The work of SBI researchers has been widely published in leading scientific journals. Here is a list of synthetic biology articles -- appearing in the past three months -- of which one or more members of the SBI faculty were authors. The citations are listed by Institute member with links to abstracts or open-access full articles, when available:
J. Christopher Anderson:
Leguia M, Brophy J, Densmore D, Anderson JC. Automated assembly of standard biological parts.
Methods Enzymol. 2011;498:363-97 (abstract).
Xia B, Bhatia S, Bubenheim B, Dadgar M, Densmore D, Anderson JC. Developer's and user's guide to Clotho v2.0 A software platform for the creation of synthetic biological systems.
Methods Enzymol. 2011;498:97-135 (abstract).
Bates JT, Chivian D, Arkin AP. GLAMM: Genome-Linked Application for Metabolic Maps.
Nucleic Acids Res. 2011 Jul;39 Suppl 2:W400-5. Epub 2011 May 29 (full article).
Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP. Versatile RNA-sensing transcriptional regulators for engineering genetic networks.Proc Natl Acad Sci U S A. 2011 May 24;108(21):8617-22. Epub 2011 May 9 (full article).
Adam Arkin and Jennifer A. Doudna:
Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure.
Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11069-74. Epub 2011 Jun 3 (full article).
Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11063-8. Epub 2011 Jun 3 (full article).
Harvey Blanch and Douglas Clark:
Graham JE, Clark ME, Nadler DC, Huffer S, Chokhawala HA, Rowland SE, Blanch HW, Clark DS, Robb FT. Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment.Nat Commun. 2011 Jul 5;2:375 (abstract).
Levine SE, Fox JM, Clark DS, Blanch HW. A mechanistic model for rational design of optimal cellulase mixtures.Biotechnol Bioeng. 2011 Jun 23 (Epub ahead of print) (abstract).
Trinh CT, Li J, Blanch HW, Clark DS. Redesigning Escherichia coli Metabolism for Anaerobic Production of Isobutanol. Appl Environ Microbiol. 2011 Jul;77(14):4894-904. Epub 2011 Jun 3 (abstract).
Galazka JM, Cate JH. A new diet for yeast to improve biofuel production. Bioeng Bugs. 2011 Jul 1;2(4). (Epub ahead of print) (abstract)
Brown ME, Walker MC, Nakashige TG, Iavarone AT, Chang MC. Discovery and Characterization of Heme Enzymes from Unsequenced Bacteria: Application to Microbial Lignin Degradation. J Am Chem Soc. 2011 Jun 14. (Epub ahead of print) (abstract)
Weeks AM, Chang MC. Constructing de Novo Biosynthetic Pathways for Chemical Synthesis inside Living Cells. Biochemistry. 2011 Jun 21;50(24):5404-18. Epub 2011 May 26 (abstract).
Jennifer A. Doudna:
Sashital DG, Jinek M, Doudna JA. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct Mol Biol. 2011 Jun;18(6):680-7. Epub 2011 May 15 (abstract)
Whitaker WR, Dueber JE. Metabolic pathway flux enhancement by synthetic protein scaffolding. Methods Enzymol. 2011;497:447-68 (abstract).
Richmond DL, Schmid EM, Martens S, Stachowiak JC, Liska N, Fletcher DA. Forming giant vesicles with controlled membrane composition, asymmetry, and contents. Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9431-6. Epub 2011 May 18 (abstract).
Beller HR, Goh EB, Keasling JD. Definitive alkene identification needed for in vitro studies with ole (olefin biosynthesis) proteins. (Letter to the editor) J Biol Chem. 2011 Jul 1;286(26):le11.
Zhang F, Keasling J. Biosensors and their applications in microbial metabolic engineering. Trends Microbiol. 2011 Jul;19(7):323-9. Epub 2011 Jun 12 (abstract).
Zhang F, Rodriguez S, Keasling JD. Metabolic engineering of microbial pathways for advanced biofuels production. Curr Opin Biotechnol. 2011 May 25. (Epub ahead of print) (abstract).