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Mark Gerstein: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Kei-Hoi Cheung, Yang Liu, Anuj Kumar, Michael Snyder, Mark Gerstein, Perry L. Miller
    An XML Application For Genomic Data Interoperation. [Citation Graph (0, 0)][DBLP]
    BIBE, 2001, pp:97-103 [Conf]
  2. Mark Gerstein
    Computational Proteomics: Genome-scale Analysis of Protein Structure, Function, & Evolution(Invited Talk). [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2003, pp:53- [Conf]
  3. Mark Gerstein
    [Invited Lecture] A Structural Census of Genomes: Comparing Bacterial, Eukaryotic, and Archaea Genomes in Terms of Protein Structure. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 1998, pp:- [Conf]
  4. Russ B. Altman, Mark Gerstein
    Finding an Average Core Structure: Application to the Globins. [Citation Graph (0, 0)][DBLP]
    ISMB, 1994, pp:19-27 [Conf]
  5. Kei-Hoi Cheung, Kevin Y. Yip, Andrew Smith, Remko de Knikker, Andy Masiar, Mark Gerstein
    YeastHub: a semantic web use case for integrating data in the life sciences domain. [Citation Graph (0, 0)][DBLP]
    ISMB (Supplement of Bioinformatics), 2005, pp:85-96 [Conf]
  6. Mark Gerstein, Michael Levitt
    Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures. [Citation Graph (0, 0)][DBLP]
    ISMB, 1996, pp:59-67 [Conf]
  7. Kei-Hoi Cheung, Deyun Pan, Andrew Smith, Michael Seringhaus, Shawn M. Douglas, Mark Gerstein
    A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data. [Citation Graph (0, 0)][DBLP]
    METMBS, 2004, pp:236-242 [Conf]
  8. Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder
    Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. [Citation Graph (0, 0)][DBLP]
    WABI, 2002, pp:419-433 [Conf]
  9. Joel S. Rozowsky, Paul Bertone, Thomas E. Royce, Sherman Weissman, Michael Snyder, Mark Gerstein
    Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites. [Citation Graph (0, 0)][DBLP]
    BSB, 2005, pp:28-29 [Conf]
  10. Mark Gerstein
    Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1998, v:14, n:8, pp:707-714 [Journal]
  11. Mark Gerstein, Russ B. Altman
    Using a measure of structural variation to define a core for the globins. [Citation Graph (0, 0)][DBLP]
    Computer Applications in the Biosciences, 1995, v:11, n:6, pp:633-644 [Journal]
  12. Dov Greenbaum, Ronald Jansen, Mark Gerstein
    Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2002, v:18, n:4, pp:585-596 [Journal]
  13. Jiang Qian, Jimmy Lin, Nicholas M. Luscombe, Haiyuan Yu, Mark Gerstein
    Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:15, pp:1917-1926 [Journal]
  14. Jerry Tsai, Mark Gerstein
    Calculations of protein volumes: sensitivity analysis and parameter database. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2002, v:18, n:7, pp:985-995 [Journal]
  15. Jerry Tsai, Neil Voss, Mark Gerstein
    Determining the minimum number of types necessary to represent the sizes of protein atoms. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2001, v:17, n:10, pp:949-956 [Journal]
  16. Anne E. Counterman Burba, Ursula Lehnert, Eric Z. Yu, Mark Gerstein
    Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:22, pp:2735-2738 [Journal]
  17. Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein
    Predicting interactions in protein networks by completing defective cliques. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:7, pp:823-829 [Journal]
  18. Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John Karro, Paul M. Harrison, Mark Gerstein
    PseudoPipe: an automated pseudogene identification pipeline. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:12, pp:1437-1439 [Journal]
  19. Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein
    The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:23, pp:2968-2970 [Journal]
  20. Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, Martin H. Schultz, Michael Snyder, Mark Gerstein
    A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:24, pp:3016-3024 [Journal]
  21. Vadim Alexandrov, Mark Gerstein
    Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2004, v:5, n:, pp:2- [Journal]
  22. Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao
    Information assessment on predicting protein-protein interactions. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2004, v:5, n:, pp:154- [Journal]
  23. Mark Gerstein, Dov Greenbaum, Kei Cheung, Perry L. Miller
    An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective. [Citation Graph (0, 0)][DBLP]
    Journal of Biomedical Informatics, 2007, v:40, n:1, pp:73-79 [Journal]
  24. Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder
    Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2004, v:11, n:4, pp:766-785 [Journal]
  25. Paul Bertone, Yuval Kluger, Ning Lan, Deyou Zheng, Dinesh Christendat, Adelinda Yee, Aled M. Edwards, Cheryl H. Arrowsmith, Gaetano T. Montelione, Mark Gerstein
    SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2001, v:29, n:13, pp:2884-2898 [Journal]
  26. Nathaniel Echols, Duncan Milburn, Mark Gerstein
    MolMovDB: analysis and visualization of conformational change and structural flexibility. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2003, v:31, n:1, pp:478-482 [Journal]
  27. Nicholas M. Luscombe, Thomas E. Royce, Paul Bertone, Nathaniel Echols, Christine E. Horak, Joseph T. Chang, Michael Snyder, Mark Gerstein
    ExpressYourself: a modular platform for processing and visualizing microarray data [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2003, v:31, n:13, pp:3477-3482 [Journal]
  28. Dov Greenbaum, Andrew Smith, Mark Gerstein
    Editorial. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:3-4 [Journal]
  29. Samuel Flores, Nathaniel Echols, Duncan Milburn, Brandon Hespenheide, Kevin Keating, Jason Lu, Stephen Wells, Eric Z. Yu, Michael Thorpe, Mark Gerstein
    The Database of Macromolecular Motions: new features added at the decade mark. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2006, v:34, n:Database-Issue, pp:296-301 [Journal]
  30. John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul M. Harrison, Mark Gerstein
    Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2007, v:35, n:Database-Issue, pp:55-60 [Journal]
  31. Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein
    The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2007, v:23, n:8, pp:1048- [Journal]
  32. Thomas E. Royce, Joel S. Rozowsky, Mark Gerstein
    Assessing the need for sequence-based normalization in tiling microarray experiments. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2007, v:23, n:8, pp:988-997 [Journal]

  33. Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. [Citation Graph (, )][DBLP]


  34. Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. [Citation Graph (, )][DBLP]


  35. An integrated system for studying residue coevolution in proteins. [Citation Graph (, )][DBLP]


  36. Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. [Citation Graph (, )][DBLP]


  37. Using semantic web rules to reason on an ontology of pseudogenes. [Citation Graph (, )][DBLP]


  38. PARE: A tool for comparing protein abundance and mRNA expression data. [Citation Graph (, )][DBLP]


  39. FlexOracle: predicting flexible hinges by identification of stable domains. [Citation Graph (, )][DBLP]


  40. Hinge Atlas: relating protein sequence to sites of structural flexibility. [Citation Graph (, )][DBLP]


  41. LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. [Citation Graph (, )][DBLP]


  42. Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. [Citation Graph (, )][DBLP]


  43. Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. [Citation Graph (, )][DBLP]


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