相关论文: Viral RNA replication modes: evolutionary and dyna…
For many viruses assembly and budding occur simultaneously during virion formation. Understanding the mechanisms underlying this process could promote biomedical efforts to block viral propagation and enable use of capsids in nanomaterials…
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…
A stochastic model for the growth of a virus in a cell population is introduced. The virus has two ways of spreading: either by allowing its host cell to live on and duplicate, or else by multiplying in large numbers within the host cell…
Accurately modeling malware propagation is essential for designing effective cybersecurity defenses, particularly against adaptive threats that evolve in real time. While traditional epidemiological models and recent neural approaches offer…
Most existing swarm pattern formation methods depend on a predefined gene regulatory network (GRN) structure that requires designers' priori knowledge, which is difficult to adapt to complex and changeable environments. To dynamically adapt…
Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
We propose Deep Residual Mixture Models (DRMMs), a novel deep generative model architecture. Compared to other deep models, DRMMs allow more flexible conditional sampling: The model can be trained once with all variables, and then used for…
The dynamics of wild-type (wt) RNA viruses and their defective viral genomes (DVGs) have been extensively studied both experimentally and theoretically. This research has paid special attention to the interference effects of DVGs on wt…
We introduce a novel generative smoothness regularization on manifolds (SToRM) model for the recovery of dynamic image data from highly undersampled measurements. The proposed generative framework represents the image time series as a…
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…
The outbreak of mutant strains and vaccination behaviors have been the focus of recent epidemiological research, but most existing epidemic models failed to simultaneously capture viral mutation and consider the complexity and behavioral…
We develop a stochastic framework for viral population dynamics at the cellular level that explicitly incorporates the replication cycle with random stage durations. The model is formulated as a structured birth-death process coupled with a…
This study presents a neural network-enhanced approach to modeling disease spread dynamics over time and space. Neural networks are used to estimate time-varying parameters, with two calibration methods explored: Approximate Bayesian…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
Background. A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk multi-region…
DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
It is estimated that approximately 15% of cancers worldwide can be linked to viral infections. The viruses that can cause or increase the risk of cancer include human papillomavirus, hepatitis B and C viruses, Epstein-Barr virus, and human…
Epidemic processes are common out-of-equilibrium phenomena of broad interdisciplinary interest. Recently, dynamic message-passing (DMP) has been proposed as an efficient algorithm for simulating epidemic models on networks, and in…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…