相关论文: Integrating influenza antigenic dynamics with mole…
In temperate regions, respiratory virus epidemics recur on a yearly basis, primarily during the winter season. This is believed to be induced by seasonal forcing, where the rate at which the virus can be transmitted varies cyclically across…
The impact of climate conditions on influenza epidemiology has mostly been studied by addressing a singular aspect of transmission and a climate variable correlating to it. As climate change unfolds at an unprecedented rate, we urgently…
Somatic hypermutations of immunoglobulin (Ig) genes occuring during affinity maturation drive B-cell receptors' ability to evolve strong binding to their antigenic targets. The landscape of these mutations is highly heterogeneous, with…
The evolution of the adaptive immune system is characterized by changes in the relative abundances of the B- and T-cell clones that make up its repertoires. To fully capture this evolution, we need to describe the complex dynamics of the…
We develop a multiple compartment Susceptible-Infected-Recovered (SIR) model to analyze the spread of several infectious diseases through different geographic areas. Additionally, we propose a data-quality sensitive optimization framework…
Viral zoonoses have emerged as the key drivers of recent pandemics. Human infection by zoonotic viruses are either spillover events -- isolated infections that fail to cause a widespread contagion -- or species jumps, where successful…
Myriad experiments have identified an important role for $\rm CD8^+$ T cell response mechanisms in determining recovery from influenza A virus infection. Animal models of influenza infection further implicate multiple elements of the immune…
We study the global spatio-temporal patterns of influenza dynamics. This is achieved by analysing and modelling weekly laboratory confirmed cases of influenza A and B from 138 countries between January 2006 and May 2014. The data were…
How will the novel coronavirus evolve? I study a simple epidemiological model, in which mutations may change the properties of the virus and its associated disease stochastically and antigenic drifts allow new variants to partially evade…
The aftermath of influenza infection is determined by a complex set of host-pathogen interactions, where genomic variability on both viral and host sides influences the final outcome. Although there exists large body of literature…
Epidemiological models for the spread of pathogens in a population are usually only able to describe a single pathogen. This makes their application unrealistic in cases where multiple pathogens with similar symptoms are spreading…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
High order structures (cavities and cliques) of the gene network of influenza A virus reveal tight associations among viruses during evolution and are key signals that indicate viral cross-species infection and cause pandemics. As…
In this paper, we carry out a computational study using the spectral decomposition of the fluctuations of a two-pathogen epidemic model around its deterministic attractor, i.e., steady state or limit cycle, to examine the role of partial…
Evidence-based knowledge of infectious disease burden, including prevalence, incidence, severity and transmission, in different population strata and locations, and possibly in real time, is crucial to the planning and evaluation of public…
Background: The pandemic of influenza A (H1N1) is a serious on-going global public crisis. Understanding its spreading dynamics is of fundamental importance for both public health and scientific researches. Recent studies have focused…
Many infectious diseases are comprised of multiple strains with examples including Influenza, tuberculosis, and Dengue virus. The time evolution of such systems is linked to a complex landscape shaped by interactions between competing…
In this work, we aim to formalize a novel scientific machine learning framework to reconstruct the hidden dynamics of the transmission rate, whose inaccurate extrapolation can significantly impair the quality of the epidemic forecasts, by…
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…
Influenza remains a significant burden on health systems. Effective responses rely on the timely understanding of the magnitude and the evolution of an outbreak. For monitoring purposes, data on severe cases of influenza in England are…