Dr Nicolae-Radu Zabet

Research Associate

Group: Paszkowski Lab

Affiliations

The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR

Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK

Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK

Contact details

Address: The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR

Email: n.r.zabet@gen.cam.ac.uk

Other websites: Linkedin, Academia.edu, ResearchGate

 

Software

Gene Regulation in Prokaryotes (GRiP)

Description: GRiP is an agent based model of the transcription factors (TFs) search process for their target sites, which is written in Java 1.6. The software represents the DNA sequence, TFs and the interaction between TFs and the DNA (facilitated diffusion mechanism), or between various TFs (cooperative behaviour). The software will output both information on the dynamics associated with the search process (locations of molecules) and also steady state results (affinity landscape, occupancy-bias, collision hotspots, search times, the times the target sites were occupied and statistics about the 1D random walk process).

Webpage: http://logic.sysbiol.cam.ac.uk/grip/

Publication: GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Nicolae Radu Zabet and Boris Adryan. Bioinformatics, 28 (9): 1287-1289, 2012, doi:10.1093/bioinformatics/bts132. link to download

Translation Particle Simulator (TPS)

Description: TPS is a highly efficient software tool written in Java 1.6, which models the translation process in eukaryotic systems with high level of details. The tool is an agent based simulator which includes among others the following features: representation of exhaustible tRNA pools, ribosome–ribosome interactions and differential initiation rates for different mRNA species.

Webpage: http://www.cs.kent.ac.uk/people/staff/dfc/site/translation/

Publication: A novel and versatile computational tool to model translation. Dominique Chu, Nicolae Zabet and Tobias von der Haar. Bioinformatics, 28 (2): 292-293, 2012, doi:10.1093/bioinformatics/btr650. link to download

 

Publications

Publication period   (April 2009 onwards)   -   ordered by publication type and date

Journal Papers

Estimating binding properties of transcription factors from genome-wide binding profiles Nicolae Radu Zabet and Boris Adryan. Nucleic Acids Research, 43 (1): 84-94, 2015, doi:10.1093/nar/gku1269. link to download

Facilitated diffusion buffers noise in gene expression Armin P. Schoech and Nicolae Radu Zabet. Physical Review E, 90 (3): 032701, 2014, doi:10.1103/PhysRevE.90.032701. link to download

Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression Daphne Ezer, Nicolae Radu Zabet and Boris Adryan. Computational and Structural Biotechnology Journal, 10 (17): 63-69, 2014, doi:10.1016/j.csbj.2014.07.005. (Review Article) link to download

Physical constraints determine the logic of bacterial promoter architectures Daphne Ezer, Nicolae Radu Zabet and Boris Adryan. Nucleic Acids Research, 42 (7): 4196-4207, 2014, doi:10.1093/nar/gku078. link to download

The influence of transcription factor competition on the relationship between occupancy and affinity Nicolae Radu Zabet, Robert Foy and Boris Adryan. PLoS ONE, 8 (9): e73714, 2013, doi:10.1371/journal.pone.0073714. link to download

The effects of transcription factor competition on gene regulation Nicolae Radu Zabet and Boris Adryan. Frontiers in Genetics, 4: 197, 2013, doi:10.3389/fgene.2013.00197. link to download

System size reduction in stochastic simulations of the facilitated diffusion mechanism Nicolae Radu Zabet BMC Systems Biology, 6 (1): 121, 2012, doi:10.1186/1752-0509-6-121. link to download

Computational models for large-scale simulations of facilitated diffusion Nicolae Radu Zabet and Boris Adryan. Molecular BioSystems, 8 (11): 2815-2827, 2012, doi:10.1039/C2MB25201E. (Review Article) link to download

A comprehensive computational model of facilitated diffusion in prokaryotes. Nicolae Radu Zabet and Boris Adryan. Bioinformatics, 28 (11): 1517-1524, 2012, doi:10.1093/bioinformatics/bts178. link to download

GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Nicolae Radu Zabet and Boris Adryan. Bioinformatics, 28 (9): 1287-1289, 2012, doi:10.1093/bioinformatics/bts132. link to download

A novel and versatile computational tool to model translation. Dominique Chu, Nicolae Zabet and Tobias von der Haar. Bioinformatics, 28 (2): 292-293, 2012, doi:10.1093/bioinformatics/btr650. link to download

Negative Feedback and Physical Limits of Genes. Nicolae Radu Zabet Journal of Theoretical Biology , 248(1):82-91, September 2011, doi:10.1016/j.jtbi.2011.06.021. link to download

Optimal parameter settings for information processing in gene regulatory networks. Dominique F. Chu, Nicolae Radu Zabet, and Andrew N. W. Hone. BioSystems, 104(2-3):99-108, May-June 2011, doi:10.1016/j.biosystems.2011.01.006. link to download

Computational limits to binary genes. Nicolae Radu Zabet and Dominique F. Chu. Journal of the Royal Society Interface , 7:945-954, June 2010, doi:10.1098/rsif.2009.0474. link to download

Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Dominique Chu, Nicolae Radu Zabet, and Boris Mitavskiy. Journal of Theoretical Biology , 257(3):419-429, April 2009, doi:10.1016/j.jtbi.2008.11.026. link to download

Conference Papers

A Comprehensive Computational Model to Simulate Transcription Factor Binding in Prokaryotes. Nicolae Radu Zabet and Boris Adryan In Information Processign in Cells and Tissues, volume 7223, pages 35-37. Springer Berlin / Heidelberg, Lecture Notes in Computer Science, 2012, doi:10.1007/978-3-642-28792-3_6. link to download

Design principles of transcriptional logic circuits. Nicolae Radu Zabet, Andrew N. W. Hone, and Dominique F. Chu. In Artificial Life XII Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, pages 186-193. MIT Press, August 2010, URL:http://mitpress.mit.edu/catalog/item/default.asp?ttype=2 ttid=12433. link to download

Stochasticity and robustness in bi-stable systems. Nicolae Radu Zabet and Dominique F. Chu. In Bioinformatics and Biomedical Engineering (iCBBE), 2010 4th International Conference on pages 1-4. IEEE Xplore, June 2010, doi:10.1109/ICBBE.2010.5518099. link to download

Miscellaneous

Towards modular, scalable and optimal design of transcriptional logic systems. Nicolae Radu Zabet. PhD thesis, School of Computing, University of Kent, UK, October 2010. link to download