Related papers: tRNA-isoleucine-tryptophan Composite Gene
Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…
In this paper we compute the limit distributions of the numbers of hairpin-loops, interior-loops and bulges in k-noncrossing RNA structures. The latter are coarse grained RNA structures allowing for cross-serial interactions, subject to the…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
Thru-hole epitaxy has recently been reported to be able to grow readily detachable domains crystallographically aligned with the underlying substrate over 2D mask material transferred onto a substrate. [Jang \textit{et al.}, \textit{Adv.…
Determining the mechanism by which transfer RNAs (tRNAs) rapidly and precisely transit through the ribosomal A, P and E sites during translation remains a major goal in the study of protein synthesis. Here, we report the real-time dynamics…
The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…
When many fundamental strings are stacked together, they puff up into D-branes. BIons and giant gravitons are the examples of such D-brane configurations that arise from coincident strings. We propose and demonstrate analogous transitions…
In the work the process of the energy transfer in the cell microtubules is simulated. A system of tryptophans connected by Coulomb dipole-dipole interaction is discussed as the energy carriers. The work models the conditions under which the…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Results of experiments probing the structure of the pomeron at hadron colliders and at HERA are reviewed. By renormalizing the pomeron flux factor in diffraction dissociation as dictated by unitarity, a picture emerges from the data in…
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
Transition metal dichalcogenide heterobilayers offer attractive opportunities to realize lattices of interacting bosons with several degrees of freedom. Such heterobilayers can feature moir\'e patterns that modulate their electronic band…
The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur, definitive concrete cases have been…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…