{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T19:52:15Z","timestamp":1790970735398,"version":"4.1.0"},"reference-count":93,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T00:00:00Z","timestamp":1776816000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Infectious Medicine"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1016\/j.imj.2026.100254","type":"journal-article","created":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T07:04:49Z","timestamp":1776927889000},"page":"100254","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"title":["Next-generation sequencing: Driving a paradigm shift from pathogen detection to systems-level analysis"],"prefix":"10.1016","volume":"5","author":[{"given":"Yu","family":"Peng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yupu","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liwen","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanyue","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ranran","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zujiang","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"12","key":"10.1016\/j.imj.2026.100254_bib0001","doi-asserted-by":"crossref","DOI":"10.1002\/jmv.70106","article-title":"Unusual G9P[4]rotavirus emerged after the dynamic changes in rotavirus genotypes from equine-like G3 to typical human G1\/G3 in Indonesia","volume":"96","author":"Dinana","year":"2024","journal-title":"J Med Virol"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0002","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1128\/microbiolspec.AME-0005-2018","article-title":"Platforms and analytical tools used in nucleic acid sequence-based microbial genotyping procedures","volume":"7","author":"MacCannell","year":"2019","journal-title":"Microbiol Spectr"},{"issue":"31","key":"10.1016\/j.imj.2026.100254_bib0003","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.2174\/1381612825666190911155508","article-title":"Next-generation sequencing: an emerging tool for drug designing","volume":"25","author":"Tripathi","year":"2019","journal-title":"Curr Pharm Des"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0004","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1080\/22221751.2020.1765704","article-title":"Isolation and characterization of a duck-origin goose astrovirus in China","volume":"9","author":"Wei","year":"2020","journal-title":"Emerg Microbes Infect"},{"issue":"11\/12","key":"10.1016\/j.imj.2026.100254_bib0005","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1016\/j.drudis.2011.03.006","article-title":"The application of next-generation sequencing technologies to drug discovery and development","volume":"16","author":"Woollard","year":"2011","journal-title":"Drug Discov Today"},{"issue":"9","key":"10.1016\/j.imj.2026.100254_bib0006","doi-asserted-by":"crossref","first-page":"4924","DOI":"10.21037\/jtd-20-930","article-title":"Comparison of the next-generation sequencing (NGS) technology with culture methods in the diagnosis of bacterial and fungal infections","volume":"12","author":"Chen","year":"2020","journal-title":"J Thorac Dis"},{"issue":"6","key":"10.1016\/j.imj.2026.100254_bib0007","doi-asserted-by":"crossref","DOI":"10.1016\/j.jinf.2024.106166","article-title":"Molecular rapid diagnostic testing for bloodstream infections: nanopore targeted sequencing with pathogen-specific primers","volume":"88","author":"Han","year":"2024","journal-title":"J Infect"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0008","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1111\/jdv.19938","article-title":"Evolution of genome diagnostics in epidermolysis bullosa: unveiling the power of next-generation sequencing","volume":"39","author":"Baardman","year":"2025","journal-title":"J Eur Acad Dermatol Venereol"},{"issue":"4","key":"10.1016\/j.imj.2026.100254_bib0009","doi-asserted-by":"crossref","DOI":"10.1016\/j.jinf.2025.106459","article-title":"Rapid and accurate diagnosis of urinary tract infections using targeted next-generation sequencing: a multicenter comparative study with metagenomic sequencing and traditional culture methods","volume":"90","author":"Chang","year":"2025","journal-title":"J Infect"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0010","article-title":"Metagenomic next-generation sequencing reveals respiratory flora distribution in COVID-19","volume":"15","author":"Wang","year":"2025","journal-title":"Sci Rep"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0011","doi-asserted-by":"crossref","DOI":"10.1002\/smtd.202000792","article-title":"High-throughput metagenomics for identification of pathogens in the clinical settings","volume":"5","author":"Li","year":"2021","journal-title":"Small Methods"},{"key":"10.1016\/j.imj.2026.100254_bib0012","doi-asserted-by":"crossref","first-page":"5378","DOI":"10.1016\/j.csbj.2022.09.028","article-title":"High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance","volume":"20","author":"Suminda","year":"2022","journal-title":"Comput Struct Biotechnol J"},{"issue":"8","key":"10.1016\/j.imj.2026.100254_bib0013","doi-asserted-by":"crossref","first-page":"995","DOI":"10.3390\/pathogens12080995","article-title":"Usefulness of next-generation sequencing in excluding bovine leukemia virus as a cause of adult camel leukosis in dromedaries","volume":"12","author":"Wernery","year":"2023","journal-title":"Pathogens"},{"issue":"5","key":"10.1016\/j.imj.2026.100254_bib0014","doi-asserted-by":"crossref","first-page":"4124","DOI":"10.3390\/cimb45050262","article-title":"Cycle threshold (ct) values of SARS-CoV-2 detected with the GeneXpert\u00ae system and a mutation associated with different target gene failure","volume":"45","author":"Yamashita","year":"2023","journal-title":"Curr Issues Mol Biol"},{"issue":"Suppl 3","key":"10.1016\/j.imj.2026.100254_bib0015","article-title":"Next generation sequencing and bioinformatics methodologies for infectious disease research and public health: approaches, applications, and considerations for development of laboratory capacity","volume":"221","author":"Maljkovic Berry","year":"2020","journal-title":"J Infect Dis"},{"key":"10.1016\/j.imj.2026.100254_bib0016","doi-asserted-by":"crossref","DOI":"10.1016\/j.meegid.2021.105192","article-title":"Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia","volume":"97","author":"G\u00e1lvez","year":"2022","journal-title":"Infect Genet Evol"},{"key":"10.1016\/j.imj.2026.100254_bib0017","article-title":"Looking for a needle in a haystack. SARS-CoV-2 variant characterization in sewage","volume":"24","author":"Itarte","year":"2021","journal-title":"Curr Opin Environ Sci Health"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0018","doi-asserted-by":"crossref","first-page":"311","DOI":"10.20506\/rst.36.1.2631","article-title":"Developing a framework to assess the costeffectiveness of COMPARE - a global platform for the exchange of sequence-based pathogen data","volume":"36","author":"Alleweldt","year":"2017","journal-title":"Rev Sci Tech"},{"issue":"2","key":"10.1016\/j.imj.2026.100254_bib0019","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1177\/1040638720937015","article-title":"Next-generation sequencing capacity and capabilities within the national animal health laboratory network","volume":"33","author":"Harris","year":"2021","journal-title":"J Vet Diagn Invest"},{"issue":"3","key":"10.1016\/j.imj.2026.100254_bib0020","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.02449-24","article-title":"Detection of tick-borne pathogens in blood-fed ticks from animals across nine Asian countries","volume":"13","author":"Byun","year":"2025","journal-title":"Microbiol Spectr"},{"issue":"10","key":"10.1016\/j.imj.2026.100254_bib0021","doi-asserted-by":"crossref","first-page":"2738","DOI":"10.1038\/s41564-024-01809-4","article-title":"Pathogen genomic surveillance status among lower resource settings in Asia","volume":"9","author":"Getchell","year":"2024","journal-title":"Nat Microbiol"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0022","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/s41591-020-1105-z","article-title":"Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids","volume":"27","author":"Gu","year":"2021","journal-title":"Nat Med"},{"issue":"12","key":"10.1016\/j.imj.2026.100254_bib0023","doi-asserted-by":"crossref","first-page":"3522","DOI":"10.1038\/s41591-024-03275-1","article-title":"Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections","volume":"30","author":"Benoit","year":"2024","journal-title":"Nat Med"},{"issue":"13","key":"10.1016\/j.imj.2026.100254_bib0024","doi-asserted-by":"crossref","DOI":"10.1097\/MD.0000000000010245","article-title":"Central nervous system histoplasmosis: multicenter retrospective study on clinical features, diagnostic approach and outcome of treatment","volume":"97","author":"Wheat","year":"2018","journal-title":"Medicine"},{"issue":"6","key":"10.1016\/j.imj.2026.100254_bib0025","doi-asserted-by":"crossref","DOI":"10.1016\/j.jinf.2025.106661","article-title":"Comparative diagnostic accuracy of metagenomic next-generation sequencing and targeted next-generation sequencing for periprosthetic joint infection: a systematic review and meta-analysis","volume":"91","author":"Wang","year":"2025","journal-title":"J Infect"},{"key":"10.1016\/j.imj.2026.100254_bib0026","doi-asserted-by":"crossref","DOI":"10.1016\/j.ebiom.2024.105307","article-title":"Enhancing lower respiratory tract infection diagnosis: implementation and clinical assessment of multiplex PCR-based and hybrid capture-based targeted next-generation sequencing","volume":"107","author":"Yin","year":"2024","journal-title":"eBioMedicine"},{"issue":"7399","key":"10.1016\/j.imj.2026.100254_bib0027","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1038\/nature11071","article-title":"Melanoma genome sequencing reveals frequent PREX2 mutations","volume":"485","author":"Berger","year":"2012","journal-title":"Nature"},{"issue":"6215","key":"10.1016\/j.imj.2026.100254_bib0028","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.1126\/science.1259037","article-title":"Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element","volume":"346","author":"Mansour","year":"2014","journal-title":"Science"},{"issue":"7","key":"10.1016\/j.imj.2026.100254_bib0029","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1038\/ng.2295","article-title":"Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma","volume":"44","author":"Sung","year":"2012","journal-title":"Nat Genet"},{"issue":"7","key":"10.1016\/j.imj.2026.100254_bib0030","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1038\/s41592-024-02298-3","article-title":"Systematic assessment of long-read RNA-seq methods for transcript identification and quantification","volume":"21","author":"Pardo-Palacios","year":"2024","journal-title":"Nat Methods"},{"issue":"6","key":"10.1016\/j.imj.2026.100254_bib0031","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1038\/s41596-023-00815-w","article-title":"Full-length circular RNA profiling by nanopore sequencing with CIRI-long","volume":"18","author":"Hou","year":"2023","journal-title":"Nat Protoc"},{"issue":"5","key":"10.1016\/j.imj.2026.100254_bib0032","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet Med"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0033","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1080\/22221751.2020.1773745","article-title":"Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries","volume":"9","author":"Yang","year":"2020","journal-title":"Emerg Microbes Infect"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0034","doi-asserted-by":"crossref","first-page":"5006","DOI":"10.1038\/s41467-020-18836-4","article-title":"Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase","volume":"11","author":"Wang","year":"2020","journal-title":"Nat Commun"},{"issue":"9","key":"10.1016\/j.imj.2026.100254_bib0035","doi-asserted-by":"crossref","first-page":"1634","DOI":"10.1002\/jmv.25773","article-title":"A doubt of multiple introduction of SARS-CoV-2 in Italy: a preliminary overview","volume":"92","author":"Giovanetti","year":"2020","journal-title":"J Med Virol"},{"issue":"6","key":"10.1016\/j.imj.2026.100254_bib0036","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1009620","article-title":"Dating first cases of COVID-19","volume":"17","author":"Roberts","year":"2021","journal-title":"PLoS Pathog"},{"issue":"3","key":"10.1016\/j.imj.2026.100254_bib0037","doi-asserted-by":"crossref","first-page":"494","DOI":"10.24272\/j.issn.2095-8137.2022.535","article-title":"Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model","volume":"44","author":"Cheng","year":"2023","journal-title":"Zool Res"},{"key":"10.1016\/j.imj.2026.100254_bib0038","article-title":"Characteristics of SARS-CoV-2 Omicron BA.5 variants in Shanghai after ending the zero-COVID policy in December 2022: a clinical and genomic analysis","volume":"15","author":"Liu","year":"2024","journal-title":"Front Microbiol"},{"issue":"2","key":"10.1016\/j.imj.2026.100254_bib0039","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/veac105","article-title":"Gene amplification acts as a molecular foothold to facilitate cross-species adaptation and evasion of multiple antiviral pathways","volume":"8","author":"Banerjee","year":"2022","journal-title":"Virus Evol"},{"issue":"6","key":"10.1016\/j.imj.2026.100254_bib0040","doi-asserted-by":"crossref","first-page":"1689","DOI":"10.1111\/tbed.12928","article-title":"Isolation and genomic characterization of gosling gout caused by a novel goose astrovirus","volume":"65","author":"Yang","year":"2018","journal-title":"Transbound Emerg Dis"},{"key":"10.1016\/j.imj.2026.100254_bib0041","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.virol.2018.02.016","article-title":"Characterization of H9N2 avian influenza viruses from the Middle East demonstrates heterogeneity at amino acid position 226 in the hemagglutinin and potential for transmission to mammals","volume":"518","author":"Chrzastek","year":"2018","journal-title":"Virology"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0042","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1186\/s40168-024-01955-1","article-title":"Unveiling bat-borne viruses: a comprehensive classification and analysis of virome evolution","volume":"12","author":"Wang","year":"2024","journal-title":"Microbiome"},{"issue":"3","key":"10.1016\/j.imj.2026.100254_bib0043","doi-asserted-by":"crossref","first-page":"412","DOI":"10.3390\/v13030412","article-title":"Current developments and challenges in plant viral diagnostics: a systematic review","volume":"13","author":"Mehetre","year":"2021","journal-title":"Viruses"},{"key":"10.1016\/j.imj.2026.100254_bib0044","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2023.1329330","article-title":"Application of next-generation sequencing to identify different pathogens","volume":"14","author":"Nafea","year":"2024","journal-title":"Front Microbiol"},{"issue":"5","key":"10.1016\/j.imj.2026.100254_bib0045","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.gpb.2015.08.002","article-title":"PacBio sequencing and its applications","volume":"13","author":"Rhoads","year":"2015","journal-title":"Genomics Proteomics Bioinformatics"},{"issue":"2","key":"10.1016\/j.imj.2026.100254_bib0046","doi-asserted-by":"crossref","DOI":"10.1016\/j.bj.2024.100770","article-title":"The establishment of a molecular diagnostic platform for mitochondrial diseases: from conventional to next-generation sequencing","volume":"48","author":"Tsai","year":"2025","journal-title":"Biomed J"},{"issue":"11","key":"10.1016\/j.imj.2026.100254_bib0047","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1038\/s41565-022-01193-2","article-title":"Nanopore-based technologies beyond DNA sequencing","volume":"17","author":"Ying","year":"2022","journal-title":"Nat Nanotechnol"},{"issue":"5","key":"10.1016\/j.imj.2026.100254_bib0048","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1016\/j.jmoldx.2021.02.001","article-title":"Nanopore flongle sequencing as a rapid, single-specimen clinical test for fusion detection","volume":"23","author":"Jeck","year":"2021","journal-title":"J Mol Diagn"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0049","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1186\/s13059-021-02553-2","article-title":"Flimma: a federated and privacy-aware tool for differential gene expression analysis","volume":"22","author":"Zolotareva","year":"2021","journal-title":"Genome Biol"},{"issue":"11","key":"10.1016\/j.imj.2026.100254_bib0050","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0224847","article-title":"Ion torrent high throughput mitochondrial genome sequencing (HTMGS)","volume":"14","author":"Harvey","year":"2019","journal-title":"PLoS One"},{"issue":"4","key":"10.1016\/j.imj.2026.100254_bib0051","doi-asserted-by":"crossref","DOI":"10.5808\/gi.23072","article-title":"Comparative analysis of HiSeq3000 and BGISEQ-500 sequencing platform over whole genome sequencing metagenomics data","volume":"21","author":"Kumar","year":"2023","journal-title":"Genomics Inform"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0052","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13040-019-0209-9","article-title":"SEQdata-BEACON: a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500","volume":"12","author":"Zhou","year":"2019","journal-title":"BioData Min"},{"issue":"4","key":"10.1016\/j.imj.2026.100254_bib0053","doi-asserted-by":"crossref","DOI":"10.1128\/aac.01373-23","article-title":"Preclinical characterization of a non-peptidomimetic HIV protease inhibitor with improved metabolic stability","volume":"68","author":"Mulato","year":"2024","journal-title":"Antimicrob Agents Chemother"},{"issue":"7","key":"10.1016\/j.imj.2026.100254_bib0054","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/s41573-023-00692-8","article-title":"Accelerating antiviral drug discovery: lessons from COVID-19","volume":"22","author":"von Delft","year":"2023","journal-title":"Nat Rev Drug Discov"},{"issue":"41","key":"10.1016\/j.imj.2026.100254_bib0055","doi-asserted-by":"crossref","first-page":"7117","DOI":"10.1016\/j.vaccine.2011.05.071","article-title":"Ensuring the safety of vaccine cell substrates by massively parallel sequencing of the transcriptome","volume":"29","author":"Onions","year":"2011","journal-title":"Vaccine"},{"issue":"9","key":"10.1016\/j.imj.2026.100254_bib0056","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.tibtech.2012.05.005","article-title":"Next generation deep sequencing and vaccine design: today and tomorrow","volume":"30","author":"Luciani","year":"2012","journal-title":"Trends Biotechnol"},{"issue":"5","key":"10.1016\/j.imj.2026.100254_bib0057","doi-asserted-by":"crossref","first-page":"568","DOI":"10.3390\/pathogens11050568","article-title":"Phage Immunoprecipitation sequencing (PhIP-seq): the promise of high throughput serology","volume":"11","author":"Tiu","year":"2022","journal-title":"Pathogens"},{"issue":"12","key":"10.1016\/j.imj.2026.100254_bib0058","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1039\/C5IB00169B","article-title":"Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing","volume":"7","author":"Tsioris","year":"2015","journal-title":"Integr Biol"},{"key":"10.1016\/j.imj.2026.100254_bib0059","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2022.974428","article-title":"Clinical utility of target amplicon sequencing test for rapid diagnosis of drug-resistant Mycobacterium tuberculosis from respiratory specimens","volume":"13","author":"Leung","year":"2022","journal-title":"Front Microbiol"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0060","article-title":"Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines","volume":"14","author":"Wang","year":"2024","journal-title":"Sci Rep"},{"issue":"10","key":"10.1016\/j.imj.2026.100254_bib0061","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1038\/s41573-023-00772-9","article-title":"Antimalarial drug discovery: progress and approaches","volume":"22","author":"Siqueira-Neto","year":"2023","journal-title":"Nat Rev Drug Discov"},{"issue":"10","key":"10.1016\/j.imj.2026.100254_bib0062","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1016\/S1473-3099(24)00263-9","article-title":"Targeted next-generation sequencing to diagnose drug-resistant tuberculosis: a systematic review and meta-analysis","volume":"24","author":"Schwab","year":"2024","journal-title":"Lancet Infect Dis"},{"key":"10.1016\/j.imj.2026.100254_bib0063","doi-asserted-by":"crossref","DOI":"10.3389\/fpubh.2023.1206056","article-title":"Direct detection of drug-resistant Mycobacterium tuberculosis using targeted next generation sequencing","volume":"11","author":"Murphy","year":"2023","journal-title":"Front Public Health"},{"key":"10.1016\/j.imj.2026.100254_bib0064","article-title":"Case Report: metagenomic next-generation sequencing assists in dynamic pathogen monitoring: powerful tool for progressing severe pneumonia","volume":"13","author":"Li","year":"2023","journal-title":"Front Cell Infect Microbiol"},{"issue":"4","key":"10.1016\/j.imj.2026.100254_bib0065","doi-asserted-by":"crossref","first-page":"153","DOI":"10.6026\/97320630014153","article-title":"Biomarker identification from RNA-seq data using a robust statistical approach","volume":"14","author":"Akond","year":"2018","journal-title":"Bioinformation"},{"issue":"3","key":"10.1016\/j.imj.2026.100254_bib0066","doi-asserted-by":"crossref","first-page":"293","DOI":"10.3390\/pathogens14030293","article-title":"Unlocking the interactions between the whole-body microbiome and HPV infection: a literature review","volume":"14","author":"Papamentzelopoulou","year":"2025","journal-title":"Pathogens"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0067","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1186\/s13104-020-05287-9","article-title":"Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis","volume":"13","author":"Chan","year":"2020","journal-title":"BMC Res Notes"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0068","doi-asserted-by":"crossref","first-page":"2089","DOI":"10.1038\/s41598-023-28715-9","article-title":"Simultaneous detection of Omicron and other SARS-CoV-2 variants by multiplex PCR MassARRAY technology","volume":"13","author":"Wacharapluesadee","year":"2023","journal-title":"Sci Rep"},{"issue":"3","key":"10.1016\/j.imj.2026.100254_bib0069","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/d41573-023-00014-y","article-title":"Error-corrected next-generation sequencing to advance nonclinical genotoxicity and carcinogenicity testing","volume":"22","author":"Marchetti","year":"2023","journal-title":"Nat Rev Drug Discov"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0070","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.jmb.2018.06.034","article-title":"Functional genomics via CRISPR-cas","volume":"431","author":"Ford","year":"2019","journal-title":"J Mol Biol"},{"issue":"6711","key":"10.1016\/j.imj.2026.100254_bib0071","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1126\/science.adn5371","article-title":"Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips","volume":"385","author":"Aguirre Rivera","year":"2024","journal-title":"Science"},{"key":"10.1016\/j.imj.2026.100254_bib0072","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2022.757844","article-title":"Potential opportunities and challenges of deploying next generation sequencing and CRISPR-cas systems to support diagnostics and surveillance towards malaria control and elimination in Africa","volume":"12","author":"Lyimo","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0073","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s13073-019-0672-4","article-title":"Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients","volume":"11","author":"Peters","year":"2019","journal-title":"Genome Med"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0074","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1186\/s13073-025-01478-w","article-title":"Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples","volume":"17","author":"Cunningham-Oakes","year":"2025","journal-title":"Genome Med"},{"issue":"7","key":"10.1016\/j.imj.2026.100254_bib0075","article-title":"Artificial intelligence and infectious diseases: Scope and perspectives","volume":"55","author":"Abbara","year":"2025","journal-title":"Infect Dis Now"},{"key":"10.1016\/j.imj.2026.100254_bib0076","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2025.1634194","article-title":"Enhancing pathogen identification through AI-assisted metagenomic sequencing","volume":"16","author":"Peng","year":"2025","journal-title":"Front Microbiol"},{"issue":"7","key":"10.1016\/j.imj.2026.100254_bib0077","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btaf370","article-title":"SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing","volume":"41","author":"Ludwig","year":"2025","journal-title":"Bioinformatics"},{"issue":"6","key":"10.1016\/j.imj.2026.100254_bib0078","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.02492-24","article-title":"Development of a culture-independent whole-genome sequencing of Nipah virus using the MinION Oxford Nanopore platform","volume":"13","author":"Rahman","year":"2025","journal-title":"Microbiol Spectr"},{"issue":"11","key":"10.1016\/j.imj.2026.100254_bib0079","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1038\/s41587-021-01108-x","article-title":"Nanopore sequencing technology, bioinformatics and applications","volume":"39","author":"Wang","year":"2021","journal-title":"Nat Biotechnol"},{"issue":"2","key":"10.1016\/j.imj.2026.100254_bib0080","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gky1142","article-title":"Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples","volume":"47","author":"Haile","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0081","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-023-47135-3","article-title":"Evaluating the performance of low-frequency variant calling tools for the detection of variants from short-read deep sequencing data","volume":"13","author":"Xiang","year":"2023","journal-title":"Sci Rep"},{"issue":"5","key":"10.1016\/j.imj.2026.100254_bib0082","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1007\/s40291-025-00797-3","article-title":"Optimization of metagenomic next-generation sequencing workflow with a novel host depletion method for enhanced pathogen detection","volume":"29","author":"Chen","year":"2025","journal-title":"Mol Diagn Ther"},{"key":"10.1016\/j.imj.2026.100254_bib0083","article-title":"Enhancing bloodstream infection diagnostics: a novel filtration and targeted next-generation sequencing approach for precise pathogen identification","volume":"16","author":"Lin","year":"2025","journal-title":"Front Microbiol"},{"issue":"10","key":"10.1016\/j.imj.2026.100254_bib0084","doi-asserted-by":"crossref","first-page":"2320","DOI":"10.3390\/microorganisms13102320","article-title":"Typing of Yersinia pestis in challenging forensic samples through targeted next-generation sequencing of multilocus variable number tandem repeat regions","volume":"13","author":"Yun","year":"2025","journal-title":"Microorganisms"},{"issue":"2","key":"10.1016\/j.imj.2026.100254_bib0085","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/s41436-018-0063-z","article-title":"The impact of variant classification on the clinical management of hereditary cancer syndromes","volume":"21","author":"Turner","year":"2019","journal-title":"Genet Med"},{"key":"10.1016\/j.imj.2026.100254_bib0086","doi-asserted-by":"crossref","first-page":"286","DOI":"10.12688\/wellcomeopenres.19453.1","article-title":"Nf-core\/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis","volume":"8","author":"West","year":"2023","journal-title":"Wellcome Open Res"},{"issue":"3","key":"10.1016\/j.imj.2026.100254_bib0087","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat Biotechnol"},{"issue":"6","key":"10.1016\/j.imj.2026.100254_bib0088","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1200\/JCO.23.02761","article-title":"Large-scale pharmacogenomics analysis of patients with cancer within the 100, 000 genomes project combining whole-genome sequencing and medical records to inform clinical practice","volume":"43","author":"Leong","year":"2025","journal-title":"J Clin Oncol"},{"issue":"1","key":"10.1016\/j.imj.2026.100254_bib0089","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1163\/157180904323042399","article-title":"International declaration on human genetic data","volume":"11","author":"Abbing","year":"2004","journal-title":"Eur J Health Law"},{"issue":"7","key":"10.1016\/j.imj.2026.100254_bib0090","doi-asserted-by":"crossref","DOI":"10.1136\/bmjgh-2024-018494","article-title":"WHO guidance for human genome data collection, access, use and sharing: why granularity maximisation in informed consent should be reconsidered","volume":"10","author":"Thaldar","year":"2025","journal-title":"BMJ Glob Health"},{"issue":"12","key":"10.1016\/j.imj.2026.100254_bib0091","doi-asserted-by":"crossref","DOI":"10.1016\/j.patter.2021.100366","article-title":"Differential privacy for public health data: an innovative tool to optimize information sharing while protecting data confidentiality","volume":"2","author":"Dyda","year":"2021","journal-title":"Patterns"},{"issue":"6","key":"10.1016\/j.imj.2026.100254_bib0092","doi-asserted-by":"crossref","DOI":"10.1016\/j.patter.2024.101006","article-title":"Recent methodological advances in federated learning for healthcare","volume":"5","author":"Zhang","year":"2024","journal-title":"Patterns"},{"issue":"6","key":"10.1016\/j.imj.2026.100254_bib0093","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1093\/bioinformatics\/btaa764","article-title":"Mainzelliste SecureEpiLinker (MainSEL): privacy-preserving record linkage using secure multi-party computation","volume":"38","author":"Stammler","year":"2022","journal-title":"Bioinformatics"}],"container-title":["Infectious Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2772431X26000201?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2772431X26000201?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T16:21:34Z","timestamp":1781022094000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2772431X26000201"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6]]},"references-count":93,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,6]]}},"alternative-id":["S2772431X26000201"],"URL":"https:\/\/doi.org\/10.1016\/j.imj.2026.100254","relation":{},"ISSN":["2772-431X"],"issn-type":[{"value":"2772-431X","type":"print"}],"subject":[],"published":{"date-parts":[[2026,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Next-generation sequencing: Driving a paradigm shift from pathogen detection to systems-level analysis","name":"articletitle","label":"Article Title"},{"value":"Infectious Medicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.imj.2026.100254","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Ltd on behalf of Tsinghua University Press.","name":"copyright","label":"Copyright"}],"article-number":"100254"}}