5 Responses to “Discovering Genomics, Proteomics and Bioinformatics”

1. By Larissa Gallo on Feb 1, 2010 | Reply

   This was a great textbook. The website was very helpful and I liked how the author did not waste paper/printing/money on images and half of the information was on the web. It was nice not carrying around a heavy text all semester, even if half my reading/work was done in front of a computer. A lot of information packed into this book. One sentence sometimes requires a lot of knowledge (thank goodness for my professor who explained it all). I would have to say, without a lecture, I would walk away from this text thinking I knew something but not knowing much at all. For an amature like me, I definitely need a lecture to go along with this text. Although some mistakes were found, a lot less than the first edition (so I’m told). Rating: 5 / 5

2. By Donald L. Copeland, MD on Feb 1, 2010 | Reply

   This book is for students who have considerable knowledge of Biology that has included basic Genetics and Genomics. For those of us who studied Human Genetics in the 1960′s it is a challenge to read and understand. If one is willing to study and learn completely new information including many new words and terms this book will enlighten one as to where we are in Genomics today and give insight into the future of Medicine. In the forty-five years that I have been a Family Physician there is nothing that has changed the practice of Medicine like this new field of Genomics and Proteomics most likely will. My suggestion to any physician who plans to practice more than five years
   
   is to buy this book and find a Professor like Dr. Campbell to guide you to understand this new and exciting subject. Rating: 5 / 5

3. By J. Estill on Feb 2, 2010 | Reply

   This book follows a convoluted path to describe basic methodologies that could be taught in a much more straightforward manner. The authors get so mired down in the biology of specific applications of bioinformatic tools that the tool itself falls into the background. The poor layout of the book even makes it difficult to read. The main text of the book is interspersed with examples, “Math Minutes” and other text which are not properly set off from the main text.

   The web links associated with the book are outdated and do not appear to be updated by the publisher to keep up with changes. If a web site is associated with a book, it should at the very least keep up with changes. In a quickly changing field such as bioinformatics these updates are absolutely critical.

   The book is also overpriced given the low quality content and paperback binding. The figures are subpar with only purple and gray coloring. I would expect at least a few full color figures for a book at this price point.

   Overall I would say that this book is not a useful tool for teaching bioinformatics or genomics. Rating: 1 / 5

4. By John Matlock on Feb 2, 2010 | Reply

   This book represents a breakthrough in textbook design. It starts with a ‘case study’ for a child visiting you the physician. You get the basic symptoms from the mother, then you are sent to the web to go attempt to establish a diagnosis. And you are not sent to some private web site, but to the Online Mendelian Inheitance in Man (OMIN) database of human diseases and genes, and to the National Center for Biotechnology Information. Immediately the student is exposed to a wealth of information far beyond what any book could provide. It’s rare that you see a textbook that attempts to take the student into the real world.

   Intermixed with the case studies is textual materials that provide the student with the basic background that they need. In addition there are almost random Math Minutes and Discovery Questions that direct the student into further depth of understanding.

   If you are planning to teach this kind of class, you owe it to yourself to at least investigate this book before selecting a text. Rating: 5 / 5

5. By Anonymous on Feb 2, 2010 | Reply

   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 DNAStar
   20. 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: 4 / 5