| 2011 | RECOMB | Experiment Specific Expression Patterns. | Tobias Petri, Robert Kffner, Ralf Zimmer |
| 2008 | ECCB | Protein structure alignment considering phenotypic plasticity. | Gergely Csaba, Fabian Birzele, Ralf Zimmer |
| 2008 | GI | Veranstaltung zum Tagungsmotto: Bioinformatik und Biotechnologie. | Volker Heun, Ralf Zimmer |
| 2008 | RECOMB | Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. | Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer |
| 2005 | ECCB | Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. | Robert Kffner, Katrin Fundel, Ralf Zimmer |
| 2005 | ECCB | Identifying active transcription factors and kinases from expression data using pathway queries. | Florian Sohler, Ralf Zimmer |
| 2005 | ECCB | Web servicing the biological office. | Martin Szugat, Daniel Gttler, Katrin Fundel, Florian Sohler, Ralf Zimmer |
| 2003 | PSB | Playing Biology's Name Game: Identifying Protein Names in Scientific Text. | Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer |
| 2003 | PSB | Profile-Profile Alignment: A Powerful Tool for Protein Structure Prediction. | Niklas von hsen, Ingolf Sommer, Ralf Zimmer |
| 2002 | ISMB | Co-clustering of biological networks and gene expression data. | Daniel Hanisch, Alexander Zien, Ralf Zimmer, Thomas Lengauer |
| 2002 | RECOMB | Microarrays: how many do you need? | Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer |
| 2001 | ISMB | Centralization: a new method for the normalization of gene expression data. | Alexander Zien, Thomas Aigner, Ralf Zimmer, Thomas Lengauer |
| 2001 | WABI | Improving Profile-Profile Alignments via Log Average Scoring. | Niklas von hsen, Ralf Zimmer |
| 2000 | ISMB | Analysis of Gene Expression Data with Pathway Scores. | Alexander Zien, Robert Kffner, Ralf Zimmer, Thomas Lengauer |
| 2000 | RECOMB | A simple iterative approach to parameter optimization. | Alexander Zien, Ralf Zimmer, Thomas Lengauer |
| 1999 | PSB | Application of Parameter Optimization to Molecular Comparison Problems. | Christian Lemmen, Alexander Zien, Ralf Zimmer, Thomas Lengauer |
| 1997 | RECOMB | Fast and numerically stable parametric alignment of biosequences. | Ralf Zimmer, Thomas Lengauer |
| 1995 | ISMB | Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment. | Ralf Thiele, Ralf Zimmer, Thomas Lengauer |