List of works by Hadi Quesneville

A Genomic Survey of Mayetiola destructor Mobilome Provides New Insights into the Evolutionary History of Transposable Elements in the Cecidomyiid Midges

scientific article published on 11 October 2021

A call for benchmarking transposable element annotation methods

scientific article published on 4 August 2015

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

scientific article published on 11 June 2018

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

A model of segmental duplication formation in Drosophila melanogaster

scientific article

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

scientific article

Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS)

Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Triticum aestivum L.).

scientific article published on 14 November 2017

Combined evidence annotation of transposable elements in genome sequences

scientific article

Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation

scientific article published on 12 April 2005

Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening

scientific article

Considering transposable element diversification in de novo annotation approaches

scientific article

Correlation of LNCR rasiRNAs expression with heterochromatin formation during development of the holocentric insect Spodoptera frugiperda

scientific article

De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue

article

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

scientific article

Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter

scientific article published in 2014

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

scientific article published in January 2003

Detection of transposable elements by their compositional bias

scientific article

Developing data interoperability using standards: A wheat community use case

scientific article published in 2017

Developing data interoperability using standards: A wheat community use case.

scientific article published on 16 October 2017

Discovering and detecting transposable elements in genome sequences

scientific article published on 10 October 2007

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

scientific article

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

scientific article

Efficient comparison of sets of intervals with NC-lists

scientific article published on 14 February 2013

Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

scientific article

Erratum to: Understanding Brassicaceae evolution through ancestral genome reconstruction. ⬇️

scientific article published on 4 April 2016

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon

scientific article published on 10 November 2015

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

scientific article published on 16 January 2017

Formation of plant metabolic gene clusters within dynamic chromosomal regions.

scientific article

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

scientific article published in Science

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

scientific article published on 2 February 2015

Genome sequence of Aedes aegypti, a major arbovirus vector

scientific article

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

scientific article

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

scientific article

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

scholarly article

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

scientific article

GnpIS: an information system to integrate genetic and genomic data from plants and fungi

scientific article (publication date: 2013)

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

scientific article published on 05 June 2017

Hoppel, a P-like element without introns: a P-element ancestral structure or a retrotranscription derivative?

scientific article published on 25 April 2003

Impact and insights from ancient repetitive elements in plant genomes

scientific article published on 09 February 2016

Impact of transposable elements on insect genomes and biology

scientific article published on 03 February 2015

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.

scientific article published on 14 March 2008

In search of lost trajectories: Recovering the diversification of transposable elements

scientific article published on July 2011

International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories

scientific article (publication date: 30 October 2012)

International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany.

scientific article published on 20 October 2016

Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops

scientific article published on 29 January 2015

LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss

scientific article

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

scientific article published on 17 August 2018

Mining Plant Genomic and Genetic Data Using the GnpIS Information System

scientific article

Oak genome reveals facets of long lifespan

scientific article published on 18 June 2018

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

scientific article

Organization and evolution of transposable elements along the bread wheat chromosome 3B

scientific article

P elements and MITE relatives in the whole genome sequence of Anopheles gambiae

scientific article

PASTEC: an automatic transposable element classification tool

scientific article

Progress in single-access information systems for wheat and rice crop improvement

scientific article published on 01 March 2019

Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells

scientific article

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

scientific article

Reconciling the evolutionary origin of bread wheat (Triticum aestivum).

scientific article published on 23 August 2016

Recurrent exon shuffling between distant P-element families.

scientific article published in February 2003

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

scientific article

RepetDB: a unified resource for transposable element references

scientific article published on 29 January 2019

Roadmap for annotating transposable elements in eukaryote genomes

scientific article published in January 2012

S-MART, a software toolbox to aid RNA-Seq data analysis

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

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

scientific article published on January 2014

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

scientific article

Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8

scientific article published in 2007

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

scientific article published on 12 February 2019

Structural and functional partitioning of bread wheat chromosome 3B.

scientific article

Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremula provides insights into a leaf beetle genome

scientific article published on 23 January 2014

Tedna: a transposable element de novo assembler

scientific article

The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 subunit LHP1 function in concert to regulate the transcription of stress-responsive genes.

scientific article published on 5 August 2016

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

scientific article (publication date: July 2015)

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

scientific article

The Ectocarpus Genome and Brown Algal Genomics

article published in 2012

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

scientific article

The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

scientific article

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

scientific article published on 30 April 2018

The genome of the stress-tolerant wild tomato species Solanum pennellii.

scientific article published on 27 July 2014

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

scientific article

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

scientific article published on 14 July 2013

Towards an open grapevine information system

scientific article

Transposable Element Annotation in Completely Sequenced Eukaryote Genomes

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

scientific article

Twenty years of transposable element analysis in the Arabidopsis thaliana genome

scientific article published on 27 July 2020

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges.

scientific article published on 25 September 2017

Understanding Brassicaceae evolution through ancestral genome reconstruction.

scientific article published on 10 December 2015

Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots".

scientific article

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

scientific article published on 29 November 2013

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

transPLANT Resources for Triticeae Genomic Data.

scientific article

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