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Bioinformatics Books for the Technically Inclined? 27

Posted by Cliff from the night-before-the-interview-reading dept.
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?"
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Bioinformatics Books for the Technically Inclined? More

Bioinformatics Books for the Technically Inclined?

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  • If there arn't any books on the subject, I seriously doupt very many people know as much as you. I seriously doupt the people interviewing you will know more. So why worry, your probably exactly what they are looking for, and anything that you do need to know, I'm sure they will teach you on the job. Its the general knowledge and ability to learn that companies look for, they prefer it if they can teach you something.

  • What field is the job in? (Score:3, Informative)

    by Otter ( 3800 ) on Friday December 07, 2001 @03:59PM (#2672286) Journal
    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 (Score:2, Insightful)

    by lfettner ( 542135 )
    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 (Score:2, Informative)

    by stelo ( 542140 )
    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

  • there's a new book by o'reilly about bioninformatics - "Developing Bioinformatics Computer Skills" - see http://www.oreilly.de/catalog/bioskills/ [oreilly.de]
    • 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.

  • Biological Sequence Analysis (Score:3, Insightful)

    by woggo ( 11781 ) on Friday December 07, 2001 @04:41PM (#2672558) Journal
    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.
  • O'Reilly seems to be getting into bioinformatics pretty heavily and while I don't think any of their more advanced books will be out in time for you, a search for 'bioinformatics' on their website turns up a rather large list of hits.

    I agree with the other poster who said you're probably perfect for the job as it is. Sounds like you've got good qualifications and in my opinion anybody who get any degree in biology can learn anything they put their mind to. :)

  • Textbooks I've used (Score:2, Informative)

    by EthOnto ( 542186 )
    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.
  • There's hardly any trained professionals in the field. These guys probably have something similar to your background. Just promise to be flexible and to learn whatever language/skills the job requires.

    I got into the biz three years ago (as a biologist) and I'm still learning new languages.
    Mostly C and XML transformation stuff, cause I honestly believe Perl & Lisp are not up to the massive amount of data challenge.

  • Bioinformatics Books (Score:1, Informative)

    by glenix ( 85526 )
    I highly recommend "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins" by Baxevanis and Ouellette-published by Wiley-Interscience; "Bioinformatics: Methods and Protocols" by Misener and Krawetz-published by Hamana Press; and "Bioinformatics: The Machine Learning Approach" by Baldi and Bruank-published by MIT Press.

  • Do a search at www.mightywords.com (Score:1, Informative)

    by Anonymous Coward
    There are three ebooks on the subject at www.mightywords.com

    Data Analysis for Bioinformatics : Part 1: Probability, Statistics, Information Theory, Clusters
    by Arun Jagota $10.00 Publisher: Arun Jagota Pub Date: 05/09/00

    Data Classification for Bioinformatics : Supervised Methods
    by Arun Jagota $10.00 Publisher: Arun Jagota Pub Date: 07/14/00

    Perl for Bioinformatics
    by Arun Jagota $9.95 Publisher: MightyWords Inc. Pub Date: 03/15/01
  • For my entire undergrad career while I was a double major in Math and Bio people kept asking me wtf I was doing. Now that these stupid idiots know what bioinformatics is too I have to compete with them for jobs that they are not qualified for. Here are my demands:

    1.)An O'Reilly book deal. I know a *lot* of programming and UNIX system adminstration. A lot more than the crack users who they got to write these dreadful bioinformatics books.

    2.)A lot of money. Especially in a position where I get to boss around straight-up bio geeks. My first order of business will be banning the reading of slashdot at work.

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