A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome
Preferred in vivo ubiquitination sites
Accuracy improvement for identifying translation initiation sites in microbial genomes
Effects of pooling mRNA in microarray class comparisons
MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanks
DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria
Conserved network motifs allow protein–protein interaction prediction
A graph-theoretic approach to testing associations between disparate sources of functional genomics data
Reducing storage requirements for biological sequence comparison
Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser
A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences
An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites
Mining HIV protease cleavage data using genetic programming with a sum-product function
Dimension reduction methods for microarrays with application to censored survival data
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions
Gene selection using a two-level hierarchical Bayesian model
Limited agreement among three global gene expression methods highlights the requirement for non-global validation
Data exploration tools for the Gene Ontology database
A probabilistic measure for alignment-free sequence comparison
ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms
Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach
DIVAA: analysis of amino acid diversity in multiple aligned protein sequences
Predicting GPCR–G-protein coupling using hidden Markov models
Exploring protein fold space by secondary structure prediction using data distribution method on Grid platform
Modeling interactome: scale-free or geometric?
Comparative analysis of methods for representing and searching for transcription factor binding sites
Primer Design and Marker Clustering for Multiplex SNP-IT Primer Extension Genotyping Assay using Statistical Modeling
Accurate detection of aneuploidies in array CGH and gene expression microarray data
The ‘subsequent artificial neural network’ (SANN) approach might bring more classificatory power to ANN-based DNA microarray analyses
The Baumgartner-Weiß-Schindler test for the detection of differentially expressed genes in replicated microarray experiments
Discovery of meaningful associations in genomic data using partial correlation coefficients
Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum
BagBoosting for tumor classification with gene expression data
Advances to Bayesian network inference for generating causal networks from observational biological data
Discovering patterns to extract protein–protein interactions from full texts
Training HMM structure with genetic algorithm for biological sequence analysis
Highly specific prediction of phosphorylation sites in proteins
Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting
Breakpoint identification and smoothing of array comparative genomic hybridization data
SARGE: a tool for creation of putative genetic networks
Importing MAGE-ML format microarray data into BioConductor
DAGchainer: a tool for mining segmental genome duplications and synteny
CSB.DB: a comprehensive systems-biology database
PLPMDB: Pyridoxal-5′-phosphate dependent enzymes mutants database
VisRD—visual recombination detection
DNMAD: web-based diagnosis and normalization for microarray data
MedlineR: an open source library in R for Medline literature data mining
Interactive gene-order comparison for multiple small genomes
CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome
EC_oligos: automated and whole-genome primer design for exons within one or between two genomes
GenePicker: replicate analysis of Affymetrix gene expression microarrays
SelSim: a program to simulate population genetic data with natural selection and recombination
DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions
The JigCell Model Builder and Run Manager
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data
Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data
GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data
ViTO: tool for refinement of protein sequence–structure alignments
PCOAT: positional correlation analysis using multiple methods
Ontologies for Behavior
CLANS: a Java application for visualizing protein families based on pairwise similarity
limmaGUI: A graphical user interface for linear modeling of microarray data
NMRb: a web-site repository for raw NMR datasets
GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
Erratum