PUBLICATIONS
Verdonck R, Legrand D, Jacob S, Philippe H
(2022) - Phenotypic plasticity through disposable genetic adaptation in ciliates - Trends in Microbiology 30(2):120-130Cayuela H, Jacob S, Schtickzelle N, Verdonck R, Philippe H, Laporte M, Huet M, Bernatchez L, Legrand D
(2022) - Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences - Oikos e08846Van Vlierberghe M., Philippe H., Baurain D.
(2021) - Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages - BMC Res Notes 14(1):143Van Vlierberghe M., Di Franco A., Philippe H., Baurain D.
(2021) - Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project - BMC Res Notes 14(1):306Kapli P., Natsidis P., Leite D.J., Fursman M., Jeffrie N., Rahman I.A., Philippe H., Copley R.R., Telford M.J.
(2021) - Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria - Science Advanced 7(12):eabe2741Junker A.D., Jacob S., Philippe H., Legrand D., Pearson CG
(2021) - Plastic cell morphology changes during dispersal - IScience 24,102915Yahalomia D., Atkinson S.D., Neuhof M., Chang E.S., Philippe H., Cartwright P., Bartholome J.L. & Huchon D.
(2020) - An animal without a mitochondrial genome. - Proceedings of the National Academy of Sciences in pressSouchet J., Gangloff E.J., Micheli G., Bossu C., Trochet A., Bertrand R., Clobert J., Calvez O., Martinez-Silvestre A., Darnet E., Le Chevalier H., Guillaume O., Mossoll-Torres M., Barthe L., Pottier G., Philippe H. & Aubret F.
(2020) - High-elevation hypoxia impacts perinatal physiology and performance in a potential montane colonizer. - Integrative Zoology 0: 1–14Garcia-Porta J., Irisarri I., Kirchner M., Rodriguez A., Kirchhof S., Brown J.L., MacLeod A., Turner A.P., Ahmadzadeh F., Albaladejo G., Crnobrnja-Isailovic J., De la Riva I., Fawzi A., Galan P., Goçmen B., Harris D.J., Jiminez-Robles O., Joger U., Jovanovic Glavas O., Karis M., Koziel G., Kunzel S., Lyra M., Miles D., Nogales M., Oguz M.A., Pafilis P., Rancilhac L., Rodriguez N., Rodriguez Concepcion B., Sanchez E., Salvi D., Slimani T., S'khifa A., Qashqaei A.T., Zagar A., Lemmon A., Moriarty Lemmon E., Carretero M.A., Carranza S., Philippe H., Sinervo B., Müller J., Vences M. & Wollenberg Valero K.C.
(2019) - Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards. - Nature Communications 10(1): 4077Di Franco A., Poujol R., Baurain D. & Philippe H.
(2019) - Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. - BMC Evolutionary Biology 19: 21Philippe H., Poustka A.J., Chiodin M., Hoff K.J., Dessimoz C., Tomiczek B., Schiffer P.H., Müller S., Domman D., Horn M., Kuhl H., Timmermann B., Satoh N., Hikosaka-Katayama T., Nakano H., Rowe M.L., Elphick M.R., Thomas-Chollier M., Hankeln T., Mertes F., Wallberg A., Copley R.R., Martinez P. & Telford M.J.
(2019) - Mitigating anticipated effects of systematic errors supports sister-group relationship between Xenacoelomorpha and Ambulacraria. - Current Biology 29: 1818-1826Delaux P.M., Hetherington A.J., Coudert Y., Delwiche C., Dunand C., Gould S., Kenrick P., Li F.W., Philippe H., Rensing S.A., Rich M., Strullu-Derrien C. & de Vries J.
(2019) - Reconstructing trait evolution in plant evo-devo studies. - Current Biology 29:R1110-R1118Delsuc F., Philippe H., Tsagkogeorga G., Simion P., Tilak M.-K., Turon X., López-Legentil S., Piette J., Lemaire P. & Douzery E.J.P.
(2018) - A phylogenomic framework and timescale for comparative studies of tunicates. - BMC Biology 16: 39Simion P., Belkhir K., François C., Veyssier J., Rink J.C., Manuel M., Philippe H. and Telford M.J.
(2018) - A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data. - BMC Biology 16: 28Laurin-Lemay S., Rodrigue N., Lartillot N. & Philippe H.
(2018) - Conditional Approximate Bayesian Computation, a new approach for across-site dependency in high-dimensional mutation-selection models. - Molecular Biology and Evolution 35: 2819-2834Cornet L., Meunier L., Van Vlierberghe M., Léonard R.R., Durieu B., Lara Y., Misztak A., Sirjacobs D., Javaux E.J., Philippe H., Wilmotte A. and Baurain D.
(2018) - Consensus assessment of the contamination level of publicly available cyanobacterial genomes - PLoS One 13: e0200323Laurin-Lemay S., Philippe H. & Rodrigue N.
(2018) - Multiple factors confounding phylogenetic detection of selection on codon usage. - Molecular Biology and Evolution 35: 1463-1472Simion P., Philippe H., Baurain D., Jager M., Richter D.J., Di Franco A., Roure B., Satoh N., Quéinnec E., Ereskovsky A., Lapébie P., Corre E., Delsuc F., King N., Wörheide G. & Manuel M.
(2017) - A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals. - Current Biology 27 (7), 958-967Delsuc F., Philippe H., Tsagkogeorga G., Simion P., Tilak M.K. & Turon X.
(2017) - A phylogenomicframework and timescale for comparative genomics and evolutionary developmental biologyof tunicates. - bioRxiv 236448Feuda R., Dohrmann M., Pett W., Philippe H., Rota-Stabelli O. & Lartillot N.
(2017) - Improved modeling of compositional heterogeneity supports sponges as sister to all other animals. - Current Biology 27(24): 3864-3870Rodríguez A., Burgon J.D., Lyra M., Irisarri I., Baurain D., Blaustein L., Göcmen B., Künzel S., Mable B., Nolte A.W., Veith M., Steinfartz S., Elmer K.R., Philippe H. & Vences M.
(2017) - Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches. - Molecular phylogenetics and evolution 115: 16-26Irisarri I., Baurain D., Brinkmann H., Delsuc F., Sire J.-Y., Kupfer A., Petersen J., Jarek M., Meyer A. , Vences M. & Philippe H.
(2017) - Phylotranscriptomic consolidation of the jawed vertebrate timetree - Nature Ecology & Evolution 1: 1370-1378Philippe H., de Vienne D.M.D, Ranwez V., Roure B., Baurain D. & Delsuc F.
(2017) - Pitfalls in supermatrix phylogenomics. - European Journal of Taxonomy 283: 1-25Zinger L. & Philippe H.
(2016) - Coalescing molecular evolution and DNA barcoding. - Molecular Ecology 25: 1908-1910Pisani D., Pett W., Dohrmann M., Feuda R., Rota-Stabelli O., Philippe H., Lartillot N. & Wörheide G.
(2016) - Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets. - Proceedings of the National Academy of Sciences 113: E948-949Pisani D., Pett W., Dohrmann M., Feuda R., Rota-Stabelli O., Philippe H., Lartillot N. & Wörheide G.
(2015) - Genomic data do not support comb jellies as the sister group to all other animals. - Proceedings of the National Academy of Sciences 112: 15402-15407Chang E.S., Neuhof M., Rubinstein N.D., Diamant A., Philippe H., Huchon D. & Cartwright P.
(2015) - Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. - Proceedings of the National Academy of Sciences 112: 14912-14917Telford M.J., Budd G.E. & Philippe H.
(2015) - Phylogenomic insights into animal evolution. - Current Biology 25: R876–R887Gouy R., Baurain D. & Philippe H.
(2015) - Rooting the tree of life: the phylogenetic jury is still out. - Philosophical Transactions of the Royal Society B - Biological Sciences 370: 20140329Matasci N., Hung L-H., Yan Z., Carpenter E.J., Wickett N.J., Mirarab S., Nguyen N., Warnow T., Ayyampalayam S., Barker M., Burleigh J.G., Gitzendanner M.A., Wafula E., Der J.P., Roure B., Philippe H., Ruhfel B.R., Miles N.W., Graham S.W., Mathews S., Surek B., Melkonian M., Soltis D.E., Soltis P.S., Rothfels C., Pokorny L., Shaw J.A., DeGironimo L., Stevenson D.W., Villarreal J.C., Chen T., Kutchan T.M., Rolf M., Baucom R.S., Deyholos M.K., Samudrala R., Tian Z., Wu X., Sun X., Zhang Y., Wang J., Leebens-Mack J. & Wong GK-S.
(2014) - Data access for the 1,000 plants (1KP) project. - GigaScience 3: 17Wickett N.J., Mirarab S., Nguyen N., Warnow T., Carpenter E., Matasci N., Ayyampalayam S., Barker B.J.G., Gitzendanner M.A., Ruhfel B.R., Wafula E., Der J.P., Graham S.W., Mathews S., Melkonian M., Soltis D.E., Soltis P.S., Miles N.W., Rothfels C.J., Pokorny L., Shaw A.J., DeGironimo L., Stevenson D.W., Surek B., Villarreal J.C., Roure B., Philippe H., de Pamphilis C.W., Chen T., Deyholos M.K., Baucom R.S., Kutchan T.M., Augustin M.M., Wang J., Zhang Y., Tian Z., Yan Z., Wu X., Sun X., Wong GK-S. & Leebens-Mack J.
(2014) - Phylotranscriptomic analysis of the origin and early diversification of land plants. - Proceedings of the National Academy of Sciences 111: E4859-E4868