Olli Yli-Harja
About me
Prof. Olli Yli-Harja is leading the Computational Systems Biology and Complex Systems group at Tampere University, where he works in close collaboration with Prof. Frank Emmert-Streib (TaU) on Data Science and Digital Twins, and Dr. Meenakshisundaram Kandhavelu (TaU) on drug repurposing. Dr. Yli-Harja is also an Affiliate Professor in Institute for Systems Biology (ISB), Seattle, where he has ongoing collaborations on complex systems with Dr Stuart Kauffman (ISB), and on AML Digital Twins with Dr Ilya Shmulevich (ISB). Prof. Yli-Harja has supervised 38 PhD theses. He is an expert in modeling and simulation of complex systems, including biological and medical systems, and software development digital twins.
Latest publications
A2A receptor antagonist 4-(2-((6-Amino-9-ethyl-8-(furan-2-yl)-9H-purin-2-yl)amino)ethyl)phenol, a promising adenosine derivative for glioblastoma treatment
Murugesan, A., Smirnov, A., Alonso, A. V., Buccioni, M., Cui, C., Dal Ben, D., Francucci, B., Lambertucci, C., Marucci, G., Volpini, R., Konda Mani, S., Devanesan, S., AlSalhi, M. S., Yli-Harja, O., Spinaci, A. & Kandhavelu, M., 1 Apr 2025, In: European Journal of Pharmaceutical Sciences. 207, 107039.Research output: Contribution to journal › Article › Scientific › peer-review
Comparative analysis of the antiglioblastoma activity of adenosine A2A receptor and CK1δ blockers
Murugesan, A., Alonso, A. V., Konda Mani, S., Sarkar, P., Smirnov, A., Francucci, B., Marucci, G., Buccioni, M., Abass, K. S., Sureka, C., Yli-Harja, O. & Kandhavelu, M., 5 Sept 2025, In: European Journal of Pharmacology. 1002, 177864.Research output: Contribution to journal › Article › Scientific › peer-review
Digital twin models for predicting venetoclax and azacitidine-induced neutropenia in patients with acute myeloid leukemia
Zhang, Y., Martinez, J., Tercan, B., Kuusanmäki, H., Emmert-Streib, F., Chandraseelan, J. G., Farea, A., Yli-Harja, O., Heckman, C. A., Gibbs, D. L., Thorsson, V., Shmulevich, I., Kontro, M., Qin, G. & Aguilar, B., 2025, In: Npj digital medicine. 8, 11 p., 596.Research output: Contribution to journal › Article › Scientific › peer-review
Sensing Cyclic Adenosine Monophosphate and Guanine Nucleotide Exchange Factor Communication Through Rluc-Epac-Citrine2 BRET Sensor in Live GBM Cells
Dilek, E., Naidoo, V., Abraham, B. G., Mani, S. K., Abass, K. S., Devanesan, S., AlSalhi, M. S., Chandrabose, S., Yli-Harja, O., Murugesan, A. & Kandhavelu, M., 2025, In: IEEE Transactions on Molecular, Biological, and Multi-Scale Communications. 11, 3, p. 395-404Research output: Contribution to journal › Article › Scientific › peer-review
Using Physics-Informed Neural Networks for Modeling Biological and Epidemiological Dynamical Systems
Farea, A., Yli-Harja, O. & Emmert-Streib, F., May 2025, In: Mathematics. 13, 10, 1664.Research output: Contribution to journal › Article › Scientific › peer-review
Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors
Pekkarinen, M., Nordfors, K., Uusi-Mäkelä, J., Kytölä, V., Hartewig, A., Huhtala, L., Rauhala, M., Urhonen, H., Häyrynen, S., Afyounian, E., Yli-Harja, O., Zhang, W., Helen, P., Lohi, O., Haapasalo, H., Haapasalo, J., Nykter, M., Kesseli, J. & Rautajoki, K. J., 2024, In: Life science alliance. 7, 6, 18 p., e202302088.Research output: Contribution to journal › Article › Scientific › peer-review
Advanced Scientometric Analysis of Scientific Machine Learning and PINNs: Topic Modeling and Trend Analysis
Emmert-Streib, F., Tripathi, S., Farea, A. & Yli-Harja, O., 2024, In: IEEE Access. 12, p. 153253-153272 20 p.Research output: Contribution to journal › Article › Scientific › peer-review
Complexity data science: A spin-off from digital twins
Emmert-Streib, F., Cherifi, H., Kaski, K., Kauffman, S. & Yli-Harja, O., Nov 2024, In: PNAS Nexus. 3, 11, 7 p., pgae456.Research output: Contribution to journal › Article › Scientific › peer-review
Understanding Physics-Informed Neural Networks: Techniques, Applications, Trends, and Challenges
Farea, A., Yli-Harja, O. & Emmert-Streib, F., Sept 2024, In: AI. 5, 3, p. 1534-1557 24 p.Research output: Contribution to journal › Review Article › peer-review
Genomic characterization of IDH-mutant astrocytoma progression to grade 4 in the treatment setting
Rautajoki, K. J., Jaatinen, S., Hartewig, A., Tiihonen, A. M., Annala, M., Salonen, I., Valkonen, M., Simola, V., Vuorinen, E. M., Kivinen, A., Rauhala, M. J., Nurminen, R., Maass, K. K., Lahtela, S. L., Jukkola, A., Yli-Harja, O., Helén, P., Pajtler, K. W., Ruusuvuori, P. & Haapasalo, J. & 3 others, , Nov 2023, In: Acta Neuropathologica Communications. 11, 1, 20 p., 176.Research output: Contribution to journal › Article › Scientific › peer-review