• J Mol Diagn  ·  November 2018

    Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer

    Wrzeszczynski KO, Felice V, Abhyankar A, Kozon L, Geiger H, Manaa D, London F, Robinson D, Fang X, Lin D, Lamendola-Essel MF, Khaira D, Dikoglu E, Emde AK, Robine N, Shah M, Arora K, Basturk O, Bhanot U, Kentsis A, Mansukhani MM, Bhagat G, Jobanputra V.

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  • Proc Natl Acad Sci USA  ·  October 15, 2018

    Impaired hematopoiesis and leukemia development in mice with a conditional knock-in allele of a mutant splicing factor gene U2af1.

    Fei DL, Zhen T, Durham B, Ferrarone J, Zhang T, Garrett L, Yoshimi A, Abdel-Wahab O, Bradley RK, Liu P, Varmus H.

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  • Elife  ·  May 8, 2018

    Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes.

    Knowles DA, Burrows CK, Blischak JD, Patterson KM, Serie DJ, Norton N, Ober C, Pritchard JK, Gilad Y.

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  • Nature Methods  ·  May 22, 2017

    Allele-specific expression reveals interactions between genetic variation and environment.

    Knowles DA, Davis JR, Edgington H, Raj A, Favé MJ, Zhu X, Potash JB, Weissman MM, Shi J, Levinson DF, Awadalla P, Mostafavi S, Montgomery SB, Battle A.

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  • Nature Genetics  ·  December 11, 2017

    Annotation-free quantification of RNA splicing using LeafCutter.

    Li YI, Knowles DA, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK.

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  • Nature  ·  July 3, 2019

    Somatic mutations and cell identity linked by Genotyping of Transcriptomes

    Nam AS, Kim K-T, Chaligne R, Izzo F, Ang C, Abu-Zeinah G, Omans ND, Pastore A, Taylor J, Alonso A, Mariani M, Cubillos-Ruiz JR, Tam W, Hoffman R, .Scandura, JM, Rabadan R, Abdel-Wahab O, Smibert P, Landau DA.

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  • The Journal of experimental medicine  ·  October 5, 2018

    Kinetics of adult hematopoietic stem cell differentiation in vivo.

    Upadhaya S, Sawai CM, Papalexi E, Rashidfarrokhi A, Jang G, Chattopadhyay P, Satija R, Reizis B.

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  • Nature Communications  ·  October 2, 2018

    Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects.

    Regier AA, Farjoun Y, Larson DE, Krasheninina O, Kang HM, Howrigan DP, Chen BJ, Kher M, Banks E, Ames DC, English AC, Li H, Xing J, Zhang Y, Matise T, Abecasis GR, Salerno W, Zody MC, Neale BM, Hall IM.

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  • Nature  ·  September 24, 2018

    Discovery of a periosteal stem cell mediating intramembranous bone formation.

    Debnath S, Yallowitz AR, McCormick J, Lalani S, Zhang T, Xu R, Li N, Liu Y, Yang YS, Eiseman M, Shim JH, Hameed M, Healey JH, Bostrom MP, Landau DA, Greenblatt MB.

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  • Science  ·  August 31, 2018

    Fusion oncogenes-genetic musical chairs.

    Imielinski M, Ladanyi M.
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  • Science Translational Medicine  ·  August 8, 2018

    A genome-wide net to catch and understand cancer

    Sanjana, NE.

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  • American Journal of Medical Genetics  ·  May 7, 2018

    Two Angelman families with unusually advanced neurodevelopment carry a start codon variant in the most highly expressed UBE3A isoform.

    Sadhwani A, Sanjana NE, Willen JM, Calculator SN, Black ED, Bean LJH, Li H., Tan WH.

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  • Micro and Nano Systems Letters  ·  June 21, 2018

    High-throughput magnetic particle washing in nanoliter droplets using serial injection and splitting.

    Stephenson W.

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  • Proc Natl Acad Sci USA  ·  June 6, 2018

    YES1 amplification is a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics.

    Fan PD, Narzisi G, Jayaprakash AD, Venturini E, Robine N, Smibert P, Germer S, Yu HA, Jordan EJ, Paik PK, Janjigian YY, Chaft JE, Wang L, Jungbluth AA, Middha S, Spraggon L, Qiao H, Lovly CM, Kris MG, Riely GJ, Politi K, Varmus H, Ladanyi M.

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  • Cell  ·  June 9, 2018

    Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features.

    Konstantinides N, Kapuralin K, Fadil C, Barboza L, Satija R, Desplan C.

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  • Cancer Discovery  ·  May 31, 2018

    Organoid profiling identifies common responders to chemotherapy in pancreatic cancer.

    Tiriac H, Belleau P, Engle DD, Plenker D, Deschênes A, Somerville T, Froeling FEM, Burkhart RA, Denroche RE, Jang GH, Miyabayashi K, Young CM, Patel H, Ma M, LaComb JF, Palmaira RLD, Javed AA, Huynh JA, Johnson M, Arora K, Robine N, Shah M, Sanghvi R, Goetz AB, Lowder CY, Martello L, Driehuis E, Lecomte N, Askan G, Iacobuzio-Donahue CA, Clevers H, Wood LD, Hruban RH, Thompson ED, Aguirre AJ, Wolpin BM, Sasson A, Kim J, Wu M, Bucobo JC, Allen PJ, Sejpal DV, Nealon W, Sullivan JD, Winter JM, Gimotty PA, Grem JL, DiMaio DJ, Buscaglia JM, Grandgenett PM, Brody JR, Hollingsworth MA, O’Kane GM, Notta F, Kim EJ, Crawford JM, Devoe CE, Ocean A, Wolfgang CL, Yu KH, Li E, Vakoc CR, Hubert B, Fischer SE, Wilson JM, Moffitt RA, Knox JJ, Krasnitz A, Gallinger S, Tuveson DA.

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  • Genome Research  ·  May 15, 2018

    Mapping and characterizing N6-methyladenine in eukaryotic genomes using single molecule real-time sequencing.

    Zhu S, Beaulaurier J, Deikus G, Wu T, Strahl M, Hao Z, Luo G, Gregory JA, Chess A, He C, Xiao A, Sebra R, Schadt EE, Fang G.

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  • Nature Biomedical Engineering  ·  April 9, 2018

    Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons.

    Tekin H, Simmons S, Cummings B, Gao L, Adiconis X, Hession CC, Ghoshal A, Dionne D, Choudhury SR, Yesilyurt V, Sanjana NE, Shi X, Lu C, Heidenreich, Pan JQ, Levin JZ & Zhang F.

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  • Nature protocols  ·  April 12, 2018

    Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

    Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP, Pinello L.

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  • Genome Research  ·  March 27, 2018

    taxMaps: Comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.

    Corvelo A, Clarke WE, Robine N, Zody MC.

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  • Neuron  ·  March 21, 2018

    Genome-wide Analyses Identify KIF5A as a Novel ALS Gene.

    Nicolas A, Kenna KP, Renton AE, Ticozzi N, Faghri F, Chia R, Dominov JA, Kenna BJ, Nalls MA, Keagle P, Rivera AM, van Rheenen W, Murphy NA, van Vugt JJFA, Geiger JT, Van der Spek RA, Pliner HA, Shankaracharya, Smith BN, Marangi G, Topp SD, Abramzon Y, Gkazi AS, Eicher JD, Kenna A; ITALSGEN Consortium, Mora G, Calvo A, Mazzini L, Riva N, Mandrioli J, Caponnetto C, Battistini S, Volanti P, La Bella V, Conforti FL, Borghero G, Messina S, Simone IL, Trojsi F, Salvi F, Logullo FO, D’Alfonso S, Corrado L, Capasso M, Ferrucci L; Genomic Translation for ALS Care (GTAC) Consortium, Moreno CAM, Kamalakaran S, Goldstein DB; ALS Sequencing Consortium, Gitler AD, Harris T, Myers RM; NYGC ALS Consortium, Phatnani H, Musunuri RL, Evani US, Abhyankar A, Zody MC; Answer ALS Foundation, Kaye J, Finkbeiner S, Wyman SK, LeNail A, Lima L, Fraenkel E, Svendsen CN, Thompson LM, Van Eyk JE, Berry JD, Miller TM, Kolb SJ, Cudkowicz M, Baxi E; Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, Benatar M, Taylor JP, Rampersaud E, Wu G, Wuu J; SLAGEN Consortium, Lauria G, Verde F, Fogh I, Tiloca C, Comi GP, Sorarù G, Cereda C; French ALS Consortium, Corcia P, Laaksovirta H, Myllykangas L, Jansson L, Valori M, Ealing J, Hamdalla H, Rollinson S, Pickering-Brown S, Orrell RW, Sidle KC, Malaspina A, Hardy J, Singleton AB, Johnson JO, Arepalli S, Sapp PC, McKenna-Yasek D, Polak M, Asress S, Al-Sarraj S, King A, Troakes C, Vance C, de Belleroche J, Baas F, Ten Asbroek ALMA, Muñoz-Blanco JL, Hernandez DG, Ding J, Gibbs JR, Scholz SW, Floeter MK, Campbell RH, Landi F, Bowser R, Pulst SM, Ravits JM, MacGowan DJL, Kirby J, Pioro EP, Pamphlett R, Broach J, Gerhard G, Dunckley TL, Brady CB, Kowall NW, Troncoso JC, Le Ber I, Mouzat K, Lumbroso S, Heiman-Patterson TD, Kamel F, Van Den Bosch L, Baloh RH, Strom TM, Meitinger T, Shatunov A, Van Eijk KR, de Carvalho M, Kooyman M, Middelkoop B, Moisse M, McLaughlin RL, Van Es MA, Weber M, Boylan KB, Van Blitterswijk M, Rademakers R, Morrison KE, Basak AN, Mora JS, Drory VE, Shaw PJ, Turner MR, Talbot K, Hardiman O, Williams KL, Fifita JA, Nicholson GA, Blair IP, Rouleau GA, Esteban-Pérez J, García-Redondo A, Al-Chalabi A; Project MinE ALS Sequencing Consortium, Rogaeva E, Zinman L, Ostrow LW, Maragakis NJ, Rothstein JD, Simmons Z, Cooper-Knock J, Brice A, Goutman SA, Feldman EL, Gibson SB, Taroni F, Ratti A, Gellera C, Van Damme P, Robberecht W, Fratta P, Sabatelli M, Lunetta C, Ludolph AC, Andersen PM, Weishaupt JH, Camu W, Trojanowski JQ, Van Deerlin VM, Brown RH Jr., van den Berg LH, Veldink JH, Harms MB, Glass JD, Stone DJ, Tienari P, Silani V, Chiò A, Shaw CE, Traynor BJ, Landers JE.

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