• bioRxiv  ·  December 2, 2025  ·  Preprint

    Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization.

    Bereket Tesfay Berackey, Zhiqun Tan, Ginny Wu, Sujan C Das, Ren Li, Benjamin Esser, Qiao Ye, Mahsa Nafisi, Samuel S Park, Pedro Adolfo Sequeira Mendieta, Jillian Berry, Firoza Mamdani, Quan Zhu, Todd C Holmes, Daofeng Li, Ting Wang, M. Margarita Behrens, Bing Ren, Joseph R Ecker, Bogdan Bintu, Xiangmin Xu.

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  • medRxiv  ·  December 3, 2025  ·  Preprint

    Machine Learning-Based Prediction of Cell-type Resolved Brain eQTLs Enhances Discovery of Variants Explainin.g Alzheimer’s Disease Heritability

    Chirag M Lakhani, Giacomo Cavalca, Anjing Liu, Rohan Nidumbur, Ru Feng, Towfique Raj, Philip De Jager, The Alzheimer’s Disease Functional Genomics Consortium, Gao Wang, David A. Knowles.

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  • Cancer Discovery  ·  December 6, 2025

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

    Ke Wang, Shayan Saniei, Nikita Poddar, Isabella G Martinez, Clifford Chao, Subrina Autar, Persephone Fiore, Saul Carcamo, Meghana Sreenath, Jack H Peplinski, Rhonda E Ries, Anna Huo-Chang Mei, Noshin Azra Rahman, Levan Mekerishvili, Miguel Quijada-Álamo, Grace Freed, Mimi Zhang, Katherine Lachman, Zayna Diaz, Manuel M Gonzalez, Jing Zhang, Giang Pham, Dan Filipescu, Mirela Berisa, Tommaso Balestra, Noelle Wheeler, 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, Christopher M Sturgeon, Dan A Landau, Zhihong Chen, Eirini P Papapetrou, Franco Izzo, Soheil Meshinchi, Dan Hasson, Elvin Wagenblast.

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  • HGG Adv .  ·  December 4, 2025

    Epigenome-wide association study meta-analysis of BMI in African Americans

    Kendra Ferrier, Mariaelisa Graff, Iain R Konigsberg, Maggie Stanislawski, Heather M Highland, Laura M Raffield, April P Carson, Eric Boerwinkle, Jill M Norris, Chris R Gignoux, Audrey E Hendricks, Sridharan Raghavan, Kari E North, Kristin L Young, Anne E Justice, Matthew A Allison, Mathew J Budoff, Silva Kasela, François Aguet, Joshua J Joseph, Charles Kooperberg, Stephen S Rich, Jerome I Rotter, Ethan M Lange, Leslie A Lange.

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  • Nucleic Acids Research  ·  December 3, 2025

    FAVOR 2.0: A reengineered functional annotation of variants online resource for interpreting genomic variation.

    Hufeng Zhou, Vineet Verma, Xihao Li, Zilin Li, Nicole Shedd, Thomas Cheng Li, Haoyu Yang, Alvin Zhang, Beatrice Borsari, Steven Buyske, Mark Gerstein, Tara Matise, Michael C Zody, Benjamin Neale, Zhiping Weng, Shamil R Sunyaev, Xihong Lin

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  • Stem Cells and Development  ·  December 3, 2025

    The Specification and Functional Maturation of Sub-Cerebral Projection Neurons Derived from Human Induced Pluripotent Stem Cells.

    Zachary Jordan, Anukriti Singh, Seth Kattapong-Graber, Sonal Goswami, Neville E. Sanjana, Emanuela Zuccaro, Feng Zhang, Kevin Eggan, Jenny Hsieh, Brian P. Hermann, Jean M. Hebert, and Asif Mirza Maroof

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  • medRxiv  ·  December 2, 2025  ·  Preprint

    Sex-Specific Genetic Architecture and Comorbidities of Alcohol Use Behaviors.

    Laura Vilar-Ribó, Mariela V Jennings, Aisha Sallah, Zeal Jinwala, Hayley HA Thorpe, Sevim B Bianchi, John Meredith, Kyra Feuer, Lydia Rader, Natasia Courchesne-Krak, Maria Niarchou, Jared Balbona, 23andMe Research Team, Sarah L Elson, Pierre Fontanillas, Emma C Johnson, Lea K Davis, Alexander S Hatoum, Travis T Mallard, Daniel E Gustavson, Hang Zhou, Abraham A Palmer, Jeanne E Savage, Rachel L Kember, Sandra Sanchez-Roige

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  • Nature Communications  ·  December 2, 2025

    Epigenome-wide association study of nuclear DNA methylation in relation to mitochondrial heteroplasmy.

    Meng Lai, Kyeezu Kim, Yinan Zheng, Christina A. Castellani, Scott M. Ratliff, Mengyao Wang, Xue Liu, Jeffrey Haessler, Tianxiao Huan, Kwadwo Bonsu, Charles Newcomb, Kyler McKessy, Lawrence F. Bielak, Wei Zhao, Roby Joehanes, Jiantao Ma, Xiuqing Guo, JoAnn E. Manson, Megan L. Grove, Jan Bressler, Kent D. Taylor, Tuuli Lappalainen, Silva Kasela, Thomas W. Blackwell, Nicole J. Lake, Jessica D. Faul, Kendra R. Ferrier, Stephen C. Ekker, Lifang Hou, Charles Kooperberg, Alexander P. Reiner, Kai Zhang, Patricia A. Peyser, Myriam Fornage, Eric Boerwinkle, Laura M. Raffield, April P. Carson, Stephen S. Rich, Yongmei Liu, Daniel Levy, Jerome I. Rotter, Jennifer A. Smith, Dan E. Arking, Chunyu Liu & NHLBI Trans-Omics for Precision Medicine (TOPMed) mtDNA Working Group

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  • bioRxiv  ·  December 1, 2025  ·  Preprint

    Robust Integration of Sparse Single-Cell Alternative Splicing and Gene Expression Data with SpliceVI.

    Smriti Vaidyanathan, Keren Isaev, Aaron Zweig, David A Knowles

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  • Molecular Psychiatry  ·  November 28, 2025

    3D genetic architecture of schizophrenia risk across three neuronal subtypes.

    Samuel K. Powell, Will Liao, Sadaf Ghorbani, Raymond Rigat, Callan O’Shea, Sarah Kammourh, Rahat Elahi, Dana Infante, PJ Michael Deans, Derek J. Le, Poonam Agarwal, Wei Qiang Seow, Novin Balafkan, Kevin C. Wang, Schahram Akbarian, Kristen J. Brennand

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  • Npj Breast Cancer  ·  November 27, 2025

    Functional and clinical significance of the RNA m6A methyltransferase complex in breast cancer.

    Anna E. Harris, Jennifer Lothion-Roy, Rachel L. Thompson, Maria Haque, Corinne L. Woodcock, Mansour A. Alsaleem, Alexander Dean, Yousif Kariri, Michael S. Toss, Lorraine J. Gudas, Andrew R. Green, Cinzia Allegrucci, Melissa B. Davis, Sheeba Irshad, Kyong-Hwa Park, Srinivasan Madhusudan, Rupert G. Fray, Jennie N. Jeyapalan, Catrin S. Rutland, Emad A. Rakha, Nigel P. Mongan

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  • Nature Genetics  ·  November 27, 2025

    Passenger mutations link cellular origin and transcriptional identity in human lung adenocarcinomas.

    Sukanya Panja, Padmaja Mantri, Kofi Ennu Johnson, Juan Sebastian Andrade-Martinez, Soo-Ryum Yang, Aditya Deshpande, Huasong Tian, Shaham Beg, Kentaro Ohara, Alessandro Leal, Joel Rosiene, Marlon Stoeckius, Peter Smibert, William D. Travis, Juan Miguel Mosquera, Paz Polak, Marcin Imieliński

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  • Molecular Psychiatry  ·  November 25, 2025

    Genome-wide association study of delay discounting identifies 11 loci and reveals transdiagnostic associations across mental and physical health.

    Hayley H. A. Thorpe, Renata B. Cupertino, Shreya Reddy Pakala, Pierre Fontanillas, Mariela V. Jennings, Jane Yang, John J. Meredith, Tiffany Greenwood, Sevim B. Bianchi, Laura Vilar-Ribó & Maria Niarchou, on behalf of the 23andMe Research Team, Sarah L. Elson, Trey Ideker, Lea K. Davis, James MacKillop, Harriet deWit, Daniel E. Gustavson, Travis T. Mallard, Abraham A. Palmer & Sandra Sanchez-Roige

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  • bioRxiv  ·  November 25, 2025  ·  Preprint

    Transcriptome-wide profiling of alternative splicing regulators with CRISPore-seq.

    Simon Müller, Nathanael Andrews, Rachel E. Yan, Akash Sookdeo, Wells H. Burrell, Xiaoguang Dai, Priyesh Rughani, Zharko Daniloski, Sissel Juul, Neville E. Sanjana

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  • Nature Methods  ·  November 24, 2025

    From slices to deep dishes: spatial transcriptomics and translatomics of thick tissue blocks.

    Maroš Pleška, Sanja Vickovic

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  • medRxiv  ·  November 22, 2025  ·  Preprint

    Biobank-scale Bayesian TWAS reveals splicing-mediated mechanisms of complex disease.

    Alex Tokolyi, Saikat Banerjee, David A Knowles

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  • medRxiv  ·  November 19, 2025  ·  Preprint

    Common and rare variant genetic contributions in African Americans with autism.

    Matilde Cirnigliaro, Jennifer K. Lowe, Alexander O. Flynn-Carroll, Michi E. Kumagai, David S. Gibson, Jack M. Fu, Shan Dong, Kangcheng Hou, Vamsee Pillalamarri, Anna M. Abbacchi, Amanda C. Gulsrud, Janet Miller, Yi Zhang, Erin T. Graham, Elizabeth O. Akinyemi, Marshel F. Adams, Amaris N. Clay, Stephanie A. Arteaga, Hailey Choi, Ryan M. Kochis, Jorge E. Peña-Velasco, Jackson N. Hoekstra, Aaron D. Besterman, Sunil Mehta, Tarik Hadzic, Rujuta B. Wilson, Tashalee R. Brown, Leanna M. Hernandez, Natasha Marrus, Sophie Molholm, Cheryl Klaiman, Rita M. Cantor, Michael E. Talkowski, Stephan J. Sanders, Dan E. Arking, Bogdan Pasaniuc, Ami Klin, John N. Constantino, Genetics of Neurodevelopment in African Americans (GENAA) Consortium, Daniel H. Geschwind

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  • bioRxiv  ·  November 10, 2025  ·  Preprint

    Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism.

    Guohua Yuan, Varun Suresh, Emilie Wigdor, Yuhan Hao, Rachel Leonard, Marilyn Steyert, Michael Griffiths, Clements Evans, Narjes Rohani, Jakob Weiss, Frederick H. Lassen, Nicole Schafer, Shan Dong, Duncan S. Palmer, Stephan J. Sanders, Tomasz J. Nowakowski.

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  • Nature Biomedical Engineering  ·  November 9, 2025

    Neuroimaging endophenotypes reveal underlying mechanisms and genetic factors contributing to progression and development of four brain disorders.

    Junhao Wen, Ioanna Skampardoni, Ye Ella Tian, Zhijian Yang, Yuhan Cui, Guray Erus, Gyujoon Hwang, Erdem Varol, Aleix Boquet-Pujadas, Ganesh B. Chand, Ilya M. Nasrallah, Theodore D. Satterthwaite, Haochang Shou, Li Shen, Arthur W. Toga, Andrew Zalesky & Christos Davatzikos

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  • bioRxiv  ·  November 5, 2025  ·  Preprint

    Distinct patterns of de novo coding variants contribute to Tourette Syndrome etiology.

    Lingyu Zhan, Dongmei Yu, Franjo Ivankovic, Maria Niarchou, Laura Domenech-Salgado, Cathy L. Barr, Fortu Benarroch, Cathy L. Budman, Danielle C. Cath, Nelson B. Freimer, Helena Garrido, Marco A. Grados, Varda Gross-Tsur, Luis Herrera-Amighetti, Robert A. King, Roger Kurlan, James F. Leckman, Gholson J. Lyon, William M. McMahon, David L. Pauls, Yehuda Pollak, Mary M. Robertson, Roxana Romero, Guy A. Rouleau, Paul Sandor, Harvey S. Singer, Paola Giusti-Rodriguez, Lea K. Davis, Carol A. Mathews, Jeremiah M. Scharf, Roel A. Ophoff

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  • bioRxiv  ·  November 5, 2025  ·  Preprint

    Large-scale discovery of neural enhancers for cis-regulation therapies.

    Troy A. McDiarmid, Nicholas F. Page, Florence M. Chardon, Riza M. Daza, George T. Chen, Michael Kosicki, Lucas M. James, Hannah C. Nourie, Dianne Laboy-Cintron, Arthur S. Lee, Paula Vij, Diego Calderon, Jean-Benoit Lalanne, Beth K. Martin, Kyle Fink, Michael E. Talkowski, Alysson R. Muotri, Benjamin D. Philpot, Len A. Pennacchio, Daniel H. Geschwind, Stephan J. Sanders, Nadav Ahituv, Jay Shendure.

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