Related papers: Infectious diseases, imposing density-dependent mo…
Type 1 diabetes (T1D) is a highly metabolically heterogeneous disease that cannot be adequately characterized by conventional biomarkers such as glycated hemoglobin (HbA1c). This study proposes an explainable deep learning framework that…
Cholera, a severe gastrointestinal infection caused by the bacterium Vibrio cholerae, remains a major threat to public health with a yearly estimated global burden of 2.9 million cases. Although the majority of existing models for the…
Cohort studies employ pairwise measures of association to quantify dependencies among conditions and exposures. To reliably use these measures to draw conclusions about the underlying association strengths requires that the measures be…
We study a well mixed SIR epidemic model with heterogeneous susceptibility and infectivity, allowing for an arbitrary joint distribution of these traits. Using an exact final size formulation and a branching process approximation for early…
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations, and to look for genomic regions with…
Inspired by DNA data of the human cytomegalovirus we propose a model of a two-type parasite population distributed over its hosts. The parasite is capable to persist in its host till the host dies, and to reinfect other hosts. To maintain…
Large populations may contain numerous simultaneously segregating polymorphisms subject to natural selection. Since selection acts on individuals whose fitness depends on many loci, different loci affect each other's dynamics. This leads to…
During an infection, HIV experiences strong selection by immune system T cells. Recent experimental work has shown that MHC escape mutations form an important pathway for HIV to avoid such selection. In this paper, we study a model of MHC…
Initial hours of hospital admission impact clinical trajectory, but early clinical decisions often suffer due to data paucity. With clustering analysis for vital signs within six hours of admission, patient phenotypes with distinct…
The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…
Mathematical models of infectious disease transmission typically neglect within-host dynamics. Yet within-host dynamics - including pathogen replication, host immune responses, and interactions with microbiota - are crucial not only for…
We have investigated the role that the mutation rate and the structure of genetic variation at a locus play in determining whether a gene is involved in disease. We predict that the mutation rate and its genetic diversity should be higher…
In this paper we study a class of stochastic individual-based models that describe the evolution of haploid populations where each individual is characterised by a phenotype and a genotype. The phenotype of an individual determines its…
In the Admixture Model, the probability that an individual carries a certain allele at a specific marker depends on the allele frequencies in $K$ ancestral populations and the proportion of the individual's genome originating from these…
We study an individual-based stochastic SIR epidemic model with infection-age dependent infectivity on a large random graph, capturing individual heterogeneity and non-homogeneous connectivity. Each individual is associated with particular…
Seasonal influenza kills hundreds of thousands every year, with multiple constantly-changing strains in circulation at any given time. A high mutation rate enables the influenza virus to evade recognition by the human immune system,…
This paper presents a non-parametric classification technique for identifying a candidate bi-allelic genetic marker set that best describes disease susceptibility in gene-gene interaction studies. The developed technique functions by…
Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a…
In medicine, comorbidities refer to the presence of multiple, co-occurring diseases. Due to their co-occurring nature, the course of one comorbidity is often highly dependent on the course of the other disease and, hence, treatments can…
Infectious pathogens often propagate by superspreading, which focusses onward transmission on disproportionately few infected individuals. At the same time, infector-infectee pairs tend to have more similar transmission potentials than…