Jarkko Koivunen
Docent
jarkko.koivunen@utu.fi +358 29 450 4927 +358 50 449 4932 Tykistökatu 6 Turku ORCID identifier: https://orcid.org/0000-0001-8060-555X |
Academia – Industry collaboration; Academia – Industry funding; drug discovery; cell signaling; research funding
I obtained my Master's degree in Organic Chemistry in 2007 and my Ph.D. in Cellular and Molecular Biology in 2011, both from the University of Jyväskylä. After completing my doctorate, I relocated to Oulu, where I worked as a researcher for over ten years. Since January 2022, I have served as the Research Manager for the InFLAMES Flagship here in Turku.
I possess robust industrial and academic networks across various fields, ranging from high-content screening to cancer research. My experience includes preparing major international applications, seeking new partners, providing feedback on application texts, various tasks related to the compilation of funding applications, advocacy actions, and science politics. I am well-acquainted with numerous national and international foundations, MSCA, Horizon Europe, Business Finland, and the Research Council of Finland calls.
I completed my Master's degree in Organic Chemistry, which was followed by a Ph.D. in Cellular and Molecular Biology in collaboration with Biotie Therapies Corporation. My doctoral thesis was centered on integrin research, employing a diverse array of methods from molecular modeling to cellular assays.
Over the past ten years, my research has focused on matrix biology, specifically emphasizing tissue homeostasis, fibrosis, and cancer. My methodological expertise includes a wide range of techniques, such as mouse models and bone marrow transplants, confocal and electron microscopy, CRISPR/Cas9, lentiviral transduction, high-content imaging, cancer biology, organ-on-a-chip technology, and organ cultures. Beyond matrix biology, I have been involved in several drug discovery projects targeting different types of cancers.
I have been teaching biochemistry and medical students for over a decade. My teaching responsibilities have included laboratory courses and lectures covering topics such as metabolism, matrix biology, structural biology, and cell biology. In addition, I have been involved in preparing and grading entrance exams for biochemistry students, as well as developing laboratory courses and a course on data management.
I have successfully supervised three doctoral theses to completion and am a co-supervisor for two doctoral candidates. Additionally, I have supervised six Master's theses, three Bachelor's theses, and multiple trainees.
- Temporally and spatially regulated collagen XVIII isoforms are involved in ureteric tree development via the TSP1-like domain (2023)
- Matrix Biology
(Refereed journal article or data article (A1)) - Analysis of extracellular matrix network dynamics in cancer using the MatriNet database (2022)
- Matrix Biology
(Refereed journal article or data article (A1)) - Identification of suitable reference genes for normalization of reverse transcription quantitative real-time PCR (RT-qPCR) in the fibrotic phase of the bleomycin mouse model of pulmonary fibrosis. (2022)
- PLoS ONE
(Refereed journal article or data article (A1)) - The CMS19 disease model specifies a pivotal role for collagen XIII in bone homeostasis (2022)
- Scientific Reports
(Refereed journal article or data article (A1)) - Upregulated integrin α11 in the stroma of cutaneous squamous cell carcinoma promotes skin carcinogenesis (2022)
- Frontiers in Oncology
(Refereed journal article or data article (A1)) - Integrin alpha 11 beta 1 is a receptor for collagen XIII (2021)
- Cell and Tissue Research
(Refereed journal article or data article (A1)) - The Burden of Post-Translational Modification (PTM)-Disrupting Mutations in the Tumor Matrisome (2021)
- Cancers
(Refereed journal article or data article (A1)) - Exploring the roles of MACIT and multiplexin collagens in stem cells and cancer (2020)
- Seminars in Cancer Biology
(Refereed journal article or data article (A1)) - Lack of collagen XVIII leads to lipodystrophy and perturbs hepatic glucose and lipid homeostasis (2020)
- Journal of Physiology
(Refereed journal article or data article (A1)) - Machine Learning Identifies Robust Matrisome Markers and Regulatory Mechanisms in Cancer (2020)
- International Journal of Molecular Sciences
(Refereed journal article or data article (A1)) - Collagen XIII-derived ectodomain regulates bone angiogenesis and intracortical remodeling (2019)
- Matrix Biology
(Refereed journal article or data article (A1)) - 2-Phenylquinazolinones as dual-activity tankyrase-kinase inhibitors (2018)
- Scientific Reports
(Refereed journal article or data article (A1)) - The N-terminal domain of unknown function (DUF959) in collagen XVIII is intrinsically disordered and highly O-glycosylated (2018)
- Biochemical Journal
(Refereed journal article or data article (A1)) - Highly Potent and Isoform Selective Dual Site Binding Tankyrase/Wnt Signaling Inhibitors That Increase Cellular Glucose Uptake and Have Antiproliferative Activity (2017)
- Journal of Medicinal Chemistry
(Refereed journal article or data article (A1)) - Small-Molecule Chemical Probe Rescues Cells from Mono-ADP-Ribosyltransferase ARTD10/PARP10-Induced Apoptosis and Sensitizes Cancer Cells to DNA Damage (2016)
- Cell Chemical Biology
(Refereed journal article or data article (A1)) - Discovery of potent and selective nonplanar tankyrase inhibiting nicotinamide mimics (2015)
- Bioorganic and Medicinal Chemistry
(Refereed journal article or data article (A1)) - Discovery of Tankyrase Inhibiting Flavones with Increased Potency and Isoenzyme Selectivity (2013)
- Journal of Medicinal Chemistry
(Refereed journal article or data article (A1)) - para-Substituted 2-Phenyl-3,4-dihydroquinazolin-4-ones As Potent and Selective Tankyrase Inhibitors (2013)
- ChemMedChem
(Refereed journal article or data article (A1)) - Novel alpha 2 beta 1 Integrin Inhibitors Reveal That Integrin Binding to Collagen under Shear Stress Conditions Does Not Require Receptor Preactivation (2012)
- Journal of Biological Chemistry
(Refereed journal article or data article (A1)) - Blockage of collagen binding to integrin alpha 2 beta 1: structure-activity relationship of protein-protein interaction inhibitors (2011)
- MedChemComm
(Refereed journal article or data article (A1))