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Faculty Detail    
Name ELLIOT J LEFKOWITZ
Professor, Department of Microbiology
Director of Informatics, Center for Clinical and Translational Science
Director, Molecular and Genetic Bioinformatics Facility, Center for AIDS Research
Director, Bioinformatics Core, Microbiome Facility		  
Campus Address BBRB 276 Zip 2170
Phone  (205) 934-1946
E-mail  ElliotL@uab.edu
Other websites UAB Scholars Profile
Virus Taxonomy
CCTS Informatics
     

Education
Undergraduate  University of Maryland  1973  1977  BS Microbiology 
Graduate  University of Texas Medical Branch  1978  1983  PhD Microbiology 
Fellowship  University of Wisconsin, Madison  1983  1987  Postdoctoral Fellowship, Virology 


Faculty Appointment(s)
Appointment Type Department Division Rank
Primary  Microbiology  Microbiology Professor
Secondary  Genetic & Translational Med  Genetic & Translational Med Professor
Center  Center for AIDS Research  Center for AIDS Research Professor
Center  Center for Biophysical Sciences/Engineering  Center for Biophysical Sciences/Engineering Professor
Center  Civitan International Research Center  Civitan International Research Center Professor
Center  Comp Arthritis, MSK, Bone & Autoimmunity Ctr  Comp Arthritis, MSK, Bone & Autoimmunity Ctr Professor
Center  Comprehensive Cancer Center  Comprehensive Cancer Center Professor
Center  Ctr for Clinical & Translational Sci  Ctr for Clinical & Translational Sci Professor
Center  Informatics Institute  Informatics Institute Professor

Graduate Biomedical Sciences Affiliations
Biochemistry and Structural Biology 
Cell, Molecular, & Developmental Biology 
Genetics, Genomics and Bioinformatics 
Medical Scientist Training Program 
Microbiology 

Biographical Sketch 
Elliot Lefkowitz (b. 1955) 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 that is now part of the institution-wide Biomedical Informatics Component (BMI) of the UAB Center for Clinical and Translational Science. In these positions, he oversees 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 of their informatics needs. These efforts have resulted in the establishment of informatics-related research collaborations across many of the Divisions, Departments, and Schools at UAB. His responsibilities extend to the development of UAB’s overall informatics programs, including oversight and support of activities related to informatics research, service, and teaching. Dr. Lefkowitz and the staff of BMI work to assist UAB investigators with obtaining access to the data they need to support their own research; providing expertise in the management and analysis of that data; and especially to assist the research community in deriving biological knowledge and meaning from the available data. His educational activities include the organization and participation in 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. In addition, he also helps coordinate and teach introductory and advanced virology, emphasizing molecular virology and virus evolution. Dr. Lefkowitz has joint academic appointments in the UAB Departments of Genetics, Mechanical Engineering (School of Engineering), and Computer and Information Sciences (College of Arts and Sciences). He has 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. He currently serves as Data Secretary for the International Committee on Taxonomy of Viruses (ICTV). In this role, he provides 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.

Society Memberships
Organization Name Position Held Org Link
American Society for Microbiology    http://www.asm.org 
American Society for Virology    http://www.asv.org 
International Committee on Taxonomy of Viruses  Data Secretary  http://www.ictvonline.org/ 
 



Research/Clinical Interest
Title
Microbial Genomics and Evolution; Bioinformatics, and Clinical Informatics
Description
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 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 and Grid Computing tools for bioinformatics analysis; and the development and use of tools for analyzing patterns of viral evolution. I have also been involved in the development of databases, web applications, and analysis tools for the sequencing and annotation of several complete bacterial and viral genomes. This includes development of the Viral Bioinformatics Resource Center, one of the original NIH-sponsored Bioinformatics Resource Centers (BRCs) for Biodefense and Emerging or Re-Emerging Infectious Diseases. My work includes research on the genomics and evolutionary history of large DNA viruses as well as several different RNA virus species including Human papillomavirus, Hepatitis C virus and Dengue virus. Ongoing research projects in my group are focused on the analysis of, and the development of tools to support the analysis of the genomics and evolution of the large DNA viruses in the family Poxviridae. Poxviruses are highly successful pathogens, known to infect a variety of hosts. The family Poxviridae includes variola virus, the causative agent of smallpox, which has been eradicated as a public health threat but could potentially reemerge as a bioterrorist threat. The risk scenario includes other animal poxviruses as well as genetically engineered or synthetically derived poxviruses. Past research on orthologous viral gene sets has defined some of the evolutionary relationships between members of the Poxviridae family. But it has not been clear how variation between family members arose in the past—an important issue in understanding how these viruses may vary and possibly produce future threats. Therefore the goal of our research has been to better understand the viral genotypic-phenotypic relationships that result in wide differences in host range and pathogenicity, as well as the evolutionary mechanisms involved in genome variation. Our work has included a comprehensive analysis of all proteins encoded by viruses of the family Poxviridae, to assess the evolutionary history of genes likely acquired through horizontal gene transfer. This effort has allowed us to predict and date the patterns of host gene acquisition throughout the evolutionary history of this virus family, and helps us to better understand the molecular mechanisms of survival and pathogenesis employed by viruses of this family at different stages of their evolution. A complete list of published work is available in NCBI's MyBibliography: http://www.ncbi.nlm.nih.gov/sites/myncbi/elliot j..lefkowitz.1/bibliography/40353132/public/?sort=date&direction=descending

Selected Publications 
Publication PUBMEDID
Li G, Chen N, Roper RL, Feng Z, Hunter A, Danila M, Lefkowitz EJ, Buller RM, Upton C. 2005. Complete coding sequences of the rabbitpox virus genome.
J Gen Virol. 86:2969-77.  		 16227218 
Wang C, Lefkowitz EJ. Genomic multiple sequence alignments: refinement using a genetic algorithm. BMC Bioinformatics. 2005 Aug 8;6:200.  16086841 
Wang C, Lefkowitz EJ. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters. BMC Bioinformatics. 2004 Oct 28;5(1):171  15511296 
Minion FC, Lefkowitz EJ, Madsen ML, Cleary BJ, Swartzell SM, Mahairas GG. The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J Bacteriol. 2004 Nov;186(21):7123-33.  15489423 
Chen N, Danila MI, Feng Z, Buller RM, Wang C, Han X, Lefkowitz EJ, Upton C. The genomic sequence of ectromelia virus, the causative agent of mousepox. Virology. 2003 Dec 5;317(1):165-86.  14675635 
Xiaoying Hou, Michal Mrug, Bradley K. Yoder, Elliot J. Lefkowitz, Gabriel Kremmidiotis, Peter DEustachio, David R. Beier, and Lisa M. Guay-Woodford. 2002. Cystin, a novel cilia-associated protein, is disrupted in the cpk mouse model of polycystic kidney disease. Journal of Clinical Investigation 109:533-540.  11854326 
Hoskins,J.A., Alborn,W. Jr., Arnold,J., Blaszczak,L., Burgett,S., DeHoff,B.S., Estrem,S., Fritz,L., Fu,D.-J., Fuller,W., Geringer,C., Gilmour,R., Glass,J.S., Khoja,H., Kraft,A., LaGace,R., LeBlanc,D.J., Lee,L.N., Lefkowitz,E.J., Lu,J., Matsushima,P., McAhren,S., McHenney,M., McLeaster,K., Mundy,C., Nicas,T.I., Norris,F.H., OGara,M., Peery,R., Robertson,G.T., Rockey,P., Sun,P.-M., Winkler,M.E., Yang,Y., Young-Bellido,M., Zhao,G., Zook,C., Baltz,R.H., Jaskunas,S.Richard, Rosteck,P.R. Jr., Skatrud,P.L. and Glass,J.I. 2001. The Genome of the Bacterium Streptococcus pneumoniae strain R6. Journal of Bacteriology. 183:5709-5717.  11544234 
Glass, J. I., Lefkowitz, E. J., Glass, J. S., Heiner, C.R., Chen, E.Y., and Cassell, G.H. 2000. The complete genome sequence of the mucosal pathogen Ureaplasma urealyticum. Nature 407:757-762.  11048724 
Chen, L., Puri, R., Lefkowitz, E.J., and Kakar, S.S. 2000. Identification of the Human Pituitary Tumor Transforming Gene (hPTTG) Family: Molecular Structure, Expression, and Chromosomal Location. Gene, 248:41-50.  10806349 
Zou, N., Lin, B.Y., Duan, F., Lee, K.-Y., Jin, G., Guan, R., Yao, G., Lefkowitz, E.J., Broker, T.R., and Chow, L.T.. 2000. The Hinge of the Human Papillomavirus Type 11 E2 Protein Contains Major Determinants for Nuclear Localization and Nuclear Matrix Association. J. Virology, 74:3761-70.  10729151 
Virus taxonomy: classification and nomenclature of viruses: Ninth Report of the International Committee on Taxonomy of Viruses. (2012) Ed: King, A.M.Q., Adams, M.J., Carstens, E.B. and Lefkowitz, E.J. San Diego: Elsevier.    
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Keywords
Viruses, Evolution, Genomics, Bioinformatics, Biomedical Informatics