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

Nucleic acids research, 2023

doi:10.1093/nar/gkad943.

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

Nature medicine, 2022

doi:10.1038/s41591-022-01913-0.

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.

Khedkar S, Smyshlyaev G, Letunic I, Maistrenko OM, Coelho LP, Orakov A, Forslund SK, Hildebrand F, Luetge M, Schmidt TSB, Barabas O, Bork P

Nucleic acids research, 2022

doi:10.1093/nar/gkac163.

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

Gut, 2022

doi:10.1136/gutjnl-2021-324755.

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

Nature, 2021

doi:10.1038/s41586-021-04233-4.

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

Genome biology, 2021

doi:10.1186/s13059-021-02393-0.

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

Nucleic acids research, 2019

doi:10.1093/nar/gkz1002.