The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
Open accessAbstract
Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. Here we developed an algorithm that can infer the local network of gene–gene interactions surrounding a gene of interest. This is achieved by a perturbation of the gene of interest and subsequently measuring the gene expression profiles at multiple time points. We applied this algorithm to computer simulated data and to experimental data on a nine gene network in Escherichia coli. Results: In this paper we show that it is possible to recover the gene regulatory network from a time series data of gene expression following a perturbation to the cell. We show this both on simulated data and on a nine gene subnetwork part of the DNA-damage response pathway (SOS pathway) in the bacteria E. coli. Contact: dibernardo@tigem.it Supplementary information: Supplementary data are available at
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Cites
Transcriptional Regulatory Networks in Saccharomyces cerevisiae
Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science · doi:10.1126/science.1075090 · Cited by 2,956
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
Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling
Gardner, T. S., di Bernardo, D., Lorenz, D., & Collins, J. J. (2003) · Science · doi:10.1126/science.1081900 · Cited by 1,117
Cited by
Modelling and analysis of gene regulatory networks
Karlebach, G., & Shamir, R. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2503 · Cited by 1,296
Gene regulatory network inference: Data integration in dynamic models—A review
Hecker, M., Lambeck, S., Toepfer, S., van Someren, E., & Guthke, R. (2009) · Biosystems · doi:10.1016/j.biosystems.2008.12.004 · Cited by 755
Matsumoto, H., Kiryu, H., Furusawa, C., Ko, M. S. H., Ko, S. B. H., Gouda, N., Hayashi, T., & Nikaido, I. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx194 · Cited by 439
Elucidating Compound Mechanism of Action by Network Perturbation Analysis
Woo, J. H., Shimoni, Y., Yang, W. S., Subramaniam, P., Iyer, A., Nicoletti, P., Rodríguez Martínez, M., López, G., Mattioli, M., Realubit, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.056 · Cited by 351
Self-citationGreenfield, A., Madar, A., Ostrer, H., & Bonneau, R. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013397 · Cited by 255
Metadata
- Authors
- Bansal, M., Gatta, G. D., & di Bernardo, D.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-01-17
- Volume
- 22
- Issue
- 7
- Pages
- 815-822
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2122342005
- Cited by
- 382
- References
- 3
- FWCI
- 8.84
- Type
- journal article
- Language
- en
- Open access
- bronze
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