Bioinformatique


Person in charge

Jean-Christophe Gelly

Objectives

To understand the theoretical concepts, issues, and applications of bioinformatics necessary for current research work in the fields of life sciences and health.

Lectures 15h

  • Introduction to bioinformatics
  • Biology and Bioinformatics Information System
  • Metrics for sequence comparison (substitution matrix)
  • Global and local pairwise alignment (dynamic programming, Needleman-Wunsch and Smith-Waterman algorithms)
  • Alignment for sequence search (BLAST, PSI-BLAST, HMM (Hmmer, HHblits)) – Significance of an alignment score (E-Value; P-value; law of extreme values)
  • Multiple alignment (exact, progressive, iterative, by consistency: ClustalW, Muscle, MAFFT, Probcons, T-COFFEE)
  • Inference in molecular phylogeny and tree construction (UPGMA, Neighbor Joining, Maximum Parsimony, Maximum Likelihood, Bootstrap)
  • Bioinformatics Genomics (genome assembly, structural annotation of genomes (ab initio and by similarity), comparison of genomes, functional annotation (by similarity and neighbourhood exploration) – Metagenomics – Functional genomics – Whole Genome Association Study (GWAS)
  • Systemic and integrative bioinformatics (notions of network and graph, network inference in biology, ontology)
  • Structural Bioinformatics: structure analysis (solvent accessibility, assignment of secondary structures structural alignment), classification and structure banks, structure prediction)
  • Bioimage informatics: Image analysis in biology and bioinformatics
  • Transcriptomics bioinformatics (analysis and processing of seq RNA data and DNA chips (image analysis, data processing, clustering)

Tutorial works 6h

Study of concrete examples from the scientific literature

Pratical works 2h

2 themes to choose from :
       1- Strucural bioinformatic
       2- Genomics

Targeted skills

  • Theoretical skills on new biological and bioinformatics approaches
  • Autonomy and ability to analyze, understand and develop a bioinformatics study