Publications

-- in press - 10 --

107. J Tsai, M Gerstein.
"Voronoi Calculations of Macromolecular Volumes: Sensitivity Analysis and Parameter Database."
Bioinformatics (in press)

106. A Kumar, S Agarwal, J Heyman, S Matson, M Heidtman, S Piccirillo, L Umansky, A Drawid, R Jansen, Y Liu, K Cheung, P Miller, M Gerstein, G S Roeder, M Snyder.
"Subcellular Localization of the Yeast Proteome."

Genes & Development (in press)

105. D Greenbaum, R Jansen, M Gerstein.
"Analysis of mRNA expression and protein abundance data on a genomic scale: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts."
Bioinformatics (in press).

104. H Hegyi, J Lin, D Greenbaum, M Gerstein.
"Structural Genomics Analysis: Phylogenetic Patterns of Unique, Shared, and Common Folds in 20 Genomes."
Proteins (in press).

*103. P Harrison, A Kumar, N Lan, N Echols, M Snyder, M Gerstein

"A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution."
J Mol Biol (in press)

102. M Gerstein, J Junker.
"Blurring the boundaries between scientific 'papers' and biological databases,"
Nature Yearbook of Science and Technology (in press)
From on-line web debate piece at www.nature.com/nature/debates/e-access .

101. C Horak, M Mahajan, N Luscombe, M Gerstein, S Weissman, M Snyder.
"Novel GATA-1 binding sites mapped in the beta-globin locus using mammalian chIp-chip analysis."
Proc. Natl. Acad. Sciences USA (in press)

100. P Harrison, M Gerstein
"Studying Genomes through the Aeons: Protein families, Pseudogenes, and Proteome Evolution,"
J Mol Biol (in press)

99. W Krebs, J Tsai, V Alexandrov, N Echols, R Jansen, J Junker, M Gerstein
"Studying Protein Flexibility in a Statistical Framework: Tools and Databases for Analyzing Structures and Approaches for Mapping this onto Sequences."
Methods in Enzymology (in press)

98. P Harrison, A Kumar, N Lan, M Snyder, M Gerstein.

"A question of size: the eukaryotic proteome and the problems in defining it."
Nuc. Acids Res (in press)

-- 2002 - 5 --

97. P Harrison, H Hegyi, P Bertone, N Echols, T Johnson, S Balasubramanian, N Luscombe, M Gerstein

"Molecular fossils in the human genome: Identification and analysis of pseudogenes in chromosomes 21 and 22."
Genome Research 12: 272-280 (2002)

96. Y Liu, N Luscombe, V Alexandrov, P Bertone, P Harrison, Z Zhang, M Gerstein

"Structural Genomics: A new era for pharmaceutical research."

GenomeBiology 3: reports4004 (2002)

95. R Jansen, D Greenbaum, M Gerstein.
"Relating whole-genome expression data with protein-protein interactions."
Genome Research 12: 37-46 (2002).

94. A Kumar, P Harrison, K Cheung, N Lan, P Bertone, N Echols, P Miller, M Gerstein, M Snyder.

"An integrated approach for finding overlooked genes in yeast."
Nature Biotech. 20: 58-63 (2002).

#93. Gerstein M, Lan N, Jansen R.
"Proteomics. Integrating interactomes."
Science 295:284-7. (2002)

-- 2001 - 21 --

92. J Qian, N Luscombe, M Gerstein.

"Protein Fold and Family Occurrence in Genomes: Power-Law Behaviour and Evolutionary Model."
J Mol Biol 313: 673-681 (2001).

*91. J Qian, M Dolled-Filhart, J Lin, H Yu, M Gerstein.
"Beyond synexpression relationships: Local Clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions."
J Mol Biol 314:1053-66 (2001).

90. K Cheung, Y Liu, A Kumar, M Snyder, M Gerstein, P Miller.
"An XML Application for Genomic Data Interoperation,"
IEEE International Symp. on Bioinformatics & Biomedical Engineering (BIBE) 97-103 (2001).

89. H Hegyi, M Gerstein.
"Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-domain Proteins,"
Genome Research 11: 1632-1640 (2001).

88. N Luscombe, D Greenbaum, M Gerstein.
"What is Bioinformatics? A Proposed Definition,"
Methods of Information in Medicine 40: 346-58 (2001).

87. R Das, J Junker, D Greenbaum, M Gerstein.
"Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond,"
The Pharmacogenomics Journal 1:115 - 125 (2001)

86. H Zhu, M Bilgin, R Bangham, D Hall, A Casamayor, P Bertone, N Lan, R Jansen, S Bidlingmaier, T Houfek, T Mitchell, P Miller, RA Dean, M Gerstein, M Snyder.
"Global Analysis of Protein Activities Using Proteome Chips."
Science 293: 2101-5 (2001)

85. V Alexandrov, M Gerstein.
"Calculating populations of subcellular compartments using density matrix formalism,"
International Journal of Quantum Chemistry 85: 693-696 (2001).

84. W Olson, M Bansal, S Burley, R Dickerson, M Gerstein, S Harvey, U Heinemann, S Neidle, Z Shakked, H Sklenar, M Suzuki, C Tung, E Westhof, C Wolberger, H Berman.
"Nomenclature: A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry."
J Mol Biol 313: 229-337 (2001).

83. J Tsai, N Voss, M Gerstein.
"Determining the minimum number of types necessary to represent the sizes of protein atoms."
Bioinformatics 17: 949-56 (2001).

82. D Greenbaum, N M Luscombe, R Jansen, J Qian, M Gerstein.

"Interrelating Different Types of Whole-genome Data, from Proteome to Secretome: 'Oming in on Function."

Genome Research 11: 1463-1468 (2001).

81. M Gerstein, FM Richards.
"Protein Geometry: Distances, Areas, and Volumes."
International Tables for Crystallography (Volume F, Chapter 22.1.1, pages 531-539; M Rossmann & E Arnold, editors; Dordrecht: Kluwer; 2001).

80. P Harrison, M Gerstein.
"A Bauhaus for Biologists: An Introduction to Protein Architecture by A. M. Lesk."
Trends Biochem Sci 26 : 204-5 (2001).

79. P Bertone, M Gerstein.
"The new direction in bioinformatics: Integrative data mining for genomics and proteomics."
IEEE Engineering in Medicine & Biology 20: 33-40 (2001).

78. Z Lian, L Wang, S Yamaga, W Bonds, Y Beazer-Barclay, Y Kluger, M Gerstein, P Newburger, N Berliner, S Weissman.
"Genomic and proteomic analysis of the myeloid differentiation program. "
Blood 98: 513-24 (2001).

77. Y Subrahmanyam, S Yamaga, Y Prashar, H Lee, N Hoe, Y Kluger, M Gerstein, J Goguen, P Newburger, S Weissman.
"RNA expression patterns change dramatically in human neutrophils exposed to bacteria."
Blood 97 : 3458-3468 (2001).

*76. P Bertone, Y Kluger, N Lan, D Zheng, D Christendat, A Yee, A Edwards, C Arrowsmith, G Montelione,
M Gerstein.
"SPINE: An integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics."
Nucleic Acids Res 29: 2884-98 (2001).

75. B Honig, M Gerstein.
"Sequences & Topology: Editorial Overview,"
Curr. Opin. Struc. Biol. 11: 327-9 (2001).

74. N Luscombe, D Greenbaum, M Gerstein.
"What is bioinformatics? An introduction and overview."
Intl. Medical Informatics Association (Yearbook, Pages 83-99, 2001).

*73. P Harrison, N Echols, M Gerstein.
"Digging for Dead Genes: An Analysis of the Characteristics of the Pseudogene Population in the C. elegans Genome."
Nuc. Acids. Res. 29 : 818-30 (2001).

*72. J Qian, B Stenger, C Wilson, J Lin, R Jansen, W Krebs, V Alexandrov, N Echols, S Teichmann, J Park, M Gerstein.
"PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information."
Nucleic Acids Res 29: 1750-64 (2001).

-- 2000 - 18 --

71. M Gerstein.
"Integrative database analysis in structural genomics."
Nat Struct Biol 7 : 960-3 (2000).

70. R Das, H Hegyi, M Gerstein.
"Genome analyses of spirochetes: a study of the protein structures, functions and metabolic pathways in Treponema pallidum and Borrelia burgdorferi."
J Mol Microbiol Biotechnol 2 : 387-92 (2000).

69. D Christendat, A Yee, A Dharamsi, Y Kluger, M Gerstein, CH Arrowsmith, AM Edwards.
"Structural proteomics: prospects for high throughput sample preparation."
Prog Biophys Mol Biol 73 : 339-345 (2000).

68. H Zhu, JF Klemic, S Chang, P Bertone, A Casamayor, KG Klemic, D Smith, M Gerstein, MA Reed, M Snyder.
"Analysis of yeast protein kinases using protein chips."
Nat Genet 26 : 283-289 (2000).

67. A Drawid, R Jansen, M Gerstein.
"Genome-wide analysis relating expression level with protein subcellular localization."
Trends Genet 16 : 426-30 (2000).

66. M Gerstein, R Jansen.
"The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?"
Curr Opin Struct Biol 10 : 574-84 (2000).

65. R Das, M Gerstein.
"The Stability of Thermophilic Proteins: A Study Based on Comprehensive Genome Comparison."
Func Integ Genomics 1 : 76-88 (2000).

64. GJ Naylor, M Gerstein.
"Measuring shifts in function and evolutionary opportunity using variability profiles: A case study of the globins."
J Mol Evol 51 : 223-33 (2000).

63. D Christendat, A Yee, A Dharamsi, Y Kluger, A Savchenko, JR Cort, V Booth, CD Mackereth, V Saridakis, I Ekiel, G Kozlov, KL Maxwell, N Wu, LP McIntosh, K Gehring, MA Kennedy, AR Davidson, EF Pai, M Gerstein, AM Edwards, CH Arrowsmith.
"Structural proteomics of an archaeon."
Nat Struct Biol 7 : 903-9 (2000).

*62. A Drawid, M Gerstein.
"A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome."
J Mol Biol 301 : 1059-75 (2000).

61. S Balasubramanian, T Schneider, M Gerstein, L Regan.
"Proteomics of Mycoplasma genitalium: identification and characterization of unannotated and atypical proteins in a small model genome."
Nucleic Acids Res 28 : 3075-82 (2000).

60. M Gerstein, J Lin, H Hegyi.
"Protein folds in the worm genome."
Pac Symp Biocomput 4 : 30-41 (2000).

59. M Gerstein.
"Annotation of the human genome."
Science 288 : 1590 (2000).

*58. J Lin, M Gerstein.
"Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels."
Genome Res 10 : 808-18 (2000).

57. W Krebs, M Gerstein.
"The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework."
Nucleic Acids Res 28 : 1665-75 (2000).

56. A Senes, M Gerstein, DM Engelman.
"Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions."
J Mol Biol 296 : 921-36 (2000).

*55. C Wilson, J Kreychman, M Gerstein.
"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 (2000).

54. R Jansen, M Gerstein.
"Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins."
Nucleic Acids Res 28 : 1481-8 (2000).

-- 1999 - 10 --

53. P Ross-Macdonald, PS Coelho, T Roemer, S Agarwal, A Kumar, R Jansen, KH Cheung,
A Sheehan, D Symoniatis, L Umansky, M Heidtman, FK Nelson, H Iwasaki, K Hager,
M Gerstein, P Miller, GS Roeder, M Snyder.
"Large-scale analysis of the yeast genome by transposon tagging and gene disruption."
Nature 402 : 413-8 (1999).

52. M Gerstein, C Chothia.
"Proteins in motion."
Science 285 : 1682-3 (1999).

51. M Gerstein, R Jansen, T Johnson, J Tsai, W Krebs.
"Studying Macromolecular Motions in a Database Framework: from Structure to Sequence."
Rigidity theory and applications 401-442 (ed. M F Thorpe and P M Duxbury, Kluwer Academic/Plenum Publishers, 1999).

50. M Gerstein.
"E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics."
Bioinformatics 15 : 429-31 (1999).

49. E Brodkin, M Gerstein.
"'E-biomed' and clinical research."
N Engl J Med 341 : 1080 (1999).

*48. J Tsai, R Taylor, C Chothia, M Gerstein.
"The packing density in proteins: standard radii and volumes."
J Mol Biol 290 : 253-66 (1999).

47. S Teichmann, C Chothia, M Gerstein.
"Advances in structural genomics."
Curr Opin Struct Biol 9 : 390-9 (1999).

46. M Gerstein.
"Building the future of biocomputing."
Nature 399 : 101 (1999).

*45. H Hegyi, M Gerstein.
"The relationship between protein structure and function: a comprehensive survey with application to the yeast genome."
J Mol Biol 288 : 147-64 (1999).

44. M Gerstein.
"Forging links in an electronic paper chain."
Nature 398 : 20 (1999).

-- 1998 - 9 --

43. M Gerstein, H Hegyi.
"Comparing genomes in terms of protein structure: surveys of a finite parts list."
FEMS Microbiol Rev 22 : 277-304 (1998).

42. M Gerstein.
"How representative are the known structures of the proteins in a complete genome? A comprehensive structural census."
Folding & Design 3 : 497-512 (1998).

41. M Gerstein.
"Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census."
Proteins 33 : 518-34 (1998).

40. M Gerstein, M Levitt.
"Simulating water and the molecules of life."
Sci Am 279 : 100-5 (1998).

39. M Gerstein.
"Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence."
Bioinformatics 14 : 707-14 (1998).

*38. M Gerstein, W Krebs.
"A database of macromolecular motions."
Nucleic Acids Res 26 : 4280-90 (1998).

37. J Fu, M Gerstein, PR David, AL Gnatt, DA Bushnell, AM Edwards, RD Kornberg.
"Repeated tertiary fold of RNA polymerase II and implications for DNA binding."
J Mol Biol 280 : 317-22 (1998).

36. M Levitt, M Gerstein.
"A unified statistical framework for sequence comparison and structure comparison."
Proc Natl Acad Sci U S A 95 : 5913-20 (1998).

35. M Gerstein, M Levitt.
"Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins."
Protein Sci 7 : 445-56 (1998).

-- 1997 - 6 --

*34. M Gerstein.
"A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure."
J Mol Biol 274 : 562-76 (1997).

33. J Tsai, M Gerstein, M Levitt.
"Simulating the minimum core for hydrophobic collapse in globular proteins."
Protein Sci 6 : 2606-16 (1997).

32. M Gerstein, M Levitt.
"A structural census of the current population of protein sequences."
Proc Natl Acad Sci U S A 94 : 11911-6 (1997).

31. C Chothia, M Gerstein.
"Protein evolution. How far can sequences diverge?"
Nature 385 : 579, 581 (1997).

30. M Levitt, M Gerstein, E Huang, S Subbiah, J Tsai.
"Protein folding: the endgame."
Annu Rev Biochem 66 : 549-79 (1997).

29. R Schmidt, M Gerstein, RB Altman.
"LPFC: an Internet library of protein family core structures."
Protein Sci 6 : 246-8 (1997).

Reverse Chronological List of 28 Publications Before Lab Opened in 1/97

-- 1996 - 3 --

28. M Gerstein & M Levitt.
"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, 1996).

27. J Tsai, M Gerstein & M Levitt.
"Keeping the Shape but Changing the Charges: A Simulation Study of Urea and its Isosteric Analogues."
Journal of Chemical Physics 104: 9417-9430 (1996).

26. M Gerstein, C Chothia.
"Packing at the Protein-Water Interface."
Proceedings of the National Academy of Sciences USA 93: 10167-10172 (1996).

-- 1995 - 7--

25. M Gerstein, J Tsai & M Levitt.
"The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra."
Journal of Molecular Biology 249: 955-966 (1995).

24. M Suzuki, N Yagi & M Gerstein.
"DNA-recognition and superstructure-formation by helix-turn-helix proteins."
Protein Engineering 8: 329-338 (1995).

23. R Altman, C Hughes & M Gerstein.
"Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins.”
Journal of Molecular Graphics 13: 142-152 (1995).

22. M Suzuki, S Brenner, M Gerstein & N Yagi.
"DNA recognition code of transcription factors.”
Protein Engineering 8: 319-328 (1995).

21. M Gerstein & R Altman.
"Average core structures and variability measures for protein families: Application to the immunoglobulins."
Journal of Molecular Biology 251: 161-175 (1995).

20. M Suzuki & M Gerstein.
"The geometry of alpha-helices binding to DNA."
Proteins: Structure, Function, Genetics 23: 525-535 (1995).

19. M Gerstein & R Altman.
"A Structurally Invariant Core for the Globins."
Computer Applications in the Biosciences 11: 633-644 (1995).

-- 1994 - 7 --

18. M Gerstein, E Sonnhammer & C Chothia.
"Volume Changes on Protein Evolution.”
Journal of Molecular Biology 236: 1067-1078 (1994).

17. M Gerstein.
"Purcell's early work on NMR: Contingency versus Inevitability.”
American Journal of Physics 62: 596-601 (1994).

16. M Suzuki, D Neuhaus, M Gerstein & S Aimoto.
"Solution structure of the DNA binding octapeptide repeat of the K10 gene product."
Protein Engineering 7: 461-470 (1994).

15. M Gerstein, A Lesk & C Chothia.
"Structural Mechanisms for Domain Movements."
Biochemistry 33: 6739-6749 (1994).

14. Y Harpaz, M Gerstein & C Chothia.
"Volume Changes on Protein Folding."
Structure 2: 641-649 (1994).

13. R Altman & M Gerstein.
"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, 1994).

12. M Suzuki, M Gerstein & N Yagi.
"The stereochemical basis for DNA recognition by Zn fingers."
Nucleic Acids Research 22: 3397-3405 (1994).

-- 1993 - 7 --

11. S Subramaniam, M Gerstein, D Oesterhelt & R Henderson.
"Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin."
EMBO Journal 12: 1-8 (1993).

10. M Gerstein, G Schulz & C Chothia.
"Domain Closure in Adenylate Kinase: Joints on Either Side of Two Helices Close Like Neighboring Fingers."
Journal of Molecular Biology 229: 494-501 (1993).

9. M Gerstein & R Lynden-Bell.
"Simulation of Water around a Model Protein Helix. 1. Two-dimensional Projections of Solvent Structure."
Journal of Physical Chemistry 97: 2982-2991 (1993).

8. M Gerstein & R Lynden-Bell.
"What is the natural boundary for a protein in solution?."
Journal of Molecular Biology 230: 641-650 (1993).

7. M Gerstein & R Lynden-Bell.
"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 (1993).

6. M Suzuki, M Gerstein & T Johnson.
"An NMR study of the DNA-binding 'SPKK' motif and a model for its interaction with DNA."
Protein Engineering 6: 565-574 (1993).

5. M Gerstein, A Lesk, E Baker, B Anderson, G Norris & C Chothia.
"Domain Closure in Lactoferrin: Two Hinges produce a See-saw Motion between Alternative Close-Packed Interfaces."
Journal of Molecular Biology 234: 357-372 (1993).

-- 1992 - 2 --

4. M Gerstein.
"A Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining Sites."
Acta Crystallographica A48: 271-276 (1992).

3. I De Baere, L Liu, L Moens, J Van Beeumen, C Gielens, J Richelle, C Trotman, J Finch, M Gerstein & M Perutz.
"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 (1992).

-- 1991 - 1 --

2. M Gerstein & C Chothia.
"Analysis of Protein Loop Closure: Two Types of Hinges Produce One Motion in Lactate Dehydrogenase."
Journal of Molecular Biology 220: 133-149 (1991).

-- 1987 - 1 --

1. N Fisch, A Kritz & M Gerstein.
"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, 1987).