Transcriptomic & Applied Genomic

Plateformes Lilloises en Biologie & Santé – PLBS – UMS 2014 – US 41

Transcriptomique et génomique appliquée


Trancriptomic & Applied Genomic (TAG) laboratory is a technical platform of the Institute Pasteur of Lille specialized in genomic. Its know-how is based on the use and development of molecular biology applications derived from high throughput sequencing technology. TAG is one of the two platforms forming the GO@L network (GenOmic at Lille) belonging to the UMS (Unité Mixte de Service) PLBS (Plateformes Lilloises en Biologie & Santé) UMS2014 US41.

TAG has developed a recognized expertize in genomic of microorganisms and their impact in human health. The skills were developed in three different domains: (i) the study, using metagenomics approach, of microbiota (mainly bacterial) to determine their compositions and evolutions, (ii) the study of microorganisms genomic at the entire genome scale in order to determine, to study and to follow their characteristics and finally (iii) the study of microbial genomes’ transcriptomic expression as well as transcriptomic of model organisms used in microbiology.

TAG interacts mainly in collaboration with Lille’s biology and health research stakeholders and also develops analytical solutions and tools and implements them through its own study subjects. TAG is one of the two platforms forming the GO@L network (GenOmics at Lille) belonging to the service unit PLBS – UMS 2014 – US 41.


  • January 2021 : The GO@L (GenOmics at Lille) network joining TAG and GFS is certified by the Infrastructure in BioHealth/Agriculture label (GIS IBiSA – “Infrastructure en Biologie Sante et Agronomie“).
  • Development of a new protocol for full length coronavirus genome sequencing and assembly directly from patient sample. Development of an analysis tool for reference free genome assembly: V-ASAP (Virus Amplicon Sequencing Assembly Pipeline).
  • Development of a pipeline for automatic analysis of full length microbial genome sequencing: MICRA (Microbial Identification and Characterization through Reads Analysis).

Transversal project

  H2020-SC1-BHC. Acronyme : FAIR :

Flagellin Aerosol Therapy as an Immunomodulatory Adjunct to the Antibiotic Treatment of Drug-Resistant Bacterial Pneumonia. In collaboration with JC Sirard (Center for Infection & Immunity of Lille).


David HOT
Team leader

Ségolène CABOCHE
Engineer in Bioinformatics

Delphine BEURY
Engineer in molecular biology

Florence MAURIER
Engineer in Bioanalysis

Engineer in Biostatistics

Engineer in Bioanalysis

Technician in molecular biology


Ayari A, Rosa-Calatrava M, Lancel S, Barthelemy J, Pizzorno A, Mayeuf- Louchart A, Baron M, Hot D, Deruyter L, Soulard D, Julien T, Faveeuw C, Molendi-Coste O, Dombrowicz D, Sedano L, Sencio V, Le Goffic R, Trottein F, Wolowczuk I.
Influenza infection rewires energy metabolism and induces browning features in adipose cells and tissues.
Commun Biol. 2020 May 14;3(1):237. doi: 10.1038/s42003-020-0965-6. PMID: 32409640; PMCID: PMC7224208.

Maurier F, Beury D, Fléchon L, Varré JS, Touzet H, Goffard A, Hot D, Caboche S.
A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43.
Virology. 2019 Mar 9; 531:141-148. doi: 10.1016/j.virol.2019.03.006. [Epub ahead of print] PubMed PMID: 30878524.

Caboche S, Even G, Loywick A, Audebert C, Hot D.
MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data.
Genome Biol. 2017 Dec 19;18(1):233. doi: 10.1186/s13059-017-1367-z. PubMed PMID: 29258574; PubMed Central PMCID: PMC5738152.

Amman F, D’Halluin A, Antoine R, Huot L, Bibova I, Keidel K, Slupek S, Bouquet P, Coutte L, Caboche S, Locht C, Vecerek B, Hot D.
Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape of Bordetella pertussis.
RNA Biol. 2018 May 18:1-9. doi: 10.1080/15476286.2018.1462655. [Epub ahead of print] PubMed PMID: 29683387.

Siegwald L, Touzet H, Lemoine Y, Hot D, Audebert C, Caboche S.
Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics.
PLoS One. 2017 Jan 4;12(1):e0169563. doi: 10.1371/journal.pone.0169563. PubMed PMID: 28052134; PubMed Central PMCID: PMC5215245.


Microbial genomic ; Transcriptomic ; High-throughput sequencing

Team contact

David Hot
Team leader
03 20 87 72 09