Strategies for systems‐level metabolic engineering

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

Datsenko, K., & Wanner, B. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.120163297 · Cited by 15,902 · see citing works

Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection

Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858 · see citing works

From genomics to chemical genomics: new developments in KEGG

Kanehisa, M. I. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj102 · Cited by 3,126 · see citing works

Production of the antimalarial drug precursor artemisinic acid in engineered yeast

Ro, D.-K., Paradise, E. M., Ouellet, M., Fisher, K. J., Newman, K. L., Ndungu, J. M., Ho, K. A., Eachus, R. A., Ham, T. S., Kirby, J., et al. (2006) · Nature · doi:10.1038/nature04640 · Cited by 2,805 · see citing works

New heterologous modules for classical or PCR‐based gene disruptions in Saccharomyces cerevisiae

Wach, A., Brachat, A., Pöhlmann, R., & Philippsen, P. (1994) · Yeast · doi:10.1002/yea.320101310 · Cited by 2,532 · see citing works

Engineering a mevalonate pathway in Escherichia coli for production of terpenoids

Martin, V. J. J., Pitera, D. J., Withers, S. T., Newman, J. D., & Keasling, J. D. (2003) · Nature Biotechnology · doi:10.1038/nbt833 · Cited by 1,720 · see citing works

Analysis of optimality in natural and perturbed metabolic networks

Segrè, D., Vitkup, D., & Church, G. M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.232349399 · Cited by 1,375 · see citing works

A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information

Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., Broadbelt, L. J., Vassily Hatzimanikatis, A., & Palsson, B. Ø. (2007) · Molecular Systems Biology · doi:10.1038/msb4100155 · Cited by 1,367 · see citing works

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

Burgard, A. P., Pharkya, P., & Maranas, C. D. (2003) · Biotechnology and Bioengineering · doi:10.1002/bit.10803 · Cited by 1,262 · see citing works

Metabolic Engineering: Principles and Methodologies

Stephanopoulos, G. N., Aristidou, A. A., & NIELSEN, J. K. (1998) · Thammasat University Digital Collections · Cited by 1,184 · see citing works

Genome-scale models of microbial cells: evaluating the consequences of constraints

Price, N. D., Reed, J. L., & Palsson, B. Ø. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro1023 · Cited by 1,024 · see citing works

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

Reed, J. L., Vo, T. D., Schilling, C. H., & Palsson, B. Ø. (2003) · Genome biology · doi:10.1186/gb-2003-4-9-r54 · Cited by 1,001 · see citing works

Biotechnology of succinic acid production and markets for derived industrial products

Zeikus, J. G., Jain, M. K., & Elankovan, P. (1999) · Applied Microbiology and Biotechnology · doi:10.1007/s002530051431 · Cited by 964 · see citing works

The <i>Escherichia coli</i> MG1655 <i>in silico</i> metabolic genotype: Its definition, characteristics, and capabilities

Edwards, J. S., & Palsson, B. O. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.10.5528 · Cited by 875 · see citing works

Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production

Alper, H., Moxley, J., Nevoigt, E., Fink, G. R., & Stephanopoulos, G. (2006) · Science · doi:10.1126/science.1131969 · Cited by 823 · see citing works

Production of succinic acid by bacterial fermentation

Song, H., & Lee, S. Y. (2006) · Enzyme and Microbial Technology · doi:10.1016/j.enzmictec.2005.11.043 · Cited by 816 · see citing works

The model organism as a system: integrating 'omics' data sets

Joyce, A. R., & Palsson, B. Ø. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1857 · Cited by 790 · see citing works

EcoCyc: a comprehensive database resource for Escherichia coli

Keseler, I. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki108 · Cited by 737 · see citing works

Global organization of metabolic fluxes in the bacterium Escherichia coli

Almaas, E., Kovács, B., Vicsek, T., Oltvai, Z. N., & Barabási, A.-Ĺ. (2004) · Nature · doi:10.1038/nature02289 · Cited by 710 · see citing works

MetaCyc: a multiorganism database of metabolic pathways and enzymes

Caspi, R. R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj128 · Cited by 620 · see citing works

Metabolic engineering of <i>Escherichia coli</i> for the production of <scp>l</scp> -valine based on transcriptome analysis and <i>in silico</i> gene knockout simulation

Park, J. H., Lee, K. H., Kim, T. Y., & Lee, S. Y. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702609104 · Cited by 592 · see citing works

Dynamic modeling of the central carbon metabolism of Escherichia coli

Chassagnole, C., Noisommit‐Rizzi, N., Schmid, J. W., Mauch, K., & Reuß, M. (2002) · Biotechnology and Bioengineering · doi:10.1002/bit.10288 · Cited by 553 · see citing works

OptStrain: A computational framework for redesign of microbial production systemsPreprint

Pharkya, P., Burgard, A. P., & Maranas, C. D. (2004) · Genome Research · doi:10.1101/gr.2872004 · Cited by 498 · see citing works

Systems metabolic engineering of Escherichia coli for L‐threonine production

Lee, K. H., Park, J. H., Kim, T. Y., Kim, H. U., & Lee, S. Y. (2007) · Molecular Systems Biology · doi:10.1038/msb4100196 · Cited by 488 · see citing works

Prospects for a bio-based succinate industry

McKinlay, J. B., Vieille, C., & Zeikus, J. G. (2007) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-007-1057-y · Cited by 472 · see citing works

Regulatory on/off minimization of metabolic flux changes after genetic perturbations

Shlomi, T., Berkman, O., & Ruppin, E. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406346102 · Cited by 458 · see citing works

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli

Alper, H. S., Jin, Y., Moxley, J. F., & Stephanopoulos, G. N. (2005) · Metabolic Engineering · doi:10.1016/j.ymben.2004.12.003 · Cited by 450 · see citing works

Global transcription machinery engineering: A new approach for improving cellular phenotype

Alper, H. S., & Stephanopoulos, G. N. (2007) · Metabolic Engineering · doi:10.1016/j.ymben.2006.12.002 · Cited by 448 · see citing works

Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli

Pitera, D. J., Paddon, C. J., Newman, J. D., & Keasling, J. D. (2006) · Metabolic Engineering · doi:10.1016/j.ymben.2006.11.002 · Cited by 440 · see citing works

Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets

Alper, H. S., Miyaoku, K., & Stephanopoulos, G. N. (2005) · Nature Biotechnology · doi:10.1038/nbt1083 · Cited by 433 · see citing works

Comparison of network-based pathway analysis methods

Papin, J. A., Stelling, J., Price, N. D., Klamt, S., Schuster, S., & Palsson, B. Ø. (2004) · Trends in biotechnology · doi:10.1016/j.tibtech.2004.06.010 · Cited by 370 · see citing works

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production

Bro, C., Regenberg, B., FORSTER, J., & Nielsen, J. (2005) · Metabolic Engineering · doi:10.1016/j.ymben.2005.09.007 · Cited by 367 · see citing works

Engineering Escherichia coli for production of functionalized terpenoids using plant P450s

Chang, M. C. Y., Eachus, R. A., Trieu, W., Ro, D.-K., & Keasling, J. D. (2007) · Nature Chemical Biology · doi:10.1038/nchembio875 · Cited by 364 · see citing works

In silico design and adaptive evolution of Escherichia coli for production of lactic acid

Fong, S. S., Burgard, A. P., Herring, C. D., Knight, E. M., Blattner, F. R., Maranas, C. D., & Palsson, B. Ø. (2005) · Biotechnology and Bioengineering · doi:10.1002/bit.20542 · Cited by 363 · see citing works

Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout Simulation

Lee, S. J., Lee, D., Kim, B. H., Kim, B. H., Lee, S. Y., & Lee, S. Y. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.7880-7887.2005 · Cited by 309 · see citing works

Systems biotechnology for strain improvement

Lee, S. Y., Lee, D., & Kim, T. Y. (2005) · Trends in biotechnology · doi:10.1016/j.tibtech.2005.05.003 · Cited by 295 · see citing works

Two approaches for metabolic pathway analysis?

Klamt, S., & Stelling, J. (2003) · Trends in biotechnology · doi:10.1016/s0167-7799(02)00034-3 · Cited by 293 · see citing works

Genomes OnLine Database (GOLD): a monitor of genome projects world-wide

Bernal, A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.126 · Cited by 285 · see citing works

Systems approach to refining genome annotation

Reed, J. L., Patel, T., Chen, K. H., Joyce, A. R., Applebee, M. K., Herring, C. D., Bui, O., Knight, E. M., Fong, S. S., & Palsson, B. Ø. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603364103 · Cited by 283 · see citing works

A genome‐scale computational study of the interplay between transcriptional regulation and metabolism

Shlomi, T., Eisenberg, Y., Sharan, R., & Ruppin, E. (2007) · Molecular Systems Biology · doi:10.1038/msb4100141 · Cited by 254 · see citing works

The Essence of Metabolic Engineering

Stephanopoulos, G. N., Aristidou, A. A., & NIELSEN, J. K. (1998) · Metabolic Engineering · doi:10.1016/b978-012666260-3/50002-9 · Cited by 237 · see citing works

L-Tyrosine production by deregulated strains of Escherichia coli

Lütke‐Eversloh, T., & Stephanopoulos, G. N. (2007) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-006-0792-9 · Cited by 209 · see citing works

GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosismetabolism

Beste, D. J. V., Hooper, T., Stewart, G. R., Bonde, B. K., Avignone-Rossa, C. A., Bushell, M. E., Wheeler, P. R., Klamt, S., Kierzek, A. M., & McFadden, J. (2007) · Genome biology · doi:10.1186/gb-2007-8-5-r89 · Cited by 204 · see citing works

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

Hoppe, A., Hoffmann, S., & Holzhütter, H. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-23 · Cited by 158 · see citing works

Construction of an Escherichia coli K-12 Mutant for Homoethanologenic Fermentation of Glucose or Xylose without Foreign Genes

Kim, Y., Ingram, L. O., & Shanmugam, K. T. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02456-06 · Cited by 143 · see citing works

Metabolite essentiality elucidates robustness of Escherichia coli metabolism

Kim, P., Lee, D., Kim, T. Y., Lee, K. H., Jeong, H., Lee, S. Y., & Park, S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703262104 · Cited by 137 · see citing works

Gene-expression tools for the metabolic engineering of bacteria

Keasling, J. D. (1999) · Trends in biotechnology · doi:10.1016/s0167-7799(99)01376-1 · Cited by 117 · see citing works

Systems biology as a foundation for genome-scale synthetic biology

Barrett, C. L., Kim, T. Y., Kim, H. U., Palsson, B. Ø., & Lee, S. Y. (2006) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2006.08.001 · Cited by 115 · see citing works

Genome‐scale analysis of Mannheimia succiniciproducens metabolism

Kim, T. Y., Kim, H. U., Park, J. M., Song, H., Kim, J. S., & Lee, S. Y. (2007) · Biotechnology and Bioengineering · doi:10.1002/bit.21433 · Cited by 105 · see citing works

Evolution of selenium utilization traits

Romero, H., Zhang, Y., Gladyshev, V. N., & Salinas, G. (2005) · Genome biology · doi:10.1186/gb-2005-6-8-r66 · Cited by 100 · see citing works

Fueling Industrial Biotechnology Growth with Bioethanol

Otero, J. M., Panagiotou, G., & Lisbeth Olsson, A. (2007) · Springer eBooks · doi:10.1007/10_2007_071 · Cited by 88 · see citing works

The economics of synthetic biology

Henkel, J., & Maurer, S. M. (2007) · Molecular Systems Biology · doi:10.1038/msb4100161 · Cited by 66 · see citing works

Hybrid dynamic/static method for large-scale simulation of metabolism

Yugi, K., Nakayama, Y., Kinoshita, A., & Tomita, M. (2005) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-2-42 · Cited by 36 · see citing works

Genetic manipulation of a primary metabolic pathway for l-ornithine production in Escherichia coli

Lee, Y. J., & Cho, J. (2006) · Biotechnology Letters · doi:10.1007/s10529-006-9163-y · Cited by 35 · see citing works

Metabolic pathway structures for recombinant protein synthesis in Escherichia coli

Vijayasankaran, N., Carlson, R. P., & Srienc, F. (2005) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-005-1920-7 · Cited by 30 · see citing works

Oxygen effect on lactose catabolism by a Leuconostoc mesenteroides strain: Modeling of general O2‐dependent stoichiometry

Plihon, F., Taillandier, P., & Strehaiano, P. (1996) · Biotechnology and Bioengineering · doi:10.1002/(sici)1097-0290(19960105)49:1 · Cited by 2 · see citing works

Adaptive laboratory evolution—Principles and applications for biotechnology

Dragosits, M., & Mattanovich, D. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-64 · Cited by 827 · see citing works

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

Feist, A. M., Zielinski, D. C., Orth, J. D., Schellenberger, J., Herrgard, M. J., & Palsson, B. Ø. (2010) · Metabolic Engineering · doi:10.1016/j.ymben.2009.10.003 · Cited by 238 · see citing works

Metabolic engineering and dynamic modelling of E. coli for the production of chemicals from renewable resources

Beauprez, J. J., Maertens, J., Foulquié-Moreno, M. R., et al. (2007) · Ghent University Academic Bibliography (Ghent University)

Systems biology and metabolic engineering for obtaining E. coli mutants capable to produce succinate from renewable resources

Bodor, Z., FAZAKAS, A., Bérczi‐Kovács, E. R., et al. (2014) · ROMANIAN BIOTECHNOLOGICAL LETTERS · Cited by 6 · see citing works

A Review of Computational Approaches for In Silico Metabolic Engineering for Microbial Fuel Production

Chan, W. H., Mohamad, M. S., Deris, S., et al. (2013) · Current Bioinformatics · doi:10.2174/1574893611308020013 · Cited by 8 · see citing works

Metabolic Engineering in Plants

Kumar, A. (2015) · Springer eBooks · doi:10.1007/978-81-322-2283-5_26 · Cited by 14 · see citing works

Flux balance analysis of metabolic networks for efficient engineering of microbial cell factories

Sen, P. (2022) · Biotechnology and Genetic Engineering Reviews · doi:10.1080/02648725.2022.2152631 · Cited by 26 · see citing works