Related papers: Integrating influenza antigenic dynamics with mole…
Consider a birth and death chain to model the number of types of a given virus. Each type gives birth to a new type at rate $\lambda$ and dies at rate 1. Each type is also assigned a fitness. When a death occurs either the least fit type…
The increase in the connectivity between hosts in recent times has facilitated the emergence of more aggressive mutant viral strains, making their containment and eradication significantly more challenging compared to the original variants.…
During chronic infection, HIV-1 engages in a rapid coevolutionary arms race with the host's adaptive immune system. While it is clear that HIV exerts strong selection on the adaptive immune system, the characteristics of the somatic…
Protein-protein interactions (PPIs) between a virus and its host govern infection, replication, and pathogenesis. While high-throughput mapping has identified thousands of virus-host associations, much of the virus-host interactome remains…
Influenza, an infectious disease, causes many deaths worldwide. Predicting influenza victims during epidemics is an important task for clinical, hospital, and community outbreak preparation. On-line user-generated contents (UGC), primarily…
Transmission rates are key in understanding the spread of infectious diseases. Using the framework of compartmental models, we introduce a simple method that enables us to reconstruct time series of transmission rates directly from…
Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality…
Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…
The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, as well as antigenic changes that reduce the cross-immunity…
Massive datasets in the gigabyte and terabyte range combined with the availability of increasingly sophisticated statistical tools yield analyses at the boundary of what is computationally feasible. Compromising in the face of this…
Persistent homology computes topological invariants from point cloud data. Recent work has focused on developing statistical methods for data analysis in this framework. We show that, in certain models, parametric inference can be performed…
Bacteria and phages have been in an ongoing arms race for billions of years. To resist phages bacteria have evolved numerous defense systems, which nevertheless are still overcome by counter-defense mechanisms of specific phages. These…
Common respiratory viruses cause seasonal epidemics in sequential patterns. The underlying mechanisms for this pattern have been debated for some time. For influenza, contenders include temperature, humidity, and vitamin D levels. While…
Here we examine the evolution of beta-2 microglobulin in terms of its hydropathic shapes, a theoretical construct that has revealed important trends. The dynamics of many proteins are largely driven by interactions between the protein…
In early HIV infection, the virus population escapes from multiple CD8+ cell responses. The later an escape mutation emerges, the slower it outgrows its competition, i. e. the escape rate is lower. This pattern could indicate that the…
Viral infections trigger complex immune responses with heterogeneous outcomes shaped by nonlinear feedbacks. An ordinary differential equation model is developed to investigate immune response dynamics during viral infection, incorporating…
There is a rich history of models for the interaction of a biological contagion like influenza with the spread of related information such as an influenza vaccination campaign. Recent work on the spread of interacting contagions on networks…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…
The unfolding of pandemic influenza A(H1N1) for Fall 2009 in the Northern Hemisphere is still uncertain. Plans for vaccination campaigns and vaccine trials are underway, with the first batches expected to be available early October. Several…