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List of works by Hadi Quesneville

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Evolution of genes and genomes on the Drosophila phylogeny

scientific article
Genome sequence of Aedes aegypti, a major arbovirus vector

scientific article
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

scientific article
The BioMart community portal: an innovative alternative to large, centralized data repositories

scientific article (publication date: July 2015)
The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

scientific article
The Ectocarpus genome and the independent evolution of multicellularity in brown algae

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

scientific article
Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

scientific article
Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

scientific article published in Science
Obligate biotrophy features unraveled by the genomic analysis of rust fungi

scientific article
Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

scientific article
Structural and functional partitioning of bread wheat chromosome 3B.

scientific article
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

scientific article
Considering transposable element diversification in de novo annotation approaches

scientific article
Combined evidence annotation of transposable elements in genome sequences

scientific article
Genome-wide studies highlight indirect links between human replication origins and gene regulation.

scholarly article
The Capsella rubella genome and the genomic consequences of rapid mating system evolution

scientific article
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

scientific article published on 05 June 2017
The genome of the stress-tolerant wild tomato species Solanum pennellii.

scientific article published on 27 July 2014
The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

scientific article published on 14 July 2013
Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots".

scientific article
Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome

scientific article
Formation of plant metabolic gene clusters within dynamic chromosomal regions.

scientific article
Discovering and detecting transposable elements in genome sequences

scientific article published on 10 October 2007
Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

scientific article
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

scientific article published on 16 January 2017
PASTEC: an automatic transposable element classification tool

scientific article
Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation.

scientific article published on 2 February 2015
LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss

scientific article published on 6 July 2007
Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells

scientific article
A model of segmental duplication formation in Drosophila melanogaster

scientific article
The Rosa genome provides new insights into the domestication of modern roses.

scientific article published on 30 April 2018
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

scientific article
Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes

scientific article published on 28 February 2015
Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

scientific article
Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes

scientific article published on 29 November 2013
Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

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

scientific article published on January 2014
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets

scientific article published on 14 March 2008
Oak genome reveals facets of long lifespan

scientific article published on 18 June 2018
Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges.

scientific article published on 25 September 2017
A call for benchmarking transposable element annotation methods

scientific article published on 4 August 2015
Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

scientific article
Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes

scientific article published in January 2003
Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

scientific article published on June 23, 2014
A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

scientific article published on 11 June 2018
Organization and evolution of transposable elements along the bread wheat chromosome 3B

scientific article
Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus

scientific article published on 16 June 2015
P elements and MITE relatives in the whole genome sequence of Anopheles gambiae

scientific article published on 18 August 2006
GnpIS: an information system to integrate genetic and genomic data from plants and fungi

scientific article (publication date: 2013)

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