ReviewNucleic acids research2015
Design and bioinformatics analysis of genome-wide CLIP experiments.
Review in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed.
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- Structural Characterization of Protein-Nucleic Acid Complexes: An Overview of the Recent Innovation in the Analytic Methods.International journal of molecular sciences · 2025Review
- iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites.PLoS computational biology · 2024Article
- Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions.PLoS computational biology · 2024Article
- Inhibition of UHRF1 Improves Motor Function in Mice with Spinal Cord Injury.Cellular and molecular neurobiology · 2024Article
- The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infectivemSphere · 2023Article
- FMRP binds Per1 mRNA and downregulates its protein expression in mice.Molecular brain · 2023Article
- RNA-Binding Proteins in Bladder Cancer.Cancers · 2023Review
- The role of N6-methyladenosine-modified non-coding RNAs in the pathological process of human cancer.Cell death discovery · 2022Review
- Next-generation sequencing: A new avenue to understand viral RNA-protein interactions.The Journal of biological chemistry · 2022Review
- MicroRNA Targeting.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding.Nucleic acids research · 2021Article
- ELAVL1 primarily couples mRNA stability with the 3' UTRs of interferon-stimulated genes.Cell reports · 2021Article
- Comprehensive machine-learning-based analysis of microRNA-target interactions reveals variable transferability of interaction rules across species.BMC bioinformatics · 2021Article
- Noncoding RNAs in B cell responses.RNA biology · 2021Review
- Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks.PLoS computational biology · 2021Article
- Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing.Computational and structural biotechnology journal · 2021Review
- ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins.Bioinformatics (Oxford, England) · 2020Article
- Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners.Biochemical Society transactions · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The past decades have witnessed a surge of discoveries revealing RNA regulation as a central player in cellular processes. RNAs are regulated by RNA-binding proteins (RBPs) at all post-transcriptional stages, including splicing, transportation, stabilization and translation. Defects in the functions of these RBPs underlie a broad spectrum of human pathologies. Systematic identification of RBP functional targets is among the key biomedical research questions and provides a new direction for drug discovery. The advent of cross-linking immunoprecipitation coupled with high-throughput sequencing (genome-wide CLIP) technology has recently enabled the investigation of genome-wide RBP-RNA binding at single base-pair resolution. This technology has evolved through the development of three distinct versions: HITS-CLIP, PAR-CLIP and iCLIP. Meanwhile, numerous bioinformatics pipelines for handling the genome-wide CLIP data have also been developed. In this review, we discuss the genome-wide CLIP technology and focus on bioinformatics analysis. Specifically, we compare the strengths and weaknesses, as well as the scopes, of various bioinformatics tools. To assist readers in choosing optimal procedures for their analysis, we also review experimental design and procedures that affect bioinformatics analyses.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.