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Reverse-engineering transcription control networks.
Gardner TS, Faith JJ. Gardner TS, et al. Phys Life Rev. 2005 Mar;2(1):65-88. doi: 10.1016/j.plrev.2005.01.001. Phys Life Rev. 2005. PMID: 20416858
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. Among authors: gardner ts. 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.
Inferring genetic networks and identifying compound mode of action via expression profiling.
Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Gardner TS, et al. Science. 2003 Jul 4;301(5629):102-5. doi: 10.1126/science.1081900. Science. 2003. PMID: 12843395
A theory for controlling cell cycle dynamics using a reversibly binding inhibitor.
Gardner TS, Dolnik M, Collins JJ. Gardner TS, et al. Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14190-5. doi: 10.1073/pnas.95.24.14190. Proc Natl Acad Sci U S A. 1998. PMID: 9826676 Free PMC article.
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. Among authors: gardner ts. 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)....
The mode-of-action by network identification (MNI) algorithm: a network biology approach for molecular target identification.
Xing H, Gardner TS. Xing H, et al. Among authors: gardner ts. Nat Protoc. 2006;1(6):2551-4. doi: 10.1038/nprot.2006.300. Nat Protoc. 2006. PMID: 17406508
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.
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. Among authors: gardner ts. 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.
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.
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
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