5 citations · 9 across the 9 of their papers we have counts for
6 papers · 1 filter
Sampling-based Continuous Optimization for Messenger RNA Design
Feipeng Yue, Ning Dai, Wei Yu Tang +3
Designing messenger RNA (mRNA) sequences for a fixed target protein requires searching an exponentially large synonymous space while optimizing properties that affect stability and…
Fast and Versatile RNA Design via Motif-level Divide-and-Conquer and Structure-level Rival Search
Tianshuo Zhou, David H. Mathews, Liang Huang
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on…
Sampling-based Continuous Optimization with Coupled Variables for RNA Design
Wei Yu Tang, Ning Dai, Tianshuo Zhou +2
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 prov…
Messenger RNA Design via Expected Partition Function and Continuous Optimization
Ning Dai, Wei Yu Tang, Tianshuo Zhou +2
The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we form…
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition
Tianshuo Zhou, Wei Yu Tang, David H. Mathews +1
RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design m…
LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments
Apoorv Malik, Liang Zhang, Milan Gautam +5
Predicting the consensus structure of a set of aligned RNA homologs is a convenient method to find conserved structures in an RNA genome, which has many applications including vira…