Related papers: Gene expression from polynomial dynamics in the 2-…
The advent of new experimental genomic technologies and the massive increase of DNA sequence information is helping researchers better understand how our genes work. Recently, experiments on mRNA abundance (gene expression) have revealed…
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…
We describe the theoretical and computational framework for the Dynamic Signatures for Genetic Regulatory Network (DSGRN) database. The motivation stems from urgent need to understand the global dynamics of biologically relevant signal…
Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…
Discrete dynamical systems defined by the iteration of a polynomial map of the unit simplex to itself appear in the context of population genetic systems evolving under mutation, recombination and weak selection. Although exceptional…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
The expression of genes usually follows a two-step procedure. First, a gene (encoded in the genome) is transcribed resulting in a strand of (messenger) RNA. Afterwards, the RNA is translated into protein. Classically, this gene expression…
In this work, we propose a new deep learning model for Genomic Prediction (GP), which involves correlating genotypic data with phenotypic. The genotypes are typically fed as a sequence of characters to the 1D-Convolution Neural Network…
We present the extention and application of a new unsupervised statistical learning technique--the Partition Decoupling Method--to gene expression data. Because it has the ability to reveal non-linear and non-convex geometries present in…
Ultrametric approach to the genetic code and the genome is considered and developed. $p$-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any…
We discuss a model of genome as a program with functional architecture and consider the approach to Darwinian evolution as a learning problem for functional programming. In particular we introduce a model of learning for some class of…
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
Graphs as a type of data structure have recently attracted significant attention. Representation learning of geometric graphs has achieved great success in many fields including molecular, social, and financial networks. It is natural to…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…