Gerstein Lab Publications

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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.
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Relating three-dimensional structures to protein networks provides evolutionary insights.
PM Kim, LJ Lu, Y Xia, MB Gerstein (2006). Science 314:1938-41.
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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.
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Genomic analysis of the hierarchical structure of regulatory networks.
H Yu, M Gerstein (2006). Proc Natl Acad Sci U S A 103:14724-31.
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The real life of pseudogenes.
M Gerstein, D Zheng (2006). Sci Am 295:48-55.
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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 (2005). Nucleic Acids Res 34:D296-301.
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PubNet: a flexible system for visualizing literature derived networks.
SM Douglas, GT Montelione, M Gerstein (2005). Genome Biol 6:R80.
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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.
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Global identification of human transcribed sequences with genome tiling arrays.
P Bertone, V Stolc, TE Royce, JS Rozowsky, AE Urban, X Zhu, JL Rinn, W Tongprasit, M Samanta, S Weissman, M Gerstein, M Snyder (2004). Science 306:2242-6.
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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.
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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.
 
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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.
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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.
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A universal legal framework as a prerequisite for database interoperability.
D Greenbaum, M Gerstein (2003). Nat Biotechnol 21:979-82.
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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.
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Genomics. Defining genes in the genomics era.
M Snyder, M Gerstein (2003). Science 300:258-60.
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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.
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Relating whole-genome expression data with protein-protein interactions.
R Jansen, D Greenbaum, M Gerstein (2002). Genome Res 12:37-46.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Perspectives: signal transduction. Proteins in motion.
M Gerstein, C Chothia (1999). Science 285:1682-3.
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The packing density in proteins: standard radii and volumes.
J Tsai, R Taylor, C Chothia, M Gerstein (1999). J Mol Biol 290:253-66.
 
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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.
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A database of macromolecular motions.
M Gerstein, W Krebs (1998). Nucleic Acids Res 26:4280-90.
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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.
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A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure.
M Gerstein (1998). J Mol Biol 274:562-76.
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