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Faculty Detail     Name ELLIOT J LEFKOWITZ Associate Professor, Department of Microbiology Director, Biomedical 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 http://bioinformatics.uab.edu http://ictvonline.org/

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 Associate Professor Secondary  Genetics   Genetic & Translational Med Associate Professor Center  Arthritis & Musculoskeletal Diseases Center  Arthritis & Musculoskeletal Diseases Center Associate Professor Center  Center for AIDS Research  Center for AIDS Research Associate Professor Center  Civitan International Research Center  Civitan International Research Center Associate Professor Center  Comprehensive Cancer Center  Comprehensive Cancer Center Associate Professor Center  General Clinical Research Center  Ctr for Clinical & Translational Sci Associate 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 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  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  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  First Prev   1 2 3 4 of  4  Next Last

Keywords Viruses, Evolution, Genomics, Bioinformatics, Biomedical Informatics

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