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Vincent Ranwez

Full professor at Institut Agro Montpellier. Team Ge2pop, UMR AGAP Institut.
93%
Open access
70
Documents
Current affiliations
Web site
  • https://sites.google.com/site/ranwez/

Publications

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Des séquences moléculaires à l’arbre de la vie : résultats théoriques, algorithmes et outils pour la phylogénomique

Vincent Ranwez
Sciences du Vivant [q-bio]. Université Montpellier 2 (Sciences et Techniques), 2010
Habilitation à diriger des recherches tel-02824963v1
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Méthodes efficaces pour reconstruire de grandes phylogénies suivant le principe du maximum de vraisemblance

Vincent Ranwez
Bio-informatique [q-bio.QM]. Université Montpellier II - Sciences et Techniques du Languedoc, 2002. Français. ⟨NNT : ⟩
Theses tel-00843175v1
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Aligning Protein-Coding Nucleotide Sequences with MACSE

Vincent Ranwez , Nathalie Chantret , Frédéric Delsuc
Methods in Molecular Biology vol. 2231: Multiple Sequence Alignment., 2231, pp.51-70, 2021, ⟨10.1007/978-1-0716-1036-7_4⟩
Book sections hal-03099847v1
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Accurate alignment of (meta)barcoding data sets using MACSE

Frédéric Delsuc , Vincent Ranwez
Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas. Phylogenetics in the Genomic Era, 2.3, No commercial publisher | Authors open access book, pp.2.3:1--2.3:31, 2020
Book sections hal-02541199v1
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Strengths and Limits of Multiple Sequence Alignment and Filtering Methods

Vincent Ranwez , Nathalie N. Chantret
Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas. Phylogenetics in the Genomic Era, No commercial publisher | Authors open access book, pp.2.2:1-2.2:36, 2020
Book sections hal-02535389v2
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How ontology based information retrieval systems may benefit from lexical text analysis

Sylvie Ranwez , Benjamin Duthil , Mohameth-François Sy , Jacky Montmain , Patrick Augereau
Oltramari, Alessandro; Vossen, Piek; Qin, Lu; Hovy, Eduard. New Trends of Research in Ontologies and Lexical Resources, 15, Springer, pp.209-230, 2013, Theory and Applications of Natural Language Processing, 978-3-642-31781-1
Book sections hal-00797143v1

Phylogénie moléculaire

Samuel Blanquart , Alexis Criscuolo , Christophe J Douady , Emmanuel Douzery , Nicolas Lartillot
Thierry Lefèvre; Michel Raymond; Frédéric Thomas. Biologie évolutive, De Boeck, 2010, 9782804101619
Book sections hal-04001134v1
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An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers

Jean-Philippe Doyon , Celine Scornavacca , Yu Gorbunov , Gergely J. Szöllősi , Vincent Ranwez
Eric Tannier. Comparative Genomics. RECOMB-CG 2010, LNCS (6398), Springer Berlin Heidelberg, pp.93-108, 2010, 978-3-642-16181-0. ⟨10.1007/978-3-642-16181-0_9⟩
Book sections lirmm-00818889v1
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OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics

Rémi Allio , Frédéric Delsuc , Khalid Belkhir , Emmanuel J P Douzery , Vincent Ranwez
Nucleic Acids Research, 2024, 52 (D1), pp.D529-D535. ⟨10.1093/nar/gkad834⟩
Journal articles hal-04266876v2
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Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift

Laurène Gay , Julien Dhinaut , Margaux Jullien , Renaud Vitalis , Miguel Navascués
Ecology and Evolution, 2022, 12 (1), ⟨10.1002/ece3.8555⟩
Journal articles hal-02922123v1
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Post-hoc recommendation explanations through an efficient exploitation of the DBpedia category hierarchy

Yu Du , Sylvie Ranwez , Nicolas Sutton-Charani , Vincent Ranwez
Knowledge-Based Systems, 2022, 245, ⟨10.1016/j.knosys.2022.108560⟩
Journal articles hal-03623354v1
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Is diversity optimization always suitable? Toward a better understanding of diversity within recommendation approaches

Yu Du , Sylvie Ranwez , Nicolas Sutton-Charani , Vincent Ranwez
Information Processing and Management, 2021, 58 (6), ⟨10.1016/j.ipm.2021.102721⟩
Journal articles hal-03335198v1
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EBCR: Empirical Bayes concordance ratio method to improve similarity measurement in memory-based collaborative filtering

Yu Du , Nicolas Sutton-Charani , Sylvie Ranwez , Vincent Ranwez
PLoS ONE, 2021, pp.1-19. ⟨10.1371/journal.pone.0255929⟩
Journal articles hal-03319825v1
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A new comprehensive annotation of leucine‐rich repeat‐containing receptors in rice

Céline Gottin , Anne Dievart , Marilyne Summo , Gaëtan Droc , Christophe Périn
Plant Journal, 2021, ⟨10.1111/tpj.15456⟩
Journal articles hal-03346283v1

Origin and Diversity of Plant Receptor-Like Kinases

Anne Diévart , Céline Gottin , Christophe Perin , Vincent Ranwez , Nathalie Chantret
Annual Review of Plant Biology, 2020, 71 (1), pp.131-156. ⟨10.1146/annurev-arplant-073019-025927⟩
Journal articles hal-02766945v1
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OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes

Celine Scornavacca , Khalid Belkhir , Jimmy Lopez , Rémy Dernat , Frédéric Delsuc
Molecular Biology and Evolution, 2019, 36 (4), pp.861-862. ⟨10.1093/molbev/msz015⟩
Journal articles hal-02139915v1
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Enseignement et recherche - Au cœur de #DigitAg, l'Institut Convergences Agriculture Numérique, une Graduate School innovante

Vincent Ranwez , Nina Lachia , Tewfik Sari
Sciences Eaux & Territoires, 2019, 29, pp.1-4. ⟨10.14758/SET-REVUE.2019.3.13⟩
Journal articles hal-03999235v1
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Pervasive hybridizations in the history of wheat relatives

Sylvain Glémin , Celine Scornavacca , Jacques Dainat , Concetta Burgarella , Veronique Viader
Science Advances , 2019, 5 (5), pp.eaav9188. ⟨10.1126/sciadv.aav9188⟩
Journal articles hal-02144799v1
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MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

Vincent Ranwez , Emmanuel J.P. Douzery , Cédric Cambon , Nathalie N. Chantret , Frédéric Delsuc
Molecular Biology and Evolution, 2018, 35 (10), pp.2582 - 2584. ⟨10.1093/molbev/msy159⟩
Journal articles hal-01925698v1
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Efficient algorithms for Longest Common Subsequence of two bucket orders to speed up pairwise genetic map comparison

Lisa de Mattéo , Yan Holtz , Vincent Ranwez , Sèverine Bérard
PLoS ONE, 2018, 13 (12), pp.e0208838. ⟨10.1371/journal.pone.0208838⟩
Journal articles hal-02134202v1

Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus

Yan Holtz , Michel Bonnefoy , Veronique Viader , Morgane Ardisson , Nicolas O. Rode
TAG Theoretical and Applied Genetics, 2017, 130 (7), pp.1491-1505. ⟨10.1007/s00122-017-2904-6⟩
Journal articles hal-01605947v1
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Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations

Yao-Ban Chan , Vincent Ranwez , Celine Scornavacca
Journal of Theoretical Biology, 2017, 432, pp.1-13. ⟨10.1016/j.jtbi.2017.08.008⟩
Journal articles hal-02154862v1
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Pitfalls in supermatrix phylogenomics

Herve Philippe , Damien M. de Vienne , Vincent Ranwez , Béatrice Roure , Denis Baurain
European Journal of Taxonomy, 2017, 283, pp.1-25. ⟨10.5852/ejt.2017.283⟩
Journal articles hal-01606389v1

The genetic map comparator: a user-friendly application to display and compare genetic maps

Yan Holtz , Jacques David , Vincent Ranwez
Bioinformatics, 2017, 33 (9), pp.1387-1388. ⟨10.1093/bioinformatics/btw816⟩
Journal articles hal-01604150v1
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Domestication reduces alternative splicing expression variations in sorghum

Vincent Ranwez , Audrey Serra , David Pot , Nathalie Chantret
PLoS ONE, 2017, 12 (9), pp.1-20. ⟨10.1371/journal.pone.0183454⟩
Journal articles hal-01608379v1
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Inferring gene duplications, transfers and losses can be done in a discrete framework

Vincent Ranwez , Celine Scornavacca , Jean-Philippe Doyon , Vincent Berry
Journal of Mathematical Biology, 2016, 72 (7), pp.1811-1844. ⟨10.1007/s00285-015-0930-z⟩
Journal articles hal-01370854v1
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Fast and reliable inference of semantic clusters

Nicolas Fiorini , Sébastien Harispe , Sylvie Ranwez , Jacky Montmain , Vincent Ranwez
Knowledge-Based Systems, 2016, 111, pp.133-143. ⟨10.1016/j.knosys.2016.08.008⟩
Journal articles hal-01506505v1
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Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment

Vincent Ranwez
PLoS ONE, 2016, 11 (8), ⟨10.1371/journal.pone.0160043⟩
Journal articles hal-01594194v1
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Genotyping by sequencing using specific allelic capture to build a high-density genetic map of durum wheat

Yan Holtz , Morgane Ardisson , Vincent Ranwez , Alban Besnard , Philippe Leroy
PLoS ONE, 2016, 11 (5), ⟨10.1371/journal.pone.0154609⟩
Journal articles hal-02639025v1
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A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality

Thu Hien To , Edwin Jacox , Vincent Ranwez , Celine Scornavacca
BMC Bioinformatics, 2015, 16, pp.1-15. ⟨10.1186/s12859-015-0803-x⟩
Journal articles hal-01595105v1
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USI: a fast and accurate approach for conceptual document annotation

Nicolas Fiorini, , Sylvie Ranwez , Jacky Montmain , Vincent Ranwez
BMC Bioinformatics, 2015, 16 (83), pp.1-10. ⟨10.1186/s12859-015-0513-4⟩
Journal articles hal-01288389v1
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Exploring the space of gene/species reconciliations with transfers

Yao-Ban Chan , Vincent Ranwez , Celine Scornavacca
Journal of Mathematical Biology, 2015, 71 (5), pp.1179-1209. ⟨10.1007/s00285-014-0851-2⟩
Journal articles hal-01268903v1

Genotyping by sequencing transcriptomes in an evolutionary pre-breeding durum wheat population

Jacques David , Yan Holtz , Vincent Ranwez , Sylvain Santoni , Gautier Sarah
Molecular Breeding, 2014, 34 (4), pp.1531-1548. ⟨10.1007/s11032-014-0179-z⟩
Journal articles hal-01123443v1

An information theoretic approach to improve semantic similarity assessments across multiple ontologies

Montserrat Batet , Sébastien Harispe , Sylvie Ranwez , David Sanchez , Vincent Ranwez
Information Sciences, 2014, 283, pp.197-210. ⟨10.1016/j.ins.2014.06.039⟩
Journal articles hal-01268902v1
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Impact of recurrent gene duplication on adaptation of plant genomes

Iris Fischer , Jacques Dainat , Vincent Ranwez , Sylvain Glémin , Jean-François Dufayard
BMC Plant Biology, 2014, 14, pp.151. ⟨10.1186/1471-2229-14-151⟩
Journal articles hal-01129945v1
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Evolutionary tinkering of the expression of PDF1s suggests their joint effect on zinc tolerance and the response to pathogen attack

Thi Ngoc Nga Nguyen , Vincent Ranwez , Denis Vile , Marie-Christine Soulie , Alia Dellagi
Frontiers in Plant Science, 2014, 5, ⟨10.3389/fpls.2014.00070⟩
Journal articles hal-01137561v1
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OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals

Emmanuel J.P. Douzery , Celine Scornavacca , Jonathan Romiguier , Khalid Belkhir , Nicolas Galtier
Molecular Biology and Evolution, 2014, 31 (7), pp.1923-1928. ⟨10.1093/molbev/msu132⟩
Journal articles hal-01133634v1
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Genomic evidence for large, long-lived ancestors to placental mammals.

Jonathan Romiguier , Vincent Ranwez , Emmanuel J.P. Douzery , Nicolas Galtier
Molecular Biology and Evolution, 2013, 30 (1), pp.5-13. ⟨10.1093/molbev/mss211⟩
Journal articles hal-01268010v1
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Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods

Thi-Hau Nguyen , Vincent Ranwez , Vincent Berry , Celine Scornavacca
PLoS ONE, 2013, 8 (10), pp.e73667. ⟨10.1371/journal.pone.0073667⟩
Journal articles hal-01189798v1
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Representing a set of reconciliations in a compact way

Celine Scornavacca , Wojciech Paprotny , Vincent Berry , Vincent Ranwez
Journal of Bioinformatics and Computational Biology, 2013, 11 (2), pp.1250025. ⟨10.1142/S0219720012500254⟩
Journal articles lirmm-00818801v1
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Sub-ontology extraction using hyponym and hypernym closure on is-a directed acyclic graphs

Vincent Ranwez , Sylvie Chabert-Ranwez , Stefan Janaqi
IEEE Transactions on Knowledge and Data Engineering, 2013, 24 (12), pp.2288-2300
Journal articles hal-02645875v1
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Reconciliation-based detection of co-evolving gene families

Yao-Ban Chan , Vincent Ranwez , Celine Scornavacca
BMC Bioinformatics, 2013, 14, 15 p. ⟨10.1186/1471-2105-14-332⟩
Journal articles hal-01189789v1

Plant Defensin type 1 (PDF1): protein promiscuity and expression variation within the Arabidopsis genus shed light on zinc tolerance acquisition in Arabidopsis halleri.

Zaigham Shahzad , Vincent Ranwez , Cécile Fizames , Laurence Marquès , Bénédicte Le Martret
New Phytologist, 2013, 200 (3), pp.820-33. ⟨10.1111/nph.12396⟩
Journal articles hal-00921194v1
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Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placentalmammals

Jonathan Romiguier , Vincent Ranwez , Frédéric Delsuc , Nicolas Galtier , Emmanuel J.P. Douzery
Molecular Biology and Evolution, 2013, 30 (9), pp.2134-2144. ⟨10.1093/molbev/mst116⟩
Journal articles hal-01268462v1

Plant Defensin type 1 (PDF1): Protein promiscuity and expression variation within the Arabidopsis genus shed light on zinc tolerance acquisition in Arabidopsis halleri

Z. Shahzad , Vincent Ranwez , C. Fizames , L. Marquès , B. Le Martret
New Phytologist, 2013, 200, pp.820-833. ⟨10.1111/nph.12396⟩
Journal articles hal-01110824v1
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Reconciliation and local gene tree rearrangement can be of mutual profit

Thi Nguyen , Vincent Ranwez , Stéphanie Pointet , Anne-Muriel Arigon Chifolleau , Jean-Philippe Doyon
Algorithms for Molecular Biology, 2013, 8 (12), ⟨10.1186/1748-7188-8-12⟩
Journal articles lirmm-00812726v1
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A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

Matthieu Leray , Joy Y. Yang , Christopher P. Meyer , Suzanne C. Mills , Natalia Agudelo
Frontiers in Zoology, 2013, 10, 14 p
Journal articles hal-01268031v1

Reference-free transcriptome assembly in non-model animals from next generation sequencing data

V. Cahais , P. Gayral , G. Tsagkogeorga , M. Ballenghien , L. Weinert
Molecular Ecology, 2012, 12 (5), pp.834-845. ⟨10.1111/j.1755-0998.2012.03148.x⟩
Journal articles hal-01267810v1
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An O(n.m) algorithm for calculating the closure of lca-type operators

Vincent Ranwez , Stefan Janaqi , Sylvie Ranwez
Ars Combinatoria, 2012, 104, pp.107-128
Journal articles hal-00797153v1
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Subontology Extraction Using Hyponym and Hypernym Closure on is-a Directed Acyclic Graphs

Vincent Ranwez , Sylvie Ranwez , Stefan Janaqi
IEEE Transactions on Knowledge and Data Engineering, 2012, 24 (12), pp.2288-2300
Journal articles hal-00797150v1
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User centered and ontology based information retrieval system for life sciences.

Mohameth-François Sy , Sylvie Ranwez , Jacky Montmain , Armelle Regnault , Michel Crampes
BMC Bioinformatics, 2012, 13 Suppl 1 (Suppl 1), pp.S4. ⟨10.1186/1471-2105-13-S1-S4⟩
Journal articles inserm-00662993v1
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Sequencing of the smallest apicomplexan genome from the human pathogen Babesia Microti

Emmanuel Cornillot , Kamel Hadj-Kaddour , Amina Dassouli , Benjamin Noel , Vincent Ranwez
Nucleic Acids Research, 2012, 40 (18), pp.9102-9114. ⟨10.1093/nar/gks700⟩
Journal articles lirmm-00818833v1
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Extraction de sous-ontologies autonomes par fermeture des opérateurs hyponymie et hyperonymie

Vincent Ranwez , Sylvie Ranwez , Stefan Janaqi
Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, 2012, 31 (1), pp.11-38. ⟨10.3166/tsi.31.11.38⟩
Journal articles hal-00797170v1
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Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.

Jonathan Romiguier , Emeric Figuet , Nicolas Galtier , Emmanuel J.P. Douzery , Bastien Boussau
PLoS ONE, 2012, 7 (3), pp.e33852. ⟨10.1371/journal.pone.0033852⟩
Journal articles hal-00965722v1
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Efficient selection of branch-specific models of sequence evolution.

Julien y Dutheil , Nicolas Galtier , Jonathan Romiguier , Emmanuel J.P. Douzery , Vincent Ranwez
Molecular Biology and Evolution, 2012, 29 (7), pp.1861-1874. ⟨10.1093/molbev/mss059⟩
Journal articles hal-00965698v1
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Building species trees from larger parts of phylogenomic databases

Celine Scornavacca , Vincent Berry , Vincent Ranwez
Information and Computation, 2011, 209 (3), pp.590-605. ⟨10.1016/j.ic.2010.11.022⟩
Journal articles lirmm-00825050v1
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Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)

Juan-Sebastian Escobar , Celine Scornavacca , Alberto Cenci , Claire Guilhaumon , Sylvain Santoni
BMC Evolutionary Biology, 2011, 11 (181), 17 p. ⟨10.1186/1471-2148-11-181⟩
Journal articles hal-01499047v1
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Models, algorithms, and programs for phylogeny reconciliation

Jean-Philippe Doyon , Vincent Ranwez , Vincent Daubin , Vincent Berry
Briefings in Bioinformatics, 2011, 12 (5), pp.392-400. ⟨10.1093/bib/bbr045⟩
Journal articles lirmm-00825041v1
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MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

Vincent Ranwez , Sébastien Harispe , Frédéric Delsuc , Emmanuel J.P. Douzery
PLoS ONE, 2011, 6 (9), ⟨10.1371/journal.pone.0022594⟩
Journal articles hal-01773250v1

Super Triplets : a triplet-based supertree approach to phylogenomics

Vincent Ranwez , Alexis Criscuolo , Emmanuel J.P. Douzery
Bioinformatics, 2010, 26 (12), pp.i115-i123. ⟨10.1093/bioinformatics/btq196⟩
Journal articles hal-04001017v1
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Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

Jonathan Romiguier , Vincent Ranwez , Emmanuel J P Douzery , Nicolas Galtier
Genome Research, 2010, 20 (8), pp.1001 - 1009. ⟨10.1101/gr.104372.109⟩
Journal articles hal-03327982v1

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

N. Galtier , L. Duret , S. Glémin , Vincent Ranwez
Trends in Genetics, 2009, 25(1), pp.1-5
Journal articles hal-00428324v1
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PhyloExplorer: a web server to validate, explore and query phylogenetic trees

Vincent Ranwez , Nicolas Clairon , Frédéric Delsuc , Saeed Pourali , Nicolas Auberval
BMC Evolutionary Biology, 2009, 9, pp.108. ⟨10.1186/1471-2148-9-108⟩
Journal articles lirmm-00396040v1
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PhySIC IST : cleaning source trees to infer more informative supertrees

Celine Scornavacca , Vincent Berry , Vincent Lefort , Emmanuel J.P. Douzery , Vincent Ranwez
BMC Bioinformatics, 2008, 9 (413), pp.1471-2105. ⟨10.1186/1471-2105-9-413⟩
Journal articles lirmm-00324069v1
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OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics.

Vincent Ranwez , Frédéric Delsuc , Sylvie Ranwez , Khalid Belkhir , Marie-Ka Tilak
BMC Evolutionary Biology, 2007, 7, pp.241. ⟨10.1186/1471-2148-7-241⟩
Journal articles halsde-00315511v1
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PhySIC: A Veto Supertree Method with Desirable Properties

Vincent Ranwez , Vincent Berry , Alexis Criscuolo , Pierre-Henri Fabre , Sylvain Guillemot
Systematic Biology, 2007, 56 (5), pp.798-817. ⟨10.1080/10635150701639754⟩
Journal articles lirmm-00194235v1

Multiple molecular evidences for a living mammalian fossil

Dorothée Huchon , Pascale Chevret , Ursula Jordan , William C. Kilpatrick , Vincent Ranwez
Proceedings of the National Academy of Sciences of the United States of America, 2007, 104 (18), pp.7495-7499. ⟨10.1073/pnas.0701289104⟩
Journal articles halsde-00453695v1
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Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics

Julien Dutheil , Sylvain Gaillard , Eric Bazin , Sylvain Glémin , Vincent Ranwez
BMC Bioinformatics, 2006, 7, pp.188. ⟨10.1186/1471-2105-7-188⟩
Journal articles halsde-00323971v1
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Improvement of Distance-Based Phylogenetic Methods by a Local Maximul Likelihood Approach Using Triplets

Vincent Ranwez , Olivier Gascuel
Molecular Biology and Evolution, 2002, 19 (11), pp.1952-1963. ⟨10.1093/oxfordjournals.molbev.a004019⟩
Journal articles lirmm-00268613v1

Quartet-Based Phylogenetic Inference: Improvements and Limits

Olivier Gascuel , Vincent Ranwez
Molecular Biology and Evolution, 2001, 18 (6), pp.1103-1116. ⟨10.1093/oxfordjournals.molbev.a003881⟩
Journal articles hal-04000964v1