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List of works by Patrick Wincker

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

scientific article

A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

scientific article

A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome

scientific article

A gene graveyard in the genome of the fungus Podospora comata

article

A holistic approach to marine eco-systems biology

scientific article

A new genomic resource dedicated to wood formation in Eucalyptus

scientific article

A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications

scientific article

A panoramic view of gene expression in the human kidney ⬇️

scientific article published on October 31, 2003

A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae).

scientific article published on 29 May 2012

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

scientific article published on 29 January 2009

A thousand plants' phylogeny

scientific article published on 01 November 2019

A vesicular glutamate transporter in lampreys: cDNA cloning and early expression in the nervous system

scientific article published on 2 April 2010

ASEtrap: a biological method for speeding up the exploration of spliceomes

scientific article

Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance.

scientific article published on 25 January 2007

Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes.

scientific article

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

scientific article published on 6 February 2008

Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome

scientific article (publication date: 27 May 2010)

Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2/4 revealed by gene regulatory network analysis in an echinoderm

scientific article (publication date: 2010)

Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome

scientific article published on 18 May 2006

Annotating genomes with massive-scale RNA sequencing

scientific article

Annotation of microsporidian genomes using transcriptional signals.

scientific article

AphanoDB: a genomic resource for Aphanomyces pathogens

scientific article

Are Hox genes ancestrally involved in axial patterning? Evidence from the hydrozoan Clytia hemisphaerica (Cnidaria).

scientific article

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

scientific article

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

scientific article

BAC ends library generation for Illumina sequencing

Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity

scholarly article by Battle Karimi et al published 7 March 2019 in Scientific Reports

Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions

scientific article published on 07 September 2020

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

scientific article

Bracovirus gene products are highly divergent from insect proteins

scientific article

Chaetognath phylogenomics: a protostome with deuterostome-like development

scientific article

Chaetognath transcriptome reveals ancestral and unique features among bilaterians

scientific article (publication date: 2008)

Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy.

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

scientific article published on 12 April 2005

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

scientific article (publication date: 4 October 2002)

Comparative genomics of emerging pathogens in the Candida glabrata clade

scientific article

Comparative genomics of protoploid Saccharomycetaceae

scientific article

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 circular DNA in the mitochondria-like organelles of Blastocystis hominis

scientific article published on 23 July 2008

Complete genome sequence of the clinical Streptococcus salivarius strain CCHSS3

scientific article

Complete genome sequence of the commensal Streptococcus salivarius strain JIM8777.

scientific article published on 08 July 2011

Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila

scientific article

Complete genome sequence of the highly hemolytic strain Bacillus cereus F837/76.

scientific article published on March 2012

Complete nucleotide sequence of the mitochondrial DNA from Kluyveromyces lactis

scientific article

Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

scientific article

Convergent genomic signatures of domestication in sheep and goats

scientific article published on 6 March 2018

Convergent origins and rapid evolution of spliced leader trans-splicing in metazoa: insights from the ctenophora and hydrozoa

scientific article

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

scientific article (publication date: 22 July 2012)

Correction: Mapping and predictive variations of soil bacterial richness across France

scientific article published on 18 December 2017

Corrigendum: Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

scientific article published on 30 July 2015

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

scientific article

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

Deciphering the evolution and metabolism of an anammox bacterium from a community genome

scientific article

Deciphering the genome structure and paleohistory of Theobroma cacao

Deciphering the genome structure and paleohistory of Theobroma cacao

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

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

Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome

scientific article

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

scientific article

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria

scientific article

Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts

scientific article

Detection of Trypanosoma cruzi and Leishmania using the polymerase chain reaction

scientific article published in 1994

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

scientific article published on 25 June 2015

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

scientific article published in 2023

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

scientific article

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

scientific article published in 2023

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

scientific article

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118.

scientific article published on 09 September 2009

Evolution of Hox gene clusters in gnathostomes: insights from a survey of a shark (Scyliorhinus canicula) transcriptome.

scientific article published on 8 July 2010

Evolution of axis specification mechanisms in jawed vertebrates: insights from a chondrichthyan

scientific article published on 18 April 2007

Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis

scientific article

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

scientific article

Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes

scientific article

Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus

scientific article

Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity

scientific article published on 12 March 2007

Extreme Diversity of Diplonemid Eukaryotes in the Ocean

scientific article

Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation

scientific article

Feminizing Wolbachia: a transcriptomics approach with insights on the immune response genes in Armadillidium vulgare

scientific article

Fifty thousand years of Arctic vegetation and megafaunal diet

scientific article (publication date: 6 February 2014)

Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination

scientific article published on 11 August 2017

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

scientific article

Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase

scientific article published on 29 July 2009

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

scientific article

Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea

scientific article

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 in yeasts

scientific article

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

scientific article

Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

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

scientific article published in 2022

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

Genomics and fruit crop selection ⬇️

scientific article published on January 1, 2013

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

scientific article published on 06 July 2021

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 coding density on the largest Paramecium tetraurelia somatic chromosome

scientific 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

Host gene response to endosymbiont and pathogen in the cereal weevil Sitophilus oryzae ⬇️

scientific article published on January 18, 2012

Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica

scientific article

Human neural crest cells display molecular and phenotypic hallmarks of stem cells

scientific article published on 08 August 2008

Hunting down fungal secretomes using liquid-phase IEF prior to high resolution 2-DE.

scientific article

Hyposoter didymator uses a combination of passive and active strategies to escape from the Spodoptera frugiperda cellular immune response

scientific article

Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells

scientific article

Identification of the Anopheles gambiae ATP-binding cassette transporter superfamily genes

scientific article

Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation

scientific article

In vitro propagation of the microsporidian pathogen Brachiola algerae and studies of its chromosome and ribosomal DNA organization in the context of the complete genome sequencing project

scientific article published on 20 September 2007

Influence of Wolbachia on host gene expression in an obligatory symbiosis.

scientific article

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

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

scientific article

Insights into metazoan evolution from Alvinella pompejana cDNAs

scientific article (publication date: 16 November 2010)

Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)

scientific article (publication date: 2006)

Large-scale identification of human genes implicated in epidermal barrier function

scientific article published in 2007

Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

scientific article

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria

scientific article published on 12 February 2018

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

scientific article

Maintaining two mating types: structure of the mating type locus and its role in heterokaryosis in Podospora anserina

scientific article

Mapping and predictive variations of soil bacterial richness across France

scientific article published on 23 October 2017

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

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

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

Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

scientific article

Mutator-like element in the yeast Yarrowia lipolytica displays multiple alternative splicings

scientific article

Neurodevelopment genes in lampreys reveal trends for forebrain evolution in craniates

scientific article

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

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach

scientific article

Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection

scientific article

Ocean plankton. Determinants of community structure in the global plankton interactome

scientific article published on May 2015

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport

scientific article

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

scientific article published on May 2015

Ocean plankton. Patterns and ecological drivers of ocean viral communities

scientific article published on May 2015

Ocean plankton. Structure and function of the global ocean microbiome

scientific article published on May 2015

OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica.

scientific article

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

scientific article

Patterns of rare and abundant marine microbial eukaryotes

scientific article

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

article

Phylogenomics revives traditional views on deep animal relationships

scientific article (publication date: 28 April 2009)

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

scientific article published on February 2012

Pilot Anopheles gambiae full-length cDNA study: sequencing and initial characterization of 35,575 clones

scientific article

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)

Polydnaviruses of braconid wasps derive from an ancestral nudivirus

scientific article

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

Quantitative gene expression profiling of mouse brain regions reveals differential transcripts conserved in human and affected in disease models

scientific article published on 5 February 2008

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

scientific article

Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica.

scientific article published in January 2005

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

scientific article

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

scientific article (publication date: July 2014)

Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti

scientific article

Sequencing platform and library preparation choices impact viral metagenomes

scientific article

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

scientific article

Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes

scientific article

Stage-specific gene expression during spermatogenesis in the dogfish (Scyliorhinus canicula).

scientific article

Structural and functional partitioning of bread wheat chromosome 3B.

scientific article

Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep‐sea hydrothermal gastropod <i>Ifremeria nautilei</i>

scientific article published in 2022

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

scientific article

Tara Oceans: towards global ocean ecosystems biology

scientific article published on 12 May 2020

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

scientific article published on 07 September 2021

The DNA sequence and analysis of human chromosome 14

scientific article (publication date: 6 February 2003)

The Dogfish Scyliorhinus canicula: A Reference in Jawed Vertebrates

scientific article published on 01 December 2008

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 Eukaryote Genome Annotation Platform at Genoscope

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

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

scientific article

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest

scientific article

The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications

scientific article

The complete mitochondrial genome of the yeast Pichia sorbitophila.

scientific article published on 12 June 2009

The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata

scientific article published on January 2003

The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii

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 sequence of the model ascomycete fungus Podospora anserina

scientific article

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

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

Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

scientific article

Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina

scientific article

Transcriptome analyses to investigate symbiotic relationships between marine protists

scientific article

Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell

scientific article (publication date: 2009)

Transcriptome of Aphanomyces euteiches: new oomycete putative pathogenicity factors and metabolic pathways

scientific article

Transcriptomics of actinorhizal symbioses reveals homologs of the whole common symbiotic signaling cascade

scientific article (publication date: June 2011)

Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping.

scientific article

Translational control of intron splicing in eukaryotes

scientific article published in Nature

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

article

Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium

scientific article

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.

scientific article

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii

scientific article

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

scientific article

Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome

scientific article

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

scientific article

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

scientific article

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

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