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 EU project: Searching for oil and gas with molecular biological methods

26.05.2021 CUBE

Despite all efforts to switch to renewable energies, fossil fuels will continue to play a role in energy supply for several decades to come. An EU…

New master thesis project opened: microbe-host interactions in ancient bacteria

18.05.2021 CUBE

We have opened a new project for a bachelor or master project at CUBE:

Welcome Johann and Michael, our new IT team

04.04.2021 CUBE

After Florian Goldenberg's move to the Vienna Scientific Cluster, we were searching for a new IT and system administrator. We were glad to find two :)…

Thomas Rattei is Highly Cited Researcher 2020

18.11.2020 CUBE

Clarivate analytics has released the Highly Cited Researchers list of 2020. This list contains scientists who are among the 1% most cited researchers…

Dr. Roman Feldbauer

02.10.2020 CUBE

Roman has very successfully passed the defensio of his dissertation. Roman presented his results on "Hubness in the protein sequence universe" and…

Annual Meeting 2020 of the Austrian Life Science Community - virtual meeting with Life Science Tuesdays

13.07.2020 CUBE

Our Annual Meeting is the melting pot of the Austrian Life Science Community - a place to listen to renowned speakers, for participants to present…

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 May 6. 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