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

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…

Welcome Nick!

29.04.2024 CUBE

We're happy to announce that CUBies are strenghtening in numbers!

Welcome Lukas!

29.04.2024 CUBE

We're happy to announce that CUBies are strenghtening in numbers!

Univie Teaching Award 2024: CeMESS

08.03.2024 CeMESS

The Centre for Microbiology and Environmental Systems Science (CeMESS) at the University of Vienna is proud to announce the establishment of the…

Women in Science 2024 @ CeMESS

09.02.2024 CeMESS

To celebrate the International Day of Women and Girls in Science (February 11th), CeMESS is once again shining the spotlight on our remarkable female…

Gender Diversity Symposium champions inclusivity in science

10.11.2023 CeMESS

How can we promote a culture of openness and inclusivity in the sciences? This was a key question posed at our recent Diversity Symposium, hosted by…

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

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

Granehall L, Huang KD, Tett A, Manghi P, Paladin A, O'Sullivan N et al. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. Microbiome. 2021 Sept 30;9(1):197. doi: 10.1186/s40168-021-01132-8

All publications