Publications - New York Genome Center

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.

Science · August 31, 2018

Fusion oncogenes-genetic musical chairs.

Imielinski M, Ladanyi M.

Imieliński Lab

Science Translational Medicine · August 8, 2018

A genome-wide net to catch and understand cancer

Sanjana, NE.

Sanjana Lab

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.

Sanjana Lab

Micro and Nano Systems Letters · June 21, 2018

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

Stephenson W.

Technology Innovation

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.

Computational Biology Lab

Technology Innovation

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.

Satija Lab

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.

Computational Biology Lab

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.

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.

Sanjana Lab

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.

Sanjana Lab

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.

Computational Biology Lab

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.

Phatnani Lab

Molecular Systems Biology · March 15, 2018

Molecular transitions in early progenitors during human cord blood hematopoiesis.

Zheng S, Papalexi E, Butler A, Stephenson W, Satija R.

Genome Research · March 13, 2018

SvABA: genome-wide detection of structural variants and indels by local assembly.

Wala JA, Bandopadhayay P, Greenwald N, O’Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.

Am J Respir Crit Care Med · March 6, 2018

Whole Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma.

Mak AC, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD, Burchard EG; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium.

Clinical and translational gastroenterology · February 20, 2018

Barrett’s esophagus is associated with a distinct oral microbiome.

Snider EJ, Compres G, Freedberg DE, Giddins MJ, Khiabanian H, Lightdale CJ, Nobel YR, Toussaint NC, Uhlemann AC, Abrams JA.

Computational Biology Lab

Arthritis Rheumatol · February 22, 2018

Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data

Orange DE, Agius P, DiCarlo EF, Robine N, Geiger H, Szymonifka J, McNamara M, Cummings R, Andersen KM, Mirza S, Figgie M, Ivashkiv L, Pernis AB, Jiang C, Frank M, Darnell R, Lingampali N, William R, Gravallese E, Bykerk VP, Goodman SM, Donlin LT; Accelerating Medicine Partnership: RA/SLE Network.

Computational Biology Lab

Nature Communications · February 23, 2018

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.

Stephenson W, Donlin LT, Butler A, Rozo C, Bracken B, Rashidfarrokhi A, Goodman SM, Ivashkiv LB, Bykerk VP, Orange DE, Darnell RB, Swerdlow HP, Satija R.

Satija Lab

Technology Innovation

Int J Mol Med · February 12, 2018

microRNA expression profiles of scar and normal tissue from patients with posterior urethral stricture caused by pelvic fracture urethral distraction defects.

Zhang K, Chen J, Zhang D, Wang L, Zhao W, Lin DY, Chen R, Xie H, Hu X, Fang X, Fu Q.

Computational Biology Lab

Methods Mol Biol · February 2, 2018

Whole Genome Sequencing-Based Discovery of Structural Variants in Glioblastoma.

Wrzeszczynski KO, Felice V, Shah M, Rahman S, Emde AK, Jobanputra V, O Frank M, Darnell RB.

Phatnani Lab

Computational Biology Lab

Our Scientific Publications

Discovery of a periosteal stem cell mediating intramembranous bone formation.

Fusion oncogenes-genetic musical chairs.

A genome-wide net to catch and understand cancer

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

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

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

Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features.

Organoid profiling identifies common responders to chemotherapy in pancreatic cancer.

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

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

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

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

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

Molecular transitions in early progenitors during human cord blood hematopoiesis.

SvABA: genome-wide detection of structural variants and indels by local assembly.

Whole Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma.

Barrett’s esophagus is associated with a distinct oral microbiome.

Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.

microRNA expression profiles of scar and normal tissue from patients with posterior urethral stricture caused by pelvic fracture urethral distraction defects.

Whole Genome Sequencing-Based Discovery of Structural Variants in Glioblastoma.