Related papers: Comparative statistical analysis of bacteria genom…
Transcription factors are short stretches of DNA (or $k$-mers) mainly located in promoters sequences that enhance or repress gene expression. With respect to an initial distribution of letters on the DNA alphabet, Behrens and Vingron…
Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural language, prior studies have attempted to model genomic k-mer…
Biomolecular phase separation is typically attributed to the polymer physics of long, disordered chains. However, the underlying chemical grammar, i.e. the specific interactions between protein and RNA building blocks, remains poorly…
Generating semantic lexicons semi-automatically could be a great time saver, relative to creating them by hand. In this paper, we present an algorithm for extracting potential entries for a category from an on-line corpus, based upon a…
Complex systems, such as life and languages, are governed by principles of evolution. The analogy and comparison between biology and linguistics\cite{alphafold2, RoseTTAFold, lang_virus, cell language, faculty1, language of gene, Protein…
The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…
Some genes can promote or repress their own expressions, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
Long Short-Term Memory (LSTM) networks have recently shown remarkable performance in several tasks dealing with natural language generation, such as image captioning or poetry composition. Yet, only few works have analyzed text generated by…
This paper describes the results of some experiments exploring statistical methods to infer syntactic behavior of words and morphemes from a raw corpus in an unsupervised fashion. It shares certain points in common with Brown et al (1992)…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, sharing a specific functional annotation across genomes of given size.…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
Identifying which taxa in our microbiota are associated with traits of interest is important for advancing science and health. However, the identification is challenging because the measured vector of taxa counts (by amplicon sequencing) is…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known…