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Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

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What this work says

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

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High throughput sequencing reveals diversity of Human Papillomaviruses in cutaneous lesions

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Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure

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Merkel Cell Polyomavirus and Two Previously Unknown Polyomaviruses Are Chronically Shed from Human Skin

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Ultra-deep sequencing for the analysis of viral populations

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Human papillomavirus genotyping by 454 next generation sequencing technology

inferredcites →https://doi.org/10.1016/j.nbt.2008.12.009openalex-snapshot

Next-generation DNA sequencing techniques

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New dimensions of the virus world discovered through metagenomics

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Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses

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Clinical resistance to vicriviroc through adaptive V3 loop mutations in HIV-1 subtype D gp120 that alter interactions with the N-terminus and ECL2 of CCR5

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Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments

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Identification of HIV integration sites in infected host genomic DNA

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Pathogen discovery from human tissue by sequence-based computational subtraction

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Rapid viral quasispecies evolution: implications for vaccine and drug strategies

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Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease

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Lentivirus-mediated Reprogramming of Somatic Cells in the Absence of Transgenic Transcription Factors

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The Human Microbiome Project

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Viruses in the faecal microbiota of monozygotic twins and their mothers

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Next-generation DNA sequencing

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Identification of foreign gene sequences by transcript filtering against the human genome

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Comprehensive genomic access to vector integration in clinical gene therapy

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Identification of a new human coronavirus

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High-resolution insertion-site analysis by linear amplification–mediated PCR (LAM-PCR)

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Sequencing technologies — the next generation

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Genome-wide analysis of retroviral DNA integration

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Microbiology in the post-genomic era

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In the News

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Cloning of a human parvovirus by molecular screening of respiratory tract samples

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Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs

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Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines

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Direction of transneuronal transport of herpes simplex virus 1 in the primate motor system is strain-dependent.

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Identification of two flavivirus-like genomes in the GB hepatitis agent.

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Minority Quasispecies of Drug‐Resistant HIV‐1 That Lead to Early Therapy Failure in Treatment‐Naive and ‐Adherent Patients

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Transmission of HIV‐1 Drug‐Resistant Variants: Prevalence and Effect on Treatment Outcome

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HIV Type 1 from a Patient with Baseline Resistance to CCR5 Antagonists Uses Drug-Bound Receptor for Entry

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Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

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A window into third-generation sequencing

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DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations

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Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

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A method to sequence and quantify DNA integration for monitoring outcome in gene therapy

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Detection of Minority Populations of HIV-1 Expressing the K103N Resistance Mutation in Patients Failing Nevirapine

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Transmission of HIV-1 minority-resistant variants and response to first-line antiretroviral therapy

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Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing

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Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection

inferredcites →https://doi.org/10.1097/qad.0b013e32834b34deopenalex-snapshot

Switching between raltegravir resistance pathways analyzed by deep sequencing

inferredcites →https://doi.org/10.1099/vir.0.009381-0openalex-snapshot

Improved strategies for sequence-independent amplification and sequencing of viral double-stranded RNA genomes

inferredcites →https://doi.org/10.1099/vir.0.024612-0openalex-snapshot

Metagenomic sequencing for virus identification in a public-health setting

inferredcites →https://doi.org/10.1101/gr.085464.108openalex-snapshot

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

inferredcites →https://doi.org/10.1101/gr.180501openalex-snapshot

Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification

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HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications

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Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance

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Metagenomic analysis of viruses in reclaimed water

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Direct pathogen detection from swab samples using a new high-throughput sequencing technology

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Viral metagenome analysis to guide human pathogen monitoring in environmental samples

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Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma

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High Diversity of the Viral Community from an Antarctic Lake

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Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

inferredcites →https://doi.org/10.1126/science.1905842openalex-snapshot

Identification of the Envelope V3 Loop as the Primary Determinant of Cell Tropism in HIV-1

inferredcites →https://doi.org/10.1126/science.7997879openalex-snapshot

Identification of Herpesvirus-Like DNA Sequences in AIDS-Sssociated Kaposi's Sarcoma

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Comparative Study of the Genetic Barriers and Pathways towards Resistance of Selective Inhibitors of Hepatitis C Virus Replication

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Unbiased Parallel Detection of Viral Pathogens in Clinical Samples by Use of a Metagenomic Approach

inferredcites →https://doi.org/10.1128/jcm.00804-11openalex-snapshot

Identification of HIV Superinfection in Seroconcordant Couples in Rakai, Uganda, by Use of Next-Generation Deep Sequencing

inferredcites →https://doi.org/10.1128/jcm.00850-11openalex-snapshot

Evaluation of High-Throughput Sequencing for Identifying Known and Unknown Viruses in Biological Samples

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Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experienced Patients Are Missed by Standard Genotype Analysis

inferredcites →https://doi.org/10.1128/jvi.00028-07openalex-snapshot

Identification of a Third Human Polyomavirus

inferredcites →https://doi.org/10.1128/jvi.00312-10openalex-snapshot

Sequence Variability in Clinical and Laboratory Isolates of Herpes Simplex Virus 1 Reveals New Mutations

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In Vivo Emergence of Vicriviroc Resistance in a Human Immunodeficiency Virus Type 1 Subtype C-Infected Subject

inferredcites →https://doi.org/10.1128/jvi.00475-10openalex-snapshot

Deep Sequencing Reveals Highly Complex Dynamics of Human Cytomegalovirus Genotypes in Transplant Patients over Time

inferredcites →https://doi.org/10.1128/jvi.00698-10openalex-snapshot

Human Enterovirus 109: a Novel Interspecies Recombinant Enterovirus Isolated from a Case of Acute Pediatric Respiratory Illness in Nicaragua

inferredcites →https://doi.org/10.1128/jvi.01109-10openalex-snapshot

A Maraviroc-Resistant HIV-1 with Narrow Cross-Resistance to Other CCR5 Antagonists Depends on both N-Terminal and Extracellular Loop Domains of Drug-Bound CCR5

inferredcites →https://doi.org/10.1128/jvi.01217-10openalex-snapshot

Tracking the Evolution of MultipleIn VitroHepatitis C Virus Replicon Variants under Protease Inhibitor Selection Pressure by 454 Deep Sequencing

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A Novel Human Polyomavirus Closely Related to the African Green Monkey-Derived Lymphotropic Polyomavirus

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Memory in Viral Quasispecies

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inferredcites →https://doi.org/10.1128/jvi.79.13.8230-8236.2005openalex-snapshot

New DNA Viruses Identified in Patients with Acute Viral Infection Syndrome

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Identification of a Severe Acute Respiratory Syndrome Coronavirus-Like Virus in a Leaf-Nosed Bat in Nigeria

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Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1

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Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients

inferredcites →https://doi.org/10.1182/blood-2010-05-283523openalex-snapshot

High-definition mapping of retroviral integration sites identifies active regulatory elements in human multipotent hematopoietic progenitors

inferredcites →https://doi.org/10.1186/1471-2105-12-38openalex-snapshot

Removing Noise From Pyrosequenced Amplicons

inferredcites →https://doi.org/10.1186/1471-2105-12-5openalex-snapshot

Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing

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Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of Iridoviridae

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The complete genome of klassevirus – a novel picornavirus in pediatric stool

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Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing

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Evaluation of next generation sequencing platforms for population targeted sequencing studies

inferredcites →https://doi.org/10.1371/journal.pbio.0000002openalex-snapshot

Viral Discovery and Sequence Recovery Using DNA Microarrays

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The Marine Viromes of Four Oceanic Regions

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Viral Population Estimation Using Pyrosequencing

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Minority HIV-1 Drug Resistance Mutations Are Present in Antiretroviral Treatment–Naïve Populations and Associate with Reduced Treatment Efficacy

inferredcites →https://doi.org/10.1371/journal.pntd.0000878openalex-snapshot

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Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach

inferredcites →https://doi.org/10.1371/journal.pone.0005683openalex-snapshot

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Low-Abundance HIV Drug-Resistant Viral Variants in Treatment-Experienced Persons Correlate with Historical Antiretroviral Use

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inferredcites →https://doi.org/10.1371/journal.pone.0013381openalex-snapshot

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A Comprehensive Deep Sequencing Strategy for Full-Length Genomes of Influenza A

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Rhinovirus Genome Variation during Chronic Upper and Lower Respiratory Tract Infections

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Performance of Ultra-Deep Pyrosequencing in Analysis of HIV-1 pol Gene Variation

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Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections

inferredcites →https://doi.org/10.1371/journal.ppat.1000011openalex-snapshot

Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

inferredcites →https://doi.org/10.1371/journal.ppat.1000455openalex-snapshot

Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa

inferredcites →https://doi.org/10.1371/journal.ppat.1001005openalex-snapshot

Quasispecies Theory and the Behavior of RNA Viruses

inferredcites →https://doi.org/10.1371/journal.ppat.1001024openalex-snapshot

Discovery of a New Human Polyomavirus Associated with Trichodysplasia Spinulosa in an Immunocompromized Patient

inferredcites →https://doi.org/10.1371/journal.ppat.1001344openalex-snapshot

Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants

inferredcites →https://doi.org/10.1371/journal.ppat.1002106openalex-snapshot

Detection of Inferred CCR5- and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing

inferredcites →https://doi.org/10.1371/journal.ppat.1002243openalex-snapshot

Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection

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Metagenomic Pyrosequencing and Microbial Identification

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Fibroblast-Derived Induced Pluripotent Stem Cells Show No Common Retroviral Vector Insertions

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Metagenomics for the Discovery of Novel Human Viruses

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Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases

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Astrovirus Encephalitis in Boy with X-linked Agammaglobulinemia

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Human Polyomavirus Related to African Green Monkey Lymphotropic Polyomavirus

What points at this work

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

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inferred← citeshttps://doi.org/10.1007/978-981-16-4554-9_5openalex-snapshot

Avian Influenza

inferred← citeshttps://doi.org/10.1007/978-981-33-6191-1_14openalex-snapshot

Next Generation Sequencing

inferred← citeshttps://doi.org/10.1007/978-981-92-0533-2_1openalex-snapshot

Next-Generation Sequencing for Plant Genomics

inferred← citeshttps://doi.org/10.1007/978-981-99-8369-8_23openalex-snapshot

Using Next Generation Sequencing to Evaluate the Genetic Mutations Responsible for Increased Antimicrobial Resistance in Escherichia Coli

inferred← citeshttps://doi.org/10.1007/s00284-023-03451-5openalex-snapshot

Recent Advances in Metagenomic Approaches, Applications, and Challenges

inferred← citeshttps://doi.org/10.1007/s00414-019-02124-yopenalex-snapshot

Optimizing DNA recovery and forensic typing of degraded blood and dental remains using a specialized extraction method, comprehensive qPCR sample characterization, and massively parallel sequencing

inferred← citeshttps://doi.org/10.1007/s00586-021-07026-5openalex-snapshot

The potential of metagenomic next-generation sequencing in diagnosis of spinal infection: a retrospective study

inferred← citeshttps://doi.org/10.1007/s00586-026-09806-3openalex-snapshot

Clinical utility of metagenomic next-generation sequencing in diagnosing spinal infections: a systematic review and meta-analysis

inferred← citeshttps://doi.org/10.1007/s00705-016-2871-2openalex-snapshot

Beak and feather disease virus in wild and captive parrots: an analysis of geographic and taxonomic distribution and methodological trends

inferred← citeshttps://doi.org/10.1007/s10529-014-1635-xopenalex-snapshot

Principles and application of antibody libraries for infectious diseases

inferred← citeshttps://doi.org/10.1007/s13337-013-0133-4openalex-snapshot

Applications of Next Generation High Throughput Sequencing Technologies in Characterization, Discovery and Molecular Interaction of Plant Viruses

inferred← citeshttps://doi.org/10.1007/s13337-017-0415-3openalex-snapshot

Application of viromics: a new approach to the understanding of viral infections in humans

inferred← citeshttps://doi.org/10.1007/s40265-016-0685-xopenalex-snapshot

Genotype 3 Infection: The Last Stand of Hepatitis C Virus

inferred← citeshttps://doi.org/10.1007/s43538-022-00098-xopenalex-snapshot

The application of next generation sequencing technology in medical diagnostics: a perspective

inferred← citeshttps://doi.org/10.1016/b978-0-12-384890-1.00027-3openalex-snapshot

Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology

inferred← citeshttps://doi.org/10.1016/b978-0-12-799942-5.00026-3openalex-snapshot

Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology

inferred← citeshttps://doi.org/10.1016/b978-0-12-805306-5.00003-1openalex-snapshot

Laboratory Diagnostics

inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20114-3openalex-snapshot

Genetics and Population Analysis

inferred← citeshttps://doi.org/10.1016/b978-0-12-813679-9.00007-5openalex-snapshot

Pathogen Identification Using Novel Sequencing Methods

inferred← citeshttps://doi.org/10.1016/b978-0-12-814515-9.00124-7openalex-snapshot

Sequencing Strategies

inferred← citeshttps://doi.org/10.1016/b978-0-12-816352-8.00002-3openalex-snapshot

Metagenomics revealing new virus species in farm and pet animals and aquaculture

inferred← citeshttps://doi.org/10.1016/b978-0-12-821406-0.00016-3openalex-snapshot

Recent developments in detection and diagnosis of plant viruses

inferred← citeshttps://doi.org/10.1016/b978-0-12-824315-2.01188-xopenalex-snapshot

Next generation sequencing in toxicology

inferred← citeshttps://doi.org/10.1016/b978-0-323-88464-8.00018-xopenalex-snapshot

Computational biology and biosensors as surveillance tools for emerging and re-emerging infectious diseases

inferred← citeshttps://doi.org/10.1016/b978-0-323-90261-8.00013-4openalex-snapshot

Gut microbe interactions: roles, benefits, and applications

inferred← citeshttps://doi.org/10.1016/b978-0-323-91900-5.00017-5openalex-snapshot

Depleted mineralization of pesticides on soil microbial diversity

inferred← citeshttps://doi.org/10.1016/b978-0-443-13659-7.00008-4openalex-snapshot

Next-generation sequencing technologies for microbial communities’ identification and characterization from aquatic and soil ecosystems for integrated management

inferred← citeshttps://doi.org/10.1016/b978-0-443-21980-1.00002-4openalex-snapshot

Genome-based approaches for disease diagnosis

inferred← citeshttps://doi.org/10.1016/b978-0-444-63492-4.00008-3openalex-snapshot

Big Data Applications in Health Sciences and Epidemiology

inferred← citeshttps://doi.org/10.1016/bs.agron.2021.02.002openalex-snapshot

Application of molecular biotechnology to manage biotic stress affecting crop enhancement and sustainable agriculture

inferred← citeshttps://doi.org/10.1016/bs.aivir.2017.08.004openalex-snapshot

Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”

inferred← citeshttps://doi.org/10.1016/bs.mcb.2022.02.001openalex-snapshot

Discovery of Virus-Host interactions using bioinformatic tools

inferred← citeshttps://doi.org/10.1016/j.actatropica.2022.106500openalex-snapshot

Description of the mitogenome and phylogeny of Aedes spp. (Diptera: Culicidae) from the Amazon region

inferred← citeshttps://doi.org/10.1016/j.actatropica.2025.107601openalex-snapshot

Sequencing and description of mitochondrial genome of Coquillettidia venezuelensis, Trichoprosopon digitatum and Uranotaenia calosomata (Diptera: Culicidae)

inferred← citeshttps://doi.org/10.1016/j.arcmed.2018.01.005openalex-snapshot

Human Virome

inferred← citeshttps://doi.org/10.1016/j.bios.2023.115407openalex-snapshot

Electrochemical nucleic acid sensors: Competent pathways for mobile molecular diagnostics

inferred← citeshttps://doi.org/10.1016/j.biotechadv.2020.107537openalex-snapshot

Library preparation for next generation sequencing: A review of automation strategies

inferred← citeshttps://doi.org/10.1016/j.chom.2016.04.016openalex-snapshot

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology

inferred← citeshttps://doi.org/10.1016/j.cofs.2016.04.002openalex-snapshot

Foodborne viruses

inferred← citeshttps://doi.org/10.1016/j.copbio.2012.09.004openalex-snapshot

Transcriptome analysis using next-generation sequencing

inferred← citeshttps://doi.org/10.1016/j.coviro.2013.02.003openalex-snapshot

Surveillance strategy for early detection of unusual infectious disease events

inferred← citeshttps://doi.org/10.1016/j.funbio.2023.04.005openalex-snapshot

Long-term impact of pulses crop rotation on soil fungal diversity in aerobic and wetland rice cultivation

inferred← citeshttps://doi.org/10.1016/j.hjb.2016.12.007openalex-snapshot

Next-Generation Sequencing and Influenza Virus: A Short Review of the Published Implementation Attempts

inferred← citeshttps://doi.org/10.1016/j.jcv.2013.03.003openalex-snapshot

Next-generation sequencing technologies in diagnostic virology

inferred← citeshttps://doi.org/10.1016/j.jcv.2013.04.021openalex-snapshot

Molecular epidemiology of viral diseases in the era of next generation sequencing

inferred← citeshttps://doi.org/10.1016/j.jcv.2013.07.009openalex-snapshot

Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencing drug resistance assay in a routine diagnostic laboratory

inferred← citeshttps://doi.org/10.1016/j.jcv.2015.04.010openalex-snapshot

Viral subpopulation diversity in influenza virus isolates compared to clinical specimens

inferred← citeshttps://doi.org/10.1016/j.jcv.2018.09.001openalex-snapshot

Genetic diversity of Hepatitis C Virus in Pakistan using Next Generation Sequencing

inferred← citeshttps://doi.org/10.1016/j.jcv.2018.09.014openalex-snapshot

Virome definition in cerebrospinal fluid of patients with neurological complications after hematopoietic stem cell transplantation

inferred← citeshttps://doi.org/10.1016/j.jmoldx.2015.07.004openalex-snapshot

Next-Generation Sequencing for Infectious Disease Diagnosis and Management

inferred← citeshttps://doi.org/10.1016/j.jmoldx.2017.06.005openalex-snapshot

Calling Chromosome Alterations, DNA Methylation Statuses, and Mutations in Tumors by Simple Targeted Next-Generation Sequencing

inferred← citeshttps://doi.org/10.1016/j.jss.2014.05.003openalex-snapshot

Comparison of culture and molecular techniques for microbial community characterization in infected necrotizing pancreatitis

inferred← citeshttps://doi.org/10.1016/j.jviromet.2013.07.001openalex-snapshot

Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform

inferred← citeshttps://doi.org/10.1016/j.jviromet.2014.07.001openalex-snapshot

An evaluation of the Qiagen HPV sign for the detection and genotyping of cervical lesions and oropharyngeal squamous cell carcinomas

inferred← citeshttps://doi.org/10.1016/j.jviromet.2014.07.023openalex-snapshot

A new approach to determining whole viral genomic sequences including termini using a single deep sequencing run

inferred← citeshttps://doi.org/10.1016/j.jviromet.2015.04.009openalex-snapshot

Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq®)

inferred← citeshttps://doi.org/10.1016/j.jviromet.2015.04.022openalex-snapshot

Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants

inferred← citeshttps://doi.org/10.1016/j.jviromet.2015.05.010openalex-snapshot

Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples

inferred← citeshttps://doi.org/10.1016/j.jviromet.2016.07.001openalex-snapshot

Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control

inferred← citeshttps://doi.org/10.1016/j.jviromet.2017.08.019openalex-snapshot

Metagenomic arbovirus detection using MinION nanopore sequencing

inferred← citeshttps://doi.org/10.1016/j.jviromet.2017.10.019openalex-snapshot

Application of next-generation sequencing to detect acyclovir-resistant herpes simplex virus type 1 variants at low frequency in thymidine kinase gene of the isolates recovered from patients with hematopoietic stem cell transplantation

inferred← citeshttps://doi.org/10.1016/j.jviromet.2023.114807openalex-snapshot

A rapid and affordable amplicon-based method for next-generation genome sequencing of the infectious bursal disease virus

inferred← citeshttps://doi.org/10.1016/j.meegid.2016.06.021openalex-snapshot

The application of HIV molecular epidemiology to public health

inferred← citeshttps://doi.org/10.1016/j.micpath.2014.09.002openalex-snapshot

Arthropods as a source of new RNA viruses

inferred← citeshttps://doi.org/10.1016/j.micpath.2024.106971openalex-snapshot

The current status and development forecasts of vaccines for aquaculture and its effects on bacterial and viral diseases

inferred← citeshttps://doi.org/10.1016/j.prp.2024.155606openalex-snapshot

Next Generation Sequencing: Latent applications in clinical diagnostics with the advent of bioinformatic frameworks

inferred← citeshttps://doi.org/10.1016/j.sbsr.2023.100601openalex-snapshot

CRISPR-based biosensor for the detection of Marburg and Ebola virus

inferred← citeshttps://doi.org/10.1016/j.tig.2013.07.006openalex-snapshot

Finding the lost treasures in exome sequencing data

inferred← citeshttps://doi.org/10.1016/j.trac.2022.116686openalex-snapshot

Genosensors as an alternative diagnostic sensing approaches for specific detection of virus species: A review of common techniques and outcomes

inferred← citeshttps://doi.org/10.1016/j.tvjl.2016.05.007openalex-snapshot

Recent developments in the diagnosis of avian influenza

inferred← citeshttps://doi.org/10.1016/j.vaccine.2022.12.040openalex-snapshot

NGS method by library enrichment for rapid pestivirus purity testing in biologics

inferred← citeshttps://doi.org/10.1016/j.virol.2017.06.027openalex-snapshot

Complete genome sequence of Ostreid herpesvirus type 1 µVar isolated during mortality events in the Pacific oyster Crassostrea gigas in France and Ireland

inferred← citeshttps://doi.org/10.1016/j.virol.2021.06.011openalex-snapshot

Novel Paju Apodemus paramyxovirus 1 and 2, harbored by Apodemus agrarius in the Republic of Korea

inferred← citeshttps://doi.org/10.1016/j.virusres.2013.09.018openalex-snapshot

Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis

inferred← citeshttps://doi.org/10.1016/j.virusres.2017.10.014openalex-snapshot

A decade of RNA virus metagenomics is (not) enough

inferred← citeshttps://doi.org/10.1016/j.virusres.2020.197963openalex-snapshot

Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies

inferred← citeshttps://doi.org/10.1016/j.watres.2015.10.024openalex-snapshot

Temporal dynamics of norovirus determined through monitoring of municipal wastewater by pyrosequencing and virological surveillance of gastroenteritis cases

inferred← citeshttps://doi.org/10.1016/s1473-3099(23)00394-8openalex-snapshot

Boosting pathogen genomics and bioinformatics workforce in Africa

inferred← citeshttps://doi.org/10.1021/acs.jproteome.9b00358openalex-snapshot

Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium

inferred← citeshttps://doi.org/10.1038/s41598-017-08139-yopenalex-snapshot

Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus

inferred← citeshttps://doi.org/10.1038/s41598-018-33909-7openalex-snapshot

Early Post-Transplant Torquetenovirus Viremia Predicts Cytomegalovirus Reactivations In Solid Organ Transplant Recipients

inferred← citeshttps://doi.org/10.1038/s41598-019-42605-zopenalex-snapshot

Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing

inferred← citeshttps://doi.org/10.1038/s41598-020-68159-zopenalex-snapshot

A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting

inferred← citeshttps://doi.org/10.1038/s41598-020-73790-xopenalex-snapshot

Mitochondrial genome sequencing and phylogeny of Haemagogus albomaculatus, Haemagogus leucocelaenus, Haemagogus spegazzinii, and Haemagogus tropicalis (Diptera: Culicidae)

inferred← citeshttps://doi.org/10.1038/s41598-022-20701-xopenalex-snapshot

Establishing farm dust as a useful viral metagenomic surveillance matrix

inferred← citeshttps://doi.org/10.1038/srep14727openalex-snapshot

Isolation and molecular characterization of newly emerging avian reovirus variants and novel strains in Pennsylvania, USA, 2011–2014

inferred← citeshttps://doi.org/10.1039/c8ra00888dopenalex-snapshot

The unequivocal preponderance of biocomputation in clinical virology

inferred← citeshttps://doi.org/10.1080/08820538.2019.1620800openalex-snapshot

A Review of Next-Generation Sequencing (NGS): Applications to the Diagnosis of Ocular Infectious Diseases

inferred← citeshttps://doi.org/10.1080/10408363.2018.1526164openalex-snapshot

Clinical laboratory utilization management and improved healthcare performance

inferred← citeshttps://doi.org/10.1080/14737159.2016.1217158openalex-snapshot

Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis

inferred← citeshttps://doi.org/10.1089/aid.2012.0382openalex-snapshot

Human T Cell Lymphotropic Virus Type 1 Infection Among U.S. Thalassemia Patients

inferred← citeshttps://doi.org/10.1089/omi.2022.0042openalex-snapshot

Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2

inferred← citeshttps://doi.org/10.1089/vim.2014.0108openalex-snapshot

Multiple Circulating Infections Can Mimic the Early Stages of Viral Hemorrhagic Fevers and Possible Human Exposure to Filoviruses in Sierra Leone Prior to the 2014 Outbreak

inferred← citeshttps://doi.org/10.1093/bib/bbu032openalex-snapshot

Alternative applications for distinct RNA sequencing strategies

inferred← citeshttps://doi.org/10.1093/bioinformatics/btv101openalex-snapshot

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum

inferred← citeshttps://doi.org/10.1093/bioinformatics/bty128openalex-snapshot

PriLive: privacy-preserving real-time filtering for next-generation sequencing

inferred← citeshttps://doi.org/10.1093/infdis/jiu340openalex-snapshot

Deep-Sequencing Analysis of the Gene Encoding the Hepatitis C Virus Nonstructural 3–4A Protease Confirms a Low Prevalence of Telaprevir-Resistant Variants at Baseline and the End of the REALIZE Study

inferred← citeshttps://doi.org/10.1094/pdis-03-17-0306-reopenalex-snapshot

Application of Next Generation Sequencing for Diagnostic Testing of Tree Fruit Viruses and Viroids

inferred← citeshttps://doi.org/10.1094/phyto-06-14-0165-ropenalex-snapshot

Comparison of Next-Generation Sequencing Versus Biological Indexing for the Optimal Detection of Viral Pathogens in Grapevine

inferred← citeshttps://doi.org/10.1097/cpm.0000000000000374openalex-snapshot

Laboratory Diagnosis of COVID-19

inferred← citeshttps://doi.org/10.1097/md.0000000000001876openalex-snapshot

Dynamic of Mixed HCV Infection in Plasma and PBMC of HIV/HCV Patients Under Treatment With Peg-IFN/Ribavirin

inferred← citeshttps://doi.org/10.1097/pat.0000000000000241openalex-snapshot

Rapid identification of pathogens using molecular techniques

inferred← citeshttps://doi.org/10.1097/qco.0000000000000113openalex-snapshot

Developments in the treatment of severe influenza

inferred← citeshttps://doi.org/10.1098/rsif.2017.0968openalex-snapshot

Model-based estimation of superinfection prevalence from limited datasets

inferred← citeshttps://doi.org/10.1099/acmi.0.000127openalex-snapshot

Using next-generation sequencing of microRNAs to identify host and/or pathogen nucleic acid signatures in samples from children with biliary atresia – a pilot study

inferred← citeshttps://doi.org/10.1099/jgv.0.000231openalex-snapshot

Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model

inferred← citeshttps://doi.org/10.1099/jgv.0.002331openalex-snapshot

Enhanced recovery of terminal sequences of viral RNAs via fine-tuning of the high-throughput sequencing library preparation and evidence of a non-templated nucleotide addition at the 3′ end of the minus strand in members of the genus Ilarvirus

inferred← citeshttps://doi.org/10.1101/2023.01.11.523546openalex-snapshot

Virome analyses by next-generation sequencing (NGS) in chilli ( Capsicum anuum L.) presented with diverse symptoms phenotype revealed the association of seven plant viruses

inferred← citeshttps://doi.org/10.1101/800995openalex-snapshot

BiomeSeq: A Tool for the Characterization of Animal Microbiomes from Metagenomic Data

inferred← citeshttps://doi.org/10.1111/1469-0691.12056openalex-snapshot

Next-generation sequencing technology in clinical virology

inferred← citeshttps://doi.org/10.1111/aab.12572openalex-snapshot

The virome of maize rough dwarf disease: Molecular genome diversification, phylogeny and selection

inferred← citeshttps://doi.org/10.1111/jam.12907openalex-snapshot

High prevalence of type 41 and high sequence diversity of partial hexon gene of human adenoviruses in municipal raw sewage and activated sludge

inferred← citeshttps://doi.org/10.1111/raq.12870openalex-snapshot

Emerging technologies revolutionising disease diagnosis and monitoring in aquatic animal health

inferred← citeshttps://doi.org/10.1111/tbed.12251openalex-snapshot

False-Positive Results in Metagenomic Virus Discovery: A Strong Case for Follow-Up Diagnosis

inferred← citeshttps://doi.org/10.1111/trf.13600openalex-snapshot

Two human immunodeficiency virus Type 2 cases in US blood donors including serologic, molecular, and genomic characterization of an epidemiologically unusual case

inferred← citeshttps://doi.org/10.1128/9781555819156.ch15openalex-snapshot

DNA Sequencing for Clinical and Public Health Virology: Some Assembly Required

inferred← citeshttps://doi.org/10.1128/aac.01490-15openalex-snapshot

HIV Drug Resistance Testing by High-Multiplex “Wide” Sequencing on the MiSeq Instrument

inferred← citeshttps://doi.org/10.1128/jcm.01389-14openalex-snapshot

Comprehensive Human Virus Screening Using High-Throughput Sequencing with a User-Friendly Representation of Bioinformatics Analysis: a Pilot Study

inferred← citeshttps://doi.org/10.1128/jcm.01881-16openalex-snapshot

Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections

inferred← citeshttps://doi.org/10.1128/jcm.02593-12openalex-snapshot

Point-Counterpoint: Is the Era of Viral Culture Over in the Clinical Microbiology Laboratory?

inferred← citeshttps://doi.org/10.1128/jcm.02652-12openalex-snapshot

Evaluation of a Benchtop HIV Ultradeep Pyrosequencing Drug Resistance Assay in the Clinical Laboratory

inferred← citeshttps://doi.org/10.1128/microbiolspec.ame-0003-2018openalex-snapshot

Laboratory Methods in Molecular Epidemiology: Viral Infections

inferred← citeshttps://doi.org/10.1136/jitc-2025-012444openalex-snapshot

Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study

inferred← citeshttps://doi.org/10.1136/vr.105125openalex-snapshot

Exploratory metagenomic analyses of periweaning failure‐to‐thrive syndrome‐affected pigs

inferred← citeshttps://doi.org/10.1145/3809986.3809999openalex-snapshot

Transformer Model-Driven Targeted Sequencing Data Mining for Pathogens in Childhood Community-Acquired Pneumonia (CAP)

inferred← citeshttps://doi.org/10.1146/annurev-phyto-080614-120030openalex-snapshot

Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms

inferred← citeshttps://doi.org/10.1155/2013/626083openalex-snapshot

Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis

inferred← citeshttps://doi.org/10.11606/t.42.2017.tde-15052017-154549openalex-snapshot

Estudo da diversidade genética do HIV inter e intra-hospedeiro em pacientes soroconvertores recentes.

inferred← citeshttps://doi.org/10.11606/t.60.2016.tde-02052016-104428openalex-snapshot

Caracterização do potencial patogênico de linhagens de Yersinia enterocolitica-like

inferred← citeshttps://doi.org/10.1177/1040638720978381openalex-snapshot

Evaluation of targeted next-generation sequencing for detection of equine pathogens in clinical samples

inferred← citeshttps://doi.org/10.1177/15353702221102895openalex-snapshot

Revolutionized virome research using systems microbiology approaches

inferred← citeshttps://doi.org/10.1186/1471-2105-15-254openalex-snapshot

ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset

inferred← citeshttps://doi.org/10.1186/1471-2164-14-501openalex-snapshot

Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias

inferred← citeshttps://doi.org/10.1186/1471-2334-13-554openalex-snapshot

Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak

inferred← citeshttps://doi.org/10.1186/1742-4690-11-s1-p54openalex-snapshot

Human T-cell lymphotropic virus type 1 infection among U.S. Thalassemia patients

inferred← citeshttps://doi.org/10.1186/1743-422x-11-146openalex-snapshot

Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA

inferred← citeshttps://doi.org/10.1186/s12859-015-0607-zopenalex-snapshot

Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data

inferred← citeshttps://doi.org/10.1186/s12859-015-0812-9openalex-snapshot

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

inferred← citeshttps://doi.org/10.1186/s12859-023-05187-2openalex-snapshot

PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach

inferred← citeshttps://doi.org/10.1186/s12879-019-4716-6openalex-snapshot

Fatal hemorrhagic varicella in a patient with abdominal pain: a case report

inferred← citeshttps://doi.org/10.1186/s12929-019-0541-xopenalex-snapshot

Genomic analysis of serologically untypable human enteroviruses in Taiwan

inferred← citeshttps://doi.org/10.1186/s12985-019-1205-xopenalex-snapshot

Rapid detection of human herpes virus by next-generation sequencing in a patient with encephalitis

inferred← citeshttps://doi.org/10.1186/s12985-023-02237-2openalex-snapshot

Molecular characterization of a reptarenavirus detected in a Colombian Red-Tailed Boa (Boa constrictor imperator)

inferred← citeshttps://doi.org/10.1186/s13023-015-0327-5openalex-snapshot

Large animal models of rare genetic disorders: sheep as phenotypically relevant models of human genetic disease

inferred← citeshttps://doi.org/10.1186/s13062-016-0105-xopenalex-snapshot

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

inferred← citeshttps://doi.org/10.1186/s40001-021-00554-2openalex-snapshot

Clinical study on the diagnosis of porcine streptococcal meningitis with negative blood and cerebrospinal fluid culture by next-generation sequencing

inferred← citeshttps://doi.org/10.1186/s40738-021-00105-7openalex-snapshot

Onco-fertility and personalized testing for potential for loss of ovarian reserve in patients undergoing chemotherapy: proposed next steps for development of genetic testing to predict changes in ovarian reserve

inferred← citeshttps://doi.org/10.1186/s44149-026-00229-7openalex-snapshot

Viral metagenomic analysis of the upper respiratory tract virome and identification of novel viruses in giant pandas

inferred← citeshttps://doi.org/10.11979/idtm.201502006openalex-snapshot

Diagnosis of Ebola Virus Disease: Progress and Prospects

inferred← citeshttps://doi.org/10.1212/con.0000000000000661openalex-snapshot

Herpesvirus Infections of the Nervous System

inferred← citeshttps://doi.org/10.1212/nxi.0000000000000251openalex-snapshot

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system

inferred← citeshttps://doi.org/10.12677/hjbm.2022.122009openalex-snapshot

Relevant Principles of Next-Generation Sequencing

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004344openalex-snapshot

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing

inferred← citeshttps://doi.org/10.1371/journal.pone.0047046openalex-snapshot

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

inferred← citeshttps://doi.org/10.1371/journal.pone.0058026openalex-snapshot

Detection of Arboviruses and Other Micro-Organisms in Experimentally Infected Mosquitoes Using Massively Parallel Sequencing

inferred← citeshttps://doi.org/10.1371/journal.pone.0064785openalex-snapshot

Simplified Large-Scale Sanger Genome Sequencing for Influenza A/H3N2 Virus

inferred← citeshttps://doi.org/10.1371/journal.pone.0067010openalex-snapshot

Using High-Throughput Sequencing to Leverage Surveillance of Genetic Diversity and Oseltamivir Resistance: A Pilot Study during the 2009 Influenza A(H1N1) Pandemic

inferred← citeshttps://doi.org/10.1371/journal.pone.0122812openalex-snapshot

SNPer: An R Library for Quantitative Variant Analysis on Single Nucleotide Polymorphisms among Influenza Virus Populations

inferred← citeshttps://doi.org/10.1371/journal.pone.0130022openalex-snapshot

Rapid, Sensitive, and Accurate Evaluation of Drug Resistant Mutant (NS5A-Y93H) Strain Frequency in Genotype 1b HCV by Invader Assay

inferred← citeshttps://doi.org/10.1371/journal.pone.0139810openalex-snapshot

Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes

inferred← citeshttps://doi.org/10.1371/journal.pone.0149215openalex-snapshot

HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China

inferred← citeshttps://doi.org/10.14800/pm.604openalex-snapshot

West Nile Virus, a Reemerging Virus

inferred← citeshttps://doi.org/10.1533/9780857098870.2.97openalex-snapshot

Molecular detection of viruses in water and sewage

inferred← citeshttps://doi.org/10.1586/14787210.2015.1007044openalex-snapshot

Latest developments and challenges in the diagnosis of human West Nile virus infection

inferred← citeshttps://doi.org/10.21037/962openalex-snapshot

Common applications of next-generation sequencing technologies in genomic research

inferred← citeshttps://doi.org/10.21203/rs.3.rs-129066/v1openalex-snapshot

Evaluation of Hepatitis B Virus Nucleos(t)ide Analogues Resistance mutations in Treatment-Naïve Patients: A Systematic Review and Meta-Analysis

inferred← citeshttps://doi.org/10.21276/apjhs.2021.8.3.11openalex-snapshot

An Overview of Epidemiology and Diagnostic Techniques for Emerging and Re-emerging Viral Infections

inferred← citeshttps://doi.org/10.2174/0122113525303969240624071851openalex-snapshot

Mutations Unveiled: Navigating the Ever-changing Landscape of SARS-CoV-2 in the COVID-19 Saga

inferred← citeshttps://doi.org/10.2174/0126664844274727231218061037openalex-snapshot

Review of Six Different Next Generation Sequencing (NGS) Techniques for Forensic Science, including Advantages and Disadvantages

inferred← citeshttps://doi.org/10.2208/jscejer.71.iii_339openalex-snapshot

SELECTIVE METAGENOMIC ANALYSIS OF POSITIVE-STRAND RNA VIRUSES IN WASTEWATER

inferred← citeshttps://doi.org/10.2217/ebo.12.208openalex-snapshot

Comprehensive whole genome and transcriptome analysis for novel diagnostics

inferred← citeshttps://doi.org/10.2217/fvl.12.45openalex-snapshot

Large-Scale Sequencing and the Natural History of Model Human RNA Viruses

inferred← citeshttps://doi.org/10.22541/au.169219983.38601687/v1openalex-snapshot

Application of Next Generation Sequencing in identifying different pathogens

inferred← citeshttps://doi.org/10.25259/gjms.2023.3.1.7openalex-snapshot

A Deep Dive into Next Generation Sequencing: A Review

inferred← citeshttps://doi.org/10.26512/2015.02.d.18300openalex-snapshot

Caracterização molecular de Johnsongrass mosaic virus em plantas forrageiras dos gêneros brachiaria, panicum e pennisetum

inferred← citeshttps://doi.org/10.26512/2016.10.d.22532openalex-snapshot

Identificação de vírus em tomateiro através de análise por sequenciamento de alto desempenho

inferred← citeshttps://doi.org/10.26512/2017.02.d.23716openalex-snapshot

Caracterização molecular e biológica de vírus da família Potyviridae infectando leguminosas forrageiras da espécie Stylosanthes guianensis

inferred← citeshttps://doi.org/10.26512/2018.02.t.32186openalex-snapshot

Viroma de batata-doce no Brasil e limpeza clonal de cultivares ricas em beta-caroteno

inferred← citeshttps://doi.org/10.26821/ijshre.8.9.2020.8901openalex-snapshot

Investigation of ChIP-Seq Technology

inferred← citeshttps://doi.org/10.3103/s0891416826700072openalex-snapshot

Molecular Techniques for Influenza Virus Identification and Typing: A Comprehensive Review

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