Ontology Modeling Lab Meeting

Probabilistic Models on Bioinformatics Ontologies

Date/time/place: 5/2/2007, noon, 425 HMMB. See Lab Meeting.

Bayesian networks (graphical models) and related methods for modeling and predicting relationships in structured ontologies, particularly the Gene Ontology.

One goal of this study could be the development of models for predicting GO terms associated with metagenomics samples.

Main assignments (15 minutes each)

Models for ontology associations...

• Troyanskaya, Barutcuoglu et al (Barbara)
  • Barutcuoglu et al.: Hierarchical multi-label prediction of gene function. Bioinformatics 2006;22:830-6.

• Fritz Roth et al (Avinash)
  • King et al.: Predicting phenotype from patterns of annotation. Bioinformatics 2003;19 Suppl 1:i183-9.
  • King et al.: Predicting gene function from patterns of annotation. Genome Res. 2003;13:896-904.

• Carroll et al (Rob)
  • Carroll & Pavlovic: Protein classification using probabilistic chain graphs and the Gene Ontology structure. Bioinformatics 2006;22:1871-8.

Evolution

• Jordan, Engelhardt, Brenner: Sifter (Barbara)
  • Engelhardt et al.: Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput. Biol. 2005;1:e45.

Re-engineering the Gene Ontology using information content

• Gil Alterovitz et al (Berkeley Bop (Chris, Suzi, etc.) and Ian)
  • http://gocwiki.geneontology.org/index.php/Collaboration_with_MIT_GO-Engineering (requires registration/login)

Ideas for followup meetings

Protein-protein interactions

• Lee et al.: An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics 2006;7:269.
• Lin et al.: Information assessment on predicting protein-protein interactions. BMC Bioinformatics 2004;5:154.

• (and maybe...?) Joshi et al.: Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. OMICS 2004;8:322-33.

NLP and literature mining

• Jordan, Mian et al
  • Blei et al.: Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span. BMC Bioinformatics 2006;7:250.

• Zheng et al
  • Zheng et al.: Identifying biological concepts from a protein-related corpus with a probabilistic topic model. BMC Bioinformatics 2006;7:58.

-- Ian Holmes - 20 Jan 2007