I am guest member in the lab of Dr. Eli Zamir, "Systems Biology of Cell Matrix Adhesion" at Max-Planck-Institute of Molecular Physiology Dortmund.

My Diploma thesis was "Propagating Interaction Logic toward Predictive Protein Hypernetworks". It was awarded with the Uhde-Preis 2011.

Peer-Reviewed

Althoff K, Beckers A, Odersky A, Mestdagh P, Köster J, Bray IM, Bryan K, Vandesompele J, Speleman F, Stallings RL, Schramm A, Eggert A, Sprüssel A, Schulte JH. MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A. Int J Cancer. 2013

Sven Rahmann, Marcel Martin, Johannes H. Schulte, Johannes Köster, Tobias Marschall, Alexander Schramm. "Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data". Methods 2012.

A Schramm, B Schowe, K Fielitz, M Heilmann, M Martin, T Marschall, J Köster, J Vandesompele, J Vermeulen, K de Preter, J Koster, R Versteeg, R Noguera, F Speleman, S Rahmann, A Eggert, K Morik and J H Schulte. "Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome". British Journal of Cancer 2012.

Köster, Johannes and Sven Rahmann. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012.

Köster, Johannes, Eli Zamir, and Sven Rahmann. "Efficiently Mining Protein Interaction Dependencies from Large Text Corpora“. Integrative Biology 2012.

Schramm A, Köster J, Marschall T, Martin M, Heilmann M, Fielitz K, Büchel G, Barann M, Esser D, Rosenstiel P, Rahmann S, Eggert A, Schulte JH. "Next-generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN-amplified neuroblastoma". Int J Cancer 2012

Köster, Johannes and Sven Rahmann. "Building and Documenting Bioinformatics Workflows with Python-based Snakemake". Proceedings of the GCB 2012.

Other

Johannes Köster, Eli Zamir, Sven Rahmann. Protein Hypernetworks: a Logic Framework for Interaction Dependencies and Perturbation Effects in Protein Networks; a preprint including the supplement is available at arXiv: 1106.2562.

Johannes Köster, Eli Zamir, Sven Rahmann. Protein Hypernetworks. It got an "honorable mention" at the Doktorantenkolleg Informatik Ruhr 2011, and a Poster Award at the Forschungstag 2011 of the University Hospital Essen. (poster as PDF)

Mini-Workshop Theoretical Computer Science in Dortmund, May 2011, on theoretical aspects of protein hypernetworks. (slides as PDF)

9th International Conference on Pathways, Networks and Systems Medicine on Crete, June 2011, on protein hypernetworks. It was honored with a Travel Award. (slides as PDF)
German Conference on Bioinformatics, September 2012, on "Building and Documenting Bioinformatics Workflows with Python-based Snakemake". (slides as PDF)

Teaching

Teaching Assistant (TU Dortmund):

Summer Term 2011: Datenstrukturen Algorithmen und Programmierung (DAP1)

Theses co-supervised:

Finished:

Michael Nimbs: Konstruktion von Protein-Hypernetzwerken durch Text-Mining in der PubMed Datenbank (Bachelor)

Christiane Küch: Entwurf einer Datenstruktur für Pangenome (Diploma)