Related papers: Toward a systems-level view of mitotic checkpoints
Using Monte Carlo model of biological evolution we have discovered that populations can switch between two different strategies of their genomes' evolution; Darwinian purifying selection and complementing the haplotypes. The first one is…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
The proliferative activity of breast tumors, which is routinely estimated by counting of mitotic figures in hematoxylin and eosin stained histology sections, is considered to be one of the most important prognostic markers. However, mitosis…
We study theoretically the replication of Kinetoplast DNA consisting of several thousands separate mini-circles found in organisms of the class Kinetoplastida. When the cell is not actively dividing these are topologically connected in a…
Medical images acquired from standardized protocols show consistent macroscopic or microscopic anatomical structures, and these structures consist of composable/decomposable organs and tissues, but existing self-supervised learning (SSL)…
Biological mixtures such as the cytosol may consist of thousands of distinct components. There is now a substantial body of evidence showing that, under physiological conditions, intracellular mixtures can phase separate into spatially…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Synthetic molecular communication (MC) is a new communication engineering paradigm which is expected to enable revolutionary applications such as smart drug delivery and real-time health monitoring. The design and implementation of…
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
The ocean is filled with phytoplankton that contribute as much photosynthesis as all land plants combined, making them vital to the carbon cycle and climate system. Recent advances in flow cytometry allow oceanographers to measure the…
The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms. While…
Autocatalysis is thought to have played an important role in the earliest stages of the origin of life. An autocatalytic cycle (AC) is a set of reactions that results in stoichiometric increase in its constituent chemicals. When the…
Mitotic activity is a crucial proliferation biomarker for the diagnosis and prognosis of different types of cancers. Nevertheless, mitosis counting is a cumbersome process for pathologists, prone to low reproducibility, due to the large…
Cancer cells are widely known to be protected from apoptosis, which is a major hurdle to successful anti-cancer therapy. Over-expression of several anti-apoptotic proteins, or mutations in pro-apoptotic factors, has been recognized to…
To separate the overlapped cells, a bottleneck detection approach is proposed in this paper. The cell image is segmented by slope difference distribution (SDD) threshold selection. For each segmented binary clump, its one-dimensional…
The saddle-node bifurcation on an invariant circle (SNIC) is one of the codimension-one routes to creation or destruction of a periodic orbit in a continuous-time dynamical system. It governs the transition from resting behaviour to…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
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…