• bioRxiv  ·  October 13, 2025  ·  Preprint

    Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data.

    Yoo-Jin Jiny Ha, Dominika Maziec, Julia Markowski, Stephanie J Georges, Nancy L Parmalee, Michele Berselli, Tim HH Coorens, Shihua Dong, Stephanie Gardiner, Divya Kalra, Daofeng Li, Benpeng Miao, Rajeeva Musunuri, Liying Xue, Zhi Yu, Kimberly Walker, Lisa Anderson, Natalie YT Au, Carrie Cibulskis, Harsha Doddapaneni, Christopher M Grochowski, Dana M Jensen, Tina Lindsay, Kelsey Loy, Azeet Narayan, Giuseppe Narzisi, Jeffrey Ou, Meranda M Pham, Alexi M Runnels, Andrew B Stergachis, Lila M Sutherlin, Ting Wang, Hu Jin, William C Feng, Yuwei Zhang, Alexander D Veit, Clara TaeHee Kim, Hye-Jung E Chun, Kristin Ardlie, Robert S Fulton, Soren Germer, Richard A Gibbs, Gabor T Marth, James T Bennett, Peter J Park

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  • Mol Psychiatry.  ·  October 13, 2025

    Genome-wide association studies of lifetime and frequency of cannabis use in 131,895 individuals.

    Hayley H A Thorpe, Pierre Fontanillas, John J Meredith, Mariela V Jennings, Renata B Cupertino, Shreya R Pakala; 23andMe Research Team; Sarah L Elson, Jibran Y Khokhar, Lea K Davis, Emma C Johnson, Abraham A Palmer, Sandra Sanchez-Roige.

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  • Nature  ·  October 14, 2025

    Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells.

    Joseph N. Pucella, Raul A. Maqueda-Alfaro, Hai Ni, Fernando Bandeira Sulczewski, Anna Eichinger, Eduardo Esteva, Ai C. Ra, Annesa Das, Oriana A. Perez, Jue Feng, Marlon Stoeckius, Peter Smibert, Alireza Khodadadi-Jamayran, Igor Dolgalev, Ellie Ivanova, Stela Sota, Ken Cadwell, Sergei B. Koralov, Judy Zhong, Chetna Soni, Daniel B. Stetson, Stuart P. Weisberg, Donna L. Farber, Juliana Idoyaga & Boris Reizis.

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  • medRxiv  ·  October 13, 2025  ·  Preprint

    Genomic analyses reveal new insights into Alzheimer’s disease.

    Emil Uffelmann, Douglas P Wightman, Shahram Bahrami, Alexey A Shadrin, Vera Fominykh, Takafumi Ojima, Chenyang Jiang, Christian Benner, Elisa Moreno, Adrian I Campos, Jesper Q Thomassen, Emmanuel Minois-Genin, Hei Man Wu, G. Bragi Walters, Richard Sherva, Tian Lin, Julien Bryois, Kristi Krebs, Marijn Schipper, Akira Narita, Alessandro Serretti, Anja H Simonsen, Anna L van Seumeren, Anne Corbett, Anne-Brita Knapskog, Annette M Hartmann, Anouk den Braber, Argonde C van Harten, Arvid Harder, Arvid Rongve, Bengt O Madsen, Betty M Tijms, Bitten Aagaard, Bjorn Lichtwarck, Bjorn E Kirsebom, Byron Creese, Chandra A Reynolds, Sara Hagg, Ida Karlsson, Christian Erikstrup, Christina Mikkelsen, Clive Ballard, Dag Aarsland, Daichi Shigemizu, Dan Rujescu, Daniel Gudbjartsson, Eivind Aakhus, Erik Sorensen, Eystein Stordal, Flora H Duits, Frank J Wolters, Frederic Blanc, Geert Jan Biessels, Geir Selbaek, Geir Brathen, Gen Tamiya, Gunhild Waldemar, Harro Seelaar, Helga Eyjolfsdottir, Henne Holstege, Henning Bundgaard, Henrik Zetterberg, Henrik Ullum, Ingmar Skoog, Ingrid T Medboen, Ingvild Saltvedt, Ingvild H Feiring, Irena Rektorova, J. Michael Gaziano, Jan Haavik, Jens Hjerling-Leffler, Jiao Luo, Jon Snaedal, Everard GB Vijverberg, Julia M Sealock, Kaj Blennow, Kaja Nordengen, Karin Persson, Katja Scheffler, Koichi Matsuda, Kouichi Ozaki, Lasse Pihlstrom, Lavinia Athanasiu, Lene Palhaugen, Marc Hulsman, Margda Waern, Maria Averina, Marianne Wettergreen, Marta R Moksnes, Martijn Huisman, Masayuki Yamamoto, Mathias Toft, Matthew S Panizzon, Mie Topholm Bruun, Mohsen Ghanbari, Monique Franc, Nancy L Pedersen, Nathaniel Y Bell, Niccolo Tesi, Ole B Pedersen, Oleksandr Frei, Olivier Bousiges, Per Svenningsson, Pieter J Visser, Qingqin S Li, Richard Hauger, Rui Zhang, Shinichi Namba, Sigrid B Sando, Silke Kern, Srdjan Djurovic, Steinunn Thordardottir, Tanya N Phung, Thomas Truelsen, Thomas Werge, Thomas F Hansen, Tomoki Kyosaka, Torgeir Engstad, Tormod Fladby, Victoria Merritt, Sverre Bergh, Wiesje M van der Flier, Rujin Wang, Eli A Stahl, Basavaraj Hooli, 23andMe Research Institute, LifeLines Cohort Study, DBDS Genomic consortium, Regeneron Genetics Center, Penn Medicine Biobank, GHS-RGC DiscovEHR collaboration, Mayo Clinic-RGC Project Generation, Colorado Center for Personalized Medicine – RGC Collaboration, UCLA-RGC ATLAS collaboration, INDIANA-CHALASANI, Mount Sinai Million Health Discoveries Program, Estonian Biobank research team, VA Million Veteran Program, Lea K Davis, Mark W Logue, Kelli Lehto, Anna Zettergren, Ben M Brumpton, Jian Zeng, Peter M Visscher, Paul F O’Reilly, Anubha Mahajan, Manuel Ferreira, Yukinori Okada, Sven J van der Lee, Sisse R Ostrowski, Ruth Frikke-Schmidt, Hreinn Stefansson, Karl Heilbron, Ole A Andreassen, Danielle Posthuma.

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  • bioRxiv  ·  October 13, 2025  ·  Preprint

    Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus.

    Tamara Prieto, Dennis J Yuan, John Zinno, Clayton Hughes, Nicholas Midler, Sheng Kao, Jani Huuhtanen, Ramya Raviram, Fenia Fotopoulou, Neil Ruthen, Srinivas Rajagopalan, Joshua S Schiffman, Andrew R D Avino, Sang-Ho Yoon, Jesus Sotelo, Nathaniel D Omans, Noelle Wheeler, Alejandro Garces, Barun Pradhan, Alexandre Pellan Cheng, Nicolas Robine, Catherine Potenski, Katharine Godfrey, Nobuyuki Kakiuchi, Akira Yokoyama, Seishi Ogawa, Julian Abrams, Ivan Raimondi, Dan A Landau.

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  • bioRxiv  ·  October 10, 2025  ·  Preprint

    A Physically-Realistic Simulator and Cosine-Based Decoder for MERFISH Spatial Transcriptomics.

    Jenkin Tsui, Naila Adam, Woongcheol Choi, Luna Liu, Cristina Flores, Shadi Ansari, Esther Kong, Yukta Thapliyal, Hakwoo Lee, Shahid Haider, Isaac Von Riedemann, Ciara O’Flanagan, IMAXT Cancer Grand Challenges Consortium, Samuel Aparicio, Andrew Roth.

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  • bioRxiv  ·  October 8, 2025  ·  Preprint

    African Green Monkeys Respond to Synthetic AB Oligomers with Persistent Alzheimers-like Activation.

    Bianca Brown, Xiaoting Li, Monica R Grasty, Isabela Lopez, Sara Dzigurski, Maya Geradi, Matthew Lawrence, John Elsworth, Matthew Lawrence, Micahel Weed, Gamze Gursoy, Andrew David Miranker.

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  • medRxiv  ·  September 30, 2025  ·  Preprint

    Meta-analysis of genetic regulation of RNA editing in the human brain identifies new genes underlying neurological disease.

    Winston H Dredge, Kailash BP, Aline Réal, Benjamin Z Muller, Beomjin Jang, Ting Fu, Hyomin Seo, Hong-Hee Won, Michael S Breen, Xinshu Xiao, David A Knowles, Jack Humphrey, Towfique Raj.

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  • bioRxiv  ·  October 3, 2025  ·  Preprint

    A conserved logic for the development of cortical layering in tetrapods.

    Astrid Deryckere, Saket Choudhary, Connor Lynch, Lian Kirit V. P. Limperis, Pauline Affatato, Jamie Woych, Elias Gumnit, Alonso Ortega Gurrola, Rahul Satija, Christian Mayer, Maria Antonietta Tosches.

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  • Genome Research  ·  October 1, 2025

    Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform.

    Liubomir Chorbadjiev, Murat Cokol, Zohar Weinstein, Kevin Shi, Christopher Fleisch, Nikolay Dimitrov, Svetlin Mladenov, Ivo Todorov, Iordan Ivanov, Simon Xu, Steven Ford, Yoon-ha Lee, Boris Yamrom, Steven Marks, Adriana Munoz, Alex Lash, Natalia Volfovsky and Ivan Iossifov.

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  • Nature Communications  ·  October 1, 2025

    Polygenic risk score for type 2 diabetes shows context-dependent effects across populations.

    Boya Guo, Yanwei Cai, Daeeun Kim, Roelof A. J. Smit, Zhe Wang, Kruthika R. Iyer, Austin T. Hilliard, Jeffrey Haessler, Ran Tao, K. Alaine Broadaway, Yujie Wang, Nikita Pozdeyev, Frederik F. Stæger, Chaojie Yang, Brett Vanderwerff, Amit D. Patki, Lauren Stalbow, Meng Lin, Nicholas Rafaels, Jonathan Shortt, Laura Wiley, Maggie Stanislawski, Jack Pattee, Lea Davis, Peter S. Straub, Megan M. Shuey, Nancy J. Cox, Nanette R. Lee, Marit E. Jørgensen, Peter Bjerregaard, Christina Larsen, Torben Hansen, Ida Moltke, James B. Meigs, Daniel O. Stram, Xianyong Yin, Xiang Zhou, Kyong-Mi Chang, Shoa L. Clarke, Rodrigo Guarischi-Sousa, Joanna Lankester, Philip S. Tsao, Steven Buyske, Mariaelisa Graff, Laura M. Raffield, Quan Sun, Lynne R. Wilkens, Christopher S. Carlson, Charles B. Easton, Simin Liu, JoAnn E. Manson, Loïc L. Marchand, Christopher A. Haiman, Karen L. Mohlke, Penny Gordon-Larsen, Anders Albrechtsen, Michael Boehnke, Stephen S. Rich, Ani Manichaikul, Jerome I. Rotter, Noha A. Yousri, Ryan M. Irvin, The biobank at the Colorado Center for Personalized Medicine (CCPM), VA Million Veteran Program (MVP), Chris Gignoux, Kari E. North, Ruth J. F. Loos, Themistocles L. Assimes, Ulrike Peters, Charles Kooperberg, Sridharan Raghavan, Heather M. Highland & Burcu F. Darst.

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  • bioRxiv  ·  September 29, 2025  ·  Preprint

    Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer’s Disease.

    Wenliang Wang, Peter Berube, Bing Yang, Rosa Castanon, Anna Bartlett, Kaushik Komandur, Joseph R. Nery, Cesar Barragan, Mia Kenworthy, Cynthia Valadon, Jordan Altshul, Alaina Petrella, Derek Chan, Chumo Chen, Andrea Saldana Acerbo, Jammy Luo, Manya Jain, Eshaan Soma, Huaming Chen, Michelle Liem, Mikayla Marrin, Caz O’Connor, Nathan Zemke, Derek H. Oakley, Bing Ren, Bradley T. Hyman, Joseph R. Ecker.

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  • Nature  ·  September 30, 2025

    Brain-heart-eye axis revealed by multi-organ imaging genetics and proteomics.

    The MULTI Consortium, Aleix Boquet-Pujadas, Filippos Anagnostakis, Michael R. Duggan, Cassandra M. Joynes, Arthur W. Toga, Zhijian Yang, Keenan A. Walker, Christos Davatzikos & Junhao Wen.

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  • Genome Biology  ·  September 27, 2025

    Hybrid BAG-seq: DNA and RNA from the same single nucleus reveals interactions between genomic and transcriptomic landscapes in human tumor samples.

    Siran Li, Joan Alexander, Jude Kendall, Peter Andrews, Elizabeth Rose, Hope Orjuela, Sarah Park, Craig Podszus, Liam Shanley, Nissim Ranade, Patrick Morris, Danielle Stauder, Daniel Bradford, Zachary Laster, Michael Ronemus, Arvind Rishi, Marina Frimer, Rong Ma, David L. Donoho, Gary L. Goldberg, Michael Wigler & Dan Levy.

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  • medRxiv  ·  September 26, 2025  ·  Preprint

    Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk.

    Aline Réal, B P Kailash, Winston H Cuddleston, Benjamin Z Muller, Beomjin Jang, Alex Tokolyi, Hong-Hee Won, Jack Humphrey, Towfique Raj, David A Knowles.

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  • Journal of Microbiology & Biology Education  ·  September 25, 2025

    Teaching molecular genetics using Paramecium and RNA interference: research-based learning and project ownership.

    M. S. Valentine, K. Johnson, M. B. Veramendi, C. James, J. Kozak, A. Patwardhan, R. Quartey.

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  • International Journal of Molecular Sciences  ·  September 22, 2025

    Stratifying ALS Patients by Mode of Inheritance Reveals Transcriptomic Signatures Specific to sALS and fALS.

    Alexandria Awai, Erica L. Johnson, Tiandong Leng, John Patrickson, Michael C. Zody, James W. Lillard, Jr. and on behalf of the NYGC ALS Consortium.

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  • medRxiv  ·  September 21, 2025  ·  Preprint

    Uncovering splicing-mediated disease associations in the UK Biobank and All of Us using a TWAS with Bayesian joint fine-mapping.

    Alex Tokolyi, Saikat Banerjee, David A Knowles.

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  • bioRxiv  ·  September 20, 2025  ·  Preprint

    Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.

    Isabella N Grabski, Junsuk Lee, John Blair, Carol Dalgarno, Isabella Mascio, Alexandra Bradu, David A Knowles, Rahul Satija.

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  • Nature  ·  September 17, 2025

    CRISPR activation for SCN2A-related neurodevelopmental disorders.

    Serena Tamura, Andrew D. Nelson, Perry W. E. Spratt, Elizabeth C. Hamada, Xujia Zhou, Henry Kyoung, Zizheng Li, Coline Arnould, Vladyslav Barskyi, Beniamin Krupkin, Kiana Young, Jingjing Zhao, Stephanie S. Holden, Atehsa Sahagun, Caroline M. Keeshen, Congyi Lu, Roy Ben-Shalom, Sunrae E. Taloma, Selin Schamiloglu, Ying C. Li, Lia Min, Paul M. Jenkins, Jen Q. Pan, Jeanne T. Paz, Stephan J. Sanders, Navneet Matharu, Nadav Ahituv & Kevin J. Bender.

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  • Dermatologic Surgery  ·  September 17, 2025

    Survival Outcomes in Cutaneous Angiosarcoma: A Meta Analysis.

    Aneri Bhargav Patel, William Driscoll, Ajay Nair Sharma, Luke Horton, Janellen Smith.

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