相关论文: Symmetry Analysis Of Genetic Code And Determinativ…
In genetic systems there is a non-trivial interface between the sequence of symbols which constitutes the chromosome, or ``genotype'', and the products which this sequence encodes --- the ``phenotype''. This interface can be thought of as a…
Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (Austin…
Two-component mixture models are particularly useful for identifying differentially expressed genes, but their performance can deteriorate markedly when the alternative distribution departs from parametric assumptions or symmetry. We…
Nuclear pleomorphism, defined herein as the extent of abnormalities in the overall appearance of tumor nuclei, is one of the components of the three-tiered breast cancer grading. Given that nuclear pleomorphism reflects a continuous…
We propose and apply a novel paradigm for characterization of genome data quality, which quantifies the effects of intentional degradation of quality. The rationale is that the higher the initial quality, the more fragile the genome and the…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
By starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient subspaces of the…
In this the first of an anticipated four paper series, fundamental results of quantitative genetics are presented from a first principles approach. While none of these results are in any sense new, they are presented in extended detail to…
In this paper, we study arbitrary infinite binary information systems each of which consists of an infinite set called universe and an infinite set of two-valued functions (attributes) defined on the universe. We consider the notion of a…
DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
Y-chromosomal and mitochondrial DNA profiles have been used as evidence in courts for decades, yet the problem of evaluating the weight of evidence has not been adequately resolved. Both are lineage markers (inherited from just one parent),…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
The origin of life is one of the greatest mysteries. The mechanism for the synthesis of DNA is synonymous with the chemical origin of life, and theories have been developed along many lines of reasoning, but resolving all requirements…
In clinical prediction settings the importance of a high-dimensional feature like genomics is often assessed by evaluating the change in predictive performance when adding it to a set of traditional clinical variables. This approach is…
Higher-dimensional analogs of the predictable degree property and column reducedness are defined, and it is proved that the two properties are equivalent. It is shown that every multidimensional convolutional code has, what is called, a…
Machine learning and deep learning have been celebrating many successes in the application to biological problems, especially in the domain of protein folding. Another equally complex and important question has received relatively little…
A new class of distances appropriate for measuring similarity relations between sequences, say one type of similarity per distance, is studied. We propose a new ``normalized information distance'', based on the noncomputable notion of…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
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…
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…