相关论文: Symmetry and Codon Usage Correlations in the Genet…
Modern genomics experiments measure functional behaviors for many thousands of DNA sequences. We suggest that, especially when these sequences are chosen at random, it is natural to compute correlation functions between sequences and…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…
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…
In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…
Constant-dimension codes have recently received attention due to their significance to error control in noncoherent random network coding. In this paper, we show that constant-rank codes are closely related to constant-dimension codes and…
Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our…
Surface codes are promising for practical quantum error correction due to their high threshold and experimental feasibility. However, their performance under realistic noise conditions, particularly those involving correlated errors,…
Parton distributions in a {\it{valon}} in the next-to-leading order is used to determine the patron distributions in pion and kaon. The validity of the valon model is tested and shown that the partonic content of the valon is universal and…
Quark-lepton symmetric models are a class of gauge theories motivated by the similarities between the quarks and leptons. In these models the gauge group of the standard model is extended to include a ``color'' group for the leptons.…
Present day data allow significant reconsideration of ideas on mechanisms underlying the degeneracy in the genetic code. Here a hypothesis is presented which links the degeneracy to possible conformational alterations in the codon-anticodon…
The class of poset metrics is very large and contains some interesting families of metrics. A family of metrics, based on posets which are formed from disjoint chains which have the same size, is examined. A necessary and sufficient…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
The optimal capacity of graded-response perceptrons storing biased and spatially correlated patterns with non-monotonic input-output relations is studied. It is shown that only the structure of the output patterns is important for the…
The use of partial geometries to construct parity-check matrices for LDPC codes has resulted in the design of successful codes with a probability of error close to the Shannon capacity at bit error rates down to $10^{-15}$. Such…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
This paper explores properties and applications of an ordered subset of the quadratic integer ring $\mathbb{Z}\left[\frac{1+\sqrt{5}}{2}\right]$. The numbers are shown to exhibit a parity triplet, as opposed to the familiar even/odd doublet…
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…