Bioinformatics Books for the Technically Inclined?

bookEnders asks: "I hold a BS and MS in Biology. For the past 6 years, I have worked as a computer programmer not in field of Biology. I have an upcoming interview (several weeks from now) for a Bioinformatics programmer position. It appears to be a great job for me - a marriage of University training and professional experience. As LISP is a requirement, I have been burrowing through David Lamkins's Successful LISP tutorial. However, I am having trouble finding Bioinformatics books that are geared toward my skills: most are written for Biologists who don't know Linux or PERL. Others are written for Computer Scientists who don't know squat about Biology. I know enough about both that neither set of these books is too valuable. Can someone (hopefully those in the field) suggest reference or tutorial materials to help me prepare for this interview?"

Comments

Re:Hmmm...

[babbage]

Well, he seems to know enough to know that he doesn't really care about Perl. He's a Lisp guy that's going for a Lisp job. Why would Perl's case sensitivity make a whiff of difference to him? Lay off already...

I think Bioinformatics is still too new of a field for there to be many books out there. O'Reilly has two books, but one is aimed at absolute newbies that are looking for the ON button, while the others is for people that have found the ON button and are trying to start out with Perl.

I'd also be interested in finding something a bit more advanced, but as of yet it doesn't seem to exist, and it seems like a perfect opportunity for someone to step in and write one. I'm an intermediate Perl monkey and I remember a bit of my last biology class back in high school, but that doesn't put me in a strong enough position to be trying to teach anything to anyone else yet. This doesn't sound like a problem for the original poster. Maybe he could spend the time waiting for this job by writing the first Lisp for Biologists book? I know I'd be interested in it...

What field is the job in?

[Otter]

As a biologist who struggles to keep up with informatics, I can sympathize. The problem is that the field is so new and so fast moving that good books are nearly impossible to write.

What area of biology does the job involve? With that, people could give you more specific pointers. Failing that, I'd suggest going to some web sites -- NCBI, ensembl.org, genome.ucsc.edu -- and looking at what's around. (Of course, my list is biased towards sequence-based genomics. If the job you're eyeing is in proteomics or arrays or some other functional genomics, it won't help as much which is why it would be useful to have a more specific pointer.)

Bioinformatics Links

[lfettner]

http://www.biolisp.org has a lot of information about Lisp and bioinformatics on their site...resources and code that you can play with. Franz Inc. also has a free "Basic Lisp Techniques" book that can be downloaded, and BioDB-Loader, a toolkit created by Peter Karp of SRI for loading and querying databases.

Bioinformatics Books

[stelo]

You should take a look at

http://www.cs.ucr.edu/~stelo/pattern.html#Resource s

under "Books". I agree that the there is no book that cover 100% of Bioinformatics, but a a subset of these will definitely do.
I particularly like the book by Gusfield for the algorithms.
Regarding Perl, you are probably aware of a new book by O'Reilly about "Perl for Bioinformatics"

http://www.oreilly.com/catalog/begperlbio/

Regards,
Stefano

Biological Sequence Analysis

[woggo]

by Durbin et al. (Cambridge) is a good bet. It's mostly about the central algorithms (Smith-Waterman, Baum-Welch, etc.) -- as a LISP wonk, you'll be able to implement them efficiently.

Textbooks I've used

[EthOnto]

I sat in on a Bioinformatics course last spring. We used texts by Pevzner and Gusfield. I would recommend looking at Gusfield. It's definitely from the CS side, but that's probably more approach anyway, since you said the job required you to know Lisp, not how to run gels. Pevzner tries to straddle both sides, but doesn't always succeed. I would also second the Lisp in Biology site. P.

Re:have you checked the stuff by o'reilly?

[Daniel Dvorkin]

Yes, Developing Bioinformatics Computer Skills is one of my favorites (BTW, the authors are Gibas and Jambeck.) I think this is probably the book that some previous poster characterized as being "for absolute newbies who are looking for the ON button," but the point he's probably missing is that the book isn't intended to be an end in itself -- one of its major functions (for me) is as a list of resources. I'd say it averages about one useful URL per page ... and while the idea of storing URL's in dead tree form may seem kind of silly, I don't know of any bioinformatics Web sites' "links" sections that have this wealth of information (and the dead tree bibliography is pretty useful too.) As a student of bioinformatics and a biotech software engineer, I strongly recommend this book.