• Tracing back primed resistance in cancer via sister cells.Dai J, Zheng S, Falco MM, Bao J, Eriksson J, Pikkusaari S, Forsten S, Jiang J, Wang W, Gao L, Perez-Villatoro F, Dufva O, Saeed K, Wang Y, Amiryousefi A, Farkkila A, Mustjoki S, Kauppi L, Tang J, Vaharautio A.Nat Commun. 2024 Feb 7;15(1):1158. doi: 10.1038/s41467-024-45478-7. PMID: 38326354; PMCID: PMC10850087. 
• Dysregulated germinal center reaction with expanded T follicular helper cells in autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy lymph nodes.Hetemaki I, Sarkkinen J, Heikkila N, Drechsel K, Mayranpaa MI, Farkkila A, Laakso S, Makitie O, Arstila TP, Kekalainen E. J Allergy Clin Immunol. 2023 Dec 19:S0091-6749(23)02454-5. doi: 10.1016/j.jaci.2023.12.004. Epub ahead of print. PMID: 38128835.
• The Emerging Role of the Single-Cell and Spatial Tumor Microenvironment in High-Grade Serous Ovarian Cancer. Launonen IM, Vähärautio A, Färkkilä A. Cold Spring Harb Perspect Med. 2023 Oct 3;13(10):a041314. doi: 10.1101/cshperspect.a041314. PMID: 37553211; PMCID: PMC10547388.
• 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 UM, Lassus H, Hautaniemi S, Farkkila A, Hynninen J, Hietanen S, Carpén O, Kauppi L. BMC Cancer. 2022 Apr 4;22(1):344. doi: 10.1186/s12885-022-09357-w. PMID: 35220285; PMCID: PMC9083297.
• STING agonism overcomes STAT3-mediated immunosuppression and adaptive resistance to PARP inhibition in ovarian cancer. Ding L, Wang Q, Martincuks A, Kearns MJ, Jiang T, Lin Z, Cheng X, Qian C, Xie S, Kim HJ, Launonen IM, Farkkila A, Roberts TM, Freeman GJ, Liu JF, Konstantinopoulos PA, Matulonis U, Yu H, Zhao JJ. Nat Commun. 2021 May 17;12(1):2655. doi: 10.1038/s41467-021-22906-8. PMID: 34001843; PMCID: PMC8120338.
• Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer. Perez-Villatoro F, Oikkonen J, Casado J, Chernenko A, Gulhan DC, Tumiati M, Li Y, Lavikka K, Hietanen S, Hynninen J, Haltia UM, Tyrmi JS, Laivuori H, Konstantinopoulos PA, Hautaniemi S, Kauppi L, Farkkila A. Sci Rep. 2021 Aug 16;11(1):16704. doi: 10.1038/s41598-021-96111-1. PMID: 34400728; PMCID: PMC8371525.
• Analysis of Non-Relapsed and Relapsed Adult Type Granulosa Cell Tumors Suggests Stable Transcriptomes during Tumor Progression. Andersson N, Haltia UM, Farkkila A, Wong SC, Eloranta K, Wilson DB, Unkila-Kallio L, Pihlajoki M, Kyrönlahti A, Heikinheimo M. Curr Issues Mol Biol. 2022 Jan 28;44(2):686-698. DOI: 10.3390/cimb44020048 PMID: 35723333; PMCID: PMC8837628.
• Tumor-Derived Lysophosphatidic Acid Blunts Protective Type I Interferon Responses in Ovarian Cancer. Chae CS, Sandoval TA, Hwang SM, Park ES, Giovanelli P, Awasthi D, Salvagno C, Emmanuelli A, Tan C, Chaudhary V, Casado J, Kossenkov AV, Song M, Barrat FJ, Holcomb K, Romero-Sandoval EA, Zamarin D, Pépin D, D’Andrea AD, Farkkila A , Cubillos-Ruiz JR. Cancer Discov. 2022 Aug 5;12(8):1904-1921. doi: 10.1158/2159-8290.CD-21-1181. PMID: 355526183
• Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer. Launonen IM, Lyytikäinen N, Casado J, Anttila EA, Szabó A, Haltia UM, Jacobson CA, Lin JR, Maliga Z, Howitt BE, Strickland KC, Santagata S, Elias K, D’Andrea AD, Konstantinopoulos PA, Sorger PK, Farkkila A. Nat Commun. 2022 Feb 11;13(1):835. doi: 10.1038/s41467-022-28389-3. PMID: 35149709; PMCID: PMC8837628.
• Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation. Duraiswamy J, Turrini R, Minasyan A, Barras D, Crespo I, Grimm AJ, Casado J, Genolet R, Benedetti F, Wicky A, Ioannidou K, Castro W, Neal C, Moriot A, Renaud-Tissot S, Anstett V, Fahr N, Tanyi JL, Eiva MA, Jacobson CA, Montone KT, Westergaard MCW, Svane IM, Kandalaft LE, Delorenzi M, Sorger PK, Farkkila A, Michielin O, Zoete V, Carmona SJ, Foukas PG, Powell DJ Jr, Rusakiewicz S, Doucey MA, Dangaj Laniti D, Coukos G. Cancer Cell. 2021 Dec 13;39(12):1623-1642.e20. doi: 10.1016/j.ccell.2021.10.008. Epub 2021 Nov 4. PMID: 34739845
• A Replication stress biomarker is associated with response to gemcitabine versus combined gemcitabine and ATR inhibitor therapy in ovarian cancer. Konstantinopoulos PA, da Costa AABA, Gulhan D, Lee EK, Cheng SC, Hendrickson AEW, Kochupurakkal B, Kolin DL, Kohn EC, Liu JF, Stover EH, Curtis J, Tayob N, Polak M, Chowdhury D, Matulonis UA, Farkkila A, D’Andrea AD, Shapiro GI.Nat Commun. 2021 Sep 22;12(1):5574. doi: 10.1038/s41467-021-25904-w.
• A first-in-class Polymerase Theta Inhibitor selectively targets Homologous-Recombination-Deficient Tumors. Zhou J, Gelot C, Pantelidou C, Li A, Yücel H, Davis RE, Farkkila A, Kochupurakkal B, Syed A, Shapiro GI, Tainer JA, Blagg BSJ, Ceccaldi R, D’Andrea AD.Nat Cancer. 2021 Jun;2(6):598-610. doi: 10.1038/s43018-021-00203-x. Epub 2021 Jun 17.
• Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells. Farkkila A, Rodríguez A, Oikkonen J, Gulhan DC, Nguyen H, Domínguez J, Ramos S, Mills CE, Pérez-Villatoro F, Lazaro JB, Zhou J, Clairmont CS, Moreau LA, Park PJ, Sorger PK, Hautaniemi S, Frias S, D’Andrea AD.Cancer Res. 2021 May 15;81(10):2774-2787. doi: 10.1158/0008-5472.CAN-20-2912. Epub 2021 Jan 29.
• Genetically Defined Syngeneic Mouse Models of Ovarian Cancer as Tools for the Discovery of Combination Immunotherapy. Iyer S, Zhang S, Yucel S, Horn H, Smith SG, Reinhardt F, Hoefsmit E, Assatova B, Casado J, Meinsohn MC, Barrasa MI, Bell GW, Pérez-Villatoro F, Huhtinen K, Hynninen J, Oikkonen J, Galhenage PM, Pathania S, Hammond PT, Neel BG, Farkkila A, Pépin D, Weinberg RA.Cancer Discov. 2021 Feb;11(2):384-407. doi: 10.1158/2159-8290.CD-20-0818. Epub 2020 Nov 6.
• Agile workflow for interactive analysis of mass cytometry data. Casado J, Lehtonen O, Rantanen V, Kaipio K, Pasquini L, Häkkinen A, Petrucci E, Hynninen J, Hietanen S, Carpén O, Biffoni M, Farkkila A, Hautaniemi S.Bioinformatics. 2021 Jun 9;37(9):1263-1268. doi: 10.1093/bioinformatics/btaa946.
• MYC Promotes Bone Marrow Stem Cell Dysfunction in Fanconi Anemia. Rodríguez A, Zhang K, Farkkila A, Filiatrault J, Yang C, Velázquez M, Furutani E, Goldman DC, García de Teresa B, Garza-Mayén G, McQueen K, Sambel LA, Molina B, Torres L, González M, Vadillo E, Pelayo R, Fleming WH, Grompe M, Shimamura A, Hautaniemi S, Greenberger J, Frías S, Parmar K, D’Andrea AD.Cell Stem Cell. 2021 Jan 7;28(1):33-47.e8. doi: 10.1016/j.stem.2020.09.004. Epub 2020 Sep 29.
• Berzosertib plus gemcitabine versus gemcitabine alone in platinum-resistant high-grade serous ovarian cancer: a multicentre, open-label, randomised, phase 2 trial. Konstantinopoulos PA, Cheng SC, Wahner Hendrickson AE, Penson RT, Schumer ST, Doyle LA, Lee EK, Kohn EC, Duska LR, Crispens MA, Olawaiye AB, Winer IS, Barroilhet LM, Fu S, McHale MT, Schilder RJ, Farkkila A, Chowdhury D, Curtis J, Quinn RS, Bowes B, D’Andrea AD, Shapiro GI, Matulonis UA.Lancet Oncol. 2020 Jul;21(7):957-968. doi: 10.1016/S1470-2045(20)30180-7. Epub 2020 Jun 15.
• Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Farkkila A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D’Andrea AD, Konstantinopoulos PA.Nat Commun. 2020 Mar 19;11(1):1459. doi: 10.1038/s41467-020-15315-8.
• The CHK1 Inhibitor Prexasertib Exhibits Monotherapy Activity in High-Grade Serous Ovarian Cancer Models and Sensitizes to PARP Inhibition. Parmar K, Kochupurakkal BS, Lazaro JB, Wang ZC, Palakurthi S, Kirschmeier PT, Yang C, Sambel LA, Farkkila A, Reznichenko E, Reavis HD, Dunn CE, Zou L, Do KT, Konstantinopoulos PA, Matulonis UA, Liu JF, D’Andrea AD, Shapiro GI.Clin Cancer Res. 2019 Oct 15;25(20):6127-6140. doi: 10.1158/1078-0432.CCR-19-0448. Epub 2019 Aug 13.
• Single-Arm Phases 1 and 2 Trial of Niraparib in Combination With Pembrolizumab in Patients With Recurrent Platinum-Resistant Ovarian Carcinoma. Konstantinopoulos PA, Waggoner S, Vidal GA, Mita M, Moroney JW, Holloway R, Van Le L, Sachdev JC, Chapman-Davis E, Colon-Otero G, Penson RT, Matulonis UA, Kim YB, Moore KN, Swisher EM, Färkkilä A, D’Andrea A, Stringer-Reasor E, Wang J, Buerstatte N, Arora S, Graham JR, Bobilev D, Dezube BJ, Munster P.JAMA Oncol. 2019 Aug 1;5(8):1141-1149. doi: 10.1001/jamaoncol.2019.1048.