| 2011 | ICML | Support Vector Machines as Probabilistic Models. | Vojtech Franc, Alexander Zien, Bernhard Schlkopf |
| 2008 | ISMB | POIMs: positional oligomer importance matrices - understanding support vector machine-based signal detectors. | Sren Sonnenburg, Alexander Zien, Petra Philips, Gunnar Rtsch |
| 2008 | WABI | An Automated Combination of Kernels for Predicting Protein Subcellular Localization. | Cheng Soon Ong, Alexander Zien |
| 2007 | ICML | Transductive support vector machines for structured variables. | Alexander Zien, Ulf Brefeld, Tobias Scheffer |
| 2007 | ICML | Multiclass multiple kernel learning. | Alexander Zien, Cheng Soon Ong |
| 2006 | ICML | A continuation method for semi-supervised SVMs. | Olivier Chapelle, Mingmin Chi, Alexander Zien |
| 2006 | ISMB | ARTS: accurate recognition of transcription starts in human. | Sren Sonnenburg, Alexander Zien, Gunnar Rtsch |
| 2005 | AISTATS | Semi-Supervised Classification by Low Density Separation. | Olivier Chapelle, Alexander Zien |
| 2005 | ICML | Large margin non-linear embedding. | Alexander Zien, Joaquin Quionero Candela |
| 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 |
| 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 |