| 2026 | AIME | Inferring Chronic Treatment Onset from ePrescription Data: A Renewal Process Approach. | Pavlin G. Policar, Dalibor Stanimirovic, Blaz Zupan |
| 2024 | DIS | Latent Embedding Based on a Transcription-Decay Decomposition of mRNA Dynamics Using Self-supervised CoxPH. | Martin Spendl, Tomaz Curk, Blaz Zupan |
| 2023 | AIME | Nation-Wide ePrescription Data Reveals Landscape of Physicians and Their Drug Prescribing Patterns in Slovenia. | Pavlin G. Policar, Dalibor Stanimirovic, Blaz Zupan |
| 2023 | AIME | Ranking of Survival-Related Gene Sets Through Integration of Single-Sample Gene Set Enrichment and Survival Analysis. | Martin Spendl, Jaka Kokosar, Ela Praznik, Luka Ausec, Blaz Zupan |
| 2023 | DIS | Gene Interactions in Survival Data Analysis: A Data-Driven Approach Using Restricted Mean Survival Time and Literature Mining. | Jaka Kokosar, Martin Spendl, Blaz Zupan |
| 2023 | DIS | Refining Temporal Visualizations Using the Directional Coherence Loss. | Pavlin G. Policar, Blaz Zupan |
| 2019 | DIS | Embedding to Reference t-SNE Space Addresses Batch Effects in Single-Cell Classification. | Pavlin G. Policar, Martin Strazar, Blaz Zupan |
| 2016 | PSB | Collective Pairwise Classification for Multi-Way Analysis of Disease and Drug Data. | Marinka Zitnik, Blaz Zupan |
| 2014 | PSB | Matrix Factorization-Based Data Fusion for Gene Function Prediction in Baker's Yeast and Slime Mold. | Marinka Zitnik, Blaz Zupan |
| 2014 | RECOMB | Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion. | Marinka Zitnik, Blaz Zupan |
| 2011 | AIME | A Data Mining Library for miRNA Annotation and Analysis. | Angelo Nuzzo, Riccardo Beretta, Francesca Mulas, Valerie Roobrouck, Catherine M. Verfaillie, Blaz Zupan, Riccardo Bellazzi |
| 2011 | AIME | Ranking and 1-Dimensional Projection of Cell Development Transcription Profiles. | Lan Zagar, Francesca Mulas, Riccardo Bellazzi, Blaz Zupan |
| 2009 | AIME | On Quality of Different Annotation Sources for Gene Expression Analysis. | Francesca Mulas, Tomaz Curk, Riccardo Bellazzi, Blaz Zupan |
| 2009 | AIME | Subgroup Discovery in Data Sets with Multi-dimensional Responses: A Method and a Case Study in Traumatology. | Lan Umek, Blaz Zupan, Marko Toplak, Annie Morin, Jean-Hugues Chauchat, Gregor Makovec, Dragica Smrke |
| 2005 | AIME | Conquering the Curse of Dimensionality in Gene Expression Cancer Diagnosis: Tough Problem, Simple Models. | Minca Mramor, Gregor Leban, Janez Demsar, Blaz Zupan |
| 2005 | KDD | Nomograms for visualizing support vector machines. | Aleks Jakulin, Martin Mozina, Janez Demsar, Ivan Bratko, Blaz Zupan |
| 2005 | KDD | Simple and effective visual models for gene expression cancer diagnostics. | Gregor Leban, Minca Mramor, Ivan Bratko, Blaz Zupan |
| 2003 | AIME | Attribute Interactions in Medical Data Analysis. | Aleks Jakulin, Ivan Bratko, Dragica Smrke, Janez Demsar, Blaz Zupan |
| 2002 | AMIA | Prognostic Model for Terminally Ill Cancer Patients on Laboratory Data. | Kenji Hira, Noriaki Aoki, Akitoshi Hayashi, Janez Demsar, Blaz Zupan, Kim Dunn, William Jack Schull, Tsuguya Fukui |
| 2001 | AIME | Abductive Inference of Genetic Networks. | Blaz Zupan, Ivan Bratko, Janez Demsar, J. Robert Beck, Adam Kuspa, Gad Shaulsky |
| 2000 | ICML | Induction of Concept Hierarchies from Noisy Data. | Blaz Zupan, Ivan Bratko, Marko Bohanec, Janez Demsar |
| 1999 | ILP | Rule Evaluation Measures: A Unifying View. | Nada Lavrac, Peter A. Flach, Blaz Zupan |
| 1997 | AIME | Acquiring and Validating Background Knowledge for Machine Learning Using Function Decomposition. | Blaz Zupan, Saso Dzeroski |
| 1997 | CBMS | Relating clinical and neurophysiological assessment of spasticity by machine learning. | Blaz Zupan, Dobrivoje S. Stokic, Marko Bohanec, Michael M. Priebe, Arthur M. Sherwood |
| 1997 | ICML | Machine Learning by Function Decomposition. | Blaz Zupan, Marko Bohanec, Ivan Bratko, Janez Demsar |
| 1997 | KDD | A Dataset Decomposition Approach to Data Mining and Machine Discovery. | Blaz Zupan, Marko Bohanec, Ivan Bratko, Bojan Cestnik |