Research graph
References from Enriching Public Pathogen Genomic Records With Patient Metadata: Quantitative Study and Exploratory Case Analysis. Local targets link to admitted publications; unresolved targets remain external evidence.
Database resources of the national center for biotechnology information
10.1093/nar/gkab1112 · External reference
GISAID: global initiative on sharing all influenza data - from vision to reality
10.2807/1560-7917.es.2017.22.13.30494 · External reference
Structural and functional impact by SARS-CoV-2 Omicron spike mutations
10.1016/j.celrep.2022.110729 · External reference
Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022
10.1128/msphere.00232-23 · External reference
Improved SARS-CoV-2 sequencing surveillance allows the identification of new variants and signatures in infected patients
10.1186/s13073-022-01098-8 · External reference
COVID-19 pandemic reveals the peril of ignoring metadata standards
10.1038/s41597-020-0524-5 · External reference
Shortcomings of SARS-CoV-2 genomic metadata
10.1186/s13104-021-05605-9 · External reference
Estimating the deferred value of pathogen genomic data for secondary use
10.1038/s41597-025-05049-x · External reference
SARS-CoV-2 entry related viral and host genetic variations: implications on COVID-19 severity, immune escape, and infectivity
10.3390/ijms22063060 · External reference
Associations between clinical data, vaccination status, antibody responses, and post-COVID-19 symptoms in Thais infected with SARS-CoV-2 Delta and Omicron variants: a 1-year follow-up study
10.1186/s12879-024-09999-2 · External reference
Integration of individualized and population-level molecular epidemiology data to model COVID-19 outcomes
10.1016/j.xcrm.2023.101361 · External reference
Impact of obesity-associated SARS-CoV-2 mutations on COVID-19 severity and clinical outcomes
10.3390/v17010038 · External reference
SARS-CoV-2 alchemy: understanding the dynamics of age, vaccination, and geography in the evolution of SARS-CoV-2 in India
10.1371/journal.pntd.0012918 · External reference
Evidence of SARS-CoV-2 convergent evolution in immunosuppressed patients treated with antiviral therapies
10.1186/s12985-024-02378-y · External reference
Modeling the onset of symptoms of COVID-19: effects of SARS-CoV-2 variant
10.1371/journal.pcbi.1009629 · External reference
Global landscape of SARS-CoV-2 genomic surveillance and data sharing
10.1038/s41588-022-01033-y · External reference
Unresolved reference
External reference
Enhancing phylogeography by improving geographical information from GenBank
10.1016/j.jbi.2011.06.005 · External reference
Going back to the roots: evaluating Bayesian phylogeographic models with discrete trait uncertainty
10.1016/j.meegid.2020.104501 · External reference
Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography
10.1093/ve/vey043 · External reference
Knowledge-driven geospatial location resolution for phylogeographic models of virus migration
10.1093/bioinformatics/btv259 · External reference
LitCovid: an open database of COVID-19 literature
10.1093/nar/gkaa952 · External reference
Entrez: molecular biology database and retrieval system
10.1016/s0076-6879(96)66012-1 · External reference
A new method of classifying prognostic comorbidity in longitudinal studies: development and validation
10.1016/0021-9681(87)90171-8 · External reference
SNOMED CT standard ontology based on the ontology for general medical science
10.1186/s12911-018-0651-5 · External reference
Unresolved reference
External reference
Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp
10.1002/imt2.107 · External reference
Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler
10.1186/s12864-016-3030-6 · External reference
BLAST+: architecture and applications
10.1186/1471-2105-10-421 · External reference
Nextclade: clade assignment, mutation calling and quality control for viral genomes
10.21105/joss.03773 · External reference
Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants
10.1038/s41467-023-38867-x · External reference
Dynamic diversity of SARS-CoV-2 genetic mutations in a lung transplantation patient with persistent COVID-19
10.1038/s41467-024-47941-x · External reference
Immune system deficiencies do not alter SARS-CoV-2 evolutionary rate but favour the emergence of mutations by extending viral persistence
10.3390/v16030447 · External reference
Persistence of SARS-CoV-2 infection and viral intra- and inter-host evolution in COVID-19 hospitalized patients
10.1002/jmv.29708 · External reference
Identification of various recombinants in a patient coinfected with the different SARS-CoV-2 variants
10.1111/irv.13340 · External reference
Investigation of the individual genetic evolution of SARS-CoV-2 in a small cluster during the rapid spread of the BF.5 lineage in Tokyo, Japan
10.3389/fmicb.2023.1229234 · External reference
Quantitative and qualitative subgenomic RNA profiles of SARS-CoV-2 in respiratory samples: a comparison between Omicron BA.2 and non-VOC-D614G
10.1016/j.virs.2024.01.010 · External reference
Emergence of SARS-CoV-2 Omicron sub-lineage JN.1 in Bangladesh
10.1128/mra.00130-24 · External reference
Epidemiology and analysis of SARS-CoV-2 Omicron subvariants BA.1 and 2 in Taiwan
10.1038/s41598-023-43357-7 · External reference
A regional genomic surveillance program is implemented to monitor the occurrence and emergence of SARS-CoV-2 variants in Yubei District, China
10.1186/s12985-023-02279-6 · External reference
Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India
10.1038/s41598-023-42065-6 · External reference
A mutation responsible for impaired detection by the Xpert SARS-CoV-2 assay independently emerged in different lineages during the SARS-CoV-2 pandemic
10.1186/s12866-023-02924-8 · External reference
Detection of high level of co-infection and the emergence of novel SARS CoV-2 Delta-Omicron and Omicron-Omicron recombinants in the epidemiological surveillance of Andalusia
10.3390/ijms24032419 · External reference
Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron variants BA.2, BA.5 and BQ.1.1 in critically ill patients with COVID-19: a prospective, multicenter cohort study
10.1186/s40635-023-00536-0 · External reference
Clinical characteristics and novel mutations of omicron subvariant XBB in Tamil Nadu, India - a cohort study
10.1016/j.lansea.2023.100272 · External reference
Genomic characterization of Influenza A (H1N1)pdm09 and SARS-CoV-2 from influenza like illness (ILI) and severe acute respiratory illness (SARI) cases reported between July-December, 2022
10.1038/s41598-024-58993-w · External reference
SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico
10.1099/mgen.0.001120 · External reference
Coding-complete genomes of 18 SARS-CoV-2 Omicron JN.1, JN.1.4, and JN.1.11 sub-lineages in Bangladesh
10.1128/mra.00135-24 · External reference
The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan
10.1016/j.jiph.2024.102556 · External reference
Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations
10.1099/mgen.0.000991 · External reference
Genomic epidemiology reveals the variation and transmission properties of SARS-CoV-2 in a single-source community outbreak
10.1093/ve/veae085 · External reference
IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era
10.1093/molbev/msaa015 · External reference
Scalable relaxed clock phylogenetic dating
10.1093/ve/vex025 · External reference
Controlling the false discovery rate: a practical and powerful approach to multiple testing
10.1111/j.2517-6161.1995.tb02031.x · External reference
Unresolved reference
External reference
Building predictive models in R using the caret package
10.18637/jss.v028.i05 · External reference
Global lineage evolution pattern of SARS-CoV-2 in Africa, America, Europe, and Asia: a comparative analysis of variant clusters and their relevance across continents
10.2478/jtim-2023-0118 · External reference
Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2
10.7554/elife.94836 · External reference
Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons
10.1371/journal.pone.0261045 · External reference
Patient-related metadata reported in sequencing studies of SARS-CoV-2: protocol for a scoping review and bibliometric analysis
10.2196/58567 · External reference
Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data
10.1038/s41467-022-32812-0 · External reference
Automated encoding of clinical documents based on natural language processing
10.1197/jamia.m1552 · External reference
10.1101/2025.04.25.25326298
10.1101/2025.04.25.25326298 · External reference
SARS-CoV-2 evolution during prolonged infection in immunocompromised patients
10.1128/mbio.00110-24 · External reference
Two-step fitness selection for intra-host variations in SARS-CoV-2
10.1016/j.celrep.2021.110205 · External reference
Determinants of spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2
10.1016/j.chom.2022.07.006 · External reference
The D405N mutation in the spike protein of SARS-CoV-2 Omicron BA.5 inhibits spike/integrins interaction and viral infection of human lung microvascular endothelial cells
10.3390/v15020332 · External reference
Characterization of intrinsic and effective fitness changes caused by temporarily fixed mutations in the SARS-CoV-2 spike E484 epitope and identification of an epistatic precondition for the evolution of E484A in variant Omicron
10.1186/s12985-023-02154-4 · External reference
Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2
10.1038/s41586-021-04388-0 · External reference
Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations
10.1002/1873-3468.14076 · External reference
Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition
10.1016/j.chom.2020.11.007 · External reference
Longitudinal analysis of genomic mutations in SARS-CoV-2 isolates from persistent COVID-19 patient
10.1016/j.isci.2024.109597 · External reference
Manipulation of innate immune signaling pathways by SARS-CoV-2 non-structural proteins
10.3389/fmicb.2022.1027015 · External reference
The role of S477N mutation in the molecular behavior of SARS-CoV-2 spike protein: an in-silico perspective
10.1002/jcb.30367 · External reference
The SARS-CoV-2 Omicron BA.1 spike G446S mutation potentiates antiviral T-cell recognition
10.1038/s41467-022-33068-4 · External reference
SARS-CoV-2 Omicron variants harbor spike protein mutations responsible for their attenuated fusogenic phenotype
10.1038/s42003-023-04923-x · External reference
Future-proofing and maximizing the utility of metadata: the PHA4GE SARS-CoV-2 contextual data specification package
10.1093/gigascience/giac003 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
External reference
