Related papers: Beta sheet propensity and the genetic code
This paper presents an overview of recent computer simulations of grain boundary (GB) diffusion focusing on atomistic understanding of diffusion mechanisms. At low temperatures when GB structure is ordered, diffusion is mediated by point…
The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of…
The beta model is the most important distribution for fitting data with the unit interval. However, the beta distribution is not suitable to model bimodal unit interval data. In this paper, we propose a bimodal beta distribution constructed…
Recent work has studied the interplay between a galaxy's history and its observable properties using "genetically modified" cosmological zoom simulations. The approach systematically generates alternative histories for a halo, while keeping…
Consider a supercritical birth and death process where the children acquire mutations. We study the mutation rates along the ancestral lineages in a sample of size $n$ from the population at time $T$. The mutation rate is time-inhomogenous…
The Protein Data Bank (PDB) today contains more than 153,000 entries with the 3-dimensional structures of biological macromolecules. Using the rich resources of this repository, it is possible identifying subsets with specific, interesting…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially…
Cell type (e.g. pluripotent cell, fibroblast) is the end result of many complex processes that unfold due to evolutionary, developmental, and transformational stimuli. A cell's phenotype and the discrete, a priori states that define various…
A population genetics model based on a multitype branching process, or equivalently a Galton-Watson branching process for multiple alleles, is pre- sented. The diffusion limit forward Kolmogorov equation is derived for the case of neutral…
All stem cell fate transitions, including the metabolic reprogramming of stem cells and the somatic reprogramming of fibroblasts into pluripotent stem cells, can be understood from a unified theoretical model of cell fates. Each cell fate…
Whole genome sequencing (WGS) is quickly becoming the customary means for identification of antimicrobial resistance (AMR) due to its ability to obtain high resolution information about the genes and mechanisms that are causing resistance…
We investigate the process of fixation of advantageous mutations in an asexual population. We assume that the effect of each beneficial mutation is exponentially distributed with mean value $\omega_{med}=1/\beta$. The model also considers…
Deviations from scale invariance resulting from small perturbations of a general two dimensional conformal field theory are studied. They are expressed in terms of beta functions for renormalization of general couplings under local change…
A good feature representation is a determinant factor to achieve high performance for many machine learning algorithms in terms of classification. This is especially true for techniques that do not build complex internal representations of…
Grain boundaries (GBs) are planar lattice defects that govern the properties of many types of polycrystalline materials. Hence, their structures have been investigated in great detail. However, much less is known about their chemical…
The evolution of the allelic proportion $x$ of a biallelic locus subject to the forces of mutation and drift is investigated in a diffusion model, assuming small scaled mutation rates. The overall scaled mutation rate is parametrized with…
Transforming growth factor (TGF) $\beta$ is known to have properties of both a tumor suppressor and a tumor promoter. While it inhibits cell proliferation, it also increases cell motility and decreases cell--cell adhesion. Coupling…
In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which…