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Bayesian modeling of recombination events in bacterial populations.

Marttinen P, Baldwin A, Hanage WP, Dowson C, Mahenthiralingam E, Corander J.

BMC Bioinformatics. 2008 Oct 7;9:421. doi: 10.1186/1471-2105-9-421.


Bayesian semi-supervised classification of bacterial samples using MLST databases.

Cheng L, Connor TR, Aanensen DM, Spratt BG, Corander J.

BMC Bioinformatics. 2011 Jul 26;12:302. doi: 10.1186/1471-2105-12-302.


SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.

Paraskevis D, Deforche K, Lemey P, Magiorkinis G, Hatzakis A, Vandamme AM.

Bioinformatics. 2005 Apr 1;21(7):1274-5. Epub 2004 Nov 16.


Identifying currents in the gene pool for bacterial populations using an integrative approach.

Tang J, Hanage WP, Fraser C, Corander J.

PLoS Comput Biol. 2009 Aug;5(8):e1000455. doi: 10.1371/journal.pcbi.1000455. Epub 2009 Aug 7.


Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations.

Corander J, Marttinen P, Sirén J, Tang J.

BMC Bioinformatics. 2008 Dec 16;9:539. doi: 10.1186/1471-2105-9-539.


TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments.

Milne I, Wright F, Rowe G, Marshall DF, Husmeier D, McGuire G.

Bioinformatics. 2004 Jul 22;20(11):1806-7. Epub 2004 Feb 26.


GARD: a genetic algorithm for recombination detection.

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD.

Bioinformatics. 2006 Dec 15;22(24):3096-8. Epub 2006 Nov 16.


PhyloPat: phylogenetic pattern analysis of eukaryotic genes.

Hulsen T, de Vlieg J, Groenen PM.

BMC Bioinformatics. 2006 Sep 1;7:398.


Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences.

Mrázek J, Xie S.

Bioinformatics. 2006 Dec 15;22(24):3099-100. Epub 2006 Nov 8.


Dual multiple change-point model leads to more accurate recombination detection.

Minin VN, Dorman KS, Fang F, Suchard MA.

Bioinformatics. 2005 Jul 1;21(13):3034-42. Epub 2005 May 24.


Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.

Brendel V, Xing L, Zhu W.

Bioinformatics. 2004 May 1;20(7):1157-69. Epub 2004 Feb 5.


Haplotypes histories as pathways of recombinations.

El-Mabrouk N, Labuda D.

Bioinformatics. 2004 Aug 12;20(12):1836-41. Epub 2004 Feb 26.


Splice site identification by idlBNs.

Castelo R, Guigó R.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i69-76.


Detecting interspecific recombination with a pruned probabilistic divergence measure.

Husmeier D, Wright F, Milne I.

Bioinformatics. 2005 May 1;21(9):1797-806. Epub 2004 Nov 30.


RDP2: recombination detection and analysis from sequence alignments.

Martin DP, Williamson C, Posada D.

Bioinformatics. 2005 Jan 15;21(2):260-2. Epub 2004 Sep 17.


Spectrum: joint Bayesian inference of population structure and recombination events.

Sohn KA, Xing EP.

Bioinformatics. 2007 Jul 1;23(13):i479-89.


Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures.

Chowdhary R, Tan SL, Ali RA, Boerlage B, Wong L, Bajic VB.

Bioinformatics. 2006 Sep 15;22(18):2310-2. Epub 2006 Apr 13.

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