Publications

Our Scientific Publications

  • Genome Biology  ·  December 6, 2021

    The SEQC2 epigenomics quality control (EpiQC) study.

    Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE.
    Biology, Genomics & Technology Computational Biology Lab
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  • bioRxiv  ·  November 20, 2021  ·  Preprint

    Antigen presentation by type 3 innate lymphoid cells instructs the differentiation of gut microbiota-specific regulatory T cells.

    Ranit Kedmi, Tariq Najar, Kailin R. Mesa, Allyssa Grayson, Lina Kroehling, Yuhan Hao, Stephanie Hao, Maria Pokrovskii, Mo Xu, Jhimmy Talbot, Jiaxi Wang, Mark S. Anderson, James M. Gardner, Terri M. Laufer, Iannis Aifantis, Juliet M. Bartleson, Paul M. Allen, Marlon Stoeckius, Dan R. Littman

    Biology, Genomics & Technology Computational Biology Lab
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  • Molecular Psychiatry  ·  November 19, 2021

    The benefit of diagnostic whole genome sequencing in schizophrenia and other psychotic disorders.

    Alkelai A, Greenbaum L, Docherty AR, Shabalin AA, Povysil G, Malakar A, Hughes D, Delaney SL, Peabody EP, McNamara J, Gelfman S, Baugh EH, Zoghbi AW, Harms MB, Hwang HS, Grossman-Jonish A, Aggarwal V, Heinzen EL, Jobanputra V, Pulver AE, Lerer B, Goldstein DB.
    Biology, Genomics & Technology Neuropsychiatric Disease Computational Biology Lab Clinical Genetics
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  • Microbiology Spectrum  ·  November 17, 2021

    Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study.

    Barun Mathema, Liang Chen, Kar Fai Chow, Yanan Zhao, Michael C Zody, Jose R Mediavilla, Marcus H Cunningham, Kaelea Composto, Annie Lee, Dayna M Oschwald, Soren Germer, Samantha Fennessey, Kishan Patel, David Wilson, Ann Cassell, Lauren Pascual, Andrew Ip, André Corvelo, Sophia Dar, Yael Kramer, Tom Maniatis, David S Perlin, Barry N Kreiswirth

    Maniatis Lab Biology, Genomics & Technology Computational Biology Lab
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  • 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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