相关论文: Identifying RNA contacts from SHAPE-MaP by partial…

On social networks, while nodes bear rich attributes, we often lack the `semantics' of why each link is formed-- and thus we are missing the `road signs' to navigate and organize the complex social universe. How to identify relationship…

We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…

Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…

Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that binding of RNA with SHAPE reagents is affected by cooperative…

Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open…

Evolution in its course found a variety of solutions to the same optimisation problem. The advent of high-throughput genomic sequencing has made available extensive data from which, in principle, one can infer the underlying structure on…

Solving point-wise feature correspondence in visual data is a fundamental problem in computer vision. A powerful model that addresses this challenge is to formulate it as graph matching, which entails solving a Quadratic Assignment Problem…

Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…

Joint modeling of a large number of variables often requires dimension reduction strategies that lead to structural assumptions of the underlying correlation matrix, such as equal pair-wise correlations within subsets of variables. The…

Many man-made objects are characterised by a shape that is symmetric along one or more planar directions. Estimating the location and orientation of such symmetry planes can aid many tasks such as estimating the overall orientation of an…

The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…

We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely available at…

Nonlinear relations, such as the curvilinear relationship between childhood trauma and resilience in patients with schizophrenia and the moderation relationship between mentalizing, and internalizing and externalizing symptoms and quality…

We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of…

A topological RNA structure is derived from a diagram and its shape is obtained by collapsing the stacks of the structure into single arcs and by removing any arcs of length one. Shapes contain key topological, information and for fixed…

Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive,…

Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based…

In this report, correlation of the pixels comprising a microarray spot is investigated. Subsequently, correlation statistics namely: Pearson correlation and Spearman rank correlation are used to segment the foreground and background…

Identifying causality is fundamental for human understanding of the world, where complex non-autonomous systems such as species population changes, brain activities, etc. are extensively existed. Since the phase spaces of such systems are…