• Research Square  ·  March 2, 2021  ·  Preprint

    Somatic whole genome dynamics of precancer in Barrett’s Esophagus.

    Thomas Paulson, Patricia Galipeau, Kenji Oman, Carissa Sanchez, Mary Kuhner, Lucian Smith, Kevin Hadi, Minita Shah, Kanika Arora, Jennifer Shelton, André Corvelo, Molly Johnson, Anne-Kathrin Emde, Carlo Maley, Xiaotong Yao, Rashesh Sanghvi, Elisa Venturini, Benjamin Hubert, Marcin Imielinski, Nicolas Robine, Brian Reid, Xiaohong Li

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  • Nature Genetics  ·  March 1, 2021

    Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens.

    Efthymia Papalexi, Eleni P. Mimitou, Andrew W. Butler, Samantha Foster, Bernadette Bracken, William M. Mauck III, Hans-Hermann Wessels, Yuhan Hao, Bertrand Z. Yeung, Peter Smibert & Rahul Satija

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  • Science  ·  February 25, 2021

    Haplotype-resolved diverse human genomes and integrated analysis of structural variation

    Peter Ebert, Peter A. Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari, Feyza Yilmaz, Xuefang Zhao, PingHsun Hsieh, Joyce Lee, Sushant Kumar, Jiadong Lin, Tobias Rausch, Yu Chen, Jingwen Ren, Martin Santamarina, Wolfram Hoeps, Hufsah Ashraf, Nelson T. Chuang, Xiaofei Yang, Katy M. Munson, Alexandra P. Lewis, Susan Fairley, Luke J. Tallon, Wayne E. Clarke, Anna O. Basile, Marta Byrska-Bishop, Andre Corvelo, Mark J.P. Chaisson, Junjie Chen, Chong Li, Harrison Brand, Aaron M. Wenger, Maryam Ghareghani, William Harvey, Benjamin Raeder, Patrick Hasenfeld, Allison Regier, Haley Abel, Ira Hall, Paul Flicek, Oliver Stegle, Mark B. Gerstein, Jose M.C. Tubio, Zepeng Mu, Yang I. Li, Xinghua Shi, Alex R. Hastie, Kai Ye, Zechen Chong, Ashley D. Sanders, Michael C. Zody, Michael E. Talkowski, Ryan E. Mills, Scott E. Devine, Charles Lee, Jan O. Korbel, Tobias Marschall, Evan E. Eichler

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  • bioRxiv  ·  February 11, 2021  ·  Preprint

    A like-for-like comparison of lightweight-mapping pipelines for single-cell RNA-seq data pre-processing.

    Mohsen Zakeri, Avi Srivastava, Hirak Sarkar, Rob Patro

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  • eLife  ·  February 11, 2021

    The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types.

    Zharko Daniloski, Tristan X. Jordan, Juliana K. Ilmain, Xinyi Guo, Gira Bhabha, Benjamin R. tenOever, Neville E. Sanjana

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  • Nature  ·  February 10, 2021

    Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.

    A list of authors and their affiliations appears at the end of the paper; include André Corvelo, Anne-Katrin Emde, Wayne E. Clarke, Soren Germer, Michael Zody

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  • Journal of Neuroscience  ·  February 3, 2021

    Reduced Motivation in Perinatal Fluoxetine-Treated Mice: A Hypodopaminergic Phenotype.

    Menezes EC, Shah R, Laughlin L, Vinod KY, Smiley JF, Cunha C, Balla A, Sershen H, Castellanos FX, Corvelo A, Teixeira CM.

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  • Cell Reports  ·  February 2, 2021

    Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.

    Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, Lee JJ, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N; TCGA Research Network, Meyerson M, Govindan R, Imielinski M

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  • Investigative Ophthalmology & Visual Science  ·  February 1, 2021

    The Role of Genetic Ancestry as a Risk Factor for Primary Open-angle Glaucoma in African Americans.

    Cole BS, Gudiseva HV, Pistilli M, Salowe R, McHugh CP, Zody MC, Chavali VRM, Ying GS, Moore JH, O’Brien JM.

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  • Genome Biology  ·  January 26, 2021

    Exploiting the GTEx resources to decipher the mechanisms at GWAS loci.

    Alvaro N Barbeira, Rodrigo Bonazzola, Eric R Gamazon, Yanyu Liang, YoSon Park, Sarah Kim-Hellmuth, Gao Wang, Zhuoxun Jiang, Dan Zhou, Farhad Hormozdiari, Boxiang Liu, Abhiram Rao, Andrew R Hamel, Milton D Pividori, François Aguet, GTEx GWAS Working Group, Lisa Bastarache, Daniel M Jordan, Marie Verbanck, Ron Do, GTEx Consortium, Matthew Stephens, Kristin Ardlie, Mark McCarthy, Stephen B Montgomery, Ayellet V Segrè, Christopher D. Brown, Tuuli Lappalainen, Xiaoquan Wen, Hae Kyung Im.

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  • American Journal of Human Genetics  ·  January 25, 2021

    De novo TRIM8 variants impair its protein localization to nuclear bodies and cause developmental delay, epilepsy, and focal segmental glomerulosclerosis.

    Weng PL, Majmundar AJ, Khan K, Lim TY, Shril S, Jin G, Musgrove J, Wang M, Ahram DF, Aggarwal VS, Bier LE, Heinzen EL, Onuchic-Whitford AC, Mann N, Buerger F, Schneider R, Deutsch K, Kitzler TM, Klämbt V, Kolb A, Mao Y, Moufawad El Achkar C, Mitrotti A, Martino J, Beck BB, Altmüller J, Benz MR, Yano S, Mikati MA, Gunduz T, Cope H, Shashi V; Undiagnosed Diseases Network, Trachtman H, Bodria M, Caridi G, Pisani I, Fiaccadori E, AbuMaziad AS, Martinez-Agosto JA, Yadin O, Zuckerman J, Kim A; UCLA Clinical Genomics Center, John-Kroegel U, Tyndall AV, Parboosingh JS, Innes AM, Bierzynska A, Koziell AB, Muorah M, Saleem MA, Hoefele J, Riedhammer KM, Gharavi AG, Jobanputra V, Pierce-Hoffman E, Seaby EG, O’Donnell-Luria A, Rehm HL, Mane S, D’Agati VD, Pollak MR, Ghiggeri GM, Lifton RP, Goldstein DB, Davis EE, Hildebrandt F, Sanna-Cherchi S

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  • bioRxiv  ·  January 19, 2021  ·  Preprint

    Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism.

    Avi Srivastava, Mohsen Zakeri, Hirak Sarkar, Charlotte Soneson, Carl Kingsford, Rob Patro

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  • Trials  ·  January 14, 2021

    The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children.

    Odgis JA, Gallagher KM, Suckiel SA, Donohue KE, Ramos MA, Kelly NR, Bertier G, Blackburn C, Brown K, Fielding L, Lopez J, Aguiniga KL, Maria E, Rodriguez JE, Sebastin M, Teitelman N, Watnick D, Yelton NM, Abhyankar A, Abul-Husn NS, Baum A, Bauman LJ, Beal JC, Bloom T, Cunningham-Rundles C, Diaz GA, Dolan S, Ferket BS, Jobanputra V, Kovatch P, McDonald TV, McGoldrick PE, Rhodes R, Rinke ML, Robinson M, Rubinstein A, Shulman LH, Stolte C, Wolf SM, Yozawitz E, Zinberg RE, Greally JM, Gelb BD, Horowitz CR, Wasserstein MP, Kenny EE.

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  • bioRxiv  ·  January 11, 2021  ·  Preprint

    The landscape of human brain immune response in patients with severe COVID-19.

    John F Fullard, Hao chih Lee, Georgios Voloudakis, Shengbao Suo, Zhiping Shao, Cyril Peter, Behnam Javidfar, Wen Zhang, Shan Jiang, André Corvelo, Emma Woodoff-Leith, Dushyant P Purohit, Gabriel E Hoffman, Schahram Akbarian, Mary Fowkes, John Crary, Guo-Cheng Yuan, Panos Roussos

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  • Nature Structural & Molecular Biology  ·  January 4, 2021

    Structural and functional characterization of the Spo11 core complex.

    Corentin Claeys Bouuaert, Sam E. Tischfield, Stephen Pu, Eleni P. Mimitou, Ernesto Arias-Palomo, James M. Berger & Scott Keeney

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  • Nature Methods  ·  January 4, 2021

    Quantum computing at the frontiers of biological sciences.

    Prashant S. Emani, Jonathan Warrell, Alan Anticevic, Stefan Bekiranov, Michael Gandal, Michael J. McConnell, Guillermo Sapiro, Alán Aspuru-Guzik, Justin T. Baker, Matteo Bastiani, John D. Murray, Stamatios N. Sotiropoulos, Jacob Taylor, Geetha Senthil, Thomas Lehner, Mark B. Gerstein & Aram W. Harrow

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