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Publications

  • Statistical analysis and optimality of biological systems
    W Młynarski, M Hledík, TR Sokolowski, G Tkačik, Neuron 109 (7), P1227-1241.e5 (2021)
  • A Tight Upper Bound on Mutual Information
    M Hledík, TR Sokolowski, G Tkačik , 2019 IEEE Information Theory Workshop, 1-5 (2019)
  • eGFRD in all dimensions
    TR Sokolowski, J Paijmans, L Bossen, M Wehrens, T Miedema, NB Becker, K Kaizu, K Takahashi, M Dogterom, PR ten Wolde, J Chem Phys 150 (5), 054108 (2019)
    [Featured Article]
  • Spatial-Stochastic Simulation of Reaction-Diffusion Systems
    TR Sokolowski & PR ten Wolde, in: B Munsky, WS Hlavacek, LS Tsimring (ed.), "Quantitative Biology: Theory, Computational Methods, and Models", ISBN: 9780262038089 (2018)
  • Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells
    P Recouvreux, TR Sokolowski, A Grammoustianou, PR ten Wolde, M Dogterom,
    Proc Natl Acad Sci USA 113 (7), 1811-1816 (2016)
  • Extending the dynamic range of transcription factor action by translational regulation
    TR Sokolowski, AM Walczak, W Bialek, G Tkačik , Phys Rev E 93 (2), 022404 (2016)
  • Optimizing information flow in small genetic networks. IV. Spatial coupling
    TR Sokolowski, G Tkačik , Phys Rev E 91 (6), 062710 (2015)
    [Editor's Pick]
  • Mutual repression enhances the steepness and precision of gene expression boundaries
    TR Sokolowski, T Erdmann, PR Ten Wolde , PLoS Comput Biol 8 (8), e1002654 (2012)
  • Green’s Function Reaction Dynamics—An Exact and Efficient Way To simulate Intracellular Pattern Formation
    T Sokolowski, L Bossen, T Miedema, N Becker , AIP Conf Proc 1281 (1), 1342-1345 (2010)
  • Long-range k-core percolation
    CF Moukarzel, T Sokolowski, J Phys: Conf Ser 246, 012019 (2010)

Published Software

  • eGFRD2
    Event-driven particle-based spatial-stochastic simulator for biochemical systems
    See github repository and gfrd.org
  • GGG ("Gap Gene Gillespie")
    Lattice-based spatial-stochastic simulator for fly embryo patterning
    See github repository

Useful technical reference for eGFRD2

  • A computational study of robust formation of spatial protein patterns 
    TR Sokolowski , PhD thesis, Vrije Universiteit Amsterdam, ISBN 978-90-77209-72-1 (2013)

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