Gerstein Lab Publications
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Main Scientific Publications

Total papers: 378

(Last updated Tue Aug 17 15:08:46 EDT 2010 )

-- In Press (0)--

-- 2010 (24) --

Annotating non-coding regions of the genome.
RP Alexander, G Fang, J Rozowsky, M Snyder, MB Gerstein (2010) Nat Rev Genet 11: 559-71.
Segmental duplications in the human genome reveal details of pseudogene formation.
E Khurana, HY Lam, C Cheng, N Carriero, P Cayting, MB Gerstein (2010) Nucleic Acids Res
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.
A Agarwal, D Koppstein, J Rozowsky, A Sboner, L Habegger, LW Hillier, R Sasidharan, V Reinke, RH Waterston, M Gerstein (2010) BMC Genomics 11: 383.
Using semantic web rules to reason on an ontology of pseudogenes.
ME Holford, E Khurana, KH Cheung, M Gerstein (2010) Bioinformatics 26: i71-8.
Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.
N Bhardwaj, MB Carson, A Abyzov, KK Yan, H Lu, MB Gerstein (2010) PLoS Comput Biol 6: e1000755.
3V: cavity, channel and cleft volume calculator and extractor.
NR Voss, M Gerstein (2010) Nucleic Acids Res 38 Suppl: W555-62.
MOTIPS: automated motif analysis for predicting targets of modular protein domains.
HY Lam, PM Kim, J Mok, R Tonikian, SS Sidhu, BE Turk, M Snyder, MB Gerstein (2010) BMC Bioinformatics 11: 243.
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010) Proc Natl Acad Sci U S A 107: 9186-91.
Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families.
PV Patel, TA Gianoulis, RD Bjornson, KY Yip, DM Engelman, MB Gerstein (2010) Genome Res 20: 960-71.
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.
Getting started in gene orthology and functional analysis.
G Fang, N Bhardwaj, R Robilotto, MB Gerstein (2010) PLoS Comput Biol 6: e1000703.
Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels.
N Bhardwaj, KK Yan, MB Gerstein (2010) Proc Natl Acad Sci U S A 107: 6841-6.
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.
Molecular sampling of prostate cancer: a dilemma for predicting disease progression.
A Sboner, F Demichelis, S Calza, Y Pawitan, SR Setlur, Y Hoshida, S Perner, HO Adami, K Fall, LA Mucci, PW Kantoff, M Stampfer, SO Andersson, E Varenhorst, JE Johansson, MB Gerstein, TR Golub, MA Rubin, O Andrén (2010) BMC Med Genomics 3: 8.
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.
ZD Zhang, A Frankish, T Hunt, J Harrow, M Gerstein (2010) Genome Biol 11: R26.
Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique.
N Bhardwaj, M Gerstein, H Lu (2010) BMC Bioinformatics 11 Suppl 1: S6.
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.
Personal genome sequencing: current approaches and challenges.
M Snyder, J Du, M Gerstein (2010) Genes Dev 24: 423-31.
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.
M Zhong, W Niu, ZJ Lu, M Sarov, JI Murray, J Janette, D Raha, KL Sheaffer, HY Lam, E Preston, C Slightham, LW Hillier, T Brock, A Agarwal, R Auerbach, AA Hyman, M Gerstein, SE Mango, SK Kim, RH Waterston, V Reinke, M Snyder (2010) PLoS Genet 6: e1000848.
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.
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.
Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data.
KY Yip, RP Alexander, KK Yan, M Gerstein (2010) PLoS One 5: e8121.
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
HY Lam, XJ Mu, AM Stütz, A Tanzer, PD Cayting, M Snyder, PM Kim, JO Korbel, MB Gerstein (2010) Nat Biotechnol 28: 47-55.
RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes.
A Abyzov, R Bjornson, M Felipe, M Gerstein (2010) Proteins 78: 309-24.

-- 2009 (39) --

Science and the Law: Grappling with the Gulf
D Greenbaum, MB Gerstein (2009) Science 323: 210.
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.
Social networking and personal genomics: suggestions for optimizing the interaction.
D Greenbaum, M Gerstein (2009) Am J Bioeth 9: 15-9.
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.
Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.
YJ Liu, D Zheng, S Balasubramanian, N Carriero, E Khurana, R Robilotto, MB Gerstein (2009) BMC Genomics 10: 480.
Robust-linear-model normalization to reduce technical variability in functional protein microarrays.
A Sboner, A Karpikov, G Chen, M Smith, D Mattoon, M Dawn, L Freeman-Cook, B Schweitzer, MB Gerstein (2009) J Proteome Res 8: 5451-64.
The relationship between the evolution of microRNA targets and the length of their UTRs.
C Cheng, N Bhardwaj, M Gerstein (2009) BMC Genomics 10: 431.
Computational analysis of membrane proteins: the largest class of drug targets.
Y Arinaminpathy, E Khurana, DM Engelman, MB Gerstein (2009) Drug Discov Today 14: 1130-5.
mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer.
C Cheng, X Fu, P Alves, M Gerstein (2009) Genome Biol 10: R90.
Mapping accessible chromatin regions using Sono-Seq.
RK Auerbach, G Euskirchen, J Rozowsky, N Lamarre-Vincent, Z Moqtaderi, P Lefrançois, K Struhl, M Gerstein, M Snyder (2009) Proc Natl Acad Sci U S A 106: 14926-31.
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.
KY Yip, PM Kim, D McDermott, M Gerstein (2009) BMC Bioinformatics 10: 241.
Getting started in text mining: part two.
A Rzhetsky, M Seringhaus, MB Gerstein (2009) PLoS Comput Biol 5: e1000411.
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.
Small RNAs originated from pseudogenes: cis- or trans-acting?
X Guo, Z Zhang, MB Gerstein, D Zheng (2009) PLoS Comput Biol 5: e1000449.
Understanding modularity in molecular networks requires dynamics.
RP Alexander, PM Kim, T Emonet, MB Gerstein (2009) Sci Signal 2: pe44.
An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping.
R Sasidharan, A Agarwal, J Rozowsky, M Gerstein (2009) BMC Res Notes 2: 150.
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.
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.
Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.
J Du, RD Bjornson, ZD Zhang, Y Kong, M Snyder, MB Gerstein (2009) PLoS Comput Biol 5: e1000432.
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.
Integrated assessment of genomic correlates of protein evolutionary rate.
Y Xia, EA Franzosa, MB Gerstein (2009) PLoS Comput Biol 5: e1000413.
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.
Relating protein conformational changes to packing efficiency and disorder.
N Bhardwaj, M Gerstein (2009) Protein Sci 18: 1230-40.
Personal phenotypes to go with personal genomes.
M Snyder, S Weissman, M Gerstein (2009) Mol Syst Biol 5: 273.
Systematic identification of transcription factors associated with patient survival in cancers.
C Cheng, LM Li, P Alves, M Gerstein (2009) BMC Genomics 10: 225.
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.
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
JO Korbel, A Abyzov, XJ Mu, N Carriero, P Cayting, Z Zhang, M Snyder, MB Gerstein (2009) Genome Biol 10: R23.
StoneHinge: hinge prediction by network analysis of individual protein structures.
KS Keating, SC Flores, MB Gerstein, LA Kuhn (2009) Protein Sci 18: 359-71.
Quantifying environmental adaptation of metabolic pathways in metagenomics.
TA Gianoulis, J Raes, PV Patel, R Bjornson, JO Korbel, I Letunic, T Yamada, A Paccanaro, LJ Jensen, M Snyder, P Bork, MB Gerstein (2009) Proc Natl Acad Sci U S A 106: 1374-9.
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.
P Lefrançois, GM Euskirchen, RK Auerbach, J Rozowsky, T Gibson, CM Yellman, M Gerstein, M Snyder (2009) BMC Genomics 10: 37.
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.
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.
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.
S Balasubramanian, D Zheng, YJ Liu, G Fang, A Frankish, N Carriero, R Robilotto, P Cayting, M Gerstein (2009) Genome Biol 10: R2.
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
J Rozowsky, G Euskirchen, RK Auerbach, ZD Zhang, T Gibson, R Bjornson, N Carriero, M Snyder, MB Gerstein (2009) Nat Biotechnol 27: 66-75.
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.
MSB: a mean-shift-based approach for the analysis of structural variation in the genome.
LY Wang, A Abyzov, JO Korbel, M Snyder, M Gerstein (2009) Genome Res 19: 106-17.
RNA-Seq: a revolutionary tool for transcriptomics.
Z Wang, M Gerstein, M Snyder (2009) Nat Rev Genet 10: 57-63.
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions.
KY Yip, M Gerstein (2009) Bioinformatics 25: 243-50.
Pseudofam: the pseudogene families database.
HY Lam, E Khurana, G Fang, P Cayting, N Carriero, KH Cheung, MB Gerstein (2009) Nucleic Acids Res 37: D738-43.

-- 2008 (25) --

Genomics Confounds Gene Classification
M Seringhaus, M Gerstein (2008) American Scientist 96:466-473 (Nov-Dec).
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.
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.
Genomic anonymity: have we already lost it?
D Greenbaum, J Du, M Gerstein (2008) Am J Bioeth 8: 71-4.
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.
Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history.
PM Kim, HY Lam, AE Urban, JO Korbel, J Affourtit, F Grubert, X Chen, S Weissman, M Snyder, MB Gerstein (2008) Genome Res 18: 1865-74.
Modeling ChIP sequencing in silico with applications.
ZD Zhang, J Rozowsky, M Snyder, J Chang, M Gerstein (2008) PLoS Comput Biol 4: e1000158.
Transmembrane protein oxygen content and compartmentalization of cells.
R Sasidharan, A Smith, M Gerstein (2008) PLoS One 3: e2726.
Seeking a new biology through text mining.
A Rzhetsky, M Seringhaus, M Gerstein (2008) Cell 134: 9-13.
Genomics: protein fossils live on as RNA.
R Sasidharan, M Gerstein (2008) Nature 453: 729-31.
The current excitement about copy-number variation: how it relates to gene duplications and protein families.
JO Korbel, PM Kim, X Chen, AE Urban, S Weissman, M Snyder, MB Gerstein (2008) Curr Opin Struct Biol 18: 366-74.
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.
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.
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.
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.
HingeMaster: normal mode hinge prediction approach and integration of complementary predictors.
SC Flores, KS Keating, J Painter, F Morcos, K Nguyen, EA Merritt, LA Kuhn, MB Gerstein (2008) Proteins 73: 299-319.
Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates.
ZD Zhang, G Weinstock, M Gerstein (2008) J Mol Evol 66: 446-56.
Open access: taking full advantage of the content.
PE Bourne, JL Fink, M Gerstein (2008) PLoS Comput Biol 4: e1000037.
The role of disorder in interaction networks: a structural analysis.
PM Kim, A Sboner, Y Xia, M Gerstein (2008) Mol Syst Biol 4: 179.
Manually structured digital abstracts: a scaffold for automatic text mining.
M Seringhaus, M Gerstein (2008) FEBS Lett 582: 1170.
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.
Uncovering trends in gene naming.
MR Seringhaus, PD Cayting, MB Gerstein (2008) Genome Biol 9: 401.
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.
Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.
ZD Zhang, P Cayting, G Weinstock, M Gerstein (2008) Mol Biol Evol 25: 131-43.
An integrated system for studying residue coevolution in proteins.
KY Yip, P Patel, PM Kim, DM Engelman, D McDermott, M Gerstein (2008) Bioinformatics 24: 290-2.

-- 2007 (45) --

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.
Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007) Proc Natl Acad Sci U S A 104: 20274-9.
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.
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
A Smith, K Cheung, M Krauthammer, M Schultz, M Gerstein (2007) Bioinformatics 23: 3073-9.
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.
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.
PARE: a tool for comparing protein abundance and mRNA expression data.
EZ Yu, AE Burba, M Gerstein (2007) BMC Bioinformatics 8: 309.
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.
The minimum information required for reporting a molecular interaction experiment (MIMIx).
S Orchard, L Salwinski, S Kerrien, L Montecchi-Palazzi, M Oesterheld, V Stümpflen, 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.
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.
TE Royce, JS Rozowsky, MB Gerstein (2007) Nucleic Acids Res 35: e99.
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.
FlexOracle: predicting flexible hinges by identification of stable domains.
SC Flores, MB Gerstein (2007) BMC Bioinformatics 8: 215.
Comparing classical pathways and modern networks: towards the development of an edge ontology.
LJ Lu, A Sboner, YJ Huang, HX Lu, TA Gianoulis, KY Yip, PM Kim, GT Montelione, MB Gerstein (2007) Trends Biochem Sci 32: 320-31.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
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 Hackermüller, 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 Karaöz, 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 Löytynoja, 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 Hallgrímsdóttir, 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) Nature 447: 799-816.
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.
Structured RNAs in the ENCODE selected regions of the human genome.
S Washietl, JS Pedersen, JO Korbel, C Stocsits, AR Gruber, J Hackermüller, 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) Genome Res 17: 852-64.
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
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) Genome Res 17: 839-51.
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.
ZD Zhang, A Paccanaro, Y Fu, S Weissman, Z Weng, J Chang, M Snyder, MB Gerstein (2007) Genome Res 17: 787-97.
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
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) Genome Res 17: 732-45.
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.
ND Trinklein, U Karaöz, 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.
What is a gene, post-ENCODE? History and updated definition.
MB Gerstein, C Bruce, JS Rozowsky, D Zheng, J Du, JO Korbel, O Emanuelsson, ZD Zhang, S Weissman, M Snyder (2007) Genome Res 17: 669-81.
An efficient pseudomedian filter for tiling microrrays.
TE Royce, NJ Carriero, MB Gerstein (2007) BMC Bioinformatics 8: 186.
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.
JO Korbel, AE Urban, F Grubert, J Du, TE Royce, P Starr, G Zhong, BS Emanuel, SM Weissman, M Snyder, MB Gerstein (2007) Proc Natl Acad Sci U S A 104: 10110-5.
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.
H Yu, R Jansen, G Stolovitzky, M Gerstein (2007) Bioinformatics 23: 2163-73.
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.
Hinge Atlas: relating protein sequence to sites of structural flexibility.
SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007) BMC Bioinformatics 8: 167.
Tilescope: online analysis pipeline for high-density tiling microarray data.
ZD Zhang, J Rozowsky, HY Lam, J Du, M Snyder, M Gerstein (2007) Genome Biol 8: R81.
Structured digital abstract makes text mining easy.
M Gerstein, M Seringhaus, S Fields (2007) Nature 447: 142.
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.
AK Smith, KH Cheung, KY Yip, M Schultz, MK Gerstein (2007) BMC Bioinformatics 8 Suppl 3: S5.
Getting connected: analysis and principles of biological networks.
X Zhu, M Gerstein, M Snyder (2007) Genes Dev 21: 1010-24.
RNAi development.
M Gerstein, SM Douglas (2007) PLoS Comput Biol 3: e80.
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.
H Yu, PM Kim, E Sprecher, V Trifonov, M Gerstein (2007) PLoS Comput Biol 3: e59.
Assessing the need for sequence-based normalization in tiling microarray experiments.
TE Royce, JS Rozowsky, MB Gerstein (2007) Bioinformatics 23: 988-97.
The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
D Zheng, MB Gerstein (2007) Trends Genet 23: 219-24.
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.
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.
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.
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.
Publishing perishing? Towards tomorrow's information architecture.
MR Seringhaus, MB Gerstein (2007) BMC Bioinformatics 8: 17.
Chemistry Nobel rich in structure.
M Seringhaus, M Gerstein (2007) Science 315: 40-1.
Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.
H Yu, K Nguyen, T Royce, J Qian, K Nelson, M Snyder, M Gerstein (2007) Nucleic Acids Res 35: e8.
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.
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
JE Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrrison, M Gerstein (2007) Nucleic Acids Res 35: D55-60.
An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.
M Gerstein, D Greenbaum, K Cheung, PL Miller (2007) J Biomed Inform 40: 73-9.

-- 2006 (31) --

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.
Novel transcribed regions in the human genome.
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) Cold Spring Harb Symp Quant Biol 71: 111-6.
Relating three-dimensional structures to protein networks provides evolutionary insights.
PM Kim, LJ Lu, Y Xia, MB Gerstein (2006) Science 314: 1938-41.
Data mining on the web.
A Smith, M Gerstein (2006) Science 314: 1682; author reply 1682.
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.
ProCAT: a data analysis approach for protein microarrays.
X Zhu, M Gerstein, M Snyder (2006) Genome Biol 7: R110.
BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments.
LY Wang, M Snyder, M Gerstein (2006) Genome Biol 7: R102.
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
AE Burba, U Lehnert, EZ Yu, M Gerstein (2006) Bioinformatics 22: 2735-8.
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
J Du, JS Rozowsky, JO Korbel, ZD Zhang, TE Royce, MH Schultz, M Snyder, M Gerstein (2006) Bioinformatics 22: 3016-24.
Integration of curated databases to identify genotype-phenotype associations.
CS Goh, TA Gianoulis, Y Liu, J Li, A Paccanaro, YA Lussier, M Gerstein (2006) BMC Genomics 7: 257.
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006) Bioinformatics 22: 2968-70.
Genomic analysis of the hierarchical structure of regulatory networks.
H Yu, M Gerstein (2006) Proc Natl Acad Sci U S A 103: 14724-31.
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.
Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
TE Royce, JS Rozowsky, NM Luscombe, O Emanuelsson, H Yu, X Zhu, M Snyder, MB Gerstein (2006) Methods Enzymol 411: 282-311.
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.
R Pinard, A de Winter, GJ Sarkis, MB Gerstein, KR Tartaro, RN Plant, M Egholm, JM Rothberg, JH Leamon (2006) BMC Genomics 7: 216.
A computational approach for identifying pseudogenes in the ENCODE regions.
D Zheng, MB Gerstein (2006) Genome Biol 7 Suppl 1: S13.1-10.
Predicting essential genes in fungal genomes.
M Seringhaus, A Paccanaro, A Borneman, M Snyder, M Gerstein (2006) Genome Res 16: 1126-35.
The real life of pseudogenes.
M Gerstein, D Zheng (2006) Sci Am 295: 48-55.
Design principles of molecular networks revealed by global comparisons and composite motifs.
H Yu, Y Xia, V Trifonov, M Gerstein (2006) Genome Biol 7: R55.
The geometry of the ribosomal polypeptide exit tunnel.
NR Voss, M Gerstein, TA Steitz, PB Moore (2006) J Mol Biol 360: 893-906.
Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.
M Seringhaus, A Kumar, J Hartigan, M Snyder, M Gerstein (2006) Nucleic Acids Res 34: e57.
Tools needed to navigate landscape of the genome.
M Gerstein (2006) Nature 440: 740.
PseudoPipe: an automated pseudogene identification pipeline.
Z Zhang, N Carriero, D Zheng, J Karro, PM Harrison, M Gerstein (2006) Bioinformatics 22: 1437-9.
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 Peregrín-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.
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.
Predicting interactions in protein networks by completing defective cliques.
H Yu, A Paccanaro, V Trifonov, M Gerstein (2006) Bioinformatics 22: 823-9.
Target hub proteins serve as master regulators of development in yeast.
AR Borneman, JA Leigh-Bell, H Yu, P Bertone, M Gerstein, M Snyder (2006) Genes Dev 20: 435-48.
Integrated prediction of the helical membrane protein interactome in yeast.
Y Xia, LJ Lu, M Gerstein (2006) J Mol Biol 357: 339-49.
The Database of Macromolecular Motions: new features added at the decade mark.
S Flores, N Echols, D Milburn, B Hespenheide, K Keating, J Lu, S Wells, EZ Yu, M Thorpe, M Gerstein (2006) Nucleic Acids Res 34: D296-301.
Design optimization methods for genomic DNA tiling arrays.
P Bertone, V Trifonov, JS Rozowsky, F Schubert, O Emanuelsson, J Karro, MY Kao, M Snyder, M Gerstein (2006) Genome Res 16: 271-81.

-- 2005 (24) --

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).
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.
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.
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.
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.
Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.
A Smith, D Greenbaum, SM Douglas, M Long, M Gerstein (2005) Genome Biol 6: 119.
PubNet: a flexible system for visualizing literature derived networks.
SM Douglas, GT Montelione, M Gerstein (2005) Genome Biol 6: R80.
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.
Assessing the limits of genomic data integration for predicting protein networks.
LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein (2005) Genome Res 15: 945-53.
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M Snyder, M Gerstein (2005) Trends Genet 21: 466-75.
YeastHub: a semantic web use case for integrating data in the life sciences domain.
KH Cheung, KY Yip, A Smith, R Deknikker, A Masiar, M Gerstein (2005) Bioinformatics 21 Suppl 1: i85-96.
Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
D Zheng, Z Zhang, PM Harrison, J Karro, N Carriero, M Gerstein (2005) J Mol Biol 349: 27-45.
Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery.
P Bertone, M Gerstein, M Snyder (2005) Chromosome Res 13: 259-74.
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.
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.
PM Harrison, D Zheng, Z Zhang, N Carriero, M Gerstein (2005) Nucleic Acids Res 33: 2374-83.
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.
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.
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.
S Balasubramanian, Y Xia, E Freinkman, M Gerstein (2005) Nucleic Acids Res 33: 1710-21.
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.
Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.
V Alexandrov, U Lehnert, N Echols, D Milburn, D Engelman, M Gerstein (2005) Protein Sci 14: 633-43.
Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly.
NR Voss, M Gerstein (2005) J Mol Biol 346: 477-92.
Impediments to database interoperation: legal issues and security concerns.
D Greenbaum, A Smith, M Gerstein (2005) Nucleic Acids Res 33: D3-4.
A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.
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) J Am Med Inform Assoc 12: 90-8.

-- 2004 (31) --

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.
Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.
U Lehnert, Y Xia, TE Royce, CS Goh, Y Liu, A Senes, H Yu, ZL Zhang, DM Engelman, M Gerstein (2004) Q Rev Biophys 37: 121-46.
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 Schübeler (2004) Proc Natl Acad Sci U S A 101: 17771-6.
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.
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.
The ENCODE (ENCyclopedia Of DNA Elements) Project.
ENCODE Project Consortium (2004) Science 306: 636-40.
Information assessment on predicting protein-protein interactions.
N Lin, B Wu, R Jansen, M Gerstein, H Zhao (2004) BMC Bioinformatics 5: 154.
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.
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.
Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction.
R Jansen, M Gerstein (2004) Curr Opin Microbiol 7: 535-45.
Genomic analysis of regulatory network dynamics reveals large topological changes.
NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein (2004) Nature 431: 308-12.
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.
Y Liu, PM Harrison, V Kunin, M Gerstein (2004) Genome Biol 5: R64.
Large-scale analysis of pseudogenes in the human genome.
Z Zhang, M Gerstein (2004) Curr Opin Genet Dev 14: 328-35.
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.
Structure and evolution of transcriptional regulatory networks.
MM Babu, NM Luscombe, L Aravind, M Gerstein, SA Teichmann (2004) Curr Opin Struct Biol 14: 283-91.
Analyzing cellular biochemistry in terms of molecular networks.
Y Xia, H Yu, R Jansen, M Seringhaus, S Baxter, D Greenbaum, H Zhao, M Gerstein (2004) Annu Rev Biochem 73: 1051-87.
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.
Computer security in academia-a potential roadblock to distributed annotation of the human genome.
D Greenbaum, SM Douglas, A Smith, J Lim, M Fischer, M Schultz, M Gerstein (2004) Nat Biotechnol 22: 771-2.
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein (2004) Genome Res 14: 1107-18.
Genomic analysis of essentiality within protein networks.
H Yu, D Greenbaum, H Xin Lu, X Zhu, M Gerstein (2004) Trends Genet 20: 227-31.
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.
Conformational changes associated with protein-protein interactions.
CS Goh, D Milburn, M Gerstein (2004) Curr Opin Struct Biol 14: 104-9.
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.
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.
R Das, M Gerstein (2004) Proteins 55: 455-63.
Exploring the range of protein flexibility, from a structural proteomics perspective.
M Gerstein, N Echols (2004) Curr Opin Chem Biol 8: 14-9.
Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism.
Y Liu, M Gerstein, DM Engelman (2004) Proc Natl Acad Sci U S A 101: 3495-7.
Comparative analysis of processed pseudogenes in the mouse and human genomes.
Z Zhang, N Carriero, M Gerstein (2004) Trends Genet 20: 62-7.
Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.
CS Goh, N Lan, SM Douglas, B Wu, N Echols, A Smith, D Milburn, GT Montelione, H Zhao, M Gerstein (2004) J Mol Biol 336: 115-30.
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics.
H Yu, X Zhu, D Greenbaum, J Karro, M Gerstein (2004) Nucleic Acids Res 32: 328-37.
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.
V Alexandrov, M Gerstein (2004) BMC Bioinformatics 5: 2.
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.

-- 2003 (33) --

Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences.
WG Krebs, J Tsai, V Alexandrov, J Junker, R Jansen, M Gerstein (2003) Methods Enzymol 374: 544-84.
An analysis of the present system of scientific publishing: what's wrong and where to go from here
D Greenbaum, J Lim, M Gerstein (2003) Interdiscip Sci Rev 28: 293-302.
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.
Relationship between gene co-expression and probe localization on microarray slides.
Y Kluger, H Yu, J Qian, M Gerstein (2003) BMC Genomics 4: 49.
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.
Z Zhang, PM Harrison, Y Liu, M Gerstein (2003) Genome Res 13: 2541-58.
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.
Reconstructing genetic networks in yeast.
Z Zhang, M Gerstein (2003) Nat Biotechnol 21: 1295-7.
A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs.
PM Harrison, N Carriero, Y Liu, M Gerstein (2003) J Mol Biol 333: 885-92.
A Bayesian networks approach for predicting protein-protein interactions from genomic data.
R Jansen, H Yu, D Greenbaum, Y Kluger, NJ Krogan, S Chung, A Emili, M Snyder, JF Greenblatt, M Gerstein (2003) Science 302: 449-53.
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
J Qian, J Lin, NM Luscombe, H Yu, M Gerstein (2003) Bioinformatics 19: 1917-26.
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.
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes.
Z Zhang, M Gerstein (2003) Nucleic Acids Res 31: 5338-48.
Comparing protein abundance and mRNA expression levels on a genomic scale.
D Greenbaum, C Colangelo, K Williams, M Gerstein (2003) Genome Biol 4: 117.
A universal legal framework as a prerequisite for database interoperability.
D Greenbaum, M Gerstein (2003) Nat Biotechnol 21: 979-82.
The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse.
Z Zhang, M Gerstein (2003) Gene 312: 61-72.
Genomic analysis of gene expression relationships in transcriptional regulatory networks.
H Yu, NM Luscombe, J Qian, M Gerstein (2003) Trends Genet 19: 422-7.
Identification and correction of spurious spatial correlations in microarray data.
J Qian, Y Kluger, H Yu, M Gerstein (2003) Biotechniques 35: 42-4, 46, 48.
Sequences and topology.
M Gerstein, JM Thornton (2003) Curr Opin Struct Biol 13: 341-3.
ExpressYourself: A modular platform for processing and visualizing microarray data.
NM Luscombe, TE Royce, P Bertone, N Echols, CE Horak, JT Chang, M Snyder, M Gerstein (2003) Nucleic Acids Res 31: 3477-82.
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.
Z Zhang, M Gerstein (2003) J Biol 2: 11.
A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes.
PM Harrison, M Gerstein (2003) Genome Biol 4: R40.
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.
SPINE 2: a system for collaborative structural proteomics within a federated database framework.
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) Nucleic Acids Res 31: 2833-8.
Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.
Z Zhang, M Gerstein (2003) Genomics 81: 468-80.
Genomics. Defining genes in the genomics era.
M Snyder, M Gerstein (2003) Science 300: 258-60.
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.
R Jansen, HJ Bussemaker, M Gerstein (2003) Nucleic Acids Res 31: 2242-51.
Spectral biclustering of microarray data: coclustering genes and conditions.
Y Kluger, R Basri, JT Chang, M Gerstein (2003) Genome Res 13: 703-16.
Structural genomics: current progress.
M Gerstein, A Edwards, CH Arrowsmith, GT Montelione (2003) Science 299: 1663.
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.
Identification of pseudogenes in the Drosophila melanogaster genome.
PM Harrison, D Milburn, Z Zhang, P Bertone, M Gerstein (2003) Nucleic Acids Res 31: 1033-7.
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.
Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level.
N Lan, GT Montelione, M Gerstein (2003) Curr Opin Chem Biol 7: 44-54.
MolMovDB: analysis and visualization of conformational change and structural flexibility.
N Echols, D Milburn, M Gerstein (2003) Nucleic Acids Res 31: 478-82.

-- 2002 (32) --

Calculations of protein volumes: sensitivity analysis and parameter database.
J Tsai, M Gerstein (2002) Bioinformatics 18: 985-95.
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.
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.
D Greenbaum, R Jansen, M Gerstein (2002) Bioinformatics 18: 585-96.
Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds.
H Hegyi, J Lin, D Greenbaum, M Gerstein (2002) Proteins 47: 126-41.
A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.
P Harrison, A Kumar, N Lan, N Echols, M Snyder, M Gerstein (2002) J Mol Biol 316: 409-19.
Studying genomes through the aeons: protein families, pseudogenes and proteome evolution.
PM Harrison, M Gerstein (2002) J Mol Biol 318: 1155-74.
A question of size: the eukaryotic proteome and the problems in defining it.
PM Harrison, A Kumar, N Lang, M Snyder, M Gerstein (2002) Nucleic Acids Res 30: 1083-90.
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.
PM Harrison, H Hegyi, S Balasubramanian, NM Luscombe, P Bertone, N Echols, T Johnson, M Gerstein (2002) Genome Res 12: 272-80.
Relating whole-genome expression data with protein-protein interactions.
R Jansen, D Greenbaum, M Gerstein (2002) Genome Res 12: 37-46.
Proteomics. Integrating interactomes.
M Gerstein, N Lan, R Jansen (2002) 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 .
Blurring the boundaries between scientific 'papers' and biological databases
M Gerstein, J Junker (2002) 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 .
Integration of genomic datasets to predict protein complexes in yeast.
R Jansen, N Lan, J Qian, M Gerstein (2002) J Struct Funct Genomics 2: 71-81.
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.
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.
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.
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.
Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes.
ZL Zhang, PM Harrison, M Gerstein (2002) J Mol Biol 323: 811-22.
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.
J Lin, J Qian, D Greenbaum, P Bertone, R Das, N Echols, A Senes, B Stenger, M Gerstein (2002) Nucleic Acids Res 30: 4574-82.
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.
Genomic analysis of membrane protein families: abundance and conserved motifs.
Y Liu, DM Engelman, M Gerstein (2002) Genome Biol 3: research0054.
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.
Z Zhang, P Harrison, M Gerstein (2002) Genome Res 12: 1466-82.
Bridging structural biology and genomics: assessing protein interaction data with known complexes.
AM Edwards, B Kus, R Jansen, D Greenbaum, J Greenblatt, M Gerstein (2002) Trends Genet 18: 529-36.
Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.
WG Krebs, V Alexandrov, CA Wilson, N Echols, H Yu, M Gerstein (2002) Proteins 48: 682-95.
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.
NM Luscombe, J Qian, Z Zhang, T Johnson, M Gerstein (2002) Genome Biol 3: RESEARCH0040.
Functional profiling of the Saccharomyces cerevisiae genome.
G Giaever, AM Chu, L Ni, C Connelly, L Riles, S Véronneau, S Dow, A Lucau-Danila, K Anderson, B André, 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 Güldener, JH Hegemann, S Hempel, Z Herman, DF Jaramillo, DE Kelly, SL Kelly, P Kötter, 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.
SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.
S Balasubramanian, P Harrison, H Hegyi, P Bertone, N Luscombe, N Echols, P McGarvey, Z Zhang, M Gerstein (2002) Pharmacogenomics 3: 393-402.
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
N Echols, P Harrison, S Balasubramanian, NM Luscombe, P Bertone, Z Zhang, M Gerstein (2002) Nucleic Acids Res 30: 2515-23.
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.
Structural genomics: a new era for pharmaceutical research.
Y Liu, NM Luscombe, V Alexandrov, P Bertone, P Harrison, Z Zhang, M Gerstein (2002) Genome Biol 3: REPORTS4004.
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.

-- 2001 (21) --

Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model.
J Qian, NM Luscombe, M Gerstein (2001) J Mol Biol 313: 673-81.
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.
J Qian, M Dolled-Filhart, J Lin, H Yu, M Gerstein (2001) J Mol Biol 314: 1053-66.
Annotation transfer for genomics: measuring functional divergence in multi-domain proteins.
H Hegyi, M Gerstein (2001) Genome Res 11: 1632-40.
What is bioinformatics? A proposed definition and overview of the field.
NM Luscombe, D Greenbaum, M Gerstein (2001) Methods Inf Med 40: 346-58.
Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond.
R Das, J Junker, D Greenbaum, MB Gerstein (2001) Pharmacogenomics J 1: 115-25.
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.
Calculating populations of subcellular compartments using density matrix formalism
V Alexandrov, M Gerstein (2001) International Journal of Quantum Chemistry 85: 693-696.
A standard reference frame for the description of nucleic acid base-pair geometry.
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) J Mol Biol 313: 229-37.
Determining the minimum number of types necessary to represent the sizes of protein atoms.
J Tsai, N Voss, M Gerstein (2001) Bioinformatics 17: 949-56.
Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
D Greenbaum, NM Luscombe, R Jansen, J Qian, M Gerstein (2001) Genome Res 11: 1463-8.
Protein Geometry: Distances, Areas, and Volumes
M Gerstein, F M Richards (2001) International Tables for Crystallography (Volume F, Chapter 22.1.1, pages 531-539; M Rossmann & E Arnold, editors; Dordrecht: Kluwer).
A Bauhaus for Biologists: An Introduction to Protein Architecture by A. M. Lesk
P Harrison, M Gerstein (2001) Trends Biochem Sci 26: 204-205.
Integrative data mining: the new direction in bioinformatics.
P Bertone, M Gerstein (2001) IEEE Eng Med Biol Mag 20: 33-40.
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.
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.
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.
P Bertone, Y Kluger, N Lan, D Zheng, D Christendat, A Yee, AM Edwards, CH Arrowsmith, GT Montelione, M Gerstein (2001) Nucleic Acids Res 29: 2884-98.
Sequences and Topology
M Gerstein, B Honig (2001) Current Opinion in Structural Biology 11: 327-329.
What is Bioinformatics? A Proposed Definition and Overview of the Field
N Luscombe, D Greenbaum, M Gerstein (2001) Intl. Medical Informatics Association (Yearbook, Pages 83-99).
Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome.
PM Harrison, N Echols, MB Gerstein (2001) Nucleic Acids Res 29: 818-30.
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.
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) 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 (18) --

Integrative database analysis in structural genomics.
M Gerstein (2000) Nat Struct Biol 7 Suppl: 960-3.
Genome analyses of spirochetes: a study of the protein structures, functions and metabolic pathways in Treponema pallidum and Borrelia burgdorferi.
R Das, H Hegyi, M Gerstein (2000) J Mol Microbiol Biotechnol 2: 387-92.
Structural proteomics: prospects for high throughput sample preparation.
D Christendat, A Yee, A Dharamsi, Y Kluger, M Gerstein, CH Arrowsmith, AM Edwards (2000) Prog Biophys Mol Biol 73: 339-45.
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.
Genome-wide analysis relating expression level with protein subcellular localization.
A Drawid, R Jansen, M Gerstein (2000) Trends Genet 16: 426-30.
The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?
M Gerstein, R Jansen (2000) Curr Opin Struct Biol 10: 574-84.
The stability of thermophilic proteins: a study based on comprehensive genome comparison.
R Das, M Gerstein (2000) Funct Integr Genomics 1: 76-88.
Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins.
GJ Naylor, M Gerstein (2000) J Mol Evol 51: 223-33.
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.
A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome.
A Drawid, M Gerstein (2000) J Mol Biol 301: 1059-75.
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.
Protein folds in the worm genome.
M Gerstein, J Lin, H Hegyi (2000) Pac Symp Biocomput 30-41.
Annotation of the human genome.
M Gerstein (2000) Science 288: 1590.
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.
J Lin, M Gerstein (2000) Genome Res 10: 808-18.
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.
WG Krebs, M Gerstein (2000) Nucleic Acids Res 28: 1665-75.
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.
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.
CA Wilson, J Kreychman, M Gerstein (2000) J Mol Biol 297: 233-49.
Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins.
R Jansen, M Gerstein (2000) Nucleic Acids Res 28: 1481-8.

-- 1999 (10) --

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

-- 1998 (9) --

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

-- 1997 (6) --

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

-- 1996 (4) --

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.
Packing at the protein-water interface.
M Gerstein, C Chothia (1996) Proc Natl Acad Sci U S A 93: 10167-72.
Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures.
M Gerstein, M Levitt (1996) Proc Int Conf Intell Syst Mol Biol 4: 59-67.

-- 1995 (7) --

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

-- 1994 (7) --

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

-- 1993 (7) --

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

-- 1992 (2) --

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. .
Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum: amino acid sequence and structural interpretation.
I De Baere, L Liu, L Moens, J Van Beeumen, C Gielens, J Richelle, C Trotman, J Finch, M Gerstein, M Perutz (1992) Proc Natl Acad Sci U S A 89: 4638-42.

-- 1991 (1) --

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

-- 1987 (1) --

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)..