Related papers: Population genomics of intrapatient HIV-1 evolutio…
Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both…
How does immune system evolve functional proteins - potent antibodies - in such a short time? We address this question using a microscopic, protein-level, sequence-based model of humoral immune response with explicitly defined interactions…
Background: High HIV transmission persists in many U.S. jurisdictions despite prevention efforts. HIV self-testing offers a means to overcome barriers associated with routine laboratory-based testing but carries a risk of increasing…
Heterogeneity is a hallmark of all cancers. Tumor heterogeneity is found at different levels -- interpatient, intrapatient, and intratumor heterogeneity. All of them pose challenges for clinical treatments. The latter two scenarios can also…
We generalize the Susceptible-Infected-Removed model for epidemics to take into account generic effects of heterogeneity in the degree of susceptibility to infection in the population. We introduce a single new parameter corresponding to a…
We investigate the long-time dynamics of a SIR epidemic model with infinitely many pathogen variants infecting a homogeneous host population. We show that the basic reproduction number $\mathcal{R}_0$ of the pathogen can be defined in that…
We have simulated the evolution of sexually reproducing populations composed of individuals represented by diploid genomes. A series of eight bits formed an allele occupying one of 128 loci of one haploid genome (chromosome). The…
Variation and selection are the core principles of Darwinian evolution, yet quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in…
We consider a spatially-heterogeneous generalization of a well-established model for the dynamics of the Human Immunodeficiency Virus-type 1 (HIV) within a susceptible host. The model consists of a nonlinear system of three coupled…
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…
One of the famous results of network science states that networks with heterogeneous connectivity are more susceptible to epidemic spreading than their more homogeneous counterparts. In particular, in networks of identical nodes it has been…
We consider an asexual population under strong selection-weak mutation conditions evolving on rugged fitness landscapes with many local fitness peaks. Unlike the previous studies in which the initial fitness of the population is assumed to…
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…
The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein…
In this paper, we extend a model of host-parasite co-evolution to incorporate the semi-conservative nature of DNA replication for both the host and the parasite. We find that the optimal mutation rate for the semi-conservative and…
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…
In this paper, we focus on susceptible-infected-susceptible dynamics on metapopulation networks, where nodes represent subpopulations, and where agents diffuse and interact. Recent studies suggest that heterogeneous network structure…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
Epidemiological processes are studied within a recently proposed hierarchical network model using the susceptible-infected-refractory dynamics of an epidemic. Within the network model, a population may be characterized by $H$ independent…
We study the influence of the rate of the attainment of herd immunity (HI), in the absence of an approved vaccine, on the vulnerable population. We essentially ask the question: how hard the evolution towards the desired herd immunity could…