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Biological cells are built up from many different constituents of varying size and stiffness which all contribute to the cell's mechanical properties. Despite this heterogeneity, in the analysis of experimental measurements such as atomic…

Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…

Understanding to what extent stem cell potential is a cell-intrinsic property, or an emergent behavior coming from global tissue dynamics and geometry, is a key outstanding question of systems and stem cell biology. Here, we propose a…

Experiments show that the movement of eukaryotic cells is regulated by a process of phase separation of two competing enzymes on the cell membrane, that effectively amplifies shallow external gradients of chemical attractant. Notably, the…

First order phase transitions proceed via nucleation. The rate of nucleation varies exponentially with the free-energy barrier to nucleation, and so is highly sensitive to variations in this barrier. In practice, very few systems are…

Major efforts to sequence cancer genomes are now occurring throughout the world. Though the emerging data from these studies are illuminating, their reconciliation with epidemiologic and clinical observations poses a major challenge. In the…

Cell motility is one of the most fundamental phenomena underlying biological processes that maintain living organisms alive. Here we introduce a simple model to describe the motility of cells which include not only time-correlated internal…

Experimental studies of cell motility in culture have shown that under adequate conditions these living organisms possess the ability to organize themselves into complex structures. Such structures may exhibit a synergy that greatly…

Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…

Single-cell sequencing has a significant role to explore biological processes such as embryonic development, cancer evolution, and cell differentiation. These biological properties can be presented by a two-dimensional scatter plot.…

When analyzing the individual positional dynamics of an ensemble of moving objects, the extracted parameters that characterize the motion of individual objects, such as the mean-squared instantaneous velocity or the diffusivity, exhibit a…

We investigate the Susceptible-Infectious-Recovered contagion dynamics in a system of self-propelled particles with polar alignment. Using agent-based simulations, we analyze the outbreak process for different combinations of the spatial…

Experiments and simulations have established that dynamics in a class of living and abiotic systems that are far from equilibrium exhibit super diffusive behavior at long times, which in some cases (for example evolving tumor) is preceded…

Phase transitions ruled by nucleation and growth can occur by nonrandom arrangement of nuclei. This is verified, for instance, in thin film growth at solid surfaces by vapor condensation or by electrodeposition where, around each nucleus, a…

Feature representation is an important aspect of remote-sensing based image classification. While deep convolutional neural networks are able to effectively amalgamate information, large numbers of parameters often make learned features…

We consider a class of biologically-motivated stochastic processes in which a unicellular organism divides its resources (volume or damaged proteins, in particular) symmetrically or asymmetrically between its progeny. Assuming the final…

This paper presents a kernelized version of the t-SNE algorithm, capable of mapping high-dimensional data to a low-dimensional space while preserving the pairwise distances between the data points in a non-Euclidean metric. This can be…

Understanding tumor invasion and metastasis is of crucial importance for both fundamental cancer research and clinical practice. In vitro experiments have established that the invasive growth of malignant tumors is characterized by the…

Cancer results from a sequence of genetic and epigenetic changes which lead to a variety of abnormal phenotypes including increased proliferation and survival of somatic cells, and thus, to a selective advantage of pre-cancerous cells. The…

Phase separation in a low-density gas-like phase and a high-density liquid-like one is a common trait of biological and synthetic self-propelling particles' systems. The competition between motility and stochastic forces is assumed to fix…