Related papers: Infectious diseases, imposing density-dependent mo…
Chronic viral infections can persist in an infected person for decades. From the perspective of the virus, a single infection can span thousands of generations, leading to a highly diverse population of viruses with its own complex…
The complex interplay between population movements in space and non-homogeneous mixing patterns have so far hindered the fundamental understanding of the conditions for spatial invasion through a general theoretical framework. To address…
How self-organization leads to the emergence of structure in social populations remains a fascinating and open question in the study of complex systems. One frequently observed structure that emerges again and again across systems is that…
Human mobility, contact patterns, and their interplay are key aspects of our social behavior that shape the spread of infectious diseases across different regions. In the light of new evidence and data sets about these two elements,…
The emerging research shows that lncRNAs are associated with a series of complex human diseases. However, most of the existing methods have limitations in identifying nonlinear lncRNA-disease associations (LDAs), and it remains a huge…
Biochemical and regulatory interactions central to biological networks are expected to cause extensive genetic interactions or epistasis affecting the heritability of complex traits and the distribution of genotypes in populations. However,…
Accurate diagnosis and treatment of complex diseases require integrating histological, molecular, and clinical data, yet in practice these modalities are often incomplete owing to tissue scarcity, assay cost, and workflow constraints.…
The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the…
Immunological self/not-self discrimination is conventionally seen as an extracellular event, involving interactions been receptors on T cells pre-educated to discriminate, and peptides bound to major histocompatibility complex proteins…
While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated…
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…
A haplotype block, or simply a block, is a chromosomal segment, DNA base sequence or string that occurs in only a few variants or types in the genomes of a population of interest, and that has an encapsulated or 'private' frequency…
Haplotype Inference is a challenging problem in bioinformatics that consists in inferring the basic genetic constitution of diploid organisms on the basis of their genotype. This information allows researchers to perform association studies…
The study proposes a modeling framework for investigating the disease dynamics with adaptive human behavior during a disease outbreak, considering the impacts of both local observations and global information. One important application…
Vector-borne diseases often infect multiple host species, increasing the likelihood of disease persistence due to the presence of multiple reservoirs. Vector biting patterns and feeding preferences can shift in response to selective…
Many complex disease syndromes such as asthma consist of a large number of highly related, rather than independent, clinical phenotypes, raising a new technical challenge in identifying genetic variations associated simultaneously with…
How does the interplay between selection, mutation and horizontal gene transfer modify the phenotypic distribution of a bacterial or cell population? While horizontal gene transfer, which corresponds to the exchange of genetic material…
The shape of an epidemic wave in simple epidemic models applies to a homogeneous distribution of infected people in the population. In large inhomogeneous systems, at country-scale for instance, the wave shape is similar except for the…
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…
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…