Experience: 25+ years creating algorithms and software tools to enable study of genomes and non-coding RNAs. Designed, published (Lowe et al., Nucleic Acids Research, 1990) , and eventually sold software for primer design through Clontech starting freshman year in college. After undergrad, spent a year in the Basic Research Branch at NCBI, where I learned large-scale genomic analysis, implemented EST library annotation (dbEST, Boguski et al., Nature Genetics, 1993) and studied rapid protein annotation methods. In graduate school at Washington University in St. Louis, I acquired a love of RNA biology in Sean Eddy's lab, and created algorithms to identify different classes of non-coding RNA genes (tRNAs, snoRNAs) that are still in regular use today. As a postdoc at Stanford in the Brown/Botstein microarray group, I designed and built DNA microarrays to study gene expression in microbial thermophiles. I was recruited to UC Santa Cruz in 2001 to co-found a new department integrating molecular and computational biology. Since then, I have been applying comparative genomics to discover novel small RNAs and study RNA-based gene regulation. My academic lab continues to integrate molecular biology and computational approaches for broad-based gene discovery. Graduate students and postdocs in my group often have projects which combine gene modeling with experimental genomics. Our current tools of choice are comparative RNA-seq and ChIP-seq, evolutionary genomics, and probabilistic modeling of RNA genes. Research Goal: Uncover the multitude of RNA genes and RNA-based regulatory mechanisms by studying the unannotated "dark matter" in genomesPersonal Goal: Make state-of-the-art bioinformatics accessible to all biomedical researchersSpecialties: Computational biology, non-coding RNA research (tRNAs, snoRNAs, regulatory RNAs), comparative genomics, human genome, extremophile biology, genome evolution, small RNA-seq analyses