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Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The…
Epidemiologic and genetic studies in chronic obstructive pulmonary disease (COPD) and many complex diseases suggest subgroup disparities (e.g., by sex). We consider this problem from the standpoint of integrative analysis where we combine…
Horizontal transfer (HT) of heritable information or `traits' (carried by genetic elements, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is limited. We present…
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…
The movie Ben-Hur highlights the dynamics of contagion associated with leprosy, a pattern of forced aggregation driven by the emergence of symptoms and the fear of contagion. The 2014 Ebola outbreaks reaffirmed the dynamics of…
The spatial structure of populations is a key element in the understanding of the large scale spreading of epidemics. Motivated by the recent empirical evidence on the heterogeneous properties of transportation and commuting patterns among…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
We describe the phenomenon of localization in the epidemic SIS model on highly heterogeneous networks in which strongly connected nodes (hubs) play the role of centers of localization. We find that in this model the localized states below…
Globally, we are witnessing the rise of complex, non-communicable diseases (NCDs) related to changes in our daily environments. Obesity, asthma, cardiovascular disease, and type 2 diabetes are part of a long list of "lifestyle" diseases…
Many supervised machine learning frameworks have been proposed for disease classification using functional magnetic resonance imaging (fMRI) data, producing important biomarkers. More recently, data pooling has flourished, making the result…
The host immune response can often efficiently suppress a virus infection, which may lead to selection for immune-resistant viral variants within the host. For example, during HIV infection, an array of CTL immune response populations…
Gene duplication is believed to play a major role in the evolution of genomic complexity. The presence of a duplicate removes the constraint of natural selection upon the gene, leading to its likely loss of function or, occasionally, the…
In many epidemiological models a nonlinear transmission function is used in the form of power law relationship. It is constantly argued that such form reflects population heterogeneities including differences in the mixing pattern,…
Metapopulation models are commonly used in ecology, evolution, and epidemiology. These models usually entail homogeneity assumptions within patches and study networks of migration between patches to generate insights into conservation of…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…
Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…
The uniform sampling of convex polytopes is an interesting computational problem with many applications in inference from linear constraints, but the performances of sampling algorithms can be affected by ill-conditioning. This is the case…
Emerging infectious diseases and climate change are two of the major challenges in 21st century. Although over the past decades, highly-resolved mathematical models have contributed in understanding dynamics of infectious diseases and are…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
In this study, we investigated the application of bio-inspired optimization algorithms, including Genetic Algorithm, Particle Swarm Optimization, and Whale Optimization Algorithm, for feature selection in chronic disease prediction. The…