An R package for multi-objective parameter selection for classifiers: TunePareto R package
McKmeans: A highly efficient multi-core k-means algorithm for clustering extremely large datasets.
An R package that analyzes cluster alternatives based on multi-objective optimization of cluster validation indices: MOCCA R package
An R package for the generation, reconstruction, simulation and analysis of Boolean networks: BoolNet R package
A new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes: HCMV drug resistance mutations
An open-source Java program for visualizing genomic abnormalities: IdeogramBrowser Software
An open-source Java program for drawing area proportional Venn/Euler diagrams: VennMaster Software
A Microsoft Excel add-in that visualizes gene expression ratios. The software is freely available upon request.
Software to analyze array CGH data with direct GPR import (Microsoft Excel add-in, Windows): MCGH Analyzer Software.
Perl program to create receiver operator charateristic (ROC) curves: http://www.CPAN.org.
A document-centered environment for simulation and visualization of algorithms: Vital
Structural RNA alignment by multi-objective optimization: RNA-Pareto
Visualization of Ant Colony Optimization (contributed by Michael Grönert): Swarm
Swat is a java commandline software based on dynamic programming to calculate optimal local alignments of DNA/ RNA sequences and protein sequences.
Differential expression analysis for sequence count data: RNASeq Count Analyzer
Clojure Framework for parallelization: Sputnik
Our paper "A model of the onset of the Senescence Associated Secretory Phenotype after DNA damage induced Senescence" has been accepted for publishing in PLOS Computational Biology.
Our paper "The influence of multi-class feature selection on the prediction of diagnostic phenotypes" has been accepted for publishing in Neural Processing Letters.