Selected Publications

1. da Silva, J., M. Coetzer, R. Nedellec, C. Pastore, and D. E. Mosier. 2010. Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region. Genetics 185: 293-303.
2. da Silva, J. 2010. An adaptive walk by human immunodeficiency virus type 1 on a fluctuating fitness landscape. Evolution 64: 1160-1165.
3. da Silva, J. 2009. Amino acid covariation in a functionally important human immunodeficiency virus type 1 protein region is associated with population subdivision. Genetics 182: 265-275.
4. da Silva, J. 2006. Site-specific amino acid frequency, fitness and the mutational landscape model of adaptation in human immunodeficiency virus type 1. Genetics 174: 1689-1694.
5. da Silva, J. 2006. Parallel Monte Carlo simulation of HIV molecular evolution in response to immune surveillance, pp. 29-57 in Parallel Computing for Bioinformatics and Computational Biology, edited by A. Y. Zomaya. Wiley Interscience, Hoboken, New Jersey.
6. Hughes, A.L., K. Westover, J. da Silva, D.H. O’Connor, and D.I. Watkins. 2001. Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus. Journal of Virology 75: 7966-7972.
7. Hughes, A.L., J. da Silva, and R. Friedman. 2001. Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Research 11: 771-780.
8. Evans, D. T., D. H. O’Connor, P. Jing, J. Dzuris, J. Sydney, J. da Silva, T.M. Allen, H. Horton, J.E. Venham, R.A. Rudersdorf, C.D. Pauza, R.E. Bontrop, R. DeMars, A. Sette, A.L. Hughes, and D.I. Watkins. 1999. Virus-specific cytotoxic T-lymphocyte responses select for amino acid variation in simian immunodeficiency virus Env and Nef. Nature Medicine 5: 1270-1276.
9. da Silva, J. and A.L. Hughes. 1999. Molecular phylogenetic evidence of cytotoxic T-lymphocyte (CTL) selection on human immunodeficiency virus type 1 (HIV-1). Molecular Biology and Evolution 16: 1420-1422.
10. da Silva, J. and A.L. Hughes. 1998. Conservation of cytotoxic T-lymphocyte (CTL) epitopes as a host strategy to constrain parasite adaptation: evidence from the nef gene of human immunodeficiency virus 1 (HIV-1). Molecular Biology and Evolution 15: 1259-1268.
11. da Silva, J. and G. Bell. 1996. The ecology and genetics of fitness in Chlamydomonas. VII. The effect of sex on the variance in fitness and mean fitness. Evolution 50: 1705-1713.
12. da Silva, J. and G. Bell. 1992. The ecology and genetics of fitness in Chlamydomonas VI. Antagonism between natural selection and sexual selection. Proceedings of the Royal Society of London, series B 249: 227-233.
13. da Silva, J. 1991. Male swords and female preferences. Science 253: 1426.