A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
coMOTIF : a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data
FDM : a graph-based statistical method to detect differential transcription using RNA-seq data
Tree-structured algorithm for long weak motif discovery
Exome sequencing-based copy-number variation and loss of heterozygosity detection : ExomeCNV
A phylogenetic mixture model for the identification of functionally divergent protein residues
Reconstructing the architecture of the ancestral amniote genome
A powerful and flexible approach to the analysis of RNA sequence count data
Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer
Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis
Inferring disease and gene set associations with rank coherence in networks
Robust synthetic gene network design via library-based search method
Contextual analysis of RNAi-based functional screens using interaction networks
Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli
OrganismTagger : detection, normalization and grounding of organism entities in biomedical documents
Automatic extraction of angiogenesis bioprocess from text
A biclustering algorithm for extracting bit-patterns from binary datasets
A framework for analytical characterization of monoclonal antibodies based on reactivity profiles in different tissues
Gee Fu : a sequence version and web-services database tool for genomic assembly, genome feature and NGS data
Mauve Assembly Metrics
ReplacementMatrix : a web server for maximum-likelihood estimation of amino acid replacement rate matrices
JMassBalance : mass-balanced randomization and analysis of metabolic networks
METANNOGEN : annotation of biological reaction networks
GlobalMIT : learning globally optimal dynamic bayesian network with the mutual information test criterion
NetDS : a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks
The GNAT library for local and remote gene mention normalization
NeuroPedia : neuropeptide database and spectral library