1. Cervera A*, Rausio H*, Kähkönen T, Andersson N, Partel G, Rantanen V, Paciello G, Ficarra E, Hynninen J, Hietanen S, Carpén O, Lehtonen R, Hautaniemi S, Huhtinen K. Comprehensive gene fusion analysis pipeline reveals novel fusion genes in ovarian cancer. Bioinformatics. 2021
    2. Salminen L, Braicu E, Lääperi M, Jylhä A, Oksa S, Hietanen S, Sehouli J, Kulbe H, DuBois A, Mahner S, Harter P, Carpen O, Huhtinen K, Hynninen J, Hilvo M. A novel two-lipid signature is a strong and independent prognostic factor in ovarian cancer. Cancers. 2021
    3. Jukonen J, Moyano-Galceran L, Höpfner K, Pietilä EA, Lehtinen L, Huhtinen K, Gucciardo E, Hynninen J, Hietanen S, Grénman S, Ojala PM, Carpén O, Lehti K. Aggressive and recurrent ovarian cancers upregulate ephrinA5, a non-canonical effector of EphA2 signaling duality. Sci Rep. 2021
    4. Häkkinen A, Zhang K, Alkodsi A, Andersson N, Erkan EP, Dai J, Kaipio K, Lamminen T, Mansuri N, Huhtinen K, Vähärautio A, Carpén O, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S. PRISM: Recovering cell type specific expression profiles from composite RNA-seq data. Bioinformatics. 2021 Mar 15. doi: 10.1093/bioinformatics/btab178
    5. Iyer S, Zhang S, Yucel S, Horn H, Smith S, Reinhardt F, Hoefsmit E, Assatova B, Casado J, Meinsohn M, Barrasa M, Bell G, Perez-Villatoro F, Huhtinen K, Hynninen J, Oikkonen J, Galhenage P, Pathania S, Hammond P, Neel B, Färkkilä A, Pépin D, Weinberg R. Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy. Cancer Discov. 2020 Nov 6:CD-20-0818. doi: 10.1158/2159-8290.CD-20-0818.
    6. Salminen L, Gidwani K, Grènman S, Carpén 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 Oncol. 2020 Dec;59(12):1461-1468. doi: 10.1080/0284186X.2020.1827157.</li
    7. Häkkinen A, Koiranen J, Casado J, Kaipio K, Lehtonen O, Petrucci E, Hynninen J, Hietanen S, Carpén O, Pasquini L, Biffoni M, Lehtonen R, Hautaniemi S. qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets, Bioinformatics, Volume 36, Issue 20, 15 October 2020, Pages 5086–5092
    8. Laasik M, Hynninen J, Forsback S, Noponen T, Seppänen M, Hietanen S. The feasibility of [18F]EF5-PET/CT to image hypoxia in ovarian tumors: a clinical study.  EJNMMI Res. 2020 Sep 10;10(1):103. doi:10.1186/s13550-020-00689-z.
    9. Bayoumy S, Hyytiä H, Leivo J, Talha SM, Huhtinen K, Poutanen M, Hynninen J, Perheentupa A, Lamminmäki U, Gidwani K, Pettersson K. Glycovariant-based lateral flow immunoassay to detect ovarian cancer-associated serum CA125. Commun Biol. 2020 Aug 21;3(1):460. doi: 10.1038/s42003-020-01191-x.
    10. Salminen L, Nadeem N, Jain S, Grènman S, Carpén O, Hietanen S, Oksa S, Lamminmäki 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 Mar;156(3):689-694. doi: 10.1016/j.ygyno.2019.12.025.
    11. Salminen L, Nadeem N, Rolfsen A, Dørum A, Grénman S, Hietanen S, Heinosalo T, Perheentupa A, Poutanen M, Bolstad N, Carpén O, Lamminmäki U, Pettersson K, Gidwani K, Hynninen J, and Huhtinen K. Exploratory analysis of CA125-MGL and -STn glycoforms in the differential diagnostics of pelvic masses.J Appl Lab Med. 2020 Mar 1;5(2):263-272. doi: 10.1093/jalm/jfz012.
    12. Kaipio K, Chen P, Roering P, Huhtinen K, Mikkonen P, Östling P, Lehtinen L, Korpela T, Potdar S, Hynninen J, Auranen A, Grénman S, Wennerberg K, Hautaniemi S and Carpén 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. J Pathol. 2019 Oct 9. doi: 10.1002/path.5356.
    13. Gidwani K, Nadeem N, Huhtinen K, Kekki H, Heinosalo T, Hynninen J, Perheentupa A, Poutanen M, Carpen O, Pettersson K, and Lamminmäki U. Europium Nanoparticle-Based Sialyl-Tn monoclonal antibody discriminates Epithelial Ovarian Cancer -associated CA125 from benign sources. J Appl Lab Med. 2019; 4(3):299-310.
    14. Oikkonen J, Zhang K, Salminen L, Schulman I, Lavikka K, Andersson N, Ojanperä E, Hietanen S, Grénman S, Lehtonen R, Huhtinen K, Carpén O, Hynninen J, Färkkilä A and Hautaniemi A. Prospective longitudinal ctDNA workflow reveals clinically actionable alterations in ovarian cancer. JCO Precision Oncology. DOI:10.1200/PO.18.00343. Published May 3, 2019
    15. Tumiati M, Hietanen S, Hynninen J, Pietilä E, Färkkilä A, Kaipio K, Roering P, Huhtinen K, Alkodsi A, Li Y, Lehtonen R, Erkan EP, Tuominen M, Lehti K, Hautaniemi S, Vähärautio A, Grénman S, Carpén O, and Kauppi L. A functional homologous recombination assay predicts primary chemotherapy response and long-term survival in ovarian cancer patients. Clin Cancer Res. 2018 Jun 1. doi: 10.1158/1078-0432.CCR-17-3770
    16. Häkkinen A, Alkodsi A, Facciotto C, Zhang K, Kaipio K, Leppä S, Carpén O, Grénman S, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S. Identifying differentially methylated sites in samples with varying tumor purity. Bioinformatics, 34:3078-85, 2018
    17. Kozlowska E, Färkkilä A, Vallius T, Carpén O, Kemppainen J, Grénman S, Lehtonen R, Hynninen J, Hietanen S, Hautaniemi S. Mathematical model predicts response to chemotherapy and drug combinations in ovarian cancer. Cancer Res. 78:4036-44, 2018
    18. Kemiläinen H, Huhtinen K, Auranen A, Carpén O, Strauss L, Poutanen M. The expression of HSD17B12 is associated with COX2, and is increased in high-grade epithelial ovarian cancer. Oncology. 2018, 94: 233-242.
    19. Nguyen EV*, Huhtinen K*, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR. Proteomic and phosphoproteomic analysis of cisplatin resistance in patient derived serous ovarian cancer cells. Mol Cell Proteomics. 2017, 16: 1377-1392. *equal contribution
    20. Lund RJ*, Huhtinen K*, Salmi J, Nguyen EV, Moulder R, Goodlett DR, Lahesmaa R, Carpén O. DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer. Sci Rep. 2017, 7: 1469. *equal contribution
    21. Gidwani K*, Huhtinen K*, Kekki H, van Vliet S, Koivuviita N, Perheentupa A, Poutanen M, Hynninen J, Auranen A, Grenman S, Lamminmäki U, Carpen O, van Kooyk Y, Pettersson K. A nanoparticle-lectin-immunoassay improves discrimination of serum CA125 from malignant 1 and benign sources. Clinical Chemistry. 2016, 62:1390-400. *equal contribution
    22. Tambe M, Pruikkonen S, Mäki-Jouppila J, Chen P, Elgaaen BV, Birkeland EE, Huhtinen K, Cárpen O, Lønning PE, Davidson B, Hautaniemi S, and Kallio MJ. Mad2 targeting miR-493-3p perturbs spindle assembly checkpoint signalling and confers resistance to paclitaxel. Oncotarget. 2016, 7: 12267-85
    23. Chen P*, Huhtinen K*, Kaipio K, Mikkonen P, Aittomäki V, Lindell R, Hynninen J, Auranen A, Grenman S, Lehtonen R, Carpen O, Hautaniemi S. Identification of Prognostic Groups in High-Grade Serous Ovarian Cancer Treated with Platinum-Taxane Chemotherapy. Cancer Res. 2015, 75: 2987-2998. *equal contribution
    24. Vallius T, Hynninen J, Auranen A, Carpén O, Matomäki J, Oksa S, Virtanen J, Grénman S: Serum HE4 and CA125 as predictors of response and outcome during neoadjuvant chemotherapy of advanced high grade serous ovarian cancer. Tumor Biology 2014 Dec;35(12):12389-95
    25. Vallius T, Peter A, Auranen A, Carpén O, Kemppainen J, Matomäki J, Oksa S, Roering P, Seppänen M, Grénman S, Hynninen J: 118F-FDG-PET/CT can identify histopathological non-responders to platinum-based neoadjuvant chemotherapy in advanced epithelial ovarian cancer. Gynecol Oncol 2016 Jan; 140(1):29-35.
    26. Hynninen J, Auranen A, Carpén O, Dean K, Seppänen M, Kemppainen J, Lavonius M, Lisinen I, Virtanen J, Grénman S: FDG PET/CT in staging of advanced epithelial ovarian cancer: frequency of supradiaphragmatic lymph node metastasis challenges the traditional pattern of disease spread. Gynecol Oncol. 2012 Jul; 126(1): 64-8.
    27. Hynninen J, Lavonius M, Oksa S, Grénman S, Carpén Olli, Auranen Annika: Is perioperative visual estimation of intra-abdominal tumor spread reliable in ovarian cancer surgery after neoadjuvant chemotherapy? Gynecol Oncol 2013 Feb; 128(2): 229-232.
    28. Hynninen J, Kemppainen J, Lavonius M, Virtanen J, Matomäki J, Oksa S, Carpén O, Grénman S, Seppänen M, Auranen A: A prospective comparison of integrated FDG-PET/contrast-enhanced CT and contrast-enhanced CT for pretreatment imaging of advanced epithelial ovarian cancer. Gynecol Oncol 2013 Nov; 131(2): 389-394