Related papers: Universal relationship in gene-expression changes …
It is tempting to believe that we now own the genome. The ability to read and re-write it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles heel exposed by all of the genomic data that has…
Cellular phenotype is characterized by different components such as cell size, protein content and cell cycle time. These are global variables that are the outcome of multiple internal microscopic processes. Accordingly, they display some…
Cells can often choose among several stably heritable phenotypes. Examples are the expression of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states, that may be associated…
Inside individual cells, expression of genes is stochastic across organisms ranging from bacterial to human cells. A ubiquitous feature of stochastic expression is burst-like synthesis of gene products, which drives considerable…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Cells control their size to cope with noise during growth and division. Eukaryotic cells exhibiting "sizer" control (targeting a specific size before dividing) may rely on molecular concentration thresholds, but simple implementations of…
A fundamental question in biology is how cell populations evolve into different subtypes based on homogeneous processes at the single cell level. Here we show that population bimodality can emerge even when biological processes are…
The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
Gene sequences of a deme evolve over time as new chromosome inversions appear in a population via mutations, some of which will replace an existing sequence. The underlying biochemical processes that generates these and other mutations are…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
Growth in confined spaces can drive cellular populations through a jamming transition from a fluid-like state to a solid-like state. Experiments have found that jammed budding yeast populations can build up extreme compressive pressures…
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…
In this paper we study an important global regulation mechanism of transcription of biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S RNAs is of blocking the transcription of RNAs when the environment…
Living cells respond to mechanical changes in the matrix surrounding them by applying contractile forces that are in turn transmitted to distant cells. We calculate the mechanical work that each cell performs in order to deform the matrix,…
Proliferating cell populations at steady state growth often exhibit broad protein distributions with exponential tails. The sources of this variation and its universality are of much theoretical interest. Here we address the problem by…
Genetic oscillators are present in the cells of many organisms and control several biological processes. The common feature of such oscillators is the presence of a protein which represses the transcription of its own gene. Recently, it has…
Gene expression is inherently noisy as many steps in the read-out of the genetic information are stochastic. To disentangle the effect of different sources of stochasticity in such systems, we consider various models that describe some…