491 citations · 584 across the 6 of their papers we have counts for
6 papers
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…
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…
Analysis and visualization of spatial transcriptomic data
Boxiang Liu, Yanjun Li, Liang Zhang
Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from…
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…
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…