My favorite microarrays, protein microarrays, biochip/ lab-on-a-chip, microarray data analysis reference, general data analysis and statistics reference & experimental design reference books

Microarray books
Protein microarray books
Biochip/ Lab-on-a-chip books
Microarray data analysis reference books
General data analysis and statistics reference books
Experimental design reference books

Price: US$45.00 
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Reviewer: A reader from SEATTLE 
"Very complete : covers both the experimental and the computational methods with specific examples. Written by two top scientists who  have worked hard at complementing each other's strengths. I particularly enjoyed the last chapter on Systems Biology which provides a masterful overview of current resaerch trends." 

Price: $89.95 
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Microarrays, widely recognized as the next revolution in molecular biology, enable scientists to analyze genes, proteins and other biological molecules on a genomic scale. This emerging technology, used in more than 10,000 laboratories already, is having an enormous impact in all areas of biomedicine and across the agricultural, biotechnology, and pharmaceutical industries. Mark Schena’s Microarray Analysis is the first textbook in this revolutionary new field of study. This comprehensive and multidisciplinary text begins with an introduction to microarray analysis, and explores basic chemistry, biochemistry, and genomics. Separate chapters are devoted to surface chemistry, target and probe preparation, microarray manufacture and detection, and data analysis and modeling. Methodology, cleanroom technology, gene expression profiling, genetic screening and diagnostics, and novel technologies round out this classic textbook. Microarray Analysis provides any science student or professional all the tools required to understand this revolutionary technology. Rapidly teaches students the fundamentals of microarrays Describes protein microarrays and other rapidly advancing forefronts Builds a conceptual foundation for the entire field Presents commercial opportunities in microarray science Emphasizes the exciting clinical applications of microarrays 

Price: US$125.00
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DNA microarray, or DNA chip, technology is a new and powerful means of discovering, characterizing, and analyzing genes and their expression patterns. The potential of this technology is huge and its applications are widespread across the many fields of biological and biomedical research. This manual assembles and synthesizes the expertise of over 30 innovators in this emerging field to provide authoritative, detailed instruction on the design, construction, and applications of microarrays, as well as comprehensive descriptions of the software tools and strategies required for extensive image and data analysis. Designed to extend and to complement the information in the best-selling laboratory manual Molecular Cloning, and presented in the same clear, user-friendly format, this book is an essential resource for investigators studying the molecular profiles of gene expression in any experimental system.

Price: US$135.00
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Microarrays, patterns of gene expression that elucidate chemical pathways, provide an improved understanding of the cause of diseases and can lead to the discovery of new biomarkers and drug targets. Here contributors from US and Italian institutions summarize research in expression analysis using microarrays, experimental approaches for microarray analysis in tumor biology, and the microarray analysis of human solid tumors.Book News, Inc.®, Portland, OR

Price: US$55.00
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This book provides a comprehensive guide to the use of DNA microarrays in neuroscience and provides approaches that are applicable to other complex biological systems. Human nervous system tissue is remarkably complex. The number of cell types, the architecture, the developmental program, and the importance of environmental factors in development and functioning all pose particular challenges to the researcher using gene expression studies. After an overview of the technology, the book discusses array scanning and image application, statistical methods for array analysis, specific applications of gene expression studies in the central nervous system, the use of postmortem human tissue, and novel methods for using microarray data to develop hypotheses about regulatory networks.

Price: US$119.95
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A quantum leap in technology took place a few years ago with the introduction of cDNA arrays that have been developed in response to the need for simultaneous analysis of the patterns of expression of thousands of genes. DNA Arrays: Technologies and Experimental Strategies offers a view of different aspects of this rapidly developing technology, including oligonucleotide and electrochemical arrays. Distinguished investigators from academia  and industry provide up-to-date insights into methodological fundamentals of construction of DNA arrays, optimization of hybridization conditions, the use of expression data in bioinformatics, different software tools, and the application of microarray technology for drug discovery process.

Price: US$49.00
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Marseille-Genopole, Cedex, France. Provides a comprehensive and practical survey of expression measurement using DNA arrays.  Covers existing methods and includes detailed protocols. Advice and hints on setting up these methods are included.

Price: US $1,250.00
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Industry leaders agree that multiplex array technologies are a key to realizing the therapeutic potential of genomic data. While pioneering companies like Affymetrix offer high-quality product lines, companies with creative technologies--such as Nanogen and Gene Logic--are making gains by offering flexible products for specialized applications such as single nucleotide polymorphism analysis, diagnostics, and high-throughput screening. In addition, emerging technologies such as protein chips and bead-based arrays promise to extend the range and potential of hybridization arrays. This report reviews dozens of companies offering DNA array technology (and related technologies, such as protein chips and microfluidic chips), reviews business issx

Price: US$89.50
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Reviewer: bjdc from Pomona, CA United States: 
The individual articles are fine in this collection but there is no singular focus. The collection skews more potential applications than lab practicals. You'll want to look through the table of contents to determine whether you need a particular chapter(s) before getting this book.

Editorial Reviews From Book News, Inc. 
Researchers, engineers, and technologists explain in detail how to design and construct DNA microarrays, as well as how to hybridize them with biological  samples for analysis. They offer step-by-step instructions for attaching and printing arrays on various matrices, and for biological sample preparation,  hybridization conditions, signal detection, probe optimization, different printing technologies, and data collection and analysis (bioinformatics). Additional topics covered include genotyping, sequencing by hybridization, and HLA-DQA typing techniques. For biological and biomedical researchers. Rampal works in the private sector.Book News, Inc.®, Portland, OR

Price: US$1,190.00
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Biochip is a broad term indicating the use of microchip technology in molecular biology. DNA microarray is a rapid method of sequencing and analysing genes. Microarray technology is rapidly becoming a central platform for functional genomics and has been applied to gene discovery, gene expression, detection of mutation or polymorphism and gene mapping. Biochip technology has an important role to play in pharmacogenomics and molecular diagnostics. This report describes the new developments in biochip technology as well as an evaluation of their potential applications. Biochips will play an important role in drug discovery as differential gene expression can be monitored by microarrays. A comparison of thousands of genes between 'disease' and 'normal' tissues will facilitate the identification of multiple potential targets for new drugs. Drug development time can be reduced. Biochip technology is likely to become as commonplace as polymerase chain reaction is now and will enable molecular diagnosis at the point of care.

Price: US$45.95
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Price: US$55
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My comments:
It is the first book on DNA microarrays. It discusses the microarray issues from printing to scanning data management and mining. It also covers some commerical technologies that did not discuss in the Microarray Biochip Technology book like the active microelectronic arrays by Nanogen, the basics of ScanArray confocal scanner by GSI lumonics. It is a very good book although some of the techniques and the commerical platforms discussed were outdated.

Price: US$36.95
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This book covers several recent high-throughput publications in Biotechniques including microarrays for high-through DNA and RNA screening, high-throughput protein screening and functional analysis. This book also contains a great chapter on protocols of aRNA preparation from single cell which is very useful for microarray research.

Price: US$105.00
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Price: US$135.00
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Microarrays, patterns of gene expression that elucidate chemical pathways, provide an improved understanding of the cause of diseases and can lead to the discovery of new biomarkers and drug targets. Here contributors from US and Italian institutions summarize research in expression analysis using microarrays, experimental approaches for microarray analysis in tumor biology, and the microarray analysis of human solid tumors.Book News, Inc.®, Portland, OR

Price: US$110.00
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Proteins interacting with diverse ligands - proteins, peptides or DNA - are the basic principles underlying many biological processes, such as antigen-antibody binding, signal transduction or receptor binding. The technique of oligopeptide synthesis on a cellulose membrane and the subsequent binding assays allow the investigation of protein interactions. A particular advantage of these peptide arrays (SPOT - technology) is the high number of oligopeptide probes that can be  tested in parallel. Detailed protocols for peptide synthesis, and the analysis of protein-protein, protein-DNA interactions as well as epitope mapping are presented in this manual. It is ideally suited not only for basic research laboratories but also for diagnostic and therapeutic applications since many diseases are related to dysfunctions in protein recognition and binding. 

Price: US$100.00

Price: US$175.00

Editorial Reviews
This book is a comprehensive guide to all of the mathematics, statistics and computing you will need to successfully operate DNA microarray experiments. It is written for researchers, clinicians, laboratory heads and managers, from both biology and bioinformatics backgrounds, who work with, or who intend to work with microarrays. The book covers all aspects of microarray bioinformatics, giving you the tools to design arrays and experiments, to analyze your data, and to share your results with your organisation or with the international community. There are chapters covering sequence databases, oligonucleotide design, experimental design, image processing, normalisation, identifying differentially expressed genes, clustering, classification and data standards. The book is based on the highly successful Microarray Bioinformatics course at Oxford University, and therefore is ideally suited for teaching the subject at postgraduate or professional level.

Price: US$75.55      

Price: US$57.95

From Book News, Inc.
Emphasizing underlying concepts and principles, this concise guide describes the design of microarray experiments and the analysis of the data they produce. Intended for graduate students and bioinformatics researchers, the book stresses the conceptual aspects of analysis and keeps mathematical complexities to a minimum. The authors are scientists with the University of London, The Institute for Genomic Research, and the European Bioinformatics Institute.

Price: US$69.95
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Written by the pre-eminent world authorities in the field, this book will be the basic reference guide to the statistical analysis of genetic microarray data. Starting from the first steps of genetic microarray data analysis, the book covers the most important topics and common methodologies for analyzing gene expression data, including preprocessing issues, experiment design, and classification and clustering. These will provide the tools and guidance needed by biologists, geneticists, and statisticians working in the analysis of genetic data. The presentation level is appropriate for a quantitative biologist or geneticist, as well as for computer scientists working in the area. 

Price:  US$109.00

Book Description
A Practical Approach to Microarray Data Analysis is for all life scientists, statisticians, computer experts, technology developers, managers, and other professionals tasked with developing, deploying, and using microarray technology including the necessary computational infrastructure and analytical tools. The book addresses the requirement of scientists and researchers to gain a basic understanding of microarray analysis methodologies and tools. It is intended for students, teachers, researchers, and research managers who want to understand the state of the art and of the presented methodologies and the areas in which gaps in our knowledge demand further research and development. The book is designed to be used by the practicing professional tasked with the design and analysis of microarray experiments or as a text for a senior undergraduate- or graduate level course in analytical genetics, biology, bioinformatics, computational biology, statistics and data mining, or applied computer science.

Price: US$29.95 
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Reviewer: A reader from Palo Alto, CA United States 
The topic of microarray image analysis has always been on the backburner. However, it is a very crucial step in the microarray experiment and is misunderstood by many colleagues. This book covers the basics of microarray imagea analysis, as well as some advanced topics. It is a really helpful reference. Good to includ in class studies. 

Price: US$40.00
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Reviewer: Asher Schachter from Needham, MA United States 
This book is an excellent educational source for the rapidly exploding field of bioinformatics, particularly in the area of functional genomics- i.e. teasing out the functions of the thousands of genes in the genome. Described in clear detail are many approaches to the complex analysis of RNA expression array data, including the appropriate situations for use and advantages and pitfalls inherent in each approach. The reader will learn biological theory integrated with mathematical concepts. The authors also clearly have a lucid understanding of the technical strengths and weaknesses of microarray technology. 

Price: US$99.50
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Microarray technology is a major experimental tool for functional genomic explorations, and will continue to be a major tool throughout this decade and beyond. The recent explosion of this technology threatens to overwhelm the scientific community with massive quantities of data. Because microarray data analysis is an emerging field, very few analytical models currently exist. Methods of Microarray Data Analysis II is the second book in this pioneering series dedicated to this exciting new field. In a single reference, readers can learn about the most up-to-date methods, ranging from data normalization, feature selection, and discriminative analysis to machine learning techniques. Currently, there are no standard procedures for the design and analysis of microarray experiments. Methods of Microarray Data Analysis II focuses on a single data set, using a different method of analysis in each chapter. Real examples expose the strengths  and weaknesses of each method for a given situation, aimed at helping readers choose appropriate protocols and utilize them for their own data set. In addition, web links are provided to the programs and tools discussed in several chapters. This book is an excellent reference not only for academic and industrial researchers, but also for core bioinformatics/genomics courses in undergraduate and graduate programs. 

Price: US $99.50
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Editorial Reviews From Book News, Inc.
Seventeen contributions cover a wide range of topics and span a number of disciplines such as image analysis, statistics, machine learning, pattern recognition, time-frequency and nonlinear signal processing, parallel computing, molecular biology, and others. Each chapter follows the various stages from data and analysis through synthesis and application. Topics include an overview of the role of supercomputers and other tools; approaches to the global modeling and analysis of gene regulatory networks and transcriptional control; state-of-the-art tools in Boolean function theory, time-frequency analysis, pattern recognition, and unsupervised learning; crucial issues associated with statistical analysis of microarray data, statistics and stochastic analysis of gene expression levels; and biological and medical implications of genomics research. Appropriate for use as an advanced level textbook, as well as for researchers. Edited by Zhang and Shmulevich (U. of Texas M.D. Anderson Cancer Center).Book News, Inc.®, Portland, OR 

Price: US$44.95
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This introductory book details reliable approaches to problems met in standard microarray data analyses. Providing examples of established approaches such as cluster analysis, function prediction, and principle component analysis, this book offers real examples to illustrate the key concepts of data analysis. 

Price: US$99.50
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Microarray technology is a major experimental tool for functional genomic explorations, and will continue to be a major tool throughout this decade and beyond. The recent explosion of this technology threatens to overwhelm the scientific community with massive quantities of data. Because microarray data analysis is an emerging field, very few analytical models currently exist. Methods of Microarray Data Analysis is one of the first books dedicated to this exciting new field. In a single reference, readers can learn about the most up-to-date methods ranging from data normalization, feature selection and discriminative analysis to machine learning techniques. Currently, there are no standard procedures for the design and analysis of microarray experiments. Methods of Microarray Data Analysis focuses on two well-known data sets, using a different method of analysis in each chapter. Real examples expose the strengths and weaknesses of each method for a given situation, aimed at helping readers choose appropriate protocols and utilize them for their own data set. In addition, web links are provided to the programs and tools discussed in several chapters. This book is an excellent reference not only for academic and industrial researchers, but also for core bioinformatics/genomics courses in undergraduate and graduate programs. 

Price: US$29.95
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See my comments on this book entitled "Microarray data analysis for dummies .... and experts too?" in Trends Biochem Sci. 2002 Aug;27(8):433-4. 

Reviewer: A reader from United States
This is a very thin book, and I use the term "book" loosely. It appears to be a hastily-typeset and published collection of terse lecture notes in near-outline form. It doesn't explain microarray data analysis, but is rather more of an annotated listing of statistical methods useful in analyzing microarray data. For the biologist looking for conceptual content, it is nearly useless. It lists a lot of equations without explaining how and why they are used, or under what circumstances. A much better book is Steen Knudsen's A Biologists Guide to Analysis of DNA Microarray Data. Paradoxically, to find Jagota's book useful, you would have to already understand its content. This book might therefore serve as a quick reference for seasoned statisticians who are suddenly tasked with having to work on someone else's microarray project. This serves to show how new the field of microarray data analysis is, and how sorely a good and thorough treatment of the subject is needed.

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: 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$44.95
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Reviewer: A reader 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.

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Price: US$29.95
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Reviewer: hanako1 from Bay Area, CA, USA
This book has been used at UCSC extension, and seems most of the students are using this book like a lecture/summary notes, not as a full textbook. Without attending the class, it is VERY difficult to understand. However, once you attended the class (and study hard with some supplement textbooks if you are a beginner), you will realize that this book summarizes key points very well.  So... if you are a beginner to this field, you might want to look for an alternative. If you are already comfortable with statistics and bioinformatics, and want  to check-out key points, maybe you are interested.

Book Description
This book explains the basics of S-PLUS in a clear style at a level suitable for people with little computing or statistical knowledge. Unlike the S-PLUS manuals, it is not comprehensive, but instead introduces the most important ideas of S-PLUS through the use of many examples. Each chapter also includes a collection of exercises that are accompanied by fully worked-out solutions and detailed comments. The volume is rounded off with practical hints on how efficient work can be performed in S-PLUS. The book is well suited for self-study and as a textbook. The third edition is based on S-PLUS Version 6 for Windows and Unix and has been completely updated. It covers the underlying S Version 4 and the graphical user interfaces for Windows and Unix. A new section of the details of factor objects has been added, Trellis graphs are used in more depth, and new exercises (and solutions) were written. The book serves equally well as an introduction to the R system, and concludes with a comparison of S-PLUS and R. 

Price: US$64.53
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Book Description
S is a powerful environment for the statistical and graphical analysis of data. It provides the tools to implement many statistical ideas that have been made possible by the widespread availability of workstations having good graphics and computational capabilities. This book is a guide to using S environments to perform statistical analyses and provides both an introduction to the use of S and a course in modern statistical methods. Implementations of S are available commercially in S-PLUS(R) workstations and as the Open Source R for a wide range of computer systems. The aim of this book is to show how to use S as a powerful and graphical data analysis system. Readers are assumed to have a basic grounding in statistics, and so the book is intended for would-be users of S-PLUS or R and both students and researchers using statistics. Throughout, the emphasis is on presenting practical problems and full analyses of real data sets. Many of the methods discussed are state of the art approaches to topics such as linear, nonlinear and smooth regression models, tree-based methods, multivariate analysis, pattern recognition, survival analysis, time series and spatial statistics. Throughout modern techniques such as robust methods, non-parametric smoothing and bootstrapping are used where appropriate. This fourth edition is intended for users of S-PLUS 6.0 or R 1.5.0 or later. A substantial change from the third edition is updating for the current versions of S-PLUS and adding coverage of R. The introductory material has been rewritten to emphasis the import, export and manipulation of data. Increased computational power allows even more computer-intensive methods to be used, and methods such as GLMMs, MARS, SOM and support vector machines are considered. 

Price: US$64.00
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My comments:
This is a very good introductory book for data analysis. It includes most of the fundamentals on testing hypothesis and examining relationships. The text is very well written and easy to understand. You also learn how to use SPSS, a powerful statistics program during the course of study. This book has helped me a lot on understand the basis of statistical analysis.

Price: US$52.50
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This is a great book I used to learn R/ S-plus. If you have some basic backgrounds of statistics, you will find this book extremely helpful to learn how to apply various statistical analysis. One excellent point of this book is it has step by step codes for almost all topics covered, which helps a biological novice like me learning the language while reinforcing the statistics fundamental! Highly recommended!

Editorial Reviews Book Description 
Statistical analysis typically involves applying theoretically generated techniques to the description and interpretation of collected data. In this text, theory, application and interpretation are combined to present the entire biostatistical process for a series of elementary and intermediate analytic methods. The theoretical basis for each method is discussed with a minimum of mathematics and is applied to a research data example using a computer system called S-PLUS. This system produces concrete numerical results and increases one's understanding of the fundamental concepts and methodology of statistical analysis. 

This text is not a computer manual, even though it makes extensive use of computer language to describe and illustrate applied statistical techniques. This makes the details of the statistical process readily accessible, providing insight into how and why a statistical method identifies the properties of sampled data. The first chapter gives a simple overview of the S-PLUS language. The subsequent chapters use this valuable statistical tool to present a variety of analytic approaches. Combining statistical logic, data and computer tools, the author explores such topics as random number generation, general linear models, estimation, analysis of tabular data, analysis of variance and survival analysis. The end result is a clear and complete explanation of the way statistical methods can help one gain an understanding of collected data. 

Modern Applied Biostatistical Methods is unlike other statistical texts, which usually deal either with theory or with applications. It integrates the two  elements into a single presentation of theoretical background, data, interpretation, graphics, and implementation. This all-around approach will be particularly helpful to students in various biostatistics and advanced epidemiology courses, and will interest all researchers involved in biomedical data analysis. 

Price: US$34.95
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Reviewer: statman13 (see more about me) from Princeton, NJ USA
I took my introductory mathematical statistics course from Brad Efron and Charles Stein at Stanford. It gave me a strong foundation and understanding of decision theory, hypothesis testing and the power of exponential families of distributions. Although I understood the Neyman - Pearson theory of hypothesis testing and confidence intervals, I was not completely comfortable applying what I had learn when confronted with real problems. Students even at the best universities in the US still need consulting experience before they are comfortable with the tools they learn.

That is why this book so intrigued me. It approaches the theory and methods from applications first. Each chapter poses an interesting real problem and then progresses to a solution, introducing only the necessary tools. Many important statistical tools and topics are covered this way. It is particularly good for students interested in biostatistics as many of the applications fall in that area. In fact the subject of maternal smoking and infant health is treated in Chapter 1 and revisited in Chapter 10 with additional data to consider.

It is designed for an advanced undergraduate course for statistics majors and has been successfully implemented by the authors at Berkeley. I think this can really work and make mathematical statistics interesting. However, the student should not think that he or she can come out of this class and jump right into consulting. The biggest problem in consulting is working with the client to pose a well formulated problems that address their questions. In this text the authors have already done that long and difficult task for us and we are left in a position to learn the subject matter and the statistical tools needed for the solution.

Price: US$34.95
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My comments:
Although the book is only distantly related with microarray analysis, but it helped me to clear up many confusing statistical ideas in clinical studies. The book teaches you how to critically read the statistical results from the literature and find the pitfalls. A great aid for designing a statistically sound experiment and a handful reference book for basic statistics. Must read for beginner!