Bioinformatics Books

Introductory Statistics with R (Statistics and Computing)

Peter Dalgaard

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Total reviews: 18 Average rating: 4.5 of 5

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R is an Open Source implementation of the S language. It works on multiple computing platforms and can be freely downloaded. R is now in widespread use for teaching at many levels as well as for practical data analysis and methodological development.

This book provides an elementary-level introduction to R, targeting both non-statistician scientists in various fields and students of statistics. The main mode of presentation is via code examples with liberal commenting of the code and the output, from the computational as well as the statistical viewpoint. A supplementary R package can be downloaded and contains the data sets.

The statistical methodology includes statistical standard distributions, one- and two-sample tests with continuous data, regression analysis, one- and two-way analysis of variance, regression analysis, analysis of tabular data, and sample size calculations. In addition, the last six chapters contain introductions to multiple linear regression analysis, linear models in general, logistic regression, survival analysis, Poisson regression, and nonlinear regression.

In the second edition, the text and code have been updated to R version 2.6.2. The last two methodological chapters are new, as is a chapter on advanced data handling. The introductory chapter has been extended and reorganized as two chapters. Exercises have been revised and answers are now provided in an Appendix.

The Elements of Statistical Learning

T. Hastie, R. Tibshirani, J. H. Friedman

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Total reviews: 27 Average rating: 4.0 of 5

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During the past decade there has been an explosion in computation and information technology. With it have come vast amounts of data in a variety of fields such as medicine, biology, finance, and marketing. The challenge of understanding these data has led to the development of new tools in the field of statistics, and spawned new areas such as data mining, machine learning, and bioinformatics. Many of these tools have common underpinnings but are often expressed with different terminology. This book describes the important ideas in these areas in a common conceptual framework. While the approach is statistical, the emphasis is on concepts rather than mathematics. Many examples are given, with a liberal use of color graphics. It should be a valuable resource for statisticians and anyone interested in data mining in science or industry. The book's coverage is broad, from supervised learning (prediction) to unsupervised learning. The many topics include neural networks, support vector machines, classification trees and boosting---the first comprehensive treatment of this topic in any book.

This major new edition features many topics not covered in the original, including graphical models, random forests, ensemble methods, least angle regression & path algorithms for the lasso, non-negative matrix factorization, and spectral clustering. There is also a chapter on methods for ``wide'' data (p bigger than n), including multiple testing and false discovery rates.

Trevor Hastie, Robert Tibshirani, and Jerome Friedman are professors of statistics at Stanford University. They are prominent researchers in this area: Hastie and Tibshirani developed generalized additive models and wrote a popular book of that title. Hastie co-developed much of the statistical modeling software and environment in R/S-PLUS and invented principal curves and surfaces. Tibshirani proposed the lasso and is co-author of the very successful An Introduction to the Bootstrap. Friedman is the co-inventor of many data-mining tools including CART, MARS, projection pursuit and gradient boosting.

Bioinformatics For Dummies (For Dummies (Math & Science))

Jean-Michel, Ph. D. Claverie, Cedric, Ph.D. Notredame

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Total reviews: 16 Average rating: 4.5 of 5

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Were you always curious about biology but were afraid to sit through long hours of dense reading? Did you like the subject when you were in high school but had other plans after you graduated? Now you can explore the human genome and analyze DNA without ever leaving your desktop!

Bioinformatics For Dummies is packed with valuable information that introduces you to this exciting new discipline. This easy-to-follow guide leads you step by step through every bioinformatics task that can be done over the Internet. Forget long equations, computer-geek gibberish, and installing bulky programs that slow down your computer. You’ll be amazed at all the things you can accomplish just by logging on and following these trusty directions. You get the tools you need to:

• Analyze all types of sequences
• Use all types of databases
• Work with DNA and protein sequences
• Conduct similarity searches
• Build a multiple sequence alignment
• Edit and publish alignments
• Visualize protein 3-D structures
• Construct phylogenetic trees

This up-to-date second edition includes newly created and popular databases and Internet programs as well as multiple new genomes. It provides tips for using servers and places to seek resources to find out about what’s going on in the bioinformatics world. Bioinformatics For Dummies will show you how to get the most out of your PC and the right Web tools so you’ll be searching databases and analyzing sequences like a pro!

Valuation in Life Sciences: A Practical Guide

Boris Bogdan, Ralph Villiger

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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

Beginning Perl for Bioinformatics

James Tisdall

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Total reviews: 25 Average rating: 4.5 of 5

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Biology, it seems, is a good showcase for the talents of Perl. Newcomers to Perl who understand biological information will find James Tisdall's Beginning Perl for Bioinformatics to be an excellent compendium of examples. Teachers of Perl will likewise find the text to be filled with fresh programming illustrations of growing scientific importance. Seasoned Perlmongers who want to learn biology, however, should search elsewhere, as Tisdall's emphasis is on Perl's logic rather than Mother Nature's.

Departing from O'Reilly's earlier monograph Developing Bioinformatic Computer Skills, Tisdall's text is organized aggressively along didactic lines. Nearly all of the 13 chapters begin with twin bullet lists of Perl programming tools and the bioinformatic methods that require them. Likewise, the chapters end with exercises. String concatenation is illustrated with gene splicing, and regular expressions are taught with gene transcription and motif searching.

Tisdall emphasizes sequence examples throughout, leading up to an introduction to a Perl interface for the NIH GenBank biological database and the widely used BLAST sequence alignment tool. After a brief discussion of three-dimensional protein structure, he returns to sequence extraction and secondary structure prediction.

Tisdall's goal is to boost the beginning programmer into a domain of self-learning. He imparts essential etiquette for the success of programming newbies: use the wealth or resources available, from user documentation to Web site surveys to FAQs to How-To's to news groups and finally to direct personal appeals for help from a senior colleague. A well-plugged-in bioinformatics Perl student will soon discover Bioperl, an open-source effort to bring research-grade bioinformatic tools to the Perl community. Bioperl is described briefly at the end of Tisdall's book and will reportedly be a forthcoming title of its own in the O'Reilly bioinformatics series.

Although he introduces bioinformatics as an academic discipline, Tisdall treats it as a trade throughout his book. He indicates that open questions and computational hard problems exist, but does not describe what they are or how they are being tackled. Ultimately, Tisdall presents bioinformatics as another arrow in a bench scientist's quiver, very much like HPLC, 2D-PAGE, and the various spectroscopies.

As odd as a "bioinformatics-as-tool" book may be to its research proponents, the reduction of bioinformatics to trade status both deflates and vindicates the years of research, as Tisdall's work attests. --Peter Leopold

Python For Bioinformatics (Jones and Bartlett Series in Biomedical Informatics)

Jason Kinser

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Subjects -> Computers & Internet -> Programming -> Languages & Tools -> Python
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Editorial Review:

Bioinformatics is a growing field that attracts researchers from many different backgrounds who are unfamiliar with the algorithms commonly used in the field. Python for Bioinformatics provides a clear introduction to the Python programming language and instructs beginners on the development of simple programming exercises . Ideal for those with some knowledge of computer programming languages, this book emphasizes Python syntax and methodologies. The text is divided into three complete sections; the first provides an explanation of general Python programming, the second includes a detailed discussion of the Python tools typically used in bioinformatics including clustering, associative memories, and mathematical analysis techniques, and the third section demonstrates how these tools are implemented through numerous applications.

Mastering Perl for Bioinformatics

James D. Tisdall

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Total reviews: 9 Average rating: 4.0 of 5

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Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with Beginning Perl for Bioinformatics, forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics. Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.

Bioconductor Case Studies (Use R)

Florian Hahne, Wolfgang Huber, Robert Gentleman, Seth Falcon

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Bioconductor software has become a standard tool for the analysis and comprehension of data from high-throughput genomics experiments. Its application spans a broad field of technologies used in contemporary molecular biology. In this volume, the authors present a collection of cases to apply Bioconductor tools in the analysis of microarray gene expression data. Topics covered include

* import and preprocessing of data from various sources

* statistical modeling of differential gene expression

* biological metadata

* application of graphs and graph rendering

* machine learning for clustering and classification problems

* gene set enrichment analysis

Each chapter of this book describes an analysis of real data using hands-on example driven approaches. Short exercises help in the learning process and invite more advanced considerations of key topics. The book is a dynamic document. All the code shown can be executed on a local computer, and readers are able to reproduce every computation, figure, and table.

Biomedical Informatics: Computer Applications in Health Care and Biomedicine (Health Informatics)

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Total reviews: 5 Average rating: 4.0 of 5

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The practice of modern medicine requires sophisticated information technologies with which to manage patient information, plan diagnostic procedures, interpret laboratory results, and conduct research. This book, inspired by a Stanford University training program developed to introduce health professionals to computer applications in modern medical care, fills the need for a high quality text in computers and medicine, and meets the growing demand by practitioners, researchers, and students for a comprehensive introduction to key topics in the field. The work is designed for a broad audience interested in the intersection of computer science and medicine.

Completely revised and expanded, the Third Edition (previously titled "Medical Informatics") includes several new chapters filled with brand new material. This book will provide both a conceptual framework and a practical approach for the implementation and management of IT used to improve the delivery of health care. Designed for use by professors and students of medical informatics and for practicing professionals, this book will focus on the role of computers in the provision of medical services. Biomedial Informatics, Third Edition, provides the conceptual base needed to comprehend and utilize medical informatics through easy to understand examples that demonstrate how computers assist in the delivery of health care. This text also includes pointers to additional literature, chapter summaries, and concise definition of recurring terms for self-study or classroom use.

An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)

Neil C. Jones, Pavel A. Pevzner

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Subjects -> Computers & Internet -> Programming -> Algorithms -> General AAS

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Total reviews: 7 Average rating: 4.5 of 5

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This introductory text offers a clear exposition of the algorithmic principles driving advances in bioinformatics. Accessible to students in both biology and computer science, it strikes a unique balance between rigorous mathematics and practical techniques, emphasizing the ideas underlying algorithms rather than offering a collection of apparently unrelated problems.

The book introduces biological and algorithmic ideas together, linking issues in computer science to biology and thus capturing the interest of students in both subjects. It demonstrates that relatively few design techniques can be used to solve a large number of practical problems in biology, and presents this material intuitively.

An Introduction to Bioinformatics Algorithms is one of the first books on bioinformatics that can be used by students at an undergraduate level. It includes a dual table of contents, organized by algorithmic idea and biological idea; discussions of biologically relevant problems, including a detailed problem formulation and one or more solutions for each; and brief biographical sketches of leading figures in the field. These interesting vignettes offer students a glimpse of the inspirations and motivations for real work in bioinformatics, making the concepts presented in the text more concrete and the techniques more approachable.

PowerPoint presentations, practical bioinformatics problems, sample code, diagrams, demonstrations, and other materials can be found at the Authors' website.