Introduction to Bioinformatics [Paperback]

Arthur Lesk (Author)

Book Description

ISBN-10: 0199208042 | ISBN-13: 978-0199208043 | Publication Date: June 2, 2008 | Edition: 3

An Introduction to Bioinformatics introduces students to the immense power of bioinformatics as a set of scientific tools. The book explains how to access the data archives of genomes and proteins, and the kinds of questions these data and tools can answer, such as how to make inferences from data archives and how to make connections among them to derive useful and interesting predictions.

Blending factual content with many opportunities for active learning, An Introduction to Bioinformatics offers a truly reader-friendly way to get to grips with this subject, making it the ideal resource for anyone new to the field.

Features
- Strikes a careful balance between biology and computer science, introducing those aspects of computer science which underpin the subject without demanding detailed prior knowledge.
- Contains numerous learning features, including exercises, problems, and WebLems.
- Retains the eloquent style and clarity of explanation for which the author is renowned.
- An Online Resource Centre includes figures from the book available to download to facilitate lecture preparation, as well as a variety of interactive resources, including web links, 3D structures, and data sets.
ew to this Edition
- New chapter on biological organization in space and reflects recent advances in genomics, transcriptomics, proteomics, and metabolomics.
- New chapter on scientific publications and archives provides a state of the art inventory on sourcing scientific literature.
- Expanded coverage of structural bioinformatics.
- Enhanced Online Resource Centre, with new guided tours of key websites, and lab assignments to support the in-depth exploration of concepts and themes covered in the book.

Editorial Reviews

Review

`Review from previous edition I have a very favourable opinion of this book. It covers the basics of all aspects of bioinformatics at a level that is very compatible with how I teach. The amount of material presented is appropriate for a one semester class. The problems are excellent: well thought out and plentiful.' Dr Mitrick A. Johns, Northern Illinois University, USA

`I like Lesk's conceptual style. It is close to how I teach...it provides a little bit of web sites, a little bit of algorithms, a little bit of theory, and much casual exposure to a range of bioinformatics topics. It is easy to use as a text. ' Dr Lorraine Marsh, Long Island University, USA

`This is a very good introductory textbook in bioinformatics. It is well-structured and nicely laid out. There are numerous examples and problems attached to each chapter, including the novel Weblems.' Dr Karen Page, University College London, UK

`Overall the book is well laid out. There is a good mixture between information text and case studies. There is a good selection of recommended reading and problems at the end of each chapter. I like the learning goals at the beginning of each chapter and the plan of the book before chapter 1.' Dr Dawn Louise Arnold, University of the West of England, UK

About the Author

Arthur M. Lesk is Professor of Biochemistry and Molecular Biology at The Pennsylvania State University, USA.

Product Details

• Paperback: 432 pages
• Publisher: Oxford University Press, USA; 3 edition (June 2, 2008)
• Language: English
• ISBN-10: 0199208042
• ISBN-13: 978-0199208043
• Product Dimensions: 9.6 x 7.4 x 0.7 inches
• Shipping Weight: 2.4 pounds (View shipping rates and policies)
• Average Customer Review: 5.0 out of 5 stars  See all reviews (1 customer review)
• Amazon Best Sellers Rank: #270,185 in Books (See Top 100 in Books)
  • #38 in Books > Professional & Technical > Professional Science > Biological Sciences > Bioinformatics

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Customer Reviews

Most Helpful Customer Reviews

2 of 2 people found the following review helpful:

5.0 out of 5 stars Excellent introduction, but a bit light, September 11, 2011

By 

Eric "Siggy" Scott (Annandale, VA) - See all my reviews

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This review is from: Introduction to Bioinformatics (Paperback)

Lesk's introduction is an excellent guide for the newcomer to the world of large-scale genomic data. It is my opinion that you can end your search here for an entry point to the modern field of bioinformatics. It's organized around tools of the trade rather than grandiose theory (systems biology discussions left off till the last chapter), and will serve better as a introduction for undergraduates or researchers new to the field than a reference book for experts. It's biggest perk is the lucidness of discussion and readability.

As best I can tell, the target audience is undergraduate biology students who have basic familiarity with computer programming. Virtually no mathematical sophistication is required -- there is not a proof in sight, and complex mathematical topics like Hidden Markov Models and Monte Carlo algorithms are explained in an unintimidating, intuitive manner. Computer science knowledge such as graph theory, dynamic programming, and computational complexity are introduced minimally and only when they are needed.

Biological concepts are also sufficiently explained, except for perhaps a term here and there, and as a computer scientist I found the book a cinch to read.

Lesk's writing style is lucid and motivated. You know not only what you're learning, but why you're learning it and what you can do with it. Therefore, the book is self-contained and is excellent for self-study.

The first half of the book (Chapter 1-4) are a high-level overview, and a practical summary of existing databases of genetic and proteomic data. This serves an excellent guide for those who A) need to become familiar with the websites that "everybody" in the field knows about, or B) are eager to get their paws on sequence data and start playing! Chapter 3 even gives a (very) brief introduction to data mining and natural language processing for extracting information from the literature.

Chapters 5-7 are the meat of the matter. Sequence alignment (chapter 5) is "THE basic tool of bioinformatics" (p. 243), and is what much of the technical material is organized around. Dotplots, single and multiple sequence alignment, profiling, BLAST, PSI-BLAST, Hidden Markov Models, and phylogenetic trees are all discussed and situated so that the read knows the advantages and disadvantages of each tool, and their limitations used to motivated future chapters on protein structure.

Chapter 6 covers protein folding, structure prediction, classification, and function prediction, as well as applications to drug discovery.

Chapter 7 ends the book with a more theoretical, big-picture discussion of systems biology, information theory, and regulatory networks.

Overall, I think this book is great. It will give you a solid, if low-resolution understanding of the field, and the writing style ensures that you have a genuine understanding of the tools' relationship to scientific questions. The book is full of practical tips like "Visual examination of multiple sequence alignment tables is one of the most profitable activities that a molecular biologist can undertake away from the lab bench. Don't even THINK about not displaying them with different colors for amino acids of different physiochemical type" (p. 271). He also is careful to emphasize difficulties in, for instance, inferring homology from sequence similarity, and in making assumptions about mutation rate. And if you are a biologist who doesn't need more than a basic understanding of the most effective tools, maybe this is sufficient.

Perhaps best of all, you can actually *read* a book like this from cover to cover! And you will actually *remember* what you read!

That said, as a computer scientist with a math degree under my belt, I did miss the presence of rigorous mathematics. The academic field of bioinformatics is much more technical than this introduction-for-mathophobes would imply, as other books like Waterman's (now outdated) Introduction to Computational Biology: Maps, Sequences and Genomes (Chapman & Hall/CRC Interdisciplinary Statistics) makes painfully clear. Then again, that's probably why I didn't ever finish reading Waterman!

That said, I should point out that I was never bored with Lesk's description of algorithms.