相关论文: Viral RNA replication modes: evolutionary and dyna…

Cellular response to environmental and internal signals can be modeled by dynamical gene regulatory networks (GRN). In the literature, three main classes of gene network models can be distinguished: (i) non-quantitative (or data-based)…

RNA velocity is an important model that combines cellular spliced and unspliced RNA counts to infer dynamical properties of various regulatory functions. Despite its wide applicability and many variants used in practice, the model has not…

Viral quasispecies can be regarded as a swarm of genetically related mutants or a quasispecies (QS). A common formalism to approach QS is the replicator-mutator equation (RME). However, a problem with the RME is how to quantify the…

We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…

Within the germinal center in follicles, B-cells proliferate, mutate and differentiate, while being submitted to a powerful selection~: a micro-evolutionary mechanism at the heart of adaptive immunity. A new foreign pathogen is confronted…

The density ratio model (DRM) is a semiparametric model that relates the distributions from multiple samples to a nonparametrically defined reference distribution via exponential tilting, with finite-dimensional parameters governing their…

Motivation: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in…

Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins.…

Effective and efficient mitigation of malware is a long-time endeavor in the information security community. The development of an anti-malware system that can counteract an unknown malware is a prolific activity that may benefit several…

Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and…

Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…

We present the R-package mgm for the estimation of k-order Mixed Graphical Models (MGMs) and mixed Vector Autoregressive (mVAR) models in high-dimensional data. These are a useful extensions of graphical models for only one variable type,…

The majority of research on epidemics relies on models which are formulated in continuous-time. However, real-world epidemic data is gathered and processed in a digital manner, which is more accurately described by discrete-time epidemic…

Budding allows virus replication and macromolecular secretion in cells. It involves the formation of a bud, i.e. an outgrowth from the cell membrane that evolves into an envelope. The largest energetic barrier to bud formation is membrane…

The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…

We analyze 14,651 HIV1 reverse transcriptase (HIV RT) sequences from the Stanford HIV Drug Resistance Database labeled with treatment regimen in order to study the evolution this enzyme under drug selection in the clinic. Our goal is to…

Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence…

The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the…

The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used…

It has been known for some time that human autoimmune diseases can be triggered by viral infections. Several possible mechanisms of interactions between a virus and immune system have been analysed, with a prevailing opinion being that the…