Related papers: Stochastic Models for Replication Origin Spacings …
DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
Genome replication, a key process for a cell, relies on stochastic initiation by replication origins, causing a variability of replication timing from cell to cell. While stochastic models of eukaryotic replication are widely available, the…
Eukaryotic cells are often exposed to fluctuations in growth conditions as well as endogenous and exogenous stress-related agents. In addition, during development global patterns of gene transcription change dramatically, and these changes…
We generalize a stochastic model of DNA replication to the case where replication-origin-initiation rates vary locally along the genome and with time. Using this generalized model, we address the inverse problem of inferring initiation…
We formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. The model describes well a large amount of…
This paper details an observation that for more primitive organisms, such as some yeasts, the statistical distribution of the origins of replication sometimes looks remarkably like the distribution of eigenvalues from the Circular…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Genome length varies widely among organisms, from compact genomes of prokaryotes to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome…
How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell…
Gene expression is significantly stochastic making modeling of genetic networks challenging. We present an approximation that allows the calculation of not only the mean and variance but also the distribution of protein numbers. We assume…
Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence-dependence of the local unzipping of double-stranded DNA, the first step…
A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or…
This paper investigates the stochastic fluctuations of the number of copies of a given protein in a cell. This problem has already been addressed in the past and closed-form expressions of the mean and variance have been obtained for a…
We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
In eukaryotes, DNA replication is initiated along each chromosome at multiple sites called replication origins. Locally, each replication origin is "licensed", or specified, at the end of the M and the beginning of G1 phases of the cell…
Following genetic ancestry in eukaryote populations poses several open problems due to sexual reproduction and recombination. The history of extant genetic material is usually modeled backwards in time, but tracking chromosomes at a large…
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic…