Concepts in Bioinformatics and Genomics

Author: Alison McCurdy
Publisher: Oxford University Press, USA
ISBN: 0199936994
Release Date: 2016-07-01
Genre: Bioinformatics

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
Publisher: Oxford University Press, USA
ISBN: 0190610549
Release Date: 2016-07-01
Genre: Bioinformatics

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.

Concepts in Bioinformatics and Genomics

Author: Jamil Momand
Publisher: Oxford University Press, USA
ISBN: 0190610530
Release Date: 2016-07-01
Genre: Bioinformatics

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-coding methodology underpinning this exciting field.

Bioinformatics and Functional Genomics

Author: Jonathan Pevsner
Publisher: John Wiley & Sons
ISBN: 9781118581780
Release Date: 2015-11-02
Genre: Science

Bioinformatics and Functional Genomics, Third Edition is the latest revision of this bestselling and indispensible text book. Thoroughly updated to encompass the latest advances in the field the book retains its broad and accessible approach. Divided into three parts the book deals first with bioinformatics, the use of computer databases and computer algorithms in the study of proteins and genes. The first section includes sequence alignment, database searches and phylogeny. The second section of the book focuses on functional genomics and includes approaches such as gene expression profiling and proteomics that are used to study cellular function. The final part of the book deals with genomics which is the study of the collection of DNA that comprises an organism, using the tools of bioinformatics. Bioinformatics and Functional Genomics, Third Edition will serve as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It will also provide an essential 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.

Fundamental Concepts of Bioinformatics

Author: Dan E. Krane
Publisher:
ISBN: 032119022X
Release Date: 2003
Genre: Bioinformatics

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.

Genomics and Bioinformatics

Author: Tore Samuelsson
Publisher: Cambridge University Press
ISBN: 9781107378339
Release Date: 2012-06-07
Genre: Science

With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.

Essential Bioinformatics

Author: Jin Xiong
Publisher: Cambridge University Press
ISBN: 9781139450621
Release Date: 2006-03-13
Genre: Science

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.

Bioinformatics for Beginners

Author: Supratim Choudhuri
Publisher: Elsevier
ISBN: 9780124105102
Release Date: 2014-05-09
Genre: Medical

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

Introduction to Genomics

Author: Arthur Lesk
Publisher: Oxford University Press
ISBN: 9780198754831
Release Date: 2017-03-30
Genre:

Our genome is the blueprint for our existence: it encodes all the information we need to develop from a single cell into a hugely complicated functional organism. Yet it is more than a static information store: our genome is a dynamic, tightly-regulated collection of genes, which switch on andoff in many combinations to give the variety of cells from which our bodies are formed. But how do we identify the genes that make up our genome? How do we determine their function? And how do different genes form the regulatory networks that direct the processes of life? Introduction to Genomics is the most up-to-date and complete textbook for students approaching the subject for the first time. Lesk's engaging writing style brings a narrative to a disparate field of study and offers a fascinating insight into what can be revealed from the study of genomes. The bookcovers: the similarities and differences between organisms; how different organisms evolved; how the genome is constructed and how it operates; and what our understanding of genomics means in terms of our future health and wellbeing. The Online Resource Centre accompanying Introduction to Genomics features: For students: * Extensive and imaginative weblems (web-based problems) for each chapter designed to give you practice with the tools required for further study and research in the field* Hints and answers to end-of-chapter problems and exercises support your self-directed learning* Guided tour of websites and major archival databanks in genomics offer a wealth of resources to springboard your own research * Journal club: links to related research articles on topics covered in the book are paired with engaging questions to improve your interpretation of the primary literature* Rotating figures allow you to visualize complex structuresFor registered adopters: * Downloadable figures from the book.

Computing for Comparative Microbial Genomics

Author: David Wayne Ussery
Publisher: Springer Science & Business Media
ISBN: 9781848002548
Release Date: 2009-02-26
Genre: Science

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.

Computational Genome Analysis

Author: Richard C. Deonier
Publisher: Springer Science & Business Media
ISBN: 9780387288079
Release Date: 2005-12-27
Genre: Computers

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.

Evolutionary Genomics and Systems Biology

Author: Gustavo Caetano-Anollés
Publisher: Wiley-Blackwell
ISBN: 9780470570401
Release Date: 2010-07-08
Genre: Science

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.

Phylogenetic Networks

Author: Daniel H. Huson
Publisher: Cambridge University Press
ISBN: 9781139492874
Release Date: 2010-12-02
Genre: Science

The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.

Bioinformatics

Author: David W. Mount
Publisher: CSHL Press
ISBN: 0879697121
Release Date: 2004
Genre: Science

As more species' genomes are sequenced, computational analysis of these data has become increasingly important. The second, entirely updated edition of this widely praised textbook provides a comprehensive and critical examination of the computational methods needed for analyzing DNA, RNA, and protein data, as well as genomes. The book has been rewritten to make it more accessible to a wider audience, including advanced undergraduate and graduate students. New features include chapter guides and explanatory information panels and glossary terms. New chapters in this second edition cover statistical analysis of sequence alignments, computer programming for bioinformatics, and data management and mining. Practically oriented problems at the ends of chapters enhance the value of the book as a teaching resource. The book also serves as an essential reference for professionals in molecular biology, pharmaceutical, and genome laboratories.

Bioinformatics

Author: Andreas D. Baxevanis
Publisher: John Wiley & Sons
ISBN: 9780471461012
Release Date: 2004-03-24
Genre: Computers

"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.