Pareto-optimal balancing conflicting objectives in genome subgroup analysis
A Microsoft Excel add-in that visualizes gene expression ratios. The software is freely available upon request.
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
Software to analyze array CGH data with direct GPR import (Microsoft Excel add-in, Windows): MCGH Analyzer Software.
McKmeans: A highly efficient multi-core k-means algorithm for clustering extremely large datasets.
Structural RNA alignment by multi-objective optimization: RNA-Pareto
Differential expression analysis for sequence count data: RNASeq Count Analyzer
Perl program to create receiver operator charateristic (ROC) curves: http://www.CPAN.org.
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.
An open-source Java program for drawing area proportional Venn/Euler diagrams:VennMaster Software
ViSiBooL-visualization and simulation of Boolean networks with temporal constraints
An R package for the generation, reconstruction, simulation and analysis of Boolean networks: BoolNet R package
An R package toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets: GiANT R package
An R package that analyzes cluster alternatives based on multi-objective optimization of cluster validation indices: MOCCA R package
An R package that provides fast screening procedures for reflections of ordinal phenotype relations in highdimensional feature representations. It allows the detection of evidence for hypothesised orderings and explorative screenings for unknown relationships.
An R package for multi-objective parameter selection for classifiers: TunePareto R package
Our paper "Chained correlations for feature selection" has been published in Advances in Data Analysis and Classification.
Our paper "Constraining classifiers in molecular analysis: invariance and robustness" has been published in Journal of the Royal Society Interface.