Research

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 iD iconORCID: 0000-0002-0208-7758 | SCOPUS | Google Scholar
 

Popular science

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.
 

Selected scientific publications

T Hell, A Ruth, 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.
 
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, BioRxiv, 2021.
 
P Ender, PA Gagliardi, M Dobrzyński, et al., Spatio-temporal control of ERK pulse frequency coordinates fate decisions during mammary acinar morphogenesis, BioRxiv, 2020.
 
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.
 
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.
 
M Dobrzyński, M-A Jacques, and O Pertz, Mining single-cell time-series datasets with Time-Course Inspector, Bioinformatics, 2020.
 
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.
 
H Ryu, M Chung, M Dobrzyński et al., Frequency modulation of ERK activation dynamics rewires cell fate, Mol Syst Biol 11:838, 2015.
 
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.
 

Book chapters

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.
 

Theses

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.
 

About me

Experiment NL - wetenschap in Nederland, Wiskunde verwangt proefdieren, PDF (0.6MB)
 
In De Verdediging, PDF (0.1MB)
(c)2015, All Rights Reserved