Chromosomal breakpoint detection in human cancer
EvoWorkshops'03 Proceedings of the 2003 international conference on Applications of evolutionary computing
A novel approach to detect copy number variation using segmentation and genetic algorithm
Proceedings of the 2009 ACM symposium on Applied Computing
A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
Computational Biology and Chemistry
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Heuristic Bayesian Segmentation for Discovery of Coexpressed Genes within Genomic Regions
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Framework for identifying common aberrations in DNA copy number data
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
GIMscan: a new statistical method for analyzing whole-genome array CGH data
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
A hidden Markov model approach for prediction of genomic alterations from gene expression profiling
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Sticky hidden Markov modeling of comparative genomic hybridization
IEEE Transactions on Signal Processing
A coarse-to-fine approach to computing the k-best Viterbi paths
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Approximation algorithms for speeding up dynamic programming and denoising aCGH data
Journal of Experimental Algorithmics (JEA)
Detection of chromosomal abnormalities using high resolution arrays in clinical cancer research
Journal of Biomedical Informatics
Simultaneous identification of causal genes and dys-regulated pathways in complex diseases
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Computational Statistics & Data Analysis
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The development of solid tumors is associated with acquisition of complex genetic alterations, indicating that failures in the mechanisms that maintain the integrity of the genome contribute to tumor evolution. Thus, one expects that the particular types of genomic alterations seen in tumors reflect underlying failures in maintenance of genetic stability, as well as selection for changes that provide growth advantage. In order to investigate genomic alterations we are using microarray-based comparative genomic hybridization (array CGH). The computational task is to map and characterize the number and types of copy number alternations present in the tumors, and so define copy number phenotypes and associate them with known biological markers.To utilize the spatial coherence between nearby clones. we use an unsupervised hidden Markov models approach. The clones are partitioned into the states which represent the underlying copy number of the group of clones. The method is demonstrated on the two cell line datasets, one with known copy number alterations. The biological conclusions drawn from the analyses are discussed.