Lista de obras - Jean-Marc Aury - Dominio Público Uruguay

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

artículo científico publicado en 2008

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

artículo científico

A global ocean atlas of eukaryotic genes.

artículo científico publicado en 2018

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

artículo científico publicado en 2014

A reference genome for pea provides insight into legume genome evolution

artículo científico publicado en 2019

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

artículo científico publicado en 2016

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

artículo científico publicado en 2019

Amphioxus functional genomics and the origins of vertebrate gene regulation

artículo científico publicado en 2018

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

artículo científico publicado en 2008

Annotating genomes with massive-scale RNA sequencing

artículo científico publicado en 2008

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

artículo científico publicado en 2003

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

artículo científico publicado en 2020

BoardION: real-time monitoring of Oxford Nanopore sequencing instruments

artículo científico publicado en 2021

Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2018

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

artículo científico publicado en 2012

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

artículo científico publicado en 2022

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

artículo científico publicado en 2020

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

artículo científico publicado en 2019

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2014

Diversity and ecological footprint of Global Ocean RNA viruses

artículo científico publicado en 2022

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

artículo científico publicado en 2023

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

artículo científico publicado en 2023

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

artículo científico publicado en 2024

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

artículo científico publicado en 2020

Extensive recent secondary contacts between four European white oak species.

artículo científico publicado en 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

artículo científico publicado en 2006

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

artículo científico publicado en 2020

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

artículo científico publicado en 2015

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

artículo científico publicado en 2004

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

scientific article published in Nature

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

artículo científico publicado en 2008

Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite

artículo científico publicado en 2011

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

artículo científico publicado en 2013

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

artículo científico publicado en 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

artículo científico publicado en 2020

Genome-wide analyses based on comparative genomics.

artículo científico publicado en 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

artículo científico publicado en 2013

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

artículo científico publicado en 2018

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

artículo científico publicado en 2006

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

artículo científico publicado en 2021

Hardwood Tree Genomics: Unlocking Woody Plant Biology

article

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

artículo científico publicado en 2008

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

artículo científico

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

artículo científico publicado en 2021

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2016

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

artículo científico publicado en 2011

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

artículo científico publicado en 2021

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

artículo científico publicado en 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

artículo científico publicado en 2016

Mapping the epigenetic basis of complex traits.

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2015

Oak genome reveals facets of long lifespan

scientific article published on 18 June 2018

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

artículo científico publicado en 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).

artículo científico publicado en 2016

Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle

artículo científico publicado en 2018

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

artículo científico publicado en 2014

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

artículo científico publicado en 2010

Population genomics of apricots unravels domestication history and adaptive events

artículo científico publicado en 2021

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

artículo científico publicado en 2010

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

artículo científico publicado en 2021

Reconstructing The Gigabase Plant Genome Of Solanum pennellii Using Nanopore Sequencing

article

Recurrent DNA virus domestication leading to different parasite virulence strategies.

artículo científico publicado en 2015

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

artículo científico publicado en 2015

Shared pedigree relationships and transmission of unreduced gametes in cultivated banana

artículo científico publicado en 2023

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

artículo científico publicado en 2018

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

artículo científico publicado en 2018

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

artículo científico publicado en 2015

Structural and functional partitioning of bread wheat chromosome 3B.

artículo científico publicado en 2014

Survey of the green picoalga Bathycoccus genomes in the global ocean

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2021

The Ectocarpus Genome and Brown Algal Genomics

article published in 2012

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

artículo científico publicado en 2010

The Eukaryote Genome Annotation Platform at Genoscope

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

artículo científico publicado en 2012

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

artículo científico publicado en 2018

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

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

The genome of Theobroma cacao

artículo científico publicado en 2010

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

artículo científico publicado en 2008

The genomic history and global expansion of domestic donkeys

artículo científico publicado en 2022

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

artículo científico publicado en 2007

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

artículo científico publicado en 2015

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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

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

artículo científico publicado en 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.

artículo científico publicado en 2017

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

artículo científico publicado en 2024

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

artículo científico publicado en 2017

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

artículo científico publicado en 2004

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

artículo científico publicado en 2024

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

artículo científico publicado en 2017

Lista de obras de 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