Questions regarding undergrad research, Bioinformatics

[Bruster32]

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Hey all,


I've been a (fairly) long time lurker on this forum, and I've read through the stickies, but I've had a few questions bumping around in my mind for a while now and decided to finally register. I was hoping you could give me some advice on two major issues regarding my future application:


I'm currently studying for the MCAT and preparing to enter my senior year but am not applying to MD/PhD programs this cycle. Although my numbers look like they'll be fairly good (~3.9 GPA, averaging 36-37-ish on MCAT practice tests), I don't currently have any major research experiences. This is partly because of scheduling issues and partly because I did not realize my interest in pure science until around my Junior year. I am starting undergraduate research in a Microbiology lab in a couple of weeks and plan on continuing with this for the remainder of the academic year.


I previously planned to apply to the NIH IRTA program or full-time research assistant positions to spend a year after graduation working on this weakness in my application (I figure that would grant me ~1.5 years by interview time, which would be weak but not absolutely pitiful), but I've had a bit of a wrench thrown into my plan. As a result of my coursework and random-article reading, I've started to become increasingly interested in the genomic/bioinformatic side of Microbiology, particularly surrounding things like virulence and antibiotic resistance. I know that some of this type of work gets kind of “mathy,” and I have little to no background in statistics or computer science (I've had a semester of calculus and statistics). In light of this, I've now been wondering if I ought to just take an additional year of undergrad to take more math and computer science courses while continuing to work in a lab part-time.


Another option would be to apply to Microbiology, Statistical Genetics, and/or Bioinformatics masters programs. Although an M.S. program would take 2+ years, I feel like I'd come out with a bit more to show for it than one or more “super-senior” years. Of course, my lack of undergraduate math/computer science experience might be a hindrance for applying to even M.S. programs, and I'd probably have to carry out remedial coursework. Finances could also be a potential issue there.


In any case, does anyone have any advice about what the best way to go would be? Can anyone share any insight about their own experiences with entering Bioinformatics related MD/PhD programs (About what kind of background is needed)? I'd greatly appreciate any advice anyone could give, and I apologize for the rambley nature of my post.


TLDR version: The research part of my application stinks; how should I go about fixing it while shifting fields at the same time?

 

[computerdorkdan]

I think the masters might be a bit of a waste of time.

Go check out WashU's computational courses that bioinformatics majors take. Lots of the classes (maybe all?) post their powerpoints. You'll notice it's pretty basic stuff.

I'd do some kind of statistics work and skip the comp sci classes. Try some Perl, Ruby, Python or R on your own in conjunction with the classes. Starting with Perl would give you a good foundation but I'm biased towards Perl, so take my advice with a grain of NaCl.

Just my .02.

 

[Bruster32]

I think the masters might be a bit of a waste of time.

Go check out WashU's computational courses that bioinformatics majors take. Lots of the classes (maybe all?) post their powerpoints. You'll notice it's pretty basic stuff.

I'd do some kind of statistics work and skip the comp sci classes. Try some Perl, Ruby, Python or R on your own in conjunction with the classes. Starting with Perl would give you a good foundation but I'm biased towards Perl, so take my advice with a grain of NaCl.

Just my .02.

Yeah, I've been looking at some "intro to bioinformatics" style books on my own time, and it doesn't seem like most of the actual programming is that complex; however, I just look at the admissions pages for most computational biology/ bioinformatics graduate programs, and a good number usually seem to require that students have taken at least a few formal computer science classes. Does this "rule" not carry as much weight when students are coming in from the MD/PhD side of things?

Also, you wouldn't happen to have a direct link to the WashU powerpoints that you're referring to, would you? I've found one or two classes through google. It's not a big deal if not, though.

I greatly appreciate your response and the advice!

 

[Naijaba]

I'll make this brief:

If you want to be a basic bioinformatics researcher, you're going to need to know at least one scripting language and/or beginner database design.

If you want to make strides in bioinformatics, you're going to need to know a hardcore programming language (read: C++) like the back of your hand. I won't lie to you, proficiency in C++ takes nearly a decade to obtain.

Bioinformatics researchers of the former type pull data and analyze it using tools available to everyone, while researchers in the latter category may develop their own tools.

 

[Neuronix]

I won't lie to you, proficiency in C++ takes nearly a decade to obtain.

I disagree. With good instruction and practice I'd say a year tops. Maybe less depending if you have previous programming experience. Then again it might take more to break all the bad habits you have to learn to get by with scripting languages or Java. I always recommend C or C++ as a first language to learn. Yes, it's hard. But, it teaches you all the fundamentals you need to know to be a competent computer (based) scientist.

 

[Bruster32]

First, I apologize if I've underestimated the difficulty of the field to the point of sounding insulting, as that was not my intention.

If you want to be a basic bioinformatics researcher, you're going to need to know at least one scripting language and/or beginner database design.

If you want to make strides in bioinformatics, you're going to need to know a hardcore programming language (read: C++) like the back of your hand. I won't lie to you, proficiency in C++ takes nearly a decade to obtain.

Bioinformatics researchers of the former type pull data and analyze it using tools available to everyone, while researchers in the latter category may develop their own tools.

If this is true, then it seems that I might honestly fall more in line with the former as opposed to the latter, as I think I might be more interested in using computer science as a tool for tackling biological problems, as opposed to an end in and of itself.

I know a lot of graduate programs allow you to take bioinformatics courses alongside standard biomedical coursework in the form of a "certification" or "minor." Perhaps I would be better suited towards pursuing a PhD in Microbiology (or something related) and doing something like that instead of a full PhD in something like bioinformatics or computational biology.

In any case, I think it would still be beneficial for me to take some programming/quantitative coursework while doing more research. Thankfully, I don't have to come to a decision immediately, and so I still have time to mill over things and continue to formalize my goals. Once again, I appreciate the advice, and I welcome anyone else who wants to share their perspective on this.

 

[WNT Signaling]

You do not necessarily have to be a straight-up bioinformatics researcher to use bioinformatics: I'm a developmental biologist, and I do bioinformatics (mostly with R) fairly frequently. An option might be to find a tech position at a university because in addition to gaining more experience, many universities (Harvard affiliates, Penn, and BU, amongst others, are great at this) allow you to take discounted or free classes, and some universities, like the one I'm at now, allow techs to sit-in on graduate classes, including bioinformatics. One more thing, not to start a flame war, but remember, you don't necessarily need a Ph.D. to be able to do great research as an M.D.