Univ. Prof. Dr. Thomas Rattei

 

 

 

 

 

Head of the Division of Computational Systems Biology
Vice-head of the Department of Microbiology and Ecosystem Science

☎ +43 1 4277 91280

thomas.rattei@univie.ac.at 

Thomas Rattei’s work covers a wide spectrum of topics from bioinformatics, genome and metagenome analysis and systems biology. He has long-standing expertise in developing and applying computational methods for the interpretation of large-scale sequence information. The international reputation of his research group triggered their involvement in numerous international (meta-) genome sequencing and analysis consortia.

Thomas’ research activities not only cover individual, project-specific questions but also general problems in bioinformatics, computational infrastructure, and large-scale biological databases. Furthermore, his group develops novel, genome-based computational approaches for studying molecular inter-species interactions, such as between hosts and pathogens, between symbionts, or in microbial ecosystems.

Thomas and his team maintain and develop internationally relevant resources in computational biology, such as the web portals phendb.org, vogdb.org and effectivedb.org for microbial trait prediction, virus orthologous groups and protein families, and bacterial secreted proteins and secretion systems.

Links

Teaching

To explore Thomas' teaching activities at the University of Vienna, visit u:find.

Join the Team

If you are interested in joining the lab, explore open positions here or email Thomas directly.

Group Members

  • Michael Neumayer
  • Alexander Pfundner
  • Michael Predl
  • Roko Sango
  • Lovro Trgovec-Greif

 Publications

Doncheva NT, Morris JH, Holze H, Kirsch R, Nastou KC, Cuesta-Astroz Y et al. Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks. Journal of Proteome Research. 2023 Feb 3;22(2):637-646. doi: 10.1021/acs.jproteome.2c00651

Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta M-C, Bäckhed F, Bork P et al. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature. 2023 Jan 26;613(7945):639-649. doi: 10.1038/s41586-022-05546-8

Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR et al. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research. 2023 Jan 6;51(D1):D389-D394. doi: 10.1093/nar/gkac1022

Bernard C, Locard-Paulet M, Noël C, Duchateau M, Giai Gianetto Q, Moumen B et al. A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. Nature Communications. 2022 Jul 14;13(1):4104. doi: 10.1038/s41467-022-31832-0

Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S et al. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Current Biology. 2021 Dec 6;31(23):5149-5162. Epub 2021 Oct 13. doi: 10.1016/j.cub.2021.09.031

Majek P, Lueftinger L, Beisken S, Rattei T, Materna A. Genome-Wide Mutation Scoring for Machine-Learning-Based Antimicrobial Resistance Prediction. International Journal of Molecular Sciences. 2021 Dec 2;22(23):13049. doi: 10.3390/ijms222313049

Flieder M, Buongiorno J, Herbold CW, Hausmann B, Rattei T, Lloyd KG et al. Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. The ISME Journal. 2021 Nov 1;15(11):3159-3180. Epub 2021 May 12. doi: 10.1038/s41396-021-00992-0

Hanson BT, Dimitri Kits K, Löffler J, Burrichter AG, Fiedler A, Denger K et al. Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. The ISME Journal. 2021 Sep 1;15(9):2779-2791. Epub 2021 Mar 31. doi: 10.1038/s41396-021-00968-0

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