• 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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  • bioRxiv  ·  July 19, 2024  ·  Preprint

    ALS molecular subtypes are a combination of cellular, genetic, and pathological features learned by deep multiomics classifiers.

    Kathryn ONeill, Regina Shaw, Isobel Bolger, NYGC ALS Consortium, Oliver H Tam, Hemali Phatnani, Molly Gale Hammell

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  • Genome Biology  ·  July 18, 2024

    Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE.

    Alsu Missarova, Emma Dann, Leah Rosen, Rahul Satija & John Marioni

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  • American Journal of Human Genetics  ·  July 11, 2024

    The DARC side of genetics in cancer: Breast cancer disparities.

    Rachel Martini, Melissa B. Davis

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  • The EMBO Journal  ·  July 1, 2024

    YTHDC1 m6A-dependent and m6A-independent functions converge to preserve the DNA damage response.

    Daniel Elvira-Blázquez, José Miguel Fernández-Justel, Aida Arcas, Luisa Statello, Enrique Goñi, Jovanna González, Benedetta Ricci, Sara Zaccara, Ivan Raimondi, Maite Huarte

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  • Chest Journal  ·  June 28, 2024

    Clinical Impact of Telomere Length Testing for Interstitial Lung Disease.

    David Zhang, Christina M Eckhardt, Claire McGroder, Shannon Benesh, Julie Porcelli, Christopher Depender, Kelsie Bogyo, Joseph Westrich, Amanda Thomas-Wilson, Vaidehi Jobanputra, Christine K Garcia

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  • BMC Genomics  ·  June 29, 2024

    Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies ANTXR2 as a candidate in PLS.

    Tess D. Pottinger, Joshua E. Motelow, Gundula Povysil, Cristiane A. Martins Moreno, Zhong Ren, Hemali Phatnani, The New York Genome Center ALS Sequencing Consortium, Timothy J. Aitman, Javier Santoyo-Lopez, Scottish Genomes Partnership, Hiroshi Mitsumoto, ALS COSMOS Study Group, PLS COSMOS Study Group, GTAC Investigators, David B. Goldstein & Matthew B. Harms

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  • Journal of Biomedical Informatics  ·  June 25, 2024

    Privacy-preserving model evaluation for logistic and linear regression using homomorphically encrypted genotype data.

    Seungwan Hong, Yoolim A Choi, Daniel S Joo, Gamze Gürsoy

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  • Bioinformatics  ·  June 20, 2024

    SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis.

    Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F Miller, Rahul Satija, John W Hickey, Jean Fan

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