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

Nucleic acids research, 2022

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Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.

Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S

Microbiome, 2022

doi:10.1186/s40168-022-01410-z.

Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems.

Bobonis J, Mitosch K, Mateus A, Karcher N, Kritikos G, Selkrig J, Zietek M, Monzon V, Pfalz B, Garcia-Santamarina S, Galardini M, Sueki A, Kobayashi C, Stein F, Bateman A, Zeller G, Savitski MM, Elfenbein JR, Andrews-Polymenis HL, Typas A

Nature, 2022

doi:10.1038/s41586-022-05091-4.

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.

Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G

Genome biology, 2021

doi:10.1186/s13059-021-02306-1.

The gut microbiome in solid organ transplantation.

Baghai Arassi M, Zeller G, Karcher N, Zimmermann M, Toenshoff B

Pediatric transplantation, 2020

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