Related papers: Positioning Crenarchaeal tRNA-Introns
We investigate topological properties of a completely integrable system on $S^2\times S^2 \times S^2$ which was recently shown to have a Lagrangian fiber diffeomorphic to $\mathbb{R} P^3$ not displaceable by a Hamiltonian isotopy [Oakley…
Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model…
Bound states of 7-branes known as 'T-branes' have properties that defy usual geometric intuition. For instance, the gauge group of n coincident branes may not be U(n). More surprisingly, matter may show up at unexpected loci, such as…
This methods paper presents computational protocols for the identification of non-coding RNA genes or RNA motifs within genomic sequences. An application to bacterial small RNA is proposed.
Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide an…
Tumor samples are heterogeneous. They consist of different subclones that are characterized by differences in DNA nucleotide sequences and copy numbers on multiple loci. Heterogeneity can be measured through the identification of the…
Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely…
We are interested in the comparison of transcript boundaries from cells which originated in different environments. The goal is to assess whether this phenomenon, called differential splicing, is used to modify the transcription of the…
We introduce a novel model for DNA condensation (whip-toroid transition) using the path integral method in the framework of the non-linear sigma model on a line segment. We show that some of its classical configurations exhibit toroidal…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
Decoding the internal structure of the proton is a fundamental challenge in physics. Historically, any new discovery about the proton has fuelled advances in several scientific fields. We have reported that gluons inside the proton…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
The Ribonucleic Acid (RNA) inverse folding problem, designing nucleotide sequences that fold into specific tertiary structures, is a fundamental computational biology problem with important applications in synthetic biology and…
Recent genome-wide measurements of binding preferences of ~200 transcription regulators in the vicinity of transcription start sites in yeast, have provided a unique insight into the cis- regulatory code of a eukaryotic genome (Venters et…
With the advent of high-resolution high-sensitivity observations, spiral patterns have been revealed around several asymptotic giant branch (AGB) stars. Such patterns can provide possible evidence for the existence of central binary stars…
Animal mitochondrial genomes usually have two transfer RNAs for Leucine: one, with anticodon UAG, translates the four-codon family CUN, whilst the other, with anticodon UAA, translates the two-codon family UUR. These two genes must differ…
A survey for line profile variability in early A-type stars has been performed in order to detect nonradial pulsation signatures. The star HR 6139, with spectral type A2V and estimated T_eff=8800 K, shows evident line profile variations…
The current picture of bacterial evolution is based largely on studies of 16S rRNA. However, this is just one gene. It is known that horizontal gene transfer can occur between bacterial species, although the frequency and implications of…