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HIV-1: Molecular Biology and Pathogenesis - Clinical Applications
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August, J.1
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Evolution of Phenotypic Drug Susceptibility and Viral Replication Capacity during Long-Term Virologic Failure of Protease Inhibitor Therapy in Human Immunodeficiency Virus-Infected Adults
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Jason D. Barbour, Terri Wrin, Robert M. Grant, Jeffrey N. Martin, Mark R. Segal, Christos J. Petropoulos, and Steven G. Deeks. Evolution of Phenotypic Drug Susceptibility and Viral Replication Capacity during Long-Term Virologic Failure of Protease Inhibitor Therapy in Human Immunodeficiency Virus-Infected Adults. Journal of Virology, 76(21):11104-11112, 2002.
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Treatment of Antiretroviral-drug-resistant HIV-1 Infection
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Steven G. Deeks. Treatment of Antiretroviral-drug-resistant HIV-1 Infection. The Lancet, 362:2002-2011, 2003.
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Virologic and Immunologic Consequences of Discontinuing Combination Antiretroviral Drug Therapy in HIV-infected Patients with Detectable Viremia
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Steven G. Deeks, Terri Wrin, Teri Liegler, Rebecca Hoh, Matthew Hayden, Jason D. Barbour, Nicholas S. Hellmann, Christos J. Petropoulos, Joseph M. McCune, Marc K. Hellerstein, and Robert M. Grant. Virologic and Immunologic Consequences of Discontinuing Combination Antiretroviral Drug Therapy in HIV-infected Patients with Detectable Viremia. New England Journal of Medicine, 344(7):472-480, 2001.
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Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates
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Article 13
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Sandrine Dudoit, Mark J. van der Laan, and Katherine S. Pollard. Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates. Statistical Applications in Genetics and Molecular Biology, 3(1), 2004. URL http://www.bepress.com/sagmb/vol3/iss1/art13. Article 13.
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Matthew J. Gonzales, Ilana Belitskaya, Kathryn M. Dupnik, Soo-Yon Rhee, and Robert W. Shafer. Protease and Reverse Transcriptase Mutation Patterns in HIV Type 1 Isolates from Heavily Treated Persons: Comparison of Isolates from Northern California with Isolates from Other Regions. AIDS Reseach and Human Retroviruses, 19(10):909-915, 2003.
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Broad Spectrum of in Vivo Fitness of Human Immunodeficiency Virus Type 1 Subpopulations Differing at Reverse Transcriptase Codons 41 and 215
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Jaap Goudsmit, Anthony de Ronde, Ester de Rooij, and Rob de Boer. Broad Spectrum of in Vivo Fitness of Human Immunodeficiency Virus Type 1 Subpopulations Differing at Reverse Transcriptase Codons 41 and 215. Journal of Virology, 71(6):4479-4484, 1997.
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Replicative Fitness of Protease Inhibitor-Resistant Mutants of Human Immunodeficiency Virus Type 1
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Javier Martinez-Picado, Anu V. Savara, Lorraine Sutton, and Richard T. D'Aquila. Replicative Fitness of Protease Inhibitor-Resistant Mutants of Human Immunodeficiency Virus Type 1. Journal of Virology, 73(5):3744-3752, 1999.
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1642405834
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Technical Report 121, Division of Biostatistics, University of California, Berkeley, June
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Katherine S. Pollard and Mark J. van der Laan. Resampling-based Multiple Testing: Asymptotic Control of Type I error and Applications to Gene Expression Data. Technical Report 121, Division of Biostatistics, University of California, Berkeley, June 2003. URL http://www.bepress.com/ucbbiostat/paper121.
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Resampling-based Multiple Testing: Asymptotic Control of Type I Error and Applications to Gene Expression Data
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Pollard, K.S.1
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Amprenavir-Resistant HIV-1 Exhibits Lopinavir Cross-Resistance and Reduced Replication Capacity
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Julia G. Prado, Terri Wrin, Je Beauchaine, Lidia Ruiz, Christos J. Petropoulos, Simon D.W. Frost, Bonaventura Clotet, Richard T. D'Aquila, and Javier Martinez-Picado. Amprenavir-Resistant HIV-1 Exhibits Lopinavir Cross-Resistance and Reduced Replication Capacity. AIDS, 16 (7):1009-1017, 2002.
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Relating HIV-1 Sequence Variation to Replication Capacity via Trees and Forests
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Mark R. Segal, Jason D. Barbour, and Robert M. Grant. Relating HIV-1 Sequence Variation to Replication Capacity via Trees and Forests. Statistical Applications in Genetics and Molecular Biology, 3(1), 2004. URL http://www.bepress.com/sagmb/vol3/iss1/art2. Article 2.
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Multiple Concurrent Reverse Transcriptase and Protease Mutations and Multidrug Resistance of HIV-1 Isolates from Heavily Treated Patients
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Robert W. Shafer, Mark A. Winters, Sarah Palmer, and Thomas C. Merigan. Multiple Concurrent Reverse Transcriptase and Protease Mutations and Multidrug Resistance of HIV-1 Isolates from Heavily Treated Patients. Annals of Internal Medicine, 128(11):906-911, 1998.
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0038064877
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A Guide to HIV-1 Reverse Transcriptase and Protease Sequencing for Drug Resistance Studies
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Theoretical Biology and Biophysics Group at Los Alamos National Laboratory
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Robert W. Shafer, Kathryn M. Dupnik, Mark A. Winters, and Susan H. Eshleman. A Guide to HIV-1 Reverse Transcriptase and Protease Sequencing for Drug Resistance Studies. In HIV Sequencing Compendium, pages 83-133. Theoretical Biology and Biophysics Group at Los Alamos National Laboratory, 2001.
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HIV Sequencing Compendium
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Shafer, R.W.1
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18544371304
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Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics
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Article 18
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Sandra E. Sinisi and Mark J. van der Laan. Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics. Statistical Applications in Genetics and Molecular Biology, 3(1), 2004. URL http://www.bepress.com/sagmb/ vol3/iss1/art18. Article 18.
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Effect of Polymorphisms on the Replication Capacity of Protease Inhibitor-Resistant HIV-1 Variants under Drug Pressure
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Carlos Sune, Lyndall Brennan, David R. Stover, and Thomas Klimkait. Effect of Polymorphisms on the Replication Capacity of Protease Inhibitor-Resistant HIV-1 Variants under Drug Pressure. Clinical Microbiology and Infection, 10(2):119-129, 2004.
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Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives
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Article 15
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Mark J. van der Laan, Sandrine Dudoit, and Katherine S. Pollard. Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives. Statistical Applications in Genetics and Molecular Biology, 3(1), 2004. URL http://www.bepress.com/sagmb/vol3/iss1/art15. Article 15.
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Mutation Patterns and Structural Correlates in Human Immunodeficiency Virus Type 1 Protease following Different Protease Inhibitor Treatment
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Thomas D. Wu, Celia A. Schi er, Matthew J. Gonzales, Jonathan Tyalor, Rami Kantor, Sunwen Chou, Dennis Israelski, Andrew R. Zolopa, W. Jeffrey Fessel, and Robert W. Shafer. Mutation Patterns and Structural Correlates in Human Immunodeficiency Virus Type 1 Protease following Different Protease Inhibitor Treatment. Journal of Virology, 77(8):4836-4847, 2003.
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Loss of Viral Fitness Associated with Multiple Gag and Gag-Pol Processing Defects in Human Immunodeficiency Virus Type 1 Variants Selected for Resistance to Protease Inhibitors in vivo
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Veronique Zennou, Fabrizio Mammano, Sylvie Paulous, Dominique Mathez, and Francois Clavel. Loss of Viral Fitness Associated with Multiple Gag and Gag-Pol Processing Defects in Human Immunodeficiency Virus Type 1 Variants Selected for Resistance to Protease Inhibitors in vivo. Journal of Virology, 72(4):3300-3306, 1998.
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