Poisson factor models with applications to non-normalized microRNA profiling
Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package
PeptideLocator: prediction of bioactive peptides in protein sequences
Specificity and affinity quantification of protein–protein interactions
Peakr: simulating solid-state NMR spectra of proteins
SplicingCompass: differential splicing detection using RNA-Seq data
Modeling risk stratification in human cancer
A temporal switch model for estimating transcriptional activity in gene expression
A rate-distortion theory for gene regulatory networks and its application to logic gate consistency
Identification of cancer fusion drivers using network fusion centrality
ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data
Parametric Bayesian priors and better choice of negative examples improve protein function prediction
Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context
CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks
freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers
MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis
FunFrame: functional gene ecological analysis pipeline
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots
JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models
Enabling interspecies epigenomic comparison with CEpBrowser
NTFD—a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data
The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions
HExpoChem: a systems biology resource to explore human exposure to chemicals
Galaxy LIMS for next-generation sequencing
RCPedia: a database of retrocopied genes
Brain: biomedical knowledge manipulation