Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Online ISBN: 9780470011539

DOI: 10.1002/047001153X

Table of Contents

Planned Table of Contents



Genetic Variation & Evolution

Section Editor: David B. Goldstein, University College London, UK

Genetic signatures of natural selection

Studies of Human Genetic History ising the mtDNA variation

Homeobox Genes: Implications for the evolution of Diversity and human disease

Population Genomics: The genetic basis of evolutionary change within populations

The Genetic Structure of Human Pathogens

Geographic Structure of Human Genetic Variation: Medical and Evolutionary


Modeling Human Genetic History

Modeling Protein Evolution

Sequence function and phylogenetic shadowing

The role of Gene Regulation in Evolution

Evolution of drug-metabolizing enzymes

Comparative Genomics: Inferences about evolution through whole genome sequences

Studies of Human genetic History using the Y Chromosome

Measuring Genetic Variation in Natural Populations: A primer


Section Editor: Terry Hassold, Case Western Reserve University, Ohio, USA

Acquired Chromosome Abnormalities: The Cytogenetics of cancer

Cytogenetics of Infertility

Visualising Human Chromosomes

Uniparental Disomy

Studies of Sperm

Analysis of Lymphomas

Human X chromosome inactivation


Fluorescence in Situ Hybridisation

Comparative Genomic Hybridisation (CGH)

Meiosis and Meiotic Errors


Chromosome and Chromosome Abnormalities

Prenatal Diagnosis


Pre-implantation Diagnosis


Section Editor: Robert Nicholls, University of Pennsylvania, Philadelphia, USA

Transcription factors and epigenetic regulation

Epigenetic reprogramming in germ cells and preimplantation embryos

Evolution of genomic imprinting in mammals

Techniques in imprinting research and epigenetics

UPD in human and mouse and role in identification of imprinted loci

Imprinting and epigenetic inheritance in human disease

Bioinformatics and identification of imprinted genes in mammals

Epigenetic inheritance and RNAi at the centromere and heterochromatin

Epigenetics and imprint resetting in cloned animals

DNA methylation in epigenetics, imprinting and development

Rapidly evolving imprinted loci

Imprinting, growth and body composition in livestock

Spreading of X chromosome inactivation

Epigenetics and variable expressivity

Mechanisms of epigenetic loss of chromosomes in insects

Imprinting and behaviour

Imprinting at the GNAS1 locus and endocrine disease

Epigenetics and imprinting in cancer and Beckwith-Wiedemann syndrome

Imprinting in Prader-Willi and Angelman syndromes

Initiation of X chromosome inactivation

Imprinting and epigenetics in mouse models and embryogenesis

The histone code and epigenetic inheritance

Gene Mapping

Section Editor: Nancy J. Cox, University of Chicago, Illinois, USA

Introduction to gene mapping

Algorithmic improvements in gene mapping

Information content in gene mapping

Genotyping error in gene mapping

Gene mapping, imprinting and epigenetics

Polymorphic inversions, duplications and deletions in gene mapping

Choices in gene mapping: populations and family structures

Gene mapping and the transition from STRPs to SNPs

Sex-specific maps and consequences for linkage mapping

Parametric vs. Non-parametric and Two-point vs. Multipoint: Controversies in Gene Mapping

LOD scores: Worked examples

Complex Traits & Diseases

Section Editor: Leena Peltonen, Biomedicum Helsinki, Finland

Cardiovascular disease: mouse

General overview

Neurodegenerative disease

Mitochondrial variation in human degenerative disease and ageing

Allergy and asthma


Population selection in complex disease gene mapping

Concept of complex trait genetics

Cognitive Disorders

Inflammation and inflammatory bowel disease

Comparative genomics

Cardiovasular disease: human structural heart disorders

Linkage and association

Common disease variant concept

Importance of complex traits


Diabetes and autoimmune disease

Genetic medicine & clinical genetics

Section Editor: Bruce Korf, University of Alabama at Birmingham, USA

Ethical and legal issues in medical genetics

Advances in newborn screening and biochemical genetics

The clinical and economic implications of pharmacogenomics

Pharmacogenomics: advances, challenges and implications of 'personalized' medicine

Family history, pedigree analysis, risk assessment

Approach to common chronic disorders of adulthood

Changing paradigms of genetic counselling

Tut: Carrier screen

Use of databases

Assessment of predisposition to cancer

Current approaches to molecular diagnosis

Molecular dysmorphology

Advances in cytogenetic diagnosis

Treatment of mongenic disorders

Genetic testing and genotype-phenotype correlations

Approach to Rare Monogenic and Chromosomal Disorders

Mechanisms of inheritance

Tut: Monogenic molecular diagnosis

Tut: Prenatal diagnosis

The Physical Examination in Clinical Genetics

Genetic counseling process

Tut: Microdeletion syndrome

Tut: Common disorder

Current approaches to carrier screening and prenatal diagnosis

Tut: Cancer genetics

Gene Therapy

Section Editor: Olivier Danos, Genthon, Evry, France

Artificial self-assembling systems for gene therapy

Adeno-associated viral vectors


Gene therapy vectors as medicinal products

Retro/lentivirus vectors

Control of transgene expression in mammalian cells

Gene therapy in hematopoietic stem cells

Cardiovascular gene therapy

Gene transfer to the skin

Gene transfer and immunity

Gene therapy in the central nervous system

Adenovirus vectors

Gene transfer to skeletal muscle

Gene therapy for cancer

Gene transfer to the liver



Genome Sequencing

Section Editor: Bruce A. Roe, University of Oklahoma, Oklahoma, USA

Finishing strategies, alternative technologies, problems, unsequencable regions, PCR versus primer walking off shotgun or large insert clones

Single molecule array-based sequencing

Real-time DNA Sequencing

Higher eukaryotes

Hierarchical, ordered mapped large insert clone shotgun sequencing

Robotics and Automation

BAC and Fosmid libraries

Microbial genomes

Sequencing templates - shotgun clone isolation vs amplification approaches

Massively parallel genome sequencing

Microelectrophoresis devices for DNA sequencing


Single molecule fluorescence


Section Editor: Marco A. Marra, Genome Sciences Centre, Vancouver, Canada

Linkage mapping

YAC-STS content mapping

Fingerprint mapping

Microarray comparative genomic hybridization for mapping

Linkage disequilibrium and whole genome association studies

Synteny mapping

Hitchhiking mapping

Haplotype mapping

Mapping informatics

QTL mapping in agro species

Radiation hybrid mapping

Overview of genome mapping

Happy mapping

Mapping complex disease phenotypes

The Human Genome

Section Editor: Richard K. Wilson, Genome Sequencing Center, Washington University, St. Louis, USA

The Human Genome Project

Alternative splicing: conservation and function

Transcriptional Promoters

Endogenous Retroviruses

GC-content and gene distribution

Overlapping genes in the human genome

Repeats and Genome Evolution

Variation in the Human Genome

Segmental Duplication

The Technology tour de force of the HGP

Non-coding RNA genes

Genome Assembly


Comparisons with Primate Genomes


Model organisms, functional and comparative genomics

Section Editor: Steve D. M. Brown, MRC Mammalian Genetics Unit, Harwell, UK

Genome Archaeology

Systematic mutagenesis of non-mammalian model species

Mouse mutagenesis and gene function

Studying gene function and genetic pathways across species

The Mouse Genome sequence


The C. elegans Genome

The Fugu and zebrafish genomes

Farm animals

The rat as a model physiological system

Comparative Vertebrate sequencing

Mouse models

Functional Genomics in Saccharomyces cerevisiae

The Drosophila Genome


Section Editor: Julian Parkhill, The Wellcome Trust Sanger Institute, Cambridge, UK



Eukaryotic parasite genome projects

Genomics in Vaccine Development

Methods for detecting horizontal transfer of genes Rickettsia


Bacterial pathogens of man


Comparative genomics of the e-proteobacterial human pathogens Helicobacter pylori and Campylobacter jejun

The Enteric family



Sequencing for detection and study of unculturable microbes

Mycoplasmas and the minimal genome


Apicomplexan parasites



Section Editor: Mark Daly, Whitehead Institute Center for Genome Research, Massachusetts, USA

Avoiding stratification in association studies

SNPs and human history

Genotyping technology: the present and the future

Creating LD maps of the genome

History of genetic mapping

Pharmacogenetics and personalised medicine

Identifying and using haplotype blocks

Mapping by admixture linkage disequilibrium

Evolutionary modelling in haplotype analysis

Reliability of SNPs in association studies

Human genetic variation

The Human Haplotype Map Project

EST's: Cancer Genes & Anatomy Project

Section Editor: Winston Hide, SANBI/UWC, Bellville, South Africa

What are ESTs?

Tut: EST clustering

Gene expression technologies

EST resources, clone sets and databases

Disease gene candidacy and ESTs

Using ORESTES ESTs to mine gene cancer expression

Pilot gene discovery in plasmodial pathogens

Using ESTs for genome annotation - predicting the Transcriptome

Tut: Manufacturing EST libraries

Alternate splicing

Nonsense-mediated RNA decay

Plant EST pilot gene discovery

Using Unigene, TIGRs indices and STACK

Cancer Gene Anatomy Project

TMAP, an expression database for cancer samples

Expression Profiling

Section Editor: John Quackenbush, The Institute for Genomic Research, Rockville, USA

From expression to biology

Protein Expression Profiling

Expression and diagnostics

Creating and hybridizing spotted DNA arrays

Microarrays for Comparative Genome Hybridization

Microarray Overview

Host-pathogen interactions

SAGE for Expression Analysis

Microbial expression profiling

Inkjet technologies for expression analysis

Tissue Microarrays

Using oligonucleotide arrays

The use of external controls in microarray experiments

Seven years of yeast microarray analysis

Protein microarrays

Studying gene expression patterns



Core Methodologies

Section Editor: Peter James, University of Lund, Lund, Sweden

Interpreting tandem mass spectra of peptides

Sample preparation for Proteomics

Ion scanning methods

Handling Membrane proteins

Tut: Peptide fingerprint Searching

Peptide fingerprinting

Hybrid MS



Protein fingerprinting

Tut: Protein fingerprint searching

Nano-MALDI & Nano-ESI MS


Digestion & coverage

Multi-Dimensional Liquid Chromatography Tandem Mass Spectrometry for Biological Discovery

Quadrupole MS

Tut: Making nano-columns and tips

Quadrupole Ion Traps and a New Era of Evolution

MALDI prep & ESI prep

Laser-based microdissection approaches and applications

Expression Proteomics

Section Editor: Stephen Pennington, University of Liverpool, Liverpool, UK

Separation dependent approaches for protein expression profiling

Two-dimensional gel electrophoresis (2-DE)

Real time measurements of protein dynamics

Image analysis

Two-dimensional gel electrophoresis

MS based methods for identification of 2-DE resolved proteins

Arraying proteins and antibodies

Detection of proteins (dyes and labels)

Protein arrays

ICAT and other labelling strategies for semi-quantitative LC based expression profiling

Separation independent approaches for expression profiling


Commercial protein chips for expression profiling


Affinity capture arrays

Mapping of Biochemical Networks

Section Editor: Pierre Legrain, Direction des Sciences du Vivant, CEA, France

Computational methods for the prediction of protein interaction partners

Protein interactions in cell signalling

Human signaling pathways analyzed by protein interaction mapping

Membrane-anchored protein complexes

Database for protein interactions

Small molecule and protein interactions

Mammalian based assays for protein-protein interaction

Energy transfer-based approaches to study G-protein coupled receptor dimerization and activation

Functional classification of proteins based on protein interaction data

Investigating protein-protein interactions in multi-subunit proteins: the case of eukaryotic RNA polymerases

C. elgans interactome

Biochemistry of protein complexes

Structural biology of protein complexes

Yeast interactome

Functional Proteomics

Section Editor: Jeremy M. Tavare, University of Bristol, Bristol, UK

Immunofluorescent labelling and fluorescent dyes

Elucidating protein dynamics and function using Fluorescence Correlation Spectroscopy (FCS)

siRNA Approaches in Cell Biology

Probing protein function using fluroescence imaging

Quantum dots and novel imaging techniques

High Content Screening

Photobleaching (FRAP/FLIP) and dynamic imaging

Using kindling GFPs to study protein dynamics and function

FRET-based reporters for intracellular enzyme activity

Probing cellular function with bioluminescence imaging

Small molecule fluorescent probes for protein labelling and their applications to cell-based imaging (including F1AsH etc.)

Probing protein function in cells using CALI

Quantiative data analysis and the "Open Microscopy Environment"

Proteome Diversity

Section Editor: Pauline M. Rudd, University of Oxford, Oxford, UK

Structure/function of O-glycans

Structure/function of N-glycans

Glycosylation in bacteria: that, what, how, why, now what?

N- and O-glycan analysis


Mass spectrometry

Nitrosylation aand thiolylation

O-glycan processing

GPI anchors

Post-translational cleavage of cell-surface receptors

Phosphorylation (worked example)




Glycosylphosphatidylinositol anchors- a structural perspective

Overview including phosphorylation/nitrosylation/post translational cleavages


Proteome Families

Section Editor: Rolf Apweiler, European Bioinformatics Institute, Cambridge, UK

Equivalog protein families in the TIGRFAMs database


Classification of proteins into families

Peptidases, families and clans

Pfam: The protein families database

The PRINTS protein fingerprint database: functional and evolutionary applications

Classification of proteins by clustering techniques


Functionally and structurally relevant residues in PROSITE motif descriptors


The PIR SuperFamily (PIRSF) classification system


Tutorial: Getting most out of protein family classification resources

Structural classification of proteins

Classification of proteins by sequence signatures

Transport protein families

Structural Proteomics

Section Editor: David Westhead, University of Leeds, Leeds, UK

Target selection for structural genomics

Fundamentals of protein structure and function

X-ray crystallography

What use is a protein structure?

Determination of membrane protein structures

Electron microscopy

Large complexes by X-ray methods

The importance of protein structural dynamics and the contribution of NMR spectroscopy

Structural genomics


Modelling membrane protein structures

Large complexes and molecular machines by electron microscopy

Structure prediction

The history and future of protein structure determination

Molecular dynamics and simulation

Systems Biology

Section Editor: Raimond L. Winslow, Whitaker Biomedical Engineering Institute, John Hopkins University School of Medicine, Baltimore, USA

Metabolic dynamics in cells viewed as multi-layered, distributed, mass-energy-information networks

Reverse engineering the structure of gene regulatory networks

Integrative modeling of the pancreatic beta cell

Constraint-based modeling of metabolomic systems

Systems biology of the heart

Global analysis of protein interaction networks

Cell motility

Functional Networks in Mammalian Cells

Quantitative modeling of gene regulatory networks

Integrative approaches to biology in the 21st century

Computational modeling of the EGF receptor system

Data collection and analysis in systems biology



Genome Assembly/Sequencing

Section Editor: Adam Kuspa, Baylor College of Medicine, Texas, USA

Statistical signals

Tut: Polymorphisms and sequence assembly

Errors in sequence assembly and corrections

Tut: Algorithms for sequence errors

Contig mapping and analysis

Repeat Finder

Tut: Graphs and metrics

Genome signals and assembly

Algorithmic challenges in mammalian whole genome assembly

Comparative analysis for sequence assembly

Microbial sequence assembly

Physical maps and use in sequence assembly

Sequence assembly algorithms

Shotgun sequencing strategies

Algorithmic issues in microbial genome assembly

Gene Finding/Gene Structure

Section Editor: Steven L. Salzberg, The Institute for Genomic Research, Rockville, USA

Dynamic programming for gene finders

Searching for genes and biologically related signals in DNA sequences

Spliced alignment

Computational motif discovery

Information theory-based models of genomic sequences

Operon finding in bacteria

Gene structure prediction by genomic sequence alignment

Alternative splicing in humans

Promoter prediction

Prokaryotic gene identification in silico

Exon splicing enhancers

Pair HMMs

Yeast gene finding by sequencing multiple strains of yeast

Eukaryotic gene finding

Gene finding pipelines

Gene structure prediction in plant genomes

Bayesian methods for combining predictions

Eukaryotic regulatory sequences

Protein Function & Annotation

Section Editor: L Aravind , National Institutes of Health, Bethesda, USA

IMPALA/RPS-BLAST/PSI-BLAST in protein sequence analysis

Proteins in bacterial signal transduction


Protein function and annotation

Chromatin proteins: sequence, structure and function

Functional annotation of proteins

Transmembrane topology prediction

Sequence complexity of proteins and its significance in annotation

Large-scale protein annotation

Protein repeats

Protein domains in eukaryotic signal transduction systems

Contextual inference of protein function

Signal peptides and protein localization prediction

Protein structure-sequence analysis

Annotation and comparisons of metabolic pathways

Membrane proteins

Comparative Analysis & Phylogeny

Section Editor: Harris Lewin, Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, USA

Bayesian methods for phylogenetics

Domains of Life on Earth

Reconstructing vertebrate phylogenetic trees

Phylogenomic approaches to bacterial phylogeny

Phylogenomic analysis of BLAST results

Phylogenomic approach to microbial evolution

Phylogenetic profiling

Phylogenetic inference and functional networks

Mapping mutations on phylogenies

Chromosome phylogeny

Phylogenetic analysis: parsimony methods and maximum likelihood methods

Evolution of regulatory pathways

Computational Methods for High Throughput Genetic Analysis - Expression profiling

Section Editor: John Quackenbush, The Institute for Genomic Research, Rockville, USA

Data normalization and transformation for microarrays

Experimental design

Relevance networks

CGH data analysis

An overview of algorithms for expression analysis

Data standardization and the Protein Standards Initiative

Mass Spectometry and Computational Proteomics

Mass spectrometric data mining for protein sequences

Assessing microarray data quality

Oligonucleotide chip analysis

Statistical methods for gene expression analysis

Error models for expression

The Bioconductor project

Integrating statistical approaches in experimental design and data analysis

Extracting networks from expression data

Statistical analysis of microarrays (SAM)

Comparative Methods for Structure Analysis and Prediction

Section Editor: William Ramsay Taylor, National Institute for Medical Research, London, UK

DNA/protein modelling

Analysis and prediction

Ab initio prediction

Protein folds

Analysis and prediction of membrane protein structure

Amino acid scoring

Structure comparison

Secondary structure

Homology modelling

The Protein Data Bank (PDB) and the World Wide PDB


Domain prediction


Molecular dynamics

Threading methods

Structuring and Integrating Data

Section Editor: Russ B. Altman, Stanford University, USA

Merging and comparing ontologies

Ontologies for information retrieval

Representing and reasoning about pathways

Ontologies for data integration

Introduction to ontologies in biomedicine

Ontologies for three-dimensional molecular structure

Description Logics: OWL and DAML+OIL

The Gene Ontology project

Automatic concept identification in biomedical literature

Ontologies for natural language processing

UMLS and associated vocabularies

TAMBIS: Transparent access to multiple bioinformatics services

Ontologies for proteomics

Frame based systems: Protégé

Modern Programming Paradigms in Biology

Section Editor: Peter Clote, Boston College, Massachusetts, USA

Simulation of biochemical networks

Integrated bioinformatics software at NCBI

Bioinformatics (or Genomic Datamining) programming in Perl

Protein threading

Bioinformatics scripting languages

Support vector machine software

The MATLAB Bioinformatics Toolbox

Ensembl-Swiss Prot

Applications of support vector machines in bioinformatics

Hidden Markov models and neural networks

Design of KEGG and GO

ACEDB genome database

Cluster architecture

Bioconductor: software and development strategies for statistical genomics

Detecting protein homology using NCBI tools

Relational databases in bioinformatics

Bioinformatics (or Genomic Datamining) programming in Perl

Gibbs Samplers and Bioinformatics

RNA Secondary Structure Prediction

Tutorial: Python