Mendell, Joshua T.2018-01-042018-01-042015-122015-11-18December 2https://hdl.handle.net/2152.5/4457The past decades have witnessed a surge of discoveries revealing RNA regulation as a central player in cellular processes. The advent of cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) technology has recently enabled the investigation of genome-wide RNA binding protein-RNA interactions, which is a very important component of RNA-regulation. However, proper and systematic bioinformatics analysis of CLIP-Seq data is still lacking and challenging. For the past few years, I have been devoting my research to methodological developments of CLIP-Seq data analysis, and developed MiClip and dCLIP for peak calling and differential analysis of CLLIP-Seq data, respectively. I have also applied my CLIP-Seq analysis pipelines in on-campus collaborating projects, in which I identified ORF57 and nuclear AGO2 binding sites. Finally, I conducted analysis of public CLIP-Seq datasets to systematically characterize RNA binding protein targeting sites on circular RNAs.application/pdfenGenomicsHigh-Throughput Nucleotide SequencingRNARNA-Binding ProteinsSequence Analysis, RNAThesis2018-01-041017760201