Dennis Vitkup

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. ncbi Biological networks: from physical principles to biological insights
    Dennis Vitkup
    Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 5:313. 2004
  2. ncbi Expression dynamics of a cellular metabolic network
    Peter Kharchenko
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    Mol Syst Biol 1:2005.0016. 2005
  3. ncbi Identifying metabolic enzymes with multiple types of association evidence
    Peter Kharchenko
    Department of Genetics, New Research Building NRB Room 238, 77 Ave, Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA
    BMC Bioinformatics 7:177. 2006
  4. ncbi Filling gaps in a metabolic network using expression information
    Peter Kharchenko
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 20:i178-85. 2004
  5. ncbi Predicting genes for orphan metabolic activities using phylogenetic profiles
    Lifeng Chen
    Center for Computational Biology and Bioinformatics and Department of Biomedical Informatics, Columbia University, St Nicholas Avenue, Irving Cancer Research Center, New York, NY 10032, USA
    Genome Biol 7:R17. 2006
  6. ncbi Influence of metabolic network structure and function on enzyme evolution
    Dennis Vitkup
    Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, Russ Berrie Pavilion, St Nicholas Avenue, New York, NY 10032, USA
    Genome Biol 7:R39. 2006
  7. ncbi Distribution of orphan metabolic activities
    Lifeng Chen
    Center for Computational Biology and Bioinformatics and Department of Biomedical Informatics, Columbia University, 1130 Nicholas Ave, Irving Cancer Research Center, New York, NY 10032, USA
    Trends Biotechnol 25:343-8. 2007
  8. ncbi New surveyor tools for charting microbial metabolic maps
    Rainer Breitling
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
    Nat Rev Microbiol 6:156-61. 2008
  9. ncbi 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

Collaborators

Detail Information

Publications9

  1. ncbi Biological networks: from physical principles to biological insights
    Dennis Vitkup
    Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 5:313. 2004
  2. ncbi Expression dynamics of a cellular metabolic network
    Peter Kharchenko
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    Mol Syst Biol 1:2005.0016. 2005
    ..We show that basic topological motifs of the metabolic network exhibit statistically significant differences in coexpression behavior...
  3. ncbi Identifying metabolic enzymes with multiple types of association evidence
    Peter Kharchenko
    Department of Genetics, New Research Building NRB Room 238, 77 Ave, Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA
    BMC Bioinformatics 7:177. 2006
    ..Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes...
  4. ncbi Filling gaps in a metabolic network using expression information
    Peter Kharchenko
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 20:i178-85. 2004
    ..AVAILABILITY: Freely available (in Supplementary information)...
  5. ncbi Predicting genes for orphan metabolic activities using phylogenetic profiles
    Lifeng Chen
    Center for Computational Biology and Bioinformatics and Department of Biomedical Informatics, Columbia University, St Nicholas Avenue, Irving Cancer Research Center, New York, NY 10032, USA
    Genome Biol 7:R17. 2006
    ..We show that our method should be easily transferable to other organisms, and that it is robust to errors in incomplete metabolic networks...
  6. ncbi Influence of metabolic network structure and function on enzyme evolution
    Dennis Vitkup
    Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, Russ Berrie Pavilion, St Nicholas Avenue, New York, NY 10032, USA
    Genome Biol 7:R39. 2006
    ..The ability to consider fluxes in a metabolic network allows us to relate the functional role of each enzyme in a network to its rate of evolution...
  7. ncbi Distribution of orphan metabolic activities
    Lifeng Chen
    Center for Computational Biology and Bioinformatics and Department of Biomedical Informatics, Columbia University, 1130 Nicholas Ave, Irving Cancer Research Center, New York, NY 10032, USA
    Trends Biotechnol 25:343-8. 2007
    ..Shrinking the space of orphan activities will likely require a close collaboration between computational and experimental laboratories...
  8. ncbi New surveyor tools for charting microbial metabolic maps
    Rainer Breitling
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
    Nat Rev Microbiol 6:156-61. 2008
    ..Data integration will play a particularly important part in exploiting the new experimental opportunities...
  9. ncbi 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...