jacques Lagnel

Documents

Présentation

Publications

	Phytophthora capsici genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing Emmanuel Szadkowski , Jacques Lagnel , Nasradin Touhami , Amalia Sayeh , Céline Lopez-Roques Microbiology Resource Announcements, 2023, 12 (12), ⟨10.1128/mra.00196-23⟩ Article dans une revue hal-04521837v1
	Crop domestication as a step towards reproductive isolation M. I. Tenaillon , E Burban , S Huynh , A Wojcik , Anne-Claire Thuillet American Journal of Botany, 2023, ⟨10.1002/ajb2.16173⟩ Article dans une revue hal-04088575v1
	SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments Nelina Angelova , Theodoros Danis , Jacques Lagnel , Costas S Tsigenopoulos , Tereza Manousaki BMC Research Notes, 2022, 15 (1), pp.98. ⟨10.1186/s13104-022-05978-5⟩ Article dans une revue hal-03842053v1
	The Rm1 and Rm2 Resistance Genes to Green Peach Aphid (Myzus persicae) Encode the Same TNL Proteins in Peach (Prunus persica L.) Henri Duval , Laure Heurtevin , Naïma Dlalah , Caroline Callot , Jacques Lagnel Genes, 2022, 13 (8), ⟨10.3390/genes13081489⟩ Article dans une revue hal-03837796v1
	Building a cluster of NLR genes conferring resistance to pests and pathogens: the story of the Vat gene cluster in cucurbits Véronique Chovelon , Rafael Feriche-Linares , Guillaume Barreau , Joël Chadoeuf , Caroline Callot Horticulture research, 2021, 8 (1), ⟨10.1038/s41438-021-00507-0⟩ Article dans une revue hal-03216497v1
	0s and 1s in marine molecular research: a regional HPC perspective Jacques Lagnel , Haris Zafeiropoulos , Anastasia Gioti , Stelios Ninidakis , Antonis Potirakis GigaScience, 2021, 10 (8), pp.1-12. ⟨10.1093/gigascience/giab053⟩ Article dans une revue hal-03659669v1
	Gearing Up for Warmer Times: Transcriptomic Response of Spongia officinalis to Elevated Temperatures Reveals Recruited Mechanisms and Potential for Resilience Vasiliki Koutsouveli , Tereza Manousaki , Ana Riesgo , Jacques Lagnel , Spyros Kollias Frontiers in Marine Science, 2020, 6, ⟨10.3389/fmars.2019.00786⟩ Article dans une revue hal-03167192v1
	Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis Elisavet Kaitetzidou , Ioanna Katsiadaki , Jacques Lagnel , Efthimia Antonopoulou , Elena Sarropoulou Scientific Reports, 2019, 9, ⟨10.1038/s41598-019-40127-2⟩ Article dans une revue hal-02627533v1
	The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics Alexandros Tsakogiannis , Tereza Manousaki , Jacques Lagnel , Nikolaos Papanikolaou , Nikos Papandroulakis Frontiers in Genetics, 2019, 9, ⟨10.3389/fgene.2018.00749⟩ Article dans une revue hal-02620563v1
	The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish A. Tsakogiannis , T. Manousaki , Jacques Lagnel , A. Sterioti , M. Pavlidis Scientific Reports, 2018, 8 (1), pp.1-17. ⟨10.1038/s41598-018-21992-9⟩ Article dans une revue hal-02620154v1
	The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird Mathieu Gautier , Junichi Yamaguchi , Julien Foucaud , Anne Loiseau , Aurélien Ausset Current Biology - CB, 2018, 28 (20), pp.1-7. ⟨10.1016/j.cub.2018.08.023⟩ Article dans une revue hal-01864435v1
	Muscle and liver transcriptome characterization and genetic marker discovery in the farmed meagre, Argyrosomus regius T. Manousaki , A. Tsakogiannis , Jacques Lagnel , D. Kyriakis , N. Duncan Marine Genomics, 2018, 39, pp.39-44. ⟨10.1016/j.margen.2018.01.002⟩ Article dans une revue hal-02621545v1
	Exploring a Nonmodel Teleost Genome Through RAD Sequencing—Linkage Mapping in Common Pandora, Pagellus erythrinus and Comparative Genomic Analysis Tereza Manousaki , Alexandros Tsakogiannis , John B. Taggart , Christos Palaiokostas , Dimitris Tsaparis G3, 2016, 6 (3), pp.509-519. ⟨10.1534/g3.115.023432⟩ Article dans une revue hal-02632190v1
	Transcriptome Profiling and Genetic Study Reveal Amplified Carboxylesterase Genes Implicated in Temephos Resistance, in the Asian Tiger Mosquito Aedes albopictus Linda Grigoraki , Jacques Lagnel , Ilias Kioulos , Anastasia Kampouraki , Evangelia Morou PLoS Neglected Tropical Diseases, 2015, 9 (5), pp.e0003771. ⟨10.1371/journal.pntd.0003771⟩ Article dans une revue hal-01938133v1
	Transcription analysis of neonicotinoid resistance in Mediterranean (MED) populations of B. tabaci reveal novel cytochrome P450s, but no nAChR mutations associated with the phenotype Aris Ilias , Jacques Lagnel , Despoina E. Kapantaidaki , Emmanouil Roditakis , Costas S. Tsigenopoulos BMC Genomics, 2015, 16, ⟨10.1186/s12864-015-2161-5⟩ Article dans une revue hal-02641522v1
	Second generation genetic linkage map for the gilthead sea bream Sparus aurata L. Costas S. Tsigenopoulos , Bruno Louro , Dimitrios Chatziplis , Jacques Lagnel , Emmanouella Vogiatzi Marine Genomics, 2014, 18, pp.77 - 82. ⟨10.1016/j.margen.2014.09.008⟩ Article dans une revue hal-02630750v1
	The sex-specific transcriptome of the hermaphrodite sparid sharpsnout seabream (Diplodus puntazzo) Tereza Manousaki , Alexandros Tsakogiannis , Jacques Lagnel , Elena Sarropoulou , Jenny Z. Xiang BMC Genomics, 2014, 15, ⟨10.1186/1471-2164-15-655⟩ Article dans une revue hal-02637653v1
	Reconfiguring the Bioinformatics Computational Spectrum: Challenges and Opportunities of FPGA-Based Bioinformatics Acceleration Platforms Grigorios Chrysos , Euripides Sotiriades , Christos Rousopoulos , Kostas Pramataris , Ioannis Papaefstathiou IEEE Design & Test, 2014, 31 (1), pp.62 - 73. ⟨10.1109/MDAT.2013.2284191⟩ Article dans une revue hal-02637115v1
	In silico mining and characterization of simple sequence repeats from gilthead sea bream (Sparus aurata) expressed sequence tags (EST-SSRs); PCR amplification, polymorphism evaluation and multiplexing and cross-species assays Emmanouella Vogiatzi , Jacques Lagnel , Victoria Pakaki , Bruno Louro , Adelino V. M. Canario Marine Genomics, 2011, 4 (2), pp.83 - 91. ⟨10.1016/j.margen.2011.01.003⟩ Article dans une revue hal-02650290v1
	Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers Bruno Louro , Ana Lucia S. Passos , Erika L. Souche , Costas Tsigenopoulos , Alfred Beck Marine Genomics, 2010, 3 (3-4), pp.179 - 191. ⟨10.1016/j.margen.2010.09.005⟩ Article dans une revue hal-02666990v1
	NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results Jacques Lagnel , Costas S. Tsigenopoulos , Ioannis Iliopoulos Bioinformatics, 2009, 25 (6), pp.824-826. ⟨10.1093/bioinformatics/btp067⟩ Article dans une revue hal-02659946v1
	A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bassDicentrarchus labraxL. D. A. Chistiakov , C. S. Tsigenopoulos , Jacques Lagnel , Y.-M. Guo , B. Hellemans Animal Genetics, 2008, 39 (6), pp.623-634. ⟨10.1111/j.1365-2052.2008.01786.x⟩ Article dans une revue hal-02657212v1
	Characterization of nine polymorphic microsatellite markers in sprat (Sprattus sprattusL.) T. Dailianis , M. Limborg , R. Hanel , D. Bekkevold , Jacques Lagnel Molecular Ecology Resources, 2008, 8 (4), pp.861-863. ⟨10.1111/j.1755-0998.2008.02091.x⟩ Article dans une revue hal-02664905v1
	Biotype status and genetic polymorphism of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in Greece: mitochondrial DNA and microsatellites. A Tsagkarakou , C S Tsigenopoulos , K Gorman , Jacques Lagnel , I D Bedford Bulletin of Entomological Research, 2007, 97 (1), pp.29-40. ⟨10.1017/S000748530700466X⟩ Article dans une revue hal-02667439v1
	FDC-specific functions of p55TNFR and IKK2 in the development of FDC networks and of antibody responses. Panayiotis Victoratos , Jacques Lagnel , Sotiria Tzima , Marat B Alimzhanov , Klaus Rajewsky Immunity, 2006, 24 (1), pp.65-77. ⟨10.1016/j.immuni.2005.11.013⟩ Article dans une revue hal-02664288v1
	Extrachromosomal DNA of the symbiont Sodalis glossinidius. a C Darby , Jacques Lagnel , C Z Matthew , K Bourtzis , I Maudlin Journal of Bacteriology, 2005, 187 (14), pp.5003-5007. ⟨10.1128/JB.187.14.5003-5007.2005⟩ Article dans une revue hal-02678823v1
	Transposable element polymorphism of Wolbachia in the mosquito Culex pipiens: evidence of genetic diversity, super-infection and recombination Olivier Duron , Jacques Lagnel , Michel Raymond , Kostas Bourtzis , Philippe Fort Molecular Ecology, 2005, 14 (5), pp.1561-1573. ⟨10.1111/j.1365-294X.2005.02495.x⟩ Article dans une revue halsde-00193163v1
	Inducible transgenic mice reveal resting dendritic cells as potent inducers of CD8+ T cell tolerance. Hans Christian Probst , Jacques Lagnel , George Kollias , Maries van den Broek Immunity, 2003, 18 (5), pp.713-20. ⟨10.1016/S1074-7613(03)00120-1⟩ Article dans une revue hal-02683091v1
	Genetic structure of a greenhouse population of the spider mite Tetranychus urticae: spatio-temporal analysis with microsatellite markers. Maria Navajas , Marie-Jeanne Cezilly , Jacques Lagnel , Alain Migeon , T Bourse Insect Molecular Biology, 2002, 11 (2), pp.157-65 Article dans une revue hal-02679319v1
	Field releases of the predatory mite Neoseiulus fallacis (Acari : Phytoseiidae) in Canada, monitored by pyrethroid resistance and allozyme markers Maria Navajas , H. Thistlewood , Jacques Lagnel , D. Marshall , Anastasia Tsagkarakou Biological Control, 2001, 20 (3), pp.191-198. ⟨10.1006/bcon.2000.0896⟩ Article dans une revue halsde-00201056v1
	Isolation and characterization by direct amplification of length polymorphisms (DALP) of codominant genetic markers with Mendelian inheritance in Neoseiulus californicus (Acari: Phytoseiidae). Marie-Jeanne Perrot-Minnot , Jacques Lagnel , E Desmarais , Maria Navajas Experimental and Applied Acarology, 2000, 24 (10-11), pp.795-803. ⟨10.1023/A:1006457310697⟩ Article dans une revue hal-02696448v1
	Genetic differentiation in Tetranychus urticae (Acari: Tetranychidae): polymorphism, host races or sibling species? Maria Navajas , A Tsagkarakov , Jacques Lagnel , M J Perrot-Minnot Experimental and Applied Acarology, 2000, 24 (5-6), pp.365-376. ⟨10.1023/A:1006432604611⟩ Article dans une revue hal-02699110v1
	Tracking paternal genes with DALP markers in a pseudoarrhenotokous reproductive system: biparental transmission but haplodiploid-like inheritance in the mite Neoseiulus californicus. M J Perrot-Minnot , Jacques Lagnel , Alain Migeon , Maria Navajas Navarro Heredity, 2000, 84 ( Pt 6), pp.702-709 Article dans une revue hal-02694021v1
	Comparison of ribosomal ITS regions among Androctonus spp. sorpions (Scorpionida: Buthidae) from Tunisia. Z Ben Ali , P Boursot , K Said , Jacques Lagnel , N Chatti Journal of Medical Entomology, 2000, 37 (6), pp.787-790. ⟨10.1603/0022-2585-37.6.787⟩ Article dans une revue hal-02698084v1
	Mechanisms of insecticide resistance in the aphid Nasonovia ribisnigri (Mosley) (Homoptera : Aphididae) from France Catherine Rufingier , Nicole Pasteur , Jacques Lagnel , C. Martin , Maria Navajas Insect Biochemistry and Molecular Biology, 1999, 29 (4), pp.385-391. ⟨10.1016/S0965-1748(99)00014-4⟩ Article dans une revue halsde-00201906v1
	Sequence variation of ribosomal internal transcribed spacers (ITS) in commercially important Phytoseiidae mites Maria M. Navajas Navarro , Jacques Lagnel , G. Fauvel , G. de Moraes Experimental and Applied Acarology, 1999, 23, pp.851-859. ⟨10.1023/A:1006251220052⟩ Article dans une revue hal-02695950v1
	Microsatellite sequences are under-represented in two mite genomes. Maria Navajas , H. M. Thistlewood , Jacques Lagnel , C Hughes Insect Molecular Biology, 1998, 7 (3), pp.249-56. ⟨10.1111/j.1365-2583.1998.00066.x⟩ Article dans une revue hal-02697825v1
	Species-wide homogeneity of nuclear ribosomal ITS2 sequences in the spider mite Tetranychus urticae contrasts with extensive mitochondrial COI polymorphism. Maria Navajas , Jacques Lagnel , Juliana Guttierez , P Boursot Heredity, 1998, 80 (6), pp.742-52. ⟨10.1046/j.1365-2540.1998.00349.x⟩ Article dans une revue hal-02699169v1
	Direct amplification of length polymorphisms (DALP), or how to get and characterize new genetic markers in many species. Eric Desmarais , I. Lanneluc , Jacques Lagnel Nucleic Acids Research, 1998, 26 (6), pp.1458-1465 Article dans une revue hal-02694020v1
	Population structure in the spider mite Tetranychus urticae (Acari: Tetranychidae) from Crete based on multiple allozymes Anastasia Tsagkarakou , Maria Navajas , Jacques Lagnel , Nicole Pasteur Heredity, 1997, 78, pp.84-92. ⟨10.1038/hdy.1997.10⟩ Article dans une revue halsde-00201298v1
	Genetic variability in Tetranychus urticae ( Acari : Tetranychidae ) from Greece : insecticide resistance and isozymes. Anastasia Tsagkarakou , Maria M. Navajas Navarro , Jacques Lagnel , J. Gutíerrez , N. Pasteur Journal of Economic Entomology, 1996, 89, 5 p Article dans une revue hal-02688550v1
	Population structure in the spider mite Tetranychus urticae (Acari: Tetranychidae) from Crete based on multiple allozymes Anastasia Tsagkarakou , Maria M. Navajas Navarro , Jacques Lagnel , N. Pasteur Heredity, 1996, 78 (1), pp.84-92. ⟨10.1038/hdy.1997.10⟩ Article dans une revue hal-02696589v1
	Mitochondrial cytochrome oxidase I in tetranychid mites : a comparison between molecular phylogeny and changes of morphological and life history traits. Maria M. Navajas Navarro , J. Gutíerrez , Jacques Lagnel , Pierre Boursot Bulletin of Entomological Research, 1996, 86, pp.407-417 Article dans une revue hal-02693555v1
	Mitochondrial COI sequences in mites : evidence for variations in base composition. Maria M. Navajas Navarro , Dominique Fournier , Jacques Lagnel , J. Gutíerrez , P. Boursot Insect Molecular Biology, 1996, 5 (4), pp.281-285. ⟨10.1111/j.1365-2583.1996.tb00102.x⟩ Article dans une revue hal-02699203v1
	Genetic variability in Tetranychus urticae (Acari: Tetranychidae) from Greece: Insecticide resistance and isozymes Anastasia Tsagkarakou , Maria Navajas , Jacques Lagnel , Jean Gutierrez , Nicole Pasteur Journal of Economic Entomology, 1996, 89 (6), pp.1354-1358. ⟨10.1093/jee/89.6.1354⟩ Article dans une revue halsde-00201336v1
	Cytotoxic activity in culture filtrates from the entomopathogenic fungus Beauveria sulfurescens Pascale Mollier , Jacques Lagnel , J.M. Quiot , Agnes Aioun , Guy Riba Journal of Invertebrate Pathology, 1994, 64, pp.208-213 Article dans une revue hal-02714982v1
	A glycoprotein highly toxic for Galleria mellonella larvae secreted by the entomopathogenic fungus Beauveria sulfurescens Pascale Mollier , Jacques Lagnel , B. Fournet , Agnes Aioun , Guy Riba Journal of Invertebrate Pathology, 1994, 64 (3), pp.200-207. ⟨10.1016/S0022-2011(94)90175-9⟩ Article dans une revue hal-02715841v1

	Change of paradigm for breeding disease resistant cultivars robust to varying environments: estimators of the robustness of plant immunity and promising genes for the future William Billaud , Thibaud Jayet , Valentin Ribaut , Lucie Tamisier , Anne Massire European Scientific Conference – Towards Pesticide Free Agriculture “What research to meet the pesticides reduction objectives embedded in the European Green Deal?”, French Research Institute for Agriculture, Food and Environment (INRAE), Jun 2022, Dijon, France Communication dans un congrès hal-03737211v1
	Robustesse de l'immunité du piment à Phytophthora capsici face à une perturbation thermique William Billaud , Thibaud Jayet , Valentin Ribaut , Lucie Tamisier , Anne Massire 13. Rencontres de Phytopathologie - Mycologie, Sep 2022, Aussois (France), France. 1p Communication dans un congrès hal-04133317v1
	Bioinformatique et reproductibilité au sein de l’unité Génétique et Amélioration des Fruits et Légumes (GAFL): mise en place et retour d'expérience. Jacques Lagnel Journées du PEPI IBIS 2019, Jun 2019, Paris, France Communication dans un congrès hal-02613718v1
	Apport de la technologie Oxford NanoPore pour l’assemblage de novo du génome d’espèces non-modèles : le cas de la coccinelle asiatique Harmonia axyridis Jacques Lagnel , Arnaud A Estoup , Cecile Donnadieu , Celine Lopez-Roques , Maxime Manno Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM 2018), Société Française de Bio-Informatique (SFBI). FRA. GdR 3003 Bioinformatique Moléculaire (GdR BiM), FRA. Institut Français de Bioinformatique (IFB), FRA. Aix Marseille Université (AMU), FRA. Institut National de la Santé et de la Recherche Médicale (INSERM), FRA. Centre National de la Recherche Scientifique (CNRS), FRA., Jul 2018, Marseille, France Communication dans un congrès hal-02733723v1
	Apport de la technologie Oxford NanoPore pour l’assemblage de novo du génome d’espèces non-modèles : le cas de la coccinelle asiatique Harmonia axyridis Jacques Lagnel , Arnaud A Estoup , Cecile Donnadieu , Celine Lopez-Roques , Maxime Manno Montpellier Omics days 2018, Université de Montpellier (UM). Montpellier, FRA., Feb 2018, Montpellier, France Communication dans un congrès hal-02737315v1
	Contribution of Oxford NanoPore technology for the de novo genome assembly of nonmodel species: the case of the Asian ladybird Harmonia axyridis Jacques Lagnel , Arnaud A Estoup , Cecile Donnadieu , Celine Lopez-Roques , Maxime Manno Réunion France Génomique, Nov 2018, Evry, France Communication dans un congrès hal-02785309v1
	Differential gene expression analysis in the threatened sponge Spongia officinalis following exposure to different temperature conditions. V Koutsouveli , Tereza Manousaki , Jacques Lagnel , S Kollias , Costas Tsigenopoulos 10. World Sponge Conference, National University of Ireland Galway. IRL., Jun 2017, Galway, Ireland Communication dans un congrès hal-02733624v1
	Evaluating the performance of available tools for building de novo transcriptome hybrid assemblies by combining reads of different length Jacques Lagnel , Tereza Manousaki , Costas Tsigenopoulos , Anastasia Tsagkarakou 9. Hellenic Bioinformatics 2016, Hellenic Bioinformatics (H.bioinfo). GRC., Nov 2016, Thessalonica, Greece Communication dans un congrès hal-02801754v1

	A reference genome of Solanum habrochaites Bernard Caromel , Jacques Lagnel , Carole Iampietro , Marie-Claire Le Coant , Marine Sallaberry XVII SOLANACEAE2022 International Conference on the Plant Family of Solanaceae, Nov 2022, THESSALONIKI, Greece Poster de conférence hal-04136943v1
	Development of a Snakemake “framework/templates” to study the whole-genome transcriptional profiling from a blood-flesh trait (bf) and non blood-flesh trait (non-bf) cultivars in Prunus persica Laure Heurtevin , Thierry Pascal , Bénédicte Quilot-Turion , Martin-Magniette Marie-Laure , Jacques Lagnel JOBIM 2020 Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier, France. ⟨10.13140/RG.2.2.15060.63366⟩ Poster de conférence hal-03267808v1
	Research of candidate genes in peach for resistance to root-knot nematodes and resistance to aphids Myzus persicae Henri Duval , Laure Heurtevin , Naïma Dlalah , Jacques Lagnel , Caroline Callot 10th Rosaceae Genomics Conference, Dec 2020, Barcelona, Spain Poster de conférence hal-03267708v1
	Hybrid de novo genome assembly using Oxford Nanopore Technology, 10X Genomics Linked-Reads sequencing, and Bionano optical map of a non-model species: the case of the melon-cotton aphid Aphis gossypii Jacques Lagnel , Rafael Feriche-Linares , Pierre Bertrand , William Marande , Anne Loiseau JOBIM, 2020, En ligne, France Poster de conférence hal-04009338v1
	Small deletion in a photosynthesis-related gene is involved in anthocyanin accumulation in the mesocarp of bf blood-flesh peaches Laure Heurtevin , Carole Confolent , Bénédicte Quilot-Turion , Sylvie Bureau , Carine Le Bourvellec 10th Rosaceae Genomics Conference, Dec 2020, Barcelone, Spain Poster de conférence hal-03267672v1
	AllMine, a flexible pipeline for allele mining Thomas Bersez , Jean-Luc Gallois , Jacques Lagnel JOBIM (Journées Ouvertes Biologie, Informatique et Mathématiques), Jul 2019, Nantes, France Poster de conférence hal-02613672v1
	A high-density genotyping strategy based on gene capture in pepper: perspectives for genome wide association study and genetic mapping Sonia Elbelt , Jacques Lagnel , Bernard Caromel , Jacques David , Judith Hirsch 17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2019, Avignon, France. INRA, Centre de recherche Provence-Alpes-Côte d’Azur, 263 p., 2019, Innovations in Genetics and Breeding of Capsicum and Eggplant. Proceedings of the 17th EUCARPIA Meeting on Genetics and Breeding of Capsicum and Eggplant September 11-13, 2019 \| Avignon - France Poster de conférence hal-02737663v1
	Biocluster: an NGS-dedicated HPC cluster in IMBBC, HCMR Upcoming Upgrade Usage/Partners Training Jacques Lagnel , Tereza Manousaki , Georgios Kotoulas , Antonios Magoulas 9. Hellenic Bioinformatics 2016, Nov 2016, Thessalonica, Greece. 2016 Poster de conférence hal-02799037v1

	The genomic basis of colour pattern polymorphism in the harlequin ladybird Mathieu Gautier , Junichi Yamaguchi , Julien Foucaud , Anne Loiseau , Aurélien Ausset 2020 Pré-publication, Document de travail hal-02791082v1
	New tools to optmise the analysis of a large RNA-Seq dataset from non model species: development of a hybrid assembly strategy and assessment of library complexity from raw sequencing output. Jacques Lagnel , - Khalid Belkhir , - Tereza Manousaki , - Erick Desmarais , - Anastasia Tsagkarakou 2014 Pré-publication, Document de travail hal-02799163v1

jacques Lagnel

Présentation

Publications

Phytophthora capsici genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing

Crop domestication as a step towards reproductive isolation

SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments

The Rm1 and Rm2 Resistance Genes to Green Peach Aphid (Myzus persicae) Encode the Same TNL Proteins in Peach (Prunus persica L.)

Building a cluster of NLR genes conferring resistance to pests and pathogens: the story of the Vat gene cluster in cucurbits

0s and 1s in marine molecular research: a regional HPC perspective

Gearing Up for Warmer Times: Transcriptomic Response of Spongia officinalis to Elevated Temperatures Reveals Recruited Mechanisms and Potential for Resilience

Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis

The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics

The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish

The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

Muscle and liver transcriptome characterization and genetic marker discovery in the farmed meagre, Argyrosomus regius

Exploring a Nonmodel Teleost Genome Through RAD Sequencing—Linkage Mapping in Common Pandora, Pagellus erythrinus and Comparative Genomic Analysis

Transcriptome Profiling and Genetic Study Reveal Amplified Carboxylesterase Genes Implicated in Temephos Resistance, in the Asian Tiger Mosquito Aedes albopictus

Transcription analysis of neonicotinoid resistance in Mediterranean (MED) populations of B. tabaci reveal novel cytochrome P450s, but no nAChR mutations associated with the phenotype

Second generation genetic linkage map for the gilthead sea bream Sparus aurata L.

The sex-specific transcriptome of the hermaphrodite sparid sharpsnout seabream (Diplodus puntazzo)

Reconfiguring the Bioinformatics Computational Spectrum: Challenges and Opportunities of FPGA-Based Bioinformatics Acceleration Platforms

In silico mining and characterization of simple sequence repeats from gilthead sea bream (Sparus aurata) expressed sequence tags (EST-SSRs); PCR amplification, polymorphism evaluation and multiplexing and cross-species assays

Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers

NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results

A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bassDicentrarchus labraxL.

Characterization of nine polymorphic microsatellite markers in sprat (Sprattus sprattusL.)

Biotype status and genetic polymorphism of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in Greece: mitochondrial DNA and microsatellites.

FDC-specific functions of p55TNFR and IKK2 in the development of FDC networks and of antibody responses.

Extrachromosomal DNA of the symbiont Sodalis glossinidius.

Transposable element polymorphism of Wolbachia in the mosquito Culex pipiens: evidence of genetic diversity, super-infection and recombination

Inducible transgenic mice reveal resting dendritic cells as potent inducers of CD8+ T cell tolerance.

Genetic structure of a greenhouse population of the spider mite Tetranychus urticae: spatio-temporal analysis with microsatellite markers.

Field releases of the predatory mite Neoseiulus fallacis (Acari : Phytoseiidae) in Canada, monitored by pyrethroid resistance and allozyme markers

Isolation and characterization by direct amplification of length polymorphisms (DALP) of codominant genetic markers with Mendelian inheritance in Neoseiulus californicus (Acari: Phytoseiidae).

Genetic differentiation in Tetranychus urticae (Acari: Tetranychidae): polymorphism, host races or sibling species?

Tracking paternal genes with DALP markers in a pseudoarrhenotokous reproductive system: biparental transmission but haplodiploid-like inheritance in the mite Neoseiulus californicus.

Comparison of ribosomal ITS regions among Androctonus spp. sorpions (Scorpionida: Buthidae) from Tunisia.

Mechanisms of insecticide resistance in the aphid Nasonovia ribisnigri (Mosley) (Homoptera : Aphididae) from France

Sequence variation of ribosomal internal transcribed spacers (ITS) in commercially important Phytoseiidae mites

Microsatellite sequences are under-represented in two mite genomes.

Species-wide homogeneity of nuclear ribosomal ITS2 sequences in the spider mite Tetranychus urticae contrasts with extensive mitochondrial COI polymorphism.

Direct amplification of length polymorphisms (DALP), or how to get and characterize new genetic markers in many species.

Population structure in the spider mite Tetranychus urticae (Acari: Tetranychidae) from Crete based on multiple allozymes

Genetic variability in Tetranychus urticae ( Acari : Tetranychidae ) from Greece : insecticide resistance and isozymes.

Population structure in the spider mite Tetranychus urticae (Acari: Tetranychidae) from Crete based on multiple allozymes

Mitochondrial cytochrome oxidase I in tetranychid mites : a comparison between molecular phylogeny and changes of morphological and life history traits.

Mitochondrial COI sequences in mites : evidence for variations in base composition.

Genetic variability in Tetranychus urticae (Acari: Tetranychidae) from Greece: Insecticide resistance and isozymes

Cytotoxic activity in culture filtrates from the entomopathogenic fungus Beauveria sulfurescens

A glycoprotein highly toxic for Galleria mellonella larvae secreted by the entomopathogenic fungus Beauveria sulfurescens

Change of paradigm for breeding disease resistant cultivars robust to varying environments: estimators of the robustness of plant immunity and promising genes for the future

Robustesse de l'immunité du piment à Phytophthora capsici face à une perturbation thermique

Bioinformatique et reproductibilité au sein de l’unité Génétique et Amélioration des Fruits et Légumes (GAFL): mise en place et retour d'expérience.

Apport de la technologie Oxford NanoPore pour l’assemblage de novo du génome d’espèces non-modèles : le cas de la coccinelle asiatique Harmonia axyridis

Apport de la technologie Oxford NanoPore pour l’assemblage de novo du génome d’espèces non-modèles : le cas de la coccinelle asiatique Harmonia axyridis

Contribution of Oxford NanoPore technology for the de novo genome assembly of nonmodel species: the case of the Asian ladybird Harmonia axyridis

Differential gene expression analysis in the threatened sponge Spongia officinalis following exposure to different temperature conditions.

Evaluating the performance of available tools for building de novo transcriptome hybrid assemblies by combining reads of different length

A reference genome of Solanum habrochaites

Development of a Snakemake “framework/templates” to study the whole-genome transcriptional profiling from a blood-flesh trait (bf) and non blood-flesh trait (non-bf) cultivars in Prunus persica

Research of candidate genes in peach for resistance to root-knot nematodes and resistance to aphids Myzus persicae

Hybrid de novo genome assembly using Oxford Nanopore Technology, 10X Genomics Linked-Reads sequencing, and Bionano optical map of a non-model species: the case of the melon-cotton aphid Aphis gossypii

Small deletion in a photosynthesis-related gene is involved in anthocyanin accumulation in the mesocarp of bf blood-flesh peaches

AllMine, a flexible pipeline for allele mining

A high-density genotyping strategy based on gene capture in pepper: perspectives for genome wide association study and genetic mapping

Biocluster: an NGS-dedicated HPC cluster in IMBBC, HCMR Upcoming Upgrade Usage/Partners Training

The genomic basis of colour pattern polymorphism in the harlequin ladybird

New tools to optmise the analysis of a large RNA-Seq dataset from non model species: development of a hybrid assembly strategy and assessment of library complexity from raw sequencing output.