• Cell Reports  ·  June 23, 2020

    Epigenomically Bistable Regions across Neuron-Specific Genes Govern Neuron Eligibility to a Coding Ensemble in the Hippocampus.

    Odell SC, Taki F, Klein SL, Chen RJ, Levine OB, Skelly MJ, Nabila A, Brindley E, Gal Toth J, Dündar F, Sheridan CK, Fetcho RN, Alonso A, Liston C, Landau DA, Pleil KE, Toth M

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  • PLOS Computational Biology  ·  June 19, 2020

    A crowdsourced set of curated structural variants for the human genome.

    Lesley M. Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc Salit, Justin M. Zook

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  • bioRxiv  ·  June 20, 2020  ·  Preprint

    Phenome-scale causal network discovery with bidirectional mediated Mendelian randomization.

    Brielin C Brown, David A Knowles
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  • PLOS Computational Biology  ·  June 19, 2020

    A Crowdsourcing app to visualize evidence of structural variants for the human genome.

    Lesley M Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc Salit, Justin M. Zook.
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  • bioRxiv  ·  June 16, 2020  ·  Preprint

    Improving oligo-conjugated antibody signal in multimodal single-cell analysis.

    Terkild Brink Buus, Alberto Herrera, Ellie Ivanova, Eleni Mimitou, Anthony Cheng, Thales Papagiannakopoulos, Peter Smibert, Niels Ødum, Sergei B. Koralov
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  • Cells  ·  June 5, 2020

    Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models.

    James A. Gregory, Emily Hoelzli, Rawaan Abdelaal, Catherine Braine, Miguel Cuevas, Madeline Halpern, Natalie Barretto, Nadine Schrode, Güney Akbalik, Kristy Kang, Esther Cheng, Kathryn Bowles, Steven Lotz, Susan Goderie, Celeste M. Karch, Sally Temple, Alison Goate, Kristen Brennand, Hemali Phatnani.

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  • Cell Reports  ·  June 2, 2020

    Acute Myeloid Leukemia iPSCs Reveal a Role for RUNX1 in the Maintenance of Human Leukemia Stem Cells.

    Wesely J, Kotini AG, Izzo F, Luo H, Yuan H, Sun J, Georgomanoli M, Zviran A, Deslauriers AG, Dusaj N, Nimer SD, Leslie C, Landau DA, Kharas MG, Papapetrou EP.

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  • bioRxiv  ·  June 1, 2020  ·  Preprint

    Direct detection of RNA modifications and structure using single molecule nanopore sequencing.

    William Stephenson, Roham Razaghi, Steven Busan, Kevin M. Weeks, Winston Timp, Peter Smibert

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  • Nature Medicine  ·  June 1, 2020

    Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring.

    Asaf Zviran, Rafael C. Schulman, Minita Shah, Steven T. K. Hill, Sunil Deochand, Cole C. Khamnei, Dillon Maloney, Kristofer Patel, Will Liao, Adam J. Widman, Phillip Wong, Margaret K. Callahan, Gavin Ha, Sarah Reed, Denisse Rotem, Dennie Frederick, Tatyana Sharova, Benchun Miao, Tommy Kim, Greg Gydush, Justin Rhoades, Kevin Y. Huang, Nathaniel D. Omans, Patrick O. Bolan, Andrew H. Lipsky, Chelston Ang, Murtaza Malbari, Catherine F. Spinelli, Selena Kazancioglu, Alexi M. Runnels, Samantha Fennessey, Christian Stolte, Federico Gaiti, Giorgio G. Inghirami, Viktor Adalsteinsson, Brian Houck-Loomis, Jennifer Ishii, Jedd D. Wolchok, Genevieve Boland, Nicolas Robine, Nasser K. Altorki & Dan A. Landau

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  • Genome Medicine  ·  May 27, 2020

    The Medical Genome Initiative: Moving Whole-Genome Sequencing for Rare Disease Diagnosis to the Clinic.

    Marshall CR, Bick D, Belmont JW, Taylor SL, Ashley E, Dimmock D, Jobanputra V, Kearney HM, Kulkarni S, Rehm H; Medical Genome Initiative.

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  • Am J Respir Crit Care Med  ·  May 27, 2020

    Whole Genome Sequencing Identifies Novel Functional Loci Associated with Lung Function in Puerto Rican Youth.

    Lee EY, Mak AC, Hu D, Sajuthi S, White MJ, Keys KL, Eckalbar W, Bonser L, Huntsman S, Urbanek C, Eng C, Jain D, Abecasis G, Kang HM, Germer S, Zody MC, Nickerson DA, Erle D, Ziv E, Rodriguez-Santana J, Seibold MA, Burchard EG.

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  • Nature  ·  May 27, 2020

    Mapping and characterization of structural variation in 17,795 human genomes.

    Haley J. Abel, David E. Larson, Allison A. Regier, Colby Chiang, Indraniel Das, Krishna L. Kanchi, Ryan M. Layer, Benjamin M. Neale, William J. Salerno, Catherine Reeves, Steven Buyske, NHGRI Centers for Common Disease Genomics, Tara C. Matise, Donna M. Muzny, Michael C. Zody, Eric S. Lander, Susan K. Dutcher, Nathan O. Stitziel & Ira M. Hall

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  • The Lancet Psychiatry  ·  May 20, 2020

    Mental Health Delivery and Neurogenetics Discovery in Africa.

    Dan J Stein , Thomas Lehner, Zane Lombard, Beverly Pringle, Geetha Senthil, Monica Uddin

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  • Genome Biology  ·  April 28, 2020

    ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data.

    Egor Dolzhenko, Mark F Bennett, Phillip A Richmond, Brett Trost, Sai Chen, Joke JFA van Vugt, Charlotte Nguyen, Giuseppe Narzisi, Vladimir G Gainullin, Andrew Gross, Bryan Lajoie, Ryan J Taft, Wyeth W Wasserman, Stephen W Scherer, Jan H Veldink, David R Bentley, Ryan KC Yuen, Melanie Bahlo, Michael A Eberle

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  • Genetics  ·  April 23, 2020

    Novel KITLG/SCF regulatory variants are associated with lung function in African American children with asthma.

    Angel Mak, Satria Sajuthi, Jaehyun Joo, Shujie Xiao, Patrick Sleiman, Marquitta J White, Eunice Y Lee, Benjamin Saef, Donglei Hu, Hongsheng Gui, Kevin L Keys, Fred Lurmann, Deepti Jain, Goncalo Abecasis, Hyun Min Kang, Deborah A Nickerson, Soren Germer, Michael C Zody, Lara Winterkorn, Catherine Reeves, Scott Huntsman, Celeste Eng, Sandra Salazar, Sam S Oh, Frank Gilliland, Zhanghua Chen, Rajesh Kumar, Fernando D Martinez, Ann Chen Wu, Elad Ziv, Hakon Hakonarson, Blanca E Himes, L Keoki Williams, Max A Seibold, Esteban G Burchard

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  • Nature Communications  ·  April 20, 2020

    High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange.

    Sarah A. Overall, Jugmohit S. Toor, Stephanie Hao, Mark Yarmarkovich, Sara M. O’Rourke, Giora I. Morozov, Son Nguyen, Alberto Sada Japp, Nicolas Gonzalez, Danai Moschidi, Michael R. Betts, John M. Maris, Peter Smibert & Nikolaos G. Sgourakis

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  • Neuron  ·  March 27, 2020

    The Loss of TBK1 Kinase Activity in Motor Neurons or in All Cell Types Differentially Impacts ALS Disease Progression in SOD1 Mice.

    Valeria Gerbino, Esther Kaunga, Junqiang Ye, Daniele Canzio, Sean O’Keeffe, Noam D. Rudnick Paolo Guarnieri, Cathleen M. Lutz, Tom Maniatis

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  • Nature Genetics  ·  March 23, 2020

    DNA methylation disruption reshapes the hematopoietic differentiation landscape.

    Izzo F, Lee SC, Poran A, Chaligne R, Gaiti F, Gross B, Murali RR, Deochand SD, Ang C, Jones PW, Nam AS, Kim KT, Kothen-Hill S, Schulman RC, Ki M, Lhoumaud P, Skok JA, Viny AD, Levine RL, Kenigsberg E, Abdel-Wahab O, Landau DA.

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  • Nature Biotechnology  ·  March 16, 2020

    Massively parallel Cas13 screens reveal principles for guide RNA design.

    Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Xinyi Guo, Mateusz Legut, Zharko Daniloski & Neville E. Sanjana.

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  • bioRxiv  ·  February 24, 2020  ·  Preprint

    An autoimmune disease risk variant has a trans master regulatory effect mediated by IRF1 under immune stimulation.

    Margot K Brandt, Sarah Kim-Hellmuth, Marcello Ziosi, Alper Gokden, Aaron Wolman, Nora Lam, Yocelyn Recinos, Veit K Hornung, Johannes Schumacher, Tuuli Lappalainen

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  • Cell Reports  ·  March 3, 2020

    High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation.

    Legut M, Daniloski Z, Xue X, McKenzie D, Guo X, Wessels HH, Sanjana NE.

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