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Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
A number of factors, such as, cell-cell interactions and self-propulsion of cells driven by cytoskeletal forces determine tissue morphologies and dynamics. To explore the interplay between these factors in controlling the dynamics at the…
Decisions in the cell that lead to its ultimate fate are important for cellular functions such as proliferation, growth, differentiation, development and death. Understanding this decision process is imperative for advancements in the…
We are living in an uncertain and dynamically changing world, where optimal decision-making under uncertainty is directly linked to the survival of species. However, evolutionary selection pressures that shape value-based decision-making…
Cancer is a disease of cellular regulation, often initiated by genetic mutation within cells, and leading to a heterogeneous cell population within tissues. In the competition for nutrients and growth space within the tumors the phenotype…
Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
A dynamical systems scenario for developmental cell biology is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Diversification, formation of discrete and recursive types, and…
Biological cells can actively tune their intracellular architecture according to their overall shape. Here we explore the rheological implication of such coupling in a minimal model of a dense cellular material where each cell exerts an…
Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Cells are known to sense and respond to their mechanical microenvironment in profound ways. Various evidence has implicated the adhesome, a body of adhesion associated proteins, in several cell fate decisions, including differentiation and…
Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…
Existing studies comparing individual-based models of growing cell populations and their continuum counterparts have mainly focused on homogeneous populations, in which all cells have the same phenotypic characteristics. However,…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
A cell routinely responds to one of many competing environmental cues. A fundamental question is whether the cell follows the cue prioritized by its internal signaling network or the cue that carries the most external information. We…
All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which…
We study the asymptotic behaviors of stochastic cell fate decision between proliferation and differentiation. We propose a model of a self-replicating Langevin system, where cells choose their fate (i.e. proliferation or differentiation)…