Four new publications

August 07, 2025

We have four new peer-reviewed publications, including two main works by the Kuijjer group and two collaborations!

In an application note in Bioinformatics, we present SPONGE, a computational tool developed by Ladislav to generate prior data for gene regulatory network modeling.

In an article in Briefings in Bioinformatics, we show how incorporating patient-specific gene regulatory network models in multi-omics integrative approaches, using MARMOT (by Romana) can improve detection of clinically important factors.

In a study in NPJ Systems Biology and Applications, Patrick shows how patient-specific mutual information networks identifies new subtypes and predictive biomarkers in lung adenocarcinoma. This was a collaboration with Patrick's Master's thesis supervisor Jesús Espinal-Enríquez.

Finally, we collaborated on a study with researchers from the National Autonomous University of Mexico on a study that identified KChIP3 as driver of Alzheimer's disease, published in the Journal of Neuroinflammation. Ladislav contributed to this study with bioinformatic analyses to identify novel target genes of KChIP3.

For detailed information, see the publications section of our website.