Related papers: RNA structure characterization from chemical mappi…
Chemical structure elucidation is a serious bottleneck in analytical chemistry today. We address the problem of identifying an unknown chemical threat given its mass spectrum and its chemical formula, a task which might take well trained…
The chemical master equation (CME), which describes the discrete and stochastic molecule number dynamics associated with biological processes like transcription, is difficult to solve analytically. It is particularly hard to solve for…
Computer-driven molecular design combines the principles of chemistry, physics, and artificial intelligence to identify novel chemical compounds and materials with desired properties for a specific application. In particular,…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
Structural quantities such as order parameters and correlation functions are often employed to gain insight into the physical behavior and properties of condensed matter systems. While standard quantities for characterizing structure exist,…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
Matched case-control studies are commonly employed in epidemiological research for their convenience and efficiency. Analysis of secondary outcomes can yield valuable insights into biological pathways and help identify genetic variants of…
Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic…
Nuclear Magnetic Resonance (NMR) spectroscopy is particularly well-suited to determine the structure of molecules and materials in powdered form. Structure determination usually proceeds by finding the best match between experimentally…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
Structural prediction has long been considered critical in RNA research, especially following the success of AlphaFold2 in protein studies, which has drawn significant attention to the field. While recent advances in machine learning and…
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…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
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…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
High-throughput RNA-sequencing (RNA-seq) technologies are powerful tools for understanding cellular state. Often it is of interest to quantify and summarize changes in cell state that occur between experimental or biological conditions.…
The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an…