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Gardner TS, di Bernardo D, Lorenz D, Collins JJ. “Inferring genetic networks and identifying compound mode of action via expression profiling”, Science 2003; 301:102-5.

Di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliott SJ, Schaus SE, Collins JJ, “Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks”, Nat. Biotechnol., 2005; 23:377-83.

Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS, “Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles”, PLoS Biol. 2007; 5:54-66.

Lu TK & Collins JJ, “Dispersing Biofilms with Engineered Enzymatic Bacteriophage”, PNAS 2007;104:11197-11202.

Ergun, A, Lawrence CA, Kohanski MA, Brennan TA, Collins JJ, “A network biology approach to prostate cancer”, Mol. Syst. Biol. 2007; 3:82.

Allison KR, Brynildsen MP, Collins JJ, “Metabolite-enabled eradication of bacterial persisters by aminoglycosides”, Nature 2011; 473:216-20.

Allison KR, Brynildsen MP, Collins JJ, “Heterogeneous bacterial persisters and engineering approaches to eliminate them”, Curr. Opin. Microbiol. 2011; 14:593-8.

Kwong LN, Costello JC, Liu H, Jiang S, Helms TL, Langsdorf AE, Jakubosky D, Genovese G, Muller FL, Jeong JH, Bender RP, Chu GC, Flaherty KT, Wargo JA, Collins JJ, Chin L, “Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma”, Nat. Med. 2012; 18:1503-10.

D Ewen Cameron & James J Collins, “Tunable protein degradation in bacteria”Nature Biotechnology (2014) doi:10.1038/nbt.3053