Publications - New York Genome Center

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.

Genome Research 19, 826—837 · January 30, 2015

Signals of recent positive selection in a worldwide sample of human populations.

Pickrell JK, Coop, G., Novembre, J., Kudaravalli, S., Li, J.Z., Absher, D., Srinivasan, B.S., Barsh, G.S., Myers, R.M., Feldman, M.W., Pritchard, J.K.

Nature Communications 3, 1143 · January 30, 2015

The genetic prehistory of southern Africa.

Pickrell JK, Patterson, N., Barbieri, C., Berthold, F., Gerlach, L., Güldemann, T., Kure, B., Mpoloka, S.W., Nakagawa, H., Naumann, C., Lipson, M., Loh, P.-R., Lachance, J., Mountain, J., Bustamante, C.D., Berger, B., Tishkoff, S.A., Henn, B.M., Stoneking, M., Reich, D., Pakendorf, B., 2012.

PLoS Genetics 8, e1002967 · January 30, 2015

Inference of population splits and mixtures from genome-wide allele frequency data.

Pickrell, J.K., Pritchard, J.K., 2012.

January 30, 2015

Ancient west Eurasian ancestry in southern and eastern Africa.

Pickrell et al.

PLoS Genetics 6, e1001236 · January 30, 2015

Noisy splicing drives mRNA isoform diversity in human cells.

Pickrell, J.K., Pai, A.A., Gilad, Y., Pritchard, J.K.

Nature 464, 768—772 · January 30, 2015

Understanding mechanisms underlying human gene expression variation with RNA sequencing.

Pickrell, J.K., Marioni, J.C., Pai, A.A., Degner, J.F., Engelhardt, B.E., Nkadori, E., Veyrieras, J.-B., Stephens, M., Gilad, Y., Pritchard, J.K.

Proc Natl Acad Sci U S A 93, 4529-4536. PMC39311 · January 30, 2015

Onconeural antigens and the paraneoplastic neurologic disorders: at the intersection of cancer, immunity, and the brain.

Darnell, R. B.

Nat Med 4, 1321-1324 · January 30, 2015

Tumor-specific killer cells in paraneoplastic cerebellar degeneration.

Albert, M. L., Darnell, J. C., Bender, A., Francisco, L. M., Bhardwaj, N. & Darnell, R. B.

Science 302, 1212-1215 · January 30, 2015

CLIP identifies Nova-regulated RNA networks in the brain.

Ule, J., Jensen, K. B., Ruggiu, M., Mele, A., Ule, A. & Darnell, R. B.

N Engl J Med 349, 1543-1554 · January 30, 2015

Paraneoplastic syndromes involving the nervous system.

Darnell, R. B. & Posner, J. B.

Prostate Cancer Prostatic Dis 7, 63-72 · January 30, 2015

Effective antigen cross-presentation by prostate cancer patients’ dendritic cells: implications for prostate cancer immunotherapy.

Orange, D. E., Jegathesan, M., Blachere, N. E., Frank, M. O., Scher, H. I., Albert, M. L. & Darnell, R. B.

Our Scientific Publications

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.

Signals of recent positive selection in a worldwide sample of human populations.

The genetic prehistory of southern Africa.

Inference of population splits and mixtures from genome-wide allele frequency data.

Ancient west Eurasian ancestry in southern and eastern Africa.

Noisy splicing drives mRNA isoform diversity in human cells.

Understanding mechanisms underlying human gene expression variation with RNA sequencing.

Onconeural antigens and the paraneoplastic neurologic disorders: at the intersection of cancer, immunity, and the brain.

Tumor-specific killer cells in paraneoplastic cerebellar degeneration.

CLIP identifies Nova-regulated RNA networks in the brain.

Paraneoplastic syndromes involving the nervous system.

Effective antigen cross-presentation by prostate cancer patients’ dendritic cells: implications for prostate cancer immunotherapy.