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For: Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G. Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox. Genome Biol 2021;22:93. [PMID: 33785070 DOI: 10.1186/s13059-021-02306-1] [Cited by in Crossref: 6] [Cited by in F6Publishing: 6] [Article Influence: 6.0] [Reference Citation Analysis]
Number Citing Articles
1 Abbas-Egbariya H, Haberman Y, Braun T, Hadar R, Denson L, Gal-Mor O, Amir A. Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal. Genome Biol 2022;23:61. [PMID: 35197084 DOI: 10.1186/s13059-022-02637-7] [Reference Citation Analysis]
2 Qing Y, Xu L, Cui G, Sun L, Hu X, Yang X, Jiang J, Zhang J, Zhang T, Wang T, He L, Wang J, Wan C. Salivary microbiome profiling reveals a dysbiotic schizophrenia-associated microbiota. NPJ Schizophr 2021;7:51. [PMID: 34711862 DOI: 10.1038/s41537-021-00180-1] [Reference Citation Analysis]
3 Clausen DS, Willis AD. Evaluating replicability in microbiome data. Biostatistics 2021:kxab048. [PMID: 34969071 DOI: 10.1093/biostatistics/kxab048] [Reference Citation Analysis]
4 García-Jiménez B, Muñoz J, Cabello S, Medina J, Wilkinson MD. Predicting microbiomes through a deep latent space. Bioinformatics 2021;37:1444-51. [PMID: 33289510 DOI: 10.1093/bioinformatics/btaa971] [Reference Citation Analysis]
5 Sorbie A, Delgado Jiménez R, Benakis C. Increasing transparency and reproducibility in stroke-microbiota research: A toolbox for microbiota analysis. iScience 2022;25:103998. [DOI: 10.1016/j.isci.2022.103998] [Reference Citation Analysis]
6 Saboo K, Petrakov NV, Shamsaddini A, Fagan A, Gavis EA, Sikaroodi M, McGeorge S, Gillevet PM, Iyer RK, Bajaj JS. Stool microbiota are superior to saliva in distinguishing cirrhosis and hepatic encephalopathy using machine learning. J Hepatol 2021:S0168-8278(21)02183-8. [PMID: 34793867 DOI: 10.1016/j.jhep.2021.11.011] [Reference Citation Analysis]
7 Lee KA, Thomas AM, Bolte LA, Björk JR, de Ruijter LK, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Leeming ER, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Vijay A, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Bataille V, Hospers GAP, Spector TD, Weersma RK, Segata N. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nat Med 2022;28:535-44. [PMID: 35228751 DOI: 10.1038/s41591-022-01695-5] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
8 Han W, Tang H, Ye Y. Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype. J Comput Biol 2022. [PMID: 35584271 DOI: 10.1089/cmb.2021.0640] [Reference Citation Analysis]
9 Intze  E, Lagkouvardos  I. DivCom: A Tool for Systematic Partition of Groups of Microbial Profiles Into Intrinsic Subclusters and Distance-Based Subgroup Comparisons. Front Bioinform 2022;2:864382. [DOI: 10.3389/fbinf.2022.864382] [Reference Citation Analysis]
10 Tataru C, Eaton A, David MM. GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data. Front Bioinform 2022;2:828703. [DOI: 10.3389/fbinf.2022.828703] [Reference Citation Analysis]
11 Kishikawa T, Tomofuji Y, Inohara H, Okada Y. OMARU: a robust and multifaceted pipeline for metagenome-wide association study. NAR Genomics and Bioinformatics 2022;4:lqac019. [DOI: 10.1093/nargab/lqac019] [Reference Citation Analysis]
12 Liu B, Sträuber H, Saraiva J, Harms H, Silva SG, Kasmanas JC, Kleinsteuber S, Nunes da Rocha U. Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture. Microbiome 2022;10:48. [PMID: 35331330 DOI: 10.1186/s40168-021-01219-2] [Reference Citation Analysis]
13 Gaio D, DeMaere MZ, Anantanawat K, Chapman TA, Djordjevic SP, Darling AE. Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes. Microb Genom 2021;7. [PMID: 34370660 DOI: 10.1099/mgen.0.000501] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
14 Fishbein SR, Robinson JI, Hink T, Reske KA, Newcomer EP, Burnham CD, Henderson JP, Dubberke ER, Dantas G. Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis. Elife 2022;11:e72801. [PMID: 35083969 DOI: 10.7554/eLife.72801] [Reference Citation Analysis]
15 Vänni P, Tejesvi MV, Ainonen S, Renko M, Korpela K, Salo J, Paalanne N, Tapiainen T. Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome. Sci Rep 2021;11:17483. [PMID: 34471207 DOI: 10.1038/s41598-021-97007-x] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
16 Curry KD, Nute MG, Treangen TJ. It takes guts to learn: machine learning techniques for disease detection from the gut microbiome. Emerg Top Life Sci 2021;5:815-27. [PMID: 34779841 DOI: 10.1042/ETLS20210213] [Reference Citation Analysis]
17 Kartal E, Schmidt TSB, Molina-Montes E, Rodríguez-Perales S, Wirbel J, Maistrenko OM, Akanni WA, Alashkar Alhamwe B, Alves RJ, Carrato A, Erasmus HP, Estudillo L, Finkelmeier F, Fullam A, Glazek AM, Gómez-Rubio P, Hercog R, Jung F, Kandels S, Kersting S, Langheinrich M, Márquez M, Molero X, Orakov A, Van Rossum T, Torres-Ruiz R, Telzerow A, Zych K, Benes V, Zeller G, Trebicka J, Real FX, Malats N, Bork P; MAGIC Study investigators., PanGenEU Study investigators. A faecal microbiota signature with high specificity for pancreatic cancer. Gut 2022:gutjnl-2021-324755. [PMID: 35260444 DOI: 10.1136/gutjnl-2021-324755] [Reference Citation Analysis]
18 de Jesus VC, Khan MW, Mittermuller BA, Duan K, Hu P, Schroth RJ, Chelikani P. Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood Caries. Front Microbiol 2021;12:683685. [PMID: 34248903 DOI: 10.3389/fmicb.2021.683685] [Cited by in F6Publishing: 2] [Reference Citation Analysis]
19 Podlesny D, Arze C, Dörner E, Verma S, Dutta S, Walter J, Fricke WF. Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation. Microbiome 2022;10:53. [PMID: 35337386 DOI: 10.1186/s40168-022-01251-w] [Reference Citation Analysis]
20 Robertson RC, Church JA, Edens TJ, Mutasa K, Min Geum H, Baharmand I, Gill SK, Ntozini R, Chasekwa B, Carr L, Majo FD, Kirkpatrick BD, Lee B, Moulton LH, Humphrey JH, Prendergast AJ, Manges AR; SHINE Trial Team. The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants. Vaccine 2021;39:5391-400. [PMID: 34393020 DOI: 10.1016/j.vaccine.2021.07.076] [Reference Citation Analysis]
21 David MM, Tataru C, Pope Q, Baker LJ, English MK, Epstein HE, Hammer A, Kent M, Sieler MJ Jr, Mueller RS, Sharpton TJ, Tomas F, Vega Thurber R, Fern XZ. Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning. mSystems 2022;:e0105821. [PMID: 35040699 DOI: 10.1128/msystems.01058-21] [Reference Citation Analysis]
22 Voigt AY, Emiola A, Johnson JS, Fleming ES, Nguyen H, Zhou W, Tsai KY, Fink C, Oh J. Skin microbiome variation with cancer progression in human cutaneous squamous cell carcinoma. J Invest Dermatol 2022:S0022-202X(22)00261-5. [PMID: 35390349 DOI: 10.1016/j.jid.2022.03.017] [Reference Citation Analysis]
23 Sim CK, Kashaf SS, Stacy A, Proctor DM, Almeida A, Bouladoux N, Chen M, Finn RD, Belkaid Y, Conlan S, Segre JA; NISC Comparative Sequencing Program. A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae. Microbiome 2022;10:43. [PMID: 35272717 DOI: 10.1186/s40168-021-01207-6] [Reference Citation Analysis]
24 Sundh J, Tanash H, Arian R, Neves-Guimaraes A, Broberg K, Lindved G, Kern T, Zych K, Nielsen HB, Halling A, Ohlsson B, Jönsson D. Advanced Dental Cleaning is Associated with Reduced Risk of COPD Exacerbations - A Randomized Controlled Trial. Int J Chron Obstruct Pulmon Dis 2021;16:3203-15. [PMID: 34858021 DOI: 10.2147/COPD.S327036] [Reference Citation Analysis]