• 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 observes the mercury transit

    09.05.16
    Event

    During the afternoon of May 9th the planet mercury has (slightly) obstructed the sun. Mercury became visible in front of the sun at 13:12 and did not leave the sun until sunset. CUBE has observed the cosmic spectacle on the ...

  • CAMI project featured in Nature Methods

    05.05.16
    Publication

    COMPETITIVE BUT SENSITIVE: TOOL BENCHMARKING IN METAGENOMICS

    The Critical Assessment of Metagenome Interpretation (CAMI) competition has been featured in a recent Nature Methods technology article. CAMI was launched by Alice McHardy from the Helmholtz Center for Infection Research, Alexander Sczyrba at ...

  • Mag. Andreas Bachmayr

    18.04.16
    Event

    Andreas graduated in the master course "Genetics and developmental biology" by successfully defending his master thesis today. In his master project entitled "Computational analysis of plastid DNA insertions into nuclear and mitochondrial genomes in non-photosynthetic parasitic plants from next generation sequencing data" ...

  • Challenges in microbial ecology: Let's join forces between experimentalists and modellers!

    31.03.16
    News

    ISME Journal recently published our paper on  'Challenges in microbial ecology: building predictive understanding of community function and dynamics' (Widder S et al. (March 2016)). The manuscript focuses the ideas of experimental and theoretical scientists engaged with microbial communties and ...

Latest publications

Suppressed recombination and unique candidate genes in the divergent haplotype encoding Fhb1, a major Fusarium head blight resistance locus in wheat.

Fine mapping and sequencing revealed 28 genes in the non-recombining haplotype containing Fhb1 . Of these, only a GDSL lipase gene shows a pathogen-dependent expression pattern. Fhb1 is a prominent Fusarium head blight resistance locus of wheat, which has been successfully introgressed in adapted breeding material, where it confers a significant increase in overall resistance to the causal pathogen Fusarium graminearum and the fungal virulence factor and mycotoxin deoxynivalenol. The Fhb1 region has been resolved for the susceptible wheat reference genotype Chinese Spring, yet the causal gene itself has not been identified in resistant cultivars. Here, we report the establishment of a 1 Mb contig embracing Fhb1 in the donor line CM-82036. Sequencing revealed that the region of Fhb1 deviates from the Chinese Spring reference in DNA size and gene content, which explains the repressed recombination at the locus in the performed fine mapping. Differences in genes expression between near-isogenic lines segregating for Fhb1 challenged with F. graminearum or treated with mock were investigated in a time-course experiment by RNA sequencing. Several candidate genes were identified, including a pathogen-responsive GDSL lipase absent in susceptible lines. The sequence of the Fhb1 region, the resulting list of candidate genes, and near-diagnostic KASP markers for Fhb1 constitute a valuable resource for breeding and further studies aiming to identify the gene(s) responsible for F. graminearum and deoxynivalenol resistance.

Schweiger W, Steiner B, Vautrin S, Nussbaumer T, Siegwart G, Zamini M, Jungreithmeier F, Gratl V, Lemmens M, Mayer KF, Bérgès H, Adam G, Buerstmayr H
2016 - Theor. Appl. Genet., in press

High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved.

The systems biology of microbial communities, organismal communities inhabiting all ecological niches on earth, has in recent years been strongly facilitated by the rapid development of experimental, sequencing and data analysis methods. Novel experimental approaches and binning methods in metagenomics render the semi-automatic reconstructions of near-complete genomes of uncultivable bacteria possible, while advances in high-resolution amplicon analysis allow for efficient and less biased taxonomic community characterization. This will also facilitate predictive modeling approaches, hitherto limited by the low resolution of metagenomic data. In this review, we pinpoint the most promising current developments in metagenomics. They facilitate microbial systems biology towards a systemic understanding of mechanisms in microbial communities with scopes of application in many areas of our daily life.

2016 - Curr. Opin. Biotechnol., 174-181

Transcriptomic and Proteomic Analysis of Arion vulgaris-Proteins for Probably Successful Survival Strategies?

The Spanish slug, Arion vulgaris, is considered one of the hundred most invasive species in Central Europe. The immense and very successful adaptation and spreading of A. vulgaris suggest that it developed highly effective mechanisms to deal with infections and natural predators. Current transcriptomic and proteomic studies on gastropods have been restricted mainly to marine and freshwater gastropods. No transcriptomic or proteomic study on A. vulgaris has been carried out so far, and in the current study, the first transcriptomic database from adult specimen of A. vulgaris is reported. To facilitate and enable proteomics in this non-model organism, a mRNA-derived protein database was constructed for protein identification. A gel-based proteomic approach was used to obtain the first generation of a comprehensive slug mantle proteome. A total of 2128 proteins were unambiguously identified; 48 proteins represent novel proteins with no significant homology in NCBI non-redundant database. Combined transcriptomic and proteomic analysis revealed an extensive repertoire of novel proteins with a role in innate immunity including many associated pattern recognition, effector proteins and cytokine-like proteins. The number and diversity in gene families encoding lectins point to a complex defense system, probably as a result of adaptation to a pathogen-rich environment. These results are providing a fundamental and important resource for subsequent studies on molluscs as well as for putative antimicrobial compounds for drug discovery and biomedical applications.

Bulat T, Smidak R, Sialana FJ, Jung G, Rattei T, Bilban M, Sattmann H, Lubec G, Aradska J
2016 - PloS one, 3: e0150614