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 Blood RNA Signature Detecting Severe Disease in Young Dengue Patients at Hospital Arrival, J. Infect. Dis. 2018 May;217(11):1690-1698.
2016From the exposome to mechanistic understanding of chemical-induced adverse effects, Environ Int 2017 02;99:97-106.
2015Bacterial Internalization, Localization, and Effectors Shape the Epithelial Immune Response during Shigella flexneri Infection, Infect. Immun. 2015 Sep;83(9):3624-37.
2015Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis, BMC Genet. 2015;16:11.
2015Automated flow cytometric analysis across large numbers of samples and cell types, Clin. Immunol. 2015 Apr;157(2):249-60.
2014The Cyni framework for network inference in Cytoscape, Bioinformatics 2015 May;31(9):1499-501.
2014The Cytoscape app article collection, F1000Res 2014;3:138.
2013Analysis of time-resolved gene expression measurements across individuals, PLoS ONE 2013;8(12):e82340.
2013TLM-Quant: an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells, PLoS ONE 2013;8(7):e68696.
2013Identification of additional proteins in differential proteomics using protein interaction networks, Proteomics 2013 Apr;13(7):1065-76.
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