Publications

Our Scientific Publications

  • Nature Communications  ·  March 10, 2025

    Secure and scalable gene expression quantification with pQuant.

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

    Gürsoy Lab
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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

    L. Davis Lab Neuropsychiatric Disease
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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

    Computational Biology Lab Research Sequencing
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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

    Sanders Lab Neurodegenerative Disease Polyethnic-1000
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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

    Knowles Lab
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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

    Knowles Lab
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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

    Phatnani Lab Neurodegenerative Disease
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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

    Satija Lab
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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
    Gürsoy Lab
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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

    Computational Biology Lab
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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

    Cancer
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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

    Satija Lab
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  • bioRxiv  ·  February 20, 2025  ·  Preprint

    Uncovering the Signatures of Cellular Senescence in the Human Dorsolateral Prefrontal Cortex.

    Nicholas Sloan, Jason Mares, Aidan C Daly, Lilian Coie, Shaunice Grier, Natalie Barretto, Obadele Casel, Kristy Kang, Chris Jackson, Maria Pedersen, Shruti Khiste, Ben Fullerton, Joana Petrescu, Courteney Mattison, Colin Smith, Yousin Suh, Vilas Menon, Hemali Phatnani.

    Phatnani Lab Neurodegenerative Disease
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  • Nature Genetics  ·  February 17, 2025

    Multiomic single-cell profiling identifies critical regulators of postnatal brain.

    Research Sequencing
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  • Nature Communications  ·  February 13, 2025

    Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers.

    Christina M. Caragine, Victoria T. Le, Meer Mustafa, Bianca Jay Diaz, John A. Morris, Simon Müller, Alejandro Mendez-Mancilla, Evan Geller, Noa Liscovitch-Brauer & Neville E. Sanjana

    Sanjana Lab Cancer
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  • arXiv  ·  February 12, 2025  ·  Preprint

    PLayer-FL: A Principled Approach to Personalized Layer-wise Cross-Silo Federated Learning.

    Ahmed Elhussein, Gamze Gürsoy

    Gürsoy Lab
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  • Cell Genomics  ·  February 12, 2025

    Secure and federated quantitative trait loci mapping with privateQTL.

    Yoolim Annie Choi, Yebin Kim, Peihan Miao, Tuuli Lappalainen, Gamze Gürsoy

    Gürsoy Lab Lappalainen Lab
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  • Nature Biotechnology  ·  February 11, 2025

    Precise RNA targeting with CRISPR–Cas13d.

    Sydney K. Hart, Simon Müller, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Gediminas Drabavicius, Olivia Choi & Neville E. Sanjana

    Sanjana Lab
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  • Nature Computational Science  ·  February 7, 2025

    A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies.

    Xihao Li, Han Chen, Margaret Sunitha Selvaraj, Eric Van Buren, Hufeng Zhou, Yuxuan Wang, Ryan Sun, Zachary R. McCaw, Zhi Yu, Min-Zhi Jiang, Daniel DiCorpo, Sheila M. Gaynor, Rounak Dey, Donna K. Arnett, Emelia J. Benjamin, Joshua C. Bis, John Blangero, Eric Boerwinkle, Donald W. Bowden, Jennifer A. Brody, Brian E. Cade, April P. Carson, Jenna C. Carlson, Nathalie Chami, Yii-Der Ida Chen, Joanne E. Curran, Paul S. de Vries, Myriam Fornage, Nora Franceschini, Barry I. Freedman, Charles Gu, Nancy L. Heard-Costa, Jiang He, Lifang Hou, Yi-Jen Hung, Marguerite R. Irvin, Robert C. Kaplan, Sharon L. R. Kardia, Tanika N. Kelly, Iain Konigsberg, Charles Kooperberg, Brian G. Kral, Changwei Li, Yun Li, Honghuang Lin, Ching-Ti Liu, Ruth J. F. Loos, Michael C. Mahaney, Lisa W. Martin, Rasika A. Mathias, Braxton D. Mitchell, May E. Montasser, Alanna C. Morrison, Take Naseri, Kari E. North, Nicholette D. Palmer, Patricia A. Peyser, Bruce M. Psaty, Susan Redline, Alexander P. Reiner, Stephen S. Rich, Colleen M. Sitlani, Jennifer A. Smith, Kent D. Taylor, Hemant K. Tiwari, Ramachandran S. Vasan, Satupa’itea Viali, Zhe Wang, Jennifer Wessel, Lisa R. Yanek, Bing Yu, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Josée Dupuis, James B. Meigs, Paul L. Auer, Laura M. Raffield, Alisa K. Manning, Kenneth M. Rice, Jerome I. Rotter, Gina M. Peloso, Pradeep Natarajan, Zilin Li, Zhonghua Liu & Xihong Lin

    Computational Biology Lab Research Sequencing
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  • Scientific Reports  ·  February 5, 2025

    Whole genome sequencing in early onset advanced heart failure.

    Erik Linnér, Tomasz Czuba, Olof Gidlöf, Jakob Lundgren, Entela Bollano, Maria Hellberg, Selvi Celik, Neha Pimpalwar, Philipp Rentzsch, Molly Martorella, Anders Gummesson, Olle Melander, Sebastian Albinsson, Göran Dellgren, Jan Borén, Anders Jeppsson, R. Thomas Lumbers, Sonia Shah, Johan Nilsson, Pradeep Natarajan, Tuuli Lappalainen, Malin Levin, Hans Ehrencrona & J. Gustav Smith

    Lappalainen Lab Biology, Genomics & Technology
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