Search Results for author: David H. Mathews

Found 6 papers, 4 papers with code

Messenger RNA Design via Expected Partition Function and Continuous Optimization

1 code implementation29 Dec 2023 Ning Dai, Wei Yu Tang, Tianshuo Zhou, David H. Mathews, Liang Huang

We then use gradient descent-based optimization methods to improve the extended objective function, and the distribution will gradually shrink towards a one-hot sequence (i. e., a single sequence).

Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition

1 code implementation14 Nov 2023 Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang

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.

LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules

no code implementations26 Oct 2022 He Zhang, Sizhen Li, Liang Zhang, David H. Mathews, Liang Huang

Vienna RNAcofold, which reduces the problem into the classical single sequence folding by concatenating two strands, scales in cubic time against the combined sequence length, and is slow for long sequences.

LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments

1 code implementation29 Jun 2022 Liang Zhang, Sizhen Li, He Zhang, David H. Mathews, Liang Huang

We present LinearAlifold, an efficient algorithm for folding aligned RNA homologs that scales linearly with both the sequence length and the number of sequences, based on our recent work LinearFold that folds a single RNA in linear time.

Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity

2 code implementations21 Apr 2020 He Zhang, Liang Zhang, Ang Lin, Congcong Xu, Ziyu Li, Kaibo Liu, Boxiang Liu, Xiaopin Ma, Fanfan Zhao, Weiguo Yao, Hangwen Li, David H. Mathews, Yujian Zhang, Liang Huang

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, distribution, and efficacy of the vaccine.

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