Research Interests

• Genetic diversity of HIV and other lentiviruses
• Molecular evolution and phylogenetic reconstruction
• Modeling evolution of proteins
• Multiple sequence alignment

I am interested in describing and understanding patterns of evolution of Human Immunodeficiency Virus Type 1, and comparing these patterns to those found in other lentiviruses. Describing the current diversity of these viruses, and projecting into the near future are critical for designing vaccines and therapeutic drugs. Understanding the natural history of lentiviruses could provide insight into many aspects of the HIV pandemic. Most current phylogentic reconstruction algorithms are designed for use on non-coding DNA under no selection pressure, whereas almost all regions of the lentiviral genomes are under strong selection. For this reason, exploring new methods of phylogenetic reconstruction will be necessary for understanding the natural history of the lentiviruses.

Recent Publications

1. Apetrei C, Becker J, Metzger M, Gautam R, Engle J, Wales AK, Eyong M, Enyong P, Sama M, Foley BT, Drucker E, Marx PA. Potential for HIV transmission through unsafe injections. AIDS. 20(7):1074-1076. (2006)

2. Blay W, Gnanakaran S, Foley B, Doria-Rose NA, Korber BT and Haigwood NL. Consistent Patterns of Change During Divergence of Human Immunodeficiency Virus Type 1 Envelope in SHIV Infected Macaques J. Virol. 80(2): 999-1014 (2006)

3. Eshleman SH, Crutcher G, Petrauskene O, Kunstman K, Cunningham SP, Trevino C, Davis C, Kennedy J, Fairman J, Foley B and Kop J. Sensitivity and Specificity of the ViroSeq¨ HIV-1 Genotyping System for detection of HIV-1 drug resistance mutations using an ABI PRISM¨ 3100 Genetic Analyzer J. Clin. Microbiol. 43(2):813-7. (2005)

4. Philpott S, Burger H, Tsoukas C, Foley B, Anastos K, Kitchen C, and Weiser B. Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: compartmentalization and intrapatient recombination. J. Virol. 79(1):353-63. (2005)

5. Zhang M, Gaschen B, Blay W, Foley B, Haigwood N, Kuiken C, Korber B. Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes, and influenza hemagglutinin. Glycobiology. 14(12):1229-46. (2004) PMID: 15175256

6. Matveeva OV, Foley BT, Nemtsov VA, Gesteland RF, Matsufuji S, Atkins JF, Ogurtsov AY, Shabalina SA. Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. BMC Bioinformatics. 29;5(1):44. (2004) PMID: 15115544

7. Delwart EL, Kalmin ND, Jones TS, Ladd DJ, Foley B, Tobler LH, Tsui RC, Busch MP. First report of human immunodeficiency virus transmission via an RNA-screened blood donation. Vox Sang. 86(3):171-7. (2004) PMID: 15078251

8. Kemal KS, Foley B, Burger H, Anastos K, Minkoff H, Kitchen C, Philpott SM, Gao W, Robison E, Holman S, Dehner C, Beck S, Meyer WA 3rd, Landay A, Kovacs A, Bremer J, Weiser B. HIV-1 in Genital Tract and Plasma of Women: Compartmentalization of Viral Sequences, Coreceptor Usage and Glycosylation. Proc Natl Acad Sci U S A. 100(22): 12972-7 (2003)

9. B. Gaschen, C. Kuiken, B. Korber and B. Foley (2001) Retrieval and on-the-fly alignment of sequence fragments from the HIV database. Bioinformatics May;17(5):415-8. PMID: 11331235

10. B.T. Foley (2000) Accessing HIV Molecular Information. In: Computational Analysis of HIV Molecular Sequences

11. Allen G. Rodrigo and Gerald H. Learn, eds. Dordrecht, Netherlands: Kluwer Academic Publishers, A Rodrigo and G Learn, editors

12. D.L. Robertson, J.P. Anderson, J.A. Bradac, J.K. Carr, B. Foley, R.K. Funkhouser, F. Gao, B.H. Hahn, M.L. Kalish, C. Kuiken, G.H. Learn, T. Leitner, F. McCutchan, S. Osmanov, M. Peeters, D. Pieniazek, M. Salminen, P.M. Sharp, S. Wolinsky and B. Korber (2000) HIV-1 nomenclature proposal. Science 288(5463): 55-56.

13. B.T. Korber, B.T. Foley, B.K. Gaschen, and C.L. Kuiken (2000) Epidemiological and Immunological Implications of the Global Variability of HIV-1. In: Retroviral Immunology The Humana Press Inc., Totowa, NJ USA, B. Walker and G. Pantaleo, editors.

14. V. Novitsky, M. Montano, M.-F. McLane, B. Renjefo, F. Vannberg, B. Foley, T. Ndung'u, R. Marlink, B. Korber and M. Essex (1999) Molecular Cloning and Phylogenetic Analysis of HIV-1 Subtype C: A Set of 23 Complete Genome Clones from Botswana. J. Virol 73(5): 4427-4432. [MEDLINE abstract]

15. S.Y. Se-Thoe, B.T. Foley, S.Y. Chan, R.V. Lin, H.M. Oh, A.E. Ling, S.K. Chew, I. Snodgrass and J.E. Sng (1998) Analysis of sequence diversity in the C2-V3 regions of the external glycoproteins of HIV type 1 in Singapore. AIDS Res Hum Retroviruses 14(17): 1601-1604 [MEDLINE abstract]