Francis D Gibbons

Summary

Affiliation: Harvard University
Country: USA

Publications

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

Detail Information

Publications9

  1. ncbi 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. ncbi 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. ncbi 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. ncbi 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
    ..AVAILABILITY: FuncBase as well as all underlying data and annotations are freely available via http://func.med.harvard.edu/..
  5. ncbi 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. ncbi 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 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. ncbi 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 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...