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| <h1><center>Publications</center></h1> | | <font face="trebuchet ms" size="+1" style="color:#000000">Our website has moved to its new [http://smolkelab.stanford.edu location]. |
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| __TOC__
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| ==Refereed Publications== | |
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| # Chang AL, McKeague M, Liang JC, Smolke CD. 2014. Kinetic and equilibrium binding characterization of aptamers to small molecules using a label-free, sensitive, and scalable platform. Analytical Chemistry. DOI: 10.1021/ac5001527. [http://pubs.acs.org/doi/abs/10.1021/ac5001527 link]
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| # Galloway KE, Franco E, Smolke CD. 2013. Dynamically reshaping signaling networks to program cell fate via genetic controllers. Science. DOI: 10.1126/science.1235005. [http://www.sciencemag.org/content/341/6152/1235005 link] | |
| # Galanie S, Siddiqui MS, Smolke CD. 2013. Molecular tools for chemical biotechnology. Curr. Opin. Biotechnol. DOI: 10.1016/j.copbio.2013.03.001. [http://www.sciencedirect.com/science/article/pii/S0958166913000554 link]
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| # Wang YH, Wei KY, Smolke CD. 2013. Synthetic Biology: Advancing the design of diverse genetic systems. Annu. Rev. Chem. Biomol. Eng. DOI: 10.1146/annurev-chembioeng-061312-103351. [http://www.annualreviews.org/doi/abs/10.1146/annurev-chembioeng-061312-103351 link]
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| # Wei KY, Chen YY, Smolke CD. 2013. A yeast-based rapid prototype platform for gene-control elements in mammalian cells. Biotechnol. Bioeng. DOI: 10.1002/bit.24792. [http://onlinelibrary.wiley.com/doi/10.1002/bit.24792/full link]
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| # Kennedy AB, Liang JC, Smolke CD. 2012. A versatile cis-blocking and trans-activation strategy for ribozyme characterization. Nuc. Acids Res. DOI: 10.1093/nar/gks1036 [http://nar.oxfordjournals.org/content/early/2012/11/15/nar.gks1036.long link]
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| # Michener JK, Nielsen J, Smolke CD. 2012. Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases. Proc. Natl. Acad. Sci. USA. DOI: 10.1073/pnas.1212287109 [http://www.pnas.org/content/109/47/19504.long link]
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| # Liang JC, Chang AL, Kennedy AB, Smolke CD. 2012. A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity. Nuc. Acids Res. 40: e154. [http://nar.oxfordjournals.org/content/40/20/e154.full link]
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| # Michener JK, Smolke CD. 2012. High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab. Eng. 14: 306-16. [http://www.sciencedirect.com/science/article/pii/S109671761200047X link]
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| # Chen YY, Galloway KE, Smolke CD. 2012. Synthetic biology: advancing biological frontiers by building synthetic systems. Genome Biol. 13: 240. [http://genomebiology.com/2012/13/2/240/ link]
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| # Chang AL, Wolf JJ, Smolke CD. 2012. Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr. Opin. Biotechnol. 23: 679-88. [http://www.sciencedirect.com/science/article/pii/S0958166912000171 link]
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| # Siddiqui MS, Thodey K, Trenchard I, Smolke CD. 2012. Advancing secondary metabolite biosynthesis in yeast with synthetic biology tools. FEMS Yeast Research. 12: 144-70. [http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2011.00774.x/full link]
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| # Chen YY, Smolke CD. 2011. From DNA to targeted therapeutics: bringing synthetic biology to the clinic. Sci. Transl. Med. 3: 106ps42. [http://stm.sciencemag.org/content/3/106/106ps42.full link]
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| # Michener JK, Thodey K, Liang JC, Smolke CD. 2012. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab. Eng. 14: 212-22. [http://www.sciencedirect.com/science/article/pii/S1096717611000942 link]
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| # Liang JC, Bloom RJ, Smolke CD. 2011. Engineering biological systems with synthetic RNA molecules. Mol. Cell. 43: 915-26. [http://www.sciencedirect.com/science/article/pii/S1097276511006447 link]
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| # Babiskin AH, Smolke CD. 2011. Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity. Nuc. Acids Res. 39: 8651-64. [http://nar.oxfordjournals.org/content/39/19/8651.long link]
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| # Smolke CD, Silver PA. 2011. Informing biological design by integration of systems and synthetic biology. Cell. 144: 855-9. [http://www.sciencedirect.com/science/article/pii/S0092867411001723 link]
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| # Babiskin AH, Smolke CD. 2011. Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules. Nuc. Acids Res. 39: 5299-311. [http://nar.oxfordjournals.org/content/early/2011/02/25/nar.gkr090.full link]
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| # Babiskin AH, Smolke CD. 2011. A synthetic library of RNA control modules for predictable tuning of gene expression in yeast. Mol. Sys. Biol. 7:471. [http://www.nature.com/msb/journal/v7/n1/full/msb20114.html link]
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| # Beisel CL, Chen YY, Culler SJ, Hoff KG, Smolke CD. 2010. Design of small molecule-responsive miRNAs based on structural requirements for Drosha processing. Nuc. Acids Res. 39: 2981-94. [http://nar.oxfordjournals.org/content/early/2010/12/11/nar.gkq954.full link]
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| # Culler SJ, Hoff KG, Smolke CD. 2010. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science. 330: 1251-5. Perspective: Cell biology. The case for RNA. 330: 1185-6. [http://www.sciencemag.org/content/330/6008/1251.full link]
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| # Chen YY, Jensen MC, Smolke CD. 2010. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc. Natl. Acad. Sci. USA. 107: 8531-6. [http://www.pnas.org/content/early/2010/04/23/1001721107.abstract link]
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| # Culler SJ, Hoff KG, Voelker RB, Berglund JA, Smolke CD. 2010. Feature Article: Functional selection and systematic analysis of intronic splicing elements identifies active sequence motifs and associated splicing factors. Nuc. Acids Res. 38: 5152-65. [http://nar.oxfordjournals.org/content/38/15/5152.full link]
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| # Hoff KG, Culler SJ, Nguyen PQ, McGuire RM, Silberg JJ, Smolke CD. 2009. In vivo fluorescent detection of Fe-S clusters coordinated by human GRX2. Chem. Biol. 16: 1299-308. Commentary: Lights on iron-sulfur clusters. 16: 1213-4. [http://www.sciencedirect.com/science/article/pii/S1074552109004025 link]
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| # Beisel CL, Smolke CD. 2009. Design principles for riboswitch function. PLoS Comp. Biol. 5: e1000363. [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 link]
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| # Win MN, Liang JC, Smolke CD. 2009. Frameworks for programming biological function through RNA parts and devices. Chem. Biol. 16: 298-310. [http://www.sciencedirect.com/science/article/pii/S1074552109000775 link]
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| # Bayer TS, Hoff KG, Beisel CL, Lee JJ, Smolke CD. 2009. Synthetic control of a fitness tradeoff in yeast nitrogen metabolism. J. Biol. Eng. 3: 1. [http://www.jbioleng.org/content/3/1/1 link]
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| # Hoff KG, Goodlitt R, Li R, Smolke CD, Silberg JJ. 2009. Fluorescence detection of a protein-bound 2Fe2S cluster. Chembiochem. 10: 667-70. [http://onlinelibrary.wiley.com/doi/10.1002/cbic.200800747/full link]
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| # Beisel CL, Bayer TS, Hoff KG, Smolke CD. 2008. Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol. Sys. Biol. 4: 224. News and Views: Small hairpin RNA as a small molecule sensor. 4: 227. [http://www.nature.com/msb/journal/v4/n1/full/msb200862.html link]
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| # Hawkins KM, Smolke CD. 2008. Cover article: Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae. Nat. Chem. Biol. 4: 564-73. News and Views: From yeast to alkaloids. 4: 524-5. [http://www.nature.com/nchembio/journal/v4/n9/full/nchembio.105.html link]
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| # Win MN, Smolke CD. 2008. Higher-order cellular information processing with synthetic RNA devices. Science. 322: 456-60. Perspective: Cell biology. RNA computing in a living cell. 322: 387-8. (Additional detail on data processing and raw data is provided [[Media:Fulldata.pdf|here]] and as an E-letter attached to this article.) [http://www.sciencemag.org/content/322/5900/456.full link]
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| # Win MN, Smolke CD. 2007. From the cover: A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc. Natl. Acad. Sci. USA. 104: 14283-8. Commentary: Targeted cleavage: tuneable cis-cleaving ribozymes. 104: 14881-2. Erratum: Proc. Natl. Acad. Sci. USA. 2009. 106: 15514. (An early online correction was published [http://hdl.handle.net/1721.1/45668 here].) [http://www.pnas.org/content/104/36/14283.abstract link]
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| # Win MN, Klein JS, Smolke CD. 2006. Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay. Nuc. Acids Res. 34: 5670-82. [http://nar.oxfordjournals.org/content/34/19/5670.long link]
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| # Pfleger BF, Pitera DJ, Smolke CD, Keasling JD. 2006. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotech. 24: 1027-32. [http://www.nature.com/nbt/journal/v24/n8/full/nbt1226.html link]
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| # Hawkins KM, Smolke CD. 2006. The regulatory roles of the galactose permease and kinase in the induction response of the GAL network in Saccharomyces cerevisiae. J. Biol. Chem. 281: 13485-92. [http://www.jbc.org/content/281/19/13485.long link]
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| # Bayer TS, Smolke CD. 2005. Programmable, ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotech. 23: 337-43. News and Views: Plug and play with RNA. 23: 306-7. [http://www.nature.com/nbt/journal/v23/n3/full/nbt1069.html link]
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| # Smolke CD, Keasling JD. 2002. Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon. Biotech. Bioeng. 80: 762-76. [http://onlinelibrary.wiley.com/doi/10.1002/bit.10434/abstract link]
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| # Smolke CD, Keasling JD. 2002. Effect of copy number and mRNA processing and stabilization on transcript and protein levels from an engineered dual-gene operon. Biotech. Bioeng. 78: 412-24. [http://onlinelibrary.wiley.com/doi/10.1002/bit.10218/abstract link]
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| # Smolke CD, Khlebnikov A, Keasling JD. 2001. Effects of transcription induction homogeneity and transcript stability on expression of two genes in a constructed operon. Appl. Micro. Biotech. 57: 689-96. [http://www.springerlink.com/content/ranhuv18kx33p9qx/ link]
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| # Smolke CD, Martin VJJ, Keasling JD. 2001. Controlling the metabolic flux through the carotenoid pathway using directed mRNA processing and stabilization. Met. Eng. 3: 313-21. [http://www.sciencedirect.com/science/article/pii/S1096717601901946 link]
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| # Smolke CD, Carrier TA, Keasling JD. 2000. Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures. Appl. Environ. Microbiol. 66: 5399-405. [http://aem.asm.org/content/66/12/5399.full link]
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| ==Non-Refereed Publications==
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| # Smolke CD, Tyo KE. 2012. Synthetic biology: Emerging methodologies to catalyze the metabolic engineering design cycle. Met. Eng. [http://www.sciencedirect.com/science/article/pii/S1096717612000341 link]
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| # Thodey K, Smolke CD. 2011. Cell Biology. Bringing it together with RNA. Science. 333: 412-3. [http://www.sciencemag.org/content/333/6041/412.full link]
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| # Smolke CD. 2009. Building outside of the box: iGEM and the BioBricks Foundation. Nat. Biotech. 27:1099-102. [http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1099.html link]
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| # Smolke CD. 2009. Cell Biology. It’s the DNA that counts. Science. 324: 1156-7. [http://www.sciencemag.org/content/324/5931/1156.full link]
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| # Win MN, Smolke CD. 2007. RNA as a versatile and powerful platform for engineering genetic regulatory tools. Biotechnology and Genetic Engineering Reviews. 24: 311-46.
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| # Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R. 2006. Engineering life: building a Fab for biology. Scientific American. 294: 44-51.
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| # Martin VJJ, Smolke CD, Keasling JD. 2002. Redesigning cells for the production of complex organic molecules. ASM News. 68: 336-43. [http://newsarchive.asm.org/jul02/feature3.asp link]
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| ==Books and Book Chapters==
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| # Liang JC, Smolke CD. 2012. Rational design and tuning of ribozyme-based devices. In: Hartig J, editor. Methods in Molecular Biology. 848:439-54. [http://www.springerprotocols.com/Full/doi/10.1007/978-1-61779-545-9_27?encCode=T0lCOjcyXzktNTQ1LTk3NzE2LTEtODc5&tokenString=NgevSbxhzQ/5JDUFp0DUPg== link]
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| # Win MN, Liang JC, Smolke CD. 2010. Frameworks for programming RNA devices. In: Mayer G, editor. The Chemical Biology of Nucleic Acids. U.K.: John Wiley & Sons, Ltd. pp. 323-38. [http://onlinelibrary.wiley.com/doi/10.1002/9780470664001.ch15/summary link]
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| # Win MN, Smolke CD. 2009. Regulating gene expression through engineered RNA technologies. In: Smolke CD, editor. Handbook for Metabolic Pathway Engineering: Tools and Applications. San Diego: CRC Press.
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| # Smolke CD, Martin VJJ, Keasling JD. 2004. Tools for metabolic engineering in Escherichia coli. In: Baneyx F, editor. Protein Expression Technologies: Current Status and Future Trends. U.K.: Horizon Scientific Press.
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| ==Edited Works in Print==
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| # Smolke CD, editor. 2009. Handbook for Metabolic Pathway Engineering: Fundamentals (volume I). San Diego: CRC Press. [http://books.google.com/books/about/The_Metabolic_Pathway_Engineering_Handbo.html?id=wzAPgK1ulBQC Google Books] [http://www.amazon.com/The-Metabolic-Pathway-Engineering-Handbook/dp/1439802963 Amazon]
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| # Smolke CD, editor. 2009. Handbook for Metabolic Pathway Engineering: Tools and Applications (volume II). San Diego: CRC Press. [http://books.google.com/books/about/The_Metabolic_Pathway_Engineering_Handbo.html?id=zCqHswQYAfgC Google Books] [http://www.amazon.com/The-Metabolic-Pathway-Engineering-Handbook/dp/1420077651 Amazon]
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