2024
A single workflow for multi-species blood transcriptomics
Authors: Elody Orcel, Hayat Hage, May Taha, Noémie Boucher, Emilie Chautard, Virginie Courtois & Adrien Saliou
Doi
Development of Mass Spectrometry Imaging on skeletal muscle to characterize the local pro-inflammatory and pro-resolution lipid responses in a vaccination context
Authors: Thomas Ribette, Yannick Charretier, Sébastien Laurent, Patrick Syntin, Emilie Chautard, Xavier Meniche, Marion Darnaud, Frédéric Becquet, Laurent Beloeil, Fabienne Piras-Douce, Josephine Abi-Ghanem
Doi
2023
Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach
Authors: Hugo Roume, Stanislas Mondot, Adrien Saliou, Sophie Le Fresne-Languille & Joël Doré
Doi
Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study
Authors: Morgane Heitz, Albrice Levrat, Vladimir Lazarevic, Olivier Barraud, Stéphane Bland, Emmanuelle Santiago-Allexant, Karen Louis, Jacques Schrenzel & Sébastien Hauser
Doi
- Cysteamine-mediated blockade of the glycine cleavage system modulates epithelial cell inflammatory and innate immune responses to viral infection
Authors: Douglas Fraser-Pitt, Derry K. Mercer, Marie-Louise Francis, David Toledo-Aparicio, Daniel W. Smith, Deborah A. O’Neil
Doi
- Multispectral in-line hologram reconstruction with aberration compensation applied to Gram-stained bacteria microscopy
In collaboration with bioMérieux & LaHC
Authors: Dylan Brault, Thomas Olivier, Nicolas Faure, Sophie Dixneuf, Chloé Kolytcheff, Elodie Charmette, Ferréol Soulez & Corinne Fournier
Doi
- Single-cell scattering and auto-fluorescence-based fast antibiotic susceptibility testing for gram-negative & gram-positive bacteria
In collaboration with bioMérieux
Authors: Sophie Dixneuf, Anne-Coline Chareire-Kleiberg, Pierre Mahé, Meriem El Azami, Chloé Kolytcheff, Samuel Bellais, Cyril Guyard, Christophe Védrine, Frédéric Mallard, Quentin Josso, Fabian Rol
Doi
- Interspecies comparison of the early transcriptomic changes associated with hepatitis B virus exposure in human and macaque immune cell populations
Authors: Armando Andres Roca Suarez, Séverine Planel, Xavier Grand, Céline Couturier, Trang Tran, Fabrice Porcheray, Jérémie Becker, Frédéric Reynier, Ana Delgado, Elodie Cascales, Loïc Peyrot, Andrea Tamellini, Adrien Saliou, Céline Elie, Chloé Baum, Bao Quoc Vuong, Barbara Testoni, Pierre Roques, Fabien Zoulim, Uzma Hasan, Isabelle Chemin
https://www.frontiersin.org/articles/10.3389/fcimb.2023.1248782/full
- Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 – A pilot Study.
In collaboration with Genetic Analysis SA
Authors: Kristin Gravdal, Katrine H. Kirste, Krzysztofa Grzelak, Graceline Tina Kirubakaran, Philippe Leissner, Adrien Saliou & Christina Casèn
https://bmcendocrdisord.biomedcentral.com/articles/10.1186/s12902-023-01432-0
- Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome.
Authors: Céline Elie, Magali Perret, Hayat Hage, Erwin Sentausa, Amy Hesketh, Karen Louis, Asmaà Fritah-Lafont, Philippe Leissner, Carole Vachon, Hervé Rostaing, Frédéric Reynier, Gaspard Gervasi & Adrien Saliou
https://doi.org/10.1038/s41598-023-33959-6
- Antimicrobial Resistance: a Biochemical Society position statement.
Authors: Tailise De Souza; G. Rodrigues; Anthony Maxwell; Derry K. Mercer; Orla Lappin
https://doi.org/10.1042/bio_2022_148
- Prior SARS-CoV-2 infection enhances and reshapes spike protein-specific induced by vaccination.
Authors: Véronique Barateau, Loïc Peyrot, Carla Saade, Bruno Pozzetto, Karen Brengel-Pesce, Mad-Hélénie Elsensohn, Omran Allatif, Nicolas Guibert, Christelle Compagnon, Natacha Mariano, Julie Chaix, Sophia Djeballi, Jean-Baptiste Fassier, Bruno Lina, Katia Lefsihane, Maxime Espi, Olivier Thaunat, Jacqueline Marvel, Manuel Rosa-Calatrava, Andres Pizzorno, Delphine Maucourt-Boulch, Laetitia Henaff, Mitra Saadatian-Elahi, Philippe Vanheims, Stéphane Paul, Thierry Walzer, Sophie Trouillet-Assant and Thierry Defrance
DOI: 10.1126/scitranslmed.ade0550
Authors: Asare Paul-Tetteh, Lee Chi-Hsien, Hürlimann Vera, Teo Youzheng, Cuénod Aline, Akduman Nermin, Gekeler Cordula, Afrizal Afrizal, Corthesy Myriam, Kohout Claire, Thomas Vincent, de Wouters Tomas, Greub Gilbert, Clavel Thomas, Pamer Eric- G, Egli Adrian, Maier Lisa, Vonaesch Pascale
DOI: 10.3389/fmicb.2023.1104707
Authors: Anziani Paul, Becker Jérémie, Mignon Charlotte, Arnaud-Barbe Nadège, Courtois Virginie, Izac Marie, Pizzato Romain, Abi-Ghanem Joséphine, Tran Viet-Dung, Sarafian Magali, Bunescu Andrei, Garnier Dominique, Abachin Eric, Renauld-Mongénie Geneviève, Guyard Cyril.
DOI: 10.3389/fmicb.2023.1104707
2022
- A gaps-and-needs analysis of vaccine R&D in Europe: Recommendations to improve the research infrastructure
Authors: Stefan Jungblut, Hilde Depraetere, Monika Slezak, Dennis Christensen, Norbert Stockhofe, Laurent Beloeil
10.1016/j.biologicals.2022.02.003
- Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions
Authors: Samuel Bellais, Mélanie Nehlich, Maryne Ania, Aurore Duquenoy, Wilfrid Mazier, Ger van den Engh, Jan Baijer, Nicole Simone Treichel, Thomas Clavel, Ilia Belotserkovsky & Vincent Thomas
https://doi.org/10.1186/s40168-021-01206-7
2021
Monocyte Trajectories Endotypes Are Associated With Worsening in Septic Patients
Authors: Bodinier M, Peronnet E, Brengel-Pesce K , Conti F, Rimmelé T, Textoris J, Vedrine C, Quemeneur L, Griffiths A. D., Tan L. K. , Venet F, Maucort-Boulch D, Monneret G, for the REALISM study group
https://doi.org/10.3389/fimmu.2021.795052
A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes
Authors: Darnaud M, De Vadder F, Bogeat P, Boucinha L, Bulteau A. L, Bunescu A, Couturier C, Delgado A, Dugua H, Elie C, Mathieu A, Novotnà T, Ouattara D. A, Planel S, Saliou A, Srutkova D, Yansouni J, Stecher B, Schwarzer M. , Leulier F, Tamellini A
https://doi.org/10.1038/s41467-021-26963-9
Herpes DNAemia and TTV Viraemia in Intensive Care Unit Critically III patients: A single-Centre Propsective Longitudinal study
Authors: Mallet F, Diouf L, Meunier B, Perret M, Reynier F, Leissner P, Quemeneur L , Griffiths A.D, Moucadel V, PachotA , Venet F, Monneret G, Lepape A, Rimmelé T, TanL. K, Brengel-Pesce K and Textoris J on behalf of the REALISM Study Group
https://doi.org/10.3389/fimmu.2021.698808
Blood transcriptomics reveal the evolution and resolution of the immune response in tuberculosis
Authors: Tabone O, Verma R, Singhania A, Chakravarty P, Branchett W.J, Graham C.M, Lee J, Trang T, Reynier F, Leissner P, Kaiser K, Rodrigue M, Woltmann G, Haldar P, O’Garra A.
https://doi.org/10.1084/jem.20210915
Assessing the Functional Heterogeneity of Monocytes in Human Septic Shock: a Proof-of-Concept Microfluidic Assay of TNFα Secretion
Authors: Llitjos JF, Bounab Y, Rousseau C, Dixneuf S, Rimbault B, Chiche JF, Textoris J, Pène F. Védrine C.
Front. Immunol., 05 July 2021 | https://doi.org/10.3389/fimmu.2021.686111
Antibody avidity, persistence, and response to antigen recall: comparison of vaccine adjuvants
Authors: Budroni S, Buricchi F, Cavallone A, Bourguignon P, Caubet M, Dewar V, D’Oro U, Finco O, Garçon N, El Idrissi M, Janssens M, Leroux-Roels G, Marchant A, Schwarz T, Van Damme P, Volpini G, van der Most R, Didierlaurent AM, Burny W.
NPJ Vaccines. 2021 May 21;6(1):78. doi: 10.1038/s41541-021-00337-0.
Fast Antibiotic Susceptibility testing via Raman Microspectrometry on Single Bacteria: An MRSA Case study
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ACS Omega. 2021 Jun 15;6(25):16273-16279. doi: 10.1021/acsomega.1c00170
Author Correction: Dynamic single-cell phenotyping of immune cells using the microfluidic platform DropMap
Authors: Bounab Y, Eyer K, Dixneuf S, Rybczynska M, Chauvel C, Mistretta M, Tran T, Aymerich N, Chenon G, Llitjos JF, Venet F, Monneret G, Gillespie IA, Cortez P, Moucadel V, Pachot A, Troesch A, Leissner P, Textoris J, Bibette J, Guyard C, Baudry J, Griffiths AD, Védrine C.
Nat Protoc. 2021 Jan 13. doi: 10.1038/s41596-021-00492-7.
2020
Clinical metagenomics bioinformatics pipeline for the identification of hospital-acquired pneumonia pathogens antibiotic resistance genes form bronchoalveolar lavage samples
Authors:Maud Tournoud, Etienne Ruppé, Guillaume Perrin, Stéphane Schicklin, Ghislaine Guigon, Pierre Mahé, Vladimir Lazarevic, Sébastien Hauser, Caroline Mirande, Albrice Levrat, Karen Louis, Gaspard Gervasi, Jacques Schrenzel
https://doi.org/10.1101/2020.02.26.966309
The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives.
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FEMS Microbiol Rev. 2020 Nov 24:fuaa060. doi: 10.1093/femsre/fuaa060.
Safety biomarkers for development of vaccines and biologics: Report from the safety biomarkers symposium held on November 28-29, 2017, Marcy l’Etoile, France.
Authors: Doubovetzky M, Ataman-Önal Y, Chousterman B, Feroldi E, Garçon N, Grillet MH, Kramer D, Laurent S, Lewis DJM, Luna E, Manigold T, Syntin P, Burdin N, Fraisse L, Jackson N.Vaccine. 2020 Dec 3;38(51):8055-8063. doi: 10.1016/j.vaccine.2020.10.015.
An integrated transcriptomics and metabolomics study of the immune response of newly hatched chicks to the cytosine-phosphate-guanine oligonucleotide stimulation.
Authors: Ouattara DA, Remolue L, Becker J, Perret M, Bunescu A, Hennig K, Biliaut E, Badin A, Giacomini C, Reynier F, Andreoni C, Béquet F, Lecine P, De Luca K.
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Draft Genome Sequences of 15 Bacterial Species Constituting the Stable Defined Intestinal Microbiota of the GM15 Gnotobiotic Mouse Model.
Authors: Elie C, Mathieu A, Saliou A, Villain A, Darnaud M, Leulier F, Tamellini A.
Microbiol Resour Announc. 2020 Aug 27;9(35):e00686-20. doi: 10.1128/MRA.00686-20
Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity
Authors: Duquenoy A, Ania M, Boucher N, Reynier F, Boucinha L, Andreoni C, Thomas V.
PLoS One. 2020 Aug 24;15(8):e0237541. doi: 10.1371/journal.pone.0237541
Dynamic single-cell phenotyping of immune cells using the microfluidic platform DropMap
Authors: Bounab Y, Eyer K, Dixneuf S, Rybczynska M, Chauvel C, Mistretta M, Tran T, Aymerich N, Chenon G, Llitjos JF, Venet F, Monneret G, Gillespie IA, Cortez P, Moucadel V, Pachot A, Troesch A, Leissner P, Textoris J, Bibette J, Guyard C, Baudry J, Griffiths AD, Védrine C.
Nat Protoc. 2020 Sep;15(9):2920-2955. doi: 10.1038/s41596-020-0354-0
Assessment of Gram- and Viability-Staining Methods for Quantifying Bacterial Community Dynamics Using Flow Cytometry
Duquenoy A, Bellais S, Gasc C, Schwintner C, Dore J, Thomas V.
Front Microbiol. 2020 Jun 26;11:1469. doi: 10.3389/fmicb.2020.01469
The science of vaccine safety: Summary of meeting at Wellcome Trust.
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Therapie. 2020 Jan-Feb;75(1):7-12. doi: 10.1016/j.therap.2019.12.003. Epub 2019 Dec 16.
Stiffness, pain and joint counts in chronic chikungunya disease: relevance to disability and quality of life
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Characterization and analytical validation of a new antigenic rapid diagnostic test for Ebola virus disease detection
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PLoS Negl Trop Dis. 2020 Jan 17;14(1):e0007965. doi: 10.1371/journal.pntd.0007965
Evaluation of integrative clustering methods for the analysis of multi-omics data
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Brief Bioinform. 2020 Feb 14. pii: bbz015. doi: 10.1093/bib/bbz015
2019
Chagas Disease Drug Discovery: Multiparametric Lead Optimization against Trypanosoma cruzi in Acylaminobenzothiazole Series
Authors: Charlotte Fleau, Angel Padilla, Juan Miguel-Siles, Maria T. Quesada-Campos, Isabel Saiz-Nicolas, Ignacio Cotillo, Juan Cantizani Perez, Rick L. Tarleton, Maria Marco and Gilles Courtemanche.
J. Med. Chem. 2019, 62, 10362−10375
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Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients.
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Front Microbiol. 2019 Sep 18;10:1898. doi: 10.3389/fmicb.2019.01898.
2HybridTools, a handy software to facilitate clone identification and mutation mapping from yeast two-hybrid screening
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PeerJ. 2019 Jul 3;7:e7245. doi: 10.7717/peerj.7245. eCollection 2019.
SATQPCR: Website or statistical analysis of real-timequantitative PCR data
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Metabolomics, lipidomics and proteomics profiling of myoblasts infected with Trypanosoma cruzi after treatment with different drugs against Chagas disease
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Metabolomics (2019) 15:117 https://doi.org/10.1007/s11306-019-1583-5
Early herpes and TTV DNAemia in septic shock patients: a pilot study
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Journal Intensive Care Med Exp. 2019
Combination of ribosome display and next generation sequencing as a powerful method for identification of affibody binders against β-lactamase CTX-M15
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Safety of AS03-adjuvanted influenza vaccines: A review of the evidence.
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Polymorphisms of a Collagen-Like Adhesin Contributes to Legionella pneumophila Adhesion, Biofilm Formation Capacity and Clinical Prevalence.
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Translocation and calmodulin-activation of the adenylate cyclase toxin (CyaA) of Bordetella pertussis
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Metagenomics next generation sequencing reveals individual composition and dynamics of anelloviruses during autologous stem cell Transplant Recipient Management
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Journal: Viruses
Simultaneous surface display and cargo loading of encapsulin nanocompartments and their use for rational vaccine design
Authors: Lagoutte P, Mignon C, Stadthagen G, Potisopon S, Donnat S, Mast J, Lugari A, Werle B.
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Biosensors for the Detection of Interaction between Legionella pneumophila Collagen-Like Protein and Glycosaminoglycans
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A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection
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Small Rho GTPases and the Effector VipA Mediate the Invasion of Epithelial Cells by Filamentous Legionella pneumophila
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Culture-free Antibiotic-susceptibility Determination From Single-bacterium Raman Spectra
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Codon harmonization – going beyond the speed limit for protein expression
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The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect?
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Lactobacillus paracasei feeding improves immune control of influenza infection in mice
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Signal management in pharmacovigilance and human risk assessment of CpG 7909, integrating embryo-fetal and post-natal developmental toxicity studies in rats and rabbits
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Cellular and molecular synergy in AS01-adjuvanted vaccines results in an early IFNγ response promoting vaccine immunogenicity
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Different Adjuvants Induce Common Innate Pathways That Are Associated with Enhanced Adaptive Responses against a Model Antigen in Humans
Authors: Burny W, Callegaro A, Bechtold V, Clement F, Delhaye S, Fissette L, Janssens M, Leroux-Roels G, Marchant A, van den Berg R. A, Garçon N, van der Most R and Didierlaurent Arnaud M. On Behalf of the ECR-002 Study Group
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The REAnimation Low Immune Status Markers (REALISM) project: a protocol for broad characterisation and follow-up of injury-induced immunosuppression in intensive care unit (ICU) critically ill patients
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Intramuscularly administered herpes zoster subunit vaccine has no effects on fertility, pre- and post-natal development in Sprague-Dawley rats
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Clinical, virological, and biological parameters associated with outcomes of Ebola virus infection in Macenta, Guinea
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Chapitre: Les vaccins ou deux siècles de biotechnologies
Authors: Sodoyer R, Drouet E, Werle B
Book: Les biotechnologies en santé tome1.
From discovery to licensure, the Adjuvant System story
Authors: Garçon N, Di Pasquale A.
Journal: Hum Vaccin Immunother.
Vaccine safety evaluation: Practical aspects in assessing benefits and risks
Authors: Di Pasquale A, Bonanni P, Garçon N, Stanberry LR, El-Hodhod M, Tavares Da Silva F.
Journal: Vaccine
Vaccine provision: Delivering sustained & widespread use
Authors: Preiss S, Garçon N, Cunningham AL, Strugnell R, Friedland LR.
Journal: Vaccine
Vaccine development: From concept to early clinical testing
Authors: Cunningham AL, Garçon N, Leo O, Friedland LR, Strugnell R, Laupèze B, Doherty M, Stern P.
Journal: Vaccine
Zika antiviral chemotherapy: identification of drugs and promising starting points for drug discovery from an FDA-approved library
Authors: Pascoalino B.S, Courtemanche G, Cordeiro M.T, Gil L. H. V. G. , Freitas-Junior L
Journal: F1000Research
Impact of adjuvants on CD4(+) T cell and B cell responses to a protein antigen vaccine: Results from a phase II, randomized, multicenter trial
Authors: Leroux-Roels G, Marchant A, Levy J, Van Damme P, Schwarz TF, Horsmans Y, Jilg W, Kremsner PG, Haelterman E, Clément F, Gabor JJ, Esen M, Hens A, Carletti I, Fissette L, Tavares Da Silva F, Burny W, Janssens M, Moris P, Didierlaurent AM, Van Der Most R, Garçon N, Van Belle P, Van Mechelen M.
Journal: Clin Immunol.
Reducing hypoxia and inflammation during invasive pulmonary aspergillosis by targeting the Interleukin-1 receptor
Authors: Gresnigt M.S. , Rekiki A, Rasid O, Savers A, Jouvion G, Dannaoui E, Parlato M, Fitting C, Brock M, Cavaillon J-M, van de Veerdonk F. L. & Ibrahim-Granet O
Journal: Nature Scientific Reports
Chapter 5: Hydrophilic Interaction Liquid Chromatography (HILIC) and Perfluorinated Stationary Phases, pp. 149-184
Authors: Cristina C. JACOB
Book: Fast Liquid Chromatography – Mass Spectrometry Methods in Food and Environmental Analysis (Imperial College Press)
Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen
Authors: Rao C, Guyard C, Pelaz C, Wasserscheid J, Bondy-Denomy J, Dewar K, Ensminger AW.
Journal: Cell Microbiol.
Scalable chromatography-based purification of virus-like particle carrier for epitope based Influenza A vaccine produced in Escherichia coli
Authors: Lagoutte P, Mignon C, Donnat S, Stadthagen G, Mast J, Sodoyer R, Lugari A and Werle B
Journal: J. Virol. Methods
Non-clinical safety evaluation of repeated intramuscular administration of the AS15 immunostimulant combined with various antigens in rabbits and cynomolgus monkeys
Authors: Garçon N, Silvano J, Kuper CF, Baudson N, Gérard C, Forster R, Segal L.
Journal: J Appl Toxicol.
2015
Differential proteomic analysis of virus-enriched fractions obtained from plasma pools of patients with dengue fever or severe dengue
Authors: Fragnoud R, Flamand M, Reynier F, Buchy P, Duong V, Pachot A, Paranhos-Baccala G, Bedin F.
Journal: BMC Infect Dis.
Draft Genome Sequences of Acinetobacter parvus CM11, Acinetobacter radioresistens CM38, and Stenotrophomonas maltophilia BR12, Isolated from Murine Proximal Colonic Tissue
Authors: Saffarian A, Mulet C, Naito T, Bouchier C, Tichit M, Ma L, Grompone G, Sansonetti PJ, Pédron T.
Journal: Genome Announc.
Vaccine Adjuvants: from 1920 to 2015 and Beyond
Authors: Di Pasquale A, Preiss S, Tavares Da Silva F, Garçon N.
Journal: Vaccines
Antibiotic free selection in Biotherapeutics
Authors: Mignon C. , Sodoyer R. , Werle B.
Journal: Antibiotic free selection in Biotherapeutics: Now and Forever, Pathogens
A FACS-optimized screen identifies regulators of genome stability in Candida albicans
Authors: Loll-Krippleber R, Feri A, Nguyen M, Maufrais C, Yansouni J, d’Enfert C, Legrand M
Journal: Eukaryot Cell.
Non clinical reproductive and developmental safety evaluation of he MAGE-A3 Cancer Immunotherapeutic, a therapeutic vaccine for cancer treatment
Authors: Destexhe E, Stannard D, Wilby OK, Grosdidier E, Baudson N, Forster R, Gérard CM, Garçon N, Segal L.
Journal: Elsevier, Reproductive toxicology Volume 51