Related papers: Novel Generic Models for Differentiating Stem Cell…
The design of biological systems is hindered by uncertainty arising from both intrinsic stochasticity of biomolecular reactions and variability across laboratory or experimental conditions. In this work, we present a sequential framework to…
Synchronization of mobile oscillators occurs in numerous contexts, including physical, chemical, biological and engineered systems. In vertebrate embryonic development, a segmental body structure is generated by a population of mobile…
Cell functional diversity is a significant determinant on how biological processes unfold. Most accounts of diversity involve a search for sequence or expression differences. Perhaps there are more subtle mechanisms at work. Using the…
Stem cells are characterized by their ability to self-renew, as well as to differentiate and give rise to new populations of cells. Stem cell divisions are crucial for generative processes that occur during early development, and later in…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
One of the fundamental cellular processes governed by genetic regulatory networks in cells is the transition among different states under the intrinsic and extrinsic noise. Based on a two-state genetic switching model with positive…
We propose a probabilistic framework for developing computational models of biological neural systems. In this framework, physiological recordings are viewed as discrete-time partial observations of an underlying continuous-time stochastic…
Controlling growth via cell division is crucial in the development of higher organisms, and yet the mechanisms through which this is achieved, e.g., in epithelial tissue, is not yet fully understood. We show that by coupling the cell cycle…
We investigate the oscillatory dynamics and bifurcation structure of a reaction-diffusion system with bistable nonlinearity and mass conservation, which was proposed by [Otsuji et al, PLoS Comp. Biol. 3 (2007), e108]. The system is a useful…
Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We…
We present a novel mathematical model of heterogeneous cell proliferation where the total population consists of a subpopulation of slow-proliferating cells and a subpopulation of fast-proliferating cells. The model incorporates two…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
A key problem in computational biology is discovering the gene expression changes that regulate cell fate transitions, in which one cell type turns into another. However, each individual cell cannot be tracked longitudinally, and cells at…
In the human immune system, T-helper cells are able to differentiate into two lymphocyte subsets: Th1 and Th2. The intracellular signaling pathways of differentiation form a dynamic regulation network by secreting distinctive types of…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Stem cells have the potential to produce lineages of non-stem cell populations (differentiated cells) via a ubiquitous hierarchal division scheme. Differentiation of a stem cell into (partially) differentiated cells can happen either…
We model intracellular regulatory dynamics with threshold-type state-dependent delay and investigate the effect of the state-dependent diffusion time. A general model which is an extension of the classic differential equation models with…