University Term Professor
Professor, Department of Biology and the
UF Genetics Institute.
In my academic research I develop and employ computational, comparative and functional genomics approaches to study genome architecture, function and evolution. I am a recognized expert in the field of genome analysis with an independent research program that currently spans 12 years. During this time I have been involved as a PI or Co-PI on federal grant awards in excess of $18M, have published over 80 articles and book chapters on genetics and genome analysis, and mentored 10 undergraduate researchers, 10 graduate students, 4 research technicians and 7 post-doctorate fellows. I have also served as the graduate coordinator for Biology, and as such, led the UF department of Biology’s graduate program and it’s 100+ students. While I was a post-doc working on the human genome project it became clear to me that the genome era would not only influence the scope and type of questions that would be investigated in biology, it would require a paradigm shift in the way experimentation and data analysis were performed. I work with large and complex plant and animal genomes where we apply computational sequence analysis methods to assemble and annotate large genome and transcriptomes, investigate within species and between species sequence variation, genome structure, gene structure, gene content, gene/genome organization and gene regulation. My research projects involve collecting primary genome annotation data in the form of genome sequences and catalogues of genes, developing methods and tools to leverage next generation sequence capacities, examining gene-expression, identifying targets of RNA and DNA binding proteins, analyzing alternatively spliced isoform expression, leveraging genomic data and approaches to address fundamental evolutionary questions concerning genome evolution, and examining the function and regulation of RNA processing. I have recently overseen a large spiny mouse RNA-Seq analysis, and I have sequenced and assembled a whole genome reference sequence for spiny mouse. I also teach and mentor undergraduates and graduate students in computational genomics and bioinformatics. I am a member of the HHMI Science Education Alliance, and have been teaching an undergraduate course based research experience on genome annotation at the undergraduate level for 5 years.
I am also the Faculty Director of Bioinformatics for the ICBR core facility at UFL, and in this capacity I have worked in collaboration with multiple faculty at UFL on multiple complex data analyses including RNA-Seq, scRNA-Seq, alternative splicing analysis and whole genome assembly and annotation. Additionally, I work closely with the additional ICBR core labs that provide NGS library construction, scRNA library construction, flow cytometry and NGS sequencing services. Thus I will provide expert oversight in the genomics data collection and informatics to ensure the use of rigorous analysis approaches.
Complete List of Published Work in MyBibliography: