RAHUL SIDDHARTHAN'S HOMEPAGE

Welcome to my internet abode. Here you will find a brief description of what I do.

Most of my time these days is spent on computational regulatory genomics: that is, trying to understand, from DNA sequence and other data, how genes are regulated. My major project is PhyloGibbs, a motif finder whose published version may be found here, but much work has been done since that will be made available at some point in the hopefully near future.

Apart from developing algorithms and writing code, I am interested in biological issues that involve gene regulation, which means a lot of biology. Specifically, I am currently collaborating with biologists on fruitfly mesoderm development and on human immune response. I am also interested in questions of evolution: it is reasonably clear today that much evolution is driven by changes in gene expression, rather than changes in the genes themselves.

This is a huge field that is getting bigger. For example, most past work focuses on transcription factors (DNA-binding proteins that recruit the RNA polymerase) but it is now becoming clear that much regulation happens at other levels (eg chromatin remodelling, post-transcriptional, RNA interference, ...) and computational biologists are barely beginning to get a grip on this. There is much that physicists can contribute here.

I am part of a small but growing group of physicists at IMSc who are interested in biology, including Gautam Menon, Sitabhra Sinha, Sudeshna Sinha and Ramesh Anishetty.

More details, and a couple of links, are available on the research page. My earlier research work, in condensed matter physics, is also described there, and you can see my research papers and other writings here.

If you're easily amused, you can also see my separate (and very out-of-date) personal webpage here.

If you want to work with me:

• If you're a researcher elsewhere who finds what I do interesting, and wants to explore collaboration or just discuss stuff, contact me.
• If you're already at IMSc: drop in anytime.
• If you want to be a student with me: you first need to join IMSc, see here. We presently have no biology programme but people in the physics programme can work with me. I may also be able to work with computer science or math students, but not as the primary thesis advisor: don't join those programmes with the goal of working with me.
• If you want to be a postdoc with me: you first need to join IMSc, see here. You will apply to the institute directly, but drop me a note about your application and I will keep an eye on it.
• Students and postdocs need to have sound mathematical skills and physical intuition (which most people who get in here do), and be comfortable with computer programming (which many people aren't, but if you can think clearly, programming is easy to pick up). Needless to say, you should have an interest in biology, though prior training isn't needed.
• If you want to do a short-term project: I have no paid positions at the moment but may in the future. I am happy to give students short projects to do as part of their course requirements, but I require you to be a competent programmer already (I will verify this before agreeing to take you on). Unfortunately many students come out of so-called "bioinformatics" or "biotechnology" courses with almost no programming skills. Above all, you should enjoy programming.

The languages I use are C, python and ocaml but you don't need to use them if you're comfortable in another language.