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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: pujolassos 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.
Microbiome signatures of progression toward celiac disease onset in at-risk children in a longitudinal prospective cohort study.
Leonard MM, Valitutti F, Karathia H, Pujolassos M, Kenyon V, Fanelli B, Troisi J, Subramanian P, Camhi S, Colucci A, Serena G, Cucchiara S, Trovato CM, Malamisura B, Francavilla R, Elli L, Hasan NA, Zomorrodi AR, Colwell R, Fasano A; CD-GEMM Team. Leonard MM, et al. Among authors: pujolassos m. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29):e2020322118. doi: 10.1073/pnas.2020322118. Proc Natl Acad Sci U S A. 2021. PMID: 34253606 Free PMC article.
Microbiome compositional data analysis for survival studies.
Pujolassos M, Susín A, Calle ML. Pujolassos M, et al. NAR Genom Bioinform. 2024 Apr 25;6(2):lqae038. doi: 10.1093/nargab/lqae038. eCollection 2024 Jun. NAR Genom Bioinform. 2024. PMID: 38666212 Free PMC article.
Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease.
Leonard MM, Karathia H, Pujolassos M, Troisi J, Valitutti F, Subramanian P, Camhi S, Kenyon V, Colucci A, Serena G, Cucchiara S, Montuori M, Malamisura B, Francavilla R, Elli L, Fanelli B, Colwell R, Hasan N, Zomorrodi AR, Fasano A; CD-GEMM Team. Leonard MM, et al. Among authors: pujolassos m. Microbiome. 2020 Sep 11;8(1):130. doi: 10.1186/s40168-020-00906-w. Microbiome. 2020. PMID: 32917289 Free PMC article.