Related papers: Alternative Splicing and Genomic Stability
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
We explore the interaction between two genetic incompatibilities (underdominant loci in diploid organisms) in a population occupying a one-dimensional space. We derive a system of partial differential equations describing the dynamics of…
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…
We study the emergence of cell differentiation under the assumption of the existence of a given number of tradeoffs between genes encoding different functions. In the model the viability of colonies is determined by the capability of their…
In this paper we consider the anharmonic corrections to the anisotropic elastic rod model for DNA. Our model accounts for the difference between the bending energies of positive and negative rolls, which comes from the asymmetric structure…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
Niching enables a genetic algorithm (GA) to maintain diversity in a population. It is particularly useful when the problem has multiple optima where the aim is to find all or as many as possible of these optima. When the fitness landscape…
Large populations may contain numerous simultaneously segregating polymorphisms subject to natural selection. Since selection acts on individuals whose fitness depends on many loci, different loci affect each other's dynamics. This leads to…
Reprogramming is a process of transforming differentiated cells into pluripotent stem cells by inducing specific modifying factors in the cells. Reprogramming is a non-equilibrium process involving a collaboration at levels separated by…
Human embryonic stem cells (ESC) are undifferentiated and are endowed with the capacities of self renewal and pluripotential differentiation. Adult stem cells renew their own tissue, but whether they can trans-differentiate to other tissues…
Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
It is a well-known fact that genetic sequences may contain sections with repeated units, called repeats, that differ in length over a population, with a length distribution of geometric type. A simple class of recombination models with…
Environmental heterogeneity can drive genetic heterogeneity in expanding populations; mutant strains may emerge that trade overall growth rate for an improved ability to survive in patches that are hostile to the wild type. This…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
Researchers puzzle over questions as to how rare species survive extinction, and why a significant proportion of microbial taxa are dormant. Computational simulation modeling by a genetic algorithm provides some answers. First, a…
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…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
This paper develops simplified mathematical models describing the mutation-selection balance for the asexual and sexual replication pathways in {\it Saccharomyces cerevisiae}. We assume diploid genomes consisting of two chromosomes, and we…