Related papers: Package models and the information crisis of prebi…
During an epidemic, the information available to individuals in the society deeply influences their belief of the epidemic spread, and consequently the preventive measures they take to stay safe from the infection. In this paper, we develop…
"Evolution behaves like a tinkerer" (Francois Jacob, Science, 1977). Software systems provide a unique opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to…
We consider information filtering, in which we face a stream of items too voluminous to process by hand (e.g., scientific articles, blog posts, emails), and must rely on a computer system to automatically filter out irrelevant items. Such…
Simulations of the coevolution of many interacting species are performed using the Webworld model. The model has a realistic set of predator-prey equations that describe the population dynamics of the species for any structure of the food…
Translating the relevance of preclinical models ($\textit{in vitro}$, animal models, or organoids) to their relevance in humans presents an important challenge during drug development. The rising abundance of single-cell genomic data from…
In survival analysis, longitudinal information on the health status of a patient can be used to dynamically update the predicted probability that a patient will experience an event of interest. Traditional approaches to dynamic prediction…
The productivity of a planetary biosphere is limited by how its free-energy budget is partitioned between maintaining a habitable environment, driving metabolism, and processing heritable information. We derive an upper bound on net primary…
In this paper we study a nonlinear reaction-diffusion system which models an infectious disease caused by bacteria such as those for cholera. One of the significant features in this model is that a certain portion of the recovered human…
We consider models of growing multi-level systems wherein the growth process is driven by rules of tournament selection. A system can be conceived as an evolving tree with a new node being attached to a contestant node at the best hierarchy…
The aims of this paper are to propose, construct and analyse microscopic kinetic models for the emergence of long chains of RNA from monomeric beta-D-ribonucleotide precursors in prebiotic circumstances. Our theory starts out from similar…
A steadily growing computational power is employed to perform molecular dynamics simulations of biological macromolecules, which represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data…
A common theme among the proposed models for network epidemics is the assumption that the propagating object, i.e., a virus or a piece of information, is transferred across the nodes without going through any modification or evolution.…
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…
Discrete diffusion models have recently shown significant progress in modeling complex data, such as natural languages and DNA sequences. However, unlike diffusion models for continuous data, which can generate high-quality samples in just…
The Internet contains a wealth of knowledge -- from the birthdays of historical figures to tutorials on how to code -- all of which may be learned by language models. However, while certain pieces of information are ubiquitous on the web,…
Self-organization is a fundamental process of complex biological systems, particularly during the early stages of development. In the mammalian embryo, blastocyst formation exemplifies a self-organized system, involving the correct…
The origin of life is often approached through the lens of replication, heredity, or molecular specificity. This paper proposes a thermodynamic framework in which the emergence of life is driven by the persistence of reaction pathways that…
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model…
Recent outbreaks of infectious diseases have been monitored closely from an epidemiological and microbiological perspective. Extracting from this wealth of data the information that is relevant for the evolution of the pathogen and predict…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…