Concepts in Bioinformatics and Genomics

Author: Alison McCurdy

Publisher: Oxford University Press, USA

ISBN: 9780199936991

Category: Bioinformatics

Page: 560

View: 8681

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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: 366

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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 for Biologists

Author: Pavel Pevzner,Ron Shamir

Publisher: Cambridge University Press

ISBN: 1139501615

Category: Science

Page: N.A

View: 4436

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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.

Essential Bioinformatics

Author: Jin Xiong

Publisher: Cambridge University Press

ISBN: 113945062X

Category: Science

Page: N.A

View: 2376

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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.

Fundamental Concepts of Bioinformatics

Author: Dan E. Krane,Michael L. Raymer

Publisher: N.A

ISBN: 9780321190222

Category: Bioinformatics

Page: 314

View: 4954

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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.

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: 3118

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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.

Genome Analysis And Bioinformatics: A Practical Approach

Author: T. R. Sharma

Publisher: N.A

ISBN: 9789380026367

Category: Bioinformatics

Page: 222

View: 5813

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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.

Introduction to Genomics

Author: Arthur Lesk

Publisher: Oxford University Press

ISBN: 0199564353

Category: Medical

Page: 397

View: 2465

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Introduction to Genomics is a fascinating insight into what can be revealed from the study of genomes: how organisms differ or match; how different organisms evolved; how the genome is constructed and how it operates; and what our understanding of genome structure and function means in terms of our future health and wellbeing.

Bioinformatics

A Concept-Based Introduction

Author: Venkatarajan Mathura,Pandjassarame Kangueane

Publisher: Springer Science & Business Media

ISBN: 0387848703

Category: Science

Page: 190

View: 6207

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Bioinformatics is an evolving field that is gaining popularity due to genomics, proteomics and other high-throughput biological methods. The function of bioinformatic scientists includes biological data storage, retrieval and in silico analysis of the results from large-scale experiments. This requires a grasp of knowledge mining algorithms, a thorough understanding of biological knowledge base, and the logical relationship of entities that describe a process or the system. Bioinformatics researchers are required to be trained in multidisciplinary fields of biology, mathematics and computer science. Currently the requirements are satisfied by ad hoc researchers who have specific skills in biology or mathematics/computer science. But the learning curve is steep and the time required to communicate using domain specific terms is becoming a major bottle neck in scientific productivity. This workbook provides hands-on experience which has been lacking for qualified bioinformatics researchers.

Introduction to Bioinformatics

Author: Arthur Lesk

Publisher: Oxford University Press

ISBN: 0199651566

Category: Science

Page: 371

View: 3298

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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.

Introduction to Evolutionary Genomics

Author: Naruya Saitou

Publisher: Springer Science & Business Media

ISBN: 1447153049

Category: Computers

Page: 461

View: 492

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This book is the first of its kind to explain the fundamentals of evolutionary genomics. The comprehensive coverage includes concise descriptions of a variety of genome organizations, a thorough discussion of the methods used, and a detailed review of genome sequence processing procedures. The opening chapters also provide the necessary basics for readers unfamiliar with evolutionary studies. Features: introduces the basics of molecular biology, DNA replication, mutation, phylogeny, neutral evolution, and natural selection; presents a brief evolutionary history of life from the primordial seas to the emergence of humans; describes the genomes of prokaryotes, eukaryotes, vertebrates, and humans; reviews methods for genome sequencing, phenotype data collection, homology searches and analysis, and phylogenetic tree and network building; discusses databases of genome sequences and related information, evolutionary distances, and population genomics; provides supplementary material at an associated website.

Bioinformatics for Beginners

Genes, Genomes, Molecular Evolution, Databases and Analytical Tools

Author: Supratim Choudhuri

Publisher: Elsevier

ISBN: 0124105106

Category: Medical

Page: 238

View: 7094

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Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools provides a coherent and friendly treatment of bioinformatics for any student or scientist within biology who has not routinely performed bioinformatic analysis. The book discusses the relevant principles needed to understand the theoretical underpinnings of bioinformatic analysis and demonstrates, with examples, targeted analysis using freely available web-based software and publicly available databases. Eschewing non-essential information, the work focuses on principles and hands-on analysis, also pointing to further study options. Avoids non-essential coverage, yet fully describes the field for beginners Explains the molecular basis of evolution to place bioinformatic analysis in biological context Provides useful links to the vast resource of publicly available bioinformatic databases and analysis tools Contains over 100 figures that aid in concept discovery and illustration

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: 9893

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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.

Clinical Genomics

Author: Shashikant Kulkarni,John Pfeifer

Publisher: Academic Press

ISBN: 0124051731

Category: Science

Page: 488

View: 3310

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Clinical Genomics provides an overview of the various next-generation sequencing (NGS) technologies that are currently used in clinical diagnostic laboratories. It presents key bioinformatic challenges and the solutions that must be addressed by clinical genomicists and genomic pathologists, such as specific pipelines for identification of the full range of variants that are clinically important. This book is also focused on the challenges of diagnostic interpretation of NGS results in a clinical setting. Its final sections are devoted to the emerging regulatory issues that will govern clinical use of NGS, and reimbursement paradigms that will affect the way in which laboratory professionals get paid for the testing. Simplifies complexities of NGS technologies for rapid education of clinical genomicists and genomic pathologists towards genomic medicine paradigm Tried and tested practice-based analysis for precision diagnosis and treatment plans Specific pipelines and meta-analysis for full range of clinically important variants

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: 4579

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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.

Discovering Genomics, Proteomics, and Bioinformatics

Author: A. Malcolm Campbell,Laurie J. Heyer

Publisher: Benjamin-Cummings Publishing Company

ISBN: 9780805382198

Category: Science

Page: 447

View: 7457

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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.

Genome-Scale Algorithm Design

Biological Sequence Analysis in the Era of High-Throughput Sequencing

Author: Veli Mäkinen,Djamal Belazzougui,Fabio Cunial,Alexandru I. Tomescu

Publisher: Cambridge University Press

ISBN: 1316342948

Category: Science

Page: N.A

View: 5547

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High-throughput sequencing has revolutionised the field of biological sequence analysis. Its application has enabled researchers to address important biological questions, often for the first time. This book provides an integrated presentation of the fundamental algorithms and data structures that power modern sequence analysis workflows. The topics covered range from the foundations of biological sequence analysis (alignments and hidden Markov models), to classical index structures (k-mer indexes, suffix arrays and suffix trees), Burrows–Wheeler indexes, graph algorithms and a number of advanced omics applications. The chapters feature numerous examples, algorithm visualisations, exercises and problems, each chosen to reflect the steps of large-scale sequencing projects, including read alignment, variant calling, haplotyping, fragment assembly, alignment-free genome comparison, transcript prediction and analysis of metagenomic samples. Each biological problem is accompanied by precise formulations, providing graduate students and researchers in bioinformatics and computer science with a powerful toolkit for the emerging applications of high-throughput sequencing.