NestedMICA as an ab initio protein motif discovery tool. [Citation Graph (, )][DBLP]
LeARN: a platform for detecting, clustering and annotating non-coding RNAs. [Citation Graph (, )][DBLP]
Extension of the COG and arCOG databases by amino acid and nucleotide sequences. [Citation Graph (, )][DBLP]
Prediction of specificity-determining residues for small-molecule kinase inhibitors. [Citation Graph (, )][DBLP]
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. [Citation Graph (, )][DBLP]
Strategies for measuring evolutionary conservation of RNA secondary structures. [Citation Graph (, )][DBLP]
Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. [Citation Graph (, )][DBLP]
Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins. [Citation Graph (, )][DBLP]
Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs. [Citation Graph (, )][DBLP]
PatternLab for proteomics: a tool for differential shotgun proteomics. [Citation Graph (, )][DBLP]
MetaMine - A tool to detect and analyse gene patterns in their environmental context. [Citation Graph (, )][DBLP]
Prediction of the outcome of preoperative chemotherapy in breast cancer using DNA probes that provide information on both complete and incomplete responses. [Citation Graph (, )][DBLP]
Flexible boosting of accelerated failure time models. [Citation Graph (, )][DBLP]
The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. [Citation Graph (, )][DBLP]
Highly accurate sigmoidal fitting of real-time PCR data by introducing a parameter for asymmetry. [Citation Graph (, )][DBLP]
Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures. [Citation Graph (, )][DBLP]
A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. [Citation Graph (, )][DBLP]
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. [Citation Graph (, )][DBLP]
Structural assembly of two-domain proteins by rigid-body docking. [Citation Graph (, )][DBLP]
Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification. [Citation Graph (, )][DBLP]
A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays. [Citation Graph (, )][DBLP]
Assessing probe-specific dye and slide biases in two-color microarray data. [Citation Graph (, )][DBLP]
Envelope: interactive software for modeling and fitting complex isotope distributions. [Citation Graph (, )][DBLP]
PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies. [Citation Graph (, )][DBLP]
Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data. [Citation Graph (, )][DBLP]
caBIGTM VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data. [Citation Graph (, )][DBLP]
FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects. [Citation Graph (, )][DBLP]
Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. [Citation Graph (, )][DBLP]
Automatic detection of exonic splicing enhancers (ESEs) using SVMs. [Citation Graph (, )][DBLP]
Effects of dependence in high-dimensional multiple testing problems. [Citation Graph (, )][DBLP]
A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data. [Citation Graph (, )][DBLP]
The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences. [Citation Graph (, )][DBLP]
Interrogating domain-domain interactions with parsimony based approaches. [Citation Graph (, )][DBLP]
Fregene: Simulation of realistic sequence-level data in populations and ascertained samples. [Citation Graph (, )][DBLP]
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. [Citation Graph (, )][DBLP]
Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification. [Citation Graph (, )][DBLP]
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. [Citation Graph (, )][DBLP]
Computational evaluation of TIS annotation for prokaryotic genomes. [Citation Graph (, )][DBLP]
Partial mixture model for tight clustering of gene expression time-course. [Citation Graph (, )][DBLP]
MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level. [Citation Graph (, )][DBLP]
SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes. [Citation Graph (, )][DBLP]
A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips. [Citation Graph (, )][DBLP]
Towards an automatic classification of protein structural domains based on structural similarity. [Citation Graph (, )][DBLP]
Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. [Citation Graph (, )][DBLP]
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. [Citation Graph (, )][DBLP]
Clustering exact matches of pairwise sequence alignments by weighted linear regression. [Citation Graph (, )][DBLP]
A simplified approach to disulfide connectivity prediction from protein sequences. [Citation Graph (, )][DBLP]
Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis. [Citation Graph (, )][DBLP]
Optimizations for the EcoPod field identification tool. [Citation Graph (, )][DBLP]
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions. [Citation Graph (, )][DBLP]
Fuzzy association rules for biological data analysis: A case study on yeast. [Citation Graph (, )][DBLP]
A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles. [Citation Graph (, )][DBLP]
Large-scale identification of polymorphic microsatellites using an in silico approach. [Citation Graph (, )][DBLP]
Parameter estimation for robust HMM analysis of ChIP-chip data. [Citation Graph (, )][DBLP]
Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats. [Citation Graph (, )][DBLP]
Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data. [Citation Graph (, )][DBLP]
How reliably can we predict the reliability of protein structure predictions? [Citation Graph (, )][DBLP]
Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. [Citation Graph (, )][DBLP]
An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments. [Citation Graph (, )][DBLP]
t2prhd: a tool to study the patterns of repeat evolution. [Citation Graph (, )][DBLP]
Gene prediction in metagenomic fragments: A large scale machine learning approach. [Citation Graph (, )][DBLP]
Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data. [Citation Graph (, )][DBLP]
ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use. [Citation Graph (, )][DBLP]
CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments. [Citation Graph (, )][DBLP]
LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method. [Citation Graph (, )][DBLP]
GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique. [Citation Graph (, )][DBLP]
A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics. [Citation Graph (, )][DBLP]
SynBlast: Assisting the analysis of conserved synteny information. [Citation Graph (, )][DBLP]
Computational identification of ubiquitylation sites from protein sequences. [Citation Graph (, )][DBLP]
Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments. [Citation Graph (, )][DBLP]
The combination approach of SVM and ECOC for powerful identification and classification of transcription factor. [Citation Graph (, )][DBLP]
Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis. [Citation Graph (, )][DBLP]
VariVis: a visualisation toolkit for variation databases. [Citation Graph (, )][DBLP]
MetaboMiner - semi-automated identification of metabolites from 2D NMR spectra of complex biofluids. [Citation Graph (, )][DBLP]
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. [Citation Graph (, )][DBLP]
Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models? [Citation Graph (, )][DBLP]
GraphCrunch: A tool for large network analyses. [Citation Graph (, )][DBLP]
A gene pattern mining algorithm using interchangeable gene sets for prokaryotes. [Citation Graph (, )][DBLP]
A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards. [Citation Graph (, )][DBLP]
PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes. [Citation Graph (, )][DBLP]
A simple and fast heuristic for protein structure comparison. [Citation Graph (, )][DBLP]
A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions. [Citation Graph (, )][DBLP]
Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling. [Citation Graph (, )][DBLP]
OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature. [Citation Graph (, )][DBLP]
Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments. [Citation Graph (, )][DBLP]
Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation. [Citation Graph (, )][DBLP]
Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy. [Citation Graph (, )][DBLP]
A nonparametric model for quality control of database search results in shotgun proteomics. [Citation Graph (, )][DBLP]
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. [Citation Graph (, )][DBLP]
Prediction of protein-protein binding site by using core interface residue and support vector machine. [Citation Graph (, )][DBLP]
Highly sensitive feature detection for high resolution LC/MS. [Citation Graph (, )][DBLP]
miRNAminer: A tool for homologous microRNA gene search. [Citation Graph (, )][DBLP]
Snagger: A user-friendly program for incorporating additional information for tagSNP selection. [Citation Graph (, )][DBLP]
Kismeth: Analyzer of plant methylation states through bisulfite sequencing. [Citation Graph (, )][DBLP]
Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. [Citation Graph (, )][DBLP]
Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens. [Citation Graph (, )][DBLP]
MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data. [Citation Graph (, )][DBLP]
Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking. [Citation Graph (, )][DBLP]
Assessment of composite motif discovery methods. [Citation Graph (, )][DBLP]
MSDmotif: exploring protein sites and motifs. [Citation Graph (, )][DBLP]
HAPSIMU: a genetic simulation platform for population-based association studies. [Citation Graph (, )][DBLP]
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. [Citation Graph (, )][DBLP]
Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles. [Citation Graph (, )][DBLP]
Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases. [Citation Graph (, )][DBLP]
Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. [Citation Graph (, )][DBLP]
PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data. [Citation Graph (, )][DBLP]
Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data. [Citation Graph (, )][DBLP]
Allowing for mandatory covariates in boosting estimation of sparse high-dimensional survival models. [Citation Graph (, )][DBLP]
Background correction using dinucleotide affinities improves the performance of GCRMA. [Citation Graph (, )][DBLP]
K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space. [Citation Graph (, )][DBLP]
High-precision high-coverage functional inference from integrated data sources. [Citation Graph (, )][DBLP]
A genetic approach for building different alphabets for peptide and protein classification. [Citation Graph (, )][DBLP]
A copula method for modeling directional dependence of genes. [Citation Graph (, )][DBLP]
Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools. [Citation Graph (, )][DBLP]
Gene set analyses for interpreting microarray experiments on prokaryotic organisms. [Citation Graph (, )][DBLP]
CBESW: Sequence Alignment on the Playstation 3. [Citation Graph (, )][DBLP]
Statistical methodology for the analysis of dye-switch microarray experiments. [Citation Graph (, )][DBLP]
Chromhome: A rich internet application for accessing comparative chromosome homology maps. [Citation Graph (, )][DBLP]
High-throughput bioinformatics with the Cyrille2 pipeline system. [Citation Graph (, )][DBLP]
MetaMQAP: A meta-server for the quality assessment of protein models. [Citation Graph (, )][DBLP]
JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. [Citation Graph (, )][DBLP]
uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts. [Citation Graph (, )][DBLP]
A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis. [Citation Graph (, )][DBLP]
Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory. [Citation Graph (, )][DBLP]
Bayesian modeling of recombination events in bacterial populations. [Citation Graph (, )][DBLP]
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. [Citation Graph (, )][DBLP]
Conditional variable importance for random forests. [Citation Graph (, )][DBLP]
Mining protein networks for synthetic genetic interactions. [Citation Graph (, )][DBLP]
Response projected clustering for direct association with physiological and clinical response data. [Citation Graph (, )][DBLP]
minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information. [Citation Graph (, )][DBLP]
Compressing DNA sequence databases with coil. [Citation Graph (, )][DBLP]
ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). [Citation Graph (, )][DBLP]
SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis. [Citation Graph (, )][DBLP]
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis. [Citation Graph (, )][DBLP]
Abbreviation definition identification based on automatic precision estimates. [Citation Graph (, )][DBLP]
A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations. [Citation Graph (, )][DBLP]
Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster. [Citation Graph (, )][DBLP]
Improving protein function prediction methods with integrated literature data. [Citation Graph (, )][DBLP]
Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features. [Citation Graph (, )][DBLP]
Microarray-based gene set analysis: a comparison of current methods. [Citation Graph (, )][DBLP]
catmap: Case-control And TDT Meta-Analysis Package. [Citation Graph (, )][DBLP]
PEPOP: Computational design of immunogenic peptides. [Citation Graph (, )][DBLP]
Methods for evaluating gene expression from Affymetrix microarray datasets. [Citation Graph (, )][DBLP]
The meaning of alignment: lessons from structural diversity. [Citation Graph (, )][DBLP]
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. [Citation Graph (, )][DBLP]
H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments. [Citation Graph (, )][DBLP]
Gene set enrichment analysis for non-monotone association and multiple experimental categories. [Citation Graph (, )][DBLP]
OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. [Citation Graph (, )][DBLP]
Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs. [Citation Graph (, )][DBLP]
Stability of gene contributions and identification of outliers in multivariate analysis of microarray data. [Citation Graph (, )][DBLP]
A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins. [Citation Graph (, )][DBLP]
CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies. [Citation Graph (, )][DBLP]
CellProfiler Analyst: data exploration and analysis software for complex image-based screens. [Citation Graph (, )][DBLP]
Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. [Citation Graph (, )][DBLP]
Discovering biclusters in gene expression data based on high-dimensional linear geometries. [Citation Graph (, )][DBLP]
Validation of protein models by a neural network approach. [Citation Graph (, )][DBLP]
Virtual screening of GPCRs: An in silico chemogenomics approach. [Citation Graph (, )][DBLP]
Clustering cancer gene expression data: a comparative study. [Citation Graph (, )][DBLP]
Integration of relational and hierarchical network information for protein function prediction. [Citation Graph (, )][DBLP]
SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles. [Citation Graph (, )][DBLP]
Precise detection of rearrangement breakpoints in mammalian chromosomes. [Citation Graph (, )][DBLP]
anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. [Citation Graph (, )][DBLP]
GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors. [Citation Graph (, )][DBLP]
A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics. [Citation Graph (, )][DBLP]
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach. [Citation Graph (, )][DBLP]
Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. [Citation Graph (, )][DBLP]
RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays. [Citation Graph (, )][DBLP]
Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons. [Citation Graph (, )][DBLP]
Presenting and exploring biological pathways with PathVisio. [Citation Graph (, )][DBLP]
Shape-IT: new rapid and accurate algorithm for haplotype inference. [Citation Graph (, )][DBLP]
Improving peptide-MHC class I binding prediction for unbalanced datasets. [Citation Graph (, )][DBLP]
Enhancing the prediction of protein pairings between interacting families using orthology information. [Citation Graph (, )][DBLP]
SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data. [Citation Graph (, )][DBLP]
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions. [Citation Graph (, )][DBLP]
Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. [Citation Graph (, )][DBLP]
RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences. [Citation Graph (, )][DBLP]
Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection. [Citation Graph (, )][DBLP]
Identifying differential correlation in gene/pathway combinations. [Citation Graph (, )][DBLP]
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. [Citation Graph (, )][DBLP]
Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems. [Citation Graph (, )][DBLP]
Integrated multi-level quality control for proteomic profiling studies using mass spectrometry. [Citation Graph (, )][DBLP]
AccPbFRET: An ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images. [Citation Graph (, )][DBLP]
Impact of residue accessible surface area on the prediction of protein secondary structures. [Citation Graph (, )][DBLP]
SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences. [Citation Graph (, )][DBLP]
Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores. [Citation Graph (, )][DBLP]
Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction. [Citation Graph (, )][DBLP]
A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data. [Citation Graph (, )][DBLP]
A new method for class prediction based on signed-rank algorithms applied to Affymetrix® microarray experiments. [Citation Graph (, )][DBLP]
Prediction of enzyme function by combining sequence similarity and protein interactions. [Citation Graph (, )][DBLP]
Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data. [Citation Graph (, )][DBLP]
mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences. [Citation Graph (, )][DBLP]
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. [Citation Graph (, )][DBLP]
Corpus annotation for mining biomedical events from literature. [Citation Graph (, )][DBLP]
ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences. [Citation Graph (, )][DBLP]
Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain. [Citation Graph (, )][DBLP]
CMA - a comprehensive Bioconductor package for supervised classification with high dimensional data. [Citation Graph (, )][DBLP]
Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments. [Citation Graph (, )][DBLP]
Optimal neighborhood indexing for protein similarity search. [Citation Graph (, )][DBLP]
Feature selection environment for genomic applications. [Citation Graph (, )][DBLP]
Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable. [Citation Graph (, )][DBLP]
Alignment of protein structures in the presence of domain motions. [Citation Graph (, )][DBLP]
A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation. [Citation Graph (, )][DBLP]
BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments. [Citation Graph (, )][DBLP]
Ranking analysis of F-statistics for microarray data. [Citation Graph (, )][DBLP]
A fast structural multiple alignment method for long RNA sequences. [Citation Graph (, )][DBLP]
PDTD: a web-accessible protein database for drug target identification. [Citation Graph (, )][DBLP]
Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations. [Citation Graph (, )][DBLP]
Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces. [Citation Graph (, )][DBLP]
The C1C2: A framework for simultaneous model selection and assessment. [Citation Graph (, )][DBLP]
DBMLoc: a Database of proteins with multiple subcellular localizations. [Citation Graph (, )][DBLP]
Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction. [Citation Graph (, )][DBLP]
Evaluation of two methods for computational HLA haplotypes inference using a real dataset. [Citation Graph (, )][DBLP]
Statistical issues in the analysis of Illumina data. [Citation Graph (, )][DBLP]
A comparison of four clustering methods for brain expression microarray data. [Citation Graph (, )][DBLP]
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. [Citation Graph (, )][DBLP]
Mining phenotypes for gene function prediction. [Citation Graph (, )][DBLP]
Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions. [Citation Graph (, )][DBLP]
Nuclear staining and relative distance for quantifying epidermal differentiation in biomarker expression profiling. [Citation Graph (, )][DBLP]
I-TASSER server for protein 3D structure prediction. [Citation Graph (, )][DBLP]
Structural descriptor database: a new tool for sequence-based functional site prediction. [Citation Graph (, )][DBLP]
13C labeling experiments at metabolic nonstationary conditions: An exploratory study. [Citation Graph (, )][DBLP]
Probe signal correction for differential methylation hybridization experiments. [Citation Graph (, )][DBLP]
Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis. [Citation Graph (, )][DBLP]
Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA). [Citation Graph (, )][DBLP]
A Java-based tool for the design of classification microarrays. [Citation Graph (, )][DBLP]
A perl package and an alignment tool for phylogenetic networks. [Citation Graph (, )][DBLP]
Determining gene expression on a single pair of microarrays. [Citation Graph (, )][DBLP]
Predicting cancer involvement of genes from heterogeneous data. [Citation Graph (, )][DBLP]
Testing gene set enrichment for subset of genes: Sub-GSE. [Citation Graph (, )][DBLP]
c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression. [Citation Graph (, )][DBLP]
A mixture model approach to sample size estimation in two-sample comparative microarray experiments. [Citation Graph (, )][DBLP]
Subfamily specific conservation profiles for proteins based on n-gram patterns. [Citation Graph (, )][DBLP]
Deducing topology of protein-protein interaction networks from experimentally measured sub-networks. [Citation Graph (, )][DBLP]
Sequence based residue depth prediction using evolutionary information and predicted secondary structure. [Citation Graph (, )][DBLP]
M-BISON: Microarray-based integration of data sources using networks. [Citation Graph (, )][DBLP]
An efficient visualization tool for the analysis of protein mutation matrices. [Citation Graph (, )][DBLP]
Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes. [Citation Graph (, )][DBLP]
An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance. [Citation Graph (, )][DBLP]
Extended Newick: it is time for a standard representation of phylogenetic networks. [Citation Graph (, )][DBLP]
Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides. [Citation Graph (, )][DBLP]
SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. [Citation Graph (, )][DBLP]
Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. [Citation Graph (, )][DBLP]
A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods. [Citation Graph (, )][DBLP]
Mixture models for analysis of melting temperature data. [Citation Graph (, )][DBLP]
New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background. [Citation Graph (, )][DBLP]
MScanner: a classifier for retrieving Medline citations. [Citation Graph (, )][DBLP]
A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time. [Citation Graph (, )][DBLP]
AnEnPi: identification and annotation of analogous enzymes. [Citation Graph (, )][DBLP]
Evolutionary Pareto-optimization of stably folding peptides. [Citation Graph (, )][DBLP]
MiMiR - an integrated platform for microarray data sharing, mining and analysis. [Citation Graph (, )][DBLP]
SODa: An Mn/Fe superoxide dismutase prediction and design server. [Citation Graph (, )][DBLP]
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. [Citation Graph (, )][DBLP]
TOBFAC: the database of tobacco transcription factors. [Citation Graph (, )][DBLP]
SPIKE - a database, visualization and analysis tool of cellular signaling pathways. [Citation Graph (, )][DBLP]
Combining transcriptional datasets using the generalized singular value decomposition. [Citation Graph (, )][DBLP]
Investigating selection on viruses: a statistical alignment approach. [Citation Graph (, )][DBLP]
Information transfer in signaling pathways: A study using coupled simulated and experimental data. [Citation Graph (, )][DBLP]
Protein contact order prediction from primary sequences. [Citation Graph (, )][DBLP]
Stability analysis of mixtures of mutagenetic trees. [Citation Graph (, )][DBLP]
BibGlimpse: The case for a light-weight reprint manager in distributed literature research. [Citation Graph (, )][DBLP]
Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem. [Citation Graph (, )][DBLP]
Functional discrimination of membrane proteins using machine learning techniques. [Citation Graph (, )][DBLP]
Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data. [Citation Graph (, )][DBLP]
Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites. [Citation Graph (, )][DBLP]
An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast. [Citation Graph (, )][DBLP]
A new protein linear motif benchmark for multiple sequence alignment software. [Citation Graph (, )][DBLP]
Major copy proportion analysis of tumor samples using SNP arrays. [Citation Graph (, )][DBLP]
Missing value imputation improves clustering and interpretation of gene expression microarray data. [Citation Graph (, )][DBLP]
Pathological rate matrices: from primates to pathogens. [Citation Graph (, )][DBLP]
MetWAMer: eukaryotic translation initiation site prediction. [Citation Graph (, )][DBLP]
Defining functional distances over Gene Ontology. [Citation Graph (, )][DBLP]
SciDBMaker: new software for computer-aided design of specialized biological databases. [Citation Graph (, )][DBLP]
VisualRepbase: an interface for the study of occurrences of transposable element families. [Citation Graph (, )][DBLP]
Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration. [Citation Graph (, )][DBLP]
Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions. [Citation Graph (, )][DBLP]
A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data. [Citation Graph (, )][DBLP]
ElliPro: a new structure-based tool for the prediction of antibody epitopes. [Citation Graph (, )][DBLP]
BatchPrimer3: A high throughput web application for PCR and sequencing primer design. [Citation Graph (, )][DBLP]
iRefIndex: A consolidated protein interaction database with provenance. [Citation Graph (, )][DBLP]
Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation. [Citation Graph (, )][DBLP]
annot8r: GO, EC and KEGG annotation of EST datasets. [Citation Graph (, )][DBLP]
CompMoby: Comparative MobyDick for detection of cis-regulatory motifs. [Citation Graph (, )][DBLP]
Inferring the role of transcription factors in regulatory networks. [Citation Graph (, )][DBLP]
Efficient computation of absent words in genomic sequences. [Citation Graph (, )][DBLP]
Modularization of biochemical networks based on classification of Petri net t-invariants. [Citation Graph (, )][DBLP]
Prioritization of gene regulatory interactions from large-scale modules in yeast. [Citation Graph (, )][DBLP]
Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure. [Citation Graph (, )][DBLP]
SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. [Citation Graph (, )][DBLP]
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. [Citation Graph (, )][DBLP]
An incremental approach to automated protein localisation. [Citation Graph (, )][DBLP]
Using the longest significance run to estimate region-specific p-values in genetic association mapping studies. [Citation Graph (, )][DBLP]
poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening. [Citation Graph (, )][DBLP]
MausDB: An open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects. [Citation Graph (, )][DBLP]
ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data. [Citation Graph (, )][DBLP]
Predicting biological system objectives de novo from internal state measurements. [Citation Graph (, )][DBLP]
Adaptive diffusion kernel learning from biological networks for protein function prediction. [Citation Graph (, )][DBLP]
Normalization for triple-target microarray experiments. [Citation Graph (, )][DBLP]
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. [Citation Graph (, )][DBLP]
The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks. [Citation Graph (, )][DBLP]
Visualizing and clustering high throughput sub-cellular localization imaging. [Citation Graph (, )][DBLP]
GBParsy: A GenBank flatfile parser library with high speed. [Citation Graph (, )][DBLP]
Studying the functional conservation of cis-regulatory modules and their transcriptional output. [Citation Graph (, )][DBLP]
Merging microarray data from separate breast cancer studies provides a robust prognostic test. [Citation Graph (, )][DBLP]
Towards a lightweight generic computational grid framework for biological research. [Citation Graph (, )][DBLP]
Combining classifiers for improved classification of proteins from sequence or structure. [Citation Graph (, )][DBLP]
A novel representation of RNA secondary structure based on element-contact graphs. [Citation Graph (, )][DBLP]
Use of normalization methods for analysis of microarrays containing a high degree of gene effects. [Citation Graph (, )][DBLP]
IDEA: Interactive Display for Evolutionary Analyses. [Citation Graph (, )][DBLP]
Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient. [Citation Graph (, )][DBLP]
OpenMS - An open-source software framework for mass spectrometry. [Citation Graph (, )][DBLP]
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. [Citation Graph (, )][DBLP]
PURE: A webserver for the prediction of domains in unassigned regions in proteins. [Citation Graph (, )][DBLP]
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family. [Citation Graph (, )][DBLP]
Gene and pathway identification with Lp penalized Bayesian logistic regression. [Citation Graph (, )][DBLP]
Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands. [Citation Graph (, )][DBLP]
Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information. [Citation Graph (, )][DBLP]
SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase. [Citation Graph (, )][DBLP]
Prediction of regulatory elements in mammalian genomes using chromatin signatures. [Citation Graph (, )][DBLP]
AWclust: point-and-click software for non-parametric population structure analysis. [Citation Graph (, )][DBLP]
Comparative optimism in models involving both classical clinical and gene expression information. [Citation Graph (, )][DBLP]
TiGER: A database for tissue-specific gene expression and regulation. [Citation Graph (, )][DBLP]
A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition. [Citation Graph (, )][DBLP]
Prediction of TF target sites based on atomistic models of protein-DNA complexes. [Citation Graph (, )][DBLP]
Empirical Bayes models for multiple probe type microarrays at the probe level. [Citation Graph (, )][DBLP]
LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. [Citation Graph (, )][DBLP]
Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes. [Citation Graph (, )][DBLP]
A dynamic Bayesian network approach to protein secondary structure prediction. [Citation Graph (, )][DBLP]
EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries. [Citation Graph (, )][DBLP]
SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool. [Citation Graph (, )][DBLP]
Automating dChip: toward reproducible sharing of microarray data analysis. [Citation Graph (, )][DBLP]
Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis. [Citation Graph (, )][DBLP]
Generating samples for association studies based on HapMap data. [Citation Graph (, )][DBLP]
Systematic identification of yeast cell cycle transcription factors using multiple data sources. [Citation Graph (, )][DBLP]
PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval. [Citation Graph (, )][DBLP]
Supervised inference of gene-regulatory networks. [Citation Graph (, )][DBLP]
Protein structure search and local structure characterization. [Citation Graph (, )][DBLP]
Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles. [Citation Graph (, )][DBLP]
Natural computation meta-heuristics for the in silico optimization of microbial strains. [Citation Graph (, )][DBLP]
Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. [Citation Graph (, )][DBLP]
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation. [Citation Graph (, )][DBLP]
Methodology capture: discriminating between the "best" and the rest of community practice. [Citation Graph (, )][DBLP]
MeInfoText: associated gene methylation and cancer information from text mining. [Citation Graph (, )][DBLP]
The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. [Citation Graph (, )][DBLP]
StAR: a simple tool for the statistical comparison of ROC curves. [Citation Graph (, )][DBLP]
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays. [Citation Graph (, )][DBLP]
VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens. [Citation Graph (, )][DBLP]
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast. [Citation Graph (, )][DBLP]
EzArray: A web-based highly automated Affymetrix expression array data management and analysis system. [Citation Graph (, )][DBLP]
A Population Proportion approach for ranking differentially expressed genes. [Citation Graph (, )][DBLP]
Local conservation scores without a priori assumptions on neutral substitution rates. [Citation Graph (, )][DBLP]
SNPFile - A software library and file format for large scale association mapping and population genetics studies. [Citation Graph (, )][DBLP]
Missing value imputation for microarray gene expression data using histone acetylation information. [Citation Graph (, )][DBLP]
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening. [Citation Graph (, )][DBLP]
ConStruct: Improved construction of RNA consensus structures. [Citation Graph (, )][DBLP]
New resampling method for evaluating stability of clusters. [Citation Graph (, )][DBLP]
Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks. [Citation Graph (, )][DBLP]
Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes. [Citation Graph (, )][DBLP]
A novel method for high accuracy sumoylation site prediction from protein sequences. [Citation Graph (, )][DBLP]
easyExon - A Java-based GUI tool for processing and visualization of Affymetrix exon array data. [Citation Graph (, )][DBLP]
Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics. [Citation Graph (, )][DBLP]
EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management. [Citation Graph (, )][DBLP]
Determining significance of pairwise co-occurrences of events in bursty sequences. [Citation Graph (, )][DBLP]
LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens. [Citation Graph (, )][DBLP]
Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis. [Citation Graph (, )][DBLP]
Extraction of semantic biomedical relations from text using conditional random fields. [Citation Graph (, )][DBLP]
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure. [Citation Graph (, )][DBLP]
Classification of drug molecules considering their IC50 values using mixed-integer linear programming based hyper-boxes method. [Citation Graph (, )][DBLP]
GENOMEPOP: A program to simulate genomes in populations. [Citation Graph (, )][DBLP]
Systems biology driven software design for the research enterprise. [Citation Graph (, )][DBLP]
PocketMatch: A new algorithm to compare binding sites in protein structures. [Citation Graph (, )][DBLP]
Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations. [Citation Graph (, )][DBLP]
SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis. [Citation Graph (, )][DBLP]
A unified approach to false discovery rate estimation. [Citation Graph (, )][DBLP]
Building pathway clusters from Random Forests classification using class votes. [Citation Graph (, )][DBLP]
Improved identification of conserved cassette exons using Bayesian networks. [Citation Graph (, )][DBLP]
Variable selection for large p small n regression models with incomplete data: Mapping QTL with epistases. [Citation Graph (, )][DBLP]
A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. [Citation Graph (, )][DBLP]
PhySIC_IST: cleaning source trees to infer more informative supertrees. [Citation Graph (, )][DBLP]
Significance analysis of microarray for relative quantitation of LC/MS data in proteomics. [Citation Graph (, )][DBLP]
SQUAT: A web tool to mine human, murine and avian SAGE data. [Citation Graph (, )][DBLP]
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. [Citation Graph (, )][DBLP]
A simple and robust method for connecting small-molecule drugs using gene-expression signatures. [Citation Graph (, )][DBLP]
Identification of a small optimal subset of CpG sites as bio-markers from high-throughput DNA methylation profiles. [Citation Graph (, )][DBLP]
GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed. [Citation Graph (, )][DBLP]
Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset. [Citation Graph (, )][DBLP]
FCI: an R-based algorithm for evaluating uncertainty of absolute real-time PCR quantification. [Citation Graph (, )][DBLP]
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. [Citation Graph (, )][DBLP]
Predicting protein linkages in bacteria: Which method is best depends on task. [Citation Graph (, )][DBLP]
The Average Mutual Information Profile as a Genomic Signature. [Citation Graph (, )][DBLP]
A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge. [Citation Graph (, )][DBLP]
Gene Ontology term overlap as a measure of gene functional similarity. [Citation Graph (, )][DBLP]
Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols. [Citation Graph (, )][DBLP]
Relating gene expression data on two-component systems to functional annotations in Escherichia coli. [Citation Graph (, )][DBLP]
Binning sequences using very sparse labels within a metagenome. [Citation Graph (, )][DBLP]
In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites. [Citation Graph (, )][DBLP]
A perspective for biomedical data integration: Design of databases for flow cytometry. [Citation Graph (, )][DBLP]
Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes. [Citation Graph (, )][DBLP]
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. [Citation Graph (, )][DBLP]
Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. [Citation Graph (, )][DBLP]
Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. [Citation Graph (, )][DBLP]
Discovering gene annotations in biomedical text databases. [Citation Graph (, )][DBLP]
SCOWLP classification: Structural comparison and analysis of protein binding regions. [Citation Graph (, )][DBLP]
GenomeMatcher: A graphical user interface for DNA sequence comparison. [Citation Graph (, )][DBLP]
SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics. [Citation Graph (, )][DBLP]
E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). [Citation Graph (, )][DBLP]
A machine vision system for automated non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification. [Citation Graph (, )][DBLP]
Semantic role labeling for protein transport predicates. [Citation Graph (, )][DBLP]
A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information. [Citation Graph (, )][DBLP]
The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem. [Citation Graph (, )][DBLP]
An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories. [Citation Graph (, )][DBLP]
Novel methodology for construction and pruning of quasi-median networks. [Citation Graph (, )][DBLP]
CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. [Citation Graph (, )][DBLP]
FERN - a Java framework for stochastic simulation and evaluation of reaction networks. [Citation Graph (, )][DBLP]
Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method. [Citation Graph (, )][DBLP]
NullHap - a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of null alleles. [Citation Graph (, )][DBLP]
ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins. [Citation Graph (, )][DBLP]
Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'. [Citation Graph (, )][DBLP]
Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge. [Citation Graph (, )][DBLP]
Using a logical model to predict the growth of yeast. [Citation Graph (, )][DBLP]
Reranking candidate gene models with cross-species comparison for improved gene prediction. [Citation Graph (, )][DBLP]
"TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis. [Citation Graph (, )][DBLP]
TileQC: A system for tile-based quality control of Solexa data. [Citation Graph (, )][DBLP]
Empirical Bayes analysis of single nucleotide polymorphisms. [Citation Graph (, )][DBLP]
Improved machine learning method for analysis of gas phase chemistry of peptides. [Citation Graph (, )][DBLP]
GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach. [Citation Graph (, )][DBLP]
AMYPdb: A database dedicated to amyloid precursor proteins. [Citation Graph (, )][DBLP]
EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration. [Citation Graph (, )][DBLP]
Probabilistic base calling of Solexa sequencing data. [Citation Graph (, )][DBLP]
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model. [Citation Graph (, )][DBLP]
Synonym set extraction from the biomedical literature by lexical pattern discovery. [Citation Graph (, )][DBLP]
A high-throughput pipeline for designing microarray-based pathogen diagnostic assays. [Citation Graph (, )][DBLP]
Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies. [Citation Graph (, )][DBLP]
CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions. [Citation Graph (, )][DBLP]
Multidimensional scaling for large genomic data sets. [Citation Graph (, )][DBLP]
Algorithm of OMA for large-scale orthology inference. [Citation Graph (, )][DBLP]
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. [Citation Graph (, )][DBLP]
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. [Citation Graph (, )][DBLP]
Microarray data mining using landmark gene-guided clustering. [Citation Graph (, )][DBLP]
Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization. [Citation Graph (, )][DBLP]
2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments. [Citation Graph (, )][DBLP]
Estimating the size of the solution space of metabolic networks. [Citation Graph (, )][DBLP]
Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. [Citation Graph (, )][DBLP]
Multi-label literature classification based on the Gene Ontology graph. [Citation Graph (, )][DBLP]
Exon level integration of proteomics and microarray data. [Citation Graph (, )][DBLP]
A relation based measure of semantic similarity for Gene Ontology annotations. [Citation Graph (, )][DBLP]
Position dependent mismatch discrimination on DNA microarrays - experiments and model. [Citation Graph (, )][DBLP]
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. [Citation Graph (, )][DBLP]
WGCNA: an R package for weighted correlation network analysis. [Citation Graph (, )][DBLP]
Novel computational methods for increasing PCR primer design effectiveness in directed sequencing. [Citation Graph (, )][DBLP]
MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. [Citation Graph (, )][DBLP]
NITPICK: peak identification for mass spectrometry data. [Citation Graph (, )][DBLP]
QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR. [Citation Graph (, )][DBLP]
Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. [Citation Graph (, )][DBLP]
Simultaneous fitting of real-time PCR data with efficiency of amplification modeled as Gaussian function of target fluorescence. [Citation Graph (, )][DBLP]
A visual analytics approach for understanding biclustering results from microarray data. [Citation Graph (, )][DBLP]
Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer. [Citation Graph (, )][DBLP]
MAID : An effect size based model for microarray data integration across laboratories and platforms. [Citation Graph (, )][DBLP]
Identification of hot-spot residues in protein-protein interactions by computational docking. [Citation Graph (, )][DBLP]
Multi-agent systems in epidemiology: a first step for computational biology in the study of vector-borne disease transmission. [Citation Graph (, )][DBLP]
A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model. [Citation Graph (, )][DBLP]
Extending pathways based on gene lists using InterPro domain signatures. [Citation Graph (, )][DBLP]
The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation. [Citation Graph (, )][DBLP]
Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification. [Citation Graph (, )][DBLP]
Function approximation approach to the inference of reduced NGnet models of genetic networks. [Citation Graph (, )][DBLP]
DOVIS: an implementation for high-throughput virtual screening using AutoDock. [Citation Graph (, )][DBLP]
OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. [Citation Graph (, )][DBLP]
Examining the significance of fingerprint-based classifiers. [Citation Graph (, )][DBLP]
Using an evolutionary algorithm and parallel computing for haplotyping in a general complex pedigree with multiple marker loci. [Citation Graph (, )][DBLP]
RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. [Citation Graph (, )][DBLP]
Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research. [Citation Graph (, )][DBLP]
Using quality scores and longer reads improves accuracy of Solexa read mapping. [Citation Graph (, )][DBLP]
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. [Citation Graph (, )][DBLP]
Gene function prediction using labeled and unlabeled data. [Citation Graph (, )][DBLP]
New time-scale criteria for model simplification of bio-reaction systems. [Citation Graph (, )][DBLP]
Normalization of oligonucleotide arrays based on the least-variant set of genes. [Citation Graph (, )][DBLP]
HECTAR: A method to predict subcellular targeting in heterokonts. [Citation Graph (, )][DBLP]
Evaluation of time profile reconstruction from complex two-color microarray designs. [Citation Graph (, )][DBLP]
Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes. [Citation Graph (, )][DBLP]
Shape based indexing for faster search of RNA family databases. [Citation Graph (, )][DBLP]
IgTM: An algorithm to predict transmembrane domains and topology in proteins. [Citation Graph (, )][DBLP]
Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes. [Citation Graph (, )][DBLP]
Evaluation of genomic island predictors using a comparative genomics approach. [Citation Graph (, )][DBLP]
A comparison of common programming languages used in bioinformatics. [Citation Graph (, )][DBLP]
Goldsurfer2 (Gs2): A comprehensive tool for the analysis and visualization of genome wide association studies. [Citation Graph (, )][DBLP]
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence. [Citation Graph (, )][DBLP]
Aspects of coverage in medical DNA sequencing. [Citation Graph (, )][DBLP]
Information-based methods for predicting gene function from systematic gene knock-downs. [Citation Graph (, )][DBLP]
Conditional clustering of temporal expression profiles. [Citation Graph (, )][DBLP]
Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. [Citation Graph (, )][DBLP]
A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification. [Citation Graph (, )][DBLP]
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. [Citation Graph (, )][DBLP]
SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. [Citation Graph (, )][DBLP]
PseudoGeneQuest - Service for identification of different pseudogene types in the human genome. [Citation Graph (, )][DBLP]
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords. [Citation Graph (, )][DBLP]
A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data. [Citation Graph (, )][DBLP]
Simple integrative preprocessing preserves what is shared in data sources. [Citation Graph (, )][DBLP]
NOTICE1
System may not be available sometimes or not working properly, since it is still in development with continuous upgrades
NOTICE2
The rankings that are presented on this page should NOT be considered as formal since the citation info is incomplete in DBLP
