Nicolas Lapalu

62
Documents

Publications

Publications

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MSpangepop: Simulating complex structural variants under advanced demographic scenarios using the coalescent

Lucien Piat , Sukanya Denni , Siegfried Dubois , Florent Couturier , Nicolas Lapalu et al.

JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. pp.1-1, 2025

Poster de conférence hal-05219528v1
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GrAuFlow: A snakemake workflow for pangenome graph augmentation using short read data

Antoine Malet , Fabrice Legeai , Ludovic Duvaux , Elisabeth Fournier , Pierre Gladieux et al.

Journées Ouvertes Biologie, Informatique, Mathématiques (JOBIM2025), Jul 2025, Bordeaux, France

Poster de conférence hal-05209521v1
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Establishment of pangenome graphs for the analysis and monitoring of fungal plant pathogen populations

Nicolas Lapalu , Antoine Loth , Fabrice Legeai , Ludovic Duvaux , Elisabeth Fournier et al.

ISCLB 2024 International Symposium on Cereal Leaf Blights, Jun 2024, Zürich, Switzerland. ⟨10.15454/1.5572369328961167E12⟩

Poster de conférence hal-04623680v1
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Investigating the involvement of the chromatin state in the control of gene expression in Leptospharia maculans

Colin Clairet , Jessica L. Soyer , Elise Gay , Nicolas Lapalu , Adeline Simon et al.

Fungal Genetics Conference, Mar 2019, Asiomar, United States

Poster de conférence hal-04456403v1

Insights into chromosome structure, transposable elements and secondary metabolite gene clusters from the complete genome sequence of Colletotrichum higginsianum

Jean-Félix Dallery , Nicolas Lapalu , M.R. Thon , Richard O'Connell

ECFG14 European conference on fungal genetics, Feb 2018, Haifa, Israel

Poster de conférence hal-04282959v1
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Investigating the involvement of the chromatin state in the control of effector gene expression in Leptospharia maculans

Colin Clairet , Nicolas Lapalu , Adeline Simon , Francoise Blaise , Julie Gervais et al.

40th New Phytologist Symposium, Sep 2017, Vienne, Austria. 2017

Poster de conférence hal-02786095v1
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Integration of transcriptomic and proteomics approaches in characterizing short-term gravi-perception signaling networks in poplar wood.

Nicolas N. Richet , Mélanie Mauriat , Marie-Claude Lesage Descauses , Odile Rogier , Françoise F. Laurans et al.

8. Plant Biomechanics International Conference PBM8, Nov 2015, Nagoya, Japan. Nagoya University, Proceedings of the Plant Biomechanics Conference, 253 p., 2015, 8th Plant Biomechanics International Conference

Poster de conférence hal-02744040v1

The first set of expressed sequence TAGS (ESTS) in the medicinal mushroom Agaricus subrufescens provides opportunitgies to discover production pathways of bioactive compounds and develop molecular breeding

Marie Foulongne-Oriol , Nicolas Lapalu , Joelle J. Amselem , Jean-Michel Savoie

12th European conference on fungal genetics, Mar 2014, Séville, Spain. , p.315, 2014

Poster de conférence hal-02797498v1
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Analysis of fungal communities associated with grapevine wood diseases, based on fungal ITS pyrosequencing.

Nicolas Lapalu , Angelique Gautier , Laetitia Brigitte , Jessica Vallance , Emilie Bruez et al.

27th Fungal Genetics Conference - Asilomar Conference Grounds,, Mar 2013, Asilomar, United States. 2013

Poster de conférence hal-01190538v1
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Isochores and effectors: genome reshaping and the birth of highly pathogenic species in fungal phytopathogens.

Jonathan Grandaubert , Marie-Helene Balesdent , Isabelle Fudal-Grolier , Joelle J. Amselem , Jonathan Kreplak et al.

Plant Genomics Seminar,, Apr 2012, Pont Royal en Provence, France. 2012, FungIsochores

Poster de conférence hal-01190821v1

FungIsochores : Isochores and effectors : genome reshaping and the birth of highly pathogenic species in fungal phytopathogens

J. Grandaubert , Marie-Hélène Balesdent , Isabelle Fudal , Joëlle Amselem , J. Kreplak et al.

Colloque Plant Genomics, 2012, Pont Royal en Provence, France. 2012

Poster de conférence hal-03283788v1

Improved Gene Annotation of the Fungal Wheat Pathogen Zymoseptoria tritici Based on Combined Iso-Seq and RNA-Seq Evidence

Nicolas Lapalu , Lucie Lamothe , Yohann Petit , Anne Genissel , Camille Delude et al.

Molecular Plant-Microbe Interactions, 2025, ⟨10.1094/MPMI-07-25-0077-TA⟩

Article dans une revue hal-05290062v1
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Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome

Nicolas Lapalu , Adeline Simon , Antoine Lu , Peter-Louis Plaumann , Joëlle Amselem et al.

Microbial Genomics, 2024, 10 (8), ⟨10.1099/mgen.0.001283⟩

Article dans une revue hal-04683720v1
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Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing

Reda Amezrou , Aurélie Ducasse , Jérôme Compain , Nicolas Lapalu , Anais Pitarch et al.

Nature Communications, 2024, 15 (1), pp.1933. ⟨10.1038/s41467-024-46191-1⟩

Article dans une revue hal-04498577v1
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A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat

Reda Amezrou , Colette Audéon , Jérôme Compain , Sandrine Gélisse , Aurélie Ducasse et al.

PLoS Pathogens, 2023, 19 (5), pp.e1011376. ⟨10.1371/journal.ppat.1011376⟩

Article dans une revue hal-04102220v1
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Quantitative and qualitative plant-pathogen interactions call upon similar pathogenicity genes with a spectrum of effects

Camilla Langlands-Perry , Anaïs Pitarch , Nicolas Lapalu , Murielle Cuenin , Christophe Bergez et al.

Frontiers in Plant Science, 2023, 14, pp.1128546. ⟨10.3389/fpls.2023.1128546⟩

Article dans une revue hal-04125786v1
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Location and timing govern tripartite interactions of fungal phytopathogens and host in the stem canker species complex

Elise Gay , Noémie Jacques , Nicolas Lapalu , Corinne Cruaud , Valerie Laval et al.

BMC Biology, 2023, 21 (1), pp.247. ⟨10.1186/s12915-023-01726-8⟩

Article dans une revue hal-04281614v1

Complete Genome Sequences of Septoria linicola : A Resource for Studying a Damaging Flax Pathogen

Nicolas Lapalu , Adeline Simon , Boris Demenou , Delphine Paumier , Marie-Pierre Guillot et al.

Molecular Plant-Microbe Interactions, 2023, 36 (1), pp.59-63. ⟨10.1094/MPMI-09-22-0185-A⟩

Article dans une revue hal-03920575v1
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Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures

Colin Clairet , Nicolas Lapalu , Adeline Simon , Jessica Soyer , Muriel Viaud et al.

Peer Community Journal, 2023, 3, pp.e13. ⟨10.24072/pcjournal.227⟩

Article dans une revue hal-04088414v1
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Population genomics reveals molecular determinants of specialization to tomato in the polyphagous fungal pathogen Botrytis cinerea in France

Alex Mercier , Adeline Simon , Nicolas Lapalu , Tatiana E Giraud , Marc Bardin et al.

Phytopathology, 2021, 111, pp.2355-2366. ⟨10.1094/PHYTO-07-20-0302-FI⟩

Article dans une revue hal-03197705v1
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Identification of Copper-Containing Oxidoreductases in the Secretomes of Three Colletotrichum Species with a Focus on Copper Radical Oxidases for the Biocatalytic Production of Fatty Aldehydes

David Ribeaucourt , Safwan Saker , David Navarro , Bastien Bissaro , Elodie Drula et al.

Applied and Environmental Microbiology, 2021, 87 (24), pp.e01526-21. ⟨10.1128/AEM.01526-21⟩

Article dans une revue hal-03619439v1
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Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization

Jessica Soyer , Colin Clairet , Elise Gay , Nicolas Lapalu , Thierry Rouxel et al.

Chromosome Research, 2021, 29 (2), pp.219-236. ⟨10.1007/s10577-021-09658-1⟩

Article dans une revue hal-03266749v1
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Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Elise J Gay , Jessica L Soyer , Nicolas Lapalu , Juliette Linglin , Isabelle Fudal et al.

BMC Biology, 2021, 19 (1), pp.e041118. ⟨10.1186/s12915-021-00989-3⟩

Article dans une revue hal-03190704v1
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pH effect on strain-specific transcriptomes of the take-all fungus

Kévin Gazengel , Lionel Lebreton , Nicolas Lapalu , Joëlle Amselem , Anne-Yvonne Guillerm-Erckelboudt et al.

PLoS ONE, 2020, 15 (7), pp.e0236429. ⟨10.1371/journal.pone.0236429⟩

Article dans une revue hal-02979591v1
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De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

Fabien Dutreux , Corinne da Silva , Léo d'Agata , Arnaud Couloux , Elise Gay et al.

Scientific Data , 2018, 5 (180235), 11 p. ⟨10.1038/sdata.2018.235⟩

Article dans une revue (data paper) hal-02621276v1
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Subcellular Localization Screening of Colletotrichum higginsianum Effector Candidates Identifies Fungal Proteins Targeted to Plant Peroxisomes, Golgi Bodies, and Microtubules

Guillaume Robin , Jochen Kleemann , Ulla Neumann , Lisa Cabre , Jean-Felix Dallery et al.

Frontiers in Plant Science, 2018, 9, ⟨10.3389/fpls.2018.00562⟩

Article dans une revue hal-02622767v1

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

Jean-Félix Dallery , Nicolas Lapalu , Antonios Zampounis , Sandrine Pigné , Isabelle Luyten et al.

BMC Genomics, 2017, 18 (1), pp.667. ⟨10.1186/s12864-017-4083-x⟩

Article dans une revue hal-04011133v1

A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene

Ziming Zhong , Thierry Marcel , Fanny E. Hartmann , Xin Ma , Clémence Plissonneau et al.

New Phytologist, 2017, 214 (2), pp.619 - 631. ⟨10.1111/nph.14434⟩

Article dans une revue hal-01530838v1
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Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

Jean-Felix Dallery , Nicolas Lapalu , Antonios Zampounis , Sandrine Pigné , Isabelle Luyten et al.

BMC Genomics, 2017, 18, ⟨10.1186/s12864-017-4083-x⟩

Article dans une revue hal-01608503v1

The first set of expressed sequence tags (EST) from the medicinal mushroom Agaricus subrufescens delivers resource for gene discovery and marker development

Marie Foulongne-Oriol , Nicolas Lapalu , Cyril Férandon , Cathy Spataro , Nathalie Ferrer et al.

Applied Microbiology and Biotechnology, 2014, 98 (18), pp.7879-92. ⟨10.1007/s00253-014-5844-y⟩

Article dans une revue hal-02631326v1
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Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens

Jonathan J. Grandaubert , Rohan G.T. Lowe , Jessica L. Soyer , C.L. Schoch , Angela P van de Wouw et al.

BMC Genomics, 2014, 15 (891), pp.OA. ⟨10.1186/1471-2164-15-891⟩

Article dans une revue hal-02631920v1
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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 et al.

Database - The journal of Biological Databases and Curation, 2013, 2013, pp.1-9. ⟨10.1093/database/bat058⟩

Article dans une revue hal-02648084v1

Le génome de Botrytis décrypté

Muriel Viaud , Anne-Francoise A.-F. Adam-Blondon , Joelle J. Amselem , Pascal P. Bally , Agnes Cimerman et al.

La revue des œnologues et des techniques vitivinicoles et œnologiques, 2012, 142, pp.9-11

Article dans une revue hal-00999949v1
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Incidence of Genome Structure, DNA Asymmetry, and Cell Physiology on T-DNA Integration in Chromosomes of the Phytopathogenic Fungus Leptosphaeria maculans

Ahmed Salim A. S. Bourras , Michel M. Meyer , Jonathan J. Grandaubert , Nicolas Lapalu , Isabelle Fudal-Grolier Fudal et al.

G3, 2012, 2 (8), pp.891-904. ⟨10.1534/g3.112.002048⟩

Article dans une revue hal-01000638v1
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Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Joelle J. Amselem , Christina A. Cuomo , Jan A. L. van Kan , Muriel Viaud , Ernesto P. Benito et al.

PLoS Genetics, 2011, 7 (8), ⟨10.1371/journal.pgen.1002230⟩

Article dans une revue hal-01190236v1
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Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Thierry Rouxel , J. Grandaubert , Jk. Hane , Claire Hoede , Angela P. van de Wouw et al.

Nature Communications, 2011, 2, pp.202. ⟨10.1038/ncomms1189⟩

Article dans une revue hal-00841751v1

Antagonistic pleiotropic effects reduce adaptation in a Major wheat pathogen

Reda Amezrou , Gwilherm Gazeau , Nicolas Lapalu , L. Meyer , Frédéric Suffert et al.

20th Reinhardsbrunn symposium on modern fungicides and andi-fungal compounds, DpG, Apr 2023, Friedrichroda, Germany

Communication dans un congrès hal-04286767v1

Antagonistic pleiotropic effects reduce adaptation in a major wheat pathogen

R. Amezrou , Gwilherm Gazeau , Nicolas Lapalu , L. Meyer , Frédéric Suffert et al.

20th International Reinhardsbrunn symposium on modern fungicides and antifungal compounds, Apr 2023, Frierichroda, Germany

Communication dans un congrès hal-04314029v1

Adaptation of Leptosphaeria maculans to a nonhost species which genes are involved?

Julie Noah , Mathilde Gorse , Nicolas Lapalu , Thierry Rouxel , Marie-Hélène Balesdent et al.

16th European Conference on Fungal Genetics, Susanne Zeilinger-Migsich; Hubertus Haas, Mar 2023, Innsbruck,, Austria. pp.376

Communication dans un congrès hal-04095698v1

Of the fungal wheat pathogen Zymoseptoria tritici using ISO-SEQ and RNA-SEQ DATA

Marc-Henri Lebrun , Nicolas Lapalu , Lucie Lamothe , Yohann Petit , Scalliet Gabriel

16TH EUROPEAN CONFERENCE ON FUNGAL GENETICS, Susanne Zeilinger-Migsich; Hubertus Haas, Mar 2023, Innsbruck, Austria. pp.625

Communication dans un congrès hal-04102741v1

Antagonistic pleiotropic effecs reduce adaptation in a major wheat pathogen

R. Amezrou , Gwilherm Gazeau , Nicolas Lapalu , Frédéric Suffert , Sabine Fillinger et al.

International symposium on cereal leaf blights, May 2022, Gammarth, Tunisia

Communication dans un congrès hal-04312259v1

Identification of the determinants involved in the adaptation of Leptosphaeria maculans to different Brassica species

Julie Noah , Mathilde Gorse , Nicolas Lapalu , Thierry Rouxel , Marie-Hélène Balesdent et al.

Fungal Genetics IDF Symposium, Nov 2021, Paris, France

Communication dans un congrès hal-04230215v1

Cloning of AvrStb9, a gene of Zymoseptoria tritici conferring avirulence on wheat cultivars carrying the Stb9 resistance gene

Thierry Marcel , Colette Audéon , Jérôme Compain , Gélisse Sandrine , Aurélie Ducasse et al.

ECFG15 - 15th European conference on fungal genetics, ECFG15, Feb 2020, Rome, Italy. pp.340-341

Communication dans un congrès hal-04273732v1
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Analyse de l'interaction entre les membres d'un complexe d'espèces pathogènes du colza (Leptosphaeria maculans et L.biglobosa) par une approche transcriptomique

Elise Gay , Marie-Helene Balesdent , Thierry Rouxel , Nicolas Lapalu , Juliette Linglin et al.

Journées Jean Chevauchon JJC2018 - 12èmes Rencontres de Phytopathologie & Mycologie,, Jan 2018, Aussois, France. p.40

Communication dans un congrès hal-02790241v1
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Investigating the involvement of histone modifications in the control of effector gene expression in Leptospharia maculans, the fungus causing stem canker of oilseed rape

Jessica L Soyer , Isabelle Fudal , Colin Clairet , Nicolas Lapalu , Adeline Simon et al.

21th Crucifer Genetics Conference, Jul 2018, saint-Malo, France

Communication dans un congrès hal-02786161v1
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Investigating the involvement of the chromatin state in the control of effector gene expression in Leptosphaeria maculans

Colin Clairet , Jessica L. Soyer , Nicolas Lapalu , Adeline Simon , Francoise Blaise et al.

Journées Jean Chevauchon JJC2018 - 12èmes Rencontres de Phytopathologie & Mycologie,, Jan 2018, Aussois, France. p.14

Communication dans un congrès hal-02785896v1

A first glimpse into the genetic architecture of pathogenicity of Zymoseptoria tritici on bread wheat

Thierry Marcel , Aurélie Ducasse , Jérome Compain , Nicolas Lapalu , Z Chang Zhong Chen et al.

29. Fungal genetics conference Asilomar 17, Mar 2017, Pacific Grove, CA, United States. p.246

Communication dans un congrès hal-01530825v1
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URGI plant and fungi platform: distributed resources through GMOD tools

Joelle J. Amselem , Michael M. Alaux , Nathalie Choisne , Olivier Inizan , Nicolas Lapalu et al.

Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego, United States

Communication dans un congrès hal-02796293v1
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Métagénomique de la microflore du bois de la vigne.

Angelique A. Gautier , Laetitia L. Brigitte , Jessica J. Vallance , Emilie E. Bruez , Nicolas Lapalu et al.

9èmes Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP),, Jan 2012, Aussois, France. p. 69

Communication dans un congrès hal-01001057v1
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Analyse bioinformatique des données de métagénomique fongique

Laetitia L. Brigitte , Joelle J. Amselem , Nicolas Lapalu , Angelique A. Gautier , Jessica J. Vallance et al.

9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.23-23

Communication dans un congrès hal-00999906v1
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Fungal species resources: an integrated system for structural and functional genome annotation

Nicolas Lapalu , Joelle J. Amselem , Baptiste B. Brault , Laetitia L. Brigitte , Jonathan J. Kreplak et al.

9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.81-81

Communication dans un congrès hal-00999954v1
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Métagénomique de la microflore du bois de la vigne

Angelique A. Gautier , Laetitia L. Brigitte , Jessica J. Vallance , Emilie E. Bruez , Nicolas Lapalu et al.

9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.69-69

Communication dans un congrès hal-01000210v1
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Botrytis/Sclerotinia resources: an integrated system for structural and functional genome annotation

Joelle J. Amselem , Nicolas Lapalu , Julien J. Brault , Laetitia L. Brigitte , Jonathan J. Kreplak et al.

BSPGW 2011 : Botrytis/Sclerotinia Post-Genome Workshop, Sep 2011, Lyon, France. pp.71

Communication dans un congrès hal-00999928v1
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URGI genome annotation system:an integrated system for structural and functional genome annotation

Joelle J. Amselem , Michael Alaux , Nathalie Choisne , Nicolas Lapalu , Baptiste Brault et al.

12. Edition du colloque JOBIM : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2 p

Communication dans un congrès hal-01019754v1

What large-scale T-DNA insertional mutagenesis tells us about pathogenicity?A functional genomics analysis in the dothieomycete Leptosphaeria maculans

Ahmed Salim A. S. Bourras , Michel M. Meyer , Jonathan J. Grandaubert , Nicolas Lapalu , Marie-Helene Balesdent et al.

ECFG10 : 10. European conference on fungal genetics, Mar 2010, Noordwijkerhout, Netherlands. pp.60

Communication dans un congrès hal-02820119v1
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Comparative genomics of Botrytis cinerea and related Ascomycota species

Nicolas Lapalu , Joelle J. Amselem , Hadi Quesneville , Marc-Henri M.-H. Lebrun

8. Rencontres de Phytopathologie - Mycologie de la Société Française de Phytopathologie (SFP), Jan 2010, Aussois, France

Communication dans un congrès hal-02751266v1
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Mining plant genomic and genetic data using the GnpIS information system

Anne-Francoise Adam-Blondon , Michael Alaux , Sophie Durand , Thomas Letellier , Guillaume Merceron et al.

Aalt D.J van Dijk. Plant Genomics Databases. Methods and Protocols, 1533, Springer, 2017, Methods in Molecular Biology, 978-1-4939-6658-5. ⟨10.1007/978-1-4939-6658-5_5⟩

Chapitre d'ouvrage hal-03206731v1