Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Online ISBN: 9780470011539

DOI: 10.1002/047001153X

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  1. Glossary Terms
  2. Part 1 Genetics
    1. 1.1 Genetic Variation and Evolution
      1. Introductory Review
        1. 1 Population genomics: patterns of genetic variation within populations
      2. Specialist Review
        1. 2 Modeling human genetic history
        2. 3 Homeobox gene repertoires: implications for the evolution of diversity
        3. Geographic structure of human genetic variation: medical and evolutionary implications
      3. Short Specialist Review
        1. 4 Studies of human genetic history using the Y chromosome
        2. 5 Studies of human genetic history using mtDNA variation
        3. 6 The genetic structure of human pathogens
        4. 7 Genetic signatures of natural selection
        5. 8 The role of gene regulation in evolution
        6. 9 Modeling protein evolution
      4. Basic Techniques and Approaches
        1. 10 Measuring variation in natural populations: a primer
    2. 1.2 Cytogenetics
      1. Introductory Review
        1. 11 Human cytogenetics and human chromosome abnormalities
        2. 12 The visualization of chromosomes
      2. Specialist Review
        1. 13 Meiosis and meiotic errors
        2. 14 Acquired chromosome abnormalities: the cytogenetics of cancer
        3. 15 Human X chromosome inactivation
      3. Short Specialist Review
        1. 16 Nondisjunction
        2. 17 Microdeletions
        3. 18 Mosaicism
        4. 19 Uniparental disomy
        5. 20 Cytogenetics of infertility
        6. 21 Preimplantation genetic diagnosis for chromosome abnormalities
      4. Basic Techniques and Approaches
        1. 22 FISH
        2. 23 Comparative genomic hybridization
        3. 24 Cytogenetic analysis of lymphomas
        4. 25 Human sperm–FISH for identifying potential paternal risk factors for chromosomally abnormal reproductive outcomes
    3. 1.3 Epigenetics
      1. Introductory Review
        1. 26 Imprinting and epigenetic inheritance in human disease
        2. Regulation of DNA methylation by Dnmt3L
      2. Specialist Review
        1. 27 The histone code and epigenetic inheritance
        2. 28 Imprinting and epigenetics in mouse models and embryogenesis: understanding the requirement for both parental genomes
        3. 29 Imprinting in Prader–Willi and Angelman syndromes
        4. 30 Beckwith–Wiedemann syndrome
        5. 31 Imprinting at the GNAS locus and endocrine disease
        6. Developmental regulation of DNA methyltransferases
        7. Epigenetic variation: amount, causes, and consequences
        8. How to get extra performance from a chromosome: recognition and modification of the X chromosome in male Drosophila melanogaster
      3. Short Specialist Review
        1. 32 DNA methylation in epigenetics, development, and imprinting
        2. 33 Epigenetic reprogramming in germ cells and preimplantation embryos
        3. 34 Epigenetics and imprint resetting in cloned animals
        4. 35 Imprinted QTL in farm animals: a fortuity or a common phenomenon?
        5. 36 Variable expressivity and epigenetics
        6. 37 Evolution of genomic imprinting in mammals
        7. 38 Rapidly evolving imprinted loci
        8. 39 Imprinting and behavior
        9. 40 Spreading of X-chromosome inactivation
        10. 41 Initiation of X-chromosome inactivation
        11. 42 Mechanisms of epigenetic loss of chromosomes in insects
        12. 43 Epigenetic inheritance and RNAi at the centromere and heterochromatin
      4. Basic Techniques and Approaches
        1. 44 Techniques in genomic imprinting research
        2. 45 Bioinformatics and the identification of imprinted genes in mammals
        3. 46 UPD in human and mouse and role in identification of imprinted loci
    4. 1.4 Gene Mapping
      1. Introductory Review
        1. 47 Introduction to gene mapping: linkage at a crossroads
        2. 48 Parametric versus nonparametric and two-point versus multipoint: controversies in gene mapping
      2. Specialist Review
        1. 49 Gene mapping, imprinting, and epigenetics
        2. 50 Gene mapping and the transition from STRPs to SNPs
        3. Consequences of error
      3. Short Specialist Review
        1. 51 Choices in gene mapping: populations and family structures
        2. 52 Algorithmic improvements in gene mapping
        3. 53 Information content in gene mapping
        4. 54 Sex-specific maps and consequences for linkage mapping
        5. 55 Polymorphic inversions, deletions, and duplications in gene mapping
        6. Impact of linkage disequilibrium on multipoint linkage analysis
      4. Basic Techniques and Approaches
        1. 56 Computation of LOD scores
    5. 1.5 Complex Traits and Diseases
      1. Introductory Review
        1. 57 Genetics of complex diseases: lessons from type 2 diabetes
        2. Importance of complex traits
      2. Specialist Review
        1. 58 Concept of complex trait genetics
        2. 59 The common disease common variant concept
        3. 60 Population selection in complex disease gene mapping
      3. Short Specialist Review
        1. 61 Allergy and asthma
        2. 62 Inflammation and inflammatory bowel disease
        3. 63 Hypertension genetics: under pressure
        4. 64 Genetics of cognitive disorders
        5. 65 Complexity of cancer as a genetic disease
        6. 66 The mitochondrial genome
    6. 1.6 Genetic Medicine and Clinical Genetics
      1. Introductory Review
        1. 67 Approach to rare monogenic and chromosomal disorders
        2. 68 Approach to common chronic disorders of adulthood
      2. Specialist Review
        1. 69 Current approaches to prenatal screening and diagnosis
        2. 70 Advances in newborn screening for biochemical genetic disorders
        3. 71 Advances in cytogenetic diagnosis
        4. 72 Current approaches to molecular diagnosis
        5. 73 The clinical and economic implications of pharmacogenomics
      3. Short Specialist Review
        1. 74 Molecular dysmorphology
        2. 75 Changing paradigms of genetic counseling
        3. 76 Ethical and legal issues in medical genetics
      4. Basic Techniques and Approaches
        1. 77 Mechanisms of inheritance
        2. 78 Genetic family history, pedigree analysis, and risk assessment
        3. 79 The physical examination in clinical genetics
        4. 80 Genetic testing and genotype–phenotype correlations
        5. 81 Genetic counseling process
        6. 82 Treatment of monogenic disorders
        7. 83 Carrier screening: a tutorial
        8. 84 Prenatal aneuploidy screening
        9. 85 Gene identification in common disorders: a tutorial
        10. 86 Uses of databases
        11. 87 The microdeletion syndromes
        12. 88 Cancer genetics
        13. 89 Familial adenomatous polyposis
    7. 1.7 Gene Therapy
      1. Introductory Review
        1. 90 Gene therapy I: principles and clinical applications
        2. 91 Gene therapy II: viral vectors and treatment modalities
      2. Specialist Review
        1. 92 Hematopoietic stem cell gene therapy
        2. 93 Gene therapy in the central nervous system
        3. 94 Cardiovascular gene therapy
      3. Short Specialist Review
        1. 95 Artificial self-assembling systems for gene therapy
        2. 96 Adenovirus vectors
        3. 97 Adeno-associated viral vectors: depend(o)ble stability
        4. 98 Retro/lentiviral vectors
        5. 99 Immunity and tolerance induction in gene therapy
        6. 100 Gene transfer vectors as medicinal products: risks and benefits
      4. Basic Techniques and Approaches
        1. 101 Gene transfer to skeletal muscle
        2. 102 Gene transfer to the liver
        3. 103 Gene transfer to the skin
        4. 104 Control of transgene expression in mammalian cells
  3. Part 2 Genomics
    1. 2.1 Genome Sequencing
      1. Introductory Review
        1. 1 Eukaryotic genomics
        2. 2 Genome sequencing of microbial species
        3. 3 Hierarchical, ordered mapped large insert clone shotgun sequencing
      2. Specialist Review
        1. 4 Sequencing templates – shotgun clone isolation versus amplification approaches
        2. 5 Robotics and automation
      3. Short Specialist Review
        1. 6 Microelectrophoresis devices for DNA sequencing
        2. 7 Single molecule array-based sequencing
        3. 8 Real-time DNA sequencing
    2. 2.2 Mapping
      1. Introductory Review
        1. 9 Genome mapping overview
        2. 10 Linking DNA to production: the mapping of quantitative trait loci in livestock
      2. Specialist Review
        1. 11 Mapping complex disease phenotypes
        2. 12 Haplotype mapping
        3. 13 YAC-STS content mapping
        4. 14 The construction and use of radiation hybrid maps in genomic research
        5. 15 Linkage mapping
      3. Short Specialist Review
        1. 16 Microarray comparative genome hybridization
        2. 17 Linkage disequilibrium and whole-genome association studies
        3. 18 Fingerprint mapping
        4. 19 Restriction fragment fingerprinting software
        5. 20 Synteny mapping
        6. 21 Hitchhiking mapping
        7. 22 The Happy mapping approach
        8. Digital karyotyping: a powerful tool for cancer gene discovery
    3. 2.3 The Human Genome
      1. Introductory Review
        1. 23 The technology tour de force of the Human Genome Project
        2. 24 The Human Genome Project
      2. Specialist Review
        1. 25 Genome assembly
        2. 26 Segmental duplications and the human genome
        3. 27 Noncoding RNAs in mammals
      3. Short Specialist Review
        1. 28 The distribution of genes in human genome
        2. 29 Pseudogenes
        3. 30 Alternative splicing: conservation and function
        4. 31 Overlapping genes in the human genome
        5. 32 Comparisons with primate genomes
        6. 33 Transcriptional promoters
        7. 34 Human microRNAs
        8. 35 Endogenous retroviruses
    4. 2.4 Model Organisms: Functional and Comparative Genomics
      1. Introductory Review
        1. 36 Genome archaeology
        2. 37 Functional analysis of genes
      2. Specialist Review
        1. 38 Mouse models
        2. 39 The rat as a model physiological system
        3. 40 Farm animals
        4. 41 Mouse mutagenesis and gene function
        5. 42 Systematic mutagenesis of nonmammalian model species
      3. Short Specialist Review
        1. 43 Functional genomics in Saccharomyces cerevisiae
        2. 44 The C. elegans genome
        3. 45 The Drosophila genome(s)
        4. 46 The Fugu and Zebrafish genomes
        5. 47 The mouse genome sequence
        6. 48 Comparative sequencing of vertebrate genomes
        7. The chimpanzee genome
        8. Functional annotation of the mouse genome: the challenge of phenotyping
    5. 2.5 Bacteria and Other Pathogens
      1. Introductory Review
        1. 49 Bacterial pathogens of man
        2. 50 Eukaryotic parasite genome projects
      2. Specialist Review
        1. 51 Genomics of enterobacteriaceae
        2. 52 Genomics of the Mycobacterium tuberculosis complex and Mycobacterium leprae
        3. 53 The Mycoplasmas – a congruent path toward minimal life functions
        4. 54 The nuclear genome of apicomplexan parasites
        5. 55 Reverse vaccinology: a critical analysis
      3. Short Specialist Review
        1. 56 The staphylococci
        2. 57 Genome-wide analysis of group A Streptococcus
        3. 58 Yersinia
        4. 59 Chlamydiae
        5. 60 Spirochete genomes
        6. 61 Comparative genomics of the ɛ-proteobacterial human pathogens Helicobacter pylori and Campylobacter jejuni
        7. 62 The neisserial genomes: what they reveal about the diversity and behavior of these species
        8. 63 Kinetoplastid genomics
        9. 64 The organelles of apicomplexan parasites
        10. 65 Environmental shotgun sequencing
        11. 66 Methods for detecting horizontal transfer of genes
        12. Genomics of Rickettsia
        13. Listeriae
    6. 2.6 SNPs/Haplotypes
      1. Introductory Review
        1. 67 History of genetic mapping
        2. 68 Normal DNA sequence variations in humans
      2. Specialist Review
        1. 69 Reliability and utility of single nucleotide polymorphisms for genetic association studies
        2. 70 Pharmacogenetics and the future of medicine
        3. 71 SNPs and human history
      3. Short Specialist Review
        1. 72 Evolutionary modeling in haplotype analysis
        2. 73 Creating LD maps of the genome
        3. 74 Finding and using haplotype blocks in candidate gene association studies
        4. 75 Avoiding stratification in association studies
        5. 76 Mapping by admixture linkage disequilibrium (MALD)
        6. 77 Genotyping technology: the present and the future
    7. 2.7 ESTs: Cancer Genes and the Anatomy Project
      1. Introductory Review
        1. 78 What is an EST?
        2. 79 Technologies for systematic analysis of eukaryotic transcriptomes
      2. Specialist Review
        1. 80 EST resources, clone sets, and databases
        2. 81 Using ESTs for genome annotation – predicting the transcriptome
        3. 82 Using ORESTES ESTs to mine gene cancer expression data
        4. 83 Proteome knowledge bases in the context of cancer
      3. Short Specialist Review
        1. 84 Disease gene candidacy and ESTs
        2. 85 The role of nonsense-mediated decay in physiological and pathological processes
        3. 86 Pilot gene discovery in plasmodial pathogens
      4. Basic Techniques and Approaches
        1. 87 Manufacturing EST libraries
        2. 88 EST clustering: a short tutorial
        3. 89 Using UniGene, STACK, and TIGR indices
    8. 2.8 Expression Profiling
      1. Introductory Review
        1. 90 Microarrays: an overview
      2. Specialist Review
        1. 91 Creating and hybridizing spotted DNA arrays
        2. 92 Using oligonucleotide arrays
        3. 93 Microarray CGH
        4. 94 Expression and localization of proteins in mammalian cells
        5. 95 Integrating genotypic, molecular profiling, and clinical data to elucidate common human diseases
        6. 96 The promise of gene signatures in cancer diagnosis and prognosis
      3. Short Specialist Review
        1. 97 Seven years of yeast microarray analysis
        2. 98 Bacterial genome organization: comparative expression profiling, operons, regulons, and beyond
        3. 99 Genomic analysis of host pathogen interactions
        4. 100 Protein microarrays as an emerging tool for proteomics
        5. 101 Tissue microarrays
      4. Basic Techniques and Approaches
        1. 102 The use of external controls in microarray experiments
        2. 103 SAGE
  4. Part 3 Proteomics
    1. 3.1 Core Methodologies
      1. Introductory Review
        1. 1 Core methodologies
        2. Advances of LC-MS and CZE-MS in proteome analysis
      2. Specialist Review
        1. 2 Sample preparation for proteomics
        2. 3 Tandem mass spectrometry database searching
        3. 4 Interpreting tandem mass spectra of peptides
        4. 5 FT-ICR
        5. 6 Laser-based microdissection approaches and applications
        6. Orbitrap mass analyzer
      3. Short Specialist Review
        1. 7 Time-of-flight mass spectrometry
        2. 8 Quadrupole mass analyzers: theoretical and practical considerations
        3. 9 Quadrupole ion traps and a new era of evolution
        4. 10 Hybrid MS
        5. 11 Nano-MALDI and Nano-ESI MS
        6. 12 Protein fingerprinting
        7. 13 Multidimensional liquid chromatography tandem mass spectrometry for biological discovery
      4. Basic Techniques and Approaches
        1. 14 Sample preparation for MALDI and electrospray
        2. 15 Handling membrane proteins
        3. 16 Improvement of sequence coverage in peptide mass fingerprinting
        4. 17 Tutorial on tandem mass spectrometry database searching
        5. 18 Techniques for ion dissociation (fragmentation) and scanning in MS/MS
        6. 19 Making nanocolumns and tips
      5. Tutorial
        1. Tutorial on protein fingerprinting
    2. 3.2 Expression Proteomics
      1. Introductory Review
        1. 20 Separation-dependent approaches for protein expression profiling
        2. 21 Separation-independent approaches for protein expression profiling
      2. Specialist Review
        1. 22 Two-dimensional gel electrophoresis
        2. 23 ICAT and other labeling strategies for semiquantitative LC-based expression profiling
        3. 24 Protein arrays
      3. Short Specialist Review
        1. 25 2D DIGE
        2. 26 Image analysis
        3. 27 Detecting protein posttranslational modifications using small molecule probes and multiwavelength imaging devices
        4. 28 Real-time measurements of protein dynamics
      4. Basic Techniques and Approaches
        1. 29 Two-dimensional gel electrophoresis (2-DE)
        2. 30 2-D Difference Gel Electrophoresis – an accurate quantitative method for protein analysis
        3. 31 MS-based methods for identification of 2-DE-resolved proteins
        4. 32 Arraying proteins and antibodies
        5. 33 Basic techniques for the use of reverse phase protein microarrays for signal pathway profiling
    3. 3.3 Mapping of Biochemical Networks
      1. Introductory Review
        1. 34 Protein interactions in cellular signaling
        2. 35 Structural biology of protein complexes
      2. Specialist Review
        1. 36 Biochemistry of protein complexes
        2. 37 Inferring gene function and biochemical networks from protein interactions
        3. 38 The C. elegans interactome project
        4. 39 The yeast interactome
      3. Short Specialist Review
        1. 40 Human signaling pathways analyzed by protein interaction mapping
        2. 41 Investigating protein–protein interactions in multisubunit proteins: the case of eukaryotic RNA polymerases
        3. 42 Membrane-anchored protein complexes
        4. 43 Energy transfer–based approaches to study G protein–coupled receptor dimerization and activation
        5. 44 Protein interaction databases
        6. 45 Computational methods for the prediction of protein interaction partners
        7. 46 Functional classification of proteins based on protein interaction data
        8. Analyzing proteomic, genomic and transcriptomic elemental compositions to uncover the intimate evolution of biopolymers
        9. Topology of protein interaction networks and cell physiology
      4. Basic Techniques and Approaches
        1. 47 Bioluminescence resonance energy transfer
    4. 3.4 Functional Proteomics
      1. Introductory Review
        1. 48 Probing cellular function with bioluminescence imaging
      2. Specialist Review
        1. 49 Small molecule fluorescent probes for protein labeling and their application to cell-based imaging (including FlAsH etc.)
        2. 50 Using photoactivatable GFPs to study protein dynamics and function
        3. 51 FRET-based reporters for intracellular enzyme activity
        4. Quantitative EM techniques
      3. Short Specialist Review
        1. 52 High content screening
        2. 53 Photobleaching (FRAP/FLIP) and dynamic imaging
        3. 54 Probing protein function in cells using CALI
        4. 55 Imaging protein function using fluorescence lifetime imaging microscopy (FLIM)
        5. 56 Elucidating protein dynamics and function using fluorescence correlation spectroscopy (FCS)
        6. 57 Quantum dots for multiparameter measurements
      4. Basic Techniques and Approaches
        1. 58 Immunofluorescent labeling and fluorescent dyes
        2. 59 Quantitative image analysis and the Open Microscopy Environment
        3. 60 siRNA approaches in cell biology
    5. 3.5 Proteome Diversity
      1. Introductory Review
        1. 61 Posttranslational modification of proteins
        2. 62 Glycosylation
      2. Specialist Review
        1. 63 Protein phosphorylation analysis by mass spectrometry
        2. 64 Structure/function of N-glycans
        3. 65 Structure/function of O-glycans
        4. 66 GPI anchors
        5. Glycosylation and hepatacellular carcinoma
        6. Protein glycosylation and renal cancer
      3. Short Specialist Review
        1. 67 Posttranslational cleavage of cell-surface receptors
        2. 68 S-nitrosylation and thiolation
        3. 69 Glycosylation in bacteria: that, what, how, why, now what?
        4. 70 O-glycan processing
        5. 71 O-Mannosylation
        6. 72 O-linked N-acetylglucosamine (O-GlcNAc)
        7. Posttranslational modifications to plants – glycosylation
      4. Basic Techniques and Approaches
        1. 73 Protein phosphorylation analysis – a primer
        2. 74 Glycoproteomics
        3. 75 Mass spectrometry
        4. 76 Analysis of N- and O-linked glycans of glycoproteins
        5. 77 Glycosylphosphatidylinositol anchors – a structural perspective
    6. 3.6 Proteome Families
      1. Introductory Review
        1. 78 Classification of proteins into families
      2. Specialist Review
        1. 79 Metalloproteins
        2. 80 Peptidases, families, and clans
        3. 81 Transporter protein families
        4. 82 Structure comparison and protein structure classifications
      3. Short Specialist Review
        1. 83 InterPro
        2. 84 Functionally and structurally relevant residues in PROSITE motif descriptors
        3. The PRINTS protein fingerprint database: functional and evolutionary applications
        4. 86 Pfam: the protein families database
        5. 87 The PIR SuperFamily (PIRSF) classification system
        6. 88 Equivalog protein families in the TIGRFAMs database
        7. 89 The CATH domain structure database
        8. 90 COGs: an evolutionary classification of genes and proteins from sequenced genomes
        9. PANTHER: Protein families and subfamilies modeled on the divergence of function
        10. Functional prediction through phylogenetic inference and structural classification of proteins
      4. Basic Techniques and Approaches
        1. 91 Classification of proteins by sequence signatures
        2. 92 Classification of proteins by clustering techniques
        3. 93 Getting the most out of protein family classification resources
    7. 3.7 Structural Proteomics
      1. Introductory Review
        1. 94 What use is a protein structure?
        2. 95 History and future of X-ray structure determination
      2. Specialist Review
        1. 96 Fundamentals of protein structure and function
        2. 97 Structural genomics – expanding protein structural universe
        3. 98 Target selection for structural genomics
        4. Protein–ligand docking and structure-based drug design
      3. Short Specialist Review
        1. 99 Large complexes by X-ray methods
        2. 100 Large complexes and molecular machines by electron microscopy
        3. 101 The importance of protein structural dynamics and the contribution of NMR spectroscopy
        4. 102 New approaches to bridging the timescale gap in the computer simulation of biomolecular processes
        5. 103 Modeling membrane protein structures
      4. Basic Techniques and Approaches
        1. 104 X-ray crystallography
        2. 105 NMR
        3. 106 Electron microscopy as a tool for 3D structure determination in molecular structural biology
    8. 3.8 Systems Biology
      1. Introductory Review
        1. 107 Integrative approaches to biology in the twenty-first century
      2. Specialist Review
        1. 108 Functional networks in mammalian cells
        2. 109 Analyzing and reconstructing gene regulatory networks
        3. 110 Reverse engineering gene regulatory networks
        4. 111 Functional inference from probabilistic protein interaction networks
        5. 112 Constraint-based modeling of metabolomic systems
        6. 113 Metabolic dynamics in cells viewed as multilayered, distributed, mass-energy-information networks
        7. 114 A complex systems approach to understand how cells control their shape and make cell fate decisions
        8. 115 Systems biology of the heart
        9. 116 Integrative modeling of the pancreatic β-cell
      3. Short Specialist Review
        1. 117 EGFR network
      4. Basic Techniques and Approaches
        1. 118 Data collection and analysis in systems biology
  5. Part 4 Bioinformatics
    1. 4.1 Genome Assembly and Sequencing
      1. Introductory Review
        1. 1 Contig mapping and analysis
      2. Specialist Review
        1. 2 Algorithmic challenges in mammalian whole-genome assembly
        2. 3 Genome signals and assembly
      3. Short Specialist Review
        1. 4 Microbial sequence assembly
        2. 5 Comparative analysis for mapping and sequence assembly
        3. 6 Statistical signals
        4. 7 Errors in sequence assembly and corrections
      4. Basic Techniques and Approaches
        1. 8 Genome maps and their use in sequence assembly
        2. 9 Repeatfinding
        3. 10 Graphs and metrics
        4. 11 Algorithms for sequence errors
        5. 12 Polymorphism and sequence assembly
    2. 4.2 Gene Finding and Gene Structure
      1. Introductory Review
        1. 13 Prokaryotic gene identification in silico
        2. 14 Eukaryotic gene finding
      2. Specialist Review
        1. 15 Spliced alignment
        2. 16 Searching for genes and biologically related signals in DNA sequences
        3. 17 Pair hidden Markov models
        4. 18 Information theory as a model of genomic sequences
      3. Short Specialist Review
        1. 19 Promoter prediction
        2. 20 Operon finding in bacteria
        3. 21 Gene structure prediction in plant genomes
        4. 22 Eukaryotic regulatory sequences
        5. 23 Alternative splicing in humans
        6. 24 Exonic splicing enhancers and exonic splicing silencers
        7. 25 Gene finding using multiple related species: a classification approach
      4. Basic Techniques and Approaches
        1. 26 Dynamic programming for gene finders
        2. 27 Gene structure prediction by genomic sequence alignment
        3. 28 Computational motif discovery
    3. 4.3 Protein Function and Annotation
      1. Introductory Review
        1. 29 In silico approaches to functional analysis of proteins
      2. Specialist Review
        1. 30 Contextual inference of protein function
        2. 31 Protein domains in eukaryotic signal transduction systems
      3. Short Specialist Review
        1. 32 Sequence complexity of proteins and its significance in annotation
        2. 33 Protein repeats
        3. 34 Large-scale protein annotation
        4. 35 Measuring evolutionary constraints as protein properties reflecting underlying mechanisms
        5. 36 Large-scale, classification-driven, rule-based functional annotation of proteins
      4. Basic Techniques and Approaches
        1. 37 Signal peptides and protein localization prediction
        2. 38 Transmembrane topology prediction
        3. 39 IMPALA/RPS-BLAST/PSI-BLAST in protein sequence analysis
    4. 4.4 Comparative Analysis and Phylogeny
      1. Introductory Review
        1. 40 The domains of life and their evolutionary implications
        2. 41 Phylogenetic profiling
      2. Specialist Review
        1. 42 Reconstructing vertebrate phylogenetic trees
        2. 43 Evolution of regulatory networks
      3. Short Specialist Review
        1. 44 Phylogenomic approaches to bacterial phylogeny
        2. 45 Phylogenomics for studies of microbial evolution
        3. 46 Mapping mutations on phylogenies
        4. 47 Phylogenetic analysis of BLAST results
        5. 48 Connecting genes by comparative genomics
        6. 49 Chromosome phylogeny
    5. 4.5 Computational Methods for High-throughput Genetic Analysis: Expression Profiling
      1. Introductory Review
        1. 50 Integrating statistical approaches in experimental design and data analysis
        2. 51 Mass spectrometry and computational proteomics
      2. Specialist Review
        1. 52 Experimental design
        2. 53 Statistical methods for gene expression analysis
        3. 54 Algorithms for gene expression analysis
        4. 55 Differential expression with the Bioconductor Project
        5. 56 Mass spectrometric data mining for protein sequences
      3. Short Specialist Review
        1. 57 Low-level analysis of oligonucleotide expression arrays
        2. 58 CGH data analysis
        3. 59 A comparison of existing tools for ontological analysis of gene expression data
        4. 60 Extracting networks from expression data
        5. 61 Data standardization and the HUPO proteomics standards initiative
      4. Basic Techniques and Approaches
        1. 62 Large error models for microarray intensities
        2. 63 Relevance networks
    6. 4.6 Methods for Structure Analysis and Prediction
      1. Introductory Review
        1. 64 Protein structure analysis and prediction
      2. Specialist Review
        1. 65 Analysis and prediction of membrane protein structure
        2. 66 Ab initio structure prediction
        3. 67 Score functions for structure prediction
        4. 68 Protein domains
        5. 69 Complexity in biological structures and systems
        6. 70 Modeling by homology
      3. Short Specialist Review
        1. 71 The Protein Data Bank (PDB) and the Worldwide PDB http://www.wwpdb.org
        2. 72 Threading for protein-fold recognition
        3. 73 CASP
        4. 74 Molecular simulations in structure prediction
        5. 75 Protein structure comparison
        6. 76 Secondary structure prediction
        7. 77 DNA/protein modeling
        8. 78 Modeling tertiary structure of RNA
    7. 4.7 Structuring and Integrating Data
      1. Introductory Review
        1. 79 Introduction to ontologies in biomedicine: from powertools to assistants
        2. BioPAX – biological pathway data exchange format
      2. Specialist Review
        1. 80 Ontologies for the life sciences
        2. 81 Unified Medical Language System and associated vocabularies
        3. 82 The Gene Ontology project
        4. 83 Ontologies for information retrieval
        5. 84 Ontologies for natural language processing
        6. 85 TAMBIS: transparent access to multiple bioinformatics services
      3. Short Specialist Review
        1. 86 Automatic concept identification in biomedical literature
        2. 87 Merging and comparing ontologies
        3. 88 Bioinformatics pathway representations, databases, and algorithms
        4. 89 Proteomics data representation and management
        5. 90 Ontologies for three-dimensional molecular structure
        6. MAGE-OM: An object model for the communication of microarray data
      4. Basic Techniques and Approaches
        1. 91 Frame-based systems: Protégé
        2. 92 Description logics: OWL and DAML + OIL
    8. 4.8 Modern Programming Paradigms in Biology
      1. Introductory Review
        1. 93 Detecting protein homology using NCBI tools
        2. 94 Integrated bioinformatics software at NCBI
      2. Specialist Review
        1. 95 Bioconductor: software and development strategies for statistical genomics
        2. 96 RNA secondary structure prediction
        3. 97 Ensembl and UniProt (Swiss-Prot)
        4. 98 Hidden Markov models and neural networks
        5. 99 Threading algorithms
      3. Short Specialist Review
        1. 100 Acedb genome database
        2. 101 Design of KEGG and GO
        3. 102 Simulation of biochemical networks
        4. 103 Using the Python programming language for bioinformatics
        5. 104 Perl in bioinformatics
        6. 105 The MATLAB bioinformatics toolbox
        7. 106 Gibbs sampling and bioinformatics
        8. 107 Applications of RNA minimum free energy computations
      4. Basic Techniques and Approaches
        1. 108 Cluster architecture
        2. 109 Relational databases in bioinformatics
        3. 110 Support vector machine software
        4. 111 Brief Python tutorial for bioinformatics
        5. 112 A brief Perl tutorial for bioinformatics
      5. Tutorial
        1. Grid technologies
        2. Attacking performance bottlenecks

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