Discovering Genomics, Proteomics, and Bioinformatics / Edition 1

Discovering Genomics, Proteomics, and Bioinformatics / Edition 1

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Benjamin Cummings

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Discovering Genomics, Proteomics, and Bioinformatics / Edition 1

Discovering Genomics, Proteomics, and Bioinformatics combines integrated Web exercises with a problem-solving approach to train readers in basic hands-on genomic analysis. The authors present global problems, then provide the tools of genomic analysis to help readers dissect the answer, thus encouraging critical thinking skills. Short boxed readings called "Math Minutes" explain the math behind the biology. For anyone interested in genomics, proteomics, or bioinformatics.

Product Details

ISBN-13: 9780805347227
Publisher: Benjamin Cummings
Publication date: 09/13/2002
Edition description: BK&CD-ROM
Pages: 352
Product dimensions: 8.50(w) x 10.72(h) x 0.59(d)

Table of Contents

Unit 1Genome Sequences1
Chapter 1Genome Sequence Acquisition and Analysis2
1.1Defining Genomes3
What Is Genomics?3
How Are Whole Genomes Sequenced?3
Math Minute 1.1What Is an E-Value?5
Why Do the Databases Contain So Many Partial Sequences?6
How Do We Make Sense of All These Bases?9
Box 1.1Which Draft Sequence Is Better?9
Can We Predict Protein Functions?10
How Well Are Genes Conserved in Diverse Species?12
How Do You Know Which Bases Form a Gene?14
How Many Proteins Can One Gene Make?15
Summary 1.116
1.2What Have We Learned from the Human Genome Draft Sequences?17
Overview of Human Genome First Draft17
Summary Statements17
Box 1.2Whose DNA Did We Sequence?17
Math Minute 1.2How Do You Fit a Line to Data?18
Can We Describe a Typical Human Gene?20
When Are the Data Sufficient?24
Can the Genome Alter Gene Expression Without Changing the DNA Sequence?25
Summary 1.228
Chapter 1 Conclusions28
Chapter 2Genome Sequences Answer Interesting Questions30
2.1Evolution of Genomes31
How Did Eukaryotes Evolve?31
Math Minute 2.1Are the Hit Numbers Significantly Different?33
What Is the Origin of Our Species?41
Math Minute 2.2How Do You Know if the Tree Is Right?45
Summary 2.146
2.2Genomic Identifications46
How Can We Identify Biological Weapons?47
How Long Can DNA Survive?49
How Did Tuberculosis Reach North America?50
How Are Newly Emerging Diseases Identified?53
Summary 2.257
2.3Biomedical Genome Research57
Can We Use Genomic Sequences to Make New Vaccines?57
Can We Make New Types of Antibiotics?59
Can We Invent New Types of Medication?62
How Can E. coli Be Lethal and in Our Intestines at the Same Time?64
Math Minute 2.3How Can You Tell if Base Compositions Are Different?65
Summary 2.366
Chapter 2 Conclusions66
Chapter 3Genomic Variations69
3.1Environmental Case Study70
Can Genomic Diversity Affect Global Warming?70
Math Minute 3.1How Do You Measure Genetic Variation?72
Math Minute 3.2How Are Populations Modeled?74
Summary 3.176
3.2Human Genomic Variation76
How Much Variation Is in the Human Genome?76
Math Minute 3.3Are All SNPs Really SNPs?78
Why Should We Care About SNPs?79
Box 3.1What's the Difference Between a Mutation and an Allele?80
Are There Any Known Examples of SNPs That Cause Diseases?82
Are There Any Known Changes in Nondisease QTL Due to SNPs?84
Box 3.2Patent Law and Genomics85
Why the SNP Frenzy? Pharmacogenomics!86
Summary 3.288
3.3The Ultimate Genomic Phenotype--Death?89
Why Do We Age?89
Are There Hidden Costs for a Prolonged Life?90
Do Bacteria Experience Genomic Trade-offs Too?91
Summary 3.393
3.4Ethical Consequences of Genomic Variations93
Are Genetically Modified Organisms Bad?93
Is Genetic Testing Good?95
Are There Simple Applications for Complex Genomes?99
Box 3.3Should I Get a Genetic Test?99
Summary 3.4101
Chapter 3 Conclusions102
Unit 2Genome Expression105
Chapter 4Basic Research with DNA Microarrays106
4.1Introduction to Microarrays107
What Happened to My Home Brew?107
Math Minute 4.1How Do You Transform the Data to Avoid Fractions?112
Math Minute 4.2How Do You Measure Similarity Between Expression Patterns?113
Math Minute 4.3How Do You Cluster Genes?114
What Can We Learn from Stressed-out Yeast?124
Why Are There So Many Copies of Some Genes but Not Others?125
How Well Do Promoters Control Gene Expression?126
Are Promoters Able to Work in Reverse?127
Summary 4.1128
4.2Alternative Uses of DNA Microarrays128
Why Do So Many Unrelated Genes Share the Same Expression Profile?128
Math Minute 4.4Is It Useful to Compare the Columns of a Gene Expression Matrix?129
Can Cells Verify Their Own Genes?131
Summary 4.2133
Chapter 4 Conclusions135
Chapter 5Applied Research with DNA Microarrays137
5.1Cancer and Genomic Microarrays138
Are There Better Ways to Diagnose Cancer?138
Math Minute 5.1What Are Signature Genes, and How Do You Use Them?139
Can Breast Cancer Be Categorized with Microarrays, too?141
What Genomic Changes Occur in Cancer Cells?143
Summary 5.1146
5.2Improving Health Care with DNA Microarrays146
Why Is the Tuberculosis Vaccine Less Effective Now?146
How Does This Drug Work?149
Can We Predict Which Drugs Will Be Effective in Different Cancers?152
What Happens When You Accumulate Fat?154
Summary 5.2158
Chapter 5 Conclusions158
Chapter 6Proteomics161
What Do All These Proteins Do?162
Which Proteins Are Needed in Different Conditions?166
Math Minute 6.1How Do You Know if You Have Sampled Enough Cells?168
Can You Live Without Some Proteins?170
Summary 6.1171
6.2Protein 3D Structures171
Does a Protein's Shape Reveal Its Function?172
Can We Use Structures to Develop Better Drugs?173
Can One Protein Kill You?174
6.2 Summary176
6.3Protein Interaction Networks176
Which Proteins Interact with Each Other?176
How Can We Measure Protein Interactions?177
Math Minute 6.2Is Sup35 a Central Protein in the Network?179
Is It Possible to Understand Proteome-wide Interactions?181
Summary 6.3183
6.4Measuring Proteins183
How Do We Know Which Proteins Are Present?184
What Proteins Do Our White Blood Cells Need to Kill a Pathogen?187
How Much of Each Protein Is Present?189
Can We Make Protein Chips?195
Are All Cells Equal?198
What Does a Proteome Produce?200
Summary 6.4202
Chapter 6 Conclusions202
Unit 3Whole Genome Perspective205
Chapter 7Genomic Circuits in Single Genes206
7.1Dissecting a Gene's Circuitry207
How Do Genomes Control Individual Genes?207
How does a Gene Control Location, Timing, and Quantity of Transcription?210
What Does Module G Do?216
Can We Apply Engineering and Computer Science Concepts to Genes?226
Summary 7.1229
7.2Integrating Single-Gene Circuits229
How Can We Describe to Others What We Know About a Genome Circuit?229
Technical Hints230
Can We Visualize Circuits for Protein Interaction and DNA Binding?230
Summary 7.2230
Chapter 7 Conclusions230
Chapter 8Integrated Genomic Circuits232
8.1Simple Integrated Circuits233
Can Genes Form Toggle Switches and Make Choices?233
Math Minute 8.1How Are Stochastic Models Applied to Cellular Processes?234
Can Humans Engineer a Genetic Toggle Switch?238
Can Humans Build a Synthetic Circadian Clock from a Toggle Switch Design?240
If Toggle Switches Are So Noisy, How Can Multicellular Organisms Develop?241
Redundancy: Is It Really Beneficial to Have More Than One Copy of a Gene?242
Summary 8.1244
8.2Complex Integrated Circuits244
Are Circuits the Key to Learning?244
Math Minute 8.2Is It Possible to Predict Steady-state Behavior?250
Can We Understand Cancer Better by Understanding Its Circuitry?257
If Circuits Are Interconnected, Does Gene Order Matter?259
Summary 8.2263
Chapter 8 Conclusions263
Chapter 9Modeling Whole-Genome Circuits265
9.1Is Genomics a New Perspective?266
The People Involved: Who Is Doing Systems Biology?266
The Quality of the Message: What Questions Do Systems Biologists Ask?267
9.2Can We Model Entire Eukaryotes with a Systems Approach?267
Genomics versus Proteomics271
Building a Systems Model272
Context of the Message273
9.3Will Systems Biology Go Systemic?274
Chapter 9 Conclusions274
Unit 4Transition from Genetics to Genomics: Medical Case Studies277
Chapter 10What's Wrong with My Child?278
10.1First Patients279
Phase IClinical Presentation279
Phase IIFamily Pedigree280
Phase IIIKaryotyping and Linkage Analysis280
Phase IVDNA Sequence Analysis281
Summary 10.1283
10.2The Next Steps in Understanding the Disease284
We Need an Animal Model System284
What Was That Other Protein I Got Lots of Hits For?284
Does Utrophin Play a Role in Muscular Dystrophy, Too?284
What Does Dystrophin Do Anyway?285
Math Minute 10.1What's Special about This Graph?286
Why Do DMD Patients' Muscles Deteriorate After the First Three Years?287
Is It Possible to Have DMD and Be Wild-Type for Dystrophin?288
How Can They Have Muscular Dystrophy if Their Dystrophin Genes Are Normal?288
Math Minute 10.2What Do You Mean by Highly Unlikely?289
Where Is the Muscular Dystrophy Field Now?293
Math Minute 10.3Is cGMP Production Elevated?301
Summary 10.2: Your Final Thoughts303
Chapter 10 Conclusions303
Chapter 11Why Can't I Just Take a Pill to Lose Weight?306
Hungry for Knowledge307
Saturday, 21 October. 7:30 A.M.307
Building a Model for Weight Homeostasis308
Cloning the Leptin Gene308
Functional Tests for Leptin310
Time to Visit Grandma311
Grandma Gives You Homework!311
Chapter 11 Conclusions319
Chapter 12Why Can't We Cure More Diseases?320
How to Develop a New Medication321
Define the Problem and Devise a Solution321
Focus 1Location, Location, Location321
Focus 2Delivery Vehicles321
Focus 3Specificity--"If It Ain't Broke, Don't Fix It"323
Math Minute 12.1What's the Right Dose?324
Eye of Newt...?326
Don't Treat the Symptom, Treat the Cause327
Chapter 12 Conclusions329

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