Related papers: Multitype PCR branching processes
The Poland-Scheraga model for DNA denaturation, besides playing a central role in applications, has been widely studied in the physical and mathematical literature over the past decades. More recently a natural generalization has been…
Clustering is one of the most widely used procedures in the analysis of microarray data, for example with the goal of discovering cancer subtypes based on observed heterogeneity of genetic marks between different tissues. It is well-known…
The shapes of branching trees have been linked to disease transmission patterns. In this paper we use the general Crump-Mode-Jagers branching process to model an outbreak of an infectious disease under mild assumptions. Introducing a new…
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…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
This paper discusses the possible ways to analyse the data, adopting a matrix notation, so often used in Bioassays. The paper also reviews the Multistage Models (MM). The MM class of models is applied for extrapolation, to the region of…
We develop clustering procedures for longitudinal trajectories based on a continuous-time hidden Markov model (CTHMM) and a generalized linear observation model. Specifically in this paper, we carry out finite and infinite mixture…
In this paper we present an extension of population-based Markov chain Monte Carlo (MCMC) to the trans-dimensional case. One of the main challenges in MCMC-based inference is that of simulating from high and trans-dimensional target…
In a multitype branching process, it is assumed that immigrants arrive according to a nonhomogeneous Poisson or a generalized Polya process (both processes are formulated as a nonhomogeneous birth process with an appropriate choice of…
This paper investigates the problem of simultaneously predicting multiple binary responses by utilizing a shared set of covariates. Our approach incorporates machine learning techniques for binary classification, without making assumptions…
Efficient and stable algorithms for the calculation of spectral quantities and correlation functions are some of the key tools in computational condensed matter physics. In this article we review basic properties and recent developments of…
Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these…
The paper studies an improved estimate for the rate of convergence for nonlinear homogeneous discrete-time Markov chains. These processes are nonlinear in terms of the distribution law. Hence, the transition kernels are dependent on the…
MicroRNAs (miRNAs) are small non-coding RNAs that function as regulators of gene expression. In recent years, there has been a tremendous and growing interest among researchers to investigate the role of miRNAs in normal cellular as well as…
Important information on the structure of complex systems, consisting of more than one component, can be obtained by measuring to which extent the individual components exchange information among each other. Such knowledge is needed to…
Multiple myeloma cancer is a type of blood cancer that happens when the growth of abnormal plasma cells becomes out of control in the bone marrow. There are various ways to diagnose multiple myeloma in bone marrow such as complete blood…
Ordinary differential equations obtained as limits of Markov processes appear in many settings. They may arise by scaling large systems, or by averaging rapidly fluctuating systems, or in systems involving multiple time-scales, by a…
Motivated by the study of rare events for a typical genetic switching model in systems biology, in this paper we aim to establish the general two-scale large deviations for chemical reaction systems. We build a formal approach to explicitly…
Counterexample generation is an indispensable part of model checking process. In stochastic model checking, counterexample generation is a challenging problem as it is not enough to find a single trace that violates the given property.…
All biological processes are controlled by complex systems of enzymatic chemical reactions. Although the majority of enzymatic networks have very elaborate structures, there are many experimental observations indicating that some turnover…