Publications

Last papers

  • Pignal, M., Laudereau, C., Gâteblé, G., & Laudereau, P.-L. (2022). Dendrobium petrophilum (Kraenzl.) Garay ex N. Hallé, a well-named species describing its unusual chasmophytic ecology. Adansonia, 44(1), 1–9. https://doi.org/10.5252/adansonia2022v44a1. https://hal.sorbonne-universite.fr/hal-03574302/ 
  • Saliba, E. M. (2022).  Reflections on Pavlinov (2021): understanding and expanding the study of the history and philosophy of nomenclature, a comprehensive state of the art. Bionomina, 31, 88–96. https://doi.org/10.11646/bionomina.31.1.5
  • Gourraud, A., Vignes-Lebbe, R., Kerner, A. & Pignal, M. (2021) Architectural Pattern: Study of orchid architecture using tools to take quick measurements of virtual specimens. Biodiversity Information Science and Standards, 5, Art. e75752. https://doi.org/10.3897/biss.5.75752
  • Saliba, E. M., Vignes-Lebbe R., Dubois A., & Ohler A. (2021). ZooNom: an online thesaurus for alleviating ambiguity in the terminology of zoological nomenclature. Zootaxa, 5071(1), 42–50. https://doi.org/10.11646/zootaxa.5071.1.2   https://hal-cnrs.archives-ouvertes.fr/hal-03451775
  • Bourgoin, T., Bailly, N., Zaragüeta-Bagils, R., & Vignes-Lebbe, R. (2021). Complete formalization of taxa with their names, contents and descriptions improves taxonomic databases and access to the taxonomic knowledge they support. Systematics and Biodiversity, 19, 738–746. https://doi.org/10.1080/14772000.2021.1915895
  • Worsaae, K., Kerbl, A., Domenico, M. D., Gonzalez, B. C., Bekkouche, N., & Martínez, A. (2021). Interstitial Annelida. Diversity, 13(2), Art. 77. https://doi.org/10.3390/d13020077
  • Saucède, T., Eléaume, M., Jossart, Q., Moreau, C., Downey, R., Bax, N., . . . Vignes-Lebbe, R. (2021). Taxonomy 2.0: Computer-aided identification tools to assist Antarctic biologists in the field and in the laboratory. Antarctic Science, 33(1), 39–51. https://doi.org/10.1017/S0954102020000462
  • Ksepka, D. T., Balanoff, A. M., Smith, N. A., Bever, G. S., Bhullar, B. S., Bourdon, E., … Smaers, J. B. (2020). Tempo and pattern of avian brain size evolution. Current Biology, 30(11), 2026–2036.e3. https://doi.org/10.1016/j.cub.2020.03.060
  • Darlu, P., Tassy, P., d’Haese, C., & Zaragüeta-Bagils, R. (2019). La reconstruction phylogénétique : concepts et méthodes. Paris : Editions Matériologiques.
  • Bourgoin, T., Vignes Lebbe, R., & Bailly, N. (2019). Visualisation of Taxonomic Knowledge: Exploring and reporting taxonomic data, training students in taxonomy. Biodiversity Information Science and Standards, 3, Art. e37730. https://doi.org/10.3897/biss.3.37730
  • Kerner, A., & Vignes Lebbe, R. (2019). Multi-context knowledge base using calculated descriptors from Xper3: The Archaeocyaths knowledge base example. Biodiversity Information Science and Standards, 3, Art. e37083. https://doi.org/10.3897/biss.3.37083
  • Dubuisson, J.-Y., Bouquin S. & Vignes-Lebbe R. (2018). Computer assisted identification: Xper and Orchids of France. L’Orchidophile, 219, 311–318.
  • Rineau V., Zaragüeta-Bagils R., & Laurin M. (2018). Impact of errors on cladistic inference: simulation-based comparison between parsimony and three-taxon analysis. Contributions to Zoology, 87(1), 25–40. https://doi.org/10.1163/18759866-08701003
  • Vignes-Lebbe, R. (2018). Natural language, formal language and the description of the living world. In T. Gaudin, D. Lacroix, M.-C. Maurel & J. C. Pomerol (Eds.), Life Sciences, Information Sciences (pp. 250–258). London: ISTE Editions. https://doi.org/10.1002/9781119452713.ch23
  • Troudet, J., Vignes-Lebbe, R., Grandcolas, P., & Legendre, F. (2018). The increasing disconnection of primary biodiversity data from specimens: How does it happen and how to handle it? Systematic biology, 67(6), 1110–1119. https://doi.org/10.1093/sysbio/syy044
  • Jouveau, S., Delaunay, M., Vignes-Lebbe, R., & Nattier, R. (2018). A multi-access identification key based on colour patterns in ladybirds (Coleoptera, Coccinellidae). ZooKeys, 758, 55–73. https://doi.org/10.3897/zookeys.758.22171
  • Troudet, J., Grandcolas, P., Blin, A., Vignes-Lebbe, R., & Legendre, F. (2017). Taxonomic bias in biodiversity data and societal preferences. Scientific Reports, 7(1), Art. 9132. https://doi.org/10.1038/s41598-017-09084-6
  • Joly, P., & Vignes-Lebbe, R. (2017). Les collections muséologiques. In M. Bouzeghoub & R. Mosseri (Eds.), Les Big Data à découvert (pp. 50–51). Paris : CNRS.
  • Vignes-Lebbe, R. (2017). Langage naturel, langage formel et description du vivant. In T. Gaudin, D. Lacroix, M.-C. Maurel & J. C. Pomerol (Eds.), Sciences de la Vie et Sciences de l’Information. Londres : ISTE Editions.
  • Pellen, F., Bouquin, S., Mougenot, I., & Vignes-Lebbe, R. (2018). Building an OWL ontology with Xper3. Biodiversity Information Science and Standards, 2, Art. e25614. https://doi.org/10.3897/biss.2.25614
  • Vignes-Lebbe, R., Bouquin, S., Kerner, A., & Bourdon, E. (2017). Desktop or remote knowledge base management systems for taxonomic data and identification keys: Xper2 and Xper3. Biodiversity Information Science and Standards, 1, Art. e19911. https://doi.org/10.3897/tdwgproceedings.1.19911
  • Pinel, A., Bouquin, S., Bourdon, E., Kerner, A., & Vignes-Lebbe, R. (2017). Three years of Xper3 assessment: towards sharing semantic taxonomic content of identification keys. Biodiversity Information Science and Standards, 1, Art. e20382. https://doi.org/10.3897/tdwgproceedings.1.20382
  • Diep Thi, M.-H., Gurgand, J., Vignes-Lebbe, R., Nguyen, H.-P., Nguyen, B.-L., Haevermans, T. (2016). Bambous d’Indochine : descripteurs morphologiques pour l’identification. Science and Technology Committee. Vietnam National University of Ho Chi Minh City.
  • Vignes-Lebbe, R., Chesselet, P., Diep Thi, M.-H. (2016). Xper3: New tools for collaborating, training and transmitting knowledge on botanical phenotypes. In N. R. Rakotoarisoa, S. Blackmore & B. Riera (eds.), Botanists of the twenty-first century: roles, challenges and opportunities (228–239). Paris: UNESCO.
  • Lecointre, G., De Wever, P., Ekström, S., Gargaud, M., Gounelle, M., Klein, E., Longo, G., Martin, H., Pavé, A., Walliser, B., Zanda,B., & Zaragüeta-Bagils, R. (2015). Catégories et classification face au changement. In M. Gargaud, & G.  Lecointre (dirs.), L’évolution, de l’univers aux sociétés : Objets et concepts (pp. 421–454). Paris : Éditions Matériologiques.
  • Cecca, F., & Zaragüeta Bagils, R. (2015). Paléobiogéographie. Collection Géosphères dirigée par P. de Wever. Les Ulis : EDP Sciences. https://doi.org/10.1051/978-2-7598-1895-2
  • Zaragüeta-Bagils, R. (2015). Les deux biogéographies : Biogéographie historique vs histoire géographique. Biosystema, 30, 133–154.
  • Rineau, V., Grand, A., Zaragüeta-Bagils, R., Laurin, M. (2015). Experimental systematics: sensitivity of cladistic methods to polarization and character ordering schemes. Contributions to Zoology, 84 (2) 129–148. https://doi.org/10.1163/18759866-08402003
  • Cavoto, P., Cardoso, V., Vignes-Lebbe, R., & Santanchè, A. (2015). FishGraph: A Network-Driven Data Analysis. 2015 IEEE 11th International Conference on e-Science, 177–186. https://doi.org/10.1109/eScience.2015.61
  • Ung, V., Zaragüeta-Bagils, R., & Williams, D. (2014). Comparative biogeography of Southeast Asia and the West Pacific region. Biological Journal of the Linnean Society, 117(2), 372–385. https://doi.org/10.1111/bij.12670
  • Grand, A., Vignes-Lebbe, R., & Santanchè, A. (2014). from phenotypes to trees of life: A metamodel-driven approach for the integration of taxonomy models. 2014 IEEE 10th International Conference on e-Science, 1, 65–72. https://doi.org/10.1109/eScience.2014.48
  • Grand, A., Zaragüeta-Bagils, R., Vélez, L. M., & Ung, V. (2014). A cladistic re-analysis of the Gadiformes (Teleostei, Paracanthopterygii) using three-item analysis. Zootaxa, 3889(4), 525–552. https://doi.org/10.11646/zootaxa.3889.4.3
  • Thacker, R. W., Díaz, M. C., Kerner, A., Vignes-Lebbe, R., Segerdell, E., Haendel, M. A., & Mungall, C. J. (2014). The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. Journal of Biomedical Semantics, 5(1), Art. 39. https://doi.org/10.1186/2041-1480-5-39
  • Corvez, A., & Grand, A. (2014). Enabling comparisons of characters using an Xper2 based knowledge-base of fern morphology. Phytotaxa, 183(3), 145–158. https://doi.org/10.11646/phytotaxa.183.3.2
  • Chrétiennot-Dinet, M. J., Desreumaux, N., & Vignes-Lebbe, R. (2014). An interactive key to the Chrysochromulina species (Haptophyta) described in the literature. PhytoKeys, 34, 47–60. https://doi.org/10.3897/phytokeys.34.6242
  • GBIF France (L’équipe GBIF France 2013 comprend/GBIF France 2013 was constituted by Anne-Sophie Archambeau, Eric Chenin, Marie-Elise Lecoq, Pere Roca Ristol, et Régine Vignes Lebbe). (2013). Le GBIF : Ouvrir l’accès aux données primaires sur la biodiversité. Networks and Communication Studies, 27(1-2), 154–164. https://doi.org/10.4000/netcom.1390
  • Burguière, T., Causse, F., Ung, V., & Vignes-Lebbe, R. (2013). IKey+: a new single-access key generation web service. Systematic biology, 62(1), 157–161. https://doi.org/10.1093/sysbio%2Fsys069
  • Zaragüeta-Bagils, R., Ung, V., Grand, A., Vignes-Lebbe, R., Cao, N., & Ducasse, J. (2012). LisBeth : New cladistics for phylogenetics and biogeography. Comptes Rendus Palevol, 11(8), 563–566. https://doi.org/10.1016/j.crpv.2012.07.002
  • Mathieu, B., Cetre-Sossah, C., Garros, C., Chavernac, D., Balenghien, T., Setier-Rio, M.L., Vignes-Lebbe, R., Ung, V., Candolfi, E., Delecolle, J. C. (2012). Development and validation of IIKC: an interactive identification key for Culicoides (Diptera: Ceratopogonidae) females from the Western Palaearctic region. Parasites and Vectors, 5, Art. 137. http://dx.doi.org/10.1186/1756-3305-5-137
  • Kerner, A. (2012). Archaeocyatha, a computer-aided identification of genera. Geologica Belgica, 15(4), 209–214.
  • Kerner, A., Vignes-Lebbe, R., & Debrenne, F. (2011). Computer-aided identification of the Archaeocyatha genera now available online. Carnet de Géologie, 11(Letters 02), 99–102. https://doi.org/10.4267/2042%2F42329
  • Kerner, A., Debrenne, F., & Vignes-Lebbe, R. (2011). Cambrian archaeocyathan metazoans: revision of morphological characters and standardization of genus descriptions to establish an online identification tool. Zookeys, 150, 381–395. https://doi.org/10.3897/zookeys.150.1566
  • Nimis, P. L., & Vignes-Lebbe R. (eds.). (2010). Tools for identifying biodiversity: Progress and problems. Trieste: Edizioni Universitàdi Trieste.
  • Ung, V., Dubus, G., Zaragüeta-Bagils, R., & Vignes-Lebbe, R. (2010). Xper²: introducing e-Taxonomy. Bioinformatics, 26(5), 703–704. https://doi.org/10.1093/bioinformatics/btp715
  • Diep, M. H., Vignes-Lebbe, R., Nguyen H. P. et Nguyen Thi B. L. (2010).  Indochinese bamboos: biodiversity informatics to assist the identification of vernacular taxa. In P. L. Nimis & R. Vignes-Lebbe (eds.), Tools for identifying biodiversity: Progress and problems (pp. 213-216). Trieste: Edizioni Universitàdi Trieste.
  • Zaragüeta-Bagils, R., Bourdon, E., Ung, V., Vignes-Lebbe, R., & Malécot, V. (2009). On the International Code of Area Nomenclature. Journal of Biogeography, 38(8), 1617–1619. https://doi.org/10.1111/j.1365-2699.2009.02106.x
  • Khalloufi, B., Zaragüeta Bagils, R., & Lelièvre, H. (2010). Rhombichthys intoccabilis, gen. et sp. nov. (Ellimmichthyiformes, Clupeomorpha, Teleostei) from the Cenomanian (Upper Cretaceous) of Ein Yabrud, Middle East. Anatomical description and phylogenetic implications. Journal of Vertebrate Paleontology, 30(1), 57–67. https://doi.org/10.1080/02724630903409089
  • Cao, N., Bourdon, E., El Azawi, M., & Zaragüeta-Bagils, R. (2009). Three-item analysis and parsimony, intersection tree and strict consensus: a biogeographical example. Bulletin de la Société Géologique de France, 180(1), 13–15. https://doi.org/10.2113/gssgfbull.180.1.13
  • Morille, C. H., Dequaire, A., Hortault, G., Péquignot, A., & Aragon, S. (2008). Un conservatoire de faune : La collection zoologique de l’Université Pierre et Marie Curie (Paris VI). In P.-A. Girard (dir.), Actes des 2ème Journées Cuénot, Les collections scientifiques des universités (pp. 81-97). Nancy : Presses universitaires de Nancy.
  • Cao N., Le Péchon T., & Zaragüeta-Bagils R. (2008). Does minimizing homoplasy really maximize homology? MaHo: A method for evaluating homology among most parsimonious trees. Comptes Rendus Palevol, 7(1), 17–26. https://doi.org/10.1016/j.crpv.2007.12.008
  • Lelièvre, H., Zaragüeta-Bagils, R., & Rouget, I. (2008). Temporal information, fossil record and phylogeny. Comptes Rendus Palevol, 7(1), 27–36. https://doi.org/10.1016/j.crpv.2007.12.007
  • Zaragüeta-Bagils, R., & Bourdon, E., (2007). Three-item analysis: Hierarchical representation and treatment of missing and inapplicable data. Comptes Rendus Palevol, 6(6-7), 527–534. https://doi.org/10.1016/j.crpv.2007.09.013
  • Cao, N., Zaragüeta-Bagils, R., & Vignes-Lebbe, R. (2007). Hierarchical representation of the hypotheses of homology. Geodiversitas, 29(1), 5–15.
  • Jacques, F. M. B., Gallut, C., Vignes-Lebbe, R., & Zaragüeta-Bagils, R. (2007). Resolving phylogenetic reconstruction in Menispermaceae (Ranunculales) using fossils and a novel statistical test. Taxon, 56(2), 379–392. https://doi.org/10.1002/tax.562010
  • Zaragüeta-Bagils, R., Bourdon, E., Rouget, I & Lelièvre, H. (2006). Arbres phylogénétiques et chronologie. Géochronique, 98, 44–45.
  • Zaragüeta-Bagils, R., Lelièvre, H., & Tassy, P. (2004). Temporal paralogy, cladograms, and the quality of the fossil record. Geodiversitas, 26(3), 381–389.
  • Vignes-Lebbe, R. (2000). Caractère pour le biologiste, caractère pour l’informaticien. In V. Barriel & T. Bourgoin (eds). Biosystema 18 : Caractères (61-70). Paris : Société Française de Systématique.
  • Vignes-Lebbe, R., Rechenmann, F., Gautier, C., & Tillier, S. (2000). Informatique et Systématique. In S. Tillier (ed.), Systématique : ordonner la diversité du vivant (pp. 132–143). Cachan : Lavoisier, Tec & Doc.
  • Lebbe, J. (1991). Représentation des concepts en biologie et médecine. Introduction à l’analyse des connaissances et à l’identification assistée par ordinateur [Thèse de doctorat Paris : Université Pierre et Marie Curie]. 281 pp.
  • Lebbe, J., & Vignes, R. (1991). Génération de graphes d’identification à partir de descriptions de concepts. In Y. Kodratoff et E. Diday (eds.), Induction Symbolique et Numérique (pp. 193–239). Toulouse : Cépaduès.
  • Vignes, R. (1991). Caractérisation automatique de groupes biologiques [Thèse de doctorat ; Paris : Université Pierre et Marie Curie]. 268 pp.