Gerstein Lab Publications

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Additional papers


An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium (2012). Nature 491:56-65
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An integrated encyclopedia of DNA elements in the human genome.
The ENCODE Project Consortium (2012). Nature 489: 57-74.
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GENCODE: the reference human genome annotation for The ENCODE Project.
J Harrow, A Frankish, JM Gonzalez, E Tapanari, M Diekhans, F Kokocinski, BL Aken, D Barrell, A Zadissa, S Searle, I Barnes, A Bignell, V Boychenko, T Hunt, M Kay, G Mukherjee, J Rajan, G Despacio-Reyes, G Saunders, C Steward, R Harte, M Lin, C Howald, A Tanzer, T Derrien, J Chrast, N Walters, S Balasubramanian, B Pei, M Tress, JM Rodriguez, I Ezkurdia, J van Baren, M Brent, D Haussler, M Kellis, A Valencia, A Reymond, M Gerstein, R Guigo, TJ Hubbard (2012). Genome Res 22: 1760-74.
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Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.
J Cotney, J Leng, S Oh, LE DeMare, SK Reilly, MB Gerstein, JP Noonan (2012). Genome Res 22: 1069-80.
 
 
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The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare.
M Vidal, DW Chan, M Gerstein, M Mann, GS Omenn, D Tagle, S Sechi, Workshop Participants (2012). Clin Proteomics 9: 6.
 
 
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The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions.
MJ Bamshad, JA Shendure, D Valle, A Hamosh, JR Lupski, RA Gibbs, E Boerwinkle, RP Lifton, M Gerstein, M Gunel, S Mane, DA Nickerson, Centers for Mendelian Genomics (2012). Am J Med Genet A 158A: 1523-5.
 
 
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Personal omics profiling reveals dynamic molecular and medical phenotypes.
R Chen, GI Mias, J Li-Pook-Than, L Jiang, HY Lam, R Chen, E Miriami, KJ Karczewski, M Hariharan, FE Dewey, Y Cheng, MJ Clark, H Im, L Habegger, S Balasubramanian, M O'Huallachain, JT Dudley, S Hillenmeyer, R Haraksingh, D Sharon, G Euskirchen, P Lacroute, K Bettinger, AP Boyle, M Kasowski, F Grubert, S Seki, M Garcia, M Whirl-Carrillo, M Gallardo, MA Blasco, PL Greenberg, P Snyder, TE Klein, RB Altman, AJ Butte, EA Ashley, M Gerstein, KC Nadeau, H Tang, M Snyder (2012). Cell 148: 1293-307.
 
 
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Mapping copy number variation by population-scale genome sequencing.
RE Mills, K Walter, C Stewart, RE Handsaker, K Chen, C Alkan, A Abyzov, SC Yoon, K Ye, RK Cheetham, A Chinwalla, DF Conrad, Y Fu, F Grubert, I Hajirasouliha, F Hormozdiari, LM Iakoucheva, Z Iqbal, S Kang, JM Kidd, MK Konkel, J Korn, E Khurana, D Kural, HY Lam, J Leng, R Li, Y Li, CY Lin, R Luo, XJ Mu, J Nemesh, HE Peckham, T Rausch, A Scally, X Shi, MP Stromberg, AM Stutz, AE Urban, JA Walker, J Wu, Y Zhang, ZD Zhang, MA Batzer, L Ding, GT Marth, G McVean, J Sebat, M Snyder, J Wang, K Ye, EE Eichler, MB Gerstein, ME Hurles, C Lee, SA McCarroll, JO Korbel, 1000 Genomes Project (2011). Nature 470: 59-65.
 
 
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AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
A Abyzov, M Gerstein (2011). Bioinformatics 27: 595-603.
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Gene inactivation and its implications for annotation in the era of personal genomics.
S Balasubramanian, L Habegger, A Frankish, DG MacArthur, R Harte, C Tyler-Smith, J Harrow, M Gerstein (2011). Genes Dev 25: 1-10.
 
 
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Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.
ZD Zhang, MB Gerstein (2010). BMC Bioinformatics 11: 539.
 
 
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A map of human genome variation from population-scale sequencing
1000 Genomes Project Consortium (2010). Nature 467:1061-73
 
 
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Personal genome sequencing: current approaches and challenges.
M Snyder, J Du, M Gerstein (2010). Genes Dev 24: 423-31.
 
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Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
HY Lam, XJ Mu, AM Stutz, A Tanzer, PD Cayting, M Snyder, PM Kim, JO Korbel, MB Gerstein (2010). Nat Biotechnol 28: 47-55.
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Social networking and personal genomics: suggestions for optimizing the interaction.
D Greenbaum, M Gerstein (2009). Am J Bioeth 9: 15-9.
 
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Personal phenotypes to go with personal genomes.
M Snyder, S Weissman, M Gerstein (2009). Mol Syst Biol 5: 273.
 
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MSB: a mean-shift-based approach for the analysis of structural variation in the genome.
LY Wang, A Abyzov, JO Korbel, M Snyder, M Gerstein (2009). Genome Res 19: 106-17.
 
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Genomic anonymity: have we already lost it?
D Greenbaum, J Du, M Gerstein (2008). Am J Bioeth 8: 71-4.
 
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High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution.
Y Hasin, T Olender, M Khen, C Gonzaga-Jauregui, PM Kim, AE Urban, M Snyder, MB Gerstein, D Lancet, JO Korbel (2008). PLoS Genet 4: e1000249.
 
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The current excitement about copy-number variation: how it relates to gene duplications and protein families.
JO Korbel, PM Kim, X Chen, AE Urban, S Weissman, M Snyder, MB Gerstein (2008). Curr Opin Struct Biol 18: 366-74.
 
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Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104: 20274-9.
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Paired-end mapping reveals extensive structural variation in the human genome.
JO Korbel, AE Urban, JP Affourtit, B Godwin, F Grubert, JF Simons, PM Kim, D Palejev, NJ Carriero, L Du, BE Taillon, Z Chen, A Tanzer, AC Saunders, J Chi, F Yang, NP Carter, ME Hurles, SM Weissman, TT Harkins, MB Gerstein, M Egholm, M Snyder (2007). Science 318: 420-6.
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Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.
JO Korbel, AE Urban, F Grubert, J Du, TE Royce, P Starr, G Zhong, BS Emanuel, SM Weissman, M Snyder, MB Gerstein (2007). Proc Natl Acad Sci U S A 104: 10110-5.
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Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.
R Pinard, A de Winter, GJ Sarkis, MB Gerstein, KR Tartaro, RN Plant, M Egholm, JM Rothberg, JH Leamon (2006). BMC Genomics 7: 216.
 
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High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays.
AE Urban, JO Korbel, R Selzer, T Richmond, A Hacker, GV Popescu, JF Cubells, R Green, BS Emanuel, MB Gerstein, SM Weissman, M Snyder (2006). Proc Natl Acad Sci U S A 103: 4534-9.
 
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Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.
S Balasubramanian, Y Xia, E Freinkman, M Gerstein (2005). Nucleic Acids Res 33: 1710-21.
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