Publications - New York Genome Center

Bioinformatics · May 21, 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

Proc Natl Acad Sci USA · May 21, 2015

Structural insights into mis-regulation of protein kinase A in human tumors

Cheung J, Ginter C, Cassidy M, Franklin MC, Rudolph MJ, Robine N, Darnell RB, Hendrickson WA.

Cell · May 21, 2015

Hepatitis C virus RNA functionally sequesters miR-122

Luna JM, Scheel TK, Danino T, Shaw KS, Mele A, Fak JJ, Nishiuchi E, Takacs CN, Catanese MT, de Jong YP, Jacobson IM, Rice CM, Darnell RB.

Science · May 21, 2015

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens

Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A.

Nature Biotechnology · May 20, 2015

Spatial reconstruction of single-cell gene expression data

Satija R, Farrell JA, Gennert D, Schier AF, Regev A

Genetics 193: 911-28 · February 8, 2015

The variance of identity-by-descent sharing in the Wright-Fisher model.

Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, Pe’er I.

Journal of Translational Medicine · February 2, 2015

Dendritic cell vaccines containing lymphocytes produce improved immunogenicity in patients with cancer.

Frank, M. O., Kaufman, J., Parveen, S., Blachère, N. E., Orange, D. E., Darnell, R. B.

Phatnani Lab

PLoS Computational Biology 8: e1002709 · February 2, 2015

Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder.

Vacic V, Markwick PRL, Oldfield CJ, Zhao X, Haynes C, Uversky VN, Iakoucheva LM.

Science 344: 921-5 · February 2, 2015

The cellular and molecular origin of tumor-associated macrophages.

Franklin RA, Liao W, Sarkar A, Kim MV, Bivona MR, Liu K, Pamer EG, Li MO.

Computational Biology Lab

Nature Methods 11: 1033-6 · February 2, 2015

Accurate de novo and transmitted indel detection in exome-capture data using microassembly.

Narzisi G, O’Rawe JA, Iossifov I, Fang H, Lee YH, Wang Z, Wu Y, Lyon GJ, Wigler M, Schatz MC.

Iossifov Lab Wigler Lab

Computational Biology Lab

Cell 158: 705-21 · February 2, 2015

Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences.

Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D,Zárate Rodriguez JG, Rogers AB, Robine N, Loke P, Blaser MJ.

Computational Biology Lab

Science 343:1010-4 · February 2, 2015

Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma.

Honeyman JN, Simon EP, Robine N, Chiaroni-Clarke R, Darcy DG, Lim IIP, Gleason CE, Murphy JM, Rosenberg BR, Teegan L, Takacs CN, Botero S, Belote R, Germer S, Emde A-K, Vacic V, Bhanot U, LaQuaglia MP, Simon SM.

Computational Biology Lab

Nature Communications 5: 3650 · February 2, 2015

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.

Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM.

Human Molecular Genetics 23: 4693-702 · February 2, 2015

Genome-wide mapping of identical-by-descent segments in an Ashkenazi PD cohort identifies associated haplotypes.

Vacic V, Ozelius LJ, Clark LN, Bar-Shira A, Gana-Weisz M, Gurevich T, Gusev A, Kedmi M, Kenny EE, Liu X, Mejia-Santana H, Mirelman A, Raymond D, Saunders-Pullman R, Desnick RJ, Atzmon G, Burns ER, Ostrer H, Hakonarson H, Bergman A, Barzilai N, Darvasi A, Peter I, Guha S, Lencz T, Giladi N, Marder K, Pe’er I, Bressman SB, Orr-Urtreger A.

Molecular Genetics & Genomic Medicine 2: 438-50 · February 2, 2015

Disease variants in genomes of 44 centenarians.

Freudenberg-Hua Y, Freudenberg J, Vacic V, Abhyankar A, Emde A-K, Ben-Avraham D, Barzilai N, Oschwald DM, Christen E, Koppel J, Greenwald B, Darnell RB, Germer S, Atzmon G, Davies P.

Computational Biology Lab

Genome Biology 15: 454 · February 2, 2015

Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions.

Brannon AR, Vakiani E, Sylvester BE, Scott SN, McDermott G, Shah RN, Kania K, Viale A, Oschwald DM, Vacic V, Emde A-K, Cercek A, Yaeger R, Kemeny NE, Saltz LB, Shia J, D‘Angelica MI, Weiser MR, Solit DB, Berger MF.

Computational Biology Lab

Pigment Cell Melanoma Research 27: 671-3 · February 2, 2015

In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival.

Menzel M, Meckbach D, Weide B, Toussaint NC, Schilbach K, Noor S, Eigentler T, Ikenberg K, Busch C, Qunitanilla-Martinez L, Göke S, Göke F, Handgretinger R, Ottmann C, Bastian B, Garbe C, Röcken M, Perner S, Kohlbacher O, Bauer J.

Transplantation 98: 697-705 · February 2, 2015

Gut Microbial Community Structure and Complications Following Kidney Transplantation: A Pilot Study.

Lee JR, Muthukumar T, Dadhania D, Toussaint NC, Ling L, Pamer E, Suthanthiran M.

Nature · February 2, 2015

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E, van den Brink MRM, Jenq RR, Taur Y, Sander C, Cross J, Toussaint NC, Xavier JB, Pamer E.

Am J Hum Genet 94: 559-73 · January 30, 2015

Joint Analysis of Functional Genomic Data and Genome-wide Associate Studies of 18 Human Traits.

Pickrell JK.

Trends in Genetics 30: 377-89 · January 30, 2015

Toward a new history and geography of human informed by ancient DNA.

Pickrell JK, Reich D.

Our Scientific Publications

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

Structural insights into mis-regulation of protein kinase A in human tumors

Hepatitis C virus RNA functionally sequesters miR-122

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens

Spatial reconstruction of single-cell gene expression data

The variance of identity-by-descent sharing in the Wright-Fisher model.

Dendritic cell vaccines containing lymphocytes produce improved immunogenicity in patients with cancer.

Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder.

The cellular and molecular origin of tumor-associated macrophages.

Accurate de novo and transmitted indel detection in exome-capture data using microassembly.

Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences.

Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma.

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.

Genome-wide mapping of identical-by-descent segments in an Ashkenazi PD cohort identifies associated haplotypes.

Disease variants in genomes of 44 centenarians.

Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions.

In melanoma, Hippo signaling is affected by copy number alterations and YAP1 overexpression impairs patient survival.

Gut Microbial Community Structure and Complications Following Kidney Transplantation: A Pilot Study.

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Joint Analysis of Functional Genomic Data and Genome-wide Associate Studies of 18 Human Traits.

Toward a new history and geography of human informed by ancient DNA.