List of works - Hervé Philippe

A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

scientific article

A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata

scientific article

A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests.

scientific article published on 12 October 2009

A maximum likelihood framework for protein design

scientific article

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

A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data.

scientific article published on 5 March 2018

Acoel flatworms are not platyhelminthes: evidence from phylogenomics

scientific article

Acoelomorph flatworms are deuterostomes related to Xenoturbella

scientific article (publication date: 10 February 2011)

Additional molecular support for the new chordate phylogeny

scientific article

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.

scientific article published in October 2005

An unusual choanoflagellate protein released by Hedgehog autocatalytic processing

scientific article

Archaeal phylogeny based on ribosomal proteins

scholarly article by Oriane Matte-Tailliez et al published May 2002 in Molecular Biology and Evolution

Assessing site-interdependent phylogenetic models of sequence evolution

scientific article published on 20 June 2006

Bayesian comparisons of codon substitution models

scientific article published on 14 September 2008

Broccoli: combining phylogenetic and network analyses for orthology assignment

scientific article published on 30 June 2020

Cnidarian phylogenetic relationships as revealed by mitogenomics

scientific article (publication date: 9 January 2013)

Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons.

scientific article published on 21 April 2009

Computing Bayes factors using thermodynamic integration.

scientific article published in April 2006

Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models

scientific article published on 01 November 2018

Consensus assessment of the contamination level of publicly available cyanobacterial genomes

scientific article published on 25 July 2018

Data access for the 1,000 Plants (1KP) project

scientific article

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

scientific article published on 01 June 2007

Difficult phylogenetic questions: more data, maybe; better methods, certainly

scientific article

Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards

scientific article published on 09 September 2019

Eubacterial phylogeny based on translational apparatus proteins

scientific article published in January 2002

Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences

scientific article published on 11 January 2019

Evaluation of the models handling heterotachy in phylogenetic inference

scientific article

Evolution of eukaryotic translation elongation and termination factors: variations of evolutionary rate and genetic code deviations

scientific article published on 01 February 2002

Exploring fast computational strategies for probabilistic phylogenetic analysis

scientific article published on October 2007

Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin

scientific article published on 27 June 2003

Genomic data do not support comb jellies as the sister group to all other animals

scientific article

Heterotachy and long-branch attraction in phylogenetics

scientific article

Heterotachy, an important process of protein evolution

scientific article (publication date: 2002)

Human myosin VIIA responsible for the Usher 1B syndrome: a predicted membrane-associated motor protein expressed in developing sensory epithelia

scientific article

Impact of missing data on phylogenies inferred from empirical phylogenomic data sets

scientific article

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

scientific article published on 22 November 2017

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

scientific article (publication date: 27 April 2008)

Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches.

scientific article published on 14 July 2017

Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?

scientific article

Large-scale sequencing and the new animal phylogeny

scientific article published on 17 August 2006

Mechanistic revisions of phenomenological modeling strategies in molecular evolution

scientific article published on 6 May 2010

MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda

scientific article

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria

scientific article published on 16 May 2019

Molecular dating in the genomic era

Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes

scientific article published in July 2005

Multiple factors confounding phylogenetic detection of selection on codon usage.

scientific article published on 27 March 2018

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

scientific article

Origin of land plants revisited in the light of sequence contamination and missing data

scientific article published in August 2012

Origin of land plants: do conjugating green algae hold the key?

scientific article

Origine des vertébrés : la tunique fait-elle le moine ?

Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta

scientific article

Phylogenomic Insights into Animal Evolution

scientific article published on October 2015

Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support

scientific article published in 2009

Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts

scientific article published on 14 October 2008

Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles

scientific article

Phylogenomics

scientific article published in 2005

Phylogenomics and the reconstruction of the tree of life

scientific article (publication date: May 2005)

Phylogenomics revives traditional views on deep animal relationships

scientific article (publication date: 28 April 2009)

Phylogenomics: the beginning of incongruence?

scientific article

Phylotranscriptomic analysis of the origin and early diversification of land plants

scientific article

Phylotranscriptomic consolidation of the jawed vertebrate timetree.

scientific article

Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders

scientific article published on 05 October 2020

Pitfalls in supermatrix phylogenomics

scientific article published on 21 February 2017

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

scientific article (publication date: 3 December 2010)

Plastid Origin: Replaying the Tape

scientific article published on 01 January 2006

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada

scientific article

Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase ⬇️

scientific article published on October 30, 2003

Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets

scientific article published on 9 February 2016

Resolving difficult phylogenetic questions: why more sequences are not enough

scientific article published in March 2011

Rooting the tree of life: the phylogenetic jury is still out

scientific article (publication date: 26 September 2015)

SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics

scientific article

Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study

scientific article

Site interdependence attributed to tertiary structure in amino acid sequence evolution

scientific article published on 19 February 2005

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

scientific article

State-of the art methodologies dictate new standards for phylogenetic analysis

scientific article

Statistical potentials for improved structurally constrained evolutionary models.

scientific article

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

scientific article

The African coelacanth genome provides insights into tetrapod evolution

scientific article

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba

scientific article

The potential value of indels as phylogenetic markers: position of trichomonads as a case study

scientific article published on 01 June 2002

The product of the mammalian orthologue of the Saccharomyces cerevisiae HBS1 gene is phylogenetically related to eukaryotic release factor 3 (eRF3) but does not carry eRF3-like activity

scientific article

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

scientific article (publication date: 26 October 2004)

Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans.

scientific article

Tunicates and not cephalochordates are the closest living relatives of vertebrates

scientific article

Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models

scientific article published on 14 November 2007

List of works by Hervé Philippe

A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals

A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata

A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests.

A maximum likelihood framework for protein design

A phylogenomic framework and timescale for comparative studies of tunicates

A phylogenomic framework and timescale for comparative studies of tunicates.

A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data.

Acoel flatworms are not platyhelminthes: evidence from phylogenomics

Acoelomorph flatworms are deuterostomes related to Xenoturbella

Additional molecular support for the new chordate phylogeny

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.

An unusual choanoflagellate protein released by Hedgehog autocatalytic processing

Archaeal phylogeny based on ribosomal proteins

Assessing site-interdependent phylogenetic models of sequence evolution

Bayesian comparisons of codon substitution models

Broccoli: combining phylogenetic and network analyses for orthology assignment

Cnidarian phylogenetic relationships as revealed by mitogenomics

Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons.

Computing Bayes factors using thermodynamic integration.

Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models

Consensus assessment of the contamination level of publicly available cyanobacterial genomes

Data access for the 1,000 Plants (1KP) project

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

Difficult phylogenetic questions: more data, maybe; better methods, certainly

Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards

Eubacterial phylogeny based on translational apparatus proteins

Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences

Evaluation of the models handling heterotachy in phylogenetic inference

Evolution of eukaryotic translation elongation and termination factors: variations of evolutionary rate and genetic code deviations

Exploring fast computational strategies for probabilistic phylogenetic analysis

Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin

Genomic data do not support comb jellies as the sister group to all other animals

Heterotachy and long-branch attraction in phylogenetics

Heterotachy, an important process of protein evolution

Human myosin VIIA responsible for the Usher 1B syndrome: a predicted membrane-associated motor protein expressed in developing sensory epithelia

Impact of missing data on phylogenies inferred from empirical phylogenomic data sets

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches.

Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?

Large-scale sequencing and the new animal phylogeny

Mechanistic revisions of phenomenological modeling strategies in molecular evolution

MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria

Molecular dating in the genomic era

Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes

Multiple factors confounding phylogenetic detection of selection on codon usage.

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

Origin of land plants revisited in the light of sequence contamination and missing data

Origin of land plants: do conjugating green algae hold the key?

Origine des vertébrés : la tunique fait-elle le moine ?

Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta

Phylogenomic Insights into Animal Evolution

Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support

Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts

Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles

Phylogenomics

Phylogenomics and the reconstruction of the tree of life

Phylogenomics revives traditional views on deep animal relationships

Phylogenomics: the beginning of incongruence?

Phylotranscriptomic analysis of the origin and early diversification of land plants

Phylotranscriptomic consolidation of the jawed vertebrate timetree.

Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders

Pitfalls in supermatrix phylogenomics

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

Plastid Origin: Replaying the Tape

Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada

Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase ⬇️

Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets

Resolving difficult phylogenetic questions: why more sequences are not enough

Rooting the tree of life: the phylogenetic jury is still out

SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics

Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study

Site interdependence attributed to tertiary structure in amino acid sequence evolution

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

State-of the art methodologies dictate new standards for phylogenetic analysis

Statistical potentials for improved structurally constrained evolutionary models.

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

The African coelacanth genome provides insights into tetrapod evolution