• Nature Methods  ·  March 24, 2025

    Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability.

    Dongsheng Bai, Zhenkun Cao, Nivedita Attada, Jinghui Song & Chenxu Zhu

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  • bioRxiv  ·  March 20, 2025  ·  Preprint

    Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia.

    Ke Wang, Shayan Saniei, Nikita Poddar, Subrina Autar, Saul Carcamo, Meghana Sreenath, Jack H Peplinski, Rhonda E Ries, Isabella G Martinez, Clifford Chao, Anna Huo-Chang Mei, Noshin Rahman, Levan Mekerishvili, Miguel Quijada-Alamo, Grace Freed, Mimi Zhang, Katherine Lachman, Zayna Diaz, Manuel M Gonzalez, Jing Zhang, Giang Pham, Dan Filipescu, Mirela Berisa, Tommaso Balestra, Julie A Reisz, Angelo D’Alessandro, Daniel J Puleston, Emily Bernstein, Jerry E Chipuk, Mark Wunderlich, Sarah K Tasian, Bridget K Marcellino, Ian A Glass, BDRL, Christopher M Sturgeon, Dan A Landau, Zhihong Chen, Eirini P Papapetrou, Franco Izzo, Soheil Meshinchi, Dan Hasson, Elvin Wagenblast

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  • bioRxiv  ·  March 19, 2025  ·  Preprint

    Measuring Longitudinal Genome-wide Clonal Evolution of Pediatric Acute Lymphoblastic Leukemia at Single-Cell Resolution.

    Yakun Pang, Tamara Prieto, Veronica Gonzalez-Pena, Athena Aragon, Yuntao Xia, Sheng Kao, Sri Rajagopalan, John Zinno, Jean Quentin, Julien Laval, Dennis Yuan, Shulz Shawn, Nathaniel Omans, David Klein, Matthew MacKay, Iwijn De Vlaminck, John Easton, William Evans, Dan A. Landau, Charles Gawad

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  • Translational Oncology  ·  March 15, 2025

    Cardiotoxicity of breast cancer drug treatments.

    Maria Haque, Nehal Atallah, Rodhan Patke, Anna E Harris, Corinne L Woodcock, Dhruvika Varun, Rachel L Thompson, Jorja Jackson-Oxley, Cyntholia H Okui, Alexander Dean, Mansour Alsaleem, Emad Rakha, Sheeba Irshad, Melissa B Davis, Jennie N Jeyapalan, Nigel P Mongan, Catrin S Rutland

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  • Nature Methods  ·  March 13, 2025

    Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage.

    Katy Börner, Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo, Rahul Satija, Sarah A. Teichmann, Gloria J. Pryhuber, Ravi S. Misra, Jeffrey M. Purkerson, Jean Fan, John W. Hickey, Gesmira Molla, Chuan Xu, Yun Zhang, Griffin M. Weber, Yashvardhan Jain, Danial Qaurooni, Yongxin Kong, HRA Team, Andreas Bueckle & Bruce W. Herr II

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  • Cell Reports Methods  ·  March 12, 2025

    A sequence context-based approach for classifying tumor structural variants without paired normal samples.

    Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Sophie Webster, Oumayma Dakhama, Ipsa Mittra, Carlos Rauert, Marcin Imielinski, Rameen Beroukhim, Frank Dubois, Simona Dalin

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  • Cell Reports  ·  March 10, 2025

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

    Kathryn O’Neill, Regina Shaw, Isobel Bolger, NYGC ALS Consortium, Oliver H. Tam, Hemali Phatnani, Molly Gale Hammell

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  • Nature Communications  ·  March 10, 2025

    Secure and scalable gene expression quantification with pQuant.

    Seungwan Hong, Conor R. Walker, Yoolim A. Choi & Gamze Gürsoy

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  • medRxiv  ·  March 7, 2025  ·  Preprint

    SingleBrain: A Meta-Analysis of Single-Nucleus eQTLs Linking Genetic Risk to Brain Disorders.

    Beomjin Jang, Kailash BP, Alex Tokolyi, Winston H. Cuddleston, Ashvin Ravi, Sanghyuk Jung, Tatsuhiko Naito, Beomsu Kim, Min Seo Kim, Minyoung Cho, Mi-So Park, Mikaela Rosen, Joel Blanchard, Jack Humphrey, David A Knowles, Hong-Hee Won, Towfique Raj

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  • Nature Genetics  ·  March 7, 2025

    Comparison of the multivariate genetic architecture of eight major psychiatric disorders across sex.

    Ted Schwaba, Travis T. Mallard, Adam X. Maihofer, Mijke Rhemtulla, Phil H. Lee, Jordan W. Smoller, Lea K. Davis, Michel G. Nivard, Andrew D. Grotzinger & Elliot M. Tucker-Drob

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  • Nature Genetics  ·  March 6, 2025

    Sequencing in over 50,000 cases identifies coding and structural variation underlying atrial fibrillation risk.

    Seung Hoan Choi, Sean J. Jurgens, Ling Xiao, Matthew C. Hill, Christopher M. Haggerty, Garðar Sveinbjörnsson, Valerie N. Morrill, Nicholas A. Marston, Lu-Chen Weng, James P. Pirruccello, David O. Arnar, Daniel Fannar Gudbjartsson, Helene Mantineo, Aenne S. von Falkenhausen, Andrea Natale, Arnljot Tveit, Bastiaan Geelhoed, Carolina Roselli, David R. Van Wagoner, Dawood Darbar, Doreen Haase, Elsayed Z. Soliman, Giovanni E. Davogustto, Goo Jun, Hugh Calkins, Jeffrey L. Anderson, Jennifer A. Brody, Jennifer L. Halford, John Barnard, John E. Hokanson, Jonathan D. Smith, Joshua C. Bis, Kendra Young, Linda S. B. Johnson, Lorenz Risch, Lorne J. Gula, Lydia Coulter Kwee, Mark D. Chaffin, Michael Kühne, Michael Preuss, Namrata Gupta, Navid A. Nafissi, Nicholas L. Smith, Peter M. Nilsson, Pim van der Harst, Quinn S. Wells, Renae L. Judy, Renate B. Schnabel, Renee Johnson, Roelof A. J. Smit, Stacey Gabriel, Stacey Knight, Tetsushi Furukawa, Thomas W. Blackwell, Victor Nauffal, Xin Wang, Yuan-I Min, Zachary T. Yoneda, Zachary W. M. Laksman, Connie R. Bezzina, Alvaro Alonso, Bruce M. Psaty, Christine M. Albert, Dan E. Arking, Dan M. Roden, Daniel I. Chasman, Daniel J. Rader, David Conen, David D. McManus, Diane Fatkin, Emelia J. Benjamin, Eric Boerwinkle, Gregory M. Marcus, Ingrid E. Christophersen, J. Gustav Smith, Jason D. Roberts, Laura M. Raffield, M. Benjamin Shoemaker, Michael H. Cho, Michael J. Cutler, Michiel Rienstra, Mina K. Chung, Morten S. Olesen, Moritz F. Sinner, Nona Sotoodehnia, Paulus Kirchhof, Ruth J. F. Loos, Saman Nazarian, Sanghamitra Mohanty, Scott M. Damrauer, Stefan Kaab, Susan R. Heckbert, Susan Redline, Svati H. Shah, Toshihiro Tanaka, Yusuke Ebana, Regeneron Genetics Center, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Hilma Holm, Kari Stefansson, Christian T. Ruff, Marc S. Sabatine, Kathryn L. Lunetta, Steven A. Lubitz & Patrick T. Ellinor

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  • bioRxiv  ·  March 4, 2025  ·  Preprint

    Targeted BDNF upregulation via upstream open reading frame disruption.

    Ning Feng, Thomas Goedert, Nenad Svrzikapa, Dongnan Yan, Britt Hanson, Alicia Ljungdahl, Ruxandra Dafinca, Kevin Talbot, Stephan J Sanders, Dhanu Gupta, Matthew Wood, Thomas C Roberts

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  • bioRxiv  ·  March 3, 2025  ·  Preprint

    Inferring fungal cis-regulatory networks from genome sequences.

    Alan M. Moses, Jason E. Stajich, Audrey P Gasch, David A Knowles

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  • bioRxiv  ·  March 1, 2025  ·  Preprint

    Multi-sample, multi-platform isoform quantification using empirical Bayes.

    Arghamitra Talukder, Shree Thavarekere, Madison Mehlferber, Gloria M Sheynkman, David A Knowles

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  • bioRxiv  ·  February 27, 2025  ·  Preprint

    Differential Cellular Mechanisms Underlie Language and Executive Decline in Amyotrophic Lateral Sclerosis.

    Joana Petrescu, Claudio Gouveia Roque, Chris Jackson, Aidan Daly, Kristy Kang, Obadele Casel, Mathew Leung, Luke Reilly, Jacqueline Eschbach, Karina McDade, Jenna M Gregory, Colin Smith, Hemali Phatnani

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  • Nature Cell Biology  ·  February 26, 2025

    Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens.

    Longda Jiang, Carol Dalgarno, Efthymia Papalexi, Isabella Mascio, Hans-Hermann Wessels, Huiyoung Yun, Nika Iremadze, Gila Lithwick-Yanai, Doron Lipson & Rahul Satija

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  • bioRxiv  ·  February 23, 2025  ·  Preprint

    ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads.

    Rashid Al-Abri, Gamze Gürsoy
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  • bioRxiv  ·  February 23, 2025  ·  Preprint

    Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graph.

    Rajeeva Lochan Musunuri, Wayne E. Clarke, Bryan Zhu, William Hooper, Timothy Chu, Jennifer Shelton, André Corvelo, Dickson Chung, Shreya Sundar, Adam M Novak, Benedict Paten, Michael C Zody, Nicolas Robine, Giuseppe Narzisi

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  • PLOS Biology  ·  February 21, 2025

    Caspase 3 and caspase 7 promote cytoprotective autophagy and the DNA damage response during non-lethal stress conditions in human breast cancer cells.

    Gayathri Samarasekera, Nancy E. Go, Courtney Choutka, Jing Xu,Yuka Takemon, Jennifer Chan, Michelle Chan, Shivani Perera, Samuel Aparicio, Gregg B. Morin, Marco A. Marra, Suganthi Chittaranjan, Sharon M. Gorski

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  • eLife  ·  February 20, 2025

    Systems genomics of salinity stress response in rice.

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

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