• bioRxiv  ·  May 20, 2024  ·  Preprint

    Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome.

    Saravanan Ganesan, Rebecca M. Murray, Jesus Sotelo, Elliot O Eton, Kouhei Takashima, Theo Botella, Kai Beattie, Alyssa C. Indart, Nada Chraiki, Carolyne Croizier, Franco Izzo, Catherine Potenski, Samuele Marro, Zhijie Wu, Shouguo Gao, Neal S. Young, John D. Blair, Rahul Satija, Benjamin Terrier, Mael Heiblig, Eirini P Papapetrou, Pierre Sujobert, Olivier Kosmider, David B. Beck and Dan A Landau

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  • bioRxiv  ·  May 14, 2024  ·  Preprint

    Low copy CRISPR-Cas13d mitigates collateral RNA cleavage.

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

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  • Proceedings of the National Academy of Sciences of the United States of America  ·  May 14, 2024

    Genome-wide CRISPR screens in spheroid culture reveal that the tumor suppressor LKB1 inhibits growth via the PIKFYVE lipid kinase.

    John R Ferrarone, Jerin Thomas, Arun M Unni, Yuxiang Zheng, Michal J Nagiec, Eric E Gardner, Oksana Mashadova, Kate Li, Nikos Koundouros, Antonino Montalbano, Meer Mustafa, Lewis C Cantley, John Blenis, Neville E Sanjana, Harold Varmus

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  • Cell  ·  May 9, 2024

    The future of rapid and automated single-cell data analysis using reference mapping.

    Mohammad Lotfollahi, Yuhan Hao, Fabian J. Theis, Rahul Satija

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  • Communications Medicine  ·  May 9, 2024

    A comprehensive AI model development framework for consistent Gleason grading.

    Xinmi Huo, Kok Haur Ong, Kah Weng Lau, Laurent Gole, David M. Young, Char Loo Tan, Xiaohui Zhu, Chongchong Zhang, Yonghui Zhang, Longjie Li, Hao Han, Haoda Lu…Haotian Cao, Xiaozhen Yu, Yabin Shi, Ziling Huang, Gabriel Marini, Jun Xu, Bingxian Liu, Bingxian Chen, Qiang Wang, Kun Gui, Wenzhao Shi, Yingying Sun, Wanyuan Chen, Dalong Cao, Stephan J. Sanders, Hwee Kuan Lee, Susan Swee-Shan Hue, Weimiao Yu & Soo Yong Tan

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  • Nature  ·  May 8, 2024

    Mapping genotypes to chromatin accessibility profiles in single cells.

    Franco Izzo, Robert M. Myers, Saravanan Ganesan, Levan Mekerishvili, Sanjay Kottapalli, Tamara Prieto, Elliot O. Eton, Theo Botella, Andrew J. Dunbar, Robert L. Bowman, Jesus Sotelo, Catherine Potenski, Eleni P. Mimitou, Maximilian Stahl, Sebastian El Ghaity-Beckley, JoAnn Arandela, Ramya Raviram, Daniel C. Choi, Ronald Hoffman, Ronan Chaligné, Omar Abdel-Wahab, Peter Smibert, Irene M. Ghobrial, Joseph M. Scandura, Bridget Marcellino, Ross L. Levine & Dan A. Landau

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  • medRxiv  ·  April 25, 2024  ·  Preprint

    Mitochondrial genome variants associated with Amyotrophic Lateral Sclerosis and their haplogroup distribution.

    Marcelo R. S. Briones, João H. Campos, Renata C. Ferreira, Lisa Schneper, Ilda M. Santos, Fernando M. Antoneli, NYGC ALS Consortium, James R. Broach

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  • bioRxiv  ·  April 20, 2024  ·  Preprint

    Ultra-secure storage and analysis of genetic data for the advancement of precision medicine.

    Jacob Blindenbach, Jiayi Kang, Seungwan Hong, Caline Karam, Thomas Lehner, Gamze Gürsoy

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  • arXiv  ·  April 29, 2024  ·  Preprint

    A Universal Metric of Dataset Similarity for Cross-silo Federated Learning.

    Ahmed Elhussein and Gamze Gürsoy

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  • bioRxiv  ·  April 26, 2024  ·  Preprint

    Tissue and cellular spatiotemporal dynamics in colon aging.

    Aidan C. Daly, Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Marjanovic, Olena Kuksenko, Matthew Smith-Erb, Sara Fernandez, Daniel Domovic, Nicholas Van Wittenberghe, Eugene Drokhlyansky, Gabriel K Griffin, Hemali Phatnani, Richard Bonneau, Aviv Regev, Sanja Vicković

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  • JAMA Psychiatry  ·  April 17, 2024

    Examining Sex Differences in Autism Heritability.

    Sven Sandin, Benjamin H K Yip, Weiyao Yin, Lauren A Weiss, Joseph D Dougherty, Stuart Fass, John N Constantino, Zhu Hailin, Tychele N Turner, Natasha Marrus, David H Gutmann, Stephan J Sanders, Benjamin Christoffersson

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  • Nature Reviews Genetics  ·  April 12, 2024

    SIMPLE-seq to decode DNA methylation dynamics in single cells.

    Dongsheng Bai & Chenxu Zhu

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  • Acta Neuropathologica  ·  April 10, 2024

    Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer’s disease.

    Prabesh Bhattarai, Tamil Iniyan Gunasekaran, … Andrew F. Teich, Dennis W. Dickson, Scott Holley, Michael Greicius, Clifton L. Dalgard, Michael Zody, Richard Mayeux, Caghan Kizil & Badri N. Vardarajan

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  • bioRxiv  ·  April 10, 2024  ·  Preprint

    Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes.

    Philipp RentzschAaron Kollotzek, Pejman MohammadiTuuli Lappalainen

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  • Cancer Cell  ·  April 2, 2024

    Mutant IDH inhibitors induce lineage differentiation in IDH-mutant oligodendroglioma.

    Avishay Spitzer, Simon Gritsch, Masashi Nomura, Alexander Jucht, Jerome Fortin, Ramya Raviram, Hannah R Weisman, L Nicolas Gonzalez Castro, Nicholas Druck, Rony Chanoch-Myers, John J Y Lee, Ravindra Mylvaganam, Rachel Lee Servis, Jeremy Man Fung, Christine K Lee, Hiroaki Nagashima, Julie J Miller, Isabel Arrillaga-Romany, David N Louis, Hiroaki Wakimoto, Will Pisano, Patrick Y Wen, Tak W Mak, Marc Sanson, Mehdi Touat, Dan A Landau, Keith L Ligon, Daniel P Cahill, Mario L Suvà, Itay Tirosh

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  • NPJ Genomic Medicine  ·  March 27, 2024

    Advancing access to genome sequencing for rare genetic disorders: recent progress and call to action.

    Vaidehi Jobanputra, Brock Schroeder, Heidi L. Rehm, Wei Shen, Elizabeth Spiteri, Ghunwa Nakouzi, Stacie Taylor, Christian R. Marshall, Linyan Meng, Stephen F. Kingsmore, Katarzyna Ellsworth, Euan Ashley & Ryan J. Taft on behalf of the Medical Genome Initiative

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  • Science Advances  ·  March 22, 2024

    Childhood cancer mutagenesis caused by transposase-derived PGBD5.

    Makiko Yamada, Ross R Keller, Rodrigo Lopez Gutierrez, Daniel Cameron, Hiromichi Suzuki, Reeti Sanghrajka, Jake Vaynshteyn, Jeffrey Gerwin, Francesco Maura, William Hooper, Minita Shah, Nicolas Robine, Phillip Demarest, N Sumru Bayin, Luz Jubierre Zapater, Casie Reed, Steven Hébert, Ignas Masilionis, Ronan Chaligne, Nicholas D Socci, Michael D Taylor, Claudia L Kleinman, Alexandra L Joyner, G Praveen Raju, Alex Kentsis

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  • NPJ Genomic Medicine  ·  March 22, 2024

    Genomic analysis of 116 autism families strengthens known risk genes and highlights promising candidates.

    Marta Viggiano, Fabiola Ceroni, Paola Visconti, Annio Posar, Maria Cristina Scaduto, Laura Sandoni, Irene Baravelli, Cinzia Cameli, Magali J. Rochat, Alessandra Maresca, Alessandro Vaisfeld, Davide Gentilini, Luciano Calzari, Valerio Carelli, Michael C. Zody, Elena Maestrini & Elena Bacchelli

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  • STAR Protocols  ·  March 20, 2024

    GoT-Splice protocol for multi-omics profiling of gene expression, cell-surface proteins, mutational status, and RNA splicing in human cells.

    Ganesan S, Cortés-López M, Swett AD, Dai X, Hickey S, Chamely P, Hawkins AG, Juul S, Landau DA, Gaiti F.

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  • JMIR Publications  ·  March 15, 2024

    A Closed-Loop Digital Health Tool to Improve Depression Care in Multiple Sclerosis: Iterative Design and Cross-Sectional Pilot Randomized Controlled Trial and its Impact on Depression Care.

    Kyra Henderson, Jennifer Reihm, Kanishka Koshal, Jaeleene Wijangco, Narender Sara, Nicolette Miller, Marianne Doyle, Alicia Mallory, Judith Sheridan, Chu-Yueh Guo, Lauren Oommen, Katherine P Rankin, Stephan Sanders, Anthony Feinstein, Christina Mangurian, Riley Bove

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