Publications
All my publications in descending order of the year published.
Supervised Phd students and Master students
Articles
- [1] Thibault Leroy, Yoann Anselmetti, Marie-Ka Tilak, Sèverine Bérard, Laura Csukonyi, Maeva Gabrielli, Celine Scornavacca, Borja Mila, Christophe Thebaud and Benoit Nabholz. A bird’s white-eye view on avian sex chromosome evolution, Peer Community Journal Volume 1, article no. e63. 2021. (initialement bioRχiv, 505610, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology en 2019)
Article : DOI
- [2] Robert M. Waterhouse, Sergey Aganezov, Yoann Anselmetti, Jiyoung Lee,
Livio Ruzzante, Maarten J.M.F. Reijnders, Romain Feron, Sèverine Bérard, Phillip George,
Matthew W. Hahn, Paul I Howell, Maryam Kamali, Sergey Koren, Daniel Lawson, Gareth Maslen, Ashley Peery, Adam M. Phillippy, Maria V. Sharakhova, Éric Tannier, Maria F. Unger, Simo V. Zhang, Max A. Alekseyev, Nora J. Besansky, Cedric Chauve, Scott J. Emrich and Igor
V. Sharakhov. Evolutionary superscaffolding and chromosome anchoring to improve
Anopheles genome assemblies, BMC Biology 18(1). 2020.
Article : DOI
- [3] Lisa De Mattéo, Yann Holtz, Vincent Ranwez, and Sèverine Bérard. Efficient algorithms for Longest Common Subsequence of two bucket orders to speed up pairwise genetic map comparison, PLoS ONE 13(12): e0208838. 2018.
ISEM 2018-308 SUD
Article : .pdf DOI
- [4] Yoann Anselmetti, Wandrille Duchemin, Éric Tannier, Cedric Chauve, and Sèverine Bérard. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes, BMC Genomics 19(Suppl 2):96. 2018. ISEM 2018-016
Article : .pdf
- [5] Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, Cedric Chauve, Celine Scornavacca, Vincent Daubin and Éric Tannier. DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies. Genome Biology and Evolution, vol. 9 pp.1312-1319. 2017. ISEM 2017-098
Article : .pdf
- [6] Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron and Krister Swenson. Aligning the unalignable: bacteriophage whole genome alignments. BMC Bioinformatics 17:30 DOI: 10.1186/s12859-015-0869-5. 2016. ISEM 2016-018
Article : .pdf
- [7] Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Éric Tannier and Sèverine Bérard. Ancestral gene synteny reconstruction improves extant species scaffolding, BMC Genomics 16(Suppl 10):S11 DOI:10.1186/1471-2164-16-S10-S11, 2015. ISEM 2015-158
Article : .pdf
- [8] Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely J. Szollosi, Vincent Daubin and Éric Tannier. Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics 28 (18): i382-i388. doi: 10.1093/bioinformatics/bts374, 2012.
Article : .pdf
- [9] Cédric Gaucherel, Sèverine Bérard and François Munoz. Equation or algorithm: differences and choosing between them, Acta Biotheoretica. 59(1): 67-79, 2010.
Article : .pdf
- [10] Sèverine Bérard, Annie Chateau, Cedric Chauve, Christophe Paul and Éric Tannier. Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes, Journal of Computational biology (JCB), Volume 16, Number 10, pages 1287-1309, Mary-Ann Liebert Inc. publishers, 2009.
Article : .pdf
- [11] Carl Herrmann, Sèverine Bérard and Laurent Tichit. SimCT: a generic tool to visualize ontology-based relationships for biological objects, Bioinformatics 25(23): 3197-3198, 2009.
Article : .pdf - Supplementary material: .pdf
- [12] Sèverine Bérard, Cedric Chauve and Christophe Paul. A more efficient algorithm for perfect sorting by reversals}, Information Processing Letters (IPL), Volume 106, Issue 3, 30 April 2008, Pages 90-95.
Article : .pdf
- [13] Sèverine Bérard, Anne Bergeron, Cedric Chauve and Christophe Paul. Perfect sorting by reversal is not always difficult}, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 4, no 1, p 4-16, 2007.
Article : .pdf
- [14] Sèverine Bérard, François Nicolas, Jérôme Buard, Olivier Gascuel and Éric Rivals. A fast and specific alignment method for minisatellite maps, Evolutionary Bioinformatics Online (EBO) 2006:2 327-344/
Article : .ps, .pdf
- [15] Sèverine Bérard and Éric Rivals. Comparison of Minisatellites, Journal of Computational biology (JCB), 10(3-4), pages 357-72, Mary-Ann Liebert Inc. publishers, 2003.
Article : .ps, .pdf - Ref : .bib
Internationals conferences
- [1] Yoann Anselmetti, Wandrille Duchemin, Éric Tannier, Cedric Chauve, and Sèverine Bérard. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes, APBC 2018, The Sixteenth Asia Pacific Bioinformatics Conference, Yokohama, Japan, 15-17 January 2018
Article : .pdf
- [2] Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Éric Tannier and Sèverine Bérard. Ancestral gene synteny reconstruction improves extant species scaffolding, RECOMB-CG, 4-7 October 2015, Frankfurt, Germany.
- [3] Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely J. Szollosi, Vincent Daubin and Éric Tannier. Evolution of gene neighborhoods within reconciled phylogenies, 11th European Conference on Computational Biology (ECCB'12), 9-12 September 2012, Basel, Switzerland.
- [4] Sèverine Bérard, Annie Chateau, Cedric Chauve, Christophe Paul and Éric Tannier. Perfect DCJ rearrangement, 6th RECOMB Comparative Genomics
Satellite Workshop, 13-15 October 2008, Paris, France.
Article : .pdf
- [5] Cédric Gaucherel, François Munoz and Sèverine Bérard. Equation against Algorithm: Which differences and which one to choose?, European conference on Computing And Philosophy (E-CAP 2008), 16-18 June 2008, Montpellier, France.
Article : .doc
- [6] Sèverine Bérard, Anne Bergeron, Cedric Chauve and Christophe Paul. Perfect sorting by reversal is not always difficult,
5th Workshop on Algorithms in Bioinformatics (WABI05), 3-6 October 2005, Palma de Majorque.
Article : .pdf
- [7] Sèverine Bérard, Anne Bergeron and Cedric Chauve. Conservation
of Combinatorial Structures in Evolution Scenarios,
2nd RECOMB Comparative Genomics Satellite Workshop (RGC), 16-19
October 2004, University of Bologna, Italy.
Series: Lecture Notes in Computer Science, Subseries: Lecture Notes in Bioinformatics, Vol. 3388, Pages 1-15. Lagergren, Jens (Ed.)
Article: .ps - Slides : .ppt - Ref : .bib
- [8] Sèverine Bérard and Éric Rivals. Comparison of Minisatellites, Proceedings of the Sixth Annual International Conference on Computational Biology (RECOMB02), pages 67-76, Washington, DC, USA, ACM press, 2002.
Article : .ps, .pdf - Slides : .ps, .pdf - Ref : .bib
Book chapter
- [1] Éric Tannier, Adelme Bazin, Adrian Davin, Laurent Guéguen, Sèverine Bérard, and Cedric Chauve. Ancestral genome organization as a diagnosis tool for phylogenomics, pp.2.5:1–2.5:19, in Scornavacca, Celine ; Delsuc, Frédéric ; Galtier, Nicolas. Phylogenetics in the
Genomic Era, No commercial publisher | Authors open access book. 2020.
- [2] Yoann Anselmetti, Nina Luhmann, Sèverine Bérard, Éric Tannier and Cedric Chauve. Comparative Methods for Reconstructing Ancient
Genomes Organization, p. 343-362, in J. Setubal, J. Stoye, P. Stadler (eds) Comparative Genomics. Methods in Molecular Biology, vol 1704. Humana Press, New York, NY
DOI. 2018. ISEM 2016-102
Nationals conferences
- [1] Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Éric Tannier and Sèverine Bérard. Comment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels, Actes des Journées Ouvertes Biologie Informatique Mathématiques (JOBIM16), pages 83-87, Lyon, 2016.
Article : .pdf
- [2] Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron and Krister Swenson. Aligning the unalignable: bacteriophage whole genome alignments. Colloque Interactions Phages-Bactéries : du
fondamental à l'appliqué, 19-20 novembre, Montpellier. 2015.
Slides : .pdf
- [3] Sèverine Bérard, Laurent Tichit and Carl Herrmann.
ClusterInspector SimCT, a tool to visualize ontology based relationships, Actes des Journées Ouvertes Biologie Informatique Mathématiques (JOBIM05), pages 447-457, Lyon, 2005.
Article : .pdf - Slides : .pdf - Ref : .bib - Logiciel : SimCT
- [4] Éric Rivals and Sèverine Bérard. Alignement de séquences avec
opérations non-commutatives, Actes des quatrièmes journées
francophones de recherche opérationnelle (FRANCORO IV), page 16, Fribourg, Suisse, 2004.
Résumé dans les actes - Ref : .bib
- [5] Sèverine Bérard and Éric Rivals. Comparaison de séquences avec amplifications et contractions, 5ème congrès de la société Française de Recherche Opérationnelle et d'Aide à la Décision (ROADEF'03), pages 169-170, Avignon, 2003.
Article : .ps, .pdf - Slides : .ps, .pdf - Ref : .bib
- [6] Sèverine Bérard and Éric Rivals. Comparaison de minisatellites, Actes des Journées Ouvertes Biologie Informatique Mathématiques (JOBIM02), pages 261-262, Saint-Malo, 2002.
Article : .ps, .pdf - Slides : .ps, .pdf - Ref : .bib
- [7] Sèverine Bérard and Éric Rivals. Comparaison de minisatellites, Actes de la 24ème réunion annuelle du Groupe de Génétique et Biologie des Populations (PPD), page 128, Montpellier, 2002.
Article : .ps, .pdf - Slides : .ps, .pdf - Ref : .bib
PhD thesis/H.D.R. (in french only)
- [1] Sèverine Bérard. Comparaison de séquences répétées en tandem et application à la génétique, Université Montpellier II, LIRMM, 2003.
Thesis : .ps, .pdf - Slides : .pdf - Ref : .bib
- [2] Sèverine Bérard. Histoires évolutives et autres comptes. Algorithmes et graphes pour la bioinformatique, Université de Montpellier, 2016.
H.D.R. : website
Miscellaneous (in french only)
- [1] Sèverine Bérard. Alignement de séquences : application à la comparaison de chaînes d'ADN, Proceedings J'Docs 2003 XIèmes Journées des Doctorants, Université Montpellier II, 2003.
Article : .ps, .pdf - Slides : .ps, .pdf
- [2] Sèverine Bérard. Reconstruction d'histoire de répétitions en tandem, Rapport de DEA, Tuteur de stage : Éric Rivals, Université Montpellier II, LIRMM, 2000.
Rapport : .ps
