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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: nap b. Front Microbiol. 2023 Nov 22;14:1250806. doi: 10.3389/fmicb.2023.1250806. eCollection 2023. Front Microbiol. 2023. PMID: 38075858 Free PMC article. Review.
APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.
Heinken A, Hulshof TO, Nap B, Martinelli F, Basile A, O'Brolchain A, O'Sullivan NF, Gallagher C, Magee E, McDonagh F, Lalor I, Bergin M, Evans P, Daly R, Farrell R, Delaney RM, Hill S, McAuliffe SR, Kilgannon T, Fleming RMT, Thinnes CC, Thiele I. Heinken A, et al. Among authors: nap b. bioRxiv [Preprint]. 2023 Oct 3:2023.10.02.560573. doi: 10.1101/2023.10.02.560573. bioRxiv. 2023. PMID: 37873072 Free PMC article. Preprint.
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.
Heinken A, Hertel J, Acharya G, Ravcheev DA, Nyga M, Okpala OE, Hogan M, Magnúsdóttir S, Martinelli F, Nap B, Preciat G, Edirisinghe JN, Henry CS, Fleming RMT, Thiele I. Heinken A, et al. Among authors: nap b. Nat Biotechnol. 2023 Sep;41(9):1320-1331. doi: 10.1038/s41587-022-01628-0. Epub 2023 Jan 19. Nat Biotechnol. 2023. PMID: 36658342 Free PMC article.