Identifying and characterizing tRNAs and other non-coding RNAs through computational and experimental genomics and transcriptomics
Our research uses a mixture of computational and experimental methods to identify and characterize the function and regulation of non-coding RNAs (ncRNAs) in many species including human, mouse, yeast, and archaea (microbes that live in extreme environments).
On the experimental side, we study ncRNAs with high-throughput RNA sequencing techniques in human and model organisms, augmented by molecular characterization via CRISPR, RNAi and other genetic manipulation tools. We have also developed a method for sequencing transfer RNA-derived small RNAs which can detect RNA modifications in addition to expression analysis. Integration of theoretical and experimental approaches is the quickest, most efficient path to new biology.
On the computational side, we design and develop algorithms, such as the widely adopted tRNAscan-SE, to identify tRNA genes in genomic sequences using probabilistic models and comparative genomics. We have developed a robust, specialized tRNA-seq data analysis pipeline for studying small non-coding RNA gene expression (tRAX). We have also designed a purely genomic method for improving tRNA characterization by inferring gene activity state (tRAP). In the dry lab, database development is a major task for continuation of data curation from our discoveries and providing latest resources to the research communities.
Our lab trains both molecular biology and bioinformatics graduate students who have a keen interest in RNA biology. Postdocs with strong backgrounds in computational RNA analysis or non-coding RNA biochemistry are encouraged to apply to the lab (please send an email and CV). If you are not currently a graduate student at UCSC, please see information for the Graduate Program in Biomedical Sciences and Engineering (PBSE). Please do not email requests for direct admittance to the program through my lab.