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 (PDF), in Polish: "Czas medycyny skrojonej na miarę", Spider's Web, December 2015.
 
M Dobrzyński, Solving the human brain (PDF), in Polish: "Na tropie rozwiązania zagadek ludzkiego mózgu", Spider's Web, November 2015.
 
M Dobrzyński, Healing with a computer (PDF), in Polish: "Era leczenia przez komputer", Polityka, June 2012.
 

Selected scientific publications

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, edited by: Zhike Zi and Xuedong Liu, Methods in Molecular Biology, 2021 (in press).
 
D Fey, M Dobrzyński, and BN Kholodenko, "Modeling with Ordinary Differential Equations", in Quantitative Biology Theory, Computational Methods, and Models, MIT Press.
 
BC Daniels, M Dobrzyński, and D Fey, "Parameter Estimation, Sloppiness, and Model Identifiability", in Quantitative Biology Theory, Computational Methods, and Models, MIT Press.
 
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, 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, 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)
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