Related papers: Multisite Population Epigenetic Model of Passive D…
Multisite phosphorylation plays an important role in intracellular signaling. There has been much recent work aimed at understanding the dynamics of such systems when the phosphorylation/dephosphorylation mechanism is distributive, that is,…
Genetic diversity is central to the process of evolution. Both natural selection and random genetic drift are influenced by the level of genetic diversity of a population; selection acts on diversity while drift samples from it. At a given…
We consider a nonlinear coupled discrete-time model of population dynamics. This model describes the movement of populations within a heterogeneous landscape, where the growth of subpopulations are modelled by (possibly different) bounded…
The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects.…
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…
Data taking values on discrete sample spaces are the embodiment of modern biological research. "Omics" experiments produce millions of symbolic outcomes in the form of reads (i.e., DNA sequences of a few dozens to a few hundred…
As the first step in an investigation of the origin of genetic information, we study how some species of molecules are preserved over cell generations and play an important role in controlling the growth of a cell. We consider a model…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
Major Depressive Disorder (MDD) is a clinically heterogeneous syndrome with diverse etiological pathways. Traditional Epigenome-Wide Association Studies (EWAS) have successfully identified risk loci based on differential methylation…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
Gene duplication is believed to play a major role in the evolution of genomic complexity. The presence of a duplicate removes the constraint of natural selection upon the gene, leading to its likely loss of function or, occasionally, the…
This paper addresses mechanisms for boundedly rational decision makers in discrete choice problem. First, we introduce two mathematical models of population dynamics with conformity biases. We next analyze the models in terms of…
The active sites of enzymes consist of residues necessary for catalysis, and structurally important non-catalytic residues that together maintain the architecture and function of the active site. Examples of evolutionary interactions…
A novel method to classify human cells is presented in this work based on the transform-domain method on DNA methylation data. DNA methylation profile variations are observed in human cells with the progression of disease stages, and the…
Many patterning events in multi-cellular organisms rely on cell-to-cell contact signaling, such as the Notch pathway in metazoans. A particularly interesting phenomenon in this form of communication is lateral inhibition where a cell that…