Zobrazeno 1 - 10
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pro vyhledávání: '"Mathews, David H"'
Motivation: RNA design aims to find at least one sequence that folds with the highest probability into a designated target structure, but some structures are undesignable in the sense that no sequence folds into them. Identifying undesignable structu
Externí odkaz:
http://arxiv.org/abs/2402.17206
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 formulate these problems as continuous optimization and develop a general
Externí odkaz:
http://arxiv.org/abs/2401.00037
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition
Publikováno v:
International Conference on Research in Computational Molecular Biology, pp. 270-287. Cham: Springer Nature Switzerland, 2024
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 methods have been invented to find sequences capable of folding into a
Externí odkaz:
http://arxiv.org/abs/2311.08339
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 efficiency and modeling power. First, it takes $O(n^6)$ for two sequences where
Externí odkaz:
http://arxiv.org/abs/2307.09580
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 accurate due to omitting the competing of intermolecular and intramolecula
Externí odkaz:
http://arxiv.org/abs/2210.14982
Autor:
Malik, Apoorv, Zhang, Liang, Gautam, Milan, Dai, Ning, Li, Sizhen, Zhang, He, Mathews, David H., Huang, Liang
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 viral diagnostics and therapeutics. However, the most commonly used tool f
Externí odkaz:
http://arxiv.org/abs/2206.14794
Publikováno v:
In Journal of Molecular Biology 1 September 2024 436(17)
Autor:
Zhang, He, Zhang, Liang, Lin, Ang, Xu, Congcong, Li, Ziyu, Liu, Kaibo, Liu, Boxiang, Ma, Xiaopin, Zhao, Fanfan, Yao, Weiguo, Li, Hangwen, Mathews, David H., Zhang, Yujian, Huang, Liang
Publikováno v:
Nature (621), 396-403, 2023
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. Previous work showed that op
Externí odkaz:
http://arxiv.org/abs/2004.10177
Publikováno v:
Bioinformatics, July 2020 (Proceedings of ISMB 2020)
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 partition function-based methods that account for folding ensembles and can th
Externí odkaz:
http://arxiv.org/abs/1912.13190
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 partition function-based ones that assemble structures using base-pairing p
Externí odkaz:
http://arxiv.org/abs/1912.12796