Publications

Our Scientific Publications

  • The Plant Cell  ·  November 15, 2021

    Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems.

    Simon C Groen, Zoe Joly-Lopez, Adrian E Platts, Mignon Natividad, Zoe Fresquez, William M Mauck III, Marinell R Quintana, Carlo LU Cabral, Rolando O Torres, Rahul Satija, Michael D Purugganan, Amelia Henry
    Satija Lab Biology, Genomics & Technology
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  • bioRxiv  ·  November 10, 2021  ·  Preprint

    High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.

    Marta Byrska-Bishop, Uday S Evani, Xuefang Zhao, Anna O Basile, Haley J Abel, Allison A Regier, André Corvelo, Wayne E Clarke, Rajeeva Musunuri, Kshithija Nagulapalli, Susan Fairley, Alexi Runnels, Lara Winterkorn, Ernesto Lowy, The Human Genome Structural Variation Consortium, Paul Flicek, Soren Germer, Harrison Brand, Ira M Hall, Michael E Talkowski, Giuseppe Narzisi, Michael C Zody

    Biology, Genomics & Technology Computational Biology Lab
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  • Genes  ·  October 30, 2021

    Molecular Classification and Interpretation of Amyotrophic Lateral Sclerosis Using Deep Convolution Neural Networks and Shapley Values.

    Abdul Karim, Zheng Su, Phillip K. West, Matthew Keon, The NYGC ALS Consortium, Jannah Shamsani, Samuel Brennan, Ted Wong, Ognjen Milicevic, Guus Teunisse, Hima Nikafshan Rad and Abdul Sattar

    Phatnani Lab Neurodegenerative Disease
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  • PLOS Biology  ·  October 7, 2021

    A field guide to cultivating computational biology.

    Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley SD, Gosline SJC, Lȇ Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, Fertig EJ.

    Biology, Genomics & Technology Computational Biology Lab
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  • Annals of the New York Academy of Sciences  ·  October 3, 2021

    Single cell biology-a Keystone Symposia report.

    Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon U, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M.Ann
    Landau Lab Cancer Biology, Genomics & Technology Computational Biology Lab
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  • Nature Genetics  ·  September 30, 2021

    Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states.

    Ronan Chaligne, Federico Gaiti, Dana Silverbush, Joshua S. Schiffman, Hannah R. Weisman, Lloyd Kluegel, Simon Gritsch, Sunil D. Deochand, L. Nicolas Gonzalez Castro, Alyssa R. Richman, Johanna Klughammer, Tommaso Biancalani, Christoph Muus, Caroline Sheridan, Alicia Alonso, Franco Izzo, Jane Park, Orit Rozenblatt-Rosen, Aviv Regev, Mario L. Suvà & Dan A. Landau

    Landau Lab Cancer Biology, Genomics & Technology Computational Biology Lab
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  • American Journal of Human Genetics  ·  September 27, 2021

    An integrated approach to identify environmental modulators of genetic risk factors for complex traits.

    Balliu B, Carcamo-Orive I, Gloudemans MJ, Nachun DC, Durrant MG, Gazal S, Park CY, Knowles DA, Wabitsch M, Quertermous T, Knowles JW, Montgomery SB.
    Knowles Lab Biology, Genomics & Technology Computational Biology Lab
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  • Nature Communications  ·  September 13, 2021

    Multi-platform profiling characterizes molecular subgroups and resistance networks in chronic lymphocytic leukemia.

    Bloehdorn J, Braun A, Taylor-Weiner A, Jebaraj BMC, Robrecht S, Krzykalla J, Pan H, Giza A, Akylzhanova G, Holzmann K, Scheffold A, Johnston HE, Yeh RF, Klymenko T, Tausch E, Eichhorst B, Bullinger L, Fischer K, Weisser M, Robak T, Schneider C, Gribben J, Dahal LN, Carter MJ, Elemento O, Landau DA, Neuberg DS, Cragg MS, Benner A, Hallek M, Wu CJ, Döhner H, Stilgenbauer S, Mertens D.
    Cancer Biology, Genomics & Technology Computational Biology Lab
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  • Nature Communications  ·  September 13, 2021

    Multi-platform profiling characterizes molecular subgroups and resistance networks in chronic lymphocytic leukemia.

    Bloehdorn J, Braun A, Taylor-Weiner A, Jebaraj BMC, Robrecht S, Krzykalla J, Pan H, Giza A, Akylzhanova G, Holzmann K, Scheffold A, Johnston HE, Yeh RF, Klymenko T, Tausch E, Eichhorst B, Bullinger L, Fischer K, Weisser M, Robak T, Schneider C, Gribben J, Dahal LN, Carter MJ, Elemento O, Landau DA, Neuberg DS, Cragg MS, Benner A, Hallek M, Wu CJ, Döhner H, Stilgenbauer S, Mertens D.

    Landau Lab Cancer Biology, Genomics & Technology Computational Biology Lab
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  • Nature  ·  September 8, 2021

    A roadmap for the Human Developmental Cell Atlas.

    Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A, Etchevers HC, Giacobini P, Göttgens B, Guo G, Hupalowska A, James KR, Kirby E, Kriegstein A, Lundeberg J, Marioni JC, Meyer KB, Niakan KK, Nilsson M, Olabi B, Pe’er D, Regev A, Rood J, Rozenblatt-Rosen O, Satija R, Teichmann SA, Treutlein B, Vento-Tormo R, Webb S; Human Cell Atlas Developmental Biological Network.
    Satija Lab Biology, Genomics & Technology Computational Biology Lab
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  • Nature Biotechnology  ·  September 9, 2021

    Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.

    Jonathan Foox, Scott W. Tighe, Charles M. Nicolet, Justin M. Zook, Marta Byrska-Bishop, Wayne E. Clarke, Michael M. Khayat, Medhat Mahmoud, Phoebe K. Laaguiby, Zachary T. Herbert, Derek Warner, George S. Grills, Jin Jen, Shawn Levy, Jenny Xiang, Alicia Alonso, Xia Zhao, Wenwei Zhang, Fei Teng, Yonggang Zhao, Haorong Lu, Gary P. Schroth, Giuseppe Narzisi, William Farmerie, Fritz J. Sedlazeck, Don A. Baldwin & Christopher E. Mason

    Biology, Genomics & Technology Computational Biology Lab
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  • Molecular Psychiatry  ·  September 7, 2021

    Induction of dopaminergic neurons for neuronal subtype-specific modeling of psychiatric disease risk.

    Powell SK, O’Shea C, Townsley K, Prytkova I, Dobrindt K, Elahi R, Iskhakova M, Lambert T, Valada A, Liao W, Ho SM, Slesinger PA, Huckins LM, Akbarian S, Brennand KJ. doi: 10.1038/s41380-021-01273-0.

    Biology, Genomics & Technology Neuropsychiatric Disease Computational Biology Lab
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  • Cell Genomics  ·  September 3, 2021

    Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens.

    Xinyi Guo, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Daniel Haro, Neville E. Sanjana

    Sanjana Lab Biology, Genomics & Technology
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  • medRxiv  ·  September 2, 2021  ·  Preprint

    Integrative genetic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes.

    Jack Humphrey, Sanan Venkatesh, Rahat Hasan, Jake T Herb, Katia de Paiva Lopes, Fahri Kucukali, Marta Byrska-Bishop, Uday S Evani, Giuseppe Narzisi, Delphine Fagegaltier, NYGC ALS Consortium, Kristel Sleegers, Hemali Phatnani, David A Knowles, Pietro Fratta, Towfique Raj

    Knowles Lab Phatnani Lab Biology, Genomics & Technology Neurodegenerative Disease Computational Biology Lab
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