• Nature  ·  December 9, 2020

    Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture.

    Nevin Yusufova, Andreas Kloetgen, Matt Teater, Adewola Osunsade, Jeannie M. Camarillo, Christopher R. Chin, Ashley S. Doane, Bryan J. Venters, Stephanie Portillo-Ledesma, Joseph Conway, Jude M. Phillip, Olivier Elemento, David W. Scott, Wendy Béguelin, Jonathan D. Licht, Neil L. Kelleher, Louis M. Staudt, Arthur I. Skoultchi, Michael-Christopher Keogh, Effie Apostolou, Christopher E. Mason, Marcin Imielinski, Tamar Schlick, Yael David, Aristotelis Tsirigos, C. David Allis, Alexey A. Soshnev, Ethel Cesarman & Ari M. Melnick.

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  • Neuron  ·  November 26, 2020

    Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis.

    Ramita Dewan, Ruth Chia, Jinhui Ding, Richard A Hickman, Thor D Stein, Yevgeniya Abramzon, Sarah Ahmed, Marya S Sabir, Makayla K Portley, Arianna Tucci, Kristina Ibáñez, F N U Shankaracharya, Pamela Keagle, Giacomina Rossi, Paola Caroppo, Fabrizio Tagliavini, Maria L Waldo, Per M Johansson, Christer F Nilsson, American Genome Center (TAGC); FALS Sequencing Consortium; Genomics England Research Consortium; International ALS/FTD Genomics Consortium (iAFGC); International FTD Genetics Consortium (IFGC); International LBD Genomics Consortium (iLBDGC); NYGC ALS Consortium; PROSPECT Consortium; James B Rowe, Luisa Benussi , Giuliano Binetti, Roberta Ghidoni, Edwin Jabbari, Coralie Viollet, Jonathan D Glass 19, Andrew B Singleton, Vincenzo Silani, Owen A Ross, Mina Ryten, Ali Torkamani, Toshiko Tanaka, Luigi Ferrucci, Susan M Resnick, Stuart Pickering-Brown, Christopher B Brady, Neil Kowal, John A Hardy, Vivianna Van Deerlin, Jean Paul Vonsattel, Matthew B Harms, Huw R Morris, Raffaele Ferrari, John E Landers, Adriano Chiò, J Raphael Gibbs, Clifton L Dalgard, Sonja W Scholz, Bryan J Traynor

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  • PLoS One  ·  November 25, 2020

    Asthma and its relationship to mitochondrial copy number: Results from the Asthma Translational Genomics Collaborative (ATGC) of the Trans-Omics for Precision Medicine (TOPMed) program.

    Cocco MP, White E, Xiao S, Hu D, Mak A, Sleiman P, Yang M, Bobbitt KR, Gui H, Levin AM, Hochstadt S, Whitehouse K, Rynkowski D, Barczak AJ, Abecasis G, Blackwell TW, Kang HM, Nickerson DA, Germer S, Ding J, Lanfear DE, Gilliland F, Gauderman WJ, Kumar R, Erle DJ, Martinez F, Hakonarson H, Burchard EG, Williams LK.

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  • bioRxiv  ·  November 23, 2020

    The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes.

    Görkem Garipler, Congyi Lu, Alexis Morrissey, Lorena S. Lopez-Zepeda, Simon E. Vidal, Begüm Aydin, Matthias Stadtfeld, Uwe Ohler, Shaun Mahony, Neville E. Sanjana, Esteban O. Mazzoni

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  • Molecular Cell  ·  November 19, 2020

    Impact of Lineage Plasticity to and from a Neuroendocrine Phenotype on Progression and Response in Prostate and Lung Cancers.

    Mark A Rubin, Robert G. Bristow, Phillip D. Thienger, Caroline Dive, Marcin Imielinski

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  • bioRxiv  ·  November 12, 2020  ·  Preprint

    Pangenome-based genome inference.

    Jana Ebler, Wayne E. Clarke, Tobias Rausch, Peter A. Audano, Torsten Houwaart, Jan Korbel, Evan E. Eichler, Michael C. Zody, Alexander T. Dilthey, Tobias Marschall
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  • Nature  ·  November 11, 2020

    Dense sampling of bird diversity increases power of comparative genomics.

    Shaohong Feng, Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve, Duo Xie, Guangji Chen, Chunxue Guo, Brant C. Faircloth, Bent Petersen, Zongji Wang, Qi Zhou, Mark Diekhans, Wanjun Chen, Sergio Andreu-Sánchez, Ashot Margaryan, Jason Travis Howard, Carole Parent, George Pacheco, Mikkel-Holger S. Sinding, Lara Puetz, Emily Cavill, Ângela M. Ribeiro, Leopold Eckhart, Jon Fjeldså, Peter A. Hosner, Robb T. Brumfield, Les Christidis, Mads F. Bertelsen, Thomas Sicheritz-Ponten, Dieter Thomas Tietze, Bruce C. Robertson, Gang Song, Gerald Borgia, Santiago Claramunt, Irby J. Lovette, Saul J. Cowen, Peter Njoroge, John Philip Dumbacher, Oliver A. Ryder, Jérôme Fuchs, Michael Bunce, David W. Burt, Joel Cracraft, Guanliang Meng, Shannon J. Hackett, Peter G. Ryan, Knud Andreas Jønsson, Ian G. Jamieson, Rute R. da Fonseca, Edward L. Braun, Peter Houde, Siavash Mirarab, Alexander Suh, Bengt Hansson, Suvi Ponnikas, Hanna Sigeman, Martin Stervander, Paul B. Frandsen, Henriette van der Zwan, Rencia van der Sluis, Carina Visser, Christopher N. Balakrishnan, Andrew G. Clark, John W. Fitzpatrick, Reed Bowman, Nancy Chen, Alison Cloutier, Timothy B. Sackton, Scott V. Edwards, Dustin J. Foote, Subir B. Shakya, Frederick H. Sheldon, Alain Vignal, André E. R. Soares, Beth Shapiro, Jacob González-Solís, Joan Ferrer-Obiol, Julio Rozas, Marta Riutort, Anna Tigano, Vicki Friesen, Love Dalén, Araxi O. Urrutia, Tamás Székely, Yang Liu, Michael G. Campana, André Corvelo, Robert C. Fleischer, Kim M. Rutherford, Neil J. Gemmell, Nicolas Dussex, Henrik Mouritsen, Nadine Thiele, Kira Delmore, Miriam Liedvogel, Andre Franke, Marc P. Hoeppner, Oliver Krone, Adam M. Fudickar, Borja Milá, Ellen D. Ketterson, Andrew Eric Fidler, Guillermo Friis, Ángela M. Parody-Merino, Phil F. Battley, Murray P. Cox, Nicholas Costa Barroso Lima, Francisco Prosdocimi, Thomas Lee Parchman, Barney A. Schlinger, Bette A. Loiselle, John G. Blake, Haw Chuan Lim, Lainy B. Day, Matthew J. Fuxjager, Maude W. Baldwin, Michael J. Braun, Morgan Wirthlin, Rebecca B. Dikow, T. Brandt Ryder, Glauco Camenisch, Lukas F. Keller, Jeffrey M. DaCosta, Mark E. Hauber, Matthew I. M. Louder, Christopher C. Witt, Jimmy A. McGuire, Joann Mudge, Libby C. Megna, Matthew D. Carling, Biao Wang, Scott A. Taylor, Glaucia Del-Rio, Alexandre Aleixo, Ana Tereza Ribeiro Vasconcelos, Claudio V. Mello, Jason T. Weir, David Haussler, Qiye Li, Huanming Yang, Jian Wang, Fumin Lei, Carsten Rahbek, M. Thomas P. Gilbert, Gary R. Graves, Erich D. Jarvis, Benedict Paten & Guojie Zhang

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  • Genome Biology  ·  November 10, 2020

    Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel.

    Marco Gerdol, Rebeca Moreira, Fernando Cruz, Jessica Gómez-Garrido, Anna Vlasova, Umberto Rosani, Paola Venier, Miguel A. Naranjo-Ortiz, Maria Murgarella, Samuele Greco, Pablo Balseiro, André Corvelo, Leonor Frias, Marta Gut, Toni Gabaldón, Alberto Pallavicini, Carlos Canchaya, Beatriz Novoa, Tyler S. Alioto, David Posada and Antonio Figueras

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  • Current Genetic Medicine Reports  ·  November 7, 2020

    Genetics of Amyotrophic Lateral Sclerosis.

    Jenna M. Gregory, Delphine Fagegaltier, Hemali Phatnani & Matthew B. Harms

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  • Nature Communications  ·  October 30, 2020

    Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis.

    Mandric I, Schwarz T, Majumdar A, Hou K, Briscoe L, Perez R, Subramaniam M, Hafemeister C, Satija R, Ye CJ, Pasaniuc B, Halperin E.

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  • American Journal of Human Genetics  ·  October 26, 2020

    Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies.

    Laura M Amendola, Kathleen Muenzen, Leslie G Biesecker, Kevin M Bowling, Greg M Cooper, Michael O Dorschner, Catherine Driscoll, Ann Katherine M Foreman, Katie Golden-Grant, John M Greally, Lucia Hindorff, Dona Kanavy , Vaidehi Jobanputra, Jennifer J Johnston, Eimear E Kenny, Shannon McNulty, Priyanka Murali, Jeffrey Ou, Bradford C Powell, Heidi L Rehm, Bradley Rolf, Tamara S Roman, Jessica Van Ziffle, Saurav Guha, Avinash Abhyankar, David Crosslin, Eric Venner, Bo Yuan, Hana Zouk, CSER Sequencing and Diagnostic Yield working group; Gail P Jarvik

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  • Cell  ·  October 24, 2020

    Identification of required host factors for SARS-CoV-2 infection in human cells.

    Zharko Daniloski, Tristan X. Jordan, Hans-Hermann Wessels, Daisy A. Hoagland, Silva Kasela, Mateusz Legut, Silas Maniatis, Eleni P. Mimitou, Lu Lu, Evan Geller, Oded Danziger, Brad R. Rosenberg, Hemali Phatnani, Peter Smibert, Tuuli Lappalainen, Benjamin R. tenOever, Neville E. Sanjana

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  • The Journal of Molecular Diagnostics  ·  October 23, 2020

    Detection of Copy Number Variants by Short Multiply Aggregated Sequence Homologies.

    Vaidehi Jobanputra, Peter Andrews, Vanessa Felice, Avinash Abhyankar, Lukasz Kozon, Dino Robinson, Ferrah London, Inessa Hakker, Kazimierz Wrzeszczynski, Michael Ronemus

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  • Nature  ·  October 23, 2020

    Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease.

    Christian R. Marshall, Shimul Chowdhury, Ryan J. Taft, Mathew S. Lebo, Jillian G. Buchan, Steven M. Harrison, Ross Rowsey, Eric W. Klee, Pengfei Liu, Elizabeth A. Worthey, Vaidehi Jobanputra, David Dimmock, Hutton M. Kearney, David Bick, Shashikant Kulkarni, Stacie L. Taylor, John W. Belmont, Dimitri J. Stavropoulos, Niall J. Lennon & Medical Genome Initiative

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  • Journal of Investigative Dermatology  ·  October 19, 2020

    Targeted knockout of β-catenin in adult melanocyte stem cells using a mouse line, Dct::CreERT2, results in disrupted stem cell renewal and pigmentation defects.

    Madeleine Le. Coz, Zackie Aktary, Natsuki Watanabe, Ichiro Yajima, Marie Pouteaux, Nisamanee Charoenchon, Tsutomu Motohashi, Takahiro Kunisada, André Corvelo, Lionel Larue

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  • Nature Communications  ·  October 14, 2020

    Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants.

    Zhao X, Qiao D, Yang C, Kasela S, Kim W, Ma Y, Shrine N, Batini C, Sofer T, Taliun SAG, Sakornsakolpat P, Balte PP, Prokopenko D, Yu B, Lange LA, Dupuis J, Cade BE, Lee J, Gharib SA, Daya M, Laurie CA, Ruczinski I, Cupples LA, Loehr LR, Bartz TM, Morrison AC, Psaty BM, Vasan RS, Wilson JG, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Ardlie KG, Aguet F, VanDenBerg DJ, Papanicolaou GJ, Rotter JI, Barnes KC, Jain D, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Dugan-Perez S, Gupta N, Gabriel S, Rich SS, O’Connor GT, Redline S, Reed RM, Laurie CC, Daviglus ML, Preudhomme LK, Burkart KM, Kaplan RC, Wain LV, Tobin MD, London SJ, Lappalainen T, Oelsner EC, Abecasis GR, Silverman EK, Barr RG; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lung Working Group, Cho MH, Manichaikul A.

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  • Nature Communications  ·  October 12, 2020

    Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium.

    Satria P Sajuthi, Peter DeFord, Nathan D Jackson, Michael T Montgomery, Jamie L Everman, Cydney L Rios, Elmar Pruesse, James D Nolin, Elizabeth G Plender, Michael E Wechsler, Angel CY Mak, Celeste Eng, Sandra Salazar, Vivian Medina, Eric M Wohlford, Scott Huntsman, Deborah A Nickerson, Soren Germer, Michael C Zody, Goncalo Abecasis, Hyun Min Kang, Kenneth M Rice, Rajesh Kumar, Sam Oh, Jose Rodriguez-Santana, Esteban G Burchard, Max A Seibold

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  • Cell  ·  October 9, 2020

    Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

    Daniel K. Wells, Marit M. van Buuren, Kristen K. Dang, Vanessa M. Hubbard-Lucey, Kathleen C.F. Sheehan, Katie M. Campbell, Andrew Lamb, Jeffrey P. Ward, John Sidney,Ana B. Blazquez,Andrew J. Rech, Jesse M. Zaretsky, Begonya Comin-Anduix, Alphonsus H.C. Ng, William Chour, Thomas V. Yu, Hira Rizvi, Jia M. Chen, Patrice Manning, Gabriela M. Steiner, Xengie C. Doan, The Tumor Neoantigen Selection Alliance, Taha Merghoub,Justin Guinney, Adam Kolom, Cheryl Selinsky, Antoni Ribas, Matthew D. Hellmann, Nir Hacohen, Alessandro Sette, James R. Heath, Nina Bhardwaj, Fred Ramsdell, Robert D. Schreiber, Ton N. Schumacher, Pia Kvistborg, and Nadine A. Defranoux

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  • Annals of the Rheumatic Diseases  ·  October 7, 2020

    Machine learning integration of scleroderma histology and gene expression identifies fibroblast polarisation as a hallmark of clinical severity and improvement.

    Showalter K, Spiera R, Magro C, Agius P, Martyanov V, Franks JM, Sharma R, Geiger H, Wood TA, Zhang Y, Hale CR, Finik J, Whitfield ML, Orange DE, Gordon JK.

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  • Cell  ·  October 1, 2020

    Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.

    Kevin Hadi, Xiaotong Yao, Julie M. Behr, Aditya Deshpande, Charalampos Xanthopoulakis, Huasong Tian,Sarah Kudman, Joel Rosiene, Madison Darmofal, Joseph DeRose, Rick Mortensen, Emily M. Adney, Alon Shaiber, Zoran Gajic, Michael Sigouros, Kenneth Eng, Jeremiah A. Wala, Kazimierz O. Wrzeszczynski Kanika Arora, Minita Shah, Anne-Katrin Emde, Vanessa Felice, Mayu O. Frank, Robert B. Darnell, Mahmoud Ghandi, Franklin Huang, Sally Dewhurst, John Maciejowski,Titia de Lange, Jeremy Setton, Nadeem Riaz, Jorge S. Reis-Filho, Simon Powell, David A. Knowles, Ed Reznik, Bud Mishra, Rameen Beroukhim, Michael C. Zody, Nicolas Robine, Kenji M. Oman, Carissa A. Sanchez, Mary K. Kuhner, Lucian P. Smith, Patricia C. Galipeau, Thomas G. Paulson, Brian J. Reid, Xiaohong Li, David Wilkes, Andrea Sboner,Juan Miguel Mosquera, Olivier Elemento, and Marcin Imielinski

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