BioHMM: a heterogeneous hidden Markov model for se...[Bioinformatics. 2006]

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1: Bioinformatics. 2006 May 1;22(9):1144-6. Epub 2006 Mar 13. Links

BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data.

Marioni JC, Thorne NP, Tavaré S.

Hutchison-MRC Research Centre, Department of Oncology, Computational Biology Group, University of Cambridge Hills Road, Cambridge. J.Marioni@damtp.cam.ac.uk

SUMMARY: We have developed a new method (BioHMM) for segmenting array comparative genomic hybridization data into states with the same underlying copy number. By utilizing a heterogeneous hidden Markov model, BioHMM incorporates relevant biological factors (e.g. the distance between adjacent clones) in the segmentation process.

PMID: 16533818 [PubMed - indexed for MEDLINE]

Continuous-index hidden Markov modelling of array CGH copy number data.
Bioinformatics. 2007 Apr 15; 23(8):1006-14. Epub 2007 Feb 19.

[Bioinformatics. 2007]
A segmentation/clustering model for the analysis of array CGH data.
Biometrics. 2007 Sep; 63(3):758-66.

[Biometrics. 2007]
A segmental maximum a posteriori approach to genome-wide copy number profiling.
Bioinformatics. 2008 Mar 15; 24(6):751-8. Epub 2008 Jan 19.

[Bioinformatics. 2008]
ReviewRecent advances in array comparative genomic hybridization technologies and their applications in human genetics.
Eur J Hum Genet. 2006 Feb; 14(2):139-48.

[Eur J Hum Genet. 2006]
ReviewAn introduction to hidden Markov models.
Curr Protoc Bioinformatics. 2007 Jun; Appendix 3:Appendix 3A.

[Curr Protoc Bioinformatics. 2007]
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Cited by 15 PubMed Central articles

Normalized, Segmented or Called aCGH Data?
van Wieringen WN, van de Wiel MA, Ylstra B. Cancer Inform. 2007 Sep 17; 3:321-7. Epub 2007 Sep 17.

[Cancer Inform. 2007]
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.
Bengtsson H, Ray A, Spellman P, Speed TP. Bioinformatics. 2009 Apr 1; 25(7):861-7. Epub 2009 Feb 4.

[Bioinformatics. 2009]
Bayesian DNA copy number analysis.
Rancoita PM, Hutter M, Bertoni F, Kwee I. BMC Bioinformatics. 2009 Jan 8; 10:10. Epub 2009 Jan 8.

[BMC Bioinformatics. 2009]
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