Algorithms and tools for protein–protein interaction networks clustering, with a special focus on population-based stochastic methods
A new era in bioimage informatics
BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
Bayesian joint analysis of heterogeneous genomics data
Composition of seed sequence is a major determinant of microRNA targeting patterns
G-BLASTN: accelerating nucleotide alignment by graphics processors
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models
Modeling tissue contamination to improve molecular identification of the primary tumor site of metastases
Adaption of the global test idea to proteomics data with missing values
Reference-free cell mixture adjustments in analysis of DNA methylation data
Comparison of approaches for parameter identifiability analysis of biological systems
Network orientation via shortest paths
Combinatorial therapy discovery using mixed integer linear programming
h5vc: scalable nucleotide tallies with HDF5
ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications
PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
NGSANE: a lightweight production informatics framework for high-throughput data analysis
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
PUmPER: phylogenies updated perpetually
MEMBPLUGIN: studying membrane complexity in VMD
ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
ngsTools : methods for population genetics analyses from next-generation sequencing data
Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics
Bio Simulators: a web UI for biological simulation