Related papers: Combinatorial analysis of interacting RNA molecule…
We investigate the nonlocal structure of optical model potentials for nucleon-nucleus scattering based on microscopic approaches. To this purpose, \emph{in-medium} folding optical potentials are calculated in momentum space and their…
Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints on each residue site. Selective constraints on residue sites are…
The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy…
Feature interaction is crucial in predictive machine learning models, as it captures the relationships between features that influence model performance. In this work, we focus on pairwise interactions and investigate their importance in…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and…
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…
Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate three-dimensional structures is one of the remarkable examples of biological self-organization. We investigated native state structures of…
We propose a new toy model of a heteropolymer chain capable of forming planar secondary structures typical for RNA molecules. In this model the sequential intervals between neighboring monomers along a chain are considered as quenched…
Heterogeneous information network (HIN) embedding aims to embed multiple types of nodes into a low-dimensional space. Although most existing HIN embedding methods consider heterogeneous relations in HINs, they usually employ one single…
The ability of oligonucleotide microarrays to measure gene expression has been hindered by an imperfect understanding of the relationship between input RNA concentrations and output signals. We argue that this relationship can be understood…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
Arc-annotated sequences are useful for representing structural information of RNAs and have been extensively used for comparing RNA structures in both terms of sequence and structural similarities. Among the many paradigms referring to…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
A network is scale-free if its connectivity density function is proportional to a power-law distribution. Scale-free networks may provide an explanation for the robustness observed in certain physical and biological phenomena, since the…
We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
In this paper we study $k$-noncrossing RNA structures with minimum arc-length 4 and at most $k-1$ mutually crossing bonds. Let ${\sf T}_{k}^{[4]}(n)$ denote the number of $k$-noncrossing RNA structures with arc-length $\ge 4$ over $n$…
Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary-structure are thermodynamic methods. These predict the most stable RNA structure, but do not consider the process of structure…