What do we do?
At the Computational Cancer Genomics Group, we are interested in gene regulation both in healthy and diseased cells. Breakthroughs in genomics technologies have led to the production of large volumes of data that could potentially tell us something about how gene regulatory instructions are encoded in our DNA. Our group develops new algorithms, computer programs, web services and databases that will help us and others to extract knowledge and understanding from such data.
- Promoter collections for two new model organisms were added, honey bee and maize. The human promoter collection has grown to more than 25’000 entries after processing of new CAGE data from FANTOM5.
- A joint paper with Bernard Moret’s group, entitled “A Maximum-likelihood approach for building cell-type trees by lifting”, received the best paper award at the 2016 Asia Pacific Bioinformatics Conference in San Francisco.
- To mark the 30th anniversary of the Eukaryotic Promoter Database EPD, we organized a symposium “Promoter Research: Past, Present and Future” at the Starling hotel on the EPFL campus. We had outstanding talks by speakers from three continents and lively discussions among all participants.
- At the SIB Days 2016, our workshop entitled “Facilitating Reproducibility of Computational Research in Bioinformatics” attracted over 50 participants.
- An article presenting our ChIP-Seq tools was finally published, more than 5 years after the web server went online.
Main publications 2016
- Kumar S, Bucher P. Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. BMC Bioinformatics. 2016;17 Suppl 1:4.
- Dreos R, Ambrosini G, Bucher P. Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. PLoS Comput Biol. 2016;12(10):e1005144.
- Ambrosini G, Dreos R, Kumar S, Bucher P. The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data. BMC Genomics. 2016;17(1):938.