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Science

Bioinformatics Graduate Schools? 14

Posted by Cliff from the flying-above-higher-education dept.
coopergm asks: "I am an undergraduate nearing graduation, majoring in Biology and Mathematics & Statistics, with a bit of Computer Science as support. What graduate school (PhD) programs out there are the best for computational biology and bioinformatics? Obviously, Stanford, MIT, and Washington University in St. Louis have a serious edge by virtue of being associated with one of the major human and mouse Genome Sequencing Centers. How would one differentiate between these three? Are there other schools offering competitive bioinformatics programs in terms of reputation, quality of research and educational experience?"
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Bioinformatics Graduate Schools? More

Bioinformatics Graduate Schools?

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  • Our bioinformatics program here at RIT is starting next quarter and should be offering a joint bio/computer science grad program starting next year. I'll be taking the undergrad classes as part of my parallel computing program and can let you know more once they've started next month. I don't even think the course web pages are up yet but if you contact me in a month there should be more information for you.
  • You are correct -- grad school labs are a real world environment research environment. I was wrong to have described industry as being 'real world'. The feeling that I was trying to get across is that I think that I have learned more interesting things faster and with less effort by being involved directly in the industrial/commercial side of things. I have the ability to throw myself directly into interesting problems and areas without having to worry about resource constraints, teaching assistant responsibilities and required-but-not-useful classes etc. etc. This approach worked out nicely for me but may certaintly not be the norm. Heck I still need grad school to pick up those MS level degrees...

    -c


  • I've been working in bioinformatics for 5+ years now and this topic is of extreme interest to me because I went straight from undergrad into a commercial biotech outfit. Generally speaking I'm very happy I did that and I honestly believe that I learned more by working in a real world discovery research environment than I could have in graduate school.

    I've often considered going back to grad school but have always come to the conclusion that I am learning more by being in the real world. Getting paid to learn also does not hurt :)

    Practically speaking you only need a phD level degree if you want to (a) be in academia or (b) manage your own group or lab someday or (c) apply for grants or teach in a university setting. For everything else the doctoral degree is (I think) pretty much a multi-year waste of time. My eventual goal is to go for the generalist approach -- multiple master's level degrees spanning computer science and molecular biology.

    The best thing about industry is that I am judged only on my abilities and accomplishments. They don't give a darn about my academic pedigree and I don't have to deal with status-obsessed ivory tower types who look down on anyone without an advanced degree.

    I live and work in the Boston/Cambridge area but if I had to pick any one school for graduate studies it would be UC Berkeley. They have by far the best mix of old school pioneers and young hotshot scientists/faculty. I would love the opportunity to work with people like Steven Brenner and Suzi Lewis. I have a disctinct feeling that over the next 5-10 years some amazing science is going to come out of the UCBerkeley folks.

    The reason it is so hard to pick a grad school (or even undergrad for that matter) is that there was a period a few years ago where practically everyone who had done anything with bioinformatics was hired away from the unversities by the big pharma companies. There were whole departments that were essentially gutted by faculty leaving for industry positions. This left a HUGE hole for people looking to learn. This is slowly changing but has not been totally fixed. There are still lots of schools offerning computational biology or bioinformatics programs that only have 1 or 2 'real' faculty capable of mentoring and teaching well. UCBerkeley is (I think) the exception here.

    Just my .02. Your experience/opinions may vary.

    -c

  • Check Waterloo out. It's CS program now has a bioinformatics option.

    =)
  • Check out BU's program. http://bioinformatics.bu.edu
  • Thanks for the insights. The problem is I'm not sure exactly what I'll be going into. That's why I picked schools that are strong in CS, mol bio, and have good associations with clinical environments as well. One of my biggest concerns is the Celera kind of problem you mentioned. I'm definitely scoping out these schools to ensure that there are more than a few faculty I could work with. Thanks again.
  • Oregon Health Sciences University. Don't know much about it, but did some work with them in the past.
  • UC Santa Cruz has a surprisingly strong bioinformatics program, lead by David Haussleur. Lots of cool little startups have been spawned out by David's students (one of my friend's companies was just bought by Affymetrix), as well as some smart PhD-types. The engineering department at UCSC is expanding, so don't let the hippie-reputation of UCSC cancel it out as an option.

    And, by the way, the UCSC campus is about the most beautiful you will ever have the opportunity to go to. And it's only three miles from the Pacific Ocean and some of the world's most popular surfing. Visit and check it out.

  • I'm at UCSF's relatively new biomedical informatics program, which of course I recommend. They restarted the program 2-3 years ago, but of course there's been a lot of active research in spite of that. I hear Columbia is trying to increase their bioinformatics focus (after having a strong clinical informatics program already). You might also want to look into biophysics and similar programs, which have strong math and biology focuses.
  • Check out RPI, http://www.rpi.edu, they have a brand spanking new bio-informatics programs with all the cool toys. A recent USD $130 million from an anonymous donor is also slated to go towards the most advanced bio-tech building. The undergrad part is a "concentration" under the "IT" degree program, and I'm not sure of the state of the Grad program. The basic idea is that RPI is gunning for MIT, since they got ranked in the top tier of schools by US News and World Report. All I know is they have a kick ass IT program, and an awesome bio program, which they joined for the whole bioinformatics thing.
  • Check out the Watson School [cshl.org]. There are a number of bioinformatic groups there, and I hear they are pretty good.

    However, I'd recommend going to a school with a very strong CS curriculum. There are lots of people interested in bioinformatics right now, but unfortunately most think some perl or python will serve all their computing needs. It won't. The bioinformatics community needs more people with both biology knowledge _and_ a strong grounding in algorithms.

    I'd say MIT certainly has the computing knowledge, and I know several CS profs at Wash U who were heavily into the genome when I was there. So one of those would be good. You'll be much better able to advance the woeful state of bioinformatics if you can help come up with better ways to store and search things, than if you spend your time writing slow and crappy cgi scripts [mcgill.ca].
  • I don't know where you learned about grad school, but grad school _is_ a real world discovery research environment. What else do you think you'd be doing if you were in a lab?
  • I actually don't know much about their bioinformatics program (other than the fact that it's new, and only for Graduate students...but that's another rant), but UC Davis has one. I don't imagine it can be too bad, being at a school already reasonably well known for it's biotech and medical programs...
    ---
    "They have strategic air commands, nuclear submarines, and John Wayne. We have this"

  • Anybody know of any good Undergraduate programs that at least include actual bioinformatics in the curriculum?

    I'm an interested, independent (read:I have to pay for everything myself) adult student, having recently returned to college. The community college I attend (American River College in the Sacramento, California area, if it matters) recently started up a biotech program, but they've yet to offer anything involving bioinformatics, and as my previous post mentioned, UC Davis only offers it as a graduate program...

    (In a related but otherwise irrelevant note - it looks like the MPI port of fastDNAml is now available for download here [indiana.edu]. Time to play!)


    ---
    "They have strategic air commands, nuclear submarines, and John Wayne. We have this"

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