Related papers: Genetic Code and Number Theory
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Decoding the genome confers the capability to predict characteristics of the organism(phenotype) from DNA (genotype). We describe the present status and future prospects of genomic prediction of complex traits in humans. Some highly…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
Biology-derived algorithms are an important part of computational sciences, which are essential to many scientific disciplines and engineering applications. Many computational methods are derived from or based on the analogy to natural…
A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick…
Throughout the evolution of biological species on Earth, cells and organs have developed many complex structures and processes to ensure their interactions with individual chemical molecules (small and macromolecular) and nanoscale objects…
The interpretation of recent environmental genomics data exposes the far-reaching influence of horizontal gene transfer, and is changing our basic concepts of organism, species and evolution itself.
Scientific code is not production software. Scientific code participates in the evaluation of a scientific hypothesis. This imposes specific constraints on the code that are often overlooked in practice. We articulate, with a small example,…
We study the problem of building generative models of natural source code (NSC); that is, source code written and understood by humans. Our primary contribution is to describe a family of generative models for NSC that have three key…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored…
Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. Families of genetic (4*4)- and (8*8)-matrices show unexpected connections of the genetic system…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
A codon table is a useful tool for mapping codons to amino acids as they have been assigned by nature. It has become a scientific icon because of the way it embodies our understanding of this natural process and the way it immediately…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
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…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…