NetworkLab@LMU

We provide software and expertise for

the analysis of experimental interaction networks
modeling and simulation of biological networks
textmining interactions from literature
identifying miRNA target networks

Research Team

Researchers

Funding

Collaborations

We already cooperate with a number of partners from universities, e.g.

Jürgen Haas (University of Edinburgh, Division of Pathway Medicine): Systems biology of herpesvirus infections
Lars Dölken (LMU München, Max-von-Pettenkofer Institut): Systems biology of herpesvirus infections
Susanne Bailer (LMU München, Max-von-Pettenkofer Institut)
Albrecht von Brunn (LMU München, Max-von-Pettenkofer Institut): Analysis of the SARS interactome
Ania C. Muntau (LMU München, Dr. von Haunersches Kinderspital)

Selected publications

2012

Papers

Robert Küffner, Tobias Petri, Pegah Tavakkolkhah, Lukas Windhager, Ralf Zimmer. Inferring Gene Regulatory Networks by ANOVA. Bioinformatics, vol 28, no. 10, pp. 1376-1382, March 2012.

BibTex

2011

Papers

Naeem H, Küffner R, Zimmer R.. MIRTFnet: analysis of miRNA regulated transcription factors. PLoS One, pp. 6(8):e22519, August 2011.

BibTex

2009

Papers

Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer. Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. Journal of Computational Biology, vol 16, no. 8, pp. 1-17, 2009.

BibTex

2008

Papers

Caroline C. Friedel, Ralf Zimmer. Identifying the topology of protein complexes from affinity purification assays. Proceedings of the German Conference on Bioinformatics (GCB 2008), September 9-12, 2008, Dresden, Germany, Lecture Notes in Informatics, vol P-136, pp. 30-43, GI, 2008.

BibTex

Florian Erhard, Caroline C. Friedel, Ralf Zimmer. FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics, vol 9, no. 1, pp. 356, 2008.

BibTex

Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer. ProCope–protein complex prediction and evaluation. Bioinformatics, vol 24, no. 18, pp. 2115–2116, Sep 2008.

BibTex

2007

Papers

Albrecht von Brunn, Carola Teepe, Jeremy C. Simpson, Rainer Pepperkok, Caroline C. Friedel, Ralf Zimmer, Rhonda Roberts, Jürgen Haas. Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS ONE, vol 2, no. 5, pp. e459, 2007.

BibTex

Katrin Fundel, R. Küffner, Ralf Zimmer. RelEx - Relation extraction using dependency parse trees. Bioinformatics, vol 23, no. 3, pp. 365-371, 2007.

BibTex

2006

Papers

R. Küffner, T. Duchrow, Katrin Fundel, Ralf Zimmer. Characterization of Protein Interactions. Daniel Huson, Oliver Kohlbacher, Andrei Lupas, Kay Nieselt, Andreas Zell (eds.): German Conference on Bioinformatics (GCB), Tübingen, Germany, September 19-22, 2006, Lecture Notes in Informatics, vol P-83, pp. 64-73, Gesellschaft für Informatik, 2006.

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