• 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

  • Happy birthday, Gabi!

    28.03.18
    Personal

    Today, Gabi Kaindl is celebrating her 60th birthday. Dear Gabi, we all congratulate and wish you all the best. Thanks for your great work and the continuous support in solving all the big and small CUBE issues every day... ...

  • CAMI paper published in Nature Methods

    03.10.17
    Publication

    The paper about the first round of the "Critical Assessment of Metagenome Interpretation" (CAMI) challenge was published in Nature Methods. The challenge was organized and run by an international team, including Dmitrij Turaev and Thomas Rattei from CUBE.

    That's not the ...

  • Harald Marx starts Computational Peptidomics Group at CUBE

    21.08.17
    Personal

    Dr. Harald Marx is a Bioinformatician by training. During his PhD in Bernhard Kuster's Lab at TU Munich he developed tools and statistical approaches for proteogenomics and structural genome annotation. As a PostDoc fellow in Joshua Coon's lab at the University of ...

  • Symposium "Computational Approaches in Precision Medicine" Jul 27/28 in Vienna

    27.07.17
    Event

    The CUBE team and the research focus "Computational Life Sciences" teamed up with David Kreil and Pawel Labaj (BOKU University) in organizing the symposium "Computational Approaches in Precision Medicine" Jul 27/28. The meeting takes place in the BIG lecture hall ...

Latest publications

Genome sequencing of Chlamydia trachomatis serovars E and F reveals substantial genetic variation.

Chlamydia trachomatis (Ctr) is a bacterial pathogen that causes ocular, urogenital and lymph system infections in humans. It is highly abundant and among its serovars, E, F and D are most prevalent in sexually transmitted disease. However, the number of publicly available genome sequences of the serovars E and F, and thereby our knowledge about the molecular architecture of these serovars, is low. Here we sequenced the genomes of six E and F clinical isolates and one E lab strain, in order to study the genetic variance in these serovars. As observed before, the genomic variation inside the Ctr genomes is very low and the phylogenetic placement in comparison to publicly available genomes is as expected by ompA gene serotyping. However, we observed a large InDel carrying four to five open reading frames in one clinical E sample and in the E lab strain. We have also observed substantial variation on nucleotide and amino acid levels, especially in membrane proteins and secreted proteins. Furthermore, these two groups of proteins are also target for recombination events. One clinical F isolate was genetically heterogeneous and revealed the highest differences on nucleotide level in the pmpE gene.

Eder T, Kobus S, Stallmann S, Stepanow S, Köhrer K, Hegemann JH, Rattei T
2017 - Pathog Dis, in press

Coral-associated viral communities show high levels of diversity and host auxiliary functions.

Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent. Most sequences with matches to eukaryotic viruses were assigned to six viral families, including four Nucleocytoplasmic Large DNA Viruses (NCLDVs) families: Iridoviridae, Phycodnaviridae, Mimiviridae, and Poxviridae, as well as Retroviridae and Polydnaviridae. Contrary to previous findings, Herpesvirales were rare in these GBR corals. Sequences of a ssRNA virus with similarities to the dinornavirus, Heterocapsa circularisquama ssRNA virus of the Alvernaviridae that infects free-living dinoflagellates, were observed in three coral species. We also detected viruses previously undescribed from the coral holobiont, including a virus that targets fungi associated with the coral species Acropora tenuis. Functional analysis of the assembled contigs indicated a high prevalence of latency-associated genes in the coral-associated viral assemblages, several host-derived auxiliary metabolic genes (AMGs) for photosynthesis (psbA, psbD genes encoding the photosystem II D1 and D2 proteins respectively), as well as potential nematocyst toxins and antioxidants (genes encoding green fluorescent-like chromoprotein). This study expands the currently limited knowledge on coral-associated viruses by characterising viral composition and function across seven GBR coral species.

Weynberg KD, Laffy PW, Wood-Charlson EM, Turaev D, Rattei T, Webster NS, van Oppen MJH
2017 - PeerJ, e4054

Peripheral blood vessels are a niche for blood-borne meningococci.

Neisseria meningitidis is the causative agent of cerebrospinal meningitis and that of a rapidly progressing fatal septic shock known as purpura fulminans. Meningococcemia is characterized by bacterial adhesion to human endothelial cells of the microvessels. Host specificity has hampered studies on the role of blood vessels colonization in N. meningitidis associated pathogenesis. In this work, using a humanized model of SCID mice allowing the study of bacterial adhesion to human cells in an in vivo context we demonstrate that meningococcal colonization of human blood vessels is a prerequisite to the establishment of sepsis and lethality. To identify the molecular pathways involved in bacterial virulence, we performed transposon insertion site sequencing (Tn-seq) in vivo. Our results demonstrate that 36% of the genes that are important for growth in the blood of mice are dispensable when bacteria colonize human blood vessels, suggesting that human endothelial cells lining the blood vessels are feeding niches for N. meningitidis in vivo. Altogether, our work proposes a new paradigm for meningococcal virulence in which colonization of blood vessels is associated with metabolic adaptation and sustained bacteremia responsible for sepsis and subsequent lethality.

Capel E, Barnier JP, Zomer AL, Bole-Feysot C, Nussbaumer T, Jamet A, Lécuyer H, Euphrasie D, Virion Z, Frapy E, Pélissier P, Join-Lambert O, Rattei T, Bourdoulous S, Nassif X, Coureuil M
2017 - Virulence, in press