Related papers: Semi-phenomenological classification models of the…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
Given a first-order sentence, a model-checking computation tests whether the sentence holds true in a given finite structure. Data provenance extracts from this computation an abstraction of the manner in which its result depends on the…
Let $\mathbb{F}_q$ be a finite field with $q$ elements and denote by $\theta : \mathbb{F}_q\to\mathbb{F}_q$ an automorphism of $\mathbb{F}_q$. In this paper, we deal with linear codes of $\mathbb{F}_q^n$ invariant under a semi-linear map…
We present a coherent Bayesian framework for selection of the most likely model from the five genetic models (genotypic, additive, dominant, co-dominant, and recessive) commonly used in genetic association studies. The approach uses a…
Nonextensive statistical mechanics has been a source of investigation in mathematical structures such as deformed algebraic structures. In this work, we present some consequences of $q$-operations on the construction of $q$-numbers for all…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The purpose of this article is to introduce q-deformed Stirling numbers of the first and second kinds. Relations between these numbers, Riemann zeta function and q-Bernoulli numbers of higher order are given. Some relations related to the…
Using concepts of physics of elementary particles concerning the breaking of symmetry and grannd unified theory we propose to study with the algebraic approximation the degeneracy finded in the genetic code with the incorporation of a…
It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In the…
This article gives a brief introduction to $q$-special functions, i.e., $q$-analogues of the classical special functions. Here $q$ is a deformation parameter, usually $0<q<1$, where $q=1$ is the classical case. The main topics to be treated…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
A new numerical characterization of symbolic sequences is proposed. The partition of sequence based on Ke and Tong algorithm is a starting point. Algorithm decomposes original sequence into set of distinct subsequences - a patterns. The set…
We consider a novel group testing procedure, termed semi-quantitative group testing, motivated by a class of problems arising in genome sequence processing. Semi-quantitative group testing (SQGT) is a non-binary pooling scheme that may be…
This article is partly a survey and partly a research paper. It tackles the use of Groebner bases for addressing problems of numerical semigroups, which is a topic that has been around for some years, but it does it in a systematic way…
Integrating heterogeneous datasets across different measurement platforms is a fundamental challenge in many scientific applications. A common example arises in deconvolution problems, such as cell type deconvolution, where one aims to…
The main aim of this work is to introduce and justify the study of semi-covarities. A {\it semi-covariety} is a non-empty family $\mathcal{F}$ of numerical semigroups such that it is closed under finite intersections, has a minimum,…
In this article, we propose a topological model to encode partial equivariance in neural networks. To this end, we introduce a class of operators, called P-GENEOs, that change data expressed by measurements, respecting the action of certain…
We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…