Since 1992, I have played a significant role in the development and provision of bioinformatics support and resources at the University of Alabama at Birmingham (UAB). I am currently Director of Informatics for the UAB Center for Clinical and Translational Sciences (CCTS), an NIH/NCATS Clinical and Translational Science Award site; Director of the UAB AIDS Center (CFAR) Bioinformatics Facility; and Director of the Bioinformatics Core for the UAB Microbiome Facility. As Director of these Informatics facilities, I oversee a team of Bioinformaticians and Systems Analysts who work and collaborate with UAB investigators to provide them with the broad range of tools and expertise necessary to support all their informatics needs. These responsibilities extend to the development of UAB’s overall informatics programs, including oversight and support of activities related to research, service and teaching. We assist investigators in the analysis of a wide range of data types including those derived from the use of next generation sequencing, including whole genome, exome, transcriptome, microbiome, and metagenomic sequence data. By providing these services, we help to ensure that each individual and laboratory can maximize their ability to publish and obtain funding, and especially to derive biological knowledge and meaning from their data. Since 2011, CCTS Informatics has also served as the analytical component of the UAB Microbiome Facility. In this role, we have developed an automated analytical pipeline for the processing and visualization of 16S rRNA sequencing data, as well as a similar pipeline for the processing of shotgun metagenomic data.
My own personal research interests are directed at contributing to the understanding of microbial genomics and evolution by developing and utilizing computational tools and bioinformatics techniques to mine sequence and other data for significant patterns characteristic of function and/or evolution. This includes research on the genomics and evolutionary history of many virus species, as well as the complete genomic sequencing and annotation of various bacterial species. I have been part of the teams that have sequenced the complete genomes of ectromelia virus, monkeypox virus, rabbitpox virus, Ureaplasma urealyticum, Streptococcus pneumoniae strain R6, and Mycoplasma hyopneumoniae. My work on basic bioinformatics tool development has included the development of new algorithms for the detection of viral regulatory motifs; tools for the identification of viral genes; the development and utilization of High Performance Computing tools for bioinformatics analysis; and the development and use of tools for analyzing patterns of viral evolution. I have also been Principal Investigator of the Viral Bioinformatics Resource Center, an NIH-sponsored effort to develop Bioinformatics Resource Centers (BRCs) for Biodefense and Emerging or Re-Emerging Infectious Diseases. I also serve as Data Secretary for the International Committee on Taxonomy of Viruses (ICTV). In this role, I provide support to the ICTV for handling of viral taxonomy proposals; communicate the results of ICTV deliberations to the scientific community; and interact with various international agencies such as the NIH National Center for Biotechnology Information to incorporate the official, ICTV virus taxonomy into their own taxonomic databases.
As Director of CCTS and CFAR Informatics, in addition to providing informatics research support and collaboration, I am also responsible for providing educational opportunities to campus investigators to enhance their knowledge, understanding, and application of informatics data and analytical tools in support of their own research interests. These opportunities include the organization and participation in for-credit courses covering various aspects of informatics education; organization of seminars and workshops targeted to specific informatics problems; providing informatics training opportunities to students, fellows, and staff from across campus; and supporting the integration of informatics training opportunities into campus NIH training (T) and development (K) award programs. I have personally mentored graduate students and postgraduate fellows throughout my research career. This includes students obtaining their degree in my own lab; serving on student dissertation committees; mentoring students on training grants; and mentoring fellows seeking and working on development awards as well as K award scholars.
