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Page 1
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. Among authors: fullam a. Nucleic Acids Res. 2024 Jan 5;52(D1):D777-D783. doi: 10.1093/nar/gkad943. Nucleic Acids Res. 2024. PMID: 37897342 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. Nucleic Acids Res. 2023 Jan 6;51(D1):D760-D766. doi: 10.1093/nar/gkac1078. Nucleic Acids Res. 2023. PMID: 36408900 Free PMC article.
GUNC: detection of chimerism and contamination in prokaryotic genomes.
Orakov A, Fullam A, Coelho LP, Khedkar S, Szklarczyk D, Mende DR, Schmidt TSB, Bork P. Orakov A, et al. Among authors: fullam a. Genome Biol. 2021 Jun 13;22(1):178. doi: 10.1186/s13059-021-02393-0. Genome Biol. 2021. PMID: 34120611 Free PMC article.
Drivers and determinants of strain dynamics following fecal microbiota transplantation.
Schmidt TSB, Li SS, Maistrenko OM, Akanni W, Coelho LP, Dolai S, Fullam A, Glazek AM, Hercog R, Herrema H, Jung F, Kandels S, Orakov A, Thielemann R, von Stetten M, Van Rossum T, Benes V, Borody TJ, de Vos WM, Ponsioen CY, Nieuwdorp M, Bork P. Schmidt TSB, et al. Among authors: fullam a. Nat Med. 2022 Sep;28(9):1902-1912. doi: 10.1038/s41591-022-01913-0. Epub 2022 Sep 15. Nat Med. 2022. PMID: 36109636 Free PMC article.
A faecal microbiota signature with high specificity for pancreatic cancer.
Kartal E, Schmidt TSB, Molina-Montes E, Rodríguez-Perales S, Wirbel J, Maistrenko OM, Akanni WA, Alashkar Alhamwe B, Alves RJ, Carrato A, Erasmus HP, Estudillo L, Finkelmeier F, Fullam A, Glazek AM, Gómez-Rubio P, Hercog R, Jung F, Kandels S, Kersting S, Langheinrich M, Márquez M, Molero X, Orakov A, Van Rossum T, Torres-Ruiz R, Telzerow A, Zych K; MAGIC Study investigators; PanGenEU Study investigators; Benes V, Zeller G, Trebicka J, Real FX, Malats N, Bork P. Kartal E, et al. Among authors: fullam a. Gut. 2022 Jul;71(7):1359-1372. doi: 10.1136/gutjnl-2021-324755. Epub 2022 Mar 8. Gut. 2022. PMID: 35260444 Free PMC article.
A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog.
Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, Kuhn M, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J. Van Espen L, et al. Among authors: fullam a. mSystems. 2021 Oct 26;6(5):e0038221. doi: 10.1128/mSystems.00382-21. Epub 2021 Oct 19. mSystems. 2021. PMID: 34665009 Free PMC article.
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: fullam a. 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.
A catalog of small proteins from the global microbiome.
Duan Y, Santos-Júnior CD, Schmidt TS, Fullam A, de Almeida BLS, Zhu C, Kuhn M, Zhao XM, Bork P, Coelho LP. Duan Y, et al. Among authors: fullam a. Nat Commun. 2024 Aug 31;15(1):7563. doi: 10.1038/s41467-024-51894-6. Nat Commun. 2024. PMID: 39214983 Free PMC 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: fullam a. 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.
Terlipressin therapy is associated with increased risk of colonisation with multidrug-resistant bacteria in patients with decompensated cirrhosis.
Mücke MM, Hernández-Tejero M, Gu W, Kuhn M, Janz M, Keller MI, Fullam A, Altepeter L, Mücke VT, Finkelmeier F, Schwarzkopf KM, Cremonese C, Hunyady PM, Heilani MW, Uschner FE, Schierwagen R, Brol MJ, Fischer J, Klein S, Peiffer KH, Hogardt M, Shoaie S, Coenraad MJ, Bojunga J, Arroyo V, Zeuzem S, Kempf VAJ, Welsch C, Laleman W, Bork P, Fernandez J, Trebicka J; MICROB-PREDICT and PREDICT Study Group of the EASL-CLIF Consortium. Mücke MM, et al. Among authors: fullam a. Aliment Pharmacol Ther. 2024 Apr;59(7):877-888. doi: 10.1111/apt.17899. Epub 2024 Feb 27. Aliment Pharmacol Ther. 2024. PMID: 38414095
24 results