Hercules Project


Isoviita V-M, Salminen L, Azar J, Lehtonen R, Roering P, Carpen O, Hietanen S, Grenman S, Hynninen J, Farkkila A, Hautaniemi S.
Open source infrastructure for healthcare data integration and machine learning analyses.
JCO Clinical Cancer Informatics, 2019, 3:1-16. Author manuscript can be downloaded from here.

Oikkonen J, Zhang K, Salminen L, Schulman I, Lavikka K, Andersson N, Ojanpera E, Hietanen S, Grenman S, Lehtonen R, Huhtinen K, Carpen O, Hynninen J, Farkkila A, Hautaniemi S.
Prospective longitudinal ctDNA workflow reveals clinically actionable alterations in ovarian cancer.
JCO Precision Oncology, 2019, 3:1-12. Open access.

Cervera A, Rantanen V, Ovaska K, Laakso M, Nunez-Fontarnau J, Alkodsi A, Casado J, Facciotto C, Hakkinen A, Louhimo R, Karinen S, Zhang K, Lavikka K, Lyly L, Pal Singh M, Hautaniemi S.
Anduril 2: Upgraded large-scale data integration framework.
Bioinformatics, 2019, pii: btz133, Epub ahead of print. Author manuscript can be downloaded from here.

Hynninen J, Laasik M, Vallius T, Kemppainen J, Gronroos S, Virtanen J, Casado J, Hautaniemi S, Grenman S, Seppanen M, Auranen A.
Clinical value of 18 F-fluorodeoxyglucose Positron Emission Tomography/Computed Tomography in response evaluation after primary treatment of advanced epithelial ovarian cancer.
Clinical Oncology, 2018, 30(8):507-514. Open access.

Kozlowska E, Farkkila A, Vallius T, Carpen O, Kemppainen J, Grenman S, Lehtonen R, Hynninen J, Hietanen S, Hautaniemi S.
Mathematical modeling predicts response to chemotherapy and drug combinations in ovarian cancer.
Cancer Research, 2018, 78(14):4036-4044. Author manuscript can be downloaded from here.

Hakkinen A, Alkodsi A, Facciotto C, Zhang K, Kaipio K, Leppa S, Carpen O, Grenman S, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S.
Identifying differentially methylated sites in samples with varying tumor purity
Bioinformatics, 2018, 34(18):3078-3085. Link to pre-print in BiorXivs.

Nikolayeva I, Guitart Pla O, Schwikowski B.
Network module identification - A widespread theoretical bias and best practices
Methods. 2017 Sep 21. pii: S1046-2023(17)30037-3. Open access.