Training – Linking gene and function, comparative genomics tools for biologists.

EVENT : C3BI Training

Linking gene and function, comparative genomics tools for biologists.

Main speaker : Valerie Crecy-Lagard, from University of Florida · Department of Microbiology and Cell Science
Date : 24/10/2017 at 08:00 am
Location : Bime meeting room 28-01-01E – BIME (28) ,Institut Pasteur, Paris

Students will need to bring their laptop.

More than twenty years after the first bacterial genome has been sequenced, microbiologists are faced with an avalanche of genomic data. However the quality of the functional annotations of the sequenced proteome is very poor with more than half of the sequenced proteins remaining of unknown function. After taking this course, students should master an array of web-based tools to help to predict gene function. This will allow them to generate in silico based functional predictions and produce illustration for manuscripts that use comparative genomic methods. For background read (

Target audience: PhD students in biological sciences with a strong focus on microbiology/biochemical applications.
Instructor: Prof. Valérie de Crécy-Lagard is a pioneer in the use of comparative genomic methods to characterize protein families of unknown function. She is spending time on sabbatical from U. of Florida as invited researcher in the Group of Eduardo Rocha.

Module organization

The course uses a blend of lectures and hands-on application exercises :
  • M1( October 24, Morning): Basic bioinformatics tools.This module is to bring everyone up to date on the basic tools that will be routinely used in the course. These will include data extraction from major biological databases such as NCBI and Uniprot, Blast, multiple alignments, accessing precomputed phylogenetic trees and genome browsers.
  • M2  (October 24, afternoon): Linking genes to pathway and pathway to genes.This module will focus on pathway databases, metabolic reconstruction and models and how mapping a gene to a pathway or more generally to biological system can ground truth a functional annotation.
  • M3 (October 25, morning): Non homology based association methodsPhysical clustering, phylogenetic distribution, comparing whole genomes, iTOL visualization tools
  • M4 (October 25, afternoon): Paralogs a blessing and a curseThis module will focus on the tools and strategy to disambiguate paralog families. This includes, Basic phylogenetic tree building, paralog separation tools, building and comparing logos
  • M5 (October 26, 8 am to 11): Regulatory based association.This module focuses on identifying regulatory sites, predicting regulatory networks, mining transcriptome data, and generating heatmaps and venn diagrams.
  • M6 (October 26, 11 am to 2h30 pm): Beyond transcriptomics, mining other types of high throughput experimental dataThis module focuses on mining other types of experimental data Phenotype/fitness, protein interaction and complexes, localization, metabolomics.


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