Publications - New York Genome Center

Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1016). Chapter First Online: 2017 · November 13, 2017

Target Discovery for Precision Medicine Using High-Throughput Genome Engineering.

Guo X, Chitale P, Sanjana NE.

Sanjana Lab

Cell · November 2, 2017

SnapShot: Discovering Genetic Regulatory Variants by QTL Analysis.

Brandt M, Lappalainen T.

Lappalainen Lab

Nature Communications · October 26, 2017

Resistance to checkpoint blockade therapy through inactivation of antigen presentation.

Sade-Feldman M, Jiao YJ, Chen JH, Rooney MS, Barzily-Rokni M, Eliane JP, Bjorgaard SL, Hammond MR, Vitzthum H, Blackmon SM, Frederick DT, Hazar-Rethinam M, Nadres BA, Van Seventer EE, Shukla SA, Yizhak K, Ray JP, Rosebrock D, Livitz D, Adalsteinsson V, Getz G, Duncan LM, Li B, Corcoran RB, Lawrence DP, Stemmer-Rachamimov A, Boland GM, Landau DA, Flaherty KT, Sullivan RJ, Hacohen N.

Landau Lab

Nature · October 11, 2017

Landscape of X chromosome inactivation across human tissues.

Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG.

Lappalainen Lab Satija Lab

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

Molecular Cell · October 5, 2017

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

Montalbano A, Canver, MC and Sanjana NE.

Sanjana Lab

Nature · March 5, 2018

Developmental diversification of cortical inhibitory interneurons.

Mayer C, Hafemeister C, Bandler RC, , Allaway K, , Brito RB, Butler A, , Satija R.

Satija Lab

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

Nature Genetics · September 11, 2017

Interpreting short tandem repeat variations in humans using mutational constraint.

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

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

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

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

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.

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

Current Opinion in Systems Biology · December 9, 2016

Modeling cancer rearrangement landscapes.

Maciejowski J, Imielinski M.

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

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

PLOS Biology · September 5, 2017

Identifying genetic variants that affect viability in large cohorts.

Mostafavi H, Berisa T, Day FR, Perry JRB, Przeworski M, Pickrell JK.

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

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

Nature Reviews Immunology · August 7, 2017

Single-cell RNA sequencing to explore immune cell heterogeneity.

Papalexi E, Satija R.

Satija Lab

Our Scientific Publications

Target Discovery for Precision Medicine Using High-Throughput Genome Engineering.

SnapShot: Discovering Genetic Regulatory Variants by QTL Analysis.

Resistance to checkpoint blockade therapy through inactivation of antigen presentation.

Landscape of X chromosome inactivation across human tissues.

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

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

Developmental diversification of cortical inhibitory interneurons.

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

Interpreting short tandem repeat variations in humans using mutational constraint.

Genomic Patterns of De Novo Mutation in Simplex Autism.

Whole-Genome Bisulphite Sequencing With Improved Accuracy and Cost

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

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

Genomic complexity of multiple myeloma and its clinical implications.

Modeling cancer rearrangement landscapes.

Chromosomal Instability as a Driver of Tumor Heterogeneity and Evolution.

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

Identifying genetic variants that affect viability in large cohorts.

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

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

Single-cell RNA sequencing to explore immune cell heterogeneity.