Considerations when using the significance analysis of microarrays (SAM) algorithm
2005; 6: 129
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
2005; 6: 132
Empirical codon substitution matrix
2005; 6: 134
Which gene did you mean?
2005; 6: 142
CAGER: classification analysis of gene expression regulation using multiple information sources
2005; 6: 114
Gene finding in the chicken genome
2005; 6: 131
libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny
2005; 6: 138
transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences
2005; 6: 156
Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking
2005; 6: 125
YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities
2005; 6: 135
AVID: An integrative framework for discovering functional relationships among proteins
2005; 6: 136
PentaPlot: A software tool for the illustration of genome mosaicism
2005; 6: 139
AnovArray: a set of SAS macros for the analysis of variance of gene expression data
2005; 6: 150
Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation
2005; 6: 157
SplitTester : software to identify domains responsible for functional divergence in protein family
2005; 6: 137
Visualization-based discovery and analysis of genomic aberrations in microarray data
2005; 6: 146
Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system
2005; 6: 147
Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes
2005; 6: 148
Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection
2005; 6: 154
Normal uniform mixture differential gene expression detection for cDNA microarrays
2005; 6: 173
Satellog: A database for the identification and prioritization of satellite repeats in disease association studies
2005; 6: 145
Sequence signature analysis of chromosome identity in three Drosophila species
2005; 6: 158
AutoFACT: An Automatic Functional Annotation and Classification Tool
2005; 6: 151
pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties
2005; 6: 152
Multiple sequence alignments of partially coding nucleic acid sequences
2005; 6: 160
Species-specific analysis of protein sequence motifs using mutual information
2005; 6: 164
Prediction of twin-arginine signal peptides
2005; 6: 167
DCD – a novel plant specific domain in proteins involved in development and programmed cell death
2005; 6: 169
SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures
2005; 6: 170
PAGE: Parametric Analysis of Gene Set Enrichment
2005; 6: 144
Thesaurus-based disambiguation of gene symbols
2005; 6: 149
CGH-Profiler: Data mining based on genomic aberration profiles
2005; 6: 188
Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates
2005; 6: 190
Signal transduction pathway profiling of individual tumor samples
2005; 6: 163
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein
2005; 6: 176
Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi
2005; 6: 178
Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops
2005; 6: 171
MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays
2005; 6: 175
Processing methods for differential analysis of LC/MS profile data
2005; 6: 179
Communication and re-use of chemical information in bioscience
2005; 6: 180
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability
2005; 6: 185
Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data
2005; 6: 187
Storing, linking, and mining microarray databases using SRS
2005; 6: 192
An empirical analysis of training protocols for probabilistic gene finders
2005; 6: 193
Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
2005; 6: 183
A computational approach for identifying pathogenicity islands in prokaryotic genomes
2005; 6: 184
FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform
2005; 6: 198
Iterative approach to model identification of biological networks
2005; 6: 155
FACT – a framework for the functional interpretation of high-throughput experiments
2005; 6: 161
Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases
2005; 6: 166
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
2005; 6: 172
Dissecting systems-wide data using mixture models: application to identify affected cellular processes
2005; 6: 177
Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm
2005; 6: 195
Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach
2005; 6: 165
Theme discovery from gene lists for identification and viewing of multiple functional groups
2005; 6: 162
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)
2005; 6: 168
Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines
2005; 6: 174
Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds
2005; 6: 181
GObar: A Gene Ontology based analysis and visualization tool for gene sets
2005; 6: 189
Functional annotation by identification of local surface similarities: a novel tool for structural genomics
2005; 6: 194
Squid – a simple bioinformatics grid
2005; 6: 197
PALSSE: A program to delineate linear secondary structural elements from protein structures
2005; 6: 202
Full cyclic coordinate descent: solving the protein loop closure problem in Cα space
2005; 6: 159
Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity
2005; 6: 182
Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments
2005; 6: 186
COPASAAR – A database for proteomic analysis of single amino acid repeats
2005; 6: 196
A comparative review of estimates of the proportion unchanged genes and the false discovery rate
2005; 6: 199
DynGO: a tool for visualizing and mining of Gene Ontology and its associations
2005; 6: 201
Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants
2005; 6: 203
FiatFlux – a software for metabolic flux analysis from 13C-glucose experiments
2005; 6: 209
Evaluation of normalization methods for cDNA microarray data by k-NN classification
2005; 6: 191
Genomic multiple sequence alignments: refinement using a genetic algorithm
2005; 6: 200
Tandem machine learning for the identification of genes regulated by transcription factors
2005; 6: 204
stam – a Bioconductor compliant R package for structured analysis of microarray data
2005; 6: 211
Improved prediction of critical residues for protein function based on network and phylogenetic analyses
2005; 6: 213
JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture
2005; 6: 216
Effective ambiguity checking in biosequence analysis
2005; 6: 153
Variation in structural location and amino acid conservation of functional sites in protein domain families
2005; 6: 210
TmaDB: a repository for tissue microarray data
2005; 6: 218
A comparative study of discriminating human heart failure etiology using gene expression profiles
2005; 6: 205