Related papers: Encoding folding paths of RNA switches
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such…
Emerging high-throughput technologies have led to a deluge of putative non-coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology…
Coupling, synchronization, and non-linear dynamics of resonator modes are omnipresent in nature and highly relevant for a multitude of applications ranging from lasers to Josephson arrays and spin torque oscillators. Nanomechanical…
The paper proposes to employ deep convolutional neural networks (CNNs) to classify noncoding RNA (ncRNA) sequences. To this end, we first propose an efficient approach to convert the RNA sequences into images characterizing their…
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…
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…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and…
Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames and which have been termed long non-coding RNAs (lncRNAs). Despite the existence of several well-characterized…
The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions…
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
Neural networks are typically represented as data structures that are traversed either through iteration or by manual chaining of method calls. However, a deeper analysis reveals that structured recursion can be used instead, so that…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…