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Maciej Dobrzynski

Post-Doc

Systems Biology Ireland
F117
University College Dublin
Belfield
Dublin 4

Tel: +353 1 716 6328
Email: maciej.dobrzynski@ucd.ie

Biography

I come from Northern Poland from a city of Slupsk. In 2003 I earned Masters degree in Physics in the field of theoretical Biophysics at the Warsaw University. I spent last year of my Masters studies at Free University (VU) Amsterdam as part of Socrates/Erasmus programme. At VU, I worked on a particle-based algorithm for spatial-stochastic simulations of biochemical networks (link to thesis). Further on, I pursued my PhD studies at the Centre for Mathematics & Computer Science (CWI) in Amsterdam. The topic of my PhD thesis was a theoretical and computational study of noise in gene expression and cell signaling (link to thesis). After my time in Amsterdam I moved to the Institute of Theoretical Biology at Humboldt University in Berlin and since August 2010 I started as a post-doc here at SBI. My major line of research revolves around theoretical and experimental investigations of cellular processes that contribute to cell-to-cell heterogeneity involved in drug resistance of cancer cells.

Professional

               

Education

Year 2011 Institution: University of Amsterdam
Qualification: PhD Subject: Science, Mathematics and Computer Science
Year 2003 Institution:
Qualification: MSc Subject: MSc Physics

Languages

Dutch:
English:
Polish:
       

Publications

 

Book Chapters

Dobrzyński, M; Bernatowicz, P; Kloc, M; Kubiak, J (2011) 'Evolution of bet-hedging mechanisms in cell cycle and embryo development stimulated by weak linkage of stochastic processes' In: Kubiak, JZ (eds). Cell Cycle in Development. Berlin Heidelberg: Springer-Verlag. , pp.11-30 Available Online [DOI] [Details]
Schwabe, A; Dobrzyński, M; Rybakova, K; Verschure, P; Bruggeman, FJ (2011) 'Origins of Stochastic Intracellular Processes and Consequences for Cell-to-Cell Variability and Cellular Survival Strategies' In: Daniel Jameson, Malkhey Verma, and Hans V. Westerhoff (eds). Methods in enzymology. Elsevier: Academic Press. , pp.597-625 Available Online [DOI] [Details]
 

Peer Reviewed Journals

Dobrzyński M, Nguyen LK, Birtwistle MR, von Kriegsheim A, Blanco Fernández A, Cheong A, Kolch W, Kholodenko BN (2014) 'Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses'. Journal of the Royal Society Interface, 11 (98). Available Online [DOI] [Details]
Lan K Nguyen, Maciej Dobrzyński, Dirk Fey, and Boris N Kholodenko (2014) 'Polyubiquitin chain assembly and organization determine the dynamics of protein activation and degradation'. Frontiers in physiology, 5 :1-13. Available Online [DOI] [Details]
Vidal Rodriguez, J; Kaandorp, JA; Dobrzyński, M; Blom, JG (2006) 'Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli'. Bioinformatics (Oxford, England), 22 (15):1895-1901. Available Online [DOI] [Details]
Dobrzyński, M; Vidal Rodriguez, J; Kaandorp, JA; Blom, JG (2007) 'Computational methods for diffusion-influenced biochemical reactions'. Bioinformatics (Oxford, England), 23 (15):1969-1977. Available Online [DOI] [Details]
Dobrzyński, M; Bruggeman, FJ (2009) 'Elongation dynamics shape bursty transcription and translation'. PNAS, 106 (8). Available Online [DOI] [Details]
Birtwistle, M.R. and von Kriegsheim, A. and Dobrzy\'nski, M. and Kholodenko, B. and Kolch, W. (2012) 'Mammalian Protein Expression Noise: Scaling Principles and the Implications for Knockdown Experiments'. Molecular BioSystems, 8 (11):3068-3076. Available Online [DOI] [Details]
Birtwistle, MR; Rauch, J; Kiyatkin, A; Aksamitiene, E; Dobrzyński, M; Hoek, JB; Kolch, W; Ogunnaike, BA; Kholodenko, BN (2012) 'Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise'. BMC systems biology, 6 (1). Available Online [DOI] [Details]
 

Conference Publications

Dobrzyński, M (2008) When do diffusion-limited trajectories become memoryless? . In: Gauges, R; Kummer, U; Pahle, J; Willy, PM eds. 5th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg Available Online [Details]
Dobrzyński, M; Fey, D; Nguyen, LK; Kholodenko, BN (2012) Bimodal Protein Distributions in Heterogeneous Oscillating Systems . In: Gilbert, David and Heiner, Monika eds. 10th International Conference, CMSB 2012, London, UK Available Online [Details]
       

Newspaper Articles

Dobrzyński, M. (2012) Era leczenia przez komputer: Obliczanie człowieka. Newspaper Articles Available Online [Details]

Dissertations/Theses

Dobrzyński, M. (2003) Particle-based algorithm for modeling of simple biochemical networks in space and time. Dissertations/Theses Available Online [Details]
Dobrzyński, M. (2011) Molecules in Motion: A Theoretical Study of Noise in Gene Expression and Cell Signaling. Dissertations/Theses Available Online [Details]
                                                                             

Research

Research Interests

  • The effect of biochemical noise on performance of eukaryotic signaling networks.
  • Single-cell mechanism that contribute to population-level cell-to-cell heterogeneity.
  • The effect of population-level heterogeneity on drug resistance of cancer cells.
  • Modeling cell-fate decisions via quasi-potential landscape formalism.
  • Single-cell imaging experimental techniques.