Metabolic Engineering: Methodologies and Applications

Volk, Michael J.; Tran, Vinh G.; Tan, Shih-I; Mishra, Shekhar; Fatma, Zia; Boob, Aashutosh; Li, Hongxiang; Xue, Pu; Martin, Teresa A.; Zhao, Huimin

doi:10.1021/acs.chemrev.2c00403

Metabolic Engineering: Methodologies and Applications

Journal Article · Thu Dec 29 23:00:00 EST 2022 · Chemical Reviews

DOI:https://doi.org/10.1021/acs.chemrev.2c00403· OSTI ID:2420746

Volk, Michael J. ^[1]; Tran, Vinh G. ^[2]; Tan, Shih-I ^[3]; Mishra, Shekhar ^[2]; Fatma, Zia ^[4]; Boob, Aashutosh ^[2]; Li, Hongxiang ^[5]; ^[2]; Martin, Teresa A. ^[2]; ^[6]

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; OSTI
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States; Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States

Not provided.

Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: SC0018260; SC0018420

OSTI ID:: 2420746

Journal Information:: Chemical Reviews, Journal Name: Chemical Reviews Journal Issue: 9 Vol. 123; ISSN 0009-2665

Publisher:: American Chemical Society

Country of Publication:: United States

Language:: English

References (447)

A machine learning Automated Recommendation Tool for synthetic biology Radivojević, Tijana; Costello, Zak; Workman, Kenneth Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-18008-4	journal	September 2020
Expanded synthetic small regulatory RNA expression platforms for rapid and multiplex gene expression knockdown Yang, Dongsoo; Yoo, Seung Min; Gu, Changdai Metabolic Engineering, Vol. 54 https://doi.org/10.1016/j.ymben.2019.04.003	journal	July 2019
Modular enzyme assembly for enhanced cascade biocatalysis and metabolic flux Kang, Wei; Ma, Tian; Liu, Min Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12247-w	journal	September 2019
Functional Reconstitution of a Pyruvate Dehydrogenase in the Cytosol of Saccharomyces cerevisiae through Lipoylation Machinery Engineering Lian, Jiazhang; Zhao, Huimin ACS Synthetic Biology, Vol. 5, Issue 7 https://doi.org/10.1021/acssynbio.6b00019	journal	March 2016
Genome-scale promoter engineering by coselection MAGE Wang, Harris H.; Kim, Hwangbeom; Cong, Le Nature Methods, Vol. 9, Issue 6, p. 591-593 https://doi.org/10.1038/nmeth.1971	journal	April 2012
Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering Alonso-Gutierrez, Jorge; Kim, Eun-Mi; Batth, Tanveer S. Metabolic Engineering, Vol. 28 https://doi.org/10.1016/j.ymben.2014.11.011	journal	March 2015
Metabolic engineering of Escherichia coli for the production of 1,3-diaminopropane, a three carbon diamine Chae, Tong Un; Kim, Won Jun; Choi, Sol Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep13040	journal	August 2015
High-level secretion of human growth hormone by Escherichia coli Chang, Chung Nan; Key, Michael; Bochner, Barry Gene, Vol. 55, Issue 2-3 https://doi.org/10.1016/0378-1119(87)90279-4	journal	January 1987
Engineering of yeast hexose transporters to transport D-xylose without inhibition by D-glucose Farwick, A.; Bruder, S.; Schadeweg, V. Proceedings of the National Academy of Sciences, Vol. 111, Issue 14 https://doi.org/10.1073/pnas.1323464111	journal	March 2014
DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency Conrado, Robert J.; Wu, Gabriel C.; Boock, Jason T. Nucleic Acids Research, Vol. 40, Issue 4 https://doi.org/10.1093/nar/gkr888	journal	October 2011
The Gibberellin Producer Fusarium fujikuroi: Methods and Technologies in the Current Toolkit Cen, Yu-Ke; Lin, Jian-Guang; Wang, You-Liang Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.00232	journal	March 2020
Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration Ng, Chiam Yu; Farasat, Iman; Maranas, Costas D. Metabolic Engineering, Vol. 29 https://doi.org/10.1016/j.ymben.2015.03.001	journal	May 2015
Effects of metabolic pathway gene copy numbers on the biosynthesis of (2S)-naringenin in Saccharomyces cerevisiae Li, Hongbiao; Gao, Song; Zhang, Siqi Journal of Biotechnology, Vol. 325 https://doi.org/10.1016/j.jbiotec.2020.11.009	journal	January 2021
Engineering of Ralstonia eutropha H16 for Autotrophic and Heterotrophic Production of Methyl Ketones Muller, J.; MacEachran, D.; Burd, H. Applied and Environmental Microbiology, Vol. 79, Issue 14 https://doi.org/10.1128/AEM.00973-13	journal	May 2013
Machine learning methods for metabolic pathway prediction Dale, Joseph M.; Popescu, Liviu; Karp, Peter D. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-15	journal	January 2010
Evolving Small-Molecule Biosensors with Improved Performance and Reprogrammed Ligand Preference Using OrthoRep Javanpour, Alex A.; Liu, Chang C. ACS Synthetic Biology, Vol. 10, Issue 10 https://doi.org/10.1021/acssynbio.1c00316	journal	October 2021
Enhancing Tolerance to Short-Chain Alcohols by Engineering the Escherichia coli AcrB Efflux Pump to Secrete the Non-native Substrate n-Butanol Fisher, Michael A.; Boyarskiy, Sergey; Yamada, Masaki R. ACS Synthetic Biology, Vol. 3, Issue 1, p. 30-40 https://doi.org/10.1021/sb400065q	journal	September 2013
Compartmentalized Metabolic Engineering for Artemisinin Biosynthesis and Effective Malaria Treatment by Oral Delivery of Plant Cells Malhotra, Karan; Subramaniyan, Mayavan; Rawat, Khushboo Molecular Plant, Vol. 9, Issue 11 https://doi.org/10.1016/j.molp.2016.09.013	journal	November 2016
Engineering Static and Dynamic Control of Synthetic Pathways Holtz, William J.; Keasling, Jay D. Cell, Vol. 140, Issue 1 https://doi.org/10.1016/j.cell.2009.12.029	journal	January 2010
Orthogonal monoterpenoid biosynthesis in yeast constructed on an isomeric substrate Ignea, Codruta; Raadam, Morten H.; Motawia, Mohammed S. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11290-x	journal	August 2019
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism Zhang, Jie; Petersen, Søren D.; Radivojevic, Tijana Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-17910-1	journal	September 2020
Identification of novel metabolic engineering targets for S-adenosyl-L-methionine production in Saccharomyces cerevisiae via genome-scale engineering Dong, Chang; Schultz, J. Carl; Liu, Wei Metabolic Engineering, Vol. 66 https://doi.org/10.1016/j.ymben.2021.03.005	journal	July 2021
Dual regulation of cytoplasmic and mitochondrial acetyl-CoA utilization for improved isoprene production in Saccharomyces cerevisiae Lv, Xiaomei; Wang, Fan; Zhou, Pingping Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12851	journal	September 2016
Biosystems Design by Machine Learning Volk, Michael Jeffrey; Lourentzou, Ismini; Mishra, Shekhar ACS Synthetic Biology, Vol. 9, Issue 7 https://doi.org/10.1021/acssynbio.0c00129	journal	June 2020
Complete biosynthesis of noscapine and halogenated alkaloids in yeast Li, Yanran; Li, Sijin; Thodey, Kate Proceedings of the National Academy of Sciences, Vol. 115, Issue 17 https://doi.org/10.1073/pnas.1721469115	journal	April 2018
From zero to hero—Design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production Becker, Judith; Zelder, Oskar; Häfner, Stefan Metabolic Engineering, Vol. 13, Issue 2 https://doi.org/10.1016/j.ymben.2011.01.003	journal	March 2011
Programming cells by multiplex genome engineering and accelerated evolution Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A. Nature, Vol. 460, Issue 7257, p. 894-898 https://doi.org/10.1038/nature08187	journal	July 2009
Quantitative Evaluation of Intracellular Metabolite Extraction Techniques for Yeast Metabolomics Canelas, André B.; ten Pierick, Angela; Ras, Cor Analytical Chemistry, Vol. 81, Issue 17 https://doi.org/10.1021/ac900999t	journal	September 2009
A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast Gueldener, U. Nucleic Acids Research, Vol. 30, Issue 6 https://doi.org/10.1093/nar/30.6.e23	journal	March 2002
In Vivo Packaging of Triacylglycerols Enhances Arabidopsis Leaf Biomass and Energy Density Winichayakul, Somrutai; Scott, Richard William; Roldan, Marissa Plant Physiology, Vol. 162, Issue 2 https://doi.org/10.1104/pp.113.216820	journal	April 2013
Gene Expression Knockdown by Modulating Synthetic Small RNA Expression in Escherichia coli Noh, Minho; Yoo, Seung Min; Kim, Won Jun Cell Systems, Vol. 5, Issue 4 https://doi.org/10.1016/j.cels.2017.08.016	journal	October 2017
A Gram-Scale Limonene Production Process with Engineered Escherichia coli Rolf, Jascha; Julsing, Mattijs K.; Rosenthal, Katrin Molecules, Vol. 25, Issue 8 https://doi.org/10.3390/molecules25081881	journal	April 2020
Deletion of d-ribulose-5-phosphate 3-epimerase (RPE1) induces simultaneous utilization of xylose and glucose in xylose-utilizing Saccharomyces cerevisiae Shen, Ming-Hua; Song, Hao; Li, Bing-Zhi Biotechnology Letters, Vol. 37, Issue 5 https://doi.org/10.1007/s10529-014-1759-z	journal	December 2014
Subcellular engineering of lipase dependent pathways directed towards lipid related organelles for highly effectively compartmentalized biosynthesis of triacylglycerol derived products in Yarrowia lipolytica Yang, Kaixin; Qiao, Yangge; Li, Fei Metabolic Engineering, Vol. 55 https://doi.org/10.1016/j.ymben.2019.08.001	journal	September 2019
Engineering of a butyraldehyde dehydrogenase of Clostridium saccharoperbutylacetonicum to fit an engineered 1,4‐butanediol pathway in Escherichia coli Hwang, Hee Jin; Park, Jin Hwan; Kim, Jin Ho Biotechnology and Bioengineering, Vol. 111, Issue 7 https://doi.org/10.1002/bit.25196	journal	February 2014
The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology Sandberg, Troy E.; Salazar, Michael J.; Weng, Liam L. Metabolic Engineering, Vol. 56 https://doi.org/10.1016/j.ymben.2019.08.004	journal	December 2019
Functional characterization of a highly specific l-arabinose transporter from Trichoderma reesei Havukainen, Sami; Pujol-Giménez, Jonai; Valkonen, Mari Microbial Cell Factories, Vol. 20, Issue 1 https://doi.org/10.1186/s12934-021-01666-4	journal	September 2021
Corynebacterium Cell Factory Design and Culture Process Optimization for Muconic Acid Biosynthesis Lee, Han-Na; Shin, Woo-Shik; Seo, Seung-Yeul Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-36320-4	journal	December 2018
Production of 2,3-butanediol from glucose and cassava hydrolysates by metabolically engineered industrial polyploid Saccharomyces cerevisiae Lee, Ye-Gi; Seo, Jin-Ho Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1545-1	journal	August 2019
Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Na, Dokyun; Yoo, Seung Min; Chung, Hannah Nature Biotechnology, Vol. 31, Issue 2 https://doi.org/10.1038/nbt.2461	journal	January 2013
Metabolic engineering for valorization of macroalgae biomass Sasaki, Yusuke; Yoshikuni, Yasuo Metabolic Engineering, Vol. 71 https://doi.org/10.1016/j.ymben.2022.01.005	journal	May 2022
Synthetic RNA Polymerase III Promoters Facilitate High-Efficiency CRISPR–Cas9-Mediated Genome Editing in Yarrowia lipolytica Schwartz, Cory M.; Hussain, Murtaza Shabbir; Blenner, Mark ACS Synthetic Biology, Vol. 5, Issue 4 https://doi.org/10.1021/acssynbio.5b00162	journal	January 2016
DeepTFactor: A deep learning-based tool for the prediction of transcription factors Kim, Gi Bae; Gao, Ye; Palsson, Bernhard O. Proceedings of the National Academy of Sciences, Vol. 118, Issue 2 https://doi.org/10.1073/pnas.2021171118	journal	December 2020
Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae Tang, Hongting; Wu, Yanling; Deng, Jiliang Metabolites, Vol. 10, Issue 8 https://doi.org/10.3390/metabo10080320	journal	August 2020
Enabling inverse metabolic engineering through genomics Gill, Ryan T. Current Opinion in Biotechnology, Vol. 14, Issue 5 https://doi.org/10.1016/S0958-1669(03)00116-2	journal	October 2003
RetroBioCat as a computer-aided synthesis planning tool for biocatalytic reactions and cascades Finnigan, William; Hepworth, Lorna J.; Flitsch, Sabine L. Nature Catalysis, Vol. 4, Issue 2 https://doi.org/10.1038/s41929-020-00556-z	journal	January 2021
Production of isopropanol by metabolically engineered Escherichia coli Jojima, Toru; Inui, Masayuki; Yukawa, Hideaki Applied Microbiology and Biotechnology, Vol. 77, Issue 6, p. 1219-1224 https://doi.org/10.1007/s00253-007-1246-8	journal	November 2007
Redirection of flux through the FPP branch-point in Saccharomyces cerevisiae by down-regulating squalene synthase Paradise, Eric M.; Kirby, James; Chan, Rossana Biotechnology and Bioengineering, Vol. 100, Issue 2 https://doi.org/10.1002/bit.21766	journal	June 2008
Industrial biomanufacturing: The future of chemical production Clomburg, James M.; Crumbley, Anna M.; Gonzalez, Ramon Science, Vol. 355, Issue 6320 https://doi.org/10.1126/science.aag0804	journal	January 2017
Microbial production of multiple short-chain primary amines via retrobiosynthesis Kim, Dong In; Chae, Tong Un; Kim, Hyun Uk Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-020-20423-6	journal	January 2021
Animal-free heme production for artificial meat in Corynebacterium glutamicum via systems metabolic and membrane engineering Ko, Young Jin; Kim, Minhye; You, Seung Kyou Metabolic Engineering, Vol. 66 https://doi.org/10.1016/j.ymben.2021.04.013	journal	July 2021
Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways Shen, C. R.; Liao, J. C. Metabolic Engineering, Vol. 10, Issue 6 https://doi.org/10.1016/j.ymben.2008.08.001	journal	November 2008
Metabolic engineering of Yarrowia lipolytica for itaconic acid production Blazeck, John; Hill, Andrew; Jamoussi, Mariam Metabolic Engineering, Vol. 32 https://doi.org/10.1016/j.ymben.2015.09.005	journal	November 2015
Biosynthesis of medicinal tropane alkaloids in yeast Srinivasan, Prashanth; Smolke, Christina D. Nature, Vol. 585, Issue 7826 https://doi.org/10.1038/s41586-020-2650-9	journal	September 2020
Metabolic engineering of Escherichia coli for α-farnesene production Wang, Chonglong; Yoon, Sang-Hwal; Jang, Hui-Jeong Metabolic Engineering, Vol. 13, Issue 6 https://doi.org/10.1016/j.ymben.2011.08.001	journal	November 2011
Enhanced Butanol Production Obtained by Reinforcing the Direct Butanol-Forming Route in Clostridium acetobutylicum Jang, Yu-Sin; Lee, Jin Young; Lee, Joungmin mBio, Vol. 3, Issue 5 https://doi.org/10.1128/mBio.00314-12	journal	October 2012
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models Heckmann, David; Lloyd, Colton J.; Mih, Nathan Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07652-6	journal	December 2018
Engineering Robust Production Microbes for Large-Scale Cultivation Wehrs, Maren; Tanjore, Deepti; Eng, Thomas Trends in Microbiology, Vol. 27, Issue 6 https://doi.org/10.1016/j.tim.2019.01.006	journal	June 2019
A Decade of Riboswitches Serganov, Alexander; Nudler, Evgeny Cell, Vol. 152, Issue 1-2 https://doi.org/10.1016/j.cell.2012.12.024	journal	January 2013
Orthogonal Engineering of Biosynthetic Pathway for Efficient Production of Limonene in Saccharomyces cerevisiae Cheng, Si; Liu, Xue; Jiang, Guozhen ACS Synthetic Biology, Vol. 8, Issue 5 https://doi.org/10.1021/acssynbio.9b00135	journal	April 2019
Chloroplastic metabolic engineering coupled with isoprenoid pool enhancement for committed taxanes biosynthesis in Nicotiana benthamiana Li, Jianhua; Mutanda, Ishmael; Wang, Kaibo Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12879-y	journal	October 2019
Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform Mikkelsen, Michael Dalgaard; Buron, Line Due; Salomonsen, Bo Metabolic Engineering, Vol. 14, Issue 2 https://doi.org/10.1016/j.ymben.2012.01.006	journal	March 2012
Targeting pathway expression to subcellular organelles improves astaxanthin synthesis in Yarrowia lipolytica Ma, Yongshuo; Li, Jingbo; Huang, Sanwen Metabolic Engineering, Vol. 68 https://doi.org/10.1016/j.ymben.2021.10.004	journal	November 2021
Development of a CRISPR/Cas9 system for high efficiency multiplexed gene deletion in Rhodosporidium toruloides Schultz, J. Carl; Cao, Mingfeng; Zhao, Huimin Biotechnology and Bioengineering, Vol. 116, Issue 8 https://doi.org/10.1002/bit.27001	journal	May 2019
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression Qi, Lei S.; Larson, Matthew H.; Gilbert, Luke A. Cell, Vol. 152, Issue 5, p. 1173-1183 https://doi.org/10.1016/j.cell.2013.02.022	journal	February 2013
MiYA, an efficient machine-learning workflow in conjunction with the YeastFab assembly strategy for combinatorial optimization of heterologous metabolic pathways in Saccharomyces cerevisiae Zhou, Yikang; Li, Gang; Dong, Junkai Metabolic Engineering, Vol. 47 https://doi.org/10.1016/j.ymben.2018.03.020	journal	May 2018
Building a global alliance of biofoundries Hillson, Nathan; Caddick, Mark; Cai, Yizhi Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10079-2	journal	May 2019
Automated design of synthetic ribosome binding sites to control protein expression Salis, Howard M.; Mirsky, Ethan A.; Voigt, Christopher A. Nature Biotechnology, Vol. 27, Issue 10, p. 946-950 https://doi.org/10.1038/nbt.1568	journal	October 2009
Metabolic engineering of Clostridium beijerinckii to improve glycerol metabolism and furfural tolerance Agu, Chidozie Victor; Ujor, Victor; Ezeji, Thaddeus Chukwuemeka Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1388-9	journal	March 2019
A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data Jansen, R. Science, Vol. 302, Issue 5644 https://doi.org/10.1126/science.1087361	journal	October 2003
Metabolic engineering for the production of shikimic acid in an evolved Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system Escalante, Adelfo; Calderón, Rocío; Valdivia, Araceli Microbial Cell Factories, Vol. 9, Issue 1, Article No. 21 https://doi.org/10.1186/1475-2859-9-21	journal	January 2010
A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae Deng, Jiliang; Wu, Yanling; Zheng, Zhaohui Microbial Cell Factories, Vol. 20, Issue 1 https://doi.org/10.1186/s12934-021-01691-3	journal	October 2021
Inhibitor tolerance and bioethanol fermentability of levoglucosan-utilizing Escherichia coli were enhanced by overexpression of stress-responsive gene ycfR: The proteomics-guided metabolic engineering Chang, Dongdong; Islam, Zia Ul; Zheng, Junfang Synthetic and Systems Biotechnology, Vol. 6, Issue 4 https://doi.org/10.1016/j.synbio.2021.11.003	journal	December 2021
In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner Sachdeva, Gairik; Garg, Abhishek; Godding, David Nucleic Acids Research, Vol. 42, Issue 14 https://doi.org/10.1093/nar/gku617	journal	July 2014
Gene-expression tools for the metabolic engineering of bacteria Keasling, Jay D. Trends in Biotechnology, Vol. 17, Issue 11, p. 452-460 https://doi.org/10.1016/S0167-7799(99)01376-1	journal	November 1999
Saturated mutagenesis of ketoisovalerate decarboxylase V461 enabled specific synthesis of 1-pentanol via the ketoacid elongation cycle Chen, Grey S.; Siao, Siang Wun; Shen, Claire R. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-11624-z	journal	September 2017
Multiple gene-mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae Lewis Liu, Z.; Moon, Jaewoong; Andersh, Brad J. Applied Microbiology and Biotechnology, Vol. 81, Issue 4, p. 743-753 https://doi.org/10.1007/s00253-008-1702-0	journal	September 2008
Balancing the carbon flux distributions between the TCA cycle and glyoxylate shunt to produce glycolate at high yield and titer in Escherichia coli Deng, Yu; Ma, Ning; Zhu, Kangjia Metabolic Engineering, Vol. 46 https://doi.org/10.1016/j.ymben.2018.02.008	journal	March 2018
Third-generation biorefineries as the means to produce fuels and chemicals from CO2 Liu, Zihe; Wang, Kai; Chen, Yun Nature Catalysis, Vol. 3, Issue 3 https://doi.org/10.1038/s41929-019-0421-5	journal	March 2020
A microbial biomanufacturing platform for natural and semisynthetic opioids Thodey, Kate; Galanie, Stephanie; Smolke, Christina D. Nature Chemical Biology, Vol. 10, Issue 10 https://doi.org/10.1038/nchembio.1613	journal	August 2014
Metabolic control analysis: a survey of its theoretical and experimental development Fell, D. A. Biochemical Journal, Vol. 286, Issue 2 https://doi.org/10.1042/bj2860313	journal	September 1992
A microbial supply chain for production of the anti-cancer drug vinblastine Zhang, Jie; Hansen, Lea G.; Gudich, Olga Nature, Vol. 609, Issue 7926 https://doi.org/10.1038/s41586-022-05157-3	journal	August 2022
Enhanced itaconic acid production in Yarrowia lipolytica via heterologous expression of a mitochondrial transporter MTT Zhao, Chen; Cui, Zhiyong; Zhao, Xiangying Applied Microbiology and Biotechnology, Vol. 103, Issue 5 https://doi.org/10.1007/s00253-019-09627-z	journal	January 2019
Enhanced Biotransformation of Furfural and Hydroxymethylfurfural by Newly Developed Ethanologenic Yeast Strains Liu, Z. Lewis; Slininger, Patricia J.; Gorsich, Steve W. Applied Biochemistry and Biotechnology, Vol. 121, Issue 1-3 https://doi.org/10.1385/ABAB:121:1-3:0451	journal	January 2005
One hundred years of clostridial butanol fermentation Moon, Hyeon Gi; Jang, Yu-Sin; Cho, Changhee FEMS Microbiology Letters https://doi.org/10.1093/femsle/fnw001	journal	January 2016
Using deep learning to model the hierarchical structure and function of a cell Ma, Jianzhu; Yu, Michael Ku; Fong, Samson Nature Methods, Vol. 15, Issue 4 https://doi.org/10.1038/nmeth.4627	journal	March 2018
Metabolic engineering of monoterpene synthesis in yeast Fischer, Marc J. C.; Meyer, Sophie; Claudel, Patricia Biotechnology and Bioengineering, Vol. 108, Issue 8 https://doi.org/10.1002/bit.23129	journal	March 2011
Production of itaconic acid from alkali pretreated lignin by dynamic two stage bioconversion Elmore, Joshua R.; Dexter, Gara N.; Salvachúa, Davinia Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-22556-8	journal	April 2021
Flux analysis and metabolomics for systematic metabolic engineering of microorganisms Toya, Yoshihiro; Shimizu, Hiroshi Biotechnology Advances, Vol. 31, Issue 6 https://doi.org/10.1016/j.biotechadv.2013.05.002	journal	November 2013
Combining Gal4p-mediated expression enhancement and directed evolution of isoprene synthase to improve isoprene production in Saccharomyces cerevisiae Wang, Fan; Lv, Xiaomei; Xie, Wenping Metabolic Engineering, Vol. 39 https://doi.org/10.1016/j.ymben.2016.12.011	journal	January 2017
Engineered protein degradation of farnesyl pyrophosphate synthase is an effective regulatory mechanism to increase monoterpene production in Saccharomyces cerevisiae Peng, Bingyin; Nielsen, Lars K.; Kampranis, Sotirios C. Metabolic Engineering, Vol. 47 https://doi.org/10.1016/j.ymben.2018.02.005	journal	May 2018
How to measure metabolic fluxes: a taxonomic guide for 13 C fluxomics Niedenführ, Sebastian; Wiechert, Wolfgang; Nöh, Katharina Current Opinion in Biotechnology, Vol. 34 https://doi.org/10.1016/j.copbio.2014.12.003	journal	August 2015
Rewiring the microbial metabolic network for efficient utilization of mixed carbon sources An, Ning; Chen, Xin; Sheng, Huakang Journal of Industrial Microbiology and Biotechnology, Vol. 48, Issue 9-10 https://doi.org/10.1093/jimb/kuab040	journal	July 2021
Sequential control of biosynthetic pathways for balanced utilization of metabolic intermediates in Saccharomyces cerevisiae Xie, Wenping; Ye, Lidan; Lv, Xiaomei Metabolic Engineering, Vol. 28 https://doi.org/10.1016/j.ymben.2014.11.007	journal	March 2015
Metabolic engineering of cyanobacteria for the synthesis of commodity products Angermayr, S. Andreas; Gorchs Rovira, Aleix; Hellingwerf, Klaas J. Trends in Biotechnology, Vol. 33, Issue 6 https://doi.org/10.1016/j.tibtech.2015.03.009	journal	June 2015
Rewiring FadR regulon for the selective production of ω-hydroxy palmitic acid from glucose in Escherichia coli Kim, Joonwon; Yoo, Hee-Wang; Kim, Minsuk Metabolic Engineering, Vol. 47 https://doi.org/10.1016/j.ymben.2018.04.021	journal	May 2018
A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast Podolsky, Igor A.; Seppälä, Susanna; Xu, Haiqing Metabolic Engineering, Vol. 66 https://doi.org/10.1016/j.ymben.2021.04.009	journal	July 2021
13C metabolic flux analysis at a genome-scale Gopalakrishnan, Saratram; Maranas, Costas D. Metabolic Engineering, Vol. 32 https://doi.org/10.1016/j.ymben.2015.08.006	journal	November 2015
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems DiCarlo, James E.; Norville, Julie E.; Mali, Prashant Nucleic Acids Research, Vol. 41, Issue 7, p. 4336-4343 https://doi.org/10.1093/nar/gkt135	journal	March 2013
Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production Liu, Yi; Liu, Quanli; Krivoruchko, Anastasia Nature Chemical Biology, Vol. 16, Issue 2 https://doi.org/10.1038/s41589-019-0431-2	journal	December 2019
Engineering cellular metabolite transport for biosynthesis of computationally predicted tropane alkaloid derivatives in yeast Srinivasan, Prashanth; Smolke, Christina D. Proceedings of the National Academy of Sciences, Vol. 118, Issue 25 https://doi.org/10.1073/pnas.2104460118	journal	June 2021
Custom-made transcriptional biosensors for metabolic engineering Koch, Mathilde; Pandi, Amir; Borkowski, Olivier Current Opinion in Biotechnology, Vol. 59 https://doi.org/10.1016/j.copbio.2019.02.016	journal	October 2019
The era of big data: Genome-scale modelling meets machine learning Antonakoudis, Athanasios; Barbosa, Rodrigo; Kotidis, Pavlos Computational and Structural Biotechnology Journal, Vol. 18 https://doi.org/10.1016/j.csbj.2020.10.011	journal	January 2020
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale Liew, Fungmin Eric; Nogle, Robert; Abdalla, Tanus Nature Biotechnology https://doi.org/10.1038/s41587-021-01195-w	journal	February 2022
Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping Lian, Jiazhang; Schultz, Carl; Cao, Mingfeng Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13621-4	journal	December 2019
Cellular and metabolic engineering: An overview Cameron, Douglas C.; Tong, I-Teh Applied Biochemistry and Biotechnology, Vol. 38, Issue 1-2 https://doi.org/10.1007/BF02916416	journal	January 1993
Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network Forster, J. Genome Research, Vol. 13, Issue 2 https://doi.org/10.1101/gr.234503	journal	February 2003
Additivity of inhibitory effects in multidrug combinations Russ, D.; Kishony, R. Nature Microbiology, Vol. 3, Issue 12 https://doi.org/10.1038/s41564-018-0252-1	journal	October 2018
Design of a programmable biosensor-CRISPRi genetic circuits for dynamic and autonomous dual-control of metabolic flux in Bacillus subtilis Wu, Yaokang; Chen, Taichi; Liu, Yanfeng Nucleic Acids Research, Vol. 48, Issue 2 https://doi.org/10.1093/nar/gkz1123	journal	December 2019
Cloning and expression of the structural gene for pyruvate decarboxylase of Zymomonas mobilis in Escherichia coli Br�u, Barbara; Sahm, Hermann Archives of Microbiology, Vol. 144, Issue 3 https://doi.org/10.1007/BF00410966	journal	April 1986
Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers Robinson, Christopher J.; Carbonell, Pablo; Jervis, Adrian J. Metabolic Engineering, Vol. 60 https://doi.org/10.1016/j.ymben.2020.04.008	journal	July 2020
Construction of plasmids with tunable copy numbers in Saccharomyces cerevisiae and their applications in pathway optimization and multiplex genome integration : Plasmid Copy Number Engineering Lian, Jiazhang; Jin, Run; Zhao, Huimin Biotechnology and Bioengineering, Vol. 113, Issue 11 https://doi.org/10.1002/bit.26004	journal	June 2016
Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803 Zhu, Hongji; Ren, Xiaoyue; Wang, Jiangxin Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-106	journal	January 2013
A comprehensive metabolic map for production of bio-based chemicals Lee, Sang Yup; Kim, Hyun Uk; Chae, Tong Un Nature Catalysis, Vol. 2, Issue 1 https://doi.org/10.1038/s41929-018-0212-4	journal	January 2019
Improving medium chain fatty acid production in Escherichia coli by multiple transporter engineering Wu, Junjun; Wang, Zhe; Zhang, Xia Food Chemistry, Vol. 272 https://doi.org/10.1016/j.foodchem.2018.08.102	journal	January 2019
Toward glycerol biorefinery: metabolic engineering for the production of biofuels and chemicals from glycerol Chen, Zhen; Liu, Dehua Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0625-8	journal	October 2016
Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli Atsumi, Shota; Wu, Tung‐Yun; Machado, Iara M. P. Molecular Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1038/msb.2010.98	journal	January 2010
Lessons from Two Design–Build–Test–Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning Opgenorth, Paul; Costello, Zak; Okada, Takuya ACS Synthetic Biology, Vol. 8, Issue 6 https://doi.org/10.1021/acssynbio.9b00020	journal	May 2019
Metabolic Engineering of Escherichia coli for the Production of 3-Hydroxypropionic Acid and Malonic Acid through β-Alanine Route Song, Chan Woo; Kim, Je Woong; Cho, In Jin ACS Synthetic Biology, Vol. 5, Issue 11 https://doi.org/10.1021/acssynbio.6b00007	journal	March 2016
Efficient and selective degradation of polyethylenes into liquid fuels and waxes under mild conditions Jia, Xiangqing; Qin, Chuan; Friedberger, Tobias Science Advances, Vol. 2, Issue 6 https://doi.org/10.1126/sciadv.1501591	journal	June 2016
Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes Pfleger, Brian F.; Pitera, Douglas J.; Smolke, Christina D. Nature Biotechnology, Vol. 24, Issue 8 https://doi.org/10.1038/nbt1226	journal	July 2006
Recent advances in the applications of promoter engineering for the optimization of metabolite biosynthesis Xu, Ning; Wei, Liang; Liu, Jun World Journal of Microbiology and Biotechnology, Vol. 35, Issue 2 https://doi.org/10.1007/s11274-019-2606-0	journal	January 2019
Global transcription machinery engineering: A new approach for improving cellular phenotype Alper, H.; Stephanopoulos, G. Metabolic Engineering, Vol. 9, Issue 3, p. 258-267 https://doi.org/10.1016/j.ymben.2006.12.002	journal	May 2007
Metabolically engineered Escherichia coli for efficient production of glycosylated natural products Peirú, Salvador; Rodríguez, Eduardo; Menzella, Hugo G. Microbial Biotechnology, Vol. 1, Issue 6 https://doi.org/10.1111/j.1751-7915.2008.00046.x	journal	October 2008
Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR Sievert, Christian; Nieves, Lizbeth M.; Panyon, Larry A. Proceedings of the National Academy of Sciences, Vol. 114, Issue 28 https://doi.org/10.1073/pnas.1700345114	journal	June 2017
Production of 2-methyl-1-butanol and 3-methyl-1-butanol in engineered Corynebacterium glutamicum Vogt, Michael; Brüsseler, Christian; Ooyen, Jan van Metabolic Engineering, Vol. 38 https://doi.org/10.1016/j.ymben.2016.10.007	journal	November 2016
Release of glucose repression on xylose utilization in Kluyveromyces marxianus to enhance glucose-xylose co-utilization and xylitol production from corncob hydrolysate Hua, Yan; Wang, Jichao; Zhu, Yelin Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1068-2	journal	February 2019
Systems metabolic engineering of microorganisms for natural and non-natural chemicals Lee, Jeong Wook; Na, Dokyun; Park, Jong Myoung Nature Chemical Biology, Vol. 8, Issue 6 https://doi.org/10.1038/nchembio.970	journal	May 2012
Energy densification in vegetative biomass through metabolic engineering Vanhercke, Thomas; Petrie, James R.; Singh, Surinder P. Biocatalysis and Agricultural Biotechnology, Vol. 3, Issue 1 https://doi.org/10.1016/j.bcab.2013.11.010	journal	January 2014
Biochemical and Structural Insights into Bacterial Organelle Form and Biogenesis Parsons, Joshua B.; Dinesh, Sriramulu D.; Deery, Evelyne Journal of Biological Chemistry, Vol. 283, Issue 21 https://doi.org/10.1074/jbc.M709214200	journal	March 2008
Directed evolution of a highly efficient cellobiose utilizing pathway in an industrial Saccharomyces cerevisiae strain : Directed Evolution of a Cellobiose Pathway Yuan, Yongbo; Zhao, Huimin Biotechnology and Bioengineering, Vol. 110, Issue 11 https://doi.org/10.1002/bit.24946	journal	June 2013
Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing Li, Yifan; Lin, Zhenquan; Huang, Can Metabolic Engineering, Vol. 31, p. 13-21 https://doi.org/10.1016/j.ymben.2015.06.006	journal	September 2015
Enabling Biocatalysis by High-Throughput Protein Engineering Using Droplet Microfluidics Coupled to Mass Spectrometry Diefenbach, Xue W.; Farasat, Iman; Guetschow, Erik D. ACS Omega, Vol. 3, Issue 2 https://doi.org/10.1021/acsomega.7b01973	journal	February 2018
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use Varma, Amit; Palsson, Bernhard O. Bio/Technology, Vol. 12, Issue 10 https://doi.org/10.1038/nbt1094-994	journal	October 1994
Robust succinic acid production from crude glycerol using engineered Yarrowia lipolytica Gao, Cuijuan; Yang, Xiaofeng; Wang, Huaimin Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0597-8	journal	August 2016
Transcription-Factor-based Biosensor Engineering for Applications in Synthetic Biology Ding, Nana; Zhou, Shenghu; Deng, Yu ACS Synthetic Biology, Vol. 10, Issue 5 https://doi.org/10.1021/acssynbio.0c00252	journal	April 2021
Production of ethylene glycol from xylose by metabolically engineeredEscherichia coli Chae, Tong Un; Choi, So Young; Ryu, Jae Yong AIChE Journal, Vol. 64, Issue 12 https://doi.org/10.1002/aic.16339	journal	July 2018
Microdroplet-Assisted Screening of Biomolecule Production for Metabolic Engineering Applications Bowman, Emily K.; Alper, Hal S. Trends in Biotechnology, Vol. 38, Issue 7 https://doi.org/10.1016/j.tibtech.2019.11.002	journal	July 2020
Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae Bao, Zehua; Xiao, Han; Liang, Jing ACS Synthetic Biology, Vol. 4, Issue 5 https://doi.org/10.1021/sb500255k	journal	September 2014
Production of the antimalarial drug precursor artemisinic acid in engineered yeast Ro, Dae-Kyun; Paradise, Eric M.; Ouellet, Mario Nature, Vol. 440, Issue 7086, p. 940-943 https://doi.org/10.1038/nature04640	journal	April 2006
Reinforcement Learning for Bioretrosynthesis Koch, Mathilde; Duigou, Thomas; Faulon, Jean-Loup ACS Synthetic Biology, Vol. 9, Issue 1 https://doi.org/10.1021/acssynbio.9b00447	journal	December 2019
Using gas mixtures of CO, CO ₂ and H ₂ as microbial substrates: the do's and don'ts of successful technology transfer from laboratory to production scale Takors, Ralf; Kopf, Michael; Mampel, Joerg Microbial Biotechnology, Vol. 11, Issue 4 https://doi.org/10.1111/1751-7915.13270	journal	May 2018
Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models Andreozzi, Stefano; Chakrabarti, Anirikh; Soh, Keng Cher Metabolic Engineering, Vol. 35 https://doi.org/10.1016/j.ymben.2016.01.009	journal	May 2016
Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica Xue, Zhixiong; Sharpe, Pamela L.; Hong, Seung-Pyo Nature Biotechnology, Vol. 31, Issue 8 https://doi.org/10.1038/nbt.2622	journal	July 2013
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity Phaneuf, Patrick V.; Yurkovich, James T.; Heckmann, David BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-06920-4	journal	July 2020
Tuning genetic control through promoter engineering Alper, H.; Fischer, C.; Nevoigt, E. Proceedings of the National Academy of Sciences, Vol. 102, Issue 36, p. 12678-12683 https://doi.org/10.1073/pnas.0504604102	journal	August 2005
Construction of a metabolome library for transcription factor-related single gene mutants of Saccharomyces cerevisiae Hashim, Zanariah; Teoh, Shao Thing; Bamba, Takeshi Journal of Chromatography B, Vol. 966 https://doi.org/10.1016/j.jchromb.2014.05.041	journal	September 2014
Modular engineering for microbial production of carotenoids Li, Cheng; Swofford, Charles A.; Sinskey, Anthony J. Metabolic Engineering Communications, Vol. 10 https://doi.org/10.1016/j.mec.2019.e00118	journal	June 2020
Progress in metabolic engineering Farmer, William R.; Liao, James C. Current Opinion in Biotechnology, Vol. 7, Issue 2 https://doi.org/10.1016/S0958-1669(96)80013-9	journal	April 1996
A system for multilocus chromosomal integration and transformation-free selection marker rescue Siddiqui, Michael S.; Choksi, Atri; Smolke, Christina D. FEMS Yeast Research, Vol. 14, Issue 8 https://doi.org/10.1111/1567-1364.12210	journal	October 2014
EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae Maury, Jérôme; Germann, Susanne M.; Baallal Jacobsen, Simo Abdessamad PLOS ONE, Vol. 11, Issue 3 https://doi.org/10.1371/journal.pone.0150394	journal	March 2016
Genetically assembled fluorescent biosensor for in situ detection of bio-synthesized alkanes Wu, Wei; Zhang, Lei; Yao, Lun Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep10907	journal	June 2015
Evolution of an alkane-inducible biosensor for increased responsiveness to short-chain alkanes Reed, Ben; Blazeck, John; Alper, Hal Journal of Biotechnology, Vol. 158, Issue 3 https://doi.org/10.1016/j.jbiotec.2012.01.028	journal	April 2012
Transporter engineering in microbial cell factories: the ins, the outs, and the in-betweens van der Hoek, Steven A.; Borodina, Irina Current Opinion in Biotechnology, Vol. 66 https://doi.org/10.1016/j.copbio.2020.08.002	journal	December 2020
Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering He, Fei; Murabito, Ettore; Westerhoff, Hans V. Journal of The Royal Society Interface, Vol. 13, Issue 117 https://doi.org/10.1098/rsif.2015.1046	journal	April 2016
Development of a CRISPR/Cas9-Based Tool for Gene Deletion in Issatchenkia orientalis Tran, Vinh G.; Cao, Mingfeng; Fatma, Zia mSphere, Vol. 4, Issue 3 https://doi.org/10.1128/mSphere.00345-19	journal	June 2019
Synthesis of Polyhydroxyalkanoate in the Peroxisome of Saccharomyces cerevisiae by Using Intermediates of Fatty Acid β-Oxidation Poirier, Yves; Erard, Nadine; Petétot, Jean MacDonald-Comber Applied and Environmental Microbiology, Vol. 67, Issue 11 https://doi.org/10.1128/AEM.67.11.5254-5260.2001	journal	November 2001
Metabolic engineering of Escherichia coli for 2,3-butanediol production from cellulosic biomass by using glucose-inducible gene expression system Sathesh-Prabu, Chandran; Kim, Donghyuk; Lee, Sung Kuk Bioresource Technology, Vol. 309 https://doi.org/10.1016/j.biortech.2020.123361	journal	August 2020
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers Heckmann, David; Campeau, Anaamika; Lloyd, Colton J. Proceedings of the National Academy of Sciences, Vol. 117, Issue 37 https://doi.org/10.1073/pnas.2001562117	journal	September 2020
Direct production of fatty alcohols from glucose using engineered strains of Yarrowia lipolytica Cordova, Lauren T.; Butler, Jonathan; Alper, Hal S. Metabolic Engineering Communications, Vol. 10 https://doi.org/10.1016/j.mec.2019.e00105	journal	June 2020
Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher Biotechnology Journal, Vol. 8, Issue 9 https://doi.org/10.1002/biot.201300091	journal	August 2013
Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production Alper, H.; Moxley, J.; Nevoigt, E. Science, Vol. 314, Issue 5805, p. 1565-1568 https://doi.org/10.1126/science.1131969	journal	December 2006
Tailoring the Saccharomyces cerevisiae endoplasmic reticulum for functional assembly of terpene synthesis pathway Kim, Jae-Eung; Jang, In-Seung; Son, So-Hee Metabolic Engineering, Vol. 56 https://doi.org/10.1016/j.ymben.2019.08.013	journal	December 2019
Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis Yu, Tao; Zhou, Yongjin J.; Huang, Mingtao Cell, Vol. 174, Issue 6 https://doi.org/10.1016/j.cell.2018.07.013	journal	September 2018
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules Levy, R.; Borenstein, E. Proceedings of the National Academy of Sciences, Vol. 110, Issue 31 https://doi.org/10.1073/pnas.1300926110	journal	July 2013
Unified rational protein engineering with sequence-based deep representation learning Alley, Ethan C.; Khimulya, Grigory; Biswas, Surojit Nature Methods, Vol. 16, Issue 12 https://doi.org/10.1038/s41592-019-0598-1	journal	October 2019
High-Yield Resveratrol Production in Engineered Escherichia coli Lim, Chin Giaw; Fowler, Zachary L.; Hueller, Thomas Applied and Environmental Microbiology, Vol. 77, Issue 10 https://doi.org/10.1128/AEM.02186-10	journal	March 2011
Recent advances in FRET-Based biosensors for biomedical applications Imani, Mahsa; Mohajeri, Nasrin; Rastegar, Mojgan Analytical Biochemistry, Vol. 630 https://doi.org/10.1016/j.ab.2021.114323	journal	October 2021
Biofuel metabolic engineering with biosensors Morgan, Stacy-Anne; Nadler, Dana C.; Yokoo, Rayka Current Opinion in Chemical Biology, Vol. 35 https://doi.org/10.1016/j.cbpa.2016.09.020	journal	December 2016
Conversion of Escherichia coli to Generate All Biomass Carbon from CO2 Gleizer, Shmuel; Ben-Nissan, Roee; Bar-On, Yinon M. Cell, Vol. 179, Issue 6 https://doi.org/10.1016/j.cell.2019.11.009	journal	November 2019
Thermodynamics-Based Metabolic Flux Analysis Henry, Christopher S.; Broadbelt, Linda J.; Hatzimanikatis, Vassily Biophysical Journal, Vol. 92, Issue 5 https://doi.org/10.1529/biophysj.106.093138	journal	March 2007
Synthetic protein scaffolds provide modular control over metabolic flux Dueber, John E.; Wu, Gabriel C.; Malmirchegini, G. Reza Nature Biotechnology, Vol. 27, Issue 8, p. 753-759 https://doi.org/10.1038/nbt.1557	journal	August 2009
Advances in promoter engineering: Novel applications and predefined transcriptional control Cazier, Andrew P.; Blazeck, John Biotechnology Journal, Vol. 16, Issue 10 https://doi.org/10.1002/biot.202100239	journal	August 2021
Development of an autonomous and bifunctional quorum-sensing circuit for metabolic flux control in engineered Escherichia coli Dinh, Christina V.; Prather, Kristala L. J. Proceedings of the National Academy of Sciences, Vol. 116, Issue 51 https://doi.org/10.1073/pnas.1911144116	journal	December 2019
Engineering microbial biofuel tolerance and export using efflux pumps Dunlop, Mary J.; Dossani, Zain Y.; Szmidt, Heather L. Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.21	journal	January 2011
Co-utilization of multiple lignocellulose-derived sugars and inhibitors by the robust mutant Kluyveromyces marxianus through adaptive laboratory evolution Du, Cong; Li, Yimin; Xiang, Ruijuan Fuel, Vol. 315 https://doi.org/10.1016/j.fuel.2021.122816	journal	May 2022
Discovery and characterization of a fourth class of guanidine riboswitches Lenkeit, Felina; Eckert, Iris; Hartig, Jörg S. Nucleic Acids Research, Vol. 48, Issue 22 https://doi.org/10.1093/nar/gkaa1102	journal	November 2020
Cofactor engineering for more efficient production of chemicals and biofuels Wang, Meng; Chen, Biqiang; Fang, Yunming Biotechnology Advances, Vol. 35, Issue 8 https://doi.org/10.1016/j.biotechadv.2017.09.008	journal	December 2017
Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli Ajikumar, P. K.; Xiao, W.-H.; Tyo, K. E. J. Science, Vol. 330, Issue 6000, p. 70-74 https://doi.org/10.1126/science.1191652	journal	September 2010
A comparison of stress tolerance in YPD and industrial lignocellulose-based medium among industrial and laboratory yeast strains Albers, Eva; Larsson, Christer Journal of Industrial Microbiology & Biotechnology, Vol. 36, Issue 8 https://doi.org/10.1007/s10295-009-0592-1	journal	May 2009
Degradation and metabolism of synthetic plastics and associated products by Pseudomonas sp.: capabilities and challenges Wilkes, R. A.; Aristilde, L. Journal of Applied Microbiology, Vol. 123, Issue 3 https://doi.org/10.1111/jam.13472	journal	May 2017
FÖrster resonance energy transfer (FRET)-based biosensors for biological applications Zhang, Xiaojing; Hu, Yue; Yang, Xiaotong Biosensors and Bioelectronics, Vol. 138 https://doi.org/10.1016/j.bios.2019.05.019	journal	August 2019
Transporter Engineering for Microbial Manufacturing Zhu, Ying; Zhou, Chen; Wang, Ying Biotechnology Journal, Vol. 15, Issue 9 https://doi.org/10.1002/biot.201900494	journal	May 2020
Portable bacterial CRISPR transcriptional activation enables metabolic engineering in Pseudomonas putida Kiattisewee, Cholpisit; Dong, Chen; Fontana, Jason Metabolic Engineering, Vol. 66 https://doi.org/10.1016/j.ymben.2021.04.002	journal	July 2021
Increasing the flux in metabolic pathways: A metabolic control analysis perspective Fell, David A. Biotechnology and Bioengineering, Vol. 58, Issue 2-3 https://doi.org/10.1002/(SICI)1097-0290(19980420)58:2/3<121::AID-BIT2>3.0.CO;2-N	journal	April 1998
Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains Rodriguez, Angelica; Chen, Yun; Khoomrung, Sakda Metabolic Engineering, Vol. 44 https://doi.org/10.1016/j.ymben.2017.10.013	journal	November 2017
Metabolic Engineering in the -omics Era: Elucidating and Modulating Regulatory Networks Vemuri, Goutham N.; Aristidou, Aristos A. Microbiology and Molecular Biology Reviews, Vol. 69, Issue 2 https://doi.org/10.1128/MMBR.69.2.197-216.2005	journal	June 2005
Overcoming glutamate auxotrophy in Escherichia coli itaconate overproducer by the Weimberg pathway Lu, Ken W.; Wang, Chris T.; Chang, Hengray Metabolic Engineering Communications, Vol. 13 https://doi.org/10.1016/j.mec.2021.e00190	journal	December 2021
Hyperproduction of 3-hydroxypropionate by Halomonas bluephagenesis Jiang, Xiao-Ran; Yan, Xu; Yu, Lin-Ping Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21632-3	journal	March 2021
Design and development of a “Y-shaped” microbial consortium capable of simultaneously utilizing biomass sugars for efficient production of butanol Zhao, Chunhua; Sinumvayo, Jean Paul; Zhang, Yanping Metabolic Engineering, Vol. 55 https://doi.org/10.1016/j.ymben.2019.06.012	journal	September 2019
In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing Wang, Yu; Cheng, Haijiao; Liu, Yang Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21003-y	journal	January 2021
Promoter engineering enables overproduction of foreign proteins from a single copy expression cassette in Bacillus subtilis Zhou, Chaoyang; Ye, Bin; Cheng, Shan Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1159-0	journal	June 2019
Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data Toya, Yoshihiro; Nakahigashi, Kenji; Tomita, Masaru Molecular BioSystems, Vol. 8, Issue 10, p. 2593-2604 https://doi.org/10.1039/c2mb25069a	journal	January 2012
Complete biosynthesis of opioids in yeast Galanie, S.; Thodey, K.; Trenchard, I. J. Science, Vol. 349, Issue 6252 https://doi.org/10.1126/science.aac9373	journal	August 2015
Modified bacteriophage lambda promoter vectors for overproduction of proteins in Escherichia coli Elvin, Christopher M.; Thompson, Phillip R.; Argall, Mary E. Gene, Vol. 87, Issue 1 https://doi.org/10.1016/0378-1119(90)90503-J	journal	March 1990
Metabolic Engineering To Produce Tyrosine or Phenylalanine in a Tryptophan-Producing Corynebacterium glutamicum Strain Ikeda, Masato; Katsumata, Ryoichi Applied and Environmental Microbiology, Vol. 58, Issue 3 https://doi.org/10.1128/aem.58.3.781-785.1992	journal	March 1992
Genetically switched d-lactate production in Escherichia coli Zhou, Li; Niu, Dan-Dan; Tian, Kang-Ming Metabolic Engineering, Vol. 14, Issue 5 https://doi.org/10.1016/j.ymben.2012.05.004	journal	September 2012
Genetic Biosensor Design for Natural Product Biosynthesis in Microorganisms Hossain, Gazi Sakir; Saini, Mukesh; Miyake, Ryoma Trends in Biotechnology, Vol. 38, Issue 7 https://doi.org/10.1016/j.tibtech.2020.03.013	journal	July 2020
Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons Cetnar, Daniel P.; Salis, Howard M. ACS Synthetic Biology, Vol. 10, Issue 2 https://doi.org/10.1021/acssynbio.0c00471	journal	January 2021
Escherichia coli hydrogenase 3 is a reversible enzyme possessing hydrogen uptake and synthesis activities Maeda, Toshinari; Sanchez-Torres, Viviana; Wood, Thomas K. Applied Microbiology and Biotechnology, Vol. 76, Issue 5 https://doi.org/10.1007/s00253-007-1086-6	journal	August 2007
A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information Feist, Adam M.; Henry, Christopher S.; Reed, Jennifer L. Molecular Systems Biology, Vol. 3, Issue 1 https://doi.org/10.1038/msb4100155	journal	January 2007
Phage serine integrase-mediated genome engineering for efficient expression of chemical biosynthetic pathway in gas-fermenting Clostridium ljungdahlii Huang, He; Chai, Changsheng; Yang, Sheng Metabolic Engineering, Vol. 52 https://doi.org/10.1016/j.ymben.2019.01.005	journal	March 2019
Gene Therapy and Metabolic Engineering Wang, Fubao; Raab, R. Michael; Washabaugh, Michael W. Metabolic Engineering, Vol. 2, Issue 2 https://doi.org/10.1006/mben.1999.0144	journal	April 2000
Evolutionary engineering of multiple-stress resistant Cakar, Z.; Seker, U.; Tamerler, C. FEMS Yeast Research, Vol. 5, Issue 6-7 https://doi.org/10.1016/j.femsyr.2004.10.010	journal	April 2005
Tools and strategies of systems metabolic engineering for the development of microbial cell factories for chemical production Ko, Yoo-Sung; Kim, Je Woong; Lee, Jong An Chemical Society Reviews, Vol. 49, Issue 14 https://doi.org/10.1039/D0CS00155D	journal	January 2020
Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli Harder, Björn-Johannes; Bettenbrock, Katja; Klamt, Steffen Metabolic Engineering, Vol. 38 https://doi.org/10.1016/j.ymben.2016.05.008	journal	November 2016
Directed Evolution: Methodologies and Applications Wang, Yajie; Xue, Pu; Cao, Mingfeng Chemical Reviews, Vol. 121, Issue 20 https://doi.org/10.1021/acs.chemrev.1c00260	journal	July 2021
Identification of major malate export systems in an engineered malate-producing Escherichia coli aided by substrate similarity search Kurgan, Gavin; Kurgan, Logan; Schneider, Aidan Applied Microbiology and Biotechnology, Vol. 103, Issue 21-22 https://doi.org/10.1007/s00253-019-10164-y	journal	October 2019
Site-specific genome integration in alphaproteobacteria mediated by TG1 integrase Morita, Kentaro; Morimura, Kohji; Fusada, Naoki Applied Microbiology and Biotechnology, Vol. 93, Issue 1 https://doi.org/10.1007/s00253-011-3545-3	journal	September 2011
A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo Moore, Christopher L.; Papa, Louis J.; Shoulders, Matthew D. Journal of the American Chemical Society, Vol. 140, Issue 37 https://doi.org/10.1021/jacs.8b04001	journal	July 2018
Directed evolution of a cellobiose utilization pathway in Saccharomyces cerevisiae by simultaneously engineering multiple proteins Eriksen, Dawn T.; Hsieh, Pei Chiun; Lynn, Patrick Microbial Cell Factories, Vol. 12, Issue 1 https://doi.org/10.1186/1475-2859-12-61	journal	January 2013
RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering Si, Tong; Luo, Yunzi; Bao, Zehua ACS Synthetic Biology, Vol. 4, Issue 3 https://doi.org/10.1021/sb500074a	journal	May 2014
Homology-dependent recombination of large synthetic pathways into E. coli genome via λ-Red and CRISPR/Cas9 dependent selection methodology Su, Buli; Song, Dandan; Zhu, Honghui Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-01360-x	journal	May 2020
Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals Borodina, Irina; Nielsen, Jens Biotechnology Journal, Vol. 9, Issue 5 https://doi.org/10.1002/biot.201300445	journal	February 2014
Metabolic Engineering Strategies for Co-Utilization of Carbon Sources in Microbes Wu, Yifei; Shen, Xiaolin; Yuan, Qipeng Bioengineering, Vol. 3, Issue 1 https://doi.org/10.3390/bioengineering3010010	journal	February 2016
Complete biosynthesis of cannabinoids and their unnatural analogues in yeast Luo, Xiaozhou; Reiter, Michael A.; d’Espaux, Leo Nature, Vol. 567, Issue 7746 https://doi.org/10.1038/s41586-019-0978-9	journal	February 2019
Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations Lenski, Richard E.; Rose, Michael R.; Simpson, Suzanne C. The American Naturalist, Vol. 138, Issue 6 https://doi.org/10.1086/285289	journal	December 1991
Enhanced 2′-Fucosyllactose production by engineered Saccharomyces cerevisiae using xylose as a co-substrate Lee, Jae Won; Kwak, Suryang; Liu, Jing-Jing Metabolic Engineering, Vol. 62 https://doi.org/10.1016/j.ymben.2020.10.003	journal	November 2020
Optogenetic approaches to cell migration and beyond Weitzman, Matthew; Hahn, Klaus M. Current Opinion in Cell Biology, Vol. 30 https://doi.org/10.1016/j.ceb.2014.08.004	journal	October 2014
CRISPR-based metabolic engineering in non-model microorganisms Lu, Liangyu; Shen, Xiaolin; Sun, Xinxiao Current Opinion in Biotechnology, Vol. 75 https://doi.org/10.1016/j.copbio.2022.102698	journal	June 2022
Engineering Saccharomyces cerevisiae for co-utilization of d-galacturonic acid and d-glucose from citrus peel waste Protzko, Ryan J.; Latimer, Luke N.; Martinho, Ze Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07589-w	journal	November 2018
Metabolic engineering of Corynebacterium glutamicum for hyperproduction of polymer-grade l- and d-lactic acid Tsuge, Yota; Kato, Naoto; Yamamoto, Shogo Applied Microbiology and Biotechnology, Vol. 103, Issue 8 https://doi.org/10.1007/s00253-019-09737-8	journal	March 2019
Hydrogenated monoterpenes as diesel fuel additives Tracy, Noah I.; Chen, Daichuan; Crunkleton, Daniel W. Fuel, Vol. 88, Issue 11 https://doi.org/10.1016/j.fuel.2009.02.002	journal	November 2009
A genetically encoded Förster resonance energy transfer sensor for monitoring in vivo trehalose-6-phosphate dynamics Peroza, Estevão A.; Ewald, Jennifer C.; Parakkal, Geetha Analytical Biochemistry, Vol. 474 https://doi.org/10.1016/j.ab.2014.12.019	journal	April 2015
Customized optimization of metabolic pathways by combinatorial transcriptional engineering Du, Jing; Yuan, Yongbo; Si, Tong Nucleic Acids Research, Vol. 40, Issue 18 https://doi.org/10.1093/nar/gks549	journal	June 2012
An evolutionary strategy for isobutanol production strain development in Escherichia coli Smith, Kevin M.; Liao, James C. Metabolic Engineering, Vol. 13, Issue 6 https://doi.org/10.1016/j.ymben.2011.08.004	journal	November 2011
RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization HamediRad, Mohammad; Lian, Jiazhang; Li, Hejun Biotechnology and Bioengineering, Vol. 115, Issue 6 https://doi.org/10.1002/bit.26570	journal	March 2018
Metabolic engineering for drug discovery and development Khosla, Chaitan; Keasling, Jay D. Nature Reviews Drug Discovery, Vol. 2, Issue 12 https://doi.org/10.1038/nrd1256	journal	December 2003
Accelerating strain engineering in biofuel research via build and test automation of synthetic biology Zhang, Jianzhi; Chen, Yongcan; Fu, Lihao Current Opinion in Biotechnology, Vol. 67 https://doi.org/10.1016/j.copbio.2021.01.010	journal	February 2021
Metabolic engineering for the utilization of carbohydrate portions of lignocellulosic biomass Kim, Jiwon; Hwang, Sungmin; Lee, Sun-Mi Metabolic Engineering, Vol. 71 https://doi.org/10.1016/j.ymben.2021.10.002	journal	May 2022
Synthetic Biology-Driven Microbial Production of Resveratrol: Advances and Perspectives Feng, Chao; Chen, Jing; Ye, Wenxin Frontiers in Bioengineering and Biotechnology, Vol. 10 https://doi.org/10.3389/fbioe.2022.833920	journal	January 2022
Multiplexed site-specific genome engineering for overproducing bioactive secondary metabolites in actinomycetes Li, Lei; Zheng, Guosong; Chen, Jun Metabolic Engineering, Vol. 40 https://doi.org/10.1016/j.ymben.2017.01.004	journal	March 2017
Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System Lian, Jiazhang; HamediRad, Mohammad; Zhao, Huimin Biotechnology Journal, Vol. 13, Issue 9 https://doi.org/10.1002/biot.201700601	journal	April 2018
Sensor-regulator and RNAi based bifunctional dynamic control network for engineered microbial synthesis Yang, Yaping; Lin, Yuheng; Wang, Jian Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05466-0	journal	August 2018
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains Khodayari, Ali; Maranas, Costas D. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13806	journal	December 2016
Dynamic metabolic control: towards precision engineering of metabolism Liu, Di; Mannan, Ahmad A.; Han, Yichao Journal of Industrial Microbiology & Biotechnology, Vol. 45, Issue 7 https://doi.org/10.1007/s10295-018-2013-9	journal	January 2018
A Transcription Factor-Based Biosensor for Detection of Itaconic Acid Hanko, Erik K. R.; Minton, Nigel P.; Malys, Naglis ACS Synthetic Biology, Vol. 7, Issue 5 https://doi.org/10.1021/acssynbio.8b00057	journal	April 2018
Frontiers in microbial 1-butanol and isobutanol production Chen, Chang-Ting; Liao, James C. FEMS Microbiology Letters, Vol. 363, Issue 5 https://doi.org/10.1093/femsle/fnw020	journal	January 2016
RNAi expression tuning, microfluidic screening, and genome recombineering for improved protein production in Saccharomyces cerevisiae Wang, Guokun; Björk, Sara M.; Huang, Mingtao Proceedings of the National Academy of Sciences, Vol. 116, Issue 19 https://doi.org/10.1073/pnas.1820561116	journal	April 2019
Overcoming lignocellulose‐derived microbial inhibitors: advancing the Saccharomyces cerevisiae resistance toolbox Brandt, Bianca A.; Jansen, Trudy; Görgens, Johann F. Biofuels, Bioproducts and Biorefining, Vol. 13, Issue 6 https://doi.org/10.1002/bbb.2042	journal	August 2019
Synthetic biology toolkit for engineering Cupriviadus necator H16 as a platform for CO2 valorization Pan, Haojie; Wang, Jia; Wu, Haoliang Biotechnology for Biofuels, Vol. 14, Issue 1 https://doi.org/10.1186/s13068-021-02063-0	journal	November 2021
Technoeconomic Analysis of Alternative Pathways of Isopropanol Production Panjapakkul, Warissara; El-Halwagi, Mahmoud M. ACS Sustainable Chemistry & Engineering, Vol. 6, Issue 8 https://doi.org/10.1021/acssuschemeng.8b01606	journal	July 2018
Metabolic Engineering of Escherichia coli for Efficient Conversion of Glycerol to Ethanol Trinh, C. T.; Srienc, F. Applied and Environmental Microbiology, Vol. 75, Issue 21 https://doi.org/10.1128/AEM.00670-09	journal	September 2009
Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds Ravikumar, Arjun; Arzumanyan, Garri A.; Obadi, Muaeen K. A. Cell, Vol. 175, Issue 7 https://doi.org/10.1016/j.cell.2018.10.021	journal	December 2018
Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids Zhang, Fuzhong; Carothers, James M.; Keasling, Jay D. Nature Biotechnology, Vol. 30, Issue 4 https://doi.org/10.1038/nbt.2149	journal	March 2012
Extended Metabolic Biosensor Design for Dynamic Pathway Regulation of Cell Factories Boada, Yadira; Vignoni, Alejandro; Picó, Jesús iScience, Vol. 23, Issue 7 https://doi.org/10.1016/j.isci.2020.101305	journal	July 2020
The development and characterization of synthetic minimal yeast promoters Redden, Heidi; Alper, Hal S. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms8810	journal	July 2015
End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis Linshiz, Gregory; Jensen, Erik; Stawski, Nina Journal of Biological Engineering, Vol. 10, Issue 1 https://doi.org/10.1186/s13036-016-0024-5	journal	February 2016
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Burgard, Anthony P.; Pharkya, Priti; Maranas, Costas D. Biotechnology and Bioengineering, Vol. 84, Issue 6 https://doi.org/10.1002/bit.10803	journal	October 2003
Materials Synthesis Insights from Scientific Literature via Text Extraction and Machine Learning Kim, Edward; Huang, Kevin; Saunders, Adam Chemistry of Materials, Vol. 29, Issue 21 https://doi.org/10.1021/acs.chemmater.7b03500	journal	October 2017
Functional reconstitution of a bacterial CO2 concentrating mechanism in Escherichia coli Flamholz, Avi I.; Dugan, Eli; Blikstad, Cecilia eLife, Vol. 9 https://doi.org/10.7554/eLife.59882	journal	October 2020
Quantitative Trait Loci (QTL)-Guided Metabolic Engineering of a Complex Trait Maurer, Matthew J.; Sutardja, Lawrence; Pinel, Dominic ACS Synthetic Biology, Vol. 6, Issue 3 https://doi.org/10.1021/acssynbio.6b00264	journal	November 2016
Flux Control at the Malonyl-CoA Node through Hierarchical Dynamic Pathway Regulation in Saccharomyces cerevisiae David, Florian; Nielsen, Jens; Siewers, Verena ACS Synthetic Biology, Vol. 5, Issue 3 https://doi.org/10.1021/acssynbio.5b00161	journal	January 2016
Quorum sensing-mediated protein degradation for dynamic metabolic pathway control in Saccharomyces cerevisiae Yang, Xiaoyu; Liu, Jianhui; Zhang, Jin Metabolic Engineering, Vol. 64 https://doi.org/10.1016/j.ymben.2021.01.010	journal	March 2021
An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals Carbonell, Pablo; Jervis, Adrian J.; Robinson, Christopher J. Communications Biology, Vol. 1, Issue 1 https://doi.org/10.1038/s42003-018-0076-9	journal	June 2018
Dynamic Control of Metabolism Ni, Cynthia; Dinh, Christina V.; Prather, Kristala L. J. Annual Review of Chemical and Biomolecular Engineering, Vol. 12, Issue 1 https://doi.org/10.1146/annurev-chembioeng-091720-125738	journal	June 2021
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D. PLoS Computational Biology, Vol. 10, Issue 2 https://doi.org/10.1371/journal.pcbi.1003487	journal	February 2014
Metabolic flux analysis and metabolic engineering of microorganisms Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup Mol. BioSyst., Vol. 4, Issue 2 https://doi.org/10.1039/B712395G	journal	January 2008
Automated multiplex genome-scale engineering in yeast Si, Tong; Chao, Ran; Min, Yuhao Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15187	journal	May 2017
Metabolic engineering for the microbial production of 1,3-propanediol Nakamura, Charles E; Whited, Gregory M Current Opinion in Biotechnology, Vol. 14, Issue 5, p. 454-459 https://doi.org/10.1016/j.copbio.2003.08.005	journal	October 2003
Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi Cacho, Ralph A.; Tang, Yi; Chooi, Yit-Heng Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00774	journal	January 2015
Biocatalysed synthesis planning using data-driven learning Probst, Daniel; Manica, Matteo; Nana Teukam, Yves Gaetan Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-28536-w	journal	February 2022
Systematic Optimization of Limonene Production in Engineered Escherichia coli Wu, Jihua; Cheng, Si; Cao, Jiayu Journal of Agricultural and Food Chemistry, Vol. 67, Issue 25 https://doi.org/10.1021/acs.jafc.9b01427	journal	May 2019
Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin Westfall, P. J.; Pitera, D. J.; Lenihan, J. R. Proceedings of the National Academy of Sciences, Vol. 109, Issue 3, p. E111-E118 https://doi.org/10.1073/pnas.1110740109	journal	January 2012
SCScore: Synthetic Complexity Learned from a Reaction Corpus Coley, Connor W.; Rogers, Luke; Green, William H. Journal of Chemical Information and Modeling, Vol. 58, Issue 2 https://doi.org/10.1021/acs.jcim.7b00622	journal	January 2018
What is flux balance analysis? Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø Nature Biotechnology, Vol. 28, Issue 3 https://doi.org/10.1038/nbt.1614	journal	March 2010
Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels Atsumi, Shota; Hanai, Taizo; Liao, James C. Nature, Vol. 451, Issue 7174, p. 86-89 https://doi.org/10.1038/nature06450	journal	January 2008
Enhanced limonene production in a fast-growing cyanobacterium through combinatorial metabolic engineering Lin, Po-Cheng; Zhang, Fuzhong; Pakrasi, Himadri B. Metabolic Engineering Communications, Vol. 12 https://doi.org/10.1016/j.mec.2021.e00164	journal	June 2021
Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols Avalos, José L.; Fink, Gerald R.; Stephanopoulos, Gregory Nature Biotechnology, Vol. 31, Issue 4 https://doi.org/10.1038/nbt.2509	journal	February 2013
From Laboratory to Field. Using Information from Arabidopsis to Engineer Salt, Cold, and Drought Tolerance in Crops Zhang, James Z.; Creelman, Robert A.; Zhu, Jian-Kang Plant Physiology, Vol. 135, Issue 2 https://doi.org/10.1104/pp.104.040295	journal	June 2004
A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Sikorski, R. S.; Hieter, P. Genetics, Vol. 122, Issue 1 https://doi.org/10.1093/genetics/122.1.19	journal	May 1989
A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases Cahn, Jackson K. B.; Werlang, Caroline A.; Baumschlager, Armin ACS Synthetic Biology, Vol. 6, Issue 2 https://doi.org/10.1021/acssynbio.6b00188	journal	October 2016
An Engineered B. subtilis Inducible Promoter System with over 10 000-Fold Dynamic Range Castillo-Hair, Sebastian M.; Fujita, Masaya; Igoshin, Oleg A. ACS Synthetic Biology, Vol. 8, Issue 7 https://doi.org/10.1021/acssynbio.8b00469	journal	June 2019
CRISPRi-dCas12a: A dCas12a-Mediated CRISPR Interference for Repression of Multiple Genes and Metabolic Engineering in Cyanobacteria Choi, Sun Young; Woo, Han Min ACS Synthetic Biology, Vol. 9, Issue 9 https://doi.org/10.1021/acssynbio.0c00091	journal	May 2020
Fermentation of Glycerol to Succinate by Metabolically Engineered Strains of Escherichia coli Zhang, X.; Shanmugam, K. T.; Ingram, L. O. Applied and Environmental Microbiology, Vol. 76, Issue 8 https://doi.org/10.1128/AEM.02902-09	journal	February 2010
CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window Halperin, Shakked O.; Tou, Connor J.; Wong, Eric B. Nature, Vol. 560, Issue 7717 https://doi.org/10.1038/s41586-018-0384-8	journal	August 2018
Improving Metabolic Pathway Efficiency by Statistical Model-Based Multivariate Regulatory Metabolic Engineering Xu, Peng; Rizzoni, Elizabeth Anne; Sul, Se-Yeong ACS Synthetic Biology, Vol. 6, Issue 1 https://doi.org/10.1021/acssynbio.6b00187	journal	August 2016
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways Shao, Zengyi; Zhao, Hua; Zhao, Huimin Nucleic Acids Research, Vol. 37, Issue 2 https://doi.org/10.1093/nar/gkn991	journal	December 2008
Metabolic engineering strategies to enable microbial utilization of C1 feedstocks Jiang, Wei; Hernández Villamor, David; Peng, Huadong Nature Chemical Biology, Vol. 17, Issue 8 https://doi.org/10.1038/s41589-021-00836-0	journal	July 2021
Top Value Added Chemicals from Biomass: Volume I -- Results of Screening for Potential Candidates from Sugars and Synthesis Gas Werpy, T.; Petersen, G. https://doi.org/10.2172/15008859	report	August 2004
Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch Soma, Yuki; Tsuruno, Keigo; Wada, Masaru Metabolic Engineering, Vol. 23 https://doi.org/10.1016/j.ymben.2014.02.008	journal	May 2014
Futuristic avenues of metabolic engineering techniques in bioremediation Sharma, Babita; Shukla, Pratyoosh Biotechnology and Applied Biochemistry, Vol. 69, Issue 1 https://doi.org/10.1002/bab.2080	journal	December 2020
Recent advances in the microbial production of isopentanol (3-Methyl-1-butanol) Runguphan, Weerawat; Sae-Tang, Kittapong; Tanapongpipat, Sutipa World Journal of Microbiology and Biotechnology, Vol. 37, Issue 6 https://doi.org/10.1007/s11274-021-03074-7	journal	May 2021
GroESL overexpression imparts Escherichia coli tolerance to i-, n-, and 2-butanol, 1,2,4-butanetriol and ethanol with complex and unpredictable patterns Zingaro, Kyle A.; Terry Papoutsakis, Eleftherios Metabolic Engineering, Vol. 15 https://doi.org/10.1016/j.ymben.2012.07.009	journal	January 2013
Integrated knowledge mining, genome-scale modeling, and machine learning for predicting Yarrowia lipolytica bioproduction Czajka, Jeffrey J.; Oyetunde, Tolutola; Tang, Yinjie J. Metabolic Engineering, Vol. 67 https://doi.org/10.1016/j.ymben.2021.07.003	journal	September 2021
Automated engineering of synthetic metabolic pathways for efficient biomanufacturing Otero-Muras, Irene; Carbonell, Pablo Metabolic Engineering, Vol. 63 https://doi.org/10.1016/j.ymben.2020.11.012	journal	January 2021
Metabolic engineering of a tyrosine-overproducing yeast platform using targeted metabolomics Gold, Nicholas D.; Gowen, Christopher M.; Lussier, Francois-Xavier Microbial Cell Factories, Vol. 14, Issue 1 https://doi.org/10.1186/s12934-015-0252-2	journal	May 2015
SteadyCom: Predicting microbial abundances while ensuring community stability Chan, Siu Hung Joshua; Simons, Margaret N.; Maranas, Costas D. PLOS Computational Biology, Vol. 13, Issue 5 https://doi.org/10.1371/journal.pcbi.1005539	journal	May 2017
A FRET-based biosensor for the quantification of glucose in culture supernatants of mL scale microbial cultivations Otten, Julia; Tenhaef, Niklas; Jansen, Roman P. Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1193-y	journal	August 2019
High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal Baez, Antonino; Cho, Kwang-Myung; Liao, James C. Applied Microbiology and Biotechnology, Vol. 90, Issue 5 https://doi.org/10.1007/s00253-011-3173-y	journal	March 2011
A new efficient gene disruption cassette for repeated use in budding yeast Guldener, U. Nucleic Acids Research, Vol. 24, Issue 13 https://doi.org/10.1093/nar/24.13.2519	journal	July 1996
Metabolic division of labor in microbial systems Tsoi, Ryan; Wu, Feilun; Zhang, Carolyn Proceedings of the National Academy of Sciences, Vol. 115, Issue 10 https://doi.org/10.1073/pnas.1716888115	journal	February 2018
Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols Ferreira, Raphael; Teixeira, Paulo Gonçalves; Gossing, Michael Metabolic Engineering Communications, Vol. 6 https://doi.org/10.1016/j.meteno.2018.01.002	journal	June 2018
Adaptive laboratory evolution and reverse engineering enhances autotrophic growth in Pichia pastoris Gassler, Thomas; Baumschabl, Michael; Sallaberger, Jakob Metabolic Engineering, Vol. 69 https://doi.org/10.1016/j.ymben.2021.11.007	journal	January 2022
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products Datsenko, K. A.; Wanner, B. L. Proceedings of the National Academy of Sciences, Vol. 97, Issue 12, p. 6640-6645 https://doi.org/10.1073/pnas.120163297	journal	May 2000
An artificial transport metabolon facilitates improved substrate utilization in yeast Thomik, Thomas; Wittig, Ilka; Choe, Jun-yong Nature Chemical Biology, Vol. 13, Issue 11 https://doi.org/10.1038/nchembio.2457	journal	September 2017
Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption Wang, Benjamin L.; Ghaderi, Adel; Zhou, Hang Nature Biotechnology, Vol. 32, Issue 5 https://doi.org/10.1038/nbt.2857	journal	April 2014
Engineering Robustness of Microbial Cell Factories Gong, Zhiwei; Nielsen, Jens; Zhou, Yongjin J. Biotechnology Journal, Vol. 12, Issue 10 https://doi.org/10.1002/biot.201700014	journal	September 2017
High-level semi-synthetic production of the potent antimalarial artemisinin Paddon, C. J.; Westfall, P. J.; Pitera, D. J. Nature, Vol. 496, Issue 7446 https://doi.org/10.1038/nature12051	journal	April 2013
Metabolic engineering of Escherichia coli for high-yield uridine production Wu, Heyun; Li, Yanjun; Ma, Qian Metabolic Engineering, Vol. 49 https://doi.org/10.1016/j.ymben.2018.09.001	journal	September 2018
Biosensors Used for Quantification of Nitrates in Plants Raul, Romero-Galindo; Irineo, Torres-Pacheco; Gerardo, Guevara-Gonzalez Ramon Journal of Sensors, Vol. 2016 https://doi.org/10.1155/2016/1630695	journal	January 2016
Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes Atsumi, Shota; Wu, Tung-Yun; Eckl, Eva-Maria Applied Microbiology and Biotechnology, Vol. 85, Issue 3 https://doi.org/10.1007/s00253-009-2085-6	journal	July 2009
The evolution, evolvability and engineering of gene regulatory DNA Vaishnav, Eeshit Dhaval; de Boer, Carl G.; Molinet, Jennifer Nature, Vol. 603, Issue 7901 https://doi.org/10.1038/s41586-022-04506-6	journal	March 2022
Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system Lian, Jiazhang; HamediRad, Mohammad; Hu, Sumeng Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01695-x	journal	November 2017
Microbial production of advanced biofuels Keasling, Jay; Garcia Martin, Hector; Lee, Taek Soon Nature Reviews Microbiology, Vol. 19, Issue 11 https://doi.org/10.1038/s41579-021-00577-w	journal	June 2021
Towards a fully automated algorithm driven platform for biosystems design HamediRad, Mohammad; Chao, Ran; Weisberg, Scott Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13189-z	journal	November 2019
A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnological producer of β-carotene Larroude, Macarena; Celinska, Ewelina; Back, Alexandre Biotechnology and Bioengineering, Vol. 115, Issue 2 https://doi.org/10.1002/bit.26473	journal	November 2017
A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data Costello, Zak; Martin, Hector Garcia npj Systems Biology and Applications, Vol. 4, Issue 1 https://doi.org/10.1038/s41540-018-0054-3	journal	May 2018
The yeast peroxisome: A dynamic storage depot and subcellular factory for squalene overproduction Liu, Guo-Song; Li, Tian; Zhou, Wei Metabolic Engineering, Vol. 57 https://doi.org/10.1016/j.ymben.2019.11.001	journal	January 2020
Current and future modalities of dynamic control in metabolic engineering Lalwani, Makoto A.; Zhao, Evan M.; Avalos, José L. Current Opinion in Biotechnology, Vol. 52 https://doi.org/10.1016/j.copbio.2018.02.007	journal	August 2018
Application of Next-Generation Sequencing Following Tandem Mass Spectrometry to Expand Newborn Screening for Inborn Errors of Metabolism: A Multicenter Study Yang, Yuqi; Wang, Leilei; Wang, Benjing Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00086	journal	February 2019
d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities Zomorrodi, Ali R.; Islam, Mohammad Mazharul; Maranas, Costas D. ACS Synthetic Biology, Vol. 3, Issue 4 https://doi.org/10.1021/sb4001307	journal	November 2013
Scale-up of industrial microbial processes Crater, Jason S.; Lievense, Jefferson C. FEMS Microbiology Letters, Vol. 365, Issue 13 https://doi.org/10.1093/femsle/fny138	journal	June 2018
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast Wang, Zhuo; Danziger, Samuel A.; Heavner, Benjamin D. PLOS Computational Biology, Vol. 13, Issue 5 https://doi.org/10.1371/journal.pcbi.1005489	journal	May 2017
Producing human ceramide-NS by metabolic engineering using yeast Saccharomyces cerevisiae Murakami, Suguru; Shimamoto, Toshi; Nagano, Hideaki Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep16319	journal	November 2015
Designing, construction and characterization of genetically encoded FRET-based nanosensor for real time monitoring of lysine flux in living cells Ameen, Seema; Ahmad, Mohammad; Mohsin, Mohd. Journal of Nanobiotechnology, Vol. 14, Issue 1 https://doi.org/10.1186/s12951-016-0204-y	journal	June 2016
Use of Bacteriophage λ Recombination Functions To Promote Gene Replacement in Escherichia coli Murphy, Kenan C. Journal of Bacteriology, Vol. 180, Issue 8 https://doi.org/10.1128/JB.180.8.2063-2071.1998	journal	April 1998
Improvement of glucaric acid production in E. coli via dynamic control of metabolic fluxes Reizman, Irene M. Brockman; Stenger, Andrew R.; Reisch, Chris R. Metabolic Engineering Communications, Vol. 2 https://doi.org/10.1016/j.meteno.2015.09.002	journal	December 2015
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism Lu, Hongzhong; Li, Feiran; Sánchez, Benjamín J. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11581-3	journal	August 2019
Bioconversion of lignocellulose: inhibitors and detoxification Jönsson, Leif J.; Alriksson, Björn; Nilvebrant, Nils-Olof Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-16	journal	January 2013
Discovery and characterization of novel d-xylose-specific transporters from Neurospora crassa and Pichia stipitis Du, Jing; Li, Sijin; Zhao, Huimin Molecular BioSystems, Vol. 6, Issue 11 https://doi.org/10.1039/c0mb00007h	journal	January 2010
Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae Jakočiūnas, Tadas; Bonde, Ida; Herrgård, Markus Metabolic Engineering, Vol. 28 https://doi.org/10.1016/j.ymben.2015.01.008	journal	March 2015
Recent Advances in Metabolic Engineering, Protein Engineering, and Transcriptome-Guided Insights Toward Synthetic Production of Taxol Mutanda, Ishmael; Li, Jianhua; Xu, Fanglin Frontiers in Bioengineering and Biotechnology, Vol. 9 https://doi.org/10.3389/fbioe.2021.632269	journal	February 2021
Overcoming glucose repression in mixed sugar fermentation by co-expressing a cellobiose transporter and a β-glucosidase in Saccharomyces cerevisiae Li, Sijin; Du, Jing; Sun, Jie Molecular BioSystems, Vol. 6, Issue 11 https://doi.org/10.1039/c0mb00063a	journal	January 2010
Engineering biological systems using automated biofoundries Chao, Ran; Mishra, Shekhar; Si, Tong Metabolic Engineering, Vol. 42 https://doi.org/10.1016/j.ymben.2017.06.003	journal	July 2017
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation Phaneuf, Patrick V.; Gosting, Dennis; Palsson, Bernhard O. Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky983	journal	October 2018
Engineering alcohol tolerance in yeast Lam, Felix H.; Ghaderi, Adel; Fink, Gerald R. Science, Vol. 346, Issue 6205 https://doi.org/10.1126/science.1257859	journal	October 2014
A rapid and reliable strategy for chromosomal integration of gene(s) with multiple copies Gu, Pengfei; Yang, Fan; Su, Tianyuan Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep09684	journal	April 2015
A genetic toolbox for metabolic engineering of Issatchenkia orientalis Cao, Mingfeng; Fatma, Zia; Song, Xiaofei Metabolic Engineering, Vol. 59 https://doi.org/10.1016/j.ymben.2020.01.005	journal	May 2020
Construction of Biologically Functional Bacterial Plasmids In Vitro Cohen, S. N.; Chang, A. C. Y.; Boyer, H. W. Proceedings of the National Academy of Sciences, Vol. 70, Issue 11 https://doi.org/10.1073/pnas.70.11.3240	journal	November 1973
Cytochrome b5 Increases the Rate of Product Formation by Cytochrome P450 2B4 and Competes with Cytochrome P450 Reductase for a Binding Site on Cytochrome P450 2B4 Zhang, Haoming; Im, Sang-Choul; Waskell, Lucy Journal of Biological Chemistry, Vol. 282, Issue 41 https://doi.org/10.1074/jbc.M703845200	journal	October 2007
Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli Bastian, Sabine; Liu, Xiang; Meyerowitz, Joseph T. Metabolic Engineering, Vol. 13, Issue 3, p. 345-352 https://doi.org/10.1016/j.ymben.2011.02.004	journal	May 2011
Engineered Synthetic Pathway for Isopropanol Production in Escherichia coli Hanai, T.; Atsumi, S.; Liao, J. C. Applied and Environmental Microbiology, Vol. 73, Issue 24, p. 7814-7818 https://doi.org/10.1128/AEM.01140-07	journal	October 2007
Synthetic Consortium of Escherichia coli for n-Butanol Production by Fermentation of the Glucose–Xylose Mixture Saini, Mukesh; Lin, Li-Jen; Chiang, Chung-Jen Journal of Agricultural and Food Chemistry, Vol. 65, Issue 46 https://doi.org/10.1021/acs.jafc.7b04275	journal	November 2017
Biofuels in the long-run global energy supply mix for transportation Timilsina, Govinda R. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 372, Issue 2006 https://doi.org/10.1098/rsta.2012.0323	journal	January 2014
Enhanced hydrogen production from glucose by metabolically engineered Escherichia coli Maeda, Toshinari; Sanchez-Torres, Viviana; Wood, Thomas K. Applied Microbiology and Biotechnology, Vol. 77, Issue 4 https://doi.org/10.1007/s00253-007-1217-0	journal	October 2007
Intelligent Microbial Heat-Regulating Engine (IMHeRE) for Improved Thermo-Robustness and Efficiency of Bioconversion Jia, Haiyang; Sun, Xiangying; Sun, Huan ACS Synthetic Biology, Vol. 5, Issue 4 https://doi.org/10.1021/acssynbio.5b00158	journal	February 2016
Pathway design using de novo steps through uncharted biochemical spaces Kumar, Akhil; Wang, Lin; Ng, Chiam Yu Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-017-02362-x	journal	January 2018
Heterologous production of raspberry ketone in the wine yeast Saccharomyces cerevisiae via pathway engineering and synthetic enzyme fusion Lee, Danna; Lloyd, Natoiya D. R.; Pretorius, Isak S. Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-016-0446-2	journal	March 2016
Mass Spectrometry-based Workflow for Accurate Quantification of Escherichia coli Enzymes: How Proteomics Can Play a Key Role in Metabolic Engineering Trauchessec, Mathieu; Jaquinod, Michel; Bonvalot, Aline Molecular & Cellular Proteomics, Vol. 13, Issue 4 https://doi.org/10.1074/mcp.M113.032672	journal	April 2014
A biosensor for the direct visualization of auxin Herud-Sikimić, Ole; Stiel, Andre C.; Kolb, Martina Nature, Vol. 592, Issue 7856 https://doi.org/10.1038/s41586-021-03425-2	journal	April 2021
The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2 Gassler, Thomas; Sauer, Michael; Gasser, Brigitte Nature Biotechnology, Vol. 38, Issue 2 https://doi.org/10.1038/s41587-019-0363-0	journal	December 2019
Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development Paddon, Chris J.; Keasling, Jay D. Nature Reviews Microbiology, Vol. 12, Issue 5 https://doi.org/10.1038/nrmicro3240	journal	April 2014
Bacterial synthesis of C3-C5 diols via extending amino acid catabolism Wang, Jian; Li, Chenyi; Zou, Yusong Proceedings of the National Academy of Sciences, Vol. 117, Issue 32 https://doi.org/10.1073/pnas.2003032117	journal	July 2020
A comparative analysis of single cell and droplet-based FACS for improving production phenotypes: Riboflavin overproduction in Yarrowia lipolytica Wagner, James M.; Liu, Leqian; Yuan, Shuo-Fu Metabolic Engineering, Vol. 47 https://doi.org/10.1016/j.ymben.2018.04.015	journal	May 2018
Advanced Strategies for Production of Natural Products in Yeast Chen, Ruibing; Yang, Shan; Zhang, Lei iScience, Vol. 23, Issue 3 https://doi.org/10.1016/j.isci.2020.100879	journal	March 2020
Altered sterol composition renders yeast thermotolerant Caspeta, Luis; Chen, Yun; Ghiaci, Payam Science, Vol. 346, Issue 6205 https://doi.org/10.1126/science.1258137	journal	October 2014
Targeting metabolic driving and intermediate influx in lysine catabolism for high-level glutarate production Li, Wenna; Ma, Lin; Shen, Xiaolin Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11289-4	journal	July 2019
Delete and Repeat: A Comprehensive Toolkit for Sequential Gene Knockout in the Budding Yeast Saccharomyces cerevisiae Hegemann, Johannes H.; Heick, Sven Boris Methods in Molecular Biology https://doi.org/10.1007/978-1-61779-197-0_12	book	January 2011
Combining CRISPR and CRISPRi Systems for Metabolic Engineering of E. coli and 1,4-BDO Biosynthesis Wu, Meng-Ying; Sung, Li-Yu; Li, Hung ACS Synthetic Biology, Vol. 6, Issue 12 https://doi.org/10.1021/acssynbio.7b00251	journal	September 2017
Advances in RNAi-Assisted Strain Engineering in Saccharomyces cerevisiae Chen, Yongcan; Guo, Erpeng; Zhang, Jianzhi Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.00731	journal	July 2020
Cell-Free Metabolic Engineering: Production of Chemicals by Minimized Reaction Cascades Guterl, Jan-Karl; Garbe, Daniel; Carsten, Jörg ChemSusChem, Vol. 5, Issue 11 https://doi.org/10.1002/cssc.201200365	journal	October 2012
Toward industrial production of isoprenoids in Escherichia coli : Lessons learned from CRISPR‐Cas9 based optimization of a chromosomally integrated mevalonate pathway Alonso‐Gutierrez, Jorge; Koma, Daisuke; Hu, Qijun Biotechnology and Bioengineering, Vol. 115, Issue 4 https://doi.org/10.1002/bit.26530	journal	February 2018
Growth of E. coli on formate and methanol via the reductive glycine pathway Kim, Seohyoung; Lindner, Steffen N.; Aslan, Selçuk Nature Chemical Biology, Vol. 16, Issue 5 https://doi.org/10.1038/s41589-020-0473-5	journal	February 2020
Engineering Escherichia coli for production of 4-hydroxymandelic acid using glucose–xylose mixture Li, Fei-Fei; Zhao, Ying; Li, Bing-Zhi Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-016-0489-4	journal	May 2016
Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts Zelezniak, Aleksej; Vowinckel, Jakob; Capuano, Floriana Cell Systems, Vol. 7, Issue 3 https://doi.org/10.1016/j.cels.2018.08.001	journal	September 2018
Ustilago maydis produces itaconic acid via the unusual intermediate trans -aconitate: Itaconic acid biosynthesis in U. maydis Geiser, Elena; Przybilla, Sandra K.; Friedrich, Alexandra Microbial Biotechnology, Vol. 9, Issue 1 https://doi.org/10.1111/1751-7915.12329	journal	December 2015
Constraint-based models predict metabolic and associated cellular functions Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A. Nature Reviews Genetics, Vol. 15, Issue 2 https://doi.org/10.1038/nrg3643	journal	January 2014
Improvement of cis , cis -Muconic Acid Production in Saccharomyces cerevisiae through Biosensor-Aided Genome Engineering Wang, Guokun; Øzmerih, Süleyman; Guerreiro, Rogério ACS Synthetic Biology, Vol. 9, Issue 3 https://doi.org/10.1021/acssynbio.9b00477	journal	February 2020
Engineering Yarrowia lipolytica for the selective and high-level production of isocitric acid through manipulation of mitochondrial dicarboxylate–tricarboxylate carriers Yuzbasheva, Evgeniya Y.; Scarcia, Pasquale; Yuzbashev, Tigran V. Metabolic Engineering, Vol. 65 https://doi.org/10.1016/j.ymben.2020.11.001	journal	May 2021
Metabolic engineering of Escherichia coli for high-level astaxanthin production with high productivity Park, Seon Young; Binkley, Robert M.; Kim, Won Jun Metabolic Engineering, Vol. 49 https://doi.org/10.1016/j.ymben.2018.08.002	journal	September 2018
Development of a commercial scale process for production of 1,4-butanediol from sugar Burgard, Anthony; Burk, Mark J.; Osterhout, Robin Current Opinion in Biotechnology, Vol. 42 https://doi.org/10.1016/j.copbio.2016.04.016	journal	December 2016
13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids Ghosh, Amit; Ando, David; Gin, Jennifer Frontiers in Bioengineering and Biotechnology, Vol. 4 https://doi.org/10.3389/fbioe.2016.00076	journal	October 2016
Combined evolutionary engineering and genetic manipulation improve low pH tolerance and butanol production in a synthetic microbial Clostridium community Wen, Zhiqiang; Ledesma‐Amaro, Rodrigo; Lu, Minrui Biotechnology and Bioengineering, Vol. 117, Issue 7 https://doi.org/10.1002/bit.27333	journal	April 2020
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities Edwards, J. S.; Palsson, B. O. Proceedings of the National Academy of Sciences, Vol. 97, Issue 10 https://doi.org/10.1073/pnas.97.10.5528	journal	May 2000
Improvement of isopropanol production by metabolically engineered Escherichia coli using gas stripping Inokuma, Kentaro; Liao, James C.; Okamoto, Masahiro Journal of Bioscience and Bioengineering, Vol. 110, Issue 6 https://doi.org/10.1016/j.jbiosc.2010.07.010	journal	December 2010
Development of an anhydrotetracycline-inducible gene expression system for solvent-producing Clostridium acetobutylicum: A useful tool for strain engineering Dong, Hongjun; Tao, Wenwen; Zhang, Yanping Metabolic Engineering, Vol. 14, Issue 1 https://doi.org/10.1016/j.ymben.2011.10.004	journal	January 2012
CRISPRi-mediated metabolic engineering of E. coli for O-methylated anthocyanin production Cress, Brady F.; Leitz, Quentin D.; Kim, Daniel C. Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-016-0623-3	journal	January 2017
Metabolic Engineering of Corynebacterium glutamicum for the High-Level Production of Cadaverine That Can Be Used for the Synthesis of Biopolyamide 510 Kim, Hee Taek; Baritugo, Kei-Anne; Oh, Young Hoon ACS Sustainable Chemistry & Engineering, Vol. 6, Issue 4 https://doi.org/10.1021/acssuschemeng.8b00009	journal	February 2018
Engineering efficient production of itaconic acid from diverse substrates in Escherichia coli Chang, Peiching; Chen, Grey S.; Chu, Hsiang-Yuan Journal of Biotechnology, Vol. 249 https://doi.org/10.1016/j.jbiotec.2017.03.026	journal	May 2017
Modeling metabolism of the human gut microbiome Magnúsdóttir, Stefanía; Thiele, Ines Current Opinion in Biotechnology, Vol. 51 https://doi.org/10.1016/j.copbio.2017.12.005	journal	June 2018
Directed Evolution of Methanococcus jannaschii Citramalate Synthase for Biosynthesis of 1-Propanol and 1-Butanol by Escherichia coli Atsumi, S.; Liao, J. C. Applied and Environmental Microbiology, Vol. 74, Issue 24 https://doi.org/10.1128/AEM.02046-08	journal	October 2008
In vivo hypermutation and continuous evolution Molina, Rosana S.; Rix, Gordon; Mengiste, Amanuella A. Nature Reviews Methods Primers, Vol. 2, Issue 1 https://doi.org/10.1038/s43586-022-00119-5	journal	May 2022
Stable high-copy-number bacteriophage λ promoter vectors for overproduction of proteins in Escherichia coli Love, Christopher A.; Lilley, Penelope E.; Dixon, Nicholas E. Gene, Vol. 176, Issue 1-2 https://doi.org/10.1016/0378-1119(96)00208-9	journal	October 1996
Optogenetic switch for controlling the central metabolic flux of Escherichia coli Tandar, Sebastian Tommi; Senoo, Sachie; Toya, Yoshihiro Metabolic Engineering, Vol. 55 https://doi.org/10.1016/j.ymben.2019.06.002	journal	September 2019
Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering Liu, Yang; Liu, Ye; Wang, Meng Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02012	journal	October 2017
Improving lycopene production in Escherichia coli by engineering metabolic control Farmer, William R.; Liao, James C. Nature Biotechnology, Vol. 18, Issue 5 https://doi.org/10.1038/75398	journal	May 2000
Exploiting transcriptomic data for metabolic engineering: toward a systematic strain design Kim, Minsuk; Park, Beom Gi; Kim, Joonwon Current Opinion in Biotechnology, Vol. 54 https://doi.org/10.1016/j.copbio.2018.01.020	journal	December 2018
Temperature-dependent dynamic control of the TCA cycle increases volumetric productivity of itaconic acid production by Escherichia coli Harder, Björn-Johannes; Bettenbrock, Katja; Klamt, Steffen Biotechnology and Bioengineering, Vol. 115, Issue 1 https://doi.org/10.1002/bit.26446	journal	October 2017
Metabolic engineering of Escherichia coli for the de novo stereospecific biosynthesis of 1,2-propanediol through lactic acid Niu, Wei; Kramer, Levi; Mueller, Joshua Metabolic Engineering Communications, Vol. 8 https://doi.org/10.1016/j.mec.2018.e00082	journal	June 2019
Determination of the fluxes in the central metabolism ofCorynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing Marx, Achim; de Graaf, Albert A.; Wiechert, Wolfgang Biotechnology and Bioengineering, Vol. 49, Issue 2 https://doi.org/10.1002/(SICI)1097-0290(19960120)49:2<111::AID-BIT1>3.0.CO;2-T	journal	January 1996
Toward a science of metabolic engineering Bailey, J. E. Science, Vol. 252, Issue 5013, p. 1668-1675 https://doi.org/10.1126/science.2047876	journal	June 1991
Molecular characterization of KU70 and KU80 homologues and exploitation of a KU70-deficient mutant for improving gene deletion frequency in Rhodosporidium toruloides Koh, Chong Mei; Liu, Yanbin BMC Microbiology, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2180-14-50	journal	January 2014
Effective CRISPR interference of an endogenous gene via a single transgene in mice MacLeod, Ryan S.; Cawley, Keisha M.; Gubrij, Igor Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-53611-6	journal	November 2019
MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis Willemsen, A. Marcel; Hendrickx, Diana M.; Hoefsloot, Huub C. J. Molecular BioSystems, Vol. 11, Issue 1 https://doi.org/10.1039/C4MB00510D	journal	January 2015
Substrate Channeling by a Rationally Designed Fusion Protein in a Biocatalytic Cascade Kummer, Matthew J.; Lee, Yoo Seok; Yuan, Mengwei JACS Au, Vol. 1, Issue 8 https://doi.org/10.1021/jacsau.1c00180	journal	July 2021
Machine and deep learning meet genome-scale metabolic modeling Zampieri, Guido; Vijayakumar, Supreeta; Yaneske, Elisabeth PLOS Computational Biology, Vol. 15, Issue 7 https://doi.org/10.1371/journal.pcbi.1007084	journal	July 2019
Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories Zhou, Yongjin J.; Buijs, Nicolaas A.; Zhu, Zhiwei Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11709	journal	May 2016
Electrical-biological hybrid system for CO2 reduction Tashiro, Yohei; Hirano, Shinichi; Matson, Morgan M. Metabolic Engineering, Vol. 47 https://doi.org/10.1016/j.ymben.2018.03.015	journal	May 2018
Manipulating multi-system of NADPH regulation in Escherichia coli for enhanced S-adenosylmethionine production Chen, Yawei; Xu, Duanbin; Fan, Lihai RSC Advances, Vol. 5, Issue 51 https://doi.org/10.1039/C5RA02937F	journal	January 2015
Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli Pitera, Douglas J.; Paddon, Chris J.; Newman, Jack D. Metabolic Engineering, Vol. 9, Issue 2 https://doi.org/10.1016/j.ymben.2006.11.002	journal	March 2007
Achievements and Perspectives in 1,4-Butanediol Production from Engineered Microorganisms Cheng, Jie; Li, Juan; Zheng, Linggang Journal of Agricultural and Food Chemistry, Vol. 69, Issue 36 https://doi.org/10.1021/acs.jafc.1c03769	journal	September 2021
A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae Shi, Shuobo; Liang, Youyun; Zhang, Mingzi M. Metabolic Engineering, Vol. 33 https://doi.org/10.1016/j.ymben.2015.10.011	journal	January 2016
Integrating continuous hypermutation with high‐throughput screening for optimization of cis,cis ‐muconic acid production in yeast Jensen, Emil D.; Ambri, Francesca; Bendtsen, Marie B. Microbial Biotechnology, Vol. 14, Issue 6 https://doi.org/10.1111/1751-7915.13774	journal	March 2021
Towards bio-upcycling of polyethylene terephthalate Tiso, Till; Narancic, Tanja; Wei, Ren Metabolic Engineering, Vol. 66 https://doi.org/10.1016/j.ymben.2021.03.011	journal	July 2021
Characterization and engineering of a two-enzyme system for plastics depolymerization Knott, Brandon C.; Erickson, Erika; Allen, Mark D. Proceedings of the National Academy of Sciences, Vol. 117, Issue 41 https://doi.org/10.1073/pnas.2006753117	journal	September 2020
Ensemble Modeling of Metabolic Networks Tran, Linh M.; Rizk, Matthew L.; Liao, James C. Biophysical Journal, Vol. 95, Issue 12 https://doi.org/10.1529/biophysj.108.135442	journal	December 2008
Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints Li, Feiran; Chen, Yu; Qi, Qi Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-30689-7	journal	May 2022
A Hierarchical Transcriptional Regulatory Network Required for Long-Term Thermal Stress Tolerance in an Industrial Saccharomyces cerevisiae Strain Gan, Yuman; Qi, Xianni; Lin, Yuping Frontiers in Bioengineering and Biotechnology, Vol. 9 https://doi.org/10.3389/fbioe.2021.826238	journal	January 2022
A Method to Constrain Genome-Scale Models with 13C Labeling Data García Martín, Héctor; Kumar, Vinay Satish; Weaver, Daniel PLOS Computational Biology, Vol. 11, Issue 9 https://doi.org/10.1371/journal.pcbi.1004363	journal	September 2015
Machine learning framework for assessment of microbial factory performance Oyetunde, Tolutola; Liu, Di; Martin, Hector Garcia PLOS ONE, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pone.0210558	journal	January 2019
Engineering Halomonas species TD01 for enhanced polyhydroxyalkanoates synthesis via CRISPRi Tao, Wei; Lv, Li; Chen, Guo-Qiang Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0655-3	journal	April 2017
Controlling Citrate Synthase Expression by CRISPR/Cas9 Genome Editing for n -Butanol Production in Escherichia coli Heo, Min-Ji; Jung, Hwi-Min; Um, Jaeyong ACS Synthetic Biology, Vol. 6, Issue 2 https://doi.org/10.1021/acssynbio.6b00134	journal	October 2016
Serine Integrases: Advancing Synthetic Biology Merrick, Christine A.; Zhao, Jia; Rosser, Susan J. ACS Synthetic Biology, Vol. 7, Issue 2 https://doi.org/10.1021/acssynbio.7b00308	journal	January 2018
Glutaric acid production by systems metabolic engineering of an l -lysine–overproducing Corynebacterium glutamicum Han, Taehee; Kim, Gi Bae; Lee, Sang Yup Proceedings of the National Academy of Sciences, Vol. 117, Issue 48 https://doi.org/10.1073/pnas.2017483117	journal	November 2020
PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction Enghiad, Behnam; Xue, Pu; Singh, Nilmani Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-30355-y	journal	May 2022
Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli Jervis, Adrian J.; Carbonell, Pablo; Vinaixa, Maria ACS Synthetic Biology, Vol. 8, Issue 1 https://doi.org/10.1021/acssynbio.8b00398	journal	December 2018
Light-based control of metabolic flux through assembly of synthetic organelles Zhao, Evan M.; Suek, Nathan; Wilson, Maxwell Z. Nature Chemical Biology, Vol. 15, Issue 6 https://doi.org/10.1038/s41589-019-0284-8	journal	May 2019
Engineered mitochondrial production of monoterpenes in Saccharomyces cerevisiae Yee, Danielle A.; DeNicola, Anthony B.; Billingsley, John M. Metabolic Engineering, Vol. 55 https://doi.org/10.1016/j.ymben.2019.06.004	journal	September 2019
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model Ding, Shaozhen; Tian, Yu; Cai, Pengli Nucleic Acids Research, Vol. 48, Issue W1 https://doi.org/10.1093/nar/gkaa230	journal	April 2020
Metabolic Engineering of a Pentose Metabolism Pathway in Ethanologenic Zymomonas mobilis Zhang, M.; Eddy, C.; Deanda, K. Science, Vol. 267, Issue 5195 https://doi.org/10.1126/science.267.5195.240	journal	January 1995
Optogenetic regulation of engineered cellular metabolism for microbial chemical production Zhao, Evan M.; Zhang, Yanfei; Mehl, Justin Nature, Vol. 555, Issue 7698 https://doi.org/10.1038/nature26141	journal	March 2018
Metabolic engineering of Saccharomyces cerevisiae for efficient production of glucaric acid at high titer Chen, Na; Wang, Jingya; Zhao, Yunying Microbial Cell Factories, Vol. 17, Issue 1 https://doi.org/10.1186/s12934-018-0914-y	journal	May 2018
SCPD: a promoter database of the yeast Saccharomyces cerevisiae Zhu, J.; Zhang, M. Q. Bioinformatics, Vol. 15, Issue 7 https://doi.org/10.1093/bioinformatics/15.7.607	journal	July 1999
Harnessing yeast organelles for metabolic engineering Hammer, Sarah K.; Avalos, José L. Nature Chemical Biology, Vol. 13, Issue 8 https://doi.org/10.1038/nchembio.2429	journal	July 2017
Microbially Derived Artemisinin: A Biotechnology Solution to the Global Problem of Access to Affordable Antimalarial Drugs Keasling, Jay D.; Diagana, Thierry T.; Hale, Victoria The American Journal of Tropical Medicine and Hygiene, Vol. 77, Issue 6_Suppl https://doi.org/10.4269/ajtmh.2007.77.198	journal	December 2007
Efficient L-Alanine Production by a Thermo-Regulated Switch in Escherichia coli Zhou, Li; Deng, Can; Cui, Wen-Jing Applied Biochemistry and Biotechnology, Vol. 178, Issue 2 https://doi.org/10.1007/s12010-015-1874-x	journal	October 2015
Application of an oxygen‐inducible nar promoter system in metabolic engineering for production of biochemicals in Escherichia coli Hwang, Hee J.; Kim, Jin W.; Ju, Si Y. Biotechnology and Bioengineering, Vol. 114, Issue 2 https://doi.org/10.1002/bit.26082	journal	September 2016
Promoter engineering strategies for the overproduction of valuable metabolites in microbes Jin, Li-Qun; Jin, Wei-Rong; Ma, Zhang-Chi Applied Microbiology and Biotechnology, Vol. 103, Issue 21-22 https://doi.org/10.1007/s00253-019-10172-y	journal	October 2019
Machine learning applications in systems metabolic engineering Kim, Gi Bae; Kim, Won Jun; Kim, Hyun Uk Current Opinion in Biotechnology, Vol. 64 https://doi.org/10.1016/j.copbio.2019.08.010	journal	August 2020
Synergistic improvement of N-acetylglucosamine production by engineering transcription factors and balancing redox cofactors Deng, Chen; Lv, Xueqin; Li, Jianghua Metabolic Engineering, Vol. 67 https://doi.org/10.1016/j.ymben.2021.07.012	journal	September 2021
Increased isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance Matsuda, Fumio; Ishii, Jun; Kondo, Takashi Microbial Cell Factories, Vol. 12, Issue 1 https://doi.org/10.1186/1475-2859-12-119	journal	January 2013
Machine learning for metabolic engineering: A review Lawson, Christopher E.; Martí, Jose Manuel; Radivojevic, Tijana Metabolic Engineering, Vol. 63 https://doi.org/10.1016/j.ymben.2020.10.005	journal	January 2021
Isopropanol production with engineered Cupriavidus necator as bioproduction platform Grousseau, Estelle; Lu, Jingnan; Gorret, Nathalie Applied Microbiology and Biotechnology, Vol. 98, Issue 9 https://doi.org/10.1007/s00253-014-5591-0	journal	March 2014
Microdroplet-based system for culturing of environmental microorganisms using FNAP-sort Saito, Kanako; Ota, Yuri; Tourlousse, Dieter M. Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-88974-2	journal	May 2021
Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol Kim, Taeho; Stogios, Peter J.; Khusnutdinova, Anna N. Journal of Biological Chemistry, Vol. 295, Issue 2 https://doi.org/10.1074/jbc.RA119.011363	journal	January 2020
Effects of Growth Mode and Pyruvate Carboxylase on Succinic Acid Production by Metabolically Engineered Strains of Escherichia coli Vemuri, G. N.; Eiteman, M. A.; Altman, E. Applied and Environmental Microbiology, Vol. 68, Issue 4 https://doi.org/10.1128/AEM.68.4.1715-1727.2002	journal	April 2002
Exploiting tandem repetitive promoters for high-level production of 3-hydroxypropionic acid Zhao, Peng; Ma, Chunlu; Xu, Lida Applied Microbiology and Biotechnology, Vol. 103, Issue 10 https://doi.org/10.1007/s00253-019-09772-5	journal	March 2019
Stereospecific Microbial Conversion of Lactic Acid into 1,2-Propanediol Niu, Wei; Guo, Jiantao ACS Synthetic Biology, Vol. 4, Issue 4 https://doi.org/10.1021/sb500240p	journal	July 2014
Engineering the Lipid and Fatty Acid Metabolism in Yarrowia lipolytica for Sustainable Production of High Oleic Oils Wang, Kaifeng; Shi, Tian-Qiong; Wang, Jinpeng ACS Synthetic Biology, Vol. 11, Issue 4 https://doi.org/10.1021/acssynbio.1c00613	journal	March 2022
Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control Leonard, E.; Ajikumar, P. K.; Thayer, K. Proceedings of the National Academy of Sciences, Vol. 107, Issue 31, p. 13654-13659 https://doi.org/10.1073/pnas.1006138107	journal	July 2010
In silico evolution of Aspergillus niger organic acid production suggests strategies for switching acid output Upton, Daniel J.; McQueen-Mason, Simon J.; Wood, A. Jamie Biotechnology for Biofuels, Vol. 13, Issue 1 https://doi.org/10.1186/s13068-020-01678-z	journal	February 2020
Network rigidity and metabolic engineering in metabolite overproduction Stephanopoulos, G.; Vallino, J. Science, Vol. 252, Issue 5013 https://doi.org/10.1126/science.1904627	journal	June 1991
Hyperproduction of Tryptophan in Corynebacterium glutamicum by Pathway Engineering Katsumata, Ryoichi; Ikeda, Masato Nature Biotechnology, Vol. 11, Issue 8 https://doi.org/10.1038/nbt0893-921	journal	August 1993
Developing an industrial artemisinic acid fermentation process to support the cost-effective production of antimalarial artemisinin-based combination therapies Lenihan, Jacob R.; Tsuruta, Hiroko; Diola, Don Biotechnology Progress, Vol. 24, Issue 5 https://doi.org/10.1002/btpr.27	journal	September 2008
Advances in the development and application of microbial consortia for metabolic engineering Jawed, Kamran; Yazdani, Syed Shams; Koffas, Mattheos AG. Metabolic Engineering Communications, Vol. 9 https://doi.org/10.1016/j.mec.2019.e00095	journal	December 2019
Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach Blazeck, John; Liu, Leqian; Redden, Heidi Applied and Environmental Microbiology, Vol. 77, Issue 22 https://doi.org/10.1128/AEM.05763-11	journal	September 2011
Applications and advances of metabolite biosensors for metabolic engineering Liu, Di; Evans, Trent; Zhang, Fuzhong Metabolic Engineering, Vol. 31 https://doi.org/10.1016/j.ymben.2015.06.008	journal	September 2015
In vivo biosensors: mechanisms, development, and applications Shi, Shuobo; Ang, Ee Lui; Zhao, Huimin Journal of Industrial Microbiology and Biotechnology, Vol. 45, Issue 7 https://doi.org/10.1007/s10295-018-2004-x	journal	July 2018
High-Throughput Quantitative Metabolomics: Workflow for Cultivation, Quenching, and Analysis of Yeast in a Multiwell Format Ewald, Jennifer Christina; Heux, Stéphanie; Zamboni, Nicola Analytical Chemistry, Vol. 81, Issue 9 https://doi.org/10.1021/ac900002u	journal	March 2009
Sugar Synthesis from CO2 in Escherichia coli Antonovsky, Niv; Gleizer, Shmuel; Noor, Elad Cell, Vol. 166, Issue 1 https://doi.org/10.1016/j.cell.2016.05.064	journal	June 2016
Automated Planning Enables Complex Protocols on Liquid-Handling Robots Whitehead, Ellis; Rudolf, Fabian; Kaltenbach, Hans-Michael ACS Synthetic Biology, Vol. 7, Issue 3 https://doi.org/10.1021/acssynbio.8b00021	journal	February 2018
Dynamic control in metabolic engineering: Theories, tools, and applications Hartline, Christopher J.; Schmitz, Alexander C.; Han, Yichao Metabolic Engineering, Vol. 63 https://doi.org/10.1016/j.ymben.2020.08.015	journal	January 2021
Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry Chao, Ran; Liang, Jing; Tasan, Ipek ACS Synthetic Biology, Vol. 6, Issue 4 https://doi.org/10.1021/acssynbio.6b00293	journal	January 2017
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities Zomorrodi, Ali R.; Maranas, Costas D. PLoS Computational Biology, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pcbi.1002363	journal	February 2012
Pathway-based signature transcriptional profiles as tolerance phenotypes for the adapted industrial yeast Saccharomyces cerevisiae resistant to furfural and HMF Liu, Z. Lewis; Ma, Menggen Applied Microbiology and Biotechnology, Vol. 104, Issue 8 https://doi.org/10.1007/s00253-020-10434-0	journal	February 2020
Optimized gene expression from bacterial chromosome by high-throughput integration and screening Saleski, Tatyana E.; Chung, Meng Ting; Carruthers, David N. Science Advances, Vol. 7, Issue 7 https://doi.org/10.1126/sciadv.abe1767	journal	February 2021

Similar Records

Directed Evolution: Methodologies and Applications

Journal Article · Fri Jul 23 00:00:00 EDT 2021 · Chemical Reviews · OSTI ID:1977811

Identification of novel metabolic engineering targets for S-adenosyl-L-methionine production in Saccharomyces cerevisiae via genome-scale engineering

Journal Article · Thu Jul 01 00:00:00 EDT 2021 · Metabolic Engineering · OSTI ID:1852565

Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications

Journal Article · Sun Jan 24 23:00:00 EST 2021 · ACS Synthetic Biology · OSTI ID:1853117

Related Subjects

Chemistry

Metabolic Engineering: Methodologies and Applications

Citation Formats

References (447)

Similar Records

Related Subjects