Core competence of the group is in the methods of computer science, statistical modeling, and machine learning. We often utilize a data-driven approach based on high-throughput genomic, epigenomic, transcriptomic and/or proteomic data. These data are integrated and analyzed computationally in an effort to better understand the biological processes and networks driving a disease or phenotype. The generated hypotheses are then validated and refined experimentally. In addition to computational work we also pursue experimental research within the research group in collaboration with Tampere University Hospital.


Selected research directions:

Integrative tumor data analysis

We develop and apply computational methods for integration of multilevel genomics and proteomics data from in-house and public data sets. We have actively participated in international networks including the Cancer Genome Atlas. Here our main focus is on understanding the mechanisms that are driving tumor progression and evolution. We study how heterogeneous genomic aberrations in clinical tissue samples affect tumor phenotypes and converge through gene regulatory networks. We mainly focus on prostate cancer and brain tumors.

Main collaborators: Prof. Tapio Visakorpi, Prof. G. Steven Bova, Prof. Ilya Shmulevich, Adj. Prof. Olli Lohi, Adj. Prof. Merja Heinäniemi

Circulating tumor DNA analysis

We develop computational methods for reconstructing the genomic landscape of cancer cells in a patient’s body, based on fragments of tumor DNA in their bloodstream. These minimally invasive “liquid biopsies” (10 mL blood sample) enable clinicians to understand the mutations driving a patient’s cancer, and allow them to better guide patient treatment. In collaboration with the Vancouver Prostate Centre, we use liquid biopsies to study mechanisms of resistance against approved and experimental cancer therapies in internationally leading clinical trials, particularly in the context of prostate cancer and bladder cancer.

Main collaborators: Dr. Alexander Wyatt, Prof. Teuvo Tammela, Prof. Tapio Visakorpi