Panagiotis Papastamoulis

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MOTIVATION Assigning RNA-seq reads to their transcript of origin is a fundamental task in transcript expression estimation. Where ambiguities in assignments exist due to transcripts sharing sequence, e.g. alternative isoforms or alleles, the problem can be solved through probabilistic inference. Bayesian methods have been shown to provide accurate(More)
RNA-seq studies allow for the quantification of transcript expression by aligning millions of short reads to a reference genome. However, transcripts share much of their sequence, so that many reads map to more than one place and their origin remains uncertain. This problem can be dealt using mixtures of distributions and transcript expression reduces to(More)
Label switching is a well-known phenomenon that occurs in MCMC outputs targeting the parameters’ posterior distribution of many latent variable models. Although its appearence is necessary for the convergence of the simulated Markov chain, it turns out to be a problem in the estimation procedure. In a recent paper, Papastamoulis and Iliopoulos (2010)(More)
February 20, 2015 Type Package Title Relabelling MCMC outputs of mixture models Version 1.3 Date 2014-11-04 Author Panagiotis Papastamoulis Maintainer Panagiotis Papastamoulis <papapast@yahoo.gr> Description The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output(More)
July 2, 2014 Type Package Title Relabelling MCMC outputs of mixture models Version 1.2 Date 2013-12-04 Author Panagiotis Papastamoulis Maintainer Panagiotis Papastamoulis <papapast@yahoo.gr> Description The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output(More)
Next generation sequencing allows the identification of genes consisting of differentially expressed transcripts, a term which usually refers to changes in the overall expression level. A specific type of differential expression is differential transcript usage (DTU) and targets changes in the relative within gene expression of a transcript. The(More)
Recent advances in molecular biology allow the quantification of the transcriptome and scoring transcripts as differentially or equally expressed between two biological conditions. Although these two tasks are closely linked, the available inference methods treat them separately: a primary model is used to estimate expression and its output is(More)