Difference between revisions of "Ian Holmes Old Page"
(Imported from TWiki)
m (Move page script moved page IanHolmesOldPage to Ian Holmes Old Page: Rename from TWiki to MediaWiki style)
Latest revision as of 23:42, 1 January 2017
Associate Professor, Computational Biology, Berkeley.
For a list of current/past members of my group and their interests, please see our lab page.
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, cis-regulatory networks 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.
Computational tools for synthetic biology are also an ongoing interest.
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:
Here are some (mostly retro) games that I've enjoyed over the years: