Publications - New York Genome Center

December 14, 2015

A quantitative proteomics-based signature of platinum sensitivity in ovarian cancer cell lines

Fan G, Wrzeszczynski KO, Fu C, Su G, Pappin DJ, Lucito R, Tonks NK

Gastroenterology · December 14, 2015

Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial

Freedberg DE, Toussaint NC, Chen SP, Ratner AJ, Whittier S, Wang TC, Wang HH, Abrams JA (2015)

Molecular Cell

Interferon α/β Enhances the Cytotoxic Response of MEK Inhibition in Melanoma

Litvin O, Schwartz S, Wan Z, Schild T, Rocco M, Oh NL, Chen BJ, Goddard N, Pratilas C, Pe’er D (2015)

PLoS One · December 14, 2015

Context Sensitive Modeling of Cancer Drug Sensitivity

Chen BJ, Litvin O, Ungar L, Pe’er D (2015)

Frontiers in Bioengineering and Biotechnology · December 14, 2015

The challenge of small-scale repeats for indel discovery

Narzisi G, Schatz MC. (2015)

Am J Med Genet B. Neuropsychiatr Genet · December 14, 2015

Genome-wide association study of schizophrenia in Ashkenazi Jews

Goes FS, McGrath J, Avramopoulos D, Wolyniec P, Pirooznia M, Ruczinski I, Nestadt G, Kenny EE, Vacic V, Peters I, Lencz T, Darvasi A, Mulle JG, Warren ST, Pulver AE

The Journal of Urology · December 14, 2015

MP47-09 Molecular Characterization of sarcomatoid clear cell renal cell carcinoma

Roy Mano, William Lee, Alexander Sankin, Michael Chevinsky, Patricia Wang, Almedina Djesevic, Robert Motzer, Emily Cheng, Paul Russo, Dayna Oschwald, Umeshkumar Bhanot, Satish Tickoo, A. Ari Hakimi, James Hsieh

Building highly-optimized, low-latency pipelines for genomic data analysis

Y. Diao, A. Roy, and T. Bloom

Nature · October 1, 2015

A global reference for human genetic variation.

The 1000 Genomes Project Consortium (Including Lappalainen T., Erlich Y.)

Lappalainen Lab

Genome Research · October 1, 2015

Functional genomics bridges the gap between quantitative genetics and molecular biology.

Lappalainen T.

Lappalainen Lab

Genome Research · October 1, 2015

A vision for ubiquitous sequencing.

Erlich Y.

Genes & Dev · September 25, 2015

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation.

Shengdong Ke, Endalkachew A. Alemu, Claudia Mertens, Emily Conn Gantman, John J. Fak, Aldo Mele, Bhagwattie Haripal, Ilana Zucker-Scharff, Michael J. Moore, Christopher Y. Park, Cathrine Broberg Vågbø, Anna Kus´nierczyk, Arne Klungland, James E. Darnell Jr., Robert B. Darnell.

Neuron · September 25, 2015

De Novo Gene Disruptions in Children on the Autistic Spectrum.

Ivan Iossifov, Michael Ronemus, Dan Levy, Zihua Wang, Inessa Hakker, Julie Rosenbaum, Boris Yamrom, Yoon-ha Lee, Giuseppe Narzisi, Anthony Leotta, Jude Kendall, Ewa Grabowska, Beicong Ma, Steven Marks, Linda Rodgers, Asya Stepansky, Jennifer Troge, Peter Andrews, Mitchell Bekritsky, Kith Pradhan, Elena Ghiban, Melissa Kramer, Jennifer Parla, Ryan Demeter, Lucinda L. Fulton, Robert S. Fulton, Vincent J. Magrini, Kenny Ye, Jennifer C. Darnell, Robert B. Darnell, Elaine R. Mardis, Richard K. Wilson, Michael C. Schatz, W. Richard McCombie, and Michael Wigler.

Iossifov Lab

PNAS · September 25, 2015

Low load for disruptive mutations in autism genes and their biased transmission.

Ivan Iossifov, Dan Levya, Jeremy Allena, Kenny Yec, Michael Ronemusa, Yoon-ha Leea, Boris Yamroma, Michael Wigler.

Iossifov Lab

Bioinformatics. Epub · September 22, 2015

Approximately independent linkage disequilibrium blocks in human populations.

Berisa T, Pickrell JK.

Genome Biology · September 18, 2015

Tools and best practices for data processing in allelic expression analysis.

Stephane E. Castel, Ami Levy-Moonshine, Pejman Mohammadi, Eric Banks and Tuuli Lappalainen

Lappalainen Lab

Annals of Neurology · August 4, 2015

A destructive feedback loop mediated by CXCL10 in CNS inflammatory disease.

Wendy K. Roberts, Ph.D., Nathalie E. Blachère, Ph.D., Mayu O. Frank, M.S., Athanasios Dousmanis, M.D., Ph.D., Richard M. Ransohoff, M.D., Robert B. Darnell, M.D., Ph.D.

Nat Methods · July 6, 2015

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes.

Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM, Smith M, Van der Aa N, Banerjee R, Ellis PD, Quail MA, Swerdlow HP, Zernicka-Goetz M, Livesey FJ, Ponting CP, Voet T.

Cell · July 1, 2015

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA.

JAMA Oncology · July 1, 2015

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.

Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Paul C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Robinson BD, Nanus DM, Tagawa ST, Campagne F, Xiang JZ, Smogorzewska A, Demichelis F, Rickman D, Sboner A, Elemento O, Rubin MA.

PLoS ONE · June 23, 2015

Gut Microbiota and Tacrolimus Dosing in Kidney Transplantation.

Lee JR, Muthukumar T, Dadhania D, Taur Y, Jenq RR, Toussaint NC, Ling L, Pamer EG, Suthanthiran M.

Our Scientific Publications

A quantitative proteomics-based signature of platinum sensitivity in ovarian cancer cell lines

Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial

Interferon α/β Enhances the Cytotoxic Response of MEK Inhibition in Melanoma

Context Sensitive Modeling of Cancer Drug Sensitivity

The challenge of small-scale repeats for indel discovery

Genome-wide association study of schizophrenia in Ashkenazi Jews

MP47-09 Molecular Characterization of sarcomatoid clear cell renal cell carcinoma

Building highly-optimized, low-latency pipelines for genomic data analysis

A global reference for human genetic variation.

Functional genomics bridges the gap between quantitative genetics and molecular biology.

A vision for ubiquitous sequencing.

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation.

De Novo Gene Disruptions in Children on the Autistic Spectrum.

Low load for disruptive mutations in autism genes and their biased transmission.

Approximately independent linkage disequilibrium blocks in human populations.

Tools and best practices for data processing in allelic expression analysis.

A destructive feedback loop mediated by CXCL10 in CNS inflammatory disease.

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes.

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.

Gut Microbiota and Tacrolimus Dosing in Kidney Transplantation.