bioRxiv Channel: Fred Hutchinson Cancer Center https://biorxiv.org This feed contains articles for bioRxiv Channel "Fred Hutchinson Cancer Center" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ The Rosetta all-atom energy function for macromolecular modeling and design ]]> https://biorxiv.org/content/10.1101/106054v1?rss=1 Alford, R. F. Leaver-Fay, A. Jeliazkov, J. R. O'Meara, M. J. DiMaio, F. P. Park, H. Shapovalov, M. V. Renfrew, P. D. Mulligan, V. K. Kappel, K. Labonte, J. W. Pacella, M. S. Bonneau, R. Bradley, P. Dunbrack, R. L. Das, R. Baker, D. Kuhlman, B. Kortemme, T. Gray, J. J. 2017-02-07 doi:10.1101/106054 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ BayesDeBulk: A Flexible Bayesian Algorithm for the Deconvolution of Bulk Tumor Data ]]> https://biorxiv.org/content/10.1101/2021.06.25.449763v1?rss=1 Petralia, F. Calinawan, A. P. Feng, S. Gosline, S. J. Pugliese, P. Ceccarelli, M. Wang, P. 2021-06-25 doi:10.1101/2021.06.25.449763 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ Multifactorial chromatin regulatory landscapes at single cell resolution ]]> https://biorxiv.org/content/10.1101/2021.07.08.451691v1?rss=1 Meers, M. P. Janssens, D. H. Henikoff, S. 2021-07-09 doi:10.1101/2021.07.08.451691 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Dynamic structural cell responses in the thymus to acute injury, regeneration, and age ]]> https://biorxiv.org/content/10.1101/2021.12.16.472014v1?rss=1 Jahn, L. L. Kousa, A. I. Sikkema, L. Flores, A. E. Argyropoulos, K. V. Tsai, J. Lazrak, A. Nichols, K. Lee, N. Malard, F. Andrlova, H. Gomes, A. L. Velardi, E. Youssef, S. da Silva, M. B. Docampo, M. Sharma, R. Mazoutis, L. Setty, M. Pe'er, D. Manley, N. R. Dudakov, J. A. van den Brink, M. R. 2021-12-17 doi:10.1101/2021.12.16.472014 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ KAT5 activity regulates G0-like states in human gliomas ]]> https://biorxiv.org/content/10.1101/2022.03.17.484768v1?rss=1 Mihalas, A. Arora, S. O'Connor, S. Feldman, H. Bassett, J. Mitchell, K. Jin, K. Hoellerbauer, P. Ling, M. Jenkins, W. Kufeld, M. Corrin, P. Carter, L. Aronow, B. J. Plaisier, C. J. Patel, A. PADDISON, P. 2022-03-19 doi:10.1101/2022.03.17.484768 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ A paracrine circuit of IL-1b/IL-1R1 between myeloid and tumor cells drives glioblastoma progression ]]> https://biorxiv.org/content/10.1101/2022.04.03.486888v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@1c99e57org.highwire.dtl.DTLVardef@1ba9d24org.highwire.dtl.DTLVardef@a2c418org.highwire.dtl.DTLVardef@1f8091c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, Z. Giotti, B. Kaluzova, M. Herting, C. Pinero, G. vallcorba, m. p. Cristea, S. Ross, J. L. Ackley, J. Maximov, V. Szulzewsky, F. Marquez-Ropero, M. Angione, A. Nichols, N. Tsankkova, N. Michor, F. Shayakhmetov, D. M. Gutmann, D. H. Tsankov, A. M. Hambardzumyan, D. 2022-04-05 doi:10.1101/2022.04.03.486888 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Cell wound repair requires the coordinated action of linear and branched actin nucleation factors ]]> https://biorxiv.org/content/10.1101/2022.04.14.488397v1?rss=1 Hui, J. Nakamura, M. Dubrulle, J. Parkhurst, S. M. 2022-04-14 doi:10.1101/2022.04.14.488397 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Robust Normalization and Integration of Single-cell Protein Expression across CITE-seq Datasets ]]> https://biorxiv.org/content/10.1101/2022.04.29.489989v1?rss=1 Zheng, Y. Jun, S.-H. Tian, Y. Florian, M. Gottardo, R. 2022-05-01 doi:10.1101/2022.04.29.489989 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation ]]> https://biorxiv.org/content/10.1101/2022.05.02.490302v1?rss=1 Khyzha, N. Henikoff, S. Ahmad, K. 2022-05-03 doi:10.1101/2022.05.02.490302 Cold Spring Harbor Laboratory Press 2022-05-03 <![CDATA[ Expression of YAP1-MAML2 and constitutively active YAP1 drive the formation of meningioma-like tumors in mice that resemble NF2-mutant meningiomas ]]> https://biorxiv.org/content/10.1101/2022.05.02.490337v1?rss=1 Szulzewsky, F. Arora, S. Arakaki, A. Sievers, P. Bonnin, D. A. A. Paddison, P. J. Sahm, F. Cimino, P. J. Gujral, T. Holland, E. C. 2022-05-02 doi:10.1101/2022.05.02.490337 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Targeting advanced prostate cancer with STEAP1 chimeric antigen receptor T cell therapy ]]> https://biorxiv.org/content/10.1101/2022.05.16.492156v1?rss=1 Bhatia, V. Kamat, N. V. Pariva, T. E. Wu, L.-T. Tsao, A. Sasaki, K. Wiest, L. T. Zhang, A. Rudoy, D. Gulati, R. Patel, R. A. Roudier, M. P. True, L. D. Haffner, M. C. Nelson, P. S. Priceman, S. J. Ishihara, J. Lee, J. K. 2022-05-17 doi:10.1101/2022.05.16.492156 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Liver humanized NSG-PiZ mice support the study of chronic hepatitis B virus infection and antiviral therapies ]]> https://biorxiv.org/content/10.1101/2022.05.17.492375v1?rss=1 Colon-Thillet, R. Stone, D. Loprieno, M. A. Klouser, L. Roychoudhury, P. Santo, T. K. Xie, H. Stensland, L. Upham, S. L. Pepper, G. Huang, M. Aubert, M. Jerome, K. R. 2022-05-17 doi:10.1101/2022.05.17.492375 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Oncogenic KRAS alters splicing factor phosphorylation and alternative splicing in lung cancer ]]> https://biorxiv.org/content/10.1101/2022.05.20.492866v1?rss=1 Lo, A. McSharry, M. Berger, A. 2022-05-20 doi:10.1101/2022.05.20.492866 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Chemical degradation of BTK/TEC as a novel approach to inhibit platelet function and thrombosis. ]]> https://biorxiv.org/content/10.1101/2022.05.30.493973v1?rss=1 Trory, J. S. Munkacsi, A. Sledz, K. Goudswaard, L. J. Heesom, K. J. Moore, S. F. Nabet, B. Aggarwal, V. K. Hers, I. 2022-05-30 doi:10.1101/2022.05.30.493973 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Gene amplification acts as a molecular foothold to facilitate cross-species adaptation and evasion of multiple antiviral pathways ]]> https://biorxiv.org/content/10.1101/2022.06.06.494757v1?rss=1 Banerjee, S. Smith, C. Geballe, A. P. Rothenburg, S. Kitzman, J. O. Brennan, G. 2022-06-08 doi:10.1101/2022.06.06.494757 Cold Spring Harbor Laboratory Press 2022-06-08 <![CDATA[ Helicobacter pylori chronic infection selects for effective colonizers of metaplastic glands ]]> https://biorxiv.org/content/10.1101/2022.06.13.496036v1?rss=1 O'Brien, V. P. Jackson, L. K. Frick, J. Rodriguez Martinez, A. E. Jones, D. S. Johnston, C. D. Salama, N. R. 2022-06-15 doi:10.1101/2022.06.13.496036 Cold Spring Harbor Laboratory Press 2022-06-15 <![CDATA[ Nucleosome patterns in circulating tumor DNA reveal transcriptional regulation of advanced prostate cancer phenotypes ]]> https://biorxiv.org/content/10.1101/2022.06.21.496879v1?rss=1 De Sarkar, N. Patton, R. D. Doebley, A.-L. Hanratty, B. Kreitzman, A. J. Sarthy, J. F. Ko, M. Adil, M. Brahma, S. Meers, M. P. Janssens, D. H. Ang, L. S. Coleman, I. Bose, A. Dumpit, R. F. Lucas, J. M. Nunez, T. A. Nguyen, H. M. McClure, H. M. Pritchard, C. C. Schweizer, M. T. Morrissey, C. Choudhury, A. D. Baca, S. C. Berchuck, J. E. Freedman, M. L. Ahmad, K. Haffner, M. C. Montgomery, B. Corey, E. Henikoff, S. Nelson, P. S. Ha, G. 2022-06-25 doi:10.1101/2022.06.21.496879 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ Cross-Protective Antibodies Against Common Endemic Respiratory Viruses ]]> https://biorxiv.org/content/10.1101/2022.06.26.497647v1?rss=1 Caban, M. Rodarte, J. Bibby, M. Gray, M. D. Taylor, J. J. Pancera, M. Boonyaratanakornkit, J. 2022-06-26 doi:10.1101/2022.06.26.497647 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ XDec Simplex Map of Breast Cancer Cell States Enables Precise Modeling and Targeting of Breast Cancer ]]> https://biorxiv.org/content/10.1101/2022.07.06.498858v1?rss=1 Murillo, O. D. Petrosyan, V. LaPlante, E. L. Dobrolecki, L. E. Lewis, M. T. Milosavljevic, A. 2022-07-07 doi:10.1101/2022.07.06.498858 Cold Spring Harbor Laboratory Press 2022-07-07 <![CDATA[ Transient T cell expansion, activation, and proliferation in therapeutically vaccinated SIV+ macaques treated with N-803 ]]> https://biorxiv.org/content/10.1101/2022.07.08.499199v1?rss=1 Harwood, O. E. Balgeman, A. J. Weaver, A. J. Ellis-Connell, A. L. Weiler, A. M. Erickson, K. N. Matschke, L. M. Golfinos, A. E. Vezys, V. Skinner, P. J. Safrit, J. T. Edlefsen, P. T. Reynolds, M. R. Friedrich, T. C. O'Connor, S. L. 2022-07-08 doi:10.1101/2022.07.08.499199 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ Extrachromosomal DNA in the cancerous transformation of Barrett's esophagus ]]> https://biorxiv.org/content/10.1101/2022.07.25.501144v1?rss=1 Luebeck, J. Ng, A. W. T. Galipeau, P. C. Li, X. Sanchez, C. A. Katz-Summercorn, A. Kim, H. Jammula, S. He, Y. Lippman, S. M. Verhaak, R. G. W. Maley, C. C. Alexandrov, L. B. Reid, B. J. Fitzgerald, R. C. Paulson, T. G. Chang, H. Y. Wu, S. Bafna, V. Mischel, P. S. 2022-07-25 doi:10.1101/2022.07.25.501144 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Deep molecular, cellular and temporal phenotyping of developmental perturbations at whole organism scale ]]> https://biorxiv.org/content/10.1101/2022.08.04.502764v1?rss=1 Saunders, L. M. Srivatsan, S. R. Duran, M. Dorrity, M. W. Ewing, B. Linbo, T. Shendure, J. Raible, D. Moens, C. B. Kimelman, D. Trapnell, C. 2022-08-05 doi:10.1101/2022.08.04.502764 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ State-dependent evolutionary models reveal modes of solid tumor growth ]]> https://biorxiv.org/content/10.1101/2022.08.05.502978v1?rss=1 Lewinsohn, M. A. Bedford, T. Müller, N. F. Feder, A. F. 2022-08-06 doi:10.1101/2022.08.05.502978 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency ]]> https://biorxiv.org/content/10.1101/2022.08.23.504195v1?rss=1 Hsieh, E. Janssens, D. H. Paddison, P. J. Browne, E. P. Henikoff, S. Ohainle, M. Emerman, M. 2022-08-23 doi:10.1101/2022.08.23.504195 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Safety switch optimization enhances antibody-mediated elimination of CAR T cells ]]> https://biorxiv.org/content/10.1101/2022.08.24.505164v1?rss=1 Shabaneh, T. B. Moffett, H. F. Stull, S. M. Derezes, T. Tait, L. J. Park, S. Riddell, S. R. Lajoie, M. J. 2022-08-24 doi:10.1101/2022.08.24.505164 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Receptor binding domain (RBD) antibodies contribute more to SARS-CoV-2 neutralization when target cells express high levels of ACE2 ]]> https://biorxiv.org/content/10.1101/2022.08.29.505713v1?rss=1 Farrell, A. G. Dadonaite, B. Greaney, A. J. Eguia, R. Loes, A. N. Francko, N. M. Logue, J. Carreno, J. M. Abbad, A. Chu, H. Y. Matreyek, K. A. Bloom, J. D. 2022-08-30 doi:10.1101/2022.08.29.505713 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Influenza virus transcription and progeny production are poorly correlated in single cells ]]> https://biorxiv.org/content/10.1101/2022.08.30.505828v1?rss=1 Bacsik, D. J. Dadonaite, B. Butler, A. Greaney, A. J. Heaton, N. S. Bloom, J. D. 2022-08-30 doi:10.1101/2022.08.30.505828 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ Fanconi anemia-isogenic head and neck cancer cell line pairs - a basic and translational science resource ]]> https://biorxiv.org/content/10.1101/2022.09.11.507488v1?rss=1 Nguyen, H. T. Tang, W. Webster, A. L. H. Whiteaker, J. R. Chandler, C. M. Errazquin, R. Sullivan, L. B. Jonlin, E. Hoskins, E. E. Chen, E. Y. Fritzke, M. Paulovich, A. G. Wells, S. I. Roohollahi, K. Dorsman, J. Brakenhoff, R. Garcia-Escudero, R. Smogorzewska, A. Wakefield, L. Grompe, M. Monnat, R. J. 2022-09-13 doi:10.1101/2022.09.11.507488 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ A biophysical model of viral escape from polyclonal antibodies ]]> https://biorxiv.org/content/10.1101/2022.09.17.508366v1?rss=1 Yu, T. C. Thornton, Z. T. Hannon, W. H. DeWitt, W. S. Radford, C. E. Matsen, F. A. Bloom, J. D. 2022-09-17 doi:10.1101/2022.09.17.508366 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains ]]> https://biorxiv.org/content/10.1101/2022.09.20.508745v1?rss=1 Starr, T. N. Greaney, A. J. Stewart, C. M. Walls, A. C. Hannon, W. W. Veesler, D. Bloom, J. D. 2022-09-20 doi:10.1101/2022.09.20.508745 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ A human-specific motif facilitates CARD8 inflammasome activation after HIV-1 infection ]]> https://biorxiv.org/content/10.1101/2022.10.04.510817v1?rss=1 Kulsuptrakul, J. Turcotte, E. Emerman, M. Mitchell, P. 2022-10-04 doi:10.1101/2022.10.04.510817 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ An optimized gene knock-out strategy for human CD34+ hematopoietic stem and progenitor cells. ]]> https://biorxiv.org/content/10.1101/2022.10.06.511235v1?rss=1 Kuppers, D. Linton, J. PADDISON, P. Rongvaux, A. 2022-10-07 doi:10.1101/2022.10.06.511235 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ MR1-restricted T cell clonotypes are associated with 'resistance' to M.tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2022.10.12.511825v1?rss=1 Cross, D. L. Layton, E. D. Yu, K. K. Smith, M. T. Aguilar, M. S. Li, S. Mayanja-Kizza, H. Stein, C. M. Boom, W. H. Hawn, T. R. Bradley, P. Newell, E. Seshadri, C. 2022-10-13 doi:10.1101/2022.10.12.511825 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike ]]> https://biorxiv.org/content/10.1101/2022.10.13.512056v1?rss=1 Dadonaite, B. Crawford, K. H. Radford, C. E. Farrell, A. G. Yu, T. C. Hannon, W. W. Zhou, P. Andrabi, R. Burton, D. R. Liu, L. Ho, D. D. Neher, R. A. Bloom, J. D. 2022-10-13 doi:10.1101/2022.10.13.512056 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants ]]> https://biorxiv.org/content/10.1101/2022.10.21.513237v1?rss=1 Desautels, T. A. Arrildt, K. T. Zemla, A. T. Lau, E. Y. Zhu, F. Ricci, D. Cronin, S. Zost, S. Binshtein, E. Scheaffer, S. M. Engdahl, T. B. Chen, E. Goforth, J. W. Vashchenko, D. Nguyen, S. Weilhammer, D. R. Lo, J. K.-Y. Rubinfeld, B. Saada, E. A. Weisenberger, T. Lee, T.-H. Whitener, B. Case, J. B. Ladd, A. Silva, M. S. Haluska, R. M. Grzesiak, E. A. Bates, T. W. Petersen, B. K. Thackray, L. B. Segelke, B. W. Lillo, A. M. Sundaram, S. Diamond, M. S. Crowe, J. E. Carnahan, R. H. Faissol, D. M. 2022-10-24 doi:10.1101/2022.10.21.513237 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation ]]> https://biorxiv.org/content/10.1101/2022.10.22.513040v1?rss=1 Schulz, M. Teissandier, A. de la Mata-Santaella, E. Armand, M. Iranzo, J. El Marjou, F. Gestraud, P. Walter, M. Kinston, S. Göttgens, B. Greenberg, M. V. C. Bourc'his, D. 2022-10-22 doi:10.1101/2022.10.22.513040 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Validation of antigen tetramers for the detection of antigen-specific B cells ]]> https://biorxiv.org/content/10.1101/2022.10.24.513230v1?rss=1 Fitzpatrick, K. S. Poljakov, K. Bibby, M. G. Remington, A. J. Gray, M. D. Boonyaratanakornkit, J. Taylor, J. J. 2022-10-24 doi:10.1101/2022.10.24.513230 Cold Spring Harbor Laboratory Press 2022-10-24 <![CDATA[ Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-κB binding ]]> https://biorxiv.org/content/10.1101/2022.10.25.513724v1?rss=1 50 million years ago (MYA)) before stabilizing since the separation of Old World monkeys (< 50 MYA). Taken together, our results suggest ancient and lineage-specific transposon subfamilies contributed to mammalian NF-{kappa}B regulatory networks. ]]> Wang, L. Alizada, A. Rathnakumar, K. Khyzha, N. Taylor, T. Campitelli, L. Patel, Z. M. Antounians, L. Hughes, T. Roy, S. Mitchell, J. A. Fish, J. E. Wilson, M. D. 2022-10-26 doi:10.1101/2022.10.25.513724 Cold Spring Harbor Laboratory Press 2022-10-26 <![CDATA[ Tracking the horizontal transfer of plasmids in Shigella sonnei and Shigella flexneri using phylogenetics ]]> https://biorxiv.org/content/10.1101/2022.10.27.514108v1?rss=1 Müller, N. F. Duchene, S. Williamson, D. A. Howden, B. Ingle, D. J. 2022-10-28 doi:10.1101/2022.10.27.514108 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ An information theoretic approach to detecting spatially varying genes ]]> https://biorxiv.org/content/10.1101/2022.11.02.514777v1?rss=1 Jones, D. C. Danaher, P. Kim, Y. Beechem, J. M. Gottardo, R. Newell, E. W. 2022-11-03 doi:10.1101/2022.11.02.514777 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ A Virus-Packageable CRISPR System Identifies Host Dependency Factors Across Multiple HIV-1 Strains ]]> https://biorxiv.org/content/10.1101/2022.11.03.515041v1?rss=1 Montoya, V. R. Ready, T. M. Felton, A. Fine, S. R. OhAinle, M. Emerman, M. 2022-11-04 doi:10.1101/2022.11.03.515041 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity ]]> https://biorxiv.org/content/10.1101/2022.11.03.515066v1?rss=1 Schofield, J. A. Hahn, S. 2022-11-04 doi:10.1101/2022.11.03.515066 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ G Protein-Coupled Receptor Kinase-2 (GRK-2) regulates exploration through neuropeptide signaling in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2022.11.05.515252v1?rss=1 Davis, K. Mitchell, C. Podhaisky, O. Bai, J. Raizen, D. M. Ailion, M. Topalidou, I. 2022-11-05 doi:10.1101/2022.11.05.515252 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Uptake of tumor-derived microparticles induces metabolic reprogramming of macrophages in the early metastatic lung. ]]> https://biorxiv.org/content/10.1101/2022.11.15.516217v1?rss=1 Kersten, K. You, R. Liang, S. Tharp, K. Pollack, J. Weaver, V. M. Krummel, M. F. Headley, M. B. 2022-11-17 doi:10.1101/2022.11.15.516217 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ The Centralspindlin proteins Pavarotti and Tumbleweed work with WASH to regulate Nuclear Envelope budding ]]> https://biorxiv.org/content/10.1101/2022.11.16.516846v1?rss=1 Davidson, K. A. Nakamura, M. Verboon, J. M. Parkhurst, S. M. 2022-11-17 doi:10.1101/2022.11.16.516846 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ FBXO42 activity is required to prevent mitotic arrest, spindle assembly checkpoint activation, and lethality in glioblastoma and other cancers ]]> https://biorxiv.org/content/10.1101/2022.11.29.518420v1?rss=1 Hoellerbauer, P. Kufeld, M. Arora, S. Girard, E. Herman, J. Olson, J. PADDISON, P. 2022-12-01 doi:10.1101/2022.11.29.518420 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Novel populations of Tr1 cells contribute to the resolution of acute influenza A virus infection. ]]> https://biorxiv.org/content/10.1101/2022.12.06.519368v1?rss=1 Abbott, C. A. Freimayer, E. L. Tyllis, T. S. Norton, T. S. Alsharifi, M. Heng, A. H. Pederson, S. M. Qu, Z. Armstrong, M. Hill, G. R. McColl, S. R. Comerford, I. 2022-12-06 doi:10.1101/2022.12.06.519368 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Statistical inference reveals the role of length, breathing, and nucleotide identity in V(D)J nucleotide trimming ]]> https://biorxiv.org/content/10.1101/2022.12.08.519635v1?rss=1 Russell, M. L. Simon, N. Bradley, P. Matsen, F. A. 2022-12-12 doi:10.1101/2022.12.08.519635 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection ]]> https://biorxiv.org/content/10.1101/2022.12.15.520606v1?rss=1 Guenthoer, J. Lilly, M. Starr, T. N. Dadonaite, B. Lovendahl, K. N. Croft, J. T. Stoddard, C. I. Chohan, V. Ding, S. Ruiz, F. Kopp, M. S. Finzi, A. Bloom, J. D. Chu, H. Y. Lee, K. K. Overbaugh, J. 2022-12-16 doi:10.1101/2022.12.15.520606 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Focal adhesion assembly requires phosphorylation signaling ]]> https://biorxiv.org/content/10.1101/2022.12.19.521109v1?rss=1 Kumar, S. Stainer, A. Dubrulle, J. Simpkins, C. Cooper, J. 2022-12-19 doi:10.1101/2022.12.19.521109 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Single-cell profiling uncovers a Muc4-expressing metaplastic gastric cell type sustained by Helicobacter pylori-specific inflammation ]]> https://biorxiv.org/content/10.1101/2022.12.20.521287v1?rss=1 O'Brien, V. P. Kang, Y. Shenoy, M. K. Finak, G. Young, W. C. Dubrulle, J. Koch, L. Martinez, A. E. R. Snow, J. A. Williams, J. Donato, E. Batra, S. K. Yeung, C. C. Bullman, S. Koch, M. A. Gottardo, R. Salama, N. R. 2022-12-20 doi:10.1101/2022.12.20.521287 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Recursive splicing discovery using lariats in total RNA sequencing ]]> https://biorxiv.org/content/10.1101/2022.12.22.521701v1?rss=1 Hoppe, E. R. Udy, D. B. Bradley, R. K. 2022-12-23 doi:10.1101/2022.12.22.521701 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Epithelia delimits glial apical polarity against mechanical shear to maintain glia-neuron architecture ]]> https://biorxiv.org/content/10.1101/2022.12.26.521704v1?rss=1 Martin, C. G. Bent, J. S. Singhvi, A. 2022-12-27 doi:10.1101/2022.12.26.521704 Cold Spring Harbor Laboratory Press 2022-12-27 <![CDATA[ An RNA seq-based reference landscape of human normal and neoplastic brain ]]> https://biorxiv.org/content/10.1101/2023.01.03.522658v1?rss=1 Arora, S. Szulzewsky, F. Jensen, M. Nuechterlein, N. Pattwell, S. S. Holland, E. C. 2023-01-03 doi:10.1101/2023.01.03.522658 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Functional genomic analysis of adult and pediatric brain tumor isolates ]]> https://biorxiv.org/content/10.1101/2023.01.05.522885v1?rss=1 900 cancer cell lines. ResultsWe found that >50% of candidate dependencies of 280 identified were shared between adult GBM tumors and individual pediatric tumor isolates. 68% of screen hits were found as nodes in our network models, along with shared and tumor-specific predictors of gene dependencies. We investigated network predictors associated with ADAR, EFR3A, FGFR1 (pediatric-specific), and SMARCC2 (ATRT-specific) gene dependency among our tumor isolates. ConclusionsThe results suggest that, despite harboring disparate genomic signatures, adult and pediatric tumor isolates share a preponderance of genetic dependences. Further, combining data from primary brain tumor lethality screens with large cancer cell line datasets produced valuable insights into biomarkers of gene dependency, even for rare cancers. Importance of the StudyOur results demonstrate that large cancer cell lines data sets can be computationally mined to identify known and novel gene dependency relationships in adult and pediatric human brain tumor isolates. Gene dependency networks and lethality screen results represent a key resource for neuro-oncology and cancer research communities. We also highlight some of the challenges and limitations of this approach. ]]> Hoellerbauer, P. Biery, M. Arora, S. Rao, Y. Girard, E. Mitchell, K. Dighe, P. Kufeld, M. Kuppers, D. Herman, J. Holland, E. Soroceanu, L. Vitanza, N. Olson, J. Pritchard, J. PADDISON, P. 2023-01-06 doi:10.1101/2023.01.05.522885 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Somatic mutation but not aneuploidy differentiates lung cancer in never-smokers and smokers. ]]> https://biorxiv.org/content/10.1101/2023.01.05.522947v1?rss=1 Moorthi, S. Paguirigan, A. Ko, M. Pettinger, M. Hoge, A. C. H. Nag, A. Patel, N. A. Wu, F. Sather, C. Fitzgibbon, M. P. Thorner, A. R. Anderson, G. L. Ha, G. Berger, A. H. 2023-01-06 doi:10.1101/2023.01.05.522947 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Genetics of Latin American Diversity (GLAD) Project: insights into population genetics and association studies in recently admixed groups in the Americas ]]> https://biorxiv.org/content/10.1101/2023.01.07.522490v1?rss=1 Borda, V. Loesch, D. P. Guo, B. Laboulaye, R. Veliz-Otani, D. French-Kwawu, J. N. Peixoto Leal, T. Gogarten, S. M. Ikpe, S. Gouveia, M. H. Mendes, M. Abecasis, G. R. Alvim, I. Arboleda-Bustos, C. E. Arboleda, G. Arboleda, H. Barreto, M. L. Barwick, L. Bezzera, M. A. Blangero, J. Borges, V. Caceres, O. Cai, J. Chana-Cuevas, P. Chen, Z. Custer, B. Dean, M. Dinardo, C. Domingos, I. Duggirala, R. Dieguez, E. Fernandez, W. Ferraz, H. B. Gilliland, F. D. Guio, H. Horta, B. Curran, J. E. Johnsen, J. M. Kaplan, R. C. Kelly, S. Kenny, E. E. Kittner, S. Konkle, 2023-01-09 doi:10.1101/2023.01.07.522490 Cold Spring Harbor Laboratory Press 2023-01-09 <![CDATA[ Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters ]]> https://biorxiv.org/content/10.1101/2023.01.09.523323v1?rss=1 Wooten, M. Takushi, B. Ahmad, K. Henikoff, S. 2023-01-10 doi:10.1101/2023.01.09.523323 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection ]]> https://biorxiv.org/content/10.1101/2023.01.10.523535v1?rss=1 Dwivedi, A. K. Siegel, D. A. Thanh, C. Hoh, R. Hobbs, K. S. Pan, T. Gibson, E. A. Martin, J. Hecht, F. Pilcher, C. Milush, J. Busch, M. P. Stone, M. Huang, M.-L. Levy, C. N. Roychoudhury, P. Hladik, F. Jerome, K. R. Henrich, T. J. Deeks, S. G. Lee, S. A. 2023-01-11 doi:10.1101/2023.01.10.523535 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ Damage-induced pyroptosis drives endogenous thymic regeneration viainduction of Foxn1 by purinergic receptor activation ]]> https://biorxiv.org/content/10.1101/2023.01.19.524800v1?rss=1 Kinsella, S. Evandy, C. A. Cooper, K. Cardinale, A. Iovino, L. deRoos, P. Hopwo, K. S. Smith, C. W. Granadier, D. W. Sullivan, L. B. Velardi, E. Dudakov, J. 2023-01-21 doi:10.1101/2023.01.19.524800 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ. ]]> https://biorxiv.org/content/10.1101/2023.01.19.524825v1?rss=1 Tsue, A. F. Kania, E. E. Lei, D. Q. Fields, R. McGann, C. C. Hershberg, E. A. Deng, X. Kihiu, M. Ong, S.-E. Disteche, C. M. Kugel, S. Beliveau, B. Schweppe, D. K. Shechner, D. M. 2023-01-20 doi:10.1101/2023.01.19.524825 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Single molecule visualization of native centromeric nucleosome formation reveals coordinated deposition by kinetochore proteins and centromere DNA sequence ]]> https://biorxiv.org/content/10.1101/2023.01.20.524981v1?rss=1 Popchock, A. Larson, J. Dubrulle, J. Asbury, C. L. Biggins, S. 2023-01-21 doi:10.1101/2023.01.20.524981 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Mitochondrial diabetes in mice expressing a dominant-negative allele of nuclear respiratory factor-1 (NRF-1) in pancreatic and β-cells ]]> https://biorxiv.org/content/10.1101/2023.01.22.524153v1?rss=1 Morrish, F. Sweet, I. R. Hockenbery, D. M. 2023-01-22 doi:10.1101/2023.01.22.524153 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ RNA Polymerase II, the BAF remodeler and transcription factors synergize to evict nucleosomes ]]> https://biorxiv.org/content/10.1101/2023.01.22.525083v1?rss=1 Brahma, S. Henikoff, S. 2023-01-22 doi:10.1101/2023.01.22.525083 Cold Spring Harbor Laboratory Press 2023-01-22 <![CDATA[ Polypharmacology-based kinome screen identifies new regulators of KSHV reactivation ]]> https://biorxiv.org/content/10.1101/2023.02.01.526589v1?rss=1 Olson, A. T. Kang, Y. Ladha, A. M. Lim, C. B. Lagunoff, M. Gujral, T. S. Geballe, A. P. 2023-02-01 doi:10.1101/2023.02.01.526589 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers ]]> https://biorxiv.org/content/10.1101/2023.02.06.527330v1?rss=1 Stoddard, C. I. Sung, K. Yaffe, Z. A. Weight, H. Beaudoin-Bussieres, G. Galloway, J. G. Gantt, S. Adhiambo, J. Begnel, E. R. Ojee, E. Slyker, J. Wamalwa, D. Kinuthia, J. Finzi, A. Matsen, F. A. Lehman, D. A. Overbaugh, J. 2023-02-07 doi:10.1101/2023.02.06.527330 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4+ T cells ]]> https://biorxiv.org/content/10.1101/2023.02.07.527545v1?rss=1 Itell, H. L. Humes, D. Overbaugh, J. 2023-02-07 doi:10.1101/2023.02.07.527545 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ The Regulation of Nucleic Acid Vaccine Responses by the Microbiome ]]> https://biorxiv.org/content/10.1101/2023.02.18.529093v1?rss=1 Johnson, A. M. F. Hager, K. Alameh, M.-G. Van, P. Potchen, N. Mayer-Blackwell, K. Fiore-Gartland, A. Minot, S. Lin, P. J. C. Tam, Y. K. Weissman, D. Kublin, J. G. 2023-02-19 doi:10.1101/2023.02.18.529093 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Validation of the association between MRI and gene signatures in facioscapulohumeral dystrophy muscle: implications for clinical trial design ]]> https://biorxiv.org/content/10.1101/2023.02.20.529303v1?rss=1 Wong, C.-J. Friedman, S. D. Snider, L. Bennett, S. R. Jones, T. I. Jones, P. L. Shaw, D. W. Blemker, S. S. Riem, L. DuCharme, O. Lemmers, R. J. van der Maarel, S. M. Wang, L. H. Tawil, R. Statland, J. M. Tapscott, S. J. 2023-02-20 doi:10.1101/2023.02.20.529303 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Multiplex Base Editing to Protect from CD33-Directed Therapy: Implications for Immune and Gene Therapy ]]> https://biorxiv.org/content/10.1101/2023.02.23.529353v1?rss=1 70%) multiplexed adenine base editing of the CD33 and gamma globin genes, resulting in long-term persistence of dual gene-edited cells with HbF reactivation in NHPs. In vitro, dual gene-edited cells could be enriched via treatment with the CD33 antibody-drug conjugate, gemtuzumab ozogamicin (GO). Together, our results highlight the potential of adenine base editors for improved immune and gene therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/529353v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@70c99dorg.highwire.dtl.DTLVardef@c46ef4org.highwire.dtl.DTLVardef@505fd2org.highwire.dtl.DTLVardef@c30b8c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Borot, F. Humbert, O. Newby, G. A. Fields, E. Kohli, S. Radtke, S. Laszlo, G. S. Mayuranathan, T. Ali, A. M. Weiss, M. J. Yen, J. S. Walter, R. B. Liu, D. R. Mukherjee, S. Kiem, H.-P. 2023-02-23 doi:10.1101/2023.02.23.529353 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Chromosome-specific maturation of the epigenome in the Drosophila male germline ]]> https://biorxiv.org/content/10.1101/2023.02.24.529909v1?rss=1 Anderson, J. Henikoff, S. Ahmad, K. 2023-02-25 doi:10.1101/2023.02.24.529909 Cold Spring Harbor Laboratory Press 2023-02-25 <![CDATA[ Hypercholesterolemia aggravates in-stent restenosis in rabbits: a mitigating effect of stent surface modification with CD47-derived peptide. ]]> https://biorxiv.org/content/10.1101/2023.02.27.530304v1?rss=1 Fishbein, I. Inamdar, V. V. Alferiev, I. S. Bratinov, G. Zviman, M. M. Yekhilevsky, A. Nagaswami, C. Gardiner, K. L. Levy, R. J. Stachelek, S. J. 2023-02-28 doi:10.1101/2023.02.27.530304 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Olfactory and neuropeptide inputs to appetite neurons in the arcuate nucleus ]]> https://biorxiv.org/content/10.1101/2023.02.28.530282v1?rss=1 Kuang, D. Hanchate, N. K. Lee, C.-Y. Heck, A. Ye, X. Erdenebileg, M. Buck, L. B. 2023-03-01 doi:10.1101/2023.02.28.530282 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut. ]]> https://biorxiv.org/content/10.1101/2023.02.28.530516v1?rss=1 Bohmann, N. Wilmanski, T. Levy, L. Lampe, J. Gurry, T. Rappaport, N. Diener, C. Gibbons, S. M. 2023-03-01 doi:10.1101/2023.02.28.530516 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Lethal giant larvae gene family (Llgl1 and Llgl2) functions as a tumor suppressor in mouse skin epidermis ]]> https://biorxiv.org/content/10.1101/2023.03.06.531408v1?rss=1 Bii, V. M. Rudoy, D. Klezovitch, O. Vasioukhin, V. 2023-03-08 doi:10.1101/2023.03.06.531408 Cold Spring Harbor Laboratory Press 2023-03-08 <![CDATA[ Diet-induced glial insulin resistance impairs the clearance of neuronal debris ]]> https://biorxiv.org/content/10.1101/2023.03.09.531940v1?rss=1 Alassaf, M. Rajan, A. 2023-03-10 doi:10.1101/2023.03.09.531940 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Neuron cilia constrain glial regulators to microdomains around distal neurons ]]> https://biorxiv.org/content/10.1101/2023.03.18.533255v1?rss=1 Ray, S. Gurung, P. Manning, R. S. Kravchuk, A. Singhvi, A. 2023-03-19 doi:10.1101/2023.03.18.533255 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ Quantification of elongation stalls and impact on gene expression in yeast ]]> https://biorxiv.org/content/10.1101/2023.03.19.533377v1?rss=1 Hou, W. Harjono, V. Harvey, A. T. Subramaniam, A. R. Zid, B. M. 2023-03-20 doi:10.1101/2023.03.19.533377 Cold Spring Harbor Laboratory Press 2023-03-20 <![CDATA[ Molecular heterogeneity of C. elegans glia across sexes ]]> https://biorxiv.org/content/10.1101/2023.03.21.533668v1?rss=1 Purice, M. D. Quitevis, E. J. A. Manning, R. S. Severs, L. J. Tran, N. T. Sorrentino, V. Setty, M. Singhvi, A. 2023-03-24 doi:10.1101/2023.03.21.533668 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning ]]> https://biorxiv.org/content/10.1101/2023.03.23.533993v1?rss=1 Radford, C. E. Schommers, P. Gieselmann, L. Crawford, K. H. Dadonaite, B. Yu, T. C. Dingens, A. S. Overbaugh, J. Klein, F. Bloom, J. D. 2023-03-24 doi:10.1101/2023.03.23.533993 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Cadherin-mediated cell-cell adhesion regulates collective pediatric glioma cell migration ]]> https://biorxiv.org/content/10.1101/2023.04.04.535599v1?rss=1 Kim, D. Olson, J. M. Cooper, J. A. 2023-04-05 doi:10.1101/2023.04.04.535599 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup ]]> https://biorxiv.org/content/10.1101/2023.04.05.535726v1?rss=1 500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life. ]]> Qiu, C. Martin, B. K. Welsh, I. C. Daza, R. M. Le, T.-M. Huang, X. Nichols, E. K. Taylor, M. L. Fulton, O. O'Day, D. R. Gomes, A. R. Ilcisin, S. Srivatsan, S. Deng, X. Disteche, C. M. Noble, W. S. Hamazaki, N. Moens, C. B. Kimelman, D. Cao, J. Schier, A. F. Spielmann, M. Murray, S. A. Trapnell, C. Shendure, J. 2023-04-05 doi:10.1101/2023.04.05.535726 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Antibodies that neutralize all current SARS-CoV-2 variants of concern by conformational locking ]]> https://biorxiv.org/content/10.1101/2023.04.08.536123v1?rss=1 Liu, L. Casner, R. G. Guo, Y. Wang, Q. Iketani, S. Chan, J. F.-W. Yu, J. Dadonaite, B. Nair, M. S. Mohri, H. Reddem, E. R. Yuan, S. Poon, V. K.-M. Chan, C. C.-S. Yuen, K.-Y. Sheng, Z. Huang, Y. Bloom, J. D. Shapiro, L. Ho, D. D. 2023-04-10 doi:10.1101/2023.04.08.536123 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses ]]> https://biorxiv.org/content/10.1101/2023.04.09.536175v1?rss=1 Lubow, J. Levoir, L. M. Ralph, D. K. Belmont, L. Contreras, M. Cartwright-Acar, C. H. Kikawa, C. Kannan, S. Davidson, E. Doranz, B. J. Duran, V. Sanchez, D. E. Sanz, A. M. Rosso, F. Einav, S. Matsen, F. A. Goo, L. 2023-04-11 doi:10.1101/2023.04.09.536175 Cold Spring Harbor Laboratory Press 2023-04-11 <![CDATA[ Estimating heritability explained by local ancestry and evaluating stratification bias in admixture mapping from summary statistics ]]> https://biorxiv.org/content/10.1101/2023.04.10.536252v1?rss=1 Chan, T. F. Rui, X. Conti, D. V. Fornage, M. Graff, M. Haessler, J. Haiman, C. Highland, H. M. Jung, S. Y. Kenny, E. Kooperberg, C. Le Marchland, L. North, K. E. Tao, R. Wojcik, G. Gignoux, C. R. PAGE Consortium, Chiang, C. W. Mancuso, N. 2023-04-10 doi:10.1101/2023.04.10.536252 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ ME-Bayes SL: Enhanced Bayesian Polygenic Risk Prediction Leveraging Information across Multiple Ancestry Groups ]]> https://biorxiv.org/content/10.1101/2023.04.12.536510v1?rss=1 Jin, J. Zhan, J. Zhang, J. Zhao, R. O'Connell, J. Jiang, Y. 23andMe Research Team, Buyske, S. Gignoux, C. R. Haiman, C. A. Kenny, E. Kooperberg, C. North, K. E. Koelsch, B. L. Wojcik, G. L. Zhang, H. Chatterjee, N. 2023-04-13 doi:10.1101/2023.04.12.536510 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Carcinoma-associated fibroblast-like tumor cells remodel the Ewing sarcoma tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2023.04.12.536619v1?rss=1 Wrenn, E. D. Apfelbaum, A. A. Rudzinski, E. R. Deng, X. Jiang, W. Sud, S. Van Noord, R. A. Newman, E. A. Garcia, N. M. Hoglund, V. J. Bhise, S. S. Kanaan, S. B. Waltner, O. G. Furlan, S. N. Lawlor, E. R. 2023-04-13 doi:10.1101/2023.04.12.536619 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations ]]> https://biorxiv.org/content/10.1101/2023.04.12.536652v1?rss=1 Li, S. Wong, A. Sun, H. Bhatia, V. Javier, G. Jana, S. Mongomery, R. B. Wright, J. L. Lam, H.-M. Hsieh, A. C. Faltas, B. M. Haffner, M. C. Lee, J. K. 2023-04-14 doi:10.1101/2023.04.12.536652 Cold Spring Harbor Laboratory Press 2023-04-14 <![CDATA[ Adenovirus protein VII binds the A-box of HMGB1 to repress interferon responses. ]]> https://biorxiv.org/content/10.1101/2023.04.17.537247v1?rss=1 Arnold, E. A. Kaai, R. J. Leung, K. Brinkley, M. R. Kelnhofer-Millevolte, L. E. Guo, M. S. Avgousti, D. C. 2023-04-18 doi:10.1101/2023.04.17.537247 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ CDK7 is a Novel Therapeutic Vulnerability in Fibrolamellar Carcinoma ]]> https://biorxiv.org/content/10.1101/2023.04.22.537934v1?rss=1 Nukaya, M. Cafferty, C. Zahed, K. Yun, I. Al-Adra, D. P. Kazim, N. A. Farghli, A. R. Chan, M. Kratz, J. D. Berres, M. E. Yen, A. Gujral, T. Sethupathy, P. Bradfield, C. A. Ronnekleiv-Kelly, S. M. 2023-04-23 doi:10.1101/2023.04.22.537934 Cold Spring Harbor Laboratory Press 2023-04-23 <![CDATA[ Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk ]]> https://biorxiv.org/content/10.1101/2023.04.24.538128v1?rss=1 Behera, S. Belyeu, J. Chen, X. Paulin, L. F. Nguyen, N. Q. Newman, E. Mahmoud, M. Menon, V. K. Qi, Q. Joshi, P. Marcovina, S. Rossi, M. Roller, E. Han, J. Onuchic, V. Avery, C. L. Ballantyne, C. M. Rodriguez, C. J. Kaplan, R. C. Muzny, D. M. Metcalf, G. A. Gibbs, R. Yu, B. Boerwinkle, E. Eberle, M. A. Sedlazeck, F. J. 2023-04-27 doi:10.1101/2023.04.24.538128 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Machine vision reveals micronucleus rupture as a potential driver of the transcriptomic response to aneuploidy ]]> https://biorxiv.org/content/10.1101/2023.05.04.539483v1?rss=1 DiPeso, L. Pendyala, S. Huang, H. Z. Fowler, D. M. Hatch, E. M. 2023-05-05 doi:10.1101/2023.05.04.539483 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Within-host rhinovirus evolution in upper and lower respiratory tract highlights capsid variability and mutation-independent compartmentalization ]]> https://biorxiv.org/content/10.1101/2023.05.11.540440v1?rss=1 Makhsous, N. Goya, S. Avendano, C. Rupp, J. Kuypers, J. Jerome, K. R. Boeckh, M. Waghmare, A. Greninger, A. L. 2023-05-11 doi:10.1101/2023.05.11.540440 Cold Spring Harbor Laboratory Press 2023-05-11 <![CDATA[ Oncogenic reactivation of young L1s is a hallmark of colon cancer ]]> https://biorxiv.org/content/10.1101/2023.05.17.541189v1?rss=1 Neu, D. Hung, S. Bartels, C. F. Faber, Z. J. Lovrenert, K. Pontius, W. D. Morgan, L. Chakraborty, M. Liao, W. Chin, D. Hong, E. S. Gray, J. Moreno, V. Kalady, M. Peters, U. Gryder, B. Sallari, R. C. Scacheri, P. C. 2023-05-21 doi:10.1101/2023.05.17.541189 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry ]]> https://biorxiv.org/content/10.1101/2023.05.24.542133v1?rss=1 Zimmer, J. T. Vock, I. W. Schofield, J. A. Kiefer, L. Moon, M. H. Simon, M. D. 2023-05-24 doi:10.1101/2023.05.24.542133 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Neural Network Models for Sequence-Based TCR and HLA Association Prediction ]]> https://biorxiv.org/content/10.1101/2023.05.25.542327v1?rss=1 Liu, S. Bradley, P. Sun, W. 2023-05-26 doi:10.1101/2023.05.25.542327 Cold Spring Harbor Laboratory Press 2023-05-26 <![CDATA[ Tracking the Metabolic Fate of Exogenous Arachidonic Acid in Ferroptosis Using Dual-Isotope Labeling Lipidomics ]]> https://biorxiv.org/content/10.1101/2023.05.28.542640v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@6bbc67org.highwire.dtl.DTLVardef@11e3a84org.highwire.dtl.DTLVardef@193ce6eorg.highwire.dtl.DTLVardef@d5b757_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Reimers, N. Do, Q. Zhang, R. Guo, A. Ostrander, R. Shoji, A. T. Vuong, C. Xu, L. 2023-05-28 doi:10.1101/2023.05.28.542640 Cold Spring Harbor Laboratory Press 2023-05-28 <![CDATA[ A single polymorphic residue in humans underlies species-specific restriction of HSV-1 by the antiviral protein MxB ]]> https://biorxiv.org/content/10.1101/2023.05.30.542951v1?rss=1 Bayer, A. Child, S. J. Malik, H. S. Geballe, A. P. 2023-05-30 doi:10.1101/2023.05.30.542951 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ A Highly Efficient and Faithful MDS Patient-Derived Xenotransplantation Model for Pre-Clinical Studies ]]> https://biorxiv.org/content/10.1101/265082v1?rss=1 Song, Y. Rongvaux, A. Taylor, A. Jiang, T. Tebaldi, T. Balasubramanian, K. Bagale, A. Terzi, Y. K. Gbyli, R. Wang, X. Zhao, J. Podoltsev, N. Xu, M. Neparidze, N. Wong, E. Torres, R. Bruscia, E. M. Kluger, Y. Manz, M. G. Flavell, R. A. Halene, S. 2018-02-14 doi:10.1101/265082 Cold Spring Harbor Laboratory Press 2018-02-14 <![CDATA[ Hierarchical modeling of the effect of pre-exposure prophylaxis on HIV in the US ]]> https://biorxiv.org/content/10.1101/285940v1?rss=1 Dale, R. Chen, Y. He, H. 2018-03-22 doi:10.1101/285940 Cold Spring Harbor Laboratory Press 2018-03-22 <![CDATA[ Comprehensive 2D and 3D phenotypic characterization of human invasive lobular carcinoma cell lines ]]> https://biorxiv.org/content/10.1101/341313v1?rss=1 Tasdemir, N. Bossart, E. Li, Z. Li, Z. Levine, K. M. Jacobsen, B. M. Tseng, G. C. Davidson, N. E. Oesterreich, S. 2018-06-07 doi:10.1101/341313 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ The splicing factor U2AF1 contributes to cancer progression through a non-canonical role in translation regulation ]]> https://biorxiv.org/content/10.1101/371492v1?rss=1 Palangat, M. Anastsakis, D. Liang, F. Lindblad, K. Bradley, R. Hourigan, C. Hafner, M. Larson, D. 2018-07-18 doi:10.1101/371492 Cold Spring Harbor Laboratory Press 2018-07-18 <![CDATA[ Identification of antibodies targeting the H3N2 hemagglutinin receptor binding site following vaccination of humans ]]> https://biorxiv.org/content/10.1101/675272v1?rss=1 Zost, S. J. Lee, J. Gumina, M. E. Parkhouse, K. Henry, C. Wilson, P. C. Bloom, J. D. Hensley, S. E. 2019-06-19 doi:10.1101/675272 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Software for the analysis and visualization of deep mutational scanning data ]]> https://biorxiv.org/content/10.1101/013623v1?rss=1 Jesse D Bloom 2015-01-10 doi:10.1101/013623 Cold Spring Harbor Laboratory Press 2015-01-10 <![CDATA[ Immunosequencing reveals diagnostic signatures of chronic viral infection in T cell memory ]]> https://biorxiv.org/content/10.1101/026567v1?rss=1 Ryan Emerson William DeWitt Marissa Vignali Jenna Gravley Cindy Desmarais Christoper Carlson John Hansen Mark Rieder Harlan Robins 2015-09-10 doi:10.1101/026567 Cold Spring Harbor Laboratory Press 2015-09-10 <![CDATA[ Conjecture: Some auto-immune diseases are caused by the tissue, not a problem with the immune system ]]> https://biorxiv.org/content/10.1101/032300v1?rss=1 Harlan S Robins 2015-11-20 doi:10.1101/032300 Cold Spring Harbor Laboratory Press 2015-11-20 <![CDATA[ Winners curse correction and variable thresholding improve performance of polygenic risk modeling based on summary-level data from genome-wide association studies ]]> https://biorxiv.org/content/10.1101/034082v1?rss=1 Jianxin Shi JuHyun Park Jubao Duan Sonja Berndt Winton Moy William Wheeler Xing Hua Debra Silverman Montserrat Garcia-Closas Chao Agnes Hsiung Jonine D. Figueroa Victoria K. Cortessis Nuria Malats Margaret R. Karagas Paolo Vineis I-Shou Chang Dongxin Lin Baosen Zhou Adeline Seow Keitaro Matsuo Yun-Chul Hong Neil E. Caporaso Brian Wolpin Eric Jacobs Gloria Petersen Donghui Li Harvey Risch Alan R. Sanders Li Hsu Robert E. Schoen Hermann Brenner Rachael Stolzenberg-Solomon Pablo Gejman Qing Lan Nathaniel Rothman Laufey T. Amundadottir Alison P. Klein Maria Teresa Landi Douglas F. Levinson Stephen 2016-01-10 doi:10.1101/034082 Cold Spring Harbor Laboratory Press 2016-01-10 <![CDATA[ Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population ]]> https://biorxiv.org/content/10.1101/038687v1?rss=1 Sujatha Jagannathan Robert K. Bradley 2016-02-04 doi:10.1101/038687 Cold Spring Harbor Laboratory Press 2016-02-04 <![CDATA[ Cryopreservation of human mucosal leukocytes ]]> https://biorxiv.org/content/10.1101/039578v1?rss=1 Sean M. Hughes Zhiquan Shu Claire N. Levy April L. Ferre Heather Hartig Cifeng Fang Gretchen Lentz Michael Fialkow Anna C Kirby Kristina M Adams Waldorf Ronald S Veazey Anja Germann Hagen von Briesen M. Juliana McElrath Charlene S Dezzutti Elizabeth Sinclair Chris A. R. Baker Barbara L Shacklett Dayong Gao Florian Hladik 2016-03-24 doi:10.1101/039578 Cold Spring Harbor Laboratory Press 2016-03-24 <![CDATA[ Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer ]]> https://biorxiv.org/content/10.1101/048215v1?rss=1 Safiye Celik Benjamin A Logsdon Stephanie Battle Charles W Drescher Mara Rendi David Hawkins Su-In Lee 2016-04-13 doi:10.1101/048215 Cold Spring Harbor Laboratory Press 2016-04-13 <![CDATA[ The validity of pairwise models in predicting community dynamics ]]> https://biorxiv.org/content/10.1101/060988v1?rss=1 Babak Momeni Li Xie Wenying Shou 2016-06-27 doi:10.1101/060988 Cold Spring Harbor Laboratory Press 2016-06-27 <![CDATA[ A compound interest approach to HIV cure ]]> https://biorxiv.org/content/10.1101/063305v1?rss=1 Daniel Reeves Elizabeth Duke Martin Prlic Florian Hladik Joshua Schiffer 2016-07-12 doi:10.1101/063305 Cold Spring Harbor Laboratory Press 2016-07-12 <![CDATA[ Massively parallel digital transcriptional profiling of single cells ]]> https://biorxiv.org/content/10.1101/065912v1?rss=1 Grace X.Y. Zheng Jessica M Terry Phillip Belgrader Paul Ryvkin Zachary W. Bent Ryan Wilson Solongo B. Ziraldo Tobias D. Wheeler Geoff P. McDermott Junjie Zhu Mark T. Gregory Joe Shuga Luz Montesclaros Donald A Masquelier Stefanie Y. Nishimura Michael Schnall-Levin Paul W Wyatt Christopher M. Hindson Rajiv Bharadwaj Alexander Wong Kevin D. Ness Lan W. Beppu Joachim Deeg Christopher McFarland Keith R. Loeb William J. Valente Nolan G. Ericson Emily A. Stevens Jerald P. Radich Tarjei S. Mikkelsen Benjamin J. Hindson Jason H Bielas 2016-07-26 doi:10.1101/065912 Cold Spring Harbor Laboratory Press 2016-07-26 <![CDATA[ Experimental estimation of the effects of all amino-acid mutations to HIV Env ]]> https://biorxiv.org/content/10.1101/067470v1?rss=1 Hugh K Haddox Adam S Dingens Jesse Bloom 2016-08-02 doi:10.1101/067470 Cold Spring Harbor Laboratory Press 2016-08-02 <![CDATA[ Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA ]]> https://biorxiv.org/content/10.1101/071969v1?rss=1 Orr Ashenberg Jai Padmakumar Michael B Doud Jesse Bloom 2016-08-28 doi:10.1101/071969 Cold Spring Harbor Laboratory Press 2016-08-28 <![CDATA[ Seasonal influenza circulation patterns and projections for 2016-2017 ]]> https://biorxiv.org/content/10.1101/076638v1?rss=1 Trevor Bedford Richard Neher 2016-09-21 doi:10.1101/076638 Cold Spring Harbor Laboratory Press 2016-09-21 <![CDATA[ Complete mapping of viral escape from neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/086611v1?rss=1 Doud, M. B. Hensley, S. E. Bloom, J. D. 2016-11-09 doi:10.1101/086611 Cold Spring Harbor Laboratory Press 2016-11-09 <![CDATA[ Modern-Day SIV viral diversity generated by extensive recombination and cross-species transmission ]]> https://biorxiv.org/content/10.1101/101725v1?rss=1 Bell, S. M. Bedford, T. 2017-01-19 doi:10.1101/101725 Cold Spring Harbor Laboratory Press 2017-01-19 <![CDATA[ Seasonal influenza circulation patterns and projections for 2017-2018 ]]> https://biorxiv.org/content/10.1101/113035v1?rss=1 Bedford, T. Neher, R. A. 2017-03-02 doi:10.1101/113035 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ Genetic characterization of the Zika virus epidemic in the US Virgin Islands ]]> https://biorxiv.org/content/10.1101/113100v1?rss=1 Black, A. Potter, B. Dudas, G. Feldstein, L. Grubaugh, N. D. Andersen, K. G. Ellis, B. R. Ellis, E. M. Bedford, T. 2017-03-03 doi:10.1101/113100 Cold Spring Harbor Laboratory Press 2017-03-03 <![CDATA[ Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody ]]> https://biorxiv.org/content/10.1101/117705v1?rss=1 Dingens, A. S. Haddox, H. K. Overbaugh, J. Bloom, J. D. 2017-03-18 doi:10.1101/117705 Cold Spring Harbor Laboratory Press 2017-03-18 <![CDATA[ Brain connectivity-informed regularization methods for regression ]]> https://biorxiv.org/content/10.1101/117945v1?rss=1 Karas, M. Brzyski, D. Dzemidzic, M. Goni, J. Kareken, D. A. Randolph, T. W. Harezlak, J. 2017-03-18 doi:10.1101/117945 Cold Spring Harbor Laboratory Press 2017-03-18 <![CDATA[ Phandango: an interactive viewer for bacterial population genomics. ]]> https://biorxiv.org/content/10.1101/119545v1?rss=1 Hadfield, J. Croucher, N. J. Goater, R. J. Abudahab, K. Aanensen, D. M. Harris, S. R. 2017-03-22 doi:10.1101/119545 Cold Spring Harbor Laboratory Press 2017-03-22 <![CDATA[ phydms: Software for phylogenetic analyses informed by deep mutational scanning ]]> https://biorxiv.org/content/10.1101/121830v1?rss=1 Hilton, S. K. Doud, M. B. Bloom, J. D. 2017-03-29 doi:10.1101/121830 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ Comprehensive characterization of pediatric acute myeloid leukemia reveals novel molecular features and age-specific interactions ]]> https://biorxiv.org/content/10.1101/125609v1?rss=1 2% of cases. In contrast, somatic structural variants, including novel gene fusions and focal MBNL1, ZEB2, and ELF1 deletions, were disproportionately prevalent in young as compared to adult patients. Conversely, DNMT3A and TP53 mutations, common in adults, are conspicuously absent from virtually all pediatric cases. Novel GATA2, FLT3, and CBL mutations, recurrent MYC-ITD, NRAS, KRAS, and WT1 mutations are frequent in pediatric AML. Deletions, mutations, and promoter DNA hypermethylation convergently impact Wnt signaling, Polycomb repression, innate immune cell interactions, and a cluster of zinc finger genes associated with KMT2A rearrangements. These results highlight the need for, and facilitate the development of age-tailored targeted therapies for the treatment of pediatric AML. ]]> Bolouri, H. Farrar, J. E. Triche, T. J. Ries, R. E. Lim, E. L. Alonzo, T. A. Ma, Y. Moore, R. Mungall, A. Marra, M. A. Zhang, J. Ma, X. Liu, Y. Liu, Y. Guidry Auvil, J. M. Davidsen, T. M. Gesuwan, P. Hermida, L. C. Salhia, B. Capone, S. Ramsingh, G. Zwaan, C. M. Noort, S. Piccolo, S. Kolb, E. A. Gamis, A. S. Smith, M. A. Gerhard, D. S. Meshinchi, S. 2017-06-13 doi:10.1101/125609 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Mapping Tumor-Specific Expression QTLs In Impure Tumor Samples ]]> https://biorxiv.org/content/10.1101/136614v1?rss=1 Wilson, D. R. Sun, W. Ibrahim, J. G. 2017-05-11 doi:10.1101/136614 Cold Spring Harbor Laboratory Press 2017-05-11 <![CDATA[ Biochemical Adaptations Of The Retina And Retinal Pigment Epithelium Support A Metabolic Ecosystem In The Vertebrate Eye ]]> https://biorxiv.org/content/10.1101/143347v1?rss=1 Kanow, M. A. Giarmarco, M. M. Jankowski, C. Tsantilas, K. Engel, A. L. Du, J. Linton, J. D. Farnsworth, C. C. Sloat, S. R. Lindsay, K. J. Parker, E. D. Brockerhoff, S. E. Sadilek, M. Chao, J. R. Hurley, J. B. 2017-05-29 doi:10.1101/143347 Cold Spring Harbor Laboratory Press 2017-05-29 <![CDATA[ HIV persistence during antiviral therapy occurs due to cellular proliferation ]]> https://biorxiv.org/content/10.1101/146977v1?rss=1 99% of infected cells are members of clonal populations after one year of ART. We reconcile our results with observations from the first months of ART, demonstrating mathematically how a "fossil record" of historic HIV replication permits observed viral evolution even while most new infected cells arise from proliferation. Together, our results imply cellular proliferation generates a majority of infected cells during ART. Therefore, reducing proliferation could decrease the size of the HIV reservoir and help achieve a functional cure. ]]> Reeves, D. B. Duke, E. R. Wagner, T. A. Palmer, S. E. Spivak, A. M. Schiffer, J. T. 2017-06-07 doi:10.1101/146977 Cold Spring Harbor Laboratory Press 2017-06-07 <![CDATA[ Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/165639v1?rss=1 Meers, M. P. Adelman, K. Duronio, R. J. Strahl, B. D. McKay, D. J. Matera, A. G. 2017-07-19 doi:10.1101/165639 Cold Spring Harbor Laboratory Press 2017-07-19 <![CDATA[ Expanding the Atlas of Functional Missense Variation for Human Genes ]]> https://biorxiv.org/content/10.1101/166595v1?rss=1 Weile, J. Sun, S. Cote, A. G. Knapp, J. Verby, M. Mellor, J. C. Wu, Y. Pons, C. Wong, C. van Lieshout, N. Yang, F. Tasan, M. Tan, G. Yang, S. Fowler, D. M. Nussbaum, R. Bloom, J. D. Vidal, M. Hill, D. E. Aloy, P. Roth, F. P. 2017-07-27 doi:10.1101/166595 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ beachmat: a Bioconductor C++ API for accessing single-cell genomics data from a variety of R matrix types ]]> https://biorxiv.org/content/10.1101/167445v1?rss=1 Lun, A. T. L. Pages, H. Smith, M. L. 2017-07-24 doi:10.1101/167445 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018 ]]> https://biorxiv.org/content/10.1101/191676v1?rss=1 3 years, but 3c3.a viruses continue to persist. The common ancestor of circulating H3N2 viruses is now more than 5 years old, which is rare for H3N2. Despite extensive genetic diversity, serological assays suggest limited, but non-zero, antigenic evolution. We expect multiple competing clades within 3c2.a to persist into the future with no clear immediate winner.nnA/H1N1pdmA clade comprising mutations S74R and I295V has recently risen to >60% global frequency. Although it shows no antigenic distinction by ferret HI data, the rapidity of its rise suggests a selective origin.nnB/VicA clade with a two amino acid deletion 162-/163-has altered serological properties and is increasing in frequency, albeit slowly. Two other clades (carrying mutations K209N and V87A/I175V) have increased in frequency moderately.nnB/YamA clade comprising M251V within clade 3 viruses continues to dominate. The is little genetic differentiation within this clade and no evidence of antigenic evolution. ]]> Bedford, T. Neher, R. 2017-09-26 doi:10.1101/191676 Cold Spring Harbor Laboratory Press 2017-09-26 <![CDATA[ Extreme heterogeneity of influenza virus infection in single cells ]]> https://biorxiv.org/content/10.1101/193995v1?rss=1 Russell, A. B. Trapnell, C. Bloom, J. D. 2017-09-27 doi:10.1101/193995 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ A high-throughput screen for transcription activation domains reveals their sequence characteristics and permits reliable prediction by deep learning ]]> https://biorxiv.org/content/10.1101/2019.12.11.872986v1?rss=1 Erijman, A. Kozlowski, L. Sohrabi-Jahromi, S. Fishburn, J. Warfield, L. Schreiber, J. Noble, W. S. Soeding, J. Hahn, S. 2019-12-12 doi:10.1101/2019.12.11.872986 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Wash and the WASH Regulatory Complex function in Nuclear Envelope budding ]]> https://biorxiv.org/content/10.1101/2019.12.18.881763v1?rss=1 Verboon, J. M. Nakamura, M. Decker, J. R. Davidson, K. A. Nandakumar, V. Parkhurst, S. M. 2019-12-19 doi:10.1101/2019.12.18.881763 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Single-Cell Map of Diverse Immune Phenotypes in the Metastatic Brain Tumor Microenvironment of Non Small Cell Lung Cancer ]]> https://biorxiv.org/content/10.1101/2019.12.30.890517v1?rss=1 Wang, L. Dai, J. Han, R.-R. Dong, L. Feng, D. Zhu, G. Guo, W. Wang, Y. Chao, M. Jin, M.-Z. Jin, S.-J. Wei, D.-P. Sun, W. Jin, W.-L. 2019-12-30 doi:10.1101/2019.12.30.890517 Cold Spring Harbor Laboratory Press 2019-12-30 <![CDATA[ BAF facilitates interphase nuclear envelope repair through recruitment of nuclear transmembrane proteins. ]]> https://biorxiv.org/content/10.1101/2020.01.10.902296v1?rss=1 Young, A. M. Gunn, A. L. Hatch, E. M. 2020-01-11 doi:10.1101/2020.01.10.902296 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Individual yeast cells signal at different levels but each with good precision ]]> https://biorxiv.org/content/10.1101/2020.01.15.906867v1?rss=1 Andrews, S. S. Brent, R. 2020-01-15 doi:10.1101/2020.01.15.906867 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Mechanical Instability of Adherens Junctions Overrides Intrinsic Quiescence of Hair Follicle Stem Cells ]]> https://biorxiv.org/content/10.1101/2020.01.17.909937v1?rss=1 Biswas, R. Banerjee, A. Lembo, S. Zhao, Z. Lakshmanan, V. Nakasaki, M. Kutyavin, V. Wright, G. Palakodeti, D. Ross, R. Jamora, C. Vasioukhin, V. Yan, J. Raghavan, S. 2020-01-17 doi:10.1101/2020.01.17.909937 Cold Spring Harbor Laboratory Press 2020-01-17 <![CDATA[ Estimation of Full-Length TprK Diversity in Treponema pallidum subspecies pallidum ]]> https://biorxiv.org/content/10.1101/2020.01.23.917484v1?rss=1 Addetia, A. Lin, M. J. Phung, Q. Xie, H. Huang, M. Ciccarese, G. Dal Conte, I. Cusini, M. Drago, F. Giacani, L. Greninger, A. L. 2020-01-24 doi:10.1101/2020.01.23.917484 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Continual inactivation of stem cell functional identity genes stabilizes progenitor commitment ]]> https://biorxiv.org/content/10.1101/2020.02.03.931972v1?rss=1 Quinto-Rives, N. Komori, H. Janssens, D. H. Kondo, S. Dai, Q. Moore, A. W. Lee, C.-Y. 2020-02-03 doi:10.1101/2020.02.03.931972 Cold Spring Harbor Laboratory Press 2020-02-03 <![CDATA[ Polymorphisms in human APOBEC3H differentially regulate ubiquitination and antiviral activity ]]> https://biorxiv.org/content/10.1101/2020.02.07.939439v1?rss=1 Chesarino, N. M. Emerman, M. 2020-02-09 doi:10.1101/2020.02.07.939439 Cold Spring Harbor Laboratory Press 2020-02-09 <![CDATA[ Optimal timing for cancer screening and adaptive surveillance using mathematical modeling ]]> https://biorxiv.org/content/10.1101/2020.02.11.927475v1?rss=1 50 years). These ages are in a cost-effective range to start screening and were independently validated by data used in current guidelines. Our framework captures critical aspects of cancer evolution within BE patients for a more personalized screening design. SignificanceOur study demonstrates how mathematical modeling of cancer evolution can be used to optimize screening regimes. Surveillance regimes could also be improved if they were based on these models. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/927475v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@6f9324org.highwire.dtl.DTLVardef@1254188org.highwire.dtl.DTLVardef@f1777eorg.highwire.dtl.DTLVardef@dc0e66_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Curtius, K. Dewanji, A. Hazelton, W. D. Rubenstein, J. H. Luebeck, E. G. 2020-02-11 doi:10.1101/2020.02.11.927475 Cold Spring Harbor Laboratory Press 2020-02-11 <![CDATA[ A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2020.02.11.941351v1?rss=1 Lopez de Maturana, E. Rodriguez, J. Alonso, L. Lao, O. Molina-Montes, E. Martin-Antoniano, I. Gomez-Rubio, P. Lawlor, R. Carrato, A. Hidalgo, M. Iglesias, M. Molero, X. Lohr, M. Michalski, C. Perea, J. O'Rorke, M. Barbera, V. Tardon, A. Farre, A. Munoz-Bellvis, L. Crnogorac-Jurcevic, T. Dominguez-Munoz, E. Gress, T. Greenhaf, W. Sharp, L. Arnes, L. Cecchini, L. Balsells, J. Costello, E. Ilzarbe, L. Kleeff, J. Kong, B. Marquez, M. Mora, J. O'Driscoll, D. Scarpa, A. Ye, W. Yu, J. Investigators, P. Garcia-Closas, M. Kogevinas, M. Rothman, N. Silverman, D. 2020-02-12 doi:10.1101/2020.02.11.941351 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Retrocopying expands the functional repertoire of APOBEC3 antiviral proteins in primates ]]> https://biorxiv.org/content/10.1101/2020.02.12.944629v1?rss=1 Yang, L. Emerman, M. Malik, H. S. McLaughlin, R. N. 2020-02-13 doi:10.1101/2020.02.12.944629 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Proteogenomic heterogeneity of localized human prostate cancer progression ]]> https://biorxiv.org/content/10.1101/2020.02.16.950378v1?rss=1 Charmpi, K. Guo, T. Zhong, Q. Wagner, U. Sun, R. Toussaint, N. C. Fritz, C. Yuan, C. Chen, H. Rupp, N. J. Christiansen, A. Rutishauser, D. Ruschoff, J. H. Fankhauser, C. Saba, K. Poyet, C. Hermanns, T. Oehl, K. Moore, A. L. Beisel, C. Calzone, L. MARTIGNETTI, L. Zhang, Q. Zhu, Y. J. Martinez, M. R. Manica, M. Haffner, M. C. Aebersold, R. Wild, P. J. Beyer, A. 2020-02-16 doi:10.1101/2020.02.16.950378 Cold Spring Harbor Laboratory Press 2020-02-16 <![CDATA[ Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein ]]> https://biorxiv.org/content/10.1101/2020.02.19.956581v1?rss=1 Walls, A. C. Park, Y.-J. Tortorici, M. A. Wall, A. McGuire, A. T. Veesler, D. 2020-02-20 doi:10.1101/2020.02.19.956581 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Evolutionarily conserved regulation of embryonic fast-twitch skeletal muscle differentiation by Pbx factors ]]> https://biorxiv.org/content/10.1101/2020.02.21.960484v1?rss=1 Farr, G. H. Li, B. Risolino, M. Johnson, N. M. Yao, Z. Kao, R. M. Majesky, M. W. Tapscott, S. J. Selleri, L. Maves, L. 2020-02-22 doi:10.1101/2020.02.21.960484 Cold Spring Harbor Laboratory Press 2020-02-22 <![CDATA[ Single-cell transcriptomics of allo-reactive CD4+ T cells over time reveals divergent fates during gut GVHD ]]> https://biorxiv.org/content/10.1101/2020.03.08.978239v1?rss=1 Engel, J. A. Lee, H. J. Williams, C. G. Kuns, R. Olver, S. Lansink, L. I. M. Soon, M. S. F. Andersen, S. B. Powell, J. E. Svensson, V. Teichmann, S. A. Hill, G. R. Varelias, A. Koyama, M. Haque, A. 2020-03-09 doi:10.1101/2020.03.08.978239 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ A single cell atlas reveals distinct immune landscapes in transplant and primary tumors that determine response or resistance to immunotherapy ]]> https://biorxiv.org/content/10.1101/2020.03.11.978387v1?rss=1 Wisdom, A. J. Mowery, Y. M. Hong, C. S. Qin, X. Zhang, D. Himes, J. E. Chen, L. Fradin, H. Muise, E. S. Xu, E. S. Carpenter, D. J. Kent, C. L. Smythe, K. S. Williams, N. Luo, L. Ma, Y. Owzar, K. Bradley, T. Kirsch, D. G. 2020-03-12 doi:10.1101/2020.03.11.978387 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWAB USING QIAGEN RNEASY KITS OR DIRECTLY VIA OMISSION OF AN RNA EXTRACTION STEP ]]> https://biorxiv.org/content/10.1101/2020.03.20.001008v1?rss=1 Bruce, E. A. Tighe, S. Hoffman, J. J. Laaguiby, P. Gerrard, D. L. Diehl, S. A. Leonard, D. G. B. Huston, C. D. Kirkpatrick, B. D. Crothers, J. W. Dragon, J. Botten, J. W. 2020-03-21 doi:10.1101/2020.03.20.001008 Cold Spring Harbor Laboratory Press 2020-03-21 <![CDATA[ APOBEC3C tandem domain proteins create super restriction factors against HIV-1 ]]> https://biorxiv.org/content/10.1101/2020.03.27.012963v1?rss=1 McDonnell, M. M. Crawford, K. H. Dingens, A. S. Bloom, J. D. Emerman, M. 2020-03-29 doi:10.1101/2020.03.27.012963 Cold Spring Harbor Laboratory Press 2020-03-29 <![CDATA[ High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters ]]> https://biorxiv.org/content/10.1101/2020.04.03.023135v1?rss=1 Egli, A. Goldman, N. Müller, N. F. Brunner, M. Wuethrich, D. Tschudin-Sutter, S. Hodcroft, E. Neher, R. Saalfrank, C. Hadfield, J. Bedfors, T. Syedbasha, M. Vogel, T. Augustin, N. Bauer, J. Sailer, N. Amar-Sliwad, N. Lang, D. Seth-Smith, H. M. Blaich, A. Hollenstein, Y. Dubuis, O. Naegele, M. Buser, A. Nickel, C. Ritz, N. Zeller, A. Stadler, T. Battegay, M. Schneider-Sliwa, R. 2020-04-04 doi:10.1101/2020.04.03.023135 Cold Spring Harbor Laboratory Press 2020-04-04 <![CDATA[ Autocrine insulin pathway signaling regulates actin dynamics in cell wound repair ]]> https://biorxiv.org/content/10.1101/2020.04.06.028662v1?rss=1 Nakamura, M. Dominguez, A. N. M. Verboon, J. M. Abreu-Blanco, M. T. Liu, R. Delrow, J. J. Parkhurst, S. M. 2020-04-07 doi:10.1101/2020.04.06.028662 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Mapping the unique and shared functions of oncogenic KRAS and RIT1 with proteome and transcriptome profiling ]]> https://biorxiv.org/content/10.1101/2020.04.10.030460v1?rss=1 Lo, A. Holmes, K. Mundt, F. Moorthi, S. Fung, I. Fereshetian, S. Watson, J. Carr, S. A. Mertins, P. Berger, A. 2020-04-11 doi:10.1101/2020.04.10.030460 Cold Spring Harbor Laboratory Press 2020-04-11 <![CDATA[ Chloroquine Kills Hair Cells in Zebrafish Lateral Line and Murine Cochlear Cultures: Implications for Ototoxicity ]]> https://biorxiv.org/content/10.1101/2020.04.14.041731v1?rss=1 Davis, S. N. Wu, P. Camci, E. D. Simon, J. A. Rubel, E. W. Raible, D. W. 2020-04-16 doi:10.1101/2020.04.14.041731 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Profiling the epigenome at home ]]> https://biorxiv.org/content/10.1101/2020.04.15.043083v1?rss=1 Henikoff, S. Henikoff, J. G. 2020-04-17 doi:10.1101/2020.04.15.043083 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Repairing neural damage in a C. elegans chemosensory circuit using genetically engineered synapses ]]> https://biorxiv.org/content/10.1101/2020.04.16.045443v1?rss=1 Rabinowitch, I. Upadhyaya, B. Pant, A. Bai, J. 2020-04-17 doi:10.1101/2020.04.16.045443 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays ]]> https://biorxiv.org/content/10.1101/2020.04.20.051219v1?rss=1 Crawford, K. H. D. Eguia, R. Dingens, A. S. Loes, A. N. Malone, K. D. Wolf, C. R. Chu, H. Y. Tortorici, M. A. Veesler, D. Murphy, M. Pettie, D. King, N. P. Balazs, A. B. Bloom, J. D. 2020-04-20 doi:10.1101/2020.04.20.051219 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Preliminary support for a 'dry swab, extraction free' protocol for SARS-CoV-2 testing via RT-qPCR ]]> https://biorxiv.org/content/10.1101/2020.04.22.056283v1?rss=1 Srivatsan, S. Han, P. D. van Raay, K. Wolf, C. R. McCulloch, D. J. Kim, A. E. Brandstetter, E. Martin, B. Gehring, J. Chen, W. Seattle Flu Study Investigators, Kosuri, S. Konnick, E. Q. Lockwood, C. M. Reider, M. J. Nickerson, D. A. Chu, H. Y. Shendure, J. Starita, L. M. 2020-04-23 doi:10.1101/2020.04.22.056283 Cold Spring Harbor Laboratory Press 2020-04-23 <![CDATA[ Using B cell receptor lineage structures to predict affinity ]]> https://biorxiv.org/content/10.1101/2020.04.24.060194v1?rss=1 Ralph, D. K. Matsen, F. A. 2020-04-25 doi:10.1101/2020.04.24.060194 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics ]]> https://biorxiv.org/content/10.1101/2020.04.27.052225v1?rss=1 Müller, N. F. Wüthrich, D. Goldman, N. Sailer, N. Saalfrank, C. Brunner, M. Augustin, N. Seth-Smith, H. M. Hollenstein, Y. Syedbasha, M. Lang, D. Neher, R. A. Dubuis, O. Naegele, M. Buser, A. Nickel, C. H. Ritz, N. Zeller, A. Lang, B. M. Hadfield, J. Bedford, T. Battegay, M. Schneider-Sliwa, R. Egli, A. Stadler, T. 2020-04-29 doi:10.1101/2020.04.27.052225 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains ]]> https://biorxiv.org/content/10.1101/2020.04.27.064774v1?rss=1 Dearlove, B. L. Lewitus, E. Bai, H. Li, Y. Reeves, D. B. Joyce, M. G. Scott, P. Amare, M. Vasan, S. Michael, N. L. Modjarrad, K. Rolland, M. 2020-04-27 doi:10.1101/2020.04.27.064774 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Tumor-specific changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma ]]> https://biorxiv.org/content/10.1101/2020.05.04.076638v1?rss=1 Santiago, C. Goldman, J. D. Zhao, H. Pankow, A. P. Okuku, F. Schmitt, M. W. Chen, L. H. Hill, C. A. Casper, C. Phipps, W. T. Mullins, J. I. 2020-05-04 doi:10.1101/2020.05.04.076638 Cold Spring Harbor Laboratory Press 2020-05-04 <![CDATA[ Antibody neutralization of an influenza virus that uses neuraminidase for receptor binding ]]> https://biorxiv.org/content/10.1101/2020.05.08.084954v1?rss=1 Gentles, L. E. Wan, H. Eichelberger, M. Bloom, J. D. 2020-05-09 doi:10.1101/2020.05.08.084954 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ Phage-DMS: a comprehensive method for fine mapping of antibody epitopes ]]> https://biorxiv.org/content/10.1101/2020.05.11.089342v1?rss=1 Garrett, M. E. Itell, H. L. Crawford, K. H. D. Basom, R. Bloom, J. D. Overbaugh, J. 2020-05-13 doi:10.1101/2020.05.11.089342 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Characterization of neutralizing antibodies from a SARS-CoV-2 infected individual ]]> https://biorxiv.org/content/10.1101/2020.05.12.091298v1?rss=1 Seydoux, E. Homad, L. J. MacCamy, A. J. Parks, K. R. Hurlburt, N. K. Jennewein, M. F. Akins, N. R. Stuart, A. B. Wan, Y.-H. Feng, J. Nelson, R. Singh, S. Cohen, K. W. McElrath, J. M. Englund, J. A. Chu, H. Y. Pancera, M. McGuire, A. T. Stamatatos, L. 2020-05-12 doi:10.1101/2020.05.12.091298 Cold Spring Harbor Laboratory Press 2020-05-12 <![CDATA[ Integrin αvβ8 on T cells is responsible for suppression of anti-tumor immunity in multiple syngeneic models and is a promising target for tumor immunotherapy ]]> https://biorxiv.org/content/10.1101/2020.05.14.084913v1?rss=1 Dodagatta-Marri, E. Ma, H.-Y. Liang, B. Li, J. Meyer, D. S. Sun, K.-H. Ren, X. Zirak, B. Rosenblum, M. D. Headley, M. Pinzas, L. Reed, N. I. Del Cid, J. S. Adoumie, M. Hann, B. C. Yang, S. Giddabasappa, A. Noorbehesht, K. Yang, B. Dal Porto, J. Tsukui, T. Niessen, K. Atakilit, A. Akhurst, R. J. Sheppard, D. 2020-05-15 doi:10.1101/2020.05.14.084913 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ dms-view: Interactive visualization tool for deep mutational scanning data ]]> https://biorxiv.org/content/10.1101/2020.05.14.096842v1?rss=1 Hilton, S. K. Huddleston, J. L. Black, A. North, K. Dingens, A. S. Bedford, T. Bloom, J. D. 2020-05-15 doi:10.1101/2020.05.14.096842 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ A system-view of B. pertussis booster vaccine responses in adults primed with whole-cell vs. acellular vaccine in infancy ]]> https://biorxiv.org/content/10.1101/2020.05.15.098830v1?rss=1 da Silva Antunes, R. Pomaznoy, M. Soldevila, F. Babor, M. Bennett, J. Tian, Y. Khalil, N. Qian, Y. Mandava, A. Scheuermann, R. H. Cortese, M. Pulendran, B. Petro, C. D. Gilkes, A. Purcell, L. A. Sette, A. Peters, B. 2020-05-16 doi:10.1101/2020.05.15.098830 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones ]]> https://biorxiv.org/content/10.1101/2020.05.18.101709v1?rss=1 Sarthy, J. F. Meers, M. P. Janssens, D. Henikoff, J. G. Morris, S. Biery, M. Feldman, H. Paddison, P. J. Vitanza, N. Olson, J. M. Ahmad, K. Henikoff, S. 2020-05-19 doi:10.1101/2020.05.18.101709 Cold Spring Harbor Laboratory Press 2020-05-19 <![CDATA[ Multi-ancestry genome-wide gene-sleep interactions identify novel loci for blood pressure ]]> https://biorxiv.org/content/10.1101/2020.05.29.123505v1?rss=1 Wang, H. Noordam, R. Cade, B. E. Schwander, K. Winkler, T. W. Lee, J. Sung, Y. J. Bentley, A. R. Manning, A. K. Aschard, H. Kilpelainen, T. O. Ilkov, M. Brown, M. R. Horimoto, A. R. Richard, M. Bartz, T. M. Vojinovic, D. Lim, E. Nierenberg, J. L. Liu, Y. Chitrala, K. Rankinen, T. Musani, S. K. Franceschini, N. Rauramaa, R. Alver, M. Zee, P. Harris, S. E. van der Most, P. J. Nolte, I. M. Munroe, P. B. Palmer, N. D. Kuhnel, B. Weiss, S. Wen, W. Hall, K. A. Lyytikainen, L.-P. O'Connell, J. R. Eiriksdottir, G. Launer, L. J. de Vries, P. S. Arking, D. Chen, 2020-05-31 doi:10.1101/2020.05.29.123505 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ In vitro and in vivo characterization of a recombinant rhesus cytomegalovirus containing a complete genome ]]> https://biorxiv.org/content/10.1101/2020.06.02.129486v1?rss=1 Taher, H. Mahyari, E. Kreklywich, C. Uebelhoer, L. S. McArdle, M. R. Moström, M. J. Bhusari, A. Nekorchuk, M. Whitmer, T. Scheef, E. A. Sprehe, L. M. Roberts, D. Hughes, C. M. Jackson, K. A. Selseth, A. N. Ventura, A. B. Yue, Y. Schmidt, K. A. Shao, J. Edlefsen, P. T. Smedley, J. Stanton, R. J. Axthelm, M. K. Estes, J. D. Hansen, S. G. Kaur, A. Barry, P. A. Bimber, B. N. Picker, L. J. Streblow, D. N. Früh, K. Malouli, D. 2020-06-02 doi:10.1101/2020.06.02.129486 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Lactoferrin retargets adenoviruses to TLR4 to induce an abortive NLRP3-associated pyroptotic response in human dendritic cells ]]> https://biorxiv.org/content/10.1101/2020.06.03.131664v1?rss=1 Cheneau, C. Eichholz, K. Tran, T. H. Tran, T. T. P. Paris, O. Henriquet, C. Pugniere, M. Kremer, E. J. 2020-06-03 doi:10.1101/2020.06.03.131664 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Linking T cell receptor sequence to transcriptional profiles with clonotype neighbor graph analysis (CoNGA) ]]> https://biorxiv.org/content/10.1101/2020.06.04.134536v1?rss=1 Schattgen, S. Guion, K. Crawford, J. C. Souquette, A. Martinez Barrio, A. Stubbington, M. J. T. Thomas, P. G. Bradley, P. 2020-06-05 doi:10.1101/2020.06.04.134536 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Increased demand for NAD+ relative to ATP drives aerobic glycolysis ]]> https://biorxiv.org/content/10.1101/2020.06.08.140558v1?rss=1 Luengo, A. Li, Z. Gui, D. Y. Sullivan, L. B. Zagorulya, M. Do, B. T. Ferriera, R. Naamati, A. Ali, A. Lewis, C. A. Thomas, C. J. Spranger, S. Matheson, N. J. Vander Heiden, M. G. 2020-06-09 doi:10.1101/2020.06.08.140558 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes ]]> https://biorxiv.org/content/10.1101/2020.06.10.144071v1?rss=1 Jackson, L. K. Potter, B. Schneider, S. E. Fitzgibbon, M. Blair, K. Farah, H. Krishna, U. Peek, R. Bedford, T. Salama, N. R. 2020-06-10 doi:10.1101/2020.06.10.144071 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation ]]> https://biorxiv.org/content/10.1101/2020.06.12.148692v1?rss=1 Hurlburt, N. K. Wan, Y.-H. Stuart, A. B. Feng, J. McGuire, A. T. Stamatatos, L. Pancera, M. 2020-06-12 doi:10.1101/2020.06.12.148692 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ Mutational resilience of antiviral restriction favors primate TRIM5α in host-virus evolutionary arms races ]]> https://biorxiv.org/content/10.1101/2020.06.12.149088v1?rss=1 Tenthorey, J. Young, C. Sodeinde, A. Emerman, M. Malik, H. S. 2020-06-13 doi:10.1101/2020.06.12.149088 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ PROTECTIVE ANTIBODIES AGAINST HPIV3 INFECTION ]]> https://biorxiv.org/content/10.1101/2020.06.15.153478v1?rss=1 Boonyaratanakornkit, J. Weidle, C. Singh, S. Bakthavatsalam, R. Perkins, J. Stewart-Jones, G. B. E. Kwong, P. D. McGuire, A. T. Pancera, M. Taylor, J. J. 2020-06-15 doi:10.1101/2020.06.15.153478 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ Combining genome-wide studies of breast, prostate, ovarian and endometrial cancers maps cross-cancer susceptibility loci and identifies new genetic associations ]]> https://biorxiv.org/content/10.1101/2020.06.16.146803v1?rss=1 1Mb from previously identified risk loci for the four cancers and an additional 23 lead variant-cancer associations were novel for one of the cancers. Bayesian models supported pleiotropic effects involving at least two cancers at 222/465 lead variants in 118/192 regions. Gene-level association analysis identified 13 shared susceptibility genes (P<2.6x10-6) in 13 regions not previously implicated in any of the four cancers and not uncovered by our variant-level meta-analysis. Several lead variants had opposite effects across cancers, including a cluster of such variants in the TP53 pathway. Fifty-four lead variants were associated with blood cell traits and suggested genetic overlaps with clonal hematopoiesis. Our study highlights the remarkable pervasiveness of pleiotropy across hormone-related cancers, further illuminating their shared genetic and mechanistic origins at variant- and gene-level resolution. ]]> Kar, S. P. Lindstroem, S. Hung, R. Lawrenson, K. Schmidt, M. O'Mara, T. Glubb, D. Tyrer, J. Schildkraut, J. Chang-Claude, J. Alsulimani, A. Anton, F. Beeghly-Fadiel, A. Bjorge, L. Bodelon, C. Brauch, H. Burghaus, S. Campa, D. Carney, M. Chen, Z. Daly, M. du Bois, A. Ekici, A. Ewing, A. Fasching, P. Flanagan, J. M. Gawelko, J. Giles, G. Hamilton, R. Harris, H. Heitz, F. Hildebrandt, M. Hillemanns, P. Huang, R.-Y. Imaz, L. Irmejs, A. Jakubowska, A. Jensen, A. John, E. Kannisto, P. Karlan, B. Khusnutdinova, E. Kiemeney, L. Kjaer, S. Klapdor, R. Kleiblo 2020-06-19 doi:10.1101/2020.06.16.146803 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Infinity Flow: High-throughput single-cell quantification of 100s of proteins using conventional flow cytometry and machine learning ]]> https://biorxiv.org/content/10.1101/2020.06.17.152926v1?rss=1 Becht, E. Tolstrup, D. Dutertre, C.-A. Ginhoux, F. Newell, E. W. Gottardo, R. Headley, M. B. 2020-06-19 doi:10.1101/2020.06.17.152926 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding ]]> https://biorxiv.org/content/10.1101/2020.06.17.157982v1?rss=1 Starr, T. N. Greaney, A. J. Hilton, S. K. Crawford, K. H. Navarro, M. J. Bowen, J. E. Tortorici, M. A. Walls, A. C. Veesler, D. Bloom, J. D. 2020-06-17 doi:10.1101/2020.06.17.157982 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Mathematical modeling explains differential SARS CoV-2 kinetics in lung and nasal passages in remdesivir treated rhesus macaques ]]> https://biorxiv.org/content/10.1101/2020.06.21.163550v1?rss=1 Goyal, A. Duke, E. R. Cardozo-Ojeda, E. F. Schiffer, J. T. 2020-06-22 doi:10.1101/2020.06.21.163550 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age ]]> https://biorxiv.org/content/10.1101/2020.06.22.165225v1?rss=1 Lieberman, N. A. P. Peddu, V. Xie, H. Shrestha, L. Huang, M. Mears, M. C. Cajimat, M. N. Bente, D. A. Shi, P.-Y. Bovier, F. Roychoudhury, P. Jerome, K. R. Moscona, A. Porotto, M. Greninger, A. L. 2020-06-22 doi:10.1101/2020.06.22.165225 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ Super LeArner Prediction of NAb Panels (SLAPNAP): A Containerized Tool for Predicting Combination Monoclonal Broadly Neutralizing Antibody Sensitivity ]]> https://biorxiv.org/content/10.1101/2020.06.23.167718v1?rss=1 Benkeser, D. Williamson, B. D. Magaret, C. A. Nizam, S. Gilbert, P. B. 2020-06-24 doi:10.1101/2020.06.23.167718 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries ]]> https://biorxiv.org/content/10.1101/2020.06.23.167759v1?rss=1 Kwong, A. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Blackwell, T. W. TOPMed Analysis Working Group, LeFaive, J. de Andrade, M. Barnard, J. Barnes, K. C. Blangero, J. Boerwinkle, E. Burchard, E. G. Cade, B. E. Chasman, D. Chen, H. Conomos, M. Cupples, L. A. Ellinor, P. T. Eng, C. Gao, Y. Guo, X. Irvin, M. R. Kelly, T. Kim, W. Kooperberg, C. Lubitz, S. A. Mak, A. C. Y. Manichaikul, A. W. Mathias, R. A. Montasser, M. E. Montgomery, C. G. Musani, S. Palmer, N. D. Peloso, G. Qiao, D. Reiner, A. P. Roden, D. M. Shoemaker, M. B. Smith, J. A 2020-06-24 doi:10.1101/2020.06.23.167759 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Identification of cellular context sensitive regulatory variation in mouse genomes ]]> https://biorxiv.org/content/10.1101/2020.06.27.175422v1?rss=1 Maurano, M. T. Halow, J. Byron, R. Groudine, M. Bender, M. A. Stamatoyannopoulos, J. A. 2020-06-28 doi:10.1101/2020.06.27.175422 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ A simple and highly efficient method for multi-allelic CRISPR-Cas9 editing in primary cell cultures ]]> https://biorxiv.org/content/10.1101/2020.07.01.183145v1?rss=1 Hoellerbauer, P. Kufeld, M. Arora, S. Wu, H.-J. Feldman, H. PADDISON, P. 2020-07-01 doi:10.1101/2020.07.01.183145 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ An integrative oncogene-dependency map identifies unique vulnerabilities of oncogenic RIT1 in lung cancer ]]> https://biorxiv.org/content/10.1101/2020.07.03.187310v1?rss=1 Vichas, A. Nkinsi, N. T. Riley, A. Parrish, P. C. R. Duke, F. Chen, J. Watson, J. Rees, M. Lee, J. K. Piccioni, F. Hatch, E. M. Berger, A. H. 2020-07-04 doi:10.1101/2020.07.03.187310 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ B cells and HSV-specific antibodies respond to HSV-2 reactivation in skin ]]> https://biorxiv.org/content/10.1101/2020.07.08.192542v1?rss=1 Emily S. Ford Anton M. Sholukh RuthMabel Boytz Savanna S. Carmack Alexis Klock Khamsone Phasouk Jason Shao Raabya Rossenkhan Paul T. Edlefsen Tao Peng Christine Johnston Anna Wald Jia Zhu Lawrence Corey 2020-07-08 doi:10.1101/2020.07.08.192542 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Cell Type Aware analysis of RNA-seq data(CARseq) reveals difference and similarities ofthe molecular mechanisms of Schizophrenia andAutism ]]> https://biorxiv.org/content/10.1101/2020.07.13.201061v1?rss=1 Jin, C. Chen, M. Lin, D. Sun, W. 2020-07-14 doi:10.1101/2020.07.13.201061 Cold Spring Harbor Laboratory Press 2020-07-14 <![CDATA[ Bystander CD4+ T cells infiltrate human tumors and are phenotypically distinct ]]> https://biorxiv.org/content/10.1101/2020.07.15.204172v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@13de05org.highwire.dtl.DTLVardef@553e34org.highwire.dtl.DTLVardef@66e9f1org.highwire.dtl.DTLVardef@8903ca_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> SIMONI, y. LI, S. ZHUANG, S. HEIT, A. KOO, S.-L. CHOW, I.-T. KWOK, W. W. TAN, I. B. TAN, D. S. W. NEWELL, E. W. 2020-07-16 doi:10.1101/2020.07.15.204172 Cold Spring Harbor Laboratory Press 2020-07-16 <![CDATA[ SARS-CoV-2 ORF6 disrupts nucleocytoplasmic transport through interactions with Rae1 and Nup98 ]]> https://biorxiv.org/content/10.1101/2020.08.03.234559v1?rss=1 Addetia, A. Lieberman, N. A. P. Phung, Q. Xie, H. Roychoudhury, P. Loprieno, M. A. Huang, M. Shrestha, L. Jerome, K. R. Greninger, A. L. 2020-08-03 doi:10.1101/2020.08.03.234559 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ chTOG is a conserved mitotic error correction factor ]]> https://biorxiv.org/content/10.1101/2020.08.03.235325v1?rss=1 Herman, J. A. Miller, M. P. Biggins, S. 2020-08-04 doi:10.1101/2020.08.03.235325 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-based Multiple Sequence Alignment ]]> https://biorxiv.org/content/10.1101/2020.08.07.242305v1?rss=1 Roe, D. Vierra-Green, C. Pyo, C.-W. Geraghty, D. E. Spellman, S. R. Maiers, M. Kuang, R. 2020-08-09 doi:10.1101/2020.08.07.242305 Cold Spring Harbor Laboratory Press 2020-08-09 <![CDATA[ Attenuated influenza virions expressing the SARS- CoV-2 receptor-binding domain induce neutralizing antibodies in mice ]]> https://biorxiv.org/content/10.1101/2020.08.12.248823v1?rss=1 Loes, A. N. Gentles, L. E. Greaney, A. J. Crawford, K. H. Bloom, J. D. 2020-08-13 doi:10.1101/2020.08.12.248823 Cold Spring Harbor Laboratory Press 2020-08-13 <![CDATA[ A combined proteomics and Mendelian randomization approach to investigate the effects of aspirin-targeted proteins on colorectal cancer ]]> https://biorxiv.org/content/10.1101/2020.08.14.239871v1?rss=1 Nounu, A. Greenhough, A. Heesom, K. J. Richmond, R. C. Zheng, J. Weinstein, S. J. Albanes, D. Baron, J. A. Hopper, J. L. Figueiredo, J. C. Newcomb, P. A. Lindor, N. M. Casey, G. Platz, E. A. Le Marchand, L. Ulrich, C. M. Li, C. I. van Duijnhoven, F. J. Gsur, A. Campbell, P. T. Moreno, V. Vodicka, P. Vodickova, L. Brenner, H. Chang-Claude, J. Hoffmeister, M. Sakoda, L. C. Slattery, M. L. Schoen, R. E. Gunter, M. J. Castellvi-Bel, S. Rok Kim, H. Kweon, S.-S. Chan, A. T. Li, L. Zheng, W. Bishop, D. T. Buchanan, D. D. Giles, G. G. Gruber, S. B. Rennert, G. 2020-08-14 doi:10.1101/2020.08.14.239871 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ The origins and consequences of UPF1 variants in pancreatic adenosquamous carcinoma ]]> https://biorxiv.org/content/10.1101/2020.08.14.248864v1?rss=1 Polaski, J. T. Udy, D. B. Escobar-Hoyos, L. F. Askan, G. Leach, S. D. Ventura, A. Kannan, R. Bradley, R. K. 2020-08-14 doi:10.1101/2020.08.14.248864 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response ]]> https://biorxiv.org/content/10.1101/2020.08.15.250589v1?rss=1 McGowan, E. Rosenthal, R. Fiore-Gartland, A. Macharia, G. Balinda, S. Kapaata, A. Muok, E. Umviligihozo, G. Dalel, J. Streatfield, C. Coutinho, H. Monaco, D. Morrison, D. Yue, L. Hunter, E. Nielsen, M. Gilmour, J. Hare, J. 2020-08-15 doi:10.1101/2020.08.15.250589 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Cooperative Binding of Transcription Factors is a Hallmark of Active Enhancers ]]> https://biorxiv.org/content/10.1101/2020.08.17.253146v1?rss=1 Rao, S. Ahmad, K. Ramachandran, S. 2020-08-18 doi:10.1101/2020.08.17.253146 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ A CAR RNA FISH assay reveals functional and spatial heterogeneity of chimeric antigen receptor T cells in tissue ]]> https://biorxiv.org/content/10.1101/2020.08.21.260935v1?rss=1 Eichholz, K. Li, A. Z. Diem, K. Tareen, S. U. Jensen, M. Zhu, J. Corey, L. 2020-08-24 doi:10.1101/2020.08.21.260935 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ A JAK/STAT-Mediated Inflammatory Signaling Cascade Drives Oncogenesis In AF10-Rearranged AML ]]> https://biorxiv.org/content/10.1101/2020.08.31.273631v1?rss=1 Chen, B. Deshpande, A. Barbosa, K. O. Kleppe, M. Lei, X. Yeddula, N. Rosa Campos, A. Wechsler-Reya, R. Bagchi, A. Meshinchi, S. Eaves, C. J. Jeremias, I. Haferlach, T. Frank, D. Ronai, Z. Chanda, S. Armstrong, S. Adams, P. Levine, R. Deshpande, A. 2020-08-31 doi:10.1101/2020.08.31.273631 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Attenuation of homeostatic signaling from apoptotic thymocytes triggers a global regenerative response in the thymus ]]> https://biorxiv.org/content/10.1101/2020.08.31.275834v1?rss=1 Kinsella, S. Evandy, C. A. Cooper, K. Iovino, L. deRoos, P. C. Hopwo, K. S. Granadier, D. W. Smith, C. W. Rafii, S. Dudakov, J. A. 2020-09-01 doi:10.1101/2020.08.31.275834 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ Single-cell analysis of chromatin silencing programs in developmental and tumor progression ]]> https://biorxiv.org/content/10.1101/2020.09.04.282418v1?rss=1 Wu, S. J. Furlan, S. N. Mihalas, A. B. Kaya-Okur, H. Feroze, A. H. Emerson, S. N. Zheng, Y. Carson, K. Cimino, P. J. Keene, C. D. Holland, E. C. Sarthy, J. F. Gottardo, R. Ahmad, K. Henikoff, S. Patel, A. P. 2020-09-04 doi:10.1101/2020.09.04.282418 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ BayesSpace enables the robust characterization of spatial gene expression architecture in tissue sections at increased resolution ]]> https://biorxiv.org/content/10.1101/2020.09.04.283812v1?rss=1 Zhao, E. Stone, M. R. Ren, X. Pulliam, T. Nghiem, P. Bielas, J. H. Gottardo, R. 2020-09-05 doi:10.1101/2020.09.04.283812 Cold Spring Harbor Laboratory Press 2020-09-05 <![CDATA[ Joint Microbial and Metabolomic Network Estimation with the Censored Gaussian Graphical Model ]]> https://biorxiv.org/content/10.1101/2020.09.07.286880v1?rss=1 Ma, J. 2020-09-09 doi:10.1101/2020.09.07.286880 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Antibody binding to SARS-CoV-2 S glycoprotein correlates with, but does not predict neutralization ]]> https://biorxiv.org/content/10.1101/2020.09.08.287482v1?rss=1 Ding, S. Laumaea, A. Gasser, R. Medjahed, H. Pancera, M. Stamatatos, L. McGuire, A. Bazin, R. Finzi, A. 2020-09-08 doi:10.1101/2020.09.08.287482 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition ]]> https://biorxiv.org/content/10.1101/2020.09.10.292078v1?rss=1 Greaney, A. J. Starr, T. N. Gilchuk, P. Zost, S. J. Binshtein, E. Loes, A. N. Hilton, S. K. Huddleston, J. Eguia, R. Crawford, K. H. Dingens, A. S. Nargi, R. S. Sutton, R. E. Suryadevara, N. Rothlauf, P. W. Liu, Z. Whelan, S. P. Carnahan, R. H. Crowe, J. E. Bloom, J. D. 2020-09-10 doi:10.1101/2020.09.10.292078 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Baseline T cell immune phenotypes predict virologic and disease control upon SARS-CoV infection ]]> https://biorxiv.org/content/10.1101/2020.09.21.306837v1?rss=1 Graham, J. Swarts, J. Leist, S. R. Schafer, A. Menachery, V. D. Gralinski, L. Jeng, S. Miller, D. R. Mooney, M. McWeeney, S. Ferris, M. T. Pardo-Manuel de Villena, F. Heise, M. T. Baric, R. S. Lund, J. M. 2020-09-21 doi:10.1101/2020.09.21.306837 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies ]]> https://biorxiv.org/content/10.1101/2020.09.24.312066v1?rss=1 Doepker, L. E. Danon, S. Harkins, E. Ralph, D. Yaffe, Z. Dhar, A. Wagner, C. Stumpf, M. Arenz, D. Williams, J. A. Jaoko, W. Mandaliya, K. Lee, K. K. Matsen, F. A. Overbaugh, J. 2020-09-25 doi:10.1101/2020.09.24.312066 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ An optimal set of inhibitors for Reverse Engineering via Kinase Regularization. ]]> https://biorxiv.org/content/10.1101/2020.09.26.312348v1?rss=1 Rata, S. Gruver, J. S. Trikoz, N. Lukyanov, A. Vultaggio, J. Ceribelli, M. Thomas, C. Gujral, T. S. Kirschner, M. W. Peshkin, L. 2020-09-28 doi:10.1101/2020.09.26.312348 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ A rapidly evolving actin mediates fertility and developmental tradeoffs in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.09.28.317503v1?rss=1 Schroeder, C. M. Tomlin, S. A. Valenzuela, J. R. Malik, H. S. 2020-09-28 doi:10.1101/2020.09.28.317503 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ AcrIIA22 is a novel anti-CRISPR that impairs SpyCas9 activity by relieving DNA torsion of target plasmids ]]> https://biorxiv.org/content/10.1101/2020.09.28.317578v1?rss=1 Forsberg, K. J. Schmidtke, D. T. Werther, R. Hausman, D. Stoddard, B. L. Kaiser, B. K. Malik, H. S. 2020-09-29 doi:10.1101/2020.09.28.317578 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Modulation of MHC-E transport by viral decoy ligands is required for RhCMV/SIV vaccine efficacy ]]> https://biorxiv.org/content/10.1101/2020.09.30.321158v1?rss=1 Verweij, M. Hansen, S. G. Iyer, R. John, N. Malouli, D. Morrow, D. Scholz, I. Womack, J. Abdulhaqq, S. Gilbride, R. M. Hughes, C. M. Ventura, A. B. Ford, J. C. Selseth, A. N. Oswald, K. Shoemaker, R. Berkemeier, B. Borsche, W. J. Hull, M. Shao, J. Sacha, J. Axthelm, M. K. Edlefsen, P. Lifson, J. D. Picker, L. J. Früh, K. 2020-10-02 doi:10.1101/2020.09.30.321158 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Cytomegaloviral determinants of CD8+ T cell programming and RhCMV/SIV vaccine efficacy ]]> https://biorxiv.org/content/10.1101/2020.09.30.321349v1?rss=1 Malouli, D. Hansen, S. G. Hancock, M. H. Hughes, C. M. Ford, J. C. Gilbride, R. M. Ventura, A. B. Morrow, D. Taher, H. Uebelhoer, L. S. McArdle, M. R. Papen, C. R. Espinosa Trethewy, R. Oswald, K. Shoemaker, R. Berkemeier, B. Bosche, W. Hull, M. Green, J. Axthelm, M. K. Shao, J. Edlefsen, P. Grey, F. Nelson, J. A. Lifson, J. D. Streblow, D. N. Sacha, J. Früh, K. Picker, L. J. 2020-10-01 doi:10.1101/2020.09.30.321349 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Helicobacter pylori accelerates KRAS-dependent gastric dysplasia ]]> https://biorxiv.org/content/10.1101/2020.10.06.328518v1?rss=1 O'Brien, V. P. Koehne, A. Dubrulle, J. Rodriguez, A. Leverich, C. Kong, P. Campbell, J. Pierce, R. Goldenring, J. Choi, E. Salama, N. 2020-10-06 doi:10.1101/2020.10.06.328518 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia ]]> https://biorxiv.org/content/10.1101/2020.10.06.328948v1?rss=1 Janssens, D. Meers, M. P. Wu, S. J. Babaeva, E. Meshinchi, S. Sarthy, J. F. Ahmad, K. Henikoff, S. 2020-10-08 doi:10.1101/2020.10.06.328948 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ CD8+ T cell responses in convalescent COVID-19 individuals target epitopes from the entireSARS-CoV-2 proteome and show kinetics of early differentiation ]]> https://biorxiv.org/content/10.1101/2020.10.08.330688v1?rss=1 Kared, H. Redd, A. D. Bloch, E. M. Bonny, T. S. Sumatoh, H. Kairi, F. Carbajo, D. Abel, B. Newell, E. W. Bettinotti, M. P. Benner, S. E. Patel, E. U. Littlefield, K. Laeyendecker, O. Shoham, S. Sullivan, D. Casadevall, A. Pekosz, A. Nardin, A. Fehlings, M. Tobian, A. A. Quinn, T. C. 2020-10-08 doi:10.1101/2020.10.08.330688 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics ]]> https://biorxiv.org/content/10.1101/2020.10.09.331900v1?rss=1 Strom, A. R. Biggs, R. J. Banigan, E. J. Wang, X. Chiu, K. Herman, C. Collado, J. Yue, F. Ritland Politz, J. C. Tait, L. J. Scalzo, D. Telling, A. Groudine, M. Brangwynne, C. P. Marko, J. Stephens, A. D. 2020-10-09 doi:10.1101/2020.10.09.331900 Cold Spring Harbor Laboratory Press 2020-10-09 <![CDATA[ Gene-level metagenomics identifies genome islands associated with immunotherapy response ]]> https://biorxiv.org/content/10.1101/2020.10.09.333971v1?rss=1 Minot, S. S. Barry, K. C. Kasman, C. Golob, J. L. Willis, A. D. 2020-10-10 doi:10.1101/2020.10.09.333971 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Innate behavior sequence progression by peptide-mediated interorgan crosstalk ]]> https://biorxiv.org/content/10.1101/2020.10.10.334540v1?rss=1 Heredia, F. Volonte, Y. Pereirinha, J. Fernandez-Acosta, M. Casimiro, A. P. Belem, C. G. Viegas, F. Tanaka, K. Arana, M. Cardoso, G. A. Macedo, A. Kotowicz, M. Prado Spalm, F. H. Dibo, M. Monfardini, R. D. Torres, T. T. Mendes, C. S. Garelli, A. Gontijo, A. M. 2020-10-10 doi:10.1101/2020.10.10.334540 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Integrated analysis of multimodal single-cell data ]]> https://biorxiv.org/content/10.1101/2020.10.12.335331v1?rss=1 Hao, Y. Hao, S. Andersen-Nissen, E. Mauck, W. M. Zheng, S. Butler, A. Lee, M. J. Wilk, A. J. Darby, C. Zagar, M. Hoffman, P. Stoeckius, M. Papalexi, E. Mimitou, E. P. Jain, J. Srivastava, A. Stuart, T. Fleming, L. B. Yeung, B. Rogers, A. J. McElrath, J. M. Blish, C. A. Gottardo, R. Smibert, P. Satija, R. 2020-10-12 doi:10.1101/2020.10.12.335331 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Collective nuclear behavior shapes bilateral nuclear symmetry for subsequent left-right asymmetric morphogenesis in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.10.15.340521v1?rss=1 Shin, D. Nakamura, M. Morishita, Y. Eiraku, M. Yamakawa, T. Y. Sasamura, T. S. Akiyama, M. A. Inaki, M. Matsuno, K. M. 2020-10-15 doi:10.1101/2020.10.15.340521 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Loss of MGA mediated Polycomb repression promotes tumor progression and invasiveness ]]> https://biorxiv.org/content/10.1101/2020.10.16.334714v1?rss=1 Mathsyaraja, H. Catchpole, J. Eastwood, E. Babaeva, E. Geuenich, M. J. Cheng, P.-F. Freie, B. Ayers, J. L. Yu, M. Wu, N. Poudel, K. R. Koehne, A. Grady, W. Houghton, A. M. Shiio, Y. MacPherson, D. P. Eisenman, R. N. 2020-10-17 doi:10.1101/2020.10.16.334714 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Multi-omic Single-cell Atlas Reveals Broad Ex Vivo Effects on Human Immunobiology ]]> https://biorxiv.org/content/10.1101/2020.10.18.344663v1?rss=1 Savage, A. K. Gutschow, M. V. Chiang, T. Henderson, K. Green, R. Chaudhari, M. Swanson, E. Heubeck, A. T. Kondza, N. Burley, K. C. Genge, P. C. Lord, C. Smith, T. Beaubien, A. Goldy, J. Bolouri, H. Buckner, J. H. Meijer, P. Coffey, E. M. Li, X.-j. Skene, P. J. Torgerson, T. R. Bumol, T. F. 2020-10-19 doi:10.1101/2020.10.18.344663 Cold Spring Harbor Laboratory Press 2020-10-19 <![CDATA[ High-resolution mapping of the neutralizing and binding specificities of polyclonal rabbit serum elicited by HIV Env trimer immunization ]]> https://biorxiv.org/content/10.1101/2020.10.21.348623v1?rss=1 Dingens, A. S. Pratap, P. Malone, K. Hilton, S. K. Ketas, T. Cottrell, C. A. Overbaugh, J. Moore, J. P. Klasse, P. J. Ward, A. B. Bloom, J. D. 2020-10-21 doi:10.1101/2020.10.21.348623 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ B LYMPHOCYTES, BUT NOT DENDRITIC CELLS, EFFICIENTLY HIV-1 TRANS-INFECT NAÏVE CD4+ T CELLS: IMPLICATIONS FOR THE VIRAL RESERVOIR ]]> https://biorxiv.org/content/10.1101/2020.10.22.351627v1?rss=1 Gerberick, A. DeLucia, D. C. Piazza, P. A. Alaoui-El-Azher, M. Rinaldo, C. R. Sluis-Cremer, N. Rappocciolo, G. 2020-10-23 doi:10.1101/2020.10.22.351627 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Epitope profiling reveals binding signatures of SARS-CoV-2 immune response and cross-reactivity with endemic HCoVs ]]> https://biorxiv.org/content/10.1101/2020.10.29.360800v1?rss=1 Stoddard, C. I. Galloway, J. Chu, H. Y. Shipley, M. M. Itell, H. L. Wolf, C. R. Logue, J. K. Magedson, A. Sung, K. Garrett, M. Crawford, K. H. Laserson, U. Matsen, F. A. Overbaugh, J. 2020-10-29 doi:10.1101/2020.10.29.360800 Cold Spring Harbor Laboratory Press 2020-10-29 <![CDATA[ Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates ]]> https://biorxiv.org/content/10.1101/2020.11.04.368597v1?rss=1 Klein, A. Solinski, H. J. Malewicz, N. Ieong, H. F.-h. Shimada, S. Hartke, T. V. Wooten, M. Wu, G. Hoon, M. A. LaMotte, R. H. Ringkamp, M. 2020-11-04 doi:10.1101/2020.11.04.368597 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Rapid adaptation to human protein kinase R by a unique genomic rearrangement in rhesus cytomegalovirus. ]]> https://biorxiv.org/content/10.1101/2020.11.06.371047v1?rss=1 Child, S. J. Greninger, A. L. Geballe, A. P. 2020-11-06 doi:10.1101/2020.11.06.371047 Cold Spring Harbor Laboratory Press 2020-11-06 <![CDATA[ The role of XPB/Ssl2 double-stranded DNA translocase processivity in transcription start-site scanning. ]]> https://biorxiv.org/content/10.1101/2020.11.09.375329v1?rss=1 Tomko, E. J. Luyties, O. Rimel, J. K. Tsai, C.-L. Fuss, J. O. Fishburn, J. Hahn, S. Tsutakawa, S. E. Taatjes, D. J. Galburt, E. A. 2020-11-10 doi:10.1101/2020.11.09.375329 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ The H3.3K27M oncohistone antagonizes reprogramming in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.11.10.375881v1?rss=1 Ahmad, K. Henikoff, S. 2020-11-11 doi:10.1101/2020.11.10.375881 Cold Spring Harbor Laboratory Press 2020-11-11 <![CDATA[ Glia actively sculpt sensory neurons by controlled phagocytosis to tune animal behavior ]]> https://biorxiv.org/content/10.1101/2020.11.11.378893v1?rss=1 Raiders, S. Black, E. C. Bae, A. MacFarlane, S. Shaham, S. Singhvi, A. 2020-11-12 doi:10.1101/2020.11.11.378893 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Massively parallel phenotyping of variant impact in cancer with Perturb-seq reveals a shift in the spectrum of cell states induced by somatic mutations ]]> https://biorxiv.org/content/10.1101/2020.11.16.383307v1?rss=1 300,000 single lung cancer cells, and used the profiles to categorize variants into phenotypic subsets to distinguish gain-of-function, loss-of-function and dominant negative variants, which we validated by comparison to orthogonal assays. Surprisingly, KRAS variants did not merely fit into discrete functional categories, but rather spanned a continuum of gain-of-function phenotypes driven by quantitative shifts in cell composition at the single cell level. We further discovered novel gain-of-function KRAS variants whose impact could not have been predicted solely by their occurrence in patient samples. Our work provides a scalable, gene-agnostic method for coding variant impact phenotyping, which can be applied in cancer and other diseases driven by somatic or germline coding mutations. ]]> Ursu, O. Neal, J. T. Shea, E. Thakore, P. I. Jerby-Arnon, L. Nguyen, L. Dionne, D. Diaz, C. Bauman, J. Mosaad, M. Fagre, C. Giacomelli, A. Ly, S. H. Rozenblatt-Rosen, O. Hahn, W. Aguirre, A. Berger, A. Regev, A. Boehm, J. S. 2020-11-17 doi:10.1101/2020.11.16.383307 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies ]]> https://biorxiv.org/content/10.1101/2020.11.16.385278v1?rss=1 Garrett, M. E. Galloway, J. Chu, H. Y. Itell, H. L. Stoddard, C. I. Wolf, C. R. Logue, J. K. McDonald, D. Matsen, F. A. Overbaugh, J. 2020-11-16 doi:10.1101/2020.11.16.385278 Cold Spring Harbor Laboratory Press 2020-11-16 <![CDATA[ A functional module states framework reveals cell states for drug and target prediction ]]> https://biorxiv.org/content/10.1101/2020.11.24.394932v1?rss=1 Qin, G. Knijnenburg, T. Gibbs, D. Moser, R. Monnat, R. J. Kemp, C. Shmulevich, I. 2020-11-25 doi:10.1101/2020.11.24.394932 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells ]]> https://biorxiv.org/content/10.1101/2020.11.24.396713v1?rss=1 Swygert, S. G. Lin, D. Portillo-Ledesma, S. Lin, P.-Y. Hunt, D. R. Kao, C.-F. Schlick, T. Noble, W. S. Tsukiyama, T. 2020-11-24 doi:10.1101/2020.11.24.396713 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ 3D Adaptive Optical Nanoscopy for Thick Specimen Imaging at sub-50 nm Resolution ]]> https://biorxiv.org/content/10.1101/2020.11.25.398958v1?rss=1 Hao, X. Allgeyer, E. S. Antonello, J. Watters, K. Gerdes, J. A. Schroeder, L. K. Bottanelli, F. Zhao, J. Kidd, P. Lessard, M. D. Rothman, J. E. Cooley, L. Biederer, T. Booth, M. J. Bewersdorf, J. 2020-11-27 doi:10.1101/2020.11.25.398958 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Prospective mapping of viral mutations that escape antibodies used to treat COVID-19 ]]> https://biorxiv.org/content/10.1101/2020.11.30.405472v1?rss=1 Starr, T. N. Greaney, A. J. Addetia, A. Hannon, W. H. Choudhary, M. C. Dingens, A. S. Li, J. Z. Bloom, J. D. 2020-12-01 doi:10.1101/2020.11.30.405472 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Designed proteins assemble antibodies into modular nanocages ]]> https://biorxiv.org/content/10.1101/2020.12.01.406611v1?rss=1 Divine, R. Dang, H. V. Ueda, G. Fallas, J. A. Vulovic, I. Sheffler, W. Saini, S. Zhao, Y. T. Raj, I. X. Morawski, P. A. Jennewein, M. F. Homad, L. J. Wan, Y.-H. Tooley, M. R. Seeger, F. Fahning, M. L. Etemadi, A. Lazarovits, J. Roederer, A. Walls, A. C. Stewart, L. Mazloomi, M. King, N. P. Campbell, D. J. McGuire, A. T. Stamatatos, L. Ruohola-Baker, H. Mathieu, J. Veesler, D. Baker, D. 2020-12-01 doi:10.1101/2020.12.01.406611 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study ]]> https://biorxiv.org/content/10.1101/2020.12.07.415653v1?rss=1 Kim, A. E. Brandstetter, E. Wilcox, N. Heimonen, J. Graham, C. Han, P. D. Starita, L. M. McCulloch, D. J. Casto, A. M. Nickerson, D. A. Van de Loo, M. M. Mooney, J. Ilcisin, M. Fay, K. A. Lee, J. Sibley, T. R. Lyon, V. Geyer, R. E. Thompson, M. Lutz, B. R. Rieder, M. J. Bedford, T. Boeckh, M. Englund, J. A. Chu, H. 2020-12-08 doi:10.1101/2020.12.07.415653 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Integrative genomics identifies lncRNA regulatory networks across 1,044 pediatric leukemias and solid tumors ]]> https://biorxiv.org/content/10.1101/2020.12.10.420257v1?rss=1 Modi, A. Lopez, G. Conkrite, K. L. Leung, T. C. Ramanan, S. Cheung, D. Su, C. Manduchi, E. Johnson, M. E. Gadd, S. Zhang, J. Smith, M. A. Guidry Auvil, J. M. Gerhard, D. S. Meshinchi, S. Perlman, E. J. Hunger, S. P. Maris, J. M. Wells, A. D. Grant, S. F. A. Diskin, S. J. 2020-12-11 doi:10.1101/2020.12.10.420257 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ A viral histone-like protein exploits H1-HMGB1 antagonism for chromatin invasion ]]> https://biorxiv.org/content/10.1101/2020.12.11.418129v1?rss=1 Lynch, K. L. Bat-Erdene, M. Dillon, M. R. Lewis, H. C. Avgousti, D. C. 2020-12-11 doi:10.1101/2020.12.11.418129 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Identification of Celastrol as a novel HIV-1 Latency Reversal Agent by an Image-Based Screen ]]> https://biorxiv.org/content/10.1101/2020.12.17.423211v1?rss=1 Rice, A. P. Liu, H. Hu, P.-W. P. Dubrulle, J. P. Stossi, F. Mancini, M. Nikolai, B. 2020-12-17 doi:10.1101/2020.12.17.423211 Cold Spring Harbor Laboratory Press 2020-12-17 <![CDATA[ A human coronavirus evolves antigenically to escape antibody immunity ]]> https://biorxiv.org/content/10.1101/2020.12.17.423313v1?rss=1 1:100 do not detectably neutralize strains isolated 8-17 years later. The decreased neutralization of "future" viruses is due to antigenic evolution of the viral spike, especially in the receptor-binding domain. If these results extrapolate to other coronaviruses, then it may be advisable to periodically update SARS-CoV-2 vaccines. ]]> Eguia, R. Crawford, K. H. D. Stevens-Ayers, T. Kelnhofer-Millevolte, L. Greninger, A. L. Englund, J. A. Boeckh, M. J. Bloom, J. D. 2020-12-18 doi:10.1101/2020.12.17.423313 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Discovery of synthetic lethal and tumor suppressive paralog pairs in the human genome ]]> https://biorxiv.org/content/10.1101/2020.12.20.423710v1?rss=1 Parrish, P. C. R. Thomas, J. D. Kamlapurkar, S. Gabel, A. Bradley, R. K. Berger, A. H. 2020-12-21 doi:10.1101/2020.12.20.423710 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Multistability and consequent phenotypic plasticity in AMPK-Akt double negative feedback loop in cancer cells ]]> https://biorxiv.org/content/10.1101/2020.12.21.423274v1?rss=1 Chedere, A. Hari, K. Kumar, S. Rangarajan, A. Jolly, M. K. 2020-12-22 doi:10.1101/2020.12.21.423274 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Rare coding variants in 35 genes associate with circulating lipid levels: a multi-ancestry analysis of 170,000 exomes ]]> https://biorxiv.org/content/10.1101/2020.12.22.423783v1?rss=1 170,000 individuals from multiple ancestries: 97,493 European, 30,025 South Asian, 16,507 African, 16,440 Hispanic/Latino, 10,420 East Asian, and 1,182 Samoan. We identified 35 genes associated with circulating lipid levels. Ten of these: ALB, SRSF2, JAK2, CREB3L3, TMEM136, VARS, NR1H3, PLA2G12A, PPARG and STAB1 have not been implicated for lipid levels using rare coding variation in population-based samples. We prioritize 32 genes identified in array-based genome-wide association study (GWAS) loci based on gene-based associations, of which three: EVI5, SH2B3, and PLIN1, had no prior evidence of rare coding variant associations. Most of the associated genes showed evidence of association in multiple ancestries. Also, we observed an enrichment of gene-based associations for low-density lipoprotein cholesterol drug target genes, and for genes closest to GWAS index single nucleotide polymorphisms (SNP). Our results demonstrate that gene-based associations can be beneficial for drug target development and provide evidence that the gene closest to the array-based GWAS index SNP is often the functional gene for blood lipid levels. ]]> Hindy, G. Dornbos, P. Chaffin, M. D. Liu, D. J. Wang, M. X. Aguilar-Salinas, C. A. Antonacci-Fulton, L. Ardissino, D. Arnett, D. K. Aslibekyan, S. Atzmon, G. Ballantyne, C. M. Barajas-Olmos, F. Barzilai, N. Becker, L. C. Bielak, L. F. Bis, J. C. Blangero, J. Boerwinkle, E. Bonnycastle, L. L. Bottinger, E. Bowden, D. W. Bown, M. J. Brody, J. A. Broome, J. G. Burtt, N. P. Cade, B. E. Centeno-Cruz, F. Chan, E. Chang, Y.-C. Chen, Y.-D. I. Cheng, C.-Y. Choi, W. J. Chowdhury, R. Contreras-Cubas, C. Cordova, E. J. Correa, A. Cupples, L. A. Curran, J. E. Danesh, 2020-12-23 doi:10.1101/2020.12.22.423783 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis ]]> https://biorxiv.org/content/10.1101/2020.12.23.424063v1?rss=1 Carroll, P. Cheng, P.-F. Freie, B. W. Kasinathan, S. Gu, H. Hedrich, T. Dowdle, J. A. Venkataramani, V. Ramani, V. Raftery, D. Shendure, J. Ayer, D. E. Muller, C. H. Eisenman, R. N. N. 2020-12-23 doi:10.1101/2020.12.23.424063 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ TCR meta-clonotypes for biomarker discovery with tcrdist3: quantification of public, HLA-restricted TCR biomarkers of SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2020.12.24.424260v1?rss=1 Mayer-Blackwell, K. Schattgen, S. Cohen-Lavi, L. Crawford, J. C. Souquette, A. Gaevert, J. A. Hertz, T. Thomas, P. G. Bradley, P. H. Fiore-Gartland, A. 2020-12-26 doi:10.1101/2020.12.24.424260 Cold Spring Harbor Laboratory Press 2020-12-26 <![CDATA[ Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies ]]> https://biorxiv.org/content/10.1101/2020.12.31.425021v1?rss=1 10-fold by several mutations, including one in emerging viral lineages in South Africa and Brazil. Going forward, these serum escape maps can inform surveillance of SARS-CoV-2 evolution. ]]> Greaney, A. J. Loes, A. N. Crawford, K. H. Starr, T. N. Malone, K. D. Chu, H. Y. Bloom, J. D. 2021-01-04 doi:10.1101/2020.12.31.425021 Cold Spring Harbor Laboratory Press 2021-01-04 <![CDATA[ Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM ]]> https://biorxiv.org/content/10.1101/2021.01.06.425610v1?rss=1 Shen, B. W. Quispe, J. D. Luyten, Y. McGeough, B. C. Morgan, R. D. Stoddard, B. L. 2021-01-06 doi:10.1101/2021.01.06.425610 Cold Spring Harbor Laboratory Press 2021-01-06 <![CDATA[ Extracellular Matrix Dysfunction in Sorsby Patient-Derived Retinal Pigment Epithelium ]]> https://biorxiv.org/content/10.1101/2021.01.06.425613v1?rss=1 Engel, A. L. Wang, Y. Khuu, T. Worrall, E. Manson, M. A. Knight, K. Yanagida, A. Qi, J. H. Ramakrishnan, A. Weleber, R. G. Klein, M. Wilson, D. J. Anand-Apte, B. Hurley, J. B. Du, J. L. Chao, J. R. 2021-01-07 doi:10.1101/2021.01.06.425613 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Enhanced Solid Tumor Recognition and T cell Stemness with SynNotch CAR Circuits ]]> https://biorxiv.org/content/10.1101/2021.01.06.425642v1?rss=1 Hyrenius-Wittsten, A. Su, Y. Park, M. Garcia, J. M. Perry, N. Montgomery, G. Liu, B. Roybal, K. T. 2021-01-07 doi:10.1101/2021.01.06.425642 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Distinct spermiogenic phenotypes underlie sperm elimination in the Segregation Distorter meiotic drive system ]]> https://biorxiv.org/content/10.1101/2021.01.08.425928v1?rss=1 2000), spermatid nuclear compaction defects reach a threshold that triggers a checkpoint controlling sperm chromatin quality to eliminate abnormal spermatids during individualization. ]]> Herbette, M. Wei, X. Chang, C.-H. Larracuente, A. M. Loppin, B. Dubruille, R. 2021-01-09 doi:10.1101/2021.01.08.425928 Cold Spring Harbor Laboratory Press 2021-01-09 <![CDATA[ Cysteine is a limiting factor for glioma proliferation and survival ]]> https://biorxiv.org/content/10.1101/2021.01.08.425930v1?rss=1 Larion, M. Ruiz-Rodado, V. Dowdy, T. Lita, A. Kramp, T. Zhang, M. Jung, J. Dios-Esponera, A. Herold-Mende, C. C. Camphausen, K. Gilbert, M. R. 2021-01-08 doi:10.1101/2021.01.08.425930 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Targeting glucose metabolism sensitizes pancreatic cancer to MEK inhibition ]]> https://biorxiv.org/content/10.1101/2021.01.09.425923v1?rss=1 Yan, L. Tu, B. Yao, J. Gong, J. Carugo, A. Bristow, C. Wang, Q. Zhu, C. Dai, B. Kang, Y. Han, L. Feng, N. Jin, Y. Fleming, J. Heffernan, T. Yao, W. Ying, H. 2021-01-11 doi:10.1101/2021.01.09.425923 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Sustained IL-15 response signature predicts RhCMV/SIV vaccine efficacy ]]> https://biorxiv.org/content/10.1101/2021.01.11.426199v1?rss=1 Barrenäs, F. Hansen, S. G. Law, L. Driscoll, C. Green, R. R. Smith, E. Chang, J. Golez, I. Urion, T. Peng, X. Whitmore, L. Newhouse, D. Hughes, C. M. Morrow, D. Randall, K. T. Selseth, A. Ford, J. C. Gilbride, R. M. Randall, B. Ainslie, E. Oswald, K. Shoemaker, R. Fast, R. Bosche, W. J. Axthelm, M. K. Fukazawa, Y. Pavlakis, G. N. Felber, B. K. Fourati, S. Sekaly, R.-P. Lifson, J. D. Komorowski, J. Kosmider, E. Shao, J. Song, W. Edlefsen, P. T. Picker, L. J. Gale, M. 2021-01-11 doi:10.1101/2021.01.11.426199 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging ]]> https://biorxiv.org/content/10.1101/2021.01.14.426654v1?rss=1 Fragoza, R. Blengini, C. S. Tran, T. N. Pannafino, G. Al-Sweel, N. Schimenti, K. Schindler, K. Alani, E. Yu, H. Schimenti, J. C. 2021-01-14 doi:10.1101/2021.01.14.426654 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ DNA-based copy number analysis confirms genomic evolution of PDX models ]]> https://biorxiv.org/content/10.1101/2021.01.15.426865v1?rss=1 Hoge, A. Getz, M. Beroukhim, R. Golub, T. Ha, G. Ben-David, U. 2021-01-17 doi:10.1101/2021.01.15.426865 Cold Spring Harbor Laboratory Press 2021-01-17 <![CDATA[ Dynamics and turnover of memory CD8 T cell responses following yellow fever vaccination ]]> https://biorxiv.org/content/10.1101/2021.01.23.427919v1?rss=1 Zarnitsyna, V. I. Akondy, R. S. Ahmed, H. McGuire, D. J. Zarnitsyn, V. G. Moore, M. Johnson, P. L. F. Ahmed, R. Li, K. Hellerstein, M. Antia, R. 2021-01-23 doi:10.1101/2021.01.23.427919 Cold Spring Harbor Laboratory Press 2021-01-23 <![CDATA[ Engineering a niche supporting haematopoietic stem cell development using integrated single cell transcriptomics ]]> https://biorxiv.org/content/10.1101/2021.01.25.427999v1?rss=1 Hadland, B. Varnum-Finney, B. Dozono, S. Dignum, T. Nourigat-McKay, C. Jackson, D. L. Itkin, T. Butler, J. M. Rafii, S. Trapnell, C. Bernstein, I. D. 2021-01-26 doi:10.1101/2021.01.25.427999 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail ]]> https://biorxiv.org/content/10.1101/2021.01.27.428529v1?rss=1 Dong, J. Zost, S. Greaney, A. Starr, T. N. Dingens, A. S. Chen, E. C. Chen, R. Case, B. Sutton, R. Gilchuk, P. Rodriguez, J. Armstrong, E. Gainza, C. Nargi, R. Binshtein, E. Xie, X. Zhang, X. Shi, P.-Y. Logue, J. Weston, S. McGrath, M. Frieman, M. Brady, T. Tuffy, K. Bright, H. Loo, Y.-M. McvTamney, P. Esser, M. Carnahan, R. Diamond, M. Bloom, J. Crowe, J. E. 2021-01-28 doi:10.1101/2021.01.27.428529 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ RSC primes the quiescent genome for hypertranscription upon cell cycle re-entry ]]> https://biorxiv.org/content/10.1101/2021.01.28.428695v1?rss=1 Cucinotta, C. E. Dell, R. H. Braceros, K. C. A. Tsukiyama, T. 2021-01-28 doi:10.1101/2021.01.28.428695 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ A Cas-BCAR3 co-regulatory circuit controls lamellipodia dynamics ]]> https://biorxiv.org/content/10.1101/2021.01.29.428899v1?rss=1 Steenkiste, E. M. Berndt, J. D. Pilling, C. Simpkins, C. Cooper, J. A. 2021-01-29 doi:10.1101/2021.01.29.428899 Cold Spring Harbor Laboratory Press 2021-01-29 <![CDATA[ Atg8 licenses adipokine nuclear exit ]]> https://biorxiv.org/content/10.1101/2021.01.29.428913v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@1826425org.highwire.dtl.DTLVardef@17cca52org.highwire.dtl.DTLVardef@1c70ac7org.highwire.dtl.DTLVardef@94a024_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIIn fed state Upd2 requires Atg8 for nuclear exit and cytosolic localization. C_LIO_LIAtg8s lipidation on starvation results in Upd2s nuclear accumulation. C_LIO_LIUpd2 nuclear retention on starvation increases fat mobilization and post-starvation hunger. C_LIO_LIOn starvation Upd2 nuclear retention increases expression of a secreted innate immune signature. C_LI ]]> Poling, M. E. Sullivan, C. E. Brent, A. E. Hafer, T. L. Rajan, A. 2021-01-31 doi:10.1101/2021.01.29.428913 Cold Spring Harbor Laboratory Press 2021-01-31 <![CDATA[ Signaling amplitude molds the Ras mutation tropism of urethane ]]> https://biorxiv.org/content/10.1101/2021.02.09.430515v1?rss=1 Counter, C. Li, s. 2021-02-10 doi:10.1101/2021.02.09.430515 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ An improved ChEC-seq method accurately maps the genome-wide binding of transcription coactivators and sequence-specific transcription factors ]]> https://biorxiv.org/content/10.1101/2021.02.12.430999v1?rss=1 Donczew, R. Lalou, A. Devys, D. Tora, L. Hahn, S. 2021-02-12 doi:10.1101/2021.02.12.430999 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.02.16.431009v1?rss=1 Jun, S.-H. Toosi, H. Mold, J. Engblom, C. Chen, X. O'Flanagan, C. Hagemann-Jensen, M. Sandberg, R. Aparicio, S. Hartman, J. Roth, A. Lagergren, J. 2021-02-17 doi:10.1101/2021.02.16.431009 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016 ]]> https://biorxiv.org/content/10.1101/2021.02.17.431683v1?rss=1 Starr, T. N. Greaney, A. J. Dingens, A. S. Bloom, J. D. 2021-02-22 doi:10.1101/2021.02.17.431683 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Dopamine receptor DOP-1 engages a sleep pathway to modulate swimming in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.02.17.431715v1?rss=1 Xu, Y. Zhang, L. Liu, Y. Topalidou, I. Hassinan, C. Ailion, M. Zhao, Z. Wang, T. Chen, Z. Bai, J. 2021-02-18 doi:10.1101/2021.02.17.431715 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ Pregnancy and weaning regulate human maternal liver size and function ]]> https://biorxiv.org/content/10.1101/2021.02.18.431862v1?rss=1 Bartlett, A. Q. Francisco, M. Goddard, E. DeBarber, A. Leo, M. C. Baetscher, E. Rooney, W. Naugler, W. Catalano, P. Guimaraes, A. Purnell, J. Q. Vesco, K. K. Schedin, P. J. 2021-02-18 doi:10.1101/2021.02.18.431862 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ A large-scale transcriptome-wide association study (TWAS) of ten blood cell phenotypes reveals complexities of TWAS fine-mapping ]]> https://biorxiv.org/content/10.1101/2021.02.23.432444v1?rss=1 Tapia, A. L. Rowland, B. T. Rosen, J. D. Preuss, M. Young, K. Graff, M. Choquet, H. Couper, D. J. Buyske, S. Bien, S. A. Jorgenson, E. Kooperberg, C. Loos, R. J. F. Morrison, A. C. North, K. E. Yu, B. Reiner, A. P. Li, Y. Raffield, L. M. 2021-02-23 doi:10.1101/2021.02.23.432444 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Odor Blocking Of Stress ]]> https://biorxiv.org/content/10.1101/2021.02.24.432809v1?rss=1 Lee, E. J. Saraiva, L. R. Hanchate, N. K. Ye, X. Asher, G. Ho, J. Buck, L. B. 2021-02-25 doi:10.1101/2021.02.24.432809 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ A public broadly neutralizing antibody class targets a membrane-proximal anchor epitope of influenza virus hemagglutinin ]]> https://biorxiv.org/content/10.1101/2021.02.25.432905v1?rss=1 Guthmiller, J. J. Han, J. Utset, H. A. Li, L. Lan, L. Y.-L. Henry, C. Stamper, C. T. Stovicek, O. Gentles, L. Dugan, H. L. Zheng, N.-Y. Richey, S. T. Tepora, M. E. Bitar, D. J. Changrob, S. Strohmeier, S. Huang, M. Garcia-Sastre, A. Nachbagauer, R. Palese, P. Bloom, J. D. Krammer, F. Coughlan, L. Ward, A. B. Wilson, P. C. 2021-02-27 doi:10.1101/2021.02.25.432905 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Factors influencing maternal microchimerism throughout infancy and its impact on infant T cell immunity ]]> https://biorxiv.org/content/10.1101/2021.03.02.432825v1?rss=1 Balle, C. Kiravu, A. Hoffmann, A. Happel, A.-U. Kanaan, S. B. Nelson, J. L. Gray, C. Jaspan, H. B. Harrington, W. E. 2021-03-02 doi:10.1101/2021.03.02.432825 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Differential condensation of sister chromatids coordinates with Cdc6 to ensure distinct cell cycle progression in Drosophila male germline stem cell lineage ]]> https://biorxiv.org/content/10.1101/2021.03.08.434490v1?rss=1 Chen, X. Ranjan, R. Snedeker, J. Wooten, M. Chu, C. Bracer, S. Mouton, T. 2021-03-09 doi:10.1101/2021.03.08.434490 Cold Spring Harbor Laboratory Press 2021-03-09 <![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[ Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila ]]> https://biorxiv.org/content/10.1101/2021.03.10.434844v1?rss=1 Larson, E. D. Komori, H. Gibson, T. J. Ostgaard, C. M. Hamm, D. C. Schnell, J. M. Lee, C.-Y. Harrison, M. M. 2021-03-10 doi:10.1101/2021.03.10.434844 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Functional development of a V3-specific broadly neutralizing antibody isolated from a case of HIV superinfection ]]> https://biorxiv.org/content/10.1101/2021.03.15.435484v1?rss=1 Shipley, M. M. Mangala Prasad, V. Doepker, L. E. Dingens, A. S. Ralph, D. K. Harkins, E. Dhar, A. Arenz, D. Chohan, V. Weight, H. Mandaliya, K. Bloom, J. D. Matsen, F. Lee, K. K. Overbaugh, J. M. 2021-03-17 doi:10.1101/2021.03.15.435484 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Inflammatory signals are sufficient to elicit TOX expression in mouse and human CD8 T cells ]]> https://biorxiv.org/content/10.1101/2021.03.15.435527v1?rss=1 Maurice, N. J. Berner, J. Taber, A. K. Zehn, D. Prlic, M. 2021-03-16 doi:10.1101/2021.03.15.435527 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies ]]> https://biorxiv.org/content/10.1101/2021.03.17.435863v1?rss=1 Greaney, A. J. Starr, T. N. Barnes, C. O. Weisblum, Y. Schmidt, F. Caskey, M. Gaebler, C. Agudelo, M. Finkin, S. Wang, Z. Poston, D. Muecksch, F. Hatziioannou, T. Bieniasz, P. D. Robbiani, D. F. Nussenzweig, M. C. Bjorkman, P. J. Bloom, J. D. 2021-03-18 doi:10.1101/2021.03.17.435863 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ High throughput genome-wide single cell protein:DNA binding site mapping by targeted insertion of promoters (TIP-seq) ]]> https://biorxiv.org/content/10.1101/2021.03.17.435909v1?rss=1 Bartlett, D. A. Dileep, V. Henikoff, S. Gilbert, D. M. 2021-03-19 doi:10.1101/2021.03.17.435909 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Live imaging of SARS-CoV-2 infection in mice reveals neutralizing antibodies require Fc function for optimal efficacy ]]> https://biorxiv.org/content/10.1101/2021.03.22.436337v1?rss=1 Ullah, I. Prevost, J. Ladinsky, M. S. Stone, H. Lu, M. Anand, S. P. Beaudoin-Bussieres, G. Benlarbi, M. Ding, S. Gasser, R. Fink, C. Chen, Y. Tauzin, A. Goyette, G. Bourassa, C. Medjahed, H. Mack, M. Chung, K. Wilen, C. B. Dekaban, G. A. Dikeakos, J. D. Bruce, E. A. Kaufmann, D. E. Stamatatos, L. McGuire, A. Richard, J. Pazgier, M. Bjorkman, P. Mothes, W. Finzi, A. Kumar, P. Uchil, P. D. 2021-03-22 doi:10.1101/2021.03.22.436337 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Isolation and Characterization of Cross-Neutralizing Coronavirus Antibodies from COVID-19+ Subjects ]]> https://biorxiv.org/content/10.1101/2021.03.23.436684v1?rss=1 Jennewein, M. MacCamey, A. Akins, N. Feng, J. Homad, L. Hurlburt, N. Seydoux, E. Wang, Y.-H. Stuart, A. B. Edara, V. V. Floyd, K. Vanderheiden, A. Mascola, J. R. Doria-Rose, N. Wang, L. Yang, E. Chu, H. Torres, J. Ozorowski, G. Ward, A. Whaley, R. Cohen, K. Pancera, M. McElrath, J. Englund, J. A. Finzi, A. Suthar, M. McGuire, A. Stamatatos, L. 2021-03-24 doi:10.1101/2021.03.23.436684 Cold Spring Harbor Laboratory Press 2021-03-24 <![CDATA[ Highly-potent, synthetic APOBEC3s restrict HIV-1 through deamination-independent mechanisms ]]> https://biorxiv.org/content/10.1101/2021.04.06.438583v1?rss=1 McDonnell, M. M. Karvonen, S. C. Gaba, A. Flath, B. Chelico, L. Emerman, M. 2021-04-06 doi:10.1101/2021.04.06.438583 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape ]]> https://biorxiv.org/content/10.1101/2021.04.06.438709v1?rss=1 Starr, T. N. Czudnochowski, N. Zatta, F. Park, Y.-J. Liu, Z. Addetia, A. Pinto, D. Beltramello, M. Hernandez, P. Greaney, A. J. Marzi, R. Glass, W. G. Zhang, I. Dingens, A. S. Bowen, J. E. Wojcechowskyj, J. A. De Marco, A. Rosen, L. E. Zhou, J. Montiel-Ruiz, M. Kaiser, H. Tucker, H. Housley, M. P. Di Iulio, J. Lombardo, G. Agostini, M. Sprugasci, N. Culap, K. Jaconi, S. Meury, M. Dellota, E. Cameroni, E. Croll, T. I. Nix, J. C. Havenar-Daughton, C. Telenti, A. Lempp, F. A. Pizzuto, M. S. Chodera, J. D. Hebner, C. M. Whelan, S. P. Virgin, H. W. Veesler, 2021-04-08 doi:10.1101/2021.04.06.438709 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody ]]> https://biorxiv.org/content/10.1101/2021.04.07.438818v1?rss=1 Tortorici, M. A. Czudnochowski, N. Starr, T. N. Marzi, R. Walls, A. C. Zatta, F. Bowen, J. E. Jaconi, S. di Iulio, J. Wang, Z. De Marco, A. Zepeda, S. Pinto, D. Liu, Z. Beltramello, M. Bartha, I. Housley, M. P. Lempp, F. A. Rosen, L. E. Dellota, E. Kaiser, H. Montiel-Ruiz, M. Zhou, J. Addetia, A. Guarino, B. Culap, K. Sprugasci, N. Saliba, C. Vetti, E. Giacchetto-Sasselli, I. Silacci Fregni, C. Abdelnabi, R. Foo, C. S.-Y. Havenar-Daughton, C. Schmid, M. A. Benigni, F. Cameroni, E. Neyts, J. Telenti, A. Snell, G. Virgin, H. W. Whelan, S. P. J. Bloom, J. 2021-04-08 doi:10.1101/2021.04.07.438818 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Machine Learning Identifies Ponatinib as a Potent Inhibitor of SARS-CoV2-induced Cytokine Storm ]]> https://biorxiv.org/content/10.1101/2021.04.07.438871v1?rss=1 Chan, M. Vijay, S. McElrath, M. J. Holland, E. C. Gujral, T. S. 2021-04-09 doi:10.1101/2021.04.07.438871 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Structurally related but genetically unrelated antibody lineages converge on an immunodominantHIV-1 Env neutralizing determinant following trimer immunization ]]> https://biorxiv.org/content/10.1101/2021.04.09.439148v1?rss=1 Aljedani, S. Liban, T. J. Tran, K. Phad, G. Singh, S. Dubrovskaya, V. Pushparaj, P. Martinez-Murillo, P. Rodarte, J. Mileant, A. Mangala, V. Kinzelman, R. O'Dell, S. Mascola, J. R. Lee, K. K. Karlsson Hedestam, G. B. Wyatt, R. T. Pancera, M. 2021-04-09 doi:10.1101/2021.04.09.439148 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Polypharmacological Re-programming of Tumor-associated Macrophages Restores Antitumor Immunity ]]> https://biorxiv.org/content/10.1101/2021.04.10.439265v1?rss=1 Nishida-Aoki, N. Gujral, T. S. 2021-04-11 doi:10.1101/2021.04.10.439265 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Multipotent progenitors and hematopoietic stem cells arise independently during the endothelial to hematopoietic transition in the early mouse embryo ]]> https://biorxiv.org/content/10.1101/2021.04.13.439736v1?rss=1 Dignum, T. Varnum-Finney, B. Srivatsan, S. Dozono, S. Waltner, O. Heck, A. Nourigat-McKay, C. Jackson, D. L. Rafii, S. Trapnell, C. Bernstein, I. D. Hadland, B. K. 2021-04-14 doi:10.1101/2021.04.13.439736 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD ]]> https://biorxiv.org/content/10.1101/2021.04.14.439844v1?rss=1 Greaney, A. J. Loes, A. N. Gentles, L. E. Crawford, K. H. Starr, T. N. Malone, K. D. Chu, H. Y. Bloom, J. D. 2021-04-14 doi:10.1101/2021.04.14.439844 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum a Candidate Beneficial Bacterium from the Human Microbiome ]]> https://biorxiv.org/content/10.1101/2021.04.16.440249v1?rss=1 Flores Ramos, S. Brugger, S. D. Fernandez Escapa, I. Skeete, C. A. Cotton, S. L. Eslami, S. M. Gao, W. Bomar, L. Tran, T. H. Jones, D. S. Minot, S. Roberts, R. J. Johnston, C. D. Lemon, K. P. 2021-04-18 doi:10.1101/2021.04.16.440249 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Redefining replication in multi-ancestry genome-wide association studies ]]> https://biorxiv.org/content/10.1101/2021.04.20.440612v1?rss=1 Smith, S. P. Shahamatdar, S. Cheng, W. Zhang, S. Paik, J. Graff, M. Haiman, C. A. Matise, T. C. North, K. E. Peters, U. Kenny, E. Gignoux, C. R. Wojcik, G. L. Crawford, L. Ramachandran, S. 2021-04-20 doi:10.1101/2021.04.20.440612 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2021.04.20.440672v1?rss=1 Donczew, R. Hahn, S. 2021-04-20 doi:10.1101/2021.04.20.440672 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Multi-omics profiling of U2AF1 mutants dissects pathogenic mechanisms affecting RNA granules in myeloid malignancies ]]> https://biorxiv.org/content/10.1101/2021.04.22.441020v1?rss=1 Biancon, G. Joshi, P. Zimmer, J. T. Hunck, T. Gao, Y. Lessard, M. D. Courchaine, E. Barentine, A. E. Machyna, M. Botti, V. Qin, A. Gbyli, R. Patel, A. Song, Y. Kiefer, L. Viero, G. Neuenkirchen, N. Lin, H. Bewersdorf, J. Simon, M. D. Neugebauer, K. M. Tebaldi, T. Halene, S. 2021-04-23 doi:10.1101/2021.04.22.441020 Cold Spring Harbor Laboratory Press 2021-04-23 <![CDATA[ Kinetochore-associated Mps1 regulates the strength of kinetochore-microtubule attachments via Ndc80 phosphorylation ]]> https://biorxiv.org/content/10.1101/2021.04.25.441339v1?rss=1 Sarangapani, K. K. Koch, L. B. Nelson, C. R. Asbury, C. L. Biggins, S. 2021-04-26 doi:10.1101/2021.04.25.441339 Cold Spring Harbor Laboratory Press 2021-04-26 <![CDATA[ A Pan-Cancer Census of Dominant Tumor Immune Archetypes ]]> https://biorxiv.org/content/10.1101/2021.04.26.441344v1?rss=1 View larger version (77K): org.highwire.dtl.DTLVardef@55a5ccorg.highwire.dtl.DTLVardef@f8205corg.highwire.dtl.DTLVardef@1480b8org.highwire.dtl.DTLVardef@eb94e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Combes, A. J. Samad, B. Tsui, J. Chew, N. W. Yan, P. Reeder, G. C. Kushnoor, D. Shen, A. Davidson, B. Barczac, A. J. Adkisson, M. Edwards, A. Naser, M. Barry, K. C. Courau, T. Hammoudi, T. Arguello, R. J. Rao, A. A. Olshen, A. B. Immunoprofiler Consortium, Cai, C. Zhan, J. Davis, K. C. Kelley, R. K. Chapman, J. S. Attreya, C. E. Patel, A. Daud, A. I. Ha, P. Diaz, A. Kratz, J. R. Collisson, E. A. Fragiadakis, G. K. Erle, D. J. Boissonnas, A. Asthana, S. Chan, V. Krummel, M. F. 2021-04-27 doi:10.1101/2021.04.26.441344 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Identification of DAXX As A Restriction Factor Of SARS-CoV-2 Through A CRISPR/Cas9 Screen ]]> https://biorxiv.org/content/10.1101/2021.05.06.442916v1?rss=1 Mac Kain, A. Maarifi, G. Aicher, S.-M. Arhel, N. Baidaliuk, A. Vallet, T. Tran, Q. D. Hardy, A. Chazal, M. Porrot, F. Ohainle, M. Carlson-Stevermer, J. Oki, J. Holden, K. Simon-Loriere, E. Bruel, T. Schwartz, O. Jouvenet, N. Nisole, S. Vignuzzi, M. Roesch, F. 2021-05-06 doi:10.1101/2021.05.06.442916 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Individual Level Differential Expression Analysis for Single Cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.05.10.443350v1?rss=1 Zhang, M. Liu, S. Miao, Z. Han, F. Gottardo, R. Sun, W. 2021-05-10 doi:10.1101/2021.05.10.443350 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ Therapeutic reversal of prenatal pontine ID1 signaling in DIPG ]]> https://biorxiv.org/content/10.1101/2021.05.10.443452v1?rss=1 Yadav, V. N. Harris, M. K. Messinger, D. Thomas, C. Cummings, J. R. Yang, T. Woo, R. Siddaway, R. Burkert, M. Stallard, S. Qin, T. Mullan, B. Siada, R. Ravindran, R. Niculcea, M. Ginn, K. Gener, M. A. H. Dorris, K. Vitanza, N. A. Schmidt, S. Spitzer, J. Jiang, L. Filbin, M. Cao, X. Castro, M. Lowenstein, P. Mody, R. Chinnaiyan, A. Desprez, P.-Y. McAllister, S. Hawkins, C. Waszak, S. Venneti, S. Koschmann, C. 2021-05-11 doi:10.1101/2021.05.10.443452 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. ]]> https://biorxiv.org/content/10.1101/2021.05.10.443524v1?rss=1 Gupta, M. Azumaya, C. M. Moritz, M. Pourmal, S. Diallo, A. Merz, G. E. Jang, G. M. Bouhaddou, M. Fossati, A. Brilot, A. F. Diwanji, D. Hernandez, E. Herrera, N. Kratochvil, H. T. Lam, V. L. Li, F. Li, Y. Nguyen, H. C. Nowotny, C. Owens, T. W. Peters, J. K. Rizo, A. N. Schulze-Gahmen, U. Smith, A. M. Young, I. D. Yu, Z. Asarnow, D. Billesbolle, C. Campbell, M. G. Chen, J. Chen, K.-H. Chio, U. S. Dickinson, M. S. Doan, L. Jin, M. Kim, K. Li, J. Li, Y.-L. Linossi, E. Liu, Y. Lo, M. Lopez, J. Lopez, K. E. Mancino, A. Moss, F. R. Paul, M. D. Pawar, K. I 2021-05-12 doi:10.1101/2021.05.10.443524 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Comprehensive profiling of mutations to influenza virus PB2 that confer resistance to the cap-binding inhibitor pimodivir ]]> https://biorxiv.org/content/10.1101/2021.05.11.443605v1?rss=1 Soh, Y. Q. S. Malone, K. D. Eguia, R. T. Bloom, J. D. 2021-05-11 doi:10.1101/2021.05.11.443605 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ A graphical, interactive and GPU-enabled workflow to process long-read sequencing data ]]> https://biorxiv.org/content/10.1101/2021.05.11.443665v1?rss=1 Reddy, S. Hung, L.-H. Sala-Torra, O. Radich, J. Yeung, C. C. Yeung, K. Y. 2021-05-13 doi:10.1101/2021.05.11.443665 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ Chromosome length and gene density contribute to micronuclear membrane stability ]]> https://biorxiv.org/content/10.1101/2021.05.12.443914v1?rss=1 Mammel, A. Huang, H. Z. Gunn, A. L. Choo, E. Hatch, E. M. 2021-05-14 doi:10.1101/2021.05.12.443914 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ Stabilization of the SARS-CoV-2 Spike receptor-binding domain using deep mutational scanning and structure-based design ]]> https://biorxiv.org/content/10.1101/2021.05.15.444222v1?rss=1 Ellis, D. Brunette, N. Crawford, K. H. D. Walls, A. C. Pham, M. N. Chen, C. Herpoldt, K.-L. Fiala, B. Murphy, M. Pettie, D. Kraft, J. C. Malone, K. D. Navarro, M. J. Ogohara, C. Kepl, E. Ravichandran, R. Sydeman, C. Ahlrichs, M. Johnson, M. Blackstone, A. Carter, L. Starr, T. N. Greaney, A. J. Lee, K. K. Veesler, D. Bloom, J. D. King, N. P. 2021-05-16 doi:10.1101/2021.05.15.444222 Cold Spring Harbor Laboratory Press 2021-05-16 <![CDATA[ Patients with mesenchymal tumours and high Fusobacteriales prevalence have worse prognosis in colorectal cancer (CRC) ]]> https://biorxiv.org/content/10.1101/2021.05.17.444326v1?rss=1 Salvucci, M. Crawford, N. T. Stott, K. Bullman, S. Longley, D. B. Prehn, J. H. 2021-05-18 doi:10.1101/2021.05.17.444326 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Functional dissection of human mitotic proteins using CRISPR-Cas9 tiling screens ]]> https://biorxiv.org/content/10.1101/2021.05.20.445000v1?rss=1 Herman, J. A. Carter, L. Arora, S. Zhu, J. Biggins, S. Paddison, P. 2021-05-20 doi:10.1101/2021.05.20.445000 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Superscan: Supervised Single-Cell Annotation ]]> https://biorxiv.org/content/10.1101/2021.05.20.445014v1?rss=1 Shasha, C. Tian, Y. Mair, F. Miller, H. E. R. Gottardo, R. 2021-05-22 doi:10.1101/2021.05.20.445014 Cold Spring Harbor Laboratory Press 2021-05-22 <![CDATA[ Transcriptional and Functional Activity of Canine Hemangiosarcoma to Support Hematopoiesis Demonstrate Bone Marrow Nurse Cell Ontogeny ]]> https://biorxiv.org/content/10.1101/2021.05.21.445198v1?rss=1 Kim, J. H. Schulte, A. J. Sarver, A. L. Angelos, M. G. Frantz, A. M. Foster, C. L. O'Brien, T. D. Cornax, I. O'Sullivan, M. G. Cheng, N. Lewellen, M. Oseth, L. Kumar, S. Bullman, S. Pedamallu, C. S. Goyal, S. M. Meyerson, M. Lund, T. C. Alfoldi, J. Lindblad-Toh, K. Breen, M. Dickerson, E. B. Kaufman, D. S. Modiano, J. F. 2021-05-23 doi:10.1101/2021.05.21.445198 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Met is required for oligodendrocyte progenitor cell migration in Danio rerio ]]> https://biorxiv.org/content/10.1101/2021.05.21.445204v1?rss=1 Ali, M. F. Latimer, A. J. Wang, Y. Hogenmiller, L. Fontenas, L. Isabella, A. J. Moens, C. B. Yu, G. Kucenas, S. 2021-05-23 doi:10.1101/2021.05.21.445204 Cold Spring Harbor Laboratory Press 2021-05-23 <![CDATA[ Nonsense-mediated mRNA decay utilizes complementary mechanisms to suppress mRNA and protein accumulation ]]> https://biorxiv.org/content/10.1101/2021.05.24.445486v1?rss=1 Udy, D. B. Bradley, R. K. 2021-05-25 doi:10.1101/2021.05.24.445486 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence ]]> https://biorxiv.org/content/10.1101/2021.05.26.442666v1?rss=1 80%) have mild symptoms and recover in the outpatient setting, but detailed studies of immune responses have focused primarily on moderate to severe COVID-19. We deeply profiled the longitudinal immune response in individuals with mild COVID-19 beginning with early time points post-infection (1-15 days) and proceeding through convalescence to >100 days after symptom onset. We correlated data from single cell analyses of peripheral blood cells, serum proteomics, virus-specific cellular and humoral immune responses, and clinical metadata. Acute infection was characterized by vigorous coordinated innate and adaptive immune activation that differed in character by age (young vs. old). We then characterized signals associated with recovery and convalescence to define and validate a new signature of inflammatory cytokines, gene expression, and chromatin accessibility that persists in individuals with post-acute sequelae of SARS-CoV-2 infection (PASC). ]]> Talla, A. Vasaikar, S. V. Lemos, M. P. Moodie, Z. Pebworth, M.-P. L. Henderson, K. E. Cohen, K. W. Czartoski, J. L. Lai, L. Suthar, M. S. Heubeck, A. T. Genge, P. C. Roll, C. M. Weiss, M. Reading, J. Kondza, N. MacMillan, H. Fong, O. C. Thomson, Z. J. Graybuck, L. T. Newell, E. W. Coffey, E. M. Meijer, P. Becker, L. A. De Rosa, S. C. Torgerson, T. R. Skene, P. J. Li, X. Szeto, G. L. McElrath, M. J. Bumol, T. F. 2021-05-26 doi:10.1101/2021.05.26.442666 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Identifying strengths and weaknesses of methods for computational network inference from single cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2021.06.01.446671v1?rss=1 Stone, M. McCalla, S. G. Fotuhi Siahpirani, A. Periyasamy, V. Shin, J. Roy, S. 2021-06-02 doi:10.1101/2021.06.01.446671 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ T helper 2 transcriptional profile predicts single-cell HIV envelope-specific polyfunctional CD4+ T cells correlated with reduced risk of infection in RV144 trial ]]> https://biorxiv.org/content/10.1101/2021.06.07.447395v1?rss=1 Cohen, K. W. Tian, Y. Thayer, C. Seese, A. Amezquita, R. McElrath, M. J. De Rosa, S. Gottardo, R. 2021-06-07 doi:10.1101/2021.06.07.447395 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ The atypical RNA-binding protein TAF15 regulates dorsoanterior neural development through diverse mechanisms in Xenopus tropicalis. ]]> https://biorxiv.org/content/10.1101/2021.06.14.041913v1?rss=1 DeJong, C. S. Dichmann, D. S. Exner, C. R. T. Xu, Y. Harland, R. M. 2021-06-14 doi:10.1101/2021.06.14.041913 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy ]]> https://biorxiv.org/content/10.1101/2021.06.15.448495v1?rss=1 10% on at least one day). Unsupervised learning was then applied to hierarchically organize VRVs by spatiotemporal patterns and identify VRV-haplotypes. Finally, homology modelling was performed to gain insight into potential impact of VRVs on Spike protein structure. We identified 90 VRVs, 71 of which have not previously been observed in a VOI/VOC, and 35 of which have emerged recently and are durably present. Our analysis identifies 17 VRVs [~]91 days earlier than their first corresponding VOI/VOC publication. Unsupervised learning revealed eight VRV-haplotypes of 4 VRVs or more, suggesting two emerging strains (B1.1.222 and B.1.234). Structural modeling supported potential functional impact of the D1118H and L452R mutations. The SLS approach equally monitors all Spike residues over time, independently of existing phylogenic classifications, and is complementary to existing genomic surveillance methods. ]]> Zhao, L. P. Lybrand, T. P. Gilbert, P. B. Hawn, T. R. Schiffer, J. T. Stamatatos, L. Payne, T. H. Carpp, L. Geraghty, D. E. Jerome, K. R. 2021-06-15 doi:10.1101/2021.06.15.448495 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic ]]> https://biorxiv.org/content/10.1101/2021.06.18.449051v1?rss=1 Bloom, J. D. 2021-06-22 doi:10.1101/2021.06.18.449051 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Mammalian UPF3A and UPF3B activate NMD independently of their EJC binding ]]> https://biorxiv.org/content/10.1101/2021.07.02.450872v1?rss=1 Yi, Z. Arvola, R. M. Myers, S. Dilsavor, C. N. Abu Alhasan, R. Carter, B. N. Patton, R. D. Bundschuh, R. Singh, G. 2021-07-03 doi:10.1101/2021.07.02.450872 Cold Spring Harbor Laboratory Press 2021-07-03 <![CDATA[ Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma ]]> https://biorxiv.org/content/10.1101/2021.07.03.450733v1?rss=1 Freeman, S. S. Sade-Feldman, M. Kim, J. Stewart, C. Gonye, A. L. K. Ravi, A. Arniella, M. B. Gushterova, I. LaSalle, T. J. Blaum, E. M. Yizhak, K. Frederick, D. T. Sharova, T. Leshchiner, I. Elagina, L. Spiro, O. G. Livitz, D. Rosebrock, D. Aguet, F. Carrot-Zhang, J. Ha, G. Lin, Z. Chen, J. H. Barzily-Rokni, M. Hammond, M. R. Vitzthum von Eckstaedt, H. C. Blackmon, S. M. Jiao, Y. J. Gabriel, S. Lawrence, D. P. Duncan, L. M. Stemmer-Rachamimov, A. O. Wargo, J. A. Flaherty, K. T. Sullivan, R. J. Boland, G. M. Meyerson, M. Getz, G. Hacohen, N. 2021-07-04 doi:10.1101/2021.07.03.450733 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ eQTL mapping using allele-specific gene expression ]]> https://biorxiv.org/content/10.1101/2021.07.03.450987v1?rss=1 Zhabotynsky, V. Huang, L. Little, P. Hu, Y. Pardo Manuel de Villena, F. F. Zou, F. Sun, W. 2021-07-04 doi:10.1101/2021.07.03.450987 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ PHENOTYPIC CHARACTERIZATION OF TWO NOVEL CELL LINE MODELS OF CASTRATION RESISTANT PROSTATE CANCER. ]]> https://biorxiv.org/content/10.1101/2021.07.04.450352v1?rss=1 Haffner, M. C. Bhamidipati, A. Tsai, H. K. Esopi, D. M. Vaghasia, A. M. Low, J.-Y. Patel, R. A. Guner, G. Pham, M.-T. Castagna, N. Hicks, J. Wyhs, N. Aebersold, R. De Marzo, A. M. Nelson, W. G. Guo, T. Yegnasubramanian, S. 2021-07-05 doi:10.1101/2021.07.04.450352 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Multivalent designed proteins protect against SARS-CoV-2 variants of concern ]]> https://biorxiv.org/content/10.1101/2021.07.07.451375v1?rss=1 Hunt, A. C. Case, J. B. Park, Y.-J. Cao, L. Wu, K. Walls, A. C. Liu, Z. Bowen, J. E. Yeh, H.-W. Saini, S. Helms, L. Zhao, Y. T. Hsiang, T.-Y. Starr, T. N. Goreshnik, I. Kozodoy, L. Carter, L. Ravichandran, R. Green, L. B. Matochko, W. L. Thomson, C. A. Vogeli, B. Kruger-Gericke, A. VanBlargan, L. A. Chen, R. E. Ying, B. Bailey, A. L. Kafai, N. M. Boyken, S. Ljubetic, A. Edman, N. Ueda, G. Chow, C. Addetia, A. Panpradist, N. Gale, M. Freedman, B. Lutz, B. Bloom, J. D. Ruohola-Baker, H. Whelan, S. P. J. Stewart, L. Diamond, M. S. Veesler, D. Jewett, M. 2021-07-07 doi:10.1101/2021.07.07.451375 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer ]]> https://biorxiv.org/content/10.1101/2021.07.07.451502v1?rss=1 Mujal, A. M. Combes, A. J. Rao, A. A. Binnewies, M. Samad, B. Tsui, J. Boissonnas, A. Pollack, J. L. Arguello, R. J. Ruhland, M. K. Barry, K. C. Chan, V. Krummel, M. F. 2021-07-08 doi:10.1101/2021.07.07.451502 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Pooled screening of CAR T cells identifies non-native signaling domains for next- generation immunotherapies ]]> https://biorxiv.org/content/10.1101/2021.07.11.451980v1?rss=1 Goodman, D. B. Azimi, C. S. Kearns, K. Garakani, K. Garcia, J. Patel, N. Hwang, B. Lee, D. Park, E. Ye, C. J. Marson, A. Bluestone, J. Roybal, K. 2021-07-12 doi:10.1101/2021.07.11.451980 Cold Spring Harbor Laboratory Press 2021-07-12 <![CDATA[ Active enhancers strengthen TAD insulation by bRNA mediated CTCF enrichment at the TAD boundaries ]]> https://biorxiv.org/content/10.1101/2021.07.13.452118v1?rss=1 Islam, Z. Saravanan, B. Walavalkar, K. Farooq, U. Singh, A. K. Thakur, J. Pandit, A. Sabarinathan, R. Henikoff, S. Notani, D. 2021-07-14 doi:10.1101/2021.07.13.452118 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Divergence in dimerization and activity of primate APOBEC3C ]]> https://biorxiv.org/content/10.1101/2021.07.13.452235v1?rss=1 Gaba, A. Hix, M. A. Suhail, S. Flath, B. Boysan, B. Williams, D. R. Pelletier, T. Emerman, M. Morcos, F. Cisneros, G. A. Chelico, L. 2021-07-13 doi:10.1101/2021.07.13.452235 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ ACE2 binding is an ancestral and evolvable trait of sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2021.07.17.452804v1?rss=1 Starr, T. N. Zepeda, S. K. Walls, A. C. Greaney, A. J. Veesler, D. Bloom, J. D. 2021-07-19 doi:10.1101/2021.07.17.452804 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Vaccinia Virus Arrests and Shifts the Cell Cycle ]]> https://biorxiv.org/content/10.1101/2021.07.19.452625v1?rss=1 Martin, C. K. Samolej, J. Olson, A. T. Bertoli, C. Wiebe, M. S. de Bruin, R. A. M. Mercer, J. 2021-07-19 doi:10.1101/2021.07.19.452625 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Systems analysis of immune responses to attenuated P. falciparum malaria sporozoite vaccination reveals excessive inflammatory signatures correlating with impaired immunity ]]> https://biorxiv.org/content/10.1101/2021.07.28.454252v1?rss=1 Du, Y. Hertoghs, N. Carnes, J. McDermott, S. M. Neal, M. L. Schwedhelm, K. V. McElrath, M. J. De Rosa, S. C. Aitchison, J. D. Stuart, K. D. 2021-07-29 doi:10.1101/2021.07.28.454252 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Engineering adoptive T cell therapy to co-opt Fas ligand-mediated death signaling in ovarian cancer enhances therapeutic efficacy ]]> https://biorxiv.org/content/10.1101/2021.07.30.454539v1?rss=1 Anderson, K. G. Oda, S. K. Bates, B. M. Burnett, M. G. Rodgers Suarez, M. Ruskin, S. L. Greenberg, P. D. 2021-07-31 doi:10.1101/2021.07.30.454539 Cold Spring Harbor Laboratory Press 2021-07-31 <![CDATA[ Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit. ]]> https://biorxiv.org/content/10.1101/2021.08.02.454829v1?rss=1 Hurlburt, N. Homad, L. Siha, I. Jenewein, M. F. MacCamy, A. Wan, Y.-H. Boonyaratanakornkit, J. Sholukh, A. M. Zhou, P. Burton, D. Andrabi, R. Stamatatos, L. Pancera, M. McGuire, A. 2021-08-03 doi:10.1101/2021.08.02.454829 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia ]]> https://biorxiv.org/content/10.1101/2021.08.03.454902v1?rss=1 Harada, T. Heshmati, Y. Kalfon, J. Ferrucio, J. X. Perez, M. Ewers, J. Kossenkov, A. Ellegast, J. M. Yi, J. S. Bowker, A. Zhu, Q. Eagle, K. Dempster, J. M. Kugener, G. Wickramasinghe, J. Herbert, Z. T. Li, C. H. Koren, J. V. Weinstock, D. M. Paralkar, V. R. Nabet, B. Lin, C. Y. Dharia, N. V. Stegmaier, K. Orkin, S. H. Pimkin, M. 2021-08-04 doi:10.1101/2021.08.03.454902 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ Coordinated Cross-Talk Between the Myc and Mlx Networks in Liver Regeneration and Neoplasia ]]> https://biorxiv.org/content/10.1101/2021.08.05.455215v1?rss=1 Wang, H. Lu, J. Alencastro, F. Roberts, A. Fiedor, J. Carroll, P. Eisenman, R. Ranganathan, S. Torbenson, M. Duncan, A. W. Prochownik, E. V. 2021-08-06 doi:10.1101/2021.08.05.455215 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Quantitative Restoration of Immune Defense in Old Animals Determined by Naive Antigen-Specific CD8 T cell Numbers ]]> https://biorxiv.org/content/10.1101/2021.08.09.453882v1?rss=1 four-fold) and NS4b:H-2Db-restricted antigen-specific CD8 T cells (two-fold). This improved the numbers of NS4b-specific CD8 T cells detected at the peak of the response against WNV, but not survival of WNV challenge. IL-7C treated old animals also showed no improvement in WNV-specific effector immunity (neutralizing antibody and in vivo T cell cytotoxicity). To test quantitative limits to which CD8 Tn cell restoration could improve protective immunity, we transferred graded doses of Ag-specific precursors into old mice and showed that injection of 5,400 (but not of 1,800 or 600) adult naive WNV-specific CD8 T cells significantly increased survival after WNV. These results set quantitative limits to the level of Tn reconstitution necessary to improve immune defense in older organisms and are discussed in light of targets of immune reconstitution. ]]> Uhrlaub, J. Jergovic, M. Bradshaw, C. M. Sonar, S. Coplen, C. P. Dudakov, J. Murray, K. O. Lanteri, M. C. Busch, M. P. van den Brink, M. R. M. Nikolich-Zugich, J. 2021-08-10 doi:10.1101/2021.08.09.453882 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ The light chain of the L9 antibody is critical for binding circumsporozoite protein minor repeats and preventing malaria ]]> https://biorxiv.org/content/10.1101/2021.08.11.455919v1?rss=1 Wang, L. T. Hurlburt, N. K. Schon, A. Flynn, B. J. Pereira, L. S. Dillon, M. Flores-Garcia, Y. Bonilla, B. Zavala, F. Idris, A. H. Francica, J. R. Pancera, M. Seder, R. A. 2021-08-11 doi:10.1101/2021.08.11.455919 Cold Spring Harbor Laboratory Press 2021-08-11 <![CDATA[ Autoimmune Alleles at the Major Histocompatibility Locus Modify Melanoma Susceptibility ]]> https://biorxiv.org/content/10.1101/2021.08.12.456166v1?rss=1 1%). However, autoimmune alleles showed higher affinity relative to common alleles for particular windows of melanocyte conserved antigens suggesting a potential relationship between antigen processing, binding, and cell-surface presentation. Overall, this study presents evidence that MHC-I autoimmune risk alleles modulate melanoma risk unaccounted for by current PRS. ]]> Talwar, J. Laub, D. Pagadala, M. Castro, A. Lewis, M. Luebeck, G. E. Morris, G. P. Salem, R. M. Thompson, W. K. Curtius, K. Zanetti, M. Carter, H. 2021-08-13 doi:10.1101/2021.08.12.456166 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes ]]> https://biorxiv.org/content/10.1101/2021.08.16.456461v1?rss=1 98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism generally contributes to the convergent evolution of Y chromosome organization. ]]> Chang, C.-H. Gregory, L. E. Gordon, K. E. Meiklejohn, C. D. Larracuente, A. 2021-08-16 doi:10.1101/2021.08.16.456461 Cold Spring Harbor Laboratory Press 2021-08-16 <![CDATA[ SOX2-phosphorylation toggles a bistable differentiation-switch in squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2021.08.18.455699v1?rss=1 Hoang-Phou, S. Sastre-Perona, A. Abbruzzese, M. Ying, Z. Siegle, J. Aranda Orgilles, B. Rocha, P. P. Aifantis, I. Skok, J. Beronja, S. Schober, M. 2021-08-18 doi:10.1101/2021.08.18.455699 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Different adjuvanted pediatric HIV envelope vaccines induced distinct plasma antibody responses despite similar B cell receptor repertoires in infant rhesus macaques. ]]> https://biorxiv.org/content/10.1101/2021.08.18.456876v1?rss=1 Fouda, G. G. Berendam, S. J. Morgan-Asiedu, P. K. Mangan, R. J. Li, S. Heimsath, H. Luo, K. Curtis, A. D. Eudailey, J. A. Fox, C. B. Tomai, M. A. Phillips, B. Itell, H. L. Kunz, E. Hudgens, M. Cronin, K. Wiehe, K. Alam, S. M. Van Rompay, K. K. A. De Paris, K. Permar, S. R. Moody, M. A. 2021-08-20 doi:10.1101/2021.08.18.456876 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Characterization of a vaccine-elicited human antibody with sequence homology to VRC01-class antibodies that binds the C1C2 gp120 domain ]]> https://biorxiv.org/content/10.1101/2021.08.21.457217v1?rss=1 Gray, M. D. Feng, J. Weidle, C. E. Cohen, K. W. Ballweber-Fleming, L. MacCamy, A. J. Huynh, C. N. Trichka, J. J. Montefiori, D. Ferrari, G. Pancera, M. McElrath, M. J. Stamatatos, L. 2021-08-23 doi:10.1101/2021.08.21.457217 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Coordinately regulated interbacterial antagonism defense pathways constitute a bacterial innate immune system ]]> https://biorxiv.org/content/10.1101/2021.08.22.457286v1?rss=1 Ting, S.-Y. LaCourse, K. D. Ledvina, H. E. Zhang, R. Radey, M. C. Kulasekara, H. D. Somavanshi, R. Bertolli, S. K. Gallagher, L. A. Kim, J. Penewit, K. M. Salipante, S. J. Xu, L. Peterson, S. B. Mougous, J. D. 2021-08-23 doi:10.1101/2021.08.22.457286 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ HIV-1 Vif gained breadth in APOBEC3G specificity after cross-species transmission of its precursors ]]> https://biorxiv.org/content/10.1101/2021.08.23.457421v1?rss=1 Chesarino, N. M. Emerman, M. 2021-08-23 doi:10.1101/2021.08.23.457421 Cold Spring Harbor Laboratory Press 2021-08-23 <![CDATA[ Activation of the Zinc-sensing receptor GPR39 promotes T cell reconstitution after hematopoietic stem cell transplant ]]> https://biorxiv.org/content/10.1101/2021.09.02.458741v1?rss=1 Iovino, L. Cooper, K. deRoos, P. Kinsella, S. Evandy, C. Ugrai, T. Mazziotta, F. Ensbey, K. S. Granadier, D. Hopwo, K. Smith, C. Gagnon, A. Galimberti, S. Petrini, M. Hill, G. R. Dudakov, J. A. 2021-09-03 doi:10.1101/2021.09.02.458741 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Multiplexed triage of candidate biomarkers in plasma using internal standard triggered-parallel reaction monitoring mass spectrometry ]]> https://biorxiv.org/content/10.1101/2021.09.02.458791v1?rss=1 Kennedy, J. J. Whiteaker, J. R. Ivey, R. G. Burian, A. Chowdhury, S. Tsai, C.-F. Liu, T. Lin, C. Murillo, O. Lundeen, R. A. Jones, L. A. Gafken, P. R. Longton, G. Rodland, K. D. Skates, S. Landua, J. Wang, P. Lewis, M. T. Paulovich, A. G. 2021-09-03 doi:10.1101/2021.09.02.458791 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ Pro-apoptotic caspase deficiency reveals a cell-extrinsic mechanism of NK cell regulation ]]> https://biorxiv.org/content/10.1101/2021.09.09.459676v1?rss=1 Olsen, T. M. Tan, W. H. Knudsen, A. C. Rongvaux, A. 2021-09-10 doi:10.1101/2021.09.09.459676 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ A faithful in vivo model of human macrophages in metastatic melanoma ]]> https://biorxiv.org/content/10.1101/2021.09.09.459682v1?rss=1 Voillet, V. Berger, T. R. McKenna, K. M. Paulson, K. G. Smythe, K. S. Hunter, D. S. Valente, W. J. Weaver, S. J. Campbell, J. S. Kim, T. S. Byrd, D. R. Bielas, J. H. Pierce, R. H. Chapuis, A. G. Gottardo, R. Rongvaux, A. 2021-09-11 doi:10.1101/2021.09.09.459682 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2021.09.11.459844v1?rss=1 Kistler, K. Huddleston, J. Bedford, T. 2021-09-12 doi:10.1101/2021.09.11.459844 Cold Spring Harbor Laboratory Press 2021-09-12 <![CDATA[ Convergent clonal selection of donor- and recipient-derived CMV-specific T cells in hematopoietic stem cell transplant patients ]]> https://biorxiv.org/content/10.1101/2021.09.14.458942v1?rss=1 Erickson, J. R. Stevens-Ayers, T. Mair, F. Edmison, B. Boeckh, M. Bradley, P. H. Prlic, M. 2021-09-15 doi:10.1101/2021.09.14.458942 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Mechanism of broad-spectrum Cas9 inhibition by AcrIIA11 ]]> https://biorxiv.org/content/10.1101/2021.09.15.460536v1?rss=1 Dillard, K. E. Terrace, C. Javanmardi, K. Kim, W. Forsberg, K. J. Finkelstein, I. J. 2021-09-15 doi:10.1101/2021.09.15.460536 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities ]]> https://biorxiv.org/content/10.1101/2021.09.17.460747v1?rss=1 Russell, M. L. Souquette, A. Levine, D. M. Allen, E. K. Kuan, G. Simon, N. Balmaseda, A. Gordon, A. Thomas, P. Matsen, F. A. Bradley, P. G. 2021-09-20 doi:10.1101/2021.09.17.460747 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ SL-Cloud: A Computational Resource to Support Synthetic Lethal Interaction Discovery ]]> https://biorxiv.org/content/10.1101/2021.09.18.459450v1?rss=1 Tercan, B. Qin, G. Kim, T. Aguilar, B. Kemp, C. J. Chambwe, N. Shmulevich, I. 2021-09-19 doi:10.1101/2021.09.18.459450 Cold Spring Harbor Laboratory Press 2021-09-19 <![CDATA[ Brain I3 Binding Protein regulates K-Ras4B membrane localization and signaling ]]> https://biorxiv.org/content/10.1101/2021.09.21.461216v1?rss=1 McCabe, I. Zhang, H. Cooper, J. A. Turner, D. L. Vojtek, A. B. 2021-09-22 doi:10.1101/2021.09.21.461216 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Hematopoietic recovery after transplantation is primarily derived from the stochastic contribution of hematopoietic stem cells ]]> https://biorxiv.org/content/10.1101/2021.09.21.461235v1?rss=1 Radtke, S. Enstrom, M. Pande, D. P. Cui, M. L. Madhu, R. Perez, A. Kiem, H.-P. 2021-09-21 doi:10.1101/2021.09.21.461235 Cold Spring Harbor Laboratory Press 2021-09-21 <![CDATA[ Batch effects removal for microbiome data via conditional quantile regression (ConQuR) ]]> https://biorxiv.org/content/10.1101/2021.09.23.461592v1?rss=1 Ling, W. Zhao, N. Lulla, A. Plantinga, A. M. Fu, W. Zhang, A. Liu, H. Li, Z. Chen, J. Randolph, T. Koay, W. L. A. White, J. R. Launer, L. J. Fodor, A. A. Meyer, K. A. Wu, M. C. 2021-09-24 doi:10.1101/2021.09.23.461592 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Prioritizing candidate peptides for cancer vaccines by PEPPRMINT: a statistical model to predict peptide presentation by HLA-I proteins ]]> https://biorxiv.org/content/10.1101/2021.09.24.461596v1?rss=1 Zhou, L. Y. Zou, F. Sun, W. 2021-09-26 doi:10.1101/2021.09.24.461596 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Single-cell RNA Sequencing Reveals Immunosuppressive Myeloid Cell Diversity and Restricted Cytotoxic Effector Cell Trafficking and Activation During Malignant Progression in Glioma ]]> https://biorxiv.org/content/10.1101/2021.09.24.461735v1?rss=1 Rajendran, S. Peterson, C. Canella, A. Hu, Y. Gross, A. Cam, M. Serin Harmanci, A. Distefano, R. Nigita, G. Wang, W. Miller, K. E. Elemento, O. Roberts, R. D. Holland, E. C. Rao, G. Mardis, E. R. Rajappa, P. 2021-09-25 doi:10.1101/2021.09.24.461735 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ An innate immune activation state prior to vaccination predicts responsiveness to multiple vaccines ]]> https://biorxiv.org/content/10.1101/2021.09.26.461847v1?rss=1 Fourati, S. Tomalin, L. E. Mule, M. P. Chawla, D. G. Gerritsen, B. Rychkov, D. Henrich, E. Miller, H. E. Hagan, T. Diray-Arce, J. Dunn, P. The Human Immunology Project Consortium (HIPC), Levy, O. Gottardo, R. Sarwal, M. Tsang, J. Suarez-Farinas, M. Pulendran, B. Sekaly, R.-P. Kleinstein, S. H. 2021-09-26 doi:10.1101/2021.09.26.461847 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ An international report on bacterial communities in esophageal squamous cell carcinoma ]]> https://biorxiv.org/content/10.1101/2021.09.29.462325v1?rss=1 Nomburg, J. Bullman, S. Nasrollahzadeh, D. Collisson, E. A. Abedi-Ardekani, B. Akoko, L. O. Atkins, J. R. Buckle, G. C. Gopal, S. Hu, N. Kaimila, B. Khoshnia, M. Malekzadeh, R. Menya, D. Mmbaga, B. T. Moody, S. Mulima, G. Mushi, B. P. Mwaiselage, J. Mwanga, A. Newton, Y. Ng, D. L. Radenbaugh, A. Rwakatema, D. S. Selekwa, M. Schüz, J. Taylor, P. R. Vaske, C. Goldstein, A. Stratton, M. R. McCormack, V. Brennan, P. DeCaprio, J. A. Meyerson, M. Mmbaga, E. J. Van Loon, K. 2021-09-29 doi:10.1101/2021.09.29.462325 Cold Spring Harbor Laboratory Press 2021-09-29 <![CDATA[ Structures of core eukaryotic protein complexes ]]> https://biorxiv.org/content/10.1101/2021.09.30.462231v1?rss=1 Humphreys, I. R. Pei, J. Baek, M. Krishnakumar, A. Anishchenko, I. Ovchinnikov, S. R. Zheng, J. Ness, T. Banjade, S. Bagde, S. R. Stancheva, V. Li, X. Liu, K. Zheng, Z. Barerro, D. Roy, U. Fernandez, I. S. Szakal, B. Branzei, D. Greene, E. C. Biggins, S. Keeney, S. Miller, E. A. Fromme, J. C. Hendrickson, T. Cong, Q. Baker, D. 2021-09-30 doi:10.1101/2021.09.30.462231 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Cx43 carboxyl terminal domain determines AQP4 and Cx30 endfoot organization and blood brain barrier permeability ]]> https://biorxiv.org/content/10.1101/2021.09.30.462547v1?rss=1 Cibelli, A. Stout, R. Timmermann, A. de Menezes, L. Guo, P. Maass, K. Seifert, G. Steinhaeuser, C. Spray, D. C. Scemes, E. 2021-10-01 doi:10.1101/2021.09.30.462547 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein after infection and/or vaccination ]]> https://biorxiv.org/content/10.1101/2021.10.05.463210v1?rss=1 Garrett, M. E. Galloway, J. G. Wolf, C. Logue, J. K. Franko, N. Chu, H. Y. Matsen, F. Overbaugh, J. M. 2021-10-07 doi:10.1101/2021.10.05.463210 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Whole genome sequence analysis of blood lipid levels in >66,000 individuals ]]> https://biorxiv.org/content/10.1101/2021.10.11.463514v1?rss=1 Selvaraj, M. S. Li, X. Li, Z. Pampana, A. Zhang, D. Y. Park, J. Aslibekyan, S. Bis, J. C. Brody, J. A. Cade, B. E. Chuang, L.-M. Chung, R.-H. Curran, J. E. de las Fuentes, L. de Vries, P. S. Duggirala, R. Freedman, B. I. Graff, M. Guo, X. Heard-Costa, N. Hidalgo, B. Hwu, C.-M. Irvin, M. R. Kelly, T. N. Kral, B. G. Lange, L. Li, X. Lisa, M. Lubitz, S. A. Manichaikul, A. W. Michael, P. Montasser, M. E. Morrison, A. C. Naseri, T. O'Connell, J. R. Palmer, N. D. Peyser, P. A. Reupena, M. S. Smith, J. A. Sun, X. Taylor, K. D. Tracy, R. P. Tsai, M. Y. Wang, 2021-10-12 doi:10.1101/2021.10.11.463514 66,000 individuals]]> Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ In vivo versus in silico assessment of potentially pathogenic missense variants in human reproductive genes ]]> https://biorxiv.org/content/10.1101/2021.10.12.464112v1?rss=1 Ding, X. Singh, P. Tran, T. N. Fragoza, R. Yu, H. Schimenti, J. C. 2021-10-12 doi:10.1101/2021.10.12.464112 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy ]]> https://biorxiv.org/content/10.1101/2021.10.12.464114v1?rss=1 Greaney, A. J. Starr, T. N. Eguia, R. T. Loes, A. N. Khan, K. Karim, F. Cele, S. Bowen, J. E. Logue, J. K. Corti, D. Veesler, D. Chu, H. Y. Sigal, A. Bloom, J. D. 2021-10-13 doi:10.1101/2021.10.12.464114 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity ]]> https://biorxiv.org/content/10.1101/2021.10.15.464608v1?rss=1 Liu, H. Ling, W. Hua, X. Moon, J.-Y. Williams-Nguyen, J. S. Zhan, X. Plantinga, A. M. Zhao, N. Zhang, A. Knight, R. Qi, Q. Burk, R. D. Kaplan, R. C. Wu, M. C. 2021-10-16 doi:10.1101/2021.10.15.464608 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ Global and context-specific transcriptional consequences of oncogenic Fbw7 mutations ]]> https://biorxiv.org/content/10.1101/2021.10.19.464955v1?rss=1 Thirmanne, H. N. Wu, F. Janssens, D. H. Swanger, J. Feldman, H. Amezquita, R. Gottardo, R. Paddison, P. J. Henikoff, S. Clurman, B. E. 2021-10-21 doi:10.1101/2021.10.19.464955 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ The endophilin curvature-sensitive motif requires electrostatic guidance to recycle synaptic vesicles in vivo ]]> https://biorxiv.org/content/10.1101/2021.10.20.465157v1?rss=1 Zhang, L. Wang, Y. Dong, Y. Pant, A. Liu, Y. Masserman, L. McLaughlin, R. N. Bai, J. 2021-10-21 doi:10.1101/2021.10.20.465157 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data ]]> https://biorxiv.org/content/10.1101/2021.10.22.465520v1?rss=1 Shen, S. Zheng, Y. Keles, S. 2021-10-24 doi:10.1101/2021.10.22.465520 Cold Spring Harbor Laboratory Press 2021-10-24 <![CDATA[ Subtype transcriptomic profiling of myeloid cells in Alzheimer Disease brain illustrates the diversity in active microglia phenotypes ]]> https://biorxiv.org/content/10.1101/2021.10.25.465802v1?rss=1 Prater, K. E. Green, K. J. Smith, C. Sun, W. Chiou, K. L. Heath, L. M. Rose, S. Shojaie, A. Snyder-Mackler, N. Keene, C. D. Blue, E. Young, J. E. Logsdon, B. Garden, G. A. Jayadev, S. 2021-10-26 doi:10.1101/2021.10.25.465802 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Adenovirus-α-defensin complexes induce NLRP3-associated maturation of human phagocytes via TLR4 engagement ]]> https://biorxiv.org/content/10.1101/2021.10.26.465098v1?rss=1 Eichholz, K. Tran, H. T. Cheneau, C. Tran, T. T. P. Paris, O. Pugniere, M. Kremer, E. J. 2021-10-26 doi:10.1101/2021.10.26.465098 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ Multilineage plasticity in prostate cancer through expansion of stem-like luminal epithelial cells with elevated inflammatory signaling ]]> https://biorxiv.org/content/10.1101/2021.11.01.466599v1?rss=1 Zaidi, S. Zhao, J. L. Chan, J. M. Roudier, M. P. Wadosky, K. M. Gopalan, A. Karthaus, W. R. Choi, J. Lawrence, K. Chaudhary, O. Xu, T. Masilionis, I. Mazutis, L. Chaligne, R. Linkov, I. Barlas, A. Jungbluth, A. Rekhtman, N. Silber, J. Manova Todorova, K. Watson, P. A. True, L. D. Nelson, P. S. Scher, H. I. Rathkopf, D. E. Morris, M. J. Haffner, M. C. Goodrich, D. W. Pe'er, D. Sawyers, C. L. 2021-11-03 doi:10.1101/2021.11.01.466599 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Reversal of lineage plasticity in RB1/TP53-deleted prostate cancer through FGFR and Janus kinase inhibition ]]> https://biorxiv.org/content/10.1101/2021.11.01.466615v1?rss=1 Karthaus, W. Chan, J. Setty, M. Love, J. Zaidi, S. Choo, Z.-N. Persad, S. LaClair, J. Lawrence, K. Chaudhary, O. Xu, T. Masilionis, I. Mazutis, L. Chaligne, R. Pe'er, D. Sawyers, C. 2021-11-01 doi:10.1101/2021.11.01.466615 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ The Immune Signatures Data Resource: A compendium of systems vaccinology datasets ]]> https://biorxiv.org/content/10.1101/2021.11.05.465336v1?rss=1 Diray-Arce, J. Miller, H. E. R. Henrich, E. Gerritsen, B. Mule, M. P. Fourati, S. Gygi, J. Hagan, T. Tomalin, L. Rychov, D. Kazmin, D. Chawla, D. G. Meng, H. Dunn, P. Campbell, J. The Human Immunology Project Consortium (HIPC), Sarwal, M. Tsang, J. Levy, O. Pulendran, B. Sekaly, R.-P. Floratos, A. Gottardo, R. Kleinstein, S. Suarez-Farinas, M. 2021-11-08 doi:10.1101/2021.11.05.465336 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies ]]> https://biorxiv.org/content/10.1101/2021.11.05.467531v1?rss=1 Li, Z. Li, X. Zhou, H. Gaynor, S. M. Selvaraj, M. S. Arapoglou, T. Quick, C. Liu, Y. Chen, H. Sun, R. Dey, R. Arnett, D. K. Bielak, L. F. Bis, J. C. Blackwell, T. Blangero, J. Boerwinkle, E. Bowden, D. W. Brody, J. A. Cade, B. E. Conomos, M. Correa, A. Cupples, L. A. Curran, J. E. de Vries, P. S. Duggirala, R. Freedman, B. I. Goring, H. H. H. Guo, X. Kalyani, R. R. Kooperberg, C. Kral, B. G. Lange, L. A. Manichaikul, A. W. Martin, L. W. Mitchell, B. D. Montasser, M. Morrison, A. Naseri, T. O'Connell, J. R. Palmer, N. D. Peyser, P. A. Psaty, B. M. Raff 2021-11-08 doi:10.1101/2021.11.05.467531 Cold Spring Harbor Laboratory Press 2021-11-08 <![CDATA[ Computational design of nanoscale rotational mechanics in de novo protein assemblies ]]> https://biorxiv.org/content/10.1101/2021.11.11.468255v1?rss=1 Courbet, A. Hansen, J. P. Hsia, Y. Bethel, N. Park, Y.-J. Xu, C. Moyer, A. Boyken, S. E. Ueda, G. Nattermann, U. Nagarajan, D. Silva, D. Sheffler, W. Quispe, J. King, N. P. Bradley, P. H. Veesler, D. Kollman, J. M. Baker, D. 2021-11-12 doi:10.1101/2021.11.11.468255 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Cell Painting predicts impact of lung cancer variants ]]> https://biorxiv.org/content/10.1101/2021.11.18.469171v1?rss=1 Caicedo, J. C. Arevalo, J. Piccioni, F. Bray, M.-A. Hartland, C. L. Wu, X. Brooks, A. N. Berger, A. Boehm, J. S. Carpenter, A. E. Singh, S. 2021-11-20 doi:10.1101/2021.11.18.469171 Cold Spring Harbor Laboratory Press 2021-11-20 <![CDATA[ Early age-related atrophy of cutaneous lymph nodes precipitates an early functional decline in skin immunity in mice with aging ]]> https://biorxiv.org/content/10.1101/2021.11.22.469479v1?rss=1 Sonar, S. A. Uhrlaub, J. L. Coplen, C. P. Sempowski, G. D. Dudakov, J. A. van den Brink, M. R. M. LaFleur, B. J. Jergovic, M. Nikolich-Zugich, J. 2021-11-23 doi:10.1101/2021.11.22.469479 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Macaque-human differences in SARS-CoV-2 Spike antibody response elicited by vaccination or infection ]]> https://biorxiv.org/content/10.1101/2021.12.01.470697v1?rss=1 Willcox, A. Sung, K. Garrett, M. E. Galloway, J. G. OConnor, M. A. Erasmus, J. H. Logue, J. K. Hawman, D. W. Chu, H. Y. Hasenkrug, K. J. Fuller, D. H. Matsen, F. A. Overbaugh, J. 2021-12-03 doi:10.1101/2021.12.01.470697 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ A Co-abundant Gene Analysis for Identification of Gut Microbial Strains Associated with Immune Responses to Oral Cholera Vaccine ]]> https://biorxiv.org/content/10.1101/2021.12.01.470820v1?rss=1 Heller, F. J. Banna, H. A. Kaisar, M. H. Chac, D. Chowdhury, F. Bhuiyan, T. R. Akter, A. Khan, A. I. Karmakar, P. C. Dash, P. LaRocque, R. C. Ryan, E. T. Minot, S. S. Harris, J. B. Qadri, F. Weil, A. A. 2021-12-01 doi:10.1101/2021.12.01.470820 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ An antibody-escape calculator for mutations to the SARS-CoV-2 receptor-binding domain ]]> https://biorxiv.org/content/10.1101/2021.12.04.471236v1?rss=1 Greaney, A. J. Starr, T. N. Bloom, J. D. 2021-12-07 doi:10.1101/2021.12.04.471236 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ]]> https://biorxiv.org/content/10.1101/2021.12.07.470215v1?rss=1 Ramdas, S. Judd, J. Graham, S. E. Kanoni, S. Wang, Y. Surakka, I. Wenz, B. Clarke, S. L. Chesi, A. Wells, A. Bhatti, K. F. Vedantam, S. Winkler, T. W. Locke, A. E. Marouli, E. Zajac, G. J. Wu, K.-H. H. Ntalla, I. Hui, Q. Klarin, D. Hilliard, A. T. Wang, Z. Xue, C. Thorleifsson, G. Helgadottir, A. Gudbjartsson, D. F. Holm, H. Olafsson, I. Hwang, M. Y. Han, S. Akiyama, M. Sakaue, S. Terao, C. Kanai, M. Zhou, W. Brumpton, B. M. Rasheed, H. Havulinna, A. S. Veturi, Y. Pacheco, J. A. Rosenthal, E. A. Lingren, T. Feng, Q. Kullo, I. J. Narita, A. Takayama, 2021-12-08 doi:10.1101/2021.12.07.470215 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ The structural basis of mRNA recognition and binding by eukaryotic pseudouridine synthase PUS1 ]]> https://biorxiv.org/content/10.1101/2021.12.08.471817v1?rss=1 Gruenberg, S. Doyle, L. A. Dai, N. Correa, I. R. Yigit, E. Stoddard, B. L. 2021-12-08 doi:10.1101/2021.12.08.471817 Cold Spring Harbor Laboratory Press 2021-12-08 <![CDATA[ Clonal hematopoiesis is driven by aberrant activation of TCL1A ]]> https://biorxiv.org/content/10.1101/2021.12.10.471810v1?rss=1 Weinstock, J. S. Gopakumar, J. Burugula, B. B. Uddin, M. M. Jahn, N. Belk, J. A. Daniel, B. Ly, N. Mack, T. M. Laurie, C. A. Broome, J. G. Taylor, K. D. Guo, X. Sinner, M. F. von Falkenhausen, A. S. Kaab, S. Shuldiner, A. R. O'Connell, J. R. Lewis, J. P. Boerwinkle, E. Barnes, K. C. Chami, N. Kenny, E. E. Loos, R. J. F. Fornage, M. Hou, L. Lloyd-Jones, D. M. Redline, S. Cade, B. E. Psaty, B. M. Bis, J. C. Brody, J. A. Silverman, E. K. Yun, J. H. Qiao, D. Palmer, N. D. Freedman, B. I. Bowden, D. W. Cho, M. H. DeMeo, D. L. Vasan, R. S. Johnson, A. D. Mat 2021-12-13 doi:10.1101/2021.12.10.471810 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Fat Body Phospholipid State Dictates Hunger Driven Feeding Behavior ]]> https://biorxiv.org/content/10.1101/2021.12.16.472854v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@1ecf3eorg.highwire.dtl.DTLVardef@b800f2org.highwire.dtl.DTLVardef@461a7eorg.highwire.dtl.DTLVardef@75651c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kelly, K. P. Alassaf, M. Sullivan, C. E. Brent, A. E. Goldberg, Z. H. Poling, M. E. Dubrulle, J. Rajan, A. 2021-12-17 doi:10.1101/2021.12.16.472854 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Identification and characterization of BrxR as a regulatory gene in the BREX phage restriction system ]]> https://biorxiv.org/content/10.1101/2021.12.19.473356v1?rss=1 Luyten, Y. Hausman, D. Young, J. C. Doyle, L. A. Ubilla-Rodriguez, N. C. Lambert, A. R. Arroyo, C. Forsberg, K. J. Morgan, R. D. Stoddard, B. L. Kaiser, B. K. 2021-12-19 doi:10.1101/2021.12.19.473356 Cold Spring Harbor Laboratory Press 2021-12-19 <![CDATA[ Simultaneous CUT&Tag profiling of the accessible and silenced regulome in single cells ]]> https://biorxiv.org/content/10.1101/2021.12.19.473377v1?rss=1 Janssens, D. H. Otto, D. J. Setty, M. Ahmad, K. Henikoff, S. 2021-12-21 doi:10.1101/2021.12.19.473377 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Mediator is broadly recruited to gene promoters via a Tail-independent mechanism ]]> https://biorxiv.org/content/10.1101/2021.12.21.473728v1?rss=1 Warfield, L. Donczew, R. Mahendrawada, L. Hahn, S. 2021-12-21 doi:10.1101/2021.12.21.473728 Cold Spring Harbor Laboratory Press 2021-12-21 <![CDATA[ Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load ]]> https://biorxiv.org/content/10.1101/2021.12.22.473781v1?rss=1 Navarro-Dominguez, B. Chang, C.-H. Brand, C. Muirhead, C. Presgraves, D. Larracuente, A. M. 2021-12-24 doi:10.1101/2021.12.22.473781 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ ROKET: Associating Somatic Mutation with Clinical Outcomes through Kernel Regression and Optimal Transport ]]> https://biorxiv.org/content/10.1101/2021.12.23.474064v1?rss=1 Little, P. Hsu, L. Sun, W. 2021-12-24 doi:10.1101/2021.12.23.474064 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Translational buffering by ribosome stalling in upstream open reading frames ]]> https://biorxiv.org/content/10.1101/2022.01.06.475296v1?rss=1 Bottorff, T. A. Geballe, A. P. Subramaniam, A. R. 2022-01-07 doi:10.1101/2022.01.06.475296 Cold Spring Harbor Laboratory Press 2022-01-07 <![CDATA[ Oncogenic role of a developmentally regulated NTRK2 splice variant ]]> https://biorxiv.org/content/10.1101/2022.01.07.475392v1?rss=1 Pattwell, S. S. Arora, S. Nuechterlein, N. Zager, M. Loeb, K. R. Cimino, P. J. Holland, N. C. Reche-Ley, N. Bolouri, H. Bonin, D. A. A. Szulzewsky, F. Phadnis, V. V. Ozawa, T. Wagner, M. J. Haffner, M. C. Cao, J. Shendure, J. Holland, E. C. 2022-01-09 doi:10.1101/2022.01.07.475392 Cold Spring Harbor Laboratory Press 2022-01-09 <![CDATA[ Patterns of Structural Variation Define Prostate Cancer Across Disease States ]]> https://biorxiv.org/content/10.1101/2022.01.09.475586v1?rss=1 Zhou, M. Ko, M. Hoge, A. C. Luu, K. Liu, Y. Russell, M. L. Hannon, W. W. Zhang, Z. Carrot-Zhang, J. Beroukhim, R. Van Allen, E. Choudhury, A. D. Nelson, P. S. Freedman, M. L. Taplin, M.-E. Meyerson, M. Viswanathan, S. R. Ha, G. 2022-01-11 doi:10.1101/2022.01.09.475586 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ Myeloid-biased HSC require Semaphorin 4A from the bone marrow niche for self-renewal under stress and life-long persistence ]]> https://biorxiv.org/content/10.1101/2022.01.12.476097v1?rss=1 Toghani, D. Zeng, S. Mahammadov, E. Crosse, E. I. Seyedhassantehrani, N. Burns, C. Gravano, D. Radtke, S. Kiem, H.-P. Rodriguez, S. Carlesso, N. Pradeep, A. Wilson, N. K. Kinston, S. J. Gottgens, B. Nerlov, C. Pietras, E. Mesnieres, M. Maes, C. Kumanogoh, A. Worzfeld, T. Kharchenko, P. Scialdone, A. Spencer, J. A. Silberstein, L. 2022-01-12 doi:10.1101/2022.01.12.476097 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ A giant virus genome is densely packaged by stable nucleosomes ]]> https://biorxiv.org/content/10.1101/2022.01.15.476465v1?rss=1 Bryson, T. D. De Ioannes, P. Valencia-Sanchez, M. I. Henikoff, J. G. Talbert, P. B. La Scola, B. Armache, K.-J. Henikoff, S. 2022-01-16 doi:10.1101/2022.01.15.476465 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ Single-Cell Transcriptomic Analyses of Tumor Ecosystems and Spatial Architectures in Human Small Cell Lung Cancers ]]> https://biorxiv.org/content/10.1101/2022.01.19.475968v1?rss=1 Ouyang, H. Chen, J. Xu, C. He, C. Sheng, L. Wang, J. Pan, D. Augert, A. Lin, J. Zhu, Y. Jia, D. 2022-01-21 doi:10.1101/2022.01.19.475968 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ mTOR-regulated Mitochondrial Metabolism Limits Mycobacterium-induced Cytotoxicity ]]> https://biorxiv.org/content/10.1101/2022.01.30.478369v1?rss=1 Pagan, A. J. Lee, L. J. Edwards-Hicks, J. Moens, C. B. Tobin, D. M. Busch-Nentwich, E. M. Pearce, E. L. Ramakrishnan, L. 2022-01-30 doi:10.1101/2022.01.30.478369 Cold Spring Harbor Laboratory Press 2022-01-30 <![CDATA[ HOXD13 is a direct EWS-FLI1 target and moderates fusion-dependent transcriptional states ]]> https://biorxiv.org/content/10.1101/2022.01.31.478548v1?rss=1 Apfelbaum, A. A. Wu, F. Hawkins, A. Jimenez, J. A. Taylor, S. D. Pfaltzgraff, E. R. Song, J. Y. Hall, C. Wellik, D. M. Ljungman, M. Furlan, S. N. Ryan, R. J. H. Sarthy, J. F. Lawlor, E. R. 2022-02-01 doi:10.1101/2022.01.31.478548 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Antibody affinity and concentration of convalescent sera provide context for reduced SARS-CoV-2 Omicron spike affinity of therapeutic antibodies ]]> https://biorxiv.org/content/10.1101/2022.02.03.478946v1?rss=1 Fiedler, S. Devenish, S. R. A. Morgunov, A. S. Ilsley, A. Ricci, F. Emmenegger, M. Kosmoliaptsis, V. Theel, E. S. Mills, J. R. Sholukh, A. M. Aguzzi, A. A. A. Iwasaki, A. Lynn, A. K. Knowles, T. P. J. 2022-02-04 doi:10.1101/2022.02.03.478946 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Olverembatinib inhibits SARS-CoV-2-Omicron variant-mediated cytokine release ]]> https://biorxiv.org/content/10.1101/2022.02.07.479443v1?rss=1 Chan, M. Holland, E. Gujral, T. 2022-02-09 doi:10.1101/2022.02.07.479443 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat ]]> https://biorxiv.org/content/10.1101/2022.02.09.479546v1?rss=1 Hannon, W. H. Roychoudhury, P. Xie, H. Shrestha, L. Addetia, A. Jerome, K. R. Greninger, A. L. Bloom, J. D. 2022-02-09 doi:10.1101/2022.02.09.479546 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ Immunization with a self-assembling nanoparticle vaccine displaying EBV gH/gL protects humanized mice against lethal viral challenge ]]> https://biorxiv.org/content/10.1101/2022.02.17.480914v1?rss=1 Malhi, H. Homad, L. J. Wan, Y.-H. Poudel, B. Fiala, B. Borst, A. J. Wang, J. Y. Walkey, C. Price, J. Wall, A. Singh, S. Moodie, Z. Handa, S. Correnti, C. Stoddard, B. L. Veesler, D. Pancera, M. Olson, J. King, N. P. McGuire, A. 2022-02-19 doi:10.1101/2022.02.17.480914 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution ]]> https://biorxiv.org/content/10.1101/2022.02.24.481899v1?rss=1 Starr, T. N. Greaney, A. J. Hannon, W. W. Loes, A. N. Hauser, K. Dillen, J. R. Ferri, E. Ghez Farrell, A. Dadonaite, B. McCallum, M. Matreyek, K. A. Corti, D. Veesler, D. Snell, G. Bloom, J. D. 2022-02-26 doi:10.1101/2022.02.24.481899 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Distinct gene expression by expanded clones of quiescent memory CD4+ T cells harboring intact latent HIV-1 proviruses ]]> https://biorxiv.org/content/10.1101/2022.03.02.482683v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@19e89d2org.highwire.dtl.DTLVardef@16a5685org.highwire.dtl.DTLVardef@563a97org.highwire.dtl.DTLVardef@120a224_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Weymar, G. H. Bar-On, Y. Oliveira, T. Y. Gaebler, C. Ramos, V. Hartweger, H. Breton, G. Caskey, M. Cohn, L. B. Jankovic, M. Nussenzweig, M. C. 2022-03-02 doi:10.1101/2022.03.02.482683 Cold Spring Harbor Laboratory Press 2022-03-02 <![CDATA[ Defining cellular population dynamics at single cell resolution during prostate cancer progression ]]> https://biorxiv.org/content/10.1101/2022.03.02.482711v1?rss=1 Germanos, A. A. Arora, S. Zheng, Y. Goddard, E. T. Coleman, I. M. Ku, A. T. Wilkinson, S. Amezquita, R. A. Zager, M. Long, A. Yang, Y. C. Bielas, J. H. Gottardo, R. Ghajar, C. M. Nelson, P. S. Sowalsky, A. G. Setty, M. Hsieh, A. C. 2022-03-04 doi:10.1101/2022.03.02.482711 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ Activation of targetable inflammatory immune signaling is seen in Myelodysplastic Syndromes with SF3B1 mutations ]]> https://biorxiv.org/content/10.1101/2022.03.09.483595v1?rss=1 Choudhary, G. Pellagatti, A. Agianian, B. Smith, M. Bhagat, T. D. Gordon-Mitchell, S. Pandey, S. Shah, N. Aluri, S. Schwartz, L. Steeples, V. Booher, R. Ramachandra, M. Samson, M. Carbajal, M. Pradhan, K. Bowman, T. Pillai, M. M. Will, B. Wickrema, A. Shastri, A. Bradley, R. K. Martell, R. E. Steidl, U. Gavathiotis, E. Boultwood, J. Starczynowski, D. T. Verma, A. 2022-03-09 doi:10.1101/2022.03.09.483595 Cold Spring Harbor Laboratory Press 2022-03-09 <![CDATA[ The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes ]]> https://biorxiv.org/content/10.1101/2022.03.12.484088v1?rss=1 Greaney, A. J. Eguia, R. T. Starr, T. N. Khan, K. Franko, N. Logue, J. K. Lord, S. M. Speake, C. Chu, H. Y. Sigal, A. Bloom, J. D. 2022-03-14 doi:10.1101/2022.03.12.484088 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ The cancer chemotherapeutic 5-fluorouracil is a potent inhibitor of Fusobacterium nucleatum and its activity is modified by the intratumoral microbiota ]]> https://biorxiv.org/content/10.1101/2022.03.12.484096v1?rss=1 LaCourse, K. D. Baryiames, A. Kempchinsky, A. G. Johnston, C. D. Bullman, S. 2022-03-13 doi:10.1101/2022.03.12.484096 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Mitochondrial Redox Adaptations Enable Aspartate Synthesis in SDH-deficient Cells ]]> https://biorxiv.org/content/10.1101/2022.03.14.484352v1?rss=1 Hart, M. L. Quon, E. Vigil, A.-L. B. G. Engstrom, I. A. Newsom, O. J. Davidsen, K. Hoellerbauer, P. Carlisle, S. M. Sullivan, L. B. 2022-03-14 doi:10.1101/2022.03.14.484352 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models ]]> https://biorxiv.org/content/10.1101/2022.03.25.485875v1?rss=1 Cohen, A. A. van Doremalen, N. A. Greaney, A. J. Andersen, H. Sharma, A. Starr, T. N. Keeffe, J. R. Fan, C. Schulz, J. E. Gnanapragasam, P. N. P. Kakutani, L. M. West, A. P. Saturday, G. Lee, Y. E. Gao, H. Jette, C. A. Lewis, M. G. Tan, T. K. Townsend, A. R. Bloom, J. D. Munster, V. J. Bjorkman, P. J. 2022-03-28 doi:10.1101/2022.03.25.485875 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Cell type-specific Expression Quantitative Trait Loci ]]> https://biorxiv.org/content/10.1101/2022.03.31.486605v1?rss=1 Little, P. Zhabotynsky, V. Li, Y. Lin, D. Sun, W. 2022-04-01 doi:10.1101/2022.03.31.486605 Cold Spring Harbor Laboratory Press 2022-04-01 <![CDATA[ SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data ]]> https://biorxiv.org/content/10.1101/2022.04.02.486748v1?rss=1 Persad, S. Choo, Z.-N. Dien, C. Masilionis, I. Chaligne, R. Nawy, T. Brown, C. C. Pe'er, I. Setty, M. Pe'er, D. 2022-04-03 doi:10.1101/2022.04.02.486748 Cold Spring Harbor Laboratory Press 2022-04-03 <![CDATA[ Integrative analysis of metabolite GWAS illuminates the molecular basis of pleiotropy and genetic correlation ]]> https://biorxiv.org/content/10.1101/2022.04.02.486791v1?rss=1 Smith, C. J. Sinnott-Armstrong, N. Cichonska, A. Julkunen, H. Fauman, E. Wurtz, P. Pritchard, J. K. 2022-04-04 doi:10.1101/2022.04.02.486791 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ The E2 glycoprotein holds key residues for Mayaro virus adaptation to the urban Aedes aegypti mosquito ]]> https://biorxiv.org/content/10.1101/2022.04.05.487100v1?rss=1 Roesch, F. Cereghino, C. Carrau, L. Hardy, A. Ribeiro-Filho, H. Henrion Lacritick, A. Koh, C. Marano, J. Bates, T. A. Rai, P. Chuong, C. Akter, S. Vallet, T. Blanc, H. Elliot, T. Brown, A. M. Michalak, P. LeRoith, T. Bloom, J. Marques, R. E. Saleh, M.-C. Vignuzzi, M. Weger-Lucarelli, J. 2022-04-05 doi:10.1101/2022.04.05.487100 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Distinct regions of H. pylori's bactofilin regulate protein interactions to control cell shape ]]> https://biorxiv.org/content/10.1101/2022.04.05.487110v1?rss=1 Sichel, S. R. Bratton, B. P. Salama, N. 2022-04-05 doi:10.1101/2022.04.05.487110 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Broadly neutralizing antibodies target the coronavirus fusion peptide ]]> https://biorxiv.org/content/10.1101/2022.04.11.487879v1?rss=1 Dacon, C. Tucker, C. Peng, L. Lee, C.-C. D. Lin, T.-H. Yuan, M. Cong, Y. Wang, L. Purser, L. Williams, J. K. Pyo, C.-W. Kosik, I. Hu, Z. Zhao, M. Mohan, D. Cooper, A. Peterson, M. Skinner, J. Dixit, S. Kollins, E. Huzella, L. Perry, D. Byrum, R. Lembirik, S. Zhang, Y. Yang, E. S. Chen, M. Leung, K. Weinberg, R. S. Pegu, A. Geraghty, D. Davidson, E. Douagi, I. Moir, S. Yewdell, J. W. Schmaljohn, C. Crompton, P. D. Holbrook, M. R. Nemazee, D. Mascola, J. R. Wilson, I. A. Tan, J. 2022-04-12 doi:10.1101/2022.04.11.487879 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Adaptive immunity is required for durable responses to alectinib in murine models of EML4-ALK lung cancer ]]> https://biorxiv.org/content/10.1101/2022.04.14.488385v1?rss=1 Kleczko, E. K. Hinz, T. K. Nguyen, T. T. Gurule, N. J. Navarro, A. Le, A. T. Johnson, A. M. Kwak, J. Polhac, D. I. Clambey, E. T. Weiser-Evans, M. C. Patil, T. Schenk, E. L. Heasley, L. E. Nemenoff, R. A. 2022-04-14 doi:10.1101/2022.04.14.488385 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.04.20.488892v1?rss=1 chen, t. Wei, X. Courret, C. cui, m. Cheng, L. wu, j. Ahmad, K. Larracuente, A. M. rong, y. 2022-04-22 doi:10.1101/2022.04.20.488892 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses ]]> https://biorxiv.org/content/10.1101/2022.04.20.488939v1?rss=1 Hagan, T. Gerristen, B. Tomalin, L. E. Fourati, S. Mule, M. P. Chawla, D. G. Rychkov, D. Henrich, E. Miller, H. E. Diray-Arce, J. Dunn, P. Lee, A. The Human Immunology Project Consortium (HIPC), Levy, O. Gottardo, R. Sarwal, M. M. Tsang, J. Suarez-Farinas, M. Sekaly, R.-P. Kleinstein, S. Pulendran, B. 2022-04-26 doi:10.1101/2022.04.20.488939 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ Evolutionarily conserved effects of Notch signaling drive intestinal graft-versus-host disease in mice and non-human primates ]]> https://biorxiv.org/content/10.1101/2022.04.23.488844v1?rss=1 Tkachev, V. Vanderbeck, A. Perkey, E. Furlan, S. N. McGuckin, C. Gomez Atria, D. Gerdemann, U. Rui, X. Lane, J. Hunt, D. J. Zheng, H. Colonna, L. Hoffman, M. Yu, A. Kelly, S. Allman, A. Burbach, B. Shimizu, Y. Panoskaltsis-Mortari, A. Chen, G. Carpenter, S. Harari, O. Kuhnert, F. Thurston, G. Blazar, B. R. Kean, L. S. Maillard, I. 2022-04-27 doi:10.1101/2022.04.23.488844 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ Evaluation of Cognitive Function in the Dog Aging Project: Associations with Baseline Canine Characteristics ]]> https://biorxiv.org/content/10.1101/2022.05.04.490636v1?rss=1 Yarborough, S. Fitzpatrick, A. Schwartz, S. Dog Aging Project Consortium, 2022-05-05 doi:10.1101/2022.05.04.490636 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Persistent serum protein signatures define an inflammatory subset of long COVID ]]> https://biorxiv.org/content/10.1101/2022.05.09.491196v1?rss=1 Talla, A. Vasaikar, S. V. Szeto, G. Lemos, M. P. Czartoski, J. L. MacMillan, H. Moodie, Z. Cohen, K. W. Fleming, L. B. Thomson, Z. Okada, L. Becker, L. A. Coffey, E. M. DeRosa, S. C. Newell, E. W. Skene, P. J. Li, X. Bumol, T. F. McElrath, M. J. Torgerson, T. R. 2022-05-10 doi:10.1101/2022.05.09.491196 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Coenzyme A binding sites induce proximal acylation across protein families ]]> https://biorxiv.org/content/10.1101/2022.05.24.493335v1?rss=1 Carrico, C. Cruz, A. Walter, M. Meyer, J. G. Wehrfritz, C. Shah, S. Wei, L. Schilling, B. Verdin, E. 2022-05-25 doi:10.1101/2022.05.24.493335 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ An in vivo biomarker to characterize ototoxic compounds and novel protective therapeutics ]]> https://biorxiv.org/content/10.1101/2022.05.31.493913v1?rss=1 Bellairs, J. A. Redila, V. Wu, P. Tong, L. Webster, A. Simon, J. A. Rubel, E. W. Raible, D. W. 2022-06-01 doi:10.1101/2022.05.31.493913 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ Androgen receptor inhibition induces metabolic reprogramming and increased reliance on oxidative mitochondrial metabolism in prostate cancer ]]> https://biorxiv.org/content/10.1101/2022.05.31.494200v1?rss=1 Crowell, P. Giafaglione, J. Jones, A. Nunley, N. Hashimoto, T. Delcourt, A. Petcherski, A. Bernard, M. Huang, R. R. Low, J.-Y. Matulionis, N. Guan, X. Navone, N. Alumkal, J. Haffner, M. Ye, H. Zoubeidi, A. Christofk, H. Shirihai, O. S. Divakaruni, A. S. Goldstein, A. S. 2022-06-01 doi:10.1101/2022.05.31.494200 Cold Spring Harbor Laboratory Press 2022-06-01 <![CDATA[ HSV-1 exploits host heterochromatin for egress ]]> https://biorxiv.org/content/10.1101/2022.05.31.494218v1?rss=1 Lewis, H. C. Kelnhofer-Millevolte, L. E. Brinkley, M. R. Arbach, H. E. Arnold, E. A. Ramachandran, S. Avgousti, D. C. 2022-05-31 doi:10.1101/2022.05.31.494218 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Distinct antibody responses to endemic coronaviruses pre- and post-SARS-CoV-2 infection in Kenyan infants and mothers ]]> https://biorxiv.org/content/10.1101/2022.06.02.493651v1?rss=1 Stoddard, C. I. Sung, K. Ojee, E. Adhiambo, J. Begnel, E. R. Slyker, J. Gantt, S. Matsen, F. A. Kinuthia, J. Wamalwa, D. Overbaugh, J. Lehman, D. A. 2022-06-03 doi:10.1101/2022.06.02.493651 Cold Spring Harbor Laboratory Press 2022-06-03 <![CDATA[ State-dependent protein-protein interactions mediating 4-1BB CAR Signaling ]]> https://biorxiv.org/content/10.1101/2022.06.07.495180v1?rss=1 Ritmeester-Loy, S. A. Lautz, J. D. Zhang-Wong, Y. Gustafson, J. A. Wilson, A. L. Lin, C. Gafken, P. R. Jensen, M. C. Orentas, R. Smith, S. E. 2022-06-09 doi:10.1101/2022.06.07.495180 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Genetic conflicts between sex chromosomes drive expansion and loss of sperm nuclear basic protein genes in Drosophila ]]> https://biorxiv.org/content/10.1101/2022.06.08.495379v1?rss=1 Chang, C.-H. Malik, H. S. 2022-06-09 doi:10.1101/2022.06.08.495379 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Adjuvants influence the maturation of VRC01-like antibodies during immunization ]]> https://biorxiv.org/content/10.1101/2022.06.10.495681v1?rss=1 Kudsen, M. L. Agrawal, P. MacCamy, A. Parks, R. K. Gray, M. D. Takushi, B. Khechaduri, A. Coler, R. LaBranche, C. Montefiori, D. Stamatatos, L. 2022-06-13 doi:10.1101/2022.06.10.495681 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ An anti-steatosis response regulated by oleic acid through lipid droplet-mediated ERAD enhancement ]]> https://biorxiv.org/content/10.1101/2022.06.15.496302v1?rss=1 Castillo-Quan, J. I. Steinbaugh, M. J. Fernandez-Cardenas, L. P. Pohl, N. K. Wu, Z. Zhu, F. Moroz, N. Teixeira, V. Bland, M. S. Lehrbach, N. J. Mazzeo, L. E. M. Teufl, M. Blackwell, T. K. 2022-06-16 doi:10.1101/2022.06.15.496302 Cold Spring Harbor Laboratory Press 2022-06-16 <![CDATA[ Co-immunization with pre-erythrocytic antigens alongside circumsporozoite protein can enhance sterile protection against Plasmodium sporozoite infection. ]]> https://biorxiv.org/content/10.1101/2022.06.17.496580v1?rss=1 Vigdorovich, V. Patel, H. Watson, A. Raappana, A. Reynolds, L. Selman, W. Beeman, S. Edlefsen, P. T. Kappe, S. H. I. Sather, D. N. 2022-06-17 doi:10.1101/2022.06.17.496580 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Novel engineered chimeric engulfment receptors trigger T-cell effector functions against SIV infected CD4+ T cells ]]> https://biorxiv.org/content/10.1101/2022.06.21.495546v1?rss=1 Corey, D. Haeseleer, F. Corey, L. 2022-06-25 doi:10.1101/2022.06.21.495546 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ The Functional Landscape of SARS-CoV-2 3CL Protease ]]> https://biorxiv.org/content/10.1101/2022.06.23.497404v1?rss=1 Iketani, S. Hong, S. J. Sheng, J. Bahari, F. Culbertson, B. Atanaki, F. F. Aditham, A. K. Kratz, A. F. Luck, M. I. Tian, R. Goff, S. P. Montazeri, H. Sabo, Y. Ho, D. D. Chavez, A. 2022-06-24 doi:10.1101/2022.06.23.497404 Cold Spring Harbor Laboratory Press 2022-06-24 <![CDATA[ A 96-WELL VALVED MICROFLUIDIC DEVICE FOR TESTING OF LIVE INTACT TUMOR CUBOIDS ]]> https://biorxiv.org/content/10.1101/2022.07.07.499178v1?rss=1 Lockhart, E. Horowitz, L. F. Lim, C. Nguyen, T. Mehrabi, M. Gujral, T. Folch, A. 2022-07-08 doi:10.1101/2022.07.07.499178 Cold Spring Harbor Laboratory Press 2022-07-08 <![CDATA[ Peptide binding specificity prediction using fine-tuned protein structure prediction networks ]]> https://biorxiv.org/content/10.1101/2022.07.12.499365v1?rss=1 Motmaen, A. Dauparas, J. Baek, M. Abedi, M. Baker, D. Bradley, P. H. 2022-07-13 doi:10.1101/2022.07.12.499365 Cold Spring Harbor Laboratory Press 2022-07-13 <![CDATA[ Robust Harmonization of Microbiome Studies by Phylogenetic Scaffolding with MaLiAmPi ]]> https://biorxiv.org/content/10.1101/2022.07.26.501561v1?rss=1 Minot, S. S. Garb, B. Roldan, A. Tang, A. Oskotsky, T. Rosenthal, C. Hoffman, N. G. Sirota, M. Golob, J. L. 2022-07-27 doi:10.1101/2022.07.26.501561 Cold Spring Harbor Laboratory Press 2022-07-27 <![CDATA[ Beta human papillomavirus 8E6 promotes alternative end-joining ]]> https://biorxiv.org/content/10.1101/2022.07.29.501983v1?rss=1 Hu, C. Bugbee, T. Palinski, R. Akinyemi, I. McIntosh, M. T. MacCarthy, T. Bhaduri-McIntosh, S. Wallace, N. 2022-07-30 doi:10.1101/2022.07.29.501983 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ Structure-based prediction of T cell receptor:peptide-MHC interactions ]]> https://biorxiv.org/content/10.1101/2022.08.05.503004v1?rss=1 Bradley, P. H. 2022-08-06 doi:10.1101/2022.08.05.503004 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Human DUX4 and mouse Dux interact with STAT1 and broadly inhibit interferon-stimulated gene induction ]]> https://biorxiv.org/content/10.1101/2022.08.09.503314v1?rss=1 Spens, A. E. Sutliff, N. A. Bennett, S. R. Campbell, A. E. Tapscott, S. J. 2022-08-11 doi:10.1101/2022.08.09.503314 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ The Drosophila AWP1 ortholog Doctor No regulates JAK/STAT signaling for left-right asymmetry in the gut by promoting receptor endocytosis ]]> https://biorxiv.org/content/10.1101/2022.08.20.504629v1?rss=1 Lai, Y.-T. Sasamura, T. Kuroda, J. Maeda, R. Nakamura, M. Hatori, R. Ishibashi, T. Taniguchi, K. Ooike, M. Taguchi, T. Nakazawa, N. Hozumi, S. Okumura, T. Aigaki, T. Inaki, M. Matsuno, K. 2022-08-20 doi:10.1101/2022.08.20.504629 Cold Spring Harbor Laboratory Press 2022-08-20 <![CDATA[ Molecular fate-mapping of serum antibodies reveals the effects of antigenic imprinting on repeated immunization ]]> https://biorxiv.org/content/10.1101/2022.08.29.505743v1?rss=1 Schiepers, A. van 't Wout, M. F. Greaney, A. J. Zang, T. Muramatsu, H. Lin, P. J. Tam, Y. K. Mesin, L. Starr, T. N. Bieniasz, P. D. Pardi, N. Bloom, J. D. Victora, G. D. 2022-08-30 doi:10.1101/2022.08.29.505743 Cold Spring Harbor Laboratory Press 2022-08-30 <![CDATA[ High-risk microbial signatures are associated with severe parasitemia in controlled Plasmodium infections of both humans and rhesus macaques ]]> https://biorxiv.org/content/10.1101/2022.09.06.506695v1?rss=1 Gustin, A. T. Broedlow, C. A. Coronado, E. Wangari, S. Iwayama, N. Ahrens, C. Y. Garrison, W. D. Guerriero, K. A. De Paris, K. Gale, M. Klatt, N. R. Kublin, J. G. Manuzak, J. A. 2022-09-07 doi:10.1101/2022.09.06.506695 Cold Spring Harbor Laboratory Press 2022-09-07 <![CDATA[ CD4-binding site immunogens elicit heterologous anti-HIV-1 neutralizing antibodies in transgenic and wildtype animals ]]> https://biorxiv.org/content/10.1101/2022.09.08.507086v1?rss=1 Gristick, H. B. Hartweger, H. Loewe, M. van Schooten, J. Ramos, V. Oliviera, T. Y. Nishimura, Y. Koranda, N. S. Wall, A. Yao, K.-H. Poston, D. Gazumyan, A. Wiatr, M. Horning, M. Keeffe, J. R. Hoffmann, M. A. Yang, Z. Abernathy, M. E. Dam, K.-M. A. Gao, H. Gnanapragasam, P. N. Kakutani, L. M. Pavlovitch-Bedzyk, A. J. Seaman, M. S. Howarth, M. McGuire, A. T. Stamatatos, L. Martin, M. A. West, A. P. Nussenzweig, M. C. Bjorkman, P. J. 2022-09-12 doi:10.1101/2022.09.08.507086 Cold Spring Harbor Laboratory Press 2022-09-12 <![CDATA[ The glutathione S-transferase Gstt1 is a robust driver of survival and dissemination in metastases ]]> https://biorxiv.org/content/10.1101/2022.09.10.507413v1?rss=1 Ferrer, C. M. Boon, R. Cho, H. Bernasocchi, T. Wong, L. P. Cetinbas, M. Haggerty, E. R. Mitsiades, I. Wojtkiewicz, G. R. McLoughlin, D. E. Rheinbay, E. Sadreyev, R. Juric, D. Mostoslavsky, R. 2022-09-13 doi:10.1101/2022.09.10.507413 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution ]]> https://biorxiv.org/content/10.1101/2022.09.13.507781v1?rss=1 Moulana, A. Dupic, T. Phillips, A. M. Chang, J. Roffler, A. A. Greaney, A. J. Starr, T. N. Bloom, J. D. Desai, M. M. 2022-09-14 doi:10.1101/2022.09.13.507781 Cold Spring Harbor Laboratory Press 2022-09-14 <![CDATA[ Evolution of antibody immunity following Omicron BA.1 breakthrough infection ]]> https://biorxiv.org/content/10.1101/2022.09.21.508922v1?rss=1 Kaku, C. I. Starr, T. N. Zhou, P. Dugan, H. L. Khalife, P. Song, G. Champney, E. R. Mielcarz, D. W. Geoghegan, J. C. Burton, D. R. Andrabi, R. Bloom, J. D. Walker, L. M. 2022-09-22 doi:10.1101/2022.09.21.508922 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ AAV-delivered gene editing for latent genital or orofacial herpes simplex virus infection reduces ganglionic viral load and minimizes subsequent viral shedding in mice ]]> https://biorxiv.org/content/10.1101/2022.09.23.509057v1?rss=1 Aubert, M. Haick, A. K. Strongin, D. E. Klouser, L. M. Loprieno, M. A. Stensland, L. Santo, T. K. Huang, M.-l. Hyrien, O. Stone, D. Jerome, K. R. 2022-09-26 doi:10.1101/2022.09.23.509057 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-specific effects via GAUDI ]]> https://biorxiv.org/content/10.1101/2022.10.06.511219v1?rss=1 Sun, Q. Rowland, B. T. Chen, J. Mikhaylova, A. V. Avery, C. Peters, U. Lundin, J. Matise, T. Buyske, S. Tao, R. Mathias, R. A. Reiner, A. P. Auer, P. L. Cox, N. J. Kooperberg, C. Thornton, T. Raffield, L. M. Li, Y. 2022-10-08 doi:10.1101/2022.10.06.511219 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Structural basis of epitope selectivity and potent protection from malaria by PfCSP antibody L9 ]]> https://biorxiv.org/content/10.1101/2022.10.07.511358v1?rss=1 Martin, G. Fernandez Quintero, M. L. Lee, W.-H. Pholcharee, T. Eshun-Wilson, L. Liedl, K. R. Pancera, M. Seder, R. A. Wilson, I. A. Ward, A. B. 2022-10-07 doi:10.1101/2022.10.07.511358 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ ACSM1 and ACSM3 regulate prostate cancer fatty acid metabolism to promote tumour growth and constrain ferroptosis ]]> https://biorxiv.org/content/10.1101/2022.10.13.511039v1?rss=1 Shrestha, R. Nassar, Z. D. Hanson, A. R. Iggo, R. Townley, S. L. Dehairs, J. Mah, C. Y. Helm, M. Alizadeh-Ghodsi, M. Pickering, M. Watt, M. J. Quek, L.-E. Hoy, A. J. Tilley, W. D. Swinnen, J. V. Butler, L. M. Selth, L. A. 2022-10-14 doi:10.1101/2022.10.13.511039 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Intermittent hypoxia therapy engages multiple longevity pathways to double lifespan in C.elegans ]]> https://biorxiv.org/content/10.1101/2022.10.13.512140v1?rss=1 Pitt, J. N. Chavez, E. Provencher, K. M. Chen, M. Tran, C. Tran, J. Huang, K. Vaid, A. Abadir, M. L. Arang, N. Leiser, S. F. Roth, M. B. Kaeberlein, M. 2022-10-17 doi:10.1101/2022.10.13.512140 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Mosaic chromosomal alterations in blood across ancestries via whole-genome sequencing ]]> https://biorxiv.org/content/10.1101/2022.11.07.515222v1?rss=1 Auer, P. L. Jakubek, Y. A. Zhou, Y. Stilp, A. M. Bacon, J. Wong, J. Mitchell, B. Lewis, J. Boerwinkle, E. Loos, R. J. F. Preuss, M. Barnes, K. Pankratz, N. Fornage, M. Redline, S. Psaty, B. M. Bis, J. C. Silverman, E. Cho, M. Yun, J. Ramachandran, V. Mathias, R. A. Taub, M. Peyser, P. A. Smith, J. A. Kardia, S. Arnett, D. North, K. E. Raffield, L. M. Carson, A. Doyle, M. Rich, S. Rotter, J. Guo, X. Cox, N. Mack, T. Chasman, D. Machiela, M. Ozcan, Z. Conomos, M. Li, Y. Desai, P. Bick, A. Reiner, A. P. Scheet, P. 2022-11-08 doi:10.1101/2022.11.07.515222 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Transcriptional reprogramming of natural killer cells by vaccinia virus shows both distinct and conserved features with mCMV ]]> https://biorxiv.org/content/10.1101/2022.11.10.516015v1?rss=1 Depierreux, D. M. Smith, G. L. Ferguson, B. J. 2022-11-10 doi:10.1101/2022.11.10.516015 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Evolution of the SARS-CoV-2 mutational spectrum ]]> https://biorxiv.org/content/10.1101/2022.11.19.517207v1?rss=1 Bloom, J. D. Beichman, A. C. Neher, R. A. Harris, K. 2022-11-21 doi:10.1101/2022.11.19.517207 Cold Spring Harbor Laboratory Press 2022-11-21 <![CDATA[ Autorepression-based conditional gene expression system in yeast for variation-suppressed control of protein dosage ]]> https://biorxiv.org/content/10.1101/2022.12.05.519107v1?rss=1 Azizoglu, A. Loureiro, C. Venetz, J. Brent, R. 2022-12-08 doi:10.1101/2022.12.05.519107 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Distinct immune responses associated with vaccination status and protection outcomes after malaria challenge ]]> https://biorxiv.org/content/10.1101/2022.12.09.519706v1?rss=1 Oyong, D. A. Duffy, F. J. Neal, M. L. Du, Y. Carnes, J. Schwedhelm, K. V. Hertoghs, N. Jun, S.-H. Miller, H. Aitchison, J. D. De Rosa, S. C. Newell, E. W. McElrath, M. J. McDermott, S. M. Stuart, K. D. 2022-12-10 doi:10.1101/2022.12.09.519706 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Sex-biased Yap1 oncogene function ]]> https://biorxiv.org/content/10.1101/2022.12.21.521494v1?rss=1 Abdelfattah, N. Natarajan, S. Maldonado, J. Tran, H. N. McMinimy, R. Borland, H. Chen, S.-h. Camargo, F. Olson, J. George, J. Yun, K. 2022-12-22 doi:10.1101/2022.12.21.521494 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Antigen-dependent IL-12 signaling in CAR T cells promotes regional to systemic disease targeting ]]> https://biorxiv.org/content/10.1101/2023.01.06.522784v1?rss=1 Lee, E. Cullen, C. Murad, J. P. Gumber, D. Park, A. Yang, J. Stern, L. Adkins, L. Dhapola, G. Gittins, B. Chang, W.-C. Martinez, C. Woo, Y. Cristea, M. Rodriguez, L. Ishihara, J. Lee, J. K. Forman, S. J. Wang, L. Priceman, S. J. 2023-01-07 doi:10.1101/2023.01.06.522784 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ RepairSwitch: simultaneous functional assessment of homologous recombination and end joining DNA repair pathways in living cells ]]> https://biorxiv.org/content/10.1101/2023.01.17.524235v1?rss=1 Steinberg, R. C. Liu, J. Vaghasia, A. M. Giovinazzo, H. Pham, M.-T. N. Tselenchuk, D. Chikarmane, R. Haffner, M. C. Nelson, W. G. Yegnasubramanian, S. 2023-01-17 doi:10.1101/2023.01.17.524235 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Development and characterization of new patient-derived xenograft (PDX) models of osteosarcoma with distinct metastatic capacities ]]> https://biorxiv.org/content/10.1101/2023.01.19.524562v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@17ea2a8org.highwire.dtl.DTLVardef@e8fcc7org.highwire.dtl.DTLVardef@2b9f8corg.highwire.dtl.DTLVardef@1f7b802_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Schott, C. R. Koehne, A. L. Sayles, L. C. Young, E. P. Luck, C. Yu, K. Lee, A. G. Breese, M. R. Leung, S. G. Shah, A. T. Xu, H. Liu, H.-Y. Spillinger, A. Behroozfard, I. H. Marini, K. D. Dinh, P. T. Pons Ventura, M. V. Vanderboon, E. N. Hazard, F. K. Cho, S.-J. Avedian, R. S. Mohler, D. G. Zimel, M. Wustrack, R. Curtis, C. Sirota, M. Sweet-Cordero, E. A. 2023-01-20 doi:10.1101/2023.01.19.524562 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ A Distinct Phenotype of Polarized Memory B cell holds IgE Memory ]]> https://biorxiv.org/content/10.1101/2023.01.25.525495v1?rss=1 Koenig, J. F. Knudsen, N. P. H. Phelps, A. Bruton, K. Hoof, I. Lund, G. Libera, D. D. Lund, A. Christensen, L. Glass, D. R. Walker, T. D. Fang, A. Waserman, S. Jordana, M. Andersen, P. S. 2023-01-25 doi:10.1101/2023.01.25.525495 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Myeloperoxidase promotes a tumorigenic microenvironment in non-small cell lungcancer ]]> https://biorxiv.org/content/10.1101/2023.01.28.526014v1?rss=1 Valadez-Cosmes, P. Kathrin, M. Kindler, O. Cosic-Mujkanovic, N. Lueger, A. Raftopoulou, S. Kienzl, M. Mihalic, Z. N. Santiso, A. Sarsembayeva, A. Brcic, L. Lindenmann, J. Sattler, W. Heinemann, A. Schicho, R. Marsche, G. Houghton, A. M. Kargl, J. 2023-01-29 doi:10.1101/2023.01.28.526014 Cold Spring Harbor Laboratory Press 2023-01-29 <![CDATA[ Fitness effects of mutations to SARS-CoV-2 proteins ]]> https://biorxiv.org/content/10.1101/2023.01.30.526314v1?rss=1 Bloom, J. D. Neher, R. A. 2023-01-31 doi:10.1101/2023.01.30.526314 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ A comprehensive rRNA variation atlas in health and disease ]]> https://biorxiv.org/content/10.1101/2023.01.30.526360v1?rss=1 Rothschild, D. Susanto, T. T. Spence, J. P. Genuth, N. R. Sinnott-Armstrong, N. Pritchard, J. K. Barna, M. 2023-02-02 doi:10.1101/2023.01.30.526360 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Genetic control of mRNA splicing as a potential mechanism for incomplete penetrance of rare coding variants ]]> https://biorxiv.org/content/10.1101/2023.01.31.526505v1?rss=1 Einson, J. Glinos, D. Boerwinkle, E. Castaldi, P. Darbar, D. de Andrade, M. Ellinor, P. Fornage, M. Gabriel, S. Germer, S. Gibbs, R. Hersh, C. Johnsen, J. Kaplan, R. Konkle, B. Kooperberg, C. Nassir, R. Loos, R. J. F. Meyers, D. A. Mitchell, B. D. Psaty, B. Vasan, R. S. Rich, S. S. Rienstra, M. Rotter, J. I. Saferali, A. Shoemaker, M. B. Silverman, E. Smith, A. V. Mohammadi, P. Castel, S. E. Iossifov, I. Lappalainen, T. 2023-01-31 doi:10.1101/2023.01.31.526505 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ BAF chromatin complexes do not mediate GLI transcriptional repression of Hedgehog target genes ]]> https://biorxiv.org/content/10.1101/2023.02.03.527038v1?rss=1 Ramachandran, J. Chen, W. Lex, R. K. Windsor, K. Lee, H. Wang, T. Zhou, W. Ji, H. Vokes, S. A. 2023-02-08 doi:10.1101/2023.02.03.527038 Cold Spring Harbor Laboratory Press 2023-02-08 <![CDATA[ Type I interferon dynamics determines memory B cell epigenetic identity in chronic viral infection ]]> https://biorxiv.org/content/10.1101/2023.03.02.530850v1?rss=1 Cooper, L. Xu, H. Polmear, J. Szeto, C. Pang, E. S. Gupta, M. Taylor, J. J. Jackson, K. J. L. Nguyen, A. La Gruta, N. Martelotto, L. G. Parish, I. A. O'Keeffe, M. Scharer, C. D. Gras, S. Good-Jacobson, K. L. 2023-03-02 doi:10.1101/2023.03.02.530850 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling ]]> https://biorxiv.org/content/10.1101/2023.03.05.531201v1?rss=1 Booth, G. T. Daza, R. M. Srivatsan, S. R. McFaline-Figueroa, J. L. Green Gladden, R. Furlan, S. N. Shendure, J. Trapnell, C. 2023-03-06 doi:10.1101/2023.03.05.531201 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops ]]> https://biorxiv.org/content/10.1101/2023.03.13.532438v1?rss=1 Harada, T. Kalfon, J. Perez, M. W. Eagle, K. Braes, F. D. Batley, R. Heshmati, Y. Ferrucio, J. X. Ewers, J. Mehta, S. Kossenkov, A. Ellegast, J. M. Bowker, A. Wickramasinghe, J. Nabet, B. Paralkar, V. R. Dharia, N. V. Stegmaier, K. Orkin, S. H. Pimkin, M. 2023-03-15 doi:10.1101/2023.03.13.532438 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection ]]> https://biorxiv.org/content/10.1101/2023.03.19.533358v1?rss=1 Wilk, A. J. Marceau, J. O. Kazer, S. W. Fleming, I. Miao, V. N. Galvez-Reyes, J. Shalek, A. K. Holmes, S. Overbaugh, J. Blish, C. A. 2023-03-19 doi:10.1101/2023.03.19.533358 Cold Spring Harbor Laboratory Press 2023-03-19 <![CDATA[ HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. ]]> https://biorxiv.org/content/10.1101/2023.03.21.533528v1?rss=1 Virgilio, M. C. Disbennett, W. M. Chen, T. Lubow, J. Welch, J. D. Collins, K. L. 2023-03-21 doi:10.1101/2023.03.21.533528 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Assessing vaccine-mediated protection in an ultra-low dose Mycobacterium tuberculosis murine model ]]> https://biorxiv.org/content/10.1101/2023.03.22.533820v1?rss=1 Plumlee, C. R. Barrett, H. W. Shao, D. E. Lien, K. A. Cross, L. M. Cohen, S. B. Edlefsen, P. T. Urdahl, K. B. 2023-03-22 doi:10.1101/2023.03.22.533820 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Analysis of evolutionary dynamics and clonal architecture in prostate cancer ]]> https://biorxiv.org/content/10.1101/2023.03.23.533974v1?rss=1 Conway, J. Tewari, A. K. Camp, S. Y. Han, S. Crowdis, J. He, M. X. Nyame, Y. A. AlDubayan, S. H. Schultz, N. Szallasi, Z. Pomerantz, M. M. Freedman, M. L. Fong, L. Nelson, P. S. Brown, M. Salari, K. Van Allen, E. 2023-03-25 doi:10.1101/2023.03.23.533974 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Primate TRIM34 is a broadly-acting, TRIM5-dependent lentiviral restriction factor ]]> https://biorxiv.org/content/10.1101/2023.03.24.534139v1?rss=1 Twentyman, J. Khalifeh, A. Felton, A. Emerman, M. Ohainle, M. 2023-03-25 doi:10.1101/2023.03.24.534139 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing ]]> https://biorxiv.org/content/10.1101/2023.03.27.534417v1?rss=1 Itkin, T. Houghton, S. Schreiner, R. Lin, Y. Badwe, C. Voisin, V. Murison, A. Seyedhassantehrani, N. Kaufmann, K. B. Garcia-Prat, L. Booth, G. T. Geng, F. Liu, Y. Gomez-Salinero, J. M. Shieh, J.-H. Redmond, D. Xiang, J. Z. Josefowicz, S. Z. Trapnell, C. Spencer, J. A. Zangi, L. Hadland, B. Dick, J. E. Xie, S. Z. Rafii, S. 2023-03-29 doi:10.1101/2023.03.27.534417 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities ]]> https://biorxiv.org/content/10.1101/2023.03.28.534648v1?rss=1 Garg, V. Yang, Y. Nowotschin, S. Setty, M. Kuo, Y.-Y. Sharma, R. Polyzos, A. Salataj, E. Murphy, D. Jang, A. Pe'er, D. Apostolou, E. Hadjantonakis, A.-K. 2023-03-29 doi:10.1101/2023.03.28.534648 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Stepwise design of pseudosymmetric protein hetero-oligomers ]]> https://biorxiv.org/content/10.1101/2023.04.07.535760v1?rss=1 Kibler, R. D. Lee, S. Kennedy, M. A. Wicky, B. I. M. Lai, S. M. Kostelic, M. M. Li, X. Chow, C. M. Carter, L. Wysocki, V. H. Stoddard, B. L. Baker, D. 2023-04-07 doi:10.1101/2023.04.07.535760 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Rapid-kinetics degron benchmarking reveals off-target activities and mixed agonism-antagonism of MYB inhibitors ]]> https://biorxiv.org/content/10.1101/2023.04.07.536032v1?rss=1 Harada, T. Perez, M. W. Kalfon, J. Dievenich Braes, F. Batley, R. Eagle, K. Nabet, B. Leifer, B. Kruell, J. Paralkar, V. R. Stegmaier, K. Koehler, A. N. Orkin, S. H. Pimkin, M. 2023-04-07 doi:10.1101/2023.04.07.536032 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Identification of 1600 replication origins in S. cerevisiae ]]> https://biorxiv.org/content/10.1101/2023.04.11.536402v1?rss=1 Foss, E. J. Lichauco, C. Gatbonton-Schwager, T. Lofts, B. Lao, U. Bedalov, A. 2023-04-12 doi:10.1101/2023.04.11.536402 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Imetelstat-Mediated Alterations in Fatty Acid Metabolism To Induce Ferroptosis As Therapeutic Strategy for Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2023.04.25.538357v1?rss=1 Bruedigam, C. Porter, A. H. Song, A. Vroeg in de Wei, G. Stoll, T. Straube, J. Cooper, L. Cheng, G. Kahl, V. F. S. Sobinoff, A. P. Ling, V. Y. Jebaraj, B. M. C. Janardhanan, Y. Haldar, R. Bray, L. J. Bullinger, L. Heidel, F. H. Kennedy, G. A. Hill, M. M. Pickett, H. A. Abdel-Wahab, O. Hartel, G. Lane, S. W. 2023-04-28 doi:10.1101/2023.04.25.538357 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ Common Analysis of Direct RNA SequencinG CUrrently Leads to Misidentification of 5-Methylcytosine Modifications at GCU Motifs ]]> https://biorxiv.org/content/10.1101/2023.05.03.539298v1?rss=1 Watson, K. Bromley, R. Sparklin, B. C. Gasser, M. Bhattacharya, T. Lebov, J. F. Tyson, T. Teigen, L. Graf, K. T. Michalski, M. Bruno, V. M. Lindsey, A. R. I. Hardy, R. W. Newton, I. L. G. Dunning Hotopp, J. C. 2023-05-03 doi:10.1101/2023.05.03.539298 Cold Spring Harbor Laboratory Press 2023-05-03 <![CDATA[ CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation ]]> https://biorxiv.org/content/10.1101/2023.05.04.539469v1?rss=1 Fang, H. Tronco, A. R. Bonora, G. Nguyen, T. Thakur, J. Berletch, J. B. Filippova, G. N. Henikoff, S. Shendure, J. Noble, W. S. Disteche, C. M. Deng, X. 2023-05-04 doi:10.1101/2023.05.04.539469 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ An Atlas of Adaptive Evolution in Endemic Human Viruses ]]> https://biorxiv.org/content/10.1101/2023.05.19.541367v1?rss=1 Kistler, K. Bedford, T. 2023-05-22 doi:10.1101/2023.05.19.541367 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Quantifying the ease of viral escape from broad and narrow antibodies to influenza hemagglutinin ]]> https://biorxiv.org/content/10.1101/210468v1?rss=1 Doud, M. B. Lee, J. M. Bloom, J. D. 2017-10-28 doi:10.1101/210468 Cold Spring Harbor Laboratory Press 2017-10-28 <![CDATA[ Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data ]]> https://biorxiv.org/content/10.1101/220285v1?rss=1 Ralph, D. K. Matsen, F. A. 2017-11-16 doi:10.1101/220285 Cold Spring Harbor Laboratory Press 2017-11-16 <![CDATA[ Transcription activator-coactivator specificity is mediated by a large and dynamic fuzzy protein-protein complex ]]> https://biorxiv.org/content/10.1101/221747v1?rss=1 Tuttle, L. M. Pacheco, D. Warfield, L. Luo, J. Ranish, J. Hahn, S. Klevit, R. E. 2017-11-18 doi:10.1101/221747 Cold Spring Harbor Laboratory Press 2017-11-18 <![CDATA[ Developing a low-cost milliliter-scale chemostat array for precise control of cellular growth ]]> https://biorxiv.org/content/10.1101/223594v1?rss=1 Skelding, D. H. Hart, S. F. M. Vidyasagar, T. Pozhitkov, A. E. Shou, W. 2017-11-22 doi:10.1101/223594 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples ]]> https://biorxiv.org/content/10.1101/223677v1?rss=1 Xue, K. S. Greninger, A. L. Perez-Osorio, A. Bloom, J. D. 2017-11-23 doi:10.1101/223677 Cold Spring Harbor Laboratory Press 2017-11-23 <![CDATA[ Nextstrain: real-time tracking of pathogen evolution ]]> https://biorxiv.org/content/10.1101/224048v1?rss=1 Hadfield, J. Megill, C. Bell, S. M. Huddleston, J. Potter, B. Callender, C. Sagulenko, P. Bedford, T. Neher, R. A. 2017-11-22 doi:10.1101/224048 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Transcription activation domains of the yeast factors Met4 and Ino2: tandem activation domains with properties similar to the yeast Gcn4 activator ]]> https://biorxiv.org/content/10.1101/228536v1?rss=1 Pacheco, D. warfield, l. brajcich, m. robbins, h. luo, j. ranish, j. Hahn, S. 2017-12-04 doi:10.1101/228536 Cold Spring Harbor Laboratory Press 2017-12-04 <![CDATA[ Mapping mutational effects along the evolutionary landscape of HIV envelope ]]> https://biorxiv.org/content/10.1101/235630v1?rss=1 100 residues. Most mutations similarly affect both Envs, but the amino-acid preferences of a minority of sites have clearly shifted. These shifted sites usually prefer a specific amino acid in one Env, but tolerate many amino acids in the other. Surprisingly, shifts are only slightly enriched at sites that have substituted between the Envs -- and many occur at residues that do not even contact substitutions. Therefore, long-range epistasis can unpredictably shift Env's mutational tolerance during HIV evolution, although the amino-acid preferences of most sites are conserved between moderately diverged viral strains. ]]> Haddox, H. K. Dingens, A. S. Hilton, S. K. Overbaugh, J. Bloom, J. D. 2017-12-16 doi:10.1101/235630 Cold Spring Harbor Laboratory Press 2017-12-16 <![CDATA[ Viral diversity is an obligate consideration in CRISPR/Cas9 designs for HIV cure ]]> https://biorxiv.org/content/10.1101/255133v1?rss=1 Roychoudhury, P. De Silva Feelixge, H. Reeves, D. B. Mayer, B. T. Stone, D. Schiffer, J. T. Jerome, K. R. 2018-01-27 doi:10.1101/255133 Cold Spring Harbor Laboratory Press 2018-01-27 <![CDATA[ Cryopreservation of human mucosal tissues ]]> https://biorxiv.org/content/10.1101/262519v1?rss=1 Hughes, S. M. Ferre, A. L. Yandura, S. E. Shetler, C. Baker, C. A. R. Calienes, F. Levy, C. N. Astronomo, R. D. Shu, Z. Lentz, G. M. Fialkow, M. Kirby, A. C. McElrath, M. J. Sinclair, E. Rohan, L. C. Anderson, P. L. Shacklett, B. L. Dezzutti, C. S. Gao, D. Hladik, F. 2018-03-14 doi:10.1101/262519 Cold Spring Harbor Laboratory Press 2018-03-14 <![CDATA[ Seasonal influenza circulation patterns and projections for Feb 2018 to Feb 2019 ]]> https://biorxiv.org/content/10.1101/271114v1?rss=1 Bedford, T. Neher, R. 2018-02-25 doi:10.1101/271114 Cold Spring Harbor Laboratory Press 2018-02-25 <![CDATA[ Isw2 and Ino80 chromatin remodeling factors regulate chromatin, replication, and copy number at the yeast ribosomal DNA locus ]]> https://biorxiv.org/content/10.1101/291971v1?rss=1 Cutler, S. Lee, L. J. Tsukiyama, T. 2018-03-30 doi:10.1101/291971 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments ]]> https://biorxiv.org/content/10.1101/293639v1?rss=1 Bloom, J. D. 2018-04-02 doi:10.1101/293639 Cold Spring Harbor Laboratory Press 2018-04-02 <![CDATA[ Functional Analysis of Metagenomes by Likelihood Inference (FAMLI) Successfully Compensates for Multi-Mapping Short Reads from Metagenomic Samples ]]> https://biorxiv.org/content/10.1101/295352v1?rss=1 Golob, J. L. Minot, S. S. 2018-04-05 doi:10.1101/295352 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants ]]> https://biorxiv.org/content/10.1101/298364v1?rss=1 Lee, J. M. Huddleston, J. Doud, M. B. Hooper, K. A. Wu, N. C. Bedford, T. Bloom, J. D. 2018-04-10 doi:10.1101/298364 Cold Spring Harbor Laboratory Press 2018-04-10 <![CDATA[ EZH2 co-opts gain-of-function p53 mutants to promote cancer growth and metastasis ]]> https://biorxiv.org/content/10.1101/298737v1?rss=1 Zhao, Y. Ding, L. Wang, D. Ye, Z. Pan, Y. Ma, L. Coleman, R. Coleman, I. Karnes, R. J. Zhang, J. Nelson, P. S. Wang, L. Zhu, R. Huang, H. 2018-04-10 doi:10.1101/298737 Cold Spring Harbor Laboratory Press 2018-04-10 <![CDATA[ Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral divergence ]]> https://biorxiv.org/content/10.1101/302703v1?rss=1 Hilton, S. K. Bloom, J. D. 2018-04-17 doi:10.1101/302703 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV ]]> https://biorxiv.org/content/10.1101/307587v1?rss=1 Dingens, A. S. Acharya, P. Haddox, H. K. Rawi, R. Xu, K. Chuang, G.-Y. Wei, H. Mascola, J. R. Carragher, B. Potter, C. S. Overbaugh, J. Kwong, P. D. Bloom, J. D. 2018-04-24 doi:10.1101/307587 Cold Spring Harbor Laboratory Press 2018-04-24 <![CDATA[ Benchmarking tree and ancestral sequence inference for B cell receptor sequences ]]> https://biorxiv.org/content/10.1101/307736v1?rss=1 Davidsen, K. Matsen, F. 2018-04-25 doi:10.1101/307736 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity ]]> https://biorxiv.org/content/10.1101/313106v1?rss=1 DeWitt, W. S. Smith, A. Schoch, G. Hansen, J. A. Matsen, F. A. Bradley, P. H. 2018-05-02 doi:10.1101/313106 Cold Spring Harbor Laboratory Press 2018-05-02 <![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[ Translational control through differential ribosome pausing during amino acid limitation in mammalian cells ]]> https://biorxiv.org/content/10.1101/321448v1?rss=1 Darnell, A. M. Subramaniam, A. R. O'Shea, E. K. 2018-05-14 doi:10.1101/321448 Cold Spring Harbor Laboratory Press 2018-05-14 <![CDATA[ Connectivity-Informed Adaptive Regularization for Generalized Outcomes ]]> https://biorxiv.org/content/10.1101/322420v1?rss=1 Brzyski, D. Karas, M. Ances, B. Dzemidzic, M. Goni, J. Randolph, T. W. Harezlak, J. 2018-05-15 doi:10.1101/322420 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ Microscopy quantification of microbial birth and death dynamics ]]> https://biorxiv.org/content/10.1101/324269v1?rss=1 Hart, S. F. M. Skelding, D. Waite, A. J. Burton, J. Xie, L. Shou, W. 2018-05-17 doi:10.1101/324269 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Sera from individuals with narrowly focused influenza virus antibodies rapidly select viral escape mutations in ovo ]]> https://biorxiv.org/content/10.1101/324707v1?rss=1 Davis, A. K. F. McCormick, K. Gumina, M. E. Petrie, J. Martin, E. T. Xue, K. S. Bloom, J. D. Monto, A. Bushman, F. Hensley, S. E. 2018-05-17 doi:10.1101/324707 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ ICeD-T Provides Accurate Estimates of Immune Cell Abundance in Tumor Samples by Allowing For Aberrant Gene Expression Patterns ]]> https://biorxiv.org/content/10.1101/326421v1?rss=1 Wilson, D. R. Ibrahim, J. G. Sun, W. 2018-05-21 doi:10.1101/326421 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Comprehensive profiling of translation initiation in influenza virus infected cells ]]> https://biorxiv.org/content/10.1101/326967v1?rss=1 Machkovech, H. M. Bloom, J. D. Subramaniam, A. R. 2018-05-21 doi:10.1101/326967 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing ]]> https://biorxiv.org/content/10.1101/326983v1?rss=1 Dvinge, H. Guenthoer, J. Porter, P. L. Bradley, R. K. 2018-05-21 doi:10.1101/326983 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ CD32+ and PD-1+ Lymph Node CD4 T Cells Support Persistent HIV-1 Transcription in Treated Aviremic Individuals ]]> https://biorxiv.org/content/10.1101/329938v1?rss=1 Noto, A. Procopio, F. Banga, R. Suffiotti, M. Corpataux, J.-M. Cavassini, M. Fenwick, C. Gottardo, R. Perreau, M. Pantaleo, G. 2018-05-24 doi:10.1101/329938 Cold Spring Harbor Laboratory Press 2018-05-24 <![CDATA[ Ultrasensitive capture of human herpes simplex virus genomes directly from clinical samples reveals extraordinarily limited evolution in cell culture ]]> https://biorxiv.org/content/10.1101/330860v1?rss=1 99% of the HSV genome at >100X coverage in 72 hours at viral loads that allow whole genome recovery from latently-infected ganglia. We also report a new computational pipeline for rapid HSV genome assembly and annotation. Using the above tools and a series of 17 HSV-1-positive clinical swabs sent to our laboratory for viral isolation, we show limited evolution of HSV-1 during viral isolation in human fibroblast cells compared to the original clinical samples. Our data indicate that previous studies using low passage clinical isolates of herpes simplex viruses are reflective of the viral sequences present in the lesion and thus can be used in phylogenetic analyses. We also detect superinfection within a single sample with unrelated HSV-1 strains recovered from separate oral lesions in an immunosuppressed patient during a 2.5-week period, illustrating the power of direct-from-specimen sequencing of HSV.nnImportanceHerpes simplex viruses affect more than 4 billion people across the globe, constituting a large burden of disease. Understanding global diversity of herpes simplex viruses is important for diagnostics and therapeutics as well as cure research and tracking transmission among humans. To date, most HSV genomics has been performed on culture isolates and DNA swabs with high quantities of virus. We describe the development of wet-lab and computational tools that enable the accurate sequencing of near-complete genomes of HSV-1 and HSV-2 directly from clinical specimens at abundances >50,000-fold lower than previously sequenced and at significantly reduced cost. We use these tools to profile circulating HSV-1 strains in the community and illustrate limited changes to the viral genome during the viral isolation process. These techniques enable cost-effective, rapid sequencing of HSV-1 and HSV-2 genomes that will help enable improved detection, surveillance, and control of this human pathogen. ]]> Greninger, A. L. Roychoudhury, P. Xie, H. Casto, A. Cent, A. Pepper, G. Koelle, D. M. Huang, M.-L. Wald, A. Johnston, C. Jerome, K. 2018-05-25 doi:10.1101/330860 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Characterization of influenza B virus variants with reduced neuraminidase inhibitor susceptibility ]]> https://biorxiv.org/content/10.1101/334201v1?rss=1 Farrukee, R. Alex, Z. E. James, M. Bloom, J. D. Reading, P. Hurt, A. C. 2018-05-30 doi:10.1101/334201 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ cytometree: a binary tree algorithm for automatic gating in cytometry analysis ]]> https://biorxiv.org/content/10.1101/335554v1?rss=1 Commenges, D. Alkhassim, C. Gottardo, R. Hejblum, B. Thiebaut, R. 2018-05-31 doi:10.1101/335554 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Bayesian Classification of Microbial Communities Based on 16S rRNA Metagenomic Data ]]> https://biorxiv.org/content/10.1101/340653v1?rss=1 Bahadorinejad, A. Ivanov, I. Lampe, J. Hullar, M. Chapkin, R. Braga-Neto, U. 2018-06-06 doi:10.1101/340653 Cold Spring Harbor Laboratory Press 2018-06-06 <![CDATA[ DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis. ]]> https://biorxiv.org/content/10.1101/342907v1?rss=1 Finak, G. Mayer, B. Fulp, W. Obrecht, P. Sato, A. Chung, E. Holman, D. Gottardo, R. 2018-06-08 doi:10.1101/342907 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Microbial coexistence through chemical-mediated interactions ]]> https://biorxiv.org/content/10.1101/358481v1?rss=1 Niehaus, L. Boland, I. Liu, M. Chen, K. Fu, D. Henckel, C. Chaung, K. Espinoza Miranda, S. Dyckman, S. Crum, M. Dedrick, S. Shou, W. Momeni, B. 2018-06-29 doi:10.1101/358481 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ A Virus-Packageable CRISPR Screen Identifies Host Factors Mediating Interferon Inhibition of HIV ]]> https://biorxiv.org/content/10.1101/363432v1?rss=1 Ohainle, M. Pendergast, L. Vermeire, J. Roesch, F. Humes, D. Basom, R. Delrow, J. J. Overbaugh, J. Emerman, M. 2018-07-20 doi:10.1101/363432 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Reconciling disparate estimates of viral genetic diversity during human influenza infections ]]> https://biorxiv.org/content/10.1101/364430v1?rss=1 Xue, K. S. Bloom, J. D. 2018-07-08 doi:10.1101/364430 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ An assay for de novo kinetochore assembly reveals a key role for the CENP-T pathway in budding yeast ]]> https://biorxiv.org/content/10.1101/381897v1?rss=1 Lang, J. Barber, A. Biggins, S. 2018-08-07 doi:10.1101/381897 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ L. pneumophila deploys a self-active inhibitor for inter-Legionella competition ]]> https://biorxiv.org/content/10.1101/383018v1?rss=1 Levin, T. C. Goldspiel, B. P. Malik, H. S. 2018-08-02 doi:10.1101/383018 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ RNA sequencing of the in vivo human herpesvirus 6B transcriptome to identify targets for clinical assays distinguishing between latent and active infections ]]> https://biorxiv.org/content/10.1101/397679v1?rss=1 Hill, J. A. Ikoma, M. Zerr, D. M. Basom, R. S. Peddu, V. Huang, M.-L. Hall Sedlak, R. Jerome, K. Boeckh, M. Barcy, S. 2018-08-22 doi:10.1101/397679 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ A natural history model for planning prostate cancer testing: calibration and validation using Swedish registry data ]]> https://biorxiv.org/content/10.1101/402743v1?rss=1 Karlsson, A. Jauhiainen, A. Gulati, R. Eklund, M. Grönberg, H. Etzioni, R. Clements, M. 2018-08-28 doi:10.1101/402743 Cold Spring Harbor Laboratory Press 2018-08-28 <![CDATA[ An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/406355v1?rss=1 Dingens, A. S. Arenz, D. Weight, H. Overbaugh, J. Bloom, J. D. 2018-08-31 doi:10.1101/406355 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Limited marginal utility of deep sequencing for HIV drug resistance testing in the age of integrase inhibitors ]]> https://biorxiv.org/content/10.1101/414995v1?rss=1 20% frequency) found by Sanger sequencing, with greater accuracy in one instance of a Sanger-detected false positive. Freely available online NGS variant callers Hydra and PASeq were superior to Sanger methods for interpretations of allele linkage and automated variant calling. NGS additionally detected low frequency mutations (1-20% frequency) associated with higher levels of drug resistance in 30/105 (29%) of protease-reverse transcriptase tests and 4/39 (10%) of integrase tests. Clinical follow-up of 69 individuals for a median of 674 days found no difference in rates of virological failure between individuals with and without low frequency mutations, although rates of virological failure were higher for individuals with drug-relevant low frequency mutations. However, all 27 individuals who experienced virological failure reported poor adherence to their drug regimen during preceding follow-up time, and all 19 who subsequently improved their adherence achieved viral suppression at later time points consistent with a lack of clinical resistance. In conclusion, in a population with low antiviral resistance emergence, NGS methods detected numerous instances of minor alleles that did not result in subsequent bona fide virological failure due to antiviral resistance.nnImportanceGenotypic antiviral resistance testing for HIV is an essential component of the clinical microbiology and virology laboratory. Next-generation sequencing (NGS) has emerged as a powerful tool for the detection of low frequency sequence variants (allele frequencies <20%). Whether detecting these low frequency mutations in HIV contributes to improved patient health, however, remains unclear. We compared NGS to conventional Sanger sequencing for detecting resistance mutations for 144 HIV drug resistance tests submitted to our clinical virology laboratory and detected low frequency mutations in 24% of tests. Over approximately two years of follow-up for 69 patients for which we had access to electronic health records, no patients had virological failure due to antiviral resistance. Instead, virological failure was entirely explained by medication non-adherence. While larger studies are required, we suggest that detection of low frequency variants by NGS presents limited marginal clinical utility when compared to standard of care. ]]> Dalmat, R. R. Makhsous, N. Pepper, G. Magaret, A. Jerome, K. R. Wald, A. Greninger, A. L. 2018-09-12 doi:10.1101/414995 Cold Spring Harbor Laboratory Press 2018-09-12 <![CDATA[ Rapid development of an infant-derived HIV-1 broadly neutralizing antibody lineage ]]> https://biorxiv.org/content/10.1101/416032v1?rss=1 Simonich, C. A. Doepker, L. Ralph, D. Williams, J. A. Dhar, A. Yaffe, Z. Gentles, L. Small, C. T. Oliver, B. Vigdorovich, V. Mangala Prasad, V. Nduati, R. Sather, D. N. Lee, K. K. Matsen, F. A. Overbaugh, J. 2018-09-13 doi:10.1101/416032 Cold Spring Harbor Laboratory Press 2018-09-13 <![CDATA[ Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD ]]> https://biorxiv.org/content/10.1101/417790v1?rss=1 Jagannathan, S. Ogata, Y. Gafken, P. Tapscott, S. J. Bradley, R. K. 2018-09-14 doi:10.1101/417790 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Trans-ethnic genome-wide association study provides insight into effector genes and molecular mechanisms for kidney function and highlights a causal effect on kidney-specific disease aetiologies ]]> https://biorxiv.org/content/10.1101/420273v1?rss=1 Morris, A. P. Le, T. H. Wu, H. Akbarov, A. van der Most, P. P. Mahajan, A. Hemani, G. Gaulton, K. J. Nadkarni, G. Valladares-Salgado, A. Wacher-Rodarte, N. Mychaleckyj, J. C. Dueker, N. D. Guo, X. Hai, Y. Haessler, J. Kamatani, Y. Stilp, A. Zhu, G. Cook, J. P. Arnlov, J. Blanton, S. H. de Borst, M. Bottinger, E. P. Buchanan, T. A. Charchar, F. J. Damman, J. Eales, J. M. Gharavi, A. G. Giedraitis, V. Heath, A. C. Ipp, E. Kiryluk, K. Kubo, M. Larsson, A. Lindgren, C. Lu, Y. Madden, P. A. Kramer, H. J. Montgomery, G. W. Papanicolaou, G. J. Raffel, L. J. S 2018-09-18 doi:10.1101/420273 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ Successes and failures of the live-attenuated influenza vaccine, can we do better? ]]> https://biorxiv.org/content/10.1101/424275v1?rss=1 Matrajt, L. Halloran, M. E. Antia, R. 2018-09-28 doi:10.1101/424275 Cold Spring Harbor Laboratory Press 2018-09-28 <![CDATA[ SWI/SNF coordinates transcriptional activation through Rpd3-mediated histone hypoacetylation during quiescence entry ]]> https://biorxiv.org/content/10.1101/426288v1?rss=1 Spain, M. M. Braceros, K. C. A. Tsukiyama, T. 2018-09-26 doi:10.1101/426288 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Differences in protein dosage underlie nongenetic differences in traits ]]> https://biorxiv.org/content/10.1101/431643v1?rss=1 Burnaevskiy, N. Sands, B. Yun, S. Tedesco, P. M. Johnson, T. E. Kaeberlein, M. Brent, R. Mendenhall, A. R. 2018-10-01 doi:10.1101/431643 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ Distinct gene-selective roles for a network of core promoter factors in Drosophila neural stem cell identity. ]]> https://biorxiv.org/content/10.1101/434597v1?rss=1 Neves, A. Eisenman, R. N. 2018-10-03 doi:10.1101/434597 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Single-cell virus sequencing of influenza infections that trigger innate immunity ]]> https://biorxiv.org/content/10.1101/437277v1?rss=1 Russell, A. B. Kowalsky, J. R. Bloom, J. D. 2018-10-07 doi:10.1101/437277 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Errors in RNA-seq transcript abundance estimates ]]> https://biorxiv.org/content/10.1101/445601v1?rss=1 12% of protein-coding genes, in at least 1% of samples, current best-in-class RNA-seq processing pipelines differ in their abundance estimates by more than four-fold using the same samples and the same set of RNA-seq reads, raising clinical concern. ]]> Arora, S. Pattwell, S. S. Holland, E. C. Bolouri, H. 2018-10-17 doi:10.1101/445601 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ CRISPR-Cas9 Screens Reveal Genes Regulating a G0-like State in Human Neural Progenitors ]]> https://biorxiv.org/content/10.1101/446344v1?rss=1 Feldman, H. Toledo, C. Arora, S. Hoellerbauer, P. Corrin, P. Carter, L. Kufeld, M. Bolouri, H. Basom, R. Delrow, J. Meier, J. Zhang, F. McFaline-Figueroa, J. Trapnell, C. Pollard, S. Plaisier, C. PADDISON, P. 2018-10-17 doi:10.1101/446344 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ A Stu2-mediated intrinsic tension-sensing pathway promotes chromosome biorientation in vivo ]]> https://biorxiv.org/content/10.1101/453811v1?rss=1 Miller, M. P. Evans, R. Zelter, A. Geyer, E. MacCoss, M. Rice, L. Davis, T. Asbury, C. Biggins, S. 2018-10-25 doi:10.1101/453811 Cold Spring Harbor Laboratory Press 2018-10-25 <![CDATA[ Connect-seq to superimpose molecular on anatomical neural circuit maps ]]> https://biorxiv.org/content/10.1101/454835v1?rss=1 Hanchate, N. K. Lee, E. J. Ellis, A. Kondoh, K. Kuang, D. Basom, R. Trapnell, C. Buck, L. B. 2018-10-27 doi:10.1101/454835 Cold Spring Harbor Laboratory Press 2018-10-27 <![CDATA[ Lineage-dependent differences and the role of IFITM3 in the type-I interferon-induced restriction of Zika virus ]]> https://biorxiv.org/content/10.1101/455972v1?rss=1 Gobillot, T. Humes, D. Sharma, A. Overbaugh, J. 2018-10-29 doi:10.1101/455972 Cold Spring Harbor Laboratory Press 2018-10-29 <![CDATA[ High-Risk Human Papillomavirus Oncogenes Disrupt the Fanconi Anemia DNA repair Pathway by Impairing Localization and De-ubiquitination of FancD2 ]]> https://biorxiv.org/content/10.1101/457176v1?rss=1 Khanal, S. Galloway, D. A. 2018-10-30 doi:10.1101/457176 Cold Spring Harbor Laboratory Press 2018-10-30 <![CDATA[ N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis ]]> https://biorxiv.org/content/10.1101/457648v1?rss=1 200 m6A marked mRNAs, including those coding for SETD methyltransferase, ribosome, and polyA RNA binding proteins. Remarkably, loss of m6A marks resulted in dramatic loss of H3K4me3 across key erythroid-specific KLF1 transcriptional targets (e.g., Heme biosynthesis genes). Further, each m6A MTase subunit and a subset of their mRNAs targets, including BRD7, CXXC1, PABPC1, PABPC4, STK40, and TADA2B, were required for erythroid specification. Thus, m6A mRNA marks promote the translation of a network of genes required for human erythropoiesis. ]]> Kuppers, D. Arora, S. Lim, Y. Lim, A. Carter, L. Corrin, P. Plasier, C. Basom, R. Delrow, J. Wang, S. He, H. Torok-Storb, B. Hsieh, A. Paddison, P. 2018-10-31 doi:10.1101/457648 Cold Spring Harbor Laboratory Press 2018-10-31 <![CDATA[ Killer meiotic drive and dynamic evolution of the wtf gene family ]]> https://biorxiv.org/content/10.1101/461004v1?rss=1 Eickbush, M. T. Young, J. M. Zanders, S. E. 2018-11-03 doi:10.1101/461004 Cold Spring Harbor Laboratory Press 2018-11-03 <![CDATA[ Transgenic mice expressing tunable levels of DUX4 develop characteristic facioscapulohumeral muscular dystrophy-like pathophysiology ranging in severity ]]> https://biorxiv.org/content/10.1101/471094v1?rss=1 Jones, T. I. Chew, G.-L. Barraza-Flores, P. Schreier, S. Ramirez, M. Wuebbles, R. D. Burkin, D. J. Bradley, R. K. Jones, P. L. 2018-11-15 doi:10.1101/471094 Cold Spring Harbor Laboratory Press 2018-11-15 <![CDATA[ Massively parallel profiling of HIV-1 resistance to the fusion inhibitor enfuvirtide ]]> https://biorxiv.org/content/10.1101/472746v1?rss=1 Dingens, A. S. Arenz, D. Overbaugh, J. Bloom, J. D. 2018-11-19 doi:10.1101/472746 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ Separate Polycomb Response Elements control chromatin state and activation of the vestigial gene ]]> https://biorxiv.org/content/10.1101/488478v1?rss=1 Ahmad, K. Spens, A. E. 2018-12-05 doi:10.1101/488478 Cold Spring Harbor Laboratory Press 2018-12-05 <![CDATA[ Comprehensive mapping of avian influenza polymerase adaptation to the human host ]]> https://biorxiv.org/content/10.1101/512525v1?rss=1 Soh, Y. Q. S. Moncla, L. H. Eguia, R. Bedford, T. Bloom, J. D. 2019-01-04 doi:10.1101/512525 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ RNAIndel: a machine-learning framework for discovery of somatic coding indels using tumor RNA-Seq data ]]> https://biorxiv.org/content/10.1101/512749v1?rss=1 Hagiwara, K. Ding, L. Edmonson, M. N. Rice, S. V. Newman, S. Meshinchi, S. Ries, R. E. Rusch, M. Zhang, J. 2019-01-07 doi:10.1101/512749 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores ]]> https://biorxiv.org/content/10.1101/526475v1?rss=1 Lewis, V. Saunders, L. Larson, T. A. Bain, E. Sturiale, S. Gur, D. Chowdhury, S. Flynn, J. Allen, M. Deheyn, D. Lee, J. Simon, J. Lippincott-Schwartz, J. Raible, D. Parichy, D. 2019-01-22 doi:10.1101/526475 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ Antigen-specific humoral immune responses by CRISPR/Cas9-edited B cells ]]> https://biorxiv.org/content/10.1101/530832v1?rss=1 Hartweger, H. McGuire, A. T. Horning, M. Taylor, J. J. Dosenovic, P. Yost, D. Gazumyan, A. Seaman, M. S. Stamatatos, L. Jankovic, M. Nussenzweig, M. C. 2019-01-26 doi:10.1101/530832 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Tumor-Intrinsic Response to IFNgamma Shapes the Tumor Microenvironment and Anti-PD-1 Response in NSCLC ]]> https://biorxiv.org/content/10.1101/531236v1?rss=1 Bullock, B. L. Kimball, A. K. Poczobutt, J. M. Li, H. Y. Kwak, J. W. Neuwelt, A. J. Johnson, A. M. Kleczko, E. Kaspar, R. Hopp, K. Schenk, E. Weiser-Evans, M. C. Clambey, E. T. Nemenoff, R. A. 2019-01-27 doi:10.1101/531236 Cold Spring Harbor Laboratory Press 2019-01-27 <![CDATA[ B cells engineered to express pathogen-specific antibodies using CRISPR/Cas9 protect against infection ]]> https://biorxiv.org/content/10.1101/541979v1?rss=1 Moffett, H. F. Harms, C. K. Fitzpatrick, K. S. Tooley, M. R. Boonyaratankornkit, J. Taylor, J. J. 2019-02-06 doi:10.1101/541979 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Proteomic and Transcriptomic Profiling Identifies Mediators of Anchorage-Independent Growth and Roles of Inhibitor of Differentiation Proteins in Invasive Lobular Breast Cancer ]]> https://biorxiv.org/content/10.1101/543132v1?rss=1 Tasdemir, N. Ding, K. Levine, K. M. Du, T. Bossart, E. A. Lee, A. V. Davidson, N. E. Oesterreich, S. 2019-02-07 doi:10.1101/543132 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Max deletion destabilizes MYC protein and abrogates Eμ-Myc lymphomagenesis ]]> https://biorxiv.org/content/10.1101/556522v1?rss=1 Mathsyaraja, H. Freie, B. Cheng, P.-F. Babaeva, E. Janssens, D. Henikoff, S. Eisenman, R. N. 2019-02-21 doi:10.1101/556522 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ Evolution-guided design of super-restrictor antiviral proteins reveals a breadth-versus-specificity tradeoff ]]> https://biorxiv.org/content/10.1101/557264v1?rss=1 Colon-Thillet, R. S. Hsieh, E. S. Graf, L. McLaughlin, R. Kochs, G. Emerman, M. S. Malik, H. S. 2019-02-22 doi:10.1101/557264 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ The kinesin-like protein Pavarotti functions non-canonically to regulate actin dynamics ]]> https://biorxiv.org/content/10.1101/561936v1?rss=1 Nakamura, M. Verboon, J. M. Prentiss, C. L. Parkhurst, S. M. 2019-02-26 doi:10.1101/561936 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ Inverted translational control of eukaryotic gene expression by ribosome collisions ]]> https://biorxiv.org/content/10.1101/562371v1?rss=1 Park, H. Subramaniam, A. R. 2019-02-27 doi:10.1101/562371 Cold Spring Harbor Laboratory Press 2019-02-27 <![CDATA[ Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease ]]> https://biorxiv.org/content/10.1101/567818v1?rss=1 Minot, S. S. Willis, A. D. 2019-03-05 doi:10.1101/567818 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome ]]> https://biorxiv.org/content/10.1101/569095v1?rss=1 Forsberg, K. J. Bhatt, I. V. Schmidtke, D. T. Stoddard, B. L. Kaiser, B. K. Malik, H. S. 2019-03-06 doi:10.1101/569095 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ A streamlined protocol and analysis pipeline for CUT&RUN chromatin profiling ]]> https://biorxiv.org/content/10.1101/569129v1?rss=1 Meers, M. P. Bryson, T. D. Henikoff, S. 2019-03-06 doi:10.1101/569129 Cold Spring Harbor Laboratory Press 2019-03-06 <![CDATA[ Quantitation of cis-translational control by general mRNA sequence features in five eukaryotes ]]> https://biorxiv.org/content/10.1101/587584v1?rss=1 Li, J. J. Chew, G.-L. Biggin, M. D. 2019-03-24 doi:10.1101/587584 Cold Spring Harbor Laboratory Press 2019-03-24 <![CDATA[ Orchestrating Single-Cell Analysis with Bioconductor ]]> https://biorxiv.org/content/10.1101/590562v1?rss=1 Amezquita, R. A. Carey, V. J. Carpp, L. N. Geistlinger, L. Lun, A. T. Marini, F. Rue-Albrecht, K. Risso, D. Soneson, C. Waldron, L. Pages, H. Smith, M. Huber, W. Morgan, M. Gottardo, R. Hicks, S. C. 2019-03-27 doi:10.1101/590562 Cold Spring Harbor Laboratory Press 2019-03-27 <![CDATA[ Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome ]]> https://biorxiv.org/content/10.1101/598771v1?rss=1 0.5 log10 occurred when relative abundance was <10%. Many errors occurred during early bacterial expansion or late contraction. When relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR. However, targeted qPCR is required to capture bacteria at low relative abundance, particularly with BV-associated bacteria during the early onset of bacterial vaginosis. ]]> Tettamanti Boshier, F. Srinivasan, S. Lopez, A. Hoffman, N. G. Proll, S. Fredricks, D. N. Schiffer, J. T. 2019-04-05 doi:10.1101/598771 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Elimination of HSV-2 infected cells is mediated predominantly by paracrine effects of tissue-resident T cell derived cytokines ]]> https://biorxiv.org/content/10.1101/610634v1?rss=1 Roychoudhury, P. Swan, D. A. Duke, E. Corey, L. Zhu, J. Dave, V. Richert Spuhler, L. Lund, J. M. Prlic, M. Schiffer, J. 2019-04-18 doi:10.1101/610634 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Thresholds for post-rebound viral control after CCR5 gene-edited autologous hematopoietic cell transplantation ]]> https://biorxiv.org/content/10.1101/629717v1?rss=1 Cardozo-Ojeda, E. F. Duke, E. R. Peterson, C. W. Reeves, D. B. Mayer, B. T. Kiem, H.-P. Schiffer, J. T. 2019-05-07 doi:10.1101/629717 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk ]]> https://biorxiv.org/content/10.1101/632166v1?rss=1 Smith, J. Maden, S. Lee, D. Buie, R. Peddu, V. Shean, R. Busby, B. 2019-05-10 doi:10.1101/632166 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Impact of rare and common genetic variants on diabetes diagnosis by hemoglobin A1c in multi-ancestry cohorts: The Trans-Omics for Precision Medicine Program. ]]> https://biorxiv.org/content/10.1101/643932v1?rss=1 Sarnowski, C. Leong, A. Raffield, L. M. Wu, P. de Vries, P. S. DiCorpo, D. Guo, X. Xu, H. Liu, Y. Zheng, X. Hu, Y. Brody, J. A. Goodarzi, M. O. Hidalgo, B. A. Highland, H. M. Jain, D. Liu, C.-T. Naik, R. P. Perry, J. A. Porneala, B. C. Selvin, E. Wessel, J. Psaty, B. M. Curran, J. E. Peralta, J. M. Blangero, J. Kooperberg, C. Mathias, R. Johnson, A. D. Reiner, A. P. Mitchell, B. D. Cupples, L. A. Vasan, R. S. Correa, A. Morrison, A. C. Boerwinkle, E. Rotter, J. I. Rich, S. S. Manning, A. K. Dupuis, J. Meigs, J. B. the TOPMed Diabetes working group, t 2019-05-28 doi:10.1101/643932 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ Reply to \"A discriminative learning approach to differential expression analysis for single-cell RNA-seq\" ]]> https://biorxiv.org/content/10.1101/648733v1?rss=1 Becht, E. Zhao, E. Amezquita, R. A. Gottardo, R. 2019-05-30 doi:10.1101/648733 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Multi-ethnic genome-wide association study of decomposed cardioelectric phenotypes illustrates strategies to identify and characterize evidence of shared genetic effects for complex traits ]]> https://biorxiv.org/content/10.1101/654012v1?rss=1 Baldassari, A. R. Avery, C. L. Highland, H. M. Arking, D. R. Buyske, S. Darbar, D. Gondalia, R. Graff, M. R. Guo, X. R. Heckbert, S. R. Hindorff, L. A. Hodonsky, C. J. Ida Chen, Y.-D. Kaplan, R. C. Peters, U. Post, W. Reiner, A. P. Shohet, R. V. Sotoodehnia, N. Tao, R. Taylor, K. D. Yao, J. D. Kenny, E. D. Lin, H. J. Soliman, E. Z. Whitsel, E. A. North, K. E. Kooperberg, C. Rotters, j. Seyerle, A. A. 2019-05-31 doi:10.1101/654012 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ A new colorectal cancer risk prediction model incorporating family history, personal and environmental factors ]]> https://biorxiv.org/content/10.1101/662106v1?rss=1 Zheng, Y. Hua, X. Win, A. K. MacInnis, R. J. Gallinger, S. Le Marchand, L. Lindor, N. M. Baron, J. A. Hopper, J. L. Dowty, J. G. Antoniou, A. C. Zheng, J. Jenkins, M. A. Newcomb, P. A. 2019-06-07 doi:10.1101/662106 Cold Spring Harbor Laboratory Press 2019-06-07 <![CDATA[ Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin ]]> https://biorxiv.org/content/10.1101/670497v1?rss=1 Lee, J. M. Eguia, R. Zost, S. J. Choudhary, S. Wilson, P. C. Bedford, T. Stevens-Ayers, T. Boeckh, M. Hurt, A. Lakdawala, S. S. Hensley, S. E. Bloom, J. D. 2019-06-13 doi:10.1101/670497 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ Persistence and plasticity of T follicular memory cells ]]> https://biorxiv.org/content/10.1101/677559v1?rss=1 Künzli, M. Schreiner, D. P. Pereboom, T. Swarnalekha, N. Lötscher, J. Ertuna, Y. I. Roux, J. Geier, F. Hess, C. Taylor, J. T. King, C. G. 2019-06-23 doi:10.1101/677559 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ Pulmonary natural killer cells control neutrophil intravascular motility and response to acute inflammation ]]> https://biorxiv.org/content/10.1101/680611v1?rss=1 Secklehner, J. De Filippo, K. Mackey, J. B. G. Vuononvirta, J. Raffo Iraolagoitia, X. L. McFarlane, A. J. Neilson, M. Headley, M. B. Krummel, M. F. Guerra, N. Carlin, L. 2019-06-23 doi:10.1101/680611 Cold Spring Harbor Laboratory Press 2019-06-23 <![CDATA[ Trans- and cis-acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosome ]]> https://biorxiv.org/content/10.1101/687236v1?rss=1 FANG, H. Bonora, G. Lewandowski, J. Thakur, J. Filippova, G. N. Henikoff, S. Shendure, J. Duan, Z. Rinn, J. Deng, X. Noble, W. S. Disteche, C. M. 2019-06-30 doi:10.1101/687236 Cold Spring Harbor Laboratory Press 2019-06-30 <![CDATA[ Partial absence of PD-1 expression by tumor-specific CD8+ T cells in EBV-driven lymphoepithelioma-like carcinoma: a case report ]]> https://biorxiv.org/content/10.1101/696278v1?rss=1 SIMONI, Y. Becht, E. Li, S. LOH, C. Y. YEONG, J. P. S. LIM, T. K. H. TAKANO, A. TAN, D. S. W. NEWELL, E. W. 2019-07-09 doi:10.1101/696278 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level ]]> https://biorxiv.org/content/10.1101/700534v1?rss=1 Mair, F. Erickson, J. R. Voillet, V. Simoni, Y. Bi, T. Tyznik, A. J. Martin, J. Gottardo, R. Newell, E. W. Prlic, M. 2019-07-14 doi:10.1101/700534 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Oral tenofovir disoproxil fumarate/emtricitabine for HIV pre-exposure prophylaxis increases expression of type I/III interferon-stimulated factors in the gastrointestinal tract but not in the blood ]]> https://biorxiv.org/content/10.1101/701961v1?rss=1 Hughes, S. M. Levy, C. N. Calienes, F. Stekler, J. D. Pandey, U. Vojtech, L. Berard, A. R. Birse, K. Noel-Romas, L. Richardson, B. Golden, J. Cartwright, M. Collier, A. C. Stevens, C. E. Curlin, M. E. Holtz, T. H. Mugo, N. Irungu, E. Katabira, E. Muwonge, T. Lama, J. R. Baeten, J. M. Burgener, A. Lingappa, J. R. McElrath, M. J. Mackelprang, R. McGowan, I. Cranston, R. D. Cameron, M. J. Hladik, F. 2019-07-13 doi:10.1101/701961 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ A new data-driven cell population discovery and annotation method for single-cell data, FAUST, reveals correlates of clinical response to cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/702118v1?rss=1 Greene, E. Finak, G. D'Amico, L. A. Bhardwaj, N. Church, C. D. Morishima, C. Ramchurren, N. Taube, J. M. Nghiem, P. T. Cheever, M. A. Fling, S. P. Gottardo, R. 2019-07-13 doi:10.1101/702118 Cold Spring Harbor Laboratory Press 2019-07-13 <![CDATA[ The Effects of Genotype x Phenotype Interactions on Silver Nanoparticle Toxicity in Organotypic Cultures of Murine Tracheal Epithelial Cells ]]> https://biorxiv.org/content/10.1101/722009v1?rss=1 Nicholas, T. P. Haick, A. K. Workman, T. W. Griffith, W. C. Nolin, J. D. Kavanagh, T. J. Faustman, E. M. Altemeier, W. A. 2019-08-01 doi:10.1101/722009 Cold Spring Harbor Laboratory Press 2019-08-01 <![CDATA[ Deep mutational scanning comprehensively maps how Zika envelope protein mutations affect viral growth and antibody escape ]]> https://biorxiv.org/content/10.1101/725556v1?rss=1 Sourisseau, M. Lawrence, D. J. P. Schwarz, M. C. Storrs, C. H. Veit, E. C. Bloom, J. D. Evans, M. J. 2019-08-05 doi:10.1101/725556 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ INX-18 and INX-19 play distinct roles in electrical synapses that modulate aversive behavior in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/725903v1?rss=1 Voelker, L. Upadhyaya, B. Ferkey, D. M. Woldemariam, S. L'Etoile, N. D. Rabinowitch, I. Bai, J. 2019-08-05 doi:10.1101/725903 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double stranded RNA foci in human cell models of FSHD ]]> https://biorxiv.org/content/10.1101/734541v1?rss=1 Shadle, S. C. Bennett, S. R. Wong, C.-J. Karreman, N. A. Campbell, A. E. van der Maarel, S. M. Bass, B. L. Tapscott, S. J. 2019-08-13 doi:10.1101/734541 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Chromosomal Mcm2-7 distribution is a primary driver of genome replication timing in budding yeast, fission yeast and mouse ]]> https://biorxiv.org/content/10.1101/737742v1?rss=1 Foss, E. J. Sripathy, S. Gatobonton-Schwager, T. Kwak, H. Thiesen, A. H. Lao, U. Bedalov, A. 2019-08-16 doi:10.1101/737742 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Inherited chromosomally integrated HHV-6 demonstrates tissue-specific RNA expression in vivo that correlates with increased antibody immune response. ]]> https://biorxiv.org/content/10.1101/741025v1?rss=1 Peddu, V. Dubuc, I. Gravel, A. Xie, H. Huang, M. Tenenbaum, D. Jerome, K. Tardif, J.-C. Dube, M.-P. Flamand, L. Greninger, A. L. 2019-08-21 doi:10.1101/741025 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA ]]> https://biorxiv.org/content/10.1101/745059v1?rss=1 Donczew, R. Warfield, L. Erijman, A. Hahn, S. 2019-08-22 doi:10.1101/745059 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Sensitive detection of highly fragmented cytomegalovirus nucleic acid in human cfDNA ]]> https://biorxiv.org/content/10.1101/748434v1?rss=1 0.3) and 107 as intermediate positive (0.01 Peddu, V. Bradley, B. Shree, S. Colbert, B. Xie, H. Santo, T. Huang, M. Cheng, E. Konnick, E. Salipante, S. Jerome, K. Lockwood, C. Greninger, A. L. 2019-08-28 doi:10.1101/748434 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Physical activity and risks of breast and colorectal cancer: A Mendelian randomization analysis ]]> https://biorxiv.org/content/10.1101/762484v1?rss=1 Papadimitriou, N. Dimou, N. Tsilidis, K. K. Banbury, B. Martin, R. Lewis, S. Kazmi, N. Robinson, T. M. Albanes, D. Aleksandrova, K. Berndt, S. I. Bishop, D. T. Brenner, H. Buchanan, D. D. Bueno-de-Mesquita, B. Campbell, P. T. Castellvi-Bel, S. Chan, A. T. Chang-Claude, J. Ellingjord-Dale, M. Figueiredo, J. C. Gallinger, S. J. Giles, G. G. Giovannucci, E. Gruber, S. B. Gsur, A. Hampe, J. Hampel, H. Harlid, S. Harrison, T. A. Hoffmeister, M. Hopper, J. L. Hsu, L. Huerta, J. M. Huyghe, J. R. Jenkins, M. A. Keku, T. O. Kuhn, T. La Vecchia, C. Le Marchand, L. 2019-09-09 doi:10.1101/762484 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ New mutant mouse models clarify the role of NAIPs, phosphorylation, NLRP3, and tumors in NLRC4 inflammasome activation ]]> https://biorxiv.org/content/10.1101/765313v1?rss=1 Tenthorey, J. Chavez, R. A. Thompson, T. W. Deets, K. A. Vance, R. E. Rauch, I. 2019-09-18 doi:10.1101/765313 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Progressive differentiation of memory CD8 T cells in the cervicovaginal tissue ]]> https://biorxiv.org/content/10.1101/769711v1?rss=1 Dave, V. Cardozo Ojeda, E. F. Mair, F. Erickson, J. Woodward-Davis, A. Soerens, A. Czartoski, J. Teague, C. Oberle, S. Zehn, D. Schiffer, J. Lund, J. M. Prlic, M. 2019-09-14 doi:10.1101/769711 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Diversity and function of maternal HIV-1-specific antibodies at the time of vertical transmission ]]> https://biorxiv.org/content/10.1101/776856v1?rss=1 Doepker, L. Simonich, C. Ralph, D. Gobillot, T. A. Garrett, M. Vigdorovich, V. Sather, D. N. Nduati, R. Matsen, F. Overbaugh, J. 2019-09-23 doi:10.1101/776856 Cold Spring Harbor Laboratory Press 2019-09-23 <![CDATA[ Seasonal influenza circulation patterns and projections for September 2019 to September 2020 ]]> https://biorxiv.org/content/10.1101/780627v1?rss=1 Bedford, T. Huddleston, J. Potter, B. Neher, R. 2019-09-24 doi:10.1101/780627 Cold Spring Harbor Laboratory Press 2019-09-24 <![CDATA[ Adipokines set neural tone by regulating synapse number ]]> https://biorxiv.org/content/10.1101/781526v1?rss=1 Brent, A. E. Rajan, A. 2019-09-25 doi:10.1101/781526 Cold Spring Harbor Laboratory Press 2019-09-25 <![CDATA[ Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes ]]> https://biorxiv.org/content/10.1101/782748v1?rss=1 Bick, A. G. Weinstock, J. Nandakumar, S. K. Fulco, C. P. Leventhal, M. J. Bao, E. L. Nasser, J. Zekavat, S. M. Szeto, M. D. Laurie, C. Taub, M. Mitchell, B. Barnes, K. Moscati, A. Fornage, M. Redline, S. Psaty, B. M. Silverman, E. Weiss, S. Palmer, N. Ramachandran, V. Burchard, E. Kardia, S. He, J. Kaplan, R. Smith, N. L. Arnett, D. Schwartz, D. Correa, A. de Andrade, M. Guo, X. Konkle, B. A. Custer, B. Peralta, J. Gui, H. Meyers, D. McGarvey, S. T. Chen, I. Shoemaker, M. B. Peyser, P. A. Broome, J. Gogarten, S. Wang, F. F. Wong, Q. Montasser, M. Da 2019-09-27 doi:10.1101/782748 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ A High-Resolution Landscape of Mutations in the BCL6 Super-Enhancer in Normal Human B-Cells ]]> https://biorxiv.org/content/10.1101/783118v1?rss=1 T/G>A and A>G/T>C substitutions, consistent with the activities of activation-induced-cytidine deaminase (AID) and the A-T mutator, DNA Polymerase {eta}, respectively, in mutagenesis in normal B-cells. Analyses of mutational signatures further corroborate the participation of these factors in this process. Single base substitution signature SBS85, SBS37, and SBS39 were found in the BCL6 SE. While SBS85 is a denoted signature of AID in lymphoid cells, the etiologies of SBS37 and SBS39 are still unknown. Our analysis suggests the contribution of error-prone DNA polymerases to the latter signatures. The high-resolution mutation landscape has enabled accurate profiling of subclonal mutations in B-cell SEs in normal individuals. By virtue of the fact that subclonal SE mutations are clonally expanded in B-cell lymphomas, our studies also offer the potential for early detection of neoplastic alterations.nnSignificanceWe used Duplex Sequencing to detect low-frequency mutations in the BCL6 super-enhancer locus in normal human B-cells. The landscape of pre-existing mutations is remarkably conserved across different ethnicities and reveals clustered mutational hotspots that correlate with reported sites of clonal mutations and translocation breakpoints in human B-cell lymphomas. This high-resolution genomic landscape revealed by Duplex Sequencing offers accurate and thorough profiling of low frequency, pre-existing mutations in normal individuals, and the potential for early detection of neoplastic alterations. ]]> Shen, J.-C. Kamath-Loeb, A. S. Kohrn, B. F. Loeb, K. R. Preston, B. D. Loeb, L. A. 2019-09-26 doi:10.1101/783118 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Architectural RNA is required for heterochromatin organization ]]> https://biorxiv.org/content/10.1101/784835v1?rss=1 Thakur, J. Fang, H. Llagas, T. Disteche, C. M. Henikoff, S. 2019-09-27 doi:10.1101/784835 Cold Spring Harbor Laboratory Press 2019-09-27 <![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[ When Two are Better than One: Modeling the Mechanisms of Antibody Mixtures ]]> https://biorxiv.org/content/10.1101/808394v1?rss=1 Einav, T. Bloom, J. D. 2019-10-17 doi:10.1101/808394 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Linking influenza virus evolution within and between human hosts ]]> https://biorxiv.org/content/10.1101/812016v1?rss=1 Xue, K. S. Bloom, J. D. 2019-10-21 doi:10.1101/812016 Cold Spring Harbor Laboratory Press 2019-10-21 <![CDATA[ A comparative study of topology-based pathway enrichment analysis methods ]]> https://biorxiv.org/content/10.1101/814145v1?rss=1 Ma, J. Shojaie, A. Michailidis, G. 2019-10-22 doi:10.1101/814145 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ The GMD-biplot and its application to microbiome data ]]> https://biorxiv.org/content/10.1101/814269v1?rss=1 Wang, Y. Randolph, T. Shojaie, A. Ma, J. 2019-10-22 doi:10.1101/814269 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[ Retinoic acid organizes the vagus motor topographic map via spatiotemporal regulation of Hgf/Met signaling ]]> https://biorxiv.org/content/10.1101/826735v1?rss=1 Isabella, A. J. Barsh, G. R. Stonick, J. A. Moens, C. B. 2019-10-31 doi:10.1101/826735 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ Detection and treatment strategy for Tritrichomonas muris in the common laboratory mouse ]]> https://biorxiv.org/content/10.1101/827055v1?rss=1 Da Costa, A. S. Graham, T. M. Duncan, J. A. Pillai, S. P. S. Lund, J. M. 2019-11-01 doi:10.1101/827055 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Novel patterns of complex structural variation revealed across thousands of cancer genome graphs ]]> https://biorxiv.org/content/10.1101/836296v1?rss=1 Hadi, K. Yao, X. Behr, J. M. Deshpande, A. Xanthopoulakis, C. Rosiene, J. Darmofal, M. Tian, H. DeRose, J. Mortensen, R. Adney, E. Gajic, Z. Eng, K. Wala, J. A. Wrzeszczynski, K. O. Arora, K. Shah, M. Emde, A.-K. Felice, V. Frank, M. O. Darnell, R. Ghandi, M. Huang, F. Maciejowski, J. De Lange, T. Setton, J. Riaz, N. Reis-Filho, J. S. Powell, S. Knowles, D. Reznik, E. Mishra, B. Beroukhim, R. Zody, M. Robine, N. Oman, K. Sanchez, C. A. Kuhner, M. K. Smith, L. P. Galipeau, P. C. Paulson, T. G. Reid, B. J. Li, X. Wilkes, D. Sboner, A. Mosquera, J. M. 2019-11-09 doi:10.1101/836296 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Aurora B-dependent Ndc80 Degradation Regulates Kinetochore Composition in Meiosis ]]> https://biorxiv.org/content/10.1101/836668v1?rss=1 Chen, J. Liao, A. Powers, E. N. Liao, H. Kohlstaedt, L. A. Evans, R. Holly, R. M. Kim Kim, J. Jovanovic, M. Unal, E. 2019-11-09 doi:10.1101/836668 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Beyond Conventional Models: Recreating the Initiation, Evolution, and Genome of GBM ]]> https://biorxiv.org/content/10.1101/837138v1?rss=1 Bohm, A. DePetro, J. Binding, C. Gerber, A. Chahley, N. Ware, M. Thomas, K. Bukhari, S. Chen, C. Chahley, E. Grisdale, C. Berger, N. D. Lawn, S. Yu, Y. Wong, R. Shen, Y. Omairi, H. Mirzaei, R. Maxwell, L. Pedersen, H. Yong, V. W. Weiss, S. Chan, J. A. Cimino, P. J. Kelly, J. Jones, S. J. M. Holland, E. Blough, M. D. Cairncross, G. 2019-11-09 doi:10.1101/837138 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Mediator subunit Med15 dictates the conserved 'fuzzy' binding mechanism of yeast transcription activators Gal4 and Gcn4 ]]> https://biorxiv.org/content/10.1101/840348v1?rss=1 Tuttle, L. M. Pacheco, D. Warfield, L. Hahn, S. Klevit, R. E. 2019-11-13 doi:10.1101/840348 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Comparative Genomics and Full-Length TprK Profiling of Treponema pallidum subsp. pallidum Reinfection ]]> https://biorxiv.org/content/10.1101/841395v1?rss=1 Addetia, A. Tantalo, L. C. Lin, M. J. Xie, H. Huang, M.-L. Marra, C. Greninger, A. L. 2019-11-13 doi:10.1101/841395 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Distinct roles for the Charcot-Marie-Tooth disease-causing endosomal regulators Mtmr5 and Mtmr13 in axon radial sorting and Schwann cell myelination ]]> https://biorxiv.org/content/10.1101/843219v1?rss=1 Mammel, A. E. Delgado, K. C. Chin, A. L. Condon, A. F. Hill, J. Q. Aicher, S. A. Wang, Y. Fedorov, L. M. Robinson, F. L. 2019-11-15 doi:10.1101/843219 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ Enhancers predominantly regulate gene expression in vivo via transcription initiation. ]]> https://biorxiv.org/content/10.1101/844191v1?rss=1 Larke, M. S. C. Nojima, T. Telenius, J. M. Sharpe, J. A. Stanley, J. A. Butler, S. Beagrie, R. A. Downes, D. J. Schwessinger, R. Oudelaar, M. Truch, J. Crompton, B. Bender, M. A. Proudfoot, N. J. Higgs, D. R. Hughes, J. R. 2019-11-16 doi:10.1101/844191 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Kinome-centric pharmacoproteomics identifies signaling pathways underlying cellular responses to targeted cancer drugs ]]> https://biorxiv.org/content/10.1101/849281v1?rss=1 Golkowski, M. Lau, H.-T. Chan, M. Kenerson, H. Vidadala, V. N. Shoemaker, A. Maly, D. J. Yeung, R. S. Gujral, T. S. Ong, S.-E. 2019-11-20 doi:10.1101/849281 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ alignparse: A Python package for parsing complex features from high-throughput long-read sequencing ]]> https://biorxiv.org/content/10.1101/850404v1?rss=1 Crawford, K. H. Bloom, J. D. 2019-11-21 doi:10.1101/850404 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Sort-purification of human CD34+CD90+ cells reduces target cell population and improves lentiviral transduction ]]> https://biorxiv.org/content/10.1101/850479v1?rss=1 Radtke, S. Pande, D. Cui, M. Perez, A. M. Chan, Y.-Y. Enstrom, M. Schmuck, S. Berger, A. Eunson, T. Adair, J. E. Kiem, H.-P. 2019-11-26 doi:10.1101/850479 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Visual Cell Sorting: A High-throughput, Microscope-based Method to Dissect Cellular Heterogeneity ]]> https://biorxiv.org/content/10.1101/856476v1?rss=1 Hasle, N. Cooke, A. Srivatsan, S. Huang, H. Stephany, J. J. Krieger, Z. Jackson, D. L. Tang, W. Monnat, R. J. Trapnell, C. Hatch, E. M. Fowler, D. 2019-11-26 doi:10.1101/856476 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5 ]]> https://biorxiv.org/content/10.1101/863043v1?rss=1 Roop, J. I. Cassidy, N. A. Dingens, A. S. Bloom, J. D. Overbaugh, J. 2019-12-03 doi:10.1101/863043 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants ]]> https://biorxiv.org/content/10.1101/872028v1?rss=1 Thornton, A. M. Fang, L. O'Brian, C. Berger, A. H. Giannakis, M. Brooks, A. N. 2019-12-11 doi:10.1101/872028 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ A high-content siRNA screen reveals new regulators of nuclear membrane stability ]]> https://biorxiv.org/content/10.1101/2023.05.30.542944v1?rss=1 Gunn, A. L. Yashchenko, A. I. Hatch, E. L. 2023-05-31 doi:10.1101/2023.05.30.542944 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment ]]> https://biorxiv.org/content/10.1101/2023.06.01.543064v1?rss=1 Walas, N. Müller, N. F. Parker, E. Henderson, A. Capone, D. Brown, J. Barker, T. Graham, J. P. 2023-06-03 doi:10.1101/2023.06.01.543064 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Atg8-LC3 controls systemic nutrient surplus signaling from flies to humans. ]]> https://biorxiv.org/content/10.1101/2023.05.31.543119v1?rss=1 Madan, A. Kelly, K. P. Sullivan, C. E. Poling, M. E. Brent, A. E. Alassaf, M. Dubrulle, J. Rajan, A. 2023-06-04 doi:10.1101/2023.05.31.543119 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma ]]> https://biorxiv.org/content/10.1101/2023.06.02.543290v1?rss=1 View larger version (56K): org.highwire.dtl.DTLVardef@20e0f2org.highwire.dtl.DTLVardef@904fbborg.highwire.dtl.DTLVardef@62af84org.highwire.dtl.DTLVardef@f114be_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ma, R. K. Tsai, P.-Y. Farghli, A. R. Shumway, A. J. Kanke, M. Gordan, J. D. Gujral, T. Vakili, K. Nukaya, M. Noetzli, L. Ronnekleiv-Kelly, S. Broom, W. Barrow, J. Sethupathy, P. 2023-06-04 doi:10.1101/2023.06.02.543290 Cold Spring Harbor Laboratory Press 2023-06-04 <![CDATA[ Differentiation latency and dormancy signatures define fetal liver HSCs at single cell resolution ]]> https://biorxiv.org/content/10.1101/2023.06.01.543314v1?rss=1 Ishida, T. Heck, A. M. Varnum-Finney, B. Dozono, S. Nourigat-McKay, C. Kraskouskas, K. Wellington, R. Waltner, O. Root, C. Jackson, D. L. Delaney, C. Rafii, S. Bernstein, I. D. Trapnell, C. Hadland, B. 2023-06-05 doi:10.1101/2023.06.01.543314 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ A Quantitative Analysis of Locomotor Patterns in Developing C. elegans ]]> https://biorxiv.org/content/10.1101/2023.06.03.543584v1?rss=1 Hassinan, C. W. Sterrett, S. C. Summy, B. Khera, A. Wang, A. Bai, J. 2023-06-06 doi:10.1101/2023.06.03.543584 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Ablation of Max expression induces meiotic onset in sexually undifferentiated germ cells ]]> https://biorxiv.org/content/10.1101/2023.06.10.544477v1?rss=1 Suzuki, A. Uranishi, K. Nishimoto, M. Mizuno, Y. Mizuno, S. Takahashi, S. Eisenman, R. N. Okuda, A. 2023-06-11 doi:10.1101/2023.06.10.544477 Cold Spring Harbor Laboratory Press 2023-06-11 <![CDATA[ De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8 ]]> https://biorxiv.org/content/10.1101/2023.06.12.544624v1?rss=1 1000-fold selectivity over other RGD integrins. CryoEM structures are within 0.6-0.7[A] root-mean-square deviation (RMSD) to the computational design models; the designed v{beta}6 inhibitor and native ligand stabilize the open conformation in contrast to the therapeutic anti-v{beta}6 antibody BG00011 that stabilizes the bent-closed conformation and caused on-target toxicity in patients with lung fibrosis, and the v{beta}8 inhibitor maintains the constitutively fixed extended-closed v{beta}8 conformation. In a mouse model of bleomycin-induced lung fibrosis, the v{beta}6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics when delivered via oropharyngeal administration mimicking inhalation, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity. ]]> Roy, A. Shi, L. Chang, A. Dong, X. Fernandez, A. Kraft, J. C. Li, J. Le, V. Q. Winegar, R. V. Cherf, G. M. Slocum, D. Poulson, P. D. casper, G. E. Vallecillo-Zuniga, M. L. Valdoz, J. C. Miranda, M. C. Bai, H. Kipnis, Y. Olshefsky, A. Priya, T. Carter, L. Ravichandran, R. Chow, C. Johnson, M. R. Chang, S. Roy, A. Overed-Sayer, C. Finch, D. K. Lowe, D. Bera, A. K. Matute-Bello, G. Birkland, T. P. DiMaio, F. Raghu, G. Cochran, J. R. Stewart, L. Campbell, M. G. Van Ry, P. M. Springer, T. A. Baker, D. 2023-06-12 doi:10.1101/2023.06.12.544624 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Fusobacterium sphaericum sp. nov., isolated from a human colon tumor, is prevalent in various human body sites and induces IL-8 secretion from colorectal cancer cells ]]> https://biorxiv.org/content/10.1101/2023.06.16.545380v1?rss=1 20,000 human metagenomic samples shows that it is a low-prevalence member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche, and given its interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation. ]]> Zepeda-Rivera, M. A. Eisele, Y. Baryiames, A. Wu, H. LaCourse, K. D. Jones, D. S. Hauner, H. Dewhirst, F. E. Minot, S. S. Johnston, C. D. Bullman, S. 2023-06-16 doi:10.1101/2023.06.16.545380 Cold Spring Harbor Laboratory Press 2023-06-16 <![CDATA[ Design of four component T=4 tetrahedral, octahedral, and icosahedral protein nanocages through programmed symmetry breaking ]]> https://biorxiv.org/content/10.1101/2023.06.16.545341v1?rss=1 Lee, S. Kibler, R. D. Hsia, Y. Borst, A. J. Philomin, A. Kennedy, M. A. Stoddard, B. L. Baker, D. 2023-06-17 doi:10.1101/2023.06.16.545341 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ MOCHA: Advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human disease cohorts ]]> https://biorxiv.org/content/10.1101/2023.06.23.544827v1?rss=1 Rachid Zaim, S. Pebworth, M.-P. McGrath, I. Okada, L. Weiss, M. Reading, J. Czartoski, J. L. Torgerson, T. McElrath, M. J. Bumol, T. F. Skene, P. J. Li, X.-j. 2023-06-24 doi:10.1101/2023.06.23.544827 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ An engineered biosensor enables dynamic aspartate measurements in living cells ]]> https://biorxiv.org/content/10.1101/2023.06.27.546775v1?rss=1 Davidsen, K. Marvin, J. S. Aggarwal, A. Brown, T. A. Sullivan, L. B. 2023-06-27 doi:10.1101/2023.06.27.546775 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Mechanical coupling coordinates microtubule growth ]]> https://biorxiv.org/content/10.1101/2023.06.29.547092v1?rss=1 Leeds, B. K. Kostello, K. F. Liu, Y. Y. Biggins, S. Asbury, C. L. 2023-06-30 doi:10.1101/2023.06.29.547092 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ A Compound that Inhibits Glycolysis in Prostate Cancer Controls Growth of Advanced Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2023.07.01.547355v1?rss=1 Uo, T. Ojo, K. K. Sprenger, C. C. Epilepsia, K. S. Perera, B. G. K. Damodarasamy, M. Sun, S. Kim, S. Hogan, H. H. Hulverson, M. A. Choi, R. Whitman, G. R. Barrett, L. K. Michaels, S. A. Xu, L. H. Pang, H. J. Nguyen, M. M. Vigil, A.-L. B. G. Kamat, V. Sullivan, L. B. Sweet, I. R. Vidadala, R. Maly, D. J. Van Voorhis, W. C. Plymate, S. R. 2023-07-03 doi:10.1101/2023.07.01.547355 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ APOBEC3 activity promotes the survival and evolution of drug-tolerant persister cells during acquired resistance to EGFR inhibitors in lung cancer ]]> https://biorxiv.org/content/10.1101/2023.07.02.547443v1?rss=1 Garcia, N. M. G. Becerra, J. N. McKinney, B. J. DiMarco, A. V. Wu, F. Fitzgibbon, M. Alvarez, J. V. 2023-07-03 doi:10.1101/2023.07.02.547443 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon ]]> https://biorxiv.org/content/10.1101/2023.07.09.548272v1?rss=1 Otto, D. J. Jordan, C. Dury, B. Dien, C. Setty, M. 2023-07-10 doi:10.1101/2023.07.09.548272 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers ]]> https://biorxiv.org/content/10.1101/2023.07.10.548412v1?rss=1 Pineda, J. M. B. Bradley, R. K. 2023-07-11 doi:10.1101/2023.07.10.548412 Cold Spring Harbor Laboratory Press 2023-07-11 <![CDATA[ Validation of human telomere length trans-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as novel human telomere length regulation genes ]]> https://biorxiv.org/content/10.1101/2023.07.12.548702v1?rss=1 Keener, R. Chhetri, S. B. Connelly, C. J. Taub, M. A. Conomos, M. P. Weinstock, J. S. Ni, B. Strober, B. J. Aslibekyan, S. Auer, P. L. Barwick, L. Becker, L. C. Blangero, J. Bleecker, E. R. Brody, J. A. Cade, B. E. Celedon, J. C. Chang, Y.-C. Cupples, L. A. Custer, B. Freedman, B. I. Gladwin, M. T. Heckbert, S. R. Hou, L. Irvin, M. R. Isasi, C. R. Johnsen, J. M. Kenny, E. E. Kooperberg, C. Minster, R. L. Nekhai, S. Pankratz, N. Peyser, P. A. Rotter, J. I. Taylor, K. D. Telen, M. J. Wu, B. Yanek, L. R. Yang, I. V. Albert, C. Arnett, D. K. Ashley-Koch, A. 2023-07-14 doi:10.1101/2023.07.12.548702 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Transposable elements regulate thymus development and function ]]> https://biorxiv.org/content/10.1101/2023.07.12.548732v1?rss=1 Larouche, J.-D. Laumont, C. M. Trofimov, A. Vincent, K. Hesnard, L. Brochu, S. Cote, C. Humeau, J. Bonneil, E. Lanoix, J. Durette, C. Gendron, P. Laverdure, J.-P. Richie, E. R. Lemieux, S. Thibault, P. Perreault, C. 2023-07-14 doi:10.1101/2023.07.12.548732 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice ]]> https://biorxiv.org/content/10.1101/2023.07.17.549345v1?rss=1 Ouwendijk, W. J. Roychoudhury, P. Cunningham, A. L. Jerome, K. R. Koelle, D. M. Kinchington, P. R. Mohr, I. Wilson, A. C. Verjans, G. M. G. M. Depledge, D. P. 2023-07-18 doi:10.1101/2023.07.17.549345 Cold Spring Harbor Laboratory Press 2023-07-18 <![CDATA[ Human Plasma Proteomic Profile of Clonal Hematopoiesis ]]> https://biorxiv.org/content/10.1101/2023.07.25.550557v1?rss=1 Yu, Z. Vromman, A. Nguyen, N. Q. H. Vellarikkal, S. K. Uddin, M. M. Niroula, A. Griffin, G. Honigberg, M. C. Lin, A. E. Gibson, C. J. Katz, D. H. Tahir, U. Haidermota, S. Ganesh, S. Antoine, T. Weinstock, J. Austin, T. R. Vasan, R. S. peloso, G. M. Hornsby, W. Ganz, P. Manson, J. E. Haring, B. Kooperberg, C. L. Reiner, A. P. Bis, J. C. Psaty, B. M. Min, Y.-I. Correa, A. Lange, L. A. Post, W. Rotter, J. I. Rich, S. S. Wilson, J. G. Ebert, B. L. Yu, B. Ballantyne, C. M. Coresh, J. Sankaran, V. G. Bick, A. G. Jaiswal, S. Libby, P. Gerszten, R. E. NHLBI T 2023-07-27 doi:10.1101/2023.07.25.550557 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Surprising connections between DNA binding and function for the near-complete set of yeast transcription factors ]]> https://biorxiv.org/content/10.1101/2023.07.25.550593v1?rss=1 Mahendrawada, L. Warfield, L. Donczew, R. hahn, s. 2023-07-27 doi:10.1101/2023.07.25.550593 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ A CRISPR screen of HIV dependency factors reveals CCNT1 is non-essential in T cells but required for HIV-1 reactivation from latency ]]> https://biorxiv.org/content/10.1101/2023.07.28.551016v1?rss=1 Hafer, T. L. Felton, A. Delgado, Y. Srinivasan, H. Emerman, M. 2023-07-28 doi:10.1101/2023.07.28.551016 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ TGF-β broadly modifies rather than specifically suppresses reactivated memory CD8 T cells in a dose-dependent manner ]]> https://biorxiv.org/content/10.1101/2023.07.27.550871v1?rss=1 Taber, A. Konecny, A. Scott-Browne, J. Prlic, M. 2023-07-29 doi:10.1101/2023.07.27.550871 Cold Spring Harbor Laboratory Press 2023-07-29 <![CDATA[ A multiplex, prime editing framework for identifying drug resistance variants at scale ]]> https://biorxiv.org/content/10.1101/2023.07.27.550902v1?rss=1 Chardon, F. M. Suiter, C. Daza, R. Smith, N. T. Parrish, P. McDiarmid, T. Lalanne, J.-B. Martin, B. K. Calderon, D. Ellison, A. Berger, A. Shendure, J. Starita, L. M. 2023-07-30 doi:10.1101/2023.07.27.550902 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ A robust method for measuring aminoacylation through tRNA-Seq ]]> https://biorxiv.org/content/10.1101/2023.07.31.551363v1?rss=1 Davidsen, K. Sullivan, L. B. 2023-08-01 doi:10.1101/2023.07.31.551363 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs ]]> https://biorxiv.org/content/10.1101/2023.07.31.551037v1?rss=1 1,000-fold in the impact of the same mutation on spike-mediated viral infection across spikes from different SARS-CoV-2 variants. Overall, our work establishes a general approach for comparing sets of DMS experiments to identify biologically important shifts in mutational effects. Significance StatementAmino-acid mutations to a protein have effects that can shift as the protein evolves or is put under new selective pressure. The effects of amino-acid mutations to a specific protein under a defined selective pressure can be measured by deep mutational scanning experiments. Here, we devise an approach to quantify shifts in mutational effects between experiments performed on different homologs (i.e. variants) of the same protein, or on the same protein selected under different conditions. We use this approach to compare experiments performed on three homologs of SARS-CoV-2 spike, identifying mutations that have shifted in their effect on spike-mediated viral infection by >1,000 fold across SARS-CoV-2 variants. ]]> Haddox, H. K. Galloway, J. G. Dadonaite, B. Bloom, J. D. Matsen, F. A. DeWitt, W. S. 2023-08-02 doi:10.1101/2023.07.31.551037 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Unraveling the Global Proteome and Phosphoproteome of Prostate Cancer Patient-Derived Xenografts ]]> https://biorxiv.org/content/10.1101/2023.08.02.551697v1?rss=1 Sychev, Z. E. Day, A. Bergom, H. E. Larson, G. Ali, A. Ludwig, M. Boytim, E. Ilsa, C. Corey, E. Plymate, S. R. Nelson, P. S. Hwang, J. H. Drake, J. M. 2023-08-05 doi:10.1101/2023.08.02.551697 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Targeting CD19-positive lymphomas with the antibody-drug conjugate (ADC) loncastuximab tesirine: preclinical evidence as single agent and as combinatorial approach ]]> https://biorxiv.org/content/10.1101/2023.08.17.553668v1?rss=1 Tarantelli, C. Wald, D. Munz, N. Spriano, F. Bruscaggin, A. Cannas, E. Cascione, L. Gaudio, E. Arribas, A. J. Manjappa, S. Golino, G. Scalise, L. Zucca, E. Stathis, A. Van Berkel, P. H. Rossi, D. Caimi, P. F. Zammarchi, F. Bertoni, F. 2023-08-18 doi:10.1101/2023.08.17.553668 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ KinCytE- a Kinase to Cytokine Explorer to Identify Molecular Regulators and Potential Therapeutic Opportunities ]]> https://biorxiv.org/content/10.1101/2023.08.20.554063v1?rss=1 Chan, M. Kang, Y. Osborne, S. Zager, M. Gujral, T. 2023-08-21 doi:10.1101/2023.08.20.554063 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ MADDD-seq, a novel massively parallel sequencing tool for simultaneous detection of DNA damage and mutations ]]> https://biorxiv.org/content/10.1101/2023.08.27.555013v1?rss=1 Vermulst, M. Paskvan, S. Chung, C. Franke, K. Clegg, N. Madeoy, J. Long, A. N. Gout, J.-F. Bielas, J. H. 2023-08-27 doi:10.1101/2023.08.27.555013 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Unraveling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors ]]> https://biorxiv.org/content/10.1101/2023.08.30.555623v1?rss=1 Favaro, P. Glass, D. R. Borges, L. Reemar, R. B. Reynolds, W. Ho, D. Bruce, T. Tebaykin, D. Scalon, V. M. Shestopalov, I. Bendall, S. C. 2023-08-31 doi:10.1101/2023.08.30.555623 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Chromatin Profiling of CBFA2T3-GLIS2 AMLs Identifies Key Transcription Factor Dependencies and BRG1 Inhibition as a Novel Therapeutic Strategy ]]> https://biorxiv.org/content/10.1101/2023.08.30.555598v1?rss=1 Kaonis, S. Smith, J. L. Katiyar, N. Merrill, M. Hylkema, T. Namciu, S. Le, Q. Babaeva, E. Ikeda, T. Morris, S. M. Girard, E. Furuyama, S. Ries, R. Bernstein, I. Meshinchi, S. Henikoff, S. Meers, M. P. Hadland, B. K. Sarthy, J. F. 2023-09-01 doi:10.1101/2023.08.30.555598 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Versatile Tissue-Injectable Hydrogels with Extended Hydrolytic Release of Bioactive Protein Therapeutics ]]> https://biorxiv.org/content/10.1101/2023.09.01.554391v1?rss=1 Nealy, E. S. Reed, S. J. Badeau, B. A. Adelmund, S. M. Shadish, J. A. Pakiam, F. J. Girard, E. J. Price, J. P. Mhyre, A. J. Kalia, V. Sarkar, S. DeForest, C. A. Olson, J. M. 2023-09-02 doi:10.1101/2023.09.01.554391 Cold Spring Harbor Laboratory Press 2023-09-02 <![CDATA[ Host cell glycosylation selects for infection with CCR5- versus CXCR4-tropic HIV-1 ]]> https://biorxiv.org/content/10.1101/2023.09.05.556399v1?rss=1 Itell, H. L. Humes, D. Baumgarten, N. E. Overbaugh, J. 2023-09-05 doi:10.1101/2023.09.05.556399 Cold Spring Harbor Laboratory Press 2023-09-05 <![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[ Position-independent refinement of vagus motor neuron wiring ]]> https://biorxiv.org/content/10.1101/2023.09.11.557289v1?rss=1 Kaneko, T. Boulanger-Weill, J. Isabella, A. J. Moens, C. B. 2023-09-13 doi:10.1101/2023.09.11.557289 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Structure and dynamics of the contractile vacuole complex in Tetrahymena thermophila ]]> https://biorxiv.org/content/10.1101/2023.09.13.557576v1?rss=1 Cheng, C.-Y. Romero, D. P. Zoltner, M. Yao, M.-C. Turkewitz, A. 2023-09-14 doi:10.1101/2023.09.13.557576 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Regulation of interferon signaling by transposon exonization ]]> https://biorxiv.org/content/10.1101/2023.09.11.557241v1?rss=1 Pasquesi, G. I. M. Allen, H. Ivancevic, A. Barbachano-Guerrero, A. Joyner, O. Guo, K. Simpson, D. M. Gapin, K. Horton, I. Nguyen, L. Yang, Q. Warren, C. J. Florea, L. D. Bitler, B. G. Santiago, M. L. Sawyer, S. L. Chuong, E. B. 2023-09-15 doi:10.1101/2023.09.11.557241 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ The diverse evolutionary histories of domesticated metaviral capsid genes in mammals ]]> https://biorxiv.org/content/10.1101/2023.09.17.558119v1?rss=1 Henriques, W. S. Young, J. M. Nemudryi, A. Nemudraia, A. Wiedenheft, B. Malik, H. S. 2023-09-17 doi:10.1101/2023.09.17.558119 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Alternate splice variants of the mitochondrial fission protein DNM1L/Drp1 regulate mitochondrial dynamics and cell fate in ovarian cancer. ]]> https://biorxiv.org/content/10.1101/2023.09.20.558501v1?rss=1 Javed, Z. Shin, D. H. Pan, W. White, S. R. Kim, Y. S. Elhaw, A. T. Kamlapurkar, S. Cheng, Y.-Y. Benson, J. C. Abdelnaby, A. E. Phaeton, R. Wang, H.-G. Yang, S. Sullivan, M. L. G. Watkins, S. C. Mullett, S. J. Gelhaus, S. L. Lee, N. Y. Coffman, L. Aird, K. M. Trebak, M. Karthikeyan, M. Walter, V. Hempel, N. 2023-09-20 doi:10.1101/2023.09.20.558501 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Computational design of sequence-specific DNA-binding proteins ]]> https://biorxiv.org/content/10.1101/2023.09.20.558720v1?rss=1 Glasscock, C. J. Pecoraro, R. McHugh, R. Doyle, L. A. Chen, W. Boivin, O. Lonnquist, B. Na, E. Politanska, Y. Haddox, H. K. Cox, D. Norn, C. Coventry, B. Goreshnik, I. Vafeados, D. Lee, G. R. Gordan, R. Stoddard, B. L. DiMaio, F. Baker, D. 2023-09-21 doi:10.1101/2023.09.20.558720 Cold Spring Harbor Laboratory Press 2023-09-21 <![CDATA[ SurvBal: Compositional Microbiome Balances for Survival Outcomes ]]> https://biorxiv.org/content/10.1101/2023.09.22.559069v1?rss=1 Li, Y. Lee, T. Marin, K. Hua, X. Srinivasan, S. Fredricks, D. N. Lee, J. R. Ling, W. 2023-09-24 doi:10.1101/2023.09.22.559069 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ RADIF(C1orf112)-FIGNL1 Complex Regulates RAD51 Chromatin Association to Promote Viability After Replication Stress ]]> https://biorxiv.org/content/10.1101/2023.09.25.556595v1?rss=1 Tischler, J. D. Tsuchida, H. Bosire, R. Oda, T. T. Park, A. Adeyemi, R. O. 2023-09-25 doi:10.1101/2023.09.25.556595 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies ]]> https://biorxiv.org/content/10.1101/2023.09.13.557606v1?rss=1 Goo, L. Kikawa, C. Cartwright-Acar, C. H. Stuart, J. B. Contreras, M. Levoir, L. M. Evans, M. J. Bloom, J. D. 2023-09-26 doi:10.1101/2023.09.13.557606 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control ]]> https://biorxiv.org/content/10.1101/2023.09.27.559793v1?rss=1 Chen, K. Y. Park, H. Subramaniam, A. R. 2023-09-27 doi:10.1101/2023.09.27.559793 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Forward genetic screens identify mechanisms of resistance to small molecule lactate dehydrogenase inhibitors ]]> https://biorxiv.org/content/10.1101/2023.09.30.560315v1?rss=1 Frank, A. R. Vandiver, F. McFadden, D. G. 2023-09-30 doi:10.1101/2023.09.30.560315 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2023.09.28.560025v1?rss=1 View larger version (41K): org.highwire.dtl.DTLVardef@13278a4org.highwire.dtl.DTLVardef@8e82aeorg.highwire.dtl.DTLVardef@25a115org.highwire.dtl.DTLVardef@728eb4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic AbstractC_FLOATNO C_FIG Androgen receptor-(AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that the HOX/CUT transcription factor ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 targets include the glucocorticoid receptor and the NE splicing factor SRRM4, among others. OC2 regulates gene expression by promoter binding, enhancement of chromatin accessibility, and formation of novel super-enhancers. OC2 also activates glucuronidation genes that irreversibly disable androgen, thereby evoking phenotypic heterogeneity indirectly by hormone depletion. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC. Our findings support enhanced efforts to therapeutically target this protein as a means of suppressing treatment-resistant disease. ]]> Qian, C. Yang, Q. Rotinen, M. Huang, R. Kim, h. Gallent, B. Yan, Y. Cadaneanu, R. M. Zhang, B. Kaochar, S. Freedland, S. J. Posadas, E. M. Ellis, L. Di Vizio, D. Morrissey, C. Nelson, P. S. Brady, L. Murali, R. Campbell, M. J. Yang, W. Knudsen, B. S. Mostaghel, E. A. Ye, H. Garraway, I. P. You, S. Freeman, M. R. 2023-10-01 doi:10.1101/2023.09.28.560025 Cold Spring Harbor Laboratory Press 2023-10-01 <![CDATA[ ATF7IP2/MCAF2 directs H3K9 methylation and meiotic gene regulation in the male germline ]]> https://biorxiv.org/content/10.1101/2023.09.30.560314v1?rss=1 Alavattam, K. G. Esparza, J. M. Hu, M. Shimada, R. Kohrs, A. R. Abe, H. Munakata, Y. Otsuka, K. Yoshimura, S. Kitamura, Y. Yeh, Y.-H. Hu, Y.-C. Kim, J. Andreassen, P. R. Ishiguro, K.-i. Namekawa, S. H. 2023-10-02 doi:10.1101/2023.09.30.560314 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Arrested Agonist Paradigm For Selective Radiosensitization of Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2023.10.01.560227v1?rss=1 Coulter, J. B. Haffner, M. Zhang, Y. Zhou, H. Pham, M.-T. N. Chen, J. Chikarmane, R. Mishra, A. Mehl, M. S. Kazibwe, S. Choi, K. Archey, A. Valluri, S. Lupold, S. E. Song, D. De Marzo, A. M. Nelson, W. G. DeWeese, T. L. Yegnasubramanian, S. 2023-10-02 doi:10.1101/2023.10.01.560227 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Therapeutic Targeting of TIM-4-L With Engineered T Cells for Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2023.10.03.560752v1?rss=1 Cieniewicz, B. Oliveira, E. Saxton, M. Torabi, D. Bhatta, A. Kukutla, P. Arballo, A. Yang, Z. Yu, B. Fate, M. Ning, H. Corey, L. Maiti, A. Corey, D. 2023-10-04 doi:10.1101/2023.10.03.560752 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ Natural malaria infection elicits rare but potent neutralizing antibodies to the blood-stage antigen RH5 ]]> https://biorxiv.org/content/10.1101/2023.10.04.560669v1?rss=1 Wang, L. T. Cooper, A. J. R. Farrell, B. Miura, K. Diouf, A. Muller-Sienerth, N. Crosnier, C. Purser, L. Maciuszek, M. Barrett, J. R. McHugh, K. Tucker, C. Li, S. Doumbo, S. Doumtabe, D. Pyo, C.-W. Nielsen, C. M. Silk, S. E. Kayentao, K. Ongoiba, A. Zhao, M. Nguyen, D. C. Lee, F. E.-H. Minassian, A. M. Geraghty, D. E. Traore, B. Seder, R. A. Crompton, P. D. Wright, G. J. Long, C. A. Draper, S. J. Higgins, M. K. Tan, J. 2023-10-06 doi:10.1101/2023.10.04.560669 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Deep mutational scanning of CYP2C19 reveals a substrate specificity-abundance tradeoff ]]> https://biorxiv.org/content/10.1101/2023.10.06.561250v1?rss=1 Boyle, G. E. Sitko, K. Galloway, J. G. Haddox, H. K. Bianchi, A. H. Dixon, A. Thomson, R. E. S. Garge, R. K. Rettie, A. E. Rubin, A. F. Geck, R. C. Gillam, E. M. J. DeWitt, W. S. Matsen, F. A. Fowler, D. M. 2023-10-08 doi:10.1101/2023.10.06.561250 Cold Spring Harbor Laboratory Press 2023-10-08 <![CDATA[ Antigen-level resolution of commensal-specific B cell responses enabled by phage-display screening and B cell tetramers ]]> https://biorxiv.org/content/10.1101/2023.10.13.562275v1?rss=1 Verma, S. Dufort, M. J. Olsen, T. M. Labuda, J. C. Kimmel, S. Scharffenberger, S. McGuire, A. Harrison, O. J. 2023-10-17 doi:10.1101/2023.10.13.562275 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus 'fossil record'. ]]> https://biorxiv.org/content/10.1101/2023.10.17.562709v1?rss=1 Blanco-Melo, D. Campbell, M. A. Zhu, H. Dennis, T. Mohda, S. Lytras, S. Hughes, J. J. Gatseva, A. Gifford, R. J. 2023-10-19 doi:10.1101/2023.10.17.562709 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Terpenoid balance in Aspergillus nidulans unveiled by heterologous squalene synthase expression ]]> https://biorxiv.org/content/10.1101/2023.10.20.563295v1?rss=1 Park, S. C. Steffan, B. N. Lim, F. Y. Gupta, R. Butun, F. A. Chen, H. Ye, R. Decker, T. Wu, C. C. Kelleher, N. L. Bok, J. W. Keller, N. P. 2023-10-20 doi:10.1101/2023.10.20.563295 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Genotype prediction of 336,463 samples from public expression data ]]> https://biorxiv.org/content/10.1101/2023.10.21.562237v1?rss=1 Razi, A. Lo, C. C. Wang, S. Leek, J. T. Hansen, K. D. 2023-10-22 doi:10.1101/2023.10.21.562237 Cold Spring Harbor Laboratory Press 2023-10-22 <![CDATA[ The Ribosome Assembly Factor Reh1 is Released from the Polypeptide Exit Tunnel in the Pioneer Round of Translation ]]> https://biorxiv.org/content/10.1101/2023.10.23.563604v1?rss=1 Musalgaonkar, S. Yelland, J. Chitale, R. Rao, S. Ozadam, H. Cenik, C. Taylor, D. Johnson, A. W. 2023-10-23 doi:10.1101/2023.10.23.563604 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Germline novelty through recurrent copy-number, protein, and regulatory evolution of the synaptonemal complex ]]> https://biorxiv.org/content/10.1101/2023.10.20.563324v1?rss=1 Wei, K. H. Chang, C.-H. Chatla, K. Krishnapura, A. Appiah, S. P. Zhang, J. Unckless, R. L. Blumenstiel, J. Bachtrog, D. 2023-10-24 doi:10.1101/2023.10.20.563324 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ A quantitative genetics framework for understanding the selection response of microbial communities ]]> https://biorxiv.org/content/10.1101/2023.10.24.563725v1?rss=1 Xie, L. Yuan, A. E. Shou, W. 2023-10-24 doi:10.1101/2023.10.24.563725 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies ]]> https://biorxiv.org/content/10.1101/2023.10.23.563660v1?rss=1 Freie, B. Carroll, P. A. Varnum-Finney, B. J. Ramani, V. Bernstein, I. Eisenman, R. N. 2023-10-25 doi:10.1101/2023.10.23.563660 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Widespread fungal-bacterial competition for magnesium enhances antibiotic resistance ]]> https://biorxiv.org/content/10.1101/2023.10.25.563990v1?rss=1 Hsieh, Y.-Y. P. Sun, W. W. Young, J. M. Cheung, R. Hogan, D. A. Dandekar, A. A. Malik, H. S. 2023-10-26 doi:10.1101/2023.10.25.563990 Cold Spring Harbor Laboratory Press 2023-10-26 <![CDATA[ dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets ]]> https://biorxiv.org/content/10.1101/2023.10.29.564578v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@6c623forg.highwire.dtl.DTLVardef@1a62199org.highwire.dtl.DTLVardef@1e7d71eorg.highwire.dtl.DTLVardef@1dc1252_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Large mutation-associated datasets are used in a variety of experimental contexts. They can be used to map antibody footprints on viral glycoproteins, assess the impact of mutations on protein function in a laboratory setting, and identify patterns of selection from natural mutation frequencies. C_FIG The mutation-based data generated by these approaches is often best understood in the context of a proteins 3D structure; for instance, to assess questions like how mutations that affect antibody escape relate to the physical antibody binding epitope on the protein. However, current approaches for visualizing mutation data in the context of a proteins structure are often cumbersome and require multiple steps and softwares. To streamline the visualization of mutation-associated data in the context of a protein structure, we developed a web-based tool, dms-viz. With dms-viz, users can straightforwardly visualize mutation-based data such as those from DMS experiments in the context of a 3D protein model in an interactive format. See https://dms-viz.github.io/ to use dms-viz. ]]> Hannon, W. W. Bloom, J. D. 2023-11-01 doi:10.1101/2023.10.29.564578 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies ]]> https://biorxiv.org/content/10.1101/2023.10.30.564764v1?rss=1 Li, X. Chen, H. Selvaraj, M. S. Van Buren, E. Zhou, H. Wang, Y. Sun, R. McCaw, Z. R. Yu, Z. Arnett, D. K. Bis, J. C. Blangero, J. Boerwinkle, E. Bowden, D. W. Brody, J. A. Cade, B. E. Carson, A. P. Carlson, J. C. Chami, N. Chen, Y.-D. I. Curran, J. E. de Vries, P. S. Fornage, M. Franceschini, N. Freedman, B. I. Gu, C. Heard-Costa, N. L. He, J. Hou, L. Hung, Y.-J. Irvin, M. R. Kaplan, R. C. Kardia, S. L. R. Kelly, T. Konigsberg, I. Kooperberg, C. Kral, B. G. Li, C. Loos, R. J. F. Mahaney, M. C. Martin, L. W. Mathias, R. A. Minster, R. L. Mitchell, B. D 2023-11-02 doi:10.1101/2023.10.30.564764 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Small-molecule binding and sensing with a designed protein family ]]> https://biorxiv.org/content/10.1101/2023.11.01.565201v1?rss=1 Lee, G. R. Pellock, S. J. Norn, C. Tischer, D. Dauparas, J. Anishchenko, I. Mercer, J. A. M. Kang, A. Bera, A. Nguyen, H. Goreshnik, I. Vafeados, D. Roullier, N. Han, H. L. Coventry, B. Haddox, H. K. Liu, D. R. Yeh, A. H.-W. Baker, D. 2023-11-02 doi:10.1101/2023.11.01.565201 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Evolutionary origin and structural ligand mimicry by the inserted domain of alpha-integrin proteins ]]> https://biorxiv.org/content/10.1101/2023.11.05.565221v1?rss=1 Hollis, J. A. Chan, M. C. Malik, H. S. Campbell, M. G. 2023-11-06 doi:10.1101/2023.11.05.565221 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Infection pressure in apes has driven selection for CD4 alleles that resist lentivirus (HIV/SIV) infection ]]> https://biorxiv.org/content/10.1101/2023.11.13.566830v1?rss=1 Warren, C. Barbachano-Guerrero, A. DuMont, V. Stabell, A. Dirasantha, O. Yang, Q. Sawyer, S. L. 2023-11-13 doi:10.1101/2023.11.13.566830 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades ]]> https://biorxiv.org/content/10.1101/2023.11.13.566961v1?rss=1 9,000 mutations across the full XBB.1.5 and BA.2 spikes affect ACE2 binding, cell entry, or escape from human sera. We find that mutations outside the receptor-binding domain (RBD) have meaningfully impacted ACE2 binding during SARS-CoV-2 evolution. We also measure how mutations to the XBB.1.5 spike affect neutralization by serum from individuals who recently had SARS-CoV-2 infections. The strongest serum escape mutations are in the RBD at sites 357, 420, 440, 456, and 473--however, the antigenic impacts of these mutations vary across individuals. We also identify strong escape mutations outside the RBD; however many of them decrease ACE2 binding, suggesting they act by modulating RBD conformation. Notably, the growth rates of human SARS-CoV-2 clades can be explained in substantial part by the measured effects of mutations on spike phenotypes, suggesting our data could enable better prediction of viral evolution. ]]> Dadonaite, B. Brown, J. McMahon, T. E. Farrell, A. G. Asarnow, D. Stewart, C. Logue, J. Murrell, B. Chu, H. Y. Veesler, D. Bloom, J. D. 2023-11-14 doi:10.1101/2023.11.13.566961 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Expansion of human centromeric arrays in cells undergoing break-induced replication ]]> https://biorxiv.org/content/10.1101/2023.11.11.566714v1?rss=1 Showman, S. Talbert, P. B. Xu, Y. Adeyemi, R. O. Henikoff, S. 2023-11-15 doi:10.1101/2023.11.11.566714 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ High-throughput thermodynamic and kinetic measurements of transcription factor/DNA mutations reveal how conformational heterogeneity can shape motif selectivity ]]> https://biorxiv.org/content/10.1101/2023.11.13.566946v1?rss=1 1700 Kds and >500 rate constants for Pho4 and MAX mutant libraries binding multiple DNA sequences and comparing these measurements with thermodynamic and kinetic models, we identify the biophysical mechanisms by which changes to TF sequence alter both bound and unbound conformational ensembles to shape specificity landscapes. These results highlight the importance of conformational heterogeneity in determining sequence specificity and selectivity and can guide future efforts to engineer nucleic acid-binding proteins with enhanced selectivity. ]]> Fordyce, P. M. Hastings, R. Aditham, A. DelRosso, N. Suzuki, P. 2023-11-16 doi:10.1101/2023.11.13.566946 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Two Septin Complexes Mediate Actin Dynamics During Cell Wound Repair ]]> https://biorxiv.org/content/10.1101/2023.11.14.567084v1?rss=1 Stjepic, V. Nakamura, M. Hui, J. Parkhurst, S. M. 2023-11-16 doi:10.1101/2023.11.14.567084 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ A novel non-invasive method to sample immune cells in the lower female genital tract ]]> https://biorxiv.org/content/10.1101/2023.11.16.567469v1?rss=1 Peters, M. Q. Domenjo-Vila, E. Carlson, M. Edlefsen, P. T. Gasper, M. Dabee, S. Armistead, B. Whidbey, C. Jaspan, H. B. Prlic, M. Harrington, W. E. 2023-11-17 doi:10.1101/2023.11.16.567469 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Whole genome association testing in 333,100 individuals across three biobanks identifies rare non-coding single variant and genomic aggregate associations with height ]]> https://biorxiv.org/content/10.1101/2023.11.19.566520v1?rss=1 Hawkes, G. Beaumont, R. N. Li, Z. Mandla, R. Li, X. Albert, C. M. Arnett, D. K. Ashley-Koch, A. E. Ashrani, A. A. Barnes, K. C. Boerwinkle, E. Brody, J. A. Carson, A. P. Chami, N. Chen, Y.-D. I. Chung, M. K. Curran, J. E. Darbar, D. Ellinor, P. T. Fornage, M. Gordeuk, V. R. Guo, X. He, J. Hwu, C.-M. Kalyani, R. R. Kaplan, R. Kardia, S. L. R. Kooperberg, C. Loos, R. J. F. Lubitz, S. A. Minster, R. L. Mitchell, B. D. Murabito, J. M. Palmer, N. D. Psaty, B. M. Redline, S. Shoemaker, M. B. Silverman, E. K. Telen, M. J. Weiss, S. T. Yanek, L. R. Zhou, H. NH 2023-11-20 doi:10.1101/2023.11.19.566520 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes ]]> https://biorxiv.org/content/10.1101/2023.11.30.569313v1?rss=1 Riley, A. K. Grant, M. Snell, A. Vichas, A. Moorthi, S. Urisman, A. Castel, P. Wan, L. Berger, A. 2023-12-01 doi:10.1101/2023.11.30.569313 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Calcium influx rapidly establishes distinct spatial recruitments of Annexins to cell wounds ]]> https://biorxiv.org/content/10.1101/2023.12.03.569799v1?rss=1 Nakamura, M. Parkhurst, S. M. 2023-12-04 doi:10.1101/2023.12.03.569799 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ snPATHO-seq: unlocking the pathology archives ]]> https://biorxiv.org/content/10.1101/2023.12.07.570700v1?rss=1 Wang, T. Harvey, K. Escudero Morales, J. Kiedik, B. Al-Eryani, G. Greenwald, A. C. Kalavros, N. SegatovDezem, F. Ma, Y. Pita-Juarez, Y. Wise, K. Degletagne, C. Elz, A. Johanneson, J. Pakiam, F. Ryu, H. Newell, E. W. Tonon, L. Kohlway, A. Drennon, T. Hadadianpour, A. Abousoud, J. Scott, R. Lund, P. Durruthy, J. Vallejos, A. F. Kaczorowski, D. Warren, J. Butler, L. M. O'Toole, S. Plummer, J. T. Vlachos, I. Lundeberg, J. Swarbrick, A. Martelotto, L. G. 2023-12-08 doi:10.1101/2023.12.07.570700 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Viral gene drive spread during herpes simplex virus 1 infection in mice ]]> https://biorxiv.org/content/10.1101/2023.12.07.570711v1?rss=1 Walter, M. Riley, R. Haick, A. K. Massa, P. A. Strongin, D. E. Klouser, L. M. Loprieno, M. A. Stensland, L. Santo, T. K. Taylor, M. P. Jerome, K. R. Verdin, E. 2023-12-08 doi:10.1101/2023.12.07.570711 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ SIRPα controls CD47-dependent platelet clearance in mice and humans ]]> https://biorxiv.org/content/10.1101/2023.12.09.570874v1?rss=1 Shoham, M. Yiu, Y. Y. Hansen, P. Subramaniam, A. Broberg, M. Gars, E. Raveh, T. FinnGen, Weissman, I. L. Sinnott-Armstrong, N. Krishnan, A. Ollila, H. Tal, M. C. 2023-12-10 doi:10.1101/2023.12.09.570874 Cold Spring Harbor Laboratory Press 2023-12-10 <![CDATA[ 50-color phenotyping of the human immune system with in-depth assessment of T cells and dendritic cells ]]> https://biorxiv.org/content/10.1101/2023.12.14.571745v1?rss=1 Konecny, A. J. Mage, P. Tyznik, A. J. Prlic, M. Mair, F. 2023-12-15 doi:10.1101/2023.12.14.571745 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ KMT2A oncoproteins induce epigenetic resistance to targeted therapies ]]> https://biorxiv.org/content/10.1101/2023.12.29.573681v1?rss=1 Janssens, D. H. Duran, M. Otto, D. J. Kirkey, D. Yi, J. S. Meshinchi, S. Sarthy, J. F. Ahmad, K. Henikoff, S. 2023-12-30 doi:10.1101/2023.12.29.573681 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ LSD1 inhibition suppresses ASCL1 and de-represses YAP1 to drive potent activity against neuroendocrine prostate cancer ]]> https://biorxiv.org/content/10.1101/2024.01.17.576106v1?rss=1 Mandl, A. Jasmine, S. Krueger, T. E. G. Kumar, R. Coleman, I. M. Dalrymple, S. L. Antony, L. Rosen, D. M. Jing, Y. Hanratty, B. Patel, R. A. Low, J.-Y. Dias, J. Celatka, C. A. Tapper, A. E. Kleppe, M. Kanayama, M. Speranzini, V. Wang, Y. Luo, J. Corey, E. Sena, L. A. Casero, R. A. Lotan, T. Trock, B. J. Kachhap, S. K. Denmeade, S. R. Carducci, M. A. Mattevi, A. Haffner, M. C. Nelson, P. S. Rienhoff, H. H. Isaacs, J. T. Brennen, W. N. 2024-01-22 doi:10.1101/2024.01.17.576106 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ CYpHER: Catalytic extracellular targeted protein degradation with high potency and durable effect ]]> https://biorxiv.org/content/10.1101/2024.02.21.581471v1?rss=1 Crook, Z. R. Sevilla, G. P. Young, P. Girard, E. J. Phi, T.-D. Howard, M. Olson, J. M. Nairn, N. W. 2024-02-23 doi:10.1101/2024.02.21.581471 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Prevalent fast evolution of genes involved in heterochromatin functions ]]> https://biorxiv.org/content/10.1101/2024.03.03.583199v1?rss=1 Lin, L. Huang, Y. McIntyre, J. Chang, C.-H. Colmenares, S. S. Lee, G. Y. C. 2024-03-06 doi:10.1101/2024.03.03.583199 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data ]]> https://biorxiv.org/content/10.1101/2024.03.08.584117v1?rss=1 Samorodnitsky, S. N. Campbell, K. M. Ribas, A. Wu, M. C. 2024-03-13 doi:10.1101/2024.03.08.584117 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation ]]> https://biorxiv.org/content/10.1101/2024.03.08.584120v1?rss=1 Kubinski, H. C. Despres, H. W. Johnson, B. A. Schmidt, M. M. Jaffrani, S. A. Mills, M. G. Lokugamage, K. Dumas, C. M. Shirley, D. J. Estes, L. K. Pekosz, A. Crothers, J. W. Roychoudhury, P. Greninger, A. L. Jerome, K. R. Martorelli Di Genova, B. Walker, D. H. Ballif, B. A. Ladinsky, M. S. Bjorkman, P. J. Menachery, V. D. Bruce, E. A. 2024-03-11 doi:10.1101/2024.03.08.584120 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Transcriptional bursting, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single cell RNA-seq ]]> https://biorxiv.org/content/10.1101/2024.03.08.584165v1?rss=1 Schofield, J. A. Hahn, S. 2024-03-13 doi:10.1101/2024.03.08.584165 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains ]]> https://biorxiv.org/content/10.1101/2024.03.08.584176v1?rss=1 Loes, A. N. Tarabi, R. A. L. Huddleston, J. Touyon, L. Wong, S. S. Cheng, S. M. Leung, N. H. Hannon, W. W. Bedford, T. Cobey, S. Cowling, B. J. Bloom, J. D. 2024-03-09 doi:10.1101/2024.03.08.584176 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV ]]> https://biorxiv.org/content/10.1101/2024.03.13.584735v1?rss=1 Chao, C. W. Sprouse, K. R. Miranda, M. C. Catanzaro, N. J. Hubbard, M. L. Addetia, A. Stewart, C. Brown, J. T. Dosey, A. Valdez, A. Ravichandran, R. Hendricks, G. G. Ahlrichs, M. Dobbins, C. Hand, A. Treichel, C. Willoughby, I. Walls, A. C. McGuire, A. T. Leaf, E. M. Baric, R. S. Schaefer, A. Veesler, D. King, N. P. 2024-03-14 doi:10.1101/2024.03.13.584735 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Development of a series of genetically engineered NTRK fusion-driven pediatric-type high-grade glioma mouse models ]]> https://biorxiv.org/content/10.1101/2024.03.13.584849v1?rss=1 Schmid, S. Russell, Z. R. Yamashita, A. S. West, M. E. Parrish, A. G. Walker, J. Rudoy, D. Yan, J. Z. Quist, D. C. Gessesse, B. N. Alvinez, N. Cimino, P. J. Kumasaka, D. K. Parchment, R. E. Holland, E. C. Szulzewsky, F. 2024-03-13 doi:10.1101/2024.03.13.584849 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Sir2 and Fun30 regulate ribosomal DNA replication timing via Mcm helicase positioning and nucleosome occupancy ]]> https://biorxiv.org/content/10.1101/2024.03.21.586113v1?rss=1 Lichauco, C. Foss, E. J. Gatbonton-Schwager, T. Athow, N. F. Lofts, B. Acob, R. Taylor, E. Lao, U. Miles, s. Bedalov, A. 2024-03-26 doi:10.1101/2024.03.21.586113 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ MICROMANIPULATION OF LIVE MICRODISSECTED TISSUES WITH A LOW-COST INTEGRATED ROBOTIC PLATFORM ]]> https://biorxiv.org/content/10.1101/2024.03.21.586169v1?rss=1 Gottshall, N. R. Stepanov, I. Ahmadianyazdi, A. Sinha, D. Lockhart, E. Nguyen, T. N. Hassan, S. Horowitz, L. Yeung, R. Gujral, T. S. Folch, A. 2024-03-27 doi:10.1101/2024.03.21.586169 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Microdissected tumor cuboids: a microscale cancer model that retains a complex tumor microenvironment ]]> https://biorxiv.org/content/10.1101/2024.03.22.586189v1?rss=1 Horowitz, L. F. Rodriguez-Mias, R. A. Zhu, S. Gottshall, N. R. Stepanov, I. Stiles, C. Yeung, M. Nguyen, T. N. Lockhart, E. J. Yeung, R. S. Villen, J. Gujral, T. S. Folch, A. 2024-03-27 doi:10.1101/2024.03.22.586189 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Carbon dioxide shapes parasite-host interactions in a human-infective nematode ]]> https://biorxiv.org/content/10.1101/2024.03.28.587273v1?rss=1 Banerjee, N. Gang, S. S. Castelletto, M. L. Ruiz, F. Hallem, E. A. 2024-03-31 doi:10.1101/2024.03.28.587273 Cold Spring Harbor Laboratory Press 2024-03-31 <![CDATA[ Cas9 RNP Physiochemical Analysis for Enhanced CRISPR-AuNP Assembly and Function ]]> https://biorxiv.org/content/10.1101/2024.04.02.586657v1?rss=1 Lane, D. D. Gottimukkala, K. S. V. Cunningham, R. Cassidy, M. E. Jwa, Y. Castelli, J. M. P. Adair, J. E. 2024-04-02 doi:10.1101/2024.04.02.586657 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Adjusting for principal components can induce spurious associations in genome-wide association studies in admixed populations ]]> https://biorxiv.org/content/10.1101/2024.04.02.587682v1?rss=1 Grinde, K. Browning, B. L. Reiner, A. P. Thornton, T. A. Browning, S. R. 2024-04-03 doi:10.1101/2024.04.02.587682 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Merkel cell polyomavirus protein ALTO modulates TBK1 activity to support persistent infection ]]> https://biorxiv.org/content/10.1101/2024.04.05.588227v1?rss=1 Wang, R. Senay, T. E. Luo, T. T. Regan, J. M. Salisbury, N. Galloway, D. You, J. 2024-04-05 doi:10.1101/2024.04.05.588227 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ Single Cell Analysis of Treatment-Resistant Prostate Cancer: Implications of Cell State Changes for Cell Surface Antigen Targeted Therapies ]]> https://biorxiv.org/content/10.1101/2024.04.09.588340v1?rss=1 Zaidi, S. Park, J. Chan, J. M. Roudier, M. Zhao, J. L. Gopalan, A. Wadosky, K. M. Patel, R. A. Sayar, E. Karthaus, W. R. Kates, D. H. Chaudhary, O. Xu, T. Masilionis, I. Mazutis, L. Chaligne, R. Obradovic, A. Linkov, I. Barlas, A. Jungbluth, A. Rekhtman, N. Silber, J. Manova-Todorova, K. Watson, P. A. True, L. D. Morrissey, C. M. Scher, H. I. Rathkopf, D. Morris, M. J. Goodrich, D. W. Choi, J. Nelson, P. S. Haffner, M. Sawyers, C. 2024-04-12 doi:10.1101/2024.04.09.588340 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ All-trans retinoic acid induces durable tumor immunity in IDH-mutant gliomas by rescuing transcriptional repression of the CRBP1-retinoic acid axis ]]> https://biorxiv.org/content/10.1101/2024.04.09.588752v1?rss=1 Rao, A. Zhang, X. Cillo, A. Sussman, J. H. Sandlesh, P. Tarbay, A. C. Mallela, A. N. Cardello, C. Krueger, K. Xu, J. Li, A. Xu, J. Patterson, J. Akca, E. Angione, A. Jaman, E. Kim, W. J. Allen, J. Venketeswaran, A. Zinn, P. O. Parise, R. Beumer, J. Duensing, A. Holland, E. C. Ferris, R. Bagley, S. J. Bruno, T. C. Vignali, D. A. A. Agnihotri, S. Amankulor, N. M. 2024-04-13 doi:10.1101/2024.04.09.588752 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Centromeric localization of KNL2 and CENP-C proteins in plants depends on their centromere-targeting domain and DNA-binding regions ]]> https://biorxiv.org/content/10.1101/2024.04.11.588992v1?rss=1 Yalagapati, S. P. Ahmadli, U. Sinha, A. Kalidass, M. Dabravolski, S. Zuo, S. Yadala, R. Rutten, T. Talbert, P. Lermontova, I. 2024-04-11 doi:10.1101/2024.04.11.588992 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ Breaking out of the cell cycle: Including quiescence in cell cycle classification ]]> https://biorxiv.org/content/10.1101/2024.04.16.589816v1?rss=1 O'Connor, S. A. Garcia, L. Patel, A. P. Hugnot, J.-P. PADDISON, P. Plaisier, C. L. 2024-04-20 doi:10.1101/2024.04.16.589816 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Functional and antigenic landscape of the Nipah virus receptor binding protein ]]> https://biorxiv.org/content/10.1101/2024.04.17.589977v1?rss=1 Larsen, B. B. McMahon, T. Brown, J. T. Wang, Z. Radford, C. E. Crowe, J. E. Veesler, D. Bloom, J. D. 2024-04-19 doi:10.1101/2024.04.17.589977 Cold Spring Harbor Laboratory Press 2024-04-19 <![CDATA[ Antigen affinity and site of immunization dictate B cell recall responses ]]> https://biorxiv.org/content/10.1101/2024.04.19.590239v1?rss=1 Termote, M. Marques, R. C. Hyllner, E. Guryleva, M. V. Henskens, M. Brutscher, A. Baken, I. J. L. Castro Dopico, X. Dalmau Gasull, A. Murrell, B. Stamatatos, L. Westerberg, L. S. Dosenovic, P. 2024-04-23 doi:10.1101/2024.04.19.590239 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses ]]> https://biorxiv.org/content/10.1101/2024.04.24.590836v1?rss=1 Ruiz, F. Foreman, W. Lilly, M. Baharani, V. A. Depierreux, D. M. Chohan, V. Taylor, A. L. Guenthoer, J. Ralph, D. Matsen, F. A. Chu, H. Y. Bieniasz, P. D. Cote, M. Starr, T. N. Overbaugh, J. 2024-04-25 doi:10.1101/2024.04.24.590836 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Cell Simulation as Cell Segmentation ]]> https://biorxiv.org/content/10.1101/2024.04.25.591218v1?rss=1 Jones, D. C. Elz, A. E. Hadadianpour, A. Ryu, H. Glass, D. R. Newell, E. W. 2024-04-28 doi:10.1101/2024.04.25.591218 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Functional genomics screens reveal a role for TBC1D24 and SV2B in antibody-dependent enhancement of dengue virus infection ]]> https://biorxiv.org/content/10.1101/2024.04.26.591029v1?rss=1 Belmont, L. Contreras, M. Cartwright-Acar, C. H. Marceau, C. D. Agrawal, A. Levoir, L. M. Lubow, J. Goo, L. 2024-04-27 doi:10.1101/2024.04.26.591029 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Reduced Levels of Lagging Strand Polymerases Shape Stem Cell Chromatin ]]> https://biorxiv.org/content/10.1101/2024.04.26.591383v1?rss=1 Snedeker, J. Davis, B. E. M. Ranjan, R. Wooten, M. I. Blundon, J. Chen, X. 2024-04-29 doi:10.1101/2024.04.26.591383 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Tumor microenvironment noise-induced polarization: the main challenge in macrophages' immunotherapy for cancer. ]]> https://biorxiv.org/content/10.1101/2024.05.02.592270v1?rss=1 Sierra, J. Avila-Ponce de Leon, U. Padilla-Longoria, P. 2024-05-05 doi:10.1101/2024.05.02.592270 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Bispecific antibodies with broad neutralization potency against SARS-CoV-2 variants of concern ]]> https://biorxiv.org/content/10.1101/2024.05.05.592584v1?rss=1 Rubio, A. A. Baharani, V. A. Dadonaite, B. Parada, M. Abernathy, M. E. Wang, Z. Lee, Y. E. Eso, M. Phung, J. Ramos, I. Chen, T. El Nesr, G. Bloom, J. D. Bieniasz, P. D. Nussenzweig, M. C. Barnes, C. O. 2024-05-06 doi:10.1101/2024.05.05.592584 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations ]]> https://biorxiv.org/content/10.1101/2024.05.07.592993v1?rss=1 Tenthorey, J. del Banco, S. Ramzan, I. Klingenberg, H. Liu, C. Emerman, M. Malik, H. S. 2024-05-10 doi:10.1101/2024.05.07.592993 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ EZH2-driven immune evasion defines high-risk pediatric AML with t(16;21) FUS::ERG gene fusion. ]]> https://biorxiv.org/content/10.1101/2024.05.14.594150v1?rss=1 Buteyn, N. J. Burke, C. G. Sartori, V. J. Deering-Gardner, E. DeBruine, Z. J. Kamarudin, D. Chandler, D. P. Monovich, A. C. Perez, M. W. Yi, J. S. Ries, R. E. Alonzo, T. A. Ryan, R. J. Meshinchi, S. Triche, T. J. 2024-05-17 doi:10.1101/2024.05.14.594150 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Apoptotic cells promote circulating tumor cell survival and metastasis ]]> https://biorxiv.org/content/10.1101/2024.05.21.595217v1?rss=1 View larger version (70K): org.highwire.dtl.DTLVardef@889460org.highwire.dtl.DTLVardef@c55e30org.highwire.dtl.DTLVardef@1aac38forg.highwire.dtl.DTLVardef@cf7ae_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hagan, C. E. Snyder, A. G. Headley, M. Oberst, A. 2024-05-22 doi:10.1101/2024.05.21.595217 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ A Rigorous Multi-Laboratory Study of Known PDAC Biomarkers Identifies Increased Sensitivity and Specificity Over CA19-9 Alone ]]> https://biorxiv.org/content/10.1101/2024.05.22.595399v1?rss=1 Haab, B. Qian, L. Staal, B. Jain, M. Fahrmann, J. F. Worthington, C. Prosser, D. Velikokhatnaya, L. Lopez, C. Tang, R. Hurd, M. Gopalakrishnan, N. Kumar, S. Smith, L. Hanash, S. Batra, S. K. Maitra, A. Lokshin, A. Huang, Y. Brand, R. 2024-05-26 doi:10.1101/2024.05.22.595399 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Multiplexed single cell transcriptomics optimizes mesodermal patterning and hemogenic endothelial output from murine embryonic stem cells ]]> https://biorxiv.org/content/10.1101/2024.05.24.595249v1?rss=1 Varnum-Finney, B. Heck, A. M. Srivatsan, S. Dozono, S. Wellington, R. Nourigat-McKay, C. Dignum, T. Trapnell, C. 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W. 2024-06-04 doi:10.1101/2024.06.03.597178 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Converging cytokine and metabolite networks shape asymmetric T cell fate at the term human maternal-fetal interface ]]> https://biorxiv.org/content/10.1101/2024.06.10.598377v1?rss=1 Maurice, N. J. Erickson, J. R. DeJong, C. S. Mair, F. Taber, A. K. Frutoso, M. Islas, L. V. Vigil, A.-L. B. Lawler, R. L. McElrath, M. J. Newell, E. W. Sullivan, L. B. Shree, R. McCartney, S. A. 2024-06-12 doi:10.1101/2024.06.10.598377 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Prevalent chromosome fusion in Vibrio cholerae O1 ]]> https://biorxiv.org/content/10.1101/2024.06.12.598706v1?rss=1 Cuenod, A. Chac, D. Khan, A. I. Chowdhury, F. Hyppa, R. W. Markiewicz, S. M. Calderwood, S. B. Ryan, E. T. Harris, J. B. LaRocque, R. C. Bhuiyan, T. R. Smith, G. R. Qadri, F. Lypaczewski, P. Weil, A. A. Shapiro, B. J. 2024-06-12 doi:10.1101/2024.06.12.598706 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Human cytomegalovirus induces neuronal gene expression for viral maturation ]]> https://biorxiv.org/content/10.1101/2024.06.13.598910v1?rss=1 Kelnhofer-Millevolte, L. E. Smith, J. R. Nguyen, D. H. Wilson, L. S. Lewis, H. C. Arnold, E. A. Brinkley, M. R. Geballe, A. P. Ramachandran, S. Avgousti, D. C. 2024-06-13 doi:10.1101/2024.06.13.598910 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ Proteogenomic Reprogramming to a Functional Human Totipotent Stem Cell State via a PARP-DUX4 Regulatory Axis ]]> https://biorxiv.org/content/10.1101/2024.06.14.598510v1?rss=1 Zimmerlin, L. Angarita, A. Park, T. S. Evans-Moses, R. Thomas, J. Yan, S. Uribe, I. Vegas, I. Kochendoerfer, C. Buys, W. Leung, A. Zambidis, E. T. 2024-06-15 doi:10.1101/2024.06.14.598510 Cold Spring Harbor Laboratory Press 2024-06-15 <![CDATA[ Weighted variance component test for the integrative multi-omics analysis of microbiome data ]]> https://biorxiv.org/content/10.1101/2024.06.14.599073v1?rss=1 Zhang, A. Ling, W. Little, A. Williams-Nguyen, J. S. Moon, J.-Y. Burk, R. D. Knight, R. Wang, D. D. Qi, Q. Kaplan, R. Zhao, N. Wu, M. 2024-06-17 doi:10.1101/2024.06.14.599073 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ RBM10 loss induces aberrant splicing of cytoskeletal and extracellular matrix mRNAs and promotes metastatic fitness. ]]> https://biorxiv.org/content/10.1101/2024.07.09.602730v1?rss=1 Krishnamoorthy, G. P. Glover, A. R. Untch, B. R. Sigcha-Coello, N. F. Xu, B. Vukel, D. Liu, Y. Tiedje, V. Berman, K. Tamarapu, P. P. Acuna-Ruiz, A. Saqcena, M. de Stanchina, E. Boucai, L. Ghossein, R. A. Knauf, J. A. Abdel-Wahab, O. Bradley, R. Fagin, J. A. 2024-07-10 doi:10.1101/2024.07.09.602730 Cold Spring Harbor Laboratory Press 2024-07-10 <![CDATA[ Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases ]]> https://biorxiv.org/content/10.1101/2024.07.11.603080v1?rss=1 Jiang, J. Gwee, J. Fang, J. Leichter, S. M. Sanders, D. Ji, X. Song, J. Zhong, X. 2024-07-16 doi:10.1101/2024.07.11.603080 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning ]]> https://biorxiv.org/content/10.1101/2024.07.16.603579v1?rss=1 Estevam, G. O. Linossi, E. M. Rao, J. Macdonald, C. B. Ravikumar, A. Chrispens, K. M. Capra, J. A. Coyote-Maestas, W. Pimentel, H. Collisson, E. A. Jura, N. Fraser, J. S. 2024-07-18 doi:10.1101/2024.07.16.603579 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ Molecular consequences of acute versus chronic CDK12 loss in prostate carcinoma nominates distinct therapeutic strategies ]]> https://biorxiv.org/content/10.1101/2024.07.16.603734v1?rss=1 Frank, S. Persse, T. Coleman, I. M. Bankhead, A. Li, D. DeSarkar, N. Wilson, D. Rudoy, D. Vashisth, M. Galipeau, P. Yang, M. Hanratty, B. Dumpit, R. Morrissey, c. Corey, E. Montgomery, R. Haffner, M. Pritchard, C. Vasioukhin, V. Ha, G. Nelson, P. S. 2024-07-19 doi:10.1101/2024.07.16.603734 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Multiple dermal cell types support productive infection and dynamic translocation of infectious Ebola virus to the apical surface of human skin ]]> https://biorxiv.org/content/10.1101/2024.07.19.604135v1?rss=1 Messingham, K. Richards, P. T. Fleck, A. Patel, R. A. Djurkovic, M. Elliff, J. Connell, S. Gonzalez, J. P. M. Gourronc, F. A. Dillard, J. A. Davey, R. A. Klingelhutz, A. J. Shtanko, O. Maury, W. 2024-07-19 doi:10.1101/2024.07.19.604135 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Oxygen is Toxic in the Cold in C. elegans. ]]> https://biorxiv.org/content/10.1101/2024.07.17.603990v1?rss=1 Suraci, C. M. Morrison, M. L. Roth, M. B. 2024-07-22 doi:10.1101/2024.07.17.603990 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Genetic variants affect diurnal glucose levels throughout the day ]]> https://biorxiv.org/content/10.1101/2024.07.22.604631v1?rss=1 Sinnott-Armstrong, N. Strausz, S. Urpa, L. Abner, E. Valliere, J. Estonian Biobank Research Team, Palta, P. Dashti, H. S. Daly, M. Pritchard, J. K. Saxena, R. Jones, S. E. Ollila, H. M. 2024-07-23 doi:10.1101/2024.07.22.604631 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Genetic Architecture and Analysis Practices of Circulating Metabolites in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program ]]> https://biorxiv.org/content/10.1101/2024.07.23.604849v1?rss=1 Wang, N. Ockerman, F. P. Zhou, L. Y. Grove, M. L. Alkis, T. Barnard, J. Bowler, R. P. Clish, C. B. Chung, S. Drzymalla, E. Evans, A. M. Franceschini, N. Gerszten, R. E. Gillman, M. G. Hutton, S. R. Kelly, R. S. Kooperberg, C. Larson, M. G. Lasky-Su, J. A. Meyers, D. A. Woodruff, P. G. Reiner, A. P. Rich, S. S. Rotter, J. Silverman, E. K. Ramachandran, V. S. Weiss, S. T. Wong, K. E. Wood, A. C. Wu, L. NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Yarden, R. Blackwell, T. Smith, A. V. Chen, H. Raffield, L. M. Yu, B. 2024-07-24 doi:10.1101/2024.07.23.604849 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ The battle of the sexes in humans is highly polygenic ]]> https://biorxiv.org/content/10.1101/2024.07.23.604850v1?rss=1 Cole, J. M. Scott, C. B. Johnson, M. M. Golightly, P. R. Carlson, J. Ming, M. J. Harpak, A. Kirkpatrick, M. 2024-07-24 doi:10.1101/2024.07.23.604850 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Stable centromere association of the yeast histone variant Cse4 requires its essential N-terminal domain ]]> https://biorxiv.org/content/10.1101/2024.07.24.604937v1?rss=1 Popchock, A. R. Hedouin, S. Mao, Y. Asbury, C. L. Stergachis, A. B. Biggins, S. 2024-07-24 doi:10.1101/2024.07.24.604937 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Decoding RNA Metabolism by RNA-linked CRISPR Screening in Human Cells ]]> https://biorxiv.org/content/10.1101/2024.07.25.605204v1?rss=1 Nugent, P. J. Park, H. Wladyka, C. L. Chen, K. Y. Bynum, C. Quarterman, G. Hsieh, A. C. Subramaniam, A. R. 2024-07-26 doi:10.1101/2024.07.25.605204 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ A targeted CRISPR screen identifies ETS1 as a regulator of HIV latency. ]]> https://biorxiv.org/content/10.1101/2024.08.03.606477v1?rss=1 Ashokkumar, M. Hafer, T. L. Felton, A. Archin, N. Margolis, D. M. Emerman, M. Browne, E. P. 2024-08-03 doi:10.1101/2024.08.03.606477 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ CARD8 inflammasome activation during HIV-1 cell-to-cell transmission ]]> https://biorxiv.org/content/10.1101/2024.08.21.608981v1?rss=1 Kulsuptrakul, J. Emerman, M. Mitchell, P. S. 2024-08-22 doi:10.1101/2024.08.21.608981 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses ]]> https://biorxiv.org/content/10.1101/2024.08.21.609082v1?rss=1 Bhattacharya, T. Alleman, E. M. Noyola, A. C. Emerman, M. Malik, H. S. 2024-08-22 doi:10.1101/2024.08.21.609082 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Post-translational modifications on protein VII are important during the early stages of adenovirus infection. ]]> https://biorxiv.org/content/10.1101/2024.08.21.609089v1?rss=1 Arnold, E. A. Smith, J. R. Leung, K. Nguyen, D. H. Kelnhofer-Millevolte, L. E. Guo, M. S. Smith, J. G. Avgousti, D. C. 2024-08-22 doi:10.1101/2024.08.21.609089 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Multiplexed Glycan Immunofluorescence Identification of Pancreatic Cancer Cell Subpopulations in Both Tumor and Blood Samples ]]> https://biorxiv.org/content/10.1101/2024.08.22.609143v1?rss=1 Binkowski, B. Klamer, Z. Gao, C. Staal, B. Repesh, A. Tran, H.-L. Brass, D. M. Bartlett, P. Gallinger, S. Blomqvist, M. Morrow, J. B. Allen, P. Shi, C. Singhi, A. Brand, R. Huang, Y. Hostetter, G. Haab, B. B. 2024-08-23 doi:10.1101/2024.08.22.609143 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Microenvironment T-Type calcium channels regulate neuronal and glial processes to promote glioblastoma growth ]]> https://biorxiv.org/content/10.1101/2024.08.22.609229v1?rss=1 Dube, C. J. Zhang, Y. Saha, S. Lai, M. Gibert, M. K. Escalante, M. Hudson, K. Wong, D. Marcinkiewicz, P. Yener, U. Sun, Y. Xu, E. Sorot, A. Mulcahy, E. Kefas, B. A. Hanif, F. Guessous, F. Patel, M. K. Schiff, D. Zong, H. Purow, B. W. Holland, E. Sonkusare, S. K. Sontheimer, H. Abounader, R. 2024-08-23 doi:10.1101/2024.08.22.609229 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Breastmilk IgG engages the neonatal immune system to instruct host-microbiota mutualism ]]> https://biorxiv.org/content/10.1101/2024.08.23.609293v1?rss=1 Shenoy, M. K. Rico, D. Gordon, S. Milburn, L. Schwensen, J. Caban, M. Koch, M. A. 2024-08-23 doi:10.1101/2024.08.23.609293 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ Chronic innate immune impairment and ZIKV persistence in the gastrointestinal tract during SIV infection in pigtail macaques ]]> https://biorxiv.org/content/10.1101/2024.08.23.609309v1?rss=1 Tisoncik-Go, J. Lewis, T. B. Whitmore, L. S. Voss, K. Niemeyer, S. Dai, J. Kim, P. Hubbell, K. Iwayama, N. Ahrens, C. Wangari, S. Murnane, R. Edlefsen, P. T. Guerriero, K. A. Gale, M. Fuller, D. H. O'Connor, M. 2024-08-24 doi:10.1101/2024.08.23.609309 Cold Spring Harbor Laboratory Press 2024-08-24 <![CDATA[ Molecular basis of pathogenicity of the recently emerged FCoV-23 coronavirus ]]> https://biorxiv.org/content/10.1101/2024.08.25.607996v1?rss=1 Tortorici, M. A. Choi, A. Gibson, C. Lee, J. Brown, J. T. Stewart, C. Joshi, A. Harari, S. Willoughby, I. Treichel, C. Leif, E. Bloom, J. D. King, N. P. Tait-Burkard, C. Whittaker, G. R. Veesler, D. 2024-08-26 doi:10.1101/2024.08.25.607996 Cold Spring Harbor Laboratory Press 2024-08-26 <![CDATA[ Spatiotemporal dynamics of tumor-CAR T-cell interaction following local administration in solid cancers ]]> https://biorxiv.org/content/10.1101/2024.08.29.610392v1?rss=1 Owens, K. Rahman, A. Bozic, I. 2024-08-30 doi:10.1101/2024.08.29.610392 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal ]]> https://biorxiv.org/content/10.1101/2024.08.30.610517v1?rss=1 Gray, C. N. Ashokkumar, M. Janssens, D. H. Kirchherr, J. L. Allard, B. Hsieh, E. Hafer, T. L. Archin, N. M. Browne, E. P. Emerman, M. 2024-08-31 doi:10.1101/2024.08.30.610517 Cold Spring Harbor Laboratory Press 2024-08-31 <![CDATA[ RCC1 depletion drives protein transport defects and rupture in micronuclei ]]> https://biorxiv.org/content/10.1101/2024.09.04.611299v1?rss=1 Zych, M. G. Contreras, M. Vashisth, M. Mammel, A. E. Ha, G. Hatch, E. M. 2024-09-05 doi:10.1101/2024.09.04.611299 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ High Resolution Class I HLA -A, -B, and -C Diversity in Eastern and Southern African Populations ]]> https://biorxiv.org/content/10.1101/2024.09.04.611164v1?rss=1 Ndhlovu, Z. Banjoko, A. W. Ng'uni, T. Naidoo, N. Ramsuran, V. Hyrien, O. 2024-09-08 doi:10.1101/2024.09.04.611164 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes ]]> https://biorxiv.org/content/10.1101/2024.09.04.611290v1?rss=1 Shinde, P. Willemsen, L. Anderson, M. Aoki, M. Basu, S. Burel, J. G. Cheng, P. Dastidar, S. G. Dunleavy, A. Einav, T. Forschmiedt, J. Fourati, S. Garcia, J. Gibson, W. Greenbaum, J. A. Guan, L. Guan, W. Gygi, J. P. Ha, B. Hou, J. Hsiao, J. Huang, Y. Jansen, R. Kakoty, B. Kang, Z. Kobie, J. J. Kojima, M. Konstorum, A. Lee, J. Lewis, S. A. Li, A. Lock, E. F. Mahita, J. Mendes, M. Meng, H. Neher, A. Nili, S. Orfield, S. Overton, J. Pai, N. Parker, C. Qian, B. Rasmussen, M. Reyna, J. Richardson, E. Safo, S. Sorenson, J. Srinivasan, A. Thrupp, N. Tip 2024-09-08 doi:10.1101/2024.09.04.611290 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Rare twin cysteine residues in the HIV-1 envelope variable region 1 link to neutralization escape and breadth development ]]> https://biorxiv.org/content/10.1101/2024.09.05.611179v1?rss=1 65,000 V1 sequences from the CATNAP database, the AMP trials and three large longitudinal HIV infection cohorts, the SHCS, ZPHI and CAPRISA studies, we show that Env variants with extra V1 Cys are present at low levels throughout infection and fluctuate in frequency over time within participants. We demonstrate an independent association of extra V1 Cys with elite plasma neutralization, and a strong preference for two versus one extra Cys, suggesting certain Envs introduce an additional disulfide bond for stabilization. We observed high levels of neutralization resistance among Envs from 34 bNAb donors, of which 17.6% had elongated V1 regions with extra Cys. We show that extra V1 Cys moderately increase neutralization resistance in an Env from a V2- Apex bNAb-inducer. Modulation of the accessibility of bNAb epitopes on this Env by extra V1 Cys enhanced epitope shielding of several regions, but increased V2 exposure. This suggests that escape from autologous neutralizing activity drove insertion of the extra V1 Cys, creating a modified antigen that may have favored V2 bNAb induction in this donor. Overall, we identify a rare motif of twin Cys in V1 that confers increased neutralization resistance and Env stabilization, is associated with bNAb induction, and may hold potential for incorporation into future HIV bNAb immunogens. ]]> Hesselman, M. C. Zeeb, M. Rusert, P. Pasin, C. Mamrosh, J. Kariuki, S. Sickmann, M. Kaufmann, M. M. Schmidt, D. Friedrich, N. Metzner, K. J. Rindler, A. Kuster, H. Adams, C. Thebus, R. Huber, M. Yerly, S. Leuzinger, K. Perreau, M. Koller, R. Dollenmaier, G. Frigerio, S. Westfall, D. H. Deng, W. DeCamp, A. C. Juraska, M. Edupuganti, S. Mgodi, N. Murrell, H. Garrett, N. Wagh, K. Mullins, J. I. Williamson, C. Moore, P. L. Günthard, H. F. Kouyos, R. D. Trkola, A. 2024-09-10 doi:10.1101/2024.09.05.611179 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ Merkel cell carcinoma-derived macrophage migration inhibitory factor (MIF) may promote persistence of Chronic Lymphocytic Leukemia ]]> https://biorxiv.org/content/10.1101/2024.09.09.611517v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@188968forg.highwire.dtl.DTLVardef@54c084org.highwire.dtl.DTLVardef@2b3a14org.highwire.dtl.DTLVardef@1f20eba_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Alencar, G. F. Rodriguez, H. J. Pulliam, T. H. Remington, A. S. Gilmour, M. W. Alam, R. Jabbour, A. J. Mullen, L. J. DeBuysscher, B. L. Nghiem, P. Taylor, J. J. 2024-09-13 doi:10.1101/2024.09.09.611517 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ The Drosophila maternal-effect gene abnormal oocyte (ao) does not repress histone gene expression ]]> https://biorxiv.org/content/10.1101/2024.09.17.613536v1?rss=1 Takenaka, R. Simmerman, S. M. Schmidt, C. A. Albanese, E. H. Rieder, L. E. Malik, H. S. 2024-09-18 doi:10.1101/2024.09.17.613536 Cold Spring Harbor Laboratory Press 2024-09-18 <![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[ Overcoming immune evasion from post-translational modification of a mutant KRAS epitope to achieve TCR-engineered T cell-mediated antitumor activity ]]> https://biorxiv.org/content/10.1101/2024.09.18.612965v1?rss=1 Lee, J. W. Chen, E. Y. Hu, T. Perret, R. Chaffee, M. E. Martinov, T. Mureli, S. McCurdy, C. L. Jones, L. A. Gafken, P. R. Chanana, P. Su, Y. Chapuis, A. G. Bradley, P. Schmitt, T. M. Greenberg, P. D. 2024-09-22 doi:10.1101/2024.09.18.612965 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ MAX inactivation deregulates the MYC network and induces neuroendocrine neoplasia in multiple tissues ]]> https://biorxiv.org/content/10.1101/2024.09.21.614255v1?rss=1 Freie, B. Ibrahim, A. H. Carroll, P. A. Bronson, R. T. Augert, A. MacPherson, D. Eisenman, R. N. 2024-09-24 doi:10.1101/2024.09.21.614255 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2024.09.24.612755v1?rss=1 Wellington, R. Cheng, X. Campbell, C. A. Trapnell, C. Espin-Palazon, R. Hadland, B. Doulatov, S. 2024-09-24 doi:10.1101/2024.09.24.612755 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213 ]]> https://biorxiv.org/content/10.1101/2024.09.24.614677v1?rss=1 Crespillo-Casado, A. Pothukuchi, P. Naydenova, K. Yip, M. C. J. Young, J. M. Boulanger, J. Dharamdasani, V. Harper, C. Hammoudi, P.-M. Otten, E. G. Boyle, K. B. Gogoi, M. Malik, H. S. Randow, F. 2024-09-26 doi:10.1101/2024.09.24.614677 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma ]]> https://biorxiv.org/content/10.1101/2024.09.25.615007v1?rss=1 Kader, T. Lin, J.-R. Hug, C. Coy, S. Chen, Y.-A. de Bruijn, I. Shih, N. Jung, E. Pelletier, R. J. Leon, M. L. Mingo, G. Omran, D. K. Lee, J. S. Yapp, C. Satravada, B. A. Kundra, R. Xu, Y. Chan, S. Tefft, J. Muhlich, J. L. Kim, S. Gysler, S. M. Agudo, J. Heath, J. R. Schultz, N. Drescher, C. Sorger, P. K. Drapkin, R. Santagata, S. 2024-09-27 doi:10.1101/2024.09.25.615007 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Endocrine persistence in ER+ breast cancer is accompanied by metabolic vulnerability in oxidative phosphorylation ]]> https://biorxiv.org/content/10.1101/2024.09.26.615177v1?rss=1 Tau, S. Chamberlin, M. D. Yang, H. Marotti, J. D. Roberts, A. M. Carmichael, M. M. Cressey, L. Dragnev, C. P. Demidenko, E. Hampsch, R. A. Soucy, S. M. Kolling, F. W. Samkoe, K. S. Alvarez, J. V. Kettenbach, A. Miller, T. W. 2024-09-27 doi:10.1101/2024.09.26.615177 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Damage-induced IL-18 stimulates thymic NK Cells limiting endogenous tissue regeneration ]]> https://biorxiv.org/content/10.1101/2024.09.27.615528v1?rss=1 Granadier, D. Cooper, K. Kousa, A. Acenas, D. Lemarquis, A. Hernandez, V. Warren, M. Iovino, L. deRoos, P. Lederer, E. Shannon-Sevillano, S. Kinsella, S. Evandy, C. van den Brink, M. Dudakov, J. 2024-09-30 doi:10.1101/2024.09.27.615528 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ Conserved chromatin regulators control the transcriptional immune response to intracellular pathogens in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2024.10.03.616425v1?rss=1 Tecle, E. Li, S. Blanchard, M. J. Bui, T. Chhan, C. B. Underwood, R. S. Bakowski, M. A. Troemel, E. R. Lazetic, V. 2024-10-04 doi:10.1101/2024.10.03.616425 Cold Spring Harbor Laboratory Press 2024-10-04 <![CDATA[ Heterozygous and generalist MxA super-restrictors overcome breadth-specificity tradeoffs in antiviral restriction ]]> https://biorxiv.org/content/10.1101/2024.10.10.617484v1?rss=1 Geiger, R. A. Khera, D. Tenthorey, J. Kochs, G. Graf, L. Emerman, M. Malik, H. S. 2024-10-10 doi:10.1101/2024.10.10.617484 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ Computational Microbiome Pharmacology Analysis Elucidates the Anti-Cancer Potential of Vaginal Microbes and Metabolites ]]> https://biorxiv.org/content/10.1101/2024.10.10.616351v1?rss=1 Lawore, D. C. Jena, S. Berard, A. R. Birse, K. Lamont, A. Mackelprang, R. D. Noel-Romas, L. Perner, M. Hou, X. Irungu, E. Mugo, N. Knodel, S. Muwonge, T. R. Katabira, E. Hughes, S. M. Levy, C. Calienes, F. L. Baeten, J. M. Celum, C. Hladik, F. Lingappa, J. R. Burgener, A. D. Green, L. N. Brubaker, D. K. 2024-10-11 doi:10.1101/2024.10.10.616351 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ SUMOylation differentially regulates SMCHD1 complex formation and function in a genomic context-specific manner ]]> https://biorxiv.org/content/10.1101/2024.10.13.618066v1?rss=1 Goossens, R. Tihaya, M. S. Willemsen, I. M. Straasheijm, K. R. van der Vliet, P. J. Gonzalez-Prieto, R. Vertegaal, A. C. O. Tapscott, S. J. Balog, J. van der Maarel, S. M. 2024-10-13 doi:10.1101/2024.10.13.618066 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Sugar-rich foods exacerbate antibiotic-induced microbiome injury ]]> https://biorxiv.org/content/10.1101/2024.10.14.617881v1?rss=1 Dai, A. Adintori, P. A. Funnell, T. Jogia, W. P. Fei, T. Waters, N. R. Rangesa, M. Ballweg, A. Gipson, B. Raj, S. Hayase, E. Markey, K. A. Burgos da Silva, M. Miltiadous, O. Brambilla, C. Z. Buchan, M. L. Peets, T. Gradissimo, A. Smith, N. Katsamakis, Z. Warren, A. Amoretti, L. A. Duan, C. Zhang, C. Matheis, F. Sullivan, A. P. Slingerland, J. B. Clurman, A. Brereton, D. G. Giardina, P. A. Gomes, A. L. C. Johnson, A. J. Knights, D. Jenq, R. R. Perales, M.-A. Giralt, S. A. Schluter, J. van den Brink, M. R. M. Peled, J. 2024-10-17 doi:10.1101/2024.10.14.617881 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ A Comprehensive Engineering Strategy Improves Potency and Manufacturability of a Near Pan-neutralizing Antibody Against HIV ]]> https://biorxiv.org/content/10.1101/2024.10.14.618178v1?rss=1 Sajadi, M. Abbasi, A. Rikhtegaran Tehrani, Z. Siska, C. Clark, R. Chi, W. Seaman, M. S. Mielke, D. Wagh, K. Liu, Q. Jumpa, T. Ketchem, R. R. Nguyen, D. N. Tolbert, W. D. Pierce, B. G. Atkinson, B. Deming, D. Sprague, M. Asakawa, A. Ferrer, D. Dunn, Y. Calvillo, S. Yin, R. Guest, J. D. Korber, B. Mayer, B. T. Sato, A. H. Ouyang, X. Foulke, S. Habibzadeh, P. Karimi, M. Aslanabadi, A. Hojabri, M. Saadat, S. Zareidoodeji, R. Kedzior, M. Pozharski, E. Heredia, A. Montefiori, D. Ferrari, G. Pazgier, M. Lewis, G. K. Jardine, J. G. Lusso, P. Devico, A. 2024-10-17 doi:10.1101/2024.10.14.618178 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ Statistical analysis of repertoire data demonstrates the influence of microhomology in V(D)J recombination ]]> https://biorxiv.org/content/10.1101/2024.10.16.618753v1?rss=1 Russell, M. L. Trofimov, A. Bradley, P. Matsen, F. A. 2024-10-18 doi:10.1101/2024.10.16.618753 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Protein catabolites as blood-based biomarkers of aging physiology: Findings from the Dog Aging Project ]]> https://biorxiv.org/content/10.1101/2024.10.17.618956v1?rss=1 Harrison, B. R. Partida-Aguilar, M. Marye, A. Djukovic, D. Kauffman, M. Dunbar, M. D. Mariner, B. L. McCoy, B. M. Algavi, Y. M. Muller, E. Baum, S. Bamberger, T. Raftery, D. Creevy, K. E. Dog Aging Project Consortium, Avery, A. Borenstein, E. Snyder-Mackler, N. Promislow, D. E. 2024-10-21 doi:10.1101/2024.10.17.618956 Cold Spring Harbor Laboratory Press 2024-10-21 <![CDATA[ Transcriptomic landscape identifies two unrecognized ependymoma subtypes and novel pathways in medulloblastoma ]]> https://biorxiv.org/content/10.1101/2024.10.21.619495v1?rss=1 Arora, S. Holland, E. Vardharajan, S. Taylor, M. Sahm, F. Mack, S. C. Sievers, P. Korshunov, A. Nuechterlein, N. Jensen, M. Glatzer, G. 2024-10-22 doi:10.1101/2024.10.21.619495 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Long-term hybridization in a karst window reveals the genetic basis of eye loss in cavefish ]]> https://biorxiv.org/content/10.1101/2024.10.25.620266v1?rss=1 Kellermeyer, R. Seidel, C. Redwine, W. B. Moran, R. L. Bertho, S. Ornelas-Garcia, C. P. Alegre, D. Weaver, K. J. Unruh, J. Troutwine, B. Wang, Y. Collins, E. Rutkowski, J. McGaugh, S. E. Espinasa, L. Rohner, N. 2024-10-28 doi:10.1101/2024.10.25.620266 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Antigen-Specific T Cell Receptor Discovery for Treating Progressive Multifocal Leukoencephalopathy ]]> https://biorxiv.org/content/10.1101/2024.11.04.621904v1?rss=1 Gupta, S. Martinov, T. Thelen, A. Sunahara, M. Mureli, S. Vazquez, A. Gerdts, J. Dandekar, R. Cortese, I. Fouassier, C. Schanzer, E. Urnov, F. D. Marson, A. Shy, B. R. Greenberg, P. D. Wilson, M. R. 2024-11-04 doi:10.1101/2024.11.04.621904 Cold Spring Harbor Laboratory Press 2024-11-04 <![CDATA[ MOSAIC: A Pipeline for MicrobiOme Studies Analytical Integration and Correction ]]> https://biorxiv.org/content/10.1101/2024.11.07.622561v1?rss=1 Fu, C. Lu, J. Zhao, N. Ling, W. 2024-11-11 doi:10.1101/2024.11.07.622561 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images ]]> https://biorxiv.org/content/10.1101/2024.11.10.622859v1?rss=1 Wu, E. Bieniosek, M. Wu, Z. Thakkar, N. Charville, G. W. Makky, A. Schürch, C. Huyghe, J. R. Peters, U. Li, C. I. Li, L. Giba, H. Behera, V. Raman, A. Trevino, A. E. Mayer, A. T. Zou, J. 2024-11-11 doi:10.1101/2024.11.10.622859 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Mutant RIT1 cooperates with YAP to drive an EMT-like lung cancer state ]]> https://biorxiv.org/content/10.1101/2024.11.11.623044v1?rss=1 Rominger, M. C. Gupta, S. Moorthi, S. McSharry, M. Kamlapurkar, S. O'Brien, S. Waldum, A. Lo, A. Duke, F. Lowe, A. Cromwell, E. Glabman, R. Koehne, A. Berger, A. 2024-11-12 doi:10.1101/2024.11.11.623044 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Semaphorin 4A maintains functional diversity of the hematopoietic stem cell pool ]]> https://biorxiv.org/content/10.1101/2024.11.12.622506v1?rss=1 Toghani, D. Gupte, S. Zeng, S. Mahammadov, E. Crosse, E. Seyedhassantehrani, N. Burns, C. Gravano, D. Radtke, S. Kiem, H.-P. Rodriguez, S. Carlesso, N. Pradeep, A. Georgiades, A. Lucas, F. Wilson, N. K. Kinston, S. J. Gottgens, B. Zong, L. Beerman, I. Park, B. Janssens, D. Jones, D. Toghani, A. Nerlov, C. Pietras, E. C. Mesnieres, M. Maes, C. Kumanogoh, A. Worzfeld, T. Cheong, J.-G. Josefowicz, S. Z. Kharchenko, P. Scadden, D. Scialdone, A. Spencer, J. A. Silberstein, L. 2024-11-13 doi:10.1101/2024.11.12.622506 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ Exploration of the Roles of HLAs When Predicting Infection Status by T Cell Receptors ]]> https://biorxiv.org/content/10.1101/2024.11.18.624054v1?rss=1 Ding, F. Liu, S. Sun, W. 2024-11-21 doi:10.1101/2024.11.18.624054 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ PFAS Compounds PFOA and Gen X are Teratogenic to Sea Urchin Embryos ]]> https://biorxiv.org/content/10.1101/2024.11.21.624751v1?rss=1 Lion, A. T. Bodine, S. M. McCutcheon, K. R. Ghogale, M. Chandragiri, S. Abayawardena, D. Shrestha, B. D. Descoteaux, A. E. Alvarez, K. Balkman, J. A. Cocke, B. Wikramanayake, A. Schlezinger, J. Wong, J. Y. Prakash, V. N. Bradham, C. 2024-11-21 doi:10.1101/2024.11.21.624751 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Improving antibody-mediated protection against HSV infection by eliminating interactions with the viral Fc receptor gE/gI ]]> https://biorxiv.org/content/10.1101/2024.11.20.624598v1?rss=1 Slein, M. D. Backes, I. M. Kelkar, N. S. Garland, C. R. Khanwalkar, U. S. Sholukh, A. M. Johnston, C. M. Leib, D. A. Ackerman, M. E. 2024-11-22 doi:10.1101/2024.11.20.624598 Cold Spring Harbor Laboratory Press 2024-11-22 <![CDATA[ Improved Deep Learning Prediction of TCR-HLA Association ]]> https://biorxiv.org/content/10.1101/2024.11.22.624910v1?rss=1 Li, F. Liu, S. Sun, W. 2024-11-25 doi:10.1101/2024.11.22.624910 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Association between COVID-19 Disease Severity and T Cell Receptor Repertoire ]]> https://biorxiv.org/content/10.1101/2024.11.26.625333v1?rss=1 Chen, X. Su, Y. Dai, C. Goldman, J. D. Heath, J. R. Liu, S. Sun, W. 2024-11-26 doi:10.1101/2024.11.26.625333 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Thrifty wide-context models of B cell receptor somatic hypermutation ]]> https://biorxiv.org/content/10.1101/2024.11.26.625407v1?rss=1 Sung, K. Johnson, M. M. Dumm, W. Simon, N. Haddox, H. Fukuyama, J. Matsen, F. A. 2024-12-01 doi:10.1101/2024.11.26.625407 Cold Spring Harbor Laboratory Press 2024-12-01 <![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[ E-box independent chromatin recruitment turns MYOD into a transcriptional repressor ]]> https://biorxiv.org/content/10.1101/2024.12.05.627024v1?rss=1 Nicoletti, C. Massenet, J. Pintado-Urbanc, A. P. Connor, L. J. Nicolau, M. Sundar, S. Xu, M. Schmitt, A. Zhang, W. Fang, Z. Chan, T. C. I. Tapscott, S. J. Cheung, T. H. Simon, M. D. Caputo, L. Puri, P. L. 2024-12-05 doi:10.1101/2024.12.05.627024 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X ]]> https://biorxiv.org/content/10.1101/2024.12.08.627395v1?rss=1 Baele, G. Carvalho, L. M. Brusselmans, M. Dudas, G. Ji, X. McCrone, J. T. Lemey, P. Suchard, M. A. Rambaut, A. 2024-12-10 doi:10.1101/2024.12.08.627395 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Single-cell multi-omic analysis of fibrolamellar carcinoma reveals rewired cell-to-cell communication patterns and unique vulnerabilities ]]> https://biorxiv.org/content/10.1101/2024.12.11.627911v1?rss=1 Farghli, A. R. Chan, M. Sherman, M. S. Dickerson, L. K. Shui, B. Nukaya, M. Stephanou, A. Ma, R. K. Pepe-Mooney, B. J. Smith, C. J. Long, D. Munn, P. R. McNairn, A. Grenier, J. K. Karski, M. Ronnekleiv-Kelly, S. M. Pillarisetty, V. G. Goessling, W. Gujral, T. Vakili, K. Sethupathy, P. 2024-12-12 doi:10.1101/2024.12.11.627911 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Sir2 is required for the quiescence-specific condensed three-dimensional chromatin structure of rDNA ]]> https://biorxiv.org/content/10.1101/2024.12.12.628092v1?rss=1 Cucinotta, C. Dell, R. Alavattam, K. Tsukiyama, T. 2024-12-12 doi:10.1101/2024.12.12.628092 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ DUX4-induced HSATII RNA accumulation drives protein aggregation impacting RNA processing pathways. ]]> https://biorxiv.org/content/10.1101/2024.12.17.628988v1?rss=1 Arends, T. Bennett, S. R. Tapscott, S. J. 2024-12-18 doi:10.1101/2024.12.17.628988 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Deciphering single-cell heterogeneity and cellular ecosystem dynamics during prostate cancer progression ]]> https://biorxiv.org/content/10.1101/2024.12.18.629070v1?rss=1 Zhao, F. Zeng, J. Chen, C. Zhao, X. Zhang, T. Thomas, G. V. Sears, R. C. Alumkal, J. J. Moran, A. E. Mills, G. B. Nelson, P. S. Xia, Z. 2024-12-20 doi:10.1101/2024.12.18.629070 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ The first comorbidity networks in companion dogs in the Dog Aging Project ]]> https://biorxiv.org/content/10.1101/2024.12.18.629088v1?rss=1 Fang, A. Kumar, L. Creevy, K. E. Promislow, D. E. L. Ma, J. 2024-12-20 doi:10.1101/2024.12.18.629088 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Detecting Clinically Relevant Topological Structures in Multiplexed Spatial Proteomics Imaging Using TopKAT ]]> https://biorxiv.org/content/10.1101/2024.12.18.628976v1?rss=1 Samorodnitsky, S. Campbell, K. M. Little, A. Ling, W. Zhao, N. Chen, Y.-C. Wu, M. 2024-12-21 doi:10.1101/2024.12.18.628976 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics ]]> https://biorxiv.org/content/10.1101/2024.12.22.629997v1?rss=1 600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties. ]]> Park, J. Prokopchuk, G. Popchock, A. R. Hao, J. Liao, T.-W. Yan, S. Hedman, D. J. Larson, J. D. Walther, B. Becker, N. A. Basu, A. Maher, L. J. Wheeler, R. J. Asbury, C. L. Biggins, S. Lukes, J. Ha, T. 2024-12-23 doi:10.1101/2024.12.22.629997 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Histone H4 limits transcription of the histone locus in Drosophila ]]> https://biorxiv.org/content/10.1101/2024.12.23.630206v1?rss=1 Ahmad, K. Wooten, M. Takushi, B. N. Vidaurre, V. Chen, X. Henikoff, S. 2024-12-24 doi:10.1101/2024.12.23.630206 Cold Spring Harbor Laboratory Press 2024-12-24 <![CDATA[ Inflammatory Monocytes Increase Prior to Detectable HIV-1 Rebound Viremia ]]> https://biorxiv.org/content/10.1101/2024.12.24.630257v1?rss=1 Farrell-Sherman, A. de la Force, N. Prator, C. Valieris, R. Azam, W. Silva, I. Deeks, S. Thanh, C. Bosch, R. Henrich, T. J. Cohn, L. B. 2024-12-25 doi:10.1101/2024.12.24.630257 Cold Spring Harbor Laboratory Press 2024-12-25 <![CDATA[ The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure ]]> https://biorxiv.org/content/10.1101/2025.01.07.631013v1?rss=1 Haddox, H. K. Angehrn, G. Sesta, L. Jennings-Shaffer, C. Temple, S. D. Galloway, J. G. DeWitt, W. S. Bloom, J. D. Matsen, F. A. Neher, R. A. 2025-01-08 doi:10.1101/2025.01.07.631013 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization. ]]> https://biorxiv.org/content/10.1101/2025.01.07.631807v1?rss=1 Tang, G. Carr, A. V. Perez, C. Ramos Sarmiento, K. Levy, L. Lampe, J. Diener, C. Gibbons, S. M. 2025-01-08 doi:10.1101/2025.01.07.631807 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ A fast numerical integration scheme for clonal expansion processes on graphs ]]> https://biorxiv.org/content/10.1101/2025.01.13.632690v1?rss=1 Paterson, C. G. B. Gao, M. Hellier, J. Luebeck, G. Wedge, D. C. Bozic, I. 2025-01-15 doi:10.1101/2025.01.13.632690 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Combinatorial phenotypic landscape enables bacterial resistance to phage infection ]]> https://biorxiv.org/content/10.1101/2025.01.13.632860v1?rss=1 Gupta, A. Morella, N. Sutormin, D. Li, N. Gaisser, K. Robertson, A. Ispolatov, Y. Seelig, G. Dey, N. Kuchina, A. 2025-01-15 doi:10.1101/2025.01.13.632860 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Pretransplant targeting of TNFRSF25 and CD25 stimulates recipient Tregs in target tissues ameliorating GVHD post-HSCT ]]> https://biorxiv.org/content/10.1101/2025.01.16.633453v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@10ef7aforg.highwire.dtl.DTLVardef@1a70f03org.highwire.dtl.DTLVardef@caa144org.highwire.dtl.DTLVardef@121b657_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> McManus, D. Copsel, S. Pfieffer, B. J. Wolf, D. Barreras, H. Ma, S. Khodor, A. Komai, S. Burgos da Silva, M. Hazime, H. Gallardo, M. van den Brink, M. R. Abreu, M. T. Hill, G. R. Perez, V. L. Levy, R. B. 2025-01-21 doi:10.1101/2025.01.16.633453 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies ]]> https://biorxiv.org/content/10.1101/2025.01.22.634135v1?rss=1 Haddox, H. K. Abdel Aziz, O. Galloway, J. G. Kent, J. Cooper, C. R. Bloom, J. D. Matsen, F. A. 2025-01-24 doi:10.1101/2025.01.22.634135 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Centromeres in the thermotolerant yeast K. marxianusmediate attachment to a single microtubule ]]> https://biorxiv.org/content/10.1101/2025.01.24.634737v1?rss=1 Barrero, D. J. Hedouin, S. Mao, Y. Asbury, C. L. Stergachis, A. O'Toole, E. Biggins, S. 2025-01-27 doi:10.1101/2025.01.24.634737 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Protein sequence editing defines distinct and overlapping functions of SKN-1A/Nrf1 and SKN-1C/Nrf2. ]]> https://biorxiv.org/content/10.1101/2025.01.29.635299v1?rss=1 Jochim, B. E. Topalidou, I. Lehrbach, N. J. 2025-01-29 doi:10.1101/2025.01.29.635299 Cold Spring Harbor Laboratory Press 2025-01-29 <![CDATA[ Modeling of hepatitis B virus infection spread in primary human hepatocytes ]]> https://biorxiv.org/content/10.1101/2025.02.05.636596v1?rss=1 Shi, Z. Tsuge, M. Collier, N. Takeuchi, Y. Uchida, T. Rutter, C. Teraoka, Y. Uprichard, S. L. Ishida, Y. Tateno, C. Ozik, J. Dahari, H. Chayama, K. 2025-02-07 doi:10.1101/2025.02.05.636596 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Systems Pharmacology Screening Reveals Mertk and other Targetable Kinases in Supratentorial Ependymomas ]]> https://biorxiv.org/content/10.1101/2025.02.06.636949v1?rss=1 Chan, M. Zhu, S. Russell, Z. Arora, S. Arakaki, A. Kumasaka, D. Szulzewsky, F. Michealraj, A. Holland, E. Gujral, T. 2025-02-08 doi:10.1101/2025.02.06.636949 Cold Spring Harbor Laboratory Press 2025-02-08 <![CDATA[ Precise engineering of chimeric antigen receptor expression levels defines T cell identity and function ]]> https://biorxiv.org/content/10.1101/2025.02.10.637482v1?rss=1 Ramos, A. S. Simon, S. Siller-Farfan, J. Rajan, A. Revale, S. Zanchini di Castiglionchio, E. Pelea, O. Fulga, T. A. Riddell, S. Dushek, O. Michaels, Y. S. Sauka-Spengler, T. 2025-02-11 doi:10.1101/2025.02.10.637482 Cold Spring Harbor Laboratory Press 2025-02-11 <![CDATA[ NF-κB dependent gene expression and plasma IL-1β, TNFα and GCSF drive transcriptomic diversity and CD4:CD8 ratio in people with HIV on ART. ]]> https://biorxiv.org/content/10.1101/2025.02.14.638232v1?rss=1 Wang, Y. Gornalusse, G. Siegel, D. Barbehenn, A. Hoh, R. Martin, J. Hecht, F. Pilcher, C. Semenova, L. Murdoch, D. M. Margolis, D. M. Levy, C. N. Jerome, K. R. Rudin, C. D. Hladik, F. Deeks, S. G. Lee, S. A. Browne, E. P. 2025-02-14 doi:10.1101/2025.02.14.638232 Cold Spring Harbor Laboratory Press 2025-02-14 <![CDATA[ Defined cellular reprogramming of androgen receptor-active prostate cancer to neuroendocrine prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.02.12.637904v1?rss=1 Li, S. Song, K. Sun, H. Tao, Y. Huang, A. Bhatia, V. Hanratty, B. Patel, R. A. Long, H. W. Morrissey, C. Haffner, M. C. Nelson, P. S. Graeber, T. G. Lee, J. K. 2025-02-17 doi:10.1101/2025.02.12.637904 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Defined media reveals the essential role of lipid scavenging to support cancer cell proliferation ]]> https://biorxiv.org/content/10.1101/2025.02.12.637975v1?rss=1 Newsom, O. J. Sullivan, L. B. 2025-02-17 doi:10.1101/2025.02.12.637975 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Accuracy and Scalability of Machine Learning Methods for Genotype-Phenotype Association Data ]]> https://biorxiv.org/content/10.1101/2025.02.13.638022v1?rss=1 Collienne, K. Zhang, L. Gavryushkin, A. 2025-02-17 doi:10.1101/2025.02.13.638022 Cold Spring Harbor Laboratory Press 2025-02-17 <![CDATA[ Succinate Dehydrogenase loss causes cascading metabolic effects that impair pyrimidine biosynthesis ]]> https://biorxiv.org/content/10.1101/2025.02.18.638948v1?rss=1 Hart, M. L. Davidsen, K. Danquah, S. Zheng, E. Sokolov, D. Sullivan, L. B. 2025-02-19 doi:10.1101/2025.02.18.638948 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ A Syntenic Pangenome for Gardnerella Reveals Taxonomic Boundaries and Stratification of Metabolic and Virulence Potential across Species ]]> https://biorxiv.org/content/10.1101/2025.02.19.636902v1?rss=1 Bouzek, H. Srinivasan, S. Jones, D. S. McMahon, E. F. Strenk, S. M. Fiedler, T. L. Fredricks, D. N. Johnston, C. D. 2025-02-19 doi:10.1101/2025.02.19.636902 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ Multi-scale machine learning model predicts muscle and functional disease progression in FSHD ]]> https://biorxiv.org/content/10.1101/2025.02.19.639046v1?rss=1 Blemker, S. S. Riem, L. DuCharme, O. Pinette, M. Costanzo, K. E. Weatherley, E. Statland, J. Tapscott, S. J. Wang, L. H. Shaw, D. W. W. The Move+ Investigator Team, Song, X. Leung, D. Friedman, S. 2025-02-20 doi:10.1101/2025.02.19.639046 Cold Spring Harbor Laboratory Press 2025-02-20 <![CDATA[ A discrete region of the D4Z4 is sufficient to initiate epigenetic silencing ]]> https://biorxiv.org/content/10.1101/2025.02.19.639175v1?rss=1 Paatela, E. M. St. Amant, F. G. Hamm, D. C. Bennett, S. R. Gujral, T. S. van der Maarel, S. M. Tapscott, S. J. 2025-02-23 doi:10.1101/2025.02.19.639175 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Pooled CAR-T screening in nonhuman primates identifies designs with enhanced proliferation, trafficking, and persistence ]]> https://biorxiv.org/content/10.1101/2025.03.05.640197v1?rss=1 Maynard, L. H. Cavanaugh, E. J. Zhu, H. Starke, C. E. Doherty, S. M. Einhaus, T. Perez, A. Stensland, L. Hoffman, M. Nelson, V. Herrin, S. Littlewood, C. Camou, K. Wilson, E. Wessel, C. Jerome, K. R. Kiem, H.-P. Peterson, C. W. 2025-03-10 doi:10.1101/2025.03.05.640197 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ Total whole-arm chromosome losses predict malignancy in human cancer ]]> https://biorxiv.org/content/10.1101/2025.03.09.642243v1?rss=1 Zheng, Y. Ahmad, K. Henikoff, S. 2025-03-11 doi:10.1101/2025.03.09.642243 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ Delta-catenin is required for cell proliferation in virus positive Merkel cell carcinoma cell lines but not in human fibroblasts ]]> https://biorxiv.org/content/10.1101/2025.03.12.642815v1?rss=1 Landazuri Vinueza, J. Salisbury, N. J. H. Dye, K. Roman, A. Galloway, D. A. 2025-03-14 doi:10.1101/2025.03.12.642815 Cold Spring Harbor Laboratory Press 2025-03-14 <![CDATA[ Capsule-Based Single-Cell Genome Sequencing ]]> https://biorxiv.org/content/10.1101/2025.03.14.643253v1?rss=1 Mullaney, D. B. Sgrizzi, S. R. Mai, D. Campbell, I. Huang, Y. Sinkunas, A. Kerr, D. L. Browning, V. E. Eisenach, H. E. Sims, J. N. Nichols, E. K. Lapointe, C. P. Amimura, Y. Harris, K. Zilionis, R. Srivatsan, S. R. 2025-03-17 doi:10.1101/2025.03.14.643253 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Collagen-binding IL-12 expressing STEAP1 CAR-T cells reduce toxicity and eradicate mouse prostate cancer in combination with checkpoint inhibitors ]]> https://biorxiv.org/content/10.1101/2025.03.19.644145v1?rss=1 Sasaki, K. Bhatia, V. Asano, Y. Bakhtiari, J. Kaur, P. Wang, C. Matsuo, T. Nikolaidi, M. Chiu, P.-C. Dubois, O. Chong, T. Javier, G. Priceman, S. J. Chapuis, A. G. Lee, J. K. Ishihara, J. 2025-03-19 doi:10.1101/2025.03.19.644145 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB ]]> https://biorxiv.org/content/10.1101/2025.03.26.645558v1?rss=1 Readshaw, J. Doyle, L. Puiu, M. Kelly, A. Nelson, A. Kaiser, A. McGuire, S. Peralata-Acosta, J. Smith, D. Stoddard, B. L. Kaiser, B. K. Blower, T. R. 2025-03-26 doi:10.1101/2025.03.26.645558 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ TP53 Inactivation Confers Resistance to the Menin Inhibitor Revumenib in Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2025.03.24.644993v1?rss=1 D'Souza, J. Leung, C. J. Ballapuram, A. C. Lin, A. S. Batingana, A. R. Lamble, A. J. Ries, R. E. Morales, C. E. Cottonham, C. Gona, P. Fan, L. Ma, X. Shannon, K. Meshinchi, S. Braun, B. S. Huang, B. J. 2025-03-27 doi:10.1101/2025.03.24.644993 Cold Spring Harbor Laboratory Press 2025-03-27 <![CDATA[ The bone marrow niche and hematopoietic system are distinctly remodeled by CD45-targeted astatine-211 radioimmunotherapy ]]> https://biorxiv.org/content/10.1101/2025.04.04.645037v1?rss=1 Hagen, M. W. Setiawan, N. J. Dexter, S. L. Woodruff, K. A. Gaerlan, F. K. Orozco, J. J. Termini, C. M. 2025-04-05 doi:10.1101/2025.04.04.645037 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Implementation of an adaptive-optics assisted isoSTED nanoscope ]]> https://biorxiv.org/content/10.1101/2025.04.02.645322v1?rss=1 Li, Y. Lee, D. Allgeyer, E. S. Schroeder, L. K. Tu, S. Bewersdorf, J. Hao, X. 2025-04-06 doi:10.1101/2025.04.02.645322 Cold Spring Harbor Laboratory Press 2025-04-06 <![CDATA[ HPV16 neutralizing monoclonal antibodies show evidence for common developmental pathways and public epitopes ]]> https://biorxiv.org/content/10.1101/2025.03.31.646278v1?rss=1 Carter, J. J. Hurlburt, N. K. Scherer, E. M. Singh, S. Rodarte, J. V. Smith, R. A. Lewis, P. Kinzelman, R. J. Kieltyka, J. Caban, M. E. Wipf, G. C. Pancera, M. Galloway, D. A. 2025-04-07 doi:10.1101/2025.03.31.646278 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Targeting the ITGA3B1 Complex with A Novel Antibody-Drug Conjugate for Metastatic Bladder Cancer ]]> https://biorxiv.org/content/10.1101/2025.04.06.647354v1?rss=1 Jung, H. Lee, J. Kim, E. G. Ahn, J. Haffner, M. Nelson, P. S. Kim, K. Lee, J. K. Yi, E. C. Kim, K. M. 2025-04-07 doi:10.1101/2025.04.06.647354 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Mucosal tissue NK cells tune their function between optimal anti-pathogen activity and tissue protection ]]> https://biorxiv.org/content/10.1101/2025.04.04.647286v1?rss=1 Vick, S. C. Domenjo-Vila, E. Frutoso, M. Glabman, R. A. Warrier, L. S. Hughes, S. M. Kirby, A. C. Fialkow, M. F. Hladik, F. Prlic, M. Lund, J. M. 2025-04-09 doi:10.1101/2025.04.04.647286 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ C-terminal fusion partner activity contributes to the oncogenic functions of YAP1::TFE3 ]]> https://biorxiv.org/content/10.1101/2025.04.04.647316v1?rss=1 Cimino, P. J. Keiser, D. J. Parrish, A. G. Holland, E. C. Szulzewsky, F. 2025-04-09 doi:10.1101/2025.04.04.647316 Cold Spring Harbor Laboratory Press 2025-04-09 <![CDATA[ Designed NGF mimetics with reduced nociceptive signatures in neurons ]]> https://biorxiv.org/content/10.1101/2025.04.14.648806v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@c48066org.highwire.dtl.DTLVardef@c9c5a7org.highwire.dtl.DTLVardef@cf8ebdorg.highwire.dtl.DTLVardef@a4345a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Schlichthaerle, T. Yang, A. Detraux, D. Johnson, D. E. Peach, C. J. Edman, N. I. Sniezek, C. Williams, C. A. Arora, S. Katiyar, N. Chen, I. Etemadi, A. Favor, A. Lee, D. Kubo, C. Coventry, B. Huang, B. Gerben, S. Ennist, N. M. Milles, L. Sankaran, B. Kang, A. Nguyen, H. Bera, A. K. Negahdari, B. Hamazaki, N. Schweppe, D. K. Stewart, L. Young, J. E. Bunnett, N. W. Ruohola-Baker, H. Mathieu, J. Pattwell, S. Garcia, K. C. Baker, D. 2025-04-14 doi:10.1101/2025.04.14.648806 Cold Spring Harbor Laboratory Press 2025-04-14 <![CDATA[ Modulating AP-1 enables CAR-T cells to establish an intratumoral PD-1+Tcf1+ stem-like reservoir and overcomes resistance to PD-1 axis blockade ]]> https://biorxiv.org/content/10.1101/2025.04.10.648245v1?rss=1 Snyder, A. J. Shasha, C. Ho, T. Garrison, S. Wilhelm, A. R. Kluesner, M. G. Ortiz, S. Nutt, W. S. Bingham, E. Bhise, S. S. Fan, E. Zepeda, V. Sarvothama, M. Wang, X. Potluri, S. Long, A. Elz, A. Furlan, S. Newell, E. W. Srivastava, S. 2025-04-15 doi:10.1101/2025.04.10.648245 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ Muc6-expressing gastric isthmus progenitors contribute to regeneration and metaplasia supported by myeloid-mesenchymal interactions ]]> https://biorxiv.org/content/10.1101/2025.04.15.648856v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@10fc2eaorg.highwire.dtl.DTLVardef@1c5b82corg.highwire.dtl.DTLVardef@1be747dorg.highwire.dtl.DTLVardef@d1d722_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Arai, J. Iwata, Y. Tsubosaka, A. Kinoshita, H. Shinohara, S. Abe, S. Shiokawa, T. Oura, K. Suzuki, N. Hata, M. Kurokawa, K. Oya, Y. Tsuboi, M. Ihara, S. Murakami, K. Shiomi, C. Uekura, C. Fujiwara, H. Tateno, H. Mizuno, S. Takahashi, S. Kanai, A. Suzuki, Y. Ushiku, T. Ijichi, H. Hirata, Y. Kasuga, M. O'Brien, V. P. Salama, N. Kakiuchi, M. Ishikawa, S. WANG, T. C. Hayakawa, Y. Fujishiro, M. 2025-04-16 doi:10.1101/2025.04.15.648856 Cold Spring Harbor Laboratory Press 2025-04-16 <![CDATA[ Measurement and prediction of unmixing-dependent spreading in spectral flow cytometry panels ]]> https://biorxiv.org/content/10.1101/2025.04.17.649396v1?rss=1 Mage, P. L. Konecny, A. J. Mair, F. 2025-04-23 doi:10.1101/2025.04.17.649396 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Whole-Proteome Screening and Multi-Modal Profiling of Antigen-Specific CD4+ T Cells at Single-Cell Resolution ]]> https://biorxiv.org/content/10.1101/2025.04.21.649828v1?rss=1 Zhang, R. Qi, J. McKasson, M. Choi, J. Gutierrez, V. Brennan, C. Hong, S. Chour, W. Ng, R. H. Xie, J. Yuan, D. Webster, A. Sidhu, S. K. Anderson, A. Chen, D. Edmark, R. Murray, K. M. Li, S. McDonald, C. Rowen, L. Wang, S. Rasheed, Y. Su, Y. Wagner, J. R. Chen, J. Narwaly, K. Fu, J. Duven, A. Forman, S. J. Song, M. Priceman, S. Brown, C. E. Ribas, A. Wong, D. Paulson, K. G. Drescher, C. W. Puig-Saus, C. Goldman, J. D. Trimble, C. L. Heath, J. R. 2025-04-23 doi:10.1101/2025.04.21.649828 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ Interprotomer Crosstalk in Mosaic Viral Glycoprotein Trimers Provides Insight into Polyvalent Immunogen Co-assembly ]]> https://biorxiv.org/content/10.1101/2025.04.22.649918v1?rss=1 Chen, C. Lovendahl, K. Overbaugh, J. Lee, K. K. 2025-04-23 doi:10.1101/2025.04.22.649918 Cold Spring Harbor Laboratory Press 2025-04-23 <![CDATA[ In vivo production of an anti-HIV antibody from primate hematopoietic cells by non-viral knock-in ]]> https://biorxiv.org/content/10.1101/2025.05.02.651933v1?rss=1 Castelli, J. M. Poljakov, K. Youngseo, J. Cassidy, M. E. Gray, M. D. Sanchez Gaytan, J. N. Enstrom, M. R. Linton, J. D. Rongvaux, A. Taylor, J. J. Adair, J. E. 2025-05-08 doi:10.1101/2025.05.02.651933 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ Bone marrow lymphocyte dynamics during chemotherapy in pediatric acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2025.05.04.652110v1?rss=1 Koedijk, J. B. Barneh, F. Meesters-Ensing, J. I. van Tuil, M. Sonneveld, E. Lambo, S. Perzolli, A. Schweighart, E. K. Ferrao Blanco, M. N. van der Meulen, M. Deli, A. Haasjes, E. Bang Christensen, K. de Groot-Kruseman, H. A. Meshinchi, S. Hasle, H. Belderbos, M. Luesink, M. Goemans, B. F. Nierkens, S. Hehir-Kwa, J. Zwaan, C. M. Heidenreich, O. 2025-05-09 doi:10.1101/2025.05.04.652110 Cold Spring Harbor Laboratory Press 2025-05-09 <![CDATA[ Intracellular and extracellular dynamics of herpes simplex virus 1 DNA and infectious particles in epithelial and neuronal cells ]]> https://biorxiv.org/content/10.1101/2025.05.13.653775v1?rss=1 Esmaeili, S. Swan, D. A. Jerome, K. R. Schiffer, J. T. Walter, M. 2025-05-13 doi:10.1101/2025.05.13.653775 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Spatial control of secretory vesicle targeting by the Ync13-Rga7-Rng10 complex during cytokinesis ]]> https://biorxiv.org/content/10.1101/2025.05.13.653810v1?rss=1 Zhang, S. Singh, D. Zhu, Y.-H. Zhang, K. J. Melero, A. Martin, S. G. Wu, J.-Q. 2025-05-14 doi:10.1101/2025.05.13.653810 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Efficacy of DNA Methyltransferase Inhibitor Immune Priming Therapy in Combination with PD-1 Inhibitors to Treat High-Risk Pediatric Brain Tumors ]]> https://biorxiv.org/content/10.1101/2025.05.14.654106v1?rss=1 Mishra, D. K. Morris, S. M. Popovski, D. Girard, E. J. Bondoc, A. Kumar, S. S. Andrade, A. F. Zhu, X. Yao, F. Brusniak, M.-Y. Umaru, B. Crotty, E. E. Brasel, K. Pakiam, F. Russo, C. Zeinieh, M. Biery, M. C. Coxon, M. Conti, H. Clarke, M. Lu, M. Rutka, J. Llivichuzhca-Loja, D. Konnikova, L. Fouladi, M. Jabado, N. Huang, A. Olson, J. M. Drissi, R. 2025-05-18 doi:10.1101/2025.05.14.654106 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ Determining preclinical safety of Aclarubicin in pediatric malignancies ]]> https://biorxiv.org/content/10.1101/2025.05.20.654130v1?rss=1 Tu, D. S. Olson, A. K. Waggie, K. S. Garcia, N. M. Hoglund, V. J. Walter, S. Rosinski, J. R. Sadeeshkumar, H. Patel, R. Sayar, E. Haffner, M. Maves, L. Neefjes, J. Sarthy, J. F. Lawlor, E. R. Ganapathi, S. S. 2025-05-24 doi:10.1101/2025.05.20.654130 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Identification and Characterization of PLUTO-201, a Novel Long Non-Coding RNA Associated with Poor Outcomes in Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2025.05.21.655369v1?rss=1 Li, H. Younger, N. S. Malik, B. Shin, H. J. Zhang, C. Niknafs, Y. Zhao, S. Wilder-Romans, K. Pitchiaya, S. Han, S. Barnard, T. J. Lloyd, P. Zhang, M. Chesner, L. N. Calvert, M. Egusa, E. A. Zhu, J. Chou, J. Das, R. Kothari, V. Shenoy, T. Diolaiti, M. E. Malik, R. Prensner, J. R. Burlingame, A. L. Ashworth, A. Chinnaiyan, A. M. Feng, F. Li, H. 2025-05-24 doi:10.1101/2025.05.21.655369 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Differential HIV-1 Proviral Defects in Children vs. Adults on Antiretroviral Therapy ]]> https://biorxiv.org/content/10.1101/2025.05.23.655786v1?rss=1 80% contained two or more defects, most commonly stop codons and/or gag start mutations. Significantly fewer defects in the major splice donor site (MSD) and packaging signal were found in the children on short or long-term ART compared to the adults, and tat was more frequently defective in children. These results suggest that different selection pressures shape the proviral landscape in children compared to adults and reveal potentially different genetic regions to target for measuring the intact HIV reservoir and for achieving HIV remission in children. ]]> Hasson, J. M. Katusiime, M. G. Capoferri, A. A. Bale, M. J. Luke, B. T. Shao, W. Cotton, M. F. Van Zyl, G. Patro, S. C. Kearney, M. F. 2025-05-27 doi:10.1101/2025.05.23.655786 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Graphical and Interactive Spatial Proteomics Image Analysis Workflow ]]> https://biorxiv.org/content/10.1101/2025.05.23.655879v1?rss=1 Singh, P. Wright, J. H. Smythe, K. S. Fukuda, B. N. Hung, L.-H. Yeung, C. C. Yeung, K. Y. 2025-05-27 doi:10.1101/2025.05.23.655879 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Genome-wide CRISPR screens identify PTGES3 as a novel AR modulator ]]> https://biorxiv.org/content/10.1101/2025.05.29.656244v1?rss=1 Li, H. Melnyk, J. E. Fu, B. X. H. Shrestha, R. Zhang, M. Sjostrom, M. Feng, S. Anderson, J. Han, W. Chesner, L. N. Shin, H. J. Farsh, T. Suarez, H. J. Nath, S. Chou, J. Das, R. Egusa, E. A. Calvert, M. Kishishita, A. Barpanda, A. Zhu, J. Maheshwari, A. Chen, W. S. Alshalalfa, M. Winters, A. Hua, J. T. Liu, T. Davicioni, E. Wiita, A. P. Stohr, B. A. Siddiqui, J. Huang, B. Small, E. J. Shokat, K. M. Nelson, P. Quigley, D. A. Wasmuth, E. V. Gilbert, L. A. Feng, F. Y. 2025-05-30 doi:10.1101/2025.05.29.656244 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Engineering Sustained-Release Broadly Neutralizing Antibody Formulations ]]> https://biorxiv.org/content/10.1101/2025.05.27.656504v1?rss=1 Jons, C. K. Kasse, C. M. Mayer, B. T. Hyrien, O. Sen, S. Meany, E. L. d'Aquino, A. I. Ganesh, P. Eckman, N. Dong, C. Yan, J. Nguyen, L. T. Doulames, V. M. Song, Y. E. Saouaf, O. M. Williams, C. M. Williams, S. C. Paredes, J. Raghavan, R. Palomares, M. Alpert, M. Yates, N. L. Tomaras, G. Seaman, M. S. Farzan, M. Appel, E. A. 2025-06-01 doi:10.1101/2025.05.27.656504 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ OGDHL regulates nucleotide metabolism, tumor growth, and neuroendocrine marker expression in prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.05.28.656673v1?rss=1 Bernard, M. Ruiz, A. Diaz, J. Nunley, N. Dove, R. Heering, K. Bopardikar, S. Gallardo, A. Hashimoto, T. Agrawal, R. Smith, C. Wilde, B. Matulionis, N. Richards, H. Sharifi, M. Lang, J. Zhao, S. Haffner, M. Boutros, P. C. Christofk, H. Goldstein, A. S. 2025-06-01 doi:10.1101/2025.05.28.656673 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Chorionic Gonadotropin Beta 7 is a marker of immune evasion in cancer ]]> https://biorxiv.org/content/10.1101/2025.05.28.656535v1?rss=1 McKellar, S. A. Pineda, J. M. B. Lattupally, R. Codd, A. S. Newell, E. Lu, S. X. Bradley, R. K. 2025-06-02 doi:10.1101/2025.05.28.656535 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ Active learnings impact on student course performance in STEM varies by type and intensity ]]> https://biorxiv.org/content/10.1101/2025.06.01.657285v1?rss=1 Xu, S. Velasco, V. Hill, M. J. Tran, E. Agrawal, S. Arroyo, E. N. Behling, S. Chambwe, N. Cintron, D. L. Cooper, J. D. Dunster, G. Grummer, J. A. Hennessey, K. Hsiao, J. Iranon, N. Jones, L. Jordt, H. Keller, M. Lacey, M. E. Littlefield, C. E. Lowe, A. Newman, S. Okolo, V. Olroyd, S. Peecook, B. R. Pickett, S. B. Slager, D. L. Caviedes-Solis, I. W. Stanchak, K. E. Sundaravaradan, V. Valdebenito, C. Williams, C. R. Zinsli, K. A. Freeman, S. Theobald, E. J. 2025-06-02 doi:10.1101/2025.06.01.657285 Cold Spring Harbor Laboratory Press 2025-06-02 <![CDATA[ Diverse modes of T cell receptor sequence convergence define unique functional and cellular phenotypes ]]> https://biorxiv.org/content/10.1101/2025.05.31.657155v1?rss=1 Schattgen, S. Vegesana, K. Hazelton, W. D. Minervina, A. Valkiers, S. Slowikowski, K. Smith, N. P. MGH COVID-19 Team, Villani, A.-C. Thomas, P. G. Bradley, P. 2025-06-03 doi:10.1101/2025.05.31.657155 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Lack of synergy between AR targeted therapies and PARP inhibitors in homologous recombination-proficient prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.06.02.657429v1?rss=1 Traphagen, N. A. Wheeler, E. Li, R. Lu, F. Ahmed, B. Tewari, A. K. Balk, S. P. Nelson, P. S. Corey, E. Long, H. D'Andrea, A. D. Qiu, X. Brown, M. 2025-06-03 doi:10.1101/2025.06.02.657429 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Replaying germinal center evolution on a quantified affinity landscape ]]> https://biorxiv.org/content/10.1101/2025.06.02.656870v1?rss=1 DeWitt, W. S. S. Vora, A. A. Araki, T. Galloway, J. G. Alkutkar, T. Bortolatto, J. Castro, T. B. Dumm, W. Jennings-Schaffer, C. Jia, T. Mesin, L. Ozorowski, G. Pae, J. Ralph, D. K. Bloom, J. D. Nourmohammad, A. Song, Y. S. Ward, A. Starr, T. N. Matsen, F. A. Victora, G. D. 2025-06-05 doi:10.1101/2025.06.02.656870 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Comparing phenotypic manifolds with Kompot: Detecting differential abundance and gene expression at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2025.06.03.657769v1?rss=1 Otto, D. J. Arriaga-Gomez, E. Thieme, E. Yang, R. Lee, S. C. Setty, M. 2025-06-07 doi:10.1101/2025.06.03.657769 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Abrogating TGFβ signaling in TCR-engineered T cells and enhancing antigen processing by tumor cells promotes sustained therapeutic activity in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2025.06.04.657887v1?rss=1 Tsai, A. K. Rollins, M. R. Ellefson, M. A. Schmiechen, Z. C. Burrack, A. L. Hulbert, A. Qian, G. Zhang, H. Provenzano, P. Cruz-Hinojoza, E. Butler, J. Z. Smith, O. C. G. O'Flanagan, S. D. Krause, J. Hickok, G. H. Masopust, D. Hingorani, S. R. Greenberg, P. D. Stromnes, I. M. 2025-06-08 doi:10.1101/2025.06.04.657887 Cold Spring Harbor Laboratory Press 2025-06-08 <![CDATA[ DEVELOPMENT OF A POTENT MONOCLONAL ANTIBODY FOR TREATMENT OF HUMAN METAPNEUMOVIRUS INFECTIONS ]]> https://biorxiv.org/content/10.1101/2025.06.09.657676v1?rss=1 Harris, E. D. McGovern, M. Pernikoff, S. Ikeda, R. Kipnis, L. Hannon, W. Sobolik, E. B. Gray, M. Greninger, A. L. He, S. Chin, C.-N. Fu, T.-M. Pancera, M. Boonyaratanakornkit, J. 2025-06-11 doi:10.1101/2025.06.09.657676 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ Biological causes and impacts of rugged tree landscapes in phylodynamic inference ]]> https://biorxiv.org/content/10.1101/2025.06.10.657742v1?rss=1 Gao, J. Brusselmans, M. Carvalho, L. M. Suchard, M. A. Baele, G. Matsen, F. A. 2025-06-12 doi:10.1101/2025.06.10.657742 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Seasonal influenza viruses show distinct adaptive dynamics during growth in chicken eggs ]]> https://biorxiv.org/content/10.1101/2025.06.12.659400v1?rss=1 Kistler, K. Bedford, T. 2025-06-17 doi:10.1101/2025.06.12.659400 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Nucleotide context models outperform protein language models for predicting antibody affinity maturation ]]> https://biorxiv.org/content/10.1101/2025.06.16.659977v1?rss=1 Johnson, M. M. Sung, K. Haddox, H. K. Vora, A. A. Araki, T. Victora, G. D. Song, Y. S. Fukuyama, J. Matsen, F. A. 2025-06-18 doi:10.1101/2025.06.16.659977 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ Learning Human T Cell Behaviors through Generative AI Embeddings of T Cell Receptors ]]> https://biorxiv.org/content/10.1101/2025.06.16.660016v1?rss=1 1M sequences) TCR atlases across human development and diseases into actionable insights. Tarpon creates: 1) bespoke sampling functions generating realistic Ag-specific TCRs, 2) embeddings revealing CD4+ and CD8+ single-positive TCR repertoires as distinct with divergent physiochemical properties, and 3) cross-dataset mappings of T cell states that validate fetal CD4+ versus CD8+ TCR differences in adults and find fetal type I innate T cells to map to MAIT and KIR+ adult CD8+ T cells which we verify via whole transcriptome analysis. Tarpon is a resource as a reference of TCRs across human physiological states and as a computational framework to create interpretable TCR embeddings, via physicochemical associations, that have broad implications for the field. ]]> Chen, D. G. Su, Y. Heath, J. R. 2025-06-22 doi:10.1101/2025.06.16.660016 Cold Spring Harbor Laboratory Press 2025-06-22 <![CDATA[ Development of PROTACs for targeted degradation of oncogenic TRK fusions ]]> https://biorxiv.org/content/10.1101/2025.06.18.660465v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@6c78f7org.highwire.dtl.DTLVardef@179dcdeorg.highwire.dtl.DTLVardef@1939988org.highwire.dtl.DTLVardef@144c718_HPS_FORMAT_FIGEXP M_FIG C_FIG JWJ-01-378 recruits cereblon (CRBN) to induce potent and selective degradation of oncogenic TRK fusions, leading to a collapse in downstream signaling and loss of cancer cell viability. Graphical abstract was created using Biorender.com. ]]> Kumar, S. Jiang, J. Donald-Paladino, M. S. Chen, J. Gutierrez, A. Federation, A. J. Szulzewsky, F. Holland, E. C. Ferguson, F. M. Nabet, B. 2025-06-24 doi:10.1101/2025.06.18.660465 Cold Spring Harbor Laboratory Press 2025-06-24 <![CDATA[ Obesity promotes conserved inflammatory and metabolic transcriptional programs in mouse and human colon tumors ]]> https://biorxiv.org/content/10.1101/2025.06.19.660576v1?rss=1 Glenny, E. M. Lin, T. Bandera, V. M. Mirminachi, B. Khumukcham, S. S. Gigic, B. Warby, C. A. Aksonova, O. Coleman, M. F. Carpanese, A. Busch, C. Himbert, C. Ose, J. Nix, D. A. Boucher, K. Schirmacher, P. Strehli, I. Hardikar, S. Cohan, J. N. Jedrzkiewicz, J. Brobeil, A. Schneider, M. A. Kahlert, C. Siegel, E. M. Byrd, D. A. Toriola, A. T. Shibata, D. Li, C. I. Figueiredo, J. C. Tan, A. C. Roper, J. Ulrich, C. M. Hursting, S. D. 2025-06-25 doi:10.1101/2025.06.19.660576 Cold Spring Harbor Laboratory Press 2025-06-25 <![CDATA[ Herpes simplex virus 1 strain 17+ with R2 mutation in UL37 has residual retrograde transport ]]> https://biorxiv.org/content/10.1101/2025.06.25.661543v1?rss=1 Walter, M. Haick, A. K. Massa, P. A. Klouser, L. M. Stensland, L. Santo, T. K. Xie, H. Jerome, K. R. 2025-06-26 doi:10.1101/2025.06.25.661543 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Direct observation of interdependent and hierarchical kinetochore assembly on individual centromeres ]]> https://biorxiv.org/content/10.1101/2025.06.25.661565v1?rss=1 View larger version (14K): org.highwire.dtl.DTLVardef@bcc252org.highwire.dtl.DTLVardef@79b6b2org.highwire.dtl.DTLVardef@c974e0org.highwire.dtl.DTLVardef@184689_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hu, C. Popchock, A. R. Latino, A. A. Asbury, C. L. Biggins, S. 2025-06-26 doi:10.1101/2025.06.25.661565 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Genital herpes shedding episodes associate with alterations in the spatial organization and activation of mucosal immune cells ]]> https://biorxiv.org/content/10.1101/2025.06.24.661157v1?rss=1 MacLean, F. Zemek, R. M. Tsegaye, A. T. Graham, J. B. Swarts, J. L. Vick, S. C. Potchen, N. B. Talavera, I. C. Warrier, L. Dubrulle, J. Schroeder, L. K. Elz, A. Sowerby, D. Saito, A. Thomas, K. K. Mack, M. Schiffer, J. McClelland, R. S. Jerome, K. R. Chohan, B. H. Ngure, K. Mugo, N. R. Newell, E. W. Lingappa, J. R. Lund, J. M. 2025-06-27 doi:10.1101/2025.06.24.661157 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ Differential Assembly of Mouse and Human Tumor Microenvironments ]]> https://biorxiv.org/content/10.1101/2025.07.01.661217v1?rss=1 View larger version (71K): org.highwire.dtl.DTLVardef@22bcf7org.highwire.dtl.DTLVardef@a410b7org.highwire.dtl.DTLVardef@1455eb5org.highwire.dtl.DTLVardef@14cc6f5_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Courau, T. Jaszczak, R. G. Samad, B. Flynn, E. Reeder, G. C. Chew, N. W. Tsui, J. Ray, A. Wismer, H. Bunis, D. Lupin-Jimenez, L. Gavil, N. V. Masopust, D. Graham, J. P. Skelly, D. A. Vesco, X. Liu, E. T. Fragiadakis, G. K. Combes, A. J. Krummel, M. F. 2025-07-05 doi:10.1101/2025.07.01.661217 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ PDL1 CHECKPOINT BLOCKADE SYNERGIZES WITH NILOTINIB BUT NOT DASATINIB TO PREVENT LEUKEMIA RELAPSE ]]> https://biorxiv.org/content/10.1101/2025.07.02.662848v1?rss=1 Morgan, E. C. Venkatesh, H. Centenos, E. G. Heltemes-Harris, L. M. Hubbard, G. Maiers, T. L. Dileepan, T. Tracy, S. I. Farrar, M. A. 2025-07-05 doi:10.1101/2025.07.02.662848 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials ]]> https://biorxiv.org/content/10.1101/2025.07.01.659979v1?rss=1 3-fold different) was observed in 40% of multilineage infections, with a trend toward greater intra-host neutralization differences with increasing VRC01 dose (Jonckheere-Terpstra test, p=0.072). In six VRC01 treated participants who acquired both sensitive (IC80<1{micro}g/ml) and resistant viruses (IC80>3{micro}g/ml), the sensitive lineages declined over time. Recombination was pervasive, observed in 63% of multilineage infections at the time of HIV diagnosis. In one treated participant infected with VRC01 discordant lineages, recombinant viruses preferentially inherited the resistance mutation (binomial p=0.004). In conclusion, our in-depth analysis of breakthrough viruses in the AMP trials revealed a high frequency of multilineage infections, including infections with viruses with different VRC01 sensitivities. This analysis also highlights the role of recombination in shaping intra-host viral evolution and facilitating escape from VRC01. SignificanceThis work advances our understanding of the diversity of initial viral infection and evolution and in vivo activity of broadly neutralizing antibodies (bNAbs). Deep sequencing revealed [~]38% of HIV acquisitions with multiple transmitted founder lineages, higher than previous studies. These occurrences were similar in the placebo and VRC01 groups. Viral recombination among post-acquisition variants was common under antibody selection and appeared to favor resistant sequences in the treatment group. These data suggest as with single antiviral therapy, passive and active immunization of bNAbs should be directed at multiple antigen targets of HIV-1. ]]> Williamson, C. Moodley, C. Magaret, C. A. Giorgi, E. E. Rolland, M. Westfall, D. H. Yssel, A. Deng, W. Rossenkhan, R. Mkhize, N. N. Chen, L. H. Zhao, H. Bhattacharya, T. Pankow, A. Murrell, B. York, T. Gwashu-Nyangiwe, A. Ndabambi, N. Thebus, R. Cohen, P. Lambson, B. E. Kaldine, H. Bhebhe, S. Juraska, M. Bai, H. deCamp, A. C. Miner, M. Ludwig, J. Molitor, C. Beaume, N. Matten, D. Huang, Y. Zhang, L. Reeves, D. B. Mayer, B. Karuna, S. T. Hural, J. A. Morris, L. Montefiori, D. Bumgarner, R. E. Moore, P. Edlefsen, P. T. Edupuganti, S. Mgodi, N. McElrath 2025-07-10 doi:10.1101/2025.07.01.659979 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ A Singular Base Editing Platform for Polyfunctional Multiplex Engineering of Immune Cells ]]> https://biorxiv.org/content/10.1101/2025.07.11.664404v1?rss=1 95% quadplex gene KO (B2M/CD3{varepsilon}/PDCD1/CISH), we achieve single-step generation of highly functional off-the-shelf CAR T cell products with enhanced function. Importantly, we found no detectable translocations or significant off-target edits and demonstrated efficacy against multiple cancer lines, and a suppressive 3D spheroid culture model. This efficient engineering process of Iterative Nicking for Synchronous Engineered Reprogramming of T cells (INSERT) establishes a safe, simplified platform for advanced therapeutic CAR T engineering. ]]> Skeate, J. G. Slipek, N. J. Lahr, W. S. Roy, S. Wick, B. J. Stelljes, E. M. Gilkey, A. K. Thenge, P. P. Diers, M. D. Kar, B. Krueger, J. B. Niemeyer, E. M. Lonetree, C.-l. Kluesner, M. G. Bell, J. B. Clement, K. Provenzano, P. Moriarity, B. S. Webber, B. R. 2025-07-16 doi:10.1101/2025.07.11.664404 Cold Spring Harbor Laboratory Press 2025-07-16 <![CDATA[ Humanized mice enable in vivo evaluation of engineered plasma cell biology and therapeutic function ]]> https://biorxiv.org/content/10.1101/2025.07.14.664835v1?rss=1 Hill, T. F. Helmers, A. E. Cheng, R. Y. Singh, S. Homad, L. J. Narvekar, P. Asher, G. D. Camp, N. D. Suchland, E. R. Ott, A. R. Hale, M. Thouvenel, C. D. Stoffers, C. Lachkar, S. McGuire, A. Rawlings, D. J. James, R. G. 2025-07-18 doi:10.1101/2025.07.14.664835 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ TCR2HLA: calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes ]]> https://biorxiv.org/content/10.1101/2025.07.18.665436v1?rss=1 0.9) across common HLA-A (9/12), B (9/12), C (6/13), DRB1 (11/11) alleles and prevalent DPA1/DPB1 (6/10), DQA1/DQB1 (8/17) heterodimers. We also introduced a high-sensitivity calibration to support predictions in samples with as few as 5,000 unique clonotypes. Calibrated predictions with confidence filtering improved reliability. Beyond genotype imputation, TCR2HLA enables the discovery of novel HLA- and exposure-associated TCRs, as shown by the identification of SARS-CoV-2 related TCRs in a large COVID-19 dataset lacking HLA data. TCR2HLA provides a scalable framework for bridging the gap between TCRseq data and HLA genotype for biomarker discovery. ]]> Mayer-Blackwell, K. Minervina, A. Pogorelyy, M. Rawat, P. Shapiro, M. R. Peters, L. D. Ford, E. S. Posgai, A. L. Vengesana, K. Minot, S. Koelle, D. M. Greiff, V. Bradley, P. Brusko, T. M. Thomas, P. G. Fiore-Gartland, A. 2025-07-23 doi:10.1101/2025.07.18.665436 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ B cells specific for polyomavirus-derived oncoprotein are predictive of Merkel cell carcinoma progression ]]> https://biorxiv.org/content/10.1101/2025.07.22.666002v1?rss=1 Rodriguez Chevez, H. J. Remington, A. J. Gray, M. M. Alam, R. Gilmour, M. W. Morningstar, C. Alencar, G. F. Pulliam, T. McClure, E. Singh, N. Urselli, F. Poljakov, K. Smythe, K. S. Kulikauskas, R. M. Robinson, K. L. Moshiri, A. S. Yeung, C. C. Lin, M. Shimp, K. R. Schwartz, A. Macy, A. M. Tooley, M. R. Baker, M. L. Carter, J. J. Hopwo, K. Singhi, N. Bakhtiari, J. Ruterbusch, M. Shasha, C. G. Iuliano, M. Mullen, L. J. Debuysscher, B. L. Veatch, J. R. Koelle, D. M. Galloway, D. A. Nghiem, P. Taylor, J. J. 2025-07-24 doi:10.1101/2025.07.22.666002 Cold Spring Harbor Laboratory Press 2025-07-24 <![CDATA[ Q4ddPCR (May the Fourth Be Precise): A Flexible, 4-Target Assay for High-Resolution HIV Reservoir Profiling ]]> https://biorxiv.org/content/10.1101/2025.07.28.667202v1?rss=1 Scheck, R. Melzer, M. Gladkov, G. Ward, A. R. Reeves, D. B. Perkins, N. Huynh, T. T. McMahon, D. K. Bosch, R. J. Macatangay, B. J. Cyktor, J. C. Eron, J. J. Mellors, J. W. Gandhi, R. T. Buchauer, L. Jones, R. B. Gaebler, C. 2025-07-31 doi:10.1101/2025.07.28.667202 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Cellular heterogeneity and therapeutic response profiling of human IDH+ glioma stem cell cultures ]]> https://biorxiv.org/content/10.1101/2025.07.29.667532v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@82aceeorg.highwire.dtl.DTLVardef@1277c18org.highwire.dtl.DTLVardef@144188eorg.highwire.dtl.DTLVardef@1a84bb3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chambwe, N. Kennedy, S. R. Kohrn, B. F. Lazarchuk, P. Leutert, M. Qin, G. Tercan, B. Sanchez-Contreras, M. Tang, W. Graber, J. PADDISON, P. Villen, J. Shmulevich, I. Monnat, R. J. 2025-08-01 doi:10.1101/2025.07.29.667532 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Stabilization of H5 highly pathogenic avian influenza hemagglutinin improves vaccine-elicited neutralizing antibody responses ]]> https://biorxiv.org/content/10.1101/2025.07.30.667762v1?rss=1 Dosey, A. Dadonaite, B. Gillespie, R. A. Leaf, E. M. Vukovich, M. J. McGowan, J. Grey, E. Muramatsu, H. Jun, R. H. Pardi, N. Kanekiyo, M. Bloom, J. D. King, N. P. 2025-08-02 doi:10.1101/2025.07.30.667762 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ A bone marrow stromal secretome screen identifies semaphorin 3A as a regulator of hematopoiesis ]]> https://biorxiv.org/content/10.1101/2025.08.07.669162v1?rss=1 Borger, D. K. Mitchell, S. P. Nakahara, F. Colombo, D. F. Torres, L. S. Garforth, S. J. Sidoli, S. Krijgsveld, J. Silberstein, L. Frenette, P. S. Gritsman, K. 2025-08-07 doi:10.1101/2025.08.07.669162 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Genetic and Epigenetic Reprogramming of Transposable Elements Drives ecDNA-Mediated Metastatic Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2025.08.08.668693v1?rss=1 Mout, L. Moreno-Rodriguez, T. Grillo, G. Nand, A. Keshavarzian, T. Bahl, S. Kang, K. Bootsma, M. Minnee, E. Zhou, S. Burns, K. H. Corey, E. Nelson, P. Dehm, S. M. Zhao, S. G. Zwart, W. Feng, F. Quigley, D. Lupien, M. 2025-08-12 doi:10.1101/2025.08.08.668693 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ RHOV is a Detachment-Responsive Rho GTPase Necessary for Ovarian Cancer Peritoneal Metastasis ]]> https://biorxiv.org/content/10.1101/2025.08.12.669944v1?rss=1 Elhaw, A. T. Tang, P. W. Cheng, Y.-Y. Kamlapurkar, S. Javed, Z. Al-Saad, S. White, S. R. Abdelnaby, A. E. Khan, H. Choi, A. S. Cole, A. R. Kim, Y.-S. Atiya, H. I. Trebak, M. Zervantonakis, I. K. Buckanovich, R. J. Aird, K. M. Coffman, L. G. Mythreye, K. Hempel, N. 2025-08-13 doi:10.1101/2025.08.12.669944 Cold Spring Harbor Laboratory Press 2025-08-13 <![CDATA[ Pro-inflammatory role of granzyme K producing bystander CD8+ T cells in acute myeloid leukemia ]]> https://biorxiv.org/content/10.1101/2025.08.12.669682v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@1fc9798org.highwire.dtl.DTLVardef@4491b1org.highwire.dtl.DTLVardef@1b8feadorg.highwire.dtl.DTLVardef@58515d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Aziez, L. Deredec, N. Boussaid, I. Shasha, C. G. Vazquez, R. Friedrich, C. Alik, A. Manasse, K. Fremont-Debaene, Z. Barthelemy, A. Catelain, C. Rameau, P. Vignon, M. Decroocq, J. Kosmider, O. Selimoglu-Buet, D. Newell, E. W. Solary, E. Delhommeau, F. Herault, O. TARTOUR, E. Birsen, R. Bouscary, D. Fontenay, M. Chapuis, N. Simoni, Y. 2025-08-15 doi:10.1101/2025.08.12.669682 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ MDS-associated SF3B1 mutations promote aberrant fate choice of hematopoietic stem cell via mis-splicing of mediator kinase module component CDK8 ]]> https://biorxiv.org/content/10.1101/2025.08.14.670174v1?rss=1 Bonner, E. A. Hsueh, T.-Y. Song, A. Arriaga-Gomez, E. A. Venkataraman, R. Sinha, S. Nguyen, E. Ferrell, P. B. Welner, R. S. Lu, R. Stirewalt, D. L. Doulatov, S. Lee, S. C. 2025-08-19 doi:10.1101/2025.08.14.670174 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants ]]> https://biorxiv.org/content/10.1101/2025.08.18.671001v1?rss=1 Dadonaite, B. Harari, S. Larsen, B. B. Kampman, L. Harteloo, A. Elias-Warren, A. Chu, H. Y. Bloom, J. D. 2025-08-19 doi:10.1101/2025.08.18.671001 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ An emergent disease-associated motor neuron state precedes cell death in a mouse model of ALS ]]> https://biorxiv.org/content/10.1101/2025.08.21.671404v1?rss=1 Gautier, O. Blum, J. A. Nguyen, T. P. Klemm, S. Yamakawa, M. Sinnott-Armstrong, N. Zeng, Y. Davis, C.-H. O. Bombosch, J. Nakayama, L. Guttenplan, K. A. Chen, D. Kathira, A. Zhao, L. Y. Rexach, J. E. Greenleaf, W. E. Gitler, A. D. 2025-08-25 doi:10.1101/2025.08.21.671404 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ An Efficient Lasso Framework for Admixture-Aware Polygenic Scores ]]> https://biorxiv.org/content/10.1101/2025.08.26.671106v1?rss=1 Ockerman, F. P. Chen, B. D. Sun, Q. Kharitonova, E. V. Chen, C. Zhou, L. Y. Loos, R. J. Kooperberg, C. Peters, U. Haessler, J. Reiner, A. P. Jung, S. Y. Manson, J. E. Nassir, R. North, K. E. Buyske, S. Haiman, C. A. Conti, D. V. Wilkens, L. R. Lange, E. M. Cox, N. J. Cao, H. Raffield, L. M. Li, Y. Tao, R. 2025-08-27 doi:10.1101/2025.08.26.671106 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Determinants of Natural Killer Cell-Mediated Antibody Dependent Cellular Cytotoxicity in SARS-CoV-2 Antibodies ]]> https://biorxiv.org/content/10.1101/2025.08.28.672949v1?rss=1 Depierreux, D. M. Ruiz, F. M. Lilly, M. Guenthoer, J. Chohan, V. Overbaugh, J. 2025-08-29 doi:10.1101/2025.08.28.672949 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Distinct modes of evolution drive HIV escape from two broadly neutralizing antibodies. ]]> https://biorxiv.org/content/10.1101/2025.08.29.673185v1?rss=1 Romero, E. V. Clyde, A. E. Giorgi, E. E. Westfall, D. H. Azam, W. Taylor, M. L. Caskey, M. Feder, A. F. Cohn, L. B. 2025-08-30 doi:10.1101/2025.08.29.673185 Cold Spring Harbor Laboratory Press 2025-08-30 <![CDATA[ Rapid protamine evolution suppresses meiotic drive in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.09.03.674087v1?rss=1 Chang, C.-H. de la Cruz, A. F. Natividad, I. M. Noyola, A. Malik, H. S. 2025-09-05 doi:10.1101/2025.09.03.674087 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Transcriptional Rewiring of BET Inhibitor Treated Ewing Sarcoma Cells Augments their Dependency on Focal Adhesion Kinase ]]> https://biorxiv.org/content/10.1101/2025.09.02.673849v1?rss=1 Ganapathi, S. S. Wrenn, E. D. Garcia, N. M. Katiyar, N. Walter, S. I. Miyaki, A. Valenti, J. Kang, Y. Chan, M. Gujral, T. S. Lawlor, E. R. 2025-09-06 doi:10.1101/2025.09.02.673849 Cold Spring Harbor Laboratory Press 2025-09-06 <![CDATA[ MondoA mediates transcriptional coordination between the MYC network and the integrated stress response in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2025.09.03.674106v1?rss=1 Ramsey, E. L. Dobersch, S. Freie, B. Hong, N. H. Wu, X. Kugel, S. Eisenman, R. N. Carroll, P. A. 2025-09-08 doi:10.1101/2025.09.03.674106 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ BIOPRINTING OF MICRODISSECTED TUMOR CUBOIDS IN HYDROGELS ]]> https://biorxiv.org/content/10.1101/2025.09.05.671932v1?rss=1 View larger version (30K): org.highwire.dtl.DTLVardef@e1d020org.highwire.dtl.DTLVardef@1271797org.highwire.dtl.DTLVardef@17de734org.highwire.dtl.DTLVardef@d62b97_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Bansal, A. M. Horowitz, L. Yeung, M. Gujral, T. M. Folch, A. 2025-09-10 doi:10.1101/2025.09.05.671932 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ Identification of a broad and potent V3 glycan site bNAb targeting anN332gp120 glycan-independent epitope ]]> https://biorxiv.org/content/10.1101/2025.09.05.674437v1?rss=1 Gieselmann, L. DeLaitsch, A. T. Rohde, M. Radford, C. Worczinski, J. Momot, A. Ahmadov, E. Burger, J. A. Havenar-Daughton, C. Deshpande, S. Giovannoni, F. Corti, D. Kreer, C. Ercanoglu, M. S. Schommers, P. Georgiev, I. West, A. P. Knuefer, J. Stumpf, R. Kroidl, A. Geldmacher, C. Maganga, L. William, W. Ntinginya, N. E. Hoelscher, M. Yang, Z. Wei, Q. Renfrow, M. Green, T. J. Novak, J. van Gils, M. Gristick, H. B. Gruell, H. Bloom, J. D. Seaman, M. S. Bjorkman, P. Klein, F. 2025-09-10 doi:10.1101/2025.09.05.674437 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ Genotoxic antibody-drug conjugates combined with Bcl-xL inhibitors enhance therapeutic efficacy in metastatic castration-resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.09.05.674562v1?rss=1 Semenova, G. Frank, S. Dumpit, R. Han, W. Coleman, I. Gulati, R. Morrissey, C. Haffner, M. Nelson, P. S. Lee, J. K. 2025-09-11 doi:10.1101/2025.09.05.674562 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Quantifying HLA transcripts by genotype in chimeric mixtures at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2025.09.12.675951v1?rss=1 Kanaan, S. B. Underwood, J. G. Green Gladden, R. Fan, E. Bhise, S. S. Thakar, M. S. Jaeger-Ruckstuhl, C. A. Stevens, J. Gray, A. N. Riddell, S. R. Bleakley, M. Meshinchi, S. Furlan, S. N. 2025-09-17 doi:10.1101/2025.09.12.675951 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Identification of protective human monoclonal antibodies using a K18 hACE2 transgenic mouse SARS-CoV-2 challenge model ]]> https://biorxiv.org/content/10.1101/2025.09.13.675985v1?rss=1 Borate, B. Pino, P. A. Hicks, A. Garcia, J. I. Garcia-Vilanova, A. Ye, C. Park, J.-G. Maingot, B. Rodriguez, O. Saveria, T. Holman, D. Schendel, S. L. Saphire, E. O. Martinez-Sobrido, L. Torrelles, J. B. Fiore-Gartland, A. 2025-09-19 doi:10.1101/2025.09.13.675985 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ A connexin 43 targeting peptide prevents blood vessel neointima formation ]]> https://biorxiv.org/content/10.1101/2025.09.22.677165v1?rss=1 Sedovy, M. W. Renton, M. C. Leng, X. Iqbal, F. Leaf, M. Roberts, K. Joshi, R. C. Malek, A. Dennison, C. Best, A. K. Baker, J. W. Joseph, M. Lampe, P. D. Isakson, B. E. Johnstone, S. R. 2025-09-24 doi:10.1101/2025.09.22.677165 Cold Spring Harbor Laboratory Press 2025-09-24 <![CDATA[ HRDPath: An Explainable Multi-Model Deep Learning Architecture for Predicting Homologous Recombination Deficiency from Histopathology Images ]]> https://biorxiv.org/content/10.1101/2025.09.24.678258v1?rss=1 Wu, C.-i. Banda, K. Arora, R. Soong, T. R. Radke, M. Dillon, M. Nik-Zainal, S. Swisher, E. Sailem, H. 2025-09-26 doi:10.1101/2025.09.24.678258 Cold Spring Harbor Laboratory Press 2025-09-26 <![CDATA[ Plasma nirmatrelvir and molnupiravir concentrations required for inhibition of SARS CoV-2 replication differ between rhesus macaques and humans ]]> https://biorxiv.org/content/10.1101/2025.09.25.678525v1?rss=1 Avila-Ponce de Leon, U. Esmaeili, S. Owens, K. Schiffer, J. T. 2025-10-01 doi:10.1101/2025.09.25.678525 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Clinical cure of chronic hepatitis B is dependent on activation and perpetuation of robust CD4+ T cell responses ]]> https://biorxiv.org/content/10.1101/2025.09.29.677401v1?rss=1 Jespersen, J. M. Avanesyan, L. Publicover, J. Carey, N. D. Patel, R. K. Edwards, A. W. Stenske, S. Shin, J. Li, J. Simone, M. Chew, N. W. Wong, N. Trilok, S. Erickson, A. Rao, A. Loo, C. P. Stec, M. Anderson, M. Cloherty, G. Sarkar, M. Combes, A. J. Wakil, A. E. Segal, M. R. Fragiadakis, G. K. Cooper, S. Baron, J. L. 2025-10-01 doi:10.1101/2025.09.29.677401 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Ontogeny and functional potential of founding dendritic cells in the developing lung ]]> https://biorxiv.org/content/10.1101/2025.09.30.679620v1?rss=1 Headley, M. B. Soysa, R. Abideen, S. Reyes, V. Z. 2025-10-02 doi:10.1101/2025.09.30.679620 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Population-level migration modeling of North American birds through data integration with BirdFlow ]]> https://biorxiv.org/content/10.1101/2025.09.30.679621v1?rss=1 Chen, Y. Slager, D. L. Plunkett, E. Fuentes, M. Deng, Y. Mackenzie, S. A. Berrigan, L. E. Fink, D. Sheldon, D. Van Doren, B. M. Dokter, A. M. 2025-10-02 doi:10.1101/2025.09.30.679621 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ spCorr: flexible and scalable inference of spatially varying correlation in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.09.30.679684v1?rss=1 Jiang, C. Yin, Y. Robson, P. Li, J. Y. H. Li, J. J. Song, D. 2025-10-02 doi:10.1101/2025.09.30.679684 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ De novo design of RNA and nucleoprotein complexes ]]> https://biorxiv.org/content/10.1101/2025.10.01.679929v1?rss=1 Favor, A. H. Quijano, R. Chernova, E. Kubaney, A. Weidle, C. Esler, M. A. McHugh, L. Carr, A. Hsia, Y. Juergens, D. Carr, K. D. Kim, P. T. Politanska, Y. Sehgal, E. Kwon, P. S. Pecoraro, R. J. Glasscock, C. Borst, A. J. DiMaio, F. Stoddard, B. L. Baker, D. 2025-10-02 doi:10.1101/2025.10.01.679929 Cold Spring Harbor Laboratory Press 2025-10-02 <![CDATA[ Re-infection with SARS-CoV-2 is associated with increased antibody breadth and potency against diverse sarbecovirus strains ]]> https://biorxiv.org/content/10.1101/2025.10.03.679858v1?rss=1 Lilly, M. Ruiz, F. Foreman, W. Chohan, V. Guenthoer, J. Depierreux, D. Baharani, V. Ralph, D. Harteloo, A. Chu, H. Bieniasz, P. D. Starr, T. Overbaugh, J. 2025-10-06 doi:10.1101/2025.10.03.679858 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Characterization of quiescent subpopulations and proliferative compartments in glioblastoma ]]> https://biorxiv.org/content/10.1101/2025.10.03.680278v1?rss=1 Mihalas, A. Mitchell, K. Arora, S. O'Connor, S. Patel, A. Plaisier, C. L. PADDISON, P. 2025-10-06 doi:10.1101/2025.10.03.680278 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ A searchable database of publications using fluorescent probes and flow cytometry to study antigen-specific B cells ]]> https://biorxiv.org/content/10.1101/2025.10.08.680531v1?rss=1 View larger version (6K): org.highwire.dtl.DTLVardef@f07f5forg.highwire.dtl.DTLVardef@13a3b95org.highwire.dtl.DTLVardef@1dcd79org.highwire.dtl.DTLVardef@9cddaa_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Palani, S. Kong, A. X. Buetow, A. Yousif, A. S. Say, A. Wang, Z. Biswas, K. Blaszczyk, J. Rodrigues-Jesus, M. J. Malave Ramos, D. R. Senthilkumar, V. Chappell, S. Koenig, J. F. Taylor, J. J. 2025-10-09 doi:10.1101/2025.10.08.680531 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ RNA regulates repeat-associated non-AUG (RAN) translation initiation in C9orf72 FTD/ALS ]]> https://biorxiv.org/content/10.1101/2025.10.09.681477v1?rss=1 Grosely, R. Yamada-Hunter, S. Puglisi, A. Palo, M. Z. Alvarado, C. Lapointe, C. P. Gitler, A. D. Puglisi, J. D. 2025-10-09 doi:10.1101/2025.10.09.681477 Cold Spring Harbor Laboratory Press 2025-10-09 <![CDATA[ Obesity Impairs the Antitumor Activity of CAR-T Cells in Triple-Negative Breast Cancer ]]> https://biorxiv.org/content/10.1101/2025.10.10.681694v1?rss=1 Malian, H. M. Marnata Pellegry, C. Oh, H. M. Glenny, E. M. Ho, A. N. Dotti, G. Hursting, S. D. Coleman, M. F. 2025-10-13 doi:10.1101/2025.10.10.681694 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ A telomere-to-telomere map of somatic mutation burden and functional impact in cancer ]]> https://biorxiv.org/content/10.1101/2025.10.10.681725v1?rss=1 Sohn, M.-H. Dubocanin, D. Vollger, M. R. Kwon, Y. Minkina, A. Munson, K. M. Hart, S. F. Ranchalis, J. E. Parmalee, N. L. Sedeno-Cortes, A. E. Ou, J. Au, N. Y. Bohaczuk, S. Carroll, B. Frazar, C. D. Harvey, W. T. Hoekzema, K. Huang, M.-F. Jacques, C. N. Jensen, D. M. Kolar, J. T. Lee, R. Lin, J. Loy, K. Mack, T. Mao, Y. Pham, M. M. Ryke, E. Smith, J. D. Sutherlin, L. Swanson, E. G. Weiss, J. M. SMaHT Assembly Working Group, Carvalho, C. Coorens, T. H. Harris, K. Wei, C.-L. Eichler, E. E. Altemose, N. Bennett, J. T. Stergachis, A. B. 2025-10-13 doi:10.1101/2025.10.10.681725 Cold Spring Harbor Laboratory Press 2025-10-13 <![CDATA[ Moving Beyond Binary Biomarkers: Machine Learning Model Resolves Concurrent and Molecularly Heterogeneous Mismatch Repair and Homologous Recombination Deficiencies in Prostate Cancer ]]> https://biorxiv.org/content/10.1101/2025.10.08.680958v1?rss=1 Sharma, K. Wilson, D. A. Wang, Y. Haider, S. Bhatlapenumarthi, V. Boiarsky, D. Cipriaso, J. M. Yermakov, L. Dutta, R. Coleman, I. M. Bankhead, A. Jadhav, S. K. Neupane, B. Taylor, B. W. Morrissey, C. Schweitzer, M. T. Montgomery, R. B. Rao, S. Nevalainen, M. T. Nelson, A. A. Antonarakis, E. S. Pilea, P. G. Berchuk, J. E. Zarrabi, K. K. Pritchard, C. Kothari, A. Chen, H.-Z. George, B. Kurzrock, R. Ha, G. Nelson, P. S. Banerjee, A. Auer, P. L. Kilari, D. De Sarkar, N. 2025-10-14 doi:10.1101/2025.10.08.680958 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Pervasive suppressors halt the spread of selfish Segregation Distorter in a natural population ]]> https://biorxiv.org/content/10.1101/2025.10.13.681989v1?rss=1 Chang, C.-H. Handler, T. Fuda, N. Pascua, D. Mouton, T. Larracuente, A. M. 2025-10-14 doi:10.1101/2025.10.13.681989 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Nascent CUT&Tag captures transcription factor binding after chromatin duplication ]]> https://biorxiv.org/content/10.1101/2025.10.13.682212v1?rss=1 Wooten, M. Nguyen, K. Takushi, B. N. Ahmad, K. Henikoff, S. 2025-10-15 doi:10.1101/2025.10.13.682212 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Functional and antigenic constraints on the Nipah virus fusion protein ]]> https://biorxiv.org/content/10.1101/2025.10.15.682664v1?rss=1 Larsen, B. B. Harari, S. Gen, R. Stewart, C. Veesler, D. Bloom, J. D. 2025-10-15 doi:10.1101/2025.10.15.682664 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics ]]> https://biorxiv.org/content/10.1101/2025.10.17.683141v1?rss=1 McCrone, J. T. Baele, G. Omah, I. F. Kinganda-Lusamaki, E. Brew, J. A. Carvalho, L. M. Dudas, G. Mbala-Kingebeni, P. Suchard, M. A. Rambaut, A. 2025-10-18 doi:10.1101/2025.10.17.683141 Cold Spring Harbor Laboratory Press 2025-10-18 <![CDATA[ Cross-Species Morphology Learning Enables Nucleic Acid-Independent Detection of Live Mutant Blood Cells ]]> https://biorxiv.org/content/10.1101/2025.10.20.682949v1?rss=1 Khan, S. A. Faerber, D. Kirkey, D. Raffel, S. Hadland, B. Deininger, M. Buettner, F. Zhao, H. G. 2025-10-21 doi:10.1101/2025.10.20.682949 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Separating selection from mutation in antibody language models ]]> https://biorxiv.org/content/10.1101/2025.10.21.683652v1?rss=1 Matsen, F. A. Dumm, W. Sung, K. Johnson, M. M. Rich, D. Starr, T. Song, Y. S. Fukuyama, J. Haddox, H. K. 2025-10-22 doi:10.1101/2025.10.21.683652 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Inflammatory Biomarkers of Asymptomatic and Symptomatic Tuberculosis ]]> https://biorxiv.org/content/10.1101/2025.10.26.684319v1?rss=1 Awany, D. Ariefdien, D. Mendelsohn, S. Rozot, V. Mulenga, H. Nyangu, S. Tameris, M. Moloantoa, T. Katona, A. Maruri, F. Noor, F. Panchiar, R. Hlongwane, K. Stanley, K. Van der Heijden, Y. Hadley, K. Fiore-Gartland, A. Innes, C. Brumskine, W. Dheda, K. Jaumdally, S. Perumal, T. Martinson, N. Leslie, A. Fourie, B. Hiemstra, A. Malherbe, S. Walzl, G. Naidoo, K. Churchyard, G. Chegou, N. Sterling, T. Hatherill, M. Scriba, T. J. 2025-10-29 doi:10.1101/2025.10.26.684319 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ VRC01 Selects Rare HIV Escape Mutations After Acquisition in Antibody-Mediated Prevention Trials ]]> https://biorxiv.org/content/10.1101/2025.10.29.685411v1?rss=1 12,000 HIV env sequences from 47 participants from the AMP trials, identifying VRC01-mediated de novo escape mutations in 8 of 26 VRC01-treated participants but none in 21 placebo participants. These mutations were found at very low frequency (<1%) in global viruses. Escape mutations, primarily located in the Loop-D and {beta}23/V5 regions of Env, conferred cross-resistance to several CD4bs bnAbs, while more potent CD4bs bnAbs like N6 and 1-18 largely retained their activity. Our findings demonstrate that prophylactic VRC01 can select for viral escape after infection, underscoring the need for next-generation bnAbs with improved breadth and potency to enhance durability and efficacy of antibody-based HIV prevention. ]]> Williamson, C. Curry, L. Mkhize, N. N. Giorgi, E. E. Magaret, C. A. Lambson, B. E. Bhebhe, S. Kaldine, H. Moyo-Gwete, T. Rolland, M. Rossenkhan, R. Garcia, N. M. G. Moodley, C. Yssel, A. Huang, Y. Marsden, A. A. Reeves, D. B. Mayer, B. T. Bumgarner, R. E. Beaume, N. Westfall, D. H. Juraska, M. DeCamp, A. C. Murrell, H. G. Bai, H. Deng, W. Pankow, A. Bhattacharya, T. York, T. Ndabambi, N. Chen, L. Zhao, H. Gwashu-Nyangiri, A. Thebus, R. Cohen, P. Murrell, B. Karuna, S. Hural, J. Mgodi, N. Edupuganti, S. Morris, L. Montefiori, D. McElrath, M. J. Cohen, 2025-10-29 doi:10.1101/2025.10.29.685411 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Characterization of Cancer-Reactive T Cells and Neoantigen-specific T Cell Receptors ]]> https://biorxiv.org/content/10.1101/2025.10.29.685473v1?rss=1 Sun, W. Liu, S. Yu, B. Zhang, Z. Bradley, P. Bleakley, M. 2025-10-30 doi:10.1101/2025.10.29.685473 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ larch: mapping the parsimony-optimal landscape of trees for directed exploration ]]> https://biorxiv.org/content/10.1101/2025.10.29.685337v1?rss=1 Barker, M. Milanov, O. Dumm, W. Rich, D. Turakhia, Y. Matsen, F. A. 2025-10-31 doi:10.1101/2025.10.29.685337 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ ADAPTIVE MULTI-SCALE GRAPH TRANSFORMER FRAMEWORK FORHISTOPATHOLOGICAL IMAGES ]]> https://biorxiv.org/content/10.1101/2025.10.30.685502v1?rss=1 Wu, C.-i. Banda, K. Swisher, E. Sailem, H. 2025-10-31 doi:10.1101/2025.10.30.685502 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Inhibition of farnesyltransferase activity diminishes hematopoietic stem cell ex vivo expansion ability ]]> https://biorxiv.org/content/10.1101/2025.10.30.685582v1?rss=1 Newman, C. Alves, I. M. Hagen, M. W. Wellington, R. Hadland, B. K. Quintana, A. M. Termini, C. M. 2025-10-31 doi:10.1101/2025.10.30.685582 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Depletion of microenvironmental syndecan-2 impairs hematopoietic stem cell self-renewal and cytokine responses ]]> https://biorxiv.org/content/10.1101/2025.11.07.687077v1?rss=1 Hagen, M. W. Setiawan, N. J. Wellington, R. Woodruff, K. A. Newman, C. Billings, T. M. Nazzaro, M. N. Hadland, B. Termini, C. M. 2025-11-09 doi:10.1101/2025.11.07.687077 Cold Spring Harbor Laboratory Press 2025-11-09 <![CDATA[ Hidden Markov Models Detect Recombination and Ancestry of SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2025.11.08.687354v1?rss=1 Masaki, N. Bedford, T. 2025-11-10 doi:10.1101/2025.11.08.687354 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCF ]]> https://biorxiv.org/content/10.1101/2025.11.10.687711v1?rss=1 Henikoff, S. Henikoff, J. G. 2025-11-12 doi:10.1101/2025.11.10.687711 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ N6-methyladenosine regulation of mRNA translation is essential for early human erythropoiesis ]]> https://biorxiv.org/content/10.1101/2025.11.10.687731v1?rss=1 Kuppers, D. Arora, S. Wladyka, C. Ge, R. Liu, S. Peng, Y. Su, R. Wilhite, A. Chen, J. He, C. Hsieh, A. Paddison, P. 2025-11-12 doi:10.1101/2025.11.10.687731 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Elucidating Neurodevelopmental Trajectories in Cancer with Topic Modeling: Revealing Persistent External Granule Layer Lineages in Medulloblastoma ]]> https://biorxiv.org/content/10.1101/2025.11.12.687706v1?rss=1 Rajendran, A. Haldipur, P. Arora, S. Grama, K. Subramanian, S. S. Galan, L. M. Johnson, D. Aldinger, K. A. Shendure, J. Millen, K. J. Gennari, J. H. Pattwell, S. S. 2025-11-13 doi:10.1101/2025.11.12.687706 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Acute Myeloid Leukemia Relapse after Bromodomain Inhibitor Treatment or Chemotherapy is Characterized by Myc-Ras Transcriptional Remodeling ]]> https://biorxiv.org/content/10.1101/2025.11.13.688312v1?rss=1 Huang, B. J. D'Souza, J. Batingana, A. R. Harris, M. D. Wang, X. Hwang, E. Wandler, A. M. Burgess, M. R. Li, Q. Meshinchi, S. Bollag, G. Shannon, K. 2025-11-14 doi:10.1101/2025.11.13.688312 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ E2F1-3 activate polyomavirus early transcription and viral replication ]]> https://biorxiv.org/content/10.1101/2025.11.15.688648v1?rss=1 Salisbury, N. J. H. Amonkar, S. Roman, A. Galloway, D. A. 2025-11-16 doi:10.1101/2025.11.15.688648 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024 ]]> https://biorxiv.org/content/10.1101/2025.11.14.688517v1?rss=1 Isaac, K. J. Cox, K. E. L. Ho, K. Y. Humphries, E. M. Kucher, N. Leek, J. T. Mosher, S. Schatz, M. C. Tan, F. J. Hoffman, A. M. 2025-11-17 doi:10.1101/2025.11.14.688517 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Targeting peptide-MHC complexes with designed T cell receptors and antibodies ]]> https://biorxiv.org/content/10.1101/2025.11.19.689381v1?rss=1 Motmaen, A. Jude, K. M. Wang, N. Minervina, A. Feldman, D. Lichtenstein, M. A. Ebenezer, A. Correnti, C. Thomas, P. G. Garcia, K. C. Baker, D. Bradley, P. 2025-11-20 doi:10.1101/2025.11.19.689381 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ Orchestrating Spatial Transcriptomics Analysis with Bioconductor ]]> https://biorxiv.org/content/10.1101/2025.11.20.688607v1?rss=1 Crowell, H. L. Dong, Y. Billato, I. Cai, P. Emons, M. Gunz, S. Guo, B. Li, M. Mahmoud, A. Manukyan, A. Pages, H. Panwar, P. Rao, S. Sargeant, C. J. Shepherd Kern, L. Ramos, M. Sun, J. Totty, M. Carey, V. J. Chen, Y. Collado-Torres, L. Ghazanfar, S. Hansen, K. D. Martinowich, K. Maynard, K. R. Patrick, E. Righelli, D. Risso, D. Tiberi, S. Waldron, L. Gottardo, R. Robinson, M. D. Hicks, S. C. Weber, L. M. 2025-11-21 doi:10.1101/2025.11.20.688607 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Tom70-mediated mitochondria-nuclear envelope contacts regulate nuclear pore complex inheritance during gametogenesis ]]> https://biorxiv.org/content/10.1101/2025.11.20.689567v1?rss=1 Ruediger, C. T. Styler, B. S. Sawyer, E. S. Spiri, S. King, G. A. Walsh, M. E. Brar, G. A. Jorgens, D. M. Ünal, E. 2025-11-21 doi:10.1101/2025.11.20.689567 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ 3D pathology-guided microdissection ]]> https://biorxiv.org/content/10.1101/2025.11.20.689586v1?rss=1 Hsieh, H.-C. Gao, G. Han, Q. Brenes, D. Baraznenok, E. Yan, R. Serafin, R. Bishop, K. W. Wang, R. Konnick, E. Q. Pritchard, C. C. Figiel, S. Hamdy, F. C. Mills, I. G. Reder, N. P. Reddi, D. M. Paulson, T. G. Grady, W. M. Valk, J. E. True, L. D. Haffner, M. C. Rao, S. R. Woodcock, D. J. Liu, J. T. C. 2025-11-21 doi:10.1101/2025.11.20.689586 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Contemporary HIV-1 envelope pseudovirus panels for detecting and assessing B cell lineages with broadly neutralizing antibody potential ]]> https://biorxiv.org/content/10.1101/2025.11.21.689752v1?rss=1 Korber, B. Seaman, M. S. Mkhize, N. N. Greene, K. Gao, H. Shen, X. Domin, E. Tang, H. Theiler, J. Wagh, K. Moore, P. L. Williamson, C. Mullins, J. I. Doria-Rose, N. A. Montefiori, D. Giorgi, E. E. 2025-11-24 doi:10.1101/2025.11.21.689752 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ The BRCA1- RAD51 Axis Regulates SCAI/REV3 Dependent Replication Fork Maintenance ]]> https://biorxiv.org/content/10.1101/2025.11.25.689574v1?rss=1 Unterseher, C. Tsuchida, H. Bosire, R. Jin, X. Kieffer, S. Adeyemi, R. 2025-11-27 doi:10.1101/2025.11.25.689574 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome ]]> https://biorxiv.org/content/10.1101/2025.11.29.690828v1?rss=1 Shen, B. A. Asfahl, K. L. Lim, B. Bertolli, S. K. Minot, S. S. Radey, M. C. Penewit, K. Ngo, B. Salipante, S. J. Johnston, C. D. Peterson, S. B. Goodman, A. D. Mougous, J. D. 2025-11-30 doi:10.1101/2025.11.29.690828 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Dissecting type I and II interferon impacts on human immune cells in disease by a cell type-specific interferon response atlas ]]> https://biorxiv.org/content/10.64898/2025.12.02.691676v1?rss=1 Moss, N. Sakai, C. Kaul, S. N. Graybuck, L. T. Rachid Zaim, S. Angus-Hill, M. L. He, Y. D. Layton, E. D. Bouvatte, P. Wittig, P. J. La France, C. M. Peng, T. Glass, M. C. Krishnan, U. Chander, A. Kawelo, E. K. Garber, J. Reading, J. Anover-Sombke, S. D. Kwok, M. Green, D. J. Goldrath, A. W. Sigvardsson, M. Skene, P. J. Li, X.-j. Torgerson, T. R. Kuan, E. L. 2025-12-05 doi:10.64898/2025.12.02.691676 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Inhibitory potential of autologous neutralizing antibodies sets quantitative limits on the rebound-competent HIV-1 reservoir ]]> https://biorxiv.org/content/10.64898/2025.12.07.692769v1?rss=1 Garcia, M. A. Farrell-Sherman, A. Zhuo, J. Fray, E. J. Zinsser, A. M. Aydin, B. Sowers, K. Li, H. Lopez, B. M. Abeyta-Lopez, A. Chu, T. Lubbeck, D. Chae, M. Varriale, J. Westfall, D. H. Lai, J. Hoh, R. Dalhuisen, T. Simonetti, F. R. Peluso, M. J. Deeks, S. G. Siliciano, R. F. Cohn, L. B. Siliciano, J. D. 2025-12-09 doi:10.64898/2025.12.07.692769 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Armoring STEAP1 CAR T cells with IL-18 potentiates antitumor activity in Ewing sarcoma ]]> https://biorxiv.org/content/10.64898/2025.12.08.693072v1?rss=1 Bhatia, V. Tsao, A. Chong, T. Challita, P. P. Liang, K. Sayar, E. Huang, J. Lawlor, E. R. Haffner, M. C. Nabet, B. Lee, J. K. 2025-12-11 doi:10.64898/2025.12.08.693072 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Using experimental results of protein design to guide biomolecular energy-function development ]]> https://biorxiv.org/content/10.64898/2025.12.12.691241v1?rss=1 Haddox, H. K. Rocklin, G. J. Motta, F. C. Strickland, D. Halabiya, S. F. Cordray, C. Park, H. Klavins, E. Baker, D. DiMaio, F. 2025-12-13 doi:10.64898/2025.12.12.691241 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals ]]> https://biorxiv.org/content/10.64898/2025.12.12.693809v1?rss=1 Raman, P. Khan, H. Young, J. M. Tsukiyama, T. Malik, H. S. 2025-12-13 doi:10.64898/2025.12.12.693809 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ Retention of a single Cenp-C gene in different syntenic locations in the montium group of Drosophila species ]]> https://biorxiv.org/content/10.64898/2025.12.11.693522v1?rss=1 Soares, R. F. Chang, C.-H. Koerich, L. B. Malik, H. S. KUHN, G. C. S. 2025-12-15 doi:10.64898/2025.12.11.693522 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ NKTR-255, a polymer-conjugated IL-15, synergizes with CAR-T cell therapy to activate endogenous anti-tumor immunity and improve tumor control ]]> https://biorxiv.org/content/10.64898/2025.12.11.693768v1?rss=1 Nutt, W. S. Kluesner, M. G. Bingham, E. Gad, E. Miller, D. Zepeda, V. Snyder, A. J. Marsh, S. A. Liudahl, S. M. Hoffman, M. LeBlanc, L. Volfbeyn, M. E. Garrison, S. M. Sarvothama, M. Barry, K. C. Headley, M. B. Marcondes, M. Srivastava, S. 2025-12-15 doi:10.64898/2025.12.11.693768 Cold Spring Harbor Laboratory Press 2025-12-15 <![CDATA[ Metaplasia Enables Stomach Colonization by Fusobacterium animalis ]]> https://biorxiv.org/content/10.64898/2025.12.16.694801v1?rss=1 Gomez-Garzon, C. Chen, Q. O'Brien, V. P. Salama, N. 2025-12-18 doi:10.64898/2025.12.16.694801 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ PTEN deficiency linked to chromosome 10q loss leads to aggressive NF2mutant meningioma biology ]]> https://biorxiv.org/content/10.64898/2025.12.21.695820v1?rss=1 Parrish, A. G. Thirmanne, H. N. Arora, S. Herold-Mende, C. Sievers, P. Sahm, F. Szulzewsky, F. Holland, E. 2025-12-22 doi:10.64898/2025.12.21.695820 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ Mitochondrial ROS-induced metabolic alterations differentially regulate ferroptosis sensitivity ]]> https://biorxiv.org/content/10.64898/2025.12.21.695848v1?rss=1 Banerjee, S. Smith, M. R. Wang, Y. I. Wang, M. Gratz, D. Tharp, G. K. Kang, S. He, P. 2025-12-23 doi:10.64898/2025.12.21.695848 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Chromatin profiling for everyone: FFPE-CUTAC for the theory and practice of modern molecular biology ]]> https://biorxiv.org/content/10.64898/2025.12.24.696395v1?rss=1 Xu, Y. Henikoff, S. Ahmad, K. 2025-12-26 doi:10.64898/2025.12.24.696395 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Generative AI Enables Breast Cancer Genomic Subtype Prediction from Histology Images ]]> https://biorxiv.org/content/10.64898/2025.12.29.692457v1?rss=1 Simon, B. G. Weiss, C. L. G. Chan, D. Mangiante, L. Ma, Z. Smith, N. H. Meisner, A. Rae, J. M. Speers, C. W. Albain, K. S. Karakas, C. Bean, G. R. Mouron, S. Quintela-Fandino, M. Curtis, C. 2025-12-29 doi:10.64898/2025.12.29.692457 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Pre-Human Immunodeficiency Virus (HIV) infection Th17 CD4+ T cells as predictors of early HIV disease progression ]]> https://biorxiv.org/content/10.64898/2025.12.29.696811v1?rss=1 Omole, T. E. Nguyen, H. M. Marcinow, A. Jahan, N. Severini, G. Naicker, N. Thomas, K. Celum, C. Mugo, N. Mujugira, A. Kublin, J. Corey, L. Sivro, A. Lingappa, J. Gray, G. McKinnon, L. 2025-12-29 doi:10.64898/2025.12.29.696811 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ Lysine deficiency within a conserved lysine desert is critical for EEL-1/HUWE1 to support ubiquitin proteasome system function. ]]> https://biorxiv.org/content/10.64898/2025.12.29.696916v1?rss=1 Yanagi, K. S. Chen, B. J. Kunjo, S. O. Topalidou, I. Lehrbach, N. J. 2025-12-30 doi:10.64898/2025.12.29.696916 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ CausalGRN: deciphering causal gene regulatory networks from single-cell CRISPR screens ]]> https://biorxiv.org/content/10.64898/2025.12.30.692369v1?rss=1 Yu, B. Liu, D. Qi, G. Huangfu, D. Hsu, L. Shojaie, A. Sun, W. 2025-12-31 doi:10.64898/2025.12.30.692369 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Developmental programming of hematopoietic stem cell dormancy by evasion of Notch signaling ]]> https://biorxiv.org/content/10.64898/2026.01.02.697352v1?rss=1 Herrero-Molinero, P. Canton, E. Maqueda, M. Ruiz-Herguido, C. Iglesias, A. Gonzalez, J. Hadland, B. Espinosa, L. Bigas, A. 2026-01-04 doi:10.64898/2026.01.02.697352 Cold Spring Harbor Laboratory Press 2026-01-04 <![CDATA[ Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures ]]> https://biorxiv.org/content/10.64898/2026.01.05.697808v1?rss=1 Ahn, J. J. Yu, T. C. Dadonaite, B. Radford, C. E. Bloom, J. D. 2026-01-06 doi:10.64898/2026.01.05.697808 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Hypatia: a set of quantitative methods for profiling isoform across cell populations ]]> https://biorxiv.org/content/10.64898/2026.01.13.699341v1?rss=1 Pan, T. Shiau, C.-K. S. Lu, L. Wang, C. Wang, M. He, Y. Bhimaraj, A. Brat, D. J. Huse, J. T. Li, J. J. Gao, R. 2026-01-14 doi:10.64898/2026.01.13.699341 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Unifying phylogenetic traversal and deep learning to guide tree exploration ]]> https://biorxiv.org/content/10.64898/2026.01.14.699358v1?rss=1 Collienne, L. Richman, H. Rich, D. H. Barker, M. Jennings-Shaffer, C. Matsen, F. A. 2026-01-14 doi:10.64898/2026.01.14.699358 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Ribosome-associated quality control of aberrant protein production during amino acid limitation ]]> https://biorxiv.org/content/10.64898/2026.01.14.699605v1?rss=1 Darnell, A. M. Chidley, C. Paradise, V. Cui, D. S. Davidsen, K. Lincoln, S. C. Abbott, K. L. Elbashir, R. Vander Heiden, C. P. Sorger, P. K. Sullivan, L. B. Davis, J. H. Vander Heiden, M. G. 2026-01-15 doi:10.64898/2026.01.14.699605 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ B Lymphocyte Protein Factories produced by Hematopoietic Stem Cell Gene Editing ]]> https://biorxiv.org/content/10.64898/2026.01.16.699998v1?rss=1 Hartweger, H. Ruprecht, C. Yao, K.-H. Laffont, P. Lima dos Reis, G. Zhou, P. Hägglöf, T. Binet, L. Loewe, M. Hong, J. P. Xiao, T. Sefik, E. Hernandez, B. Gazumyan, A. Jankovic, M. Seaman, M. S. Costa, G. Nelson, S. A. Clark, J. Kanatani, S. Wilson, P. C. Krammer, F. Levashina, E. A. Julien, J.-P. Wardemann, H. Sinnis, P. Stamatatos, L. Flavell, R. A. Nussenzweig, M. C. 2026-01-18 doi:10.64898/2026.01.16.699998 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ Kinetochore clustering is mediated by Mps1 phosphorylation of conserved MELT motifs in Stu1 ]]> https://biorxiv.org/content/10.64898/2026.01.23.701336v1?rss=1 Mallet, D. R. Jiang, M. Minnuto, G. M. Biggins, S. 2026-01-25 doi:10.64898/2026.01.23.701336 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ Modeling HIV infection, treatment, rebound, and intervention in human immune organoids ]]> https://biorxiv.org/content/10.64898/2026.01.25.701611v1?rss=1 Sackey, S. A. Schrum, J. E. Mangalanathan, U. M. Fish, R. S. Sola, E. Selehi, A. Pi, R. Zack, J. A. Kim, J. T. Lehman, D. A. Davis, M. M. Blish, C. A. 2026-01-27 doi:10.64898/2026.01.25.701611 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Recovery of an 18th Century Rhinovirus Genome through Ancient RNA Isolation of Human Lungs ]]> https://biorxiv.org/content/10.64898/2026.01.29.702071v1?rss=1 Barnett, E. E. Castillo, A. Du Plessis, I. A. Kistler, K. Carrillo, L. Leon, A. S. Liu, T. Rutherford, M. G. Ploug, J. McCrone, J. T. Arcos, M. C. A. Melo, D. B. 2026-01-30 doi:10.64898/2026.01.29.702071 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Shared Maturation Pathways of HIV-1 Envelope-reactive V3-glycan bnAb Lineages in Human and Rhesus Macaque ]]> https://biorxiv.org/content/10.64898/2026.01.29.702664v1?rss=1 Clark, M. Li, H. Martin, M. Evangelous, T. Gobeil, S. Berry, M. Wagh, K. Giorgi, E. Hogarty, M. Zhao, C. Wang, S. Marchitto, L. Ding, W. Park, Y. Rando, J. Carey, J. Connell, A. Skelly, A. Chen, Y. Rohr, S. Jiang, C. Venkatayogi, S. Mansouri, K. Edwards, R. J. Lindenberger, J. Hora, B. Doria-Rose, N. A. Mascola, J. van Gils, M. J. Sanders, R. W. Korber, B. Hahn, B. H. Saunders, K. O. Acharya, P. Wiehe, K. Haynes, B. F. Shaw, G. M. Williams, W. B. 2026-01-30 doi:10.64898/2026.01.29.702664 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Genetic engineering of Staphylococcus haemolyticus: Overcoming Restriction-Modification Barriers and Targeting Virulence Genes ]]> https://biorxiv.org/content/10.64898/2026.02.03.702568v1?rss=1 Venter, H. J. Cavanagh, J. P. Wolden, R. Jones, D. Roberts, R. J. Rivera, M. Z. Christensen, M. O. Johnston, C. D. 2026-02-03 doi:10.64898/2026.02.03.702568 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Intranasal Delivery of HIV/SIV Antigens with NE/AS01B Adjuvants Enhances Cellular Immunity and Reduces Viral Loads in SHIV-Challenged Macaques ]]> https://biorxiv.org/content/10.64898/2026.02.04.703720v1?rss=1 Thurman, M. Chokkavelu, V. Johnson, S. D. Olwenyi, O. A. Kathamuthu, G. R. Yu, J. Adeniji, S. Hong, K. Y. Johnston, M. Bose, D. Pandey, K. Gao, H. Shen, X. Montefiori, D. Wong, P. T. Baker, J. R. Villinger, F. Kane, M. A. Abdel-Mohsen, M. Byrareddy, S. 2026-02-05 doi:10.64898/2026.02.04.703720 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Structural determinants of broadly neutralizing human antibodies binding to morphological dengue virus variants. ]]> https://biorxiv.org/content/10.64898/2026.02.07.704521v1?rss=1 Mangala Prasad, V. Chatterjee, A. Roy, A. Srinivasan, S. Charles, S. Lubow, J. goo, l. 2026-02-08 doi:10.64898/2026.02.07.704521 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ Deep learning-based non-invasive profiling of tumor transcriptomes from cell-free DNA for precision oncology ]]> https://biorxiv.org/content/10.64898/2026.02.10.705188v1?rss=1 Patton, R. D. Netzley, A. Persse, T. W. Nair, A. Galipeau, P. C. Coleman, I. M. Itagi, P. Chandra, P. Adil, M. Vashisth, M. Sayar, E. Hiatt, J. B. Dumpit, R. Kollath, L. Demirci, R. A. Ghodsi, A. Lam, H.-M. Morrissey, C. Iravani, A. Chen, D. L. Hsieh, A. C. MacPherson, D. Haffner, M. C. Nelson, P. S. Ha, G. 2026-02-12 doi:10.64898/2026.02.10.705188 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Complete definition of how mutations affect antibodies used to prevent RSV ]]> https://biorxiv.org/content/10.64898/2026.02.12.705519v1?rss=1 Simonich, C. A. McMahon, T. E. Kampman, L. Chu, H. Y. Bloom, J. D. 2026-02-12 doi:10.64898/2026.02.12.705519 Cold Spring Harbor Laboratory Press 2026-02-12 <![CDATA[ Intellectual disability risk gene RFX4 regulates cortical neurogenesis by restraining neuronal differentiation ]]> https://biorxiv.org/content/10.64898/2026.02.11.705165v1?rss=1 Kroll, K. L. Determan, J. J. Chapman, G. Crump, S. R. Batool, F. Malik, S. Gujral, T. Buchser, W. Valentine, C. Elia, S. Sentmanat, M. Jetter, H. 2026-02-14 doi:10.64898/2026.02.11.705165 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Vicious circle of amyloid and leptomeningeal macrophages evokes vascular dysfunction in CAA ]]> https://biorxiv.org/content/10.64898/2026.02.12.705483v1?rss=1 Wake, H. Hartantyo, R. Y. TSUJI, T. Hou, L. Saito, R. Yamasaki, A. Kochi, T. Saito, Y. Tada, M. Cheung, D. L. Moorhouse, A. J. Prinz, M. Masuda, T. Kakita, A. 2026-02-14 doi:10.64898/2026.02.12.705483 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection ]]> https://biorxiv.org/content/10.64898/2026.02.18.706711v1?rss=1 Kikawa, C. Huddleston, J. Turner, S. A. Loes, A. N. Liu, J. Gang, S. Griffiths, T. Drapeau, E. M. Cowling, B. J. Ho, F. Leung, N. H. Englund, J. A. Lacombe, K. Watanabe, S. Hasegawa, H. Busch, M. Lanteri, M. Stone, M. Spencer, B. Neher, R. A. Smith, D. J. Bedford, T. Hensley, S. E. Bloom, J. D. 2026-02-19 doi:10.64898/2026.02.18.706711 Cold Spring Harbor Laboratory Press 2026-02-19 <![CDATA[ Differential effects of two common GVHD prophylaxis regimens on the gut microbiome: Results from the BMT CTN 1801 study ]]> https://biorxiv.org/content/10.64898/2026.02.19.706769v1?rss=1 Wirbel, J. Saber, W. Martens, M. J. Peled, J. U. Andermann, T. M. Fei, T. Brooks, E. F. Doyle, B. Pincus, N. B. Jenq, R. R. Bar, M. Bolanos-Meade, J. Bratrude, B. Chhabra, S. Choi, S. W. Clark, W. Das, S. Elmariah, H. Gooptu, M. Holtan, S. G. Jones, R. J. Levine, J. E. Logan, B. R. Al Malki, M. M. Murthy, H. S. Rashidi, A. Rezvani, A. R. Riches, M. L. Runaas, L. Sandhu, K. Spahn, A. Sung, A. D. van den Brink, M. R. M. Horowitz, M. M. Hamadani, M. Kean, L. S. Perales, M.-A. Bhatt, A. S. 2026-02-20 doi:10.64898/2026.02.19.706769 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Mutations to the HCoV-229E spike have counterbalancing effects on serum antibody neutralization and receptor binding ]]> https://biorxiv.org/content/10.64898/2026.02.22.707297v1?rss=1 Harari, S. Eguia, R. T. Dadonaite, B. Radford, C. E. Stewart, C. Veesler, D. Bloom, J. D. 2026-02-23 doi:10.64898/2026.02.22.707297 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines ]]> https://biorxiv.org/content/10.64898/2026.02.23.707528v1?rss=1 Loes, A. N. Tarabi, R. A. Li, S. H. Atkinson, R. K. Huddleston, J. Kikawa, C. Griffths, T. Drapeau, E. M. Wong, S.-S. Cheng, S. M. Leung, N. H. Cobey, S. Cowling, B. J. Bedford, T. Hensley, S. E. Bloom, J. D. 2026-02-23 doi:10.64898/2026.02.23.707528 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ scDesignPop generates realistic population-scale single-cell RNA-seq for power analysis, benchmarking, and privacy protection ]]> https://biorxiv.org/content/10.64898/2026.02.23.707578v1?rss=1 Dong, C. Y. Cen, Y. Song, D. Li, J. J. 2026-02-25 doi:10.64898/2026.02.23.707578 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Topological Data Analysis of Spatial Protein Expression in Multiplexed Spatial Proteomics Studies ]]> https://biorxiv.org/content/10.64898/2026.02.25.707521v1?rss=1 Samorodnitsky, S. N. Wu, M. 2026-02-27 doi:10.64898/2026.02.25.707521 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Regulatory T cells restrain IL-15-mediated cytotoxic and bystander T cell activity in mucosal tissue without compromising antigen-driven memory ]]> https://biorxiv.org/content/10.64898/2026.02.25.708034v1?rss=1 Cruz Talavera, I. Graham, J. B. Swarts, J. L. Traxinger, B. R. Peters, M. Q. Warrier, L. Koehne, A. L. Arkatkar, T. Jerome, K. R. Prlic, M. Lund, J. M. 2026-02-27 doi:10.64898/2026.02.25.708034 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Evaluation of an H5 influenza virus mRNA-lipid nanoparticle (LNP) vaccine in lactating dairy cows ]]> https://biorxiv.org/content/10.64898/2026.03.03.709308v1?rss=1 Santos, J. J. S. Souza, C. K. Zanella, G. C. Goulart, D. B. Arruda, B. Boggiatto, P. Palmer, M. V. Snyder, C. A. Kristula, M. A. Dickens, C. Webb, T. L. Atkinson, R. K. Dadonaite, B. Dwivedi, G. Alameh, M.-G. Bloom, J. D. Weissman, D. Althouse, G. C. Baker, A. L. Hensley, S. E. 2026-03-04 doi:10.64898/2026.03.03.709308 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Neuroepithelial reprogramming and ERBB vulnerability in canine acanthomatous ameloblastoma ]]> https://biorxiv.org/content/10.64898/2026.03.03.709191v1?rss=1 Stephanou, A. Shui, B. Mische, D. Byron, M. Katt, W. P. Chan, M. Grenier, J. K. De Vlaminck, I. Duhamel, G. E. Gujral, T. S. Sethupathy, P. Peralta, S. 2026-03-05 doi:10.64898/2026.03.03.709191 Cold Spring Harbor Laboratory Press 2026-03-05 <![CDATA[ Remote homology and functional genetics unmask deeply preserved Scm3/HJURP orthologs in metazoans ]]> https://biorxiv.org/content/10.64898/2026.03.04.709615v1?rss=1 Hollis, J. A. Stonick, J. A. Topalidou, I. Young, J. M. Moens, C. B. Lehrbach, N. J. Campbell, M. G. Malik, H. S. 2026-03-06 doi:10.64898/2026.03.04.709615 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Hunting for microsatellite instability in long-read data with Owl ]]> https://biorxiv.org/content/10.64898/2026.03.08.708905v1?rss=1 Kronenberg, Z. Chua, K. P. Chaisson, M. J. P. Yoo, B. Lansdon, L. Rowell, W. J. Brandine, G. d. S. Dolzhenko, E. Ikegami, K. Huang, K. K. Tan, P. Bhise, S. Fan, E. Mendoza, M. O'Donnell, E. Pastinen, T. Lawlor, E. R. Furlan, S. N. Farooqi, M. S. Eberle, M. A. 2026-03-10 doi:10.64898/2026.03.08.708905 Cold Spring Harbor Laboratory Press 2026-03-10 <![CDATA[ Therapeutic scheduling of WEE1 inhibition preserves T cell function and promotes immune control of HPV⁺ tumors ]]> https://biorxiv.org/content/10.64898/2026.03.10.710574v1?rss=1 Liu, Y. Zhang, Z. Tao, Y. Rahgav, L. Gray-Gaillard, S. Hussaini, Y. Pan, M. Shamber, J. Kwak, J. Park, S. L. Cramer, J. Stoltz, R. Patria, J. Swanger, J. Liu, K. Sannigrahi, M. K. Houghton, M. Rodriguez, C. Carey, R. M. Brody, R. Rajasekaran, K. Weinstein, G. Linette, G. P. Carreno, B. M. Painter, M. M. Wherry, E. J. Clurman, B. Basu, D. Diab, A. 2026-03-12 doi:10.64898/2026.03.10.710574 Cold Spring Harbor Laboratory Press 2026-03-12 <![CDATA[ Proteomics reveals extensive phosphoregulation of outer kinetochore protein KNL1 ]]> https://biorxiv.org/content/10.64898/2026.03.13.711714v1?rss=1 Jurasin, A. C. Frank, A. R. Biggins, S. 2026-03-15 doi:10.64898/2026.03.13.711714 Cold Spring Harbor Laboratory Press 2026-03-15 <![CDATA[ Estrogen receptor-positive cell line xenograft models recapitulate metastatic dissemination and endocrine response of invasive lobular breast carcinoma ]]> https://biorxiv.org/content/10.64898/2026.03.17.712396v1?rss=1 Tasdemir, N. Savariau, L. Scott, J. Latoche, J. Biery, K. Li, Z. Bossart, E. Sreekumar, S. Brown, D. Wang, S. Watters, R. Nasrazadani, A. Qin, Y. Cao, Y. Chen, F. Tseng, G. Castro, C. Anderson, C. J. Atkinson, J. Hooda, J. Lucas, P. C. Davidson, N. LEE, A. V. Oesterreich, S. 2026-03-18 doi:10.64898/2026.03.17.712396 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Translating Histopathology Foundation Model Embeddings into Cellular and Molecular Features for Clinical Studies ]]> https://biorxiv.org/content/10.64898/2026.03.17.711896v1?rss=1 Cui, S. Sui, Z. Li, Z. Matkowskyj, K. A. Yu, M. Grady, W. M. Sun, W. 2026-03-19 doi:10.64898/2026.03.17.711896 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ Metabolic specialization structures gut bacterial niches and drives colorectal cancer progression ]]> https://biorxiv.org/content/10.64898/2026.03.21.712571v1?rss=1 Xu, L.-L. Seelbinder, B. Zhou, Z. Kuo, T.-H. Sae-Ong, T. Treibmann, S. Damerell, V. Brobeil, A. Richter, K. M. Mueller, M. Toriola, A. T. Shibata, D. Li, C. I. Byrd, D. A. Figueiredo, J. C. Hardikar, S. Zielinski, C. E. Bleckmann, A. Ni, Y. Correia-Melo, C. Zimmermann, M. Ulrich, C. M. Gigic, B. Panagiotou, G. 2026-03-23 doi:10.64898/2026.03.21.712571 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ Pluripotency Factors Modulate Interferon Signaling in Embryonic Stem Cells ]]> https://biorxiv.org/content/10.64898/2026.03.23.713714v1?rss=1 Yang, Q. Padilla-Galvez, M. Uhl, S. Eggenberger, J. Kogut, S. Becker, S. Chen, S. Rosenberg, B. R. Blanco-Melo, D. 2026-03-25 doi:10.64898/2026.03.23.713714 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Nextstrain automates real-time phylodynamic analysis of open data for endemic and emerging pathogens ]]> https://biorxiv.org/content/10.64898/2026.03.23.713807v1?rss=1 Andrews, K. R. Chang, J. Roemer, C. Hadfield, J. Lin, V. Brito, A. F. Daodu, R. Joia, I. A. Kistler, K. Li, A. W. Moncla, L. H. Paredes, M. I. Kuhnert, D. Torres, L. M. Voitl, L. Aksamentov, I. Hodcroft, E. B. Huddleston, J. McCrone, J. T. Anderson, J. S. Sibley, T. R. Lee, J. Neher, R. A. Bedford, T. 2026-03-26 doi:10.64898/2026.03.23.713807 Cold Spring Harbor Laboratory Press 2026-03-26 <![CDATA[ A codon-sensitive conformational switch gates commitment to translation start sites ]]> https://biorxiv.org/content/10.64898/2026.03.24.713952v1?rss=1 McGuire, S. F. Chan, M. C. Chan, T. C. Pachikara, N. Alleman, E. M. Sikora, V. M. Subramaniam, A. R. Campbell, M. G. Lapointe, C. P. 2026-03-27 doi:10.64898/2026.03.24.713952 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ An interdependent Cbf1-CCAN interaction stabilizes the budding yeast kinetochore ]]> https://biorxiv.org/content/10.64898/2026.03.25.714319v1?rss=1 Hedouin, S. Hu, C. Biggins, S. 2026-03-27 doi:10.64898/2026.03.25.714319 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ High-dimensional multiomics reveals perturbations to IL-6/IL-6R axis and RUNX3 in CD4+ T cells during third trimester pregnancy ]]> https://biorxiv.org/content/10.64898/2026.03.26.711478v1?rss=1 37 weeks), and non-pregnant blood. >350 surface proteins were screened via flow cytometry, and transcriptomes were analysed using single-cell RNA sequencing with >130 CITE-seq barcoded antibodies. ResultsSurface protein screening identified changes to ILT4/CD85d, CD9, IFN-{gamma} receptor {beta}-chain, CX3CR1 and CCR5 in the pregnant blood and decidual CD4+ T cells. CX3CR1 and CCR5 had the highest expression on the effector-memory T cell (TEM) subset in the blood, with expression consistent across subsets in decidua. CD126/IL-6R was lower in pregnant blood and decidual CD4+ T cells, while scRNAseq identified enrichment in the IL-6R signalling pathway in naive CD4+ T cells in pregnant blood. Both sIL-6R and IL-6 concentrations were increased in plasma during pregnancy, suggesting perturbations to the IL-6/IL-6R signalling axis. Meanwhile, decidual CD4+ T cells had increased expression of transcription factor RUNX3 in the CD69+ tissue-resident-like subset. ConclusionsOur findings demonstrate altered molecular expression in CD4+ T cells during pregnancy. This provides important mechanistic insight of their adaptation and regulation during placental development, which may drive placental dysfunction or pregnancy complications including preeclampsia, fetal growth restriction and stillbirth. These new data may inform future studies that focus on determining the significance of differentially- expressed immune features in pregnancy to identify potential targets for immune modulation to treat pregnancy complications and infections. ]]> Habel, J. Nguyen, T. H. O. de Alwis, N. Allen, E. K. Li, S. Juno, J. A. Kent, S. J. Bond, K. Williamson, D. Lappas, M. Hannan, N. Walker, S. Schroeder, J. Crawford, J. C. Thomas, P. Kedzierska, K. Rowntree, L. 2026-03-30 doi:10.64898/2026.03.26.711478 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Cellector: A tool to detect foreign genotype cells in scRNAseq data with applications in leukemia and microchimerism. ]]> https://biorxiv.org/content/10.64898/2026.03.26.714571v1?rss=1 Heaton, H. Behboudi, R. Ward, C. Weerakoon, M. Kanaan, S. Reichle, S. Hunter, N. Furlan, S. 2026-03-30 doi:10.64898/2026.03.26.714571 Cold Spring Harbor Laboratory Press 2026-03-30 <![CDATA[ Fc receptor dependent and independent mechanisms of antibody-mediatedenhancement of immune responses ]]> https://biorxiv.org/content/10.64898/2026.03.27.714269v1?rss=1 Cipolla, M. MacLean, A. J. Hernandez, B. Silva Santos, G. S. Stamatatos, L. Gazumyan, A. Hartweger, H. Merkenschlager, J. Bournazos, S. Ravetch, J. Nussenzweig, M. 2026-03-31 doi:10.64898/2026.03.27.714269 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ IMMREP25: Unseen Peptides ]]> https://biorxiv.org/content/10.64898/2026.03.30.715276v1?rss=1 Richardson, E. Aarts, Y. J. M. Altin, J. A. Baakman, C. A. B. Bradley, P. Chen, B. Clifford, J. Dhar, M. Diepenbroek, D. Fast, E. Gowthaman, R. He, J. Karnaukhov, V. Marzella, D. F. Meysman, P. Nielsen, M. Nilsson, J. B. Deleuran, S. N. Parizi, F. M. Pelissier, A. Pierce, B. G. Rodriguez Martinez, M. Roran A R, D. Saravanakumar, S. Shao, Y. Smit, N. Van Houcke, M. Visani, G. M. Wan, Y.-T. R. Wang, X. Woods, L. Wuyts, S. Xiao, C. Xue, L. C. IMMREP25 Participant Consortium, Barton, J. Noakes, M. May, D. H. Peters, B. 2026-04-01 doi:10.64898/2026.03.30.715276 Cold Spring Harbor Laboratory Press 2026-04-01 <![CDATA[ Aurora kinase A enables collective invasion and metastasis by endowing a leader cell phenotype and stabilizing Eplin-mediated cohesion with follower cells ]]> https://biorxiv.org/content/10.64898/2026.03.31.715024v1?rss=1 Zhou, B. P. Chu, T. L. H. Gallant, A. K. Wang, S. Bhat, T. A. Ghorayeb, R. Gough, C. Garcia, R. E. Pujana, M. A. Lim, C. J. Maxwell, C. A. 2026-04-02 doi:10.64898/2026.03.31.715024 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Bovine H5N1 influenza viruses have adapted to more efficiently use receptors abundant in cattle ]]> https://biorxiv.org/content/10.64898/2026.04.02.715584v1?rss=1 Hassard, J. A. Yang, J. Dadonaite, B. Pekar, J. E. Yu, J. Richardson, S. A. S. Pinto, R. M. Ramirez Valdez, K. Lemey, P. Quantrill, J. L. Xue, J. Masonou, T. Case, K.-M. Ajeian, J. Woodall, M. N. J. Ross, R. A. Hudson, N. Zhong, K. Cao, H. Jones, S. Klim, H. J. Wasik, B. R. Dermawan, D. N. Sadeyen, J.-R. Werling, D. Yaffy, D. James, J. Nunez, A. Digard, P. Brown, I. H. Goldhill, D. H. Murcia, P. R. Smith, C. M. Liu, Y. Bloom, J. D. Iqbal, M. Barclay, W. S. Haslam, S. M. Peacock, T. P. 2026-04-06 doi:10.64898/2026.04.02.715584 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Multi-omic profiling of human antibody-secreting cells reveals diverse subsets sustain durable humoral immunity ]]> https://biorxiv.org/content/10.64898/2026.04.13.717827v1?rss=1 Glass, D. R. Dornisch, E. M. Yin, H. Ludmann, S. A. Samudre, A. Kuhl, S. Malone, J. Chander, A. Kaul, S. N. Phalen, C. G. Parthasarathy, V. Dillon, M. A. Genge, P. C. Stuckey, T. J. Anover-Sombke, S. D. Wittig, P. J. Pebworth, M.-P. He, Z. Henderson, K. E. Ravisankar, P. Hernandez, V. Musgrove, B. Mishra, S. Krishnan, U. Thomson, Z. J. Weiss, M. Estep, N. Graybuck, L. T. Angus-Hill, M. L. Gustafson, C. E. Kopp, M. S. Reading, J. Li, X.-j. Viana, M. P. Bumol, T. F. Goldrath, A. W. Sigvardsson, M. Bendall, S. C. Skene, P. J. Green, D. J. Newell, E. W. Tor 2026-04-17 doi:10.64898/2026.04.13.717827 Cold Spring Harbor Laboratory Press 2026-04-17