Related papers: A Mutagenetic Tree Hidden Markov Model for Longitu…

Hidden Markov models provide a natural statistical framework for the detection of the copy number variations (CNV) in genomics. In this paper, we consider a Hidden Markov Model involving several correlated hidden processes at the same time.…

Massive research efforts are now underway to develop a cure for HIV infection, allowing patients to discontinue lifelong combination antiretroviral therapy (ART). New latency-reversing agents (LRAs) may be able to purge the persistent…

This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted…

One way in which the human immunodeficiency virus (HIV-1) replicates within a host is by infecting activated CD4+ T-cells, which then produce additional copies of the virus. Even with the introduction of antiretroviral drug therapy, which…

We present a new joint longitudinal and survival model aimed at estimating the association between the risk of an event and the change in and history of a biomarker that is repeatedly measured over time. We use cubic B-splines models for…

HIV virus replication is a time-related process that includes several stages. Focusing on the core steps, RNA polymerase II transcripts in an early stage pre-mRNA containing regulator proteins (i.e nef,tat,rev,vif,vpr,vpu), which are…

Oxidative stress, a reaction caused by the imbalance between the reactive oxygen species of human organism and its ability to detoxify reactive intermediates and to repair the resulting damage plays an important role in HIV-infections. On…

Hidden Markov Models (HMMs) are powerful tools for modeling sequential data, where the underlying states evolve in a stochastic manner and are only indirectly observable. Traditional HMM approaches are well-established for linear sequences,…

Mixture models provide a flexible representation of heterogeneity in a finite number of latent classes. From the Bayesian point of view, Markov Chain Monte Carlo methods provide a way to draw inferences from these models. In particular,…

With the launch of second line anti-retroviral therapy for HIV infected individuals, there has been an increased expectation on surviving period of people with HIV. We consider previously well-known models in HIV epidemiology where the…

HIV/AIDs Regimen specification one of many problems for which bioinformaticians have implemented and trained machine learning methods such as neural networks. Predicting HIV resistance would be much easier, but unfortunately we rarely have…

Can we understand and predict the evolutionary pathways by which bacteria acquire multi-drug resistance (MDR)? These questions have substantial potential impact in basic biology and in applied approaches to address the global health…

RNA secondary structure is modeled with the novel arbitrary-order hidden Markov model ({\alpha}-HMM). The {\alpha}-HMM extends over the traditional HMM with capability to model stochastic events that may be in influenced by historically…

Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of…

An exactly solvable model based on the topology of a protein native state is applied to identify bottlenecks and key-sites for the folding of HIV-1 Protease. The predicted sites are found to correlate well with clinical data on resistance…

People living with HIV on antiretroviral therapy often have undetectable virus levels by standard assays, but "latent" HIV still persists in viral reservoirs. Eliminating these reservoirs is the goal of HIV cure research. The quantitative…

Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…

Analyzing disease progression patterns can provide useful insights into the disease processes of many chronic conditions. These analyses may help inform recruitment for prevention trials or the development and personalization of treatments…

To investigate interactions between parasite species in a host, a population of field voles was studied longitudinally, with presence or absence of six different parasites measured repeatedly. Although trapping sessions were regular, a…

Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins.…