TY - JOUR AU - Drummond, A. J. AU - Nicholls, G. K. AU - Rodrigo, A. G. AU - Solomon, W. PY - 2002 DA - 2002// TI - Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data JO - Genetics VL - 161 ID - Drummond2002 ER - TY - JOUR AU - Leigh-Brown, A. J. PY - 1997 DA - 1997// TI - Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population JO - Proc Natl Acad Sci USA VL - 94 UR - https://doi.org/10.1073/pnas.94.5.1862 DO - 10.1073/pnas.94.5.1862 ID - Leigh-Brown1997 ER - TY - JOUR AU - Achaz, G. AU - Palmer, S. AU - Kearney, M. AU - Maldarelli, F. AU - Mellors, J. W. AU - Coffin, J. M. AU - Wakeley, J. PY - 2004 DA - 2004// TI - A Robust Measure of HIV-1 Population Turnover within Chronically Infected Individuals JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh196 DO - 10.1093/molbev/msh196 ID - Achaz2004 ER - TY - JOUR AU - Seo, T. -. K. AU - Thorne, J. L. AU - Hasegawa, M. AU - Kishino, H. PY - 2002 DA - 2002// TI - Estimation of Effective Population Size of HIV-1 Within a Host: A Pseudomaximum-Likelihood Approach JO - Genetics VL - 160 ID - Seo2002 ER - TY - JOUR AU - Shriner, D. AU - Shankarappa, R. AU - Jensen, M. A. AU - Nickle, D. C. AU - Mittler, J. E. AU - Margolick, J. B. AU - Mullins, J. I. PY - 2004 DA - 2004// TI - Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection JO - Genetics VL - 166 UR - https://doi.org/10.1534/genetics.166.3.1155 DO - 10.1534/genetics.166.3.1155 ID - Shriner2004 ER - TY - JOUR AU - Rouzine, I. M. AU - Coffin, J. M. PY - 1999 DA - 1999// TI - Linkage disequilibrium test implies a large effective population number for HIV in vivo JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.19.10758 DO - 10.1073/pnas.96.19.10758 ID - Rouzine1999 ER - TY - JOUR AU - Haase, A. T. PY - 1999 DA - 1999// TI - Population biology of HIV-1 infection: viral and CD4+ T cell demographics and dynamics in lymphatic tissues JO - Annu Rev Immunol VL - 17 UR - https://doi.org/10.1146/annurev.immunol.17.1.625 DO - 10.1146/annurev.immunol.17.1.625 ID - Haase1999 ER - TY - JOUR AU - Kouyos, R. D. AU - Althaus, C. L. AU - Bonhoeffer, S. PY - 2006 DA - 2006// TI - Stochastic or deterministic: what is the effective population size of HIV-1? JO - Trends Microbiol VL - 14 UR - https://doi.org/10.1016/j.tim.2006.10.001 DO - 10.1016/j.tim.2006.10.001 ID - Kouyos2006 ER - TY - JOUR AU - Haddad, D. N. AU - Birch, C. AU - Middleton, T. AU - Dwyer, D. E. AU - Cunningham, A. L. AU - Saksena, N. K. PY - 2000 DA - 2000// TI - Evidence for late stage compartmentalization of HIV-1 resistance mutations between lymph node and peripheral blood mononuclear cells JO - AIDS VL - 14 UR - https://doi.org/10.1097/00002030-200010200-00008 DO - 10.1097/00002030-200010200-00008 ID - Haddad2000 ER - TY - JOUR AU - Fulcher, J. A. AU - Hwangbo, Y. AU - Zioni, R. AU - Nickle, D. AU - Lin, X. AU - Heath, L. AU - Mullins, J. I. AU - Corey, L. AU - Zhu, T. PY - 2004 DA - 2004// TI - Compartmentalization of human immunodeficiency virus type 1 between blood monocytes and CD4+ T cells during infection JO - J Virol VL - 78 UR - https://doi.org/10.1128/JVI.78.15.7883-7893.2004 DO - 10.1128/JVI.78.15.7883-7893.2004 ID - Fulcher2004 ER - TY - JOUR AU - Wong, J. K. AU - Ignacio, C. C. AU - Torriani, F. AU - Havler, D. AU - Fitch, N. J. S. AU - Richman, D. D. PY - 1997 DA - 1997// TI - In vivo compartmentalization of human immunodeficiency virus: evidence from the examination of polsequences from autopsy tissues JO - J Virol VL - 71 ID - Wong1997 ER - TY - JOUR AU - Shriner, D. AU - Liu, Y. AU - Nickle, D. C. AU - Mullins, J. I. PY - 2006 DA - 2006// TI - Evolution of intrahost HIV-1 genetic diversity during chronic infection JO - Int J Org Evolution VL - 60 ID - Shriner2006 ER - TY - JOUR AU - Barton, N. H. PY - 2000 DA - 2000// TI - Genetic hitchhiking JO - Philos Trans R Soc Lond B Biol Sci VL - 355 UR - https://doi.org/10.1098/rstb.2000.0716 DO - 10.1098/rstb.2000.0716 ID - Barton2000 ER - TY - JOUR AU - Mansky, L. M. PY - 1996 DA - 1996// TI - Forward mutation rate of Human Immunodeficiency Virus Type 1 in a T lymphoid cell line JO - AIDS Res Hum Retroviruses VL - 12 UR - https://doi.org/10.1089/aid.1996.12.307 DO - 10.1089/aid.1996.12.307 ID - Mansky1996 ER - TY - JOUR AU - O'Neil, P. K. AU - Sun, G. AU - Yu, H. AU - Ron, Y. AU - Dougherty, J. P. AU - Preston, B. D. PY - 2002 DA - 2002// TI - Mutational analysis of HIV-1 long terminal repeats to explore the relative contribution of reverse transcriptase and RNA polymerase II to viral mutagenesis JO - J Biol Chem VL - 277 UR - https://doi.org/10.1074/jbc.M204774200 DO - 10.1074/jbc.M204774200 ID - O'Neil2002 ER - TY - JOUR AU - Shriner, D. AU - Rodrigo, A. G. AU - Nickle, D. C. AU - Mullins, J. I. PY - 2004 DA - 2004// TI - Pervasive genomic recombination of HIV-1 in vivo JO - Genetics VL - 167 UR - https://doi.org/10.1534/genetics.103.023382 DO - 10.1534/genetics.103.023382 ID - Shriner2004 ER - TY - JOUR AU - Zhuang, J. AU - Jetzt, A. E. AU - Sun, G. AU - Yu, H. AU - Klarmann, G. AU - Ron, Y. AU - Preston, B. D. AU - Dougherty, J. P. PY - 2002 DA - 2002// TI - Human Immunodeficiency Virus Type 1 Recombination: Rate, Fidelity, and Putative Hot Spots JO - J Virol VL - 76 UR - https://doi.org/10.1128/JVI.76.22.11273-11282.2002 DO - 10.1128/JVI.76.22.11273-11282.2002 ID - Zhuang2002 ER - TY - JOUR AU - Jetzt, A. E. AU - Yu, H. AU - Klarmann, G. J. AU - Ron, Y. AU - Preston, B. D. AU - Dougherty, J. P. PY - 2000 DA - 2000// TI - High rate of recombination throughout the human immunodeficiency virus type 1 genome JO - J Virol VL - 74 UR - https://doi.org/10.1128/JVI.74.3.1234-1240.2000 DO - 10.1128/JVI.74.3.1234-1240.2000 ID - Jetzt2000 ER - TY - JOUR AU - Levy, D. N. AU - Aldrovandi, G. M. AU - Kutsch, O. AU - Shaw, G. M. PY - 2004 DA - 2004// TI - Dynamics of HIV-1 recombination in its natural target cells JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0306764101 DO - 10.1073/pnas.0306764101 ID - Levy2004 ER - TY - JOUR AU - Rhodes, T. AU - Wargo, H. AU - Hu, W. S. PY - 2003 DA - 2003// TI - High rates of human immunodeficiency virus type 1 recombination: near-random segregation of markers one kilobase apart in one round of viral replication JO - J Virol VL - 77 UR - https://doi.org/10.1128/JVI.77.20.11193-11200.2003 DO - 10.1128/JVI.77.20.11193-11200.2003 ID - Rhodes2003 ER - TY - JOUR AU - Robertson, A. PY - 1961 DA - 1961// TI - Inbreeding in artificial selection programmes JO - Genet Res VL - 2 UR - https://doi.org/10.1017/S0016672300000690 DO - 10.1017/S0016672300000690 ID - Robertson1961 ER - TY - JOUR AU - Woolliams, J. A. AU - Bijma, P. PY - 2000 DA - 2000// TI - Predicting rates of inbreeding in populations undergoing selection JO - Genetics VL - 154 ID - Woolliams2000 ER - TY - JOUR AU - Wray, N. R. AU - Thompson, R. PY - 1990 DA - 1990// TI - Prediction of rates of inbreeding in selected populations JO - Genet Res VL - 55 UR - https://doi.org/10.1017/S0016672300025180 DO - 10.1017/S0016672300025180 ID - Wray1990 ER - TY - JOUR AU - Ewens, W. J. PY - 1982 DA - 1982// TI - On the concept of the effective population size JO - Theor Popul Biol VL - 21 UR - https://doi.org/10.1016/0040-5809(82)90024-7 DO - 10.1016/0040-5809(82)90024-7 ID - Ewens1982 ER - TY - JOUR AU - Kimura, M. AU - Crow, J. F. PY - 1963 DA - 1963// TI - The measurement of effective population numbers JO - Evolution VL - 17 UR - https://doi.org/10.2307/2406157 DO - 10.2307/2406157 ID - Kimura1963 ER - TY - JOUR AU - Wright, S. PY - 1931 DA - 1931// TI - Evolution in Mendelian Populations JO - Genetics VL - 16 ID - Wright1931 ER - TY - CHAP AU - Hartl, D. L. AU - Clark, A. G. PY - 1989 DA - 1989// BT - Principles of Population Genetics PB - Sinauer Associates CY - Sunderland, MA ID - Hartl1989 ER - TY - JOUR AU - Allen, T. M. AU - Altfeld, M. AU - Geer, S. C. AU - Kalife, E. T. AU - Moore, C. AU - O'Sullivan, K. M. AU - Desouza, I. AU - Feeney, M. E. AU - Eldridge, R. L. AU - Maier, E. L. PY - 2005 DA - 2005// TI - Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution JO - J Virol VL - 79 UR - https://doi.org/10.1128/JVI.79.21.13239-13249.2005 DO - 10.1128/JVI.79.21.13239-13249.2005 ID - Allen2005 ER - TY - JOUR AU - Jones, N. A. AU - Wei, X. AU - Flower, D. R. AU - Wong, M. AU - Michor, F. AU - Saag, M. S. AU - Hahn, B. H. AU - Nowak, M. A. AU - Shaw, G. M. AU - Borrow, P. PY - 2004 DA - 2004// TI - Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response JO - J Exp Med VL - 200 UR - https://doi.org/10.1084/jem.20040511 DO - 10.1084/jem.20040511 ID - Jones2004 ER - TY - JOUR AU - Liu, Y. AU - McNevin, J. AU - Cao, J. AU - Zhao, H. AU - Genowati, I. AU - Wong, K. AU - McLaughlin, S. AU - McSweyn, M. AU - Diem, K. AU - Stevens, C. PY - 2006 DA - 2006// TI - Selection on the human immunodeficiency virus type 1 proteome following primary infection JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.00575-06 DO - 10.1128/JVI.00575-06 ID - Liu2006 ER - TY - JOUR AU - Liu, Y. AU - McNevin, J. AU - Zhao, H. AU - Tebit, D. M. AU - Troyer, R. M. AU - McSweyn, M. AU - Ghosh, A. K. AU - Shriner, D. AU - Arts, E. J. AU - McElrath, M. J. PY - 2007 DA - 2007// TI - Evolution of HIV-1 CTL epitopes: Fitness-Balanced Escape JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.01277-07 DO - 10.1128/JVI.01277-07 ID - Liu2007 ER - TY - JOUR AU - Jung, A. AU - Maier, R. AU - Vartanian, J. -. P. AU - Bocharov, G. AU - Jung, V. AU - Fischer, U. AU - Meese, E. AU - Wain-Hobson, S. AU - Meyerhans, A. PY - 2002 DA - 2002// TI - Multiply infected spleen cells in HIV patients JO - Nature VL - 418 UR - https://doi.org/10.1038/418144a DO - 10.1038/418144a ID - Jung2002 ER - TY - JOUR AU - Chun, T. -. W. AU - Carruth, L. AU - Finzi, D. AU - Shen, X. AU - DiGiuseppe, J. A. AU - Taylor, H. AU - Hermankova, M. AU - Chadwick, K. AU - Margolick, J. AU - Quinn, T. C. PY - 1997 DA - 1997// TI - Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection JO - Nature VL - 387 UR - https://doi.org/10.1038/387183a0 DO - 10.1038/387183a0 ID - Chun1997 ER - TY - CHAP AU - Nei, M. PY - 1987 DA - 1987// BT - Molecular Evolutionary Genetics PB - Columbia University Press CY - New York ID - Nei1987 ER - TY - JOUR AU - Kimura, M. AU - Crow, J. F. PY - 1964 DA - 1964// TI - The Number of Alleles That Can Be Maintained in a Finite Population JO - Genetics VL - 49 ID - Kimura1964 ER -