Related papers: Weighted-Codon-Usage Based Phylogeny In Ectocarpal…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a…
Interacting particle systems undergoing repeated mutation and selection steps model genetic evolution, and also describe a broad class of sequential Monte Carlo methods. The genealogical tree embedded into the system is important in both…
Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the…
Ocean worlds are considered as targets for life detection missions because they meet several key requirements for habitability. However, identifying potential life on other worlds requires observing clear and unambiguous biosignature…
Identifying significant subsets of the genes, gene shaving is an essential and challenging issue for biomedical research for a huge number of genes and the complex nature of biological networks,. Since positive definite kernel based methods…
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…
We revisit Cox's proportional hazard models and LASSO in the aim of improving feature selection in survival analysis. Unlike traditional methods relying on cross-validation or BIC, the penalty parameter $\lambda$ is directly tuned for…
Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…
Evolution algebras were introduced into Genetics to deal with the mechanism of inheritance of asexual organisms. Their distribution into isotopism classes is uniquely related with the mutation of alleles in non-Mendelian Genetics. This…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
We investigate the influence of the nucleon-nucleon collision profile (probability of interaction as a function of the nucleon-nucleon impact parameter) in the wounded nucleon model and its extensions on several observables measured in…
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary…
The alpha model, a parametrized family of probabilities on cladograms (rooted binary leaf labeled trees), is introduced. This model is Markovian self-similar, deletion-stable (sampling consistent), and passes through the Yule, Uniform and…
It is increasingly recognized that participation bias can pose problems for genetic studies. Recently, to overcome the challenge that genetic information of non-participants is unavailable, it is shown that by comparing the IBD (identity by…
We give an analytical form for the weighted correlation function of peaks in a Gaussian random field. In a cosmological context, this approach strictly describes the formation bias and is the main result here. Nevertheless, we show its…
Using QCD motivated and phenomenological considerations, we construct x- dependent polarized parton distributions, which evolve under GLAP evolution, satisfy DIS data and are within positivity constraints. Each flavor is done separately and…