Ian Holmes Assistant Professor, Department of 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

Joined the UC Berkeley Faculty in 2004

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.

Education

1995     First-class BA in Physics & Theoretical Physics, University of Cambridge
1997     Honorary MA, University of Cambridge
1998     PhD in Genetics, University of Cambridge

Major Awards

Professional Experience

1999            Fulbright-Zeneca Research Fellow
1999-2002     Associate, Howard Hughes Medical Institute, Berkeley Drosophila Genome Project
2002            Researcher, ENSEMBL Human Genome Annotation Project, European Molecular Biology Laboratory, Hinxton, UK
2002-2004    Lecturer in Bioinformatics, Department of Statistics, University of Oxford
2004-present     Assistant Professor, Department of Bioengineering, University of California, Berkeley

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.