Related papers: Optimal Placement of Origins for DNA Replication
Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we…
Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach,…
The origin of heredity is studied as a recursive state in a replicating proto-cell consisting of many molecule species in mutually catalyzing reaction networks. Protocells divide when the number of molecules, increasing due to replication,…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and tradeoffs of DNA-based storage systems under a simple model, motivated by current…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
Tomasetti and Vogelstein recently proposed that the majority of variation in cancer risk among tissues is due to "bad luck," that is, random mutations arising during DNA replication in normal noncancerous stem cells. They generalize this…
Even the simplest organisms are too complex to have spontaneously arisen fully-formed, yet precursors to first life must have emerged ab initio from their environment. A watershed event was the appearance of the first entity capable of…
The Poisson distribution is the probability distribution of the number of independent events in a given period of time. Although the Poisson distribution appears ubiquitously in various stochastic dynamics of gene expression, both as…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
In this paper we study the evolution of the mutation rate for simple organisms in dynamic environments. A model with multiple fitness coding loci tracking a moving fitness peak is developed and an analytical expression for the optimal…
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are…
Alternative splicing allows an organism to make different proteins in different cells at different times, all from the same gene. In a cell that uses alternative splicing, the total length of all the exons is much shorter than in a cell…
We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
The expression of genes usually follows a two-step procedure. First, a gene (encoded in the genome) is transcribed resulting in a strand of (messenger) RNA. Afterwards, the RNA is translated into protein. Classically, this gene expression…
Stochastic restart may drastically reduce the expected run time of a computer algorithm, expedite the completion of a complex search process, or increase the turnover rate of an enzymatic reaction. These diverse first-passage-time (FPT)…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
The amplification cycle of many replicators (natural or artificial) involves the usage of a host compartment, inside of which the replicator express phenotypic compounds necessary to carry out its genetic replication. For example, viruses…
We propose an alternative to the prevailing two origin of life narratives, one based on a replicator first hypothesis, and one based on a metabolism first hypothesis. Both hypotheses have known difficulties: All known evolvable molecular…