Quantitative Biology
Why do biological and artificial neurons sometimes modularise, each encoding a single meaningful variable, and sometimes entangle their representation of many variables? In this work, we develop a theory of when biologically inspired…
Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…
Bacteria and phages have been in an ongoing arms race for billions of years. To resist phages bacteria have evolved numerous defense systems, which nevertheless are still overcome by counter-defense mechanisms of specific phages. These…
The spotted lanternfly (Lycorma delicatula) has recently spread from its native range to several other countries and forecasts predict that it may become a global invasive pest. In particular, since its confirmed presence in the United…
In neural-decoding studies, recordings of participants' responses to stimuli are used to train models. In recent years, there has been an explosion of publications detailing applications of innovations from deep-learning research to…
Populations evolving in fluctuating environments face the fundamental challenge of balancing adaptation to current conditions against preparation for uncertain futures. Here, we study microbial evolution in partially predictable…
Animals employ different strategies for relating sensory input to behavioral output to navigate sensory environments, but what strategy to use, when to switch and why remain unclear. In C. elegans, navigation is composed of 'steering' and…
Toy models are highly idealized and deliberately simplified models that retain only the essential features of a system in order to explore specific theoretical questions. Long used in physics and other sciences, they have recently begun to…
A population of individuals with the same genes can present heterogeneous traits (phenotypes). The prevalence of this heterogeneity can be explained as a bet-hedging strategy that improves the population proliferation rate (fitness) in…
Mathematical models of cardiac cell electrical activity include numerous parameters, making calibration to experimental data and individual-specific modeling challenging. This study applies Sobol sensitivity analysis, a global…
The boreal forest plays a crucial role as a global carbon sink. This study uses two 250-year simulations of Canada's Taiga Plains, an area targeted by the 2 Billion Trees Program to evaluate afforestation and reforestation strategies that…
Prokaryotes have evolved various mechanisms to counter viruses, which in their turn developed numerous strategies to avoid defenses of the hosts. Dozens of such defense and counter-defense mechanisms have recently been discovered, yet the…
The true slime mold \textit{Physarum polycephalum} has the remarkable capability to perform self-organized activities such as network formation among food sources. Despite well reproducing the emergence of slime networks, existing models…
Continuous glucose monitoring (CGM) combined with AI offers new opportunities for proactive diabetes management through real-time glucose forecasting. However, most existing models are task-specific and lack generalization across patient…
Computational multi-scale pandemic modelling remains a major and timely challenge. Here we identify specific requirements for a new class of models simulating pandemics across three scales: (1) pathogen evolution, often punctuated by the…
Polynomial dynamical systems (DSs) can model a wide range of physical processes. A special subset of these DSs that can model chemical reactions under mass-action kinetics is called chemical dynamical systems (CDSs). A fundamental problem,…
Chemotaxis, the movement of an organism in response to chemical stimuli, is a typical feature of many microbiological systems. In particular, the social amoeba \textit{Disctyostelium discoideum} is widely used as a model organism, but it is…
If brain anatomy and dynamics have a genuine complex network structure as it has become standard to posit, it is also reasonable to assume that such a structure should play a key role not only in brain function but also in brain…
The release of Wolbachia-infected mosquitoes into Aedes aegypti infested areas is a promising strategy for localised eradication of dengue infection. Ae aegypti mosquitoes favour urban environments as breeding habitats, so are often found…
Background:Chronic kidney disease is one of the most prevalent non-communicable health issues globally, and high body mass index plays a significant role in the onset and progression of chronic kidney disease. Methods: Data on the disease…