ID Numbers for Cross Referencing : Volume 4 Bioinformatics This list will help you include cross references to other articles in GGPB. Find the article that you wish to cross refer to, note its corresponding unique ID number e.g (g203206) and then insert that unique ID number into your text. Please do not insert the article title, just its unique ID number. This makes your work easier (less typing) and it gives us a unique identifier to ensure that accurate and unambiguous cross-referencing is obtained. Thank you for using the unique ID numbers. Please remember you can cross reference to articles outside the section in which your article appears. 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 http://www.wwpdb.org 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