I am Ian Holmes. In May 2002 I moved from Berkeley to the University of Oxford, UK, to take up a position as a lecturer in Bioinformatics in the Department of Statistics. My new group homepage is here.

This page is preserved, since I am still actively collaborating with the Drosophila genome project, creating software and algorithms for the identification of regulatory elements from analysis of sequence, expression and GO annotation data. I return to Berkeley frequently and am interested in forming international collaborations with scientists in industry and academia.


From December 1999 to January 2002, I worked as a bioinformatics scientist for the Berkeley Drosophila Genome Project on DNA, RNA and protein sequence and expression analysis informatics, funded by the Howard Hughes Medical Institute. During 1999 I held a Fulbright research fellowship and worked with Bill Bruno of group T10, Los Alamos National Laboratory. Before that, I wrote a PhD on probabilistic modeling and C.elegans evolution at the Sanger Centre.


kimono is an integrated likelihood sampler for clustering sequence and expression data

Handel is a package for doing multiple sequence alignment using the single-residue indel process of Thorne, Kishino & Felsenstein