Patrick Wincker

Affiliations

Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France.

Publications (86)

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

BMC biology

Avec: Sarah Farhat , Phuong Le , Ehsan Kayal , Benjamin Noel , Estelle Bigeard , Erwan Corre , Florian Maumus , Isabelle Florent , Adriana Alberti , Jean-Marc Aury , Tristan Barbeyron , Ruibo Cai , Corinne Da Silva , Benjamin Istace , Karine Labadie , Dominique Marie , Jonathan Mercier , Tsinda Rukwavu , Jeremy Szymczak , Thierry Tonon , Catharina Alves-de-Souza , Pierre Rouzé , Yves Van de Peer , Patrick Wincker , Stephane Rombauts , Betina M Porcel , Laure Guillou

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

Nature ecology & evolution

Avec: Lucas Leclère , Coralie Horin , Sandra Chevalier , Pascal Lapébie , Philippe Dru , Sophie Peron , Muriel Jager , Thomas Condamine , Karen Pottin , Séverine Romano , Julia Steger , Chiara Sinigaglia , Carine Barreau , Gonzalo Quiroga Artigas , Antonella Ruggiero , Cécile Fourrage , Johanna E M Kraus , Julie Poulain , Jean-Marc Aury , Patrick Wincker , Eric Quéinnec , Ulrich Technau , Michaël Manuel , Tsuyoshi Momose , Evelyn Houliston , Richard R Copley

Global Trends in Marine Plankton Diversity across Kingdoms of Life.

Cell

Avec: Federico M Ibarbalz , Nicolas Henry , Manoela C Brandão , Séverine Martini , Greta Busseni , Hannah Byrne , Luis Pedro Coelho , Hisashi Endo , Josep M Gasol , Ann C Gregory , Frédéric Mahé , Janaina Rigonato , Marta Royo-Llonch , Guillem Salazar , Isabel Sanz-Sáez , Eleonora Scalco , Dodji Soviadan , Ahmed A Zayed , Adriana Zingone , Karine Labadie , Joannie Ferland , Claudie Marec , Stefanie Kandels , Marc Picheral , Céline Dimier , Julie Poulain , Sergey Pisarev , Margaux Carmichael , Stéphane Pesant , Auteur inconnu , Marcel Babin , Emmanuel Boss , Daniele Iudicone , Olivier Jaillon , Silvia G Acinas , Hiroyuki Ogata , Eric Pelletier , Lars Stemmann , Matthew B Sullivan , Shinichi Sunagawa , Laurent Bopp , Colomban de Vargas , Lee Karp-Boss , Patrick Wincker , Fabien Lombard , Chris Bowler , Lucie Zinger

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

Genome research

Avec: Alexey Vorobev , Marion Dupouy , Quentin Carradec , Tom O Delmont , Anita Annamalé , Patrick Wincker , Eric Pelletier

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

Nature microbiology

Avec: Marta Royo-Llonch , Pablo Sánchez , Clara Ruiz-González , Guillem Salazar , Carlos Pedrós-Alió , Marta Sebastián , Karine Labadie , Lucas Paoli , Federico M Ibarbalz , Lucie Zinger , Benjamin Churcheward , Auteur inconnu , Samuel Chaffron , Damien Eveillard , Eric Karsenti , Shinichi Sunagawa , Patrick Wincker , Lee Karp-Boss , Chris Bowler , Silvia G Acinas

Correction: Mapping and predictive variations of soil bacterial richness across France.

PloS one

Avec: Sébastien Terrat , Walid Horrigue , Samuel Dequiedt , Nicolas P A Saby , Mélanie Lelièvre , Virginie Nowak , Julie Tripied , Tiffanie Régnier , Claudy Jolivet , Dominique Arrouays , Patrick Wincker , Corinne Cruaud , Battle Karimi , Antonio Bispo , Pierre Alain Maron , Nicolas Chemidlin Prévost-Bouré , Lionel Ranjard

Biosynthetic potential of the global ocean microbiome.

Nature

Avec: Lucas Paoli , Hans-Joachim Ruscheweyh , Clarissa C Forneris , Florian Hubrich , Satria Kautsar , Agneya Bhushan , Alessandro Lotti , Quentin Clayssen , Guillem Salazar , Alessio Milanese , Charlotte I Carlström , Chrysa Papadopoulou , Daniel Gehrig , Mikhail Karasikov , Harun Mustafa , Martin Larralde , Laura M Carroll , Pablo Sánchez , Ahmed A Zayed , Dylan R Cronin , Silvia G Acinas , Peer Bork , Chris Bowler , Tom O Delmont , Josep M Gasol , Alvar D Gossert , André Kahles , Matthew B Sullivan , Patrick Wincker , Georg Zeller , Serina L Robinson , Jörn Piel , Shinichi Sunagawa

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

Communications biology

Avec: Nina Guérin , Marta Ciccarella , Elisa Flamant , Paul Frémont , Sophie Mangenot , Benjamin Istace , Benjamin Noel , Caroline Belser , Laurie Bertrand , Karine Labadie , Corinne Cruaud , Sarah Romac , Charles Bachy , Martin Gachenot , Eric Pelletier , Adriana Alberti , Olivier Jaillon , Patrick Wincker , Jean-Marc Aury , Quentin Carradec

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

Scientific reports

Avec: Marine Canesi , Eric Douville , Paolo Montagna , Marco Taviani , Jarosław Stolarski , Louise Bordier , Arnaud Dapoigny , Gninwoyo Eric Hermann Coulibaly , Anne-Catherine Simon , Mathieu Agelou , Jonathan Fin , Nicolas Metzl , Guillaume Iwankow , Denis Allemand , Serge Planes , Clémentine Moulin , Fabien Lombard , Guillaume Bourdin , Romain Troublé , Sylvain Agostini , Bernard Banaigs , Emilie Boissin , Emmanuel Boss , Chris Bowler , Colomban de Vargas , Michel Flores , Didier Forcioli , Paola Furla , Eric Gilson , Pierre E Galand , Stéphane Pesant , Shinichi Sunagawa , Olivier P Thomas , Rebecca Vega Thurber , Christian R Voolstra , Patrick Wincker , Didier Zoccola , Stéphanie Reynaud

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean.

Nature communications

Avec: Corentin Hochart , Lucas Paoli , Hans-Joachim Ruscheweyh , Guillem Salazar , Emilie Boissin , Sarah Romac , Julie Poulain , Guillaume Bourdin , Guillaume Iwankow , Clémentine Moulin , Maren Ziegler , Barbara Porro , Eric J Armstrong , Benjamin C C Hume , Jean-Marc Aury , Claudia Pogoreutz , David A Paz-García , Maggy M Nugues , Sylvain Agostini , Bernard Banaigs , Emmanuel Boss , Chris Bowler , Colomban de Vargas , Eric Douville , Michel Flores , Didier Forcioli , Paola Furla , Eric Gilson , Fabien Lombard , Stéphane Pesant , Stéphanie Reynaud , Olivier P Thomas , Romain Troublé , Patrick Wincker , Didier Zoccola , Denis Allemand , Serge Planes , Rebecca Vega Thurber , Christian R Voolstra , Shinichi Sunagawa , Pierre E Galand

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

Scientific data

Avec: Fabien Lombard , Guillaume Bourdin , Stéphane Pesant , Sylvain Agostini , Alberto Baudena , Emilie Boissin , Nicolas Cassar , Megan Clampitt , Pascal Conan , Ophélie Da Silva , Céline Dimier , Eric Douville , Amanda Elineau , Jonathan Fin , J Michel Flores , Jean-François Ghiglione , Benjamin C C Hume , Laetitia Jalabert , Seth G John , Rachel L Kelly , Ilan Koren , Yajuan Lin , Dominique Marie , Ryan McMinds , Zoé Mériguet , Nicolas Metzl , David A Paz-García , Maria Luiza Pedrotti , Julie Poulain , Mireille Pujo-Pay , Joséphine Ras , Gilles Reverdin , Sarah Romac , Alice Rouan , Eric Röttinger , Assaf Vardi , Christian R Voolstra , Clémentine Moulin , Guillaume Iwankow , Bernard Banaigs , Chris Bowler , Colomban de Vargas , Didier Forcioli , Paola Furla , Pierre E Galand , Eric Gilson , Stéphanie Reynaud , Shinichi Sunagawa , Matthew B Sullivan , Olivier P Thomas , Romain Troublé , Rebecca Vega Thurber , Patrick Wincker , Didier Zoccola , Denis Allemand , Serge Planes , Emmanuel Boss , Gaby Gorsky

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

Nature communications

Avec: Leandro Quadrana , Mathilde Etcheverry , Arthur Gilly , Erwann Caillieux , Mohammed-Amin Madoui , Julie Guy , Amanda Bortolini Silveira , Stefan Engelen , Victoire Baillet , Patrick Wincker , Jean-Marc Aury , Vincent Colot

Marine DNA Viral Macro- and Microdiversity from Pole to Pole.

Cell

Avec: Ann C Gregory , Ahmed A Zayed , Nádia Conceição-Neto , Ben Temperton , Ben Bolduc , Adriana Alberti , Mathieu Ardyna , Ksenia Arkhipova , Margaux Carmichael , Corinne Cruaud , Céline Dimier , Guillermo Domínguez-Huerta , Joannie Ferland , Stefanie Kandels , Yunxiao Liu , Claudie Marec , Stéphane Pesant , Marc Picheral , Sergey Pisarev , Julie Poulain , Jean-Éric Tremblay , Dean Vik , Auteur inconnu , Marcel Babin , Chris Bowler , Alexander I Culley , Colomban de Vargas , Bas E Dutilh , Daniele Iudicone , Lee Karp-Boss , Simon Roux , Shinichi Sunagawa , Patrick Wincker , Matthew B Sullivan

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

Nucleic acids research

Avec: Laurence Garczarek , Ulysse Guyet , Hugo Doré , Gregory K Farrant , Mark Hoebeke , Loraine Brillet-Guéguen , Antoine Bisch , Mathilde Ferrieux , Jukka Siltanen , Erwan Corre , Gildas Le Corguillé , Morgane Ratin , Frances D Pitt , Martin Ostrowski , Maël Conan , Anne Siegel , Karine Labadie , Jean-Marc Aury , Patrick Wincker , David J Scanlan , Frédéric Partensky

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

Scientific reports

Avec: Quentin Carradec , Julie Poulain , Emilie Boissin , Benjamin C C Hume , Christian R Voolstra , Maren Ziegler , Stefan Engelen , Corinne Cruaud , Serge Planes , Patrick Wincker

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

Frontiers in microbiology

Avec: Hugo Doré , Gregory K Farrant , Ulysse Guyet , Julie Haguait , Florian Humily , Morgane Ratin , Frances D Pitt , Martin Ostrowski , Christophe Six , Loraine Brillet-Guéguen , Mark Hoebeke , Antoine Bisch , Gildas Le Corguillé , Erwan Corre , Karine Labadie , Jean-Marc Aury , Patrick Wincker , Dong Han Choi , Jae Hoon Noh , Damien Eveillard , David J Scanlan , Frédéric Partensky , Laurence Garczarek

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

Molecular ecology resources

Avec: Miriam I Brandt , Blandine Trouche , Laure Quintric , Babett Günther , Patrick Wincker , Julie Poulain , Sophie Arnaud-Haond

Male Differentiation in the Marine Copepod

Biology

Avec: Kevin Sugier , Romuald Laso-Jadart , Benoît Vacherie , Jos Käfer , Laurie Bertrand , Karine Labadie , Nathalie Martins , Céline Orvain , Emmanuelle Petit , Patrick Wincker , Jean-Louis Jamet , Adriana Alberti , Mohammed-Amin Madoui

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

GigaScience

Avec: Jean-Marc Aury , Stefan Engelen , Benjamin Istace , Cécile Monat , Pauline Lasserre-Zuber , Caroline Belser , Corinne Cruaud , Hélène Rimbert , Philippe Leroy , Sandrine Arribat , Isabelle Dufau , Arnaud Bellec , David Grimbichler , Nathan Papon , Etienne Paux , Marion Ranoux , Adriana Alberti , Patrick Wincker , Frédéric Choulet

Tempo and drivers of plant diversification in the European mountain system.

Nature communications

Avec: Jan Smyčka , Cristina Roquet , Martí Boleda , Adriana Alberti , Frédéric Boyer , Rolland Douzet , Christophe Perrier , Maxime Rome , Jean-Gabriel Valay , France Denoeud , Kristýna Šemberová , Niklaus E Zimmermann , Wilfried Thuiller , Patrick Wincker , Inger G Alsos , Eric Coissac , Auteur inconnu , Sébastien Lavergne

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

eLife

Avec: Daniel J Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont , Gabriel Reygondeau , Nicolas Maillet , Nicolas Henry , Gaëtan Benoit , Ophélie Da Silva , Tom O Delmont , Antonio Fernàndez-Guerra , Samir Suweis , Romain Narci , Cédric Berney , Damien Eveillard , Frederick Gavory , Lionel Guidi , Karine Labadie , Eric Mahieu , Julie Poulain , Sarah Romac , Simon Roux , Céline Dimier , Stefanie Kandels , Marc Picheral , Sarah Searson , Auteur inconnu , Stéphane Pesant , Jean-Marc Aury , Jennifer R Brum , Claire Lemaitre , Eric Pelletier , Peer Bork , Shinichi Sunagawa , Fabien Lombard , Lee Karp-Boss , Chris Bowler , Matthew B Sullivan , Eric Karsenti , Mahendra Mariadassou , Ian Probert , Pierre Peterlongo , Patrick Wincker , Colomban de Vargas , Maurizio Ribera d'Alcalà , Daniele Iudicone , Olivier Jaillon

Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean.

Nature communications

Avec: Eric J Armstrong , Julie Lê-Hoang , Quentin Carradec , Jean-Marc Aury , Benjamin Noel , Benjamin C C Hume , Christian R Voolstra , Julie Poulain , Caroline Belser , David A Paz-García , Corinne Cruaud , Karine Labadie , Corinne Da Silva , Clémentine Moulin , Emilie Boissin , Guillaume Bourdin , Guillaume Iwankow , Sarah Romac , Sylvain Agostini , Bernard Banaigs , Emmanuel Boss , Chris Bowler , Colomban de Vargas , Eric Douville , Michel Flores , Didier Forcioli , Paola Furla , Pierre E Galand , Eric Gilson , Fabien Lombard , Stéphane Pesant , Stéphanie Reynaud , Matthew B Sullivan , Shinichi Sunagawa , Olivier P Thomas , Romain Troublé , Rebecca Vega Thurber , Didier Zoccola , Serge Planes , Denis Allemand , Patrick Wincker

Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation.

ISME communications

Avec: Isabel Sanz-Sáez , Pablo Sánchez , Guillem Salazar , Shinichi Sunagawa , Colomban de Vargas , Chris Bowler , Matthew B Sullivan , Patrick Wincker , Eric Karsenti , Carlos Pedrós-Alió , Susana Agustí , Takashi Gojobori , Carlos M Duarte , Josep M Gasol , Olga Sánchez , Silvia G Acinas

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

Nature

Avec: Pablo Librado , Gaetan Tressières , Lorelei Chauvey , Antoine Fages , Naveed Khan , Stéphanie Schiavinato , Laure Calvière-Tonasso , Mariya A Kusliy , Charleen Gaunitz , Xuexue Liu , Stefanie Wagner , Clio Der Sarkissian , Andaine Seguin-Orlando , Aude Perdereau , Jean-Marc Aury , John Southon , Beth Shapiro , Olivier Bouchez , Cécile Donnadieu , Yvette Running Horse Collin , Kristian M Gregersen , Mads Dengsø Jessen , Kirsten Christensen , Lone Claudi-Hansen , Mélanie Pruvost , Erich Pucher , Hrvoje Vulic , Mario Novak , Andrea Rimpf , Peter Turk , Simone Reiter , Gottfried Brem , Christoph Schwall , Éric Barrey , Céline Robert , Christophe Degueurce , Liora Kolska Horwitz , Lutz Klassen , Uffe Rasmussen , Jacob Kveiborg , Niels Nørkjær Johannsen , Daniel Makowiecki , Przemysław Makarowicz , Marcin Szeliga , Vasyl Ilchyshyn , Vitalii Rud , Jan Romaniszyn , Victoria E Mullin , Marta Verdugo , Daniel G Bradley , João L Cardoso , Maria J Valente , Miguel Telles Antunes , Carly Ameen , Richard Thomas , Arne Ludwig , Matilde Marzullo , Ornella Prato , Giovanna Bagnasco Gianni , Umberto Tecchiati , José Granado , Angela Schlumbaum , Sabine Deschler-Erb , Monika Schernig Mráz , Nicolas Boulbes , Armelle Gardeisen , Christian Mayer , Hans-Jürgen Döhle , Magdolna Vicze , Pavel A Kosintsev , René Kyselý , Lubomír Peške , Terry O'Connor , Elina Ananyevskaya , Irina Shevnina , Andrey Logvin , Alexey A Kovalev , Tumur-Ochir Iderkhangai , Mikhail V Sablin , Petr K Dashkovskiy , Alexander S Graphodatsky , Ilia Merts , Viktor Merts , Aleksei K Kasparov , Vladimir V Pitulko , Vedat Onar , Aliye Öztan , Benjamin S Arbuckle , Hugh McColl , Gabriel Renaud , Ruslan Khaskhanov , Sergey Demidenko , Anna Kadieva , Biyaslan Atabiev , Marie Sundqvist , Gabriella Lindgren , F Javier López-Cachero , Silvia Albizuri , Tajana Trbojević Vukičević , Anita Rapan Papeša , Marcel Burić , Petra Rajić Šikanjić , Jaco Weinstock , David Asensio Vilaró , Ferran Codina , Cristina García Dalmau , Jordi Morer de Llorens , Josep Pou , Gabriel de Prado , Joan Sanmartí , Nabil Kallala , Joan Ramon Torres , Bouthéina Maraoui-Telmini , Maria-Carme Belarte Franco , Silvia Valenzuela-Lamas , Antoine Zazzo , Sébastien Lepetz , Sylvie Duchesne , Anatoly Alexeev , Jamsranjav Bayarsaikhan , Jean-Luc Houle , Noost Bayarkhuu , Tsagaan Turbat , Éric Crubézy , Irina Shingiray , Marjan Mashkour , Natalia Ya Berezina , Dmitriy S Korobov , Andrey Belinskiy , Alexey Kalmykov , Jean-Paul Demoule , Sabine Reinhold , Svend Hansen , Barbara Wallner , Natalia Roslyakova , Pavel F Kuznetsov , Alexey A Tishkin , Patrick Wincker , Katherine Kanne , Alan Outram , Ludovic Orlando

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

Molecular ecology

Avec: Jianfei Pan , Xuexue Liu , Mateusz Baca , Laure Calvière-Tonasso , Stéphanie Schiavinato , Loreleï Chauvey , Gaétan Tressières , Aude Perdereau , Jean-Marc Aury , Pedro H Oliveira , Patrick Wincker , Aida Abdykanova , Juan Luis Arsuaga , Jamsranjav Bayarsaikhan , Andrey B Belinskiy , Eudald Carbonell , Hossein Davoudi , Jaime Lira Garrido , Allan S Gilbert , Taylor Hermes , Christina Warinner , Alexey A Kalmykov , David Lordkipanidze , Paweł Mackiewicz , Azadeh F Mohaseb , Kristine Richter , Nuritdin Sayfullaev , Beth Shapiro , Svetlana Shnaider , John Southon , Krzysztof Stefaniak , Geoffrey D Summers , Eline Naomi van Asperen , Nikoloz Vanishvili , Eden A Hill , Pavel Kuznetsov , Sabine Reinhold , Svend Hansen , Marjan Mashkour , Rémi Berthon , William Timothy Treal Taylor , Jean-Luc Houle , Evon Hekkala , Danijela Popović , Ludovic Orlando

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.

Scientific reports

Avec: Shinya Sato , Deepak Nanjappa , Richard G Dorrell , Fabio Rocha Jimenez Vieira , Elena Kazamia , Leila Tirichine , Alaguraj Veluchamy , Roland Heilig , Jean-Marc Aury , Olivier Jaillon , Patrick Wincker , Zoltan Fussy , Miroslav Obornik , Sergio A Muñoz-Gómez , David G Mann , Chris Bowler , Adriana Zingone

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

The Plant journal : for cell and molecular biology

Avec: Julie Ferreira de Carvalho , Jérémy Lucas , Gwenaëlle Deniot , Cyril Falentin , Olivier Filangi , Marie Gilet , Fabrice Legeai , Maryse Lode , Jérôme Morice , Gwenn Trotoux , Jean-Marc Aury , Valérie Barbe , Jean Keller , Rod Snowdon , Zhesi He , France Denoeud , Patrick Wincker , Ian Bancroft , Anne-Marie Chèvre , Mathieu Rousseau-Gueutin

A gene graveyard in the genome of the fungus Podospora comata.

Molecular genetics and genomics : MGG

Avec: Philippe Silar , Jean-Marc Dauget , Valérie Gautier , Pierre Grognet , Michelle Chablat , Sylvie Hermann-Le Denmat , Arnaud Couloux , Patrick Wincker , Robert Debuchy

Late Quaternary dynamics of Arctic biota from ancient environmental genomics.

Nature

Avec: Yucheng Wang , Mikkel Winther Pedersen , Inger Greve Alsos , Bianca De Sanctis , Fernando Racimo , Ana Prohaska , Eric Coissac , Hannah Lois Owens , Marie Kristine Føreid Merkel , Antonio Fernandez-Guerra , Alexandra Rouillard , Youri Lammers , Adriana Alberti , France Denoeud , Daniel Money , Anthony H Ruter , Hugh McColl , Nicolaj Krog Larsen , Anna A Cherezova , Mary E Edwards , Grigory B Fedorov , James Haile , Ludovic Orlando , Lasse Vinner , Thorfinn Sand Korneliussen , David W Beilman , Anders A Bjørk , Jialu Cao , Christoph Dockter , Julie Esdale , Galina Gusarova , Kristian K Kjeldsen , Jan Mangerud , Jeffrey T Rasic , Birgitte Skadhauge , John Inge Svendsen , Alexei Tikhonov , Patrick Wincker , Yingchun Xing , Yubin Zhang , Duane G Froese , Carsten Rahbek , David Nogues Bravo , Philip B Holden , Neil R Edwards , Richard Durbin , David J Meltzer , Kurt H Kjær , Per Möller , Eske Willerslev

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient.

Frontiers in microbiology

Avec: Blandine Trouche , Miriam I Brandt , Caroline Belser , Covadonga Orejas , Stéphane Pesant , Julie Poulain , Patrick Wincker , Jean-Christophe Auguet , Sophie Arnaud-Haond , Loïs Maignien

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

The ISME journal

Avec: Tom O Delmont , Juan José Pierella Karlusich , Iva Veseli , Jessika Fuessel , A Murat Eren , Rachel A Foster , Chris Bowler , Patrick Wincker , Eric Pelletier

Comparative genomics reveals new functional insights in uncultured MAST species.

The ISME journal

Avec: Aurelie Labarre , David López-Escardó , Francisco Latorre , Guy Leonard , François Bucchini , Aleix Obiol , Corinne Cruaud , Michael E Sieracki , Olivier Jaillon , Patrick Wincker , Klaas Vandepoele , Ramiro Logares , Ramon Massana

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

GigaScience

Avec: Mathieu Rousseau-Gueutin , Caroline Belser , Corinne Da Silva , Gautier Richard , Benjamin Istace , Corinne Cruaud , Cyril Falentin , Franz Boideau , Julien Boutte , Regine Delourme , Gwenaëlle Deniot , Stefan Engelen , Julie Ferreira de Carvalho , Arnaud Lemainque , Loeiz Maillet , Jérôme Morice , Patrick Wincker , France Denoeud , Anne-Marie Chèvre , Jean-Marc Aury

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

BMC bioinformatics

Avec: Christophe Djemiel , Samuel Dequiedt , Battle Karimi , Aurélien Cottin , Thibault Girier , Yassin El Djoudi , Patrick Wincker , Mélanie Lelièvre , Samuel Mondy , Nicolas Chemidlin Prévost-Bouré , Pierre-Alain Maron , Lionel Ranjard , Sébastien Terrat

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

BMC biology

Avec: Elise J Gay , Jessica L Soyer , Nicolas Lapalu , Juliette Linglin , Isabelle Fudal , Corinne Da Silva , Patrick Wincker , Jean-Marc Aury , Corinne Cruaud , Anne Levrel , Jocelyne Lemoine , Regine Delourme , Thierry Rouxel , Marie-Hélène Balesdent

Sequencing and Chromosome-Scale Assembly of Plant Genomes,

Biology

Avec: Benjamin Istace , Caroline Belser , Cyril Falentin , Karine Labadie , Franz Boideau , Gwenaëlle Deniot , Loeiz Maillet , Corinne Cruaud , Laurie Bertrand , Anne-Marie Chèvre , Patrick Wincker , Mathieu Rousseau-Gueutin , Jean-Marc Aury

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

The ISME journal

Avec: Clemens Schauberger , Ronnie N Glud , Bela Hausmann , Blandine Trouche , Lois Maignien , Julie Poulain , Patrick Wincker , Sophie Arnaud-Haond , Frank Wenzhöfer , Bo Thamdrup

A robust approach to estimate relative phytoplankton cell abundances from metagenomes.

Molecular ecology resources

Avec: Juan José Pierella Karlusich , Eric Pelletier , Lucie Zinger , Fabien Lombard , Adriana Zingone , Sébastien Colin , Josep M Gasol , Richard G Dorrell , Nicolas Henry , Eleonora Scalco , Silvia G Acinas , Patrick Wincker , Colomban de Vargas , Chris Bowler

Diversity and ecological footprint of Global Ocean RNA viruses.

Science (New York, N.Y.)

Avec: Guillermo Dominguez-Huerta , Ahmed A Zayed , James M Wainaina , Jiarong Guo , Funing Tian , Akbar Adjie Pratama , Benjamin Bolduc , Mohamed Mohssen , Olivier Zablocki , Eric Pelletier , Erwan Delage , Adriana Alberti , Jean-Marc Aury , Quentin Carradec , Corinne da Silva , Karine Labadie , Julie Poulain , Auteur inconnu , Chris Bowler , Damien Eveillard , Lionel Guidi , Eric Karsenti , Jens H Kuhn , Hiroyuki Ogata , Patrick Wincker , Alexander Culley , Samuel Chaffron , Matthew B Sullivan

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

ISME communications

Avec: Blandine Trouche , Clemens Schauberger , Feriel Bouderka , Jean-Christophe Auguet , Caroline Belser , Julie Poulain , Bo Thamdrup , Patrick Wincker , Sophie Arnaud-Haond , Ronnie N Glud , Loïs Maignien

The genomic history and global expansion of domestic donkeys.

Science (New York, N.Y.)

Avec: Evelyn T Todd , Laure Tonasso-Calvière , Loreleï Chauvey , Stéphanie Schiavinato , Antoine Fages , Andaine Seguin-Orlando , Pierre Clavel , Naveed Khan , Lucía Pérez Pardal , Laura Patterson Rosa , Pablo Librado , Harald Ringbauer , Marta Verdugo , John Southon , Jean-Marc Aury , Aude Perdereau , Emmanuelle Vila , Matilde Marzullo , Ornella Prato , Umberto Tecchiati , Giovanna Bagnasco Gianni , Antonio Tagliacozzo , Vincenzo Tinè , Francesca Alhaique , João Luís Cardoso , Maria João Valente , Miguel Telles Antunes , Laurent Frantz , Beth Shapiro , Daniel G Bradley , Nicolas Boulbes , Armelle Gardeisen , Liora Kolska Horwitz , Aliye Öztan , Benjamin S Arbuckle , Vedat Onar , Benoît Clavel , Sébastien Lepetz , Ali Akbar Vahdati , Hossein Davoudi , Azadeh Mohaseb , Marjan Mashkour , Olivier Bouchez , Cécile Donnadieu , Patrick Wincker , Samantha A Brooks , Albano Beja-Pereira , Dong-Dong Wu , Ludovic Orlando

Analysis of the

Cell genomics

Avec: Ferdinand Marlétaz , Arnaud Couloux , Julie Poulain , Karine Labadie , Corinne Da Silva , Sophie Mangenot , Benjamin Noel , Albert J Poustka , Philippe Dru , Cinta Pegueroles , Marco Borra , Elijah K Lowe , Guy Lhomond , Lydia Besnardeau , Stéphanie Le Gras , Tao Ye , Daria Gavriouchkina , Roberta Russo , Caterina Costa , Francesca Zito , Letizia Anello , Aldo Nicosia , Maria Antonietta Ragusa , Marta Pascual , M Dolores Molina , Aline Chessel , Marta Di Carlo , Xavier Turon , Richard R Copley , Jean-Yves Exposito , Pedro Martinez , Vincenzo Cavalieri , Smadar Ben Tabou de Leon , Jenifer Croce , Paola Oliveri , Valeria Matranga , Maria Di Bernardo , Julia Morales , Patrick Cormier , Anne-Marie Geneviève , Jean Marc Aury , Valérie Barbe , Patrick Wincker , Maria Ina Arnone , Christian Gache , Thierry Lepage

The defensome of complex bacterial communities.

Nature communications

Avec: Angelina Beavogui , Auriane Lacroix , Nicolas Wiart , Julie Poulain , Tom O Delmont , Lucas Paoli , Patrick Wincker , Pedro H Oliveira

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

Nature communications

Avec: Ana Paula Zotta Mota , Georgios D Koutsovoulos , Laetitia Perfus-Barbeoch , Evelin Despot-Slade , Karine Labadie , Jean-Marc Aury , Karine Robbe-Sermesant , Marc Bailly-Bechet , Caroline Belser , Arthur Péré , Corinne Rancurel , Djampa K Kozlowski , Rahim Hassanaly-Goulamhoussen , Martine Da Rocha , Benjamin Noel , Nevenka Meštrović , Patrick Wincker , Etienne G J Danchin

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

Cell

Avec: Guillem Salazar , Lucas Paoli , Adriana Alberti , Jaime Huerta-Cepas , Hans-Joachim Ruscheweyh , Miguelangel Cuenca , Christopher M Field , Luis Pedro Coelho , Corinne Cruaud , Stefan Engelen , Ann C Gregory , Karine Labadie , Claudie Marec , Eric Pelletier , Marta Royo-Llonch , Simon Roux , Pablo Sánchez , Hideya Uehara , Ahmed A Zayed , Georg Zeller , Margaux Carmichael , Céline Dimier , Joannie Ferland , Stefanie Kandels , Marc Picheral , Sergey Pisarev , Julie Poulain , Auteur inconnu , Silvia G Acinas , Marcel Babin , Peer Bork , Chris Bowler , Colomban de Vargas , Lionel Guidi , Pascal Hingamp , Daniele Iudicone , Lee Karp-Boss , Eric Karsenti , Hiroyuki Ogata , Stephane Pesant , Sabrina Speich , Matthew B Sullivan , Patrick Wincker , Shinichi Sunagawa

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

Molecular ecology

Avec: Paolo Sordino , Salvatore D'Aniello , Eric Pelletier , Patrick Wincker , Valeria Nittoli , Lars Stemmann , Maria Grazia Mazzocchi , Fabien Lombard , Daniele Iudicone , Luigi Caputi

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

PLoS biology

Avec: Serge Planes , Denis Allemand , Sylvain Agostini , Bernard Banaigs , Emilie Boissin , Emmanuel Boss , Guillaume Bourdin , Chris Bowler , Eric Douville , J Michel Flores , Didier Forcioli , Paola Furla , Pierre E Galand , Jean-François Ghiglione , Eric Gilson , Fabien Lombard , Clémentine Moulin , Stephane Pesant , Julie Poulain , Stéphanie Reynaud , Sarah Romac , Matthew B Sullivan , Shinichi Sunagawa , Olivier P Thomas , Romain Troublé , Colomban de Vargas , Rebecca Vega Thurber , Christian R Voolstra , Patrick Wincker , Didier Zoccola , Auteur inconnu

Meta-Omics Reveals Genetic Flexibility of Diatom Nitrogen Transporters in Response to Environmental Changes.

Molecular biology and evolution

Avec: Greta Busseni , Fabio Rocha Jimenez Vieira , Alberto Amato , Eric Pelletier , Juan J Pierella Karlusich , Maria I Ferrante , Patrick Wincker , Alessandra Rogato , Chris Bowler , Remo Sanges , Luigi Maiorano , Maurizio Chiurazzi , Maurizio Ribera d'Alcalà , Luigi Caputi , Daniele Iudicone

A reference genome for pea provides insight into legume genome evolution.

Nature genetics

Avec: Jonathan Kreplak , Mohammed-Amin Madoui , Petr Cápal , Petr Novák , Karine Labadie , Grégoire Aubert , Philipp E Bayer , Krishna K Gali , Robert A Syme , Dorrie Main , Anthony Klein , Aurélie Bérard , Iva Vrbová , Cyril Fournier , Leo d'Agata , Caroline Belser , Wahiba Berrabah , Helena Toegelová , Zbyněk Milec , Jan Vrána , HueyTyng Lee , Ayité Kougbeadjo , Morgane Térézol , Cécile Huneau , Chala J Turo , Nacer Mohellibi , Pavel Neumann , Matthieu Falque , Karine Gallardo , Rebecca McGee , Bunyamin Tar'an , Abdelhafid Bendahmane , Jean-Marc Aury , Jacqueline Batley , Marie-Christine Le Paslier , Noel Ellis , Thomas D Warkentin , Clarice J Coyne , Jérome Salse , David Edwards , Judith Lichtenzveig , Jiří Macas , Jaroslav Doležel , Patrick Wincker , Judith Burstin

Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea.

Molecular ecology resources

Avec: Majda Arif , Jérémy Gauthier , Kevin Sugier , Daniele Iudicone , Olivier Jaillon , Patrick Wincker , Pierre Peterlongo , Mohammed-Amin Madoui

Tara Oceans: towards global ocean ecosystems biology.

Nature reviews. Microbiology

Avec: Shinichi Sunagawa , Silvia G Acinas , Peer Bork , Chris Bowler , Auteur inconnu , Damien Eveillard , Gabriel Gorsky , Lionel Guidi , Daniele Iudicone , Eric Karsenti , Fabien Lombard , Hiroyuki Ogata , Stephane Pesant , Matthew B Sullivan , Patrick Wincker , Colomban de Vargas

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

BMC genomics

Avec: Aurélie Canaguier , Romane Guilbaud , Erwan Denis , Ghislaine Magdelenat , Caroline Belser , Benjamin Istace , Corinne Cruaud , Patrick Wincker , Marie-Christine Le Paslier , Patricia Faivre-Rampant , Valérie Barbe

Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria.

Genome biology and evolution

Avec: Théophile Grébert , Laurence Garczarek , Vincent Daubin , Florian Humily , Dominique Marie , Morgane Ratin , Alban Devailly , Gregory K Farrant , Isabelle Mary , Daniella Mella-Flores , Gwenn Tanguy , Karine Labadie , Patrick Wincker , David M Kehoe , Frédéric Partensky

Environmental vulnerability of the global ocean epipelagic plankton community interactome.

Science advances

Avec: Samuel Chaffron , Erwan Delage , Marko Budinich , Damien Vintache , Nicolas Henry , Charlotte Nef , Mathieu Ardyna , Ahmed A Zayed , Pedro C Junger , Pierre E Galand , Connie Lovejoy , Alison E Murray , Hugo Sarmento , Auteur inconnu , Silvia G Acinas , Marcel Babin , Daniele Iudicone , Olivier Jaillon , Eric Karsenti , Patrick Wincker , Lee Karp-Boss , Matthew B Sullivan , Chris Bowler , Colomban de Vargas , Damien Eveillard

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

Communications biology

Avec: Caroline Belser , Franc-Christophe Baurens , Benjamin Noel , Guillaume Martin , Corinne Cruaud , Benjamin Istace , Nabila Yahiaoui , Karine Labadie , Eva Hřibová , Jaroslav Doležel , Arnaud Lemainque , Patrick Wincker , Angélique D'Hont , Jean-Marc Aury

Diversity of the Pacific Ocean coral reef microbiome.

Nature communications

Avec: Pierre E Galand , Hans-Joachim Ruscheweyh , Guillem Salazar , Corentin Hochart , Nicolas Henry , Benjamin C C Hume , Pedro H Oliveira , Aude Perdereau , Karine Labadie , Caroline Belser , Emilie Boissin , Sarah Romac , Julie Poulain , Guillaume Bourdin , Guillaume Iwankow , Clémentine Moulin , Eric J Armstrong , David A Paz-García , Maren Ziegler , Sylvain Agostini , Bernard Banaigs , Emmanuel Boss , Chris Bowler , Colomban de Vargas , Eric Douville , Michel Flores , Didier Forcioli , Paola Furla , Eric Gilson , Fabien Lombard , Stéphane Pesant , Stéphanie Reynaud , Olivier P Thomas , Romain Troublé , Didier Zoccola , Christian R Voolstra , Rebecca Vega Thurber , Shinichi Sunagawa , Patrick Wincker , Denis Allemand , Serge Planes

Pervasive tandem duplications and convergent evolution shape coral genomes.

Genome biology

Avec: Benjamin Noel , France Denoeud , Alice Rouan , Carol Buitrago-López , Laura Capasso , Julie Poulain , Emilie Boissin , Mélanie Pousse , Corinne Da Silva , Arnaud Couloux , Eric Armstrong , Quentin Carradec , Corinne Cruaud , Karine Labadie , Julie Lê-Hoang , Sylvie Tambutté , Valérie Barbe , Clémentine Moulin , Guillaume Bourdin , Guillaume Iwankow , Sarah Romac , Sylvain Agostini , Bernard Banaigs , Emmanuel Boss , Chris Bowler , Colomban de Vargas , Eric Douville , J Michel Flores , Didier Forcioli , Paola Furla , Pierre E Galand , Fabien Lombard , Stéphane Pesant , Stéphanie Reynaud , Matthew B Sullivan , Shinichi Sunagawa , Olivier P Thomas , Romain Troublé , Rebecca Vega Thurber , Denis Allemand , Serge Planes , Eric Gilson , Didier Zoccola , Patrick Wincker , Christian R Voolstra , Jean-Marc Aury

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

Molecular ecology

Avec: Stefanie Wagner , Andaine Seguin-Orlando , Jean-Charles Leplé , Thibault Leroy , Céline Lalanne , Karine Labadie , Jean-Marc Aury , Sandy Poirier , Patrick Wincker , Christophe Plomion , Antoine Kremer , Ludovic Orlando

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

Science (New York, N.Y.)

Avec: William Timothy Treal Taylor , Pablo Librado , Chief Joseph American Horse , Carlton Shield Chief Gover , Jimmy Arterberry , Antonia Loretta Afraid of Bear-Cook , Harold Left Heron , Robert Milo Yellow Hair , Mario Gonzalez , Bill Means , Sam High Crane , Wendell W. Yellow Bull , Barbara Dull Knife , Anita Afraid of Bear , Cruz Tecumseh Collin , Chance Ward , Theresa A Pasqual , Lorelei Chauvey , Laure Tonasso-Calviere , Stéphanie Schiavinato , Andaine Seguin-Orlando , Antoine Fages , Naveed Khan , Clio Der Sarkissian , Xuexue Liu , Stefanie Wagner , Beth Ginondidoy Leonard , Bruce L Manzano , Nancy O'Malley , Jennifer A Leonard , Eloísa Bernáldez-Sánchez , Eric Barrey , Léa Charliquart , Emilie Robbe , Thibault Denoblet , Kristian Gregersen , Alisa O Vershinina , Jaco Weinstock , Petra Rajić Šikanjić , Marjan Mashkour , Irina Shingiray , Jean-Marc Aury , Aude Perdereau , Saleh Alquraishi , Ahmed H Alfarhan , Khaled A S Al-Rasheid , Tajana Trbojević Vukičević , Marcel Buric , Eberhard Sauer , Mary Lucas , Joan Brenner-Coltrain , John R Bozell , Cassidee A Thornhill , Victoria Monagle , Angela Perri , Cody Newton , W Eugene Hall , Joshua L Conver , Petrus Le Roux , Sasha G Buckser , Caroline Gabe , Juan Bautista Belardi , Christina I Barrón-Ortiz , Isaac A Hart , Christina Ryder , Matthew Sponheimer , Beth Shapiro , John Southon , Joss Hibbs , Charlotte Faulkner , Alan Outram , Laura Patterson Rosa , Katelyn Palermo , Marina Solé , Alice William , Wayne McCrory , Gabriella Lindgren , Samantha Brooks , Camille Eché , Cécile Donnadieu , Olivier Bouchez , Patrick Wincker , Gregory Hodgins , Sarah Trabert , Brandi Bethke , Patrick Roberts , Emily Lena Jones , Yvette Running Horse Collin , Ludovic Orlando

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

iScience

Avec: Xuexue Liu , Andaine Seguin-Orlando , Lorelei Chauvey , Gaëtan Tressières , Stéphanie Schiavinato , Laure Tonasso-Calvière , Jean-Marc Aury , Aude Perdereau , Stefanie Wagner , Pierre Clavel , Oscar Estrada , Jianfei Pan , Yuehui Ma , Jacob Enk , Alison Devault , Jennifer Klunk , Sébastien Lepetz , Benoit Clavel , Lin Jiang , Patrick Wincker , Yvette Running Horse Collin , Clio Der Sarkissian , Ludovic Orlando

The NEREA Augmented Observatory: an integrative approach to marine coastal ecology.

Scientific data

Avec: Lucia Campese , Luca Russo , Maria Abagnale , Adriana Alberti , Giancarlo Bachi , Cecilia Balestra , Daniele Bellardini , Angela Buondonno , Ulisse Cardini , Ylenia Carotenuto , Giovanni Checcucci , Maria Luisa Chiusano , Isabella D'Ambra , Giuliana d'Ippolito , Iole Di Capua , Vincenzo Donnarumma , Angelo Fontana , Marta Furia , Denisse Galarza-Verkovitch , Roberto Gallia , Karine Labadie , Serena Leone , Priscilla Licandro , Antonio Longo , Maira Maselli , Louise Merquiol , Carola Murano , Pedro H Oliveira , Augusto Passarelli , Isabella Percopo , Aude Perdereau , Roberta Piredda , Francesca Raffini , Vittoria Roncalli , Hans-Joachim Ruscheweyh , Ennio Russo , Maria Saggiomo , Chiara Santinelli , Diana Sarno , Shinichi Sunagawa , Ferdinando Tramontano , Anna Chiara Trano , Marco Uttieri , Patrick Wincker , Gianpaolo Zampicinini , Raffaella Casotti , Fabio Conversano , Domenico D'Alelio , Daniele Iudicone , Francesca Margiotta , Marina Montresor

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

npj biodiversity

Avec: Ann M Mc Cartney , Giulio Formenti , Alice Mouton , Diego De Panis , Luísa S Marins , Henrique G Leitão , Genevieve Diedericks , Joseph Kirangwa , Marco Morselli , Judit Salces-Ortiz , Nuria Escudero , Alessio Iannucci , Chiara Natali , Hannes Svardal , Rosa Fernández , Tim De Pooter , Geert Joris , Mojca Strazisar , Jonathan M D Wood , Katie E Herron , Ole Seehausen , Phillip C Watts , Felix Shaw , Robert P Davey , Alice Minotto , José M Fernández , Astrid Böhne , Carla Alegria , Tyler Alioto , Paulo C Alves , Isabel R Amorim , Jean-Marc Aury , Niclas Backstrom , Petr Baldrian , Laima Baltrunaite , Endre Barta , Bertrand BedHom , Caroline Belser , Johannes Bergsten , Laurie Bertrand , Helena Bilandija , Mahesh Binzer-Panchal , Iliana Bista , Mark Blaxter , Paulo A V Borges , Guilherme Borges Dias , Mirte Bosse , Tom Brown , Rémy Bruggmann , Elena Buena-Atienza , Josephine Burgin , Elena Buzan , Alessia Cariani , Nicolas Casadei , Matteo Chiara , Sergio Chozas , Fedor Čiampor , Angelica Crottini , Corinne Cruaud , Fernando Cruz , Love Dalen , Alessio De Biase , Javier Del Campo , Teo Delic , Alice B Dennis , Martijn F L Derks , Maria Angela Diroma , Mihajla Djan , Simone Duprat , Klara Eleftheriadi , Philine G D Feulner , Jean-François Flot , Giobbe Forni , Bruno Fosso , Pascal Fournier , Christine Fournier-Chambrillon , Toni Gabaldon , Shilpa Garg , Carmela Gissi , Luca Giupponi , Jessica Gomez-Garrido , Josefa González , Miguel L Grilo , Björn Grüning , Thomas Guerin , Nadege Guiglielmoni , Marta Gut , Marcel P Haesler , Christoph Hahn , Balint Halpern , Peter W Harrison , Julia Heintz , Maris Hindrikson , Jacob Höglund , Kerstin Howe , Graham M Hughes , Benjamin Istace , Mark J Cock , Franc Janžekovič , Zophonias O Jonsson , Sagane Joye-Dind , Janne J Koskimäki , Boris Krystufek , Justyna Kubacka , Heiner Kuhl , Szilvia Kusza , Karine Labadie , Meri Lähteenaro , Henrik Lantz , Anton Lavrinienko , Lucas Leclère , Ricardo Jorge Lopes , Ole Madsen , Ghislaine Magdelenat , Giulia Magoga , Tereza Manousaki , Tapio Mappes , Joao Pedro Marques , Gemma I Martinez Redondo , Florian Maumus , Shane A McCarthy , Hendrik-Jan Megens , Jose Melo-Ferreira , Sofia L Mendes , Matteo Montagna , Joao Moreno , Mai-Britt Mosbech , Mónica Moura , Zuzana Musilova , Eugene Myers , Will J Nash , Alexander Nater , Pamela Nicholson , Manuel Niell , Reindert Nijland , Benjamin Noel , Karin Noren , Pedro H Oliveira , Remi-Andre Olsen , Lino Ometto , Rebekah A Oomen , Stephan Ossowski , Vaidas Palinauskas , Snaebjorn Palsson , Jerome P Panibe , Joana Pauperio , Martina Pavlek , Emilie Payen , Julia Pawlowska , Jaume Pellicer , Graziano Pesole , Joao Pimenta , Martin Pippel , Anna Maria Pirttilä , Nikos Poulakakis , Jeena Rajan , Rúben M C Rego , Roberto Resendes , Philipp Resl , Ana Riesgo , Patrik Rodin-Morch , Andre E R Soares , Carlos Rodriguez Fernandes , Maria M Romeiras , Guilherme Roxo , Lukas Rüber , Maria Jose Ruiz-Lopez , Urmas Saarma , Luis P da Silva , Manuela Sim-Sim , Lucile Soler , Vitor C Sousa , Carla Sousa Santos , Alberto Spada , Milomir Stefanovic , Viktor Steger , Josefin Stiller , Matthias Stöck , Torsten H Struck , Hiranya Sudasinghe , Riikka Tapanainen , Christian Tellgren-Roth , Helena Trindade , Yevhen Tukalenko , Ilenia Urso , Benoit Vacherie , Steven M Van Belleghem , Kees Van Oers , Carlos Vargas-Chavez , Nevena Velickovic , Noel Vella , Adriana Vella , Cristiano Vernesi , Sara Vicente , Sara Villa , Olga Vinnere Pettersson , Filip A M Volckaert , Judit Voros , Patrick Wincker , Sylke Winkler , Claudio Ciofi , Robert M Waterhouse , Camila J Mazzoni

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

Scientific reports

Avec: M E Sieracki , N J Poulton , O Jaillon , P Wincker , C de Vargas , L Rubinat-Ripoll , R Stepanauskas , R Logares , R Massana

Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity.

Scientific reports

Avec: Battle Karimi , Samuel Dequiedt , Sébastien Terrat , Claudy Jolivet , Dominique Arrouays , Patrick Wincker , Corinne Cruaud , Antonio Bispo , Nicolas Chemidlin Prévost-Bouré , Lionel Ranjard

Genome Resolved Biogeography of Mamiellales.

Genes

Avec: Jade Leconte , L Felipe Benites , Thomas Vannier , Patrick Wincker , Gwenael Piganeau , Olivier Jaillon

Investigating population-scale allelic differential expression in wild populations of

Ecology and evolution

Avec: Romuald Laso-Jadart , Kevin Sugier , Emmanuelle Petit , Karine Labadie , Pierre Peterlongo , Christophe Ambroise , Patrick Wincker , Jean-Louis Jamet , Mohammed-Amin Madoui

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

Nature ecology & evolution

Avec: Hisashi Endo , Romain Blanc-Mathieu , Yanze Li , Guillem Salazar , Nicolas Henry , Karine Labadie , Colomban de Vargas , Matthew B Sullivan , Chris Bowler , Patrick Wincker , Lee Karp-Boss , Shinichi Sunagawa , Hiroyuki Ogata

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

Nature

Avec: Pablo Librado , Naveed Khan , Antoine Fages , Mariya A Kusliy , Tomasz Suchan , Laure Tonasso-Calvière , Stéphanie Schiavinato , Duha Alioglu , Aurore Fromentier , Aude Perdereau , Jean-Marc Aury , Charleen Gaunitz , Lorelei Chauvey , Andaine Seguin-Orlando , Clio Der Sarkissian , John Southon , Beth Shapiro , Alexey A Tishkin , Alexey A Kovalev , Saleh Alquraishi , Ahmed H Alfarhan , Khaled A S Al-Rasheid , Timo Seregély , Lutz Klassen , Rune Iversen , Olivier Bignon-Lau , Pierre Bodu , Monique Olive , Jean-Christophe Castel , Myriam Boudadi-Maligne , Nadir Alvarez , Mietje Germonpré , Magdalena Moskal-Del Hoyo , Jarosław Wilczyński , Sylwia Pospuła , Anna Lasota-Kuś , Krzysztof Tunia , Marek Nowak , Eve Rannamäe , Urmas Saarma , Gennady Boeskorov , Lembi Lōugas , René Kyselý , Lubomír Peške , Adrian Bălășescu , Valentin Dumitrașcu , Roxana Dobrescu , Daniel Gerber , Viktória Kiss , Anna Szécsényi-Nagy , Balázs G Mende , Zsolt Gallina , Krisztina Somogyi , Gabriella Kulcsár , Erika Gál , Robin Bendrey , Morten E Allentoft , Ghenadie Sirbu , Valentin Dergachev , Henry Shephard , Noémie Tomadini , Sandrine Grouard , Aleksei Kasparov , Alexander E Basilyan , Mikhail A Anisimov , Pavel A Nikolskiy , Elena Y Pavlova , Vladimir Pitulko , Gottfried Brem , Barbara Wallner , Christoph Schwall , Marcel Keller , Keiko Kitagawa , Alexander N Bessudnov , Alexander Bessudnov , William Taylor , Jérome Magail , Jamiyan-Ombo Gantulga , Jamsranjav Bayarsaikhan , Diimaajav Erdenebaatar , Kubatbeek Tabaldiev , Enkhbayar Mijiddorj , Bazartseren Boldgiv , Turbat Tsagaan , Mélanie Pruvost , Sandra Olsen , Cheryl A Makarewicz , Silvia Valenzuela Lamas , Silvia Albizuri Canadell , Ariadna Nieto Espinet , Ma Pilar Iborra , Jaime Lira Garrido , Esther Rodríguez González , Sebastián Celestino , Carmen Olària , Juan Luis Arsuaga , Nadiia Kotova , Alexander Pryor , Pam Crabtree , Rinat Zhumatayev , Abdesh Toleubaev , Nina L Morgunova , Tatiana Kuznetsova , David Lordkipanize , Matilde Marzullo , Ornella Prato , Giovanna Bagnasco Gianni , Umberto Tecchiati , Benoit Clavel , Sébastien Lepetz , Hossein Davoudi , Marjan Mashkour , Natalia Ya Berezina , Philipp W Stockhammer , Johannes Krause , Wolfgang Haak , Arturo Morales-Muñiz , Norbert Benecke , Michael Hofreiter , Arne Ludwig , Alexander S Graphodatsky , Joris Peters , Kirill Yu Kiryushin , Tumur-Ochir Iderkhangai , Nikolay A Bokovenko , Sergey K Vasiliev , Nikolai N Seregin , Konstantin V Chugunov , Natalya A Plasteeva , Gennady F Baryshnikov , Ekaterina Petrova , Mikhail Sablin , Elina Ananyevskaya , Andrey Logvin , Irina Shevnina , Victor Logvin , Saule Kalieva , Valeriy Loman , Igor Kukushkin , Ilya Merz , Victor Merz , Sergazy Sakenov , Victor Varfolomeyev , Emma Usmanova , Viktor Zaibert , Benjamin Arbuckle , Andrey B Belinskiy , Alexej Kalmykov , Sabine Reinhold , Svend Hansen , Aleksandr I Yudin , Alekandr A Vybornov , Andrey Epimakhov , Natalia S Berezina , Natalia Roslyakova , Pavel A Kosintsev , Pavel F Kuznetsov , David Anthony , Guus J Kroonen , Kristian Kristiansen , Patrick Wincker , Alan Outram , Ludovic Orlando

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

Scientific reports

Avec: Miriam I Brandt , Florence Pradillon , Blandine Trouche , Nicolas Henry , Cathy Liautard-Haag , Marie-Anne Cambon-Bonavita , Valérie Cueff-Gauchard , Patrick Wincker , Caroline Belser , Julie Poulain , Sophie Arnaud-Haond , Daniela Zeppilli

Population genomics of apricots unravels domestication history and adaptive events.

Nature communications

Avec: Alexis Groppi , Shuo Liu , Amandine Cornille , Stéphane Decroocq , Quynh Trang Bui , David Tricon , Corinne Cruaud , Sandrine Arribat , Caroline Belser , William Marande , Jérôme Salse , Cécile Huneau , Nathalie Rodde , Wassim Rhalloussi , Stéphane Cauet , Benjamin Istace , Erwan Denis , Sébastien Carrère , Jean-Marc Audergon , Guillaume Roch , Patrick Lambert , Tetyana Zhebentyayeva , Wei-Sheng Liu , Olivier Bouchez , Céline Lopez-Roques , Rémy-Félix Serre , Robert Debuchy , Joseph Tran , Patrick Wincker , Xilong Chen , Pierre Pétriacq , Aurélien Barre , Macha Nikolski , Jean-Marc Aury , Albert Glenn Abbott , Tatiana Giraud , Véronique Decroocq

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods.

Nature communications

Avec: Juan José Pierella Karlusich , Eric Pelletier , Fabien Lombard , Madeline Carsique , Etienne Dvorak , Sébastien Colin , Marc Picheral , Francisco M Cornejo-Castillo , Silvia G Acinas , Rainer Pepperkok , Eric Karsenti , Colomban de Vargas , Patrick Wincker , Chris Bowler , Rachel A Foster

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

Science advances

Avec: Tristan Cordier , Inès Barrenechea Angeles , Nicolas Henry , Franck Lejzerowicz , Cédric Berney , Raphaël Morard , Angelika Brandt , Marie-Anne Cambon-Bonavita , Lionel Guidi , Fabien Lombard , Pedro Martinez Arbizu , Ramon Massana , Covadonga Orejas , Julie Poulain , Craig R Smith , Patrick Wincker , Sophie Arnaud-Haond , Andrew J Gooday , Colomban de Vargas , Jan Pawlowski

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

Science (New York, N.Y.)

Avec: Ahmed A Zayed , James M Wainaina , Guillermo Dominguez-Huerta , Eric Pelletier , Jiarong Guo , Mohamed Mohssen , Funing Tian , Akbar Adjie Pratama , Benjamin Bolduc , Olivier Zablocki , Dylan Cronin , Lindsey Solden , Erwan Delage , Adriana Alberti , Jean-Marc Aury , Quentin Carradec , Corinne da Silva , Karine Labadie , Julie Poulain , Hans-Joachim Ruscheweyh , Guillem Salazar , Elan Shatoff , Auteur inconnu , Ralf Bundschuh , Kurt Fredrick , Laura S Kubatko , Samuel Chaffron , Alexander I Culley , Shinichi Sunagawa , Jens H Kuhn , Patrick Wincker , Matthew B Sullivan , Silvia G Acinas , Marcel Babin , Peer Bork , Emmanuel Boss , Chris Bowler , Guy Cochrane , Colomban de Vargas , Gabriel Gorsky , Lionel Guidi , Nigel Grimsley , Pascal Hingamp , Daniele Iudicone , Olivier Jaillon , Stefanie Kandels , Lee Karp-Boss , Eric Karsenti , Fabrice Not , Hiroyuki Ogata , Nicole Poulton , Stéphane Pesant , Christian Sardet , Sabrinia Speich , Lars Stemmann , Matthew B Sullivan , Shinichi Sungawa , Patrick Wincker

Mirusviruses link herpesviruses to giant viruses.

Nature

Avec: Morgan Gaïa , Lingjie Meng , Eric Pelletier , Patrick Forterre , Chiara Vanni , Antonio Fernandez-Guerra , Olivier Jaillon , Patrick Wincker , Hiroyuki Ogata , Mart Krupovic , Tom O Delmont

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

ISME communications

Avec: Clemens Schauberger , Bo Thamdrup , Clarisse Lemonnier , Blandine Trouche , Julie Poulain , Patrick Wincker , Sophie Arnaud-Haond , Ronnie N Glud , Lois Maignien

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

Molecular ecology

Avec: Adrien Tran Lu Y , Stéphanie Ruault , Claire Daguin-Thiébaut , Jade Castel , Nicolas Bierne , Thomas Broquet , Patrick Wincker , Aude Perdereau , Sophie Arnaud-Haond , Pierre-Alexandre Gagnaire , Didier Jollivet , Stéphane Hourdez , François Bonhomme

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

The ISME journal

Avec: Hugo Doré , Ulysse Guyet , Jade Leconte , Gregory K Farrant , Benjamin Alric , Morgane Ratin , Martin Ostrowski , Mathilde Ferrieux , Loraine Brillet-Guéguen , Mark Hoebeke , Jukka Siltanen , Gildas Le Corguillé , Erwan Corre , Patrick Wincker , David J Scanlan , Damien Eveillard , Frédéric Partensky , Laurence Garczarek

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

Nature communications

Avec: Alice Rouan , Melanie Pousse , Nadir Djerbi , Barbara Porro , Guillaume Bourdin , Quentin Carradec , Benjamin Cc Hume , Julie Poulain , Julie Lê-Hoang , Eric Armstrong , Sylvain Agostini , Guillem Salazar , Hans-Joachim Ruscheweyh , Jean-Marc Aury , David A Paz-García , Ryan McMinds , Marie-Josèphe Giraud-Panis , Romane Deshuraud , Alexandre Ottaviani , Lycia Die Morini , Camille Leone , Lia Wurzer , Jessica Tran , Didier Zoccola , Alexis Pey , Clémentine Moulin , Emilie Boissin , Guillaume Iwankow , Sarah Romac , Colomban de Vargas , Bernard Banaigs , Emmanuel Boss , Chris Bowler , Eric Douville , Michel Flores , Stéphanie Reynaud , Olivier P Thomas , Romain Troublé , Rebecca Vega Thurber , Serge Planes , Denis Allemand , Stephane Pesant , Pierre E Galand , Patrick Wincker , Shinichi Sunagawa , Eric Röttinger , Paola Furla , Christian R Voolstra , Didier Forcioli , Fabien Lombard , Eric Gilson

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

Scientific data

Avec: Caroline Belser , Julie Poulain , Karine Labadie , Frederick Gavory , Adriana Alberti , Julie Guy , Quentin Carradec , Corinne Cruaud , Corinne Da Silva , Stefan Engelen , Paul Mielle , Aude Perdereau , Gaelle Samson , Shahinaz Gas , Auteur inconnu , Christian R Voolstra , Pierre E Galand , J Michel Flores , Benjamin C C Hume , Gabriela Perna , Maren Ziegler , Hans-Joachim Ruscheweyh , Emilie Boissin , Sarah Romac , Guillaume Bourdin , Guillaume Iwankow , Clémentine Moulin , David A Paz García , Sylvain Agostini , Bernard Banaigs , Emmanuel Boss , Chris Bowler , Colomban de Vargas , Eric Douville , Didier Forcioli , Paola Furla , Eric Gilson , Fabien Lombard , Stéphane Pesant , Stéphanie Reynaud , Shinichi Sunagawa , Olivier P Thomas , Romain Troublé , Rebecca Vega Thurber , Didier Zoccola , Claude Scarpelli , E' Krame Jacoby , Pedro H Oliveira , Jean-Marc Aury , Denis Allemand , Serge Planes , Patrick Wincker

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

Communications biology

Avec: Alex J Veglia , Kalia S I Bistolas , Christian R Voolstra , Benjamin C C Hume , Hans-Joachim Ruscheweyh , Serge Planes , Denis Allemand , Emilie Boissin , Patrick Wincker , Julie Poulain , Clémentine Moulin , Guillaume Bourdin , Guillaume Iwankow , Sarah Romac , Sylvain Agostini , Bernard Banaigs , Emmanuel Boss , Chris Bowler , Colomban de Vargas , Eric Douville , Michel Flores , Didier Forcioli , Paola Furla , Pierre E Galand , Eric Gilson , Fabien Lombard , Stéphane Pesant , Stéphanie Reynaud , Shinichi Sunagawa , Olivier P Thomas , Romain Troublé , Didier Zoccola , Adrienne M S Correa , Rebecca L Vega Thurber

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

Cell genomics

Avec: Tom O Delmont , Morgan Gaia , Damien D Hinsinger , Paul Frémont , Chiara Vanni , Antonio Fernandez-Guerra , A Murat Eren , Artem Kourlaiev , Leo d'Agata , Quentin Clayssen , Emilie Villar , Karine Labadie , Corinne Cruaud , Julie Poulain , Corinne Da Silva , Marc Wessner , Benjamin Noel , Jean-Marc Aury , Auteur inconnu , Colomban de Vargas , Chris Bowler , Eric Karsenti , Eric Pelletier , Patrick Wincker , Olivier Jaillon

Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.

Life science alliance

Avec: Richard G Dorrell , Alan Kuo , Zoltan Füssy , Elisabeth H Richardson , Asaf Salamov , Nikola Zarevski , Nastasia J Freyria , Federico M Ibarbalz , Jerry Jenkins , Juan Jose Pierella Karlusich , Andrei Stecca Steindorff , Robyn E Edgar , Lori Handley , Kathleen Lail , Anna Lipzen , Vincent Lombard , John McFarlane , Charlotte Nef , Anna Mg Novák Vanclová , Yi Peng , Chris Plott , Marianne Potvin , Fabio Rocha Jimenez Vieira , Kerrie Barry , Colomban de Vargas , Bernard Henrissat , Eric Pelletier , Jeremy Schmutz , Patrick Wincker , Joel B Dacks , Chris Bowler , Igor V Grigoriev , Connie Lovejoy

Ocean-wide comparisons of mesopelagic planktonic community structures.

ISME communications

Avec: Janaina Rigonato , Marko Budinich , Alejandro A Murillo , Manoela C Brandão , Juan J Pierella Karlusich , Yawouvi Dodji Soviadan , Ann C Gregory , Hisashi Endo , Florian Kokoszka , Dean Vik , Nicolas Henry , Paul Frémont , Karine Labadie , Ahmed A Zayed , Céline Dimier , Marc Picheral , Sarah Searson , Julie Poulain , Stefanie Kandels , Stéphane Pesant , Eric Karsenti , Auteur inconnu , Peer Bork , Chris Bowler , Colomban de Vargas , Damien Eveillard , Marion Gehlen , Daniele Iudicone , Fabien Lombard , Hiroyuki Ogata , Lars Stemmann , Matthew B Sullivan , Shinichi Sunagawa , Patrick Wincker , Samuel Chaffron , Olivier Jaillon

Predicting global distributions of eukaryotic plankton communities from satellite data.

ISME communications

Avec: Hiroto Kaneko , Hisashi Endo , Nicolas Henry , Cédric Berney , Frédéric Mahé , Julie Poulain , Karine Labadie , Odette Beluche , Roy El Hourany , Auteur inconnu , Samuel Chaffron , Patrick Wincker , Ryosuke Nakamura , Lee Karp-Boss , Emmanuel Boss , Chris Bowler , Colomban de Vargas , Kentaro Tomii , Hiroyuki Ogata

Imputed genomes of historical horses provide insights into modern breeding.

iScience

Avec: Evelyn T Todd , Aurore Fromentier , Richard Sutcliffe , Yvette Running Horse Collin , Aude Perdereau , Jean-Marc Aury , Camille Èche , Olivier Bouchez , Cécile Donnadieu , Patrick Wincker , Ted Kalbfleisch , Jessica L Petersen , Ludovic Orlando

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

npj biodiversity

Avec: Christian R Voolstra , Benjamin C C Hume , Eric J Armstrong , Guinther Mitushasi , Barbara Porro , Nicolas Oury , Sylvain Agostini , Emilie Boissin , Julie Poulain , Quentin Carradec , David A Paz-García , Didier Zoccola , Hélène Magalon , Clémentine Moulin , Guillaume Bourdin , Guillaume Iwankow , Sarah Romac , Bernard Banaigs , Emmanuel Boss , Chris Bowler , Colomban de Vargas , Eric Douville , Michel Flores , Paola Furla , Pierre E Galand , Eric Gilson , Fabien Lombard , Stéphane Pesant , Stéphanie Reynaud , Matthew B Sullivan , Shinichi Sunagawa , Olivier P Thomas , Romain Troublé , Rebecca Vega Thurber , Patrick Wincker , Serge Planes , Denis Allemand , Didier Forcioli

Réseau de co-auteurs

Jean-Marc Aury 34 collaborations

Chris Bowler 32 collaborations

Julie Poulain 30 collaborations

Karine Labadie 29 collaborations

Colomban de Vargas 27 collaborations

Shinichi Sunagawa 23 collaborations

Fabien Lombard 19 collaborations

Corinne Cruaud 19 collaborations

Matthew B Sullivan 18 collaborations

Caroline Belser 16 collaborations

Stéphane Pesant 15 collaborations

None None 15 collaborations

Eric Pelletier 15 collaborations

Emmanuel Boss 14 collaborations

Adriana Alberti 12 collaborations

Daniele Iudicone 12 collaborations

Olivier Jaillon 12 collaborations

Sarah Romac 12 collaborations

Serge Planes 12 collaborations

Emilie Boissin 12 collaborations

Pierre E Galand 12 collaborations

Christian R Voolstra 12 collaborations

Eric Karsenti 11 collaborations

Eric Douville 11 collaborations

Denis Allemand 11 collaborations

Clémentine Moulin 11 collaborations

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Romain Troublé 11 collaborations

Sylvain Agostini 11 collaborations

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Didier Forcioli 11 collaborations

Paola Furla 11 collaborations

Eric Gilson 11 collaborations

Olivier P Thomas 11 collaborations

Didier Zoccola 11 collaborations

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Aude Perdereau 11 collaborations

Nicolas Henry 10 collaborations

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Silvia G Acinas 10 collaborations

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Benjamin Noel 9 collaborations

Benjamin Istace 9 collaborations

Hiroyuki Ogata 9 collaborations

Lee Karp-Boss 9 collaborations

Hans-Joachim Ruscheweyh 9 collaborations

Ludovic Orlando 9 collaborations

Corinne Da Silva 8 collaborations

Ahmed A Zayed 8 collaborations

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J Michel Flores 4 collaborations

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