相关论文: A Solvable Sequence Evolution Model and Genomic Co…

We investigate symbolic sequences and in particular information carriers as e.g. books and DNA-strings. First the higher order Shannon entropies are calculated, a characteristic root law is detected. Then the algorithmic entropy is…

When mutation rates are low, natural selection remains effective, and increasing the mutation rate can give rise to an increase in adaptation rate. When mutation rates are high to begin with, however, increasing the mutation rate may have a…

Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…

The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…

Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…

Developing models with high interpretability and even deriving formulas to quantify relationships between biological data is an emerging need. We propose here a framework for ab initio derivation of sequence motifs and linear formula using…

Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…

Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…

Sequence-to-sequence transduction is the core problem in language processing applications as diverse as semantic parsing, machine translation, and instruction following. The neural network models that provide the dominant solution to these…

We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…

Abstract Recent advances in immunology and synthetic biology have accelerated the development of deep generative methods for DNA sequence design. Two dominant approaches in this field are AutoRegressive (AR) models and Diffusion Models…

We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…

{\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…

The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…

Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…

In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…

The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we…

As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our…

We present new techniques for synthesizing programs through sequences of mutations. Among these are (1) a method of local scoring assigning a score to each expression in a program, allowing us to more precisely identify buggy code, (2)…

A nucleotides sequence is identified, in the two (four) letters alphabet, by the the labels of a vector state of an irreducible representation of U_q(sl(2)) (U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the distribution…