Bioinformatics

The Bioinformatics Facility was created in March 2013 to foster the implementation of bioinformatics applications in projects of the Life Science Research Unit (LSRU). As bioinformatics becomes more and more important in many areas of Life Sciences Research, the Bioinformatics Facility aims at providing expertise in this field to the researchers of LSRU.

Mission

The missions of this core facility are mainly data analysis and teaching.

Data analysis

  •     Applying up-to-date analysis methods to LSRU projects
  •     Developing specific tools and methods for LSRU projects

The general data science’s workflow used is from Hadley Wickham:

It applies to any projects since the generic involved steps are most of the time similar.

Teaching

Expertise

Any LSRU member has access to the facility and can ask for advice or help in their projects. The fields of expertise of the bioinformatic facility include:

Statistics

  • Hypothesis testing, comparison of n samples with correction for multiple testing
  • Regression model: linear, generalised linear, mixed, non-linear
  • Global model or many per atomic elements

Computational biology

  • Next-Generation Sequencing, mapping, from raw sequence files to alignments
  • Intensive computation is performed on the ULHPC clusters.

Genomics

  • Copy Number Variation, variant calling together with Dr. Patrick May, Head of Genome Analysis, LCSB.
  • Genomic scans for genes underlying selective sweeps
  • Population splits and demographic inferences

Functional Genomics

  • ChIP-seq, DNA methylation with Dr. Lasse Sinkkonen, Head of the Epigenetics team
  • Gene expression, microarray pre-processing and comparative analyses
  • RNA-seq
  • Functional enrichments (GSEA, IPA ingenuity)

Phylogeny

Proteomics

Reproducible science

  • all code is versioned via git hosted at r3 LCSB gitlab
  • an online lab-book (access restricted within UNI) keeps track of daily actions and summarised statistics
    • git commits, code insertions / deletions
    • per project, per team and per year
  • reports as Rmarkdown documents. Those text files are versioned and contain all code and links to import raw data, tidying methods and transformation and plotting.

Data visualisation

  • Proficient in using the R package ggplot2
  • Interactive documents, R package shiny

dataviz

Collaboration

The Bioinformatics Facility interacts closely the LCSBBioinformatics Core.

External collaboration within Luxembourg is also established with:

 

Contact

Aurélien Ginolhac

  • Life Sciences Research Unit.
  • University of Luxembourg
  • Campus Belval - 6 avenue du Swing, 
  • L-4367 Belvaux
  • Phone office: +352 46 66 44 6560
  • Biotech II – Office 4.22
  • E-mail: aurelien.ginolhac@uni.lu