AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context
Profile-based detection of microRNA precursors in animal genomes
ColorHOR—novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome
BACCardI—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data
Theoretical and practical advances in genome halving
Operon prediction without a training set
A parallel graph decomposition algorithm for DNA sequencing with nanopores
Accurate identification of alternatively spliced exons using support vector machine
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
Fast and accurate database homology search using upper bounds of local alignment scores
Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites
Rapid motif-based prediction of circular permutations in multi-domain proteins
Relation between weight matrix and substitution matrix: motif search by similarity
Predicting protein localization in budding Yeast
Protein homology detection by HMM–HMM comparison
A simple statistical method for discriminating outer membrane proteins with better accuracy
DPRml: distributed phylogeny reconstruction by maximum likelihood
An alternative model of amino acid replacement
A new approach to prediction of short-range conformational propensities in proteins
PDBML: the representation of archival macromolecular structure data in XML
Statistical analysis of domains in interacting protein pairs
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins
Predicting fold novelty based on ProtoNet hierarchical classification
Solving and analyzing side-chain positioning problems using linear and integer programming
Local correlation of expression profiles with gene annotations—proof of concept for a general conciliatory method
Superior feature-set ranking for small samples using bolstered error estimation
A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples
Extracting relations between promoter sequences and their strengths from microarray data
Clustering of gene expression data using a local shape-based similarity measure
Normalization of two-channel microarray experiments: a semiparametric approach
Identifying differentially expressed genes from microarray experiments via statistic synthesis
GoArrays: highly dynamic and efficient microarray probe design
Classification using partial least squares with penalized logistic regression
Validation of alternative methods of data normalization in gene co-expression studies
Probabilities of spurious connections in gene networks: application to expression time series
Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression
Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays
Quantile smoothing of array CGH data
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm
Comparison of computational methods for the identification of cell cycle-regulated genes
Finding regulatory modules through large-scale gene-expression data analysis
Evolutionary optimization with data collocation for reverse engineering of biological networks
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling
An improved algorithm for stoichiometric network analysis: theory and applications
Intervention in context-sensitive probabilistic Boolean networks
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
Automatic extraction of gene/protein biological functions from biomedical text
In silico gene function prediction using ontology-based pattern identification
ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems
CRAVE: a database, middleware and visualization system for phenotype ontologies
Primaclade—a flexible tool to find conserved PCR primers across multiple species
MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly
SABmark—a benchmark for sequence alignment that covers the entire known fold space
NetAcet: prediction of N-terminal acetylation sites
Multiple sequence alignment with user-defined constraints at GOBICS
SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates
A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns
PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order
CyDAS: a cytogenetic data analysis system
Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processes
hp-DPI: Helicobacter pylori Database of Protein Interactomes—embracing experimental and inferred interactions
BRAGI: linking and visualization of database information in a 3D viewer and modeling tool