Book reviews

Discovering Genomics, the concept of homology and how the

Proteomics and Bioinformatics relatedness of genes can be described in
Edited by A. Campbell and L. Heyer terms of their similarity to each other.
Pearson Education, Harlow; 2003; The BLAST programs are introduced as a
ISBN 0-8053-4722-4; 352 pp.; popular similarity search method. Next, it
£35.37; Paperback deals with the utility of genome
sequences: phylogenetic trees allow us to
The advent of rapid DNA sequencing visualise the ancestral relationships
techniques has allowed us to accumulate between species; our ability to identify
genomic information at an unprecedented organisms from gene sequence will help
rate; the determination of viral and other us to diagnose existing, and newly
small genomes is now commonplace and emerging, diseases; and the field of
the human genome sequencing project is biomedical genome research may
nearing completion. Importantly, the field accelerate the development of new

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of bioinformatics has emerged to supply medications. The unit concludes with
us with the tools to store, handle and genomic variation, the existence of single
interpret the enormous quantity of data nucleotide polymorphisms (SNPs) and the
now available. As a result, biology field of pharmacogenomics, which is
students are now able to think in more concerned with how variations at the
global terms, towards entire genomes and genetic level translate to altered efficacy of
the proteins which they encode. drugs in the clinic. Some ethical
Discovering Genomics, Proteomics, and implications are considered, such as the
Bioinformatics, edited by A. Malcolm consequences of genetic testing and the
Campbell and Laurie J. Heyer, introduces use of genetically modified organisms
students to this new perspective, by (GMOs).
combining a text book with an interactive Unit 2 deals with genome expression,
teaching resource on the web and devotes much of its time to DNA
(www.geneticsplace.com). A free CD- microarrays. The impact of DNA chips
ROM accompanies the text and features on health care, particularly cancer, is
all figures and tables in colour. The book discussed and numerous case studies
is composed of four units and takes the demonstrate the enormous potential of
reader from DNA sequence acquisition to this technology. The remainder of the
the analysis of microarray data and the unit comprises several sections on
concept of genomic circuits and protein proteomics — addressing protein
interaction networks. Case studies are structure, function and the interaction
used for illustrative purposes throughout, networks in which they take part. Some
and exemplify the role of the genomic of the quantitative and qualitative
sciences in society. Chapters are methods available for proteome analysis
punctuated with ‘math minutes’, which are described, from traditional two-
provide mathematical background to the dimensional electrophoresis-based
biology, and ‘discovery questions’, which approaches to state-of-the-art techniques
encourage students to critique published that utilise mass spectrometry and the
literature, use online tools and databases emergence of protein chips.
and draw their own conclusions from the Unit 3 is concerned with genomic
data presented. circuits, building from what we know
Unit 1 focuses on genome sequences: about a well-characterised single gene, sea
how they are determined, methods used urchin Endo16, to integrated multi-gene
in their characterisation and the databases networks. It takes the reader from a single
which house the information. It describes gene perspective towards the idea of a

& HENRY STEWART PUBLICATIONS 1473-9550. B R I E F I N G S I N F U N C T I O N A L G E N O M I C S A N D P R O T E O M I C S . VOL 2. NO 2. 159–163. JULY 2003 159
Book reviews

cellular ‘web’, in which genes interact and databases. More importantly, it would
regulate each other’s transcription. The have illustrated the collaborative nature of
concept of genetic toggle switches is the nucleotide sequence data resources
introduced; these allow the genome to which help to fuel the genomic sciences.
make ‘decisions’ and regulate its own The companion website provides
activity in response to a changing useful background on some of the more
environment. The emergence of systems commonly-used analytical methods, a
biology is touched upon, showing how collection of three-dimensional structures
models of interaction can be built which to accompany the text, some sample
closely mimic experimental systems. amino acid and nucleotide sequences for
The majority of Unit 4 is presented as cut-and-paste submission to online tools,
case studies, which bring together various and some links to online databases and
elements of the book into a set of problem bioinformatics resources. The CD-ROM
solving exercises. The book concludes proves particularly useful for the
with some of the challenges which lie microarray images, where spot patterns
ahead in our ability to dissect and treat can be visualised in full colour. Overall,
disease at the genetic level. Genomic the general approach of the book sets it

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diversity amongst individuals and the apart from related texts; the writing style
polygenic nature of most diseases are is relaxed and the emphasis on published
highlighted as major obstacles in creating literature and current research seems
treatments that are effective in all cases. appropriate for a discipline in its infancy.
The extent of this problem is illustrated by The companion website allows students
the difficulties experienced in altering the to inspect data firsthand and equips them
specificity of aspirin, a simple and well- to perform basic genomic analysis. Besides
characterised small molecule with a long biology students, this would be a useful
history of use in health care. guide for anyone wishing to familiarise
The scope of the book is intentionally themselves with the genomic sciences and
broad and covers a great deal of ground in the wide range of bioinformatics tools
a little over 300 pages. Naturally, there is publicly available on the internet.
a trade-off in that some topics are under-
addressed. In particular, I felt that the Paul Bradley,
introduction to sequence analysis in European Bioinformatics Institute,
Chapter 1 could have been expanded Wellcome Trust Genome Campus,
upon. In addition to the pairwise Cambridge, UK
alignment methods described, those
which utilise multiple sequence
alignments are widely used. Alignments of
gene families and domain families reveal
Analyzing Medical Data Using
the existence of conserved motifs, which S-plus (Statistics for Biology
provide us with signatures that can be and Health Series)
used to characterise a novel protein or Brian Everitt and Sophia
nucleotide sequence. A description of Rabe-Hesketh
some of the more common secondary, or Springer Verlag GmBH & Co. KG,
pattern, databases would have been useful Tiergartenstrasse 17, D-69121
to supplement those sections dealing with Heidelberg, Germany
prediction of gene function from December 2001
sequence. Also, an explanation of the ISBN 0-387 98862 9; pp. 485;
relationship between GenBank, the £56.00; US$79.95; A 79.95
European Molecular Biology Laboratory
(EMBL) and the DNA DataBank of Japan The analysis of massive amounts of data
(DDBJ) would have bridged the sections that has become possible through the new
dealing with sequence acquisition, and methodologies is still a debated and highly

160 & HENRY STEWART PUBLICATIONS 1473-9550. B R I E F I N G S I N F U N C T I O N A L G E N O M I C S A N D P R O T E O M I C S . VOL 2. NO 2. 159–163. JULY 2003