ArticleRNA (New York, N.Y.)2016
CLIPSeqTools--a novel bioinformatics CLIP-seq analysis suite.
Article in RNA (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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.
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Who cites it
22 citing papers in PubMed, 49 citations in OpenAlex.
- Unlocking the potential of non-coding RNAs in cancer research and therapy.Translational oncology · 2023Article
- A network of DZF proteins controls alternative splicing regulation and fidelity.Nucleic acids research · 2023Article
- Solid-Support Directional (SSD) RNA-Seq as a Companion Method to CLIP-Seq.Methods in molecular biology (Clifton, N.J.) · 2022Article
- TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization.Nucleic acids research · 2021Article
- Modulation of Aub-TDRD interactions elucidates piRNA amplification and germplasm formation.Life science alliance · 2021Article
- Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.GigaScience · 2020Article
- Clip for studying protein-RNA interactions that regulate virus replication.Methods (San Diego, Calif.) · 2020Review
- Autoregulation of JARID2 through PRC2 interaction with its antisense ncRNA.BMC research notes · 2020Article
- Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction.Circulation · 2020Article
- Mobile genomics: tools and techniques for tackling transposons.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Capturing 5' and 3' native ends of mRNAs concurrently with Akron sequencing.Nature protocols · 2019Article
- Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions.Methods (San Diego, Calif.) · 2019Review
- Recent computational developments on CLIP-seq data analysis and microRNA targeting implications.Briefings in bioinformatics · 2018Review
- Amyotrophic Lateral Sclerosis associated FUS mutation shortens mitochondria and induces neurotoxicity.Scientific reports · 2018Article
- Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs.Quantitative biology (Beijing, China) · 2018Article
- CLIP-related methodologies and their application to retrovirology.Retrovirology · 2018Review
- Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis.Nature structural & molecular biology · 2018Article
- Bioinformatic tools for analysis of CLIP ribonucleoprotein data.Wiley interdisciplinary reviews. RNA · 2017Review
- From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data.Nucleic acids research · 2017Article
- Kc167, a widely used Drosophila cell line, contains an active primary piRNA pathway.RNA (New York, N.Y.) · 2017Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely diverse and depending on the RBPs that are analyzed, the approaches vary significantly, necessitating the development of flexible and efficient informatics tools. In this study, we present CLIPSeqTools, a novel, highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. It contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains.
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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.