Publications - New York Genome Center

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

Nature Genetics · January 26, 2018

DNA.Land is a framework to collect genomes and phenomes in the era of abundant genetic information.

Yuan J, Gordon A, Speyer D, Aufrichtig R, Zielinski D, Pickrell J, Erlich Y.

Bioinformatics · March 19, 2018

A Bayesian Framework for Multiple Trait Colocalization from Summary Association Statistics

Giambartolomei C, Liu JZ, Zhang W, Hauberg M, Shi H, Boocock J, Pickrell J, Jaffe AE, the CommonMind

Consortium, Pasaniuc B*, Roussos P.

Genetics · January 18, 2018

Detecting Polygenic Adaptation in Admixture Graphs.

Racimo F, Berg JJ, Pickrell JK.

Genome Biol · August 15, 2018

Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons.

Yuan Y, Xie S, Darnell JC, Darnell AJ, Saito Y, Phatnani H, Murphy EA, Zhang C, Maniatis T, Darnell RB.

Phatnani Lab

PNAS · February 6, 2018

Damaging de novo mutations diminish motor skills in children on the autism spectrum.

Buja A, Volfovsky N, Krieger AM, Lord C, Lash AE, Wigler M, Iossifov I.

Iossifov Lab Wigler Lab

Nature · February 7, 2018

Asparagine bioavailability governs metastasis in a model of breast cancer.

Knott SRV, Wagenblast E, Khan S, Kim SY, Soto M, Wagner M, Turgeon M-O, Fish L, Erard N, Gable AL, Maceli AR, Dickopf S, Papachristou EK, D’Santos CS, Carey LA, Wilkinson JE, Harrell JC, Perou CM, Goodarzi H, Poulogiannis G, Hannon GJ.

Cell Rep · May 19, 2015

An epigenetic memory of pregnancy in the mouse mammary gland.

Dos Santos CO, Dolzhenko E, Hodges E, Smith AD, Hannon GJ.

Nature · April 16, 2015

A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis.

Wagenblast E, Soto M, Gutiérrez-Ángel, Hartl CA, Gable AL, Maceli AR, Erard N, Williams AM, Kim SY, Dickopf S, Harrell JC, Smith AD, Perou CM, Wilkinson JE, Hannon GJ, Knott SR.

Genome Research · December 19, 2017

Evolutionary expansion of DNA hypomethylation in the mammalian germline genome.

Qu J, Hodges E, Molaro A, Gagneux P, Dean MD, Hannon GJ, Smith AD.

Molecular Cell · July 20, 2017

A CRISPR Resource for Individual, Combinatorial, or Multiplexed Gene Knockout.

Erard N, Knott SRV, Hannon GJ.

Nature Biotechnology · January 10, 2018

Strength in numbers from integrated single-cell neuroscience.

Satija, R.

Satija Lab

Nature Methods · July 31, 2017

Simultaneous epitope and transcriptome measurement in single cells.

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Swerdlow H, Satija R, Smibert, P

Satija Lab

Technology Innovation

Nature Communications · December 19, 2017

The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy.

Landau DA, Sun C, Rosebrock D, Herman SEM, Fein J, Sivina M, Underbayev C, Liu D, Hoellenriegel J, Ravichandran S, Farooqui MZH, Zhang W, Cibulskis C, Zviran A, Neuberg DS, Livitz D, Bozic I, Leshchiner I, Getz G, Burger JA, Wiestner A & Wu, CJ.

Landau Lab

Our Scientific Publications

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.

DNA.Land is a framework to collect genomes and phenomes in the era of abundant genetic information.

A Bayesian Framework for Multiple Trait Colocalization from Summary Association Statistics

Detecting Polygenic Adaptation in Admixture Graphs.

Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons.

Damaging de novo mutations diminish motor skills in children on the autism spectrum.

Asparagine bioavailability governs metastasis in a model of breast cancer.

An epigenetic memory of pregnancy in the mouse mammary gland.

A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis.

Evolutionary expansion of DNA hypomethylation in the mammalian germline genome.

A CRISPR Resource for Individual, Combinatorial, or Multiplexed Gene Knockout.

Strength in numbers from integrated single-cell neuroscience.

Simultaneous epitope and transcriptome measurement in single cells.

The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy.