Related papers: Signalling Entropy: a novel network-theoretical fr…
With the advancement of high-throughput biotechnologies, we increasingly accumulate biomedical data about diseases, especially cancer. There is a need for computational models and methods to sift through, integrate, and extract new…
Many dynamical phenomena in complex systems concern spreading that plays out on top of networks with changing architecture over time -- commonly known as temporal networks. A complex system's proneness to facilitate spreading phenomena,…
A rigorous understanding of how multicellular behaviors arise from the actions of single cells requires quantitative frameworks that bridge the gap between genetic circuits, the arrangement of cells in space, and population-level behaviors.…
The existence of the {\em typical set} is key for data compression strategies and for the emergence of robust statistical observables in macroscopic physical systems. Standard approaches derive its existence from a restricted set of…
Resistance to therapy remains a significant challenge in cancer treatment, often due to the presence of a stem-like cell population that drives tumor recurrence post-treatment. Moreover, many anticancer therapies induce plasticity,…
Mathematical modeling of disease outbreaks can infer the future trajectory of an epidemic, which can inform policy decisions. Another task is inferring the origin of a disease, which is relatively difficult with current mathematical models.…
Entropy is one of the key thermodynamic variables reflecting changes in the state of matter. Unlike other thermodynamic variables, it is well-defined also for nonequilibrium steady states through its relation to information. Applying this…
We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combinatorial therapy against cancer. The experiments are…
Quantification of complexity in neurophysiological signals has been studied using different methods, especially those from information or dynamical system theory. These studies revealed the dependence on different states of consciousness,…
The knowledge of cell molecular mechanisms implicated in human diseases is expanding and should be converted into guidelines for deciphering pathological cell signaling and suggesting appropriate treatment. The basic assumption is that…
This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…
The classification of electron systems according to their topology has been at the forefront of condensed matter research in recent years. It has been found that systems of the same symmetry, previously thought of as equivalent, may in fact…
Recent developments enable the quantification of causal control given a structural causal model (SCM). This has been accomplished by introducing quantities which encode changes in the entropy of one variable when intervening on another.…
Cell migration is crucial to many physiological and pathological processes. During migration, a cell adapts its morphology, including the overall morphology and nucleus morphology, in response to various cues in complex microenvironments,…
Entropy rate of sequential data-streams naturally quantifies the complexity of the generative process. Thus entropy rate fluctuations could be used as a tool to recognize dynamical perturbations in signal sources, and could potentially be…
Graph based entropy, an index of the diversity of events in their distribution to parts of a co-occurrence graph, is proposed for detecting signs of structural changes in the data that are informative in explaining latent dynamics of…
Recent evidence suggests that nongenetic (epigenetic) mechanisms play an important role at all stages of cancer evolution. In many cancers, these mechanisms have been observed to induce dynamic switching between two or more cell states,…
Mechanics and biochemical signaling are both often deregulated in cancer, leading to cancer cell phenotypes that exhibit increased invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control…
Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and…