Animal Phylogeny
Jimenez-Guri E, Philippe H, Okamura B, Holland PW.
Buddenbrockia is a cnidarian worm.
Science. 2007 Jul 6;317(5834):116-8.
Delsuc F, Brinkmann H, Chourrout D, Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates
Nature. 2006 Feb 23;439(7079):965-8.
Philippe H, Lartillot N, Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
Mol Biol Evol. 2005 May;22(5):1246-53.
Philippe H., A. Chenuil and A. Adoutte. Can the cambrian explosion be inferred through molecular phylogeny?
Development. 1994;120(Supplement):15-25.
Eukaryotic Phylogeny
Brinkmann H, van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H.
An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics
Syst Biol. 2005 Oct;54(5):743-57
Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Loffelhardt W, Bohnert HJ, Philippe H, Lang BF.
Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes
Curr Biol. 2005 Jul 26;15(14):1325-30
Douzery EJ, Snell EA, Bapteste E, Delsuc F, Philippe H. The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?
Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15386-91
Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, Gordon P, Durufle L, Gaasterland T, Lopez P, Muller M, Philippe H. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba.
Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1414-9
Brochier C, Bapteste E, Moreira D, Philippe H. Eubacterial phylogeny based on translational apparatus proteins.
Trends Genet. 2002 Jan;18(1):1-5
Philippe H, Lopez P, Brinkmann H, Budin K, Germot A, Laurent J, Moreira D, Muller M, Le Guyader H. Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions.
Proc Biol Sci. 2000 Jun 22;267(1449):1213-21
Moreira D, Le Guyader H, Philippe H. The origin of red algae and the evolution of chloroplasts.
Nature. 2000 May 4;405(6782):69-72
Universal Tree of Life
Brochier C, Philippe H.
Phylogeny: a non-hyperthermophilic ancestor for bacteria.
Nature. 2002 May 16;417(6886):244
Forterre P, Philippe H. Where is the root of the universal tree of life?
Bioessays. 1999 Oct;21(10):871-9
Brinkmann H, Philippe H. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies.
Mol Biol Evol. 1999 Jun;16(6):817-25
Heterotachy
Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F.
Heterotachy and long-branch attraction in phylogenetics
BMC Evol Biol. 2005 Oct 6;5:50
Gribaldo S, Casane D, Lopez P, Philippe H. Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin.
Mol Biol Evol. 2003 Nov;20(11):1754-9
Lopez P, Casane D, Philippe H. Heterotachy, an important process of protein evolution.
Mol Biol Evol. 2002 Jan;19(1):1-7
Philippe H, Germot A. Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution.
Mol Biol Evol. 2000 May;17(5):830-4. No abstract available
Lopez P, Forterre P, Philippe H. The root of the tree of life in the light of the covarion model.
J Mol Evol. 1999 Oct;49(4):496-508
Philippe H., G. Lecointre, H.L.V. L�and H. Le Guyader. A critical study of homoplasy in molecular data with the use of a morphologically based cladogram.
Mol. Biol. Evol. 1996;13:1174-1186
Phylogenomics and Tree building
Rodriguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H.
Detecting and overcoming systematic errors in genome-scale phylogenies.
Syst Biol. 2007 Jun;56(3):389-99.
Lartillot N, Brinkmann H, Philippe H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model.
BMC Evol Biol. 2007 Feb 8;7 Suppl 1:S4
Jeffroy O, Brinkmann H, Delsuc F, Philippe H. Phylogenomics: the beginning of incongruence?
Trends Genet. 2006 Apr;22(4):225-31
Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life
Nat Rev Genet. 2005 May;6(5):361-75
Lartillot N, Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
Mol Biol Evol. 2004 Jun;21(6):1095-109
Lecointre G, Philippe H, Van Le HL, Le Guyader H. How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences.
Mol Phylogenet Evol. 1994 Dec;3(4):292-309
Lecointre G, Philippe H, Van Le HL, Le Guyader H. Species sampling has a major impact on phylogenetic inference.
Mol Phylogenet Evol. 1993 Sep;2(3):205-24