Related papers: Embedded transfer RNA Genes
This paper aims at identifying the information flow in state-of-the-art machine translation systems, taking as example the transfer of gender when translating from French into English. Using a controlled set of examples, we experiment…
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…
Motivation: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in…
We investigate the number of inverted repeats observed in 37 complete genomes of bacteria. The number of inverted repeats observed is much higher than expected using Markovian models of DNA sequences in most of the eubacteria. By using the…
Interactions are ubiquitous across biological systems. These interactions can be abstracted as patterns of connections among distinct units such as genes, proteins, individual organisms, or species which form a hierarchy of biological…
The effects of the residual proton-neutron interactions on bandcrossing features are studied by means of shell model calculations for nucleons in a high-j intruder orbital. The presence of an odd-nucleon shifts the frequency of the…
State-of-the-art named entity recognition (NER) systems have been improving continuously using neural architectures over the past several years. However, many tasks including NER require large sets of annotated data to achieve such…
We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…
We introduce the software tool NTRFinder to find the complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that nested…
The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
Patchy particles have received great attention due to their ability to develop directional and selective interactions and serve as building units for the self-assembly of innovative colloidal molecules and crystalline structures. Although…
Several recent studies show that companion cells in flowering plant gametophytes relax epigenetic control of transposable elements (TEs) to promote production of small RNA that presumably assist nearby reproductive cells in management of…
We present Transfer Orthology Networks (TRON), a novel neural network architecture designed for cross-species transfer learning. TRON leverages orthologous relationships, represented as a bipartite graph between species, to guide knowledge…
Gene essentiality refers to the degree to which a gene is necessary for the survival and reproductive efficacy of a living organism. Although the essentiality of non-coding genes has been documented, there are still aspects of non-coding…
MicroRNAs (miRNAs) are small non-coding RNAs which regulate gene expression by binding to the 3' UTR of the corresponding messenger RNAs. We construct miRNA co-target networks for 22 different species using a target prediction database,…
We consider a one-dimensional (1D) structure where non-interacting spin-$s$ scattering centers, such as quantum impurities or multi-level atoms, are embedded at given positions. We show that the injection into the structure of unpolarized…
Experimental evidences show that in gene transcription, RNA polymerase has the possibility to be stalled at certain position of the transcription template. This may be due to the template damage, or protein barriers. Once stalled,…
Transcription is one of the essential processes for cells to read genetic information encoded in genes, which is initiated by the binding of RNA polymerase to related promoter. Experiments have found that the nucleotide sequence of promoter…
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…