Related papers: Theory for stability and regulation of epigenetic …
Complex gene regulatory networks often display emergent simple behavior. Sometimes this simplicity can be traced to a nearly equivalent energy landscape, but not always. Here, we show how a topological theory for stochastic and biochemical…
Motile eukaryotic cells display distinct modes of migration that often occur within the same cell type. It remains unclear, however, whether transitions between the migratory modes require changes in external conditions, or whether the…
Boolean networks have been widely used to explore aspects of gene regulation, traditionally with a single network. A modified form of the model to explore the effects of increasing the number of gene states has also recently been…
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature…
The dynamical behavior of two types of non-equilibrium systems is discussed: $(a)$ two-dimensional cellular structures, and $(b)$ living polymers. Simple models governing their evolution are introduced and steady state distributions (cell…
The mechanism through which cells determine their fate is intimately related to the spreading of certain biochemical (so-called epigenetic) marks along their genome. The mechanisms behind mark spreading and maintenance are not yet fully…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
In biology and ecology, individuals or communities of individuals living in unpredictable environments often alternate between different evolutionary strategies to spread and reduce risks. Such behavior is commonly referred to as…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…
We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…
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…
Cells adapt to different conditions by altering a vast number of components, which is measurable using transcriptome analysis. Given that a cell undergoing steady growth is constrained to sustain each of its internal components, the…
Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…