Andrey Rzhetsky

Summary

Affiliation: Columbia University
Country: USA

Publications

  1. pmc A recipe for high impact
    Murat Cokol
    Genome Biol 8:406. 2007
  2. pmc Self-correcting maps of molecular pathways
    Andrey Rzhetsky
    Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics and Joint Centers for Systems Biology, Columbia University, New York, New York, USA
    PLoS ONE 1:e61. 2006
  3. pmc Microparadigms: chains of collective reasoning in publications about molecular interactions
    Andrey Rzhetsky
    Department of Biomedical Informatics, Columbia Genome Center, Columbia University, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 103:4940-5. 2006
  4. ncbi request reprint GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data
    Andrey Rzhetsky
    Columbia Genome Center, Columbia University, New York, NY 10032, USA
    J Biomed Inform 37:43-53. 2004
  5. ncbi request reprint Probabilistic inference of molecular networks from noisy data sources
    Ivan Iossifov
    Department of Medical Informatics, Columbia University, New York, NY 10032, USA
    Bioinformatics 20:1205-13. 2004
  6. pmc Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
    Ivan Iossifov
    Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA
    Genome Res 18:1150-62. 2008
  7. ncbi request reprint Emergent behavior of growing knowledge about molecular interactions
    Murat Cokol
    Department of Biological Sciences, Columbia University, New York, New York 10032, USA
    Nat Biotechnol 23:1243-7. 2005
  8. pmc Imitating manual curation of text-mined facts in biomedicine
    Raul Rodriguez-Esteban
    Department of Electrical Engineering, Columbia University, New York, New York, United States of America
    PLoS Comput Biol 2:e118. 2006
  9. pmc Novel opportunities for computational biology and sociology in drug discovery
    Lixia Yao
    Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
    Trends Biotechnol 28:161-70. 2010
  10. ncbi request reprint Two biomedical sublanguages: a description based on the theories of Zellig Harris
    Carol Friedman
    Department of Medical Informatics, Columbia University, VC5, Vanderbilt Building, 622 West 168th Street, New York, NY 10032 3720, USA
    J Biomed Inform 35:222-35. 2002

Collaborators

Detail Information

Publications27

  1. pmc A recipe for high impact
    Murat Cokol
    Genome Biol 8:406. 2007
    ..Our analysis highlights common statistical features of high-impact articles; we also show how information flows among various publication types...
  2. pmc Self-correcting maps of molecular pathways
    Andrey Rzhetsky
    Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics and Joint Centers for Systems Biology, Columbia University, New York, New York, USA
    PLoS ONE 1:e61. 2006
    ..Our approach can be directly applied to an array of diverse problems including those encountered in molecular biology, ecology, economics, politics, and sociology...
  3. pmc Microparadigms: chains of collective reasoning in publications about molecular interactions
    Andrey Rzhetsky
    Department of Biomedical Informatics, Columbia Genome Center, Columbia University, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 103:4940-5. 2006
    ..Our computations deem highly unlikely any milder intermediate explanation between these two extremes...
  4. ncbi request reprint GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data
    Andrey Rzhetsky
    Columbia Genome Center, Columbia University, New York, NY 10032, USA
    J Biomed Inform 37:43-53. 2004
    ..GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information...
  5. ncbi request reprint Probabilistic inference of molecular networks from noisy data sources
    Ivan Iossifov
    Department of Medical Informatics, Columbia University, New York, NY 10032, USA
    Bioinformatics 20:1205-13. 2004
    ..We further explore the prediction limits, given experimental data that cover only part of the underlying protein networks. This approach can be extended naturally to include other types of biological data sources...
  6. pmc Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network
    Ivan Iossifov
    Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA
    Genome Res 18:1150-62. 2008
    ....
  7. ncbi request reprint Emergent behavior of growing knowledge about molecular interactions
    Murat Cokol
    Department of Biological Sciences, Columbia University, New York, New York 10032, USA
    Nat Biotechnol 23:1243-7. 2005
  8. pmc Imitating manual curation of text-mined facts in biomedicine
    Raul Rodriguez-Esteban
    Department of Electrical Engineering, Columbia University, New York, New York, United States of America
    PLoS Comput Biol 2:e118. 2006
    ..We illustrated our analysis by visualizing the predicted accuracy of the text-mined relations involving the term cocaine...
  9. pmc Novel opportunities for computational biology and sociology in drug discovery
    Lixia Yao
    Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
    Trends Biotechnol 28:161-70. 2010
    ..Attention to these opportunities could promise punctuated advance and will complement the well-established computational work on which drug discovery currently relies...
  10. ncbi request reprint Two biomedical sublanguages: a description based on the theories of Zellig Harris
    Carol Friedman
    Department of Medical Informatics, Columbia University, VC5, Vanderbilt Building, 622 West 168th Street, New York, NY 10032 3720, USA
    J Biomed Inform 35:222-35. 2002
    ..The two domains and their associated sublanguages discussed are: the clinical domain, where the text consists of patient reports, and the biomolecular domain, where the text consists of complete journal articles...
  11. pmc Novel opportunities for computational biology and sociology in drug discovery
    Lixia Yao
    Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
    Trends Biotechnol 27:531-40. 2009
    ..Attention to these opportunities could promise punctuated advance and will complement the well-established computational work on which drug discovery currently relies...
  12. pmc Six senses in the literature. The bleak sensory landscape of biomedical texts
    Raul Rodriguez-Esteban
    Department of Electrical Engineering, Columbia University, New York, NY, USA
    EMBO Rep 9:212-5. 2008
  13. pmc Benchmarking ontologies: bigger or better?
    Lixia Yao
    Department of Biomedical Informatics, Columbia University, New York, New York, USA
    PLoS Comput Biol 7:e1001055. 2011
    ....
  14. ncbi request reprint Automatically identifying gene/protein terms in MEDLINE abstracts
    Hong Yu
    Department of Computer Science, Columbia University, 1214 Amsterdam Avenue, New York, NY 10027, USA
    J Biomed Inform 35:322-30. 2002
    ..We found that many of the pairs in our knowledge source do not appear in the current GenBank database. Therefore our methods may also be used for automatic lexicon generation...
  15. pmc Probing genetic overlap among complex human phenotypes
    Andrey Rzhetsky
    Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics and Joint Centers for Systems Biology, Columbia University, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 104:11694-9. 2007
    ..Our disease network hypothesis can be immediately exploited in the design of genetic mapping approaches that involve joint linkage or association analyses of multiple seemingly disparate phenotypes...
  16. pmc Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease
    Michael Krauthammer
    Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 101:15148-53. 2004
    ..We propose that this strategy will provide a valuable means to bridge genetic and genomic knowledge in the search for genetic determinants of multifactorial disorders...
  17. pmc Looking at cerebellar malformations through text-mined interactomes of mice and humans
    Ivan Iossifov
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
    PLoS Comput Biol 5:e1000559. 2009
    ..Further, we observed that cerebellar malformation phenotypes tend to be associated with highly connected genes. This tendency was stronger for developmental phenotypes and weaker for cerebellar degeneration...
  18. pmc The BioPAX community standard for pathway data sharing
    Emek Demir
    Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    Nat Biotechnol 28:935-42. 2010
    ..This large amount of pathway data in a computable form will support visualization, analysis and biological discovery...
  19. ncbi request reprint Of truth and pathways: chasing bits of information through myriads of articles
    Michael Krauthammer
    Department of Medical Informatics, Columbia University, New York, NY 10032, USA
    Bioinformatics 18:S249-57. 2002
    ..We hope that in the future such a model can be useful for automatically producing consensus views of molecular interaction data...
  20. pmc Quantitative systems-level determinants of human genes targeted by successful drugs
    Lixia Yao
    Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA
    Genome Res 18:206-13. 2008
    ..Our study provides quantitative guidelines that could aid in the computational screening of new drug targets in human cells...
  21. pmc Network properties of genes harboring inherited disease mutations
    Igor Feldman
    Department of Biomedical Informatics, Center of Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 105:4323-8. 2008
    ..These clusters are likely to represent disorder-specific functional modules and suggest a framework for identifying yet-undiscovered disease genes...
  22. ncbi request reprint Listening to viral tongues: comparing viral trees using a stochastic context-free grammar
    Andrey Rzhetsky
    Department of Biomedical Informatics, Columbia Genome Center, Columbia University, New York, USA
    Mol Biol Evol 22:905-13. 2005
    ..The proposed methodology is applicable to a broad class of problems that require comparison of the topological properties of various dendrograms...
  23. pmc Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users
    Hagit Shatkay
    The Computational Biology and Machine Learning Lab, School of Computing, Queen s University, Kingston, Ontario, Canada
    Bioinformatics 24:2086-93. 2008
    ....
  24. pmc Seeking a new biology through text mining
    Andrey Rzhetsky
    University of Chicago, Chicago, IL 60637, USA
    Cell 134:9-13. 2008
    ..Hence, there is much interest in text mining, the use of computational tools to enhance the human ability to parse and understand complex text...
  25. ncbi request reprint Learning to predict protein-protein interactions from protein sequences
    Shawn M Gomez
    Unité de Biochimie et Biologie Moléculaire des Insectes, Institut Pasteur, 75724 Paris Cedex 15, France
    Bioinformatics 19:1875-81. 2003
    ..The model is efficient to compute and scales well to very large collections of data. In a cross-validated comparison using known yeast interactions, the attraction-repulsion method performs better than several competing techniques...
  26. pmc New directions in biomedical text annotation: definitions, guidelines and corpus construction
    W John Wilbur
    National Center for Biotechnology Information NLM, NIH, Bethesda, MD, USA
    BMC Bioinformatics 7:356. 2006
    ..Our ultimate goal is to annotate a significant corpus of biomedical text and train machine learning methods to automatically categorize such text along certain dimensions that we have defined...
  27. ncbi request reprint Immunity-related genes and gene families in Anopheles gambiae
    George K Christophides
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Science 298:159-65. 2002
    ..Representative expression profiles confirm that sequence diversification is accompanied by specific responses to different immune challenges. Alternative RNA splicing may also contribute to expansion of the immune repertoire...