Our publications

Our publications


A Cervix Detection Driven Deep Learning Approach for Cow Heat Analysis from Endoscopic Images.
He R, Benhabiles H, Windal F, Even G, Audebert C, Collard D, Taleb-Ahmed A

Conference: IEEE International Conference on Image Processing (2022)

A CNN-based methodology for cow heat analysis from endoscopic images.

Ruiwen He, Halim Benhabiles, Feryal Windal, Gaël Even, Christophe Audebert, Agathe Decherf, Dominique Collard & Abdelmalik Taleb-Ahmed

Applied Intelligence (2022)

Prevalence, Subtype Distribution and Zoonotic Significance of Blastocystis sp. Isolates from Poultry, Cattle and Pets in Northern Egypt.
Naguib D, Gantois N, Desramaut J, Arafat N, Even G, Certad G, Chabé M, Viscogliosi E. 

Microorganisms (2022)

Putative SET-domain methyltransferases in Cryptosporidium parvum and histone methylation during infection.
Sawant M, Benamrouz-Vanneste S, Meloni D, Gantois N, Even G, Guyot K, Creusy C, Duval E, Wintjens R, B. Weitzman J, Chabe M, Viscogliosi E & Certad G

Virulence (2022)

Animal, Herd and Feed Characteristics Associated with Blastocystis Prevalence and Molecular Diversity in Dairy Cattle from the North of France.
Audebert C, Gantois N, Ducrocq S, Darras M, Merlin S, Martel S, Viscogliosi E, Even G, Chabé M

Parasitologia (2022)

Detection, Molecular Identification and Transmission of the Intestinal Protozoa Blastocystis sp. in Guinea from a Large-Scale Epidemiological Study Conducted in the Conakry Area.
Guilavogui T, Gantois N, Even G, Desramaut J, Dautel E, Denoyelle C, Ibrahima Cissé F, Cherif Touré S, Luther Kourouma B, Sawant M, Chabé M, Certad G, Viscogliosi E

Microorganisms (2022)

A multiplex serological assay for the characterization of IgG immune response to SARS-CoV-2.
Brochot E., Souplet V. , Follet P., Ponthieu P., Olivier C., Even G., Audebert C., Malbec R.

Plos One (2022)


A multiplex serological assay for the characterization of IgG immune response to SARS-CoV-2.
Brochot E., Souplet V., Follet P., Ponthieu P., Olivier C., Even G., Audebert C., Malbec R.

medRxiv.org, September 2021

Blastocystis sp. Prevalence and Subtypes Distribution amongst Syrian Refugee Communities Living in North Lebanon.

Khaled S, Gantois N, Ayoubi A, Even G, Sawant M, El Houmayraa J, Nabot M, Benamrouz-Vanneste S, Chabé M, Certad G, El Safadi D, Dabboussi F, Hamze M, Viscogliosi, E. 

MDPI, January 2021

Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations.
Even G, Lokmer A, Rodrigues J, Audebert C, Viscogliosi E, Ségurel L and Chabé M

Front. Cell. Infect. Microbiol., March 2021


Prevalence and Subtype Distribution of Blastocystis sp. in Senegalese School Children.
Khaled S, Gantois N, Ly A.T, Senghor S, Even G, Dautel E, Dejager R, Sawant M, Baydoun M, Benamrouz-Vanneste S, Chabé M, Ndiaye S, Schacht A.-M, Certad G, Riveau G, Viscogliosi E.

MDPI, September 2020

Agrodiag PorCoV: A multiplex immunoassay for the differential diagnosis of porcine enteric coronaviruses.

Malbec R, Kimpston-Burkgren K, Vandenkoornhuyse E, Olivier C, Souplet V, Audebert C, Carrillo-Ávila JA, Baum D, Giménez-Lirola L.

J Immunol Methods. 2020 Aug

Genetic basis for virulence differences of various Cryptosporidium parvum carcinogenic isolates.

Audebert C, Bonardi F, Caboche S, Guyot K, Touzet H, Merlin S, Gantois N, Creusy C, Meloni D, Mouray A, Viscogliosi E, Certad G, Benamrouz-Vanneste S, Chabé M.

Sci Rep. 2020 Apr

Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis.

Soret P, Vandenborght LE, Francis F, Coron N, Enaud R, Avalos M, Schaeverbeke T, Berger P, Fayon M, Thiebaut R, Delhaes L; Mucofong Investigation Group.

Sci Rep. 2020 Feb 27

Porcine bacteriospermia examined by high-throughput sequencing.

Even G, Mottais D, Morien F, Pham MD, Ostergaard A, Martel S, Merlin S, Audebert C.

Theriogenology. 2020 Jan


The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?

Siegwald L., Caboche S., Even G., Viscogliosi E, Chabé M. and Audebert C.

MDPI, September 2019

Prevalence, Molecular Identification, and Risk Factors for Cryptosporidium Infection in Edible Marine Fish: A Survey Across Sea Areas Surrounding France.

Certad Gabriela, Follet Jérôme, Gantois Nausicaa, Hammouma-Ghelboun Ourida, Guyot Karine, Benamrouz-Vanneste Sadia, Fréalle Emilie, Seesao Yuwalee, Delaire Baptiste, Creusy Colette, Even Gaël, Verrez-Bagnis Veronique, Ryan Una, Gay Mélanie, Aliouat-Denis Cécile, Viscogliosi Eric

Frontiers in Microbiology, May 2019

The Formation of Glycan-Specific Natural Antibodies Repertoire in GalT-KO Mice Is Determined by Gut Microbiota.

Daniel Bello-Gil, Christophe Audebert, Sara Olivera-Ardid, Magdiel Pérez-Cruz, Gaël Even, Nailya Khasbiullina, Nausicaa Gantois, Nadezhda Shilova, Sophie Merlin, Cristina Costa, Nicolai Bovin and Rafael Mañez

Frontiers in Immunology, March 2019


Prospects for applications in human health of nanopore-based sequencing.

Audebert C., Hot D., & Caboche S.

Medecine Science, April 2018


Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics.

Siegwald L., Touzet H., Lemoine Y., Hot D., Audebert C. & Caboche S.

PLOS ONE, 2017 Jan

Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis. colonization.

Siegwald L., Audebert C., Even G., Viscogliosi E., Caboche S. & Chabé M.


MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data.

Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert and David Hot


High association of Cryptosporidium spp. infection with colon adenocarcinoma in Lebanese patients.

Marwan Osman, Sadia Benamrouz, Karine Guyot, Martha Baydoun, Emilie Frealle, Magali Chabe, Nausicaa Gantois, Baptiste Delaire, Anne Goffard, Albert Aoun, Nawaf Jurdi, Fouad Dabboussi, Gael Even, Christian Slomianny, Pierre Gosset, Monzer Hamze, Colette Creusy, Eric Viscogliosi, Gabriela Certad.

PLOS ONE, 2017 Dec


Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota.

Audebert C., Even G., Cian A., The Blastocystis Investigation Group, Loywick A., Merlin S., Viscogliosi E. & Chabé M.

Scientific Reports, 2016 May

A review of methods for nematode identification.

Seesao Y, Gay M, Merlin S, Viscogliosi E, Aliouat-Denis CM, Audebert C.

J Microbiol Methods, 2016 Jun

Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation.

Nguyen LD., Deschaght P., Merlin S., Loywick A., Audebert C., Van Daele S., Viscogliosi E., Vaneechoutte M., Delhaes L.

PLoS One, 2016 Dec


Photodynamic therapy relieves colitis and prevents colitis-associated carcinogenesis in mice.

Reinhard A., Bressenot A., Dassonneville R., Loywick A., Hot D., Audebert C., Marchal S., Guillemin F., Chamaillard M., Peyrin-Biroulet L., Bezdetnaya L.

Inflamm Bowel Dis. 2015 May

49 Propidium monoazide (PMA) sample pretreatment impacts the abundance of rare populations in high-throughput sequencing analysis of CF lung mycobiome and bacteriome.

Nguyena L., Deschaght P., Merlin S., Loywick A., Audebert C., Viscogliosi E., Vaneechoutte M., Delhaes L.

Journal of Cystic Fibrosis, Volume 14, Supplement 1, June 2015, Pages S70, Abstracts of the 38th European Cystic Fibrosis Conference

Relationship Between Pneumocystis carinii Burden and the Degree of Host Immunosuppression in an Airborne Transmission Experimental Model.

Khalife S., Chabé M., Gantois N., Audebert C, Pottier M., Hlais S., Pinçon C., Chassat T., Pierrot C., Khalife J., Aliouat-Denis CM., Aliouat EM.

J Eukaryot Microbiol. 2015 Oct 28


High-Throughput Sequencing, a Versatile Weapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology.

Caboche S, Audebert C, Hot D

Pathogens 2014 2 Apr 2, 3, 258-279

Cryptosporidium parvum-induced ileo-caecal adenocarcinoma and WNT signaling in a rodent model.

Benamrouz S, Conseil V, Chabe M, Praet M, Audebert C, Blervaque R, Guyot K, Gazzola S, Mouray A, Chassat T, Delaire B, Goetinck N, Gantois N, Osman M, Slomianny C, Dehennaut V, Lefebvre T, Viscogliosi E, Cuvelier C, Dei-Cas E, Creusy C, Certad G.

Dis Model Mech. 2014 Mar 2

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

Caboche S, Audebert C, Lemoine Y, Hot D

BMC Genomics. 2014 Apr 5;15(1):264

Monitoring of four DNA extraction methods upstream of high-throughput sequencing of Anisakidae nematodes.

Seesao Y, Audebert C, Verrez-Bagnis V, Merlin S, Jérôme M, Viscogliosi E, Dei-Cas E, Aliouat-Denis CM, Gay M.

J Microbiol Methods. 2014 May 15, pii: S0167-7012(14)00125-0

An improved single-round PCR leads to rapid and highly sensitive detection of Pneumocystis spp.

Chabé M, Khalife S, Gantois N, Even G, Audebert C

Med Mycol. 2014 Nov 1;52(8):841-6. doi: 10.1093/mmy/myu032. Epub 2014 Jun 25.

Le séquençage haut-débit – Vers un diagnostic basé sur la séquence complète du génome de l’agent infectieux (High-throughput sequencing: towards a genome-based diagnosis in infectious diseases).

Audebert C,Hot D, Lemoine Y and Caboche S

Med Sci (Paris). 2014 Dec;30(12):1144-51