Amos Bairoch & Lydie Lane
Computer and Laboratory Investigation of Proteins of Human Origin (CALIPHO)
Geneva, Centre Médical Universitaire (CMU)
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What do we do?

At the CALIPHO Group, which stands for “Computer and Laboratory Investigation of Proteins of Human Origin”, we aim to use a combination of bioinformatics and experimental methodologies to increase the knowledge about the function of the 20,000 or so protein-coding genes that exist in the human genome. Our main mission is the development of neXtProt, a human protein knowledge resource.
Recently, we focused on annotating the effects of human protein variations in the context of cancers and genetic diseases, and analyzing results of high-throughput experiments to shed light on the function of selected sets of uncharacterized human proteins.
We are part of the HUPO Human Protein Project, which aims at validating the existence of all predicted human proteins in biological samples by mass spectrometry.
We are also active in the development of ontologies/standardization resources, such as Cellosaurus for cell lines and ICEPO for ion channel electrophysiology.

Highlights 2016

In 2016, we continued to develop the new generation of the neXtProt platform. The new neXtProt site allows power users and software developers to make use of all of the integrated data in software tools (with our new API) or in powerful cross-resources queries (thanks to our SPARQL endpoint).
We also started to integrate the results of our effort to annotate the phenotypic effect of protein variants in cancers and genetic diseases in a new phenotype view, and through specific portals such as the one for ion channels.

Main publications 2016

  • Gaudet P et al. The neXtProt knowledgebase on human proteins: 2017 update. Nucleic Acids Res 2016; pii: gkw1062.
  • Hinard V et al. ICEPO: the ion channel electrophysiology ontology. Database (Oxford) 2016; pii: baw017.
  • Omenn GS et al. Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications. J Proteome Res. 2016 Nov 4;15(11):3951-3960.
  • Duek P et al. Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status. J Proteome Res. 2016 Nov 4;15(11):3971-3978.

Our research topics: