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

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