Discovering Genomics, Proteomics, and Bioinformatics

Rating:
Summary: A novel approach!
Review: Abstract: great and innovative book. I have seen many books, but none like this. It is still concise in this first edition, yet could become the "Lewin" of genomics.
Score: 9/10.

Recommended to students: yes, together with classic works like Brown.

Recommended to Central Library: yes.

1. The supplied CD-ROM is a nice teaching aid. Yet, it is difficult to "extract" pictures from it for teaching purposes. It would be much more useful if the pictures were individually supplied in standard high-quality graphic formats like TIFF, instead of PDF. The later is perfect for distributing text with pictures, but not to retrieve such pictures. Other publishers distribute the book artwork as individual TIFF files. That approach greatly enhances the book and boost sales. This is particularly useful for teachers. Actually, it is a must for us these days. Please, make sure that future versions of the CD-ROM or DVD-ROM are --as this one-- compatible with the open-source Unix-based Mac OS X platform. Thanks.

2. The associated web page "Instructor's Guide"3. The discovering questions are terrific. Please, expand them in future versions.

4. Math minutes are an excellent idea.

5. Boxes are welcome. Please, include more.

6. Also helpful are the boldface words on each chapter. Perhaps they could be also included in a keywords at the beginning of each chapter.

7. The index should be more comprehensive and should have all main entries in boldface. This is important to any index and very few books have it right.

8. The glossary is helpful. It should be more comprehensive,
including more terms.

9. The summaries and conclusions are great, yet should be expanded to include more relevant information. They should be like a "minichapter" an the end of each chapter or --better-- at the beginning. All partial summaries could be pooled into a larger summary that way.

10. Addendum sections could be included as separate notes or boxes.

11. The pronunciation tips for new words are also an excellent idea; mostly for non-English speakers.

12. The classified references are really useful. Well done. If they were commented or "annotated" they would be just perfect.

13. A list of abbreviations would be welcome. A list sorted by the full name would be very handy as well.

14. What about telomerase and aging? What about the fact that
unicellular organisms are immortal? Or stem cells? Or tumor cells? Death is a tax that multicellular organisms have to pay to nature in order to evolve. Yet we humans might change that soon.

15. It should be clearly indicated the organisms with genomes made of dsDNA, ssDNA, dsRNA and ssRNA.

16. Missing bioinformatics tools and step-by-step analysis of genes and mRNA (see next) and whole genomes.

17. It would be really helpful to explain clearly and analyze --even from a bioinformatics point of view-- the structure of genes, mRNA, CDS, introns, exons, promoters and terminators. It is not clear where do these elements start or end or how to recognize them. Diagrams and graphs would greatly help to explain these absolutely basic and fundamental concepts. In other words, imagine that you have cloned and sequenced a genomic gene as well as a full mRNA (cDNA). Now you want to publish your results and for that you do a comprehensive description of your gene (chromosome) and cDNA (mRNA). That is precisely the kind of information that is missing as a diagram and explanation. In this way, it should be indicated that you may encounter several ATG (or other) starting coding triplets in the mRNA, that if the 20 or so amino acid residues of the 5'-end of a peptide have a high percentage of hydrophobic residues, they are likely part of a leading peptide which would be further excised, that you may encounter several polyadenylation signals, etc. On the genome side, the promoter and terminator structures should be analyzed, as well as the intron-exon boundaries.

18. Likewise, it should be indicated the tools and current
possibilities to determine or predict the 3D structure of a protein (folding) from the primary structure of the peptide.

19. Does not mention Lasergene package of DNAStar20. Which genes are best to draw dendrograms? Differentiation between genes from the nucleus or organelles (mitochondrion or chloroplast). Likewise for DNA fingerprinting and molecular markers.

21. Differential display methodologies are missing (as well as other methodologies of gene expression like subtractive hybridization).

22. Large-scale sequencing is missing. For instance, sequencing of single-molecules will allow the sequencing of whole chromosomes or genomes.

23. Missing tables comparing different genomes with full details
(size, ploidy, percentage of genes, introns, exons, repetitive DNA, junk DNA, etc).

24. Reference to manufacturers is very useful. Please, include also links to web sites. Best if all manufacturers are included as an appendix.

25. All web sites (NCBI, etc) and web-based applications (BLAST, ORF Finder, etc) should be clearly indicted in an appendix.

26. It is not indicated that the PCR was in fact described with full details by Khorana et al 14 years before Mullis et al.

27. Please, include more drawings and pictures in the printed book and CD-ROM.

28. Suggestion: including chapters on eukaryotic-genomic DNA
libraries, cDNA libraries, subtractive libraries.

29. Suggestion: including chapters on plant and animal transformation.

30. Suggestion: including drawing of Maxam-Gilbert sequencing method and Sanger method (Applied Biosystems electropherograms,
electrofluorograms).

31. Prions, viroids and viruses could be also included.

32. A title index at the beginning of each chapter would be very
useful. Besides the goals for chapter, which are quite useful.

33. Bioinformatics could be significantly expanded.

34. QuickTime videos explaining some topics would be fantastic.
Please, make them in QuickTime (best quality, platform-independent).

35. All in all, a great novel approach. Keep up the great work!

Rating:
Summary: Simply fascinating
Review: The sheer number of books in the area of bioinformatics is growing rapidly, and each author takes a different approach to the topic: Bergeron's Bioinformatics Computing uses concepts from Information Theory, while Pervzner's Computational Molecular Biology uses Graph Theory and Durbin et. al. Biological Sequence Analysis use Statistics and hard core mathematical analysis to get the point across. Campbell and Heyer, the authors of Discovering Genomics, Proteomics, & Bioinformatics use concepts from Electrical Engineering and Control Engineering to prescribe some of the details of genomics and proteomics. As an instructor you need to choose the right book to meet the needs and understanding level of your target audience. For biology students that have little mathematics or statistics knowledge but have taken Physics II (E&M), this would be the perfect book. The authors are a little heaving on the biological terminologies, so a sophomore level Computer Science major with little or no biology background would have a difficult time coming up to speed at the beginning, but the glossary of terms at the end of the book is comprehensive enough that can aid the learning process.

The approach to figuring out what, where and how genes are controlled using what are called circuits is simply fascinating. Genes are controlled in three ways: location of the gene, the time of control and the amount. These three metrics can easily be mapped to circuit diagram in Electrical Engineering using the concept of switches (transistors) and time varying influencers (control theory and feedback loops), the authors describe of genes are regulated. One can imagine that the process of mapping genes into circuits is a difficult task, and one would be right. In fact, only one gene, the Endo16, has been fully expressed in circuit diagrams and that task took years of research. Imagine the amount of man power and hours it would take to draw the circuit diagram for the entire human genome of over 35000 genes! Even the concepts of noise in the circuit and complex integrated circuits are explored in details. The authors make no hesitation in telling the readers what the unknowns are and what topics are under intense investigation. It is amazing to realize that we still a long way to go, and what we are seeing thus far is just the beginning on a very long journey.

In general, the book is very interactive filled with Discovery Questions, Math Minutes and a CD simply filled with tons and tons of pictures that are in PDF format that can be printed in need be. There is also a Web site that accompanies this book that explains various bioinformatics methods, and contains information required by some of the Discovery Questions. The text itself is divided into four units:
1) Genomic Sequences which talks about the whole picture of genomic analysis and its benefits. The question of why this field of study is so important and what we hope to gain from in the coming years and decades is also answered. The students are exposed to topics in the areas of biological weapons, antibiotics and how they work, the evolution and survival of DNA and ethical consequences of genetics and genetic engineering.
2) Genomic Expressions in which the how and where questions are answered in detail. How did we gather all of this information? DNA microarrays are discussed in detail including advanced research in the area and who is doing in. Proteins microarrays are also discussed, but not in as much details due to the fact that protein microarrays are very much in their infancies. The authors do make a number of predictions in terms of where the proteomics area of research is heading and what we need to get there.
3) Whole Genome Perspective. The bottom up approach takes the readers to the whole genome analysis, and that's where the authors discuss the notions of electronic circuits in describing the genome and proteins prescription.
4) Medical Case studies in the areas of drug discovery bring this book to an end. The authors tackle questions such as how a disease is discovered and researched, and go into some of the misconceptions of drug discovery and end the book with why discovering a new drug is such a difficult task.

A complete text with the entire information one would need to come up to speed with the area of life sciences. A good mix of biology, mathematics, statistics, engineering and computer science give the reader a comprehensive overview of the current problems, research areas and new developments in the field of bioinformatics.

I recommend this text for a bioinformatics course with students of biology with little mathematics and statistics background. The text is easy to read and follow. The accompanying CD-Rom is field with relevant pictures, graphs, etc, that can further the learning process.