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Page 1
Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.
Nishijima S, Stankevic E, Aasmets O, Schmidt TSB, Nagata N, Keller MI, Ferretti P, Juel HB, Fullam A, Robbani SM, Schudoma C, Hansen JK, Holm LA, Israelsen M, Schierwagen R, Torp N, Telzerow A, Hercog R, Kandels S, Hazenbrink DHM, Arumugam M, Bendtsen F, Brøns C, Fonvig CE, Holm JC, Nielsen T, Pedersen JS, Thiele MS, Trebicka J, Org E, Krag A, Hansen T, Kuhn M, Bork P; GALAXY and MicrobLiver Consortia. Nishijima S, et al. Among authors: schmidt tsb. Cell. 2024 Nov 4:S0092-8674(24)01204-2. doi: 10.1016/j.cell.2024.10.022. Online ahead of print. Cell. 2024. PMID: 39541968 Free article.
Discovery of antimicrobial peptides in the global microbiome with machine learning.
Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP. Santos-Júnior CD, et al. Among authors: schmidt tsb. Cell. 2024 Jul 11;187(14):3761-3778.e16. doi: 10.1016/j.cell.2024.05.013. Epub 2024 Jun 5. Cell. 2024. PMID: 38843834 Free article.
Paternal microbiome perturbations impact offspring fitness.
Argaw-Denboba A, Schmidt TSB, Di Giacomo M, Ranjan B, Devendran S, Mastrorilli E, Lloyd CT, Pugliese D, Paribeni V, Dabin J, Pisaniello A, Espinola S, Crevenna A, Ghosh S, Humphreys N, Boruc O, Sarkies P, Zimmermann M, Bork P, Hackett JA. Argaw-Denboba A, et al. Among authors: schmidt tsb. Nature. 2024 May;629(8012):652-659. doi: 10.1038/s41586-024-07336-w. Epub 2024 May 1. Nature. 2024. PMID: 38693261 Free PMC article.
Functional and evolutionary significance of unknown genes from uncultivated taxa.
Rodríguez Del Río Á, Giner-Lamia J, Cantalapiedra CP, Botas J, Deng Z, Hernández-Plaza A, Munar-Palmer M, Santamaría-Hernando S, Rodríguez-Herva JJ, Ruscheweyh HJ, Paoli L, Schmidt TSB, Sunagawa S, Bork P, López-Solanilla E, Coelho LP, Huerta-Cepas J. Rodríguez Del Río Á, et al. Among authors: schmidt tsb. Nature. 2024 Feb;626(7998):377-384. doi: 10.1038/s41586-023-06955-z. Epub 2023 Dec 18. Nature. 2024. PMID: 38109938 Free PMC article.
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P. Schmidt TSB, et al. Nucleic Acids Res. 2024 Jan 5;52(D1):D777-D783. doi: 10.1093/nar/gkad943. Nucleic Acids Res. 2024. PMID: 37897342 Free PMC article.
Computational exploration of the global microbiome for antibiotic discovery.
Santos-Júnior CD, Der Torossian Torres M, Duan Y, Del Río ÁR, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP. Santos-Júnior CD, et al. Among authors: schmidt tsb. bioRxiv [Preprint]. 2023 Sep 11:2023.08.31.555663. doi: 10.1101/2023.08.31.555663. bioRxiv. 2023. Update in: Cell. 2024 Jul 11;187(14):3761-3778.e16. doi: 10.1016/j.cell.2024.05.013. PMID: 37693522 Free PMC article. Updated. Preprint.
Consistency across multi-omics layers in a drug-perturbed gut microbial community.
Wuyts S, Alves R, Zimmermann-Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P. Wuyts S, et al. Among authors: schmidt tsb. Mol Syst Biol. 2023 Sep 12;19(9):e11525. doi: 10.15252/msb.202311525. Epub 2023 Jul 24. Mol Syst Biol. 2023. PMID: 37485738 Free PMC article.
Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.
Kunath BJ, Hickl O, Queirós P, Martin-Gallausiaux C, Lebrun LA, Halder R, Laczny CC, Schmidt TSB, Hayward MR, Becher D, Heintz-Buschart A, de Beaufort C, Bork P, May P, Wilmes P. Kunath BJ, et al. Among authors: schmidt tsb. Microbiome. 2022 Dec 28;10(1):243. doi: 10.1186/s40168-022-01435-4. Microbiome. 2022. PMID: 36578059 Free PMC article.
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR. Fullam A, et al. Among authors: schmidt tsb. Nucleic Acids Res. 2023 Jan 6;51(D1):D760-D766. doi: 10.1093/nar/gkac1078. Nucleic Acids Res. 2023. PMID: 36408900 Free PMC article.
35 results