5 citations · 9 across the 9 of their papers we have counts for
9 papers
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…
Designing RNAs with Language Models
Milan Gautam, Ning Dai, Tianshuo Zhou +3
RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to t…
Probabilistic RNA Designability via Interpretable Ensemble Approximation and Dynamic Decomposition
Tianshuo Zhou, David H. Mathews, Liang Huang
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures…
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…
Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance
Tianshuo Zhou, Wei Yu Tang, Apoorv Malik +2
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fol…
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…