List of publications
Zi Z.
Molecular Engineering of the TGF-β Signaling Pathway.
J Mol Biol. 2019, 431:2644-2654.
PMID:31121181
Han H, Wu G, Li Y, Zi Z.
eDetect: A Fast Error Detection and Correction Tool for Live Cell Imaging Data Analysis
iScience, 2019. 13:1-8.
PMID:30785030
van Jaarsveld MTM, Deng D, Wiemer EAC, Zi Z.
Tissue-Specific Chk1 Activation Determines Apoptosis by Regulating the Balance of p53 and p21.
iScience. 2019, 12:27-40.
PMID: 30665195
Li Y, Lee M, Kim N, Wu G, Deng D, Kim JM, Liu X, Heo WD, Zi Z.
Spatiotemporal Control of TGF-β Signaling with Light.
ACS Synth Biol. 2018, 7:443–451.
PMID: 29241005
Feng Z, Zi Z, Liu X. Measuring TGF-β Ligand Dynamics in Culture Medium.
Methods Mol Biol. 2016,1344:379-89. (Book chapter)
PMID: 26520139
Huang X, Zi Z.
Inferring cellular regulatory networks with Bayesian model averaging for linear regression (BMALR).
Mol Biosyst. 2014, 10:2023-2030.
PMID: 24899235
Rigbolt KT, Zarei M, Sprenger A, Becker AC, Diedrich B, Huang X, Eiselein S, Kristensen AR, Gretzmeier C, Andersen JS, Zi Z, Dengjel J.
Characterization of early autophagy signaling by quantitative phosphoproteomics.
Autophagy. 2014,10:356-71.
PMID: 24275748
Zi Z.
A tutorial on mathematical modeling of biological signaling pathways.
Methods Mol Biol. 2012, 880:41-51. (Book chapter)
PMID: 23361980
Zi Z, Chapnick DA, Liu X.
Dynamics of TGF-β/Smad signaling.
FEBS Lett. 2012, 586:1921-8. (Review)
PMID: 22710166
Adrover MÀ#, 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.
Sci Signal. 2011, 4:ra63. (# contributed equally)
PMID: 21954289
Zi Z#,*, Feng Z#, Chapnick DA, Dahl M, Deng D, Klipp E, Moustakas A, Liu X*.
Quantitative analysis of transient and sustained transforming growth factor-β signaling dynamics.
( # contributed equally, * corresponding authors)
Mol Syst Biol. 2011, 7:492.
PMID: 21613981
Zi Z.
SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.
Bioinformatics. 2011, 27:1028-9.
PMID: 21303862
Zi Z.
Sensitivity analysis approaches applied to systems biology models.
IET Syst Biol. 2011, 5:336-6. (Review)
PMID: 22129029
Zi Z*, Liebermeister W, Klipp E*.
A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae.
PLoS One. 2010, 5:e9522. (* corresponding authors)
PMID: 20209100
Zi Z, Zheng Y, Rundell AE, Klipp E.
SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.
BMC Bioinformatics. 2008, 9:342.
PMID: 18706080
Zi Z, Klipp E.
Steady state analysis of signal response in receptor trafficking networks.
Genome Inform. 2007, 18:100-8.
PMID: 18546478
Zi Z, Klipp E.
Constraint-based modeling and kinetic analysis of the Smad dependent TGF-β signaling pathway.
PLoS One. 2007, 2:e936.
PMID: 17895977
Zi Z, Klipp E.
Cellular signaling is potentially regulated by cell density in receptor trafficking networks.
FEBS Lett. 2007, 581:4589-95.
PMID: 17825822
Zi Z, Klipp E.
SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.
Bioinformatics. 2006, 22:2704-5.
PMID: 16926221
Zi Z, Cho KH, Sung MH, Xia X, Zheng J, Sun Z.
In silico identification of the key components and steps in IFN-γ induced JAK-STAT signaling pathway.
FEBS Lett. 2005, 579:1101-8.
PMID: 15710397