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We report new statistical time-series analysis tools providing significant improvements in the rapid, precision extraction of discrete state dynamics from large databases of experimental observations of molecular machines. By building…
Computational modeling of cancer can help unveil dynamics and interactions that are hard to replicate experimentally. Thanks to the advancement in cancer databases and data analysis technologies, these models have become more robust than…
Collectively coordinated cell migration plays a role in tissue embryogenesis, cancer, homeostasis and healing. To study these processes, different cell-based modelling approaches have been developed, ranging from lattice-based cellular…
This article presents an algorithm that allows modeling of biological networks in a qualitative framework with continuous time. Mathematical modeling is used as a systems biology tool to answer biological questions, and more precisely, to…
The growth of several biological tissues is known to be controlled in part by local geometrical features, such as the curvature of the tissue interface. This control leads to changes in tissue shape that in turn can affect the tissue's…
Several models have been proposed to describe the dynamics of epithelial tissues undergoing morphogenetic changes driven by apical constriction pulses, which differ in where the constriction is applied, either at the perimeter or medial…
Mathematical modelling of biological population dynamics often involves proposing high fidelity discrete agent-based models that capture stochasticity and individual-level processes. These models are often considered in conjunction with an…
Human blood flow is a multi-scale problem: in first approximation, blood is a dense suspension of plasma and deformable red cells. Physiological vessel diameters range from about one to thousands of cell radii. Current computational models…
One of the essential functions of living organisms is spontaneous migration through the deformation of their body, such as crawling, swimming, and walking. Depending on the size of the object, the efficient migratory mode should be altered…
Statistical tools are crucial for studying and modeling turbulent flows, where chaotic velocity fluctuations span a wide range of spatial and temporal scales. Advances in image velocimetry, especially in tracking-based methods, now allow…
Tuning cell rearrangements is essential in collective cell movement that underlies cancer progression, wound repair, and embryonic development. A key question is how tissue material properties and morphology emerge from cellular factors…
Chemotaxis is a ubiquitous biological phenomenon in which cells detect a spatial gradient of chemoattractant, and then move towards the source. Here we present a position-dependent advection-diffusion model that quantitatively describes the…
The migratory dynamics of cells can be influenced by the complex micro-environment through which they move. It remains unclear how the motility machinery of confined cells responds and adapts to their micro-environment. Here, we propose a…
Cell biomechanics involve a great number of complex phenomena that are fundamental to the evolution of life itself and other associated processes, ranging from the very early stages of embryo-genesis to the maintenance of damaged structures…
Fluorescence microscopy has led to impressive quantitative models and new insights gained from richer sets of biomedical imagery. However, there is a dearth of rigorous and established bioimaging strategies for modeling spatiotemporal…
Brownian motion is a universal characteristic of colloidal particles embedded in a host medium, and it is the fingerprint of molecular transport or diffusion, a generic feature of relevance not only in Physics but also in several branches…
In the emerging field of 3D bioprinting, cell damage due to large deformations is considered a main cause for cell death and loss of functionality inside the printed construct. Those deformations, in turn, strongly depend on the…
A variety of enhanced statistical and numerical methods are now routinely used to extract comprehensible and relevant thermodynamic information from the vast amount of complex, high-dimensional data obtained from intensive molecular…
A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for…
Widefield calcium imaging has recently emerged as a powerful experimental technique to record coordinated large-scale brain activity. These measurements present a unique opportunity to characterize spatiotemporal coherent structures that…