• Science  ·  August 7, 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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  • medRxiv  ·  August 7, 2025  ·  Preprint

    Development and validation of electronic health record-based ascertainment of obsessive-compulsive disorder cases and controls.

    Bo Wang, Tyne W Miller-Fleming, Dongmei Yu, Donald Hucks, Emily Gantz, Rebecca Johnston, Angela Maxwell-Horn, Nancy Cox, James Sutcliffe, Carol A Mathews, Evonne McArthur, Helen Hatfield, Dia Kabir, Evan J Giangrande, Rebecca G Fortgang, Shirley B Wang, Rakesh Karmacharya, Joshua L Roffman, Jeremiah M Scharf, Jordan W Smoller, Takahiro Soda, James J Crowley, Lea K Davis.

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  • bioRxiv  ·  August 7, 2025  ·  Preprint

    Non-linear transcriptional responses to gradual modulation of transcription factor dosage.

    Júlia Domingo, Mariia Minaeva, John A. Morris, Samuel Ghatan, Marcello Ziosi, Neville E. Sanjana, Tuuli Lappalainen

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  • Frontiers in Systems Biology  ·  July 2, 2025

    Learning Gaussian Graphical Models from Correlated Data.

    Zeyuan Song, Sophia Gunn, Stefano Monti, Gina Marie Peloso, Ching-Ti Liu, Kathryn Lunetta, Paola Sebastiani.

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  • JAMA Internal Medicine  ·  August 1, 2025

    Diseases Common in Persons With Cystic Fibrosis Among CFTR Heterozygotes.

    Chenjie Zeng, Sangwoo T Han, Thomas A Cassini, Karen S Raraigh, Tam C Tran, James Yang, Garry R Cutting, Joshua C Denny.

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  • Genetics in Medicine  ·  July 2, 2025

    Venous thromboembolism laboratory testing (factor V Leiden and factor II c.∗97G>A), 2025 revision: A technical standard of the American College of Medical Genetics and Genomics (ACMG).

    Benjamin E Kang, Shulin Zhang, Harry Lesmana, Jeffrey Dungan, Kara Reynolds, Saurav Guha, Hunter Best.

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  • Biological Psychiatry: Cognitive Neuroscience and Neuroimaging  ·  August 1, 2025

    Deriving Mendelian Randomization-based Causal Networks of Brain Imaging Phenotypes and Bipolar Disorder.

    Shane O’Connell, Brielin C Brown, Dara M Cannon, Pilib Ó Broin, Nadine Parker, Dag Alnæs, Lars T Westlye, Saikat Banerjee, Leila Nabulsi, Emma Corley, Ole A Andreassen, David A Knowles, Niamh Mullins.

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  • bioRxiv  ·  August 2, 2025  ·  Preprint

    Targeting CyclinD1-CDK6 to Mitigate Senescence-Driven Inflammation and Age-Associated Functional Decline.

    Adarsh Rajesh, Aaron P. Havas, Rouven Arnold, Kathryn Lande, K. Garrett Evensen, Kelly Yichen Li, Sainath Mamde, Qian Yang, Armin Gandhi, Karl N. Miller, Marcos Garcia Teneche, Zoe Yao, Jessica Proulx, Andrew Davis, Laurence Haddadin, Michael Alcaraz, Carolina Cano Macip, Brightany Li, Xue Lei, Charlene Miciano, Elizabeth Smoot, Allen Wang, Jeffrey H. Albrecht, April E. Williams, Bing Ren, Kevin Y. Yip, Peter D. Adams.

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  • American Journal of Respiratory and Critical Care Medicine.  ·  August 2, 2025

    Deficient FANCL Predisposes to Endothelial Damage: A New Therapeutic Target for Pulmonary Hypertension.

    Shiyun Liu, Xiaoqian Shan, Yufei Sun, Haixia Chen, Huazhuo Feng, Shaocong Mo, Changlei Bao, Junqi Zhu, Zizhou Zhang, Feng Wei, Xiuzhen Bai, Ran Xu, Jiaxuan Lai, Haiyun Luo, Chenting Zhang, Xiaoyun Luo, Qian Jiang, Yuqin Chen, Yuqi Zhou, Haiyang Tang, Lei Xu, Wenju Lu, Rong Guo, Chunli Liu, Zifeng Yang, Jason X.-J. Yuan, Xinlin XuXinlin Xu, Dongyi XuDongyi Xu, Jian WangJian Wang, and Kai YangKai Yang.

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  • NPJ Digit Med.  ·  August 2, 2025

    Multi-domain rule-based phenotyping algorithms enable improved GWAS signal.

    Abigail Newbury, Ahmed Elhussein, Gamze Gürsoy.

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  • Immunity  ·  July 29, 2025

    Asynchronous aging and turnover of human circulating and tissue-resident memory T cells across sites.

    Nora Lam, J Carlos Angel, Bruce A Buchholz, YoonSeung Lee , Stuart P Weisberg, Brea H Brown, Julia Davis-Porada, Daniel P Caron, Isaac J Jensen, Peter A Szabo, Basak B Ural, Steven B Wells, Masaru Kubota, Rei Matsumoto, Maigan Brusko, Todd M Brusko, Chao Lu, Andrew J Yates, Donna L Farber.

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  • Nature Communications  ·  July 29, 2025

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

    Megan D. Schertzer, Andrew Stirn, Keren Isaev, Laura Pereira, Stella H. Park, Anjali Das, Aline Réal, Erin D. Jeffery, Claire Harbison, Hans-Hermann Wessels, Gloria M. Sheynkman, Neville E. Sanjana & David A. Knowles

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  • Acta Neuropathol  ·  July 29, 2025

    Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord.

    John F. Tuddenham, Masashi Fujita, Emily Lee, Nivedita Nimmagadda, Anthony Khairallah, Claire Harbison, Xena E. Flowers, Guillermo Coronas-Samano, Silas Maniatis, Aidan Daly, Julie A. Schneider, Andrew F. Teich, Jean Paul G. Vonsattel, Peter A. Sims, Wassim Elyaman, Elizabeth M. Bradshaw, Lyle W. Ostrow, Hemali Phatnani, Neil A. Shneider, David A. Bennett, Philip L. De Jager, Serge Przedborski, Vilas Menon & Marta Olah

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  • Scandinavian Journal of Immunology  ·  July 28, 2025

    Multiparametric Optimization of Human Primary B-Cell Cultures Using Design of Experiments.

    Anne Bruun Rovsing, Kenneth Green, Lisbeth Jensen, Ian Helstrup Nielsen, Jacob Giehm Mikkelsen, Søren E. Degn

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  • Proceedings of the National Academy of Sciences of the United States of America  ·  July 28, 2025

    Rare variants in BMAL1 are associated with a neurodevelopmental syndrome.

    Vishnu Anand Cuddapah, Dechun Chen, Bumsik Cho, Rebecca Moore, Mohnish Suri, Hana Safraou, Frederic Tran-Mau-Them, Ashley Wilson, Jacqueline Odgis, Atteeq U Rehman, Carol Saunders, Shiva Ganesan, Vaidehi Jobanputra, Stephen W Scherer, Ingo Helbig, Amita Sehgal.

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  • Cell Reports Method  ·  July 25, 2025

    Recent advances and future prospects for blockchain in biomedicine.

    Eric Ni, Xiangru Tang, Xiao Zhou, Danielle Lee, Ahmed Elhussein, Elizabeth Knight, Gamze Gürsoy, Mark Gerstein

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  • Genetics in Medicine Open  ·  July 24, 2025

    Laboratory considerations for GRCh37 to GRCh38 reference genome transition: A laboratory quality assurance bulletin of the American College of Medical Genetics and Genomics (ACMG).

    Vimla S. Aggarwal, Saurav Guha, Matthew S. Lebo, Kyle Retterer, Curt Scharfe, Lora J.H. Bean, on behalf of the ACMG Laboratory Quality Assurance Committee.

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  • Nature  ·  July 23, 2025

    Complex genetic variation in nearly complete human genomes.

    Glennis A. Logsdon, Peter Ebert, Peter A. Audano, Mark Loftus, David Porubsky, Jana Ebler, Feyza Yilmaz, Pille Hallast, Timofey Prodanov, DongAhn Yoo, Carolyn A. Paisie, William T. Harvey, Xuefang Zhao, Gianni V. Martino, Mir Henglin, Katherine M. Munson, Keon Rabbani, Chen-Shan Chin, Bida Gu, Hufsah Ashraf, Stephan Scholz, Olanrewaju Austine-Orimoloye, Parithi Balachandran, Marc Jan Bonder, Haoyu Cheng, Zechen Chong, Jonathan Crabtree, Mark Gerstein, Lisbeth A. Guethlein, Patrick Hasenfeld, Glenn Hickey, Kendra Hoekzema, Sarah E. Hunt, Matthew Jensen, Yunzhe Jiang, Sergey Koren, Youngjun Kwon, Chong Li, Heng Li, Jiaqi Li, Paul J. Norman, Keisuke K. Oshima, Benedict Paten, Adam M. Phillippy, Nicholas R. Pollock, Tobias Rausch, Mikko Rautiainen, Yuwei Song, Arda Söylev, Arvis Sulovari, Likhitha Surapaneni, Vasiliki Tsapalou, Weichen Zhou, Ying Zhou, Qihui Zhu, Michael C. Zody, Ryan E. Mills, Scott E. Devine, Xinghua Shi, Michael E. Talkowski, Mark J. P. Chaisson, Alexander T. Dilthey, Miriam K. Konkel, Jan O. Korbel, Charles Lee, Christine R. Beck, Evan E. Eichler & Tobias Marschall

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  • Cell  ·  July 22, 2025

    SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress.

    Erica Wolin, Jimmy K. Guo, Mario R. Blanco, Isabel N. Goronzy, Darvesh Gorhe, Wenzhao Dong, Andrew A. Perez, Abdurrahman Keskin, Elizabeth Valenzuela, Ahmed A. Abdou, Carl R. Urbinati, Ross Kaufhold, H. Tomas Rube, Jailson Brito Querido, Mitchell Guttman, Marko Jovanovic

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  • eLife  ·  July 22, 2025

    Metastatic small cell lung cancer arises from TP53/RB1-deficient and MYC overproduction hESC-derived PNECs.

    Huanhuan Joyce Chen, Eric E Gardner, Yajas Shah, Kui Zhang, Abhimanyu Thakur, Chen Zhang, Olivier Elemento, Harold Varmus

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  • Human Genetics and Genomics Advances  ·  July 18, 2025

    Genotypic, functional, and phenotypic characterization in CTNNB1 neurodevelopmental syndrome.

    Nina Žakelj, David Gosar, Špela Miroševič, Stephan J. Sanders, Alicia Ljungdhal, Sayeh Kohani, Shouhe Huang, Lok I. Leong, Ying An, Miou-Jing Teo, Fiona Moultrie, Roman Jerala, Duško Lainšček, Vida Forstnerič, Petra Sušjan, Leszek Lisowski, Andrea Perez-Iturralde, Jasna Oražem Mrak, Ho Yin Edwin Chan, Damjan Osredkar

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