Kari Lavikka

Name Kari Antero Lavikka
Date of Birth
E-mail kari.lavikka@helsinki.fi
ORCiD 0000-0002-4163-4945

Summary

I am a doctoral researcher specializing in interactive data visualization within the field of life sciences. With a strong background in software design and development, gained through extensive industry experience, I possess practical skills essential for developing innovative tools and methods to assist fellow researchers in their work.

Degrees

University of Helsinki, Ph.D Student
Doctoral Programme in Biomedicine
Supervisor: Prof. Sampsa Hautaniemi
University of Helsinki, Master of Science
Master's Programme in Data Science
Thesis title: Grammar-Based Interactive Genome Visualization
University of Helsinki, Bachelor of Science
Biology, Faculty of Biological and Environmental Sciences
Thesis title: Visualizing Cancer Genomes

Employment

The Systems Biology of Drug Resistance in Cancer group, University of Helsinki
  • Developing GenomeSpy, an interactive visualization toolkit for genomic data
  • Researching tumor evolution, developing methods for its visualization
  • Doing bioinformatics, particularly copy-number analysis
  • Teaching on the Clinical Data Mining course
Somia Dynamoid Oy
  • Developed an Android mobile app for a chat platform
Dynamoid Oy, later Sulake Dynamoid Oy
  • Chief technology officer (CTO), member of the executive board
  • Led the development of the technical architecture of IRC-Galleria, a trailblazing finnish social media website.
  • Designed and maintained IRC-Galleria's relational database
  • Designed and implemented user interfaces
  • Designed and implemented software
eQ Pankki Oy
  • Software development for stock trading
  • Maintenance of servers
  • Technical support, customer service
Business DataBases Oy
  • Developed customer relationship management (CRM) software as a part-time job

Awards

Best Abstract Award, BioVis COSI, ISMB/ECCB 2023
Abstract title: Visualizing temporal and multi-regional evolution of tumor subclones with Jellyfish plots
Best Poster Award, BioVis COSI, ISMB 2020
Poster title: Grammar-Based Interactive Genome Visualization

Grants

Young Investigator's Grant, Biomedicum Helsinki Foundation
Proposal title: Accelerating Cancer Research through Interactive Visualization Techniques
Dates: 1.12.2023 - 31.3.2024
Amount: 6000 €

Journal Articles

  • Lahtinen, A., Lavikka, K., Virtanen, A., Li, Y., Jamalzadeh, S., Skorda, A., Lauridsen, A. R., Zhang, K., Marchi, G., Isoviita, V.-M., Ariotta, V., Lehtonen, O., Muranen, T. A., Huhtinen, K., Carpén, O., Hietanen, S., Senkowski, W., Kallunki, T., Häkkinen, A., … Hautaniemi, S. (2023). Evolutionary states and trajectories characterized by distinct pathways stratify patients with ovarian high grade serous carcinoma. Cancer Cell. https://doi.org/10.1016/j.ccell.2023.04.017
  • Senkowski, W., Gall-Mas, L., Falco, M. M., Li, Y., Lavikka, K., Kriegbaum, M. C., Oikkonen, J., Bulanova, D., Pietras, E. J., Voßgröne, K., Chen, Y.-J., Erkan, E. P., Dai, J., Lundgren, A., Grønning Høg, M. K., Larsen, I. M., Lamminen, T., Kaipio, K., Huvila, J., … Wennerberg, K. (2023). A platform for efficient establishment and drug-response profiling of high-grade serous ovarian cancer organoids. Developmental Cell. https://doi.org/10.1016/j.devcel.2023.04.012
  • Perez-Villatoro, F., Oikkonen, J., Casado, J., Chernenko, A., Gulhan, D. C., Tumiati, M., Li, Y., Lavikka, K., Hietanen, S., Hynninen, J., Haltia, U.-M., Tyrmi, J. S., Laivuori, H., Konstantinopoulos, P. A., Hautaniemi, S., Kauppi, L., & Färkkilä, A. (2022). Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer. Npj Precision Oncology, 6(1), 96. https://doi.org/10.1038/s41698-022-00339-8
  • 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. (2019). Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer. JCO Precision Oncology, 3, 1–12. https://doi.org/10.1200/PO.18.00343
  • Cervera, A., Rantanen, V., Ovaska, K., Laakso, M., Nuñez-Fontarnau, J., Alkodsi, A., Casado, J., Facciotto, C., Häkkinen, A., Louhimo, R., Karinen, S., Zhang, K., Lavikka, K., Lyly, L., Pal Singh, M., & Hautaniemi, S. (2019). Anduril 2: upgraded large-scale data integration framework. Bioinformatics, 35(19), 3815–3817. https://doi.org/10.1093/bioinformatics/btz133