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For: Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R. Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel. J Clin Microbiol 2016;54:1000-7. [PMID: 26818672 DOI: 10.1128/JCM.03060-15] [Cited by in Crossref: 132] [Cited by in F6Publishing: 139] [Article Influence: 18.9] [Reference Citation Analysis]
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2 Liang Y, Feng Q, Wei K, Hou X, Song X, Li Y. Potential of metagenomic next-generation sequencing in detecting infections of ICU patients. Mol Cell Probes 2023;68:101898. [PMID: 36764622 DOI: 10.1016/j.mcp.2023.101898] [Reference Citation Analysis]
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6 Almas S, Carpenter RE, Singh A, Rowan C, Tamrakar VK, Sharma R. Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential. Adv Respir Med 2023;91:49-65. [PMID: 36825940 DOI: 10.3390/arm91010006] [Reference Citation Analysis]
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12 Niles DT, Lee RA, Lamb GS, Dhaheri FA, Boguniewicz J. Plasma Cell-Free Metagenomic Next Generation Sequencing in the Clinical Setting for the Diagnosis of Infectious Diseases: A Systematic Review and Meta-Analysis. Diagnostic Microbiology and Infectious Disease 2022. [DOI: 10.1016/j.diagmicrobio.2022.115838] [Reference Citation Analysis]
13 Gemler BT, Mukherjee C, Howland C, Fullerton PA, Spurbeck RR, Catlin LA, Smith A, Minard-smith AT, Bartling C. UltraSEQ: a universal bioinformatic platform for information-based clinical metagenomics and beyond.. [DOI: 10.1101/2022.08.24.505213] [Reference Citation Analysis]
14 Ogunbayo AE, Mogotsi MT, Sondlane H, Nkwadipo KR, Sabiu S, Nyaga MM. Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa. Int J Environ Res Public Health 2022;19:10418. [PMID: 36012053 DOI: 10.3390/ijerph191610418] [Cited by in F6Publishing: 2] [Reference Citation Analysis]
15 Wang X, Stelzer-Braid S, Scotch M, Rawlinson WD. Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use. Rev Med Virol 2022;:e2375. [PMID: 35775736 DOI: 10.1002/rmv.2375] [Reference Citation Analysis]
16 Chen Z, Tian Y, Wang Y, Zhao H, Chen C, Zhang F. Profile of the Lower Respiratory Tract Microbiome in Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome and Lung Disease. Front Microbiol 2022;13:888996. [DOI: 10.3389/fmicb.2022.888996] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
17 Havasi A, Visan S, Cainap C, Cainap SS, Mihaila AA, Pop L. Influenza A, Influenza B, and SARS-CoV-2 Similarities and Differences – A Focus on Diagnosis. Front Microbiol 2022;13:908525. [DOI: 10.3389/fmicb.2022.908525] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
18 Lamoureux C, Surgers L, Fihman V, Gricourt G, Demontant V, Trawinski E, N'Debi M, Gomart C, Royer G, Launay N, Le Glaunec JM, Wemmert C, La Martire G, Rossi G, Lepeule R, Pawlotsky JM, Rodriguez C, Woerther PL. Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections. Front Microbiol 2022;13:761873. [PMID: 35464955 DOI: 10.3389/fmicb.2022.761873] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
19 Soto RA, Paul L, Porucznik CA, Xie H, Stinnett RC, Briggs B, Biggerstaff M, Stanford JB, Schlaberg R. Improving Pandemic Preparedness Through Metagenomics-Based Detection and Genotyping of Respiratory Viruses in Self-Collected, Ambient Temperature-Preserved Nasal Swabs (Preprint).. [DOI: 10.2196/preprints.32848] [Reference Citation Analysis]
20 Tosta E. The adaptation of SARS-CoV-2 to humans. Mem Inst Oswaldo Cruz 2022;116:e210127. [PMID: 35019068 DOI: 10.1590/0074-02760210127] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
21 Goswami S, Kumar V, Chakraborty J. Computational biology and biosensors as surveillance tools for emerging and re-emerging infectious diseases. Biosensors for Emerging and Re-Emerging Infectious Diseases 2022. [DOI: 10.1016/b978-0-323-88464-8.00018-x] [Reference Citation Analysis]
22 Zhang Z, Ma P, Ahmed R, Wang J, Akin D, Soto F, Liu BF, Li P, Demirci U. Advanced Point-of-Care Testing Technologies for Human Acute Respiratory Virus Detection. Adv Mater 2022;34:e2103646. [PMID: 34623709 DOI: 10.1002/adma.202103646] [Cited by in Crossref: 24] [Cited by in F6Publishing: 28] [Article Influence: 24.0] [Reference Citation Analysis]
23 Boix-amorós A, Lee AG, Clemente JC. The Rest Is Noise: Finding Signals in Lung Microbiome Data Analysis. The Microbiome in Respiratory Disease 2022. [DOI: 10.1007/978-3-030-87104-8_3] [Reference Citation Analysis]
24 Bartlow AW, Stromberg ZR, Gleasner CD, Hu B, Davenport KW, Jakhar S, Li PE, Vosburg M, Garimella M, Chain PSG, Erkkila TH, Fair JM, Mukundan H. Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods. PLOS Glob Public Health 2022;2:e0000811. [PMID: 36962439 DOI: 10.1371/journal.pgph.0000811] [Cited by in Crossref: 3] [Article Influence: 3.0] [Reference Citation Analysis]
25 van Zyl GU. New Technological Developments in Identification and Monitoring of New and Emerging Infections. Encyclopedia of Infection and Immunity 2022. [DOI: 10.1016/b978-0-12-818731-9.00094-x] [Reference Citation Analysis]
26 Redd TK, Lalitha P, Prajna NV, Sikha M, Gunasekaran R, Hinterwirth A, Chen C, Zhong L, Liu Z, Lietman TM, Keenan JD, Doan T, Seitzman GD. Impact of Sample Collection Order on the Diagnostic Performance of Metagenomic Deep Sequencing for Infectious Keratitis. Cornea 2022;41:39-44. [PMID: 34870622 DOI: 10.1097/ICO.0000000000002766] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
27 Kim SH, Kwon YK, Park CK, Kim HR. Identification of Campylobacter jejuni and Chlamydia psittaci from cockatiel (Nymphicus hollandicus) using metagenomics. BMC Genomics 2021;22:797. [PMID: 34742232 DOI: 10.1186/s12864-021-08122-y] [Reference Citation Analysis]
28 Mu S, Hu L, Zhang Y, Liu Y, Cui X, Zou X, Wang Y, Lu B, Zhou S, Liang X, Liang C, Xiao N, O'Grady J, Lee S, Cao B. Prospective Evaluation of a Rapid Clinical Metagenomics Test for Bacterial Pneumonia. Front Cell Infect Microbiol 2021;11:684965. [PMID: 34737971 DOI: 10.3389/fcimb.2021.684965] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
29 Suman S, Kumar A, Saxena I, Kumar M. Fungal Keratitis: Recent Advances in Diagnosis and Treatment. Infectious Eye Diseases - Recent Advances in Diagnosis and Treatment 2021. [DOI: 10.5772/intechopen.98411] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
30 Courtney SJ, Stromberg ZR, Myers Y Gutiérrez A, Jacobsen D, Stromberg LR, Lenz KD, Theiler J, Foley BT, Gans J, Yusim K, Kubicek-Sutherland JZ. Optical Biosensor Platforms Display Varying Sensitivity for the Direct Detection of Influenza RNA. Biosensors (Basel) 2021;11:367. [PMID: 34677323 DOI: 10.3390/bios11100367] [Cited by in Crossref: 3] [Cited by in F6Publishing: 4] [Article Influence: 1.5] [Reference Citation Analysis]
31 Zheng Y, Qiu X, Wang T, Zhang J. The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection. Front Cell Infect Microbiol 2021;11:694756. [PMID: 34568089 DOI: 10.3389/fcimb.2021.694756] [Cited by in Crossref: 4] [Cited by in F6Publishing: 5] [Article Influence: 2.0] [Reference Citation Analysis]
32 Han D, Diao Z, Lai H, Han Y, Xie J, Zhang R, Li J. Multilaboratory assessment of metagenomic next-generation sequencing for unbiased microbe detection. Journal of Advanced Research 2021. [DOI: 10.1016/j.jare.2021.09.011] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 0.5] [Reference Citation Analysis]
33 Diao Z, Han D, Zhang R, Li J. Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections. Journal of Advanced Research 2021. [DOI: 10.1016/j.jare.2021.09.012] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 2.0] [Reference Citation Analysis]
34 Tosta E. The protective immunity induced by SARS-CoV-2 infection and vaccination: a critical appraisal. Explor Immunol. [DOI: 10.37349/ei.2021.00014] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 2.5] [Reference Citation Analysis]
35 Govender KN, Street TL, Sanderson ND, Eyre DW. Metagenomic Sequencing as a Pathogen-Agnostic Clinical Diagnostic Tool for Infectious Diseases: a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies. J Clin Microbiol 2021;59:e0291620. [PMID: 33910965 DOI: 10.1128/JCM.02916-20] [Cited by in Crossref: 13] [Cited by in F6Publishing: 15] [Article Influence: 6.5] [Reference Citation Analysis]
36 Ramchandar N, Burns J, Coufal NG, Pennock A, Briggs B, Stinnett R, Bradley J, Arnold J, Liu GY, Pring M, Upasani VV, Rickert K, Dimmock D, Chiu C, Farnaes L, Cannavino C. Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections. Open Forum Infect Dis 2021;8:ofab346. [PMID: 34322569 DOI: 10.1093/ofid/ofab346] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 2.0] [Reference Citation Analysis]
37 Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St Hilaire M, Austin S, Landis RC, Steininger C. Viral metagenomics reveals the presence of novel Zika virus variants in Aedes mosquitoes from Barbados. Parasit Vectors 2021;14:343. [PMID: 34187544 DOI: 10.1186/s13071-021-04840-0] [Cited by in Crossref: 7] [Cited by in F6Publishing: 7] [Article Influence: 3.5] [Reference Citation Analysis]
38 Chen H, Li J, Yan S, Sun H, Tan C, Liu M, Liu K, Zhang H, Zou M, Xiao X. Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study. PeerJ 2021;9:e11699. [PMID: 34249516 DOI: 10.7717/peerj.11699] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 0.5] [Reference Citation Analysis]
39 Xu J, Yu Y, Lv J, Yang S, Wu J, Chen J, Peng W. Application of Metagenomic Next-Generation Sequencing to Diagnose Pneumocystis jirovecii Pneumonia in Kidney Transplantation Recipients. Ann Transplant 2021;26:e931059. [PMID: 34099614 DOI: 10.12659/AOT.931059] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 2.0] [Reference Citation Analysis]
40 Valença IN, Santos RBD, Peronni KC, Sauvage V, Vandenbogaert M, Caro V, Silva Junior WAD, Covas DT, Silva-Pinto AC, Laperche S, Kashima S, Slavov SN. Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia. Rev Inst Med Trop Sao Paulo 2021;63:e40. [PMID: 34037156 DOI: 10.1590/S1678-9946202163040] [Reference Citation Analysis]
41 Waweru JW, de Laurent Z, Kamau E, Said K, Gicheru E, Mutunga M, Kibet C, Kinyua J, Nokes DJ, Sande C, Githinji G. Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples. Wellcome Open Res 2021;6:99. [DOI: 10.12688/wellcomeopenres.16756.1] [Reference Citation Analysis]
42 Ramchandar N, Coufal NG, Warden AS, Briggs B, Schwarz T, Stinnett R, Xie H, Schlaberg R, Foley J, Clarke C, Waldeman B, Enriquez C, Osborne S, Arrieta A, Salyakina D, Janvier M, Sendi P, Totapally BR, Dimmock D, Farnaes L. Metagenomic Next-Generation Sequencing for Pathogen Detection and Transcriptomic Analysis in Pediatric Central Nervous System Infections. Open Forum Infect Dis 2021;8:ofab104. [PMID: 34104666 DOI: 10.1093/ofid/ofab104] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 2.5] [Reference Citation Analysis]
43 Courtney SJ, Stromberg ZR, Kubicek-Sutherland JZ. Nucleic Acid-Based Sensing Techniques for Diagnostics and Surveillance of Influenza. Biosensors (Basel) 2021;11:47. [PMID: 33673035 DOI: 10.3390/bios11020047] [Cited by in Crossref: 6] [Cited by in F6Publishing: 7] [Article Influence: 3.0] [Reference Citation Analysis]
44 Acera Mateos P, Balboa RF, Easteal S, Eyras E, Patel HR. PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses. Sci Rep 2021;11:3209. [PMID: 33547380 DOI: 10.1038/s41598-021-82043-4] [Cited by in Crossref: 7] [Cited by in F6Publishing: 7] [Article Influence: 3.5] [Reference Citation Analysis]
45 Filkins L, Schlaberg R. Metagenomic Applications for Infectious Disease Testing in Clinical Laboratories. Application and Integration of Omics-powered Diagnostics in Clinical and Public Health Microbiology 2021. [DOI: 10.1007/978-3-030-62155-1_7] [Reference Citation Analysis]
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47 Plyusnin I, Kant R, Jääskeläinen AJ, Sironen T, Holm L, Vapalahti O, Smura T. Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types. Virus Evol 2020;6:veaa091. [PMID: 33408878 DOI: 10.1093/ve/veaa091] [Cited by in Crossref: 17] [Cited by in F6Publishing: 17] [Article Influence: 5.7] [Reference Citation Analysis]
48 Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020;8:E1539. [PMID: 33036303 DOI: 10.3390/microorganisms8101539] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 1.7] [Reference Citation Analysis]
49 Thi Kha Tu N, Thi Thu Hong N, Thi Han Ny N, My Phuc T, Thi Thanh Tam P, Doorn HRV, Dang Trung Nghia H, Thao Huong D, An Han D, Thi Thu Ha L, Deng X, Thwaites G, Delwart E, Virtala AK, Vapalahti O, Baker S, Van Tan L. The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections. Viruses 2020;12:E960. [PMID: 32872469 DOI: 10.3390/v12090960] [Cited by in Crossref: 9] [Cited by in F6Publishing: 9] [Article Influence: 3.0] [Reference Citation Analysis]
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51 Mateos PA, Balboa RF, Easteal S, Eyras E, Patel HR. PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses.. [DOI: 10.1101/2020.07.24.219097] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.3] [Reference Citation Analysis]
52 Wang H, Lu Z, Bao Y, Yang Y, de Groot R, Dai W, de Jonge MI, Zheng Y. Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia. PLoS One 2020;15:e0232610. [PMID: 32497137 DOI: 10.1371/journal.pone.0232610] [Cited by in Crossref: 17] [Cited by in F6Publishing: 18] [Article Influence: 5.7] [Reference Citation Analysis]
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55 Li G, Huang J, Li Y, Feng J. The Value of Combined Radial Endobronchial Ultrasound-Guided Transbronchial Lung Biopsy and Metagenomic Next-Generation Sequencing for Peripheral Pulmonary Infectious Lesions. Can Respir J 2020;2020:2367505. [PMID: 32322324 DOI: 10.1155/2020/2367505] [Cited by in Crossref: 5] [Cited by in F6Publishing: 7] [Article Influence: 1.7] [Reference Citation Analysis]
56 Shami A, Al-mijalli S, Somily A, Albarakaty FM, Abdurahim SA. Incidence and susceptibility patterns of urine bacterial flora in young females.. [DOI: 10.1101/2020.03.18.996793] [Reference Citation Analysis]
57 Thoendel M, Jeraldo P, Greenwood-Quaintance KE, Yao J, Chia N, Hanssen AD, Abdel MP, Patel R. Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis. J Clin Microbiol 2020;58:e00981-19. [PMID: 31826963 DOI: 10.1128/JCM.00981-19] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 1.7] [Reference Citation Analysis]
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62 van Rijn AL, van Boheemen S, Sidorov I, Carbo EC, Pappas N, Mei H, Feltkamp M, Aanerud M, Bakke P, Claas ECJ, Eagan TM, Hiemstra PS, Kroes ACM, de Vries JJC. The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. PLoS One 2019;14:e0223952. [PMID: 31647831 DOI: 10.1371/journal.pone.0223952] [Cited by in Crossref: 40] [Cited by in F6Publishing: 40] [Article Influence: 10.0] [Reference Citation Analysis]
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64 Altan E, Dib JC, Gulloso AR, Escribano Juandigua D, Deng X, Bruhn R, Hildebrand K, Freiden P, Yamamoto J, Schultz-Cherry S, Delwart E. Effect of Geographic Isolation on the Nasal Virome of Indigenous Children. J Virol 2019;93:e00681-19. [PMID: 31189707 DOI: 10.1128/JVI.00681-19] [Cited by in Crossref: 7] [Cited by in F6Publishing: 8] [Article Influence: 1.8] [Reference Citation Analysis]
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