Gerstein Lab Publications

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Sixty years of genome biology.
WF Doolittle, P Fraser, MB Gerstein, BR Graveley, S Henikoff, C Huttenhower, A Oshlack, CP Ponting, JL Rinn, MC Schatz, J Ule, D Weigel, GM Weinstock (2013). Genome Biol 14: 113.
 
 
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Genomics: ENCODE leads the way on big data.
M Gerstein (2012). Nature 489: 208.
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The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare.
M Vidal, DW Chan, M Gerstein, M Mann, GS Omenn, D Tagle, S Sechi, Workshop Participants (2012). Clin Proteomics 9: 6.
 
 
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The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions.
MJ Bamshad, JA Shendure, D Valle, A Hamosh, JR Lupski, RA Gibbs, E Boerwinkle, RP Lifton, M Gerstein, M Gunel, S Mane, DA Nickerson, Centers for Mendelian Genomics (2012). Am J Med Genet A 158A: 1523-5.
 
 
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Closure of the NCBI SRA and implications for the long-term future of genomics data storage.
D Lipman, P Flicek, S Salzberg, M Gerstein, R Knight (2011). Genome Biol 12: 402.
 
 
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The role of cloud computing in managing the deluge of potentially private genetic data.
D Greenbaum, M Gerstein (2011). Am J Bioeth 11: 39-41.
 
 
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Social considerations in research: consider them but don't use them.
D Greenbaum, M Gerstein (2011). Am J Bioeth 11: 31-2.
 
 
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A user's guide to the encyclopedia of DNA elements (ENCODE).
The ENCODE Project Consortium (2011). PLoS Biol 9: e1001046.
 
 
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Tiling array data analysis: a multiscale approach using wavelets.
A Karpikov, J Rozowsky, M Gerstein (2011). BMC Bioinformatics 12: 57.
 
 
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Reproducible Research: Addressing the need for data and code sharing in computational science
Yale Law School Roundtable on Data and Code Sharing (2010). Computing in Science & Engineering 12(5): 8-13 (Sept/Oct).
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Science and the Law: Grappling with the Gulf
D Greenbaum, MB Gerstein (2009). Science 323: 210.
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Social networking and personal genomics: suggestions for optimizing the interaction.
D Greenbaum, M Gerstein (2009). Am J Bioeth 9: 15-9.
 
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An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping.
R Sasidharan, A Agarwal, J Rozowsky, M Gerstein (2009). BMC Res Notes 2: 150.
 
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Unlocking the secrets of the genome.
SE Celniker, LA Dillon, MB Gerstein, KC Gunsalus, S Henikoff, GH Karpen, M Kellis, EC Lai, JD Lieb, DM MacAlpine, G Micklem, F Piano, M Snyder, L Stein, KP White, RH Waterston, modENCODE Consortium (2009). Nature 459: 927-30.
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Integrated assessment of genomic correlates of protein evolutionary rate.
Y Xia, EA Franzosa, MB Gerstein (2009). PLoS Comput Biol 5: e1000413.
 
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Genomic anonymity: have we already lost it?
D Greenbaum, J Du, M Gerstein (2008). Am J Bioeth 8: 71-4.
 
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Seeking a new biology through text mining.
A Rzhetsky, M Seringhaus, M Gerstein (2008). Cell 134: 9-13.
 
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Open access: taking full advantage of the content.
PE Bourne, JL Fink, M Gerstein (2008). PLoS Comput Biol 4: e1000037.
 
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Manually structured digital abstracts: a scaffold for automatic text mining.
M Seringhaus, M Gerstein (2008). FEBS Lett 582: 1170.
 
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Uncovering trends in gene naming.
MR Seringhaus, PD Cayting, MB Gerstein (2008). Genome Biol 9: 401.
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Semantic Web Approach to Database Integration in the Life Sciences
KH Cheung, AK Smith, KYL Yip, CJO Baker, MB Gerstein (2007). in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 11-30
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Semantic Web Standards: Legal and Social Issues and Implications
D Greenbaum, M Gerstein (2007). in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), pp. 413-433
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Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
A Smith, K Cheung, M Krauthammer, M Schultz, M Gerstein (2007). Bioinformatics 23: 3073-9.
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Structured digital abstract makes text mining easy.
M Gerstein, M Seringhaus, S Fields (2007). Nature 447: 142.
 
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RNAi development.
M Gerstein, SM Douglas (2007). PLoS Comput Biol 3: e80.
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Chemistry Nobel rich in structure.
M Seringhaus, M Gerstein (2007). Science 315: 40-1.
 
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The Death of the Scientific Paper
Seringhaus M, Gerstein M (2006). The Scientist. 20(9): 25
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Data mining on the web.
A Smith, M Gerstein (2006). Science 314: 1682; author reply 1682.
 
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The real life of pseudogenes.
M Gerstein, D Zheng (2006). Sci Am 295: 48-55.
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Tools needed to navigate landscape of the genome.
M Gerstein (2006). Nature 440: 740.
 
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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)
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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.
 
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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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Impediments to database interoperation: legal issues and security concerns.
D Greenbaum, A Smith, M Gerstein (2005). Nucleic Acids Res 33: D3-4.
 
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A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.
N Carriero, MV Osier, KH Cheung, PL Miller, M Gerstein, H Zhao, B Wu, S Rifkin, J Chang, H Zhang, K White, K Williams, M Schultz (2005). J Am Med Inform Assoc 12: 90-8.
 
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An analysis of the present system of scientific publishing: what's wrong and where to go from here
D Greenbaum, J Lim, M Gerstein (2003). Interdiscip Sci Rev 28:293-302
 
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Reconstructing genetic networks in yeast.
Z Zhang, M Gerstein (2003). Nat Biotechnol 21: 1295-7.
 
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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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Sequences and topology.
M Gerstein, JM Thornton (2003). Curr Opin Struct Biol 13: 341-3.
 
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Structural genomics: current progress.
M Gerstein, A Edwards, CH Arrowsmith, GT Montelione (2003). Science 299: 1663.
 
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Blurring the boundaries between scientific 'papers' and biological databases
M Gerstein, J Junker (2002). Nature Yearbook of Science and Technology 210-212 (ed. D Butler, Palgrave Macmillan Publishers)
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Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
D Greenbaum, NM Luscombe, R Jansen, J Qian, M Gerstein (2001). Genome Res 11: 1463-8.
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Protein Geometry: Distances, Areas, and Volumes
M Gerstein, F M Richards (2001). International Tables for Crystallography (Volume F, Chapter 22.1.1, pages 531-539; M Rossmann & E Arnold, editors; Dordrecht: Kluwer)
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A Bauhaus for Biologists: An Introduction to Protein Architecture by A. M. Lesk
P Harrison, M Gerstein (2001). Trends Biochem Sci 26:204-205
 
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Sequences and Topology
M Gerstein, B Honig (2001). Current Opinion in Structural Biology 11: 327-329.
 
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What is Bioinformatics? A Proposed Definition and Overview of the Field
N Luscombe, D Greenbaum, M Gerstein (2001). Intl. Medical Informatics Association (Yearbook, Pages 83-99)
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Annotation of the human genome.
M Gerstein (2000). Science 288: 1590.
 
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E-biomed and clinical research.
ES Brodkin, M Gerstein (1999). N Engl J Med 341: 1080; author reply 1081.
 
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Building the future of biocomputing.
M Gerstein (1999). Nature 399: 101.
 
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Forging links in an electronic paper chain.
M Gerstein (1999). Nature 398: 20.
 
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Simulating water and the molecules of life.
M Gerstein, M Levitt (1998). Sci Am 279: 100-5.
 
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Protein evolution. How far can sequences diverge?
C Chothia, M Gerstein (1997). Nature 385: 579, 581.
 
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Practicing Cyberlaw in the Year 2000.
R Becker, M Gerstein (1996). New Jersey Lawyer Magazine 179: 12-27 (September).
 
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Keeping the Shape but Changing the Charges: A Simulation Study of Urea and its Isosteric Analogues
J Tsai, M Gerstein, M Levitt (1996). Journal of Chemical Physics 104: 9417-9430
 
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Packing at the protein-water interface.
M Gerstein, C Chothia (1996). Proc Natl Acad Sci U S A 93: 10167-72.
 
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Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures.
M Gerstein, M Levitt (1996). Proc Int Conf Intell Syst Mol Biol 4: 59-67.
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Using a measure of structural variation to define a core for the globins.
M Gerstein, RB Altman (1995). Comput Appl Biosci 11: 633-44.
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Binding geometry of alpha-helices that recognize DNA.
M Suzuki, M Gerstein (1995). Proteins 23: 525-35.
 
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Average core structures and variability measures for protein families: application to the immunoglobulins.
M Gerstein, RB Altman (1995). J Mol Biol 251: 161-75.
 
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The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra.
M Gerstein, J Tsai, M Levitt (1995). J Mol Biol 249: 955-66.
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Methods for displaying macromolecular structural uncertainty: application to the globins.
RB Altman, C Hughes, MB Gerstein (1995). J Mol Graph 13: 142-52, 109-2.
 
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DNA recognition and superstructure formation by helix-turn-helix proteins.
M Suzuki, N Yagi, M Gerstein (1995). Protein Eng 8: 329-38.
 
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Purcell's early work on NMR: Contingency versus Inevitability
M Gerstein (1994). American Journal of Physics 62: 596-601
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Stereochemical basis of DNA recognition by Zn fingers.
M Suzuki, M Gerstein, N Yagi (1994). Nucleic Acids Res 22: 3397-405.
 
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Volume changes on protein folding.
Y Harpaz, M Gerstein, C Chothia (1994). Structure 2: 641-9.
 
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Solution structure of the DNA binding octapeptide repeat of the K10 gene product.
M Suzuki, D Neuhaus, M Gerstein, S Aimoto (1994). Protein Eng 7: 461-70.
 
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Volume changes in protein evolution.
M Gerstein, EL Sonnhammer, C Chothia (1994). J Mol Biol 236: 1067-78.
 
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Finding an average core structure: application to the globins.
RB Altman, M Gerstein (1994). Proc Int Conf Intell Syst Mol Biol 2: 19-27.
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Simulation of Water around a Model Protein Helix. 1. Two-dimensional Projections of Solvent Structure.
M Gerstein, R Lynden-Bell (1993). Journal of Physical Chemistry 97: 2982-2991.
 
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Simulation of Water around a Model Protein Helix. 2. The Relative Contributions of Packing, Hydrophobicity, and Hydrogen Bonding.
M Gerstein, R Lynden-Bell (1993). Journal of Physical Chemistry 97: 2991-2999.
 
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Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces.
M Gerstein, BF Anderson, GE Norris, EN Baker, AM Lesk, C Chothia (1993). J Mol Biol 234: 357-72.
 
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An NMR study on the DNA-binding SPKK motif and a model for its interaction with DNA.
M Suzuki, M Gerstein, T Johnson (1993). Protein Eng 6: 565-74.
 
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What is the natural boundary of a protein in solution?
M Gerstein, RM Lynden-Bell (1993). J Mol Biol 230: 641-50.
 
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Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers.
M Gerstein, G Schulz, C Chothia (1993). J Mol Biol 229: 494-501.
 
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Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin.
S Subramaniam, M Gerstein, D Oesterhelt, R Henderson (1993). EMBO J 12: 1-8.
 
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A Resolution-Sensitive Procedure for Comparing Protein Surfaces and its Application to the Comparison of Antigen-Combining Sites.
M Gerstein (1992). Acta Crystallographica A48: 271-276.
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Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum: amino acid sequence and structural interpretation.
I De Baere, L Liu, L Moens, J Van Beeumen, C Gielens, J Richelle, C Trotman, J Finch, M Gerstein, M Perutz (1992). Proc Natl Acad Sci U S A 89: 4638-42.
 
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Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase.
M Gerstein, C Chothia (1991). J Mol Biol 220: 133-49.
 
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Inverse Problem for Synchrotron Radiation in the Presence of Noise
N Fisch, A Kritz, M Gerstein (1987). 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).
 
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