Related papers: Codon Capture and Ambiguous Intermediate Scenarios…
DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
Soft context formation is a lossless image coding method for screen content. It encodes images pixel by pixel via arithmetic coding by collecting statistics for probability distribution estimation. Its main pipeline includes three stages,…
The process of translation is ambiguous, in that there are typically many valid trans- lations for a given sentence. This gives rise to significant variation in parallel cor- pora, however, most current models of machine translation do not…
Large-scale simultaneous mRNA translation and the resulting competition for the available ribosomes has important implications to the cell's functioning and evolution. Developing a better understanding of the intricate correlations between…
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…
Colorization is an ambiguous problem, with multiple viable colorizations for a single grey-level image. However, previous methods only produce the single most probable colorization. Our goal is to model the diversity intrinsic to the…
A key problem in computational biology is discovering the gene expression changes that regulate cell fate transitions, in which one cell type turns into another. However, each individual cell cannot be tracked longitudinally, and cells at…
RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with…
We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…
In this study, we build upon a previously proposed neuroevolution framework to evolve deep convolutional models. Specifically, the genome encoding and the crossover operator are extended to make them applicable to layered networks. We also…
Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…
We present a computer simulation, which is inspired by Penna model, to help understanding the effect of genetic coding tables on population dynamics. To represent populations we used real and artificial gene sequences in this model. We…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
The evolution of genetic systems has been analyzed through the use of modifier gene models, in which a neutral gene is posited to control the transmission of other genes under selection. Analysis of modifier gene models has found the…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
Trapped Bosons exhibit fundamental physical phenomena and are potentially useful for quantum technologies. We present a method for simulating Bosons using path integral molecular dynamics. A main challenge for simulations is including all…