Publications

 My Google Scholar: here

Feel free to contact me to have a pdf version of one of my articles.

2017

Yao-ban Chan, Vincent Ranwez, Celine Scornavacca. Inferring incomplete lineage sorting, duplica- tions, transfers and losses with reconciliations. Accepted for publication in Journal of Theoretical Biology.

Cedric Chauve, Mark Jones, Manuel Lafond, Celine Scornavacca, Mathias Weller. Constructing a Consensus Phylogeny from a Leaf-Removal Distance. Accepted to SPIRE 2017.

Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi and Celine Scornavacca. Rearrangement Moves on Rooted Phylogenetic Networks. Accepted for publication in PLOS Computational Biology.

Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, Cedric Chauve, Celine Scornavacca, Vincent Daubin, Eric Tannier. DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies. Accepted for publication in Genome Biology and Evolution 9(2017), no. 5, pp. 1312-1319.

Manuel Lafond, Celine Scornavacca. On the Weighted Quartet Consensus problem. CPM 2017. LIPIcs, vol. 78, Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, 2017, pp. 28:1-28:18.

Julia Matsieva, Steven Kelk,   Celine Scornavacca, Chris Whidden, and Dan Gusfield.  A Resolution of the Static Formulation Question for the Problem of Computing the History Bound}. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14(2017), no. 2, pp 404-417.

Edwin Jacox, Mathias Weller, Eric Tannier and Celine Scornavacca . Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses. Bioinformatics 33(2017) no. 7, pp 980-987.

Julien Baste, Christophe Paul, Ignasi Sau, Celine Scornavacca. Efficient FPT algorithms for (strict) compatibility of unrooted phylogenetic trees. Bulletin of Mathematical Biology 79(2017), no. 4, pp 920-938

Celine Scornavacca, Joan Carles  Pons Mayol,  Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. Journal of Theoretical Biology 418(2017), pp 129–137.

Celine Scornavacca, Nicolas Galtier. Incomplete Lineage Sorting in Mammalian Phylogenomics. Systematic Biology 66(2017), no. 1, pp 112–120.

Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca, Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. Algorithmica 77(2017), no. 1, pp 173–200.

Magnus Bordewich, Celine Scornavacca, Nihan Tokac, Mathias Weller.  On the fixed parameter tractability of agreement-based phylogenetic distances. Journal of Mathematical Biology 74(2017), pp 239–257.

2016

Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi, Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? Bulletin of Mathematical Biology  78(2016) no. 9, pp  1773–1795.

Mark Jones, Christophe Paul, Celine Scornavacca. On the consistency of orthology relationships. BMC Bioinformatics 17(2016)  no. 14, pp. 416 (RECOMB CG  proceedings).

Julien Baste, Christophe Paul, Ignasi Sau, Celine Scornavacca. Efficient FPT algorithms for (strict) compatibility of unrooted phylogenetic trees. AAIM 2016. LNCS, vol. 9778,  Springer-Verlag, 2016, pp.  53-64.

Edwin Jacox, Cedric Chauve, Gergely J. Szöllősi, Yann Ponty, Celine Scornavacca. ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics 32(2016) no. 13, pp 2056–2058.

François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Emmanuelle Jousselin,  Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. Bioinformatics 32(2016) no. 4, pp 608–610.

Leo van Iersel, Steven Kelk, Celine Scornavacca. Kernelizations for the hybridization number problem on multiple nonbinary trees. Journal of Computer and System Sciences  82(2016) no. 6, pp 1075–1089.

Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon and Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. Journal of Mathematical Biology , 72(2016) no.  7, pp 1811–1844 .

Steven Kelk, Leo van Iersel, Celine Scornavacca, Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. Journal of Graph Algorithms and Applications 20(2016), no. 2, pp. 189–215.

Brozovic, Matija; Martin, Cyril; Dantec, Christelle; Dauga, Delphine; Mendez, Mickael; Simion, Paul; Percher, Madeline; Laporte, Baptiste; Scornavacca, Céline; Fujiwara, Shigeki; Gineste, Mathieu; Lowe, Elijah; Piette, Jacques; Sasakura, Yasunori; Takatori, Naohito; Brown, Titus C; Delsuc, Frederic; Gissi, Carmela; DOUZERY, Emmanuel; McDougall, Alex; NISHIDA, Hiroki; Sawada, Hitoshi; Swalla, Billie; Yasuo, Hitoyoshi; Lemaire, Patrick. ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acid Research 44(2016) no. D1, pp. D808–D818.

Manuel Binet, Olivier Gascuel,  Celine Scornavacca, Emmanuel J.P. Douzery, Fabio Pardi. Fast and accurate branch lengths estimation for phylogenomic trees. BMC Bioinformatics 17(2016), no. 1, pp. 1–18.

2015

Thu-Hien To, Edwin Jacox, Vincent Ranwez, Celine Scornavacca. A Fast Method for Calculating Reliable Event Supports in Tree Reconciliations via Pareto optimality. BMC Bioinformatics 6(2015) no. 1, pp 1–15.

Thu-Hien To and Celine Scornavacca.  Efficient algorithms for reconciling gene trees and species networks via duplication and loss events. BMC genomics 2015(16) no. 10, S6. pdf (the article on the BMC website is badly formatted)

Mareike Fischer, Leo van Iersel, Steven Kelk, and Celine Scornavacca.  On Computing the Maximum Parsimony Score of a Phylogenetic Network. SIAM Journal on Discrete Mathematics – SIDMA 29(2015), no. 1, pp. 559-585.

Fabio Pardi, Celine Scornavacca. Reconstructible phylogenetic networks: do not distinguish the indistinguishable. PLOS Computational Biology. 2015(11), no 4:e1004135. doi:10.1371/journal.pcbi.1004135. pdf (the article on the PLOS website is badly formatted)

Yao-ban Chan, Vincent Ranwez, Celine Scornavacca. Exploring the space of gene/species reconciliations with transfers. Journal of Mathematical Biology 71(2015), pp. 1179-1209.

Celine Scornavacca, Edwin Jacox and Gergely Szöllősi. Joint amalgamation of most parsimonious reconciled gene treesBioinformatics 31(2015) no. 6, pp 841–848.

2014

Leo van Iersel, Steven Kelk, and Celine Scornavacca. Exact reconciliation of undated trees. ArXiv http://arxiv.org/abs/1410.7004

The agreement problem for unrooted phylogenetic trees is FPT. Celine Scornavacca, Leo van Iersel, Steven Kelk and  David Bryant. Journal of Graph Algorithms and Application  18(2014) no.3, pp. 385-392

A practical approximation algorithm for solving massive instances of hybridization number forbinary and nonbinary trees.  Leo Van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. BMC Bioinformatics 15(2014):127.

OrthoMaM v8: a database of orthologous exons and coding sequences for com- parative genomics in mammals. Emmanuel J. P. Douzery, Celine Scornavacca, Jonathan Romiguier, Khalid Belkhir, Nicolas Galtier, Frédéric Delsuc  and Vincent Ranwez.  Molecular Biology and Evolution. In print. doi: 10.1093/molbev/msu132

2013

Reconciliation-based detection of co-evolving gene families.  Yao-ban Chan, Vincent Ranwez, Celine Scornavacca.  BMC Bioinformatics. 14(2013), p 332. doi:10.1186/1471-2105-14-332

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

Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, Nicolas C Rochette, Thomas Bigot, David Fournier, Fanny Pouyet, Vincent Cahais, Aurelien Bernard, Celine Scornavacca, Benoit Nabholz, Annabelle Haudry, Loic Dachary, Nicolas Galtier, Khalid Belkhir, Julien Y Dutheil.  Bio++: efficient, extensible libraries and tools for computational molecular evolution. Molecular Biology and Evolution (2013), doi: 10.1093/molbev/mst097

Celine Scornavacca, Wojciech Paprotny, Vincent Berry and Vincent Ranwez. Representing a set of reconciliations in a compact way. Journal of Bioinformatics and Computational Biology. 11(2013) no. 2, pp. 1250025.

2012

Steven Kelk and Celine Scornavacca. Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable. Published online  in Algorithmica in 2012. 68(2014) no. 4, pp. 886-915.

Cycle killer…qu’est-ce que c’est? On the comparative approximability of hybridization number and directed feedback vertex set, Steven Kelk, Leo van Iersel, Nela Lekic, Simone Linz, Celine Scornavacca, Leen Stougie.  SIAM Journal on Discrete Mathematics. 26(2012) no. 4, pp. 1635–1656.

Daniel H. Huson and Celine Scornavacca. Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Systematic Biology. 61(2012) no. 6, pp. 1061–1067 .

Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number. WABI 2012. LNBI, vol. 7534, Springer- Verlag, 2012, pp. 430–440.

Celine Scornavacca, Benjamin Albrecht, Alberto Cenci and Daniel H. Huson. Fast computation of minimum hybridization networks. Bionformatics. 28(2012) no. 2, pp. 191-197.

Steven Kelk, Celine Scornavacca, and Leo van Iersel. On the elusiveness of clusters. IEEE/ACM Transactions on Computational Biology and Bioinformatics.  9(2012), pp. 517-534.

2011

Daniel H. Huson, Regula Rupp and Celine Scornavacca. Phylogenetic NetworksCambridge University Press. 2011 (http://www.phylogenetic-networks.org/).

Juan S. Escobar, Celine Scornavacca, Alberto Cenci, Claire Guilhaumon, Sylvain Santoni, Emmanuel J. P. Douzery, Vincent Ranwez, Sylvain Glémin and Jacques David. Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)BMC Evolutionary Biology 11(2011), pp. 181.

Celine Scornavacca and Daniel H. Huson. A survey of combinatorial methods for phylogenetic networks. Genome Biology and Evolution. 3(2011), pp. 23-35.

Celine Scornavacca, Vincent Berry and Vincent Ranwez. Building species trees from larger parts of phylogenomic databasesInformation and Computation. 209(2011), no. 3, pp. 590–605.

Celine Scornavacca, Franziska Zickmann and Daniel H. Huson. Tanglegrams for rooted phylogenetic trees and networksBioinformatics. 27(2011), no. 13, pp. i248-i256.

2010

Jean-Philippe Doyon, Celine Scornavacca, Gergely J. Szöllösi, Vincent Ranwez and Vincent Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. Eighth Annual RECOMB Satellite Workshop on Comparative Genomics, RECOMB GC 2010, LNCS, vol. 6398, Springer-Verlag, 2010. pp. 93-108.

Jean-Philippe Doyon, Celine Scornavacca, Gergely J. Szöllösi, Vincent Ranwez and Vincent Berry. Un algorithme de parcimonie efficace pour la réconciliation d’arbres de gènes/espèces avec pertes, duplications and transfertsJOBIM 2010.

2009

Celine Scornavacca, Vincent Berry and Vincent Ranwez. From Gene Trees to Species Trees through a Supertree Approach. Third International Conference on Language and Automata Theory and Applications, LATA 2009, LNCS, vol. 5457, Springer-Verlag, 2009, pp. 702-714.

2008

Celine Scornavacca, Vincent Berry, Lefort Vincent, Emmanuel J. P. Douzery and Vincent Ranwez. PhySIC IST : cleaning source trees to infer more informative supertrees. BMC Bioinformatics, 9(2008), pp. 413.

Marilia D. V. Braga, Marie-France Sagot, Celine Scornavacca and Eric Tannier. Exploring the solution space of sorting by reversals and an application in evolution. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(2008) no. 3, pp. 348–56.

2007

Vincent Ranwez, Vincent Berry, Alexis Criscuolo, Pierre-Henri Fabre, Sylvain Guillemot, Celine Scornavacca and Emmanuel J. P. Douzery. PhySIC : a Veto Supertree Method with Desirable PropertiesSystematic Biology, 56(2007), no. 5, pp. 798-817.

Marilia D. V. Braga, Marie-France Sagot, Celine Scornavacca and Eric Tannier. The solution space of sorting by reversals. Third International Symposium on Bioinformatics Research and Applications, ISBRA 2007, LNCS, vol. 4463, Springer-Verlag, 2007, pp. 293-304.

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: