List of works - Jean-Marc Aury

"Changing by doubling", the impact of Whole Genome Duplications in the evolution of eukaryotes

scientific article

A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs

scientific article published on 08 February 2022

A global ocean atlas of eukaryotic genes.

scientific article published on 25 January 2018

A haploid system of sex determination in the brown alga Ectocarpus sp.

scientific article published on 28 August 2014

A reference genome for pea provides insight into legume genome evolution

scientific article published on 02 September 2019

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation.

scientific article published in February 2016

Adaptive introgression as a driver of local adaptation to climate in European white oaks

scientific article published on 08 August 2019

Amphioxus functional genomics and the origins of vertebrate gene regulation

scientific article published in Nature

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline

scientific article published on 6 February 2008

Annotating genomes with massive-scale RNA sequencing

scientific article

Assessing the Drosophila melanogaster and Anopheles gambiae genome annotations using genome-wide sequence comparisons

scientific article

Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

scientific article published in 2021

BAC ends library generation for Illumina sequencing

BiSCoT: improving large eukaryotic genome assemblies with optical maps

scientific article published on 05 November 2020

BoardION: real-time monitoring of Oxford Nanopore sequencing instruments

scientific article published on 13 May 2021

Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

scientific article published on 22 January 2021

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

article

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

article

Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Strains

article

Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

scientific article published on 24 June 2019

Comparative assessment of long-read error-correction software applied to RNA-sequencing data:

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

scientific article

Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina)

scientific article

Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland.

scientific article

Coprolites as a source of information on the genome and diet of the cave hyena

scientific article (publication date: 22 July 2012)

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

scientific article published on 8 April 2022

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

scientific article published on 30 October 2020

Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

scientific article published on 25 February 2019

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.

scientific article published on 12 October 2017

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

De novo clustering of long reads by gene from transcriptomics data

article

Deciphering metatranscriptomic data

scientific article

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

scientific article

Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus.

scientific article

Diversity and ecological footprint of Global Ocean RNA viruses

scientific article published on 10 June 2022

Early dispersal of domestic horses into the Great Plains and northern Rockies

scientific article published on 31 March 2023

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

scientific article published in 2023

Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets

scientific article published in 2024

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

scientific article published on 15 September 2020

Extensive recent secondary contacts between four European white oak species.

scientific article published on 13 January 2017

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

scientific article published in 2022

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

scientific article published on 29 June 2006

Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in <i>Brassica rapa</i>

scientific article published on 12 November 2020

Genome assembly using Nanopore-guided long and error-free DNA reads

scientific article published on 20 April 2015

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

scientific article

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

scientific article published in Nature

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

scientific article

Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite

scientific article

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

scientific article

Genome-defence small RNAs exapted for epigenetic mating-type inheritance.

scientific article published on 7 May 2014

Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

scientific article published on 10 June 2020

Genome-wide analyses based on comparative genomics.

scientific article published in January 2003

Genome-wide evolutionary response of European oaks during the Anthropocene

publication published on 05 January 2022

Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence

scientific article published in 2022

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

scientific article

Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation.

scientific article published on 18 April 2018

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

scientific article

Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

scientific article published on 03 May 2021

Hardwood Tree Genomics: Unlocking Woody Plant Biology

article

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

scientific article

High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Isolate Using Nanopore MinION Sequencing

scientific article published on 09 August 2017

High-quality de novo genome assembly of the Dekkera bruxellensis UMY321 yeast isolate using Nanopore MinION sequencing

Historical management of equine resources in France from the Iron Age to the Modern Period

scientific article published in 2021

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

scientific article

Implication of the suberin pathway in adaptation to waterlogging and hypertrophied lenticels formation in pedunculate oak (Quercus robur L.).

scientific article published on 29 June 2016

Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods

scientific article

In silico survey of the mitochondrial protein uptake and maturation systems in the brown alga Ectocarpus siliculosus

scientific article

Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

scientific article published on 23 March 2021

Long-read assembly of the Brassica napus reference genome Darmor-bzh

scientific article published on 01 December 2020

MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

scientific article

Mapping the epigenetic basis of complex traits.

scientific article published on 6 February 2014

Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

scientific article published on 29 July 2021

Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers

article

Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers

scientific article published on 02 July 2019

Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

scientific article published on 15 April 2015

Oak genome reveals facets of long lifespan

scientific article published on 18 June 2018

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

scientific article published on May 2015

Peculiar hybrid genomes of devastating plant pests promote plasticity in the absence of sex and meiosis

article

Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).

scientific article published on 14 January 2016

Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle

scientific article published on 12 November 2018

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

scientific article published on 21 August 2014

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

scientific article (publication date: 3 December 2010)

Population genomics of apricots unravels domestication history and adaptive events

scientific article published on 25 June 2021

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

scientific article

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

scientific article published on 06 January 2021

Reconstructing The Gigabase Plant Genome Of Solanum pennellii Using Nanopore Sequencing

article

Recurrent DNA virus domestication leading to different parasite virulence strategies.

scientific article

Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses

scientific article

Shared pedigree relationships and transmission of unreduced gametes in cultivated banana

scientific article published in 2023

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

scientific article

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

scientific article published on 22 January 2018

Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?

scientific article published on 19 February 2015

Structural and functional partitioning of bread wheat chromosome 3B.

scientific article

Survey of the green picoalga Bathycoccus genomes in the global ocean

scientific article

TE-Tracker: systematic identification of transposition events through whole-genome resequencing

scientific article

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

scientific article published on 07 September 2021

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 Eukaryote Genome Annotation Platform at Genoscope

The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences

scientific article

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

scientific article published on 30 April 2018

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

scientific article

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.

scientific article published on 15 September 2017

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

scientific article

The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution.

scientific article

The genome of Theobroma cacao

scientific article

The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

scientific article published on 11 March 2019

The genome sequence of the model ascomycete fungus Podospora anserina

scientific article

The genomic history and global expansion of domestic donkeys

scientific article published on 9 September 2022

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

scientific article

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

scientific article

The origins and spread of domestic horses from the Western Eurasian steppes

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

scientific article

The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants

scientific article

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

scientific article published on 17 October 2019

Translational control of intron splicing in eukaryotes

scientific article published in Nature

Transposition favors the generation of large effect mutations that may facilitate rapid adaption

scientific article published on 31 July 2019

Transposon accumulation lines uncover histone H2A.Z-driven integration bias towards environmentally responsive genes

article

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

scientific article published on 25 September 2017

Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

scholarly article

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

scientific article

Virus-host coexistence in phytoplankton through the genomic lens

scientific article published on 01 April 2020

Virus-host coexistence in phytoplankton through the genomic lens: Supplementary Material

scholarly article published 7 January 2019

Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation

scientific article

Widespread horse-based mobility arose around 2,200 BCE in Eurasia

scientific article published on 6 June 2024

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

scientific article

List of works by Jean-Marc Aury

"Changing by doubling", the impact of Whole Genome Duplications in the evolution of eukaryotes

A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs

A global ocean atlas of eukaryotic genes.

A haploid system of sex determination in the brown alga Ectocarpus sp.

A reference genome for pea provides insight into legume genome evolution

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation.

Adaptive introgression as a driver of local adaptation to climate in European white oaks

Amphioxus functional genomics and the origins of vertebrate gene regulation

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline

Annotating genomes with massive-scale RNA sequencing

Assessing the Drosophila melanogaster and Anopheles gambiae genome annotations using genome-wide sequence comparisons

Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

BAC ends library generation for Illumina sequencing

BiSCoT: improving large eukaryotic genome assemblies with optical maps

BoardION: real-time monitoring of Oxford Nanopore sequencing instruments

Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

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

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Strains

Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

Comparative assessment of long-read error-correction software applied to RNA-sequencing data:

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data

Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina)

Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland.

Coprolites as a source of information on the genome and diet of the cave hyena

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

De novo clustering of long reads by gene from transcriptomics data

Deciphering metatranscriptomic data

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

Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus.

Diversity and ecological footprint of Global Ocean RNA viruses

Early dispersal of domestic horses into the Great Plains and northern Rockies

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Extensive recent secondary contacts between four European white oak species.

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in <i>Brassica rapa</i>

Genome assembly using Nanopore-guided long and error-free DNA reads

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

Genome-defence small RNAs exapted for epigenetic mating-type inheritance.

Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

Genome-wide analyses based on comparative genomics.

Genome-wide evolutionary response of European oaks during the Anthropocene

Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation.

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

Hardwood Tree Genomics: Unlocking Woody Plant Biology

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Isolate Using Nanopore MinION Sequencing

High-quality de novo genome assembly of the Dekkera bruxellensis UMY321 yeast isolate using Nanopore MinION sequencing

Historical management of equine resources in France from the Iron Age to the Modern Period

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

Implication of the suberin pathway in adaptation to waterlogging and hypertrophied lenticels formation in pedunculate oak (Quercus robur L.).

Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods

In silico survey of the mitochondrial protein uptake and maturation systems in the brown alga Ectocarpus siliculosus

Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

Long-read assembly of the Brassica napus reference genome Darmor-bzh

MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

Mapping the epigenetic basis of complex traits.

Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers

Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers

Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

Oak genome reveals facets of long lifespan

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

Peculiar hybrid genomes of devastating plant pests promote plasticity in the absence of sex and meiosis