• Our aim is to advance our understanding of biological systems,

    ranging from single species to multi-species systems and ecosystems,

    based on data from large-scale bioanalytical methods.

  • We develop, improve and apply

    computational methods

    for the interpretation of molecular information in biology.

  • We establish and analyse

    quantitative mathematical models.

CUBE News

  • CUBE coordinates federal project to establish national bioinformatics infrastructure

    10.01.17
    News

    The Federal Ministry of Science, Research and Economics has granted a federal project to establish software and database infrastructure for life science. CUBE will coordinate this project, which has a total volume of 660k EUR from 2017 to 2020. The main ...

  • HAPPY NEW YEAR!

    02.01.17
    Event

    We wish all our team, our students, and our collaboration partners a happy, successful and peaceful new year!

  • Job opening: Group Leader Position

    27.10.16
    Personal

    The Division of Computational Systems Biology at the University of Vienna is offering a

    Group Leader Position in Bioinformatics

    CUBE - the division of Computational Systems Biology - is part of the Department of Microbiology and Ecosystem Science of the ...

  • Virus Orthologous Groups: A novel resource for virus (meta)genomics

    21.08.16
    News

    Orthologous groups are a central resource for comparative (meta-)genomics. At CUBE we have established a novel resource of Virus Orthologous Groups (VOGs), which is based all current RefSeq genomes. It therefore represents all viral lineages of which complete genomes are available. ...

Latest publications

PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data.

Plant Genome and Systems Biology (PGSB), formerly Munich Institute for Protein Sequences (MIPS) PlantsDB, is a database framework for the integration and analysis of plant genome data, developed and maintained for more than a decade now. Major components of that framework are genome databases and analysis resources focusing on individual (reference) genomes providing flexible and intuitive access to data. Another main focus is the integration of genomes from both model and crop plants to form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny). Data exchange and integrated search functionality with/over many plant genome databases is provided within the transPLANT project.

Spannagl M, Nussbaumer T, Bader K, Gundlach H, Mayer KF
2017 - Methods Mol. Biol., 33-44

A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model.

In our mouse model, gastric acid-suppression is associated with antigen-specific IgE and anaphylaxis development. We repeatedly observed non-responder animals protected from food allergy. Here, we aimed to analyse reasons for this protection. Ten out of 64 mice, subjected to oral ovalbumin (OVA) immunizations under gastric acid-suppression, were non-responders without OVA-specific IgE or IgG1 elevation, indicating protection from allergy. In these non-responders, allergen challenges confirmed reduced antigen uptake and lack of anaphylactic symptoms, while in allergic mice high levels of mouse mast-cell protease-1 and a body temperature reduction, indicative for anaphylaxis, were determined. Upon OVA stimulation, significantly lower IL-4, IL-5, IL-10 and IL-13 levels were detected in non-responders, while IL-22 was significantly higher. Comparison of fecal microbiota revealed differences of bacterial communities on single bacterial Operational-Taxonomic-Unit level between the groups, indicating protection from food allergy being associated with a distinct microbiota composition in a non-responding phenotype in this mouse model.

Diesner SC, Bergmayr C, Pfitzner B, Assmann V, Krishnamurthy D, Starkl P, Endesfelder D, Rothballer M, Welzl G, Rattei T, Eiwegger T, Szépfalusi Z, Fehrenbach H, Jensen-Jarolim E, Hartmann A, Pali-Schöll I, Untersmayr E
2016 - Clin. Immunol., 10-18

The origin and evolution of cell types.

Cell types are the basic building blocks of multicellular organisms and are extensively diversified in animals. Despite recent advances in characterizing cell types, classification schemes remain ambiguous. We propose an evolutionary definition of a cell type that allows cell types to be delineated and compared within and between species. Key to cell type identity are evolutionary changes in the 'core regulatory complex' (CoRC) of transcription factors, that make emergent sister cell types distinct, enable their independent evolution and regulate cell type-specific traits termed apomeres. We discuss the distinction between developmental and evolutionary lineages, and present a roadmap for future research.

Arendt D, Musser JM, Baker CV, Bergman A, Cepko C, Erwin DH, Pavličev M, Schlosser G, Widder S, Laubichler MD, Wagner GP
2016 - Nat. Rev. Genet., 12: 744-757