viPEr-networks of Statin-treated human hepatocytes. (A) Focus network of all differentially regulated genes upon Atorvastatin treatement and direct Atorvastatin targets. (B) Focus networks based on same data between the Transcription Factors FoxA1/A2/A3 and all the main Atorvastatin target, HMGCR.
Biological networks in space and time
Biological networks such as protein-protein interaction networks or gene regulatory networks are an integral part to understand biological systems. Yet, our current representations of biological networks are mostly static: the factor of time (for instance coming from time-series data) or event-driven interaction (as is found in cell cycle regulation) are not accounted for.
In collaboration with groups from the CPT (Alain Barrat) and I2M (Laurent Tichit), we are working on implementing the aspect of time in biological networks.
Previous work we have done in network biology for interpretation and integration of large-scale data coming from -omics studies we have published here:
1) miMerge and miScore for the generation of non-redundant protein interaction networks (Villaveces, et al., Database, 2015, doi: 10.1093/database/bau131)
2) KEGGViewer (Villaveces, et al., F1000Res 3:43, 2014, doi: 10.12688/f1000research.3-43.v1) for the visualization and integration of pathway data; and PsiquicGraph (Villaveces, et al., F1000Res 3:44, 2014, doi: 10.12688/f1000research.3-44.v1) both available via the BioJS platform;
3) the Cytoscape plugins viPEr for generating focus networks based on -omics data and PEANUT for pathway enrichment of focus networks (Garmhausen et al., BMC Genomics 16:790, 2015, doi: 10.1186/s12864-015-2017-z).
Current funding for these projects come from ANR and CENTURI.
Part of these projects were funded by the BMBF grants 'HEPATOSYS' and 'SYBACOL'. and the Max Planck Society.