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
An edit script for taxonomic classifications
2005; 6: 208
Sources of variation in Affymetrix microarray experiments
2005; 6: 214
A protein domain interaction interface database: InterPare
2005; 6: 207
A new dynamical layout algorithm for complex biochemical reaction networks
2005; 6: 212
Generalizations of Markov model to characterize biological sequences
2005; 6: 219
A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage
2005; 6: 220
Assessing local structural perturbations in proteins
2005; 6: 226
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
2005; 6: 227
ProbeMaker: an extensible framework for design of sets of oligonucleotide probes
2005; 6: 229
Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"
2005; 6: 206
Micro-Mar: a database for dynamic representation of marine microbial biodiversity
2005; 6: 222
SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design
2005; 6: 223
Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software
2005; 6: 228
Versatile and declarative dynamic programming using pair algebras
2005; 6: 224
Pathway level analysis of gene expression using singular value decomposition
2005; 6: 225
Chromosomal clustering of a human transcriptome reveals regulatory background
2005; 6: 230
EXPANDER – an integrative program suite for microarray data analysis
2005; 6: 232
GeneRank: Using search engine technology for the analysis of microarray experiments
2005; 6: 233
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
2005; 6: 236
Measuring similarities between transcription factor binding sites
2005; 6: 237
Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data
2005; 6: 239
Sequence variation in ligand binding sites in proteins
2005; 6: 240
Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks
2005; 6: 242
A linear memory algorithm for Baum-Welch training
2005; 6: 231
Quality determination and the repair of poor quality spots in array experiments
2005; 6: 234
An analysis of extensible modelling for functional genomics data
2005; 6: 235
Mathematical design of prokaryotic clone-based microarrays
2005; 6: 238
Phylogenetic detection of conserved gene clusters in microbial genomes
2005; 6: 243
T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory
2005; 6: 246
htSNPer1.0: software for haplotype block partition and htSNPs selection
2005; 6: 38
CoPub Mapper: mining MEDLINE based on search term co-publication
2005; 6: 51
WEBnm@: a web application for normal mode analyses of proteins
2005; 6: 52
Evolutionary sequence analysis of complete eukaryote genomes
2005; 6: 53
In silico microdissection of microarray data from heterogeneous cell populations
2005; 6: 54
Speeding disease gene discovery by sequence based candidate prioritization
2005; 6: 55
TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
2005; 6: 56
Combining Affymetrix microarray results
2005; 6: 57
Towards precise classification of cancers based on robust gene functional expression profiles
2005; 6: 58
SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management
2005; 6: 60
Graphical representation of ribosomal RNA probe accessibility data using ARB software package
2005; 6: 61