University Logo WebPortal Logo LCSB Logo

Bioinformatics Softare Portal - Tools for analysing omics data and general gene and protein lists
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).
GenePEN logo
GenePEN, 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) logo
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)
EnrichNet logo
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)
PathVar logo
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)
TopoGSA logo
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)
PathExpand logo
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)
SeedNet logo
SeedNet Online
VRMLGen, a free R software package to generate 3D representations of biological data in the Virtual Reality Markup Language (Journal of Statistical Software, 2010).
VRMLGen logo
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.
RepExplore logo
FastMotif, A sequence motif discovery algorithm for large DNA datasets, based on spectral methods (, Download source code).
FastMotif logo