Related papers: Horizontal gene transfer: numerical comparison bet…
The purpose of this paper is to analyze the mechanism for the interplay of deterministic and stochastic models for contagious diseases. Deterministic models for contagious diseases are prone to predict global stability. Small natural birth…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
We investigate the interplay between two fundamental mechanisms of microbial population dynamics and evolution called dormancy and horizontal gene transfer. The corresponding traits come in many guises and are ubiquitous in microbial…
In this work, we characterize the solution of a system of elliptic integro-differential equations describing a phenotypically structured population subject to mutation, selection and migration between two habitats. Assuming that the effects…
Stochastic gene expression has been implicated in a variety of cellular processes, including cell differentiation and disease. In this issue of Cell, Weinberger et al. (2005) take an integrated computational-experimental approach to study…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
We consider a stochastic model of gene expression in which transcription depends on a multistate promoter, including the famous two-state model and refractory promoters as special cases, and focus on deriving the exact stationary…
Lateral gene transfer (LGT) is a common mechanism of non-vertical evolution where genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
A prevailing trend in neural network research suggests that model performance improves with increasing depth and capacity - often at the cost of integrability and efficiency. In this paper, we propose a strategy to optimize small,…
In this paper, we study an integro-differential equation which describes the evolutionary dynamics of a population structured by a phenotypic trait. This population undergoes asexual reproduction, competition, selection, and mutation. We…
The evolution of dispersal is a classical question in evolutionary biology, and it has been studied in a wide range of mathematical models. A selection-mutation model, in which the population is structured by space and a phenotypic trait,…
Multiple mechanisms in the HIV lifecycle play a role in its ability to evade therapy and become a chronic, difficult-to-treat infection. Within its major cellular target, the activated T cell, many steps occur between viral entry and viral…
In this paper we analyze a continuous-time epidemic model and its discrete counterpart, where infection spreads both horizontally and vertically. We consider three cases: model with horizontal and imperfect vertical transmissions, model…
In this note, we characterize the solution of a system of elliptic integro-differential equations describing a phe-notypically structured population subject to mutation, selection and migration. Generalizing an approach based on…
Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses…
Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Fluctuating environments pose tremendous challenges to bacterial populations. It is observed in numerous bacterial species that individual cells can stochastically switch among multiple phenotypes for the population to survive in rapidly…