GenePEN, an efficient machine learning approach to identify coordinated alterations of genes or proteins in biological networks using omics data, providing provably optimal results in few seconds. Example code can be downloaded for testing (Stat. Appl. Genet. Mol. Biol., in press).

ArrayMining.net, a server for automatic analysis of DNA-microarray data, providing Cross-study normalisation, Feature selection, Clustering, Prediction, Co-Expression Network Analysis and Gene Set analysis. (BMC Bioinformatics, 2009)

EnrichNet, a web-service mapping gene sets onto a human protein-protein interaction network and analyzing their network associations with mapped cellular pathways, processes and complexes (Bioinformatics 2012, ECCB 2012)

PathVar, a web-application to study how the variance of expression levels across genes/proteins in cellular pathways changes under different experimental conditions, and to extract patterns for sample clustering and classification (Bioinformatics, 2012)

TopoGSA, a web-server mapping gene or protein sets onto molecular interaction networks to characterise their topological properties, providing within- and between-gene-set comparisons using interactive 2D- and 3D-visualisations and similarity ranking tables (Bioinformatics, 2010)

PathExpand, a web- application extending pre-defined protein sets representing cellular processes by mapping them onto an interaction network and expanding them to include densely interconnected interaction partners (BMC Bioinformatics, 2010, RECOMB CCB 2010)

SeedNet Online, an interactive gene co-expression network visualisation to investigate transcriptional inter-actions between dormant and germinating Arabidopsis thaliana seeds (Proceedings of the National Academy of Sciences USA, 2011)

VRMLGen, a free R software package to generate 3D representations of biological data in the Virtual Reality Markup Language (Journal of Statistical Software, 2010).

RepExplore, a web-service for omics data analysis exploiting the information captured in the variance of technical replicates to provide more reliable and informative differential expression and abundance statistics, as well as low-dimensional data visualizations.

FastMotif, A sequence motif discovery algorithm for large DNA datasets, based on spectral methods (http://arxiv.org/abs/1407.6125e, Download source code).