ArticleNucleic acids research2013
COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- UFold-X: an enhanced Dual & Dynamic U-Mamba model for long-range RNA secondary structure prediction.Nucleic acids research · 2026Article
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- miRNA-lncRNA Cross-Regulation Landscape in Cancer: From Molecular Mechanisms to Therapeutic and Diagnostic Applications.Cancers · 2026Review
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Tissue-specific modulation of CRISPR activity by miRNA-sensing guide RNAs.Nucleic acids research · 2025Article
- Functional Validation of SAM Riboswitch Element A fromBiochemistry · 2024Article
- Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform fromMicrobiology spectrum · 2024Article
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- Long Noncoding RNAs CAT2064 and CAT2042 may Function as Diagnostic Biomarkers for Prostate Cancer by Affecting Target MicrorRNAs.Indian journal of clinical biochemistry : IJCB · 2024Article
- Deciphering the evolutionary landscape of severe fever with thrombocytopenia syndrome virus across East Asia.Virus evolution · 2024Article
- Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.Nature communications · 2023Article
- e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.Nucleic acids research · 2023Article
- Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks.Nature biotechnology · 2023Article
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing.NPJ systems biology and applications · 2023Article
- Fast RNA-RNA Interaction Prediction Methods for Interaction Analysis of Transcriptome-Scale Large Datasets.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Upstream Flanking Sequence Assists Folding of an RNA Thermometer.Journal of molecular biology · 2022Article
- Women in the European Virus Bioinformatics Center.Viruses · 2022Article
- Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids.Journal of the Royal Society, Interface · 2022Review
- A novel end-to-end method to predict RNA secondary structure profile based on bidirectional LSTM and residual neural network.BMC bioinformatics · 2021Article
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2 authors.
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Abstract
Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary structure are thermodynamic methods. These aim to predict the most stable RNA structure. There exists by now ample experimental and theoretical evidence that the process of structure formation matters and that sequences in vivo fold while they are being transcribed. None of the thermodynamic methods, however, consider the process of structure formation. Here, we present a conceptually new method for predicting RNA secondary structure, called CoFold, that takes effects of co-transcriptional folding explicitly into account. Our method significantly improves the state-of-art in terms of prediction accuracy, especially for long sequences of >1000 nt in length.
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