Gerstein Lab Publications
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Main Scientific Publications

Total papers: 335

(Last updated Sat Jun 20 15:53:54 EDT 2009 )

-- In Press (0)--

-- 2009 (20) --

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 Lefrancois, 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 Stumpflen, A Ceol, A Chatr-aryamontri, J Armstrong, P Woollard, JJ Salama, S Moore, J Wojcik, GD Bader, M Vidal, ME Cusick, M Gerstein, AC Gavin, G Superti-Furga, J Greenblatt, J Bader, P Uetz, M Tyers, P Legrain, S Fields, N Mulder, M Gilson, M Niepmann, L Burgoon, J De Las Rivas, C Prieto, VM Perreau, C Hogue, HW Mewes, R Apweiler, I Xenarios, D Eisenberg, G Cesareni, H Hermjakob (2007) Nat Biotechnol 25: 894-8.
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 Guigo, 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 Hallgrimsdottir, 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 Hackermuller, J Hertel, M Lindemeyer, K Reiche, A Tanzer, C Ucla, C Wyss, SE Antonarakis, F Denoeud, J Lagarde, J Drenkow, P Kapranov, TR Gingeras, R Guigo, M Snyder, MB Gerstein, A Reymond, IL Hofacker, PF Stadler (2007) Genome Res 17: 852-64.
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 Guigo, 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 Guigo, 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 Karaoz, J Wu, A Halees, S Force Aldred, PJ Collins, D Zheng, ZD Zhang, MB Gerstein, M Snyder, RM Myers, Z Weng (2007) Genome Res 17: 720-31.
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, X Wang 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 Peregrin-Alvarez, M Shales, X Zhang, M Davey, MD Robinson, A Paccanaro, JE Bray, A Sheung, B Beattie, DP Richards, V Canadien, A Lalev, F Mena, P Wong, A Starostine, MM Canete, J Vlasblom, S Wu, C Orsi, SR Collins, S Chandran, R Haw, JJ Rilstone, K Gandi, NJ Thompson, G Musso, P St Onge, S Ghanny, MH Lam, G Butland, AM Altaf-Ul, S Kanaya, A Shilatifard, E O'Shea, JS Weissman, CJ Ingles, TR Hughes, J Parkinson, M Gerstein, SJ Wodak, A Emili, JF Greenblatt (2006) Nature 440: 637-43.
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.