相似文献
1
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.
Bioinformatics. 2017 Feb 15;33(4):566-567. doi: 10.1093/bioinformatics/btw653.
2
PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis.
Genome Biol. 2014 Jan 22;15(1):R18. doi: 10.1186/gb-2014-15-1-r18.
3
PAR-CLIP for Discovering Target Sites of RNA-Binding Proteins.
Methods Mol Biol. 2018;1720:55-75. doi: 10.1007/978-1-4939-7540-2_5.
4
omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data.
Genome Biol. 2018 Nov 1;19(1):183. doi: 10.1186/s13059-018-1521-2.
5
PAR-CLIP and streamlined small RNA cDNA library preparation protocol for the identification of RNA binding protein target sites.
Methods. 2017 Apr 15;118-119:41-49. doi: 10.1016/j.ymeth.2016.11.009. Epub 2016 Nov 18.
6
Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.
Nat Protoc. 2014 Feb;9(2):263-93. doi: 10.1038/nprot.2014.012. Epub 2014 Jan 9.
7
dCLIP: a computational approach for comparative CLIP-seq analyses.
Genome Biol. 2014 Jan 7;15(1):R11. doi: 10.1186/gb-2014-15-1-r11.
8
Computational Analysis of RNA-Protein Interactions via Deep Sequencing.
Methods Mol Biol. 2018;1751:171-182. doi: 10.1007/978-1-4939-7710-9_12.
9
Discovering circRNA-microRNA Interactions from CLIP-Seq Data.
Methods Mol Biol. 2018;1724:193-207. doi: 10.1007/978-1-4939-7562-4_16.
10
Transcriptome-wide Identification of RNA-binding Protein Binding Sites Using Photoactivatable-Ribonucleoside-Enhanced Crosslinking Immunoprecipitation (PAR-CLIP).
Curr Protoc Mol Biol. 2017 Apr 3;118:27.6.1-27.6.19. doi: 10.1002/cpmb.35.
引用本文的文献
1
Dysregulated RNA splicing impairs regeneration in alcohol-associated liver disease.
Nat Commun. 2025 Sep 10;16(1):8049. doi: 10.1038/s41467-025-63251-2.
2
Analysis of the mRNA modification machinery alterations in breast cancer through the SCAN-B cohort.
NAR Cancer. 2025 Sep 3;7(3):zcaf027. doi: 10.1093/narcan/zcaf027. eCollection 2025 Sep.
3
Transcriptomic analysis reveals lung cancer and subtype-specific alternative splicing biomarkers regulated by RNA-binding proteins.
Mol Ther Nucleic Acids. 2025 Aug 12;36(3):102681. doi: 10.1016/j.omtn.2025.102681. eCollection 2025 Sep 9.
4
TDP-43 binds to RNA G-quadruplex structure and regulates mRNA stability and translation.
Nucleic Acids Res. 2025 Aug 27;53(16). doi: 10.1093/nar/gkaf820.
5
Cytoplasmic PXR regulates glucose metabolism by binding mRNAs and modulating their stability.
Nat Struct Mol Biol. 2025 Aug 12. doi: 10.1038/s41594-025-01614-5.
6
Isoform characterization of mA in single cells identifies its role in RNA surveillance.
Nat Commun. 2025 Jul 1;16(1):5828. doi: 10.1038/s41467-025-60869-0.
7
Integrative characterization of MYC RNA-binding function.
Cell Genom. 2025 Jul 9;5(7):100878. doi: 10.1016/j.xgen.2025.100878. Epub 2025 May 15.
8
Ku limits RNA-induced innate immunity to allow Alu expansion in primates.
Nature. 2025 Jul;643(8071):562-571. doi: 10.1038/s41586-025-09104-w. Epub 2025 May 15.
9
Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential.
Genome Biol. 2025 May 8;26(1):119. doi: 10.1186/s13059-025-03590-x.
10
mA alters ribosome dynamics to initiate mRNA degradation.
Cell. 2025 May 5. doi: 10.1016/j.cell.2025.04.020.
本文引用的文献
1
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Nat Methods. 2016 Jun;13(6):508-14. doi: 10.1038/nmeth.3810. Epub 2016 Mar 28.
2
CLIPdb: a CLIP-seq database for protein-RNA interactions.
BMC Genomics. 2015 Feb 5;16(1):51. doi: 10.1186/s12864-015-1273-2.
3
HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.
Cell Rep. 2014 Mar 27;6(6):1139-1152. doi: 10.1016/j.celrep.2014.02.005. Epub 2014 Mar 6.
4
PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis.
Genome Biol. 2014 Jan 22;15(1):R18. doi: 10.1186/gb-2014-15-1-r18.
5
Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.
Nat Protoc. 2014 Feb;9(2):263-93. doi: 10.1038/nprot.2014.012. Epub 2014 Jan 9.
6
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges.
Nat Struct Mol Biol. 2013 Dec;20(12):1434-42. doi: 10.1038/nsmb.2699. Epub 2013 Nov 10.
7
Site identification in high-throughput RNA-protein interaction data.
Bioinformatics. 2012 Dec 1;28(23):3013-20. doi: 10.1093/bioinformatics/bts569. Epub 2012 Sep 28.
8
HITS-CLIP: panoramic views of protein-RNA regulation in living cells.
Wiley Interdiscip Rev RNA. 2010 Sep-Oct;1(2):266-86. doi: 10.1002/wrna.31. Epub 2010 Aug 2.
9
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.
Nat Biotechnol. 2011 Jun 1;29(7):607-14. doi: 10.1038/nbt.1873.
10
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
Nat Struct Mol Biol. 2010 Jul;17(7):909-15. doi: 10.1038/nsmb.1838. Epub 2010 Jul 4.
Zotero 插件