[BiO BB] Bioinformatics reading list (Was Introducing into Bioinformatics)

miller miller at pharm.sunysb.edu
Wed Feb 14 11:13:03 EST 2001

Hi Everyone!

I think that Marielle has a great idea here. We could start with the books and
information provided by Gary and Deanne and expand from there. I would be
willing to work on this if you like.

Let me take this opportunity to introduce myself. I am a biochemist. I am not a
programmer (yet) but I really love working with computers and would like to move
further in that direction. I feel that bioinformatics is really an exciting area
and I would like to work in this field. In addition, I am a strong supporter of
open source software and free access to information.



Holly Miller, Ph.D.              voice: 631 444-8018
Res. Asst. Prof.                 FAX:  631 444-7641
Dept. Pharm. Sci.                http://www.pharm.sunysb.edu/faculty/miller/
SUNY Stony Brook                 miller at pharm.sunysb.edu
Stony Brook, NY 11794-8651

             BioMail--New references from Medline to your e-mail account

"Taylor, Deanne" wrote:

> Besides the books that Gary listed, there really aren't any "Here's how to
> become a cutting-edge bioinformaticist" books out there. Bioinformatics is
> so new that most books that come out are all about the tools that exist, not
> how to build new or better tools. As a programmer, I doubt you'll want to
> sit back and use other people's tools. :) but those are just the books!
> There is so much for a programmer to do in bioinformatics that books just
> can't touch.
> Ah, but one or two more books. :)  If you're of a mathematical bent, you may
> want to at least check out of the library Eddy's book  "Biological Sequence
> Analysis" by Durbin, Eddy, Krogh and Mitchison. There are several new
> bioinformatics books out there that have just come out (search
> "bioinformatics" on Amazon.com), though from what I've seen they're on the
> level of Baxevanis, which is pretty much user-level stuff....how to use
> other people's software.
> Now, as a programmer, bioinformatics can become pretty much just about
> handling data sets. If you want to do the science of bioinformatics, you
> should follow what Gary said, definitely, and read up on the Mol. Bio of the
> Cell. Also is the book GENES VII by Ben Lewin for genomic info. If you want
> to work with genome or sequence information, you should know about stuff
> like open reading frames, restriction sites, and how the data is generated
> (PCR, etc).
> In addition to sequence manipulation, there are several avenues a programmer
> can explore. One is pure database handling, which reduces the bioinformatics
> problem down to a data structure level. For instance, expression profiles
> from chip data can be pretty  big databases at big companies. Oracle is used
> a lot in many companies for this purpose. Additionally, data analysis and
> statistics are valuable, though many chip manufacturers supply the analysis
> programs so there isn't a need to do any more than understand what's going
> on when one is doing this kind of analysis.
> The bioinformatics field is really wide open as far as what one can do with
> the data sets. Manipulating large data sets is going to become very
> important in industry soon, including database work, because the real
> information isn't in the "genome"...it's in how the cells express it, and to
> do true expression profiling work takes thousands of experiments with many
> many data points.
> Also coming up in importance in industry is pharmo-chemical profiling...mix
> expression profiling with chemical profiles. Again, all database work but
> statistics become important since there are no commercial/validated programs
> for pharmochemical profiling so someone has to both set up the database
> schema as well as work on the validation of data sets.
> Summary:  iif you want to be on the cutting-edge of bioinformatics, have a
> basic knowledge of statistics and validation, Perl and/or Python,
> Oracle/SQL, molecular biology and genetics. You can be a bioinformaticist
> without knowing much about mol bio and genetics, but you'll be more like a
> data handler (which most bioinf programmers are these days).
> Deanne Taylor
> -----Original Message-----
> From: Gary Van Domselaar [mailto:gvd at penguin.pharmacy.ualberta.ca]
> Sent: Wednesday, February 14, 2001 9:30 AM
> To: im99_foa at nada.kth.se
> Cc: BIO Bulletin Board
> Subject: Re: [BiO BB] Introducing into Bioinformatics
> Marielle,
> One of the best-selling books on bioinformatics is "Bioinformatics - A
> Practical Guide to the Analysis of Genes and Proteins," Baxevanis and
> Oulette (Wiley, 1998)".  I found it to be very accessible.  Another early,
> but still valuable book is "Sequence Analysis Primer" by Gribskov (1991).
> A less accessible, but still valuable book IMO, is "Bioinformatics, The
> Machine Learning Approach" by Baldi and Brunak.  If you have no biology
> background, you might want to pick up a good molecular biology text.
> "Molecular Biology of the Cell" by James Watson (of Watson/Crick fame) is
> very good.
> Regards,
> g.
> --                                                                   --
>                              Gary Van Domselaar
> Ph.D. Candidate,                                    Associate Director,
> Faculty of Pharmacy,                   Bioinformatics.org: The Open Lab
> University of Alberta                           gary at bioinformatics.org
> gary at penguin.pharmacy.ualberta.ca        http://bioinformatics.org/gary
> --                                                                   --
> On Wed, 14 Feb 2001, Marielle Fois wrote:
> > Hello,
> >
> > Does anybody have an idea of a good way of getting into bioinformatics
> > for someone on computer science with no biology background? I wonder
> > if there is a book or article considered the standard in
> > bioinformatics. Wouldn't this be a good information to have in this
> > site?
> >
> > Thanks,
> > Marielle

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