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Main Scientific Publications

In Press

Rapid Evolution by Positive Darwinian Selection in T-cell Antigen CD4 in Primates. ZD Zhang, G Weinstock, M Gerstein (In press) Journal of Molecular Evolution .

-- 2008 --

PE Bourne, JL Fink, M Gerstein (2008). "Open access: taking full advantage of the content." PLoS Comput Biol 4: e1000037.
PM Kim, A Sboner, Y Xia, M Gerstein (2008). "The role of disorder in interaction networks: a structural analysis." Mol Syst Biol 4: 179.
M Seringhaus, M Gerstein (2008). "Manually structured digital abstracts: A scaffold for automatic text mining." FEBS Lett 582: 1170.
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). "Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets." Genome Res 18: 393-403.
MR Seringhaus, PD Cayting, MB Gerstein (2008). "Uncovering trends in gene naming." Genome Biol 9: 401.
JQ Wu, J Du, J Rozowsky, Z Zhang, AE Urban, G Euskirchen, S Weissman, M Gerstein, M Snyder (2008). "Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome." Genome Biol 9: R3.
ZD Zhang, P Cayting, G Weinstock, M Gerstein (2008). "Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories." Mol Biol Evol 25: 131-43.
KY Yip, P Patel, PM Kim, DM Engelman, D McDermott, M Gerstein (2008). "An integrated system for studying residue coevolution in proteins." Bioinformatics 24: 290-2.

-- 2007 --

Semantic Web Approach to Database Integration in the Life Sciences. KH Cheung, AK Smith, KYL Yip, CJO Baker, MB Gerstein (2007) in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 11-30.
Semantic Web Standards: Legal and Social Issues and Implications. D Greenbaum, M Gerstein (2007) in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 413-433.
PM Kim, JO Korbel, MB Gerstein (2007). "Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context." Proc Natl Acad Sci U S A 104: 20274-9.
SR Setlur, TE Royce, A Sboner, JM Mosquera, F Demichelis, MD Hofer, KD Mertz, M Gerstein, MA Rubin (2007). "Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer." Cancer Res 67: 10296-303.
A Smith, K Cheung, M Krauthammer, M Schultz, M Gerstein (2007). "Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics." Bioinformatics 23: 3073-9.
AJ McClellan, Y Xia, AM Deutschbauer, RW Davis, M Gerstein, J Frydman (2007). "Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches." Cell 131: 121-35.
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). "Paired-end mapping reveals extensive structural variation in the human genome." Science 318: 420-6.
EZ Yu, AE Burba, M Gerstein (2007). "PARE: a tool for comparing protein abundance and mRNA expression data." BMC Bioinformatics 8: 309.
AR Borneman, TA Gianoulis, ZD Zhang, H Yu, J Rozowsky, MR Seringhaus, LY Wang, M Gerstein, M Snyder (2007). "Divergence of transcription factor binding sites across related yeast species." Science 317: 815-9.
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). "The minimum information required for reporting a molecular interaction experiment (MIMIx)." Nat Biotechnol 25: 894-8.
TE Royce, JS Rozowsky, MB Gerstein (2007). "Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification." Nucleic Acids Res 35: e99.
AR Borneman, ZD Zhang, J Rozowsky, MR Seringhaus, M Gerstein, M Snyder (2007). "Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms." Funct Integr Genomics 7: 335-45.
SC Flores, MB Gerstein (2007). "FlexOracle: predicting flexible hinges by identification of stable domains." BMC Bioinformatics 8: 215.
LJ Lu, A Sboner, YJ Huang, HX Lu, TA Gianoulis, KY Yip, PM Kim, GT Montelione, MB Gerstein (2007). "Comparing classical pathways and modern networks: towards the development of an edge ontology." Trends Biochem Sci 32: 320-31.
ENCODE Project Consortium, E Birney, JA Stamatoyannopoulos, A Dutta, R Guigó, TR Gingeras, EH Margulies, Z Weng, M Snyder, ET Dermitzakis, RE Thurman, MS Kuehn, CM Taylor, S Neph, CM Koch, S Asthana, A Malhotra, I Adzhubei, JA Greenbaum, RM Andrews, P Flicek, PJ Boyle, H Cao, NP Carter, GK Clelland, S Davis, N Day, P Dhami, SC Dillon, MO Dorschner, H Fiegler, PG Giresi, J Goldy, M Hawrylycz, A Haydock, R Humbert, KD James, BE Johnson, EM Johnson, TT Frum, ER Rosenzweig, N Karnani, K Lee, GC Lefebvre, PA Navas, F Neri, SC Parker, PJ Sabo, R Sandstrom, A Shafer, D Vetrie, M Weaver, S Wilcox, M Yu, FS Collins, J Dekker, JD Lieb, TD Tullius, GE Crawford, S Sunyaev, WS Noble, I Dunham, F Denoeud, A Reymond, P Kapranov, J Rozowsky, D Zheng, R Castelo, A Frankish, J Harrow, S Ghosh, A Sandelin, IL Hofacker, R Baertsch, D Keefe, S Dike, J Cheng, HA Hirsch, EA Sekinger, J Lagarde, JF Abril, A Shahab, C Flamm, C Fried, J Hackermuller, J Hertel, M Lindemeyer, K Missal, A Tanzer, S Washietl, J Korbel, O Emanuelsson, JS Pedersen, N Holroyd, R Taylor, D Swarbreck, N Matthews, MC Dickson, DJ Thomas, MT Weirauch, J Gilbert, J Drenkow, I Bell, X Zhao, KG Srinivasan, WK Sung, HS Ooi, KP Chiu, S Foissac, T Alioto, M Brent, L Pachter, ML Tress, A Valencia, SW Choo, CY Choo, C Ucla, C Manzano, C Wyss, E Cheung, TG Clark, JB Brown, M Ganesh, S Patel, H Tammana, J Chrast, CN Henrichsen, C Kai, J Kawai, U Nagalakshmi, J Wu, Z Lian, J Lian, P Newburger, X Zhang, P Bickel, JS Mattick, P Carninci, Y Hayashizaki, S Weissman, T Hubbard, RM Myers, J Rogers, PF Stadler, TM Lowe, CL Wei, Y Ruan, K Struhl, M Gerstein, SE Antonarakis, Y Fu, ED Green, U Karaoz, A Siepel, J Taylor, LA Liefer, KA Wetterstrand, PJ Good, EA Feingold, MS Guyer, GM Cooper, G Asimenos, CN Dewey, M Hou, S Nikolaev, JI Montoya-Burgos, A Loytynoja, S Whelan, F Pardi, T Massingham, H Huang, NR Zhang, I Holmes, JC Mullikin, A Ureta-Vidal, B Paten, M Seringhaus, D Church, K Rosenbloom, WJ Kent, EA Stone, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, S Batzoglou, N Goldman, RC Hardison, D Haussler, W Miller, A Sidow, ND Trinklein, ZD Zhang, L Barrera, R Stuart, DC King, A Ameur, S Enroth, MC Bieda, J Kim, AA Bhinge, N Jiang, J Liu, F Yao, VB Vega, CW Lee, P Ng, A Shahab, A Yang, Z Moqtaderi, Z Zhu, X Xu, S Squazzo, MJ Oberley, D Inman, MA Singer, TA Richmond, KJ Munn, A Rada-Iglesias, O Wallerman, J Komorowski, JC Fowler, P Couttet, AW Bruce, OM Dovey, PD Ellis, CF Langford, DA Nix, G Euskirchen, S Hartman, AE Urban, P Kraus, S Van Calcar, N Heintzman, TH Kim, K Wang, C Qu, G Hon, R Luna, CK Glass, MG Rosenfeld, SF Aldred, SJ Cooper, A Halees, JM Lin, HP Shulha, X Zhang, M Xu, JN Haidar, Y Yu, Y Ruan, VR Iyer, RD Green, C Wadelius, PJ Farnham, B Ren, RA Harte, AS Hinrichs, H Trumbower, H Clawson, J Hillman-Jackson, AS Zweig, K Smith, A Thakkapallayil, G Barber, RM Kuhn, D Karolchik, L Armengol, CP Bird, PI de Bakker, AD Kern, N Lopez-Bigas, JD Martin, BE Stranger, A Woodroffe, E Davydov, A Dimas, E Eyras, IB Hallgrimsdóttir, J Huppert, MC Zody, GR Abecasis, X Estivill, GG Bouffard, X Guan, NF Hansen, JR Idol, VV Maduro, B Maskeri, JC McDowell, M Park, PJ Thomas, AC Young, RW Blakesley, DM Muzny, E Sodergren, DA Wheeler, KC Worley, H Jiang, GM Weinstock, RA Gibbs, T Graves, R Fulton, ER Mardis, RK Wilson, M Clamp, J Cuff, S Gnerre, DB Jaffe, JL Chang, K Lindblad-Toh, ES Lander, M Koriabine, M Nefedov, K Osoegawa, Y Yoshinaga, B Zhu, PJ de Jong (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature 447: 799-816.
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). "Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies." Genome Res 17: 898-909.
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 Guigó, M Snyder, MB Gerstein, A Reymond, IL Hofacker, PF Stadler (2007). "Structured RNAs in the ENCODE selected regions of the human genome." Genome Res 17: 852-64.
D Zheng, A Frankish, R Baertsch, P Kapranov, A Reymond, SW Choo, Y Lu, F Denoeud, SE Antonarakis, M Snyder, Y Ruan, CL Wei, TR Gingeras, R Guigó, J Harrow, MB Gerstein (2007). "Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution." Genome Res 17: 839-51.
ZD Zhang, A Paccanaro, Y Fu, S Weissman, Z Weng, J Chang, M Snyder, MB Gerstein (2007). "Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions." Genome Res 17: 787-97.
JS Rozowsky, D Newburger, F Sayward, J Wu, G Jordan, JO Korbel, U Nagalakshmi, J Yang, D Zheng, R Guigó, TR Gingeras, S Weissman, P Miller, M Snyder, MB Gerstein (2007). "The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci." Genome Res 17: 732-45.
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). "Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome." Genome Res 17: 720-31.
MB Gerstein, C Bruce, JS Rozowsky, D Zheng, J Du, JO Korbel, O Emanuelsson, ZD Zhang, S Weissman, M Snyder (2007). "What is a gene, post-ENCODE? History and updated definition." Genome Res 17: 669-81.
TE Royce, NJ Carriero, MB Gerstein (2007). "An efficient pseudomedian filter for tiling microrrays." BMC Bioinformatics 8: 186.
JO Korbel, AE Urban, F Grubert, J Du, TE Royce, P Starr, G Zhong, BS Emanuel, SM Weissman, M Snyder, MB Gerstein (2007). "Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome." Proc Natl Acad Sci U S A 104: 10110-5.
H Yu, R Jansen, G Stolovitzky, M Gerstein (2007). "Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications." Bioinformatics 23: 2163-73.
L Wu, SI Hwang, K Rezaul, LJ Lu, V Mayya, M Gerstein, JK Eng, DH Lundgren, DK Han (2007). "Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling." Mol Cell Proteomics 6: 1343-53.
SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007). "Hinge Atlas: relating protein sequence to sites of structural flexibility." BMC Bioinformatics 8: 167.
ZD Zhang, J Rozowsky, HY Lam, J Du, M Snyder, M Gerstein (2007). "Tilescope: online analysis pipeline for high-density tiling microarray data." Genome Biol 8: R81.
M Gerstein, M Seringhaus, S Fields (2007). "Structured digital abstract makes text mining easy." Nature 447: 142.
AK Smith, KH Cheung, KY Yip, M Schultz, MK Gerstein (2007). "LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics." BMC Bioinformatics 8 Suppl 3: S5.
X Zhu, M Gerstein, M Snyder (2007). "Getting connected: analysis and principles of biological networks." Genes Dev 21: 1010-24.
M Gerstein, SM Douglas (2007). "RNAi development." PLoS Comput Biol 3: e80.
H Yu, PM Kim, E Sprecher, V Trifonov, M Gerstein (2007). "The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics." PLoS Comput Biol 3: e59.
TE Royce, JS Rozowsky, MB Gerstein (2007). "Assessing the need for sequence-based normalization in tiling microarray experiments." Bioinformatics 23: 988-97.
D Zheng, MB Gerstein (2007). "The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?" Trends Genet 23: 219-24.
L Li, X Wang, R Sasidharan, V Stolc, W Deng, H He, J Korbel, X Chen, W Tongprasit, P Ronald, R Chen, M Gerstein, X Wang Deng (2007). "Global identification and characterization of transcriptionally active regions in the rice genome." PLoS ONE 2: e294.
SC Popescu, GV Popescu, S Bachan, Z Zhang, M Seay, M Gerstein, M Snyder, SP Dinesh-Kumar (2007). "Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays." Proc Natl Acad Sci U S A 104: 4730-5.
MG Smith, TA Gianoulis, S Pukatzki, JJ Mekalanos, LN Ornston, M Gerstein, M Snyder (2007). "New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis." Genes Dev 21: 601-14.
Z Zhang, AW Pang, M Gerstein (2007). "Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human." BMC Evol Biol 7 Suppl 1: S14.
MR Seringhaus, MB Gerstein (2007). "Publishing perishing? Towards tomorrow's information architecture." BMC Bioinformatics 8: 17.
M Seringhaus, M Gerstein (2007). "Chemistry Nobel rich in structure." Science 315: 40-1.
H Yu, K Nguyen, T Royce, J Qian, K Nelson, M Snyder, M Gerstein (2007). "Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool." Nucleic Acids Res 35: e8.
O Emanuelsson, U Nagalakshmi, D Zheng, JS Rozowsky, AE Urban, J Du, Z Lian, V Stolc, S Weissman, M Snyder, MB Gerstein (2007). "Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome." Genome Res 17: 886-97.
JE Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrrison, M Gerstein (2007). "Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation." Nucleic Acids Res 35: D55-60.
M Gerstein, D Greenbaum, K Cheung, PL Miller (2007). "An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective." J Biomed Inform 40: 73-9.

-- 2006 --

The Death of the Scientific Paper. Seringhaus M, Gerstein M (2006). The Scientist. 20(9): 25.
Analytical Evolutionary Model for Protein Fold Occurrence in Genomes, Accounting for the Effects of Gene Duplication, Deletion, Acquisition and Selective Pressure. M Kamal, N Luscombe, J Qian, M Gerstein (2006) in Power Laws, Scale-Free Networks and Genome Biology (edited by EV Koonin, YI Wolf, GP Karev; Springer, New York), pages 165-193.
J Rozowsky, J Wu, Z Lian, U Nagalakshmi, JO Korbel, P Kapranov, D Zheng, S Dyke, P Newburger, P Miller, TR Gingeras, S Weissman, M Gerstein, M Snyder (2006). "Novel transcribed regions in the human genome." Cold Spring Harb Symp Quant Biol 71: 111-6.
PM Kim, LJ Lu, Y Xia, MB Gerstein (2006). "Relating three-dimensional structures to protein networks provides evolutionary insights." Science 314: 1938-41.
A Smith, M Gerstein (2006). "Data mining on the web." Science 314: 1682; author reply 1682.
Y Liu, J Li, L Sam, CS Goh, M Gerstein, YA Lussier (2006). "An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits." PLoS Comput Biol 2: e159.
X Zhu, M Gerstein, M Snyder (2006). "ProCAT: a data analysis approach for protein microarrays." Genome Biol 7: R110.
LY Wang, M Snyder, M Gerstein (2006). "BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments." Genome Biol 7: R102.
AE Burba, U Lehnert, EZ Yu, M Gerstein (2006). "Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins." Bioinformatics 22: 2735-8.
J Du, JS Rozowsky, JO Korbel, ZD Zhang, TE Royce, MH Schultz, M Snyder, M Gerstein (2006). "A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge." Bioinformatics 22: 3016-24.
CS Goh, TA Gianoulis, Y Liu, J Li, A Paccanaro, YA Lussier, M Gerstein (2006). "Integration of curated databases to identify genotype-phenotype associations." BMC Genomics 7: 257.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). "The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks." Bioinformatics 22: 2968-70.
H Yu, M Gerstein (2006). "Genomic analysis of the hierarchical structure of regulatory networks." Proc Natl Acad Sci U S A 103: 14724-31.
T Srikantha, AR Borneman, KJ Daniels, C Pujol, W Wu, MR Seringhaus, M Gerstein, S Yi, M Snyder, DR Soll (2006). "TOS9 regulates white-opaque switching in Candida albicans." Eukaryot Cell 5: 1674-87.
TE Royce, JS Rozowsky, NM Luscombe, O Emanuelsson, H Yu, X Zhu, M Snyder, MB Gerstein (2006). "Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies." Methods Enzymol 411: 282-311.
R Pinard, A de Winter, GJ Sarkis, MB Gerstein, KR Tartaro, RN Plant, M Egholm, JM Rothberg, JH Leamon (2006). "Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing." BMC Genomics 7: 216.
D Zheng, MB Gerstein (2006). "A computational approach for identifying pseudogenes in the ENCODE regions." Genome Biol 7 Suppl 1: S13.1-10.
M Seringhaus, A Paccanaro, A Borneman, M Snyder, M Gerstein (2006). "Predicting essential genes in fungal genomes." Genome Res 16: 1126-35.
M Gerstein, D Zheng (2006). "The real life of pseudogenes." Sci Am 295: 48-55.
H Yu, Y Xia, V Trifonov, M Gerstein (2006). "Design principles of molecular networks revealed by global comparisons and composite motifs." Genome Biol 7: R55.
NR Voss, M Gerstein, TA Steitz, PB Moore (2006). "The geometry of the ribosomal polypeptide exit tunnel." J Mol Biol 360: 893-906.
M Seringhaus, A Kumar, J Hartigan, M Snyder, M Gerstein (2006). "Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae." Nucleic Acids Res 34: e57.
M Gerstein (2006). "Tools needed to navigate landscape of the genome." Nature 440: 740.
Z Zhang, N Carriero, D Zheng, J Karro, PM Harrison, M Gerstein (2006). "PseudoPipe: an automated pseudogene identification pipeline." Bioinformatics 22: 1437-9.
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). "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae." Nature 440: 637-43.
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). "High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays." Proc Natl Acad Sci U S A 103: 4534-9.
H Yu, A Paccanaro, V Trifonov, M Gerstein (2006). "Predicting interactions in protein networks by completing defective cliques." Bioinformatics 22: 823-9.
AR Borneman, JA Leigh-Bell, H Yu, P Bertone, M Gerstein, M Snyder (2006). "Target hub proteins serve as master regulators of development in yeast." Genes Dev 20: 435-48.
Y Xia, LJ Lu, M Gerstein (2006). "Integrated prediction of the helical membrane protein interactome in yeast." J Mol Biol 357: 339-49.
S Flores, N Echols, D Milburn, B Hespenheide, K Keating, J Lu, S Wells, EZ Yu, M Thorpe, M Gerstein (2006). "The Database of Macromolecular Motions: new features added at the decade mark." Nucleic Acids Res 34: D296-301.
P Bertone, V Trifonov, JS Rozowsky, F Schubert, O Emanuelsson, J Karro, MY Kao, M Snyder, M Gerstein (2006). "Design optimization methods for genomic DNA tiling arrays." Genome Res 16: 271-81.

-- 2005 --

Inferring Protein-Protein Interactions Using Interaction Network Topologies. A Paccanaro, V Trifonov, H Yu, M Gerstein (2005). International Joint Conference on Neural Networks (IJCNN, Jul. 31-Aug. 4, Montreal, Canada), pages 161 - 166, vol. 1.
Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis. LJ Lu, Y Xia, H Yu, A Rives, H Lu, F Schubert, M Gerstein (2005). Data Analysis and Visualization in Genomics and Proteomics (Wiley, NY).
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). "Biochemical and genetic analysis of the yeast proteome with a movable ORF collection." Genes Dev 19: 2816-26.
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). "Global analysis of protein phosphorylation in yeast." Nature 438: 679-84.
SE Hartman, P Bertone, AK Nath, TE Royce, M Gerstein, S Weissman, M Snyder (2005). "Global changes in STAT target selection and transcription regulation upon interferon treatments." Genes Dev 19: 2953-68.
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). "A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray." Plant Mol Biol 59: 137-49.
A Smith, D Greenbaum, SM Douglas, M Long, M Gerstein (2005). "Network security and data integrity in academia: an assessment and a proposal for large-scale archiving." Genome Biol 6: 119.
SM Douglas, GT Montelione, M Gerstein (2005). "PubNet: a flexible system for visualizing literature derived networks." Genome Biol 6: R80.
T Coric, D Zheng, M Gerstein, CM Canessa (2005). "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." J Physiol 568: 725-35.
LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein (2005). "Assessing the limits of genomic data integration for predicting protein networks." Genome Res 15: 945-53.
TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M Snyder, M Gerstein (2005). "Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping." Trends Genet 21: 466-75.
KH Cheung, KY Yip, A Smith, R Deknikker, A Masiar, M Gerstein (2005). "YeastHub: a semantic web use case for integrating data in the life sciences domain." Bioinformatics 21 Suppl 1: i85-96.
D Zheng, Z Zhang, PM Harrison, J Karro, N Carriero, M Gerstein (2005). "Integrated pseudogene annotation for human chromosome 22: evidence for transcription." J Mol Biol 349: 27-45.
P Bertone, M Gerstein, M Snyder (2005). "Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery." Chromosome Res 13: 259-74.
Y Gilad, SA Rifkin, P Bertone, M Gerstein, KP White (2005). "Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles." Genome Res 15: 674-80.
PM Harrison, D Zheng, Z Zhang, N Carriero, M Gerstein (2005). "Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability." Nucleic Acids Res 33: 2374-83.
D Huber, D Boyd, Y Xia, MH Olma, M Gerstein, J Beckwith (2005). "Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation." J Bacteriol 187: 2983-91.
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). "Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium." Methods Enzymol 394: 210-43.
S Balasubramanian, Y Xia, E Freinkman, M Gerstein (2005). "Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms." Nucleic Acids Res 33: 1710-21.
H Grosshans, T Johnson, KL Reinert, M Gerstein, FJ Slack (2005). "The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans." Dev Cell 8: 321-30.
V Alexandrov, U Lehnert, N Echols, D Milburn, D Engelman, M Gerstein (2005). "Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool." Protein Sci 14: 633-43.
NR Voss, M Gerstein (2005). "Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly." J Mol Biol 346: 477-92.
D Greenbaum, A Smith, M Gerstein (2005). "Impediments to database interoperation: legal issues and security concerns." Nucleic Acids Res 33: D3-4.
N Carriero, MV Osier, KH Cheung, PL Miller, M Gerstein, H Zhao, B Wu, S Rifkin, J Chang, H Zhang, K White, K Williams, M Schultz (2005). "A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies." J Am Med Inform Assoc 12: 90-8.

-- 2004 --

An XML-Based Approach to Integrating Heterogeneous Yeast Genome Data. KH Cheung, D Pan, A Smith, M Seringhaus, SM Douglas, M Gerstein. 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS); pp 236-242.
U Lehnert, Y Xia, TE Royce, CS Goh, Y Liu, A Senes, H Yu, ZL Zhang, DM Engelman, M Gerstein (2004). "Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions." Q Rev Biophys 37: 121-46.
EJ White, O Emanuelsson, D Scalzo, T Royce, S Kosak, EJ Oakeley, S Weissman, M Gerstein, M Groudine, M Snyder, D Schubeler (2004). "DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states." Proc Natl Acad Sci U S A 101: 17771-6.
P Berman, P Bertone, B Dasgupta, M Gerstein, MY Kao, M Snyder (2004). "Fast optimal genome tiling with applications to microarray design and homology search." J Comput Biol 11: 766-85.
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). "Global identification of human transcribed sequences with genome tiling arrays." Science 306: 2242-6.
ENCODE Project Consortium (2004). "The ENCODE (ENCyclopedia Of DNA Elements) Project." Science 306: 636-40.
N Lin, B Wu, R Jansen, M Gerstein, H Zhao (2004). "Information assessment on predicting protein-protein interactions." BMC Bioinformatics 5: 154.
DA Hall, H Zhu, X Zhu, T Royce, M Gerstein, M Snyder (2004). "Regulation of gene expression by a metabolic enzyme." Science 306: 482-4.
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). "Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon." Genome Res 14: 1975-86.
R Jansen, M Gerstein (2004). "Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction." Curr Opin Microbiol 7: 535-45.
NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein (2004). "Genomic analysis of regulatory network dynamics reveals large topological changes." Nature 431: 308-12.
Y Liu, PM Harrison, V Kunin, M Gerstein (2004). "Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes." Genome Biol 5: R64.
Z Zhang, M Gerstein (2004). "Large-scale analysis of pseudogenes in the human genome." Curr Opin Genet Dev 14: 328-35.
Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione (2004). "The protein target list of the Northeast Structural Genomics Consortium." Proteins 56: 181-7.
MM Babu, NM Luscombe, L Aravind, M Gerstein, SA Teichmann (2004). "Structure and evolution of transcriptional regulatory networks." Curr Opin Struct Biol 14: 283-91.
Y Xia, H Yu, R Jansen, M Seringhaus, S Baxter, D Greenbaum, H Zhao, M Gerstein (2004). "Analyzing cellular biochemistry in terms of molecular networks." Annu Rev Biochem 73: 1051-87.
JL Rinn, JS Rozowsky, IJ Laurenzi, PH Petersen, K Zou, W Zhong, M Gerstein, M Snyder (2004). "Major molecular differences between mammalian sexes are involved in drug metabolism and renal function." Dev Cell 6: 791-800.
D Greenbaum, SM Douglas, A Smith, J Lim, M Fischer, M Schultz, M Gerstein (2004). "Computer security in academia-a potential roadblock to distributed annotation of the human genome." Nat Biotechnol 22: 771-2.
H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein (2004). "Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs." Genome Res 14: 1107-18.
H Yu, D Greenbaum, H Xin Lu, X Zhu, M Gerstein (2004). "Genomic analysis of essentiality within protein networks." Trends Genet 20: 227-31.
LL Freeman-Cook, AM Dixon, JB Frank, Y Xia, L Ely, M Gerstein, DM Engelman, D DiMaio (2004). "Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor." J Mol Biol 338: 907-20.
CS Goh, D Milburn, M Gerstein (2004). "Conformational changes associated with protein-protein interactions." Curr Opin Struct Biol 14: 104-9.
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). "CREB binds to multiple loci on human chromosome 22." Mol Cell Biol 24: 3804-14.
R Das, M Gerstein (2004). "A method using active-site sequence conservation to find functional shifts in protein families: application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens." Proteins 55: 455-63.
M Gerstein, N Echols (2004). "Exploring the range of protein flexibility, from a structural proteomics perspective." Curr Opin Chem Biol 8: 14-9.
Y Liu, M Gerstein, DM Engelman (2004). "Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism." Proc Natl Acad Sci U S A 101: 3495-7.
Z Zhang, N Carriero, M Gerstein (2004). "Comparative analysis of processed pseudogenes in the mouse and human genomes." Trends Genet 20: 62-7.
CS Goh, N Lan, SM Douglas, B Wu, N Echols, A Smith, D Milburn, GT Montelione, H Zhao, M Gerstein (2004). "Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis." J Mol Biol 336: 115-30.
H Yu, X Zhu, D Greenbaum, J Karro, M Gerstein (2004). "TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics." Nucleic Acids Res 32: 328-37.
V Alexandrov, M Gerstein (2004). "Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures." BMC Bioinformatics 5: 2.
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). "A map of the interactome network of the metazoan C. elegans." Science 303: 540-3.

-- 2003 --

WG Krebs, J Tsai, V Alexandrov, J Junker, R Jansen, M Gerstein (2003). "Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences." Methods Enzymol 374: 544-84.
D Greenbaum, J Lim, M Gerstein (2003). "An analysis of the present system of scientific publishing: what's wrong and where to go from here" Interdiscip Sci Rev 28: 293-302.
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). "Identification of novel functional elements in the human genome." Cold Spring Harb Symp Quant Biol 68: 317-22.
Y Kluger, H Yu, J Qian, M Gerstein (2003). "Relationship between gene co-expression and probe localization on microarray slides." BMC Genomics 4: 49.
Z Zhang, PM Harrison, Y Liu, M Gerstein (2003). "Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome." Genome Res 13: 2541-58.
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). "A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development." Plant Physiol 133: 1480-93.
Z Zhang, M Gerstein (2003). "Reconstructing genetic networks in yeast." Nat Biotechnol 21: 1295-7.
PM Harrison, N Carriero, Y Liu, M Gerstein (2003). "A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs." J Mol Biol 333: 885-92.
R Jansen, H Yu, D Greenbaum, Y Kluger, NJ Krogan, S Chung, A Emili, M Snyder, JF Greenblatt, M Gerstein (2003). "A Bayesian networks approach for predicting protein-protein interactions from genomic data." Science 302: 449-53.
J Qian, J Lin, NM Luscombe, H Yu, M Gerstein (2003). "Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data." Bioinformatics 19: 1917-26.
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). "Distribution of NF-kappaB-binding sites across human chromosome 22." Proc Natl Acad Sci U S A 100: 12247-52.
Z Zhang, M Gerstein (2003). "Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes." Nucleic Acids Res 31: 5338-48.
D Greenbaum, C Colangelo, K Williams, M Gerstein (2003). "Comparing protein abundance and mRNA expression levels on a genomic scale." Genome Biol 4: 117.
D Greenbaum, M Gerstein (2003). "A universal legal framework as a prerequisite for database interoperability." Nat Biotechnol 21: 979-82.
Z Zhang, M Gerstein (2003). "The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse." Gene 312: 61-72.
H Yu, NM Luscombe, J Qian, M Gerstein (2003). "Genomic analysis of gene expression relationships in transcriptional regulatory networks." Trends Genet 19: 422-7.
J Qian, Y Kluger, H Yu, M Gerstein (2003). "Identification and correction of spurious spatial correlations in microarray data." Biotechniques 35: 42-4, 46, 48.
M Gerstein, JM Thornton (2003). "Sequences and topology." Curr Opin Struct Biol 13: 341-3.
NM Luscombe, TE Royce, P Bertone, N Echols, CE Horak, JT Chang, M Snyder, M Gerstein (2003). "ExpressYourself: A modular platform for processing and visualizing microarray data." Nucleic Acids Res 31: 3477-82.
Z Zhang, M Gerstein (2003). "Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements." J Biol 2: 11.
PM Harrison, M Gerstein (2003). "A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes." Genome Biol 4: R40.
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). "Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens." Proteins 51: 562-8.
CS Goh, N Lan, N Echols, SM Douglas, D Milburn, P Bertone, R Xiao, LC Ma, D Zheng, Z Wunderlich, T Acton, GT Montelione, M Gerstein (2003). "SPINE 2: a system for collaborative structural proteomics within a federated database framework." Nucleic Acids Res 31: 2833-8.
Z Zhang, M Gerstein (2003). "Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome." Genomics 81: 468-80.
M Snyder, M Gerstein (2003). "Genomics. Defining genes in the genomics era." Science 300: 258-60.
R Jansen, HJ Bussemaker, M Gerstein (2003). "Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models." Nucleic Acids Res 31: 2242-51.
Y Kluger, R Basri, JT Chang, M Gerstein (2003). "Spectral biclustering of microarray data: coclustering genes and conditions." Genome Res 13: 703-16.
M Gerstein, A Edwards, CH Arrowsmith, GT Montelione (2003). "Structural genomics: current progress." Science 299: 1663.
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). "The transcriptional activity of human Chromosome 22." Genes Dev 17: 529-40.
PM Harrison, D Milburn, Z Zhang, P Bertone, M Gerstein (2003). "Identification of pseudogenes in the Drosophila melanogaster genome." Nucleic Acids Res 31: 1033-7.
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). "Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches." Proteins 50: 392-9.
N Lan, GT Montelione, M Gerstein (2003). "Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level." Curr Opin Chem Biol 7: 44-54.
N Echols, D Milburn, M Gerstein (2003). "MolMovDB: analysis and visualization of conformational change and structural flexibility." Nucleic Acids Res 31: 478-82.

-- 2002 --

J Tsai, M Gerstein (2002). "Calculations of protein volumes: sensitivity analysis and parameter database." Bioinformatics 18: 985-95.
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). "Subcellular localization of the yeast proteome." Genes Dev 16: 707-19.
D Greenbaum, R Jansen, M Gerstein (2002). "Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts." Bioinformatics 18: 585-96.
H Hegyi, J Lin, D Greenbaum, M Gerstein (2002). "Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds." Proteins 47: 126-41.
P Harrison, A Kumar, N Lan, N Echols, M Snyder, M Gerstein (2002). "A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution." J Mol Biol 316: 409-19.
PM Harrison, M Gerstein (2002). "Studying genomes through the aeons: protein families, pseudogenes and proteome evolution." J Mol Biol 318: 1155-74.
PM Harrison, A Kumar, N Lang, M Snyder, M Gerstein (2002). "A question of size: the eukaryotic proteome and the problems in defining it." Nucleic Acids Res 30: 1083-90.
PM Harrison, H Hegyi, S Balasubramanian, NM Luscombe, P Bertone, N Echols, T Johnson, M Gerstein (2002). "Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22." Genome Res 12: 272-80.
R Jansen, D Greenbaum, M Gerstein (2002). "Relating whole-genome expression data with protein-protein interactions." Genome Res 12: 37-46.
M Gerstein, N Lan, R Jansen (2002). "Proteomics. Integrating interactomes." Science 295: 284-7.
Towards a systematic definition of protein function that scales to the genome level: Defining function in terms of interactions. N Lan, R Jansen, M Gerstein (2002). Proceedings of the IEEE 90:1848-1858 .
M Gerstein, J Junker (2002). "Blurring the boundaries between scientific 'papers' and biological databases" Nature Yearbook of Science and Technology : 210-212 (ed. D Butler, Palgrave Macmillan Publishers).
Fast optimal genome tiling with applications to microarray design and homology search. P Berman, P Bertone, B DasGupta, M Gerstein, M-Y Kao, M Snyder. (2002) Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics. Springer-Verlag LNCS 2452: 419-433 .
R Jansen, N Lan, J Qian, M Gerstein (2002). "Integration of genomic datasets to predict protein complexes in yeast." J Struct Funct Genomics 2: 71-81.
CE Horak, NM Luscombe, J Qian, P Bertone, S Piccirrillo, M Gerstein, M Snyder (2002). "Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae." Genes Dev 16: 3017-33.
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). "YMD: a microarray database for large-scale gene expression analysis." Proc AMIA Symp : 140-4.
D Schneider, Y Liu, M Gerstein, DM Engelman (2002). "Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis." FEBS Lett 532: 231-6.
A Mateos, J Dopazo, R Jansen, Y Tu, M Gerstein, G Stolovitzky (2002). "Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons." Genome Res 12: 1703-15.
ZL Zhang, PM Harrison, M Gerstein (2002). "Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes." J Mol Biol 323: 811-22.
J Lin, J Qian, D Greenbaum, P Bertone, R Das, N Echols, A Senes, B Stenger, M Gerstein (2002). "GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing." Nucleic Acids Res 30: 4574-82.
Z Lian, Y Kluger, DS Greenbaum, D Tuck, M Gerstein, N Berliner, SM Weissman, PE Newburger (2002). "Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line." Blood 100: 3209-20.
Y Liu, DM Engelman, M Gerstein (2002). "Genomic analysis of membrane protein families: abundance and conserved motifs." Genome Biol 3: research0054.
Z Zhang, P Harrison, M Gerstein (2002). "Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome." Genome Res 12: 1466-82.
AM Edwards, B Kus, R Jansen, D Greenbaum, J Greenblatt, M Gerstein (2002). "Bridging structural biology and genomics: assessing protein interaction data with known complexes." Trends Genet 18: 529-36.
WG Krebs, V Alexandrov, CA Wilson, N Echols, H Yu, M Gerstein (2002). "Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic." Proteins 48: 682-95.
NM Luscombe, J Qian, Z Zhang, T Johnson, M Gerstein (2002). "The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties." Genome Biol 3: RESEARCH0040.
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). "Functional profiling of the Saccharomyces cerevisiae genome." Nature 418: 387-91.
S Balasubramanian, P Harrison, H Hegyi, P Bertone, N Luscombe, N Echols, P McGarvey, Z Zhang, M Gerstein (2002). "SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes." Pharmacogenomics 3: 393-402.
N Echols, P Harrison, S Balasubramanian, NM Luscombe, P Bertone, Z Zhang, M Gerstein (2002). "Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes." Nucleic Acids Res 30: 2515-23.
CE Horak, MC Mahajan, NM Luscombe, M Gerstein, SM Weissman, M Snyder (2002). "GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis." Proc Natl Acad Sci U S A 99: 2924-9.
Y Liu, NM Luscombe, V Alexandrov, P Bertone, P Harrison, Z Zhang, M Gerstein (2002). "Structural genomics: a new era for pharmaceutical research." Genome Biol 3: REPORTS4004.
A Kumar, PM Harrison, KH Cheung, N Lan, N Echols, P Bertone, P Miller, MB Gerstein, M Snyder (2002). "An integrated approach for finding overlooked genes in yeast." Nat Biotechnol 20: 58-63.

-- 2001 --

J Qian, NM Luscombe, M Gerstein (2001). "Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model." J Mol Biol 313: 673-81.
J Qian, M Dolled-Filhart, J Lin, H Yu, M Gerstein (2001). "Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions." J Mol Biol 314: 1053-66.
H Hegyi, M Gerstein (2001). "Annotation transfer for genomics: measuring functional divergence in multi-domain proteins." Genome Res 11: 1632-40.
NM Luscombe, D Greenbaum, M Gerstein (2001). "What is bioinformatics? A proposed definition and overview of the field." Methods Inf Med 40: 346-58.
R Das, J Junker, D Greenbaum, MB Gerstein (2001). "Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond." Pharmacogenomics J 1: 115-25.
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). "Global analysis of protein activities using proteome chips." Science 293: 2101-5.
V Alexandrov, M Gerstein (2001). "Calculating populations of subcellular compartments using density matrix formalism" International Journal of Quantum Chemistry 85: 693-696.
WK Olson, M Bansal, SK Burley, RE Dickerson, M Gerstein, SC Harvey, U Heinemann, XJ Lu, S Neidle, Z Shakked, H Sklenar, M Suzuki, CS Tung, E Westhof, C Wolberger, HM Berman (2001). "A standard reference frame for the description of nucleic acid base-pair geometry." J Mol Biol 313: 229-37.
J Tsai, N Voss, M Gerstein (2001). "Determining the minimum number of types necessary to represent the sizes of protein atoms." Bioinformatics 17: 949-56.
D Greenbaum, NM Luscombe, R Jansen, J Qian, M Gerstein (2001). "Interrelating different types of genomic data, from proteome to secretome: 'oming in on function." Genome Res 11: 1463-8.
M Gerstein, F M Richards (2001). "Protein Geometry: Distances, Areas, and Volumes" International Tables for Crystallography : (Volume F, Chapter 22.1.1, pages 531-539; M Rossmann & E Arnold, editors; Dordrecht: Kluwer).
P Harrison, M Gerstein (2001). " A Bauhaus for Biologists: An Introduction to Protein Architecture by A. M. Lesk" Trends Biochem Sci 26: 204-205.
P Bertone, M Gerstein (2001). "Integrative data mining: the new direction in bioinformatics." IEEE Eng Med Biol Mag 20: 33-40.
Z Lian, L Wang, S Yamaga, W Bonds, Y Beazer-Barclay, Y Kluger, M Gerstein, PE Newburger, N Berliner, SM Weissman (2001). "Genomic and proteomic analysis of the myeloid differentiation program." Blood 98: 513-24.
YV Subrahmanyam, S Yamaga, Y Prashar, HH Lee, NP Hoe, Y Kluger, M Gerstein, JD Goguen, PE Newburger, SM Weissman (2001). "RNA expression patterns change dramatically in human neutrophils exposed to bacteria." Blood 97: 2457-68.
P Bertone, Y Kluger, N Lan, D Zheng, D Christendat, A Yee, AM Edwards, CH Arrowsmith, GT Montelione, M Gerstein (2001). "SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics." Nucleic Acids Res 29: 2884-98.
M Gerstein, B Honig (2001). "Sequences and Topology" Current Opinion in Structural Biology 11: 327-329.
N Luscombe, D Greenbaum, M Gerstein (2001). "What is Bioinformatics? A Proposed Definition and Overview of the Field" Intl. Medical Informatics Association : (Yearbook, Pages 83-99).
PM Harrison, N Echols, MB Gerstein (2001). "Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome." Nucleic Acids Res 29: 818-30.
J Qian, B Stenger, CA Wilson, J Lin, R Jansen, SA Teichmann, J Park, WG Krebs, H Yu, V Alexandrov, N Echols, M Gerstein (2001). "PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information." Nucleic Acids Res 29: 1750-64.
An XML Application for Genomic Data Interoperation. Cheung KH, Liu Y, Kumar K, Snyder M, Gerstein M, Miller P. IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE) 2001, pp. 97-103 .

-- 2000 --

M Gerstein (2000). "Integrative database analysis in structural genomics." Nat Struct Biol 7 Suppl: 960-3.
R Das, H Hegyi, M Gerstein (2000). "Genome analyses of spirochetes: a study of the protein structures, functions and metabolic pathways in Treponema pallidum and Borrelia burgdorferi." J Mol Microbiol Biotechnol 2: 387-92.
D Christendat, A Yee, A Dharamsi, Y Kluger, M Gerstein, CH Arrowsmith, AM Edwards (2000). "Structural proteomics: prospects for high throughput sample preparation." Prog Biophys Mol Biol 73: 339-45.
H Zhu, JF Klemic, S Chang, P Bertone, A Casamayor, KG Klemic, D Smith, M Gerstein, MA Reed, M Snyder (2000). "Analysis of yeast protein kinases using protein chips." Nat Genet 26: 283-9.
A Drawid, R Jansen, M Gerstein (2000). "Genome-wide analysis relating expression level with protein subcellular localization." Trends Genet 16: 426-30.
M Gerstein, R Jansen (2000). "The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?" Curr Opin Struct Biol 10: 574-84.
R Das, M Gerstein (2000). "The stability of thermophilic proteins: a study based on comprehensive genome comparison." Funct Integr Genomics 1: 76-88.
GJ Naylor, M Gerstein (2000). "Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins." J Mol Evol 51: 223-33.
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). "Structural proteomics of an archaeon." Nat Struct Biol 7: 903-9.
A Drawid, M Gerstein (2000). "A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome." J Mol Biol 301: 1059-75.
S Balasubramanian, T Schneider, M Gerstein, L Regan (2000). "Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome." Nucleic Acids Res 28: 3075-82.
M Gerstein, J Lin, H Hegyi (2000). "Protein folds in the worm genome." Pac Symp Biocomput : 30-41.
M Gerstein (2000). "Annotation of the human genome." Science 288: 1590.
J Lin, M Gerstein (2000). "Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels." Genome Res 10: 808-18.
WG Krebs, M Gerstein (2000). "The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework." Nucleic Acids Res 28: 1665-75.
A Senes, M Gerstein, DM Engelman (2000). "Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions." J Mol Biol 296: 921-36.
CA Wilson, J Kreychman, M Gerstein (2000). "Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores." J Mol Biol 297: 233-49.
R Jansen, M Gerstein (2000). "Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins." Nucleic Acids Res 28: 1481-8.

-- 1999 --

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). "Large-scale analysis of the yeast genome by transposon tagging and gene disruption." Nature 402: 413-8.
M Gerstein, C Chothia (1999). "Perspectives: signal transduction. Proteins in motion." Science 285: 1682-3.
M Gerstein, R Jansen, T Johnson, J Tsai, W Krebs (1999). " Motions in a Database Framework: from Structure to Sequence" Rigidity Theory and Applications : 401-442 (ed. M F Thorpe and P M Duxbury, Kluwer Academic/Plenum Publishers).
M Gerstein (1999). "E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics." Bioinformatics 15: 429-31.
ES Brodkin, M Gerstein (1999). ""E-biomed" and clinical research." N Engl J Med 341: 1080; author reply 1081.
J Tsai, R Taylor, C Chothia, M Gerstein (1999). "The packing density in proteins: standard radii and volumes." J Mol Biol 290: 253-66.
SA Teichmann, C Chothia, M Gerstein (1999). "Advances in structural genomics." Curr Opin Struct Biol 9: 390-9.
M Gerstein (1999). "Building the future of biocomputing." Nature 399: 101.
H Hegyi, M Gerstein (1999). "The relationship between protein structure and function: a comprehensive survey with application to the yeast genome." J Mol Biol 288: 147-64.
M Gerstein (1999). "Forging links in an electronic paper chain." Nature 398: 20.

-- 1998 --

M Gerstein, H Hegyi (1998). "Comparing genomes in terms of protein structure: surveys of a finite parts list." FEMS Microbiol Rev 22: 277-304.
M Gerstein (1998). "How representative are the known structures of the proteins in a complete genome? A comprehensive structural census." Fold Des 3: 497-512.
M Gerstein (1998). "Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census." Proteins 33: 518-34.
M Gerstein, M Levitt (1998). "Simulating water and the molecules of life." Sci Am 279: 100-5.
M Gerstein (1998). "Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence." Bioinformatics 14: 707-14.
M Gerstein, W Krebs (1998). "A database of macromolecular motions." Nucleic Acids Res 26: 4280-90.
J Fu, M Gerstein, PR David, AL Gnatt, DA Bushnell, AM Edwards, RD Kornberg (1998). "Repeated tertiary fold of RNA polymerase II and implications for DNA binding." J Mol Biol 280: 317-22.
M Levitt, M Gerstein (1998). "A unified statistical framework for sequence comparison and structure comparison." Proc Natl Acad Sci U S A 95: 5913-20.
M Gerstein, M Levitt (1998). "Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins." Protein Sci 7: 445-56.

-- 1997 --

M Gerstein (1997). "A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure." J Mol Biol 274: 562-76.
M Gerstein, M Levitt (1997). "A structural census of the current population of protein sequences." Proc Natl Acad Sci U S A 94: 11911-6.
C Chothia, M Gerstein (1997). "Protein evolution. How far can sequences diverge?" Nature 385: 579, 581.
M Levitt, M Gerstein, E Huang, S Subbiah, J Tsai (1997). "Protein folding: the endgame." Annu Rev Biochem 66: 549-79.
R Schmidt, M Gerstein, RB Altman (1997). "LPFC: an Internet library of protein family core structures." Protein Sci 6: 246-8.

-- 1996 --

Practicing Cyberlaw in the Year 2000. R Becker, M Gerstein (1996) New Jersey Lawyer Magazine 179: 12-27 (September)..
Keeping the Shape but Changing the Charges: A Simulation Study of Urea and its Isosteric Analogues. J Tsai, M Gerstein, M Levitt (1996) Journal of Chemical Physics 104: 9417-9430.
M Gerstein, C Chothia (1996). "Packing at the protein-water interface." Proc Natl Acad Sci U S A 93: 10167-72.
M Gerstein, M Levitt (1996). "Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures." Proc Int Conf Intell Syst Mol Biol 4: 59-67.

-- 1995 --

M Gerstein, RB Altman (1995). "Using a measure of structural variation to define a core for the globins." Comput Appl Biosci 11: 633-44.
M Suzuki, M Gerstein (1995). "Binding geometry of alpha-helices that recognize DNA." Proteins 23: 525-35.
M Gerstein, RB Altman (1995). "Average core structures and variability measures for protein families: application to the immunoglobulins." J Mol Biol 251: 161-75.
M Gerstein, J Tsai, M Levitt (1995). "The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra." J Mol Biol 249: 955-66.
RB Altman, C Hughes, MB Gerstein (1995). "Methods for displaying macromolecular structural uncertainty: application to the globins." J Mol Graph 13: 142-52, 109-2.
M Suzuki, N Yagi, M Gerstein (1995). "DNA recognition and superstructure formation by helix-turn-helix proteins." Protein Eng 8: 329-38.
M Suzuki, SE Brenner, M Gerstein, N Yagi (1995). "DNA recognition code of transcription factors." Protein Eng 8: 319-28.

-- 1994 --

Purcell's early work on NMR: Contingency versus Inevitability . M Gerstein (1994) American Journal of Physics 62: 596-601.
M Suzuki, M Gerstein, N Yagi (1994). "Stereochemical basis of DNA recognition by Zn fingers." Nucleic Acids Res 22: 3397-405.
Y Harpaz, M Gerstein, C Chothia (1994). "Volume changes on protein folding." Structure 2: 641-9.
M Gerstein, AM Lesk, C Chothia (1994). "Structural mechanisms for domain movements in proteins." Biochemistry 33: 6739-49.
M Suzuki, D Neuhaus, M Gerstein, S Aimoto (1994). "Solution structure of the DNA binding octapeptide repeat of the K10 gene product." Protein Eng 7: 461-70.
M Gerstein, EL Sonnhammer, C Chothia (1994). "Volume changes in protein evolution." J Mol Biol 236: 1067-78.
RB Altman, M Gerstein (1994). "Finding an average core structure: application to the globins." Proc Int Conf Intell Syst Mol Biol 2: 19-27.

-- 1993 --

Simulation of Water around a Model Protein Helix. 1. Two-dimensional Projections of Solvent Structure. M Gerstein, R Lynden-Bell (1993) Journal of Physical Chemistry 97: 2982-2991. .
Simulation of Water around a Model Protein Helix. 2. The Relative Contributions of Packing, Hydrophobicity, and Hydrogen Bonding. M Gerstein, R Lynden-Bell (1993) Journal of Physical Chemistry 97: 2991-2999..
M Gerstein, BF Anderson, GE Norris, EN Baker, AM Lesk, C Chothia (1993). "Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces." J Mol Biol 234: 357-72.
M Suzuki, M Gerstein, T Johnson (1993). "An NMR study on the DNA-binding SPKK motif and a model for its interaction with DNA." Protein Eng 6: 565-74.
M Gerstein, RM Lynden-Bell (1993). "What is the natural boundary of a protein in solution?" J Mol Biol 230: 641-50.
M Gerstein, G Schulz, C Chothia (1993). "Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers." J Mol Biol 229: 494-501.
S Subramaniam, M Gerstein, D Oesterhelt, R Henderson (1993). "Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin." EMBO J 12: 1-8.

-- 1992 --

A Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining Sites. M Gerstein (1992) Acta Crystallographica A48: 271-276. .
I De Baere, L Liu, L Moens, J Van Beeumen, C Gielens, J Richelle, C Trotman, J Finch, M Gerstein, M Perutz (1992). "Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum: amino acid sequence and structural interpretation." Proc Natl Acad Sci U S A 89: 4638-42.

-- 1991 --

M Gerstein, C Chothia (1991). "Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase." J Mol Biol 220: 133-49.

-- 1987 --

Inverse Problem for Synchrotron Radiation in the Presence of Noise. N Fisch, A Kritz, M Gerstein (1987) Proceedings of the Sixth Joint Workshop on Electron Cyclotron Emission and Electron Cyclotron Resonance Heating. (eds. A Riviere, A Costley), 23-30 (Oxford, 16-17 September)..