Basic Applied Bioinformatics

Praise for the third edition of Bioinformatics “This book is a gem to read and use in practice.” — Briefings in Bioinformatics "This volume has a distinctive, special value as it offers an unrivalled level of details and unique expert insights from the leading computational biologists, including the very creators of popular bioinformatics tools." — ChemBioChem “A valuable survey of this fascinating field. . . I found it to be the most useful book on bioinformatics that I have seen and recommend it very highly.” — American Society for Microbiology News “This should be on the bookshelf of every molecular biologist.” — The Quarterly Review of Biology The field of bioinformatics is advancing at a remarkable rate. With the development of new analytical techniques that make use of the latest advances in machine learning and data science, today’s biologists are gaining fantastic new insights into the natural world’s most complex systems. These rapidly progressing innovations can, however, be difficult to keep pace with. The expanded fourth edition of the best-selling Bioinformatics aims to remedy this by providing students and professionals alike with a comprehensive survey of the current field. Revised to reflect recent advances in computational biology, it offers practical instruction on the gathering, analysis, and interpretation of data, as well as explanations of the most powerful algorithms presently used for biological discovery. Bioinformatics, Fourth Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists at all levels, covering both key concepts that have stood the test of time and the new and important developments driving this fast-moving discipline forwards. This new edition features:  New chapters on metabolomics, population genetics, metagenomics and microbial community analysis, and translational bioinformatics A thorough treatment of statistical methods as applied to biological data 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 is an indispensable companion for researchers, instructors, and students of all levels in molecular biology and computational biology, as well as investigators involved in genomics, clinical research, proteomics, and related fields.

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 Reviews from the First Edition «…provides a broad overview of the basic tools for sequence analysis … 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.» —Nature Structural Biology «…should be in the personal library of any biologist who uses the Internet for the analysis of DNA and protein sequence data.» —Science «…a wonderful primer designed to navigate the novice through the intricacies of in scripto analysis … The accomplished gene searcher will also find this book a useful addition to their library … an excellent reference to the principles of bioinformatics.» —Trends in Biochemical Sciences This new edition of the highly successful Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins provides a sound foundation of basic concepts, with practical discussions and comparisons of both computational tools and databases relevant to biological research. Equipping biologists with the modern tools necessary to solve practical problems in sequence data analysis, the Second Edition covers the broad spectrum of topics in bioinformatics, ranging from Internet concepts to predictive algorithms used on sequence, structure, and expression data. With chapters written by experts in the field, this up-to-date reference thoroughly covers vital concepts and is appropriate for both the novice and the experienced practitioner. Written in clear, simple language, the book is accessible to users without an advanced mathematical or computer science background. This new edition includes: All new end-of-chapter Web resources, bibliographies, and problem sets Accompanying Web site containing the answers to the problems, as well as links to relevant Web resources New coverage of comparative genomics, large-scale genome analysis, sequence assembly, and expressed sequence tags A glossary of commonly used terms in bioinformatics and genomics Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second 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, positional cloning, clinical research, and computational biology.

This book is an excellent introductory text describing the use of bioinformatics to analyze genomic and post-genomic data. It has been translated from the original popular French edition, which was based on a course taught at the well-respected ?cole Polytechnique in Palaiseau. This edition has been fully revised and updated by the authors. After a brief introduction to gene structure and sequence determination, it describes the techniques used to identify genes, their protein-coding sequences and regulatory regions. The book discusses the methodology of comparative genomics, using information from different organisms to deduce information about unknown sequences. There is a comprehensive chapter on structure prediction, covering both RNA and protein. Finally, the book describes the complex networks of RNA and protein that exist within the cell and their interactions, ending with a discussion of the simulation approaches that can be used to model these networks. Praise from the reviews: “In context of the new developments the genomic era has brought, Bioinformatics: Genomics and Post-Genomics becomes a fundamental and indispensable resource for undergraduate and early graduate students…insightfully authored…will immensely help students…in establishing important foundations while shaping their careers.” NEWSLETTER, BRITISH SOCIETY OF CELL BIOLOGY

Bioinformatics is contributing to some of the most important advances in medicine and biology. At the forefront of this exciting new subject are techniques known as artificial intelligence which are inspired by the way in which nature solves the problems it faces. This book provides a unique insight into the complex problems of bioinformatics and the innovative solutions which make up ‘intelligent bioinformatics’. Intelligent Bioinformatics requires only rudimentary knowledge of biology, bioinformatics or computer science and is aimed at interested readers regardless of discipline. Three introductory chapters on biology, bioinformatics and the complexities of search and optimisation equip the reader with the necessary knowledge to proceed through the remaining eight chapters, each of which is dedicated to an intelligent technique in bioinformatics. The book also contains many links to software and information available on the internet, in academic journals and beyond, making it an indispensable reference for the 'intelligent bioinformatician'. Intelligent Bioinformatics will appeal to all postgraduate students and researchers in bioinformatics and genomics as well as to computer scientists interested in these disciplines, and all natural scientists with large data sets to analyse.

Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers: General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.

“… this book was written from start to finish by one extremely dedicated and erudite individual. The author has done an excellent job of covering the many topics that fall under the umbrella of computational biology for vaccine design, demonstrating an admirable command of subject matter in fields as disparate as object-oriented databases and regulation of T cell response. Simply put, it has just the right breadth and depth, and it reads well. In fact, readability is one of its virtues—making the book enticing and useful, all at once…” Human Vaccines, 2010 «… This book has several strong points. Although there are many textbooks that deal with vaccinology, few attempts have been made to bring together descriptions of vaccines in history, basic bioinformatics, various computational solutions and challenges in vaccinology, detailed experimental methodologies, and cutting-edge technologies… This book may well serve as a first line of reference for all biologists and computer scientists…» –Virology Journal, 2009 Vaccines have probably saved more lives and reduced suffering in a greater number of people than any other medical intervention in human history, succeeding in eradicating smallpox and significantly reducing the mortality and incidence of other diseases. However, with the emergence of diseases such as SARS and the threat of biological warfare, vaccination has once again become a topic of major interest in public health. Vaccinology now has at its disposal an array of post-genomic approaches of great power. None has a more persuasive potential impact than the application of computational informatics to vaccine discovery; the recent expansion in genome data and the parallel increase in cheap computing power have placed the bioinformatics exploration of pathogen genomes centre stage for vaccine researchers. This is the first book to address the area of bioinformatics as applied to rational vaccine design, discussing the ways in which bioinformatics can contribute to improved vaccine development by introducing the subject of harnessing the mathematical and computing power inherent in bioinformatics to the study of vaccinology putting it into a historical and societal context, and exploring the scope of its methods and applications. Bioinformatics for Vaccinology is a one-stop introduction to computational vaccinology. It will be of particular interest to bioinformaticians with an interest in immunology, as well as to immunologists, and other biologists who need to understand how advances in theoretical and computational immunobiology can transform their working practices.

ALGORITHMS IN BIOINFORMATICS Explore a comprehensive and insightful treatment of the practical application of bioinformatic algorithms in a variety of fields Algorithms in Bioinformatics: Theory and Implementation delivers a fulsome treatment of some of the main algorithms used to explain biological functions and relationships. It introduces readers to the art of algorithms in a practical manner which is linked with biological theory and interpretation. The book covers many key areas of bioinformatics, including global and local sequence alignment, forced alignment , detection of motifs, Sequence logos, Markov chains or information entropy. Other novel approaches are also described, such as Self-Sequence alignment, Objective Digital Stains (ODSs) or Spectral Forecast and the Discrete Probability Detector (DPD) algorithm. The text incorporates graphical illustrations to highlight and emphasize the technical details of computational algorithms found within, to further the reader’s understanding and retention of the material. Throughout, the book is written in an accessible and practical manner, showing how algorithms can be implemented and used in JavaScript on Internet Browsers. The author has included more than 120 open-source implementations of the material, as well as 33 ready-to-use presentations. The book contains original material that has been class-tested by the author and numerous cases are examined in a biological and medical context. Readers will also benefit from the inclusion of: A thorough introduction to biological evolution, including the emergence of life, classifications and some known theories and molecular mechanismsA detailed presentation of new methods, such as Self-sequence alignment, Objective Digital Stains and Spectral Forecast A treatment of sequence alignment, including local sequence alignment, global sequence alignment and forced sequence alignment with full implementationsDiscussions of position-specific weight matrices, including the count, weight, relative frequencies, and log-likelihoods matricesA detailed presentation of the methods related to Markov Chains as well as a description of their implementation in Bioinformatics and adjacent fieldsAn examination of information and entropy, including sequence logos and explanations related to their meaningAn exploration of the current state of bioinformatics, including what is known and what issues are usually avoided in the fieldA chapter on philosophical transactions that allows the reader a broader view of the prediction processNative computer implementations in the context of the field of BioinformaticsExtensive worked examples with detailed case studies that point out the meaning of different results Perfect for professionals and researchers in biology, medicine, engineering, and information technology, as well as upper level undergraduate students in these fields, Algorithms in Bioinformatics: Theory and Implementation will also earn a place in the libraries of software engineers who wish to understand how to implement bioinformatic algorithms in their products.

Bioinformatics Software Engineering: Delivering Effective Applications will be useful to anyone who wants to understand how successful software can be developed in a rapidly changing environment. A handbook, not a textbook, it is not tied to any particular operating system, platform, language, or methodology. Instead it focuses on principles and practices that have been proven in the real world. It is pragmatic, emphasizing the importance of what the author calls Adaptive Programming – doing what works in your situation, and it is concise, covering the whole software development lifecycle in one slim volume. At each stage, it describes common pitfalls, explains how these can be avoided, and suggests simple techniques which make it easier to deliver better solutions. «Well thought-out … addresses many of the key issues facing developers of bioinformatics software.» (Simon Dear, Director, UK Technology and Development, Bioinformatics Engineering and Integration, Genetics Research, GlaxoSmithKline) Here are some examples from the book itself. On software development: “Writing software properly involves talking to people – often lots of people – and plenty of non-coding work on your part. It requires the ability to dream up new solutions to problems so complicated that they are hard to describe.” From description to specification: “Look for verbs – action words, such as ‘does’, ‘is’ and ‘views’. Identify nouns – naming words, like ‘user’, ‘home’ and ‘sequence’. List the adjectives – describing words, for example ‘quick’, ‘simple’ or ‘precise’. The verbs are the functions that must be provided by your application. The nouns define the parameters to those functions, and the adjectives specify the constraint conditions under which your program must operate.” On how to start writing software: “Handle errors. Take in data. Show output. Get going!” On testing: “It may not be physically possible to test every potential combination of situations that could occur as users interact with a program. But one thing that can be done is to test an application at the agreed extremes of its capability: the maximum number of simultaneous users it has to support, the minimum system configuration it must run on, the lowest communication speed it must cope with, and the most complex operations it must perform. If your program can cope with conditions at the edge of its performance envelope, it is less likely to encounter difficulties in dealing with less challenging situations.” On showing early versions of software to users: “It can be hard explaining the software development process to people who are unfamiliar with it. Code that to you is nearly finished is simply not working to them, and seeing their dream in bits on the workbench can be disappointing to customers, especially when they were expecting to be able to take it for a test drive.” On bugs: “If your users find a genuinely reproducible bug in production code, apologize, fix it fast, and then fix the system that allowed it through. And tell your customers what you are doing, and why, so they will be confident that it will not happen again. Everybody makes mistakes. Don’t make the same ones twice.” And one last thought on successful software development: "You have to be a detective, following up clues and examining evidence to discover what has gone wrong and why. And you have to be a politician, underst

In the current era of complete genome sequencing, Bioinformatics and Molecular Evolution provides an up-to-date and comprehensive introduction to bioinformatics in the context of evolutionary biology. This accessible text: provides a thorough examination of sequence analysis, biological databases, pattern recognition, and applications to genomics, microarrays, and proteomics emphasizes the theoretical and statistical methods used in bioinformatics programs in a way that is accessible to biological science students places bioinformatics in the context of evolutionary biology, including population genetics, molecular evolution, molecular phylogenetics, and their applications features end-of-chapter problems and self-tests to help students synthesize the materials and apply their understanding is accompanied by a dedicated website – www.blackwellpublishing.com/higgs – containing downloadable sequences, links to web resources, answers to self-test questions, and all artwork in downloadable format (artwork also available to instructors on CD-ROM). This important textbook will equip readers with a thorough understanding of the quantitative methods used in the analysis of molecular evolution, and will be essential reading for advanced undergraduates, graduates, and researchers in molecular biology, genetics, genomics, computational biology, and bioinformatics courses.

Combining biology, computer science, mathematics, and statistics, the field of bioinformatics has become a hot new discipline with profound impacts on all aspects of biology and industrial application. Now, Computational Intelligence in Bioinformatics offers an introduction to the topic, covering the most relevant and popular CI methods, while also encouraging the implementation of these methods to readers' research.