CUBE

Division of Computational Systems Biology

Centre for Microbiology and Environmental Systems Science

About CUBE

The Division of Computational Systems Biology | CUBE at the Centre for Microbiology and Environmental Systems Science | CeMESS is a group of bioinformaticians and computational biologists. CUBE focuses on understanding biological systems, ranging from single species to multi-species systems and ecosystems.

Our research is based on data from large-scale bioanalytical methods. Researchers in our group develop, improve and apply computational methods for the interpretation of molecular information in biology. We establish and analyse quantitative mathematical models.

More about CeMESS

Research Topics

New paper in Nature clarifies controversy around foetal microbiome

19.01.2023 CUBE

Scientific claims that babies already harbour living bacteria in the womb are incorrect - this has been proven by international researchers involving…

Funding for “DataLife” Project: New node in European research infrastructure

22.12.2022 CeMESS

A novel infrastructure for life science data: The project “DataLife - Data Infrastructure for Life Sciences”, coordinated by CUBE head Thomas Rattei,…

Thomas Rattei is Highly Cited Researcher 2022

15.11.2022 CUBE

CUBE member Thomas Rattei is among the most cited researchers in the world. Alongside his CMESS colleagues Andreas Richter (TER), Michael Wagner…

CMESS celebrates four Highly Cited Researchers 2022

15.11.2022 CeMESS

Our Centre once again features four scientists listed as most cited researchers worldwide. Thomas Rattei (CUBE), Andreas Richter (TER), Michael Wagner…

Start of CMESS Lecture Series – winter 2022/2023 edition

27.10.2022 CeMESS

The CMESS Lecture Series has started with a talk by Peter Fineran from the University of Otago (New Zealand). He granted insights into “The…

Insights into the world of microbes: CMESS joins European Researchers’ Nights 2022

29.09.2022 CeMESS

CMESS researchers are part of this year’s European Researchers’ Night (ERN) that is taking place on Friday, September 30. From 3pm until midnight…

Software & Databases

We develop and provide access to various software and databases, including: PhenDB, VOGDB, NVT, HoloVir, SIMAP, EffectiveDB, PICA, Gepard, and GenSkew.
Life Science Compute Cluster

We operate and administer Life Science Compute Cluster (LiSC), a specialized high-performance computing infrastructure which is available to life scientists across the University of Vienna.

Recent Publications

2026

Yu XA, Strachan CR, Herbold CW, Lang M, Gasche C, Makristathis A et al. Genome-wide sweeps create ecological units in the human gut microbiome. Nature. 2026 Jul 2;655(8121):202-209. doi: 10.1038/s41586-026-10476-w

2023

Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology. 2023 Nov;41(11):1633-1644. Epub 2023 Feb 23. doi: 10.1038/s41587-023-01688-w

Valles-Colomer M, Blanco-Míguez A, Manghi P, Asnicar F, Dubois L, Golzato D et al. The person-to-person transmission landscape of the gut and oral microbiomes. Nature. 2023 Feb 2;614(7946):125-135. doi: 10.1038/s41586-022-05620-1

2021

Sarhan MS, Lehmkuhl A, Straub R, Tett AJ, Wieland G, Franken M et al. Ancient DNA diffuses from human bones to cave stones. iScience. 2021 Dec 17;24(12):103397. 103397. Epub 2021 Nov 23. doi: 10.1016/j.isci.2021.103397

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

All publications