Caroline Menguy

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Publications

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

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

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

Article dans une revue (data paper) hal-05480555v1
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A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution

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

Plant Biotechnology Journal, 2026, 24 (5), pp.3345-3367. ⟨10.1111/pbi.70553⟩

Article dans une revue hal-05247455v1
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Emergent patterns of patchiness differ between physical and planktonic properties in the ocean

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

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

Article dans une revue hal-04976225v1

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

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

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

Article dans une revue hal-05505155v1
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The Silene latifolia genome and its giant Y chromosome

Carol Moraga , Catarina Branco , Quentin Rougemont , Paris Veltsos , Pavel Jedlička et al.

Science, 2025, 387 (6734), pp.630-636. ⟨10.1126/science.adj7430⟩

Article dans une revue hal-04293712v1
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First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples

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

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

Article dans une revue (data paper) cea-05046943v1
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Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors

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

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

Article dans une revue hal-04911301v1
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Plant Genetic Bases Associated With Microbiota Descriptors Shed Light Into a Novel Holobiont Generalist Genes Theory

Loeiz Maillet , Manon Norest , Adam Kautsky , Anna Geraci , Elisabetta Oddo et al.

Environmental Microbiology, 2025, 27 (5), pp.e70108. ⟨10.1111/1462-2920.70108⟩

Article dans une revue hal-05090352v1
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Omics exploration of deep-sea biodiversity: data from the “Pourquoi Pas les Abysses?” and eDNAbyss projects

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

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

Article dans une revue hal-05434404v1
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On the way to diploidization and unexpected ploidy in the grass Sporobolus section Spartina mesopolyploids

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

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

Article dans une revue hal-04976572v1
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High diversity of crustose coralline algae microbiomes across species and islands, and implications for coral recruits

Corentin Hochart , Héloïse Rouzé , Béatrice Rivière , Hans-Joachim Ruscheweyh , Laetitia Hédouin et al.

Environmental Microbiome, 2024, 19 (1), pp.112. ⟨10.1186/s40793-024-00640-y⟩

Article dans une revue hal-04888274v1
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Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

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

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

Article dans une revue hal-04489824v1
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Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres

Franz Boideau , Virginie Huteau , Loeiz Maillet , Anael Brunet , Olivier Coriton et al.

The Plant cell, 2024, 36 (10), pp.4472-4490. ⟨10.1093/plcell/koae208⟩

Article dans une revue hal-04682098v1
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The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

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

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

Article dans une revue hal-05248491v1
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Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments

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

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

Article dans une revue hal-04388214v1
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Diversity of the Pacific Ocean coral reef microbiome

Pierre Galand , Hans-Joachim Ruscheweyh , Guillem Salazar , Corentin Hochart , Nicolas Henry et al.

Nature Communications, 2023, 14 (1), pp.3039. ⟨10.1038/s41467-023-38500-x⟩

Article dans une revue hal-04176291v1
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Host transcriptomic plasticity and photosymbiotic fidelity underpin $Pocillopora$ acclimatization across thermal regimes in the Pacific Ocean

Eric J Armstrong , Julie Lê-Hoang , Quentin Carradec , Jean-Marc Aury , Benjamin Noel et al.

Nature Communications, 2023, 14, pp.3056. ⟨10.1038/s41467-023-38610-6⟩

Article dans une revue cea-04171796v1
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Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

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

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

Article dans une revue hal-04176297v3

Epigenomic and structural events preclude recombination in Brassica napus

Franz Boideau , Gautier Richard , Olivier Coriton , Virginie Huteau , Caroline Belser et al.

New Phytologist, 2022, 234 (2), pp.545-559. ⟨10.1111/nph.18004⟩

Article dans une revue hal-03651949v1
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Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection

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

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

Article dans une revue hal-03977388v1

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

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

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

Article dans une revue hal-04382382v1
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Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

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

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

Article dans une revue hal-03658639v1
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Genomic adaptation of the picoeukaryote $Pelagomonas\ calceolata$ to iron-poor oceans revealed by a chromosome-scale genome sequence

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

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

Article dans une revue cea-03791710v1
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Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case

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

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

Article dans une revue hal-03318024v1
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Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

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

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

Article dans une revue hal-03198097v1
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Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

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

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

Article dans une revue hal-03352701v1
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Diversity and biogeography of bathyal and abyssal seafloor bacteria and archaea along a Mediterranean-Atlantic gradient

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

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

Article dans une revue hal-03589735v1
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Population genomics of apricots unravels domestication history and adaptive events

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

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

Article dans une revue hal-03282504v1
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Chromosome-scale assembly of the yellow mealworm genome

Evangelia Eleftheriou , Jean-Marc Aury , Benoît Vacherie , Benjamin Istace , Caroline Belser et al.

Open Research Europe, 2021, 1, pp.94. ⟨10.12688/openreseurope.13987.3⟩

Article dans une revue hal-03770436v1
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BiSCoT: improving large eukaryotic genome assemblies with optical maps

Benjamin Istace , Caroline Belser , Jean-Marc Aury

PeerJ, 2020, 8, pp.e10150. ⟨10.7717/peerj.10150⟩

Article dans une revue hal-04290135v1
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Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa

Julien Boutte , Loeiz Maillet , Thomas Chaussepied , Sébastien Letort , Jean-Marc Aury et al.

Frontiers in Plant Science, 2020, 11, pp.577536. ⟨10.3389/fpls.2020.577536⟩

Article dans une revue hal-03137565v1
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Long-read assembly of the Brassica napus reference genome Darmor-bzh

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

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

Article dans une revue (data paper) hal-03283975v1
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The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean

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

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

Article dans une revue hal-02402685v1

A reference genome for pea provides insight into legume genome evolution

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

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

Article dans une revue hal-02278272v1
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Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers

Thibault Leroy , Quentin Rougemont , Jean-Luc Dupouey , Catherine Bodenes , Céline Lalanne et al.

New Phytologist, 2019, online fisrt, pp.1-15. ⟨10.1111/nph.16039⟩

Article dans une revue hal-02622295v1
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Draft Genome Sequence of Tubulinosema ratisbonensis , a Microsporidian Species Infecting the Model Organism Drosophila melanogaster

Valérie Polonais , Sebastian Niehus , Ivan Wawrzyniak , Adrien Franchet , Christine Gaspin et al.

Microbiology Resource Announcements, 2019, 8 (31), ⟨10.1128/MRA.00077-19⟩

Article dans une revue hal-02276377v1

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

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

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

Article dans une revue hal-01977046v1
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Oak genome reveals facets of long lifespan

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

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

Article dans une revue hal-01820559v1
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Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

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

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

Article dans une revue (data paper) hal-01771844v1
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Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

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

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

Article dans une revue hal-01633879v1

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

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

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

Article dans une revue istex hal-01579667v1
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Genome assembly using Nanopore-guided long and error-free DNA reads

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

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

Article dans une revue hal-04361027v1
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The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Isabelle Lesur , Grégoire G. Le Provost , Pascal Bento , Corinne da Silva , Jean-Charles Leplé et al.

BMC Genomics, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩

Article dans une revue hal-02285504v1
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Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

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

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

Article dans une revue hal-02503091v1

The DNA sequence and analysis of human chromosome 14

Roland Heilig , Ralph Eckenberg , Jean-Louis Petit , Núria Fonknechten , Corinne da Silva et al.

Nature, 2003, 421 (6923), pp.601-607. ⟨10.1038/nature01348⟩

Article dans une revue hal-04312826v1
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Approches bioinformatiques pour l'exploration des génomes et de la biodiversité

Caroline Belser

Génomique, Transcriptomique et Protéomique [q-bio.GN]. Université Paris-Saclay, 2022. Français. ⟨NNT : 2022UPASB073⟩

Thèse tel-03994054v1
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European mink (Mustela lutreola) reference genome and population genomics

Alice Mouton , Christine Fournier-Chambrillon , Pascal Fournier , Jakub Skorupski , Przemysław Śmietana et al.

34th European Mustelid Colloquium, Sep 2022, Online conference, France

Communication dans un congrès hal-03787589v1

The Pisum Genus: Getting out of Pea Soup!

Jonathan Kreplak , Mohammed-Amin Madoui , Karine Labadie , Grégoire Aubert , Petr Capal et al.

Plant and Animal Genome XXVI Conference, 2018, San Diego (CA), United States

Communication dans un congrès hal-04331722v1
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The pea genome

Jonathan Kreplak , Mohammed-Amin Madoui , Karine Labadie , Gregoire Aubert , Philippe Bayer et al.

8. International Conference on Legume Genetics and Genomics (ICLGG), Noble Research Institute., Sep 2017, Siófok, Hungary. 128 p

Communication dans un congrès hal-02735156v1
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Towards the genome sequence of pea : a tribute to Mendel

Mohammed-Amin Madoui , K. Labadie , Jonathan Kreplak , Gregoire Aubert , Léo d'Agata et al.

2. International Legume Society Conference - Legumes for a Sustainable World, Legume Society., Oct 2016, Lisbonne, Portugal. 358 p

Communication dans un congrès hal-01602206v1

Genomic resources for functional analysis in <em>Medicago truncatula</em> and related crop species

Frederic Debellé , C. Belser , J.M. Aury , K. Labadie , Brice Roux et al.

6. International Conference on Legume Genetics and Genomics, International Crops Research Institute for the Semi-Arid Tropics, CGIAR (ICRISAT). Patancheru, IND., Oct 2012, Hyderabad, India

Communication dans un congrès hal-02747944v1

TARA Pacific bleaching prevalence of sampling sites (Islands)

Christian R Voolstra , Benjamin C.C Hume , Kyra Pikaar , Guillaume Bourdin , Stéphane Pesant et al. Autre publication scientifique hal-04384087v1

TARA Pacific CTAX colony morphological annotations release version 1_1

Guinther Mitushasi , Sylvain Algostini , Benjamin Hume , Yuko Kitano , Julie Poulain et al. Autre publication scientifique hal-04384090v1

Tara Pacific V9 18S rDNA metabarcoding dataset

Frédéric Mahé , Nicolas Henry , Cédric Berney , Julie Poulain , Sarah Romac et al. Autre publication scientifique hal-04384095v1

Tara Pacific metabarcoding sequencing (16S, 18S, ITS2) reference & replication tables version 1

Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh et al. Autre publication scientifique hal-04384100v1

Tara Pacific 16S rRNA data analysis release

Hans-Joachim Ruscheweyh , Guillem Salazar , Julie Poulain , Caroline Belser , Quentin Clayssen et al. Autre publication scientifique hal-04384109v1

Tara Pacific ITS2 Symbiodiniaceae data release version 1

Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh et al. Autre publication scientifique hal-04384112v1

Tara Pacific 18S-based coral host genetic analysis data release version 1

Benjamin C.C. Hume , Julie Poulain , Stéphane Pesant , Caroline Belser , Hans-Joachim Ruscheweyh et al. Autre publication scientifique hal-04384097v1
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LONG DNA TECHNOLOGIES EVALUATION FOR PLANT STRUCTURAL VARIATIONS DETECTION : NANOPORE ONT SEQUENCING vs BIONANO GENOMICS OPTICAL MAPPING

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

Plant and Animal Genome XXVIII Conference, Jan 2020, San Diego, United States.

Poster de conférence hal-02925940v1

Long DNA technologies evaluation for plant structural variations detection: Nanopore ONT sequencing vs Bionano Genomics optical mapping

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

- Plant and Animal Genome XXVIII Conference, 2020, San Diego, CA, United States

Poster de conférence hal-04331757v1

Chromosome-scale assemblies of Brassica oleracea and Brassica rapa using nanopore long reads and optical maps

Caroline Belser , Bejamin Istace , Denis Engemann , M Dubarry , Cyril Falentin et al.

21st Crucifer Genetics Conference on Brassica - Bassica 2018, Jul 2018, Saint-Malo, France

Poster de conférence hal-03318378v1

Optical Mapping with the Saphyr System on Plant Genomes

Erwan Denis , Caroline Belser , Wahiba Berrabah , Ghislaine Magdelenat , Corinne Cruaud et al.

- Plant and Animal Genome XXVI Conference, 2018, San Diego (CA), United States

Poster de conférence hal-04331771v1

From whole-genome scans for divergence to the discovery of speciation genes in oaks

Thibault Leroy , Jean Marc Aury , Catherine Bodenes-Brezard Bodénès , Laure Villate , Grégoire G. Le Provost et al.

15. Congress of the European Society for Evolutionary Biology (ESEB), Aug 2015, Lausanne, Switzerland. , 1 p., 2015

Poster de conférence hal-02797182v1
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Genome assembly using Nanopore-guided Long and Error-free DNA reads

Guillaume Gautreau , Mohammed‐amin Madoui , Stefan Engelen , Adriana A. Alberti , Caroline Belser et al.

Journées Ouvertes en Biologie, Informatique et Mathématiques 2015, Jul 2015, Clermont-Ferrand, France

Poster de conférence hal-04862540v1