Related papers: Cell biology: Networks, regulation, pathways
Scientific research is a major driving force in a knowledge based economy. Income, health and wellbeing depend on scientific progress. The better we understand the inner workings of the scientific enterprise, the better we can prompt,…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
We will review some of the theoretical progresses that have been in the study of complex systems in physics and of their applications to biology.
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…
Boolean networks have been used in a variety of settings, as models for general complex systems as well as models of specific systems in diverse fields, such as biology, engineering, and computer science. Traditionally, their properties as…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
Research on probabilistic models of networks now spans a wide variety of fields, including physics, sociology, biology, statistics, and machine learning. These efforts have produced a diverse ecology of models and methods. Despite this…
Theory and empirical science should be in constant dialogue, but often find it hard to understand one another. Here we describe a graduate-level university course we developed to improve matters. The course was designed to help…
Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body, while at the same time raising the need to formalise this new knowledge. Here, we review current cell ontology efforts to…
We analyze the structure of two dimensional disordered cellular systems generated by extensive computer simulations. These cellular structures are studied as topological trees rooted on a central cell or as closed shells arranged…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Physicists study a wide variety of phenomena creating new interdisciplinary research fields by applying theories and methods originally developed in physics in order to solve problems in economics, social science, biology, medicine,…
Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
Multicellular self-organization drives development in biological organisms, yet a comprehensive theory is lacking as basic properties of cells can complicate common approaches. Framing such properties by dynamic graphs led to new…
Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…
Correlation is not causation. As simple as this widely agreed-upon statement may seem, scientifically defining causality and using it to drive our modern biomedical research is immensely challenging. In this perspective, we attempt to…
This limited review is intended as an introduction to the fast growing subject of mathematical modelling of cell metabolism and its biochemical pathways, and more precisely on pathways linked to apoptosis of cancerous cells. Some basic…
The lecture summarises main results of my team over last five years in the field of technical experiment design and interpretation of results of experiments for cell bi-ology. I introduce the theoretical concept of the experiment, based…
It has long been known that photonic science and especially photonic communications can raise the speed of technologies and producing manufacturing. More recently, photonic science has also been interested in its capabilities to implement…