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Maximum likelihood tree estimation using codon substitution models with multiple partitions.

Zoller S, Boskova V, Anisimova M.

Mol Biol Evol. 2015 Apr 23. pii: msv097. [Epub ahead of print]


Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.

Anisimova M, Pečerska J, Schaper E.

Front Bioeng Biotechnol. 2015 Mar 17;3:31. doi: 10.3389/fbioe.2015.00031. eCollection 2015. Review.


Antibody-specific model of amino acid substitution for immunological inferences from alignments of antibody sequences.

Mirsky A, Kazandjian L, Anisimova M.

Mol Biol Evol. 2015 Mar;32(3):806-19. doi: 10.1093/molbev/msu340. Epub 2014 Dec 21.


The evolution and function of protein tandem repeats in plants.

Schaper E, Anisimova M.

New Phytol. 2015 Apr;206(1):397-410. doi: 10.1111/nph.13184. Epub 2014 Nov 24.


Natural selection on coding and noncoding DNA sequences is associated with virulence genes in a plant pathogenic fungus.

Rech GE, Sanz-Martín JM, Anisimova M, Sukno SA, Thon MR.

Genome Biol Evol. 2014 Sep 4;6(9):2368-79. doi: 10.1093/gbe/evu192.


Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families.

Dimitrieva S, Anisimova M.

PLoS One. 2014 Jun 4;9(6):e95034. doi: 10.1371/journal.pone.0095034. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e102721.


Deep conservation of human protein tandem repeats within the eukaryotes.

Schaper E, Gascuel O, Anisimova M.

Mol Biol Evol. 2014 May;31(5):1132-48. doi: 10.1093/molbev/msu062. Epub 2014 Feb 3.


Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex.

Peeters N, Carrère S, Anisimova M, Plener L, Cazalé AC, Genin S.

BMC Genomics. 2013 Dec 6;14:859. doi: 10.1186/1471-2164-14-859.


State-of the art methodologies dictate new standards for phylogenetic analysis.

Anisimova M, Liberles DA, Philippe H, Provan J, Pupko T, von Haeseler A.

BMC Evol Biol. 2013 Aug 1;13:161. doi: 10.1186/1471-2148-13-161. Review.


Graph-based modeling of tandem repeats improves global multiple sequence alignment.

Szalkowski AM, Anisimova M.

Nucleic Acids Res. 2013 Sep;41(17):e162. doi: 10.1093/nar/gkt628. Epub 2013 Jul 22.


CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models.

Gil M, Zanetti MS, Zoller S, Anisimova M.

Mol Biol Evol. 2013 Jun;30(6):1270-80. doi: 10.1093/molbev/mst034. Epub 2013 Feb 23.


Repeat or not repeat?--Statistical validation of tandem repeat prediction in genomic sequences.

Schaper E, Kajava AV, Hauser A, Anisimova M.

Nucleic Acids Res. 2012 Nov 1;40(20):10005-17. doi: 10.1093/nar/gks726. Epub 2012 Aug 25.


Gene copy number variation and its significance in cyanobacterial phylogeny.

Schirrmeister BE, Dalquen DA, Anisimova M, Bagheri HC.

BMC Microbiol. 2012 Aug 15;12:177. doi: 10.1186/1471-2180-12-177.


Selection on the protein-coding genome.

Kosiol C, Anisimova M.

Methods Mol Biol. 2012;856:113-40. doi: 10.1007/978-1-61779-585-5_5.


ALF--a simulation framework for genome evolution.

Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C.

Mol Biol Evol. 2012 Apr;29(4):1115-23. doi: 10.1093/molbev/msr268. Epub 2011 Dec 8.


Evolution of cyanobacterial morphotypes: Taxa required for improved phylogenomic approaches.

Schirrmeister BE, Anisimova M, Antonelli A, Bagheri HC.

Commun Integr Biol. 2011 Jul;4(4):424-7. doi: 10.4161/cib.4.4.16183. Epub 2011 Jul 1.


Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco.

Wang M, Kapralov MV, Anisimova M.

BMC Evol Biol. 2011 Sep 23;11:266. doi: 10.1186/1471-2148-11-266.


Functional diversification of the GALA type III effector family contributes to Ralstonia solanacearum adaptation on different plant hosts.

Remigi P, Anisimova M, Guidot A, Genin S, Peeters N.

New Phytol. 2011 Dec;192(4):976-87. doi: 10.1111/j.1469-8137.2011.03854.x. Epub 2011 Sep 8.


Complex interplay of evolutionary forces in the ladybird homeobox genes of Drosophila melanogaster.

Balakirev ES, Anisimova M, Ayala FJ.

PLoS One. 2011;6(7):e22613. doi: 10.1371/journal.pone.0022613. Epub 2011 Jul 22.

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