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Raphael-Gauthier Flores

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List of the publications I am involved in.
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Publications

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SyntenyViewer: a comparative genomics-driven translational research tool

Raphael Flores , Cécile Huneau , Laura Burlot , Mathilde Lainé , Erik Kimmel
Database - The journal of Biological Databases and Curation, 2023, 2023, ⟨10.1093/database/baad027⟩
Journal articles hal-04099923v1
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Applying FAIR principles to plant phenotypic data management in GnpIS

Cyril Pommier , Célia Michotey , Guillaume Cornut , Pierre Roumet , Eric Duchêne
Plant Phenomics, 2019, 2019, pp.1-15. ⟨10.34133/2019/1671403⟩
Journal articles hal-02624031v1
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Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Michael Alaux , Jane Rogers , Thomas Letellier , Raphaël Flores , Françoise Alfama
Genome Biology, 2018, 19 (1), pp.905-911. ⟨10.1186/s13059-018-1491-4⟩
Journal articles hal-02278879v1

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

. International Wheat Genome Sequencing Consortium (iwgsc) , Arnaud Bellec , Helene Berges , Sonia Vautrin , Michael Alaux
Science, 2018, 361 (6403), pp.7191. ⟨10.1126/science.aar7191⟩
Journal articles hal-01885399v1
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Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Triticum aestivum L.)

Umar Quraishi , Caroline Pont , Qurat-Ul Ain , Raphaël Flores , Laura Burlot
Frontiers in Plant Science, 2017, 8, pp.1-12. ⟨10.3389/fpls.2017.01843⟩
Journal articles hal-02285542v1

Reconciling the evolutionary origin of bread wheat (Triticum aestivum)

Moaine El Baidouri , Florent Murat , Maeva Veyssière , Mélanie Molinier , Raphaël-Gauthier Flores
New Phytologist, 2016, 213 (3), ⟨10.1111/nph.14113⟩
Journal articles hal-01361976v1
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TransPLANT resources for triticeae genomic data

Manuel Spannagl , Michael M. Alaux , Matthias Lange , Dan M. Bolser , Kai Christian Bader
PLANT GENOME, 2016, 9 (1), 13 p. ⟨10.3835/plantgenome2015.06.0038⟩
Journal articles hal-02635899v1
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Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops

Florent Murat , Rongzhi R. Zhang , Sébastien Guizard , Haris Gavranovic , Raphael Flores
Genome Biology and Evolution, 2015, 7 (3), pp.735-749. ⟨10.1093/gbe/evv014⟩
Journal articles hal-01133906v1
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GnpIS: an information system to integrate genetic and genomic data from plants and fungi

Delphine D. Steinbach , Michael M. Alaux , Joelle J. Amselem , Nathalie Choisne , Sophie S. Durand
Database - The journal of Biological Databases and Curation, 2013, 2013, pp.1-9. ⟨10.1093/database/bat058⟩
Journal articles hal-02648084v1

Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction

Olivier Langella , Benoit B. Valot , Daniel Jacob , Thierry T. Balliau , Raphaël-Gauthier Flores
Proteomics, 2013, 13 (9), pp.1457-1466. ⟨10.1002/pmic.201200564⟩
Journal articles hal-02651260v1
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Shared sub-genome dominance following polyploidization explains grass genome evolutionary plasticity from a 7 protochromosome ancestor with 16K protogenes

Florent Murat , Rongzhi R. Zhang , Sébastien S. Guizard , Raphaël-Gauthier R.-G. Flores , Alix A. Armero Villanueva
Genome Biology and Evolution, 2013, 6 (1), pp.12-33. ⟨10.1093/gbe/evt200⟩
Journal articles hal-00964190v1

Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes.

Florent Murat , Rongzhi Zhang , Sébastien Guizard , Raphael Flores , Alix Armero
Genome Biology and Evolution, 2013, 6 (1), pp.12-33
Journal articles hal-01218128v1
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Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes

Caroline C. Pont , Florent Murat , Sébastien S. Guizard , Raphaël-Gauthier R.-G. Flores , Séverine S. Foucrier
Plant Journal, 2013, pp.1-29. ⟨10.1111/tpj.12366⟩
Journal articles hal-00964421v1

Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes

Baptiste Imbert, , Jonathan Kreplak , Raphaël Flores , Grégoire Aubert , Judith Burstin
Forum des Jeunes Chercheurs UBFC 2023, Jun 2023, Besancon, France
Conference papers hal-04130857v1

Exploitation des graphes de connaissance pour dynamiser la recherche translationnelle chez les protéagineux

Baptiste Imbert , Jonathan Kreplak , Raphaël Flores , Grégoire Aubert , Judith Burstin
Journée doctorants UMR Agroécologie, Nov 2023, Dijon, France
Conference papers hal-04318079v1

RepetDB: a unified resource for transposable element references

Mariène Wan , Nicolas Francillonne , Raphaël Flores , Françoise Alfama , Johann Confais
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2022, SFBI; IFB; GDR BIM, Jul 2022, Rennes, France
Conference papers hal-03819882v1
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Developing infrastructures for FAIR data in plant biology

Cyril Pommier , Guillaume Cornut , Michael Alaux , Windpouire Esther Dzale Yeumo , Raphaël Flores
Gatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany
Conference papers hal-03316569v1

BreedWheat GWAS data in GnpIS information system

Mathilde Lainé , Thomas Letellier , Raphaël Flores , Nacer Mohellibi , Cyril Pommier
Eucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France
Conference papers hal-02340450v1
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Improving the « FAIRness » of Inra’s data for plant biology and breeding

Michael Alaux , Cyril Pommier , Esther Dzale Yeumo , Sophie Durand , Raphaël Flores
PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides
Conference papers hal-02790227v1
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The IWGSC Data repository and wheat data resources hosted at URGI: Overview and perspectives

Michael Alaux , Jane Rogers , Thomas Letellier , Raphaël Flores , Cyril Pommier
PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides
Conference papers hal-02788401v1

Developing grapevine FAIR Data

Cyril Pommier , Eric Duchêne , Thierry Lacombe , Timothée Flutre , Michael Alaux
PAG Conference 2018, Jan 2018, San Diego, United States
Conference papers hal-02738117v1

The IWGSC Reference genome browser, data mining and beyond

Michael Alaux , Thomas Letellier , Françoise Alfama Depauw , Jane Rogers , Frédéric Choulet
PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States
Conference papers hal-02788141v1
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Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA

Sophie Durand , Windpouire Esther Dzale Yeumo , Cyril Pommier , Michael Alaux , Guillaume Cornut
4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides
Conference papers hal-02791168v1
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Contribution to a European roadmap for data standardisation in Plant Science at URGI-INRA

Cyril Pommier , Michael M. Alaux , Windpouire Esther Dzale Yeumo , Guillaume Cornut , Sophie S. Durand
Plant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic
Conference papers hal-02794139v1

IWGSC Sequence Repository: Moving towards tools to facilitate data integration for the reference sequence of wheat

Michael Alaux , Thomas Letellier , Françoise Alfama-Depauw , Véronique Jamilloux , Jane Rogers
PAG XXIV - Plant and Animal Genome Conference, Jan 2016, San Diego, United States
Conference papers hal-01266518v1

GnpIS-Asso : A Generic Database for Managing and Exploiting Plant Genetic Association Studies Results Using High Throughput Genotyping and Phenotyping Data

Delphine Steinbach , Guillaume Merceron , Célia Michotey , Raphaël-Gauthier Flores , Nacer Mohellibi
23. Plant and Animal Genome, Jan 2015, San Diego, United States
Conference papers hal-01174322v1
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Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii

Cyril Pommier , Pawel Krajewski , Thomas Letellier , Hanna Cwiek , Célia Michotey
23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States
Conference papers hal-02739236v1
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Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource

Nacer Mohellibi , Nathalie Choisne , Aminah A. Keliet , Daphné Verdelet , Françoise Alfama
23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, Californie, United States. pp.24 slides
Conference papers hal-02741780v1
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IWGSC sequence repository : how to facilitate pseudomolecule assembly?

Michael M. Alaux , Frédéric Choulet , Loïc Couderc , Françoise F. Alfama-Depauw , Véronique Jamilloux
PAG XXIII - Plant and Animal Genome Conference, Jan 2015, San Diego, United States
Conference papers hal-02741662v1

Information system for phenotype data: trait, trials and genotypes identification and integration

Cyril Pommier , Michael M. Alaux , Sophie S. Durand , Raphaël-Gauthier R.-G. Flores , Aminah A. Keliet
22. Conference Plant and Animal Genome, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). GBR., Jan 2014, San Diego, United States
Conference papers hal-02795958v1
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Plant biology open data interoperability in the big data era

Anne-Francoise Adam-Blondon , Sophie S. Durand , Erik Kimmel , Raphaël-Gauthier R.-G. Flores , Cyril Pommier
Plant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany
Conference papers hal-02801067v1

IWGSC Sequence repository : Blast your favorite gene against the wheat survey sequence

Michael Alaux , Françoise Alfama-Depauw , Véronique Jamilloux , Raphaël Flores , Daphné Verdelet
PAG XXI - Plant and Animal Genome, Jan 2013, San Diego, United States
Conference papers hal-02804578v1

A generic tool for managing and exploiting genetic association studies results using high throughput genotyping and phenotyping

Célia Michotey , Frédéric Sapet , Pierre Dubreuil , Jacques Le Gouis , Mathilde Causse
Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France
Conference papers hal-01268379v1

Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case study on grain legumes

Baptiste Imbert , Jonathan Kreplak , Raphaël Flores , Grégoire Aubert , Judith Burstin
JOBIM 2023 Edition multisite, Jun 2023, Nancy, Nice,, France
Conference poster hal-04279248v1

Translational research opportunities in grain legumes: where are we?

Nadim Tayeh , Baptiste Imbert , Jonathan Kreplak , Raphaël Flores , Grégoire Aubert
ILS4 Fourth International Legume Society Conference 2023, Sep 2023, Grenade, France
Conference poster hal-04230581v1

Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case study on grain legumes

Baptiste Imbert , Jonathan Kreplak , Raphaël Flores , Grégoire Aubert , Judith Burstin
JOBIM 2023 Edition multisite, Jun 2023, Nancy, Nice, Plouzané, Pointe à Pitre, Tours, Virtuel, France
Conference poster hal-04331568v1
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FG-iRODS : un service de gestion de données pour les communautés scientifiques à l'échelle nationale et européenne basé une infrastructure fédérée

Emmanuel Medernach , Jérôme Pansanel , Raphaël Flores , Christine Gondrand , Patrick Moreau
JCAD 2019 - Journées Calcul Données, Oct 2019, Toulouse, France. , 1 p., 2019
Conference poster hal-02786994v1
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Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA

Sophie Durand , Esther Dzale Yeumo , Cyril Pommier , Michaël Alaux , Guillaume Cornut
Crop diversification in a changing world : Mobilizing the green gold of plant genetic resources, May 2017, Montpellier, France. , 2017, EUCARPIA Genetic Resources 2017
Conference poster hal-01606277v1

Data integration in the agronomic domain : national and international data discovery system

Florian Philippe , Aravind Venkatesan , Nordine El Hassouni , Cyril Pommier , Manuel Ruiz
JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-105 (#59), 2015
Conference poster lirmm-01274725v1
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BreedWheat genotyping and phenotyping data in GnpIS information system

Marie Laine , Thomas Letellier , Raphaël-Gauthier R.-G. Flores , Loïc Couderc , Nacer Mohellibi
JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015
Conference poster hal-02801654v1