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Journal articles36 documents

  • Michel Laurin, Gilles Didier, Rachel Warnock. Editorial: Timetrees: Incorporating fossils and molecules. Frontiers in Genetics, Frontiers, 2022, 13, ⟨10.3389/fgene.2022.937763⟩. ⟨hal-03709640⟩
  • Gilles Didier, Michel Laurin. Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions. PeerJ, PeerJ, 2021, 9, pp.e12577. ⟨10.7717/peerj.12577⟩. ⟨hal-03258099v3⟩
  • Gilles Didier. Probabilities of tree topologies with temporal constraints and diversification shifts. Peer Community Journal, Peer Community In/Centre Mersenne, 2021, 1, pp.e65. ⟨10.24072/pcjournal.73⟩. ⟨hal-01865425⟩
  • Gilles Didier, Michel Laurin. Exact distribution of divergence times from fossil ages and tree topologies. Systematic Biology, Oxford University Press (OUP), 2020, 69 (6), pp.1068-1087. ⟨10.1101/490003⟩. ⟨hal-01952736⟩
  • Denis Geraads, Gilles Didier, Andrew Barr, Denné Reed, Michel Laurin. The fossil record of camelids demonstrates a late divergence between Bactrian camel and dromedary. Acta Palaeontologica Polonica, Polskiej Akademii Nauk, Instytut Paleobiologii, 2020, 65 (2), pp.251-260. ⟨10.4202/app.00727.2020⟩. ⟨hal-02895911⟩
  • Gilles Didier, Olivier Chabrol, Michel Laurin. Parsimony‐based test for identifying changes in evolutionary trends for quantitative characters: implications for the origin of the amniotic egg. Cladistics, Wiley, 2019, 35 (5), pp.576-599. ⟨10.1111/cla.12371⟩. ⟨hal-01609238⟩
  • Manuela Royer-Carenzi, Gilles Didier. Testing for correlation between traits under directional evolution. Journal of Theoretical Biology, Elsevier, 2019, 482, ⟨10.1016/j.jtbi.2019.08.013⟩. ⟨hal-02057232⟩
  • Gilles Didier. Optimal pattern matching algorithms. Journal of Complexity, Elsevier, 2019, 51, pp.79 - 109. ⟨10.1016/j.jco.2018.10.003⟩. ⟨hal-01310164⟩
  • Gilles Didier, Alberto Valdeolivas, Anaïs Baudot. Identifying communities from multiplex biological networks by randomized optimization of modularity. F1000Research, Faculty of 1000, 2018, ⟨10.12688/f1000research.15486.2⟩. ⟨hal-01881798⟩
  • Emmanuel Paradis, Simon Blomberg, Ben Bolker, Joseph Brown, Julien Claude, et al.. Package ‘ape’. Analyses of phylogenetics and evolution, version, 2018, pp.2--4. ⟨hal-01800058⟩
  • Olivier Chabrol, Manuela Royer-Carenzi, Pierre Pontarotti, Gilles Didier. Detecting the molecular basis of phenotypic convergence. Methods in Ecology and Evolution, Wiley, 2018, 9 (11), pp.2170-2180. ⟨10.1111/2041-210X.13071⟩. ⟨hal-01532965⟩
  • Gilles Didier, Marine Fau, Michel Laurin. Likelihood of tree topologies with fossils and diversification rate estimation. Systematic Biology, Oxford University Press (OUP), 2017, ⟨10.1093/sysbio/syx045⟩. ⟨hal-01270368⟩
  • Gilles Didier. Time-dependent-asymmetric-linear-parsimonious ancestral state reconstruction. Bulletin of Mathematical Biology, Springer Verlag, 2017, ⟨10.1007/s11538-017-0332-z⟩. ⟨hal-01410313⟩
  • Gilles Didier, Laurent Tichit. Designing optimal-and fast-on-average pattern matching algorithms. Journal of Discrete Algorithms, Elsevier, 2017, 42, pp.45-60. ⟨hal-01310165⟩
  • Manuela Royer-Carenzi, Gilles Didier. A comparison of ancestral state reconstruction methods for quantitative characters. Journal of Theoretical Biology, Elsevier, 2016, 404, pp. 126--142. ⟨10.1016/j.jtbi.2016.05.029⟩. ⟨hal-01261430⟩
  • Gilles Didier, Christine Brun, Anaïs Baudot. Identifying communities from multiplex biological networks. . PeerJ, PeerJ, 2015, 3:e1525, ⟨10.7717/peerj.1525⟩. ⟨hal-01255282⟩
  • Manuela Royer-Carenzi, Pierre Pontarotti, Gilles Didier. Choosing the best ancestral character state reconstruction method.. Mathematical Biosciences, Elsevier, 2013, 242 (1), pp.95-109. ⟨10.1016/j.mbs.2012.12.003⟩. ⟨hal-00830797⟩
  • Gilles Didier, Eduardo L Corel, Ivan Laprevotte, Alex Grossmann, Claudine Landès-Devauchelle. Variable length local decoding and alignment-free sequence comparison. Theoretical Computer Science, Elsevier, 2012, 462, pp.1 - 11. ⟨10.1016/j.tcs.2012.08.005⟩. ⟨hal-01614104⟩
  • Gilles Didier, Elisabeth Remy. Relations between gene regulatory networks and cell dynamics in Boolean models. Discrete Applied Mathematics, Elsevier, 2012, 160 (15), pp.2147 - 2157. ⟨10.1016/j.dam.2012.05.010⟩. ⟨hal-01258494⟩
  • Gilles Didier, Manuela Royer-Carenzi, Michel Laurin. The reconstructed evolutionary process with the fossil record. Journal of Theoretical Biology, Elsevier, 2012, 315, pp.26-37. ⟨10.1016/j.jtbi.2012.08.046⟩. ⟨hal-01105197⟩
  • Gilles Didier, Elisabeth Remy, Claudine Chaouiya. Mapping multivalued onto Boolean dynamics. Journal of Theoretical Biology, Elsevier, 2011, 270 (1), pp.177. ⟨10.1016/j.jtbi.2010.09.017⟩. ⟨hal-00656334⟩
  • Gilles Didier. Parametric Maximum Parsimonious Reconstruction on Trees. Bulletin of Mathematical Biology, Springer Verlag, 2011, 73, pp.1477-1502. ⟨10.1007/s11538-010-9574-8⟩. ⟨hal-01258496⟩
  • Gilles Didier, Eduardo L Corel, Florian Pitschi, Ivan Laprevotte, Gilles Grasseau, et al.. MS4 - Multi-Scale Selector of Sequence Signatures: an alignment-free method for the classification of biological sequences. BMC Bioinformatics, BioMed Central, 2010, 11 (1), ⟨10.1186/1471-2105-11-406⟩. ⟨hal-01614124⟩
  • F. Lopez, J. Textoris, A. Bergon, G. Didier, E. Rémy, et al.. TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS ONE, Public Library of Science, 2008, 3 (12), pp.e4001. ⟨10.1371/journal.pone.0004001⟩. ⟨hal-01595819⟩
  • Gilles Didier, Laurent Debomy, Maude Pupin, Ming Zhang, Alexander Grossmann, et al.. Comparing sequences without using alignments: application to HIV/SIV subtyping. BMC Bioinformatics, BioMed Central, 2007, 8 (1), ⟨10.1186/1471-2105-8-1⟩. ⟨inria-00289069⟩
  • Gilles Didier, Carito Guziolowski. Mapping sequences by parts. Algorithms for Molecular Biology, BioMed Central, 2007, 2, pp.11. ⟨10.1186/1748-7188-2-11⟩. ⟨inria-00180004⟩
  • Gilles Didier, Thomas Schmidt, Jens Stoye, Dekel Tsur. Character sets of strings. Journal of Discrete Algorithms, Elsevier, 2007, 5 (2), pp.330 - 340. ⟨10.1016/j.jda.2006.03.021⟩. ⟨hal-01614122⟩
  • Gilles Didier, Vicente Acuña, Alejandro Maass. Coding with variable block maps. Theoretical Computer Science, Elsevier, 2006, 369 (1-3), pp.396 - 405. ⟨10.1016/j.tcs.2006.09.024⟩. ⟨hal-01614117⟩
  • Gilles Didier, Ivan Laprevotte, Maude Pupin, Alain Hénaut. Local Decoding of Sequences and Alignment-Free Comparison. Journal of Computational Biology, Mary Ann Liebert, 2006, 13 (8), pp.1465-1476. ⟨10.1089/cmb.2006.13.1465⟩. ⟨inria-00289089⟩
  • Gilles Didier, Anne-Sophie Carpentier, Alessandra Riva, Pierre Tisseur, Alain Hénaut. The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA. Computational Biology and Chemistry, Elsevier, 2004, 28 (1), pp.3 - 10. ⟨10.1016/j.compbiolchem.2003.12.001⟩. ⟨hal-01614113⟩
  • Gilles Didier, P. Brezellec, E. Remy, A. Henaut. GeneANOVA--gene expression analysis of variance. Bioinformatics, Oxford University Press (OUP), 2002, 18 (3), pp.490 - 491. ⟨10.1093/bioinformatics/18.3.490⟩. ⟨hal-01614111⟩
  • Gilles Didier, I. Laprevotte, M. Pupin, E. Coward, C. Terzian, et al.. HIV-1 and HIV-2 LTR Nucleotide Sequences: Assessment of the Alignment by N-block Presentation, "Retroviral Signatures" of Overrepeated Oligonucleotides, and a Probable Important Role of Scrambled Stepwise Duplications/Deletions in Molecular Evolution. Molecular Biology and Evolution, Oxford University Press (OUP), 2001, 18 (7), pp.1231 - 1245. ⟨10.1093/oxfordjournals.molbev.a003909⟩. ⟨hal-01614106⟩
  • Gilles Didier. Caractérisation des N-écritures et application à l'étude des suites de complexité ultimement n + cste. Theoretical Computer Science, Elsevier, 1999, 215 (1-2), pp.31 - 49. ⟨10.1016/S0304-3975(97)00122-9⟩. ⟨hal-01614129⟩
  • Gilles Didier. Combinatoire des codages de rotations. Acta Arithmetica, Instytut Matematyczny PAN, 1998, 85 (2), pp.157 - 177. ⟨10.4064/aa-85-2-157-177⟩. ⟨hal-01614102⟩
  • Gilles Didier. Codages de rotations et fractions continues. Journal of Number Theory, Elsevier, 1998, 71 (2), pp.275 - 306. ⟨10.1006/jnth.1998.2246⟩. ⟨hal-01614096⟩
  • Gilles Didier. Échanges de trois d'intervalles et suites sturmiennes. Journal de Théorie des Nombres de Bordeaux, Société Arithmétique de Bordeaux, 1997, 9 (2), pp.463-478. ⟨hal-01948117⟩

Conference papers2 documents

  • Michel Laurin, Gilles Didier. Extinction des ophiacodontidés, édaphosauridés et sphenacodontidés vers la fin du Cisuralien. Congrès annuel de l'Association Française de Paléontologie, Assocation Française de Paléontologie et Association Géologique Auboise, Aug 2021, Troyes, France. pp.22. ⟨hal-03512140⟩
  • Gilles Didier, Olivier Chabrol, Michel Laurin. Origine de l'œuf amniotique étudiée à l'aide de deux nouvelles méthodes. Annual meeting of the Association Paléontologique Française, Apr 2019, Aix-En-Provence, France. pp.38. ⟨hal-02612671⟩

Preprints, Working Papers, ...2 documents

  • Gilles Didier, Claudine Landès, Alain Hénaut, Bruno Torrésani. Four billion years: the story of an ancient protein family. 2021. ⟨hal-03264942⟩
  • Gilles Didier, Stéphane Guindon. Arbres : Combinatoire et Modèles. 2021. ⟨hal-03485566⟩