The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS
Abstract
We describe Dizzy, a software tool for stochastically and deterministically modeling the spatially homogeneous kinetics of integrated large-scale genetic, metabolic, and signaling networks. Notable features include a modular simulation framework, reusable modeling elements, complex kinetic rate laws, multi-step reaction processes, steady-state noise estimation, and spatial compartmentalization.
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Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Stochastic Gene Expression in a Single Cell
Elowitz, M. B., Levine, A. J., Siggia, E. D., & Swain, P. S. (2002) · Science · doi:10.1126/science.1070919 · Cited by 5,441
A genomic regulatory network for development
Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C.-H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., et al. (2002) · Science · doi:10.1126/science.1069883 · Cited by 1,567
Self-citationE-CELL: software environment for whole-cell simulation
Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T. S., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J. C., et al. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.1.72 · Cited by 764
Quantitative model for gene regulation by lambda phage repressor.
Ackers, G. K., Johnson, A. D., & Shea, M. A. (1982) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.79.4.1129 · Cited by 590
Web-based kinetic modelling using JWS Online
Olivier, B. G., & Snoep, J. L. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth200 · Cited by 326
Cited by
An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems
Gupta, A., & Mendes, P. (2018) · Computation · doi:10.3390/computation6010009 · Cited by 17
Paul, D., & Radde, N. (2018) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2018.07.012 · Cited by 1
Metadata
- Authors
- RAMSEY, S., ORRELL, D., & BOLOURI, H.
- Venue
- Journal of Bioinformatics and Computational Biology
- Publisher
- World Scientific Pub Co Pte Lt
- Published
- 2005-04
- Volume
- 03
- Issue
- 02
- Pages
- 415-436
- ISSN
- 0219-7200 (ISSN-L)
- 1757-6334
- OpenAlex
- W2065219357
- Cited by
- 253
- References
- 6
- FWCI
- 9.33
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
