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Articles

2024
  • Barcia-Cruz R, Goudenège D, Moura de Sousa JA, Piel D, Marbouty M, Rocha EPC, Le Roux F. (2024) Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages. Nat Commun. 15(1):664 DOI
  • Reignier O., Bormans M., Hervé F., Robert E., Savar V., Tanniou S., Amzil Z., Noël C. and Briand E. (2024). Spatio-temporal connectivity of a toxic cyanobacterial community and its associated microbiome along a freshwater-marine continuum. Harmful Algae, 134:102627. DOI
  • Migaou M., Macé S., Maalej H., Marchand L., Bonnetot S., Noël C., Sinquin C., Jérôme M., Zykwinska A., Colliec-Jouault S., Maaroufi Raoui M. and Delbarre-Ladrat C. (2024). Exploring the Exopolysaccharide Production Potential of Bacterial Strains Isolated from Tunisian Blue Crab Portunus segnis Microbiota. Molecules, 29(4), 774 (17p.). DOI
  • Dourdin, T. S., Guyomard, K., Rabiller, M., Houssais, N., Cormier, A., Monier, P. L., Sussarellu, R., and Rivière, G. (2024). Ancestors’ Gift: Parental Early Exposure to the Environmentally Realistic Pesticide Mixture Drives Offspring Phenotype in a Larger Extent Than Direct Exposure in the Pacific Oyster, Crassostrea gigas. Environmental Science and Technology. 58, 1865–1876. DOI
  • Carrier G., Berthelier J., Maupetit A., Nicolau E., Marbouty M., Schreiber N., Charrier A., Carcopino C., Leroi L. and Saint-Jean B. (2024). Genetic and phenotypic intra-species diversity of alga Tisochrysis lutea reveals original genetic structure and domestication potential. European Journal of Phycology, 59(1): 94–111. DOI
2023
  • Cahier K, Piel D, Barcia-Cruz R, Goudenège D, Wegner KM, Monot M, Romalde JL, Le Roux F. (2023) Environmental vibrio phage-bacteria interaction networks reflect the genetic structure of host populations. Environ Microbiol. 25(8):1424-1438. DOI
  • Sauvage, T., Cormier, A., and Delphine, P. (2023). A comparison of Oxford nanopore library strategies for bacterial genomics. BMC Genomics. 24, 627. DOI
  • Dourdin, T. S., Rivière, G., Cormier, A., Poi, C. D., Guyomard, K., Rabiller, M., Akcha, F., Sadialiou, T. B., Monier, P. L., and Sussarellu, R. (2023). Molecular and phenotypic effects of early exposure to an environmentally relevant pesticide mixture in the Pacific oyster, Crassostrea gigas. Environmental Pollution. 326, 121472. DOI
  • Auffret P., Servili A., Gonzalez A.A., Fleury M.L., Mark F.C. and Mazurais D. (2023). Transgenerational exposure to ocean acidification impacts the hepatic transcriptome of European sea bass (Dicentrarchus labrax). BMC Genomics 24, 331. DOI
  • Roux P., Schapira M., Mertens K.N., André C., Terre-Terrillon A., Schmitt A., Manach S., Collin K., Serghine J., Noel C., and Raffaele Siano. (2023). When phytoplankton do not bloom: the case of the dinoflagellate Lepidodinium chlorophorum in southern Brittany (France) assessed by environmental DNA. Progress in Oceanography, 212. DOI
  • Philippe A., Noël C., Eyheraguibel B., Briand J.F., Paul-Pont I., Ghiglione J.F., Coton E. and Burgaud G. (2023). Fungal diversity and dynamics during long-term immersion of conventional and biodegradable plastics in the marine environment. Diversity, 15(4): 579. DOI
  • Oury N., Noël C., Mona S., Aurelle D. and Magalon H. (2023). From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Molecular Phylogenetics and Evolution. DOI
2022
  • Piel D, Bruto M, Labreuche Y, Blanquart F, Goudenège D, Barcia-Cruz R, Chenivesse S, Le Panse S, James A, Dubert J, Petton B, Lieberman E, Wegner KM, Hussain FA, Kauffman KM, Polz MF, Bikard D, Gandon S, Rocha EPC, Le Roux F. (2022) Phage-host coevolution in natural populations. Nat Microbiol. 7(7):1075-1086. DOI
  • Gourmelon M., Boukerb A.M., Nabi N., Banerji S., Joensen K.G., Serghine J., Cormier A., Megraud F., Lehours P., Alter T., Ingle D.J., Kirk M.D. and Nielsen E.M. (2022). Genomic Diversity of Campylobacter lari Group Isolates from Europe and Australia in a One Health Context. Applied And Environmental Microbiology, 88(23), 21p. DOI.
  • Bernard C.*, Locard-Paulet M.*, Noël C.*, Duchateau M., Giai Gianetto Q., Moumen B., Rattei T., Héchard Y., Jensen L., Matondo M., and Samba Louaka A. (2022). A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. Nature Communications. DOI (*) These authors contributed equally
  • Nef C., Dittami S.,, Kaas R., Briand E., Noël C., Mairet F., and Garnier M. (2022). Sharing vitamins, or not? Co-cultures of two known vitamin B12-producing bacteria does not allow growth of B12-starved Tisochrysis lutea, but its natural microbial consortium does. Microorganisms. DOI
  • Cohen-Rengifo M., Danion M., Gonzalez A.A., Bégout M.L., Cormier A., Noël C., Cabon J., Vitré T., Mark F.C., and Mazurais D. (2022). The extensive transgenerational transcriptomic effects of ocean acidification on the olfactory epithelium of a marine fish are associated with a better viral resistance. BMC Genomics, 23(1):1-18. DOI
  • Tilloy V, Cuzin P, Leroi L, Guérin E, Durand P, and Alain S (2022). ASPICov: An automated pipeline for identification of SARS-Cov2 nucleotidic variants. PLoS ONE, 17(1):e0262953. DOI
2021
  • Boukerb M, Noël C, Quenot E, Cadiou B, Chevé J, Quintric L, Cormier A, Dantan L, Gourmelon M. (2021). Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach. Frontiers in Microbiology, 12(697553):21. DOI
  • Mathon L, Valentini A, Guérin PE, Normandeau E, Noel C, Lionnet C, Boulanger E, Thuillier W, Bernatchez L, Mouillot D, Dejean T, Manel S. Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification. Molecular Ecology Resources. DOI
  • Siano R, Lassudrie M, Cuzin P, Briant N, Loizeau V, Schmidt S, Ehrhold A, Mertens KN, Lambert C, Quintric L, Noël C, Latimier M, Quéré J, Durand P, Penaud A. (2021) Sediment archives reveal irreversible shifts in plankton communities after World War II and agricultural pollution. Curr Biol. S0960-9822(21)00452-8. DOI.
  • Stenger PL, Ky CL, Reisser C, Duboisset J, Dicko H, Durand P, Quintric L, Planes S, Vidal-Dupiol J. (2021). Molecular pathways and pigments underlying the colors of the pearl oyster Pinctada margaritifera var. cumingii (Linnaeus 1758). Genes, 12(3), 421. DOI.
2020
  • Brandt MI, Trouche B, Quintric L, Wincker P, Poulain J, Arnaud-Haond S. (2020). A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding. bioRxiv, 7717355, ver. 3 recommended and peer-reviewed by Peer Community In Ecology. DOI.
  • Mazurais D, Servili A, Noel C, Cormier A, Collet S, Leseur R, Le Roy M, Vitré T, Madec L, Zambonino-Infante JL. (2020). Transgenerational regulation of cbln11 gene expression in the olfactory rosette of the European sea bass (Dicentrarchus labrax) exposed to ocean acidification. Marine Environmental Research. DOI.
  • Rolland S, Mengue L, Noël C, Crapart S, Mercier A, Aucher W, Héchard Y, Samba-Louaka A. (2020). Encystment Induces Down-Regulation of an Acetyltransferase-Like Gene in Acanthamoeba castellanii. Pathogens. 9(5), 321. DOI.
2016
  • Epelboin Y, Quintric L, Guévélou E, Boudry P, Pichereau V, Corporeau C (2016). The Kinome of Pacific Oyster Crassostrea gigas, Its Expression during Development and in Response to Environmental Factors. PLoS One. 11(5):e0155435. DOI.

Conferences

2024
  • Bretaudeau A., Durand P., Corre E. (2024). BYTE-SEA: l’infrastructure numérique au service du PEPR ATLASea de séquençage de génomes d’organismes marins. Contribution des plateformes bretonnes de l’axe Bio-informatique de Biogenouest. Congrès Gen2Bio, 14-15 mars 2024, St Malo, France. Programme
2022
  • Sol Dourdin T., Cormier A., Guyomard K., Rabiller M., Sussarellu R. and Riviere G. (2022). Multigenerational Effects of Early Exposure to an Environmentally Relevant Pesticide Mixture in the Pacific Oyster, C. gigas. EPIMAR 2022 - 2nd Epigenetics in Marine Biology Conference 2022. October 11-14, 2022, Woods Hole, Massachusetts, USA.
  • Sol Dourdin T., Cormier A., Guyomard K., Rabiller M., Sussarellu R., and Riviere G. (2022). Phenotypic and molecular effects of early exposure to environmentally relevant pesticide mixture in the Pacific oyster, Crassostrea gigas . PRIMO 2021- 21st International Symposium on Pollutant Responses In Marine arine Organisms. May 22-25, 2022, Gothenburg, Sweden.
  • André C., Hoebeke M., Henry N., Noel C., Durand P. and Corre E. (2022) MyGOD: Visualization and analysis interface for marine genomic observatories data. Gen2Bio, La Baule, 24-25 mars 2022. Poster. Screencast.
2019
  • Siano R., Lassudrie Duchesne M., Cuzin P., Mertens K., Schmidt S., Quintric L., Durand P. (2019) Long-term dynamics of protist paleocommunities over 5000 years in the Bay of Brest (Brittany, France). 5e Colloque du GDR de Génomique Environnementale. 8-10 Octobre 2019, La Rochelle. Lien.
2018
  • Marcon V., Quintric L., Durand P., Inizan O., Dussart C., Loux V., Bernard M., Pascal G. (2018) A journey of a team of engineers in learning packaging technology. GCC Conference, June 2018, Portland, USA. Lien.

Posters

2023
  • Auffret P., Leroi L., Clément J. Bardon A., Cormier A., Noel C., de Massy B., Durand P. (2023). athENA: a Nextflow pipeline for sequencing data brokering to ENA. JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques. 27-30 Juin 2023, Rennes. Lien.
  • Durand P. (2023). BeeDeeM: a general-purpose bioinformatics databank manager system. JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques. 27-30 Juin 2023, Rennes. Lien.
  • Battistel C., Mouren J.-C., Morga B., Pelletier C., Canier L., Garcia C., Arzul I., Leroi L., Durand P., Chevignon G., Jacquot M. (2023). MoPSeq-DB: the reference database and visualisation platform for marine mollusc pathogens genomes. JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques. 27-30 Juin 2023, Rennes. Lien.
  • Leroi L., Noel C., Cormier A., Auffret P., Bardon A., Durand P. (2023). SeBiMER: the bioinformatics platform of Ifremer. JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques. 27-30 Juin 2023, Rennes. Lien.
  • Cormier A., Durand P. (2023). ToolDirectory: Dynamic visualization of softwares managed by Bioinformatics Core Facilities. JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques. 27-30 Juin 2023, Rennes. Lien.
  • Boudet M., Brillet-Guéguen L., Le Bars A., Massau K., Leroi L., Cormier A., Durand P., Corre., Bretaudeau A. (2023). BEAURIS: an automated, modular, and FAIR system for large-scale genome data management. JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques. 27-30 Juin 2023, Rennes. Lien.
2022
  • Jacquot M., Mouren J.C., Battistel C., Morga B., Pelletier C., Canier L., Garcia C., Arzul I., Leroi L., Durand P. and Chevignon G. (2022). MoPSeq-DB: a web platform to share, visualise and analyse sequence data of mollusc pathogens . ISEEMPD 2022 - International Symposium on Ecology and Evolution of Marine Parasites and Diseases. 15-18 November 2022, La Rochelle, France. Lien.
  • Brocard S., Cormier A., Noel C., Berthelier J., Carrier G., Sussarellu R. (2022). MAM : Methylation Analysis of Microalgae. JOBIM 2022 - Journées Ouvertes en Biologie, Informatique et Mathématiques. 05-08 Juillet 2022, Rennes. Lien.
  • Passerini D., Kolypczuk L., Cormier A., Sauvage T. and Leroi F (2022). Diversité des PAMs dans le microbiote des produits de la mer . MuFoPAM 2022 - 9èmes journées du GDR. 19-21 octobre 2022, Amboise.
  • Passerini D., Kolypczuk L., Cormier A. and Leroi F. (2022). Etude des réseaux d’interactions bactériennes dans le microbiome des produits de la mer, en vue d’un procédé de biopréservation dirigé. Microbes 2022 - 17e Congrès National de la SFM « La microbiologie dans tous ses états » . 3-5 octobre 2022, Montpellier. Lien.
2021
  • Noël C., Cuzin P., Leroi L., Cormier A. and Durand P. (2021). ORSON: a nextflow workflow for transcriptome and proteome annotation. Proceedings JOBIM Conference, Paris.
  • Carcopino C., Cuzin P., Leroi L., Noël C., Cormier A. and Durand P. (2021). OMICS-CATALOG: a FAIR toolkit for fast visualization of omics data and metadata. Proceedings JOBIM Conference, Paris.
  • Tilloy V., Cuzin P., Leroi L., Durand P. and Alain S. (2021). ASPICov: an automated pipeline for identification of SARS-Cov-2 nucleotidic variants. Proceedings JOBIM Conference, Paris.
2020
  • Quintric L., Noël C., Leroi L., Cormier A. and Durand P. (2020). SAMBA: a flexible automated workflow for the reproducible and standardized processing of eDNA metabarcoding data. Proceedings JOBIM Conference, Montpellier. Lien.
  • Cuzin P., Lassudrie Duchesne M., Quintric L., Noel C., Durand P., Siano R. (2020) Long-term dynamics of protist paleocommunities in a coastal marine ecosystem(Bay of Brest, NW France) revealed by DNA metabarcoding. Proceedings JOBIM Conference, Montpellier. Lien.
2019
  • Dumont E., Malo F., Durand P., Quintric L., Siano R., Briand E. (2019). Bacterial communities associated with Alexandrium: study of their structure and composition in culture and in situ by a metabarcoding and network analyses approach. Phycotox2019 : Conférence nationale sur les algues toxiques GdR Phycotox. 15-16 mai 2019, Brest. Lien.
  • Lassudrie M., Cuzin P., Mertens K., Quintric L., Durand P., Schmidt S., Siano R. (2019). Long-term dynamics of protist paleocommunities in a coastal marine ecosystem (Bay of Brest, NW France) by DNA metabarcoding. ASLO 2019 - Aquatic Science Meeting "Planet Water Challenges and Successes". 22 Feb -2 Mars, San Juan, Puerto Rico, USA. Lien.
  • Pépin J.F., Bouget J.F., Chabirand J.M. , Chasselin L., Costes L., Grizon J., Lejolivet A., Le Noc S, Palvadeau H, Schmitt A., Seugnet J.L., P. Soletchnik, Travers M.A., Tourbiez D., Guesdon S. (2019) Première évaluation de la diversité des communautés microbiennes planctoniques au cours d’épisodes de mortalité des moules bleues en france : utilisation de l’approche de métabarcoding pour l’analyse de l’adn environnemental. Journées Scientifiques et Techniques de l’AFB, 11-12 juin 2019 Brest.
2018
  • Dussart C., Brandt M., Arnaud-Haond S., Quintric L. (2018). Metabarcoding on the deep seafloor: optimizing multigene approaches for large-scale biodiversity assessments. Proceedings JOBIM Conference, Marseille. Lien.
  • Marcon V., Quintric L., Durand P., Inizan O., Dussart C., Loux V., Bernard M., Pascal G. (2018) A journey of a team of engineers in learning packaging technology. Proceedings JOBIM, Marseille. Lien.
2017
  • Cozien J., Leroi L., Jacquin J., Quintric L., Marquer F., Dussart C., Travers M.A. and Hervio-Heath D. (2017). Gènes de ménage et NGS afin d'explorer la dynamique et la structure des communautés Vibrio spp. dans les milieux marins côtiers.
2016
  • Guesdon S., Travers M.A., Hervio-Heath D., Derrien A., Genauzeau S., Schmitt A., Quintric L., Leroi L., Pépin J.F. (2016) Equilibre microbien et initiation des épisodes de mortalité de moules Y aurait-il un lien ?
  • Leroi L., Cozien J., Marquer F. , Quintric L., Travers M.A. and Hervio-Heath D. (2016). Housekeeping gene targets and NGS to explore Vibrio spp. communities in coastal environments. Proceedings JOBIM, Lyon. Lien.
2014
  • Messaoudi S., Barbeyron T., Quintric L., Colliec-Jouault S., Czjzek M., Michel G., Delbarre-Ladrat C. (2014). A computational genomics pipeline for prokaryotic sequencing projects: application on marine bacteria producing sulfated exopolysaccharides.
2013
  • Bienvenu B., Goudenège D., Le Roux F., Quintric L, Compère C, Dreanno C (2013). Genome sequence of Pseudoalteromonas sp. D41, a pioneer bacterium in marine biofouling.

How to cite the Ifremer Bioinformatics Service (SeBiMER)?

Either we are co-authors, affiliation to quote:
  • Ifremer, IRSI, SeBiMER Service de Bioinformatique de l'Ifremer, F-29280 Plouzané, France
Or we appear in the acknowledgements; example of citations:
  • SeBiMER support: "We are grateful to Ifremer Bioinformatics Core Facility (SeBiMER; https://bioinfo.ifremer.fr/), for providing technical help and scientific support for bioinformatics analysis".
  • Use of DATARMOR / DATAREF : "The authors acknowledge the Pôle de Calcul et de Données Marines (PCDM; https://wwz.ifremer.fr/en/Research-Technology/Research-Infrastructures/Digital-infrastructures/Computation-Centre) for providing DATARMOR computing and storage resources."
  • Use of Galaxy DATARMOR: "Analyses were done on the Galaxy instance of the Ifremer (https://galaxy-datarmor.ifremer.fr/)."