An edit script for taxonomic classifications.
Non-linear mapping for exploratory data analysis in functional genomics.
The Gene Set Builder: collation, curation, and distribution of sets of genes.
Mathematical design of prokaryotic clone-based microarrays.
Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells.
Online tool for the discrimination of equi-distributions.
A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage.
Bias in error estimation when using cross-validation for model selection.
A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets.
Combining gene expression data from different generations of oligonucleotide arrays.
pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties.
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome.
Selection of informative clusters from hierarchical cluster tree with gene classes.
Integrated analysis of gene expression by association rules discovery.
Noncoding RNA gene detection using comparative sequence analysis.
PCOGR: Phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms.
Application of machine learning in SNP discovery.
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.
Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser.
Identifying biological concepts from a protein-related corpus with a probabilistic topic model.
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.
PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.
Inter-residue distances derived from fold contact propensities correlate with evolutionary substitution costs.
Constraint Logic Programming approach to protein structure prediction.
BioWarehouse: a bioinformatics database warehouse toolkit.
Evaluation of methods for oligonucleotide array data via quantitative real-time PCR.
Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach.
TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.
Bayesian models for pooling microarray studies with multiple sources of replications.
A standard curve based method for relative real time PCR data processing.
Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthetic lethality.
CoaSim: A flexible environment for simulating genetic data under coalescent models.
Microbial identification by mass cataloging.
GeneRank: Using search engine technology for the analysis of microarray experiments.
Statistical significance for hierarchical clustering in genetic association and microarray expression studies.
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases.
Comparative analysis of haplotype association mapping algorithms.
Correction: Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment.
An improved procedure for gene selection from microarray experiments using false discovery rate criterion.
AnovArray: a set of SAS macros for the analysis of variance of gene expression data.
COPASAAR - A database for proteomic analysis of single amino acid repeats.
Multiple sequence alignments of partially coding nucleic acid sequences.
Two-stage normalization using background intensities in cDNA microarray data.
BioBuilder as a database development and functional annotation platform for proteins.
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models.
libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny.
A methodology for the structural and functional analysis of signaling and regulatory networks.
The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins.
"Harshlighting" small blemishes on microarrays.
RNA: (guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited - bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.
Parameter estimation for stiff equations of biosystems using radial basis function networks.
SED, a normalization free method for DNA microarray data analysis.
SNP haplotype tagging from DNA pools of two individuals.
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods.
Metabolite coupling in genome-scale metabolic networks.
In search of functional association from time-series microarray data based on the change trend and level of gene expression.
Computational method for reducing variance with Affymetrix microarrays.
Spotting effect in microarray experiments.
Automated modelling of signal transduction networks.
Effective ambiguity checking in biosequence analysis.
LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates.
UVPAR: fast detection of functional shifts in duplicate genes.
Evolutionary models for insertions and deletions in a probabilistic modeling framework.
Principal component analysis for predicting transcription-factor binding motifs from array-derived data.
Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region.
The relationship between the L1 and L2 domains of the insulin and epidermal growth factor receptors and leucine-rich repeat modules.
Exploring supervised and unsupervised methods to detect topics in biomedical text.
GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes.
A knowledge discovery object model API for Java.
Low degree metabolites explain essential reactions and enhance modularity in biological networks.
The COG database: an updated version includes eukaryotes.
SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.
SIMAGE: simulation of DNA-microarray gene expression data.
Quantifying robustness of biochemical network models.
Biologically relevant effects of mRNA amplification on gene expression profiles.
Variation in structural location and amino acid conservation of functional sites in protein domain families.
htSNPer1.0: software for haplotype block partition and htSNPs selection.
preAssemble: a tool for automatic sequencer trace data processing.
Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data.
Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity.
d-matrix - database exploration, visualization and analysis.
Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.
A new dynamical layout algorithm for complex biochemical reaction networks.
Two-part permutation tests for DNA methylation and microarray data.
Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments.
How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results.
Evolutionary distance estimation and fidelity of pair wise sequence alignment.
A database for G proteins and their interaction with GPCRs.
Internet-based profiler system as integrative framework to support translational research.
in silicoreconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence.
Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals.
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments.
Biclustering of gene expression data by non-smooth non-negative matrix factorization.
OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies.
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila.
Probabilistic estimation of microarray data reliability and underlying gene expression.
ESTIMA, a tool for EST management in a multi-project environment.
Kalign - an accurate and fast multiple sequence alignment algorithm.
Columba: an integrated database of proteins, structures, and annotations.
ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification.
Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator.
ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes.
prot4EST: Translating Expressed Sequence Tags from neglected genomes.
FastGroup: A program to dereplicate libraries of 16S rDNA sequences.
Normal uniform mixture differential gene expression detection for cDNA microarrays.
Content-rich biological network constructed by mining PubMed abstracts.
CoPub Mapper: mining MEDLINE based on search term co-publication.
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.
Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model.
rpoBMycobacterium tuberculosis.
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.
Scoredist: A simple and robust protein sequence distance estimator.
Spectral embedding finds meaningful (relevant) structure in image and microarray data.
JColorGrid: software for the visualization of biological measurements.
SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.
Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data.
STEM: a tool for the analysis of short time series gene expression data.
Automatic annotation of protein motif function with Gene Ontology terms.
Computational verification of protein-protein interactions by orthologous co-expression.
Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST).
Escherichia coliwith wavelets transforms.
OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments.
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification.
Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics.
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.
Kangaroo - A pattern-matching program for biological sequences.
Haplotype frequency estimation error analysis in the presence of missing genotype data.
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data.
Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML Database - Xindice.
TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes.
Comparison of mode estimation methods and application in molecular clock analysis.
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases.
Incremental genetic K-means algorithm and its application in gene expression data analysis.
Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast.
Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource.
A statistical approach for array CGH data analysis.
The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison.
More robust detection of motifs in coexpressed genes by using phylogenetic information.
DNA microarray data and contextual analysis of correlation graphs.
Assessing stability of gene selection in microarray data analysis.
GECKO: a complete large-scale gene expression analysis platform.
Integration of the Gene Ontology into an object-oriented architecture.
An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem.
An analysis of extensible modelling for functional genomics data.
Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities.
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.
Auto-validation of fluorescent primer extension genotyping assay using signal clustering and neural networks.
BayGO: Bayesian analysis of ontology term enrichment in microarray data.
Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants.
BIPAD: A web server for modeling bipartite sequence elements.
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
Assessing local structural perturbations in proteins.
An SVM-based system for predicting protein subnuclear localizations.
Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data.
Integrating alternative splicing detection into gene prediction.
An analysis of the Sargasso Sea resource and the consequences for database composition.
A new pooling strategy for high-throughput screening: the Shifted Transversal Design.
Clustering proteins from interaction networks for the prediction of cellular functions.
EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance.
Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis.
Tools for loading MEDLINE into a local relational database.
Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays.
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions.
Functionally specified protein signatures distinctive for each of the different blue copper proteins.
Comparison of normalization methods for CodeLink Bioarray data.
Automated methods of predicting the function of biological sequences using GO and BLAST.
Clustering the annotation space of proteins.
Identifying metabolic enzymes with multiple types of association evidence.
The distance-profile representation and its application to detection of distantly related protein families.
Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality.
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.
Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments.
galaxieEST: addressing EST identity through automated phylogenetic analysis.
PentaPlot: A software tool for the illustration of genome mosaicism.
Quality determination and the repair of poor quality spots in array experiments.
ASAView: Database and tool for solvent accessibility representation in proteins.
Providing visualisation support for the analysis of anatomy ontology data.
Profiling alternatively spliced mRNA isoforms for prostate cancer classification.
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.
Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays.
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.
Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock.
Harshlight: a "corrective make-up" program for microarray chips.
GONOME: measuring correlations between GO terms and genomic positions.
Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data.
Computation of elementary modes: a unifying framework and the new binary approach.
GO-Diff: Mining functional differentiation between EST-based transcriptomes.
A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions.
Information extraction from full text scientific articles: Where are the keywords?
Confirmation of human protein interaction data by human expression data.
CGH-Profiler: Data mining based on genomic aberration profiles.
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.
TMTMprobe-to-gene annotations.
Evaluating concentration estimation errors in ELISA microarray experiments.
Domain-based small molecule binding site annotation.
A two-way interface between limited Systems Biology Markup Language and R.
Estimating mutual information using B-spline functions - an improved similarity measure for analysing gene expression data.
Using hexamers to predict cis-regulatory motifs in Drosophila.
Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals.
Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data.
Modeling Sage data with a truncated gamma-Poisson model.
Tests for finding complex patterns of differential expression in cancers: towards individualized medicine.
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa.
Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA.
SPOC: A widely distributed domain associated with cancer, apoptosis and transcription.
An interactive tool for visualization of relationships between gene expression profiles.
Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE).
Extending the mutual information measure to rank inferred literature relationships.
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools.
Characterizing disease states from topological properties of transcriptional regulatory networks.
Enhanced protein domain discovery using taxonomy.
Entropy-based gene ranking without selection bias for the predictive classification of microarray data.
JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture.
Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR.
Development of an unbiased statistical method for the analysis of unigenic evolution.
A study of quality measures for protein threading models.
EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments.
Versatile and declarative dynamic programming using pair algebras.
Querying the public databases for sequences using complex keywords contained in the feature lines.
Instance-based concept learning from multiclass DNA microarray data.
Multipolar representation of protein structure.
Chaos game representation for comparison of whole genomes.
AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis.
A robust two-way semi-linear model for normalization of cDNA microarray data.
A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images.
An adaptive method for cDNA microarray normalization.
A functional hierarchical organization of the protein sequence space.
Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets.
The SGS3 protein involved in PTGS finds a family.
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.
Can Zipf's law be adapted to normalize microarrays?
Fast-Find: A novel computational approach to analyzing combinatorial motifs.
Simplifying gene trees for easier comprehension.
Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function.
Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach.
Chromosomal clustering of a human transcriptome reveals regulatory background.
Protein kinases associated with the yeast phosphoproteome.
Identification of significant periodic genes in microarray gene expression data.
Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries.
SimArray: a user-friendly and user-configurable microarray design tool.
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements.
Improvement of alignment accuracy utilizing sequentially conserved motifs.
GeneXplorer: an interactive web application for microarray data visualization and analysis.
ArrayQuest: a web resource for the analysis of DNA microarray data.
A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles.
Various criteria in the evaluation of biomedical named entity recognition.
Development and implementation of an algorithm for detection of protein complexes in large interaction networks.
Improved hit criteria for DNA local alignment.
Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins.
Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs.
A format for databasing and comparison of AFLP fingerprint profiles.
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis.
Accelerated probabilistic inference of RNA structure evolution.
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs.
VANTED: A system for advanced data analysis and visualization in the context of biological networks.
Reproducibility of gene expression across generations of Affymetrix microarrays.
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein.
GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease.
Optimizationof neural network architecture using genetic programming improvesdetection and modeling of gene-gene interactions in studies of humandiseases.
A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models.
ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations.
REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance.
stam - a Bioconductor compliant R package for structured analysis of microarray data.
Structural comparison of metabolic networks in selected single cell organisms.
MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences.
MB2Plasmodiumspecies has a unique combination of S1 and GTP-binding domains.
A Taxonomic Search Engine: Federating taxonomic databases using web services.
Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data.
t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies.
S-adenosylmethionine to three crystal structures.
Discriminative topological features reveal biological network mechanisms.
A power law global error model for the identification of differentially expressed genes in microarray data.
MolTalk - a programming library for protein structures and structure analysis.
SuperLigands - a database of ligand structures derived from the Protein Data Bank.
In silicodiscovery of human natural antisense transcripts.
SIMMAP: Stochastic character mapping of discrete traits on phylogenies.
Communication and re-use of chemical information in bioscience.
Alternative splicing and protein function.
A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions.
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics.
An empirical analysis of training protocols for probabilistic gene finders.
SUPFAM: A database of sequence superfamilies of protein domains.
The 3of5 web application for complex and comprehensive pattern matching in protein sequences.
Visualizing the genome: techniques for presenting human genome data and annotations.
An algorithm for mapping positively selected members of quasispecies-type viruses.
PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability.
Speeding disease gene discovery by sequence based candidate prioritization.
Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features.
GenomeViz: visualizing microbial genomes.
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution.
Detailed protein sequence alignment based on Spectral Similarity Score (SSS).
Fast and sensitive multiple alignment of large genomic sequences.
Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables.
The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource.
Are scale-free networks robust to measurement errors?
Sources of variation in Affymetrix microarray experiments.
Expression profiling of human renal carcinomas with functional taxonomic analysis.
GNU polyxmass: a software framework for mass spectrometric simulations of linear (bio-)polymeric analytes.
Linear fuzzy gene network models obtained from microarray data by exhaustive search.
Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering.
eL-DASionator: an LDAS upload file generator.
JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases.
Exploration of biological network centralities with CentiBiN.
SpectralNET - an application for spectral graph analysis and visualization.
Gene selection and classification of microarray data using random forest.
A simple method for assessing sample sizes in microarray experiments.
Transcriptomic response to differentiation induction.
In silicomicrodissection of microarray data from heterogeneous cell populations.
Ancestral sequence alignment under optimal conditions.
LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles.
Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiaebased on codon composition.
VKCDB: Voltage-gated potassium channel database.
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method.
2DDB - a bioinformatics solution for analysis of quantitative proteomics data.
The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks.
An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification.
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network.
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.
Correction: versatile and declarative dynamic programming using pair algebras.
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.
IsoSVM - Distinguishing isoforms and paralogs on the protein level.
Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis.
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server.
Applying dynamic Bayesian networks to perturbed gene expression data.
Improved prediction of critical residues for protein function based on network and phylogenetic analyses.
Effect of data normalization on fuzzy clustering of DNA microarray data.
A stable gene selection in microarray data analysis.
MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation.
A case study in pathway knowledgebase verification.
PREP-Mt: predictive RNA editor for plant mitochondrial genes.
Length-dependent prediction of protein intrinsic disorder.
Combining Affymetrix microarray results.
K-SPMM: a database of murine spermatogenic promoters modules & motifs.
A new mixture model approach to analyzing allelic-loss data using Bayes factors.
A novel method for prokaryotic promoter prediction based on DNA stability.
A comparative review of estimates of the proportion unchanged genes and the false discovery rate.
A two-stage approach for improved prediction of residue contact maps.
A double classification tree search algorithm for index SNP selection.
Storing, linking, and mining microarray databases using SRS.
Trustworthiness and metrics in visualizing similarity of gene expression.
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps.
Identification of consensus RNA secondary structures using suffix arrays.
Genome comparison without alignment using shortest unique substrings.
Satellog: A database for the identification and prioritization of satellite repeats in disease association studies.
Asynchronous adaptive time step in quantitative cellular automata modeling.
MASQOT: a method for cDNA microarray spot quality control.
pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files.
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins.
Bayesian detection of periodic mRNA time profiles without use of training examples.
The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD).
MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools.
mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.
Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis.
A factor analysis model for functional genomics.
Automation of gene assignments to metabolic pathways using high-throughput expression data.
AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.
NBLAST: a cluster variant of BLAST for NxN comparisons.
Processing methods for differential analysis of LC/MS profile data.
An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments.
ArrayD: A general purpose software for Microarray design.
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks.
CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting.
Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation.
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.
A SNP-centric database for the investigation of the human genome.
WebArray: an online platform for microarray data analysis.
A proposed metric for assessing the measurement quality of individual microarrays.
An Entropy-based gene selection method for cancer classification using microarray data.
Approaching the taxonomic affiliation of unidentified sequences in public databases - an example from the mycorrhizal fungi.
Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation.
PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine.
Feature selection for splice site prediction: A new method using EDA-based feature ranking.
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs.
Detection of transposable elements by their compositional bias.
Delayed impact: ISI's citation tracking choices are keeping scientists in the dark.
Cluster stability scores for microarray data in cancer studies.
The Gaggle: An open-source software system for integrating bioinformatics software and data sources.
EpiJen: a server for multistep T cell epitope prediction.
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability.
cDNA2Genome: A tool for mapping and annotating cDNAs.
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms.
Calibration and assessment of channel-specific biases in microarray data with extended dynamical range.
Escherichia colitranscriptional regulatory network.
Evolutionary sequence analysis of complete eukaryote genomes.
Approximation properties of haplotype tagging.
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.
Iterative approach to model identification of biological networks.
Visualising very large phylogenetic trees in three dimensional hyperbolic space.
Functional annotation by identification of local surface similarities: a novel tool for structural genomics.
FRAGS: estimation of coding sequence substitution rates from fragmentary data.
A normalization strategy applied to HiCEP (an AFLP-based expression profiling) analysis: Toward the strict alignment of valid fragments across electrophoretic patterns.
Computational models with thermodynamic and composition features improve siRNA design.
CARMA: A platform for analyzing microarray datasets that incorporate replicate measures.
FunSpec: a web-based cluster interpreter for yeast.
Multiscale Hy3S: Hybrid stochastic simulation for supercomputers.
Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling.
PASBio: predicate-argument structures for event extraction in molecular biology.
Iterative class discovery and feature selection using Minimal Spanning Trees.
A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationships: an application to papillomavirus DNA sequences.
WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.
Sequence variation in ligand binding sites in proteins.
Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery.
A comparative study of discriminating human heart failure etiology using gene expression profiles.
VisANT: an online visualization and analysis tool for biological interaction data.
Prediction of twin-arginine signal peptides.
A probabilistic model for the evolution of RNA structure.
Conservation of regulatory elements between two species of Drosophila.
Dissecting systems-wide data using mixture models: application to identify affected cellular processes.
Computing expectation values for RNA motifs using discrete convolutions.
Inconsistencies over time in 5% of NetAffx probe-to-gene annotations.
Computational protein biomarker prediction: a case study for prostate cancer.
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.
Using large-scale perturbations in gene network reconstruction.
Theme discovery from gene lists for identification and viewing of multiple functional groups.
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.
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).
Interaction profile-based protein classification of death domain.
Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking.
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.
INTEGRATOR: interactive graphical search of large protein interactomes over the Web.
Detecting overlapping coding sequences in virus genomes.
Visualization of comparative genomic analyses by BLAST score ratio.
An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage.
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information.
TmaDB: a repository for tissue microarray data.
Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).
Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences.
Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae.
Support Vector Machines for predicting protein structural class.
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions.
GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions.
Dynamic covariation between gene expression and proteome characteristics.
An integrated system for genetic analysis.
Frequent occurrence of recognition Site-like sequences in the restriction endonucleases.
Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays.
Detection of divergent genes in microbial aCGH experiments.
SuperMimic - Fitting peptide mimetics into protein structures.
Predicting population coverage of T-cell epitope-based diagnostics and vaccines.
Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases.
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications.
A structural study for the optimisation of functional motifs encoded in protein sequences.
Microarray results: how accurate are they?
Choosing the best heuristic for seeded alignment of DNA sequences.
Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation.
Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma.
CAGER: classification analysis of gene expression regulation using multiple information sources.
CGHPRO - A comprehensive data analysis tool for array CGH.
A note on generalized Genome Scan Meta-Analysis statistics.
Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.
Multivariate search for differentially expressed gene combinations.
XcisClique: analysis of regulatory bicliques.
A hidden Markov model approach for determining expression from genomic tiling micro arrays.
Proteins with two SUMO-like domains in chromatin-associated complexes: The RENi (Rad60-Esc2-NIP45) family.
Statistical distributions of optimal global alignment scores of random protein sequences.
Shortest triplet clustering: reconstructing large phylogenies using representative sets.
A multistep bioinformatic approach detects putative regulatory elements in gene promoters.
FOUNTAIN: A JAVA open-source package to assist large sequencing projects.
A web services choreography scenario for interoperating bioinformatics applications.
Feature selection and nearest centroid classification for protein mass spectrometry.
Integrating partonomic hierarchies in anatomy ontologies.
Extraction of phylogenetic network modules from the metabolic network.
Recent Hits Acquired by BLAST (ReHAB): A tool to identify new hits in sequence similarity searches.
GDRosaceae): integrated web resources for Rosaceae genomics and genetics research.
Array-A-Lizer: A serial DNA microarray quality analyzer.
Ontological visualization of protein-protein interactions.
Predicting functional sites with an automated algorithm suitable for heterogeneous datasets.
Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm.
Optimized LOWESS normalization parameter selection for DNA microarray data.
Evaluation of normalization methods for microarray data.
Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system.
Eval: A software package for analysis of genome annotations.
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes.
Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data.
Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment.
Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA.
Modeling of cell signaling pathways in macrophages by semantic networks.
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits.
The Use of Functional Domains to Improve Transmembrane Protein Topology Prediction.
J. Bioinformatics and Computational Biology
Discovering Protein-protein Interactions.
Heuristic Search in Constrained Bipartite Matching with Applications to Protein Nmr Backbone Resonance Assignment.
Automated Identification of Single Nucleotide Polymorphismsfrom Sequencing Data.
Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints.
Prediction of Protein Coarse Contact Maps.
Multiple Sequence Alignment Using an Exhaustive and Greedy Algorithm.
Dynamic Model-based Clustering for Time-course Gene Expression Data.
The Incomplete Perfect Phylogeny Haplotype Problem.
Identifying Patterns of Dna for Tumor Diagnosis Using Capillary Electrophoresis-amplified Fragment Length Polymorphism (ce-aflp) Screening.
Approximate Matching of Structured Motifs in Dna Sequences.
Cluster Analysis of Dynamic Parameters of Gene Expression.
Supersequences of Masks for Oligo-chips.
An Ancova Approach to Normalize Microarray Data, and its Performance to Existing Methods.
a PrioriContact Preferences in Molecular Recognition.
Cwinnower Algorithm for Finding Fuzzy Dna Motifs.
A Dimensionless Fit Measure for Phylogenetic Distance Trees.
Exploring Alternative Transcript Structure in the Humangenome Using Blocks and Interpro.
Active Site Prediction for Comparative Model Structures with Thematics.
A Statistical Framework for Haplotype Block Inference.
Coopps: a System for the Cooperative Prediction of Protein Structures.
A Theoretical Analysis of the Selection of Differentially Expressed Genes.
Prediction of Protein Subcellular Locations Using a New Measure of Information Discrepancy.
Erratum: Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics.
Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach.
Robustness, Stability and Efficiency of Phage lambda Genetic Switch: Dynamical Structure Analysis.
Rank-based Methods as a Non-parametric Alternative of the T-statistic for the Analysis of Biological Microarray Data.
Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models.
Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type-1.
Active Site Driven Ligand Design: an Evolutionary Approach.
Computing Highly Specific and Noise-tolerant Oligomers Efficiently.
Using Weighted Permutation Scores to Detect Differential Gene Expression with Microarray Data.
Robustness of Metabolic Map Reconstruction.
Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination.
Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks (supplementary Material).
Development of Image Processing Program for Yeast Cell Morphology.
Index-based Similarity Search for Protein Structure Databases.
Cubic: Identification of Regulatory Binding Sites through Data Clustering.
Improving Gene Network Inference by Comparing Expression Time-series across Species, Developmental Stages or Tissues.
An Integrated Feature Selection and Classification Method to Select Minimum Number of Variables on the Case Study of Gene Expression Data.
Clustering Gene Expression Data with Kernel Principal Components.
Predicting Risk of Coronary Artery Disease from Dna Microarray-based Genotyping Using Neural Networks and Other Statistical Analysis Tool.
An Interactive Tool for Extracting Exons and Snp from Genomic Sequence: Isolation of Hcn1 and Hcn3 Ion Channel Genes.
Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks.
Pops: a Computational Tool for Modeling and Predicting Protease Specificity.
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network.
Gene Function Prediction by a Combined Analysis of Gene Expression Data and Protein-protein Interaction Data.
Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering.
Determining Relevant Features to Recognize Electron Density Patterns in X-ray Protein Crystallography.
Protein Folding on the Hexagonal Lattice in the Hp Model.
Integration of Bioinformatics and Computational Biology to Understand Protein-dna Recognition Mechanism.
Use of Gene Networks for Identifying and Validating Drug Targets.
Bayesian Network Learning with Feature Abstraction for Gene-drug Dependency Analysis.
Pairwise Protein Structure Alignment Based on an Orientation-independent Backbone Representation.
Recognizing Complex, Asymmetric Functional Sites in Protein Structures Using a Bayesian Scoring Function.
Ruleminer: a Knowledge System for Supporting High-throughput Protein Function Annotations.
A New Regulatory Interaction Suggested by Simulations for Circadian Genetic Control Mechanism in Mammals.
Raptor: Optimal Protein Threading by Linear Programming.
Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets.
Improved Parameter Estimation for Variance-stabilizing Transformation of Gene-expression Microarray Data.
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks.
Searching for Transcription Factor Binding Site Clusters: How True Are True Positives?
Shannon Information in Complete Genomes.
Modeling and Simulation of Molecular Biology Systems Using Petri Nets: Modeling Goals of Various Approaches.
Patternhunter Ii: Highly Sensitive and Fast Homology Search.
Exploring Protein's Optimal Hp Configurations by Self-organizing Mapping.
Progressive Multiple Alignment Using Sequence Triplet Optimizations and Three-residue Exchange Costs.
Linear Independence of Pairwise Comparisons of Dna Microarray Data.
Reconstructing Genetic Networks from Time Ordered Gene Expression Data Using Bayesian Method with Global Search Algorithm.
Bioie: Retargetable Information Extraction and Ontological Annotation of Biological Interactions from the Literature.
Prima: Peptide Robust Identification from Ms/ms Spectra.
Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic Approach.
Complexity and Approximability of Double Digest.
Techniques for Optimization of Queries on Integrated Biological Resources.
Unique Peptide Identification of Rnasea Superfamily Sequences Based on Reinforced Merging Algorithms.
Support Vector Machines for Prediction and Analysis of Beta and Gamma-turns in Proteins.
A Wavelet Approach for the Analysis of Folding Trajectory of Protein Trp-cage.
Assessing the Impact of Predictive Biosimulation on Drug Discovery and Development.
A Hybrid Genetic Algorithm and Expectation Maximization Method for Global Gene Trajectory Clustering.
Generation of a Large Gene/protein Lexicon by Morphological Pattern Analysis.
in SilicoPhenotypic Screening Method of Mutants Based on Statistical Modeling of Genetically Mixed Samples.
Clustering and re-clustering for Pattern Discovery in Gene Expression Data.
A Tabu Search Algorithm for Post-processing Multiple Sequence Alignment.
Bioinformatics Meets Proteomics - Bridging the Gap between Massspectrometry Data Analysis and Cell Biology.
Prediction of Protein Secondary Structure Based on Residue Pairs.
Aligning Multiple Protein Structures by Deterministic Annealing.
Identifying Uniformly Mutated Segments within Repeats.
Histogram-based Scoring Schemes for Protein Nmr Resonance Assignment.
Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms.
A Tutorial on Markov Models Based on Mendel's Classical Experiments.
A Comprehensive Whole Genome Bacterial Phylogeny Using Correlated Peptide Motifs Defined in a High Dimensional Vector Space.
Kernel-based Self-organized Maps Trained with Supervised Bias for Gene Expression Data Analysis.
Covariation Analysis of Local Amino Acid Sequences in Recurrent Protein Local Structures.
Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function.
Valid: Validation of Protein Sequence Quality Based on Multiple Alignment Data.
Reduced Bio-basis Function Neural Networks for Protease Cleavage Site Prediction.
Conservation of Amino Acids into Multiple Alignments Involved in Pairwise Interactions in Three-dimensional Protein Structures.
Randomized Algorithms for Motif Detection.
Computational Strategies for Analyzing Data in Gene Expression Microarray Experiments.
High Torsional Energy Disulfides: Relationship between Cross-strand Disulfides and Right-handed Staples.
Characterization of the Splice Sites in Gt-ag and Gc-ag Introns in Higher Eukaryotes Using Full-length Cdnas.
Multiclass Molecular Cancer Classification by Kernel Subspace Methods with Effective Kernel Parameter Selection.
Dynamic Integration of Gene Annotation and its Application to Microarray Analysis.
Suregene, a Scalable System for Automated Term Disambiguation of Gene and Protein Names.
An Empirical Study of the Universal Chemical Key Algorithm for Assigning Unique Keys to Chemical Compounds.
arabidopsis in SilicoPhenotypic Analysis.
An Optimization Method for the Identification of Minimal Sets of Discriminating Gene Markers: Application to Cultivar Identification in Wheat.
Bteval: a Server for Evaluation of beta-turn Prediction Methods.
Noise-robust Soft Clustering of Gene Expression Time-course Data.
Systematic Variation Normalization in Microarray Data to Get Gene Expression Comparison Unbiased.
Computational Identification of Transcription Factors Involved in Early Cellular Response to a Stimulus.
Guest Editor's Introduction: Advanced Techniques for Bioinformatics.
Binding Matrix: a Novel Approach for Binding Site Recognition.
Genome Wide Identification of Dna Binding Motifs of Nodd-factor in Sinorhizobium Meliloti and Mesorhizobium Loti.
Developing Optimal Prediction Models for Cancer Classification Using Gene Expression Data.
Ancestral Maximum Likelihood of Evolutionary Trees Is Hard.
A Fast and Sensitive Algorithm for Aligning Ests to the Human Genome.
Decision Tree Based Information Integration for Automated Protein Classification.
Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data.
Hidden Markov Models, Grammars, and Biology: a Tutorial.
Protein Structure and Fold Prediction Using Tree-augmented Naïve Bayesian Classifier.
Adaptive Control of Hybridization Noise in Dna Sequencing-by-hybridization.
Neural Models for Predicting Viral Vaccine Targets.
The Probability Distribution for a Random Match between an Experimental-theoretical Spectral Pair in Tandem Mass Spectrometry.
Evolution of the Nadr Regulon in Enterobacteriaceae.
Algorithms for Challenging Motif Problems.
Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics.
Efficient Inference of Haplotypes from Genotypes on a Pedigree.
Effective Algorithms for Tag Snp Selection.
A Tutorial of Recent Developments in the Seeding of Local Alignment.
Data Mining Tools for Biological Sequences.
Integrated Statistical Analysis of Cdna Microarray and Nir Spectroscopic Data Applied to a Hemp Dataset.
Multivariate Entropy Distance Method for Prokaryotic Gene Identification.
Direct Prediction of T-cell Epitopes Using Support Vector Machines with Novel Sequence Encoding Schemes.
A Quantitative Analysis of Interfacial Amino Acid Conservation in Protein-protein Hetero Complexes.
A Robust Algorithm for Ratio Estimation in Two-color Microarray Experiments.
Optimal Spaced Seeds for Homologous Coding Regions.
Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information.
Dissecting the Human Spliceosome through Bioinformatics and Proteomics Approaches.
Protein Classification Using Comparative Molecular Interaction Profile Analysis System.
Identification of Biological Relationships from Text Documentsusing Efficient Computational Methods.
Discovery of Highly Differentiative Gene Groups from Microarray Gene Expression Data Using the Gene Club Approach.
Protein Structure Alignment and Fast Similarity Search Using Local Shape Signatures.
Clustering of Amino Acids for Protein Secondary Structure Prediction.