List of works - Jean-François Flot

A Feulgen glimpse into genome evolution during range expansion: a case study of the subterranean amphipod Niphargus schellenbergi

scientific article published in 2022

A coral spawning calendar for Sesoko Station, Okinawa, Japan

scientific article published on 18 November 2021

A genomic glance through the fog of plasticity and diversification in Pocillopora.

scientific article

Against All Odds: Trehalose-6-Phosphate Synthase and Trehalase Genes in the Bdelloid Rotifer Adineta vaga Were Acquired by Horizontal Gene Transfer and Are Upregulated during Desiccation

scientific article published on 10 July 2015

An Indo-Pacific coral spawning database

scientific article published on 29 January 2021

Brazilian cave heritage under siege ⬇️

scientific article published on 18 March 2022

Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

scientific article published on 17 December 2022

Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer <i>Adineta vaga</i>

scientific article published on 06 October 2021

Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

scientific article published on 08 March 2022

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

scientific article published on 14 December 2017

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments.

scientific article published on 27 April 2019

Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures

scientific article

DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe

scientific article (publication date: 29 November 2016)

Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC.

scientific article published on 19 January 2015

Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants

scientific article published in 2017

Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex.

scientific article

Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system

scientific article published in 2013

Genome Assembly of the Cold-Tolerant Leaf Beetle Gonioctena quinquepunctata, an Important Resource for Studying Its Evolution and Reproductive Barriers between Species

publication published on 01 July 2021

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

scientific article

Guidelines for DNA taxonomy, with a focus on the meiofauna

HaplowebMaker and CoMa: Two web tools to delimit species using haplowebs and conspecificity matrices

scientific article published in 2020

Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton

scientific article

High-quality genome (re)assembly using chromosomal contact data

scientific article

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

scientific article

ITS1 variation among Stichopathes cf. maldivensis (Hexacorallia: Antipatharia) whip black corals unveils conspecificity and population connectivity at local and global scales across the Indo-Pacific

scientific article published on 11 January 2021

Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization?

scientific article

Integrating multiple species criteria and species hypotheses in subterranean biology

Lophelia pertusa corals from the Ionian and Barents seas share identical nuclear ITS2 and near-identical mitochondrial genome sequences

scientific article

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

scientific article

Molecular phylogeny of Alpine groundwater Niphargidae (Crustacea, Amphipoda) reveals the effects of Quaternary climate fluctuations

scientific article published on 14 July 2022

Molecular taxonomy, phylogeny and biogeography of the Niphargus tatrensis species complex (Amphipoda, Niphargidae) in Austria ⬇️

scholarly article by Fabio Stoch et al published 6 October 2020 in Organisms Diversity and Evolution

Morphological evolution of coexisting amphipod species pairs from sulfidic caves suggests competitive interactions and character displacement, but no environmental filtering and convergence

scientific article published on 23 April 2015

Niphargus dancaui sp. nov. (Amphipoda, Niphargidae) – a new species thriving in sulfidic groundwaters in southeastern Romania

scientific article published on 16 December 2015

Niphargus-Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania

scientific article

Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology

scientific article

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

article

Phylogenetic structure and molecular species delimitation hint a complex evolutionary history in an Alpine endemic Niphargus clade (Crustacea, Amphipoda)

scientific article published in 2023

Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean

scientific article published on 29 October 2020

Quantification of complex modular architecture in plants

scientific article published on 22 February 2018

Rediscovery and redescription of Niphargus enslini Karaman, 1932 (Amphipoda, Niphargidae) in southern Germany

Response to Signorovitch et al.

scientific article published in August 2016

Solving the Coral Species Delimitation Conundrum

scientific article published on 18 September 2021

Species Delimitation's Coming of Age.

scientific article

Speleomics: omics insights into subterranean ecosystems

scientific article published on 14 July 2022

Sulfur Cave (Romania), an extreme environment with microbial mats in a CO2-H2S/O2 gas chemocline dominated by mycobacteria

The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes

scientific article

The era of reference genomes in conservation genomics

scientific article published in March 2022

The first record of a stygobiotic form of Garra rufa (Heckel, 1843), sympatric with Garra tashanensis Mousavi-Sabet, Vatandoust, Fatemi &amp; Eagderi, 2016 (Teleostei, Cyprinidae), in Iranian subterranean waters

scientific article published on 17 October 2023

The hitchhiker's guide to single-locus species delimitation

scientific article published on 05 July 2018

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

scientific article published on 31 July 2017

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

scholarly article published 8 February 2017

The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: the putative D-loop and a novel ORF of unknown function

scientific article published in 2007

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

scientific article published on 01 March 2020

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

scientific article published on 01 January 2020

Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecosystem of Frasassi, central Italy

scientific article

List of works by Jean-François Flot

A Feulgen glimpse into genome evolution during range expansion: a case study of the subterranean amphipod Niphargus schellenbergi

A coral spawning calendar for Sesoko Station, Okinawa, Japan

A genomic glance through the fog of plasticity and diversification in Pocillopora.

Against All Odds: Trehalose-6-Phosphate Synthase and Trehalase Genes in the Bdelloid Rotifer Adineta vaga Were Acquired by Horizontal Gene Transfer and Are Upregulated during Desiccation

An Indo-Pacific coral spawning database

Brazilian cave heritage under siege ⬇️

Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer <i>Adineta vaga</i>

Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments.

Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures

DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe

Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC.

Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants

Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex.

Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system

Genome Assembly of the Cold-Tolerant Leaf Beetle Gonioctena quinquepunctata, an Important Resource for Studying Its Evolution and Reproductive Barriers between Species

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

Guidelines for DNA taxonomy, with a focus on the meiofauna

HaplowebMaker and CoMa: Two web tools to delimit species using haplowebs and conspecificity matrices

Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton

High-quality genome (re)assembly using chromosomal contact data

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

ITS1 variation among Stichopathes cf. maldivensis (Hexacorallia: Antipatharia) whip black corals unveils conspecificity and population connectivity at local and global scales across the Indo-Pacific

Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization?

Integrating multiple species criteria and species hypotheses in subterranean biology

Lophelia pertusa corals from the Ionian and Barents seas share identical nuclear ITS2 and near-identical mitochondrial genome sequences

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

Molecular phylogeny of Alpine groundwater Niphargidae (Crustacea, Amphipoda) reveals the effects of Quaternary climate fluctuations

Molecular taxonomy, phylogeny and biogeography of the Niphargus tatrensis species complex (Amphipoda, Niphargidae) in Austria ⬇️

Morphological evolution of coexisting amphipod species pairs from sulfidic caves suggests competitive interactions and character displacement, but no environmental filtering and convergence

Niphargus dancaui sp. nov. (Amphipoda, Niphargidae) – a new species thriving in sulfidic groundwaters in southeastern Romania

Niphargus-Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania

Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology

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

Phylogenetic structure and molecular species delimitation hint a complex evolutionary history in an Alpine endemic Niphargus clade (Crustacea, Amphipoda)

Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean

Quantification of complex modular architecture in plants

Rediscovery and redescription of Niphargus enslini Karaman, 1932 (Amphipoda, Niphargidae) in southern Germany

Response to Signorovitch et al.

Solving the Coral Species Delimitation Conundrum

Species Delimitation's Coming of Age.

Speleomics: omics insights into subterranean ecosystems

Sulfur Cave (Romania), an extreme environment with microbial mats in a CO2-H2S/O2 gas chemocline dominated by mycobacteria

The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes

The era of reference genomes in conservation genomics

The first record of a stygobiotic form of Garra rufa (Heckel, 1843), sympatric with Garra tashanensis Mousavi-Sabet, Vatandoust, Fatemi &amp;amp; Eagderi, 2016 (Teleostei, Cyprinidae), in Iranian subterranean waters

The hitchhiker's guide to single-locus species delimitation

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: the putative D-loop and a novel ORF of unknown function

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecosystem of Frasassi, central Italy

The first record of a stygobiotic form of Garra rufa (Heckel, 1843), sympatric with Garra tashanensis Mousavi-Sabet, Vatandoust, Fatemi & Eagderi, 2016 (Teleostei, Cyprinidae), in Iranian subterranean waters