Identification of novel transcripts in annotated genomes using RNA-Seq
TOTALRECALLER : improved accuracy and performance via integrated alignment and base-calling
A novel signal processing approach for the detection of copy number variations in the human genome
Sufficient statistics and expectation maximization algorithms in phylogenetic tree models
Tissue-specific prediction of directly regulated genes
DECOD : fast and accurate discriminative DNA motif finding
Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins
Elemental composition determination based on MS n
A Grid-enabled web portal for NMR structure refinement with AMBER
Annotation concept synthesis and enrichment analysis : a logic-based approach to the interpretation of high-throughput experiments
A rank-based statistical test for measuring synergistic effects between two gene sets
A Lasso regression model for the construction of microRNA-target regulatory networks
Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases
BRISK—research-oriented storage kit for biology-related data
Making whole genome multiple alignments usable for biologists
PGAT : a multistrain analysis resource for microbial genomes
Simple high-throughput annotation pipeline (SHAP)
SpEED : fast computation of sensitive spaced seeds
MethylCoder : software pipeline for bisulfite-treated sequences
spacodiR : structuring of phylogenetic diversity in ecological communities
DivBayes and SubT : exploring species diversification using Bayesian statistics
ModeRNA server : an online tool for modeling RNA 3D structures
NASP : a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments
PREDA : an R-package to identify regional variations in genomic data
IRiS : Construction of ARG networks at genomic scales
CytoscapeRPC : a plugin to create, modify and query Cytoscape networks from scripting languages
Simple Neurite Tracer : open source software for reconstruction, visualization and analysis of neuronal processes
MetATT : a web-based metabolomics tool for analyzing time-series and two-factor datasets
StochKit2 : software for discrete stochastic simulation of biochemical systems with events
Simulating systems genetics data with SysGenSIM
APCluster : an R package for affinity propagation clustering
RxnFinder : biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity
ontoCAT : an R package for ontology traversal and search
CSO validator : improving manual curation workflow for biological pathways