• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4681712)   Today's Articles (3412)
For: Marcos-Zambrano LJ, Karaduzovic-Hadziabdic K, Loncar Turukalo T, Przymus P, Trajkovik V, Aasmets O, Berland M, Gruca A, Hasic J, Hron K, Klammsteiner T, Kolev M, Lahti L, Lopes MB, Moreno V, Naskinova I, Org E, Paciência I, Papoutsoglou G, Shigdel R, Stres B, Vilne B, Yousef M, Zdravevski E, Tsamardinos I, Carrillo de Santa Pau E, Claesson MJ, Moreno-Indias I, Truu J. Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. Front Microbiol 2021;12:634511. [PMID: 33737920 PMCID: PMC7962872 DOI: 10.3389/fmicb.2021.634511] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/01/2021] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
1
Bakir-Gungor B, Temiz M, Canakcimaksutoglu B, Yousef M. Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach. Comput Biol Med 2025;187:109813. [PMID: 39929003 DOI: 10.1016/j.compbiomed.2025.109813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 01/09/2025] [Accepted: 02/05/2025] [Indexed: 02/12/2025]
2
Mikles B, Schmidt CJ, Benbow ME, Jordan HR, Pechal JL. Potential postmortem microbial biomarkers of infant and younger children death investigation. J Forensic Sci 2025;70:607-618. [PMID: 39682072 PMCID: PMC11874197 DOI: 10.1111/1556-4029.15677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/08/2024] [Accepted: 11/13/2024] [Indexed: 12/18/2024]
3
Wu J, Xiao L, Fan L, Wang L, Zhu X. Dual graph-embedded fusion network for predicting potential microbe-disease associations with sequence learning. Front Genet 2025;16:1511521. [PMID: 40008230 PMCID: PMC11850361 DOI: 10.3389/fgene.2025.1511521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 01/15/2025] [Indexed: 02/27/2025]  Open
4
Iqbal S, Begum F, Ullah I, Jalal N, Shaw P. Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities. Crit Rev Microbiol 2025;51:1-21. [PMID: 38385313 DOI: 10.1080/1040841x.2024.2319669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/13/2023] [Accepted: 02/10/2024] [Indexed: 02/23/2024]
5
Przymus P, Rykaczewski K, Martín-Segura A, Truu J, Carrillo De Santa Pau E, Kolev M, Naskinova I, Gruca A, Sampri A, Frohme M, Nechyporenko A. Deep learning in microbiome analysis: a comprehensive review of neural network models. Front Microbiol 2025;15:1516667. [PMID: 39911715 PMCID: PMC11794229 DOI: 10.3389/fmicb.2024.1516667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Accepted: 12/16/2024] [Indexed: 02/07/2025]  Open
6
Karwowska Z, Aasmets O, Kosciolek T, Org E. Effects of data transformation and model selection on feature importance in microbiome classification data. MICROBIOME 2025;13:2. [PMID: 39754220 PMCID: PMC11699698 DOI: 10.1186/s40168-024-01996-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 12/04/2024] [Indexed: 01/06/2025]
7
Kim S, Lee HC, Sim JE, Park SJ, Oh HH. Bacterial profile-based body fluid identification using a machine learning approach. Genes Genomics 2025;47:87-98. [PMID: 39503932 DOI: 10.1007/s13258-024-01594-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Accepted: 10/23/2024] [Indexed: 01/16/2025]
8
Tsoumtsa Meda L, Lagarde J, Guillier L, Roussel S, Douarre PE. Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits. Methods Mol Biol 2025;2852:223-253. [PMID: 39235748 DOI: 10.1007/978-1-0716-4100-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
9
Patel RA, Panche AN, Harke SN. Gut microbiome-gut brain axis-depression: interconnection. World J Biol Psychiatry 2025;26:1-36. [PMID: 39713871 DOI: 10.1080/15622975.2024.2436854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 11/26/2024] [Accepted: 11/28/2024] [Indexed: 12/24/2024]
10
Monshizadeh M, Hong Y, Ye Y. Multitask knowledge-primed neural network for predicting missing metadata and host phenotype based on human microbiome. BIOINFORMATICS ADVANCES 2024;5:vbae203. [PMID: 39735577 PMCID: PMC11676323 DOI: 10.1093/bioadv/vbae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 11/27/2024] [Accepted: 12/11/2024] [Indexed: 12/31/2024]
11
Hosseiniyan Khatibi SM, Dimaano NG, Veliz E, Sundaresan V, Ali J. Exploring and exploiting the rice phytobiome to tackle climate change challenges. PLANT COMMUNICATIONS 2024;5:101078. [PMID: 39233440 PMCID: PMC11671768 DOI: 10.1016/j.xplc.2024.101078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 08/07/2024] [Accepted: 09/02/2024] [Indexed: 09/06/2024]
12
Chang CC, Liu TC, Lu CJ, Chiu HC, Lin WN. Explainable machine learning model for identifying key gut microbes and metabolites biomarkers associated with myasthenia gravis. Comput Struct Biotechnol J 2024;23:1572-1583. [PMID: 38650589 PMCID: PMC11035017 DOI: 10.1016/j.csbj.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/14/2024] [Accepted: 04/07/2024] [Indexed: 04/25/2024]  Open
13
Oh VKS, Li RW. Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2400458. [PMID: 39535493 DOI: 10.1002/advs.202400458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 09/16/2024] [Indexed: 11/16/2024]
14
Tian H, Tang R. Prediction of Crohn's disease based on deep feature recognition. Comput Biol Chem 2024;113:108231. [PMID: 39362115 DOI: 10.1016/j.compbiolchem.2024.108231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 09/21/2024] [Accepted: 09/28/2024] [Indexed: 10/05/2024]
15
Han H, Choi YH, Kim SY, Park JH, Chung J, Na HS. Optimizing microbiome reference databases with PacBio full-length 16S rRNA sequencing for enhanced taxonomic classification and biomarker discovery. Front Microbiol 2024;15:1485073. [PMID: 39654676 PMCID: PMC11625778 DOI: 10.3389/fmicb.2024.1485073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 10/28/2024] [Indexed: 12/12/2024]  Open
16
Zou B, Xenakis JG, Xiao M, Ribeiro A, Divaris K, Wu D, Zou F. A deep learning feature importance test framework for integrating informative high-dimensional biomarkers to improve disease outcome prediction. Brief Bioinform 2024;26:bbae709. [PMID: 39815828 PMCID: PMC11735761 DOI: 10.1093/bib/bbae709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 12/01/2024] [Accepted: 12/26/2024] [Indexed: 01/18/2025]  Open
17
Han J, Zhang H, Ning K. Techniques for learning and transferring knowledge for microbiome-based classification and prediction: review and assessment. Brief Bioinform 2024;26:bbaf015. [PMID: 39820436 PMCID: PMC11737891 DOI: 10.1093/bib/bbaf015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 12/10/2024] [Accepted: 01/06/2025] [Indexed: 01/19/2025]  Open
18
Neiroukh D, Hajdarpasic A, Ayhan C, Sultan S, Soliman O. Gut Microbial Taxonomy and Its Role as a Biomarker in Aortic Diseases: A Systematic Review and Future Perspectives. J Clin Med 2024;13:6938. [PMID: 39598083 PMCID: PMC11594723 DOI: 10.3390/jcm13226938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 10/31/2024] [Accepted: 11/11/2024] [Indexed: 11/29/2024]  Open
19
Bašić-Čičak D, Hasić Telalović J, Pašić L. Utilizing Artificial Intelligence for Microbiome Decision-Making: Autism Spectrum Disorder in Children from Bosnia and Herzegovina. Diagnostics (Basel) 2024;14:2536. [PMID: 39594202 PMCID: PMC11592508 DOI: 10.3390/diagnostics14222536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Revised: 10/17/2024] [Accepted: 10/21/2024] [Indexed: 11/28/2024]  Open
20
Bakir-Gungor B, Temiz M, Inal Y, Cicekyurt E, Yousef M. CCPred: Global and population-specific colorectal cancer prediction and metagenomic biomarker identification at different molecular levels using machine learning techniques. Comput Biol Med 2024;182:109098. [PMID: 39293338 DOI: 10.1016/j.compbiomed.2024.109098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 08/29/2024] [Accepted: 08/31/2024] [Indexed: 09/20/2024]
21
Akhmedov M, Espinoza JL. Addressing the surge of infections by multidrug-resistant Enterobacterales in hematopoietic cell transplantation. Blood Rev 2024;68:101229. [PMID: 39217051 DOI: 10.1016/j.blre.2024.101229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 08/17/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
22
Porreca A, Ibrahimi E, Maturo F, Marcos Zambrano LJ, Meto M, Lopes MB. Robust prediction of colorectal cancer via gut microbiome 16S rRNA sequencing data. J Med Microbiol 2024;73. [PMID: 39377779 DOI: 10.1099/jmm.0.001903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]  Open
23
Obeagu EI, Okoroiwu GI, Ubosi NI, Obeagu GU, Onohuean H, Muhammad T, Adias TC. Revolution in malaria detection: unveiling current breakthroughs and tomorrow's possibilities in biomarker innovation. Ann Med Surg (Lond) 2024;86:5859-5876. [PMID: 39359838 PMCID: PMC11444567 DOI: 10.1097/ms9.0000000000002383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/06/2024] [Indexed: 10/04/2024]  Open
24
Kostic T, Schloter M, Arruda P, Berg G, Charles TC, Cotter PD, Kiran GS, Lange L, Maguin E, Meisner A, van Overbeek L, Sanz Y, Sarand I, Selvin J, Tsakalidou E, Smidt H, Wagner M, Sessitsch A. Concepts and criteria defining emerging microbiome applications. Microb Biotechnol 2024;17:e14550. [PMID: 39236296 PMCID: PMC11376781 DOI: 10.1111/1751-7915.14550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024]  Open
25
Kundu P, Beura S, Mondal S, Das AK, Ghosh A. Machine learning for the advancement of genome-scale metabolic modeling. Biotechnol Adv 2024;74:108400. [PMID: 38944218 DOI: 10.1016/j.biotechadv.2024.108400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 05/13/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
26
Khan MW, Fung DLX, Schroth RJ, Chelikani P, Hu P. A cross-cohort analysis of dental plaque microbiome in early childhood caries. iScience 2024;27:110447. [PMID: 39104404 PMCID: PMC11298647 DOI: 10.1016/j.isci.2024.110447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/05/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024]  Open
27
Chibwe K, Sundararaju S, Zhang L, Tsui C, Tang P, Ling F. Intra-hospital microbiome variability is driven by accessibility and clinical activities. Microbiol Spectr 2024;12:e0029624. [PMID: 38940596 PMCID: PMC11302010 DOI: 10.1128/spectrum.00296-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024]  Open
28
Chen J, Zhu Y, Yuan Q. Predicting potential microbe-disease associations based on dual branch graph convolutional network. J Cell Mol Med 2024;28:e18571. [PMID: 39086148 PMCID: PMC11291560 DOI: 10.1111/jcmm.18571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/15/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024]  Open
29
Wang Z, Peng X, Hülpüsch C, Khan Mirzaei M, Reiger M, Traidl-Hoffmann C, Deng L, Schloter M. Distinct prophage gene profiles of Staphylococcus aureus strains from atopic dermatitis patients and healthy individuals. Microbiol Spectr 2024;12:e0091524. [PMID: 39012113 DOI: 10.1128/spectrum.00915-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/13/2024] [Indexed: 07/17/2024]  Open
30
Yehuala TZ, Agimas MC, Derseh NM, Wubante SM, Fente BM, Yismaw GA, Tesfie TK. Machine learning algorithms to predict healthcare-seeking behaviors of mothers for acute respiratory infections and their determinants among children under five in sub-Saharan Africa. Front Public Health 2024;12:1362392. [PMID: 38962762 PMCID: PMC11220189 DOI: 10.3389/fpubh.2024.1362392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/03/2024] [Indexed: 07/05/2024]  Open
31
Tamayo M, Olivares M, Ruas-Madiedo P, Margolles A, Espín JC, Medina I, Moreno-Arribas MV, Canals S, Mirasso CR, Ortín S, Beltrán-Sanchez H, Palloni A, Tomás-Barberán FA, Sanz Y. How Diet and Lifestyle Can Fine-Tune Gut Microbiomes for Healthy Aging. Annu Rev Food Sci Technol 2024;15:283-305. [PMID: 38941492 DOI: 10.1146/annurev-food-072023-034458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
32
Ayub H, Khan MA, Shehryar Ali Naqvi S, Faseeh M, Kim J, Mehmood A, Kim YJ. Unraveling the Potential of Attentive Bi-LSTM for Accurate Obesity Prognosis: Advancing Public Health towards Sustainable Cities. Bioengineering (Basel) 2024;11:533. [PMID: 38927769 PMCID: PMC11200407 DOI: 10.3390/bioengineering11060533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/19/2024] [Indexed: 06/28/2024]  Open
33
Liu Q, Zhai Y, Hui Y, Chen J, Mi Y, Wang J, Wei H. Identification of red blood cell distribution width as a prognostic factor in acute myeloid leukemia. Exp Hematol 2024;133:104206. [PMID: 38508299 DOI: 10.1016/j.exphem.2024.104206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024]
34
Pais N, Ravishanker N, Rajasekaran S, Weinstock G, Tran DB. Randomized feature selection based semi-supervised latent Dirichlet allocation for microbiome analysis. Sci Rep 2024;14:8855. [PMID: 38632488 PMCID: PMC11024186 DOI: 10.1038/s41598-024-59682-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/13/2024] [Indexed: 04/19/2024]  Open
35
Manrique P, Montero I, Fernandez-Gosende M, Martinez N, Cantabrana CH, Rios-Covian D. Past, present, and future of microbiome-based therapies. MICROBIOME RESEARCH REPORTS 2024;3:23. [PMID: 38841413 PMCID: PMC11149097 DOI: 10.20517/mrr.2023.80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 06/07/2024]
36
Gradisteanu Pircalabioru G, Raileanu M, Dionisie MV, Lixandru-Petre IO, Iliescu C. Fast detection of bacterial gut pathogens on miniaturized devices: an overview. Expert Rev Mol Diagn 2024;24:201-218. [PMID: 38347807 DOI: 10.1080/14737159.2024.2316756] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024]
37
Baddal B, Taner F, Uzun Ozsahin D. Harnessing of Artificial Intelligence for the Diagnosis and Prevention of Hospital-Acquired Infections: A Systematic Review. Diagnostics (Basel) 2024;14:484. [PMID: 38472956 DOI: 10.3390/diagnostics14050484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/23/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]  Open
38
Walsh C, Stallard-Olivera E, Fierer N. Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology. mBio 2024;15:e0205023. [PMID: 38126787 PMCID: PMC10865974 DOI: 10.1128/mbio.02050-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]  Open
39
Kumar B, Lorusso E, Fosso B, Pesole G. A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions. Front Microbiol 2024;15:1343572. [PMID: 38419630 PMCID: PMC10900530 DOI: 10.3389/fmicb.2024.1343572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024]  Open
40
Li H, Yu Z, Du F, Song L, Gao Y, Shi F. sscNOVA: a semi-supervised convolutional neural network for predicting functional regulatory variants in autoimmune diseases. Front Immunol 2024;15:1323072. [PMID: 38380333 PMCID: PMC10876991 DOI: 10.3389/fimmu.2024.1323072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/15/2024] [Indexed: 02/22/2024]  Open
41
Ramon E, Obón-Santacana M, Khannous-Lleiffe O, Saus E, Gabaldón T, Guinó E, Bars-Cortina D, Ibáñez-Sanz G, Rodríguez-Alonso L, Mata A, García-Rodríguez A, Moreno V. Performance of a Shotgun Prediction Model for Colorectal Cancer When Using 16S rRNA Sequencing Data. Int J Mol Sci 2024;25:1181. [PMID: 38256252 PMCID: PMC10816515 DOI: 10.3390/ijms25021181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]  Open
42
Peralta-Marzal LN, Rojas-Velazquez D, Rigters D, Prince N, Garssen J, Kraneveld AD, Perez-Pardo P, Lopez-Rincon A. A robust microbiome signature for autism spectrum disorder across different studies using machine learning. Sci Rep 2024;14:814. [PMID: 38191575 PMCID: PMC10774349 DOI: 10.1038/s41598-023-50601-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024]  Open
43
Staab S, Cardénas A, Peixoto RS, Schreiber F, Voolstra CR. Coracle-a machine learning framework to identify bacteria associated with continuous variables. Bioinformatics 2024;40:btad749. [PMID: 38123508 PMCID: PMC10766586 DOI: 10.1093/bioinformatics/btad749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/06/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023]  Open
44
Lee S, Lee I. Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data. Gut Microbes 2024;16:2375679. [PMID: 38972064 PMCID: PMC11229738 DOI: 10.1080/19490976.2024.2375679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024]  Open
45
Fonseca DC, Marques Gomes da Rocha I, Depieri Balmant B, Callado L, Aguiar Prudêncio AP, Tepedino Martins Alves J, Torrinhas RS, da Rocha Fernandes G, Linetzky Waitzberg D. Evaluation of gut microbiota predictive potential associated with phenotypic characteristics to identify multifactorial diseases. Gut Microbes 2024;16:2297815. [PMID: 38235595 PMCID: PMC10798365 DOI: 10.1080/19490976.2023.2297815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]  Open
46
Vänni P, Tejesvi MV, Paalanne N, Aagaard K, Ackermann G, Camargo CA, Eggesbø M, Hasegawa K, Hoen AG, Karagas MR, Kolho KL, Laursen MF, Ludvigsson J, Madan J, Ownby D, Stanton C, Stokholm J, Tapiainen T. Machine-learning analysis of cross-study samples according to the gut microbiome in 12 infant cohorts. mSystems 2023;8:e0036423. [PMID: 37874156 PMCID: PMC10734493 DOI: 10.1128/msystems.00364-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/13/2023] [Indexed: 10/25/2023]  Open
47
Feng K, Ren F, Xing Z, Zhao Y, Yang C, Liu J, Shang Q, Wang X, Wang X. Microbiome and its implications in oncogenesis: a Mendelian randomization perspective. Am J Cancer Res 2023;13:5785-5804. [PMID: 38187050 PMCID: PMC10767327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/02/2023] [Indexed: 01/09/2024]  Open
48
Mouratidis I, Chantzi N, Khan U, Konnaris MA, Chan CSY, Mareboina M, Moeckel C, Georgakopoulos-Soares I. Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis. BMC Genomics 2023;24:768. [PMID: 38087204 PMCID: PMC10714505 DOI: 10.1186/s12864-023-09861-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]  Open
49
Peng C, May A, Abeel T. Unveiling microbial biomarkers of ruminant methane emission through machine learning. Front Microbiol 2023;14:1308363. [PMID: 38143860 PMCID: PMC10749206 DOI: 10.3389/fmicb.2023.1308363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023]  Open
50
Angelova IY, Kovtun AS, Averina OV, Koshenko TA, Danilenko VN. Unveiling the Connection between Microbiota and Depressive Disorder through Machine Learning. Int J Mol Sci 2023;24:16459. [PMID: 38003647 PMCID: PMC10671666 DOI: 10.3390/ijms242216459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]  Open
PrevPage 1 of 3 123Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA