Related papers: Sum rules of codon usage probabilities
New sets (typically found by computer search) with Sidon constant equal to the square root of their cardinalities are given. For each integer $N$ there are only a finite number of groups of prime order containing $N$-element extreme sets.…
We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the…
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as…
We introduce the simple parametrization for the space of codons (triples of nucleotides) by 8\times 8 table. This table (which we call the dyadic plane) possesses the natural 2-adic ultrametric. We show that after this parametrization the…
Traditional Quartet Puzzling algorithms use maximum likelihood methods to reconstruct quartet trees, and a puzzling algorithm to combine these quartets into a tree for the full collection of $n$ taxa. We propose a variation of Quartet…
Compositional data (i.e., data comprising random variables that sum up to a constant) arises in many applications including microbiome studies, chemical ecology, political science, and experimental designs. Yet when compositional data serve…
We study the learnability of sums of independent integer random variables given a bound on the size of the union of their supports. For $\mathcal{A} \subset \mathbf{Z}_{+}$, a sum of independent random variables with collective support…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
Background. The large-scale pattern of distribution of genes on the chromosomes in the known animal genomes is not well characterized. We hypothesized that individual genes will be distributed on chromosomes in a mathematically ordered…
The presence of clusters of rare codons is known to negatively impact the efficiency and accuracy of protein production. In this paper, we demonstrate a statistical method of identifying such clusters in the coding sequence of a gene. Using…
This review article discusses the experimental and theoretical status of various Parton Model sum rules. The basis of the sum rules in perturbative QCD is discussed. Their use in extracting the value of the strong coupling constant is…
We investigate the semileptonic decays of B and D mesons into $\pi$ and $\rho$ mesons, respectively, by means of QCD sum rules. We find that for the vector formfactors involved the pole dominance hypothesis is valid to good accuracy with…
It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In the…
Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In…
Materials property predictions have improved from advances in machine learning algorithms, delivering materials discoveries and novel insights through data-driven models of structure-property relationships. Nearly all available models rely…
This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as…
We calculate the almost sure dimension for a general class of random affine code tree fractals in $\mathbb R^d$. The result is based on a probabilistic version of the Falconer-Sloan condition $C(s)$ introduced in \cite{FS}. We verify that,…
In this report, the explicit probability density functions of the random Euclidean distances associated with regular hexagons are given, when the two endpoints of a link are randomly distributed in the same hexagon, and two adjacent…
We describe a probabilistic method of cross-identifying astrophysical sources in two catalogs from their positions and positional uncertainties. The probability that an object is associated with a source from the other catalog, or that it…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…