Related papers: Molecular Clock Dating using MrBayes

The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…

Complex data features, such as unmodelled censored event times and variables with time-dependent effects, are common in cancer recurrence studies and pose challenges for Bayesian survival modelling. Current methodologies for predictive…

We propose a new statistical approach to obtain differential gene expression of non-detects in quantitative real-time PCR (qPCR) experiments through Bayesian hierarchical modeling. We propose to treat non-detects as non-random missing data,…

Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…

In this dissertation, we develop nonparametric Bayesian models for biomedical data analysis. In particular, we focus on inference for tumor heterogeneity and inference for missing data. First, we present a Bayesian feature allocation model…

Evolutionary modeling applications are the best way to provide full information to support in-depth understanding of evaluation of organisms. These applications mainly depend on identifying the evolutionary history of existing organisms and…

We present the public release of MrMoose, a fitting procedure that is able to perform multi-wavelength and multi-object spectral energy distribution (SED) fitting in a Bayesian framework. This procedure is able to handle a large variety of…

With the routine collection of massive-dimensional predictors in many application areas, screening methods that rapidly identify a small subset of promising predictors have become commonplace. We propose a new MOdular Bayes Screening (MOBS)…

Markov Chain Monte Carlo (MCMC) is a well-established family of algorithms primarily used in Bayesian statistics to sample from a target distribution when direct sampling is challenging. Existing work on Bayesian decision trees uses MCMC.…

Being able to measure time, whether directly or indirectly, is a significant advantage for an organism. It permits it to predict regular events, and prepare for them on time. Thus, clocks are ubiquitous in biology. In the present paper, we…

We present a novel probabilistic clustering model for objects that are represented via pairwise distances and observed at different time points. The proposed method utilizes the information given by adjacent time points to find the…

The study of mouse social behaviours has been increasingly undertaken in neuroscience research. However, automated quantification of mouse behaviours from the videos of interacting mice is still a challenging problem, where object tracking…

Establishing that a set of population-splitting events occurred at the same time can be a potentially persuasive argument that a common process affected the populations. Oaks et al. (2013) assessed the ability of an approximate-Bayesian…

The R package (R Core Team (2016)) genMOSS is specifically designed for the Bayesian analysis of genome-wide association study data. The package implements the mode oriented stochastic search (MOSS) procedure as well as a simple moving…

MultiBUGS (https://www.multibugs.org) is a new version of the general-purpose Bayesian modelling software BUGS that implements a generic algorithm for parallelising Markov chain Monte Carlo (MCMC) algorithms to speed up posterior inference…

More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…

Identifying overlapping communities in networks is a challenging task. In this work we present a novel approach to community detection that utilises the Bayesian non-negative matrix factorisation (NMF) model to produce a probabilistic…

We introduce a multiple criteria Bayesian preference learning framework incorporating behavioral cues for decision aiding. The framework integrates pairwise comparisons, response time, and attention duration to deepen insights into…

Multimodal manifold modeling methods extend the spectral geometry-aware data analysis to learning from several related and complementary modalities. Most of these methods work based on two major assumptions: 1) there are the same number of…

Molecular assembly offers a promising path to detect life beyond Earth, while minimizing assumptions based on terrestrial life. As mass spectrometers will be central to upcoming Solar System missions, predicting molecular assembly from…