相关论文: Revisiting Waiting Times in DNA evolution

Motivated by the randomized generation of slowly synchronizing automata, we study automata made of permutation letters and a merging letter of rank $ n\!-\!1 $. We present a constructive randomized procedure to generate synchronizing…

Transposable Elements (TEs) or jumping genes are the DNA sequences that have an intrinsic capability to move within a host genome from one genomic location to another. Studies show that the presence of a TE within or adjacent to a…

Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA…

Recursive processing is considered a hallmark of human linguistic abilities. A recent study evaluated recursive processing in recurrent neural language models (RNN-LMs) and showed that such models perform below chance level on embedded…

The delay time distribution of neutron star mergers provides critical insights into binary evolution processes and the merger rate evolution of compact object binaries. However, current observational constraints on this delay time…

Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…

The power of natural language generation models has provoked a flurry of interest in automatic methods to detect if a piece of text is human or machine-authored. The problem so far has been framed in a standard supervised way and consists…

Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life', has been analyzed for a multitude of…

Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…

Using recent results on the occurrence times of a string of symbols in a stochastic process with mixing properties, we present a new method for the search of rare words in biological sequences generally modelled by a Markov chain. We obtain…

Real time, or quantitative, PCR typically starts from a very low concentration of initial DNA strands. During iterations the numbers increase, first essentially by doubling, later predominantly in a linear way. Observation of the number of…

Protein sequences are abundant in repeating segments, both as exact copies and as approximate segments with mutations. These repeats are important for protein structure and function, motivating decades of algorithmic work on repeat…

Understanding the merging behavior patterns at freeway on-ramps is important for assistanting the decisions of autonomous driving. This study develops a primitive-based framework to identify the driving patterns during merging processes and…

Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parameters (e.g., k-mer size) are…

Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…

Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…

We study various aspects of Dyck words appearing in binary sequences, where $0$ is treated as a left parenthesis and $1$ as a right parenthesis. We show that binary words that are $7/3$-power-free have bounded nesting level, but this no…

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…

Consider infinite random words over a finite alphabet where the letters occur as an i.i.d. sequence according to some arbitrary distribution on the alphabet. The expectation and the variance of the waiting time for the first completed…

Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…