What do we do?
At the EPFL Bioinformatics and Biostatistics Core Facility (BBCF) we provide research labs with extensive support in bioinformatics and biostatistics. Our main competences are in management and analysis of genomic data, mathematical modelling and statistical analysis of quantitative biological data. We provide support for the analysis of large or complex data sets, the development of data management pipelines for new high-throughput technologies (e.g. high-density arrays, high-throughput sequencing), and the statistical planning in complex experimental designs. We also help researchers in the areas of mining public data, designing and setting up local databases, building mathematical models from experimental data and running simulations to evaluate a model.
Highlights 2016In 2016, the BBCF had the opportunity to participate in a pilot analysis with Pierre Fabre, PhD - from Prof. Duboule’s group (EPFL) - whose aim was to highlight specific expression patterns of the Hox genes into different mouse tissues using Single-cell RNA-seq (scRNA-seq). This study should now be extended, and most probably completed with chromatin accessibility (ATAC-Seq or scATAC-seq) and chromatin folding (FISH and 4C-seq) data in order to understand specific cis-regulation at the single cell level.
With Prof. Deplancke's group (EPFL, SIB) we started the development of ASAP (Automated Single-cell Analysis Pipeline), a fully integrated, web-based platform aimed at the complete analysis of single-cell and bulk RNA-seq data post genome alignment: from the parsing, filtering and normalization of the input count data files to the visual representation of the data, identification of cell clusters, differentially expressed genes (including cluster-specific marker genes), and functional gene set enrichment.
In collaboration with Prof. Van der Goot's group (EPFL) we continued the development of SwissPalm, and developed a tool to compare inter-species palmitoyl-proteomes. This new tool allows to identify – with higher confidence – truly palmitoylated proteins from proteomic screens.
Main publications 2016
- Loviglio M.N., et al. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Molecular Psychiatry. 2016-05
- Deluz C, et al. A role for mitotic bookmarking of SOX2 in pluripotency and differentiation. Genes & Development 2016; 30:2538-2550
- Zeng YX, et al. Extension of least squares spectral resolution algorithm to high-resolution lipidomics data. Anal Chim Acta. 2016 Mar 31;914:35-46