Introduction to Bioinformatics with R by
In biological research, the amount of data available to researchers has increased so much over recent years, it is becoming increasingly difficult to understand the current state of the art without some experience and understanding of data analytics and bioinformatics. An Introduction to Bioinformatics with R: A Practical Guide for Biologists leads the reader through the basics of computational analysis of data encountered in modern biological research. With no previous experience with statistics or programming required, readers will develop the ability to plan suitable analyses of biological datasets, and to use the R programming environment to perform these analyses. This is achieved through a series of case studies using R to answer research questions using molecular biology datasets. Broadly applicable statistical methods are explained, including linear and rank-based correlation, distance metrics and hierarchical clustering, hypothesis testing using linear regression, proportional hazards regression for survival data, and principal component analysis. These methods are then applied as appropriate throughout the case studies, illustrating how they can be used to answer research questions. Key Features: · Provides a practical course in computational data analysis suitable for students or researchers with no previous exposure to computer programming. · Describes in detail the theoretical basis for statistical analysis techniques used throughout the textbook, from basic principles · Presents walk-throughs of data analysis tasks using R and example datasets. All R commands are presented and explained in order to enable the reader to carry out these tasks themselves. · Uses outputs from a large range of molecular biology platforms including DNA methylation and genotyping microarrays; RNA-seq, genome sequencing, ChIP-seq and bisulphite sequencing; and high-throughput phenotypic screens. · Gives worked-out examples geared towards problems encountered in cancer research, which can also be applied across many areas of molecular biology and medical research. This book has been developed over years of training biological scientists and clinicians to analyse the large datasets available in their cancer research projects. It is appropriate for use as a textbook or as a practical book for biological scientists looking to gain bioinformatics skills.
Bioinformatics for Dummies by
Bioinformatics - the process of searching biological databases, comparing sequences, examining protein structures, and researching biological questions with a computer - is one of the marvels of modern technology that can save you months of lab work. And the most amazing part is that, if you know how, you can use highly sophisticated programs over the Internet without paying a dime and sometimes, without installing anything new on your own computer. All you need to know is how to use these technological miracles. That's where Bioinformatics For Dummies comes in. If you want to know what bioinformatics is all about and how to use it without wading through pages of computer gibberish or taking a course full of theory, this book has the answers in plain English. You'll find out how to Use Internet resources Understand bioinformatics jargon Research biological databases Locate the sequences you need Perform specific tasks, step by step Written by two experts who helped develop the science, Bioinformatics For Dummies is all about getting things done. If you're just getting your feet wet, start at the beginning with a quick review of those necessary parts of microbiology and an overview of the tools available. If you already know what you want to do, you can go directly to a chapter that shows you how. Get the lowdown on Researching and analyzing DNA and protein sequences Gathering information from all published sources Searching databases for similar sequences and acquiring information about gene functions through sequence comparisons Producing and editing multiple sequence comparisons for presentation Predicting protein structures and RNA structures Doing phylogenetic analysis With an Internet connection and Bioinformatics For Dummies, you'll discover how to peruse databases that contain virtually everything known about human biology. It's like having access to the world's largest lab, right from your desk. This book is your lab assistant - one that never takes a day off, never argues when you ask it for help, and won't demand a benefits package.
Understanding Bioinformatics by
Suitable for advanced undergraduates and postgraduates, Understanding Bioinformatics provides a definitive guide to this vibrant and evolving discipline. The book takes a conceptual approach. It guides the reader from first principles through to an understanding of the computational techniques and the key algorithms. Understanding Bioinformatics is an invaluable companion for students from their first encounter with the subject through to more advanced studies. The book is divided into seven parts, with the opening part introducing the basics of nucleic acids, proteins and databases. Subsequent parts are divided into 'Applications' and 'Theory' Chapters, allowing readers to focus their attention effectively. In each section, the Applications Chapter provides a fast and straightforward route to understanding the main concepts and 'getting started'. Each of these is then followed by Theory Chapters which give greater detail and present the underlying mathematics. In Part 2, Sequence Alignments, the Applications Chapter shows the reader how to get started on producing and analyzing sequence alignments, and using sequences for database searching, while the next two chapters look closely at the more advanced techniques and the mathematical algorithms involved. Part 3 covers evolutionary processes and shows how bioinformatics can be used to help build phylogenetic trees. Part 4 looks at the characteristics of whole genomes. In Parts 5 and 6 the focus turns to secondary and tertiary structure - predicting structural conformation and analysing structure-function relationships. The last part surveys methods of analyzing data from a set of genes or proteins of an organism and is rounded off with an overview of systems biology. The writing style of Understanding Bioinformatics is notable for its clarity, while the extensive, full-color artwork has been designed to present the key concepts with simplicity and consistency. Each chapter uses mind-maps and flow diagrams to give an overview of the conceptual links within each topic.
Developing Bioinformatics Computer Skills by
Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving scientific discipline. Genome sequencing projects are producing vast amounts of biological data for many different organisms, and, increasingly, storing these data in public databases. Such biological databases are growing exponentially, along with the biological literature. It's impossible for even the most zealous researcher to stay on top of necessary information in the field without the aid of computer-based tools. Bioinformatics is all about building these tools.Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology for the first time, as well as for experienced biology researchers who are just starting to use computers to handle their data. The book covers the Unix file system, building tools and databases for bioinformatics, computational approaches to biological problems, an introduction to Perl for bioinformatics, data mining, and data visualization.Written in a clear, engaging style, Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze the data.
Beginning Perl for Bioinformatics by
With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.The book covers: Programming basics and working with DNA sequences and strings Debugging your code Simulating gene mutations using random number generators Regular expressions and finding motifs in data Arrays, hashes, and relational databases Regular expressions and restriction maps Using Perl to parse PDB records, annotations in GenBank, and BLAST output
Bioinformatics for Biologists by
The computational education of biologists is changing to prepare students for facing the complex datasets of today's life science research. In this concise textbook, the authors' fresh pedagogical approaches lead biology students from first principles towards computational thinking. A team of renowned bioinformaticians take innovative routes to introduce computational ideas in the context of real biological problems. Intuitive explanations promote deep understanding, using little mathematical formalism. Self-contained chapters show how computational procedures are developed and applied to central topics in bioinformatics and genomics, such as the genetic basis of disease, genome evolution or the tree of life concept. Using bioinformatic resources requires a basic understanding of what bioinformatics is and what it can do. Rather than just presenting tools, the authors - each a leading scientist - engage the students' problem-solving skills, preparing them to meet the computational challenges of their life science careers.
Bioinformatics and Functional Genomics by
The bestselling introduction to bioinformatics and functional genomics-now in an updated edition Widely received in its previous edition, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded Second Edition, it continues to be the go-to source for students and professionals involved in biomedical research. This edition provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include: Several fundamentally important proteins, such as globins, histones, insulin, and albumins, are included to better show how to apply bioinformatics tools to basic biological questions. A completely updated companion web site, which will be updated as new information becomes available - visit www.wiley.com/go/pevsnerbioinformatics Descriptions of genome sequencing projects spanning the tree of life. A stronger focus on how bioinformatics tools are used to understand human disease. The book is complemented by lavish illustrations and more than 500 figures and tables-fifty of which are entirely new to this edition. Each chapter includes a Problem Set, Pitfalls, Boxes explaining key techniques and mathematics/statistics principles, Summary, Recommended Reading, and a list of freely available software. Readers may visit a related Web page for supplemental information at www.wiley.com/go/pevsnerbioinformatics. Bioinformatics and Functional Genomics, Second Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It is also an indispensable resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases. Praise for the first edition: "...ideal both for biologists who want to master the application of bioinformatics to real-world problems and for computer scientists who need to understand the biological questions that motivate algorithms." Quarterly Review of Biology "... an excellent textbook for graduate students and upper level undergraduate students." Annals of Biomedical Engineering "...highly recommended for academic and medical libraries, and for researchers as an introduction and reference..." E-Streams
Practical Computing for Biologists by
Practical Computing for Biologists is an effective guide to using the many freely available computing tools in order to work more powerfully and effectively. This text helps readers to overcome the most frustrating aspects of data processing to focus on the pleasures of scientific inquiry.Although many of the techniques are relevant to molecular bioinformatics, the motivation for the text is much broader, focusing on topics and techniques that are applicable to a range of scientific endeavors.
Problem Solving Handbook for Computational Biology and Bioinformatics by
Bioinformatics is growing by leaps and bounds; theories/algorithms/statistical techniques are constantly evolving. Nevertheless, a core body of algorithmic ideas have emerged and researchers are beginning to adopt a "problem solving" approach to bioinformatics, wherein they use solutions to well-abstracted problems as building blocks to solve larger scope problems. Problem Solving Handbook for Computational Biology and Bioinformatics is an edited volume contributed by world renowned leaders in this field. This comprehensive handbook with problem solving emphasis, covers all relevant areas of computational biology and bioinformatics. Web resources and related themes are highlighted at every opportunity in this central easy-to-read reference. Designed for advanced-level students, researchers and professors in computer science and bioengineering as a reference or secondary text, this handbook is also suitable for professionals working in this industry.
Bioinformatics for Geneticists by
Praise from the reviews: "Without reservation, I endorse this text as the best resource I've encountered that neatly introduces and summarizes many points I've learned through years of experience. The gems of truth found in this book will serve well those who wish to apply bioinformatics in their daily work, as well as help them advise others in this capacity." CIRCGENETICS "This book may really help to get geneticists and bioinformaticians on 'speaking-terms'... contains some essential reading for almost any person working in the field of molecular genetics." EUROPEAN JOURNAL OF HUMAN GENETICS "... an excellent resource... this book should ensure that any researcher's skill base is maintained." GENETICAL RESEARCH "... one of the best available and most accessible texts on bioinformatics and genetics in the postgenome age... The writing is clear, with succinct subsections within each chapter....Without reservation, I endorse this text as the best resource I've encountered that neatly introduces and summarizes many points I've learned through years of experience. The gems of truth found in this book will serve well those who wish to apply bioinformatics in their daily work, as well as help them advise others in this capacity." CIRCULATION: CARDIOVASCULAR GENETICS A fully revised version of the successful First Edition, this one-stop reference book enables all geneticists to improve the efficiency of their research. The study of human genetics is moving into a challenging new era. New technologies and data resources such as the HapMap are enabling genome-wide studies, which could potentially identify most common genetic determinants of human health, disease and drug response. With these tremendous new data resources at hand, more than ever care is required in their use. Faced with the sheer volume of genetics and genomic data, bioinformatics is essential to avoid drowning true signal in noise. Considering these challenges, Bioinformatics for Geneticists, Second Edition works at multiple levels: firstly, for the occasional user who simply wants to extract or analyse specific data; secondly, at the level of the advanced user providing explanations of how and why a tool works and how it can be used to greatest effect. Finally experts from fields allied to genetics give insight into the best genomics tools and data to enhance a genetic experiment. Hallmark Features of the Second Edition: Illustrates the value of bioinformatics as a constantly evolving avenue into novel approaches to study genetics The only book specifically addressing the bioinformatics needs of geneticists More than 50% of chapters are completely new contributions Dramatically revised content in core areas of gene and genomic characterisation, pathway analysis, SNP functional analysis and statistical genetics Focused on freely available tools and web-based approaches to bioinformatics analysis, suitable for novices and experienced researchers alike Bioinformatics for Geneticists, Second Edition describes the key bioinformatics and genetic analysis processes that are needed to identify human genetic determinants. The book is based upon the combined practical experience of domain experts from academic and industrial research environments and is of interest to a broad audience, including students, researchers and clinicians working in the human genetics domain.
Bioinformatics for High Throughput Sequencing by
Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein - DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.