Publications

Citation system

Complete references to use as signature for the authors or co-authors ABiMS.

Principle : Downward addressing : Organism, laboratory, team and minimal address: postal code, town, country

CNRS officer :

CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique, 29680, Roscoff, France

Sorbonne Université officer :

Sorbonne Université, CNRS, FR2424, ABiMS, Station Biologique, 29680, Roscoff, France

JOBIM format

ABiMS, FR2424 CNRS - Sorbonne Université, Station Biologique, Place Georges Teissier, 29680, Roscoff, France

Acknowledgement example

We are grateful to the Roscoff Bioinformatics platform ABiMS (http://abims.sb-roscoff.fr), part of the Institut Français de Bioinformatique (ANR-11-INBS-0013) and BioGenouest network, for providing help and/or computing and/or storage resources... .

2024

Publications

Lisa Mazéas, Ahlem Bouguerba-Collin, J. Mark Cock, France Denoeud, Olivier Godfroy, Loraine Brillet-Guéguen, Tristan Barbeyron, Agnieszka P. Lipinska, Ludovic Delage, Erwan Corre, Elodie Drula, Bernard Henrissat, Mirjam Czjzek, Nicolas Terrapon & Cécile Hervé. Candidate genes involved in biosynthesis and degradation of the main extracellular matrix polysaccharides of brown algae and their probable evolutionary history. BMC Genomics 25, 950 (2024). https://doi.org/10.1186/s12864-024-10811-3
Gross, M., Rajter, Ľ., Mahe, F., Bass, D., Berney, C., Henry, N., de Vargas, C., & Dunthorn, M. (2024). O Short-branch Microsporidia, Where Art Thou? Identifying diversity hotspots for future sampling. European Journal of Protistology, 126119. doi: 10.1016/j.ejop.2024.126119
Morard R, Darling KF, Weiner AKM, Hassenrück C, Vanni C, Cordier T, Henry N, Greco M, Vollmar NM, Milivojevic T, Rahman SN, Siccha M, Meilland J, Jonkers L, Quillévéré F, Escarguel G, Douady CJ, de Garidel-Thoron T, de Vargas C, Kucera M. The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton. Biol Rev Camb Philos Soc. 2024 Aug;99(4):1218-1241. doi: 10.1111/brv.13065. Epub 2024 Feb 13. PMID: 38351434.
Zavadska D, Henry N, Auladell A, Berney C, Richter DJ. Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes. PLoS One. 2024 Jun 6;19(6):e0303697. doi: 10.1371/journal.pone.0303697. PMID: 38843225; PMCID: PMC11156365.
Useros F, García-Cunchillos I, Henry N, Berney C, Lara E. How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation. Environ Microbiol. 2024 Mar;26(3):e16606. doi: 10.1111/1462-2920.16606. PMID: 38509748.
Hiroki Ban, Hisashi Endo, The EukBank Team, Akira Kuwata, Hiroyuki Ogata, Global Distribution and Diversity of Marine Parmales, Microbes and Environments, 2024, Volume 39, Issue 1, Released on J-STAGE March 23, 2024, Online ISSN 1347-4405, Print ISSN 1342-6311, https://doi.org/10.1264/jsme2.ME23093.
Rondon R, Valdés C, Cosseau C, Bergami E, Cárdenas CA, Balbi T, Pérez-Toledo C, Garrido I, Perrois G, Chaparro C, Corre E, Corsi I, González-Aravena M. Transcriptomic responses of Antarctic clam Laternula elliptica to nanoparticles, at single and combined exposures reveal ecologically relevant biomarkers. Ecotoxicol Environ Saf. 2024 Jul 15;280:116523. doi: 10.1016/j.ecoenv.2024.116523. Epub 2024 Jun 8. PMID: 38850707.
Banchi E, Corre E, Del Negro P, Celussi M, Malfatti F. Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment. Mar Life Sci Technol. 2023 Nov 3;6(1):126-142. doi: 10.1007/s42995-023-00192-z. PMID: 38433960; PMCID: PMC10902248.
Finn RD, Balech B, Burgin J Physilia Chua, Erwan Corre et al. Establishing the ELIXIR Microbiome Community. F1000Research 2024, 13(ELIXIR):50 (https://doi.org/10.12688/f1000research.144515.1)
Bérénice Batut, Gildas Le Corguillé, Yvan Le Bras, Loraine Brillet-Guéguen, Fabien Mareuil, et al.. Exploring the richness of the French Galaxy Ecosystem. GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. , pp.1-1, 2024, ⟨10.7490/f1000research.1119765.1⟩. ⟨hal-04644779⟩
Clea Siguret, Thomas Chaussepied, Romane Libouban, Eva Mercier, Julien Seiler, et al.. Galaxy France: an example of a national UseGalaxy server. GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. pp.1-15, ⟨10.7490/f1000research.1119767.1⟩. ⟨hal-04644627⟩
Julie Lao, Raphael Tackx, Pierre Marin, Amanda Dieuaide, Thomas Mignon, et al.. The ABRomics platform — a One Health Antimicrobial resistance analysis service. Journées Ouvertes en Biologie, Informatique, et Mathématiques - 2024, Jun 2024, Toulouse, France. ⟨hal-04618645⟩
Frédéric de Lamotte, Laurent Bouri, Konogan Bourhy, Christophe Bruley, Olivier Collin, et al.. Orchestrating data flows throughout their whole life cycle: Key stages and partners for success. JOBIM2024 : Journées Ouvertes en Biologie, Informatique, et Mathématiques - 2024, Jun 2024, Toulouse, France. 2024. ⟨hal-04665629⟩
Pierre Marin, Bérénice Batut, Kenzo-Hugo Hillion, Clea Siguret, Raphael Tackx, et al.. ABRomics: A Galaxy-based one health antimicrobial resistance platform. GCC 2024 - Galaxy Community Conference 2024, Jun 2024, Brno, Czech Republic. , ⟨10.7490/f1000research.1119762.1⟩. ⟨hal-04619528⟩
David Benaben, Christophe Blanchet, Matéo Boudet, Guillaume Brysbaert, Anthony Bretaudeau, et al.. Services deployed on the IFB National Network of Computing Resources (NNCR). JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques, Jun 2024, Toulouse, France. , 2024. ⟨hal-04618059⟩
Konogan Bourhy, Laurent Bouri, Christophe Bruley, Olivier Collin, Frédéric De Lamotte, et al.. Orchestrating data flows throughout their whole life cycle: Key stages and partners for success. JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques, Jun 2024, Toulouse, France. , 2024. ⟨hal-04618277⟩

Datasets

Alric Benjamin, Lemoine Maud, Claquin Pascal, Abadie Eric, Arnaud Christophe, Artigas Felipe, Belin Catherine, Blondel Camille, Breton Elsa, Carpentier Liliane et al. (2024). PHYTOBS-MARCOBOLO dataset - Phytoplankton time series in French coastal waters. SEANOE. https://doi.org/10.17882/99107
BenthOBS dataset - French National Observation Service for benthic macrofauna in coastal waters. SEANOE. https://doi.org/10.17882/94768
Henry, N., Mahé, F., Berney, C., Poulain, J., Romac, S., Bourdin, G., Ruscheweyh, H.-J., Salazar, G., Belser, C., Clayssen, Q., Hume, B., Boissin, E., Galand, P. E., Pesant, S., Lombard, F., Armstrong, E., Lang-Yona, N., McMinds, R., Vega Thurber, R., … de Vargas, C. (2024). rDNA 18S V9 ASVs (DADA2) from the Tara Pacific Expedition (v1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.13837785
Mahé, F., Henry, N., Berney, C., Poulain, J., Romac, S., Bourdin, G., Ruscheweyh, H.-J., Salazar, G., Belser, C., Clayssen, Q., Hume, B. C. C., Boissin, E., Galand, P. E., Pesant, S., Lombard, F., Armstrong, E., Lang Yona, N., Klinges, G., McMinds, R., … de Vargas, C. (2024). rDNA 18S V9 ASV tables (SWARM) for Tara Pacific Expedition [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10822169
Lombard, F., Guidi, L., Brandão, M. C., Coelho, L. P., Colin, S., Dolan, J. R., Elineau, A., Gasol, J. M., Grondin, P. L., Henry, N., Ibarbalz, F. M., Jalabert, L., Picheral, M., Pierella Karlusich, J. J., Rainer, P., Romagnan, J.-B., Stemmann, L., Acinas, A., Karp-Boss, L., … Gorsky, G. (2024). Dataset originating from various imaging devices used during the Tara Ocean Cruise and associated with the manuscript "Ubiquity of inverted 'gelatinous' ecosystem pyramids in the global ocean" (Version v1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10478781
Schmitt Aurélien, Hoebeke Mark (2024). HYDROMED : Physical & biogeochemical dataset for North-Western Mediterranean Stations. SEANOE. https://doi.org/10.17882/101587
Useros, F., García-Cunchillos, I., Henry, N., Berney, C., & Lara, E. (2024). Data from: How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation. [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10720956

2023

Publications

Daryna Zavadska, Nicolas Henry, Adrià Auladell,Cédric Berney, Daniel J. Richter. On the relationship between protist metabarcoding and protist metagenome-assembled genomes. https://www.biorxiv.org/. doi: https://doi.org/10.1101/2023.10.09.561583
Choquet M, Lenner F, Cocco A, Toullec G, Corre E, Toullec JY, Wallberg A. Comparative population transcriptomics provide new insight into the evolutionary history and adaptive potential of World Ocean krill. Mol Biol Evol. 2023 Oct 10:msad225. doi: 10.1093/molbev/msad225. Epub ahead of print. PMID: 37816123.
Kaneko, H., Endo, H., Henry, N. et al. Predicting global distributions of eukaryotic plankton communities from satellite data. ISME COMMUN. 3, 101 (2023). https://doi.org/10.1038/s43705-023-00308-7
Stéphane Mauger, Aurélien Baud, Gildas Le Corguillé, Gwenn Tanguy, Erwan Legeay, Emeline Creis, Myriam Valero, Philippe Potin, Christophe Destombe. Genetic resources of macroalgae: Development of an efficient method using microsatellite markers in non-model organisms, Algal Research, Volume 75,2023,103251,ISSN 2211-9264,https://doi.org/10.1016/j.algal.2023.103251
Federico M. Ibarbalz, Nicolas Henry, Frédéric Mahé, Mathieu Ardyna, Adriana Zingone, Eleonora Scalco, Connie Lovejoy, Fabien Lombard, Olivier Jaillon, Daniele Iudicone, Shruti Malviya, Tara Oceans Coordinators, Matthew B. Sullivan, Samuel Chaffron, Eric Karsenti, Marcel Babin, Emmanuel Boss, Patrick Wincker, Lucie Zinger, Colomban de Vargas, Chris Bowler, Lee Karp-Boss. Pan-Arctic plankton community structure and its global connectivity. Elementa: Science of the Anthropocene (2023) 11 (1): 00060. https://doi.org/10.1525/elementa.2022.00060
Qikun Xing, Lea Cabioch, Antoine Desrut, Gildas Le Corguille, Sylvie Rousvoal, Laurence Dartevelle ,Elodie Rolland, Yann Guitton, Philippe Potin, Gabriel V. Markov, Sylvain Faugeron and Catherine Leblanc. Aldehyde perception induces specific molecular responses in Laminaria digitata and affects algal consumption by a specialist grazer. The Plant Journal (2023) doi: 10.1111/tpj.16450
Pascoal, F., Tomasino, M.P., Piredda, R. , Henry N. et al. Inter-comparison of marine microbiome sampling protocols. ISME COMMUN. 3, 84 (2023). https://doi.org/10.1038/s43705-023-00278-w
Rigonato, J., Budinich, M., Murillo, A.A., Henry N. et al. Ocean-wide comparisons of mesopelagic planktonic community structures. ISME COMMUN. 3, 83 (2023). https://doi.org/10.1038/s43705-023-00279-9
Galand, P.E., Ruscheweyh, HJ., Salazar, G., Henry N. et al. Diversity of the Pacific Ocean coral reef microbiome. Nat Commun 14, 3039 (2023). https://doi.org/10.1038/s41467-023-38500-x
Delgado, S., Fernandez-Trujillo, M., Houée, G. J Silvent, X Liu, E Corre & JY Sire . Expression of 20 SCPP genes during tooth and bone mineralization in Senegal bichir. Dev Genes Evol (2023). https://doi.org/10.1007/s00427-023-00706-w
Anaïs Rey, Frédérique Viard, Anne Lizé, Erwan Corre , Alice Valentini, Pierre Thiriet .Coastal rocky reef fish monitoring in the context of the Marine Strategy Framework Directive: Environmental DNA metabarcoding complements underwater visual census. Ocean & Coastal Management Volume 241, 1 July 2023, 106625 https://doi.org/10.1016/j.ocecoaman.2023.106625
Rapport d’activités du pôle ODATIS 2022. https://archimer.ifremer.fr/doc/00839/95127/102815.pdf
Federico M. Ibarbalz , Nicolas Henry et al.- Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell Volume 179, Issue 5, 14 November 2019, Pages 1084-1097.e21. https://doi.org/10.1016/j.cell.2019.10.008
Hugo Doré, Jade Leconte, Ulysse Guyet, Solène Breton, Gregory K. Farrant, David Demory, Morgane Ratin, Mark Hoebeke, Erwan Corre, Frances D. Pitt, Martin Ostrowski, David J. Scanlan, Frédéric Partensky, Christophe Six, Laurence Garczarek. Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts. mSystems. Vol. 7, No. 6. https://doi.org/10.1128/msystems.00656-22
Hetty KleinJan, Clémence Frioux, Gianmaria Califano, Méziane Aite, Enora Fremy, Elham Karimi, Erwan Corre, Thomas Wichard, Anne Siegel, Catherine Boyen, Simon M. Dittami. Insights into the potential for mutualistic and harmful host–microbe interactions affecting brown alga freshwater acclimation. Molecular Ecology . Volume32, Issue3 February 2023. https://doi.org/10.1111/mec.16766
M Stam, P Lelièvre, M Hoebeke, E Corre, T Barbeyron… - Nucleic Acids Research, 2022 . SulfAtlas, the sulfatase database: state of the art and new developments. Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D647–D653, https://doi.org/10.1093/nar/gkac977
Mariana Câmara dos Reis, Sarah Romac, Florence Le Gall, Dominique Marie, Miguel J. Frada, Gil Koplovitz, Thierry Cariou, Nicolas Henry, Colomban de Vargas, Christian Jeanthon. Exploring the phycosphere of Emiliania huxleyi: From bloom dynamics to microbiome assembly experiments. Molecular Ecology https://doi.org/10.1111/mec.16829

Citations

Q Zeng, A Lebreton, L Auer, X Man, L Jia, G WangStable functional structure despite high taxonomic variability across fungal communities in soils of old-growth montane forests - Microbiome, 2023 https://doi.org/10.1186/s40168-023-01650-7
R Stetsenko. The evolution of recombination in self-fertilising species: theoretical approach and genomic study of linkage disequilibrium between deleterious mutations in several …- 2023 HALId:tel-04220046 https://theses.hal.science/tel-04220046
Claire Golléty, Jon Yearsley, Aline Migné, Dominique Davoult. Functioning of a canopy-dominated intertidal community during emersion: highly productive but heterotrophic at the annual scale. https://doi.org/10.21203/rs.3.rs-3096636/v1
Belcour A, Got J, Aite M, Delage L, Collén J, Frioux C, Leblanc C, Dittami SM, Blanquart S, Markov GV, Siegel A. Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe. Genome Res. 2023 Jul 19. doi: 10.1101/gr.277056.122. Epub ahead of print. PMID: 37468308.
Tristan Barbeyron, Nolwen Le Duff , Eric Duchaud, François Thomas. Zobellia alginiliquefaciens sp. nov., a novel member of the flavobacteria isolated from the epibiota of the brown alga Ericaria zosteroides (C. Agardh) Molinari & Guiry 2020 .IJSME. 02 June 2023 https://doi.org/10.1099/ijsem.0.005924
Franck Dorkeld, Réjane Streiff , Laure Sauné , Guillaume Castel , Mylène Ogliastro , Carole Kerdelhué. Sequence, assembly and count datasets of viruses associated to the pine processionary moth Thaumetopoea pityocampa (Denis & Schiffermüller) (Lepidoptera, Notodontidae) identified from transcriptomic high-throughput sequencing. Data in Brief Volume 48, June 2023, 109180. https://doi.org/10.1016/j.dib.2023.109180
Portanier et al. Coupling large-spatial scale larval dispersal modelling with barcoding to refine the amphi-Atlantic connectivity hypothesis in deep-sea seep mussels. Front. Mar. Sci., 12 April 2023 | https://doi.org/10.3389/fmars.2023.1122124
Karine Cahier, Damien Piel, Rubén Barcia-Cruz, David Goudenège, K. Mathias Wegner, Marc Monot, Jesús L. Romalde, Frédérique Le Roux. Environmental vibrio phage–bacteria interaction networks reflect the genetic structure of host populationsFirst published: 06 March 2023 https://doi.org/10.1111/1462-2920.16366
Ansgar Gruber, Cedar McKay, Miroslav Oborník, Gabrielle Rocap. Multi class intracellular protein targeting predictions in diatoms and other algae with complex plastids: ASAFind 2.0. https://arxiv.org/pdf/2303.02488.pdf
Théophile Grébert, Laurence Garczarek, Vincent Daubin, Florian Humily, Dominique Marie, Morgane Ratin, Alban Devailly, Gregory K Farrant, Isabelle Mary, Daniella Mella-Flores, Gwenn Tanguy, Karine Labadie, Patrick Wincker, David M Kehoe, Frédéric Partensky, Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria, Genome Biology and Evolution, Volume 14, Issue 4, April 2022, evac035, https://doi.org/10.1093/gbe/evac035
Jolien J.E. van Hooff, Laura Eme . Lateral gene transfer leaves lasting traces in Rhizaria. 2023 https://www.biorxiv.org/. https://doi.org/10.1101/2023.01.27.525846
Maria Luiza Pedrotti ,Ana Luzia de Figueiredo Lacerda ,Stephanie Petit,Jean François Ghiglione,Gabriel Gorsky. Vibrio spp and other potential pathogenic bacteria associated to microfibers in the North-Western Mediterranean Sea. 2022 https://doi.org/10.1371/journal.pone.0275284
Metz, S., Itoïz, S., Obiol, A. et al. Global perspective of environmental distribution and diversity of Perkinsea (Alveolata) explored by a meta-analysis of eDNA surveys. Sci Rep 13, 20111 (2023). https://doi.org/10.1038/s41598-023-47378-0
Hoste, A., Capblancq, T., Broquet, T. et al. Projection of current and future distribution of adaptive genetic units in an alpine ungulate. Heredity (2023). https://doi-org.inee.bib.cnrs.fr/10.1038/s41437-023-00661-2

Datasets

Bureau Sarah, Hoebeke Mark, Breton Elsa, Cariou Thierry, Dauvin Jean-Claude, Macé Éric, Morin Pascal, Thiébaut Éric (2023). ASTAN temperature & salinity historical time series (1952 - 1999). SEANOE. https://doi.org/10.17882/95911
Henry, N., Caracciolo, M., Romac, S., Rigaut-Jalabert, F., & Simon, N. (2023). SOMLIT-Astan time-series (2009-2016) rDNA 18S V4 ASV table (dada2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8392525
Delage, E., Salazar, G., Ruscheweyh, H.-J., Henry, N., Poulain, J., de Vargas, C., Sunagawa, S., & Chaffron, S. (2023). Tara Oceans (2009-2013) rDNA 16S V4V5 ASV table (dada2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7551744
Delage, E., Henry, N., Salazar, G., Ruscheweyh, H.-J., Poulain, J., Sunagawa, S., de Vargas, C., & Chaffron, S. (2023). Tara Oceans (2009-2013) rDNA 18S V4 ASV table (dada2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7551644
Delage, E., Henry, N., Salazar, G., Ruscheweyh, H.-J., Poulain, J., Sunagawa, S., de Vargas, C., & Chaffron, S. (2023). Tara Oceans (2009-2013) rDNA 18S V9 ASV table (dada2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7548227
Berney, C., Mahé, F., Henry, N., Lara, E., de Vargas, C., & EukBank consortium. (2023). EukBank 18S V4 dataset [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7804946

2022

Publications

KleinJan, H., Frioux, C., Califano, G., Aite, M., Fremy, E., Karimi, E., Corre, E., Wichard, T., Siegel, A., Boyen, C. and Dittami, S.M. (2022), Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation. Mol Ecol. https://doi.org/10.1111/mec.16766
Mark Stam, Pernelle Lelièvre, Mark Hoebeke, Erwan Corre, Tristan Barbeyron, Gurvan Michel, SulfAtlas, the sulfatase database: state of the art and new developments, Nucleic Acids Research, 2022;, gkac977, https://doi.org/10.1093/nar/gkac977
Endress, M.; Zatylny-Gaudin, C.; Leprince, J.; Lefranc, B.; Corre, E.; Le Corguillé, G.; Bernay, B.; Leduc, A.; Rangama, J.; Mouret, L.; Lafont, A.-G.; Bondon, A.; Henry, J. Structural and Functional Characterization of Orcokinin B-like Neuropeptides in the Cuttlefish (Sepia officinalis). Mar. Drugs 2022,20,505.https://doi.org/10.3390/md20080505
C. Thomas-Bulle, D. Bertrand, N. Nagarajan, R. R. Copley, E. Corre, S. Hourdez, É. Bonnivard, A. Claridge-Chang, and D. Jollivet, “Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella,” BMC Ecology and Evolution, vol. 22, no. 1, p. 106, 2022. https://doi.org/10.1186/s12862-022-02057-y
de Vargas Colomban, Le Bescot Noan, Pollina Thibaut, Henry Nicolas, Romac Sarah, Colin Sébastien, Haëntjens Nils, Carmichael Margaux, Berger Calixte, Le Guen David, Decelle Johan, Mahé Frédéric, Poulain Julie, Malpot Emmanuel, Beaumont Carole, Hardy Michel, Guiffant Damien, Probert Ian, Gruber David F., Allen Andrew E., Gorsky Gabriel, Follows Michael J., Pochon Xavier, Troublé Romain, Cael B. B., Lombard Fabien, Boss Emmanuel, Prakash Manu, the Plankton Planet core team, Bazile Romain, Boss Emmanuel, Bourdin Guillaume, Cael BB, Casati Roberto, Colin Sébastien, Vargas Colomban de, Gorsky Gabriel, Guiffant Damien, Haentjens Nils, Henry Nicolas, Larson Adam, Bescot Noan Le, Lombard Fabien, Mirambeau Gilles, Moulin Clémentine, Oddone Anna, Prakash Manu, Prazuck Christophe, Raimbault Vincent, Trellu Clara, Troublé Romain. Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale. Frontiers in Marine Science. 9-2022.https://www.frontiersin.org/articles/10.3389/fmars.2022.936972.
Daniel J Richter, Romain Watteau, Thomas Vannier, Jade Leconte, Paul Frémont, Gabriel Reygondeau, Nicolas Maillet, Nicolas Henry, Gaëtan Benoit, Ophélie Da Silva, Tom O Delmont, Antonio Fernàndez-Guerra, Samir Suweis, Romain Narci, Cédric Berney, Damien Eveillard, Frederick Gavory, Lionel Guidi, Karine Labadie, Eric Mahieu, Julie Poulain, Sarah Romac, Simon Roux, Céline Dimier, Stefanie Kandels, Marc Picheral, Sarah Searson, Tara Oceans Coordinators, Stéphane Pesant, Jean-Marc Aury, Jennifer R Brum, Claire Lemaitre, Eric Pelletier, Peer Bork, Shinichi Sunagawa, Fabien Lombard, Lee Karp-Boss, Chris Bowler, Matthew B Sullivan, Eric Karsenti, Mahendra Mariadassou, Ian Probert, Pierre Peterlongo, Patrick Wincker, Colomban de Vargas, Maurizio Ribera d'Alcalà, Daniele Iudicone, Olivier Jaillon.(2022). Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife; 11:e78129.. https://doi.org/10.7554/eLife.78129
Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Donat Agosti3 Petr Baldrian, Bachir Balech, Erwan Corre, Robert P. Davey, Henrik Lantz, Graziano Pesole5, Christian Quast, Frank Oliver Glöckner, Niels Raes, Anna Sandionigi, Monica Santamaria, Wouter Addink, Jiri Vohradsky, Amandine Nunes-Jorge, Nils Peder Willassen, Jerry Lanfear. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR F1000Research 2022, 10(ELIXIR):1238 (https://doi.org/10.12688/f1000research.73825.2)
Mariarita Caracciolo,Fabienne Rigaut-Jalabert,Sarah Romac,Frédéric Mahé,Samuel Forsans,Jean-Philippe Gac,Laure Arsenieff,Maxime Manno,Samuel Chaffron,Thierry Cariou,Mark Hoebeke,Yann Bozec,Eric Goberville,Florence Le Gall,Loïc Guilloux,Anne-Claire Baudoux,Colomban de Vargas,Fabrice Not,Eric Thiébaut, Nicolas Henry,Nathalie Simon. Seasonal dynamics of marine protist communities in tidally mixed coastal waters. Molecular Ecology.20 May 2022 https://doi.org/10.1111/mec.16539
Santi, Ioulia, Cancio, Ibon, Corre, Erwan, Cox, Cymon J., Exter, Katrina, Hoebeke, Mark, Kervella, Anne Emmanuelle, Laroquette, Arnaud, Pavloudi, Christina, Portier, Marc and Pade, Nicolas (2022) European Marine Omics Biodiversity Observation Network (EMO BON) – Data Management Plan. (Version 1.0). Paris, France, EMBRC-ERIC, 33pp. http://dx.doi.org/10.25607/OBP-1743
Ferrieux Mathilde, Dufour Louison, Doré Hugo, Ratin Morgane, Guéneuguès Audrey, Chasselin Léo, Marie Dominique, Rigaut-Jalabert Fabienne, Le Gall Florence, Sciandra Théo, Monier Garance, Hoebeke Mark, Corre Erwan, Xia Xiaomin, Liu Hongbin, Scanlan David J., Partensky Frédéric, Garczarek Laurence. Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas, Frontiers in Microbiology (2022) https://doi.org/10.3389/fmicb.2022.893413
Castel, J.; Hourdez, S.; Pradillon, F.; Daguin-Thiébaut, C.; Ballenghien, M.; Ruault, S.; Corre, E.; Tran Lu Y, A.; Mary, J.; Gagnaire, P.-A.; et al. Inter-Specific Genetic Exchange Despite Strong Divergence in Deep-Sea Hydrothermal Vent Gastropods of the Genus Alviniconcha.Genes,13,985. https://doi.org/10.3390/genes13060985
Gaudin-Zatylny, C., Corre, E., Zanuttini, B. et al. Identification of a New Set of Polypeptidic Sex Pheromones from Cuttlefish (Sepia officinalis). Mar Biotechnol (2022). https://doi.org/10.1007/s10126-022-10126-y
Koua, N.D.; Henry, J.; Corre, E.; Pontin, J.; Bernay, B.; Nunez, J. Immuno-Enzymatic and Proteomic Approaches for Sexing the African Bonytongue (Heterotis niloticus Cuvier, 1829). Fishes 2022, 7, 106. https://doi.org/10.3390/ fishes7030106

Citations

Marjorie Couton, Laurent Lévêque, Claire Daguin-Thiébaut, Thierry Comtet & Frédérique Viard (2022) Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring, Biofouling, 38:4, 367-383, https://doi.org/10.1080/08927014.2022.2075739
Brunet, M., Le Duff, N., Barbeyron, T. et al. Consuming fresh macroalgae induces specific catabolic pathways, stress reactions and Type IX secretion in marine flavobacterial pioneer degraders. ISME J 16, 2027–2039 (2022). https://doi.org/10.1038/s41396-022-01251-6
Nathan Foulquier, Christelle Le Dantec, Eleonore Bettacchioli, Christophe Jamin, Marta E. Alarcon-Riquelme, and Jacques-Olivier Pers. Machine Learning for the Identification of a Common Signature for Anti–SSA/Ro 60 Antibody Expression Across Autoimmune Diseases. Arthritis & Rheumatology Vol. 74, No. 10, October 2022, pp 1706–1719 DOI 10.1002/art.42243.
Luis, A.S., Baslé, A., Byrne, D.P. et al. Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota. Nat Chem Biol 18, 841–849 (2022). https://doi.org/10.1038/s41589-022-01039-x
Piel, D., Bruto, M., Labreuche, Y. et al. Phage–host coevolution in natural populations. Nat Microbiol 7, 1075–1086 (2022). https://doi.org/10.1038/s41564-022-01157-1
Mohamed Sassi et al. Forecasting Staphylococcus aureus Infections Using GenomeWide Association Studies, Machine Learning, and Transcriptomic Approaches, 2022,mSystems. https://doi.org/10.1128/msystems.00378-22
Decelle, J., Kayal, E., Bigeard, E. et al. Intracellular development and impact of a marine eukaryotic parasite on its zombified microalgal host. ISME J 16, 2348–2359 (2022). https://doi.org/10.1038/s41396-022-01274-z
Thomas Lenormand, Denis Roze. Y recombination arrest and degeneration in the absence of sexual dimorphism. Science, 2022, 375 (6581),pp.663-666. https://doi.org/ff10.1126/science.abj1813
Walter Santana-Garcia, Jaime A Castro-Mondragon, Mónica Padilla-Gálvez, Nga Thi Thuy Nguyen, Ana Elizondo-Salas, Najla Ksouri, François Gerbes, Denis Thieffry, Pierre Vincens, Bruno Contreras-Moreira, Jacques van Helden, Morgane Thomas-Chollier, Alejandra Medina-Rivera, RSAT 2022: regulatory sequence analysis tools, Nucleic Acids Research, 2022;, gkac312, https://doi.org/10.1093/nar/gkac312
JJ Pierella Karlusich, E Pelletier, L Zinger, F Lombard et al. A robust approach to estimate relative phytoplankton cell abundances from metagenomes. Mol Ecol Resour. 2022;00:1–25. DOI: 10.1111/1755-0998.13592
Vaulot D, Hung Sim CW, Ong D, Teo B, Biwer C, Jamy M, dos Santos AL. metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Preprint from bioRxiv, 06 Feb 2022. DOI: 10.1101/2022.02.04.479133
R Stetsenko, D Roze. The evolution of recombination in self-fertilizing organisms. bioRxiv, 2022. https://doi.org/10.1101/2022.02.24.481800
Charbonnel, E., Daguin-Thiébaut, C., Caradec, L. et al. Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations. Heredity 128, 364–376 (2022). https://doi.org/10.1038/s41437-022-00515-3
Josselin Gueno, Michael Borg, Simon Bourdareau, Guillaume Cossard, Olivier Godfroy, Agnieszka Lipinska, Leila Tirichine, J Mark Cock, Susana M Coelho, Chromatin landscape associated with sexual differentiation in a UV sex determination system, Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3307–3322, https://doi.org/10.1093/nar/gkac145
T Grébert, L Garczarek, V Daubin, F Humily, D Marie et al. Diversity and evolution of pigment types in marine Synechococcus cyanobacteria Genome Biol. Evol. 14(4) https://doi.org/10.1093/gbe/evac035
M Ferrieux, L Dufour, H Doré, M Ratin, A Guéneuguès…et al. Comparative thermophysiology of marine Synechococcus CRD1 strains isolated from different thermal niches in iron-depleted areas bioRxiv, 2022. doi: https://doi.org/10.1101/2022.03.09.483587
C Jiang, H Jiang, T Zhang, Z Lu, X Mao. Enzymatic Verification and Comparative Analysis of Carrageenan Metabolism Pathways in Marine Bacterium Flavobacterium algicola. Applied and Environmental Microbiology, 2022. DOI https://doi.org/10.1128/aem.00256-22
Lisa Mazéas, Rina Yonamine, Tristan Barbeyron, Bernard Henrissat, Elodie Drula, Nicolas Terrapon, Chikako Nagasato, Cécile Hervé. Assembly and synthesis of the extracellular matrix in brown algae,. Seminars in Cell & Developmental Biology, 2022, https://doi.org/10.1016/j.semcdb.2022.03.005.
A Tran Lu Y, S Ruault, C Daguin‐Thiébaut, J Castel…et al. Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep‐sea hydrothermal gastropod Ifremeria nautilei Molecular Ecology, 2022. https://doi.org/10.1111/mec.16430
Cossard, G.G., Godfroy, O., Nehr, Z. et al. Selection drives convergent gene expression changes during transitions to co-sexuality in haploid sexual systems. Nat Ecol Evol 6, 579–589 (2022). https://doi.org/10.1038/s41559-022-01692-4
Flurin Leugger, Thomas Broquet, Dirk Nikolaus Karger et al. Dispersal and habitat dynamics shape the genetic structure of the Northern chamois in the Alps. Journal of Biogeography. 2022;00:1–14. DOI: 10.1111/jbi.14363

2021

Publications

González-Aravena M, Rondon R, Font A, Cárdenas CA, Toullec J-Y, Corre E and Paschke K (2021) Low Transcriptomic Plasticity of Antarctic Giant Isopod Glyptonotus antarcticus Juveniles Exposed to Acute Thermal Stress. Front. Mar. Sci. 8:761866. doi: 10.3389/fmars.2021.761866
Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Donat Agosti, Petr Baldrian, Bachir Balech, Erwan Corre, Robert P. Davey, Henrik Lantz , Graziano Pesole, Christian Quast, Frank Oliver Glöckner, Niels Raes, Anna Sandionigi14, Monica Santamaria, Wouter Addink15, Jiri Vohradsky, Amandine Nunes-Jorge, Nils Peder Willassen, Jerry Lanfear. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR. F1000Research 2021, 10(ELIXIR):1238 https://doi.org/10.12688/f1000research.73825.1
Xing Q, Bernard M, Rousvoal S, Corre E, Markov GV, Peters AF and Leblanc C (2021) Different Early Responses of Laminariales to an Endophytic Infection Provide Insights About Kelp Host Specificity. Front. Mar. Sci. 8:742469. https://doi.org/10.3389/fmars.2021.742469 
Baptiste Houyvet ,Yolande Bouchon-Navaro, Claude Bouchon, Erwan Corre and Céline Zatylny-Gaudin. Marine Transcriptomics Analysis for the Identification of New Antimicrobial Peptides. Mar. Drugs 2021, 19(9), 490; https://doi.org/10.3390/md19090490
Christophe Six, Morgane Ratin, Dominique Marie, and Erwan Corre. Marine Synechococcus Picocyanobacteria: Light Utilization Across Latitudes. PNAS September 21, 2021 118 (38) e2111300118; https://doi.org/10.1073/pnas.2111300118
Mariarita Caracciolo, Fabienne Rigaut-Jalabert, Sarah Romac, Frédéric Mahé, Samuel Forsans, Jean-Philippe Gac, Laure Arsenieff, Maxime Manno, Samuel Chaffron, Thierry Cariou, Mark Hoebeke, Yann Bozec, Eric Goberville, Florence Le Gall, Loïc Guilloux, Anne-Claire Baudoux, Colomban de Vargas, Fabrice Not, Eric Thiébaut, Nicolas Henry, Nathalie Simon.Seasonal temporal dynamics of marine protists communities in tidally mixed coastal waters.biorxiv.org. doi: https://doi.org/10.1101/2021.09.15.460302
Tristan Barbeyron; Manon Thiébaud; Nolwen Le Duff; Marjolaine Martin; Erwan Corre; Gwenn Tanguy; Micheline Vandenbol; François Thomas. Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov., two flavobacteria from the epiphytic microbiota of the brown alga Ascophyllum nodosum, and emended description of the genus Zobellia. IJSME. Vol 71. Issue8. https://doi.org/10.1099/ijsem.0.004913
Karimi E, Geslain E, Belcour A, Frioux C, Aïte M, Siegel A, Corre E, Dittami SM. 2021. Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines. PeerJ 9:e11344 https://doi.org/10.7717/peerj.11344
Couton, Marjorie; Baud, Aurélien; Daguin-Thiébaut, Claire; Corre Erwan; Comtet, Thierry; Viard, Frédérique. High-Throughput Sequencing on preservative ethanol is effective at jointly examining infra-specific and taxonomic diversity, although bioinformatics pipelines do not perform equally. Methods in Ecology and Evolution. https://doi.org/10.1002/ece3.7453
Alexandre Leduc, Samia Chaouni, Frédéric Pouzoulet, Ludovic De Marzi, Frédérique Megnin-Chanet, Erwan Corre, Dinu Stefan, Jean-Louis Habrand, François Sichel, Carine Laurent .Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams. Scientific Reports. https://doi.org/10.1038/s41598-021-85394-0
Sarah Farhat, Phuong Le, Ehsan Kayal, Benjamin Noel, Estelle Bigeard, Erwan Corre, Florian Maumus, Isabelle Florent, Adriana Alberti, Jean-Marc Aury, Tristan Barbeyron, Ruibo Cai, Corinne Da Silva, Benjamin Istace, Karine Labadie, Dominique Marie, Jonathan Mercier, Tsinda Rukwavu, Jeremy Szymczak, Thierry Tonon, Catharina Alves-de-Souza, Pierre Rouzé, Yves Van de Peer, Patrick Wincker, Stephane Rombauts, Betina M. Porcel & Laure Guillou.Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biology volume 19, Article number: 1 (2021). DOI :10.1186/s12915-020-00927-9
Richard G. Dorrell, Adrien Villain, Benoît Perez-Lamarque, Guillemette Audren de Kerdrel, Giselle McCallum, Andrew K. Watson, Ouardia Ait-Mohamed, Adriana Alberti, Erwann Corre, Kyle R. Frischkorn, Juan J. Pierella Karlusich, Eric Pelletier, Hélène Morlon, Chris Bowler, and Guillaume Blanc. Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes . PNAS January 26, 2021 118 (4) e2009974118; https://doi.org/10.1073/pnas.2009974118
Rémi Allio, Marie-Ka Tilak, Celine Scornavacca, Nico L Avenant, Andrew C Kitchener, Erwan Corre, Benoit Nabholz, Frédéric Delsuc. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021;10:e63167 DOI: 10.7554/eLife.63167

Citations

Roman Stetsenko, View ORCID ProfileDenis Roze. The evolution of recombination in self-fertilizing organisms. https://doi.org/10.1101/2022.02.24.481800
Thomas LENORMAND and Denis ROZE.Y recombination arrest and degeneration in the absence of sexual dimorphism. SCIENCE.2022 Vol 375, Issue 6581 pp. 663-666 • DOI: 10.1126/science.abj1813
Nicole Hugouvieux-Cotte-Pattat, Monique Royer, Erwan Gueguen, Paul Le Guen, Roderich D. Süssmuth, Sylvie Reverchon and Stéphane Cociancich. Specificity and genetic polymorphism in the Vfm quorum sensing system of plant pathogenic bacteria of the genus Dickeya. Environmental Microbiology (2022), doi:10.1111/1462-2920.15889
Shingo Akita, Christophe Vieira, Takeaki Hanyuda, Florence Rousseau, Corinne Cruaud, Arnaud Couloux, Svenja Heesch, J. Mark Cock, Hiroshi Kawai. Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences. Molecular Phylogenetics and Evolution, Volume 168, 2022, 107408, https://doi.org/10.1016/j.ympev.2022.107408.
Banchi E, Del Negro P, Celussi M and Malfatti F (2021) Sediment Features and Human Activities Structure the Surface Microbial Communities of the Venice Lagoon. Front. Mar. Sci. 8:762292. doi: 10.3389/fmars.2021.762292
Savary O, Coton M, Frisvad JC, Nodet P, Ropars J, Coton E. and Jany J-L. Unexpected Nectriaceae species diversity in cheese, description of Bisifusarium allantoides sp. nov., Bisifusarium penicilloides sp. nov., Longinectria gen. nov. lagenoides sp. nov. and Longinectriaverticilliforme sp. nov. Mycosphere 12(1): 1077–1100 (2021). Doi: 10.5943/mycosphere/12/1/13
Mauger, S., Fouqueau, L., Avia, K. et al. Development of tools to rapidly identify cryptic species and characterize their genetic diversity in different European kelp species. J Appl Phycol (2021). https://doi.org/10.1007/s10811-021-02613-x
Luis, A.S., Jin, C., Pereira, G.V. et al. A single sulfatase is required to access colonic mucin by a gut bacterium. Nature 598, 332–337 (2021). https://doi.org/10.1038/s41586-021-03967-5
Bruno Francesco Rodriguesde Oliveira, Isabelle RodriguesLopes, Anna Luiza Bauer Canellas, Guilherme Muricy, Stephen Anthony Jacksonb, Alan D.W.Dobson, Marinella Silva Laport. Genomic and in silico protein structural analyses provide insights into marine polysaccharide-degrading enzymes in the sponge-derived Pseudoalteromonas sp. PA2MD11. International Journal of Biological Macromolecules Volume 191, 30 November 2021, Pages 973-995.https://doi.org/10.1016/j.ijbiomac.2021.09.076
Pavla Debeljak,Stéphane Blain,Andrew Bowie,Pier van der Merwe,Barbara Bayer,Ingrid Obernosterer. Homeostasis drives intense microbial trace metal processing on marine particles. https://doi.org/10.1002/lno.11923
Hagestad, O.C., Hou, L., Andersen, J.H. et al. Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation. IMA Fungus 12, 21 (2021). https://doi.org/10.1186/s43008-021-00072-0
Stéphane Hourdez, Céline Boidin-Wichlacz, Didier Jollivet, François Massol, Maria Claudia Rayol, Renato Bruno, Daniela Zeppilli, Frédéric Thomas, Ludovic Lesven, Gabriel Billon, Sébastien Duperron, Aurélie Tasiemski .Investigation of Capitella spp. symbionts in the context of varying anthropic pressures: First occurrence of a transient advantageous epibiosis with the giant bacteria Thiomargarita sp. to survive seasonal increases of sulfides in sediments.Science of The Total Environment Volume 798, 1 December 2021, 149149. https://doi.org/10.1016/j.scitotenv.2021.149149
Yacine Badis,Delphine Scornet,Minori Harada,Céline Caillard,Olivier Godfroy,Morgane Raphalen,Claire M. M. Gachon,Susana M. Coelho,Taizo Motomura,Chikako Nagasato,J. Mark Cock.Targeted CRISPR-Cas9-based gene knockouts in the model brown alga Ectocarpus. New Phytologist.Volume231, Issue5 September 2021 Pages 2077-209102 June 2021 https://doi.org/10.1111/nph.17525
Mikkelsen, M.D., Cao, H.T.T., Roret, T. et al. A novel thermostable prokaryotic fucoidan active sulfatase PsFucS1 with an unusual quaternary hexameric structure. Sci Rep 11, 19523 (2021). https://doi.org/10.1038/s41598-021-98588-3
Trefault, N., De la Iglesia, R., Moreno-Pino, M., Lopes dos Santos, A., Gérikas Ribeiro, C., Parada-Pozo, G., Cristi, A. et al. 2021. Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula. Scientific Reports. 11.
Vaulot, D., Mahé, F., Bass, D. & Geisen, S. 2021. pr2-primer: an 18S rRNA primer database for protists. Molecular Ecology Resources. in press.
Grébert T., Garczarek L., Daubin V., Humily F., Marie D., Ratin M., Devailly A., Farrant G. K., Mary I., Mella-Flores D., Tanguy G., Labadie K., Wincker P., Kehoe D.M. and Partensky F. Diversity and evolution of pigment types and the phycobilisome rod gene region of marine Synechococcus cyanobacteria. bioRxiv preprint doi: https://doi.org/10.1101/2021.06.21.449213 (Submitted to GBE)
Kayal E, Smith DR. 2021. Is the dinoflagellate Amoebophrya really missing a mtDNA? Molecular Biology and Evolution 38(6): 2493–2496.
Thomas, F., Le Duff, N., Wu, TD. et al. Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria. ISME J (2021). https://doi.org/10.1038/s41396-021-00987-x
Julien Kincaid-Smith,Eglantine Mathieu-Bégné, Cristian Chaparro,Marta Reguera-Gomez,Stephen Mulero,Jean-Francois Allienne,Eve Toulza,Jérôme Boissier . No pre-zygotic isolation mechanisms between Schistosoma haematobium and Schistosoma bovis parasites: From mating interactions to differential gene expression. https://doi.org/10.1371/journal.pntd.0009363
Sun, Y., Debeljak, P. & Obernosterer, I. Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean. ISME J (2021). https://doi.org/10.1038/s41396-021-00973-3
Denis Roze. A simple expression for the strength of selection on recombination generated by interference among mutations. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, In press.https://hal.sorbonne-universite.fr/hal-03185704/document
Louise Fouqueau, Denis Roze. The evolution of sex along an environmental gradient. Evolution - International Journal of Organic Evolution, Wiley, In press, ff10.5281/zenodo.4643637 hal-03185708
Stenger, P.-L.; Ky, C.-L.; Reisser, C.; Duboisset, J.; Dicko, H.; Durand, P.; Quintric, L.; Planes, S.; Vidal-Dupiol, J. Molecular Pathways and Pigments Underlying the Colors of the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus 1758). Genes 2021, 12, 421. https://doi.org/10.3390/genes12030421
Trefault Nicole; De la Iglesia Rodrigo; Moreno-Pino, Mario; Lopes dos Santos Adriana; Gérikas Ribeiro Catherine; et al. Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula.Scientific Reports (Nature Publisher Group); London Vol. 11, N° 1, (2021).DOI:10.1038/s41598-020-80568-8
Cormier A, Wattier R, Giraud I, Teixeira M, Grandjean F, Rigaud T, Cordaux R. 2021. Draft genome sequences of Thelohania contejeani and Cucumispora dikerogammari, pathogenic microsporidia of freshwater crustaceans. Microbiol Resour Announc 10:e01346-20. https://doi.org/10.1128/MRA .01346-20.
Ana S. Luis, Chunsheng Jin, Gabriel Vasconcelos Pereira, Robert W. P. Glowacki, Sadie Gugel, Shaleni Singh, Dominic P. Byrne, Nicholas Pudlo,James A London, Arnaud Baslé, Mark Reihill, Stefan Oscarson, Patrick A. Eyers, Mirjam, Czjzek, Gurvan Michel, Tristan Barbeyron, Edwin A Yates, Gunnar C. Hansson,Niclas G. Karlsson,Alan Cartmell, Eric C. Martens. A single bacterial sulfatase is required for metabolism of colonic mucin O-glycans 3 and intestinal colonization by a symbiotic human gut bacterium. https://assets.researchsquare.com/files/rs-113032/v1_stamped.pdf
Haidara, N and O. Porrua. Modulated termination of non-coding transcription partakes in the regulation of gene expression. : https://doi.org/10.1101/2021.01.06.425579;
Maéva Brunet , Florian de Bettignies , Nolwen Le Duff , Gwenn Tanguy , Dominique Davoult , Catherine Leblanc , Angélique Gobet, François Thomas. Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities. Environmental Microbiology https://doi.org/10.1111/1462-2920.15389

2020

Publications

Ehsan Kayal, Catharina Alves-de-Souza, Sarah Farhat, Lourdes Velo-Suarez, Joanne Monjol, Jeremy Szymczak, Estelle Bigeard, Dominique Marie, Benjamin Noel, Betina M. Porcel, Erwan Corre, Christophe Six, Laure Guillou. Dinoflagellate host chloroplasts and mitochondria remain functional during Amoebophrya infection. Accepted in Frontiers in Microbiology, section Microbial Symbioses. https://doi.org/10.3389/fmicb.2020.600823
Huiru Li, Lydia Scheschonk, Sandra Heinrich, Klaus Valentin, Lars Harms, Gernot Glöckner, Erwan Corre, Kai Bischof. Transcriptomic responses to darkness and the survival strategy of the kelp <i>Saccharina latissima </i> during the Polar night .Front. Mar. Sci. - Marine Molecular Biology and Ecology.https://doi.org/10.3389/fmars.2020.592033
Laurence Garczarek, Ulysse Guyet, Hugo Doré, Gregory K. Farrant, Mark Hoebeke, Loraine Brillet-Guéguen, Antoine Bisch, Mathilde Ferrieux, Jukka Siltanen, Erwan Corre, Gildas Le Corguillé , Morgane Ratin, Frances D. Pitt, Martin Ostrowski, Maël Conan, Anne Siegel, Karine Labadie, Jean-Marc Aury, Patrick Wincker, David J. Scanlan and Frédéric Partensky. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. 2020 Nucleic Acids Research, gkaa958, https://doi.org/10.1093/nar/gkaa958.
Guillaume Dubrulle, Adeline Picot, Stéphanie Madec, Erwan Corre, Audrey Pawtowski, Riccardo Baroncelli, Michel Zivy, Thierry Balliau, Gaétan Le Floch, and Flora Pensec. Deciphering the infectious process of Colletotrichum lupini in lupin through transcriptomic and proteomic analysis. Microorganisms https://doi.org/10.3390/microorganisms8101621
Xi Liu, Frédéric Hérault, Christian Diot, Erwan Corre. Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific Mule and Hinny hybrids fed ad libitum and overfed. BMC Genomics https://doi.org/10.21203/rs.3.rs-18946/v2
Jean-Philippe Mevy, Beatrice Loriod, Xi Liu, Erwan Corre, Magali Torres, Michael Büttner, Anne Haguenauer, Ilja Marco Reiter, Catherine Fernandez, Thierry Gauquelin. Downy oak (Quercus pubescens Willd.) response to climate change: transcriptome assembly, differential genes analysis and targeted metabolomics. Plants 2020, 9(9), 1149; https://doi.org/10.3390/plants9091149 
Hugo Doré,Gregory K. Farrant,Ulysse Guyet,Julie Haguait,Florian Humily,Morgane Ratin, Frances D. Pitt,Martin Ostrowski,Christophe Six,Loraine Brillet-Guéguen,Mark Hoebeke, Antoine Bisch,Gildas Lecorguillé,Erwan Corre,Karine Labadie,Jean-Marc Aury, Patrick Wincker,Dong H. Choi,Jae H Noh,Damien Eveillard,David J. Scanlan, Frédéric Partensky,Laurence Garczarek. Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria. Front. Microbiol. - Aquatic Microbiology, https://doi.org/10.3389/fmicb.2020.567431
Louis Benoist , Baptiste Houyvet, Joël Henry, Erwan Corre , Bruno Zanuttini and Céline Zatylny-Gaudin. Using in-depth in silico search to identify antimicrobials peptides from haemocytes in the cuttlefish Sepia officinalis after bacterial challenge. Mar. Drugs 2020, 18(9), 439; https://doi.org/10.3390/md18090439
Albane Jouault, Angélique Gobet, Marjolaine Simon, Emilie Portier, Morgan Perennou, Erwan Corre, Fanny Gaillard, Eric Duchaud, David Vallenet, Gurvan Michel, Yannick Fleury Alexis Bazire Alain Dufour. Alterocin is an antibiofilm protein secreted by Pseudoalteromonas sp. 3J6. AEM https://doi.org/10.1128/AEM.00893-20
Benoist, Louis; Corre, Erwan; Bernay, Benoit; Henry, Joël; Zatylny-Gaudin, Céline . Omic analysis of Sepia officinalis white body: new insights into multifunctionality and haematopoiesis regulation" . Journal proteome research . https://doi.org/10.1021/acs.jproteome.0c00100
Ulysse Guyet, Ngoc A. Nguyen, Hugo Doré, Julie Haguait, Justine Pittera, Maël Conan, Morgane Ratin, Erwan Corre, Gildas Le Corguillé, Loraine Brillet-Guéguen, Mark Hoebeke, Christophe Six, Claudia Steglich, Anne Siegel, Damien Eveillard, Frédéric Partensky, Laurence Garczarek. Synergic effects of temperature and irradiance on the physiology of the marine Synechococcus strain WH7803. Frontiers in Microbiology, section Aquatic Microbiology. https://doi.org/10.3389/fmicb.2020.01707
L’Haridon S, Haroun H, Corre E, Roussel E, Morgane C, Pignet P, Balie`re C, la Cono V, Jebbar M, Yakimov M, Toffin L, Methanohalophilus profundi sp. nov., a methylotrophic halophilic piezophilic methanogen isolated from a deep hypersaline anoxic basin, Systematic and Applied Microbiology (2020), doi: https://doi.org/10.1016/j.syapm.2020.126107
Anna P Muir, Stanislas F Dubois, Rebecca E Ross, Louise B Firth, Antony M Knights, Fernando P Lima, Rui Seabra, Erwan Corre, Gildas Le Corguillé, Flavia LD Nunes. Seascape genomics reveals population isolation in the reef-building honeycomb worm, Sabellaria alveolata (L.). BMVCevolutionary biology. https://doi.org/10.21203/rs.2.11848/v2
N'Zi Daniel Koua, Jésus Nú ñez-Rodriguez, Julie Orjuela, Céline Zatylny- Gaudin, Marie-Pierre Dubos, Benoît Bernay, Julien Pontin, Erwan Corre, Joël Henry. Identification and structural characterization of the factors involved in vitellogenesis and its regulation in the African Osteoglossiforme of aquacultural interest Heterotis niloticus (Cuvier, 1829). General and Comparative Endocrinology. https://doi.org/10.1016/j.ygcen.2020.113532
S. Dupont; A. Lokmer; E. Corre; J.-C. Auguet; B. Petton; E. Toulza; C. Montagnani; G. Tanguy; D. Pecqueur; C. Salmeron; L. Guillou; C. Desnues; B. La Scola; J. Bou Khalil; J. de Lorgeril; G. Mitta; Y. Gueguen; Jean-Michel Escoubas. Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses. https://doi.org/10.1186/s42523-020-00032-w
Ruibo Cai, Ehsan Kayal, Catharina Alves-de-Souza, Estelle Bigeard, Erwan Corre, Christian Jeanthon, Dominique Marie, Betina M. Porcel, Raffaele Siano, Jeremy Szymczak, Matthias Wolf & Laure Guillou . Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach. Scientific Reports volume 10, Article number: 2531 (2020). https://doi.org/10.1038/s41598-020-59524-z
Bertille Burgunter-Delamare, Hetty KleinJan, Clemence Frioux, Enora Fremy, Margot Wagner, Erwan Corre, Alicia Le Salver, Cédric Leroux, Catherine Leblanc, Catherine Boyen, Anne Siegel, Simon M. Dittami. Metabolic complementarity between a brown alga and associated cultivable bacteria provide indications of mutually beneficial interactions. Frontiers in Marine sciences Front. Mar. Sci., 21 February 2020 | https://doi.org/10.3389/fmars.2020.00085
Annie Lebreton; Erwan Corre; Jean-Luc Jany; Loraine Brillet-Guegen; Carlos Perez-Arques; Victoriano Garre; Misharl Monsoor; Robert Debuchy; Christophe Le Meur; Emmanuel Coton; Georges Barbier; Laurence Meslet Cladiere. 2020. Comparative genomics applied to Mucor species with different lifestyles. BMC Genomics. https://doi.org/10.1186/s12864-019-6256-2.
Dittami, Simon; Corre, Erwan; Guéguen, Loraine; Pontoizeau, Noé; Aite, Meziane; Avia, Komlan; Caron, Christophe; Cho, Chung Hyun; Collén, Jonas; Cormier, Alexandre; Delage, Ludovic; Doubleau, Sylvie; Frioux , Clémence; Gobet, Angélique; González-Navarrete, Irene; Grosillier, Agnes; Hervé, Cécile; Jollivet, Didier; Kleinjan, Hetty; Leblance, Catherine; Lipinska, Agnieszka; Liu, Xi; Marie, Dominique; Markov, Gabriel; Minoche, André; Monsoor, Misharl; Pericard, Pierre; Perrineau, Marie-Mathilde; Peters, Akira; Siegel, Anne; Siméon, Amandine; Trottier, Camille; Yoon, Hwan Su; Himmelbauer, Heinz; Boyen, Catherine; Tonon, Thierry. The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga. Marine Genomics. https://doi.org/10.1016/j.margen.2020.100740
Arnaud Belcour, Jean Girard, Méziane Aite, Ludovic Delage, Camille Trottier, Charlotte Marteau, Cédric Leroux, Simon M. Dittami, Pierre Sauleau, Erwan Corre, Jacques Nicolas, Catherine Boyen, Catherine Leblanc, Jonas Collén, Anne Siegel, Gabriel V. Markov. Inferring biochemical reactions and metabolite structures to cope with metabolic pathway drift. accepted in iScience, Volume 23, Issue 2, 21 February 2020, https://doi.org/10.1016/j.isci.2020.100849

Citations

Daniel Vaulot , Stefan Geisen , Frédéric Mahé , David Bass. pr2-primers: an 18S rRNA primer database for protists. : https://doi.org/10.1101/2021.01.04.425170;
Lipinska, Collén;, Krueger-Hadfield, Mora Ficko-Blean. To gel or not to gel: differential expression of carrageenan-related genes between the gametophyte and tetasporophyte life cycle stages of the red alga Chondrus crispus. Scientific Reports, 13 Jul 2020, 10(1):11498 DOI: 10.1038/s41598-020-67728-6
Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient. Guzinski J, Ruggeri P, Ballenghien M, Mauger S, Jacquemin B, Jollivet C, Coudret J, Jaugeon L, Destombe C, Valero M. Genes (Basel), 11(12), 13 Dec 2020. DOI: 10.3390/genes11121503
Complete mitogenome data from a European specimen of Ostrinia scapulalis (Walker, 1859) (Lepidoptera, Pyraloidea, Crambidae, Pyraustinae). Gschloessl B, Audiot P, Nidelet S, Kergoat GJ, Streiff R. Data Brief, 33:106427, 22 Oct 2020 DOI: 10.1016/j.dib.2020.106427
Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing. Auffret P, Le Luyer J, Sham Koua M, Quillien V, Ky CL. BMC Genomics, 21(1):662, 25 Sep 2020. DOI : 10.1186/s12864-020-07015-w
Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1. Han Z, Jasnovidova O, Haidara N, Tudek A, Kubicek K, Libri D, Stefl R, Porrua O. EMBO J, 39(7):e101548, 28 Feb 2020 . DOI: 10.15252/embj.2019101548
Histone modifications during the life cycle of the brown alga Ectocarpus Simon Bourdareau1 , Leila Tirichine2 , Bérangère Lombard3 , Damarys Loew3 , Delphine Scornet1 , Susana M. Coelho1,*, J. Mark Cock1,*i: https://doi.org/10.1101/2020.03.09.980763;
Sichert, A., Corzett, C.H., Schechter, M.S. et al. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol 5, 1026–1039 (2020). https://doi.org/10.1038/s41564-020-0720-2
Thomas Lenormand, FredericFyon, EricSun, DenisRoze. Sex Chromosome Degeneration by Regulatory Evolution . Current Biology Volume 30, Issue 15, 3 August 2020, Pages 3001-3006.e5. https://doi.org/10.1016/j.cub.2020.05.052
Deb, S., Das, L. & Das, S.K. Composition and functional characterization of the gut microbiome of freshwater pufferfish (Tetraodon cutcutia). Arch Microbiol 202, 2761–2770 (2020). https://doi.org/10.1007/s00203-020-01997-7
Qikun Xing, Guiqi Bi, Min Cao, Arnaud Belcour, Méziane Aite, Yunxiang Mao. Comparative Transcriptome Analysis Provides Insights into The Response of Ulva Compressa to The Fluctuating Salinity Conditions. DOI: 10.21203/rs.3.rs-47388/v1
Kolchina, N.V., Rychkov, G.N., Kulminskaya, A.A. et al. Structural Organization of the Active Center of Unmodified Recombinant Sulfatase from the Mycelial Fungi Fusarium proliferatum LE1. Russ J Bioorg Chem 46, 563–571 (2020). https://doi.org/10.1134/S1068162020040081
Synthèse d’inhibiteurs d’endosulfatases humaines : vers de nouveaux outils thérapeutiques contre le cancer et les maladies inflammatoires. Thèse Pauline Quellier 2020. https://tel.archives-ouvertes.fr/tel-02987041/
Burgunter-Delamare, B., Boyen, C. & Dittami, S.M. Effect of essential oil- and iodine treatments on the bacterial microbiota of the brown alga Ectocarpus siliculosus. J Appl Phycol 33, 459–470 (2021). https://doi.org/10.1007/s10811-020-02286-y
Xing, Q., Rousvoal, S. & Leblanc, C. Transcriptome-wide identification and evaluation of optimal reference genes for RT-qPCR expression analysis of Saccharina latissima responses to biotic and abiotic stress. J Appl Phycol 33, 617–627 (2021). https://doi.org/10.1007/s10811-020-02279-x
Alexandre Cormier , Mohamed Amine Chebbi , Isabelle Giraud, Remi Wattier , Maria Teixeira , Clement Gilbert , Thierry Rigaud , and Richard Cordaux. Comparative Genomics of Strictly Vertically Transmitted, Feminizing Microsporidia Endosymbionts of Amphipod Crustaceans. Biol. Evol. 13(1) doi:10.1093/gbe/evaa245

Oral communications/ Posters

Gildas Le Corguillé, Julien Seiler, François Gerbes et al. , What's new on the IFB NNCR Cluster(s) ?. JOBIM2020, Visio, June 2020
Gildas Le Corguillé, Les outils de bioinfo : plus simple à installer et donc à réutiliser. BGO Axe Bioinfo, December 2020

2019

Publications

Cátia Monteiro, Sandra Heinrich, Inka Bartsch, Klaus Valentin, Erwan Corre, Jonas Collén, Lars Harms, Gernot Glöckner and Kai Bischof. Temperature Modulates Sex-Biased Gene Expression in the Gametophytes of the Kelp Saccharina latissima. Frontiers in Marine Science. 1 December 2019 | Volume 6 | Article 769 doi: 10.3389/fmars.2019.00769
Elham Karimi, Enora Geslain, Hetty KleinJan, Gwenn Tanguy, Erwan Legeay, Erwan Corre, Simon M Dittami. Genome sequences of seventy-two bacterial strains isolated from Ectocarpus subulatus: a resource for algal microbiology. Genome Biology and Evolution, 2019 . evz278, https://doi.org/10.1093/gbe/evz278
Monteiro, Catia; Li, Huiru; Bischof, Kai; Bartsch, Inka; Valentin, Klaus; Corre, Erwan; Collen, Jonas; Harms, Lars; Glöckner, Gernot; Heinrich, Sandra. Is local adaptation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima?" BMC Plant Biology .https://doi.org/10.1186/s12870-019-2124-0 />
Nègre, Aite, Belcour, Frioux, Brillet-Guéguen, Liu, Bordron, Godfroy, Lipinska, Leblanc, Siegel, Dittami, Corre, and Markov, “Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus,” Antioxidants, vol. 8, no. 11, pp. 564–23, Nov. 2019.DOI: 10.3390/antiox8110564
Dittami SM, Arboleda E, Auguet J-C, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen A, Eveillard D, Gachon CMM, Griffiths S, Harder T, Kayal E, Kazamia E, Lallier FH, Media M, Marzinelli EM, Morganti T, Pons LN, Prado S, Pintado J, Saha M, Selosse M-A, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. 2019. A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions.PeerJ Preprints: No. e27519v1. https://doi.org/10.7287/peerj.preprints.27519v3
Ohdera A, Ames CL, Dikow RB. Kayal E, Chiodin M, Busby B, La S, Pirro S, Collins AG, Medina M, Ryan JF. 2019. Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa). GigaScience 8(7): giz069. https://doi.org/10.1093/gigascience/giz069
Kayal M, Lewis H, Ballard J,Kayal E. 2019. Humanity and the 21st century’s resource gauntlet: a commentary on Ripple et al.'s article “World scientists’ warning to humanity: a second notice”.Rethinking Ecology. doi: 10.3897/rethinkingecology.4.32116
Marjorie Couton, Thierry Comtet, Sabrina Le Cam, Erwan Corre, Frédérique Viard. Metabarcoding on planktonic larval stages: an efficient approach for detecting and investigating life cycle dynamics of benthic aliens. accepted in Management of Biological Invasions.
Alexandra Rahmani, Erwan Corre,Gaëlle Richard,Adeline Bidauld,Christophe Lambert, Louisi Oliveira, Cristiane Thompson, Fabiano Thompson, Vianney Pichereau, Christine Paillard. Transcriptomic analysis of clam extra pallial fluids reveals immunity and cytoskeleton alterations in the first week of Brown Ring Disease development. Fish & Shellfish Immunology. https://doi.org/10.1016/j.fsi.2019.08.025
Huiru Li, Cátia Monteiro, Sandra Heinrich, Inka Bartsch, Klaus Valentin, Lars Harms, Gernot Glöckne, Erwan Corre, Kai Bischof. Responses of the kelp Saccharina latissima (Phaeophyceae) to the warming Arctic: from physiology to transcriptomics. Physiologia Plantarum, https://doi.org/10.1111/ppl.13009.
François Thomas,Erwan Corre & Aurélie Cébron .Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil. The ISME Journal (2019).https://doi.org/10.1038/s41396-019-0394-z
Rombouts, I., Simon, N., Aubert, A., Cariou, T., Feunteun, E., Guérin, L., Hoebeke, M., McQuatters-Gollop, A., Rigaut-Jalabert, F., Artigas, L.F. Changes in marine phytoplankton diversity: assessment under the Marine Strategy Framework Directive. Ecological Indicators. https://doi.org/10.1016/j.ecolind.2019.02.009
Laure Arsenieff, Nathalie Simon, Fabienne Rigaut-Jalabert, Florence Le Gall, Samuel Chaffron, Erwan Corre, Emmanuelle Com, Estelle Bigeard, Anne-Claire Baudoux. First Viruses Infecting the Marine Diatom Guinardia delicatula. Frontiers in Microbiology, section Aquatic Microbiology. 09 January 2019 | https://doi.org/10.3389/fmicb.2018.03235

Remerciements

L Reisky et al., A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nature chemical …, 2019
B Pilgaard et al. Proteomic enzyme analysis of the marine fungus Paradendryphiella salina reveals alginate lyase as a minimal adaptation strategy for brown algae …- Scientific reports, 2019 -
J Le Luyere et al. , Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada … BMC genomics…, 2019
P Debeljak et al. Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes. Environmental Microbiology. https://doi.org/10.1111/1462-2920.14621
E Ruppé et al. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nature Microbiology
Z Han et al. Termination of non-coding transcription in yeast relies on both a CTD-interaction domain and a CTD-mimic in Sen1 BioRxiv 2019
W Santana-Garcia et al. ,RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding
J Vidal-Dupiol et al., Sequencing, de novo assembly and annotation of the genome of the scleractinian coral, Pocillopora acuta. bioRxiv, 2019 -
MM Sandinet et al., Time calibrated morpho-molecular classification of Nassellaria (Radiolaria) - Protist, 2019 -
D Piel et al. Selection of Vibrio crassostreae relies on a plasmid expressing a type 6 secretion system cytotoxic for host immune cells Environmental Microbiology …, 2019 -
S Lambert et al., Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations. The ISME …, 2019 - nature.com
ECP Catãoet al., Shear stress as a major driver of marine biofilm communities in the NW Mediterranean Sea. Frontiers inMicrobiology, 2019
A Gutierrez-Rodriguez et al., High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding. The ISME …, 2019
M Tragin, D Vaulot . Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding - Scientific reports, 2019
S Le Cam et al. , A genome‐wide investigation of the worldwide invader Sargassum muticum shows high success albeit (almost) no genetic diversity. Evolutionary application 2019
A Arun et al., Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae. eLife. 2019

Oral communications/ Posters

Les réseaux métaboliques à l’échelle des génomes : des outils pour intégrer les données et ouvrir de nouvelles questions biologiques. Delphine Negre et Gabriel Markov. Gen2Bio, March 2019, Angers (FR)
Update from the Galaxy Comminity. Gruening B. and Le Corguillé G. ELIXIR All-Hands, 17 Jun 2019, Lisbonne (PL)
Workflow4Metabolomics: an international computing infrastructure for Metabolomics. Pétéra M, Dallet R, Le Corguillé G, et al. Galaxy Community Conference (GCC2019). June 2019. Freiburg (DE).
Metabolomics data analysis. Pétéra M, Le Corguillé G, et al. Galaxy Community Conference (GCC2019). June 2019. Freiburg (DE). Training session

2018

Publications

Jacquemot L., Bettarel Y., Monjol J. , Corre E., Halary S. , Desnues C., Ferrier-Pagès C., Bouvier T. , Baudoux A-C. Therapeutic potential of a new jumbo phage that infects the coral pathogen Vibrio coralliilyticus . Front. Microbiol. | doi: 10.3389/fmicb.2018.02501
Baptiste Houyvet; Bruno Zanuttini; Erwan Corre; Gildas Le Corguillé; Joël Henry; Céline Zatylny-Gaudin. "Design of antimicrobial peptides from a cuttlefish database ». Amino Acids. 2018 Nov;50(11):1573-1582. doi: 10.1007/s00726-018-2633-4
Ehsan Kayal,Bastian Bentlage,,M. Sabrina Pankey, Aki H. Ohdera,Monica Medina, David C. Plachetzki, Allen G. Collins and Joseph F. Ryan. Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. BMC Evolutionary Biology201818:68. https://doi.org/10.1186/s12862-018-1142-0
Annie Lebreton, Laurence Meslet-Cladière, Stéphanie Morin-Sardin, Emmanuel Coton, Jean-Luc Jany, Georges Barbier, Erwan Corre .Comparative analysis of five Mucor species transcriptomes. 2018.Genomics.https://doi.org/10.1016/j.ygeno.2018.09.003
Soleilhac, E.; Brillet-Guéguen, L.; Roussel, V.; Prudent, R.; Touquet, B.; Dass, S.; Aci-Sèche, S.; Kasam, V.; Barette, C.; Imberty, A.; Breton, V.; Vantard, M.; Horvath, D.; Botté, C.; Tardieux, I.; Roy, S.; Maréchal, E.; Lafanechère, L. Specific Targeting of Plant and Apicomplexa Parasite Tubulin through Differential Screening Using In Silico and Assay-Based Approaches. Int. J. Mol. Sci. 2018, 19, 3085.https://doi.org/10.3390/ijms19103085
Sarah Farhat, Isabelle Florent, Benjamin Noel, Ehsan Kayal, Corinne Da Silva, Estelle Bigeard, Adriana Alberti, Karine Labadie, Erwan Corre, Jean-Marc Aury, Stephane Rombauts, Patrick Wincker, Laure Guillou, Betina M. Porcel. Comparative time-scale gene expression analysis highlights the infection processes of two Amoebophrya strains. Front. Microbiol., 02 October 2018 | https://doi.org/10.3389/fmicb.2018.02251 
Simon M. Dittami, Erwan Corre, Loraine Brillet-Gueguen, Noe Pontoizeau, Meziane Aite, Komlan Avia, Christophe Caron, Chung Hyun Cho, Jonas Collen, Alexandre Cormier, Ludovic Delage, Sylvie Doubleau, Clemence Frioux, Angelique Gobet, Irene Gonzalez-Navarrete, Agnes Groisillier, Cecile Herve, Didier Jollivet, Hetty KleinJan, Catherine Leblanc, Agnieszka P. Lipinska, Xi Liu, Dominique Marie, Gabriel V. Markov, Andre E. Minoche, Misharl Monsoor, Pierre Pericard, Marie-Mathilde Perrineau, Akira F. Peters, Anne Siegel, Amandine Simeon, Camille Trottier, Hwan So Yoon, Heinz Himmelbauer, Catherine Boyen, Thierry Tonon (2018) The genome of Ectocarpus subulatus highlights unique mechanisms for stress tolerance in brown algae. bioRxiv, 307165. doi : 10.1101/307165
Alexandre Leduc; Céline Zatylny-Gaudin, PhD; Marie Robert, PhD; Erwan Corre, PhD; Gildas Le Corguillé; Hélène Castel, PhD; Antoine Lefevre-Scelles, PhD; Vincent Fournier, PhD; Enric Gisbert, PhD; Karl Blyth Andree, PhD; joel henry, PhD. Dietary aquaculture by-product hydrolysates: impact on the transcriptomic response of the intestinal mucosa of European seabass (Dicentrarchus labrax) fed low fish meal diets.BMC Genomics (2018) 19:396 https://doi.org/10.1186/s12864-018-4780-0
Arnaud Meng; Camille Marchet; Erwan Corre; Pierre Peterlongo; Adriana Alberti; Corinne Da Silva; Patrick Wincker; Eric Pelletier; Ian Probert; Johan Decelle; Stéphane Le Crom; Fabrice Not; Lucie Bittner. A de novo approach to disentangle/decouple partner identity and function in holobiont systems. Microbiome may 2018. https://doi.org/10.1186/s40168-018-0481-9
Héloïse Chassé, Julie Aubert, Sandrine Boulben; Gildas Le Corguillé; Erwan Corre, Patrick Cormier, Julia Morales. 2018. "Translatome analysis at oocyte-to-embryo transition in sea urchin ». NAR .DOI:10.1093/nar/gky258
Arnaud Meng, Erwan Corre, Ian Probert, Andres Gutierrez-Rodriguez, Raffaele Siano, Anita Annamale, Adriana Alberti, Corinne Da Silva, Patrick Wincker, Stephane Le Crom, Fabrice Not, Lucie Bittner. Analysis Of The Genomic Basis Of Functional Diversity In Dinoflagellates Using A Transcriptome-Based Sequence Similarity Network. Molecular Ecology. https://doi.org/10.1111/mec.14579
Jean-Philippe Buffet, Erwan Corre, Evelyne Duvernois-Berthet, Jérôme Fournier, and Pascal Jean Lopez. Adhesive gland transcriptomics uncovers a diversity of proteins and enzymes involved in glue formation in marine tube-building polychaetes.Acta Biomaterialia.DOI:10.1016/j.actbio.2018.03.037
Stéphane L’Haridon, Erwan Corre, Yue Guan, Manikandan Vinu, Violetta La Cono, Michail Yakimov, Ulrich Stingl, Laurent Toffin and Mohamed Jebbar. Complete Genome Sequence of the Halophilic Methylotrophic Methanogen. Archaeon Methanohalophilus portucalensis Strain FDF-1^T. Genome Announc. January 2018 6:e01482-17; doi:10.1128/genomeA.01482-17

Remerciements

B.Gschloessl et al.. De novo genome and transcriptome resources of the Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae). Data in Brief, Volume 17, April 2018, Pages 781-787
Eloïse Vanhoenacker et al.. Stabilizing selection, mutational bias, and the evolution of sex. Evolution. 11 July 2018. https://doi.org/10.1111/evo.13547
Angélique Gobet et al.. Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore. Microbiome20186:60. https://doi.org/10.1186/s40168-018-0430-7
Komlan Avia et al.. Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus. Genes 2018, 9(6), 286; https://doi.org/10.3390/genes9060286
Alexandre Cormier et al.. The complete mitochondrial genome of Gammarus roeselii (Crustacea, Amphipoda): insights into mitogenome plasticity and evolution. December 2018, Volume 825, Issue 1, pp 197–210
Alok Arun et al.. Convergent recruitment of life cycle regulators to direct sporophyte development in two eukaryotic supergroups. biorxiv.org. https://doi.org/10.1101/460436
Théophile Grébert et al.. Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria. PNAS February 27, 2018 115 (9) E2010-E2019; https://doi.org/10.1073/pnas.1717069115
Justine Pittera et al.. Thermoacclimation and genome adaptation of the membrane lipidome in marine Synechococcus. Environmental microbiology. 10 November 2017 https://doi.org/10.1111/1462-2920.13985
Akira Kuwata et al.. Bolidophyceae, a Sister Picoplanktonic Group of Diatoms – A Review. Front. Mar. Sci. 29 October 2018. https://doi.org/10.3389/fmars.2018.00370
Catherine Gérikas Ribeiro et al.. Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria. The ISME Journal 12, 1360–1374 (2018)
Sheree Yau et al.. Mantoniella Beaufortii and Mantoniella Baffinensis sp. nov. (Mamiellales, Mamiellophyceae), Two New Green Algal Species from the High Arctic. biorxiv.org. https://doi.org/10.1101/506915
Nga Thi Thuy Nguyen et al.. RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W209–W214, https://doi.org/10.1093/nar/gky317
Margot Tragin & Daniel Vaulot. Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset. Scientific Reports 8, Article number: 14020 (2018)
Maxime Bruto et al.. Ancestral gene acquisition as the key to virulence potential in environmental Vibrio populations. The ISME Journal 12, 2954–2966 (2018)
Sophie Rodrigues et al.. Relation between Biofilm and Virulence in Vibrio tapetis: A Transcriptomic Study. Pathogens 2018, 7(4), 92; https://doi.org/10.3390/pathogens7040092
Arnaud Belcour et al.. Inferring biochemical reactions and metabolite structures to cope with metabolic pathway drift. biorxiv.org. https://doi.org/10.1101/462556
Diala Abu Awad Denis Roze. Effects of partial selfing on the equilibrium genetic variance, mutation load, and inbreeding depression under stabilizing selection. Evolution. 14 February 2018. https://doi.org/10.1111/evo.13449
B. Gschloessl et al.. Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae). Molecular Ecology Resources. 20 January 2018 https://doi.org/10.1111/1755-0998.12756
Ewan Harney et al.. Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata. Aquaculture. Volume 491, 1 April 2018, Pages 105-113. https://doi.org/10.1016/j.aquaculture.2018.03.006

2017

Publications

Baptiste Houyvet; Yolande Bouchon-Navaro; Bouchon Claude; Didier Goux; Benoit Bernay; Erwan Corre; Celine Zatylny-Gaudin. Identification of a moronecidin-like antimicrobial peptide in the venomous fish Pterois volitans: functional and structural study of pteroicidin-<alpha>. Fish and Shellfish Immunology. 02/11/2017.DOI:10.1016/j.fsi.2017.11.003
Simon M. Dittami, Erwan Corre. Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast. accepted in PeerJ. 30/10/2017. DOI:10.7717/peerj.4073
Björn Grüning, Ryan Dale, Andreas Sjödin, Jillian Rowe, Brad A. Chapman, Christopher H. Tomkins-Tinch, Renan Valieris, The Bioconda Team (Gildas le Corguillé inside), Johannes Köster.Bioconda: A sustainable and comprehensive software distribution for the life sciences. bioRxiv 207092, October 2017. doi: https://doi.org/10.1101/207092.NAture Methods 2018 : https://doi.org/10.1038/s41592-018-0046-7
Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Lariviere, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon Ryan, Florian Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Rolf Backofen, Anton Nekrutenko, Björn Grüning. Community-driven data analysis training for biology. Cell Systems. Volume 6, Issue 6, p752–758.e1, 27 June 2018. https://doi.org/10.1016/j.cels.2018.05.012. bioRxiv 225680; doi: https://doi.org/10.1101/225680
Adriana Lopes dos Santos, Thibaut Pollina, Priscillia Gourvila, Erwan Corre, Dominique Marie , José Luis Garrido , Francisco Rodríguez , Mary-Hélène Noële, Daniel Vaulot and Wenche Eikrem. Chloropicophyceae, a new class of picoplanktonic prasinophytes from the sunlit oceans.Scientific Reports accepted (1):1-20 · October 2017. DOI: 10.1038/s41598-017-12412-5.
Ehsan Kayal, Bastian Bentlage, M. Sabrina Pankey, Aki H. Ohdera, Monica Medina, David C. Plachetzki, Allen G. Collins, Joseph F. Ryan. Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits. 2017. Accepted in BMC Evolutionary Biology.
Lina-Juana Dolch, Guillaume Tourcier, Mariette Bedhomme, Séverine Collin, Leonardo Magneschi, Melissa Conte, Khawla Seddiki, Josselin Lupette, Erwan Corre, Dimitris Petroutsos, Laurent Fourage, Giovanni Finazzi, Fabrice Rébeillé, Juliette Jouhet, Patrick McGuinn, Eric Maréchal. Nitric oxide mediates nitrite-sensing and adaptation and triggers a remodeling of glycerolipids in Phaeodactylum . Plant Physiology. DOI: https://doi.org/10.1104/pp.17.01042
Thomas F, Bordron P, Eveillard D, Michel G (2017) Gene expression analysis of of Zobellia galactanivorans during the degradation of algal polysaccharides reveals both substrate-specific and shared transcriptome-wide responses. Frontiers in Microbiology, in the press. doi: 10.3389/fmicb.2017.01808
Guitton Y, Tremblay-Franco M, Le Corguillé G, Martin JF, Pétéra M, Roger-Mele P, Delabrière A, Goulitquer S, Monsoor M, Duperier C, Canlet C, Servien R, Tardivel P, Caron C, Giacomoni F, Thévenot. E. 2017. Create, run, share, publish, and reference your LC-MS, FIA-MS, GC-MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics. Int J Biochem Cell Biol. 2017 Jul 12. pii: S1357-2725(17)30157-7. doi: 10.1016/j.biocel.2017.07.002.
Jean-Yves Toullec, Erwan Corre, Perrine Mandon, Marcelo Gonzalez-Aravena, Céline Ollivaux and Chi-Ying Lee. Characterization of the neuropeptidome of a Southern Ocean decapod, the shrimp Chorismus antarcticus. Focus on a new decapod ITP-like belonging to the CHH peptide family. General and Comparative Endocrinology ;252:60-78 · July 2017. DOI: 10.1016/j.ygcen.2017.07.015
Petra ten Hoopen; Robert D Finn; Lars Ailo Bongo; Erwan Corre; Bruno Fosso; Folker Meyer; Alex Mitchell; Eric Pelletier; Graziano Pesole; Monica Santamaria; Nils Peder Willassen; Guy Cochrane.2017. The metagenomic data life-cycle: standards and best practices. GigaScience · June 2017. DOI: 10.1093/gigascience/gix047
Ritter A., Cabioch L., Brillet-Guéguen L., Corre E., Cosse A., Dartevelle L., Duruflé H., Fasshauer C., Goulitquer S., Thomas F., Correa J. A., Potin P, Faugeron S. and Leblanc C. (2017). Herbivore-induced chemical and molecular responses of the kelps Laminaria digitata and Lessonia spicata. PLOS ONE 12(3): e0173315. doi: 10.1371/journal.pone.0173315
Paul Simion, Hervé Philippe, Denis Baurain, Muriel Jager, Daniel J. Richter, Arnaud Di Franco, Béatrice Roure, Nori Satoh, Éric Quéinnec, Alexander Ereskowsky, Pascal Lapébie, Erwan Corre, Frédéric Delsuc, Nicole King, Gert Wörheide & Michaël Manuel A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals. Current Biology. Volume 27, Issue 7, 3 April 2017, Pages 958-967.https://doi.org/10.1016/j.cub.2017.02.031
Stephane L'Haridon, Erwan Corre, Yue Guan, Manikandan Vinu, Violetta La Cono, Michail Yakimov, Ulrich Stingl, Laurent Toffin, and Mohamed Jebbar. 2017. Complete genome sequence of Methanohalophilus halophilus DSM 3094T. Genome Announcements 5(7) · February 2017. DOI: 10.1128/genomeA.01604-16.
Dorrell, Richard G and Gile, Gillian and McCallum, Giselle and Méheust, Raphaël and Bapteste, Eric P and Klinger, Christen M and Brillet-Guéguen, Loraine and Freeman, Katalina D and Richter, Daniel J and Bowler, Chris. (2017). Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. eLife, 6, [e23717]. DOI: 10.7554/eLife.23717
van Rijswijk M, Beirnaert C, Caron C, Le Corguillé G., et al. The future of metabolomics in ELIXIR. F1000Research 2017, 6 (ELIXIR):1649 (doi: 10.12688/f1000research.12342.1

Oral communications/ Posters

Barbeyron T, Brillet-Guéguen L, Carré W., Carrière C, Caron C, Czjzek M, Hoebeke M, Michel G. Matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity. EnzyBio 2017 (GT Enzymes – SFBBM), Le Croisic (9-12 mai 2017). Oral presentation.
Houyvet B., Bouchon-Navaro Y., Bouchon C., Bernay B., Corre E., Zatylny-Gaudin C . Antimicrobial peptides in venomous fish Pterois volitans. 7th International Meeting on Antimicrobial Peptides IMAP University of Copenhagen (Denmark) August 25 -27, 2017.
Houyvet B., Zanuttini B., Corre E., Henry J., Zatylny-Gaudin C. Design of antimicrobial peptides from a cuttlefish database. 7th International Meeting on Antimicrobial Peptides IMAP University of Copenhagen ( Denmark) August 25 -27, 2017
Ehsan Kayal, Lourdes Velo Suarez,Laure Guillou, Erwan Corre, Christophe Six, Estelle Bigeard, Dominique Marie. Possible hijacking of the host plastids by an intracellular parasite (Amoebophrya sp., Syndiniales) of microalgae. 15th International Congress of Protistology. 30/7 4/08/2017 Prague Czech Republic
Annie Lebreton, Stéphanie Morin-Sardin, Laurence Meslet-Cladière, Jean-Luc Jany, Emmanuel Coton, Georges Barbier, Erwan Corre. Transcriptional studies of five fungal Mucor species. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), 2017. Lille, 3-6 juillet 2017.
Jean-Michel Escoubas, Samuel Dupont, Bruno Petton, Ana Lokmer, Eve Toulza, Caroline Montagnani, David Pecqueur, Laure Guillou, Christelle Desnues, Julien De Lorgeril, Yannick Gueguen, Guillaume Mitta and Erwan Core. A holistic approach to investigate the establishment and dynamics of the blood-microbiota (bacteria, protists and viruses) in a marine invertebrate. IWH17: Interdisciplinary Workshop on Holobionts. University of Bordeaux. BORDEAUX, France, November 6-8, 2017
Gobet, A., Corre, E., Correc, G., Delage, L., Dittami, S., Kleinjan, H., Rousvoal, S., Tanguy, G. and Leblanc, C..Characterization of the epiphytic bacterial community associated to the kelp laminaria digitata. IPC 11 11th International Phycological Congress. 13-19 August 2017. Szczecin, Poland.
Fabrice Not,Emilie Villar,Arnaud Meng,Charles Bachy,Christophe Six,Lucie Bittner,Cédric Leroux,Adriana Alberti,Damien Eveillar, Erwan Corre. Ecophysiology of plankton photosymbiosis. 15th International Congress of Protistology. 30/7 4/08/2017 Prague Czech Republic
Gabriel MARKOV, Jean GIRARD, Camille TROTTIER, Cédric LEROUX, Elodie LACROIX, Ludovic DELAGE, Jonas COLLÉN, Simon DITTAMI, Erwan CORRE, Catherine BOYEN, Anne SIEGEL, Catherine LEBLANC. Patchwork evolution of cholesterol biosynthetic pathway in the model red alga Chondrus crispus. Symposium Substances Naturelles ICSN-UPSACLAY (15ème Symposium ICSN).Gif-sur-Yvette, IMAGIF, 29 et 30 juin 2017.
Markov G., Girard J., Trottier C., Guéguen L., Leroux C., Lacroix E., Delage L., Collén J., Dittami S., Corre E., Boyen C., Siegel A., Leblanc C. (2017). Patchwork evolution of metabolic pathways in red and brown macroalgae. Communication orale, 8th annual meeting of the EFOR network, Algae Workshop, 3d May 2017, Paris.
THOMAS François, CORRE Erwan, CEBRON Aurélie. DNA-SIP and metagenomic revealsshifts in active phenanthrene-degrading bacteria of rhizosphere and bulk soil from a historically contaminated site. 14th Symposium on Bacterial Genetics and Ecology "Talking with the neighbours" 4–8 June 2017. Aberdeen, Scotland
Laure Guillou, Erwan Corre, Christophe Six, Lourdes Velo Suarez, Ehsan Kayal. Possible hijacking of the host plastids by an intracellular parasite (Amoebophrya spp., Syndiniales) of microalgae. Microbiology Society 3-7April2017. Edinburgh UK
Poster: Barbeyron T, Brillet-Guéguen L, Carré W., Carrière C, Caron C, Czjzek M, Hoebeke M, Michel G. Matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity. CBM12 - The 12th Carbohydrate Bioengineering Meeting, Vienna, Austria (April 23-26, 2017).
Hugo Doré, Mark Hoebeke. Cyanorak V2: Un système d’information pour la comparaison des génomes des picocyanobactéries marines. Gen2Bio 2017 - Nantes. Oral presentation.
Hugo DORE, Gregory FARRANT, Frédéric PARTENSKY, Florian HUMILY, Morgane RATIN, Antoine BISCH, Loraine GUÉGUEN, Mark HOEBEKE, Erwann CORRE, Gildas LE CORGUILLÉ, David J. SCANLAN and Laurence GARCZAREK. Genomic bases of long-term adaptation to environmental conditions in Prochlorococcus and Synechococcus. Annual Conference of the Microbiology Society, Edinburgh, April 2017. Oral presentation.
Gobet A., Corre E., Correc G., Delage L., Dittami S., Kleinjan H., Rousvoal S., Tanguy G. and Leblanc C. Characterization of the epiphytic bacterial community associated to the kelp Laminaria digitata.- 11th International Phycological Congress, 13-19 August 2017, Szczecin, Poland
Gildas Le Corguillé, Franck Giacomoni, Pierrick Roger-Mele, Christophe Duperier, Mélanie Pétéra, Yann Guitton, Marie Tremblay-Franco, Jean-François Martin, Cécile Canlet, Alexis Delabrière, Etienne Thévenot, Christophe Caron. Workflow4Metabolomics:Towards an international computing infrastructure and a tools showcase for Metabolomics. GCC2017, Montepellier, June 2017. Oral presentation.

2016

Publications

Alexandre Cormier, Komlan Avia, Lieven Sterck, Thomas Derrien, Valentin Wucher, Gwendoline Andres;,Misharl Monsoor, Olivier Godfroy, Agnieszka Lipinska, Marie-Mathilde Perrineau, Yves Van De Peer, Christophe Hitte, Erwan Corre, Susana M. Coelho, J. Mark Cock. 2016. "Re-annotation, improved large-scale assembly and establishment of a catalogue of non-coding loci for the genome of the model brown alga Ectocarpus. New Phytologist. November 2016. DOI: 10.1111/nph.14321
Tristan Barbeyron, Loraine Brillet-Guéguen, Wilfrid Carré, Cathelène Carrière, Christophe Caron, Mirjam Czjzek, Mark Hoebeke and Gurvan Michel. Matching The Diversity Of Sulfated Biomolecules: Creation Of A Classification Database For Sulfatases Reflecting Their Substrate Specificity. PLOS ONE 11(10): e0164846. doi: 10.1371/journal.pone.016484
S. Djebali, V. Wucher, S. Foissac, C. Hitte, E. Corre, and T. Derrien, “Bioinformatics Pipeline for Transcriptome Sequencing Analysis,” in Methods in Molecular Biology, vol. 1468, no. 14, New York, NY: Springer New York, 2016, pp. 201–219.
Kim Huenerlage, Kévin Cascella, Erwan Corre, Lola Toomey, Friedrich Buchholz, Jean-Yves Toullec. The arctoboreal krill species Thysanoessa inermis and climate change: Linking transcriptomics and physiological responses to variations in environmental temperatures. Cell Stress and Chaperones August 2016 DOI: 10.1007/s12192-016-0720-6
Bussard A, Corre E, Hubas C, Duvernois-Berthet E, Le Corguillé G, Jourdren L, Coulpier F, Claquin P, Lopez PJ. Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms. Environ Microbiol. 2016 May 28. doi: 10.1111/1462-2920.13398.
K. Wang, C. Del Castillo, E. Corre, E. Pales-Espinosa, and B. Allam. Clam focal and systemic immune responses to QPX infection revealed by RNA-seq technology. BMC Genomics, vol. 17, no. 1, p. 146, 201
Varet H, Brillet-Guéguen L, Coppée J-Y, Dillies M-A (2016) SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data. PLoS ONE 11 (6): e0157022. doi:10.1371/journal.pone.0157022

Oral communications

P. Potin, E. Corre and IDEALG WP leaders (2016) Ten years of French and EU integrative research projects to capitalize on the breakthroughs in algal biotechnology. Bioinformatics, Metabolic Engineering and Genomics in Biotechnological Applications. V Workshop CeBiB – 30 Nov–2 Dec 2016, Puerto Varas Chili. invited plenary lecture.
E. Corre. Les outils de bioinformatique au service de l’exploration des génomes d’algues marines.IDEALG Annual meeting Lorient France, 7 nov. 2016
E. Corre. La plate-forme bioinformatique ABiMS : un outil et des services dédiés au service du traitement de la donnée en biotechnologies marines. conférence Biosciences en Finistère. 12 octobre 2016 CCI de Brest
Loraine Brillet-Guéguen, Misharl Monsoor. Environment for analysis and annotation of macro algae genomes, infrastructure example on the ABiMS platform with GMOD tools. AG IDEALG, 8-9 November 2016, Lorient
Laure Guillou, Erwan Corre , Phuong Le, Dominique Marie, Estelle Bigeard ,Yves Van der Peer ,Stephane Rombauts ,Patrick Winker, Betina Porcel, Sarah Faraht.The paradox of being a specialist for a parasite of marine blooming dinoflagellates .A New Age of Discovery for Aquatic Microeukaryotes.EMBL Heidelberg, Germany Tuesday 26 January - Friday 29 January 2016

Posters

Arnaud Meng, Lucie Bittner, Stéphane Le Crom, Fabrice Not and Erwan Corre. De novo transcriptome assembly dedicated pipeline and its specific application to non-model, marine planktonic organisms. ECCB2016
L. Jacquemot, J. P. Monjol, Y. Bettarel, E. Corre, C. Ferrier-Pagès, T. Bouvier, C. Desnues, A-C. Baudoux.Phage therapy for diseased corals? Potential of a novel giant virus as biocontrol agent against coral pathogens.2016. 13th International Coral Reef Symposium, HAWAI'I, 19-24 June, 2016
Arnaud Meng, Lucie Bittner, Stéphane Le Crom, Fabrice Not and Erwan Corre. De novo transcriptome assembly dedicated pipeline and its specific application to non-model, marine planktonic organisms. ECCB2016
Lebreton Annie, Meslet-Cladière Laurence, Jany Jean-Luc, Barbier Georges, Corre Erwan. Etude comparative des génomes et transcriptomes de Mucor spp.. JOBIM 2016 Lyon 28 au 30 juin
Monsoor Misharl, Eric Fontanillas, Julie Baffard, Pierre-Guillaume Brun, Erwan Corre, Christophe Caron, Didier Jollivet. « AdaptSearch » : a galaxy pipeline for the search of adaptive mutations and positively selected genes from RNASeq orthologs . JOBIM 2016 Lyon 28 au 30 juin

2015

Publications

Alexis Dereeper, Felix Homa, Gwendoline Andres, Guilhem Sempere, Gautier Sarah, Yann Hueber, Jean-François Dufayard and Manuel Ruiz. 2015. SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations. Nucl. Acids Res. doi: 10.1093/nar/gkv351
Ronan Lagadec, Laurent Laguerre, Arnaud Menuet, Anis Amara, Claire Rocancourt, Pierre Péricard, Benoît G. Godard, Maria Celina Rodicio, Isabel Rodriguez-Moldes, Hélène Mayeur, Quentin Rougemont, Sylvie Mazan & Agnès Boutet. 2015. The ancestral role of nodal signalling in breaking L/R symmetry in the vertebrate forebrain. Nature Communications 6, doi:10.1038/ncomms7686
James E. Tarver, Alexandre Cormier, Natalia Pinzón, Richard S. Taylor, Wilfrid Carré, Martina Strittmatter, Hervé Seitz, Susana M. Coelho and J. Mark Cock. microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus. Nucl. Acids Res. (27 July 2015) 43 (13): 6384-6398.; doi: 10.1093/nar/gkv578
Alejandra Medina-Rivera, Matthieu Defrance, Olivier Sand, Carl Herrmann, Jaime A. Castro-Mondragon, Jeremy Delerce,Sébastien Jaeger, Christophe Blanchet, Pierre Vincens, Christophe Caron, Daniel M. Staines, Bruno Contreras-Moreira, Marie Artufel, Lucie Charbonnier-Khamvongsa,Céline Hernandez, Denis Thieffry, Morgane Thomas-Chollier, Jacques van Helden. RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Res (2015) 43 (W1): W50-W56. DOI: https://doi.org/10.1093/nar/gkv362
Dominique Boeuf, Stephane Audic, Loraine Brillet-Gueguen, Christophe Caron, Christian Jeanthon. 2015. MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution Database 2015; doi: 10.1093/database/bav080
Marie Robert, Céline Zatylny-Gaudin, Vincent Fournier, Erwan Corre, Gildas Le Corguillé, Benoît Bernay, Joël Henry. (2015). Molecular characterization of peptide fractions of a Tilapia (Oreochromis niloticus) by-product hydrolysate and in vitro evaluation of antibacterial activity. Process Biochemestry. 12/2014; DOI:10.1016/j.procbio.2014.12.022
V. Cornet,B.Houyvet, J.Henry, B.Bernay,E.Corre, G. Le Corguillé, C. Zatylny-Gaudin. The Toll/NF-<kappa>B pathway in cuttlefish symbiotic accessory nidamental gland. Developmental Comparative Immunology Volume 53, Issue 1, November 2015,Pages 42–46
Zatylnyc-Gaudin Celine, Cornet Valérie, Leduc Alexandre, Zanuttini Bruno, Corre Erwan, Le Corguillé Gildas, Bernay Benoît, Garderes Johan, Kraut Alexandra, Couté Yohann & Henry Joël. Neuropeptidome of the cephalopod Sepia officinalis identification tissue mapping and expression pattern of neurotransmitters and neurohormones during egg-laying. Journal of Proteome Research. Decembre 2015 DOI: 10.1021/acs.jproteome.5b00463
Gregory Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Erwan Corre and Laurence Garczarek. WiseScaffolder : an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data. BMC Bioinformatics. 2015; 16(1): 281. doi: 10.1186/s12859-015-0705-y
Barbara Gasse; Xi Liu, Erwan Corre, Jean-Yves Sire. Amelotin gene structure and expression during enamel formation in the opossum Monodelphis domestica. PLoS One. 2015; 10(7): e0133314.
Cornet V, Henry J, Goux D, Duval E, Bernay B, Le Corguillé G, Corre E, et al. (2015) How Egg Case Proteins Can Protect Cuttlefish Offspring? PLoS One 10(7): e0132836. doi:10.1371/journal.pone.0132836
Simon M. Dittami, Laëtitia Duboscq-Bidot, Morgan Perennou, Angélique Gobet, Erwan Corre, Catherine Boyen, Thierry Tonon. Host-microbe interactions as a driver of brown algal acclimation to salinity gradients. The ISME Journal , (26 June 2015) | doi:10.1038/ismej.2015.104
Sergio Balzano, Erwan Corre, Johan Decelle, Roberto Sierra, Patrick Wincker, Corinne Da Silva, Julie Poulain, Jan Pawlowski, Fabrice Not. Transcriptome analyses to investigate symbiotic relationships between marine protists. Front Microbiol. 2015 Mar 17;6:98, section Microbial Physiology and Metabolism

Oral communications

Olivier Inizan, Gildas Le Corguillé et al. An initiative to federate the galactic community in France: the IFB Galaxy Working Group. GCC2015 Norwich. 7-8 of July
Thierry Tonon et al. Comparative analysis of marine and freshwater brown algae: insights into the biology and evolution of an extremophile Ectocarpus (9OR.14) EPC6 Londres. 23-28 August 2015
Simon Dittami et al. Microbiomes impact algal acclimation: the example of a freshwater strain of Ectocarpus (4KN.2) EPC6 Londres. 23-28 August 2015
Andres Gutierrez-Rodriguez, Daniel Richter, Arnaud Meng, Lucie Bittner, Erwan Corre, Fabrice Not. A physio-molecular integrative approach to assess global patterns of microalgal and photosymbiotic oxidative stress in marine environment. Conferences Jacques Monod. Marine Eco-Systems Biology. Roscoff (Brittany), France June 22-26, 2015.
Simon M. Dittami , Laëtitia Duboscq-Bidot , Morgan Perennou , Angélique Gobet , Erwan Corre , Thierry Tonon, Boyen Catherine. The association of marine bacteria with the brown alga Ectocarpus: a stress-resistant holobiont. Conferences Jacques Monod. Marine Eco-Systems Biology. Roscoff (Brittany), France June 22-26, 2015.
V. Cornet, B.Houyvet, J.Henry, D.Goux, E. Duval, B.Bernay, E.Corre, G. Le Corguillé, C. Zatylny-Gaudin. How cuttlefish protect their offsprin? Annual meeting of the society of Experimental Biology 30 june –3 july 2015, Pragues (Czech Republic).
C Zatylny-Gaudin, V. Cornet, M. Endress, B. Houyvet, B. Bernay, G. Le Corguillé, E. Corre, J. Henry. The impact of “omics” approaches in the understanding of reproduction and predation in the cuttlefish Sepia officinalis. Annual meeting of the society of Experimental Biology 30 june –3 july 2015, Pragues (Czech Republic). Communication affichée
V. Cornet, B.Houyvet, J.Henry, , B.Bernay, E.Corre, G. Le Corguillé, C. Zatylny-Gaudin. The Toll/NF-κB pathway: a key to beneficial bacterial symbiosis in cuttlefish reproductive glands. Annual meeting of the society of Experimental Biology 30 june –3 july 2015, Pragues (Czech Republic).
Joël Henry, Valérie Cornet, Alexandre Leduc, Bruno Zanuttini, Erwan Corre, Gildas Le Corguillé, Benoît Bernay, A Kraut, Céline Zatylny-Gaudin . Caractérisation du neuropeptidome de la seiche Sepia officinalis : identification des neuropeptides impliqués dans la ponte. 19ème Congrès du Groupe Français des Peptides et des Protéines .17-22 mai 2015 . Portbail, Normandie, France
Marie Robert, Alexandre Leduc, CéLine Zatylny-Gaudin, Benoit Bernay, Erwan Corre, Gildas Le Corguillé, Vincent Fournier et Joël Henry. Caractérisation structurale et fonctionnelle de deux hydrolysats fonctionnels destinés à l’alimentation d’espèces aquacoles. 19ème Congrès du Groupe Français des Peptides et des Protéines .17-22 mai 2015 . Portbail, Normandie, France.
V. Cornet, J. Henry, Didier Goux, E. Duval, E. Corre, G. Le Corguillé, B. Bernay, C. Zatylny-Gaudin. Les SepECPs : Une nouvelle classe de protéines capsulaires impliquées dans la protection de l’œuf chez Sepia officinalis.19ème Congrès du Groupe Français des Peptides et des Protéines .17-22 mai 2015 . Portbail, Normandie, France
Gildas Le Corguillé, Misharl Monsoor, W4M group et Christophe Caron, Workflow4Metabolomics : un environnement pour l’analyse à haut-débit. Gen2Bio. 26 mars. La Baule
Vaulot, D.; Lopes dos Santos, A.; Pollina, T.; Corre, E.: Picoeucaryote Metagenomes From The South-Eastern Pacific Ocean. ASLO 2015. Aquatic Sciences Meeting. 22-27 February 2015. Granada Spain
Lopes, A. S.; Gourvil, P.; Romac, S.; Pollina, T.; Corre, E.; Rodriguez-Hernandez, F.; Garrido, J. L.; Audic, S.; de Vargas, C.; Vaulot, D.: Ecological Diversity Of Prasinophytes Clade Vii, The Dominant Green Algae In Open Oceans. ASLO 2015. Aquatic Sciences Meeting: 22-27 February 2015. Granada Spain
L. Brillet-Guéguen, G. Le Corguillé, G. Andres, C. Caron, V. Loux. Planemo: no more crap! Galaxy Day 2015, Paris

Posters

Marie TREMBLAY-FRANCO, Cécile CANLET, Yann GUITTON, Daniel JACOB, Gildas LE CORGUILLE, Jean-François MARTIN, Misharl MONSOOR, Nils PAULHE, Mélanie PETERA, Camille VACQUIE, Franck GIACOMONI, Estelle PUJOS-GUILLOT, Christophe CARON, Etienne THEVENOT. New tools and workflows on W4M, The Galaxy matabolomic infrastructure. RFMF. 9 au 11 juin 2015. Lilles
Gildas Le Corguillé, Misharl Monsoor, W4M group et Christophe Caron, Workflow4Metabolomics : un environnement pour l’analyse à haut-débit. Gen2Bio. 26 mars 2015. La Baule
L. Brillet- Guéguen, C. Caron, V. Loux and the French Galaxy Working Group. A French Galaxy Tool Shed to federate the national infrastructures and offering quality assessed tools. Galaxy Community Conference 2015 et Actes Jobim 2015
Liu X, Corre E and Sire JY. Looking for Secretory Calcium-Binding PhosphoProtein (SCPP) transcripts in jaw transcriptomes. F1000Research 2015, 4:874 (doi: 10.7490/f1000research.1110625.1)
Arnaud Meng, Lucie Bittner, Anita Annamale, Fabrice Not, Erwan Corre, Stéphane Le Crom. De novo assembly pipeline for transcriptomic analysis. JOBIM 2015. F1000Research 2015, 4:533 (doi: 10.7490/f1000research.1110281.1)
Noé Pontoizeau, Simon M. Dittami, Irene Gonzàlez, André E. Minoche, Alexandre Cormier, Pierre Pericard, Erwan Corre, Catherine Boyen, Heinz Himmelbauer, Thierry Tonon. Comparative Analysis of Marine and Freshwater Brown Algae: Insights Into the Biology and Evolution of an Extremophile Ectocarpus. Actes Jobim 2015
Caroline VERNETTE, Emma PRUDENT, Erwan CORRE, Gildas LE CORGUILLÉ, Christophe CARON. Enhanced Blast on Galaxy. Actes Jobim 2015

2014

Publications

Franck Giacomoni,†, Gildas Le Corguillé,†, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot, Christophe Caron. (2014). Workflow4Metabolomics: A collaborative research infrastructure forin computational metabolomics. Bioinformatics, doi: 10.1093/bioinformatics/btu813
Robert, M., Zatylny-Gaudin, C., Fournier, V., Corre, E., Le Corguillé, G., Bernay, B., & Henry, J. (2014). Transcriptomic and peptidomic analysis of protein hydrolysates from the white shrimp (L. vannamei). Journal of Biotechnology, 186C, 30–37. doi:10.1016/j.jbiotec.2014.06.020
Sophia Ahmed, J Mark Cock, Eugenie Pessia, Remy Luthringer, Alexandre Cormier, Marine Robuchon, Lieven Sterck, Akira F Peters, Simon M Dittami, Erwan Corre, Myriam Valero, Jean-Marc Aury, Denis Roze, Yves Van de Peer, John Bothwell, Gabriel A B Marais, Susana M Coelho (2014). A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp. Current Biology : CB, 24(17), 1945–1957.
Godard, B. G., Coolen, M., Le Panse, S., Gombault, A., Ferreiro-Galve, S., Laguerre, L., Ronan Lagadec, Patrick Wincker, Julie Poulain, Corinne Da Silva, Shigehiro Kuraku, Wilfrid Carre, Agnes Boutet and Sylvie Mazan. (2014). Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates. Biology Open, 3(11), 1098–1107. doi:10.1242/bio.20148037
Valérie Cornet, Joël Henry, Erwan Corre, Gildas Le Corguille, Bruno Zanuttini, Céline Zatylny-Gaudin. (2014). Dual role of the cuttlefish salivary proteome in defense and predation ». Journal of Proteomics, 108, 209–222. doi:10.1016/j.jprot.2014.05.019.
Gregory Carrier, Matthieu Garnier, Loic Le Cunff, Gael Bougaran, Ian Probert, Colomban De Vargas, Erwan Corre, Jean-Paul Cadoret and Bruno Saint-Jean. 2014 Comparative transcriptome of wild type and selected strains of the microalgae Tisochrysis lutea provides insights into the genetic basis, lipid metabolism and the life cycle. PLoS ONE, 9(1), e86889. doi:10.1371/journal.pone.0086889
Emmanuelle Pales Espinosa, Erwan Corre and Bassem Allam. 2014. Pallial mucus of the oyster Crassostrea virginica regulates the expression of putative virulence genes of its pathogen Perkinsus marinus. International Journal for Parasitology, 44(5), 305–317. doi:10.1016/j.ijpara.2014.01.006
Lipinska A, Cormier A, Luthringer R, Peters AF, Corre E, Gachon CMM, Cock JM, Coelho SM. 2014. Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga Ectocarpus. Mol Biol Evol. 2015 Jun;32(6):1581-97

Oral communications

E. Corre. Marine microbial and metagenomic developement : Data & Tools. Réunion Bioinformatique microbienne - IFB et FG WP Variants - 25 Septembre 2014 - Institut Pasteur
Stéphane L’Haridon, Morgane Chalopin, Erwan Roussel, Erika Arcadi, Violetta La Cono, Mickael Yakimov, Erwan Corre, Laurent Toffin and Mohamed Jebbar. Methanohalophilus From Deep-sea Hypersaline Anoxic Lakes. Extremophiles 2014. 10th International Congress on Extremophiles ( Extremophiles 2014), September 7 - 11, 2014, Saint Petersburg, Russia (Poster).
Emma Prudent, Gildas Le Corguillé. Private BLAST: Using Galaxy. Lightning Talk. Galaxy Community Conference (GCC2014) June 30 July 2, 2014 Johns Hopkins University, Baltimore, USA
Stéphane Audic, Erwan Corre. Metagenic data analysis in the TARA project. Galaxy pipeline. WP2.7.2 France genomique. Metagenomic . 26 Mai 2014 -Lyon
Morales, Julia ; Chassé, Héloïse ; Boulben, Sandrine ; Corre, Erwann; Le Corguillé, Gildas ; Glippa, Virginie ; Coson, Bertrand ; Belle, Robert ; Mulner-Lorillon, Odile; Cormier, Patrick. Translatome analysis following fertilization. Developmental Biology of the Sea Urchin XXII. April 23-27, 2014. Woods Hole. USA
O. Godfroy, G. Le Corguillé, D. Scornet, M. Perennou, E. Corre, S. Coelho, M. Cock. EctoTILLING, a reverse genetic tool for Ectocarpus. Journées du PEPI IBIS les 31 mars et 1er avril 2014 à Paris
J Henry, V Cornet, A Leduc, B Zanuttini, E Corre, G Le Corguille, B Bernay, A Kraut, C Zatylny-Gaudin.Egg-Laying Regulation In The Cephalopod Sepia Officinalis: Identification And Mapping Of The Neuropeptidome Overexpressed During Spawning. 20th International Symposium On Regulatory Peptides (Regpep2014). September 7 - 10, 2014. Kyoto Garden Palace, Kyoto, Japan. Journal Of Molecular Neuroscience .Volume 53. Pages S142-S142.
C Zatylny-Gaudin, M Endress, V Cornet, B Bernay, E Corre, G Lecorguille, J Henry. Female Sex Peptides In The Control Of Cuttlefish Reproduction. 20th International Symposium On Regulatory Peptides (Regpep2014). September 7 - 10, 2014. Kyoto Garden Palace, Kyoto, Japan. Journal Of Molecular Neuroscience .Volume 53. Pages S144-S144.
L. Brillet-Guéguen, C. Caron, V. Loux, Groupe de Travail Galaxy IFB. Developing a sharing strategy for tools and workflows between France Génomique platforme with Galaxy. Galaxy Day 2014, Paris

Posters

Monsoor M., Le Corguille G., Landi M., Petera M., Pericard P., Duperier C., Tremblay-Franco M., Martin J., Goulitquer S., Thévenot E., Giacomoni F. and Caron C. (2014). workflow4metabolomics.org. Galaxy Community Conference 2014, Baltimore
Gregory Carrier, Matthieu Garnier, Loïc Le Cunff, Gaël Bougaran , Ian Probert, Colomban De Vargas, Erwan Corre, Catherine Rouxel, Aurélie Charrier, Bruno Saint-Jean and Jean-Paul Cadoret.. Comparative transcriptome of wild type and selected strains of the microalgae Tisochrysis lutea provides insights into the genetic basis, lipid metabolism and the life cycle. Alg’n’Chem - 3& March - 3 April 2014 - Montpellier France.

2013

Publications

Janouškovec J, Liu SL, Martone PT, Carré W, Leblanc C, Collén J, Keeling PJ. 2013.Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers.PLoS One. 2013;8(3):e59001. doi: 10.1371/journal.pone.0059001. Epub 2013 Mar 25.
Collén J., Porcel B., Carré W., Ball S., Chaparro C., Tonon T., Barbeyron T., Michel G., Noel B., Valentin K., Elias M., Artiguenave F., Arun A., Aury J.M., Barbosa-Neto J.F., Bothwell J.H., Bouget F.Y., Brillet L., Cabello-Hurtado F., Capella-Gutíerrez S., Charrier B., Cladière L., Cock J.M., Coelho S.M., Colleoni C., Czjzek M., Da Silva C., Delage L., Denoeud F., Deschamps P., Dittami S.M., Gabaldón T., Gachon C.M., Groisillier A., Hervé C., Jabbari K., Katinka M., Kloareg B., Kowalczyk N., Labadie K., Leblanc C., Lopez P.J., McLachlan D., Meslet-Cladiere L., Moustafa A., Nehr Z., Nyvall Collén P., Panaud O., Partensky F., Poulain J., Rensing S.A., Rousvoal S., Samson G., Symeonidi A., Weissenbach J., Zambounis A., Wincker P., Boyen C. 2013, Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proc Natl Acad Sci U S A. 2013 Mar 26;110(13):5247-52. doi: 10.1073/pnas.1221259110.
Gosselin P, Martineau Y, Morales J, Czjzek M, Glippa V, Gauffeny I, Morin E, Le Corguillé G, Pyronnet S, Cormier P, Cosson B. Tracking a refined eIF4E-binding motif reveals Angel1 as a new partner of eIF4E. Nucleic Acids Res. 2013 Sep;41(16):7783-92. doi: 10.1093/nar/gkt569.
Dupont, Samuel; Corre, Erwan; Li, Yanyan; Vacelet, Jean; Bourguet-Kondracki, Marie-Lise. 2013. First insights into the microbiome of a carnivorous sponge. FEMS Microbiol Ecol. 2013 Jul 12. doi: 10.1111/1574-6941.12178.
Toullec J-Y, Corre E, Bernay B, Thorne MAS, Cascella K, et al. (2013) Transcriptome and Peptidome Characterisation of the Main Neuropeptides and Peptidic Hormones of a Euphausiid: The Ice Krill, Euphausia crystallorophias. PLoS ONE 8(8): e71609. doi:10.1371/journal.pone.0071609

Oral communications

A.Cormier, J. Bothwell, M. Cock, E. Corre and S. Coelho (2013). Sex determination and differentiation in the brown alga Ectocarpus. Journées de la Société Phycologique de France, Roscoff – 16 au 18 décembre 2013.
Luthringer R., Cormier, A., Peters AF., Corre, E., Cock JM., Coelho SM. Evolution of sexual dimorphism in the brown algae. Journées de la Société Phycologique de France, Roscoff – 16 au 18 décembre 2013.
Simon M. Dittami, Laëtitia Duboscq-Bidot, Morgan Perennou, Erwan Corre, Catherine Boyen, Thierry Tonon. Diversity of bacteria associated to brown algae of the genus Ectocarpus and their importance for acclimation. Journées de la Société Phycologique de France, Roscoff – 16 au 18 décembre 2013.
Gildas Le Corguillé, Misharl Monsoor, Christophe Caron. GalaxyDay. Paris 04/12/2013.
Gildas Le Corguillé. Journée Axe Bioinformatique Biogenouest. Rennes. 29/11/2013.
Samuel Dupont, Erwan Corre, Alyssa Carré-Mlouka, Yanyan Li, Isabelle Domart- Coulon, Jean Vacelet and Marie-Lise Bourguet-Kondracki. EXPLORING THE MICROBIAL DIVERSITY ASSOCIATED WITH A CARNIVOROUS SPONGE. 14th International Symposium on Marine Natural Products / 8th European Conference on Marine Natural Products. September 15th - 20th, 2013 La Toja Island, Galicia Spain.
Gregory Farrant, Erwan Corre, Christophe Caron, Frédéric Partensky and Laurence Garczarek. Model organisms-oriented metagenomics: recruitment of Illumina reads on marine picocyanobacterial genomes. Session plénière Jobim 2013.
Ahmed S , Cock JM, Pessia E Luthringer R , Cormier A , Robuchon M , Sterck L , Peters AF, DittamiS ,Corre E,Valero,M,AuryJ-M,RozeD,VandePeerY ,BothwellJH,MaraisG, Coelho Susana M. Evolution of an ancient pair of haploid sex chromosomes. Jacques Monod conferences . Recent advences on the evolution of sex and genetic systemes. Roscoff, 22-26 may 2013.
Pierre Pericard, Gildas Le Corguillé, Urszula Czerwinska, Marion Landi, Franck Giacomoni, Christophe Duperier, Jean-François Martin, Sophie Goulitquer, Estelle Pujos-Guillot and Christophe Caron. A Small Step into Galaxy, a Faster Pace for Metabolomics. Session parallèle Jobim 2013 & RFMF Amiens 2013.
Gildas Le Corguillé, Pierre Pericard, Urszula Czerwinska, Marion Landi, Franck Giacomoni, Christophe Duperier, Jean-François Martin, Sophie Goulitquer, Estelle Pujos-Guillot and Christophe Caron. A Small Step into Galaxy, a Faster Pace for Metabolomics. Lightning Talk. Galaxy Community Conference (GCC2013) June 30 July 2, 2013 University of Oslo, Oslo, Norway
Antoine Gravot, Misharl Monsoor. Approches métabolomiques pour l’étude de la résistance quantitative à la hernie chez les crucifères. Journée Corsaire. Novembre 2013. Rennes

Posters

Samuel DUPONT , Erwan CORRE , Isabelle DOMART-COULON, Yan-yan LI , Jean VACELET and Marie-Lise BOURGUET-KONDRACKI. EXPLORING THE MICROBIAL DIVERSITY IN THE MARINE CARNIVOROUS SPONGE ASBESTOPLUMA HYPOGEA. FEMS. 5th congress of european microbiologists. 2013. july 21-25
Christophe Caron, Wilfrid Carré, Alexandre Cormier, Sandra Derozier, Franck Giacomoni, Olivier Inizan, Gildas Le Corguillé, Alban Lermine, Sarah Maman, Pierre Pericard and Franck Samson. Toward a cyber Galaxy ? Actes Jobim 2013.
Nicolas Guilhot, Sébastien Theil, Frederic Choulet, Christophe Caron, Alexandre Cormier, Catherine Feuillet and Philippe Leroy. TriAnnot : un outil bioinformatique puissant pour l’identification de gènes d’intérêt agronomique dans les génomes des plantes. Actes Jobim 2013.
Gwendoline Andres, Alexandre Cormier, Mylene Lorre-Guidt, Mark Hoebeke, Michel Groc, Philippe Dru and Christophe Caron. EMBRC-France e-infrastructure.Actes Jobim 2013.
Alexandre Cormier, John Bothwell, Mark Cock, Erwan Corre and Susana Coelho. Identification of female sex locus in the brown alga Ectocarpus. Actes Jobim 2013.

2012

Publications

Bretaudeau A, Coste F, Humily F, Garczarek L, Le Corguillé; G, Six C, Ratin M, Collin O, Schluchter WM, Partensky F. CyanoLyase: a database of phycobilin lyase sequences, motifs and functions. Nucleic Acids Res. 2012 Nov 21.
Mella-Flores D, Six C, Ratin M, Partensky F, Boutte C, Le Corguillé G, Marie D, Blot N, Gourvil P, Kolowrat C, Garczarek L. Prochlorococcus and Synechococcus have Evolved Different Adaptive Mechanisms to Cope with Light and UV Stress. Front Microbiol. 2012;3:285. Epub 2012 Aug 8.
J. Mark Cock et al. The Ectocarpus Genome and Brown Algal Genomics. Genomic Insights into the Biology of Algae. Vol. 64. 2012.

Posters

Christophe BLANCHET, Clément GAUTHEY, Christophe CARON, Olivier COLLIN, Stéphane DELMOTTE, Tiphaine MARTIN, Simon PENEL, Aurélien ROULT, Franck SAMSON and Bruno SPATARO. Towards a Distributed Infrastructure for Bioinformatics: French GRISBI Perspective. Actes Jobim 2012
Loraine GUÉGUEN, Gregory FARRANT , Gildas LE CORGUILLÉ, Erwan CORRE, Wilfrid CARRÉ, Laurence GARCZAREK, Frédéric PARTENSKY, Christophe CARON and Mark HOEBEKE. Cyanorak v2 An information management system for annotating cyanobacterial orthogroups. Actes JOBIM 2012
Alexandre CORMIER, Susana COELHO, Mark COCK and Erwan CORRE.Analysis of sexual differentiation in the brown alga Ectocarpus by RNA-seq Reference genome and de novo approaches comparison. Actes JOBIM 2012.
Pierre Pericard, Wilfrid Carre, Christophe Caron, Erwan Corre and Sylvie Mazan. de novo transcriptome assembly pipeline for Scyliorhinus canicula NGS data. Actes JOBIM 2012
Pierre Pericard, Wilfrid Carre, Christophe Caron, Erwan Corre and Sylvie Mazan. Development of a pipeline for Scyliorhinus canicula miRNA identification from NGS data. Actes JOBIM 2012.
Gregory Farrant, Erwan Corre, Mark Hoebeke, Wilfrid Carré, Christophe Caron, Frédéric Partensky and Laurence Garczarek. Microbial de novo genome assembly: Comparison of CLC Genomics & VELVET for assembly of contaminated but deeply covered Illumina 1.5 single reads. Actes JOBIM 2012.
Nathalie Kowalczyk, Wilfrid Carre, Lorraine Brillet, Erwan Corre, Bettina Porcel, Corine Da Silva, Catherine Boyen, Jonas Collen. Analysis Of Life Stages Of The Red Alga Chondrus Crispus. 04/2012. Roscoff. Esil 2012: Algal Post Genomics. 5Th International Meeting On The Model Brown Alga Ectocarpus
Ritter A., Goulitquer S., Cosse A., Thomas F., Fasshauer C., Brillet L., Corre E., Potin P., Faugeron S., Leblanc C. Transcriptomic And Metabolomic Approaches To Study Defense Responses Against Grazers In Kelps. 04/2012. Roscoff. Esil 2012: Algal Post Genomics. 5Th International Meeting On The Model Brown Alga Ectocarpus
Alexandre Cormier, Rémy Luthringer, Sophia Ahmed, Akira Peters, Wilfrid Carre, Mark Cock, Erwan Corre, Susana Coelho. Transcriptomic Analysis Of Sexual Differentiation In Ectocarpus Using Rna-Seq. 04/2012. Roscoff. Esil 2012: algal post genomics. 5th international meeting on the model brown alga ectocarpus
Sergio Balzano, Erwan Corre, Johan Decelle, Roberto Sierra, Jan Pawlowski, Corinne Da Silva, Patrick Wincker, And Fabrice Not.Transcriptome Analyses To Investigate Relationships Between Rhizaria And Their Eukaryotic Symbionts. Aussois 04/2012. Ecole Thematique Expert Genomique Environnementale
Dupont, S. ; Corre, E. ;Li, Y.Y. ; Vacelet, J.; Bourguet-Kondracki, M.L. Etude du microbiote associé à l’éponge carnivore .Asbestopluma hypogea par pyroséquençage 454. Journées de rentrée de l’école doctorale iViv (ED387), 14-05 novembre 2012, Paris, France
Dupont, S. ; Corre E. ; Li, Y.Y. ; Vacelet, J.; Bourguet-Kondracki, M.L. Etude métagénomique (Pyrosequençage 454) du microbiome associé à l’éponge carnivore Asbestopluma hypogea. AG4 du GDR BioChiMar , 10-12 novembre 2012, Gif-Sur-Yvette, France
K. Cascella1, E. Corre, J-Y. Toullec. Réponses physiologiques du krill à une augmentation de la température de l’Océan Antarctique. Poster : Comité National Français des Recherches Arctiques et Antarctiques (CNFRA) - 8èmes Journées Scientifiques, Plouzané, 10 et 11 mai 2012.
K. Cascella, L. Vouillot, N. Leger, E. Corre, D. Jollivet, J. Ravaux, A. Tanguy, J.-Y. Toullec. Physiological impact of temperature increase on ice krill (Euphausia crystallorophias) : HSP70 response. Poster : 29Juin-2 Juillet 2012. SEB Meeting (Salzburg)

2011

Publications

Susana M. Coelho, Olivier Godfroy, Alok Arun, Gildas Le Corguillé, Akira F. Peters and J. Mark Cock. Genetic regulation of life cycle transitions in the brown alga Ectocarpus. Plant Signal Behav. 2011 Nov 1;6(11).
Pagarete A, Le Corguillé G, Tiwari B, Ogata H, de Vargas C, Wilson WH, Allen MJ. Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms. FEMS Microbiol Ecol. 2011 Dec;78(3):555-64.
Isabelle Boutet, Nicolas Gagnière, Odile Lecompte, Carole Dossat, Erwan Corre, Arnaud Tanguy, François H. Lallier. 2011. Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels. Accepted in BMC Genomics.
Coelho SM, Godfroy O, Arun A, Le Corguillé G, Peters AF, Cock JM. OUROBOROS is a master regulator of the gametophyte to sporophyte life cycle transition in the brown alga Ectocarpus. Proc Natl Acad Sci U S A. 2011 Jul 12;108(28):11518-23.
Blot N, Mella-Flores D, Six C, Le Corguillé G, Boutte C, Peyrat A, Monnier A, Ratin M, Gourvil P, Campbell DA, Garczarek L. Light History Influences the Response of the Marine Cyanobacterium Synechococcus sp. WH7803 to Oxidative Stress. Plant Physiol. 2011 Aug;156(4):1934-54.

Posters

Goudenège D., E. Krin, E. Corre, C. Médigue, D. Mazel and F. Le Roux. Vibrios Infecting Marine Invertebrates: New Insights into Vibrio Virulence and their Adaptive Gene Reservoirs. Actes Jobim 2011.
Habib C., G. Le Corguillé, E. Corre, L. Brillet, M. Hoebeke, W. Carre, L. Garczarek, F. Partensky and C. Caron. PELICAN: Orthologous Groups and Gene Lateral Transfers for Comparative Genomic Analysis of Marine Cyanobacteria. Actes Jobim 2011.
Blanchet C., C. Gauthey, C. Caron, O. Collin, S. Delmotte, T. Martin, A. Roult, F. Samson and B. Spataro. RENABI GRISBI -Infrastructure Distribuée pour la Bioinformatique. Actes Jobim 2011.

2010

Publications

Kolowrat C, Partensky F, Mella-Flores D, Le Corguillé G, Boutte C, Blot N, Ratin M, Ferréol M, Lecomte X, Gourvil P, Lennon JF, Kehoe DM, Garczarek L. Ultraviolet stress delays chromosome replication in light/dark synchronized cells of the marine cyanobacterium Prochlorococcus marinus PCC9511. BMC Microbiol. 2010 Jul 29;10:204.
Heesch S, Cho GY, Peters AF, Le Corguillé G, Falentin C, Boutet G, Coëdel S, Jubin C, Samson G, Corre E, Coelho SM, Cock JM. A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence. New Phytol. 2010 Oct;188(1):42-51. Epub 2010 Apr 28.
J. Mark Cock, Lieven Sterck, Pierre Rouzé, Delphine Scornet, Andrew E. Allen, Grigoris Amoutzias, Veronique Anthouard, François Artiguenave, Jean-Marc Aury, Jonathan H. Badger, Bank Beszteri, Kenny Billiau, Eric Bonnet, John H. F. Bothwell, Chris Bowler, Catherine Boyen, Colin Brownlee, Carl J. Carrano, Bénédicte Charrier, Ga Youn Cho, Susana M. Coelho, Jonas Collén, Erwan Corre, Corinne Da Silva, Ludovic Delage, Nicolas Delaroque, Simon M. Dittami, Sylvie Doulbeau, Marek Elias, Garry Farnham, Claire M.M. Gachon, Bernhard Gschloessl, Svenja Heesch, Kamel Jabbari, Claire Jubin, Hiroshi Kawai, Kei Kimura, Bernard Kloareg, Frithjof C. Küpper, Daniel Lang, Aude Le Bail, Catherine Leblanc, Patrice Lerouge, Martin Lohr, Pascal J. Lopez, Cindy Martens, Florian Maumus, Gurvan Michel, Diego Miranda-Saavedra, Julia Morales, Hervé Moreau, Taizo Motomura, Chikako Nagasato, Carolyn A. Napoli, David R. Nelson, Pi Nyvall-Collén, Akira F. Peters, Cyril Pommier, Philippe Potin, Julie Poulain, Hadi Quesneville, Betsy Read, Stefan A. Rensing, Andrés Ritter, Sylvie Rousvoal, Manoj Samanta, Gaelle Samson, Declan C. Schroeder, Béatrice Ségurens, Martina Strittmatter, Thierry Tonon, James Tregear, Klaus Valentin, Peter von Dassow, Takahiro Yamagishi, Yves Van de Peer & Patrick Wincker. 2010.The Ectocarpus genome and the independent evolution of multicellularity in the brown algae. Nature. 2010 Jun 3;465(7298):617-21.

Posters

Célia Michotey, Ludovic Legrand, Hélène Chiapello, Valentin Loux, Annie Gendrault, Jean-François Gibrat and Christophe Caron. Web Services for MIcrobial Genome Annotation using Data Integration. Actes JOBIM 2010.
Philippe Picouet, Zakaria Doughi, Loraine Brillet, Erwan Corre, Christophe Caron, Olivier Collin, François Moreews and Xavier Bailly. BioDesc : gestion d’un entrepôt multiformat de descriptions de ressources bioinformatique. Actes JOBIM 2010.
Christophe Blanchet and Christophe Caron. RENABI GRISBI - Grande Infrastructure pour la Bioinformatique. Actes JOBIM 2010.

2009

Publications

Gildas Le Corguillé, Gareth Pearson, Marta Valente, Carla Viegas, Bernhard Gschloessl, Erwan Corre, Xavier Bailly, Akira F. Peters, Claire Jubin, Benoit Vacherie, J. Mark Cock and Catherine Leblanc. 2009. Chloroplast genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus : further insights on the evolution of red-algal derived plastids. BMC Evol Biol. 2009 Oct 16;9:253.
Gareth A. Pearson, Galice Hoarau, Asuncion Lago-Leston, James A. Coyer, Nicholas J. Miller, Michael Kube, Kolja Henckel, Ester T.A. Serrão, Erwan Corre, Wytze T. Stam and Jeanine L. Olsen. 2009. An Expressed Sequence Tag (EST) Analysis of the Intertidal Brown Seaweeds Fucus serratus (L.) and F. vesiculosus (L.) (Heterokontophyta, Phaeophyceae) in Response to Abiotic Stressors. Marine Biotechnology. doi 10.1007/s10126-009-9208-z.
Simon M Dittami, Delphine Scornet, Erwan Corre, Michael Dondrup, Karl-Heinz Glatting, Rainer König, J Mark Cock, Catherine Boyen and Thierry Tonon. 2009. Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress.Genome Biology. 2009;10(6):R66.
Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz-Tamayo R, Nalin R, Le Paslier D, Doré J and Leclerc M. Toward the Human intestinal microbiota phylogenetic core. Environmental Microbiology. EMI-2008-0847.R2

2008

Publications

Hélène Chiapello, Annie Gendrault, Christophe Caron, Jérome Blum, Marie-Agnès Petit and Meriem El Karoui. MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level. BMC Bioinformatics 2008, 9:498doi:10.1186/1471-2105-9-498
Peters AF, Scornet D, Ratin M, Charrier B, Monnier A, Merrien Y, Corre E, Coelho SM, Cock JM.2008. Life-cycle-generation-specific developmental processes are modified in the immediate upright mutant of the brown alga Ectocarpus siliculosus. Development;135(8):1503-12
O. Filangi, Y. Beausse, A. Assi, L. Legrand, JM. Larré, V. Martin, O. Collin, C. Caron, H. Leroy, D. Allouche. BioMAJ: A flexible framework for databanks synchronization and processing. Bioinformatics 2008 24(16):1823-1825; doi:10.1093/bioinformatics/btn325 (2008)

Posters

Marc Wessner, Martin Senger, Franck Samson, Philippe Picouet, François Moreews, Hervé Ménager, Véronique Martin, Sébastien Letort, Catherine Letondal, Mark Hoebeke, Jérome Gouzy, Jean-françois Gibrat, Erwan Corre, Olivier Collin, Sébastien Carrere, Christophe Caron, Pierre Tufféry and Bertrand Néron. BioWorkflow: Web Services toolkit and pipeline applications evaluation to deploy a confidence network . JOBIM 2008

2007-2006

Publications

Morales J, Mulner-Lorillon O, Cosson B, Morin E, Bellé R, Bradham C.A., Beane W S, Cormier P. 2006. Translational control genes in the sea urchin genome. Dev Biol. 300(1):293-307.
Moussard H., Corre E., Cambon-Bonavita M._A., Fouquet Y., Jeanthon C..Novel uncultured 'Epsilonproteobacteria' dominate a filamentous sulphur mat from the 13°N hydrothermal vent field, East Pacific Rise.2006. FEMS Microbiol Ecol.;58(3):449-63
Herve C, Tonon T, Collen J, Corre E., Boyen C. 2006. NADPH oxidases in Eukaryotes: red algae provide new hints! Curr Genet. Mar;49(3):190-204.
Xavier Bailly, S. Bigaret, P. Tanguy, O. Collin and P. Picouet . 2006. BioSide, a biologist dedicated environment for bioinformatics programs, , 10th Evolutionary Biology Meeting at Marseille, 20-22 September 2006
Collen J, Roeder V, Rousvoal S, Collin O, Kloareg B, Boyen C. 2006. An expressed sequence tag analysis of thallus and regenerating protoplasts of Chondrus crispus (Gigartinales, Rhodophyceae) J. Phycol 42 (1): 104-112 FEB 2006

2005

Publications

Roeder V, Collen J, Rousvoal S, Corre E, Leblanc C, Boyen C .2005. Identification of stress genes transcripts in Laminaria digitata (Phaeophyceae) protoplast cultures by expressed sequence tag analysis. J Phycol 41:1227–1235
Jeanthon C., Nercessian O., Corre E. , Grabowski-Lux A.. 2005. Hyperthermophilic and Methanogenic Archaea in Oil Fields in Petroleum Microbiology. p 55-70

2004

Publications

Jolivet E, Corre E, L'Haridon S, Forterre P, Prieur D. 2004. Thermococcus marinus sp. nov. and Thermococcus radiotolerans sp. nov., two hyperthermophilic archaea from deep-sea hydrothermal vents that resist ionizing radiation.Extremophiles. Jun;8(3):219-27.

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