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Pascal Hingamp





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The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes

Caroline Vernette , Julien Lecubin , Pablo Sánchez , (team) Tara Oceans Coordinators , Shinichi Sunagawa
Nucleic Acids Research, 2022, 11, ⟨10.1093/nar/gkac420⟩
Journal articles hal-03696136v1
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Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

Silvia Acinas , Pablo Sánchez , Guillem Salazar , Francisco Cornejo-Castillo , Marta Sebastián
Communications Biology, 2021, 4 (1), ⟨10.1038/s42003-021-02112-2⟩
Journal articles hal-03238997v1

The Ocean Barcode Atlas: a web service to explore the biodiversity and biogeography of marine organisms.

Caroline Vernette , Nicolas Henry , Julien Lecubin , Colomban de Vargas , Pascal Hingamp
Molecular Ecology Resources, 2021, ⟨10.1111/1755-0998.13322⟩
Journal articles hal-03115219v1
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Macroscale patterns of oceanic zooplankton composition and size structure

Manoela Brandão , Fabio Benedetti , Séverine Martini , Yawouvi Dodji Soviadan , Jean-Olivier Irisson
Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-94615-5⟩
Journal articles hal-03318806v1
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Diversity and evolution of bacterial bioluminescence genes in the global ocean

Thomas Vannier , Pascal Hingamp , Floriane Turrel , Lisa Tanet , Magali Lescot
NAR Genomics and Bioinformatics, 2020, 2 (2), ⟨10.1093/nargab/lqaa018⟩
Journal articles hal-02514159v1
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Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Luigi Caputi , Quentin Carradec , Damien Eveillard , Amos Kirilovsky , Eric Pelletier
Global Biogeochemical Cycles, 2019, 33 (3), pp.391-419. ⟨10.1029/2018GB006022⟩
Journal articles hal-02999805v1
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Minimum Information about an Uncultivated Virus Genome (MIUViG)

Simon Roux , Evelien M. Adriaenssens , Bas E. Dutilh , Eugene V. Koonin , Andrew M. Kropinski
Nature Biotechnology, 2019, 37 (1), pp.29-37. ⟨10.1038/nbt.4306⟩
Journal articles pasteur-01977322v1

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Guillem Salazar , Lucas Paoli , Adriana A. Alberti , Jaime Huerta-Cepas , Hans-Joachim Ruscheweyh
Cell, 2019, 179 (5), pp.1068-1083.e21. ⟨10.1016/j.cell.2019.10.014⟩
Journal articles hal-02964513v1
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Microbial abundance, activity and population genomic profiling with mOTUs2

Alessio Milanese , Daniel Mende , Lucas Paoli , Guillem Salazar , Hans-Joachim Ruscheweyh
Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-08844-4⟩
Journal articles hal-02281129v1
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Marine DNA viral macro- and microdiversity from Pole to Pole

Ann Gregory , Ahmed Zayed , Nádia Conceição-Neto , Ben Temperton , Ben Bolduc
Cell, 2019, 177 (5), pp.1109-1123.e14. ⟨10.1016/j.cell.2019.03.040⟩
Journal articles hal-02387010v1
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The Ocean Gene Atlas: exploring the biogeography of plankton genes online

Emilie Villar , Thomas Vannier , Caroline Vernette , Magali Lescot , Miguelangel Cuenca
Nucleic Acids Research, 2018, 46 (W1), pp.gky376. ⟨10.1093/nar/gky376⟩
Journal articles hal-01803597v1
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Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan

Takashi Yoshida , Yosuke Nishimura , Hiroyasu Watai , Nana Haruki , Daichi Morimoto
The International Society of Microbiologial Ecology Journal, 2018, ⟨10.1038/s41396-018-0052-x⟩
Journal articles hal-01771838v1
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Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Yoann Seeleuthner , Samuel Mondy , Vincent Lombard , Quentin Carradec , Eric Pelletier
Nature Communications, 2018, 9, pp.310. ⟨10.1038/s41467-017-02235-3⟩
Journal articles hal-01771839v1
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Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters

Yanze Li , Pascal Hingamp , Hiroyasu Watai , Hisashi Endo , Takashi Yoshida
Viruses, 2018, 10 (9), pp.496. ⟨10.3390/v10090496⟩
Journal articles hal-01874850v1
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Taxon Richness of “Megaviridae” Exceeds those of Bacteria and Archaea in the Ocean

Tomoko Mihara , Hitoshi Koyano , Pascal Hingamp , Nigel Grimsley , Susumu Goto
Microbes and environments / JSME, 2018, 33 (2), pp.162-171. ⟨10.1264/jsme2.me17203⟩
Journal articles hal-01978927v1
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A global ocean atlas of eukaryotic genes

Quentin Carradec , Eric Pelletier , Corinne da Silva , Adriana A. Alberti , Yoann Seeleuthner
Nature Communications, 2018, 9 (1), pp.373. ⟨10.1038/s41467-017-02342-1⟩
Journal articles cea-01874711v1
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Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Adriana A. Alberti , Julie Poulain , Stefan Engelen , Karine Labadie , Sarah Romac
Scientific Data , 2017, 4, ⟨10.1038/sdata.2017.93⟩
Journal articles hal-01771844v1
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Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean

Yosuke Nishimura , Hiroyasu Watai , Takashi Honda , Tomoko Mihara , Kimiho Omae
MSphere, 2017, 2 (2), ⟨10.1128/mSphere.00359-16⟩
Journal articles hal-01771841v1
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Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

Francisco M. Cornejo-Castillo , Ana M. Cabello , Guillem Salazar , Patricia Sánchez-Baracaldo , Gipsi Lima-Mendez
Nature Communications, 2016, 7, pp.11071. ⟨10.1038/ncomms11071⟩
Journal articles hal-01295207v1
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Plankton networks driving carbon export in the oligotrophic ocean

Lionel Guidi , Samuel Chaffron , Lucie Bittner , Damien Eveillard , Abdelhalim Larhlimi
Nature, 2016, 532, pp.465-470. ⟨10.1038/nature16942⟩
Journal articles hal-01275276v1

Linking Virus Genomes with Host Taxonomy.

Tomoko Mihara , Yosuke Nishimura , Yugo Shimizu , Hiroki Nishiyama , Genki Yoshikawa
AIDS Research and Human Retroviruses, 2016, 8 (3), pp.66. ⟨10.3390/v8030066⟩
Journal articles hal-01435950v1
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Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

Camille Clerissi , Yves Desdevises , Sarah Romac , Stéphane Audic , Colomban de Vargas
Environmental Microbiology Reports, 2015, 7 (6), pp.979-989. ⟨10.1111/1758-2229.12345⟩
Journal articles hal-01246259v1
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Structure and function of the global ocean microbiome

Shinichi Sunagawa , Luis Pedro Coelho , Samuel Chaffron , Jens Roat Kultima , Karine Labadie
Science, 2015, 348 (6237), pp.1261359. ⟨10.1126/science.1261359⟩
Journal articles hal-01233742v1
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Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

Magali Lescot , Pascal Hingamp , Kenji K Kojima , Emilie Villar , Sarah Romac
The International Society of Microbiologial Ecology Journal, 2015, 10 (5), pp.1134-1146. ⟨10.1038/ismej.2015.192⟩
Journal articles hal-01258212v1
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Patterns and ecological drivers of ocean viral communities

Jennifer Brum , J Cesar Ignacio-Espinoza , Simon Roux , Guilhem Doulcier , Silvia G. Acinas
Science, 2015, 348 (6237), pp.1261498. ⟨10.1126/science.1261498⟩
Journal articles hal-01768331v1

Environmental characteristics of Agulhas rings affect interocean plankton transport

Emilie Villar , Gregory Farrant , Michael Follows , Laurence Garczarek , Sabrina Speich
Science, 2015, 348 (6237), pp.1261447 - 1261447. ⟨10.1126/science.1261447⟩
Journal articles hal-01893637v1
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Open science resources for the discovery and analysis of Tara Oceans data

Stéphane Pesant , Fabrice Not , Marc Picheral , Stefanie Kandels-Lewis , Noan Le Bescot
Scientific Data , 2015, 2, pp.150023. ⟨10.1038/sdata.2015.23⟩
Journal articles hal-01253984v1
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Eukaryotic plankton diversity in the sunlit ocean

Noan Le Bescot , Ian Probert , Margaux Carmichael , Julie Poulain , Sarah Romac
Science, 2015, 348 (6237), pp.1261605. ⟨10.1126/science.1261605⟩
Journal articles hal-01253979v1

QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate

Emese Meglécz , Nicolas Pech , André Gilles , Vincent Dubut , Pascal Hingamp
Molecular Ecology Resources, 2014, 14 (6), pp.1302-1313. ⟨10.1111/1755-0998.12271⟩
Journal articles hal-02356473v1
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Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Ramiro Logares , Shinichi Sunagawa , Guillem Salazar , Francisco M. Cornejo-Castillo , Isabel Ferrera
Environmental Microbiology, 2014, 16 (9, SI), pp.2659-2671. ⟨10.1111/1462-2920.12250⟩
Journal articles hal-01258219v1
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Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Pascal Hingamp , Nigel Grimsley , Silvia G Acinas , Camille Clerissi , Lucie Subirana
The International Society of Microbiologial Ecology Journal, 2013, 7 (9), pp.1678-1695. ⟨10.1038/ismej.2013.59⟩
Journal articles hal-01258223v1
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A Holistic Approach to Marine Eco-Systems Biology

Eric Karsenti , Silvia G. Acinas , Peer Bork , Chris Bowler , Colomban de Vargas
PLoS Biology, 2011, 9 (10), pp.e1001177. ⟨10.1371/journal.pbio.1001177⟩
Journal articles hal-01893669v1

Metagenome Annotation Using a Distributed Grid of Undergraduate Students

P. Hingamp , Céline Brochier-Armanet , E. Talla , D. Gautheret , D. Thieffry
PLoS Biology, 2008, 6, pp.239-241
Journal articles hal-00697953v1
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Feature extraction and signal processing for nylon DNA microarrays.

Fabrice Lopez , Jacques Rougemont , Béatrice Loriod , Aude Bourgeois , Laurence Loï
BMC Genomics, 2004, 5 (1), pp.38. ⟨10.1186/1471-2164-5-38⟩
Journal articles inserm-00112016v1
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DNA microarray data and contextual analysis of correlation graphs.

Jacques Rougemont , Pascal Hingamp
BMC Bioinformatics, 2003, 4, pp.15. ⟨10.1186/1471-2105-4-15⟩
Journal articles inserm-00115584v1

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database

V. Lombard , E.B. Camon , H.E. Parkinson , P. Hingamp , G. Stoesser
Bioinformatics, 2002, 18, pp.763-764
Journal articles hal-00427286v1

Divergent N-terminal sequences target an inducible testis deubiquitinating enzyme to distinct subcellular structures.

L. Lin , Anne Keriel , C. Morales , N Bedard , Q. Zhao
Molecular and Cellular Biology, 2000, 20 (17), pp.6568-78
Journal articles hal-01994377v1

Divergent N-terminal sequences target an inducible testis deubiquitinating enzyme to distinct subcellular structures

H. Lin , A. Keriel , C.R. Morales , N. Bedard , Q. Zhao
Molecular and Cellular Biology, 2000, 20 (17), pp.6568-6578
Journal articles hal-02695857v1