Fabian Horn

Fabian Horn

Prediction of gene regulatory networks involved in the differentiation, secondary metabolism and cross talk of Aspergillus nidulans

Biological data is collected in many hundreds of different experiments where each consists of thousands of data points. They are published and stored in several databases and scientific jounals in different data formats and abstraction layers. The challenge for bioinformatics is to gather, preprocess and model these data consistently. By the integration of the information from several experiments, new scientific findings can be obtained with the help of methods from systems biology and comparative analysis.

Aspergillus nidulans is a filamentous fungus which is able to form sexual spores through meiosis. It is therefore used to research the eukaryotic cell biology. A.nidulans has been completely sequenced and there has been great progress in elucidaton of the molecular regulation of the biosynthesis of secondary metabolites. In this project there are two main methods which are to be applied to A.nidulans:

1. A new microarray probe design has already been developed and is currently applied to investigated the transriptome under different environmental conditions. To improve the quality of the data, published microarray data for A.nidulans can be integrated and methods which mine gene expression across different experiments are to be developed and employed.

2. We are looking for the connection of transcriptome data with metabolome data. Until now such relationships have only be analyzed for the primary metabolism, e.g. in Escherichia coli. The project aims to adapt these existing methods for the specific characteristics of secondary metabolite pathways. The methods should be applicable for organisms like A.nidulans, where less prior knowledge is available.


Horn F, Linde J, Mattern DJ, Walther G, Guthke R, Brakhage AA, Valiante V (2015) Draft Genome Sequence of the Fungus Penicillium brasilianum MG11. Genome Announc 3(5), Details PubMed

Horn F, Üzüm Z, Möbius N, Guthke R, Linde J, Hertweck C (2015) Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417. Genome Announc 3(1), Details PubMed

Linde J, Duggan S, Weber M, Horn F, Sieber P, Hellwig D, Riege K, Marz M, Martin R, Guthke R, Kurzai O (2015) Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res 43(3), 1392-1406. Details PubMed

Priebe S, Kreisel C, Horn F, Guthke R, Linde J (2015) FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics 31(3), 445-446. Details PubMed

Bohnert M, Nützmann HW, Schroeckh V, Horn F, Dahse HM, Brakhage AA, Hoffmeister D (2014) Cytotoxic and antifungal activities of melleolide antibiotics follow dissimilar structure-activity relationships. Phytochemistry 105, 101-108. Details PubMed

Horn F, Rittweger M, Taubert J, Lysenko A, Rawlings C, Guthke R (2014) Interactive exploration of integrated biological datasets using context-sensitive workflows. Front Genet 5, 21. Details PubMed

Horn F, Schroeckh V, Netzker T, Guthke R, Brakhage AA, Linde J (2014) Draft Genome Sequence of Streptomyces iranensis. Genome Announc 2(4), Details PubMed

Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldón T, Böcker S, Voigt K (2014) Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). PLoS Genet 10(8), e1004496. Details PubMed

Wartenberg A, Linde J, Martin R, Schreiner M, Horn F, Jacobsen ID, Jenull S, Wolf T, Kuchler K, Guthke R, Kurzai O, Forche A, d'Enfert C, Brunke S, Hube B (2014) Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant. PLoS Genet 10(12), e1004824. Details PubMed

Horn F, Heinekamp T, Kniemeyer O, Pollmächer J, Valiante V, Brakhage AA (2012) Systems biology of fungal infection. Front Microbiol 3, 108. Details PubMed

Nützmann HW, Reyes-Dominguez Y, Scherlach K, Schroeckh V, Horn F, Gacek A, Schümann J, Hertweck C, Strauss J, Brakhage AA (2011) Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation. Proc Natl Acad Sci U S A 108(34), 14282-14287. Details PubMed


Reinhard Guthke


Axel A. Brakhage

Start of PhD

September 1, 2009

Doctoral Disputation

February 4, 2013

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