Skip Navigation



Bioinformatics Advance Access published online on March 13, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl089
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
22/9/1144    most recent
btl089v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Marioni, J. C.
Right arrow Articles by Tavaré, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Marioni, J. C.
Right arrow Articles by Tavaré, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 24, 2005
Revised February 7, 2006
Accepted March 7, 2006

Applications note

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

J. C. Marioni 1 *, N. P. Thorne 1, and S. Tavaré 1

1 University of Cambridge, Department of Oncology, Computational Biology Group, Hutchison-MRC Research Centre, Hills Road, Cambridge; University of Cambridge, Department of Applied Mathematics and Theoretical Physics, Wilberforce Road, Cambridge

* To whom correspondence should be addressed.
J. C. Marioni, E-mail: J.Marioni{at}damtp.cam.ac.uk


  Abstract

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

Availability: BioHMM is available as part of the R library snapCGH which can be downloaded from http://www.bioconductor.org/packages/bioc/1.8/html/snapCGH.html.

Supplementary Information: Supplementary information is available at http://www.damtp.cam.ac.uk/user/jcm68/BioHMM.html.

Associate Editor: Christos Ouzounis
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BiostatisticsHome page
S. Stjernqvist and T. Ryden
A continuous-index hidden Markov jump process for modeling DNA copy number data
Biostat., October 1, 2009; 10(4): 773 - 778.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. Nicolas, A. Leduc, S. Robin, S. Rasmussen, H. Jarmer, and P. Bessieres
Transcriptional landscape estimation from tiling array data using a model of signal shift and drift
Bioinformatics, September 15, 2009; 25(18): 2341 - 2347.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Bicciato, R. Spinelli, M. Zampieri, E. Mangano, F. Ferrari, L. Beltrame, I. Cifola, C. Peano, A. Solari, and C. Battaglia
A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets
Nucleic Acids Res., August 1, 2009; 37(15): 5057 - 5070.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
O. M. Rueda and R. Diaz-Uriarte
RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions
Bioinformatics, August 1, 2009; 25(15): 1959 - 1960.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
B. Daines, H. Wang, Y. Li, Y. Han, R. Gibbs, and R. Chen
High-Throughput Multiplex Sequencing to Discover Copy Number Variants in Drosophila
Genetics, August 1, 2009; 182(4): 935 - 941.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
B. Nilsson, M. Johansson, F. Al-Shahrour, A. E. Carpenter, and B. L. Ebert
Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution
Bioinformatics, April 15, 2009; 25(8): 1078 - 1079.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Bengtsson, A. Ray, P. Spellman, and T. P. Speed
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods
Bioinformatics, April 1, 2009; 25(7): 861 - 867.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. Budinska, E. Gelnarova, and M. G. Schimek
MSMAD: a computationally efficient method for the analysis of noisy array CGH data
Bioinformatics, March 15, 2009; 25(6): 703 - 713.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Zhang
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays
Bioinformatics, December 15, 2008; 24(24): 2825 - 2831.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H.-I H. Chen, F.-H. Hsu, Y. Jiang, M.-H. Tsai, P.-C. Yang, P. S. Meltzer, E. Y. Chuang, and Y. Chen
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization
Bioinformatics, August 15, 2008; 24(16): 1749 - 1756.
[Abstract] [Full Text] [PDF]

Home page
 CSH ProtocolsHome page
K. Wang and M. Bucan
Copy Number Variation Detection via High-Density SNP Genotyping
CSH Protocols, June 1, 2008; 2008(7): pdb.top46 - pdb.top46.
[Abstract] [Full Text]

Home page
 Nucleic Acids ResHome page
P. Cahan, L. E. Godfrey, P. S. Eis, T. A. Richmond, R. R. Selzer, M. Brent, H. L. McLeod, T. J. Ley, and T. A. Graubert
wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data
Nucleic Acids Res., April 1, 2008; 36(7): e41 - e41.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Andersson, C. E. G. Bruder, A. Piotrowski, U. Menzel, H. Nord, J. Sandgren, T. R. Hvidsten, T. Diaz de Stahl, J. P. Dumanski, and J. Komorowski
A segmental maximum a posteriori approach to genome-wide copy number profiling
Bioinformatics, March 15, 2008; 24(6): 751 - 758.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Pique-Regi, J. Monso-Varona, A. Ortega, R. C. Seeger, T. J. Triche, and S. Asgharzadeh
Sparse representation and Bayesian detection of genome copy number alterations from microarray data
Bioinformatics, February 1, 2008; 24(3): 309 - 318.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W. Raffelsberger, Y. Krause, L. Moulinier, D. Kieffer, A.-L. Morand, L. Brino, and O. Poch
RReportGenerator: automatic reports from routine statistical analysis using R
Bioinformatics, January 15, 2008; 24(2): 276 - 278.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
K. Wang, M. Li, D. Hadley, R. Liu, J. Glessner, S. F.A. Grant, H. Hakonarson, and M. Bucan
PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
Genome Res., November 1, 2007; 17(11): 1665 - 1674.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. B. Gerstein, C. Bruce, J. S. Rozowsky, D. Zheng, J. Du, J. O. Korbel, O. Emanuelsson, Z. D. Zhang, S. Weissman, and M. Snyder
What is a gene, post-ENCODE? History and updated definition
Genome Res., June 1, 2007; 17(6): 669 - 681.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Stjernqvist, T. Ryden, M. Skold, and J. Staaf
Continuous-index hidden Markov modelling of array CGH copy number data
Bioinformatics, April 15, 2007; 23(8): 1006 - 1014.
[Abstract] [Full Text] [PDF]

Home page
 aacredbookHome page
P. J. Park
Integrated Analysis of Array-CGH and Expression Data
Am. Assoc. Cancer Res. Educ. Book, April 14, 2007; 2007(1): 209 - 212.
[Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Colella, C. Yau, J. M. Taylor, G. Mirza, H. Butler, P. Clouston, A. S. Bassett, A. Seller, C. C. Holmes, and J. Ragoussis
QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data
Nucleic Acids Res., March 27, 2007; (2007) gkm076v3.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Du, J. S. Rozowsky, J. O. Korbel, Z. D. Zhang, T. E. Royce, M. H. Schultz, M. Snyder, and M. Gerstein
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge
Bioinformatics, December 15, 2006; 22(24): 3016 - 3024.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.