Publications - New York Genome Center

Clin Med Insights Oncol · November 15, 2016

Key Difficulties Associated with Cancer Biology.

Fang X, Aragon-Ching J, Cidon EU.

J Exp Med · November 18, 2016

Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+ or CD141+ DCs.

Breton G, Zheng S, Valieris R, Tojal da Silva I, Satija R, Nussenzweig MC.

Satija Lab

Nucleic Acid Res · November 29, 2016

Pharos: Collating protein information to shed light on the druggable genome.

Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma’ayan A, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R.

Leukemia · December 2, 2016

Frequent evolution of copy number alterations in CLL following first-line treatment with FC(R) is enriched with TP53 alterations: results from the CLL8 trial.

Edelmann J, Tausch E, Landau DA, Robrecht S, Bahlo J, Fischer K, Fink AM, Bloehdorn J, Holzmann K, Böttcher S, Werner L, Kneba M, Gribben JG, Neuberg DS, Wu CJ, Hallek M, Döhner H, Stilgenbauer S.

Landau Lab

Nat Protoc · December 11, 2016

Indel variant analysis of short-read sequencing data with Scalpel.

Fang H, Bergmann EA, Arora K, Vacic V, Zody MC, Iossifov I, O’Rawe JA, Wu Y, Jimenez Barron LT, Rosenbaum J, Ronemus M, Lee YH, Wang Z, Dikoglu E, Jobanputra V, Lyon GJ, Wigler M, Schatz MC, Narzisi G.

Iossifov Lab Wigler Lab

Anal Biochem · June 1, 2016

Genome-scale CRISPR pooled screens

Sanjana NE

Sanjana Lab

Science · June 2, 2016

The Genome Project-Write

Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L.

Sanjana Lab

Scientific Reports 6, Article number: 28384 · June 22, 2016

Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks

Thibault Honegger, Moritz I. Thielen, Soheil Feizi, Neville E. Sanjana & Joel Voldman

Sanjana Lab

Genome Biol. PubMed, PubMedCentral · April 28, 2016

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ Jr, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R

DNA Res. pii: dsw007. [Epub ahead of print] · March 6, 2016

Whole Genome Sequencing of Turbot (Scophthalmus maximus; Pleuronectiformes): A Fish Adapted to Demersal Life

Figueras A, Robledo D, Corvelo A, Hermida M, Pereiro P, Rubiolo JA, Gómez-Garrido J, Carreté L, Bello X, Gut M, Gut IG, Marcet-Houben M, Forn-Cuní G, Galán B, García JL, Abal-Fabeiro JL, Pardo BG, Taboada X, Fernández C, Vlasova A, Hermoso-Pulido A, Guigó R, Álvarez-Dios JA, Gómez-Tato A, Viñas A, Maside X, Gabaldón T, Novoa B, Bouza C, Alioto T, Martínez P

MBio. 7(2).pii: e00431-16. doi: 10.1128/mBio.00431-16 · April 5, 2016

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharach E, Mishra N, Briese T, Zody MC, Kembou Tsofack JE, Zamostiano R, Berkowitz A, Ng J, Nitido A, Corvelo A, Toussaint NC, Abel Nielsen SC, Hornig M, Del Pozo J, Bloom T, Ferguson H, Eldar A, Lipkin WI

Nature Genetics. doi:10.1038/ng.3559 · April 28, 2016

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

G David Poznik, Yali Xue, Fernando L Mendez, Thomas F Willems, Andrea Massaia, Melissa A Wilson Sayres, Qasim Ayub, Shane A McCarthy, Apurva Narechania, Seva Kashin, Yuan Chen, Ruby Banerjee, Juan L Rodriguez-Flores, Maria Cerezo, Haojing Shao, Melissa Gymrek, Ankit Malhotra, Sandra Louzada, Rob Desalle, Graham R S Ritchie, Eliza Cerveira, Tomas W Fitzgerald, Erik Garrison, Anthony Marcketta, David Mittelman

April 28, 2016

Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates

Thomas Willems, Melissa Gymrek, G. David Poznik, Chris Tyler-Smith, The 1000 Genomes Project Chromosome Y Group, and Yaniv Erlich

Cell Rep. 2016 Mar 30. pii: S2211-1247(16)30264-9. doi: 10.1016/j.celrep.2016.03.023. [Epub ahead of print] · April 13, 2016

PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage

Hwang HW, Park CY, Goodarzi H, Fak JJ, Mele A, Moore MJ, Saito Y, Darnell RB

Elife. 5. pii: e10421. doi: 10.7554/eLife.10421 · February 19, 2016

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

Scheckel C, Drapeau E, Frias MA, Park CY, Fak J, Zucker-Scharff I, Kou Y, Haroutunian V, Ma’ayan A, Buxbaum JD, Darnell RB

Am J Hum Genet. 2016 Jan 7;98(1):58-74. doi: 10.1016/j.ajhg.2015.11.023. Epub 2015 Dec 31. · April 13, 2016

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

Turner TN, Hormozdiari F, Duyzend MH, McClymont SA, Hook PW, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman HA, Zody MC, Nelson BJ, Huddleston J, Sandstrom R, Smith JD, Hanna D, Swanson JM, Faustman EM, Bamshad MJ, Stamatoyannopoulos J, Nickerson DA, McCallion AS, Darnell R, Eichler EE.

Iossifov Lab

Nat Genet. 2016 Jan;48(1):22-9. doi: 10.1038/ng.3461. Epub 2015 Dec 7. · March 17, 2016

Abundant contribution of short tandem repeats to gene expression variation in humans

GYMREK M, WILLEMS T, GUILMATRE A, ZENG H, MARKUS B, GEORGIEV S, DALY MJ, PRICE AL, PRITCHARD JK, SHARP AJ, ERLICH Y.

Nature. 2016 Jan 28;529(7587):532-6. doi: 10.1038/nature16486. Epub 2016 Jan 20. · March 9, 2016

Graded Foxo1 Activity in Tregs Differentiates Tumor Immunity from Spontaneous Autoimmunity

Luo C, Liao W, Dadi S, Toure A, Li Mo

Genome Research · January 4, 2016

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

GTEx Consortium.

Lappalainen Lab

Pubmed · January 29, 2015

Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing

Gutierrez-Arcelus M, Ongen H, Lappalainen T, Montgomery SB, Buil A, Yurovsky A, Bryois J, Padioleau I, Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Giger T, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE, Dermitzakis ET. PLoS Genet

Lappalainen Lab

Bioinformatics · August 1, 2015

Assessing allele-specific expression across multiple tissues from RNA-seq read data

Pirinen M, Lappalainen T, Zaitlen NA; GTEx Consortium, Dermitzakis ET, Donnelly P, McCarthy MI, Rivas MA

Lappalainen Lab

Our Scientific Publications

Key Difficulties Associated with Cancer Biology.

Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+ or CD141+ DCs.

Pharos: Collating protein information to shed light on the druggable genome.

Frequent evolution of copy number alterations in CLL following first-line treatment with FC(R) is enriched with TP53 alterations: results from the CLL8 trial.

Indel variant analysis of short-read sequencing data with Scalpel.

Genome-scale CRISPR pooled screens

The Genome Project-Write

Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Whole Genome Sequencing of Turbot (Scophthalmus maximus; Pleuronectiformes): A Fish Adapted to Demersal Life

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates

PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

Abundant contribution of short tandem repeats to gene expression variation in humans

Graded Foxo1 Activity in Tregs Differentiates Tumor Immunity from Spontaneous Autoimmunity

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing

Assessing allele-specific expression across multiple tissues from RNA-seq read data