Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins

Book Description

Reviews of the Second Edition
"In this book, Andy Baxevanis and Francis Ouellette . . . have undertaken the difficult task of organizing the knowledge in this field in a logical progression and presenting it in a digestible form. And they have done an excellent job. This fine text will make a major impact on biological research and, in turn, on progress in biomedicine. We are all in their debt."
--Eric Lander, from the Foreword to the Second Edition
"The editors and the chapter authors of this book are to be applauded for providing biologists with lucid and comprehensive descriptions of essential topics in bioinformatics. This book is easy to read, highly informative, and certainly timely. It is most highly recommended for students and for established investigators alike, for anyone who needs to know how to access and use the information derived in and from genomic sequencing projects."
--Trends in Genetics
"It is an excellent general bioinformatics text and reference, perhaps even the best currently available . . . Congratulations to the authors, editors, and publisher for producing a weighty, authoritative, readable, and attractive book."
--Briefings in Bioinformatics
"This book, written by the top scientists in the field of bioinformatics, is the perfect choice for every molecular biology laboratory."
--The Quarterly Review of Biology
This fully revised version of a world-renowned bestseller provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. Using relevant biological examples, the book provides background on and strategies for using many of the most powerful and commonly used computational approaches for biological discovery. This Third Edition reinforces key concepts that have stood the test of time while making the reader aware of new and important developments in this fast-moving field. With a new full-color and enlarged page design, Bioinformatics, Third Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists.
This new edition features:
* New chapters on genomic databases, predictive methods using RNA sequences, sequence polymorphisms, protein structure prediction, intermolecular interactions, and proteomic approaches for protein identification
* Detailed worked examples illustrating the strategic use of the concepts presented in each chapter, along with a collection of expanded,more rigorous problem sets suitable for classroom use
* Special topic boxes and appendices highlighting experimental strategies and advanced concepts
* Annotated reference lists, comprehensive lists of relevant Web resources, and an extensive glossary of commonly used terms in bioinformatics, genomics, and proteomics
Bioinformatics, Third Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, clinical research, proteomics, and computational biology.

Customer Reviews:

Somewhat more than an out-of-date catalog of tools.......2004-03-27

The book is a collection of chapters by different authors addressing software tools for various problems: database search, multiple sequence alignment, gene prediction, protein structure prediction, etc. A big flaw is that all of the authors assume a different level of prior background and have rather different emphases.

I'd have to agree with the other reviewer that Chapters 1 & 17, which constitute 10% of the book, are wasted paper. No one in 2001 (when the book was published), let alone 2004, needs Chapter 1's lengthy explanation of what e-mail and web browsers are. And the perl program at the anticlimax of Chapter 17 was ... anticlimactic.

The book is to a great extent a catalog of available software tools. With the exception of the chapters on multiple alignment and phylogeny, the emphasis is on not on how the tools work but how to operate them -- to the of saying "at this URL there is a web page where you can either paste in your sequence or upload a file". The idea of invoking a program through a Unix command line is more than once presented as a truly daunting prospect. The authors generally do a good job of emphasizing that the programs are the beginning of analysis and not the end; the results must always be viewed somewhat skeptically with an expert eye.

If you're coming at the book as a biologist, you will probably find it to be a useful catalog of software, though undoubtedly dated by now. If you're coming at it from the informatics side, you're going to need some background... a book like Dwyer's, Setubal and Meidanis's, or Mount's will get you up to speed on the algorithm aspects of the field with simplified versions of many of the big problems. Then you can look at this book to find good pointers to the ways the real-world versions have been addressed.

The book was published three years ago and, being to a large extent an index of the work of others, is necessarily no longer up to date in a fast-moving field. It needs a revision and, in the meantime, it would make more sense to snag a used copy than to pay full price for a new book.

A survey for tool users.......2003-10-09

Like any survey, it seems to touch the major features only. And, as others have pointed out, the tools change but the book doesn't.

I think this is a good, brief introduction to the wide variety of bioinformatic tools and databases on the internet. It describes the major features of each, and the kinds of results that each tool is good for. After that, the serious user will go to the sources of each tool or database, to learn more about the specifics as of the moment. No book can hope to keep up with the weekly enhancements at the major repositories.

I emphasize that this is for tools users, not tool makers. It addresses the working scientists who already know their subjects and their needs. This skips over the algorithms in favor of higher level descriptions, and skips over many of the biological reasons for the tools described. Better-informed tool users get better answers from the tools, true. At some point, though, the biologists want to skip the theory, skip the introduction to subjects in which they're experts, and get on with their science. I don't think this book was ever meant for people - and I'm one - who want full details of the algorithms.

I agree, the book treats its many subjects in a shallow way. I think that is by intent, since the book's real goal is breadth and its target is a reader who knows the basic science. It's a bit off the center of my interests, but I've found it helpful.

Bioinformatic for the beginner..........2003-01-31

I guess that everybody interrested by this kind of book knows already a little about bioinformatic and wants to improve his bioinformatician skill. So forget about this book:
This is really a well-documented introduction to all the methods currently used by every biologist or biology student, such as Blast, Clustal, multiple alignement or use of web-interface for submiting sequence.
So get it if you need a clear introduction to the field, but if you already know a little bit about bioinfo, immediately choose a more detailed book.

Poorly organized overpriced book.......2002-09-30

Although the book is presented as an introduction to the topic, its organization assumes that the reader has already been working in the area. Two of the chapters (1 and 17) are a waste of space. The first chapter presents a (useless) introduction to internet, while chapter 17 attempts (and fails to do so) to explain Perl in the context of bioinformatics. For the same money you can find far better books in the market. The good thing is that I only borrowed the book :)

..........2002-06-27

I used the Baxevanis volume in coursework at Johns Hopkins Biotechnology program...several of the chapter authors are associated with the school. There's no doubt that the editor and authors are experts in their fields, but the volume seems somewhat dated, and is disjointed. I found a couple of the chapters virtually unreadable. The real killer is the price. The book is GROSSLY overpriced...

Book Description

This book is the first complete guide to valuation in life sciences for industry professionals, investors, and academics. Boris Bogdan and Ralph Villiger introduce the characteristics of drug and medical device development, explain how to translate these into the valuation, and provide valuable industry data. After guiding the reader through the theory of valuation, including discounted cash-flow and real options, the authors demonstrate how to value projects, patents, licences, firms and stocks on real-life examples, even treating complex licence and company structures. Special emphasis is put on the practicability of the proposed methods by including many hands-on examples, without compromising on realistic results. Ralph Villiger and Boris Bogdan have written what is sure to become the industry standard reference for valuation of pharmaceutical and biotechnology projects and companies. At a time when the healthcare industry is placing increasing emphasis on licensing and M&A as a core strategy this book provides a firm understanding of the way in which products and businesses can be valued at all stages of their development.

Dr. Martin Buckland, Chief Business Officer, Astex Therapeutics, Cambridge, UK

The book presents a number of innovative ideas, illustrated with practical examples that should improve decision-making in the drug development process, intellectual property evaluation, licensing and sublicensing. The authors make a persuasive case for the use of advanced techniques and the section on worked-examples should be particularly appealing to practitioners.

Dr. Martin Grossmann, Novartis Pharmaceuticals

There is no doubt that this book will become an essential reference tool for professionals in technology transfer, business developers and biotech companies, as well as the pharmaceutical industry and Life Science investors.

Jean-Pierre Saintouil, Director of Technology Transfer Department, Institut Pasteur, Paris, France

Introduction to Bioinformatics: A Theoretical and Practical Approach

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Introduction to Bioinformatics: A Theoretical and Practical Approach

Manufacturer: Humana Press
ProductGroup: Book
Binding: Paperback

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ASIN: 158829241X
Release Date: 2003-04-01

Book Description

Introduction to Bioinformatics: A Theoretical and Practical Approach was written as an introductory text for the undergraduate, graduate, or professional. This text provides scientists with both a biological framework to understand the questions life scientist confront in the context of the computational issues and tools that are currently available for scientific research It also provides the life scientist with a resource to the various computational tools that are available all supported with their underlying mathematical foundations.

The book is divided into four main sections. The first two sections provide an overview of the various biological processes that govern an organism and impact health. The first section, Biochemistry, Cell and Molecular Biology, describes basic cellular structure and the decoding of the genome. The second section, Molecular Genetics covers the regulation of genomes and the molecular genetic basis of disease as a consequence of genetic replication. Clinical human genetics and the various clinical databases are also reviewed. The third section, the Unix Operating System, demystifies the Unix system used throughout the world to support advanced computation tools. In addition to information on the installation and management of Unix-based software tools, examples of command line sequence analyses are presented that will enable the research to become as comfortable in a command-line environment as they are in the Graphical-User Interface environment. The final section, Computer Applications, provides information on the management and analysis of DNA sequencing projects, along with a review of how DNA can be modeled as a statistical series of patterns. It follows with a discussion of the various genome databases, the representation of genomes, and methods for their large scale analyses. Protein visualization, and transcription profiling including the use of analysis software for systems biology round out the coverage.

The volume also includes a bonus CD-ROM containing valuable software programs including BioDiscovery (for microarray analysis), ClustalX (a sequence alignment program) Ensembl, MicroAnalyser (for microarray analysis on the Macintosh), Staden Sequence Analysis Package, Tree View (for displaying phylogenies) an others. Also included is a complete set of color illustrations from each chapter that will prove invaluable for professors preparing their next bioinformatics course or seminar.

Bioinformatics Sequence Structure and Databanks ; A Practical Approach

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Bioinformatics Sequence Structure and Databanks ; A Practical Approach
Des Higgins
Manufacturer: Oxford University Press
ProductGroup: Book
Binding: Paperback

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ASIN: 0195667530

Bioinformatics: A Practical Approach (Chapman & Hall/Crc Mathematical & Computational Biology)

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Bioinformatics: A Practical Approach (Chapman & Hall/Crc Mathematical & Computational Biology)

Manufacturer: Chapman & Hall/CRC
ProductGroup: Book
Binding: Hardcover

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ASIN: 1584888105

Book Description

An emerging, ever-evolving branch of science, bioinformatics has paved the way for the explosive growth in the distribution of biological information to a variety of biological databases, including the National Center for Biotechnology Information. For growth to continue in this field, biologists must obtain basic computer skills while computer specialists must possess a fundamental understanding of biological problems. Bridging the gap between biology and computer science, Bioinformatics: A Practical Approach assimilates current bioinformatics knowledge and tools relevant to the omics age into one cohesive, concise, and self-contained volume. Written by expert contributors from around the world, this practical book presents the most state-of-the-art bioinformatics applications. The first part focuses on genome analysis, common DNA analysis tools, phylogenetics analysis, and SNP and haplotype analysis. After chapters on microarray, SAGE, regulation of gene expression, miRNA, and siRNA, the book presents widely applied programs and tools in proteome analysis, protein sequences, protein functions, and functional annotation of proteins in murine models. The last part introduces the programming languages used in biology, website and database design, and the interchange of data between Microsoft Excel and Access. Keeping complex mathematical deductions and jargon to a minimum, this accessible book offers both the theoretical underpinnings and practical applications of bioinformatics.

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Great book for protein lovers!
A great blend of biology and computer science

Bioinformatics: Sequence, Structure and Databanks: A Practical Approach

Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Paperback

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ASIN: 0199637903

Book Description

Bioinformatics covers practical important topics in the analysis of protein sequences and structures. It includes comparing amino acid sequences to structures comparing structures to each other, searching information on entire protein families as well as searching with single sequences, how to use the Internet and how to set up and use the SRS molecular biology database management system. Finally, there are chapters on multiple sequence alignment and protein secondary structure prediction. Bioinformatics will be invaluable to occasional users of these techniques as well as experienced professionals or researchers.

Customer Reviews:

Great book for protein lovers!.......2001-06-28

The title of this collection of texts is slightly misleading because the book is entirely devoted to proteins. It does not cover either DNA sequence analysis or nucleic acid structure prediction. Nor does it expose methods of "genome informatics" such as computer-assisted genome annotation or function-associated genome segmenting. Moreover the problematics of molecular evolution is covered only as much as protein phylogeny and homology is discussed. There is virtually no mention of methods for studying genome evolution.

Despite the above negatives the book provides a remarkable survey and tutorial of protein sequence and structure analysis. The editors introduction (Higgins and Taylor) is brief, precise and to the point. Chapter 1 (Jones and Hadley) and Chapter 2 (Johnson and Lehtonen) constitute a tutorial of protein structure analysis. Both chapters are likely to be informative for the beginners and enjoyable by the experts. Chapter 6 (Heringa) and Chapter 8 (Yona and Brenner) are real masterpieces and should be read by all practitioners of bioinformatics as well as by all individuals who want to learn methods of sequence analysis. These two chapters and the editor's introduction make the entire book a valuable desk reference for practitioners and a candidate textbook for students. Just to be completely fair I need to say that Chapter 5 (Henikoff and Henikoff) is potentially confusing and poorly written. The same - although to a lesser degree - applies to Chapter 9 (Harper.)

In summary: Higgins and Taylor have assembled a superb collection of short texts in protein sequence and structure analysis. Practitioners of both bioinformatics and protein biochemistry should use this book as a desk reference. Those who want to learn about bioinformatics will certainly benefit from reading selected chapters of this book as well. The book would not be harmed if it failed to contain confusing and poorly written Chapter 5 (Henikoff and Henikoff) and Chapter 9 (Harper.)

A great blend of biology and computer science.......2001-05-11

Gives a great overview of bioinformatic techniques in "sequence analysis and searching" and "protein structure analysis and prediction." Then it gives an overview of gene databases online as do all other bioinformatics books. The best part about it is that it spends 70% talking about new biology techniques which greatly helps a computer scientist like me to get into the field. Recommended.

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More like "Practicing Bioinformatician"

The Practical Bioinformatician

Manufacturer: World Scientific Publishing Company
ProductGroup: Book
Binding: Hardcover

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ASIN: 981238846X

Book Description

Computer scientists have increasingly been enlisted as "bioinformaticians" to assist molecular biologists in their research. This book is a practical introduction to bioinformatics for these computer scientists. The chapters are in-depth discussions by expert bioinformaticians on both general techniques and specific approaches to a range of selected bioinformatics problems. The book is organized into clusters of chapters on the following topics:

Ÿ Overview of modern molecular biology and a broad spectrum of techniques from computer science — data mining, machine learning, mathematical modeling, sequence alignment, data integration, workflow development, etc.
Ÿ In-depth discussion of computational recognition of functional and regulatory sites in DNA sequences.
Ÿ Incisive discussion of computational prediction of secondary structure of RNA sequences.
Ÿ Overview of computational prediction of protein cellular localization, and selected discussions of inference of protein function.
Ÿ Overview of methods for discovering protein-protein interactions.
Ÿ Detailed discussion of approaches to gene expression analysis for the diagnosis of diseases, the treatment of diseases, and the understanding of gene functions.
Ÿ Case studies on analysis of phylogenies, functional annotation of proteins, construction of purpose-built integrated biological databases, and development of workflows underlying the large-scale-effort gene discovery.

Customer Reviews:

More like "Practicing Bioinformatician".......2005-01-26

This is a survey book, with invited chapters covering a variety of subjects. This goes way beyond the basics. For example, it doesn't address BLAST internals or usage, but does describe how it can be used as one step in more complex computations.

The good parts are quite good. The first chapter's biology review is quick but generally adequate, except for a few over-simplifications like "the disease genes for ... breast cancer ... have been identified." They have? ALL of them, or just a few of the more important ones? The "Strategy and Planning" chapter is very weak, perhaps because it addresses such a huge and varied range of topics. Chapters on neural nets, motif finding, homology search (post-BLAST), probe design, and RNA structure are good, and have enough detail for a programmer to get started on. The data mining section has some good material, but doesn't really cover the full breadth of data mining (a book-length topic in itself). Other chapters, esp. phylogeny and database issues, don't rise to the same level.

The problems: Well, no index for one. There's a huge aggregate list of references (I would have preferred chapter by chapter), and even pictures of all the authors in the back, but no index. The table of contents is quite detailed, but hardly a replacement. Also, despite editorial policies meant to ensure uniformity between chapters, some inexplicable differences showed up. Sometimes it's a "translation start site (TSS)", other times a "translation initiation site (TIS)." The editing could have been a little tighter too. Criterion should be the singular of criteria, strata should be the plural of stratum, a few other annoyances should have been addressed as well. Editing should cover the illustrations, too. The diagram on p.411 has "mosquitoes" from poor compression, and the line drawings of ch.11 don't always connect connected lines. And of course this shows the usual problem of such books - it's an idiosyncratic selection of topics, giving erratic coverage to the field. If it hits your area of interest, great, but it may miss.

What's good here is quite good. It covers topics well into the post-genome age, using genome data rather than just trying to discover it. Still, the book as a whole is spotty - considering the price, I hoped for better. Also, readers expecting "Practical" to mean "Basic" are in for an unhappy surprise. You'd better have a very solid background before you pick this up.

//wiredweird

Practical Bioinformatics (Nucleic Acids and Molecular Biology)

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Practical Bioinformatics (Nucleic Acids and Molecular Biology)

Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 3540206132

Book Description

The book is unique in that. It bridges the gap between bioinformaticists and molecular biologists, i.e. the developers and the users of computational methods for biological data analysis and in that it presents examples of practical applications of the bioinformatics tools in the "daily practice" of an experimental research scientist.

The book starts with reviews on computational methods for protein sequence-structure-function analysis (sequence studies, structure prediction), followed by methods that explicitly utilize experimental data routinely obtained in the laboratory to improve the functional predictions. The second part comprises a series of examples on how particular applications of different types of bioinformatics methods in combination with experimental studies to validate the hypotheses have led to important scientific discoveries.

Therefore, the book is a guide to application of bioinformatics methods in molecular biology, addressed mainly to the research scientists, postdocs, and advanced graduate students.

Practical Guide to Protein Bioinformatics: Sequence, Structure and Function (Chapman & Hall/ CRC Mathematical Biology & Medicine)

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Practical Guide to Protein Bioinformatics: Sequence, Structure and Function (Chapman & Hall/ CRC Mathematical Biology & Medicine)
Shoba Ranganathan
Manufacturer: Chapman & Hall/CRC
ProductGroup: Book
Binding: Hardcover

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Book Description

While there are many textbooks available that provide all the information bench scientists, researchers, and students need to carry out "wet" laboratory experiments, very few sufficiently address computer-based functional annotation. Furthermore, most books on bioinformatics and computational biology focus on the genomic DNA aspects and all but overlook the vast and important area of protein bioinformatics. This book fills those gaps. It provides a comprehensive introduction to the computer-based analysis of proteins at the sequence, structure, and functional levels.

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Bioinformatics: Sequence, Structure and Databanks: A Practical Approach
Des Higgins
Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Paperback

Bioinformatics | Biological Sciences | Science | Subjects | Books
ASIN: B000OL5988

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