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

CeMESS joins hands with Open Science for European Researchers' Night!

05.10.2023 CeMESS

Last Friday, the Universalmuseum Joanneum in Graz played host to a unique stall: a collaborative effort between CeMESS and Open Science, as part of…

Congratulations, Dr. Lüftinger

03.08.2023 CUBE

Lukas Lüftinger defended his PhD thesis "Antibiotic Resistance Prediction from Sequencing Data by Machine Learning" with very good grades. During his…

Start of CeMESS Lecture Series – summer 2023 edition

31.03.2023 CeMESS

The CeMESS Lecture Series started with a talk by Shaul Pollak on “Combining machine-learning, ecological theory, and experiments to study bacterial…

Women in Science 2023 @ CMESS

11.02.2023 CeMESS

Spotlight on female researchers: For the International Day of Women and Girls in Science on February 11th and the International Women's Day on March…

International Women's Day 2022 @ CMESS

09.02.2023 CeMESS

For International Women's Day on 8 March, we are putting the spotlight on women at CMESS. Just over half of the CMESS staff and researchers are women.…

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…

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