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Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics

Alexey Vorobev , Marion Dupouy , Quentin Carradec , Tom O. Delmont , Anita Annamalé , et al.
Genome Research, 2020, 30 (4), pp.647-659. ⟨10.1101/gr.253070.119⟩
Journal articles hal-02573621v1
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Basin-Scale Underway Quantitative Survey of Surface Microplankton Using Affordable Collection and Imaging Tools Deployed From Tara

Zoé Mériguet , Anna Oddone , David Le Guen , Thibaut Pollina , Romain Bazile , et al.
Frontiers in Marine Science, 2022, 9, ⟨10.3389/fmars.2022.916025⟩
Journal articles hal-03877194v1
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Tracing the invertebrate herpesviruses in the global sequence datasets

Umberto Rosani , Morgan Gaia , Tom O Delmont , Mart Krupovic
Frontiers in Marine Science, 2023, 10, pp.1159754. ⟨10.3389/fmars.2023.1159754⟩
Journal articles pasteur-04162270v1

Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Christian Voolstra , Benjamin Hume , Eric Armstrong , Guinther Mitushasi , Barbara Porro , et al.
npj Biodiversity, 2023, 2 (1), pp.15. ⟨10.1038/s44185-023-00020-8⟩
Journal articles hal-04176277v1
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Host transcriptomic plasticity and photosymbiotic fidelity underpin $Pocillopora$ acclimatization across thermal regimes in the Pacific Ocean

Eric J Armstrong , Julie Lê-Hoang , Quentin Carradec , Jean-Marc Aury , Benjamin Noel , et al.
Nature Communications, 2023, 14, pp.3056. ⟨10.1038/s41467-023-38610-6⟩
Journal articles cea-04171796v1
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MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics

Benjamin Churcheward , Maxime Millet , Audrey Bihouée , Guillaume Fertin , Samuel Chaffron
mSystems, 2022, 7 (4), ⟨10.1128/msystems.00432-22⟩
Journal articles hal-03781944v1
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Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean

Maggie M Reddy , Corentine Goossens , Yuxiang Zhou , Slimane Chaib , Delphine Raviglione , et al.
Communications Earth & Environment, 2023, 4 (1), pp.281. ⟨10.1038/s43247-023-00942-y⟩
Journal articles hal-04184949v1
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Large scale patterns of marine diatom richness: Drivers and trends in a changing ocean

Greta Busseni , Luigi Caputi , Roberta Piredda , Paul Fremont , Bruno Hay Mele , et al.
Global Ecology and Biogeography, 2020, 29 (11), pp.1915-1928. ⟨10.1111/geb.13161⟩
Journal articles hal-02992584v1
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Mirusviruses link herpesviruses to giant viruses

Morgan Gaïa , Lingjie Meng , Eric Pelletier , Patrick Forterre , Chiara Vanni , et al.
Nature, 2023, 616 (7958), pp.783-789. ⟨10.1038/s41586-023-05962-4⟩
Journal articles pasteur-04085734v1

Marine snow originating from appendicularian houses: Age-dependent settling characteristics

Fabien Lombard , Thomas Kiorboe
Deep Sea Research Part I: Oceanographic Research Papers, 2010, 57 (10), pp.1304-1313. ⟨10.1016/j.dsr.2010.06.008⟩
Journal articles istex hal-04020174v1
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Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Juan José Pierella Karlusich , Eric Pelletier , Fabien Lombard , Madeline Carsique , Etienne Dvorak , et al.
Nature Communications, 2021, 12, pp.4160. ⟨10.1038/s41467-021-24299-y⟩
Journal articles hal-03334117v2

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Tom Delmont , Morgan Gaia , Damien Hinsinger , Paul Frémont , Chiara Vanni , et al.
Cell Genomics, 2022, 2 (5), pp.100123. ⟨10.1016/j.xgen.2022.100123⟩
Journal articles hal-03872935v2
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Microbial community functioning during plant litter decomposition

Simon Schroeter , Damien Eveillard , Samuel Chaffron , Johanna Zoppi , Bernd Kampe , et al.
Scientific Reports, 2022, 12 (1), pp.7451. ⟨10.1038/s41598-022-11485-1⟩
Journal articles hal-03781927v1
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MiBiOmics: an interactive web application for multi-omics data exploration and integration

Johanna Zoppi , Jean-François Guillaume , Michel Neunlist , Samuel Chaffron
BMC Bioinformatics, 2021, 22 (1), ⟨10.1186/s12859-020-03921-8⟩
Journal articles hal-03101013v1
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Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Alice Rouan , Melanie Pousse , Nadir Djerbi , Barbara Porro , Guillaume Bourdin , et al.
Nature Communications, 2023, 14 (1), pp.3038. ⟨10.1038/s41467-023-38499-1⟩
Journal articles cea-04171809v1
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Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

Magali Lescot , Pascal Hingamp , Kenji Kojima , Emilie Villar , Sarah Romac , et al.
ISME Journal, 2016, 10 (5), pp.1134-1146. ⟨10.1038/ismej.2015.192⟩
Journal articles hal-02964380v1

Linking extreme seasonality and gene expression in arctic marine protists

Magdalena Wutkowska , Anna Vader , Ramiro Logares , Eric Pelletier , Tove Gabrielsen
Preprints, Working Papers, ... cea-03480606v1
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Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)

Romuald Laso‐jadart , Kevin Sugier , Emmanuelle Petit , Karine Labadie , Pierre Peterlongo , et al.
Ecology and Evolution, 2020, 10 (16), pp.8894-8905. ⟨10.1002/ece3.6588⟩
Journal articles hal-02999798v1
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Editorial: Technological advances for measuring planktonic components of the pelagic ecosystem: An integrated approach to data collection and analysis

Sophie G. Pitois , Elaine S. Fileman , Mark C. Benfield , Peter H. Wiebe , Fabien Lombard
Frontiers in Marine Science, 2023, 10, ⟨10.3389/fmars.2023.1100998⟩
Journal articles hal-04020892v1
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Plankton biogeography in the 21st century and impacts of climate change: advances through genomics

Paul Frémont , Marion Gehlen , Olivier Jaillon
Comptes Rendus. Biologies, 2023, 346 (1), pp.13-24. ⟨10.5802/crbiol.107⟩
Journal articles hal-04026636v1
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Planktoscope protocol for plankton imaging

Fabien Lombard
Journal articles hal-04020900v1

Contribution of genome scale metabolic modeling to niche theory

Antoine Régimbeau , Marko Budinich , Abdelhalim Larhlimi , Juan Jose Pierella Karlusich , Olivier Aumont , et al.
Preprints, Working Papers, ... hal-03352833v1

Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions

Hisashi Endo , Romain Blanc Mathieu , Yanze Li , Guillem Salazar , Nicolas Henry , et al.
Nature Ecology & Evolution, 2020, 4 (12), pp.1639-1649. ⟨10.1038/s41559-020-01288-w⟩
Journal articles hal-02974168v1
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Global observation of plankton communities from space

Hiroto Kaneko , Hisashi Endo , Nicolas Henry , Cédric Berney , Frédéric Mahé , et al.
Preprints, Working Papers, ... hal-03855690v1
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Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective

Youri Timsit , Magali Lescot , Martha Valiadi , Fabrice Not
International Journal of Molecular Sciences, 2021, 22 (21), pp.11311. ⟨10.3390/ijms222111311⟩
Journal articles hal-03402318v1
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Disentangling temporal associations in marine microbial networks

Ina Maria Deutschmann , Anders Krabberød , Francisco Latorre , Erwan Delage , Cèlia Marrasé , et al.
Microbiome, 2023, 11 (83), ⟨10.1101/2021.07.13.452187⟩
Journal articles hal-03781901v2
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Diversity of the Pacific Ocean coral reef microbiome

Pierre Galand , Hans-Joachim Ruscheweyh , Guillem Salazar , Corentin Hochart , Nicolas Henry , et al.
Nature Communications, 2023, 14 (1), pp.3039. ⟨10.1038/s41467-023-38500-x⟩
Journal articles hal-04176291v1

Functional trait-based approaches as a common framework for aquatic ecologists: Synthesis and recent results

Séverine Martini , Floriane Larras , Aurélien Boyé , Emile Faure , Nicole Aberle , et al.
ALSO Aquatic Sciences Meeting, Association for the Sciences of Limnology and Oceanography (ASLO), Jun 2023, Palma de Mallorca, Balearic Islands, Spain. pp.965-994, ⟨10.1002/lno.11655⟩
Conference papers hal-04117032v1
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Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes

Greta Busseni , Fabio Rocha Jimenez Vieira , Alberto Amato , Eric Pelletier , Juan Pierella Karlusich , et al.
Molecular Biology and Evolution, 2019, 36 (11), pp.2522-2535. ⟨10.1093/molbev/msz157⟩
Journal articles hal-02184019v1

Metagenomic Mining for Amine Dehydrogenase Discovery

Adam Caparco , Eric Pelletier , Jean Louis Petit , Aurélie Jouenne , Bettina Bommarius , et al.
Advanced Synthesis and Catalysis, 2020, 362 (12), pp.2427-2436. ⟨10.1002/adsc.202000094⟩
Journal articles hal-04150129v1