• Nature  ·  October 9, 2024

    The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution.

    Duy D. Nguyen, William F. Hooper, Weisi Liu, Timothy R. Chu, Heather Geiger, Jennifer M. Shelton, Minita Shah, Zoe R. Goldstein, Lara Winterkorn, Adrienne Helland, Michael Sigouros, Jyothi Manohar, Jenna Moyer, Majd Al Assaad, Alissa Semaan, Sandra Cohen, Florencia Madorsky Rowdo, David Wilkes, Mohamed Osman, Rahul R. Singh, Andrea Sboner, Henkel L. Valentine, Phillip Abbosh, Scott T. Tagawa, David M. Nanus, Jones T. Nauseef, Cora N. Sternberg, Ana M. Molina, Douglas Scherr, Giorgio Inghirami, Juan Miguel Mosquera, Olivier Elemento, Nicolas Robine & Bishoy M. Faltas

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  • Nature Biotechnology  ·  October 7, 2024

    Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap.

    Jiacheng Gu, Abhishek Iyer, Ben Wesley, Angelo Taglialatela, Giuseppe Leuzzi, Sho Hangai, Aubrianna Decker, Ruoyu Gu, Naomi Klickstein, Yuanlong Shuai, Kristina Jankovic, Lucy Parker-Burns, Yinuo Jin, Jia Yi Zhang, Justin Hong, Xiang Niu, Jonathon A. Costa, Mikael G. Pezet, Jacqueline Chou, Hans-Willem Snoeck, Dan A. Landau, Elham Azizi, Edmond M. Chan, Alberto Ciccia & Jellert T. Gaublomme

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  • American Journal of Human Genetics  ·  October 3, 2024

    Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies.

    Derek Shyr, Rounak Dey, Xihao Li, Hufeng Zhou, Eric Boerwinkle, Steve Buyske, Mark Daly, Richard A Gibbs, Ira Hall, Tara Matise, Catherine Reeves, Nathan O Stitziel, Michael Zody, Benjamin M Neale, Xihong Lin

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  • Genome Research  ·  October 2, 2024

    High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.

    Jonas A Gustafson, Sophia B Gibson, Nikhita Damaraju, Miranda PG Zalusky, Kendra Hoekzema, David Twesigomwe, Lei Yang, Anthony A Snead, Phillip A Richmond, Wouter De Coster, Nathan D Olson, Andrea Guarracino, Qiuhui Li, Angela L Miller, Joy Goffena, Zachery B Anderson, Sophie HR Storz, Sydney A Ward, Maisha Sinha, Claudia Gonzaga-Jauregui, Wayne E Clarke, Anna O Basile, Andre Corvelo, Catherine E Reeves, Adrienne Helland, Rajeeva Lochan Musunuri, Mahler Revsine, Karynne E Patterson, Cate Paschal, Christina Zakarian, Sara Goodwin, Tanner D Jensen, Esther Robb, 1000 Genomes ONT Sequencing Consortium, University of Washington Center for Rare Disease Research (UW-CRDR), Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium, W. Richard McCombie, Fritz J Sedlazeck, Justin M Zook, Stephen B Montgomery, Erik Garrison, Mikhail Kolmogorov, Michael C Schatz, Richard N McLaughlin Jr., Harriet Dashnow, Michael C Zody, Matthew Loose, Miten Jain, Evan E Eichler and Danny E. Miller

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  • Cell  ·  October 2, 2024

    Private information leakage from single-cell count matrices.

    Conor R. Walker, Xiaoting Li, Manav Chakravarthy, William Lounsbery-Scaife, Yoolim A. Choi, Ritambhara Singh, Gamze Gürsoy

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  • bioRxiv  ·  September 25, 2024  ·  Preprint

    Complex genetic variation in nearly complete human genomes.

    Glennis A. Logsdon, Peter Ebert, Peter A. Audano, Mark Loftus, David Porubsky, Jana Ebler, Feyza Yilmaz, Pille Hallast, Timofey Prodanov, DongAhn Yoo, Carolyn A. Paisie, William T. Harvey, Xuefang Zhao, Gianni V. Martino, Mir Henglin, Katherine M. Munson, Keon Rabbani, Chen-Shan Chin, Bida Gu, Hufsah Ashraf, Olanrewaju Austine-Orimoloye, Parithi Balachandran, Marc Jan Bonder, Haoyu Cheng, Zechen Chong, Jonathan Crabtree, Mark Gerstein, Lisbeth A Guethlein, Patrick Hasenfeld, Glenn Hickey, Kendra Hoekzema, Sarah E Hunt, Matthew Jensen, Yunzhe Jiang, Sergey Koren, Youngjun Kwon, Chong Li, Heng Li, Jiaqi Li, Paul J Norman, Keisuke K. Oshima, Benedict Paten, Adam M. Phillippy, Nicholas R Pollock, Tobias Rausch, Mikko Rautiainen, Stephan Scholz, Yuwei Song, Arda Soylev, Arvis Sulovari, Likhitha Surapaneni, Vasiliki Tsapalou, Weichen Zhou, Ying Zhou, Qihui Zhu, Michael C. Zody, Ryan E. Mills, Scott E. Devine, Xinghua Shi, Mike E Talkowski, Mark J.P. Chaisson, Alexander T Dilthey, Miriam K. Konkel, Jan O. Korbel, Charles Lee, Christine R. Beck, Evan E. Eichler and Tobias Marschall

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  • Proceedings of the National Academy of Sciences  ·  September 23, 2024

    Nr2f1 enhancers have distinct functions in controlling Nr2f1 expression during cortical development.

    Zhidong Liu, Athéna R Ypsilanti, Eirene Markenscoff-Papadimitriou, Diane E Dickel, Stephan J Sanders, Shan Dong, Len A Pennacchio, Axel Visel, John L Rubenstein

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  • Nature Genetics  ·  September 24, 2024

    Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution.

    Joshua S. Schiffman, Andrew R. D’Avino, Tamara Prieto, Yakun Pang, Yilin Fan, Srinivas Rajagopalan, Catherine Potenski, Toshiro Hara, Mario L. Suvà, Charles Gawad & Dan A. Landau

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  • bioRxiv  ·  September 22, 2024  ·  Preprint

    Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks.

    Jennifer H. McDaniel, Vaidehi Patel, Nathan D. Olson, Hua-Jun He, Zhiyong He, Anthony Schmitt, Kristin Sikkink, Fritz Sedlazeck, Harsha Doddapaneni, Shalini N. Jhangiani, Donna M. Muzny, Marie-Claude Gingras, Heer Mehta, Luis F. Paulin, Alex R. Hastie, Hung-Chun Yu, Victor Weigman, Alison Rojas, Katie Kennedy, Jamie Remington, Isai Gonzalez, Mitch Sudkamp, Kelly Wiseman, Bryan Lajoie, Shawn Levy, Miten Jain, Stuart Akeson, Giuseppe Narzisi, Zoe Steinsnyder, Catherine Reeves, Jennifer Shelton, Sarah B. Kingan, Christine Lambert, Primo Bayabyan, Aaron M. Wenger, Ian J. McLaughlin, Aaron Adamson, Christopher Kingsley, Melanie Wescott, Young Kim, Benedict Paten, Jimin Park, Ivo Violich, Karen H. Miga, Joshua Gardner, Brandy McNulty, Gail Rosen, Rajiv McCoy, Lesley Chapman Hannah, Doron Lipson, Hila Benjamin, Nika Iremadze, Ilya Soifer, Stephen Eacker, Mary Wood, Erin Cross, Greg Husar, Stephen Gross, Michael Vernich, Mikhail Komogorov, Tanveer Ahmad, Ayse Keskus, Asher Bryant, Francoise Thibaud-Nissen, Jonathan Trow, Justin Wagner, Chunlin Xiao, Andrew S Liss, Justin M. Zook

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  • Muscle & Nerve  ·  September 18, 2024

    Access for ALL in ALS: A large-scale, inclusive, collaborative consortium to unlock the molecular and genetic mechanisms of amyotrophic lateral sclerosis.

    James D. Berry MD, Sabrina Paganoni MD, PhD, Matthew B. Harms MD, Neil Shneider MD, PhD, Jinsy Andrews MD, Timothy M. Miller MD, PhD, Suma Babu MBBS, Alex V. Sherman MS, Brent T. Harris MD, PhD, Frank A. Provenzano PhD, Hemali P. Phatnani PhD, Jeremy Shefner MD, PhD, Mark A. Garret MD, Shaffeeq S. Ladha MD, Amy Y. Tsou MD, Praveena Mohan PhD, Courtney Igne MS, The ALL ALS Consortium, Robert Bowser PhD

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  • Cold Spring Harbor Perspectives in Biology  ·  September 16, 2024

    Glia in Neurodegenerative Disease.

    Gerard Crowley, David Attwell, Hemali Phatnani, Harald Sontheimer and Soyon Hong

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  • American Society of Human Genetics  ·  September 12, 2024

    Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies.

    Derek Shyr, Rounak Dey, Xihao Li, Hufeng Zhou, Eric Boerwinkle, Steve Buyske, Mark Daly, Richard A Gibbs, Ira Hall, Tara Matise, Catherine Reeves, Nathan O Stitziel, Michael Zody, Benjamin M Neale, Xihong Lin

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  • Nature Medicine  ·  September 3, 2024

    A framework for sharing of clinical and genetic data for precision medicine applications.

    Ahmed Elhussein, Ulugbek Baymuradov, NYGC ALS Consortium, Noémie Elhadad, Karthik Natarajan & Gamze Gürsoy

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  • Alzheimer's & Dementia  ·  August 30, 2024

    Bridging the gap: Multi-omics profiling of brain tissue in Alzheimer’s disease and older controls in multi-ethnic populations.

    Joseph S. Reddy, Laura Heath, Abby Vander Linden, Mariet Allen, Katia de Paiva Lopes, Fatemeh Seifar, Erming Wang, Yiyi Ma, William L. Poehlman, Zachary S. Quicksall, Alexi Runnels, Yanling Wang, Duc M. Duong, Luming Yin, Kaiming Xu, Erica S. Modeste, Anantharaman Shantaraman, Eric B. Dammer, Lingyan Ping, Stephanie R. Oatman, Jo Scanlan, Charlotte Ho, Minerva M. Carrasquillo, Merve Atik, Geovanna Yepez, Adriana O. Mitchell, Thuy T. Nguyen, Xianfeng Chen, David X. Marquez, Hasini Reddy, Harrison Xiao, Sudha Seshadri, Richard Mayeux, Stefan Prokop, Edward B. Lee, Geidy E. Serrano, Thomas G. Beach, Andrew F. Teich, Varham Haroutunian, Edward J. Fox, Marla Gearing, Aliza Wingo, Thomas Wingo, James J. Lah, Allan I. Levey, Dennis W. Dickson, Lisa L. Barnes, Philip De Jager, Bin Zhang, David Bennett, Nicholas T. Seyfried, Anna K. Greenwood, Nilüfer Ertekin-Taner

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  • bioRxiv  ·  August 27, 2024  ·  Preprint

    Type 1 interferon perturbates clonal competition by reshaping human blood development.

    Chhiring Lama, Danielle Isakov, Shira Rosenberg, Miguel Quijada-Alamo, Mirca S Saurty-Seerunghen, Sara Moein, Tsega-Ab Abera, Olivia Sakaguchi, Mansi Totwani, Grace Freed, Chi-Lam Poon, Neelang Parghi, Andrea Kubas-Meyer, Amy X. Xie, Mohamed Omar, Daniel Choi, Franco Castillo-Tokumori, Ghaith Abu-Zeinah, Alicia Dillard, Nathaniel D Omans, Neville N Dusaj, Paulina Chamely, Eleni Mimitou, Peter Smibert, Heidi E. Kosiorek, Amylou C. Dueck, Rona Weinberg, Ronan Chaligne, Bridget Marcellino, Luigi Marchionni, Sanjay Patel, Paul D. Simonson, Dan A. Landau, Elvin Wagenblast, Ronald Hoffman, Anna S Nam

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  • bioRxiv  ·  August 19, 2024  ·  Preprint

    DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.

    Jimin Park, Daniel E. Cook, Pi-Chuan Chang, Alexey Kolesnikov, Lucas Brambrink, Juan Carlos Mier, Joshua Gardner, Brandy McNulty, Samuel Sacco, Ayse Keskus, Asher Bryant, Tanveer Ahmad, Jyoti Shetty, Yongmei Zhao, Bao Tran, Giuseppe Narzisi, Adrienne Helland, Byunggil Yoo, Irina Pushel, Lisa A. Lansdon, Chengpeng Bi, Adam Walter, Margaret Gibson, Tomi Pastinen, Midhat S. Farooqi, Nicolas Robine, Karen H. Miga, Andrew Carroll, Mikhail Kolmogorov, Benedict Paten, Kishwar Shafin

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  • Cell Reports  ·  August 16, 2024

    Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes.

    Platon Megagiannis, Yuan Mei, Rachel E Yan, Lin Yuan, Jonathan J Wilde, Hailey Eckersberg, Rahul Suresh, Xinzhu Tan, Hong Chen, W Todd Farmer, Kuwook Cha, Phuong Uyen Le, Helene Catoire, Daniel Rochefort, Tony Kwan, Brian A Yee, Patrick Dion, Arjun Krishnaswamy, Jean-Francois Cloutier, Stefano Stifani, Kevin Petrecca, Gene W Yeo, Keith K Murai, Guoping Feng, Guy A Rouleau, Trey Ideker, Neville E Sanjana, Yang Zhou

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  • Cell  ·  August 8, 2024

    Multiplexed single-cell characterization of alternative polyadenylation regulators.

    Madeline H Kowalski, Hans-Hermann Wessels, Johannes Linder, Carol Dalgarno, Isabella Mascio, Saket Choudhary, Austin Hartman, Yuhan Hao, Anshul Kundaje, Rahul Satija

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  • Muscle & Nerve  ·  August 9, 2024

    Mitochondrial genome variants associated with amyotrophic lateral sclerosis and their haplogroup distribution.

    Marcelo R. S. Briones PhD, João H. Campos PhD, Renata C. Ferreira PhD, Lisa Schneper PhD, Ilda M. Santos MSc, Fernando M. Antoneli PhD, NYGC ALS Consortium, James R. Broach PhD

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  • Nature Communications  ·  August 8, 2024

    Multi-omic analysis of Huntington’s disease reveals a compensatory astrocyte state.

    Fahad Paryani, Ji-Sun Kwon, Christopher W. Ng, Kelly Jakubiak, Nacoya Madden, Kenneth Ofori, Alice Tang, Hong Lu, Shengnan Xia, Juncheng Li, Aayushi Mahajan, Shawn M. Davidson, Anna O. Basile, Caitlin McHugh, Jean Paul Vonsattel, Richard Hickman, Michael C. Zody, David E. Housman, James E. Goldman, Andrew S. Yoo, Vilas Menon & Osama Al-Dalahmah

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  • Scientific Reports  ·  August 1, 2024

    A methylation risk score for chronic kidney disease: a HyperGEN study.

    Alana C. Jones, Amit Patki, Vinodh Srinivasasainagendra, Bertha A. Hidalgo, Hemant K. Tiwari, Nita A. Limdi, Nicole D. Armstrong, Ninad S. Chaudhary, Bré Minniefield, Devin Absher, Donna K. Arnett, Leslie A. Lange, Ethan M. Lange, Bessie A. Young, Clarissa J. Diamantidis, Stephen S. Rich, Josyf C. Mychaleckyj, Jerome I. Rotter, Kent D. Taylor, Holly J. Kramer, Russell P. Tracy, Peter Durda, Silva Kasela, Tuuli Lappalinen, Yongmei Liu, W. Craig Johnson, David J. Van Den Berg, Nora Franceschini, Simin Liu, Charles P. Mouton, Parveen Bhatti, Steve Horvath, Eric A. Whitsel & Marguerite R. Irvin

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