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  1. Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.

    bioRxiv : the preprint server for biology · 2026

    Crosslinking and immunoprecipitation (CLIP) methods remain the gold standard for characterizing RNA binding protein (RBP) behavior. As a result, many researchers rely on CLIP to assess how treatments targeting RBPs alter binding patterns and regulatory activity. However, current tools for …

    PMID 41959526 DOI ↗

  2. FLARE: a fast and flexible workflow for identifying RNA editing foci.

    BMC bioinformatics · 2023 · 24(1): 370

    Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable …

    PMID 37784060 DOI ↗

  3. Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.

    Cell genomics · 2023 · 3(6): 100317

    Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts …

    PMID 37388912 DOI ↗

  4. Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels.

    Molecular cell · 2018 · 69(6): 1005-1016.e7

    RNA binding proteins (RBPs) interact with primary, precursor, and mature microRNAs (miRs) to influence mature miR levels, which in turn affect critical aspects of human development and disease. To understand how RBPs contribute to miR biogenesis, we analyzed human enhanced …

    PMID 29547715 DOI ↗

  5. RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy.

    Methods in molecular biology (Clifton, N.J.) · 2011 · 729: 247-55

    Transcriptome analysis by deep sequencing, more commonly known as RNA-seq is, becoming the method of choice for gene discovery and quantitative splicing detection. We published a double-random priming RNA-seq approach capable of generating strand-specific information [Li et al., Proc Natl …

    PMID 21365495 DOI ↗

Datasets 5

GSE76008 GSE · GEO

A 17-Gene Stemness Score for Rapid Identification of High-Risk AML Patients [Illumina]

Homo sapiens · GPL10558

GSE51685 GSE · GEO

Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for amyotrophic lateral sclerosis and frontotemporal dementia (strand specific RNA-seq)

Mus musculus · GPL13112

GSE51684 GSE · GEO

Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for amyotrophic lateral sclerosis and frontotemporal dementia (Multiplex Analysis of PolyA-linked Sequences)

Homo sapiens · GPL11154

GSE215252 GSE · GEO

FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

Homo sapiens · GPL24676

GSE213867 GSE · GEO

Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in translation factor binding sites

Homo sapiens · GPL24676

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