Jaana Oikkonen

Publications

Research output per year 2011 2016 2022 2023 2024 2025

• 33 Article
• 1 Conference contribution
• 1 Meeting Abstract
• 1 Comment/debate
• 2 More
  • 1 Editorial
  • 1 Doctoral Thesis

Research output per year

Research output per year

Search results

• 2025

  Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics

  Lavikka, K., Maarala, A. I., Oikkonen, J. & Hautaniemi, S., 11 Mar 2025, In: Bioinformatics. 41, 3, 4 p., btaf091.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2024

  A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells

  Bulanova, D., Akimov, Y., Senkowski, W., Oikkonen, J., Gall-Mas, L., Timonen, S., Elmadani, M., Hynninen, J., Hautaniemi, S., Aittokallio, T. & Wennerberg, K., 23 May 2024, In: Science Advances. 10, 21, 15 p., eadj1564.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer

  Launonen, I.-M., Niemiec, I., Hincapié-Otero, M., Erkan, E. P., Junquera, A., Afenteva, D., Falco, M. M., Liang, Z., Salko, M., Chamchougia, F., Szabo, A., Perez-Villatoro, F., Li, Y., Micoli, G., Nagaraj, A., Haltia, U.-M., Kahelin, E., Oikkonen, J., Hynninen, J. & Virtanen, A. & 6 others, Nirmal, A. J., Vallius, T., Hautaniemi, S., Sorger, P. K., Vähärautio, A. & Färkkilä, A., 9 Dec 2024, In: Cancer Cell. 42, 12, p. 2045-2063.e10 29 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit

  Lavikka, K., Oikkonen, J., Li, Y., Muranen, T., Micoli, G., Marchi, G., Lahtinen, A., Huhtinen, K., Lehtonen, R., Hietanen, S., Hynninen, J., Virtanen, A. & Hautaniemi, S., 5 Aug 2024, In: GigaScience. 13, 15 p., giae040.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Extensive mutational ctDNA profiles reflect High-grade serous cancer tumors and reveal emerging mutations at recurrence

  Marchi, G., Rajavuori, A., Nguyen, M. T. N., Huhtinen, K., Oksa, S., Hietanen, S., Hautaniemi, S., Hynninen, J. & Oikkonen, J., Jan 2024, In: Translational oncology. 39, 8 p., 101814.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Genome-wide quantification of copy-number aberration impact on gene expression in ovarian high-grade serous carcinoma

  Jamalzadeh, S., Dai, J., Lavikka, K., Li, Y., Jiang, J., Huhtinen, K., Virtanen, A., Oikkonen, J., Hietanen, S., Hynninen, J., Vähärautio, A., Häkkinen, A. & Hautaniemi, S., 5 Feb 2024, In: BMC Cancer. 24, 1, 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• HRD related signature 3 predicts clinical outcome in advanced tubo-ovarian high-grade serous carcinoma

  Koskela, H., Li, Y., Joutsiniemi, T., Muranen, T., Isoviita, V. M., Huhtinen, K., Micoli, G., Lavikka, K., Marchi, G., Hietanen, S., Virtanen, A., Hautaniemi, S., Oikkonen, J. & Hynninen, J., Jan 2024, In: Gynecologic Oncology. 180, p. 91-98 8 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• PIK3R1 fusion drives chemoresistance in ovarian cancer by activating ERK1/2 and inducing rod and ring-like structures

  Rausio, H., Cervera, A., Heuser, V. D., West, G., Oikkonen, J., Pianfetti, E., Lovino, M., Ficarra, E., Taimen, P., Hynninen, J., Lehtonen, R., Hautaniemi, S., Carpén, O. & Huhtinen, K., May 2024, In: Neoplasia (United States). 51, 10 p., 100987.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• 2023

  A platform for efficient establishment and drug-response profiling of high-grade serous ovarian cancer organoids

  Senkowski, W., Gall-Mas, L., Falco, M. M., Li, Y., Lavikka, K., Kriegbaum, M. C., Oikkonen, J., Bulanova, D., Pietras, E. J., Vossgrone, K., Chen, Y.-J., Erkan, E. P., Dai, J., Lundgren, A., Hog, M. K. G., Larsen, I. M., Lamminen, T., Kaipio, K., Huvila, J. & Virtanen, A. & 9 others, Engelholm, L., Christiansen, P., Santoni-Rugiu, E., Huhtinen, K., Carpen, O., Hynninen, J., Hautaniemi, S., Vähärautio, A. & Wennerberg, K., 19 Jun 2023, In: Developmental Cell. 58, 12, p. 1106-+ 24 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Circulating tumor DNA-based copy-number profiles enable monitoring treatment effects during therapy in high-grade serous carcinoma

  Nguyen, M. T. N., Rajavuori, A., Huhtinen, K., Hietanen, S., Hynninen, J., Oikkonen, J. & Hautaniemi, S., Dec 2023, In: Biomedicine & Pharmacotherapy. 168, 8 p., 115630.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes

  Pikkusaari, S., Tumiati, M., Virtanen, A., Oikkonen, J., Li, Y., Perez-Villatoro, F., Muranen, T., Salko, M., Huhtinen, K., Kanerva, A., Koskela, H., Tapper, J., Koivisto-Korander, R., Joutsiniemi, T., Haltia, U.-M., Lassus, H., Hautaniemi, S., Färkkilä, A., Hynninen, J. & Hietanen, S. & 2 others, Carpen, O. & Kauppi, L., 15 Aug 2023, In: Clinical Cancer Research. 29, 16, p. 3110-3123 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Quantification of cell death and proliferation of patient-derived ovarian cancer organoids through 3D imaging and image analysis

  Skorda, A., Lauridsen, A. R., Huhtinen, K., Lahtinen, A., Senkowski, W., Oikkonen, J., Hynninen, J., Hautaniemi, S. & Kallunki, T., 15 Dec 2023, In: STAR protocols. 4, 4, 17 p., 102683.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Uusi työkalu räätälöityyn munasarjasyövän hoitoon

  Translated title of the contribution: Functional homologous recombination assay on FFPE specimens of advanced high-grade serous ovarian cancer predicts clinical outcomesPikkusaari, S., Tumiati, M., Virtanen, A., Oikkonen, J., Li, Y., Perez-Villatoro, F., Muranen, T., Salko, M., Huhtinen, K., Kanerva, A., Koskela, H., Tapper, J., Koivisto-Korander, R., Joutsiniemi, T., Haltia, U.-M., Lassus, H., Hautaniemi, S., Färkkilä, A., Hynninen, J. & Hietanen, S. & 2 others, Carpen, O. & Kauppi, L., 15 Aug 2023, In: Duodecim. 139, 9, p. 760 1 p.

  Research output: Contribution to journal › Article › Professional

  Open Access

  File
• 2022

  Effects of Wee1 inhibitor adavosertib on patient-derived high-grade serous ovarian cancer cells are multiple and independent of homologous recombination status

  Roering, P., Siddiqui, A., Heuser, V. D., Potdar, S., Mikkonen, P., Oikkonen, J., Li, Y., Pikkusaari, S., Wennerberg, K., Hynninen, J., Grenman, S., Huhtinen, K., Auranen, A., Carpen, O. & Kaipio, K., 23 Aug 2022, In: Frontiers in oncology . 12, 14 p., 954430.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer

  Zhang, K., Erkan, E. P., Jamalzadeh, S., Dai, J., Andersson, N., Kaipio, K., Lamminen, T., Mansuri, N., Huhtinen, K., Carpen, O., Hietanen, S., Oikkonen, J., Hynninen, J., Virtanen, A., Häkkinen, A., Hautaniemi, S. & Väharautio, A., Feb 2022, In: Science Advances. 8, 8, 18 p., 1831.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer

  Perez Villatoro, F. R., Oikkonen, J., Casado, J., Chernenko, A., Gulhan, D. C., Tumiati, M., Li, Y., Lavikka, K. A., Hietanen, S., Hynninen, J., Haltia, U.-M., Tyrmi, J. S., Laivuori, H., Konstantinopoulos, P. A., Hautaniemi, S., Kauppi, L. & Färkkilä, A., 2022, In: npj precision oncology. 6, 1, 13 p., 96.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• QuantISH: RNA in situ hybridization image analysis framework for quantifying cell type-specific target RNA expression and variability

  Jamalzadeh, S., Häkkinen, A., Andersson, N., Huhtinen, K., Laury, A., Hietanen, S., Hynninen, J., Oikkonen, J., Carpen, O., Virtanen, A. & Hautaniemi, S., Jul 2022, In: Laboratory Investigation. 102, 7, p. 753-761 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2021

  Genetically Defined Syngeneic Mouse Models of Ovarian Cancer as Tools for the Discovery of Combination Immunothrapy

  Iyer, S., Zhang, S., Yucel, S., Horn, H., Smith, S. G., Reinhardt, F., Hoefsmit, E., Assatova, B., Casado, J., Meinsohn, M.-C., Barrasa, M. I., Bell, G. W., Perez-Villatoro, F., Huhtinen, K., Hynninen, J., Oikkonen, J., Galhenage, P. M., Pathania, S., Hammond, P. T. & Neel, B. G. & 3 others, Farkkila, A., Pepin, D. & Weinberg, R. A., Feb 2021, In: Cancer Discovery. 11, 2, p. 384-407 24 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells

  Färkkilä, A., Rodriguez, A., Oikkonen, J., Gulhan, D. C., Huy Nguyen, Dominguez, J., Ramos, S., Mills, C. E., Perez-Villatoro, F., Lazaro, J.-B., Zhou, J., Clairmont, C. S., Moreau, L. A., Park, P. J., Sorger, P. K., Hautaniemi, S., Frias, S. & D'Andrea, A. D., 15 May 2021, In: Cancer Research. 81, 10, p. 2774-2787 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer

  He, L., Bulanova, D., Oikkonen, J., Häkkinen, A., Zhang, K., Zheng, S., Wang, W., Erkan, E. P., Carpén, O., Joutsiniemi, T., Hietanen, S., Hynninen, J., Huhtinen, K., Hautaniemi, S., Vähärautio, A., Tang, J., Wennerberg, K. & Aittokallio, T., 3 Nov 2021, In: Briefings in Bioinformatics. 22, 6, 12 p., 272.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2019

  Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

  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. & Hautaniemi, S., 3 May 2019, In: JCO Precision Oncology. 3, 3, p. 1-12 12 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2018

  Musiikillisen luovuuden perimänlaajuinen tutkimus

  Oikkonen, J., Kuusi, T. & Järvelä, I., 29 Jun 2018, In: Musiikki. 44, 1, p. 45-57 13 p.

  Research output: Contribution to journal › Article › General public

• 2016

  Convergent evidence for the molecular basis of musical traits

  Oikkonen, J., Onkamo, P., Järvelä, I. & Kanduri, C., 22 Dec 2016, In: Scientific Reports. 6, 10 p., 39707.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Creative Activities in Music - A Genome-Wide Linkage Analysis

  Oikkonen, J., Kuusi, T., Peltonen, P., Raijas, P., Ukkola-Vuoti, L., Karma, K., Onkamo, P. & Jarvela, I., 24 Feb 2016, In: PLoS One. 11, 2, 21 p., 0148679.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• Detecting signatures of positive selection associated with musical aptitude in the human genome

  Liu, X., Kanduri, C., Oikkonen, J., Karma, K., Raijas, P., Ukkola-Vuoti, L., Teo, Y.-Y. & Jarvela, I., 16 Feb 2016, In: Scientific Reports. 6, 9 p., 21198.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2015

  A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions

  Oikkonen, J., Huang, Y., Onkamo, P., Ukkola-Vuoti, L., Raijas, P., Karma, K., Vieland, V. J. & Jarvela, I., Feb 2015, In: Molecular Psychiatry. 20, 2, p. 275-282 8 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Association and Promoter Analysis of AVPR1A in Finnish Autism Families

  Kantojärvi, K., Oikkonen, J., Kotala, I., Kallela, J., Vanhala, R., Onkamo, P. & Jarvela, I., Oct 2015, In: Autism Research. 8, 5, p. 634-639 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2014

  Correlation between components of newly diagnosed exudative age-related macular degeneration lesion and focal retinal sensitivity

  Hautamäki, A., Oikkonen, J., Onkamo, P. & Immonen, I., 2014, In: Acta Ophthalmologica. 92, 1, p. 51-58 8 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Genomics approaches to study musical aptitude

  Oikkonen, J. & Jarvela, I., Nov 2014, In: BioEssays. 36, 11, p. 1102-1108 7 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2013

  Genome-Wide Copy Number Variation Analysis in Extended Families and Unrelated Individuals Characterized for Musical Aptitude and Creativity in Music

  Ukkola-Vuoti, L., Kanduri, C., Oikkonen, J., Buck, G., Blancher, C., Raijas, P., Karma, K., Lahdesmaki, H. & Järvelä, I., 27 Feb 2013, In: PLoS One. 8, 2, 9 p., e56356.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• The genome-wide landscape of copy number variations in the MUSGEN study provides evidence for a founder effect in the isolated Finnish population

  Kanduri, C., Ukkola-Vuoti, L., Oikkonen, J., Buck, G., Blancher, C., Raijas, P., Karma, K., Lahdesmaki, H. & Järvelä, I., Dec 2013, In: European Journal of Human Genetics. 21, 12, p. 1411-1416 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2012

  Suomalaisten musikaalisuus

  Translated title of the contribution: Musical aptitude of the Finnish populationRaijas, P., Oikkonen, J., Ukkola-Vuoti, L., Onkamo, P. & Järvelä, I., 2012, In: Musiikki. 2012, 1, p. 86-90 5 p.

  Research output: Contribution to journal › Article › General public

• 2011

  Association of the arginine vasopressin receptor 1A (AVPR1A) haplotypes with listening to music

  Ukkola-Vuoti, L., Oikkonen, J., Onkamo, P., Karma, K., Raijas, P. & Jarvela, I., 2011, In: Journal of Human Genetics. 56, 4, p. 324-329 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review