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

Three CeMESS Scientists Recognized as “Highly Cited Researchers”

19.11.2024 CeMESS

CeMESS is proud to celebrate Andreas Richter (TER), Michael Wagner (DOME), and Wolfgang Wanek (TER) for their inclusion in the 2024 Clarivate list of…

Congratulations, Dr. Trgovec-Greif!

10.09.2024 CUBE

Lovro Trgovec-Greif successfully defended his PhD thesis "Virus bioinformatics and phage-bacteria interactions".

Congratulations, Dr. Sango!

07.09.2024 CUBE

Roko Sango defended his PhD thesis "Computational metabolic modelling and multi-omics analysis of bone-marrow derived and tissue-resident macrophages"…

Congratulations, Dr. Predl

02.08.2024 CUBE

Michael Predl defended his PhD thesis "Prediction of cross-feeding interactions in microbial communities using metabolic modelling" with very good…

Austrian Bioinformatics Workshop 2024, July 3 in Graz

16.05.2024 CUBE

CUBE, the Center for Medical Research (ZMF) of the Medical University of Graz and the Austrian Bioinformatics Platform welcome you to Graz to…

We are hiring: ELIXIR Austria node coordinator

16.05.2024 CUBE

We are searching for a highly motivated person (m/f/d) with professional experience in the coordination of research infrastructures for the position…

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