Saez-Rodriguez Group

Systems Biomedicine

Jovan Tanevski

I received my Bachelor of Electrical Engineering and Information Technologies in in 2010, followed by a Master’s degree in Bioinformatics in 2011 in Skopje, Macedonia. For my PhD studies I moved to Ljubljana, Slovenia, where I started working at the Department of Knowledge Technologies at the Jožef Stefan Institute. For my thesis I developed methods for scientific knowledge discovery by modeling and design of deterministic and stochastic dynamical biological systems. Since 2016 I work as a research associate at the Jožef Stefan Institute.

In 2018 I joined the Saez-Rodriguez group at the Heidelberg University, as a postdoctoral researcher, focusing on machine learning for modeling spatially resolved omics data. Since 2022 I am a Research Area Leader, coordinating and overseeing the development and application of machine learning and optimization methods for analysis of spatial omics data within the institute.

 Tanevski Lab

Research Area Leader

I lead the research area of Machine Learning and Optimization for Spatial Omics. We focus on problem driven development of approaches to data exploration, hypothesis generation and computational scientific discovery to facilitate translational biomedicine. Our approaches are based on representation learning and supervised analysis of highly multiplexed spatial omics data. We develop new and extend existing explainable, scalable and readily deployable methods for multi-view learning, graph neural networks, metaheuristic optimization and optimal transport to:

  1. Identify clinically relevant regions and interactions by explanatory modeling and optimization of global and local tissue/condition specific persistent multicellular patterns.
  2. Learn higher order structural and functional organization to form taxonomical models of tissues for comparative analyses and generation of in-silico samples.
  3. Integrate multiomics data with databases of prior knowledge to discover context specific mechanistic insighs spanning multiple omics layers.

Our interest is to address questions of structure-function relationships in disease, progression and response to treatment. We value collaborations with clinical, experimental biology groups and groups working on the development of novel methods for the acquisition of spatially resolved data. We welcome synergistic collaborations with computational groups towards the construction of more robust theoretical and computational frameworks for the analysis of all aspects of biomedical data and beyond.

Research Interests

My research interests are at the intersection of systems sciences and machine learning. I am interested in the development of methods that combine data and prior knowledge. I have a strong background in machine learning and experience in computational systems biology. I am experienced in modeling and design of dynamical systems and their application to problems coming from the domains of systems and synthetic biology. I am currently working on developing methods for analysis of highly multiplexed and spatially resolved data. I am keen to understand the different patterns of expression within the tissue and bridge them to the underlying dynamical mechanisms that can explain the emergent functional programs and organization.

Professional Career

2022-present Research Area Leader – Institute for Computational Biomedicine, Heidelberg University, Germany
2018–2022 Postdoctoral researcher – Institute for Computational Biomedicine, Heidelberg University, Germany
2016–present Research associate – Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
2011-2016 Research assistant – Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia

Education

2011–2016 PhD in Information and Communication Technologies – Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
2010–2011 Master of Science in Bioinformatics - Ss. Cyril and Methodius University, Skopje, Macedonia
2006–2010 Bachelor of Electrical Engineering and Information Technologies – Ss. Cyril and Methodius University, Skopje, Macedonia