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Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action.
D'Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. D'Elia D, et al. Among authors: berland m. Front Microbiol. 2023 Sep 25;14:1257002. doi: 10.3389/fmicb.2023.1257002. eCollection 2023. Front Microbiol. 2023. PMID: 37808321 Free PMC article.
Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment.
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. Marcos-Zambrano LJ, et al. Among authors: berland m. Front Microbiol. 2021 Feb 19;12:634511. doi: 10.3389/fmicb.2021.634511. eCollection 2021. Front Microbiol. 2021. PMID: 33737920 Free PMC article. Review.
Machine learning approaches in microbiome research: challenges and best practices.
Papoutsoglou G, Tarazona S, Lopes MB, Klammsteiner T, Ibrahimi E, Eckenberger J, Novielli P, Tonda A, Simeon A, Shigdel R, Béreux S, Vitali G, Tangaro S, Lahti L, Temko A, Claesson MJ, Berland M. Papoutsoglou G, et al. Among authors: berland m. Front Microbiol. 2023 Sep 22;14:1261889. doi: 10.3389/fmicb.2023.1261889. eCollection 2023. Front Microbiol. 2023. PMID: 37808286 Free PMC article. Review.
A toolbox of machine learning software to support microbiome analysis.
Marcos-Zambrano LJ, López-Molina VM, Bakir-Gungor B, Frohme M, Karaduzovic-Hadziabdic K, Klammsteiner T, Ibrahimi E, Lahti L, Loncar-Turukalo T, Dhamo X, Simeon A, Nechyporenko A, Pio G, Przymus P, Sampri A, Trajkovik V, Lacruz-Pleguezuelos B, Aasmets O, Araujo R, Anagnostopoulos I, Aydemir Ö, Berland M, Calle ML, Ceci M, Duman H, Gündoğdu A, Havulinna AS, Kaka Bra KHN, Kalluci E, Karav S, Lode D, Lopes MB, May P, Nap B, Nedyalkova M, Paciência I, Pasic L, Pujolassos M, Shigdel R, Susín A, Thiele I, Truică CO, Wilmes P, Yilmaz E, Yousef M, Claesson MJ, Truu J, Carrillo de Santa Pau E. Marcos-Zambrano LJ, et al. Among authors: berland m. Front Microbiol. 2023 Nov 22;14:1250806. doi: 10.3389/fmicb.2023.1250806. eCollection 2023. Front Microbiol. 2023. PMID: 38075858 Free PMC article. Review.
Alteration of Gut Microbiome in Patients With Schizophrenia Indicates Links Between Bacterial Tyrosine Biosynthesis and Cognitive Dysfunction.
Thirion F, Speyer H, Hansen TH, Nielsen T, Fan Y, Le Chatelier E, Fromentin S, Berland M, Plaza Oñate F, Pons N, Galleron N, Levenez F, Markó L, Birkner T, Jørgensen T, Forslund SK, Vestergaard H, Hansen T, Nordentoft M, Mors O, Benros ME, Pedersen O, Ehrlich SD. Thirion F, et al. Among authors: berland m. Biol Psychiatry Glob Open Sci. 2022 Feb 10;3(2):283-291. doi: 10.1016/j.bpsgos.2022.01.009. eCollection 2023 Apr. Biol Psychiatry Glob Open Sci. 2022. PMID: 37124355 Free PMC article.
Diet Supplementation with NUTRIOSE, a Resistant Dextrin, Increases the Abundance of Parabacteroides distasonis in the Human Gut.
Thirion F, Da Silva K, Plaza Oñate F, Alvarez AS, Thabuis C, Pons N, Berland M, Le Chatelier E, Galleron N, Levenez F, Vergara C, Chevallier H, Guérin-Deremaux L, Doré J, Ehrlich SD. Thirion F, et al. Among authors: berland m. Mol Nutr Food Res. 2022 Jun;66(11):e2101091. doi: 10.1002/mnfr.202101091. Epub 2022 Apr 4. Mol Nutr Food Res. 2022. PMID: 35312171 Free PMC article.
Both Disease Activity and HLA-B27 Status Are Associated With Gut Microbiome Dysbiosis in Spondyloarthritis Patients.
Berland M, Meslier V, Berreira Ibraim S, Le Chatelier E, Pons N, Maziers N, Thirion F, Gauthier F, Plaza Oñate F, Furet JP, Leboime A, Said-Nahal R, Levenez F, Galleron N, Quinquis B, Langella P, Ehrlich SD, Breban M. Berland M, et al. Arthritis Rheumatol. 2023 Jan;75(1):41-52. doi: 10.1002/art.42289. Epub 2022 Nov 19. Arthritis Rheumatol. 2023. PMID: 35818337 Free PMC article.
Reply.
Berland M, Ehrlich D, Breban M. Berland M, et al. Arthritis Rheumatol. 2024 Feb 13. doi: 10.1002/art.42826. Online ahead of print. Arthritis Rheumatol. 2024. PMID: 38351478 No abstract available.
112 results