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Structurally informed evolutionary models improve phylogenetic reconstruction for emerging, seasonal, and pandemic influenza viruses

https://doi.org/10.1101/228692
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Evolutionary Concept in Genetics and Genomics
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A new method for calculating evolutionary substitution rates
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Respiratory Syncytial Virus—A Comprehensive Review
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Influenza virus hemagglutinin stalk-based antibodies and vaccines
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Should phylogenetic models be trying to ‘fit an elephant’?
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The prospects and challenges of universal vaccines for influenza
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Measurably evolving pathogens in the genomic era
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Structural and functional specificity of Influenza virus haemagglutinin and paramyxovirus fusion protein anchoring peptides
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Global circulation patterns of seasonal influenza viruses vary with antigenic drift
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Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection
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Efficacy of commercial vaccines against newly emerging avian influenza H5N8 virus in Egypt
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Structural basis for immunization with postfusion respiratory syncytial virus fusion F glycoprotein (RSV F) to elicit high neutralizing antibody titers
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Bayes Factors
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Computing Bayes Factors Using Thermodynamic Integration
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Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards
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Phylogenetic Systematics and Biogeography of Hummingbirds: Bayesian and Maximum Likelihood Analyses of Partitioned Data and Selection of an Appropriate Partitioning Strategy
inferredcites →https://doi.org/10.1080/10635150802206883openalex-snapshot
Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci
inferredcites →https://doi.org/10.1093/molbev/msj021openalex-snapshot
Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences
inferredcites →https://doi.org/10.1093/molbev/msn090openalex-snapshot
Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics
inferredcites →https://doi.org/10.1093/molbev/msq224openalex-snapshot
Choosing among Partition Models in Bayesian Phylogenetics
inferredcites →https://doi.org/10.1093/molbev/mss020openalex-snapshot
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/molbev/mss075openalex-snapshot
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
inferredcites →https://doi.org/10.1093/molbev/mss084openalex-snapshot
Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty
inferredcites →https://doi.org/10.1093/molbev/mss243openalex-snapshot
Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics
inferredcites →https://doi.org/10.1093/molbev/msv003openalex-snapshot
The Relationship between dN/dS and Scaled Selection Coefficients
inferredcites →https://doi.org/10.1093/sysbio/syq085openalex-snapshot
Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection
inferredcites →https://doi.org/10.1093/sysbio/syw054openalex-snapshot
Emerging Concepts of Data Integration in Pathogen Phylodynamics
inferredcites →https://doi.org/10.1111/irv.12466openalex-snapshot
Lineage‐specific epitope profiles for HPAI H5 pre‐pandemic vaccine selection and evaluation
inferredcites →https://doi.org/10.1126/science.1210724openalex-snapshot
Catching a Moving Target
inferredcites →https://doi.org/10.1128/jvi.01606-12openalex-snapshot
Insights into Avian Influenza Virus Pathogenicity: the Hemagglutinin Precursor HA0 of Subtype H16 Has an Alpha-Helix Structure in Its Cleavage Site with Inefficient HA1/HA2 Cleavage
inferredcites →https://doi.org/10.1128/jvi.03004-13openalex-snapshot
Assessment of Influenza Virus Hemagglutinin Stalk-Based Immunity in Ferrets
inferredcites →https://doi.org/10.1128/mr.56.1.152-179.1992openalex-snapshot
Evolution and ecology of influenza A viruses
inferredcites →https://doi.org/10.1142/s021972001441008xopenalex-snapshot
Co-evolution analysis to predict protein–protein interactions within influenza virus envelope
inferredcites →https://doi.org/10.1146/annurev.bi.56.070187.002053openalex-snapshot
THE STRUCTURE AND FUNCTION OF THE HEMAGGLUTININ MEMBRANE GLYCOPROTEIN OF INFLUENZA VIRUS
inferredcites →https://doi.org/10.1146/annurev.biochem.69.1.531openalex-snapshot
Receptor Binding and Membrane Fusion in Virus Entry: The Influenza Hemagglutinin
inferredcites →https://doi.org/10.1371/journal.ppat.1006885openalex-snapshot
When are pathogen genome sequences informative of transmission events?
inferredcites →https://doi.org/10.2807/1560-7917.es.2017.22.13.30494openalex-snapshot
GISAID: Global initiative on sharing all influenza data – from vision to reality
inferredcites →https://doi.org/10.4172/1747-0862.1000035openalex-snapshot
Avian influenza vaccination in Egypt: Limitations of the current strategy
inferredcites →https://doi.org/10.7554/elife.05055openalex-snapshot
The contrasting phylodynamics of human influenza B viruses
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Ventromedial hypothalamic neurons control a defensive emotion state

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41598-018-28706-1openalex-snapshot
The influenza virus hemagglutinin head evolves faster than the stalk domain
inferred← citeshttps://doi.org/10.3390/vaccines7020045openalex-snapshot
Computational Approaches and Challenges to Developing Universal Influenza Vaccines
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