Analyzing time series gene expression data
Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins
Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptor
Which is better for cDNA-microarray-based classification: ratios or direct intensities
A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions
Efficient combination of multiple word models for improved sequence comparison
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays
Class discovery and classification of tumor samples using mixture modeling of gene expression data—a unified approach
Identification of DNA regulatory motifs using Bayesian variable selection
A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments
Predicting allergenic proteins using wavelet transform
Genome wide identification and classification of alternative splicing based on EST data
Incremental generation of summarized clustering hierarchy for protein family analysis
Distribution of information in biomedical abstracts and full-text publications
A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles
GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms
A statistical framework for genomic data fusion
THEA: ontology-driven analysis of microarray data
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway
SCA db: spinocerebellar ataxia candidate gene database
DBRF–MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants
An efficient algorithm for optimizing whole genome alignment with noise
Correcting log ratios for signal saturation in cDNA microarrays
A mixture model for estimating the local false discovery rate in DNA microarray analysis
Exhaustive whole-genome tandem repeats search
Mining gene expression data for positive and negative co-regulated gene clusters
Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication
The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura
A neural network method for prediction of β-turn types in proteins using evolutionary information
Mining gene expression data based on template theory
ICBS: a database of interactions between protein chains mediated by β-sheet formation
Faster cyclic loess: normalizing RNA arrays via linear models
BacTregulators: a database of transcriptional regulators in bacteria and archaea
Qxpak: a versatile mixed model application for genetical genomics and QTL analyses
Regulatory motif finding by logic regression
STAR: an algorithm to Search for Tandem Approximate Repeats
A statistical framework for the design of microarray experiments and effective detection of differential gene expression
MathSBML: a package for manipulating SBML-based biological models
A System for Automated Bacterial (genome) Integrated Annotation—SABIA
Dblox: a genome-wide test for ancient segmental duplication
ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences
GDPC: connecting researchers with multiple integrated data sources
PaVESy: Pathway Visualization and Editing System
The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions
RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets
Gene-Ontology-based clustering of gene expression data
ASIAN: a website for network inference
A collaborative database of inbred mouse strain characteristics
TargetDB: a target registration database for structural genomics projects
Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies
LUCY2: an interactive DNA sequence quality trimming and vector removal tool
SWAPSC: sliding window analysis procedure to detect selective constraints
ClutrFree: cluster tree visualization and interpretation
Rainbow: a toolbox for phylogenetic supertree construction and analysis
Thermodynamics of enzyme-catalyzed reactions—a database for quantitative biochemistry
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
FigSearch: a figure legend indexing and classification system
GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers
CoPS: Comprehensive Peptide Signature Database
Command line tool for calculating theoretical MS spectra for given sequences