Philippe Gambette
-
LIGM, office 4B079
+33(0)1.60.95.77.34
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Publications
Topics:
Discrete mathematics and algorithmics
Computer science for biology
Computer science for natural
language and text processing
Visualization
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
).
Ideas to improve the readability of this page were taken
here
and
there
, and
there
.