Related papers: The Genetic Code revisited: Inner-to-outer map, 2D…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression measurements. Moreover, those genes are often richly annotated using GO terms that…
Genetic programming is the practice of evolving formulas using crossover and mutation of genes representing functional operations. Motivated by genetic evolution we develop and solve two combinatorial games, and we demonstrate some…
The idea of the evolution of the genetic code from the CG to the CGUA alphabet has been developed further. The assumption of the originally triplet structure of the genetic code has been substantiated. The hypothesis of the emergence of…
We revisit the notion of gene regulatory code in embryonic development in the light of recent findings about genome spatial organisation. By analogy with the genetic code, we posit that the concept of code can only be used if the…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
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…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
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…
Genetic programming is a powerful heuristic search technique that is used for a number of real world applications to solve among others regression, classification, and time-series forecasting problems. A lot of progress towards a theoretic…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
The application of genetic algorithms (GAs) to many optimization problems in organizations often results in good performance and high quality solutions. For successful and efficient use of GAs, it is not enough to simply apply simple GAs…
We Propose 22 unique Solutions to the Genetic Code. An Alternative Cracking, from the Perspective of a Mathematician.
Identifying genes associated with complex human diseases is one of the main challenges of human genetics and computational medicine. To answer this question, millions of genetic variants get screened to identify a few of importance. To…
Cell formation is a critical step in the design of cellular manufacturing systems. Recently, it was tackled using a cut-based-graph-partitioning model. This model meets real-life production systems requirements as it uses the actual amount…
A model for the information transfer from DNA to protein using quantum information and computation techniques is presented. DNA is modeled as the sender and proteins are modeled as the receiver of this information. On the DNA side, a…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
The genetic code is profoundly shaped by an origin in ancient RNA-mediated interactions, needing an extended development to reach the Standard Genetic Code (SGC). That development can serially use RNA specificities, a ribonucleopeptide…
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…