ArticleGenome biology2019
dStruct: identifying differentially reactive regions from RNA structurome profiling data.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- A Workflow for Identifying Helicase-Dependent RNA Structural Changes in Transcriptional Termination: From DMS Sequencing Analysis to Reporter Assay-Based Validation.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Deep learning for RNA secondary structure determination: gauging generalizability and broadening the scope of traditional methods.RNA (New York, N.Y.) · 2026Review
- Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.bioRxiv : the preprint server for biology · 2025Article
- Ribosome-induced mRNA pseudoknot interactions visualized by DMS MaP-Seq.bioRxiv : the preprint server for biology · 2025Article
- TDP-43 binds to RNA G-quadruplex structure and regulates mRNA stability and translation.Nucleic acids research · 2025Article
- Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) · 2025Article
- Defining the Parameters for Sorting of RNA Cargo Into Extracellular Vesicles.Journal of extracellular vesicles · 2025Article
- DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via mNature communications · 2024Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections.Human genetics · 2023Article
- Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.Nature communications · 2022Article
- Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites.RNA biology · 2021Article
- Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets.NAR genomics and bioinformatics · 2021Article
- diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data.Genome biology · 2021Article
- Probing Transcriptome-Wide RNA Structural Changes Dependent on the DEAD-box Helicase Dbp2.Methods in molecular biology (Clifton, N.J.) · 2021Article
- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP.Nature communications · 2020Article
- mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity.Genome biology · 2019Article
- Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination.Genetics · 2019Article
- dStruct: identifying differentially reactive regions from RNA structurome profiling data.Genome biology · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
RNA biology is revolutionized by recent developments of diverse high-throughput technologies for transcriptome-wide profiling of molecular RNA structures. RNA structurome profiling data can be used to identify differentially structured regions between groups of samples. Existing methods are limited in scope to specific technologies and/or do not account for biological variation. Here, we present dStruct which is the first broadly applicable method for differential analysis accounting for biological variation in structurome profiling data. dStruct is compatible with diverse profiling technologies, is validated with experimental data and simulations, and outperforms existing methods.
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Registered trials
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