Group: Paszkowski Lab
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
Address: The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR
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).
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.
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.
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.
Publication period (April 2009 onwards) - ordered by publication type and date
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)
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.
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.
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.
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.
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.
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.