Åsmund Flobak
Background and activities
Project leader for the ERA PerMed project OncoLogics and project leader for the RCN project PRESORT. Principal Investigator at St Olavs hospital for the clinical trial IMPRESS-Norway.
Twitter: https://twitter.com/asmundflobak
Video: https://www.youtube.com/watch?v=N4NzEyo_HQo
Medical doctor 2005 and Master of Science in Nanotechnology 2013. Medical internship 2006-2007, clinical oncology 2009, residential radiologist 2010-2011, PhD 2011-2016, jointly clinical oncology and research from 2016 at The Cancer Clinic, St Olavs University hospital and at The Norwegian University of Science and Technology.
My research project during medical studies focused on simulation of signal transduction, and my master project in nanotechnology focused on a transfection platform using nanowires for high throughput transfection.
Working as a residential oncologist in 2009 I was puzzled by how many novel drugs, with specific targets in signal transduction networks, only produced modest benefits and only for some of my patients. Targeted therapies are different from traditional chemotherapeutic agents in that it is not the growth capacity but rather regulators deciding on growth that are the drug targets. I started my PhD autumn 2011 to explore options for drug combination response prediction.
During my PhD I focused on a drug panel of 7 targeted drugs and the corresponding 21 pairwise combinations, and integrated prior knowledge on the signaling mechanisms affected by the drugs with specific molecular states characterizing my experimental system, the AGS cell line. I finished my PhD from NTNU in 2016, titled “Systems Medicine: From Modeling Systems Perturbations to Predicting Drug Synergies”. During my PhD I did both experiments in the wet-lab (cell lines, drug screening, xenograft experiments), and in the dry-lab (building logical models for drug combination response prediction, development of a pipeline in Java for drug synergy studies).
I’m lead developer of the DrugLogics pipeline for drug synergy and resistance predictions. Our pipeline produces models tailored to single samples for drug synergy simulation and prediction. The automated pipeline takes as input prior knowledge describing molecular mechanisms for targeted drugs, and omics data describing a given cell line or tissue. Based on these two inputs calibrated models are generated, which can predict drug synergies or resistance for single cell lines or tissues. I have also designed the high throughput experiment we currently use as a benchmark for our drug synergy predictions, encompassing 171 pairwise combinations of targeted therapies (mostly kinase inhibitors and some protein interaction inhibitors).
HealthTalk: IMPRESS-Norway - Large national cancer precision medicine trial (interview in English)
Contribution to the Different Sub-projects
Scientific, academic and artistic work
A selection of recent journal publications, artistic productions, books, including book and report excerpts. See all publications in the database
2021
- (2021) The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Briefings in Bioinformatics. vol. 22 (4).
2020
- (2020) Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine. Network and Systems Medicine.
- (2020) High-throughput screening reveals higher synergistic effect of MEK inhibitor combinations in colon cancer spheroids. Scientific Reports. vol. 10.
- (2020) Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction. Frontiers in Physiology. vol. 11.
- (2020) Tumor Targeting by αvβ3-Integrin-Specific Lipid Nanoparticles Occurs via Phagocyte Hitchhiking. ACS Nano. vol. 14 (7).
- (2020) The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics.
- (2020) A middle-out modeling strategy to extend a colon cancer logical model improves drug synergy predictions in epithelial-derived cancer cell lines. Frontiers in Molecular Biosciences. vol. 7:502573.
- (2020) emba: R package for analysis and visualization of biomarkers in boolean model ensembles. Journal of Open Source Software (JOSS).
2019
- (2019) A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines. Scientific Data. vol. 6.
- (2019) Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications. vol. 10 (2674).
2017
- (2017) CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets. Bioinformatics. vol. 33 (15).
2015
- (2015) Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Computational Biology. vol. 11 (8).
- (2015) The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. BMC Systems Biology. vol. 9 (40).