Bioinformatics books

Notes on some bioinformatics books from two perspectives. Here’s what I’m looking for: 1) advanced discussion of computational and statistical methods for genomics, especially microarray analysis, and 2) suitability for an intro and survey bioinformatics course I teach.

THE ANALYSIS OF GENE EXPRESSION DATA: METHODS AND SOFTWARE
edited by Giovanni Parmigiani, Elizabeth S Garrett, Rafael A Irizarry, Scott L Zeger
companion website
Great medium depth howto. Covers R, dChip, SAM, and packages that take more sophisticated approaches to analysis, clustering, and visualization.

Bioinformatics for Geneticists
Edited by Michael R. Barnes and Ian C. Gray
Published Online: 22 May 2003
Genomic orientation, but too light and introductory for my needs, too genomic focused for my course. Good starting point book for a geneticist.

Advances in Systems Biology
Series: Advances in Experimental Medicine and Biology, Vol. 547
Opresko, Lee K.; Gephart, Julie M.; Mann, Michaela B. (Eds.)
2004
Pulled this book for A Systems Approach to Discovering Signaling and Regulatory Pathways—or how to digest large interaction networks into relevant pieces by Trey Ideker.

Microarray Gene Expression Data Analysis: A Beginners Guide
by Helen C. Causton , John Quackenbush , Alvis Brazma
2003
What it says it is: design, image processing, normalization, basic stats, clustering.

Bioinformatics: Databases and Systems
Edited by Stan Letovsky
Kluwer Academic Press, Boston, 1999
A chapter a database. Covers the usual gang, plus chapters on WIT/WIT2, KEGG, BioWidgets (Java), and AceDB (overview).

Statistical Methods in Bioinformatics An Introduction
Series: Statistics for Biology and Health
Ewens, Warren J. and Grant, Gregory
2nd ed. , 2004, 588p
errata
Heavy statistical treatment of sequence analysis. Starts with stats, then stat properties of one seq, multiple seq alignments, BLAST, Marlov chains, HMMs.

‘In Silico’ Simulation of Biological Processes
No. 247 Novartis Foundation Symposium
270 pages January 2003
Picked this up for the GO chapter. Also has a chapter on KEGG.

Micr
oarrays Methods and Applications: Nuts and Bolts

Edited by Gary Hardiman
2003
Covers topics from basic MA howtos to more specialized applications. A mixed bag. One chapter on microarray scanner evaluation, another on C. elegans 50-mer oligos made by the Hardiman lab at UCSD. Chapter text and figures are online.


Microarray Quality Control

by Wei Zhang, Ilya Shmulevich and Jaakko Astola
136 pages February 2004
What the title says. Microarrays from a core facility perspective. Ends with normatization. Covers long oligo design.

Microarray Bioinformatics
by Dov Stekel
Cambridge University Press. 2003
Thorough and clear coverage of microarray design, construction, image proc, and normalization. What caught my eye was the chapter on oilgo design, but its all good. Best single book on microarrays I’ve seen.

Bioinformatics: Methods and Protocols
Edited by Stephen Misener, Stephen A. Krawetz
Humana Press; 1st edition 2000
Program based by chapter. Too program based for a course. Has good chpaters on Clustal and Phylip. A chapter on Trascription control regions using MatInspector/GenomeInspector, weight matrix based sequence scanning for single or paired binding sites.

Computational Molecular Biology: an Algorithmic Approach
by Pavel A. Pevzner
MIT Press, 2000
Takes a unique approach. Looks at interesting computational aspects of seqeunce-based biology, and sometimes takes an odd sideways view of problems, getting deep into the underlying mathematics. A great complement to a more straightforward survey book. The topic coverage isn’t broad enough for my course, and the topics get covered in more depth than I need. Runs thorugh algorithmics of restircition digests to microarrays including, of course, sequencing by hybridization. Covers algorithmics of genomic comparisons. Great source book for a serious comp bio student.

DNA Microarrays: A Practical Approach
Edited by Mark Schena
Oxford University Press, Oxford, UK, 1999
A book on microarray technology. From DNA spotted on glass to enzymatic oligo arrays to ink jets, to microelectronic arrays. Written early on when many different approaches were being explored. Great source for technical information.

Mathematics of Genome Analysis
by Jerome K. Percus
Cambridge University Press; 1st edition 2002
Not a genomics book, but a mathmatician’ s look at DNA sequence, from clone libraries through seq alignments.

Post-genome Informatics
by Minoru Kanehisa
Oxford University Press, Oxford, 2000
Cool cover! Written by the guy behind KEGG. An eclectic choice of topics, first databases, then sequence analysis basics, then network analysis. Had a few pages on comparing networks that I found useful.

Guide to Analysis of DNA Microarray Data
by Steen Knudsen
John Wiley and Sons, New York, 2002
A what-to-do book on microarray data analysis. Very short, too short to explain how to do things, but describes what to do, issues to consider, and what results will look like. Useful as a place to start, will show you what you don’t know. The linked site has example R and BioConductor code.

Methods of Microarray Data Analysis II
Edited by Simon M. Lin and Kimberly F. Johnson
Springer, 2002
Papers from CAMDA ‘01 Various array analysis, especially advanced clsutering methods. Particularly interesting are:

  • Biology-Driven Clustering of Microarray Data; K.R. Coombes, et al.
    GO-based clustering.
  • Analysis of Gene Expression Profiles and Drug Activity Patterns by Clustering and Bayesian Network Learning; Jeong-Ho Chang, et al.
  • Topomap and bayesian clustering

DNA Arrays: Technologies and Experimental Strategies
Edited by Elena V. Grigorenko
CRC Press, 2001
What caught my eye are the technology chapters, one on oligo arrays and another on electrochemical array detection.

DNA Arrays: Methods and Protocols
Edited by Jang B. Rampal
Humana Press, 2001
This is another array technology book. Great information on ink-jet and photolithographic oligo synthesis. There are several sequencing by hybridization articles. It starts with a chapter on the history of the field by Southern. Great book for a collection of articles!

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