Blaž Zupan

Blaž Zupan is a Slovenian computer scientist who leads a bioinformatics laboratory and researches artificial intelligence, machine learning, and data mining. He graduated in computer science from Ljubljana in 1991, earned a master’s at Houston in 1993, and completed a PhD under Ivan Bratko in 1997. He became a full professor at Ljubljana, held visiting appointments at Baylor and Pavia, founded its Bioinformatics Laboratory in 2010, and worked with colleagues on GenePath for genetic-network analysis. He coauthored the Orange toolbox paper in 2013, published matrix-factorization work on data fusion with Marinka Žitnik in 2015, and worked with colleagues on Orange-based biomedical image analysis in 2019. He and Janez Demšar received Slovenia’s Puh Prize in 2022, and as of October 2026 he leads the Bioinformatics Laboratory and a project on explainable foundation models for human gene expression.

Now at: Faculty of Computer and Information Science, University of Ljubljana
Works: 260
Citations: 13,059
h-index: 52
Badges: Wayfarer
Loyal

Publication numbers from OpenAlex, as of 19 October 2026.

Timeline

1968

Born in Postojna

He is born in Postojna, Yugoslavia, in 1968. He is a Slovenian computer scientist.
1991–1993

Computer science degrees

He graduates in computer science from the University of Ljubljana in 1991 and earns an MS in computer science from the University of Houston in 1993.
1997

A PhD under Ivan Bratko

He receives a PhD in computer science from the University of Ljubljana under Ivan Bratko's mentorship.
2000–2010

Visiting roles and GenePath

In 2000, he becomes a visiting professor at Baylor College of Medicine. He and colleagues publish GenePath in 2003, a system for automated construction of genetic networks from mutant data. In 2008, he becomes a visiting professor at the University of Pavia, becomes a full professor at Ljubljana in 2009, and founds and chairs its Bioinformatics Laboratory in 2010.
2013–2015

Orange and data fusion

In 2013, he coauthors the Orange data-mining toolbox paper, which presents analysis through Python scripting and visual programming. With Marinka Žitnik, he publishes Data Fusion by Matrix Factorization in 2015; the method uses penalized matrix tri-factorization to reveal hidden associations across data matrices.
2019–2022

Orange for biomedical images

In 2019, he and colleagues use Orange to simplify biomedical image analysis through deep-learning embedding, machine-learning procedures, and data visualization. In 2022, he and Janez Demšar receive the Puh Prize.
2025–2027

Explainable gene expression models

He leads a project to develop explainable foundation models for human gene expression from RNA-Seq data. The project aims to support biomarker discovery and personalized medicine.
As of October 2026

Bioinformatics laboratory leadership

As of October 2026, he leads the Bioinformatics Laboratory at the Faculty of Computer and Information Science, University of Ljubljana. He teaches and researches data mining, machine learning, and artificial intelligence.

Career

Since 2010Faculty of Computer and Information Science, University of LjubljanaFounder, Chair
2009–2010University of LjubljanaFull Professor
2008–2010University of PaviaVisiting Professor
2000–2010Baylor College of MedicineVisiting Professor
1997–2002Jožef Stefan International Postgraduate School
1996–2003Jožef Stefan Institute