Related papers: Positioning Crenarchaeal tRNA-Introns
A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the "fine structure" of nucleotide sequences. The approach is based on the assumption that…
S stars are late-type giants that are transition objects between M-type stars and carbon stars on the asymptotic giant branch (AGB). They are classified into two types: intrinsic or extrinsic, based on the presence or absence of technetium…
Current biological AI models lack interpretability -- their internal representations do not correspond to biological relationships that researchers can examine. Understanding gene regulation requires models whose learned structure can be…
Chaperone protein - the most disordered among all protein groups - help RNAs fold into their functional structure by destabilizing misfolded configurations or stabilizing the functional ones. But disentangling the mechanism underlying RNA…
Centaurus A (Cen A) is one of the most famous galaxies hosting an active galactic nucleus (AGN), where the interaction between AGN activities and surrounding interstellar and intergalactic media has been investigated. Recent studies…
Selected ribonucleotide sequences bind well to zwitterionic phospholipid bilayer membranes, though randomized RNAs do not. There are no evident repeated sequences in selected membrane binding RNAs. This implies small and varied motifs…
Background: Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization of transposed elements in duplicated genes than…
Integrase proteins acting on circular double-stranded DNA often change its topology by transforming unknotted circles into torus knots and links. Two systems of tangle equations--corresponding to the two initial DNA sequences--arise when…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…
We present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic integration of network inference and network topological analysis…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
We investigate possible interpretations of the new periodic B- and A-type variable stars discovered in NGC 3766. They lie in the region of the Hertzsprung-Russell diagram between slowly pulsating B and delta Sct stars, a region where no…
We develop a general theory of crystal truncation rod (CTR) scattering from vicinal surfaces with a coherently strained heteroepitaxial film. The formalism incorporates film-induced interference fringes, full elastic lattice distortion,…
Xenopus tropicalis is an anuran amphibian species used as model in vertebrate comparative genomics. It provides the same advantages as Xenopus laevis but is diploid and has a smaller genome of 1.7 Gbp. Therefore X. tropicalis is more…
Building on arXiv:1911.05827, we uncover new properties of type-B conformal anomalies for Coulomb-branch operators in continuous families of 4D $\mathcal{N}=2$ SCFTs. We study a large class of such anomalies on the Higgs branch, where…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in…
DNA methylation (meDNA) is a suspected modulator of alternative splicing, while splicing in turn is involved in tumour formations nearly as frequently as DNA mutations. Yet, the impact of meDNA on tumorigenesis via its effect on splicing…