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Number of documents

35

Publications


Journal articles33 documents

  • Gilles Didier, Michel Laurin. Exact distribution of divergence times from fossil ages and tree topologies. Systematic Biology, Oxford University Press (OUP), 2020, ⟨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, ⟨10.4202/app.00727.2020⟩. ⟨hal-02895911⟩
  • Gilles Didier. Optimal pattern matching algorithms. Journal of Complexity, Elsevier, 2019, 51, pp.79 - 109. ⟨10.1016/j.jco.2018.10.003⟩. ⟨hal-01310164⟩
  • 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, 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⟩
  • 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⟩
  • 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⟩
  • Gilles Didier, Olivier Chabrol, Manuela Royer-Carenzi, Pierre Pontarotti. 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, Laurent Tichit. Designing optimal-and fast-on-average pattern matching algorithms. Journal of Discrete Algorithms, Elsevier, 2017, 42, pp.45-60. ⟨hal-01310165⟩
  • 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, 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⟩
  • 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. ⟨10.1101/037812⟩. ⟨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, 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, Eduardo 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, 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. 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, 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, Eduardo 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, 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, 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, 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, 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, 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 papers1 document

  • Gilles Didier, Olivier Chabrol, Michel Laurin. Origine de l'oeuf amniotique étudiée à l'aide de deux nouvelles méthodes. Annual meeting of the Association Paléontologique Française, Apr 2019, Aix-En-Provence, France. p. 38. ⟨hal-02612671⟩

Preprints, Working Papers, ...1 document

  • Gilles Didier. Probabilities of tree topologies with temporal constraints and diversification shifts. 2019. ⟨hal-01865425⟩