Related papers: Branch Mode Selection during Early Lung Developmen…
When modeling of tumor-driven angiogenesis, a major source of analytical and computational complexity is the strong coupling between the kinetic parameters of the relevant stochastic branching-and-growth of the capillary network, and the…
Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear simultaneously or sequentially in long and short germ-band…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Branched actin networks at the leading edge of a crawling cell evolve via protein-regulated processes such as polymerization, depolymerization, capping, branching, and severing. A formulation of these processes is presented and analyzed to…
Morphogenesis in the central nervous system has received intensive attention as elucidating fundamental mechanisms of morphogenesis will shed light on the physiology and pathophysiology of the developing central nervous system.…
Living neuronal networks in dissociated neuronal cultures are widely known for their ability to generate highly robust spatiotemporal activity patterns in various experimental conditions. These include neuronal avalanches satisfying the…
(Multi-type) branching processes are a natural and well-studied model for generating random infinite trees. Branching processes feature both nondeterministic and probabilistic branching, generalizing both transition systems and Markov…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
We propose a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis, the process of body segmentation during embryonic development, that is invariant across all vertebrate species. This is…
We present a flexible branching process model for cell population dynamics in synchrony/time-series experiments used to study important cellular processes. Its formulation is constructive, based on an accounting of the unique cohorts in the…
The forest of mutations associated to a multitype branching forest is obtained by merging together all vertices of its clusters and by preserving connections between them. We first show that the forest of mutations of any mulitype branching…
Tissue dynamics play a crucial role in biological processes ranging from inflammation to morphogenesis. However, these noisy multicellular dynamics are notoriously hard to predict. Here, we introduce a biomimetic machine learning framework…
A new suggestion for pattern formation in biological systems is proposed. The interaction of two signaling pathways provides complex patterning. The interaction of two pathways involves few of the biochemical complexities of the pathways.…
The relative importance of the intrinsic and extrinsic factors determining the variety of geometric shapes exhibited by dendritic trees remains unclear. This question was addressed by developing a model of the growth of dendritic trees…
We investigate a model of the GnRH pulse and surge generator, with the definite aim of constraining the model GnRH output with respect to a physiologically relevant list of specifications. The alternating pulse and surge pattern of…
A blood cell lineage consists of several consecutive developmental stages from the pluripotent or multipotent stem cell to a particular stage of terminally differentiated cells. There is considerable interest in identifying the key…
The interplay between tumor cells and macrophages plays a central regulatory role in cancer progression. In this study, we developed a mathematical model that incorporates tumor cells, M1 type macrophages, M2 type macrophages and an M3 type…
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function.…
Morphogenetic dynamics of tissue sheets require coordinated cell shape changes regulated by global patterning of mechanical forces. Inspired by such biological phenomena, we propose a minimal mechanochemical model based on the notion that…