Francis D Gibbons

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization
    Francis D Gibbons
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, MA 02115, USA
    Genome Biol 6:R96. 2005
  2. pmc Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae
    Markus Proft
    Department Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Eukaryot Cell 4:1343-52. 2005
  3. pmc Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function
    Weidong Tian
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA
    Genome Biol 9:S7. 2008
  4. pmc FuncBase: a resource for quantitative gene function annotation
    John E Beaver
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 26:1806-7. 2010
  5. pmc An en masse phenotype and function prediction system for Mus musculus
    Murat Tasan
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA
    Genome Biol 9:S8. 2008
  6. pmc Predicting protein complex membership using probabilistic network reliability
    Saurabh Asthana
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:1170-5. 2004
  7. ncbi request reprint SILVER helps assign peptides to tandem mass spectra using intensity-based scoring
    Francis D Gibbons
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Am Soc Mass Spectrom 15:910-2. 2004
  8. pmc Judging the quality of gene expression-based clustering methods using gene annotation
    Francis D Gibbons
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 12:1574-81. 2002
  9. ncbi request reprint Towards a proteome-scale map of the human protein-protein interaction network
    Jean François Rual
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nature 437:1173-8. 2005

Collaborators

  • Kevin Struhl
  • Oliver D King
  • Lan V Zhang
  • Ning Li
  • Tong Hao
  • Michael E Cusick
  • David P Hill
  • Huda Y Zoghbi
  • Zeba Wunderlich
  • Niels Klitgord
  • Mike Boxem
  • Frederick P Roth
  • Murat Tasan
  • Weidong Tian
  • John E Beaver
  • Markus Proft
  • Jean François Rual
  • Saurabh Asthana
  • Timothy R Hughes
  • Judith A Blake
  • J Michael Cherry
  • Julie Park
  • Kavitha Venkatesan
  • Marc Vidal
  • Siming Li
  • Debra S Goldberg
  • Matija Dreze
  • Giovanni Franklin
  • Philippe Lamesch
  • Estelle Llamosas
  • Sebiha Cevik
  • Jean Vandenhaute
  • Sharyl L Wong
  • Jennifer Rosenberg
  • Camille Bex
  • Robert S Sikorski
  • Matthew Copeland
  • Gabriel F Berriz
  • Nono Ayivi-Guedehoussou
  • Carlene Fraughton
  • Alex Smolyar
  • Lynn Doucette-Stamm
  • Stuart Milstein
  • Joanna S Albala
  • Amelie Dricot
  • Christophe Simon
  • Reynaldo Sequerra
  • Stephanie Bosak
  • Janghoo Lim
  • Tomoko Hirozane-Kishikawa

Detail Information

Publications9

  1. pmc Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization
    Francis D Gibbons
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, MA 02115, USA
    Genome Biol 6:R96. 2005
    ..The corresponding software ('Chipper') is freely available. The method described here should help reveal an organism's transcription-regulatory 'wiring diagram'...
  2. pmc Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae
    Markus Proft
    Department Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Eukaryot Cell 4:1343-52. 2005
    ....
  3. pmc Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function
    Weidong Tian
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA
    Genome Biol 9:S7. 2008
    ....
  4. pmc FuncBase: a resource for quantitative gene function annotation
    John E Beaver
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 26:1806-7. 2010
    ..FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases...
  5. pmc An en masse phenotype and function prediction system for Mus musculus
    Murat Tasan
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA
    Genome Biol 9:S8. 2008
    ..Integration of accumulated evidence should permit researchers to form fewer - and more accurate - hypotheses for further study through experimentation...
  6. pmc Predicting protein complex membership using probabilistic network reliability
    Saurabh Asthana
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:1170-5. 2004
    ..Here we demonstrate inference of membership in a partially known protein complex by using a probabilistic network model and an algorithm previously used to evaluate reliability in communication networks...
  7. ncbi request reprint SILVER helps assign peptides to tandem mass spectra using intensity-based scoring
    Francis D Gibbons
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Am Soc Mass Spectrom 15:910-2. 2004
    ..SILVER is available online at http://llama.med.harvard.edu/Software.html...
  8. pmc Judging the quality of gene expression-based clustering methods using gene annotation
    Francis D Gibbons
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 12:1574-81. 2002
    ..We show the self-organized-map approach to be best for both measurement types at higher numbers of clusters. Clusters of genes derived from single- and average-linkage hierarchical clustering tend to produce worse-than-random results...
  9. ncbi request reprint Towards a proteome-scale map of the human protein-protein interaction network
    Jean François Rual
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nature 437:1173-8. 2005
    ..This work represents an important step towards a systematic and comprehensive human interactome project...