Research Topics
| Andrey RzhetskySummaryAffiliation: Columbia University Country: USA Publications
| Collaborators
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Detail Information
Publications
A recipe for high impactMurat 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...- Self-correcting maps of molecular pathwaysAndrey Rzhetsky
Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics and Joint Centers for Systems Biology, Columbia University, New York, New York, United States of America and Judith P Sulzberger MD Coumbia Genome Center and Department of Biology, Columbia University, New York, New York, United States of America
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... - Microparadigms: chains of collective reasoning in publications about molecular interactionsAndrey 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... 
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway dataAndrey 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...- Probabilistic inference of molecular networks from noisy data sourcesIvan 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... - Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction networkIvan 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.... - Emergent behavior of growing knowledge about molecular interactionsMurat Cokol
Department of Biological Sciences, Columbia University, New York, New York 10032, USA
Nat Biotechnol 23:1243-7. 2005 - Imitating manual curation of text-mined facts in biomedicineRaul 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... - Two biomedical sublanguages: a description based on the theories of Zellig HarrisCarol 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... - Novel opportunities for computational biology and sociology in drug discoveryLixia 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... - Benchmarking ontologies: bigger or better?Lixia Yao
Department of Biomedical Informatics, Columbia University, New York, New York, USA
PLoS Comput Biol 7:e1001055. 2011.... - Automatically identifying gene/protein terms in MEDLINE abstractsHong 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... - Novel opportunities for computational biology and sociology in drug discoveryLixia 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... - Six senses in the literature. The bleak sensory landscape of biomedical textsRaul Rodriguez-Esteban
Department of Electrical Engineering, Columbia University, New York, NY, USA
EMBO Rep 9:212-5. 2008 - Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's diseaseMichael 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... - Looking at cerebellar malformations through text-mined interactomes of mice and humansIvan 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... - Probing genetic overlap among complex human phenotypesAndrey 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... - The BioPAX community standard for pathway data sharingEmek 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... - Of truth and pathways: chasing bits of information through myriads of articlesMichael 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... - Quantitative systems-level determinants of human genes targeted by successful drugsLixia 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... - Network properties of genes harboring inherited disease mutationsIgor 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... - Listening to viral tongues: comparing viral trees using a stochastic context-free grammarAndrey 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... - Seeking a new biology through text miningAndrey 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... - Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse usersHagit Shatkay
The Computational Biology and Machine Learning Lab, School of Computing, Queen s University, Kingston, Ontario, Canada
Bioinformatics 24:2086-93. 2008..The latter strongly suggest that automatic annotation along most of the dimensions is highly feasible, and that this new framework for scientific sentence categorization is applicable in practice... - Learning to predict protein-protein interactions from protein sequencesShawn 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... - New directions in biomedical text annotation: definitions, guidelines and corpus constructionW 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... - Immunity-related genes and gene families in Anopheles gambiaeGeorge 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...