Ian Holmes

I'm an assistant professor of ComputationalBiology? (which, in my case, includes lots of BioInformatics) at the Department of Bioengineering, CalBerkeley. A description of our group's research interests can be found http://biowiki.org/ResearchTopics

I've written several free programs for doing evolutionary genomics, including one called "xrate" that uses a very fast EM (ExpectationMaximization) method for measuring evolutionary mutation rates in DNA and protein sequences. The programs are bundled into one SourceForge project called "dart", downloadable from here: http://www.biowiki.org/

Thanks be to the miracle of wiki, and to the sod(s) who added the following decorations to my page (I actually don't get wheatgrass *at all*. This always comes up in therapy with my dog)

I'm a bioinformatics scientist at the University of Oxford. No, I'm not. I'm just too lazy to update the wiki. I'm actually at Berkeley wolfing down wheatgrass shakes like there's no tomorrow. (he's actually giving a seminar on his work now. and he doesn't seem like the type to be drinking wheatgrass. more like a lager kind of guy...)

I maintain a list of wiki sites in Bioinformatics. (Again, this is a slight fib... wheatgrass has been occupying a lot more of my time recently)


Among my other projects, I'm using InterpreterPattern to build a dynamic programming compiler for sequence analysis.

I've also started going to therapy with my dog (we bring our own wheatgrass).

Feedback welcomed... mailto:ihh@fruitfly.org (or post here!)

Er.... Are You There? This stuff about dogs and wheatgrass looks like vandalism. Yeah, I'm here. I left the vandalism in place cos it's kind of cute. Do I have bad WikiNature? Will I have to be..... punished? ;)

Heh heh heh...certain other online communities would rush to make the obvious obligatory responses there, but, ahem, this is pretty much a technically-oriented wiki. :-)

You could say more about your work, though; I'm sure that would be of general interest (e.g. purely nuclear DNA? What about differing or multimodal mutation clocks? Assumptions of versus measurements of what is highly conserved and what is not? Leaping introns? Conserved exons, statistical measures of exons -- how the hell does regulatory RNA itself recognize promoters, if it's so hard for us to do so with hidden markov models?). Meanwhile I'll take a look at biowiki. -- Doug

Well, stochastic grammars are an extension of HMMs that tackle higher-order correlations. See e.g. http://biowiki.org/StochasticGrammars

There are various extensions to phylogenetic models that allow things like varying-rate mutation clocks... often by augmenting the state space. See http://biowiki.org/PhyloGrammars for some discussion of these kinds of models.

As for "leaping introns" and the like, see http://biowiki.org/TransposonPapers

The more mystical question of how biology recognizes signals that we can't pick up statistically is for experimentalists to tackle. :-)

Here's another biowiki full of bioinformatics refs: http://www.biodirectory.com/biowiki/Main_Page

The discussion on the OnTopic page mandates that I add something about software development. Personally, I'm a pragmatic XP-er, who loves the high-feedback property of open source development, and thinks that ten emails from users are worth all the XP dogma in the world. Our GBrowse development project at http://biowiki.org/view/GBrowse/WebHome is the main thing fuelling this enthusiasm.

I'm beginning to suspect that it's the dog who writes all the papers while Ian obsesses over wheat grass.


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