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Coauthors
Michael McGrath Departments of Laboratory Medicine, Pathology, and Medicine, University of California at San Francisco, USA
1 protocol

Marco Salemi Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, USA
1 protocol

James Dollar Bioinfoexperts, LLC, USA
1 protocol

Rebecca Rose Bioinfoexperts, LLC, USA
1 protocol

David J. Nolan
  • Bioinfoexperts, LLC, USA
Contributions
  • 1 Author merit

Education

Bachelors, University of Florida, USA, 2000

Current position

Biological Scientist, Pathology, Immunology and Laboratory Medicine, University of Florida, UF

Publications

  1. Blohm, G. M., Lednicky, J. A., Marquez, M., White, S. K., Loeb, J. C., Pacheco, C. A., Nolan, D. J., Paisie, T., Salemi, M., Rodriguez-Morales, A. J., Morris, J. G., Jr., Pulliam, J. R. C., Carrillo, A. S., Plaza, J. D. and Paniz-Mondolfi, A. E. (2017). Complete Genome Sequences of Identical Zika virus Isolates in a Nursing Mother and Her Infant. Genome Announc 5(17).
  2. Mallard, J., Papazian, E., Soulas, C., Nolan, D. J., Salemi, M. and Williams, K. C. (2017). A method for obtaining simian immunodeficiency virus RNA sequences from laser capture microdissected and immune captured CD68+ and CD163+ macrophages from frozen tissue sections of bone marrow and brain. J Immunol Methods 442: 59-63.
  3. Azarian, T., Ali, A., Johnson, J. A., Jubair, M., Cella, E., Ciccozzi, M., Nolan, D. J., Farmerie, W., Rashid, M. H., Sinha-Ray, S., Alam, M. T., Morris, J. G. and Salemi, M. (2016). Non-toxigenic environmental Vibrio cholerae O1 strain from Haiti provides evidence of pre-pandemic cholera in Hispaniola. Sci Rep 6: 36115.
  4. Azarian, T., Maraqa, N. F., Cook, R. L., Johnson, J. A., Bailey, C., Wheeler, S., Nolan, D., Rathore, M. H., Morris, J. G., Jr. and Salemi, M. (2016). Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit. PLoS One 11(10): e0164397.
  5. Lamers, S. L., Rose, R., Nolan, D. J., Fogel, G. B., Barbier, A. E., Salemi, M. and McGrath, M. S. (2016). HIV-1 Evolutionary Patterns Associated with Metastatic Kaposi's Sarcoma during AIDS. Sarcoma 2016: 4510483.
  6. Lamers, S. L., Rose, R., Maidji, E., Agsalda-Garcia, M., Nolan, D. J., Fogel, G. B., Salemi, M., Garcia, D. L., Bracci, P., Yong, W., Commins, D., Said, J., Khanlou, N., Hinkin, C. H., Sueiras, M. V., Mathisen, G., Donovan, S., Shiramizu, B., Stoddart, C. A., McGrath, M. S. and Singer, E. J. (2016). HIV DNA Is Frequently Present within Pathologic Tissues Evaluated at Autopsy from Combined Antiretroviral Therapy-Treated Patients with Undetectable Viral Loads. J Virol 90(20): 8968-8983.
  7. Rose, R., Lamers, S. L., Nolan, D. J., Maidji, E., Faria, N. R., Pybus, O. G., Dollar, J. J., Maruniak, S. A., McAvoy, A. C., Salemi, M., Stoddart, C. A., Singer, E. J. and McGrath, M. S. (2016). HIV Maintains an Evolving and Dispersed Population in Multiple Tissues during Suppressive Combined Antiretroviral Therapy in Individuals with Cancer. J Virol 90(20): 8984-8993.
  8. Azarian, T., Daum, R. S., Petty, L. A., Steinbeck, J. L., Yin, Z., Nolan, D., Boyle-Vavra, S., Hanage, W. P., Salemi, M. and David, M. Z. (2016). Intrahost Evolution of Methicillin-Resistant Staphylococcus aureus USA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections. J Infect Dis 214(6): 895-905.
  9. Rife, B. D., Nolan, D. J., Lamers, S. L., Autissier, P., Burdo, T., Williams, K. C. and Salemi, M. (2016). Evolution of Neuroadaptation in the Periphery and Purifying Selection in the Brain Contribute to Compartmentalization of Simian Immunodeficiency Virus (SIV) in the Brains of Rhesus Macaques with SIV-Associated Encephalitis. J Virol 90(13): 6112-6126.
  10. Lamers, S. L., Rose, R., Ndhlovu, L. C., Nolan, D. J., Salemi, M., Maidji, E., Stoddart, C. A. and McGrath, M. S. (2016). The meningeal lymphatic system: a route for HIV brain migration? J Neurovirol 22(3): 275-281.
  11. Lamers, S. L., Nolan, D. J., Rife, B. D., Fogel, G. B., McGrath, M. S., Burdo, T. H., Autissier, P., Williams, K. C., Goodenow, M. M. and Salemi, M. (2015). Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques. J Virol 89(16): 8484-8496.
  12. Campbell, J. H., Ratai, E. M., Autissier, P., Nolan, D. J., Tse, S., Miller, A. D., Gonzalez, R. G., Salemi, M., Burdo, T. H. and Williams, K. C. (2014). Anti-alpha4 antibody treatment blocks virus traffic to the brain and gut early, and stabilizes CNS injury late in infection. PLoS Pathog 10(12): e1004533.
  13. Strickland, S. L., Rife, B. D., Lamers, S. L., Nolan, D. J., Veras, N. M., Prosperi, M. C., Burdo, T. H., Autissier, P., Nowlin, B., Goodenow, M. M., Suchard, M. A., Williams, K. C. and Salemi, M. (2014). Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS. J Gen Virol 95(Pt 12): 2784-2795.
  14. Lamers, S. L., Fogel, G. B., Nolan, D. J., McGrath, M. S. and Salemi, M. (2014). HIV-associated neuropathogenesis: a systems biology perspective for modeling and therapy. Biosystems 119: 53-61.
  15. Prosperi, M. C., Yin, L., Nolan, D. J., Lowe, A. D., Goodenow, M. M. and Salemi, M. (2013). Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges. Sci Rep 3: 2837.
  16. Lamers, S. L., Nolan, D. J., Strickland, S. L., Prosperi, M., Fogel, G. B., Goodenow, M. M. and Salemi, M. (2013). Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS. J Gen Virol 94(Pt 11): 2469-2479.
  17. Prosperi, M., Veras, N., Azarian, T., Rathore, M., Nolan, D., Rand, K., Cook, R. L., Johnson, J., Morris, J. G., Jr. and Salemi, M. (2013). Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a cross-sectional study. Sci Rep 3: 1902.
  18. Lamers, S. L., Fogel, G. B., Singer, E. J., Salemi, M., Nolan, D. J., Huysentruyt, L. C. and McGrath, M. S. (2012). HIV-1 Nef in macrophage-mediated disease pathogenesis. Int Rev Immunol 31(6): 432-450.
  19. Strickland, S. L., Gray, R. R., Lamers, S. L., Burdo, T. H., Huenink, E., Nolan, D. J., Nowlin, B., Alvarez, X., Midkiff, C. C., Goodenow, M. M., Williams, K. and Salemi, M. (2012). Efficient transmission and persistence of low-frequency SIVmac251 variants in CD8-depleted rhesus macaques with different neuropathology. J Gen Virol 93(Pt 5): 925-938.
  20. Strickland, S. L., Gray, R. R., Lamers, S. L., Burdo, T. H., Huenink, E., Nolan, D. J., Nowlin, B., Alvarez, X., Midkiff, C. C., Goodenow, M. M., Williams, K. and Salemi, M. (2011). Significant genetic heterogeneity of the SIVmac251 viral swarm derived from different sources. AIDS Res Hum Retroviruses 27(12): 1327-1332.
1 Protocol published
Single Genome Sequencing of Expressed and Proviral HIV-1 Envelope Glycoprotein 120 (gp120) and nef Genes
The current study provides detailed protocols utilized to amplify the complete HIV-1 gp120 and nef genes from single copies of expressed or integrated HIV present in fresh-frozen autopsy tissues of patients who died while on ...