Preprint > Page 13
  • bioRxiv  ·  October 16, 2024  ·  Preprint

    A Reproducibility Focused Meta-Analysis Method for Single-Cell Transcriptomic Case-Control Studies Uncovers Robust Differentially Expressed Genes.

    Nathan Joel Nakatsuka, Drew Adler, Longda Jiang, Austin Hartman, Evan Cheng, Eric Klann, Rahul Satija

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  • bioRxiv  ·  October 15, 2024  ·  Preprint

    Efficient indexing and querying of annotations in a pangenome graph.

    Adam M. Novak, Dickson Chung, Glenn Hickey, Sarah Djebali, Toshiyuki T. Yokoyama, Erik Garrison, Giuseppe Narzisi, Benedict Paten, Jean Monlong

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  • bioRxiv  ·  October 11, 2024  ·  Preprint

    Targetable treatment resistance in thyroid cancer with clonal hematopoiesis.

    Vera Tiedje, Pablo Sánchez Vela, Julie L. Yang, Brian R. Untch, Laura Boucai, Aaron J. Stonestrom, Alberto Bueno Costa, Sebastià Franch Expósito, Avi Srivastava, Marina Kerpelev, Jillian Greenberg, Mathew Wereski, Amanda Kulick, Kevin Chen, Tianyue Qin, Soo-Yeon Im, Aishwarya Krishnan, Anthony R. Martinez Benitez, Raquel Pluvinet, Merve Sahin, Kamal Menghrajani, Gnana P. Krishnamoorthy, Elisa de Stanchina, Ahmet Zehir, Rahul Satija, Jeffrey Knauf, Robert L Bowman, Manel Esteller, Sean Devlin, Michael F. Berger, Richard P. Koche, James A. Fagin, Ross L Levine

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  • bioRxiv  ·  September 25, 2024  ·  Preprint

    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, 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, Stephan Scholz, Yuwei Song, Arda Soylev, Arvis Sulovari, Likhitha Surapaneni, Vasiliki Tsapalou, Weichen Zhou, Ying Zhou, Qihui Zhu, Michael C. Zody, Ryan E. Mills, Scott E. Devine, Xinghua Shi, Mike E Talkowski, Mark J.P. Chaisson, Alexander T Dilthey, Miriam K. Konkel, Jan O. Korbel, Charles Lee, Christine R. Beck, Evan E. Eichler and Tobias Marschall

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  • bioRxiv  ·  September 22, 2024  ·  Preprint

    Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks.

    Jennifer H. McDaniel, Vaidehi Patel, Nathan D. Olson, Hua-Jun He, Zhiyong He, Anthony Schmitt, Kristin Sikkink, Fritz Sedlazeck, Harsha Doddapaneni, Shalini N. Jhangiani, Donna M. Muzny, Marie-Claude Gingras, Heer Mehta, Luis F. Paulin, Alex R. Hastie, Hung-Chun Yu, Victor Weigman, Alison Rojas, Katie Kennedy, Jamie Remington, Isai Gonzalez, Mitch Sudkamp, Kelly Wiseman, Bryan Lajoie, Shawn Levy, Miten Jain, Stuart Akeson, Giuseppe Narzisi, Zoe Steinsnyder, Catherine Reeves, Jennifer Shelton, Sarah B. Kingan, Christine Lambert, Primo Bayabyan, Aaron M. Wenger, Ian J. McLaughlin, Aaron Adamson, Christopher Kingsley, Melanie Wescott, Young Kim, Benedict Paten, Jimin Park, Ivo Violich, Karen H. Miga, Joshua Gardner, Brandy McNulty, Gail Rosen, Rajiv McCoy, Lesley Chapman Hannah, Doron Lipson, Hila Benjamin, Nika Iremadze, Ilya Soifer, Stephen Eacker, Mary Wood, Erin Cross, Greg Husar, Stephen Gross, Michael Vernich, Mikhail Komogorov, Tanveer Ahmad, Ayse Keskus, Asher Bryant, Francoise Thibaud-Nissen, Jonathan Trow, Justin Wagner, Chunlin Xiao, Andrew S Liss, Justin M. Zook

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  • bioRxiv  ·  August 27, 2024  ·  Preprint

    Type 1 interferon perturbates clonal competition by reshaping human blood development.

    Chhiring Lama, Danielle Isakov, Shira Rosenberg, Miguel Quijada-Alamo, Mirca S Saurty-Seerunghen, Sara Moein, Tsega-Ab Abera, Olivia Sakaguchi, Mansi Totwani, Grace Freed, Chi-Lam Poon, Neelang Parghi, Andrea Kubas-Meyer, Amy X. Xie, Mohamed Omar, Daniel Choi, Franco Castillo-Tokumori, Ghaith Abu-Zeinah, Alicia Dillard, Nathaniel D Omans, Neville N Dusaj, Paulina Chamely, Eleni Mimitou, Peter Smibert, Heidi E. Kosiorek, Amylou C. Dueck, Rona Weinberg, Ronan Chaligne, Bridget Marcellino, Luigi Marchionni, Sanjay Patel, Paul D. Simonson, Dan A. Landau, Elvin Wagenblast, Ronald Hoffman, Anna S Nam

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  • bioRxiv  ·  July 19, 2024  ·  Preprint

    ALS molecular subtypes are a combination of cellular, genetic, and pathological features learned by deep multiomics classifiers.

    Kathryn ONeill, Regina Shaw, Isobel Bolger, NYGC ALS Consortium, Oliver H Tam, Hemali Phatnani, Molly Gale Hammell

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  • bioRxiv  ·  June 12, 2024  ·  Preprint

    Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database.

    Sanna Gudmundsson, Moriel Singer-Berk, Sarah L. Stenton, Julia K. Goodrich, Michael W. Wilson, Jonah Einson, Nicholas A Watts, Genome Aggregation Database Consortium, Tuuli Lappalainen, Heidi L. Rehm, Daniel G. MacArthur, Anne O’Donnell-Luria

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  • bioRxiv  ·  May 31, 2024  ·  Preprint

    Systems genomics of salinity stress response in rice.

    Sonal Gupta, Simon C. Groen, Maricris L. Zaidem, Andres Godwin C. Sajise, Irina Calic, Mignon A. Natividad, Kenneth L. McNally, Georgina V. Vergara, Rahul Satija, Steven J. Franks, Rakesh K. Singh, Zoé Joly-Lopez, Michael D. Purugganan

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  • 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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