Celebrating Romana's successful PhD defense

March 28, 2026

On Monday March 23, 2026, Romana successfully defended her PhD thesis "Omics data integration with gene regulatory networks in health and disease" at the Faculty of Medicine, University of Oslo!

The defense was held at Grønt auditorium in Rikshospitalet, on walking distance from NCMBM. The day started with Romana's trial lecture, titled "Computational methods for inference of trajectories in single-cell RNA-seq data." Here, Romana presented what trajectory inference can and cannot do, and gave an overview of what various computational tools for trajectory inference are based on. As many trajectory inference methods have been published in recent years, she focused on widely used approaches while also highlighting selected methods with distinct capabilities, including applications to other data types and approaches that incorporate additional information such as RNA velocity. It was nice to see that, rather than treating the lecture as a purely formal requirement, she used the opportunity to explore directions that particularly interested her.

The thesis committee, including the chair Prof. Tero Aittokallio, first opponent Group Leader Laura Cantini, second opponent Prof. Markus List, and third opponent Associate Prof. Valeria Vitelli, retreated for a short discussion, after which they announced that the trial lecture was passed, and that the defense would be held in the afternoon of the same day. The committee, supervisor, and opponents then went for a lunch in between the sessions.

At 13.15, the defense started with an introduction by faculty representative Tero Aittokallio, Professor at University of Oslo. The first opponent, Laura Cantini, Group Leader at Institut Pasteur, France, started the scientific discussions. These covered, amongst others, topics such as using prior knowledge in network modeling and multi-omics integration, as well as the challenge of benchmarking gene regulatory networks. The second opponent, Professor Markus List, Technical University of Munich, Germany, continued the discussions, covering topics including data dominance in omics integration and network modeling, and bringing new ideas on future projects with HEDGEHOG, Romana's bipartite community detection method. Both opponents discussed the use of deep learning vs linear approaches for data integration. Romana also reflected on the risks of purely data-driven analyses and emphasized the importance of being cautious in interpreting results: "If you have no prior idea what to look for, you can be conservative, because you’re going to find something anyway" (quote form the defense). At the end of the discussions, the committee retreated again, and the final verdict of pass was happily given, and it was time to congratulate the candidate, now Dr. Pop.

After the defense, the audience and committee got together for coffee, cake, and pizza at the Department of Informatics. Here, Romana received her defense hat made by members from the Mathelier and Kuijjer labs, featuring her tools MARMOT and HEDGEHOG, and various of Romana's hobbies. It was then time to grow the lab tree and sign the lab's book of PhD wisdom.

Below we share some memories (taken by Roza Lemma, Patricio López-Sánchez, and Mariike Kuijjer) and warmly congratulate Dr. Pop on completing her PhD!