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Synthetic Biology

Lu TK and Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences USA published June 25, 2007, 10.1073/pnas.0704624104

Balazsi G and Collins JJ. Taking the inventory inside single cells. Nat Chem Biol 3(3): 141-2 (2007).

Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, and Collins JJ. Phenotypic consequences of promoter-mediated transcriptional noise. Molecular Cell 24: 853-865 (2006).

Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R. Engineering life: building a FAB for biology. Scientific American 294: 44-51 (2006). [pdf file]

Isaacs FJ, Dwyer DJ and Collins JJ. RNA synthetic biology. Nature Biotechnology 24: 545-554 (2006). [pdf file]

Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC and Collins JJ. A bottom-up approach to gene regulation. Nature 439: 856-860 (2006). [pdf file]

Blake WJ and Collins JJ. And the noise played on: stochastic gene expression and HIV-1 infection. Cell 122: 147-155 (2005). [pdf file]

Kaern M, Elston TC, Blake WJ, and Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6: 451-464 (2005). [pdf file]

Isaacs FJ, Blake WJ and Collins JJ. Signal processing in single cells. Science 307: 1886-1888 (2005). [pdf file]

Isaacs FJ and Collins JJ. Plug-and-play with RNA. Nature Biotechnology 23: 306-307 (2005). [pdf file]

Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR and Collins JJ. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology 22: 841-847 (2004). [pdf file]

Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR and Collins JJ. Programmable cells: Interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences USA 101: 8414-8419 (2004). [pdf file]

Mason J, Linsay P, Collins JJ and Glass L. Evolving complex dynamics in electronic models of genetic networks. Chaos 14: 707-715 (2004). [pdf file]

Isaacs FJ, Hasty J, Cantor CR and Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proceedings of the National Academy of Sciences USA 100: 7714-7719 (2003). [pdf file]

Blake WJ, Kaern M, Cantor CR and Collins JJ. Noise in eukaryotic gene expression. Nature 422: 633-637 (2003). [pdf file]

Kaern M, Blake WJ and Collins JJ. The engineering of gene regulatory networks. Annual Review of Biomedical Engineering 5: 179-206 (2003). [pdf file]

Hasty J, McMillen D and Collins JJ. Engineered gene circuits. Nature 420: 224-230 (2002). [pdf file]

Hasty J, Dolnik M, Rottschafer V and Collins JJ. A synthetic gene network for entraining and amplifying cellular oscillations. Physical Review Letters 88: 148101 (2002). [pdf file]

McMillen D, Kopell N, Hasty J and Collins JJ. Synchronizing genetic relaxation oscillators with intercell signaling. Proceedings of the National Academy of Sciences USA 99: 679-684 (2002). [pdf file]

Hasty J and Collins JJ. Translating the noise. Nature Genetics 31: 13-14 (2002). [pdf file]

Hasty J, McMillen D, Isaacs F and Collins JJ. Computational studies of gene regulatory networks: In numero molecular biology. Nature Reviews Genetics 2: 268-279 (2001). [pdf file]

Hasty J, Isaacs F, Dolnik M, McMillen D and Collins JJ. Designer gene networks: Towards fundamental cellular control. CHAOS 11: 207-220 (2001). [pdf file]

Gardner TS and Collins JJ. Neutralizing noise in gene networks. Nature 405: 520-521 (2000). [pdf file]

Hasty J, Pradines J, Dolnik M and Collins JJ. Noise-based switches and amplifiers for gene expression. Proceedings of the National Academy of Sciences USA 97: 2075-2080 (2000). [pdf file]

Gardner TS, Cantor CR and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339-342 (2000). [pdf file]

Systems Biology

Dwyer DJ, Kohanski MA, Hayete B, Collins JJ. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol Syst Biol 3: 91 (2007).

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

Hayete B, Gardner TS, Collins JJ. Size matters: network inference tackles the genome scale. Mol Syst Biol 3: 77 (2007).

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 9;5(1):e8 (2007).

di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliot SJ, Schaus SE and Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology 23: 377-383 (2005). [pdf file]

Gardner TS, Shimer S and Collins JJ. Inferring microbial genetic networks. ASM News 70: 121-126 (2004). [pdf file]

Gardner TS, Bernardo D, Lorenz D and Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105 (2003). [pdf file]

Tegner J, Yeung MKS, Hasty J and Collins JJ. Reverse engineering gene networks - Integrating genetic perturbations with dynamical modeling. Proceedings of the National Academy of Sciences USA 100: 5944-5949 (2003). [pdf file]

Yeung MKS, Tegner J and Collins JJ. Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Sciences USA 99: 6163-6168 (2002). [pdf file]

Hasty J and Collins JJ. Protein interactions: unspinning the web. Nature 411: 30-31 (2001). [pdf file]