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Construction of a genetic toggle switch in Escherichia coli.
Gardner TS, Cantor CR, Collins JJ. Gardner TS, et al. Nature. 2000 Jan 20;403(6767):339-42. doi: 10.1038/35002131. Nature. 2000. PMID: 10659857
Quorum-sensing regulation of a copper toxicity system in Pseudomonas aeruginosa.
Thaden JT, Lory S, Gardner TS. Thaden JT, et al. Among authors: gardner ts. J Bacteriol. 2010 May;192(10):2557-68. doi: 10.1128/JB.01528-09. Epub 2010 Mar 16. J Bacteriol. 2010. PMID: 20233934 Free PMC article.
Programmable cells: interfacing natural and engineered gene networks.
Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR, Collins JJ. Kobayashi H, et al. Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8414-9. doi: 10.1073/pnas.0402940101. Epub 2004 May 24. Proc Natl Acad Sci U S A. 2004. PMID: 15159530 Free PMC article.
On the choice and number of microarrays for transcriptional regulatory network inference.
Cosgrove EJ, Gardner TS, Kolaczyk ED. Cosgrove EJ, et al. Among authors: gardner ts. BMC Bioinformatics. 2010 Sep 9;11:454. doi: 10.1186/1471-2105-11-454. BMC Bioinformatics. 2010. PMID: 20825684 Free PMC article.
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata.
Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, Gardner TS. Faith JJ, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D866-70. doi: 10.1093/nar/gkm815. Epub 2007 Oct 11. Nucleic Acids Res. 2008. PMID: 17932051 Free PMC article.
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.
Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Faith JJ, et al. PLoS Biol. 2007 Jan;5(1):e8. doi: 10.1371/journal.pbio.0050008. PLoS Biol. 2007. PMID: 17214507 Free PMC article.
Size matters: network inference tackles the genome scale.
Hayete B, Gardner TS, Collins JJ. Hayete B, et al. Mol Syst Biol. 2007;3:77. doi: 10.1038/msb4100118. Epub 2007 Feb 13. Mol Syst Biol. 2007. PMID: 17299414 Free PMC article. No abstract available.
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia.
Cosgrove EJ, Zhou Y, Gardner TS, Kolaczyk ED. Cosgrove EJ, et al. Bioinformatics. 2008 Nov 1;24(21):2482-90. doi: 10.1093/bioinformatics/btn476. Epub 2008 Sep 8. Bioinformatics. 2008. PMID: 18779235 Free PMC article.
Algorithm scripts are available at the Gardner Lab website (http://gardnerlab.bu.edu/SSEMLasso)....
Algorithm scripts are available at the Gardner Lab website (http://gardnerlab.bu.edu/SSEMLasso)....
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