Related papers: Inferring HIV escape rates from multi-locus genoty…
We consider a general mathematical model of a within-host viral infection with $n$ virus strains and explicit age-since-infection structure for infected cells. In the model, multiple virus strains compete for a population of target cells.…
The aetiology of head and neck squamous cell carcinoma (HNSCC) involves multiple carcinogens such as alcohol, tobacco and infection with human papillomavirus (HPV). As the HPV infection influences the prognosis, treatment and survival of…
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are…
Convolutional neural networks can be trained to perform histology slide classification using weak annotations with multiple instance learning (MIL). However, given the paucity of labeled histology data, direct application of MIL can easily…
We consider a simple deterministic model which describes an asymmetric competition between an immune system with a specific and powerful response, and a virus with a broad toxicity and fast mutations. Interest in this model relies on the…
During the HIV infection several quasispecies of the virus arise, which are able to use different coreceptors, in particular the CCR5 and CXCR4 coreceptors (R5 and X4 phenotypes, respectively). The switch in coreceptor usage has been…
Locating recombination hotspots in genomic data is an important but difficult task. Current methods frequently rely on estimating complicated models at high computational cost. In this paper we develop an extremely fast, scalable method for…
Populations of heterogeneous cells play an important role in many biological systems. In this paper we consider systems where each cell can be modelled by an ordinary differential equation. To account for heterogeneity, parameter values are…
The Hamiltonian Monte Carlo (HMC) sampling algorithm exploits Hamiltonian dynamics to construct efficient Markov Chain Monte Carlo (MCMC), which has become increasingly popular in machine learning and statistics. Since HMC uses the gradient…
Pathogen deep-sequencing is an increasingly routinely used technology in infectious disease surveillance. We present a semi-parametric Bayesian Poisson model to exploit these emerging data for inferring infectious disease transmission flows…
During primary HIV infection, the kinetics of plasma virus concentrations and CD4+ cell counts is very complex. Parametric and nonparametric models have been suggested for fitting repeated measurements of these markers. Alternatively,…
We propose and study a new mathematical model of the human immunodeficiency virus (HIV). The main novelty is to consider that the antibody growth depends not only on the virus and on the antibodies concentration but also on the uninfected…
We use a cellular automata model to study the evolution of HIV infection and the onset of AIDS. The model takes into account the global features of the immune response to any pathogen, the fast mutation rate of the HIV and a fair amount of…
The advent and subsequent widespread availability of preventive vaccines has altered the course of public health over the past century. Despite this success, effective vaccines to prevent many high-burden diseases, including HIV, have been…
We propose small-variance asymptotic approximations for the inference of tumor heterogeneity (TH) using next-generation sequencing data. Understanding TH is an important and open research problem in biology. The lack of appropriate…
Incidence estimation of HIV infection can be performed using recent infection testing algorithm (RITA) results from a cross-sectional sample. This allows practitioners to understand population trends in the HIV epidemic without having to…
We study the early stages of viral infection, and the distribution of times to obtain a persistent infection. The virus population proliferates by entering and reproducing inside a target cell until a sufficient number of new virus…
Chronic viral infections can persist in an infected person for decades. From the perspective of the virus, a single infection can span thousands of generations, leading to a highly diverse population of viruses with its own complex…
High throughput sequencing (HTS) continues to expand our understanding of microbial communities, despite insufficient sequencing depths to detect all rare taxa. These low abundance taxa are not accounted for in existing methods for…
In this paper we study intra-host viral adaptation by antigenic cooperation - a mechanism of immune escape that serves as an alternative to the standard mechanism of escape by continuous genomic diversification and allows to explain a…