Ian Holmes

Assistant Professor, Bioengineering Core Member, UCB/UCSF Graduate Group in Bioengineering 374C Stanley Hall mailcode: 1762 (510) 666 - 2790 fax: (866) 486 - 7316 This e-mail address is being protected from spambots. You need JavaScript enabled to view it http://biowiki.org/IanHolmes Membership effective July 2005

Research Interests

We're interested in building realistic stochastic models of all different aspects of genome evolution, and making these models useful as practical tools for biological discovery.

Research Summary

We have several areas of interest around the general theme of using bioinformatics in the investigation of genomes, their evolution and ecology.These include(1) Developing new software for genomics (from Web 2.0/AJAX genome browsers to phylogeny and molecular evolution, ');(2) Developing, analyzing and applying probabilistic models for sequence analysis (example methods include stochastic grammars or finite-state machines; example biological applications include multiple genome alignment, ncRNA gene evolution and transposon analysis, ');and (3) Developing computational methods for synthetic biology, such as ribocircuit design or metagenomics.

Selected Publications

    Holmes, I. and Bruno, W.J., Evolutionary HMMs: A Bayesian Approach to Multiple Alignment. Bioinformatics 17(9), 803-820, 2001.
    Holmes, I. and Rubin, G.M., An Expectation Maximization Algorithm for Training Hidden Substitution Models. Journal of Molecular Biology, 317(5),757-768, 2002.
    Holmes, I., Using Guide Trees to Construct Multiple-Sequence Evolutionary HMMs. Bioinformatics, 19, 147-157, 2003.
    Holmes I.  Accelerated probabilistic inference of RNA structure evolution.  BMC Bioinformatics. 2005 Mar 24;6:73.
    Klosterman PS, Uzilov AV, Bendana YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I.  XRate: a fast prototyping, training and annotation tool for phylo-grammars.  BMC Bioinformatics. 2006 Oct 3;7:428.
    Kosiol C., Holmes I. and Goldman N.  An empirical codon model for protein sequence evolution.  Mol Biol Evol. 2007 Jul;24(7):1464-79. Epub 2007 Mar 30.
    Margulies EH et al.  Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.  Genome Res. 2007 Jun;17(6):760-7.