ID Numbers for Cross Referencing : Volume 4 Bioinformatics
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Genome Assembly/Sequencing
Gene Finding/Gene Structure
Protein Function and Annotation
Comparative Analysis and Phylogeny
Computational Methods for High Throughput Genetic Analysis - Expression profiling
Comparative Methods for Structure Analysis and Prediction
Structuring and Integrating Data
Modern Programming Paradigms in Biology
Section 1 Genome Assembly/Sequencing
ID Title
g401105 Contig mapping and analysis
g401201 Algorithmic challenges in mammalian whole-genome assembly
g401210 Genome signals and assembly
g401304 Microbial sequence assembly
g401308 Statistical signals
g401312 Comparative analysis for mapping and sequence assembly
g401315 Errors in sequence assembly and corrections
g401402 Repeatfinding
g401407 Algorithms for sequence errors
g401411 Genome maps and their use in sequence assembly
g401416 Polymorphism and sequence assembly
g401417 Graphs and metrics
Section 2 Gene Finding/Gene Structure
ID Title
g402102 Prokaryotic gene identification in silico
g402107 Eukaryotic gene finding
g402204 Information theory as a model of genomic sequences
g402208 Spliced alignment
g402215 Pair hidden markov models
g402216 Searching for genes and biologically related signals in DNA sequences
g402301 Promoter prediction
g402303 Gene structure prediction in plant genomes
g402305 Alternative splicing in humans
g402306 Operon finding in bacteria
g402310 Eukaryotic regulatory sequences
g402314 Exonic splicing enhancers and exonic splicing silencers
g402319 Gene finding using multiple related species: a classification approach
g402412 Dynamic programming for gene finders
g402413 Gene structure prediction by genomic sequence alignment
g402417 Computational motif discovery
Section 3 Protein Function & Annotation
ID Title
g403102 In silico approaches to functional analysis of proteins
g403206 Protein domains in eukaryotic signal transduction systems
g403207 Contextual inference of protein function
g403301 Protein repeats
g403304 Large-scale protein annotation
g403310 Measuring evolutionary constraints as protein properties reflecting underlying mechanisms
g403313 Sequence complexity of proteins and its significance in annotation
g403314 Large-scale, classification-driven, rule-based functional annotation of proteins
g403409 Signal peptides and protein localization prediction
g403411 IMPALA/RPS-BLAST/PSI-BLAST in protein sequence analysis
g403412 Transmembrane topology prediction
Section 4 Comparative Analysis & Phylogeny
ID Title
g404104 Phylogenetic profiling
g404112 The domains of life and their evolutionary implications
g404207 Evolution of regulatory pathways
g404208 Reconstructing vertebrate phylogenetic trees
g404301 Phylogenomics for studies of microbial evolution
g404302 Phylogenetic analysis of BLAST results
g404303 Phylogenomic approaches to bacterial phylogeny
g404309 Mapping mutations on phylogenies
g404310 Chromosome phylogeny
g404314 Connecting genes by comparative genomics
Section 5 Computational Methods for High Throughput Genetic Analysis - Expression profiling
ID Title
g405101 Mass spectrometry and computational proteomics
g405115 Integrating statistical approaches in experimental design and data analysis
g405202 Algorithms for gene expression analysis
g405205 Experimental design
g405207 Mass spectrometric data mining for protein sequences
g405208 Differential expression with the bioconductor project
g405210 Statistical methods for gene expression analysis
g405306 Data standardisation and the HUPO proteomics standards initiative
g405309 Extracting networks from expression data
g405312 A comparsion of existing tools for ontological analysis of gene expression data
g405314 CGH data analysis
g405316 Low-level analysis of oligonucleotide expression arrays
g405404 Relevance networks
g405413 Error models for microarray intensities
Section 6 Comparative Methods for Structure Analysis and Prediction
ID Title
g406113 Analysis and prediction of membrane protein structure
g406119 Protein structure analysis and prediction
g406201 Ab-initio structure prediction
g406202 Score functions for structure prediction
g406204 Protein domains
g406206 Complexity in biological structures and systems
g406210 Modeling by homology
g406303 The Protein Data Bank (PDB) and the Worldwide PDB
g406305 Threading for protein-fold recognition
g406308 CASP
g406314 Molecular simulations in structure prediction
g406315 Protein structure comparison
g406316 Secondary structure prediction
g406317 DNA/protein modeling
g406318 Modeling tertiary structure of RNA
Section 8 Structuring and Integrating Data
ID Title
g408101 Introduction to ontologies in biomedicine: from powertools to assistants
g408202 The Gene Ontology project
g408206 Ontologies for information retrieval
g408207 Unified Medical Language System and associated vocabularies
g408212 Ontologies for natural language processing
g408213 Ontologies for the life sciences
g408214 TAMBIS: transparent access to multiple bioinformatics services
g408308 Bioinformatics pathway representations, databases, and algorithms
g408309 Automatic concept identification in biomedical literature
g408311 Merging and comparing ontologies
g408315 Ontologies for three-dimensional molecular structure
g408316 Proteomics data representation and management
g408404 Description logics: OWL and DAML + OIL
g408410 Frame-based systems: Protégé
Section 9 Modern Programming Paradigms in Biology  
ID Title
g409103 Integrated bioinformatics software at NCBI
g409113 Detecting protein homology using NCBI tools
g409201 Hidden Markov models and neural networks
g409202 Threading algorithms
g409207 Bioconductor: software and development strategies for statistical genomics
g409215 Ensembl and UniProt (Swiss-Prot)
g409218 RNA secondary structure prediction
g409305 Acedb genome database
g409308 The MATLAB bioinformatics toolbox
g409310 Design of KEGG and GO
g409311 Simulation of biochemical networks
g409314 Using the Python programming language for bioinformatics
g409319 Gibbs sampling and bioinformatics
g409321 Perl in bioinformatics
g409323 Applications of RNA minimum free energy computations
g409404 Cluster architecture
g409412 Relational databases in bioinformatics
g409416 Support vector machine software
g409420 A brief Perl tutorial for bioinformatics
g409422 Brief Python tutorial for bioinformatics