Patrick Wincker

466
Documents
Affiliation actuelle
  • Laboratoire d'Analyses Génomiques des Eucaryotes (LAGE)

Publications

Publications

Deposit thumbnail

A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution

Gaetan Droc , Delphine Giraud , Caroline Belser , Karine Labadie , Simone Duprat et al.

Plant Biotechnology Journal, inPress, pp.1-23. ⟨10.1111/pbi.70553⟩

Article dans une revue hal-05247455v1
Deposit thumbnail

Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2)

Ioulia Santi , Christina Pavloudi , Maria Abagnale , Iñigo Azua , Zuriñe Baña et al.

Biodiversity Data Journal, 2026, 14, pp.e178484. ⟨10.3897/BDJ.14.e178484⟩

Article dans une revue (data paper) hal-05480555v1
Deposit thumbnail

Sustainability insights from Late Pleistocene climate change and horse migration patterns

Yvette Running Horse Collin , Clément Bataille , Samantha Hershauer , Mila Hunska Tašunke Icu , Akil Nujipi et al.

Science, 2025, 388 (6748), pp.748-755. ⟨10.1126/science.adr2355⟩

Article dans une revue hal-05343796v1

Sustainability insights from Late Pleistocene climate change and horse migration patterns

Yvette Running Horse Collin , Clément Bataille , Samantha Hershauer , Mila Hunska Tašunke Icu , Akil Nujipi et al.

Science, 2025, 388 (6748), pp.748-755. ⟨10.1126/science.adr2355⟩

Article dans une revue hal-05216355v1
Deposit thumbnail

Genome sequences of four Ixodes species expands understanding of tick evolution

Alexandra Cerqueira de Araujo , Benjamin Noël , Anthony Bretaudeau , Karine Labadie , Matéo Boudet et al.

BMC Biology, 2025, 23, pp.17. ⟨10.1186/s12915-025-02121-1⟩

Article dans une revue hal-04707197v1
Deposit thumbnail

Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors

Guillaume Martin , Benjamin Istace , Franc-Christophe Baurens , Caroline Belser , Catherine Hervouet et al.

Nature Communications, 2025, 16, pp.961. ⟨10.1038/s41467-025-56329-4⟩

Article dans une revue hal-04911301v1

ERGA-BGE genome of Xanthium orientale subsp. italicum (Moretti) Greuter. A plant of American origin, now widespread and, in some cases, invasive in Europe

Salvatore Tomasello , Eleonora Manzo , Rita Monteiro , Astrid Böhne , Thomas Marcussen et al.

Open Research Europe, 2025, 5, pp.367. ⟨10.12688/openreseurope.21891.1⟩

Article dans une revue hal-05464158v1
Deposit thumbnail

First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples

Christina Pavloudi , Ioulia Santi , Iñigo Azua , Zuriñe Baña , Mauro Bastianini et al.

Biodiversity Data Journal, 2025, 13, pp.e143585. ⟨10.3897/BDJ.13.e143585⟩

Article dans une revue (data paper) cea-05046943v1
Deposit thumbnail

The late rise of sky-island vegetation in the European Alps

Lara M Wootton , Florian C Boucher , Charles Pouchon , Cristina Roquet , Eric Coissac et al.

Nature Plants, 2025, 11 (6), pp.1142-1153. ⟨10.1038/s41477-025-02001-0⟩

Article dans une revue hal-05347361v1

ERGA-BGE reference genome of Lewinskya acuminata, a common epiphytic Mediterranean moss with disjunct populations in California and Ethiopia

Pablo Aguado-Ramsay , Francisco Lara , Isabel Draper , Maria Conejero , Astrid Böhne et al.

Open Research Europe, 2025, 5, pp.357. ⟨10.12688/openreseurope.21670.1⟩

Article dans une revue cea-05483813v1
Deposit thumbnail

Origin and evolutionary trajectories of brown algal sex chromosomes

Josué Barrera-Redondo , Agnieszka Lipinska , Pengfei Liu , Erica Dinatale , Guillaume Cossard et al.

Nature Ecology & Evolution, 2025, ⟨10.1038/s41559-025-02838-w⟩

Article dans une revue hal-05224288v1
Deposit thumbnail

Omics exploration of deep-sea biodiversity: data from the “Pourquoi Pas les Abysses?” and eDNAbyss projects

Sophie Arnaud-Haond , Blandine Trouche , Cathy Liautard-Haag , Karine Alain , Johanne Aubé et al.

Scientific Data , 2025, 12 (1), pp.1982. ⟨10.1038/s41597-025-06009-1⟩

Article dans une revue hal-05434404v1
Deposit thumbnail

Patterns and drivers of diatom diversity and abundance in the global ocean

Juan Pierella Karlusich , Karen Cosnier , Lucie Zinger , Nicolas Henry , Charlotte Nef et al.

Nature Communications, 2025, 16 (1), pp.3452. ⟨10.1038/s41467-025-58027-7⟩

Article dans une revue hal-05138560v1
Deposit thumbnail

On the way to diploidization and unexpected ploidy in the grass Sporobolus section Spartina mesopolyploids

Armel Salmon , Yan Hao , Morgane Milin , Oscar Lima , Armand Cave-Radet et al.

Nature Communications, 2025, 16 (1), pp.1997. ⟨10.1038/s41467-025-56983-8⟩

Article dans une revue hal-04976572v1
Deposit thumbnail

Emergent patterns of patchiness differ between physical and planktonic properties in the ocean

Patrick Clifton Gray , Emmanuel Boss , Guillaume Bourdin , A Bourdais , C Bowler et al.

Nature Communications, 2025, 16 (1), pp.1808. ⟨10.1038/s41467-025-56794-x⟩

Article dans une revue hal-04976225v1

ERGA-BGE reference genome of Eunicella cavolini, an IUCN Near Threatened Gorgonian of the Mediterranean Sea

Didier Aurelle , Dorian Guillemain , Frédéric Zuberer , Denys Malengros , Astrid Böhne et al.

Open Research Europe, 2025, 5, pp.323. ⟨10.12688/openreseurope.21514.1⟩

Article dans une revue hal-05505155v1

Transcriptomic response of the picoalga Pelagomonas calceolata to nitrogen availability: new insights into cyanate lyase function

Nina Guérin , Chloé Seyman , Céline Orvain , Laurie Bertrand , Priscillia Gourvil et al.

Microbiology Spectrum, 2025, ⟨10.1128/spectrum.02654-24⟩

Article dans une revue cea-05010706v1

Straight from the Horse’s Mouth: Timing and Zoogeography of Domesticated Horse Arrivals in Mongolia and China

William Honeychurch , Rong Fan , Leland Rogers , Mark E. Hall , Chunag Amartuvshin et al.

Journal of Archaeological Method and Theory, 2025, 32 (1), pp.27. ⟨10.1007/s10816-024-09691-4⟩

Article dans une revue cea-05047023v1
Deposit thumbnail

Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses

Jianfei Pan , Xuexue Liu , Mateusz Baca , Laure Calvière-Tonasso , Stéphanie Schiavinato et al.

Molecular Ecology, 2024, 33 (19), pp.e17527. ⟨10.1111/mec.17527⟩

Article dans une revue hal-04729863v1
Deposit thumbnail

Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

Ana Paula Zotta Mota , Georgios Koutsovoulos , Laetitia Perfus-Barbeoch , Evelin Despot-Slade , Karine Labadie et al.

Nature Communications, 2024, 15 (1), pp.773. ⟨10.1038/s41467-024-44914-y⟩

Article dans une revue hal-04489824v1
Deposit thumbnail

Sea surface temperature reconstruction in the Pacific Ocean using multi-elemental proxy in Porites and Diploastrea corals: Application to Palau Archipelago

Marine Canesi , Éric Douville , Paolo Montagna , Louise Bordier , Sandrine Caquineau et al.

Chemical Geology, 2024, 645, pp.121884. ⟨10.1016/j.chemgeo.2023.121884⟩

Article dans une revue hal-04337163v1

High altitude horse use and early horse transport in eastern Eurasia: New evidence from melting ice

William Timothy Treal Taylor , Isaac Hart , Tumurbaatar Tuvshinjargal , Jamsranjav Bayarsaikhan , Nicholas Jarman et al.

The Holocene, 2024, 34 (9), pp.1204-1213. ⟨10.1177/09596836241254484⟩

Article dans une revue hal-04780801v1

Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood

Stefanie Wagner , Andaine Seguin-Orlando , Jean-Charles Leplé , Thibault Leroy , Céline Lalanne et al.

Molecular Ecology, 2024, 33 (3), ⟨10.1111/mec.16859⟩

Article dans une revue hal-04717422v1
Deposit thumbnail

Unraveling biogeographical patterns and environmental drivers of soil fungal diversity at the French national scale

Christophe Djemiel , Samuel Dequiedt , Walid Horrigue , Arthur Bailly , Mélanie Lelièvre et al.

Soil, 2024, 10 (1), pp.251-273. ⟨10.5194/soil-10-251-2024⟩

Article dans une revue hal-04874922v1
Deposit thumbnail

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

France Denoeud , Olivier Godfroy , Corinne Cruaud , Svenja Heesch , Zofia Nehr et al.

Cell, 2024, 187 (24), pp.6943-6965. ⟨10.1016/j.cell.2024.10.049⟩

Article dans une revue hal-04794231v1
Deposit thumbnail

The genome of the simultaneously hermaphroditic snail Lymnaea stagnalis reveals an evolutionary expansion of FMRFamide-like receptors

Joris M Koene , Daniel J. Jackson , Yumi Nakadera , Nicolas Cerveau , Mohammed‐amin Madoui et al.

Scientific Reports, 2024, 14 (1), pp.29213. ⟨10.1038/s41598-024-78520-1⟩

Article dans une revue hal-04465013v2
Deposit thumbnail

Widespread horse-based mobility arose around 2,200 BCE in Eurasia

Pablo Librado , Gaetan Tressières , Lorelei Chauvey , Antoine Fages , Naveed Khan et al.

Nature, 2024, 631 (8022), ⟨10.1038/s41586-024-07597-5⟩

Article dans une revue hal-04607980v1
Deposit thumbnail

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Ann Mc Cartney , Giulio Formenti , Alice Mouton , Diego de Panis , Luísa Marins et al.

npj Biodiversity, 2024, 3 (1), pp.28. ⟨10.1038/s44185-024-00054-6⟩

Article dans une revue hal-05248491v1
Deposit thumbnail

Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions

Clemens Schauberger , Bo Thamdrup , Clarisse Lemonnier , Blandine Trouche , Julie Poulain et al.

ISME Communications, 2024, 4 (1), pp.ycad005. ⟨10.1093/ismeco/ycad005⟩

Article dans une revue hal-04492228v1
Deposit thumbnail

DNA methylation-based profiling of horse archaeological remains for age-at-death and castration

Xuexue Liu , Andaine Seguin- Orlando , Lorelei Chauvey , Gaëtan Tressières , Laure Tonasso-Calvie et al.

iScience, 2023, 26 (3), pp.106144. ⟨10.1016/j.isci.2023.106144⟩

Article dans une revue cea-04286440v1
Deposit thumbnail

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⟩

Article dans une revue hal-04184949v1
Deposit thumbnail

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

Hugo Doré , Ulysse Guyet , Jade Leconte , Gregory Farrant , Benjamin Alric et al.

The International Society of Microbiologial Ecology Journal, 2023, 17 (5), pp.720-732. ⟨10.1038/s41396-023-01386-0⟩

Article dans une revue hal-04238382v2
Deposit thumbnail

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⟩

Article dans une revue cea-04171796v1
Deposit thumbnail

Pervasive tandem duplications and convergent evolution shape coral genomes

Benjamin Noel , France Denoeud , Alice Rouan , Carol Buitrago-López , Laura Capasso et al.

Genome Biology, 2023, 24 (1), pp.123. ⟨10.1186/s13059-023-02960-7⟩

Article dans une revue hal-04117388v1
Deposit thumbnail

Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Alice Rouan , Mélanie Pousse , Nadir Djerbi , Barbara Porro , Guillaume Bourdin et al.

Nature Communications, 2023, 14 (1), pp.3038. ⟨10.1038/s41467-023-38499-1⟩

Article dans une revue cea-04171809v1
Deposit thumbnail

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

Christian R Voolstra , Benjamin C C Hume , Eric J Armstrong , Guinther Mitushasi , Barbara Porro et al.

npj Biodiversity, 2023, 2 (1), pp.15. ⟨10.1038/s44185-023-00020-8⟩

Article dans une revue hal-04157744v1
Deposit thumbnail

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⟩

Article dans une revue pasteur-04085734v1
Deposit thumbnail

Early dispersal of domestic horses into the Great Plains and northern Rockies

William Timothy Treal Taylor , Pablo Librado , Mila Hunska Tašunke Icu , Carlton Shield Chief Gover , Jimmy Arterberry et al.

Science, 2023, 379 (6639), pp.1316-1323. ⟨10.1126/science.adc9691⟩

Article dans une revue hal-04065852v1
Deposit thumbnail

The defensome of complex bacterial communities

Angelina Beavogui , Auriane Lacroix , Nicolas Wiart , Julie Poulain , Tom O Delmont et al.

Nature Communications, 2023, 15, pp.2146. ⟨10.1101/2023.08.12.553040⟩

Article dans une revue hal-04406189v2
Deposit thumbnail

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⟩

Article dans une revue hal-04176291v1
Deposit thumbnail

Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation

Isabel Sanz-Sáez , Pablo Sánchez , Guillem Salazar , Shinichi Sunagawa , Colomban de Vargas et al.

ISME Communications, 2023, 3 (1), ⟨10.1038/s43705-023-00290-0⟩

Article dans une revue cea-04481824v1
Deposit thumbnail

Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes

Ferdinand Marlétaz , Arnaud Couloux , Julie Poulain , Karine Labadie , Corinne da Silva et al.

Cell Genomics, 2023, 3 (4), pp.100295. ⟨10.1016/j.xgen.2023.100295⟩

Article dans une revue (data paper) hal-04093287v1
Deposit thumbnail

Imputed genomes of historical horses provide insights into modern breeding

Evelyn T Todd , Aurore Fromentier , Richard Sutcliffe , Yvette Running , Horse Collin et al.

iScience, 2023, 26 (7), pp.107104. ⟨10.1016/j.isci.2023.107104⟩

Article dans une revue hal-04242127v1
Deposit thumbnail

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Caroline Belser , Julie Poulain , Karine Labadie , Frederick Gavory , Adriana Alberti et al.

Scientific Data , 2023, 10 (1), pp.326. ⟨10.1038/s41597-023-02204-0⟩

Article dans une revue hal-04176297v3
Deposit thumbnail

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Alex Veglia , Kalia Bistolas , Christian Voolstra , Benjamin Hume , Hans-Joachim Ruscheweyh et al.

Communications Biology, 2023, 6 (1), pp.566. ⟨10.1038/s42003-023-04917-9⟩

Article dans une revue hal-04176296v2
Deposit thumbnail

Pan-Arctic plankton community structure and its global connectivity

Federico M Ibarbalz , Nicolas Henry , Frédéric Mahé , Mathieu Ardyna , Adriana Zingone et al.

Elementa: Science of the Anthropocene, 2023, 11 (1), pp.00060. ⟨10.1525/elementa.2022.00060⟩

Article dans une revue hal-04267640v1
Deposit thumbnail

Mission Tara Microplastics: a holistic set of protocols and data resources for the field investigation of plastic pollution along the land-sea continuum in Europe

Jean-François Ghiglione , Valérie Barbe , Stéphane Bruzaud , Gaëtan Burgaud , Jérôme Cachot et al.

Environmental Science and Pollution Research, 2023, ⟨10.1007/s11356-023-26883-9⟩

Article dans une revue hal-04302147v1
Deposit thumbnail

Predicting global distributions of eukaryotic plankton communities from satellite data

Hiroto Kaneko , Hisashi Endo , Nicolas Henry , Cédric Berney , Frédéric Mahé et al.

ISME Communications, 2023, 3 (1), pp.101. ⟨10.1038/s43705-023-00308-7⟩

Article dans une revue hal-04394784v1
Deposit thumbnail

Ocean-wide comparisons of mesopelagic planktonic community structures

Janaina Rigonato , Marko Budinich , Alejandro Murillo , Manoela Brandão , Juan Pierella Karlusich et al.

ISME Communications, 2023, 3 (1), pp.83. ⟨10.1038/s43705-023-00279-9⟩

Article dans une revue hal-04184772v1
Deposit thumbnail

Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Fabien Lombard , Guillaume Bourdin , Stéphane Pesant , Sylvain Agostini , Alberto Baudena et al.

Scientific Data , 2023, 10 (1), pp.324. ⟨10.1038/s41597-022-01757-w⟩

Article dans une revue hal-04164118v1
Deposit thumbnail

Differences in carbonate chemistry up-regulation of long-lived reef-building corals

Marine Canesi , Éric Douville , Paolo Montagna , Marco Taviani , Jarosław Stolarski et al.

Scientific Reports, 2023, 13 (1), pp.11589. ⟨10.1038/s41598-023-37598-9⟩

Article dans une revue cea-04170119v1
Deposit thumbnail

Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments

Blandine Trouche , Clemens Schauberger , Feriel Bouderka , Jean-Christophe Auguet , Caroline Belser et al.

ISME Communications, 2023, 3 (1), pp.133. ⟨10.1038/s43705-023-00341-6⟩

Article dans une revue hal-04388214v1
Deposit thumbnail

Different environmental response strategies in sympatric corals from Pacific Islands

Barbara Porro , Thamilla Zamoum , Didier Forcioli , Eric Gilson , Adrien Poquet et al.

Communications Earth & Environment, 2023, 4 (1), pp.311. ⟨10.1038/s43247-023-00946-8⟩

Article dans une revue hal-04205154v1
Deposit thumbnail

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Corentin Hochart , Lucas Paoli , Hans-Joachim Ruscheweyh , Guillem Salazar , Emilie Boissin et al.

Nature Communications, 2023, 14 (1), pp.3037. ⟨10.1038/s41467-023-38502-9⟩

Article dans une revue hal-04176293v1

ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications

Charles Pouchon , Frédéric Boyer , Cristina Roquet , France Denoeud , Jérôme Chave et al.

Molecular Ecology Resources, 2022, 22 (5), pp.2018-2037. ⟨10.1111/1755-0998.13584⟩

Article dans une revue hal-03839343v1
Deposit thumbnail

Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

Richard Dorrell , Alan Kuo , Zoltan Füssy , Elisabeth Richardson , Asaf Salamov et al.

Life Science Alliance, 2022, 6 (3), pp.e202201833. ⟨10.26508/lsa.202201833⟩

Article dans une revue hal-03859139v1
Deposit thumbnail

Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Tristan Cordier , Inès Barrenechea Angeles , Nicolas Henry , Franck Lejzerowicz , Cédric Berney et al.

Science Advances , 2022, 8 (5), ⟨10.1126/sciadv.abj9309⟩

Article dans une revue hal-03561462v1
Deposit thumbnail

Historical management of equine resources in France from the Iron Age to the Modern Period: a cross disciplinary approach

Pierre Clavel , Jean Dumoncel , Clio Der Sarkissian , Andaine Seguin-Orlando , Laure Calvière-Tonasso et al.

Bulletins et Mémoires de la Société d'anthropologie de Paris, 2022, 34 ((S)), pp.4627-4647. ⟨10.4000/bmsap.8460⟩

Article dans une revue hal-05023241v1
Deposit thumbnail

Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection

Aurélie Canaguier , Romane Guilbaud , Erwan Denis , Ghislaine Magdelenat , Caroline Belser et al.

BMC Genomics, 2022, 23 (1), pp.317. ⟨10.1186/s12864-022-08499-4⟩

Article dans une revue hal-03977388v1
Deposit thumbnail

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⟩

Article dans une revue hal-03872935v2

Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans

Naama Lang-Yona , J. Michel Flores , Rotem Haviv , Adriana Alberti , Julie Poulain et al.

Communications Earth & Environment, 2022, 3 (1), pp.121. ⟨10.1038/s43247-022-00441-6⟩

Article dans une revue hal-04382382v1

Reply to: When did mammoths go extinct?

Yucheng Wang , Ana Prohaska , Haoran Dong , Adriana Alberti , Inger Greve Alsos et al.

Nature, 2022, 612 (7938), pp.E4-E6. ⟨10.1038/s41586-022-05417-2⟩

Article dans une revue hal-04242151v1
Deposit thumbnail

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

Jean-Marc Aury , Stefan Engelen , Benjamin Istace , Cécile Monat , Pauline Lasserre-Zuber et al.

GigaScience, 2022, 11, pp.1-18. ⟨10.1093/gigascience/giac034⟩

Article dans une revue hal-03658639v1
Deposit thumbnail

Restructuring of plankton genomic biogeography in the surface ocean under climate change

Paul Frémont , Marion Gehlen , Mathieu Vrac , Jade Leconte , Tom O. Delmont et al.

Nature Climate Change, 2022, 12 (4), pp.393-401. ⟨10.1038/s41558-022-01314-8⟩

Article dans une revue insu-03659872v1
Deposit thumbnail

A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Juan José Pierella Karlusich , Eric Pelletier , Lucie Zinger , Fabien Lombard , Adriana Zingone et al.

Molecular Ecology Resources, 2022, 23 (1), pp.16-40. ⟨10.1111/1755-0998.13592⟩

Article dans une revue hal-03559541v1
Deposit thumbnail

The genomic history and global expansion of domestic donkeys

Evelyn Todd , Laure Tonasso-Calvière , Loreleï Chauvey , Stéphanie Schiavinato , Antoine Fages et al.

Science, 2022, 377 (6611), pp.1172-1180. ⟨10.1126/science.abo3503⟩

Article dans une revue hal-03827857v1
Deposit thumbnail

Priorities for ocean microbiome research

Andre Abreu , Etienne Bourgois , Adam Gristwood , Romain Troublé , Silvia Acinas et al.

Nature Microbiology, 2022, 7 (7), pp.937-947. ⟨10.1038/s41564-022-01145-5⟩

Article dans une revue hal-03781942v1
Deposit thumbnail

Genomic adaptation of the picoeukaryote $Pelagomonas\ calceolata$ to iron-poor oceans revealed by a chromosome-scale genome sequence

Nina Guérin , Marta Ciccarella , Elisa Flamant , Paul Frémont , Sophie Mangenot et al.

Communications Biology, 2022, 5 (1), pp.983. ⟨10.1038/s42003-022-03939-z⟩

Article dans une revue cea-03791710v1
Deposit thumbnail

Author Correction: Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Yucheng Wang , Mikkel Winther Pedersen , Inger Greve Alsos , Bianca de Sanctis , Fernando Racimo et al.

Nature, 2022, 603, pp.E31-E31. ⟨10.1038/s41586-022-04628-x⟩

Article dans une revue insu-03745285v1
Deposit thumbnail

Diversity and evolution of pigment types in marine $Synechococcus$ cyanobacteria

Théophile Grébert , Laurence Garczarek , Vincent Daubin , Florian Humily , Dominique Marie et al.

Genome Biology and Evolution, 2022, 14 (4), pp.evac035. ⟨10.1093/gbe/evac035⟩

Article dans une revue hal-03641745v1
Deposit thumbnail

Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France

Benoît Clavel , Sébastien Lepetz , Loreleï Chauvey , Stéphanie Schiavinato , Laure Tonasso-Calvière et al.

Journal of Archaeological Science: Reports, 2022, 41, pp.103341. ⟨10.1016/j.jasrep.2022.103341⟩

Article dans une revue halshs-03755076v1
Deposit thumbnail

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Daniel Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont et al.

eLife, 2022, 11, pp.e78129. ⟨10.7554/eLife.78129⟩

Article dans une revue hal-02399723v2
Deposit thumbnail

Diversity and ecological footprint of Global Ocean RNA viruses

Guillermo Dominguez-Huerta , Ahmed Zayed , James Wainaina , Jiarong Guo , Funing Tian et al.

Science, 2022, 376 (6598), pp.1202-1208. ⟨10.1126/science.abn6358⟩

Article dans une revue hal-03781935v1
Deposit thumbnail

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

Ahmed Zayed , James Wainaina , Guillermo Dominguez-Huerta , Eric Pelletier , Jiarong Guo et al.

Science, 2022, 376 (6589), pp.156-162. ⟨10.1126/science.abm5847⟩

Article dans une revue hal-03781924v1
Deposit thumbnail

Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei

Adrien Tran Y. Lu , Stephanie Ruault , Claire Daguin-Thiébaut , Jade Castel , Nicolas Bierne et al.

Molecular Ecology, 2022, 31 (10), pp.2796-2813. ⟨10.1111/mec.16430⟩

Article dans une revue hal-03669635v1

Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding

Miriam Brandt , Blandine Trouche , Laure Quintric , Babett Günther , Patrick Wincker et al.

Molecular Ecology Resources, 2021, 21 (6), pp.1904-1921. ⟨10.1111/1755-0998.13398⟩

Article dans une revue hal-04203425v1
Deposit thumbnail

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

Caroline Belser , Franc-Christophe Baurens , Benjamin Noel , Guillaume Martin , Corinne Cruaud et al.

Communications Biology, 2021, 4 (1), ⟨10.1038/s42003-021-02559-3⟩

Article dans une revue hal-03352701v1
Deposit thumbnail

Environmental vulnerability of the global ocean epipelagic plankton community interactome

Samuel Chaffron , Erwan Delage , Marko Budinich , Damien Vintache , Nicolas Henry et al.

Science Advances , 2021, 7 (35), pp.eabg1921. ⟨10.1126/sciadv.abg1921⟩

Article dans une revue hal-03443359v2
Deposit thumbnail

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

Miriam I Brandt , Florence Pradillon , Blandine Trouche , Nicolas Henry , Cathy Liautard-Haag et al.

Scientific Reports, 2021, 11 (1), pp.7856. ⟨10.1038/s41598-021-86396-8⟩

Article dans une revue hal-03198097v1
Deposit thumbnail

Historical management of equine resources in France from the Iron Age to the Modern Period

Sébastien Lepetz , Benoît Clavel , Duha Alioğlu , Lorelei Chauvey , Stéphanie Schiavinato et al.

Journal of Archaeological Science: Reports, 2021, 40 (B), pp.103250. ⟨10.1016/j.jasrep.2021.103250⟩

Article dans une revue hal-03431948v1
Deposit thumbnail

Diversity and biogeography of bathyal and abyssal seafloor bacteria and archaea along a Mediterranean-Atlantic gradient

Blandine Trouche , Miriam Brandt , Caroline Belser , Covadonga Orejas , Stephane Pesant et al.

Frontiers in Microbiology, 2021, 12, pp.702016. ⟨10.3389/fmicb.2021.702016⟩

Article dans une revue hal-03589735v1
Deposit thumbnail

Population genomics of apricots unravels domestication history and adaptive events

Alexis Groppi , Shuo Liu , A. Cornille , David Tricon , Quynh Trang Bui et al.

Nature Communications, 2021, 12 (1), pp.3956. ⟨10.1038/s41467-021-24283-6⟩

Article dans une revue hal-03282504v1
Deposit thumbnail

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Laurence Garczarek , Ulysse Guyet , Hugo Doré , Gregory Farrant , Mark Hoebeke et al.

Nucleic Acids Research, 2021, 49 (D1), pp.D667-D676. ⟨10.1093/nar/gkaa958⟩

Article dans une revue hal-02988562v1
Deposit thumbnail

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⟩

Article dans une revue hal-03334117v2
Deposit thumbnail

Comparative genomics reveals new functional insights in uncultured MAST species

Aurelie Labarre , David López-Escardó , Francisco Latorre , Guy Leonard , François Bucchini et al.

The International Society of Microbiologial Ecology Journal, 2021, 15 (6), pp.1767-1781. ⟨10.1038/s41396-020-00885-8⟩

Article dans une revue hal-04288985v1
Deposit thumbnail

Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids

Pierre Clavel , Jean Dumoncel , Clio Der Sarkissian , Andaine Seguin-Orlando , Laure Calvière-Tonasso et al.

Journal of Archaeological Science, 2021, 131, pp.105383. ⟨10.1016/j.jas.2021.105383⟩

Article dans une revue hal-03413040v1
Deposit thumbnail

Male differentiation in the marine Copepod Oithona nana reveals the development of a new nervous ganglion and Lin12-Notch-repeat protein-associated proteolysis

Kevin Sugier , Romuald Laso-Jadart , Benoît Vacherie , Jos Käfer , Laurie Bertrand et al.

Biology, 2021, 10 (7), pp.657. ⟨10.3390/biology10070657⟩

Article dans une revue hal-03286235v1
Deposit thumbnail

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

Tom Delmont , Juan José Pierella Karlusich , Iva Veseli , Jessika Fuessel , A. Murat Eren et al.

The International Society of Microbiologial Ecology Journal, 2021, 16 (4), pp.927-936. ⟨10.1038/s41396-021-01135-1⟩

Article dans une revue hal-03480646v1
Deposit thumbnail

Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

Marta Royo-Llonch , Pablo Sánchez , Clara Ruiz-González , Guillem Salazar , Carlos Pedrós-Alió et al.

Nature Microbiology, 2021, 6 (12), pp.1561-1574. ⟨10.1038/s41564-021-00979-9⟩

Article dans une revue hal-03781908v1
Deposit thumbnail

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients.

Clemens Schauberger , Ronnie N. Glud , Bela Hausmann , Blandine Trouche , Lois Maignien et al.

The International Society of Microbiologial Ecology Journal, 2021, 15, pp.3455-3467. ⟨10.1038/s41396-021-01021-w⟩

Article dans une revue hal-03415694v1

Author Correction: A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Quentin Carradec , Julie Poulain , Emilie Boissin , Benjamin Hume , Christian Voolstra et al.

Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-81544-6⟩

Article dans une revue hal-03368783v1
Deposit thumbnail

The origins and spread of domestic horses from the Western Eurasian steppes

Pablo Librado , Naveed Khan , Antoine Fages , Mariya A Kusliy , Tomasz Suchan et al.

Nature, 2021, 598 (7882), pp.634-640. ⟨10.1038/s41586-021-04018-9⟩

Article dans une revue hal-03425363v1
Deposit thumbnail

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

Benjamin Istace , Caroline Belser , Cyril Falentin , Karine Labadie , Franz Boideau et al.

Biology, 2021, 10 (8), ⟨10.3390/biology10080732⟩

Article dans une revue hal-03318024v1
Deposit thumbnail

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Yucheng Wang , Mikkel Winther Pedersen , Inger Greve Alsos , Bianca de Sanctis , Fernando Racimo et al.

Nature, 2021, 598 (7882), pp.634-640. ⟨10.1038/s41586-021-04016-x⟩

Article dans une revue hal-03431961v1
Deposit thumbnail

Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Elise J Gay , Jessica L Soyer , Nicolas Lapalu , Juliette Linglin , Isabelle Fudal et al.

BMC Biology, 2021, 19 (1), pp.e041118. ⟨10.1186/s12915-021-00989-3⟩

Article dans une revue hal-03190704v1
Deposit thumbnail

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Sarah Farhat , Phuong Le , Ehsan Kayal , Benjamin Noel , Estelle Bigeard et al.

BMC Biology, 2021, 19 (1), ⟨10.1186/s12915-020-00927-9⟩

Article dans une revue hal-03114990v1
Deposit thumbnail

BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons

Christophe Djemiel , Samuel Dequiedt , Battle Karimi , Aurélien Cottin , Thibault Girier et al.

BMC Bioinformatics, 2020, 21 (1), pp.1-21. ⟨10.1186/s12859-020-03829-3⟩

Article dans une revue hal-03014150v1
Deposit thumbnail

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⟩

Article dans une revue hal-02999798v1
Deposit thumbnail

Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

Shinya Sato , Deepak Nanjappa , Richard G Dorrell , Fabio Rocha Jimenez Vieira , Elena Kazamia et al.

Scientific Reports, 2020, 10 (1), pp.9449. ⟨10.1038/s41598-020-65941-x⟩

Article dans une revue inserm-02886223v1

Biogeography of soil microbial habitats across France

Battle Karimi , Jean Villerd , Samuel Dequiedt , Sébastien Terrat , Nicolas Chemidlin Prévost-Bouré et al.

Global Ecology and Biogeography, 2020, 29 (8), pp.1399-1411. ⟨10.1111/geb.13118⟩

Article dans une revue hal-03014310v1
Deposit thumbnail

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⟩

Article dans une revue hal-02573621v1
Deposit thumbnail

Genome Resolved Biogeography of Mamiellales

Jade Leconte , L. Felipe Felipe Benites , Thomas Vannier , Patrick Wincker , Gwenael Piganeau et al.

Genes, 2020, 11 (1), pp.66. ⟨10.3390/genes11010066⟩

Article dans une revue hal-02505108v1

Tara Oceans: towards global ocean ecosystems biology

Shinichi Sunagawa , Silvia Acinas , Peer Bork , Chris Bowler , Silvia Acinas et al.

Nature Reviews Microbiology, 2020, 18 (8), pp.428-445. ⟨10.1038/s41579-020-0364-5⟩

Article dans une revue hal-04394809v1
Deposit thumbnail

Tara Pacific Expedition’s Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans: Overview and Preliminary Results

J. Flores , G. Bourdin , O. Altaratz , M. Trainic , N. Lang-Yona et al.

Bulletin of the American Meteorological Society, 2020, 101 (5), pp.E536-E554. ⟨10.1175/BAMS-D-18-0224.1⟩

Article dans une revue hal-02967981v1
Deposit thumbnail

Le RMQS au service de l'écologie microbienne des sols français

Samuel S. Dequiedt , Battle Karimi , Nicolas Chemidlin Prévost-Bouré , Sébastien Terrat , Walid Horrigue et al.

Étude et Gestion des Sols, 2020, 27 (1), pp.51-71

Article dans une revue hal-02540019v1
Deposit thumbnail

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Hugo Doré , Gregory Farrant , Ulysse Guyet , Julie Haguait , Florian Humily et al.

Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.567431⟩

Article dans une revue hal-02938656v1
Deposit thumbnail

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Quentin Carradec , Julie Poulain , Emilie Boissin , Benjamin Hume , Christian Voolstra et al.

Scientific Reports, 2020, 10 (1), pp.15893. ⟨10.1038/s41598-020-72589-0⟩

Article dans une revue hal-02964556v1
Deposit thumbnail

Long-read assembly of the Brassica napus reference genome Darmor-bzh

Mathieu Rousseau-Gueutin , Caroline Belser , Corinne Da silva , Gautier Richard , Benjamin Istace et al.

GigaScience, 2020, 9 (12), pp.giaa137. ⟨10.1093/gigascience/giaa137⟩

Article dans une revue (data paper) hal-03283975v1
Deposit thumbnail

An assessment of environmental metabarcoding protocols aiming at favoring contemporary biodiversity in inventories of deep-sea communities

Miriam Brandt , Blandine Trouche , Nicolas Henry , Cathy Liautard-Haag , Lois Maignien et al.

Frontiers in Marine Science, 2020, 7, pp.234. ⟨10.3389/fmars.2020.00234⟩

Article dans une revue hal-03410860v1
Deposit thumbnail

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⟩

Article dans une revue hal-02974168v1

A gene graveyard in the genome of the fungus Podospora comata

Philippe Silar , Jean-Marc Dauget , Valérie Gautier , Pierre Grognet , Michelle Chablat et al.

Molecular Genetics and Genomics, 2019, 294 (1), pp.177--190. ⟨10.1007/s00438-018-1497-3⟩

Article dans une revue hal-02173830v1
Deposit thumbnail

Marine DNA viral macro- and microdiversity from Pole to Pole

Ann Gregory , Ahmed Zayed , Nádia Conceição-Neto , Ben Temperton , Ben Bolduc et al.

Cell, 2019, 177 (5), pp.1109-1123.e14. ⟨10.1016/j.cell.2019.03.040⟩

Article dans une revue hal-02387010v1
Deposit thumbnail

Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)

Gabriel Gorsky , Guillaume Bourdin , Fabien Lombard , Maria Luiza Pedrotti , Samuel Audrain et al.

Frontiers in Marine Science, 2019, 6, pp.650. ⟨10.3389/fmars.2019.00750⟩

Article dans une revue hal-02407578v1
Deposit thumbnail

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean

Serge Planes , Denis Allemand , Sylvain Agostini , Bernard Banaigs , Emilie Boissin et al.

PLoS Biology, 2019, 17 (9), pp.e3000483. ⟨10.1371/journal.pbio.3000483⟩

Article dans une revue hal-02402685v1
Deposit thumbnail

Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Julie Ferreira de Carvalho , Jérémy Lucas , Gwenaëlle Deniot , Cyril Falentin , Olivier Filangi et al.

The Plant Journal, 2019, 98 (3), pp.434-447. ⟨10.1111/tpj.14228⟩

Article dans une revue hal-02019346v1

A reference genome for pea provides insight into legume genome evolution

Jonathan J. Kreplak , Mohammed-Amin Madoui , Petr Cápal , Petr Novak , Karine Labadie et al.

Nature Genetics, 2019, 51 (9), pp.1411-1422. ⟨10.1038/s41588-019-0480-1⟩

Article dans une revue hal-02278272v1
Deposit thumbnail

Transposition favors the generation of large effect mutations that may facilitate rapid adaption

Leandro Quadrana , Mathilde Etcheverry , Arthur Gilly , Erwann Caillieux , Mohammed-Amin Madoui et al.

Nature Communications, 2019, 10, ⟨10.1038/s41467-019-11385-5⟩

Article dans une revue hal-02398702v1
Deposit thumbnail

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⟩

Article dans une revue hal-02184019v1
Deposit thumbnail

Global Trends in Marine Plankton Diversity across Kingdoms of Life

Federico Ibarbalz , Nicolas Henry , Manoela Brandão , Severine Martini , Greta Busseni et al.

Cell, 2019, 179 (5), pp.1084-1097.e21. ⟨10.1016/j.cell.2019.10.008⟩

Article dans une revue hal-03094778v1
Deposit thumbnail

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Luigi Caputi , Quentin Carradec , Damien Eveillard , Amos Kirilovsky , Éric Pelletier et al.

Global Biogeochemical Cycles, 2019, 33 (3), pp.391-419. ⟨10.1029/2018GB006022⟩

Article dans une revue hal-02999805v1
Deposit thumbnail

The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

Lucas R Leclère , Coralie Horin , Sandra Chevalier , Pascal Lapébie , Philippe Dru et al.

Nature Ecology & Evolution, 2019, 3 (5), pp.801-810. ⟨10.1038/s41559-019-0833-2⟩

Article dans une revue hal-02115215v1
Deposit thumbnail

Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity

Battle Karimi , Samuel S. Dequiedt , Sébastien Terrat , Claudy C. Jolivet , Dominique D. Arrouays et al.

Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-40422-y⟩

Article dans une revue hal-02093081v1
Deposit thumbnail

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems

M. E Sieracki , N. J Poulton , O. Jaillon , P. Wincker , Colomban de Vargas et al.

Scientific Reports, 2019, 9, pp.6025. ⟨10.1038/s41598-019-42487-1⟩

Article dans une revue hal-02113815v1

A thousand plants' phylogeny

Patrick Wincker

Nature Plants, 2019, 5 (11), pp.1106-1107. ⟨10.1038/s41477-019-0555-0⟩

Article dans une revue cea-04309470v1

Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability

Paolo Sordino , Salvatore d'Aniello , Eric Pelletier , Patrick Wincker , Valeria Nittoli et al.

Molecular Ecology, 2019, 29 (2), pp.292-307. ⟨10.1111/mec.15321⟩

Article dans une revue hal-03955981v1

Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps

Caroline Belser , Benjamin Istace , Erwan Denis , Marion Dubarry , Franc-Christophe Baurens et al.

Nature Plants, 2018, 4 (11), pp.879-887. ⟨10.1038/s41477-018-0289-4⟩

Article dans une revue hal-01977046v1
Deposit thumbnail

Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy

Kevin Sugier , Benoit Vacherie , Astrid Cornils , Patrick Wincker , Jean-Louis Jamet et al.

PeerJ, 2018, 6, pp.e4685. ⟨10.7717/peerj.4685⟩

Article dans une revue hal-01979866v1
Deposit thumbnail

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region

Benjamin C C Hume , Maren Ziegler , Julie Poulain , Xavier Pochon , Sarah Romac et al.

PeerJ, 2018, 6, pp.e4816. ⟨10.7717/peerj.4816⟩

Article dans une revue hal-01822910v1

Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean

Johan Decelle , Quentin Carradec , Xavier Pochon , Nicolas Henry , Sarah Romac et al.

Current Biology, 2018, 28 (22), pp.3625-3633.e3. ⟨10.1016/j.cub.2018.09.024⟩

Article dans une revue hal-02194113v1
Deposit thumbnail

Oak genome reveals facets of long lifespan

Christophe Plomion , Jean-Marc Aury , Joelle Amselem , Thibault Leroy , Florent Murat et al.

Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩

Article dans une revue hal-01820559v1
Deposit thumbnail

A global ocean atlas of eukaryotic genes

Quentin Carradec , Eric Pelletier , Corinne da Silva , Adriana A. Alberti , Yoann Seeleuthner et al.

Nature Communications, 2018, 9 (1), pp.373. ⟨10.1038/s41467-017-02342-1⟩

Article dans une revue cea-01874711v1
Deposit thumbnail

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

Fabien Dutreux , Corinne da Silva , Léo d'Agata , Arnaud Couloux , Elise Gay et al.

Scientific Data , 2018, 5 (180235), 11 p. ⟨10.1038/sdata.2018.235⟩

Article dans une revue (data paper) hal-02621276v1

Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network.

Arnaud Meng , Erwan Corre , Ian Probert , Andres Gutierrez-Rodriguez , Raffaele Siano et al.

Molecular Ecology, 2018, 27 (10), pp.2365-2380. ⟨10.1111/mec.14579⟩

Article dans une revue hal-02879300v1

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes

Philippe Cubry , Christine Tranchant-Dubreuil , Anne-Céline Thuillet , Cécile Monat , Marie-Noelle Ndjiondjop et al.

Current Biology, 2018, 28 (14), pp.2274-2282. e6. ⟨10.1016/j.cub.2018.05.066⟩

Article dans une revue hal-03958213v1
Deposit thumbnail

Biogeography of soil bacteria and archaea across France

Battle Karimi , Sébastien Terrat , Samuel S. Dequiedt , Nicolas Saby , Walid Horrigue et al.

Science Advances , 2018, 4 (7), pp.eaat1808. ⟨10.1126/sciadv.aat1808⟩

Article dans une revue hal-01843961v1

Extracting high molecular weight genomic DNA from Saccharomyces cerevisiae

Erwan Denis , Sophie Sanchez , Barbara Mairey , Odette Beluche , Corinne Cruaud et al.

Protocol Exchange, 2018, ⟨10.1038/protex.2018.076⟩

Article dans une revue hal-04330988v1
Deposit thumbnail

Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation

Elodie Gaulin , Michiel Pel , Laurent Camborde , Hélène San Clemente , Sarah Courbier et al.

BMC Biology, 2018, 16 (1), ⟨10.1186/s12915-018-0508-5⟩

Article dans une revue hal-01891875v1
Deposit thumbnail

Amphioxus functional genomics and the origins of vertebrate gene regulation

Ferdinand Marletaz , Panos N. Firbas , Ignacio Maeso , Juan J. Tena , Ozren Bogdanovic et al.

Nature, 2018, 564 (7734), pp.64-70. ⟨10.1038/s41586-018-0734-6⟩

Article dans une revue hal-02000511v1

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Rudi Appels , Kellye Eversole , Nils Stein , Catherine Feuillet , Beat Keller et al.

Science, 2018, 361 (6403), ⟨10.1126/science.aar7191⟩

Article dans une revue hal-04331004v1
Deposit thumbnail

Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle

Claude Murat , Thibaut Payen , Benjamin Noël , Alan Kuo , Emmanuelle Morin et al.

Nature Ecology & Evolution, 2018, 2 (12), pp.1956-1965. ⟨10.1038/s41559-018-0710-4⟩

Article dans une revue hal-02094494v1
Deposit thumbnail

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria

Théophile Grébert , Hugo Doré , Frédéric Partensky , Gregory Farrant , Emmanuel Boss et al.

Proceedings of the National Academy of Sciences of the United States of America, 2018, 115 (9), pp.E2010-E2019. ⟨10.1073/pnas.1717069115⟩

Article dans une revue hal-01772758v1
Deposit thumbnail

Convergent genomic signatures of domestication in sheep and goats

Florian Alberto , Frédéric Boyer , Pablo Orozco-Terwengel , Ian Streeter , Bertrand Servin et al.

Nature Communications, 2018, 9 (1), pp.813. ⟨10.1038/s41467-018-03206-y⟩

Article dans une revue cea-01875703v1
Deposit thumbnail

A de novo approach to disentangle partner identity and function in holobiont systems

Arnaud Meng , Camille Marchet , Erwan Corre , Pierre Peterlongo , Adriana A. Alberti et al.

Microbiome, 2018, pp.1-35. ⟨10.1186/s40168-018-0481-9⟩

Article dans une revue hal-01643153v2

Status of coral reefs of Upolu (Independent State of Samoa) in the South West Pacific and recommendations to promote resilience and recovery of coastal ecosystems

Maren Ziegler , Gaëlle Quéré , Jean-François Ghiglione , Guillaume Iwankow , Valérie Barbe et al.

Marine Pollution Bulletin, 2018, 129 (1), pp.392-398. ⟨10.1016/j.marpolbul.2018.02.044⟩

Article dans une revue hal-01960450v1
Deposit thumbnail

Gene flow contributes to diversification of the major fungal pathogen $Candida\ albicans$

Jeanne Ropars , Corinne Maufrais , Dorothée Diogo , Marina Marcet-Houben , Aurélie Perin et al.

Nature Communications, 2018, 9 (1), pp.2253. ⟨10.1038/s41467-018-04787-4⟩

Article dans une revue pasteur-01815656v1
Deposit thumbnail

Discovering Millions of Plankton Genomic Markers from the Atlantic Ocean and the Mediterranean Sea

Majda Arif , Jérémy Gauthier , Kevin Sugier , Daniele Iudicone , Olivier Jaillon et al.

Molecular Ecology Resources, 2018, pp.1-24. ⟨10.1111/1755-0998.12985⟩

Article dans une revue hal-01987200v1
Deposit thumbnail

Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Amoebophrya Strains

Sarah Farhat , Isabelle Florent , Benjamin Noël , Ehsan Kayal , Corinne da Silva et al.

Frontiers in Microbiology, 2018, 9, pp.2251. ⟨10.3389/fmicb.2018.02251⟩

Article dans une revue hal-02126891v1
Deposit thumbnail

Genome evolution across 1,011 $Saccharomyces\ cerevisiae$ isolates

Jackson Peter , Matteo de Chiara , Anne Friedrich , Jia-Xing Yue , David Pflieger et al.

Nature, 2018, 556 (7701), pp.339 - 344. ⟨10.1038/s41586-018-0030-5⟩

Article dans une revue cea-01872910v1
Deposit thumbnail

The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond , Jerome Gouzy , Jérémy Just , Hélène Badouin , Marion Verdenaud et al.

Nature Genetics, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩

Article dans une revue hal-01798003v1
Deposit thumbnail

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Yoann Seeleuthner , Samuel Mondy , Vincent Lombard , Quentin Carradec , Eric Pelletier et al.

Nature Communications, 2018, 9, pp.310. ⟨10.1038/s41467-017-02235-3⟩

Article dans une revue hal-01771839v1
Deposit thumbnail

Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination

Sheng Sun , Vikas Yadav , R. Blake Billmyre , Christina A. Cuomo , Minou Nowrousian et al.

PLoS Biology, 2017, 15 (8), pp.e2002527. ⟨10.1371/journal.pbio.2002527⟩

Article dans une revue cea-04320340v1
Deposit thumbnail

High-quality $de\ novo$ genome assembly of the $Dekkera\ bruxellensis$ yeast using Nanopore MinION sequencing

Téo Fournier , Jean-Sébastien Gounot , Kelle Freel , Corinne Cruaud , Arnaud Lemainque et al.

G3, 2017, 7 (10), pp.3243-3250. ⟨10.1534/g3.117.300128⟩

Article dans une revue cea-04315763v1
Deposit thumbnail

$de\ novo$ assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

Benjamin Istace , Anne Friedrich , Léo d'Agata , Sébastien Faye , Emilie Payen et al.

Gigascience, 2017, 6 (2), pp.giw018. ⟨10.1093/gigascience/giw018⟩

Article dans une revue cea-04315750v1

A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

Roberto Arrigoni , Benoît Vacherie , Francesca Benzoni , Fabrizio Stefani , Eric Karsenti et al.

Molecular Ecology Resources, 2017, 17 (5), pp.1054-1071. ⟨10.1111/1755-0998.12640⟩

Article dans une revue hal-03971503v1

Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis

Petra Spirhanzlova , Sophie Dhorne-Pollet , J.S. Fellah , C. da Silva , T. Tlapakova et al.

Developmental Biology, 2017, 426 (2), pp.255-260. ⟨10.1016/j.ydbio.2016.05.015⟩

Article dans une revue hal-01607555v1
Deposit thumbnail

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Anaïs Gouin , Anthony Bretaudeau , Kiwoong Nam , Sylvie Gimenez , Jean-Marc Aury et al.

Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩

Article dans une revue hal-01633879v1

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona

Mohammed-Amin Madoui , Julie Poulain , Kevin Sugier , Marc Wessner , Benjamin Noel et al.

Molecular Ecology, 2017, 26 (17), pp.4467 - 4482. ⟨10.1111/mec.14214⟩

Article dans une revue hal-01621969v1
Deposit thumbnail

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Adriana A. Alberti , Julie Poulain , Stefan Engelen , Karine Labadie , Sarah Romac et al.

Scientific Data , 2017, 4, ⟨10.1038/sdata.2017.93⟩

Article dans une revue hal-01771844v1
Deposit thumbnail

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes

Romain Blanc-Mathieu , Laetitia Zurletto , Jean-Marc Aury , Martine da Rocha , Jerome Gouzy et al.

PLoS Genetics, 2017, 13 (6), pp.e1006777. ⟨10.1371/journal.pgen.1006777⟩

Article dans une revue hal-01602779v1
Deposit thumbnail

Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells

Jean-François Mangot , Ramiro Logares , Pablo Sánchez , Fran Latorre , Yoann 6 Seeleuthner et al.

Scientific Reports, 2017, 7, pp.41498. ⟨10.1038/srep41498⟩

Article dans une revue hal-01466618v1
Deposit thumbnail

Mapping and predictive variations of soil bacterial richness across France

Sébastien Terrat , Walid Horrigue , Samuel Dequietd , Nicolas Saby , Mélanie M. Lelievre et al.

PLoS ONE, 2017, 12 (0190128), pp.1-19. ⟨10.1371/journal.pone.0186766⟩

Article dans une revue hal-01843156v1
Deposit thumbnail

Benthic protists: the under-charted majority

Dominik Forster , Micah Dunthorn , Fréderic Mahé , John R. Dolan , Stéphane Audic et al.

FEMS Microbiology Ecology, 2016, 92 (8), pp.fiw120. ⟨10.1093/femsec/fiw120⟩

Article dans une revue hal-01383722v1
Deposit thumbnail

Plankton networks driving carbon export in the oligotrophic ocean

Lionel Guidi , Samuel Chaffron , Lucie Bittner , Damien Eveillard , Abdelhalim Larhlimi et al.

Nature, 2016, 532, pp.465-470. ⟨10.1038/nature16942⟩

Article dans une revue hal-01275276v1
Deposit thumbnail

Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae)

Julie Boutte , Julie Ferreira de Carvalho , Mathieu Rousseau-Gueutin , Julie Poulain , Corinne da Silva et al.

Genome Biology and Evolution, 2016, 8 (9), pp.3030-3044. ⟨10.1093/gbe/evw209⟩

Article dans une revue hal-01412081v1
Deposit thumbnail

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 et al.

Nature Communications, 2016, 7, pp.11071. ⟨10.1038/ncomms11071⟩

Article dans une revue hal-01295207v1

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

Noan Le Bescot , Frédéric Mahé , Stéphane Audic , Céline Dimier , Marie-Jose Garet et al.

Environmental Microbiology, 2016, 18 (2), pp.609-626. ⟨10.1111/1462-2920.13039⟩

Article dans une revue istex hal-01305586v1

Insights into global diatom distribution and diversity in the world's ocean

Shruti Malviya , Eleonora Scalco , Stephane Audic , Flora Vincenta , Alaguraj Veluchamy et al.

Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (11), pp.E1516-E1525. ⟨10.1073/pnas.1509523113⟩

Article dans une revue hal-01545320v1
Deposit thumbnail

Survey of the green picoalga Bathycoccus genomes in the global ocean

Thomas Vannier , Jade Leconte , Yoann Seeleuthner , Samuel Mondy , Eric Pelletier et al.

Scientific Reports, 2016, 6, pp.37900. ⟨10.1038/srep37900⟩

Article dans une revue hal-01410203v1
Deposit thumbnail

Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells

Christo Kole , Naomi Berdugo , Corinne da Silva , Najate Aït-Ali , Géraldine Millet-Puel et al.

PLoS ONE, 2016, 11 (3), pp.e0150758. ⟨10.1371/journal.pone.0150758⟩

Article dans une revue hal-01292283v1
Deposit thumbnail

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Simon Roux , Jennifer R. Brum , Bas E. Dutilh , Shinichi Sunagawa , Melissa B. Duhaime et al.

Nature, 2016, 537 (7622), pp.689-693. ⟨10.1038/nature19366⟩

Article dans une revue hal-01376822v1
Deposit thumbnail

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria

Gregory K. Farrant , Hugo Doré , Francisco M. Cornejo-Castillo , Frédéric Partensky , Morgane Ratin et al.

Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (24), pp.E3365-E3374. ⟨10.1073/pnas.1524865113⟩

Article dans une revue hal-01331214v1

Extreme Diversity of Diplonemid Eukaryotes in the Ocean

Olga Flegontova , Pavel Flegontov , Shruti Malviya , Stephane Audic , Patrick Wincker et al.

Current Biology, 2016, 26 (22), pp.3060-3065. ⟨10.1016/j.cub.2016.09.031⟩

Article dans une revue cea-04541791v1
Deposit thumbnail

Genome assembly using Nanopore-guided long and error-free DNA reads

Mohammed-Amin Madoui , Stefan Engelen , Corinne Cruaud , Caroline Belser , Laurie Bertrand et al.

BMC Genomics, 2015, 16 (1), pp.327. ⟨10.1186/s12864-015-1519-z⟩

Article dans une revue hal-04361027v1

Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides.

Pierre Czernic , Djamel Gully , Fabienne Cartieaux , Lionel Moulin , Ibtissem Guefrachi et al.

Plant Physiology, 2015, 169 (2), pp.1254-65. ⟨10.1104/pp.15.00584⟩

Article dans une revue hal-01430710v1
Deposit thumbnail

Eukaryotic plankton diversity in the sunlit ocean

Noan Le Bescot , Ian Probert , Margaux Carmichael , Julie Poulain , Sarah Romac et al.

Science, 2015, 348 (6237), pp.1261605. ⟨10.1126/science.1261605⟩

Article dans une revue hal-01253979v1

Environmental characteristics of Agulhas rings affect interocean plankton transport

Emilie Villar , Gregory Farrant , Michael J. Follows , Laurence Garczarek , Sabrina Speich et al.

Science, 2015, 348 (6237), pp.1261447 - 1261447. ⟨10.1126/science.1261447⟩

Article dans une revue hal-01893637v1
Deposit thumbnail

Open science resources for the discovery and analysis of Tara Oceans data

Stéphane Pesant , Fabrice Not , Marc Picheral , Stefanie Kandels-Lewis , Noan Le Bescot et al.

Scientific Data , 2015, 2, pp.150023. ⟨10.1038/sdata.2015.23⟩

Article dans une revue hal-01253984v1
Deposit thumbnail

Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome

Lise Pingault , Frédéric Choulet , Adriana A. Alberti , Natasha Marie Glover , Patrick Wincker et al.

Genome Biology, 2015, 16 (1), n.p. ⟨10.1186/s13059-015-0601-9⟩

Article dans une revue hal-02635440v1
Deposit thumbnail

Structure and function of the global ocean microbiome

Shinichi Sunagawa , Luis Pedro Coelho , Samuel Chaffron , Jens Roat Kultima , Karine Labadie et al.

Science, 2015, 348 (6237), pp.1261359. ⟨10.1126/science.1261359⟩

Article dans une revue hal-01233742v1
Deposit thumbnail

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

Magali Lescot , Pascal Hingamp , Kenji K Kojima , Emilie Villar , Sarah Romac et 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

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

Christophe Plomion , Jean-Marc Aury , Joëlle Amselem , Tina Alaeitabar , Valérie Barbe et al.

Molecular Ecology Resources, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩

Article dans une revue istex hal-01579667v1
Deposit thumbnail

Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

Peter von Dassow , Uwe John , Hiroyuki Ogata , Ian Probert , El Mahdi Bendif et al.

The International Society of Microbiologial Ecology Journal, 2015, 9 (6), pp.1365-1377. ⟨10.1038/ismej.2014.221⟩

Article dans une revue hal-01245155v1
Deposit thumbnail

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 et al.

Environmental Microbiology Reports, 2015, 7 (6), pp.979-989. ⟨10.1111/1758-2229.12345⟩

Article dans une revue hal-01246259v1
Deposit thumbnail

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

Guillaume Morel , Lieven Sterck , Dominique Swennen , Marina Marcet-Houben , Djamila Onesime et al.

Scientific Reports, 2015, 5, ⟨10.1038/srep11571⟩

Article dans une revue hal-01201920v1
Deposit thumbnail

Patterns and ecological drivers of ocean viral communities

Jennifer Brum , J Cesar Ignacio-Espinoza , Simon Roux , Guilhem Doulcier , Silvia G. Acinas et al.

Science, 2015, 348 (6237), pp.1261498. ⟨10.1126/science.1261498⟩

Article dans une revue hal-01768331v1

Determinants of community structure in the global plankton interactome

Gipsi Lima-Mendez , Karoline Faust , Nicolas Henry , Johan Decelle , Sébastien Colin et al.

Science, 2015, 348 (6237), pp.1262073. ⟨10.1126/science.1262073⟩

Article dans une revue hal-01234200v1

Full-length <em>de novo</em> assembly of RNA-seq data in pea (<em>Pisum sativum</em> L.) provides a gene expression atlas and gives insights into root nodulation in this species

Susete Alves Carvalho , Gregoire G. Aubert , Sebastien Carrere , Corinne Cruaud , Anne-Lise Brochot et al.

The Plant Journal, 2015, 84 (1), pp.1-19. ⟨10.1111/tpj.12967⟩

Article dans une revue (article de synthèse) hal-02631162v1

Tara Oceans studies plankton at PLANETARY SCALE

P. Bork , C. Bowler , Colomban de Vargas , G. Gorsky , E. Karsenti et al.

Science, 2015, 348 (6237), pp.873. ⟨10.1126/science.aac5605⟩

Article dans une revue hal-01258211v1

Towards the Rose Genome Sequence and Its Use in Research and Breeding

Fabrice Foucher , Laurence Hibrand-Saint Oyant , Latifa Hamama , Soulaiman Sakr , H. Nybom et al.

Acta Horticulturae, 2015, 1064, pp.167-175. ⟨10.17660/ActaHortic.2015.1064.19⟩

Article dans une revue hal-02630890v1
Deposit thumbnail

Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

Eric Fontanillas , Michael E Hood , Hélène Badouin , Elsa Petit , Valérie Barbe et al.

Molecular Biology and Evolution, 2015, 32 (4), pp.928-943. ⟨10.1093/molbev/msu396⟩

Article dans une revue hal-01302682v1
Deposit thumbnail

Transcriptome analyses to investigate symbiotic relationships between marine protists

Sergio Balzano , Erwan Corre , Johan Decelle , Roberto Sierra , Patrick Wincker et al.

Frontiers in Microbiology, 2015, 6, pp.98. ⟨10.3389/fmicb.2015.00098⟩

Article dans une revue hal-01143962v1
Deposit thumbnail

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.

Gotthard Kunze , Claude Gaillardin , Małgorzata Czernicka , Pascal Durrens , Tiphaine Martin et al.

Biotechnology for Biofuels, 2014, 7 (1), pp.66. ⟨10.1186/1754-6834-7-66⟩

Article dans une revue pasteur-00988609v1
Deposit thumbnail

The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome.

Damien Formey , Erika Sallet , Christine Lelandais-Brière , Cécile Ben , Pilar Bustos-Sanmamed et al.

Genome Biology, 2014, 15 (9), pp.457. ⟨10.1186/s13059-014-0457-4⟩

Article dans une revue hal-02635888v1
Deposit thumbnail

TE-Tracker: systematic identification of transposition events through whole-genome resequencing

Arthur Gilly , Mathilde Etcheverry , Mohammed-Amin Madoui , Julie Guy , Leandro Quadrana et al.

BMC Bioinformatics, 2014, 15 (1), ⟨10.1186/s12859-014-0377-z⟩

Article dans une revue hal-03170927v1
Deposit thumbnail

Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus

Florian Humily , Gregory K. Farrant , Dominique Marie , Frédéric Partensky , Sophie Mazard et al.

FEMS Microbiology Ecology, 2014, 88 (2), pp.231-249. ⟨10.1111/1574-6941.12285⟩

Article dans une revue hal-01100993v1
Deposit thumbnail

Structural and Functional Partitioning of Bread Wheat Chromosome 3B

Frédéric Choulet , Adriana A. Alberti , Sébastien Theil , Natasha Marie Glover , Valérie Barbe et al.

Science, 2014, 345 (6194), ⟨10.1126/science.1249721⟩

Article dans une revue hal-02638189v1

Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis

S. Ravel , P. Wincker , A. Benkahla , International Glossina Genome Initiative (iggi)

Science, 2014, 344 (6182), pp.380-386. ⟨10.1126/science.1249656⟩

Article dans une revue pasteur-02024895v1
Deposit thumbnail

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

G Albert Wu , Simon Prochnik , Jerry Jenkins , Jérôme Salse , Uffe Hellsten et al.

Nature Biotechnology, 2014, 32 (7), pp.656-662. ⟨10.1038/nbt.2906⟩

Article dans une revue hal-02285484v1
Deposit thumbnail

Patterns of Rare and Abundant Marine Microbial Eukaryotes

Ramiro Logares , Stéphane Audic , David Bass , Lucie Bittner , Christophe Boutte et al.

Current Biology, 2014, 24 (8), pp.813-821. ⟨10.1016/j.cub.2014.02.050⟩

Article dans une revue hal-01149637v1
Deposit thumbnail

Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates

Benoit G. Godard , Marion Coolen , Sophie Le Panse , Aurélie Gombault , Susana Ferreiro-Galve et al.

Biology Open, 2014, 3, pp.1098-1107. ⟨10.1242/bio.20148037⟩

Article dans une revue hal-01087670v1
Deposit thumbnail

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

Betina M Porcel , France Denoeud , Fred Opperdoes , Benjamin Noel , Mohammed-Amine Madoui et al.

PLoS Genetics, 2014, 10 (2), pp.e1004007. ⟨10.1371/journal.pgen.1004007⟩

Article dans une revue hal-04402160v1

Genome interplay in the grain transcriptome of hexaploid bread wheat

Matthias Pfeifer , Karl G. Kugler , Simen R. Sandve , Bujie Zhan , Heidi Rudi et al.

Science, 2014, 345 (6194), pp.287-287. ⟨10.1126/science.1250091⟩

Article dans une revue hal-02889033v1

Mapping the epigenetic basis of complex traits

Sandra Cortijo , Rene Wardenaar , Maria Colomé-Tatché , Arthur Gilly , Mathilde Etcheverry et al.

Science, 2014, 343 (6175), pp.1145-1148. ⟨10.1126/science.1248127⟩

Article dans une revue hal-01193838v1

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Boulos Chalhoub , France Denoeud , Shengyi Liu , Isobel A. P. Parkin , Haibao Tang et al.

Science, 2014, 345 (6199), pp.950-953. ⟨10.1126/science.1253435⟩

Article dans une revue hal-01208705v1

Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis in Podospora anserina

Pierre Grognet , Frédérique Bidard , Claire Kuchly , Laetitia Chan Ho Tong , Evelyne Coppin et al.

Genetics, 2014, 197 (1), pp.421-432. ⟨10.1534/genetics.113.159988⟩

Article dans une revue hal-03153569v1

Ancient hybridizations among the ancestral genomes of bread wheat

T. Marcussen , S. Sandve , L. Heier , M. Spannagl , M. Pfeifer et al.

Science, 2014, 345 (6194), pp.1250092-1250092. ⟨10.1126/science.1250092⟩

Article dans une revue hal-02889053v1
Deposit thumbnail

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 et al.

Environmental Microbiology, 2014, 16 (9, SI), pp.2659-2671. ⟨10.1111/1462-2920.12250⟩

Article dans une revue istex hal-01258219v1
Deposit thumbnail

Organization and evolution of transposable elements along the bread wheat chromosome 3B

Josquin Daron , Natasha Glover , Lise Pingault , Sébastien Theil , Véronique Jamilloux et al.

Genome Biology, 2014, 15 (12), pp.1-15. ⟨10.1186/s13059-014-0546-4⟩

Article dans une revue hal-02630315v1
Deposit thumbnail

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

Adriana A. Alberti , Caroline Belser , Stefan Engelen , Laurie Bertrand , Celine Orvain et al.

BMC Genomics, 2014, 15, pp.912. ⟨10.1186/1471-2164-15-912⟩

Article dans une revue hal-02503091v1
Deposit thumbnail

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

France Denoeud , Lorenzo Carretero-Paulet , Alexis Dereeper , Gaëtan Droc , Romain Guyot et al.

Science, 2014, 345 (6201), pp.1181-1184. ⟨10.1126/science.1255274⟩

Article dans une revue hal-02641562v1
Deposit thumbnail

Fifty thousand years of Arctic vegetation and megafaunal diet

Eske Willerslev , John Davison , Mari Moora , Martin Zobel , Eric Coissac et al.

Nature, 2014, 506 (7486), pp.47-51. ⟨10.1038/nature12921⟩

Article dans une revue hal-02640450v1
Deposit thumbnail

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.

Camille Berthelot , Frédéric Brunet , Domitille Chalopin , Amélie Juanchich , Maria Bernard et al.

Nature Communications, 2014, 5, pp.1-10. ⟨10.1038/ncomms4657⟩

Article dans une revue hal-01193812v1

Hyposoter didymator uses a combination of passive and active strategies to escape from the Spodoptera frugiperda cellular immune response

Tristan Doremus , Véronique Jouan , Serge Urbach , Francois Cousserans , Patrick Wincker et al.

Journal of Insect Physiology, 2013, 59 (4), pp.500-508. ⟨10.1016/j.jinsphys.2013.02.010⟩

Article dans une revue istex hal-01837247v1
Deposit thumbnail

Sequencing platform and library preparation choices impact viral metagenomes

Sergei A Solonenko , J César Ignacio-Espinoza , Adriana Alberti , Corinne Cruaud , Steven Hallam et al.

BMC Genomics, 2013, 14 (1), pp.320. ⟨10.1186/1471-2164-14-320⟩

Article dans une revue cea-04669813v1

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae)

Julie Ferreira de Carvalho , Julie Poulain , Corinne da Silva , Patrick Wincker , Sophie Michon-Coudouel et al.

Heredity, 2013, 110 (2), pp.181-193. ⟨10.1038/hdy.2012.76⟩

Article dans une revue hal-00797941v1
Deposit thumbnail

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Pascal Hingamp , Nigel Grimsley , Silvia G Acinas , Camille Clerissi , Lucie Subirana et 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
Deposit thumbnail

OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica

Gemma Danks , Coen Campsteijn , Mrutyunjaya Parida , Stephen Butcher , Harsha Doddapaneni et al.

Nucleic Acids Research, 2013, 41 (D1), pp.D845-D853. ⟨10.1093/nar/gks1159⟩

Article dans une revue cea-04667001v1

Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes

Frédéric Lehembre , Didier Doillon , Elise David , Sandrine Perrotto , Jessica Baude et al.

Environmental Microbiology, 2013, 15 (10), pp.2829-2840. ⟨10.1111/1462-2920.12143⟩

Article dans une revue istex hal-01115321v1
Deposit thumbnail

Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)

Lucia Morales , Benjamin Noel , Betina Porcel , Marina Marcet-Houben , Marie-Francoise Hullo et al.

Genome Biology and Evolution, 2013, 5 (12), pp.2524-2539. ⟨10.1093/gbe/evt201⟩

Article dans une revue cea-04669702v1

Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis

Julie Ferreira de Carvalho , Houda Chelaifa , Julien Boutte , Julie Poulain , Arnaud Couloux et al.

Plant Molecular Biology, 2013, 83 (6), pp.606. ⟨10.1007/s11103-013-0111-7⟩

Article dans une revue istex hal-00943497v1
Deposit thumbnail

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.

Jonas Collén , Betina Porcel , Wilfrid Carré , Steven G Ball , Cristian Chaparro et al.

Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (13), pp.5247-52. ⟨10.1073/pnas.1221259110⟩

Article dans une revue hal-01073830v1

Insights to Algal Evolution from the Chondrus Genome

J. Collen , G. Michel , W. Carre , B. Porcel , Jean-Marc Aury et al.

Phycologia, 2013, 52 (4)

Article dans une revue cea-04666950v1
Deposit thumbnail

Comparative genomics of emerging pathogens in the Candida glabrata clade.

Toni Gabaldón , Tiphaine Martin , Marina Marcet-Houben , Pascal Durrens , Monique Bolotin-Fukuhara et al.

BMC Genomics, 2013, 14 (1), pp.623. ⟨10.1186/1471-2164-14-623⟩

Article dans une revue inserm-00871184v1

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

Angélique d'Hont , France Denoeud , Jean-Marc Aury , Franc-Christophe Baurens , Françoise Carreel et al.

Nature, 2012, 488 (7410), pp.213-7. ⟨10.1038/nature11241⟩

Article dans une revue hal-00855582v1

The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium

J. Mark Cock , Lieven Sterck , Sophia Ahmed , Andrew E. Allen , Grigoris Amoutzias et al.

Advances in Botanical Research, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩

Article dans une revue hal-02649287v1
Deposit thumbnail

Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome

Romain Philippe , Frédéric Choulet , Etienne Paux , Jan van Oeveren , Jifeng Tang et al.

BMC Genomics, 2012, 13, ⟨10.1186/1471-2164-13-47⟩

Article dans une revue hal-01190822v1

Annotation of microsporidian genomes using transcriptional signals.

Eric Peyretaillade , Nicolas Parisot , Valérie Polonais , Sébastien Terrat , Jérémie Denonfoux et al.

Nature Communications, 2012, 3 (1), pp.1137. ⟨10.1038/ncomms2156⟩

Article dans une revue hal-00813939v1
Deposit thumbnail

Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization

Véronique Leh Louis , Laurence Despons , Anne Friedrich , Tiphaine Martin , Pascal Durrens et al.

G3, 2012, 2 (2), pp.299 - 311. ⟨10.1534/g3.111.000745⟩

Article dans une revue hal-00679348v1

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

Hervé Moreau , Bram Verhelst , Arnaud Couloux , Evelyne Derelle , Stephane Rombauts et al.

Genome Biology, 2012, 13 (8), pp.R74. ⟨10.1186/gb-2012-13-8-r74⟩

Article dans une revue hal-03160896v1
Deposit thumbnail

Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus.

Nicolas Tchitchek , Béatrice Jacquelin , Patrick Wincker , Carole Dossat , Corinne Da Silva et al.

BMC Genomics, 2012, 13 (1), pp.279. ⟨10.1186/1471-2164-13-279⟩

Article dans une revue inserm-00771549v1
Deposit thumbnail

Linkage to the mating-type locus across the genus microbotryum: insights into nonrecombining chromosomes

Elsa Petit , Tatiana Giraud , Damien M. de Vienne , Marco A Coelho , Gabriela Aguileta et al.

Evolution - International Journal of Organic Evolution, 2012, 66 (11), pp.3519-3533. ⟨10.1111/j.1558-5646.2012.01703.x⟩

Article dans une revue hal-01190628v1
Deposit thumbnail

Feminizing Wolbachia: a transcriptomics approach with insights on the immune response genes in Armadillidium vulgare

Frédéric Chevalier , Juline Herbinière-Gaboreau , Delphine Charif , Guillaume Mitta , Frédérick F. Gavory et al.

BMC Microbiology, 2012, 12 (suppl), pp.S1. ⟨10.1186/1471-2180-12-S1-S1⟩

Article dans une revue halsde-00661197v1
Deposit thumbnail

Sequencing of the smallest apicomplexan genome from the human pathogen Babesia Microti

Emmanuel Cornillot , Kamel Hadj-Kaddour , Amina Dassouli , Benjamin Noel , Vincent Ranwez et al.

Nucleic Acids Research, 2012, 40 (18), pp.9102-9114. ⟨10.1093/nar/gks700⟩

Article dans une revue lirmm-00818833v1

Genes under positive selection in a model plant pathogenic fungus, Botrytis

Gabriela G. Aguileta , Juliette J. Lengellé , Helene H. Chiapello , Tatiana T. Giraud , Muriel Viaud et al.

Infection, Genetics and Evolution, 2012, 12 (05), pp.987-996. ⟨10.1016/j.meegid.2012.02.012⟩

Article dans une revue istex hal-01000313v1

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.

Olivier Arnaiz , Nathalie Mathy , Céline Baudry , Sophie Malinsky , Jean-Marc Aury et al.

PLoS Genetics, 2012, 8 (10), pp.e1002984. ⟨10.1371/journal.pgen.1002984⟩

Article dans une revue hal-00759182v1
Deposit thumbnail

Influence of Wolbachia on host gene expression in an obligatory symbiosis.

Natacha Kremer , Delphine Charif , Hélène Henri , Frédérick F. Gavory , Patrick Wincker et al.

BMC Microbiology, 2012, 12 (Suppl 1), pp.1-16. ⟨10.1186/1471-2180-12-S1-S7⟩

Article dans une revue hal-00763438v1

Genomics and fruit crop selection

Patrick Wincker

Nature Genetics, 2012, 45 (1), pp.9-10. ⟨10.1038/Ng.2498⟩

Article dans une revue cea-04669826v1

Complete Genome Sequence of the Highly Hemolytic Strain Bacillus cereus F837/76

Sandrine Auger , Nathalie N. Galleron , Béatrice Segurens , Carole C. Dossat , Alexandre A. Bolotine et al.

Journal of Bacteriology, 2012, 194 (6), pp.1630 - 1630. ⟨10.1128/JB.06719-11⟩

Article dans une revue hal-01004271v1

Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

Sebastien Terrat , Richard Christen , Samuel S. Dequiedt , Mélanie M. Lelievre , Virginie Nowak et al.

Microbial Biotechnology, 2012, 5 (1), pp.135-141. ⟨10.1111/j.1751-7915.2011.00307.x⟩

Article dans une revue hal-01546177v1
Deposit thumbnail

Host gene response to endosymbiont and pathogen in the cereal weevil \textitSitophilus oryzae

A. Vigneron , Delphine Charif , C. Vincent-Monégat , A. Vallier , Frédérick F. Gavory et al.

BMC Microbiology, 2012, 12, pp.S14. ⟨10.1186/1471-2180-12-S1-S14⟩

Article dans une revue hal-02278586v1

Convergent origins and rapid evolution of " spliced leader " trans-splicing in Metazoa : insights from the Ctenophora and Hydrozoa.

Romain Derelle , T. Momose , Michaël Manuel , C. da Silva , P. Wincker et al.

RNA, 2011, 16 (4), pp.696-707. ⟨10.1261/rna.1975210⟩

Article dans une revue hal-00594660v1

Complete genome sequence of the clinical Streptococcus salivarius strain CCHSS3

Christine C. Delorme , Eric Guédon , Nicolas N. Pons , Corinne Cruaud , Arnaud A. Couloux et al.

Journal of Bacteriology, 2011, 193 (18), pp.5041-5042. ⟨10.1128/JB.05416-11⟩

Article dans une revue hal-01000176v1
Deposit thumbnail

Transcriptomics of Actinorhizal Symbioses Reveals Homologs of the Whole Common Symbiotic Signaling Cascade

Valerie Hocher , Nicole Alloisio , Florence Auguy , Pascale Fournier , Patrick Doumas et al.

Plant Physiology, 2011, 156 (2), pp.700-711. ⟨10.1104/pp.111.174151⟩

Article dans une revue hal-00599363v1

Atlas of gene expression in the mouse kidney: new features of glomerular parietal cells

Lydie L Cheval , Fabien Pierrat , Carole Dossat , Mathieu Genete , Martine Imbert-Teboul et al.

Physiological Genomics, 2011, 43 (3), pp.161-173. ⟨10.1152/physiolgenomics.00093.2010⟩

Article dans une revue hal-03160960v1
Deposit thumbnail

Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite.

France Denoeud , Michaël Roussel , Benjamin Noel , Ivan Wawrzyniak , Corinne da Silva et al.

Genome Biology, 2011, 12 (3), pp.R29. ⟨10.1186/gb-2011-12-3-r29⟩

Article dans une revue inserm-00617212v1

A panoramic view of gene expression in the human kidney

Danielle Chabardes-Garonne , Arnaud Mejean , Jean-Christophe Aude , Lydie L Cheval , Antonio Di Stefano et al.

Proceedings of the National Academy of Sciences of the United States of America, 2011, 100 (23), pp.13710-13715. ⟨10.1073/pnas.2234604100⟩

Article dans une revue hal-03160989v1

The Medicago genome provides insight into the evolution of rhizobial symbioses

Nevin Young , Frédéric Debellé , Giles Oldroyd , Rene Geurts , Steven Cannon et al.

Nature, 2011, 480 (7378), pp.520-524. ⟨10.1038/nature10625⟩

Article dans une revue hal-04198529v1
Deposit thumbnail

Complete Genome Sequence of the Commensal Streptococcus salivarius Strain JIM8777

Eric Guédon , Christine Delorme , Nicolas Pons , Corinne Cruaud , Valentin Loux et al.

Journal of Bacteriology, 2011, 193 (18), pp.5024-5025. ⟨10.1128/JB.05390-11⟩

Article dans une revue hal-03649194v1
Deposit thumbnail

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Joelle J. Amselem , Christina A. Cuomo , Jan A. L. van Kan , Muriel Viaud , Ernesto P. Benito et al.

PLoS Genetics, 2011, 7 (8), ⟨10.1371/journal.pgen.1002230⟩

Article dans une revue hal-01190236v1

The genome of Theobroma cacao.

Xavier Argout , Jerome Salse , Jean-Marc Aury , Mark J Guiltinan , Gaetan Droc et al.

Nature Genetics, 2011, 43 (2), pp.101-8. ⟨10.1038/ng.736⟩

Article dans une revue hal-00855922v1
Deposit thumbnail

A Holistic Approach to Marine Eco-Systems Biology

Eric Karsenti , Silvia G. Acinas , Peer Bork , Chris Bowler , Colomban de Vargas et al.

PLoS Biology, 2011, 9 (10), pp.e1001177. ⟨10.1371/journal.pbio.1001177⟩

Article dans une revue hal-01893669v1
Deposit thumbnail

Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

Carine Genet , Patrice Dehais , Yniv Y. Palti , Guangtu G. Gao , Frédérick F. Gavory et al.

BMC Genomics, 2011, 12, online (june), Non paginé. ⟨10.1186/1471-2164-12-314⟩

Article dans une revue hal-01000483v1

The Medicago genome provides insight into the evolution of rhizobial symbioses

Nevin D. Young , Frederic Debellé , Giles E. D. Oldroyd , Rene Geurts , Steven Cannon et al.

Nature, 2011, 480 (7378), pp.520-524. ⟨10.1038/nature10625⟩

Article dans une revue hal-02652790v1

Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome

Emilie Tisserant , C. da Silva , Annegret Kohler , Emmanuelle Morin , Patrick Wincker et al.

New Phytologist, 2011, 189 (3), pp.883-891. ⟨10.1111/j.1469-8137.2010.03597.x⟩

Article dans une revue hal-02645504v1
Deposit thumbnail

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Thierry Rouxel , J. Grandaubert , Jk. Hane , Claire Hoede , Angela P. van de Wouw et al.

Nature Communications, 2011, 2, pp.202. ⟨10.1038/ncomms1189⟩

Article dans une revue hal-00841751v1
Deposit thumbnail

Insights into metazoan evolution from Alvinella pompejana cDNAs.

Nicolas Gagnière , Didier Jollivet , Isabelle Boutet , Yann Brélivet , Didier Busso et al.

BMC Genomics, 2010, 11 (1), pp.634. ⟨10.1186/1471-2164-11-634⟩

Article dans une revue inserm-00617220v1

A vesicular glutamate transporter in lampreys: cDNA cloning and early expression in the nervous system.

Verona Villar-Cerviño , Claire Rocancourt , Arnaud Menuet , Corinne da Silva , Patrick Wincker et al.

Journal of Chemical Neuroanatomy, 2010, 40 (1), pp.71-81. ⟨10.1016/j.jchemneu.2010.03.009⟩

Article dans une revue istex hal-00486376v1
Deposit thumbnail

Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome.

Anne-Nathalie Volkoff , Véronique Jouan , Serge Urbach , Sylvie Samain , Max Bergoin et al.

PLoS Pathogens, 2010, 6 (5), pp.e1000923. ⟨10.1371/journal.ppat.1000923⟩

Article dans une revue inria-00537901v1
Deposit thumbnail

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

France Denoeud , Simon Henriet , Sutada Mungpakdee , Jean-Marc Aury , Corinne da Silva et al.

Science, 2010, 330 (6009), pp.1381-1385. ⟨10.1126/science.1194167⟩

Article dans une revue halsde-00544648v1
Deposit thumbnail

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

Francis Martin , Annegret Kohler , Claude Murat , Raffaella Balestrini , Pedro M Coutinho et al.

Nature, 2010, 464 (7291), pp.1033-1038. ⟨10.1038/nature08867⟩

Article dans une revue cea-00907731v1
Deposit thumbnail

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.

Saneyoshi Ueno , Grégoire Le Provost , Valérie Léger , Christophe Klopp , Céline Noirot et al.

BMC Genomics, 2010, 11, pp.650. ⟨10.1186/1471-2164-11-650⟩

Article dans une revue hal-00645933v1

Finding candidate genes under positive selection in Non-model species: examples of genes involved in host specialization in pathogens

G. Aguileta , J. Lengellé , S. Marthey , H. Chiapello , F. Rodolphe et al.

Molecular Ecology, 2010, 19 (2), pp.292-306. ⟨10.1111/j.1365-294X.2009.04454.x⟩

Article dans une revue istex hal-02333079v1

Evolution of Hox Gene Clusters in Gnathostomes: Insights from a Survey of a Shark (Scyliorhinus canicula) Transcriptome

S. Oulion , M. Debiais-Thibaud , Y d'Aubenton-Carafa , C. Thermes , C. da Silva et al.

Molecular Biology and Evolution, 2010, 27 (12), pp.2829 - 2838. ⟨10.1093/molbev/msq172⟩

Article dans une revue hal-01920896v1
Deposit thumbnail

The complete genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy actinobacterium with food and probiotic applications

Hélène Falentin , Stéphanie-Marie Deutsch , Gwénaël Jan , Valentin Loux , Anne Thierry et al.

PLoS ONE, 2010, 5 (7), pp.1-12. ⟨10.1371/journal.pone.0011748⟩

Article dans une revue hal-01204238v1

Ancestral Regulatory Circuits Governing Ectoderm Patterning Downstream of Nodal and BMP2/4 Revealed by Gene Regulatory Network Analysis in an Echinoderm

Alexandra Saudemont , Emmanuel Haillot , Flavien Mekpoh , Nathalie Bessodes , Magali Quirin et al.

PLoS Genetics, 2010, 6 (12), pp.e1001259. ⟨10.1371/journal.pgen.1001259⟩

Article dans une revue hal-02411414v1

Stage-specific gene expression during spermatogenesis in the dogfish (Scyliorhinus canicula)

Emma Redon , Adrien Bosseboeuf , Claire Rocancourt , Corinne da Silva , Patrick Wincker et al.

Reproduction [Cambridge], 2010, 140 (1), pp.57-71. ⟨10.1530/REP-10-0021⟩

Article dans une revue hal-02296535v1
Deposit thumbnail

The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae

J. Mark Cock , Lieven Sterck , Pierre Rouzé , Delphine Scornet , Andrew E. Allen et al.

Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩

Article dans une revue cea-00906990v1

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach

A. Valentini , C. Miquel , M. A. Nawaz , E. Bellemain , Eric Coissac et al.

Molecular Ecology Resources, 2009, 9 (1), pp.51-60

Article dans une revue halsde-00378004v1

Hunting down fungal secretomes using liquid-phase IEF prior to high resolution 2-DE

Delphine D. Vincent , Marie-Helene Balesdent , Julien Gibon , Stéphane Claverol , Delphine Lapaillerie et al.

Electrophoresis, 2009, 30 (23), pp.4118-4136. ⟨10.1002/elps.200900415⟩

Article dans une revue istex hal-02656973v1
Deposit thumbnail

A Plasmodium Falciparum FcB1-Schizont-EST Collection Providing Clues to Schizont Specific Gene Structure and Polymorphism

Isabelle Florent , Betina M Porcel , Elodie Guillaume , Corinne da Silva , François Artiguenave et al.

BMC Genomics, 2009, 10, pp.235-252. ⟨10.1186/1471-2164-10-235⟩

Article dans une revue lirmm-00395282v1

Are Hox Genes Ancestrally Involved in Axial Patterning? Evidence from the Hydrozoan Clytia hemisphaerica (Cnidaria).

Roxane Chiori , Muriel Jager , Elsa Denker , P. Wincker , C. da Silva et al.

PLoS ONE, 2009, 4 (1), pp.e4231

Article dans une revue hal-00594698v1
Deposit thumbnail

Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase

Elodie Fleury , Arnaud Huvet , Christophe Lelong , Julien de Lorgeril , Viviane Boulo et al.

BMC Genomics, 2009, 10 (341), pp.341. ⟨10.1186/1471-2164-10-341⟩

Article dans une revue inria-00435769v1
Deposit thumbnail

Comparative genomics of protoploid Saccharomycetaceae

Jean-Luc Souciet , Bernard Dujon , Claude Gaillardin , Mark Johnston , Philippe V Baret et al.

Genome Research, 2009, 19, pp.1696-1709. ⟨10.1101/gr.091546.109⟩

Article dans une revue inria-00407511v1

Polydnaviruses of Braconid Wasps Derive from an Ancestral Nudivirus

Annie Bézier , Marc Annaheim , Juline Herbiniere , Christoph Wetterwald , Gabor Gyapay et al.

Science, 2009, 323 (5916), pp.926-930. ⟨10.1126/science.1166788⟩

Article dans une revue hal-00402741v1
Deposit thumbnail

Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.

Yvan Zivanovic , J. Armengaud , Arnaud Lagorce , Christophe Leplat , Philippe Guerin et al.

Genome Biology, 2009, 10 (6), pp.R70. ⟨10.1186/gb-2009-10-6-r70⟩

Article dans une revue hal-00401146v1

The complete mitochondrial genome of the yeast Pichia sorbitophila

Paul P. Jung , Joseph Schacherer , Jean-Luc Souciet , Serge Potier , Patrick Wincker et al.

FEMS Yeast Research, 2009, 9 (6), pp.903--910. ⟨10.1111/j.1567-1364.2009.00540.x⟩

Article dans une revue hal-05022603v1

Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation

Eric Peyretaillade , Olivier Gonçalves , Sébastien Terrat , Eric Dugat-Bony , Patrick Wincker et al.

BMC Genomics, 2009, 10 (1), ⟨10.1186/1471-2164-10-607⟩

Article dans une revue hal-01888038v1

A Role for RNAi in the Selective Correction of DNA Methylation Defects

Felipe Karam Teixeira , Fabiana Heredia , Alexis Sarazin , François Roudier , Martine Boccara et al.

Science, 2009, 323 (5921), pp.1600-1604. ⟨10.1126/science.1165313⟩

Article dans une revue cea-00817409v1

Neurodevelopment genes in lampreys reveal trends for forebrain evolution in craniates.

Adèle Guérin , Yves d'Aubenton-Carafa , Emna Marrakchi , Corinne da Silva , Patrick Wincker et al.

PLoS ONE, 2009, 4 (4), pp.e5374. ⟨10.1371/journal.pone.0005374⟩

Article dans une revue hal-00384096v1
Deposit thumbnail

Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell

Peter Von Dassow , Hiroyuki Ogata , Ian Probert , Patrick Wincker , Corinne da Silva et al.

Genome Biology, 2009, 10 (10), pp.R114. ⟨10.1186/gb-2009-10-10-r114⟩

Article dans une revue hal-01258261v1
Deposit thumbnail

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

Maite Novo , Frederic Bigey , Emmanuelle Beyne , Virginie Galeote , Frédérick Gavory et al.

Proceedings of the National Academy of Sciences of the United States of America, 2009, 106 (38), pp.16333-16338. ⟨10.1073/pnas.0904673106⟩

Article dans une revue hal-02668729v1

Phylogenomics revives traditional views on deep animal relationships.

Herve Philippe , Romain Derelle , P. Lopez , K. Pick , Carole Borchiellini et al.

Current Biology, 2009, 19 (8), pp.706-712. ⟨10.1016/j.cub.2009.02.052⟩

Article dans une revue hal-00594690v1
Deposit thumbnail

Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes

Roxana Yockteng , Sylvain Marthey , Hélène Chiapello , Annie Gendrault , Michael E Hood et al.

BMC Genomics, 2009, 8 (1), pp.272. ⟨10.1186/1471-2164-8-272⟩

Article dans une revue hal-02333218v1
Deposit thumbnail

A new genomic resource dedicated to wood formation in Eucalyptus

D. Rengel , H.S. Clemente , F. Servant , Nathalie Ladouce , E. Paux et al.

BMC Plant Biology, 2009, 9 (36), n.p. ⟨10.1186/1471-2229-9-36⟩

Article dans une revue hal-01565048v1
Deposit thumbnail

Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation

Eric Peyretaillade , Olivier Gonçalves , Sébastien Terrat , Eric Dugat-Bony , Patrick Wincker et al.

BMC Genomics, 2009, 10, pp.607. ⟨10.1186/1471-2164-10-607⟩

Article dans une revue hal-00461524v1

A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

Isabelle Florent , Betina Porcel , Elodie Guillaume , Corinne da Silva , François Artiguenave et al.

BMC Genomics, 2009, 10 (1), pp.235. ⟨10.1186/1471-2164-10-235⟩

Article dans une revue hal-05558288v1

Isolation of 60 polymorphic microsatellite loci in EST libraries of four sibling species of the phytopathogenic fungal complex Microbotryum

T. Giraud , R. Yockteng , Sylvain S. Marthey , Hélène Chiapello , Odile Jonot et al.

Molecular Ecology Resources, 2008, 8 (2), pp.387-392. ⟨10.1111/j.1471-8286.2007.01967.x⟩

Article dans une revue istex hal-02665569v1

Bracovirus Gene Products Are Highly Divergent From Insect Proteins

Annie Bézier , Juline Herbinière , Céline Serbielle , Jérôme Lesobre , Patrick Wincker et al.

Archives of Insect Biochemistry and Physiology, 2008, 67, pp.172-187. ⟨10.1002/arch.20219⟩

Article dans une revue istex hal-00315839v1
Deposit thumbnail

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.

Alexis Dufresne , Martin Ostrowski , David J. Scanlan , Laurence Garczarek , Sophie Mazard et al.

Genome Biology, 2008, 9 (5), pp.R90. ⟨10.1186/gb-2008-9-5-r90⟩

Article dans une revue hal-00338634v1

In vitro propagation of the microsporidian pathogen Brachiola algerae and studies of its chromosome and ribosomal DNA organization in the context of the complete genome sequencing project

Abdel Belkorchia , Corinne Biderre , Cécile Militon , Valérie Polonais , Patrick Wincker et al.

Parasitology International, 2008, 57 (1), pp.62-71. ⟨10.1016/j.parint.2007.09.002⟩

Article dans une revue istex hal-00529592v1
Deposit thumbnail

Annotating genomes with massive-scale RNA sequencing

France Denoeud , Jean-Marc Aury , Corinne da Silva , Benjamin Noel , Odile Rogier et al.

Genome Biology, 2008, 9 (12), ⟨10.1186/gb-2008-9-12-r175⟩

Article dans une revue hal-02664963v1

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline.

L. Duret , Jean Cohen , Claire Jubin , Philippe Dessen , Jean-François Goût et al.

Genome Research, 2008, 18 (4), pp.585-96. ⟨10.1101/gr.074534.107⟩

Article dans une revue hal-00282468v1

Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity

Alla Lapidus , Eugene Goltsman , Sandrine Auger , Nathalie Galleron , Béatrice Ségurens et al.

Chemico-Biological Interactions, 2008, 171 (2), pp.236-249. ⟨10.1016/j.cbi.2007.03.003⟩

Article dans une revue istex hal-04314336v1
Deposit thumbnail

Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping

Luro François , Gilles Costantino , Javier Terol , Thierry Allario , Xavier Argout et al.

BMC Genomics, 2008, 9, pp.287. ⟨10.1186/1471-2164-9-287⟩

Article dans une revue hal-02661072v1
Deposit thumbnail

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

Jean-Marc Aury , Corinne Cruaud , Valérie Barbe , Odile Rogier , Sophie Mangenot et al.

BMC Genomics, 2008, 9, ⟨10.1186/1471-2164-9-603⟩

Article dans une revue hal-02659381v1

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Pierre Abad , Jerome Gouzy , Jean-Marc Aury , Philippe Castagnone-Sereno , Etienne Danchin et al.

Nature Biotechnology, 2008, 26 (8), pp.909-915. ⟨10.1038/nbt.1482⟩

Article dans une revue hal-01189285v1

The Genome of Borrelia recurrentis, the Agent of Deadly Louse-Borne Relapsing Fever, Is a Degraded Subset of Tick-Borne Borrelia duttonii

Magali Lescot , Stephane Audic , Catherine Robert , Thi Tien Nguyen , Guillaume Blanc et al.

PLoS Genetics, 2008, 4 (9), pp.e1000185. ⟨10.1371/journal.pgen.1000185⟩

Article dans une revue hal-02978141v1

Quantitative gene expression profiling of mouse brain regions reveals differential transcripts conserved in human and affected in disease models.

Camille Brochier , Marie-Claude Gaillard , Elsa Diguet , Nicolas Caudy , Carole Dossat et al.

Physiological Genomics, 2008, 33 (2), pp.170-9. ⟨10.1152/physiolgenomics.00125.2007⟩

Article dans une revue hal-00275419v1

A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome.

Lucie Hanriot , Céline Keime , Nadine Gay , Claudine Faure , Carole Dossat et al.

BMC Genomics, 2008, 9, pp.418. ⟨10.1186/1471-2164-9-418⟩

Article dans une revue hal-00425134v1
Deposit thumbnail

Translational control of intron splicing in eukaryotes

Olivier Jaillon , Khaled Bouhouche , Jean-François Gout , Jean-Marc Aury , Benjamin Noel et al.

Nature, 2008, 451 (7176), pp.359-362. ⟨10.1038/nature06495⟩

Article dans une revue cea-00945555v1

The genome sequence of the model ascomycete fungus Podospora anserina

Eric Espagne , Olivier Lespinet , Fabienne Malagnac , Corinne da Silva , Olivier Jaillon et al.

Genome Biology, 2008, 9 (5), pp.R77. ⟨10.1186/gb-2008-9-5-r77⟩

Article dans une revue hal-04011226v1

Complete circular DNA in the mitochondria-like organelles of Blastocystis hominis.

Ivan Wawrzyniak , Michaël Roussel , Marie Diogon , Arnaud Couloux , Catherine Texier et al.

International Journal for Parasitology, 2008, 38 (12), pp.1377-1382. ⟨10.1016/j.ijpara.2008.06.001⟩

Article dans une revue hal-00527813v1

Sur le terrain du respect

Dominique Bodin , P. Wincker , P. Fournel , J.-P. Dubois

Module étrange, 2008, pp.1-24

Article dans une revue halshs-00347062v1
Deposit thumbnail

The genome sequence of the model ascomycete fungus Podospora anserina.

Eric Espagne , Olivier Lespinet , Fabienne Malagnac , Corinne da Silva , Olivier Jaillon et al.

Genome Biology, 2008, 9 (5), pp.R77. ⟨10.1186/gb-2008-9-5-r77⟩

Article dans une revue hal-00286300v1
Deposit thumbnail

Transcriptome of Aphanomyces euteiches: new oomycete putative pathogenicity factors and metabolic pathways.

Elodie Gaulin , Mohammed-Amine Madoui , Arnaud Bottin , Christophe Jacquet , Catherine Mathé et al.

PLoS ONE, 2008, 3 (3), pp.e1723. ⟨10.1371/journal.pone.0001723⟩

Article dans une revue hal-00320699v1

Transcript Profiling of Poplar Leaves upon Infection with Compatible and Incompatible Strains of the Foliar Rust Melampsora larici-populina

Cecile Rinaldi , Annegret Kohler , Pascal Frey , Frédéric Duchaussoy , Francois Ningre et al.

Plant Physiology, 2007, 144 (1), pp.347-366. ⟨10.1104/pp.106.094987⟩

Article dans une revue hal-01194961v1
Deposit thumbnail

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Olivier Jaillon , Jean-Marc Aury , Benjamin Noel , Alberto Policriti , Christian Clepet et al.

Nature, 2007, 449 (7161), pp.463-7. ⟨10.1038/nature06148⟩

Article dans une revue inria-00180136v1
Deposit thumbnail

Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis.

Ana C Fierro , Raphaël Thuret , Laurent Coen , Muriel Perron , Barbara A Demeneix et al.

BMC Genomics, 2007, 8, pp.118. ⟨10.1186/1471-2164-8-118⟩

Article dans une revue hal-00159690v1
Deposit thumbnail

AphanoDB: a genomic resource for Aphanomyces pathogens.

Mohammed-Amine Madoui , Elodie Gaulin , Catherine Mathé , Hélène San Clemente , Arnaud Couloux et al.

BMC Genomics, 2007, 8, pp.471. ⟨10.1186/1471-2164-8-471⟩

Article dans une revue hal-00320701v1

Large-scale identification of human genes implicated in epidermal barrier function.

N. Mattiuzzo , E. Toulza , Mf Galliano , N. Jonca , C. Dossat et al.

Genome Biology, 2007, 8, pp.67-74

Article dans une revue hal-00306571v1
Deposit thumbnail

Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance

Javier Terol , Ana Conesa , Jose M Colmenero , Manuel Cercos , Francisco Tadeo et al.

BMC Genomics, 2007, 8, ⟨10.1186/1471-2164-8-31⟩

Article dans une revue hal-01605709v1
Deposit thumbnail

Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)

Beatriz Sabater-Munoz , Fabrice Legeai , Claude Rispe , Joël Bonhomme , Peter Dearden et al.

Genome Biology, 2006, 7-3 (r21), pp.1-11. ⟨10.1186/gb-2006-7-3-r21⟩

Article dans une revue inria-00180157v1

Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila.

Nicolas Vodovar , David Vallenet , Stéphane Cruveiller , Zoé Rouy , Valérie Barbe et al.

Nat Biotechnol, 2006, 24 (6), pp.673-9. ⟨10.1038/nbt1212⟩

Article dans une revue hal-00133119v1

Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome

Didier Lamoureux , Anne Bernole , Isabelle Le Clainche , Sarah Tual , Vincent Thareau et al.

TAG Theoretical and Applied Genetics, 2006, 113 (2), pp.344-356. ⟨10.1007/s00122-006-0301-7⟩

Article dans une revue istex inria-00180148v1

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

Jean-Marc Aury , Olivier Jaillon , L. Duret , Benjamin Noel , Claire Jubin et al.

Nature, 2006, 444 (7116), pp.171-8. ⟨10.1038/nature05230⟩

Article dans une revue hal-00132091v1

Chaetognath phylogenomics: a protostome with deuterostome-like development

E. Martin , X. Caubit , L. Fasano , F. Marletaz , Y. Perez et al.

Current Biology, 2006, 16, pp.R577-578

Article dans une revue hal-00310882v1

Mutator-like element in the yeast Yarrowia lipolytica displays multiple alternative splicings.

Cécile Neuvéglise , Fabienne Chalvet , Patrick Wincker , Claude Gaillardin , Serge Casaregola

Eukaryotic Cell, 2005, 4 (3), pp.615-624. ⟨10.1128/EC.4.3.615-624.2005⟩

Article dans une revue hal-02675656v1

Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation

Karin Eiglmeier , Patrick Wincker , Laurence Cattolico , Véronique Anthouard , Inge Holm et al.

Insect Biochemistry and Molecular Biology, 2005, 35 (8), pp.799-814. ⟨10.1016/j.ibmb.2005.02.020⟩

Article dans une revue istex hal-02683098v1

Vertebrate-Type Intron-Rich Genes in the Marine Annelid Platynereis dumerilii

Florian Raible , Kristin Tessmar-Raible , Kazutoyo Osoegawa , Patrick Wincker , Claire Jubin et al.

Science, 2005, 310 (5752), pp.1325-1326. ⟨10.1126/science.1119089⟩

Article dans une revue hal-04690301v1

Complete nucleotide sequence of the mitochondrial DNA from Kluyveromyces lactis.

Yvan Zivanovic , Patrick Wincker , Benoit Vacherie , Monique Bolotin-Fukuhara , Hiroshi Fukuhara

FEMS Yeast Research, 2005, 5 (4-5), pp.315-22. ⟨10.1016/j.femsyr.2004.09.003⟩

Article dans une revue hal-00198575v1

Whole Genome Sequence Comparisons and “Full-Length” cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation

Vanina Castelli , Jean-Marc Aury , Olivier Jaillon , Patrick Wincker , Christian Clepet et al.

Genome Research, 2004, 14 (3), pp.406-413. ⟨10.1101/gr.1515604⟩

Article dans une revue hal-04789187v1

Genome duplication in the teleost fish Tretraodon nigroviridis reveals the early vertebrate proto-karyotype

Olivier Jaillon , Jean-Marc Aury , Frédéric Brunet , Jean-Louis Petit , Nicole Stange-Thomann et al.

Nature, 2004, 431 (7011), pp.946-957. ⟨10.1038/nature03025⟩

Article dans une revue hal-02681415v1

Genome evolution in yeasts.

Bernard Dujon , David Sherman , Gilles Fischer , Pascal Durrens , Serge Casaregola et al.

Nature, 2004, 430 (6995), pp.35-44. ⟨10.1038/nature02579⟩

Article dans une revue istex hal-00104411v1

Whole genome sequence comparisons and "full-lenght" cDNA sequences: a combined approach to evaluate and improve Arabidopdid genome annotation

V. Castelli , J.M. Aury , Olivier Jaillon , Patrick Wincker , Christian Clepet et al.

Genome Research, 2004, 14 (3), pp.406-413

Article dans une revue hal-02672600v1

The complete mitochondrial genome sequence of the pathogenic yeast Candida ( Torulopsis ) glabrata

Romain Koszul , Alain Malpertuy , Lionel Frangeul , Christiane Bouchier , Patrick Wincker et al.

FEBS Letters, 2003, 534 (1-3), pp.39-48. ⟨10.1016/s0014-5793(02)03749-3⟩

Article dans une revue pasteur-02868102v1

The DNA sequence and analysis of human chromosome 14

Roland Heilig , Ralph Eckenberg , Jean-Louis Petit , Núria Fonknechten , Corinne da Silva et al.

Nature, 2003, 421 (6923), pp.601-607. ⟨10.1038/nature01348⟩

Article dans une revue hal-04312826v1

Genome sequence of the plant pathogen Ralstonia solanacearum.

Marcel Salanoubat , S. Genin , François Artiguenave , J. Gouzy , S. Mangenot et al.

Nature, 2002, 415 (6871), pp.497-502. ⟨10.1038/415497a⟩

Article dans une revue hal-00427300v2
Deposit thumbnail

The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

Alexander Bolotin , Patrick Wincker , Stéphane Mauger , Olivier Jaillon , Karine Malarme et al.

Genome Research, 2001, 11 (5), pp.731-753. ⟨10.1101/gr.gr-1697r⟩

Article dans une revue hal-04297851v1

Initial sequencing and analysis of the human genome

Eric Lander , Lauren Linton , Bruce Birren , Chad Nusbaum , Michael Zody et al.

Nature, 2001, 409 (6822), pp.860-921. ⟨10.1038/35057062⟩

Article dans une revue hal-04419732v1

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

M.D. Katinka , S. Duprat , E. Cornillot , G. Metenier , F. Thomarat et al.

Nature, 2001, 414, pp.450-453. ⟨10.1038/35106579⟩

Article dans une revue hal-00427201v1

The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403

A. Bolotin , Patrick Wincker , S. Mauger , Olivier Jaillon , Karine Malarme et al.

Genome Research, 2001, 11, pp.731-753

Article dans une revue hal-02681585v1

Genomic exploration of the hemiascomycetous yeasts: I. A set of yeast species for molecular evolution studies

Jean-Luc Souciet , Michel Aigle , François Artiguenave , Gaëlle Blandin , Monique Bolotin-Fukuhara et al.

FEBS Letters, 2000, 487 (1), pp.3-12. ⟨10.1016/S0014-5793(00)02272-9⟩

Article dans une revue hal-02694630v1

Genomic exploration of the hemiascomycetous yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

Bertrand Llorente , Pascal Durrens , Alain Malpertuy , Michel Aigle , François Artiguenave et al.

FEBS Letters, 2000, 487 (1), pp.122-133. ⟨10.1016/s0014-5793(00)02291-2⟩

Article dans une revue hal-02696721v1

Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae.

B Llorente , A Malpertuy , C Neuvéglise , Jacky de Montigny , M Aigle et al.

FEBS Letters, 2000, 487 (1), pp.101-112. ⟨10.1016/S0014-5793(00)02289-4⟩

Article dans une revue hal-05258748v1

Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes.

A Malpertuy , F Tekaia , S Casarégola , M Aigle , F Artiguenave et al.

FEBS Letters, 2000, 487 (1), pp.113-121. ⟨10.1016/S0014-5793(00)02290-0⟩

Article dans une revue istex hal-05258727v1

Genomic exploration of the hemiascomycetous yeasts: 14. Debaryomyces hansenii var. hansenii

A. Lépingle , Serge Casaregola , Cécile Neuvéglise , E. Bon , H.V. Nguyen et al.

FEBS Letters, 2000, 2000, pp.82-86

Article dans une revue hal-02694689v1

Genomic exploration of the hemiascomycetous yeasts: 6. Saccharomyces exiguus

E. Bon , Cécile Neuvéglise , A. Lépingle , Patrick Wincker , Francois Artiguenave et al.

FEBS Letters, 2000, 487, pp.42-46

Article dans une revue hal-02694290v1

Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum

E. Bon , Cécile Neuvéglise , Serge Casaregola , Francois Artiguenave , Patrick Wincker et al.

FEBS Letters, 2000, 487, pp.37-41

Article dans une revue hal-02694284v1

Genomic exploration of the hemiascomycetous yeasts: 8. Zygosaccharomyces rouxii.

Jacky de Montigny , Marie-Laure Straub , Serge Potier , F Tekaia , B Dujon et al.

FEBS Letters, 2000, 487 (1), pp.52-55. ⟨10.1016/S0014-5793(00)02279-1⟩

Article dans une revue hal-05258467v1

Genomic exploration of the hemiascomycetous yeasts: 15. Pichia sorbitophila.

Jacky de Montigny , Catherine Spehner , Jean-Luc Souciet , F Tekaia , B Dujon et al.

FEBS Letters, 2000, 487 (1), pp.87-90. ⟨10.1016/S0014-5793(00)02286-9⟩

Article dans une revue hal-05259013v1

Genomic exploration of the hemiascomycetous yeasts: 17. Yarrowia lipolytica

Serge Casaregola , Cécile Neuvéglise , A. Lépingle , E. Bon , C. Feynerol et al.

FEBS Letters, 2000, 487, pp.95-100

Article dans une revue hal-02694288v1

Genomic exploration of the hemiascomycetous yeasts: 7. Saccharomyces servazzii

Serge Casaregola , A. Lépingle , E. Bon , Cécile Neuvéglise , H.V. Nguyen et al.

FEBS Letters, 2000, 487, pp.47-51

Article dans une revue hal-02694291v1

Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes.

C. Gaillardin , G. Duchateau-Nguyen , F. Tekaia , B. Llorente , S. Casaregola et al.

FEBS Letters, 2000, 487 (1), pp.134-49. ⟨10.1016/S0014-5793(00)02292-4⟩

Article dans une revue hal-00115674v1

Genomic exploration of the hemiascomycetous yeasts: 9. Saccharomyces kluyveri

Cécile Neuvéglise , E. Bon , A. Lépingle , Patrick Wincker , Francois Artiguenave et al.

FEBS Letters, 2000, 487, pp.56-60

Article dans une revue hal-02694289v1

Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence

Hugues Roest Crollius , Olivier Jaillon , Alain Bernot , Corinne Dasilva , Laurence Bouneau et al.

Nature Genetics, 2000, 25 (2), pp.235-238. ⟨10.1038/76118⟩

Article dans une revue hal-03772374v1

PCR-based diagnosis for Chagas' disease in bolivian children living in an active transmission area : comparison with conventional serological and parasitological diagnosis

P. Wincker , Jenny Telleria , Marie-France Bosseno , M.A. Cardoso , P. Marques et al.

Memórias do Instituto Oswaldo Cruz, 1996, 91 (no spécial), pp.297

Article dans une revue hal-01257079v1

Unrelated sequences at the 5′ end of mouse LINE-1 repeated elements define two distinct sub-families

Patrick Wincker , Véronique Jubier-Maurin , Gérard Roizès

Nucleic Acids Research, 1987, 15 (21), pp.8593-8606. ⟨10.1093/nar/15.21.8593⟩

Article dans une revue hal-02170275v1

The relationships between the 5′ end repeats and the largest members of the LI interspersed repeated family in the mouse genome

Véronique Jubier-Maurin , Patrick Wincker , Gérard G. Cuny , Gérard Roizès

Nucleic Acids Research, 1987, 15 (18), pp.7395-7410. ⟨10.1093/nar/15.18.7395⟩

Article dans une revue hal-02171107v1

Genomics-based quantitative biogeography of marine plankton

Margaux Crédeville , Roy El Hourany , Swan Sow , Julie Poulain , Manon Depaty et al.

2025

Pré-publication, Document de travail hal-05363600v1
Deposit thumbnail

The JEDI marker as a universal measure of planetary biodiversity

Taylor Priest , Nicolas Henry , Thomas Weber , Laurine Planat , Coralie Rousseau et al.

2026

Pré-publication, Document de travail hal-05507468v1

Origin and evolutionary trajectories of brown algal sex chromosomes

Josué Barrera-Redondo , Agnieszka Lipinska , Pengfei Liu , Erica Dinatale , Guillaume Cossard et al.

2024

Pré-publication, Document de travail hal-04453200v1

Genome-resolved diversity and biosynthetic potential of the coral reef microbiome

Lucas Paoli , Fabienne Wiederkehr , Hans-Joachim Ruscheweyh , Samuel Miravet-Verde , Kalia S.I. Bistolas et al.

2024

Pré-publication, Document de travail hal-04807685v1
Deposit thumbnail

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Ann M Mc Cartney , Giulio Formenti , Alice Mouton , Diego de Panis , Luísa S Marins et al.

2024

Pré-publication, Document de travail hal-04406124v1
Deposit thumbnail

Mirusviruses provide a missing link in the evolution of giant viruses Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses

Morgan Gaïa , Lingjie Meng , Eric Pelletier , Patrick Forterre , Chiara Vanni et al.

2022

Pré-publication, Document de travail (preprint/prepublication) hal-03876463v1
Deposit thumbnail

Global observation of plankton communities from space

Hiroto Kaneko , Hisashi Endo , Nicolas Henry , Cédric Berney , Frédéric Mahé et al.

2022

Pré-publication, Document de travail hal-03855690v1
Deposit thumbnail

From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals,<i>Pocillopora</i>and<i>Porites</i>

Romane Deshuraud , Alexandre Ottaviani , Julie Poulain , Marine Leprêtre , Odette Beluche et al.

2023

Pré-publication, Document de travail (working paper) hal-04195332v1
Deposit thumbnail

Insights into biotic and abiotic modulation of ocean mesopelagic communities

Janaina Rigonato , Marko Budinich , Alejandro Murillo , Manoela Brandão , Juan Karlusich et al.

2022

Pré-publication, Document de travail hal-03166899v1

Changes in functional composition and gene expression in eukaryotic plankton at the Atlantic-Arctic Polar front

Paul Frémont , Corinne da Silva , Lucia Campese , Émilie Villar , Achal Rastogi et al.

2023

Pré-publication, Document de travail (preprint/prepublication) hal-04328288v1

Equatorial to Polar genomic variability of the microalgae <i>Bathycoccus prasinos</i>

Jade Leconte , Youri Timsit , Tom O Delmont , Magali Lescot , Gwenael Piganeau et al.

2023

Pré-publication, Document de travail (preprint/prepublication) hal-04308022v1
Deposit thumbnail

Restructuring of genomic provinces of surface ocean plankton under climate change

Paul Frémont , Marion Gehlen , Mathieu Vrac , Jade Leconte , Tom O. Delmont et al.

2021

Pré-publication, Document de travail cea-03166589v2
Deposit thumbnail

Ecogenomics of key prokaryotes in the arctic ocean

Marta Royo-Llonch , Pablo Sánchez , Clara Ruiz-González , Guillem Salazar , Carlos Pedrós-Alió et al.

2020

Pré-publication, Document de travail hal-02946895v1

Environmental vulnerability of the global ocean plankton community interactome

S. Chaffron , E. Delage , M. Budinich , D. Vintache , N. Henry et al.

2020

Pré-publication, Document de travail hal-03971893v1
Deposit thumbnail

Linking Allele-Specific Expression And Natural Selection In Wild Populations

Romuald Laso-Jadart , Kevin Sugier , Emmanuelle Petit , Karine Labadie , Pierre Peterlongo et al.

2019

Pré-publication, Document de travail hal-02275928v1

Prospective scientifique pour la recherche française sur la biodiversité - 2023

D. Couvet , A. Delavaud , J. Langridge , H. Soubelet , L. Abbadie et al.

Fondation pour la Recherche sur la Biodiversité, 50 p., 2023, 979-10-91015-66-0

Ouvrages hal-04637987v1

ADN et ARN environnementaux : découverte et fonctions

Patrick Wincker

Colloque ADNe/ARNe L’ADN (ADNe) : marqueurs du vivant dans les écosystèmes, Académie d'Agriculture de France, Sep 2023, Paris, France

Communication dans un congrès cea-04482722v1

Role of cyanate lyase in low-nitrate acclimation in the picophytoplankton Pelagomonas calceolata

Nina Guerin , Quentin Carradec , Patrick Wincker , Adrien Thurotte

8th European Phycological Congress, Aug 2023, Brest, France

Communication dans un congrès hal-04406043v1
Deposit thumbnail

European mink (Mustela lutreola) reference genome and population genomics

Alice Mouton , Christine Fournier-Chambrillon , Pascal Fournier , Jakub Skorupski , Przemysław Śmietana et al.

34th European Mustelid Colloquium, Sep 2022, Online conference, France

Communication dans un congrès hal-03787589v1

High-quality genome assemblies of corals highlight the specifics of their long lifespan

France Denoeud , Benjamin Noel , Julie Poulain , Carol Bruitago , Quentin Carradec et al.

EAGS, France Génomique, Oct 2021, Tours (France), France

Communication dans un congrès hal-04440766v1

Disentangling the effects of genotype, environment, and symbiotype on coral holobiont gene expression across the Pacific

Eric Armstrong , Quentin Carradec , Julie Lê-Hoang , Patrick Wincker

Environmental and Agronomical Genomics 2021 symposium, Oct 2021, Tours, France

Communication dans un congrès hal-04410520v1

La révolution génomique : de nouvelles approches pour étudier le vivant

Patrick Wincker

Colloque AFBV 2021 : les biotechnologies végétales entre science et société, Association Française des Biotechnologies Végétales, Oct 2021, Paris, France

Communication dans un congrès cea-04482731v1

Global-scale functional genomic and population genetic analyses of Millepora, Pocillopora, and Porites coral host diversity

Eric Armstrong , Quentin Carradec , Julie Lê-Hoang , Patrick Wincker

International Coral Reef Society Symposium, Jul 2020, Bremen, France

Communication dans un congrès hal-04406087v1

Co-evolution of chloroplast and nuclear genomes in flowering plants and impact of allopolyploidy on fine tune cytonuclear interactions.

Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , Jérémy Lucas , Gwenaëlle Deniot , Cyril Falentin et al.

International Conference on Polyploidy, Jun 2019, Ghent, Belgium

Communication dans un congrès hal-03318182v1

Genome-centered approaches for eukaryotes in complex microbial communities

Patrick Wincker

Fourth Microbial Single Cell Genomics (SCGC) Workshop, Sep 2019, Boothbay Harbor, United States

Communication dans un congrès cea-04482711v1

Cytonuclear interactions remain stable during allopolyploid evolution despite repeated wholegenome duplications

Julie Ferreira de Carvalho , Jérémy Lucas , Gwenaëlle Deniot , Cyril Falentin , Olivier Filangi et al.

21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2019, Saint Malo, France

Communication dans un congrès hal-04665569v1

How build up soil bacterial co-occurrence networks from wide spatial scale sampling?

Battle Karimi , Samuel Dequiedt , Sébastien Terrat , Claudy Jolivet , Dominique Arrouays et al.

JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France

Communication dans un congrès hal-02953290v1

Biogeographical design of soil microbial habitats

Battle Karimi , Jean Villerd , Samuel Dequiedt , Sébastien Terrat , Nicolas Chemidlin Prévost-Bouré et al.

5ème colloque du GDR de Génomique Environnementale, Oct 2019, La Rochelle, France

Communication dans un congrès hal-02951841v1

Structural and functional evolutionary dynamics of duplicated genes and genomes in nascent and natural B. napus

Mathieu Rousseau-Gueutin , Jérémy Lucas , France Denoeud , Julie Ferreira de Carvalho , Zhesi He et al.

21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2019, Saint-Malo, France

Communication dans un congrès hal-03318226v1

The Pisum Genus: Getting out of Pea Soup!

Jonathan Kreplak , Mohammed-Amin Madoui , Karine Labadie , Grégoire Aubert , Petr Capal et al.

Plant and Animal Genome XXVI Conference, 2018, San Diego (CA), United States

Communication dans un congrès hal-04331722v1

Mapping, understanding and predicting soil microbial diversity across France

Nicolas Chemidlin Prévost-Bouré , Sébastien Terrat , Battle Karimi , Samuel Dequiedt , Walid Horrigue et al.

21st World Congress of Soil Science, Aug 2018, Rio de Janeiro, Brazil

Communication dans un congrès hal-03102542v1

How a polyploid becomes a new species: example from the Brassica model.

Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , J. Lucas , France Denoeud , Fabrice Legeai et al.

International Conference on Environmental and Agronomical Genomics, 2018, Paris, France

Communication dans un congrès hal-03318223v1

Challenges in the analysis of large-scale meta-omics data for marine eukaryotes

Patrick Wincker

Gordon Research Conference- Marine Microbes, Gordon Research Conference, Jul 2018, Lucca (Barga), Italy

Communication dans un congrès cea-04482704v1

Innovative tools to diagnose the impact of land use practices on soil microbial communities

Sébastien Terrat , Walid Horrigue , Battle Karimi , Samuel Dequiedt , Nicolas Chemidlin Prévost-Bouré et al.

21st World Congress of Soil Science, Aug 2018, Rio de Janeiro, Brazil. pp.96

Communication dans un congrès hal-03103798v1

Cytonuclear interactions overcome inter-genomic conflict resulting from interspecific hybridization and genome doubling

Julie Ferreira de Carvalho , Jérémy Lucas , Cyril Falentin , Gwenaëlle Deniot , Olivier Filangi et al.

Second Joint Congress on Evolutionary Biology, Aug 2018, Montpellier, France

Communication dans un congrès hal-03318235v1

Bacterial social networks across the French National territory

Battle Karimi , Nicolas Chemidlin Prévost-Bouré , Sébastien Terrat , Samuel S. Dequiedt , Nicolas Saby et al.

Journée d’Ecologie Fonctionnelle AnaEE, AnaEE Analyses et Expérimentations sur les Ecosystèmes - France., Mar 2017, La Grande Motte, France

Communication dans un congrès hal-01605623v1

A transcriptomic approach to study marine plankton holobionts

Arnaud Meng , Erwan Corre , Pierre Peterlongo , Camille Marchet , Adriana A. Alberti et al.

International Conference on Holobionts, Apr 2017, Paris, France

Communication dans un congrès hal-01575069v1
Deposit thumbnail

The pea genome

Jonathan Kreplak , Mohammed-Amin Madoui , Karine Labadie , Gregoire Aubert , Philippe Bayer et al.

8. International Conference on Legume Genetics and Genomics (ICLGG), Noble Research Institute., Sep 2017, Siófok, Hungary. 128 p

Communication dans un congrès hal-02735156v1
Deposit thumbnail

Mapping and predictive variations of soil microbial richness, bacterial and archaeal phyla across France

Sébastien Terrat , Battle Karimi , Walid Horrigue , Samuel Dequiedt , Nicolas Saby et al.

4. International Conference on Microbial Diversity 2017 (MD 2017), Oct 2017, Bari, Italy. pp.209-211

Communication dans un congrès hal-02738142v1

Bacterial "social" network in french soils : a Metagenomics insight

Battle Karimi , Nicolas Chemidlin Prévost-Bouré , Sébastien Terrat , Samuel S. Dequiedt , Nicolas Saby et al.

Journée d’Ecologie Fonctionnelle AnaEE, AnaEE Analyses et Expérimentations sur les Ecosystèmes - France., Mar 2017, La Grande Motte, France

Communication dans un congrès hal-01608367v1

Soil bacterial interaction networks on a wide scale

Battle Karimi , Nicolas Chemidlin Prévost-Bouré , Sébastien Terrat , Samuel Dequiedt , Claudy Jolivet et al.

4. International Conference on Microbial Diversity 2017 (MD 2017), Oct 2017, Bari, Italy. pp.414-415

Communication dans un congrès hal-02735708v1
Deposit thumbnail

Towards the genome sequence of pea : a tribute to Mendel

Mohammed-Amin Madoui , K. Labadie , Jonathan Kreplak , Gregoire Aubert , Léo d'Agata et al.

2. International Legume Society Conference - Legumes for a Sustainable World, Legume Society., Oct 2016, Lisbonne, Portugal. 358 p

Communication dans un congrès hal-01602206v1

Biogeographical patterns of soil bacterial diversity at the scale of France

Sébastien Terrat , Samuel S. Dequiedt , Nicolas Saby , Walid Horrigue , Mélanie M. Lelievre et al.

16. International Symposium on Microbial Ecology - ISME16, Aug 2016, Montréal, Canada

Communication dans un congrès hal-01603633v1
Deposit thumbnail

Le pois, espèce modèle ?

Judith Burstin , Nadim N. Tayeh , Anthony Klein , Jonathan Kreplak , Françoise Jacquin et al.

1. Rencontres Francophones sur les Légumineuses (RFL1), Institut National de la Recherche Agronomique (INRA). FRA., May 2016, Dijon, France

Communication dans un congrès hal-02741352v1

Is soil an island for bacteria ? Contribution of the soil bacterial taxa area relationship unsing new generation sequencing

Nicolas Chemidlin Prévost-Bouré , Sébastien Terrat , Samuel Dequiedt , Nicolas Saby , Claudy Jolivet et al.

16. International Symposium on Microbial Ecology - ISME16, International Society for Microbial Ecology (ISME). INT., Aug 2016, Montréal, Canada

Communication dans un congrès hal-02798699v1

Oak genome sequencing and evolution

Jerome J. Salse , Jean Marc Aury , Florent Murat , Sébastien Faye , Karine Labadie et al.

Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p

Communication dans un congrès hal-02741698v1

Sequencing and Analysis of Wheat Chromosome 1B

Frédéric Choulet , Hélène Rimbert , Ambre-Aurore Josselin , Benoît Darrier , Pierre Sourdille et al.

Plant and Animal Genome XXIV Conference; IWGSC Standards and Protocoles Workshop, Jan 2016, San Diego, United States

Communication dans un congrès hal-02306172v1

Pea in the genomic era

Judith Burstin , Susete Alves Carvalho , Christelle Aluome , Nadim Tayeh , Anne-Lise Brochot et al.

Séminaire IFR AIB (Agrobiosciences, Interactions & Biodiversité), Feb 2015, Toulouse, France

Communication dans un congrès hal-01536570v1

Towards an universal genome-based DNA barcode-The PhyloAlps project

Eric Coissac , Pierre Taberlet , Cristina Roquet , Marti Boleda , Ludovic Gielly et al.

6th International Barcode of Life Conference, Aug 2015, Guelph, Canada. pp.206-206

Communication dans un congrès cea-04573288v1

Towards the rose genome sequence and its use in research and breeding

Fabrice Foucher , Laurence Hibrand-Saint Oyant , Latifa Hamama , Soulaiman Sakr , H. Nybom et al.

VI International Symposium on Rose Research and Cultivation, 2015, Hanovre, Germany. pp.167-175

Communication dans un congrès hal-01393815v1

A reference sequence of wheat chromosome 3B

Frédéric Choulet , Adriana A. Alberti , Sébastien Theil , Natasha Marie Glover , Valérie Barbe et al.

3. Plant Genomics Congress, May 2015, London, United Kingdom

Communication dans un congrès hal-02740971v1
Deposit thumbnail

Pea genomic tools for functional and structural approaches

Nadim N. Tayeh , Susete Alves Carvalho , Christelle Aluome , Sébastien Carrere , Jonathan Kreplak et al.

Mendel's legacy - 150 years of the genius of genetics, Masaryk University. CZE., Sep 2015, Brno, Czech Republic

Communication dans un congrès hal-02743963v1
Deposit thumbnail

Assembling a pseudomolecule for a wheat chromosome: the 3B experience

Frédéric Choulet , Adriana A. Alberti , Valérie Barbe , Sébastien Theil , Pierre Sourdille et al.

22. Conference on Plant and Animal Genome, Jan 2014, San Diego, United States

Communication dans un congrès hal-02743902v1
Deposit thumbnail

A reference sequence of wheat chromosome 3B

Frédéric Choulet , Adriana A. Alberti , Sébastien Theil , Natasha Marie Glover , Valérie Barbe et al.

22. Conference on Plant and Animal Genome, Jan 2014, San Diego, United States

Communication dans un congrès hal-02742303v1

Bac sequencing analyses in the hexaploid Spartina maritime (Poaceae): Homoeolog divergence and microsynteny in the grass family

Carine Charron , Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , Houda Chelaifa , Julien Boutte et al.

Réunion du groupe « Cytogénétique et Polyploïdie », May 2014, Clermont-Ferrand, France

Communication dans un congrès hal-01108395v1

Le séquençage massif pour caractériser la diversité microbienne des sols, standardisation et applications au sein de la plateforme GenoSol

Sébastien Terrat , Samuel Dequiedt , Nicolas Chemidlin Prévost-Bouré , Nicolas N. Saby , Mélanie M. Lelievre et al.

Colloque Etude du Polymorphisme des Génomes Végétaux (EPGV), Jun 2014, Évry, France

Communication dans un congrès hal-02740417v1

Pea in the genomic era

Susete Alves Carvalho , Christelle Aluome , Gregoire G. Aubert , Corinne Cruaud , Anthony Klein et al.

2. Adam Kondorosi Symposium "Frontiers in Legume Biology",, Dec 2014, Gif-sur-Yvette, France

Communication dans un congrès hal-02797923v1
Deposit thumbnail

Sequencing and Assembling a Reference Sequence of the 1 Gb Wheat Chromosome 3B

Frédéric Choulet , Sébastien Theil , Josquin Daron , Natasha Marie Glover , Nicolas N. Guilhot et al.

IWGSC Wheat Genome Sequencing Strategy and Funding Workshop, International Wheat Genome Sequencing Consortium (IWGSC). USA., Apr 2013, Evry, France

Communication dans un congrès hal-02747374v1

Automatized detection of duplicated copies from NGS data: Application to 45S rDNA and coding genes in the hexaploid Spartina maritime (Poaceae)

Julien Boutte , Benoit Aliaga , Julie Ferreira de Carvalho , Oscar Lima , Sophie Coudouel et al.

Rencontres ALPHY/PhyloSIB, Feb 2013, Lyon, France

Communication dans un congrès hal-01108442v1
Deposit thumbnail

Apport des nouvelles générations de séquençage pour accéder à la diversité et la richesse des communautés microbiennes de sols issus d'échantillonnage de grande ampleur

Sébastien Terrat , Samuel S. Dequiedt , Richard Christen , Dipankar Bachar , Mélanie M. Lelievre et al.

Ecole Thématique Expert Génomique Environnementale ETEGE, Apr 2012, Aussois, France

Communication dans un congrès hal-01208719v1
Deposit thumbnail

A strategy to assemble a reference sequence of the 1 Gb wheat chromosome 3B

Frédéric Choulet , Sébastien Theil , Josquin Daron , Natasha Marie Glover , Nicolas N. Guilhot et al.

TGAC/ESF-LESC workshop, Strategies for de novo assemblies of complex crop genomes, Genome Analysis Centre (TGAC). Norwich, GBR., Oct 2012, Norwich, United Kingdom

Communication dans un congrès hal-02809032v1

Genomic resources for functional analysis in <em>Medicago truncatula</em> and related crop species

Frederic Debellé , C. Belser , J.M. Aury , K. Labadie , Brice Roux et al.

6. International Conference on Legume Genetics and Genomics, International Crops Research Institute for the Semi-Arid Tropics, CGIAR (ICRISAT). Patancheru, IND., Oct 2012, Hyderabad, India

Communication dans un congrès hal-02747944v1
Deposit thumbnail

Towards a reference sequence of the 1 Gb wheat chromosome 3B

Frédéric Choulet , Sébastien Theil , Adriana A. Alberti , Valérie Barbe , Sophie Mangenot et al.

16. Annual Advances in Genome Biology and Technology (AGBT), Feb 2012, Marco Island, United States

Communication dans un congrès hal-02807639v1
Deposit thumbnail

Influence of Soil DNA Extraction Procedure to Assess Bacterial Diversity using Pyrosequencing of 16S rDNA

Sébastien Terrat , Richard Christen , Samuel S. Dequiedt , Christophe Mougel , Mélanie M. Lelievre et al.

NENUN ISME-Workshop: Extraction of Microbial DNA & RNA in Environmental Samples, Aug 2012, Copenhague, Denmark

Communication dans un congrès hal-01208718v1

Ecological genomics of invasive polyploids: Case study from hexaploid and allo-dodecaploid Spartina species colonizing salt marshes

Julie Ferreira de Carvalho , Julie Poulain , Corinne da Silva , Patrick Wincker , Sophie Coudouel et al.

International Conference of Ployploidy, Hybridization and Biodiversity (ICPHB), May 2012, Pruhonice, Czech Republic

Communication dans un congrès hal-01108907v1

GENOTROUT - Apport des nouvelles technologies de séquençage (NGS) à l'analyse du génome de la truite arc-en-ciel (2010-2013)

Yann Guiguen , Carine Genet , Edwige Quillet , Mekki Boussaha , Jean-Nicolas Volff et al.

9. Colloque Agenae/ANR, Mar 2012, La Rochelle, France. pp.18

Communication dans un congrès hal-01019800v1

Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

Sébastien Terrat , Samuel Dequiedt , Richard Christen , Mélanie M. Lelievre , Tiffanie Regnier et al.

Journées d'animation "MEM Days" organisées par l'INRA, Jan 2012, Ecully, France

Communication dans un congrès hal-02809171v1

Comparative genomics of the Nakaseomyces clade: Candida glabrata and enew merging pathogens

Cécile Fairhead , Toni Gabaldón , Tiphaine Martin , Pascal Durrens , Olivier Lespinet et al.

Comparative Genomics of Eukaryotic Microorganisms,, Oct 2011, Sant Feliu de Guixols, Spain

Communication dans un congrès hal-00674241v1

Development of genomic resources for <em>Medicago truncatula</em> and related legume crops

Frederic Debellé , Marion Verdenaud , Anne-Marie Dudez , Nicolas Samson , Olivier Saurat et al.

Model Legume Congress 2011, Institut National Polytechnique (Toulouse) (Toulouse INP). Castanet Tolosan, FRA., May 2011, Sainte Maxime, France

Communication dans un congrès hal-02746654v1
Deposit thumbnail

Influence of Soil DNA Extraction Procedure to Assess Bacterial Diversity using Pyrosequencing of 16S rDNA

Sébastien Terrat , Richard Christen , Samuel Dequiedt , Christophe Mougel , Mélanie M. Lelievre et al.

6. ISMOM: International Symposium of Interactions of Soil Minerals withOrganic Components and Microorganisms.3. InterCongress of Commission 2.5 IUSSSoil chemical, physical and biological interfacial reactions, Labo/service de l'auteur, Ville service, Pays service., Jun 2011, Montpellier, France

Communication dans un congrès hal-02746836v1
Deposit thumbnail

Report on sequencing the wheat chromosome 3B

Frédéric Choulet , Patrick Wincker , Hadi Quesneville , Dominique D. Brunel , Bikram S. Gill et al.

19. Plant and Animal Genome Conference, Jan 2011, San Diego, Californie, United States. 1 p

Communication dans un congrès hal-02808854v1

Vers la caractérisation des compartiments codant et répété du génome des spartines polyploïdes par séquençage en masse

Julie Ferreira de Carvalho , Houda Chelaifa , Jiri Macas , Oscar Lima , Sophie Coudouel et al.

Colloque « Biodiversité, Histoire des Espèces, Evolution des Génomes », Jun 2011, Rennes, France

Communication dans un congrès hal-01108953v1
Deposit thumbnail

Sequencing and Analyses of the Hexaploid Wheat Chromosome 3B

Frédéric Choulet , P. Wincker , Hadi Quesneville , Dominique D. Brunel , B. Gill et al.

19. Conference on Plant and Animal Genome, Jan 2011, San Diego, CA, United States

Communication dans un congrès hal-02747876v1

Nature, nurture and the structure of macroalgal genomes

J. Mark Cock , Jonas Collen , Lieven Sterck , Pierre Rouzé , Delphine Scornet et al.

5. European Phycological Congress, Sep 2011, Rhodes, Greece

Communication dans un congrès hal-02749757v1
Deposit thumbnail

Sequencing and analyses of the hexaploid wheat chromosome 3B

Frédéric Choulet , Etienne Paux , Philippe Leroy , Arnaud Couloux , Michaël Alaux et al.

10. conference on Genome Informatics, Sep 2010, Hinxton, United Kingdom

Communication dans un congrès hal-02753841v1
Deposit thumbnail

GENOTROUT - Apport des nouvelles technologies de séquençage (NGS) à l'analyse du génome pseudotétraploide de la truite arc-en-ciel (2010-2012)

Yann Guiguen , Carine Genet , Edwige Quillet , Jean-Nicolas Volff , Domitille Chalopin et al.

8. Journées AGENAE, Nov 2010, Bordeaux, France

Communication dans un congrès hal-01193660v1
Deposit thumbnail

Development of resources for comparative physical mapping between Muscadinia rotundifolia and Vitis vinifera

Iritche Zah-Bi , Sophie Blanc , Marc Bras , Aurelie A. Canaguier , Isabelle I. Le Clainche et al.

6. International Workshop of Grapevine Downy and Powdery Mildew. GDPM 2010, Jul 2010, BORDEAUX, France

Communication dans un congrès hal-02754937v1

Bioinformatic analysis of Sanger and 454 ESTs in oak

Saneyoshi S. Ueno , Grégoire G. Le Provost , Valérie V. Léger , Christophe Klopp , Celine C. Noirot et al.

Conference on Forest Ecosystem Genomics and Adaptation, Jun 2010, Madrid, Spain. pp.73

Communication dans un congrès hal-00964385v1
Deposit thumbnail

Naissance et diversification des effecteurs dans les génomes fongiques: le projet ANR FungIsochore

Thierry T. Rouxel , Bruno Le Cam , Joelle J. Amselem , P. Wincker , Marie-Helene Balesdent

8. Rencontres de Phytopathologie - Mycologie de la Société Française de Phytopathologie (SFP), Jan 2010, Ausois, France

Communication dans un congrès hal-02753379v1

AT-rich isochores as ecological niches for effectors in the genome of Leptosphaeria maculans

Isabelle Fudal-Grolier Fudal , Jonathan J. Grandaubert , Azita A. Dilmaghani , Nicolas Glaser , Patrick Wincker et al.

14. International Congress on Molecular Plant-Microbe Interactions, Jul 2009, Quebec City, Canada

Communication dans un congrès hal-02756559v1
Deposit thumbnail

Towards sequencing the 1 Gb wheat chromosome 3B

Frédéric Choulet , Etienne Paux , Philippe Leroy , Pierre Sourdille , Stéphane Schlub et al.

1. Workshop of StatSeq COST Action TD0801, Oct 2009, Barcelona, Spain

Communication dans un congrès hal-02818225v1

Development of genomic resources in oak to study the structure, variability, evolution and functioning of its genome

Christophe Plomion , Franck Salin , Jean-Marc Frigerio , Catherine Bodenes , Patricia Faivre Rampant et al.

International Plant & Animal genomes XV Conferences, Jan 2007, San Diego, United States

Communication dans un congrès hal-00337980v1

A SNP detection project using one million reads from WGS libraries produced from one pig from seven different breeds.

Patrice Dehais , Denis Milan , Thomas Faraut , C. Dossat , Patrick Wincker et al.

International Plant & Animal Genomes XV Conference, San Diego, 2007, California, France

Communication dans un congrès hal-02751166v1

Transcriptomic response of the picophytoplankton Pelagomonas calceolata to nitrogen depleted environments

Nina Guérin , Quentin Carradec , Patrick Wincker , Chloé Seyman , Adrien Thurotte et al.

Resilience and Recovery in Aquatic Systems, Jun 2023, Palma de Mallorca, Spain

Poster de conférence hal-04405314v1

Ocean-wide comparisons of plankton composition clarify differences in the structure and regulation of mesopelagic communities

Janaina Rigonato , Patrick Wincker , Olivier Jaillon

18th International Symposium on Microbial Ecology, Oct 2022, Lausanne ( CH), Switzerland.

Poster de conférence hal-04391705v1

Genomic adaptation of Pelagomonas calceolata to temperate iron-poor oceans revealed by a chromosome-scale assembled genome

Nina Guérin , Quentin Carradec , Marta Ciccarella , Elisa Flamant , Sophie Mangenot et al.

Environmental and Agronomical Genomics 2021 symposium, Oct 2021, Tours, France

Poster de conférence hal-04410501v1

Transcriptional and functional analyses of Symbiodiniaceae across the Pacific Ocean

Julie Lê-Hoang , Quentin Carradec , Eric Armstrong , Patrick Wincker

International Coral Reef Society Symposium, Jul 2020, Bremen, Germany

Poster de conférence hal-04405200v1
Deposit thumbnail

LONG DNA TECHNOLOGIES EVALUATION FOR PLANT STRUCTURAL VARIATIONS DETECTION : NANOPORE ONT SEQUENCING vs BIONANO GENOMICS OPTICAL MAPPING

Aurélie Canaguier , Erwan Denis , Romane Guilbaud , Ghislaine Magdelenat , Caroline Belser et al.

Plant and Animal Genome XXVIII Conference, Jan 2020, San Diego, United States.

Poster de conférence hal-02925940v1

Long DNA technologies evaluation for plant structural variations detection: Nanopore ONT sequencing vs Bionano Genomics optical mapping

Aurélie Canaguier , Erwan Denis , Romane Guilbaud , Ghislaine Magdelenat , Caroline Belser et al.

- Plant and Animal Genome XXVIII Conference, 2020, San Diego, CA, United States

Poster de conférence hal-04331757v1

Transcriptional activity of coral holobiont eukaryotes in the framework of Tara Pacific expedition

Quentin Carradec , Julie Lê-Hoang , Eric Armstrong , Julie Poulain , Karine Labadie et al.

Marine Molecular Ecology, Jul 2019, Hong-Kong, China

Poster de conférence hal-04405109v1
Deposit thumbnail

Genome skimming at the scale of the whole Alpine ecosystem : insights into genome size, gene family amplifications and functional signatures

France Denoeud , Adriana Alberti , Sébastien Lavergne , Patrick Wincker

Conference on Plant Genome Evolution, Sep 2019, Sitges, Spain

Poster de conférence hal-04440668v1

Chromosome-scale assemblies of Brassica oleracea and Brassica rapa using nanopore long reads and optical maps

Caroline Belser , Bejamin Istace , Denis Engemann , M Dubarry , Cyril Falentin et al.

21st Crucifer Genetics Conference on Brassica - Bassica 2018, Jul 2018, Saint-Malo, France

Poster de conférence hal-03318378v1

Comparative approaches for metagenomic biogeography and population structures of eukaryotes

Thomas Vannier , Jade Leconte , Patrick Wincker , Olivier Jaillon

4th Environmental Genomics symposium, Sep 2017, Marseille, France

Poster de conférence hal-04391650v1

Contrasting Spatial Patterns and Ecological Attributes of Soil Bacterial Taxa across French National Territory

Battle Karimi , Sébastien Terrat , Samuel S. Dequiedt , Nicolas Saby , Walid Horrigue et al.

Journée d’Ecologie Fonctionnelle AnaEE, Mar 2017, La Grande Motte, France. , 2017

Poster de conférence hal-01605429v1
Deposit thumbnail

Contrasting Spatial Patterns and Ecological Attributes of Soil Bacterial Taxa across French National Territory

Battle Karimi , Sébastien Terrat , Samuel S. Dequiedt , Nicolas Saby , Walid Horrigue et al.

Congrès de la Société Française d'Ecologie, Oct 2016, Marseille, France. 2016

Poster de conférence hal-01602852v1

Pea Genomics : What Else ?

Gregoire Aubert , Mohammed-Amin Madoui , Jonathan Kreplak , Nadim Tayeh , Karine Labadie et al.

ASA-CSSA-SSSA Meeting “Resilience Emerging from Scarcity and Abundance”, Nov 2016, Phoenix, United States. ASA CSSA SSSA Annual Meeting Presentations, 2016, ASA CSSA SSSA Annual Meeting Presentations

Poster de conférence hal-01607090v1
Deposit thumbnail

Genome assembly using Nanopore-guided Long and Error-free DNA reads

Guillaume Gautreau , Mohammed‐amin Madoui , Stefan Engelen , Adriana A. Alberti , Caroline Belser et al.

Journées Ouvertes en Biologie, Informatique et Mathématiques 2015, Jul 2015, Clermont-Ferrand, France

Poster de conférence hal-04862540v1

Impact of meiotic recombination on gene admixture for wheat improvement

Benoît Darrier , Frédéric Choulet , Natasha Marie Glover , Adriana A. Alberti , Sébastien Theil et al.

9. International Wheat Conference, Sep 2015, Sydney, Australia. 195 p., 2015, 9th International Wheat Conference 20-25 September 2015, Sydney, Australia : Program and Abstracts

Poster de conférence hal-02741010v1
Deposit thumbnail

Recent pea genomic resources will enhance complementary improvement strategies in this crop

Judith Burstin , Susete Alves Carvalho , Nadim N. Tayeh , Christelle Aluome , Virginie Bourion et al.

6. International Food Legumes Research Conference (IFLRC VI), Jul 2014, Saskatoon, Canada. , 225 p., 2014

Poster de conférence hal-02743375v1

Bac sequencing analyses in the hexaploid Spartina maritime (Poaceae): Homoeolog divergence and microsynteny in the grass family

Carine Charron , Mathieu Rousseau-Gueutin , Julie Ferreira de Carvalho , Houda Chelaifa , Julien Boutte et al.

International Conference on Invasive Spartina 2014, Jul 2014, Rennes, France. , 1 p., 2014

Poster de conférence hal-01109652v1

The hexaploid Spartina maritime (Poaceae, Chloridoidea) genome: Composition and evolution in the grass family

Julie Ferreira de Carvalho , Carine Charron , Houda Chelaifa , Julien Boutte , Mathieu Rousseau-Gueutin et al.

Plant Genome Evolution Meeting, Sep 2013, Amsterdam, Netherlands. , 2013

Poster de conférence hal-01110188v1
Deposit thumbnail

Deep sequencing of 16S rRNA gene to efficiently assess bacterial richness and the rare biosphere in soils

Sébastien Terrat , Samuel Dequiedt , Dipankar Bachar , Richard Christen , Christophe Mougel et al.

14. International Symposium on Microbial Ecology (ISME 14), Aug 2012, Copenhague, Danemark, Netherlands. 1 p., 2012

Poster de conférence hal-02806957v1

Genome and transcriptome analyses in hexaploid Spartina species (Poaceae) colonizing salt marshes

Julie Ferreira de Carvalho , Julie Poulain , Corinne da Silva , Patrick Wincker , Sophie Coudouel et al.

PAG XIX Plant and Animal Genome Conference, Jan 2012, San Diego, United States

Poster de conférence hal-01110212v1

Genetic diversity of Tuber aestivum / uncinatum

Virginie Molinier , Claude Murat-Furminieux , Emmanuelle Morin , Patrick Wincker , Armelle Gollotte et al.

ALPHY Meeting, Mar 2012, Banyuls sur Mer, France. , 2012

Poster de conférence hal-01268765v1

Automatized detection of duplicated copies from NGS data: Application to 45S rDNA and coding genes in hexaploid Spartina species (Poaceae)

Julien Boutte , Benoit Aliaga , Julie Ferreira de Carvalho , Oscar Lima , Sophie Coudouel et al.

International Conference of Ployploidy, Hybridization and Biodiversity (ICPHB), May 2012, Prague, Czech Republic

Poster de conférence hal-01110201v1

Optimisation du pyroséquençage haut-débit pour caractériser la diversité taxonomique des communautés bactériennes des sols

Sébastien Terrat , Pierre Plassart , R. Christen , Samuel Dequiedt , Tiffanie Régnier et al.

5ième colloque de l’Association Francophone Ecologie Microbienne (AFEM), Nov 2011, Hammamet, Tunisie. , 1 p., 2011

Poster de conférence hal-02808211v1

Optimisation du pyroséquençage haut-débit pour caractériser la diversité taxonomique des communautés bactériennes des sols

Sébastien Terrat , Pierre Plassart , R. Christen , Samuel Dequiedt , Tiffanie Régnier et al.

Colloque Génomique Environnementale, Nov 2011, Ecully, France. , 1 p., 2011

Poster de conférence hal-02807955v1

The complete genome of Propionibacterium freudenreichii CIRM 1 a hardy actinobacteria with food and probiotic applications

Hélène Falentin , Stéphanie-Marie Deutsch , Sandrine Parayre-Breton , Julien Dherbecourt , Gwénaël Jan et al.

3 International Symposium on Propionibacteria and Bifidobacteria: Dairy and Probiotic, Jun 2010, Oviédo, Spain. , International Journal of Food Microbiology, Volume 149, Issue 1, Pages 1-112 (1 September 2011), 2010, International Journal of Food Microbiology

Poster de conférence hal-01454344v1

TARA Pacific bleaching prevalence of sampling sites (Islands)

Christian R Voolstra , Benjamin C.C Hume , Kyra Pikaar , Guillaume Bourdin , Stéphane Pesant et al. Autre publication scientifique hal-04384087v1

TARA Pacific CTAX colony morphological annotations release version 1_1

Guinther Mitushasi , Sylvain Algostini , Benjamin Hume , Yuko Kitano , Julie Poulain et al. Autre publication scientifique hal-04384090v1

Tara Pacific V9 18S rDNA metabarcoding dataset

Frédéric Mahé , Nicolas Henry , Cédric Berney , Julie Poulain , Sarah Romac et al. Autre publication scientifique hal-04384095v1

Tara Pacific metabarcoding sequencing (16S, 18S, ITS2) reference & replication tables version 1

Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh et al. Autre publication scientifique hal-04384100v1

Tara Pacific 16S rRNA data analysis release

Hans-Joachim Ruscheweyh , Guillem Salazar , Julie Poulain , Caroline Belser , Quentin Clayssen et al. Autre publication scientifique hal-04384109v1

Tara Pacific ITS2 Symbiodiniaceae data release version 1

Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh et al. Autre publication scientifique hal-04384112v1

Tara Pacific 18S-based coral host genetic analysis data release version 1

Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh et al. Autre publication scientifique hal-04384097v1
Deposit thumbnail

Génétique et génomique du pois : what else ?

Judith Burstin , Nadim Tayeh , Anthony Klein , Virginie Bourion , Jonathan Kreplak et al.

Société Nationale d'Horticulture de France, pp.33-37, 2016, 978-2-913793-16-3

Proceedings/Recueil des communications hal-02794125v1

Whole genome sequencing projects of the plant pathogenic fungi Botrytis Cinerea and Sclerotinia Sclerotiorum

Sabine, Helma Fillinger , Joelle J. Amselem , Francois Artiguenave , Arnaud Billault , Mathias Choquer et al.

Macromolecules and secondary metabolites of grapevine and wine : fruit development, biotic and abiotic stresses, mechanisms of plant defense responses, proteins, glycoproteins, polysaccharides, polyphenolics, aroma compounds and secondar, EDITIONS TEC ET DOC, 2007, 978-2-7430-0965-9

Chapitre d'ouvrage hal-02820038v1