From Bioinformatics.Org Wiki
It's notoriously difficult to find any books on bioinformatics itself that cater well for all of those coming from computing, from mathematics and from biology backgrounds. The few textbooks available in the field tend to be eyewateringly expensive as well. Suggested reading below has been divided into books of general interest, those best suited to people coming from a computational/mathematical background and books for biologists interested in bioinformatics.
Many people are curious about the Human Genome (Project). The completion of the first draft probably represents bioinformatics' coming of age as a discipline. The first couple of books are aimed at the intelligent layperson.
A gossipy and insightful account of the race to sequence the genome can be found in "The Sequence" by Kevin Davies [Weidenfeld; ISBN 0297646982]. Matt Ridley's "Genome" [Fourth Estate; ISBN 185702835X] is both an interesting layperson's introduction to the issues raised by the bioinformatic revolution and an overview of its biology and enormous scope. Ridley's book received a slightly snooty review from Walter Bodmer. This is understandable, since his and Robin McKie's excellent "pre-genomic" guide to the Human Genome Mapping Project, "The Book of Life" [Oxford Paperbacks; ISBN 0195114876] was undeservedly found in a remainders bin when Damian Counsell bought his copy.
If you are a non-biological scientist (or a non-scientist) and are hooked by these, why not go back to the "real beginning" of the race and read James Watson's entertaining and indiscreet memoir of his and Francis Crick's determination of the structure of DNA, "The Double Helix" [Penguin; ISBN 0140268774]---now updated with an introduction by media don Steve Jones.
Nigel Barber at Peterborough Regional College in the UK recommends Gary Zweiger's "Transducing the Genome" [McGraw-Hill Professional Publishing; ISBN 0071369805]. The summary at Amazon makes it sound a tad pretentious, but all the reviews seem pretty positive so it might be worth a read.
If you are a quantitative scientist and would like a deeper knowledge of contemporary (molecular) biology, but you want to acquire it as painlessly as possible you could try the following:
- Donna Rae Siegfried's Biology for Dummies [Wiley; ISBN 0764553267] is fun, well thought out and a lot more informative than the title might suggest. If only all biology textbooks were this entertaining and unpretentious.
- If you already have some biological knowledge and would like to get a grip on modern biomolecular science then Richard J. Epstein's Human Molecular Biology is an elegant, colourful and detailed guide.
If you are a hardcore maths/computing person Michael Waterman's "Introduction to Computational Biology" [Chapman & Hall/CRC Statistics and Mathematics; ISBN 0412993910] and Pavel Pevzner's "Computational Molecular Biology - An Algorithmic Approach" [The MIT Press (A Bradford Book); ISBN 0262161974] will give you all the discrete maths you can shake a stick at, but perfunctory introductions to the biology.
J.W. Bizzaro recommends Dan Gusfield's "Algorithms on Strings, Trees and Sequences" [Cambridge, 1997; ISBN 0521585198], Richard Durbin, Sean Eddy, A. Krogh, G. Mitchison "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" [Cambridge, 1997; ISBN 0521629713] (which Damian Counsell thinks is one of the clearest and most comprehensive guides to alignment algorithms) and---for that full "computers-to-biology conversion"--- Geoffrey M. Cooper "The Cell: A Molecular Approach" [Sinauer Associates, 2007; ISBN 0878932194]. Jeff Ames writes that a second edition of this book is now available [Sinauer Associates, 2000; ISBN 0878931066] and that this version---if you can find it in the shops---comes with a CD.
Applying bioinformatics to biological research
One outstanding general text for the biologist is David W. Mount's "Bioinformatics" [Cold Spring Harbor Press; ISBN 0879697121]. It's not cheap, but it's the best I've seen if you are studying bioinformatics itself.
Bioinformatics has been dismissed by some as "the science of BLAST searches". The best collection of advice so far on doing BLAST searches is O'Reilly's BLAST book by Ian Korf, Mark Yandell and Joseph Bedell [O'Reilly ISBN 0596002998]. Damian Counsell reviewed it enthusiastically, but not uncritically, for the UK UNIX Users' Group magazine. I'd go as far as to say that all biologists thinking of using BLAST in their research should read the relevant sections before they even go near a computer.
If you wish to use general bioinformatics tools, especially if you are a little wary of computers, Damian Counsell's new "best" book is "Bioinformatics for Dummies" [John Wiley and Sons; ISBN 0764516965]. It is (obviously) aimed at people who are beginners, who are happier using the Web rather than typing commands, and who are more interested in learning than in impressing people---the writing is friendly clear and unpretentious. However, it concentrates on Web-based resources so it will, inevitably, date. (This is partially compensated for by there being a companion Website.)
Also, if you're coming to the subject as a computer user with a biological background, looking to exploit the many tools available, you might want to try Terry Attwood and David Parry-Smith's "Introduction to Bioinformatics" [Longman Higher Education; ISBN 0582327881], or Des Higgins and Willie Taylor's "Bioinformatics: Sequence Structure and Databanks" [Oxford University Press; ISBN 0199637903]. Another excellent practical introduction is Andreas Baxevanis and Francis Ouellette's "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins" [Wiley-Interscience; ISBN 0471478784], now in its new and improved third edition. Ouellette teaches bioinformatics all over Canada and the experience shows.
"Darwin's Radio" by Greg Bear [Ballantine Books; ISBN 0345435249] is a wonderful hard SF thriller which stretches ideas derived from genome discoveries to their breaking point. It's gripping and humane.
Leonard Crane, the author of Ninth Day of Creation kindly sent me a copy for review. So far it's an excellent read. If you'd like to read a well-researched, but speculative, novel containing actual scenes of practicing bioinformatics then try it.
Ken Allen contributed the following reviews:
"Frameshift [Tor Books; ISBN 0812571088] by Robert J. Sawyer---based around the HGP---reasonable read, but poor / confused ending."
Calculating God [Tor Books; ISBN 0812580354] by the same author---has a subtler bio connection and is a much better read. Near the start an alien spacecraft lands, the alien emerges and says 'take me to your paleontologist'