Principal Investigator
Anniina Färkkilä, MD PhD
Assistant professorAnniina Färkkilä, MD PhD, is an Assistant professor in translational gynecologic oncology and a Specialist in gynecology at the University of Helsinki, Finland.
She completed herpostdoctoral fellowship at the Dana-Farber Cancer Institute and Harvard Medical School in 2019. In 2018 she was awarded the Seth Wichmann award by the Finnish Gynecologic Society, and the Eero Saksela award by the Finnish Cancer Institute in 2022. She was the recipient of a prestigious ERC Starting grant in 2022.Dr. Färkkilä also works as a specialist for gynecologic oncology at the Helsinki University Hospital (HUH), participating in multiple clinical trials at the HUH Comprehensive cancer center.
Dr. Färkkilä coordinates the prospective Oncosys-Ova trial, and leads the Ovarian cancer project in the iCAN Digital Precision Medicine Flagship. She is a board member at the Nordic Society of Gynecologic Oncology (NSGO), the National Molecular tumor board of Finnish Cancer Center (FICAN), and the translational working group of European Network of gynecological clinical trials (ENTOG) and Gynecologic Cancer Inter Group (GCIG).
She is passionate about precision oncology, improving the treatment and outcomes of cancer patients, leadership, wellbeing, family and outdoor activities.
Research coordinator
Joonas Jukonen, PhD
Joonas works as a research/trial coordinator for Färkkilä lab, and additionally on setting up long-term organoid cultures from HGSC patient-derived material. His prior research expertise includes various molecular biology methods, utilizing both clinical samples and cell-based assays. He has previously studied oncogenic Eph-ephrin and MMP signaling in HGSC and melanoma, respectively.
Post-Docs
Sara Palomino, PhD
Sara’s research explores the role of the tumor microenvironment in ovarian cancer progression, using spatial transcriptomics, network analysis, and systems medicine. She has a background in omics analysis and in developing stratification and clustering techniques, previously applied in a multidisciplinary project on cirrhosis.
Hanna Elomaa, PhD
Hanna’s project will focus on characterizing the immune landscape and spatial interactions in the ovarian cancer microenvironment using advanced spatial profiling techniques. Previously, she has investigated immune cell infiltration and its spatial organization in the colorectal cancer microenvironment using multiplex immunohistochemistry and machine learning-based image analysis.
Doctoral researchers
Fernando Perez, MSc
Doctoral researcherHe is interested in identifying Genomic and Tumor microenviroment biomarkers that predict chemotherapy response in Ovarian Cancer. For that, he is developing algorithms to analyze fluorescence images and the detection of genomic imbalances patterns.
Iga Niemiec, MSc
Doctoral researcherIga’s project focuses on the discovery of immune escape mechanisms in the high-grade serous ovarian cancer. By combining genetics, spatial imaging and spatial transcriptomics data, Iga aims to uncover the genetic and spatial features shaping the tumor-immune interplay and leading to immune escape.
Ada Junquera, MSc
Doctoral researcher (iCANDOC)Ada’s research focuses on how current therapies shape the TME and immune dynamics. She profiles the patient-derived samples through spatial methods, such as tCycIF multiplexed imaging and GeoMx spatial transcriptomics.
Her goal is to uncover treatment-associated patterns and novel biomarkers for improved patient stratification and treatment refinement.
Matilda Salko, MD
Doctoral researcherHer work is mostly focused on the prospective Oncosys-Ova study. She is looking into the clinical characteristics and treatment responses as well as genomic data of ovarian cancer patients, aiming to better understand the real-world clinical outcomes of patients diagnosed with HGSC
Inga-Maria Launonen, MD
Doctoral researcherHer PhD projects focus on the effects of homologous recombination deficiencies and DNA damage on the tumor-immune interactions in high-grade serous ovarian cancer. She is especially interested in the spatial architecture and interactions in the tumor microenvironment that delineate therapy responses.
Ziqi Kang, MSc
Doctoral researcherHer project focuses on profiling the tissue architecture and discovering spatial-related immune response mechanisms from multiplexed images. She is developing unbiased automatic computational tools in order to deeply quantify spatial information in fluorescence images.
Pablo Siliceo Portugal, MSc
Doctoral researcher (iCANDOC)Pablo’s project is focused on understanding early immunoregulatory processes that drive tumor development in homologous recombination deficient tumors by means of spatial investigation. He is particularly interested in key spatiotemporal and topological features involved in pathogenesis and clinical outcomes.
Aleksandra Shabanova, MSc
Doctoral researcher (iCANDOC)Her PhD research focuses on identifying novel prognostic markers and therapeutic targets for personalized cancer treatment by investigating antigen presentation-driven immune evasion mechanism. By integrating spatial multi-omic analysis of tumor microenvironments and cell-cell interaction studies, she aims to uncover insights into cancer progression. Her primary research interests lie at the intersection of cancer cell biology, bioinformatics and immunology.
Zhihan Liang, MSc
Doctoral researcher (iCANDOC)His tasks involve using spatial transcriptomics data to analyze the tumor microenvironment of ovarian cancer. He is interested in genetic and spatial features related to immune evasion.
María Hincapié Otero, MSc
Doctoral researcherMaría’s project is centered on the integration of the stromal compartment into the immune-competent patient-derived cultures (iPDCs) that have been established within the lab. This initiative aims to faithfully recapitulate patients’ tumors, facilitating the utilization of these cultures as a personalized high-throughput platform to test different therapeutic agents, with a focus on addressing the challenge of chemo-resistance in high-grade serous ovarian cancer (HGSOC).
Ella Anttila, MD
Doctoral researcherHer main task in Färkkilä Lab is to help with data analysis in different projects concerning tumor microenvironment of HGSOC.
Anni Suoknuuti
Doctoral researcherAnni is a second year medical student, and her main task is to work on the clinical data of the FINPROVE trial.
Wenqing Chen, MSc
Doctoral researcher (iCANDOC)She is a PhD co-trained by Vähärautio and Färkkilä’s lab. Her project involves applying and evaluating computational methods to quantify tissue architecture in multiplexed images. The goal is to identify deficiencies in these methods, adapt and integrate the most effective methods into the tCyCIF analysis pipeline.
Master’s students
Antti Toivanen, BSc
LSI Master’s Programme Antti holds a BSc in Molecular biosciences from UH. He is currently a MSc student in the Life Science Informatics (LSI) programme here at UH. His interests include bioinformatics, molecular biology, and systems modelling. Antti’s thesis project focuses on assessing the statistical power of tissue microarrays (TMA) in sampling of HGSC.
Nika Mikhailava, BSc
Genetics and Molecular Biosciences Master’s Programme (University of Helsinki)Nika’s responsibilities include working with the establishment, maintenance, and characterization of long-term organoids, alongside other wet lab projects.
Venla Kaislo, BSc
Bioinformatics and Digital Health Master’s programme (Aalto University)Venla does omics data analysis and multimodal clinical modeling of chemo-naive ovarian cancer patients.
Elias Ruuska, BSc
Genetics and Molecular Biosciences Master’s Programme (University of Helsinki)Elias is currently developing and utilizing t-cyCIF image analysis pipelines to study spatial interactions of cells in the tumor microenvironment.
Clinical researchers
Ulla-Maija Haltia, MD PhD
Gynecologic OncologistOvarian cancer is her main interest. She shares her time between clinical duties and translational research.
Laura Haapasalo, Midwife
Study NurseLaura works as a Midwife with gynecological cancer patients at an Outpatient Clinic in Women’s Hospital. As a study nurse she mainly coordinates the recruitment process.
Maija Vääriskoski, MSocSc (Social- and Health Research and Management), Midwife
Study NurseMaija worked as a study nurse, overseeing and enhancing the recruitment process, managing clinical data and study registries, and coordinating the collection of samples.
Medical students
Anni Härkönen
Medical studentAnni is a second-year Medical Student, and her main focus is working on the clinical data of the Oncosys-ova study.
Silja Kauppila
Medical studentSilja is a second-year Medical Student, and her main focus is working with t-CycIF data from a large cohort of TNBC samples.
Andreas Hainari, BMed
Medical studentAndreas is a third-year medical student combining his medical training with technical studies in bioinformation technology. His medical thesis investigated actionable genomic aberrations in High-Grade Serous Carcinoma using multi-omic workflow integration and semantic knowledge graphs. He is currently focusing on analysing Whole Exome Sequencing and bulk RNA-seq data.
Eveliina Holappa, BSc
Medical student, PhD Study TrackEveliina is working with patient sample processing, 3D cell culture, and flow cytometry experiments.
Interns
Arttu Peltola
Mathematics BSc student (Aalto University)Arttu is helping to improve the image processing pipeline by establishing a metric and a system around it to measure and optimize segmentation methods and the impact of different filtering, denoising and enhancing methods on the segmentation alongside helping with other projects involving image processing.
Lab managers
Saundarya Shah, MSc
Spatial Transcriptomics ManagerShe coordinates tCycIF and GeoMx spatial transcriptomic experiments
Anastasia Lundgren, MSc
Lab ManagerAnastasia coordinates the ONCOSYS-Ova sample collection
Aino Elomaa, BSc
Laboratory and clinical sample coordinatorAlumni
Angéla Szabó
BioinformaticianHer tasks mainly focused on celltype calling and image analysis. She’s particularly interested in image visualization tools.
Lina Maltrovsky, BSc
Biological Chemistry Master´s programme (University of Vienna)Lina focused on combining highly multiplexed imaging with proteomics analysis and optimizing this method.
Alva Grönholm, BSc
TRANSMED Master’s programmeShe focused on performing bioinformatic analyses for the cell cycle project on highly multiplexed imaging data.
Matías Aiskovich, MSc
LSI Master’s programmeHe is interested in applying bioinformatics and machine learning to tumor omics data. He focused on developing computer vision models for CycIF multiplexed imaging and GeoMx spatial transcriptomics data.
Olavi Goussev, MSc (Tech)
Data Science Master’s programmeHe was concentrating on the development and implementation of machine learning processes and feature engineering methods for analyzing multiplex immunofluorescence image data from tumor microenvironments.
Panagiotis Lilis, BSc
GMB MSc programmeHe specialized in cell culture with a primary focus on establishing long-term 3D ovarian tumor organoid cultures
Foteini Chamchougia
Erasmus+ internship program 2023-2024Foteini was, at the time of her internship, a Biology Bachelor’s student in the University of Patras, Greece. She was involved in multiple projects analyzing patient-derived samples and utilizing spatial techniques like tCycIF multiplexed imaging.
Assel Kalmenova, MSc
Research assistanntAssel earned her B.Sc. in Biology and M.Sc. in Molecular Medicine from Nazarbayev University, Kazakhstan. During her studies she worked on cancer and hematology research. Her Internship focuses on expansion of high-grade serous ovarian cancer organoids, and on analysis of tumor microenvironment.
Ashwini Nagaraj, PhD
Postdoctoral fellowAshwini’s research is focused on establishing high-grade serous ovarian cancer (HGSC) patient-derived immunocompetent model for functional testing immunotherapeutic agents. She was also interested in understanding the tumor microenvironment in chemo-resistant HGSC using single-cell spatial omics approaches, with the aim of identifying novel biomarkers and targets for immune and combination therapies in chemo-resistant HGSC
Aditi Sirsikar, BSc
TRANSMED Master’s programmeHer responsibilities included analyzing multi-dimensional drug response data from patient-derived immunocompetent cultures (iPDCs) and examining replication stress pathway activation using CyCIF to investigate molecular pathways driving patient-specific drug responses observed in iPDCs.
Abhilash VA
Master’s student from IISER Pune (India)Abhilash performed evaluations of immune cell-specific functional response following single or combinatorial treatment with DNA damaging and immunotherapy agents using patient-derived immunocompetent cultures of High Grade Serous Ovarian Cancer.
Teodóra Faragó
LSI Master’s programme studentHer tasks mainly consisted of automatic cell-type calling and computational analysis. Her main interests are biological algorithms and machine learning in medicine.
Julia Casado, PhD
Postdoctoral fellowHer research focused on the tumor microenvironment from highly-multiplexed images of tumor tissue. She designed and integrated algorithms to perform cell type and cell state calling with an emphasis on spatial localization and cell infiltration profiling.
Elina Pietilä, PhD
Postdoctoral fellowShe worked in precision medicine in high-grade serous ovarian cancer using immunocompetent patient-derived ex vivo cultures. Her project based on screening the effect of novel combinatorial immunotherapies on single-cell level in the tumor microenvironment.