I have been working on developing computational pipelines for analysis of genomic data for more than 20 years. I enjoy teaching students, and have successfully supervised more than two-dozen Ph.D. students. As well as publishing one of the first textbooks in the field (in 2006), I’ve also published more than a hundred papers that'd been cited at least 10 times – most of those papers have Ph.D. students as first authors, and I am a senior author. I have been leading a group on Comparative Genomics since 1998. My research includes several projects focused on the high-throughput analysis of hundreds and now thousands of genome sequences for bacterial pathogens, such as Escherichia coli, Salmonella and Vibrio cholera.
We are currently building a database with more than two million viral genome sequences, and developing tools for rapid classification and analysis of viral genomes from metagenomic sequences. I am interested in developing ‘realtime’ methods for detecting microbial pathogens (e.g., C. difficile, or Zika virus) from clinical metagenomic samples, using third-generation sequencing technologies, such as Oxford Nanopore flow cells. Using this technology, we can sequence RNA transcripts directly, and we have recently deposited the first RNA sequence to the SRA (Sequence Read Archive – before this, the ‘RNA sequences’ were cDNA copies).
We are working on sequencing microbiomes and viromes – both RNA and DNA. Preliminary results indicate that it is possible to identify bacterial pathogens and obtain full-length viral genome sequences from urine samples within less than 30 minutes, allowing for rapid clinical diagnostics. I have several collaborative projects with groups in Denmark, Norway, the UK, Germany, Belgium, and Thailand. I am also mentoring several faculty in the Department of Biomedical Informatics at UAMS.