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

EMBO Practical Course Integrated multi-omic analyses of microbial communities: 23 – 29 April 2022 | Luxembourg

29.01.2022 CUBE

This EMBO Practical Course is aimed at early-stage researchers (PhD students, early PostDocs) with prior expertise in one (or more) of these “omes”…

New bachelor or master project: wavefront transformation and alignment of protein sequences

27.11.2021 CUBE

Protein sequence alignment is a fundamental and widely-used technique in bioinformatics. A new bachelor or master thesis project will enable and…

CMESS celebrates four Highly Cited Researchers 2021

17.11.2021 CeMESS

CMESS is home to four of the world's most cited researchers. Holger Daims (DOME), Thomas Rattei (CUBE), Andreas Richter (TER) and Michael Wagner…

Thomas Rattei is Highly Cited Researcher 2021

16.11.2021 CUBE

CUBE member Thomas Rattei is - just as in the past year - among the most cited researchers in the world. Alongside his CMESS colleagues Holger Daims…

Official Opening of the new biology building

13.10.2021 CeMESS

The University of Vienna Biology Building (UBB) officially starts into full operation: The University of Vienna and the Bundesimmobiliengesellschaft…

Doctoral School celebrates its first birthday

12.10.2021 CeMESS

One year of hands-on interdisciplinary training: The Doctoral School in Microbiology and Environmental Science has celebrated its first birthday. More…

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

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