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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: orakov 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.
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P. Mende DR, et al. Among authors: orakov an. Nucleic Acids Res. 2020 Jan 8;48(D1):D621-D625. doi: 10.1093/nar/gkz1002. Nucleic Acids Res. 2020. PMID: 31647096 Free PMC article.
Towards the biogeography of prokaryotic genes.
Coelho LP, Alves R, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P. Coelho LP, et al. Among authors: orakov a. Nature. 2022 Jan;601(7892):252-256. doi: 10.1038/s41586-021-04233-4. Epub 2021 Dec 15. Nature. 2022. PMID: 34912116 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: orakov 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.
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: orakov 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.
ASAR: visual analysis of metagenomes in R.
Orakov AN, Sakenova NK, Sorokin A, Goryanin II. Orakov AN, et al. Bioinformatics. 2018 Apr 15;34(8):1404-1405. doi: 10.1093/bioinformatics/btx775. Bioinformatics. 2018. PMID: 29211828 Free PMC article.