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Items: 1 to 20 of 106

1.

Linear-time algorithms for the multiple gene duplication problems.

Luo CW, Chen MC, Chen YC, Yang RW, Liu HF, Chao KM.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):260-5. doi: 10.1109/TCBB.2009.52.

PMID:
21071814
2.

Genomic duplication problems for unrooted gene trees.

Paszek J, Górecki P.

BMC Genomics. 2016 Jan 11;17 Suppl 1:15. doi: 10.1186/s12864-015-2308-4.

3.

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem.

Górecki P, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S14. doi: 10.1186/1471-2105-13-S10-S14.

4.

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence.

Chaudhary R, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S11. doi: 10.1186/1471-2105-13-S10-S11.

5.

Efficient algorithms for knowledge-enhanced supertree and supermatrix phylogenetic problems.

Wehe A, Burleigh JG, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec;10(6):1432-41. doi: 10.1109/TCBB.2012.162.

PMID:
24407302
6.

The gene-duplication problem: near-linear time algorithms for NNI-based local searches.

Bansal MS, Eulenstein O, Wehe A.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):221-31. doi: 10.1109/TCBB.2009.7.

PMID:
19407347
7.

A simple algorithm to infer gene duplication and speciation events on a gene tree.

Zmasek CM, Eddy SR.

Bioinformatics. 2001 Sep;17(9):821-8.

PMID:
11590098
8.

Species Tree Inference Using a Mixture Model.

Ullah I, Parviainen P, Lagergren J.

Mol Biol Evol. 2015 Sep;32(9):2469-82. doi: 10.1093/molbev/msv115. Epub 2015 May 11.

PMID:
25963975
9.

Optimal gene trees from sequences and species trees using a soft interpretation of parsimony.

Berglund-Sonnhammer AC, Steffansson P, Betts MJ, Liberles DA.

J Mol Evol. 2006 Aug;63(2):240-50. Epub 2006 Jul 7.

PMID:
16830091
10.

The multiple gene duplication problem revisited.

Bansal MS, Eulenstein O.

Bioinformatics. 2008 Jul 1;24(13):i132-8. doi: 10.1093/bioinformatics/btn150.

11.

Gene family evolution by duplication, speciation, and loss.

Chauve C, Doyon JP, El-Mabrouk N.

J Comput Biol. 2008 Oct;15(8):1043-62. doi: 10.1089/cmb.2008.0054.

PMID:
18781833
12.

Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants.

Burleigh JG, Bansal MS, Wehe A, Eulenstein O.

J Comput Biol. 2009 Aug;16(8):1071-83. doi: 10.1089/cmb.2009.0139.

PMID:
19689214
13.

Exact solutions for species tree inference from discordant gene trees.

Chang WC, Górecki P, Eulenstein O.

J Bioinform Comput Biol. 2013 Oct;11(5):1342005. doi: 10.1142/S0219720013420055. Epub 2013 Oct 2.

PMID:
24131054
14.

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.

Górecki P, Burleigh GJ, Eulenstein O.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S15. doi: 10.1186/1471-2105-12-S1-S15.

15.

Inferring optimal species trees under gene duplication and loss.

Bayzid MS, Mirarab S, Warnow T.

Pac Symp Biocomput. 2013:250-61.

16.

Zinc finger gene clusters and tandem gene duplication.

Tang M, Waterman M, Yooseph S.

J Comput Biol. 2002;9(2):429-46.

PMID:
12015891
17.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

18.

A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem.

Bansal MS, Shamir R.

IEEE/ACM Trans Comput Biol Bioinform. 2011 May-Jun;8(3):848-50. doi: 10.1109/TCBB.2010.74.

PMID:
20733245
19.

Reconciliation of gene and species trees.

Rusin LY, Lyubetskaya EV, Gorbunov KY, Lyubetsky VA.

Biomed Res Int. 2014;2014:642089. doi: 10.1155/2014/642089. Epub 2014 Mar 27.

20.

A hybrid micro-macroevolutionary approach to gene tree reconstruction.

Durand D, Halldórsson BV, Vernot B.

J Comput Biol. 2006 Mar;13(2):320-35.

PMID:
16597243

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