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The HMMs designed for arrayCGH data take as input log ratios of measured fluorescence, a continuous variable, while read depth data consists of discrete counts of reads. We will therefore consider Hidden Markov models are useful for segmentation of many kinds of genomic data, as they represent linear sequences of observed data made up of homogeneous stretches associated Advanced Search Include Citations.
Advanced Search Include Citations Disambiguate. HaasMax Planck circular binary segmentation bioconductor edger, Michael I. Citations A tutorial on hidden Markov models and selected applications in speech recognition - Rabiner - Show Context Citation Context A tutorial on hidden Markov models and selected applications in speech recognition - Rabiner - Show Context Citation Context Differential expression analysis for sequence count data - Anders, Huber - Computational methods for discovering structural variation with next-generation sequencing, Nat - Medvedev - Autism genome-wide copy number variation reveals ubiquitin and neuronal genes - Glessner, Wang, et al.
Epub Oct 03 - Li, Vinckenbosch, et al. RazerSfast read mapping with sensitivity control - Weese, Emde, et al.
Control-free calling of copy number alterations in deepsequencing data using GC-content normalization - Boeva - Exome sequencing-based copy-number variation and loss of heterozygosity detection: CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data - Ivakhno - Towards a comprehensive structural variation map of an individual human genome - Pang, MacDonald, et al. Sebat J Sensitive and accurate detection of copy number variants using read depth of coverage.
Genome Res 19 - Yoon, Xuan, et al. Open software development for computational biology and bioinformatics. Estimation and correction for GC-content bias in high throughput sequencing - Benjamini, Speed - Coarfa C, Milosavljevic Circular binary segmentation bioconductor edger Readdepth: A parallel r package for detecting copy number alterations from short sequencing reads. Khaja R, Scherer S Development of bioinformatics resources for display and analysis of copy number circular binary segmentation bioconductor edger other structural variants in the human genome.
Cytogenetic and Genome Research - Zhang, Feuk, et al. Identifying a common protein-coding gene set for the human and mouse genomes.