R3NG9X last accessed: 2022-11-04

Other names: NCBI Virus Variation, Dengue Virus Database, Influenza Virus Database, Rotavirus Database, West Nile Virus Database

NCBI Virus is a community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories.

Webpage:

https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/

Licence:

Name: NCBI Data Policies and Disclaimer
URL: http://www.ncbi.nlm.nih.gov/home/about/policies.shtml

Publications:

Publications
More detailed information about this field from each metasource.

NCBI viral genomes resource
PMID: 25428358
metasource: Fairsharing.org
version: None

Virus Variation Resource - improved response to emergent viral outbreaks
PMID: 27899678
metasource: Fairsharing.org
version: None

NCBI viral genomes resource PubMed citations: 236.

236 articles citing: NCBI viral genomes resource

Development of a Multiepitope Vaccine Against SARS-CoV-2: Immunoinformatics Study. PMID:35891920
FnCas9 Editor Linked Uniform Detection Assay for COVID-19. PMID:35838958
Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1. PMID:35789859
Detection of Ancient Viruses and Long-Term Viral Evolution. PMID:35746807
Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples. PMID:35695508
Thompson loop: opportunities for antitubercular drug design by targeting the weak spot in demethylmenaquinone methyltransferase protein. PMID:35520325
Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica. PMID:35499326
Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis. PMID:35477737
AutoCoV: tracking the early spread of COVID-19 in terms of the spatial and temporal patterns from embedding space by K-mer based deep learning. PMID:35468739
An overview of dinucleotide and codon usage in all viruses. PMID:35467158
The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes. PMID:35435739
Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study. PMID:35356467
Designing sensitive viral diagnostics with machine learning. PMID:35241837
Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. PMID:35228751
Bacteriophages Roam the Wheat Phyllosphere. PMID:35215838
Using networks to analyze and visualize the distribution of overlapping genes in virus genomes. PMID:35202429
Combination of antiviral drugs inhibits SARS-CoV-2 polymerase and exonuclease and demonstrates COVID-19 therapeutic potential in viral cell culture. PMID:35194144
Genetic and biological characteristics of species A rotaviruses detected in common shrews suggest a distinct evolutionary trajectory. PMID:35169491
The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine. PMID:35165687
The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease. PMID:35092426
Conserved Motifs and Domains in Members of Pospiviroidae. PMID:35053346
Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes. PMID:35027677
Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes. PMID:35022216
Development of a Genomics-Based Approach To Identify Putative Hypervirulent Nontyphoidal Salmonella Isolates: Salmonella enterica Serovar Saintpaul as a Model. PMID:34986312
Deconvoluting virome-wide antibody epitope reactivity profiles. PMID:34922324
A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design. PMID:34914686
VDA-RWLRLS: An anti-SARS-CoV-2 drug prioritizing framework combining an unbalanced bi-random walk and Laplacian regularized least squares. PMID:34902608
GenBank. PMID:34850943
Transformation of Seed Non-Transmissible Hop Viroids in Nicotiana benthamiana Causes Distortions in Male Gametophyte Development. PMID:34834761
Correcting the Estimation of Viral Taxa Distributions in Next-Generation Sequencing Data after Applying Artificial Neural Networks. PMID:34828361
Feature-extraction and analysis based on spatial distribution of amino acids for SARS-CoV-2 Protein sequences. PMID:34815067
Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications. PMID:34798370
Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples. PMID:34790908
Virtual screening and in vitro validation identifies the first reported inhibitors of Salmonella enterica HPPK. PMID:34778775
Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog's lettuce (Groenlandia densa). PMID:34748577
DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes. PMID:34724822
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer. PMID:34718715
Distribution and Pathogenicity of Two Cutthroat Trout Virus (CTV) Genotypes in Canada. PMID:34578311
VGEA: an RNA viral assembly toolkit. PMID:34567846
STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. PMID:34544477
High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome. PMID:34526611
Whole-genome-based phylogenomic analysis of the Belgian 2016-2017 influenza A(H3N2) outbreak season allows improved surveillance. PMID:34477544
Predicting hosts based on early SARS-CoV-2 samples and analyzing the 2020 pandemic. PMID:34465838
Mutational spectrum of SARS-CoV-2 during the global pandemic. PMID:34453107
Moisture modulates soil reservoirs of active DNA and RNA viruses. PMID:34446837
Development of Novel PCR Assays for Improved Detection of Enterovirus D68. PMID:34432489
Simple Classification of RNA Sequences of Respiratory-Related Coronaviruses. PMID:34395967
Nanotechnology based solutions to combat zoonotic viruses with special attention to SARS, MERS, and COVID 19: Detection, protection and medication. PMID:34390768
A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. PMID:34379778
ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach. PMID:34370725
Bacteriophages of Thermophilic 'Bacillus Group' Bacteria-A Review. PMID:34361957
Lytic archaeal viruses infect abundant primary producers in Earth's crust. PMID:34330907
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. PMID:34320186
Seq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An in silico study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculations. PMID:34305174
Haploflow: strain-resolved de novo assembly of viral genomes. PMID:34281604
Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts. PMID:34262534
Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. PMID:34261503
AAV ablates neurogenesis in the adult murine hippocampus. PMID:34259630
Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses. PMID:34234921
Interplay between SARS-CoV-2-derived miRNAs, immune system, vitamin D pathway and respiratory system. PMID:34159729
Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom. PMID:34135876
Scaling relation between genome length and particle size of viruses provides insights into viral life history. PMID:34113814
FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. PMID:34106048
A novel piperazine derivative that targets hepatitis B surface antigen effectively inhibits tenofovir resistant hepatitis B virus. PMID:34083665
Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils. PMID:34077260
Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review. PMID:34073395
Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil. PMID:34006626
Identifying biases and their potential solutions in human microbiome studies. PMID:34006335
Transcription, mRNA Export, and Immune Evasion Shape the Codon Usage of Viruses. PMID:33988683
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities. PMID:33975974
VIRUSBreakend: Viral Integration Recognition Using Single Breakends. PMID:33973999
Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. PMID:33973215
Diversity and distribution of viruses inhabiting the deepest ocean on Earth. PMID:33972725
Learning vector quantization as an interpretable classifier for the detection of SARS-CoV-2 types based on their RNA sequences. PMID:33935376
Intrahost speciations and host switches played an important role in the evolution of herpesviruses. PMID:33927887
Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies. PMID:33875001
Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis. PMID:33866136
Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota. PMID:33808469
Clinical Experience of Cerebrospinal Fluid-Based Liquid Biopsy Demonstrates Superiority of Cell-Free DNA over Cell Pellet Genomic DNA for Molecular Profiling. PMID:33781965
Field-deployable, rapid diagnostic testing of saliva for SARS-CoV-2. PMID:33750853
Pattern of genomic variation in SARS-CoV-2 (COVID-19) suggests restricted nonrandom changes: Analysis using Shewhart control charts. PMID:33709963
High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. PMID:33614906
Massive expansion of human gut bacteriophage diversity. PMID:33606979
The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus. PMID:33596252
Complete Genome Sequence of a Phapecoctavirus Isolated from a Pigeon Cloacal Swab Sample. PMID:33541888
Haploflow: Strain-resolved de novo assembly of viral genomes. PMID:33532769
Cenote-Taker 2 democratizes virus discovery and sequence annotation. PMID:33505708
Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions. PMID:33452481
Viruses in Extreme Environments, Current Overview, and Biotechnological Potential. PMID:33430116
Identification and characterization of a silent mutation in RNA binding domain of N protein coding gene from SARS-CoV-2. PMID:33407800
Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family. PMID:33398323
Revisiting Orthotospovirus phylogeny using full-genome data and testing the contribution of selection, recombination and segment reassortment in the origin of members of new species. PMID:33394171
Virxicon: A Lexicon Of Viral Sequences. PMID:33367605
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. PMID:33279989
GenBank. PMID:33196830
Virome Sequencing of the Human Intestinal Mucosal-Luminal Interface. PMID:33194818
Systems Biology Approaches for Therapeutics Development Against COVID-19. PMID:33194800
Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies. PMID:33173909
The Presence of Human Herpesvirus 6 in the Brain in Health and Disease. PMID:33172107
Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PMID:33137082
Single Cell Genomics Reveals Viruses Consumed by Marine Protists. PMID:33072003
Evolutionary Analysis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Reveals Genomic Divergence with Implications for Universal Vaccine Efficacy. PMID:33050053
Automated download and clean-up of family-specific databases for kmer-based virus identification. PMID:33031509
Structural and Proteomic Studies of the Aureococcus anophagefferens Virus Demonstrate a Global Distribution of Virus-Encoded Carbohydrate Processing. PMID:33013751
From Orphan Phage to a Proposed New Family-the Diversity of N4-Like Viruses. PMID:33008130
A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data. PMID:33003197
Five Novel Non-Sialic Acid-Like Scaffolds Inhibit In Vitro H1N1 and H5N2 Neuraminidase Activity of Influenza a Virus. PMID:32947893
CoV-Seq, a New Tool for SARS-CoV-2 Genome Analysis and Visualization: Development and Usability Study. PMID:32931441
A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase. PMID:32908149
Enhanced Detection of DNA Viruses in the Cerebrospinal Fluid of Encephalitis Patients Using Metagenomic Next-Generation Sequencing. PMID:32903437
Insights into the Evolutionary Origin of Mediterranean Sandfly Fever Viruses. PMID:32878929
Development of a Fluorescence-Based, High-Throughput SARS-CoV-2 3CLpro Reporter Assay. PMID:32843534
Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model. PMID:32793490
NCBI Taxonomy: a comprehensive update on curation, resources and tools. PMID:32761142
Assessment of Metagenomic Sequencing and qPCR for Detection of Influenza D Virus in Bovine Respiratory Tract Samples. PMID:32731471
Machine-learning approach expands the repertoire of anti-CRISPR protein families. PMID:32728052
Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease-Paving the Way for Vaccine Development. PMID:32717854
Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products. PMID:32713863
Computational approaches in viral ecology. PMID:32670501
Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents. PMID:32665274
Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. PMID:32627830
Whole genome sequencing identifies an allele responsible for clear vs. turbid plaque morphology in a Mycobacteriophage. PMID:32513117
A tissue level atlas of the healthy human virome. PMID:32493363
Predicting host taxonomic information from viral genomes: A comparison of feature representations. PMID:32453718
An effective CTL peptide vaccine for Ebola Zaire Based on Survivors' CD8+ targeting of a particular nucleocapsid protein epitope with potential implications for COVID-19 vaccine design. PMID:32418793
Phages Actively Challenge Niche Communities in Antarctic Soils. PMID:32371471
Massively multiplexed nucleic acid detection with Cas13. PMID:32349121
Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient. PMID:32336957
Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins. PMID:32218151
Experimental Evolution To Isolate Vaccinia Virus Adaptive G9 Mutants That Overcome Membrane Fusion Inhibition via the Vaccinia Virus A56/K2 Protein Complex. PMID:32132237
Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities. PMID:32075851
Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments. PMID:32071164
Variant morphology and random chromosomal integration of BK polyomavirus in posttransplant urothelial carcinomas. PMID:32047230
The evolution of protein domain repertoires: Shedding light on the origins of the Herpesviridae family. PMID:32042448
Discovery of several thousand highly diverse circular DNA viruses. PMID:32014111
LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins. PMID:32003788
Intratumoral heterogeneity and clonal evolution in liver cancer. PMID:31941899
The Microbiota in Hematologic Malignancies. PMID:31927673
Full genomic characterization of a porcine rotavirus strain detected in an asymptomatic piglet in Accra, Ghana. PMID:31924206
Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions. PMID:31866953
Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust. PMID:31848272
Exploiting the Feedstock Flexibility of the Emergent Synthetic Biology Chassis Vibrio natriegens for Engineered Natural Product Production. PMID:31801279
Are viral-infections associated with Ménière's Disease? A systematic review and meta-analysis of molecular-markers of viral-infection in case-controlled observational studies of MD. PMID:31756230
The pulmonary virome, bacteriological and histopathological findings in bovine respiratory disease from western Canada. PMID:31715071
Studying the gut virome in the metagenomic era: challenges and perspectives. PMID:31660953
Molecular characterization and In Vitro synthesis of infectious RNA of a Turnip vein-clearing virus isolated from Alliaria petiolata in Hungary. PMID:31648277
Prediction of microbial communities for urban metagenomics using neural network approach. PMID:31639050
Programmable Inhibition and Detection of RNA Viruses Using Cas13. PMID:31607545
Database resources of the National Center for Biotechnology Information. PMID:31602479
Endogenous Avian Leukosis Virus in Combination with Serotype 2 Marek's Disease Virus Significantly Boosted the Incidence of Lymphoid Leukosis-Like Bursal Lymphomas in Susceptible Chickens. PMID:31554689
A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process. PMID:31534042
Sequence determinants of polyadenylation-mediated regulation. PMID:31530582
DisCVR: Rapid viral diagnosis from high-throughput sequencing data. PMID:31528358
NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. PMID:31527408
Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds. PMID:31440273
Genomic detection and molecular characterization of two distinct isolates of cycas necrotic stunt virus from Paeonia suffruticosa and Daphne odora. PMID:31352619
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. PMID:31332386
Highly conserved influenza T cell epitopes induce broadly protective immunity. PMID:31331771
Harnessing host-virus evolution in antiviral therapy and immunotherapy. PMID:31312450
High-Throughput Sequencing Analysis of Small RNAs Derived from Coleus Blumei Viroids. PMID:31284471
Phages and Human Health: More Than Idle Hitchhikers. PMID:31252683
Vaccinia viral A26 protein is a fusion suppressor of mature virus and triggers membrane fusion through conformational change at low pH. PMID:31220181
Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches. PMID:31201356
Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains. PMID:31150425
Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages. PMID:31127947
DNAscan: personal computer compatible NGS analysis, annotation and visualisation. PMID:31029080
Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease. PMID:30873724
Piscine orthoreovirus demonstrates high infectivity but low virulence in Atlantic salmon of Pacific Canada. PMID:30867461
Vgas: A Viral Genome Annotation System. PMID:30814982
Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. PMID:30718881
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. PMID:30661755
Reduced bonobo MHC class I diversity predicts a reduced viral peptide binding ability compared to chimpanzees. PMID:30630404
Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species. PMID:30597118
A longitudinal systems immunologic investigation of acute Zika virus infection in an individual infected while traveling to Caracas, Venezuela. PMID:30596671
Minimum Information about an Uncultivated Virus Genome (MIUViG). PMID:30556814
Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution. PMID:30456441
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. PMID:30445993
Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research. PMID:30412219
Database resources of the National Center for Biotechnology Information. PMID:30395293
A planarian nidovirus expands the limits of RNA genome size. PMID:30383829
Metagenomic Sequencing of HIV-1 in the Blood and Female Genital Tract Reveals Little Quasispecies Diversity during Acute Infection. PMID:30381486
A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage. PMID:30352623
Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes. PMID:30339683
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. PMID:30320215
Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection. PMID:30262776
Genome-wide diversity in temporal and regional populations of the betabaculovirus Erinnyis ello granulovirus (ErelGV). PMID:30249206
Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes. PMID:30231528
Usability of the international HAVNet hepatitis A virus database for geographical annotation, backtracing and outbreak detection. PMID:30229723
Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. PMID:30126456
Integrated analysis of the impact of age on genetic and clinical aspects of hepatocellular carcinoma. PMID:30125264
Predicting MicroRNA Mediated Gene Regulation between Human and Viruses. PMID:30096814
Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus. PMID:29937276
Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses. PMID:29795788
Reproducible protocols for metagenomic analysis of human faecal phageomes. PMID:29631623
A comprehensive and quantitative exploration of thousands of viral genomes. PMID:29624169
A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection. PMID:29564396
The End of a 60-year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton. PMID:29487186
Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs. PMID:29354101
ReprDB and panDB: minimalist databases with maximal microbial representation. PMID:29347966
MVP: a microbe-phage interaction database. PMID:29177508
Do Viruses Exchange Genes across Superkingdoms of Life? PMID:29163404
Coral-associated viral communities show high levels of diversity and host auxiliary functions. PMID:29158985
Proofreading-Deficient Coronaviruses Adapt for Increased Fitness over Long-Term Passage without Reversion of Exoribonuclease-Inactivating Mutations. PMID:29114026
A review of methods and databases for metagenomic classification and assembly. PMID:29028872
Identification of sapovirus GV.2, astrovirus VA3 and novel anelloviruses in serum from patients with acute hepatitis of unknown aetiology. PMID:28982120
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs. PMID:28957499
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
RNA-Seq investigations of human post-mortem trigeminal ganglia. PMID:28699403
A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections. PMID:28662150
Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs. PMID:28586923
Zika virus evolution and spread in the Americas. PMID:28538734
In silico approach to designing rational metagenomic libraries for functional studies. PMID:28532384
Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses. PMID:28492506
drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes. PMID:28369462
How to Name and Classify Your Phage: An Informal Guide. PMID:28368359
Intracellular HIV-1 RNA and CD4+ T-cell activation in patients starting antiretrovirals. PMID:28358734
The blood DNA virome in 8,000 humans. PMID:28328962
Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. PMID:28102365
viruSITE-integrated database for viral genomics. PMID:28025349
Virus Variation Resource - improved response to emergent viral outbreaks. PMID:27899678
MRPrimerV: a database of PCR primers for RNA virus detection. PMID:27899620
Pharmacometabolomics Informs Viromics toward Precision Medicine. PMID:27833560
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. PMID:27789703
Identification of a Lineage D Betacoronavirus in Cave Nectar Bats (Eonycteris spelaea) in Singapore and an Overview of Lineage D Reservoir Ecology in SE Asian Bats. PMID:27637887
Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients. PMID:27618896
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts. PMID:27375564
Twenty-Five New Viruses Associated with the Drosophilidae (Diptera). PMID:27375356
Aberrant PD-L1 expression through 3'-UTR disruption in multiple cancers. PMID:27281199
Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing. PMID:26709640
Database resources of the National Center for Biotechnology Information. PMID:26615191
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. PMID:26553804
Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells. PMID:26550473
Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy. PMID:26370248
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. PMID:26137199
Advanced molecular surveillance of hepatitis C virus. PMID:25781918
Are arthropods at the heart of virus evolution? PMID:25751043
Virus Variation Resource - improved response to emergent viral outbreaks PubMed citations: 132.

132 articles citing: Virus Variation Resource - improved response to emergent viral outbreaks

Daily Reports on Phage-Host Interactions. PMID:35910653
SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development. PMID:35903104
Epidemiology of Mosquito-Borne Viruses in Egypt: A Systematic Review. PMID:35891557
Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants. PMID:35891459
The past, current and future epidemiological dynamic of SARS-CoV-2. PMID:35872966
Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina. PMID:35836127
Conserved recombination patterns across coronavirus subgenera. PMID:35814334
The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance. PMID:35758819
Revolutionized virome research using systems microbiology approaches. PMID:35723062
Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens. PMID:35664829
CoV2K model, a comprehensive representation of SARS-CoV-2 knowledge and data interplay. PMID:35650205
Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches. PMID:35639694
Word2vec neural model-based techniqueto generate protein vectors for combating COVID-19: a machine learning approach. PMID:35611155
Databases, Knowledgebases, and Software Tools for Virus Informatics. PMID:35594018
NGS data vectorization, clustering, and finding key codons in SARS-CoV-2 variations. PMID:35581558
AutoCoV: tracking the early spread of COVID-19 in terms of the spatial and temporal patterns from embedding space by K-mer based deep learning. PMID:35468739
Open reading frame dominance indicates protein-coding potential of RNAs. PMID:35438231
A Novel Lineage of Cile-Like Viruses Discloses the Phylogenetic Continuum Across the Family Kitaviridae. PMID:35418952
Global landscape of SARS-CoV-2 genomic surveillance and data sharing. PMID:35347305
Study of the SARS-CoV-2 genomic data generation to evaluate the introduction of genomics in epidemiological surveillance and public health decision making. PMID:35317482
Phages and their satellites encode hotspots of antiviral systems. PMID:35316646
Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning? PMID:35225672
Virtual Screening of Drug-Like Compounds as Potential Inhibitors of the Dengue Virus NS5 Protein. PMID:35223766
Identifying Inhibitors of -1 Programmed Ribosomal Frameshifting in a Broad Spectrum of Coronaviruses. PMID:35215770
The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine. PMID:35165687
Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic. PMID:35134624
Evolution of Viral Pathogens Follows a Linear Order. PMID:35107326
Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction. PMID:35106601
DeLUCS: Deep learning for unsupervised clustering of DNA sequences. PMID:35061715
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. PMID:35042229
Heptad stereotypy, S/Q layering, and remote origin of the SARS-CoV-2 fusion core. PMID:35039783
Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes. PMID:35022216
Comparison of COVID-19 laboratory diagnosis by commercial kits: Effectivity of RT-PCR to the RT-LAMP. PMID:34997587
Distinct codon usage bias evolutionary patterns between weakly and strongly virulent respiratory viruses. PMID:34977494
Evidence for a mouse origin of the SARS-CoV-2 Omicron variant. PMID:34954396
Identification of HLA-A*24:02-Restricted CTL Candidate Epitopes Derived from the Nonstructural Polyprotein 1a of SARS-CoV-2 and Analysis of Their Conservation Using the Mutation Database of SARS-CoV-2 Variants. PMID:34937174
HLA-A∗02:01 restricted T cell receptors against the highly conserved SARS-CoV-2 polymerase cross-react with human coronaviruses. PMID:34919800
Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk. PMID:34896769
Development of Inactivated FAKHRAVAC® Vaccine against SARS-CoV-2 Virus: Preclinical Study in Animal Models. PMID:34835202
Whole-Genome Sequences of SARS-CoV-2 Isolates from the Dominican Republic. PMID:34817214
Feature-extraction and analysis based on spatial distribution of amino acids for SARS-CoV-2 Protein sequences. PMID:34815067
PCR Primer Design for the Rapidly Evolving SARS-CoV-2 Genome. PMID:34773624
ViroidDB: a database of viroids and viroid-like circular RNAs. PMID:34751403
MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors. PMID:34750626
RESCRIPt: Reproducible sequence taxonomy reference database management. PMID:34748542
Cross-reactivity and inclusivity analysis of CRISPR-based diagnostic assays of coronavirus SARS-CoV-2. PMID:34703657
Global landscape of SARS-CoV-2 genomic surveillance, public availability extent of genomic data, and epidemic shaped by variants. PMID:34611660
A prenylated dsRNA sensor protects against severe COVID-19. PMID:34581622
Whole Genome Analysis of Human Rotaviruses Reveals Single Gene Reassortant Rotavirus Strains in Zambia. PMID:34578453
Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes. PMID:34578371
Dengue Virus Serotype 1 Conformational Dynamics Confers Virus Strain-Dependent Patterns of Neutralization by Polyclonal Sera. PMID:34549976
Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. PMID:34438144
A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome. PMID:34433827
Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. PMID:34271250
Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane. PMID:34255499
Dengue Virus is Hyperendemic in Nigeria from 2009 to 2020: A Contemporary Systematic Review. PMID:34216122
Cardiomyopathy and Death Following Chikungunya Infection: An Increasingly Common Outcome. PMID:34206332
Genome Warehouse: A Public Repository Housing Genome-scale Data. PMID:34175476
Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). PMID:34131209
The pattern of human papillomavirus infection and genotypes among Nigerian women from 1999 to 2019: a systematic review. PMID:34124973
VirusViz: comparative analysis and effective visualization of viral nucleotide and amino acid variants. PMID:34107016
Molecular Epidemiology of Citrus Leprosis Virus C: A New Viral Lineage and Phylodynamic of the Main Viral Subpopulations in the Americas. PMID:33995302
Protein Intrinsic Disorder and Evolvability of MERS-CoV. PMID:33923962
Sofosbuvir Selects for Drug-Resistant Amino Acid Variants in the Zika Virus RNA-Dependent RNA-Polymerase Complex In Vitro. PMID:33800884
The human virome: assembly, composition and host interactions. PMID:33785903
Field-deployable, rapid diagnostic testing of saliva for SARS-CoV-2. PMID:33750853
The Missing Expression Level-Evolutionary Rate Anticorrelation in Viruses Does Not Support Protein Function as a Main Constraint on Sequence Evolution. PMID:33713114
Significant non-existence of sequences in genomes and proteomes. PMID:33693858
Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter. PMID:33677572
Evaluation of the Sequence Variability within the PCR Primer/Probe Target Regions of the SARS-CoV-2 Genome. PMID:33659508
Therapeutic targeting of measles virus polymerase with ERDRP-0519 suppresses all RNA synthesis activity. PMID:33621266
A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses. PMID:33615042
Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires. PMID:33590101
Epitope mimicry analysis of SARS-COV-2 surface proteins and human lung proteins. PMID:33588349
An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. PMID:33479725
Bioinformatics resources for SARS-CoV-2 discovery and surveillance. PMID:33416890
The Skin Interactome: A Holistic "Genome-Microbiome-Exposome" Approach to Understand and Modulate Skin Health and Aging. PMID:33380819
A review on viral data sources and search systems for perspective mitigation of COVID-19. PMID:33348368
Application of CRISPR/Cas9 in Understanding Avian Viruses and Developing Poultry Vaccines. PMID:33330126
NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index. PMID:33322070
A computational approach to design potential siRNA molecules as a prospective tool for silencing nucleocapsid phosphoprotein and surface glycoprotein gene of SARS-CoV-2. PMID:33321203
Next-generation computational tools and resources for coronavirus research: From detection to vaccine discovery. PMID:33301953
Distribution pattern and prevalence of West Nile virus infection in Nigeria from 1950 to 2020: a systematic review. PMID:33254358
Computational Analysis of Targeting SARS-CoV-2, Viral Entry Proteins ACE2 and TMPRSS2, and Interferon Genes by Host MicroRNAs. PMID:33207533
Systems Biology Approaches for Therapeutics Development Against COVID-19. PMID:33194800
Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens. PMID:33103064
NCAM protein and SARS-COV-2 surface proteins: In-silico hypothetical evidence for the immunopathogenesis of Guillain-Barré syndrome. PMID:33069093
Virus database annotations assist in tracing information on patients infected with emerging pathogens. PMID:33052312
ViruSurf: an integrated database to investigate viral sequences. PMID:33045721
Potential role of cellular miRNAs in coronavirus-host interplay. PMID:32983652
Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design. PMID:32973171
A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2. PMID:32919067
Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike. PMID:32913581
CoV3D: a database of high resolution coronavirus protein structures. PMID:32890396
Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro. PMID:32853525
Time-series analyses of directional sequence changes in SARS-CoV-2 genomes and an efficient search method for candidates for advantageous mutations for growth in human cells. PMID:32835214
SARS-CoV-2 ORF8 and SARS-CoV ORF8ab: Genomic Divergence and Functional Convergence. PMID:32825438
Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products. PMID:32713863
Phylogenetic Analyses of Rotavirus A from Cattle in Uruguay Reveal the Circulation of Common and Uncommon Genotypes and Suggest Interspecies Transmission. PMID:32674420
A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2. PMID:32665985
Middle East Respiratory Syndrome Coronavirus (MERS-CoV): State of the Science. PMID:32630780
CoV3D: A database and resource for high resolution coronavirus protein structures. PMID:32577656
Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs. PMID:32575728
Targeting the SARS-CoV-2 spike glycoprotein prefusion conformation: virtual screening and molecular dynamics simulations applied to the identification of potential fusion inhibitors. PMID:32565126
The application of DNA nucleotide footprint plotting in coronavirus. PMID:32542185
Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach. PMID:32502733
VADR: validation and annotation of virus sequence submissions to GenBank. PMID:32448124
Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites. PMID:32363136
Immunogenicity and Efficacy of a Recombinant Human Adenovirus Type 5 Vaccine against Zika Virus. PMID:32272595
High-Throughput Fluorescence-Based Screen Identifies the Neuronal MicroRNA miR-124 as a Positive Regulator of Alphavirus Infection. PMID:32102877
The origins of dengue and chikungunya viruses in Ecuador following increased migration from Venezuela and Colombia. PMID:32075576
Intragenic recombination influences rotavirus diversity and evolution. PMID:31949920
Database resources of the National Center for Biotechnology Information. PMID:31602479
FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. PMID:31346170
Risk assessment and genomic characterization of Zika virus in China and its surrounding areas. PMID:31268910
Genetic analysis of Ghanaian G1P[8] and G9P[8] rotavirus A strains reveals the impact of P[8] VP4 gene polymorphism on P-genotyping. PMID:31242245
Whole genome characterization and evolutionary analysis of OP354-like P[8] Rotavirus A strains isolated from Ghanaian children with diarrhoea. PMID:31199823
Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains. PMID:31150425
Immunogenicity of Different Forms of Middle East Respiratory Syndrome S Glycoprotein. PMID:31024747
Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance. PMID:30728194
Epidemiology of West Nile Virus in the Eastern Mediterranean region: A systematic review. PMID:30695031
Simultaneous Detection of Different Zika Virus Lineages via Molecular Computation in a Point-of-Care Assay. PMID:30558136
Terrestrial Bird Migration and West Nile Virus Circulation, United States. PMID:30457531
A protective human monoclonal antibody targeting the West Nile virus E protein preferentially recognizes mature virions. PMID:30455471
Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research. PMID:30412219
Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop. PMID:30258051
Targeting intramolecular proteinase NS2B/3 cleavages for trans-dominant inhibition of dengue virus. PMID:30228122
Molecular characterisation of rotavirus strains detected during a clinical trial of the human neonatal rotavirus vaccine (RV3-BB) in Indonesia. PMID:30145099
Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs. PMID:29354101
Database resources of the National Center for Biotechnology Information. PMID:29140470
Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral". PMID:29029728
Zika genomics urgently need standardized and curated reference sequences. PMID:28880955

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curated information
metasource: Fairsharing.org
version: None

dna sequence data
metasource: Fairsharing.org
version: None

protein
metasource: Fairsharing.org
version: None

rna sequence
metasource: Fairsharing.org
version: None

viral sequence
metasource: Fairsharing.org
version: None

dengue viruses
metasource: re3data.org
version: re3data.org: NCBI Virus Variation; editing status 2020-09-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NG9X last accessed: 2022-11-04

rotaviruses
metasource: re3data.org
version: re3data.org: NCBI Virus Variation; editing status 2020-09-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NG9X last accessed: 2022-11-04

west nile virus
metasource: re3data.org
version: re3data.org: NCBI Virus Variation; editing status 2020-09-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NG9X last accessed: 2022-11-04

influenza viruses
metasource: re3data.org
version: re3data.org: NCBI Virus Variation; editing status 2020-09-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NG9X last accessed: 2022-11-04

virus sequence
metasource: re3data.org
version: re3data.org: NCBI Virus Variation; editing status 2020-09-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NG9X last accessed: 2022-11-04

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