Publications

Our Scientific Publications

  • Genome Research  ·  October 11, 2017

    Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change.

    Mohammadi P, Castel SE, Brown AA, Lappalainen T.

    Lappalainen Lab
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  • Molecular Cell  ·  October 5, 2017

    High-Throughput Approaches to Pinpoint Function within the Noncoding Genome.

    Montalbano A, Canver, MC and Sanjana NE.

    Sanjana Lab
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  • Nature  ·  March 5, 2018

    Developmental diversification of cortical inhibitory interneurons.

    Mayer C, Hafemeister C, Bandler RC, Machold R, Allaway K, Jaglin X, Brito RB, Butler A, Fishell G, Satija R.
    Satija Lab
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  • Communications Biology  ·  March 22, 2018

    Lancet: genome-wide somatic variant calling using localized colored DeBruijn graphs.

    Narzisi G, Corvelo A, Arora K, Bergmann E, Shah M, Musunuri R, Emde, A-K, Robine N, Vacic V, Zody MC.
    Computational Biology Lab
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  • Nature Genetics  ·  September 11, 2017

    Interpreting short tandem repeat variations in humans using mutational constraint.

    Gymrek M, Willems T, Reich D, Erlich Y.

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  • Cell  ·  September 28, 2017

    Genomic Patterns of De Novo Mutation in Simplex Autism.

    Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB,
    Eichler EE.

    Computational Biology Lab
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  • Genome Research  ·  August 9, 2018

    Whole-Genome Bisulphite Sequencing With Improved Accuracy and Cost

    Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM.

    Computational Biology Lab
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  • PLOS Biology  ·  December 30, 2018

    Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results.

    Alterovitz G, Dean DA II, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, King CHS IV, Johanson E, Thompson EE, Donaldson E, Tsang HS, Goecks J, Almeida JS, Guo L, Walderhaug M, Walsh P, Kahsay R, Bloom T, Lai Y, Simonyan V, Mazumder R.

    Computational Biology Lab
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  • Nature Genetics  ·  August 20, 2018

    Modified penetrance of coding variants by cis-regulatory variation shapes human traits.

    Castel SE, Cervera A, Mohammadi P, Aguet F, Reverter F, Wolman A, Guigo R, Vasileva A, Lappalainen T.
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  • Nature Reviews Clinical Oncology  ·  February 14, 2017

    Genomic complexity of multiple myeloma and its clinical implications.

    Manier S, Salem KZ, Park J, Landau DA, Getz G, Ghobrial IM.

    Landau Lab
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  • Current Opinion in Systems Biology  ·  December 9, 2016

    Modeling cancer rearrangement landscapes.

    Maciejowski J, Imielinski M.

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  • Cold Spring Harbor Perspectives in Medicine  ·  June 1, 2017

    Chromosomal Instability as a Driver of Tumor Heterogeneity and Evolution.

    Bakhoum SF, Landau DA.

    Landau Lab
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  • Immunity  ·  September 7, 2017

    An NF-kB Transcription-Factor-Dependent Lineage Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function

    Oh H, Grinberg-Bleyer Y, Liao W, Maloney D, Wang P, Wu Z, Wang J, Bhatt DM, Heise N, Schmid RM, Hayden MS, Klein U Rabadan R, Ghosh S.

    Computational Biology Lab
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  • Nature Communications  ·  August 30, 2017

    ATRX is a regulator of therapy induced senescence in human cells.

    Kovatcheva M, Liao W, Klein ME, Robine N, Geiger H, Crago AM, Dickson MA, Tap WD, Singer S, Koff A.
    Computational Biology Lab
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  • Nature Communications  ·  August 16, 2017

    Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations.

    Kim-Hellmuth S, Bechheim M, Puetz B, Mohammadi P, Nedelec Y, Giangreco N, Becker J, Kaiser V, Fricker N, Beier E, Boor P, Castel S, Noethen MM, Barreiro LB, Pickrell JK, Mueller-Myhsok, Lappalainen T, Schumacher J, Hornung, V.

    Lappalainen Lab
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  • Nature Reviews Immunology  ·  August 7, 2017

    Single-cell RNA sequencing to explore immune cell heterogeneity.

    Papalexi E, Satija R.

    Satija Lab
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  • Modern Pathology  ·  August 4, 2017

    Pancreatic intraductal tubulopapillary neoplasm is genetically distinct from intraductal papillary mucinous neoplasm and ductal adenocarcinoma.

    Basturk O, Berger MF, Yamaguchi H, Adsay V, Askan G, Bhanot UK, Zehir A, Carneiro F, Hong SM, Zamboni G, Dikoglu E, Jobanputra V, Wrzeszczynski KO, Balci S, Allen P, Ikari N, Takeuchi S, Akagawa H, Kanno A, Shimosegawa T, Morikawa T, Motoi F, Unno M, Higuchi R, Yamamoto M, Shimizu K, Furukawa T, Klimstra DS.

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  • Nature  ·  August 7, 2017

    Identification of essential genes for cancer immunotherapy.

    Patel SJ, Sanjana NE, Kishton RJ, Eidizadeh A, Vodnala SK, Cam M, Gartner JJ, Jia, L, Steinberg SM, Yamamoto TN, Merchant, AS, Mehta, GU, Chichura A, Shalem O, Tran E, Eil, R, Sukumar M, Perez Guijarro E, Day C-P, Robbins P, Feldman S, Merlino G, Zhang F, Restifo, NP.

    Sanjana Lab
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  • Nature Methods  ·  August 31, 2017

    GUIDES: sgRNA design for loss-of-function screens.

    Meier, JA, Zhang F, Sanjana, NE.
    Sanjana Lab
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  • Neurology Genetics  ·  July 11, 2017

    Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

    Wrzeszczynski KO, Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Vacic V, Norel R, Bilal E, Bergmann EA, Moore Vogel JL, Bruce JN, Lassman AB, Canoll P, Grommes C, Harvey S, Parida L, Michelini VV, Zody MC, Jobanputra V, Royyuru AK, Darnell RB.

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