List of works - Emmanuel J.P. Douzery

2. Dating Methods and Corresponding Chronometers in Astrobiology

7. Ancient Fossil Record and Early Evolution (ca. 3.8 to 0.5 Ga)

A cost-effective straightforward protocol for shotgun Illumina libraries designed to assemble complete mitogenomes from non-model species

A glimpse on the pattern of rodent diversification: a phylogenetic approach

scientific article

A mitochondrial DNA control region phylogeny of the Cervinae: speciation in Cervus and implications for conservation

scientific article (publication date: February 2001)

A new malaria agent in African hominids

scientific article published in May 2009

A phylogenetic perspective on the evolution of Mediterranean teleost fishes ⬇️

scientific article (publication date: 2012)

A phylogenomic framework and timescale for comparative studies of tunicates

A phylogenomic framework and timescale for comparative studies of tunicates.

scientific article published on 13 April 2018

ANISEED 2015: a digital framework for the comparative developmental biology of ascidians

scientific article (publication date: 4 January 2016)

Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates

article

Acetylcholinesterase genes within the Diptera: takeover and loss in true flies

scientific article (publication date: 22 October 2006)

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

scientific article

Arrival and diversification of caviomorph rodents and platyrrhine primates in South America

scientific article

Ascidian mitogenomics: comparison of evolutionary rates in closely related taxa provides evidence of ongoing speciation events

scientific article published on March 2014

Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability.

scientific article published in February 2003

Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development

scientific article

Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes

scientific article

Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae).

scientific article

Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes

scientific article (publication date: 2013)

Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach

scientific article published on 13 August 2013

Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach

scholarly article by Pierre-Henri Fabre et al published 30 October 2012 in Zoologica Scripta

Efficient selection of branch-specific models of sequence evolution

scientific article published on 2 February 2012

Environment drives high phylogenetic turnover among oceanic bacterial communities ⬇️

scientific article published on January 18, 2012

Evidence for genetic exchange and hybridization in Trypanosoma cruzi based on nucleotide sequences and molecular karyotype

scientific article

Fast and accurate branch lengths estimation for phylogenomic trees

scientific article

Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping

scientific article

FishMed: traits, phylogeny, current and projected species distribution of Mediterranean fishes, and environmental data

article

Flightless scaly-tailed squirrels never learned how to fly: A reappraisal of Anomaluridae phylogeny

scholarly article by Pierre-Henri Fabre published in June 2018

Genetic clustering of Trypanosoma cruzi I lineage evidenced by intergenic miniexon gene sequencing

scientific article published on 6 May 2007

Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications

scientific article

Identification of autophagy genes in Ciona intestinalis: a new experimental model to study autophagy mechanism

scientific article published on 13 August 2009

In Cold Blood: Compositional Bias and Positive Selection Drive the High Evolutionary Rate of Vampire Bats Mitochondrial Genomes

article

Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans

scientific article

Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach

scientific article

Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals

scientific article

Life-History Traits Evolved Jointly with Climatic Niche and Disturbance Regime in the Genus Leucadendron (Proteaceae).

scientific article

Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations

scientific article

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

scholarly article by Vincent Ranwez published in October 2018

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons

scientific article (publication date: 2011)

Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats

scientific article

Molecular and morphological phylogenies of ruminantia and the alternative position of the moschidae

scientific article (publication date: April 2003)

Molecular dating in the genomic era

Molecular estimation of eulipotyphlan divergence times and the evolution of "Insectivora".

scientific article published in August 2003

Molecular evidence for hybridisation between the two living species of South American ratites: potential conservation implications

article

Molecular phylogenetic reconstructions identify East Asia as the cradle for the evolution of the cosmopolitan genus Myotis (Mammalia, Chiroptera).

scientific article

Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos

scientific article

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

scientific article

Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes

scientific article

New DNA data from a transthyretin nuclear intron suggest an Oligocene to Miocene diversification of living South America opossums (Marsupialia: Didelphidae).

scientific article published in May 2005

Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae).

scientific article published on 10 July 2013

OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes

scientific article published in 2019

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals

scientific article published on 9 April 2014

PhySIC: a veto supertree method with desirable properties

scientific article published in October 2007

PhySIC_IST: cleaning source trees to infer more informative supertrees

scientific article (publication date: 4 October 2008)

Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences

scientific article (publication date: May 1997)

Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP.

scientific article

Projected impacts of climate warming on the functional and phylogenetic components of coastal Mediterranean fish biodiversity

article

Protected and threatened components of fish biodiversity in the Mediterranean sea.

scientific article

Rabbits, if anything, are likely Glires

scientific article published in December 2004

Representing taxonomic, phylogenetic and functional diversity: new challenges for Mediterranean marine-protected areas

scholarly article by François Guilhaumon et al published 17 November 2014 in Diversity and Distributions

Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths)

scientific article

Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes

scientific article

Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics

scientific article published in July 2014

SDM: a fast distance-based approach for (super) tree building in phylogenomics

scientific article published in October 2006

Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules

scientific article

SuperTriplets: a triplet-based supertree approach to phylogenomics

scientific article

The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies

scientific article

The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?

scientific article (publication date: 26 October 2004)

Thrice better than once: quality control guidelines to validate new mitogenomes

scientific article

List of works by Emmanuel J.P. Douzery

2. Dating Methods and Corresponding Chronometers in Astrobiology

7. Ancient Fossil Record and Early Evolution (ca. 3.8 to 0.5 Ga)

A cost-effective straightforward protocol for shotgun Illumina libraries designed to assemble complete mitogenomes from non-model species

A glimpse on the pattern of rodent diversification: a phylogenetic approach

A mitochondrial DNA control region phylogeny of the Cervinae: speciation in Cervus and implications for conservation

A new malaria agent in African hominids

A phylogenetic perspective on the evolution of Mediterranean teleost fishes ⬇️

A phylogenomic framework and timescale for comparative studies of tunicates

A phylogenomic framework and timescale for comparative studies of tunicates.

ANISEED 2015: a digital framework for the comparative developmental biology of ascidians

Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates

Acetylcholinesterase genes within the Diptera: takeover and loss in true flies

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

Arrival and diversification of caviomorph rodents and platyrrhine primates in South America

Ascidian mitogenomics: comparison of evolutionary rates in closely related taxa provides evidence of ongoing speciation events

Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability.

Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development

Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes

Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae).

Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes

Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach

Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach

Efficient selection of branch-specific models of sequence evolution

Environment drives high phylogenetic turnover among oceanic bacterial communities ⬇️

Evidence for genetic exchange and hybridization in Trypanosoma cruzi based on nucleotide sequences and molecular karyotype

Fast and accurate branch lengths estimation for phylogenomic trees

Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping

FishMed: traits, phylogeny, current and projected species distribution of Mediterranean fishes, and environmental data

Flightless scaly-tailed squirrels never learned how to fly: A reappraisal of Anomaluridae phylogeny

Genetic clustering of Trypanosoma cruzi I lineage evidenced by intergenic miniexon gene sequencing

Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications

Identification of autophagy genes in Ciona intestinalis: a new experimental model to study autophagy mechanism

In Cold Blood: Compositional Bias and Positive Selection Drive the High Evolutionary Rate of Vampire Bats Mitochondrial Genomes

Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans

Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach

Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals

Life-History Traits Evolved Jointly with Climatic Niche and Disturbance Regime in the Genus Leucadendron (Proteaceae).

Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons

Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats

Molecular and morphological phylogenies of ruminantia and the alternative position of the moschidae

Molecular dating in the genomic era

Molecular estimation of eulipotyphlan divergence times and the evolution of "Insectivora".

Molecular evidence for hybridisation between the two living species of South American ratites: potential conservation implications

Molecular phylogenetic reconstructions identify East Asia as the cradle for the evolution of the cosmopolitan genus Myotis (Mammalia, Chiroptera).

Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes

New DNA data from a transthyretin nuclear intron suggest an Oligocene to Miocene diversification of living South America opossums (Marsupialia: Didelphidae).

Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae).

OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals

PhySIC: a veto supertree method with desirable properties

PhySIC_IST: cleaning source trees to infer more informative supertrees

Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences

Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP.

Projected impacts of climate warming on the functional and phylogenetic components of coastal Mediterranean fish biodiversity

Protected and threatened components of fish biodiversity in the Mediterranean sea.

Rabbits, if anything, are likely Glires

Representing taxonomic, phylogenetic and functional diversity: new challenges for Mediterranean marine-protected areas

Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths)

Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes

Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics

SDM: a fast distance-based approach for (super) tree building in phylogenomics

Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules

SuperTriplets: a triplet-based supertree approach to phylogenomics

The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies

The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?

Thrice better than once: quality control guidelines to validate new mitogenomes