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Mark Gerstein

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Occupations

Chemicals & Drugs

Devices

Oligonucleotide Array Sequence Analysis

Concepts & Ideas

Living Beings

Saccharomyces cerevisiae

Genes & Molecular Sequences

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Publications

TOP 3
Talbert-Slagle Kristina; Marlatt Sara; Barrera Francisco N; Khurana Ekta; Oates Joanne; Gerstein Mark; Engelman Donald M; Dixon Ann M; Dimaio Daniel
Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor.
Auerbach Raymond K; Euskirchen Ghia; Rozowsky Joel; Lamarre-Vincent Nathan; Moqtaderi Zarmik; Lefrançois Philippe; Struhl Kevin; Gerstein Mark; Snyder Michael
Mapping accessible chromatin regions using Sono-Seq.
Bhardwaj Nitin; Gerstein Mark
Relating protein conformational changes to packing efficiency and disorder.

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All Publications

2009: Talbert-Slagle Kristina; Marlatt Sara; Barrera Francisco N; Khurana Ekta; Oates Joanne; Gerstein Mark; Engelman Donald M; Dixon Ann M; Dimaio Daniel
Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor.
Journal of virology 2009;83(19):9773-85.
2009: Auerbach Raymond K; Euskirchen Ghia; Rozowsky Joel; Lamarre-Vincent Nathan; Moqtaderi Zarmik; Lefrançois Philippe; Struhl Kevin; Gerstein Mark; Snyder Michael
Mapping accessible chromatin regions using Sono-Seq.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(35):14926-31.
2009: Bhardwaj Nitin; Gerstein Mark
Relating protein conformational changes to packing efficiency and disorder.
Protein science : a publication of the Protein Society 2009;18(6):1230-40.
2009: Mishima Yuichiro; Abreu-Goodger Cei; Staton Alison A; Stahlhut Carlos; Shou Chong; Cheng Chao; Gerstein Mark; Enright Anton J; Giraldez Antonio J
Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.
Genes & development 2009;23(5):619-32.
2009: Keating Kevin S; Flores Samuel C; Gerstein Mark B; Kuhn Leslie A
StoneHinge: hinge prediction by network analysis of individual protein structures.
Protein science : a publication of the Protein Society 2009;18(2):359-71.
2009: Gianoulis Tara A; Raes Jeroen; Patel Prianka V; Bjornson Robert; Korbel Jan O; Letunic Ivica; Yamada Takuji; Paccanaro Alberto; Jensen Lars J; Snyder Michael; Bork Peer; Gerstein Mark B
Quantifying environmental adaptation of metabolic pathways in metagenomics.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(5):1374-9.
2009: Rozowsky Joel; Euskirchen Ghia; Auerbach Raymond K; Zhang Zhengdong D; Gibson Theodore; Bjornson Robert; Carriero Nicholas; Snyder Michael; Gerstein Mark B
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
Nature biotechnology 2009;27(1):66-75.
2009: Popescu Sorina C; Popescu George V; Bachan Shawn; Zhang Zimei; Gerstein Mark; Snyder Michael; Dinesh-Kumar Savithramma P
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays.
Genes & development 2009;23(1):80-92.
2009: Wang Lu-Yong; Abyzov Alexej; Korbel Jan O; Snyder Michael; Gerstein Mark
MSB: a mean-shift-based approach for the analysis of structural variation in the genome.
Genome research 2009;19(1):106-17.
2009: Yip Kevin Y; Gerstein Mark
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions.
Bioinformatics (Oxford, England) 2009;25(2):243-50.
2009: Sasidharan Rajkumar; Agarwal Ashish; Rozowsky Joel; Gerstein Mark
An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping.
BMC research notes 2009;2():211.
2009: Cheng Chao; Bhardwaj Nitin; Gerstein Mark
The relationship between the evolution of microRNA targets and the length of their UTRs.
BMC genomics 2009;10():431.
2009: Cheng Chao; Fu Xuping; Alves Pedro; Gerstein Mark
mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer.
Genome biology 2009;10(9):R90.
2009: Yip Kevin Y; Kim Philip M; McDermott Drew; Gerstein Mark
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.
BMC bioinformatics 2009;10():241.
2009: Sasidharan Rajkumar; Agarwal Ashish; Rozowsky Joel; Gerstein Mark
An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping.
BMC research notes 2009;2():150.
2009: Snyder Michael; Weissman Sherman; Gerstein Mark
Personal phenotypes to go with personal genomes.
Molecular systems biology 2009;5():273.
2009: Cheng Chao; Li Lei M; Alves Pedro; Gerstein Mark
Systematic identification of transcription factors associated with patient survival in cancers.
BMC genomics 2009;10():225.
2009: Lefrançois Philippe; Euskirchen Ghia M; Auerbach Raymond K; Rozowsky Joel; Gibson Theodore; Yellman Christopher M; Gerstein Mark; Snyder Michael
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.
BMC genomics 2009;10():37.
2009: Balasubramanian Suganthi; Zheng Deyou; Liu Yuen-Jong; Fang Gang; Frankish Adam; Carriero Nicholas; Robilotto Rebecca; Cayting Philip; Gerstein Mark
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.
Genome biology 2009;10(1):R2.
2008: Kim Philip M; Lam Hugo Y K; Urban Alexander E; Korbel Jan O; Affourtit Jason; Grubert Fabian; Chen Xueying; Weissman Sherman; Snyder Michael; Gerstein Mark B
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.
Genome research 2008;18(12):1865-74.
2008: Flores Samuel C; Keating Kevin S; Painter Jay; Morcos Faruck; Nguyen Khang; Merritt Ethan A; Kuhn Leslie A; Gerstein Mark B
HingeMaster: normal mode hinge prediction approach and integration of complementary predictors.
Proteins 2008;73(2):299-319.
2008: Lian Zheng; Karpikov Alexander; Lian Jin; Mahajan Milind C; Hartman Stephen; Gerstein Mark; Snyder Michael; Weissman Sherman M
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.
Genome research 2008;18(8):1224-37.
2008: Mertz Kirsten D; Demichelis Francesca; Sboner Andrea; Hirsch Michelle S; Dal Cin Paola; Struckmann Kirsten; Storz Martina; Scherrer Simone; Schmid Daniel M; Strebel Räto T; Probst-Hensch Nicole M; Gerstein Mark; Moch Holger; Rubin Mark A
Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer.
International journal of cancer. Journal international du cancer 2008;123(3):569-76.
2008: Rzhetsky Andrey; Seringhaus Michael; Gerstein Mark
Seeking a new biology through text mining.
Cell 2008;134(1):9-13.
2008: Korbel Jan O; Kim Philip M; Chen Xueying; Urban Alexander Eckehart; Weissman Sherman; Snyder Michael; Gerstein Mark B
The current excitement about copy-number variation: how it relates to gene duplications and protein families.
Current opinion in structural biology 2008;18(3):366-74.
2008: Nagalakshmi Ugrappa; Wang Zhong; Waern Karl; Shou Chong; Raha Debasish; Gerstein Mark; Snyder Michael
The transcriptional landscape of the yeast genome defined by RNA sequencing.
Science (New York, N.Y.) 2008;320(5881):1344-9.
2008: Zhang Zhengdong D; Weinstock George; Gerstein Mark
Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates.
Journal of molecular evolution 2008;66(5):446-56.
2008: Seringhaus Michael; Gerstein Mark
Manually structured digital abstracts: a scaffold for automatic text mining.
FEBS letters 2008;582(8):1170.
2008: Zhang Zhengdong D; Cayting Philip; Weinstock George; Gerstein Mark
Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.
Molecular biology and evolution 2008;25(1):131-43.
2008: Yip Kevin Y; Patel Prianka; Kim Philip M; Engelman Donald M; McDermott Drew; Gerstein Mark
An integrated system for studying residue coevolution in proteins.
Bioinformatics (Oxford, England) 2008;24(2):290-2.
2008: Seringhaus Michael; Rozowsky Joel; Royce Thomas; Nagalakshmi Ugrappa; Jee Justin; Snyder Michael; Gerstein Mark
Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.
BMC genomics 2008;9():635.
2008: Zhang Zhengdong D; Rozowsky Joel; Snyder Michael; Chang Joseph; Gerstein Mark
Modeling ChIP sequencing in silico with applications.
PLoS computational biology 2008;4(8):e1000158.
2008: Sasidharan Rajkumar; Smith Andrew; Gerstein Mark
Transmembrane protein oxygen content and compartmentalization of cells.
PloS one 2008;3(7):e2726.
2008: Kim Philip M; Sboner Andrea; Xia Yu; Gerstein Mark
The role of disorder in interaction networks: a structural analysis.
Molecular systems biology 2008;4():179.
2007: Kim Philip M; Korbel Jan O; Gerstein Mark B
Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(51):20274-9.
2007: Setlur Sunita R; Royce Thomas E; Sboner Andrea; Mosquera Juan-Miguel; Demichelis Francesca; Hofer Matthias D; Mertz Kirsten D; Gerstein Mark; Rubin Mark A
Integrative microarray analysis of pathways dysregulated in metastatic prostate cancer.
Cancer research 2007;67(21):10296-303.
2007: Smith Andrew; Cheung Kei; Krauthammer Michael; Schultz Martin; Gerstein Mark
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
Bioinformatics (Oxford, England) 2007;23(22):3073-9.
2007: Korbel Jan O; Urban Alexander Eckehart; Affourtit Jason P; Godwin Brian; Grubert Fabian; Simons Jan Fredrik; Kim Philip M; Palejev Dean; Carriero Nicholas J; Du Lei; Taillon Bruce E; Chen Zhoutao; Tanzer Andrea; Saunders A C Eugenia; Chi Jianxiang; Yang Fengtang; Carter Nigel P; Hurles Matthew E; Weissman Sherman M; Harkins Timothy T; Gerstein Mark B; Egholm Michael; Snyder Michael
Paired-end mapping reveals extensive structural variation in the human genome.
Science (New York, N.Y.) 2007;318(5849):420-6.
2007: Borneman Anthony R; Zhang Zhengdong D; Rozowsky Joel; Seringhaus Michael R; Gerstein Mark; Snyder Michael
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
Functional & integrative genomics 2007;7(4):335-45.
2007: Borneman Anthony R; Gianoulis Tara A; Zhang Zhengdong D; Yu Haiyuan; Rozowsky Joel; Seringhaus Michael R; Wang Lu Yong; Gerstein Mark; Snyder Michael
Divergence of transcription factor binding sites across related yeast species.
Science (New York, N.Y.) 2007;317(5839):815-9.
2007: Yu Haiyuan; Jansen Ronald; Stolovitzky Gustavo; Gerstein Mark
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.
Bioinformatics (Oxford, England) 2007;23(16):2163-73.
2007: Wu Linfeng; Hwang Sun-Il; Rezaul Karim; Lu Long J; Mayya Viveka; Gerstein Mark; Eng Jimmy K; Lundgren Deborah H; Han David K
Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling.
Molecular & cellular proteomics : MCP 2007;6(8):1343-53.
2007: Lu Long J; Sboner Andrea; Huang Yuanpeng J; Lu Hao Xin; Gianoulis Tara A; Yip Kevin Y; Kim Philip M; Montelione Gaetano T; Gerstein Mark B
Comparing classical pathways and modern networks: towards the development of an edge ontology.
Trends in biochemical sciences 2007;32(7):320-31.
2007: Euskirchen Ghia M; Rozowsky Joel S; Wei Chia-Lin; Lee Wah Heng; Zhang Zhengdong D; Hartman Stephen; Emanuelsson Olof; Stolc Viktor; Weissman Sherman; Gerstein Mark B; Ruan Yijun; Snyder Michael
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.
Genome research 2007;17(6):898-909.
2007: Washietl Stefan; Pedersen Jakob S; Korbel Jan O; Stocsits Claudia; Gruber Andreas R; Hackermüller Jörg; Hertel Jana; Lindemeyer Manja; Reiche Kristin; Tanzer Andrea; Ucla Catherine; Wyss Carine; Antonarakis Stylianos E; Denoeud France; Lagarde Julien; Drenkow Jorg; Kapranov Philipp; Gingeras Thomas R; Guigó Roderic; Snyder Michael; Gerstein Mark B; Reymond Alexandre; Hofacker Ivo L; Stadler Peter F
Structured RNAs in the ENCODE selected regions of the human genome.
Genome research 2007;17(6):852-64.
2007: Zheng Deyou; Frankish Adam; Baertsch Robert; Kapranov Philipp; Reymond Alexandre; Choo Siew Woh; Lu Yontao; Denoeud France; Antonarakis Stylianos E; Snyder Michael; Ruan Yijun; Wei Chia-Lin; Gingeras Thomas R; Guigó Roderic; Harrow Jennifer; Gerstein Mark B
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
Genome research 2007;17(6):839-51.
2007: Zhang Zhengdong D; Paccanaro Alberto; Fu Yutao; Weissman Sherman; Weng Zhiping; Chang Joseph; Snyder Michael; Gerstein Mark B
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.
Genome research 2007;17(6):787-97.
2007: Rozowsky Joel S; Newburger Daniel; Sayward Fred; Wu Jiaqian; Jordan Greg; Korbel Jan O; Nagalakshmi Ugrappa; Yang Jin; Zheng Deyou; Guigó Roderic; Gingeras Thomas R; Weissman Sherman; Miller Perry; Snyder Michael; Gerstein Mark B
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
Genome research 2007;17(6):732-45.
2007: Gerstein Mark B; Bruce Can; Rozowsky Joel S; Zheng Deyou; Du Jiang; Korbel Jan O; Emanuelsson Olof; Zhang Zhengdong D; Weissman Sherman; Snyder Michael
What is a gene, post-ENCODE? History and updated definition.
Genome research 2007;17(6):669-81.
2007: Korbel Jan O; Urban Alexander Eckehart; Grubert Fabian; Du Jiang; Royce Thomas E; Starr Peter; Zhong Guoneng; Emanuel Beverly S; Weissman Sherman M; Snyder Michael; Gerstein Mark B
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(24):10110-5.
2007: Emanuelsson Olof; Nagalakshmi Ugrappa; Zheng Deyou; Rozowsky Joel S; Urban Alexander E; Du Jiang; Lian Zheng; Stolc Viktor; Weissman Sherman; Snyder Michael; Gerstein Mark B
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
Genome research 2007;17(6):886-97.
2007: Gerstein Mark; Seringhaus Michael; Fields Stanley
Structured digital abstract makes text mining easy.
Nature 2007;447(7141):142.
2007: Zhu Xiaowei; Gerstein Mark; Snyder Michael
Getting connected: analysis and principles of biological networks.
Genes & development 2007;21(9):1010-24.
2007: Zheng Deyou; Gerstein Mark B
The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
Trends in genetics : TIG 2007;23(5):219-24.
2007: Yu Haiyuan; Kim Philip M; Sprecher Emmett; Trifonov Valery; Gerstein Mark
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.
PLoS computational biology 2007;3(4):e59.
2007: Royce Thomas E; Rozowsky Joel S; Gerstein Mark B
Assessing the need for sequence-based normalization in tiling microarray experiments.
Bioinformatics (Oxford, England) 2007;23(8):988-97.
2007: Popescu Sorina C; Popescu George V; Bachan Shawn; Zhang Zimei; Seay Montrell; Gerstein Mark; Snyder Michael; Dinesh-Kumar S P
Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(11):4730-5.
2007: Smith Michael G; Gianoulis Tara A; Pukatzki Stefan; Mekalanos John J; Ornston L Nicholas; Gerstein Mark; Snyder Michael
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.
Genes & development 2007;21(5):601-14.
2007: Gerstein Mark; Greenbaum Dov; Cheung Kei; Miller Perry L
An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.
Journal of biomedical informatics 2007;40(1):73-9.
2007: Seringhaus Michael; Gerstein Mark
Chemistry Nobel rich in structure.
Science (New York, N.Y.) 2007;315(5808):40-1.
2007: Karro John E; Yan Yangpan; Zheng Deyou; Zhang Zhaolei; Carriero Nicholas; Cayting Philip; Harrrison Paul; Gerstein Mark
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
Nucleic acids research 2007;35(Database issue):D55-60.
2007: Yu Eric Z; Burba Anne E Counterman; Gerstein Mark
PARE: a tool for comparing protein abundance and mRNA expression data.
BMC bioinformatics 2007;8():309.
2007: Royce Thomas E; Rozowsky Joel S; Gerstein Mark B
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.
Nucleic acids research 2007;35(15):e99.
2007: Flores Samuel C; Gerstein Mark B
FlexOracle: predicting flexible hinges by identification of stable domains.
BMC bioinformatics 2007;8():215.
2007: Royce Thomas E; Carriero Nicholas J; Gerstein Mark B
An efficient pseudomedian filter for tiling microrrays.
BMC bioinformatics 2007;8():186.
2007: Flores Samuel C; Lu Long J; Yang Julie; Carriero Nicholas; Gerstein Mark B
Hinge Atlas: relating protein sequence to sites of structural flexibility.
BMC bioinformatics 2007;8():167.
2007: Zhang Zhengdong D; Rozowsky Joel; Lam Hugo Y K; Du Jiang; Snyder Michael; Gerstein Mark
Tilescope: online analysis pipeline for high-density tiling microarray data.
Genome biology 2007;8(5):R81.
2007: Li Lei; Wang Xiangfeng; Sasidharan Rajkumar; Stolc Viktor; Deng Wei; He Hang; Korbel Jan; Chen Xuewei; Tongprasit Waraporn; Ronald Pamela; Chen Runsheng; Gerstein Mark; Wang Deng Xing
Global identification and characterization of transcriptionally active regions in the rice genome.
PloS one 2007;2(3):e294.
2007: Zhang Zhaolei; Pang Andy Wing Chun; Gerstein Mark
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.
BMC evolutionary biology 2007;7 Suppl 1():S14.
2007: Seringhaus Michael R; Gerstein Mark B
Publishing perishing? Towards tomorrow's information architecture.
BMC bioinformatics 2007;8():17.
2007: Yu Haiyuan; Nguyen Katherine; Royce Tom; Qian Jiang; Nelson Kenneth; Snyder Michael; Gerstein Mark
Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.
Nucleic acids research 2007;35(2):e8.
2006: Kim Philip M; Lu Long J; Xia Yu; Gerstein Mark B
Relating three-dimensional structures to protein networks provides evolutionary insights.
Science (New York, N.Y.) 2006;314(5807):1938-41.
2006: Du Jiang; Rozowsky Joel S; Korbel Jan O; Zhang Zhengdong D; Royce Thomas E; Schultz Martin H; Snyder Michael; Gerstein Mark
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
Bioinformatics (Oxford, England) 2006;22(24):3016-24.
2006: Yip Kevin Y; Yu Haiyuan; Kim Philip M; Schultz Martin; Gerstein Mark
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
Bioinformatics (Oxford, England) 2006;22(23):2968-70.
2006: Liu Yang; Li Jianrong; Sam Lee; Goh Chern-Sing; Gerstein Mark; Lussier Yves A
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.
PLoS computational biology 2006;2(11):e159.
2006: Burba Anne E Counterman; Lehnert Ursula; Yu Eric Z; Gerstein Mark
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
Bioinformatics (Oxford, England) 2006;22(22):2735-8.
2006: Yu Haiyuan; Gerstein Mark
Genomic analysis of the hierarchical structure of regulatory networks.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(40):14724-31.
2006: Srikantha Thyagarajan; Borneman Anthony R; Daniels Karla J; Pujol Claude; Wu Wei; Seringhaus Michael R; Gerstein Mark; Yi Song; Snyder Michael; Soll David R
TOS9 regulates white-opaque switching in Candida albicans.
Eukaryotic cell 2006;5(10):1674-87.
2006: Seringhaus Michael; Paccanaro Alberto; Borneman Anthony; Snyder Michael; Gerstein Mark
Predicting essential genes in fungal genomes.
Genome research 2006;16(9):1126-35.
2006: Voss N R; Gerstein M; Steitz T A; Moore P B
The geometry of the ribosomal polypeptide exit tunnel.
Journal of molecular biology 2006;360(4):893-906.
2006: Zhang Zhaolei; Carriero Nicholas; Zheng Deyou; Karro John; Harrison Paul M; Gerstein Mark
PseudoPipe: an automated pseudogene identification pipeline.
Bioinformatics (Oxford, England) 2006;22(12):1437-9.
2006: Yu Haiyuan; Paccanaro Alberto; Trifonov Valery; Gerstein Mark
Predicting interactions in protein networks by completing defective cliques.
Bioinformatics (Oxford, England) 2006;22(7):823-9.
2006: Urban Alexander Eckehart; Korbel Jan O; Selzer Rebecca; Richmond Todd; Hacker April; Popescu George V; Cubells Joseph F; Green Roland; Emanuel Beverly S; Gerstein Mark B; Weissman Sherman M; Snyder Michael
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(12):4534-9.
2006: Xia Yu; Lu Long J; Gerstein Mark
Integrated prediction of the helical membrane protein interactome in yeast.
Journal of molecular biology 2006;357(1):339-49.
2006: Borneman Anthony R; Leigh-Bell Justine A; Yu Haiyuan; Bertone Paul; Gerstein Mark; Snyder Michael
Target hub proteins serve as master regulators of development in yeast.
Genes & development 2006;20(4):435-48.
2006: Bertone Paul; Trifonov Valery; Rozowsky Joel S; Schubert Falk; Emanuelsson Olof; Karro John; Kao Ming-Yang; Snyder Michael; Gerstein Mark
Design optimization methods for genomic DNA tiling arrays.
Genome research 2006;16(2):271-81.
2006: Flores Samuel; Echols Nathaniel; Milburn Duncan; Hespenheide Brandon; Keating Kevin; Lu Jason; Wells Stephen; Yu Eric Z; Thorpe Michael; Gerstein Mark
The Database of Macromolecular Motions: new features added at the decade mark.
Nucleic acids research 2006;34(Database issue):D296-301.
2006: Rozowsky J; Wu J; Lian Z; Nagalakshmi U; Korbel J O; Kapranov P; Zheng D; Dyke S; Newburger P; Miller P; Gingeras T R; Weissman S; Gerstein M; Snyder M
Novel transcribed regions in the human genome.
Cold Spring Harbor symposia on quantitative biology 2006;71():111-6.
2006: Zhu Xiaowei; Gerstein Mark; Snyder Michael
ProCAT: a data analysis approach for protein microarrays.
Genome biology 2006;7(11):R110.
2006: Goh Chern-Sing; Gianoulis Tara A; Liu Yang; Li Jianrong; Paccanaro Alberto; Lussier Yves A; Gerstein Mark
Integration of curated databases to identify genotype-phenotype associations.
BMC genomics 2006;7():257.
2006: Royce Thomas E; Rozowsky Joel S; Luscombe Nicholas M; Emanuelsson Olof; Yu Haiyuan; Zhu Xiaowei; Snyder Michael; Gerstein Mark B
Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
Methods in enzymology 2006;411():282-311.
2006: Pinard Robert; de Winter Alex; Sarkis Gary J; Gerstein Mark B; Tartaro Karrie R; Plant Ramona N; Egholm Michael; Rothberg Jonathan M; Leamon John H
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.
BMC genomics 2006;7():216.
2006: Zheng Deyou; Gerstein Mark B
A computational approach for identifying pseudogenes in the ENCODE regions.
Genome biology 2006;7 Suppl 1():S13.1-10.
2006: Yu Haiyuan; Xia Yu; Trifonov Valery; Gerstein Mark
Design principles of molecular networks revealed by global comparisons and composite motifs.
Genome biology 2006;7(7):R55.
2006: Seringhaus Michael; Kumar Anuj; Hartigan John; Snyder Michael; Gerstein Mark
Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.
Nucleic acids research 2006;34(8):e57.
2005: Ptacek Jason; Devgan Geeta; Michaud Gregory; Zhu Heng; Zhu Xiaowei; Fasolo Joseph; Guo Hong; Jona Ghil; Breitkreutz Ashton; Sopko Richelle; McCartney Rhonda R; Schmidt Martin C; Rachidi Najma; Lee Soo-Jung; Mah Angie S; Meng Lihao; Stark Michael J R; Stern David F; De Virgilio Claudio; Tyers Mike; Andrews Brenda; Gerstein Mark; Schweitzer Barry; Predki Paul F; Snyder Michael
Global analysis of protein phosphorylation in yeast.
Nature 2005;438(7068):679-84.
2005: Hartman Stephen E; Bertone Paul; Nath Anjali K; Royce Thomas E; Gerstein Mark; Weissman Sherman; Snyder Michael
Global changes in STAT target selection and transcription regulation upon interferon treatments.
Genes & development 2005;19(24):2953-68.
2005: Coric Tatjana; Zheng Deyou; Gerstein Mark; Canessa Cecilia M
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.
The Journal of physiology 2005;568(Pt 3):725-35.
2005: Stolc Viktor; Li Lei; Wang Xiangfeng; Li Xueyong; Su Ning; Tongprasit Waraporn; Han Bin; Xue Yongbiao; Li Jiayang; Snyder Michael; Gerstein Mark; Wang Jun; Deng Xing Wang
A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.
Plant molecular biology 2005;59(1):137-49.
2005: Royce Thomas E; Rozowsky Joel S; Bertone Paul; Samanta Manoj; Stolc Viktor; Weissman Sherman; Snyder Michael; Gerstein Mark
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
Trends in genetics : TIG 2005;21(8):466-75.
2005: Lu Long J; Xia Yu; Paccanaro Alberto; Yu Haiyuan; Gerstein Mark
Assessing the limits of genomic data integration for predicting protein networks.
Genome research 2005;15(7):945-53.
2005: Cheung Kei-Hoi; Yip Kevin Y; Smith Andrew; Deknikker Remko; Masiar Andy; Gerstein Mark
YeastHub: a semantic web use case for integrating data in the life sciences domain.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i85-96.
2005: Zheng Deyou; Zhang Zhaolei; Harrison Paul M; Karro John; Carriero Nick; Gerstein Mark
Integrated pseudogene annotation for human chromosome 22: evidence for transcription.
Journal of molecular biology 2005;349(1):27-45.
2005: Gilad Yoav; Rifkin Scott A; Bertone Paul; Gerstein Mark; White Kevin P
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.
Genome research 2005;15(5):674-80.
2005: Grosshans Helge; Johnson Ted; Reinert Kristy L; Gerstein Mark; Slack Frank J
The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans.
Developmental cell 2005;8(3):321-30.
2005: Alexandrov Vadim; Lehnert Ursula; Echols Nathaniel; Milburn Duncan; Engelman Donald; Gerstein Mark
Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.
Protein science : a publication of the Protein Society 2005;14(3):633-43.
2005: Voss N R; Gerstein M
Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly.
Journal of molecular biology 2005;346(2):477-92.
2005: Carriero Nicholas; Osier Michael V; Cheung Kei-Hoi; Miller Perry L; Gerstein Mark; Zhao Hongyu; Wu Baolin; Rifkin Scott; Chang Joseph; Zhang Heping; White Kevin; Williams Kenneth; Schultz Martin
A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.
Journal of the American Medical Informatics Association : JAMIA 2005;12(1):90-8.
2005: Smith Andrew; Greenbaum Dov; Douglas Shawn M; Long Morrow; Gerstein Mark
Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.
Genome biology 2005;6(9):119.
2005: Douglas Shawn M; Montelione Gaetano T; Gerstein Mark
PubNet: a flexible system for visualizing literature derived networks.
Genome biology 2005;6(9):R80.
2005: Bertone Paul; Gerstein Mark; Snyder Michael
Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery.
Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2005;13(3):259-74.
2005: Harrison Paul M; Zheng Deyou; Zhang Zhaolei; Carriero Nicholas; Gerstein Mark
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.
Nucleic acids research 2005;33(8):2374-83.
2005: Acton Thomas B; Gunsalus Kristin C; Xiao Rong; Ma Li Chung; Aramini James; Baran Michael C; Chiang Yi-Wen; Climent Teresa; Cooper Bonnie; Denissova Natalia G; Douglas Shawn M; Everett John K; Ho Chi Kent; Macapagal Daphne; Rajan Paranji K; Shastry Ritu; Shih Liang-Yu; Swapna G V T; Wilson Michael; Wu Margaret; Gerstein Mark; Inouye Masayori; Hunt John F; Montelione Gaetano T
Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium.
Methods in enzymology 2005;394():210-43.
2005: Balasubramanian Suganthi; Xia Yu; Freinkman Elizaveta; Gerstein Mark
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.
Nucleic acids research 2005;33(5):1710-21.
2004: White Eric J; Emanuelsson Olof; Scalzo David; Royce Thomas; Kosak Steven; Oakeley Edward J; Weissman Sherman; Gerstein Mark; Groudine Mark; Snyder Michael; Schübeler Dirk
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(51):17771-6.
2004: Bertone Paul; Stolc Viktor; Royce Thomas E; Rozowsky Joel S; Urban Alexander E; Zhu Xiaowei; Rinn John L; Tongprasit Waraporn; Samanta Manoj; Weissman Sherman; Gerstein Mark; Snyder Michael
Global identification of human transcribed sequences with genome tiling arrays.
Science (New York, N.Y.) 2004;306(5705):2242-6.
2004: Hall David A; Zhu Heng; Zhu Xiaowei; Royce Thomas; Gerstein Mark; Snyder Michael
Regulation of gene expression by a metabolic enzyme.
Science (New York, N.Y.) 2004;306(5695):482-4.
2004: Kumar Anuj; Seringhaus Michael; Biery Matthew C; Sarnovsky Robert J; Umansky Lara; Piccirillo Stacy; Heidtman Matthew; Cheung Kei-Hoi; Dobry Craig J; Gerstein Mark B; Craig Nancy L; Snyder Michael
Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon.
Genome research 2004;14(10A):1975-86.
2004: Luscombe Nicholas M; Babu M Madan; Yu Haiyuan; Snyder Michael; Teichmann Sarah A; Gerstein Mark
Genomic analysis of regulatory network dynamics reveals large topological changes.
Nature 2004;431(7006):308-12.
2004: Zhang ZhaoLei; Gerstein Mark
Large-scale analysis of pseudogenes in the human genome.
Current opinion in genetics & development 2004;14(4):328-35.
2004: Wunderlich Zeba; Acton Thomas B; Liu Jinfeng; Kornhaber Gregory; Everett John; Carter Phil; Lan Ning; Echols Nathaniel; Gerstein Mark; Rost Burkhard; Montelione Gaetano T
The protein target list of the Northeast Structural Genomics Consortium.
Proteins 2004;56(2):181-7.
2004: Rinn John L; Rozowsky Joel S; Laurenzi Ian J; Petersen Petur H; Zou Kaiyong; Zhong Weimin; Gerstein Mark; Snyder Michael
Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.
Developmental cell 2004;6(6):791-800.
2004: Greenbaum Dov; Douglas Shawn M; Smith Andrew; Lim Joanna; Fischer Michael; Schultz Martin; Gerstein Mark
Computer security in academia-a potential roadblock to distributed annotation of the human genome.
Nature biotechnology 2004;22(6):771-2.
2004: Yu Haiyuan; Luscombe Nicholas M; Lu Hao Xin; Zhu Xiaowei; Xia Yu; Han Jing-Dong J; Bertin Nicolas; Chung Sambath; Vidal Marc; Gerstein Mark
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
Genome research 2004;14(6):1107-18.
2004: Yu Haiyuan; Greenbaum Dov; Xin Lu Hao; Zhu Xiaowei; Gerstein Mark
Genomic analysis of essentiality within protein networks.
Trends in genetics : TIG 2004;20(6):227-31.
2004: Lehnert Ursula; Xia Yu; Royce Thomas E; Goh Chem-Sing; Liu Yang; Senes Alessandro; Yu Haiyuan; Zhang Zhao Lei; Engelman Donald M; Gerstein Mark
Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.
Quarterly reviews of biophysics 2004;37(2):121-46.
2004: Freeman-Cook Lisa L; Dixon Ann M; Frank Jennifer B; Xia Yu; Ely Lara; Gerstein Mark; Engelman Donald M; DiMaio Daniel
Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor.
Journal of molecular biology 2004;338(5):907-20.
2004: Euskirchen Ghia; Royce Thomas E; Bertone Paul; Martone Rebecca; Rinn John L; Nelson F Kenneth; Sayward Fred; Luscombe Nicholas M; Miller Perry; Gerstein Mark; Weissman Sherman; Snyder Michael
CREB binds to multiple loci on human chromosome 22.
Molecular and cellular biology 2004;24(9):3804-14.
2004: Das Rajdeep; Gerstein Mark
A method using active-site sequence conservation to find functional shifts in protein families: application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens.
Proteins 2004;55(2):455-63.
2004: Liu Yang; Gerstein Mark; Engelman Donald M
Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(10):3495-7.
2004: Goh Chern-Sing; Milburn Duncan; Gerstein Mark
Conformational changes associated with protein-protein interactions.
Current opinion in structural biology 2004;14(1):104-9.
2004: Gerstein Mark; Echols Nathaniel
Exploring the range of protein flexibility, from a structural proteomics perspective.
Current opinion in chemical biology 2004;8(1):14-9.
2004: Zhang Zhaolei; Carriero Nick; Gerstein Mark
Comparative analysis of processed pseudogenes in the mouse and human genomes.
Trends in genetics : TIG 2004;20(2):62-7.
2004: Goh Chern-Sing; Lan Ning; Douglas Shawn M; Wu Baolin; Echols Nathaniel; Smith Andrew; Milburn Duncan; Montelione Gaetano T; Zhao Hongyu; Gerstein Mark
Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.
Journal of molecular biology 2004;336(1):115-30.
2004: Alexandrov Vadim; Gerstein Mark
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.
BMC bioinformatics 2004;5():2.
2004: Berman Piotr; Bertone Paul; Dasgupta Bhaskar; Gerstein Mark; Kao Ming-Yang; Snyder Michael
Fast optimal genome tiling with applications to microarray design and homology search.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(4):766-85.
2004: Liu Yang; Harrison Paul M; Kunin Victor; Gerstein Mark
Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.
Genome biology 2004;5(9):R64.
2004: Xia Yu; Yu Haiyuan; Jansen Ronald; Seringhaus Michael; Baxter Sarah; Greenbaum Dov; Zhao Hongyu; Gerstein Mark
Analyzing cellular biochemistry in terms of molecular networks.
Annual review of biochemistry 2004;73():1051-87.
2004: Yu Haiyuan; Zhu Xiaowei; Greenbaum Dov; Karro John; Gerstein Mark
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics.
Nucleic acids research 2004;32(1):328-37.
2003: Kluger Yuval; Yu Haiyuan; Qian Jiang; Gerstein Mark
Relationship between gene co-expression and probe localization on microarray slides.
BMC genomics 2003;4(1):49.
2003: Zhang Zhaolei; Harrison Paul M; Liu Yin; Gerstein Mark
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.
Genome research 2003;13(12):2541-58.
2003: Harrison Paul M; Carriero Nicholas; Liu Yang; Gerstein Mark
A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs.
Journal of molecular biology 2003;333(5):885-92.
2003: Jansen Ronald; Yu Haiyuan; Greenbaum Dov; Kluger Yuval; Krogan Nevan J; Chung Sambath; Emili Andrew; Snyder Michael; Greenblatt Jack F; Gerstein Mark
A Bayesian networks approach for predicting protein-protein interactions from genomic data.
Science (New York, N.Y.) 2003;302(5644):449-53.
2003: Martone Rebecca; Euskirchen Ghia; Bertone Paul; Hartman Stephen; Royce Thomas E; Luscombe Nicholas M; Rinn John L; Nelson F Kenneth; Miller Perry; Gerstein Mark; Weissman Sherman; Snyder Michael
Distribution of NF-kappaB-binding sites across human chromosome 22.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(21):12247-52.
2003: Zhang Zhaolei; Gerstein Mark
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes.
Nucleic acids research 2003;31(18):5338-48.
2003: Greenbaum Dov; Gerstein Mark
A universal legal framework as a prerequisite for database interoperability.
Nature biotechnology 2003;21(9):979-82.
2003: Yu Haiyuan; Luscombe Nicholas M; Qian Jiang; Gerstein Mark
Genomic analysis of gene expression relationships in transcriptional regulatory networks.
Trends in genetics : TIG 2003;19(8):422-7.
2003: Zhang Zhaolei; Gerstein Mark
The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse.
Gene 2003;312():61-72.
2003: Qian Jiang; Kluger Yuval; Yu Haiyuan; Gerstein Mark
Identification and correction of spurious spatial correlations in microarray data.
BioTechniques 2003;35(1):42-4, 46, 48.
2003: Luscombe Nicholas M; Royce Thomas E; Bertone Paul; Echols Nathaniel; Horak Christine E; Chang Joseph T; Snyder Michael; Gerstein Mark
ExpressYourself: A modular platform for processing and visualizing microarray data.
Nucleic acids research 2003;31(13):3477-82.
2003: Goh Chern-Sing; Lan Ning; Echols Nathaniel; Douglas Shawn M; Milburn Duncan; Bertone Paul; Xiao Rong; Ma Li-Chung; Zheng Deyou; Wunderlich Zeba; Acton Tom; Montelione Gaetano T; Gerstein Mark
SPINE 2: a system for collaborative structural proteomics within a federated database framework.
Nucleic acids research 2003;31(11):2833-8.
2003: Zhang Zhaolei; Gerstein Mark
Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.
Genomics 2003;81(5):468-80.
2003: Snyder Michael; Gerstein Mark
Genomics. Defining genes in the genomics era.
Science (New York, N.Y.) 2003;300(5617):258-60.
2003: Jansen Ronald; Bussemaker Harmen J; Gerstein Mark
Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.
Nucleic acids research 2003;31(8):2242-51.
2003: Kluger Yuval; Basri Ronen; Chang Joseph T; Gerstein Mark
Spectral biclustering of microarray data: coclustering genes and conditions.
Genome research 2003;13(4):703-16.
2003: Rinn John L; Euskirchen Ghia; Bertone Paul; Martone Rebecca; Luscombe Nicholas M; Hartman Stephen; Harrison Paul M; Nelson F Kenneth; Miller Perry; Gerstein Mark; Weissman Sherman; Snyder Michael
The transcriptional activity of human Chromosome 22.
Genes & development 2003;17(4):529-40.
2003: Harrison Paul M; Milburn Duncan; Zhang Zhaolei; Bertone Paul; Gerstein Mark
Identification of pseudogenes in the Drosophila melanogaster genome.
Nucleic acids research 2003;31(3):1033-7.
2003: Echols Nathaniel; Milburn Duncan; Gerstein Mark
MolMovDB: analysis and visualization of conformational change and structural flexibility.
Nucleic acids research 2003;31(1):478-82.
2003: Lian Z; Euskirchen G; Rinn J; Martone R; Bertone P; Hartman S; Royce T; Nelson K; Sayward F; Luscombe N; Yang J; Li J L; Miller P; Urban A E; Gerstein M; Weissman S; Snyder M
Identification of novel functional elements in the human genome.
Cold Spring Harbor symposia on quantitative biology 2003;68():317-22.
2003: Krebs W G; Tsai J; Alexandrov Vadim; Junker Jochen; Jansen Ronald; Gerstein Mark
Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences.
Methods in enzymology 2003;374():544-84.
2003: Greenbaum Dov; Colangelo Christopher; Williams Kenneth; Gerstein Mark
Comparing protein abundance and mRNA expression levels on a genomic scale.
Genome biology 2003;4(9):117.
2003: Zhang Zhaolei; Gerstein Mark
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.
Journal of biology 2003;2(2):11.
2003: Harrison Paul M; Gerstein Mark
A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes.
Genome biology 2003;4(6):R40.
2002: Horak Christine E; Luscombe Nicholas M; Qian Jiang; Bertone Paul; Piccirrillo Stacy; Gerstein Mark; Snyder Michael
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.
Genes & development 2002;16(23):3017-33.
2002: Schneider Dirk; Liu Yang; Gerstein Mark; Engelman Donald M
Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis.
FEBS letters 2002;532(1-2):231-6.
2002: Zhang Zhao Lei; Harrison Paul M; Gerstein Mark
Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes.
Journal of molecular biology 2002;323(5):811-22.
2002: Lian Zheng; Kluger Yuval; Greenbaum Dov S; Tuck David; Gerstein Mark; Berliner Nancy; Weissman Sherman M; Newburger Peter E
Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line.
Blood 2002;100(9):3209-20.
2002: Lin J; Qian J; Greenbaum D; Bertone P; Das R; Echols N; Senes A; Stenger B; Gerstein M
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.
Nucleic acids research 2002;30(20):4574-82.
2002: Zhang Zhaolei; Harrison Paul; Gerstein Mark
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.
Genome research 2002;12(10):1466-82.
2002: Edwards Aled M; Kus Bart; Jansen Ronald; Greenbaum Dov; Greenblatt Jack; Gerstein Mark
Bridging structural biology and genomics: assessing protein interaction data with known complexes.
Trends in genetics : TIG 2002;18(10):529-36.
2002: Liu Yang; Engelman Donald M; Gerstein Mark
Genomic analysis of membrane protein families: abundance and conserved motifs.
Genome biology 2002;3(10):research0054.
2002: Krebs W G; Alexandrov Vadim; Wilson Cyrus A; Echols Nathaniel; Yu Haiyuan; Gerstein Mark
Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.
Proteins 2002;48(4):682-95.
2002: Luscombe Nicholas M; Qian Jiang; Zhang Zhaolei; Johnson Ted; Gerstein Mark
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.
Genome biology 2002;3(8):RESEARCH0040.
2002: Echols Nathaniel; Harrison Paul; Balasubramanian Suganthi; Luscombe Nicholas M; Bertone Paul; Zhang Zhaolei; Gerstein Mark
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
Nucleic acids research 2002;30(11):2515-23.
2002: Harrison Paul M; Gerstein Mark
Studying genomes through the aeons: protein families, pseudogenes and proteome evolution.
Journal of molecular biology 2002;318(5):1155-74.
2002: Balasubramanian Suganthi; Harrison Paul; Hegyi Hedi; Bertone Paul; Luscombe Nicholas; Echols Nathaniel; McGarvey Patrick; Zhang ZhaoLei; Gerstein Mark
SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.
Pharmacogenomics 2002;3(3):393-402.
2002: Hegyi Hedi; Lin Jimmy; Greenbaum Dov; Gerstein Mark
Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds.
Proteins 2002;47(2):126-41.
2002: Greenbaum Dov; Jansen Ronald; Gerstein Mark
Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts.
Bioinformatics (Oxford, England) 2002;18(4):585-96.
2002: Kumar Anuj; Agarwal Seema; Heyman John A; Matson Sandra; Heidtman Matthew; Piccirillo Stacy; Umansky Lara; Drawid Amar; Jansen Ronald; Liu Yang; Cheung Kei-Hoi; Miller Perry; Gerstein Mark; Roeder G Shirleen; Snyder Michael
Subcellular localization of the yeast proteome.
Genes & development 2002;16(6):707-19.
2002: Horak Christine E; Mahajan Milind C; Luscombe Nicholas M; Gerstein Mark; Weissman Sherman M; Snyder Michael
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(5):2924-9.
2002: Harrison Paul M; Kumar Anuj; Lang Ning; Snyder Michael; Gerstein Mark
A question of size: the eukaryotic proteome and the problems in defining it.
Nucleic acids research 2002;30(5):1083-90.
2002: Harrison Paul; Kumar Anuj; Lan Ning; Echols Nathaniel; Snyder Michael; Gerstein Mark
A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.
Journal of molecular biology 2002;316(3):409-19.
2002: Harrison Paul M; Hegyi Hedi; Balasubramanian Suganthi; Luscombe Nicholas M; Bertone Paul; Echols Nathaniel; Johnson Ted; Gerstein Mark
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.
Genome research 2002;12(2):272-80.
2002: Gerstein Mark; Lan Ning; Jansen Ronald
Proteomics. Integrating interactomes.
Science (New York, N.Y.) 2002;295(5553):284-7.
2002: Jansen Ronald; Greenbaum Dov; Gerstein Mark
Relating whole-genome expression data with protein-protein interactions.
Genome research 2002;12(1):37-46.
2002: Kumar Anuj; Harrison Paul M; Cheung Kei-Hoi; Lan Ning; Echols Nathaniel; Bertone Paul; Miller Perry; Gerstein Mark B; Snyder Michael
An integrated approach for finding overlooked genes in yeast.
Nature biotechnology 2002;20(1):58-63.
2002: Jansen Ronald; Lan Ning; Qian Jiang; Gerstein Mark
Integration of genomic datasets to predict protein complexes in yeast.
Journal of structural and functional genomics 2002;2(2):71-81.
2002: Cheung Kei-Hoi; White Kevin; Hager Janet; Gerstein Mark; Reinke Valerie; Nelson Kenneth; Masiar Peter; Srivastava Ranjana; Li Yuli; Li Ju; Zhao Hongyu; Li Jinming; Allison David B; Snyder Michael; Miller Perry; Williams Kenneth
YMD: a microarray database for large-scale gene expression analysis.
Proceedings / AMIA ... Annual Symposium. AMIA Symposium 2002;():140-4.
2002: Liu Yang; Luscombe Nicholas M; Alexandrov Vadim; Bertone Paul; Harrison Paul; Zhang Zhaolei; Gerstein Mark
Structural genomics: a new era for pharmaceutical research.
Genome biology 2002;3(2):REPORTS4004.
2001: Qian J; Dolled-Filhart M; Lin J; Yu H; Gerstein M
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.
Journal of molecular biology 2001;314(5):1053-66.
2001: Qian J; Luscombe N M; Gerstein M
Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model.
Journal of molecular biology 2001;313(4):673-81.
2001: Hegyi H; Gerstein M
Annotation transfer for genomics: measuring functional divergence in multi-domain proteins.
Genome research 2001;11(10):1632-40.
2001: Greenbaum D; Luscombe N M; Jansen R; Qian J; Gerstein M
Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
Genome research 2001;11(9):1463-8.
2001: Zhu H; Bilgin M; Bangham R; Hall D; Casamayor A; Bertone P; Lan N; Jansen R; Bidlingmaier S; Houfek T; Mitchell T; Miller P; Dean R A; Gerstein M; Snyder M
Global analysis of protein activities using proteome chips.
Science (New York, N.Y.) 2001;293(5537):2101-5.
2001: Lian Z; Wang L; Yamaga S; Bonds W; Beazer-Barclay Y; Kluger Y; Gerstein M; Newburger P E; Berliner N; Weissman S M
Genomic and proteomic analysis of the myeloid differentiation program.
Blood 2001;98(3):513-24.
2001: Bertone P; Kluger Y; Lan N; Zheng D; Christendat D; Yee A; Edwards A M; Arrowsmith C H; Montelione G T; Gerstein M
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.
Nucleic acids research 2001;29(13):2884-98.
2001: Qian J; Stenger B; Wilson C A; Lin J; Jansen R; Teichmann S A; Park J; Krebs W G; Yu H; Alexandrov V; Echols N; Gerstein M
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.
Nucleic acids research 2001;29(8):1750-64.
2001: Subrahmanyam Y V; Yamaga S; Prashar Y; Lee H H; Hoe N P; Kluger Y; Gerstein M; Goguen J D; Newburger P E; Weissman S M
RNA expression patterns change dramatically in human neutrophils exposed to bacteria.
Blood 2001;97(8):2457-68.
2001: Harrison P M; Echols N; Gerstein M B
Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome.
Nucleic acids research 2001;29(3):818-30.
2001: Luscombe N M; Greenbaum D; Gerstein M
What is bioinformatics? A proposed definition and overview of the field.
Methods of information in medicine 2001;40(4):346-58.
2000: Gerstein M
Integrative database analysis in structural genomics.
Nature structural biology 2000;7 Suppl():960-3.
2000: Zhu H; Klemic J F; Chang S; Bertone P; Casamayor A; Klemic K G; Smith D; Gerstein M; Reed M A; Snyder M
Analysis of yeast protein kinases using protein chips.
Nature genetics 2000;26(3):283-9.
2000: Das R; Hegyi H; Gerstein M
Genome analyses of spirochetes: a study of the protein structures, functions and metabolic pathways in Treponema pallidum and Borrelia burgdorferi.
Journal of molecular microbiology and biotechnology 2000;2(4):387-92.
2000: Drawid A; Jansen R; Gerstein M
Genome-wide analysis relating expression level with protein subcellular localization.
Trends in genetics : TIG 2000;16(10):426-30.
2000: Gerstein M; Jansen R
The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?
Current opinion in structural biology 2000;10(5):574-84.
2000: Christendat D; Yee A; Dharamsi A; Kluger Y; Savchenko A; Cort J R; Booth V; Mackereth C D; Saridakis V; Ekiel I; Kozlov G; Maxwell K L; Wu N; McIntosh L P; Gehring K; Kennedy M A; Davidson A R; Pai E F; Gerstein M; Edwards A M; Arrowsmith C H
Structural proteomics of an archaeon.
Nature structural biology 2000;7(10):903-9.
2000: Drawid A; Gerstein M
A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome.
Journal of molecular biology 2000;301(4):1059-75.
2000: Balasubramanian S; Schneider T; Gerstein M; Regan L
Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome.
Nucleic acids research 2000;28(16):3075-82.
2000: Lin J; Gerstein M
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels.
Genome research 2000;10(6):808-18.
2000: Das R; Gerstein M
The stability of thermophilic proteins: a study based on comprehensive genome comparison.
Functional & integrative genomics 2000;1(1):76-88.
2000: Krebs W G; Gerstein M
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.
Nucleic acids research 2000;28(8):1665-75.
2000: Wilson C A; Kreychman J; Gerstein M
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.
Journal of molecular biology 2000;297(1):233-49.
2000: Jansen R; Gerstein M
Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins.
Nucleic acids research 2000;28(6):1481-8.
2000: Senes A; Gerstein M; Engelman D M
Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.
Journal of molecular biology 2000;296(3):921-36.
2000: Christendat D; Yee A; Dharamsi A; Kluger Y; Gerstein M; Arrowsmith C H; Edwards A M
Structural proteomics: prospects for high throughput sample preparation.
Progress in biophysics and molecular biology 2000;73(5):339-45.
2000: Gerstein M; Lin J; Hegyi H
Protein folds in the worm genome.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000;():30-41.
1999: Ross-Macdonald P; Coelho P S; Roemer T; Agarwal S; Kumar A; Jansen R; Cheung K H; Sheehan A; Symoniatis D; Umansky L; Heidtman M; Nelson F K; Iwasaki H; Hager K; Gerstein M; Miller P; Roeder G S; Snyder M
Large-scale analysis of the yeast genome by transposon tagging and gene disruption.
Nature 1999;402(6760):413-8.
1999: Gerstein M; Chothia C
Perspectives: signal transduction. Proteins in motion.
Science (New York, N.Y.) 1999;285(5434):1682-3.
1999: Hegyi H; Gerstein M
The relationship between protein structure and function: a comprehensive survey with application to the yeast genome.
Journal of molecular biology 1999;288(1):147-64.
1998: Gerstein M
Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census.
Proteins 1998;33(4):518-34.
1998: Gerstein M; Hegyi H
Comparing genomes in terms of protein structure: surveys of a finite parts list.
FEMS microbiology reviews 1998;22(4):277-304.
1998: Gerstein M; Krebs W
A database of macromolecular motions.
Nucleic acids research 1998;26(18):4280-90.
1998: Gerstein M; Levitt M
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins.
Protein science : a publication of the Protein Society 1998;7(2):445-56.
1998: Gerstein M
How representative are the known structures of the proteins in a complete genome? A comprehensive structural census.
Folding & design 1998;3(6):497-512.
1998: Gerstein M
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence.
Bioinformatics (Oxford, England) 1998;14(8):707-14.
1997: Gerstein M
A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure.
Journal of molecular biology 1997;274(4):562-76.
1997: Gerstein M; Levitt M
A structural census of the current population of protein sequences.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(22):11911-6.

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Mark Gerstein

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