Publications

for further details, please consult
my research gate profile and my
google scholar profile




2017

  • accepted journal papers



  • journal papers

    • Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations. Y Chan, V Ranwez, C Scornavacca. Journal of Theoretical Biology (2017) 432: 1-13 PDF.
    • Domestication Reduces Alternative Splicing Expression Variations in Sorghum.  Vincent Ranwez, Audrey Serra, David Pot,  Nathalie Chantret. Accepted for publication in
       Plos One (2017) 
      12(9): e0183454 PDF.
    • Epistatic determinism of durum wheat resistance to the Wheat Spindle Streak Mosaic Virus. Y. Holtz, M. Bonnefoy, V. Viader, M. Ardisson, N. O. Rode, G. Poux, P. Roumet2, V. Marie-Jeanne, V. Ranwez, S. Santoni, D. Gouache, J. L. David.  Theoretical and Applied Genetics (2017) 130(7): 1491-1505 PDF.
    • The Genetic Map Comparator: a user-friendly application to display and compare genetic maps. Y. Holtz, J. David and  Vincent Ranwez.  Bioinformatics (2017) 33(9): 1387–1388, Web Site (online tool) PDF.
    • Pitfalls in supermatrix phylogenomics. Hervé Philippe, Damien M. de Vienne, Vincent Ranwez, Béatrice Roure, Denis Baurain and Frédéric Delsuc. Accepted for publication in European Journal of Taxonomy (2017) 283: 1-25 PDF.

2016

  • journal papers

    • Fast and reliable inference of semantic clusters.  Nicolas Fiorini, Sébastien Harispe, Sylvie Ranwez, Jacky Montmain, Vincent Ranwez. Knowledge Based System 2016 111, 133-144 PDF.
    • Two simple and efficient algorithms to compute the SP-score objective function of a multiple sequence alignment.  Vincent Ranwez. PLoS One 2016 11(8): e0160043 PDF.
    • Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat. Y Holtz, M Ardisson, V Ranwez, A Besnard, P Leroy, G Poux, P Roumet, V.Viader, S. Santoni, J. David. PloS one 2016 11 (5): e0154609 PDF
    • Inferring gene duplications, transfers and losses can be done in a discrete framework. Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon and Vincent Berry Journal of mathematical biology (2016) 72 (7), 1811-1844 PDF

2015

  • journal papers

    • 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 16:384  PDF.
    • USI: a fast and accurate approach for conceptual document annotation. Nicolas Fiorini, Sylvie Ranwez, Jacky Montmain and Vincent Ranwez. BMC Bioinformatics (2015) 16:83 PDF, WEB Site.
    • Exploring the space of gene/species reconciliations with transfers. Yao-ban Chan, Vincent Ranwez, Celine Scornavacca. Journal of Mathematical Biology (2015) 71(5): 1179-1209 PDF.
  • conférences and communications
    • USI at BioASQ 2015: a Semantic Similarity-Based Approach for Semantic Indexing. Fiorini, N., Ranwez, S., Harispe, S., Montmain, J. and Ranwez, V. InWorking Notes for the Conference and Labs of the Evaluation Forum (CLEF 2015), Toulouse, France. PDF WEB Site

2014

  • journal papers

    • Genotyping by sequencing transcriptomes in an evolutionary pre-breeding durum wheat population. Jacques David, Yan Holtz, Vincent Ranwez, Sylvain Santoni, Gautier Sarah, Morgane Ardisson, Gérard Poux Fréderic Choulet, Clémence Genthon, Pierre Roumet, Muriel Tavaud-Pirra. Molecular Breeding (2014)  34(4):1531-1548  PDF.
    • An information theoretic approach to improve semantic similarity assessments across multiple ontologies. Montserrat Batet  Sébastien Harispe, Sylvie Ranwez, David Sánchez, Vincent Ranwez. Information Sciences (2014)  283(1):197-210. PDF.
    • Impact of recurrent gene duplication on adaptation of plant genomes. I. Fischer, J. Dainat, V. Ranwez, S. Glémin, J.F. Dufayard and N. Chantret.  BMC Plant Biology (2014) 14 (151). PDF
    • Evolutionary Tinkering of the Expression of PDF1s Suggests their Joint Effect on Zinc Tolerance and the Response To Pathogen Attack. N.N.T. Nguyen, V. Ranwez, D. Vile, M.C. Soulie, A. Dellagi, D. Expert, F. Gosti. Frontiers in Plant Science (2014) 5(70) PDF.

    • OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals. E. J. P. Douzery, C. Scornavacca, J. Romiguier, K. Belkhir, N. Galtier, F. Delsuc  and V. Ranwez. 

       Molecular Biology and Evolution (2014) 31(7):1923-8. PDF

  • conférences and communications
    •  Coping with imprecision during a semi-automatic conceptual indexing process. N. Fiorini, S. Ranwez, J. Montmain and  V. Ranwez. 15th International Conference IPMU 2014, in Montpellier, France (July 15 - 19, 2014). Lecture Note in Computer Science (LNCS) : Springer Berlin / Heidelberg, volume 444, pp. 11-20 PDF.
    • Indexation conceptuelle par propagation. Application à un corpus d’articles scientifiques liés au cancer. N. Fiorini, S. Ranwez, V. Ranwez et J. Montmain.  CORIA 2014  dans le cadre de la semaine du document numérique et de la recherche d'information 19-21 Mars 2014 Nancy.
    • Broadening the genetic bases of durum wheat. Jacques David, Muriel Tavaud, Pierre Roumet, Marie-Hélène Muller, Sylvain Santoni, Sarah Gautier, Yan Holtz, Vincent Ranwez, Morgane Ardisson, Gérard Poux, Constance Vagne. 65-78. E. Porceddu, A.B. Damania, C.O. Qualset (eds.). Proceedings of the International Symposium on Genetics and Breeding of Durum Wheat - IAM Bari: CIHEAM 2014 – 636p.  (Série  A  Mediterranean  Seminars,  N°  110,  Options Méditerranéennes) PDF.

2013

  • journal papers

    • Reconciliation-based detection of co-evolving gene families. Yao-ban Chan, Vincent Ranwez and Celine Scornavacca. BMC Bioinformatics, 14:332 PDF.
    • Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat. V Ranwez, Y Holtz, G Sarah, M Ardisson, S Santoni, S Glémin, M Tavaud-Pirra, J. David . BMC Bioinformatics 14 (Suppl 15), S15 (RECOMB-CG 2013 special issue) Web Site PDF
    • Plant Defensin type 1 (PDF1): protein promiscuity and expression variation within the 2 Arabidopsis genus shed light on zinc tolerance acquisition in Arabidopsis halleri. Zaigham Shahzad, Vincent Ranwez, Cécile Fizames, Laurence Marquès, Bénédicte Le Martret, Julien Alassimone, Cécile Godé, Eric Lacombe, Teddy Castillo, Pierre Saumitou-Laprade, Pierre Berthomieu, Françoise Gosti. New Phytologist (2013) 200(3): 820-33 PDF.
    • Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods. Thi-Hau Nguyen Vincent Ranwez  Vincent Berry, Celine Scornavacca. PLoS ONE 8(10): e73667. doi:10.1371/journal.pone.0073667  PDF.
    • Less is more in mammalian phylogenomics : AT-rich genes minimize tree conflicts and unravel the root of placental mammals. J. Romiguier, V. Ranwez, F. Delsuc, N. Galtier, E.J.P. Douzery.  Molecular Biology and Evolution (2013) 30(09): 2134-44 PDF.
    • 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, Vincent Ranwez, Joel T Boehm and Ryuji J Machida. Frontiers in Zoology (2013) 10: 34 PDF.
    • Representing a set of reconciliations in a compact way. C. Scornavacca, W. Patrotny, V. Berry, V. Ranwez. Journal of Bioinformatics and Computational Biology (2013) 11(2):1250025 PDF.
    • Reconciliation and local gene tree rearrangement can be of mutual profi. Thi Hau Nguyen, Vincent Ranwez, Stephanie Pointet, Anne-MurielA. Chifolleau, Jean-Philippe Doyon and Vincent Berry. Algorithms for Molecular Biology (2013) 8(12) PDF.
    • Genomic Evidence for Large, Long-Lived Ancestors to Placental Mammals. J. Romiguier, V. Ranwez, E.J.P. Douzery, N. Galtier. Molecular Biology and Evolution  (2013) 30(1):5-13 PDF.
  • conferences and communications



2012

  • journal papers

    • Sequencing of the smallest apicomplexan genome from the human pathogen Babesia microti.  E. Cornillot, K. Hadj-Kaddour1, A. Dassouli1, B. Noel, V. Ranwez, B. Vacherie, Y. Augagneur, V. Brès, A. Duclos, S. Randazzo, B. Carcy, F. Debierre-Grockiego, S. Delbecq, K. Moubri-Ménage, H. Shams-Eldin, S. Usmani-Brown, F. Bringaud, P. Wincker, C. P. Vivarès, R. T. Schwarz, T. P. Schetters, P. J. Krause, A. Gorenflot, V. Berry, V. Barbe, C. Ben Mamoun. Nucleic Acids Research (2012) 40(18):9102-14  PDF.
    • Reference-free transcriptome assembly in non-model animals from next generation sequencing data. V. Cahais, P. Gayral, G. Tsagkogeorga, J. Melo-Ferreira, M. Ballenghien, L. Weinert, Y. Chiari, K. Belkhir, V. Ranwez , N. Galtier. Molecular Ecology Resources (2012) 12(5):834-845. PDF.
    • Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. Jonathan Romiguier, Emeric Figuet, Nicolas Galtier, Emmanuel JP Douzery, Bastien Boussau, Julien Y Dutheil, Vincent Ranwez. Plos One (2012) 7(3): e33852. PDF
    • Efficient selection of branch-specific models of sequence evolution. Julien Y. Dutheil, Nicolas Galtier, Jonathan Romiguier, Emmanuel JP Douzery, Vincent Ranwez and Bastien Boussau. Molecular Biology and Evolution, 29 (7): 1861-1874, 2012. PDF.
    • An O(n.m) algorithm for calculating the closure of lca-type operators. Vincent Ranwez, Stefan Janaqi, Sylvie Ranwez Ars Combinatoria 104: 107-128, 2012 (table of contents).
    • User Centered and Ontology Based Information Retrieval System for Life Sciences Mohameth-François Sy, Sylvie Ranwez, Jacky Montmain, Armelle Regnault, Michel Crampes, Vincent Ranwez BMC Bioinformatics 2012, 13(Suppl 1):S4 PDF WEB SITE 
    • Sub-ontology 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   vol. 24, no. 12, pp. 2288-2300, Dec. 2012 PDF.
  • book section

    • New Trends of Research in Ontologies and Lexical Resources (chapter 11). How ontology based information retrieval systems may benefit from lexical text analysis. S. Ranwez, B. Duthil, M.F. Sy, J. Montmain, P. Augereau and V. Ranwez. (to be published).

    french journal paper
    • Extraction de sous-ontologies autonomes par fermeture des opérateurs hyponymie et hyperonymie V. Ranwez, S. Ranwez, S. Janaqi. Technique et science informatiques (2012) 31(1) :11-38 PDF  RUN.

    conferences and communications

    • Une méthode de reformulation utilisant une ontologie de domaine. M.F. Sy, S. Ranwez, J. Montmain, V. Ranwez. Actes de la neuvième édition de la COnférence en Recherche d'Information et Applications CORIA 2012  dans le cadre de la semaine du document numérique et de la recherche d'information 21-23 mars 2012, Bordeaux, France (2012) : pp 135-150 PDF.
    • Accounting for gene tree uncertainty improves gene tree accuracy as well as duplications, transfers and losses  predictions. T. H. Nguyen, J.-P. Doyon, S. Pointet, A.-M. Arigon Chifolleau, V. Ranwez and V. Berry . WABI 2012 Proceedings in Lecture Notes in Computer Science (LNCS) Volume 7534, 2012, pp 123-134 PDF.

2011

  • journal papers
    • MACSE : Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. Vincent Ranwez, Sébastien Harispe, Frédéric Delsuc, Emmanuel JP Douzery Plos One 6(9) : e22594. PDF, WEB SITERUN ONLINE
    • Models, algorithms, and programs for phylogeny reconciliation. Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin, Vincent Berry Briefings in Bioinformatics (2011) 12(5):392-400. PDF WEB SITE
    • Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae). Juan S Escobar, Celine Scornavacca, Alberto Cenci, Claire Guilhaumon, Sylvain Santoni, Emmanuel JP Douzery, Vincent Ranwez, Sylvain Glemin and Jacques David BMC Evolutionary Biology, 11:181, 2011 PDF.
    • Building species trees from larger parts of phylogenomic databases. Celine Scornavacca, Vincent Berry and Vincent Ranwez Information and Computation, (209) : pp. 590-605, 2011. PDF

2010

  • Habilitation à Diriger des Recherches (HDR)
    • Des séquences moléculaires à l’Arbre de la Vie : résultats théoriques, algorithmes et outils pour la phylogénomique. V. Ranwez, HDR soutenues le 6 décembre 2010. PDF ABSTRACT
  • book section
    • Phylogénie moléculaire (chapitre 9) Samuel Blanquart, Alexis Criscuolo, Christophe Douady, Emmanuel Douzery, Nicolas Lartillot, Hervé Philippe, and Vincent Ranwez in Biologie Evolutive, (M. Raymond, T. Lefèvre, and F. Thomas, eds.), 2010 .De Boek Université, Bruxelles, Belgique
  • journal papers
    • Contrasting GC-content dynamics across 33 mammalian genomes : relationship with life-history traits and chromosome sizes. Jonathan Romiguier, Vincent Ranwez, Emmanuel J. P. DOUZERY and Nicolas GALTIER Genome Research 20(8) : 1001-1009, 2010. PDF
    • SuperTriplets : a triplet-based supertree approach to phylogenomics. Vincent Ranwez, Alexis Criscuolo and Emmanuel J. P. Douzery. Bioinformatics 26 : i115-i123. PDF, WEB SITE
  • conferences and communications
    • SWAT4LS 2010 (speaker : S. Ranwez) Sylvie Ranwez, Vincent Ranwez, Mohameth François Sy, Jacky Montmain and Michel Crampes. User Centered and Ontology Based Information Retrieval System for Life Sciences.
    • RECOMB-CG 2010 Jean-Philippe Doyon, Celine Scornavacca, K. Yu. Gorbunov, Gergely Szollosi, Vincent Ranwez and Vincent Berry. Lecture Note in Computer Science (LNCS) : Springer Berlin / Heidelberg, (RECOMB Satellite Workshop on Comparative Genomics), Volume 6398, pp. 93-108 PDF.
    • ISMB 2010 (speaker : V. Ranwez) SuperTriplets : a triplet-based supertree approach to phylogenomics.
    • Utilisation de proximités sémantiques pour améliorer la recherche et le rendu d’information. Sylvie Ranwez, Vincent Ranwez, Mohameth-François Sy, Jacky Montmain et Michel Crampes. IC 2010, 21e Journées Francophones d’Ingénierie des Connaissances, Nîmes, France, 9-11 juin 2010, pp.247-258.
    • Alphy 2010 (speaker : E. Douzery) OrthoMaM et PhyloeExplorer : deux outils pour l’exploration et l’exploitation des marqueurs et arbres phylogénétiques

2009

  • journal papers
    • PhyloExplorer : a web server to validate, explore and query phylogenetic trees. V. Ranwez, N. Clairon, F. Delsuc, S. Pourali, N. Auberval, S. Diser, V. Berry. BMC Evolutionary Biology 9(1) : 108, 2009. PDF, WEB SITE
    • GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Galtier, N., L. Duret, S. Glémin, and V. Ranwez. 2009. Trends in Genetics 25(1):1-5 PDF
  • conferences and communications
    • From gene trees to species trees through a supertree approach. Celine Scornavacca, Vincent Berry, and Vincent Ranwez. Lecture Note in Computer Science (LNCS) : Springer Berlin / Heidelberg, Volume 5457/2009, pp. 702-714, 2009 ISBN 978-3-642-00981-5 ( Language and Automata Theory and Applications : LATA 2009).
    • JFO 2009 (speaker : S. Ranwez) Extraction de sous-ontologies autonomes par fermeture des opérateurs hyponymie et hyperonymie

2008

  • journal papers
    • PhySIC_IST : healing source trees to infer healthy supertrees. Celine Scornavacca, Vincent Berry, Emmanuel J. P. Douzery and Vincent Ranwez. BMC Bioinformatics 9:413 PDF
  • conferences and communications
    • MIEP 2008 (speaker : C. Scornavacca) Healing source trees to obtain healthy supertrees
    • SMBE 2008 (speaker : C. Scornavacca) PhySICIST healing source trees to infer healthy supertrees
    • Alphy 2008 (speaker : C. Scornavacca) PhySIC_IST : healing source trees to infer healthy supertrees
    • SMBE 2008 (poster) Evolutionary dynamics and phylogenetic content of coding sequences in mammalian genomes

2007

  • journal papers
    • OrthoMaM : A database of orthologous genomic markers for placental mammal phylogenetics Ranwez V., Delsuc F., Ranwez S., Belkhir K. Tilak M. & Douzery E. J. P. BMC Evolutionary Biology 7 : 241 PDF, WEB SITE
    • PhySIC : A Veto Supertree Method with Desirable Properties. Ranwez V ; Berry V ; Criscuolo A ; Fabre PH ; Guillemot S ; Scornavacca C ; Douzery EJP. Systematic Biology, Volume 56, Issue 5 October 2007 , pages 798-817 ABSTRACT method download
    • Multiple molecular evidences for a living mammalian fossil.Huchon D, Chevret P, Jordan U, Kilpatrick CW, Ranwez V, Jenkins PD, Brosius J, Schmitz J. Proc Natl Acad Sci U S A. 2007 May 1 ;104(18):7495-9. Epub 2007 Apr 23. ABSTRACT
  • conferences and communications
    • JOBIM 2007 (speaker : V. Ranwez) Représentation matricielle sans parcimonie A Criscuolo, V Ranwez.
    • Evolution 2007 (speaker : V. Ranwez) OrthoMaM : a database of candidate coding markers for mammalian phylogenomics . V. RANWEZ, F. DELSUC, M.-K. TILAK, S. RANWEZ AND E.J. P. DOUZERY WEB SITE
    • Evolution 2007 (speaker : D. Huchon) DNA sequencing and SINE insertions support Laonastes as a "living fossil". D. HUCHON, P. CHEVRET, U. JORDAN, C. W. KILPATRICK, V. RANWEZ, J. BROSIUS AND J. SCHMITZ.
    • Dumont D’Urville Workshops on Applied Evolutionary Bioinformatics 2007 (speaker : V. Ranwez) SuperTriplet : a supertree method based on triplets. V. Ranwez, A. Criscuolo, E.J.P. Douzery.
    • Dumont D’Urville Workshops on Applied Evolutionary Bioinformatics 2007 (speaker : V. Berry) PhySIC : inferring supertrees from phylogenetic signal with induction and non-contradiction. V. Ranwez, V. Berry, A. Criscuolo, P.H. Fabre, S. Guillemot, C. Scornavacca and E.J.P. Douzery

2006

  • journal papers
    • Bio++ : a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. Dutheil J, Gaillard S, Bazin E, Glemin S, Ranwez V, Galtier N and Belkhir K. BMC Bioinformatics. 2006 Apr 4 ;7(1):188 full article
  • conferences and communications
    • Ontological ISA-Distance Measure for Information Visualisation on Conceptual Maps. Sylvie Ranwez, Vincent Ranwez, Jean Villerd, Michel Crampes. In On the Move to Meaningful Internet Systems 2006 : OTM 2006 Workshops, Lecture Notes in Computer Science, publisher (LNCS) : Springer Berlin / Heidelberg, Volume 4278/2006, ISBN 978-3-540-48273-4, pp.1050-1061, 2006.
    • JOBIM 2006 (speaker : V. Ranwez) Votez veto pour l’Arbre de la Vie : la méthode PhySIC pour reconstruire des superarbres. V. Berry, V. Ranwez, P.-H. Fabre et E.J.P. Douzery. pp251-264
    • JOBIM 2006 (presentation flash, speaker : J. Dutheil) Bio++ : a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics J. Dutheil, S. Gaillard, E. Bazin, S. Glémin, V. Ranwez, N. Galtier and K. Belkhir

2003-2005 (Clinigenetics SA)

    • CliniGenetics was a biopharmaceutical company devoted to the discovery and development of new molecules for the treatment of complex metabolic diseases and their cardiovascular complications. These diseases are the main cause of morbidity and death in the developed world.

2002

  • journal papers
    • Improvement of distance-based phylogenetic method via a local maximum likelihood approach. Vincent Ranwez, Olivier Gascuel. Molecular Biology and Evolution (MBE) 19(11):1952-1963, 2002. ABSTRACT+PDF
    • Order Independent Homotopic Thinning for binary and Grey Tone Anchored Skeletons. Vincent Ranwez, Pierre Soille. Pattern Recognition Letters (PRL) 23 (6) : 687-702, 2002.
    • Mé́thodes efficaces pour reconstruire de grandes phylogénies suivant le principe du maximum de vraisemblance. V. Ranwez. Thèse effectuée sous la direction d’Olivier Gascuel. PDF phD :Efficient methods for reconstructing large phylogenies according to the maximum likelihood principle. ABSTRACT

2001

  • journal papers
    • Quartet Based Phylogenetic Inference : Improvements and limits. Vincent Ranwez, Olivier Gascuel. Molecular Biology and Evolution (MBE) 18(6) : 1103-1116, 2001. ABSTRACT+PDF
  • conferences and communications
    • Phylogenetic Reconstruction Algorithms Based on Weighted 4-trees. Vincent Ranwez, Olivier Gascuel. Lecture Note in Computer Science (LNCS) volume 2066, pp. 86-100, 2001 (sélection d’articles de JOBIM’2000).

1999

  • conferences and communications
    • Order Independent Homotopic Thinning. Vincent Ranwez, Pierre Soille. (DGCI’99), Lecture Note in computer science (LNCS) volume 1568, pp. 337-348, 1999.
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