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 masters in organic chemistry in 2007 and my PhD in cellular and molecular biology in 2011, both from the University of Jyväskylä. After finishing my doctorate, I moved to Oulu where I worked as a researcher over ten years. I have been a research manager of InFLAMES Flagship since January 2022.
I have good industrial and academic networks in different fields, varying from high content screening to cancer research. I have been preparing big international applications, seeking new partners, commenting on the application texts and participating in other tasks related to compiling the funding applications. I am familiar with many national and international foundations, MSCA, Horizon Europe, Business Finland and Academy of Finland calls.
I did my master’s degree in organic chemistry and my PhD in cellular and molecular biology in collaboration with Biotie Therapies Corporation. My PhD thesis was based on integrin-research using multiple methods from molecular modelling to cellular assays.
For past ten years, my research focus has been in matrix biology, especially in tissue homeostasis, fibrosis and cancer. My methodological know-how includes mouse work including bone marrow transplants, confocal and electron microscopy, Crispr/Cas9, lentiviral transduction, high content imaging, cancer biology, organ-on-a-chip, and organ cultures. In addition to matrix biology, I have been involved in many drug discovery projects targeting different cancers.
I have been teaching biochemistry and medical students over a decade. Teaching tasks have included laboratory courses and lectures about metabolism, matrix biology, structural biology, and cell biology. Additionally, I have been preparing and grading the entrance exam for biochemistry students and developing laboratory courses and a data management course.
I have supervised three doctoral theses to completion and I am a co-supervisor of two doctoral researchers. I have supervised six Master’s and three bachelor theses to completion.
- 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)) - 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)) - Fluorescent Small Molecule Probe to Modulate and Explore alpha 2 beta 1 Integrin Function (2011)
- Journal of the American Chemical Society
(Refereed journal article or data article (A1))