Method for redesign of microbial production systems

Maranas, Costas D; Burgard, Anthony P; Pharkya, Priti

Title: Method for redesign of microbial production systems

Patent · Tue Nov 02 00:00:00 EDT 2010

OSTI ID:1017455

Maranas, Costas D ^[1]; Burgard, Anthony P ^[2]; Pharkya, Priti ^[2]

Port Matilda, PA
State College, PA

A computer-assisted method for identifying functionalities to add to an organism-specific metabolic network to enable a desired biotransformation in a host includes accessing reactions from a universal database to provide stoichiometric balance, identifying at least one stoichiometrically balanced pathway at least partially based on the reactions and a substrate to minimize a number of non-native functionalities in the production host, and incorporating the at least one stoichiometrically balanced pathway into the host to provide the desired biotransformation. A representation of the metabolic network as modified can be stored.

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Research Organization:: The Penn State Research Foundation (University Park, PA)

Sponsoring Organization:: USDOE

DOE Contract Number:: 58855

Assignee:: The Penn State Research Foundation (University Park, PA)

Patent Number(s):: 7,826,975

Application Number:: 10/929,091

OSTI ID:: 1017455

Country of Publication:: United States

Language:: English

References (126)

A Linear Steady-State Treatment of Enzymatic Chains. General Properties, Control and Effector Strength Heinrich, Reinhart; Rapoport, Tom A. European Journal of Biochemistry, Vol. 42, Issue 1 https://doi.org/10.1111/j.1432-1033.1974.tb03318.x	journal	February 1974
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction Overbeek, R. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.123	journal	January 2000
Metabolic pathways in the post-genome era Papin, Jason A.; Price, Nathan D.; Wiback, Sharon J. Trends in Biochemical Sciences, Vol. 28, Issue 5 https://doi.org/10.1016/S0968-0004(03)00064-1	journal	May 2003
Biochemical systems analysis Savageau, Michael A. Journal of Theoretical Biology, Vol. 25, Issue 3 https://doi.org/10.1016/S0022-5193(69)80027-5	journal	December 1969
A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Mushegian, A. R.; Koonin, E. V. Proceedings of the National Academy of Sciences, Vol. 93, Issue 19 https://doi.org/10.1073/pnas.93.19.10268	journal	September 1996
Constructing a minimal genome Huynen, Martijn Trends in Genetics, Vol. 16, Issue 3 https://doi.org/10.1016/S0168-9525(99)01972-1	journal	March 2000
Cadmium removal by a new strain of Pseudomonas aeruginosa in aerobic culture. Wang, C. L.; Michels, P. C.; Dawson, S. C. Applied and environmental microbiology, Vol. 63, Issue 10 https://doi.org/10.1128/AEM.63.10.4075-4078.1997	journal	January 1997
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth Ibarra, Rafael U.; Edwards, Jeremy S.; Palsson, Bernhard O. Nature, Vol. 420, Issue 6912 https://doi.org/10.1038/nature01149	journal	November 2002
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data Edwards, Jeremy S.; Ibarra, Rafael U.; Palsson, Bernhard O. Nature Biotechnology, Vol. 19, Issue 2 https://doi.org/10.1038/84379	journal	February 2001
Applications of Multiobjective Optimization in Chemical Engineering Bhaskar, V.; Gupta, Santosh K.; Ray, Ajay K. Reviews in Chemical Engineering, Vol. 16, Issue 1 https://doi.org/10.1515/REVCE.2000.16.1.1	journal	January 2000
Glycerol Production in a Triose Phosphate Isomerase Deficient Mutant of Saccharomyces cerevisiae Compagno, C.; Boschi, F.; Ranzi, B. M. Biotechnology Progress, Vol. 12, Issue 5 https://doi.org/10.1021/bp960043c	journal	October 1996
Production of beta-carotene in Zymomonas mobilis and Agrobacterium tumefaciens by introduction of the biosynthesis genes from Erwinia uredovora. Misawa, N.; Yamano, S.; Ikenaga, H. Applied and Environmental Microbiology, Vol. 57, Issue 6 https://doi.org/10.1128/AEM.57.6.1847-1849.1991	journal	January 1991
Computer Program for Calculating the Melting Temperature of Degenerate Oligonucleotides Used in PCR or Hybridization Chen, Haoyuan; Zhu, Guan BioTechniques, Vol. 22, Issue 6 https://doi.org/10.2144/97226bc04	journal	June 1997
Optimization of regulatory architectures in metabolic reaction networks Hatzimanikatis, Vassily; Floudas, Christodoulos A.; Bailey, James E. Biotechnology and Bioengineering, Vol. 52, Issue 4, p. 485-500 https://doi.org/10.1002/(SICI)1097-0290(19961120)52:4<485::AID-BIT4>3.0.CO;2-L	journal	November 1996
Analysis and design of metabolic reaction networks via mixed-integer linear optimization Hatzimanikatis, Vassily; Floudas, Christodoulos A.; Bailey, James E. AIChE Journal, Vol. 42, Issue 5 https://doi.org/10.1002/aic.690420509	journal	May 1996
Hierarchical optimization: An introduction Anandalingam, G.; Friesz, T. L. Annals of Operations Research, Vol. 34, Issue 1 https://doi.org/10.1007/BF02098169	journal	December 1992
Large-Scale Evaluation of In Silico Gene Deletions in Saccharomyces cerevisiae Förster, Jochen; Famili, Iman; Palsson, Bernhard Ø. OMICS: A Journal of Integrative Biology, Vol. 7, Issue 2 https://doi.org/10.1089/153623103322246584	journal	July 2003
Quantification of central metabolic fluxes in the facultative methylotrophmethylobacterium extorquens AM1 using13C-label tracing and mass spectrometry Van Dien, Stephen J.; Strovas, Tim; Lidstrom, Mary E. Biotechnology and Bioengineering, Vol. 84, Issue 1 https://doi.org/10.1002/bit.10745	journal	August 2003
Engineering the metabolism of Escherichia coli W3110 for the conversion of sugar to redox-neutral and oxidized products: Homoacetate production Causey, T. B.; Zhou, S.; Shanmugam, K. T. Proceedings of the National Academy of Sciences, Vol. 100, Issue 3, p. 825-832 https://doi.org/10.1073/pnas.0337684100	journal	January 2003
Regulation of Gene Expression in Flux Balance Models of Metabolism Covert, Markus W.; Schilling, Christophe H.; Palsson, Bernhard Journal of Theoretical Biology, Vol. 213, Issue 1 https://doi.org/10.1006/jtbi.2001.2405	journal	November 2001
Eco Cyc: Encyclopedia of Escherichia coli genes and metabolism Karp, P. D.; Riley, M.; Paley, S. M. Nucleic Acids Research, Vol. 27, Issue 1 https://doi.org/10.1093/nar/27.1.55	journal	January 1999
Cybernetic modeling of growth in mixed, substitutable substrate environments: Preferential and simultaneous utilization Ramakrishna, Ramprasad; Ramkrishna, Doraiswami; Konopka, Allan E. Biotechnology and Bioengineering, Vol. 52, Issue 1, p. 141-151 https://doi.org/10.1002/(SICI)1097-0290(19961005)52:1<141::AID-BIT14>3.0.CO;2-R	journal	October 1996
MetaCyc: a multiorganism database of metabolic pathways and enzymes Krieger, C. J. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh100	journal	January 2004
Optimization of nonlinear biotechnological processes with linear programming: Application to citric acid production by Aspergillus niger Torres, Néstor V.; Voit, Eberhard O.; González-Alcón, Carlos Biotechnology and Bioengineering, Vol. 49, Issue 3, p. 247-258 https://doi.org/10.1002/(SICI)1097-0290(19960205)49:3<247::AID-BIT2>3.0.CO;2-K	journal	March 2000
Growth energetics and metabolic fluxes in continuous cultures of Penicillium chrysogenum Henriksen, C. M.; Christensen, L. H.; Nielsen, J. Journal of Biotechnology, Vol. 45, Issue 2 https://doi.org/10.1016/0168-1656(95)00164-6	journal	February 1996
The KEGG resource for deciphering the genome Kanehisa, M. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh063	journal	January 2004
Effect of modified glucose uptake using genetic engineering techniques on high-level recombinant protein production inescherichia coli dense cultures Chou, Chih-Hsiung; Bennett, George N.; San, Ka-Yiu Biotechnology and Bioengineering, Vol. 44, Issue 8 https://doi.org/10.1002/bit.260440811	journal	October 1994
Modification of central metabolic pathway inescherichia coli to reduce acetate accumulation by heterologous expression of thebacillus subtilis acetolactate synthase gene Aristidou, Aristos A.; San, Ka-Yiu; Bennett, George N. Biotechnology and Bioengineering, Vol. 44, Issue 8 https://doi.org/10.1002/bit.260440810	journal	October 1994
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
MPW: the Metabolic Pathways Database Selkov, E. Nucleic Acids Research, Vol. 26, Issue 1 https://doi.org/10.1093/nar/26.1.43	journal	January 1998
Metabolic flux distributions in Penicillium chrysogenum during fed-batch cultivations: METABOLIC FLUX DISTRIBUTIONS IN PENICILLIUM CHRYSOGENUM Jørgensen, Henrik; Nielsen, Jens; Villadsen, John Biotechnology and Bioengineering, Vol. 46, Issue 2 https://doi.org/10.1002/bit.260460205	journal	April 1995
High cell density and high monoclonal antibody production through medium design and rational control in a bioreactor Xie, Liangzhi; Wang, Daniel I. C. Biotechnology and Bioengineering, Vol. 51, Issue 6, p. 725-729 https://doi.org/10.1002/(SICI)1097-0290(19960920)51:6<725::AID-BIT12>3.0.CO;2-C	journal	March 2000
Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments Methe, B. A.; Nelson, K. E.; Eisen, J. A. Science, Vol. 302, Issue 5652, p. 1967-1969 https://doi.org/10.1126/science.1088727	journal	December 2003
Cybernetic modeling of microbial growth on multiple substrates Kompala, Dhinakar S.; Ramkrishna, Doraiswami; Tsao, George T. Biotechnology and Bioengineering, Vol. 26, Issue 11 https://doi.org/10.1002/bit.260261103	journal	November 1984
The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining Ellis, L. B. M. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg048	journal	January 2003
Optimization in integrated biochemical systems Voit, Eberhard O. Biotechnology and Bioengineering, Vol. 40, Issue 5 https://doi.org/10.1002/bit.260400504	journal	August 1992
Analysis of optimality in natural and perturbed metabolic networks Segre, D.; Vitkup, D.; Church, G. M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 23 https://doi.org/10.1073/pnas.232349399	journal	November 2002
Identifying rate-controlling enzymes in metabolic pathways without kinetic parameters Delgado, Javier P.; Liao, James C. Biotechnology Progress, Vol. 7, Issue 1 https://doi.org/10.1021/bp00007a003	journal	January 1991
How will bioinformatics influence metabolic engineering? Edwards, Jeremy S.; Palsson, Bernhard O. Biotechnology and Bioengineering, Vol. 58, Issue 2-3, p. 162-169 https://doi.org/10.1002/(SICI)1097-0290(19980420)58:2/3<162::AID-BIT8>3.0.CO;2-J	journal	April 1998
Malonyl-Coenzyme A Reductase from Chloroflexus aurantiacus, a Key Enzyme of the 3-Hydroxypropionate Cycle for Autotrophic CO₂ Fixation Hugler, M.; Menendez, C.; Schagger, H. Journal of Bacteriology, Vol. 184, Issue 9, p. 2404-2410 https://doi.org/10.1128/JB.184.9.2404-2410.2002	journal	May 2002
Mathematical models of metabolic pathways Varner, J.; Ramkrishna, D. Current Opinion in Biotechnology, Vol. 10, Issue 2 https://doi.org/10.1016/S0958-1669(99)80025-1	journal	April 1999
The Genome-Scale Metabolic Extreme Pathway Structure in Haemophilus influenzae Shows Significant Network Redundancy Papin, Jason A.; Price, Nathan D.; Edwards, Jeremy S. Journal of Theoretical Biology, Vol. 215, Issue 1 https://doi.org/10.1006/jtbi.2001.2499	journal	March 2002
Metabolic Engineering of Propanediol Pathways Cameron, D. C.; Altaras, N. E.; Hoffman, M. L. Biotechnology Progress, Vol. 14, Issue 1 https://doi.org/10.1021/bp9701325	journal	February 1998
Applications of improved stoichiometric model in medium design and fed-batch cultivation of animal cells in bioreactor Xie, Liangzhi; Wang, Daniel I. C. Cytotechnology, Vol. 15, Issue 1-3 https://doi.org/10.1007/BF00762376	journal	January 1994
Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments Finneran, Kevin T.; Housewright, Meghan E.; Lovley, Derek R. Environmental Microbiology, Vol. 4, Issue 9 https://doi.org/10.1046/j.1462-2920.2002.00317.x	journal	September 2002
Complex biology with no parameters Bailey, James E. Nature Biotechnology, Vol. 19, Issue 6 https://doi.org/10.1038/89204	journal	June 2001
Genome evolution Snel, Berend; Bork, Peer; Huynen, Martijn Trends in Genetics, Vol. 16, Issue 1 https://doi.org/10.1016/S0168-9525(99)01924-1	journal	January 2000
The EcoCyc and MetaCyc databases Karp, P. D. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.56	journal	January 2000
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
Poly- -Hydroxybutyrate Biosynthesis in the Facultative Methylotroph Methylobacterium extorquens AM1: Identification and Mutation of gap11, gap20, and phaR Korotkova, N.; Chistoserdova, L.; Lidstrom, M. E. Journal of Bacteriology, Vol. 184, Issue 22 https://doi.org/10.1128/JB.184.22.6174-6181.2002	journal	November 2002
Genome-scale microbial in silico models: the constraints-based approach Price, Nathan D.; Papin, Jason A.; Schilling, Christophe H. Trends in Biotechnology, Vol. 21, Issue 4 https://doi.org/10.1016/S0167-7799(03)00030-1	journal	April 2003
Electricity Production by Geobacter sulfurreducens Attached to Electrodes Bond, D. R.; Lovley, D. R. Applied and Environmental Microbiology, Vol. 69, Issue 3 https://doi.org/10.1128/AEM.69.3.1548-1555.2003	journal	March 2003
Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints Ramakrishna, Ramprasad; Edwards, Jeremy S.; McCulloch, Andrew American Journal of Physiology-Regulatory, Integrative and Comparative Physiology, Vol. 280, Issue 3 https://doi.org/10.1152/ajpregu.2001.280.3.R695	journal	March 2001
Probing the performance limits of theEscherichia coli metabolic network subject to gene additions or deletions Burgard, Anthony P.; Maranas, Costas D. Biotechnology and Bioengineering, Vol. 74, Issue 5 https://doi.org/10.1002/bit.1127	journal	January 2001
GENOME SEQUENCING: Laboratory Workhorse Decoded Pennisi, E. Science, Vol. 277, Issue 5331 https://doi.org/10.1126/science.277.5331.1432	journal	September 1997
The power of public access: the human genome project and the scientific process Quackenbush, John Nature Genetics, Vol. 29, Issue 1 https://doi.org/10.1038/ng0901-4	journal	September 2001
Efficient Degradation of Trichloroethylene by a Recombinant Escherichia Coli Winter, Robert B.; Yen, Kwang-Mu; Ensley, Burt D. Nature Biotechnology, Vol. 7, Issue 3 https://doi.org/10.1038/nbt0389-282	journal	March 1989
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
A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering Hatzimanikatis, Vassily; Liao, James C. Biotechnology and Bioengineering, Vol. 79, Issue 5 https://doi.org/10.1002/bit.10406	journal	July 2002
Assessment of the Metabolic Capabilities of Haemophilus influenzae Rd through a Genome-scale Pathway Analysis Schilling, Christophe H.; Palsson, Bernhard Ø. Journal of Theoretical Biology, Vol. 203, Issue 3 https://doi.org/10.1006/jtbi.2000.1088	journal	April 2000
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps Klamt, S.; Stelling, J.; Ginkel, M. Bioinformatics, Vol. 19, Issue 2 https://doi.org/10.1093/bioinformatics/19.2.261	journal	January 2003
Multiple Formate Dehydrogenase Enzymes in the Facultative Methylotroph Methylobacterium extorquens AM1 Are Dispensable for Growth on Methanol Chistoserdova, L.; Laukel, M.; Portais, J. -C. Journal of Bacteriology, Vol. 186, Issue 1 https://doi.org/10.1128/JB.186.1.22-28.2004	journal	December 2003
Synthesis of Vanillin from Glucose Li, Kai; Frost, J. W. Journal of the American Chemical Society, Vol. 120, Issue 40 https://doi.org/10.1021/ja9817747	journal	October 1998
Microbial Production of Hydrogen: An Overview Nandi, R.; Sengupta, S. Critical Reviews in Microbiology, Vol. 24, Issue 1 https://doi.org/10.1080/10408419891294181	journal	January 1998
Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints Desai, Ruchir P.; Nielsen, Lars K.; Papoutsakis, Eleftherios T. Journal of Biotechnology, Vol. 71, Issue 1-3 https://doi.org/10.1016/S0168-1656(99)00022-X	journal	May 1999
Technological and economic potential of poly(lactic acid) and lactic acid derivatives Datta, Rathin; Tsai, Shih-Perng; Bonsignore, Patrick FEMS Microbiology Reviews, Vol. 16, Issue 2-3 https://doi.org/10.1111/j.1574-6976.1995.tb00168.x	journal	February 1995
Metabolic reconstruction using shortest paths Arita, Masanori Simulation Practice and Theory, Vol. 8, Issue 1-2 https://doi.org/10.1016/S0928-4869(00)00006-9	journal	April 2000
Reconstruction of the central carbon metabolism of Aspergillus niger: Reconstruction of Aspergillus niger metabolism David, Helga; Åkesson, Mats; Nielsen, Jens European Journal of Biochemistry, Vol. 270, Issue 21 https://doi.org/10.1046/j.1432-1033.2003.03798.x	journal	October 2003
Quantitative assessment of uncertainty in the optimization of metabolic pathways Petkov, Spas B.; Maranas, Costas D. Biotechnology and Bioengineering, Vol. 56, Issue 2, p. 145-161 https://doi.org/10.1002/(SICI)1097-0290(19971020)56:2<145::AID-BIT4>3.0.CO;2-P	journal	October 1997
Biotechnology of succinic acid production and markets for derived industrial products Zeikus, J. G.; Jain, M. K.; Elankovan, P. Applied Microbiology and Biotechnology, Vol. 51, Issue 5 https://doi.org/10.1007/s002530051431	journal	May 1999
Global Transposon Mutagenesis and a Minimal Mycoplasma Genome Hutchison III, C. A. Science, Vol. 286, Issue 5447 https://doi.org/10.1126/science.286.5447.2165	journal	December 1999
A Hierarchical Lagrangean Relaxation Procedure for Solving Midterm Planning Problems Gupta, Anshuman; Maranas, Costas D. Industrial & Engineering Chemistry Research, Vol. 38, Issue 5 https://doi.org/10.1021/ie980782t	journal	May 1999
Production of Electricity during Wastewater Treatment Using a Single Chamber Microbial Fuel Cell Liu, Hong; Ramnarayanan, Ramanathan; Logan, Bruce E. Environmental Science & Technology, Vol. 38, Issue 7 https://doi.org/10.1021/es034923g	journal	April 2004
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
A genome-based approach for the identification of essential bacterial genes Arigoni, Fabrizio; Talabot, Francois; Peitsch, Manuel Nature Biotechnology, Vol. 16, Issue 9 https://doi.org/10.1038/nbt0998-851	journal	September 1998
From Annotated Genomes to Metabolic Flux Models and Kinetic Parameter Fitting Segrè, Daniel; Zucker, Jeremy; Katz, Jeremy OMICS: A Journal of Integrative Biology, Vol. 7, Issue 3 https://doi.org/10.1089/153623103322452413	journal	September 2003
Advances in flux balance analysis Kauffman, Kenneth J.; Prakash, Purusharth; Edwards, Jeremy S. Current Opinion in Biotechnology, Vol. 14, Issue 5 https://doi.org/10.1016/j.copbio.2003.08.001	journal	October 2003
A hierarchical approach to protein molecular evolution Bogarad, L. D.; Deem, M. W. Proceedings of the National Academy of Sciences, Vol. 96, Issue 6 https://doi.org/10.1073/pnas.96.6.2591	journal	March 1999
The Lagrangian Relaxation Method for Solving Integer Programming Problems Fisher, Marshall L. Management Science, Vol. 27, Issue 1 https://doi.org/10.1287/mnsc.27.1.1	journal	January 1981
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Reed, Jennifer L.; Vo, Thuy D.; Schilling, Christophe H. Genome Biology, Vol. 4, Issue 9, p. R54 https://doi.org/10.1186/gb-2003-4-9-r54	journal	August 2003
Predicting crossover generation in DNA shuffling Moore, G. L.; Maranas, C. D.; Lutz, S. Proceedings of the National Academy of Sciences, Vol. 98, Issue 6 https://doi.org/10.1073/pnas.051631498	journal	March 2001
Inverse Flux Analysis for Reduction of Acetate Excretion in Escherichia coli Delgado, J.; Liao, J. C. Biotechnology Progress, Vol. 13, Issue 4 https://doi.org/10.1021/bp970047x	journal	August 1997
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering Schuster, S. Trends in Biotechnology, Vol. 17, Issue 2 https://doi.org/10.1016/S0167-7799(98)01290-6	journal	February 1999
Study of two-stage processes for the microbial production of 1,3-propanediol from glucose M., Hartlep; W., Hussmann; N., Prayitno Applied Microbiology and Biotechnology, Vol. 60, Issue 1-2 https://doi.org/10.1007/s00253-002-1111-8	journal	October 2002
E-CELL: software environment for whole-cell simulation Tomita, M.; Hashimoto, K.; Takahashi, K. Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1093/bioinformatics/15.1.72	journal	January 1999
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics SantaLucia, J. Proceedings of the National Academy of Sciences, Vol. 95, Issue 4 https://doi.org/10.1073/pnas.95.4.1460	journal	February 1998
The Complete Genome Sequence of Escherichia coli K-12 Blattner, F. R. Science, Vol. 277, Issue 5331 https://doi.org/10.1126/science.277.5331.1453	journal	September 1997
The underlying pathway structure of biochemical reaction networks Schilling, C. H.; Palsson, B. O. Proceedings of the National Academy of Sciences, Vol. 95, Issue 8 https://doi.org/10.1073/pnas.95.8.4193	journal	April 1998
Most of the yeast genomic sequences are not essential for cell growth and division Goebl, Mark G.; Petes, Thomas D. Cell, Vol. 46, Issue 7 https://doi.org/10.1016/0092-8674(86)90697-5	journal	September 1986
Engineering Escherichia coli for efficient conversion of glucose to pyruvate Causey, T. B.; Shanmugam, K. T.; Yomano, L. P. Proceedings of the National Academy of Sciences, Vol. 101, Issue 8, p. 2235-2240 https://doi.org/10.1073/pnas.0308171100	journal	February 2004
Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotrophMethylobacterium extorquens AM1, with application to reconstruction of C3 and C4 metabolism Van Dien, Stephen J.; Lidstrom, Mary E. Biotechnology and Bioengineering, Vol. 78, Issue 3 https://doi.org/10.1002/bit.10200	journal	March 2002
OptStrain: A computational framework for redesign of microbial production systems Pharkya, P. Genome Research, Vol. 14, Issue 11 https://doi.org/10.1101/gr.2872004	journal	November 2004
Selection analyses of insertional mutants using subgenic-resolution arrays Badarinarayana, Vasudeo; Estep, Preston W.; Shendure, Jay Nature Biotechnology, Vol. 19, Issue 11 https://doi.org/10.1038/nbt1101-1060	journal	November 2001
Biochemical production capabilities ofescherichia coli Varma, Amit; Boesch, Brian W.; Palsson, Bernhard O. Biotechnology and Bioengineering, Vol. 42, Issue 1 https://doi.org/10.1002/bit.260420109	journal	June 1993
An estimation of minimal genome size required for life Itaya, Mitsuhiro FEBS Letters, Vol. 362, Issue 3 https://doi.org/10.1016/0014-5793(95)00233-Y	journal	April 1995
Simple constrained-optimization view of acetate overflow inE. coli Majewski, R. A.; Domach, M. M. Biotechnology and Bioengineering, Vol. 35, Issue 7 https://doi.org/10.1002/bit.260350711	journal	March 1990
Gene Expression Profiling by DNA Microarrays and Metabolic Fluxes in Escherichia coli Oh, M. -K.; Liao, J. C. Biotechnology Progress, Vol. 16, Issue 2 https://doi.org/10.1021/bp000002n	journal	April 2000
Equations and calculations for fermentations of butyric acid bacteria Papoutsakis, Eleftherios Terry Biotechnology and Bioengineering, Vol. 26, Issue 2 https://doi.org/10.1002/bit.260260210	journal	February 1984
Creating multiple-crossover DNA libraries independent of sequence identity Lutz, S.; Ostermeier, M.; Moore, G. L. Proceedings of the National Academy of Sciences, Vol. 98, Issue 20 https://doi.org/10.1073/pnas.201413698	journal	September 2001
A modular minimal cell model: Purine and pyrimidine transport and metabolism Castellanos, M.; Wilson, D. B.; Shuler, M. L. Proceedings of the National Academy of Sciences, Vol. 101, Issue 17 https://doi.org/10.1073/pnas.0400962101	journal	April 2004
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
Microbial production of 1,3-propanediol Biebl, H.; Menzel, K.; Zeng, A. -P. Applied Microbiology and Biotechnology, Vol. 52, Issue 3 https://doi.org/10.1007/s002530051523	journal	September 1999
Presence of Acetyl Coenzyme A (CoA) Carboxylase and Propionyl-CoA Carboxylase in Autotrophic Crenarchaeota and Indication for Operation of a 3-Hydroxypropionate Cycle in Autotrophic Carbon Fixation † Menendez, Castor; Bauer, Zsuzsa; Huber, Harald Journal of Bacteriology, Vol. 181, Issue 4 https://doi.org/10.1128/JB.181.4.1088-1098.1999	journal	January 1999
Minimal Reaction Sets for Escherichia coli Metabolism under Different Growth Requirements and Uptake Environments Burgard, A. P.; Vaidyaraman, S.; Maranas, C. D. Biotechnology Progress, Vol. 17, Issue 5 https://doi.org/10.1021/bp0100880	journal	October 2001
The challenges of in silico biology Palsson, Bernhard Nature Biotechnology, Vol. 18, Issue 11 https://doi.org/10.1038/81125	journal	November 2000
Optimization of polyphosphate degradation and phosphate secretion using hybrid metabolic pathways and engineered host strains Van Dien, Stephen J.; Keasling, J. D. Biotechnology and Bioengineering, Vol. 59, Issue 6, p. 754-761 https://doi.org/10.1002/(SICI)1097-0290(19980920)59:6<754::AID-BIT12>3.0.CO;2-5	journal	September 1998
The EcoCyc Database Karp, P. D. Nucleic Acids Research, Vol. 30, Issue 1 https://doi.org/10.1093/nar/30.1.56	journal	January 2002
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
Toward Metabolic Phenomics: Analysis of Genomic Data Using Flux Balances Schilling, C. H.; Edwards, J. S.; Palsson, B. O. Biotechnology Progress, Vol. 15, Issue 3 https://doi.org/10.1021/bp9900357	journal	June 1999
PathMiner: predicting metabolic pathways by heuristic search McShan, D. C.; Rao, S.; Shah, I. Bioinformatics, Vol. 19, Issue 13 https://doi.org/10.1093/bioinformatics/btg217	journal	September 2003
Integrated approaches to the design of media and feeding strategies for fed-batch cultures of animal cells Xie, Liangzhi; Wang, Daniel I. C. Trends in Biotechnology, Vol. 15, Issue 3 https://doi.org/10.1016/S0167-7799(97)01014-7	journal	March 1997
Computer-aided synthesis of biochemical pathways Mavrovouniotis, Michael L.; Stephanopoulos, George; Stephanopoulos, Gregory Biotechnology and Bioengineering, Vol. 36, Issue 11 https://doi.org/10.1002/bit.260361107	journal	December 1990
Modeling DNA Mutation and Recombination for Directed Evolution Experiments Moore, Gregory L.; Maranas, Costas D. Journal of Theoretical Biology, Vol. 205, Issue 3 https://doi.org/10.1006/jtbi.2000.2082	journal	August 2000
GENETICS:Ethical Considerations in Synthesizing a Minimal Genome Cho, M. K. Science, Vol. 286, Issue 5447 https://doi.org/10.1126/science.286.5447.2087	journal	December 1999
Metabolic Engineering from a Cybernetic Perspective. 1. Theoretical Preliminaries Varner, J.; Ramkrishna, D. Biotechnology Progress, Vol. 15, Issue 3 https://doi.org/10.1021/bp990017p	journal	June 1999
The metabolic world of Escherichia coli is not small Arita, M. Proceedings of the National Academy of Sciences, Vol. 101, Issue 6 https://doi.org/10.1073/pnas.0306458101	journal	February 2004
Overproduction of glycogen inEscherichia coli blocked in the acetate pathway improves cell growth Dedhia, Neiley N.; Hottiger, Thomas; Bailey, James E. Biotechnology and Bioengineering, Vol. 44, Issue 1 https://doi.org/10.1002/bit.260440119	journal	June 1994
Genome-wide expression profiling in Escherichia coli K-12 Richmond, C. Nucleic Acids Research, Vol. 27, Issue 19 https://doi.org/10.1093/nar/27.19.3821	journal	October 1999
Combining evidence using p-values: application to sequence homology searches Bailey, T. L.; Gribskov, M. Bioinformatics, Vol. 14, Issue 1 https://doi.org/10.1093/bioinformatics/14.1.48	journal	February 1998
Stoichiometric analysis of animal cell growth and its application in medium design Xie, Liangzhi; Wang, Daniel I. C. Biotechnology and Bioengineering, Vol. 43, Issue 11 https://doi.org/10.1002/bit.260431122	journal	May 1994
Metabolic Capabilities of Escherichia coli: I. Synthesis of Biosynthetic Precursors and Cofactors Varma, Amit; Palsson, Bernhard O. Journal of Theoretical Biology, Vol. 165, Issue 4 https://doi.org/10.1006/jtbi.1993.1202	journal	December 1993
Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations Papoutsakis, Eleftherios Terry; Meyer, Charles L. Biotechnology and Bioengineering, Vol. 27, Issue 1 https://doi.org/10.1002/bit.260270108	journal	January 1985
Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns Varma, Amit; Palsson, Bernhard O. Journal of Theoretical Biology, Vol. 165, Issue 4 https://doi.org/10.1006/jtbi.1993.1203	journal	December 1993
Optimization-based framework for inferring and testing hypothesized metabolic objective functions Burgard, Anthony P.; Maranas, Costas D. Biotechnology and Bioengineering, Vol. 82, Issue 6 https://doi.org/10.1002/bit.10617	journal	June 2003
Metabolic flux distributions inCorynebacterium glutamicum during growth and lysine overproduction Vallino, Joseph J.; Stephanopoulos, Gregory Biotechnology and Bioengineering, Vol. 41, Issue 6 https://doi.org/10.1002/bit.260410606	journal	March 1993
Biochemical systems analysis Savageau, Michael A. Journal of Theoretical Biology, Vol. 25, Issue 3 https://doi.org/10.1016/S0022-5193(69)80026-3	journal	December 1969

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