Nextstrain: real-time tracking of pathogen evolution
Explore this paper's citation graph
Summary
Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform that presents a real-time view into the evolution and spread of a range of viral pathogens of high public health importance.
- Type
- preprint
- Published
- 2017-11-22
- Cited by
- 3,133
- References
- 11
- Access
- Open access
- OpenAlex
- https://openalex.org/W2769672610
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:8134099
Keywords
Viral phylodynamics, Visualization, JavaScript, Python (programming language), Public health
References
- nextflu: real-time tracking of seasonal influenza virus evolution in humans
- The application of genomics to tracing bacterial pathogen transmission.
- Epidemiology of human infections with avian influenza A(H7N9) virus in China.
- Evolutionary epidemiology: preparing for an age of genomic plenty
- Real-time, portable genome sequencing for Ebola surveillance
- Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance
- Establishment and cryptic transmission of Zika virus in Brazil and the Americas
- Three mutations switch H7N9 influenza to human-type receptor specificity
- TreeTime: Maximum-likelihood phylodynamic analysis
- Viral Phylodynamics
- Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas
Cited by
- Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Early Manifestations of COVID-19 in Israel
- Putative host-derived insertions in the genome of circulating SARS-CoV-2 variants
- Utilizing genomic signatures to gain insights into the dynamics of SARS-CoV-2 through Machine and Deep Learning techniques
- Vaccination and the evolution of seasonal influenza
- Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest
- Real-time search of all bacterial and viral genomic data
- GLUE: a flexible software system for virus sequence data
- Real-Time Analysis and Visualization of Pathogen Sequence Data
- Quantifying the Aftermath: Recent Outbreaks Among People Who Inject Drugs and the Utility of Phylodynamics.
- Nonbifurcating Phylogenetic Tree Inference via the Adaptive LASSO
- A simple influenza model with complicated dynamics
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes
- Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing
- Estimating Vaccine-Driven Selection in Seasonal Influenza
- Recent advances in computational phylodynamics.
- A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT
- Dengue antigenic relationships predict evolutionary dynamics
- The phylogenomics of evolving virus virulence
- Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia
- Reconstruction and prediction of viral disease epidemics
Related papers
- Phylodynamique des infections virales.
- Phylodynamic approaches to studying avian influenza virus
- The contrasting phylodynamics of human influenza B viruses
- Regularized Maximum Likelihood Estimation for the Random Coefficients Model in Python
- Object Oriented Javascript Generalization Technique
- Python bindings for libcloudph++
- Phylogenetic analysis of pandemic influenza A/H1N1 virus