Gerstein Lab Publications

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This is part of a disjoint subdivision of all the papers into 4 types.
(1) review = all review papers published by Gerstein Lab & colaborators
(2) informatics-research-article = informatics research article lead by the Gerstein Lab
(3) expt-collab = research article driven by an experimental or informatics lab in collaboration with Gerstein Lab
(4) otherpub = not one of the above


A comprehensive nuclear receptor network for breast cancer cells.
R Kittler, J Zhou, S Hua, L Ma, Y Liu, E Pendleton, C Cheng, M Gerstein, KP White (2013). Cell Rep 3: 538-51.
 
 
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Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.
H Tilgner, D Raha, L Habegger, M Mohiuddin, M Gerstein, M Snyder (2013). G3 (Bethesda) 3: 387-97.
 
 
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The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
SB Montgomery, DL Goode, E Kvikstad, CA Albers, ZD Zhang, XJ Mu, G Ananda, B Howie, KJ Karczewski, KS Smith, V Anaya, R Richardson, J Davis, 1000 Genomes Project Consortium, DG MacArthur, A Sidow, L Duret, M Gerstein, KD Makova, J Marchini, G McVean, G Lunter (2013). Genome Res 23: 749-61.
 
 
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Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression.
PC Lin, YL Chiu, S Banerjee, K Park, JM Mosquera, E Giannopoulou, P Alves, AK Tewari, MB Gerstein, H Beltran, AM Melnick, O Elemento, F Demichelis, MA Rubin (2012). Cancer Res 73: 1232-44.
 
 
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Landscape of transcription in human cells.
S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann, A Mortazavi, A Tanzer, J Lagarde, W Lin, F Schlesinger, C Xue, GK Marinov, J Khatun, BA Williams, C Zaleski, J Rozowsky, M Roder, F Kokocinski, RF Abdelhamid, T Alioto, I Antoshechkin, MT Baer, NS Bar, P Batut, K Bell, I Bell, S Chakrabortty, X Chen, J Chrast, J Curado, T Derrien, J Drenkow, E Dumais, J Dumais, R Duttagupta, E Falconnet, M Fastuca, K Fejes-Toth, P Ferreira, S Foissac, MJ Fullwood, H Gao, D Gonzalez, A Gordon, H Gunawardena, C Howald, S Jha, R Johnson, P Kapranov, B King, C Kingswood, OJ Luo, E Park, K Persaud, JB Preall, P Ribeca, B Risk, D Robyr, M Sammeth, L Schaffer, LH See, A Shahab, J Skancke, AM Suzuki, H Takahashi, H Tilgner, D Trout, N Walters, H Wang, J Wrobel, Y Yu, X Ruan, Y Hayashizaki, J Harrow, M Gerstein, T Hubbard, A Reymond, SE Antonarakis, G Hannon, MC Giddings, Y Ruan, B Wold, P Carninci, R Guigo, TR Gingeras (2012). Nature 489: 101-8.
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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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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, BE Bernstein, P Bickel, JB Brown, P Cayting, Y Chen, G DeSalvo, C Epstein, KI Fisher-Aylor, G Euskirchen, M Gerstein, J Gertz, AJ Hartemink, MM Hoffman, VR Iyer, YL Jung, S Karmakar, M Kellis, PV Kharchenko, Q Li, T Liu, XS Liu, L Ma, A Milosavljevic, RM Myers, PJ Park, MJ Pazin, MD Perry, D Raha, TE Reddy, J Rozowsky, N Shoresh, A Sidow, M Slattery, JA Stamatoyannopoulos, MY Tolstorukov, KP White, S Xi, PJ Farnham, JD Lieb, BJ Wold, M Snyder (2012). Genome Res 22: 1813-31.
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Modeling gene expression using chromatin features in various cellular contexts.
X Dong, MC Greven, A Kundaje, S Djebali, JB Brown, C Cheng, TR Gingeras, M Gerstein, R Guigo, E Birney, Z Weng (2012). Genome Biol 13: R53.
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Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line.
JQ Wu, M Seay, VP Schulz, M Hariharan, D Tuck, J Lian, J Du, M Shi, Z Ye, M Gerstein, MP Snyder, S Weissman (2012). PLoS Genet 8: e1002565.
 
 
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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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Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides.
TA Gianoulis, MA Griffin, DJ Spakowicz, BF Dunican, CJ Alpha, A Sboner, AM Sismour, C Kodira, M Egholm, GM Church, MB Gerstein, SA Strobel (2012). PLoS Genet 8: e1002558.
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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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Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
G Li, X Ruan, RK Auerbach, KS Sandhu, M Zheng, P Wang, HM Poh, Y Goh, J Lim, J Zhang, HS Sim, SQ Peh, FH Mulawadi, CT Ong, YL Orlov, S Hong, Z Zhang, S Landt, D Raha, G Euskirchen, CL Wei, W Ge, H Wang, C Davis, KI Fisher-Aylor, A Mortazavi, M Gerstein, T Gingeras, B Wold, Y Sun, MJ Fullwood, E Cheung, E Liu, WK Sung, M Snyder, Y Ruan (2012). Cell 148: 84-98.
 
 
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Performance comparison of whole-genome sequencing platforms.
HY Lam, MJ Clark, R Chen, R Chen, G Natsoulis, M O'Huallachain, FE Dewey, L Habegger, EA Ashley, MB Gerstein, AJ Butte, HP Ji, M Snyder (2011). Nat Biotechnol 30: 78-82.
 
 
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Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.
RR Haraksingh, A Abyzov, M Gerstein, AE Urban, M Snyder (2011). PLoS One 6: e27859.
 
 
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Identification of a disease-defining gene fusion in epithelioid hemangioendothelioma.
MR Tanas, A Sboner, AM Oliveira, MR Erickson-Johnson, J Hespelt, PJ Hanwright, J Flanagan, Y Luo, K Fenwick, R Natrajan, C Mitsopoulos, M Zvelebil, BL Hoch, SW Weiss, M Debiec-Rychter, R Sciot, RB West, AJ Lazar, A Ashworth, JS Reis-Filho, CJ Lord, MB Gerstein, MA Rubin, BP Rubin (2011). Sci Transl Med 3: 98ra82.
 
 
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The reality of pervasive transcription.
MB Clark, PP Amaral, FJ Schlesinger, ME Dinger, RJ Taft, JL Rinn, CP Ponting, PF Stadler, KV Morris, A Morillon, JS Rozowsky, MB Gerstein, C Wahlestedt, Y Hayashizaki, P Carninci, TR Gingeras, JS Mattick (2011). PLoS Biol 9: e1000625; discussion e1001102.
 
 
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Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes.
J Fasolo, A Sboner, MG Sun, H Yu, R Chen, D Sharon, PM Kim, M Gerstein, M Snyder (2011). Genes Dev 25: 767-78.
 
 
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A cis-regulatory map of the Drosophila genome.
N Negre, CD Brown, L Ma, CA Bristow, SW Miller, U Wagner, P Kheradpour, ML Eaton, P Loriaux, R Sealfon, Z Li, H Ishii, RF Spokony, J Chen, L Hwang, C Cheng, RP Auburn, MB Davis, M Domanus, PK Shah, CA Morrison, J Zieba, S Suchy, L Senderowicz, A Victorsen, NA Bild, AJ Grundstad, D Hanley, DM MacAlpine, M Mannervik, K Venken, H Bellen, R White, M Gerstein, S Russell, RL Grossman, B Ren, JW Posakony, M Kellis, KP White (2011). Nature 471: 527-31.
 
 
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Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches.
GM Euskirchen, RK Auerbach, E Davidov, TA Gianoulis, G Zhong, J Rozowsky, N Bhardwaj, MB Gerstein, M Snyder (2011). PLoS Genet 7: e1002008.
 
 
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The genomic complexity of primary human prostate cancer.
MF Berger, MS Lawrence, F Demichelis, Y Drier, K Cibulskis, AY Sivachenko, A Sboner, R Esgueva, D Pflueger, C Sougnez, R Onofrio, SL Carter, K Park, L Habegger, L Ambrogio, T Fennell, M Parkin, G Saksena, D Voet, AH Ramos, TJ Pugh, J Wilkinson, S Fisher, W Winckler, S Mahan, K Ardlie, J Baldwin, JW Simons, N Kitabayashi, TY MacDonald, PW Kantoff, L Chin, SB Gabriel, MB Gerstein, TR Golub, M Meyerson, A Tewari, ES Lander, G Getz, MA Rubin, LA Garraway (2011). Nature 470: 214-20.
 
 
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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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Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.
W Niu, ZJ Lu, M Zhong, M Sarov, JI Murray, CM Brdlik, J Janette, C Chen, P Alves, E Preston, C Slightham, L Jiang, AA Hyman, SK Kim, RH Waterston, M Gerstein, M Snyder, V Reinke (2011). Genome Res 21: 245-54.
 
 
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Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.
D Pflueger, S Terry, A Sboner, L Habegger, R Esgueva, PC Lin, MA Svensson, N Kitabayashi, BJ Moss, TY MacDonald, X Cao, T Barrette, AK Tewari, MS Chee, AM Chinnaiyan, DS Rickman, F Demichelis, MB Gerstein, MA Rubin (2011). Genome Res 21: 56-67.
 
 
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Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses.
X Li, TA Gianoulis, KY Yip, M Gerstein, M Snyder (2010). Cell 143: 639-50.
 
 
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Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis.
Y Lee, X Yang, Y Huang, H Fan, Q Zhang, Y Wu, J Li, R Hasina, C Cheng, MW Lingen, MB Gerstein, RR Weichselbaum, HR Xing, YA Lussier (2010). PLoS Comput Biol 6: e1000730.
 
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Variation in transcription factor binding among humans.
M Kasowski, F Grubert, C Heffelfinger, M Hariharan, A Asabere, SM Waszak, L Habegger, J Rozowsky, M Shi, AE Urban, MY Hong, KJ Karczewski, W Huber, SM Weissman, MB Gerstein, JO Korbel, M Snyder (2010). Science 328: 232-5.
 
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Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing.
JQ Wu, L Habegger, P Noisa, A Szekely, C Qiu, S Hutchison, D Raha, M Egholm, H Lin, S Weissman, W Cui, M Gerstein, M Snyder (2010). Proc Natl Acad Sci U S A 107: 5254-9.
 
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Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs.
J Mok, PM Kim, HY Lam, S Piccirillo, X Zhou, GR Jeschke, DL Sheridan, SA Parker, V Desai, M Jwa, E Cameroni, H Niu, M Good, A Remenyi, JL Ma, YJ Sheu, HE Sassi, R Sopko, CS Chan, C De Virgilio, NM Hollingsworth, WA Lim, DF Stern, B Stillman, BJ Andrews, MB Gerstein, M Snyder, BE Turk (2010). Sci Signal 3: ra12.
 
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Close association of RNA polymerase II and many transcription factors with Pol III genes.
D Raha, Z Wang, Z Moqtaderi, L Wu, G Zhong, M Gerstein, K Struhl, M Snyder (2010). Proc Natl Acad Sci U S A 107: 3639-44.
 
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EBNA1 regulates cellular gene expression by binding cellular promoters.
A Canaan, I Haviv, AE Urban, VP Schulz, S Hartman, Z Zhang, D Palejev, AB Deisseroth, J Lacy, M Snyder, M Gerstein, SM Weissman (2009). Proc Natl Acad Sci U S A 106: 22421-6.
 
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Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.
R Tonikian, X Xin, CP Toret, D Gfeller, C Landgraf, S Panni, S Paoluzi, L Castagnoli, B Currell, S Seshagiri, H Yu, B Winsor, M Vidal, MB Gerstein, GD Bader, R Volkmer, G Cesareni, DG Drubin, PM Kim, SS Sidhu, C Boone (2009). PLoS Biol 7: e1000218.
 
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N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer.
D Pflueger, DS Rickman, A Sboner, S Perner, CJ LaFargue, MA Svensson, BJ Moss, N Kitabayashi, Y Pan, A de la Taille, R Kuefer, AK Tewari, F Demichelis, MS Chee, MB Gerstein, MA Rubin (2009). Neoplasia 11: 804-11.
 
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Small RNAs originated from pseudogenes: cis- or trans-acting?
X Guo, Z Zhang, MB Gerstein, D Zheng (2009). PLoS Comput Biol 5: e1000449.
 
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Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor.
K Talbert-Slagle, S Marlatt, FN Barrera, E Khurana, J Oates, M Gerstein, DM Engelman, AM Dixon, D Dimaio (2009). J Virol 83: 9773-85.
 
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The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies.
JO Korbel, T Tirosh-Wagner, AE Urban, XN Chen, M Kasowski, L Dai, F Grubert, C Erdman, MC Gao, K Lange, EM Sobel, GM Barlow, AS Aylsworth, NJ Carpenter, RD Clark, MY Cohen, E Doran, T Falik-Zaccai, SO Lewin, IT Lott, BC McGillivray, JB Moeschler, MJ Pettenati, SM Pueschel, KW Rao, LG Shaffer, M Shohat, AJ Van Riper, D Warburton, S Weissman, MB Gerstein, M Snyder, JR Korenberg (2009). Proc Natl Acad Sci U S A 106: 12031-6.
 
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Unlocking the secrets of the genome.
SE Celniker, LA Dillon, MB Gerstein, KC Gunsalus, S Henikoff, GH Karpen, M Kellis, EC Lai, JD Lieb, DM MacAlpine, G Micklem, F Piano, M Snyder, L Stein, KP White, RH Waterston, modENCODE Consortium (2009). Nature 459: 927-30.
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Integrated assessment of genomic correlates of protein evolutionary rate.
Y Xia, EA Franzosa, MB Gerstein (2009). PLoS Comput Biol 5: e1000413.
 
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Dynamic and complex transcription factor binding during an inducible response in yeast.
L Ni, C Bruce, C Hart, J Leigh-Bell, D Gelperin, L Umansky, MB Gerstein, M Snyder (2009). Genes Dev 23: 1351-63.
 
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Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.
Y Mishima, C Abreu-Goodger, AA Staton, C Stahlhut, C Shou, C Cheng, M Gerstein, AJ Enright, AJ Giraldez (2009). Genes Dev 23: 619-32.
 
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Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.
P Lefrancois, GM Euskirchen, RK Auerbach, J Rozowsky, T Gibson, CM Yellman, M Gerstein, M Snyder (2009). BMC Genomics 10: 37.
 
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Distinct genomic aberrations associated with ERG rearranged prostate cancer.
F Demichelis, SR Setlur, R Beroukhim, S Perner, JO Korbel, CJ Lafargue, D Pflueger, C Pina, MD Hofer, A Sboner, MA Svensson, DS Rickman, A Urban, M Snyder, M Meyerson, C Lee, MB Gerstein, R Kuefer, MA Rubin (2009). Genes Chromosomes Cancer 48: 366-80.
 
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A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster.
X Zhang, Z Lian, C Padden, MB Gerstein, J Rozowsky, M Snyder, TR Gingeras, P Kapranov, SM Weissman, PE Newburger (2009). Blood 113: 2526-34.
 
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MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays.
SC Popescu, GV Popescu, S Bachan, Z Zhang, M Gerstein, M Snyder, SP Dinesh-Kumar (2009). Genes Dev 23: 80-92.
 
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Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.
M Seringhaus, J Rozowsky, T Royce, U Nagalakshmi, J Jee, M Snyder, M Gerstein (2008). BMC Genomics 9: 635.
 
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Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies.
AY Yam, Y Xia, HT Lin, A Burlingame, M Gerstein, J Frydman (2008). Nat Struct Mol Biol 15: 1255-62.
 
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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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Transmembrane protein oxygen content and compartmentalization of cells.
R Sasidharan, A Smith, M Gerstein (2008). PLoS One 3: e2726.
 
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Targeting the human cancer pathway protein interaction network by structural genomics.
YJ Huang, D Hang, LJ Lu, L Tong, MB Gerstein, GT Montelione (2008). Mol Cell Proteomics 7: 2048-60.
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A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.
Z Lian, A Karpikov, J Lian, MC Mahajan, S Hartman, M Gerstein, M Snyder, SM Weissman (2008). Genome Res 18: 1224-37.
 
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Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer.
KD Mertz, F Demichelis, A Sboner, MS Hirsch, P Dal Cin, K Struckmann, M Storz, S Scherrer, DM Schmid, RT Strebel, NM Probst-Hensch, M Gerstein, H Moch, MA Rubin (2008). Int J Cancer 123: 569-76.
 
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The transcriptional landscape of the yeast genome defined by RNA sequencing.
U Nagalakshmi, Z Wang, K Waern, C Shou, D Raha, M Gerstein, M Snyder (2008). Science 320: 1344-9.
 
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Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
DS Johnson, W Li, DB Gordon, A Bhattacharjee, B Curry, J Ghosh, L Brizuela, JS Carroll, M Brown, P Flicek, CM Koch, I Dunham, M Bieda, X Xu, PJ Farnham, P Kapranov, DA Nix, TR Gingeras, X Zhang, H Holster, N Jiang, RD Green, JS Song, SA McCuine, E Anton, L Nguyen, ND Trinklein, Z Ye, K Ching, D Hawkins, B Ren, PC Scacheri, J Rozowsky, A Karpikov, G Euskirchen, S Weissman, M Gerstein, M Snyder, A Yang, Z Moqtaderi, H Hirsch, HP Shulha, Y Fu, Z Weng, K Struhl, RM Myers, JD Lieb, XS Liu (2008). Genome Res 18: 393-403.
 
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Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.
JQ Wu, J Du, J Rozowsky, Z Zhang, AE Urban, G Euskirchen, S Weissman, M Gerstein, M Snyder (2008). Genome Biol 9: R3.
 
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Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer.
SR Setlur, TE Royce, A Sboner, JM Mosquera, F Demichelis, MD Hofer, KD Mertz, M Gerstein, MA Rubin (2007). Cancer Res 67: 10296-303.
 
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Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches.
AJ McClellan, Y Xia, AM Deutschbauer, RW Davis, M Gerstein, J Frydman (2007). Cell 131: 121-35.
 
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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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Divergence of transcription factor binding sites across related yeast species.
AR Borneman, TA Gianoulis, ZD Zhang, H Yu, J Rozowsky, MR Seringhaus, LY Wang, M Gerstein, M Snyder (2007). Science 317: 815-9.
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The minimum information required for reporting a molecular interaction experiment (MIMIx).
S Orchard, L Salwinski, S Kerrien, L Montecchi-Palazzi, M Oesterheld, V Stumpflen, A Ceol, A Chatr-aryamontri, J Armstrong, P Woollard, JJ Salama, S Moore, J Wojcik, GD Bader, M Vidal, ME Cusick, M Gerstein, AC Gavin, G Superti-Furga, J Greenblatt, J Bader, P Uetz, M Tyers, P Legrain, S Fields, N Mulder, M Gilson, M Niepmann, L Burgoon, J De Las Rivas, C Prieto, VM Perreau, C Hogue, HW Mewes, R Apweiler, I Xenarios, D Eisenberg, G Cesareni, H Hermjakob (2007). Nat Biotechnol 25: 894-8.
 
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Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
AR Borneman, ZD Zhang, J Rozowsky, MR Seringhaus, M Gerstein, M Snyder (2007). Funct Integr Genomics 7: 335-45.
 
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Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.
GM Euskirchen, JS Rozowsky, CL Wei, WH Lee, ZD Zhang, S Hartman, O Emanuelsson, V Stolc, S Weissman, MB Gerstein, Y Ruan, M Snyder (2007). Genome Res 17: 898-909.
 
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Structured RNAs in the ENCODE selected regions of the human genome.
S Washietl, JS Pedersen, JO Korbel, C Stocsits, AR Gruber, J Hackermuller, J Hertel, M Lindemeyer, K Reiche, A Tanzer, C Ucla, C Wyss, SE Antonarakis, F Denoeud, J Lagarde, J Drenkow, P Kapranov, TR Gingeras, R Guigo, M Snyder, MB Gerstein, A Reymond, IL Hofacker, PF Stadler (2007). Genome Res 17: 852-64.
 
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Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.
ND Trinklein, U Karaoz, J Wu, A Halees, S Force Aldred, PJ Collins, D Zheng, ZD Zhang, MB Gerstein, M Snyder, RM Myers, Z Weng (2007). Genome Res 17: 720-31.
 
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Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling.
L Wu, SI Hwang, K Rezaul, LJ Lu, V Mayya, M Gerstein, JK Eng, DH Lundgren, DK Han (2007). Mol Cell Proteomics 6: 1343-53.
 
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Global identification and characterization of transcriptionally active regions in the rice genome.
L Li, X Wang, R Sasidharan, V Stolc, W Deng, H He, J Korbel, X Chen, W Tongprasit, P Ronald, R Chen, M Gerstein, XW Deng (2007). PLoS One 2: e294.
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Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays.
SC Popescu, GV Popescu, S Bachan, Z Zhang, M Seay, M Gerstein, M Snyder, SP Dinesh-Kumar (2007). Proc Natl Acad Sci U S A 104: 4730-5.
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New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.
MG Smith, TA Gianoulis, S Pukatzki, JJ Mekalanos, LN Ornston, M Gerstein, M Snyder (2007). Genes Dev 21: 601-14.
 
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Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.
Z Zhang, AW Pang, M Gerstein (2007). BMC Evol Biol 7 Suppl 1: S14.
 
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Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
O Emanuelsson, U Nagalakshmi, D Zheng, JS Rozowsky, AE Urban, J Du, Z Lian, V Stolc, S Weissman, M Snyder, MB Gerstein (2007). Genome Res 17: 886-97.
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An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.
Y Liu, J Li, L Sam, CS Goh, M Gerstein, YA Lussier (2006). PLoS Comput Biol 2: e159.
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TOS9 regulates white-opaque switching in Candida albicans.
T Srikantha, AR Borneman, KJ Daniels, C Pujol, W Wu, MR Seringhaus, M Gerstein, S Yi, M Snyder, DR Soll (2006). Eukaryot Cell 5: 1674-87.
 
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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
NJ Krogan, G Cagney, H Yu, G Zhong, X Guo, A Ignatchenko, J Li, S Pu, N Datta, AP Tikuisis, T Punna, JM Peregrin-Alvarez, M Shales, X Zhang, M Davey, MD Robinson, A Paccanaro, JE Bray, A Sheung, B Beattie, DP Richards, V Canadien, A Lalev, F Mena, P Wong, A Starostine, MM Canete, J Vlasblom, S Wu, C Orsi, SR Collins, S Chandran, R Haw, JJ Rilstone, K Gandi, NJ Thompson, G Musso, P St Onge, S Ghanny, MH Lam, G Butland, AM Altaf-Ul, S Kanaya, A Shilatifard, E O'Shea, JS Weissman, CJ Ingles, TR Hughes, J Parkinson, M Gerstein, SJ Wodak, A Emili, JF Greenblatt (2006). Nature 440: 637-43.
 
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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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Biochemical and genetic analysis of the yeast proteome with a movable ORF collection.
DM Gelperin, MA White, ML Wilkinson, Y Kon, LA Kung, KJ Wise, N Lopez-Hoyo, L Jiang, S Piccirillo, H Yu, M Gerstein, ME Dumont, EM Phizicky, M Snyder, EJ Grayhack (2005). Genes Dev 19: 2816-26.
 
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Global analysis of protein phosphorylation in yeast.
J Ptacek, G Devgan, G Michaud, H Zhu, X Zhu, J Fasolo, H Guo, G Jona, A Breitkreutz, R Sopko, RR McCartney, MC Schmidt, N Rachidi, SJ Lee, AS Mah, L Meng, MJ Stark, DF Stern, C De Virgilio, M Tyers, B Andrews, M Gerstein, B Schweitzer, PF Predki, M Snyder (2005). Nature 438: 679-84.
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Global analysis of protein phosphorylation in yeast.
J Ptacek, G Devgan, G Michaud, H Zhu, X Zhu, J Fasolo, H Guo, G Jona, A Breitkreutz, R Sopko, RR McCartney, MC Schmidt, N Rachidi, SJ Lee, AS Mah, L Meng, MJ Stark, DF Stern, C De Virgilio, M Tyers, B Andrews, M Gerstein, B Schweitzer, PF Predki, M Snyder (2005). Nature 438: 679-84.
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Global changes in STAT target selection and transcription regulation upon interferon treatments.
SE Hartman, P Bertone, AK Nath, TE Royce, M Gerstein, S Weissman, M Snyder (2005). Genes Dev 19: 2953-68.
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Global changes in STAT target selection and transcription regulation upon interferon treatments.
SE Hartman, P Bertone, AK Nath, TE Royce, M Gerstein, S Weissman, M Snyder (2005). Genes Dev 19: 2953-68.
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A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.
V Stolc, L Li, X Wang, X Li, N Su, W Tongprasit, B Han, Y Xue, J Li, M Snyder, M Gerstein, J Wang, XW Deng (2005). Plant Mol Biol 59: 137-49.
 
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Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel.
T Coric, D Zheng, M Gerstein, CM Canessa (2005). J Physiol 568: 725-35.
 
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Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.
Y Gilad, SA Rifkin, P Bertone, M Gerstein, KP White (2005). Genome Res 15: 674-80.
 
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Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation.
D Huber, D Boyd, Y Xia, MH Olma, M Gerstein, J Beckwith (2005). J Bacteriol 187: 2983-91.
 
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Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium.
TB Acton, KC Gunsalus, R Xiao, LC Ma, J Aramini, MC Baran, YW Chiang, T Climent, B Cooper, NG Denissova, SM Douglas, JK Everett, CK Ho, D Macapagal, PK Rajan, R Shastry, LY Shih, GV Swapna, M Wilson, M Wu, M Gerstein, M Inouye, JF Hunt, GT Montelione (2005). Methods Enzymol 394: 210-43.
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The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans.
H Grosshans, T Johnson, KL Reinert, M Gerstein, FJ Slack (2005). Dev Cell 8: 321-30.
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DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.
EJ White, O Emanuelsson, D Scalzo, T Royce, S Kosak, EJ Oakeley, S Weissman, M Gerstein, M Groudine, M Snyder, D Schubeler (2004). Proc Natl Acad Sci U S A 101: 17771-6.
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Fast optimal genome tiling with applications to microarray design and homology search.
P Berman, P Bertone, B Dasgupta, M Gerstein, MY Kao, M Snyder (2004). J Comput Biol 11: 766-85.
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Global identification of human transcribed sequences with genome tiling arrays.
P Bertone, V Stolc, TE Royce, JS Rozowsky, AE Urban, X Zhu, JL Rinn, W Tongprasit, M Samanta, S Weissman, M Gerstein, M Snyder (2004). Science 306: 2242-6.
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The ENCODE (ENCyclopedia Of DNA Elements) Project.
The ENCODE Project Consortium (2004). Science 306: 636-40.
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Information assessment on predicting protein-protein interactions.
N Lin, B Wu, R Jansen, M Gerstein, H Zhao (2004). BMC Bioinformatics 5: 154.
 
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Regulation of gene expression by a metabolic enzyme.
DA Hall, H Zhu, X Zhu, T Royce, M Gerstein, M Snyder (2004). Science 306: 482-4.
 
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Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon.
A Kumar, M Seringhaus, MC Biery, RJ Sarnovsky, L Umansky, S Piccirillo, M Heidtman, KH Cheung, CJ Dobry, MB Gerstein, NL Craig, M Snyder (2004). Genome Res 14: 1975-86.
 
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The protein target list of the Northeast Structural Genomics Consortium.
Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione (2004). Proteins 56: 181-7.
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Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.
JL Rinn, JS Rozowsky, IJ Laurenzi, PH Petersen, K Zou, W Zhong, M Gerstein, M Snyder (2004). Dev Cell 6: 791-800.
 
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Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor.
LL Freeman-Cook, AM Dixon, JB Frank, Y Xia, L Ely, M Gerstein, DM Engelman, D DiMaio (2004). J Mol Biol 338: 907-20.
 
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CREB binds to multiple loci on human chromosome 22.
G Euskirchen, TE Royce, P Bertone, R Martone, JL Rinn, FK Nelson, F Sayward, NM Luscombe, P Miller, M Gerstein, S Weissman, M Snyder (2004). Mol Cell Biol 24: 3804-14.
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A map of the interactome network of the metazoan C. elegans.
S Li, CM Armstrong, N Bertin, H Ge, S Milstein, M Boxem, PO Vidalain, JD Han, A Chesneau, T Hao, DS Goldberg, N Li, M Martinez, JF Rual, P Lamesch, L Xu, M Tewari, SL Wong, LV Zhang, GF Berriz, L Jacotot, P Vaglio, J Reboul, T Hirozane-Kishikawa, Q Li, HW Gabel, A Elewa, B Baumgartner, DJ Rose, H Yu, S Bosak, R Sequerra, A Fraser, SE Mango, WM Saxton, S Strome, S Van Den Heuvel, F Piano, J Vandenhaute, C Sardet, M Gerstein, L Doucette-Stamm, KC Gunsalus, JW Harper, ME Cusick, FP Roth, DE Hill, M Vidal (2004). Science 303: 540-3.
 
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Identification of novel functional elements in the human genome.
Z Lian, G Euskirchen, J Rinn, R Martone, P Bertone, S Hartman, T Royce, K Nelson, F Sayward, N Luscombe, J Yang, JL Li, P Miller, AE Urban, M Gerstein, S Weissman, M Snyder (2003). Cold Spring Harb Symp Quant Biol 68: 317-22.
 
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A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development.
Y Jiao, H Yang, L Ma, N Sun, H Yu, T Liu, Y Gao, H Gu, Z Chen, M Wada, M Gerstein, H Zhao, LJ Qu, XW Deng (2003). Plant Physiol 133: 1480-93.
 
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Distribution of NF-kappaB-binding sites across human chromosome 22.
R Martone, G Euskirchen, P Bertone, S Hartman, TE Royce, NM Luscombe, JL Rinn, FK Nelson, P Miller, M Gerstein, S Weissman, M Snyder (2003). Proc Natl Acad Sci U S A 100: 12247-52.
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Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens.
MS Kimber, F Vallee, S Houston, A Necakov, T Skarina, E Evdokimova, S Beasley, D Christendat, A Savchenko, CH Arrowsmith, M Vedadi, M Gerstein, AM Edwards (2003). Proteins 51: 562-8.
 
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The transcriptional activity of human Chromosome 22.
JL Rinn, G Euskirchen, P Bertone, R Martone, NM Luscombe, S Hartman, PM Harrison, FK Nelson, P Miller, M Gerstein, S Weissman, M Snyder (2003). Genes Dev 17: 529-40.
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Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches.
A Savchenko, A Yee, A Khachatryan, T Skarina, E Evdokimova, M Pavlova, A Semesi, J Northey, S Beasley, N Lan, R Das, M Gerstein, CH Arrowmith, AM Edwards (2003). Proteins 50: 392-9.
 
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Subcellular localization of the yeast proteome.
A Kumar, S Agarwal, JA Heyman, S Matson, M Heidtman, S Piccirillo, L Umansky, A Drawid, R Jansen, Y Liu, KH Cheung, P Miller, M Gerstein, GS Roeder, M Snyder (2002). Genes Dev 16: 707-19.
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Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.
CE Horak, NM Luscombe, J Qian, P Bertone, S Piccirrillo, M Gerstein, M Snyder (2002). Genes Dev 16: 3017-33.
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YMD: a microarray database for large-scale gene expression analysis.
KH Cheung, K White, J Hager, M Gerstein, V Reinke, K Nelson, P Masiar, R Srivastava, Y Li, J Li, H Zhao, J Li, DB Allison, M Snyder, P Miller, K Williams (2002). Proc AMIA Symp : 140-4.
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Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis.
D Schneider, Y Liu, M Gerstein, DM Engelman (2002). FEBS Lett 532: 231-6.
 
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Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons.
A Mateos, J Dopazo, R Jansen, Y Tu, M Gerstein, G Stolovitzky (2002). Genome Res 12: 1703-15.
 
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Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line.
Z Lian, Y Kluger, DS Greenbaum, D Tuck, M Gerstein, N Berliner, SM Weissman, PE Newburger (2002). Blood 100: 3209-20.
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Functional profiling of the Saccharomyces cerevisiae genome.
G Giaever, AM Chu, L Ni, C Connelly, L Riles, S Veronneau, S Dow, A Lucau-Danila, K Anderson, B Andre, AP Arkin, A Astromoff, M El-Bakkoury, R Bangham, R Benito, S Brachat, S Campanaro, M Curtiss, K Davis, A Deutschbauer, KD Entian, P Flaherty, F Foury, DJ Garfinkel, M Gerstein, D Gotte, U Guldener, JH Hegemann, S Hempel, Z Herman, DF Jaramillo, DE Kelly, SL Kelly, P Kotter, D LaBonte, DC Lamb, N Lan, H Liang, H Liao, L Liu, C Luo, M Lussier, R Mao, P Menard, SL Ooi, JL Revuelta, CJ Roberts, M Rose, P Ross-Macdonald, B Scherens, G Schimmack, B Shafer, DD Shoemaker, S Sookhai-Mahadeo, RK Storms, JN Strathern, G Valle, M Voet, G Volckaert, CY Wang, TR Ward, J Wilhelmy, EA Winzeler, Y Yang, G Yen, E Youngman, K Yu, H Bussey, JD Boeke, M Snyder, P Philippsen, RW Davis, M Johnston (2002). Nature 418: 387-91.
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GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.
CE Horak, MC Mahajan, NM Luscombe, M Gerstein, SM Weissman, M Snyder (2002). Proc Natl Acad Sci U S A 99: 2924-9.
 
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An integrated approach for finding overlooked genes in yeast.
A Kumar, PM Harrison, KH Cheung, N Lan, N Echols, P Bertone, P Miller, MB Gerstein, M Snyder (2002). Nat Biotechnol 20: 58-63.
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Global analysis of protein activities using proteome chips.
H Zhu, M Bilgin, R Bangham, D Hall, A Casamayor, P Bertone, N Lan, R Jansen, S Bidlingmaier, T Houfek, T Mitchell, P Miller, RA Dean, M Gerstein, M Snyder (2001). Science 293: 2101-5.
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Genomic and proteomic analysis of the myeloid differentiation program.
Z Lian, L Wang, S Yamaga, W Bonds, Y Beazer-Barclay, Y Kluger, M Gerstein, PE Newburger, N Berliner, SM Weissman (2001). Blood 98: 513-24.
 
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RNA expression patterns change dramatically in human neutrophils exposed to bacteria.
YV Subrahmanyam, S Yamaga, Y Prashar, HH Lee, NP Hoe, Y Kluger, M Gerstein, JD Goguen, PE Newburger, SM Weissman (2001). Blood 97: 2457-68.
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Analysis of yeast protein kinases using protein chips.
H Zhu, JF Klemic, S Chang, P Bertone, A Casamayor, KG Klemic, D Smith, M Gerstein, MA Reed, M Snyder (2000). Nat Genet 26: 283-9.
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Structural proteomics of an archaeon.
D Christendat, A Yee, A Dharamsi, Y Kluger, A Savchenko, JR Cort, V Booth, CD Mackereth, V Saridakis, I Ekiel, G Kozlov, KL Maxwell, N Wu, LP McIntosh, K Gehring, MA Kennedy, AR Davidson, EF Pai, M Gerstein, AM Edwards, CH Arrowsmith (2000). Nat Struct Biol 7: 903-9.
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Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome.
S Balasubramanian, T Schneider, M Gerstein, L Regan (2000). Nucleic Acids Res 28: 3075-82.
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Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.
A Senes, M Gerstein, DM Engelman (2000). J Mol Biol 296: 921-36.
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Large-scale analysis of the yeast genome by transposon tagging and gene disruption.
P Ross-Macdonald, PS Coelho, T Roemer, S Agarwal, A Kumar, R Jansen, KH Cheung, A Sheehan, D Symoniatis, L Umansky, M Heidtman, FK Nelson, H Iwasaki, K Hager, M Gerstein, P Miller, GS Roeder, M Snyder (1999). Nature 402: 413-8.
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Repeated tertiary fold of RNA polymerase II and implications for DNA binding.
J Fu, M Gerstein, PR David, AL Gnatt, DA Bushnell, AM Edwards, RD Kornberg (1998). J Mol Biol 280: 317-22.
 
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LPFC: an Internet library of protein family core structures.
R Schmidt, M Gerstein, RB Altman (1997). Protein Sci 6: 246-8.
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