Research

A biophysicist with background in mathematical modelling, scientific programming, and data analysis with more than a decade of experience as a programmer, researcher, and lecturer in industry and academia. Building data analysis and visualisation pipelines for time series data from time-lapse fluorescent imaging and high-content screening. Experienced in R/Shiny, Python, Mathematica, Matlab, UNIX/command-line, HPC cluster environments. Interested in leveraging the power of modern data analysis to personalised medicine & healthcare.

 

ORCID: 0000-0002-0208-7758 | SCOPUS | Google Scholar

 

M Dobrzyński, The era of personalised medicine (in Polish: Czas medycyny skrojonej na miarę), Spider's Web (PDF), December 2015.

 

M Dobrzyński, Solving human brain (in Polish: Na tropie rozwiązania zagadek ludzkiego mózgu), Spider's Web (PDF), November 2015.

 

M Dobrzyński, Healing with computer (in Polish: Era leczenia przez komputer), Polityka (PDF), June 2012.

 

M Dobrzyński, B Grädel, PA Gagliardi, O Pertz, et al., Quantification of collective signalling in time-lapse microscopy images, Meth Microsc, 2024; Data; Code.

 

PA Gagliardi, B Grädel, et al., M Dobrzyński, Automatic detection of spatio-temporal signaling patterns in cell collectives, J Cell Biol, 2023; Data; Code.

 

P Ender, PA Gagliardi, M Dobrzyński, et al., Spatiotemporal control of ERK pulse frequency coordinates fate decisions during mammary acinar morphogenesis, Dev Cell, 2022; Data.

 

PA Gagliardi, M Dobrzyński, M-A Jacques, C Dessauges, RM Hughes, and O Pertz, Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival, Dev Cell 56(12), 2021; Data.

 

M-A Jacques, M Dobrzyński, PA Gagliardi, R Sznitman, and O Pertz, CODEX, a neural network approach to explore signaling dynamics landscapes, Mol Syst Biol 17:e10026, 2021; Data; Code.

 

M Dobrzyński, M-A Jacques, and O Pertz, Mining single-cell time-series datasets with Time-Course Inspector, Bioinformatics, 2020; Code.

 

C Dessauges, J Mikelson, M Dobrzyński, et al., Optogenetic actuator/biosensor circuits for large-scale interrogation of ERK dynamics identify sources of MAPK signaling robustness, Mol Syst Biol 18:e10670, 2022.

 

Y Blum, J Mikelson, M Dobrzyński, et al., Temporal perturbation of Erk dynamics reveals network architecture of FGF2-MAPK signaling, Mol Syst Biol 15:e8947, 2019; Data.

 

H Ryu, M Chung, M Dobrzyński et al., Frequency modulation of ERK activation dynamics rewires cell fate, Mol Syst Biol 11:838, 2015.

 

T Hell, M Dobrzyński, et al., Flavonoids from Ericameria nauseosa inhibiting PI3K/AKT pathway in human melanoma cells, Biomed Pharmacother, 2022.

 

T Hell, A Rutz, L Dürr, M Dobrzyński, et al., Combining activity profiling with advanced annotation to accelerate the discovery of natural products targeting oncogenic signaling in melanoma, J Nat Prod, 2022.

 

L Dürr, T Hell, M Dobrzyński, et al., High-content screening pipeline for natural products targeting oncogenic signaling in melanoma, J Nat Prod, 2022; Code.

 

LK Nguyen, M Dobrzyński, D Fey, BK Kholodenko, Polyubiquitin chain assembly and organization determine the dynamics of protein activation and degradation, Front Physiol, 2014.

 

M Dobrzyński et al., Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses, J R Soc Interface, 2014.

 

M Dobrzyński, D Fey, and L Nguyen, Bimodal Protein Distributions in Heterogeneous Oscillating Systems, in Comp Meth in Syst Biol, 2012.

 

M Dobrzyński and FJ Bruggeman, Elongation dynamics shape bursty transcription and translation, PNAS, 2009.

 

M Dobrzyński et al., Computational methods for diffusion-influenced biochemical reactions, Bioinformatics, 2007.

 

M Dobrzyński, Mining of single-cell signaling time-series for dynamic phenotypes with clustering, in TGF-beta Signaling: Methods and Protocols, Springer, 2022.

 

D Fey, M Dobrzyński, and BN Kholodenko, Modeling with Ordinary Differential Equations, in Quantitative Biology Theory, Computational Methods, and Models, MIT Press, 2018.

 

BC Daniels, M Dobrzyński, and D Fey, Parameter Estimation, Sloppiness, and Model Identifiability, in Quantitative Biology Theory, Computational Methods, and Models, MIT Press, 2018.

 

A Schwabe, M Dobrzyński, K Rybakova, P Verschure, FJ Bruggeman, Origins of Stochastic Intracellular Processes and Consequences for Cell-to-Cell Variability and Cellular Survival Strategies, in Methods in Enzymology, Elsevier, 2011.

 

M Dobrzyński, P Bernatowicz, M Kloc, JZ Kubiak, Evolution of Bet-Hedging Mechanisms in Cell Cycle and Embryo Development Stimulated by Weak Linkage of Stochastic Processes, in Cell Cycle in Development, Springer, 2011.

 

PhD thesis, Molecules in Motion: a theoretical study of noise in gene expression and cell signaling, PDF (6.5MB), University of Amsterdam, The Netherlands, 2011.

 

MSc thesis, Particle-based algorithm for modeling of simple biochemical networks in space and time, PDF (0.7MB), Faculty of Physics, Warsaw University, Poland, 2003.

 

Experiment NL - wetenschap in Nederland, Wiskunde verwangt proefdieren, PDF (0.6MB)

 

In De Verdediging, PDF (0.1MB)