Hidden Markov models approach to the analysis of array CGH data

DOI10.1016/j.jmva.2004.02.008zbMath1047.92026OpenAlexW2066721762WikidataQ105583680 ScholiaQ105583680MaRDI QIDQ1876991

Jane Fridlyand, Antoine M. Snijders, Donna G. Albertson, Dan Pinkel, Ajay N. Jain

Publication date: 16 August 2004

Published in: Journal of Multivariate Analysis (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jmva.2004.02.008

zbMATH Keywords

HMMMutationArray CGHCancerChromosomal aberrationsGenomic profileMMR

Mathematics Subject Classification ID

Medical applications (general) (92C50) Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08)

Related Items (27)

Fast estimation of posterior probabilities in change-point analysis through a constrained hidden Markov model ⋮ MGP-HMM: detecting genome-wide CNVs using an HMM for modeling mate pair insertion sizes and read counts ⋮ A semiparametric Bayesian model for comparing DNA copy numbers ⋮ A heuristic, iterative algorithm for change-point detection in abrupt change models ⋮ Using GWAS data to identify copy number variants contributing to common complex diseases ⋮ Prediction in Cancer Genomics Using Topological Signatures and Machine Learning ⋮ Bayesian–frequentist hybrid model with application to the analysis of gene copy number changes ⋮ Sparse latent factor models with interactions: analysis of gene expression data ⋮ Modeling read counts for CNV detection in exome sequencing data ⋮ PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data ⋮ A continuous-index hidden Markov jump process for modeling DNA copy number data ⋮ A shifting level model algorithm that identifies aberrations in array-CGH data ⋮ A Coarse-to-Fine Approach to Computing the k-Best Viterbi Paths ⋮ Identification of Differential Aberrations in Multiple-Sample Array CGH Studies ⋮ A Bayesian HMM with random effects and an unknown number of states for DNA copy number analysis ⋮ A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data ⋮ Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays ⋮ The screening and ranking algorithm to detect DNA copy number variations ⋮ A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data ⋮ Segmentation and Estimation for SNP Microarrays: A Bayesian Multiple Change-Point Approach ⋮ Detecting Genomic Aberrations Using Products in a Multiscale Analysis ⋮ A model selection approach for multiple sequence segmentation and dimensionality reduction ⋮ Quasi-hidden Markov model and its applications in change-point problems ⋮ A Latent Class Model with Hidden Markov Dependence for Array CGH Data ⋮ Multiscale Change Point Inference ⋮ Nonparametric multivariate breakpoint detection for the means, variances, and covariances of a discrete time stochastic process ⋮ A Segmentation/Clustering Model for the Analysis of Array CGH Data

Uses Software

• R
• clusfind

Cites Work

• Unnamed Item
• Estimating the dimension of a model
• Fitting autoregressive models for prediction
• Finding Groups in Data

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