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

{\it Transcription} is the process whereby RNA molecules are polymerized by molecular machines, called RNA polymerase (RNAP), using the corresponding DNA as the template. Recent {\it in-vivo} experiments with single cells have established…

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The…

The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses…

Inherent stochasticity in gene expression leads to distributions of mRNA copy numbers in a population of identical cells. These distributions are determined primarily by the multitude of states of a gene promoter, each driving transcription…

Oncolytic virotherapy - the use of viruses that specifically kill tumor cells - is an innovative and highly promising route for treating cancer. However, its therapeutic outcomes are mainly impaired by the host immune response to the viral…

Most human tumors result from the accumulation of multiple genetic and epigenetic alterations in a single cell. Mutations that confer a fitness advantage to the cell are known as driver mutations and are causally related to tumorigenesis.…

A model capturing the dynamics between virus and tumour cells in the context of oncolytic virotherapy is presented and analysed. The ability of the virus to be internalised by uninfected cells is described by an infectivity parameter, which…

Purpose: To allow fast and high-quality reconstruction of clinical accelerated multi-coil MR data by learning a variational network that combines the mathematical structure of variational models with deep learning. Theory and Methods:…

Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…

Understanding the viral dynamics and immunizing antibodies of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for devising better therapeutic and prevention strategies for COVID-19. Here, we present a Bayesian…

In this paper recent substantial progress in applying the density-matrix renormalization-group (DMRG) to the simulation of the time-evolution of strongly correlated quantum systems in one dimension is reviewed. Various approaches to…

regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal…

A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of…

Invariant risk minimization (IRM) aims to enable out-of-distribution (OOD) generalization in deep learning by learning invariant representations. As IRM poses an inherently challenging bi-level optimization problem, most existing approaches…

We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic…

The mutation-selection mechanism of Darwinian evolution gives rise not only to adaptation to environmental conditions but also to the enhancement of robustness against mutations. When two or more phenotypes have the same fitness value, the…

Short tandem repeats (STRs) are low-entropy regions in the genome, consisting of a short (1-6 bp) unit that is consecutively repeated multiple times. They are known for high mutational instability, due to so-called stutter-mutations, in…

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…

In this paper, we propose a new method remMap -- REgularized Multivariate regression for identifying MAster Predictors -- for fitting multivariate response regression models under the high-dimension-low-sample-size setting. remMap is…

Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking…