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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 CCTS Informatics
Virus Taxonomy
     

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  NSM Dean's Office   Computer Info Sci Associate Professor Research
Secondary  Genetics   Genetic & Translational Med Associate Professor
Secondary  Mechanical Engineering  Mechanical Engineering Associate Professor
Center  Arthritis & Musculoskeletal Diseases Center  Arthritis & Musculoskeletal Diseases Center 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  Comprehensive Cancer Center  Comprehensive Cancer Center Professor
Center  General Clinical Research Center  Ctr for Clinical & Translational Sci Professor

Graduate Biomedical Sciences Affiliations
Biochemistry and Structural Biology 
Cellular and Molecular Biology Program 
Genetics and Genomic Sciences 
Integrative Genetics Graduate Program 
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 also serves as Chair of the Virus Data Subcommittee of the International Committee on Taxonomy of Viruses (ICTV). In this role he provides support to the ICTV for handling of viral taxonomy proposals; communicating the results of ICTV deliberations to the scientific community; and interacting 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  Chair, Virus Data Subcommittee  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.

Selected Publications 
Publication PUBMEDID
Adams MJ, Lefkowitz EJ, King AM, Carstens EB. (2014). Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2014). Arch Virol. 2014 Jun 7.  24906522 
Stoll ML, Kumar R, Morrow C, and Lefkowitz E. (2014): Dysbiosis of the enteric microbiota in pediatric spondyloarthritis. Arthritis Rheumatol. Mar;66 Suppl 11:S228-9. doi: 10.1002/art.38601.  24677931 
Muzny CA, Sunesara IR, Kumar R, Mena LA, Griswold ME, Martin DH, Lefkowitz EJ, Schwebke JR, and Swiatlo E. (2013). Characterization of the Vaginal Microbiota among Sexual Risk Behavior Groups of Women with Bacterial Vaginosis. PLoS One, Nov 13;8(11):e80254.  24236175 
Esteban DJ, Upton C, Bartow-McKenney C, Buller RM, Chen NG, Schriewer J, Lefkowitz EJ, Wang C. (2013). Expression of a non-coding RNA in ectromelia virus is required for normal plaque formation. Virus Genes. Sep 28.  2407804 
Lazrak A, Fu L, Bali V, Bartoszewski R, Rab A, Havasi V, Keiles S, Kappes J, Kumar R, Lefkowitz E, Sorscher EJ, Matalon S, Collawn JF, Bebok Z. (2013). The silent codon change I507-ATC->ATT contributes to the severity of the ΔF508 CFTR channel dysfunction. FASEB J. 27: 4630-4645.  23907436 
Hendrickson R.C., Wang C., Hatcher E.L., Lefkowitz E.J. (2010) Orthopoxvirus Genome Evolution: The Role of Gene Loss. Viruses. 2(9):1933-1967.  21994715 
J. Rodney Brister, Yiming Bao, Carla Kuiken, Philippe Le Mercier, Elliot Lefkowitz, Raphael Leplae, Ramana Madupu, Ruchi Newman, Richard Scheuermann, Donald Seto, Susmita Shrivastava, Qiandong Zeng, William Klimke and Tatiana Tatusova (2010). Editorial: Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. Viruses. 2(10):2258-2268.  21994619 
Coggins, W. C, Lefkowitz, E. J. Sullender, W.M. 1998. Genetic variability among group A and group B Respiratory Syncytial viruses in a childrens hospital. Journal of Clinical Microbiology. 36:3552.  9817872 
Schmidt DJ, Pickett BE, Camacho D, Comach G, Xhaja K, Lennon NJ, Rizzolo K, de Bosch N, Becerra A, Nogueira ML, Mondini A, da Silva EV, Vasconcelos PF, Muñoz-Jordán JL, Santiago GA, Ocazionez R, Gehrke L, Lefkowitz EJ, Birren BW, Henn MR, Bosch I. (2011) A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals novel NS5 mutation. Infect Genet Evol.  21964598 
Banerjee S, Sullender WM, Choudekar A, John C, Tyagi V, Fowler K, Lefkowitz EJ, Broor S. (2011) Detection and genetic diversity of human metapneumovirus in hospitalized children with acute respiratory infections in India. J Med Virol. 83:1799-1810.  21837798 
Lefkowitz, E.J., A.K. Pattnaik, and L.A. Ball. 1990. Complementation of a vesicular stomatitis virus glycoprotein G mutant with wild-type protein expressed from either a bovine papilloma virus or a vaccinia virus vector system. Virology 178, 373-383.  2171187 
White, Gregory; Pickett, Brett; Lefkowitz, Elliot; Ottendorfer, Christy; Johnson, Amelia; Stark, Lillian; Unnasch, Thomas. (2011) Phylogenetic Analysis of Eastern Equine Encephalitis Virus Isolates from Florida. Am J Trop Med Hyg. 5:709-17.  21540379 
Pickett, BE, Striker, R. Lefkowitz EJ. (2010) Evidence for Separation of HCV Subtype 1a into Two Distinct Clades. Journal of Viral Hepatitis. June 2010.  20565573 
Pickett BE, Lefkowitz EJ (2009). Recombination in West Nile Virus: Minimal Contribution to Genomic Diversity. Virus Journal. 6:165.  19821990 
Odom MR, Curtis Hendrickson R, Lefkowitz EJ (2009). Poxvirus protein evolution: Family wide assessment of possible horizontal gene transfer events. Virus Res. 2009 Sep;144(1-2):233-49. Epub 2009 May 21.  19464330 
Rubins KH, Hensley LE, Bell GW, Wang C, Lefkowitz EJ, Brown PO, Relman DA. 2008. Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes. PLoS ONE. 2008 Jul 9;3(7):e2628.  18612436 
Assarsson E, Greenbaum JA, Sundström M, Schaffer L, Hammond JA, Pasquetto V, Oseroff C, Hendrickson RC, Lefkowitz EJ, Tscharke DC, Sidney J, Grey HM, Head SR, Peters B, Sette A. 2008. Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2140-5.  18245380 
Moutaftsi M, Bui HH, Peters B, Sidney J, Salek-Ardakani S, Oseroff C, Pasquetto V, Crotty S, Croft M, Lefkowitz EJ, Grey H, Sette A. Vaccinia virus-specific CD4+ T cell responses target a set of antigens largely distinct from those targeted by CD8+ T cell responses. J Immunol. 2007 Jun 1;178(11):6814-20.   17513729 
Minkah N, Hwang Y, Perry K, Van Duyne GD, Hendrickson R, Lefkowitz EJ, Hannenhalli S, Bushman FD. Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. Virology. 2007 Aug 15;365(1):60-9. Epub 2007 Apr 25.   17462694 
Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V. National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun. 2007 Jul;75(7):3212-9. Epub 2007 Apr 9  17420237 
Parveen S, Sullender WM, Fowler K, Lefkowitz EJ, Kapoor SK, Broor S.Genetic variability in the G protein gene of group A and B respiratory syncytial viruses from India. J Clin Microbiol. 2006 Sep;44(9):3055-64.   16954227  
Lefkowitz EJ, Wang C, Upton C. Poxviruses: past, present and future. Virus Res. 2006 Apr;117(1):105-18. Epub 2006 Feb 24.  16503070 
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.    
Buller, R.M., Arif, B.M., Black, D.N., Dumbell K.R., Esposito, J.J., Lefkowitz, E.J., McFadden, G., Moss, B., Mercer, A.A., Moyer, R.W., Skinner, M,A. and Tripathy, D.N. 2005. Poxviridae. In Virus Taxonomy, The VIIIth Report of the International Committee on Taxonomy of Viruses, Claude Fauquet, M.A. Mayo, J. Maniloff, U. Desselberger, L.A. Ball, (eds.) Academic Press.   
Jones, W.T., Lefkowitz, E.J., 2000. A Lite Bioinformatics Specialization: A Strategy for Initiating Computer Science/Bioinformatics Collaboration. SigBio Newsletter, 20:20-21.   
Frank J. Lebeda, Murray Wolinsky, and Elliot J. Lefkowitz. 2003. Information Resources and Database Development for Defense against Biological Weapons. In Biological Weapons Defense; Principles and Mechanisms of Infectious Disease, Luther Lindler, (ed.) Human Press.   

Keywords
Viruses, Evolution, Genomics, Bioinformatics, Biomedical Informatics