Publications of Zhike Zi

Li, Y.; Deng, D.; Höfer, C. T.; Kim, J.; Heo, W. D.; Xu, Q.; Liu, X.; Zi, Z.: Liebig's law of the minimum in the TGF-β/SMAD pathway. PLOS Computational Biology 20 (5), Article e1012072 (2024)

Shi, D.; Feng, W.; Zi, Z.: Machine learning unveils RNA polymerase II binding as a predictor for SMAD2-dependent transcription dynamics in response to Actvin signalling. IET Systems Biology 18 (1), pp. 14 - 22 (2024)

Li, Y.; Lee, H.; Heo, W. D.; Zi, Z.: Revisiting the Role of TGFβ Receptor Internalization for Smad Signaling: It is Not Required in Optogenetic TGFβ Signaling Systems. Advanced Biology, 2101008 (2021)

Zhang, X.; Xu, Q.; Zi, Z.; Liu, Z.; Wan, C.; Crisman, L.; Shen, J.; Liu, X.: Programmable Extracellular Vesicles for Macromolecule Delivery and Genome Modifications. Developmental Cell 55 (6), pp. 784 - 801 (2020)

van Jaarsveld, M. T. M.; Deng, D.; Ordoñez-Rueda, D.; Paulsen, M.; Wiemer, E. A. C.; Zi, Z.: Cell-type-specific role of CHK2 in mediating DNA damage-induced G2 cell cycle arrest. Oncogenesis 9, 35 (2020)

Zi, Z.: Molecular Engineering of the TGF-β Signaling Pathway. Journal of Molecular Biology (London) 431 (15), pp. 2644 - 2654 (2019)

Han, H.; Wu, G.; Li, Y.; Zi, Z.: eDetect: A Fast Error Detection and Correction Tool for Live Cell Imaging Data Analysis. iScience 13, pp. 1 - 8 (2019)

van Jaarsveld, M.; Deng, D.; Wiemer, E. A. C.; Zi, Z.: Tissue-Specific Chk1 Activation Determines Apoptosis by Regulating the Balance of p53 and p21. iScience 12, pp. 27 - 40 (2019)

Li, Y.; Lee, M.; Kim, N.; Wu, G.; Deng, D.; Kim, J. M.; Liu, X.; Heo, W. D.; Zi, Z.: Spatiotemporal Control of TGF-β Signaling with Light. ACS Synthetic Biology 7 (2), pp. 443 - 451 (2018)

Huang, X.; Zi, Z.: Inferring cellular regulatory networks with Bayesian model averaging for linear regression (BMALR). Molecular BioSystems 10 (8), pp. 2023 - 2030 (2014)

Rigbolt, K. T. G.; Zarei, M.; Sprenger, A.; Becker, A. C.; Diedrich, B.; Huang, X.; Eiselein, S.; Kristensen, A. R.; Gretzmeier, C.; Andersen, J. S. et al.; Zi, Z.; Dengjel, J.: Characterization of early autophagy signaling by quantitative phosphoproteomics. Autophagy 10 (2), pp. 356 - 371 (2014)

Zi, Z.; Chapnick, D. A.; Liu, X.: Dynamics of TGF-β/Smad signaling. FEBS Letters 586 (14), pp. 1921 - 1928 (2012)

Adrover, M. À.; Zi, Z.; Duch, A.; Schaber, J.; González-Novo, A.; Jimenez, J.; Nadal-Ribelles, M.; Clotet, J.; Klipp, E.; Posas, F.: Time-dependent quantitative multicomponent control of the G1-S network by the stress-activated protein kinase Hog1 upon osmostress. Science Signaling 4 (192), p. ra63 (2011)

Zi, Z.; Feng, Z.; Chapnick, D. A.; Dahl, M.; Deng, D.; Klipp, E.; Moustakas, A.; Liu, X.: Quantitative analysis of transient and sustained transforming growth factor-β signaling dynamics. Molecular Systems Biology 2011 (7), 7: 492 (2011)

Zi, Z.: Sensitivity analysis approaches applied to systems biology models. IET Systems Biology 5 (6), pp. 336 - 346 (2011)

Zi, Z.: SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models. Bioinformatics 27 (7), pp. 1028 - 1029 (2011)

Zi, Z.; Liebermeister, W.; Klipp, E.: A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae. A Quantitative Study of the Hog1 MAPK Response to Fluctuating Osmotic Stress in Saccharomyces cerevisiae 5 (3), e9522 (2010)

Zi, Z.; Zheng, Y.; Rundell, A. E.; Klipp, E.: A systems biology markup language (SBML) based sensitivity analysis tool. BMC Bioinformatics 15 (9), p. 342 - 342 (2008)

Zi, Z.; Klipp, E.: Cellular signaling is potentially regulated by cell density in receptor trafficking networks. FEBS Letters 581 (24), pp. 4589 - 4595 (2007)

Zi, Z.; Klipp, E.: Constraint-based modeling and kinetic analysis of the smad dependent TGF-ß signaling pathway. PLoS One 2 (9), p. e936 - e936 (2007)