Related papers: Positioning Crenarchaeal tRNA-Introns
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
We devise an autoencoder based strategy to facilitate anomaly detection for boosted jets, employing Graph Neural Networks (GNNs) to do so. To overcome known limitations of GNN autoencoders, we design a symmetric decoder capable of…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
We present a new algorithm that identifies reconstructed jets originating from hadronic decays of tau leptons against those from quarks or gluons. No tau lepton reconstruction algorithm is used. Instead, the algorithm represents jets as…
We show that in any nontrivial Hahn field with truncation as a primitive operation we can interpret the monadic second-order logic of the additive monoid of natural numbers and are thus undecidable. We also specify a definable binary…
We report on Australia Telescope Compact Array (ATCA) HI observations carried out in the direction of bilateral supernova remnants (SNRs) with associated neutron stars: G296.5+10.0 and G320.4--1.2, in a search for the origin of such…
Here we investigate translational regulation in bacteria by analyzing the distribution of start codons in fully assembled genomes. We report 36 genes (infC, rpoC, rnpA, etc.) showing a preference for non-AUG start codons in evolutionarily…
In this work we analyze some models used to explain the origins of intra-strand parity and strand compositional asymmetries in bacterial genomes. Due to the particular way that these two features emerge in bacterial DNA, we performed our…
As the places where most of the fuel of the cell, namely ATP, is synthesized, mitochondria are crucial organelles in eukaryotic cells. The shape of the invaginations of the mitochondria inner membrane, known as cristae, has been identified…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
To synthesize peptides alongside the RNAs making the so-called RNA world, some genetic coding involving RNA had to develop. Herein, it is proposed that the first real-coding setup was a direct one, made up of continuous poly-tRNA-like…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
It is well known that the general transcription factors (GTF) specifically recognize correct TATA boxes, distinguishing them from many others. Employing the principles of determinacy analysis (mathematical theory of rules) we analyzed a…
Elastic periodic lattices act as mechanical filters of incident vibrations. By and large, they forbid wave propagation within bandgaps and resonate outside them. However, they often encounter "truncation resonances" (TRs) inside bandgaps…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
The elucidation of the pseudogap phenomenon of the cuprates, a set of anomalous physical properties below the characteristic temperature T* and above the superconducting transition temperature Tc, has been a major challenge in condensed…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…