Perkiö A, Pradhan B, Genc F, Pirttikoski A, Pikkusaari S, Erkan EP, Falco MM, Huhtinen K, Narva S, Hynninen J, Kauppi L, Vähärautio A. Locus-specific LINE-1 expression in clinical ovarian cancer specimens at the single-cell level. Scientific Reports 2024, 1;14:4322.
Sandoval TA, Salvagno C, Chae CS, Awasthi D, Giovanelli P, Marin Falco M, Hwang SM, Teran-Cabanillas E, Suominen L, Yamazaki T, Kuo HH, Moyer JE, Martin ML, Manohar J, Kim K, Sierra MA, Ramos Y, Tan C, Emmanuelli A, Song M, Morales DK, Zamarin D, Frey MK, Cantillo E, Chapman-Davis E, Holcomb K, Mason CE, Galluzzi L, Zhou ZN, Vaharautio A, Cloonan SM, Cubillos-Ruiz JR. Iron Chelation Therapy Elicits Innate Immune Control of Metastatic Ovarian Cancer. Cancer Discovery 2024.
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 Jr Y, Amiryousefi A, Färkkilä A, Mustjoki S, Kauppi L, Tang J, Vähärautio A. Tracing back primed resistance in cancer via sister cells. Nature Communications 2024.
Senkowski W, Gall-Mas L, Falco MM, Li Y, Lavikka K, Kriegbaum MC, Oikkonen J, Bulanova D, Pietras EJ, Voßgröne K, Chen YJ, Erkan EP, Dai J, Lundgren A, Grønning Høg MK, Larsen IM, Lamminen T, Kaipio K, Huvila J, Virtanen A, Engelholm L, Christiansen P, Santoni-Rugiu E, Huhtinen K, Carpén O, Hynninen J, Hautaniemi S, Vähärautio A, Wennerberg K. A platform for efficient establishment, expansion and drug response profiling of high-grade serous ovarian cancer organoids. Developmental Cell 2023.
Zhang K, Erkan EP, Jamalzadeh S, Dai J, Andersson N, Kaipio K, Lamminen T, Mansuri N, Huhtinen K, Carpén O, Hietanen S, Oikkonen J, Hynninen J, Virtanen A, Häkkinen A, Hautaniemi S, Vähärautio A. Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer. Science Advances 2022.
He L, Bulanova D, Oikkonen J, Häkkinen A, Zhang K, Zheng S, Wang W, Erkan EP, Carpén O, Joutsiniemi T, Hietanen S, Hynninen J, Huhtinen K, Hautaniemi S, Vähärautio A, Tang J, Wennerberg K, Aittokallio T. Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer. Briefings in bioinformatics 2021.
Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA, Vähärautio A, Greene CS, Hicks SC. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS computational biology 2021.
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 individual composite RNA-seq samples. Bioinformatics 2021.
Tumiati M, Hietanen S, Hynninen J, Pietilä E, Färkkilä A, Kaipio K, Roering P, Huhtinen K, Alkodsi A, Li Y, Lehtonen R, Pekcan Erkan E, M. Tuominen M, Lehti K, K. Hautaniemi S, Vähärautio A, Grénman S, Carpén O, Kauppi L. A Functional Homologous Recombination Assay Predicts Primary Chemotherapy Response and Long-Term Survival in Ovarian Cancer Patients. Clinical Cancer Research 2018.
Launonen, I-M., Vähärautio, A., & Färkkilä, A. The Emerging Role of the Single-Cell and Spatial Tumor Microenvironment in High-Grade Serous Ovarian Cancer. Cold Spring Harbor Perspectives in Medicine. 2023.
Vähärautio A, Taipale J. Perspective: Cancer by super-enhancer. Science 2014.
Bonke M, Turunen M, Sokolova M, Vähärautio A, Kivioja T, Taipale M, Björklund M, Taipale J. Transcriptional networks controlling the cell cycle. G3 2013.
Kivioja T*, Vähärautio A*, Karlsson K, Bonke M, Enge M, Linnarsson S, Taipale J. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 2012 (*equal contribution).
Sur IK, Hallikas O, Vähärautio A, Yan J, Turunen M, Enge M, Taipale M, Karhu A, Aaltonen LA, Taipale J. Mice Lacking a Myc Enhancer That Includes Human SNP rs6983267 Are Resistant to Intestinal Tumours. Science 2012.
PRE-PRINTS:
Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer
Launonen I-M, Erkan EP, Niemiec I, Junquera A, Hincapié-Otero M, Afenteva D, Liang Z, Salko M, Szabo A, Perez-Villatoro F, Falco MM, Li Y, Micoli G, Nagaraj A, Haltia U-M, Kahelin E, Oikkonen J, Hynninen J, Virtanen A, Nirmal AJ, Vallius T, Hautaniemi S, Sorger P, Vähärautio A, Färkkilä A. Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer. doi: https://doi.org/10.1101/2024.03.19.585657
Patient-derived functional immuno-oncology platform identifies responders to ATR inhibitor and immunotherapy combinations in ovarian cancer
Nagaraj A, Salko M, Sirskikar A, Erkan EP, Pietilä EA, Niemiec I, Bao J, Marchi G, Szabó A, Lundgren A, Nowlan K, Pikkusaari S, Kanerva A, Tapper J, Koivisto-Korander R, Lassus H, Kauppi L, Hautaniemi S, Vähärautio A, Tang J, Haltia U, Kekäläinen E, Virtanen A, Salo T, Färkkilä A. Patient-derived functional immuno-oncology platform identifies responders to ATR inhibitor and immunotherapy combinations in ovarian cancer doi: https://doi.org/10.1101/2024.02.15.579904
Multi-Omics Analysis Reveals the Attenuation of the Interferon Pathway as a Driver of Chemo-Refractory Ovarian Cancer
Afenteva D, Yu R, Rajavuori A, Salvadores M, Launonen I, Lavikka K, Zhang K, Marchi G, Jamalzadeh S, Isoviita V, Li Y, Micoli G, Erkan EP, Falco MM, Ungureanu D, Lahtinen A, Oikkonen J, Hietanen S, Vähärautio A, Sur I, Virtanen A, Färkkilä A, Hynninen J, Muranen T, Taipale J, Hautaniemi S. Multi-Omics Analysis Reveals the Attenuation of the Interferon Pathway as a Driver of Chemo-Refractory Ovarian Cancer. doi: https://doi.org/10.1101/2024.03.28.587131