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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

Susanna L. Lamers
  • Bioinfoexperts, LLC, USA
  • 1 Author merit

Education

Masters of Science, New York University, USA, 2010

Current position

CEO, Research, Bioinfoexperts LLC, USA

Publications

  1. Reynolds, S. J., Ssempijja, V., Galiwango, R., Ndyanabo, A., Nakigozi, G., Lyagoba, F., Nazziwa, J., Redd, A., Lamers, S. L., Gray, R., Wawer, M., Serwadda, D. and Quinn, T. C. (2017). Low Rates of Transmitted Drug Resistance Among Newly Identified HIV-1 Seroconverters in Rural Rakai, Uganda. AIDS Res Hum Retroviruses 33(5): 448-451.
  2. Lamers, S. L., Fogel, G. B., Liu, E. S., Nolan, D. J., Salemi, M., Barbier, A. E., Rose, R., Singer, E. J. and McGrath, M. S. (2017). Predicted coreceptor usage at end-stage HIV disease in tissues derived from subjects on antiretroviral therapy with an undetectable plasma viral load. Infect Genet Evol 51: 194-197.
  3. Rose, R., Lamers, S. L., Dollar, J. J., Grabowski, M. K., Hodcroft, E. B., Ragonnet-Cronin, M., Wertheim, J. O., Redd, A. D., German, D. and Laeyendecker, O. (2017). Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. AIDS Res Hum Retroviruses 33(3): 211-218.
  4. Rainwater-Lovett, K., Ziemniak, C., Watson, D., Luzuriaga, K., Siberry, G., Petru, A., Chen, Y., Uprety, P., McManus, M., Ho, Y. C., Lamers, S. L. and Persaud, D. (2017). Paucity of Intact Non-Induced Provirus with Early, Long-Term Antiretroviral Therapy of Perinatal HIV Infection. PLoS One 12(2): e0170548.
  5. 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.
  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. Rife, B. D., Nolan, D. J., Lamers, S. L., Autissier, P., Burdo, T., Williams, K. C. and Salemi, M. (2016). Correction for Rife et al., 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(19): 8947.
  8. Lamers, S. L., Barbier, A. E., Ratmann, O., Fraser, C., Rose, R., Laeyendecker, O. and Grabowski, M. K. (2016). HIV-1 Sequence Data Coverage in Central East Africa from 1959 to 2013. AIDS Res Hum Retroviruses 32(9): 904-908.
  9. Lamers, S. L., Fogel, G. B., Liu, E. S., Salemi, M. and McGrath, M. S. (2016). On the Physicochemical and Structural Modifications Associated with HIV-1 Subtype B Tropism Transition. AIDS Res Hum Retroviruses 32(8): 829-840.
  10. 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.
  11. 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.
  12. 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.
  13. Fogel, G. B., Lamers, S. L., Liu, E. S., Salemi, M. and McGrath, M. S. (2015). Identification of dual-tropic HIV-1 using evolved neural networks. Biosystems 137: 12-19.
  14. 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.
  15. Lamers, S. L., Newman, R. M., Laeyendecker, O., Tobian, A. A., Colgrove, R. C., Ray, S. C., Koelle, D. M., Cohen, J., Knipe, D. M. and Quinn, T. C. (2015). Global Diversity within and between Human Herpesvirus 1 and 2 Glycoproteins. J Virol 89(16): 8206-8218.
  16. Newman, R. M., Lamers, S. L., Weiner, B., Ray, S. C., Colgrove, R. C., Diaz, F., Jing, L., Wang, K., Saif, S., Young, S., Henn, M., Laeyendecker, O., Tobian, A. A., Cohen, J. I., Koelle, D. M., Quinn, T. C. and Knipe, D. M. (2015). Genome Sequencing and Analysis of Geographically Diverse Clinical Isolates of Herpes Simplex Virus 2. J Virol 89(16): 8219-8232.
  17. Fogel, G. B., Lamers, S. L., Levine, A. J., Valdes-Sueiras, M., McGrath, M. S., Shapshak, P. and Singer, E. J. (2015). Factors related to HIV-associated neurocognitive impairment differ with age. J Neurovirol 21(1): 56-65.
  18. 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.
  19. Lamers, S. L. and McGrath, M. S. (2014). HIV-1 Persistence in Macrophage Reservoirs during Antiretroviral Therapy. Austin Journal of Clinical Pathology 1(4).
  20. Fogel, G. B., Liu, E. S., Salemi, M., Lamers, S. L. and McGrath, M. S. (2014). Evolved Neural Networks for HIV-1 Co-receptor Identification. 2014 IEEE Congress on Evolutionary Computation 2778-2784.
  21. 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.
  22. 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.
  23. 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.
  24. Galiwango, R. M., Lamers, S. L., Redd, A. D., Manucci, J., Tobian, A. A., Sewankambo, N., Kigozi, G., Nakigozi, G., Serwadda, D., Boaz, I., Nalugoda, F., Sullivan, D. J., Kong, X., Wawer, M. J., Gray, R. H., Quinn, T. C., Laeyendecker, O. and Rakai Health Sciences, P. (2012). HIV type 1 genetic variation in foreskin and blood from subjects in Rakai, Uganda. AIDS Res Hum Retroviruses 28(7): 729-733.
  25. 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.
  26. 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.
  27. Ng, O. T., Munshaw, S., Lamers, S. L., Chew, K. K., Lin, L., Redd, A. D., Manucci, J., Quinn, T. C., Ray, S. C., Chua, A., Leo, Y. S. and Laeyendecker, O. (2011). Molecular epidemiology of HIV type 1 in Singapore and identification of novel CRF01_AE/B recombinant forms. AIDS Res Hum Retroviruses 27(10): 1135-1137.
  28. Lamers, S. L., Poon, A. F. and McGrath, M. S. (2011). HIV-1 nef protein structures associated with brain infection and dementia pathogenesis. PLoS One 6(2): e16659.
  29. Lamers, S. L., Gray, R. R., Salemi, M., Huysentruyt, L. C. and McGrath, M. S. (2011). HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues. Infect Genet Evol 11(1): 31-37.
  30. Lamers, S. L., Fogel, G. B., Huysentruyt, L. C. and McGrath, M. S. (2010). HIV-1 nef protein visits B-cells via macrophage nanotubes: a mechanism for AIDS-related lymphoma pathogenesis? Curr HIV Res 8(8): 638-640.
  31. Lamers, S. L., Fogel, G. B. and McGrath, M. S. (2010). HIV-miR-H1 evolvability during HIV pathogenesis. Biosystems 101(2): 88-96.
  32. Lamers, S. L., Salemi, M., Galligan, D. C., Morris, A., Gray, R., Fogel, G., Zhao, L. and McGrath, M. S. (2010). Human immunodeficiency virus-1 evolutionary patterns associated with pathogenic processes in the brain. J Neurovirol 16(3): 230-241.
  33. Salemi, M., Lamers, S. L., Huysentruyt, L. C., Galligan, D., Gray, R. R., Morris, A. and McGrath, M. S. (2009). Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma. PLoS One 4(12): e8153.
  34. Collinson-Streng, A. N., Redd, A. D., Sewankambo, N. K., Serwadda, D., Rezapour, M., Lamers, S. L., Gray, R. H., Wawer, M. J., Quinn, T. C. and Laeyendecker, O. (2009). Geographic HIV type 1 subtype distribution in Rakai district, Uganda. AIDS Res Hum Retroviruses 25(10): 1045-1048.
  35. Gray, R. R., Tatem, A. J., Lamers, S., Hou, W., Laeyendecker, O., Serwadda, D., Sewankambo, N., Gray, R. H., Wawer, M., Quinn, T. C., Goodenow, M. M. and Salemi, M. (2009). Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. AIDS 23(14): F9-F17.
  36. Zhao, L., Galligan, D. C., Lamers, S. L., Yu, S., Shagrun, L., Salemi, M. and McGrath, M. S. (2009). High level HIV-1 DNA concentrations in brain tissues differentiate patients with post-HAART AIDS dementia complex or cardiovascular disease from those with AIDS. Sci China C Life Sci 52(7): 651-656.
  37. Lamers, S. L., Salemi, M., Galligan, D. C., de Oliveira, T., Fogel, G. B., Granier, S. C., Zhao, L., Brown, J. N., Morris, A., Masliah, E. and McGrath, M. S. (2009). Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology. PLoS One 4(3): e5065.
  38. Lamers, S. L., Salemi, M., McGrath, M. S. and Fogel, G. B. (2008). Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks. IEEE/ACM Trans Comput Biol Bioinform 5(2): 291-300.
  39. Salemi, M., Lamers, S. L., Yu, S., de Oliveira, T., Fitch, W. M. and McGrath, M. S. (2005). Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J Virol 79(17): 11343-11352.
  40. Lamers, S., Beason, S., Dunlap, L., Compton, R. and Salemi, M. (2004). HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data. Bioinformatics 20(3): 436-438.
  41. Tuttle, D. L., Anders, C. B., Aquino-De Jesus, M. J., Poole, P. P., Lamers, S. L., Briggs, D. R., Pomeroy, S. M., Alexander, L., Peden, K. W., Andiman, W. A., Sleasman, J. W. and Goodenow, M. M. (2002). Increased replication of non-syncytium-inducing HIV type 1 isolates in monocyte-derived macrophages is linked to advanced disease in infected children. AIDS Res Hum Retroviruses 18(5): 353-362.
  42. Perez, E. E., Rose, S. L., Peyser, B., Lamers, S. L., Burkhardt, B., Dunn, B. M., Hutson, A. D., Sleasman, J. W. and Goodenow, M. M. (2001). Human immunodeficiency virus type 1 protease genotype predicts immune and viral responses to combination therapy with protease inhibitors (PIs) in PI-naive patients. J Infect Dis 183(4): 579-588.
  43. Ping, L. H., Nelson, J. A., Hoffman, I. F., Schock, J., Lamers, S. L., Goodman, M., Vernazza, P., Kazembe, P., Maida, M., Zimba, D., Goodenow, M. M., Eron, J. J., Jr., Fiscus, S. A., Cohen, M. S. and Swanstrom, R. (1999). Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: underrepresentation of X4 variants. J Virol 73(8): 6271-6281.
  44. Skinner, L. M., Lamers, S. L., Sanders, J. C., Eyster, M. E., Goodenow, M. M. and Katzman, M. (1998). Analysis of a large collection of natural HIV-1 integrase sequences, including those from long-term nonprogressors. J Acquir Immune Defic Syndr Hum Retrovirol 19(2): 99-110.
  45. White, G. B., Pfahnl, A., Haddock, S., Lamers, S., Greenberg, R. M. and Anderson, P. A. (1998). Structure of a putative sodium channel from the sea anemone Aiptasia pallida. Invert Neurosci 3(4): 317-326.
  46. Lamers, S. L., Sleasman, J. W. and Goodenow, M. M. (1996). A model for alignment of Env V1 and V2 hypervariable domains from human and simian immunodeficiency viruses. AIDS Res Hum Retroviruses 12(12): 1169-1178.
  47. Barrie, K. A., Perez, E. E., Lamers, S. L., Farmerie, W. G., Dunn, B. M., Sleasman, J. W. and Goodenow, M. M. (1996). Natural variation in HIV-1 protease, Gag p7 and p6, and protease cleavage sites within gag/pol polyproteins: amino acid substitutions in the absence of protease inhibitors in mothers and children infected by human immunodeficiency virus type 1. Virology 219(2): 407-416.
  48. Lamers, S. L., Sleasman, J. W., She, J. X., Barrie, K. A., Pomeroy, S. M., Barrett, D. J. and Goodenow, M. M. (1994). Persistence of multiple maternal genotypes of human immunodeficiency virus type I in infants infected by vertical transmission. J Clin Invest 93(1): 380-390.
  49. Lamers, S. L., Sleasman, J. W., She, J. X., Barrie, K. A., Pomeroy, S. M., Barrett, D. J. and Goodenow, M. M. (1993). Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo. J Virol 67(7): 3951-3960.
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 ...