Best Papers [best]
- 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.
- Relating three-dimensional structures to protein networks provides evolutionary insights.
- PM Kim, LJ Lu, Y Xia, MB Gerstein (2006) Science 314: 1938-41.
- 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.
- The real life of pseudogenes.
- M Gerstein, D Zheng (2006) Sci Am 295: 48-55.
- 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.
- PubNet: a flexible system for visualizing literature derived networks.
- SM Douglas, GT Montelione, M Gerstein (2005) Genome Biol 6: R80.
- 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.
- 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.
- 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.
- 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.
- Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.
- Z Zhang, PM Harrison, Y Liu, M Gerstein (2003) Genome Res 13: 2541-58.
- A 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.
- A universal legal framework as a prerequisite for database interoperability.
- D Greenbaum, M Gerstein (2003) Nat Biotechnol 21: 979-82.
- 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.
- Genomics. Defining genes in the genomics era.
- M Snyder, M Gerstein (2003) Science 300: 258-60.
- 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.
- Relating whole-genome expression data with protein-protein interactions.
- R Jansen, D Greenbaum, M Gerstein (2002) Genome Res 12: 37-46.
- 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.
- 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.
- Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome.
- PM Harrison, N Echols, MB Gerstein (2001) Nucleic Acids Res 29: 818-30.
- PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.
- J Qian, B Stenger, CA Wilson, J Lin, R Jansen, SA Teichmann, J Park, WG Krebs, H Yu, V Alexandrov, N Echols, M Gerstein (2001) Nucleic Acids Res 29: 1750-64.
- 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.
- 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.
- 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.
- Perspectives: signal transduction. Proteins in motion.
- M Gerstein, C Chothia (1999) Science 285: 1682-3.
- The packing density in proteins: standard radii and volumes.
- J Tsai, R Taylor, C Chothia, M Gerstein (1999) J Mol Biol 290: 253-66.
- 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.
- A database of macromolecular motions.
- M Gerstein, W Krebs (1998) Nucleic Acids Res 26: 4280-90.
- 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.
- A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure.
- M Gerstein (1997) J Mol Biol 274: 562-76.
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