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

Pre-Opening Event at the UBB

26.09.2021 CeMESS

CMESS employees celebrated the move to the University of Vienna Biology Building (UBB) with a soft opening event on September 23rd: The Rectorate and…

Open: PhD student or PostDoc position in bioinformatics for marine prospecting

03.09.2021 CUBE

Despite ongoing efforts to increase the percentage of renewable energy resources, hydrocarbons (HC), i.e. oil and gas will remain an important energy…

New publication in the JACS: A Metabolite of Pseudomonas Triggers Prophage-Selective Lysogenic to Lytic Conversion in Staphylococcus aureus

17.08.2021 CeMESS

Bacteriophages are still a relatively unknown component of the human microbiome. However, they can play a powerful role in the life cycles of…

CUBE moved to new University Biology Building

12.08.2021 CUBE

CUBE has moved. We are now situated in the new University Biology Buildung at Djerassiplatz 1, 1030 Vienna. The offices of CUBE are located on the 2nd…

New CMESS report out now

25.06.2021 CeMESS

Our research, facilities, and faculty – our new CMESS report with insights into our work and organisation has just been published. The report outlines…

New publication in Nature Reviews Microbiology: Prevotella diversity, niches and interactions with the human host

03.06.2021 CUBE

Prevotella is a diverse genus that is frequently identified in the human microbiome across different body-sites.

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