1 code implementation • 29 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).
1 code implementation • 14 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.
no code implementations • 18 Jul 2023 • Sizhen Li, Ning Dai, He Zhang, Apoorv Malik, David H. Mathews, Liang Huang
First, it takes $O(n^6)$ for two sequences where n is the average sequence length.
no code implementations • 26 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.
1 code implementation • 29 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.
2 code implementations • 21 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.