491 citations · 760 across the 6 of their papers we have counts for
6 papers
LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs
Sizhen Li, Ning Dai, He Zhang +3
The classical Sankoff algorithm for the simultaneous folding and alignment of homologous RNA sequences is highly influential, but it suffers from two major limitations in efficienc…
LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules
He Zhang, Sizhen Li, Liang Zhang +2
Many ncRNAs function through RNA-RNA interactions. Fast and reliable RNA structure prediction with consideration of RNA-RNA interaction is useful. Some existing tools are less accu…
Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity
He Zhang, Liang Zhang, Ang Lin +11
Messenger RNA (mRNA) vaccines are being used for COVID-19, but still suffer from the critical issue of mRNA instability and degradation, which is a major obstacle in the storage, d…
ThreshKnot: Thresholded ProbKnot for Improved RNA Secondary Structure Prediction
Liang Zhang, He Zhang, David H. Mathews +1
RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to parti…
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search
Liang Huang, He Zhang, Dezhong Deng +4
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation:…
LinearPartition: Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities
He Zhang, Liang Zhang, David H. Mathews +1
RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy (MFE) methods to partitio…