TY - JOUR AU - Koff, W. C. AU - Johnson, P. R. AU - Watkins, D. I. AU - Burton, D. R. AU - Lifson, J. D. AU - Hasenkrug, K. J. AU - McDermott, A. B. AU - Schultz, A. AU - Zamb, T. J. AU - Boyle, R. AU - Desrosiers, R. C. PY - 2006 DA - 2006// TI - HIV vaccine design: insights from live attenuated SIV vaccines JO - Nat Immunol VL - 7 UR - https://doi.org/10.1038/ni1296 DO - 10.1038/ni1296 ID - Koff2006 ER - TY - JOUR AU - Johnson, R. P. AU - Desrosiers, R. C. PY - 1998 DA - 1998// TI - Protective immunity induced by live attenuated simian immunodeficiency virus JO - Curr Opin Immunol VL - 10 UR - https://doi.org/10.1016/S0952-7915(98)80118-0 DO - 10.1016/S0952-7915(98)80118-0 ID - Johnson1998 ER - TY - JOUR AU - Mills, J. AU - Desrosiers, R. AU - Rud, E. AU - Almond, N. PY - 2000 DA - 2000// TI - Live attenuated HIV vaccines: proposal for further research and development JO - AIDS Res Hum Retroviruses VL - 16 UR - https://doi.org/10.1089/088922200750005976 DO - 10.1089/088922200750005976 ID - Mills2000 ER - TY - JOUR AU - Whitney, J. B. AU - Ruprecht, R. M. PY - 2004 DA - 2004// TI - Live attenuated HIV vaccines: pitfalls and prospects JO - Curr Opin Infect Dis VL - 17 UR - https://doi.org/10.1097/00001432-200402000-00004 DO - 10.1097/00001432-200402000-00004 ID - Whitney2004 ER - TY - JOUR AU - Baba, T. W. AU - Jeong, Y. S. AU - Penninck, D. AU - Bronson, R. AU - Greene, M. F. AU - Ruprecht, R. M. PY - 1995 DA - 1995// TI - Pathogenicity of live, attenuated SIV after mucosal infection of neonatal macaques JO - Science VL - 267 UR - https://doi.org/10.1126/science.7892606 DO - 10.1126/science.7892606 ID - Baba1995 ER - TY - JOUR AU - Baba, T. W. AU - Liska, V. AU - Khimani, A. H. AU - Ray, N. B. AU - Dailey, P. J. AU - Penninck, D. AU - Bronson, R. AU - Greene, M. F. AU - McClure, H. M. AU - Martin, L. N. AU - Ruprecht, R. M. PY - 1999 DA - 1999// TI - Live attenuated, multiply deleted simian immunodeficiency virus causes AIDS in infant and adult macaques JO - Nat Med VL - 5 UR - https://doi.org/10.1038/8859 DO - 10.1038/8859 ID - Baba1999 ER - TY - JOUR AU - Chakrabarti, L. A. AU - Metzner, K. J. AU - Ivanovic, T. AU - Cheng, H. AU - Louis-Virelizier, J. AU - Connor, R. I. AU - Cheng-Mayer, C. PY - 2003 DA - 2003// TI - A truncated form of Nef selected during pathogenic reversion of simian immunodeficiency virus SIVmac239Deltanef increases viral replication JO - J Virol VL - 77 UR - https://doi.org/10.1128/JVI.77.2.1245-1256.2003 DO - 10.1128/JVI.77.2.1245-1256.2003 ID - Chakrabarti2003 ER - TY - JOUR AU - Whatmore, A. M. AU - Cook, N. AU - Hall, G. A. AU - Sharpe, S. AU - Rud, E. W. AU - Cranage, M. P. PY - 1995 DA - 1995// TI - Repair and evolution of nef in vivo modulates simian immunodeficiency virus virulence JO - J Virol VL - 69 ID - Whatmore1995 ER - TY - JOUR AU - Churchill, M. J. AU - Rhodes, D. I. AU - Learmont, J. C. AU - Sullivan, J. S. AU - Wesselingh, S. L. AU - Cooke, I. R. AU - Deacon, N. J. AU - Gorry, P. R. PY - 2006 DA - 2006// TI - Longitudinal analysis of human immunodeficiency virus type 1 nef/long terminal repeat sequences in a cohort of long-term survivors infected from a single source JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.80.2.1047-1052.2006 DO - 10.1128/JVI.80.2.1047-1052.2006 ID - Churchill2006 ER - TY - JOUR AU - Berkhout, B. AU - Verhoef, K. AU - van Wamel, J. L. B. AU - Back, B. PY - 1999 DA - 1999// TI - Genetic instability of live-attenuated HIV-1 vaccine strains JO - J Virol VL - 73 ID - Berkhout1999 ER - TY - JOUR AU - Verhoef, K. AU - Marzio, G. AU - Hillen, W. AU - Bujard, H. AU - Berkhout, B. PY - 2001 DA - 2001// TI - Strict control of human immunodeficiency virus type 1 replication by a genetic switch: Tet for Tat JO - J Virol VL - 75 UR - https://doi.org/10.1128/JVI.75.2.979-987.2001 DO - 10.1128/JVI.75.2.979-987.2001 ID - Verhoef2001 ER - TY - JOUR AU - Smith, S. M. AU - Khoroshev, M. AU - Marx, P. A. AU - Orenstein, J. AU - Jeang, K. T. PY - 2001 DA - 2001// TI - Constitutively dead, conditionally live HIV-1 genomes. Ex vivo implications for a live virus vaccine JO - J Biol Chem VL - 276 UR - https://doi.org/10.1074/jbc.M101604200 DO - 10.1074/jbc.M101604200 ID - Smith2001 ER - TY - JOUR AU - Berkhout, B. AU - Marzio, G. AU - Verhoef, K. PY - 2002 DA - 2002// TI - Control over HIV-1 replication by an antibiotic; a novel vaccination strategy with a drug-dependent virus JO - Virus Res VL - 82 UR - https://doi.org/10.1016/S0168-1702(01)00399-9 DO - 10.1016/S0168-1702(01)00399-9 ID - Berkhout2002 ER - TY - JOUR AU - Das, A. T. AU - Zhou, X. AU - Vink, M. AU - Klaver, B. AU - Berkhout, B. PY - 2002 DA - 2002// TI - Conditional live virus as a novel approach towards a safe live attenuated HIV vaccine JO - Expert Rev Vaccines VL - 1 UR - https://doi.org/10.1586/14760584.1.3.293 DO - 10.1586/14760584.1.3.293 ID - Das2002 ER - TY - JOUR AU - Das, A. T. AU - Verhoef, K. AU - Berkhout, B. PY - 2004 DA - 2004// TI - A conditionally replicating virus as a novel approach toward an HIV vaccine JO - Methods Enzymol VL - 388 UR - https://doi.org/10.1016/S0076-6879(04)88028-5 DO - 10.1016/S0076-6879(04)88028-5 ID - Das2004 ER - TY - JOUR AU - Baron, U. AU - Bujard, H. PY - 2000 DA - 2000// TI - Tet repressor-based system for regulated gene expression in eukaryotic cells: principles and advances JO - Methods Enzymol VL - 327 UR - https://doi.org/10.1016/S0076-6879(00)27292-3 DO - 10.1016/S0076-6879(00)27292-3 ID - Baron2000 ER - TY - JOUR AU - Marzio, G. AU - Verhoef, K. AU - Vink, M. AU - Berkhout, B. PY - 2001 DA - 2001// TI - In vitro evolution of a highly replicating, doxycycline-dependent HIV for applications in vaccine studies JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.111031498 DO - 10.1073/pnas.111031498 ID - Marzio2001 ER - TY - JOUR AU - Marzio, G. AU - Vink, M. AU - Verhoef, K. AU - de Ronde, A. AU - Berkhout, B. PY - 2002 DA - 2002// TI - Efficient human immunodeficiency virus replication requires a fine-tuned level of transcription JO - J Virol VL - 76 UR - https://doi.org/10.1128/JVI.76.6.3084-3088.2002 DO - 10.1128/JVI.76.6.3084-3088.2002 ID - Marzio2002 ER - TY - JOUR AU - Das, A. T. AU - Zhou, X. AU - Vink, M. AU - Klaver, B. AU - Verhoef, K. AU - Marzio, G. AU - Berkhout, B. PY - 2004 DA - 2004// TI - Viral evolution as a tool to improve the tetracycline-regulated gene expression system JO - J Biol Chem VL - 279 UR - https://doi.org/10.1074/jbc.M313895200 DO - 10.1074/jbc.M313895200 ID - Das2004 ER - TY - JOUR AU - Zhou, X. AU - Vink, M. AU - Klaver, B. AU - Verhoef, K. AU - Marzio, G. AU - Das, A. T. AU - Berkhout, B. PY - 2006 DA - 2006// TI - The genetic stability of a conditional-live HIV-1 variant can be improved by mutations in the Tet-On regulatory system that restrain evolution JO - J Biol Chem VL - 281 UR - https://doi.org/10.1074/jbc.M513400200 DO - 10.1074/jbc.M513400200 ID - Zhou2006 ER - TY - JOUR AU - Zhou, X. AU - Vink, M. AU - Klaver, B. AU - Berkhout, B. AU - Das, A. T. PY - 2006 DA - 2006// TI - Optimization of the Tet-On system for regulated gene expression through viral evolution JO - Gene Ther VL - 13 UR - https://doi.org/10.1038/sj.gt.3302780 DO - 10.1038/sj.gt.3302780 ID - Zhou2006 ER - TY - JOUR AU - Zhou, X. AU - Vink, M. AU - Berkhout, B. AU - Das, A. T. PY - 2006 DA - 2006// TI - Modification of the Tet-On regulatory system prevents the conditional-live HIV-1 variant from losing doxycycline-control JO - Retrovirology VL - 3 UR - https://doi.org/10.1186/1742-4690-3-82 DO - 10.1186/1742-4690-3-82 ID - Zhou2006 ER - TY - JOUR AU - Kiselyeva, Y. AU - Ito, Y. AU - Lima, R. G. AU - Grivel, J. C. AU - Das, A. T. AU - Berkhout, B. AU - Margolis, L. B. PY - 2004 DA - 2004// TI - Depletion of CD4 T lymphocytes in human lymphoid tissue infected ex vivo with doxycycline-dependent HIV-1 JO - Virol VL - 328 UR - https://doi.org/10.1016/j.virol.2004.07.014 DO - 10.1016/j.virol.2004.07.014 ID - Kiselyeva2004 ER - TY - JOUR AU - Das, A. T. AU - Baldwin, C. E. AU - Vink, M. AU - Berkhout, B. PY - 2005 DA - 2005// TI - Improving the safety of a conditional-live human immunodeficiency virus type 1 vaccine by controlling both gene expression and cell entry JO - J Virol VL - 79 UR - https://doi.org/10.1128/JVI.79.6.3855-3858.2005 DO - 10.1128/JVI.79.6.3855-3858.2005 ID - Das2005 ER - TY - JOUR AU - Das, A. T. AU - Klaver, B. AU - Harwig, A. AU - Vink, M. AU - Ooms, M. AU - Centlivre, M. AU - Berkhout, B. PY - 2007 DA - 2007// TI - Construction of a doxycycline-dependent simian immunodeficiency virus reveals a non-transcriptional function of Tat in viral replication JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.01354-07 DO - 10.1128/JVI.01354-07 ID - Das2007 ER - TY - JOUR AU - Mathews, D. H. AU - Sabina, J. AU - Zuker, M. AU - Turner, D. H. PY - 1999 DA - 1999// TI - Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure JO - J Mol Biol VL - 288 UR - https://doi.org/10.1006/jmbi.1999.2700 DO - 10.1006/jmbi.1999.2700 ID - Mathews1999 ER - TY - JOUR AU - Zuker, M. PY - 2003 DA - 2003// TI - Mfold web server for nucleic acid folding and hybridization prediction JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg595 DO - 10.1093/nar/gkg595 ID - Zuker2003 ER - TY - JOUR AU - Pachulska-Wieczorek, K. AU - Purzycka, K. J. AU - Adamiak, R. W. PY - 2006 DA - 2006// TI - New, extended hairpin form of the TAR-2 RNA domain points to the structural polymorphism at the 5' end of the HIV-2 leader RNA JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl373 DO - 10.1093/nar/gkl373 ID - Pachulska-Wieczorek2006 ER - TY - JOUR AU - Berkhout, B. AU - Jeang, K. T. PY - 1991 DA - 1991// TI - Detailed mutational analysis of TAR RNA: critical spacing between the bulge and loop recognition domains JO - Nucleic Acids Res VL - 19 UR - https://doi.org/10.1093/nar/19.22.6169 DO - 10.1093/nar/19.22.6169 ID - Berkhout1991 ER - TY - JOUR AU - Huthoff, H. AU - Berkhout, B. PY - 2001 DA - 2001// TI - Two alternating structures for the HIV-1 leader RNA JO - RNA VL - 7 UR - https://doi.org/10.1017/S1355838201001881 DO - 10.1017/S1355838201001881 ID - Huthoff2001 ER - TY - JOUR AU - Berkhout, B. AU - Ooms, M. AU - Beerens, N. AU - Huthoff, H. AU - Southern, E. AU - Verhoef, K. PY - 2002 DA - 2002// TI - In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes JO - J Biol Chem VL - 277 UR - https://doi.org/10.1074/jbc.M200950200 DO - 10.1074/jbc.M200950200 ID - Berkhout2002 ER - TY - JOUR AU - Ooms, M. AU - Huthoff, H. AU - Russell, R. AU - Liang, C. AU - Berkhout, B. PY - 2004 DA - 2004// TI - A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions JO - J Virol VL - 78 UR - https://doi.org/10.1128/JVI.78.19.10814-10819.2004 DO - 10.1128/JVI.78.19.10814-10819.2004 ID - Ooms2004 ER - TY - JOUR AU - Abbink, T. E. M. AU - Ooms, M. AU - Haasnoot, P. C. J. AU - Berkhout, B. PY - 2005 DA - 2005// TI - The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation JO - Biochem VL - 44 UR - https://doi.org/10.1021/bi0502588 DO - 10.1021/bi0502588 ID - Abbink2005 ER - TY - JOUR AU - Das, A. T. AU - Harwig, A. AU - Vrolijk, M. M. AU - Berkhout, B. PY - 2007 DA - 2007// TI - The TAR hairpin of human immunodeficiency virus type-1 can be deleted when not required for Tat-mediated activation of transcription JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.00392-07 DO - 10.1128/JVI.00392-07 ID - Das2007 ER - TY - CHAP AU - Vrolijk, M. M. AU - Ooms, M. AU - Harwig, A. AU - Das, A. T. AU - Berkhout, B. PY - 2008 DA - 2008// TI - Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA BT - Nucleic Acids Res ID - Vrolijk2008 ER - TY - JOUR AU - Regier, D. A. AU - Desrosiers, R. C. PY - 1990 DA - 1990// TI - The complete nucleotide sequence of a pathogenic molecular clone of simian immunodeficiency virus JO - AIDS Res Hum Retroviruses VL - 6 ID - Regier1990 ER - TY - JOUR AU - Guan, Y. AU - Whitney, J. B. AU - Diallo, K. AU - Wainberg, M. A. PY - 2000 DA - 2000// TI - Leader sequences downstream of the primer binding site are important for efficient replication of simian immunodeficiency virus JO - J Virol VL - 74 UR - https://doi.org/10.1128/JVI.74.19.8854-8860.2000 DO - 10.1128/JVI.74.19.8854-8860.2000 ID - Guan2000 ER - TY - JOUR AU - Auersperg, N. PY - 1964 DA - 1964// TI - Long-term cultivation of hypodiploid human tumor cells JO - J Nat Cancer Inst VL - 32 ID - Auersperg1964 ER - TY - JOUR AU - Lusso, P. AU - Cocchi, F. AU - Balotta, C. AU - Markham, P. D. AU - Louie, A. AU - Farci, P. AU - Pal, R. AU - Gallo, R. C. AU - Reitz, M. S. PY - 1995 DA - 1995// TI - Growth of macrophage-tropic and primary human immunodeficiency virus type 1 (HIV-1) isolates in a unique CD4+ T-cell clone (PM1): failure to downregulate CD4 and to interfere with cell-line-tropic HIV-1 JO - J Virol VL - 69 ID - Lusso1995 ER - TY - JOUR AU - Mills, K. H. AU - Barnard, A. L. AU - Williams, M. AU - Page, M. AU - Ling, C. AU - Stott, E. J. AU - Silvera, P. AU - Taffs, F. AU - Kingsman, A. S. AU - Adams, S. E. AU - Almond, N. AU - Kitchin, P. A. AU - Jones, W. C. PY - 1991 DA - 1991// TI - Vaccine-induced CD4+ T cells against the simian immunodeficiency virus gag protein. Epitope specificity and relevance to protective immunity JO - J Immunol VL - 147 ID - Mills1991 ER - TY - JOUR AU - Lifson, J. D. AU - Rossio, J. L. AU - Piatak, M. AU - Parks, T. AU - Li, L. AU - Kiser, R. AU - Coalter, V. AU - Fisher, B. AU - Flynn, B. M. AU - Czajak, S. AU - Hirsch, V. M. AU - Reimann, K. A. AU - Schmitz, J. E. AU - Ghrayeb, J. AU - Bischofberger, N. AU - Nowak, M. A. AU - Desrosiers, R. C. AU - Wodarz, D. PY - 2001 DA - 2001// TI - Role of CD8(+) lymphocytes in control of simian immunodeficiency virus infection and resistance to rechallenge after transient early antiretroviral treatment JO - J Virol VL - 75 UR - https://doi.org/10.1128/JVI.75.21.10187-10199.2001 DO - 10.1128/JVI.75.21.10187-10199.2001 ID - Lifson2001 ER - TY - JOUR AU - Cline, A. N. AU - Bess, J. W. AU - Piatak, M. AU - Lifson, J. D. PY - 2005 DA - 2005// TI - Highly sensitive SIV plasma viral load assay: practical considerations, realistic performance expectations, and application to reverse engineering of vaccines for AIDS JO - J Med Primatol VL - 34 UR - https://doi.org/10.1111/j.1600-0684.2005.00128.x DO - 10.1111/j.1600-0684.2005.00128.x ID - Cline2005 ER - TY - JOUR AU - Maudru, T. AU - Peden, K. W. PY - 1998 DA - 1998// TI - Adaptation of the fluorogenic 5'-nuclease chemistry to a PCR-based reverse transcriptase assay JO - Biotechn VL - 25 ID - Maudru1998 ER - TY - JOUR AU - Ruijter, J. M. AU - Thygesen, H. H. AU - Schoneveld, O. J. AU - Das, A. T. AU - Berkhout, B. AU - Lamers, W. H. PY - 2006 DA - 2006// TI - Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology JO - Retrovirology VL - 3 UR - https://doi.org/10.1186/1742-4690-3-2 DO - 10.1186/1742-4690-3-2 ID - Ruijter2006 ER -