2025
xData Unit & Microbiota Program
Automatic classification of epithelial tight junctions using graph-extracted metrics
BIMOP Unit & xData Unit & Antimicrobial Program
RaMoA: Raman micro-spectroscopy and deep learning for rapidly predicting the Mechanism of Action of an antimicrobial and its potential novelty
xData Unit & Vaccines Program
Comparative analysis of integrative classification methods for multi-omics data
Microbiota Program & xData Unit
Immunocompetent mid-throughput Gut-on-a-Chip model to study host – microbiota interaction
2024
Diagnostics Program & MIMPS Unit
Development of a new rapid diagnostic test to support onchocerciasis elimination
BIMOP Unit
COLPLEX Technology: an Innovative Approach for the Development of Multiplex Point of Care Tests
Vaccines Programme & xDATA Unit
A predictive signature of vaccine reactogenicity for human peripheral blood to benchmark novel vaccine formulations
OMICS Unit
Enhanced shotgun metagenomics using Unique Molecular Identifier-based protocol with Oxford Nanopore sequencing
BIMOP Unit
The Colicin/Immunitysystem in the service of moleculardiagnostics
MIMPS Unit & Antimicrobial programme
Acinetobacter baumannii: Setup and characterization of pneumonia and septicemia preclinical models with longitudinal monitoring using bioluminescent strains
OMICS Unit
The promise of the Orbitrap ASTRAL mass-spectrometer for proteomics analysis
xDATA Unit & CLIOP Unit & Vaccines programme
Biobank Data Harmonization Across SARS-Cov-2 Cohorts for Robust Research Outcomes
OMICS Unit
A single workflow for multi-species blood transcriptomics
xDATA Unit
Integrated analysis of humoral immune response across several COVID immunization schemes in COVIDAuRA study
OMICS Unit
Multi-omics workflow for the identification of discriminant markers associated with Trypanosoma cruzi populations.
BIMOP Unit & Antimicrobial programme
Murine in vitro alveolar macrophage model to study the effects of influenza virus infection
xDATA Unit & BIMOP Unit & MIMPS Unit & CLIOP Unit
Fecal microbiota & Immune fitness evaluation in healthy, elderly and centenarians’ populations
Microbiota programme & BIMOP Unit & MIMPS Unit
Immunocompetent mid-throughput Gut-on-a-Chip model to study intestinal inflammation and homeostasis
xDATA Unit & BIMOP Unit & Diagnostic programme
Automatic Bacteria Classification on Microscopic Images of Positive Blood Culture Gram Smears
BIMOP unit
Microfluidic chip for bacterial biofilm formation and analysis
Poster presented @ Lab-on-a-Chip and Microfluidics Europe 2024 Conference.
Best Poster Awards Sponsored by Lab-on-a-Chip Journal, Royal Society of Chemistry (RSC): third position
2023
BIMOP unit
Col/lm Technology : an innovative generic multiplex assay technology
Poster presented at I4ID congress.
VACCINE progam & CLIOPS unit
Non-International, multicentric study, aiming to constitute a collection of biological samples collected from cnetenary subjects and used for scientific purposes
Poster only available in French.
In collaboration with Gerond’If
BIMOP unit & ANTIMICROBIALS progam
HoloMoA: Digital Inline Holographic Microscopy to rapidly & Cost-effectively Determine the Mechanism of Action (MoA) of Antimicrobials
BIMOP unit
« Holographic Microscopy Data Analysis with Deep Learning for the Detection of Antimicrobial Mechanism of Action«
OMICS unit
« A quality control pipeline for Nanopore sequencing data, applicable for metagenomics«
In collaboration with bioMérieux
BIMOP unit
« Eight-wavelenght Digital In-line Holography & Brightfield Imaging in a single microscope«
In collaboration with bioMérieux & Laboratoire Hubert Curien
Omics>Proteomics unit
« Mutli-omics workflow for the identification of discriminant markers associated with Trypanosoma Cruzi populations«
In collaboration with London School of Hygiene & Tropical Medicine / DNDi
Science & Management Data unit
« Comparative analysis of supervised integrative methods for multi-omics data«
In collaboration with Bill & Melinda Gates Medical Reserach Institute
BIMOP unit
« Col/lm technology: an innovative generic multiplex assay technology«
MICROBIOME program
« Targeted culturomics: high-throughput sorting and cultivation of anaerobic commensal bacterial species form fecal microbiota«
OMICS hub unit/bioinformatics
« Comparison of DNA exctraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome«
In collaboration with BioMerieux
2022
MICROBIOME program
« Ex-vivo experimental approaches to explore the immunomodulatory and homeostatic potential of pre- and probiotics »
OMICS hub Unit
« Multi-omics workflow for the identification of dicriminant markers associated with Trypanosoma cruzi population »
BIMOP Unit / Microfluidics
« Gelatin molding and coating: applications in microfabrication, microfluidics and tissue engineering »
MICROBIOME program
« Towards an integrated in-vitro platform to investigate host-microbiota interactions using immunocompetent gut-on-chip »
2021
OMICS Hub Unit/Metabolomics
« Rapid thermal tissues stabilization for HRMAS NMR metabolic profiling »
In collaboration with Grenoble Institut Neurosciences, iRMaGe
BIMOP Unit/Microfluidics
« Optimizing the functionalization of super-paramagnetic beads for droplet-based protein secretion profiling of immune cells »
OMICs Hub Unit /Proteomics
« A Robust and Standardized Workflow to Analyze C. albicans differential Protein Expression using Tandem Mass Tag (TMT) »
in collaboration with COVARIS (www.covaris.com)
Bioassays, Microsystems & Optical engineering Unit / Holographic imaging
Bioassays, Microsystems & Optical engineering Unit/ MICROFLUIDICS
Bioassays, Microsystems & Optical engineering Unit/ Cellular Analysis & BIOASSAYS
2024
Diagnostics Program & MIMPS Unit
Development of a new rapid diagnostic test to support onchocerciasis elimination
BIMOP Unit
COLPLEX Technology: an Innovative Approach for the Development of Multiplex Point of Care Tests
Vaccines Programme & xDATA Unit
A predictive signature of vaccine reactogenicity for human peripheral blood to benchmark novel vaccine formulations
OMICS Unit
Enhanced shotgun metagenomics using Unique Molecular Identifier-based protocol with Oxford Nanopore sequencing
BIMOP Unit
The Colicin/Immunitysystem in the service of moleculardiagnostics
MIMPS Unit & Antimicrobial programme
Acinetobacter baumannii: Setup and characterization of pneumonia and septicemia preclinical models with longitudinal monitoring using bioluminescent strains
OMICS Unit
The promise of the Orbitrap ASTRAL mass-spectrometer for proteomics analysis
xDATA Unit & CLIOP Unit & Vaccines programme
Biobank Data Harmonization Across SARS-Cov-2 Cohorts for Robust Research Outcomes
OMICS Unit
A single workflow for multi-species blood transcriptomics
xDATA Unit
Integrated analysis of humoral immune response across several COVID immunization schemes in COVIDAuRA study
OMICS Unit
Multi-omics workflow for the identification of discriminant markers associated with Trypanosoma cruzi populations.
BIMOP Unit & Antimicrobial programme
Murine in vitro alveolar macrophage model to study the effects of influenza virus infection
xDATA Unit & BIMOP Unit & MIMPS Unit & CLIOP Unit
Fecal microbiota & Immune fitness evaluation in healthy, elderly and centenarians’ populations
Microbiota programme & BIMOP Unit & MIMPS Unit
Immunocompetent mid-throughput Gut-on-a-Chip model to study intestinal inflammation and homeostasis
xDATA Unit & BIMOP Unit & Diagnostic programme
Automatic Bacteria Classification on Microscopic Images of Positive Blood Culture Gram Smears
BIMOP unit
Microfluidic chip for bacterial biofilm formation and analysis
Poster presented @ Lab-on-a-Chip and Microfluidics Europe 2024 Conference.
Best Poster Awards Sponsored by Lab-on-a-Chip Journal, Royal Society of Chemistry (RSC): third position
2023
BIMOP unit
Col/lm Technology : an innovative generic multiplex assay technology
Poster presented at I4ID congress.
VACCINE progam & CLIOPS unit
Non-International, multicentric study, aiming to constitute a collection of biological samples collected from cnetenary subjects and used for scientific purposes
Poster only available in French.
In collaboration with Gerond’If
BIMOP unit & ANTIMICROBIALS progam
HoloMoA: Digital Inline Holographic Microscopy to rapidly & Cost-effectively Determine the Mechanism of Action (MoA) of Antimicrobials
BIMOP unit
« Holographic Microscopy Data Analysis with Deep Learning for the Detection of Antimicrobial Mechanism of Action«
OMICS unit
« A quality control pipeline for Nanopore sequencing data, applicable for metagenomics«
In collaboration with bioMérieux
BIMOP unit
« Eight-wavelenght Digital In-line Holography & Brightfield Imaging in a single microscope«
In collaboration with bioMérieux & Laboratoire Hubert Curien
Omics>Proteomics unit
« Mutli-omics workflow for the identification of discriminant markers associated with Trypanosoma Cruzi populations«
In collaboration with London School of Hygiene & Tropical Medicine / DNDi
Science & Management Data unit
« Comparative analysis of supervised integrative methods for multi-omics data«
In collaboration with Bill & Melinda Gates Medical Reserach Institute
BIMOP unit
« Col/lm technology: an innovative generic multiplex assay technology«
MICROBIOME program
« Targeted culturomics: high-throughput sorting and cultivation of anaerobic commensal bacterial species form fecal microbiota«
OMICS hub unit/bioinformatics
« Comparison of DNA exctraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome«
In collaboration with BioMerieux
2022
MICROBIOME program
« Ex-vivo experimental approaches to explore the immunomodulatory and homeostatic potential of pre- and probiotics »
OMICS hub Unit
« Multi-omics workflow for the identification of dicriminant markers associated with Trypanosoma cruzi population »
BIMOP Unit / Microfluidics
« Gelatin molding and coating: applications in microfabrication, microfluidics and tissue engineering »
MICROBIOME program
« Towards an integrated in-vitro platform to investigate host-microbiota interactions using immunocompetent gut-on-chip »
2021
OMICS Hub Unit/Metabolomics
« Rapid thermal tissues stabilization for HRMAS NMR metabolic profiling »
In collaboration with Grenoble Institut Neurosciences, iRMaGe
BIMOP Unit/Microfluidics
« Optimizing the functionalization of super-paramagnetic beads for droplet-based protein secretion profiling of immune cells »
OMICs Hub Unit /Proteomics
« A Robust and Standardized Workflow to Analyze C. albicans differential Protein Expression using Tandem Mass Tag (TMT) »
in collaboration with COVARIS (www.covaris.com)
Bioassays, Microsystems & Optical engineering Unit / Holographic imaging
Bioassays, Microsystems & Optical engineering Unit/ MICROFLUIDICS
Bioassays, Microsystems & Optical engineering Unit/ Cellular Analysis & BIOASSAYS
2019
Multi-omics approaches for diagnostics
Authors: Becker J, Moucadel V – With BioMérieux
Table ronde, Lyonbiopole, Lyon, France
Evaluation of integrative clustering methods for the analysis of multi-omics data
Authors: Chauvel C, Novoloaca A, Veyre P, Reynier F, Becker J
Conference: UseR 2019, Toulouse, France
BioTracs-MIMOSA: Mass spectrometry processing of Metabolomics Data
Authors: Abi-Ghanem J, Hennig K, Ouattara D;A, Bequet F.
RFMF, Clermont Ferrand, France
Identification by MALDI-TOF (VITEK® MS) of the highly pathogenic species: Burkholderia mallei and Burkholderia pseudomallei
Authors: Monnin V, Polsinelli S, Jacob D, Arend S, Boisse C, Michel F, Celliere B, Courault P, Villet R, Durand G, GirardV
Conference: ECCMID 2019, Amsterdam, the Netherlands
2018
Combination of ribosome display and next generation sequencing as a powerful method for identification of affibody binders against β-lactamase CTX-M15
Authors: Lagoutte P, Potisopon S, Elie C, Donnat S, Mignon C, Stadthagen Gomez G, Werle B
Conference: PEGS 2018, Lisbon, Portugal
GM15, a new gnotobiotic mouse model to explore interactions between microbiome and host physiology in childhood stunting induced by chronic undernutrition
Authors: Darnaud M, Bogeat P, Dugua H, Schwarzer M, Leulier F, Tamellini A
Conference: ICSB 2018, Lyon, France
Comparison DNA extraction methods for the analysis of the human gut microbiome using 16S and whole-genome sequencing
Authors: Elie C, Perret M, Louis K, Fritah-Lafont A, Laissner P, Vachon C, Rostaing H, Gervasi G, Reynier F, Saliou A – with BioMérieux
Conference: ICCMG, Geneva, Switzerland
Benchmark of unsupervised cytometry data analysis methods for the comparison of population
Authors: Courbon B, Beitz B, Delgado A, Sapay N
Conference: ICSB, Lyon, France
Encapsulin nanocages for simoultaneous surface dispaly and cargo loading
Authors: Mignon C, Lagoutte P, Donnat S, Potisopon S, Werle B
LUMI-Seq™ – Reconstruction of near full-lenght 16S rRNA genes using Illumina short reads
Authors: Elie C, Hirel j, Baum C, Reynier F, Saliou A
Conference: EMBL, Heidelberg, Germany
An automatic platform for Genome-Scale Metabolic Model reconstruction and Analysis
Authors: Ouattara D.A, Joseph C, Bunescu A, Abi-Ghanem J, Bequet F
Conference, ECCB 2018, Athens, Greece
OMICS Hub Unit/Metabolic
« InsightCell – online monitoring of living cells metabolism »
In collaboration with Bruker
Authors: Bunescu A, Codina A, Pennestri M
Conference: Translational Immunometabolism, Basel, Switzerland
Towards the deciphering of the MoA of an experimental drug against Chagas disease, using multi-omics platform
Authors: Hennig K, Abi Ghanem J, Bunescu A, Meniche X, Biliaut E, Bequet F, Lewis M, Kelly J, Braillard S, Courtemanche G, Chatelain E.
Childhood stunting model induced by chronic undernutrition in gnotobiotic mice
Authors: Darnaud M, Bogeat P, Dugua H, Schwarzer M, Leulier F, Tamellini A.
Conference: Keystone Symposia Microbiome, Banff, Canada
2017
Multi-omic Pathway Enrichment Analysis
Authors: Angelin-Bonnet O, Ouattara D. A, Reynier F., Becker J.
Conference: EMBL, Heidelberg, Germany
Development of an analytical workflow for the characterization of the microbiota metabolome using a combination of NMR and MS, through targeted & untargeted approaches
Authors: Hennig K, Bunescu A, Ouattara D.A, Meniche X, Abi Ghanem J, Biliaut E, Bequet F
Conference: HPLC 2017, Prague, Czech republic
Combinatorial design for random molecular cloning and screening of high yield expression vectors
Authors: Mariano N, Mignon C, Stadthagen Gomez G, Donnat S, Lagoutte P, Werle B
Conference: Recombinant Protein Production, Dubrovnik, Croatie
BIOSPECIMENS v1.5: a web platform to facilitate collaborative research on infectious diseases
Authors: Louis K, Rimbault B, Delestre C, Mouscaz Y, Albrieux M, Boisse C, Villet R, Boissy G
Conference: JOBIM, 2017
2016
Evaluation of integrative approaches for the analysis of multi_omics data
Authors: Novoloaca A, Reynier F, Becker J
JOBIM, 2016
Protein sequence recoding, codon usage bias on the bench
Authors: Mariano N, Mignon C, Chenavas S, Stadthagen G, Lugari A, Perot C., Donnat S, Lagoutte P, Diot F, Sodoyer R, Werle B
Conference: PEGS Boston
Met-SAMoA (Metabolic Screening of Antimicrobial Mode of Action) Development of an integrated NMR/MS metabolomics approach for the determination of the novelty of new antimicrobials mechanisms of action based on their metabolic signature
Authors: Bunescu A, Ouattara D.A, Meniche X, Billaut E, Boisse C, Tambosco J and Bequet F
Conference: ECCMID 2016, Amsterdam, NL
Development of an improved protocol for lipid analysis based on heat inactivation of enzymes
Authors: Meniche X, Ouattara D.A, Hennig K, Sköld K, Boren M, Elias Y, Biliaut E, Bogeat P, Boisse C, Peltier M, Jacob C, Bunescu A, Bequet F
Conference: IPID MAPS Annual Meeting 2016, La Jolla, US
Prevention of metabolite change due to enzymatic post-sample activity using heat based enzyme inactivation
Authors: Bunescu A, Ouattara D. A, Sköld K, Boren M, Biliaut E, Hennig K ,Bogeat P, Boisse C, Peltier M, Meniche X, Jacob C, Bequet F
Conference: 5th International Conference and Exhibition on Metabolomics, Osaka, Japan
The bioinformatics timeline of the data integration in BIOASTER
Authors: Mouscaz Y, Cauchard A, Malinovic A, Picandet L, Sapay N, Veyre P and Boissy G
Conference: JeBiF Workshop @ JOBIM 2016 Lyon
Validation of methods to characterize and monitor injury-induced immune deficiency in severe intensive care unit patients
Authors: Rol M.L, Moucadel V, Cerrato E, Riffaud C, Gallet-Gorius E, Portier A, Demaret J, Tabone O, Malcus C, Rimmele T, Monneret G, Textoris J, Venet F, On behalf of the Realism Study Group
Conference: Congres ESID Barcelona
2015
BIOSPECIMEN: a web platform developed to facilitate research on infectious diseases & microbiota
Authors: Louis K, Rimbault B, Gaillard C, Costaz L, Guyard C, Khlebnikov A and Troesch A
Conference: CCO XXXIV European Culture Collections as tools in research and biotechnology. Paris
Comparative Analysis – A Balb/c Mice Core Gut Microbiome?
Authors: Boucinha L, Reynier F, Schwarzer M, Leulier F, van Hijum S
Conference: The Human Microbiome, EMBL conference, Heidelberg, Germany, June 2015
Insight into the Protein and Expression Systems Engineering unit of Bioaster, a technology institute specialized in infectious diseases and microbiology
Authors: Donnat S, Lagoutte P, Lugari A, Mignon C, Sodoyer R, Stadthagen G and Werle B
Conference: French Brazilian Biomedical Innovation Forum, San Paoulo Instituit Butantan
Controlled ultrasound cavitation for DNA delivery into bacteria and yeast/ Award for best poster
Authors: Stadthagen G, Mignon C, Mestas J-L, Donnat S, Poncet E, Sodoyer R, Lafon C, Werle B
Conference: International Conference of Synthetic Biology, Houston, Sept 2015
Fast protein liquid chromatography based purification of MS2 bacteriophage virus-like particles
Authors: Lagoutte P, Mignon C, Donnat S, Mast J, Lugari A and Werle B
Conference: Word vaccine congres Europe, Madrid, 9 au 12 novembre 2015
A new animal facility in Lyon Gerland area to explore microbiome
Authors: Darnaud M, Peltier M, Tamellini A et al
Conference: 8ème Journée Scientifique de la SFR Biosciences, Lyon
BIOASTER: Animal models and imaging competencies to improve chlamydial studies
Authors: Rekiki A, Darnaud M, Gaudin A , Peltier M, Bogeat P, Tamellini A
Conference: European meeting on animal chlamydiosis
Multi-omics data integration platform in public-private partnership
Authors: Sapay N, Veyre P, Le Carrour T, Cauchard A, Garnier J
Conference: JOBIM, Clermont-Ferrand
Evaluation of heat stabilization for the conservation of biological samples as an approach for metabolomics: a 1H-NMR/LC-MS metabolite profiling study
Authors: Bequet F, Bunescu A, Ouattara D.A, Meniche X, Da Costa Jacob C, Billiaut E, Bogeat P, Gaillard C, Peltier M, Sköld K, Boren M, Tamellini A, Guyard C, Troesch A
Conference: Metabolomics Conference 2015 – San