A Simulation and Optimization Environment for Models in Computational Neurobiology. - Blaz Zupan; John A. Halter (EUROSIM, 1995)

Acquiring and Validating Background Knowledge for Machine Learning Using Function Decomposition. - Blaz Zupan; Saso Dzeroski (AIME, 1997)

Constructing Intermediate Concepts by Decomposition of Real Functions. - Janez Demsar; Blaz Zupan; Marko Bohanec; Ivan Bratko (ECML, 1997)

Machine Learning by Function Decomposition. - Blaz Zupan; Marko Bohanec; Ivan Bratko; Janez Demsar (ICML, 1997)

A Dataset Decomposition Approach to Data Mining and Machine Discovery. - Blaz Zupan; Marko Bohanec; Ivan Bratko; Bojan Cestnik (KDD, 1997)

Intelligent Data Analysis for Medical Diagnosis: Using Machine Learning and Temporal Abstraction. - Nada Lavrac; Blaz Zupan; Igor Kononenko 001; Matjaz Kukar; Elpida T. Keravnou (AI Commun., 1998)

Acquiring background knowledge for machine learning using function decomposition: a case study in rheumatology. - Blaz Zupan; Saso Dzeroski (Artif. Intell. Medicine, 1998)

Feature Transformation by Function Decomposition. - Blaz Zupan; Marko Bohanec; Janez Demsar; Ivan Bratko (IEEE Intell. Syst., 1998)

Relating clinical and neurophysiological assessment of spasticity by machine learning. - Blaz Zupan; Dobrivoje S. Stokic; Marko Bohanec; Michael M. Priebe; Arthur M. Sherwood (Int. J. Medical Informatics, 1998)

Experimental Evaluation of Three Partition Selection Criteria for Decision Table Decomposition. - Blaz Zupan; Marko Bohanec (Informatica (Slovenia), 1998)

Optimization of Rule-Based Systems Using State Space Graphs. - Blaz Zupan; Albert Mo Kim Cheng (IEEE Trans. Knowl. Data Eng., 1998)

Rule Evaluation Measures: A Unifying View. - Nada Lavrac; Peter A. Flach; Blaz Zupan (ILP, 1999)

Hierarchical Multi-Attribute Decision Models and Their Application in Health Care. - Marko Bohanec; Blaz Zupan; Vladislav Rajkovic (MIE, 1999)

Naive Bayesian-Based Nomogram for Prediction of Prostate Cancer Recurrence. - Janez Demsar; Blaz Zupan; Michael W. Kattan; J. Robert Beck; Ivan Bratko (MIE, 1999)

Slovenian national health insurance card: The next step. - T. Kalin; Gorazd Kandus; Denis Trcek; Blaz Zupan (MIE, 1999)

Learning by Discovering Concept Hierarchies. - Blaz Zupan; Marko Bohanec; Janez Demsar; Ivan Bratko (Artif. Intell., 1999)

Induction of Concept Hierarchies from Noisy Data. - Blaz Zupan; Ivan Bratko; Marko Bohanec; Janez Demsar (ICML, 2000)

Machine learning for survival analysis: a case study on recurrence of prostate cancer. - Blaz Zupan; Janez Demsar; Michael W. Kattan; J. Robert Beck; Ivan Bratko (Artif. Intell. Medicine, 2000)

Applications of qualitative multi-attribute decision models in health care. - Marko Bohanec; Blaz Zupan; Vladislav Rajkovic (Int. J. Medical Informatics, 2000)

Transformation of attribute space by function decomposition. - Janez Demsar; Blaz Zupan; Ivan Bratko (Data Fusion and Perception, 2001)

Function Decomposition in Machine Learning. - Blaz Zupan; Ivan Bratko; Marko Bohanec; Janez Demsar (Machine Learning and Its Applications, 2001)

Abductive Inference of Genetic Networks. - Blaz Zupan; Ivan Bratko; Janez Demsar; J. Robert Beck; Adam Kuspa; Gad Shaulsky (AIME, 2001)

Web-Enabled Knowledge-Based Analysis of Genetic Data. - Peter Juvan; Blaz Zupan; Janez Demsar; Ivan Bratko; John A. Halter; Adam Kuspa; Gad Shaulsky (ISMDA, 2001)

A Sixth International Workshop on Intelligent Data Analysis in Medicine and Pharmacology (IDAMAP-2001). - Riccardo Bellazzi; Blaz Zupan (MedInfo, 2001)

GenePath: A Computer Program for Genetic Pathway Discovery from Mutant Data. - Janez Demsar; Blaz Zupan; Ivan Bratko; Adam Kuspa; John A. Halter; Robert J. Beck; Gad Shaulsky (MedInfo, 2001)

Decisions at Hand: A Decision Support System on Handhelds. - Blaz Zupan; Ales Porenta; Gaj Vidmar; Noriaki Aoki; Ivan Bratko; J. Robert Beck (MedInfo, 2001)

Feature mining and predictive model construction from severe trauma patient's data. - Janez Demsar; Blaz Zupan; Noriaki Aoki; Matthew J. Wall; Thomas H. Granchi; J. Robert Beck (Int. J. Medical Informatics, 2001)

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 (AMIA, 2002)

Construction and application of hierarchical socioeconomic decision models. - Marjan Krisper; Blaz Zupan (Informatica (Slovenia), 2002)

Attribute Interactions in Medical Data Analysis. - Aleks Jakulin; Ivan Bratko; Dragica Smrke; Janez Demsar; Blaz Zupan (AIME, 2003)

GenePath: a system for inference of genetic networks and proposal of genetic experiments. - Blaz Zupan; Ivan Bratko; Janez Demsar; Peter Juvan; Tomaz Curk; Urban Borstnik; J. Robert Beck; John A. Halter; Adam Kuspa; Gad Shaulsky (Artif. Intell. Medicine, 2003)

GenePath: a system for automated construction of genetic networks from mutant data. - Blaz Zupan; Janez Demsar; Ivan Bratko; Peter Juvan; John A. Halter; Adam Kuspa; Gad Shaulsky (Bioinform., 2003)

Clustering gene expression data with Temporal Abstractions. - Lucia Sacchi; Riccardo Bellazzi; Cristiana Larizza; Paolo Magni; Tomaz Curk; Uros Petrovic; Blaz Zupan (MedInfo, 2004)

Orange: From Experimental Machine Learning to Interactive Data Mining. - Janez Demsar; Blaz Zupan; Gregor Leban; Tomaz Curk (PKDD, 2004)

Nomograms for Visualization of Naive Bayesian Classifier. - Martin Mozina; Janez Demsar; Michael W. Kattan; Blaz Zupan (PKDD, 2004)

A function-decomposition method for development of hierarchical multi-attribute decision models. - Marko Bohanec; Blaz Zupan (Decis. Support Syst., 2004)

Data Mining in Medicine. - Nada Lavrac; Blaz Zupan (The Data Mining and Knowledge Discovery Handbook, 2005)

Conquering the Curse of Dimensionality in Gene Expression Cancer Diagnosis: Tough Problem, Simple Models. - Minca Mramor; Gregor Leban; Janez Demsar; Blaz Zupan (AIME, 2005)

Nomograms for visualizing support vector machines. - Aleks Jakulin; Martin Mozina; Janez Demsar; Ivan Bratko; Blaz Zupan (KDD, 2005)

Simple and effective visual models for gene expression cancer diagnostics. - Gregor Leban; Minca Mramor; Ivan Bratko; Blaz Zupan (KDD, 2005)

Microarray data mining with visual programming. - Tomaz Curk; Janez Demsar; Qikai Xu; Gregor Leban; Uros Petrovic; Ivan Bratko; Gad Shaulsky; Blaz Zupan (Bioinform., 2005)

VizRank: finding informative data projections in functional genomics by machine learning. - Gregor Leban; Ivan Bratko; Uros Petrovic; Tomaz Curk; Blaz Zupan (Bioinform., 2005)

TA-clustering: Cluster analysis of gene expression profiles through Temporal Abstractions. - Lucia Sacchi; Riccardo Bellazzi; Cristiana Larizza; Paolo Magni; Tomaz Curk; Uros Petrovic; Blaz Zupan (Int. J. Medical Informatics, 2005)

GenePath: from mutations to genetic networks and back. - Peter Juvan; Janez Demsar; Gad Shaulsky; Blaz Zupan (Nucleic Acids Res., 2005)

Towards Practical PPM Spam Filtering: Experiments for the TREC 2006 Spam Track. - Andrej Bratko; Bogdan Filipic; Blaz Zupan (TREC, 2006)

Knowledge-based data analysis and interpretation. - Blaz Zupan; John H. Holmes; Riccardo Bellazzi (Artif. Intell. Medicine, 2006)

VizRank: Data Visualization Guided by Machine Learning. - Gregor Leban; Blaz Zupan; Gaj Vidmar; Ivan Bratko (Data Min. Knowl. Discov., 2006)

proDEX - A DSS tool for environmental decision-making. - Martin Znidarsic; Marko Bohanec; Blaz Zupan (Environ. Model. Softw., 2006)

Spam Filtering Using Statistical Data Compression Models. - Andrej Bratko; Gordon V. Cormack; Bogdan Filipic; Thomas R. Lynam; Blaz Zupan (J. Mach. Learn. Res., 2006)

Discovery of Genetic Networks Through Abduction and Qualitative Simulation. - Blaz Zupan; Ivan Bratko; Janez Demsar; Peter Juvan; Adam Kuspa; John A. Halter; Gad Shaulsky (Computational Discovery of Scientific Knowledge, 2007)

Visualization-based cancer microarray data classification analysis. - Minca Mramor; Gregor Leban; Janez Demsar; Blaz Zupan (Bioinform., 2007)

Polyketide synthase genes and the natural products potential of Dictyostelium discoideum. - Jurica Zucko; N. Skunca; Tomaz Curk; Blaz Zupan; Paul F. Long; John Cullum; R. H. Kessin; Daslav Hranueli (Bioinform., 2007)

Towards knowledge-based gene expression data mining. - Riccardo Bellazzi; Blaz Zupan (J. Biomed. Informatics, 2007)

FreeViz - An intelligent multivariate visualization approach to explorative analysis of biomedical data. - Janez Demsar; Gregor Leban; Blaz Zupan (J. Biomed. Informatics, 2007)

Modelling impacts of cropping systems: Demands and solutions for DEX methodology. - Martin Znidarsic; Marko Bohanec; Blaz Zupan (Eur. J. Oper. Res., 2008)

Predictive data mining in clinical medicine: Current issues and guidelines. - Riccardo Bellazzi; Blaz Zupan (Int. J. Medical Informatics, 2008)

On Quality of Different Annotation Sources for Gene Expression Analysis. - Francesca Mulas; Tomaz Curk; Riccardo Bellazzi; Blaz Zupan (AIME, 2009)

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 (AIME, 2009)

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. - Gregor Rot; Anup Parikh; Tomaz Curk; Adam Kuspa; Gad Shaulsky; Blaz Zupan (BMC Bioinform., 2009)

Textual features for corpus visualization using correspondence analysis. - Sasa Petrovic; Bojana Dalbelo Basic; Annie Morin; Blaz Zupan; Jean-Hugues Chauchat (Intell. Data Anal., 2009)

dictyBase - a Dictyostelium bioinformatics resource update. - Petra Fey; Pascale Gaudet; Tomaz Curk; Blaz Zupan; Eric M. Just; Siddhartha Basu; Sohel N. Merchant; Yulia A. Bushmanova; Gad Shaulsky; Warren A. Kibbe; Rex L. Chisholm (Nucleic Acids Res., 2009)

Data-Driven Revision of Decision Models. - Martin Znidarsic; Marko Bohanec; Blaz Zupan (Encyclopedia of Data Warehousing and Mining, 2009)

Text Mining approaches for Automated Literature Knowledge Extraction and Representation. - Angelo Nuzzo; Francesca Mulas; Matteo Gabetta; Eloisa Arbustini; Blaz Zupan; Cristiana Larizza; Riccardo Bellazzi (MedInfo, 2010)

New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. - Anup Parikh; Eryong Huang; Christopher Dinh; Blaz Zupan; Adam Kuspa; Devika Subramanian; Gad Shaulsky (BMC Bioinform., 2010)

FragViz: visualization of fragmented networks. - Miha Stajdohar; Minca Mramor; Blaz Zupan; Janez Demsar (BMC Bioinform., 2010)

On utility of gene set signatures in gene expression-based cancer class prediction. - Minca Mramor; Marko Toplak; Gregor Leban; Tomaz Curk; Janez Demsar; Blaz Zupan (MLSB, 2010)

A Subgroup Discovery Approach for Relating Chemical Structure and Phenotype Data in Chemical Genomics. - Lan Umek; Petra Kaferle; Mojca Mattiazzi; Ales Erjavec; Crtomir Gorup; Tomaz Curk; Uros Petrovic; Blaz Zupan (MLSB, 2010)

Data Mining in Medicine. - Nada Lavrac; Blaz Zupan (Data Mining and Knowledge Discovery Handbook, 2010)

A Data Mining Library for miRNA Annotation and Analysis. - Angelo Nuzzo; Riccardo Beretta; Francesca Mulas; Valerie Roobrouck; Catherine M. Verfaillie; Blaz Zupan; Riccardo Bellazzi (AIME, 2011)

Ranking and 1-Dimensional Projection of Cell Development Transcription Profiles. - Lan Zagar; Francesca Mulas; Riccardo Bellazzi; Blaz Zupan (AIME, 2011)

Similarity of Transcription Profiles for Genes in Gene Sets. - Marko Toplak; Tomaz Curk; Blaz Zupan (ICANNGA (2), 2011)

Stage prediction of embryonic stem cell differentiation from genome-wide expression data. - Lan Zagar; Francesca Mulas; Silvia Garagna; Maurizio Zuccotti; Riccardo Bellazzi; Blaz Zupan (Bioinform., 2011)

Subgroup discovery in data sets with multi-dimensional responses. - Lan Umek; Blaz Zupan (Intell. Data Anal., 2011)

SNPsyn: detection and exploration of SNP-SNP interactions. - Tomaz Curk; Gregor Rot; Blaz Zupan (Nucleic Acids Res., 2011)

Team ULjubljana's Solution to the JRS 2012 Data Mining Competition. - Jure Zbontar; Marinka Zitnik; Miha Zidar; Gregor Majcen; Matic Potocnik; Blaz Zupan (RSCTC, 2012)

NIMFA: A Python Library for Nonnegative Matrix Factorization. - Marinka Zitnik; Blaz Zupan (J. Mach. Learn. Res., 2012)

Extracting Gene Regulation Networks Using Linear-Chain Conditional Random Fields and Rules. - Slavko Zitnik; Marinka Zitnik; Blaz Zupan; Marko Bajec (BioNLP@ACL (Shared Task), 2013)

Interest Propagation for Knowledge Extraction and Representation. - Francesca Mulas; Elisa Del Fabbro; Blaz Zupan; Riccardo Bellazzi (EFMI-STC, 2013)

DEX Methodology: Three Decades of Qualitative Multi-Attribute Modeling. - Marko Bohanec; Martin Znidarsic; Vladislav Rajkovic; Ivan Bratko; Blaz Zupan (Informatica (Slovenia), 2013)

Orange: Data Mining Fruitful and Fun - A Historical Perspective. - Janez Demsar; Blaz Zupan (Informatica (Slovenia), 2013)

Orange: data mining toolbox in python. - Janez Demsar; Tomaz Curk; Ales Erjavec; Crtomir Gorup; Tomaz Hocevar; Mitar Milutinovic; Martin Mozina; Matija Polajnar; Marko Toplak; Anze Staric; Miha Stajdohar; Lan Umek; et al. (J. Mach. Learn. Res., 2013)

Matrix Factorization-Based Data Fusion for Gene Function Prediction in Baker's Yeast and Slime Mold. - Marinka Zitnik; Blaz Zupan (Pacific Symposium on Biocomputing, 2014)

Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion. - Marinka Zitnik; Blaz Zupan (RECOMB, 2014)

Gene network inference by probabilistic scoring of relationships from a factorized model of interactions. - Marinka Zitnik; Blaz Zupan (Bioinform., 2014)

Heterogeneous computing architecture for fast detection of SNP-SNP interactions. - Davor Sluga; Tomaz Curk; Blaz Zupan; Uros Lotric (BMC Bioinform., 2014)

Assessment of Machine Learning Reliability Methods for Quantifying the Applicability Domain of QSAR Regression Models. - Marko Toplak; Rok Mocnik; Matija Polajnar; Zoran Bosnic; Lars Carlsson; Catrin Hasselgren Arnby; Janez Demsar; Scott Boyer; Blaz Zupan; Jonna C. Stålring (J. Chem. Inf. Model., 2014)

Gene network inference by fusing data from diverse distributions. - Marinka Zitnik; Blaz Zupan (Bioinform., 2015)

Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion. - Marinka Zitnik; Blaz Zupan (J. Comput. Biol., 2015)

Data Fusion by Matrix Factorization. - Marinka Zitnik; Blaz Zupan (IEEE Trans. Pattern Anal. Mach. Intell., 2015)

Gene Prioritization by Compressive Data Fusion and Chaining. - Marinka Zitnik; Edward A. Nam; Christopher Dinh; Adam Kuspa; Gad Shaulsky; Blaz Zupan (PLoS Comput. Biol., 2015)

Integrative Clustering by Nonnegative Matrix Factorization Can Reveal Coherent Functional Groups From Gene Profile Data. - Sanja Brdar; Vladimir S. Crnojevic; Blaz Zupan (IEEE J. Biomed. Health Informatics, 2015)

Concurrent software architectures for exploratory data analysis. - Anze Staric; Janez Demsar; Blaz Zupan (WIREs Data Mining Knowl. Discov., 2015)

Sieve-based relation extraction of gene regulatory networks from biological literature. - Slavko Zitnik; Marinka Zitnik; Blaz Zupan; Marko Bajec (BMC Bioinform., 2015)

Collective Pairwise Classification for Multi-Way Analysis of Disease and Drug Data. - Marinka Zitnik; Blaz Zupan (PSB, 2016)

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. - Martin Strazar; Marinka Zitnik; Blaz Zupan; Jernej Ule; Tomaz Curk (Bioinform., 2016)

Jumping across biomedical contexts using compressive data fusion. - Marinka Zitnik; Blaz Zupan (Bioinform., 2016)

Scalable non-negative matrix tri-factorization. - Andrej Copar; Marinka Zitnik; Blaz Zupan (BioData Min., 2017)

dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond. - Miha Stajdohar; Rafael D. Rosengarten; Janez Kokosar; Luka Jeran; Domen Blenkus; Gad Shaulsky; Blaz Zupan (BMC Bioinform., 2017)

scOrange - a tool for hands-on training of concepts from single-cell data analytics. - Martin Strazar; Lan Zagar; Jaka Kokosar; Vesna Tanko; Ales Erjavec; Pavlin G. Policar; Anze Staric; Janez Demsar; Gad Shaulsky; Vilas Menon; Andrew Lemire; Anup Parikh; et al. (Bioinform., 2019)

RICERCANDO: Data mining toolkit for mobile broadband measurements. - Veljko Pejovic; Ivan Majhen; Miha Janez; Blaz Zupan (Comput. Networks, 2020)

Conformal prediction and its integration within visual analytics toolbox. - Tomaz Hocevar; Blaz Zupan (COPA, 2021)

Explainable Point-Based Document Visualizations. - Primoz Godec; Nikola Ðukic; Ajda Pretnar; Vesna Tanko; Lan Zagar; Blaz Zupan (CoRR, 2021)

Visualization of Biological Data - From Analysis to Communication (Dagstuhl Seminar 21401). - Karsten Klein 001; Georgeta Elisabeta Marai; Kay Katja Nieselt; Blaz Zupan (Dagstuhl Reports, 2021)

Conformal Prediction with Orange. - Tomaz Hocevar; Blaz Zupan; Jonna C. Stålring (J. Stat. Softw., 2021)

Hands-on training about overfitting. - Janez Demsar; Blaz Zupan (PLoS Comput. Biol., 2021)

Efficient Matching of Single Cells and Cell Types. - Primoz Godec; Blaz Zupan; Vesna Tanko; Martin Strazar (ICHI, 2022)

Nation-Wide ePrescription Data Reveals Landscape of Physicians and Their Drug Prescribing Patterns in Slovenia. - Pavlin G. Policar; Dalibor Stanimirovic; Blaz Zupan (AIME, 2023)

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 (AIME, 2023)

Gene Interactions in Survival Data Analysis: A Data-Driven Approach Using Restricted Mean Survival Time and Literature Mining. - Jaka Kokosar; Martin Spendl; Blaz Zupan (DS, 2023)

Refining Temporal Visualizations Using the Directional Coherence Loss. - Pavlin G. Policar; Blaz Zupan (DS, 2023)

Embedding to reference t-SNE space addresses batch effects in single-cell classification. - Pavlin G. Policar; Martin Strazar; Blaz Zupan (Mach. Learn., 2023)

Latent Embedding Based on a Transcription-Decay Decomposition of mRNA Dynamics Using Self-supervised CoxPH. - Martin Spendl; Tomaz Curk; Blaz Zupan (DS (1), 2024)

Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students. - Pavlin G. Policar; Martin Spendl; Tomaz Curk; Blaz Zupan (Bioinform., 2024)

Visualizing High-Dimensional Temporal Data Using Direction-Aware t-SNE. - Pavlin G. Policar; Blaz Zupan (CoRR, 2024)

VERA: Generating Visual Explanations of Two-Dimensional Embeddings via Region Annotation. - Pavlin G. Policar; Blaz Zupan (CoRR, 2024)

openTSNE: A Modular Python Library for t-SNE Dimensionality Reduction and Embedding. - Pavlin G. Policar; Martin Strazar; Blaz Zupan (J. Stat. Softw., 2024)

Hands-on training about data clustering with orange data mining toolbox. - Janez Demsar; Blaz Zupan (PLoS Comput. Biol., 2024)

Large scale gene set ranking for survival-related gene sets. - Martin Spendl; Jaka Kokosar; Ela Praznik; Luka Ausec; Miha Stajdohar; Blaz Zupan (Artif. Intell. Medicine, 2025)

Automated Assignment Grading with Large Language Models: Insights From a Bioinformatics Course. - Pavlin G. Policar; Martin Spendl; Tomaz Curk; Blaz Zupan (CoRR, 2025)

Uncovering temporal patterns in visualizations of high-dimensional data. - Pavlin G. Policar; Blaz Zupan (Mach. Learn., 2025)