Publications - New York Genome Center

Genetics in Medicine · December 3, 2018

Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes.

Guo H, Duyzend MH, Coe BP, Baker C, Hoekzema K, Gerdts J, Turner TN, Zody MC, Beighley JS, Murali SC, Nelson BJ; University of Washington Center for Mendelian Genomics, Bamshad MJ, Nickerson DA, Bernier RA, Eichler EE.

Computational Biology Lab

Science · December 14, 2018

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk.

Rajarajan P, Borrman T, Liao W, Schrode N, Flaherty E, Casiño C, Powell S, Yashaswini C, LaMarca EA, Kassim B, Javidfar B, Espeso-Gil S, Li A, Won H, Geschwind DH, Ho SM, MacDonald M, Hoffman GE, Roussos P, Zhang B, Hahn CG, Weng Z, Brennand KJ, Akbarian S.

Computational Biology Lab

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.

Clinical Genetics

Computational Biology Lab

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.

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.

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.

Knowles Lab

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.

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.

Landau Lab

Cancer

Technology Innovation

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.

Satija Lab

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.

Computational Biology Lab

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

Our Scientific Publications

Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes.

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk.

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

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

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

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

Annotation-free quantification of RNA splicing using LeafCutter.

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

Kinetics of adult hematopoietic stem cell differentiation in vivo.

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

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.