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A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
Chauve C, Tannier E. Chauve C, et al. Among authors: tannier e. PLoS Comput Biol. 2008 Nov;4(11):e1000234. doi: 10.1371/journal.pcbi.1000234. Epub 2008 Nov 28. PLoS Comput Biol. 2008. PMID: 19043541 Free PMC article.
Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae.
Gavranović H, Tannier E. Gavranović H, et al. Among authors: tannier e. Pac Symp Biocomput. 2010:21-30. Pac Symp Biocomput. 2010. PMID: 19908354
Yeast ancestral genome reconstructions: the possibilities of computational methods II.
Chauve C, Gavranovic H, Ouangraoua A, Tannier E. Chauve C, et al. Among authors: tannier e. J Comput Biol. 2010 Sep;17(9):1097-112. doi: 10.1089/cmb.2010.0092. J Comput Biol. 2010. PMID: 20874398
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution.
Murat F, Xu JH, Tannier E, Abrouk M, Guilhot N, Pont C, Messing J, Salse J. Murat F, et al. Among authors: tannier e. Genome Res. 2010 Nov;20(11):1545-57. doi: 10.1101/gr.109744.110. Epub 2010 Sep 28. Genome Res. 2010. PMID: 20876790 Free PMC article.
Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.
Gavranović H, Chauve C, Salse J, Tannier E. Gavranović H, et al. Among authors: tannier e. Bioinformatics. 2011 Jul 1;27(13):i257-65. doi: 10.1093/bioinformatics/btr224. Bioinformatics. 2011. PMID: 21685079 Free PMC article.
Reconstructing the architecture of the ancestral amniote genome.
Ouangraoua A, Tannier E, Chauve C. Ouangraoua A, et al. Among authors: tannier e. Bioinformatics. 2011 Oct 1;27(19):2664-71. doi: 10.1093/bioinformatics/btr461. Epub 2011 Aug 16. Bioinformatics. 2011. PMID: 21846735
ANGES: reconstructing ANcestral GEnomeS maps.
Jones BR, Rajaraman A, Tannier E, Chauve C. Jones BR, et al. Among authors: tannier e. Bioinformatics. 2012 Sep 15;28(18):2388-90. doi: 10.1093/bioinformatics/bts457. Epub 2012 Jul 20. Bioinformatics. 2012. PMID: 22820205
Linearization of ancestral multichromosomal genomes.
Maňuch J, Patterson M, Wittler R, Chauve C, Tannier E. Maňuch J, et al. Among authors: tannier e. BMC Bioinformatics. 2012;13 Suppl 19(Suppl 19):S11. doi: 10.1186/1471-2105-13-S19-S11. Epub 2012 Dec 19. BMC Bioinformatics. 2012. PMID: 23281593 Free PMC article.
FPSAC: fast phylogenetic scaffolding of ancient contigs.
Rajaraman A, Tannier E, Chauve C. Rajaraman A, et al. Among authors: tannier e. Bioinformatics. 2013 Dec 1;29(23):2987-94. doi: 10.1093/bioinformatics/btt527. Epub 2013 Sep 24. Bioinformatics. 2013. PMID: 24068034
Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence.
Duchemin W, Daubin V, Tannier E. Duchemin W, et al. Among authors: tannier e. BMC Genomics. 2015;16 Suppl 10(Suppl 10):S9. doi: 10.1186/1471-2164-16-S10-S9. Epub 2015 Oct 2. BMC Genomics. 2015. PMID: 26450112 Free PMC article.
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