• Genome Medicine  ·  April 14, 2025

    Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease.

    Alexandra C. Martin-Geary, Alexander J.M. Blakes, Ruebena Dawes, Scott D. Findlay, Jenny Lord, Shan Dong, Susan Walker, Jonathan Talbot-Martin, Nechama Wieder, Elston N. D’Souza, Maria Fernandes, Sarah Hilton, Nayana Lahiri, Christopher Campbell, Sarah Jenkinson, Christian G.E.L. DeGoede, Emily R. Anderson, Toby Candler, Helen Firth, Christopher B. Burge, Stephan J. Sanders, Jamie Ellingford, Diana Baralle, Siddharth Banka & Nicola Whiffin

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  • Nucleic Acids Research  ·  April 14, 2025

    pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data.

    J Carlos Angel, Narjis El Amraoui, Gamze Gürsoy

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  • Nature Methods  ·  April 11, 2025

    Error-corrected flow-based sequencing at whole genome scale and its application to circulating cell-free DNA profiling.

    Alexandre Pellan Cheng, Adam J. Widman, Anushri Arora, Itai Rusinek, Aaron Sossin, Srinivas Rajagopalan, Nicholas Midler,William F. Hooper, Rebecca M. Murray, Daniel Halmos, Theophile Langanay, Hoyin Chu, Giorgio Inghirami, Catherine Potenski, Soren Germer, Melissa Marton, Dina Manaa, Adrienne Helland, Rob Furatero, Jaime McClintock, Lara Winterkorn, Zoe Steinsnyder, Yohyoh Wang, Asrar I. Alimohamed, Murtaza S. Malbari, Ashish Saxena, Margaret K. Callahan, Dennie T. Frederick, Lavinia Spain, Michael Sigouros, Jyothi Manohar, Abigail King, David Wilkes, John Otilano, Olivier Elemento, Juan Miguel Mosquera, Ariel Jaimovich, Doron Lipson, Samra Turajlic, Michael C. Zody, Nasser K. Altorki, Jedd D. Wolchok, Michael A. Postow, Nicolas Robine, Bishoy M. Faltas, Genevieve Boland, Dan A. Landau

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  • Science  ·  April 11, 2025

    The genetic architecture of and evolutionary constraints on the human pelvic form.

    Liaoyi Xu, Eucharist Kun, Devansh Pandey, Joyce Y. Wang, Marianne F. Brasil, Tarjinder Singh, and Vagheesh M. Narasimhan

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  • Nature  ·  April 9, 2025

    Phenotypic complexities of rare heterozygous neurexin-1 deletions.

    Michael B. Fernando, Yu Fan, Yanchun Zhang, Alex Tokolyi, Aleta N. Murphy, Sarah Kammourh, P. J. Michael Deans, Sadaf Ghorbani, Ryan Onatzevitch, Adriana Pero, Christopher Padilla, Sarah E. Williams, Erin K. Flaherty, Iya A. Prytkova, Lei Cao, David A. Knowles, Gang Fang, Paul A. Slesinger & Kristen J. Brennand

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  • Nature Biotechnology  ·  April 4, 2025

    Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.

    Ayse G. Keskus, Asher Bryant, Tanveer Ahmad, Byunggil Yoo, Sergey Aganezov, Anton Goretsky, Ataberk Donmez, Lisa A. Lansdon, Isabel Rodriguez, Jimin Park, Yuelin Liu, Xiwen Cui, Joshua Gardner, Brandy McNulty, Samuel Sacco, Jyoti Shetty, Yongmei Zhao, Bao Tran, Giuseppe Narzisi, Adrienne Helland, Daniel E. Cook, Pi-Chuan Chang, Alexey Kolesnikov, Andrew Carroll, Erin K. Molloy, Chengpeng Bi, Adam Walter, Margaret Gibson, Irina Pushel, Erin Guest, Tomi Pastinen, Kishwar Shafin, Karen H. Miga, Salem Malikic, Chi-Ping Day, Nicolas Robine, Cenk Sahinalp, Michael Dean, Midhat S. Farooqi, Benedict Paten & Mikhail Kolmogorov

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  • Nature Medicine  ·  April 4, 2025

    Precision Omics Initiative Sweden (PROMISE) will integrate research with healthcare.

    Anders Kämpe, Sanna Gudmundsson, Colum P. Walsh, Kerstin Lindblad-Toh, Åsa Johansson, Anna Clareborn, Adam Ameur, Anders Edsjö, Thoas Fioretos, Hans Ehrencrona, Daniel Eriksson, Tove Fall, Paul W. Franks, Ulf Gyllensten, Margareta Haag, Anna Hagwall, Maria Johansson Soller, Janne Lehtiö, Yi Lu, Patrik K. E. Magnusson, Erik Melén, Beatrice Melin, Karl Michaëlsson, Ann Nordgren, Jessica Nordlund, Lao H. Saal, Jochen M. Schwenk, Per Sikora, Johan Sundström, Fulya Taylan, Bethany Van Guelpen, Mia Wadelius, Anna Wedell, Valtteri Wirta, Päivi Östling, Bo Jacobsson, Tobias Sjöblom, Bengt Persson, Richard Rosenquist, Anna Lindstrand & Tuuli Lappalainen

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  • Cell Reports  ·  April 3, 2025

    Single-cell 5-hydroxymethylcytosine landscapes of mouse early embryos at single-base resolution

    Dongsheng Bai, Jinmin Yang, Xiaohui Xue, Yun Gao, Yan Wang, Mengge Cui, Bo He, Hu Zeng, Huifen Xiang, Zijian Guo, Lan Zhu, Juan Gao, Chenxu Zhu, Fuchou Tang, Chengqi Yi.

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  • NPJ Precision Oncology  ·  March 28, 2025

    A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer.

    Jones T. Nauseef, Timothy R. Chu, William F. Hooper, Alicia Alonso, Ali Oku, Heather Geiger, Zoe R. Goldstein, Minita Shah, Michael Sigouros, Jyothi Manohar, Zoe Steinsnyder, Lara Winterkorn, Brian D. Robinson, Andrea Sboner, Himisha Beltran, Olivier Elemento, Iman Hajirasouliha, Marcin Imieliński, David M. Nanus, Scott T. Tagawa, Nicolas Robine & Juan Miguel Mosquera

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  • American Society of Human Genetics  ·  March 26, 2025

    Consensus guidelines for assessing eligibility of pathogenic DNA variants for antisense oligonucleotide treatments.

    David Cheerie, Margaret M Meserve, Danique Beijer, Charu Kaiwar, Logan Newton, Ana Lisa Taylor Tavares, Aubrie Soucy Verran, Emma Sherrill, Stefanie Leonard, Stephan J Sanders, Emily Blake, Nour Elkhateeb, Aastha Gandhi, Nicole S Y Liang, Jack T Morgan, Anna Verwillow, Jan Verheijen, Andrew Giles, Sean Williams, Maya Chopra, Laura Croft, Hormos Salimi Dafsari, Alice E Davidson, Jennifer Friedman, Anne Gregor, Bushra Haque, Rosan Lechner, Kylie-Ann Montgomery, Mina Ryten, Emil Schober, Gabriele Siegel, Patricia J Sullivan, Ella F Whittle, Bianca Zardetto, Timothy W Yu, Matthis Synofzik, Annemieke Aartsma-Rus, Gregory Costain, Marlen C Lauffer

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  • 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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