Related papers: A New Genetic Code Table
Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…
This paper proposes a new mathematical framework that can be applied to biological problems such as analysis of the structures of proteins and protein complexes. In particular, it gives a new method for encoding the three-dimensional…
The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code…
The usage frequencies for codons belonging to quartets are analized, over the whole exonic region, for 92 biological species. Correlation is put into evidence, between the usage frequencies of synonymous codons with third nucleotide A and C…
Building on recent development by Padakandla and Pradhan, and by Lim, Feng, Pastore, Nazer, and Gastpar, this paper studies the potential of structured nested coset coding as a complete replacement for random coding in network information…
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…
The classification of amino acids and their sequence analysis plays a vital role in life sciences and is a challenging task. This article uses and compares state-of-the-art deep learning models like convolution neural networks (CNN), long…
The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
Motivation: The consistent amount of different types of omics data requires novel methods of analysis and data integration. In this work we describe Regression2Net, a computational approach to analyse gene expression and methylation…
What are proteins made from, as the working parts of the living cells protein machines? To answer this question, we need a technology to disassemble proteins onto elementary func-tional details and to prepare lumped description of such…
The ultimate secret of all lives on earth is hidden in their genomes -- a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level…
This work is concerned with the development of a well-founded, theoretically justified, and least complicated metric for the classification of proteins with reference to enzymes. As the signature of an enzyme family, a catalytic domain is…
Simulating generic quantum states and dynamics is practically intractable using classical computers. However, certain special classes -- namely Clifford and matchgate circuits -- permit efficient computation. They provide invaluable tools…
This paper is dealing with DNA cyclic codes which play an important role in DNA computing and have attracted a particular attention in the literature. Firstly, we introduce a new family of DNA cyclic codes over the ring…
Recently, Graph Convolutional Networks (GCNs) have proven to be a powerful mean for Computer Aided Diagnosis (CADx). This approach requires building a population graph to aggregate structural information, where the graph adjacency matrix…
Advances in classical machine learning and single-cell technologies have paved the way to understand interactions between disease cells and tumor microenvironments to accelerate therapeutic discovery. However, challenges in these machine…
Genes carry the instructions for making proteins that are found in a cell as a specific sequence of nucleotides that are found in DNA molecules. But, the regions of these genes that code for proteins may occupy only a small region of the…
A new algorithm to compute cylindrical algebraic decompositions (CADs) is presented, building on two recent advances. Firstly, the output is truth table invariant (a TTICAD) meaning given formulae have constant truth value on each cell of…
In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which…