List of works - Julie Poulain

454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction.

scientific article published on June 2011

A global ocean atlas of eukaryotic genes.

scientific article published on 25 January 2018

A role for RNAi in the selective correction of DNA methylation defects

scientific article published on 29 January 2009

An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research

scientific article

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region.

scientific article published on 23 May 2018

Arsenic hypertolerance in the protist Euglena mutabilis is mediated by specific transporters and functional integrity maintenance mechanisms

scientific article published on 28 April 2014

Atlas of gene expression in the mouse kidney: new features of glomerular parietal cells

scientific article

BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution

scientific article

Biogeography and diversity of Collodaria (Radiolaria) in the global ocean

scientific article published on 24 March 2017

Candidate chemosensory genes in female antennae of the noctuid moth Spodoptera littoralis

scientific article

Capturing the mutational landscape of the beta-lactamase TEM-1.

scientific article published on 22 July 2013

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

article

Comparative analysis of Acinetobacters: three genomes for three lifestyles

scientific article published on 19 March 2008

Comparative genomics of emerging pathogens in the Candida glabrata clade

scientific article

Comparative genomics of protoploid Saccharomycetaceae

scientific article

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)

scientific article

Comparative venomics of Psyttalia lounsburyi and P. concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 β-glucosidase

scientific article (publication date: 25 October 2016)

Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode

scientific article published on 2 January 2012

Complete genome sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water

scientific article

Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites ⬇️

scientific article

Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis

scientific article

Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides

scientific article published on 18 August 2015

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

scientific article (publication date: 22 July 2012)

De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes

scientific article

Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

scientific article published on 16 October 2015

Degeneration of the nonrecombining regions in the mating-type chromosomes of the anther-smut fungi

scientific article

Disentangling The Causes For Faster-X Evolution In Aphids

Disentangling the causes for faster-X evolution in aphids.

scientific article published on 19 January 2018

ESTs library from embryonic stages reveals tubulin and reflectin diversity in Sepia officinalis (Mollusca — Cephalopoda).

scientific article

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

scientific article

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

scientific article

Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil

scientific article published on 14 July 2011

Enterotypes of the human gut microbiome

scientific article

Enterotypes of the human gut microbiome

scientific article published in Nature

Erratum: Addendum: Enterotypes of the human gut microbiome

scientific article published in Nature

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

scientific article

Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis.

scientific article published on 23 July 2013

Extensive inter- and intraspecific venom variation in closely related parasites targeting the same host: the case of Leptopilina parasitoids of Drosophila.

scientific article published on 2 April 2013

Functional annotation of Cotesia congregata bracovirus: identification of viral genes expressed in parasitized host immune tissues

scientific article

Gene flow contributes to diversification of the major fungal pathogen Candida albicans.

scientific article

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

scientific article

Genes under positive selection in a model plant pathogenic fungus, Botrytis

scientific article

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

scientific article

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

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

scientific article

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

scientific article

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

scientific article published on 3 September 2015

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

scientific article

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

scientific article

Identification of the main venom protein components of Aphidius ervi, a parasitoid wasp of the aphid model Acyrthosiphon pisum.

scientific article

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

scientific article

Insights into global diatom distribution and diversity in the world's ocean

scientific article

Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes

scientific article

Masculinization of the x chromosome in the pea aphid

scientific article

Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates

scientific article

Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling

scientific article

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

scientific article published on 18 September 2013

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients

scientific article published on 08 June 2021

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export

scientific article published on 5 March 2018

Neobodonids are dominant kinetoplastids in the global ocean

scientific article published on 21 December 2017

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona

scientific article published on 21 June 2017

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

scientific article published on May 2015

Ocean plankton. Structure and function of the global ocean microbiome

scientific article published on May 2015

Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection

scientific article published on 14 March 2014

Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

scientific article published on 04 February 2022

Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization

scientific article published on February 2012

Plankton networks driving carbon export in the oligotrophic ocean

scientific article

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

scientific article (publication date: 3 December 2010)

Predicted effector molecules in the salivary secretome of the pea aphid (Acyrthosiphon pisum): a dual transcriptomic/proteomic approach

scientific article

RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter

scientific article

Reference transcriptomes and detection of duplicated copies in hexaploid and allododecaploid Spartina species (Poaceae). ⬇️

scientific article

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

scientific article (publication date: July 2014)

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

scientific article published on 22 January 2018

Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes

scientific article

Structural and functional partitioning of bread wheat chromosome 3B.

scientific article

Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages

scientific article published on 7 February 2018

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 Medicago genome provides insight into the evolution of rhizobial symbioses

scientific article

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

scientific article

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

scientific article

The genome of Theobroma cacao

scientific article

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

The genome of the mesopolyploid crop species Brassica rapa ⬇️

scientific article (publication date: 28 August 2011)

The genome of the nucleopolyhedrosis-causing virus from Tipula oleracea sheds new light on the Nudiviridae family

scientific article

The genome sequence of the model ascomycete fungus Podospora anserina

scientific article

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

scientific article

The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome

scientific article

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

scientific article

The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont

scientific article

The venom composition of the parasitic wasp Chelonus inanitus resolved by combined expressed sequence tags analysis and proteomic approach

scientific article

Transcriptome analyses to investigate symbiotic relationships between marine protists

scientific article

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae). ⬇️

scientific article

Transcriptomic response of Manduca sexta immune tissues to parasitization by the bracovirus associated wasp Cotesia congregata

scientific article published on 10 January 2015

Unveiling of the diversity of Prasinoviruses (Phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-amplified DNA polymerase and major capsid protein genes

scientific article (publication date: May 2014)

Venom gland extract is not required for successful parasitism in the polydnavirus-associated endoparasitoid Hyposoter didymator (Hym. Ichneumonidae) despite the presence of numerous novel and conserved venom proteins

scientific article

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

scientific article

mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus

scientific article

List of works by Julie Poulain

454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction.

A global ocean atlas of eukaryotic genes.

A role for RNAi in the selective correction of DNA methylation defects

An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region.

Arsenic hypertolerance in the protist Euglena mutabilis is mediated by specific transporters and functional integrity maintenance mechanisms

Atlas of gene expression in the mouse kidney: new features of glomerular parietal cells

BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution

Biogeography and diversity of Collodaria (Radiolaria) in the global ocean

Candidate chemosensory genes in female antennae of the noctuid moth Spodoptera littoralis

Capturing the mutational landscape of the beta-lactamase TEM-1.

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

Comparative analysis of Acinetobacters: three genomes for three lifestyles

Comparative genomics of emerging pathogens in the Candida glabrata clade

Comparative genomics of protoploid Saccharomycetaceae

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)

Comparative venomics of Psyttalia lounsburyi and P. concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 β-glucosidase

Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode

Complete genome sequence of Flavobacterium indicum GPSTA100-9T, isolated from warm spring water

Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites ⬇️

Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis

Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides

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

De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes

Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

Degeneration of the nonrecombining regions in the mating-type chromosomes of the anther-smut fungi

Disentangling The Causes For Faster-X Evolution In Aphids

Disentangling the causes for faster-X evolution in aphids.

ESTs library from embryonic stages reveals tubulin and reflectin diversity in Sepia officinalis (Mollusca — Cephalopoda).

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

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

Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil

Enterotypes of the human gut microbiome

Enterotypes of the human gut microbiome

Erratum: Addendum: Enterotypes of the human gut microbiome

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis.

Extensive inter- and intraspecific venom variation in closely related parasites targeting the same host: the case of Leptopilina parasitoids of Drosophila.

Functional annotation of Cotesia congregata bracovirus: identification of viral genes expressed in parasitized host immune tissues

Gene flow contributes to diversification of the major fungal pathogen Candida albicans.

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage

Genes under positive selection in a model plant pathogenic fungus, Botrytis

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

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

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

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

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

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

Identification of the main venom protein components of Aphidius ervi, a parasitoid wasp of the aphid model Acyrthosiphon pisum.

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

Insights into global diatom distribution and diversity in the world's ocean

Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes

Masculinization of the x chromosome in the pea aphid

Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates

Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export

Neobodonids are dominant kinetoplastids in the global ocean

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

Ocean plankton. Structure and function of the global ocean microbiome

Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection

Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization

Plankton networks driving carbon export in the oligotrophic ocean

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

Predicted effector molecules in the salivary secretome of the pea aphid (Acyrthosiphon pisum): a dual transcriptomic/proteomic approach

RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter

Reference transcriptomes and detection of duplicated copies in hexaploid and allododecaploid Spartina species (Poaceae). ⬇️

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

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

Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes

Structural and functional partitioning of bread wheat chromosome 3B.

Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages