Patrick Wincker

Patrick Wincker

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Patrick Wincker

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A thousand plants' phylogeny.

Authors:
Patrick Wincker

Nat Plants 2019 Nov;5(11):1106-1107

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

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http://dx.doi.org/10.1038/s41477-019-0555-0DOI Listing
November 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

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

Mol Ecol Resour 2019 Mar;19(2):526-535

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

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http://doi.wiley.com/10.1111/1755-0998.12985
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http://dx.doi.org/10.1111/1755-0998.12985DOI Listing
March 2019

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

Mol Genet Genomics 2019 Feb 4;294(1):177-190. Epub 2018 Oct 4.

Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.

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http://link.springer.com/10.1007/s00438-018-1497-3
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http://dx.doi.org/10.1007/s00438-018-1497-3DOI Listing
February 2019

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

Curr Biol 2018 11 8;28(22):3625-3633.e3. Epub 2018 Nov 8.

Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2018.09.024DOI Listing
November 2018

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

Biogeography of soil bacteria and archaea across France.

Sci Adv 2018 07 4;4(7):eaat1808. Epub 2018 Jul 4.

Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, F-21000 Dijon, France.

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http://dx.doi.org/10.1126/sciadv.aat1808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031370PMC
July 2018

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

Curr Biol 2018 07 5;28(14):2274-2282.e6. Epub 2018 Jul 5.

Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; Université de Montpellier, Place Eugène Bataillon, 34000 Montpellier, France. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2018.05.066DOI Listing
July 2018

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

Microbiome 2018 06 9;6(1):105. Epub 2018 Jun 9.

Sorbonne Université, Univ Antilles, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), F-75005, Paris, France.

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http://dx.doi.org/10.1186/s40168-018-0481-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994019PMC
June 2018

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

Mol Ecol 2018 05 3;27(10):2365-2380. Epub 2018 May 3.

Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France.

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http://dx.doi.org/10.1111/mec.14579DOI Listing
May 2018

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

PeerJ 2018 14;6:e4685. Epub 2018 May 14.

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

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http://dx.doi.org/10.7717/peerj.4685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957050PMC
May 2018

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

PeerJ 2018 23;6:e4816. Epub 2018 May 23.

Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

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http://dx.doi.org/10.7717/peerj.4816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970565PMC
May 2018

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.

Mar Pollut Bull 2018 Apr 23;129(1):392-398. Epub 2018 Mar 23.

Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia.

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https://linkinghub.elsevier.com/retrieve/pii/S0025326X183013
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http://dx.doi.org/10.1016/j.marpolbul.2018.02.044DOI Listing
April 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

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

Mol Ecol 2017 Sep 25;26(17):4467-4482. Epub 2017 Jul 25.

Commissariat à l'Energie Atomique (CEA), Institut de Biologie François Jacob, Genoscope, Evry, France.

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http://dx.doi.org/10.1111/mec.14214DOI Listing
September 2017

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

Sci Rep 2017 01 27;7:41498. Epub 2017 Jan 27.

Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E-08003, Spain.

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http://www.nature.com/articles/srep41498
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http://dx.doi.org/10.1038/srep41498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5269757PMC
January 2017

Extreme Diversity of Diplonemid Eukaryotes in the Ocean.

Curr Biol 2016 11;26(22):3060-3065

Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2016.09.031DOI Listing
November 2016

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

Genome Biol Evol 2016 10 5;8(9):3030-3044. Epub 2016 Oct 5.

UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France

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http://dx.doi.org/10.1093/gbe/evw209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633685PMC
October 2016

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

Proc Natl Acad Sci U S A 2016 Mar 29;113(11):E1516-25. Epub 2016 Feb 29.

Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR 8197, INSERM U1024, F-75005 Paris, France;

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http://dx.doi.org/10.1073/pnas.1509523113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801293PMC
March 2016

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

Plant Physiol 2015 Oct 18;169(2):1254-65. Epub 2015 Aug 18.

Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)

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http://dx.doi.org/10.1104/pp.15.00584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587450PMC
October 2015

Ocean plankton. Patterns and ecological drivers of ocean viral communities.

Science 2015 May;348(6237):1261498

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA. Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA. Soil, Water, and Environmental Science, University of Arizona, Tucson, AZ 85721, USA.

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http://dx.doi.org/10.1126/science.1261498DOI Listing
May 2015

Transcriptome analyses to investigate symbiotic relationships between marine protists.

Front Microbiol 2015 17;6:98. Epub 2015 Mar 17.

UMR 7144, Université Pierre et Marie Curie Université Paris 06, Sorbonne Universités, Station Biologique de Roscoff Roscoff, France ; Centre National de la Recherche Scientifique, UMR 7144, Station Biologique de Roscoff Roscoff, France.

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http://dx.doi.org/10.3389/fmicb.2015.00098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362344PMC
April 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

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.

Environ Microbiol 2014 Sep 18;16(9):2659-71. Epub 2013 Sep 18.

Department of Marine Biology and Oceanography, Institute of Marine Science (ICM), Spanish National Research Council (CSIC), Passeig Marítim de la Barceloneta, 37-49, Barcelona, ES-08003, Spain.

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http://dx.doi.org/10.1111/1462-2920.12250DOI 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
Publisher Site
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