|cc||Elliot J. Lefkowitz, Ph.D.
Associate Professor, Department of Microbiology
Areas of Focus: virology; genomics; evolution; boinformatics
My 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 work includes the development and use of databases, analytical tools, and visualization tools to support the sequencing, annotation, and analysis of bacterial and viral genomes. I have been involved in bioinformatics-related collaborations across many of the Divisions, Departments, and Schools at UAB, including the Schools of Public Health, Engineering, and Natural Sciences & Mathematics. In addition, I have been involved in, and initiated, collaborations with research groups world-wide. My work on basic bioinformatics tool development has included the development of new algorithms for the detection of viral regulatory motifs, the development and utilization of High Performance and Grid Computing for bioinformatics analysis (with the Departments of Computer and Information Sciences and Mechanical Engineering), and the development and use of statistical genetics methods to analyze genomic and microarray gene expression data (with the Section on Statistical Genetics). My work on the development of bioinformatics resources has included the development of databases, analytical tools, and interactive applications for the sequencing, annotation, and analysis of eukaryotic, bacterial, and viral genomes. I have been the recipient of numerous U.S. Government grants and contracts awarded by the National Institutes of Health, the U.S. Army, and the Department of Energy to develop bioinformatics resources to support biodefense research. I have also been involved in the development of databases, web applications, and analysis tools for the sequencing and annotation of several complete bacterial genomes including Ureaplasma urealyticum (with Drs. John Glass and Gail Cassell of Eli Lilly), Streptococcus pneumoniae strain R6 (with Drs. John Glass and JoAnn Hoskins of Eli Lilly), and Mycoplasma hyopneumoniae (with Dr. Chris Minion of Iowa State). I am currently Principal Investigator of the Viral Bioinformatics Resource Center, one of eight NIH-sponsored contracts to develop Bioinformatics Resource Centers for Biodefense and Emerging or Re-Emerging Infectious Diseases. Prior to serving as PI on the VBRC, I was PI of one of the two NIAID Orthopoxvirus Genomic and Bioinformatics Resource Centers, the predecessor to the current BRC program. (Chris Upton of the University of Victoria and Mark Buller of St. Louis University were PIs of the second center.) The VBRC was specifically directed to study viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae and Togaviridae families.
Figure 1 - Taxonomic demarcation via sequence similarity
Panel A: Pairwise Analysis of Sequence Conservation (PASC) analysis was carried out on the viral DNA-dependent DNA polymerase gene (the vaccinia virus E9L gene homolog) for every completely sequenced poxvirus genome. Each protein was aligned to every other protein and the percent identity of each pair-wise comparison was then included in a histogram plot of all possible comparisons. Peaks are identified across the top of the figure according to the taxa represented by particular pairwise sequence comparisons.
Panel B: Phylogenetic reconstruction of the Poxviridae family of viruses based on their DNA polymerase protein sequences. Subfamily and Genera demarcations are identified. Terminal nodes are labeled according to genus. Sequences belonging to one of the genera labeled either Group A or B coincide with the A and B comparison peaks at the top of panel A.
Panel C: Phylogenetic prediction based on the multiple nucleic acid sequence alignment of the core genomic region of each representative orthopoxvirus species or strain.
Elliot Lefkowitz (b. 1955), Associate Professor, Department of Microbiology and Director of the UAB Molecular and Genetic Bioinformatics Facility, received his B.S. degree in Microbiology at the University of Maryland-College Park in 1977. He received his PhD in Microbiology from the University of Texas Medical Branch-Galveston in 1983 where he studied the regulation of interferon-gamma activity. He continued his training as a postdoctoral fellow at the University of Wisconsin-Madison where he participated in research projects involving the cloning of interferon-inducible genes and the molecular biology and evolution of vaccinia and vesicular stomatitis viruses. Dr. Lefkowitz came to UAB in 1987 and in 1991 became director of the UAB AIDS Center Biological Computing Resource Facility which is now part of the institution-wide Molecular and Genetic Bioinformatics Facility. His current work includes research on microbial genomics and evolution, and the development of bioinformatic resources (databases, analytical tools, and web-based interfaces) to support these interests.