RNA 2nd Structure Prediction

✅ : Recommended

I. RNA Secondary Structure Prediction

1. Basics

• ✅ Course: 生物信息学（清华大学）; 生物物理学（清华大学）
• ✅ Teaching Slides and Videos: Models for RNA secondary structure prediction
• Book: 《Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids》by Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison (English | 中文)

• Energy Model - RNAstructure/Mfold and RNAfold
• ✅ How do RNA folding algorithms work? (Sean R Eddy) 2004 Nature Biotech
• What is dynamic programming? (Sean R Eddy) 2004 Nature Biotech
• SCFG Model (Rfam/Infernal)
• ✅ What is a hidden Markov model? (Sean R Eddy) 2004 Nature Biotech
• You can read the SCFG section in the book above (《Biological Sequence Analysis》).

2. Recent Research Articles and Reviews

• ✅ [review] 2023 BIB - Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery
• [review] 2022 PNAS - Thoughts on how to think (and talk) about RNA structure
• 2020 ICLR - RNA Secondary Structure Prediction By Learning Unrolled Algorithms (Chinese comments)
• (Transfer learning) 2019 Nature Commn. - SPOT-RNA: RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

II. Structure Probing Experiments

1. Structure probing methods

关于RNA 二级结构高通量测序方法

2. Structure probing data analysis

• 2022 Nature Methods - RNA secondary structure packages evaluated and improved by high-throughput experiments
• 2021 Genome Biology - diffBUM-HMM a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data