Bioinformatics and Functional Genomics / Edition 1

Paperback (Print)
Used and New from Other Sellers
Used and New from Other Sellers
from $4.96
Usually ships in 1-2 business days
(Save 96%)
Other sellers (Paperback)
  • All (12) from $4.96   
  • New (3) from $97.95   
  • Used (9) from $4.97   
Close
Sort by
Page 1 of 1
Showing All
Note: Marketplace items are not eligible for any BN.com coupons and promotions
$97.95
Seller since 2010

Feedback rating:

(27)

Condition:

New — never opened or used in original packaging.

Like New — packaging may have been opened. A "Like New" item is suitable to give as a gift.

Very Good — may have minor signs of wear on packaging but item works perfectly and has no damage.

Good — item is in good condition but packaging may have signs of shelf wear/aging or torn packaging. All specific defects should be noted in the Comments section associated with each item.

Acceptable — item is in working order but may show signs of wear such as scratches or torn packaging. All specific defects should be noted in the Comments section associated with each item.

Used — An item that has been opened and may show signs of wear. All specific defects should be noted in the Comments section associated with each item.

Refurbished — A used item that has been renewed or updated and verified to be in proper working condition. Not necessarily completed by the original manufacturer.

New
Absolutely BRAND NEW ORIGINAL US Edition / Mint condition / Never been read / Paperback / ISBN: 0471210048. Shipped out in one business day with free tracking.

Ships from: Manvel, TX

Usually ships in 1-2 business days

  • Standard, 48 States
  • Standard (AK, HI)
$102.95
Seller since 2013

Feedback rating:

(10)

Condition: New
100% BRAND NEW US Edition / Mint condition / Never been read / Paperback / ISBN: 0471210048. Shipped out in one business day with free tracking.

Ships from: Manvel, TX

Usually ships in 1-2 business days

  • Canadian
  • International
  • Standard, 48 States
  • Standard (AK, HI)
  • Express, 48 States
  • Express (AK, HI)
$115.00
Seller since 2014

Feedback rating:

(148)

Condition: New
Brand new.

Ships from: acton, MA

Usually ships in 1-2 business days

  • Standard, 48 States
  • Standard (AK, HI)
Page 1 of 1
Showing All
Close
Sort by

Overview

Introduction to Bioinformatics provides a broad-based introduction to bioinformatics by following three, real-world examples throughout the book: retinol-binding protein, breast cancer, and a calcium binding site C2. The author emphasizes the use of computational tools and databases to study connections between the structure of proteins and genes to function, development, evolution, and disease. Readers will learn real skills, such as how to analyze genes and proteins, how to make trees using phylogenetic software, how to extract data, or how to identify genes and proteins implicated in diseases.
Read More Show Less

Editorial Reviews

From the Publisher
"…provides non-trivial tools and biological motivations to learn bioinformatics." (Journal of Statistical Computation & Simulation, January 2005)

"...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, March-May 2005)

"…this appears to be an excellent textbook for graduate students and upper level undergraduate students." (Annals of Biomedical Engineering, July 2004, 32, 7)

"…highly recommended for academic and medical libraries, and for researchers as an introduction and reference…" (E-Streams, Vol. 7, No. 4)

“...an intriguing work targeted toward biologists wanting to solve problems...provides a compendium of many biological insights and breakthroughs and will be a useful resource...highly recommended.” (Choice, Vol. 41, No. 7, March 2004)

Read More Show Less

Product Details

  • ISBN-13: 9780471210047
  • Publisher: Wiley, John & Sons, Incorporated
  • Publication date: 10/17/2003
  • Edition description: Older Edition
  • Edition number: 1
  • Pages: 800
  • Product dimensions: 8.52 (w) x 10.85 (h) x 1.56 (d)

Read an Excerpt

Bioinformatics and Functional Genomics


By Jonathan Pevsner

John Wiley & Sons

Copyright © 2003 Wiley-Liss
All right reserved.

ISBN: 0-471-21004-8


Chapter One

Introduction

Bioinformatics represents a new field at the interface of the twentieth-century revolutions in molecular biology and computers. A focus of this new discipline is the use of computer databases and computer algorithms to analyze proteins, genes, and the complete collections of deoxyribonucleic acid (DNA) that comprises an organism (the genome). A major challenge in biology is to make sense of the enormous quantities of sequence data and structural data that are generated by genome-sequencing projects, proteomics, and other large-scale molecular biology efforts. The tools of bioinformatics include computer programs that help to reveal fundamental mechanisms underlying biological problems related to the structure and function of macromolecules, biochemical pathways, disease processes, and evolution.

According to a National Institutes of Health (NIH) definition, bioinformatics is "research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, analyze, or visualize such data." The related discipline of computational biology is "the development and application of data-analytical and theoretical methods, mathematicalmodeling and computational simulation techniques to the study of biological, behavioral, and social systems."

While the discipline of bioinformatics focuses on the analysis of molecular sequences, genomics and functional genomics are two closely related disciplines. The goal of genomics is to determine and analyze the complete DNA sequence of an organism, that is, its genome. The DNA encodes genes, which can be expressed as ribonucleic acid (RNA) transcripts and then translated into protein. Functional genomics describes the use of genomewide assays to the study of gene and protein function.

The aim of this book is to explain both the theory and practice of bioinformatics. The book is especially designed to help the biology student use computer programs and databases to solve biological problems related to proteins, genes, and genomes. Bioinformatics is an integrative discipline, and our focus on individual proteins and genes is part of a larger effort to understand broad issues in biology such as the relationship of structure to function, development, and disease.

Organization of The Book

There are three main sections of the book. The first part explains how to access biological sequence data, particularly DNA and protein sequences (Chapter 2). Once sequences are obtained, we show how to compare two sequences (pairwise alignment; Chapter 3) and how to compare multiple sequences [primarily by the Basic Local Alignment Search Tool (BLAST); Chapters 4 and 5].

The second part of the book describes functional genomics approaches to RNA and protein. The central dogma of biology states that DNA is transcribed into RNA then translated into protein. We will examine gene expression, including a description of the emerging technology of DNA microarrays (Chapters 6 and 7). We then consider proteins from the perspective of protein families, the analysis of individual proteins, protein structure, and multiple sequence alignment (Chapters 8-10). The relationships of protein and DNA sequences that are multiply aligned can be visualized in phylogenetic trees (Chapter 11). Chapter 11 thus introduces the subject of molecular evolution.

Since 1995, the genomes have been sequenced for several hundred bacteria and archaea as well as fungi, animals, and plants. The third section of the book covers genome analysis. Chapter 12 provides an overview of the study of completed genomes and then descriptions of how the tools of bioinformatics can elucidate the tree of life. We describe bioinformatics resources for the study of viruses (Chapter 13) and bacteria and archaea (Chapter 14; these are two of the three main branches of life). Next we examine a variety of eukaryotes (from fungi to primates; Chapters 15 and 16) and then the human genome (Chapter 17). Finally, we explore bioinformatic approaches to human disease (Chapter 18).

Bioinformatics: The Big Picture

We can summarize the entire field of bioinformatics with three perspectives. The first perspective on bioinformatics is the cell (Fig. 1.1). The central dogma of molecular biology is that DNA is transcribed into RNA and translated into protein. The focus of molecular biology has been on individual genes, messenger RNA (mRNA) transcripts, and proteins. A focus of the field of bioinformatics is the complete collection of DNA (the genome), RNA (the transcriptome), and protein sequences (the proteome) that have been amassed (Henikoff, 2002). These millions of molecular sequences present both great opportunities and great challenges. A bioinformatics approach to molecular sequence data involves the application of computer algorithms and computer databases to molecular and cellular biology. Such an approach is sometimes referred to as functional genomics. This typifies the essential nature of bioinformatics: biological questions can be approached from levels ranging from single genes and proteins to cellular pathways and networks or even whole genomic responses (Ideker et al., 2001). Our goals are to understand how to study both individual genes and proteins and collections of thousands of genes/proteins.

From the cell we can focus on individual organisms, which represents the second perspective of the field of bioinformatics (Fig. 1.2). Each organism changes across different stages of development and (formulticellular organisms) across different regions of the body. For example, while we may sometimes think of genes as static entities that specify features such as eye color or height, they are in fact dynamically regulated across time and region and in response to physiological state. Gene expression varies in disease states or in response to a variety of signals, both intrinsic and environmental. Many bioinformatics tools are available to study the broad biological questions relevant to the individual: There are many databases of expressed genes and proteins derived from different tissues and conditions. One of the most powerful applications of functional genomics is the use of DNA microarrays to measure the expression of thousands of genes in biological samples.

At the largest scale is the tree of life (Fig. 1.3) (Chapter 12). There are many millions of species alive today, and they can be grouped into the three major branches of bacteria, archaea (single-celled microbes that tend to live in extreme environments), and eukaryotes. Molecular sequence databases currently hold DNA sequence from over 100,000 different organisms. The complete genome sequences of several hundred organisms will soon become available. One of the main lessons we are learning is the fundamental unity of life at the molecular level. We are also coming to appreciate the power of comparative genomics, in which genomes are compared.

Figure 1.4 on the following page presents the contents of this book in the context of the three perspectives of bioinformatics.

A Consistent Example: Retinol-Binding Protein

Throughout this book we will focus on the example of a gene and its corresponding protein product: retinol-binding protein (RBP4), a small, abundant secreted protein that binds retinol (vitamin A) in blood (Newcomer and Ong, 2000). Retinol, obtained from carrots in the form of vitamin A, is very hydrophobic. RBP4 helps transport this ligand to the eye where it is used for vision. We will study RBP4 in detail because it has a number of interesting features:

There are many proteins that are homologous to RBP4 in a variety of species, including human, mouse, and fish ("orthologs"). We will use these as examples of how to align proteins, perform database searches, and study phylogeny (Chapters 2-11). There are other human proteins that are closely related to RBP4 ("paralogs"). Altogether the family that includes RBP4 is called the lipocalins, a diverse group of small ligand-binding proteins that tend to be secreted into extracellular spaces (Akerstrom et al., 2000; Flower et al., 2000). Other lipocalins have fascinating functions such as apoliprotein D (which binds cholesterol), a pregnancy-associated lipocalin, aphrodisin (an "aphrodisiac" in hamsters), and an odorant-binding protein in mucus. There are even bacterial lipocalins, which could have a role in antibiotic resistance (Bishop, 2000). We will explore how bacterial lipocalins could be ancient genes that entered eukaryotic genomes by a process called lateral gene transfer. The gene expression levels of some lipocalins are dramatically regulated (Chapters 6 and 7). Because the lipocalins are small, abundant, and soluble proteins, their biochemical properties have been characterized in detail. The three-dimensional protein structure has been solved for several of them by X-ray crystallography (Chapter 9). Some lipocalins have been implicated in human disease (Chapter 18).

Another molecule we will introduce is the pol (polymerase) gene of human immunodeficiency virus 1 (HIV-1). HIV presents one of the greatest public health challenges in the world today. Over 42 million people are infected as of the end of the year 2002 and over 16 million people have died. The HIV-1 genome encodes just nine proteins, including pol (Frankel and Young, 1998). We will examine pol throughout the book because the properties of this gene, its protein products, and the HIV-1 genome are distinct from the lipocalins.

The pol gene is a multidomain protein: it is a single polypeptide with several structurally and functionally distinct domains. The pol gene encodes a protein of 1003 amino acids with reverse transcriptase activity (that is, an RNA-dependent DNA polymerase). It is also an aspartyl protease, and it has integrase activity. These multiple activities are typical of multidomain proteins. The modular nature of the pol protein affects our ability to perform database searches (Chapters 4 and 5) and multiple sequence alignments (Chapters 8 and 10). The pol gene incorporates substitutions extremely rapidly. A typical individual infected by HIV may have over a million variants of pol. The study of the evolution of pol complements our study of the lipocalins (Chapter 11). As a viral protein, our study of pol gives us the opportunity to learn how to access bioinformatics resources relevant to studying viruses (Chapter 13). Database searches with pol will help emphasize how to restrict searches to particular domains of the tree of life.

Organization of The Chapters

The chapters of this book are intended to provide both the theory of bioinformatics subjects as well as a practical guide to using computer databases and algorithms. Web resources are provided throughout each chapter. Chapters end with brief sections called Perspective and Pitfalls. The perspective feature describes the rate of growth of the subject matter in each chapter. For example, a perspective on Chapter 2 (access to sequence information) is that the amount of DNA sequence data deposited in GenBank is undergoing an explosive rate of growth. In contrast, an area such as pairwise sequence alignment, which is fundamental to the entire field of bioinformatics (Chapter 3), was firmly established in the 1970s and 1980s.

The pitfalls section of each chapter describes some common difficulties encountered by biologists using bioinformatics tools. Some errors might seem trivial, such as searching a DNA database with a protein sequence. Other pitfalls are more subtle, such as artifacts caused by multiple sequence alignment programs depending upon the type of algorithm that is selected. Indeed, while the field of bioinformatics depends substantially on analyzing sequence data, it is important to recognize that there are many categories of errors associated with data generation, collection, storage, and analysis.

Each chapter offers multiple-choice quizzes, which test your understanding of the chapter materials. There are also problems that require you to apply the concepts presented in each chapter. These problems may form the basis of a computer laboratory for a bioinformatics course.

The references at the end of each chapter are accompanied by an annotated list of recommended articles. This suggested reading section includes classic papers that show how the principles described in each chapter were discovered. Particularly helpful review articles and research papers are highlighted.

Suggestions For Students and Teachers: Web Exercises And Find-a-Gene

Often, students of bioinformatics have a particular research area of interest such as a gene, a physiological process, a disease, or a genome. It is hoped that by studying RBP4 and other specific proteins and genes throughout this book, students can simultaneously apply the principles of bioinformatics to their own research questions.

In teaching a course on bioinformatics at Johns Hopkins, it has been helpful to complement lectures with computer labs. All the websites described in this book are freely available on the World WideWeb, and many of the software packages are free for academic use.

Another feature of the Johns Hopkins course is that each student is required to discover a novel gene by the last day of the course. The student must begin with any protein sequence of interest and perform database searches to identify genomic DNA that encodes a protein no one has described before. This problem is described in Chapter 5 (see Fig. 5.17). The student thus chooses the name of the gene and its corresponding protein and describes information about the organism and evidence that the gene has not been described before. Then, the student creates a multiple sequence alignment of the new protein (or gene) and creates a phylogenetic tree showing its relation to other known sequences.

Each year, some beginning students are slightly apprehensive about accomplishing this exercise, but in the end all of them succeed. A benefit of this exercise is that it requires a student to actively use the principles of bioinformatics. Most students choose a gene (or protein) relevant to their own research area, while others find new lipocalins.

Teaching bioinformatics is notable for the diversity of students learning this new discipline. Each chapter provides background on the subject matter. For more advanced students, several key research papers are cited at the end of each chapter. These papers are technical, and reading them along with the chapters will provide a deeper understanding of the material. The suggested reading section also includes review articles.

Continues...


Excerpted from Bioinformatics and Functional Genomics by Jonathan Pevsner Copyright © 2003 by Wiley-Liss. Excerpted by permission.
All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
Excerpts are provided by Dial-A-Book Inc. solely for the personal use of visitors to this web site.

Read More Show Less

Table of Contents

Foreword
Preface
Pt. I Analyzing DNA, RNA, and Protein Sequences in Databases
1 Introduction 3
2 Access to Sequence Data and Literature Information 15
3 Pairwise Sequence Alignment 41
4 Basic Local Alignment Search Tool (BLAST) 87
5 Advanced BLAST Searching 127
Pt. II Genomewide Analysis of RNA and Protein
6 Bioinformatic Approaches to Gene Expression 157
7 Gene Expression: Microarray Data Analysis 189
8 Protein Analysis and Proteomics 223
9 Protein Structure 273
10 Multiple Sequence Alignment 319
11 Molecular Phylogeny and Evolution 357
Pt. III Genome Analysis
12 Completed Genomes and the Tree of Life 397
13 Completed Genomes: Viruses 437
14 Completed Genomes: Bacteria and Archaea 465
15 Eukaryotic Genomes: Fungi 503
16 Eukaryotic Genomes: From Parasites to Primates 539
17 Human Genome 607
18 Human Disease 647
Epilogue 695
App GCG for Protein and DNA Analysis 697
Glossary 717
Solutions to Self-Test Quizzes 735
Subject Index 737
Author Index 753
Read More Show Less

Customer Reviews

Be the first to write a review
( 0 )
Rating Distribution

5 Star

(0)

4 Star

(0)

3 Star

(0)

2 Star

(0)

1 Star

(0)

Your Rating:

Your Name: Create a Pen Name or

Barnes & Noble.com Review Rules

Our reader reviews allow you to share your comments on titles you liked, or didn't, with others. By submitting an online review, you are representing to Barnes & Noble.com that all information contained in your review is original and accurate in all respects, and that the submission of such content by you and the posting of such content by Barnes & Noble.com does not and will not violate the rights of any third party. Please follow the rules below to help ensure that your review can be posted.

Reviews by Our Customers Under the Age of 13

We highly value and respect everyone's opinion concerning the titles we offer. However, we cannot allow persons under the age of 13 to have accounts at BN.com or to post customer reviews. Please see our Terms of Use for more details.

What to exclude from your review:

Please do not write about reviews, commentary, or information posted on the product page. If you see any errors in the information on the product page, please send us an email.

Reviews should not contain any of the following:

  • - HTML tags, profanity, obscenities, vulgarities, or comments that defame anyone
  • - Time-sensitive information such as tour dates, signings, lectures, etc.
  • - Single-word reviews. Other people will read your review to discover why you liked or didn't like the title. Be descriptive.
  • - Comments focusing on the author or that may ruin the ending for others
  • - Phone numbers, addresses, URLs
  • - Pricing and availability information or alternative ordering information
  • - Advertisements or commercial solicitation

Reminder:

  • - By submitting a review, you grant to Barnes & Noble.com and its sublicensees the royalty-free, perpetual, irrevocable right and license to use the review in accordance with the Barnes & Noble.com Terms of Use.
  • - Barnes & Noble.com reserves the right not to post any review -- particularly those that do not follow the terms and conditions of these Rules. Barnes & Noble.com also reserves the right to remove any review at any time without notice.
  • - See Terms of Use for other conditions and disclaimers.
Search for Products You'd Like to Recommend

Recommend other products that relate to your review. Just search for them below and share!

Create a Pen Name

Your Pen Name is your unique identity on BN.com. It will appear on the reviews you write and other website activities. Your Pen Name cannot be edited, changed or deleted once submitted.

 
Your Pen Name can be any combination of alphanumeric characters (plus - and _), and must be at least two characters long.

Continue Anonymously

    If you find inappropriate content, please report it to Barnes & Noble
    Why is this product inappropriate?
    Comments (optional)