Related papers: Modeling mutations in bacteria and human tissues
We explore the connection between evolution and large-deviation theory. To do so, we study evolutionary dynamics in which individuals experience mutations, reproduction, and selection using variants of the Moran model. We show that, in the…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
Research into somatic mutations in cancer cell DNA and their role in tumour growth and progression between successive stages is crucial for improving our understanding of cancer evolution. Mathematical and computer modelling can provide…
We study the influence of the matter content of extragalactic jets on their morphology, dynamics and emission properties. For this purpose we consider jets of extremely different compositions including pure leptonic and baryonic plasmas.…
We give a very short introduction to discrete and continuum models for the evolutionary and spatial dynamics of cancer through two case studies: a model for the evolutionary dynamics of cancer cells under cytotoxic therapy and a model for…
We present a theoretical as well as experimental investigation of a population of self-replicating segments of code subject to random mutation and survival of the fittest. Under the assumption that such a system constitutes a minimal system…
Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA…
Learning meaningful causal representations from observations has emerged as a crucial task for facilitating machine learning applications and driving scientific discoveries in fields such as climate science, biology, and physics. This…
Multitype branching processes are ideal for studying the population dynamics of stem cell populations undergoing mutation accumulation over the years following transplant. In such stochastic models, several quantities are of clinical…
Over 80% of human cancers originate from the epithelium, which covers the outer and inner surfaces of organs and blood vessels. In stratified epithelium, the bottom layers are occupied by stem and stem-like cells that continually divide and…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Stem cells have the potential to produce lineages of non-stem cell populations (differentiated cells) via a ubiquitous hierarchal division scheme. Differentiation of a stem cell into (partially) differentiated cells can happen either…
Starting from a general equation for organism (or cell system) growth and attributing additional cell death rate (besides the natural rate) to therapy, we derive an equation for cell response to {\alpha} radiation. Different from previous…
In this work, we introduce a computational model for the study of the host-bacteria interaction and the influence of the intestinal microbiota on the behavior and feeding pattern of an individual. The model is based on digital entities,…
We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the…
Evolutionary algorithms borrow from biology the concepts of mutation and selection in order to evolve optimized solutions to known problems. The GENETIS collaboration is developing genetic algorithms for designing antennas that are more…
We study a model for the spread of an infectious disease which incorporates spatial and temporal effects. The model is a delayed multi-type branching process in which types represent geographic regions while infected individuals reproduce…
Mutation testing is a well-established technique for assessing a test suite's quality by injecting artificial faults into production code. In recent years, mutation testing has been extended to machine learning (ML) systems, and deep…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…