Concepts in Bioinformatics and Genomics

Author: Alison McCurdy

Publisher: Oxford University Press, USA

ISBN: 9780199936991

Category: Bioinformatics

Page: 560

View: 7920

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Concepts in Bioinformatics and Genomics takes a conceptual approach to its subject, balancing biology, mathematics, and programming, while highlighting relevant real-world applications. Topics are developed from the fundamentals up like in an introductory textbook. This is a comprehensive bookfor students enrolled in their first course in bioinformatics. A compelling case study gene, the TP53 gene, a human tumor suppressor with strong clinical applications, runs throughout, engaging students with a continuously relevant example.The textbook thoroughly describes basic principles of probability as they lead up to the concept of expectation value (E-value) and its use in sequence alignment programs. Concepts in Bioinformatics and Genomics also describes, from a mathematical perspective, the development of the Hidden MarkovModel and how it can be used to align sequences in multiple sequence alignment programs. Finally, it introduces students to programming exercises directly related to bioinformatics problems. These thought-provoking exercises stretch the students' imaginations and learning, giving them a deeperunderstanding of software programs, molecular biology, basic probability, and program-coding methodology underpinning the discipline. They will have the tools necessary to compute biological data.

Concepts in Bioinformatics and Genomics

Author: Jamil Momand,Alison McCurdy

Publisher: Oxford University Press, USA

ISBN: 9780190610548

Category: Bioinformatics

Page: 477

View: 8275

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Concepts in Bioinformatics and Genomics takes a conceptual approach to its subject, balancing biology, mathematics, and programming while highlighting relevant real-world applications and providing students with the tools to compute and analyze biological data. It presents many thought-provoking exercises to stretch students' imaginations, giving them a deeper understanding of the molecular biology, basic probability, software programs, and program-codingmethodology underpinning this exciting field.

Bioinformatics

A Practical Guide to the Analysis of Genes and Proteins

Author: Andreas D. Baxevanis,B. F. Francis Ouellette

Publisher: John Wiley & Sons

ISBN: 0471461016

Category: Computers

Page: 504

View: 7392

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"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.

Essential Bioinformatics

Author: Jin Xiong

Publisher: Cambridge University Press

ISBN: 113945062X

Category: Science

Page: N.A

View: 375

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Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.

Evolutionary Genomics and Systems Biology

Author: Gustavo Caetano-Anollés

Publisher: John Wiley & Sons

ISBN: 1118210719

Category: Science

Page: 465

View: 4933

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A comprehensive, authoritative look at an emergent area in post-genomic science, Evolutionary genomics is an up-and-coming, complex field that attempts to explain the biocomplexity of the living world. Evolutionary Genomics and Systems Biology is the first full-length book to blend established and emerging concepts in bioinformatics, evolution, genomics, and structural biology, with the integrative views of network and systems biology. Three key aspects of evolutionary genomics and systems biology are covered in clear detail: the study of genomic history, i.e., understanding organismal evolution at the genomic level; the study of macromolecular complements, which encompasses the evolution of the protein and RNA machinery that propels life; and the evolutionary and dynamic study of wiring diagrams—macromolecular components in interaction—in the context of genomic complements. The book also features: A solid, comprehensive treatment of phylogenomics, the evolution of genomes, and the evolution of biological networks, within the framework of systems biology A special section on RNA biology—translation, evolution of structure, and micro RNA and regulation of gene expression Chapters on the mapping of genotypes to phenotypes, the role of information in biology, protein architecture and biological function, chromosomal rearrangements, and biological networks and disease Contributions by leading authorities on each topic Evolutionary Genomics and Systems Biology is an ideal book for students and professionals in genomics, bioinformatics, evolution, structural biology, complexity, origins of life, systematic biology, and organismal diversity, as well as those individuals interested in aspects of biological sciences as they interface with chemistry, physics, and computer science and engineering.

Genome Analysis And Bioinformatics: A Practical Approach

Author: T. R. Sharma

Publisher: N.A

ISBN: 9789380026367

Category: Bioinformatics

Page: 222

View: 6431

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With the decoding of whole genome sequences of many organisms, new vistas of research have emerged in computational biology. The scientific community has free access to the genome sequence data from the public databases. Many times, it is really hard to make sense of these huge data of DNA and protein sequences. Therefore, bioinformatics tools are used to handle, store and analyze genome sequence data for the benefit of mankind. The book has been written in a simplest possible manner so that every one should understand the basic concepts of genome sequence analysis and bioinformatics. The book is structured in such a way so that readers should first know about how whole genome sequences are generated by using high throughput DNA sequencing technologies and then storing of sequences in biological databases. Second part deals with the basic principals involved in sequence analysis and applications of softwares along with practical exercises. Thirdly, data mining approaches for the discovery of genes and DNA markers have also been discussed. Besides, glossary of important terms and introduction to basic bioinformatics softwares has been included for the benefits of readers. The book will serve as a text book to the B. Tech (Bioinformatics & Biotechnology) students and would also be useful reference book to the postgraduate students and research scientists working in the areas of life sciences, genomics, biotechnology and molecular biology as well as Masters in Computer Applications (MCA) who are interested in bioinformatics.

Fundamental Concepts of Bioinformatics

Author: Dan E. Krane,Michael L. Raymer

Publisher: N.A

ISBN: 9780321190222

Category: Bioinformatics

Page: 314

View: 5309

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Co-authored by a biologist and computer scientist, this book is designed to make bioinformatics useful to undergraduates and prepare them for more advanced work. It covers problems at the end of each chapter, which use real data to help students apply what they have learned from both a statistical and biological point of view.

Computational Genome Analysis

An Introduction

Author: Richard C. Deonier,Simon Tavaré,Michael Waterman

Publisher: Springer Science & Business Media

ISBN: 9780387987859

Category: Computers

Page: 535

View: 5316

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This book presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. The book features a free download of the R software statistics package and the text provides great crossover material that is interesting and accessible to students in biology, mathematics, statistics and computer science. More than 100 illustrations and diagrams reinforce concepts and present key results from the primary literature. Exercises are given at the end of chapters.

Computing for Comparative Microbial Genomics

Bioinformatics for Microbiologists

Author: David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini

Publisher: Springer Science & Business Media

ISBN: 1848002548

Category: Science

Page: 270

View: 8712

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Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.

Introduction to Computational Genomics

A Case Studies Approach

Author: Nello Cristianini,Matthew W. Hahn

Publisher: Cambridge University Press

ISBN: 1139460153

Category: Computers

Page: N.A

View: 2557

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Where did SARS come from? Have we inherited genes from Neanderthals? How do plants use their internal clock? The genomic revolution in biology enables us to answer such questions. But the revolution would have been impossible without the support of powerful computational and statistical methods that enable us to exploit genomic data. Many universities are introducing courses to train the next generation of bioinformaticians: biologists fluent in mathematics and computer science, and data analysts familiar with biology. This readable and entertaining book, based on successful taught courses, provides a roadmap to navigate entry to this field. It guides the reader through key achievements of bioinformatics, using a hands-on approach. Statistical sequence analysis, sequence alignment, hidden Markov models, gene and motif finding and more, are introduced in a rigorous yet accessible way. A companion website provides the reader with Matlab-related software tools for reproducing the steps demonstrated in the book.

Discovering Genomics, Proteomics, and Bioinformatics

Author: A. Malcolm Campbell,Laurie J. Heyer

Publisher: Benjamin-Cummings Publishing Company

ISBN: 9780805382198

Category: Science

Page: 447

View: 5908

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KEY BENEFIT: Discovering Genomics is the first genomics text that combines web activities and case studies with a problem-solving approach to teach upper-level undergraduates and first-year graduate students the fundamentals of genomic analysis. More of a workbook than a traditional text, Discovering Genomics, Second Edition allows students to work with real genomic data in solving problems and provides the user with an active learning experience. KEY TOPICS: Genomic Medicine Case Study: What's wrong with my child? Genome Sequence Acquisition and Analysis, Comparative Genomics in Evolution and Medicine, Genome Variations, Genomic Medicine Case Study: Why Can't I Just Take a Pill to Lose Weight? Basic Research with DNA Microarrays, Applied Research with DNA Microarrays, Proteomics, Genomic Medicine Case Study: Why Can't We Cure More Diseases? Genomic Circuits in Single Genes, Integrated Genomic Circuits, Modeling Whole-Genome Circuits. MARKET: For all readers interested in genomics.

Bioinformatics

The Machine Learning Approach

Author: Pierre Baldi,Søren Brunak,Professor Pierre Baldi,Francis Bach

Publisher: MIT Press

ISBN: 9780262025065

Category: Computers

Page: 452

View: 5515

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Pierre Baldi and Soren Brunak present the key machine learning approaches and apply them to the computational problems encountered in the analysis of biological data. The book is aimed at two types of researchers and students. First are the biologists and biochemists who need to understand new data-driven algorithms, such as neural networks and hidden Markov models, in the context of biological sequences and their molecular structure and function. Second are those with a primary background in physics, mathematics, statistics, or computer science who need to know more about specific applications in molecular biology.

Biocode

The New Age of Genomics

Author: Dawn Field,Neil Davies

Publisher: American Chemical Society

ISBN: 0199687757

Category: Science

Page: 196

View: 4703

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The living world runs on genomic software - what Dawn Field and Neil Davies call the 'biocode' - the sum of all DNA on Earth. In Biocode, they tell the story of a new age of scientific discovery: the growing global effort to read and map the biocode, and what that might mean for the future. The structure of DNA was identified in 1953, and the whole human genome was mapped by 2003. Since then the new field of genomics has mushroomed and is now operating on an industrial scale. Genomes can now be sequenced rapidly and increasingly cheaply. The genomes of large numbers of organisms from mammals to microbes, have been mapped. Getting your genome sequenced is becoming affordable for many. You too can check paternity, find out where your ancestors came from, or whether you are at risk of some diseases. Some check out the pedigree of their pets, while others turn genomes into art. A stray hair is enough to crudely reconstruct the face of the owner. From reading to constructing: the first steps to creating artificial life have already been taken. Some may find the rapidity of developments, and the potential for misuse, alarming. But they also open up unprecedented possibilities. The ability to read DNA has changed how we view ourselves and understand our place in nature. From the largest oceans, to the insides of our guts, we are able to explore the biosphere as never before, from the genome up. Sequencing technology has made the invisible world of microbes visible, and biodiversity genomics is revealing whole new worlds within us and without. The findings are transformational: we are all ecosystems now. Already the first efforts at 'barcoding' entire ecological communities and creating 'genomic observatories' have begun. The future, the authors argue, will involve biocoding the entire planet.

Introduction to Bioinformatics

Author: Arthur Lesk

Publisher: Oxford University Press

ISBN: 0199651566

Category: Science

Page: 371

View: 4225

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Lesk provides an accessible and thorough introduction to a subject which is becoming a fundamental part of biological science today. The text generates an understanding of the biological background of bioinformatics.

Bioinformatics Data Skills

Reproducible and Robust Research with Open Source Tools

Author: Vince Buffalo

Publisher: "O'Reilly Media, Inc."

ISBN: 1449367518

Category: Computers

Page: 538

View: 6008

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Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, you’ll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand life’s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, you’re ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles

Cancer Bioinformatics

Author: Ying Xu,Juan Cui,David Puett

Publisher: Springer

ISBN: 1493913816

Category: Computers

Page: 368

View: 3701

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This book provides a framework for computational researchers studying the basics of cancer through comparative analyses of omic data. It discusses how key cancer pathways can be analyzed and discovered to derive new insights into the disease and identifies diagnostic and prognostic markers for cancer. Chapters explain the basic cancer biology and how cancer develops, including the many potential survival routes. The examination of gene-expression patterns uncovers commonalities across multiple cancers and specific characteristics of individual cancer types. The authors also treat cancer as an evolving complex system, explore future case studies, and summarize the essential online data sources. Cancer Bioinformatics is designed for practitioners and researchers working in cancer research and bioinformatics. It is also suitable as a secondary textbook for advanced-level students studying computer science, biostatistics or biomedicine.

Genomic Perl

From Bioinformatics Basics to Working Code

Author: Rex A. Dwyer

Publisher: Cambridge University Press

ISBN: 9780521801775

Category: Computers

Page: 334

View: 652

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This introduction to computational molecular biology will help programmers and biologists learn the skills needed to start work in this important, expanding field. The author explains many of the basic computational problems and gives concise, working programs to solve them in the Perl programming language. With minimal prerequisites, the author explains the biological background for each problem, develops a model for the solution, then introduces the Perl concepts needed to implement the solution. The book covers pairwise and multiple sequence alignment, fast database searches for homologous sequences, protein motif identification, genome rearrangement, physical mapping, phylogeny reconstruction, satellite identification, sequence assembly, gene finding, and RNA secondary structure. The concrete examples and step-by-step approach make it easy to grasp the computational and statistical methods, including dynamic programming, branch-and-bound optimization, greedy methods, maximum likelihood methods, substitution matrices, BLAST searching, and Karlin-Altschul statistics. Perl code is provided on the accompanying CD.

Bioinformatics: Genomics and Proteomics

Author: Ruchi Singh

Publisher: Vikas Publishing House

ISBN: 9325978555

Category: Technology & Engineering

Page: N.A

View: 1229

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This is an innovative textbook for undergraduates as well as postgraduates offering basic knowledge of biology. Its aim is to provide state-of-the-art information about this developing science that has the potential to replace existing biological approaches to study genes and proteins. The chapters are explained in a concise yet detailed manner, including ample cross-references, references to literature and databases, tables and illustrations. The book's sound approach to this intricately complex field makes it an exceptional resource for further exploration into biochemistry, molecular biology, genomics and drug designing fields. Abundant learning features make this book the ideal teaching and learning tool. KEY FEATURES • Illustrations to bolster understanding of complex biochemical relations • Tables for quick access to precise data • Extensive end-of-chapter exercises and references • The most basic details furnished for those who are new to biology • User-friendly, Internet-based bioinformatics tools that allow researchers to extract information from databases and analyze it • Analysis of one software tool discussed in each chapter step-by-step from entering the input till interpretation of the results This is an in-depth textbook written for the biologist who wants a thorough understanding of the popular bioinformatics programs and molecular databases currently in use. It provides a broad, application-oriented overview of this technology.