Using informative multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling

DOI10.1515/SAGMB-2014-0098MaRDI QIDQ5962702zbMATH OpenOpenAlexWikidataFDO

Authors Rawane Samb, Khader Khadraoui, Pascal Belleau, Astrid Deschênes, Lajmi Lakhal-Chaieb, Arnaud Droit

Publication date 16 February 2016

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1515/sagmb-2014-0098

zbMATH Keywords

nucleosome positioningreversible-jump MCMCBayesian t-mixturegenome-wide profilingmultinomial-Dirichlet prior

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) General biostatistics (92B15) Biochemistry, molecular biology (92C40)

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Cites work

• scientific article; zbMATH DE number 1085980 (Why is no real title available?)
• scientific article; zbMATH DE number 2117879 (Why is no real title available?)
• A continuous-index Bayesian hidden Markov model for prediction of nucleosome positioning in genomic DNA
• A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions
• Estimating the dimension of a model
• Markov chains for exploring posterior distributions. (With discussion)
• PICS: Probabilistic Inference for ChIP-seq
• Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
• Using informative multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling

Cited in

(10)

• DNA combinatorial messages and epigenomics: the case of chromatin organization and nucleosome occupancy in eukaryotic genomes
• Using informative multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling
• Change point analysis of histone modifications reveals epigenetic blocks linking to physical domains
• A generalized hidden Markov model for determining sequence-based predictors of nucleosome positioning
• Re-cracking the nucleosome positioning code
• Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data
• Nonparametric Bayesian bi-clustering for next generation sequencing count data
• A continuous-index Bayesian hidden Markov model for prediction of nucleosome positioning in genomic DNA
• NucPosPred: predicting species-specific genomic nucleosome positioning via four different modes of general PseKNC
• ThIEF: finding genome-wide trajectories of epigenetics marks

Describes a project that uses

Uses Software

• PICS
• nucleoSim
• PuFFIN
• nucleR
• consensusSeekeR
• VennDiagram

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