• bioRxiv  ·  July 2, 2025  ·  Preprint

    Perplexity as a Metric for Isoform Diversity in the Human Transcriptome.

    Megan D Schertzer, Stella H Park, Jiayu Su, Gloria M Sheynkman, David A Knowles

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  • Nature  ·  July 2, 2025

    The Somatic Mosaicism across Human Tissues Network.

    Tim H. H. Coorens, Ji Won Oh, Yujin Angelina Choi, Nam Seop Lim, Boxun Zhao, Adam Voshall, Alexej Abyzov, Lucinda Antonacci-Fulton, Samuel Aparicio, Kristin G. Ardlie, Thomas J. Bell, James T. Bennett, Bradley E. Bernstein, Thomas G. Blanchard, Alan P. Boyle, Jason D. Buenrostro, Kathleen H. Burns, Fei Chen, Rui Chen, Sangita Choudhury, Harsha V. Doddapaneni, Evan E. Eichler, Gilad D. Evrony, Melissa A. Faith, Thomas G. Fazzio, Robert S. Fulton, Manuel Garber, Nils Gehlenborg, Soren Germer, Gad Getz, Richard A. Gibbs, Raquel G. Hernandez, Fulai Jin, Jan O. Korbel, Dan A. Landau, Heather A. Lawson, Niall J. Lennon, Heng Li, Yan Li, Po-Ru Loh, Gabor Marth, Michael J. McConnell, Ryan E. Mills, Stephen B. Montgomery, Pradeep Natarajan, Peter J. Park, Rahul Satija, Fritz J. Sedlazeck, Diane D. Shao, Hui Shen, Andrew B. Stergachis, Hunter R. Underhill, Alexander E. Urban, Melissa W. VonDran, Christopher A. Walsh, Ting Wang, Tao P. Wu, Chenghang Zong, Eunjung Alice Lee, Flora M. Vaccarino & The Somatic Mosaicism across Human Tissues Network

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  • Nature Communications  ·  July 1, 2025

    Shared genetic architecture of posttraumatic stress disorder with cardiovascular imaging, risk, and diagnoses.

    Jie Shen, Wander Valentim, Eleni Friligkou, Cassie Overstreet, Karmel W. Choi, Dora Koller, Christopher J. O’Donnell, Murray B. Stein, Joel Gelernter, Posttraumatic Stress Disorder Working Group of the Psychiatric Genomics Consortium, Haitao Lv, Ling Sun, Guido J. Falcone, Renato Polimanti & Gita A. Pathak

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  • Nature Medicine  ·  June 27, 2025

    A reference model of circulating hematopoietic stem cells across the lifespan with applications to diagnostics.

    N. Furer, N. Rappoport, O. Milman, S. Tavor, A. Lifshitz, A. Bercovich, O. Ben-Kiki, A. Danin, M. Kedmi, Z. Shipony, D. Lipson, E. Meiri, G. Yanai, S. Shapira, N. Arber, S. Berdichevsky, J. Tyner, S. Joshi, D. Landau, S. Ganesan, N. Dusaj, P. Chamely, N. Kaushansky, N. Chapal-Ilani, R. Shamir, A. Tanay & L. Shlush

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  • The Lancet Psychiatry  ·  June 26, 2025

    The Psychiatric Genomics Consortium: discoveries and directions.

    Arpana Agrawal, Cynthia M Bulik, Dawit Shawel Abebe, Ole A Andreassen, Elizabeth G Atkinson, Karmel W Choi, Aiden Corvin, Helena L Davies, Lea K Davis, Anna R Docherty, Howard J Edenberg, Barbara Franke, Joel Gelernter, Paola Giusti-Rodríguez, John M Hettema, Jens Hjerling-Leffler, Hailiang Huang, Emma C Johnson, Cathryn M Lewis, Yi Lu, Mary-Ellen Lynall, Joanna Martin, Andrew M McIntosh, Janitza L Montalvo-Ortiz, Niamh Mullins, Caroline M Nievergelt, Kevin S O’Connell, Michael C O’Donovan, Adeniran Okewole, Roseann E Peterson, Danielle Posthuma, Jonathan Sebat, Jordan W Smoller, Reeteka Sud, Biju Viswanath, James T R Walters, Hyejung Won, Naomi R Wray, Patrick F Sullivan; Coordinating Committee of the Psychiatric Genomics Consortium

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  • medRxiv  ·  June 17, 2025  ·  Preprint

    FUS Mislocalization Rewires a Cortical Gene Network to Drive Cognitive and Behavioral Impairment in ALS.

    Raphaelle Cassel, Félicie Lorenc, Aurélie Bombardier, Claudia De Tapia, Stéphane Dieterle, Cláudio Gouveia Roque, Christopher A. Jackson, Geoffrey Stuart-Lopez, Caroline Rouaux, Simon J. Guillot, Marie-Christine Birling, Pascal Kessler, Maurizio Grassano, Bryan Traynor, Adriano Chio, Raju Roy, James Shorter, Fergal M. Waldron, Jenna M. Gregory, Hemali Phatnani, Luc Dupuis, Salim Megat

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  • Prenatal Diagnosis  ·  June 12, 2025

    Prenatally Detected Maternally Inherited Partial Duplication of 11p15.5 ICR1 Results in Phenotypes Overlapping Russell-Silver Syndrome in Infancy.

    Amanda Thomas-Wilson, Mythily Ganapathi, Nina Harkavy, Corbin Schwanke, Jessica Giordano, Abdallah F. Elias, Ronald J. Wapner, Vaidehi Jobanputra

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  • medRxiv  ·  June 11, 2025  ·  Preprint

    GXwasR: A Toolkit for Investigating Sex-Differentiated Genetic Effects on Complex Traits.

    Banabithi Bose, Freida Bolstein, Jeewoo Kim, Jessica Winters, Ky’Era Actkins, David Mayer, Maria Niarchou, Harrshavasan T.S Congivaram, Digna R Velez Edwards, Lea Davis, Barbara Stranger

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  • Alzheimer's & Dementia  ·  June 11, 2025

    GWAS links APOE to neuropsychiatric symptoms in mild cognitive impairment and dementia

    Selina M. Vattathil, Freida Blostein, Tyne W. Miller-Fleming, Lea K. Davis, Alzheimer’s Disease Genetics Consortium (ADGC), Alzheimer’s Disease Neuroimaging Initiative, Thomas S. Wingo, Aliza P. Wingo

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  • medRxiv  ·  June 10, 2025  ·  Preprint

    Unraveling temporal dynamics of the post-mortem transcriptome in amyotrophic lateral sclerosis.

    Ting Shen, Barbara E. Spencer, Pavel P. Kuksa, Vivianna M. Van Deerlin, Hemali Phatnani, NYGC ALS Consortium, Edward B. Lee, Corey T. McMillan

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  • medRxiv  ·  June 4, 2025  ·  Preprint

    Mosaic chromosomal alterations in blood are associated with an increased risk of Alzheimer’s disease.

    Tatsuhiko Naito, Kosei Hirata, Beomjin Jang, Chirag M. Lakhani, Alice Buonfiglioli, Wan-Ping Lee, Otto Valladares, Li-San Wang, Yukinori Okada, Hong-Hee Won, Eirini P. Papapetrou, Samuele G. Marro, David A. Knowles, Towfique Raj

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  • medRxiv  ·  June 2, 2025  ·  Preprint

    Omic Risk Scores are Associated with COPD-related Traits Across Three Cohorts.

    Iain R Konigsberg, Luciana B Vargas, Katherine A Pratte, Daniel E Guzman, Tess D Pottinger, Kristina L Buschur, Thomas W Blackwell, Yongmei Liu, Kent D Taylor, W Craig Johnson, Peter Durda, Russell P Tracy, Ani Manichaikul, Elizabeth C Oelsner, Stacey Gabriel, Namrata Gupta, Suna Onengut-Gumuscu, Joshua D Smith, Francois Aguet, Kristin Ardlie, Usman A Tahir, Robert E Gerszten, Clary Clish, Eugene R Bleecker, Deborah A Meyers, Victor E Ortega, Stephanie A Christenson, Dawn L DeMeo, Brian D Hobbs, Craig P Hersh, Peter J Castaldi, Jeffrey L Curtis, R Graham Barr, Jerome I Rotter, Stephen S Rich, Prescott G Woodruff, Edwin K Silverman, Michael H Cho, Katerina J Kechris, Russell P Bowler, Ethan M Lange, Leslie A Lange, Matthew R Moll, on behalf of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium

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  • Science  ·  May 29, 2025

    Predicting expression-altering promoter mutations with deep learning.

    Kishore Jaganathan, Nicole Ersaro, Gherman Novakovsky, Yuchuan Wang, Terena James, Jeremy Schwartzentruber, Petko Fiziev, Irfahan Kassam, Fan Cao, Johann Hawe, Henry Cavanagh, Ashley Lim, Grace Png, Jeremy McRae, Abhimanyu Banerjee, Arvind Kumar, Jacob Ulirsch, Yan Zhang, Francois Aguet, Pierrick Wainschtein, Laksshman Sundaram, Adriana Salcedo, Sofia Kyriazopoulou Panagiotopoulou, Delasa Aghamirzaie, Evin Padhi, Ziming Weng, Shan Dong, Damian Smedley, Mark Caulfield, Anne O’Donnell-Luria, Heidi L Rehm, Stephan J Sanders, Anshul Kundaje, Stephen B Montgomery, Mark T Ross, Kyle Kai-How Farh

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  • Nature Communications  ·  May 23, 2025

    Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity.

    Michael Kosicki, Dianne Laboy Cintrón, Pia Keukeleire, Max Schubach, Nicholas F. Page, Ilias Georgakopoulos-Soares, Jennifer A. Akiyama, Ingrid Plajzer-Frick, Catherine S. Novak, Momoe Kato, Riana D. Hunter, Kianna von Maydell, Sarah Barton, Patrick Godfrey, Erik Beckman, Stephan J. Sanders, Martin Kircher, Len A. Pennacchio & Nadav Ahituv

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  • AMIA Annual Proceedings Symposium Archive  ·  May 22, 2025

    Toward Identifying New Risk Aversions and Subsequent Limitations and Biases When Making De-identified Structured Data Sets Openly Available in a Post-LLM world.

    Fangyi Chen, Kenrick Cato, Gamze Gürsoy, Patricia C Dykes, Graham Lowenthal, Sarah Rossetti

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  • Cell Stem Cell  ·  May 22, 2025

    Deconvoluting clonal and cellular architecture in IDH-mutant acute myeloid leukemia.

    Maria Sirenko, Soobeom Lee, Zhengxi Sun, Ronan Chaligne, Sanam Loghavi, Georgios Asimomitis, Charlotte K Brierley, Elsa Bernard, Sheng F Cai, Robert M Myers, Bettina Nadorp, Junya Sango, Morgan Lallo, Max F Levine, Dylan Domenico, Juan E Arango Ossa, Juan S Medina-Martinez, Kamal Menghrajani, Audrey Lasry, Alice S Mims, Helee Desai, Andrea Laganson, Chris Famulare, Minal Patel, Gerard Lozanski, Kelly L Bolton, Aaron D Viny, Mikhail Roshal, Ross L Levine, Eirini P Papapetrou, Eytan M Stein, Dan A Landau, Ann-Kathrin Eisfeld, Iannis Aifantis, Elli Papaemmanuil.

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  • Nature Communications  ·  May 21, 2025

    APOBEC affects tumor evolution and age at onset of lung cancer in smokers.

    Tongwu Zhang, Jian Sang, Phuc H. Hoang, Wei Zhao, Jennifer Rosenbaum, Kofi Ennu Johnson, Leszek J. Klimczak, John McElderry, Alyssa Klein, Christopher Wirth, Erik N. Bergstrom, Marcos Díaz-Gay, Raviteja Vangara, Frank Colon-Matos, Amy Hutchinson, Scott M. Lawrence, Nathan Cole, Bin Zhu, Teresa M. Przytycka, Jianxin Shi, Neil E. Caporaso, Robert Homer, Angela C. Pesatori, Dario Consonni, Marcin Imieliński, Stephen J. Chanock, David C. Wedge, Dmitry A. Gordenin, Ludmil B. Alexandrov, Reuben S. Harris & Maria Teresa Landi

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  • Atherosclerosis  ·  May 20, 2025

    Epigenetic mechanisms underlying variation of IL-6, a well-established inflammation biomarker and risk factor for cardiovascular disease.

    Jessica I Lundin, Ulrike Peters, Yao Hu, Farah Ammous, Emelia J Benjamin, Joshua C Bis, Jennifer A Brody, Mary Cushman, Harriett Fuller, Chris Gignoux, Xiuqing Guo, Jeff Haessler, Chris Haiman, Roby Joehanes, Silva Kasela, Eimear Kenny, Tuuli Lappalainen, Daniel Levy, Chunyu Liu, Yongmei Liu, Ruth J F Loos, Tara Matise, Kari E North, Sungshim L Park, Scott M Ratliff, Alex Reiner, Stephen S Rich, Jerome I Rotter, Jennifer A Smith, Nona Sotoodehnia, Russell Tracy, David Van den Berg, Ting Ye, Wei Zhao, Laura M Raffield, Charles Kooperberg; PAGE Study

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  • Schizophrenia Research  ·  May 19, 2025

    Clinical Characteristics associated with functional seizures in individuals with psychosis.

    Allison M Lake, India A Reddy, Robert Havranek, Lea K Davis, Jonah Fox.

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  • bioRxiv  ·  May 16, 2025  ·  Preprint

    Single-Cell RNA Sequencing and Inferred Protein Activity Analysis Reveal a Distinct Tumor Phenotype in Early-Onset Colorectal Cancer Patients.

    David A Cohen, Aleksandar Obradovic, Luka Jovanovic, Yosuke Mitani, Tianxia Li, Soobeom Lee, Dechokyab De, Casidhe-Nicole Bethancourt, Alice Shin, Karen Dunbar, Francesco Cambuli, Christopher Lengner, Ning Li, Caitlin Rogers, Jennifer Ho, Viktoria Jakubikova, Emma Blystone, Yoanna Pumpalova, Beatrice Dionigi, Sanja Vicković, Chia-Wei Cheng, Joel Gabre

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  • Nature Genetics  ·  May 16, 2025

    Dominant variants in major spliceosome U4 and U5 small nuclear RNA genes cause neurodevelopmental disorders through splicing disruption.

    Caroline Nava, Benjamin Cogne, Amandine Santini, Elsa Leitão, François Lecoquierre, Yuyang Chen, Sarah L. Stenton, Thomas Besnard, Solveig Heide, Sarah Baer, Abhilasha Jakhar, Sonja Neuser, … Saurav Guha, Anne Guimier, Tobias B. Haack, Hamza Hadj Abdallah, Yosra Halleb, Radu Harbuz, Madeleine Harris, Julia Hentschel, Bénédicte Héron, Marc-Phillip Hitz, A. Micheil Innes, Vincent Jadas, Louis Januel, Nolwenn Jean-Marçais, Vaidehi Jobanputra, … Rami Abou Jamra, Delphine Héron, Cyril Mignot, Pierre Blanc, Anne O’Donnell-Luria, Nicola Whiffin, Camille Charbonnier, Clément Charenton, Julien Thevenon & Christel Depienne

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