Cargando…

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood and has been attributed to host genetics, host immune responses, co-infection, viral genetics, and ada...

Descripción completa

Detalles Bibliográficos
Autores principales:	Lemey, Philippe, Kosakovsky Pond, Sergei L, Drummond, Alexei J, Pybus, Oliver G, Shapiro, Beth, Barroso, Helena, Taveira, Nuno, Rambaut, Andrew
Formato:	Texto
Lenguaje:	English
Publicado:	Public Library of Science 2007
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797821/ https://www.ncbi.nlm.nih.gov/pubmed/17305421 http://dx.doi.org/10.1371/journal.pcbi.0030029

Ejemplares similares

Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril
por: Wisotsky, Sadie R, et al.
Publicado: (2020)

Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model
por: Spielman, Stephanie J, et al.
Publicado: (2018)

Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants
por: Siebenga, J. Joukje, et al.
Publicado: (2010)

Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability
por: Mannino, Frank, et al.
Publicado: (2020)

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates
por: Membrebe, Jade Vincent, et al.
Publicado: (2019)

Bayesian Phylogeography Finds Its Roots
por: Lemey, Philippe, et al.
Publicado: (2009)

Heterogeneity of synonymous substitution rates in the Xenopus frog genome
por: Lau, Quintin, et al.
Publicado: (2020)

Relax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST
por: Dellicour, Simon, et al.
Publicado: (2021)

Relative evolutionary rate inference in HyPhy with LEISR
por: Spielman, Stephanie J., et al.
Publicado: (2018)

Slow and Fast Evolving Endosymbiont Lineages: Positive Correlation between the Rates of Synonymous and Non-Synonymous Substitution
por: Silva, Francisco J., et al.
Publicado: (2015)

Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates
por: Zhang, Zhang, et al.
Publicado: (2006)

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak
por: Dellicour, Simon, et al.
Publicado: (2018)

Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography
por: Bielejec, Filip, et al.
Publicado: (2014)

Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants
por: Mower, Jeffrey P, et al.
Publicado: (2007)

Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition
por: Guéguen, Laurent, et al.
Publicado: (2018)

Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses
por: Lucaci, Alexander G, et al.
Publicado: (2023)

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
por: Suchard, Marc A, et al.
Publicado: (2018)

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences
por: Delport, Wayne, et al.
Publicado: (2010)

The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate
por: McFerrin, Lisa G, et al.
Publicado: (2011)

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates
por: Vrancken, Bram, et al.
Publicado: (2014)

Benchmarking Multi-Rate Codon Models
por: Delport, Wayne, et al.
Publicado: (2010)

Tracking virus outbreaks in the twenty-first century
por: Grubaugh, Nathan D., et al.
Publicado: (2018)

No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation
por: Hellberg, Michael E
Publicado: (2006)

Nonlinear Dynamics of Nonsynonymous (d(N)) and Synonymous (d(S)) Substitution Rates Affects Inference of Selection
por: Wolf, Jochen B. W., et al.
Publicado: (2009)

Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2
por: Lemey, Philippe, et al.
Publicado: (2014)

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen
por: MacLean, Oscar A., et al.
Publicado: (2021)

Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation
por: Baele, Guy, et al.
Publicado: (2016)

Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models
por: Sianga-Mete, Rita, et al.
Publicado: (2022)

Effects of Synonymous Mutations beyond Codon Bias: The Evidence for Adaptive Synonymous Substitutions from Microbial Evolution Experiments
por: Bailey, Susan F, et al.
Publicado: (2021)

Gene-Specific Signatures of Elevated Non-Synonymous Substitution Rates Correlate Poorly across the Plasmodium Genus
por: Weedall, Gareth D., et al.
Publicado: (2008)

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli
por: Wielgoss, Sébastien, et al.
Publicado: (2011)

Purifying Selection Can Obscure the Ancient Age of Viral Lineages
por: Wertheim, Joel O., et al.
Publicado: (2011)

Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses
por: Mei, Han, et al.
Publicado: (2021)

Non-synonymous to synonymous substitutions suggest that orthologs tend to keep their functions, while paralogs are a source of functional novelty
por: Escorcia-Rodríguez, Juan M., et al.
Publicado: (2022)

Virus evolution and transmission in an ever more connected world
por: Pybus, Oliver G., et al.
Publicado: (2015)

Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation
por: Harrison, Abby, et al.
Publicado: (2011)

Evolutionary analysis of the dynamics of viral infectious disease
por: Pybus, Oliver G., et al.
Publicado: (2009)

On the Validity of Evolutionary Models with Site-Specific Parameters
por: Scheffler, Konrad, et al.
Publicado: (2014)

A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses
por: Ghafari, Mahan, et al.
Publicado: (2021)

Persistent HIV-1 replication maintains the tissue reservoir during therapy
por: Lorenzo-Redondo, Ramon, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_q5nrhdvp4qvdg5jeqbvf2bvc7p