AI-powered simulation-based inference of a genuinely spatial-stochastic model of early mouse embryogenesis MA Ramírez-Sierra, TR Sokolowski, arXiv:2402.15330 (2024)
Stable developmental patterns of gene expression without morphogen gradients M Majka, NB Becker, PR ten Wolde, M Zagorski, TR Sokolowski, arXiv:2306.00537 (2023)
Deriving a genetic regulatory network from an optimization principle TR Sokolowski, T Gregor, W Bialek, G Tkačik, arXiv:2302.05680 (2023)
Information theory entering soils and tissues TR Sokolowski, Cell Systems 13 (7), 511-513 (2022)
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)
Publizierte 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
Nützliche theoretische und technische Referenz für 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)