Hercules Project


Publications

Hakkinen A, Zhang K, Alkodsi A, Andersson N, Pekcan Erkan E, Dai J, Kaipio K, Lamminen T, Mansuri N, Huhtinen K, Vaharautio A, Carpen O, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S.
PRISM: Recovering cell type specific expression profiles from individual composite RNA-seq samples.
Bioinformatics. 2021 Mar 15:btab178. Online publication before print. Open access.

Casado J, Lehtonen O, Rantanen V, Kaipio K, Pasquini L, Hakkinen A, Petrucci E, Hynninen J, Hietanen S, Carpen O, Biffoni M, Farkkila A, Hautaniemi S.
Agile workflow for interactive analysis of mass cytometry data.
Bioinformatics. Online publication before print. Open access.

Salminen L, Gidwani K, Grenman S, Carpen O, Hietanen S, Pettersson K, Huhtinen K Hynninen J.
HE4 in the evaluation of tumor load and prognostic stratification of high grade serous ovarian carcinoma.
Acta Oncologica, 2020, 59:12, 1461-1468. Open access.

Laasik M, Hynninen J, Forsback S, Noponen T, Seppanen M, Hietanen S.
The feasibility of [18F]EF5-PET/CT to image hypoxia in ovarian tumors: a clinical study.
EJNMMI Research, 2020, 10, 103. Open access.

Salminen L, Nadeem N, Jain S, Grenman S, Carpen O, Hietanen S, Oksa S, Lamminmaki U, Pettersson K, Gidwani K, Huhtinen K, Hynninen J.
A longitudinal analysis of CA125 glycoforms in the monitoring and follow up of high grade serous ovarian cancer.
Gynecol Oncol. 2020, 156(3):689-694. Open access.

Balduit A, Agostinis C, Mangogna A, Maggi V, Zito G, Romano F, Romano A, Ceccherini R, Grassi G, Bonin S, Bonazza D, Zanconati F, Ricci G, Bulla R.
The Extracellular matrix influences ovarian carcinoma cells' sensitivity to cisplatinum: A first step towards personalized medicine.
Cancers (Basel). 2020, 12(5):1175. Open access.

Hakkinen A, Koiranen J, Casado J, Kaipio K, Lehtonen O, Petrucci E, Hynninen J, Hietanen S, Carpen O, Pasquini L, Biffoni M, Lehtonen R, Hautaniemi S.
qSNE: Quadratic rate t-SNE optimizer with automatic parameter tuning for large data sets.
Bioinformatics, 2020. Online publication before print. Open access.

Akimov Y, Bulanova D, Timonen S, Wennerberg K, Aittokallio T.
Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics.
Molecular Systems Biology, 2020, 16:e9195. Open access.

Kaipio K, Chen P, Roering P, Huhtinen K, Mikkonen P, Ostling P, Lehtinen L, Mansuri N, Korpela T, Potdar S, Hynninen J, Auranen A, Grenman S, Wennerberg K, Hautaniemi S, Carpen O.
ALDH1A1-related stemness in high-grade serous ovarian cancer is a negative prognostic indicator but potentially targetable by EGFR/mTOR-PI3K/aurora kinase inhibitors.
Journal of Pathology, 2020, 250(2):159-169.

Azzalini E, De Martino E, Fattorini P, Canzonieri V, Stanta G, Bonin S.
Reliability of miRNA Analysis from Fixed and Paraffin-Embedded Tissues.
International Journal of Molecular Sciences. 2019;20(19):4819. Open access.

Laasik M, Kemppainen J, Auranen A, Hietanen S, Grenman S, Seppanen M, Hynninen J.
Behavior of FDG-avid supradiaphragmatic lymph nodes in PET/CT throughout primary therapy in advanced serous epithelial ovarian cancer: a prospective study.
Cancer Imaging, 2019, 29;19(1):27. Open access.

Kozlowska E, Vallius T, Hynninen J, Hietanen S, Farkkila A, Hautaniemi S.
Virtual clinical trials identify effective combination therapies in ovarian cancer.
Science Reports, 2019, 9(1):18678. Open access.

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.