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Project #3327
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#3327 : Listeriomics – Development of a web platform for visualization and analysis of Listeria omics data
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Name of Applicant : Pascale Cossart
Date of application : 27-01-2016
Unit : Bacteria-Cell Interactions
Location : Batiment Roux – Rdc
Phone : 9301
@ Mail : pascale.cossart@pasteur.fr
@ PI-Mail : pascale.cossart@pasteur.fr

Project context and summary :

Over the past three decades Listeria has become a model organism for host-pathogen interactions, leading to critical discoveries in a broad range of fields including virulence-factor regulation, cell biology, and bacterial pathophysiology. More recently, the number of Listeria “omics” data produced has increased exponentially, not only in term of number, but also in term of heterogeneity of data. There are now more than 40 published Listeria genomes, around 400 different transcriptomics data and 10 proteomics studies available. The capacity to analyze these data through a systems biology approach and generate tools for biologists to analyze these data themselves is a challenge for bioinformaticians. To tackle these challenges we are developing a web-based platform named Listeriomics which integrates different type of tools for “omics” data manipulation, the two most important being: 1) a genome viewer for displaying gene expression array, tiling array, and RNASeq data along with proteomics and genomics data. 2) An expression atlas, which is a query based tool which connects every genomics elements (genes, smallRNAs, antisenseRNAs) to the most relevant “omics” data. Our platform integrates already all genomics, and transcriptomics data ever published on Listeria and will thus allow biologists to analyze dynamically all these data, and bioinformaticians to have a central database for network analysis. Finally, it has been used already several times in our laboratory for different types of studies, including transcriptomics analysis in different biological conditions, and whole genome analysis of Listeria proteins N-termini. This project is funded by an ANR Investissement d’avenir: BACNET  10-BINF-02-01


Related team publications :
Comparative transcriptomics of pathogenic and non-pathogenic Listeria species, Mol Syst Biol. 2012 May 22;8:583. doi: 10.1038/msb.2012.11.
The Listeria transcriptional landscape from saprophytism to virulence, Nature. 2009 Jun 18;459(7249):950-6. doi: 10.1038/nature08080. Epub 2009 May 17.
Comparison of widely used Listeria monocytogenes strains EGD, 10403S, and EGD-e highlights genomic variations underlying differences in pathogenicity, MBio. 2014 Mar 25;5(2):e00969-14. doi: 10.1128/mBio.00969-14.
Service Delivery
Project Manager : christophe.becavin@pasteur.fr
Project Type : Medium
Status : Closed
Publication : https://doi.org/10.1128/mSystems.00186-16; https://doi.org/10.1038/nmicrobiol.2017.5


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