ArticleNature genetics2021
Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic.
Article in Nature genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 294 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
294 citing papers in PubMed, 456 citations in OpenAlex.
- Randomized controlled trial of molnupiravir SARS-CoV-2 viral and antibody response in at-risk adult outpatients.Nature communications · 2024Trial
- Comparing methods to estimate time-varying reproduction numbers using genomic and epidemiological data.Infectious Disease Modelling · 2026Article
- Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens.Bioinformatics (Oxford, England) · 2026Article
- Article
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- A generalized lineage nomenclature for viral genomic epidemiology.Nature microbiology · 2026Article
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data.Nature biotechnology · 2026Article
- The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California.PLOS digital health · 2026Article
- Report from the BV-BRC, CDC, NCBI, and NIAID Viral Sub-Species Classification Workshop.Journal of virology · 2026Article
- SARS-CoV-2 saltational events are recurrent and trace to persistent human infections.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary dynamics of Respiratory Syncytial Virus in pre-pandemic, pandemic, and post-pandemic periods in Houston, Texas, USA.bioRxiv : the preprint server for biology · 2026Article
- Practical phylogenetic usage of theoretical advances in distance-based tree learning.BMC bioinformatics · 2026Article
- Article
- Global approaches to infectious disease surveillance and modeling.Nature medicine · 2026Review
- Predicting the antigenic evolution of seasonal influenza viruses using phylogenetic convergence.bioRxiv : the preprint server for biology · 2026Article
- Graph transformer for ancient ancestry inference.bioRxiv : the preprint server for biology · 2026Article
- Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.bioRxiv : the preprint server for biology · 2026Article
- Extensive evolution and T cell escape by SARS-CoV-2 in a 2.5-year persistent infection of an immunocompromised host.iScience · 2026Article
234 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 6 institutions in 4 countries.
Funding
Abstract
As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering in a new era of 'genomic contact tracing'-that is, using viral genomes to trace local transmission dynamics. However, because the viral phylogeny is already so large-and will undoubtedly grow many fold-placing new sequences onto the tree has emerged as a barrier to real-time genomic contact tracing. Here, we resolve this challenge by building an efficient tree-based data structure encoding the inferred evolutionary history of the virus. We demonstrate that our approach greatly improves the speed of phylogenetic placement of new samples and data visualization, making it possible to complete the placements under the constraints of real-time contact tracing. Thus, our method addresses an important need for maintaining a fully updated reference phylogeny. We make these tools available to the research community through the University of California Santa Cruz SARS-CoV-2 Genome Browser to enable rapid cross-referencing of information in new virus sequences with an ever-expanding array of molecular and structural biology data. The methods described here will empower research and genomic contact tracing for SARS-CoV-2 specifically for laboratories worldwide.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.