I've noticed that a couple of people here describe themselves as "computer guys" working for "biologists" (just like me). I wonder if there is any one well-known like this, a computer scientist that started in a biological lab and who was successful enough in doing this to start his own group later on. Someone like a role model for computer guys that do something that "is rather desperate". If you think that a weblab is not a career-killer for bioinformatics than I would appreciate a concrete counter-example.


Comments
Pharyngula has interesting discussion on same line of thought
http://scienceblogs.com/pharyngula/2007/11/of_books_in_neurobiology.php
structural biology > bioinformatics
Hello all. I am a long time lurker, recently contemplating my future (in science). I have a chemistry/structural biology (proteins) background. My graduate work and postdoc are in the same field, though I am attempting to broaden my knowledge as far as technique applications. Most of my current work is computational, and I find myself more interested in computational biology/bioinformatics than wetlab science. Do you think making a switch to bioinformatics will help or hurt my career?
still desperate
I should probably comment, as the desperate guy :)
If I understand correctly, you're looking for examples of people from a computer science background who moved into biology and now run a laboratory. I don't know any - but I'm sure that they exist.
What's far more common is that people start with a biological background then become "computer guys", either through necessity (noone else wants the job) or choice (it's more fun than lab work) or a combination of the two. Many of those people go on to run their own labs and many of them have been named here.
In terms of career development, both routes have their problems. There are of course a few purely computational research groups but they are quite rare in any country. Remember that on average, scientists achieve research independence in their early forties and bioinformatics as we know it today is still not much more than 10 years old. So most tenured researchers in bioinformatics already have a pretty good record as wet lab researchers. This is certainly the case with the IMB here in Queensland for example. Most of the group leaders there were already established in cell biology, genetics, biochemistry and so on. For them, increased interest in bioinformatics has come at a fortuitous time as they can run labs with a bioinformatics component, but very much applied to wetlab work.
For those of us who are a little younger and enjoy bioinformatics, things are a little more difficult. If you get out of the lab and into computational work before you settle on your pet biological system, people just don't understand where you're coming from. They ask about your research interests, expecting a snappy one-line answer like "ageing" or "metalloproteins" or "fruit fly development", when what you're interested in is simply biological data. How to acquire it, store it, analyse it and present it. So there's the dilemma. Successful career scientists run a wetlab with a single focus, to which bioinformatics can be applied. Young, would-be successful career scientists love applying the bioinformatics but don't have a strong, single wetlab focus. Result: they don't understand each other very well.
All I can suggest is that if it's research success in academia that you crave, find a focused biological problem that (a) offers sufficient computational interest for you, (b) offers the chance for you to run a wetlab even if you don't necessarily want to work in it and (c) lets you apply for funding on terms that other biologists and grant bodies can understand ("my aim is to cure disease X" or whatever). Failing that, hope for a staff scientist position to come up in a field where you can use your bioinformatics (such as a sequencing centre). And failing that, just get any old job that involves programming - sysadmin, telecommunications, website design. Won't be as much fun as science though.
yes, but...
yes OK, but I assume (Eisen?) that they are many are mainly computer scientists that waited until they had their own group and then started to have a "wet lab component" instead of "computer guys working for biologists". I haven't checked their cvs yet, though...just searching for them...
Mathematicians
Would you accept mathematicians instead of CSers - biologically motivated maths problems have a longer history than the current crop of CS issues.
If so, how about Eric Lander, Andy Clark and Michael Waterman? All math-trained at PhD level or above, all would now be described as biologists, all have a wet-lab component. Oh, and they all use computers :-)
You might also want to include Ronald Fisher...
Ranganathan @ UTSW
Rama Ranganathan [http://www.utsouthwestern.edu/findfac/professional/0,2356,22254,00.html] comes close to that I feel. His lab [http://www.hhmi.swmed.edu/Labs/rr/] works "to understand the process of information flow in cell signaling systems at atomic detail".
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no
Ranganathan has done his ma and phd in biotechnology/biology. He's not a computer scientist if I haven't misunderstood something on this webpage.
Yes you are right :)
That is why I said close :) The course of BS Bioengg @ UCB has elements of Applied computing but obviously not pure Computer Science subjects like 'Theory of Computation'.
I guess another close contender to what you seek is Prof. Walter Freeman [ http://en.wikipedia.org/wiki/Walter_J._Freeman ] but again Physics and Mathematics Graduate and not Computer Science as such [Though on a crude level, I feel Physics takes care of Hardware and Mathematics takes care of Software part in CS, CS as a subject itself is an illusion].
Another close contender is Eleazar Eskin [ http://www.cs.ucla.edu/~eeskin/ ]... but again less of wetlab and more of in-silico like Pevzner @ UCSD.
But sadly I could found no one who is hard core CS guy, who worked in Bio lab [interestingly Richard Stallman, according to http://en.wikipedia.org/wiki/Richard_Stallman has a record, "Stallman was also a volunteer Laboratory Assistant in the biology department at Rockefeller University"] and made way up to establish wetlab.
______________________"The Answer Lies in Genome"______________________
http://computationalbiologynews.blogspot.com/
plenty of examples, but I am not sure what you want.
How "wet" is wet? Lots of labs do PCR, RT-PCR, sequencing for both validating computational predictions and collecting data for studies. Are you talking about someone who switched fields or someone who does both?
Michael Brent apparently has a wet lab now to test computational predictions. He made his way quite well in CS and computational linguistics before focusing on computational genomics and gene prediction.
Michael Eisen runs a successful lab using and developing computational approaches and doing lots of wet stuff in flies, yeasts, and even frogs (and frog killing fungi).
Chris Burge, Steven Brenner, and Todd Lowe (among others) have both a "wet" and "dry" component to their labs for both validation of computational predictions and generating new data regarding splicing among other things.
Just some folks I could think of off top of my head, I am sure there are many others -- this seems has a gender and nationality bias to it.
Cannot see one
Michael Brent has not a single paper published in wet biology. Burge's papers that I looked on rather look like collaborations than his own biological work (as he's not the last author). I couldn't find a web-biology paper for Todd Lower, but his lab might be one that really test their own ncRNAs, whereas they simply might have no publications yet.
I still cannot see computer scientists that started their career "working for biologists"...
Any better examples?
still not sure who you are looking for
I still don't quite understand the criteria of what you are looking for as a model. What does "working for biologists" mean? Lots of people are biologists that don't actually touch organisms. Is a biochemist more of a biologist than a theoretical ecologist? Do you just mean working for a lab that is mostly employing experimental molecular biology?
If I read it correctly you are looking for someone who:
a) was trained originally in computer science (PhD? MS? Undergraduate?)
b) Did computer science/programming in a lab that one would describe as "wet" (as a PhD student, Postdoc?). What did they do in this phase, wet or dry work?
c) Later on went on to start a lab that primarily is "wet" or "dry" research? (realizing those terms are often over simplifications).
So do you want someone who is trained in computational research and then went on to apply their skills in traditional wet labs, but later started a lab that is "dry"?
Does someone re-training later in life not count for your list? Only someone who studied (postdoc or PhD) under a "wet" lab but was previously trained as a computational scientist?
Sean Eddy did his PhD in experimental biology but dabbled in programming while at Colorado and clearly did a computationally focused postdoc with Durbin and Sulston but was motivated by experimental genomics data being generated while at the Sanger. His lab has done continued to do computational prediction and experimental validation of RNA genes among other things.
For example, Bob Waterston's lab has pioneered genome sequencing techniques and experimental questions in C. elegans. Through his work and others lots of progress was made in how we sequence genomes, assemble BAC maps, etc. Currently Zhirong Bao is a postdoc in the group, he did his grad work with Sean Eddy and developed novel computational approach to identifying repetitive sequences de novo. He is now working on applying his skills to imaging processing providing automation in analyzing images of worm development. Does Zhirong count as someone transitioning?
Do people in systematics who sequence genes (wet) for phylogenetic reconstruction that later on specialize in algorithm development meet your criteria?
Michael Brent's lab has several papers where gene predictions were made in Twinscan and validated via RT-PCR in Chicken and Cryptococcus for starters, but no I wouldn't describe the lab as primarily "wet". Neither is the Burge lab, but both are employing a hybrid for the purposes of validating computational predictions or in testing models that predict the role of sequences in enhancing splicing. Does testing the effect of moving splicing enhancers around count as a "wet lab"? What about RT-PCR to validate predictions? If you are not looking for a hybrid what exactly are you looking for?
Does having Cell & Genes & Dev papers rather than NAR & Genome Research papers to make the difference?