2023
Poster communications
- ref_biblio
- Melissa Garry, Julien Farasin, Camille Bouchez, Achim Quaiser, Bénédicte Ménez, et al.. Unraveling the role of oxygen fluctuations on microbial iron oxidation and biomass production in the fractured continental subsurface. Goldschmidt Conference 2023, Jul 2023, Lyon, France. ⟨insu-04188048⟩
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- ref_biblio
- Ivan-David Osorio-Leon, Bastien Wild, Camille Bouchez, Emmanuelle Gérard, Achim Quaiser, et al.. Mineral substrate and fluid redox conditions control cell density in attached biofilms: in-situ incubations in deep groundwater. Goldschmidt Conference 2023, Jul 2023, Lyon, France. ⟨insu-04188040⟩
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2021
Conference papers
- ref_biblio
- Ivan-David Osorio-Leon, Melissa Garry, Camille Bouchez, Julien Farasin, Eliot Chatton, et al.. In-situ biogeochemical response to oxygendelivery in a fractured-bedrock aquifer:insights from a reactive Push-Pull test. Advancing Critical Zone science. First OZCAR TERENO International Conference, Oct 2021, Strasbourg, France. pp.248. ⟨insu-03602775⟩
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2020
Journal articles
- ref_biblio
- Lorine Bethencourt, Olivier Bochet, Julien Farasin, Luc Aquilina, Tanguy Le Borgne, et al.. Genome reconstruction reveals distinct assemblages of Gallionellaceae in surface and subsurface redox transition zones. FEMS Microbiology Ecology, 2020, 96 (5), pp.fiaa036. ⟨10.1093/femsec/fiaa036⟩. ⟨insu-02509650⟩
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- ref_biblio
- Olivier Bochet, Lorine Bethencourt, Alexis Dufresne, Julien Farasin, Mathieu Pédrot, et al.. Iron-oxidizer hotspots formed by intermittent oxic–anoxic fluid mixing in fractured rocks. Nature Geoscience, 2020, 13 (2), pp.149-155. ⟨10.1038/s41561-019-0509-1⟩. ⟨insu-02395691⟩
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2019
Journal articles
- ref_biblio
- Luc Burté, Charles Cravotta, Lorine Bethencourt, Julien Farasin, Mathieu Pédrot, et al.. Kinetic study on clogging of a geothermal pumping well triggered by mixing-induced biogeochemical reactions. Environmental Science and Technology, 2019, 53 (10), pp.5848-5857. ⟨10.1021/acs.est.9b00453⟩. ⟨insu-02123861⟩
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Conference papers
- ref_biblio
- Tanguy Le Borgne, Olivier Bochet, Luc Burté, Lorine Bethencourt, Camille Bouchez, et al.. Effect of subsurface fluid mixing on microbial growth and bioclogging in fractured media: field observations and modelling. American Geophysical Union Fall Meeting 2019, American Geophysical Union, Dec 2019, San Francisco, United States. pp.B44C-02. ⟨insu-02402723⟩
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- ref_biblio
- Lorine Bethencourt, Olivier Bochet, Luc Aquilina, Achim Quaiser, Tanguy Le Borgne, et al.. Un nouveau genre de bactéries oxydant le fer domine les zones de transitions redox des aquifères fracturés. IXe Colloque de l'Association Francophone d'Ecologie Microbienne (AFEM 2019), Nov 2019, Bussang, France. ⟨hal-02390776⟩
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2018
Journal articles
- ref_biblio
- Clément Roques, Luc Aquilina, Alexandre Boisson, Virginie Vergnaud-Ayraud, Thierry Labasque, et al.. Autotrophic denitrification supported by biotite dissolution in crystalline aquifers: (2) transient mixing and denitrification dynamic during long-term pumping. Science of the Total Environment, 2018, 619-620, pp.491-503. ⟨10.1016/j.scitotenv.2017.11.104⟩. ⟨insu-01653141⟩
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- ref_biblio
- Luc Aquilina, Clément Roques, Alexandre Boisson, Virginie Vergnaud-Ayraud, Thierry Labasque, et al.. Autotrophic denitrification supported by biotite dissolution in crystalline aquifers (1): New insights from short-term batch experiments. Science of the Total Environment, 2018, 619-620, pp.842-853. ⟨10.1016/j.scitotenv.2017.11.079⟩. ⟨insu-01652576⟩
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Conference papers
- ref_biblio
- Tanguy Le Borgne, Aditya Bandopadhyay, Olivier Bochet, Alexis Dufresne, Julien Farasin, et al.. Dynamics of reactive mixing hot spots from hyporheic zones to fractured media. American Geophysical Union 2018, Fall Meeting, Dec 2018, Washington, United States. pp.H13E-01. ⟨insu-01928175⟩
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Poster communications
- ref_biblio
- Antoine Hubert, Julien Farasin, Hervé Tabuteau, Alexis Dufresne, Yves Méheust, et al.. Dynamics of reactive microbial hotspots in concentration and velocity gradients. Computer Methods in Water Resources (CMWR) 2018, Jun 2018, Saint-Malo, France. , Abstract 241, 2018, Proceedings. ⟨insu-02078847⟩
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2017
Journal articles
- ref_biblio
- Amandine Lê Van, Achim Quaiser, Marie Duhamel, Sophie Michon-Coudouel, Alexis Dufresne, et al.. Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera. PeerJ, 2017, 5, pp.e3454. ⟨10.7717/peerj.3454⟩. ⟨hal-01555396⟩
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Conference papers
- ref_biblio
- Olivier Bochet, Tanguy Le Borgne, Lorine Bethencourt, Luc Aquilina, Alexis Dufresne, et al.. Groundwater mixing at fracture intersections triggers massive iron-rich microbial mats . American Geophysical Union Fall Meeting 2017, Dec 2017, New Orleans, United States. pp.H31F-1570. ⟨insu-01731725⟩
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- ref_biblio
- Antoine Hubert, Julien Farasin, Hervé Tabuteau, Alexis Dufresne, Yves Méheust, et al.. Dynamics of Reactive Microbial Hotspots in Concentration Gradient.. American Geophysical Union Fall Meeting 2017, Dec 2017, New Orleans, United States. pp.H33E-1730. ⟨insu-01731955⟩
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- ref_biblio
- Lorine Bethencourt, Luc Aquilina, Marine Biget, Olivier Bochet, Julien Farasin, et al.. Abondance et diversité des bactéries oxydantes du fer de la famille des Gallionellaceae dans les aquifères de socle fracturé. VIIIe Colloque de l'Association Francophone d'Ecologie Microbienne, Oct 2017, Camaret, France. ⟨hal-02390754⟩
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Book sections
- ref_biblio
- Achim Quaiser, Alexis Dufresne, Sophie Michon-Coudouel, Marine Biget, Philippe Vandenkoornhuyse. Large-scale sequence-based information-novel understanding of ecology and novel avenues to test ecological hypotheses. Abad Chabbi, Henry W. Loescher Terrestrail Ecosystem Research Infrastructures: Challenges, New Developments and Perspectives, CRC Press, pp.165-192, 2017, 978-1-4987-5131-5. ⟨hal-01839582⟩
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Poster communications
- ref_biblio
- Lorine Bethencourt, Olivier Bochet, Tanguy Le Borgne, Luc Aquilina, Marine Biget, et al.. Fracture-induced mixing of recent and ancient groundwaters controls the distribution of iron-oxidizing bacteria in hard-rock aquifers. 10th International Symposium on Subsurface Microbiology (ISSM 2017), Nov 2017, Rotorua, New Zealand. ⟨hal-02390701⟩
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- ref_biblio
- Clément Roques, Luc Aquilina, Virginie Vergnaud-Ayraud, Alexandre Boisson, Thierry Labasque, et al.. Long-term Denitrification Processes and Kinetics in a Crystalline Aquifer
subject to Pumping from 1991. European Geosciences Union General Assembly 2017, Apr 2017, Vienne, Austria. Geophysical Research Abstracts, 19, pp.EGU2017-12213, 2017. ⟨insu-01534075⟩
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2016
Journal articles
- ref_biblio
- Achim Quaiser, Mart Krupovic, Alexis Dufresne, André-Jean Francez, Simon Roux. Diversity and comparative genomics of chimeric viruses in Sphagnum-dominated peatlands. Virus Evolution, 2016, 2 (2), pp.vew025. ⟨10.1093/ve/vew025⟩. ⟨pasteur-01977372⟩
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- ref_biblio
- Théodore Bouchez, A. L. Blieux, Samuel S. Dequiedt, Isabelle Domaizon, Alexis Dufresne, et al.. Molecular microbiology methods for environmental diagnosis. Environmental Chemistry Letters, 2016, 14 (4), pp.423--441. ⟨10.1007/s10311-016-0581-3⟩. ⟨hal-01413017⟩
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- ref_biblio
- Flore Ballaud, Alexis Dufresne, Andre-Jean Francez, Jonathan Colombet, Télesphore Sime-Ngando, et al.. Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat. Frontiers in Microbiology, 2016, 6, pp.1494. ⟨10.3389/fmicb.2015.01494⟩. ⟨hal-01263117⟩
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Conference papers
- ref_biblio
- Tanguy Le Borgne, Olivier Bochet, Maria Klepikova, Peter K. Kang, Alexis Shakas, et al.. Coupled transport, mixing and biogeochemical reactions in fractured media: experimental observations and modelling at the Ploemeur fractured rock observatory . American Geophysical Union Fall Meeting 2016, American Geophysical Union, Dec 2016, San Francisco, United States. pp.H54C-04. ⟨insu-01416952⟩
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Books
- ref_biblio
- Théodore Bouchez, Anne Laure Blieux, Samuel S. Dequiedt, Isabelle Domaizon, Alexis Dufresne, et al.. La microbiologie moléculaire au service du diagnostic environnemental. Synthèse de Recherche. Contrat n°1406C0050. Projet de recherche coordonné par : "Observatoire des sols vivants". ADEME Agence de l'Environnement et de la Maitrise de l'Energie, 34 p., 2016. ⟨hal-01608851⟩
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2015
Journal articles
- ref_biblio
- Achim Quaiser, Alexis Dufresne, Flore Ballaud, Simon Roux, Yvan Zivanovic, et al.. Diversity and comparative genomics of Microviridae in Sphagnum-dominated peatlands. Frontiers in Microbiology, 2015, 6, pp.375. ⟨10.3389/fmicb.2015.00375⟩. ⟨hal-01149546⟩
- Accès au texte intégral et bibtex
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- ref_biblio
- Luc Aquilina, Virginie Vergnaud-Ayraud, Antoine Armandine Les Landes, Hélène Pauwels, Philippe Davy, et al.. Impact of climate changes during the last 5 million years on groundwater in basement aquifers. Scientific Reports, 2015, 5 (1), pp.14132. ⟨10.1038/srep14132⟩. ⟨insu-01203447⟩
- Accès au texte intégral et bibtex
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- ref_biblio
- Philippe Vandenkoornhuyse, Achim Quaiser, Marie Duhamel, Amandine Lê Van, Alexis Dufresne. The importance of the microbiome of the plant holobiont. New Phytologist, 2015, 206 (4), pp.1196-1206. ⟨10.1111/nph.13312⟩. ⟨hal-01115639⟩
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- ref_biblio
- Flavia L.D. Nunes, Luc Aquilina, Jo de Ridder, Andre-Jean Francez, Achim Quaiser, et al.. Time-scales of hydrological forcing on the geochemistry and bacterial community structure of temperate peat soils. Scientific Reports, 2015, 5 (1), pp.14612. ⟨10.1038/srep14612⟩. ⟨insu-01217318⟩
- Accès au texte intégral et bibtex
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- ref_biblio
- Sarah Ben Maamar, Luc Aquilina, Achim Quaiser, Hélène Pauwels, Sophie Michon-Coudouel, et al.. Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths. Frontiers in Microbiology, 2015, 6, pp.1457. ⟨10.3389/fmicb.2015.01457⟩. ⟨insu-01249981⟩
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Conference papers
- ref_biblio
- Olivier Bochet, Alexis Dufresne, Mathieu Pédrot, Eliot Chatton, Tanguy Le Borgne, et al.. Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological measurements
. AGU Fall Meeting 2015, American Geophysical Union, Dec 2015, San Francisco, United States. pp.B53H-06. ⟨insu-01241923⟩
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Poster communications
- ref_biblio
- Olivier Bochet, Tanguy Le Borgne, Mathieu Pédrot, Thierry Labasque, Nicolas Lavenant, et al.. Biofilm development in a hotspot of mixing between shallow and deep groundwater in a fractured aquifer: field evidence from joint flow, chemical and microbiological characterization. EGU General Assembly 2015, Apr 2015, Vienne, Austria. Geophysical Research Abstracts, 17, pp.EGU2015-11928, 2015. ⟨hal-01714510⟩
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2014
Journal articles
- ref_biblio
- Maria-Cristina Ciobanu, Gaëtan Burgaud, Alexis Dufresne, Anja Breuker, Vanessa Rédou, et al.. Microorganisms persist at record depths in the subseafloor of the Canterbury Basin.. ISME Journal, 2014, 8, pp.1370-80. ⟨10.1038/ismej.2013.250⟩. ⟨hal-01056621⟩
- Accès au texte intégral et bibtex
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- ref_biblio
- Achim Quaiser, Xavier Bodi, Alexis Dufresne, Delphine Naquin, Andre-Jean Francez, et al.. Unraveling the Stratification of an Iron-Oxidizing Microbial Mat by Metatranscriptomics. PLoS ONE, 2014, 9 (7), pp.e102561. ⟨10.1371/journal.pone.0102561⟩. ⟨insu-01060225⟩
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Conference papers
- ref_biblio
- Sarah Ben Maamar, Luc Aquilina, Achim Quaiser, Hélène Pauwels, Virginie Ayraud-Vergnaud, et al.. Insight into microbial diversity and functions in hard-rock aquifers through high throughput sequencing. Ninth International Symposium of Subsurface Microbiology (ISSM 2014), Oct 2014, Pacific Pacific Grove, California, United States. ⟨hal-02399649⟩
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2013
Conference papers
- ref_biblio
- Flore Ballaud, Alexis Dufresne, Andre-Jean Francez, Jonathan Colombet, Télesphore Sime-Ngando, et al.. Patterns of viral and microbial diversity in Sphagnum-dominated peatland using meta genomics. VIème Colloque AFEM “Microbiologie environnementale : du gène à l’écosystème”, Association Francophone d’Ecologie Microbienne, Oct 2013, Clermont-Ferrand, France. ⟨hal-01156599⟩
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- ref_biblio
- Sarah Ben Maamar, Alexis Dufresne, Philippe Vandenkoornhuyse, Luc Aquilina, Virginie Vergnaud-Ayraud, et al.. Investigation of groundwater microbial diversity in hard rock aquifers. HydroEco'2013, May 2013, rennes, France. pp.132. ⟨insu-00823461⟩
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- ref_biblio
- Luc Aquilina, Pierre Marmonier, Marie-José Dole-Olivier, C. Picart, Dominique Martin, et al.. Influence of residence time on biodiversity in karstic aquifers. HydroEco'2013, May 2013, rennes, France. pp.82. ⟨insu-00823460⟩
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Poster communications
- ref_biblio
- Amandine Lê Van, Achim Quaiser, Philippe Vandenkoornhuyse, Alexandra Dheilly, Sophie Coudouel, et al.. Is the diversity of the active plant root microbiome spatially structured?. Colloque Génomique Environnementale ‘Diversité, évolution et fonctionnement du vivant à l’ère des nouvelles technologies de séquençage’, Aug 2013, Rennes, France. ⟨hal-01159027⟩
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- ref_biblio
- Flore Ballaud, Alexis Dufresne, Andre-Jean Francez, Jonathan Colombet, Télesphore Sime-Ngando, et al.. Viral and microbial diversity in a Sphagnum-dominated peatland using metagenomics. Colloque Génomique Environnementale ‘Diversité, évolution et fonctionnement du vivant à l’ère des nouvelles technologies de séquençage’, Aug 2013, Rennes, France. ⟨hal-01159031⟩
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- ref_biblio
- Sarah Ben Maamar, Luc Aquilina, Alexis Dufresne, Achim Quaiser, Virginie Vergnaud-Ayraud, et al.. High-thoughput sequencing to access microbial diversity and functions in hard-rock aquifers. Colloque Génomique Environnementale ‘Diversité, évolution et fonctionnement du vivant à l’ère des nouvelles technologies de séquençage’, Aug 2013, Rennes, France. ⟨hal-01159023⟩
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2012
Journal articles
- ref_biblio
- Stéphane Mahé, Marie Duhamel, Thomas Le Calvez, Laëtitia Guillot, Ludmila Sarbu, et al.. PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution. PLoS ONE, 2012, 7 (9), pp.e43117. ⟨10.1371/journal.pone.0043117⟩. ⟨hal-00756250⟩
- Accès au texte intégral et bibtex
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Conference papers
- ref_biblio
- Achim Quaiser, Philippe Vandenkoornhuyse, Andre-Jean Francez, Alexis Dufresne. Functional community analysis of a microbial mat involved in the oxydation of iron by metatranscriptomics. ISME 2014 Conference, Aug 2012, Copenhague, Denmark. ⟨hal-01157148⟩
- Accès au bibtex
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- ref_biblio
- Achim Quaiser, Philippe Vandenkoornhuyse, Andre-Jean Francez, Alexis Dufresne. Functional community analysis of a microbial mat involved in the oxydation of iron by metatranscriptomics. Annual Conference of the Association for General and Applied Microbiology, Mar 2012, Tübingen, France. ⟨hal-01157157⟩
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2011
Conference papers
- ref_biblio
- Achim Quaiser, Andre-Jean Francez, Alexis Dufresne, Philippe Vandenkoornhuyse. Community analysis of a microbial mat involved in the oxydation of iron by metatranscriptomics. Colloque Génomique Environnementale, Nov 2011, Lyon, France. ⟨hal-01157226⟩
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- ref_biblio
- Alexis Dufresne. Diversité microbienne et vitesse de renouvellement des eaux souterraines dans les aquifères. Journée Thématique de l'ifr 140 "Structure et Expression des génomes" (SEG), Apr 2011, Rennes, France. ⟨hal-00654089⟩
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Poster communications
- ref_biblio
- Xavier Bodi, Alexis Dufresne, Andre-Jean Francez, Philippe Vandenkoornhuyse, Achim Quaiser. Community analysis of a microbial mat involved in the oxidation of iron by metatranscriptomics. Jacques Monod Conference “Integrative Ecological Genomics”, Oct 2011, Roscoff, France. ⟨hal-01159120⟩
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2010
Journal articles
- ref_biblio
- Philippe Vandenkoornhuyse, Alexis Dufresne, Achim Quaiser, Gwenola Gouesbet, Françoise Binet, et al.. Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics. Ecology Letters, 2010, 13 (6), pp.776-791. ⟨10.1111/j.1461-0248.2010.01464.x⟩. ⟨hal-00494616⟩
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2009
Journal articles
- ref_biblio
- David J. Scanlan, Martin Ostrowski, Sophie Mazard, Alexis Dufresne, Laurence Garczarek, et al.. Ecological genomics of marine Picocyanobacteria.. Microbiology and Molecular Biology Reviews, 2009, 73 (2), pp.249-299. ⟨10.1128/MMBR.00035-08⟩. ⟨hal-00406529⟩
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Conference papers
- ref_biblio
- Aurélie Nicolas, Stéphane Avner, Alexis Dufresne, Stéphane Mahé, Eric Petit, et al.. HasSium : a bioinformatic tool for fast reliable sorting and classification of very large samples of pyrosequenced amplicons.. JOBIM 2009, Jun 2009, Nantes, France. ⟨hal-00452319⟩
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- ref_biblio
- Aurélie Nicolas, Stéphane Avner, Alexis Dufresne, Stéphane Mahé, Eric Petit, et al.. HasSium : a bioinformatic tool for fast reliable sorting and classification of very large samples of pyrosequenced amplicons. BioMarKs kickoff meeting, Jun 2009, Roscoff, France. ⟨hal-00452325⟩
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2008
Journal articles
- ref_biblio
- Alexis Dufresne, Martin Ostrowski, David J. Scanlan, Sophie Mazard, Brian P. Palenik, et al.. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.. Genome Biology, 2008, 9 (5), pp.R90. ⟨10.1186/gb-2008-9-5-r90⟩. ⟨hal-00338634⟩
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- ref_biblio
- Laurence Garczarek, Alexis Dufresne, Nicolas Blot, Amanda M. Cockshutt, Anne Peyrat, et al.. Function and evolution of the psbA gene family in marine Synechococcus: Synechococcus sp. WH7803 as a case study. ISME Journal, 2008, 2 (9), pp.937-953. ⟨10.1038/ismej.2008.46⟩. ⟨hal-00338642⟩
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2007
Journal articles
- ref_biblio
- Laurence Garczarek, Alexis Dufresne, Sylvie Rousvoal, Nyree J. West, Sophie Mazard, et al.. High vertical and low horizontal diversity of Prochlorococcus ecotypes in the Mediterranean sea in summers.. FEMS Microbiology Ecology, 2007, 60 (2), pp.189-206. ⟨10.1111/j.1574-6941.2007.00297.x⟩. ⟨hal-00476860⟩
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- ref_biblio
- Christophe Six, Jean-Claude Thomas, Laurence Garczarek, Martin Ostrowski, Alexis Dufresne, et al.. Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study. Genome Biology, 2007, 8 (12), pp.R259. ⟨10.1186/gb-2007-8-12-r259⟩. ⟨hal-00338622⟩
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2004
Theses
- ref_biblio
- Alexis Dufresne. Génomique comparée des procaryotes synthétiques marins Prochlorococcus et Synechococcus. Génomique, Transcriptomique et Protéomique [q-bio.GN]. Rennes 1, 2004. Français. ⟨NNT : ⟩. ⟨tel-01117401⟩
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