• Nature Genetics  ·  November 9, 2023

    Most large structural variants in cancer genomes can be detected without long reads.

    Zi-Ning ChooJulie M. BehrAditya Deshpande, Kevin HadiXiaotong YaoHuasong Tian, Kaori Takai, George Zakusilo, Joel Rosiene, Arnaud Da Cruz Paula, Britta Weigelt, Jeremy Setton, Nadeem Riaz, Simon N. Powell, Klaus Busam, Alexander N. Shoushtari, Charlotte Ariyan, Jorge Reis-Filho, Titia de Lange & Marcin Imieliński

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  • bioRxiv  ·  November 1, 2023  ·  Pre-Print

    Small variant benchmark from a complete assembly of X and Y chromosomes.

    Justin Wagner, Nathan D. Olson, Jennifer McDaniel, Lindsay Harris, Brendan J. Pinto, David Jáspez, Adrián Muñoz-Barrera, Luis A. Rubio-Rodríguez, José M. Lorenzo-Salazar, Carlos Flores, Sayed Mohammad Ebrahim Sahraeian, Giuseppe Narzisi, Marta Byrska-Bishop, Uday S Evani, Chunlin Xiao, Juniper A. Lake, Peter Fontana, Craig Greenberg, Donald Freed, Paul C. Boutros, Mohammed Faizal Eeman Mootor, Lisa Murray, Kishwar Shafin, Andrew Carroll, Fritz J Sedlazeck, Melissa Wilson, Justin M. Zook

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  • bioRxiv  ·  October 27, 2023  ·  Pre-Print

    AlphaMissense is better correlated with functional assays of missense impact than earlier prediction algorithms.

    Alicia Ljungdahl, Sayeh Kohani, Nicholas F. Page, Eloise S. Wells, Emilie M. Wigdor, Shan Dong, Stephan J. Sanders

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  • Frontiers in Immunology  ·  October 24, 2023

    Heterozygote advantage at HLA class I and II loci and reduced risk of colorectal cancer.

    Ya-Yu Tsai, Chenxu Qu, Joseph D Bonner, Rebeca Sanz-Pamplona, Sidney S Lindsey, Marilena Melas, Kevin J McDonnell, Gregory E Idos, Christopher P Walker, Kevin K Tsang, Diane M Da Silva, Ferran Moratalla-Navarro, Asaf Maoz, Hedy S Rennert, W Martin Kast, Joel K Greenson, Victor Moreno, Gad Rennert, Stephen B Gruber, Stephanie L Schmit

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  • bioRxiv  ·  October 20, 2023  ·  Pre-Print

    LKB1 suppresses growth and promotes the internalization of EGFR through the PIKFYVE lipid kinase.

    John Ferrarone, Jerin Thomas, Arun Unni, Yuxiang Zheng, Michal Nagiec, Eric Gardner, Oksana Mashadova, Kate Li, Nikos Koundouros, Antonino Montalbano, Meer Mustafa, Lewis Cantley, John Blenis, Neville Sanjana, Harold Varmus

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  • bioRxiv  ·  October 17, 2023  ·  Pre-Print

    Detecting significantly recurrent genomic connections from simple and complex rearrangements in the cancer genome.

    Shu Zhang, Kiran H Kumar, Ofer Shapira, Xiaotong Yao, Jeremiah Wala, Frank Dubois, Rose Gold, James E. Haber, Andrew Cherniack, Marcin Imielinski, Simona Dalin, Rameen Beroukhim

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  • bioRxiv  ·  October 12, 2023  ·  Pre-Print

    A sequence context-based germline filter for structural variant calling from tumor samples without paired normal.

    Wolu Chukwu, Siyun Lee, Alex Crane, Shu Zhang, Ipsa Mittra, Marcin Imieliński, Rameen Beroukhim, Frank Dubois, Simona Dalin

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  • Molecular Psychiatry  ·  October 5, 2023

    Astrocytic β-catenin signaling via TCF7L2 regulates synapse development and social behavior.

    Lukasz Mateusz Szewczyk, Marcin Andrzej Lipiec, Ewa Liszewska, Ksenia Meyza, Joanna Urban-Ciecko, Ludwika Kondrakiewicz, Anna Goncerzewicz, Kamil Rafalko, Tomasz Grzegorz Krawczyk, Karolina Bogaj, Ilia Davidovich Vainchtein, Hiromi Nakao-Inoue, Alicja Puscian, Ewelina Knapska, Stephan J. Sanders, Tomasz Jan Nowakowski, Anna Victoria Molofsky & Marta Barbara Wisniewska

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  • The American Journal of Human Genetics  ·  October 5, 2023

    Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed whole-genome sequencing study.

    Yuxuan Wang, Margaret Sunitha Selvaraj, Xihao Li, Zilin Li, Jacob A. Holdcraft, Donna K. Arnett, Joshua C. Bis, John Blangero, Eric Boerwinkle, Donald W. Bowden, Brian E. Cade, Jenna C. Carlson, April P. Carson, Yii-Der Ida Chen, Joanne E. Curran, Paul S. de Vries, Susan K. Dutcher, Patrick T. Ellinor, James S. Floyd, Myriam Fornage, Barry I. Freedman, Stacey Gabriel, Soren Germer, Richard A. Gibbs, Xiuqing Guo, Jiang He, Nancy Heard-Costa, Bertha Hildalgo, Lifang Hou, Marguerite R. Irvin, Roby Joehanes, Robert C. Kaplan, Sharon LR. Kardia, Tanika N. Kelly, Ryan Kim, Charles Kooperberg, Brian G. Kral, Daniel Levy, Changwei Li, Chunyu Liu, Don Lloyd-Jone, Ruth JF. Loos, Michael C. Mahaney, Lisa W. Martin, Rasika A. Mathias, Ryan L. Minster, Braxton D. Mitchell, May E. Montasser, Alanna C. Morrison, Joanne M. Murabito, Take Naseri, Jeffrey R. O’Connell, Nicholette D. Palmer, Michael H. Preuss, Bruce M. Psaty, Laura M. Raffield, Dabeeru C. Rao, Susan Redline, Alexander P. Reiner, Stephen S. Rich, Muagututi’a Sefuiva Ruepena, Wayne H.-H. Sheu, Jennifer A. Smith, Albert Smith, Hemant K. Tiwari, Michael Y. Tsai, Karine A. Viaud-Martinez, Zhe Wang, Lisa R. Yanek, Wei Zhao, Jerome I. Rotter, Xihong Lin, Pradeep Natarajan, Gina M. Peloso

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  • The American Journal of Human Genetics  ·  October 5, 2023

    Heterozygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction.

    Xi Shi, Congyi Lu, Alba Corman, Alexandra Nikish, Yang Zhou, Randy J. Platt, Ivan Iossifov, Feng Zhang, Jen Q. Pan, Neville E. Sanjana

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  • bioRxiv  ·  October 2, 2023

    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, GTAC Investigators, David B Goldstein, Matthew B Harms

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  • Acta Neuropathologica Communications  ·  September 28, 2023

    Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas.

    Vladimir Amani, Kent A. Riemondy, Rui Fu, Andrea M. Griesinger, Enrique Grimaldo, Graziella Ribeiro De Sousa, Ahmed Gilani, Molly Hemenway, Nicholas K. Foreman, Andrew M. Donson & Nicholas Willard

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  • Nature Immunology  ·  September 21, 2023

    Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection.

    Bingjie Zhang, Rabi Upadhyay, Yuhan Hao, Marie I. Samanovic, Ramin S. Herati, John D. Blair, Jordan Axelrad, Mark J. Mulligan, Dan R. Littman & Rahul Satija

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  • NPJ Precision Oncology  ·  September 13, 2023

    Evolution of structural rearrangements in prostate cancer intracranial metastases.

    Francesca Khani, William F. Hooper, Xiaofei Wang, Timothy R. Chu, Minita Shah, Lara Winterkorn, Michael Sigouros, Vincenza Conteduca, David Pisapia, Sara Wobker, Sydney Walker, Julie N. Graff, Brian Robinson, Juan Miguel Mosquera, Andrea Sboner, Olivier Elemento, Nicolas Robine & Himisha Beltran

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  • medRxiv  ·  September 12, 2023  ·  Pre-Print

    Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease.

    Alexandra C Martin Geary, Alexander JM Blakes, Ruebena Dawes, Scott D Findlay, View ORCID ProfileJenny C Lord, Susan Walker, Jonathan Talbot-Martin, Nechama Wieder, Elston N D’Souza, Maria Fernandes, Sarah Hilton, Nayana Lahiri, Christopher Campbell, Sarah Jenkinson, Christian GEL De Goede, Emily R Anderson, Christopher B Burge, Stephan J Sanders, Jamie Ellingford, Diana Baralle, Siddharth Banka, Nicola Whiffin

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  • bioRxiv  ·  September 12, 2023  ·  Pre-Print

    Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox.

    Megan D Schertzer, Andrew Stirn, Keren Isaev, Laura Pereira, Anjali Das, Claire Harbison, Stella H Park, Hans-Hermann Wessels, Neville E Sanjana, David A Knowles

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  • bioRxiv  ·  September 12, 2023  ·  Pre-Print

    Multi-OMIC analysis of Huntington disease reveals a neuroprotective astrocyte state.

    Fahad Paryani, Ji-Sun Kwon, Chris W Ng, Nacoya Madden, Kenneth Ofori, Alice Tang, Hong Lu, Juncheng Li, Aayushi Mahajan, Shawn M. Davidson, Anna Basile, Caitlin McHugh, Jean Paul Vonsattel, Richard Hickman, Michael Zody, David E. Houseman, James E. Goldman, Andrew E. Yoo, Vilas Menon, Osama Al-Dalahmah

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  • Cell Genomics  ·  September 6, 2023

    The functional impact of rare variation across the regulatory cascade.

    Taibo Li, Nicole Ferraro, Benjamin J. Strober, Francois Aguet, Silva Kasela, Marios Arvanitis, Bohan Ni, Laurens Wiel, Elliot Hershberg, Kristin Ardlie, Dan E. Arking, Rebecca L. Beer, Jennifer Brody, Thomas W. Blackwell, Clary Clish, Stacey Gabriel, Robert Gerszten, Xiuqing Guo, Namrata Gupta, W. Craig Johnson, Tuuli Lappalainen, Henry J. Lin, Yongmei Liu, Deborah A. Nickerson, George Papanicolaou, Jonathan K. Pritchard, Pankaj Qasba, Ali Shojaie, Josh Smith, Nona Sotoodehnia, Kent D. Taylor, Russell P. Tracy, David Van Den Berg, Matthew T. Wheeler, Stephen S. Rich, Jerome I. Rotter, Alexis Battle, Stephen B. Montgomery

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  • Briefing in Bioinformatics  ·  August 30, 2023

    SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data.

    Lindsay Lee, Miao Yu, Xiaoqi Li, Chenxu Zhu, Yanxiao Zhang, Hongyu Yu, Ziyin Chen, Shreya Mishra, Bing Ren, Yun Li, Ming Hu

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  • NPJ Digital Medicine  ·  August 21, 2023

    Deep learning based phenotyping of medical images improves power for gene discovery of complex disease.

    Brianna I. Flynn, Emily M. Javan, Eugenia Lin, Zoe Trutner, Karl Koenig, Kenoma O. Anighoro, Eucharist Kun, Alaukik Gupta, Tarjinder Singh, Prakash Jayakumar & Vagheesh M. Narasimhan

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