• 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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  • Cell  ·  June 20, 2024

    Multiplexed single-cell characterization of alternative polyadenylation regulators.

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

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  • Developmental Cell  ·  June 14, 2024

    Identifying FUS amyotrophic lateral sclerosis disease signatures in patient dermal fibroblasts.

    Karl Kumbier, Maike Roth, Zizheng Li, Julia Lazzari-Dean, Christopher Waters, Sabrina Hammerlindl, Capria Rinaldi, Ping Huang, Vladislav A. Korobeynikov, New York Genome Center ALS Consortium, Hemali Phatnani, Neil Shneider, Matthew P. Jacobson, Lani F. Wu, Steven J. Altschuler

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  • bioRxiv  ·  June 12, 2024  ·  Preprint

    Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database.

    Sanna Gudmundsson, Moriel Singer-Berk, Sarah L. Stenton, Julia K. Goodrich, Michael W. Wilson, Jonah Einson, Nicholas A Watts, Genome Aggregation Database Consortium, Tuuli Lappalainen, Heidi L. Rehm, Daniel G. MacArthur, Anne O’Donnell-Luria

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  • Nature Medicine  ·  June 14, 2024

    Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment.

    Adam J. Widman, Minita Shah, Amanda Frydendahl, Daniel Halmos, Cole C. Khamnei, Nadia Øgaard, Srinivas Rajagopalan, Anushri Arora, Aditya Deshpande, William F. Hooper, Jean Quentin, Jake Bass, Mingxuan Zhang, Theophile Langanay, Laura Andersen, Zoe Steinsnyder, Will Liao, Mads Heilskov Rasmussen, Tenna Vesterman Henriksen, Sarah Østrup Jensen, Jesper Nors, Christina Therkildsen, Jesus Sotelo, Ryan Brand, Joshua S. Schiffman, Ronak H. Shah, Alexandre Pellan Cheng, Colleen Maher, Lavinia Spain, Kate Krause, Dennie T. Frederick, Wendie den Brok, Caroline Lohrisch, Tamara Shenkier, Christine Simmons, Diego Villa, Andrew J. Mungall, Richard Moore, Elena Zaikova, Viviana Cerda, Esther Kong, Daniel Lai, Murtaza S. Malbari, Melissa Marton, Dina Manaa, Lara Winterkorn, Karen Gelmon, Margaret K. Callahan, Genevieve Boland, Catherine Potenski, Jedd D. Wolchok, Ashish Saxena, Samra Turajlic, Marcin Imielinski, Michael F. Berger, Sam Aparicio, Nasser K. Altorki, Michael A. Postow, Nicolas Robine, Claus Lindbjerg Andersen & Dan A. Landau

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  • Cell Reports  ·  June 7, 2024

    Five autism-associated transcriptional regulators target shared loci proximal to brain-expressed genes.

    Siavash Fazel Darbandi, Joon-Yong An, Kenneth Lim, Nicholas F. Page, Lindsay Liang, David M. Young, Athena R. Ypsilanti, Matthew W. State, Alex S. Nord, Stephan J. Sanders, John L.R. Rubenstein

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  • The New England Journal of Medicine  ·  June 5, 2024

    Genome Sequencing for Diagnosing Rare Diseases.

    Monica H Wojcik, Gabrielle Lemire, Eva Berger, Maha S Zaki, Mariel Wissmann, Wathone Win, Susan M White, Ben Weisburd, Dagmar Wieczorek, Leigh B Waddell, Jeffrey M Verboon, Grace E VanNoy, Ana Töpf, Tiong Yang Tan, Steffen Syrbe, Vincent Strehlow, Volker Straub, Sarah L Stenton, Hana Snow, Moriel Singer-Berk, Josh Silver, Shirlee Shril, Eleanor G Seaby, Ronen Schneider, Vijay G Sankaran, Alba Sanchis-Juan, Kathryn A Russell, Karit Reinson, Gianina Ravenscroft, Maximilian Radtke, Denny Popp, Tilman Polster, Konrad Platzer, Eric A Pierce, Emily M Place, Sander Pajusalu, Lynn Pais, Katrin Õunap, Ikeoluwa Osei-Owusu, Henry Opperman, Volkan Okur, Kaisa Teele Oja, Melanie O’Leary, Emily O’Heir, Chantal F Morel, Andreas Merkenschlager, Rhett G Marchant, Brian E Mangilog, Jill A Madden, Daniel MacArthur, Alysia Lovgren, Jordan P Lerner-Ellis, Jasmine Lin, Nigel Laing, Friedhelm Hildebrandt, Julia Hentschel, Emily Groopman, Julia Goodrich, Joseph G Gleeson, Roula Ghaoui, Casie A Genetti, Janina Gburek-Augustat, Hanna T Gazda, Vijay S Ganesh, Mythily Ganapathi, Lyndon Gallacher, Jack M Fu, Emily Evangelista, Eleina England, Sandra Donkervoort, Stephanie DiTroia, Sandra T Cooper, Wendy K Chung, John Christodoulou, Katherine R Chao, Liam D Cato, Kinga M Bujakowska, Samantha J Bryen, Harrison Brand, Carsten G Bönnemann, Alan H Beggs, Samantha M Baxter, Tobias Bartolomaeus, Pankaj B Agrawal, Michael Talkowski, Christina Austin-Tse, Rami Abou Jamra, Heidi L Rehm, Anne O’Donnell-Luria.

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  • Nature Reviews Molecular Cell Biology  ·  June 4, 2024

    SenNet recommendations for detecting senescent cells in different tissues.

    Vidyani Suryadevara, Adam D. Hudgins, Adarsh Rajesh, Alberto Pappalardo, Alla Karpova, Amit K. Dey, Ann Hertzel, Anthony Agudelo, Azucena Rocha, Bikem Soygur, Birgit Schilling… Francesco Cambuli, Gagandeep Kaur, George A. Kuchel, Gung Lee, Heike E. Daldrup-Link, Helene Martini, Hemali Phatnani, Iman M. Al-Naggar, Irfan Rahman, Jia Nie, João F. Passos, Jonathan C. Silverstein, Judith Campisi, Julia Wang, Kanako Iwasaki, Karina Barbosa, Kay Metis, Kerem Nernekli, Laura J. Niedernhofer, Li Ding, Lichao Wang, Lisa C. Adams, Liu Ruiyang, Madison L. Doolittle, Marcos G. Teneche, Marissa J. Schafer, Ming Xu, Mohammadjavad Hajipour, Mozhgan Boroumand, Nathan Basisty, Nicholas Sloan, Nikolai Slavov, Olena Kuksenko, Paul Robson, Paul T. Gomez, Periklis Vasilikos, Peter D. Adams, Priscila Carapeto, Quan Zhu, Ramalakshmi Ramasamy, Rolando Perez-Lorenzo, Rong Fan, Runze Dong, Ruth R. Montgomery, Sadiya Shaikh, Sanja Vicković … Nicola Neretti

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  • bioRxiv  ·  May 31, 2024  ·  Preprint

    Systems genomics of salinity stress response in rice.

    Sonal Gupta, Simon C. Groen, Maricris L. Zaidem, Andres Godwin C. Sajise, Irina Calic, Mignon A. Natividad, Kenneth L. McNally, Georgina V. Vergara, Rahul Satija, Steven J. Franks, Rakesh K. Singh, Zoé Joly-Lopez, Michael D. Purugganan

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  • Genetics in Medicine  ·  May 30, 2024

    Laboratory testing for preconception/prenatal carrier screening: A technical standard of the American College of Medical Genetics and Genomics (ACMG).

    Saurav Guha, Honey V. Reddi, Mahmoud Aarabi, Marina DiStefano, Erin Wakeling, Jeffrey S. Dungan, Anthony R. Gregg on behalf of the ACMG Laboratory Quality Assurance Committee

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  • Biological Psychiatry  ·  May 29, 2024

    Omics approaches to investigate the pathogenesis of suicide.

    Maura Boldrini, Yang Xiao, Tarjinder Singh, Chenxu Zhu, Mbemba Jabbi, Harry Pantazopoulos, Gamze Gürsoy, Keri Martinowich, Giovanna Punzi, Eric J. Vallender, Michael Zody, Sabina Berretta, Thomas M. Hyde, Joel E. Kleinman, Stefano Marenco, Panagiotis Roussos, David A. Lewis, Gustavo Turecki, Thomas Lehner, J. John Mann

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  • bioRxiv  ·  May 23, 2024  ·  Preprint

    Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts.

    Dennis J Yuan, John Zinno, Theo Botella, Dalia Dhingra, Shu Wang, Allegra Hawkins, Ariel Swett, Jesus Sotelo, Ramya Raviram, Clayton Hughes, Catherine Potenski, Akira Yokoyama, Nobuyuki Kakiuchi, Seishi Ogawa, Dan A Landau

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  • Biology  ·  May 15, 2024

    1,25-Dihydroxyvitamin D3 Suppresses Prognostic Survival Biomarkers Associated with Cell Cycle and Actin Organization in a Non-Malignant African American Prostate Cell Line.

    Jabril R Johnson, Rachel N Martini, Yate-Ching Yuan, Leanne Woods-Burnham, Mya Walker, Greisha L Ortiz-Hernandez, Firas Kobeissy, Dorothy Galloway, Amani Gaddy, Chidinma Oguejiofor, Blake Allen, Deyana Lewis, Melissa B Davis, K Sean Kimbro, Clayton C Yates, Adam B Murphy, Rick A Kittles

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  • bioRxiv  ·  May 20, 2024  ·  Preprint

    Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome.

    Saravanan Ganesan, Rebecca M. Murray, Jesus Sotelo, Elliot O Eton, Kouhei Takashima, Theo Botella, Kai Beattie, Alyssa C. Indart, Nada Chraiki, Carolyne Croizier, Franco Izzo, Catherine Potenski, Samuele Marro, Zhijie Wu, Shouguo Gao, Neal S. Young, John D. Blair, Rahul Satija, Benjamin Terrier, Mael Heiblig, Eirini P Papapetrou, Pierre Sujobert, Olivier Kosmider, David B. Beck and Dan A Landau

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  • bioRxiv  ·  May 14, 2024  ·  Preprint

    Low copy CRISPR-Cas13d mitigates collateral RNA cleavage.

    Sydney K. Hart, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Simon Müller, Gediminas Drabavicius, Olivia Choi, Neville E. Sanjana

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  • Proceedings of the National Academy of Sciences of the United States of America  ·  May 14, 2024

    Genome-wide CRISPR screens in spheroid culture reveal that the tumor suppressor LKB1 inhibits growth via the PIKFYVE lipid kinase.

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

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