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Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1001/jama.2011.375openalex-snapshot
Low-Frequency HIV-1 Drug Resistance Mutations and Risk of NNRTI-Based Antiretroviral Treatment Failure
inferredcites →https://doi.org/10.1002/9780470015902.a0001768.pub2openalex-snapshot
Mutation–Selection Balance
inferredcites →https://doi.org/10.1007/bf01732340openalex-snapshot
Two types of amino acid substitutions in protein evolution
inferredcites →https://doi.org/10.1016/0092-8674(78)90223-4openalex-snapshot
Nucleotide sequence heterogeneity of an RNA phage population
inferredcites →https://doi.org/10.1016/0378-1119(76)90004-4openalex-snapshot
The proportion of revertant and mutant phage in a growing population, as a function of mutation and growth rate
inferredcites →https://doi.org/10.1016/j.immuni.2012.11.022openalex-snapshot
Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design
inferredcites →https://doi.org/10.1016/j.tig.2014.02.002openalex-snapshot
Comparative population genomics: power and principles for the inference of functionality
inferredcites →https://doi.org/10.1016/j.virusres.2014.03.019openalex-snapshot
On the nucleotide composition and structure of retroviral RNA genomes
inferredcites →https://doi.org/10.1038/nature00939openalex-snapshot
Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein
inferredcites →https://doi.org/10.1038/nature06638openalex-snapshot
Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G
inferredcites →https://doi.org/10.1038/nature07357openalex-snapshot
Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications
inferredcites →https://doi.org/10.1038/nature08237openalex-snapshot
Architecture and secondary structure of an entire HIV-1 RNA genome
inferredcites →https://doi.org/10.1038/nature12861openalex-snapshot
Mutational and fitness landscapes of an RNA virus revealed through population sequencing
inferredcites →https://doi.org/10.1038/nature24039openalex-snapshot
CG dinucleotide suppression enables antiviral defence targeting non-self RNA
inferredcites →https://doi.org/10.1038/ncomms11660openalex-snapshot
Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable
inferredcites →https://doi.org/10.1038/ng.795openalex-snapshot
A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase
inferredcites →https://doi.org/10.1038/nm.2892openalex-snapshot
Antiretroviral dynamics determines HIV evolution and predicts therapy outcome
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.45openalex-snapshot
Highly heterogeneous mutation rates in the hepatitis C virus genome
inferredcites →https://doi.org/10.1038/nrg2146openalex-snapshot
The distribution of fitness effects of new mutations
inferredcites →https://doi.org/10.1073/pnas.0400146101openalex-snapshot
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
inferredcites →https://doi.org/10.1073/pnas.1102036108openalex-snapshot
Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection
inferredcites →https://doi.org/10.1073/pnas.1105315108openalex-snapshot
Coordinate linkage of HIV evolution reveals regions of immunological vulnerability
inferredcites →https://doi.org/10.1073/pnas.1402285111openalex-snapshot
Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses
inferredcites →https://doi.org/10.1086/430005openalex-snapshot
Estimating HIV Evolutionary Pathways and the Genetic Barrier to Drug Resistance
inferredcites →https://doi.org/10.1086/650543openalex-snapshot
Pre‐existing Minority Drug‐Resistant HIV‐1 Variants, Adherence, and Risk of Antiretroviral Treatment Failure
inferredcites →https://doi.org/10.1093/infdis/jiu677openalex-snapshot
Risk of Drug Resistance Among Persons Acquiring HIV Within a Randomized Clinical Trial of Single- or Dual-Agent Preexposure Prophylaxis
inferredcites →https://doi.org/10.1093/nar/gkg100openalex-snapshot
Human immunodeficiency virus reverse transcriptase and protease sequence database
inferredcites →https://doi.org/10.1093/nar/gku075openalex-snapshot
The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication
inferredcites →https://doi.org/10.1093/ve/vex003openalex-snapshot
In vivo mutation rates and the landscape of fitness costs of HIV-1
inferredcites →https://doi.org/10.1098/rstb.2010.0063openalex-snapshot
Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies
inferredcites →https://doi.org/10.1099/vir.0.022657-0openalex-snapshot
Resistance pathways of human immunodeficiency virus type 1 against the combination of zidovudine and lamivudine
inferredcites →https://doi.org/10.1126/science.185.4154.862openalex-snapshot
Amino Acid Difference Formula to Help Explain Protein Evolution
inferredcites →https://doi.org/10.1126/science.2460925openalex-snapshot
The Accuracy of Reverse Transcriptase from HIV-1
inferredcites →https://doi.org/10.1126/science.7824947openalex-snapshot
HIV Population Dynamics in Vivo: Implications for Genetic Variation, Pathogenesis, and Therapy
inferredcites →https://doi.org/10.1128/aac.44.9.2475-2484.2000openalex-snapshot
Human Immunodeficiency Virus Type 1 Mutations Selected in Patients Failing Efavirenz Combination Therapy
inferredcites →https://doi.org/10.1128/jvi.00302-14openalex-snapshot
Mutations in HIV-1 Reverse Transcriptase Affect the Errors Made in a Single Cycle of Viral Replication
inferredcites →https://doi.org/10.1128/jvi.00508-09openalex-snapshot
Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons
inferredcites →https://doi.org/10.1128/jvi.00915-10openalex-snapshot
Nature, Position, and Frequency of Mutations Made in a Single Cycle of HIV-1 Replication
inferredcites →https://doi.org/10.1128/jvi.01908-10openalex-snapshot
Oligonucleotide Motifs That Disappear during the Evolution of Influenza Virus in Humans Increase Alpha Interferon Secretion by Plasmacytoid Dendritic Cells
inferredcites →https://doi.org/10.1128/jvi.69.8.5087-5094.1995openalex-snapshot
Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase
inferredcites →https://doi.org/10.1128/jvi.79.21.13239-13249.2005openalex-snapshot
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
inferredcites →https://doi.org/10.1128/mmbr.65.1.151-185.2001openalex-snapshot
Transition between Stochastic Evolution and Deterministic Evolution in the Presence of Selection: General Theory and Application to Virology
inferredcites →https://doi.org/10.1146/annurev.immunol.21.120601.141053openalex-snapshot
T Cell Dynamics in HIV-1 Infection
inferredcites →https://doi.org/10.1186/1471-2148-13-1openalex-snapshot
New approaches for unravelling reassortment pathways
inferredcites →https://doi.org/10.1186/1471-2148-5-44openalex-snapshot
Quasispecies theory in the context of population genetics
inferredcites →https://doi.org/10.1371/journal.pbio.1002251openalex-snapshot
Extremely High Mutation Rate of HIV-1 In Vivo
inferredcites →https://doi.org/10.1371/journal.pcbi.1000660openalex-snapshot
Recombination Rate and Selection Strength in HIV Intra-patient Evolution
inferredcites →https://doi.org/10.1371/journal.pcbi.1002527openalex-snapshot
Standing Genetic Variation and the Evolution of Drug Resistance in HIV
inferredcites →https://doi.org/10.1371/journal.pgen.1004000openalex-snapshot
Loss and Recovery of Genetic Diversity in Adapting Populations of HIV
inferredcites →https://doi.org/10.1371/journal.pone.0000796openalex-snapshot
NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence
inferredcites →https://doi.org/10.1371/journal.pone.0074109openalex-snapshot
CpG Usage in RNA Viruses: Data and Hypotheses
inferredcites →https://doi.org/10.1371/journal.ppat.1000079openalex-snapshot
Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses
inferredcites →https://doi.org/10.1371/journal.ppat.1000367openalex-snapshot
Likely Role of APOBEC3G-Mediated G-to-A Mutations in HIV-1 Evolution and Drug Resistance
inferredcites →https://doi.org/10.1371/journal.ppat.1001005openalex-snapshot
Quasispecies Theory and the Behavior of RNA Viruses
inferredcites →https://doi.org/10.1371/journal.ppat.1001273openalex-snapshot
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
inferredcites →https://doi.org/10.1371/journal.ppat.1003461openalex-snapshot
Extreme Genetic Fragility of the HIV-1 Capsid
inferredcites →https://doi.org/10.1371/journal.ppat.1006114openalex-snapshot
Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture
inferredcites →https://doi.org/10.4161/rna.22896openalex-snapshot
The A-nucleotide preference of HIV-1 in the context of its structured RNA genome
inferredcites →https://doi.org/10.7554/elife.03300openalex-snapshot
The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
inferredcites →https://doi.org/10.7554/elife.10670openalex-snapshot
More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1
inferredcites →https://doi.org/10.7554/elife.11282openalex-snapshot
Population genomics of intrapatient HIV-1 evolution
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1371/journal.ppat.1006114openalex-snapshot
Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture
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