Bayesian Hierarchical Modeling of the HIV Evolutionary Response to Therapy

REFERENCES

• Bass , B. L. 2002 . RNA Editing by Adenosine Deaminases That Act on RNA . Annual Review of Biochemistry , 71 : 817 – 846 .
   PubMed Web of Science ®Google Scholar
• Chipman , H. , George , E. and McCulloch , R. 2008 . BART: Bayesian Additive Regression Trees . Annals of Applied Statistics , 4 : 266 – 298 .
   Google Scholar
• Fearnhead , P. and Donnelly , P. 2001 . Estimating Recombination Rates From Population Genetic Data . Genetics , 159 : 1299 – 1318 .
   PubMedGoogle Scholar
• Felsenstein , J. and Churchill , G. 1996 . A Hidden Markov Model Approach to Variation Among Sites in Rate of Evolution . Molecular Biology and Evolution , 13 : 93 – 104 .
   PubMed Web of Science ®Google Scholar
• Geman , S. and Geman , D. 1984 . Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images . IEEE Transaction on Pattern Analysis and Machine Intelligence , 6 : 721 – 741 .
   PubMedGoogle Scholar
• Green , P. J. 1995 . Reversible Jump Markov Chain Monte Carlo Computation and Bayesian Model Determination . Biometrika , 82 : 711 – 731 .
   Web of Science ®Google Scholar
• Griffiths , R. and Marjoram , P. 1996 . Ancestral Inference From Samples of DNA Sequences With Recombination . Journal of Computational Biology , 3 : 479 – 502 .
   PubMed Web of Science ®Google Scholar
• Hastings , W. 1970 . Monte Carlo Sampling Methods Using Markov Chains and Their Applications . Biometrika , 57 : 97 – 109 .
   Web of Science ®Google Scholar
• Hein , J. , Schierup , M. H. and Wiuf , C. 2005 . Gene Genealogies, Variation, and Evolution: A Primer in Coalescent Theory , New York : Oxford University Press .
   Google Scholar
• Hudson , R. 1983 . Properties of a Neutral Allele Model With Intragenic Recombination . Theoretical Population Biology , 23 : 183 – 201 .
   PubMedGoogle Scholar
• ——— . 2002 . Generating Samples Under a Wright-Fisher Neutral Model . Bioinformatics , 18 : 337 – 338 .
   PubMedGoogle Scholar
• Kingman , J. 1982 . The Coalescent . Stochastic Processes and Their Applications , 13 : 235 – 248 .
   Google Scholar
• Li , N. and Stephens , M. 2003 . Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data . Genetics , 165 : 2213 – 2233 .
   PubMed Web of Science ®Google Scholar
• Lu , X. , Yu , Q. , Binder , G. K. , Chen , Z. , Slepushkina , T. , Rossi , J. and Dropulic , B. 2004 . Antisense-Mediated Inhibition of Human Immunodeficiency Virus (HIV) Replication by Use of an HIV Type 1-Based Vector Results in Severely Attenuated Mutants Incapable of Developing Resistance . Journal of Virology , 78 : 7079 – 7088 .
   PubMed Web of Science ®Google Scholar
• McGuire , G. , Denham , M. and Balding , D. 2001 . Models of Sequence Evolution for DNA Sequences Containing Gaps . Molecular Biology and Evolution , 18 : 481 – 490 .
   PubMedGoogle Scholar
• Mukherjee , R. , Plesa , G. , Sherrill-Mix , S. , Richardson , M. W. , Riley , J. L. and Bushman , F. D. 2010 . HIV Sequence Variation Associated With env Antisense Adoptive T-Cell Therapy in the hNSG Mouse Model . Molecular Therapy , 18 : 803 – 811 .
   PubMedGoogle Scholar
• Nishikura , K. 2010 . Functions and Regulation of RNA Editing by ADAR Deaminases . Annual Review of Biochemistry , 79 : 321 – 349 .
   PubMed Web of Science ®Google Scholar
• Rabiner , L. R. 1989 . A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition . Proceedings of the IEEE , 77 : 257 – 286 .
   Web of Science ®Google Scholar
• Rambaut , A. and Grassly , N. C. 1997 . Seq-Gen: An Application for the Monte Carlo Simulation of DNA Sequence Evolution Along Phylogenetic Trees . Computer Applications in the Bioscience , 13 : 235 – 238 .
   PubMedGoogle Scholar
• Ray , N. , Harrison , J. E. , Blackburn , L. A. , Martin , J. N. , Deeks , S. G. and Doms , R. W. 2007 . Clinical Resistance to Enfuvirtide Does Not Affect Susceptibility of Human Immunodeficiency Virus Type 1 to Other Classes of Entry Inhibitors . Journal of Virology , 81 : 3240 – 3250 .
   PubMed Web of Science ®Google Scholar
• Robertson , D. L. , Sharp , P. M. , McCutchan , F. E. and Hahn , B. H. 1995 . Recombinaton in HIV-1 . Nature , 374 : 124 – 126 .
   PubMed Web of Science ®Google Scholar
• Schierup , M. H. and Hein , J. 2000 . Consequences of Recombination on Traditional Phylogenetic Analysis . Genetics , 156 : 879 – 891 .
   PubMed Web of Science ®Google Scholar
• UNAIDS . 2006 . Aids Epidemic Update: Special Report on HIV/AIDS, Joint United Nations Programme on HIV/AIDS , Geneva, Switzerland : UNAIDS .
   Google Scholar
• Wild , C. , Greenwell , T. and Matthews , T. 1993 . A Synthetic Peptide From HIV-1 gp41 is a Potent Inhibitor of Virus Mediated Cell-Cell Fusion . AIDS Research and Human Retroviruses , 9 : 1051 – 1053 .
   PubMed Web of Science ®Google Scholar
• Wilson , D. J. and McVean , G. 2006 . Estimating Diversifying Selection and Functional Constraint in the Presence of Recombination . Genetics , 172 : 1411 – 1425 .
   PubMedGoogle Scholar
• Wulff , B.-E. , Sakurai , M. and Nishikura , K. 2011 . Elucidating the Inosinome: Global Approaches to Adenosine-to-Inosine RNA Editing . Nature Reviews , 12 : 81 – 85 .
   Google Scholar
• Wyatt , R. , Moore , J. , Accola , M. , Desjardin , E. , Robinson , J. and Sodroski , J. 1995 . Involvement of the v1/v2 Variable Loop Structure in the Exposure of Human Immunodeficiency Virus Type 1 gp120 Epitopes Induced by Receptor Binding . Journal of Virology , 69 : 5723 – 5733 .
   PubMedGoogle Scholar