 Ruiz, C. F. Haley, J. A. Montal, E. D. Haley, J. D. 2020-01-15 doi:10.1101/2020.01.15.896373 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Neuroligin3 Splice Isoforms Shape Mouse Hippocampal Inhibitory Synaptic Function ]]> https://biorxiv.org/content/10.1101/2020.01.22.915801v1?rss=1 Uchigashima, M. Leung, M. Watanabe, T. Cheung, A. Watanabe, M. Imamura Kawasawa, Y. Futai, K. 2020-01-23 doi:10.1101/2020.01.22.915801 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ An atlas of cell types in the mammalian epididymis and vas deferens ]]> https://biorxiv.org/content/10.1101/2020.01.24.918979v1?rss=1 Rinaldi, V. Donnard, E. Gellatly, K. Rasmussen, M. Kucukural, A. Yukselen, O. Garber, M. Sharma, U. Rando, O. 2020-01-24 doi:10.1101/2020.01.24.918979 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Edaravone-Loaded Mesoscale Nanoparticles Treat Cisplatin-Induced Acute Kidney Injury ]]> https://biorxiv.org/content/10.1101/2020.01.24.919134v1?rss=1 Williams, R. M. Shah, J. Mercer, E. Tian, H. S. Cheung, J. M. Dorso, M. Jaimes, E. A. Heller, D. A. 2020-01-25 doi:10.1101/2020.01.24.919134 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ GS-Preprocess: Containerized GUIDE-seq Data Analysis Tools with Diverse Sequencer Compatibility ]]> https://biorxiv.org/content/10.1101/2020.01.26.914861v1?rss=1 Rodriguez, T. C. Pratt, H. E. Liu, P. Amrani, N. Zhu, L. J. 2020-01-27 doi:10.1101/2020.01.26.914861 Cold Spring Harbor Laboratory Press 2020-01-27 <![CDATA[ mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding ]]> https://biorxiv.org/content/10.1101/2020.02.05.936120v1?rss=1 Bao, C. Loerch, S. Ling, C. Korostelev, A. A. Grigorieff, N. Ermolenko, D. 2020-02-06 doi:10.1101/2020.02.05.936120 Cold Spring Harbor Laboratory Press 2020-02-06 <![CDATA[ Epstein Barr virus epitope/MHC interaction combined with convergent recombination drive selection of diverse T cell receptor a and b repertoires ]]> https://biorxiv.org/content/10.1101/2020.02.06.938241v1?rss=1 Gil, A. Kamga, L. Chirravuri-Venkata, R. Aslan, N. Clark, F. G. Ghersi, D. Luzuriaga, K. Selin, L. K. 2020-02-07 doi:10.1101/2020.02.06.938241 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Exploring the selenium-over-sulfur substrate specificity and kinetics of a bacterial selenocysteine lyase ]]> https://biorxiv.org/content/10.1101/2020.02.07.939272v1?rss=1 Johnstone, M. A. Nelson, S. J. Groesbeck, C. V. Self, W. T. 2020-02-09 doi:10.1101/2020.02.07.939272 Cold Spring Harbor Laboratory Press 2020-02-09 <![CDATA[ Cell cycle-associated expression patterns predict gene function in mycobacteria ]]> https://biorxiv.org/content/10.1101/2020.02.10.942268v1?rss=1 Bandekar, A. C. Subedi, S. Ioerger, T. R. Sassetti, C. M. 2020-02-11 doi:10.1101/2020.02.10.942268 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ Single Cell Transcriptomics Reveals Dysregulated Cellular and Molecular Networks in a Fragile X Syndrome Model ]]> https://biorxiv.org/content/10.1101/2020.02.12.946780v1?rss=1 Donnard, E. Shu, H. Garber, M. R. 2020-02-13 doi:10.1101/2020.02.12.946780 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ PEA15 loss of function and defective cerebral development in the domestic cat ]]> https://biorxiv.org/content/10.1101/2020.02.14.949214v1?rss=1 Barsh, G. Graff, E. Cochran, N. Kaelin, C. Day, K. Prokop, J. Gray-Edwards, H. Watanabe, R. Koehler, J. Falgoust, R. Martin, D. Myers, R. Cox, N. 2020-02-14 doi:10.1101/2020.02.14.949214 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Cytosine methylation dynamics during post-testicular sperm maturation in mammals ]]> https://biorxiv.org/content/10.1101/2020.02.14.949487v1?rss=1 Galan, C. Serra, R. Sun, F. Rinaldi, V. Conine, C. Rando, O. 2020-02-14 doi:10.1101/2020.02.14.949487 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Structure of the human clamp loader bound to the sliding clamp: a further twist on AAA+ mechanism ]]> https://biorxiv.org/content/10.1101/2020.02.18.953257v1?rss=1 Gaubitz, C. Liu, X. Magrino, J. Stone, N. P. Landeck, J. Hedglin, M. Kelch, B. A. 2020-02-18 doi:10.1101/2020.02.18.953257 Cold Spring Harbor Laboratory Press 2020-02-18 <![CDATA[ CRISPR-based Live Imaging of Epigenetic Modification-Mediated Genome Reorganization ]]> https://biorxiv.org/content/10.1101/2020.02.18.954610v1?rss=1 Feng, Y. Wang, Y. Yang, C. Naseri, A. Pederson, T. Zheng, J. Xiao, X. Zhang, S. Xie, W. Ma, H. 2020-02-19 doi:10.1101/2020.02.18.954610 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ "Sulcus Sink": A Compact Binary and Semi-Automated Inverse Dijkstra-based System for Describing Sulcal Trajectories ]]> https://biorxiv.org/content/10.1101/2020.02.18.955096v1?rss=1 Pienaar, R. 2020-02-19 doi:10.1101/2020.02.18.955096 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome ]]> https://biorxiv.org/content/10.1101/2020.02.25.964536v1?rss=1 Tessema, S. K. Hathaway, N. J. Teyssier, N. B. Murphy, M. Aydemir, O. Duarte, E. M. Simone, W. Colborn, J. Saute, F. Crawford, E. Aide, P. Bailey, J. A. Greenhouse, B. 2020-02-26 doi:10.1101/2020.02.25.964536 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Drug GRADE: an integrated analysis of population growth and cell death reveals drug- specific and cancer subtype-specific response profiles ]]> https://biorxiv.org/content/10.1101/2020.02.26.966689v1?rss=1 Schwartz, H. R. Richards, R. Fontana, R. E. Joyce, A. J. Honeywell, M. E. Lee, M. J. 2020-02-27 doi:10.1101/2020.02.26.966689 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model ]]> https://biorxiv.org/content/10.1101/2020.03.02.973206v1?rss=1 Na, H. Zdraljevic, S. Tanny, R. E. Walhout, M. Andersen, E. 2020-03-03 doi:10.1101/2020.03.02.973206 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Comprehensive analysis of fungal G1 cyclin docking motif sequences that control CDK regulatory potency in vivo ]]> https://biorxiv.org/content/10.1101/2020.03.02.973354v1?rss=1 Bandyopadhyay, S. Bhaduri, S. Örd, M. Davey, N. E. Loog, M. Pryciak, P. M. 2020-03-03 doi:10.1101/2020.03.02.973354 Cold Spring Harbor Laboratory Press 2020-03-03 <![CDATA[ Multi-contact 3C data reveal that the human genome is largely unentangled ]]> https://biorxiv.org/content/10.1101/2020.03.03.975425v1?rss=1 Tavares-Cadete, F. Norouzi, D. Dekker, B. Liu, Y. Dekker, J. 2020-03-04 doi:10.1101/2020.03.03.975425 Cold Spring Harbor Laboratory Press 2020-03-04 <![CDATA[ Detecting chromatin interactions along and between sister chromatids with SisterC ]]> https://biorxiv.org/content/10.1101/2020.03.10.986208v1?rss=1 Oomen, M. E. Hedger, A. K. Watts, J. K. Dekker, J. 2020-03-11 doi:10.1101/2020.03.10.986208 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Content and performance of the MiniMUGA genotyping array, a new tool to improve rigor and reproducibility in mouse research ]]> https://biorxiv.org/content/10.1101/2020.03.12.989400v1?rss=1 Sigmon, J. S. Blanchard, M. Baric, R. S. Bell, T. A. Brennan, J. Brockmann, G. A. Burks, A. W. Calabrese, M. Caron, K. M. Cheney, R. E. Ciavatta, D. Conlon, F. Darr, D. B. Faber, J. Franklin, C. Gershon, T. R. Gralinski, L. E. Gu, B. Gaines, C. H. Hagan, R. S. Heimsath, E. G. Heise, M. T. Hock, P. Ideraabdullah, F. Jennette, J. C. Kafri, T. Kashfeen, A. Kelada, S. N. P. Kulis, M. Kumar, V. Linnertz, C. L. Livraghi-Butrico, A. Lloyd, K. Loeser, R. Lutz, C. M. Lynch, R. M. Magnuson, T. Matsushima, G. K. McMullan, R. Miller, D. Mohlke, K. L. Moy, S. S. Mu 2020-03-14 doi:10.1101/2020.03.12.989400 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Flexibility and constraint in preimplantation gene regulation in mouse ]]> https://biorxiv.org/content/10.1101/2020.03.13.990275v1?rss=1 Conine, C. Krykbaeva, M. Song, L. Brewster, R. Friedman, N. Rando, O. 2020-03-14 doi:10.1101/2020.03.13.990275 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Start codon disruption with CRISPR/Cas9 prevents murine Fuchs' endothelial corneal dystrophy ]]> https://biorxiv.org/content/10.1101/2020.03.18.996728v1?rss=1 Uehara, H. Zhang, X. Pereira, F. Narendran, S. Choi, S. Bhuvanagiri, S. Liu, J. Ravi Kumar, S. Bohner, A. Carroll, L. Archer, B. Zhang, Y. Liu, W. Gao, G. Ambati, J. Jun, A. S. Ambati, B. K. 2020-03-20 doi:10.1101/2020.03.18.996728 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ SWI/SNF antagonizes SIR heterochromatin to promote transcription of genes expressed during mitotic exit in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2020.03.24.006205v1?rss=1 Rege, M. Feldman, J. L. Adkins, N. L. Peterson, C. L. 2020-03-25 doi:10.1101/2020.03.24.006205 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ ELP-dependent expression of MCL1 promotes resistance to EGFR inhibition in triple-negative breast cancer cells ]]> https://biorxiv.org/content/10.1101/2020.03.29.014894v1?rss=1 Cruz-Gordillo, P. Honeywell, M. E. Leete, T. Lee, M. J. 2020-03-30 doi:10.1101/2020.03.29.014894 Cold Spring Harbor Laboratory Press 2020-03-30 <![CDATA[ A novel CRISPR-based malaria diagnostic capable of Plasmodium detection, speciation, and drug-resistance genotyping ]]> https://biorxiv.org/content/10.1101/2020.04.01.017962v1?rss=1 Cunningham, C. H. Hennelly, C. M. Lin, J. T. Ubalee, R. Boyce, R. M. Mulogo, E. Hathaway, N. Thwai, K. L. Phanzu, F. Kalonji, A. Kashamuka, M. Tshefu, A. Meshnick, S. R. Juliano, J. J. Parr, J. B. 2020-04-02 doi:10.1101/2020.04.01.017962 Cold Spring Harbor Laboratory Press 2020-04-02 <![CDATA[ CryoEM Structure of CtBP2 Confirms Tetrameric Architecture ]]> https://biorxiv.org/content/10.1101/2020.04.06.027573v1?rss=1 Jecrois, A. M. Dcona, M. M. Deng, X. Bandyopadhyay, D. Grossman, S. R. Schiffer, C. A. Royer, W. E. 2020-04-07 doi:10.1101/2020.04.06.027573 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults ]]> https://biorxiv.org/content/10.1101/2020.04.15.042978v1?rss=1 Cao, Y. Guo, Z. Vangala, P. Donnard, E. Liu, P. McDonel, P. Ordovas-Montanes, J. Shalek, A. K. Finberg, R. W. Wang, J. P. Garber, M. 2020-04-17 doi:10.1101/2020.04.15.042978 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ A conserved neuropeptide system links head and body motor circuits to enable adaptive behavior ]]> https://biorxiv.org/content/10.1101/2020.04.27.064550v1?rss=1 Ramachandran, S. Banerjee, N. Bhattacharya, R. Touroutine, D. Lambert, C. M. Schoofs, L. Beets, I. Francis, M. M. 2020-04-28 doi:10.1101/2020.04.27.064550 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Single Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis ]]> https://biorxiv.org/content/10.1101/2020.05.04.077529v1?rss=1 Henriques, F. Bedard, A. H. Guilherme, A. Kelly, M. Chi, J. Zhang, P. Lifshitz, L. M. Bellve, K. Rowland, L. Yenilmez, B. Kumar, S. Wang, Y. Luban, J. Weinstein, L. S. Lin, J. D. Cohen, P. Czech, M. P. 2020-05-05 doi:10.1101/2020.05.04.077529 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Susceptibility trends of zoliflodacin against multidrug-resistant Neisseria gonorrhoeae clinical isolates in NanJing, China (2014-2018) ]]> https://biorxiv.org/content/10.1101/2020.05.04.078055v1?rss=1 Le, W.-J. Su, X.-H. Lou, X. Li, X. Gong, X. Wang, B.-X. Genco, C. A. Mueller, J. P. Rice, P. A. 2020-05-05 doi:10.1101/2020.05.04.078055 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Zika virus infection during pregnancy protects against secondary infection in the absence of CD8+ cells ]]> https://biorxiv.org/content/10.1101/2020.05.08.082610v1?rss=1 Schouest, B. Gilbert, M. H. Bohm, R. P. Schiro, F. Aye, P. P. Panganiban, A. T. Magnani, D. M. Maness, N. J. 2020-05-09 doi:10.1101/2020.05.08.082610 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ IgA MAb blocks SARS-CoV-2 Spike-ACE2 interaction providing mucosal immunity ]]> https://biorxiv.org/content/10.1101/2020.05.15.096719v1?rss=1 Ejemel, M. Li, Q. Hou, S. Schiller, Z. A. Wallace, A. L. Amcheslavsky, A. Kurt Yilmaz, N. Toomey, J. R. Schneider, R. Close, B. J. Chen, D.-Y. Conway, H. L. Saeed, M. Cavacini, L. A. Klempner, M. S. Schiffer, C. A. Wang, Y. 2020-05-15 doi:10.1101/2020.05.15.096719 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ SPATIAL ORGANIZATION OF TRANSCRIBED EUKARYOTIC GENES ]]> https://biorxiv.org/content/10.1101/2020.05.20.106591v1?rss=1 Leidescher, S. Nuebler, J. Feodorova, Y. Hildebrand, E. Ullrich, S. Bultmann, S. Link, S. Thanisch, K. Dekker, J. Leonhardt, H. Mirny, L. Solovei, I. 2020-05-21 doi:10.1101/2020.05.20.106591 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ High-Throughput Human Primary Cell-Based Airway Model for Evaluating Influenza, Coronavirus, or other Respiratory Viruses in vitro ]]> https://biorxiv.org/content/10.1101/2020.05.23.112797v1?rss=1 Gard, A. L. Maloney, R. Cain, B. P. Miller, C. R. Luu, R. J. Coppeta, J. R. Liu, P. Wang, J. P. Azizgolshani, H. Fezzie, R. F. Balestrini, J. L. Isenberg, B. C. Finberg, R. W. Borenstein, J. T. 2020-05-23 doi:10.1101/2020.05.23.112797 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ A developmental analysis of juxtavascular microglia dynamics and interactions with the vasculature ]]> https://biorxiv.org/content/10.1101/2020.05.25.110908v1?rss=1 Mondo, E. Becker, S. C. Kautzman, A. G. Schifferer, M. Baer, C. E. Chen, J. Huang, E. J. Simons, M. Schafer, D. P. 2020-05-25 doi:10.1101/2020.05.25.110908 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ A Specific Neuroligin3-αNeurexin1 Code Regulates GABAergic Synaptic Function in Mouse Hippocampus ]]> https://biorxiv.org/content/10.1101/2020.05.27.119024v1?rss=1 Uchigashima, M. Konno, K. Demchak, E. Cheung, A. Watanabe, T. Keener, D. Abe, M. Le, T. Sakimura, K. Sasaoka, T. Uemura, T. Kawasawa, Y. I. Watanabe, M. Futai, K. 2020-06-01 doi:10.1101/2020.05.27.119024 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome ]]> https://biorxiv.org/content/10.1101/2020.05.27.120105v1?rss=1 Ryder, S. P. 2020-05-28 doi:10.1101/2020.05.27.120105 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Core binding factor leukemia hijacks T-cell prone PU.1 antisense promoter ]]> https://biorxiv.org/content/10.1101/2020.05.29.120857v1?rss=1 van der Kouwe, E. Heller, G. Czibere, A. Castilla, L. H. Delwel, R. Di Ruscio, A. Ebralidze, A. K. Forte, M. Kazianka, L. Kornauth, C. Le, T. Lind, K. Monteiro Barbosa, I. A. Pichler, A. Pulikkan, J. A. Schmolke, A.-S. Sill, H. Sperr, W. Spittler, A. Trinh, B. Q. Valent, P. Vanura, K. Welner, R. S. Zuber, J. Tenen, D. G. Staber, P. B. 2020-05-31 doi:10.1101/2020.05.29.120857 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ STAT3 Serine phosphorylation is required for TLR4 metabolic reprogramming and IL-1β expression ]]> https://biorxiv.org/content/10.1101/2020.06.02.130716v1?rss=1 Balic, J. Albargy, H. Luu, K. Kirby, F. Jayasekara, W. Mansell, F. Garama, D. Baschuk, N. De Nardo, D. Louis, C. Humphries, F. Fitzgerald, K. A. Latz, E. Gough, D. Mansell, A. 2020-06-02 doi:10.1101/2020.06.02.130716 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Site-Specific Incorporation of Citrulline into Proteins in Mammalian Cells ]]> https://biorxiv.org/content/10.1101/2020.06.06.137885v1?rss=1 Mondal, S. Wang, S. Zheng, Y. Sen, S. Chatterjee, A. Thompson, P. 2020-06-06 doi:10.1101/2020.06.06.137885 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ Deciphering complex mechanisms of resistance and loss of potency through coupled molecular dynamics and machine learning. ]]> https://biorxiv.org/content/10.1101/2020.06.08.139105v1?rss=1 Leidner, F. Kurt-Yilmaz, N. Schiffer, C. A. 2020-06-09 doi:10.1101/2020.06.08.139105 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Chronic Effects of Indirect and Direct Cannabinoid Receptor Agonists on Addiction-Related Behaviors and Dopamine Release ]]> https://biorxiv.org/content/10.1101/2020.06.14.150755v1?rss=1 Honeywell, K. M. Freels, T. G. McWain, M. A. Chaffin, A. S. Nolen, H. G. Sable, H. J. Lester, D. B. 2020-06-14 doi:10.1101/2020.06.14.150755 Cold Spring Harbor Laboratory Press 2020-06-14 <![CDATA[ Oral administration of a single anti-CfaE nanobody provides broadly cross-protective immunity against major pathogenic Enterotoxigenic Escherichia coli strains ]]> https://biorxiv.org/content/10.1101/2020.06.16.155465v1?rss=1 Amcheslavsky, A. Wallace, A. Ejemel, M. Li, Q. McMahon, C. Stoppato, M. Giuntini, S. Schiller, Z. A. Pondish, J. Toomey, J. R. Schneider, R. Meisinger, J. Heukers, R. Kruse, A. C. Barry, E. M. Pierce, B. Klempner, M. S. Cavacini, L. A. Wang, Y. 2020-06-18 doi:10.1101/2020.06.16.155465 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ Hydrazines as versatile chemical biology probes and drug-discovery tools for cofactor-dependent enzymes ]]> https://biorxiv.org/content/10.1101/2020.06.17.154864v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1e1a54forg.highwire.dtl.DTLVardef@12be680org.highwire.dtl.DTLVardef@129e027org.highwire.dtl.DTLVardef@3b2317_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lin, Z. Wang, X. Bustin, K. A. He, L. Suciu, R. M. Schek, N. Ahmadi, M. Hu, K. Olson, E. J. Parsons, W. H. Witze, E. S. Morton, P. D. Gregus, A. M. Buczynski, M. W. Matthews, M. L. 2020-06-18 doi:10.1101/2020.06.17.154864 Cold Spring Harbor Laboratory Press 2020-06-18 <![CDATA[ C. elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor ]]> https://biorxiv.org/content/10.1101/2020.06.22.164475v1?rss=1 Walhout, M. Giese, G. Walker, M. Ponomarova, O. Zhang, H. Li, X. Minevich, G. 2020-06-23 doi:10.1101/2020.06.22.164475 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ TIR-1/SARM1 Inhibits Axon Regeneration ]]> https://biorxiv.org/content/10.1101/2020.06.23.165852v1?rss=1 Julian, V. Byrne, A. B. 2020-06-23 doi:10.1101/2020.06.23.165852 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ DGAT1 is a lipid metabolism oncoprotein that enables cancer cells to accumulate fatty acid while avoiding lipotoxicity ]]> https://biorxiv.org/content/10.1101/2020.06.23.166603v1?rss=1 Wilcock, D. J. Badrock, A. P. Owen, R. Guerin, M. Southam, A. D. Johnston, H. Ogden, S. Fullwood, P. Watson, J. Ferguson, H. Haworth, J. Richardson, D. A. Lloyd, G. R. Jankevics, A. Dunn, W. B. Wellbrock, C. Lorigan, P. Ceol, C. Francavilla, C. Smith, M. P. Hurlstone, A. F. L. 2020-06-24 doi:10.1101/2020.06.23.166603 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Differential role of cytosolic Hsp70s in longevity assurance and protein quality control ]]> https://biorxiv.org/content/10.1101/2020.06.25.170670v1?rss=1 Andersson, R. Eisele-Bürger, A. M. Hanzen, S. Vielfort, K. Öling, D. Eisele, F. Johansson, G. Gustafsson, T. Kvint, K. Nyström, T. 2020-06-25 doi:10.1101/2020.06.25.170670 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ Scalable learning of interpretable rules for the dynamic microbiome domain ]]> https://biorxiv.org/content/10.1101/2020.06.25.172270v1?rss=1 Maringanti, V. S. Bucci, V. Gerber, G. K. 2020-06-28 doi:10.1101/2020.06.25.172270 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ WNT6-ACC2-induced accumulation of triacylglycerol rich lipid droplets is exploited by Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2020.06.26.174110v1?rss=1 Brandenburg, J. Marwitz, S. Tazoll, S. C. Waldow, F. Kalsdorf, B. Vierbuchen, T. Scholzen, T. Gross, A. Goldenbaum, S. Hoelscher, A. Hein, M. Linnemann, L. Reimann, M. Kispert, A. Leitges, M. Rupp, J. Lange, C. Niemann, S. Behrends, J. Goldmann, T. Heine, H. Schaible, U. E. Hoelscher, C. Schwudke, D. Reiling, N. 2020-06-26 doi:10.1101/2020.06.26.174110 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Chromosome-scale assembly of the coral endosymbiont Symbiodinium microadriaticum genome provides insight into the unique biology of dinoflagellate chromosomes ]]> https://biorxiv.org/content/10.1101/2020.07.01.182477v1?rss=1 Nand, A. Zhan, Y. Salazar, O. R. Aranda, M. Voolstra, C. R. Dekker, J. 2020-07-02 doi:10.1101/2020.07.01.182477 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ KDM6B promotes oncogenic CDK4/6-pRB-E2F pathway via maintaining enhancer activation in high-risk neuroblastoma ]]> https://biorxiv.org/content/10.1101/2020.07.02.184986v1?rss=1 D'oto, A. Fang, J. Jin, H. Xu, B. Singh, S. Mullasseril, A. Jones, V. Von Butler, X. Cooke, B. Hu, D. Shohet, J. Murphy, A. Davidoff, A. YANG, J. 2020-07-03 doi:10.1101/2020.07.02.184986 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain ]]> https://biorxiv.org/content/10.1101/2020.07.04.187757v1?rss=1 Yurkovetskiy, L. Pascal, K. E. Tompkins-Tinch, C. Nyalile, T. Wang, Y. Baum, A. Diehl, W. E. Dauphin, A. Carbone, C. Veinotte, K. Egri, S. B. Schaffner, S. F. Lemieux, J. E. Munro, J. Sabeti, P. C. Kyratsous, C. Shen, K. Luban, J. 2020-07-04 doi:10.1101/2020.07.04.187757 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types. ]]> https://biorxiv.org/content/10.1101/2020.07.20.211276v1?rss=1 Saez-Atienzar, S. Bandres-Ciga, S. Langston, R. G. Kim, J. J. Choi, S. W. Reynolds, R. H. The International ALS Genomics Consortium, ITALSGEN, Abramzon, Y. Dewan, R. Ahmed, S. Landers, J. E. Chia, R. Ryten, M. Cookson, M. R. Nalls, M. A. Chio, A. Traynor, B. J. 2020-07-21 doi:10.1101/2020.07.20.211276 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Annotation of Chromatin States in 66 Complete Mouse Epigenomes During Development ]]> https://biorxiv.org/content/10.1101/2020.07.23.218552v1?rss=1 van der Velde, A. G. Fan, K. Tsuji, J. Moore, J. E. Purcaro, M. Pratt, H. Weng, Z. 2020-07-24 doi:10.1101/2020.07.23.218552 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Mycobacterium tuberculosis evasion of Guanylate Binding Protein-mediated host defense in mice requires the ESX1 secretion system. ]]> https://biorxiv.org/content/10.1101/2020.07.27.223362v1?rss=1 Olive, A. J. Smith, C. M. Baer, C. E. Coers, J. Sassetti, C. M. 2020-07-27 doi:10.1101/2020.07.27.223362 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ Structure and assembly of the diiron cofactor in the heme-oxygenase-like domain of the N-nitrosourea-producing enzyme SznF ]]> https://biorxiv.org/content/10.1101/2020.07.29.227702v1?rss=1 McBride, M. J. Pope, S. R. Hu, K. Slater, J. W. Okafor, C. D. Balskus, E. P. Bollinger, J. M. Boal, A. K. 2020-07-30 doi:10.1101/2020.07.29.227702 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ A Murine Model for the Transition of Streptococcus pneumoniae from Asymptomatic Colonizer to Systemic Pathogen ]]> https://biorxiv.org/content/10.1101/2020.07.29.227991v1?rss=1 Joma, B. J. Siwapornchai, N. Vanguri, V. K. Shrestha, A. Roggensack, S. E. Davidson, B. A. Tai, A. Hakansson, A. P. Meydani, S. N. Leong, J. M. Bou Ghanem, E. N. 2020-07-30 doi:10.1101/2020.07.29.227991 Cold Spring Harbor Laboratory Press 2020-07-30 <![CDATA[ The ESCRT protein CHMP5 restrains skeletal progenitor cell senescence by preserving endo-lysosomal-mitochondrial network ]]> https://biorxiv.org/content/10.1101/2020.08.03.233874v1?rss=1 Ge, X. He, L. Liu, H. Haynes, C. M. Shim, J.-H. 2020-08-04 doi:10.1101/2020.08.03.233874 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Melting dsDNA donor molecules potentiates precision genome editing in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.08.03.235036v1?rss=1 Ghanta, K. S. Mello, C. C. 2020-08-03 doi:10.1101/2020.08.03.235036 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.08.03.235143v1?rss=1 Chaves, D. A. Hui, D. Li, L. Moresco, J. J. Oh, M. E. Conte, D. Yates, J. R. Mello, C. C. Gu, W. 2020-08-04 doi:10.1101/2020.08.03.235143 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Separation and identification of permethylated glycan isomers by reversed phase nanoLC-NSI-MSn ]]> https://biorxiv.org/content/10.1101/2020.08.04.236349v1?rss=1 Kurz, S. Sheikh, M. O. Lu, S. Wells, L. Tiemeyer, M. 2020-08-04 doi:10.1101/2020.08.04.236349 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Protein arginine methyltransferase 5 promotes metastasis via enhancing EGFR transcription and modulating AKT1 activation by methylation ]]> https://biorxiv.org/content/10.1101/2020.08.12.246660v1?rss=1 Huang, L. Zhang, X.-O. Verdejo-Torres, O. Wigglesworth, K. Sun, X. Sallis, B. Moon, D. Huang, T. Rozen, E. Zhang, L. Wang, G. Shohet, J. M. Lee, M. M. Wu, J. Q. 2020-08-13 doi:10.1101/2020.08.12.246660 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ UPRmt scales mitochondrial network expansion with protein synthesis via mitochondrial import ]]> https://biorxiv.org/content/10.1101/2020.08.12.248161v1?rss=1 Shpilka, T. Du, Y. Yung, Q. Melber, A. Uma Naresh, N. Lavelle, J. Liu, P. Weidberg, H. Li, R. Yu, J. Zhu, L. J. Strittmatter, L. Haynes, C. M. 2020-08-14 doi:10.1101/2020.08.12.248161 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ A genome-wide screen in macrophages identifies new regulators of IFNγ-inducible MHCII that contribute to T cell activation ]]> https://biorxiv.org/content/10.1101/2020.08.12.248252v1?rss=1 Kiritsy, M. C. Ankley, L. M. Trombley, J. D. Huizinga, G. P. Lord, A. E. Orning, P. Elling, R. Fitzgerald, K. A. Olive, A. 2020-08-12 doi:10.1101/2020.08.12.248252 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Consequences of aneuploidy in human fibroblasts with trisomy 21 ]]> https://biorxiv.org/content/10.1101/2020.08.14.251082v1?rss=1 Hwang, S. Cavaliere, P. Li, R. Zhu, L. J. Dephoure, N. Torres, E. M. 2020-08-14 doi:10.1101/2020.08.14.251082 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ PIE-1 promotes SUMOylation and activation of HDAC1 during the C. elegans oogenesis ]]> https://biorxiv.org/content/10.1101/2020.08.17.253955v1?rss=1 Kim, H. Ding, Y.-H. Lu, S. Zuo, M.-Q. Conte, D. Dong, M.-Q. Mello, C. 2020-08-17 doi:10.1101/2020.08.17.253955 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ HDAC1 SUMOylation promotes Argonaute directed transcriptional silencing in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.08.17.254466v1?rss=1 Kim, H. Ding, Y.-H. Zhang, G. Yan, Y.-H. Conte, D. Dong, M.-Q. Mello, C. 2020-08-17 doi:10.1101/2020.08.17.254466 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Comparing Lifeact and Phalloidin for Super-resolution Imaging of Actin in Fixed Cells ]]> https://biorxiv.org/content/10.1101/2020.08.19.248898v1?rss=1 Mazloom-Farsibaf, H. Farzam, F. Fazel, M. Wester, M. J. Meddens, M. B. M. Lidke, K. A. 2020-08-20 doi:10.1101/2020.08.19.248898 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Host immunity increases Mycobacterium tuberculosis reliance on cytochrome bd oxidase ]]> https://biorxiv.org/content/10.1101/2020.08.21.260737v1?rss=1 Cai, Y. Jaecklein, E. Mackenzie, J. Papavinasasundaram, K. Olive, A. J. Chen, X. Steyn, A. J. C. Sassetti, C. M. 2020-08-21 doi:10.1101/2020.08.21.260737 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Characterization of Viral Insulins Reveals White Adipose Tissue Specific Effects in Mice ]]> https://biorxiv.org/content/10.1101/2020.08.21.261321v1?rss=1 Chrudinova, M. Moreau, F. Noh, H. L. Panikova, T. Zakova, L. Friedline, R. H. Valenzuela, F. A. Kim, J. K. Jiracek, J. Kahn, C. R. Altindis, E. 2020-08-22 doi:10.1101/2020.08.21.261321 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication Timing ]]> https://biorxiv.org/content/10.1101/2020.08.24.263459v1?rss=1 Wang, W. Klein, K. Proesmans, K. Yang, H. Marchal, C. Zhu, X. Borrman, T. Hastie, A. Weng, Z. Bechhoefer, J. Chen, C.-L. Gilbert, D. M. Rhind, N. 2020-08-24 doi:10.1101/2020.08.24.263459 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Methods for detecting PER2::LUCIFERASE bioluminescence rhythms in freely moving mice ]]> https://biorxiv.org/content/10.1101/2020.08.24.264531v1?rss=1 Martin-Burgos, B. Wang, W. William, I. Tir, S. Mohammad, I. Javed, R. Smith, S. Cui, Y. Smith, C. van der Vinne, V. Molyneux, P. C. Miller, S. C. Weaver, D. R. Leise, T. L. Harrington, M. 2020-08-24 doi:10.1101/2020.08.24.264531 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ PFRED: A computational platform for siRNA and antisense oligonucleotides design. ]]> https://biorxiv.org/content/10.1101/2020.08.25.265983v1?rss=1 Sciabola, S. Xi, H. Cruz, D. Cao, Q. Lawrence, C. Zhang, T. Rotstein, S. Hughes, J. D. Caffrey, D. R. Stanton, R. V. 2020-08-25 doi:10.1101/2020.08.25.265983 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation ]]> https://biorxiv.org/content/10.1101/2020.08.25.267666v1?rss=1 Imbalzano, A. N. Sharma, T. Witwicka, H. 2020-08-26 doi:10.1101/2020.08.25.267666 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Metformin enhances anti-mycobacterial responses by educating immunometabolic circuits of CD8+ T cells ]]> https://biorxiv.org/content/10.1101/2020.08.26.269217v1?rss=1 Bohme, J. Martinez, N. Li, S. Lee, A. Marzuki, M. Tizazu, A. Ackart, D. Frenkel, J. Todd, A. Lachmandas, E. Lum, J. Shihui, F. Ng, T. P. Lee, B. Larbi, A. Netea, M. Basaraba, R. van Crevel, R. Newell, E. Kornfeld, H. Singhal, A. 2020-08-27 doi:10.1101/2020.08.26.269217 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ dagLogo: an R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data ]]> https://biorxiv.org/content/10.1101/2020.08.28.254623v1?rss=1 Ou, J. Liu, H. Nirala, N. J. Stukalov, A. Acharya, U. Green, M. R. Zhu, L. J. 2020-08-31 doi:10.1101/2020.08.28.254623 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ A Liquid-to-Solid Phase Transition Enhances the Catalytic Activity of SARM1 ]]> https://biorxiv.org/content/10.1101/2020.08.28.272377v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@d9c222org.highwire.dtl.DTLVardef@588637org.highwire.dtl.DTLVardef@1d3a3d4org.highwire.dtl.DTLVardef@1a8e058_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Loring, H. S. Thompson, P. 2020-08-29 doi:10.1101/2020.08.28.272377 Cold Spring Harbor Laboratory Press 2020-08-29 <![CDATA[ Exploring the evolutionary history of kinetic stability in the alpha-lytic protease family ]]> https://biorxiv.org/content/10.1101/2020.08.30.274340v1?rss=1 Nixon, C. F. Lim, S. A. Sailer, Z. R. Zheludev, I. N. Gee, C. L. Kelch, B. A. Harms, M. J. Marqusee, S. 2020-08-31 doi:10.1101/2020.08.30.274340 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Ribosome inhibition by C9ORF72-ALS/FTD-associated poly-PR and poly-GR proteins revealed by cryo-EM ]]> https://biorxiv.org/content/10.1101/2020.08.30.274597v1?rss=1 Loveland, A. B. Svidritskiy, E. Susorov, D. Lee, S. Park, A. Demo, G. Gao, F.-B. Korostelev, A. A. 2020-08-31 doi:10.1101/2020.08.30.274597 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Deficient spermiogenesis in mice lacking Rlim ]]> https://biorxiv.org/content/10.1101/2020.08.31.275248v1?rss=1 Wang, F. Gervasi, M. G. Boskovic, A. Sun, F. Rinaldi, V. Yu, J. Wallingford, M. Tourzani, D. Mager, J. Zhu, L. Rando, O. Visconti, P. Strittmatter, L. Bach, I. 2020-09-01 doi:10.1101/2020.08.31.275248 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Degradation of ATFS-1 by LONP-1 promotes deleterious mitochondrial genome heteroplasmy ]]> https://biorxiv.org/content/10.1101/2020.09.01.274472v1?rss=1 Haynes, C. Yang, Q. Liu, P. Du, Y. Luk, K. Anderson, N. Lavelle, J. Zeinert, R. Chien, P. Wolfe, S. 2020-09-01 doi:10.1101/2020.09.01.274472 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Meaningful Effects in the Adolescent Brain Cognitive Development Study ]]> https://biorxiv.org/content/10.1101/2020.09.01.276451v1?rss=1 Dick, A. S. Watts, A. L. Heeringa, S. G. Lopez, D. A. Bartsch, H. Fan, C. C. Palmer, C. E. Reuter, C. Marshall, A. T. Haist, F. Hawes, S. Nichols, T. Barch, D. M. Jernigan, T. L. Garavan, H. Grant, S. Pariyadath, V. Hoffman, E. Neale, M. Paulus, M. P. Sher, K. Thompson, W. 2020-09-01 doi:10.1101/2020.09.01.276451 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Recombinant Paraprobiotics as a New Paradigm for Treating Gastrointestinal Nematode Parasites of Humans ]]> https://biorxiv.org/content/10.1101/2020.09.02.278341v1?rss=1 Li, H. Abraham, A. Gazzola, D. Hu, Y. Beamer, G. Flanagan, K. Soto, E. Rus, F. Mirza, Z. Draper, A. Vakalapudi, S. Stockman, C. Bain, P. Urban, J. F. Ostroff, G. R. Aroian, R. V. 2020-09-02 doi:10.1101/2020.09.02.278341 Cold Spring Harbor Laboratory Press 2020-09-02 <![CDATA[ Activated iPSC-microglia from C9orf72 ALS/FTD patients exhibit endosomal-lysosomal dysfunction ]]> https://biorxiv.org/content/10.1101/2020.09.03.277459v1?rss=1 Lorenzini, I. Alsop, E. Levy, J. Gittings, L. M. Rabichow, B. E. Lall, D. Moore, S. Bustos, L. Pevey, R. Burciu, C. Saul, J. McQuade, A. Tzioras, M. Mota, T. A. Logemann, A. Rose, J. Almeida, S. Gao, F.-B. Bowser, R. Spires-Jones, T. L. Blurton-Jones, M. Gendron, T. F. Baloh, R. H. Van Keuren-Jensen, K. Sattler, R. 2020-09-03 doi:10.1101/2020.09.03.277459 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ CD4 Effectors Need to Recognize Antigen Locally to Become Cytotoxic CD4 and Follicular Helper T Cells ]]> https://biorxiv.org/content/10.1101/2020.09.03.281998v1?rss=1 Devarajan, P. Vong, A. M. Castonguay, C. H. Bautista, B. L. Jones, M. C. Kugler-Umana, O. Kelly, K. A. Swain, S. L. 2020-09-03 doi:10.1101/2020.09.03.281998 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ NHR-49/PPAR-α and HLH-30/TFEB promote C. elegans host defense via a flavin-containing monooxygenase ]]> https://biorxiv.org/content/10.1101/2020.09.03.282087v1?rss=1 Wani, K. A. Goswamy, D. Taubert, S. Ratnappan, R. Ghazi, A. Irazoqui, J. E. 2020-09-03 doi:10.1101/2020.09.03.282087 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ CASCADES, a novel SOX2 super-enhancer associated long noncoding RNA, regulates cancer stem cell specification and differentiation in glioblastoma multiforme ]]> https://biorxiv.org/content/10.1101/2020.09.05.284349v1?rss=1 Shahzad, U. Li, C. Johnston, M. Wang, J. J. Sabha, N. Varn, F. S. Riemenschneider, A. Krumholtz, S. Meda, P. Smith, C. Karamchandani, J. Watts, J. K. Verhaak, R. G. W. Gallo, M. Rutka, J. T. Das, S. 2020-09-06 doi:10.1101/2020.09.05.284349 Cold Spring Harbor Laboratory Press 2020-09-06 <![CDATA[ Terminal Modification, Sequence, and Length Determine Small RNA Stability in Animals ]]> https://biorxiv.org/content/10.1101/2020.09.08.287979v1?rss=1 Gainetdinov, I. Colpan, C. Cecchini, K. Albosta, P. Jouravleva, K. Vega-Badillo, J. Lee, Y. Ozata, D. Zamore, P. D. 2020-09-08 doi:10.1101/2020.09.08.287979 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Bacterial processing of glucose modulates C. elegans lifespan and healthspan ]]> https://biorxiv.org/content/10.1101/2020.09.13.295451v1?rss=1 Kingsley, S. F. Seo, Y. Allen, C. Ghanta, K. S. Finkel, S. E. Tissenbaum, H. 2020-09-13 doi:10.1101/2020.09.13.295451 Cold Spring Harbor Laboratory Press 2020-09-13 <![CDATA[ Mitochondria surveillance systems trigger innate immune responses to bacterial pathogens via AMPK pathway in C. elegans ]]> https://biorxiv.org/content/10.1101/2020.09.17.301036v1?rss=1 Peng, D. Sun, M. Ju, S. Chen, H. Wang, S. Lin, J. Aroian, R. 2020-09-17 doi:10.1101/2020.09.17.301036 Cold Spring Harbor Laboratory Press 2020-09-17 <![CDATA[ Competition for MCM Loading at Origins Establishes Replication Timing Patterns ]]> https://biorxiv.org/content/10.1101/2020.09.20.305276v1?rss=1 Dukaj, L. Rhind, N. 2020-09-20 doi:10.1101/2020.09.20.305276 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ Single-cell characterization of transcriptomic heterogeneity in lymphoblastoid cell lines ]]> https://biorxiv.org/content/10.1101/2020.09.24.311886v1?rss=1 Sorelle, E. D. Dai, J. Zhou, J. Y. Giamberardino, S. Bailey, J. A. Gregory, S. Chan, C. Luftig, M. A. 2020-09-25 doi:10.1101/2020.09.24.311886 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ Synergistic effect of deoxynucleosides and AAV gene therapy for thymidine kinase 2 deficiency ]]> https://biorxiv.org/content/10.1101/2020.10.08.330969v1?rss=1 Lopez-Gomez, C. Sanchez-Quintero, M. J. Lee, E. J. Kleiner, G. Xie, J. Akman, H. O. Gao, G. Hirano, M. 2020-10-08 doi:10.1101/2020.10.08.330969 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Implantation and Gastrulation Abnormalities Characterize Early Embryonic Lethal Mouse Lines ]]> https://biorxiv.org/content/10.1101/2020.10.08.331587v1?rss=1 Yoon, Y. Riley, J. Gallant, J. Xu, P. Rivera-Perez, J. A. 2020-10-08 doi:10.1101/2020.10.08.331587 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Precision Cas9 Genome Editing in vivo with All-in-one, Self-targeting AAV Vectors ]]> https://biorxiv.org/content/10.1101/2020.10.09.333997v1?rss=1 Ibraheim, R. Tai, P. W. L. Mir, A. Javeed, N. Wang, J. Rodriguez, T. C. Nelson, S. Khokhar, E. Mintzer, E. Maitland, S. Cao, Y. Tsagkaraki, E. Wolfe, S. A. Wang, D. Pai, A. A. Xue, W. Gao, G. Sontheimer, E. J. 2020-10-09 doi:10.1101/2020.10.09.333997 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Elucidating the viral and host factors enabling the cross-species transmission of primate lentiviruses from simians to humans ]]> https://biorxiv.org/content/10.1101/2020.10.13.337303v1?rss=1 Tebit, D. Nickel, G. Gibson, R. Carpenter, C. Rodriguez, M. Hathaway, N. Bain, K. Reyes-Rodriguez, A. Bonogo, J. Canaday, D. McDonald, D. Bailey, J. Arts, E. 2020-10-13 doi:10.1101/2020.10.13.337303 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ CRISPR-enhanced human adipocyte 'browning' as cell therapy for metabolic disease ]]> https://biorxiv.org/content/10.1101/2020.10.13.337923v1?rss=1 Tsagkaraki, E. Nicoloro, S. De Souza, T. Solivan-Rivera, J. Desai, A. Shen, Y. Kelly, M. Guilherme, A. Henriques, F. Ibraheim, R. Amrani, N. Luk, K. Maitland, S. Friedline, R. H. Tauer, L. Hu, X. Kim, J. K. Wolfe, S. A. Sontheimer, E. J. Corvera, S. Czech, M. P. 2020-10-13 doi:10.1101/2020.10.13.337923 Cold Spring Harbor Laboratory Press 2020-10-13 <![CDATA[ Beta-cell specific insulin resistance promotes glucose-stimulated insulin hypersecretion ]]> https://biorxiv.org/content/10.1101/2020.10.15.338160v1?rss=1 Skovso, S. Panzhinskiy, E. Kolic, J. Dionne, D. A. Dai, X.-Q. Sharma, R. B. Elghazi, L. Cen, H. H. Ellis, C. E. Faulkner, K. Marcil, S. A. M. Overby, P. Noursadeghi, N. Hutchinson, D. Hu, X. Modi, H. Wildi, J. Botezelli, J. D. Noh, H. L. Suk, S. Gablaski, B. Bautista, A. Kim, R. Cras-Meneur, C. Flibotte, S. Sinha, S. Luciani, D. S. Nislow, C. Rideout, E. J. Cytrynbaum, E. N. Kim, J. Bernal-Mizrachi, E. Alonso, L. C. MacDonald, P. E. Johnson, J. D. 2020-10-15 doi:10.1101/2020.10.15.338160 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Translation-dependent and independent mRNA decay occur through mutually exclusive pathways that are defined by ribosome density during T Cell activation. ]]> https://biorxiv.org/content/10.1101/2020.10.16.341222v1?rss=1 Mercier, B. C. Labaronne, E. Cluet, D. Bicknell, A. Corbin, A. Guiguettaz, L. Aube, F. Modolo, L. Auboeuf, D. Moore, M. J. Ricci, E. P. 2020-10-17 doi:10.1101/2020.10.16.341222 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ The chromatin-binding domain of Ki-67 together with p53 protects human chromosomes from mitotic damage ]]> https://biorxiv.org/content/10.1101/2020.10.16.342352v1?rss=1 Garwain, O. Sun, X. Iyer, D. R. Li, R. Zhu, L. J. Kaufman, P. D. 2020-10-16 doi:10.1101/2020.10.16.342352 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Toll-9 interacts with Toll-1 to mediate a feedback loop during apoptosis-induced proliferation in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.10.19.346254v1?rss=1 Shields, A. Amcheslavsky, A. Brown, E. Nie, Y. Tanji, T. Ip, Y. T. Bergmann, A. 2020-10-20 doi:10.1101/2020.10.19.346254 Cold Spring Harbor Laboratory Press 2020-10-20 <![CDATA[ Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control ]]> https://biorxiv.org/content/10.1101/2020.10.24.352492v1?rss=1 Gideon, H. P. Hughes, T. K. Wadsworth, M. H. Tu, A. A. Gierahn, T. M. Hopkins, F. H. Wei, J.-R. Kummerlowe, C. Grant, N. L. Nargan, K. Phuah, J. Borish, H. J. Maiello, P. White, A. G. Ganchua, S. K. C. Myers, A. Ameel, C. Cochran, C. T. Nyquist, S. K. Peters, J. M. Tomko, J. A. Frye, L. J. Rosenberg, J. Shih, A. Chao, M. Scanga, C. Ordovas-Montanes, J. Berger, B. Mattila, J. T. Madansein, R. Love, J. C. Bryson, B. D. Lin, P. L. Leslie, A. Behar, S. M. Flynn, J. L. Fortune, S. M. Shalek, A. K. 2020-10-26 doi:10.1101/2020.10.24.352492 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ CaMKII binds both substrates and effectors at the active site ]]> https://biorxiv.org/content/10.1101/2020.10.25.354241v1?rss=1 Ozden, C. Sloutsky, R. Santos, N. Agnello, E. Gaubitz, C. Esposito, E. A. Lapinskas, E. Kelch, B. A. Garman, S. C. Hayashi, Y. Stratton, M. 2020-10-26 doi:10.1101/2020.10.25.354241 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Non-apoptotic enteroblast-specific role of the initiator caspase Dronc for development and homeostasis of the Drosophila intestine ]]> https://biorxiv.org/content/10.1101/2020.10.25.354431v1?rss=1 Lindblad, J. L. Tare, M. Amcheslavsky, A. Shields, A. Bergmann, A. 2020-10-26 doi:10.1101/2020.10.25.354431 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Pseudomonas aeruginosa PA14 biofilms produce R-bodies, extendable protein polymers with roles in host colonization and virulence ]]> https://biorxiv.org/content/10.1101/2020.10.26.356394v1?rss=1 Wang, B. Lin, Y.-C. Jo, J. Price-Whelan, A. Tao McDonald, S. Brown, L. M. Dietrich, L. E. 2020-10-27 doi:10.1101/2020.10.26.356394 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Aberrant Ca2+ homeostasis in adipocytes links inflammation to metabolic dysregulation in obesity ]]> https://biorxiv.org/content/10.1101/2020.10.28.360008v1?rss=1 Guney, E. Arruda, A. P. Parlakgul, G. Cagampan, E. Min, N. Lee, Y. Greene, L. Tsaousidou, E. Inouye, K. Han, M. S. Davis, R. J. Hotamisligil, G. S. 2020-10-29 doi:10.1101/2020.10.28.360008 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ ATF-4 and hydrogen sulfide signalling mediate longevity from inhibition of translation or mTORC1 ]]> https://biorxiv.org/content/10.1101/2020.11.02.364703v1?rss=1 Statzer, C. Venz, R. Bland, M. Robida-Stubbs, S. Meng, J. Patel, K. Emsley, R. Petrovic, D. Liu, P. Morantte, I. Haynes, C. Filipovic, M. Mair, W. B. Longchamp, A. Blackwell, T. K. Ewald, C. Y. 2020-11-02 doi:10.1101/2020.11.02.364703 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Genetic and Epigenetic Features of Promoters with Ubiquitous Chromatin Accessibility Support Ubiquitous Transcription of Cell-essential Genes ]]> https://biorxiv.org/content/10.1101/2020.11.02.364869v1?rss=1 Fan, K. Moore, J. E. Zhang, X.-o. Weng, Z. 2020-11-02 doi:10.1101/2020.11.02.364869 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Intracellular sterol sensing controls intestinal B cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.11.03.367177v1?rss=1 Trindade, B. C. Ceglia, S. Berthelette, A. Raso, F. Howley, K. Muppidi, J. R. Reboldi, A. 2020-11-05 doi:10.1101/2020.11.03.367177 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ SwarmTCR: a computational approach to predict the specificity of T Cell Receptors ]]> https://biorxiv.org/content/10.1101/2020.11.05.370312v1?rss=1 Ehrlich, R. Kamga, L. Gil, A. Luzuriaga, K. Selin, L. Ghersi, D. 2020-11-05 doi:10.1101/2020.11.05.370312 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Orthogonal CRISPR-Cas genome editing and efficient inhibition with anti-CRISPRs in zebrafish embryos ]]> https://biorxiv.org/content/10.1101/2020.11.07.372151v1?rss=1 Takasugi, P. R. Drage, E. P. Kanishka, S. N. Higbee, M. A. Gagnon, J. A. 2020-11-08 doi:10.1101/2020.11.07.372151 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ A cohort of Caenorhabditis species lacking the highly conserved let-7 microRNA ]]> https://biorxiv.org/content/10.1101/2020.11.10.377101v1?rss=1 Nelson, C. Ambros, V. 2020-11-11 doi:10.1101/2020.11.10.377101 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ The Tec kinase ITK differentially optimizes NFAT, NF-κB, and MAPK signaling during early T cell activation to regulate graded gene induction ]]> https://biorxiv.org/content/10.1101/2020.11.12.380725v1?rss=1 Gallagher, M. P. Conley, J. M. Vangala, P. Reboldi, A. Garber, M. Berg, L. J. 2020-11-14 doi:10.1101/2020.11.12.380725 Cold Spring Harbor Laboratory Press 2020-11-14 <![CDATA[ Mitochondrial respiration contributes to the interferon gamma response in antigen presenting cells ]]> https://biorxiv.org/content/10.1101/2020.11.22.393538v1?rss=1 Kiritsy, M. Mott, D. Behar, S. M. Sassetti, C. M. Olive, A. J. 2020-11-23 doi:10.1101/2020.11.22.393538 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Modelling the impact of clot fragmentation on the microcirculation after thrombectomy ]]> https://biorxiv.org/content/10.1101/2020.11.30.403808v1?rss=1 El-Bouri, W. K. MacGowan, A. Jozsa, T. I. Gounis, M. J. Payne, S. J. 2020-11-30 doi:10.1101/2020.11.30.403808 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ The Erythropoietin Receptor Stimulates Rapid Cycling and Formation of Larger Red Cells During Mouse and Human Erythropoiesis ]]> https://biorxiv.org/content/10.1101/2020.11.30.404780v1?rss=1 Hidalgo, D. Bejder, J. Pop, R. Gellatly, K. Scalf, S. M. Eastman, A. E. Chen, J.-J. Zhu, J. L. Heuberger, J. A. A. C. Guo, S. Koury, M. J. Nordsborg, N. B. Socolovsky, M. 2020-11-30 doi:10.1101/2020.11.30.404780 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice ]]> https://biorxiv.org/content/10.1101/2020.12.01.405514v1?rss=1 Smith, C. M. Baker, R. E. Proulx, M. K. Mishra, B. B. Long, J. E. Park, S. W. Lee, H.-N. Kiritsy, M. C. Bellerose, M. M. Olive, A. J. Murphy, K. C. Papavinasasundaram, K. Boehm, F. J. Reames, C. J. Meade, R. K. Hampton, B. K. Linnertz, C. Ehrt, S. Schnappinger, D. Pardo-Manuel de Villena, F. Ferris, M. T. Ioerger, T. R. Sassetti, C. M. 2020-12-01 doi:10.1101/2020.12.01.405514 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Viral Packaging ATPases Utilize a Glutamate Switch to Couple ATPase Activity and DNA Translocation ]]> https://biorxiv.org/content/10.1101/2020.12.01.406595v1?rss=1 Pajak, J. Atz, R. Hilbert, B. J. Morais, M. Kelch, B. A. Jardine, P. Arya, G. 2020-12-02 doi:10.1101/2020.12.01.406595 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Scalable production of tissue-like vascularised liver organoids from human PSCs. ]]> https://biorxiv.org/content/10.1101/2020.12.02.406835v1?rss=1 Harrison, S. P. Sillar, R. Tanaka, Y. Xiang, Y. Patterson, B. Kempf, H. Melum, E. Asrud, K. Chollet, M. E. Andersen, E. Sandset, P. M. Baumgarten, S. Bonanini, F. Kurek, D. Mathapati, S. Almaas, R. Sharma, K. Wilson, S. R. Skottvoll, F. S. Boger, I. C. Bogen, I. L. Nyman, T. A. Wu, J. J. Bezrouk, A. Cizkova, D. Mokry, J. Zweigerdt, R. Park, I.-H. Sullivan, G. J. 2020-12-02 doi:10.1101/2020.12.02.406835 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ A Budding Yeast Model for Human Disease Mutations in the EXOSC2 Cap Subunit of the RNA Exosome ]]> https://biorxiv.org/content/10.1101/2020.12.06.413658v1?rss=1 Sterrett, M. C. Enyenihi, L. Leung, S. W. Hess, L. Strassler, S. E. Farchi, D. Lee, R. S. Withers, E. S. Kremsky, I. Baker, R. E. Basrai, M. A. Van Hoof, A. Fasken, M. B. Corbett, A. H. 2020-12-07 doi:10.1101/2020.12.06.413658 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Distinct Neuropeptide-Receptor Modules Regulate a Sex-Specific Behavioral Response to a Pheromone ]]> https://biorxiv.org/content/10.1101/2020.12.09.417857v1?rss=1 Reilly, D. K. McGlame, E. J. Vandewyer, E. Robidoux, A. N. Northcott, H. T. Joyce, W. Alkema, M. J. Gegear, R. J. Beets, I. Srinivasan, J. 2020-12-10 doi:10.1101/2020.12.09.417857 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2020.12.15.422930v1?rss=1 Mangkalaphiban, K. He, F. Ganesan, R. Wu, C. Baker, R. Jacobson, A. 2020-12-15 doi:10.1101/2020.12.15.422930 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice ]]> https://biorxiv.org/content/10.1101/2020.12.15.422970v1?rss=1 Liu, P. Liang, S. Zheng, C. Mintzer, E. Zhao, Y. G. Ponnienselvan, K. Mir, A. Sontheimer, E. J. Gao, G. Flotte, T. R. Wolfe, S. Xue, W. 2020-12-16 doi:10.1101/2020.12.15.422970 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Global community effect: large-scale cooperation yields collective survival of differentiating embryonic stem cells ]]> https://biorxiv.org/content/10.1101/2020.12.20.423651v1?rss=1 Daneshpour, H. van den Bersselaar, P. Youk, H. 2020-12-21 doi:10.1101/2020.12.20.423651 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome compaction and individualization ]]> https://biorxiv.org/content/10.1101/2020.12.20.423657v1?rss=1 Choppakatla, P. Dekker, B. Cutts, E. Vannini, A. Dekker, J. Funabiki, H. 2020-12-20 doi:10.1101/2020.12.20.423657 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization ]]> https://biorxiv.org/content/10.1101/2020.12.22.424026v1?rss=1 Walker, M. D. Giese, G. E. Holdorf, A. D. Bhattacharya, S. Diot, C. Horowitz, B. B. Garcia-Gonzalez, A. P. Lee, Y.-U. Leland, T. Li, X. Mirza, Z. Na, H. Nanda, S. Ponomarova, O. Zhang, H. Zhang, J. Yilmaz, L. S. Walhout, M. 2020-12-23 doi:10.1101/2020.12.22.424026 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Systematic evaluation of chromosome conformation capture assays ]]> https://biorxiv.org/content/10.1101/2020.12.26.424448v1?rss=1 Akgol Oksuz, B. Yang, L. Abraham, S. Venev, S. V. Krietenstein, N. Parsi, K. M. Ozadam, H. Oomen, M. E. Nand, A. Mao, H. Genga, R. M. J. Maehr, R. Rando, O. Mirny, L. Gibcus, J. H. Dekker, J. 2020-12-27 doi:10.1101/2020.12.26.424448 Cold Spring Harbor Laboratory Press 2020-12-27 <![CDATA[ Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation ]]> https://biorxiv.org/content/10.1101/2020.12.29.424751v1?rss=1 Demo, G. Loveland, A. B. Svidritskiy, E. Gamper, H. B. Hou, Y.-M. Korostelev, A. A. 2020-12-29 doi:10.1101/2020.12.29.424751 Cold Spring Harbor Laboratory Press 2020-12-29 <![CDATA[ Quantifying the regulatory role of individual transcription factors in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.01.04.425191v1?rss=1 Guharajan, S. Chhabra, S. Parisutham, V. Brewster, R. C. 2021-01-04 doi:10.1101/2021.01.04.425191 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ ERK signaling licenses SKN-1A/NRF1 for proteasome production and proteasomal stress resistance ]]> https://biorxiv.org/content/10.1101/2021.01.04.425272v1?rss=1 Zhang, P. Qu, H.-Y. Wu, Z. Na, H. Hourihan, J. Zhang, F. Zhu, F. Isik, M. Walhout, A. J. M. Feng, Y.-X. Blackwell, K. 2021-01-04 doi:10.1101/2021.01.04.425272 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Human antibody immune responses are personalized by selective removal of MHC-II peptide epitopes ]]> https://biorxiv.org/content/10.1101/2021.01.15.426750v1?rss=1 Gutierrez-Gonzalez, M. Fahad, A. S. Ardito, M. Nanaware, P. Lu, L. Normandin, E. Madan, B. Tivin, J. Coates, E. Henry, A. R. Laboune, F. Graham, B. S. Douek, D. C. Ledgerwood, J. E. Mascola, J. R. Martin, W. D. Stern, L. De Groot, A. S. DeKosky, B. J. 2021-01-17 doi:10.1101/2021.01.15.426750 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Formation and Spontaneous Long-Term Repatterning of Headless Planarian Flatworms ]]> https://biorxiv.org/content/10.1101/2021.01.15.426822v1?rss=1 Bischof, J. LaPalme, J. Miller, K. Morokuma, J. Williams, K. Fields, C. Levin, M. 2021-01-17 doi:10.1101/2021.01.15.426822 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Multiple RNA regulatory pathways coordinate the activity and expression pattern of a conserved germline RNA-binding protein ]]> https://biorxiv.org/content/10.1101/2021.01.15.426877v1?rss=1 Albarqi, M. M. Y. Ryder, S. P. 2021-01-17 doi:10.1101/2021.01.15.426877 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Endometrial Gap Junction Expression - Early Indicators of Endometriosis and Integral to Invasiveness ]]> https://biorxiv.org/content/10.1101/2021.01.25.428135v1?rss=1 Nicholson, B. Kirma, N. B. Chen, C.-W. Chavez, J. B. Lin, L.-L. Wang, C.-M. Hsu, Y.-T. Hart, M. J. Ruan, J. Gillette, L. H. Burney, R. O. Schenken, R. S. Robinson, R. D. Osmulski, P. Gaczynska, M. 2021-01-26 doi:10.1101/2021.01.25.428135 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Single calcium channel nanodomains drive presynaptic calcium entry at individual lamprey reticulospinal presynaptic terminals ]]> https://biorxiv.org/content/10.1101/2021.02.02.429388v1?rss=1 Ramachandran, S. Rodriguez, S. Potcoava, M. Alford, S. 2021-02-02 doi:10.1101/2021.02.02.429388 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Host tropism determination by convergent evolution of immunological evasion in the Lyme disease system ]]> https://biorxiv.org/content/10.1101/2021.02.09.430532v1?rss=1 Hart, T. M. Dupuis, A. P. Tufts, D. M. Blom, A. M. Starkey, S. Rego, R. O. M. Ram, S. Kraiczy, P. Kramer, L. D. Diuk-Wasser, M. A. Kolokotronis, S.-O. Lin, Y.-P. 2021-02-10 doi:10.1101/2021.02.09.430532 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Quantifying and Mitigating Motor Phenotypes Induced by Antisense Oligonucleotides in the Central Nervous System ]]> https://biorxiv.org/content/10.1101/2021.02.14.431096v1?rss=1 Moazami, M. P. Rembetsy-Brown, J. M. Wang, F. Krishnamurthy, P. M. Weiss, A. Marosfoi, M. King, R. M. Motwani, M. Gray-Edwards, H. Fitzgerald, K. A. Brown, R. H. Watts, J. K. 2021-02-15 doi:10.1101/2021.02.14.431096 Cold Spring Harbor Laboratory Press 2021-02-15 <![CDATA[ YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation ]]> https://biorxiv.org/content/10.1101/2021.02.18.431832v1?rss=1 He, L. Pratt, H. Wei, F. Gao, M. Weng, Z. Struhl, K. 2021-02-18 doi:10.1101/2021.02.18.431832 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Dopaminergic Ric GTPase activity impacts amphetamine sensitivity and sleep quality in a dopamine transporter-dependent manner in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.02.18.431857v1?rss=1 Fagan, R. R. Kearney, P. J. Luethi, D. Bolden, N. C. Sitte, H. H. Emery, P. Melikian, H. E. 2021-02-18 doi:10.1101/2021.02.18.431857 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ CD4 T cell help prevents CD8 T cell exhaustion and promotes control of Mycobacterium tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2021.02.23.432461v1?rss=1 Lu, Y.-J. Barreira-Silva, P. Boyce, S. Powers, J. Cavallo, K. Behar, S. M. 2021-02-23 doi:10.1101/2021.02.23.432461 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ IFNγ and iNOS-mediated alterations in the bone marrow and thymus and its impact on Mycobacterium avium-induced thymic atrophy ]]> https://biorxiv.org/content/10.1101/2021.02.23.432464v1?rss=1 Barreira-Silva, P. Melo-Miranda, R. Nobrega, C. Roque, S. Serre-Miranda, C. Borges, M. de Sa Calcada, D. Behar, S. M. Appelberg, R. Correia-Neves, M. 2021-02-24 doi:10.1101/2021.02.23.432464 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Proanthocyanidin-enriched cranberry extract induces resilient bacterial community dynamics in a gnotobiotic mouse model ]]> https://biorxiv.org/content/10.1101/2021.02.25.432903v1?rss=1 Neto, C. C. Mortzfeld, B. M. Turbitt, J. R. Bhattarai, S. K. Yeliseyev, V. DiBenedetto, N. Bry, L. M. Bucci, V. 2021-02-25 doi:10.1101/2021.02.25.432903 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Somatic piRNAs and Transposons are Differentially Regulated During Skeletal Muscle Atrophy and Programmed Cell Death ]]> https://biorxiv.org/content/10.1101/2021.03.02.433533v1?rss=1 Tsuji, J. Thomson, T. Brown, C. Ghosh, S. Theurkauf, W. Weng, Z. Schwartz, L. M. 2021-03-02 doi:10.1101/2021.03.02.433533 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence ]]> https://biorxiv.org/content/10.1101/2021.03.03.433592v1?rss=1 Gutierrez, J. I. Brittingham, G. P. Karadeniz, Y. B. Tran, K. D. Dutta, A. Holehouse, A. S. Peterson, C. L. Holt, L. J. 2021-03-03 doi:10.1101/2021.03.03.433592 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ The landscape of accessible chromatin in quiescent and post-myocardial infarction cardiac fibroblasts ]]> https://biorxiv.org/content/10.1101/2021.03.03.433814v1?rss=1 Li, C. Sun, J. Liu, Q. Dodlapati, S. Ming, H. Wang, L. Li, Y. Li, R. Jiang, Z. Francis, J. Fu, X. 2021-03-04 doi:10.1101/2021.03.03.433814 Cold Spring Harbor Laboratory Press 2021-03-04 <![CDATA[ Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2021.03.07.434227v1?rss=1 Muecksch, F. Weisblum, Y. Barnes, C. Schmidt, F. Schaefer-Babajew, D. Lorenzi, J. Flyak, A. DeLaitsch, A. Huey-Tubman, K. Hou, S. Schiffer, C. Gaebler, C. Wang, Z. Da Silva, J. Poston, D. Finkin, S. Cho, A. Cipolla, M. Oliveira, T. Millard, K. Ramos, V. Gazumyan, A. Rutkowska, M. Caskey, M. Nussenzweig, M. Bjorkman, P. Hatziioannou, T. Bieniasz, P. 2021-03-08 doi:10.1101/2021.03.07.434227 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ RNA-silencing induces target gene relocalization toward a specialized nuage domain ]]> https://biorxiv.org/content/10.1101/2021.03.09.434681v1?rss=1 Mello, C. Yang, Y. Grunwald, D. Priess, J. 2021-03-11 doi:10.1101/2021.03.09.434681 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ FastTomo: A SerialEM Script for Collecting Electron Tomography Data ]]> https://biorxiv.org/content/10.1101/2021.03.16.435675v1?rss=1 Xu, A. Xu, C. 2021-03-17 doi:10.1101/2021.03.16.435675 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Loss of Nuclear DNA ligase III Can Revert PARP Inhibitor Resistance in BRCA1-deficient Cells by Increasing DNA Replication Stress ]]> https://biorxiv.org/content/10.1101/2021.03.24.436323v1?rss=1 Paes Dias, M. Tripathi, V. Heijden, I. v. d. Cong, K. Manolika, E.-M. Galanos, P. Bhin, J. Gogola, E. Annunziato, S. Lieftink, C. Andujar-Sanchez, M. Ven, M. v. d. Chakrabarty, S. Beijersbergen, R. L. Bartkova, J. Rottenberg, S. Cantor, S. Bartek, J. Chaudhuri, A. R. Jonkers, J. 2021-03-24 doi:10.1101/2021.03.24.436323 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Regenerating vascular mural cells in zebrafish fin blood vessels are not derived from pre-existing ones and differentially require pdgfrb signaling for their development ]]> https://biorxiv.org/content/10.1101/2021.03.27.437334v1?rss=1 Siekmann, A. F. Leonard, E. V. Figueroa, R. Bussmann, J. Amigo, J. D. Lawson, N. D. 2021-03-28 doi:10.1101/2021.03.27.437334 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Critical contribution of 3' non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA ]]> https://biorxiv.org/content/10.1101/2021.03.29.437276v1?rss=1 Duan, Y. Veksler-Lublinsky, I. Ambros, V. 2021-03-29 doi:10.1101/2021.03.29.437276 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ Conserved and context-dependent roles for Pdgfrb signaling during zebrafish vascular mural cell development ]]> https://biorxiv.org/content/10.1101/2021.03.29.437552v1?rss=1 Ando, K. Shih, Y.-H. Ebarasi, L. Grosse, A. Portman, D. Chiba, A. Mattonet, K. Gerri, C. Stainier, D. Y. R. Mochizuki, N. Fukuhara, S. Betsholtz, C. Lawson, N. D. 2021-03-29 doi:10.1101/2021.03.29.437552 Cold Spring Harbor Laboratory Press 2021-03-29 <![CDATA[ The nucleoporin Nup50 activates the Ran guanyl-nucleotide exchange factor RCC1 to promote mitotic NPC assembly ]]> https://biorxiv.org/content/10.1101/2021.03.31.437874v1?rss=1 Holzer, G. De Magistris, P. Gramminger, C. Sachdev, R. Magalska, A. Schooley, A. Scheufen, A. Lennartz, B. Tatarek-Nossol, M. Lue, H. Linder, M. I. Kutay, U. Preisinger, C. Moreno-Andres, D. Antonin, W. 2021-04-02 doi:10.1101/2021.03.31.437874 Cold Spring Harbor Laboratory Press 2021-04-02 <![CDATA[ Cell-type specific circadian bioluminescence rhythms recorded from Dbp reporter mice reveal circadian oscillator misalignment ]]> https://biorxiv.org/content/10.1101/2021.04.04.438413v1?rss=1 Smith, C. B. van der Vinne, V. McCartney, E. Stowie, A. C. Leise, T. L. Martin-Burgos, B. Molyneux, P. C. Garbutt, L. A. Brodsky, M. H. Davidson, A. J. Harrington, M. E. Dallmann, R. Weaver, D. R. 2021-04-05 doi:10.1101/2021.04.04.438413 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ The testis-specific transcription factor TCFL5 responds to A MYBto elaborate the male meiotic program in placental mammals ]]> https://biorxiv.org/content/10.1101/2021.04.04.438419v1?rss=1 Ozata, D. M. Yu, T. Cecchini, K. Mou, H. Arif, A. Colpan, C. Adriano Biasini, A. Gainetdinov, I. de Rooij, D. G. Weng, Z. Zamore, P. 2021-04-05 doi:10.1101/2021.04.04.438419 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins ]]> https://biorxiv.org/content/10.1101/2021.04.06.438740v1?rss=1 Sharma, S. Zhou, R. Wan, L. Song, K. Xu, C. Li, Y. Liao, M. 2021-04-08 doi:10.1101/2021.04.06.438740 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Oncogenic BRAF Induces Whole-Genome Doubling Through Suppression of Cytokinesis ]]> https://biorxiv.org/content/10.1101/2021.04.08.439023v1?rss=1 Darp, R. Vittoria, M. A. Ganem, N. J. Ceol, C. J. 2021-04-09 doi:10.1101/2021.04.08.439023 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy ]]> https://biorxiv.org/content/10.1101/2021.04.08.439092v1?rss=1 Koh, E.-I. Ruecker, N. Proulx, M. K. Soni, V. Murphy, K. C. Papavinasasundaram, K. G. Reames, C. J. Trujillo, C. Zaveri, A. Zimmerman, M. D. Aslebagh, R. Baker, R. E. Shaffer, S. A. Guinn, K. M. Fitzgerald, M. Dartois, V. A. Ehrt, S. Hung, D. T. Ioerger, T. R. Rubin, E. Rhee, K. Y. Schnappinger, D. Sassetti, C. M. 2021-04-09 doi:10.1101/2021.04.08.439092 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Controlling gene expression timing through gene regulatory architecture ]]> https://biorxiv.org/content/10.1101/2021.04.09.439163v1?rss=1 Ali, M. Z. Brewster, R. C. 2021-04-10 doi:10.1101/2021.04.09.439163 Cold Spring Harbor Laboratory Press 2021-04-10 <![CDATA[ Global mRNA and chromatin accessibility profiling elucidate how HIV-1 perturbs ILC and NK cell subsets ]]> https://biorxiv.org/content/10.1101/2021.04.20.440368v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@9d6be2org.highwire.dtl.DTLVardef@115f0e8org.highwire.dtl.DTLVardef@17b1a28org.highwire.dtl.DTLVardef@f262e9_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, Y. Lifshitz, L. Silverstein, N. Mintzer, E. Luk, K. StLouis, P. Brehm, M. Wolfe, S. Deeks, S. Luban, J. 2021-04-20 doi:10.1101/2021.04.20.440368 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Locating Macromolecular Assemblies in Cells by 2D Template Matching with cisTEM ]]> https://biorxiv.org/content/10.1101/2021.04.20.440648v1?rss=1 Lucas, B. A. Himes, B. A. Xue, L. Grant, T. Mahamid, J. Grigorieff, N. 2021-04-21 doi:10.1101/2021.04.20.440648 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model ]]> https://biorxiv.org/content/10.1101/2021.04.25.441198v1?rss=1 Hammer, M. Huisman, M. Rigano, A. Boehm, U. Chambers, J. J. Gaudreault, N. North, A. J. Pimentel, J. A. Sudar, D. Bajcsy, P. Brown, C. M. Corbett, A. D. Faklaris, O. Lacoste, J. Laude, A. Nelson, G. Nitschke, R. Farzam, F. Smith, C. Grunwald, D. Strambio-De-Castillia, C. 2021-04-26 doi:10.1101/2021.04.25.441198 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ In vitro efficacy of gentamicin against multidrug-resistant Neisseria gonorrhoeae: synergy of three gentamicin antimicrobial combinations ]]> https://biorxiv.org/content/10.1101/2021.04.26.441563v1?rss=1 Li, X. Le, W.-J. Lou, X. Wang, B.-w. Genco, C. A. Rice, P. A. Su, X.-H. 2021-04-27 doi:10.1101/2021.04.26.441563 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Heterogeneous pdgfrβ+ cells regulate coronary vessel development and revascularization during heart regeneration ]]> https://biorxiv.org/content/10.1101/2021.04.27.441161v1?rss=1 Lien, C.-L. Kapuria, S. Bai, H. Fierros, J. Huang, Y. Ma, F. Yoshida, T. Aguayo, A. Kok, F. Wiens, K. Yip, J. McCain, M. Pellegrini, M. Nagashima, M. Hitchcock, P. Lawson, N. Harrison, M. 2021-04-28 doi:10.1101/2021.04.27.441161 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Astrocytic GABA Transporter controls sleep by modulating GABAergic signaling in Drosophila circadian neurons ]]> https://biorxiv.org/content/10.1101/2021.04.27.441638v1?rss=1 Chaturvedi, R. Stork, T. Yuan, C. Freeman, M. R. Emery, P. 2021-04-27 doi:10.1101/2021.04.27.441638 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Simultaneous profiling of multiple chromatin proteins in the same cells ]]> https://biorxiv.org/content/10.1101/2021.04.27.441642v1?rss=1 Gopalan, S. Wang, Y. Harper, N. W. Garber, M. Fazzio, T. G. 2021-04-28 doi:10.1101/2021.04.27.441642 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Ultraspecific somatic SNV and indel detection in single neurons using primary template-directed amplification ]]> https://biorxiv.org/content/10.1101/2021.04.30.442032v1?rss=1 Luquette, L. J. Miller, M. B. Zhou, Z. Bohrson, C. L. Galor, A. Lodato, M. A. Gawad, C. West, J. Walsh, C. A. Park, P. J. 2021-05-01 doi:10.1101/2021.04.30.442032 Cold Spring Harbor Laboratory Press 2021-05-01 <![CDATA[ The tiny, conserved zinc-finger protein GTSF1helps PIWI proteins achieve their full catalytic potential ]]> https://biorxiv.org/content/10.1101/2021.05.04.442675v1?rss=1 Arif, A. Ozata, D. M. Andersson, C. Izumi, N. Tomari, Y. Zamore, P. D. 2021-05-04 doi:10.1101/2021.05.04.442675 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Kinesin-3 mediated delivery of presynaptic neurexin stabilizes growing dendritic spines and postsynaptic components in vivo ]]> https://biorxiv.org/content/10.1101/2021.05.11.443328v1?rss=1 Oliver, D. Ramachandran, S. Philbrook, A. Lambert, C. M. Nguyen, K. C. Q. Hall, D. H. Francis, M. 2021-05-11 doi:10.1101/2021.05.11.443328 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Programming large target genomic deletion and concurrent insertion via a prime editing-based method: PEDAR ]]> https://biorxiv.org/content/10.1101/2021.05.12.443800v1?rss=1 100 bp). Thus, developing a method to accurately delete insertions/duplications and repair the deletion junction could improve the scope of gene therapies. Here, we engineer a novel gene editor, PE-Cas9, by conjugating Cas9 nuclease to reverse transcriptase. Combined with two prime editing guide RNAs (pegRNAs) targeting complementary DNA strands, PE-Cas9 can direct the replacement of a genomic fragment, ranging from to ~1-kb to >10-kb, with a desired sequence at the target site without requiring an exogenous DNA template. In a reporter cell line, this PE-Cas9-based deletion and repair (PEDAR) method restored mCherry expression through in-frame deletion of a disrupted GFP sequence. We further show that PEDAR efficiency could be enhanced by using pegRNAs with high cleavage activity or increasing transfection efficiency. In tyrosinemia mice, PEDAR removed a 1.38-kb pathogenic insertion within the Fah gene and precisely repaired the deletion junction to restore FAH expression in liver. This study highlights PEDAR as a tool for correcting pathogenic mutations. ]]> Jiang, T. Zhang, X.-O. Weng, Z. Xue, W. 2021-05-13 doi:10.1101/2021.05.12.443800 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ A catalog of transcription start sites across 115 human tissue and cell types ]]> https://biorxiv.org/content/10.1101/2021.05.12.443890v1?rss=1 Moore, J. E. Zhang, X.-O. Elhajjajy, S. I. Fan, K. Reese, F. Mortazavi, A. Weng, Z. 2021-05-13 doi:10.1101/2021.05.12.443890 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Human genetic diversity modifies therapeutic gene editing off-target potential ]]> https://biorxiv.org/content/10.1101/2021.05.20.445054v1?rss=1 Cancellieri, S. Zeng, J. Lin, L. Y. Masillo, F. Nguyen, A. Bombieri, N. Ciuculescu, F. Katta, V. Tsai, S. Armant, M. Giugno, R. Bauer, D. E. Pinello, L. 2021-05-21 doi:10.1101/2021.05.20.445054 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ ZNF146/OZF and ZNF507 target LINE-1 sequences ]]> https://biorxiv.org/content/10.1101/2021.05.24.445350v1?rss=1 Creamer, K. M. Larsen, E. C. Lawrence, J. B. 2021-05-24 doi:10.1101/2021.05.24.445350 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ SCARF1-induced efferocytosis plays an immunomodulatory role in humans, and autoantibodies targeting SCARF1 are produced in patients with systemic lupus erythematosus ]]> https://biorxiv.org/content/10.1101/2021.05.24.445434v1?rss=1 Jorge, A. M. Lao, T. Kim, R. Licciardi, S. Elkhoury, J. Luster, A. D. Means, T. K. Ramirez-Ortiz, Z. G. 2021-05-25 doi:10.1101/2021.05.24.445434 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Non-neutralizing antibodies targeting the immunogenic regions of HIV-1 envelope reduce mucosal infection and virus burden in humanized mice ]]> https://biorxiv.org/content/10.1101/2021.05.24.445493v1?rss=1 Hioe, C. E. Li, G. Liu, X. Tsahouridis, O. He, X. Funaki, M. Klingler, J. Tang, A. F. Feyznezhad, R. Heindel, D. W. Wang, X.-H. Spencer, D. A. Hu, G. Satija, N. Prevost, J. Finzi, A. Hessell, A. Wang, S. Lu, S. Chen, B. K. Zolla-Pazner, S. Upadhyay, C. Alvarez, R. A. Su, L. 2021-05-24 doi:10.1101/2021.05.24.445493 Cold Spring Harbor Laboratory Press 2021-05-24 <![CDATA[ Distinct allosteric mechanisms of first-generation MsbA inhibitors ]]> https://biorxiv.org/content/10.1101/2021.05.25.445681v1?rss=1 Thelot, F. A. Zhang, W. Song, K. Xu, C. Huang, J. Liao, M. 2021-05-25 doi:10.1101/2021.05.25.445681 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ PGC1α Regulates the Endothelial Response to Fluid Shear Stress via Telomerase Reverse Transcriptase Control of Heme Oxygenase-1 ]]> https://biorxiv.org/content/10.1101/2021.05.26.445830v1?rss=1 Kant, S. Tran, K.-V. Kvandova, M. Caliz, A. D. Yoo, H.-J. Learnard, H. Craige, S. M. Hall, J. D. Jimenez, J. M. St. Hilaire, C. Schulz, E. Kroller-Schon, S. Keaney, J. F. 2021-05-27 doi:10.1101/2021.05.26.445830 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Widespread occurrence of hybrid internal-terminal exons in human transcriptomes ]]> https://biorxiv.org/content/10.1101/2021.05.27.446076v1?rss=1 Fiszbein, A. McGurk, M. Calvo-Roitberg, E. Kim, G. Burge, C. Pai, A. A. 2021-05-29 doi:10.1101/2021.05.27.446076 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications ]]> https://biorxiv.org/content/10.1101/2021.05.31.446382v1?rss=1 Rigano, A. Ehmsen, S. Ozturk, S. U. Ryan, J. Balashov, A. Hammer, M. Kirli, K. Bellve, K. Boehm, U. Brown, C. M. Chambers, J. J. Coleman, R. A. Cosolo, A. Faklaris, O. Fogarty, K. Guilbert, T. Hamacher, A. B. Itano, M. S. Keeley, D. P. Kunis, S. Lacoste, J. Laude, A. Ma, W. Marcello, M. Montero-Llopis, P. Nelson, G. Nitschke, R. Pimentel, J. A. Weidtkamp-Peters, S. Park, P. J. Alver, B. Grunwald, D. Strambio-De-Castillia, C. 2021-05-31 doi:10.1101/2021.05.31.446382 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP ]]> https://biorxiv.org/content/10.1101/2021.05.31.446434v1?rss=1 Carbone, C. E. Loveland, A. B. Gamper, H. Hou, Y.-M. Demo, G. Korostelev, A. A. 2021-05-31 doi:10.1101/2021.05.31.446434 Cold Spring Harbor Laboratory Press 2021-05-31 <![CDATA[ Non-Coding Genetic Analysis Implicates Interleukin 18 Receptor Accessory Protein 3'UTR in Amyotrophic Lateral Sclerosis ]]> https://biorxiv.org/content/10.1101/2021.06.03.446863v1?rss=1 25,000 variants in untranslated regions of 6,139 amyotrophic lateral sclerosis (ALS) whole-genomes and 70,403 non-ALS controls. We identified Interleukin-18 Receptor Accessory Protein (IL18RAP) 3'UTR variants significantly enriched in non-ALS genomes, replicated in an independent cohort, and associated with a five-fold reduced risk of developing ALS. Variant IL18RAP 3'UTR reduces mRNA stability and the binding of RNA-binding proteins. Variant IL18RAP 3'UTR further dampens neurotoxicity of human iPSC-derived C9orf72-ALS microglia that depends on NF-{kappa}B signaling. Therefore, the variant IL18RAP 3'UTR provides survival advantage for motor neurons co-cultured with C9-ALS microglia. The study reveals direct genetic evidence and therapeutic targets for neuro-inflammation, and emphasizes the importance of non-coding genetic association studies. One Sentence SummaryNon-coding genetic variants in IL-18 receptor 3UTR decrease ALS risk by modifying IL-18-NF-{kappa}B signaling in microglia. ]]> Eitan, C. Barkan, E. Olender, T. van Eijk, K. R. Moisse, M. Farhan, S. M. K. Siany, A. Hung, S.-T. Yacovzada, N. Cooper-Knock, J. Kenna, K. P. van der Spek, R. A. A. Sproviero, W. Al Khleifat, A. Iacoangeli, A. Shatunov, A. S. Jones, A. R. Chapnik, E. Rothschild, D. Weissbrod, O. Werneburg, S. Schafer, D. P. Brown, R. H. Shaw, P. J. Van Damme, P. van den Berg, L. H. Phatnani, H. P. Segal, E. Ichida, J. K. Al-Chalabi, A. Veldink, J. H. Project MinE ALS Sequencing Consortium, NYGC ALS Consortium, Hornstein, E. 2021-06-05 doi:10.1101/2021.06.03.446863 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ Presynaptic Gq-coupled receptors drive biphasic dopamine transporter trafficking that modulates dopamine clearance and motor function ]]> https://biorxiv.org/content/10.1101/2021.06.04.447129v1?rss=1 Kearney, P. J. Conklin, T. Martin, G. E. Melikian, H. E. 2021-06-05 doi:10.1101/2021.06.04.447129 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ Quantification of Antisense Oligonucleotides by Splint Ligation and Quantitative Polymerase Chain Reaction ]]> https://biorxiv.org/content/10.1101/2021.06.05.447195v1?rss=1 Shin, M. Krishnamurthy, P. M. Watts, J. K. 2021-06-05 doi:10.1101/2021.06.05.447195 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ High-affinity, neutralizing antibodies to SARS-CoV-2 can be made in the absence of T follicular helper cells ]]> https://biorxiv.org/content/10.1101/2021.06.10.447982v1?rss=1 Chen, J. S. Chow, R. D. Song, E. Mao, T. Israelow, B. Kamath, K. Bozekowski, J. Haynes, W. A. Filler, R. B. Menasche, B. L. Wei, J. Alfajaro, M. M. Song, W. Peng, L. Carter, L. Weinstein, J. S. Gowthaman, U. Chen, S. Craft, J. Shon, J. C. Iwasaki, A. Wilen, C. B. Eisenbarth, S. C. 2021-06-11 doi:10.1101/2021.06.10.447982 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Structural organization of the C1b projection within the ciliary central apparatus ]]> https://biorxiv.org/content/10.1101/2021.06.16.448709v1?rss=1 Cai, K. Zhao, Y. Zhao, L. Phan, N. Witman, G. Nicastro, D. 2021-06-17 doi:10.1101/2021.06.16.448709 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Dystrophin regulates peripheral circadian SRF signalling ]]> https://biorxiv.org/content/10.1101/2021.06.23.449492v1?rss=1 Betts, C. A. Jagannath, A. van Westering, T. Bowerman, M. Banerjee, S. Meng, J. Falzarano, M. S. Cravo, L. McClorey, G. Meijboom, K. Bhomra, A. Lim, C. Rinaldi, C. Counsell, J. Chwalenia, K. O'Donovan, E. Saleh, A. Gait, M. J. Morgan, J. Ferlini, A. Foster, R. Wood, M. 2021-06-23 doi:10.1101/2021.06.23.449492 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ MethodsJ2: A Software Tool to Improve Microscopy Methods Reporting ]]> https://biorxiv.org/content/10.1101/2021.06.23.449674v1?rss=1 Ryan, J. Pengo, T. Rigano, A. Montero-Llopis, P. Itano, M. S. Cameron, L. Marques, G. Strambio-De-Castillia, C. Sanders, M. A. Brown, C. M. 2021-06-24 doi:10.1101/2021.06.23.449674 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Mitogen Kinase Kinase (MKK7) controls cytokine production in vitro and in vivo in mice ]]> https://biorxiv.org/content/10.1101/2021.06.25.449967v1?rss=1 Caliz, A. D. Yoo, H.-J. Vertii, A. Tournier, C. Davis, R. J. Keaney, J. F. Kant, S. 2021-06-25 doi:10.1101/2021.06.25.449967 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ MicroRNA-202 prevents precocious spermatogonial differentiation and meiotic initiation during mouse spermatogenesis ]]> https://biorxiv.org/content/10.1101/2021.06.27.449895v1?rss=1 Chen, J. Gao, C. Lin, X. Ning, Y. He, W. Zheng, C. Zhang, D. Yan, L. Jiang, B. Zhao, Y. Hossen, M. A. Han, C. 2021-06-28 doi:10.1101/2021.06.27.449895 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Modeling site-specific nucleotide biases affecting Himar1 transposon insertion frequencies in TnSeq datasets ]]> https://biorxiv.org/content/10.1101/2021.07.01.450749v1?rss=1 Choudhery, S. Brown, A. J. Akusobi, C. D. Rubin, E. J. Sassetti, C. M. Ioerger, T. R. 2021-07-01 doi:10.1101/2021.07.01.450749 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Members of the CUGBP Elav-Like Family of RNA-Binding Proteins are Expressed in Distinct Populations of Primary Sensory Neurons ]]> https://biorxiv.org/content/10.1101/2021.07.05.451166v1?rss=1 Grlickova-Duzevik, E. Michael, M. McGrath-Conwell, A. Neufeld, P. K. Reimonn, T. M. Molliver, D. C. Harrison, B. J. 2021-07-06 doi:10.1101/2021.07.05.451166 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Distinct mitochondrial remodeling during early cardiomyocyte development in a human-based stem cell model ]]> https://biorxiv.org/content/10.1101/2021.07.07.451436v1?rss=1 Mostafavi, S. Balafkan, N. Pettersen, I. K. N. Nido, G. S. Siller, R. Tzoulis, C. Sullivan, G. Bindoff, L. A. 2021-07-07 doi:10.1101/2021.07.07.451436 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Age-associated changes to neuronal dynamics involve a loss of inhibitory signaling in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.07.07.451497v1?rss=1 Wirak, G. S. Florman, J. Alkema, M. J. Connor, C. W. Gabel, C. V. 2021-07-08 doi:10.1101/2021.07.07.451497 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Complete genomic and epigenetic maps of human centromeres ]]> https://biorxiv.org/content/10.1101/2021.07.12.452052v1?rss=1 Altemose, N. Logsdon, G. Bzikadze, A. V. Sidhwani, P. Langley, S. A. Caldas, G. V. Hoyt, S. J. Uralsky, L. Ryabov, F. D. Shew, C. Sauria, M. E. G. Borchers, M. Gershman, A. Mikheenko, A. Shepelev, V. A. Dvorkina, T. Kunyavskaya, O. Vollger, M. R. Rhie, A. McCartney, A. M. Asri, M. Lorig-Roach, R. Shafin, K. Aganezov, S. Olson, D. Gomes de Lima, L. Potapova, T. Hartley, G. A. Haukness, M. Kerpedjiev, P. Gusev, F. Tigyi, K. Brooks, S. Y. Young, A. Nurk, S. Koren, S. Salama, S. Paten, B. Rogaev, E. I. Streets, A. M. Karpen, G. H. Dernburg, A. Sullivan, B. 2021-07-13 doi:10.1101/2021.07.12.452052 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ c-Jun N-terminal kinase (JNK) signaling contributes to cystic burden in polycystic kidney disease ]]> https://biorxiv.org/content/10.1101/2021.07.15.452451v1?rss=1 Smith, A. O. Jonassen, J. A. Preval, K. M. Davis, R. J. Pazour, G. J. 2021-07-15 doi:10.1101/2021.07.15.452451 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ TAF4b transcription networks regulating early oocyte differentiation ]]> https://biorxiv.org/content/10.1101/2021.07.18.452838v1?rss=1 Gura, M. A. Relovska, S. Abt, K. M. Seymour, K. A. Wu, T. Kaya, H. Turner, J. Fazzio, T. G. Freiman, R. N. 2021-07-18 doi:10.1101/2021.07.18.452838 Cold Spring Harbor Laboratory Press 2021-07-18 <![CDATA[ The ASC Speck And NLRP3 Inflammasome Function Are Spatially And Temporally Distinct ]]> https://biorxiv.org/content/10.1101/2021.07.19.452947v1?rss=1 Harton, J. Nagar, A. Rahman, T. 2021-07-19 doi:10.1101/2021.07.19.452947 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ The epithelial-specific ER stress sensor IRE1β enables host-microbiota crosstalk to affect colon goblet cell development ]]> https://biorxiv.org/content/10.1101/2021.07.28.453864v1?rss=1 Grey, M. J. De Luca, H. Ward, D. V. Kreulen, I. A. M. Foley, S. E. Thiagarajah, J. R. McCormick, B. A. Turner, J. R. Lencer, W. I. 2021-07-28 doi:10.1101/2021.07.28.453864 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ A cohesin traffic pattern genetically linked to gene regulation ]]> https://biorxiv.org/content/10.1101/2021.07.29.454218v1?rss=1 Valton, A.-L. Venev, S. V. Mair, B. Khokhar, E. Tong, A. H. Usaj, M. Chan, K. S. Pai, A. Moffat, J. Dekker, J. 2021-07-30 doi:10.1101/2021.07.29.454218 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ Evolution of protection after maternal immunization for respiratory syncytial virus in cotton rats ]]> https://biorxiv.org/content/10.1101/2021.07.30.454440v1?rss=1 Blanco, J. C. G. McGinnes-Cullen, L. Kamali, A. Sylla, F. Boukhavalova, M. Morrison, T. 2021-07-30 doi:10.1101/2021.07.30.454440 Cold Spring Harbor Laboratory Press 2021-07-30 <![CDATA[ Low-level overexpression of wild type TDP-43 causes late-onset, progressive neurodegeneration and paralysis in mice ]]> https://biorxiv.org/content/10.1101/2021.08.04.455119v1?rss=1 Yang, C. Qiao, T. Yu, J. Wang, H. Guo, Y. Salameh, J. Metterville, J. Parsi, S. Brown, R. H. Cai, H. Xu, Z. 2021-08-04 doi:10.1101/2021.08.04.455119 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Sterol scarcity primes p38 immune defenses through a TIR-1/SARM1 phase transition ]]> https://biorxiv.org/content/10.1101/2021.08.05.455128v1?rss=1 Peterson, N. D. Icso, J. D. Salisbury, J. E. Rodriguez, T. C. Thompson, P. Pukkila-Worley, R. 2021-08-06 doi:10.1101/2021.08.05.455128 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers ]]> https://biorxiv.org/content/10.1101/2021.08.05.455340v1?rss=1 Spracklin, G. Abdennur, N. A. Imakaev, M. Chowdhury, N. Pradhan, S. Mirny, L. Dekker, J. 2021-08-06 doi:10.1101/2021.08.05.455340 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment ]]> https://biorxiv.org/content/10.1101/2021.08.12.455997v1?rss=1 Kotliar, D. Colubri, A. 2021-08-13 doi:10.1101/2021.08.12.455997 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Type I interferon modulates Langerhans cell ADAM17 to promote photosensitivity in lupus ]]> https://biorxiv.org/content/10.1101/2021.08.18.456792v1?rss=1 Li, T. M. Veiga, K. R. Schwartz, N. Chinenov, Y. Oliver, D. J. Lora, J. Jabbari, A. Liu, Y. Shipman, W. D. Sandoval, M. J. Sollohub, I. F. Ambler, W. G. Rashighi, M. Krueger, J. G. Anandasabapathy, N. Blobel, C. P. Lu, T. T. 2021-08-18 doi:10.1101/2021.08.18.456792 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Loops, TADs, Compartments, and Territories are Elastic and Robust to Dramatic Nuclear Volume Swelling ]]> https://biorxiv.org/content/10.1101/2021.08.20.457153v1?rss=1 Sanders, J. T. Golloshi, R. Terry, P. H. Nash, D. G. Xu, Y. Dekker, J. McCord, R. P. 2021-08-23 doi:10.1101/2021.08.20.457153 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Biochemically distinct cohesin complexes mediate positioned loops between CTCF sites and dynamic loops within chromatin domains ]]> https://biorxiv.org/content/10.1101/2021.08.24.457555v1?rss=1 Liu, Y. Dekker, J. 2021-08-26 doi:10.1101/2021.08.24.457555 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ A novel multifunctional role for Hsp70 in binding post-translational modifications on clients ]]> https://biorxiv.org/content/10.1101/2021.08.25.457671v1?rss=1 Nitika, Zheng, B. Ruan, L. Kline, J. Sikora, J. Torres, M. T. Wang, Y. Takakuwa, J. Huguet, R. Klemm, C. Segarra, V. A. Winters, M. Pryciak, P. Thorpe, P. H. Tatebayashi, K. Li, R. Fornelli, L. Truman, A. 2021-08-25 doi:10.1101/2021.08.25.457671 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Development of a flexible split prime editor using truncated reverse transcriptase ]]> https://biorxiv.org/content/10.1101/2021.08.26.457801v1?rss=1 6.3 kb) in vivo. Although PE can be split into two fragments and delivered using dual adeno-associated viruses (AAVs), choice of split sites within Cas9 - which affects editing efficiency - is limited due to the large size of PE. Furthermore, the potential effect of overexpressing RT in mammalian cells is largely unknown. Here, we developed a compact PE with complete deletion of the RNase H domain of reverse transcriptase (RT), which showed comparable editing to full-length PE. Using compact PE, we tested the effect of 4 different Cas9 split sites and found that the Glu 573 split site supports robust editing (up to 93% of full-length PE). The compact PE, but not PE2, abolished its binding to eRF1 and showed minimal effect on stop codon readthrough, which therefore might reduce the effects on protein biosynthesis. This study identifies a safe and efficient compact PE2 that enables flexible split-PE design to facilitate efficient delivery in vivo and advance the utility of prime editing. ]]> Xue, W. Zheng, C. LIANG, S. Liu, P. Liu, B. Kwan, S. Wolfe, S. 2021-08-27 doi:10.1101/2021.08.26.457801 Cold Spring Harbor Laboratory Press 2021-08-27 <![CDATA[ A Cytosolic Reductase Pathway is Required for Complete N-Glycosylation of an STT3B-Dependent Acceptor Site. ]]> https://biorxiv.org/content/10.1101/2021.08.31.458373v1?rss=1 van Lith, M. Pringle, M. A. Fleming, B. Gaeta, G. Im, J. Gilmore, J. R. Bulleid, N. J. 2021-09-01 doi:10.1101/2021.08.31.458373 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Ether Lipid Biosynthesis Promotes Lifespan Extension and Enables Diverse Prolongevity Paradigms ]]> https://biorxiv.org/content/10.1101/2021.09.02.457410v1?rss=1 Cedillo, L. Li, S. Ahsan, F. Emans, S. Adedoja, A. Dao, K. Li, Z. Peterson, N. Watrous, J. Jain, M. Das, S. Pukkila-Worley, R. Soukas, A. A. 2021-09-03 doi:10.1101/2021.09.02.457410 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Glial TGFβ activity promotes axon survival in peripheral nerves ]]> https://biorxiv.org/content/10.1101/2021.09.02.458753v1?rss=1 Lassetter, A. Corty, M. Barria, R. Sheehan, A. Aicher, S. Fox, A. N. Hill, J. Freeman, M. 2021-09-03 doi:10.1101/2021.09.02.458753 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Single-nucleus transcriptomic analyses reveal microglial activation underlying cerebellar degeneration in Ataxia Telangiectasia ]]> https://biorxiv.org/content/10.1101/2021.09.09.459619v1?rss=1 Lai, J. Kim, J. Jeffries, A. M. Tolles, A. Chittenden, T. W. Buckley, P. G. Yu, T. W. Lodato, M. A. Lee, E. A. 2021-09-09 doi:10.1101/2021.09.09.459619 Cold Spring Harbor Laboratory Press 2021-09-09 <![CDATA[ Integrated molecular analysis identifies a conserved pericyte gene signature in zebrafish ]]> https://biorxiv.org/content/10.1101/2021.09.13.459947v1?rss=1 Lawson, N. D. Shih, Y.-H. Grosse, A. Portman, D. Idrizi, F. 2021-09-13 doi:10.1101/2021.09.13.459947 Cold Spring Harbor Laboratory Press 2021-09-13 <![CDATA[ Dysregulation of the Tweak/Fn14 pathway in skeletal muscle of spinal muscular atrophy mice ]]> https://biorxiv.org/content/10.1101/2021.09.13.460053v1?rss=1 Meijboom, K. E. McFall, E. Anthony, D. Edwards, B. Kubinski, S. Hazell, G. Ahlskog, N. Claus, P. Davies, K. E. Wood, M. Bowerman, M. 2021-09-15 doi:10.1101/2021.09.13.460053 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Single residue substitution in protamine 1 disrupts sperm genome packaging and embryonic development in mice ]]> https://biorxiv.org/content/10.1101/2021.09.16.460631v1?rss=1 Moritz, L. Schon, S. Rabbani, M. Sheng, Y. Pendlebury, D. Agrawal, R. Sultan, C. Jorgensen, K. Zheng, X. Diehl, A. Ragunathan, K. Hu, Y.-C. Nandakumar, J. Li, J. Orwig, K. Redding, S. Hammoud, S. 2021-09-16 doi:10.1101/2021.09.16.460631 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Neutralizing antibody-independent immunity to SARS-CoV-2 in hamsters and hACE-2 transgenic mice immunized with a RBD/Nucleocapsid fusion protein ]]> https://biorxiv.org/content/10.1101/2021.09.16.460663v1?rss=1 Castro, J. Fumagalli, M. Hojo-Souza, N. Azevedo, P. Salazar, N. Rattis, B. Ramos, S. Faustino, L. Almeida, G. Oliveira, L. Marcal, T. Augusto, M. Magalhaes, R. D. M. Cassaro, B. Burle, G. Doro, D. Kalil, J. Durigon, E. L. Salazar, A. Caballero, O. Machado, A. da Silva, J. da Fonseca, F. Fernandes, A. P. Teixeira, S. Gazzinelli, R. 2021-09-16 doi:10.1101/2021.09.16.460663 Cold Spring Harbor Laboratory Press 2021-09-16 <![CDATA[ Small molecule screen employing patient-derived iPS hepatocytes identifies LRRK2 as a novel therapeutic target for Alpha1 Antitrypsin Deficiency ]]> https://biorxiv.org/content/10.1101/2021.09.17.460732v1?rss=1 Kent, D. Ng, S. S. Khoshkenar, P. Syanda, A. M. Chao Zheng, L. Zieger, M. Greer, C. Hatch, S. B. Segal, J. M. Blackford, S. J. I. Chowdary, V. Ismali, T. Danovi, D. Sahdeo, S. Ebner, D. Mueller, C. Rashid, S. T. 2021-09-17 doi:10.1101/2021.09.17.460732 Cold Spring Harbor Laboratory Press 2021-09-17 <![CDATA[ Cryo-EM structures reveal high-resolution mechanism of a DNA polymerase sliding clamp loader ]]> https://biorxiv.org/content/10.1101/2021.09.23.461575v1?rss=1 Gaubitz, C. Liu, X. Pajak, J. Stone, N. P. Hayes, J. A. Demo, G. Kelch, B. A. 2021-09-23 doi:10.1101/2021.09.23.461575 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Flygenvectors: The spatial and temporal structure of neural activity across the fly brain ]]> https://biorxiv.org/content/10.1101/2021.09.25.461804v1?rss=1 Schaffer, E. S. Mishra, N. Whiteway, M. R. Li, W. Vancura, M. B. Freedman, J. Patel, K. B. Voleti, V. Paninski, L. Hillman, E. M. C. Abbott, L. Axel, R. 2021-09-26 doi:10.1101/2021.09.25.461804 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Dcp2 C-terminal Cis-Binding Elements Control Selective Targeting of the Decapping Enzyme by Forming Distinct Decapping Complexes ]]> https://biorxiv.org/content/10.1101/2021.10.01.462794v1?rss=1 He, F. Wu, C. Jacobson, A. 2021-10-01 doi:10.1101/2021.10.01.462794 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Molecular structure and conformation of stereocilia tip-links elucidated by cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2021.10.01.462800v1?rss=1 Elferich, J. Clark, S. Ge, J. Goehring, A. Matsui, A. Gouaux, E. 2021-10-01 doi:10.1101/2021.10.01.462800 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites ]]> https://biorxiv.org/content/10.1101/2021.10.11.463518v1?rss=1 Pratt, H. E. Andrews, G. R. Phalke, N. Purcaro, M. J. van der Velde, A. G. Moore, J. E. Weng, Z. 2021-10-12 doi:10.1101/2021.10.11.463518 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ A Recombinant Multivalent Vaccine (rCpa1) Induces Protection for C57BL/6 and HLA Transgenic Mice Against Pulmonary Infection with Both Species of Coccidioides ]]> https://biorxiv.org/content/10.1101/2021.10.20.465232v1?rss=1 Campuzano, A. Pentakota, K. D. Liao, Y.-R. Zhang, H. Wiederhold, N. P. Ostroff, G. Hung, C.-Y. 2021-10-21 doi:10.1101/2021.10.20.465232 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ ARP2/3- and resection-coupled genome reorganization facilitates translocations ]]> https://biorxiv.org/content/10.1101/2021.10.22.465487v1?rss=1 Zagelbaum, J. Schooley, A. Zhao, J. Schrank, B. R. Callen, E. Zha, S. Gottesman, M. Nussenzweig, A. Rabadan, R. Dekker, J. Gautier, J. 2021-10-24 doi:10.1101/2021.10.22.465487 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Comparative analysis reveals the long-term co-evolutionary history of parvoviruses and vertebrates. ]]> https://biorxiv.org/content/10.1101/2021.10.25.465781v1?rss=1 Campbell, M. A. Loncar, S. Kotin, R. Gifford, R. J. 2021-10-26 doi:10.1101/2021.10.25.465781 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Cell wall damage reveals spatial flexibility in peptidoglycan synthesis and a non-redundant role for RodA in mycobacteria ]]> https://biorxiv.org/content/10.1101/2021.10.26.465981v1?rss=1 Melzer, E. S. Kado, T. Garcia-Heredia, A. Gupta, K. R. Meniche, X. Morita, Y. S. Sassetti, C. M. Rego, E. H. M. Siegrist, M. S. 2021-10-26 doi:10.1101/2021.10.26.465981 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex ]]> https://biorxiv.org/content/10.1101/2021.10.29.466335v1?rss=1 Akey, C. Singh, D. Ouch, C. Echeverria, I. Nudelman, I. Varberg, J. M. Yu, Z. Fang, F. Shi, Y. Wang, J. Saltzberg, D. Song, K. Xu, C. Gumbart, J. Suslov, S. Unruh, J. Jaspersen, S. L. Chait, B. Sali, A. Menendez-Martinez, J. Ludke, S. J. Villa, E. Rout, M. 2021-10-29 doi:10.1101/2021.10.29.466335 Cold Spring Harbor Laboratory Press 2021-10-29 <![CDATA[ Allosteric modulation of the SARS-CoV-2 spike conformation ]]> https://biorxiv.org/content/10.1101/2021.10.29.466470v1?rss=1 Diaz-Salinas, M. A. Li, Q. Ejemel, M. Wang, Y. Munro, J. B. 2021-11-01 doi:10.1101/2021.10.29.466470 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Leishmania amazonensis sabotages host cell SUMOylation for intracellular survival ]]> https://biorxiv.org/content/10.1101/2021.11.03.467107v1?rss=1 Okuda, K. Franco, M. C. Yasunaga, A. Gazzinelli, R. Rabinovitch, M. Cherry, S. Silverman, N. 2021-11-04 doi:10.1101/2021.11.03.467107 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Age-induced P-bodies become detrimental and shorten the lifespan of yeast ]]> https://biorxiv.org/content/10.1101/2021.11.05.467477v1?rss=1 Choi, J. Wang, S. Li, Y. Hao, N. Zid, B. M. 2021-11-05 doi:10.1101/2021.11.05.467477 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Bacteria modulate tamoxifen-induced death via host fatty acid metabolism ]]> https://biorxiv.org/content/10.1101/2021.11.05.467497v1?rss=1 Diot, C. Garcia-Gonzalez, A. P. Vieira, A. F. Walker, M. Honeywell, M. Doyle, H. Rivera, Y. Na, H. Zhang, H. Lee, M. Olsen, C. P. Walhout, A. J. M. 2021-11-07 doi:10.1101/2021.11.05.467497 Cold Spring Harbor Laboratory Press 2021-11-07 <![CDATA[ WormCat 2.0 defines characteristics and conservation of poorly annotated genes in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2021.11.11.467968v1?rss=1 Higgins, D. P. Weisman, C. M. Lui, D. S. D'Agostino, F. A. Walker, A. K. 2021-11-13 doi:10.1101/2021.11.11.467968 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Determinants of precocious B-cell aging in European adolescences living with perinatally acquired HIV-1 after over 10 years of suppressive therapy ]]> https://biorxiv.org/content/10.1101/2021.11.11.468189v1?rss=1 Ruggiero, A. Pascucci, G. R. Cotugno, N. Dominguez-Rodriguez, S. Stefano, R. Tagarro Garcia, A. Rojo, P. Foster, C. Bamford, A. De Rossi, A. Nastouli, E. Nigel, K. Elena, M. Fatou, B. Smolen, K. K. Ozonoff, A. Katherine, L. Steen, H. Carlo, G. Goulder, P. Rossi, P. Levy, O. Pahwa, S. Palma, P. included in the manuscript, 2021-11-13 doi:10.1101/2021.11.11.468189 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Microglial phagocytosis dysfunction during stroke is prevented by rapamycin ]]> https://biorxiv.org/content/10.1101/2021.11.12.468358v1?rss=1 Beccari, S. Sierra-Torre, V. Valero, J. Garcia-Zaballa, M. Carretero-Guillen, A. Capetillo-Zarate, E. Domercq, M. Huguet, P. Ramonet, D. Osman, A. Han, W. Dominguez, C. Faust, T. E. Touzani, O. Boya, P. Schafer, D. Marino, G. Canet-Soulas, E. Blomgren, K. Plaza-Zabala, A. Sierra, A. 2021-11-13 doi:10.1101/2021.11.12.468358 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Protection of mice against experimental cryptococcosis by synthesized peptides delivered in glucan particles ]]> https://biorxiv.org/content/10.1101/2021.11.12.468465v1?rss=1 Specht, C. Homan, E. J. Lee, C. K. Mou, Z. Gomez, C. L. Hester, M. M. Abraham, A. Rus, F. Ostroff, G. Levitz, S. M. 2021-11-13 doi:10.1101/2021.11.12.468465 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Tunable Transcription Factor Library for Robust Quantification of Gene Expression Dynamics in E. coli ]]> https://biorxiv.org/content/10.1101/2021.11.16.468742v1?rss=1 Parisutham, V. Chhabra, S. Ali, Z. Brewster, R. C. 2021-11-19 doi:10.1101/2021.11.16.468742 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Stimulation of immunity-linked genes by membrane disruption is linked to Golgi function and the ARF-1 GTPase ]]> https://biorxiv.org/content/10.1101/2021.11.16.468795v1?rss=1 Welsh, C. M. Smulan, L. J. Fanelli, M. J. Lui, D. S. Walker, A. K. 2021-11-16 doi:10.1101/2021.11.16.468795 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance ]]> https://biorxiv.org/content/10.1101/2021.11.30.470632v1?rss=1 Zephyr, J. Rao, D. N. Vo, S. V. Henes, M. Kosovrasti, K. Matthew, A. N. Hedger, A. K. Timm, J. Chan, E. T. Ali, A. Yilmaz, N. K. Schiffer, C. A. 2021-11-30 doi:10.1101/2021.11.30.470632 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Chromosome-level reference genomes for two strains of Caenorhabditis briggsae: an improved platform for comparative genomics ]]> https://biorxiv.org/content/10.1101/2021.12.01.470807v1?rss=1 Stevens, L. Moya, N. D. Tanny, R. E. Gibson, S. B. Tracey, A. Na, H. Zhan, Y. Chitrakar, R. Dekker, J. Walhout, A. J. Baugh, L. R. Andersen, E. C. 2021-12-01 doi:10.1101/2021.12.01.470807 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ HSC-independent definitive hematopoietic cells persist into adult life ]]> https://biorxiv.org/content/10.1101/2021.12.02.468909v1?rss=1 Kobayashi, M. Wei, H. Yamanashi, T. Shih, D. J. Portilho, N. A. Cornelius, S. Valiente, N. Nishida, C. Zheng, W. J. Kang, J. Seita, J. Wu, J. Yoshimoto, M. 2021-12-02 doi:10.1101/2021.12.02.468909 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ The HIV-1 capsid core is an opportunistic nuclear import receptor ]]> https://biorxiv.org/content/10.1101/2021.12.02.470925v1?rss=1 Xue, G. Yu, H. J. Goh, S. L. Gres, A. T. Guney, M. H. Sarafianos, S. G. Luban, J. KewalRamani, V. N. 2021-12-02 doi:10.1101/2021.12.02.470925 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ Progressive polysomal association of Upf1, Upf2, and Upf3 as ribosomes traverse mRNA coding regions ]]> https://biorxiv.org/content/10.1101/2021.12.03.471156v1?rss=1 Ganesan, R. Mangkalaphiban, K. Baker, R. E. He, F. Jacobson, A. 2021-12-03 doi:10.1101/2021.12.03.471156 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ SWR1C catalyzes H2A.Z deposition by coupling ATPase activity to the nucleosome acidic patch ]]> https://biorxiv.org/content/10.1101/2021.12.08.471801v1?rss=1 Gioacchini, N. Peterson, C. L. 2021-12-09 doi:10.1101/2021.12.08.471801 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Neurexins in serotonergic neurons regulate serotonin transmission and complex mouse behaviors ]]> https://biorxiv.org/content/10.1101/2021.12.09.471904v1?rss=1 Cheung, A. Matsui, A. Abe, M. Sakimura, K. Sasaoka, T. Uemura, T. Imamura Kawasawa, Y. Futai, K. 2021-12-09 doi:10.1101/2021.12.09.471904 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Quantitative Structural Analysis of Influenza Virus by Cryo-electron Tomography and Convolutional Neural Networks ]]> https://biorxiv.org/content/10.1101/2021.12.09.472010v1?rss=1 View larger version (63K): org.highwire.dtl.DTLVardef@983f56org.highwire.dtl.DTLVardef@1664734org.highwire.dtl.DTLVardef@1cce73dorg.highwire.dtl.DTLVardef@1617998_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Huang, Q. Y. Song, K. Xu, C. Bolon, D. Wang, J. P. Finberg, R. W. Schiffer, C. A. Somasundaran, M. 2021-12-09 doi:10.1101/2021.12.09.472010 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Adenine Base Editing in vivo with a Single Adeno-Associated Virus Vector ]]> https://biorxiv.org/content/10.1101/2021.12.13.472434v1?rss=1 Zhang, H. Bamidele, N. Liu, P. Ojelabi, O. Gao, X. D. Rodriguez, T. Cheng, H. Wolfe, S. A. Xue, W. Sontheimer, E. J. 2021-12-13 doi:10.1101/2021.12.13.472434 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ A reference induced pluripotent stem cell line for large-scale collaborative studies ]]> https://biorxiv.org/content/10.1101/2021.12.15.472643v1?rss=1 View larger version (84K): org.highwire.dtl.DTLVardef@cef106org.highwire.dtl.DTLVardef@31d5d8org.highwire.dtl.DTLVardef@1ce6d8corg.highwire.dtl.DTLVardef@17a19d2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pantazis, C. B. Yang, A. Lara, E. McDonough, J. A. Blauwendraat, C. Peng, L. Oguro, H. Zou, J. Sebesta, D. Pratt, G. Cross, E. Blockwick, J. Buxton, P. Kinner-Bibeau, L. Medura, C. Tompkins, C. Hughes, S. Santiana, M. Faghri, F. Nalls, M. A. Vitale, D. Qi, Y. A. Ramos, D. M. Anderson, K. Stadler, J. Narayan, P. Papademetriou, J. Reilly, L. Nelson, M. P. Aggarwal, S. Rosen, L. U. Kirwan, P. Pisupati, V. Coon, S. L. Scholz, S. W. Coccia, E. Sarrafha, L. Ahfeldt, T. Funes, S. Bosco, D. A. Beccari, M. S. Cleveland, D. W. Zanellati, M. C. Basundra, R. Des 2021-12-17 doi:10.1101/2021.12.15.472643 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ MDITRE: scalable and interpretable machine learning for predicting host status from temporal microbiome dynamics ]]> https://biorxiv.org/content/10.1101/2021.12.15.472835v1?rss=1 Maringanti, V. S. Bucci, V. Gerber, G. K. 2021-12-17 doi:10.1101/2021.12.15.472835 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ RFX6-mediated dysregulation defines human β cell dysfunction in early type 2 diabetes ]]> https://biorxiv.org/content/10.1101/2021.12.16.466282v1?rss=1 Walker, J. T. Saunders, D. C. Rai, V. Dai, C. Orchard, P. Hopkirk, A. L. Reihsmann, C. V. Tao, Y. Fan, S. Shrestha, S. Varshney, A. Wright, J. J. Pettway, Y. D. Ventresca, C. Agarwala, S. Aramandla, R. Poffenberger, G. Jenkins, R. Hart, N. J. Greiner, D. L. Shultz, L. D. Bottino, R. Human Pancreas Analysis Program, Liu, J. Parker, S. C. J. Powers, A. C. Brissova, M. 2021-12-17 doi:10.1101/2021.12.16.466282 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Microcin MccI47 selectively inhibits enteric bacteria and reduces carbapenem-resistant Klebsiella pneumoniae colonization in vivo when administered via an engineered live biotherapeutic ]]> https://biorxiv.org/content/10.1101/2021.12.17.473159v1?rss=1 Mortzfeld, B. M. Palmer, J. D. Bhattarai, S. K. Dupre, H. L. Mercado-Lubo, R. Silby, M. W. Bang, C. McCormick, B. A. Bucci, V. 2021-12-19 doi:10.1101/2021.12.17.473159 Cold Spring Harbor Laboratory Press 2021-12-19 <![CDATA[ PERIOD phosphoclusters control temperature compensation of the Drosophila circadian clock ]]> https://biorxiv.org/content/10.1101/2021.12.23.474078v1?rss=1 Emery, P. Joshi, R. Cai, Y. Xia, Y. Chiu, J. 2021-12-24 doi:10.1101/2021.12.23.474078 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ A NEUROGENIC GENE EXPRESSION SIGNATURE SUPPORTS HUMAN THERMOGENIC ADIPOSE TISSUE DEVELOPMENT IN VIVO. ]]> https://biorxiv.org/content/10.1101/2021.12.29.474474v1?rss=1 Solivan-Rivera, J. Yang Loureiro, Z. DeSouza, T. Desai, A. Yang, Q. Rojas-Rodriguez, R. Skritakis, P. Joyce, S. Zhong, D. Nguyen, T. Corvera, S. 2021-12-30 doi:10.1101/2021.12.29.474474 Cold Spring Harbor Laboratory Press 2021-12-30 <![CDATA[ Cell culture model system utilizing engineered A549 cells to express high levels of ACE2 and TMPRSS2 for investigating SARS-CoV-2 infection and antivirals ]]> https://biorxiv.org/content/10.1101/2021.12.31.474593v1?rss=1 Chang, C.-W. Parsi, K. M. Somasundaran, M. Vanderleeden, E. Cruz, J. Cousineau, A. Liu, P. Li, Q. Wang, Y. Maehr, R. Wang, J. P. Finberg, R. W. 2022-01-03 doi:10.1101/2021.12.31.474593 Cold Spring Harbor Laboratory Press 2022-01-03 <![CDATA[ Gut Microbial Trimethylamine is Elevated in Alcohol-Associated Hepatitis and Contributes to Ethanol-Induced Liver Injury in Mice ]]> https://biorxiv.org/content/10.1101/2021.12.31.474633v1?rss=1 Helsley, R. N. Miyata, T. Kadam, A. Venkateshwari, V. Sangwan, N. Huang, E. C. Banerjee, R. Brown, A. L. Fung, K. K. Massey, W. Neumann, C. Danny, O. Osborn, L. J. Schugar, R. C. McMullen, M. R. Bellar, A. Poulsen, K. L. Kim, A. Pathak, V. Mrdjen, M. Anderson, J. T. Willard, B. McClain, C. J. Mitchell, M. McCullough, A. J. Radaeva, S. Barton, B. Szabo, G. Dasarathy, S. Garcia-Garcia, J. C. Rotroff, D. M. Allende, D. S. Wang, Z. Hazen, S. L. Nagy, L. E. Brown, J. M. 2022-01-01 doi:10.1101/2021.12.31.474633 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ Molecular Dynamics of DNA Translocation by FtsK ]]> https://biorxiv.org/content/10.1101/2022.01.03.474797v1?rss=1 Pajak, J. Arya, G. 2022-01-04 doi:10.1101/2022.01.03.474797 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets ]]> https://biorxiv.org/content/10.1101/2022.01.03.474854v1?rss=1 MacMillan, H. J. Kong, Y. Calvo-Roitberg, E. Alonso, L. C. Pai, A. A. 2022-01-04 doi:10.1101/2022.01.03.474854 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Compartmentalized Cell Envelope Biosynthesis in Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.01.07.475471v1?rss=1 Puffal, J. Sparks, I. L. Brenner, J. R. Li, X. Leszyk, J. D. Hayashi, J. Shaffer, S. A. Morita, Y. S. 2022-01-08 doi:10.1101/2022.01.07.475471 Cold Spring Harbor Laboratory Press 2022-01-08 <![CDATA[ TrpA1 is a shear stress mechanosensing channel regulating intestinal homeostasis in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.01.10.475734v1?rss=1 Gong, J. Nirala, N. K. Chen, J. Wang, F. Gu, P. Wen, Q. Ip, Y. T. Xiang, Y. 2022-01-11 doi:10.1101/2022.01.10.475734 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ H2A.Z deposition by SWR1C involves multiple ATP-dependent steps ]]> https://biorxiv.org/content/10.1101/2022.01.11.475888v1?rss=1 Fan, J. Moreno, A. T. Baier, A. S. Loparo, J. J. Peterson, C. L. 2022-01-11 doi:10.1101/2022.01.11.475888 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ The C-terminal domain of SEC-10 is fundamental for exocyst function, Spitzenkorper organization and cell morphogenesis in Neurospora crassa. ]]> https://biorxiv.org/content/10.1101/2022.01.14.475644v1?rss=1 Figueroa-Melendez, A. Martinez-Nunez, L. Rico-Ramirez, A. M. Martinez-Andrade, J. M. Munson, M. Riquelme, M. 2022-01-14 doi:10.1101/2022.01.14.475644 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ Exocyst stimulates each step of exocytic SNARE complex assembly and vesicle fusion ]]> https://biorxiv.org/content/10.1101/2022.01.16.476540v1?rss=1 Lee, C. Lepore, D. Munson, M. Yoon, T.-Y. 2022-01-17 doi:10.1101/2022.01.16.476540 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ A family of C. elegans VASA homologs control Argonaute pathway specificity and promote transgenerational silencing ]]> https://biorxiv.org/content/10.1101/2022.01.18.476504v1?rss=1 Dai, S. Tang, X. Li, L. Ishidate, T. Ozturk, A. R. Chen, H. Yan, Y.-H. Dong, M.-Q. Shen, E.-Z. Mello, C. C. 2022-01-18 doi:10.1101/2022.01.18.476504 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Broadly-recognized, cross-reactive SARS-CoV-2 CD4 T cell epitopes are highly conserved across human coronaviruses and presented by common HLA alleles ]]> https://biorxiv.org/content/10.1101/2022.01.20.477107v1?rss=1 Becerra-Artiles, A. Calvo-Calle, J. M. Co, M. Nanaware, P. Cruz, J. Weaver, G. C. Lu, L. Forcini, C. Finberg, R. W. Moormann, A. Stern, L. J. 2022-01-22 doi:10.1101/2022.01.20.477107 Cold Spring Harbor Laboratory Press 2022-01-22 <![CDATA[ Impaired ERK MAPK activation in mature osteoblasts enhances bone formation via the mTOR pathway ]]> https://biorxiv.org/content/10.1101/2022.01.24.477465v1?rss=1 Kim, J.-M. Yang, Y.-S. Hong, J. Chaugule, S. Chun, H. van der Meulen, M. C. H. Xu, R. Greenblatt, M. B. Shim, J.-H. 2022-01-24 doi:10.1101/2022.01.24.477465 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Defining the Substrate Envelope of SARS-CoV-2 Main Protease to Predict and Avoid Drug Resistance ]]> https://biorxiv.org/content/10.1101/2022.01.25.477757v1?rss=1 Shaqra, A. M. Zvornicanin, S. Huang, Q. Y. Lockbaum, G. J. Knapp, M. Tandeske, L. Barkan, D. T. Flynn, J. Bolon, D. N. Moquin, S. Dovala, D. Kurt Yilmaz, N. Schiffer, C. A. 2022-01-27 doi:10.1101/2022.01.25.477757 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ In vitro activity of ertapenem against Neisseria gonorrhoeae clinical isolates with decreased susceptibility or resistance to extended spectrum cephalosporins in Nanjing, China (2013-2019) ]]> https://biorxiv.org/content/10.1101/2022.01.25.477800v1?rss=1 Su, X.-H. Li, X. Le, W.-J. Lou, X. Genco, C. A. Rice, P. A. 2022-01-26 doi:10.1101/2022.01.25.477800 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms ]]> https://biorxiv.org/content/10.1101/2022.01.26.477860v1?rss=1 Flynn, J. M. Samant, N. Schneider-Nachum, G. Barkan, D. T. Yilmaz, N. K. Schiffer, C. A. Moquin, S. A. Dovala, D. Bolon, D. N. A. 2022-01-26 doi:10.1101/2022.01.26.477860 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ Condensation of a nuclear mRNA export factor regulates mRNA transport during stress ]]> https://biorxiv.org/content/10.1101/2022.01.30.478372v1?rss=1 Heinrich, S. Hondele, M. Marchand, D. Derrer, C. P. Zedan, M. Oswald, A. Uliana, F. Mancini, R. Grunwald, D. Weis, K. 2022-01-30 doi:10.1101/2022.01.30.478372 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA ]]> https://biorxiv.org/content/10.1101/2022.01.31.478526v1?rss=1 Liu, X. Gaubitz, C. Pajak, J. Kelch, B. A. 2022-01-31 doi:10.1101/2022.01.31.478526 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Optimization of NLS Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells ]]> https://biorxiv.org/content/10.1101/2022.02.01.478672v1?rss=1 Luk, K. Liu, P. Zeng, J. Wang, Y. Maitland, S. A. Idrizi, F. Ponnienselvan, K. Zhu, L. J. Luban, J. Bauer, D. E. Wolfe, S. 2022-02-01 doi:10.1101/2022.02.01.478672 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR ]]> https://biorxiv.org/content/10.1101/2022.02.04.479139v1?rss=1 Gustafsson, T. Galan, C. Yu, T. Upton, H. Ferguson, L. Kaymak, E. Weng, Z. Collins, K. Rando, O. 2022-02-04 doi:10.1101/2022.02.04.479139 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Human XIST RNA acts early to condense architecture which facilitates A-repeat density-dependent initiation of gene silencing ]]> https://biorxiv.org/content/10.1101/2022.02.04.479153v1?rss=1 Valledor, M. Byron, M. Dumas, B. Carone, D. M. Hall, L. L. Lawrence, J. B. 2022-02-05 doi:10.1101/2022.02.04.479153 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ IgD+ Age-Associated B cells are the progenitors of the main T-independent B cell response to infection that generates protective Ab and can be induced by an inactivated vaccine in the aged ]]> https://biorxiv.org/content/10.1101/2022.02.04.479159v1?rss=1 Kugler-Umana, O. A. Zhang, W. Kuang, Y. Liang, J. Castonguay, C. Tonkonogy, S. L. Marshak-Rothstein, A. Devarajan, P. Swain, S. L. 2022-02-05 doi:10.1101/2022.02.04.479159 Cold Spring Harbor Laboratory Press 2022-02-05 <![CDATA[ Evidence for RNA or protein transport from somatic tissues to the male reproductive tract in mouse ]]> https://biorxiv.org/content/10.1101/2022.02.08.479624v1?rss=1 Rinaldi, V. Messemer, K. Desevin, K. Sun, F. Berry, B. Kukreja, S. Tapper, A. Wagers, A. Rando, O. 2022-02-10 doi:10.1101/2022.02.08.479624 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Bioframe: Operations on Genomic Intervals in Pandas Dataframes ]]> https://biorxiv.org/content/10.1101/2022.02.16.480748v1?rss=1 Open2C, Abdennur, N. Fudenberg, G. Flyamer, I. M. Galitsyna, A. A. Goloborodko, A. Imakaev, M. Venev, S. V. 2022-02-19 doi:10.1101/2022.02.16.480748 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ MafB, WDR77, and ss-catenin interact with each other and have similar genome association profiles ]]> https://biorxiv.org/content/10.1101/2022.02.17.480948v1?rss=1 He, L. Gao, M. Pratt, H. Weng, Z. Struhl, K. 2022-02-17 doi:10.1101/2022.02.17.480948 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Dilated cardiomyopathy mutation E525K in human beta-cardiac myosin stabilizes the interacting heads motif and super-relaxed state of myosin ]]> https://biorxiv.org/content/10.1101/2022.02.18.480995v1?rss=1 Rasicci, D. V. Tiwari, P. Desetty, R. Sadler, F. R. Sivaramakrishnan, S. Craig, R. Yengo, C. M. 2022-02-19 doi:10.1101/2022.02.18.480995 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Regulation of Hedgehog Signaling Through Arih2-Mediated Smoothened Ubiquitination and Endoplasmic Reticulum-Associated Degradation ]]> https://biorxiv.org/content/10.1101/2022.02.20.481183v1?rss=1 Lv, B. Zhang, X.-O. Pazour, G. J. 2022-02-20 doi:10.1101/2022.02.20.481183 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ Heat Shock Factor 1 (HSF1) specifically potentiates c-MYC-mediated transcription independently of the canonical heat-shock response ]]> https://biorxiv.org/content/10.1101/2022.02.22.481519v1?rss=1 Xu, M. Lin, L. Chuang, K.-H. Ram, B. Dai, S. Su, K.-H. Tang, Z. Dai, C. 2022-02-23 doi:10.1101/2022.02.22.481519 Cold Spring Harbor Laboratory Press 2022-02-23 <![CDATA[ Agent-based models help interpret patterns of clinical drug resistance by contextualizing competition between distinct drug failure modes. ]]> https://biorxiv.org/content/10.1101/2022.02.25.481999v1?rss=1 Leighow, S. M. Landry, B. Lee, M. J. Peyton, S. R. Pritchard, J. R. 2022-02-28 doi:10.1101/2022.02.25.481999 Cold Spring Harbor Laboratory Press 2022-02-28 <![CDATA[ Keratinocyte-tethering modification for biologics enables location-precise treatment in mouse vitiligo ]]> https://biorxiv.org/content/10.1101/2022.02.28.482387v1?rss=1 Hsueh, Y.-C. Wang, Y. Riding, R. L. Catalano, D. E. Lu, Y.-J. Richmond, J. M. Siegel, D. L. Rusckowski, M. Stanley, J. R. Harris, J. E. 2022-03-02 doi:10.1101/2022.02.28.482387 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ The little skate genome and the evolutionary emergence of wing-like fin appendages ]]> https://biorxiv.org/content/10.1101/2022.03.21.485123v1?rss=1 Marletaz, F. de la Calle-Mustienes, E. Acemel, R. D. Nakamura, T. Paliou, C. Naranjo, S. Martinez-Garcia, P. M. Cases, I. Sleight, V. A. Hirschberger, C. Marcet-Houben, M. Navon, D. Andrescavage, A. Skvortsova, K. Duckett, P. E. Gonzalez-Rajal, A. Bogdanovic, O. Gibcus, J. H. Yang, L. Gallardo-Fuentes, L. Sospedra, I. Lopez-Rios, J. Darbellay, F. Visel, A. Dekker, J. Shubin, N. Gabaldon, T. Tena, J. J. Lupianez, D. G. Rokhsar, D. S. Gomez-Skarmeta, J. L. 2022-03-22 doi:10.1101/2022.03.21.485123 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ Paradoxical activation of SREBP1c and de novo lipogenesis by hepatocyte-selective ACLY depletion in obese mice. ]]> https://biorxiv.org/content/10.1101/2022.03.21.485183v1?rss=1 Yenilmez, B. Kelly, M. Zhang, G.-F. Wetoska, N. Ilkayeva, O. Min, K. Rowland, L. DiMarzio, C. He, W. Raymond, N. Lifshitz, L. Pan, M. Han, X. Xie, J. Friedline, R. H. Kim, J. K. Gao, G. Herman, M. A. Newgard, C. Czech, M. 2022-03-21 doi:10.1101/2022.03.21.485183 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ EPHierStats: a statistical tool to model the hierarchical relationships in electrophysiological data ]]> https://biorxiv.org/content/10.1101/2022.03.23.485501v1?rss=1 100) per unit of analysis. This novel analysis framework enables encoding of the full hierarchical relationships between measurements in a mixed-effects general linear model while also analyzing the distribution of values in assessed variables. Our method can easily be adapted to analyze a wide range of repeated-measures electrophysiological experiments. Implementation of the EPHierStats tool will aid the adaption of modern statistical approaches that prevent pseudoreplication and its associated false discovery rate while enabling statistical assessments of the complex relationships inherent to the field of neuroscience. ]]> Kolpakova, J. Marvel-Zuccola, J. D. Futai, K. Martin, G. van der Vinne, V. 2022-03-26 doi:10.1101/2022.03.23.485501 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ CRISPR-induced exon skipping of β-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer ]]> https://biorxiv.org/content/10.1101/2022.03.27.485965v1?rss=1 Mou, H. Yue, J. Jin, Y. Wang, Z. Gao, Y. Janowitz, T. Meyer, H. V. Kucukural, A. Wilkinson, J. E. Ozata, D. M. Beyaz, S. 2022-03-27 doi:10.1101/2022.03.27.485965 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Identification and characterization of the T cell receptor (TCR) repertoire of the Cynomolgus macaque (Macaca Fascicularis) ]]> https://biorxiv.org/content/10.1101/2022.03.30.486315v1?rss=1 90% sequence similarity with the human TCR repertoire. These data will facilitate the analysis of T cell immunity in Cynomolgus macaques. ]]> Jaiswal, S. Boyce, S. Nyquist, S. K. Jivanjee, T. Ibrahim, S. Bromley, J. D. Gatter, G. J. Gideon, H. Patel, K. Ganchua, S. K. Berger, B. Fortune, S. M. Flynn, J. Shalek, A. K. Behar, S. M. 2022-03-31 doi:10.1101/2022.03.30.486315 Cold Spring Harbor Laboratory Press 2022-03-31 <![CDATA[ S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress ]]> https://biorxiv.org/content/10.1101/2022.03.30.486419v1?rss=1 Godbole, A. A. Gopalan, S. Nguyen, T.-K. Fazzio, T. G. Walker, A. K. 2022-03-30 doi:10.1101/2022.03.30.486419 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Different olfactory neuron classes use distinct temporal and molecular programs to complete synaptic development ]]> https://biorxiv.org/content/10.1101/2022.03.31.486637v1?rss=1 Aimino, M. A. DePew, A. T. Restrepo, L. Mosca, T. J. 2022-04-01 doi:10.1101/2022.03.31.486637 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ Centriolar satellites expedite mother centriole remodeling to promote ciliogenesis. ]]> https://biorxiv.org/content/10.1101/2022.04.04.486992v1?rss=1 Hall, E. A. Kumar, D. Prosser, S. L. Yeyati, P. L. Herranz-Pérez, V. Garcia Verdugo, J. M. Rose, L. McKie, L. Dodd, D. O. Tennant, P. A. Megaw, R. Murphy, L. C. Ferreira, M. Grimes, G. Williams, L. Pelletier, L. Quidwai, T. Reiter, J. F. Mill, P. 2022-04-04 doi:10.1101/2022.04.04.486992 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristobal Island, Galapagos archipelago ]]> https://biorxiv.org/content/10.1101/2022.04.05.487164v1?rss=1 Schoenborn, A. A. Yannarell, S. M. MacVicar, C. T. Medina, N. N. B. Markellie, L. M. Mitchell, H. Bonham, K. S. Leon-Reyes, A. Klepac-Ceraj, V. Shank, E. A. 2022-04-05 doi:10.1101/2022.04.05.487164 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Blood oxygenation-level dependent cerebrovascular reactivity imaging as strategy to monitor CSF-hemoglobin toxicity ]]> https://biorxiv.org/content/10.1101/2022.04.05.487168v1?rss=1 Thomson, B. R. Richter, H. Akeret, K. Buzzi, R. M. Anagnostakou, V. van Niftrik, B. H. B. Schwendinger, N. Kulcsar, Z. Kronen, P. W. Regli, L. Fierstra, J. Schaer, D. J. Hugelshofer, M. 2022-04-07 doi:10.1101/2022.04.05.487168 Cold Spring Harbor Laboratory Press 2022-04-07 <![CDATA[ Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons. ]]> https://biorxiv.org/content/10.1101/2022.04.05.487209v1?rss=1 Barrett, A. Varol, E. Weinreb, A. Taylor, S. R. McWhirter, R. Cros, C. Basavaraju, M. Poff, A. Tipps, J. A. Majeed, M. Vidal, B. Wang, C. Yemini, E. Bayer, E. A. Sun, H. Hobert, O. Miller, D. M. Hammarlund, M. 2022-04-08 doi:10.1101/2022.04.05.487209 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ In situ single particle classification reveals distinct 60S maturation intermediates in cells ]]> https://biorxiv.org/content/10.1101/2022.04.10.487797v1?rss=1 Lucas, B. A. Zhang, K. Loerch, S. Grigorieff, N. 2022-04-10 doi:10.1101/2022.04.10.487797 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Human and murine Cryptococcus neoformans infection selects for common genomic changes in an environmental isolate. ]]> https://biorxiv.org/content/10.1101/2022.04.12.487930v1?rss=1 Sephton-Clark, P. McConnell, S. A. Grossman, N. Baker, R. Dragotakes, Q. Fan, Y. Fu, M. S. Gerbig, G. Greengo, S. Hardwick, J. M. Kulkarni, M. Levitz, S. M. Nosanchuk, J. D. Shoham, S. Smith, D. Stempinski, P. Wear, M. Cuomo, C. A. Casadevall, A. 2022-04-12 doi:10.1101/2022.04.12.487930 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Complete mutational mapping of a GTPase switch in vivo reveals novel allosteric regulation ]]> https://biorxiv.org/content/10.1101/2022.04.13.488230v1?rss=1 Mathy, C. J. P. Mishra, P. Flynn, J. M. Perica, T. Mavor, D. Bolon, D. N. A. Kortemme, T. 2022-04-14 doi:10.1101/2022.04.13.488230 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Sequence dependencies and biophysical features both govern cleavage of diverse cut-sites by HIV protease ]]> https://biorxiv.org/content/10.1101/2022.04.18.488666v1?rss=1 Samant, N. Nachum, G. Tsepal, T. Bolon, D. 2022-04-18 doi:10.1101/2022.04.18.488666 Cold Spring Harbor Laboratory Press 2022-04-18 <![CDATA[ Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB ]]> https://biorxiv.org/content/10.1101/2022.04.19.488762v1?rss=1 Jourevleva, K. Golovenko, D. Demo, G. Dutcher, R. C. Hall, T. M. Zamore, P. D. Korostelev, A. A. 2022-04-20 doi:10.1101/2022.04.19.488762 Cold Spring Harbor Laboratory Press 2022-04-20 <![CDATA[ Stem cell heterogeneity and reiteration of developmental signaling underlie melanocyte regeneration in zebrafish ]]> https://biorxiv.org/content/10.1101/2022.04.27.489712v1?rss=1 Frantz, W. T. Iyengar, S. Neiswender, J. Cousineau, A. Maehr, R. Ceol, C. J. 2022-04-29 doi:10.1101/2022.04.27.489712 Cold Spring Harbor Laboratory Press 2022-04-29 <![CDATA[ Fc-engineered antibodies leverage neutrophils to drive control of Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.05.01.490220v1?rss=1 Irvine, E. B. Peters, J. M. Lu, R. Grace, P. S. Sixsmith, J. Wallace, A. Schneider, M. Shin, S. Karpinski, W. Hsiao, J. C. van Woudenbergh, E. Casadevall, A. Bryson, B. D. Cavacini, L. Alter, G. Fortune, S. M. 2022-05-01 doi:10.1101/2022.05.01.490220 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ ATXN2 is a target of N-terminal proteolysis ]]> https://biorxiv.org/content/10.1101/2022.05.07.491020v1?rss=1 Chitre, M. Emery, P. 2022-05-08 doi:10.1101/2022.05.07.491020 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ Peptide Avidity for TCR on CD4 Effectors Determines the Extent of Memory Generation ]]> https://biorxiv.org/content/10.1101/2022.05.09.491158v1?rss=1 Jones, M. C. Castonguay, C. Nanaware, P. P. Weaver, G. C. Stadinski, B. Kugler-Umana, O. A. Huseby, E. Stern, L. J. Devarajan, P. J. Swain, S. L. 2022-05-10 doi:10.1101/2022.05.09.491158 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Stromal Hippo-YAP signaling in stem cell niche controls intestinal homeostasis ]]> https://biorxiv.org/content/10.1101/2022.05.12.491640v1?rss=1 Mao, J. Dang, K. Singh, A. Jennifer, C. L. Tao, Z. Liu, H. Zhu, L. Wu, X. 2022-05-12 doi:10.1101/2022.05.12.491640 Cold Spring Harbor Laboratory Press 2022-05-12 <![CDATA[ D-2-Hydroxyglutarate dehydrogenase connects the propionate shunt to ketone body metabolism in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.05.16.492161v1?rss=1 Ponomarova, O. Zhang, H. Li, X. Nanda, S. Leland, T. B. Fox, B. W. Giese, G. E. Schroeder, F. C. Yilmaz, S. L. Walhout, A. J. M. 2022-05-17 doi:10.1101/2022.05.16.492161 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ CRISPR/Cas9-Mediated Excision of ALS/FTD-Causing Hexanucleotide Repeat Expansion in C9ORF72 rescues major disease mechanisms in vivo and in vitro ]]> https://biorxiv.org/content/10.1101/2022.05.17.492303v1?rss=1 Meijboom, K. E. Abdallah, A. Fordham, N. P. Nagase, H. Rodriguez, T. Kraus, C. Gendron, T. F. Krishnan, G. Esanov, R. Andrade, N. S. Rybin, M. J. Ramic, M. Stephens, Z. D. Edraki, A. Blackwood, M. T. Kahriman, A. Henninger, N. Kocher, J.-P. A. Benatar, M. Brodsky, M. H. Petrucelli, L. Gao, F.-B. Sontheimer, E. J. Brown, R. H. Zeier, Z. Mueller, C. 2022-05-17 doi:10.1101/2022.05.17.492303 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Mitochondrial genome recovery by ATFS-1 is essential for development following starvation ]]> https://biorxiv.org/content/10.1101/2022.05.19.492689v1?rss=1 Naresh, N. U. Shpilka, T. Yang, Q. Du, Y. Haynes, C. 2022-05-19 doi:10.1101/2022.05.19.492689 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Purified cytosolic crystals from Bacillus thuringiensis as a novel active pharmaceutical ingredient (API) ]]> https://biorxiv.org/content/10.1101/2022.05.20.492900v1?rss=1 Chicca, J. Cazeault, N. R. Rus, F. Abraham, A. Garceau, C. Li, H. Atwa, S. M. Flanagan, K. Soto, E. Morrison, M. S. Gazzola, D. Hu, Y. Liu, D. R. Nielsen, M. K. Urban, J. F. Ostroff, G. Aroian, R. V. 2022-05-21 doi:10.1101/2022.05.20.492900 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Discovery of a new class of reversible TEA-domain transcription factor inhibitors with a novel binding mode ]]> https://biorxiv.org/content/10.1101/2022.05.24.493232v1?rss=1 Hu, L. Sun, Y. Liu, S. Erb, H. Singh, A. Mao, J. Luo, X. Wu, X. 2022-05-24 doi:10.1101/2022.05.24.493232 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Loss-of-function mutation in human Oxidation Resistance gene 1 disrupts the spatial-temporal regulation of histone arginine methylation in early brain development ]]> https://biorxiv.org/content/10.1101/2022.05.24.493324v1?rss=1 Lin, X. Wang, W. Yang, M. Damseh, N. Sousa, M. M. L. d. Jacob, F. Lang, A. Kristiansen, E. Pannone, M. Kissova, M. Almaas, R. Kusnierczyk, A. Siller, R. Shahrour, M. Al-Ashhab, M. Abu-Libdeh, B. Tang, W. Slupphaug, G. Elpeleg, O. Boe, S. O. Eide, L. Sullivan, G. J. Rinholm, J. E. Song, H. Ming, G.-L. Van Loon, B. Edvardson, S. Ye, J. Bjoras, M. 2022-05-24 doi:10.1101/2022.05.24.493324 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ De novo lipogenesis fuels adipocyte autophagosome membrane dynamics ]]> https://biorxiv.org/content/10.1101/2022.05.25.493413v1?rss=1 Rowland, L. A. GUILHERME, A. Henriques, F. DiMarzio, C. Wetoska, N. Kelly, M. Reddig, K. Hendricks, G. Pan, M. Han, X. Ilkayeva, O. R. Newgard, C. B. Czech, M. P. 2022-05-25 doi:10.1101/2022.05.25.493413 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Modeling Down syndrome neurodevelopment with isogenic cerebral organoids ]]> https://biorxiv.org/content/10.1101/2022.05.25.493459v1?rss=1 Czerminski, J. T. King, O. D. Lawrence, J. B. 2022-05-26 doi:10.1101/2022.05.25.493459 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Multicellular Aligned Bands Disrupt Global Collective Cell Behavior ]]> https://biorxiv.org/content/10.1101/2022.05.30.494066v1?rss=1 Jebeli, M. Lopez, S. K. Goldblatt, Z. E. McCollum, D. Mana-Capelli, S. Wen, Q. Billiar, K. 2022-05-31 doi:10.1101/2022.05.30.494066 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Chromosome silencing in vitro reveals trisomy 21 causes cell-autonomous deficits in angiogenesis and early dysregulation in Notch signaling ]]> https://biorxiv.org/content/10.1101/2022.06.01.494361v1?rss=1 Moon, J. E. Lawrence, J. B. 2022-06-01 doi:10.1101/2022.06.01.494361 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC ]]> https://biorxiv.org/content/10.1101/2022.06.03.494617v1?rss=1 Liu, S. Li, L. Zhang, F. van Sambeek, B. Appleton, E. Ng, A. H. M. Khoshakhlagh, P. Chen, Y. Garcia-Corral, M. Wu, C.-T. Huang, J. Y. Tan, Y. Chao, G. Aach, J. Tam, J. Lim, E. T. Raychaudhuri, S. Church, G. 2022-06-03 doi:10.1101/2022.06.03.494617 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ A Caenorhabditis elegans nck-1 and filamentous actin-regulating protein pathway mediates a key cellular defense against bacterial pore-forming proteins ]]> https://biorxiv.org/content/10.1101/2022.06.10.495598v1?rss=1 Sitaram, A. Yin, Y. Zamaitis, T. Zhang, B. Aroian, R. V. 2022-06-10 doi:10.1101/2022.06.10.495598 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Fundamental limits to progression of cellular life in frigid environments ]]> https://biorxiv.org/content/10.1101/2022.06.10.495632v1?rss=1 Laman Trip, D. S. Maire, T. Youk, H. 2022-06-10 doi:10.1101/2022.06.10.495632 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex ]]> https://biorxiv.org/content/10.1101/2022.06.10.495637v1?rss=1 Vargas, R. Luna, M. J. Freschi, L. Murphy, K. C. Ioerger, T. R. Sassetti, C. M. Farhat, M. R. 2022-06-10 doi:10.1101/2022.06.10.495637 Cold Spring Harbor Laboratory Press 2022-06-10 <![CDATA[ Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for Label-Free Detection of Molecules across Entire Cell Sections ]]> https://biorxiv.org/content/10.1101/2022.06.13.495969v1?rss=1 Elferich, J. Schiroli, G. Scadden, D. Grigorieff, N. 2022-06-14 doi:10.1101/2022.06.13.495969 Cold Spring Harbor Laboratory Press 2022-06-14 <![CDATA[ Sparse-spectral microendoscopy for real-time visualization of tumor cell phenotype and microenvironment spatial heterogeneity in vivo ]]> https://biorxiv.org/content/10.1101/2022.06.17.496624v1?rss=1 Spring, B. Q. Palanisami, A. Saad, M. A. Kercher, E. M. Lang, R. T. Harman, R. C. Sutin, J. Mai, Z. Hasan, T. 2022-06-18 doi:10.1101/2022.06.17.496624 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ EZH2 inhibition remodels the inflammatory senescence-associated secretory phenotype to potentiate pancreatic cancer immune surveillance ]]> https://biorxiv.org/content/10.1101/2022.06.21.495523v1?rss=1 Chibaya, L. Murphy, K. C. Lopez-Diaz, Y. DeMarco, K. D. Liu, H. Gopalan, S. Faulkner, M. Li, J. Morris, J. P. Ho, Y.-J. Simon, J. Luan, W. Kulick, A. De Stanchina, E. Simin, K. Zhu, L. J. Fazzio, T. G. Lowe, S. W. Ruscetti, M. 2022-06-23 doi:10.1101/2022.06.21.495523 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.06.21.497047v1?rss=1 Farjo, M. Koelle, K. Martin, M. A. Gibson, L. L. Walden, K. K. Rendon, G. Fields, C. J. Alnaji, F. Gallagher, N. Luo, C. H. Mostafa, H. H. Manabe, Y. C. Pekosz, A. Smith, R. L. McManus, D. D. Brooke, C. B. 2022-06-22 doi:10.1101/2022.06.21.497047 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Binge alcohol drinking alters the differential control of cholinergic interneurons over nucleus accumbens D1 and D2 medium spiny neurons ]]> https://biorxiv.org/content/10.1101/2022.06.22.497229v1?rss=1 Kolpakova, J. Van der Vinne, V. Gimenez-Gomez, P. Le, T. Martin, G. 2022-06-26 doi:10.1101/2022.06.22.497229 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Silencing of ApoE with Divalent siRNAs Drives Activation of Immune Clearance Pathways and Improves Amyloid Pathology in Mouse Models of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.06.28.498012v1?rss=1 Ferguson, C. Hildebrand, S. Godinho, B. M. D. C. Buchwald, J. Echeverria, D. Coles, A. Grigorenko, A. Vanjielli, L. Sousa, J. McHugh, N. Hassler, M. Santarelli, F. Heneka, M. T. Rogaev, E. Khvorova, A. 2022-07-02 doi:10.1101/2022.06.28.498012 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Chemical engineering of therapeutic siRNAs for allele-specific gene silencing in vivo in CNS ]]> https://biorxiv.org/content/10.1101/2022.06.29.498088v1?rss=1 50-fold selectivity for the mutant HD-causing allele, based on a single nucleotide difference. The optimized compound exhibits selective silencing of mutant huntingtin (HTT) protein in patient derived cells and throughout the HD mouse brain, providing a demonstration of SNP-based allele-specific RNAi silencing of gene expression in vivo in the CNS. The ability to target a disease-causing allele using RNAi-based therapies could be applied to a wide range of dominant CNS disorders, where maintenance of wild-type expression is essential. ]]> Conroy, F. Miller, R. Alterman, J. F. Hassler, M. R. Echeverria, D. Godinho, B. M. D. C. Knox, E. G. Sapp, E. Sousa, J. Yamada, K. Mahmood, F. Boudi, A. Kegel-Gleason, K. DiFiglia, M. Aronin, N. Khvorova, A. Pfister, E. L. 2022-07-02 doi:10.1101/2022.06.29.498088 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ RNA polymerase II and PARP1 shape enhancer-promoter contacts ]]> https://biorxiv.org/content/10.1101/2022.07.07.499190v1?rss=1 Barshad, G. Lewis, J. J. Chivu, A. G. Abuhashem, A. Krietenstein, N. Rice, E. J. Rando, O. J. Hadjantonakis, A.-K. Danko, C. G. 2022-07-08 doi:10.1101/2022.07.07.499190 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ Asymmetric trichotomous data partitioning enables development of predictive machine learning models using limited siRNA efficacy datasets ]]> https://biorxiv.org/content/10.1101/2022.07.08.499317v1?rss=1 Monopoli, K. R. Korkin, D. Khvorova, A. 2022-07-10 doi:10.1101/2022.07.08.499317 Cold Spring Harbor Laboratory Press 2022-07-10 <![CDATA[ Bacterial pattern recognition in C. elegans by a nuclear hormone receptor ]]> https://biorxiv.org/content/10.1101/2022.07.12.499718v1?rss=1 Peterson, N. D. Tse, S. Y. Huang, Q. J. Schiffer, C. A. Pukkila-Worley, R. 2022-07-13 doi:10.1101/2022.07.12.499718 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Cryo-EM structure of a RAS/RAF recruitment complex ]]> https://biorxiv.org/content/10.1101/2022.07.14.500081v1?rss=1 Eck, M. J. Jeon, H. Park, E. Rawson, S. Schmoker, A. Kim, B.-W. Oh, S. Song, K. 2022-07-14 doi:10.1101/2022.07.14.500081 Cold Spring Harbor Laboratory Press 2022-07-14 <![CDATA[ Canonical Wnt Signaling Maintains Human Mesenchymal Progenitor Cell Multipotency During Adipose Tissue Development ]]> https://biorxiv.org/content/10.1101/2022.07.18.500487v1?rss=1 Loureiro, Z. Y. Joyce, S. Solivan-Rivera, J. Desai, A. Skritakis, P. Yang, Q. DeSouza, T. Nguyen, T. MacDougald, O. A. Corvera, S. 2022-07-18 doi:10.1101/2022.07.18.500487 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Cannabinoids Activate the Insulin Pathway to Modulate Mobilization of Cholesterol in C. elegans ]]> https://biorxiv.org/content/10.1101/2022.07.20.500754v1?rss=1 Hernandez-Cravero, B. Gallino, S. Florman, J. Vranich, C. Philippe, D. Elgoyhen, A. B. Alkema, M. Diego De Mendoza, D. 2022-07-21 doi:10.1101/2022.07.20.500754 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ FMRP-Regulated RNA Splicing is Mediated by Multiple Splicing Factors and Translational Control of Mbnl1 RNA ]]> https://biorxiv.org/content/10.1101/2022.08.02.502495v1?rss=1 Jung, S. Shah, S. Richter, J. D. 2022-08-03 doi:10.1101/2022.08.02.502495 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Flnc: Machine Learning Improves the Identification of Novel Full-length Long Noncoding RNAs from RNA Sequencing Data Without Transcriptional Initiation Profiles ]]> https://biorxiv.org/content/10.1101/2022.08.02.502545v1?rss=1 Li, Z. Zhou, P. Kwon, E. Fitzgerald, K. Weng, Z. Zhou, C. 2022-08-05 doi:10.1101/2022.08.02.502545 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Relaxed targeting rules allow PIWI-clade Argonaute proteins to silence ever-mutating transposons ]]> https://biorxiv.org/content/10.1101/2022.08.04.502788v1?rss=1 Gainetdinov, I. Cecchini, K. Vega-Badillo, J. Bagci, A. Colpan, C. Arif, A. Wu, P.-H. Zamore, P. D. 2022-08-05 doi:10.1101/2022.08.04.502788 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Phosphosite Scanning reveals a complex phosphorylation code underlying CDK-dependent activation of Hcm1 ]]> https://biorxiv.org/content/10.1101/2022.08.04.502803v1?rss=1 Conti, M. M. Li, R. Narvaez Ramos, M. A. Zhu, L. J. Fazzio, T. G. Benanti, J. A. 2022-08-05 doi:10.1101/2022.08.04.502803 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Reliable multiplex generation of pooled induced pluripotent stem cells for genetic testing ]]> https://biorxiv.org/content/10.1101/2022.08.10.500520v1?rss=1 Smullen, M. Reichert, J. M. Dawes, P. Wang, Q. Readhead, B. Church, G. Lim, E. T. Chan, Y. 2022-08-13 doi:10.1101/2022.08.10.500520 Cold Spring Harbor Laboratory Press 2022-08-13 <![CDATA[ Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state ]]> https://biorxiv.org/content/10.1101/2022.08.15.504001v1?rss=1 Maiti, A. Hedger, A. Myint, W. Balachandran, V. Watts, J. Schiffer, C. A. Matsuo, H. 2022-08-15 doi:10.1101/2022.08.15.504001 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ A novel batokine Breg controls adipose thermogenesis and glucose homeostasis ]]> https://biorxiv.org/content/10.1101/2022.08.16.504121v1?rss=1 Chen, Q. Huang, L. Pan, D. Hu, K. Li, R. Zhu, L. J. Guertin, D. Wang, Y.-X. 2022-08-16 doi:10.1101/2022.08.16.504121 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Dimeric G-quadruplex motifs determine a large fraction of strong replication origins in vertebrates ]]> https://biorxiv.org/content/10.1101/2022.08.17.504255v1?rss=1 Poulet-Benedetti, J. Tonnerre-Doncarli, C. Valton, A.-L. Laurent, M. Gerard, M. Barinova, N. Parisis, N. Massip, F. Picard, F. Prioleau, M.-N. 2022-08-17 doi:10.1101/2022.08.17.504255 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome ]]> https://biorxiv.org/content/10.1101/2022.08.28.505582v1?rss=1 Zhou, H. Arapoglou, T. Li, X. Li, Z. Zheng, X. Moore, J. E. Asok, A. Kumar, S. Blue, E. E. Buyske, S. Cox, N. Felsenfeld, A. Gerstein, M. Kenny, E. Li, B. Matise, T. Philippakis, A. Rehm, H. Sofia, H. J. Neale, B. Snyder, G. Weng, Z. Sunyaev, S. Lin, X. 2022-08-29 doi:10.1101/2022.08.28.505582 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Implications of the 375W mutation for HIV-1 tropism and vaccine development. ]]> https://biorxiv.org/content/10.1101/2022.08.29.505747v1?rss=1 Verdejo-Torres, O. Vargas-Pavia, T. Fatima, S. Duenas-Decamp, M. J. 2022-08-29 doi:10.1101/2022.08.29.505747 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Extensive cellular multitasking within Bacillus subtilis biofilms ]]> https://biorxiv.org/content/10.1101/2022.09.02.506450v1?rss=1 Yannarell, S. M. Beaudoin, E. S. Talley, H. S. Schoenborn, A. A. Orr, G. Anderton, C. R. Chrisler, W. B. Shank, E. A. 2022-09-03 doi:10.1101/2022.09.02.506450 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Di-valent siRNA Mediated Silencing of MSH3 Blocks Somatic Repeat Expansion in Mouse Models of Huntington's Disease ]]> https://biorxiv.org/content/10.1101/2022.09.06.506795v1?rss=1 O'Reilly, D. Belgrad, J. Ferguson, C. Summers, A. Sapp, E. McHugh, C. Mathews, E. Buchwald, J. Ly, S. Echeverria Moreno, D. Kennedy, Z. Hariharan, V. Monopoli, K. Yang, X. Carroll, J. Difiglia, M. Aronin, N. Khvorova, A. 2022-09-06 doi:10.1101/2022.09.06.506795 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Vitamin B12 produced by gut bacteria modulates excitatory neurotransmission ]]> https://biorxiv.org/content/10.1101/2022.09.06.506833v1?rss=1 Kang, W. K. Araya, A. Fox, B. W. Thackeray, A. Schroeder, F. C. Walhout, A. J. M. Alkema, M. J. 2022-09-08 doi:10.1101/2022.09.06.506833 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Generation of floxed alleles for cell-specific knockout in zebrafish ]]> https://biorxiv.org/content/10.1101/2022.09.06.506849v1?rss=1 Shin, M. Nozaki, T. Toles, B. Kolb, A. Luk, K. Isogai, S. Ishida, K. Hanasaka, T. Parsons, M. J. Wolfe, S. A. Lawson, N. D. 2022-09-06 doi:10.1101/2022.09.06.506849 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Evolved bacterial resistance to the chemotherapy gemcitabine modulates its efficacy ]]> https://biorxiv.org/content/10.1101/2022.09.07.506952v1?rss=1 Sayin, S. Rosener, B. Li, C. G. Ho, B. Ponomarova, O. Ward, D. Walhout, A. J. Mitchell, A. 2022-09-07 doi:10.1101/2022.09.07.506952 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ ATFS-1 regulates peroxisome assembly genes and protects both mitochondria and peroxisomes during peroxin perturbations ]]> https://biorxiv.org/content/10.1101/2022.09.09.507280v1?rss=1 Shpilka, T. Uma Naresh, N. Du, Y. Watts, J. L. Haynes, C. M. 2022-09-10 doi:10.1101/2022.09.09.507280 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Drosophila Males Use 5'-to-3' Phased Biogenesis to Make Stellate-silencing piRNAs that Lack Homology to Maternally Deposited piRNA Guides ]]> https://biorxiv.org/content/10.1101/2022.09.12.507655v1?rss=1 Venkei, Z. G. Gainetdinov, I. Starostik, M. Choi, C. Chen, P. Balsara, C. Whitfield, T. Bell, G. W. Feng, S. Jacobsen, S. E. Aravin, A. Kim, J. K. Zamore, P. Yamashita, Y. M. 2022-09-13 doi:10.1101/2022.09.12.507655 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Negative regulation of C. elegans innate immunity by orphan nuclear receptor NHR-42 ]]> https://biorxiv.org/content/10.1101/2022.09.12.507697v1?rss=1 Goswamy, D. Labed, S. A. Gonzalez, X. Irazoqui, J. E. 2022-09-15 doi:10.1101/2022.09.12.507697 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ The Respiratory Syncytial Virus G Protein Enhances the Immune Responses to the RSV F Protein in an Enveloped Virus-like Particle Vaccine Candidate ]]> https://biorxiv.org/content/10.1101/2022.09.12.507712v1?rss=1 McGinnes-Cullen, L. W. Luo, B. Wen, Z. Zang, L. Durr, E. Morrison, T. G. 2022-09-13 doi:10.1101/2022.09.12.507712 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Host genetic background is a barrier to vaccine-induced protection against infection ]]> https://biorxiv.org/content/10.1101/2022.09.19.508548v1?rss=1 Lai, R. Gong, D. Williams, T. Ogunsola, A. F. Cavallo, K. Arlehamn, C. L. Beamer, G. Ferris, M. Sassetti, C. M. Lauffenburger, D. Behar, S. 2022-09-19 doi:10.1101/2022.09.19.508548 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Methotrexate inhibition of muropeptide transporter SLC46A2 controls psoriatic skin inflammation ]]> https://biorxiv.org/content/10.1101/2022.09.29.509906v1?rss=1 Bharadwaj, R. Lusi, C. F. Mashayekh, S. Nagar, A. Malireddi, R. K. S. Kane, G. I. Wodzanowski, K. Brown, A. Okuda, K. Monahan, A. Paik, D. Nandy, A. Anonick, M. Goldman, W. E. Kanneganti, T.-D. Orzalli, M. H. Grimes, C. L. Atukorale, P. U. Silverman, N. 2022-09-30 doi:10.1101/2022.09.29.509906 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Mechanisms of insertions at a DNA double-strand break ]]> https://biorxiv.org/content/10.1101/2022.09.30.509517v1?rss=1 Min, J. Zhao, J. Zagelbaum, J. Takahashi, S. Cummings, P. Schooley, A. Dekker, J. Gottesman, M. E. Rabadan, R. Gautier, J. 2022-10-01 doi:10.1101/2022.09.30.509517 Cold Spring Harbor Laboratory Press 2022-10-01 <![CDATA[ Potential limitations of micro-dystrophin gene therapy for Duchenne muscular dystrophy ]]> https://biorxiv.org/content/10.1101/2022.10.02.510519v1?rss=1 Hart, C. C. Lee, Y. i. Xie, J. Gao, G. Hammers, D. W. Sweeney, L. 2022-10-05 doi:10.1101/2022.10.02.510519 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Structure and assembly of an extremely long bacteriophage tail tube ]]> https://biorxiv.org/content/10.1101/2022.10.03.510161v1?rss=1 Agnello, E. Pajak, J. Liu, X. Kelch, B. A. 2022-10-04 doi:10.1101/2022.10.03.510161 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Treg cells drive MYCN-mediated immunosuppression and tumor aggressiveness in high-risk neuroblastoma ]]> https://biorxiv.org/content/10.1101/2022.10.03.510561v1?rss=1 Qin, X. Lam, A. K. Zhang, X. Sengupta, S. Iorgulescu, B. J. Zuo, T. Floru, A. E. Meara, G. K. Lloyd, k. Kwok, L. A. Smith, K. S. Nagaraju, T. R. Meijers, R. Ceol, C. Liu, C.-T. Alexandrescu, S. Wu, C. J. Keskin, D. George, R. E. Feng, H. 2022-10-05 doi:10.1101/2022.10.03.510561 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ The nuclear Argonaute HRDE-1 directs target gene re-localization and shuttles to nuage to promote small RNA mediated inherited silencing ]]> https://biorxiv.org/content/10.1101/2022.10.04.510877v1?rss=1 Ding, Y.-H. Ochoa, H. Ishidate, T. Mello, C. 2022-10-05 doi:10.1101/2022.10.04.510877 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Restricted effects of the sole C. elegans Daughterless/E homolog, HLH-2, on nervous system development ]]> https://biorxiv.org/content/10.1101/2022.10.10.511552v1?rss=1 Masoudi, N. Schnabel, R. Yemini, E. Leyva-Diaz, E. Hobert, O. 2022-10-10 doi:10.1101/2022.10.10.511552 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Data Descriptor: Human whole exome genotype data for Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2022.10.11.511653v1?rss=1 30. Our new strategy for processing these diversely generated WES samples has shown to generate high-quality data. The improved ability to combine data sequenced in different batches benefits the whole genomics research community. The WES data are accessible to the scientific community via https://dss.niagads.org/. ]]> Leung, Y. Y. Naj, A. C. Chou, Y.-F. Valladares, O. Wheeler, N. Lin, H. Gangadharan, P. Qu, L. Clark, K. Cantwell, L. Nicaretta, H. the Alzheimer's Disease Sequencing Project, Seshadri, S. Brkanac, Z. Cruchaga, C. Pericak-Vance, M. A. Mayeux, R. Kuzma, A. B. Lee, W.-P. Bush, W. S. DeStefano, A. L. Martin, E. Schellenberg, G. D. Wang, L.-S. 2022-10-13 doi:10.1101/2022.10.11.511653 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ Chromosome decompaction and cohesin direct Topoisomerase II activity to establish and maintain an unentangled interphase genome ]]> https://biorxiv.org/content/10.1101/2022.10.15.511838v1?rss=1 Hildebrand, E. M. Polovnikov, K. Dekker, B. Liu, Y. Lafontaine, D. L. Fox, A. N. Li, Y. Venev, S. V. Mirny, L. A. Dekker, J. 2022-10-16 doi:10.1101/2022.10.15.511838 Cold Spring Harbor Laboratory Press 2022-10-16 <![CDATA[ Degradomic identification of membrane type 1-matrix metalloproteinase (MT1-MMP/MMP14) as an ADAMTS9 and ADAMTS20 substrate ]]> https://biorxiv.org/content/10.1101/2022.10.17.512574v1?rss=1 Nandadasa, S. Martin, D. Deshpande, G. Robert, K. L. Stack, M. S. Itoh, Y. APTE, S. S. 2022-10-19 doi:10.1101/2022.10.17.512574 Cold Spring Harbor Laboratory Press 2022-10-19 <![CDATA[ Development of a clot-adhesive coating to improve the performance of thrombectomy devices ]]> https://biorxiv.org/content/10.1101/2022.10.18.512663v1?rss=1 Skarbek, C. Anagnostakou, V. Procopio, E. Epshtein, M. Raskett, C. Romagnoli, R. Iviglia, G. Morra, M. Antonucci, M. Nicoletti, A. Caligiuri, G. Gounis, M. 2022-10-24 doi:10.1101/2022.10.18.512663 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Noncanonical CDK4 signaling rescues diabetes in a mouse model by promoting beta cell differentiation ]]> https://biorxiv.org/content/10.1101/2022.10.19.512511v1?rss=1 Stamateris, R. E. Sharma, R. B. Landa-Galvan, H. V. Darko, C. Redmond, D. Rane, S. G. Alonso, L. C. 2022-10-20 doi:10.1101/2022.10.19.512511 Cold Spring Harbor Laboratory Press 2022-10-20 <![CDATA[ High bacillary burden and the ESX-1 type VII secretion system promote MHC class I presentation to CD8 T-cells during Mycobacterium tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2022.10.20.513087v1?rss=1 Mott, D. Chang, E. Shinkawa, T. Yang, J. Baer, C. Papavinasasundaram, K. Sassetti, C. M. Behar, S. M. 2022-10-21 doi:10.1101/2022.10.20.513087 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Mitotic chromosomes scale to nucleo-cytoplasmic ratio and cell size in Xenopus ]]> https://biorxiv.org/content/10.1101/2022.10.20.513104v1?rss=1 Zhou, C. Y. Dekker, B. Liu, Z. Cabrera, H. Ryan, J. Dekker, J. Heald, R. 2022-10-21 doi:10.1101/2022.10.20.513104 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Career Self-Efficacy Disparities in Underrepresented Biomedical Scientist Trainees ]]> https://biorxiv.org/content/10.1101/2022.10.21.512368v1?rss=1 Chatterjee, D. Jacob, G. A. Sturzenegger Varvayanis, S. Wefes, I. Chalkley, R. Nogueira, A. T. Fuhrmann, C. Varadarajan, J. Hubbard, N. M. Gaines, C. H. Layton, R. L. Chaudhary, S. 2022-10-21 doi:10.1101/2022.10.21.512368 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Converging pathways direct synapse elimination through the homeodomain transcriptional regulator DVE-1 ]]> https://biorxiv.org/content/10.1101/2022.10.21.512874v1?rss=1 Alexander, K. D. Ramachandran, S. Lambert, C. M. Russell, J. Oliver, D. Armstrong, W. Rettler, M. Doitsidou, M. Benard, C. Francis, M. M. 2022-10-21 doi:10.1101/2022.10.21.512874 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Salt-inducible kinase inhibition promotes the adipocyte thermogenic program and adipose tissue browning ]]> https://biorxiv.org/content/10.1101/2022.10.27.514130v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@ce743org.highwire.dtl.DTLVardef@122f339org.highwire.dtl.DTLVardef@18e3013org.highwire.dtl.DTLVardef@1f65311_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractsC_FLOATNO C_FIG ObjectiveNorepinephrine stimulates the adipose tissue thermogenic program through a {beta}-adrenergic receptor ({beta}AR) - cyclic adenosine monophosphate (cAMP) - protein kinase A (PKA) signaling cascade. We discovered that a noncanonical activation of the mechanistic target of rapamycin complex 1 (mTORC1) by PKA is required for the {beta}AR-stimulation of adipose tissue browning. However, the downstream events triggered by PKA-phosphorylated mTORC1 activation that drive this thermogenic response are not well understood. MethodsWe used a proteomic approach of Stable Isotope Labeling by/with Amino acids in Cell culture (SILAC) to characterize the global protein phosphorylation profile in brown adipocytes treated with the {beta}AR agonist. We identified salt-inducible kinase 3 (SIK3) as a candidate mTORC1 substrate and further tested the effect of SIK3 deficiency or SIK inhibition on the thermogenic gene expression program in brown adipocytes and in mouse adipose tissue. ResultsSIK3 interacts with RAPTOR, the defining component of the mTORC1 complex, and is phosphorylated at Ser884 in a rapamycin-sensitive manner. Pharmacological SIK inhibition by a pan-SIK inhibitor (HG-9-91-01) in brown adipocytes increases basal Ucp1 gene expression and restores its expression upon blockade of either mTORC1 or PKA. Short-hairpin RNA (shRNA) knockdown of Sik3 augments, while overexpression of SIK3 suppresses, Ucp1 gene expression in brown adipocytes. The regulatory PKA phosphorylation domain of SIK3 is essential for its inhibition. CRISPR-mediated Sik3 deletion in brown adipocytes increases type IIa histone deacetylase (HDAC) activity and enhances the expression of genes involved in thermogenesis such as Ucp1, Pgc1, and mitochondrial OXPHOS complex protein. We further show that HDAC4 interacts with PGC1 after {beta}AR stimulation and reduces lysine acetylation in PGC1. Finally, a SIK inhibitor well-tolerated in vivo (YKL-05-099) can stimulate the expression of thermogenesis-related genes and browning of mouse subcutaneous adipose tissue. ConclusionsTaken together, our data reveal that SIK3, with the possible contribution of other SIKs, functions as a phosphorylation switch for {beta}-adrenergic activation to drive the adipose tissue thermogenic program and indicates that more work to understand the role of the SIKs is warranted. Our findings also suggest that maneuvers targeting SIKs could be beneficial for obesity and related cardiometabolic disease. ]]> Shi, F. de Fatima Silva, F. Liu, D. Turk, C. Kruger, M. Collins, S. 2022-10-28 doi:10.1101/2022.10.27.514130 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Singletrome: A method to analyze and enhance the transcriptome with long noncoding RNAs for single cell analysis ]]> https://biorxiv.org/content/10.1101/2022.10.31.514182v1?rss=1 Rahman, R.-U. U. Ahmad, I. Sparks, R. Saad, A. B. Mullen, A. 2022-11-02 doi:10.1101/2022.10.31.514182 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ Cooltools: enabling high-resolution Hi-C analysis in Python ]]> https://biorxiv.org/content/10.1101/2022.10.31.514564v1?rss=1 Open 2C, Abdennur, N. Abraham, S. Fudenberg, G. Flyamer, I. M. Galitsyna, A. A. Goloborodko, A. Imakaev, M. Oksuz, B. A. Venev, S. V. 2022-11-01 doi:10.1101/2022.10.31.514564 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ The BRCA1 isoform, BRCA1-IRIS, operates independently of the full-length BRCA1 in the Fanconi anemia pathway ]]> https://biorxiv.org/content/10.1101/2022.11.02.514969v1?rss=1 Li, A. G. Chan, B. C. Murphy, E. C. He, Y. Ors, M. Kong, Q. Cantor, S. B. Brugge, J. S. Brown, M. Livingston, D. M. 2022-11-04 doi:10.1101/2022.11.02.514969 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ PRMT5 links lipid metabolism to contractile function of skeletal muscles ]]> https://biorxiv.org/content/10.1101/2022.11.04.515165v1?rss=1 Kim, K. H. Jia, Z. Strange, M. M. Chen, J. Qiu, J. Oprescu, S. N. Chen, X. Syed, S. A. Yue, F. Roseguini, B. T. Imbalzano, A. N. Hu, C. Kuang, S. 2022-11-04 doi:10.1101/2022.11.04.515165 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Systems-level transcriptional regulation of Caenorhabditis elegans metabolism ]]> https://biorxiv.org/content/10.1101/2022.11.08.515576v1?rss=1 Walhout, A. J. Nanda, S. Jacques, M.-A. Wang, W. Myers, C. L. Yilmaz, S. 2022-11-09 doi:10.1101/2022.11.08.515576 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Differential requirement for IRGM proteins during tuberculosis infection in mice ]]> https://biorxiv.org/content/10.1101/2022.11.09.515519v1?rss=1 Wilburn, K. M. Meade, R. K. Heckenberg, E. M. Dockterman, J. Coers, J. Sassetti, C. M. Olive, A. J. Smith, C. M. 2022-11-09 doi:10.1101/2022.11.09.515519 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ A nematode model to evaluate microdeletion phenotype expression ]]> https://biorxiv.org/content/10.1101/2022.11.09.515676v1?rss=1 Antkowiak, K. R. Coskun, P. Noronha, S. T. Tavella, D. Massi, F. Ryder, S. P. 2022-11-09 doi:10.1101/2022.11.09.515676 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Cell autonomous requirement of imprinted XCI inextra-embryonic polar trophoblast cells ]]> https://biorxiv.org/content/10.1101/2022.11.10.515976v1?rss=1 Wang, F. Chander, A. Yoon, Y. Wallingford, M. Espejo-Serrano, C. Bustos, F. Findlay, G. M. Mager, J. Bach, I. 2022-11-10 doi:10.1101/2022.11.10.515976 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors ]]> https://biorxiv.org/content/10.1101/2022.11.16.516815v1?rss=1 90% yield. In standard conditions, with water as the solvent, hydrolysis of the starting material to adenosine monophosphate limits the yields. To our surprise, we find that rather than increasing adenylation yields by decreasing the rate of ImpA hydrolysis, formamide does so by increasing the reaction rate between ImpA and 5'-phosphorylated DNA by [~]10 fold. The method described here enables straightforward preparation of chemically adenylated adapters with higher than 90% yield, simplifying reagent preparation for NGS. ]]> Hildebrand, S. Hedger, A. K. Watts, J. Khvorova, A. 2022-11-16 doi:10.1101/2022.11.16.516815 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Enzyme levels broadly influence flux throughout the metabolic network ]]> https://biorxiv.org/content/10.1101/2022.11.17.516982v1?rss=1 Yilmaz, S. Walhout, M. Li, X. 2022-11-18 doi:10.1101/2022.11.17.516982 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Variation in anthelmintic responses are driven by genetic differences among diverse C. elegans strains ]]> https://biorxiv.org/content/10.1101/2022.11.26.518036v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@6222bborg.highwire.dtl.DTLVardef@d635a6org.highwire.dtl.DTLVardef@15c3935org.highwire.dtl.DTLVardef@1afe3fe_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Shaver, A. O. Wit, J. Dilks, C. M. Crombie, T. A. Li, H. Aroian, R. V. Andersen, E. C. 2022-11-26 doi:10.1101/2022.11.26.518036 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ Structural Elucidation of a Protective B cell Epitope on Outer Surface Protein C (OspC) of the Lyme disease spirochete, Borreliella burgdorferi ]]> https://biorxiv.org/content/10.1101/2022.11.28.518297v1?rss=1 Rudolph, M. J. Davis, S. Haque, H. M. E. Weis, D. D. Vance, D. J. Piazza, C. L. Ejemel, M. Cavacini, L. A. Wang, Y. Mbow, L. Gilmore, R. D. Mantis, N. J. 2022-11-29 doi:10.1101/2022.11.28.518297 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2022.12.01.518643v1?rss=1 Becerra-Artiles, A. Nanaware, P. P. Muneeruddin, K. Weaver, G. C. Shaffer, S. A. Calvo-Calle, J. M. Stern, L. J. 2022-12-01 doi:10.1101/2022.12.01.518643 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Molecular dynamics analysis of Superoxide Dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression ]]> https://biorxiv.org/content/10.1101/2022.12.05.519128v1?rss=1 Kalia, M. Miotto, M. Ness, D. Opie-Martin, S. Spargo, T. P. Di Rienzo, L. Biagini, T. Petrizzelli, F. Al-Khleifat, A. Kabiljo, R. Topp, S. Mayl, K. Fogh, I. Mehta, P. R. Williams, K. L. Jockel-Balsarotti, J. Bali, T. Self, W. Henden, L. Nicholson, G. A. Ticozzi, N. McKenna-Yasek, D. Tang, L. Shaw, P. Chio, A. Ludolph, A. Weishaupt, J. H. Landers, J. E. Glass, J. D. Mora, J. S. Robberecht, W. Van Damme, P. McLaughlin, R. Hardiman, O. van den Berg, L. H. Veldink, J. H. Corcia, P. Stevic, Z. Siddique, N. Ratti, A. Silani, V. Blair, I. P. Fan, D.-s. Essel 2022-12-05 doi:10.1101/2022.12.05.519128 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane ]]> https://biorxiv.org/content/10.1101/2022.12.05.519151v1?rss=1 Shi, W. Cai, Y. Zhu, H. Peng, H. Voyer, J. Rits-Volloch, S. Cao, H. Mayer, M. L. Song, K. Xu, C. Lu, J. Zhang, J. Chen, B. 2022-12-05 doi:10.1101/2022.12.05.519151 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus ]]> https://biorxiv.org/content/10.1101/2022.12.06.519325v1?rss=1 Jia, G.-S. Zhang, W.-C. Liang, Y. Liu, X.-H. Rhind, N. Pidoux, A. Brysch-Herzberg, M. Du, L.-L. 2022-12-09 doi:10.1101/2022.12.06.519325 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Non-allelic homologous recombination driven translocation explains histidine-rich protein 3 deletion mechanism in Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/2022.12.07.519189v1?rss=1 Hathaway, N. J. Kim, I. E. Young, N. W. Hui, S. T. DeFeo, R. Giesbrecht, D. Liang, E. Y. Nixon, C. P. Juliano, J. J. Parr, J. B. Bailey, J. A. 2022-12-08 doi:10.1101/2022.12.07.519189 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Co-evolution of human influenza A and Epstein Barr virus-specific CD8 ex vivo memory T cell receptor BV repertoires with increasing age ]]> https://biorxiv.org/content/10.1101/2022.12.15.520600v1?rss=1 60 years) donors, we demonstrate that CD8 memory TCR repertoires to three immunodominant epitopes, known to have cross-reactive responses, IAV- M158-66 (M1), EBV-BMLF1280-288 (BM), and EBV-BRLF109-117 (BR) co-evolve as individuals age. Cross-sectional studies showed that IAV-M1- and both EBV-specific repertoires narrowed their TRBV usage with increasing age manifesting to different degrees for each epitope. In fact, narrowing of EBV-BM and EBV-BR-specific TRBV usage correlated with increasing age. IAV- M1-specific TRBV usage was significantly narrowed by middle-age. There was evidence that TRBV usage was changing with increasing age. For instance, IAV-M1-specific dominant BV19 usage appeared to become bimodal showing either high or low frequency of usage in the older age group, while BV30 usage frequency directly correlated with age. For the EBV epitope-specific responses there was preferential usage of particular TRBV and changes in the hierarchy of BV family usage in the different age groups. There appeared to be focusing of the TRBV repertoire by all 3 epitopes to three common BV in the older donors, which would be consistent with retention of crossreactive TCR suggesting co-evolution. Longitudinal studies tracking two donors over 14- 15 years (middle age to older) showed that there were continuous modulations in the TCR repertoire of IAV-M1, EBV-BM and EBV-BR-specific responses over time. There was evidence that acute IAV infection could contribute to these changes in TCR repertoire. This could be occurring by the TCR cross-reactivity that is known to exist between these 3 epitopes, and which appeared to be enhanced during acute IAV infection based on increased usage of common shared TRBV. These studies suggest that virus-specific TCR repertoires change over time as individuals age leading to narrowing of the repertoire favoring retention of potentially crossreactive TCR. ]]> Clark, F. Gil, A. Aslan, N. Ghersi, D. Selin, L. K. 2022-12-18 doi:10.1101/2022.12.15.520600 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data ]]> https://biorxiv.org/content/10.1101/2022.12.16.520793v1?rss=1 Lee, L. Yu, H. Jia, B. B. Jussila, A. Zhu, C. Chen, J. Xie, L. Hafner, A. Strambio-De-Castillia, C. Boettiger, A. Ren, B. Li, Y. Hu, M. 2022-12-19 doi:10.1101/2022.12.16.520793 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Multi-center integrated analysis of non-coding CRISPR screens ]]> https://biorxiv.org/content/10.1101/2022.12.21.520137v1?rss=1 Yao, D. Tycko, J. Oh, W. Bounds, L. R. Gosai, S. J. Lataniotis, L. Mackay-Smith, A. Doughty, B. R. Gabdank, I. Schmidt, H. Youngworth, I. Andreeva, K. Ren, X. Barrera, A. Luo, Y. Siklenka, K. Yardimci, G. G. The ENCODE4 Consortium, Tewhey, R. Kundaje, A. Greenleaf, W. J. Sabeti, P. C. Leslie, C. Pritykin, Y. Moore, J. E. Beer, M. A. Gersbach, C. Reddy, T. E. Shen, Y. Engreitz, J. M. Bassik, M. C. Reilly, S. K. 2022-12-22 doi:10.1101/2022.12.21.520137 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Revisiting chromatin packaging in mouse sperm ]]> https://biorxiv.org/content/10.1101/2022.12.26.521943v1?rss=1 Yin, Q. Yang, C.-H. Strelkova, O. Sun, Y. H. Gopalan, S. Yang, L. Dekker, J. Fazzio, T. G. Li, X. G. Gibcus, J. Rando, O. 2022-12-27 doi:10.1101/2022.12.26.521943 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ pomBseen: An Automated Pipeline for Analysis of Fission Yeast Images ]]> https://biorxiv.org/content/10.1101/2022.12.27.521403v1?rss=1 Ohira, M. J. Rhind, N. 2022-12-27 doi:10.1101/2022.12.27.521403 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ A Transcriptional Cofactor Regulatory Network for the C. elegans Intestine ]]> https://biorxiv.org/content/10.1101/2023.01.05.522920v1?rss=1 Walhout, M. Horowitz, B. B. Nanda, S. 2023-01-06 doi:10.1101/2023.01.05.522920 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ A comparative analysis of microglial inducible Cre lines ]]> https://biorxiv.org/content/10.1101/2023.01.09.523268v1?rss=1 Faust, T. E. Feinberg, P. A. O'Connor, C. Kawaguchi, R. Chan, A. Strasburger, H. Masuda, T. Amann, L. Knobeloch, K.-P. E. Prinz, M. Schaefer, A. Schafer, D. P. 2023-01-09 doi:10.1101/2023.01.09.523268 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Size-Dependent Expression of the Fission Yeast Cdc13 Cyclin is Conferred by Translational Regulation ]]> https://biorxiv.org/content/10.1101/2023.01.16.524304v1?rss=1 Bashir, S. Sun, X.-M. Zhao, Y. Martinez-Illescas, N. G. Gallego-Lopez, I. Guerrero Negron, L. Keifenheim, D. Karadimitriou, T. Tran, T. Pickering, M. Marguerat, S. Rhind, N. 2023-01-16 doi:10.1101/2023.01.16.524304 Cold Spring Harbor Laboratory Press 2023-01-16 <![CDATA[ p53 controls choice between apoptotic and non-apoptotic death following DNA damage ]]> https://biorxiv.org/content/10.1101/2023.01.17.524444v1?rss=1 Honeywell, M. E. Isidor, M. S. L. Harper, N. W. Fontana, R. E. Cruz-Gordillo, P. Porto, S. A. Spinelli, J. B. Guertin, D. A. Lee, M. J. 2023-01-18 doi:10.1101/2023.01.17.524444 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Recurrent phases of strict protein limitation inhibit tumor growth and restore lifespan in a Drosophila intestinal cancer model ]]> https://biorxiv.org/content/10.1101/2023.01.18.524563v1?rss=1 Pfefferkorn, R. M. Mortzfeld, B. M. Fink, C. von Frieling, J. Bossen, J. Esser, D. Kaleta, C. M. Rosenstiel, P. Heine, H. Roeder, T. 2023-01-20 doi:10.1101/2023.01.18.524563 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Regulation of Ebola GP conformation and membrane binding by the chemical environment of the late endosome ]]> https://biorxiv.org/content/10.1101/2023.01.18.524651v1?rss=1 Jain, A. Govindan, R. Berkman, A. Luban, J. Durham, N. D. Munro, J. 2023-01-20 doi:10.1101/2023.01.18.524651 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Gut-associated lymphoid tissue attrition associates with response to anti-α4β7 therapy in ulcerative colitis ]]> https://biorxiv.org/content/10.1101/2023.01.19.524731v1?rss=1 Canales-Herrerias, P. Uzzan, M. Seki, A. Czepielewski, R. S. Verstockt, B. Livanos, A. Raso, F. Dunn, A. Dai, D. Wang, A. Al-taie, Z. Martin, J. Ko, H. M. Tokuyama, M. Tankelevich, M. Meringer, H. Cossarini, F. Jha, D. Krek, A. Paulsen, J. D. Zuber Nakadar, M. Wong, J. Erlich, E. C. Onufer, E. J. Helmink, B. A. Sharma, K. Rosenstein, A. Chung, G. Dawson, T. Juarez, J. Yajnik, V. Cerutti, A. Faith, J. Suarez-Farinas, M. Argmann, C. Petralia, F. Randolph, G. J. Polydorides, A. D. Reboldi, A. Colombel, J. F. Mehandru, S. 2023-01-20 doi:10.1101/2023.01.19.524731 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Sex differences in adolescent cannabis vapor self-administration mediate enduring effects on behavioral flexibility and prefrontal microglia activation in rats ]]> https://biorxiv.org/content/10.1101/2023.01.21.524468v1?rss=1 Freels, T. G. Westbrook, S. R. Wright, H. R. Kuyat, J. R. Zamberletti, E. Malena, A. N. Melville, M. W. Brown, A. M. Glodosky, N. C. Ginder, D. E. Klappenbach, C. M. Delevich, K. M. Rubino, T. McLaughlin, R. J. 2023-01-22 doi:10.1101/2023.01.21.524468 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils ]]> https://biorxiv.org/content/10.1101/2023.01.27.525911v1?rss=1 Zezulin, A. U. Ye, D. Howell, E. Yen, D. Bresciani, E. Diemer, J. Ren, J.-g. Ahmad, M. H. Castilla, L. H. Touw, I. P. Minn, A. J. Tong, W. Liu, P. P. Tan, K. Yu, W. Speck, N. A. 2023-01-28 doi:10.1101/2023.01.27.525911 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses ]]> https://biorxiv.org/content/10.1101/2023.02.01.526623v1?rss=1 Zvornicanin, S. N. Shaqra, A. M. Huang, Q. Y. Ornelas, E. Moghe, M. Knapp, M. Moquin, S. Dovala, D. Schiffer, C. A. Kurt Yilmaz, N. 2023-02-02 doi:10.1101/2023.02.01.526623 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ An efficient method for viable cryopreservation of hookworms and other gastrointestinal nematodes in the laboratory ]]> https://biorxiv.org/content/10.1101/2023.02.01.526637v1?rss=1 Li, H. Gazzola, D. Hu, Y. Aroian, R. V. 2023-02-01 doi:10.1101/2023.02.01.526637 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Quantification of gallium cryo-FIB milling damage in biological lamella ]]> https://biorxiv.org/content/10.1101/2023.02.01.526705v1?rss=1 Lucas, B. A. Grigorieff, N. 2023-02-03 doi:10.1101/2023.02.01.526705 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Mechanistic Modeling Explains the Production Dynamics of Recombinant Adeno-Associated Virus with the Baculovirus Expression Vector System ]]> https://biorxiv.org/content/10.1101/2023.02.04.527082v1?rss=1 Destro, F. Srinivasan, P. Kanter, J. M. Neufeld, C. Wolfrum, J. M. Barone, P. W. Springs, S. L. Sinskey, A. J. Cecchini, S. Kotin, R. M. Braatz, R. D. 2023-02-05 doi:10.1101/2023.02.04.527082 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ Pairtools: from sequencing data to chromosome contacts ]]> https://biorxiv.org/content/10.1101/2023.02.13.528389v1?rss=1 Open2C, Abdennur, N. Fudenberg, G. Flyamer, I. M. Galitsyna, A. A. Goloborodko, A. Imakaev, M. Venev, S. V. 2023-02-15 doi:10.1101/2023.02.13.528389 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States ]]> https://biorxiv.org/content/10.1101/2023.02.19.526477v1?rss=1 Chatterjee, D. Nogueira, A. T. Wefes, I. Chalkley, R. Sturzenegger Varvayanis, S. Fuhrmann, C. N. Varadarajan, J. Jacob, G. A. Gaines, C. H. Hubbard, N. M. Chaudhary, S. Layton, R. L. 2023-02-21 doi:10.1101/2023.02.19.526477 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Broadly effective ACE2 decoy proteins protect mice from lethal SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2023.02.22.529625v1?rss=1 75% animals, and increased animal survival rate from 0% (untreated) to >87.5% (treated). These results demonstrate that both proteins are good drug candidates for protecting animals from severe COVID-19. In a head-to-head comparison of these two proteins with five previously-described ACE2-Ig constructs, we found that two of these constructs, each carrying five surface mutations in the ACE2 region, had partial loss of neutralization potency against three SARS-CoV-2 variants. These data suggest that extensively mutating ACE2 residues near the RBD-binding interface should be avoided or performed with extra caution. Further, we found that both ACE2-Ig-95 and ACE2-Ig-105/106 could be produced to gram/liter level, demonstrating the developability of them as biologic drug candidates. Stress-condition stability test of them further suggests that more studies are required in the future to improve the stability of these proteins. These studies provide useful insight into critical factors for engineering and preclinical development of ACE2 decoys as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. Abstract ImportanceEngineering soluble ACE2 proteins that function as a receptor decoy to block SARS-CoV-2 infection is a very attractive approach to broadly effective and hard-to-escape anti-SARS-CoV-2 agents. This study here describes development of two antibody-like soluble ACE2 proteins that broadly block diverse SARS-CoV-2 variants including Omicron. In a stringent COVID-19 mouse model, both proteins successfully protected >87.5% animals from lethal SARS-CoV-2 infection. In addition, a head-to-head comparison of the two constructs developed in this study with five previously-described ACE2 decoy constructs were performed here. Two previously-described constructs with relatively more ACE2-surface mutations were found with less robust neutralization activities against diverse SARS-CoV-2 variants. Further, the developability of the two proteins as biologic drug candidates was also assessed here. This study provides two broadly anti-SARS-CoV-2 drug candidates and useful insight into critical factors for engineering and preclinical development of ACE2 decoy as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. TweetTwo antibody-like ACE2 decoy proteins could block diverse SARS-CoV-2 variants and prevent animals from severe COVID-19. ]]> Lu, M. Yao, W. Li, Y. Ma, D. Zhang, Z. Wang, H. Tang, X. Wang, Y. Li, C. Cheng, D. Lin, H. Yin, Y. Zhao, J. Zhong, G. 2023-02-23 doi:10.1101/2023.02.22.529625 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Epigenetic regulation of innate immune genes and enhanced interleukin-10 expression underlie chronic subclinical Plasmodium chabaudi infection ]]> https://biorxiv.org/content/10.1101/2023.02.23.529826v1?rss=1 de Souza Silva, L. Nguyen, Y. A. H. Monks, B. G. Forconi, C. S. Crabtree, J. N. Rodriguez, T. Tamburro, N. D. P. Sontheimer, E. J. Horvath, G. L. Abdullah, Z. Latz, E. Caffrey, D. R. Kurt-Jones, E. Gazzinelli, R. T. Fitzgerald, K. A. Golenbock, D. T. 2023-02-24 doi:10.1101/2023.02.23.529826 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Traumatic brain injury-induced fear generalization in mice involves hippocampal memory trace dysfunction and is alleviated by (R,S)-ketamine ]]> https://biorxiv.org/content/10.1101/2023.02.24.529876v1?rss=1 McGowan, J. C. Ladner, L. R. Shubeck, C. X. Tapia, J. LaGamma, C. T. Anqueira-Gonzalez, A. DeFrancesco, A. Chen, B. K. Hunsberger, H. C. Sydnor, E. J. Logan, R. W. Yu, T.-S. Kernie, S. G. Denny, C. A. 2023-02-27 doi:10.1101/2023.02.24.529876 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Lipofuscin-like autofluorescence within microglia and its impact on studying microglial engulfment ]]> https://biorxiv.org/content/10.1101/2023.02.28.530224v1?rss=1 Stillman, J. M. Lopes, F. M. Lin, J.-P. Hu, K. Reich, D. S. Schafer, D. P. 2023-03-01 doi:10.1101/2023.02.28.530224 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome ]]> https://biorxiv.org/content/10.1101/2023.03.01.530696v1?rss=1 Becker-Krail, D. Ketchesin, K. D. D. Xue, X. Wilson, R. Lam, T. T. Williams, K. Nairn, A. Tseng, G. Logan, R. W. 2023-03-02 doi:10.1101/2023.03.01.530696 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Systematic analyses of the resistance potential of drugs targeting SARS-CoV-2 main protease ]]> https://biorxiv.org/content/10.1101/2023.03.02.530652v1?rss=1 Flynn, J. M. Huang, Q. Y. M. Zvornicanin, S. N. Schneider-Nachum, G. Shaqra, A. M. Kurt Yilmaz, N. Moquin, S. A. Dovala, D. Schiffer, C. A. Bolon, D. N. A. 2023-03-02 doi:10.1101/2023.03.02.530652 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Genome-wide screen identifies host loci that modulate M. tuberculosis fitness in immunodivergent mice ]]> https://biorxiv.org/content/10.1101/2023.03.05.528534v1?rss=1 Meade, R. K. Long, J. E. Jinich, A. Rhee, K. Y. Ashbrook, D. G. Williams, R. W. Sassetti, C. M. Smith, C. M. 2023-03-06 doi:10.1101/2023.03.05.528534 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Differential requirements for different subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes in myoblast differentiation ]]> https://biorxiv.org/content/10.1101/2023.03.05.531193v1?rss=1 PADILLA-BENAVIDES, T. Olea-Flores, M. Sharma, T. Syed, S. A. Witwicka, H. Zuniga-Eulogio, M. D. Zhang, K. Navarro-Tito, N. Imbalzano, A. N. 2023-03-05 doi:10.1101/2023.03.05.531193 Cold Spring Harbor Laboratory Press 2023-03-05 <![CDATA[ Evolutionary constraint and innovation across hundreds of placental mammals ]]> https://biorxiv.org/content/10.1101/2023.03.09.531574v1?rss=1 Christmas, M. J. Kaplow, I. M. Genereux, D. P. Dong, M. X. Hughes, G. M. Li, X. Sullivan, P. F. Hindle, A. G. Andrews, G. Armstrong, J. C. Bianchi, M. Breit, A. M. Diekhans, M. Fanter, C. Foley, N. M. Goodman, D. B. Goodman, L. Keough, K. C. Kirilenko, B. Kowalczyk, A. Lawless, C. Lind, A. L. Meadows, J. R. S. Moreira, L. R. Redlich, R. W. Ryan, L. Swofford, R. Valenzuela, A. Wagner, F. Wallerman, O. Brown, A. R. Damas, J. Fan, K. Gatesy, J. Grimshaw, J. Johnson, J. Kozyrev, S. V. Lawler, A. J. Marinescu, V. D. Morrill, K. M. Osmanski, A. Paulat, N. S. 2023-03-09 doi:10.1101/2023.03.09.531574 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease ]]> https://biorxiv.org/content/10.1101/2023.03.10.531987v1?rss=1 Sullivan, P. F. Meadows, J. R. S. Gazal, S. Phan, B. N. Li, X. Genereux, D. P. Dong, M. X. Bianchi, M. Andrews, G. Sakthikumar, S. Nordin, J. Roy, A. Christmas, M. J. Marinescu, V. D. Wang, C. Wallerman, O. Xue, J. R. Li, Y. Yao, S. Sun, Q. Szatkiewicz, J. Wen, J. Huckins, L. M. Lawler, A. J. Keough, K. C. Zheng, Z. Zeng, J. Wray, N. R. Johnson, J. Chen, J. Zoonomia Consortium, Paten, B. Reilly, S. K. Hughes, G. M. Weng, Z. Pollard, K. S. Pfenning, A. R. Forsberg-Nilsson, K. Karlsson, E. K. Lindblad-Toh, K. 2023-03-10 doi:10.1101/2023.03.10.531987 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Distinct Th17 effector cytokines differentially promote microglial and blood-brain barrier inflammatory responses during post-infectious encephalitis ]]> https://biorxiv.org/content/10.1101/2023.03.10.532135v1?rss=1 Wayne, C. R. Bremner, L. I. Faust, T. E. Duran-Laforet, V. Ampatey, N. Ho, S. J. Feinberg, P. A. Arvanitis, P. Ciric, B. Delaney, S. L. Vargas-Deming, W. Swedo, S. Menon, V. Schafer, D. P. Cutforth, T. Agalliu, D. 2023-03-12 doi:10.1101/2023.03.10.532135 Cold Spring Harbor Laboratory Press 2023-03-12 <![CDATA[ Antigen receptor signaling and cell death resistance controls intestinal humoral response zonation. ]]> https://biorxiv.org/content/10.1101/2023.03.16.532481v1?rss=1 Raso, F. Liu, S. Willett, M. J. Barton, G. Mayer, C. T. Bannard, O. Acharya, M. Muppidi, J. Marshak-Rothstein, A. Reboldi, A. 2023-03-16 doi:10.1101/2023.03.16.532481 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Cryo-EM structure of the human Sirtuin 6-nucleosome complex ]]> https://biorxiv.org/content/10.1101/2023.03.17.533206v1?rss=1 Chio, U. S. Rechiche, O. Bryll, A. R. Zhu, J. Feldman, J. Peterson, C. Tan, S. Armache, J.-P. 2023-03-18 doi:10.1101/2023.03.17.533206 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Embryonic type 3 innate lymphoid cells sense maternal dietary cholesterol to control local Peyer's patch development ]]> https://biorxiv.org/content/10.1101/2023.03.19.533339v1?rss=1 Howley, K. Berthelette, A. Ceglia, S. Kang, J. Reboldi, A. 2023-03-23 doi:10.1101/2023.03.19.533339 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Self-delivering CRISPR RNAs for AAV Co-delivery and Genome Editing in vivo ]]> https://biorxiv.org/content/10.1101/2023.03.20.533459v1?rss=1 Zhang, H. Kelly, K. Lee, J. Echeverria, D. Cooper, D. Panwala, R. Chen, Z. Gaston, N. Newby, G. A. Xie, J. Liu, D. R. Gao, G. Wolfe, S. A. Khvorova, A. Watts, J. K. Sontheimer, E. J. 2023-03-20 doi:10.1101/2023.03.20.533459 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Synthesis and validation of click-modified of NOD1/2 agonists ]]> https://biorxiv.org/content/10.1101/2023.03.28.534546v1?rss=1 Bharadwaj, R. Anonick, M. V. Mashayekh, S. Brown, A. Wodzanowski, K. A. Okuda, K. Silverman, N. Grimes, C. L. 2023-03-28 doi:10.1101/2023.03.28.534546 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Nucleolar structure connects with global nuclear organization ]]> https://biorxiv.org/content/10.1101/2023.03.30.534966v1?rss=1 Wang, C. Ma, H. Baserga, S. Pederson, T. Huang, S. 2023-03-31 doi:10.1101/2023.03.30.534966 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness ]]> https://biorxiv.org/content/10.1101/2023.03.30.535005v1?rss=1 View larger version (50K): org.highwire.dtl.DTLVardef@8b4864org.highwire.dtl.DTLVardef@3daad9org.highwire.dtl.DTLVardef@9ba446org.highwire.dtl.DTLVardef@3e1a08_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIS:D614G is ubiquitous among SARS-CoV-2 B-lineage Spikes and is required for infectivity of the main Variants of Concern C_LIO_LIIn an example of convergent evolution, SARS-CoV-2 A lineage viruses maintained transmission chains in the absence of S:D614G, but were instead dependent upon S:Q613H or S:H655Y C_LIO_LIS:D614G and S:H655Y are both adaptations to the polybasic S1/S2 cleavage site C_LIO_LIIncreased infectivity of S:D614G and S:H655Y is associated with a more open RBD conformation and increased steady-state levels of virion-associated S1 C_LI ]]> Yurkovetskiy, L. Egri, S. Kurhade, C. Diaz-Salinas, M. A. Jaimes, J. A. Nyalile, T. Xie, X. Choudhary, M. C. Dauphin, A. Li, J. Z. Munro, J. B. Shi, P.-Y. Shen, K. Luban, J. 2023-03-31 doi:10.1101/2023.03.30.535005 Cold Spring Harbor Laboratory Press 2023-03-31 <![CDATA[ A single neuron in C. elegans orchestrates multiple motor outputs through parallel modes of transmission ]]> https://biorxiv.org/content/10.1101/2023.04.02.532814v1?rss=1 Huang, Y.-C. Luo, J. Huang, W. Baker, C. M. Gomes, M. A. Byrne, A. B. Flavell, S. W. 2023-04-02 doi:10.1101/2023.04.02.532814 Cold Spring Harbor Laboratory Press 2023-04-02 <![CDATA[ Modeling neurodevelopmental disorder-associated hAGO1 mutations in C. elegans Argonaute ALG-1 ]]> https://biorxiv.org/content/10.1101/2023.04.06.535748v1?rss=1 Duan, Y. Li, L. Panzade, G. P. PITON, A. Zinovyeva, A. Ambros, V. 2023-04-07 doi:10.1101/2023.04.06.535748 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Uncovering circadian rhythm disruptions of synaptic proteome signaling in prefrontal cortex and nucleus accumbens associated with opioid use disorder ]]> https://biorxiv.org/content/10.1101/2023.04.07.536056v1?rss=1 Puig, S. Xue, X. Salisbury, R. Shelton, M. A. Kim, S.-M. Hildebrand, M. A. Glausier, J. R. Freyberg, Z. Tseng, G. C. Yocum, A. K. Lewis, D. A. Seney, M. L. MacDonald, M. L. Logan, R. W. 2023-04-07 doi:10.1101/2023.04.07.536056 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection ]]> https://biorxiv.org/content/10.1101/2023.04.10.536057v1?rss=1 Mostrom, M. J. Yu, S. Tran, D. Saccoccio, F. Versoza, C. J. Malouli, D. J. Mirza, A. Valencia, S. Gilbert, M. Blair, R. V. Hansen, S. G. Barry, P. A. Fruh, K. Jensen, J. D. Pfeifer, S. P. Kowalik, T. F. Permar, S. R. Kaur, A. 2023-04-10 doi:10.1101/2023.04.10.536057 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Cryo-EM structure of the human cardiac myosin filament ]]> https://biorxiv.org/content/10.1101/2023.04.11.536274v1?rss=1 Dutta, D. Nguyen, V. Campbell, K. Padron, R. Craig, R. 2023-04-12 doi:10.1101/2023.04.11.536274 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ A novel mouse allele of the DNA/RNA helicase senataxin (Setxspcar3) causing meiotic arrest of spermatocytes and male infertility ]]> https://biorxiv.org/content/10.1101/2023.04.12.536672v1?rss=1 Fujiwara, Y. Saito, K. Sun, F. Inoue, E. Schimenti, J. Okada, Y. Handel, M. A. 2023-04-13 doi:10.1101/2023.04.12.536672 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Selenium reduction of ubiquinone via SQOR suppresses ferroptosis ]]> https://biorxiv.org/content/10.1101/2023.04.13.535674v1?rss=1 Lee, N. Park, S. J. Lange, M. Tseyang, T. Doshi, M. B. Kim, T. Song, Y. Kim, D. Greer, P. L. Olzmann, J. A. Spinelli, J. Kim, D. 2023-04-13 doi:10.1101/2023.04.13.535674 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Engineering Nme2Cas9 Adenine Base Editors with Improved Activity and Targeting Scope ]]> https://biorxiv.org/content/10.1101/2023.04.14.536905v1?rss=1 Bamidele, N. Zhang, H. Dong, X. Gaston, N. Cheng, H. Kelly, K. Watts, J. K. Xie, J. Gao, G. Sontheimer, E. J. 2023-04-14 doi:10.1101/2023.04.14.536905 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Gardnerella vaginolysin potentiates glycan molecular mimicry by Neisseria gonorrhoeae ]]> https://biorxiv.org/content/10.1101/2023.04.15.537036v1?rss=1 Morrill, S. R. Saha, S. Varki, A. P. Lewis, W. G. Ram, S. Lewis, A. L. 2023-04-15 doi:10.1101/2023.04.15.537036 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ The mitochondrial Ca2+ channel MCU is critical for tumor growth by supporting cell cycle progression and proliferation ]]> https://biorxiv.org/content/10.1101/2023.04.26.538295v1?rss=1 Fernandez Garcia, E. Paudel, U. Noji, M. C. Bowman, C. E. Pitarresi, J. R. Rustgi, A. K. Wellen, K. E. Arany, Z. Weissenrieder, J. S. Foskett, J. K. 2023-04-28 doi:10.1101/2023.04.26.538295 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Rit2 loss in dopaminergic neurons drives a progressive Parkinsonian phenotype ]]> https://biorxiv.org/content/10.1101/2023.04.26.538430v1?rss=1 Kearney, P. J. Zhang, Y. Tan, Y. Kahuno, E. Conklin, T. Fagan, R. R. Yue, Z. Melikian, H. E. Shaffer, S. A. Pavchinskiy, R. G. 2023-04-28 doi:10.1101/2023.04.26.538430 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Lactate transporter MCT1 in hepatic stellate cells promotes fibrotic collagen expression in nonalcoholic steatohepatitis ]]> https://biorxiv.org/content/10.1101/2023.05.03.539244v1?rss=1 Min, K. Yenilmez, B. Kelly, M. Echeverria, D. Elleby, M. Lifshitz, L. M. Raymond, N. Tsagkaraki, E. Harney, S. M. DiMarzio, C. McHugh, N. Bramato, B. Morrison, B. Rothstein, J. D. Khvorova, A. Czech, M. P. 2023-05-03 doi:10.1101/2023.05.03.539244 Cold Spring Harbor Laboratory Press 2023-05-03 <![CDATA[ Three-dimensional characterization of medium spiny neuron heterogeneity in the adult mouse striatum ]]> https://biorxiv.org/content/10.1101/2023.05.04.539488v1?rss=1 Gayden, J. Puig, S. Srinivasan, C. Buck, S. A. Gamble, M. C. Glausier, J. R. Tejeda, H. A. Dong, Y. Pfenning, A. R. Logan, R. Freyberg, Z. 2023-05-05 doi:10.1101/2023.05.04.539488 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Up-regulation of cholesterol synthesis pathways and limited neurodegeneration in a knock-in Sod1 mutant mouse model of ALS. ]]> https://biorxiv.org/content/10.1101/2023.05.05.539444v1?rss=1 Dominov, J. A. Madigan, L. A. Whitt, J. P. Rademacher, K. L. Webster, K. M. Zhang, H. Banno, H. A. Tang, S. Zhang, Y. Wightman, N. Shychuck, E. M. Page, J. Weiss, A. Kelly, K. Kucukural, A. A. Brodsky, M. H. Jaworski, A. Fallon, J. R. Lipscombe, D. Brown, R. H. 2023-05-05 doi:10.1101/2023.05.05.539444 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity ]]> https://biorxiv.org/content/10.1101/2023.05.15.540865v1?rss=1 Reese, F. Williams, B. Balderrama-Gutierrez, G. Wyman, D. Celik, M. H. Rebboah, E. Rezaie, N. Trout, D. Razavi-Mohseni, M. Jiang, Y. Borsari, B. Morabito, S. Liang, H. Y. McGill, C. J. Rahmanian, S. Sakr, J. Jiang, S. Zeng, W. Carvalho, K. Weimer, A. K. Dionne, L. A. McShane, A. Bedi, K. Elhajjajy, S. I. Upchurch, S. Jou, J. Youngworth, I. Gabdank, I. Sud, P. Jolanki, O. Strattan, J. S. Kagda, M. S. Snyder, M. P. Hitz, B. C. Moore, J. E. Weng, Z. Bennett, D. Reinholdt, L. Ljungman, M. Beer, M. A. Gerstein, M. B. Pachter, L. Guigo, R. Wold, B. J. Mort 2023-05-16 doi:10.1101/2023.05.15.540865 Cold Spring Harbor Laboratory Press 2023-05-16 <![CDATA[ Single nucleus transcriptomics of human and monkey striatum implicates DNA damage, neuroinflammation, and neurodegeneration signaling in opioid use disorder ]]> https://biorxiv.org/content/10.1101/2023.05.17.541145v1?rss=1 Phan, B. N. Ray, M. H. Xue, X. Fenster, R. J. Kohut, S. J. Bergman, J. Haber, S. N. Mccullough, K. M. Kuppe-Fish, M. K. Glausier, J. R. Su, Q. Tipton, A. E. Lewis, D. A. Freyberg, Z. Tseng, G. C. Ressler, K. J. Russek, S. J. Alekseyev, Y. Seney, M. L. Pfenning, A. R. Logan, R. W. 2023-05-17 doi:10.1101/2023.05.17.541145 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ Reduction of retinal ganglion cell death in mouse models of familial dysautonomia using AAV-mediated gene therapy and splicing modulators ]]> https://biorxiv.org/content/10.1101/2023.05.22.541535v1?rss=1 Schultz, A. Cheng, S.-Y. Kirchner, E. Costello, S. Miettinen, H. Chaverra, M. King, C. George, L. Zhao, X. Narasimhan, J. Weetall, M. Slaugenhaupt, S. Morini, E. Punzo, C. Lefcort, F. 2023-05-24 doi:10.1101/2023.05.22.541535 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo ]]> https://biorxiv.org/content/10.1101/2023.05.26.542506v1?rss=1 1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure ([~]6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions. ]]> Yamada, K. Hariharan, V. N. Caiazzi, J. Miller, R. Ferguson, C. Sapp, E. Fakih, H. Tan, Q. Yamada, N. Furgal, R. Paquette, J. Bramato, B. McHugh, N. Summer, A. Lochmann, C. Godinho, B. Hildebrand, S. Echeverria, D. Hassler, M. Alterman, J. DiFiglia, M. Aronin, N. Khvorova, A. 2023-05-26 doi:10.1101/2023.05.26.542506 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2023.05.27.542323v1?rss=1 Zeng, J. Nguyen, M. A. Liu, P. Ferreira da Silva, L. Lin, L. Y. Justus, D. G. Petri, K. Clement, K. Porter, S. N. Verma, A. Neri, N. R. Rosanwo, T. Ciuculescu, M.-F. Abriss, D. Mintzer, E. Maitland, S. A. Demirci, S. Tisdale, J. F. Williams, D. A. Zhu, L. J. Pruett-Miller, S. M. Pinello, L. Joung, J. K. Pattanayak, V. Manis, J. P. Armant, M. Pellin, D. Brendel, C. Wolfe, S. A. Bauer, D. E. 2023-05-27 doi:10.1101/2023.05.27.542323 Cold Spring Harbor Laboratory Press 2023-05-27 <![CDATA[ Structural characterization of a pathogenic antibody underlying vaccine-induced immune thrombotic thrombocytopenia (VITT) ]]> https://biorxiv.org/content/10.1101/2023.05.28.542636v1?rss=1 Nguyen, S. N. Le, S.-H. Ivanov, D. G. Ivetic, N. Nazy, I. Kaltashov, I. A. 2023-05-29 doi:10.1101/2023.05.28.542636 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Identification of 30 transition fibre proteins reveals a complex and dynamic structure with essential roles in ciliogenesis ]]> https://biorxiv.org/content/10.1101/2023.05.29.542710v1?rss=1 Ahmed, M. Wheeler, R. J. Tyc, J. Shafiq, S. Sunter, J. Vaughan, S. 2023-05-29 doi:10.1101/2023.05.29.542710 Cold Spring Harbor Laboratory Press 2023-05-29 <![CDATA[ Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay ]]> https://biorxiv.org/content/10.1101/2023.05.31.543082v1?rss=1 Mangkalaphiban, K. Ganesan, R. Jacobson, A. 2023-06-01 doi:10.1101/2023.05.31.543082 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Expression of ALS-PFN1 impairs vesicular degradation in iPSC-derived microglia ]]> https://biorxiv.org/content/10.1101/2023.06.01.541136v1?rss=1 Funes, S. Gadd, D. H. Mosqueda, M. Zhong, J. Jung, J. FNU, S. Unger, M. Cameron, D. Dawes, P. Keagle, P. J. McDonough, J. A. Boopathy, S. Sena-Esteves, M. Lutz, C. M. Skarnes, W. C. Lim, E. T. Schafer, D. P. Massi, F. Landers, J. E. Bosco, D. A. 2023-06-01 doi:10.1101/2023.06.01.541136 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Autonomous and non-cell autonomous etiology of ciliopathy associated structural birth defects ]]> https://biorxiv.org/content/10.1101/2023.06.07.544132v1?rss=1 Francis, R. J. San Agustin, J. T. Szabo Rogers, H. L. Cui, C. Jonassen, J. A. Eguether, T. Follit, J. A. Lo, C. W. Pazour, G. 2023-06-07 doi:10.1101/2023.06.07.544132 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis ]]> https://biorxiv.org/content/10.1101/2023.06.13.544859v1?rss=1 Syed, S. A. Shqillo, K. Nand, A. Zhan, Y. Dekker, J. Imbalzano, A. N. 2023-06-14 doi:10.1101/2023.06.13.544859 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ Regulatory properties of transcription factors with diverse mechanistic function ]]> https://biorxiv.org/content/10.1101/2023.06.15.545127v1?rss=1 Ali, M. Z. Guharajan, S. Parisutham, V. Brewster, R. C. 2023-06-15 doi:10.1101/2023.06.15.545127 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ The pentameric complex is not required for vertical transmission of cytomegalovirus in seronegative pregnant rhesus macaques ]]> https://biorxiv.org/content/10.1101/2023.06.15.545169v1?rss=1 Wang, H.-Y. Taher, H. Kreklywich, C. N. Schmidt, K. A. Scheef, E. A. Barfield, R. Otero, C. E. Valencia, S. Crooks, C. M. Mirza, A. Woods, K. Burgt, N. V. Kowalik, T. F. Barry, P. A. Hansen, S. G. Tarantal, A. F. Chan, C. Streblow, D. N. Picker, L. J. Kaur, A. Frueh, K. Permar, S. R. Malouli, D. 2023-06-16 doi:10.1101/2023.06.15.545169 Cold Spring Harbor Laboratory Press 2023-06-16 <![CDATA[ Genome-wide kinetic profiling of pre-mRNA 3' end cleavage ]]> https://biorxiv.org/content/10.1101/2023.06.21.545926v1?rss=1 Torres-Ulloa, L. Calvo-Roitberg, E. Pai, A. A. 2023-06-22 doi:10.1101/2023.06.21.545926 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus MT:10398A>G ]]> https://biorxiv.org/content/10.1101/2023.06.22.546129v1?rss=1 G (rs2853826) was significantly associated with overall MT-heteroplasmy in brain tissue while also being linked with the largest number of distinct disease phenotypes of all annotated MT variants in MitoMap. Using gene-expression data from our brain samples, our modeling discovered several gene networks involved in mitochondrial respiratory chain and Complex I function associated with 10398A>G. The variant was also found to be an expression quantitative trait loci (eQTL) for the gene MT-ND3. We further characterized the effect of 10398A>G by phenotyping a population of lymphoblastoid cell-lines (LCLs) with and without the variant allele. Examination of RNA sequence data from these LCLs reveal that 10398A>G was an eQTL for MT-ND4. We also observed in LCLs that 10398A>G was significantly associated with overall MT-heteroplasmy within the MT control region, confirming the initial findings observed in post-mortem brain tissue. These results provide novel evidence linking MT SNPs with MT heteroplasmy and open novel avenues for the investigation of pathomechanisms that are driven by this pleiotropic disease associated loci. ]]> Smullen, M. Olson, M. N. Murray, L. F. Suresh, M. Yan, G. Dawes, P. Barton, N. J. Mason, J. N. Zhang, Y. Fernandez-Fontaine, A. A. Church, G. M. Mastroeni, D. Wang, Q. Lim, E. T. Chan, Y. Readhead, B. 2023-06-25 doi:10.1101/2023.06.22.546129 G]]> Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Dysregulated Pulmonary Inflammatory Responses Exacerbate the Outcome of Secondary Aspergillosis Following Influenza ]]> https://biorxiv.org/content/10.1101/2023.06.27.546808v1?rss=1 Lee, C. K. Oliveira, L. V. N. Akalin, A. Specht, C. Lourenco, D. Gomez, C. L. Ramirez-Ortiz, Z. G. Wang, J. P. Levitz, S. M. 2023-06-30 doi:10.1101/2023.06.27.546808 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ FruitFire: a luciferase based on a fruit fly metabolic enzyme ]]> https://biorxiv.org/content/10.1101/2023.06.30.547126v1?rss=1 1000-fold. FruitFire enabled in vivo bioluminescence imaging in the brains of mice using the pro-luciferin CycLuc2-amide. The conversion of a fruit fly enzyme into a luciferase capable of in vivo imaging underscores the potential for bioluminescence with a range of adenylating enzymes from nonluminescent organisms, and the possibilities for application-focused design of enzyme-substrate pairs. ]]> Adams, S. T. Zephyr, J. Bohn, M. F. Schiffer, C. A. Miller, S. C. 2023-06-30 doi:10.1101/2023.06.30.547126 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Reverse engineering of a pathogenic antibody reveals the molecular mechanism of vaccine-induced immune thrombotic thrombocytopenia ]]> https://biorxiv.org/content/10.1101/2023.06.30.547300v1?rss=1 Ivanov, D. G. Ivetic, N. Du, Y. Nguyen, S. N. Le, H. S. Favre, D. Nazy, I. Kaltashov, I. A. 2023-07-01 doi:10.1101/2023.06.30.547300 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Dual targeting of hepatocyte DGAT2 and stellate cell FASN alleviates nonalcoholic steatohepatitis in mice. ]]> https://biorxiv.org/content/10.1101/2023.07.05.547848v1?rss=1 Yenilmez, B. Harney, S. M. DiMarzio, C. Kelly, M. Min, K. Echeverria, D. Bramato, B. M. Jackson, S. O. Reddig, K. Kim, J. K. Khvorova, A. Czech, M. P. 2023-07-05 doi:10.1101/2023.07.05.547848 Cold Spring Harbor Laboratory Press 2023-07-05 <![CDATA[ Aub, Vasa and Armi localization to phase separated nuage is dispensable for piRNA biogenesis and transposon silencing in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.07.25.549160v1?rss=1 Ho, S. Rice, N. P. Yu, T. Weng, Z. Theurkauf, W. E. 2023-07-26 doi:10.1101/2023.07.25.549160 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Rapid disassembly and Piwi-independent reassembly of Drosophila piRNA cluster heterochromatin following acute heat shock ]]> https://biorxiv.org/content/10.1101/2023.07.26.549158v1?rss=1 Rice, N. P. Ho, S. Weng, Z. Theurkauf, W. P. 2023-07-26 doi:10.1101/2023.07.26.549158 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Challenges in identifying mRNA transcript starts and ends from long-read sequencing data ]]> https://biorxiv.org/content/10.1101/2023.07.26.550536v1?rss=1 Calvo-Roitberg, E. Daniels, R. F. Pai, A. A. 2023-07-27 doi:10.1101/2023.07.26.550536 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Expression of a STING Gain-of-function Mutation in Endothelial Cells Initiates Lymphocytic Infiltration of the Lungs ]]> https://biorxiv.org/content/10.1101/2023.07.27.550897v1?rss=1 Gao, K. M. Chiang, K. Korkmaz, F. T. Janardhan, H. P. Trivedi, C. M. Quinton, L. J. Gingras, S. M. Fitzgerald, K. A. Marshak-Rothstein, A. 2023-07-27 doi:10.1101/2023.07.27.550897 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Activation of Autoreactive Lymphocytes in the Lung by STING Gain-of-function Mutation Radioresistant Cells ]]> https://biorxiv.org/content/10.1101/2023.07.28.551002v1?rss=1 Gao, K. M. Nundel, K. Chiang, K. Yin, X. Utz, P. J. Fitzgerald, K. A. Marshak-Rothstein, A. 2023-07-28 doi:10.1101/2023.07.28.551002 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in hepatic stellate cells ]]> https://biorxiv.org/content/10.1101/2023.07.29.551032v1?rss=1 Sun, C. Zhou, C. Daneshvar, K. Kratkiewicz, A. J. Ben Saad, A. Hess, A. Chen, J. Y. Pondick, J. V. York, S. R. Li, W. Moran, S. P. Gentile, S. Ur Rahman, R. Li, Z. Sparks, R. Habboub, T. Kim, B.-M. Choi, M. Affo, S. Schwabe, R. F. Popov, Y. V. Mullen, A. C. 2023-07-30 doi:10.1101/2023.07.29.551032 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ The ciliary MBO2 complex targets assembly of inner arm dynein b and reveals additional doublet microtubule asymmetries ]]> https://biorxiv.org/content/10.1101/2023.07.31.551375v1?rss=1 Fu, G. Augspurger, K. Sakizadeh, J. Reck, J. Bower, R. Tritschler, D. Gui, L. Nicastro, D. Porter, M. E. 2023-08-02 doi:10.1101/2023.07.31.551375 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Screening the human druggable genome identifies ABHD17B as an anti-fibrotic target in hepatic stellate cells ]]> https://biorxiv.org/content/10.1101/2023.08.07.551744v1?rss=1 9,500 genes in primary human HSCs and identify ABHD17B as a potential therapeutic target to inhibit liver fibrosis. ]]> Li, W. Sparks, R. P. Sun, C. Yang, Y. Pantano, L. Kirchner, R. Chen, J. Y. Moran, S. P. Barrera, V. Wrobel, D. Sui, S. J. H. Aspnes, G. Schuler, M. Smith, J. Medoff, B. D. Boustany-Kari, C. M. Rippmann, J. F. Santos, D. M. Doerner, J. F. Mullen, A. C. 2023-08-07 doi:10.1101/2023.08.07.551744 Cold Spring Harbor Laboratory Press 2023-08-07 <![CDATA[ CD20 is a mammalian odorant receptor expressed in a subset of olfactory sensory neurons that mediates innate avoidance of predators ]]> https://biorxiv.org/content/10.1101/2023.08.08.552498v1?rss=1 Jiang, H.-C. Park, S. J. Wang, I.-H. Bear, D. M. Nowlan, A. Greer, P. L. 2023-08-10 doi:10.1101/2023.08.08.552498 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Casein kinase II promotes piRNA production through direct phosphorylation of USTC component TOFU-4 ]]> https://biorxiv.org/content/10.1101/2023.08.09.552615v1?rss=1 Mello, C. ZHANG, G. Zheng, C. ding, y.-h. 2023-08-10 doi:10.1101/2023.08.09.552615 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Transcriptional suppression of sphingolipid catabolism controls pathogen resistance in C. elegans ]]> https://biorxiv.org/content/10.1101/2023.08.10.552843v1?rss=1 Nasrallah, M. A. Peterson, N. D. Salisbury, J. E. Liu, P. Page, A. L. Tse, S. Y. Wani, K. A. Tocheny, C. E. Pukkila-Worley, R. 2023-08-11 doi:10.1101/2023.08.10.552843 Cold Spring Harbor Laboratory Press 2023-08-11 <![CDATA[ Thyroid hormone rewires cortical circuits to coordinate body-wide metabolism and exploratory drive ]]> https://biorxiv.org/content/10.1101/2023.08.10.552874v1?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. 2023-08-10 doi:10.1101/2023.08.10.552874 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Coxsackievirus infection induces direct pancreatic β-cell killing but poor anti-viral CD8+ T-cell responses ]]> https://biorxiv.org/content/10.1101/2023.08.19.553954v1?rss=1 Vecchio, F. Carre, A. Korenkov, D. Zhou, Z. Apaolaza, P. Tuomela, S. Burgos-Morales, O. Snowhite, I. Perez-Hernandez, J. Brandao, B. Afonso, G. Halliez, C. Kaddis, J. Kent, S. C. Nakayama, M. Richardson, S. J. Vinh, J. Verdier, Y. Laiho, J. Scharfmann, R. Solimena, M. Marinicova, Z. Bismuth, E. Lucidarme, N. Sanchez, J. Bustamante, C. Gomez, P. Buus, S. the nPOD-Virus Working Group, You, S. Pugliese, A. Hyoty, H. Rodriguez-Calvo, T. Flodstrom-Tullberg, M. Mallone, R. 2023-08-21 doi:10.1101/2023.08.19.553954 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Mycobacterium tuberculosis response to cholesterol is integrated with environmental pH and potassium levels via a lipid utilization regulator ]]> https://biorxiv.org/content/10.1101/2023.08.22.554309v1?rss=1 Chen, Y. MacGilvary, N. J. Tan, S. 2023-08-25 doi:10.1101/2023.08.22.554309 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Adrenergic Reprogramming of Preexisting Adipogenic Trajectories Steer Naive Mural Cells Toward Beige Differentiation ]]> https://biorxiv.org/content/10.1101/2023.08.26.554950v1?rss=1 Kathleen, D. Cortez, B. N. Lin, J. Z. Lama, D. Layne, M. D. Farmer, S. R. Rabhi, N. 2023-08-26 doi:10.1101/2023.08.26.554950 Cold Spring Harbor Laboratory Press 2023-08-26 <![CDATA[ A distinct class of hematopoietic stem cells develop from the human yellow bone marrow ]]> https://biorxiv.org/content/10.1101/2023.08.29.555167v1?rss=1 Nguyen, T. T. Loureiro, Z. Y. Desai, A. DeSouza, T. Joyce, S. Khair, L. Samant, A. Cirka, H. Solivan-Rivera, J. Ziegler, R. Brehm, M. Messina, L. M. Corvera, S. 2023-08-31 doi:10.1101/2023.08.29.555167 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Evolutionarily related host and microbial pathways regulate fat desaturation ]]> https://biorxiv.org/content/10.1101/2023.08.31.555782v1?rss=1 Fox, B. Helf, M. Burkhardt, R. Artyukhin, A. Curtis, B. Palomino, D. F. Chaturbedi, A. Tauffenberger, A. Wrobel, C. J. Zhang, Y. Lee, S. S. Schroeder, F. 2023-08-31 doi:10.1101/2023.08.31.555782 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Identification of genome safe harbor loci for human gene therapy based on evolutionary biology and comparative genomics ]]> https://biorxiv.org/content/10.1101/2023.09.08.556857v1?rss=1 Quezada-Ramirez, M. A. Loncar, S. Campbell, M. A. Gifford, R. J. Kotin, R. M. 2023-09-10 doi:10.1101/2023.09.08.556857 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ Whole Genome Sequencing Based Analysis of Inflammation Biomarkers in the Trans-Omics for Precision Medicine (TOPMed) Consortium ]]> https://biorxiv.org/content/10.1101/2023.09.10.555215v1?rss=1 Jiang, M.-Z. Gaynor, S. M. Li, X. Van Buren, E. Stilp, A. Buth, E. Wang, F. F. Manansala, R. Gogarten, S. M. Li, Z. Polfus, L. M. Salimi, S. Bis, J. C. Pankratz, N. Yanek, L. R. Durda, P. Tracy, R. P. Rich, S. S. Rotter, J. I. Mitchell, B. D. Lewis, J. P. Psaty, B. M. Pratte, K. A. Silverman, E. K. Kaplan, R. C. Avery, C. North, K. Mathias, R. A. Faraday, N. Lin, H. Wang, B. Carson, A. P. Norwood, A. F. Gibbs, R. A. Kooperberg, C. Lundin, J. Peters, U. Dupuis, J. Hou, L. Fornage, M. Benjamin, E. J. Reiner, A. P. Bowler, R. P. Lin, X. Auer, P. L. Raf 2023-09-12 doi:10.1101/2023.09.10.555215 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Developmental priming of cancer susceptibility ]]> https://biorxiv.org/content/10.1101/2023.09.12.557446v1?rss=1 Panzeri, I. Fagnocchi, L. Apostle, S. Tompkins, M. Wolfrum, E. Madaj, Z. Hostetter, G. Liu, Y. Schaefer, K. Yang, C.-H. Bergsma, A. Drougard, A. Dror, E. PERMUTE, Chandler, D. Schramek, D. Triche, T. J. Pospisilik, J. A. 2023-09-15 doi:10.1101/2023.09.12.557446 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ A brown fat-enriched adipokine, ASRA, is a leptin receptor antagonist that stimulates appetite ]]> https://biorxiv.org/content/10.1101/2023.09.12.557454v1?rss=1 Huang, L. Liu, P. Du, Y. Pan, D. Lee, A. Wolfe, S. Wang, Y.-X. 2023-09-12 doi:10.1101/2023.09.12.557454 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease ]]> https://biorxiv.org/content/10.1101/2023.09.13.557414v1?rss=1 Yin, R. Melton, S. Huseby, E. Kardar, M. Chakraborty, A. K. 2023-09-16 doi:10.1101/2023.09.13.557414 Cold Spring Harbor Laboratory Press 2023-09-16 <![CDATA[ Nanoparticle delivery of innate immune agonists combines with senescence-inducing agents to mediate T cell control of pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2023.09.18.558307v1?rss=1 Chibaya, L. Lusi, C. F. DeMarco, K. D. Kane, G. I. Brassil, M. L. Parikh, C. N. Murphy, K. C. Li, J. Naylor, T. E. Cerrutti, J. Peura, J. Pitarresi, J. R. Zhu, L. J. Fitzgerald, K. A. Atukorale, P. U. Ruscetti, M. A. 2023-09-18 doi:10.1101/2023.09.18.558307 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Single intravitreal administration of a tetravalent siRNA exhibits robust and efficient gene silencing in rodent and swine photoreceptors ]]> https://biorxiv.org/content/10.1101/2023.09.20.558641v1?rss=1 Cheng, S.-Y. Caiazzi, J. Biscans, A. Alterman, J. F. Echeverria, D. McHugh, N. Hassler, M. Jolly, S. Giguere, D. Cipi, J. Khvorova, A. Punzo, C. 2023-09-22 doi:10.1101/2023.09.20.558641 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ A 4D transcriptomic map for the evolution of multiple sclerosis-like lesions in the marmoset brain ]]> https://biorxiv.org/content/10.1101/2023.09.25.559371v1?rss=1 Lin, J.-P. Brake, A. Donadieu, M. Lee, A. Kawaguchi, R. Sati, P. Geschwind, D. H. Jacobson, S. Schafer, D. P. Reich, D. S. 2023-09-27 doi:10.1101/2023.09.25.559371 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Contributions of hyperactive mutations in Mpro from SARS-CoV-2 to drug resistance ]]> https://biorxiv.org/content/10.1101/2023.09.28.560010v1?rss=1 Flynn, J. M. Duggan, S. N. Shaqra, A. M. Dovala, D. Schiffer, C. A. Bolon, D. 2023-09-29 doi:10.1101/2023.09.28.560010 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Mapping of multiple neurotransmitter receptor subtypes and distinct protein complexes to the connectome ]]> https://biorxiv.org/content/10.1101/2023.10.02.560011v1?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. 2023-10-02 doi:10.1101/2023.10.02.560011 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration ]]> https://biorxiv.org/content/10.1101/2023.10.02.560584v1?rss=1 Buck, S. A. Rubin, S. A. Kunkhyen, T. Treiber, C. D. Xue, X. Fenno, L. E. Mabry, S. J. Sundar, V. R. Yang, Z. Shah, D. Ketchesin, K. D. Becker-Krail, D. D. Vasylieva, I. Smith, M. C. Weisel, F. J. Wang, W. Erickson-Oberg, M. Q. O'Leary, E. I. Aravind, E. Ramakrishnan, C. Kim, Y. S. Wu, Y. Quick, M. Coleman, J. A. MacDonald, W. A. Elbakri, R. De Miranda, B. R. Palladino, M. J. McCabe, B. D. Fish, K. N. Seney, M. L. Rayport, S. Mingote, S. Deisseroth, K. Hnasko, T. S. Awatramani, R. Watson, A. M. Waddell, S. Cheetham, C. E. Logan, R. W. Freyberg, Z. 2023-10-03 doi:10.1101/2023.10.02.560584 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Neutrophil-derived IL-17 limits protective host responses and promotes tuberculosis pathogenesis ]]> https://biorxiv.org/content/10.1101/2023.10.05.561061v1?rss=1 Sharma, P. Sharma, R. D. Das, M. Sarkar, B. Singh, L. Jain, N. Chaturvedi, S. Mehra, L. Rathee, A. Sharma, S. Shihui, F. Lee, A. Kumar, P. N. Das, P. Viswanathan, V. Kornfeld, H. Howland, S. Babu, S. Nandicoori, V. Singhal, A. Kumar, D. 2023-10-06 doi:10.1101/2023.10.05.561061 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Functional genomics reveals that a divergent genetic dependency signature is not essential to the synergism of molecular-targeted agent and chemotherapeutic combinations in gastric cancer cells ]]> https://biorxiv.org/content/10.1101/2023.10.07.561351v1?rss=1 Leylek, O. Honeywell, M. E. Lee, M. J. Hemann, M. T. Ozcan, G. 2023-10-10 doi:10.1101/2023.10.07.561351 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Deep generative models predict SARS-CoV-2 Spike infectivity and foreshadow neutralizing antibody escape ]]> https://biorxiv.org/content/10.1101/2023.10.08.561389v1?rss=1 Youssef, N. A. Ghantous, F. Gurev, S. Brock, K. Jaimes, J. A. Dauphin, A. Yurkovetskiy, L. Soto, D. Estaboulieh, R. Kotzen, B. Bosso, M. Lemieux, J. Luban, J. A. Seaman, M. Marks, D. 2023-10-10 doi:10.1101/2023.10.08.561389 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Beta-catenin-mediated activation of Wnt target genes utilizes a biomolecular condensate-dependent mechanism ]]> https://biorxiv.org/content/10.1101/2023.10.09.561634v1?rss=1 Stewart, R. A. Goodman, L. B. Tran, J. J. Zientko, J. P. Sabu, M. Jeon, U. S. Cadigan, K. M. 2023-10-10 doi:10.1101/2023.10.09.561634 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells. ]]> https://biorxiv.org/content/10.1101/2023.10.11.561959v1?rss=1 Liu, H. Caliz, A. D. Learnard, H. Koupenova, M. Keaney, J. F. Kant, S. Zhu, L. J. Vertii, A. 2023-10-16 doi:10.1101/2023.10.11.561959 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ The ability of the LIMD1 and TRIP6 LIM domains to bind to f-actin under strain is critical for their tension dependent localization to adherens junctions and association with the Hippo pathway kinase LATS1. ]]> https://biorxiv.org/content/10.1101/2023.10.12.562097v1?rss=1 Ray, S. DeSilva, C. Dasgupta, I. Mana-Capelli, S. Cruz-Calderon, N. McCollum, D. 2023-10-13 doi:10.1101/2023.10.12.562097 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ An inducible ESCRT-III inhibition tool to control HIV-1 budding ]]> https://biorxiv.org/content/10.1101/2023.10.16.562494v1?rss=1 Wang, H. Gallet, B. Moriscot, C. Pezet, M. Chatellard, C. Kleman, J.-P. Gottlinger, H. Weissenhorn, W. Boscheron, C. 2023-10-16 doi:10.1101/2023.10.16.562494 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Enhancer-driven local 3D chromatin domain folding modulates transcription in human mammary tumor cells ]]> https://biorxiv.org/content/10.1101/2023.10.17.562690v1?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. 2023-10-19 doi:10.1101/2023.10.17.562690 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Inhibiting the GPI Transamidase Subunit GPAA1 Abolishes CD24 Surface Localization and Enhances Macrophage-Mediated Phagocytosis of Ovarian Cancer Cells ]]> https://biorxiv.org/content/10.1101/2023.10.21.563315v1?rss=1 Mishra, A. K. Ye, T. Banday, S. Thakare, R. P. Su, C. C. T.-T. Pham, N. N. H. Ali, A. Kulshreshtha, A. Chowdhury, S. R. Simone, T. M. Hu, K. Zhu, L. J. Eisenhaber, B. Deibler, S. K. Simin, K. Thompson, P. R. Eisenhaber, F. Malonia, S. K. Green, M. R. 2023-10-23 doi:10.1101/2023.10.21.563315 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Addressing the dNTP bottleneck restricting prime editing activity ]]> https://biorxiv.org/content/10.1101/2023.10.21.563443v1?rss=1 Ponnienselvan, K. Liu, P. Nyalile, T. Oikemus, S. Joynt, A. T. Kelly, K. Guo, D. Chen, Z. Lee, J. M. Schiffer, C. A. Emerson, C. P. Lawson, N. D. Watts, J. K. Sontheimer, E. J. Luban, J. J. Wolfe, S. A. 2023-10-21 doi:10.1101/2023.10.21.563443 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ Modular vector assembly enables rapid assessment of emerging CRISPR technologies ]]> https://biorxiv.org/content/10.1101/2023.10.25.564061v1?rss=1 McGee, A. V. Liu, Y. V. Griffith, A. L. Szegletes, Z. M. Wen, B. Kraus, C. Miller, N. W. Steger, R. J. Escude Velasco, B. Bosch, J. A. Zirin, J. D. Viswanatha, R. Sontheimer, E. J. Goodale, A. Greene, M. A. Green, T. M. Doench, J. G. 2023-10-27 doi:10.1101/2023.10.25.564061 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Arrestin-3-assisted activation of JNK3 mediates dopaminergic behavioral and signaling plasticity in vivo. ]]> https://biorxiv.org/content/10.1101/2023.10.27.564447v1?rss=1 Ahmed, M. R. Zheng, C. Dunning, J. L. Ahmed, M. S. Ge, C. Pair, F. S. Gurevich, V. Gurevich, E. V. 2023-10-30 doi:10.1101/2023.10.27.564447 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types ]]> https://biorxiv.org/content/10.1101/2023.10.29.564613v1?rss=1 Kumar, P. Gholamalamdari, O. Zhang, Y. Zhang, L. Vertii, A. van Schaik, T. Peric-Hupkes, D. Sasaki, T. Gilbert, D. M. van Steensel, B. Ma, J. Kaufman, P. D. Belmont, A. S. 2023-11-01 doi:10.1101/2023.10.29.564613 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Distinct members of the C. elegans CeMbio reference microbiota exert cryptic virulence and infection protection ]]> https://biorxiv.org/content/10.1101/2023.11.02.565327v1?rss=1 Gonzalez, X. Irazoqui, J. E. 2023-11-05 doi:10.1101/2023.11.02.565327 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ PARP knockdown promotes synapse reformation after axon injury ]]> https://biorxiv.org/content/10.1101/2023.11.03.565562v1?rss=1 Belew, M. Y. Huang, W. Florman, J. T. Alkema, M. J. Byrne, A. B. 2023-11-05 doi:10.1101/2023.11.03.565562 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ The Host-specific Microbiota is Required for Diet-Specific Metabolic Homeostasis ]]> https://biorxiv.org/content/10.1101/2023.11.05.565654v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@16a864org.highwire.dtl.DTLVardef@1894996org.highwire.dtl.DTLVardef@3e5429org.highwire.dtl.DTLVardef@77bfb_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fei, N. Xie, B. Long, T. J. StGeorge, M. Tan, A. Manzoor, S. Sidebottom, A. M. Melanie Spedale, M. Betty R Theriault, B. R. Dinanath Sulakhe, D. S. B., E. B. 2023-11-06 doi:10.1101/2023.11.05.565654 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Cell lineage analysis with somatic mutations reveals late divergence of neuronal cell types and cortical areas in human cerebral cortex ]]> https://biorxiv.org/content/10.1101/2023.11.06.565899v1?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. 2023-11-07 doi:10.1101/2023.11.06.565899 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ Single-cell transcriptomic and genomic changes in the aging human brain ]]> https://biorxiv.org/content/10.1101/2023.11.07.566050v1?rss=1 Jeffries, A. M. Yu, T. Ziegenfuss, J. S. Tolles, A. K. Kim, Y. Weng, Z. Lodato, M. A. 2023-11-07 doi:10.1101/2023.11.07.566050 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ An encyclopedia of enhancer-gene regulatory interactions in the human genome ]]> https://biorxiv.org/content/10.1101/2023.11.09.563812v1?rss=1 13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and large-scale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 element-gene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancer-promoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics. ]]> Gschwind, A. R. Mualim, K. S. Karbalayghareh, A. Sheth, M. U. Dey, K. K. Jagoda, E. Nurtdinov, R. N. Xi, W. Tan, A. S. Jones, H. Ma, X. R. Yao, D. Nasser, J. Avsec, Z. James, B. T. Shamim, M. S. Durand, N. C. Rao, S. S. P. Mahajan, R. Doughty, B. R. Andreeva, K. Ulirsch, J. C. Fan, K. Perez, E. M. Nguyen, T. C. Kelley, D. R. Finucane, H. K. Moore, J. E. Weng, Z. Kellis, M. Bassik, M. C. Price, A. L. Beer, M. A. Guigo, R. Stamatoyannopoulos, J. A. Aiden, E. L. Greenleaf, W. J. Leslie, C. S. Steinmetz, L. M. Kundaje, A. Engreitz, J. M. 2023-11-13 doi:10.1101/2023.11.09.563812 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ A human immune/muscle xenograft model of FSHD muscle pathology ]]> https://biorxiv.org/content/10.1101/2023.11.17.567590v1?rss=1 Daman, K. Yan, J. Burzenski, L. M. Kady, J. Shultz, L. D. Brehm, M. A. Emerson, C. P. 2023-11-17 doi:10.1101/2023.11.17.567590 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ IFIH1 (MDA5) is required for innate immune detection of intron-containing RNA expressed from the HIV-1 provirus ]]> https://biorxiv.org/content/10.1101/2023.11.17.567619v1?rss=1 Guney, M. H. Nagalekshmi, K. McCauley, S. M. Carbone, C. Aydemir, O. Luban, J. 2023-11-18 doi:10.1101/2023.11.17.567619 Cold Spring Harbor Laboratory Press 2023-11-18 <![CDATA[ Glucose-fed microbiota alters intestinal epithelium and increases susceptibility to bacterial pathogens ]]> https://biorxiv.org/content/10.1101/2023.11.19.567723v1?rss=1 Kingsley, S. F. Seo, Y. Wood, A. Wani, K. A. Gonzalez, X. Irazoqui, J. E. Finkel, S. E. Tissenbaum, H. A. 2023-11-21 doi:10.1101/2023.11.19.567723 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ The nematode (Ascaris suum) intestine is a location of synergistic anthelmintic effects of Cry5B and levamisole ]]> https://biorxiv.org/content/10.1101/2023.11.20.567786v1?rss=1 Williams, P. D. E. Brewer, M. Aroian, R. Robertson, A. P. Martin, R. J. 2023-11-20 doi:10.1101/2023.11.20.567786 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Mycobacterium smegmatis NucS-promoted DNA Mismatch Repair involves limited resection by a 5'-3' exonuclease and is independent of homologous recombination and NHEJ ]]> https://biorxiv.org/content/10.1101/2023.11.26.568737v1?rss=1 Rivera-Flores, I. V. Wang, E. X. Murphy, K. C. 2023-11-26 doi:10.1101/2023.11.26.568737 Cold Spring Harbor Laboratory Press 2023-11-26 <![CDATA[ Heterogeneity in lung macrophage control of Mycobacterium tuberculosis is determined by T cells ]]> https://biorxiv.org/content/10.1101/2023.11.29.569283v1?rss=1 Lai, R. Williams, T. Rakib, T. Lee, J. Behar, S. M. 2023-12-01 doi:10.1101/2023.11.29.569283 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ A novel druggable DYRK3/CAMKV signaling module for Neuroblastoma tumor growth inhibition. ]]> https://biorxiv.org/content/10.1101/2023.11.30.569438v1?rss=1 Rozen, E. J. Wigglesworth, K. Shohet, J. M. 2023-12-01 doi:10.1101/2023.11.30.569438 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Differences in clamp loader mechanism between bacteria and eukaryotes ]]> https://biorxiv.org/content/10.1101/2023.11.30.569468v1?rss=1 Landeck, J. T. Pajak, J. Norman, E. K. Sedivy, E. L. Kelch, B. A. 2023-11-30 doi:10.1101/2023.11.30.569468 Cold Spring Harbor Laboratory Press 2023-11-30 <![CDATA[ TNF-alpha promotes cilia elongation via Mixed Lineage Kinases signaling. ]]> https://biorxiv.org/content/10.1101/2023.11.30.569502v1?rss=1 Kumari, A. Caliz, A. D. Kant, S. Vertii, A. 2023-12-01 doi:10.1101/2023.11.30.569502 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Pathogen effector-triggered aggregation of TIR-1/SARM1 on lysosome-related organelles activates intestinal immunity ]]> https://biorxiv.org/content/10.1101/2023.12.04.569946v1?rss=1 Tse-Kang, S. Wani, K. A. Peterson, N. D. Page, A. Pukkila-Worley, R. 2023-12-04 doi:10.1101/2023.12.04.569946 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Phosphorylation of MYCN and MAX by PAK family kinases is a novel tumor-suppressor mechanism in neuroblastoma with potential therapeutic implications. ]]> https://biorxiv.org/content/10.1101/2023.12.04.570005v1?rss=1 Rozen, E. J. Wigglesworth, K. Shohet, J. M. 2023-12-06 doi:10.1101/2023.12.04.570005 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Expanding the toolbox: Novel class IIb microcins show activity against gram-negative ESKAPE and plant pathogens ]]> https://biorxiv.org/content/10.1101/2023.12.05.570296v1?rss=1 Mortzfeld, B. M. Bhattarai, S. K. Bucci, V. 2023-12-06 doi:10.1101/2023.12.05.570296 Cold Spring Harbor Laboratory Press 2023-12-06 <![CDATA[ Fluorescent tagging of endogenous IRS2 with an auxin-dependent degron to assess dynamic intracellular localization and function ]]> https://biorxiv.org/content/10.1101/2023.12.06.570406v1?rss=1 Jo, M. Lee, J.-S. Lero, M. W. Morgan, J. S. Shaw, L. M. 2023-12-07 doi:10.1101/2023.12.06.570406 Cold Spring Harbor Laboratory Press 2023-12-07 <![CDATA[ Mitotic chromosomes harbor cell type and species-specific structural features within a universal looping architecture ]]> https://biorxiv.org/content/10.1101/2023.12.08.570796v1?rss=1 Oomen, M. E. Fox, A. N. Gonzalez, I. Molliex, A. Papadopoulou, T. Navarro, P. Dekker, J. 2023-12-09 doi:10.1101/2023.12.08.570796 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ Structural mechanism of angiogenin activation by the ribosome ]]> https://biorxiv.org/content/10.1101/2023.12.11.570495v1?rss=1 Loveland, A. B. Koh, C. S. Ganesan, R. Jacobson, A. Korostelev, A. A. 2023-12-11 doi:10.1101/2023.12.11.570495 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Single molecule studies of the native hair cell mechanosensory transduction complex ]]> https://biorxiv.org/content/10.1101/2023.12.11.571162v1?rss=1 Clark, S. Mitra, J. Elferich, J. Goehring, A. Ge, J. Ha, T. Gouaux, E. 2023-12-12 doi:10.1101/2023.12.11.571162 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits ]]> https://biorxiv.org/content/10.1101/2023.12.18.572185v1?rss=1 Neve, R. L. Giedraitis, E. Akbari, M. S. Cohen, S. Phelan, V. V. 2023-12-18 doi:10.1101/2023.12.18.572185 Cold Spring Harbor Laboratory Press 2023-12-18 <![CDATA[ A programmable dual-targeting di-valent siRNA scaffold supports potent multi-gene modulation in the central nervous system ]]> https://biorxiv.org/content/10.1101/2023.12.19.572404v1?rss=1 Belgrad, J. Tang, Q. Hildebrand, S. Summers, A. Sapp, E. Echeverria, D. O'Reilly, D. Luu, E. Bramato, B. Allen, S. Cooper, D. Alterman, J. Yamada, K. Aronin, N. DiFiglia, M. Khvorova, A. 2023-12-19 doi:10.1101/2023.12.19.572404 Cold Spring Harbor Laboratory Press 2023-12-19 <![CDATA[ Sex-specific Effects of the Endocannabinoid Agonist 2-Arachidonoylglycerol on Sleep and Circadian Disruptions during Fentanyl Withdrawal ]]> https://biorxiv.org/content/10.1101/2023.12.19.572466v1?rss=1 Gamble, M. C. Miracle, S. Williams, B. R. Logan, R. W. 2023-12-20 doi:10.1101/2023.12.19.572466 Cold Spring Harbor Laboratory Press 2023-12-20 <![CDATA[ Dueling Endogenous Viral-Like Sequences Control Synaptic Plasticity ]]> https://biorxiv.org/content/10.1101/2023.12.20.572708v1?rss=1 M'Angale, P. G. Lemieux, A. Liu, Y. Graslie, J. Wang, S. Simkin, A. Budnik, V. Kelch, B. A. Thomson, T. 2023-12-21 doi:10.1101/2023.12.20.572708 Cold Spring Harbor Laboratory Press 2023-12-21 <![CDATA[ CDC20 determines the sensitivity to spindle assembly checkpoint (SAC) inhibitors ]]> https://biorxiv.org/content/10.1101/2023.12.21.572559v1?rss=1 Zheng, S. Raz, L. Zhou, L. Cohen-Sharir, Y. Tian, R. Wardenaar, R. Broekhuis, M. J. C. Suarez Peredo Rodriguez, M. F. Wobben, S. van den Brink, A. Bakker, P. Foijer, F. Ben-David, U. 2023-12-23 doi:10.1101/2023.12.21.572559 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ Antibody-mediated depletion of select T cell subsets in blood and tissue of nonhuman primates ]]> https://biorxiv.org/content/10.1101/2023.12.22.572898v1?rss=1 Sutton, M. S. Bucsan, A. N. Lehman, C. C. Kamath, M. Pokkali, S. Magnani, D. M. Seder, R. Darrah, P. A. Roederer, M. 2023-12-23 doi:10.1101/2023.12.22.572898 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ Metabolite profiling of human renal cell carcinoma reveals tissue-origin dominance in nutrient availability ]]> https://biorxiv.org/content/10.1101/2023.12.24.573250v1?rss=1 Abbott, K. L. Ali, A. Reinfeld, B. I. Deik, A. A. I. Subudhi, S. Landis, M. D. Hongo, R. A. Young, K. L. Kunchok, T. Nabel, C. S. Crowder, K. D. Kent, J. R. Madariaga, M. L. L. Jain, R. K. Beckermann, K. E. Lewis, C. A. Clish, C. B. Muir, A. Rathmell, W. K. Rathmell, J. C. Vander Heiden, M. G. 2023-12-24 doi:10.1101/2023.12.24.573250 Cold Spring Harbor Laboratory Press 2023-12-24 <![CDATA[ Dominant negative mutations in yeast Hsp90 reveal triage decision mechanism targeting client proteins for degradation ]]> https://biorxiv.org/content/10.1101/2024.01.02.573950v1?rss=1 Flynn, J. M. Joyce, M. E. Bolon, D. N. 2024-01-02 doi:10.1101/2024.01.02.573950 Cold Spring Harbor Laboratory Press 2024-01-02 <![CDATA[ PRMT5 orchestrates EGFR and AKT networks to activate NFκB and promote EMT ]]> https://biorxiv.org/content/10.1101/2024.01.03.574104v1?rss=1 Huang, L. Ravi, M. Zhang, X.-O. Verdejo-Torres, O. Shendy, N. A. M. Nezhady, M. A. M. Gopalan, S. Wang, G. Durbin, A. D. Fazzio, T. G. Wu, J. Q. 2024-01-04 doi:10.1101/2024.01.03.574104 Cold Spring Harbor Laboratory Press 2024-01-04 <![CDATA[ FANCJ promotes PARP1 activity during DNA replication that is essential in BRCA1 deficient cells ]]> https://biorxiv.org/content/10.1101/2024.01.04.574095v1?rss=1 Cong, K. MacGilvary, N. Lee, S. MacLeod, S. Calvo, J. Peng, M. Nedergaard Kousholt, A. Day, T. Cantor, S. 2024-01-04 doi:10.1101/2024.01.04.574095 Cold Spring Harbor Laboratory Press 2024-01-04 <![CDATA[ mRNA initiation and termination are spatially coordinated ]]> https://biorxiv.org/content/10.1101/2024.01.05.574404v1?rss=1 Calvo-Roitberg, E. Carroll, C. L. Venev, S. V. Kim, G. Mick, S. T. Dekker, J. Fiszbein, A. Pai, A. A. 2024-01-07 doi:10.1101/2024.01.05.574404 Cold Spring Harbor Laboratory Press 2024-01-07 <![CDATA[ Spatial characterization of interface dermatitis in cutaneous lupus reveals novel chemokine ligand-receptor pairs that drive disease ]]> https://biorxiv.org/content/10.1101/2024.01.05.574422v1?rss=1 View larger version (46K): org.highwire.dtl.DTLVardef@1e86dbeorg.highwire.dtl.DTLVardef@7d0208org.highwire.dtl.DTLVardef@1108aa8org.highwire.dtl.DTLVardef@ff255f_HPS_FORMAT_FIGEXP M_FIG C_FIG Model of chemokine systems governing recruitment of immune cell subsets to form interface dermatitis in cutaneous lupus. A. Summary of fresh tissue blister biopsy studies demonstrating increases in HLADR+ cells in nonlesional lupus biopsies as assessed by flow cytometry, and increased CXCL6 and CCL8 as assessed by 96 plex immunoassay. Lesional lupus biopsies also demonstrated significant increases in T cells and CXCL9/10/11 production. B. Model of chemokine-directed formation of interface dermatitis in cutaneous lupus. 1. Whole transcriptome atlas (WTA) digital spatial profiling (DSP) revealed increased AIM2 in keratinocytes proximal to inflammation, which is reported to be induced by environmental triggers including UV light and toxins. We also noted increased Caspase 8 (Casp8) and IL18 at the protein level, which can be induced downstream of AIM2. Chemokines including CXCL6 and CCL8 can be induced downstream of IL18, explaining how CCL8 and CXCL6 might be induced. 2. Recruitment of myeloid cell first responders by CCL8 and CXCL6. CD14+CD16+ myeloid cells, which were recently described in nonlesional lupus skin, express CXCR1 and migrate towards CXCL6, whereas CD14+CD16-myeloid cells express more CCR2 and migrate towards CCL8. 3. The CXCR3 ligands CXCL9/10/11 are expressed by keratinocytes, but more strongly in CD45+ immune cell and T cell regions of interest (ROIs). 4. T cells express CXCR3 and migrate towards CXCL9 and to a greater extent CXCL11. 5. The recruited HLADR+ myeloid populations and T cells contribute to formation of interface dermatitis. Thus, we propose a model in which keratinocyte/myeloid crosstalk can reinforce chemokine systems to optimally recruit lymphocytes and other immune cells to form interface dermatitis. Created with Biorender.com. Plain language summaryLupus skin rashes arise during flares, after exposure to medications or sunlight, or in response to other triggers of inflammation. To understand how white blood cells enter the skin to cause these rashes, we used new technologies to look at proteins that attract them into the skin. We found proteins that are expressed by skin cells in lesions that can recruit specific types of white blood cells that are thought to be the initiators of skin rashes. Once in the skin, these and other white blood cells can make additional proteins that bring in more and more cells. We hope that our findings will be used to test new topical treatments for lupus and other autoimmune skin rashes. ]]> Shakiba, S. Haddadi, N.-S. Afshari, K. Lubov, J. E. Raef, H. S. Li, R. Yildiz-Altay, U. Daga, M. Refat, M. A. Kim, E. Galindo de Laflin, J. Akabane, A. Sherman, S. MacDonald, E. Strassner, J. P. Zhang, L. Leon, M. Baer, C. E. Dresser, K. Liang, Y. Whitley, J. B. Skopelja-Gardner, S. Harris, J. E. Deng, A. Vesely, M. D. Rashighi, M. Richmond, J. M. 2024-01-06 doi:10.1101/2024.01.05.574422 Cold Spring Harbor Laboratory Press 2024-01-06 <![CDATA[ Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFs ]]> https://biorxiv.org/content/10.1101/2024.01.09.574742v1?rss=1 View larger version (50K): org.highwire.dtl.DTLVardef@5ac4b9org.highwire.dtl.DTLVardef@1298a63org.highwire.dtl.DTLVardef@3c8b01org.highwire.dtl.DTLVardef@c9f5f4_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lawrence, J. B. Hall, L. L. Creamer, K. M. Byron, M. F. 2024-01-09 doi:10.1101/2024.01.09.574742 Cold Spring Harbor Laboratory Press 2024-01-09 <![CDATA[ BAMBI: Integrative biostatistical and artificial-intelligence method discover coding and non-coding RNA genes as biomarkers ]]> https://biorxiv.org/content/10.1101/2024.01.12.575460v1?rss=1 Zhou, P. Li, Z. Liu, F. Kwon, E. Hsieh, T.-C. Ye, S. Vasudevan, S. Lee, J. Zhou, C. 2024-01-15 doi:10.1101/2024.01.12.575460 Cold Spring Harbor Laboratory Press 2024-01-15 <![CDATA[ Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact. ]]> https://biorxiv.org/content/10.1101/2024.01.15.575636v1?rss=1 Piekniewska, A. Anderson, N. Roelandse, M. Lloyd, K. Korf, I. Voss, S. R. de Castro, G. Magnani, D. Varga, Z. James-Zorn, C. Horb, M. Grethe, J. S. Bandrowski, A. E. 2024-01-16 doi:10.1101/2024.01.15.575636 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Structural basis of respiratory complexes adaptation to cold temperatures ]]> https://biorxiv.org/content/10.1101/2024.01.16.575914v1?rss=1 Shin, Y.-C. Latorre-Muro, P. Djurabekova, A. Zdorevskyi, O. Bennett, C. Burger, N. Song, K. Xu, C. Sharma, V. Liao, M. Puigserver, P. 2024-01-17 doi:10.1101/2024.01.16.575914 Cold Spring Harbor Laboratory Press 2024-01-17 <![CDATA[ Single-domain antibodies reveal unique borreliacidal epitopes on the Lyme disease vaccine antigen, Outer surface protein A (OspA) ]]> https://biorxiv.org/content/10.1101/2024.01.23.576890v1?rss=1 Vance, D. J. Basir, S. Piazza, C. L. Willsey, G. Haque, H. M. E. Tremblay, J. M. Rudolph, M. J. Muriuki, B. Cavacini, L. A. Weis, D. D. Shoemaker, C. B. Mantis, N. J. 2024-01-24 doi:10.1101/2024.01.23.576890 Cold Spring Harbor Laboratory Press 2024-01-24 <![CDATA[ Cholinergic agonist PNU282987 induces pro-inflammatory gene expression via the MCOLN1-TFEB pathway in murine macrophages. ]]> https://biorxiv.org/content/10.1101/2024.01.26.577408v1?rss=1 Honwad, H. H. Najibi, M. Koscso, B. Bogunovic, M. Irazoqui, J. E. 2024-01-30 doi:10.1101/2024.01.26.577408 Cold Spring Harbor Laboratory Press 2024-01-30 <![CDATA[ Microbiota encoded fatty-acid metabolism expands tuft cells to protect tissues homeostasis during Clostridioides difficile infection in the large intestine ]]> https://biorxiv.org/content/10.1101/2024.01.29.574039v1?rss=1 Kellogg, T. D. Ceglia, S. Mortzfeld, B. M. Zeamer, A. L. Foley, S. E. Ward, D. Bhattarai, S. K. McCormick, B. A. Reboldi, A. Bucci, V. 2024-02-01 doi:10.1101/2024.01.29.574039 Cold Spring Harbor Laboratory Press 2024-02-01 <![CDATA[ C. elegans Multidrug Resistance Protein 5 (MRP-5) Transports Vitamin B12 from the Intestine to the Gonad to Support Embryonic Development ]]> https://biorxiv.org/content/10.1101/204735v1?rss=1 Na, H. Ponomarova, O. Giese, G. E. Walhout, M. J. M. 2017-10-17 doi:10.1101/204735 Cold Spring Harbor Laboratory Press 2017-10-17 <![CDATA[ Fluorescence polarization control for on-off switching of single molecules at cryogenic temperatures ]]> https://biorxiv.org/content/10.1101/204776v1?rss=1 Hulleman, C. Huisman, M. Moerland, R. Grunwald, D. Stallinga, S. Rieger, B. 2017-10-17 doi:10.1101/204776 Cold Spring Harbor Laboratory Press 2017-10-17 <![CDATA[ The Fission Yeast S-Phase Cyclin Cig2 Can Drive Mitosis ]]> https://biorxiv.org/content/10.1101/213330v1?rss=1 Magner, M. Keifenheim, D. Rhind, N. 2017-11-02 doi:10.1101/213330 Cold Spring Harbor Laboratory Press 2017-11-02 <![CDATA[ Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping ]]> https://biorxiv.org/content/10.1101/214841v1?rss=1 Klein, K. Wang, W. Borrman, T. Chan, S. Zhang, D. Weng, Z. Hastie, A. Chen, C. Gilbert, D. M. Rhind, N. 2017-11-06 doi:10.1101/214841 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ A hyperthermophilic phage decoration protein suggests common evolutionary origin with Herpesvirus Triplex proteins and an anti-CRISPR protein ]]> https://biorxiv.org/content/10.1101/216911v1?rss=1 Stone, N. P. Hilbert, B. J. Hidalgo, D. Halloran, K. T. Kelch, B. A. 2017-11-09 doi:10.1101/216911 Cold Spring Harbor Laboratory Press 2017-11-09 <![CDATA[ Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series ]]> https://biorxiv.org/content/10.1101/219188v1?rss=1 Fischer, D. S. Fiedler, A. K. Kernfeld, E. Genga, R. M. J. Hasenauer, J. Maehr, R. Theis, F. J. 2017-11-14 doi:10.1101/219188 Cold Spring Harbor Laboratory Press 2017-11-14 <![CDATA[ HIV-1 unmasks the plasticity of innate lymphoid cells ]]> https://biorxiv.org/content/10.1101/221010v1?rss=1 nView larger version (32K):norg.highwire.dtl.DTLVardef@ae82a7org.highwire.dtl.DTLVardef@103b2b4org.highwire.dtl.DTLVardef@1c9585aorg.highwire.dtl.DTLVardef@1c7bb2d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG ]]> Wang, Y. Gellatly, K. Derr, A. Jaiswal, S. Kucukural, A. McDonel, P. Greenough, T. Houghton, J. Garber, M. Luban, J. 2017-11-17 doi:10.1101/221010 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ Nuclear Export Through Nuclear Envelope Remodeling in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/224055v1?rss=1 Ding, B. Mirza, A. M. Ashley, J. Budnik, V. Munson, M. 2017-11-22 doi:10.1101/224055 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Identifying the in vivo cellular correlates of antipsychotic drugs ]]> https://biorxiv.org/content/10.1101/226050v1?rss=1 Joshi, R. PANICKER, M. 2017-11-29 doi:10.1101/226050 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Uncoupling Intraflagellar Transport and Primary Cilia Formation Demonstrates Deep Integration of IFT in Hedgehog Signaling ]]> https://biorxiv.org/content/10.1101/226324v1?rss=1 Eguether, T. J. Cordelieres, F. P. Pazour, G. J. 2017-11-28 doi:10.1101/226324 Cold Spring Harbor Laboratory Press 2017-11-28 <![CDATA[ Conformational control of translation termination on the 70S ribosome ]]> https://biorxiv.org/content/10.1101/226837v1?rss=1 Svidritskiy, E. Korostelev, A. A. 2017-11-29 doi:10.1101/226837 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Transcriptome-wide analysis of the functional intronome using spliceosome profiling ]]> https://biorxiv.org/content/10.1101/226894v1?rss=1 Chen, W. Moore, J. Ozadam, H. Shulha, H. P. Rhind, N. Weng, Z. Moore, M. J. 2017-11-29 doi:10.1101/226894 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ The Phagocyte Oxidase Controls Tolerance to Mycobacterium tuberculosis infection. ]]> https://biorxiv.org/content/10.1101/232777v1?rss=1 Olive, A. J. Smith, C. M. Kiritsy, M. C. Sassetti, C. M. 2017-12-21 doi:10.1101/232777 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ ORBIT: a new paradigm for geneticengineering of mycobacterial chromosomes ]]> https://biorxiv.org/content/10.1101/249292v1?rss=1 Murphy, K. C. Nelson, S. J. Nambi, S. Papavinasasundaram, K. Baer, C. E. Sassetti, C. M. 2018-01-16 doi:10.1101/249292 Cold Spring Harbor Laboratory Press 2018-01-16 <![CDATA[ OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control ]]> https://biorxiv.org/content/10.1101/251850v1?rss=1 Rigano, A. Galli, V. Clark, J. M. Pereira, L. E. Grossi, L. Luban, J. Giulietti, R. Leidi, T. Hunter, E. Valle, M. Sbalzarini, I. F. Strambio-De-Castillia, C. 2018-02-23 doi:10.1101/251850 Cold Spring Harbor Laboratory Press 2018-02-23 <![CDATA[ Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers ]]> https://biorxiv.org/content/10.1101/251892v1?rss=1 Fu, Y. Wu, P.-H. Beane, T. Zamore, P. D. Weng, Z. 2018-01-22 doi:10.1101/251892 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ CNBP controls c-Rel dependent IL-12 β gene transcription and Th1 immunity ]]> https://biorxiv.org/content/10.1101/258731v1?rss=1 Chen, Y. Sharma, S. Assis, P. A. Jiang, Z. Olive, A. J. Hang, S. Bernier, J. Huh, J. R. Sassetti, C. M. Knipe, D. M. Gazzinelli, R. T. Fitzgerald, K. A. 2018-02-01 doi:10.1101/258731 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Herpes ICP8 protein stimulates homologous recombination in human cells ]]> https://biorxiv.org/content/10.1101/259739v1?rss=1 Valledor, M. Myers, R. S. Schiller, P. C. 2018-02-11 doi:10.1101/259739 Cold Spring Harbor Laboratory Press 2018-02-11 <![CDATA[ The TRIM-NHL protein NHL-2 is a Novel Co-Factor of the CSR-1 and HRDE-1 22G-RNA Pathways ]]> https://biorxiv.org/content/10.1101/260240v1?rss=1 Boag, P. R. Davis, G. M. Tu, S. Colson, R. N. Anderson, J. W. T. Gunzburg, M. J. Francisco, M. A. Ray, D. Maity, T. Wu, M. Z. Morris, Q. D. Hughes, T. R. Wilce, J. A. Claycomb, J. Weng, Z. 2018-02-05 doi:10.1101/260240 Cold Spring Harbor Laboratory Press 2018-02-05 <![CDATA[ PIWI Proteins Act at Multiple Steps in the Production of Their Own Guides ]]> https://biorxiv.org/content/10.1101/261545v1?rss=1 Zamore, P. Gainetdinov, I. Coplan, C. Cecchini, K. 2018-02-07 doi:10.1101/261545 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ An Automated Bayesian Pipeline for Rapid Analysis of Single-Molecule Binding Data ]]> https://biorxiv.org/content/10.1101/261917v1?rss=1 Smith, C. S. Jouravleva, K. Huisman, M. Jolly, S. M. Zamore, P. D. Grunwald, D. 2018-04-11 doi:10.1101/261917 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Emergence of the erythroid lineage from multipotent hematopoiesis ]]> https://biorxiv.org/content/10.1101/261941v1?rss=1 Khoramian Tusi, B. Wolock, S. L. Weinreb, C. Hwang, Y. Hidalgo, D. Zilionis, R. Waisman, A. Huh, J. Klein, A. M. Socolovsky, M. 2018-02-16 doi:10.1101/261941 Cold Spring Harbor Laboratory Press 2018-02-16 <![CDATA[ Identification of piRNA binding sites reveals the Argonaute regulatory landscape of the C. elegans germline ]]> https://biorxiv.org/content/10.1101/262113v1?rss=1 Shen, E.-Z. Chen, H. Ozturk, A. R. Tu, S. Shirayama, M. Tang, W. Ding, Y.-H. Dai, S.-Y. Weng, Z. Mello, C. C. 2018-02-07 doi:10.1101/262113 Cold Spring Harbor Laboratory Press 2018-02-07 <![CDATA[ Mycobacterium tuberculosis-specific CD4+ and CD8+ T cells differ in their capacity to recognize infected macrophages ]]> https://biorxiv.org/content/10.1101/262493v1?rss=1 Yang, J. Mott, D. Sutiwisesak, R. Lu, Y. J. Rosa, F. Stowell, B. Babunovic, G. Lee, J. Carpenter, S. Way, S. S. Fortune, S. Behar, S. M. 2018-02-10 doi:10.1101/262493 Cold Spring Harbor Laboratory Press 2018-02-10 <![CDATA[ The C. elegans heterochronic gene lin-28 coordinates the timing of hypodermal and somatic gonadal programs for hermaphrodite reproductive system morphogenesis ]]> https://biorxiv.org/content/10.1101/265314v1?rss=1 Choi, S. Ambros, V. 2018-02-13 doi:10.1101/265314 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Generation of functional human adipose tissue in mice from primed progenitor cells ]]> https://biorxiv.org/content/10.1101/267427v1?rss=1 Rojas-Rodriguez, R. Lujan-Hernandez, J. Min, S. Y. DeSouza, T. Teebagy, P. Desai, A. Tessier, H. Slamin, R. Siegel-Reamer, L. Berg, C. Baez, A. Lalikos, J. Corvera, S. 2018-02-18 doi:10.1101/267427 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ Diffusion rather than IFT provides most of the tubulin required for axonemal assembly ]]> https://biorxiv.org/content/10.1101/268573v1?rss=1 Harris, J. A. Van De Weghe, J. M. Kubo, T. Witman, G. B. Lechtreck, K. 2018-02-20 doi:10.1101/268573 Cold Spring Harbor Laboratory Press 2018-02-20 <![CDATA[ Integrating cross-linking experiments with ab initio protein-protein docking ]]> https://biorxiv.org/content/10.1101/275891v1?rss=1 Vreven, T. Schweppe, D. K. Chavez, J. D. Weisbrod, C. R. Shibata, S. Zheng, C. Bruce, J. E. Weng, Z. 2018-03-03 doi:10.1101/275891 Cold Spring Harbor Laboratory Press 2018-03-03 <![CDATA[ Higher-Order Organization Principles of Pre-translational mRNPs ]]> https://biorxiv.org/content/10.1101/278747v1?rss=1 Metkar, M. Ozadam, H. Lajoie, B. R. Imakaev, M. Mirny, L. A. Dekker, J. Moore, M. J. 2018-03-08 doi:10.1101/278747 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ High dimensional analyses of cells dissociated from cryopreserved synovial tissue ]]> https://biorxiv.org/content/10.1101/284844v1?rss=1 Donlin, L. T. Rao, D. A. Wei, K. Slowikowski, K. McGeachy, M. J. Turner, J. D. Meednu, N. Mizoguchi, F. Gutierrez-Arcelus, M. Lieb, D. J. Keegan, J. Muskat, K. Hillman, J. Rozo, C. Ricker, E. Eisenhaure, T. M. Li, S. Browne, E. P. Chicoine, A. Sutherby, D. Noma, A. Nusbaum, C. Kelly, S. Pernis, A. B. Ivashkiv, L. B. Goodman, S. M. Robinson, W. H. Utz, P. J. Lederer, J. A. Gravallese, E. M. Boyce, B. F. Hacohen, N. Pitzalis, C. Gregersen, P. K. Firestein, G. S. Raychaudhuri, S. Moreland, L. W. Holers, M. Bykerk, V. P. Filer, A. Boyle, D. L. Brenner, M. B 2018-03-19 doi:10.1101/284844 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Effects of larval density on gene regulation in C. elegans during routine L1 synchronization ]]> https://biorxiv.org/content/10.1101/284927v1?rss=1 Rando, O. J. Chan, I. L. Conine, C. 2018-03-19 doi:10.1101/284927 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Profiling of pluripotency factors in individual stem cells and early embryos ]]> https://biorxiv.org/content/10.1101/286351v1?rss=1 Hainer, S. J. Boskovic, A. Rando, O. J. Fazzio, T. G. 2018-03-21 doi:10.1101/286351 Cold Spring Harbor Laboratory Press 2018-03-21 <![CDATA[ Hydrophobicity drives the systemic distribution of lipid-conjugated siRNAs via lipid transport pathways ]]> https://biorxiv.org/content/10.1101/288092v1?rss=1 Osborn, M. F. Coles, A. H. Biscans, A. Haraszti, R. A. Roux, L. Davis, S. Ly, S. Echeverria, D. Hassler, M. R. Godinho, B. M. D. C. Nikan, M. Khvorova, A. 2018-03-23 doi:10.1101/288092 Cold Spring Harbor Laboratory Press 2018-03-23 <![CDATA[ Diverse lipid conjugates for functional extra-hepatic siRNA delivery in vivo ]]> https://biorxiv.org/content/10.1101/289439v1?rss=1 Biscans, A. Coles, A. Haraszti, R. Echeverria, D. Hassler, M. Osborn, M. Khvorova, A. 2018-03-26 doi:10.1101/289439 Cold Spring Harbor Laboratory Press 2018-03-26 <![CDATA[ Numerous recursive sites contribute to accuracy of splicing of long introns in flies ]]> https://biorxiv.org/content/10.1101/290007v1?rss=1 40 kb) fly introns, including many genes involved in morphogenesis and development, and tend to occur near the midpoints of introns. Suggesting a possible function for recursive splicing, we observe that fly introns with recursive sites are spliced more accurately than comparably sized non-recursive introns. ]]> Pai, A. A. Paggi, J. Adelman, K. Burge, C. B. 2018-03-27 doi:10.1101/290007 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Heavily and Fully Modified RNAs Guide Efficient SpyCas9-Mediated Genome Editing ]]> https://biorxiv.org/content/10.1101/290999v1?rss=1 Mir, A. Alterman, J. F. Hassler, M. R. Debacker, A. J. Hudgens, E. Echeverria, D. Brodsky, M. H. Khvorova, A. Watts, J. K. Sontheimer, E. J. 2018-03-28 doi:10.1101/290999 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Primate immunodeficiency virus Vpx and Vpr counteract transcriptional repression of proviruses by the HUSH complex ]]> https://biorxiv.org/content/10.1101/293001v1?rss=1 Yurkovetskiy, L. Guney, M. H. Kim, K. Goh, S. L. McCauley, S. M. Dauphin, A. Diehl, W. E. Luban, J. 2018-04-03 doi:10.1101/293001 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ Acute-stress impairs cytoprotective mechanisms through neural inhibition of the insulin pathway ]]> https://biorxiv.org/content/10.1101/294645v1?rss=1 De Rosa, M. J. Veuthey, T. Florman, J. Grant, J. Blanco, G. Andersen, N. Donnelly, J. Rayes, D. Alkema, M. 2018-04-24 doi:10.1101/294645 Cold Spring Harbor Laboratory Press 2018-04-24 <![CDATA[ All-in-One Adeno-associated Virus Delivery and Genome Editing by Neisseria meningitidis Cas9 in vivo ]]> https://biorxiv.org/content/10.1101/295055v1?rss=1 35% gene modification after two weeks of vector administration, with minimal off-target cleavage in vivo. Our findings indicate that NmeCas9 can facilitate future efforts to correct disease-causing mutations by expanding the targeting scope of RNA-guided nucleases. ]]> Ibraheim, R. Song, C.-Q. Mir, A. Amrani, N. Xue, W. Sontheimer, E. J. 2018-04-04 doi:10.1101/295055 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT ]]> https://biorxiv.org/content/10.1101/301267v1?rss=1 Harvey, S. Xu, Y. Lin, X. Gao, X. D. Qiu, Y. Ahn, J. Xiao, X. Cheng, C. 2018-04-13 doi:10.1101/301267 Cold Spring Harbor Laboratory Press 2018-04-13 <![CDATA[ A novel sialylation site on Neisseria gonorrhoeae lipooligosaccharide links heptose II lactose expression with pathogenicity ]]> https://biorxiv.org/content/10.1101/302968v1?rss=1 Ram, S. Gulati, S. Lewis, L. A. Chakraborti, S. Zheng, B. DeOliveira, R. B. Reed, G. W. Cox, A. D. Li, J. St. Michael, F. Stupak, J. Su, X.-H. Saha, S. Landig, C. S. Varki, A. RICE, P. A. 2018-04-17 doi:10.1101/302968 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Structural analysis of the active site and DNA binding of human cytidine deaminase APOBEC3B ]]> https://biorxiv.org/content/10.1101/304170v1?rss=1 Hou, S. Silvas, T. V. Leidner, F. Nalivaika, E. A. Matsuo, H. Kurt Yilmaz, N. Schiffer, C. A. 2018-04-18 doi:10.1101/304170 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Transient kinetic analysis of SWR1C-catalyzed H2A.Z deposition unravels the impact of nucleosome dynamics and the asymmetry of stepwise histone exchange ]]> https://biorxiv.org/content/10.1101/304998v1?rss=1 Singh, R. K. Watanabe, S. Bilsel, O. Peterson, C. L. 2018-04-19 doi:10.1101/304998 Cold Spring Harbor Laboratory Press 2018-04-19 <![CDATA[ Gain of Function Analysis Reveals Non-Redundant Roles for the Yersinia pestis Type III Secretion System Effectors YopJ, YopT, and YpkA ]]> https://biorxiv.org/content/10.1101/310243v1?rss=1 Palace, S. G. Proulx, M. K. Szabady, R. L. Goguen, J. D. 2018-04-28 doi:10.1101/310243 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ Small RNAs gained during epididymal transit of sperm are essential for embryonic development in mice ]]> https://biorxiv.org/content/10.1101/311670v1?rss=1 Conine, C. Sun, F. Song, L. Rivera-Perez, J. Rando, O. 2018-04-30 doi:10.1101/311670 Cold Spring Harbor Laboratory Press 2018-04-30 <![CDATA[ BZLF1 interacts with the chromatin remodeler INO80 promoting escape from latent infections with Epstein-Barr virus ]]> https://biorxiv.org/content/10.1101/317354v1?rss=1 Schaeffner, M. Mrozek-Gorska, P. Woellmer, A. Tagawa, T. Buschle, A. Krietenstein, N. Lieleg, C. Korber, P. Hammerschmidt, W. 2018-05-08 doi:10.1101/317354 Cold Spring Harbor Laboratory Press 2018-05-08 <![CDATA[ Transcriptome Analysis of Neisseria gonorrhoeae During Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants Between Men and Women ]]> https://biorxiv.org/content/10.1101/319970v1?rss=1 Nudel, K. McClure, R. Moreau, M. Abrams, A. J. Tjaden, B. Su, X.-H. Trees, D. L. RICE, P. A. Massari, P. Genco, C. A. 2018-05-11 doi:10.1101/319970 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Identification and Characterization of Human Monoclonal Antibodies for Immunoprophylaxis Against Enterotoxigenic Escherichia coli Infection ]]> https://biorxiv.org/content/10.1101/320044v1?rss=1 Giuntini, S. Stoppato, M. Sedic, M. Ejemel, M. Pondish, J. R. Wisheart, D. Schiller, Z. A. Thomas, W. D. Barry, E. Cavacini, L. Klempner, M. Wang, Y. 2018-05-11 doi:10.1101/320044 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Condensin-dependent chromatin condensation represses transcription globally during quiescence ]]> https://biorxiv.org/content/10.1101/320895v1?rss=1 Swygert, S. G. Kim, S. Wu, X. Fu, T. Hsieh, T.-H. Rando, O. J. Eisenman, R. N. Schendure, J. McKnight, J. N. Tsukiyama, T. 2018-05-12 doi:10.1101/320895 Cold Spring Harbor Laboratory Press 2018-05-12 <![CDATA[ Neuronal Modulation of Brown Adipose Activity Through Perturbation of White Adipocyte Lipogenesis ]]> https://biorxiv.org/content/10.1101/324160v1?rss=1 Guilherme, A. Pedersen, D. J. Henriques, F. Bedard, A. H. Henchey, E. Kelly, M. Rahmouni, K. Morgan, D. A. Czech, M. P. 2018-05-16 doi:10.1101/324160 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ A new in vitro assay measuring direct interaction of nonsense suppressors with the eukaryotic protein synthesis machinery ]]> https://biorxiv.org/content/10.1101/330506v1?rss=1 nView larger version (18K):norg.highwire.dtl.DTLVardef@a548dborg.highwire.dtl.DTLVardef@15237bcorg.highwire.dtl.DTLVardef@c93d3forg.highwire.dtl.DTLVardef@1d40e2c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ng, M. Y. Zhang, H. Weil, A. Singh, V. Jamiolkowski, R. M. Baradaran-Heravi, A. Roberge, M. Jacobson, A. Friesen, W. Welch, E. Goldman, Y. Cooperman, B. S. 2018-05-24 doi:10.1101/330506 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ A long-non-coding RNA, LINC00473, confers the human adipose tissue thermogenic phenotype through enhanced cAMP responsiveness. ]]> https://biorxiv.org/content/10.1101/339192v1?rss=1 Tran, K.-V. Nandrup-Bus, C. DeSouza, T. Soares, R. Jespersen, N. Z. Min, S. Y. Rojas-Rodriguez, R. Willenbrock, H. Juhlin, T. Severinsen, M. C. K. Malka, K. Pedersen, B. K. Fitzgibbons, T. Scheele, C. Corvera, S. Nielsen, S. 2018-06-05 doi:10.1101/339192 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Maelstrom Represses Canonical Polymerase II Transcription within Bi-Directional piRNA Clusters in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/344572v1?rss=1 Chang, T. H. Mattei, E. Gainetdinov, I. Weng, Z. Zamore, P. 2018-06-12 doi:10.1101/344572 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ General decapping activators target different subsets of inefficiently translated mRNAs ]]> https://biorxiv.org/content/10.1101/344937v1?rss=1 Jacobson, A. He, F. Celik, A. 2018-06-12 doi:10.1101/344937 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine ]]> https://biorxiv.org/content/10.1101/346205v1?rss=1 Ding, W. Higgins, D. P. Yadav, D. K. Pukkila-Worley, R. Walker, A. K. 2018-06-13 doi:10.1101/346205 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ SIR proteins create compact heterochromatin fibers ]]> https://biorxiv.org/content/10.1101/346296v1?rss=1 Swygert, S. Senapati, S. Bolukbasi, M. Wolfe, S. Lindsay, S. Peterson, C. L. 2018-06-13 doi:10.1101/346296 Cold Spring Harbor Laboratory Press 2018-06-13 <![CDATA[ Potent Cas9 inhibition in bacterial and human cells by new anti-CRISPR protein families ]]> https://biorxiv.org/content/10.1101/350504v1?rss=1 Lee, J. Mir, A. Edraki, A. Garcia, B. Amrani, N. Lou, H. E. Gainetdinov, I. Pawluk, A. Ibraheim, R. Gao, X. D. Liu, P. Davidson, A. R. Maxwell, K. L. Sontheimer, E. J. 2018-06-20 doi:10.1101/350504 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry ]]> https://biorxiv.org/content/10.1101/351130v1?rss=1 Zhang, F. Wei, K. Slowikowski, K. Fonseka, C. Y. Rao, D. A. Kelly, S. Goodman, S. M. Tabechian, D. Hughes, L. B. Salomon-Escoto, K. Watts, G. F. M. Apruzzese, W. Lieb, D. J. Boyle, D. L. Mandelin, A. M. Accelerating Medicines Partnership: RA Phase 1, AMP RA/SLE, Boyce, B. F. DiCarlo, E. Gravallese, E. M. Gregersen, P. K. Moreland, L. Firestein, G. S. Hacohen, N. Nusbaum, C. Lederer, J. A. Perlman, H. Pitzalis, C. Filer, A. Holers, V. M. Bykerk, V. P. Donlin, L. T. Anolik, J. H. Brenner, M. B. Raychaudhuri, S. 2018-06-20 doi:10.1101/351130 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Robust genome editing with short single-stranded and long, partially single-stranded DNA donors in C. elegans ]]> https://biorxiv.org/content/10.1101/352260v1?rss=1 Mello, C. Dokshin, G. A. Ghanta, K. S. Piscopo, K. M. 2018-06-20 doi:10.1101/352260 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ CRISPR delivery particles for developing therapeutic strategies in metabolic disease ]]> https://biorxiv.org/content/10.1101/352799v1?rss=1 Shen, Y. Cohen, J. L. Nicoloro, S. M. Kelly, M. Yenilmez, B. Henriques, F. Tsagkaraki, E. Edwards, Y. J. K. Hu, X. Friedline, R. H. Kim, J. K. Czech, M. P. 2018-06-21 doi:10.1101/352799 Cold Spring Harbor Laboratory Press 2018-06-21 <![CDATA[ Constrained mutational sampling of amino acids in HIV-1 protease evolution ]]> https://biorxiv.org/content/10.1101/354597v1?rss=1 Boucher, J. I. Whitfield, T. W. Dauphin, A. Nauchum, G. Zeldovich, K. B. Swanstrom, R. Schiffer, C. A. Luban, J. Bolon, D. N. A. 2018-06-23 doi:10.1101/354597 Cold Spring Harbor Laboratory Press 2018-06-23 <![CDATA[ Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience ]]> https://biorxiv.org/content/10.1101/354621v1?rss=1 Casadevall, A. Bik, E. M. Fang, F. C. Kullas, A. Davis, R. J. 2018-06-24 doi:10.1101/354621 Cold Spring Harbor Laboratory Press 2018-06-24 <![CDATA[ Structure of the ciliary axoneme at nanometer resolution reconstructed by TYGRESS ]]> https://biorxiv.org/content/10.1101/363317v1?rss=1 Song, K. Shang, Z. Fu, X. Lou, X. Grigorieff, N. Nicastro, D. 2018-07-06 doi:10.1101/363317 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning ]]> https://biorxiv.org/content/10.1101/365866v1?rss=1 Oomen, M. E. Hansen, A. Liu, Y. Darzacq, X. Dekker, J. 2018-07-09 doi:10.1101/365866 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ Regional collapsing of rare variation implicates specific genic regions in ALS ]]> https://biorxiv.org/content/10.1101/375774v1?rss=1 Gelfman, S. Dugger, S. A. Araujo Martins Moreno, C. Ren, Z. Wolock, C. J. Shneider, N. A. Phatnani, H. Cirulli, E. T. Lasseigne, B. N. Harris, T. Maniatis, T. Rouleau, G. A. Brown, R. H. Gitler, A. D. Myers, R. M. Petrovski, S. Allen, A. Harms, M. B. Goldstein, D. B. 2018-07-24 doi:10.1101/375774 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ An algorithm-centric Monte Carlo method to empiricallyquantify motion type estimation uncertainty in single-particle tracking ]]> https://biorxiv.org/content/10.1101/379255v1?rss=1 Rigano, A. Galli, V. Gonciarz, K. Sbalzarini, I. F. Strambio-De-Castillia, C. 2018-08-08 doi:10.1101/379255 Cold Spring Harbor Laboratory Press 2018-08-08 <![CDATA[ A Persistence Detector for Metabolic Network Rewiring in an Animal ]]> https://biorxiv.org/content/10.1101/382507v1?rss=1 Bulcha, J. T. Giese, G. E. Ali, M. Z. Lee, Y.-U. Walker, M. D. Holdorf, A. D. Yilmaz, L. S. Brewster, R. C. Walhout, A. J. 2018-08-01 doi:10.1101/382507 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ An Evolutionarily Conserved piRNA-producing Locus Required for Male Mouse Fertility ]]> https://biorxiv.org/content/10.1101/386201v1?rss=1 80% of small RNAs in the adult mouse testis, have been proposed to bind and regulate target RNAs like miRNAs, cleave targets like siRNAs, or lack biological function altogether. Although piRNA pathway protein mutants are male sterile, no biological function has been identified for any mammalian piRNA-producing locus. Here, we report that males lacking piRNAs from a conserved mouse pachytene piRNA locus on chromosome 6 (pi6) produce sperm with defects in capacitation and egg fertilization. Moreover, heterozygous embryos sired by pi6-/- fathers show reduced viability in utero. Molecular analyses suggest that pi6 piRNAs repress gene expression by cleaving mRNAs encoding proteins required for sperm function. pi6 also participates in a network of piRNA-piRNA precursor interactions that initiate piRNA production from a second piRNA locus on chromosome 10 as well as pi6 itself. Our data establish a direct role for pachytene piRNAs in spermiogenesis and embryo viability.nnHighlightsO_LINormal male mouse fertility and spermiogenesis require piRNAs from the pi6 locusnC_LIO_LISperm capacitation and binding to the zona pellucida of the egg require pi6 piRNAsnC_LIO_LIHeterozygous embryos sired by pi6-/- fathers show reduced viability in uteronC_LIO_LIDefects in pi6 mutant sperm reflect changes in the abundance of specific mRNAs.nC_LI ]]> Wu, P.-H. Fu, Y. Cecchini, K. Ozata, D. M. Weng, Z. Zamore, P. D. 2018-08-07 doi:10.1101/386201 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Multi-modal regulation of C. elegans hermaphrodite spermatogenesis by the GLD-1-FOG-2 complex ]]> https://biorxiv.org/content/10.1101/386250v1?rss=1 Hu, S. Ryan, L. E. Kaymak, E. Freeberg, L. Lo, T.-W. Kuersten, S. Ryder, S. P. Haag, E. S. 2018-08-07 doi:10.1101/386250 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ FUS/TLS undergoes calcium-mediated nuclear egress during excitotoxic stress and is required for Gria2 mRNA processing ]]> https://biorxiv.org/content/10.1101/386870v1?rss=1 Tischbein, M. Baron, D. Lin, Y.-C. Gall, K. Landers, J. Fallini, C. Bosco, D. 2018-08-07 doi:10.1101/386870 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ Photon count estimation in single-molecule localization microscopy ]]> https://biorxiv.org/content/10.1101/396424v1?rss=1 Rieger, B. Stallinga, S. Hulleman, C. N. Thorsen, R. O. Grunwald, D. Hammer, M. 2018-08-20 doi:10.1101/396424 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data ]]> https://biorxiv.org/content/10.1101/399931v1?rss=1 Kucukural, A. Yukselen, O. Ozata, D. M. Moore, M. J. Garber, M. 2018-08-24 doi:10.1101/399931 Cold Spring Harbor Laboratory Press 2018-08-24 <![CDATA[ Trans-splicing of the C. elegans let-7 primary transcript developmentally regulates let-7 microRNA biogenesis and let-7 family microRNA activity ]]> https://biorxiv.org/content/10.1101/400077v1?rss=1 Nelson, C. Ambros, V. 2018-08-24 doi:10.1101/400077 Cold Spring Harbor Laboratory Press 2018-08-24 <![CDATA[ Toll-Like Receptor-4 Disruption Suppresses Adipose Tissue Remodeling and Increases Survival During Cancer Cachexia Syndrome ]]> https://biorxiv.org/content/10.1101/400135v1?rss=1 Henriques, F. Lopes, M. Franco, F. Knobl, P. Santos, K. Bueno, L. Correa, V. Bedard, A. Guilherme, A. Birbrair, A. Peres, S. Farmer, S. Batista, M. L. 2018-08-25 doi:10.1101/400135 Cold Spring Harbor Laboratory Press 2018-08-25 <![CDATA[ SWITCH-LIKE PHOSPHORYLATION OF WRN INTEGRATES END-RESECTION WITH REPAIR OF DSBs AT REPLICATION FORKS ]]> https://biorxiv.org/content/10.1101/403808v1?rss=1 Palermo, V. Malacaria, E. Sanchez, M. Franchitto, A. Pichierri, P. 2018-08-29 doi:10.1101/403808 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Structural Adaptation of Darunavir Analogs Against Primary Resistance Mutations in HIV-1 Protease ]]> https://biorxiv.org/content/10.1101/406637v1?rss=1 Lockbaum, G. J. Leidner, F. Rusere, L. Henes, M. Kosovrasti, K. Nalivaika, E. A. Ali, A. Kurt Yilmaz, N. Schiffer, C. A. 2018-09-03 doi:10.1101/406637 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Classification and monomer-by-monomer annotation of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly ]]> https://biorxiv.org/content/10.1101/408674v1?rss=1 Uralsky, L. Shepelev, V. A. Alexandrov, A. A. Yurov, Y. B. Rogaev, E. I. Alexandrov, I. A. 2018-09-07 doi:10.1101/408674 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Transfer RNA Genes Affect Chromosome Structure and Function via Local Effects ]]> https://biorxiv.org/content/10.1101/412247v1?rss=1 Kamakaka, R. T. Hamdani, O. Dhillon, N. Hsieh, T.-H. S. Fujita, T. Ocampo, J. Kirkland, J. G. Lawrimore, J. Kobayashi, T. J. Friedman, B. Fulton, D. Wu, K. Y. Chereji, R. V. Oki, M. Bloom, K. S. Clark, D. Rando, O. J. 2018-09-10 doi:10.1101/412247 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish ]]> https://biorxiv.org/content/10.1101/414003v1?rss=1 Whitesell, T. R. Chrystal, P. Ryu, J.-R. Munsie, N. Grosse, A. French, C. Workentine, M. L. Li, R. Zhu, L. J. Waskiewicz, A. Lehmann, O. J. Lawson, N. D. Childs, S. J. 2018-09-10 doi:10.1101/414003 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Modulation of actin polymerization affects nucleocytoplasmic transport in multiple forms of Amyotrophic Lateral Sclerosis ]]> https://biorxiv.org/content/10.1101/415901v1?rss=1 Giampetruzzi, A. Danielson, E. W. Jeon, M. Gumina, V. Boopathy, S. Brown, R. Landers, J. Fallini, C. 2018-09-12 doi:10.1101/415901 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Multiple Toll-Spätzle Pathways in Drosophila melanogaster Immunity ]]> https://biorxiv.org/content/10.1101/420679v1?rss=1 Yu, X.-Q. Chowdhury, M. Li, C.-F. He, Z. Lu, Y. Liu, X. Wang, Y. Ip, Y. T. Strand, M. R. 2018-09-18 doi:10.1101/420679 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ High diversity, turnover, and structural constraints characterize TCR α and β repertoire selection ]]> https://biorxiv.org/content/10.1101/428623v1?rss=1 Kamga, L. Gil, A. Song, I. Chirravuri, R. Aslan, N. Ghersi, D. Stern, L. J. Selin, L. K. Luzuriaga, K. 2018-09-29 doi:10.1101/428623 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ The RNA-binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria ]]> https://biorxiv.org/content/10.1101/445825v1?rss=1 Ge, D. T. Wang, W. Tipping, C. Gainetdinov, I. Weng, Z. Zamore, P. D. 2018-10-17 doi:10.1101/445825 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Resistance from Afar: Distal Mutation V36M Allosterically Modulates the Active Site to Accentuate Drug Resistance in HCV NS3/4A Protease ]]> https://biorxiv.org/content/10.1101/452284v1?rss=1 Ozen, A. Lin, K.-H. Romano, K. P. Tavella, D. Newton, A. Petropoulos, C. J. Kuang, W. Aydin, C. Schiffer, C. 2018-11-05 doi:10.1101/452284 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ An emergent Ebola virus nucleoprotein variant influences virion budding, oligomerization, transcription and replication ]]> https://biorxiv.org/content/10.1101/454314v1?rss=1 Lin, A. E. Diehl, W. E. Cai, Y. Finch, C. Akusobi, C. Kirchdoerfer, R. N. Bollinger, L. Schaffner, S. F. Brown, E. A. Saphire, E. O. Andersen, K. G. Kuhn, J. H. Luban, J. Sabeti, P. C. 2018-10-29 doi:10.1101/454314 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ Image processing and analysis methods for the Adolescent Brain Cognitive Development Study ]]> https://biorxiv.org/content/10.1101/457739v1?rss=1 Hagler, D. J. Hatton, S. N. Makowski, C. Cornejo, M. D. Fair, D. A. Dick, A. S. Sutherland, M. T. Casey, B. J. Barch, D. M. Harms, M. P. Watts, R. Bjork, J. M. Garavan, H. P. Hilmer, L. Pung, C. J. Sicat, C. S. Kuperman, J. Bartsch, H. Xue, F. Heitzeg, M. M. Laird, A. R. Trinh, T. T. Gonzalez, R. Tapert, S. F. Riedel, M. C. Squeglia, L. M. Hyde, L. W. Rosenberg, M. D. Earl, E. A. Howlett, K. D. Baker, F. C. Soules, M. Diaz, J. Ruiz de Leon, O. Thompson, W. K. Neale, M. C. Herting, M. Sowell, E. R. Alvarez, R. P. Hawes, S. W. Sanchez, M. Bodurka, J. Bre 2018-11-04 doi:10.1101/457739 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Intraflagellar transport protein 74 is essential for mouse spermatogenesis and male fertility by regulating axonemal microtubule assembly in mice ]]> https://biorxiv.org/content/10.1101/457804v1?rss=1 Shi, L. Zhou, T. Huang, Q. Zhang, S. Li, W. Zhang, L. Hess, R. A. Pazour, G. J. zhang, z. 2018-10-31 doi:10.1101/457804 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure ]]> https://biorxiv.org/content/10.1101/473264v1?rss=1 Stone, N. Demo, G. Agnello, E. Kelch, B. A. 2018-11-19 doi:10.1101/473264 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin ]]> https://biorxiv.org/content/10.1101/484568v1?rss=1 Vertii, A. Ou, J. Yu, J. Yan, A. Pages, H. Liu, H. Zhu, L. J. Kaufman, P. D. 2018-12-03 doi:10.1101/484568 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Ezh2-dependent epigenetic reprogramming controls a developmental switch between modes of gastric neuromuscular regulation ]]> https://biorxiv.org/content/10.1101/486423v1?rss=1 nView larger version (38K):norg.highwire.dtl.DTLVardef@e12f42org.highwire.dtl.DTLVardef@1e5c7beorg.highwire.dtl.DTLVardef@9cbc21org.highwire.dtl.DTLVardef@34f28_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIGastric pacemaker cells (ICC) transdifferentiate into quiescent cells (FLC) in vivonC_LIO_LIICC-to-FLC shift switches neural control from nitrergic/cholinergic to purinergicnC_LIO_LIEzh2-mediated H3K27me3 represses cell-identity genes during ICC-to-FLC transitionnC_LIO_LIEzh2 inhibition restores ICC numbers, phenotype and functionnC_LInneTOC BLURBSyed et al. find aging to cause transdifferentiation of gastric pacemaker cells (interstitial cells of Cajal, ICC), which also communicate cholinergic and nitrergic neurotransmission to smooth muscle cells, into quiescent "fibroblast-like cells" (FLC), which only mediate purinergic signals. This switch is governed by Ezh2, whose inhibition can reverse ICC depletion. ]]> Syed, S. Hayashi, Y. Lee, J.-H. Yan, H. Lorincz, A. Strege, P. R. Gajdos, G. B. Milosavljevic, S. Nie, J. Rumessen, J. J. Gibbons, S. J. Horvath, V. J. Bardsley, M. R. Redelman, D. D. Klein, S. Saur, D. Farrugia, G. Zhang, Z. Urrutia, R. Ordog, T. 2018-12-04 doi:10.1101/486423 Cold Spring Harbor Laboratory Press 2018-12-04 <![CDATA[ Fission Yeast Cells Grow Approximately Exponentially ]]> https://biorxiv.org/content/10.1101/489708v1?rss=1 Pickering, M. Hollis, L. N. D'Souza, E. Rhind, N. 2018-12-06 doi:10.1101/489708 Cold Spring Harbor Laboratory Press 2018-12-06 <![CDATA[ Identification of A Disintegrin and Metalloproteinase 9 domain (ADAM9) required in the early stages of encephalomyocarditis virus infection ]]> https://biorxiv.org/content/10.1101/491068v1?rss=1 Bazzone, L. E. King, M. MacKay, C. R. Kyawe, P. P. Meraner, P. Lindstrom, D. Rojas-Quintero, J. Owen, C. A. Wang, J. P. Brass, A. L. Kurt-Jones, E. A. Finberg, R. W. 2018-12-09 doi:10.1101/491068 Cold Spring Harbor Laboratory Press 2018-12-09 <![CDATA[ Resistance to Diet Induced Obesity in the Apolipoprotein E Deficient Mouse is Associated with an Attenuated Transcriptional Response in Visceral Fat ]]> https://biorxiv.org/content/10.1101/494195v1?rss=1 Fitzgibbons, T. P. Kelly, M. Kim, J. K. Czech, M. P. 2018-12-11 doi:10.1101/494195 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ International travelers and genomics uncover a ‘hidden’ Zika outbreak ]]> https://biorxiv.org/content/10.1101/496901v1?rss=1 Grubaugh, N. Saraf, S. Gangavarapu, K. Watts, A. Tan, A. L. Roidtman, R. Ladner, J. T. Oliveira, G. Matteson, N. L. Kraemer, M. U. Vogels, C. B. Hentoff, A. Bhatia, D. Stanek, D. Scott, B. Landis, V. Stryker, I. Cone, M. Kopp, E. Cannons, A. Heberlein-Larson, L. White, S. Gillis, L. Ricciardi, M. Kwai, J. Lichtenberger, P. Magnani, D. Watkins, D. Palacios, G. Hamer, D. H. GeoSentinel Surveillance Network, Gardner, L. Perkins, T. A. Baele, G. Khan, K. Morrison, A. Isern, S. Michael, S. F. Andersen, K. G. 2018-12-14 doi:10.1101/496901 Cold Spring Harbor Laboratory Press 2018-12-14 <![CDATA[ Control of noncoding RNA production and histone levels by a 5’ tRNA fragment ]]> https://biorxiv.org/content/10.1101/498949v1?rss=1 Boskovic, A. Bing, X. Y. Kaymak, E. Rando, O. J. 2018-12-17 doi:10.1101/498949 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ PSI controls tim splicing and circadian period in Drosophila ]]> https://biorxiv.org/content/10.1101/504282v1?rss=1 Foley, L. Ling, J. Joshii, R. Evantal, N. Kadener, S. Emery, P. 2018-12-21 doi:10.1101/504282 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ The FXR2P low complexity domain drives assembly of multiple fibril types with differing ribosome association in neurons ]]> https://biorxiv.org/content/10.1101/505255v1?rss=1 Stackpole, E. E. Akins, M. R. Ivshina, M. Murthy, A. C. Fawzi, N. L. Fallon, J. R. 2018-12-22 doi:10.1101/505255 Cold Spring Harbor Laboratory Press 2018-12-22 <![CDATA[ BRG1 is a prognostic indicator and a potential therapeutic target for prostate cancer ]]> https://biorxiv.org/content/10.1101/506972v1?rss=1 Muthuswami, R. Bailey, L. Rakesh, R. Imbalzano, A. Nickerson, J. Hockensmith, J. W. 2018-12-27 doi:10.1101/506972 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Gain-of-function mutations in the UNC-2/CaV2α channel lead to hyperactivity and excitation-dominant synaptic transmission in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/509380v1?rss=1 Huang, Y.-C. Pirri, J. Rayes, D. Gao, S. Mulcahy, B. Grant, J. Saheki, Y. Francis, M. Zhen, M. Alkema, M. 2019-01-01 doi:10.1101/509380 Cold Spring Harbor Laboratory Press 2019-01-01 <![CDATA[ MTF1, a classic metal sensing transcription factor, promotes myogenesis in response to copper. ]]> https://biorxiv.org/content/10.1101/534271v1?rss=1 Tavera-Montanez, C. Hainer, S. J. Cangussu, D. Gordon, S. J. V. Xiao, Y. Reyes-Gutierrez, P. Imbalzano, A. N. Navea, J. G. Fazzio, T. G. PADILLA-BENAVIDES, T. 2019-01-29 doi:10.1101/534271 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Multiple human adipocyte subtypes and mechanisms of their development ]]> https://biorxiv.org/content/10.1101/537464v1?rss=1 Min, S. Y. Desai, A. Yang, Z. Sharma, A. Genga, R. M. J. Kucukural, A. Lifshitz, L. Maehr, R. Garber, M. Corvera, S. 2019-01-31 doi:10.1101/537464 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Oligogenic effects of 16p11.2 copy number variation on craniofacial development ]]> https://biorxiv.org/content/10.1101/540732v1?rss=1 Qiu, Y. Arbogast, T. Martin Lorenzo, S. Li, H. Shih, T. Ellen, R. Hong, O. Cho, S. Shanta, O. Timothy, P. Corsello, C. Deutsch, C. K. Chevalier, C. Davis, E. E. Iakoucheva, L. M. Herault, Y. Katasanis, N. Messer, K. Sebat, J. 2019-02-05 doi:10.1101/540732 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Clinical investigation and genetic analysis of a peripheral sclerocornea pedigree ]]> https://biorxiv.org/content/10.1101/547547v1?rss=1 Zhang, B. N. Chan, T. C. Y. Tam, P. O. S. Liu, Y. Pang, C. P. Jhanji, V. Chen, L. J. Chu, W. K. 2019-02-12 doi:10.1101/547547 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Environmental pheromone and endocrine signals correct heterochronic developmental phenotypes caused by insufficient expression of let-7 family microRNAs in C. elegans ]]> https://biorxiv.org/content/10.1101/551606v1?rss=1 Ilbay, O. Ambros, V. 2019-02-15 doi:10.1101/551606 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Sensory lesioning induces microglial synapse elimination via ADAM10 and fractalkine signaling ]]> https://biorxiv.org/content/10.1101/551697v1?rss=1 Gunner, G. Cheadle, L. Johnson, K. M. Ayata, P. Badimon, A. Mondo, E. Nagy, A. Liu, L. Bemiller, S. M. Kim, K.-w. Lira, S. A. Lamb, B. T. Tapper, A. R. Ransohoff, R. M. Greenberg, M. E. Schaefer, A. Schafer, D. P. 2019-02-15 doi:10.1101/551697 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ Evolutionary dynamics of phage resistance in bacterial biofilms ]]> https://biorxiv.org/content/10.1101/552265v1?rss=1 Simmons, M. Bond, M. C. Drescher, K. Bucci, V. Nadell, C. D. 2019-02-17 doi:10.1101/552265 Cold Spring Harbor Laboratory Press 2019-02-17 <![CDATA[ GCNA interacts with Spartan and Topoisomerase II to regulate genome stability. ]]> https://biorxiv.org/content/10.1101/570200v1?rss=1 Davis, G. M. Dokshin, G. Sawle, A. D. Eldridge, M. D. Romer, K. A. Gourley, T. E. Molesworth, L. W. Tatnell, H. R. Ozturk, A. R. de Rooij, D. G. Hannon, G. J. Page, D. C. Mello, C. C. Carmell, M. A. 2019-03-07 doi:10.1101/570200 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis. ]]> https://biorxiv.org/content/10.1101/576660v1?rss=1 Phillips, H. M. Stothard, C. A. Shaikh Qureshi, W. M. Kousa, A. I. Briones-Leon, A. Khasawneh, R. Sanders, R. Mazotta, S. Dodds, R. Seidel, K. Bates, T. Nakatomi, M. Cockell, S. Schneider, J. E. Mohun, T. J. Maehr, R. Kist, R. Peters, H. Bamforth, S. D. 2019-03-14 doi:10.1101/576660 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control ]]> https://biorxiv.org/content/10.1101/581868v1?rss=1 Viny, A. D. Bowman, R. L. Liu, Y. Lavallee, V.-P. Redlich, S. E. Xiao, W. Durham, B. H. Navitski, A. Park, J. Braunstein, S. Azizi, E. Witkin, M. Baslan, T. Ott, C. J. Pe'er, D. Dekker, J. Koche, R. Levine, R. L. 2019-03-18 doi:10.1101/581868 Cold Spring Harbor Laboratory Press 2019-03-18 <![CDATA[ Cyclophilin A protects HIV-1 from restriction by human TRIM5α ]]> https://biorxiv.org/content/10.1101/587907v1?rss=1 Kim, K. Dauphin, A. Komurlu, S. Yurkovetskiy, L. Diehl, W. E. McCauley, S. M. Carbone, C. Selyutina, A. Bulnes-Ramos, A. Diaz-Griffero, F. Strambio-De-Castillia, C. Campbell, E. M. Luban, J. 2019-03-25 doi:10.1101/587907 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ Statistical Analysis of Variability in TnSeq Data Across Conditions Using Zero-Inflated Negative Binomial Regression ]]> https://biorxiv.org/content/10.1101/590281v1?rss=1 Subramaniyam, S. DeJesus, M. A. Saveri, A. Smith, C. M. Baker, R. E. Ehrt, S. Schnappinger, D. Sassetti, C. M. Ioerger, T. R. 2019-03-28 doi:10.1101/590281 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ The piRNA Response to Retroviral Invasion of the Koala Genome ]]> https://biorxiv.org/content/10.1101/599852v1?rss=1 Yu, T. Koppetsch, B. Chappell, K. Pagliarani, S. Johnston, S. Weng, Z. Theurkauf, W. 2019-04-05 doi:10.1101/599852 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Extensive ribosome and RF2 rearrangements during translation termination ]]> https://biorxiv.org/content/10.1101/600445v1?rss=1 Svidritskiy, E. Demo, G. Loveland, A. B. Xu, C. Korostelev, A. A. 2019-04-05 doi:10.1101/600445 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ TRIM5α restricts flavivirus replication by targeting the viral protease for proteasomal degradation. ]]> https://biorxiv.org/content/10.1101/605345v1?rss=1 Chiramel, A. I. Meyerson, N. McNally, K. Broeckel, R. M. Montoya, V. Mendes-Solis, O. Robertson, S. Sturdevant, G. Lubick, K. Nair, V. Youseff, B. Ireland, R. Bosio, C. Kim, K. Luban, J. Hirsch, V. Taylor, T. R. Bouamr, F. Sawyer, S. Best, S. M. 2019-04-11 doi:10.1101/605345 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ The central role of the tail in switching off myosin II in cells ]]> https://biorxiv.org/content/10.1101/606368v1?rss=1 Craig, R. Yang, S. Lee, K. H. Woodhead, J. L. Sato, O. Ikebe, M. 2019-04-11 doi:10.1101/606368 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ Promotion of adipogenesis by JMJD6 requires the AT hook-like domain and is independent of its catalytic function ]]> https://biorxiv.org/content/10.1101/609982v1?rss=1 Reyes-Gutierrez, P. Carrasquillo-Rodriguez, J. W. Imbalzano, A. N. 2019-04-15 doi:10.1101/609982 Cold Spring Harbor Laboratory Press 2019-04-15 <![CDATA[ The coordinate actions of calcineurin and Hog1 mediate the response to cellular stress through multiple nodes of the cell cycle network ]]> https://biorxiv.org/content/10.1101/612416v1?rss=1 Leech, C. M. Flynn, M. J. Arsenault, H. E. Ou, J. Liu, H. Zhu, L. J. Benanti, J. 2019-04-17 doi:10.1101/612416 Cold Spring Harbor Laboratory Press 2019-04-17 <![CDATA[ Myosin XI Interacting with a RabE GTPase Is Required for Polarized Growth ]]> https://biorxiv.org/content/10.1101/617167v1?rss=1 Orr, R. G. Furt, F. Warner, E. L. Agar, E. M. Garbarino, J. M. Cabral, S. E. Dubuke, M. L. Butt, A. M. Munson, M. Vidali, L. 2019-04-28 doi:10.1101/617167 Cold Spring Harbor Laboratory Press 2019-04-28 <![CDATA[ The Pseudomonas aeruginosa accessory genome elements, including bacterial immune systems effect virulence towards C. elegans ]]> https://biorxiv.org/content/10.1101/621433v1?rss=1 Vasquez-Rifo, A. I. Veksler-Lublinsky, I. I. Cheng, Z. Ausubel, F. M. Ambros, V. 2019-04-29 doi:10.1101/621433 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ Free circular introns with an unusual branchpoint in neuronal projections ]]> https://biorxiv.org/content/10.1101/623447v1?rss=1 Eddy, S. R. Saini, H. Moore, M. J. Bicknell, A. A. 2019-04-30 doi:10.1101/623447 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Calcineurin broadly regulates the initiation of skeletal muscle-specific gene expression by binding target promoters and facilitating the interaction of the SWI/SNF chromatin remodeling enzyme ]]> https://biorxiv.org/content/10.1101/628768v1?rss=1 Witwicka, H. Nogami, J. Syed, S. A. Maehara, K. Padilla-Benavides, T. Ohkawa, Y. Imbalzano, A. N. 2019-05-05 doi:10.1101/628768 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Tissue-specific Genome Editing in vivo by MicroRNA-repressible Anti-CRISPR Proteins ]]> https://biorxiv.org/content/10.1101/631689v1?rss=1 Lee, J. Mou, H. Ibraheim, R. Liang, S.-Q. Xue, W. Sontheimer, E. J. 2019-05-08 doi:10.1101/631689 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Resolving the 3D landscape of transcription-linked mammalian chromatin folding ]]> https://biorxiv.org/content/10.1101/638775v1?rss=1 Hsieh, T.-H. S. Slobodyanyuk, E. Hansen, A. S. Cattoglio, C. Rando, O. J. Tjian, R. Darzacq, X. 2019-05-17 doi:10.1101/638775 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Ultrastructural details of mammalian chromosome architecture ]]> https://biorxiv.org/content/10.1101/639922v1?rss=1 Krietenstein, N. Abraham, S. Venev, S. Abdennur, N. Gibcus, J. Hsieh, T.-H. Parsi, K. M. Yang, L. Maehr, R. Mirny, L. Dekker, J. Rando, O. 2019-05-17 doi:10.1101/639922 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Probing mechanisms of transcription elongation through cell-to-cell variability of RNA polymerase ]]> https://biorxiv.org/content/10.1101/655712v1?rss=1 Ali, M. Z. Choubey, S. Das, D. Brewster, R. 2019-05-31 doi:10.1101/655712 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ The Impact of Antimalarial Resistance on the Genetic Structure of Plasmodium falciparum in the DRC ]]> https://biorxiv.org/content/10.1101/656561v1?rss=1 Verity, R. J. Aydemir, O. Brazeau, N. F. Watson, O. J. Hathaway, N. J. Mwandagalirwa, M. K. Marsh, P. W. Thwai, K. Fulton, T. Denton, M. Morgan, A. P. Parr, J. B. Tumwebaze, P. K. Conrad, M. Rosenthal, P. J. Ishengoma, D. S. Ngondi, J. Gutman, J. Mulenga, M. Norris, D. E. Moss, W. J. Mensah, B. A. Myers-Hansen, J. L. Ghansah, A. Tshefu, A. K. Ghani, A. C. Meshnick, S. R. Bailey, J. A. Juliano, J. J. 2019-05-31 doi:10.1101/656561 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Conditional, inducible gene silencing in dopamine neurons reveals a sex-specific role for Rit2 GTPase in acute cocaine response and striatal function ]]> https://biorxiv.org/content/10.1101/658856v1?rss=1 Sweeney, C. G. Kearney, P. J. Fagan, R. L. Smith, L. A. Bolden, N. C. Zhao-Shea, R. Rivera, I. V. Kolpakova, J. Xie, J. Gao, G. Tapper, A. R. Martin, G. E. Melikian, H. E. 2019-06-03 doi:10.1101/658856 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ A Novel PHOX/CD38/MCOLN1/TFEB Axis Important For Macrophage Activation During Bacterial Phagocytosis ]]> https://biorxiv.org/content/10.1101/669325v1?rss=1 Najibi, M. Moreau, J. A. Honwad, H. H. Irazoqui, J. 2019-06-13 doi:10.1101/669325 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Ste5 Membrane Localization Allows MAPK Pathway Signaling in trans Between Kinases on Separate Scaffold Molecules ]]> https://biorxiv.org/content/10.1101/673855v1?rss=1 Lamson, R. E. Winters, M. J. Pryciak, P. M. 2019-06-17 doi:10.1101/673855 Cold Spring Harbor Laboratory Press 2019-06-17 <![CDATA[ Adaptive evolution targets a piRNA precursor transcription network ]]> https://biorxiv.org/content/10.1101/678227v1?rss=1 Parhad, S. S. Yu, T. Zhang, G. Rice, N. Weng, Z. Theurkauf, W. 2019-06-21 doi:10.1101/678227 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ A chromosome folding intermediate at the condensin-to-cohesin transition during telophase ]]> https://biorxiv.org/content/10.1101/678474v1?rss=1 Abramo, K. Valton, A.-L. Venev, S. V. Ozadam, H. Fox, A. N. Dekker, J. 2019-06-21 doi:10.1101/678474 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Neonatal-derived IL-17 producing dermal gd T cells are required to prevent spontaneous atopic dermatitis ]]> https://biorxiv.org/content/10.1101/686576v1?rss=1 Spidale, N. Malhotra, N. Sylvia, K. Frascoli, M. Miu, B. Standinski, B. D. Huseby, E. S. Kang, J. 2019-06-28 doi:10.1101/686576 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Epstein Barr virus genomes reveal population structure and type 1 association with endemic Burkitt lymphoma ]]> https://biorxiv.org/content/10.1101/689216v1?rss=1 Kaymaz, Y. Oduor, C. I. Aydemir, O. Luftig, M. A. Otieno, J. A. Ong'echa, J. M. Bailey, J. A. Moormann, A. M. 2019-07-02 doi:10.1101/689216 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ DolphinNext: A distributed data processing platform for high throughput genomics ]]> https://biorxiv.org/content/10.1101/689539v1?rss=1 Yukselen, O. Turkyilmaz, O. Ozturk, A. Garber, M. Kucukural, A. 2019-07-02 doi:10.1101/689539 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Molecular and structural mechanism of pan-genotypic HCV NS3/4A protease inhibition by glecaprevir ]]> https://biorxiv.org/content/10.1101/692392v1?rss=1 Timm, J. Kosovrasti, K. Henes, M. Leidner, F. Hou, S. Ali, A. Kurt-Yilmaz, N. Schiffer, C. A. 2019-07-03 doi:10.1101/692392 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ C. elegans LIN-28 controls temporal cell-fate progression by regulating LIN-46 expression via the 5’UTR of lin-46 mRNA ]]> https://biorxiv.org/content/10.1101/697490v1?rss=1 Ilbay, O. Nelson, C. Ambros, V. 2019-07-10 doi:10.1101/697490 Cold Spring Harbor Laboratory Press 2019-07-10 <![CDATA[ Limited recognition of Mycobacterium tuberculosis-infected macrophages by polyclonal CD4 and CD8 T cells from the lungs of infected mice ]]> https://biorxiv.org/content/10.1101/697805v1?rss=1 Patankar, Y. Sutiwisesak, R. Boyce, S. Lai, R. Lindestam Arlehamn, C. Sette, A. Behar, S. M. 2019-07-11 doi:10.1101/697805 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Regulation of Nuclear-cytoplasmic Partitioning by the lin-28-lin-46 Pathway Reinforces MicroRNA Repression of HBL-1 to Confer Robust Cell-fate Progression in C. elegans ]]> https://biorxiv.org/content/10.1101/698977v1?rss=1 Ilbay, O. Ambros, V. 2019-07-11 doi:10.1101/698977 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C ]]> https://biorxiv.org/content/10.1101/704957v1?rss=1 Belaghzal, H. Borrman, T. Stephens, A. D. Lafontaine, D. L. Venev, S. V. Marko, J. F. Weng, Z. Dekker, J. 2019-07-16 doi:10.1101/704957 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ IQGAP1 connects phosphoinositide signaling to cytoskeletal reorganization ]]> https://biorxiv.org/content/10.1101/706465v1?rss=1 Yerramilli, V. S. Ross, A. H. Lindberg, S. K. Scarlata, S. Gericke, A. 2019-07-18 doi:10.1101/706465 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Regulation of melanocyte development by ligand-dependent BMP signaling underlies oncogenic BMP signaling in melanoma ]]> https://biorxiv.org/content/10.1101/708610v1?rss=1 Gramann, A. Venkatesan, A. M. Guerin, M. Ceol, C. 2019-07-19 doi:10.1101/708610 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Dopamine transporter trafficking and Rit2 GTPase:In vivo impact and mechanism of action ]]> https://biorxiv.org/content/10.1101/712448v1?rss=1 Fagan, R. R. Kearney, P. J. Sweeney, C. G. Luethi, D. Schooter Uiterkamp, F. E. Schicker, K. O'Connor, L. C. Sitte, H. H. Melikian, H. E. 2019-07-23 doi:10.1101/712448 Cold Spring Harbor Laboratory Press 2019-07-23 <![CDATA[ Lattice arrangement of myosin filaments correlates with fiber type in rat skeletal muscle ]]> https://biorxiv.org/content/10.1101/720300v1?rss=1 Ma, W. Lee, K. H. Yang, S. Irving, T. Craig, R. 2019-07-30 doi:10.1101/720300 Cold Spring Harbor Laboratory Press 2019-07-30 <![CDATA[ Whole integration of neural connectomics, dynamics and bio-mechanics for identification of behavioral sensorimotor pathways in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/724328v1?rss=1 Kim, J. Santos, J. A. Alkema, M. J. Shlizerman, E. 2019-08-03 doi:10.1101/724328 Cold Spring Harbor Laboratory Press 2019-08-03 <![CDATA[ Leptin promotes expression of EMT-related transcription factors and invasion in a Src and FAK-dependent pathway in MCF10A mammary epithelial cells ]]> https://biorxiv.org/content/10.1101/739169v1?rss=1 Olea-Flores, M. Zuniga-Eulogio, M. Tacuba-Saavedra, A. Bueno-Salgado, M. Sanchez-Carvajal, A. Vargas-Santiago, Y. Mendoza-Catalan, M. A. Perez Salazar, E. Garcia-Hernandez, A. Padilla-Benavides, T. Navarro-Tito, N. 2019-08-18 doi:10.1101/739169 Cold Spring Harbor Laboratory Press 2019-08-18 <![CDATA[ Distinct features of nucleolus-associated domains in mouse embryonic stem cells ]]> https://biorxiv.org/content/10.1101/740480v1?rss=1 Bizhanova, A. Yan, A. Yu, J. Zhu, L. J. Kaufman, P. D. 2019-08-20 doi:10.1101/740480 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ Hedgehog signaling regulates neurogenesis in the larval and adult zebrafish hypothalamus ]]> https://biorxiv.org/content/10.1101/740613v1?rss=1 Male, I. Ozacar, A. T. Fagan, R. R. Loring, M. D. Shen, M.-C. Pace, V. Devine, C. A. Lutservitz, A. Karlstrom, R. O. 2019-08-26 doi:10.1101/740613 Cold Spring Harbor Laboratory Press 2019-08-26 <![CDATA[ Association between Drusen Burden Determined by OCT and Genetic Risk in Early and Intermediate Age-Related Macular Degeneration ]]> https://biorxiv.org/content/10.1101/743633v1?rss=1 Seddon, J. M. Dossett, J. Widjajahakim, R. Rosner, B. 2019-08-24 doi:10.1101/743633 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods ]]> https://biorxiv.org/content/10.1101/745844v1?rss=1 Moore, J. E. Pratt, H. Purcaro, M. Weng, Z. 2019-08-24 doi:10.1101/745844 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Dormancy as a spectrum measuring spore’s proximity to death and to replicative life ]]> https://biorxiv.org/content/10.1101/747766v1?rss=1 Maire, T. Allertz, T. Betjes, M. A. Youk, H. 2019-08-28 doi:10.1101/747766 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Oral administration of an anti-CfaE secretory IgA antibody protects against Enterotoxigenic Escherichia coli diarrheal disease in a non-human primate model ]]> https://biorxiv.org/content/10.1101/748442v1?rss=1 Stoppato, M. Gaspar, C. Regeimbal, J. Nunez, G. giuntini, s. Gawron, M. A. Pondish, J. R. Martin, J. C. Schneider, M. Schiller, Z. A. Klempner, M. Cavacini, L. A. Wang, Y. 2019-08-28 doi:10.1101/748442 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ The aminoalkylindole, BML-190, negatively regulates chitosan synthesis via the cAMP/PKA1 pathway in Cryptococcus neoformans ]]> https://biorxiv.org/content/10.1101/751172v1?rss=1 Maybruck, B. T. Lam, W. C. Specht, C. Ilagan, M. X. G. Donlin, M. J. Lodge, J. K. 2019-08-29 doi:10.1101/751172 Cold Spring Harbor Laboratory Press 2019-08-29 <![CDATA[ Chitosan biosynthesis and virulence in the human fungal pathogen Cryptococcus gattii ]]> https://biorxiv.org/content/10.1101/759050v1?rss=1 Lam, W. C. Upadhya, R. Specht, C. Ragsdale, A. E. Hole, C. R. Levitz, S. M. Lodge, J. K. 2019-09-05 doi:10.1101/759050 Cold Spring Harbor Laboratory Press 2019-09-05 <![CDATA[ Dissection of the 4D chromatin structure of the α-globin locus through in vivo erythroid differentiation with extreme spatial and temporal resolution ]]> https://biorxiv.org/content/10.1101/763763v1?rss=1 Oudelaar, A. M. Beagrie, R. A. Gosden, M. De Ornellas, S. Georgiades, E. Kerry, J. Hidalgo, D. Carrelha, J. Shivalingam, A. El-Sagheer, A. H. Telenius, J. M. Brown, T. Buckle, V. J. Socolovsky, M. Higgs, D. R. Hughes, J. R. 2019-09-10 doi:10.1101/763763 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Signaling to TRP53 and TAp63 from CHK1/CHK2 is responsible for elimination of most oocytes defective for either chromosome synapsis or recombination ]]> https://biorxiv.org/content/10.1101/768150v1?rss=1 Schimenti, J. C. Rinaldi, V. Bloom, J. 2019-09-12 doi:10.1101/768150 Cold Spring Harbor Laboratory Press 2019-09-12 <![CDATA[ Mutations in the SPTLC1 gene are a cause of amyotrophic lateral sclerosis that may be amenable to serine supplementation ]]> https://biorxiv.org/content/10.1101/770339v1?rss=1 Johnson, J. O. Chia, R. Kumaran, R. Alahmady, N. Miller, D. E. Abramzon, Y. Faghri, F. Renton, A. E. Topp, S. D. Pliner, H. A. Gibbs, J. R. Ding, J. Smith, N. Landeck, N. Nalls, M. A. Cookson, M. R. Pletnikova, O. Troncoso, J. Scholz, S. W. Sabir, M. S. Ahmed, S. Dalgard, C. L. Troakes, C. Jones, A. R. Shatunov, A. Iacoangeli, A. Al Khleifat, A. Ticozzi, N. Silani, V. Gellera, C. Blair, I. P. Dobson-Stone, C. Kwok, J. B. England, B. K. Bonkowski, E. S. The International ALS Genomics Consortium, The ITALSGEN Consortium, The FALS Sequencing Consortium, 2019-09-19 doi:10.1101/770339 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Direct, sensitive and specific detection of individual single- or double-strand DNA breaks by fluorescence microscopy ]]> https://biorxiv.org/content/10.1101/772269v1?rss=1 Kordon, M. Zarebski, M. Solarczyk, K. Ma, H. Pederson, T. Dobrucki, J. W. 2019-09-18 doi:10.1101/772269 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Structural organization of the C1a-e-c supercomplex within the ciliary central apparatus ]]> https://biorxiv.org/content/10.1101/773416v1?rss=1 2 MDa) complex, the C1a-e-c supercomplex, that requires the PF16 protein for assembly and contains the CA components FAP76, FAP81, FAP92, and FAP216. We localized these subunits within the supercomplex using nanogold-labeling and show that loss of any one of them results in impaired ciliary motility. These data provide insight into the subunit organization and three-dimensional (3D) structure of the CA, which is a prerequisite for understanding the molecular mechanisms by which the CA regulates ciliary beating.nnSummaryFu et al. use a wild-type vs. mutant comparison and cryo-electron tomography of Chlamydomonas flagella to identify central apparatus (CA) subunits and visualize their location in the native 3D CA structure. The study provides a better understanding of the CA and how it regulates ciliary motility. ]]> Fu, G. Zhao, L. Dymek, E. Hou, Y. Song, K. Phan, N. Shang, Z. Smith, E. F. Witman, G. B. Nicastro, D. 2019-09-18 doi:10.1101/773416 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Influence of different glycoproteins and of the virion core on SERINC5 antiviral activity ]]> https://biorxiv.org/content/10.1101/780577v1?rss=1 Diehl, W. E. Guney, M. H. Kyawe, P. P. White, J. M. Pizzato, M. Luban, J. 2019-09-24 doi:10.1101/780577 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ CK2-dependent phosphorylation of the Brg1 chromatin remodeling enzyme occurs during mitosis ]]> https://biorxiv.org/content/10.1101/781781v1?rss=1 Padilla-Benavides, T. Haokip, D. T. Yoon, Y. Reyes-Gutierrez, P. Rivera-Perez, J. A. Imbalzano, A. N. 2019-09-25 doi:10.1101/781781 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Wheat Germ Agglutinin Conjugated Fluorescent pH Sensors for Visualizing Proton Fluxes ]]> https://biorxiv.org/content/10.1101/781799v1?rss=1 Zhang, L. Zhang, M. Bellve, K. Fogarty, K. Castro, M. A. Brauchi, S. Kobertz, W. R. 2019-09-25 doi:10.1101/781799 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Replication gaps underlie BRCA-deficiency and therapy response ]]> https://biorxiv.org/content/10.1101/781955v1?rss=1 Panzarino, N. J. Krais, J. Peng, M. Mosqueda, M. Nayak, S. Bond, S. Calvo, J. Cong, K. Doshi, M. Bere, M. Ou, J. Deng, B. Zhu, L. J. Johnson, N. Cantor, S. 2019-09-25 doi:10.1101/781955 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ PARPi synthetic lethality derives from replication-associated single-stranded DNA gaps ]]> https://biorxiv.org/content/10.1101/781989v1?rss=1 Cong, K. Kousholt, A. N. Peng, M. Panzarino, N. J. Lee, W. T. C. Nayak, S. Krais, J. Calvo, J. Bere, M. Rothenberg, E. Johnson, N. Jonkers, J. Cantor, S. 2019-09-25 doi:10.1101/781989 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Replication gaps are a cancer vulnerability counteracted by translesion synthesis ]]> https://biorxiv.org/content/10.1101/781997v1?rss=1 Nayak, S. Calvo, J. Cong, K. Berthiaume, E. Jackson, J. Dash, R. C. Vindigni, A. Hadden, K. M. Cantor, S. 2019-09-25 doi:10.1101/781997 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Hepatic JNK-mediated bile acid homeostasis regulates liver cancer through PPARα ]]> https://biorxiv.org/content/10.1101/783761v1?rss=1 Manieri, E. Esteban-Lafuente, L. Rodriguez, E. Leiva-Vega, L. Chen, C. Cubero, F. J. Barrett, T. Cavanagh-Kyros, J. Seruggia, D. Monte, M. J. Marin, J. J. Davis, R. R. J. Mora, A. Sabio, G. 2019-09-29 doi:10.1101/783761 Cold Spring Harbor Laboratory Press 2019-09-29 <![CDATA[ Functionally overlapping variants control TB susceptibility in Collaborative Cross mice ]]> https://biorxiv.org/content/10.1101/785725v1?rss=1 Smith, C. M. Proulx, M. K. Lai, R. Kiritsy, M. C. Bell, T. A. Hock, P. Pardo-Manuel de Villena, F. Ferris, M. T. Baker, R. E. Behar, S. M. Sassetti, C. M. 2019-09-28 doi:10.1101/785725 Cold Spring Harbor Laboratory Press 2019-09-28 <![CDATA[ Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics ]]> https://biorxiv.org/content/10.1101/790642v1?rss=1 Durham, N. D. Agrawal, A. Waltari, E. Croote, D. Zanini, F. Fouch, M. Davidson, E. Smith, O. Carabajal, E. Pak, J. E. Doranz, B. J. Robinson, M. Sanz, A. M. Albornoz, L. L. Rosso, F. Einav, S. Quake, S. R. McCutcheon, K. M. Goo, L. 2019-10-02 doi:10.1101/790642 Cold Spring Harbor Laboratory Press 2019-10-02 <![CDATA[ Evaluation of IL-1 blockade as a host-directed therapy for tuberculosis in mice and macaques ]]> https://biorxiv.org/content/10.1101/792390v1?rss=1 Winchell, C. G. M. Mishra, B. B. Phuah, J. Y. Saqib, M. Nelson, S. J. Maiello, P. Causgrove, C. M. Ameel, C. L. Stein, B. Borish, H. J. White, A. G. Klein, E. C. Zimmerman, M. D. Dartois, V. Lin, P. L. Sassetti, C. M. Flynn, J. L. 2019-10-03 doi:10.1101/792390 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Nonsense suppression position effect implicates poly(A)-binding protein in the regulation of translation termination ]]> https://biorxiv.org/content/10.1101/793158v1?rss=1 Wu, C. Roy, B. He, F. Jacobson, A. 2019-10-06 doi:10.1101/793158 Cold Spring Harbor Laboratory Press 2019-10-06 <![CDATA[ Patterned Neuronal Activities Dictate Cell Type-specific Axon Regeneration ]]> https://biorxiv.org/content/10.1101/799635v1?rss=1 Ruppell, K. T. Wang, F. Li, F. Shang, Y. Gong, J. Guttipatti, P. Song, Y. Xiang, Y. 2019-10-10 doi:10.1101/799635 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ A large inner membrane pore defines the ESX translocon ]]> https://biorxiv.org/content/10.1101/800169v1?rss=1 Poweleit, N. Czudnochowski, N. Nakagawa, R. Murphy, K. C. Sassetti, C. M. Rosenberg, O. 2019-10-10 doi:10.1101/800169 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism ]]> https://biorxiv.org/content/10.1101/801076v1?rss=1 Richter, J. Huber, K. Shah, S. Molinaro, G. Liu, B. Wang, R. 2019-10-10 doi:10.1101/801076 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Genetic Rescue of Fragile X Syndrome Links FMRP Deficiency to Codon Optimality-Dependent RNA Destabilization ]]> https://biorxiv.org/content/10.1101/801449v1?rss=1 Shu, H. R. Donnard, E. Liu, B. Richter, J. 2019-10-10 doi:10.1101/801449 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Drug Combination Antagonism and Single Agent Dominance Result from Differences in Death Activation Kinetics ]]> https://biorxiv.org/content/10.1101/805093v1?rss=1 Richards, R. Schwartz, H. R. Stewart, M. S. Cruz-Gordillo, P. Honeywell, M. E. Joyce, A. J. Landry, B. D. Lee, M. J. 2019-10-16 doi:10.1101/805093 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Dysbiosis in a canine model of human fistulizing Crohn’s disease ]]> https://biorxiv.org/content/10.1101/815589v1?rss=1 Maldonado-Contreras, A. Ferrer, L. Cawley, C. Crain, S. Toscano, J. Ward, D. V. Hoffman, A. 2019-10-22 doi:10.1101/815589 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ TRIM34 acts with TRIM5 to restrict HIV and SIV capsids ]]> https://biorxiv.org/content/10.1101/820886v1?rss=1 Ohainle, M. Kim, K. Keceli, S. Felton, A. Campbell, E. M. Luban, J. Emerman, M. 2019-10-30 doi:10.1101/820886 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Investigating the influence of environment on the evolution of Hsp90 using comprehensive fitness maps ]]> https://biorxiv.org/content/10.1101/823468v1?rss=1 Flynn, J. M. Bolon, D. N. A. Rossouw, A. Cote-Hammarlof, P. A. Fragata, I. Mavor, D. Hollins, C. Bank, C. 2019-10-30 doi:10.1101/823468 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Phosphorylation on PstP controls cell wall metabolism and antibiotic tolerance in Mycobacterium smegmatis ]]> https://biorxiv.org/content/10.1101/825588v1?rss=1 Shamma, F. Papavinasasundaram, K. Bandekar, A. Sassetti, C. M. Boutte, C. C. 2019-10-31 doi:10.1101/825588 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Mapping the growth effect of previously hidden ubiquitin alleles using an overexpression based mutational scan ]]> https://biorxiv.org/content/10.1101/831503v1?rss=1 Mavor, D. Bolon, D. N. A. Mishra, P. 2019-11-08 doi:10.1101/831503 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ Selection of HIV-1 for Resistance to Fourth Generation Protease Inhibitors Reveals Two Independent Pathways to High-Level Resistance ]]> https://biorxiv.org/content/10.1101/837120v1?rss=1 Spielvogel, E. Lee, S.-K. Zhou, S. Lockbaum, G. J. Henes, M. Sondgeroth, A. Kosovrasti, K. Ali, A. Yilmaz, N. K. Schiffer, C. A. Swanstrom, R. 2019-11-09 doi:10.1101/837120 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Astrocyte-like glia-specific gene deathstar is crucial for normal development, adult locomotion and lifespan of male Drosophila ]]> https://biorxiv.org/content/10.1101/839811v1?rss=1 Najafi, H. Wong, K. Kim, W. J. 2019-11-12 doi:10.1101/839811 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Targeted complement inhibition at synapses prevents microglial synaptic engulfment and synapse loss in demyelinating disease ]]> https://biorxiv.org/content/10.1101/841601v1?rss=1 Werneburg, S. Jung, J. Kunjamma, R. B. Ha, S.-K. Luciano, N. J. Willis, C. M. Gao, G. Crocker, S. J. Popko, B. Reich, D. S. Schafer, D. P. 2019-11-15 doi:10.1101/841601 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ WormCat: an online tool for annotation and visualization of Caenorhabditis elegans genome-scale data ]]> https://biorxiv.org/content/10.1101/844928v1?rss=1 Holdorf, A. D. Higgins, D. P. Hart, A. C. Boag, P. R. Pazour, G. Walhout, M. Walker, A. K. 2019-11-15 doi:10.1101/844928 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved AS-NMD pathways ]]> https://biorxiv.org/content/10.1101/847004v1?rss=1 Kovalak, C. A. Moore, M. J. Metkar, M. 2019-11-19 doi:10.1101/847004 Cold Spring Harbor Laboratory Press 2019-11-19 <![CDATA[ A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry ]]> https://biorxiv.org/content/10.1101/851345v1?rss=1 Hayes, J. A. Hilbert, B. J. Gaubitz, C. Stone, N. P. Kelch, B. A. 2019-11-21 doi:10.1101/851345 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ A minimal CRISPR-Cas3 system for genome engineering ]]> https://biorxiv.org/content/10.1101/860999v1?rss=1 Csorgo, B. Leon, L. M. Chau-Ly, I. J. Vasquez-Rifo, A. Berry, J. D. Mahendra, C. Crawford, E. Lewis, J. D. Bondy-Denomy, J. 2019-12-03 doi:10.1101/860999 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Corollary Discharge Promotes a Sustained Motor State in a Neural Circuit for Navigation ]]> https://biorxiv.org/content/10.1101/861559v1?rss=1 Ji, N. Venkatachalam, V. Rodgers, H. Hung, W. Kawano, T. Clark, C. Lim, M. Alkema, M. J. Zhen, M. J. Samuel, A. 2019-12-03 doi:10.1101/861559 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ Efficient Homology-directed Repair with Circular ssDNA Donors ]]> https://biorxiv.org/content/10.1101/864199v1?rss=1 Iyer, S. Mir, A. Ibraheim, R. Lee, J. VegaBadillo, J. Roscoe, B. Zhu, L. J. Liu, P. Luk, K. Mintzer, E. de Brito, J. S. Zamore, P. Sontheimer, E. J. Wolfe, S. 2019-12-05 doi:10.1101/864199 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ Regulatory asymmetry in the negative single-input module network motif: Role of network size, growth rate and binding affinity ]]> https://biorxiv.org/content/10.1101/865527v1?rss=1 Ali, M. Z. Parisutham, V. Chuobey, S. Brewster, R. C. 2019-12-05 doi:10.1101/865527 Cold Spring Harbor Laboratory Press 2019-12-05 <![CDATA[ A DNA-guided Argonaute Protein Functions in DNA Replication in Thermus thermophilus ]]> https://biorxiv.org/content/10.1101/869172v1?rss=1 Jolly, S. M. Gainetdinov, I. Jouravleva, K. Zhang, H. Strittmatter, L. Hendricks, G. M. Dhabaria, A. Ueberheide, B. Zamore, P. 2019-12-09 doi:10.1101/869172 Cold Spring Harbor Laboratory Press 2019-12-09 <![CDATA[ Spatial positioning of preimplantation mouse embryo blastomeres is regulated by mTORC1 and 7mG-cap dependent translation at the 8- to 16-cell transition. ]]> https://biorxiv.org/content/10.1101/2023.03.07.531473v1?rss=1 Gahurova, L. Tomankova, J. Cerna, P. Bora, P. Kubickova, M. Virnicchi, G. Kovacicova, K. Potesil, D. Hruska, P. Zdrahal, Z. Anger, M. Susor, A. Bruce, A. W. 2023-03-07 doi:10.1101/2023.03.07.531473 Cold Spring Harbor Laboratory Press 2023-03-07 <![CDATA[ idh-1 neomorphic mutation confers sensitivity to vitamin B12 via increased dependency on one-carbon metabolism in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.03.13.584865v1?rss=1 Ponomarova, O. Starbard, A. N. Belfi, A. Anderson, A. V. Sundaram, M. V. Walhout, A. J. 2024-03-14 doi:10.1101/2024.03.13.584865 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ High-fidelity enhanced AsCas12a knock-in mice for efficient multiplexed gene editing, disease modeling and orthogonal immunogenetics ]]> https://biorxiv.org/content/10.1101/2024.03.14.585126v1?rss=1 Tang, K. Zhou, X. Fang, S.-Y. Vandenbulcke, E. Du, A. Shen, J. Cao, H. Zhou, J. Chen, K. Xin, S. Zhou, L. Lin, S. H. Majety, M. Ling, X. Lam, S. Z. Chow, R. Bai, S. Nottoli, T. Booth, C. Liu, C. Dong, M. B. Chen, S. 2024-03-16 doi:10.1101/2024.03.14.585126 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ Post-transcriptional RNA stabilization of telomere-proximal RNAs FRG2, DBET, D4Z4 at human 4q35 in response to genotoxic stress and D4Z4 macrosatellite repeat length. ]]> https://biorxiv.org/content/10.1101/2024.03.18.585486v1?rss=1 Salsi, V. Losi, F. Salani, M. Kaufman, P. D. Tupler, R. G. 2024-03-19 doi:10.1101/2024.03.18.585486 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Single-cell genomics and regulatory networks for 388 human brains ]]> https://biorxiv.org/content/10.1101/2024.03.18.585576v1?rss=1 2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized [~]250 disease-risk genes and drug targets with associated cell types. Summary Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/585576v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@70b24org.highwire.dtl.DTLVardef@6c9eddorg.highwire.dtl.DTLVardef@131fae2org.highwire.dtl.DTLVardef@4e0f1e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Emani, P. S. Liu, J. J. Clarke, D. Jensen, M. Warrell, J. Gupta, C. Meng, R. Lee, C. Y. Xu, S. Dursun, C. Lou, S. Chen, Y. Chu, Z. Galeev, T. Hwang, A. Li, Y. Ni, P. Zhou, X. PsychENCODE Consortium, Bakken, T. E. Bendl, J. Bicks, L. Chatterjee, T. Cheng, L. Cheng, Y. Dai, Y. Duan, Z. Flaherty, M. Fullard, J. F. Gancz, M. Garrido-Martin, D. Gaynor-Gillett, S. Grundman, J. Hawken, N. Henry, E. Hoffman, G. E. Huang, A. Jiang, Y. Jin, T. Jorstad, N. L. Kawaguchi, R. Khullar, S. Liu, J. Liu, J. Liu, S. Ma, S. Margolis, M. Mazariegos, S. Moore, J. M 2024-03-19 doi:10.1101/2024.03.18.585576 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Calcineurin promotes adaptation to chronic stress through two distinct mechanisms ]]> https://biorxiv.org/content/10.1101/2024.03.19.585797v1?rss=1 Flynn, M. J. Harper, N. W. Li, R. Zhu, L. J. Lee, M. J. Benanti, J. A. 2024-03-20 doi:10.1101/2024.03.19.585797 Cold Spring Harbor Laboratory Press 2024-03-20 <![CDATA[ Traumatic injury causes selective degeneration and TDP-43 mislocalization in human iPSC-derived C9orf72-associated ALS/FTD motor neurons ]]> https://biorxiv.org/content/10.1101/2024.03.21.586073v1?rss=1 Martin, E. J. Santacruz, C. Mitevska, A. Jones, I. E. Krishnan, G. Gao, F.-B. Finan, J. D. Kiskinis, E. 2024-03-26 doi:10.1101/2024.03.21.586073 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ Reprogramming of host energy metabolism mediated by the TNF-iNOS-HIF-1alpha axis plays a key role in host resistance to Plasmodium infection ]]> https://biorxiv.org/content/10.1101/2024.03.26.586751v1?rss=1 Matteucci, K. C. Assis, P. A. Hirako, I. C. Leite, N. P. S. Pioto, F. OJELABI, O. E. TOLLER-KAWAHISA, J. Costa, D. L. S. Silva, J. Alves-Filho, J. C. Gazzinelli, R. 2024-03-29 doi:10.1101/2024.03.26.586751 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Nucleic Acid Aptamers Protect Against Lead (Pb(II)) Toxicity ]]> https://biorxiv.org/content/10.1101/2024.03.28.587288v1?rss=1 Anwar, A. Ramis De Ayreflor Reyes, S. John, A. A. Breiling, E. O'Connor, A. M. Reis, S. Shim, J.-H. Shah, A. A. Srinivasan, J. Farny, N. G. 2024-03-31 doi:10.1101/2024.03.28.587288 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ The mex-3 3' untranslated region is essential for reproduction during temperature stress ]]> https://biorxiv.org/content/10.1101/2024.04.01.587367v1?rss=1 Brown, H. E. Varderesian, H. V. Keane, S. A. Ryder, S. P. 2024-04-01 doi:10.1101/2024.04.01.587367 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Combinatorial expression of neurexin genes regulates glomerular targeting by olfactory sensory neurons ]]> https://biorxiv.org/content/10.1101/2024.04.01.587570v1?rss=1 Park, S. J. Wang, I.-H. Lee, N. Jiang, H.-C. Uemura, T. Futai, K. Kim, D. Macosko, E. Greer, P. 2024-04-02 doi:10.1101/2024.04.01.587570 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses ]]> https://biorxiv.org/content/10.1101/2024.04.01.587595v1?rss=1 Matsui, A. Spangler, C. Elferich, J. Shiozaki, M. Jean, N. Zhao, X. Qin, M. Zhong, H. Yu, Z. Gouaux, E. 2024-04-01 doi:10.1101/2024.04.01.587595 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ A single cell atlas of the mouse seminal vesicle ]]> https://biorxiv.org/content/10.1101/2024.04.08.588538v1?rss=1 Sun, F. Desevin, K. Fu, Y. Parameswaran, S. Mayall, J. Rinaldi, V. Krietenstein, N. Manukyan, A. Yin, Q. Galan, C. Yang, C.-H. Shindyapina, A. Gladyshev, V. N. Garber, M. Schjenken, J. E. Rando, O. 2024-04-11 doi:10.1101/2024.04.08.588538 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Ergothioneine boosts mitochondrial respiration and exercise performance via direct activation of MPST ]]> https://biorxiv.org/content/10.1101/2024.04.10.588849v1?rss=1 Sprenger, H.-G. Mittenbuehler, M. J. Sun, Y. Van Vranken, J. G. Schindler, S. Jayaraj, A. Khetarpal, S. A. Vargas-Castillo, A. Puszynska, A. M. Spinelli, J. B. Armani, A. Kunchok, T. Ryback, B. Seo, H.-S. Song, K. Sebastian, L. O Young, C. Braithwaite, C. Dhe-Paganon, S. Burger, N. Mills, E. L. Gygi, S. P. Arthanari, H. Chouchani, E. T. Sabatini, D. M. Spiegelman, B. M. 2024-04-10 doi:10.1101/2024.04.10.588849 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Population genomics of Plasmodium ovale species in sub-Saharan Africa ]]> https://biorxiv.org/content/10.1101/2024.04.10.588912v1?rss=1 Carey-Ewend, K. Popkin-Hall, Z. R. Simkin, A. Muller, M. Hennelly, C. He, W. Moser, K. Gaither, C. Niare, K. Aghakanian, F. Feleke, S. Brhane, B. G. Phanzu, F. Mwandagalirwa, K. Aydemir, O. Sutherland, C. Ishengoma, D. S. Ali, I. M. Ngasala, B. Kalonji, A. Tshefu, A. Parr, J. Bailey, J. A. Juliano, J. J. Lin, J. T. 2024-04-13 doi:10.1101/2024.04.10.588912 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Muscle-Specific Pyruvate Kinase Isoforms, Pkm1 and Pkm2, Regulate Mammalian SWI/SNF Proteins and Histone 3 Phosphorylation During Myoblast Differentiation ]]> https://biorxiv.org/content/10.1101/2024.04.10.588959v1?rss=1 Olea-Flores, M. Sharma, T. Verdejo-Torres, O. DiBartolomeo, I. Thompson, P. R. Padilla-Benavides, T. Imbalzano, A. N. 2024-04-11 doi:10.1101/2024.04.10.588959 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ SleepInvestigatoR: A flexible R function for analyzing scored sleep in rodents ]]> https://biorxiv.org/content/10.1101/2024.04.12.588853v1?rss=1 Gamble, M. C. Williams, B. R. McKenna, J. T. Logan, R. W. 2024-04-15 doi:10.1101/2024.04.12.588853 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ T follicular helper cell profiles differ by malaria antigen and for children compared to adults ]]> https://biorxiv.org/content/10.1101/2024.04.13.589352v1?rss=1 Forconi, C. S. Nixon, C. Wu, H. W. Odwar, B. Pond-Tor, S. Ong'echa, J. M. Kurtis, J. D. Moormann, A. M. 2024-04-16 doi:10.1101/2024.04.13.589352 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Rules of engagement for condensins and cohesins guide mitotic chromosome formation ]]> https://biorxiv.org/content/10.1101/2024.04.18.590027v1?rss=1 Samejima, K. Gibcus, J. H. Abraham, S. Cisneros-Soberanis, F. Samejima, I. Beckett, A. J. Pucekova, N. Abad, M. A. Medina-Pritchard, B. Paulson, J. R. Xie, L. Jeyaprakash, A. A. Prior, I. A. Mirny, L. A. Dekker, J. Goloborodko, A. Earnshaw, W. C. 2024-04-18 doi:10.1101/2024.04.18.590027 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ BNST GluN2D-containing NMDARs contribute to ethanol intake but not negative affective behaviors in female mice ]]> https://biorxiv.org/content/10.1101/2024.04.19.590258v1?rss=1 Doyle, M. A. Salimando, G. J. Altemus, M. E. Badt, J. K. Bedenbaugh, M. N. Vardy, A. S. Adank, D. N. Park, A. S. Winder, D. G. 2024-04-21 doi:10.1101/2024.04.19.590258 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Cross species modeling reveals a role for the unfolded protein response in shaping the transcriptional reaction to Mycobacterium tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2024.04.19.590290v1?rss=1 Pullen, K. M. Finethy, R. Ko, S.-H. B. Reames, C. J. Sassetti, C. M. Lauffenburger, D. A. 2024-04-24 doi:10.1101/2024.04.19.590290 Cold Spring Harbor Laboratory Press 2024-04-24 <![CDATA[ Association of diet and inflammation with the vaginal microbiota of pregnant individuals with or without IBD ]]> https://biorxiv.org/content/10.1101/2024.04.23.590846v1?rss=1 Vargas Robles, D. Yan Rou, Y. Singha, B. Tien, J. Purandare, M. Rojas-Correa, M. Madziar, C. Picker, M. Dumont, T. Leftwich, H. Frisard, C. F. Ward, D. V. Peter, I. Olendzki, B. Maldonado-Contreras, A. 2024-04-24 doi:10.1101/2024.04.23.590846 Cold Spring Harbor Laboratory Press 2024-04-24 <![CDATA[ mRNA nuclear clustering leads to a difference in mutant huntingtin mRNA and protein silencing by siRNAs in vivo ]]> https://biorxiv.org/content/10.1101/2024.04.24.590997v1?rss=1 Allen, S. J. O'Reilly, D. Miller, R. Sapp, E. Summers, A. Paquette, J. Moreno, D. E. Bramato, B. McHugh, N. Yamada, K. Aronin, N. DiFiglia, M. Khvorova, A. 2024-04-28 doi:10.1101/2024.04.24.590997 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Cryo-EM Structure of HRSL Domain Reveals Activating Crossed Helices at the Core of GCN2 ]]> https://biorxiv.org/content/10.1101/2024.04.24.591037v1?rss=1 Solorio - Kirpichyan, K. Golovenko, D. Korostelev, A. Yan, N. Korennykh, A. 2024-04-25 doi:10.1101/2024.04.24.591037 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Protection against experimental cryptococcosis elicited by Cationic Adjuvant Formulation 01-adjuvanted subunit vaccines ]]> https://biorxiv.org/content/10.1101/2024.04.24.591045v1?rss=1 100,000 deaths annually. No licensed vaccines are available. We explored the efficacy and immune responses of subunit cryptococcal vaccines adjuvanted with Cationic Adjuvant Formulation 01 (CAF01). CAF01 promotes humoral and T helper (Th) 1 and Th17 immune responses and has been safely used in human vaccine trials. Four subcutaneous vaccines, each containing single recombinant Cryptococcus neoformans protein antigens, partially protected mice from experimental cryptococcosis. Protection increased, up to 100%, in mice that received bivalent and quadrivalent vaccine formulations. Vaccinated mice that received a pulmonary challenge with C. neoformans had an influx of leukocytes into the lung including robust numbers of polyfunctional CD4+ T cells which produced Interferon gamma (IFN{gamma}), tumor necrosis factor alpha (TNF), and interleukin (IL)-17 upon ex vivo antigenic stimulation. Cytokine-producing lung CD8+ T cells were also found, albeit in lesser numbers. A significant, durable IFN{gamma} response was observed in the lungs, spleen, and blood. Moreover, IFN{gamma} secretion following ex vivo stimulation directly correlated with fungal clearance in the lungs. Thus, we have developed multivalent cryptococcal vaccines which protect mice from experimental cryptococcosis using an adjuvant which has been safely tested in humans. These preclinical studies suggest a path towards human cryptococcal vaccine trials. Author summaryCryptococcosis is a fungal infection that poses great challenges to public health, especially in resource-limited regions with high HIV prevalence. Despite the urgent need, no licensed vaccines are currently available. In this study, we used a lethal mouse model of cryptococcosis to explore protection and immune responses elicited by vaccines consisting of recombinant cryptococcal proteins formulated with CAF01, an adjuvant that has an established safety and immunogenicity profile in human clinical vaccine trials. We discovered that while vaccines containing a single protein partially protected mouse strains, the protection was greatly augmented when the mice received vaccines formulated with multiple antigens. The lungs of vaccinated and infected mice had a robust influx of CD4+ T cells, many of which made the cytokines IFN{gamma} and IL-17 when stimulated ex vivo. Moreover, we found the production of IFN{gamma} directly correlated with clearance of fungi from the lungs. Cytotoxic CD8+ T cell responses were also observed, albeit in lesser numbers. Our promising findings from this preclinical research paves the way for future human cryptococcal vaccine trials. ]]> Wang, R. Oliveira, L. V. N. Hester, M. M. Carlson, D. M. Christensen, D. Specht, C. A. Levitz, S. M. 2024-04-28 doi:10.1101/2024.04.24.591045 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.04.28.591397v1?rss=1 Sprague, D. Y. Rusch, K. Dunn, R. L. Borchardt, J. Bubnis, G. Chiu, G. Wen, C. Suzuki, R. Chaudhary, S. Dichter, B. Ly, R. Onami, S. Lu, H. Kimura, K. Yemini, E. I. Kato, S. 2024-04-30 doi:10.1101/2024.04.28.591397 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Structure of a human monoclonal antibody in complex with Outer surface protein C (OspC) of the Lyme disease spirochete, Borreliella burgdorferi ]]> https://biorxiv.org/content/10.1101/2024.04.29.591597v1?rss=1 Rudolph, M. Chen, Y. Vorauer, C. Vance, D. Piazza, C. L. Willsey, G. G. McCarthy, K. Muriuki, B. Cavacini, L. Guttman, M. Mantis, N. J. 2024-04-30 doi:10.1101/2024.04.29.591597 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ VGLL2 and TEAD1 fusion proteins drive YAP/TAZ-independent transcription and tumorigenesis by engaging p300 ]]> https://biorxiv.org/content/10.1101/2024.05.01.592016v1?rss=1 Guo, S. Hu, X. Cotton, J. L. Ma, L. Li, Q. Cui, J. Wang, Y. Thakare, R. P. Tao, Z. Ip, T. Wu, X. Wang, J. Mao, J. 2024-05-03 doi:10.1101/2024.05.01.592016 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Incorporation of Epstein-Barr viral variation implicates significance of LMP1 in survival prediction and prognostic subgrouping in Burkitt lymphoma ]]> https://biorxiv.org/content/10.1101/2024.05.03.592343v1?rss=1 Kim, I. E. Oduor, C. Stamp, J. Luftig, M. A. Moormann, A. M. Crawford, L. Bailey, J. 2024-05-06 doi:10.1101/2024.05.03.592343 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Genome-wide screen of Mycobacterium tuberculosis-infected macrophages identified the GID/CTLH complex as a determinant of intracellular bacterial growth. ]]> https://biorxiv.org/content/10.1101/2024.05.06.592714v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@1fc273aorg.highwire.dtl.DTLVardef@173927borg.highwire.dtl.DTLVardef@95cb02org.highwire.dtl.DTLVardef@42fcea_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Simwela, N. V. Johnston, L. Pavinski Bitar, P. Jaecklein, E. Altier, C. Sassetti, C. M. Russell, D. G. 2024-05-08 doi:10.1101/2024.05.06.592714 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Standardized Nomenclature and Reporting for PacBio HiFi Sequencing and Analysis of rAAV Gene Therapy Vectors ]]> https://biorxiv.org/content/10.1101/2024.05.07.592296v1?rss=1 Talevich, E. Tseng, E. Diallo, A. Sellami, N. Elliott, A. Cantarel, B. L. Tonthat, N. Chatterjee, P. Tai, P. W. L. Aldridge, C. 2024-05-12 doi:10.1101/2024.05.07.592296 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Peripheral opioid tolerance involves skin keratinocytes and platelet-derived growth factor type B signaling ]]> https://biorxiv.org/content/10.1101/2024.05.14.594040v1?rss=1 Posa, L. Miracle, S. A. MacDonald, A. K. Gamble, M. Albers, K. M. Freyberg, Z. Logan, R. Puig, S. 2024-05-14 doi:10.1101/2024.05.14.594040 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ PIEZO acts in an intestinal valve to regulate swallowing in C. elegans ]]> https://biorxiv.org/content/10.1101/2024.05.14.594054v1?rss=1 Park, Y.-J. Yeon, J. Cho, J. Kim, D.-Y. Bai, X. Oh, Y. Kim, J. Nam, H. Hwang, H. Heo, W. Kim, J. Jun, S. Lee, K. Kang, K. Kim, K. 2024-05-14 doi:10.1101/2024.05.14.594054 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Dual-Action Kinase Inhibitors Control p38α MAP Kinase Threonine Dephosphorylation ]]> https://biorxiv.org/content/10.1101/2024.05.15.594272v1?rss=1 Stadnicki, E. Ludewig, H. Kumar, R. P. Wang, X. Qiao, Y. Kern, D. Bradshaw, N. 2024-05-15 doi:10.1101/2024.05.15.594272 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ High-throughput screening of more than 30,000 compounds for anthelmintics against gastrointestinal nematode parasites ]]> https://biorxiv.org/content/10.1101/2024.05.16.594481v1?rss=1 Elfawal, M. A. Goetz, E. Kim, Y. Savinov, S. N. Barasa, L. Thompson, P. R. Aroian, R. V. 2024-05-18 doi:10.1101/2024.05.16.594481 Cold Spring Harbor Laboratory Press 2024-05-18 <![CDATA[ RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability ]]> https://biorxiv.org/content/10.1101/2024.05.16.594552v1?rss=1 Provasek, V. Bacolla, A. Rangaswamy, S. Mitra, J. Kodavati, M. Yusuf, I. Malojirao, V. Vasquez, V. Britz, G. W. Li, G.-M. Xu, Z. Mitra, S. Garruto, R. M. Tainer, J. Hegde, M. 2024-05-17 doi:10.1101/2024.05.16.594552 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Distinct components of nucleoside-modified messenger RNA vaccines cooperate to instruct efficient germinal center responses ]]> https://biorxiv.org/content/10.1101/2024.05.17.594726v1?rss=1 Bettini, E. Chudnovskiy, A. Protti, G. Nakadakari-Higa, S. Ceglia, S. Castano, D. Chiu, J. Muramatsu, H. Mdluli, T. Abraham, E. Lipinszki, Z. Maillard, I. Tam, Y. Reboldi, A. Pardi, N. Spreafico, R. Victora, G. D. Locci, M. 2024-05-17 doi:10.1101/2024.05.17.594726 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ A novel mouse home cage lickometer system reveals sex- and housing-based influences on alcohol drinking ]]> https://biorxiv.org/content/10.1101/2024.05.22.595186v1?rss=1 Petersen, N. Adank, D. N. Quan, Y. Edwards, C. M. Taylor, A. Winder, D. Doyle, M. A. 2024-05-23 doi:10.1101/2024.05.22.595186 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Senescent-like microglia limit remyelination through the senescence associated secretory phenotype ]]> https://biorxiv.org/content/10.1101/2024.05.23.595605v1?rss=1 Gross, P. S. Laforet, V. D. Manavi, Z. Zia, S. Lee, S. H. Shults, N. V. Selva, S. Alvarez, E. Plemel, J. R. Schafer, D. P. Huang, J. K. 2024-05-26 doi:10.1101/2024.05.23.595605 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Oxygen Sensor-Guided Fine Needle Biopsy Studies of Human Cancer Xenografts in Mice ]]> https://biorxiv.org/content/10.1101/2024.05.27.596060v1?rss=1 McDonald, R. C. Fischer, A. H. Rusckowski, M. 2024-06-01 doi:10.1101/2024.05.27.596060 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ A glial circadian gene expression atlas reveals cell type and disease-specific reprogramming in response to amyloid pathology or aging. ]]> https://biorxiv.org/content/10.1101/2024.05.28.596297v1?rss=1 Sheehan, P. W. Fass, S. B. Sapkota, D. Kang, S. Hollis, H. C. Lawrence, J. H. Anafi, R. C. Dougherty, J. D. Fryer, J. D. Musiek, E. S. 2024-06-01 doi:10.1101/2024.05.28.596297 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Marigold: A machine learning-based web app for zebrafish pose tracking ]]> https://biorxiv.org/content/10.1101/2024.05.31.596910v1?rss=1 Teicher, G. Riffe, R. M. Barnaby, W. Martin, G. Clayton, B. E. Trapani, J. G. Downes, G. B. 2024-06-01 doi:10.1101/2024.05.31.596910 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Aging disrupts the coordination between mRNA and protein expression in mouse and human midbrain ]]> https://biorxiv.org/content/10.1101/2024.06.01.596950v1?rss=1 Buck, S. A. Mabry, S. J. Glausier, J. R. Banks-Tibbs, T. Ward, C. Gayden Kozel, J. Fu, C. Fish, K. N. Lewis, D. A. Logan, R. W. Freyberg, Z. 2024-06-01 doi:10.1101/2024.06.01.596950 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ Preventing acute neurotoxicity of CNS therapeutic oligonucleotides with the addition of Ca2+ and Mg2+ in the formulation ]]> https://biorxiv.org/content/10.1101/2024.06.06.597639v1?rss=1 Miller, R. Paquette, J. Barker, A. Sapp, E. McHugh, N. Bramato, B. Yamada, N. Alterman, J. Echeveria, D. Yamada, K. Watts, J. K. Anaclet, C. DiFiglia, M. Khvorova, A. Aronin, N. 2024-06-08 doi:10.1101/2024.06.06.597639 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Ribosome-Associated Vesicles promote activity-dependent local translation ]]> https://biorxiv.org/content/10.1101/2024.06.07.598007v1?rss=1 Martin-Solana, E. Carter, S. D. Donahue, E. K. Ning, J. Glausier, J. R. Preisegger, M. A. Eisenman, L. Joseph, P. N. Bouchet-Marquis, C. Wu, K. Mobini, C. L. Frantz, A. N. Puig, S. Hampton, C. M. Kabbani, N. Jensen, G. J. Watkins, S. C. Deisseroth, K. Fenno, L. E. Gold, M. S. Wills, Z. P. Burkewitz, K. Das, S. Freyberg, Z. 2024-06-08 doi:10.1101/2024.06.07.598007 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Monocytes Mobilized by Gut Neurons Remodel the Enteric Nervous System ]]> https://biorxiv.org/content/10.1101/2024.06.09.598124v1?rss=1 Kurapati, S. Shin, C. Szabo, K. Liu, Y. Ashraf, A. Koscso, B. Dash, C. Navarro, L. Saha, M. Nagaraj, S. Wang, W. Zhu, J. Shulzhenko, N. Baer, C. Srinivasan, S. Kulkarni, S. Pasricha, P. Peters, L. Bogunovic, M. 2024-06-10 doi:10.1101/2024.06.09.598124 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Immunological correlates of protection mediated by a whole organism Cryptococcus neoformans vaccine deficient in chitosan ]]> https://biorxiv.org/content/10.1101/2024.06.12.598760v1?rss=1 100,000 deaths annually, mostly in persons with impaired CD4+ T cell function such as AIDS. There are no approved human vaccines. We previously created a genetically engineered avirulent strain of C. neoformans, designated cda1{Delta}2{Delta}3{Delta}. When used as a vaccine, cda1{Delta}2{Delta}3{Delta} protects mice against a subsequent challenge with a virulent C. neoformans strain. Here, we defined components of the immune system responsible for vaccine-mediated protection. We found that while B cells and CD8+ T cells were dispensible, protection was lost in mice genetically deficient in CD4+ T cells, and the cytokines IFN{gamma}, TNF, or IL-23. A robust influx of cytokine-producing CD4+ T cells was seen in the lungs of vaccinated mice following infection. Importantly, protection was retained in mice depleted of CD4+ T cells following vaccination, suggesting a strategy to protect persons who are at risk for future CD4+ T cell dysfunction. ]]> Specht, C. Wang, R. Oliveira, L. V. N. Hester, M. M. Gomez, C. L. Mou, Z. Carlson, D. Lee, C. K. Hole, C. R. Lam, W. C. Upadhya, R. Lodge, J. Levitz, S. M. 2024-06-14 doi:10.1101/2024.06.12.598760 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Cyclophilin A Facilitates HIV-1 DNA Integration ]]> https://biorxiv.org/content/10.1101/2024.06.15.599180v1?rss=1 Padron, A. Dwivedi, R. Chakraborty, R. Prakash, P. Kim, K. Shi, J. Ahn, J. Pandhare, J. Luban, J. Aiken, C. Balasubramaniam, M. Dash, C. 2024-06-17 doi:10.1101/2024.06.15.599180 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Colibactin-induced damage in bacteria is cell contact independent ]]> https://biorxiv.org/content/10.1101/2024.06.21.600066v1?rss=1 Lowry, E. Mitchell, A. 2024-06-21 doi:10.1101/2024.06.21.600066 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ A novel family of lncRNAs relate facioscapulohumeral muscular dystrophy to nucleolar architecture and protein synthesis rate ]]> https://biorxiv.org/content/10.1101/2024.06.29.600824v1?rss=1 Salsi, V. Losi, F. Fosso, B. Ferrarini, M. Pini, S. Manfredi, M. Vattemi, G. N. A. Mongini, T. E. Maggi, L. Pesole, G. D. Henras, A. Kaufman, P. D. McStay, B. Tupler, R. G. 2024-06-29 doi:10.1101/2024.06.29.600824 Cold Spring Harbor Laboratory Press 2024-06-29 <![CDATA[ Crk mediates Csk-Hippo signaling independently of Yap tyrosine phosphorylation to induce cell extrusion ]]> https://biorxiv.org/content/10.1101/2024.06.27.601065v1?rss=1 Hannan, A. Wang, Q. Wu, Y. Makrides, N. Qu, X. Mao, J. Que, J. Cardoso, W. V. Zhang, X. 2024-07-01 doi:10.1101/2024.06.27.601065 Cold Spring Harbor Laboratory Press 2024-07-01 <![CDATA[ A broad cathepsin inhibitor blocks crystal-stimulated inflammasome-dependent and -independent inflammation, and gout arthritis ]]> https://biorxiv.org/content/10.1101/2024.07.01.601464v1?rss=1 Orellano, L. A. A. Zeng, C. Zhu, J. Bogyo, M. Rock, K. LAI, J.-J. 2024-07-03 doi:10.1101/2024.07.01.601464 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Uridine Phosphorylase-1 supports metastasis of mammary cancer by altering immune and extracellular matrix landscapes of the lung ]]> https://biorxiv.org/content/10.1101/2024.07.02.601676v1?rss=1 Whyte, D. Vande Voorde, J. Sumpton, D. Dhayade, S. Dornier, E. Moore, M. Novo, D. Peters, J. Wiesheu, R. Mackey, J. B. McFarlane, A. J. Fercoq, F. Fisher, S. Dehesa Caballero, C. Gilroy, K. Redmond, K. L. Mitchell, L. E. Anderson, E. Thomson, G. Dzierozynski, L. N. Apiz Saab, J. J. Lewis, C. A. Muir, A. Halbrook, C. J. Strathdee, D. Jackstadt, R. Nixon, C. Dunne, P. Steele, C. W. Carlin, L. M. Macpherson, I. R. Roberts, E. W. Coffelt, S. B. Blyth, K. Sansom, O. J. Norman, J. C. Clarke, C. J. 2024-07-04 doi:10.1101/2024.07.02.601676 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ Sleep and circadian rhythm activity alterations during adolescence in a mouse model of neonatal fentanyl withdrawal syndrome ]]> https://biorxiv.org/content/10.1101/2024.07.05.602239v1?rss=1 Williams, B. Gamble, M. C. Singh, N. Bryant, C. D. Logan, B. A. Logan, R. W. 2024-07-09 doi:10.1101/2024.07.05.602239 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ Unbiased multiplex antigen screening of Cerebrospinal Fluid detects microbial and autoantigenic epitopes associated with Multiple Sclerosis ]]> https://biorxiv.org/content/10.1101/2024.07.05.602301v1?rss=1 Barton, N. J. Tran, K. Olson, M. N. Deshpande, M. Radu, I. Francis, N. Kurban, M. Orszulak, A. R. Chigas, S. M. Sundstrom, J. Dawes, P. Murray, L. F. Ionete, C. Lim, E. T. Hemond, C. C. Chan, Y. 2024-07-09 doi:10.1101/2024.07.05.602301 Cold Spring Harbor Laboratory Press 2024-07-09 <![CDATA[ IFNγ initiates TLR9-dependent autoimmune hepatitis in DNase II deficient mice ]]> https://biorxiv.org/content/10.1101/2024.07.10.602775v1?rss=1 Hao, K. Gao, K. M. Strauss, M. Subramanian, S. Marshak-Rothstein, A. 2024-07-16 doi:10.1101/2024.07.10.602775 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Impaired fatty acid import or catabolism in macrophages restricts intracellular growth of Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2024.07.22.604660v1?rss=1 Simwela, N. V. Jaecklein, E. Sassetti, C. M. Russell, D. G. M. 2024-07-23 doi:10.1101/2024.07.22.604660 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Impact of preanalytical factors on liquid biopsy in the canine cancer model ]]> https://biorxiv.org/content/10.1101/2024.07.29.605605v1?rss=1 Megquier, K. Husted, C. Rhoades, J. White, M. E. Genereux, D. P. Chen, F. L. Xiong, K. Kwon, E. Swofford, R. Painter, C. Adalsteinsson, V. London, C. A. Gardner, H. L. Karlsson, E. K. 2024-07-30 doi:10.1101/2024.07.29.605605 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Investigation of cell mechanics and migration on DDR2-expressing neuroblastoma cell line ]]> https://biorxiv.org/content/10.1101/2024.08.15.607761v1?rss=1 Vessella, T. Rozen, E. J. Shohet, J. Wen, Q. Zhou, H. S. 2024-08-16 doi:10.1101/2024.08.15.607761 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ Removal of developmentally regulated microexons has a minimal impact on larval zebrafish brain morphology and function ]]> https://biorxiv.org/content/10.1101/2024.08.19.608697v1?rss=1 Calhoun, C. C. S. Capps, M. E. S. Muya, K. Gannaway, W. C. Martina, V. Conklin, C. L. Klein, M. C. Webster, J. Torija-Olson, E. G. Thyme, S. 2024-08-20 doi:10.1101/2024.08.19.608697 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Conformational dynamics of the HIV-1 envelope glycoprotein from CRF01_AE is associated with susceptibility to antibody-dependent cellular cytotoxicity ]]> https://biorxiv.org/content/10.1101/2024.08.22.609179v1?rss=1 Diaz-Salinas, M. Chatterjee, D. Nayrac, M. Medjahed, H. Prevost, J. Pazgier, M. Finzi, A. Munro, J. 2024-08-22 doi:10.1101/2024.08.22.609179 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Inpp5e is a Critical Regulator of Protein Transport to Photoreceptor Outer Segments ]]> https://biorxiv.org/content/10.1101/2024.08.27.609873v1?rss=1 Gupta, M. Lewis, T. R. Stuck, M. W. Spencer, W. J. Klementieva, N. V. Arshavsky, V. Y. Pazour, G. J. 2024-08-28 doi:10.1101/2024.08.27.609873 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Structural and systems characterization of phosphorylation on metabolic enzymes identifies sex-specific metabolic reprogramming in obesity ]]> https://biorxiv.org/content/10.1101/2024.08.28.609894v1?rss=1 Tamir, T. Y. Chaudhary, S. Li, A. X. Trojan, S. E. Flower, C. T. Vo, P. Cui, Y. Davis, J. C. Mukkamala, R. S. Venditti, F. N. Hillis, A. L. Toker, A. Vander Heiden, M. G. Spinelli, J. B. Kennedy, N. J. Davis, R. J. White, F. M. 2024-08-29 doi:10.1101/2024.08.28.609894 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ The Initiator Caspase Dronc Drives Compensatory Proliferation of Apoptosis-Resistant Cells During Epithelial Tissue Regeneration After Ionizing Radiation ]]> https://biorxiv.org/content/10.1101/2024.09.01.610661v1?rss=1 JNK signaling pathway in DARE cells directly regulates their proliferation, which in turn influences NARE cell proliferation. Consequently, we show that maintaining proliferative homeostasis between DARE and NARE cells is vital for balanced tissue regeneration. Given the widespread use of ionizing irradiation in cancer treatment and prevention, our findings have potential implications for understanding treatment-resistant cells and cancer recurrence. ]]> Braun, T. Afgin, N. Sapozhnikov, L. Sivan, E. Bergmann, A. Baena-Lopez, L. A. Yacobi-Sharon, K. Arama, E. 2024-09-02 doi:10.1101/2024.09.01.610661 Cold Spring Harbor Laboratory Press 2024-09-02 <![CDATA[ Chemical genetic interactions elucidate pathways controlling tuberculosis antibiotic efficacy during infection ]]> https://biorxiv.org/content/10.1101/2024.09.04.609063v1?rss=1 Oluoch, P. O. Koh, E.-I. Proulx, M. K. Reames, C. J. Papavinasasundaram, K. Murphy, K. C. Zimmerman, M. Dartois, V. A. Sassetti, C. M. 2024-09-04 doi:10.1101/2024.09.04.609063 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Two functional forms of the Meckel-Gruber syndrome protein TMEM67 generated by proteolytic cleavage by ADAMTS9 mediate Wnt signaling and ciliogenesis ]]> https://biorxiv.org/content/10.1101/2024.09.04.611229v1?rss=1 Ahmed, M. Fischer, S. Robert, K. L. Lange, K. I. Stuck, M. W. Best, S. Johnson, C. A. Pazour, G. J. Blacque, O. E. Nandadasa, S. 2024-09-05 doi:10.1101/2024.09.04.611229 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Next generation APOBEC3 inhibitors: Optimally designed for potency and nuclease stability ]]> https://biorxiv.org/content/10.1101/2024.09.05.611238v1?rss=1 Hedger, A. K. Myint, W. Lee, J. M. Suchenski-Loustaunau, D. Balachandran, V. Shaqra, A. M. Kurt Yilmaz, N. Watts, J. Matsuo, H. Schiffer, C. A. 2024-09-06 doi:10.1101/2024.09.05.611238 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Disrupted development of sensory systems and the cerebellum in a zebrafish ebf3a mutant ]]> https://biorxiv.org/content/10.1101/2024.09.10.612287v1?rss=1 Dang, N. D. P. Conklin, C. L. Truong, T. Q. Vivian, M. D. Wang, J. Thomas, H. R. Parant, J. M. Yeo, N. C. Thyme, S. 2024-09-11 doi:10.1101/2024.09.10.612287 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm ]]> https://biorxiv.org/content/10.1101/2024.09.16.613305v1?rss=1 Schooley, A. Venev, S. V. Aksenova, V. Navarrete, E. Dasso, M. Dekker, J. 2024-09-16 doi:10.1101/2024.09.16.613305 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ An integrated view of the structure and function of the human 4D nucleome ]]> https://biorxiv.org/content/10.1101/2024.09.17.613111v1?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, 2024-09-19 doi:10.1101/2024.09.17.613111 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Dynamic phosphorylation of Hcm1 promotes fitness in chronic stress ]]> https://biorxiv.org/content/10.1101/2024.09.18.613713v1?rss=1 Conti, M. M. Bail, J. P. Li, R. Zhu, L. J. Benanti, J. A. 2024-09-19 doi:10.1101/2024.09.18.613713 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ A unique interplay of access and selection shapes peritoneal metastasis evolution in colorectal cancer ]]> https://biorxiv.org/content/10.1101/2024.09.25.614736v1?rss=1 Wassenaar, E. C. Gorelick, A. N. Hung, W.-T. Cheek, D. M. Kucukkose, E. Lee, I.-H. Blohmer, M. Degner, S. Giunta, P. Wiezer, R. M. Raicu, M. G. Ubink, I. Klaasen, S. J. Lansu, N. Watson, E. V. Corcoran, R. B. Boland, G. Getz, G. Kops, G. J. Juric, D. Lennerz, J. K. Boerma, D. Kranenburg, O. Naxerova, K. 2024-09-27 doi:10.1101/2024.09.25.614736 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Early zygotic engineering promotes targeted large transgene integration and direct production of fully transgenic animals ]]> https://biorxiv.org/content/10.1101/2024.09.29.615605v1?rss=1 Gupta, K. Xu, P. Gallant, J. Yoon, Y. Rivera-Perez, J. A. Lawrence, J. B. 2024-10-01 doi:10.1101/2024.09.29.615605 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ An aneuploidy epistasis map reveals metabolic vulnerabilities associated with supernumerary chromosomes in cancer ]]> https://biorxiv.org/content/10.1101/2024.09.30.615609v1?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. 2024-10-01 doi:10.1101/2024.09.30.615609 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Transcriptome-based identification of long noncoding RNAs (lncRNAs) across the genome of Anopheles gambiae ]]> https://biorxiv.org/content/10.1101/2024.10.02.616138v1?rss=1 Xu, J. Hu, K. Riehle, M. M. Khadka, V. 2024-10-02 doi:10.1101/2024.10.02.616138 Cold Spring Harbor Laboratory Press 2024-10-02 <![CDATA[ Real-Time Spatiotemporal Tracking of Infectious Outbreaks in Confined Environments with a Host-Pathogen Agent-Based System ]]> https://biorxiv.org/content/10.1101/2024.10.01.616085v1?rss=1 Srinivasan, S. King, J. Colubri, A. Korkin, D. 2024-10-03 doi:10.1101/2024.10.01.616085 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM ]]> https://biorxiv.org/content/10.1101/2024.10.01.616095v1?rss=1 Zhang, K. Cossio, P. Rangan, A. V. Lucas, B. A. Grigorieff, N. 2024-10-03 doi:10.1101/2024.10.01.616095 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Potent and durable gene modulation in heart and muscle with chemically defined siRNAs ]]> https://biorxiv.org/content/10.1101/2024.10.01.616183v1?rss=1 95% reduction of circulating MSTN for half a year, with no observed systemic or target-related toxicity. MSTN inhibition resulted in muscle growth and increased lean muscle mass, correlating with improved grip strength. Interestingly, the functional impact on muscle growth and strength significantly outlasts the target silencing, suggesting extended pharmacological effects. Systemic administration was equally efficacious in all muscle groups tested, including skeletal muscle, heart, tongue and diaphragm. The informational nature of the muscle-active chemically defined siRNA scaffold was confirmed by demonstrating muscle and heart efficacy with three additional targets. Our findings pave the way for potent and long-lasting gene modulation in muscle using chemically defined, lipophilic siRNAs, offering a new avenue for treating muscular diseases. ]]> Fakih, H. H. Lochmann, C. Gagnon, R. Summers, A. Caiazzi, J. Buchwald, J. E. Tang, Q. Maru, B. Hildebrand, S. R. Zain UI Abideen, M. Furgal, R. C. Gross, K. Y. Yang, Y.-S. Cooper, D. Monopoli, k. Echeverria, D. Shim, J.-h. Yamada, K. Alterman, J. F. Khvorova, A. 2024-10-03 doi:10.1101/2024.10.01.616183 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Lung CD4+ resident memory T cells use airway secretory cells to stimulate and regulate neutrophilic allergic airways disease. ]]> https://biorxiv.org/content/10.1101/2024.10.03.616494v1?rss=1 Ravi, V. R. Korkmaz, F. T. Lyon De Ana, C. Lu, L. Shao, F.-Z. Odom, C. V. Barker, K. A. Ramanujan, A. Niszczak, E. N. Goltry, W. N. Martin, I. M. C. Ha, C. T. Quinton, L. J. Jones, M. R. Fine, A. Welch, J. D. Chen, F. Belkina, A. C. Mizgerd, J. P. Shenoy, A. T. 2024-10-04 doi:10.1101/2024.10.03.616494 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Antisense oligonucleotide targeting pathogenic sense repeat RNA in C9ORF72 suppresses production of antisense-dependent dipeptide repeat proteins implicated in ALS/FTD ]]> https://biorxiv.org/content/10.1101/2024.10.04.616663v1?rss=1 Gu, Y. Kankel, M. W. Watts, J. Jafar-nejad, P. Almeida, S. 2024-10-05 doi:10.1101/2024.10.04.616663 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ Antibody-Fab and -Fc features promote Mycobacterium tuberculosis restriction. ]]> https://biorxiv.org/content/10.1101/2024.10.07.617070v1?rss=1 Grace, P. S. Peters, J. M. Sixsmith, J. Lu, R. Fenderson, B. A. Vickers, A. Slein, M. D. Irvine, E. B. McKitrick, T. Wei, M.-H. Cummings, R. D. Wallace, A. Cavacini, L. Choudhary, A. K. Proulx, M. K. Sundling, C. Källenius, G. Reljic, R. Ernst, J. D. Casadevall, A. Locht, C. Pinter, A. Sassetti, C. M. Bryson, B. D. Fortune, S. M. Alter, G. 2024-10-11 doi:10.1101/2024.10.07.617070 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ The EZH2 inhibitor tazemetostat mitigates HIV immune evasion, reduces reservoir formation, and promotes durable CD8+ T-cell revitalization ]]> https://biorxiv.org/content/10.1101/2024.10.11.617869v1?rss=1 Gramatica, A. Miller, I. G. Ward, A. R. Khan, F. Kemmer, T. J. Weiler, J. Huynh, T. T. Zumbo, P. Kurland, A. P. Leyre, L. Ren, Y. Klevorn, T. Copertino, D. C. Chukwukere, U. Levinger, C. Dilling, T. R. Linden, N. L. Board, N. L. Falling Iversen, E. Terry, S. Mota, T. M. Bedir, S. Clayton, K. L. Bosque, A. MacLaren Ehui, L. Kovacs, C. M. Betel, D. Johnson, J. R. Paiardini, M. Danesh, A. Jones, R. B. 2024-10-15 doi:10.1101/2024.10.11.617869 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Comet fragment-ion indexing for enhanced peptide sequencing ]]> https://biorxiv.org/content/10.1101/2024.10.11.617953v1?rss=1 McGann, C. D. Bergstrom, E. J. Sharma, V. Heil, L. R. Yu, Q. Eng, J. K. Schweppe, D. K. 2024-10-15 doi:10.1101/2024.10.11.617953 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2024.10.15.618557v1?rss=1 Huang, Q. Y. Kim, R. Song, K. Grigorieff, N. Munro, J. Schiffer, C. A. Somasundaran, M. 2024-10-18 doi:10.1101/2024.10.15.618557 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Rational Design of Enhanced Nme2Cas9 and Nme2SmuCas9 Nucleases and Base Editors ]]> https://biorxiv.org/content/10.1101/2024.10.30.620986v1?rss=1 Bamidele, N. Andosoria, A. Chen, Z. Cheng, H. Panwala, R. Jazbec, E. Sontheimer, E. J. 2024-10-30 doi:10.1101/2024.10.30.620986 Cold Spring Harbor Laboratory Press 2024-10-30 <![CDATA[ Molecular basis for the increased membrane fusion activity of the Ebola virus glycoprotein A82V variant from the 2013-2016 epidemic: insights from simulations and experiments ]]> https://biorxiv.org/content/10.1101/2024.10.28.620686v1?rss=1 Durham, N. D. Jain, A. Howard, A. Luban, J. Munro, J. 2024-10-31 doi:10.1101/2024.10.28.620686 Cold Spring Harbor Laboratory Press 2024-10-31 <![CDATA[ A quantitative intracellular peptide binding assay reveals recognition determinants and context dependence of short linear motifs ]]> https://biorxiv.org/content/10.1101/2024.10.30.621084v1?rss=1 Subbanna, M. S. Winters, M. J. Örd, M. Davey, N. E. Pryciak, P. M. 2024-11-01 doi:10.1101/2024.10.30.621084 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ Mouse Pachytene piRNAs Cleave Hundreds of Transcripts,But Alter the Steady-State Abundance of Only a Minority of Targets ]]> https://biorxiv.org/content/10.1101/2024.11.02.621675v1?rss=1 Cecchini, K. Ajaykumar, N. Bagci, A. Zamore, P. Gainetdinov, I. 2024-11-03 doi:10.1101/2024.11.02.621675 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Suppression of Huntington's Disease Somatic Instability by Transcriptional Repression and Direct CAG Repeat Binding ]]> https://biorxiv.org/content/10.1101/2024.11.04.619693v1?rss=1 Mathews, E. W. Coffey, S. R. Gaertner, A. Belgrad, J. Bragg, R. M. O'Reilly, D. Cantle, J. P. McHugh, C. Summers, A. Fentz, J. Schwagarus, T. Cornelius, A. Lingos, I. Burch, Z. Kovalenko, M. Andrew, M. A. Bennett, C. F. Kordasiewicz, H. Marchionini, D. M. Wilkinson, H. Vogt, T. F. Pinto, R. M. Khvorova, A. Howland, D. Wheeler, V. Carroll, J. B. 2024-11-04 doi:10.1101/2024.11.04.619693 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ Cocaine, via ΔFosB, remodels gene expression and excitability in ventral hippocampus ]]> https://biorxiv.org/content/10.1101/2024.11.06.621895v1?rss=1 Eagle, A. L. Doyle, M. A. Sugimoto, C. Dykstra, M. M. Kuhn, H. M. Murray, B. R. Bastle, R. M. He, J. Maze, I. Mazei-Robison, M. Robison, A. J. 2024-11-07 doi:10.1101/2024.11.06.621895 Cold Spring Harbor Laboratory Press 2024-11-07 <![CDATA[ A type-specific B cell epitope at the apex of Outer surface protein C (OspC) of the Lyme disease spirochete, Borreliella burgdorferi ]]> https://biorxiv.org/content/10.1101/2024.11.06.622094v1?rss=1 Vance, D. Freeman-Gallant, G. McCarthy, K. Piazza, C. L. Chen, Y. Vorauer, C. Muriuki, B. Rudolph, M. J. Cavacini, L. Guttman, M. MANTIS, N. J. 2024-11-08 doi:10.1101/2024.11.06.622094 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ A consensus variant-to-function score to functionally prioritize variants for disease ]]> https://biorxiv.org/content/10.1101/2024.11.07.622307v1?rss=1 0.95) variants than non-functionally informed fine-mapping. We further constructed tissue/cell line-specific cV2F scores that prioritize variants based on regulatory potential in specific tissues/cell lines, attaining high heritability enrichment for tissue-related diseases/traits (15.6x, s.e. 2.3) while providing independent information (average correlation of 0.27 with the primary cV2F score). We highlight examples of GWAS loci for which cV2F pinpoints causal variants with high confidence and elucidates their functional role. ]]> Fabiha, T. Raine, I. Kundu, S. Pampari, A. Abramov, S. Boytsov, A. Strouse, K. Dura, K. Fang, W. Kerner, G. Butts, J. Ali, T. Gschwind, A. Mualim, K. S. Moore, J. E. Weng, Z. Ulirsch, J. Ji, H. E. Vierstra, J. Reddy, T. E. Montgomery, S. B. Engreitz, J. Kundaje, A. Tewhey, R. Price, A. Dey, K. 2024-11-09 doi:10.1101/2024.11.07.622307 Cold Spring Harbor Laboratory Press 2024-11-09 <![CDATA[ Regulation of Fentanyl Reward in Male and Female Mice by the Circadian Transcription Factor NPAS2 ]]> https://biorxiv.org/content/10.1101/2024.11.12.623242v1?rss=1 Barko, K. Shelton, M. A. DePoy, L. M. Gayden, J. Kim, S.-M. Puig, S. Xue, X. Oliver-Smith, J. Zhu, X. Parekh, P. K. Tseng, G. C. Williams, B. Freyberg, Z. Logan, R. W. 2024-11-17 doi:10.1101/2024.11.12.623242 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Dynamic cytoplasmic fluidity during morphogenesis in a human fungal pathogen ]]> https://biorxiv.org/content/10.1101/2024.11.16.623909v1?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. 2024-11-17 doi:10.1101/2024.11.16.623909 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Comamonas aquatica inhibits TIR-1/SARM1 induced axon degeneration ]]> https://biorxiv.org/content/10.1101/2024.11.20.622298v1?rss=1 O'Connor, L. C. Kang, W. K. Vo, P. Spinelli, J. B. Alkema, M. J. Byrne, A. B. 2024-11-21 doi:10.1101/2024.11.20.622298 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Buprenorphine Induces Human Fetal Membrane Sterile Inflammation ]]> https://biorxiv.org/content/10.1101/2024.11.22.624850v1?rss=1 Lynn, T. Kelleher, M. E. Georges, H. M. McCauley, E. M. Logan, R. Yonkers, K. A. Abrahams, V. M. 2024-11-22 doi:10.1101/2024.11.22.624850 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Sex-specific DNA methylation differences in Amyotrophic lateral sclerosis ]]> https://biorxiv.org/content/10.1101/2024.11.22.624866v1?rss=1 Grant, O. Iacoangeli, A. Zwamborn, R. van Rheenen, W. Byrne, R. P. van Eijk, K. R. Kenna, K. Van Vugt, J. Cooper-Knock, J. Kenna, B. Vural, A. Topp, S. Smith, B. Dobson, R. van Es, M. Gotkine, M. Corcia, P. de Carvalho, M. Panades, M. Mora, J. Mill, J. Garton, F. McRae, A. Wray, N. Shaw, P. Landers, J. Glass, J. Shaw, C. Basak, N. Hardiman, O. Van Damme, P. McLaughlin, R. van den Berg, L. Veldink, J. Al Chalabi, A. Al Kheifat, A. 2024-11-25 doi:10.1101/2024.11.22.624866 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes ]]> https://biorxiv.org/content/10.1101/2024.11.26.625483v1?rss=1 Peterman, E. L. Ploessl, D. S. Love, K. S. Sanabria, V. Daniels, R. F. Johnstone, C. P. Godavarti, D. R. Kabaria, S. R. Pai, A. A. Galloway, K. E. 2024-11-26 doi:10.1101/2024.11.26.625483 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Raver1 links Ripk1 RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance ]]> https://biorxiv.org/content/10.1101/2024.11.27.625707v1?rss=1 Zhang, B. Orning, P. Lehman, J. W. Dinis, A. Torres-Ulloa, L. Elling, R. Kelliher, M. A. Bertin, J. Proulx, M. K. Ryan, L. Kandasamy, R. K. Espevik, T. Pai, A. A. Fitzgerald, K. A. Lien, E. 2024-11-29 doi:10.1101/2024.11.27.625707 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Identification and developmental profiling of microRNAs in the acoel worm Hofstenia miamia ]]> https://biorxiv.org/content/10.1101/2024.12.01.626237v1?rss=1 Duan, Y. Segev, T. Veksler-Lublinsky, I. Ambros, V. Srivastava, M. 2024-12-02 doi:10.1101/2024.12.01.626237 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection ]]> https://biorxiv.org/content/10.1101/2024.11.29.624972v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@169c77forg.highwire.dtl.DTLVardef@1a872f5org.highwire.dtl.DTLVardef@1360cforg.highwire.dtl.DTLVardef@38d7ed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Perugino, C. Liu, H. Feldman, J. Marbourg, J. Guy, T. Hui, A. Ingram, N. Liebaert, J. Chaudhary, N. Tao, W. Jacob-Dolan, C. Hauser, B. M. Mian, Z. Nathan, A. Zhao, Z. Kaseke, C. Tano-Menka, R. Getz, M. Senjobe, F. Berrios, C. Ofoman, O. Manickas-Hill, Z. Wesemann, D. Lemieux, J. Goldberg, M. B. Nundel, K. Moormann, A. M. Marshak-Rothstein, A. Larocque, R. Ryan, E. Iafrate, A. J. Lingwood, D. Gaiha, G. Charles, R. Balazs, A. B. Pandit, A. Naranbhai, V. Schmidt, A. Pillai, S. 2024-12-04 doi:10.1101/2024.11.29.624972 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ High-throughput discovery and deep characterization of cyclin-CDK docking motifs ]]> https://biorxiv.org/content/10.1101/2024.12.03.625240v1?rss=1 Ord, M. Winters, M. J. Subbanna, M. S. de Martin Garrido, N. Cushing, V. I. Kliche, J. Benz, C. Ivarsson, Y. Greber, B. J. Pryciak, P. M. Davey, N. E. 2024-12-04 doi:10.1101/2024.12.03.625240 Cold Spring Harbor Laboratory Press 2024-12-04 <![CDATA[ Pol II degradation activates cell death independently from the loss of transcription ]]> https://biorxiv.org/content/10.1101/2024.12.09.627542v1?rss=1 Harper, N. W. Birdsall, G. A. Honeywell, M. E. Pai, A. A. Lee, M. J. 2024-12-10 doi:10.1101/2024.12.09.627542 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Endosome maturation is orchestrated by inside-out proton signaling through a Na+/H+ exchanger and pH-dependent Rab GTPase cycling ]]> https://biorxiv.org/content/10.1101/2024.12.09.627558v1?rss=1 Lee, Y. Ouyang, Q. Riaz, H. A. Ma, L. Fleishman, M. Schmidt, M. Dupree, J. L. Lambright, D. G. Morrow, E. M. 2024-12-12 doi:10.1101/2024.12.09.627558 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ IL-17A primes an early progenitor compartment to tune the erythropoietic feedback circuit ]]> https://biorxiv.org/content/10.1101/2024.12.16.628761v1?rss=1 Wu, Q. C. Swaminathan, A. Winward, A. Lalonde, L. Hwang, Y. Littman, N. Socolovsky, M. Klein, A. M. 2024-12-20 doi:10.1101/2024.12.16.628761 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Acute infectious mononucleosis generates persistent, functional EBNA-1 antibodies with high cross-reactivity to alpha crystalline beta ]]> https://biorxiv.org/content/10.1101/2024.12.18.629009v1?rss=1 Ganta, K. K. McManus, M. Blanc, R. Wang, Q. Jung, W. Brody, R. Carrington, M. Paris, R. Chandramouli, S. McNamara, R. Luzuriaga, K. 2024-12-21 doi:10.1101/2024.12.18.629009 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Mapping histological and functional maturation of human endocrine pancreas across early postnatal periods ]]> https://biorxiv.org/content/10.1101/2024.12.20.629754v1?rss=1 Saunders, D. C. Hart, N. Pan, F. C. Reihsmann, C. V. Hopkirk, A. L. Izmaylov, N. Mei, S. Sherrod, B. A. Davis, C. Duryea, J. Haliyur, R. Aramandla, R. Durai, H. Poffenberger, G. Martin, A. Posgai, A. L. Kusmartseva, I. Beery, M. L. Yang, M. Kang, H. Greiner, D. L. Shultz, L. D. Cartailler, J.-P. Aamodt, K. I. Bottino, R. Atkinson, M. A. Wright, C. V. E. Powers, A. C. Brissova, M. 2024-12-22 doi:10.1101/2024.12.20.629754 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation ]]> https://biorxiv.org/content/10.1101/2024.12.26.629296v1?rss=1 Moore, J. E. Pratt, H. E. Fan, K. Phalke, N. Fisher, J. Elhajjajy, S. I. Andrews, G. Gao, M. Shedd, N. Fu, Y. Lacadie, M. C. Meza, J. Ganna, M. Choudhury, E. Swofford, R. Farrell, N. P. Pampari, A. Ramalingam, V. Reese, F. Borsari, B. Yu, X. Wattenberg, E. S. Ruiz-Romero, M. Razavi-Mohseni, M. Xu, J. Galeev, T. Beer, M. A. Guigo, R. Gerstein, M. Engreitz, J. M. Ljungman, M. Reddy, T. E. Snyder, M. Epstein, C. B. Gaskell, E. Bernstein, B. E. Dickel, D. E. Visel, A. Pennacchio, L. A. Mortazavi, A. Kundaje, A. Weng, Z. 2024-12-26 doi:10.1101/2024.12.26.629296 Cold Spring Harbor Laboratory Press 2024-12-26 <![CDATA[ Detection of HTTex1p by western blot and immunostaining of HD human and mouse brain using neo-epitope antibody P90 highlights impact of CAG repeat expansion on its size, solubility, and response to MSH3 silencing ]]> https://biorxiv.org/content/10.1101/2024.12.31.630891v1?rss=1 Sapp, E. Boudi, A. Iwanowicz, A. Belgrad, J. Miller, R. O'Reilly, D. Yamada, K. Deng, Y. Joni, M. Li, X. Kegel-Gleason, K. Khvorova, A. Reiner, A. Aronin, N. DiFiglia, M. 2025-01-01 doi:10.1101/2024.12.31.630891 Cold Spring Harbor Laboratory Press 2025-01-01 <![CDATA[ Sustained efficacy of CRISPR-Cas13b gene therapy for FSHD is challenged by immune response to Cas13b ]]> https://biorxiv.org/content/10.1101/2024.12.18.629250v1?rss=1 Rashnonejad, A. Farea, M. Chermahini, G. A. COULIS, G. Taylor, N. Fowler, A. Villalta, A. King, O. D. Harper, S. Q. 2025-01-02 doi:10.1101/2024.12.18.629250 Cold Spring Harbor Laboratory Press 2025-01-02 <![CDATA[ Transcriptional responses to prolonged oxidative stress require cholinergic activation of G-protein-coupled receptor signaling ]]> https://biorxiv.org/content/10.1101/2025.01.06.628021v1?rss=1 Biswas, K. Moore, C. Rogers, H. Wani, K. A. Higgins, D. P. Walker, A. K. Pukkila-Worley, R. Rand, J. B. Francis, M. M. 2025-01-07 doi:10.1101/2025.01.06.628021 Cold Spring Harbor Laboratory Press 2025-01-07 <![CDATA[ Intrastriatal delivery of a zinc finger protein targeting the mutant HTT gene obviates lipid phenotypes in zQ175DN HD mice ]]> https://biorxiv.org/content/10.1101/2025.01.06.630918v1?rss=1 Iwanowicz, A. Boudi, A. Seeley, C. Sapp, E. Miller, R. Liu, S. Chase, K. Shing, K. Batista, A. R. Siena-Esteves, M. Aronin, N. Difiglia, M. Kegel-Gleason, K. B. 2025-01-07 doi:10.1101/2025.01.06.630918 Cold Spring Harbor Laboratory Press 2025-01-07 <![CDATA[ AAVone: A Cost-Effective, Single-Plasmid Solution for Efficient AAV Production with Reduced DNA Impurities ]]> https://biorxiv.org/content/10.1101/2025.01.07.631712v1?rss=1 Yang, R. Tran, N. T. Chen, T. Cui, M. Wang, Y. Sharma, T. Liu, Y. Zhang, J. Yuan, X. Zhang, D. Chen, C. Shi, Z. Wang, L. Dai, Y. Zaidi, H. Liang, J. Chen, M. Jaijyan, D. Hu, H. Wang, B. Xu, C. Hu, W. Gao, G. Yu, D. Tai, P. W. L. Wang, Q. 2025-01-08 doi:10.1101/2025.01.07.631712 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ A Microphysiological Model of Progressive Human Hepatic Insulin Resistance ]]> https://biorxiv.org/content/10.1101/2025.01.08.631261v1?rss=1 Hellen, D. J. Ungerleiger, J. Tevonian, E. Sphabmixay, P. Roy, P. Chidley, C. Jeppesen, J. Demozay, D. Griffith, L. G. 2025-01-08 doi:10.1101/2025.01.08.631261 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Molecular Mechanisms of Drug Resistance and Compensation in SARS-CoV-2 Main Protease: The Interplay Between E166 and L50 ]]> https://biorxiv.org/content/10.1101/2025.01.24.634813v1?rss=1 Zvornicanin, S. N. Shaqra, A. M. Flynn, J. Carias Martinez, H. Jia, W. Moquin, S. Dovala, D. Bolon, D. N. Kurt Yilmaz, N. Schiffer, C. A. 2025-01-27 doi:10.1101/2025.01.24.634813 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ The structure of a thermostable phage's Portal Vertex and Neck Complex illuminates its maturation process ]]> https://biorxiv.org/content/10.1101/2025.04.14.648768v1?rss=1 Sedivy, E. L. Agnello, E. Hobaugh, J. E. Ahsan, R. Xu, C. Song, K. Kelch, B. A. 2025-04-15 doi:10.1101/2025.04.14.648768 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ tRNA-derived RNA processing in sperm transmits non-genetically inherited phenotypes to offspring in C. elegans ]]> https://biorxiv.org/content/10.1101/2025.04.14.648817v1?rss=1 Galambos, N. S. Crocker, O. J. Schneider, B. K. Allerton, K. S. Gross, K. E. Schneider, A. E. Lynch, J. Yukselen, O. Kucukural, A. Conine, C. C. 2025-04-16 doi:10.1101/2025.04.14.648817 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Archaeal SegAB forms a bipolar structure that promotes chromosome segregation in spherical cells ]]> https://biorxiv.org/content/10.1101/2025.04.15.649018v1?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. 2025-04-16 doi:10.1101/2025.04.15.649018 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Targeted plasma proteomics uncover novel proteins associated with KIF5A-linked SPG10 and ALS spectrum disorders ]]> https://biorxiv.org/content/10.1101/2025.04.29.651203v1?rss=1 Dulski, J. Boddapati, A. Risi, B. Iruzubieta, P. Orlacchio, A. Fernandez Torron, R. Castillo Trivino, T. Lopez De M Arregui, A. Vucic, S. Kaat, L. D. Barakat, T. S. Petrucelli, L. Prudencio, M. Landers, J. E. Prokop, A. Weishaupt, J. H. Filosto, M. Wszolek, Z. K. Pant, D. C. 2025-05-02 doi:10.1101/2025.04.29.651203 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Sex-specific transcriptional signatures of oxycodone persist during withdrawal and abstinence in the suprachiasmatic nucleus of heterogeneous stock rats ]]> https://biorxiv.org/content/10.1101/2025.04.29.651331v1?rss=1 Delorme, T. C. Sambare, S. Williams, B. R. Gamble, M. C. Solberg-Woods, L. Maturin, L. Palmer, A. A. George, O. Logan, R. 2025-05-04 doi:10.1101/2025.04.29.651331 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ The gonococcal vaccine candidate antigen NGO1701 is a N. gonorrhoeae periplasmic copper storage protein ]]> https://biorxiv.org/content/10.1101/2025.05.01.651437v1?rss=1 Roe, S. K. Mazgaj, R. Zhu, T. Esmaeeli, M. Lewis, L. A. Genco, C. Waldron, K. J. Massari, P. 2025-05-07 doi:10.1101/2025.05.01.651437 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Staphylococcus aureus-Induced Degeneration of Nociceptive Neurons in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2025.05.01.651706v1?rss=1 DiLoreto, E. M. Gonzalez, X. Wani, K. A. Shen, J. Irazoqui, J. E. Srinivasan, J. E. 2025-05-07 doi:10.1101/2025.05.01.651706 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ The phosphatases TCPTP, PTPN22, and SHP1 play unique roles in T cell phosphotyrosine maintenance and feedback regulation of the TCR ]]> https://biorxiv.org/content/10.1101/2025.05.05.652301v1?rss=1 Callahan, A. Mojumdar, A. Hu, M. Wang, A. Griffith, A. Huang, N. Chua, X. Y. Mroz, N. M. Puterbaugh, R. Z. Reilly, S. P. Salomon, A. R. 2025-05-09 doi:10.1101/2025.05.05.652301 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ A Compact Base Editor Rescues AATD-associated Liver and Lung Disease in Mouse Models ]]> https://biorxiv.org/content/10.1101/2025.05.07.652636v1?rss=1 Gao, J. Bamidele, N. Pires-Ferreira, D. Destefano, A. Tang, Q. Cao, Y. Xie, J. Gao, G. Gruntman, A. Sontheimer, E. Flotte, T. Xue, W. J. 2025-05-09 doi:10.1101/2025.05.07.652636 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Transient centrosome loss in cultured prostate epithelial cells induces chromosomal instability to produce an oncogenic genotype that correlates with poor clinical outcomes ]]> https://biorxiv.org/content/10.1101/2025.05.10.653266v1?rss=1 View larger version (55K): org.highwire.dtl.DTLVardef@ac4c9org.highwire.dtl.DTLVardef@fd9961org.highwire.dtl.DTLVardef@160e20corg.highwire.dtl.DTLVardef@198bf0e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yang, J. de Oliveira Pessoa, D. Ryniawec, J. M. Coope, M. R. Buster, D. W. Loertscher, E. Wang, M. Chen, C. Cress, A. E. Rogers, G. C. Padi, M. 2025-05-12 doi:10.1101/2025.05.10.653266 Cold Spring Harbor Laboratory Press 2025-05-12 <![CDATA[ Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice ]]> https://biorxiv.org/content/10.1101/2025.05.09.653044v1?rss=1 Saflund, M. Askari, M. Eghbali, A. Abdi, M. M. Östlund Farrants, A.-K. Yu, T. Ozata, D. M. 2025-05-14 doi:10.1101/2025.05.09.653044 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Whole-brain chemosensory responses of both C. elegans sexes ]]> https://biorxiv.org/content/10.1101/2025.05.15.654129v1?rss=1 Seyedolmohadesin, M. Fu, X. Torkashvand, M. Rasouli, S. Lang, S. Li, L. Kalinski, C. Cook, S. J. Schroeder, F. C. Yemini, E. Venkatachalam, V. 2025-05-19 doi:10.1101/2025.05.15.654129 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ Engineering novel AAV capsids by global de-targeting and subsequent muscle-specific tropism in mice and NHPs ]]> https://biorxiv.org/content/10.1101/2025.05.19.654800v1?rss=1 Pan, Y. Zhong, Y. Chen, H. Zhang, Y. Dai, Z. Chen, J. Tan, K. Chen, X. Qiu, D. Sheng, L. Tan, X. Fan, Y. Bu, Y. Zhou, Z. Yang, Z. Duan, R. Guan, M. Gao, G. Li, H. 2025-05-19 doi:10.1101/2025.05.19.654800 Cold Spring Harbor Laboratory Press 2025-05-19 <![CDATA[ The cryo-EM structure of mouse radial spoke 3 reveals a unique metabolic and regulatory hub in cilia ]]> https://biorxiv.org/content/10.1101/2025.05.19.654877v1?rss=1 Zhao, Y. Song, K. Tavakoli, A. Gui, L. Fernandez Gonzalez, A. Zhang, S. Dzeja, P. P. Mitsialis, S. A. Zhang, X. Nicastro, D. 2025-05-21 doi:10.1101/2025.05.19.654877 Cold Spring Harbor Laboratory Press 2025-05-21 <![CDATA[ Adipocyte MKK3 Increases in Human Obesity protecting against Insulin Resistance by p38-beta activation ]]> https://biorxiv.org/content/10.1101/2025.05.19.654793v1?rss=1 Bernardo, E. Matesanz, N. Torres, J. L. Herrera-Melle, L. Leiva-Vega, L. Mora, A. Rodriguez, M. E. Hernandez-Cosido, L. Nogueiras, R. Arthur, S. Nebreda, A. R. Davis, R. R. Marcos, M. Sabio, G. 2025-05-23 doi:10.1101/2025.05.19.654793 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Xist Repeat A coordinates an assembly of SR proteins to recruit SPEN and induce gene silencing ]]> https://biorxiv.org/content/10.1101/2025.05.21.655143v1?rss=1 Trotman, J. B. Porrello, A. Schactler, S. A. DeLeon, L. E. Eberhard, Q. E. Boyson, S. P. Zhang, Z. Lee, D. M. Kirik, S. E. Nguyen, S. N. Beltejar, M.-C. G. Shinn, M. K. Ong, S.-E. Gonzalez-Perez, M. P. Shaffer, S. A. Dominguez, D. Shechner, D. M. Calabrese, M. 2025-05-26 doi:10.1101/2025.05.21.655143 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ IL-6 Evades KSHV-Mediated Hyperadenylation repression via CRM1-Dependent Nuclear Export. ]]> https://biorxiv.org/content/10.1101/2025.06.05.657986v1?rss=1 Schultz, S. Miles, J. Dwyer, W. MacVeigh-Fierro, D. Muller, M. 2025-06-05 doi:10.1101/2025.06.05.657986 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Gene therapies alleviate absence epilepsy associated with Scn2a deficiency in DBA/2J mice ]]> https://biorxiv.org/content/10.1101/2025.06.03.657652v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@35374eorg.highwire.dtl.DTLVardef@1c22197org.highwire.dtl.DTLVardef@2b4582org.highwire.dtl.DTLVardef@e06e68_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefScn2a deficiency leads to absence seizures in D2J mice and neuronal hyperexcitability with compensatory KV reduction; restoring NaV1.2 or introducing human KV1.1 reduces seizure burden. HighlightsO_LIScn2a deficiency induces robust absence seizures in the DBA/2J but not the C57BL/6N strain. C_LIO_LICortical neurons in adult DBA/2J mice with Scn2a deficiency exhibit intrinsic hyperexcitability. C_LIO_LISevere Scn2a deficiency leads to downregulation of multiple potassium channel genes. C_LIO_LIGenetic restoration of NaV1.2 expression alleviates spike-wave discharges (SWDs). C_LIO_LIAAV-mediated human KV1.1 delivery substantially reduced absence seizures, demonstrating the therapeutic potential of targeted gene therapy. C_LI ]]> Zhang, Z. Zhang, J. Chen, X. Deming, B. A. Kant, S. Mandal, P. Kothandaraman, H. SanMiguel, P. J. Halurkar, M. S. Abeyaratna, A. D. Robinson, M. J. Zhao, Y. Vitko, Y. Gaykema, R. P. Yuan, C. Lanman, N. A. Tegtmeyer, M. T. Wang, D. Gao, G. Shi, R. Perez-Reyes, E. Yang, Y. 2025-06-06 doi:10.1101/2025.06.03.657652 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Pancreatic cancer cachexia is mediated by PTHrP-driven disruption of adipose de novo lipogenesis ]]> https://biorxiv.org/content/10.1101/2025.06.03.657464v1?rss=1 Bhalerao, N. U. Ogoti, Y. Peura, J. Johnson, C. Chen, Q. Korobkina, E. Keller, F. Wengyn, M. Norgard, R. J. Shamber, C. Klute, K. DiMaio, D. Sellin, K. Grandgenett, P. M. Li, R. Hollingsworth, M. A. GUILHERME, A. Czech, M. Kremer, R. Zhu, L. J. Watson, E. V. Ruscetti, M. Guertin, D. Pitarresi, J. R. 2025-06-07 doi:10.1101/2025.06.03.657464 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Lowering the HTT1a transcript as an effective therapy for Huntingtons disease ]]> https://biorxiv.org/content/10.1101/2025.06.10.658804v1?rss=1 Papadopoulou, A. S. Alterman, J. Landles, C. Smith, E. J. Conroy, F. Phillips, J. Canibano-Pico, M. Nita, I. M. Osborne, G. F. Iqbal, A. Aldous, S. G. Bondulich, M. K. Gomez-Paredes, C. Sathasivam, K. O'Reilly, D. Echeverria, D. Bobkov, K. Greene, J. R. Aronin, N. Khvorova, A. Bates, G. P. 2025-06-11 doi:10.1101/2025.06.10.658804 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ Annotating the X-ray diffraction pattern of vertebrate striated muscle ]]> https://biorxiv.org/content/10.1101/2025.06.11.659175v1?rss=1 Koubassova, N. A. Dutta, D. Ma, W. Tsaturyan, A. K. Irving, T. Padron, R. Craig, R. 2025-06-16 doi:10.1101/2025.06.11.659175 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ KRAS withdrawal in Cholangiocarcinoma leads to immune infiltration and tumor regression ]]> https://biorxiv.org/content/10.1101/2025.06.11.659210v1?rss=1 Qiao, Y. Yee, M. Parikh, C. N. Cao, Y. Shih, Y.-H. Ma, B. Wu, J. Q. Ruscetti, M. Liang, S.-Q. Xue, W. 2025-06-17 doi:10.1101/2025.06.11.659210 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Prime assembly with linear DNA donors enables large genomic insertions ]]> https://biorxiv.org/content/10.1101/2025.06.16.659978v1?rss=1 Liu, B. Petti, A. Zhou, X. Cheng, H. Zhou, L. Jiang, T. Sontheimer, E. J. Xue, W. 2025-06-17 doi:10.1101/2025.06.16.659978 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ R-loops shape chromatin architecture to promote balanced lineage allocation during differentiation ]]> https://biorxiv.org/content/10.1101/2025.06.23.661125v1?rss=1 Chao, C.-H. Fazzio, T. G. 2025-06-25 doi:10.1101/2025.06.23.661125 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Blocking somatic repeat expansion and lowering huntingtin via RNA interference synergize to prevent Huntingtons disease pathogenesis in mice ]]> https://biorxiv.org/content/10.1101/2025.06.24.661398v1?rss=1 110 CAGs), which exhibit robust expansion, mHTT inclusions, and transcriptional dysregulation by 12 months, long-term MSH3 silencing blocked expansion, reduced inclusions, and reversed gene expression changes. HTT silencing alone had limited effect, but combined MSH3/HTT targeting synergistically eliminated inclusions and restored transcriptomic profiles. Parallel treatment in wild-type mice showed no toxicity, supporting the safety of long-term intervention. These findings position somatic expansion as a promising therapeutic target and demonstrate the potential of RNAi-based co-silencing of MSH3 and HTT as a disease-modifying strategy for HD. ]]> Belgrad, J. Summers, A. Landles, C. Greene, J. R. Hildebrand, S. Knox, E. Sapp, E. Yamada, N. Furgal, R. Miller, R. Osborne, G. F. Chase, K. Luu, E. Freedman, J. Bramato, B. McHugh, N. Benoit, V. OReilly, D. Greer, P. Bates, G. P. Vogt, T. F. Lee, R. Howland, D. DiFiglia, M. Aronin, N. Khvorova, A. 2025-06-25 doi:10.1101/2025.06.24.661398 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ A global genetic interaction map of a human cell reveals conserved principles of genetic networks ]]> https://biorxiv.org/content/10.1101/2025.06.30.662193v1?rss=1 Billmann, M. Costanzo, M. Zhang, X. Hassan, A. Z. Rahman, M. Brown, K. R. Chan, K. S. Tong, A. H. Pons, C. Ward, H. N. Ross, C. van Leeuwen, J. Aregger, M. Lawson, K. A. Mair, B. Roth, A. F. Sen, N. E. Forster, D. T. Tan, G. Merro, P. Masud, S. N. Lee, Y. Aguilera-Uribe, M. Usaj, M. Almeida, S. M. Aulakh, K. Bhojoo, U. Birkadze, S. Budijono, N. Cai, X. Caumanns, J. J. Chandrashekhar, M. Chang, D. Clinie, R. Dasgupta, K. Drazic, A. Rojas Echenique, J. I. Gacesa, R. Granda Farias, A. Habsid, A. Horecka, I. Kantautas, K. Ji, F. Kim, D.-K. Lee, S. Y. Li 2025-07-02 doi:10.1101/2025.06.30.662193 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ PCNA is a Nucleotide Exchange Factor for the Clamp Loader ATPase Complex ]]> https://biorxiv.org/content/10.1101/2025.07.02.662830v1?rss=1 Pajak, J. Landeck, J. T. Liu, X. Anand, K. Litvak, S. Kelch, B. A. 2025-07-03 doi:10.1101/2025.07.02.662830 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Genome-wide analysis reveals pathways important for the development and maturation of excitatory synaptic connections to GABAergic neurons ]]> https://biorxiv.org/content/10.1101/2025.07.05.663213v1?rss=1 Oliver, D. B. Ramachandran, S. Biswas, K. McKillop, H. Genao, N. Lemons, M. L. Francis, M. M. 2025-07-06 doi:10.1101/2025.07.05.663213 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ Inhibiting Clarinet/CLA-1 restores function to injured motor neurons ]]> https://biorxiv.org/content/10.1101/2025.07.05.663315v1?rss=1 Huang, W. Min, E. Byrne, A. 2025-07-06 doi:10.1101/2025.07.05.663315 Cold Spring Harbor Laboratory Press 2025-07-06 <![CDATA[ Sterols regulate ciliary membrane dynamics and hedgehog signaling in health and disease ]]> https://biorxiv.org/content/10.1101/2025.07.15.664899v1?rss=1 Eguether, T. Lamaziere, A. kozlowski, l. Ayala-Sanmartin, J. Farhat, M. Belaid, N. Certain, A. Isidor, B. Besnard, T. Trugnan, G. Pazour, G. J. Despres, G. Deseille, C. Moreno, S. 2025-07-16 doi:10.1101/2025.07.15.664899 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Endothelial Cell Expression of STINGV154M Gain-of-Function Mutation Delays the Resolution of UVB-induced Skin Injury ]]> https://biorxiv.org/content/10.1101/2025.07.14.664621v1?rss=1 Chuprin, J. E. Lopes, C. S. Gao, K. M. Chiang, K. Afshari, K. Haddadi, N. Garber, M. Koupenova, M. Fitzgerald, K. A. Marshak-Rothstein, A. Rashighi, M. 2025-07-18 doi:10.1101/2025.07.14.664621 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ LIPL-1 and LIPL-2 are TCER-1-regulated Lysosomal Lipases with Distinct Roles in Immunity and Fertility ]]> https://biorxiv.org/content/10.1101/2025.07.14.664648v1?rss=1 Bahr, L. Amrit, F. R. Silvia, P. E. Bui, D. Wayhs, B. Choe, M. Osman, G. Naim, N. Champion, M. Shen, J. Irazoqui, J. E. Olsen, C. P. Ghazi, A. 2025-07-18 doi:10.1101/2025.07.14.664648 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ Interaction of IRS2 with PLK1 protects cells from mitotic stress ]]> https://biorxiv.org/content/10.1101/2025.07.17.665461v1?rss=1 Lee, J.-S. Bui, Q. T. Jo, M. Morgan, J. S. Nasa, I. Kettenbach, A. Shaw, L. M. 2025-07-21 doi:10.1101/2025.07.17.665461 Cold Spring Harbor Laboratory Press 2025-07-21 <![CDATA[ Rag GTPases Suppress Renal Cystic Disease by Inhibiting TFEB Independently of mTORC1 ]]> https://biorxiv.org/content/10.1101/2025.07.24.664930v1?rss=1 de Fatima Silva, F. Boucher, A. R. Li, H. Chen, Q. Gaughan, M. Korobkina, E. Isidor, M. S. Smith, A. O. Shen, K. Allison, D. B. Tran, P. Pazour, G. J. Guertin, D. A. 2025-07-24 doi:10.1101/2025.07.24.664930 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Baseline expression of c-Myc defines the tissue specificity of oncogenic K-Ras ]]> https://biorxiv.org/content/10.1101/2025.07.21.665965v1?rss=1 Popow, O. Yu, Q. Yapp, C. Hull, S. Paulo, J. A. Hanna, B. Xu, S. Kuang, Y. Sigel, C. Paweletz, C. P. Gygi, S. P. Haigis, K. M. 2025-07-25 doi:10.1101/2025.07.21.665965 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Cooperativity and Communication between the Active Sites of the Dimeric SARS-CoV-2 Main Protease ]]> https://biorxiv.org/content/10.1101/2025.07.31.667456v1?rss=1 Zvornicanin, S. N. Shaqra, A. M. Flynn, J. M. Intravaia, L. E. Martinez, H. C. Jia, W. Gupta, D. K. Moquin, S. Dovala, D. Bolon, D. N. A. Kelch, B. A. Schiffer, C. A. Kurt Yilmaz, N. 2025-07-31 doi:10.1101/2025.07.31.667456 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Therapeutic delivery of albumin-binding siRNA targeting IRS2 to diverse cell types reduces mammary tumor growth ]]> https://biorxiv.org/content/10.1101/2025.07.29.667434v1?rss=1 Tocheny, C. M. Buchwald, J. E. Dahlke, C. D. Fakih, H. H. Morgan, J. S. Summers, A. Wisniewski, C. A. Jackson, S. O. Lee, J.-S. Card, M.-A. Echeverria, D. Peterson, C. Mercurio, A. M. Khvorova, A. Shaw, L. M. 2025-08-01 doi:10.1101/2025.07.29.667434 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions ]]> https://biorxiv.org/content/10.1101/2025.07.29.667515v1?rss=1 Smith, R. G. Fu, Y. Schiela, K. L. Dautle, M. Williams, R. Wilson, H. M. Azadegan, C. Whetstine, J. R. Dekker, J. Liu, Y. 2025-08-01 doi:10.1101/2025.07.29.667515 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ UCP1 Mitigates Hepatic Steatosis and Fibrosis Independent of Cold Exposure ]]> https://biorxiv.org/content/10.1101/2025.08.05.666925v1?rss=1 Haley, J. A. Le, J. Li, R. Korobkina, E. de Fatima Silva, F. Gaughan, M. Fitzgibbons, T. P. Martinez, N. Chen, Q. Fluharty, S. M. Li, H. Lewis, C. A. Harris, J. E. Zhu, L. J. Mullen, A. C. Jang, C. Guertin, D. A. 2025-08-07 doi:10.1101/2025.08.05.666925 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Comparative analysis of plasma and bone marrow nutrient levels in pediatric B-ALL patients ]]> https://biorxiv.org/content/10.1101/2025.08.05.668707v1?rss=1 Abbott, K. L. Ali, A. Munim, M. B. Bagchi, D. P. Kunchok, T. Waite, M. Wiggers, C. R. M. Dimitrov, B. Harris, M. H. Knoechel, B. Silverman, L. B. Vander Heiden, M. G. Pikman, Y. 2025-08-07 doi:10.1101/2025.08.05.668707 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ B. pertussis tracheal cytotoxin biases NOD signaling to suppress IL-1 mediated inflammation and evade adaptive immunity ]]> https://biorxiv.org/content/10.1101/2025.08.08.669383v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@ada335org.highwire.dtl.DTLVardef@1b61a0eorg.highwire.dtl.DTLVardef@68c66eorg.highwire.dtl.DTLVardef@bb6e54_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 8.C_FLOATNO Graphic Abstract B. pertussis can produce both NOD1 and NOD2 activating PGNs. Release of TCT promotes NOD1 activation and diminishes NOD2 activation. NOD2 activation in myeloid cells drives M1 polarization of macrophages and IL-1 family cytokine production. IL-1 family cytokines skew fibroblasts towards an inflammatory phenotype, leading to chemokine release, extracellular remodeling, and recruitment of lymphocytes. Therefore, TCT release tempers long-term immunity to B. pertussis. C_FIG ]]> Rickert, D. M. Hill, E. M. Himmelberger, R. E. Rajbanshi, N. Cardozo, S. Bergamin De Castro, T. Bharadwaj, R. Scott, A. J. Silverman, N. Goldman, W. E. Carbonetti, N. H. Scanlon, K. M. Skerry, C. 2025-08-08 doi:10.1101/2025.08.08.669383 Cold Spring Harbor Laboratory Press 2025-08-08 <![CDATA[ Regulation of tension-dependent localization of LATS1 and LATS2 to adherens junctions. ]]> https://biorxiv.org/content/10.1101/2025.08.26.672419v1?rss=1 De Silva, C. Kelch, B. A. McCollum, D. 2025-08-27 doi:10.1101/2025.08.26.672419 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ An electrostatic repulsion model of centromere organisation ]]> https://biorxiv.org/content/10.1101/2025.09.01.673455v1?rss=1 Bell, C. Chen, L. Maristany, M. J. Blaukopf, C. Zhou, H. Huertas, J. Perez Lopez, J. I. Langer, C. C. H. Steinacker, T. L. Schuette, N. Doolittle, L. Espinosa, J. R. Redding, S. Collepardo-Guevara, R. Rosen, M. K. Gerlich, D. W. 2025-09-02 doi:10.1101/2025.09.01.673455 Cold Spring Harbor Laboratory Press 2025-09-02 <![CDATA[ BMP9 regulates the endothelial secretome to drive pulmonary hypertension ]]> https://biorxiv.org/content/10.1101/2025.08.29.673113v1?rss=1 Zhong, Y. Yang, P. Troncone, L. Kovalenko, O. V. Fast, E. M. Rajesh, S. Lavoie, S. Tumelty, K. E. Shin, E. Covington, T. Zeghibe, A. Wadsworth, M. H. Christensen, S. M. Nathans, R. Benard, S. A. Tang, X. Quazi, S. A. Worst, L. R. McNeil, M. E. Kim, S. S. J. Bocobo, G. D. Szulcek, R. Bogaard, H. J. Hart, K. M. Martinez-Hackert, E. M. Berasi, S. P. Huard, C. Yu, P. B. 2025-09-04 doi:10.1101/2025.08.29.673113 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ HIF2-driven PTHrP Causes Cachexia and Hypercalcemia in Kidney Cancer: Treatment with HIF2 Inhibitors ]]> https://biorxiv.org/content/10.1101/2025.09.09.675147v1?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. 2025-09-11 doi:10.1101/2025.09.09.675147 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ SARM1, the executioner of axon degeneration, is an ADP-ribosyl transferase and autoMARylation negatively regulates its activation ]]> https://biorxiv.org/content/10.1101/2025.09.12.675907v1?rss=1 Icso, J. DeOrsey, L. Barasa, L. Kelch, B. A. Thompson, P. R. 2025-09-13 doi:10.1101/2025.09.12.675907 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Next-Generation Multiplexed Targeted Proteomics Quantifies Post-Translational Modifications, Compound-Protein Interactions, and Disease Biomarkers with High Throughput ]]> https://biorxiv.org/content/10.1101/2025.09.10.675380v1?rss=1 99% of 800 peptides in a single run. We compiled a library of 23,989 human phosphorylation sites from a phosphoproteomic dataset and used it to profile kinase signaling differences across cell lines. In human brain tissue, we established a hyperphosphorylated tau assay including pTau127, revealing potential biomarkers for Alzheimers disease. We also quantified diglycyl-lysine peptides to assess polyubiquitin branching. Finally, we built a library of 20,946 reactive cysteines and profiled covalent compound-protein interactions spanning diverse pathways. GoDig 2.0 enables high-throughput analyses of site-specific protein modifications across many biological contexts. ]]> Shuken, S. R. Frere, G. A. Beard, C. R. Canterbury, J. D. Zuniga, N. R. Gassaway, B. M. Dawson, S. L. Ooi, K. H. Paulo, J. A. McNerney, M. W. Gygi, S. P. Yu, Q. 2025-09-16 doi:10.1101/2025.09.10.675380 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching ]]> https://biorxiv.org/content/10.1101/2025.09.11.675606v1?rss=1 Zhang, K. Grant, T. Grigorieff, N. 2025-09-16 doi:10.1101/2025.09.11.675606 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Somatic function of the Argonaute protein Aubergine is essential for neuromuscular development and function in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.09.17.676627v1?rss=1 M'Angale, P. Oliver, D. Alegre, G. Graslie, J. Tran, A. Ohira, A. Zinter, M. Malinkevich, A. Thomson, T. 2025-09-17 doi:10.1101/2025.09.17.676627 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions ]]> https://biorxiv.org/content/10.1101/2025.09.16.676562v1?rss=1 Bonilla, B. Patty, B. Sambare, S. Dekker, J. Fazzio, T. G. Hainer, S. J. 2025-09-18 doi:10.1101/2025.09.16.676562 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Selective chr21 homolog silencing reveals polymorphisms influence the epigenetic silencing and functional dosage of RWDD2B ]]> https://biorxiv.org/content/10.1101/2025.09.17.676855v1?rss=1 Larsen, E. C. Moon, J. E. King, O. D. Lawrence, J. B. 2025-09-18 doi:10.1101/2025.09.17.676855 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Gli3R-mediated inhibition of hedgehog signaling alters the embryonic transcriptome in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.09.18.677168v1?rss=1 Moyer, A. J. Thyme, S. B. 2025-09-18 doi:10.1101/2025.09.18.677168 Cold Spring Harbor Laboratory Press 2025-09-18 <![CDATA[ Dynamic changes in chromosome and nuclear architecture during maturation of normal and ALS C9orf72 motor neurons ]]> https://biorxiv.org/content/10.1101/2025.09.22.677835v1?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. 2025-09-22 doi:10.1101/2025.09.22.677835 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Differentiation stage-specific use of cap-independent and cap-dependent translation initiation in hematopoiesis ]]> https://biorxiv.org/content/10.1101/2025.09.24.678136v1?rss=1 Mazzola, M. C. Zhao, T. Kiem, A. Kristiansen, T. A. Gustafsson, K. Wong, L. P. Scott-Solomon, E. Fahlberg, M. D. Forward, S. Assita, E. R. Schiroli, G. Handley, M. Kfoury, Y. Fukushima, T. Keyes, S. Sharda, A. Milosevic, J. Kato, H. Ivanov, P. Sykes, D. B. Kwok, S. J. J. Sadreyev, R. I. Sankaran, V. G. Hsu, Y.-C. Scadden, D. T. 2025-09-25 doi:10.1101/2025.09.24.678136 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Atlas of Lysosomal Aging Reveals a Molecular Clock of Storage Disorder-Associated Metabolites ]]> https://biorxiv.org/content/10.1101/2025.09.25.678303v1?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. 2025-09-26 doi:10.1101/2025.09.25.678303 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Transmission network for foot-and-mouth disease epidemic in Mar Chiquita - Argentina: A spatial modeling analysis ]]> https://biorxiv.org/content/10.1101/2025.09.26.678789v1?rss=1 Musa, S. S. Lozano, L. C. Marcos, A. König, G. A. Colubri, A. 2025-09-29 doi:10.1101/2025.09.26.678789 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Imp, a key regulator of transposable elements, cell growth, and differentiation genes during embryogenesis ]]> https://biorxiv.org/content/10.1101/2025.09.30.679481v1?rss=1 Vazquez Pianzola, M. P. Beuchle, D. M'Angale, P. G. Alegre, G. Hernandez, G. Bullock, S. L. Thomson, T. Suter, B. 2025-09-30 doi:10.1101/2025.09.30.679481 Cold Spring Harbor Laboratory Press 2025-09-30 <![CDATA[ Thick filament molecular interfaces play a critical role in pathogenesis of hypertrophic and dilated cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2025.10.03.680256v1?rss=1 200 pathogenic and benign missense variants in these genes by mapping variants onto a cryo-EM-based atomic model of the human cardiac thick filament. We identified HCM variants residing in 31 molecular interfaces of the complex thick filament interactome, including the two main interfaces of the myosin interacting-heads motif (IHM), and interfaces involving the myosin heavy chain, essential and regulatory light chains, and cMyBP-C. Pathogenic DCM missense variants are rare, and altered only interfaces involving the myosin IHM and tails. None of the 21 variants classified as benign were within interfaces. We demonstrate earlier disease onset and adverse outcomes in HCM patients with pathogenic variants within versus outside of molecular interfaces, emphasizing their importance in normal thick filament function and improving risk stratification of patients. The dissimilar distribution of DCM and HCM variants could explain the different features of the two phenotypes. ]]> Dutta, D. Kim, Y. Ho, C. SHaRE Investigators, Seidman, J. Seidman, C. Craig, R. Padron, R. 2025-10-04 doi:10.1101/2025.10.03.680256 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Commensal Escherichia coli colonization triggers Peyer's patch development ]]> https://biorxiv.org/content/10.1101/2025.10.06.680803v1?rss=1 Gerner, R. R. Walker, G. T. Klaus, S. M. Melchior, K. Hossain, S. Siada, K. Hsu, C.-Y. Albicoro, F. J. Santus, W. Patkar, R. Carrillo-Terrazas, M. Norton, G. J. Thelen, F. Perez-Lopez, A. Sharma, P. Wong, M. P. Lei, V. Ransohoff, R. M. Lo, D. D. Lane, T. E. Reboldi, A. Nuccio, S.-P. Behnsen, J. Zuniga, E. I. Lu, L.-F. Tukel, C. Chu, H. Raffatellu, M. 2025-10-07 doi:10.1101/2025.10.06.680803 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Mutational scan of self-cleavage by HIV-1 protease provides new views of a conformationally dynamic mechanism ]]> https://biorxiv.org/content/10.1101/2025.10.07.680924v1?rss=1 Nachum, G. S. Boucher, J. I. Flynn, J. Quansah, P. Nachum, S. Bolon, D. N. 2025-10-07 doi:10.1101/2025.10.07.680924 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ A novel post-translational modification of fimbriae drives pathogenicity in Klebsiella pneumoniae ]]> https://biorxiv.org/content/10.1101/2025.10.03.680091v1?rss=1 Dobihal, G. S. Lewis, K. Yu, L. Herrera, C. Trent, M. S. Flores Kim, J. Uhlemann, A.-C. 2025-10-10 doi:10.1101/2025.10.03.680091 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Synergistic targeting of MCL1 and caspases for enhanced anti-tumor immunity in breast cancer. ]]> https://biorxiv.org/content/10.1101/2025.10.10.681458v1?rss=1 Yi, J. K. Lee, J.-S. Shaw, L. M. Kim, P. Spektor, A. 2025-10-10 doi:10.1101/2025.10.10.681458 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Cytokines of the Interleukin-1 superfamily and Interleukin-6 are associated with neuroinflammation and brain injury in Herpes Simplex Virus Encephalitis ]]> https://biorxiv.org/content/10.1101/2025.10.10.681150v1?rss=1 Egbe, F. N. Dunai, C. Hetherington, C. Boardman, S. A. Moreno, L. B. Facer, B. Hooper, C. Haw, D. Villani, A.-C. Lenzi, L. Haldenby, S. Patterson, S. Kurt-Jones, E. Luster, A. D. Solomon, T. Ellul, M. A. Michael, B. D. 2025-10-12 doi:10.1101/2025.10.10.681150 Cold Spring Harbor Laboratory Press 2025-10-12 <![CDATA[ QuickStainer: a rapid negative staining device for improved preservation of molecular structure ]]> https://biorxiv.org/content/10.1101/2025.10.11.681814v1?rss=1 Nguyen, V. Gautam, R. Somavarapu, A. Dutta, D. Patra, A. Ge, J. Yengo, C. Padron, R. Craig, R. 2025-10-13 doi:10.1101/2025.10.11.681814 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Multiplexed cytokine and antigen mRNA administration generates durable anti-tumor immunity against pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2025.10.13.681939v1?rss=1 Parikh, C. N. DeMarco, K. D. Kane, G. I. Bhalerao, N. Dinnell, R. W. Ma, B. Giwa, H. K. Zhao, Z. Zhou, L. Murphy, K. C. Chibaya, L. Mori, H. Qiao, Y. Lewis, B. C. Xue, W. Pitarresi, J. R. Atukorale, P. U. Ruscetti, M. 2025-10-14 doi:10.1101/2025.10.13.681939 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ The Impact of Malaria-Induced Neutrophil Subset Shift and a Link to Burkitt Lymphoma ]]> https://biorxiv.org/content/10.1101/2025.10.13.681992v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@1640dc4org.highwire.dtl.DTLVardef@1c3e794org.highwire.dtl.DTLVardef@98bf12org.highwire.dtl.DTLVardef@2851b8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Okoth, S. A. Tonui, R. K. Maina, T. K. Agwati, E. Oduor, C. I. Njuguna, F. M. Keitany, K. K. Chepsiror, D. Ayieko, C. Moormann, A. Kinyua, A. W. Forconi, C. S. 2025-10-14 doi:10.1101/2025.10.13.681992 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Murine Toll-like receptor 8 is a nucleic acid multi-sensor detecting 2',3'-cyclic monophosphate guanosine as well as combinations of ribo-, deoxy-, cyclic nucleotides, and nucleosides ]]> https://biorxiv.org/content/10.1101/2025.10.14.682277v1?rss=1 Hinkelmann, L. Brehm, M. Kumbol, V. McGurran, H. Krueger, C. Kleinau, G. Scheerer, P. Golenbock, D. Alexopoulou, L. Gantier, M. Bauer, S. Lehnardt, S. 2025-10-15 doi:10.1101/2025.10.14.682277 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ The shared selection landscape of dog and human cancers ]]> https://biorxiv.org/content/10.1101/2025.10.15.682624v1?rss=1 Genereux, D. P. MEGQUIER, K. Swofford, R. Turner-Maier, J. White, M. Sohrab, V. Husted, C. Gardner, H. Painter, C. London, C. Karlsson, E. 2025-10-15 doi:10.1101/2025.10.15.682624 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ αTAT1 defines a microtubule mechanosensing axis that drives fibroblast durotaxis and fibrosis across organs ]]> https://biorxiv.org/content/10.1101/2025.10.20.682962v1?rss=1 Santos, A. Islam, T. Chrysovergi, M.-A. Auernheimer, V. Al-Hilal, T. Lamas, S. Lagares, D. 2025-10-21 doi:10.1101/2025.10.20.682962 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ TDP-43 dysfunction leads to impaired proteostasis and predisposes mice to worse neurological outcomes after brain injury ]]> https://biorxiv.org/content/10.1101/2025.10.20.683438v1?rss=1 Rotunno, M. Fowler, M. Zhong, J. Ohara, K. Wiggin, E. Cameron, D. Stallworth, K. Bouley, J. McEachern, H. Anadolu, M. Nickerson, J. Tapper, A. Molas, S. Massi, F. Henninger, N. King, O. Bosco, D. 2025-10-21 doi:10.1101/2025.10.20.683438 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Virus-like particle capture reveals coordination of actin remodeling during Shigella flexneri entry by host proteins ]]> https://biorxiv.org/content/10.1101/2025.10.21.683715v1?rss=1 Chen, P. Goldberg, M. B. Gil-Marques, M. L. Fish, M. S. Pham, L. A. T. Kharbanda, V. Egger, K. T. 2025-10-21 doi:10.1101/2025.10.21.683715 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Exacerbation of a Subset of Behavioral Phenotypes by Early Treatment with AAV FOXG1 Gene Replacement Therapy in a Mouse Model of FOXG1 Syndrome ]]> https://biorxiv.org/content/10.1101/2025.10.22.683927v1?rss=1 Torturo, C. L. Kerker, K. Gresack, J. DeGrave, C. Du, A. Wang, D. Gao, G. Reich, S. Ramboz, S. Sah, D. W. Y. 2025-10-23 doi:10.1101/2025.10.22.683927 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Genome-wide CRISPR interference screen identifies Clip2 as a novel regulator of osteocyte maturation and morphology ]]> https://biorxiv.org/content/10.1101/2025.10.23.683957v1?rss=1 Mazur, C. M. Kotsalidis, P. E. George, M. Whalley, T. Sato, T. Doench, J. G. Surface, L. E. Wein, M. N. 2025-10-24 doi:10.1101/2025.10.23.683957 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ Cryo-EM Reveals How Cardiomyopathy Therapeutic Drugs Modulate the Myosin Motors of the Heart ]]> https://biorxiv.org/content/10.1101/2025.10.29.685122v1?rss=1 Somavarapu, A. K. Ge, J. Yengo, C. M. Craig, R. Padron, R. 2025-10-29 doi:10.1101/2025.10.29.685122 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ BCG vaccination elicits protection against Mtb infection mediated by two phases of T cell immunity ]]> https://biorxiv.org/content/10.1101/2025.10.28.685186v1?rss=1 Ogunsola, A. F. Lai, R. Cavallo, K. Beamer, G. L. Behar, S. M. 2025-10-30 doi:10.1101/2025.10.28.685186 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ VadK, a Non-Canonical Kinase that Regulates the Methylcitrate Cycle and is Essential for Mycobacterium tuberculosis Virulence ]]> https://biorxiv.org/content/10.1101/2025.10.30.685616v1?rss=1 Pascoe, J. Newcombe, J. Mendoza, J. Birua, S. Mendum, T. A. Anand, K. Singh, A. Sinha, A. Papavinasasundaram, K. Bhatt, A. Larrouy-Maumus, G. Singh, A. Goulding, C. W. Beste, D. J. 2025-10-30 doi:10.1101/2025.10.30.685616 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ CFDP1 is required for histone variant H2A.Z deposition by the human SRCAP chromatin remodeling complex ]]> https://biorxiv.org/content/10.1101/2025.10.30.685587v1?rss=1 Moro, N. Yang, D. Butty, V. L. Levine, S. S. Peterson, C. L. Boyer, L. A. Watanabe, S. 2025-10-31 doi:10.1101/2025.10.30.685587 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Gram-positive bacterial cell wall components inhibit herpes simplex virus infection. ]]> https://biorxiv.org/content/10.1101/2025.11.02.686169v1?rss=1 Adams, A. N. Griffin, L. E. Burnie, J. Powers, J. Causey, A. Glick, V. J. Gavitt, M. Richmond-Buccola, D. Kim, C. H. Ahmad, M. Jackson, M. Keiser, G. Cheng, J. L. Kumar, A. Fernando, L. D. Vlach, J. Orzalli, M. H. Corbett-Helaire, K. S. Decourt, A. Azadi, P. Gopinath, S. 2025-11-03 doi:10.1101/2025.11.02.686169 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Neutrophil Transcriptomics in SLE: Exploring Intrinsic, Ex Vivo Adaptation, and CAR T-Cell Therapy-Induced Changes ]]> https://biorxiv.org/content/10.1101/2025.11.03.686294v1?rss=1 Dehdashtian, E. Hu, G. Whiteman, L. Islam, M. T. Gallucci, S. Garber, M. Borie, D. Schett, G. Caricchio, R. 2025-11-05 doi:10.1101/2025.11.03.686294 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments ]]> https://biorxiv.org/content/10.1101/2025.11.06.687082v1?rss=1 Calvo-Roitberg, E. Lehman, J. W. Tam, E. Elhajjajy, S. Engelhardt, B. E. Pai, A. A. 2025-11-08 doi:10.1101/2025.11.06.687082 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Control of gene output by intron RNA structure ]]> https://biorxiv.org/content/10.1101/2025.11.08.687378v1?rss=1 Schärfen, L. Bech, P. Podszywałow-Bartnicka, P. Neugebauer, K. M. 2025-11-09 doi:10.1101/2025.11.08.687378 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ Depletion and recovery of IgG following treatment with Rozanoliximab and Imlifidase in pigtail macaques ]]> https://biorxiv.org/content/10.1101/2025.11.11.687913v1?rss=1 Rzasa, K. M. Zikos, J. Penney, T. Schiro, F. R. Doyle-Meyers, L. A. Aye, P. P. Veazey, R. S. Hoxie, J. A. Maness, N. J. Magnani, D. M. Ackerman, M. E. 2025-11-13 doi:10.1101/2025.11.11.687913 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Multi-dimensional regulation of LIN-28 temporal expression dynamics in the C. elegans heterochronic gene cascade ]]> https://biorxiv.org/content/10.1101/2025.11.13.688268v1?rss=1 Nelson, C. Ambros, V. 2025-11-14 doi:10.1101/2025.11.13.688268 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Reliable repurposing of antibody interactome inside the cell ]]> https://biorxiv.org/content/10.1101/2025.11.16.688718v1?rss=1 O'Shea, C. M. Shahzad, R. Aghasoleimani, K. Newman, S. Panmanee, J. Schalkwyk, L. C. Brooke, G. N. Benson, F. E. Trimmer, J. S. Bosco, D. Fujisawa, T. Ichijo, H. Cashman, N. R. Engel, S. Wright, G. S. A. 2025-11-16 doi:10.1101/2025.11.16.688718 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Inferring binding specificities of human transcription factors with the wisdom of crowds ]]> https://biorxiv.org/content/10.1101/2025.11.16.688692v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@1c6677corg.highwire.dtl.DTLVardef@b4124aorg.highwire.dtl.DTLVardef@1ce2b1org.highwire.dtl.DTLVardef@66e917_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gryzunov, N. Penzar, D. Kamenets, V. Vyaltsev, V. Kozin, I. Eliseeva, I. A. Nozdrin, V. Vorontsov, I. E. Bushuev, S. Strekalovskikh, V. Zinkevich, A. Andrews, G. Bedarew, M. Blass, I. Frolov, D. Lariushina, I. Moore, J. Orenstein, Y. Roev, G. Salimov, D. Shimshoviz, N. Tziony, I. Weng, Z. IBIS Consortium, GRECO-BIT/Codebook Consortium, Bucher, P. Deplancke, B. Fornes, O. Grau, J. Grosse, I. Jolma, A. Kolpakov, F. A. Makeev, V. J. Hughes, T. R. Kulakovskiy, I. V. 2025-11-17 doi:10.1101/2025.11.16.688692 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Condensin chromatin association is regulated by SMC head and hinge engagement and phosphorylation ]]> https://biorxiv.org/content/10.1101/2025.11.17.688780v1?rss=1 Miles, C. Yu, M. Schalbetter, S. Minchell, N. Sweet, S. Baxter, J. 2025-11-17 doi:10.1101/2025.11.17.688780 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Epo and hypoxia accelerate a pattern of gradual cell cycle shortening in BFU-e and CFU-e erythroid progenitors in vivo ]]> https://biorxiv.org/content/10.1101/2025.11.18.688855v1?rss=1 Winward, A. Lalonde, L. Nair, D. Socolovsky, M. 2025-11-18 doi:10.1101/2025.11.18.688855 Cold Spring Harbor Laboratory Press 2025-11-18 <![CDATA[ In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles ]]> https://biorxiv.org/content/10.1101/2025.11.25.690450v1?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. 2025-11-25 doi:10.1101/2025.11.25.690450 Cold Spring Harbor Laboratory Press 2025-11-25 <![CDATA[ Autoimmunity and H. pylori infection cooperatively promote epithelial tumorigenic differentiation and systemic immune modulation ]]> https://biorxiv.org/content/10.1101/2025.11.23.690054v1?rss=1 View larger version (17K): org.highwire.dtl.DTLVardef@1096623org.highwire.dtl.DTLVardef@1099e7org.highwire.dtl.DTLVardef@1e8493forg.highwire.dtl.DTLVardef@120e5d3_HPS_FORMAT_FIGEXP M_FIG C_FIG Background and contextAutoimmunity is emerging as a contributing factor for early-onset gastric cancer especially in young women, but it is unknown how it interacts with the most prevalent etiology factor, Helicobacter pylori. New findingsThis study provides the initial evidence that Helicobacter pylori and autoimmunity cooperatively cause long-lasting suppression of innate and adaptive immunity while promoting epithelial tumorigenic differentiation in the stomach. LimitationsEven with the murine-adapted Helicobacter pylori strain PMSS1, a human pathogen, the mouse modeling remains technically and conceptually challenging and can only capture some aspects of human Helicobacter pylori infection. Clinical research relevanceThis study showcases how autoimmunity predisposed by host genetics may cooperate with a prevalent environment factor, Helicobacter pylori, to promote gastric cancer development, with cellular and histopathological changes in the stomach, as well as local and systemic alteration of immune profiles. The lasting effects long after the elimination of Helicobacter pylori suggest the necessity of remedies besides Helicobacter pylori eradication. Basic research relevanceThis study provides molecular and cellular clues for how a convergence of autoimmunity and Helicobacter pylori cooperatively downregulates tumor suppressors in gastric epithelial cells while causing long-lasting suppression of innate and adaptive immunity. More studies are needed for better understanding of the interaction between Helicobacter pylori and autoimmunity, to help develop interventions against the alarming trend of early-onset gastric cancer. Lay summaryThis study provides initial insight into how autoimmunity and Helicobacter pylori in combination may impinge on multi-pronged effect on the stomach and the immune system to accelerate gastric cancer development. ]]> Vazquez, E. N. Lozano, C. Honan, A. M. Zaika, E. Houghton, J. El-Rifai, W. Zaika, A. Chen, Z. 2025-11-26 doi:10.1101/2025.11.23.690054 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ The pos-1 3' untranslated region governs germline specification and proliferation to ensure reproductive robustness ]]> https://biorxiv.org/content/10.1101/2025.11.26.690476v1?rss=1 Varderesian, H. V. Utaegbulam, J. N. Brown, H. E. Ramirez, B. Velcani, M. Ryder, S. P. 2025-11-28 doi:10.1101/2025.11.26.690476 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Loss of ADAMTS9 results in Nephronophthisis like polycystic kidneys by disrupting ciliogenesis and ECM dynamics ]]> https://biorxiv.org/content/10.64898/2025.12.02.691883v1?rss=1 Fischer, S. Robert, K. L. Ahmed, M. Kane, G. I. Atukorale, P. U. Nandadasa, S. 2025-12-03 doi:10.64898/2025.12.02.691883 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ SP140 limits type I interferon-driven pathology, preserving T cell motility and promoting resistance in tuberculosis ]]> https://biorxiv.org/content/10.64898/2025.12.05.692491v1?rss=1 Caouaille, M. Fromont, L. Shinkawa, T. Faucher, M. Abdul Hamid, A. I. Mazeres, S. Duverge, Y. Lorreyte, Y. Naser, E. Behar, S. M. Lefrancais, E. Neyrolles, O. Hudrisier, D. 2025-12-09 doi:10.64898/2025.12.05.692491 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Albumin-binding dendrimer-conjugated siRNA enables safe and effective gene silencing throughout the central nervous system ]]> https://biorxiv.org/content/10.64898/2025.12.16.694641v1?rss=1 Fakih, H. Ohara, M. Summers, A. Sarli, S. Kelly, K. Maru, B. Bramato, B. Khvorova, A. Watts, J. 2025-12-18 doi:10.64898/2025.12.16.694641 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ Insertion of rare autism variants in synaptic genes induce novel behavioral phenotypes in C. elegans ]]> https://biorxiv.org/content/10.64898/2025.12.19.695228v1?rss=1 Haskell, D. Haury, W. R. Granato, M. M. Bastien, B. L. Hart, M. P. 2025-12-21 doi:10.64898/2025.12.19.695228 Cold Spring Harbor Laboratory Press 2025-12-21 <![CDATA[ Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo ]]> https://biorxiv.org/content/10.64898/2025.12.22.695948v1?rss=1 CHEN, S. Loubiere, V. Hollingsworth, E. W. Jacinto, S. H. Dizehchi, A. Schreiber, J. Kvon, E. Z. Stark, A. 2025-12-24 doi:10.64898/2025.12.22.695948 Cold Spring Harbor Laboratory Press 2025-12-24 <![CDATA[ Prime Editing Models the MTARC1 A165T Variant in Human Liver Organoids, Demonstrating Reduced Steatosis, Inflammation, and Fibrosis ]]> https://biorxiv.org/content/10.64898/2025.12.23.696200v1?rss=1 Ben Saad, A. Weilheimer, A. D. Gentile, S. D. Arghiani, N. Toles, B. J. Tripathi, S. Mohsin Sayed, S. Chandraker, A. Mullen, A. C. 2025-12-25 doi:10.64898/2025.12.23.696200 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ HIV Nef amplifies mechanical heterogeneity to promote immune evasion ]]> https://biorxiv.org/content/10.64898/2025.12.24.696400v1?rss=1 Leyre, L. Mustapha, F. Herrera, A. Lee, E. Huntsman, E. Zumbo, P. Weiler, J. Sinha, P. Naing, E. Smith, C. Kovacs, C. Galiano, M. Wahman, N. Betel, D. Clayton, K. L. Huse, M. Jones, R. B. 2025-12-26 doi:10.64898/2025.12.24.696400 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Long-term high throughput agitation culturing with real-time metabolic profiling ]]> https://biorxiv.org/content/10.64898/2025.12.28.696554v1?rss=1 Lenzen, D. Holbrook, S. Kuan, D. Ling, Q. Tsai, C.-H. 2025-12-29 doi:10.64898/2025.12.28.696554 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Structural basis for non-AUG translation regulation by 5MPs ]]> https://biorxiv.org/content/10.64898/2025.12.28.696766v1?rss=1 Zottig, X. Huang, C.-Y. Seraj, Z. Grigorieff, N. Korostelev, A. A. 2025-12-29 doi:10.64898/2025.12.28.696766 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Structural basis for hydrolytic splicing of a circularly permuted group II intron ]]> https://biorxiv.org/content/10.64898/2025.12.30.696962v1?rss=1 Ling, X. Jinbiao, M. Fang, W. Chen, Z. 2025-12-30 doi:10.64898/2025.12.30.696962 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Multi-modal choroid plexus pathology in aging and Alzheimer's disease ]]> https://biorxiv.org/content/10.64898/2025.12.30.697051v1?rss=1 500 postmortem samples age 16 to 105, spatial transcriptomics, and functional studies in 5xFAD mice. We identify fibrosis, calcification, and macrophage abnormalities as hallmarks of ChP aging, with AD pathology conferring additional effects, including expansion of a pro-inflammatory fibroblast-macrophage signaling niche. In 5xFAD mice, macrophage dysfunction is associated with impaired epithelial barrier maintenance and repair. Together, these data provide a foundational resource for understanding ChP dysfunction in aging and AD and propose the macrophage-fibroblast-epithelial barrier axis as a driver of ChP pathology. ]]> Xu, H. Lotfy, P. Englert, B. Oberhauser, J. Byer, L. I. J. Wihlman, J. Colangelo, K. Okar, S. V. Thommana, A. Puttonen, H. Mäyränpää, M. I. Tuimala, J. Pedrosa, R. Kumar, D. Haberberger, J. F. Atkins, M. E. Alimukhamedov, S. Pragana, A. Benson, J. Gabrielle, M. E. Dong, A. DurantLaforet, V. Lin, P. B.-C. Keene, C. D. Latimer, C. S. Prater, K. E. Holtzman, D. M. Isakova, A. E. Wyss-Coray, T. Schafer, D. P. Reich, D. S. Lehtimäki, T. Karhunen, P. J. Kok, E. Jansson, D. Yang, A. C. Myllykangas, L. Ordovas-Montanes, J. Lehtinen, M. K. 2025-12-31 doi:10.64898/2025.12.30.697051 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Birth by Cesarean Section Remodels Neonatal Brain Barriers and Associated Immune and Metabolic Pathways in Mice ]]> https://biorxiv.org/content/10.64898/2026.01.06.696394v1?rss=1 Turpin, V. Morael, J. N. S. Cergneux, A. J. C. Blair, H. J. Ratsika, A. Guzzetta, K. E. Morales, L. Knox, E. G. Ventura-Silva, A. P. Majumdar, A. Cintado, E. Tessier, C. Shearer, J. Loftus, N. J. Armitage, E. G. Barnes, A. Clarke, G. Swann, J. R. Cryan, J. F. Aburto, M. R. 2026-01-07 doi:10.64898/2026.01.06.696394 Cold Spring Harbor Laboratory Press 2026-01-07 <![CDATA[ AlphaFold3-based modeling uncovers the dynamic structural interface between full-length IAP antagonists and DIAP1 for apoptosis regulation in Drosophila ]]> https://biorxiv.org/content/10.64898/2026.01.09.698746v1?rss=1 Rai, P. Bergmann, A. 2026-01-10 doi:10.64898/2026.01.09.698746 Cold Spring Harbor Laboratory Press 2026-01-10 <![CDATA[ Cell Death Induced by Homoisoflavonoid Brazilin and its Semi-synthetic Derivates on MDA-MB-231 and MCF7 Breast Cancer Cell Lines ]]> https://biorxiv.org/content/10.64898/2026.01.09.698710v1?rss=1 Zuniga-Eulogio, M. Quinteros, M. Hernandez-Moreno, A. Hernandez-Moreno, T. Sharma, T. Ordonez, M. Coste-Sanchez, C. PADILLA-BENAVIDES, T. Navarro-Tito, N. 2026-01-11 doi:10.64898/2026.01.09.698710 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ Single-cell RNA analysis reveals unexpected hemocyte plasticity and immune cell specialization in a Drosophila overgrowth model ]]> https://biorxiv.org/content/10.64898/2026.01.09.698745v1?rss=1 Yarikipati, P. Bergmann, A. 2026-01-11 doi:10.64898/2026.01.09.698745 Cold Spring Harbor Laboratory Press 2026-01-11 <![CDATA[ A hypothalamus-liver-skeletal muscle axis controlled by JNK1 and FGF21 mediates olanzapine-induced insulin resistance in an intraperitoneal treatment in male mice ]]> https://biorxiv.org/content/10.64898/2026.01.12.698937v1?rss=1 Ferreira, V. Folgueira, C. Hitos, A. B. Montes-San Lorenzo, A. Estevez-Salguero, A. Davis, R. J. Lopez, M. Sabio, G. Rada, P. Valverde, A. M. 2026-01-12 doi:10.64898/2026.01.12.698937 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ NR4A1 limits CD8⁺ T Cell effector responses and protection in tuberculosis ]]> https://biorxiv.org/content/10.64898/2026.01.12.699051v1?rss=1 Fatima, S. Chen, Y. Smulan, L. Satish, B. Jameson, M. Saini, S. Johnson, C. Tay, A. Shihui, F. Rahmathulla, H. Balachander, A. Howland, S. Kornfeld, H. Singhal, A. 2026-01-13 doi:10.64898/2026.01.12.699051 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ Multiomics reveals epigenetic control of fibroblast activity after myocardial infarction and a key role for RUNX transcription factors ]]> https://biorxiv.org/content/10.64898/2026.01.12.699153v1?rss=1 Li, Y. Zhang, X. Ghimire, K. Khatri, N. Wang, L. Liu, Q. Shiri, M. Shakoori, R. Upadhayaya, S. Li, B. Francis, J. Simintiras, C. A. Li, R. Sun, J. Fu, X. 2026-01-13 doi:10.64898/2026.01.12.699153 Cold Spring Harbor Laboratory Press 2026-01-13 <![CDATA[ Ift43 Controls the Ciliary Levels of Gli2 and Gli3 ]]> https://biorxiv.org/content/10.64898/2026.01.14.699321v1?rss=1 Stuck, M. W. Gupta, M. Knutson, L. N. Desai, P. B. Robert, K. L. Anuszczyk, J. J. Smith, A. O. Paulson, D. Nandadasa, S. Devine, W. Lo, C. W. Cox, T. Fink, D. M. Pazour, G. J. 2026-01-15 doi:10.64898/2026.01.14.699321 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity ]]> https://biorxiv.org/content/10.64898/2026.01.19.700311v1?rss=1 Liu, J. Gibcus, J. H. Dekker, J. 2026-01-20 doi:10.64898/2026.01.19.700311 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ C4BP occludes the non-opsonic interaction of Neisseria gonorrhoeae with human neutrophil CEACAMs ]]> https://biorxiv.org/content/10.64898/2026.01.19.700458v1?rss=1 Broden, M. W. Shaughnessy, J. Mohlin, F. Cardenas, A. J. Blom, A. M. Ram, S. Criss, A. K. 2026-01-20 doi:10.64898/2026.01.19.700458 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Tceal7 is a BRG1-regulated target of calcineurin signaling that promotes myoblast differentiation ]]> https://biorxiv.org/content/10.64898/2026.01.20.700469v1?rss=1 Yadav, S. Sharma, T. PADILLA-BENAVIDES, T. N. Imbalzano, A. N. 2026-01-21 doi:10.64898/2026.01.20.700469 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Reciprocal regulation between the protein arginine deiminases and mSWI/SNF chromatin remodelers controls skeletal muscle differentiation and regeneration ]]> https://biorxiv.org/content/10.64898/2026.01.20.700682v1?rss=1 Olea-Flores, M. Sharma, T. Parikh, A. Barasa, L. Hachmer, S. Dilworth, F. J. PADILLA-BENAVIDES, T. Thompson, P. Imbalzano, A. N. 2026-01-21 doi:10.64898/2026.01.20.700682 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ StrIPETrack: a real-time, ROI-flexible tracking platform for high-throughput zebrafish behavior ]]> https://biorxiv.org/content/10.64898/2026.01.29.702662v1?rss=1 Cummings, C. E. Bastien, B. L. Martinez, J. A. Luo, J. Thyme, S. B. 2026-01-30 doi:10.64898/2026.01.29.702662 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Functional Annotation of the Major Histocompatibility Complex Locus ]]> https://biorxiv.org/content/10.64898/2026.02.01.703124v1?rss=1 Bounds, L. R. Barrera, A. ter Weele, M. Liu, S. Wu, E. Li, S. Venukuttan, R. Rai, R. Mu, W. Iglesias, N. Giusti-Rodriguez, P. Reddy, T. E. Li, Y. Gordan, R. Allen, A. S. Love, M. I. Sullivan, P. F. Crawford, G. E. Gersbach, C. A. 2026-02-03 doi:10.64898/2026.02.01.703124 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming ]]> https://biorxiv.org/content/10.64898/2026.02.01.703129v1?rss=1 View larger version (34K): org.highwire.dtl.DTLVardef@b697b0org.highwire.dtl.DTLVardef@1a0b390org.highwire.dtl.DTLVardef@16ce710org.highwire.dtl.DTLVardef@b5d87a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Reisman, S. J. Zhu, W. Miller, S. E. Halabi, D. Sangvai, N. Crawford, G. E. Gordan, R. Gersbach, C. A. 2026-02-03 doi:10.64898/2026.02.01.703129 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ The CD8 immgenT framework as a universal reference of mouse CD8 Tαβ cell differentiation states ]]> https://biorxiv.org/content/10.64898/2026.02.02.703365v1?rss=1 200,000 single-cell transcriptomes and 128-plex surface proteomes from 734 samples spanning multiple perturbations, tissues, and timepoints. Unbiased analysis identifies 21 states encompassing naive, effector, circulating memory, tissue-resident memory, progenitor-exhausted, and terminally-exhausted compartments, among others. These states re-emerge with striking molecular convergence across acute/chronic infections, cancer, autoimmunity, aging, and homeostasis, showing that near-identical transcriptional programs support protective or dysfunctional outcomes depending on developmental history and microenvironment. Classic archetypes map to discrete clusters but exhibit unappreciated heterogeneity and overlap, cautioning against rigid nomenclature. We provide validated combinatorial markers, flow cytometry gating strategies, and immgenT reference-based integration for reproducible annotation of new datasets. This universal coordinate system harmonizes fragmented CD8 T cell literature and clarifies relationships across diverse immune challenges. ]]> Galletti, G. Globig, A.-M. Barreiro, O. Heim, T. A. Liu, S. Borys, S. M. Casey, O. Monell, A. T. Patravali, D. Scharping, N. E. Quon, S. Takehara, K. K. Ferry, A. Cheung, K. P. Duong, E. Shinkawa, T. Spranger, S. Behar, S. M. Kaech, S. M. Goldrath, A. W. Zemmour, D. ImmgenT Project, 2026-02-04 doi:10.64898/2026.02.02.703365 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in post-streptococcal encephalitis ]]> https://biorxiv.org/content/10.64898/2026.02.04.703836v1?rss=1 Wayne, C. R. Akcan, U. Faust, T. E. Duran-Laforet, V. Jamoul, D. Bremner, L. Ampatey, N. Akcan, B. Ho, S. J. Ciric, B. Delaney, S. Vargas, W. S. Swedo, S. Menon, V. Schafer, D. P. Cutforth, T. Agalliu, D. 2026-02-07 doi:10.64898/2026.02.04.703836 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Allele-specific rescue of neurexin behavioral phenotypes by monoamine-targeting compounds ]]> https://biorxiv.org/content/10.64898/2026.02.06.703315v1?rss=1 100 protein isoforms through alternative promoters and extensive splicing, which are differentially impacted by NRXN1 deletions found in patients. Yet pharmacologic targeting of NRXN1 isoforms or deletions has not been comprehensively studied. Here, we developed a behavioral screening approach in C. elegans to identify small molecule compounds that modify decreased activity levels caused by isoform-specific deletions of neurexin (nrx-1). Screening 190 compounds, we discovered that monoamine-targeting drugs differentially improve behavioral phenotypes depending on which nrx-1 isoforms are disrupted. Broad modulation of monoamine signaling or antagonism of specific serotonin receptors are required to increased activity of both alleles tested. Modulation of adrenergic signaling uniquely improved loss of -isoform, and additional antagonism of dopamine signaling was required to increase activity with loss of {gamma} isoform. The FDA-approved atypical antipsychotic olanzapine was the sole validated compound achieving Z-scores >2 in both screens. In Drosophila Nrx-1 mutants, olanzapine, but not the related compound asenapine maleate, significantly improved activity deficits, demonstrating evolutionary conservation of the neurexin-monoamine relationship. Multi-behavior testing revealed pharmacological specificity: olanzapine improved both activity and social feeding phenotypes of nrx-1 alleles, while asenapine maleate improved activity, but worsened social feeding, indicating distinct modifier impacts across behavioral domains. Our findings establish monoamine modulation as a conserved compensatory mechanism for neurexin loss, identify olanzapine as a lead compound for targeting neurexin loss, and demonstrate that allele stratification and pharmacogenomic approaches are needed for precision intervention in behavioral conditions. ]]> Smisko, W. R. Haury, W. R. Perni, M. Palo, J. Kalik, R. Bastien, B. L. Bilchak, J. N. Jongens, T. A. Kayser, M. S. Hart, M. P. 2026-02-07 doi:10.64898/2026.02.06.703315 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ Differential sex-dependent responses of circulating steroid hormones and cortical gene expression in a preclinical traumatic brain injury model ]]> https://biorxiv.org/content/10.64898/2026.02.06.703864v1?rss=1 Simmons, A. M. Wilferd, S. F. Campagnuolo, S. Pena, V. Bimonte-Nelson, H. Newbern, J. Sirianni, R. W. Plaisier, C. L. Stabenfeldt, S. E. 2026-02-09 doi:10.64898/2026.02.06.703864 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ EBV Type 1 versus Type 2: A determinant of NK cell anti-tumor activity in Burkitt lymphoma ]]> https://biorxiv.org/content/10.64898/2026.02.09.704808v1?rss=1 Forconi, C. S. Shumate, L. Racenet, Z. M'Bana, V. Oduor, C. Matta, A. Melo, J. Oluoch, P. O. Odwar, B. Otieno, J. Vik, T. A. N'juguna, F. Kinyua, A. W. Bailey, J. A. Munz, C. Moormann, A. M. 2026-02-10 doi:10.64898/2026.02.09.704808 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ High-throughput quantification of huntingtin mRNA expression and aggregation in mouse brain using automated RNAscope imaging. ]]> https://biorxiv.org/content/10.64898/2026.02.09.704866v1?rss=1 0.90) reflects variable probe binding along transcripts; for clusters, the linear scaling between cluster volume and mRNA content (R2 > 0.98) confirms uniform probe accessibility and enables quantitative conversion of fluorescence intensity to absolute mRNA counts. Applied to HttQ111+/- knock-in mice across multiple ages, we analyzed thousands of fields of view (FOVs), detecting >900,000 single mRNA molecules and segmenting >1.9 million mRNA clusters using two probes targeting mouse huntingtin (Htt): one detecting the spliced transcript that uses early cryptic polyadenylation sites in intron 1 (HTT1a), and one detecting full-length Htt (fl-HTT). Our analysis reveals considerable heterogeneity in mRNA accumulation: 16-63% of Q111 FOVs are classified as "extreme" (exceeding the 95th percentile of wildtype clustered mRNA levels), with striatum showing higher prevalence than cortex for both probes (HTT1a: 63% striatum, 31% cortex; fl-HTT: 44% striatum, 16%cortex). Extreme FOVs are characterized by elevated cluster numbers (2-6x more clusters per nucleus) and higher cluster density (1.3-1.7x more mRNA per {micro}m3). Cluster localization shows nuclear bias ([~]68%) in normal FOVs, but extreme FOVs exhibit a shift toward cytoplasmic localization, particularly for fl-HTT (48% nuclear vs 68% in normal FOVs), though the interpretation of this shift requires further investigation. Despite the large dataset at the cellular level, our study included only 11 mice (9 Q111, 2 wildtype), and this limited sample size precluded robust statistical inference at the animal level. Nevertheless, these quantitative metrics provide a framework for investigating disease mechanisms and evaluating therapeutic interventions using RNAscope in future studies with larger cohorts. ]]> van Velde, P. Tran, B. Allen, S. Luu, E. Furgal, R. Summers, A. Belgrad, J. Knox, E. Khvorova, A. Grunwald, D. 2026-02-11 doi:10.64898/2026.02.09.704866 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Organyl 5'-Phosphates in siRNA Guide Strands: Structure-Function Relationships Governing Anchoring in Argonaute 2 and Metabolic Stability ]]> https://biorxiv.org/content/10.64898/2026.02.13.705631v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@e6f88forg.highwire.dtl.DTLVardef@1c87dfaorg.highwire.dtl.DTLVardef@1c6e68corg.highwire.dtl.DTLVardef@14a1f60_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Carrigan-Broda, T. J. Gebert, L. F. R. Hildebrand, S. Yamada, N. Luu, E. Caiazzi, J. McHugh, N. Echeverria, D. Wagh, A. MacRae, I. J. Yamada, K. Khvorova, A. 2026-02-14 doi:10.64898/2026.02.13.705631 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Germline Blastomeres transcriptomics in the presence or absence of PIE-1 during C. elegans early embryogenesis ]]> https://biorxiv.org/content/10.64898/2026.02.14.705883v1?rss=1 Ponsard, P. Stubbe, F.-X. Tricquet, P. Mello, C. Hermand, D. 2026-02-14 doi:10.64898/2026.02.14.705883 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Breaking β-sheets in FUS prion-like domain preserves phase separation and function but prevents aggregation and toxicity ]]> https://biorxiv.org/content/10.64898/2026.02.17.706410v1?rss=1 View larger version (53K): org.highwire.dtl.DTLVardef@d15f63org.highwire.dtl.DTLVardef@1cd6221org.highwire.dtl.DTLVardef@e58126org.highwire.dtl.DTLVardef@181ec67_HPS_FORMAT_FIGEXP M_FIG C_FIG SUMMARYThe RNA-binding protein Fused in Sarcoma (FUS) undergoes phase separation as part of its physiological function but can aberrantly aggregate into solid-like assemblies in amyotrophic lateral sclerosis and frontotemporal dementia. To dissect the role of {beta}-sheets in both function and pathological transition, we engineered {beta}-sheet-preventing FUS variants via targeted proline residue insertions in the prion-like disordered region. These variants retained native structure, motions, and phase behavior yet showed dramatically reduced aggregation, both as an isolated prion-like domain and in full-length FUS. Crucially, these variants maintained a panel of FUS cellular functions that depend on FUS condensation but prevented FUS toxicity in fly models of neurodegeneration. Our findings implicate {beta}-sheets as key drivers of FUS condensate maturation and neuronal toxicity, highlighting {beta}-sheet modulation as a therapeutic strategy against FUS-related neurodegeneration. HIGHLIGHTSO_LITargeted proline additions disrupt {beta}-sheet formation in FUS without altering native conformations, dynamics, or phase separation behavior C_LIO_LI{beta}-sheet-deficient FUS variants prevent aggregation and liquid-to-solid transitions while retaining key biological functions C_LIO_LIIn vivo models reveal attenuated toxicity of {beta}-sheet-deficient FUS in Drosophila C_LIO_LI{beta}-sheets are identified as central drivers of condensate maturation and neuronal death, offering a therapeutic entry point for modulating prion-like domain pathology C_LI ]]> Wake, N. Alcalde, J. Jutzi, D. Bajaj, A. Kour, S. Barai, M. Weng, S.-L. Cummings, S. Zheng, T. Anderson, E. N. Wang, S.-H. Puterbaugh, R. Z. Bosco, D. A. Schuster, B. S. Mittal, J. Pandey, U. B. Ruepp, M.-D. Fawzi, N. L. 2026-02-18 doi:10.64898/2026.02.17.706410 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Zebrafish screen of schizophrenia risk genes reveals convergent dysregulation of cholesterol metabolism ]]> https://biorxiv.org/content/10.64898/2026.02.17.706411v1?rss=1 20 human schizophrenia-associated genes, including eight of the top ten SCHEMA genes, genes disrupted in childhood-onset schizophrenia (COS), and genes located within recurrent copy number variants. Whole-brain phospho-Erk activity mapping and behavioral profiling identified phenotypes in multiple mutant lines. We prioritized a protein-truncating mutation in sp4, which encodes an activity-dependent transcription factor, and a COS-associated missense mutation in atp1a3a, which encodes a Na+/K+ ATPase pump, for additional characterization. Both knockout and point mutations in atp1a3a disrupted brain activity and behavior in larvae and impaired navigation of a Y-maze in juveniles. Bulk RNA sequencing data from adult sp4 and atp1a3a brains highlighted convergent upregulation of sterol biosynthesis pathways, including increased expression of srebf2 and msmo1. Analysis of previously published telencephalon single-cell data demonstrated that cholesterol synthesis genes are enriched in astrocyte-like cells and increase in expression during post-larval development. Consistent with transcriptomic findings, filipin staining indicated increased free cholesterol in juvenile sp4 and atp1a3a mutant brains. Our findings identify dysregulation of glial and sterol-associated programs as a shared molecular consequence of two distinct schizophrenia risk mutations. Although whether sterol pathway dysregulation represents a primary pathogenic mechanism or a secondary response to changes in neuronal activity requires further investigation, the convergence observed between genetic models and developmental stages suggests that disruptions to lipid homeostasis could represent a shared feature of schizophrenia disease biology. ]]> Moyer, A. J. Capps, M. E. S. Conklin, C. L. Bastien, B. L. Martina, V. Gannaway, W. C. Cummings, C. E. Martinez, J. A. Chen, M. Kioschos, G. Torija-Olson, E. G. Klein, M. C. Vivian, M. D. Calhoun, C. C. S. Thyme, S. B. 2026-02-18 doi:10.64898/2026.02.17.706411 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Glycolytic Specialization Shapes Neuronal Physiology and Function in vivo ]]> https://biorxiv.org/content/10.64898/2026.02.17.706437v1?rss=1 Wolfe, A. D. Niu, L. Yilmaz, L. S. Ravikumar, S. Thomas, M. J. Walhout, A. J. M. Wang, Z.-W. Goodman, R. H. Colon-Ramos, D. A. 2026-02-18 doi:10.64898/2026.02.17.706437 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Targeting tRNA-Arg-TCT-4-1 suppresses cancer cell growth and tumorigenesis ]]> https://biorxiv.org/content/10.64898/2026.02.19.706891v1?rss=1 Orellana, E. A. Bowles, I. E. Yang, X. Torres, A. Jamieson, S. R. Ali, R. H. Gutierrez, A. Gregory, R. I. 2026-02-20 doi:10.64898/2026.02.19.706891 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Time in shells: Complex interaction between biological clock and biomineralisation in Mytilus galloprovincialis ]]> https://biorxiv.org/content/10.64898/2026.02.23.707208v1?rss=1 Louis, V. Peru, E. Paulin, C.-H. Lartaud, F. Besseau, L. 2026-02-24 doi:10.64898/2026.02.23.707208 Cold Spring Harbor Laboratory Press 2026-02-24 <![CDATA[ Elevating Neuronal CYLD Causes Frontotemporal Dementia (FTD)-Relevant Behavioral and Physiological Deficits ]]> https://biorxiv.org/content/10.64898/2026.02.24.707507v1?rss=1 Baral, A. Bilal, M. Dai, H. Jun, Y.-W. Almeida, S. Gao, F.-B. Yao, W.-D. 2026-02-26 doi:10.64898/2026.02.24.707507 Cold Spring Harbor Laboratory Press 2026-02-26 <![CDATA[ Transition from infectivity and immune escape to pure escape as an evolutionary strategy during the COVID-19 pandemic. ]]> https://biorxiv.org/content/10.64898/2026.02.26.706090v1?rss=1 Kotzen, B. Gurev, S. Youssef, N. Jaimes, J. Luban, J. Marks, D. Seaman, M. Lemieux, J. E. 2026-02-27 doi:10.64898/2026.02.26.706090 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Gene conversion is a key driver of diversity hotspots in M. tuberculosis antigens and virulence-associated loci ]]> https://biorxiv.org/content/10.64898/2026.02.26.708061v1?rss=1 Marin, M. G. Quinones-Olvera, N. Jin, H. Harris, M. A. Jeffrey, B. M. Rosenthal, A. Murphy, K. C. Sassetti, C. Li, H. Farhat, M. R. 2026-02-27 doi:10.64898/2026.02.26.708061 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Core circadian clock genes control molecular and behavioral circatidal rhythms in Parhyale hawaiensis ]]> https://biorxiv.org/content/10.64898/2026.02.27.708297v1?rss=1 Louis, V. Bellido, Z. Helfenbein, A. Rosenthal, J. J. C. Emery, P. 2026-03-02 doi:10.64898/2026.02.27.708297 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ Cbfb2 gene dosage programs the differential lymphoid lineage developmental potential of fetal and adult hematopoietic progenitors ]]> https://biorxiv.org/content/10.64898/2026.03.02.708762v1?rss=1 Berthelette, A. Newell, K. Phan, Q. Taniuchi, I. Kang, J. Frascoli, M. 2026-03-05 doi:10.64898/2026.03.02.708762 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ Arc Capsids Facilitate the Transfer of Muscleblind. ]]> https://biorxiv.org/content/10.64898/2026.03.06.708592v1?rss=1 Zinter, M. Xiao, C. M'Angale, P. G. Zhao-Shea, R. Freels, T. Tapper, A. Thomson, T. 2026-03-10 doi:10.64898/2026.03.06.708592 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Resolving thyroid lineage cell trajectories merging into a dual endocrine gland in mammals ]]> https://biorxiv.org/content/10.64898/2026.03.11.710917v1?rss=1 Lobo, M. Johansson, E. Kumari, S. Schoultz, E. Ahlinder, I. Liang, S. Carlsson, T. Johansson, B. R. Marotta, P. De Felice, M. Dahlberg, J. Guibentif, C. Fagman, H. Maehr, R. Nilsson, M. 2026-03-13 doi:10.64898/2026.03.11.710917 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Impaired Endosomal Recycling of Signaling Receptors Activates an Extracellular UPR ]]> https://biorxiv.org/content/10.64898/2026.03.12.711310v1?rss=1 Mallick, A. Du, Y. Haynes, C. M. 2026-03-13 doi:10.64898/2026.03.12.711310 Cold Spring Harbor Laboratory Press 2026-03-13 <![CDATA[ Nidogen/NID-1 guides regenerating motor axons in the mature nervous system ]]> https://biorxiv.org/content/10.64898/2026.03.13.711544v1?rss=1 Min, E. Huang, W. Byrne, A. B. 2026-03-17 doi:10.64898/2026.03.13.711544 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ Loss of C3 and CD14 reduces region-specific neuroinflammation in a murine polytrauma model ]]> https://biorxiv.org/content/10.64898/2026.03.13.711583v1?rss=1 Olde Heuvel, F. Pagliarini, M. Sun, F. Lupu, L. Zhao, Z. Cui, L. Halbgebauer, R. Mannes, M. Boeckers, T. Lien, E. Mollnes, T. E. Huber-Lang, M. Roselli, F. 2026-03-17 doi:10.64898/2026.03.13.711583 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ The glp-1 3' untranslated region regulates germline proliferation and promotes reproductive fecundity through multiple mechanisms ]]> https://biorxiv.org/content/10.64898/2026.03.23.713686v1?rss=1 Coskun, P. Ryder, S. P. 2026-03-25 doi:10.64898/2026.03.23.713686 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Folate Receptor α Contributes to Radiation Resistance in Neuroendocrine Prostate Cancer by Regulating Redox Homeostasis ]]> https://biorxiv.org/content/10.64898/2026.03.26.714502v1?rss=1 Goel, H. L. Wang, T. Dimitrov, B. S. Kumar, A. Silva, C. A. Fitzgerald, T. J. Mercurio, A. M. 2026-03-30 doi:10.64898/2026.03.26.714502 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Identifying Inheritance Patterns of Allelic Imbalance, using Integrative Modeling and Bayesian Inference ]]> https://biorxiv.org/content/10.64898/2026.03.28.714974v1?rss=1 Hoyt, S. H. Reddy, T. E. Gordan, R. Allen, A. S. Majoros, W. H. 2026-03-31 doi:10.64898/2026.03.28.714974 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Nanoparticle encapsulation enhances spatial distribution of Panobinostat to treat metastatic medulloblastoma via the intrathecal route ]]> https://biorxiv.org/content/10.64898/2026.03.31.715392v1?rss=1 Babayemi, O. Larson, J. D. Chaudhuri, S. Valesquez, F. Morton, J. Kuo, C.-F. Sablatura, L. K. Baquer, G. Reagan, M. S. Stopka, S. Sandberg, D. I. Agar, N. R. Sevick-Muraca, E. Wechsler-Reya, R. J. Sirianni, R. W. 2026-04-02 doi:10.64898/2026.03.31.715392 Cold Spring Harbor Laboratory Press 2026-04-02