Functional and Integrative Genomics
We provide advanced and personalised support and consulting in bioinformatics and biostatistics for the scientific community of EPFL as well as for other Institutes.
It covers, but is not limited to:
Main competences include:
- Experimental design of experiments
- Integrative and statistical analysis & visualisation of any kind of quantitative and multidimensional biological data (e.g, genomic, epigenetic and clinical data), including publicly available data
- Development of specific methods and pipelines
Main competences include:
- Transcriptomics: RNA-seq (bulk and single cells), Gene Expression Microarray
- Epigenetics/Epigenomics: ChIP-seq, DNase-seq, ATAC-seq, Methylation detection
- 3D-chromatin: 4C-seq. Hi-C, capture Hi-C, ChIA-PET
- Whole genome sequencing (WGS): SNP, De novo sequencing
- Mining public databases (SRA, GEO, cancer genome atlas, ...)
- Clinical data (survival curves, ...)
- Gene Ontology & Pathways
- Quantitative Data Analysis: advanced processing and statistics of any kind of quantitative biological data
|Marion is a senior bioinformatician providing support and consulting in bioinformatics and biostatistics.|
With a 10+ years experience in this field and an educational background in computer science and data mining (PhD), Marion will work in close collaboration with you to give you all the support you need.
|Bastien Mangeat||Head of GECF||SV1841||37113|
On-demand Bioinformatics Tools
We propose on-demand data integration as well as conception and development of bioinformatics databases/applications. This service is open to SV laboratories and core facilities.
- Data integration. You have produced a number of data in your lab and you want to cross them with external databases, or you want to do systematic and complex queries on publicly available datasets.
- Conception and development of dedicated applications. You would like:
- to store your data in a structured database to make complex queries or to be able to visually explore a complex or large dataset
- to make data available with innovative representations
- to have an online application allowing researchers at EPFL or more globally the scientific community to use your analysis pipelines / libraries / scripts and then increase the visibility of your work
- to get some support to develop and maintain an original web application in the field of biology or bioinformatics
|FlyGut||Buchon N et al.||Morphological and molecular characterization of adult midgut compartmentalization in Drosophila.||2013||Cell reports|
|HTSstation||David FP et al.||HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.||2014||PloS one|
|SwissPalm||Blanc M et al.||SwissPalm: Protein Palmitoylation database.||2015||F1000Research|
|GetPrime v2||David FP et al.||GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms.||2017||Nucleic acids research|
|ASAP v2||Gardeux V et al.||ASAP: a Web-based platform for the analysis and interactive visualization of single-cell RNA-seq data.||2017||Bioinformatics (Oxford, England)|