Publications

According to ACM, ArnetMiner, CSB, DBLP, Google Scholar, HAL, ORCID, Publons, SemanticScholar.

Some presentations of the results of the following publications are available on this page.

International journal articles

• [J19] 2022 : Simon Gabay, Philippe Gambette Rachel Bawden, & Benoît Sagot,
  Ancien ou moderne ? Pistes computationnelles pour l’analyse graphématique des textes écrits au XVII^e siècle (Old or Modern? Towards a Computational Graphematic Analysis of 17^th Century French Texts),
  Linx, revue des linguistes de l'Université Paris Ouest Nanterre La Défense, 85, p. 1-20 [DOI].
• [J18] 2022: Olga Seminck, Philippe Gambette, Dominique Legallois & Thierry Poibeau,
  The Evolution of the Idiolect over the Lifetime: A Quantitative and Qualitative Study of French 19th Century Literature,
  Journal of Cultural Analytics, 7(3), p. 1-26 [DOI, scripts and data].
• [J17] 2021: Olga Seminck, Philippe Gambette, Dominique Legallois & Thierry Poibeau,
  The Corpus for Idiolectal Research (CIDRE),
  JOHD (Journal of Open Humanities Data), 7, p. 15 [DOI, data].
• [J16] 2020: Mathilde Bouvel, Philippe Gambette & Marefatollah Mansouri,
  Counting Phylogenetic Networks of Level 1 and 2,
  JOMB (Journal of Mathematical Biology) 81, p. 1357-1395 [DOI].
• [J15] 2018: Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette & Louxin Zhang,
  Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks,
  DAM (Discrete Applied Mathematics) 246, p. 62-79 [DOI].
• [J14] 2017: Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi & Celine Scornavacca,
  Rearrangement Moves on Rooted Phylogenetic Networks,
  PLOS Comp Bio (PLOS Computational Biology), 13(8):e1005611, p. 1-21 [DOI].
• [J13] 2017: Philippe Gambette, Katharina Huber & Guillaume Scholz,
  Uprooted phylogenetic networks,
  BMB (Bulletin of Mathematical Biology), 79(9):2022-2048 [DOI].
• [J12] 2017: Annie Glatigny, Philippe Gambette, Alexa Bourand-Plantefol, Geneviève Dujardin, & Marie-Hélène Mucchielli-Giorgi,
  Development of an in silico method for the identification of subcomplexes involved in the biogenesis of multiprotein complexes in Saccharomyces cerevisiae,
  BMC Syst Biol (BMC Systems Biology) 11:67, p. 1-12 [DOI].
• [J11] 2017: Philippe Gambette, Katharina Huber & Steven Kelk,
  On the Challenge of Reconstructing Level-1 Phylogenetic Networks from Triplets and Clusters,
  JOMB (Journal of Mathematical Biology) 74(7), p. 1729–1751. [DOI].
• [J10] 2016: Nadège Lechevrel & Philippe Gambette,
  Une approche textométrique pour étudier la transmission des savoirs biologiques au XIX^e siècle (A Textometrical Approach to Study the Transmission of Biological Knowledge in the XIX^th Century),
  NPSS (Nouvelles perspectives en sciences sociales) 12(1), p. 221-253 [DOI].
• [J9] 2016: Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi & Celine Scornavacca,
  Do Branch Lengths Help to Locate a Tree in a Phylogenetic Network?,
  BMB (Bulletin of Mathematical Biology) 78(9), p. 1773-1795 [DOI].
• [J8] 2014: Christophe Crespelle & Philippe Gambette,
  (Nearly-)Tight Bounds on the Linearity and Contiguity of Cographs,
  TCS (Theoretical Computer Science) 522, p. 1-12 [DOI].
• [J7] 2013: Lionel Spinelli, Philippe Gambette, Charles E. Chapple, Benoît Robisson, Anaïs Baudot, Henri Garreta, Laurent Tichit, Alain Guénoche & Christine Brun,
  Clust&See: a Cytoscape plugin for the identification, visualization and manipulation of network clusters,
  BioSystems 113(2), p. 91-95 [DOI].
• [J6] 2012: Philippe Gambette & Katharina Huber,
  On Encodings of Phylogenetic Networks of Bounded Level,
  JOMB (Journal of Mathematical Biology) 61(1), p. 157-180 [DOI].
• [J5] 2012: Philippe Gambette, Vincent Berry & Christophe Paul,
  Quartets and Unrooted Phylogenetic Networks,
  JBCB (Journal of Bioinformatics and Computational Biology) 10(4), 1250004 (23 p.) [DOI].
• [J4] 2011: Philippe Gambette & Alain Guénoche,
  Bootstrap Clustering for Graph Partitioning,
  RAIRO-Operations Research 45(4), p. 339-352 [DOI].
• [J3] 2010: Christophe Crespelle & Philippe Gambette,
  Unrestricted and Complete Breadth-First Search of Trapezoid Graphs in O(n) Time,
  IPL (Information Processing Letters) 110, p. 497-502 [DOI].
• [J2] 2009: Daniel Huson, Regula Rupp, Vincent Berry, Philippe Gambette & Christophe Paul,
  Computing Galled Networks from Real Data,
  Bioinformatics 25(12) ISMB/ECCB'09 (Proceedings of the 17^th Annual Conference on Intelligent Systems for Molecular Biology & 8^th European Conference on Computational Biology), p. i85-i93 [DOI].
• [J1] 2008: Philippe Gambette & Daniel H. Huson,
  Improved Layout of Phylogenetic Networks,
  TCBB (IEEE/ACM Transactions on Computational Biology and Bioinformatics) 5(3), p. 472-479 [DOI]. (⇒ Erdős nb 3)

Peer-reviewed international conferences with proceedings

• [C18] 2023 : Pierre Bourhis, Aaron Boussidan & Philippe Gambette,
  On Distances between Words with Parameters
  CPM 2023 (Proceedings of the 33^rd Annual Symposium on Combinatorial Pattern Matching), Leibniz International Proceedings in Informatics (LIPIcs), to appear [DOI to be added, supplementary material].
• [C17] 2022: Chuanming Dong, Philippe Gambette & Catherine Dominguès,
  Classifying triggers of industrial pollution events
  JADT'22 (Proceedings of the 16^th International Conference on statistical analysis of textual data), Statistical Analysis of Textual Data, p. 354-360. [URL, script and data].
• [C16] 2022: Simon Gabay, Pedro Ortiz Suarez, Alexandre Bartz, Alix Chagué, Rachel Bawden, Philippe Gambette & Benoît Sagot,
  From FreEM to D'AlemBERT: a Large Corpus and a Language Model for Early Modern French,
  LREC 2022 (Proceedings of the 13^th Language Resources and Evaluation Conference), p. 3367-3374, [URL, video, corpus FreEM max].
• [C15] 2022: Rachel Bawden, Jonathan Poinhos, Eleni Kogkitsidou, Philippe Gambette, Benoît Sagot & Simon Gabay,
  Automatic Normalisation of Early Modern French,
  LREC 2022 (Proceedings of the 13^th Language Resources and Evaluation Conference), p. 3354-3366, [URL, video, corpus FreEM norm, demo of ABA].
• [C14] 2022: Simon Gabay, Rachel Bawden, Jonathan Poinhos, Philippe Gambette, Eleni Kogkitsidou & Benoît Sagot,
  Le changement linguistique au XVII^e siècle : nouvelles approches scriptométriques,
  CMLF 2022 (Actes du 8^e Congrès Mondial de Linguistique Française), SHS Web Conferences, volume 138, p. 02006.1-15, [DOI].
• [C13] 2022: Laurent Bulteau, Philippe Gambette & Olga Seminck,
  Reordering a tree according to an order on its leaves,
  CPM 2022 (Proceedings of the 33^rd Annual Symposium on Combinatorial Pattern Matching), Leibniz International Proceedings in Informatics (LIPIcs), volume 223, p. 24.1-15, [DOI, supplementary material].
• [C12] 2021: Chuanming Dong, Philippe Gambette & Catherine Dominguès,
  Extracting event-related information from a corpus regarding soil industrial pollution,
  KDIR 2021 (Proceedings of the 13^th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management), volume 1, p. 217-224 [DOI, supplementary material].
• [C11] 2020: Eleni Kogkitsidou & Philippe Gambette,
  Normalisation of 16^th and 17^th century texts in French and geographical named entity recognition,
  SIGSPATIAL GeoHumanities 2020 (Proceedings of the 4^th ACM SIGSPATIAL International Workshop on Geospatial Humanities), p. 28-34 [DOI, video].
• [C10] 2018: Christine Barats, Anne Dister, Philippe Gambette, Jean-Marc Leblanc & Marie Peres,
  Appeler à signer une pétition en ligne : caractéristiques linguistiques des appels,
  JADT'18 (Proceedings of the 14^th International Conference on statistical analysis of textual data), Statistical Analysis of Textual Data, p. 68-75 [URL].
• [C9] 2016: Christine Barats, Anne Dister, Philippe Gambette, Jean-Marc Leblanc & Marie Peres-Leblanc,
  Analyser des pétitions en ligne : potentialités et limites d'un dispositif d'étude pluridisciplinaire (Analyzing online petitions: potentialities and limitations of a multidisciplinary study device),
  JADT'16 (Proceedings of the 13^th International Conference on statistical analysis of textual data), Statistical Analysis of Textual Data, p. 772-781 (supplementary material) [URL].
• [C8] 2016: Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette & Louxin Zhang,
  Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time,
  IWOCA'15 (Proceedings of the 26^th International Workshop on Combinatorial Algorithms), LNCS 9538, p. 197-208 [DOI].
• [C7] 2015: Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette & Louxin Zhang,
  Locating a Tree in A Phylogenetic Network in Quadratic Time,
  RECOMB'15 (Proceedings of the 19^th Annual International Conference on Research in Computational Molecular Biology), LNCS (LNBI) 9029, p. 96-107 [DOI].
• [C6] 2013: Christophe Crespelle & Philippe Gambette,
  Linear-time Constant-ratio Approximation Algorithm and Tight Bounds for the Contiguity of Cographs,
  WALCOM'13 (Proceedings of the 7^th International Workshop on Algorithms and Computation), LNCS 7748, p. 126-136 [DOI].
• [C5] 2010: Delphine Amstutz & Philippe Gambette,
  Utilisation de la visualisation en nuage arboré pour l'analyse littéraire (Using the tree cloud visualization for literature analysis),
  JADT'10 (Proceedings of the 10^th International Conference on statistical analysis of textual data), Statistical Analysis of Textual Data, p. 227-238 (supplementary material) [URL].
• [C2] 2010: Philippe Gambette & Jean Véronis,
  Visualising a Text with a Tree Cloud,
  IFCS'09 (Proceedings of the International Federation of Classification Societies 2009 Conference), Studies in Classification, Data Analysis, and Knowledge Organization 40, p. 561-570 (supplementary material) [DOI].
• [C4] 2009: Christophe Crespelle & Philippe Gambette,
  Efficient Neighbourhood Encoding for Interval Graphs and Permutation Graphs and O(n) Breadth-First Search,
  IWOCA'09 (Proceedings of the 20^th International Workshop on Combinatorial Algorithms), LNCS 5874, p. 146-157 [DOI].
• [C3] 2009: Philippe Gambette, Vincent Berry & Christophe Paul,
  The Structure of Level-k Phylogenetic Networks,
  CPM'09 (Proceedings of the 20^th Annual Symposium on Combinatorial Pattern Matching), LNCS 5577, p. 289-300 [DOI].
• [C1] 2007: Philippe Gambette & Stéphane Vialette,
  On Restrictions of Balanced 2-Interval Graphs,
  WG'07 (Proceedings of the 33^rd International Workshop on Graph-Theoretic Concepts in Computer Science), LNCS 4769, p. 55-65 [DOI].

Peer-reviewed international conferences without proceedings

• [IC1] 2021: Philippe Gambette, Olga Seminck, Dominique Legallois & Thierry Poibeau,
  Evaluating Hierarchical Clustering Methods for Corpora with Chronological Order,
  EADH 2021 (2^nd International Conference of the European Association for Digital Humanities) [video].

Posters

• [P5] 2021: Olga Seminck, Philippe Gambette, Dominique Legallois & Thierry Poibeau,
  The Corpus for Idiolectal Research (CIDRE),
  EADH 2021 poster session (2^nd International Conference of the European Association for Digital Humanities)
• [P3] 2012: Annie Glatigny, Viet-Dung Tran, Philippe Gambette & Marie-Hélène Mucchielli
  An in silico approach to model the assembly pathway of protein respiratory complexes in Saccharomyces cerevisiae,
  JOBIM 2012 poster session.

Dissertations

• [D4] 2010: Méthodes combinatoires de reconstruction de réseaux phylogénétiques (in French, Combinatorial Methods for Phylogenetic Network Reconstruction, summary in English)
  PhD Thesis supervised by Vincent Berry & Christophe Paul at LIRMM. (⇒ grand-grand-grand-grand-grand-grand-grand-grand-grand-son of Lagrange) [a 4 page summary in English].
• [D3] 2006: Les graphes 2-intervallaires (in French, 2-Interval Graphs)
  Master Thesis supervised by Michel Habib at LIAFA.
• [D2] 2005: La représentation des réseaux phylogénétiques (in French, Representation of Phylogenetic Networks)
  Maîtrise Thesis supervised by Daniel Huson at ZBIT, Tübingen University.
• [D1] 2004: Quelques propriétés topologiques des arbres de duplication (in French, Some Topological Properties of Duplication Trees)
  Bachelor Thesis supervised by Olivier Gascuel & Denis Bertrand at LIRMM.

Technical Reports

• 2022: Variations of industrial organisation names in aligned databases related to soil pollution in France (9p, with Chuanming Dong & Catherine Dominguès)
• 2019: Cutting an alignment with Ockham's razor (23p, with Mark Jones, Leo van Iersel, Remie Janssen, Steven Kelk, Fabio Pardi & Celine Scornavacca)
• 2018: The BiodivERsA database: a mapping of research on biodiversity and ecosystem services in Europe over 2005-2015, BiodivERsA report (60p, with Lise Goudeseune, Hilde Eggermont, André Heughebaert & Xavier Le Roux).
• 2016: Who is Who in Phylogenetic Networks: Articles, Authors and Programs (5p, with Tushar Agarwal & David Morrison).
• 2015: Tree Containment in Linear Time for Nested Networks (11p, with Andreas DM Gunawan, Anthony Labarre, Stéphane Vialette & Louxin Zhang).
• 2014: Temporal and geographical trends in the type of biodiversity research funded on a competitive basis in European countries, BiodivERsA report (27p, with Hilde Eggermont & Xavier Le Roux).
• 2009: A Note on Minimum Flip Consensus and Maximum Compatible Subset (2p, complement to [C4]).
• 2008: An Obstruction Approach to Reconstruct Phylogenies and Level-k Networks from Triplets (22p, with Vincent Berry and Christophe Paul).
• 2007: Graphes 2-intervallaires, variantes et restrictions (67p, in French, 2-Interval Graphs, Variants and Restrictions, with Michel Habib & Stéphane Vialette).