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For: Kennedy CJ, Boyle PM, Waks Z, Silver PA. Systems-level engineering of nonfermentative metabolism in yeast. Genetics 2009;183:385-97. [PMID: 19564482 PMCID: PMC2746161 DOI: 10.1534/genetics.109.105254] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 06/19/2009] [Indexed: 01/30/2023]  Open
Number Cited by Other Article(s)
1
Zou G, Xiao M, Chai S, Zhu Z, Wang Y, Zhou Z. Efficient genome editing in filamentous fungi via an improved CRISPR-Cas9 ribonucleoprotein method facilitated by chemical reagents. Microb Biotechnol 2021;14:2343-2355. [PMID: 32841542 PMCID: PMC8601184 DOI: 10.1111/1751-7915.13652] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022]  Open
2
Myers KS, Riley NM, MacGilvray ME, Sato TK, McGee M, Heilberger J, Coon JJ, Gasch AP. Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. PLoS Genet 2019;15:e1008037. [PMID: 30856163 PMCID: PMC6428351 DOI: 10.1371/journal.pgen.1008037] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/21/2019] [Accepted: 02/20/2019] [Indexed: 01/08/2023]  Open
3
Development of Synthetic Microbial Platforms to Convert Lignocellulosic Biomass to Biofuels. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2016.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
4
Sánchez BJ, Nielsen J. Genome scale models of yeast: towards standardized evaluation and consistent omic integration. Integr Biol (Camb) 2016;7:846-58. [PMID: 26079294 DOI: 10.1039/c5ib00083a] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
5
Ates O. Systems Biology of Microbial Exopolysaccharides Production. Front Bioeng Biotechnol 2015;3:200. [PMID: 26734603 PMCID: PMC4683990 DOI: 10.3389/fbioe.2015.00200] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/30/2015] [Indexed: 11/23/2022]  Open
6
Heavner BD, Price ND. Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. PLoS Comput Biol 2015;11:e1004530. [PMID: 26566239 PMCID: PMC4643975 DOI: 10.1371/journal.pcbi.1004530] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 08/28/2015] [Indexed: 11/18/2022]  Open
7
Li Y, Tian P. Contemplating 3-Hydroxypropionic Acid Biosynthesis in Klebsiella pneumoniae. Indian J Microbiol 2015;55:131-9. [PMID: 25805899 DOI: 10.1007/s12088-015-0513-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/09/2015] [Indexed: 11/30/2022]  Open
8
Sandström AG, Almqvist H, Portugal-Nunes D, Neves D, Lidén G, Gorwa-Grauslund MF. Saccharomyces cerevisiae: a potential host for carboxylic acid production from lignocellulosic feedstock? Appl Microbiol Biotechnol 2014;98:7299-318. [DOI: 10.1007/s00253-014-5866-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 10/25/2022]
9
Crook N, Alper HS. Model-based design of synthetic, biological systems. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2012.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
10
Kondo A, Ishii J, Hara KY, Hasunuma T, Matsuda F. Development of microbial cell factories for bio-refinery through synthetic bioengineering. J Biotechnol 2013;163:204-16. [DOI: 10.1016/j.jbiotec.2012.05.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/10/2012] [Accepted: 05/18/2012] [Indexed: 12/24/2022]
11
Xu C, Liu L, Zhang Z, Jin D, Qiu J, Chen M. Genome-scale metabolic model in guiding metabolic engineering of microbial improvement. Appl Microbiol Biotechnol 2012. [DOI: 10.1007/s00253-012-4543-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
12
Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases. Proc Natl Acad Sci U S A 2012;109:19504-9. [PMID: 23129650 DOI: 10.1073/pnas.1212287109] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
13
A BioBrick compatible strategy for genetic modification of plants. J Biol Eng 2012;6:8. [PMID: 22716313 PMCID: PMC3537565 DOI: 10.1186/1754-1611-6-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 06/06/2012] [Indexed: 11/10/2022]  Open
14
Dueñas-Sánchez R, Gutiérrez G, Rincón AM, Codón AC, Benítez T. Transcriptional regulation of fermentative and respiratory metabolism in Saccharomyces cerevisiae industrial bakers' strains. FEMS Yeast Res 2012;12:625-36. [PMID: 22591337 DOI: 10.1111/j.1567-1364.2012.00813.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/06/2012] [Indexed: 11/30/2022]  Open
15
Ng CY, Jung MY, Lee J, Oh MK. Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering. Microb Cell Fact 2012;11:68. [PMID: 22640729 PMCID: PMC3442981 DOI: 10.1186/1475-2859-11-68] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 05/04/2012] [Indexed: 12/24/2022]  Open
16
Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 2012;10:291-305. [PMID: 22367118 DOI: 10.1038/nrmicro2737] [Citation(s) in RCA: 537] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
17
Kim IK, Roldão A, Siewers V, Nielsen J. A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 2012;12:228-48. [DOI: 10.1111/j.1567-1364.2011.00779.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 12/01/2022]  Open
18
Soh KC, Miskovic L, Hatzimanikatis V. From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks. FEMS Yeast Res 2011;12:129-43. [DOI: 10.1111/j.1567-1364.2011.00771.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/18/2011] [Accepted: 11/19/2011] [Indexed: 01/05/2023]  Open
19
Boyle PM, Silver PA. Parts plus pipes: synthetic biology approaches to metabolic engineering. Metab Eng 2011;14:223-32. [PMID: 22037345 DOI: 10.1016/j.ymben.2011.10.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 10/05/2011] [Accepted: 10/16/2011] [Indexed: 11/24/2022]
20
Agapakis CM, Silver PA. Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway. Bioeng Bugs 2011;1:413-8. [PMID: 21468209 DOI: 10.4161/bbug.1.6.12462] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 05/24/2010] [Accepted: 05/26/2010] [Indexed: 11/19/2022]  Open
21
Matsuda F, Furusawa C, Kondo T, Ishii J, Shimizu H, Kondo A. Engineering strategy of yeast metabolism for higher alcohol production. Microb Cell Fact 2011;10:70. [PMID: 21902829 PMCID: PMC3184262 DOI: 10.1186/1475-2859-10-70] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Accepted: 09/08/2011] [Indexed: 01/27/2023]  Open
22
Varman AM, Xiao Y, Leonard E, Tang YJ. Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae. Microb Cell Fact 2011;10:45. [PMID: 21689458 PMCID: PMC3145561 DOI: 10.1186/1475-2859-10-45] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 06/21/2011] [Indexed: 11/16/2022]  Open
23
Ducat DC, Way JC, Silver PA. Engineering cyanobacteria to generate high-value products. Trends Biotechnol 2011;29:95-103. [DOI: 10.1016/j.tibtech.2010.12.003] [Citation(s) in RCA: 310] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 12/06/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
24
Hasunuma T, Sung KM, Sanda T, Yoshimura K, Matsuda F, Kondo A. Efficient fermentation of xylose to ethanol at high formic acid concentrations by metabolically engineered Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2011;90:997-1004. [DOI: 10.1007/s00253-011-3085-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/17/2010] [Accepted: 12/22/2010] [Indexed: 01/10/2023]
25
Liu H, Gravelat FN, Chiang LY, Chen D, Vanier G, Ejzykowicz DE, Ibrahim AS, Nierman WC, Sheppard DC, Filler SG. Aspergillus fumigatus AcuM regulates both iron acquisition and gluconeogenesis. Mol Microbiol 2010;78:1038-54. [PMID: 21062375 DOI: 10.1111/j.1365-2958.2010.07389.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
26
Redox biocatalysis and metabolism: molecular mechanisms and metabolic network analysis. Antioxid Redox Signal 2010;13:349-94. [PMID: 20059399 DOI: 10.1089/ars.2009.2931] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
27
Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]  Open
28
Boyle PM, Silver PA. Harnessing nature's toolbox: regulatory elements for synthetic biology. J R Soc Interface 2009;6 Suppl 4:S535-46. [PMID: 19324675 DOI: 10.1098/rsif.2008.0521.focus] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
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