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For: Ainsworth D, Sternberg MJE, Raczy C, Butcher SA. k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets. Nucleic Acids Res 2017;45:1649-56. [PMID: 27965413 DOI: 10.1093/nar/gkw1248] [Cited by in Crossref: 10] [Cited by in F6Publishing: 20] [Article Influence: 2.0] [Reference Citation Analysis]
Number Citing Articles
1 Hicks SD, Uhlig R, Afshari P, Williams J, Chroneos M, Tierney-Aves C, Wagner K, Middleton FA. Oral microbiome activity in children with autism spectrum disorder. Autism Res 2018;11:1286-99. [PMID: 30107083 DOI: 10.1002/aur.1972] [Cited by in Crossref: 25] [Cited by in F6Publishing: 23] [Article Influence: 6.3] [Reference Citation Analysis]
2 Seol D, Jhang SY, Kim H, Kim SY, Kwak HS, Kim SH, Lee W, Park S, Kim H, Cho S, Kwak W. Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data. Front Microbiol 2019;10:1683. [PMID: 31440213 DOI: 10.3389/fmicb.2019.01683] [Cited by in Crossref: 9] [Cited by in F6Publishing: 6] [Article Influence: 3.0] [Reference Citation Analysis]
3 Hicks SD, Rajan AT, Wagner KE, Barns S, Carpenter RL, Middleton FA. Validation of a Salivary RNA Test for Childhood Autism Spectrum Disorder. Front Genet 2018;9:534. [PMID: 30473705 DOI: 10.3389/fgene.2018.00534] [Cited by in Crossref: 21] [Cited by in F6Publishing: 17] [Article Influence: 5.3] [Reference Citation Analysis]
4 Mihaila D, Donegan J, Barns S, LaRocca D, Du Q, Zheng D, Vidal M, Neville C, Uhlig R, Middleton FA. The oral microbiome of early stage Parkinson's disease and its relationship with functional measures of motor and non-motor function. PLoS One 2019;14:e0218252. [PMID: 31247001 DOI: 10.1371/journal.pone.0218252] [Cited by in Crossref: 20] [Cited by in F6Publishing: 18] [Article Influence: 6.7] [Reference Citation Analysis]
5 Shi W, Qi H, Sun Q, Fan G, Liu S, Wang J, Zhu B, Liu H, Zhao F, Wang X, Hu X, Li W, Liu J, Tian Y, Wu L, Ma J. gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. Nucleic Acids Res 2019;47:D637-48. [PMID: 30365027 DOI: 10.1093/nar/gky1008] [Cited by in Crossref: 23] [Cited by in F6Publishing: 17] [Article Influence: 11.5] [Reference Citation Analysis]
6 Banerjee K, Zhao N, Srinivasan A, Xue L, Hicks SD, Middleton FA, Wu R, Zhan X. An Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis. Front Genet 2019;10:350. [PMID: 31068967 DOI: 10.3389/fgene.2019.00350] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 0.7] [Reference Citation Analysis]
7 Breitwieser FP, Lu J, Salzberg SL. A review of methods and databases for metagenomic classification and assembly. Brief Bioinform 2019;20:1125-36. [PMID: 29028872 DOI: 10.1093/bib/bbx120] [Cited by in Crossref: 155] [Cited by in F6Publishing: 116] [Article Influence: 77.5] [Reference Citation Analysis]
8 Ye SH, Siddle KJ, Park DJ, Sabeti PC. Benchmarking Metagenomics Tools for Taxonomic Classification. Cell 2019;178:779-94. [PMID: 31398336 DOI: 10.1016/j.cell.2019.07.010] [Cited by in Crossref: 104] [Cited by in F6Publishing: 76] [Article Influence: 52.0] [Reference Citation Analysis]
9 Escobar-Zepeda A, Godoy-Lozano EE, Raggi L, Segovia L, Merino E, Gutiérrez-Rios RM, Juarez K, Licea-Navarro AF, Pardo-Lopez L, Sanchez-Flores A. Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics. Sci Rep 2018;8:12034. [PMID: 30104688 DOI: 10.1038/s41598-018-30515-5] [Cited by in Crossref: 38] [Cited by in F6Publishing: 27] [Article Influence: 9.5] [Reference Citation Analysis]
10 R Marcelino V, Holmes EC, Sorrell TC. The use of taxon-specific reference databases compromises metagenomic classification. BMC Genomics 2020;21:184. [PMID: 32106809 DOI: 10.1186/s12864-020-6592-2] [Cited by in Crossref: 6] [Cited by in F6Publishing: 6] [Article Influence: 3.0] [Reference Citation Analysis]
11 Itsko M, Retchless AC, Joseph SJ, Norris Turner A, Bazan JA, Sadji AY, Ouédraogo-Traoré R, Wang X. Full Molecular Typing of Neisseria meningitidis Directly from Clinical Specimens for Outbreak Investigation. J Clin Microbiol 2020;58:e01780-20. [PMID: 32938738 DOI: 10.1128/JCM.01780-20] [Cited by in Crossref: 3] [Cited by in F6Publishing: 1] [Article Influence: 1.5] [Reference Citation Analysis]
12 Osunmakinde CO, Selvarajan R, Sibanda T, Mamba BB, Msagati TAM. Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018;10:E429. [PMID: 30110939 DOI: 10.3390/v10080429] [Cited by in Crossref: 5] [Cited by in F6Publishing: 4] [Article Influence: 1.3] [Reference Citation Analysis]
13 Bowden KE, Joseph SJ, Cartee JC, Ziklo N, Danavall D, Raphael BH, Read TD, Dean D. Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs. mSphere 2021;6:e01302-20. [PMID: 33658279 DOI: 10.1128/mSphere.01302-20] [Reference Citation Analysis]
14 Bozio CH, Vuong J, Dokubo EK, Fallah MP, McNamara LA, Potts CC, Doedeh J, Gbanya M, Retchless AC, Patel JC, Clark TA, Kohar H, Nagbe T, Clement P, Katawera V, Mahmoud N, Djingarey HM, Perrocheau A, Naidoo D, Stone M, George RN, Williams D, Gasasira A, Nyenswah T, Wang X, Fox LM; Liberian Meningococcal Disease Outbreak Response Team. Outbreak of Neisseria meningitidis serogroup C outside the meningitis belt-Liberia, 2017: an epidemiological and laboratory investigation. Lancet Infect Dis 2018;18:1360-7. [PMID: 30337259 DOI: 10.1016/S1473-3099(18)30476-6] [Cited by in Crossref: 14] [Cited by in F6Publishing: 7] [Article Influence: 3.5] [Reference Citation Analysis]
15 Menegon M, Cantaloni C, Rodriguez-Prieto A, Centomo C, Abdelfattah A, Rossato M, Bernardi M, Xumerle L, Loader S, Delledonne M. On site DNA barcoding by nanopore sequencing. PLoS One 2017;12:e0184741. [PMID: 28977016 DOI: 10.1371/journal.pone.0184741] [Cited by in Crossref: 64] [Cited by in F6Publishing: 39] [Article Influence: 12.8] [Reference Citation Analysis]
16 Nasko DJ, Koren S, Phillippy AM, Treangen TJ. RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. Genome Biol 2018;19:165. [PMID: 30373669 DOI: 10.1186/s13059-018-1554-6] [Cited by in Crossref: 51] [Cited by in F6Publishing: 34] [Article Influence: 12.8] [Reference Citation Analysis]
17 Alvarenga DO, Fiore MF, Varani AM. A Metagenomic Approach to Cyanobacterial Genomics. Front Microbiol 2017;8:809. [PMID: 28536564 DOI: 10.3389/fmicb.2017.00809] [Cited by in Crossref: 48] [Cited by in F6Publishing: 37] [Article Influence: 9.6] [Reference Citation Analysis]
18 Hicks SD, Khurana N, Williams J, Dowd Greene C, Uhlig R, Middleton FA. Diurnal oscillations in human salivary microRNA and microbial transcription: Implications for human health and disease. PLoS One 2018;13:e0198288. [PMID: 30020932 DOI: 10.1371/journal.pone.0198288] [Cited by in Crossref: 12] [Cited by in F6Publishing: 12] [Article Influence: 3.0] [Reference Citation Analysis]
19 Yang C, Chowdhury D, Zhang Z, Cheung WK, Lu A, Bian Z, Zhang L. A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. Comput Struct Biotechnol J 2021;19:6301-14. [PMID: 34900140 DOI: 10.1016/j.csbj.2021.11.028] [Reference Citation Analysis]
20 Thurlow CM, Joseph SJ, Ganova-raeva L, Katz SS, Pereira L, Chen C, Debra A, Vilfort K, Workowski K, Cohen SE, Reno H, Sun Y, Burroughs M, Sheth M, Chi K, Danavall D, Philip SS, Cao W, Kersh EN, Pillay A, Marco ML. Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing. mSphere. [DOI: 10.1128/msphere.00009-22] [Reference Citation Analysis]
21 Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome 2017;5:69. [PMID: 28683828 DOI: 10.1186/s40168-017-0283-5] [Cited by in Crossref: 179] [Cited by in F6Publishing: 139] [Article Influence: 35.8] [Reference Citation Analysis]
22 Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, Han J, Holmes OB, Juan YF, King R, Kislyuk A, Lin MF, Mariano M, Morse T, Reynoso LV, Cruz DR, Sheu J, Tang J, Wang J, Zhang MA, Zhong E, Ahyong V, Lay S, Chea S, Bohl JA, Manning JE, Tato CM, DeRisi JL. IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience 2020;9:giaa111. [PMID: 33057676 DOI: 10.1093/gigascience/giaa111] [Cited by in Crossref: 10] [Cited by in F6Publishing: 18] [Article Influence: 5.0] [Reference Citation Analysis]
23 Nugent CM, Adamowicz SJ. Alignment-free classification of COI DNA barcode data with the Python package Alfie. MBMG 2020;4:e55815. [DOI: 10.3897/mbmg.4.55815] [Cited by in Crossref: 6] [Article Influence: 3.0] [Reference Citation Analysis]