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Akademický článek

ePRINT: exonuclease assisted mapping of protein-RNA interactions

Autor: Sophie Hawkins, Alexandre Mondaini, Seema C. Namboori, Grady G. Nguyen, Gene W. Yeo, Asif Javed, Akshay Bhinge

Publikováno v: Genome Biology, Vol 25, Iss 1, Pp 1-20 (2024)

Abstract RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purify

Externí odkaz: https://doaj.org/article/98cdf82927c44a94a75a95ed56f2b3cc

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Akademický článek

Protocol to process crosslinking and immunoprecipitation data into annotated binding sites

Autor: Shuhao Xu, Grady G. Nguyen, Jack T. Naritomi, Hema M. Kopalle, Brian A. Yee, Katherine L. Rothamel, Evan A. Boyle, Gene W. Yeo

Publikováno v: STAR Protocols, Vol 5, Iss 2, Pp 103040- (2024)

Summary: Here, we present a protocol for using Skipper, a pipeline designed to process crosslinking and immunoprecipitation (CLIP) data into annotated binding sites. We describe steps for partitioning annotated transcript regions and fitting data to

Externí odkaz: https://doaj.org/article/e622606ca3b6467c8ebeda72b22e1c1e

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Akademický článek

Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data

Autor: Her, Hsuanlin, Rothamel, Katherine L., Nguyen, Grady G., Boyle, Evan A., Yeo, Gene W.

Publikováno v: In Cell Genomics 10 July 2024 4(7)

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Akademický článek

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

Autor: Boyle, Evan A., Her, Hsuan-Lin, Mueller, Jasmine R., Naritomi, Jack T., Nguyen, Grady G., Yeo, Gene W.

Publikováno v: In Cell Genomics 14 June 2023 3(6)

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Akademický článek

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

Autor: Evan A. Boyle, Hsuan-Lin Her, Jasmine R. Mueller, Grady G. Nguyen, Gene W. Yeo

Technology for crosslinking and immunoprecipitation 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

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::20f3673588667e281964338fc55a00a7
https://doi.org/10.1101/2022.10.08.511447