Related papers: Embedded transfer RNA Genes
The prospect of RNA nanotechnology is increasing because of its numerous potential applications especially in medical science. The spherical Nanodiamonds (NDs) are becoming popular because of their lesser toxicity, desirable mechanical,…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
Knowledge bases of real-world facts about entities and their relationships are useful resources for a variety of natural language processing tasks. However, because knowledge bases are typically incomplete, it is useful to be able to…
We construct and study an extended random matrix model of RNA (polymer) folding. A perturbation which acts on all the nucleotides in the chain is added to the action of the RNA partition function. The effect of this perturbation on the…
Genetic variation affecting gene regulation is a central driver of phenotypic differences between individuals and can be used to uncover how biological processes are organized in a cell. Although detecting cis-eQTLs is now routine,…
The investigation of dynamical processes on networks has been one focus for the study of contagion processes. It has been demonstrated that contagions can be used to obtain information about the embedding of nodes in a Euclidean space.…
Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and…
Primary human cells offer the most faithful representation of native human physiology, yet their practical utility is constrained by the difficulty of introducing exogenous genetic material. Electroporation provides a promising non-viral…
As computer systems become more pervasive and complex, security is increasingly important. Secure Transmission refers to the transfer of data such as confidential or proprietary information over a secure channel. Many secure transmission…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
Topological entropy has been one of the most difficult to implement of all the entropy-theoretic notions. This is primarily due to finite sample effects and high-dimensionality problems. In particular, topological entropy has been…
Both genomic stability and sustenance of day-to-day life rely on efficient and accurate readout of the genetic code. Single-molecule experiments show that transcription and replication are highly stochastic and irregular processes, with the…
Transcription factors are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional…
Transfer learning leverages feature representations of deep neural networks (DNNs) pretrained on source tasks with rich data to empower effective finetuning on downstream tasks. However, the pretrained models are often prohibitively large…
DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells. For adult somatic cells, location and dynamics of methylation has been very precisely pinned down with the 5-cytosine markers on…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore…
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation. However, the experimental determination of miRNA sequence and structure is both expensive and time-consuming.…