Related papers: Model Based Framework for Estimating Mutation Rate…
We develop a Bayesian statistical model and estimation methodology based on Forward Projection Adaptive Markov chain Monte Carlo in order to perform the calibration of a high-dimensional non-linear system of Ordinary Differential Equations…
Hepatitis C virus helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by…
Multiscale mathematical models of hepatitis C infection have been instrumental in our understanding of direct acting antivirals. These models include the mechanisms driving intracellular viral production and explicitly model the…
Hepatitis type B is one of the most common infectious disease worldwide that can pose severe threats to human health up to the point that may contribute to severe liver damage or cancer. Over the past two decades a large number of dynamic…
We develop Graph-Coupled Hidden Markov Models (GCHMMs) for modeling the spread of infectious disease locally within a social network. Unlike most previous research in epidemiology, which typically models the spread of infection at the level…
In this work we develop a stochastic model of acute HIV infection, based on the well-known standard model, that allows us to simulate the complex mutation pathways of HIV escape from multiple CTL responses. Under this model, we describe two…
Human papillomavirus (HPV) infection is the most common sexually transmitted infection in the world. Persistent oncogenic Human papillomavirus infection has been a leading threat to global health and can lead to serious complications such…
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions,…
Malware evolves over time and antivirus must adapt to such evolution. Hence, it is critical to detect those points in time where malware has evolved so that appropriate countermeasures can be undertaken. In this research, we perform a…
In this paper, a mathematical analysis of the global dynamics of a viral infection model in vivo is carried out. We study the dynamics of a hepatitis C virus (HCV) model, under therapy, that considers both extracellular and intracellular…
The detection of change-points in heterogeneous sequences is a statistical challenge with many applications in fields such as finance, signal analysis and biology. A wide variety of literature exists for finding an ideal set of…
We consider a mathematical model comprising of four coupled ordinary differential equations (ODEs) for studying the hepatitis C (HCV) viral dynamics. The model embodies the efficacies of a combination therapy of interferon and ribavirin. A…
The rates of escape and reversion in response to selection pressure arising from the host immune system, notably the cytotoxic T-lymphocyte (CTL) response, are key factors determining the evolution of HIV. Existing methods for estimating…
The main focus of this work is on developing models for the activity profile of a terrorist group, detecting sudden spurts and downfalls in this profile, and, in general, tracking it over a period of time. Toward this goal, a $d$-state…
Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus…
Hepatitis B is a potentially life-threatening liver infection caused by the hepatitis B virus (HBV). In this paper, the transmission dynamics of hepatitis B is formulated with a mathematical model with considerations of different classes of…
Chromosomal DNA is characterized by variation between individuals at the level of entire chromosomes (e.g., aneuploidy in which the chromosome copy number is altered), segmental changes (including insertions, deletions, inversions, and…
We define a Hidden Markov Model (HMM) in which each hidden state has time-dependent $\textit{activity levels}$ that drive transitions and emissions, and show how to estimate its parameters. Our construction is motivated by the problem of…
VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these…
Respiratory infections and chronic respiratory diseases impose a heavy health burden worldwide. Coughing is one of the most common symptoms of many such infections, and can be indicative of flare-ups of chronic respiratory diseases. Whether…