Comprehensive characterization and effective combinatorial targeting of high-grade serous ovarian cancer via single-cell analysis (HERCULES)
In the HERCULES EU project, we are studying samples from high-grade serous ovarian cancer tumours. The samples are analysed using mass cytometry, DNA, RNA and ChIP (chromatin immunoprecipitation) sequencing; and computational tools to find […]
Systems biology of cell infection by the bacterial pathogen Listeria monocytogenes
In the context of the Swiss consortium InfectX (www.infectx.ch), we have previously performed siRNA, microRNA and drug screens to investigate signaling pathways modulating invasion of host cells by the bacterial pathogen Listeria monocytogenes. In […]
PTR 392 – Systems-wide analysis of Leishmania virulence
This PTR aims to gain novel insight into the nature, the expression, and the regulation of Leishmania virulence factors through the investigation of genetics, transcriptomics, and proteomics differences between (i) virulent and avirulent L. […]
Gravity (for Gene inteRaction Analysis of Variants in Individuals: a Tool for You) provides a visualisation of genetic data from SNP array, whole genome and whole exome data in the context of protein-protein interactions. […]
Cytoscape: Visualization and analysis of omics data in interaction networks
Cytoscape is the worldwide standard open-source platform for network visualization and data integration. This project, which we started at the Institute for Systems Biology in Seattle, provides a universal, customizable tool for the network-based […]
2018A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection., Nat Commun. 2018 Oct 24;9(1):4418.
2018Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines, Genome Med 2018 07;10(1):59.
2018The Cytoscape Automation app article collection, F1000Res 2018;7:800.
2018A Blood RNA Signature Detecting Severe Disease in Young Dengue Patients at Hospital Arrival, J. Infect. Dis. 2018 May;217(11):1690-1698.
2018Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors, Nat. Immunol. 2018 Mar;19(3):302-314.
2018Parallel derivation of isogenic human primed and naive induced pluripotent stem cells, Nat Commun 2018 01;9(1):360.
2017Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges, Proc. Natl. Acad. Sci. U.S.A. 2018 01;115(3):E488-E497.
2017Network module identification-A widespread theoretical bias and best practices, Methods 2018 01;132:19-25.
2017Common and phylogenetically widespread coding for peptides by bacterial small RNAs, BMC Genomics 2017 07;18(1):553.
2017Network-based analysis of omics data: the LEAN method, Bioinformatics 2017 03;33(5):701-709.
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