|
Undergraduate Publications [student]
Undergraduate Publications
Current undergraduates are listed at http://www.gersteinlab.org/people/
Past ones are at http://www.gersteinlab.org/people/alumni.htm
- 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.
- 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).
- 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.
- 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.
- 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.
- An XML-Based Approach to Integrating Heterogeneous Yeast Genome Data
- KH Cheung, D Pan, A Smith, M Seringhaus, SM Douglas, M Gerstein. 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS); pp 236-242.
- The protein target list of the Northeast Structural Genomics Consortium.
- Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost, GT Montelione (2004) Proteins 56: 181-7.
- 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.
- Exploring the range of protein flexibility, from a structural proteomics perspective.
- M Gerstein, N Echols (2004) Curr Opin Chem Biol 8: 14-9.
- Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.
- CS Goh, N Lan, SM Douglas, B Wu, N Echols, A Smith, D Milburn, GT Montelione, H Zhao, M Gerstein (2004) J Mol Biol 336: 115-30.
- Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
- J Qian, J Lin, NM Luscombe, H Yu, M Gerstein (2003) Bioinformatics 19: 1917-26.
- 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.
- SPINE 2: a system for collaborative structural proteomics within a federated database framework.
- CS Goh, N Lan, N Echols, SM Douglas, D Milburn, P Bertone, R Xiao, LC Ma, D Zheng, Z Wunderlich, T Acton, GT Montelione, M Gerstein (2003) Nucleic Acids Res 31: 2833-8.
- MolMovDB: analysis and visualization of conformational change and structural flexibility.
- N Echols, D Milburn, M Gerstein (2003) Nucleic Acids Res 31: 478-82.
- Subcellular localization of the yeast proteome.
- A Kumar, S Agarwal, JA Heyman, S Matson, M Heidtman, S Piccirillo, L Umansky, A Drawid, R Jansen, Y Liu, KH Cheung, P Miller, M Gerstein, GS Roeder, M Snyder (2002) Genes Dev 16: 707-19.
- Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds.
- H Hegyi, J Lin, D Greenbaum, M Gerstein (2002) Proteins 47: 126-41.
- A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.
- P Harrison, A Kumar, N Lan, N Echols, M Snyder, M Gerstein (2002) J Mol Biol 316: 409-19.
- Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.
- PM Harrison, H Hegyi, S Balasubramanian, NM Luscombe, P Bertone, N Echols, T Johnson, M Gerstein (2002) Genome Res 12: 272-80.
- GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.
- J Lin, J Qian, D Greenbaum, P Bertone, R Das, N Echols, A Senes, B Stenger, M Gerstein (2002) Nucleic Acids Res 30: 4574-82.
- Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.
- WG Krebs, V Alexandrov, CA Wilson, N Echols, H Yu, M Gerstein (2002) Proteins 48: 682-95.
- SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.
- S Balasubramanian, P Harrison, H Hegyi, P Bertone, N Luscombe, N Echols, P McGarvey, Z Zhang, M Gerstein (2002) Pharmacogenomics 3: 393-402.
- Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
- N Echols, P Harrison, S Balasubramanian, NM Luscombe, P Bertone, Z Zhang, M Gerstein (2002) Nucleic Acids Res 30: 2515-23.
- An integrated approach for finding overlooked genes in yeast.
- A Kumar, PM Harrison, KH Cheung, N Lan, N Echols, P Bertone, P Miller, MB Gerstein, M Snyder (2002) Nat Biotechnol 20: 58-63.
- Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.
- J Qian, M Dolled-Filhart, J Lin, H Yu, M Gerstein (2001) J Mol Biol 314: 1053-66.
- 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.
- Genome-wide analysis relating expression level with protein subcellular localization.
- A Drawid, R Jansen, M Gerstein (2000) Trends Genet 16: 426-30.
- 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.
- Protein folds in the worm genome.
- M Gerstein, J Lin, H Hegyi (2000) Pac Symp Biocomput 30-41.
- 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.
Return to front page
