Ian Holmes

faculty photo

Associate Professor, Bioengineering

374C Stanley Hall
Mailcode 1762

For more information, see: http://biowiki.org/IanHolmes

Research Interests

The Holmes Lab brings techniques from machine learning, statistical linguistics, phylogenetics, and web development to bear on the interpretation and analysis of genomic data. Examples include the application of context-free grammars to understanding DNA and RNA structure; the use of phylogenetic methods in genome annotation, and to detect recombination breakpoints; the development of machine learning algorithms for bioinformatics models; the reconstruction of insertion, deletion and transposition events in genome evolutionary histories; statistical algorithms for metagenomics species distribution analysis; and dynamic-HTML web applications for collaborative genomic data analysis.


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

Major Awards

  • 1998 Fulbright-Zeneca Research Fellowship

Professional Experience

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