My favorite bioinformatics books

*Please refer to Data analysis reference books section in My favorite microarray books for recommendations on data analysis references!

General introduction
Specific topics

Price: US$69.00

Price: US$95.00
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Reviewer: birgitpils (see more about me) from Redwood City, CA United States
David Mount did an excellent job introducing bioinformatics to biologists. Without a lot of Mathematics he explains the algorithms used for sequence alignments or phylogenetics, much better than any other book I have seen. Particularly, I found the chapter about Phylogenetic Prediction very helpful, that shows advantages and disadvantages of the numerous phylogenetic analysis programs with a lot of examples and helps the molecular biologist to decide which one to use. Although this book is quiet expensive, I think it is worth every penny!

Price: US$60.00
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Reviewer: A reader from Cambridge, MA USA
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.)

Price: US$24.46
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Reviewer: Thomas J. Dougherty from Cheshire, CT USA 
As a research scientist at a major pharmaceutical company, I became involved with microbial genomics four years ago. I have become familar with bioinformatics by talking and working with colleagues in my company, but on more than one occasion in the past, I found myself baffled by some detail or aspect of this new and rapidly evolving field. This book, Developing Bioinformatics Computer Skills is an outstanding introduction for the biologist attempting to become broadly familar with the basics of the bioinformatics field. The authors begin with a highly informative introduction to the Unix operating system, and then proceed to describe many of the basic tools for sequence analysis, database searching, multiple sequence alignments and  phylogenetic analysis. This section has an outstanding non-mathematical explanation of scoring matrices and dynamic programming for alignments. This  is followed by chapters on protein structure and predicting protein structure and function from sequence. They also discuss tools for sequence assembly,  annotating genomes, proteomics and biochemical pathway databases. There is an excellent chapter on analysis of large data sets using Perl scripts. The  book closes with chapters on building relational databases and data visualization. The material is well written and clearly presented, and can serve as an excellent springboard to more advanced texts in the field. I highly recommend it to those who are beginning to use bioinformatics, as well as to those more experienced who would like a ready reference with the basics all under one cover. Well worth the modest price!! 

Price: US$35
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My comments:
A well written book provides you the basic ideas about the challenges in analysing the vast amount of genome data and simple explanations of the theories behind the informatic tools. Chapter 4 discusses on the potentials of bioinformatics analysis of molecular/ metabolic pathways in future. 

Reviewer: Steven Forth (see more about me) from Vancouver, BC Canada
The author has a vision of where bioinformatics needs to go and he articulates this clearly. Most books in the field are blinkered by comparison. Chapter 4 on network analysis of  moelecular interactions is a valuable (if general) contribution to the discussion on how computational and systems models can be applied to deepening our understanding of how pathways might actually work, and how these models can be connected to existing data resources.

Price: US$89.50
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Reviewer: Pethuru Raj Chelliah  from Japan
This book gives an overview of the powerful suite of software tools available for various computer applications of molecular biology. The initial chapters talk about many programs(comparisons, Database searching, sequence analysis, Gene Finding, pattern recognition, etc.) and web-based interfaces in  addition to the utilities for sequences, databases etc., packed in Wisconsin package apart from short briefs of how to use these tools in a desktop  environment. Also this book gives the details of sequence analysis tool called Omiga and its diverse functionalities. Biological Sequence analysis software like MacVector and Lasergene gets enough attention in this book. Also sequence type-dependent and  platform-independen tools like PepTool and GeneTool are also explained in detail.  Two important applications in molecular biology, gene identification and biological pattern detection have received a greater significance here. There is  also a chapter about network computing for biologists. This book lists out a set of free molecular biology software available in different web servers. A lot of relevant information about the journals online,  research institutions and organisations and biological information repositories with their web site details and references are also accommodated. There are separate chapters for web-based resources for NCBI(National Center for Biotechnology Information)and EBI(European Bioinformatics Institute) besides a  number of computing resources for geneticists. 

Price: US$69.95
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Reviewer: bjdc from Pomona, CA United States 
I'm always looking for a good guide book for undergrads and biocomputing novices that covers the basics without getting carried away with algorithmic minutiae. I found this book a fair place to start for those who have no idea of what is out there. The tools and Web sites described are mainstays and likely won't be going anywhere. However, if you are already moderately knowledgeable, you will exhaust this book immediately. The nature of the field is constant movement toward newer and more thorough tools. This is not a users' guide: go to the referenced Web sites themselves to get the most up to date, accurate information. 

Price: US$35
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My comments:
This is a very good  introduction book. The first 2 chapters cover the basis of bioinformatics and internet infrastructure. The later chapters discuss the analysis of DNA sequences, alignments, different secondary and protein databases. The principals behind different secondary databases and alignment algorithms are clearly and simply discribed. There is one excellent chapter with online exercises that guide you step by step to build up a protocol to start from an unknown DNA sequence from primary sequence analysis to secondary and finally 3-D structural analysis. A must read for beginner!

Reviewer: Dr N.E Fisher (n.e.fisher@btinternet.com) from University College London 
This is a concise and well-written introduction to the rapidly advancing field of bioinformatics. A suitable target audience would be final year undergrads, postgrads and doctoral workers looking to be brought up to speed in this key area. Recommended, and great value for money.

Price: US$59.00
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Reviewer: a student from Taejon Korea 
This book is introductory. It deals with many topics such as biological sequence analysis, hidden markov model(HMM), gene prediction using  Neural Networks, RNA splicing signal model, evolutionary approach and protein structure modeling. It is helpful to glimpse a broad overview of these topics, however the explanations are rather superficial. Especially the chapters covering sequence analysis are too concise. 

Price: US$69.95
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My comments:
It is a good introductory book to the people interested in bioinformatics. It covers some databases structure, a lot of useful bioinformatics tools for data analysis like GCG. It is a little bit too program-oriented, so you have to sit besides your PC and try the respective program or file in order to learn efficiently. (my opinion is based on the 1st edition)

Reviewer: A reader from US
"The novice user of bioinformatics tools needs a guide that answers several fundamental questions - what are these tools designed for and what can they do; what are their limitations; how does one access them, and where can one find further information. For each of the basic sub-fields of bioinformatics, Bioinformatics provides a survey, a list of world wide web addresses (URLs), and a list of monographs and reviews to which the reader may go for further  information. Each chapter covers fundamental definitions and makes no assumptions about prior knowledge.... The book provides a broad overview of the basic tools for sequence analysis. It is a good starting point for the reader who wants to learn about the types of tools used in bioinfomatics and how to get started. For biologists approaching this subject for the first time, it will be a very useful handbook to keep on the shelf after the first reading, close to  the computer." --Terry Gaasterland, The Rockefeller University

Price: $74.00
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Editorial Reviews From Book News, Inc. 
Describes the bioinformatics needed to achieve a meaningful analysis of the unprecedented amount of research data on the human genome and presents information on the practicalities of making effective use of computing in the generation, processing, analysis, and storage of data, as well as in making the data available to the research community. This second edition provides a new chapter on the rise of the World Wide Web as a major source of access of information in the field, detailing the material and services that may be obtained. Book News, Inc. Portland, OR 

Price: US$27.97 
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Reviewer: jxgardner from davis, ca United States
The author presents Perl in a thorough, well organized fashion,always reinforcing the use of the basic tools ...scalars,arrays,hashes, regular expressions,loops and subroutines,parsing data banks,relational databases,perl modules,program design and so on.He presents clearly ,giving many examples of real life biological problems. It assumes little if any programming background, although a knowledge of C and Unix would be very helpful. This is definitely a must for anyone learning Perl for molecular biology. 5 stars ++

Price: US$44.95
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Reviewer: A reader from Cambridge, MA USA 
The title is somewhat misleading because the book is primarily devoted to combinatorial methods that could be used in genome sequencing and genomics. The selection of methods is arbitrary and does not seem to be dictated by either pedagogical or scientific vision. It mainly reflects the author's own work and interests. Contrary to what the editorial review states I find this text quite abstract and formal. I like the book very much but I don't think it should be  recommended to the beginners in computational biology. Readers who have a taste for mathematics and a strong background in combinatorics could  benefit the most from reading this book. Anybody who looks for a textbook-level guidance in computational biology should probably rely on better designed texts such as Don Gusfield's "Algorithms on strings trees and sequences" or "Biological sequence analysis" by Durbin and co-authors. However, the readers who are interested in mathematics behind designs of DNA arrays (chapter 5) or in mathematical treatment of genome rearrangements  (chapter 10) should certainly read this book in detail. 

Price: US$29.95
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Reviewer: Eser Ayanoglu from Palo Alto, CA USA 
If you are looking for a clear, brief and to the point source for probabilistic and statistical basis of data analysis for bioinformatics, I would recommend this book. Such background is critical for serious bioinformatics related research. The beginning of the book has essential introductory topics such as probability theory, distributions , information theory and clustering methods. Multiple sequence alignments, and construction of phylogenetic trees are also part of the book. Then some other topics such as probability models, model fitness, neural networks, decision trees and protein structure prediction are included. I think that literature references as concrete examples and also links to valuable sources are very beneficial. 

Price: US$49.95
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Reviewer: A reader from ILLINOIS 
Very well written, clear, and self-contained. The authors provide a masterly treatment of machine learning methods (neural networks, hidden markov  models, etc.) and their applications to fundamental problems in sequence analyis and biology. The book goes all the way from first principles to advanced  research topics and should be valuable for both students and researchers. Second edition has many new topics, including DNA microarrays. Requires some concentration but mathematical details are summarized in the appendices. I strongly recommend it for anyone with an interest in bioinformatics and/or machine learning. 

Price: US$44.95
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Reviewer: dataguru from Seattle, Washington 
This is a first book introducing support vector learning, a very hot area in machine learning, data mining, and statistics. Aside from Burges (1998)'s tutorial article and Vapnik (1995)'s book, this book by two authors actively working in this field is a welcome addition which is likely to become a standard reference and a textbook among students and researchers who want to learn this important subject. Besides tutoring systematically on the standard theory such as large margin hyperplane, nonlinear kernel classifiers, and support vector regression, this book also deals with growing new areas in this field such as random processes. More interestingly, this book discusses a lot of applications which I consider very imoportant and healthy for the advance of this  field, such as medical diagnosis, image analysis, and bioinformatics. In all, I strongly recommend this book for students, and young researchers who want to learn. I'm sure a lot of people will find this book a wise investment, since it provides a handy and timely review of a rapidly growing field. 

Price: US$55.00
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Reviewer: A reader from West Lafayette, IN USA 
I have studied this book for some time now. The book is clearly directed to researchers in the area of pattern discovery with particular attention to biomolecular data. It collects contributions from the some of the most important research groups in the field. Each chapter is written by a different group  but they are all very interesting. I have only a complaint about the quality of the print, not good enough for the cost of the book. 

Price: US$34.95
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Reviewer: Lee D Carlson from Global Mathematics, Inc St Louis, MO 
This book is a very well written overview to hidden Markov models and context-free grammar methods in computational biology. The authors have written a book that is useful to both biologists and mathematicians. Biologists with a background in probability theory equivalent to a senior-level course should be able to follow along without any trouble. The approach the author's take in the book is very intuitive and they motivate the concepts  with elementary examples before moving on to the more abstract definitions. Exercises also abound in the book, and they are straightforward enough to  work out, and should be if one desires an in-depth understanding of the main text. In addition, there is a software package called HMMER, developed by one of the authors (Eddy) that is in the public domain and can be downloaded from the Internet. The package specifically uses hidden Markov models to perform sequence analysis using the methods outlined in the book.