Related papers: Studies on the Origin and Evolution of Codon Bias
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists that, under explicit…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
Cyclic redundancy check (CRC) codes check if a codeword is correctly received. This paper presents an algorithm to design CRC codes that are optimized for the code-specific error behavior of a specified feedforward convolutional code. The…
Sensory systems across all modalities and species exhibit adaptation to continuously changing input statistics. Individual neurons have been shown to modulate their response gains so as to maximize information transmission in different…
Over repeat presentations of the same stimulus, sensory neurons show variable responses. This "noise" is typically correlated between pairs of cells, and a question with rich history in neuroscience is how these noise correlations impact…
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
Neural codes appear efficient. Naturally, neuroscientists contend that an efficient process is responsible for generating efficient codes. They argue that natural selection is the efficient process that generates those codes. Although…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick…
In 1932, Paul Erdos asked whether a random walk constructed from a binary sequence can achieve the lowest possible deviation (lowest discrepancy), for the sequence itself and for all its subsequences formed by homogeneous arithmetic…
In contrast with animal communication systems, diversity is characteristic of almost every aspect of human language. Languages variously employ tones, clicks, or manual signs to signal differences in meaning; some languages lack the…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
{\bf Background}: Several features are known to correlate with the GC-content in the human genome, including recombination rate, gene density and distance to telomere. However, by testing for pairwise correlation only, it is impossible to…
We argue that the phenomenon of symmetry breaking in genetics can enhance the adaptability of a species to changes in the environment. In the case of a virus, the claim is that the codon bias in the neutralization epitope improves the…
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…
Neural compression methods are gaining popularity due to their superior rate-distortion performance over traditional methods, even at extremely low bitrates below 0.1 bpp. As deep learning architectures, these models are prone to bias…
Neural codes are lists of subsets of neurons that fire together. Of particular interest are neurons called place cells, which fire when an animal is in specific, usually convex regions in space. A fundamental question, therefore, is to…
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show…
Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests…
In this paper we consider the class of anti-uniform Huffman codes and derive tight lower and upper bounds on the average length, entropy, and redundancy of such codes in terms of the alphabet size of the source. The Fibonacci distributions…