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Hervé Philippe

Research Profile

Concepts & Ideas

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Evolution, Molecular

Genes & Molecular Sequences

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Computer Simulation

Chemicals & Drugs

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Publications

TOP 3
Béatrice Roure; Denis BAURAIN; Hervé Philippe
Impact of missing data on phylogenies inferred from empirical phylogenomic data sets.
Simon Laurin-Lemay; Henner Brinkmann; Hervé Philippe
Origin of land plants revisited in the light of sequence contamination and missing data.
Hervé Philippe; Henner Brinkmann; Dennis Lavrov; D Timothy J Littlewood; Michael Manuel; Gert Wörheide; Denis BAURAIN
Resolving difficult phylogenetic questions: why more sequences are not enough.

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All Publications

2013: Béatrice Roure; Denis BAURAIN; Hervé Philippe
Impact of missing data on phylogenies inferred from empirical phylogenomic data sets.
Molecular biology and evolution 2013;30(1):197-214.
2012: Simon Laurin-Lemay; Henner Brinkmann; Hervé Philippe
Origin of land plants revisited in the light of sequence contamination and missing data.
Current biology : CB 2012;22(15):R593-4.
2011: Hervé Philippe; Henner Brinkmann; Dennis Lavrov; D Timothy J Littlewood; Michael Manuel; Gert Wörheide; Denis BAURAIN
Resolving difficult phylogenetic questions: why more sequences are not enough.
PLoS biology 2011;9(3):e1000602.
2011: Béatrice Roure; Hervé Philippe
Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference.
BMC evolutionary biology 2011;11():17.
2010: Denis BAURAIN; Henner Brinkmann; Jörn Petersen; Naiara Rodriguez-Ezpeleta; Alexandra Stechmann; Vincent Demoulin; Andrew J Roger; Gertraud Burger; B Franz Lang; Hervé Philippe
Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles.
Molecular biology and evolution 2010;27(7):1698-709.
2010: Claudia L Kleinman; Nicolas Rodrigue; Nicolas Lartillot; Hervé Philippe
Statistical potentials for improved structurally constrained evolutionary models.
Molecular biology and evolution 2010;27(7):1546-60.
2010: Yan Zhou; Henner Brinkmann; Nicolas Rodrigue; Nicolas Lartillot; Hervé Philippe
A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests.
Molecular biology and evolution 2010;27(2):371-84.
2009: Hervé Philippe; Romain Derelle; Philippe Lopez; Kerstin Pick; Carole Borchiellini; Nicole Boury-Esnault; Jean Vacelet; Emmanuelle Renard; Evelyn Houliston; Eric Quéinnec; Corinne Da Silva; Patrick Wincker; Hervé Le Guyader; Sally Leys; Daniel J Jackson; Fabian Schreiber; Dirk Erpenbeck; Burkhard Morgenstern; Gert Wörheide; Michaël Manuel
Phylogenomics revives traditional views on deep animal relationships.
Current biology : CB 2009;19(8):706-12.
2009: Yu Liu; Emma T Steenkamp; Henner Brinkmann; Lise Forget; Hervé Philippe; B Franz Lang
Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support.
BMC evolutionary biology 2009;9():272.
2008: Frederic Delsuc; Georgia Tsagkogeorga; Nicolas Lartillot; Hervé Philippe
Additional molecular support for the new chordate phylogeny.
Genesis (New York, N.Y. : 2000) 2008;46(11):592-604.
2008: Nicolas Rodrigue; Nicolas Lartillot; Hervé Philippe
Bayesian comparisons of codon substitution models.
Genetics 2008;180(3):1579-91.
2008: Hervé Philippe
Less is more: decreasing the number of scientific conferences to promote economic degrowth.
Trends in genetics : TIG 2008;24(6):265-7.
2008: Nicolas Lartillot; Hervé Philippe
Improvement of molecular phylogenetic inference and the phylogeny of Bilateria.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2008;363(1496):1463-72.
2008: Nicolas Rodrigue; Hervé Philippe; Nicolas Lartillot
Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models.
Bioinformatics (Oxford, England) 2008;24(1):56-62.
2007: Thomas Lepage; David Bryant; Hervé Philippe; Nicolas Lartillot
A general comparison of relaxed molecular clock models.
Molecular biology and evolution 2007;24(12):2669-80.
2007: Nicolas Rodrigue; Hervé Philippe; Nicolas Lartillot
Exploring fast computational strategies for probabilistic phylogenetic analysis.
Systematic biology 2007;56(5):711-26.
2007: Naiara Rodriguez-Ezpeleta; Henner Brinkmann; Gertraud Burger; Andrew J Roger; Michael W Gray; Hervé Philippe; B Franz Lang
Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans.
Current biology : CB 2007;17(16):1420-5.
2007: Naiara Rodriguez-Ezpeleta; Henner Brinkmann; Béatrice Roure; Nicolas Lartillot; B Franz Lang; Hervé Philippe
Detecting and overcoming systematic errors in genome-scale phylogenies.
Systematic biology 2007;56(3):389-99.
2007: Naiara Rodriguez-Ezpeleta; Hervé Philippe; Henner Brinkmann; Burkhard Becker; Michael Melkonian
Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta.
Molecular biology and evolution 2007;24(3):723-31.
2007: Henner Brinkmann; Hervé Philippe
The diversity of eukaryotes and the root of the eukaryotic tree.
Advances in experimental medicine and biology 2007;607():20-37.
2007: Yan Zhou; Nicolas Rodrigue; Nicolas Lartillot; Hervé Philippe
Evaluation of the models handling heterotachy in phylogenetic inference.
BMC evolutionary biology 2007;7():206.
2007: Hervé Philippe; Henner Brinkmann; Pedro Martinez; Marta Riutort; Jaume Baguñà
Acoel flatworms are not platyhelminthes: evidence from phylogenomics.
PloS one 2007;2(8):e717.
2007: Nicolas Lartillot; Henner Brinkmann; Hervé Philippe
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model.
BMC evolutionary biology 2007;7 Suppl 1():S4.
2007: Béatrice Roure; Naiara Rodriguez-Ezpeleta; Hervé Philippe
SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics.
BMC evolutionary biology 2007;7 Suppl 1():S2.
2007: Denis BAURAIN; Henner Brinkmann; Hervé Philippe
Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?
Molecular biology and evolution 2007;24(1):6-9.
2006: Hervé Philippe; Maximilian J Telford
Large-scale sequencing and the new animal phylogeny.
Trends in ecology & evolution 2006;21(11):614-20.
2006: Nicolas Rodrigue; Hervé Philippe; Nicolas Lartillot
Assessing site-interdependent phylogenetic models of sequence evolution.
Molecular biology and evolution 2006;23(9):1762-75.
2006: Frederic Delsuc; Denis BAURAIN; Hervé Philippe
[Vertebrate origins: does the tunic make the man?].
Médecine sciences : M/S 2006;22(8-9):688-90.
2006: Emmanuel J P Douzery; Frederic Delsuc; Hervé Philippe
[Molecular dating in the genomic era].
Médecine sciences : M/S 2006;22(4):374-80.
2006: Nicolas Lartillot; Hervé Philippe
Computing Bayes factors using thermodynamic integration.
Systematic biology 2006;55(2):195-207.
2006: Olivier Jeffroy; Henner Brinkmann; Frederic Delsuc; Hervé Philippe
Phylogenomics: the beginning of incongruence?
Trends in genetics : TIG 2006;22(4):225-31.
2006: Frederic Delsuc; Henner Brinkmann; Daniel Chourrout; Hervé Philippe
Tunicates and not cephalochordates are the closest living relatives of vertebrates.
Nature 2006;439(7079):965-8.
2006: Elizabeth A Snell; Nina M Brooke; William R Taylor; Didier Casane; Hervé Philippe; Peter W H Holland
An unusual choanoflagellate protein released by Hedgehog autocatalytic processing.
Proceedings. Biological sciences / The Royal Society 2006;273(1585):401-7.
2006: Naiara Rodriguez-Ezpeleta; Hervé Philippe
Plastid origin: replaying the tape.
Current biology : CB 2006;16(2):R53-6.
2006: Claudia L Kleinman; Nicolas Rodrigue; Cécile Bonnard; Hervé Philippe; Nicolas Lartillot
A maximum likelihood framework for protein design.
BMC bioinformatics 2006;7():326.
2005: Henner Brinkmann; Mark van der Giezen; Yan Zhou; Gaëtan Poncelin de Raucourt; Hervé Philippe
An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.
Systematic biology 2005;54(5):743-57.
2005: Naiara Rodriguez-Ezpeleta; Henner Brinkmann; Suzanne C Burey; Béatrice Roure; Gertraud Burger; Wolfgang Löffelhardt; Hans Bohnert; Hervé Philippe; B Franz Lang
Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes.
Current biology : CB 2005;15(14):1325-30.
2005: Frederic Delsuc; Henner Brinkmann; Hervé Philippe
Phylogenomics and the reconstruction of the tree of life.
Nature reviews. Genetics 2005;6(5):361-75.
2005: Hervé Philippe; Nicolas Lartillot; Henner Brinkmann
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia.
Molecular biology and evolution 2005;22(5):1246-53.
2005: Nicolas Rodrigue; Nicolas Lartillot; David Bryant; Hervé Philippe
Site interdependence attributed to tertiary structure in amino acid sequence evolution.
Gene 2005;347(2):207-17.
2005: Hervé Philippe; Yan Zhou; Henner Brinkmann; Nicolas Rodrigue; Frederic Delsuc
Heterotachy and long-branch attraction in phylogenetics.
BMC evolutionary biology 2005;5():50.
2004: Emmanuel J P Douzery; Elizabeth A Snell; Eric Bapteste; Frederic Delsuc; Hervé Philippe
The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?
Proceedings of the National Academy of Sciences of the United States of America 2004;101(43):15386-91.
2004: Hervé Philippe; Elizabeth A Snell; Eric Bapteste; Philippe Lopez; Peter W H Holland; Didier Casane
Phylogenomics of eukaryotes: impact of missing data on large alignments.
Molecular biology and evolution 2004;21(9):1740-52.
2004: Nicolas Lartillot; Hervé Philippe
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process.
Molecular biology and evolution 2004;21(6):1095-109.
2003: Simonetta Gribaldo; Didier Casane; Philippe Lopez; Hervé Philippe
Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin.
Molecular biology and evolution 2003;20(11):1754-9.
2003: Eric Bapteste; David Moreira; Hervé Philippe
Rampant horizontal gene transfer and phospho-donor change in the evolution of the phosphofructokinase.
Gene 2003;318():185-91.
2003: Hervé Philippe; Christophe J Douady
Horizontal gene transfer and phylogenetics.
Current opinion in microbiology 2003;6(5):498-505.
2003: Hervé Philippe; Didier Casane; Simonetta Gribaldo; Philippe Lopez; Julien Meunier
Heterotachy and functional shift in protein evolution.
IUBMB life 2003;55(4-5):257-65.
2003: Purificación López-García; Hervé Philippe; Françoise Gail; David Moreira
Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(2):697-702.
2002: Patrick Forterre; Céline Brochier; Hervé Philippe
Evolution of the Archaea.
Theoretical population biology 2002;61(4):409-22.
2002: Simonetta Gribaldo; Hervé Philippe
Ancient phylogenetic relationships.
Theoretical population biology 2002;61(4):391-408.
2002: Eric Bapteste; Hervé Philippe
The potential value of indels as phylogenetic markers: position of trichomonads as a case study.
Molecular biology and evolution 2002;19(6):972-7.
2002: Céline Brochier; Hervé Philippe
Phylogeny: a non-hyperthermophilic ancestor for bacteria.
Nature 2002;417(6886):244.
2002: Yvan Zivanovic; Philippe Lopez; Hervé Philippe; Patrick Forterre
Pyrococcus genome comparison evidences chromosome shuffling-driven evolution.
Nucleic acids research 2002;30(9):1902-10.
2002: Oriane Matte-Tailliez; Céline Brochier; Patrick Forterre; Hervé Philippe
Archaeal phylogeny based on ribosomal proteins.
Molecular biology and evolution 2002;19(5):631-9.
2002: Eric Bapteste; Henner Brinkmann; Jennifer A Lee; Dorothy V Moore; Christoph Wilhelm Sensen; Paul Gordon; Laure Duruflé; Terry Gaasterland; Philippe Lopez; Miklós Müller; Hervé Philippe
The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(3):1414-9.
2002: David Moreira; Stephanie Kervestin; Olivier Jean-Jean; Hervé Philippe
Evolution of eukaryotic translation elongation and termination factors: variations of evolutionary rate and genetic code deviations.
Molecular biology and evolution 2002;19(2):189-200.
2002: Philippe Lopez; Didier Casane; Hervé Philippe
Heterotachy, an important process of protein evolution.
Molecular biology and evolution 2002;19(1):1-7.
2002: Céline Brochier; Eric Bapteste; David Moreira; Hervé Philippe
Eubacterial phylogeny based on translational apparatus proteins.
Trends in genetics : TIG 2002;18(1):1-5.
2001: David Moreira; Hervé Philippe
Sure facts and open questions about the origin and evolution of photosynthetic plastids.
Research in microbiology 2001;152(9):771-80.
2000: Céline Brochier; Hervé Philippe; David Moreira
The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome.
Trends in genetics : TIG 2000;16(12):529-33.
2000: Hervé Philippe; Agnès Germot; David Moreira
The new phylogeny of eukaryotes.
Current opinion in genetics & development 2000;10(6):596-601.
2000: Hannu Myllykallio; Philippe Lopez; Purificación López-García; Roland Heilig; William Saurin; Yvan Zivanovic; Hervé Philippe; Patrick Forterre
Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon.
Science (New York, N.Y.) 2000;288(5474):2212-5.
2000: Hervé Philippe; Philippe Lopez; H Brinkmann; K Budin; Agnès Germot; Jacqueline Laurent; David Moreira; M Müller; Hervé Le Guyader
Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions.
Proceedings. Biological sciences / The Royal Society 2000;267(1449):1213-21.
2000: David Moreira; Hervé Le Guyader; Hervé Philippe
The origin of red algae and the evolution of chloroplasts.
Nature 2000;405(6782):69-72.
2000: Hervé Philippe; Agnès Germot
Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution.
Molecular biology and evolution 2000;17(5):830-4.
2000: Patrick Forterre; Claire Bouthier de La Tour; Hervé Philippe; Michel Duguet
Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from archaea to bacteria.
Trends in genetics : TIG 2000;16(4):152-4.
2000: Philippe Lopez; Patrick Forterre; Hervé Le Guyader; Hervé Philippe
Origin of replication of Thermotoga maritima.
Trends in genetics : TIG 2000;16(2):59-60.
1999: Patrick Forterre; Hervé Philippe
Where is the root of the universal tree of life?
BioEssays : news and reviews in molecular, cellular and developmental biology 1999;21(10):871-9.
1999: Hervé Philippe; Patrick Forterre
The rooting of the universal tree of life is not reliable.
Journal of molecular evolution 1999;49(4):509-23.
1999: Philippe Lopez; Patrick Forterre; Hervé Philippe
The root of the tree of life in the light of the covarion model.
Journal of molecular evolution 1999;49(4):496-508.
1999: H Brinkmann; Hervé Philippe
Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies.
Molecular biology and evolution 1999;16(6):817-25.
1999: Philippe Lopez; Hervé Philippe; Hannu Myllykallio; Patrick Forterre
Identification of putative chromosomal origins of replication in Archaea.
Molecular microbiology 1999;32(4):883-6.
1999: Agnès Germot; Hervé Philippe
Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family.
The Journal of eukaryotic microbiology 1999;46(2):116-24.
1999: Hervé Philippe; K Budin; David Moreira
Horizontal transfers confuse the prokaryotic phylogeny based on the HSP70 protein family.
Molecular microbiology 1999;31(3):1007-10.
1999: David Moreira; Hervé Le Guyader; Hervé Philippe
Unusually high evolutionary rate of the elongation factor 1 alpha genes from the Ciliophora and its impact on the phylogeny of eukaryotes.
Molecular biology and evolution 1999;16(2):234-45.
1998: C Wallrapp; S B Verrier; Galina Zhouravleva; Hervé Philippe; Michel Philippe; Thomas M Gress; Olivier Jean-Jean
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.
FEBS letters 1998;440(3):387-92.
1998: Hervé Philippe; Jacqueline Laurent
How good are deep phylogenetic trees?
Current opinion in genetics & development 1998;8(6):616-23.
1998: K Budin; Hervé Philippe
New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences.
Molecular biology and evolution 1998;15(8):943-56.
1997: Agnès Germot; Hervé Philippe; Hervé Le Guyader
Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae.
Molecular and biochemical parasitology 1997;87(2):159-68.
1996: Agnès Germot; Hervé Philippe; Hervé Le Guyader
Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial endosymbiosis in eukaryotes.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(25):14614-7.