Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design.
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Andrew L. Ferguson | Jaclyn K. Mann | B. Walker | A. Chakraborty | A. Ferguson | S. Omarjee | T. Ndung’u | J. Mann
[1] E. Jaynes. Information Theory and Statistical Mechanics , 1957 .
[2] K. Binder,et al. Spin glasses: Experimental facts, theoretical concepts, and open questions , 1986 .
[3] Jasbir S. Arora,et al. Introduction to Optimum Design , 1988 .
[4] Ina Ruck,et al. USA , 1969, The Lancet.
[5] William Bialek,et al. Entropy and Information in Neural Spike Trains , 1996, cond-mat/9603127.
[6] S O'Brien,et al. New class I and II HLA alleles strongly associated with opposite patterns of progression to AIDS. , 1999, Journal of immunology.
[7] R. Enrique,et al. Phase stability under irradiation in alloys with a positive heat of mixing: Effective thermodynamics description , 1999 .
[8] G. Learn,et al. HIV-1 Nomenclature Proposal , 2000, Science.
[9] D K Smith,et al. Numerical Optimization , 2001, J. Oper. Res. Soc..
[10] H. Erlich,et al. A Review of the Role of the Human Leukocyte Antigen ( HLA ) System as a Host Immunogenetic Factor Influencing HIV Transmission and Progression to AIDS , 2002 .
[11] C. W. Gear,et al. Equation-Free, Coarse-Grained Multiscale Computation: Enabling Mocroscopic Simulators to Perform System-Level Analysis , 2003 .
[12] Michael J. Berry,et al. Network information and connected correlations. , 2003, Physical review letters.
[13] Eric R. Ziegel,et al. The Elements of Statistical Learning , 2003, Technometrics.
[14] Todd M. Allen,et al. HIV evolution: CTL escape mutation and reversion after transmission , 2004, Nature Medicine.
[15] M. Altfeld,et al. Immune Selection for Altered Antigen Processing Leads to Cytotoxic T Lymphocyte Escape in Chronic HIV-1 Infection , 2004, The Journal of experimental medicine.
[16] John Sidney,et al. Reversion of CTL escape–variant immunodeficiency viruses in vivo , 2004, Nature Medicine.
[17] Philip J. R. Goulder,et al. HIV and SIV CTL escape: implications for vaccine design , 2004, Nature Reviews Immunology.
[18] A. E. Hirsh,et al. The application of statistical physics to evolutionary biology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[19] Christian Brander,et al. 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 , 2005, Journal of Virology.
[20] Michael J. Berry,et al. Ising models for networks of real neurons , 2006, q-bio/0611072.
[21] A. Maritan,et al. Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns , 2006, Proceedings of the National Academy of Sciences.
[22] B. Walker,et al. Fitness Cost of Escape Mutations in p24 Gag in Association with Control of Human Immunodeficiency Virus Type 1 , 2006, Journal of Virology.
[23] Todd M. Allen,et al. Escape from the Dominant HLA-B27-Restricted Cytotoxic T-Lymphocyte Response in Gag Is Associated with a Dramatic Reduction in Human Immunodeficiency Virus Type 1 Replication , 2007, Journal of Virology.
[24] Bette Korber,et al. Design and Pre-Clinical Evaluation of a Universal HIV-1 Vaccine , 2007, PloS one.
[25] James I Mullins,et al. HIV-1 Group M Conserved Elements Vaccine , 2007, PLoS pathogens.
[26] Todd M. Allen,et al. Escape and Compensation from Early HLA-B57-Mediated Cytotoxic T-Lymphocyte Pressure on Human Immunodeficiency Virus Type 1 Gag Alter Capsid Interactions with Cyclophilin A , 2007, Journal of Virology.
[27] E. Rosenberg,et al. Recognition of a Defined Region within p24 Gag by CD8+ T Cells during Primary Human Immunodeficiency Virus Type 1 Infection in Individuals Expressing Protective HLA Class I Alleles , 2007, Journal of Virology.
[28] Philip J. R. Goulder,et al. Compensatory Mutation Partially Restores Fitness and Delays Reversion of Escape Mutation within the Immunodominant HLA-B*5703-Restricted Gag Epitope in Chronic Human Immunodeficiency Virus Type 1 Infection , 2007, Journal of Virology.
[29] Zubair Anwar,et al. Enabling Microscopic Simulators to Perform System-Level Analysis of Viscoelastic Flows , 2008 .
[30] Todd M. Allen,et al. HLA-Associated Alterations in Replication Capacity of Chimeric NL4-3 Viruses Carrying gag-protease from Elite Controllers of Human Immunodeficiency Virus Type 1 , 2008, Journal of Virology.
[31] C. Melief,et al. Immunotherapy of established (pre)malignant disease by synthetic long peptide vaccines , 2008, Nature Reviews Cancer.
[32] L. Loh,et al. Rates of HIV immune escape and reversion: implications for vaccination. , 2008, Trends in microbiology.
[33] Todd M. Allen,et al. Structural and Functional Constraints Limit Options for Cytotoxic T-Lymphocyte Escape in the Immunodominant HLA-B27-Restricted Epitope in Human Immunodeficiency Virus Type 1 Capsid , 2008, Journal of Virology.
[34] B. Walker,et al. Greater viral rebound and reduced time to resume antiretroviral therapy after therapeutic immunization with the ALVAC-HIV vaccine (vCP1452) , 2008, AIDS.
[35] Bin Li,et al. HLA-B57/B*5801 Human Immunodeficiency Virus Type 1 Elite Controllers Select for Rare Gag Variants Associated with Reduced Viral Replication Capacity and Strong Cytotoxic T-Lymphotye Recognition , 2008, Journal of Virology.
[36] Alan S. Perelson,et al. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits noncommercial use, distribution, and reproduction in other forums, provided the original authors and source are credited , 2022 .
[37] C. Brander,et al. Identification and Optimal Definition of HIV-Derived Cytotoxic T Lymphocyte (CTL) Epitopes for the Study of CTL Escape, Functional Avidity and Viral Evolution , 2008 .
[38] Michael J. Berry,et al. Spin glass models for a network of real neurons , 2009, 0912.5409.
[39] Elite control of HIV infection: implications for vaccine design. , 2009, Expert opinion on biological therapy.
[40] Anthony D. Kelleher,et al. Human Immunodeficiency Virus Type 1-Specific CD8+ T-Cell Responses during Primary Infection Are Major Determinants of the Viral Set Point and Loss of CD4+ T Cells , 2009, Journal of Virology.
[41] J. Hertz,et al. Ising model for neural data: model quality and approximate methods for extracting functional connectivity. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.
[42] David W. Haas,et al. HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins , 2009, PloS one.
[43] Heng Tao Shen,et al. Principal Component Analysis , 2009, Encyclopedia of Biometrics.
[44] Erik Aurell,et al. Frontiers in Computational Neuroscience , 2022 .
[45] Todd M. Allen,et al. HLA-B57/B*5801 Human Immunodeficiency Virus Type 1 Elite Controllers Select for Rare Gag Variants Associated with Reduced Viral Replication Capacity and Strong Cytotoxic T-Lymphocyte Recognition , 2009, Journal of Virology.
[46] Eric J. Arts,et al. Variable Fitness Impact of HIV-1 Escape Mutations to Cytotoxic T Lymphocyte (CTL) Response , 2009, PLoS pathogens.
[47] T. Hwa,et al. Identification of direct residue contacts in protein–protein interaction by message passing , 2009, Proceedings of the National Academy of Sciences.
[48] David Heckerman,et al. HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering , 2009, Journal of Virology.
[49] Todd M. Allen,et al. Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic Infection , 2010, Journal of Virology.
[50] Jack T Stapleton,et al. The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation , 2010, Science.
[51] S. Buus,et al. Efficacious Early Antiviral Activity of HIV Gag- and Pol-Specific HLA-B*2705-Restricted CD8+ T Cells , 2010, Journal of Virology.
[52] Andrew L. Ferguson,et al. An experimental and computational investigation of spontaneous lasso formation in microcin J25. , 2010, Biophysical journal.
[53] E. Rosenberg,et al. Impaired Replication Capacity of Acute/Early Viruses in Persons Who Become HIV Controllers , 2010, Journal of Virology.
[54] L. Picker,et al. Addendum: Effector memory T cell responses are associated with protection of rhesus monkeys from mucosal simian immunodeficiency virus challenge , 2011, Nature Network Boston.
[55] Sebastian Bonhoeffer,et al. A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase , 2011, Nature Genetics.
[56] J. Sidney,et al. Vaccine-Induced HIV-Specific CD8+ T Cells Utilize Preferential HLA Alleles and Target-Specific Regions of HIV-1 , 2011, Journal of acquired immune deficiency syndromes.
[57] W. Bialek,et al. Are Biological Systems Poised at Criticality? , 2010, 1012.2242.
[58] Simona Cocco,et al. Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data , 2011, Physical review letters.
[59] Todd M. Allen,et al. Coordinate linkage of HIV evolution reveals regions of immunological vulnerability , 2011, Proceedings of the National Academy of Sciences.
[60] Mario Roederer,et al. Relationship between Functional Profile of HIV-1 Specific CD8 T Cells and Epitope Variability with the Selection of Escape Mutants in Acute HIV-1 Infection , 2011, PLoS pathogens.
[61] David Heckerman,et al. Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations , 2011, PloS one.
[62] Pham Phung,et al. Broad neutralization coverage of HIV by multiple highly potent antibodies , 2011, Nature.
[63] Andrew R. Jones,et al. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations , 2010, Nucleic Acids Res..
[64] C. Sander,et al. Direct-coupling analysis of residue coevolution captures native contacts across many protein families , 2011, Proceedings of the National Academy of Sciences.
[65] Matthew S. Lewis,et al. Profound early control of highly pathogenic SIV by an effector-memory T cell vaccine , 2011, Nature.
[66] Sebastian Bonhoeffer,et al. Exploring the Complexity of the HIV-1 Fitness Landscape , 2012, PLoS genetics.
[67] Huldrych F. Günthard,et al. Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection , 2012, PLoS pathogens.
[68] Zabrina L. Brumme,et al. Impact of HLA-B*81-Associated Mutations in HIV-1 Gag on Viral Replication Capacity , 2012, Journal of Virology.
[69] A. Sette,et al. Memory CD8+ T Cells Specific for a Single Immunodominant or Subdominant Determinant Induced by Peptide-Dendritic Cell Immunization Protect from an Acute Lethal Viral Disease , 2012, Journal of Virology.