We developed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) to quantify protein-RNA interactions in the whole transcriptome. We described the details of the iCLIP method and presented it in a video. We showed that the cDNAs in iCLIP truncate at crosslink sites, and developed computational methods based on cDNAs-starts for analysis of iCLIP data. We wrote three reviews on the advances in CLIP technologies: the 2012 and 2018 review describing the core steps and the variant experimental methods of iCLIP, and the 2018 computational review describing the approaches for data analysis and quality control.
Many computational tools have been developed for analysis of data produced by CLIP and its variant protocols, as described in our review. In collaboration with Tomaz Curk, we developed iCount, a Python code and associated command-line interface (CLI), which are available from GitHub, which maps, annotates and analyses iCLIP data, and defines the peaks of high-occupancy protein-RNA binding sites. This code is the basis for the web server iMaps, which enables a streamlined analysis of data produced by iCLIP and other CLIP variants, and is freely available for general use. iMaps can be used to analyse unpublished data in a secure manner, and to obtain public CLIP data in a well-annotated format, along with various forms of data quality control, visualisation and comparison.