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Prime-Bspre: A Genome-Wide Protein-Rna Binding Sites Prediction Method Based on Templates

https://doi.org/10.2139/ssrn.4889490
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RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins
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RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation
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Sequence, Structure, and Context Preferences of Human RNA Binding Proteins
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RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection
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Structural imprints in vivo decode RNA regulatory mechanisms
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Erratum: Structural imprints in vivo decode RNA regulatory mechanisms
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Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
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Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
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Context-dependent control of alternative splicing by RNA-binding proteins
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A census of human RNA-binding proteins
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iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
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Repetitive DNA: genomic dark matter matters
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A large-scale binding and functional map of human RNA-binding proteins
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Highly accurate protein structure prediction with AlphaFold
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Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq
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Systematic identification of NF90 target RNAs by iCLIP analysis
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PRIME-3D2D is a 3D2D model to predict binding sites of protein–RNA interaction
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RNA sequence‐ and shape‐dependent recognition by proteins in the ribonucleoprotein particle
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Functional diversity of the hnRNPs: past, present and perspectives
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High-throughput characterization of protein-RNA interactions
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RCK: accurate and efficient inference of sequence- and structure-based protein–RNA binding models from RNAcompete data
inferredcites →https://doi.org/10.1093/gigascience/giab008openalex-snapshot
Twelve years of SAMtools and BCFtools
inferredcites →https://doi.org/10.1093/nar/gkab1049openalex-snapshot
Ensembl 2022
inferredcites →https://doi.org/10.1093/nar/gkab1061openalex-snapshot
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
inferredcites →https://doi.org/10.1093/nar/gkac243openalex-snapshot
An atlas of posttranslational modifications on RNA binding proteins
inferredcites →https://doi.org/10.1093/nar/gkac694openalex-snapshot
PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins
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A statistical sampling algorithm for RNA secondary structure prediction
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TM-align: a protein structure alignment algorithm based on the TM-score
inferredcites →https://doi.org/10.1093/nar/gkl544openalex-snapshot
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions
inferredcites →https://doi.org/10.1093/nar/gku406openalex-snapshot
RBPmap: a web server for mapping binding sites of RNA-binding proteins
inferredcites →https://doi.org/10.1093/nar/gkz1062openalex-snapshot
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
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RNAstructure: software for RNA secondary structure prediction and analysis
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A computational approach for genome-wide mapping of splicing factor binding sites
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GraphProt: modeling binding preferences of RNA-binding proteins
inferredcites →https://doi.org/10.1186/s13059-021-02506-9openalex-snapshot
Clipper: p-value-free FDR control on high-throughput data from two conditions
inferredcites →https://doi.org/10.1186/s13059-022-02755-2openalex-snapshot
Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP
inferredcites →https://doi.org/10.1214/11-aoas466openalex-snapshot
Measuring reproducibility of high-throughput experiments
inferredcites →https://doi.org/10.1261/rna.029041.111openalex-snapshot
LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
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RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins
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Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
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Clipper: p-value-free FDR control on high-throughput data from two conditions
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