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Items: 46

1.

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

Anselmetti Y, Duchemin W, Tannier E, Chauve C, Bérard S.

BMC Genomics. 2018 May 9;19(Suppl 2):96. doi: 10.1186/s12864-018-4466-7.

2.

RecPhyloXML: a format for reconciled gene trees.

Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier É, Daubin V.

Bioinformatics. 2018 Nov 1;34(21):3646-3652. doi: 10.1093/bioinformatics/bty389.

3.

Gene transfers can date the tree of life.

Davín AA, Tannier E, Williams TA, Boussau B, Daubin V, Szöllősi GJ.

Nat Ecol Evol. 2018 May;2(5):904-909. doi: 10.1038/s41559-018-0525-3. Epub 2018 Apr 2.

4.

Comparative Methods for Reconstructing Ancient Genome Organization.

Anselmetti Y, Luhmann N, Bérard S, Tannier E, Chauve C.

Methods Mol Biol. 2018;1704:343-362. doi: 10.1007/978-1-4939-7463-4_13.

PMID:
29277873
5.

Algorithms for computing the double cut and join distance on both gene order and intergenic sizes.

Fertin G, Jean G, Tannier E.

Algorithms Mol Biol. 2017 Jun 5;12:16. doi: 10.1186/s13015-017-0107-y. eCollection 2017.

6.

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.

Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Bérard S, Chauve C, Scornavacca C, Daubin V, Tannier E.

Genome Biol Evol. 2017 May 1;9(5):1312-1319. doi: 10.1093/gbe/evx069.

7.

Francisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?

Lays C, Tannier E, Henry T.

Microb Cell. 2016 Oct 29;3(11):576-578. doi: 10.15698/mic2016.11.543.

8.

Genome rearrangements with indels in intergenes restrict the scenario space.

Bulteau L, Fertin G, Tannier E.

BMC Bioinformatics. 2016 Nov 11;17(Suppl 14):426. doi: 10.1186/s12859-016-1264-6.

9.

Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses.

Jacox E, Weller M, Tannier E, Scornavacca C.

Bioinformatics. 2017 Apr 1;33(7):980-987. doi: 10.1093/bioinformatics/btw778.

PMID:
28073758
10.

Efficient Gene Tree Correction Guided by Genome Evolution.

Noutahi E, Semeria M, Lafond M, Seguin J, Boussau B, Guéguen L, El-Mabrouk N, Tannier E.

PLoS One. 2016 Aug 11;11(8):e0159559. doi: 10.1371/journal.pone.0159559. eCollection 2016.

11.

Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation.

Biller P, Guéguen L, Knibbe C, Tannier E.

Genome Biol Evol. 2016 May 22;8(5):1427-39. doi: 10.1093/gbe/evw083.

12.

Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies.

Semeria M, Tannier E, Guéguen L.

BMC Bioinformatics. 2015;16 Suppl 14:S5. doi: 10.1186/1471-2105-16-S14-S5. Epub 2015 Oct 2.

13.

Moments of genome evolution by Double Cut-and-Join.

Biller P, Guéguen L, Tannier E.

BMC Bioinformatics. 2015;16 Suppl 14:S7. doi: 10.1186/1471-2105-16-S14-S7. Epub 2015 Oct 2.

14.

Ancestral gene synteny reconstruction improves extant species scaffolding.

Anselmetti Y, Berry V, Chauve C, Chateau A, Tannier E, Bérard S.

BMC Genomics. 2015;16 Suppl 10:S11. doi: 10.1186/1471-2164-16-S10-S11. Epub 2015 Oct 2.

15.

Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence.

Duchemin W, Daubin V, Tannier E.

BMC Genomics. 2015;16 Suppl 10:S9. doi: 10.1186/1471-2164-16-S10-S9. Epub 2015 Oct 2.

16.

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi.

Szöllősi GJ, Davín AA, Tannier E, Daubin V, Boussau B.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140335. doi: 10.1098/rstb.2014.0335.

17.

Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.

Murat F, Zhang R, Guizard S, Gavranović H, Flores R, Steinbach D, Quesneville H, Tannier E, Salse J.

Genome Biol Evol. 2015 Jan 29;7(3):735-49. doi: 10.1093/gbe/evv014.

18.

The inference of gene trees with species trees.

Szöllősi GJ, Tannier E, Daubin V, Boussau B.

Syst Biol. 2015 Jan;64(1):e42-62. doi: 10.1093/sysbio/syu048. Epub 2014 Jul 28. Review. Erratum in: Syst Biol. 2016 Jan;65(1):180.

19.

Gene tree correction guided by orthology.

Lafond M, Semeria M, Swenson KM, Tannier E, El-Mabrouk N.

BMC Bioinformatics. 2013;14 Suppl 15:S5. doi: 10.1186/1471-2105-14-S15-S5. Epub 2013 Oct 15.

20.

Lateral gene transfer, rearrangement, reconciliation.

Patterson M, Szöllősi G, Daubin V, Tannier E.

BMC Bioinformatics. 2013;14 Suppl 15:S4. doi: 10.1186/1471-2105-14-S15-S4. Epub 2013 Oct 15.

21.

FPSAC: fast phylogenetic scaffolding of ancient contigs.

Rajaraman A, Tannier E, Chauve C.

Bioinformatics. 2013 Dec 1;29(23):2987-94. doi: 10.1093/bioinformatics/btt527. Epub 2013 Sep 24.

PMID:
24068034
22.

Efficient exploration of the space of reconciled gene trees.

Szöllõsi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V.

Syst Biol. 2013 Nov;62(6):901-12. doi: 10.1093/sysbio/syt054. Epub 2013 Aug 6.

23.

Lateral gene transfer from the dead.

Szöllosi GJ, Tannier E, Lartillot N, Daubin V.

Syst Biol. 2013 May 1;62(3):386-97. doi: 10.1093/sysbio/syt003. Epub 2013 Jan 25.

24.

Linearization of ancestral multichromosomal genomes.

Maňuch J, Patterson M, Wittler R, Chauve C, Tannier E.

BMC Bioinformatics. 2012;13 Suppl 19:S11. doi: 10.1186/1471-2105-13-S19-S11. Epub 2012 Dec 19.

25.

Genome-scale coestimation of species and gene trees.

Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V.

Genome Res. 2013 Feb;23(2):323-30. doi: 10.1101/gr.141978.112. Epub 2012 Nov 6.

26.

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations.

Szöllosi GJ, Boussau B, Abby SS, Tannier E, Daubin V.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17513-8. doi: 10.1073/pnas.1202997109. Epub 2012 Oct 4.

27.

Evolution of gene neighborhoods within reconciled phylogenies.

Bérard S, Gallien C, Boussau B, Szöllősi GJ, Daubin V, Tannier E.

Bioinformatics. 2012 Sep 15;28(18):i382-i388. doi: 10.1093/bioinformatics/bts374.

28.

ANGES: reconstructing ANcestral GEnomeS maps.

Jones BR, Rajaraman A, Tannier E, Chauve C.

Bioinformatics. 2012 Sep 15;28(18):2388-90. doi: 10.1093/bioinformatics/bts457. Epub 2012 Jul 20.

PMID:
22820205
29.

Lateral gene transfer as a support for the tree of life.

Abby SS, Tannier E, Gouy M, Daubin V.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4962-7. doi: 10.1073/pnas.1116871109. Epub 2012 Mar 13.

30.

Reconstructing the architecture of the ancestral amniote genome.

Ouangraoua A, Tannier E, Chauve C.

Bioinformatics. 2011 Oct 1;27(19):2664-71. doi: 10.1093/bioinformatics/btr461. Epub 2011 Aug 16.

PMID:
21846735
31.

Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.

Gavranović H, Chauve C, Salse J, Tannier E.

Bioinformatics. 2011 Jul 1;27(13):i257-65. doi: 10.1093/bioinformatics/btr224.

32.

Bayesian sampling of genomic rearrangement scenarios via double cut and join.

Miklós I, Tannier E.

Bioinformatics. 2010 Dec 15;26(24):3012-9. doi: 10.1093/bioinformatics/btq574. Epub 2010 Oct 29.

PMID:
21037244
33.

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.

Genome Res. 2010 Nov;20(11):1545-57. doi: 10.1101/gr.109744.110. Epub 2010 Sep 28.

34.

Yeast ancestral genome reconstructions: the possibilities of computational methods II.

Chauve C, Gavranovic H, Ouangraoua A, Tannier E.

J Comput Biol. 2010 Sep;17(9):1097-112. doi: 10.1089/cmb.2010.0092.

PMID:
20874398
35.

Palaeogenomics of plants: synteny-based modelling of extinct ancestors.

Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C, Salse J.

Trends Plant Sci. 2010 Sep;15(9):479-87. doi: 10.1016/j.tplants.2010.06.001. Epub 2010 Jul 17.

PMID:
20638891
36.

Cassis: detection of genomic rearrangement breakpoints.

Baudet C, Lemaitre C, Dias Z, Gautier C, Tannier E, Sagot MF.

Bioinformatics. 2010 Aug 1;26(15):1897-8. doi: 10.1093/bioinformatics/btq301. Epub 2010 Jun 23.

37.

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.

Abby SS, Tannier E, Gouy M, Daubin V.

BMC Bioinformatics. 2010 Jun 15;11:324. doi: 10.1186/1471-2105-11-324.

39.

Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes.

Bérard S, Chateau A, Chauve C, Paul C, Tannier E.

J Comput Biol. 2009 Oct;16(10):1287-309. doi: 10.1089/cmb.2009.0088.

PMID:
19803733
40.

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation.

Lemaitre C, Zaghloul L, Sagot MF, Gautier C, Arneodo A, Tannier E, Audit B.

BMC Genomics. 2009 Jul 24;10:335. doi: 10.1186/1471-2164-10-335.

41.

Multichromosomal median and halving problems under different genomic distances.

Tannier E, Zheng C, Sankoff D.

BMC Bioinformatics. 2009 Apr 22;10:120. doi: 10.1186/1471-2105-10-120.

42.

Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes.

Lemaitre C, Braga MD, Gautier C, Sagot MF, Tannier E, Marais GA.

Genome Biol Evol. 2009 Apr 30;1:56-66. doi: 10.1093/gbe/evp006.

43.

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

Chauve C, Tannier E.

PLoS Comput Biol. 2008 Nov;4(11):e1000234. doi: 10.1371/journal.pcbi.1000234. Epub 2008 Nov 28.

44.

Exploring the solution space of sorting by reversals, with experiments and an application to evolution.

Braga MD, Sagot MF, Scornavacca C, Tannier E.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jul-Sep;5(3):348-56. doi: 10.1109/TCBB.2008.16.

PMID:
18670039
45.

Precise detection of rearrangement breakpoints in mammalian chromosomes.

Lemaitre C, Tannier E, Gautier C, Sagot MF.

BMC Bioinformatics. 2008 Jun 18;9:286. doi: 10.1186/1471-2105-9-286.

46.

Evolution under reversals: parsimony and conservation of common intervals.

Diekmann Y, Sagot MF, Tannier E.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Apr-Jun;4(2):301-9.

PMID:
17473322

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