Associate Professor, Computational Biology, Berkeley.
- Lab address: 381 Stanley Hall, UC Berkeley, CA 94720-3220
- Lab phone: (510) 666 - 2791
I am on the faculty of the Departments of Bioengineering
and Electrical Engineering & Computer Science at UC Berkeley
and the Physical Biosciences Division at Lawrence Berkeley Laboratory.
For a list of current/past members of my group and their interests, please see our lab page.
- Using computers to investigate genomes, their evolution and ecology.
- Developing the statistical bioinformatics tools for this, e.g.
- Developing "Web 2.0" genomics infrastructure, e.g. AJAX genome wikis.
- Synthetic biology, especially RNA engineering and paleo-genetics.
Computational biology needs realistic, predictive, quantitative models of the how biological sequences --- and systems --- evolve.
My lab develops & applies stochastic process models
(e.g. discrete-state continuous-time Markov chains)
for the study of molecular evolution.
The dynamics we have modeled include substitutions, insertions and deletions ("indels"), microsatellite dynamics, local duplications, inversions, transpositions, recombinations and rearrangements.
Systems we might consider include sequences, gene families,
and chemical signaling pathways.
Ancestral sequence reconstruction
One interest is in paleogenomics: using molecular evolutionary models to make inferences about the origins of life by working backwards from present-era DNA sequences,
with the goal of reconstructing those origins in the laboratory synthetically.
Other applications of the models include
genefinding, SNP analysis, simulations, and design of combinatorial libraries.
A related interest is "genome ecology": the (evolutionary) interactions of genomes with their neighbors.
Examples include the bioinformatics of transposon classification, virus phylogenetics & recombination, or the metagenomics of microbial communities.
Understanding and re-engineering genomes (and metagenomes) will require a robust set of computational tools.
We work on infrastructural components and technologies for genome annotation, such as the Gene Ontology or our genome wiki tools.
Computational tools for synthetic biology are also an ongoing interest.
For more info see the front page, the Holmes lab page or the paper archive.
I grew up in Cambridge (UK) and studied physics at the Cavendish Laboratory (TCM group) and genomics at the Sanger Institute (Informatics).
I now work at UC Berkeley and live in East Oakland.
My current NIH biosketch can be found here (MS Word doc)
A list of my published papers is here
I have written several computer games:
- Zoo Gas (2009) is a cheap and cheerful cellular automaton experiment. Not so much a game, as a very early-stage prototype for a game, experimenting with taking the components of simulations in molecular ecology and polymer physics, and trying to turn them into objects in a virtual world.
- Pipeline (1989), co-written with William Reeve, was published by Superior Software for the BBC Micro. It rates a mention on the Wikipedia page for Jupiter's moons in fiction. 8-) Here it is on YouTube. Essentially it was a fast four-way scrolling arcade/puzzle/RPG with a level designer. There's a review here, with a download you can run on an emulator. A PC version, Pipeline Plus, is available from Superior Interactive. In development it was called GuildMaster and I imagined it as a sort of medieval/fantasy guild progression thing, with alternate professions you could follow. My contributions to the code included the non-graphics components: puzzle logic, level designer, etc.
Here are some (mostly retro) games that I've enjoyed over the years:
- Exile: Newtonian physics, implacable robots, synthetic biology, jetpacks, wind, fire, water, grenades, monkeys, mutant maggots, slime molds, bees, fish, an evil genius living in an asteroid... all in 32,768 bytes
- Core Wars because programming should be Darwinian
- Not a game I played. But I just love games that are Turing-complete. The Game of Life unit cell is wonderful too
- Elite, The Sentinel and Cholo: atmospheric early 3D. I was the right age to play these
- The first two use procedural generation (as does Exile). Cholo has an intriguing post-apocalyptic thriller plot
- Interactive poetry and fiction.
- UniWar - an iPhone multiplayer turn-based strategy game. Board games in your pocket...