Positions

Overview

  • My work at the University of Alabama at Birmingham (UAB) encompasses a number of roles and interests. As a Professor of Microbiology, my research interests are directed at deriving a better understanding of the processes and consequences of microbial evolution and how variation of the genomic sequences of microbes impacts that evolution. I am also interested in the role that microbes play in human health and disease. To pursue these interests my lab focuses on bioinformatics analysis – the development and use of computational tools to analyze biological data. My interests in bioinformatics also impacts my educational activities since I serve as Co-Director of the UAB Undergraduate Bioinformatics Program. Bioinformatics also guides my service responsibilities that include serving as Director of Bioinformatics for the UAB Center for Clinical and Translational Sciences (CCTS), an NIH/NCATS Clinical and Translational Science Award site and as Director of the Bioinformatics Core for the UAB Microbiome Facility. Previously, I have also served as Director of the UAB AIDS Center (CFAR) Bioinformatics Facility enabled the formation of the CCTS and Microbiome facilities. As Director of these Informatics facilities, I oversee 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 responsibilities extend to the development of UAB’s overall informatics programs, including oversight and support of activities related to research, service and education. We assist investigators in the analysis of a wide range of data types including those derived from the use of next generation sequencing, including whole genome, exome, transcriptome, microbiome, and metagenomic sequence data. Since 2011 our work serving as the analytical component of the UAB Microbiome Facility has included development of an automated analytical pipeline for the processing and visualization of 16S rRNA sequencing data, as well as a similar pipeline for the processing of shotgun metagenomic data. These pipelines provide an initial report detailing the microbial population present in investigator samples and are followed by customized, more detailed analyses investigating the significance of differences identified between samples. Our provision of bioinformatics support helps to ensure that each individual and laboratory can maximize their ability to publish and obtain funding, and especially to derive biological knowledge and meaning from their data.

    My own personal 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 includes research on the genomics and evolutionary history of many virus species, as well as the complete genomic sequencing and annotation of various bacterial species. I have been part of the teams that have sequenced the complete genomes of ectromelia virus, monkeypox virus, rabbitpox virus, Ureaplasma urealyticum, Streptococcus pneumoniae strain R6, and Mycoplasma hyopneumoniae. My work on basic bioinformatics tool development 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 Computing tools for bioinformatics analysis; and the development and use of tools for analyzing patterns of viral evolution. I was the first 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. I also serve as Data Secretary for the International Committee on Taxonomy of Viruses (ICTV). In this role, I provide 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.

    More recently, my research interests have included a focus on the role that populations of microorganisms (the microbiota) play in health and disease by looking for associations between the populations of microbial genomes present in an environment or host (the microbiome) and phenotypic data describing that environment or host. Our work in this area encompasses both laboratory and clinical studies as well as the development of bioinformatics tools to support the analysis of the collected data.

    In addition to my research and service activities, I am also responsible for providing educational opportunities to campus investigators to enhance their knowledge, understanding, and application of informatics data and analytical tools in support of their own research interests. These opportunities include the organization and participation in for-credit 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. I have personally mentored graduate students and postgraduate fellows throughout my research career. This includes students obtaining their degree in my own lab; serving on student dissertation committees; mentoring students on training grants; and mentoring fellows seeking and working on development awards. I am currently a mentor for four K-award scholars. I also serve as Co-Director of the UAB Undergraduate Bioinformatics Bachelor’s-degree Program. This program provides undergraduate students with the opportunity to take classes from and perform research with faculty in the UAB School of Medicine and faculty in the UAB College of Arts and Sciences who have expertise in Bioinformatics, Computational Biology, Data Science, and Computer Science.
  • Selected Publications

    Academic Article

    Year Title Altmetric
    2022 Diet Quality and the Gut Microbiota in Women Living in AlabamaAmerican Journal of Preventive Medicine.  63:S37-S46. 2022
    2022 Making virus taxonomy accessible 2022
    2022 Genomic evolution of the Coronaviridae familyVirology.  570:123-133. 2022
    2022 Differentiating between viruses and virus species by writing their names correctlyArchives of Virology.  167:1231-1234. 2022
    2022 Intrinsic IL-2 production by effector CD8 T cells affects IL-2 signaling and promotes fate decisions, stemness, and protectionScience Immunology.  7. 2022
    2022 ICTV Virus Taxonomy Profile: Potyviridae 2022Journal of General Virology.  103. 2022
    2021 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and MononegaviralesArchives of Virology.  166:3513-3566. 2021
    2021 Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales (Archives of Virology, (2021), 166, 12, (3513-3566), 10.1007/s00705-021-05143-6)Archives of Virology.  166:3567-3579. 2021
    2021 Perspective on taxonomic classification of uncultivated virusesCurrent Opinion in Virology.  51:207-215. 2021
    2021 Sex-based differences in the activation of peripheral blood monocytes in early Parkinson diseasenpj Parkinson's Disease.  7. 2021
    2021 Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)Archives of Virology.  166:2633-2648. 2021
    2021 ICTV virus taxonomy profile: Marnaviridae 2021Journal of General Virology.  102. 2021
    2021 ICTV virus taxonomy profile: BornaviridaeJournal of General Virology.  102. 2021
    2021 ICTV virus taxonomy profile: Herpesviridae 2021Journal of General Virology.  102. 2021
    2021 ICTV virus taxonomy profile: InoviridaeJournal of General Virology.  102. 2021
    2021 ICTV virus taxonomy profile: PlectroviridaeJournal of General Virology.  102. 2021
    2021 The gut microbiome of extremely preterm infants randomized to the early progression of enteral feedingPediatric Research2021
    2020 Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)Archives of Virology.  165:2737-2748. 2020
    2020 Correction to: Binomial nomenclature for virus species: a consultation (Archives of Virology, (2020), 165, 2, (519-525), 10.1007/s00705-019-04477-6)Archives of Virology.  165:1263-1264. 2020
    2020 The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranksNature Microbiology.  5:668-674. 2020
    2020 Binomial nomenclature for virus species: a consultationArchives of Virology.  165:519-525. 2020
    2020 Midtrimester microbial DNA variations in maternal serum of women who experience spontaneous preterm birthThe Journal of Maternal-Fetal and Neonatal Medicine.  33:359-367. 2020
    2020 Age-related differences in the gut microbiome of rhesus macaquesJournal of Gerontology Series A: Biological Sciences and Medical Sciences.  75:1293-1298. 2020
    2020 Comprehensive analysis of iron utilization by Mycobacterium tuberculosisPLoS Pathogens.  16. 2020
    2019 Individualized recovery of gut microbial strains post antibioticsnpj Biofilms and Microbiomes.  5. 2019
    2019 Sharing of gut microbial strains between selected individual sets of twins cohabitating for decadesPLoS One.  14. 2019
    2019 Individualized recovery of gut microbial strains post antibiotics.npj Biofilms and Microbiomes.  5:30. 2019
    2019 Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)Archives of Virology.  164:2417-2429. 2019
    2019 ICTV virus taxonomy profile: FiloviridaeJournal of General Virology.  100:911-912. 2019
    2019 ICTV virus taxonomy profile: SolinviviridaeJournal of General Virology.  100:736-737. 2019
    2019 Altered DNA methylation in the developing brains of rats genetically prone to high versus low anxietyThe Journal of Neuroscience.  39:3144-3158. 2019
    2019 Gut microbiota diversity is associated with cardiorespiratory fitness in post-primary treatment breast cancer survivorsExperimental Physiology.  104:529-539. 2019
    2019 Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018)Archives of Virology.  164:943-946. 2019
    2019 ICTV virus taxonomy profile: ParvoviridaeJournal of General Virology.  100:367-368. 2019
    2019 In Silico and Experimental Evaluation of Primer Sets for Species-Level Resolution of the Vaginal Microbiota Using 16S Ribosomal RNA Gene SequencingJournal of Infectious Diseases.  219:305-314. 2019
    2019 ICTV virus taxonomy profile: BirnaviridaeJournal of General Virology.  100:5-6. 2019
    2019 ICTV virus taxonomy profile: NodaviridaeJournal of General Virology.  100:3-4. 2019
    2018 New microbe genomic variants in patients fecal community following surgical disruption of the upper human gastrointestinal tractHuman Microbiome Journal.  10:37-42. 2018
    2018 The diversity of the proline-rich domain of pneumococcal surface protein A (PspA): Potential relevance to a broad-spectrum vaccineVaccine.  36:6834-6843. 2018
    2018 ICTV virus taxonomy profile: GlobuloviridaeJournal of General Virology.  99:1357-1358. 2018
    2018 Associations between Race, Perceived Psychological Stress, and the Gut Microbiota in a Sample of Generally Healthy Black and White Women: A Pilot Study on the Role of Race and Perceived Psychological StressPsychosomatic Medicine.  80:640-648. 2018
    2018 Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)Archives of Virology.  163:2601-2631. 2018
    2018 ICTV virus taxonomy profile: BaculoviridaeJournal of General Virology.  99:1185-1186. 2018
    2018 The virology of taterapox virus in vitroViruses.  10. 2018
    2018 Identification of Key Bacteria Involved in the Induction of Incident Bacterial Vaginosis: A Prospective StudyJournal of Infectious Diseases.  218:966-978. 2018
    2018 ICTV virus taxonomy profile: PapillomaviridaeJournal of General Virology.  99:989-990. 2018
    2018 Composition and richness of the serum microbiome differ by age and link to systemic inflammationGeroscience.  40:257-268. 2018
    2018 ICTV virus taxonomy profile: AsfarviridaeJournal of General Virology.  99:613-614. 2018
    2018 ICTV virus taxonomy profile: AvsunviroidaeJournal of General Virology.  99:611-612. 2018
    2018 ICTV virus taxonomy profile: HypoviridaeJournal of General Virology.  99:615-616. 2018
    2018 ICTV virus taxonomy profile: PlasmaviridaeJournal of General Virology.  99:617-618. 2018
    2018 ICTV virus taxonomy profile: RhabdoviridaeJournal of General Virology.  99:447-448. 2018
    2018 ICTV Virus Taxonomy Profile: GuttaviridaeJournal of General Virology.  99:290-291. 2018
    2018 ICTV virus taxonomy profile: AmpullaviridaeJournal of General Virology.  99:288-289. 2018
    2018 Novel putative drivers revealed by targeted exome sequencing of advanced solid tumorsPLoS One.  13. 2018
    2018 Age and fecal microbial strain-specific differences in patients with spondyloarthritisArthritis Research and Therapy.  20. 2018
    2018 ICTV Virus taxonomy profile: ChrysoviridaeJournal of General Virology.  99:19-20. 2018
    2018 ICTV virus taxonomy profile: BicaudaviridaeJournal of General Virology.  99:864-865. 2018
    2018 ICTV virus taxonomy profile: PartitiviridaeJournal of General Virology.  99:17-18. 2018
    2018 ICTV virus taxonomy profile: TogaviridaeJournal of General Virology.  99:761-762. 2018
    2018 Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV)Nucleic Acids Research.  46:D708-D717. 2018
    2017 ICTV virus taxonomy profile: NyamiviridaeJournal of General Virology.  98:2914-2915. 2017
    2017 ICTV virus taxonomy profile: PleolipoviridaeJournal of General Virology.  98:2916-2917. 2017
    2017 ICTV virus taxonomy profile: PneumoviridaeJournal of General Virology.  98:2912-2913. 2017
    2017 Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficilenpj Biofilms and Microbiomes.  3. 2017
    2017 ICTV virus taxonomy profile: HepeviridaeJournal of General Virology.  98:2645-2646. 2017
    2017 Streptococcus pneumoniae TIGR4 phase-locked opacity variants differ in virulence phenotypesmSphere.  2. 2017
    2017 ICTV virus taxonomy profile: CystoviridaeJournal of General Virology.  98:2423-2424. 2017
    2017 ICTV virus taxonomy profile: PicornaviridaeJournal of General Virology.  98:2421-2422. 2017
    2017 Helicobacter pylori infection is associated with an altered gastric microbiota in childrenMucosal Immunology.  10:1169-1177. 2017
    2017 Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017)Archives of Virology.  162:2505-2538. 2017
    2017 ICTV virus taxonomy profile: CircoviridaeJournal of General Virology.  98:1997-1998. 2017
    2017 ICTV virus taxonomy profile: VirgaviridaeJournal of General Virology.  98:1999-2000. 2017
    2017 ICTV virus taxonomy profile: BenyviridaeJournal of General Virology.  98:1571-1572. 2017
    2017 Targeting of Streptococcus mutans Biofilms by a Novel Small Molecule Prevents Dental Caries and Preserves the Oral MicrobiomeJournal of Dental Research.  96:807-814. 2017
    2017 ICTV virus taxonomy profile: OphioviridaeJournal of General Virology.  98:1161-1162. 2017
    2017 ICTV virus taxonomy profile: PolyomaviridaeJournal of General Virology.  98:1159-1160. 2017
    2017 50 years of the International Committee on Taxonomy of Viruses: progress and prospectsArchives of Virology.  162:1441-1446. 2017
    2017 Gut microbiota composition associated with alterations in cardiorespiratory fitness and psychosocial outcomes among breast cancer survivorsSupportive Care in Cancer.  25:1563-1570. 2017
    2017 ICTV virus taxonomy profile: CorticoviridaeJournal of General Virology.  98:888-889. 2017
    2017 ICTV virus taxonomy profile: IridoviridaeJournal of General Virology.  98:890-891. 2017
    2017 ICTV virus taxonomy profile: IflaviridaeJournal of General Virology.  98:527-528. 2017
    2017 ICTV virus taxonomy profile: SecoviridaeJournal of General Virology.  98:529-531. 2017
    2017 Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated dietJournal of Microbiological Methods.  135:69-76. 2017
    2017 ICTV virus taxonomy profile: DicistroviridaeJournal of General Virology.  98:355-356. 2017
    2017 ICTV virus taxonomy profile: PotyviridaeJournal of General Virology.  98:352-354. 2017
    2017 Consensus statement: Virus taxonomy in the age of metagenomicsNature Reviews Microbiology.  15:161-168. 2017
    2017 ICTV virus taxonomy profile: GeminiviridaeJournal of General Virology.  98:131-133. 2017
    2017 ICTV virus taxonomy profile: OurmiavirusJournal of General Virology.  98:129-130. 2017
    2017 50 years of the International Committee on Taxonomy of Viruses: progress and prospectsArchives of Virology.  162:1441-1446. 2017
    2017 Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017)Archives of Virology.  162:2505-2538. 2017
    2017 Consensus statement: Virus taxonomy in the age of metagenomicsNature Reviews Microbiology.  15:161-168. 2017
    2017 Erratum: Author Correction: Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile.npj Biofilms and Microbiomes.  3:29. 2017
    2017 Gut microbiota composition associated with alterations in cardiorespiratory fitness and psychosocial outcomes among breast cancer survivorsSupportive Care in Cancer.  25:1563-1570. 2017
    2017 ICTV virus taxonomy profile: AscoviridaeJournal of General Virology.  98:4-5. 2017
    2017 ICTV virus taxonomy profile: FlaviviridaeJournal of General Virology.  98:2-3. 2017
    2017 Streptococcus pneumoniae TIGR4 Phase-Locked Opacity Variants Differ in Virulence PhenotypesmSphere.  2. 2017
    2017 Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)Nucleic Acids Research2017
    2016 Fecal metabolomics in pediatric spondyloarthritis implicate decreased metabolic diversity and altered tryptophan metabolism as pathogenic factorsGenes and Immunity.  17:400-405. 2016
    2016 Gravidas with class III obesity: evaluating the abdominal skin microbiota above and below the panniculus*The Journal of Maternal-Fetal and Neonatal Medicine.  29:3312-3316. 2016
    2016 Midtrimester cervicovaginal microbiota: Identification of microbial variations associated with puerperal infection at termAmerican Journal of Perinatology: neonatal and maternal-fetal medicine.  33:1165-1175. 2016
    2016 Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016)Archives of Virology.  161:2921-2949. 2016
    2016 The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profilesFEMS Microbiology Ecology.  92. 2016
    2016 Culture-independent diagnostics for health securityHealth security.  14:122-142. 2016
    2016 Vaginal Microbiota in Pregnancy: Evaluation Based on Vaginal Flora, Birth Outcome, and RaceAmerican Journal of Perinatology: neonatal and maternal-fetal medicine.  33:401-408. 2016
    2016 Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficileBMC Microbiology.  16. 2016
    2016 Gravidas with class III obesity: evaluating the abdominal skin microbiota above and below the panniculus*The Journal of Maternal-Fetal and Neonatal Medicine.  29:3312-3316. 2016
    2016 Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016)Archives of Virology.  161:2921-2949. 2016
    2015 Quantitative Proteomic Analysis of Enriched Nuclear Fractions from BK Polyomavirus-Infected Primary Renal Proximal Tubule Epithelial CellsJournal of Proteome Research.  14:4413-4424. 2015
    2015 Gut microbial dysbiosis due to helicobacter drives an increase in marginal zone B cells in the absence of IL-10 signaling in macrophagesJournal of Immunology.  195:3071-3085. 2015
    2015 Comparative genome analysis of Mycoplasma pneumoniaeBMC Genomics.  16. 2015
    2015 Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2015)Archives of Virology.  160:1837-1850. 2015
    2015 Tracking the changes in virus taxonomyArchives of Virology.  160:1375-1383. 2015
    2015 Genome variability and gene content in chordopoxviruses: Dependence on microsatellitesViruses.  7:2126-2146. 2015
    2015 Loss of vancomycin-resistant enterococcus fecal dominance in an organ transplant patient with Clostridium difficile colitis after fecal microbiota transplantOpen Forum Infectious Diseases.  2. 2015
    2015 An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatusFrontiers in Microbiology.  6. 2015
    2015 Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2015)Archives of Virology.  160:1837-1850. 2015
    2014 Association between BVAB1 and high Nugent scores among women with bacterial vaginosisDiagnostic Microbiology and Infectious Disease.  80:321-323. 2014
    2014 Altered microbiota associated with abnormal humoral immune responses to commensal organisms in enthesitis-related arthritisArthritis Research and Therapy.  16. 2014
    2014 Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2014)Archives of Virology.  159:2831-2841. 2014
    2014 Expression of a non-coding RNA in ectromelia virus is required for normal plaque formationVirus Genes.  48:38-47. 2014
    2014 Expression of a non-coding RNA in ectromelia virus is required for normal plaque formationVirus Genes.  48:38-47. 2014
    2014 Getting started with microbiome analysis: Sample acquisition to bioinformaticsCurrent protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.].  2014:18.8.1-18.8.29. 2014
    2014 Identification of nucleotide-level changes impacting gene content and genome evolution in orthopoxvirusesJournal of Virology.  88:13651-13668. 2014
    2014 Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2014)Archives of Virology.  159:2831-2841. 2014
    2014 Recently agreed changes to the Statutes of the International Committee on Taxonomy of VirusesArchives of Virology.  159:175-180. 2014
    2013 Recently agreed changes to the International Code of Virus Classification and NomenclatureArchives of Virology.  158:2633-2639. 2013
    2013 Characterization of the vaginal microbiota among sexual risk behavior groups of women with bacterial vaginosisPLoS One.  8. 2013
    2013 The silent codon change I507-ATC→ATT contributes to the severity of the AF508 CFTR channel dysfunctionThe FASEB Journal.  27:4630-4645. 2013
    2013 Characterization of the vaginal microbiota among sexual risk behavior groups of women with bacterial vaginosisPLoS One.  8. 2013
    2013 Correction: Characterization of the Vaginal Microbiota among Sexual Risk Behavior Groups of Women with Bacterial VaginosisPLoS One.  8. 2013
    2013 The silent codon change I507-ATC→ATT contributes to the severity of the AF508 CFTR channel dysfunctionThe FASEB Journal.  27:4630-4645. 2013
    2011 A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutationInfection, Genetics and Evolution.  11:2011-2019. 2011
    2011 Detection and genetic diversity of human metapneumovirus in hospitalized children with acute respiratory infections in IndiaJournal of Medical Virology.  83:1799-1810. 2011
    2011 Evidence for separation of HCV subtype 1a into two distinct cladesJournal of Viral Hepatitis.  18:608-618. 2011
    2011 Phylogenetic Analysis of Eastern Equine Encephalitis Virus Isolates from FloridaAmerican Journal of Tropical Medicine and Hygiene.  84:709-717. 2011
    2011 A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutationInfection, Genetics and Evolution.  11:2011-2019. 2011
    2010 Towards viral genome annotation standards, report from the 2010 NCBI annotation workshopViruses.  2:2258-2268. 2010
    2010 Orthopoxvirus genome evolution: The role of gene lossViruses.  2:1933-1967. 2010
    2009 Recombination in West Nile Virus: Minimal contribution to genomic diversityVirology Journal.  6. 2009
    2009 Poxvirus protein evolution: Family wide assessment of possible horizontal gene transfer eventsVirus Research.  144:233-249. 2009
    2009 Poxvirus protein evolution: Family wide assessment of possible horizontal gene transfer eventsVirus Research.  144:233-249. 2009
    2008 Reply to Satheshkumar and Moss: Poxvirus transcriptome analysisProceedings of the National Academy of Sciences of USA.  105. 2008
    2008 Comparative analysis of viral gene expression programs during poxvirus infection: A transcriptional map of the vaccinia and monkeypox genomesPLoS One.  3:1-12. 2008
    2008 Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes (Proceedings of the National Academy of Sciences of the United States of America (2008) 105, (2140-2145) 10.1073/pnas.0711573105)Proceedings of the National Academy of Sciences of USA.  105:6787. 2008
    2008 Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genesProceedings of the National Academy of Sciences of USA.  105:2140-2145. 2008
    2008 Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genesProceedings of the National Academy of Sciences of USA.  105:2140-2145. 2008
    2007 Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomesVirology.  365:60-69. 2007
    2007 National institute of allergy and infectious diseases bioinformatics resource centers: New assets for pathogen informaticsInfection and Immunity.  75:3212-3219. 2007
    2007 Vaccinia virus-specific CD4+ T cell responses target a set of antigens largely distinct from those targeted by CD8+ T cell responsesJournal of Immunology.  178:6814-6820. 2007
    2006 Genetic variability in the G protein gene of group A and B respiratory syncytial viruses from IndiaJournal of Clinical Microbiology.  44:3055-3064. 2006
    2006 Poxviruses: Past, present and futureVirus Research.  117:105-118. 2006
    2005 Complete coding sequences of the rabbitpox virus genomeJournal of General Virology.  86:2969-2977. 2005
    2005 Virulence differences between monkeypox virus isolates from West Africa and the Congo basinVirology.  340:46-63. 2005
    2005 Genomic multiple sequence alignments: Refinement using a genetic algorithmBMC Bioinformatics.  6. 2005
    2005 Poxvirus Bioinformatics Resource Center: A comprehensive Poxviridae informational and analytical resourceNucleic Acids Research.  33. 2005
    2004 The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosisJournal of Bacteriology.  186:7123-7133. 2004
    2004 SS-Wrapper: A package of wrapper applications for similarity searches on Linux clustersBMC Bioinformatics.  5. 2004
    2003 The genomic sequence of ectromelia virus, the causative agent of mousepoxVirology.  317:165-186. 2003
    2003 Nucleic acid probes and method for detecting ureaplasma urealyticum 2003
    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. 2002
    2002 Cystin, a novel cilia-associated protein, is disrupted in the cpk mouse model of polycystic kidney diseaseJournal of Clinical Investigation.  109:533-540. 2002
    2002 Cystin, a novel cilia-associated protein, is disrupted in the cpk mouse model of polycystic kidney diseaseJournal of Clinical Investigation.  109:533-540. 2002
    2001 Genome of the bacterium Streptococcus pneumoniae strain R6Journal of Bacteriology.  183:5709-5717. 2001
    2000 Nucleic acid probes and method for detecting Ureaplasma urealyticum 2000
    2000 The complete sequence of the mucosal pathogen Ureaplasma urealyticumNature.  407:757-762. 2000
    2000 Identification of the human pituitary tumor transforming gene (hPTTG) family: molecular structure, expression, and chromosomal localizationGene.  248:41-50. 2000
    2000 The hinge of the human papillomavirus type 11 E2 protein contains major determinants for nuclear localization and nuclear matrix associationJournal of Virology.  74:3761-3770. 2000
    1999 NUCLEIC ACID PROBES AND METHOD FOR DETECTING UREAPLASMA UREALYTICUM 1999
    1998 Genetic variability among group A and group B respiratory syncytial viruses in a children's hospitalJournal of Clinical Microbiology.  36:3552-3557. 1998
    1996 Phylogenetic analysis of the 16S-23S rRNA intergenic spacer regions of the genus UreaplasmaJournal of Veterinary Medical Science.  58:191-195. 1996
    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 systemVirology.  178:373-383. 1990
    1985 An Inhibitor of Interferon Action: I. Physical Association of the Inhibitor with Interferon-gammaJournal of interferon research.  5:85-99. 1985
    1985 An Inhibitor of Interferon Action: II. Biological Properties of the IFN-γ-Associated Inhibitor of Interferon ActionJournal of interferon research.  5:101-110. 1985
    1981 Assay and Characterization of an Inhibitor of Interferon ActionMethods in Enzymology.  79:440-448. 1981
    1981 Assay and characterization of an inhibitor of interferon action.Methods in Enzymology.  79:440-448. 1981
    1981 Control of the interferon system: An inhibitor of interferon actionTexas reports on biology and medicine.  Vol. 41:317-323. 1981
    1979 Production and function of an inhibitor of interferon action found in mouse lymphokine preparationsJournal of Clinical Hematology and Oncology.  9. 1979
    1976 Comparative Effectiveness of Six Antiviral Agents in Herpes Simplex Type I Infection of Mice (39392)Experimental Biology and Medicine.  152:337-342. 1976
    1974 Mechanism of late therapy of viral infections with interferon 1974

    Book

    Year Title Altmetric
    2012 Virus Taxonomy 2012
    2011 Virus taxonomy: Ninth report of the international committee on taxonomy of viruses 2011

    Chapter

    Year Title Altmetric
    2019 Taxonomy and Classification of Viruses 2019
    2008 Virus Databases.  348-364. 2008
    2007 Comparative genomics of viruses using bioinformatics tools.  49-72. 2007

    Research Overview

  • Microbial Genomics and Evolution; Bioinformatics; Microbiome
  • Investigator On

  • Building and InnovatinG: Digital heALTH Technology and Analytics (BIGDATA)  awarded by National Institute of Arthritis & Musculoskeletal & Skin Diseases/NIH/DHHS
  • Building and InnovatinG: Digital heAlth Technology and Analytics (BIGDATA) - Methodologic Core  awarded by National Institute of Arthritis & Musculoskeletal & Skin Diseases/NIH/DHHS
  • Center for Clinical and Translational Science (3 Linked Awards UL1, KL2, TL1)  awarded by National Center for Advancing Translational Sciences/NIH/DHHS
  • Determining the Structural- and Functional-Level Effects of Diet-Specific Interventions on the Gut Microbiota of a Racially Diverse Sample of Southern United States Adults  awarded by National Cancer Institute/NIH/DHHS
  • Dysbiosis of the Sinus Microbiota in Chronic Rhinosinusitis  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Early Life Protein-enriched Human Milk Diets to Increase Lean Body Mass Accretion and Diversity of the Gut Microbiome in Extremely Preterm Infants: A Randomized Trial  awarded by National Institute of Child Health and Human Development/NIH/DHHS
  • Emerging Antiviral Resistance in Congenital Cytomegalovirus Infection  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Enteric Flora in Newly Diagnosed Spondyloarthritis: A Collaborative Study  awarded by FRIENDS OF CARRA
  • Epigenetics, Neurodevelopment, and Emotional Behavior  awarded by National Institute of Mental Health/NIH/DHHS
  • Exploration of the Gut Microbiome in Spondyloarthritis  awarded by American College of Rheumatology
  • Interactions of Gut Microbiome, Genetic Susceptibility and Environmental Factors in Parkinson's Disease  awarded by DOD - Department of Defense
  • Mechanisms of Pulmonary Microbiota-Induced Inflammation and Vascular Dysfunction in Neonatal Lung Injury  awarded by National Heart, Lung, and Blood Institute/NIH/DHHS
  • Mixed-omics Evaluation of the Impact of Gut Microbiome on Insulin Resistance in Spinal Cord Injury  awarded by Neilsen (Craig H.) Foundation
  • Pathogenesis of Bacterial Vaginosis in Women Who Have Sex with Women  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • Prematurity Prevention and Research Related to the Microbiome (PREPARE-M)  awarded by UNIVERSITY OF ALABAMA HEALTH SERVICES FOUNDATION
  • Prematurity Prevention and Research Related to the Microbiome (PREPARE-M)  awarded by UNIVERSITY OF ALABAMA HEALTH SERVICES FOUNDATION
  • Private Grant  awarded by ALEXION PHARMACEUTICALS, INC.
  • Private Grant  awarded by BRISTOL MYERS SQUIBB PHARMACEUTICAL COMPANY
  • Private Grant  awarded by NOVARTIS PHARMACEUTICALS CORPORATION
  • Private Grant  awarded by ABBVIE INC
  • Role of Gut Microbe Composition in Psychosocial Symptom Response to Exercise Training in Breast Cancer Survivors  awarded by National Cancer Institute/NIH/DHHS
  • The UAB STI CRC - DiSCIS Biostatistics & Bioinformatics Core  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • The UAB Sexually Transmitted Infections Cooperative Research Centers (STI CRC)  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • The UAB Sexually Transmitted Infections Cooperative Research Centers (STI CRC)  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • The University of Alabama at Birmingham Spinal Cord Injury Model System of Care  awarded by Administration for Community Living/DHHS
  • Transcriptional Regulation of Metabolism in Neurons  awarded by SOUTHERN RESEARCH INSTITUTE
  • UAB Center for AIDS Research  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • UAB Center for AIDS Research  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • UAB Center for AIDS Research - DNA Sequencing  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • UAB Center for AIDS Research - Genomics Core G  awarded by National Institute of Allergy and Infectious Diseases/NIH/DHHS
  • UAB Center for Clinical and Translational Science (CCTS) (3 Linked Awards UL1, KL2, TL1)  awarded by National Center for Advancing Translational Sciences/NIH/DHHS
  • UAB Center for Clinical and Translational Science (CCTS) (3 linked awards: UL1, KL2, TL1)  awarded by National Center for Advancing Translational Sciences/NIH/DHHS
  • UAB Center for Clinical and Translational Science (CCTS) UL1  awarded by National Center for Advancing Translational Sciences/NIH/DHHS
  • UAB Multidisciplinary Clinical Research Center (P60)  awarded by National Institute of Arthritis & Musculoskeletal & Skin Diseases/NIH/DHHS
  • UAB Multidisciplinary Clinical Research Center - Core B (Methodology Core)  awarded by National Institute of Arthritis & Musculoskeletal & Skin Diseases/NIH/DHHS
  • Teaching Overview

  • Program Director
    2018 – Present Co-Director, UAB Undergraduate Bioinformatics Program

    Classes and Lectures
    1988 Undergraduate Genetics, Adjunct Professor, Department of Biology, Judson College, Marion, Alabama, Lecture and laboratory course in basic undergraduate genetics.
    1990 – 2001 Practical Applications of Sequence Analysis Software (MIC753), UAB Microbiology upper level graduate course in Bioinformatics (offered every two years)
    2001 – 2005 Bioinformatics I (CIS-640), UAB Department of Computer and Information Sciences, Graduate course in introductory bioinformatics.
    2003, 2004 Genetics in Medicine, UAB School of Medicine, Bioinformatics Lecture for this new Medical Student course.
    2003, 2004 Mass Spectrometry and Proteomics (BMG 744), UAB Department of Biochemistry and Molecular Genetics, Lecture on Proteomic Bioinformatic applications.
    2005 UAB Infectious Diseases Grand Rounds. “Viruses Biodefense and Bioinformatics”
    2005 UAB Virology Discussion Group. “Viral Genomics and Evolution: The use of Bioinformatics to make biological inferences”
    2003 – 2009 Cellular and Molecular Biology Laboratory Methods, “Biological databases: sequence, genomic, expression, and proteomic” (2 lecture hours/year)
    2004 – 2009 Advanced Human Genetics (MGE-701). Module leader, “Bioinformatics”. (3 lecture hours; 3 discussion hours/year)
    2006 – 2017 Fundamentals II, Dental and Optometric Microbiology. “RNA Viruses”. (1 lecture hour/year)
    2006 – 2019 GBS 762, GBS Virology. Lectures on “Negative-strand RNA Viruses” and “Virus Evolution” (4 lecture hours/year)
    2006 – 2020 MIC 724, GBSC 720, Virology Journal Club. (15 discussion hours/semester)
    2010 MIC 791, Advanced Topics in Virology. Co-Course Director (1.5 lecture hours; 19.5 discussion hours)
    2010 – 2019 GBS 722, GBS Bioinformatics. “Introduction to Bioinformatics”. (4 lecture hours)
    2011 – 2018 CCTS-BMI Summer Seminar Series on Informatics (1 lecture hour)
    2015 – 2016 MIC741, Topics in Professional Development: 'OMICS. “Bioinformatics: The Management and Analysis of Biological Data” (2 lecture hours)
    2015 GBSC 716, Microbiome in Health and Disease (1.5 lecture hours)
    2017 – 2019 UAB School of Medicine Virus Case Studies, Fundamentals of Medicine: Block 5
    2017, 2019 GBS 748, Bacterial Pathogenesis. Genomic Variability. (4 lecture hours)
    2018 – Present INFO 701, Introduction to Bioinformatics. Multiple sequence alignments and Phylogenetics. (4 lecture hours)
    2019 – Present MSTP 793, MSTP student Basic Research Forum: Bioinformatics
    2019 – Present Undergraduate Introductory Bioinformatics Seminar (INFO 101). Course Director. (14 lecture hours/semester)
    2020 INFO 751, Systems Biomedicine of Human Microbiota. Analysis of Microbiome Data.
    2020 GGSC 320, Undergraduate Colloquium-Genetics/Genomics. Bioinformatics Careers.
    2020 – Present GBS 762, GBS Virology. Lecture on “Virus Evolution” (2 lecture hours/year)
    2021 GGSC 320, Undergraduate Colloquium-Genetics/Genomics. Viruses and their evolution.
  • Teaching Activities

  • GBSC720 - Journal Club 2 (Fall Term 2017)
  • GBSC720 - Journal Club 2 (Fall Term 2018)
  • GBSC720 - Journal Club 2 (Fall Term 2019)
  • GBSC720 - Journal Club 2 (Spring Term 2017)
  • GBSC720 - Journal Club 2 (Spring Term 2018)
  • GBSC720 - Journal Club 2 (Spring Term 2019)
  • GBSC720 - Journal Club 2 (Spring Term 2020)
  • INFO101 - Intro Bioinformatics Sem (Spring Term 2019)
  • INFO101 - Intro Bioinformatics Sem (Spring Term 2020)
  • INFO101 - Intro Bioinformatics Sem (Spring Term 2021)
  • INFO101 - Intro Bioinformatics Sem (Spring Term 2022)
  • INFO497 - Research in Bioinformatics (Fall Term 2021)
  • INFO498 - Honors Bioinformatics Research (Fall Term 2021)
  • INFO498 - Honors Bioinformatics Research (Spring Term 2022)
  • INFO499 - Bioinformatics Capstone (Fall Term 2021)
  • INFO499 - Bioinformatics Capstone (Spring Term 2021)
  • MIC724 - Virology Journal Club (Fall Term 2007)
  • MIC724 - Virology Journal Club (Fall Term 2008)
  • MIC724 - Virology Journal Club (Fall Term 2009)
  • MIC724 - Virology Journal Club (Fall Term 2010)
  • MIC724 - Virology Journal Club (Fall Term 2011)
  • MIC724 - Virology Journal Club (Fall Term 2012)
  • MIC724 - Virology Journal Club (Fall Term 2013)
  • MIC724 - Virology Journal Club (Fall Term 2014)
  • MIC724 - Virology Journal Club (Fall Term 2015)
  • MIC724 - Virology Journal Club (Fall Term 2016)
  • MIC724 - Virology Journal Club (Spring Term 2008)
  • MIC724 - Virology Journal Club (Spring Term 2009)
  • MIC724 - Virology Journal Club (Spring Term 2010)
  • MIC724 - Virology Journal Club (Spring Term 2011)
  • MIC724 - Virology Journal Club (Spring Term 2012)
  • MIC724 - Virology Journal Club (Spring Term 2013)
  • MIC724 - Virology Journal Club (Spring Term 2015)
  • MIC724 - Virology Journal Club (Spring Term 2016)
  • MIC791 - Advanced Topics in Virology (Spring Term 2010)
  • OBHS121 - Fundamentals of Dent and Opt 2 (Fall Term 2011)
  • Education And Training

  • The University of Alabama at Birmingham Microbiology, Postdoctoral Fellowship
  • University of Wisconsin Biochemistry, Postdoctoral Fellowship
  • Doctor of Philosophy in Microbiology, University of Texas System : Medical Branch 1983
  • Full Name

  • Elliot Lefkowitz