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I'm applying for PhD programs in Computer Science, which allow a year of rotation and courses, before the student officially joins a lab for their thesis. I've had research experience in Computational Biology, but being a Math major, I've had a relatively (relative to average CS graduates) large number of courses on (or related to) Theory CS (I took quite a few advanced courses on topics closely related to Theory CS).

I have two questions:

1 - Do admissions committee generally view an applicant in my situation more qualified for doing a PhD in Theory, or in Comp bio?

2 - Assuming I'm considered more qualified for Comp Bio, is it a bad idea to express interest in working in CompBio, and claim I want to work with an advisor in that area, while I actually plan to do my PhD in TCS? I mean, given that once I get in I'll have the freedom to choose my advisor and I'll have enough time and opportunities to even gain research experience in a different area, could there be any negative consequences in expressing interest in CompBio (and even introduce some vague research ideas), and then if admitted, try to work on TCS? (moral issues with doing this are of course a different story)

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Apply for and do the PhD you actually want to do.

The skills gained by having research experience are generally subject transferable, so if you want to do theoretical computer science, explain what skills and knowledge your research experience in computational biology gave you that would be applicable to that field. It could even be something as simple as saying "my experience in researching x topic in computational biology got me interested in computer science as a field of research, which I want to explore further, focusing on theoretical topic y".

Don't try and game the system. Be honest about your interests and the experiences that have led you to them.

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Assuming that computational biology and theoretical computer science are housed in the same department, I see no reason that you would not be able to later switch as you saw fit.

When I applied to PhD programs, I expressed interest in matrix theory and abstract algebra. I ended up moving to applied math relatively quickly. I was assigned a temporary advisor when I arrived. She helped me transition administratively to the other discipline. It was a matter of her signing a form confirming I had found a permanent advisor. Note that not all programs will even assign you a temporary advisor.

I have never heard of a program that retrospectively looks back at your application and confirms whether or not you actually studied the topic you had proposed when you applied.

Such a practice as you have described is actually somewhat common I would think. Interests change. There is nothing inherently immoral about changing your research interests. (I would avoid outright lying, however).

As for how qualified you are for either subject, that is impossible for me to say. Demonstrable experience in computational biology is not going to hurt your application. Neither are numerous classes in theoretical CS. Note that, based on the research interests of the faculty, one field may be favored over the other for admissions purposes. If they have one theoretical CS professor and 10 computational biology professors, you are betting against the odds to say you really want to study theoretical CS.

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