• 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

Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide.

Characterisation of G protein-coupled receptors (GPCR) relies on the availability of a toolbox of ligands that selectively modulate different functional states of the receptors. To uncover such molecules, we explored a unique strategy for ligand discovery that takes advantage of the evolutionary conservation of the 600-million-year-old oxytocin/vasopressin signalling system. We isolated the insect oxytocin/vasopressin orthologue inotocin from the black garden ant (Lasius niger), identified and cloned its cognate receptor and determined its pharmacological properties on the insect and human oxytocin/vasopressin receptors. Subsequently, we identified a functional dichotomy: inotocin activated the insect inotocin and the human vasopressin V1b receptors, but inhibited the human V1aR. Replacement of Arg8 of inotocin by D-Arg8 led to a potent, stable and competitive V1aR-antagonist ([D-Arg8]-inotocin) with a 3,000-fold binding selectivity for the human V1aR over the other three subtypes, OTR, V1bR and V2R. The Arg8/D-Arg8 ligand-pair was further investigated to gain novel insights into the oxytocin/vasopressin peptide-receptor interaction, which led to the identification of key residues of the receptors that are important for ligand functionality and selectivity. These observations could play an important role for development of oxytocin/vasopressin receptor modulators that would enable clear distinction of the physiological and pathological responses of the individual receptor subtypes.

Di Giglio MG, Muttenthaler M, Harpsøe K, Liutkeviciute Z, Keov P, Eder T, Rattei T, Arrowsmith S, Wray S, Marek A, Elbert T, Alewood PF, Gloriam DE, Gruber CW
2017 - Sci Rep, 41002

Unraveling the microbial processes of black band disease in corals through integrated genomics.

Coral disease outbreaks contribute to the ongoing degradation of reef ecosystems, however, microbial mechanisms underlying the onset and progression of most coral diseases are poorly understood. Black band disease (BBD) manifests as a cyanobacterial-dominated microbial mat that destroys coral tissues as it rapidly spreads over coral colonies. To elucidate BBD pathogenesis, we apply a comparative metagenomic and metatranscriptomic approach to identify taxonomic and functional changes within microbial lesions during in-situ development of BBD from a comparatively benign stage termed cyanobacterial patches. Results suggest that photosynthetic CO2-fixation in Cyanobacteria substantially enhances productivity of organic matter within the lesion during disease development. Photosynthates appear to subsequently promote sulfide-production by Deltaproteobacteria, facilitating the major virulence factor of BBD. Interestingly, our metagenome-enabled transcriptomic analysis reveals that BBD-associated cyanobacteria have a putative mechanism that enables them to adapt to higher levels of hydrogen sulfide within lesions, underpinning the pivotal roles of the dominant cyanobacterium within the polymicrobial lesions during the onset of BBD. The current study presents sequence-based evidence derived from whole microbial communities that unravel the mechanism of development and progression of BBD.

Sato Y, Ling EY, Turaev D, Laffy P, Weynberg KD, Rattei T, Willis BL, Bourne DG
2017 - Sci Rep, 40455

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