Jean-Marc Aury

Jean-Marc Aury

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Jean-Marc Aury

Jean-Marc Aury

Publications by authors named "Jean-Marc Aury"

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Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules.

Sci Rep 2019 Oct 17;9(1):14908. Epub 2019 Oct 17.

Genoscope, Institut de biologie François-Jacob, Commissariat a l'Energie Atomique (CEA), Université Paris-Saclay, F-91057, Evry, France.

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http://dx.doi.org/10.1038/s41598-019-51470-9DOI Listing
October 2019

Adaptive introgression as a driver of local adaptation to climate in European white oaks.

New Phytol 2019 Aug 8. Epub 2019 Aug 8.

BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612, Cestas, France.

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http://dx.doi.org/10.1111/nph.16095DOI Listing
August 2019

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

Nat Commun 2019 Jul 31;10(1):3421. Epub 2019 Jul 31.

Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, Paris, 75005, France.

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http://dx.doi.org/10.1038/s41467-019-11385-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668482PMC
July 2019

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

Authors:
Rudi Appels Kellye Eversole Catherine Feuillet Beat Keller Jane Rogers Nils Stein Curtis J Pozniak Nils Stein Frédéric Choulet Assaf Distelfeld Kellye Eversole Jesse Poland Jane Rogers Gil Ronen Andrew G Sharpe Curtis Pozniak Gil Ronen Nils Stein Omer Barad Kobi Baruch Frédéric Choulet Gabriel Keeble-Gagnère Martin Mascher Andrew G Sharpe Gil Ben-Zvi Ambre-Aurore Josselin Nils Stein Martin Mascher Axel Himmelbach Frédéric Choulet Gabriel Keeble-Gagnère Martin Mascher Jane Rogers François Balfourier Juan Gutierrez-Gonzalez Matthew Hayden Ambre-Aurore Josselin ChuShin Koh Gary Muehlbauer Raj K Pasam Etienne Paux Curtis J Pozniak Philippe Rigault Andrew G Sharpe Josquin Tibbits Vijay Tiwari Frédéric Choulet Gabriel Keeble-Gagnère Martin Mascher Ambre-Aurore Josselin Jane Rogers Manuel Spannagl Frédéric Choulet Daniel Lang Heidrun Gundlach Georg Haberer Gabriel Keeble-Gagnère Klaus F X Mayer Danara Ormanbekova Etienne Paux Verena Prade Hana Šimková Thomas Wicker Frédéric Choulet Manuel Spannagl David Swarbreck Hélène Rimbert Marius Felder Nicolas Guilhot Heidrun Gundlach Georg Haberer Gemy Kaithakottil Jens Keilwagen Daniel Lang Philippe Leroy Thomas Lux Klaus F X Mayer Sven Twardziok Luca Venturini Rudi Appels Hélène Rimbert Frédéric Choulet Angéla Juhász Gabriel Keeble-Gagnère Frédéric Choulet Manuel Spannagl Daniel Lang Michael Abrouk Georg Haberer Gabriel Keeble-Gagnère Klaus F X Mayer Thomas Wicker Frédéric Choulet Thomas Wicker Heidrun Gundlach Daniel Lang Manuel Spannagl Daniel Lang Manuel Spannagl Rudi Appels Iris Fischer Cristobal Uauy Philippa Borrill Ricardo H Ramirez-Gonzalez Rudi Appels Dominique Arnaud Smahane Chalabi Boulos Chalhoub Frédéric Choulet Aron Cory Raju Datla Mark W Davey Matthew Hayden John Jacobs Daniel Lang Stephen J Robinson Manuel Spannagl Burkhard Steuernagel Josquin Tibbits Vijay Tiwari Fred van Ex Brande B H Wulff Curtis J Pozniak Stephen J Robinson Andrew G Sharpe Aron Cory Moussa Benhamed Etienne Paux Abdelhafid Bendahmane Lorenzo Concia David Latrasse Jane Rogers John Jacobs Michael Alaux Rudi Appels Jan Bartoš Arnaud Bellec Hélène Berges Jaroslav Doležel Catherine Feuillet Zeev Frenkel Bikram Gill Abraham Korol Thomas Letellier Odd-Arne Olsen Hana Šimková Kuldeep Singh Miroslav Valárik Edwin van der Vossen Sonia Vautrin Song Weining Abraham Korol Zeev Frenkel Tzion Fahima Vladimir Glikson Dina Raats Jane Rogers Vijay Tiwari Bikram Gill Etienne Paux Jesse Poland Jaroslav Doležel Jarmila Číhalíková Hana Šimková Helena Toegelová Jan Vrána Pierre Sourdille Benoit Darrier Rudi Appels Manuel Spannagl Daniel Lang Iris Fischer Danara Ormanbekova Verena Prade Delfina Barabaschi Luigi Cattivelli Pilar Hernandez Sergio Galvez Hikmet Budak Burkhard Steuernagel Jonathan D G Jones Kamil Witek Brande B H Wulff Guotai Yu Ian Small Joanna Melonek Ruonan Zhou Angéla Juhász Tatiana Belova Rudi Appels Odd-Arne Olsen Kostya Kanyuka Robert King Kirby Nilsen Sean Walkowiak Curtis J Pozniak Richard Cuthbert Raju Datla Ron Knox Krysta Wiebe Daoquan Xiang Antje Rohde Timothy Golds Jaroslav Doležel Jana Čížková Josquin Tibbits Hikmet Budak Bala Ani Akpinar Sezgi Biyiklioglu Gary Muehlbauer Jesse Poland Liangliang Gao Juan Gutierrez-Gonzalez Amidou N'Daiye Jaroslav Doležel Hana Šimková Jarmila Číhalíková Marie Kubaláková Jan Šafář Jan Vrána Hélène Berges Arnaud Bellec Sonia Vautrin Michael Alaux Françoise Alfama Anne-Françoise Adam-Blondon Raphael Flores Claire Guerche Thomas Letellier Mikaël Loaec Hadi Quesneville Curtis J Pozniak Andrew G Sharpe Sean Walkowiak Hikmet Budak Janet Condie Jennifer Ens ChuShin Koh Ron Maclachlan Yifang Tan Thomas Wicker Frédéric Choulet Etienne Paux Adriana Alberti Jean-Marc Aury François Balfourier Valérie Barbe Arnaud Couloux Corinne Cruaud Karine Labadie Sophie Mangenot Patrick Wincker Bikram Gill Gaganpreet Kaur Mingcheng Luo Sunish Sehgal Kuldeep Singh Parveen Chhuneja Om Prakash Gupta Suruchi Jindal Parampreet Kaur Palvi Malik Priti Sharma Bharat Yadav Nagendra K Singh JitendraP Khurana Chanderkant Chaudhary Paramjit Khurana Vinod Kumar Ajay Mahato Saloni Mathur Amitha Sevanthi Naveen Sharma Ram Sewak Tomar Jane Rogers John Jacobs Michael Alaux Arnaud Bellec Hélène Berges Jaroslav Doležel Catherine Feuillet Zeev Frenkel Bikram Gill Abraham Korol Edwin van der Vossen Sonia Vautrin Bikram Gill Gaganpreet Kaur Mingcheng Luo Sunish Sehgal Jan Bartoš Kateřina Holušová Ondřej Plíhal Matthew D Clark Darren Heavens George Kettleborough Jon Wright Miroslav Valárik Michael Abrouk Barbora Balcárková Kateřina Holušová Yuqin Hu Mingcheng Luo Elena Salina Nikolai Ravin Konstantin Skryabin Alexey Beletsky Vitaly Kadnikov Andrey Mardanov Michail Nesterov Andrey Rakitin Ekaterina Sergeeva Hirokazu Handa Hiroyuki Kanamori Satoshi Katagiri Fuminori Kobayashi Shuhei Nasuda Tsuyoshi Tanaka Jianzhong Wu Rudi Appels Matthew Hayden Gabriel Keeble-Gagnère Philippe Rigault Josquin Tibbits Odd-Arne Olsen Tatiana Belova Federica Cattonaro Min Jiumeng Karl Kugler Klaus F X Mayer Matthias Pfeifer Simen Sandve Xu Xun Bujie Zhan Hana Šimková Michael Abrouk Jacqueline Batley Philipp E Bayer David Edwards Satomi Hayashi Helena Toegelová Zuzana Tulpová Paul Visendi Song Weining Licao Cui Xianghong Du Kewei Feng Xiaojun Nie Wei Tong Le Wang Philippa Borrill Heidrun Gundlach Sergio Galvez Gemy Kaithakottil Daniel Lang Thomas Lux Martin Mascher Danara Ormanbekova Verena Prade Ricardo H Ramirez-Gonzalez Manuel Spannagl Nils Stein Cristobal Uauy Luca Venturini Nils Stein Rudi Appels Kellye Eversole Jane Rogers Philippa Borrill Luigi Cattivelli Frédéric Choulet Pilar Hernandez Kostya Kanyuka Daniel Lang Martin Mascher Kirby Nilsen Etienne Paux Curtis J Pozniak Ricardo H Ramirez-Gonzalez Hana Šimková Ian Small Manuel Spannagl David Swarbreck Cristobal Uauy

Science 2018 08 16;361(6403). Epub 2018 Aug 16.

John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK.

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http://dx.doi.org/10.1126/science.aar7191DOI Listing
August 2018

Complete Genome Sequence of the Facultative Methylotroph TK 0001 Isolated from Soil in Poland.

Genome Announc 2018 Feb 22;6(8). Epub 2018 Feb 22.

Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Evry, France

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http://dx.doi.org/10.1128/genomeA.00018-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5824006PMC
February 2018

High-Quality Genome Assembly of the Yeast Using Nanopore MinION Sequencing.

G3 (Bethesda) 2017 10 5;7(10):3243-3250. Epub 2017 Oct 5.

Génétique Moléculaire, Génomique, Microbiologie, Unité Mixte de Recherche 7156, University of Strasbourg, Centre National de la Recherche Scientifique, F-67000, France

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http://dx.doi.org/10.1534/g3.117.300128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633375PMC
October 2017

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data.

BMC Bioinformatics 2016 Mar 3;17:115. Epub 2016 Mar 3.

CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.

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http://dx.doi.org/10.1186/s12859-016-0969-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776351PMC
March 2016

Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.

BMC Genomics 2016 Mar 16;17:243. Epub 2016 Mar 16.

CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France.

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http://dx.doi.org/10.1186/s12864-016-2579-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793746PMC
March 2016

Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).

Stand Genomic Sci 2016 14;11. Epub 2016 Jan 14.

INRA, UMR 1253, Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France ; AGROCAMPUS OUEST, UMR1253, UMR Science et Technologie du Lait et de l'Oeuf, 35000 Rennes, France.

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http://dx.doi.org/10.1186/s40793-015-0120-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714504PMC
January 2016

Deciphering metatranscriptomic data.

Methods Mol Biol 2015 ;1269:279-91

LIFL, UMR CNRS 8022, Lille 1 University, Villeneuve d'Ascq, France,

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http://dx.doi.org/10.1007/978-1-4939-2291-8_17DOI Listing
September 2015

Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses.

PLoS Genet 2015 Sep 17;11(9):e1005470. Epub 2015 Sep 17.

Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université François Rabelais, Tours, France.

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http://dx.doi.org/10.1371/journal.pgen.1005470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574769PMC
September 2015

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

BMC Bioinformatics 2014 Nov 19;15:377. Epub 2014 Nov 19.

Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France.

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http://dx.doi.org/10.1186/s12859-014-0377-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279814PMC
November 2014

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

BMC Genomics 2014 Oct 20;15:912. Epub 2014 Oct 20.

CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France.

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http://dx.doi.org/10.1186/1471-2164-15-912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213505PMC
October 2014

A haploid system of sex determination in the brown alga Ectocarpus sp.

Curr Biol 2014 Sep 28;24(17):1945-57. Epub 2014 Aug 28.

Integrative Biology of Marine Models, CNRS UMR 8227, Sorbonne Universités, UPMC Université Paris 6, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2014.07.042DOI Listing
September 2014

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

Science 2014 Sep 4;345(6201):1181-4. Epub 2014 Sep 4.

Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France.

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http://albuquerque.bioinformatics.uottawa.ca/Papers/JournalP
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http://www.sciencemag.org/cgi/doi/10.1126/science.1255274
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http://dx.doi.org/10.1126/science.1255274DOI Listing
September 2014

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

Science 2014 Aug 21;345(6199):950-3. Epub 2014 Aug 21.

Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France.

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http://dx.doi.org/10.1126/science.1253435DOI Listing
August 2014

Structural and functional partitioning of bread wheat chromosome 3B.

Science 2014 Jul;345(6194):1249721

Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France.

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http://dx.doi.org/10.1126/science.1249721DOI Listing
July 2014

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

FEMS Microbiol Ecol 2014 May 24;88(2):231-49. Epub 2014 Feb 24.

UPMC-Université Paris VI, Station Biologique, Roscoff Cedex, France; CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Oceanic Plankton Group, Marine Phototrophic Prokaryotes Team, Roscoff Cedex, France.

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http://dx.doi.org/10.1111/1574-6941.12285DOI Listing
May 2014

Mapping the epigenetic basis of complex traits.

Science 2014 Mar 6;343(6175):1145-8. Epub 2014 Feb 6.

Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), UMR 8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris F-75005, France.

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http://dx.doi.org/10.1126/science.1248127DOI Listing
March 2014

The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution.

PLoS One 2013 28;8(6):e67350. Epub 2013 Jun 28.

CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, Montpellier, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067350PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696114PMC
January 2014

In silico survey of the mitochondrial protein uptake and maturation systems in the brown alga Ectocarpus siliculosus.

PLoS One 2011 18;6(5):e19540. Epub 2011 May 18.

Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019540PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097184PMC
September 2011

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

Nature 2010 Jun;465(7298):617-21

UPMC Université Paris 6, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France.

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http://dx.doi.org/10.1038/nature09016DOI Listing
June 2010

"Changing by doubling", the impact of Whole Genome Duplications in the evolution of eukaryotes.

C R Biol 2009 Feb-Mar;332(2-3):241-53. Epub 2008 Nov 29.

Genoscope (CEA), 2, rue Gaston-Crémieux, CP 5706, 91057 Evry, France.

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http://dx.doi.org/10.1016/j.crvi.2008.07.007DOI Listing
May 2009

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes.

Mol Biol Evol 2006 Sep 29;23(9):1808-16. Epub 2006 Jun 29.

Laboratoire de Biologie Moléculaire de la Cellule, INRA LA 1237, CNRS UMR5161, IFR 128 BioSciences Lyon-Gerland, Ecole Normale Supérieure de Lyon, Lyon, France.

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http://dx.doi.org/10.1093/molbev/msl049DOI Listing
September 2006