Main Scientific Publications (Last Modified on Saturday, 05-Aug-2000 21:11:57 EDT) -- In Press - 8 -- D Christendat, A Yee, A Dharamsi, Y Kluger, A Savchenko, J R Cort, V Booth, C D Mackereth, V Saridakis, I Ekiel, G Kozlov, K L Maxwell, N Wu, L P. McIntosh, K Gehring, M A. Kennedy, A R Davidson, E F Pai, M Gerstein, A M Edwards & C H Arrowsmith, "Structural Proteomics of an Archeon," Nature Structural Biology (in press). M Gerstein & F M Richards (2000). "Protein Geometry: Distances, Areas, and Volumes," International Tables for Crystallography 22. (International Union of Crystallography, Chester, UK, in press). http://bioinfo.mbb.yale.edu/e-print/geom-inttab/geom-inttab.pdf S Balasubramanian, T Schneider, M Gerstein & L Regan (2000). "Proteomics of Mycoplasma Genitalium: Identification and Characterization of Unannotated and Atypical Proteins in a Small Model Genome," Nuc. Acid Res. (in press) http://bioinfo.mbb.yale.edu/e-print/mg-cd-nar/text.pdf A Drawid, R Jansen & M Gerstein (2000). "Gene Expression Levels are Correlated with Protein Subcellular Localization," Trends in Genetics (in press). http://bioinfo.mbb.yale.edu/e-print/exploc-tig/text.pdf D Christendat, A Yee, A Dharamsi, Y Kluger, M Gerstein, C Arrowsmith, A Edwards (2000). "Structural Proteomics: Prospects for High Throughput Sample Preparation," Progress in Biophysics and Molecular Biology (in press). G Naylor & M Gerstein (2000). "Measuring Shifts In Function And Evolutionary Opportunity Using Variability Profiles: A Case Study of the Globins," Journal of Molecular Evolution (in press). http://bioinfo.mbb.yale.edu/e-print/protspace-jme/text.pdf M Gerstein & R Jansen (2000). "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 (in press). http://bioinfo.mbb.yale.edu/e-print/expclust-cosb/text.pdf http://bioinfo.mbb.yale.edu/genome/expression R Das, H Hegyi & M Gerstein (2000). "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 (in press). http://bioinfo.mbb.yale.edu/e-print/spirochete-jmmb/text.pdf -- 2000 - 9 -- A Drawid & M Gerstein (2000). "A Bayesian System Integrating Expression Data with Sequence Patterns for Localizing Proteins: Comprehensive Application to the Yeast Genome," J. Mol. Biol. 360: 1077-1093. http://bioinfo.mbb.yale.edu/e-print/bayesloc-jmb/text.pdf http://bioinfo.mbb.yale.edu/genome/localize M Gerstein, J Lin & H Hegyi (2000). "Protein Folds in the Worm Genome," Pacific Symposium on Biocomputing 5: 30-42. PUBMED-ID: 10902154 http://bioinfo.mbb.yale.edu/e-print/wormfold-psb00/text.pdf http://bioinfo.mbb.yale.edu/genome/worm_yeast/ W Krebs & M Gerstein (2000) "The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework," Nucleic Acids Res 28: 1665-75. PUBMED-ID: 10734184 http://bioinfo.mbb.yale.edu/e-print/morphs-nar/text.pdf http://bioinfo.mbb.yale.edu/MolMovDB M Gerstein (2000). "Annotation of the human genome," Science 288: 1590. PUBMED-ID: 10858136 http://bioinfo.mbb.yale.edu/e-print/genome-annotate-science/text.htm J Lin & M Gerstein (2000). "Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels," Genome Res. 10: 808-1 PUBMED-ID: 10854412 http://bioinfo.mbb.yale.edu/e-print/genome-tree-genomeres/text.pdf C Wilson, J Kreychman, & M Gerstein (2000). "Assessing Annotation Transfer for Genomics: Quantifying the relations between protein sequence, structure, and function through traditional and probabilistic scores," J. Mol. Biol. 297: 233-49. PUBMED-ID: 10704319 http://bioinfo.mbb.yale.edu/e-print/ann-xfer-jmb/ http://bioinfo.mbb.yale.edu/align/scop/ R Das & M Gerstein (2000). "The Stability of Thermophilic Proteins: A Study Based on Comprehensive Genome Comparison," Functional & Integrative Genomics 1: 76-88. http://bioinfo.mbb.yale.edu/e-print/thermo-genome-fig/text.pdf http://bioinfo.mbb.yale.edu/genome/thermophile/ R Jansen & M Gerstein (2000). "Analysis of the Yeast Transcriptome with Broad Structural and Functional Categories: Characterizing Highly Expressed Proteins," Nuc. Acids Res. 28:1481-1488 PUBMED-ID: 10684945 http://bioinfo.mbb.yale.edu/e-print/transcriptome-nar/text.pdf http://bioinfo.mbb.yale.edu/genome/expression/ A Senes, M Gerstein & D Engelman (2000). "Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif correlates with beta-branched residues in a position-dependent fashion," J. Mol. Biol. 296: 921-36. PUBMED-ID: 10677292 http://bioinfo.mbb.yale.edu/e-print/tmstat-jmb/text.pdf http://engelman.csb.yale.edu/tmstat/ -- 1999 - 10 -- M Gerstein (1999). "Forging links in an electronic paper chain," Nature 398: 20 PUBMED-ID: 9849936 http://bioinfo.mbb.yale.edu/e-print/elec-pub-nature/text.htm H Hegyi & M Gerstein (1999). "The Relationship between Protein Structure and Function: a Comprehensive Survey with Application to the Yeast Genome," J Mol. Biol. 228: 147-164. PUBMED-ID: 10329133 http://bioinfo.mbb.yale.edu/e-print/foldfunc-jmb/text-ff.pdf http://bioinfo.mbb.yale.edu/genome/foldfunc/ M Gerstein, (1999) "Building the future of biocomputing," Nature 399: 101 PUBMED-ID: 10335835 http://bioinfo.mbb.yale.edu/e-print/biocomp-nature/text.htm S Teichmann, C Chothia & M Gerstein (1999). "Advances in Structural Genomics," Curr. Opin. Struc. Biol. 9: 390-399. PUBMED-ID: 10361097 http://bioinfo.mbb.yale.edu/e-print/strucgenom-cosb/text-sg.pdf http://bioinfo.mbb.yale.edu/genome/MG/ J Tsai, R Taylor, C Chothia & M Gerstein (1999). "The Packing Density in Proteins: Standard Radii and Volumes," J. Mol. Biol. 290: 253-266. PUBMED-ID: 10388571 http://bioinfo.mbb.yale.edu/e-print/std-vols-jmb/std-vols-jmb.pdf M Gerstein (1999). "E-publishing on the Web: Promises, Pitfalls, and Payoffs for Bioinformatics," Bioinformatics 15: 429-431. PUBMED-ID: 10515701 http://bioinfo.mbb.yale.edu/e-print/epub-ed-bioinfo/ M Gerstein, R Jansen, T Johnson, J Tsai & W Krebs (1999). "Studying Macromolecular Motions in a Database Framework: from Structure to Sequence," Rigidity theory & applications (ed. M F Thorpe & P M Duxbury, Kluwer Academic/Plenum Publishers), 401-442. http://bioinfo.mbb.yale.edu/e-print/rigidity-conf.pdf M Gerstein & C Chothia (1999). "Proteins in Motion," Science 285: 1682-3. PUBMED-ID: 10523185 http://bioinfo.mbb.yale.edu/e-print/protmot-science/text.pdf E Brodkin & M Gerstein (1999). "'E-biomed? and clinical research," New Engl. J Med. 341:1080-1 http://bioinfo.mbb.yale.edu/e-print/ebiomed-nejm/text.pdf PUBMED-ID: 10507925 P Ross-Macdonald, P S R Coelho, T Roemer, S Agarwal, A Kumar, R Jansen, K Cheung, A Sheehan, D Symoniatis, L Umansky, M Heidtman, F K Nelson, H Iwasaki, K Hager, M Gerstein, P Miller, G S Roeder & M Snyder (1999). "Large-scale analysis of the yeast genome by transposon tagging and gene disruption," Nature 402: 413-418. PUBMED-ID: 10586881 http://bioinfo.mbb.yale.edu/e-print/genome-transposon-nature/text.pdf http://bioinfo.mbb.yale.edu/genome/phenotypes/ -- 1998 - 9 -- M Gerstein & M Levitt (1998). "Comprehensive Assessment of Automatic Structural Alignment against a Manual Standard, the Scop Classification of Proteins," Protein Science 7: 445-456. PUBMED-ID: 9521122 http://bioinfo.mbb.yale.edu/e-print/scop-str-prosci-reprint.pdf http://bioinfo.mbb.yale.edu/align/ J Fu, M Gerstein, P David, A Gnatt, D Bushnell, A Edwards & R Kornberg (1998). "Repeated tertiary fold of RNA polymerase II and implications for DNA binding," J. Mol. Biol. 280: 317-322. PUBMED-ID: 9665838 http://bioinfo.mbb.yale.edu/e-print/rnapol-jmb-reprint.pdf M Levitt & M Gerstein (1998). "A Unified Statistical Framework for Sequence Comparison and Structure Comparison," Proc. Natl. Acad. Sci. USA 95: 5913-5920. PUBMED-ID: 9665838 http://bioinfo.mbb.yale.edu/e-print/statframe-pnas-reprint.pdf M Gerstein & W Krebs (1998). "A Database of Macromolecular Movements," Nuc. Acid. Res. 26:4280-4290. PUBMED-ID: 98391754 http://bioinfo.mbb.yale.edu/e-print/molmovdb-nar-reprint.pdf http://bioinfo.mbb.yale.edu/MolMovDB M Gerstein & M Levitt (1998). "Simulating Water and the Molecules of Life," Scientific American 279: 100-105. PUBMED-ID: 9841379 http://bioinfo.mbb.yale.edu/sciam/ M Gerstein (1998). "Measurement of the Effectiveness of Transitive Sequence Comparison, through a Third 'Intermediate' Sequence," Bioinformatics 14: 707-14. PUBMED-ID: 9789096 http://bioinfo.mbb.yale.edu/e-print/transcmp-bioinfo-reprint.pdf M Gerstein & H Hegyi (1998). "Comparing Microbial Genomes in terms of Protein Structure: Surveys of a Finite Parts List," FEMS Microbiology Reviews 22: 277-304. PUBMED-ID: 10357579 http://bioinfo.mbb.yale.edu/e-print/surveys-fems-preprint.pdf M Gerstein (1998). "Patterns of Protein-Fold Usage in Eight Microbial Genomes: A Comprehensive Structural Census," Proteins 33: 518-534. PUBMED-ID: 9849936 http://bioinfo.mbb.yale.edu/genome/browser/ M Gerstein (1998). "How Representative are the Known Structures of the Proteins in a Complete Genome? A Comprehensive Structural Census," Folding & Design 3: 497-512. PUBMED-ID: 9889159 http://bioinfo.mbb.yale.edu/e-print/pdb-v-gen-folddes/fad-3-497-reprint.pdf -- 1997- 6 -- R Schmidt, M Gerstein & R Altman (1997). "LPFC: An Internet Library of Protein Family Core Structures," Protein Science 6: 246-248. PUBMED-ID: 9007997 http://bioinfo.mbb.yale.edu/e-print/lpfc-prosci/text.pdf M Levitt, M Gerstein, E Huang, S Subbiah & J Tsai (1997). "Protein Folding: The Endgame," Annual Reviews of Biochemistry 66: 549-579. PUBMED-ID: 9242917 http://bioinfo.mbb.yale.edu/e-print/ar96-endgame/ar96-endgame-reprint.html C Chothia & M Gerstein (1997). "Protein Evolution. How far can sequences diverge?" Nature 385:579-581. PUBMED-ID: 9024652 http://bioinfo.mbb.yale.edu/e-print/seqevol-nature/text.pdf M Gerstein & M Levitt (1997). "A Structural Census of the Current Population of Protein Sequences," Proceedings of the National Academy of Sciences USA 94: 11911-11916. PUBMED-ID: 9342336 M Gerstein (1997). "A Structural Census of Genomes: Comparing Bacterial, Eukaryotic, and Archaeal Genomes in terms of Protein Structure," Journal of Molecular Biology 274: 562-576. PUBMED-ID: 9417935 http://bioinfo.mbb.yale.edu/e-print/genome-jmb-reprint.pdf http://bioinfo.mbb.yale.edu/genome/browser/ J Tsai, M Gerstein & M Levitt (1997). "Simulating the minimum core for hydrophobic collapse in globular proteins," Protein Science 6: 2606-2616. PUBMED-ID: 9416609 http://bioinfo.mbb.yale.edu/e-print/prosci-collapse.pdf -- 1996 - 3 -- M Gerstein & M Levitt (1996). "Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures," in Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology, 59-67 (Menlo Park, CA, AAAI Press, June 12-15). PUBMED-ID: 8877505 http://bioinfo.mbb.yale.edu/hyper/mbg/AvgCore/ismb96/ J Tsai, M Gerstein & M Levitt (1996). "Keeping the Shape but Changing the Charges: A Simulation Study of Urea and its Isosteric Analogues," Journal of Chemical Physics 104: 9417-9430. M Gerstein & C Chothia (1996). "Packing at the Protein-Water Interface," Proceedings of the National Academy of Sciences USA 93: 10167-10172. PUBMED-ID: 8816770 http://bioinfo.mbb.yale.edu/e-print/surfpack-pnas/text.pdf -- 1995 - 7-- M Gerstein, J Tsai & M Levitt (1995). "The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra," Journal of Molecular Biology 249: 955-966. PUBMED-ID: 7540695 M Suzuki, N Yagi & M Gerstein (1995). "DNA-recognition and superstructure-formation by helix-turn-helix proteins," http://www.oup.co.uk/jnls/list/proeng">Protein Engineering 8: 329-338. PUBMED-ID: 7567918 R Altman, C Hughes & M Gerstein (1995). "Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins," Journal of Molecular Graphics 13: 142-152. PUBMED-ID: 7577841 M Suzuki, S Brenner, M Gerstein & N Yagi (1995). "DNA recognition code of transcription factors," Protein Engineering 8: 319-328. PUBMED-ID: 7567917 M Gerstein & R Altman (1995). "Average core structures and variability measures for protein families: Application to the immunoglobulins," Journal of Molecular Biology 251: 161-175. PUBMED-ID: 7643385 http://bioinfo.mbb.yale.edu/e-print/avgstr-jmb.pdf M Suzuki & M Gerstein (1995). "The geometry of alpha-helices binding to DNA," Proteins: Structure, Function, Genetics 23: 525-535. PUBMED-ID: 8749848 M Gerstein & R Altman (1995). "A Structurally Invariant Core for the Globins," Computer Applications in the Biosciences 11: 633-644. PUBMED-ID: 8808580 http://bioinfo.mbb.yale.edu/hyper/mbg/AvgCore/ -- 1994 - 7 -- M Gerstein, E Sonnhammer & C Chothia (1994). "Volume Changes on Protein Evolution," Journal of Molecular Biology 236: 1067-1078. PUBMED-ID: 8120887 http://bioinfo.mbb.yale.edu/hyper/mbg/ProtEvol/ M Gerstein (1994). "Purcell's early work on NMR: Contingency versus Inevitability," American Journal of Physics 62: 596-601. http://bioinfo.mbb.yale.edu/hyper/mbg/Purcell M Suzuki, D Neuhaus, M Gerstein & S Aimoto (1994). "Solution structure of the DNA binding octapeptide repeat of the K10 gene product," Protein Engineering 7: 461-470. PUBMED-ID: 8029203 M Gerstein, A Lesk & C Chothia (1994). "Structural Mechanisms for Domain Movements," Biochemistry 33: 6739-6749. PUBMED-ID: 8204609 Y Harpaz, M Gerstein & C Chothia (1994). "Volume Changes on Protein Folding," Structure 2: 641-649. PUBMED-ID: 7922041 http://bioinfo.mbb.yale.edu/e-print/volfold-structure/text.pdf R Altman & M Gerstein. (1994). "Finding an Average Core Structure: Application to the Globins," in Proceedings of the Second International Conference on Intelligent Systems in Molecular Biology, 19-27 (Menlo Park, CA, AAAI Press, August 14-17). PUBMED-ID: 7584390 http://bioinfo.mbb.yale.edu/hyper/mbg/ISMB-94-60 M Suzuki, M Gerstein & N Yagi (1994). "The stereochemical basis for DNA recognition by Zn fingers," Nucleic Acids Research 22: 3397-3405. PUBMED-ID: 8078776 -- 1993 - 7 -- S Subramaniam, M Gerstein, D Oesterhelt & R Henderson (1993). "Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin," EMBO Journal 12: 1-8. PUBMED-ID: 8428572 M Gerstein, G Schulz & C Chothia (1993). "Domain Closure in Adenylate Kinase: Joints on Either Side of Two Helices Close Like Neighboring Fingers," Journal of Molecular Biology 229: 494-501. PUBMED-ID: 8429559 M Gerstein & R Lynden-Bell (1993). "Simulation of Water around a Model Protein Helix. 1. Two-dimensional Projections of Solvent Structure," Journal of Physical Chemistry 97: 2982-2991. M Gerstein & R Lynden-Bell (1993). "What is the natural boundary for a protein in solution?," Journal of Molecular Biology 230: 641-650. PUBMED-ID: 8464069 M Gerstein & R Lynden-Bell (1993). "Simulation of Water around a Model Protein Helix. 2. The Relative Contributions of Packing, Hydrophobicity, and Hydrogen Bonding," Journal of Physical Chemistry 97: 2991-2999. M Suzuki, M Gerstein & T Johnson (1993). "An NMR study of the DNA-binding 'SPKK' motif and a model for its interaction with DNA," Protein Engineering 6: 565-574. PUBMED-ID: 8234227 M Gerstein, A Lesk, E Baker, B Anderson, G Norris & C Chothia (1993). "Domain Closure in Lactoferrin: Two Hinges produce a See-saw Motion between Alternative Close-Packed Interfaces," Journal of Molecular Biology 234: 357-372. PUBMED-ID: 8230220 -- 1992 - 2 -- M Gerstein (1992). "A Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining Sites," Acta Crystallographica A48: 271-276. http://bioinfo.mbb.yale.edu/hyper/mbg/CoarseSurf I De Baere, L Liu, L Moens, J Van Beeumen, C Gielens, J Richelle, C Trotman, J Finch, M Gerstein & M Perutz (1992). "Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum : Amino acid sequence and structural interpretation," Proceedings of the National Academy of Sciences USA 89: 4638-4642. PUBMED-ID: 1584800 -- 1991 - 1 -- M Gerstein & C Chothia (1991). "Analysis of Protein Loop Closure: Two Types of Hinges Produce One Motion in Lactate Dehydrogenase," Journal of Molecular Biology 220: 133-149. PUBMED-ID: 2067013 -- 1987 - 1 -- N Fisch, A Kritz & M Gerstein. (1987). "Inverse Problem for Synchrotron Radiation in the Presence of Noise," in Proceedings of the Sixth Joint Workshop on Electron Cyclotron Emission and Electron Cyclotron Resonance Heating. (eds. A Riviere & A Costley), 23-30 (Oxford, 16-17 September).