Medical Big Data

Genialis, BioLab to Improve Precision Medicine Using Data Mining

Long-standing relationship between the two organizations expands to develop new methods and tools for the discovery of clinically actionable biomarkers

Genialis, a leader in applied data science for the development of precision medicines, today announced together with the Bioinformatics Laboratory at the University of Ljubljana that the organizations have entered into a Sponsored Research Agreement to develop new algorithms and methods to better assign patients to therapeutic options based on disease subtypes, deepening Genialis’ investment and expertise in machine-learning-based drug discovery.

“Pubmed includes nearly one-million biomarker studies, but vanishingly few have seen success in the clinic being used to help actual patients,” said Miha Stajdohar, Ph.D., Chief Technology Officer of Genialis. “Using our experience as a baseline, we have identified key shortcomings common to the old way of doing things and have invented technologies to better identify ‘omics signatures and build predictive models to help patients most in need of precision medicines.”

Genialis has deep ties to BioLab, a renowned research group within the Faculty of Computer and Information Science at the University of Ljubljana, Slovenia. Stajdohar, a co-founder of Genialis, earned his Ph.D. at the institution and was co-mentored by Blaz Zupan, Ph.D., director of BioLab. Dr. Zupan remains a senior advisor to Genialis, and has published numerous studies on data integration with proofs of concept across a range of biomedical use cases, including target discovery and prioritization; drug-induced liver injury; and disease-disease relationships.

“At BioLab we’ve specialized in several aspects of data science that are especially relevant to the biomedical setting. These include novel methods for combining molecular, experimental and observational data with sources of prior knowledge. We’re also quite excited by data visualization and explainable AI, two separate but highly complementary disciplines,” said Dr. Zupan. “In collaborating with Genialis we have the opportunity to really advance the application of data science to drug development.”

BioLab develops and maintains the Orange data mining software, which integrates seamlessly with Genialis’ Expressions software, bridging state-of-the-art machine learning and multi-omics data analysis. Expressions enables systems-level computational biology through optimized and reproducible processing of sequencing data, including RNA, whole exome/genome, and numerous flavors of chromatin and RNA binding methods like ChIP and CLIP. Expressions also creates a foundation for Good Machine Learning Practice by enforcing metadata annotation and FAIR data standards. Orange, meanwhile, facilitates data integration and visualization, and rapid prototyping of models from its library of statistical and machine learning algorithms.


Genialis will participate in the Festival of Biologics 2021, as Dr. Rosengarten joins OncXerna Therapeutics (fka Oncologie) CEO Laura Benjamin for a virtual fireside chat. The conversation on Tuesday, March 30 at 9:00 a.m. PDT, will focus on the companies’ work together to develop a state-of-the-art RNA-based biomarker platform. At SITC 2020, OncXerna and Genialis coauthored a poster detailing how OncXerna’s TME Panel-1 matches patients to a drug whose MOA targets the dominant biology of their tumor microenvironment. Genialis is working to validate the TME Panel-1 on additional solid tumor types and to expand access to the model to the broader clinical research community.

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