Related papers: Zimin patterns in genomes
Metagenomic binning aims to cluster DNA fragments from mixed microbial samples into their respective genomes, a critical step for downstream analyses of microbial communities. Existing methods rely on deterministic representations, such as…
This paper considers the problems of modeling and predicting a long-term and ``blurry'' relapse that occurs after a medical act, such as a surgery. The relapse is observed only indirectly, in a ``blurry'' fashion, through longitudinal…
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…
We consider the communication complexity of the Hamming distance of two strings. Bille et al. [SPIRE 2018] considered the communication complexity of the longest common prefix (LCP) problem in the setting where the two parties have their…
Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores we develop a maximum…
In this paper, we study the pattern occurrence in $k$-ary words. We prove an explicit upper bound on the number of $k$-ary words avoiding any given pattern using a random walk argument. Additionally, we reproduce several already known…
The X chromosome is present as a single copy in the heterogametic sex, and this hemizygosity is expected to drive unusual patterns of evolution on the X relative to the autosomes. For example, the hemizgosity of the X may lead to a lower…
We have analyzed gene expression data from 3 different kinds of samples: normal human tissues, human cancer cell lines and leukemic cells from lymphoid and myeloid leukemia pediatric patients. We have searched for genes that are over…
Although theories regarding the role of sequence-specific DNA resonance in biology have abounded for over 40 years, the published evidence for it is lacking. Here, the authors reasoned that for sustained resonance signaling, the number of…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
We present a new approach to the problem of enumerating permutations of length n that avoid a fixed consecutive pattern of length m. We use this idea to give explicit upper and lower bounds on the number of permutations avoiding a pattern…
The ICTV develops, refines and maintains a universal virus taxonomy; Order is the highest taxon in the branching hierarchy of recognised viral taxa. Historically, ICTV (sub)committees have classified viruses on the basis of morphological…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
In a recent preprint, Mike Cummings showed that the smooth components of suitably parametrized Springer fibers are in bijection with contracted, fully reduced Pl\"ucker degree-two $\mathfrak{sl}_r$-webs of standard type and that are…
We derive theoretical upper and lower bounds on the maximum size of DNA codes of length n with constant GC-content w and minimum Hamming distance d, both with and without the additional constraint that the minimum Hamming distance between…
Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal.…
Zipf's law of abbreviation, the tendency of more frequent words to be shorter, is one of the most solid candidates for a linguistic universal, in the sense that it has the potential for being exceptionless or with a number of exceptions…
Mutually Uncorrelated (MU) codes are a class of codes in which no proper prefix of one codeword is a suffix of another codeword. These codes were originally studied for synchronization purposes and recently, Yazdi et al. showed their…
Vincular or dashed patterns resemble classical patterns except that some of the letters within an occurrence are required to be adjacent. We prove several infinite families of Wilf-equivalences for k-ary words involving vincular patterns…
Significant fraction (about 98.5% in humans, 24% in microbe Rickettsia prowazekii) of most animal genomes is non-coding DNA. Although recent studies established functions of its certain portions, it remains genomic dark matter. The paper…