Pascal Hingamp

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Article dans une revue (36)

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 Sunagawaet al. Nucleic Acids Research, 2022, 11, ⟨10.1093/nar/gkac420⟩ Article dans une revue hal-03696136v1
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 Hingampet al. Molecular Ecology Resources, 2021, ⟨10.1111/1755-0998.13322⟩ Article dans une revue hal-03115219v1
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities Silvia Acinas,Pablo Sánchez,Guillem Salazar,Francisco Cornejo-Castillo,Marta Sebastiánet al. Communications Biology, 2021, 4 (1), ⟨10.1038/s42003-021-02112-2⟩ Article dans une revue hal-03238997v1
Diversity and evolution of bacterial bioluminescence genes in the global ocean Thomas Vannier,Pascal Hingamp,Floriane Turrel,Lisa Tanet,Magali Lescotet al. NAR Genomics and Bioinformatics, 2020, 2 (2), ⟨10.1093/nargab/lqaa018⟩ Article dans une revue hal-02514159v1
Minimum Information about an Uncultivated Virus Genome (MIUViG) Simon Roux,Evelien M. Adriaenssens,Bas E. Dutilh,Eugene V. Koonin,Andrew M. Kropinskiet al. Nature Biotechnology, 2019, 37 (1), pp.29-37. ⟨10.1038/nbt.4306⟩ Article dans une revue pasteur-01977322v1
Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems Luigi Caputi,Quentin Carradec,Damien Eveillard,Amos Kirilovsky,Éric Pelletieret al. Global Biogeochemical Cycles, 2019, 33 (3), pp.391-419. ⟨10.1029/2018GB006022⟩ Article dans une revue hal-02999805v1
Marine DNA viral macro- and microdiversity from Pole to Pole Ann Gregory,Ahmed Zayed,Nádia Conceição-Neto,Ben Temperton,Ben Bolducet al. Cell, 2019, 177 (5), pp.1109-1123.e14. ⟨10.1016/j.cell.2019.03.040⟩ Article dans une revue hal-02387010v1
Microbial abundance, activity and population genomic profiling with mOTUs2 Alessio Milanese,Daniel Mende,Lucas Paoli,Guillem Salazar,Hans-Joachim Ruscheweyhet al. Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-08844-4⟩ Article dans une revue hal-02281129v1
Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans Yoann Seeleuthner,Samuel Mondy,Vincent Lombard,Quentin Carradec,Eric Pelletieret al. Nature Communications, 2018, 9, pp.310. ⟨10.1038/s41467-017-02235-3⟩ Article dans une revue hal-01771839v1
Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters Yanze Li,Pascal Hingamp,Hiroyasu Watai,Hisashi Endo,Takashi Yoshidaet al. Viruses, 2018, 10 (9), pp.496. ⟨10.3390/v10090496⟩ Article dans une revue hal-01874850v1
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 Morimotoet al. The International Society of Microbiologial Ecology Journal, 2018, ⟨10.1038/s41396-018-0052-x⟩ Article dans une revue hal-01771838v1
A global ocean atlas of eukaryotic genes Quentin Carradec,Eric Pelletier,Corinne da Silva,Adriana A. Alberti,Yoann Seeleuthneret al. Nature Communications, 2018, 9 (1), pp.373. ⟨10.1038/s41467-017-02342-1⟩ Article dans une revue cea-01874711v1
Taxon Richness of “Megaviridae” Exceeds those of Bacteria and Archaea in the Ocean Tomoko Mihara,Hitoshi Koyano,Pascal Hingamp,Nigel Grimsley,Susumu Gotoet al. Microbes and environments / JSME, 2018, 33 (2), pp.162-171. ⟨10.1264/jsme2.me17203⟩ Article dans une revue hal-01978927v1
The Ocean Gene Atlas: exploring the biogeography of plankton genes online Emilie Villar,Thomas Vannier,Caroline Vernette,Magali Lescot,Miguelangel Cuencaet al. Nucleic Acids Research, 2018, 46 (W1), pp.gky376. ⟨10.1093/nar/gky376⟩ Article dans une revue hal-01803597v1
Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean Yosuke Nishimura,Hiroyasu Watai,Takashi Honda,Tomoko Mihara,Kimiho Omaeet al. MSphere, 2017, 2 (2), ⟨10.1128/mSphere.00359-16⟩ Article dans une revue hal-01771841v1
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition Adriana A. Alberti,Julie Poulain,Stefan Engelen,Karine Labadie,Sarah Romacet al. Scientific Data , 2017, 4, ⟨10.1038/sdata.2017.93⟩ Article dans une revue hal-01771844v1
Linking Virus Genomes with Host Taxonomy. Tomoko Mihara,Yosuke Nishimura,Yugo Shimizu,Hiroki Nishiyama,Genki Yoshikawaet al. AIDS Research and Human Retroviruses, 2016, 8 (3), pp.66. ⟨10.3390/v8030066⟩ Article dans une revue hal-01435950v1
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-Mendezet al. Nature Communications, 2016, 7, pp.11071. ⟨10.1038/ncomms11071⟩ Article dans une revue hal-01295207v1
Plankton networks driving carbon export in the oligotrophic ocean Lionel Guidi,Samuel Chaffron,Lucie Bittner,Damien Eveillard,Abdelhalim Larhlimiet al. Nature, 2016, 532, pp.465-470. ⟨10.1038/nature16942⟩ Article dans une revue hal-01275276v1
Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages Magali Lescot,Pascal Hingamp,Kenji K Kojima,Emilie Villar,Sarah Romacet al. The International Society of Microbiologial Ecology Journal, 2015, 10 (5), pp.1134-1146. ⟨10.1038/ismej.2015.192⟩ Article dans une revue hal-01258212v1
Structure and function of the global ocean microbiome Shinichi Sunagawa,Luis Pedro Coelho,Samuel Chaffron,Jens Roat Kultima,Karine Labadieet al. Science, 2015, 348 (6237), pp.1261359. ⟨10.1126/science.1261359⟩ Article dans une revue hal-01233742v1
Open science resources for the discovery and analysis of Tara Oceans data Stéphane Pesant,Fabrice Not,Marc Picheral,Stefanie Kandels-Lewis,Noan Le Bescotet al. Scientific Data , 2015, 2, pp.150023. ⟨10.1038/sdata.2015.23⟩ Article dans une revue (data paper) hal-01253984v1
Environmental characteristics of Agulhas rings affect interocean plankton transport Emilie Villar,Gregory Farrant,Michael J. Follows,Laurence Garczarek,Sabrina Speichet al. Science, 2015, 348 (6237), pp.1261447 - 1261447. ⟨10.1126/science.1261447⟩ Article dans une revue hal-01893637v1
Eukaryotic plankton diversity in the sunlit ocean Noan Le Bescot,Ian Probert,Margaux Carmichael,Julie Poulain,Sarah Romacet al. Science, 2015, 348 (6237), pp.1261605. ⟨10.1126/science.1261605⟩ Article dans une revue hal-01253979v1
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 Vargaset al. Environmental Microbiology Reports, 2015, 7 (6), pp.979-989. ⟨10.1111/1758-2229.12345⟩ Article dans une revue hal-01246259v1
Patterns and ecological drivers of ocean viral communities Jennifer Brum,J Cesar Ignacio-Espinoza,Simon Roux,Guilhem Doulcier,Silvia G. Acinaset al. Science, 2015, 348 (6237), pp.1261498. ⟨10.1126/science.1261498⟩ Article dans une revue hal-01768331v1
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 Hingampet al. Molecular Ecology Resources, 2014, 14 (6), pp.1302-1313. ⟨10.1111/1755-0998.12271⟩ Article dans une revue istex hal-02356473v1
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 Ferreraet al. Environmental Microbiology, 2014, 16 (9, SI), pp.2659-2671. ⟨10.1111/1462-2920.12250⟩ Article dans une revue istex hal-01258219v1
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes Pascal Hingamp,Nigel Grimsley,Silvia G Acinas,Camille Clerissi,Lucie Subiranaet al. The International Society of Microbiologial Ecology Journal, 2013, 7 (9), pp.1678-1695. ⟨10.1038/ismej.2013.59⟩ Article dans une revue hal-01258223v1
A Holistic Approach to Marine Eco-Systems Biology Eric Karsenti,Silvia G. Acinas,Peer Bork,Chris Bowler,Colomban de Vargaset al. PLoS Biology, 2011, 9 (10), pp.e1001177. ⟨10.1371/journal.pbio.1001177⟩ Article dans une revue hal-01893669v1
Metagenome Annotation Using a Distributed Grid of Undergraduate Students P. Hingamp,Céline Brochier-Armanet,E. Talla,D. Gautheret,D. Thieffryet al. PLoS Biology, 2008, 6, pp.239-241 Article dans une revue hal-00697953v1
Feature extraction and signal processing for nylon DNA microarrays. Fabrice Lopez,Jacques Rougemont,Béatrice Loriod,Aude Bourgeois,Laurence Loïet al. BMC Genomics, 2004, 5 (1), pp.38. ⟨10.1186/1471-2164-5-38⟩ Article dans une revue inserm-00112016v1
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⟩ Article dans une revue 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. Stoesseret al. Bioinformatics, 2002, 18, pp.763-764 Article dans une revue 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. Zhaoet al. Molecular and Cellular Biology, 2000, 20 (17), pp.6568-78 Article dans une revue 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. Zhaoet al. Molecular and Cellular Biology, 2000, 20 (17), pp.6568-6578 Article dans une revue hal-02695857v1

Chapitre d'ouvrage (1)

Prognosis of breast cancer and gene expression profiling using DNA arrays F Bertucci,R Houlgatte,S Granjeaud,V Nasser,Béatrice B. Loriodet al. Microarrays, Immune Responses and Vaccines, 975, pp.217-231, 2002, 0077-8923;1-57331-446-3. ⟨10.1111/j.1749-6632.2002.tb05954.x⟩ Chapitre d'ouvrage istex hal-01612160v1