Publication Date

2019
- A rapid methods development workflow for high-throughput quantitative proteomic applications
  Chen Y, Vu J, Thompson MG, Sharpless WA, Chan LJG, Gin JW, et al. (2019) A rapid methods development workflow for high-throughput quantitative proteomic applications. PLoS ONE 14(2): e0211582. https://doi.org/10.1371/journal.pone.0211582
  Chris Petzold
- Sensor-enabled alleviation of product inhibition in chorismate pyruvate-lyase
  Chen Y, Vu J, Thompson MG, Sharpless WA, Chan LJG, Gin JW, et al. (2019) A rapid methods development workflow for high-throughput quantitative proteomic applications. PLoS ONE 14(2): e0211582. https://doi.org/10.1371/journal.pone.0211582
  Taraka Dale
- Building a global alliance of biofoundries
  Nathan Hillson, Mark Caddick, Yizhi Cai, Jose A. Carrasco, Matthew Wook Chang, Natalie C. Curach, David J. Bell, Rosalind Le Feuvre, Douglas C. Friedman, Xiongfei Fu, Nicholas D. Gold, Markus J. Herrgård, Maciej B. Holowko, James R. Johnson, Richard A. Johnson, Jay D. Keasling, Richard I. Kitney, Akihiko Kondo, Chenli Liu, Vincent J. J. Martin, Filippo Menolascina, Chiaki Ogino, Nicola J. Patron, Marilene Pavan, Chueh Loo Poh, Isak S. Pretorius, Susan J. Rosser, Nigel S. Scrutton, Marko Storch, Hille Tekotte, Evelyn Travnik, Claudia E. Vickers, Wen Shan Yew, Yingjin Yuan, Huimin Zhao & Paul S. Freemont. (2019) "Building a global alliance of biofoundries". Nature Communications, 10:2040
  Nathan Hillson
- Innovative Chemicals and Materials from Bacterial Aromatic Catabolic Pathways
  Christopher W.Johnson, Davinia Salvachúa, Nicholas A. Rorrer, Brenna A. Black, Derek R. Vardon, Peter C. St. John, Nicholas S. Cleveland, Graham Dominick, Joshua R. Elmore, Nicholas Grundl, Payal Khanna, Chelsea R. Martinez, William E. Michener, Darren J. Peterson, Kelsey J. Ramirez, Priyanka Singh, Todd A. VanderWall, A. Nolan Wilson, Gregg T. Beckham (2019) "Innovative Chemicals and Materials from Bacterial Aromatic Catabolic Pathways." Joule (available online 20 May 2019) https://doi.org/10.1016/j.joule.2019.05.011
  Gregg T. Beckham
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2018
- Parallel Integration and Chromosomal Expansion of Metabolic Pathways
  Goyal G, Costello Z, Guitierrez JA, Kang A, Lee TS, Garcia Martin H, Hillson NJ. Parallel Integration and Chromosomal Expansion of Metabolic Pathways. ACS Synth Biol. 2018 Oct 23. doi: 10.1021/acssynbio.8b00243. [Epub ahead of print] PubMed PMID: 30351913.
  Nathan Hillson
- Isolation and characterization of novel mutations in the pSC101 origin that increase copy number
  Thompson MG, Sedaghatian N, Barajas JF, Wehrs M, Bailey CB, Kaplan N, Hillson NJ, Mukhopadhyay A, Keasling JD. Isolation and characterization of novel mutations in the pSC101 origin that increase copy number. Sci Rep. 2018 Jan 25;8(1):1590. doi: 10.1038/s41598-018-20016-w. PubMed PMID: 29371642; PubMed Central PMCID: PMC5785507.
  Nathan Hillson
- Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B(2) Biosynthesis
  Barajas JF, Zargar A, Pang B, Benites VT, Gin J, Baidoo EEK, Petzold CJ, Hillson NJ, Keasling JD. Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B(2) Biosynthesis. Chembiochem. 2018 Jul 4;19(13):1391-1395. doi: 10.1002/cbic.201800169. Epub 2018 May 14. PubMed PMID: 29603548.
  Nathan Hillson
- Constraining Genome-Scale Models to Represent the Bow Tie Structure of Metabolism for (13)C Metabolic Flux Analysis.
  Backman TWH, Ando D, Singh J, Keasling JD, García Martín H. Constraining Genome-Scale Models to Represent the Bow Tie Structure of Metabolism for (13)C Metabolic Flux Analysis. Metabolites. 2018 Jan 4;8(1). pii: E3. doi: 10.3390/metabo8010003. PubMed PMID: 29300340; PubMed Central PMCID: PMC5875993.
- ClusterCAD: a computational platform for type I modular polyketide synthase design
  Eng CH, Backman TWH, Bailey CB, Magnan C, García Martín H, Katz L, Baldi P, Keasling JD. ClusterCAD: a computational platform for type I modular polyketide synthase design. Nucleic Acids Res. 2018 Jan 4;46(D1):D509-D515. doi: 10.1093/nar/gkx893. PubMed PMID: 29040649; PubMed Central PMCID: PMC5753242.
- Membrane permeability of terpenoids explored with molecular simulation
  Josh V. Vermaas, Gayle J. Bentley, Gregg T. Beckham*, Michael F. Crowley*, “Membrane permeability of terpenoids explored with molecular simulation”, in press at J. Phys. Chem. B.
  Gregg T. Beckham
- A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution
  Ramesh Jha Kumar*, Jeremy Bingen, Christopher W. Johnson, Theresa Kern, Payal Khanna, Daniel Trettel, Charlie Strauss, Gregg T. Beckham, Taraka Dale*, “A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution”, Met. Eng. Comm. (2018) 6, 33-38.
  Taraka Dale
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2017
- Metabolic engineering of Actinobacillus succinogenes provides insights into succinic acid biosynthesis
  Michael T. Guarnieri, Yat-Chen C. Chou, Davinia Salvachua, Ali Mohagheghi, Peter St. John, Yannick J. Bomble, Gregg T. Beckham, “Metabolic engineering of Actinobacillus succinogenes provides insights into succinic acid biosynthesis”, Appl. Env. Microbiol., 2017.
  Gregg T. Beckham
- Eliminating a global regulator of carbon catabolite repression enhances the conversion of aromatic lignin monomers to muconate in Pseudomonas putida KT2440
  Christopher W. Johnson, Payal Khanna, Jeffrey G. Linger, Gregg T. Beckham, “Eliminating a global regulator of carbon catabolite repression enhances the conversion of aromatic lignin monomers to muconate in Pseudomonas putida KT2440”, Metabolic Eng. Comm., 2017.
  Gregg T. Beckham
- Cellulosic ethanol: status and innovation
  Lynd, L. R., Liang, X., Biddy, M. J., et al. “Cellulosic ethanol: status and innovation.” Current Opinion in Biotechnology 45 (2017): 202-211.
  Mary J. Biddy
- Heterologous Gene Expression of N-Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N-terminus of Modular Polyketide Synthase
  Yuzawa S, Bailey CB, Fujii T, Jocic R, Barajas JF, Benites VT, Baidoo EEK, Chen Y, Petzold CJ, Katz L, Keasling JD. Heterologous Gene Expression of N-Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N-terminus of Modular Polyketide Synthase. ACS Chem Biol. 2017 Nov 17;12(11):2725-2729. doi: 10.1021/acschembio.7b00714. Epub 2017 Oct 17. PubMed PMID: 29028314.
- The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization
  Morrell WC, Birkel GW, Forrer M, Lopez T, Backman TWH, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso-Gutierrez J, George KW, Mukhopadhyay A, Vaino I, Keasling JD, Adams PD, Hillson NJ, Garcia Martin H. The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization. ACS Synth Biol. 2017 Dec 15;6(12):2248-2259. doi: 10.1021/acssynbio.7b00204. Epub 2017 Sep 8. PubMed PMID: 28826210.
  Nathan Hillson
- Engineered polyketides: Synergy between protein and host level engineering
  Barajas JF, Blake-Hedges JM, Bailey CB, Curran S, Keasling JD. Engineered polyketides: Synergy between protein and host level engineering. Synth Syst Biotechnol. 2017 Sep 7;2(3):147-166. doi: 10.1016/j.synbio.2017.08.005. eCollection 2017 Sep. Review. PubMed PMID: 29318196; PubMed Central PMCID: PMC5655351.
- Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism
  Shymansky CM, Wang G, Baidoo EEK, Gin J, Apel AR, Mukhopadhyay A, García Martín H, Keasling JD. Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism. Front Bioeng Biotechnol. 2017 May 24;5:31. doi: 10.3389/fbioe.2017.00031. eCollection 2017. PubMed PMID: 28596955; PubMed Central PMCID: PMC5443151.
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2016
- Opportunities and challenges in biological lignin valorization
  Gregg T. Beckham, Christopher W. Johnson, Eric M. Karp, Davinia Salvachúa, Derek R. Vardon, “Opportunities and challenges in biological lignin valorization”, Curr. Opin. Biotech., 2016.
  Gregg T. Beckham
- Chemicals from biomass: A market assessment of bioproducts with near-term potential
  Biddy, M. J., C. Scarlata, and C. Kinchin,; “Chemicals from biomass: A market assessment of bioproducts with near-term potential” , NREL Report No. TP-5100-65509 (2016).
  Mary J. Biddy
- The techno-economic basis for coproduct manufacturing to enable hydrocarbon fuel production from lignocellulosic biomass
  Biddy, M. J., et al. “The techno-economic basis for coproduct manufacturing to enable hydrocarbon fuel production from lignocellulosic biomass.” ACS Sustainable Chemistry & Engineering 4.6 (2016): 3196-3211.
  Mary J. Biddy
- Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae
  Wu W, Tran W, Taatjes CA, Alonso-Gutierrez J, Lee TS, Gladden JM (2016) Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae. PLoS ONE 11(2): e0146983. doi:10.1371/journal.pone.0146983.
  John Gladden
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2015
- Tunable riboregulator switches for post-transcriptional control of gene expression
  Malathy Krishnamurthy, Scott P. Hennelly, Taraka Dale, Shawn R. Starkenburg, Ricardo Marti-Arbona, David T. Fox, Scott N. Twary, Karissa Y. Sanbonmatsu, Clifford J. Unkefer, “Tunable riboregulator switches for post-transcriptional control of gene expression”, ACS Synthetic Biology, 2015.
  Taraka Dale