Related papers: Ultrametrics in the genetic code and the genome
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
We study infinite tree and ultrametric matrices, and their action on the boundary of the tree. For each tree matrix we show the existence of a symmetric random walk associated to it and we study its Green potential. We provide a…
An important application of distance geometry to biochemistry studies the embeddings of the vertices of a weighted graph in the three-dimensional Euclidean space such that the edge weights are equal to the Euclidean distances between…
Random network coding recently attracts attention as a technique to disseminate information in a network. This paper considers a non-coherent multi-shot network, where the unknown and time-variant network is used several times. In order to…
Evolutionary algorithms borrow from biology the concepts of mutation and selection in order to evolve optimized solutions to known problems. The GENETIS collaboration is developing genetic algorithms for designing antennas that are more…
Some aspects of analysis involving fields with absolute value functions are discussed, which includes the real or complex numbers with their standard absolute values, as well as ultrametric situations like the p-adic numbers.
Optimizing a neural network's performance is a tedious and time taking process, this iterative process does not have any defined solution which can work for all the problems. Optimization can be roughly categorized into - Architecture and…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
The tendencies described in this work were revealed in the course of examination of adenine and uracil distribution in the mRNA encoding sequence. The study also discusses the usage of codons occupied by the amino acid arginine in the table…
We introduce genetic algorithms as a means to estimate the accuracy required to discriminate among different models using experimental observables. We exemplify the technique in the context of the minimal supersymmetric standard model. If…
The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences,…
We introduce a formalism for the geometry of eukaryotic cells and organisms.Cells are taken to be star-convex with good biological reason. This allows for a convenient description of their extent in space as well as all manner of cell…
In this paper we consider aspects of geometric observability for hypergraphs, extending our earlier work from the uniform to the nonuniform case. Hypergraphs, a generalization of graphs, allow hyperedges to connect multiple nodes and…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical…
We investigate the large-scale geometry of the DNA-protein complex of chromatin using a generalized optimality principle, which requires that not only should all sub-parts of a natural process be optimal but also the unfolding of higher…
The proof of the theorem, which states that the Euclidean metric on the set of random points in an $n$-dimensional Euclidean space with the distribution of a special class, converges in probability in the limit $n\rightarrow\infty$ to the…
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…
We review the theory and practice of determining what parts of a data set are ultrametric. It is assumed that the data set, to begin with, is endowed with a metric, and we include discussion of how this can be brought about if a…