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New generation in vitro high-throughput screening (HTS) assays for the assessment of engineered nanomaterials provide an opportunity to learn how these particles interact at the cellular level, particularly in relation to injury pathways.…
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…
Rapid identification of outbreaks in hospitals is essential for controlling pathogens with epidemic potential. Although whole genome sequencing (WGS) remains the gold standard in outbreak investigations, its substantial costs and turnaround…
Stochastic compartmental models are important tools for understanding the course of infectious diseases epidemics in populations and in prospective evaluation of intervention policies. However, calculating the likelihood for discretely…
Proliferation of uninfected as well as infected hepatocytes and recycling of DNA-containing capsids are two major mechanisms playing significant roles in the clearance of hepatitis B virus (HBV) infection. In this study, the temporal…
We present an individual-based model for the coevolutionary dynamics between CD8+ cytotoxic T lymphocytes (CTLs) and tumour cells. In this model, every cell is viewed as an individual agent whose phenotypic state is modelled by a discrete…
Cis-regulatory modules (CRMs) composed of multiple transcription factor binding sites (TFBSs) control gene expression in eukaryotic genomes. Comparative genomic studies have shown that these regulatory elements are more conserved across…
RNA viruses are a widely used tool to study evolution experimentally. Many standard protocols of virus propagation and competition are done at nominally low multiplicity of infection (m.o.i.), but lead during one passage to two or more…
Tumor segmentation in whole-slide images of histology slides is an important step towards computer-assisted diagnosis. In this work, we propose a tumor segmentation framework based on the novel concept of persistent homology profiles…
Molecular and genomic technological advancements have greatly enhanced our understanding of biological processes by allowing us to quantify key biological variables such as gene expression, protein levels, and microbiome compositions. These…
Given a mathematical model quantifying the viral infection of pandemic influenza H1N1pdm09-H275 wild type (WT) and H1N1pdm09-H275Y mutant (MUT) strains, we describe a simple method of estimating the model's constant parameters using Monte…
B-cell repertoires are characterized by a diverse set of receptors of distinct specificities generated through two processes of somatic diversification: V(D)J recombination and somatic hypermutations. B cell clonal families stem from the…
$\textbf{Objective}$: To develop a multi-channel device event segmentation and feature extraction algorithm that is robust to changes in data distribution. $\textbf{Methods}$: We introduce an adaptive transfer learning algorithm to classify…
Antimicrobial resistance is becoming a major threat to public health throughout the world. Researchers are attempting to contrast it by developing both new antibiotics and patient-specific treatments. In the second case, whole-genome…
Safe and effective preventive vaccines have the potential to help stem the HIV epidemic. The efficacy of such vaccines is typically measured in randomized, double-blind phase IIb/III trials and described as a reduction in newly acquired HIV…
In epidemiological studies, the capture-recapture (CRC) method is a powerful tool that can be used to estimate the number of diseased cases or potentially disease prevalence based on data from overlapping surveillance systems. Estimators…
Individual-level epidemic models are increasingly being used to help understand the transmission dynamics of various infectious diseases. However, fitting such models to individual-level epidemic data is challenging, as we often only know…
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…
We consider the standard three-component differential equation model for the growth of an HIV virion population in an infected host in the absence of drug therapy. The dynamical properties of the model are determined by the set of values of…
Oncolytic virotherapy, utilizing genetically modified viruses to combat cancer and trigger anti-cancer immune responses, has garnered significant attention in recent years. In our previous work arXiv:2305.12386, we developed a stochastic…