Method for determining gene knockouts

Maranas, Costa D; Burgard, Anthony R; Pharkya, Priti

Method for determining gene knockouts

Patent · 03 June 2013

OSTI ID:1084350

Maranas, Costa D; Burgard, Anthony R; Pharkya, Priti

A method for determining candidates for gene deletions and additions using a model of a metabolic network associated with an organism, the model includes a plurality of metabolic reactions defining metabolite relationships, the method includes selecting a bioengineering objective for the organism, selecting at least one cellular objective, forming an optimization problem that couples the at least one cellular objective with the bioengineering objective, and solving the optimization problem to yield at least one candidate.

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

Sponsoring Organization:: USDOE

DOE Contract Number:: FG03-01ER25499

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

Patent Number(s):: 8,457,941

Application Number:: 13/210,484

OSTI ID:: 1084350

Country of Publication:: United States

Language:: English

References (98)

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
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
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
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock Pharkya, Priti; Burgard, Anthony P.; Maranas, Costas D. Biotechnology and Bioengineering, Vol. 84, Issue 7 https://doi.org/10.1002/bit.10857	journal	December 2003
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
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
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
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
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
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
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
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
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
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
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
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
Metabolic Flux Analysis ofEscherichia coliDeficient in the Acetate Production Pathway and Expressing theBacillus subtilisAcetolactate Synthase Yang, Yea-Tyng; Aristidou, Aristos A.; San, Ka-Yiu Metabolic Engineering, Vol. 1, Issue 1 https://doi.org/10.1006/mben.1998.0103	journal	January 1999
Bulk Chemicals from Biotechnology: The Case of 1,3-Propanediol Production and the New Trends Zeng, An-Ping; Biebl, Hanno https://doi.org/10.1007/3-540-45736-4_11	book	January 2002
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
Lagrangean relaxation for integer programming Geoffrion, A. M. Mathematical Programming Studies, Vol. 2, p. 82-114 https://doi.org/10.1007/BFb0120690	book	January 1974
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
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
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
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
Synthesis of biochemical production routes Mavrovouniotis, M.; Stephanopoulos, G.; Stephanopoulos, G. Computers & Chemical Engineering, Vol. 16, Issue 6 https://doi.org/10.1016/0098-1354(92)80071-G	journal	June 1992
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
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
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
Hydrogen production by biological processes: a survey of literature Das, D. International Journal of Hydrogen Energy, Vol. 26, Issue 1 https://doi.org/10.1016/S0360-3199(00)00058-6	journal	January 2001
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
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
Metabolic modeling of microbial strains in silico Covert, Markus W.; Schilling, Christophe H.; Famili, Iman Trends in Biochemical Sciences, Vol. 26, Issue 3 https://doi.org/10.1016/S0968-0004(00)01754-0	journal	March 2001
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
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
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
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
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
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
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
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
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
The challenges of in silico biology Palsson, Bernhard Nature Biotechnology, Vol. 18, Issue 11 https://doi.org/10.1038/81125	journal	November 2000
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
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
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
Cleaning up with genomics: applying molecular biology to bioremediation Lovley, Derek R. Nature Reviews Microbiology, Vol. 1, Issue 1 https://doi.org/10.1038/nrmicro731	journal	October 2003
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
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
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
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
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
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
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
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
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 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
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 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
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
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
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
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
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
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
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
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
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
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
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 TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species Quackenbush, J. Nucleic Acids Research, Vol. 29, Issue 1 https://doi.org/10.1093/nar/29.1.159	journal	January 2001
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Varma, A.; Palsson, B. O. Applied and Environmental Microbiology, Vol. 60, Issue 10 https://doi.org/10.1128/aem.60.10.3724-3731.1994	journal	January 1994
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
Production of succinic acid through overexpression of NAD(+)-dependent malic enzyme in an Escherichia coli mutant. Stols, L.; Donnelly, M. I. Applied and environmental microbiology, Vol. 63, Issue 7 https://doi.org/10.1128/aem.63.7.2695-2701.1997	journal	January 1997
Modeling DNA shuffling Sun, Fengzhu Proceedings of the second annual international conference on Computational molecular biology - RECOMB '98 https://doi.org/10.1145/279069.279126	conference	January 1998
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions Edwards, Jeremy S.; Palsson, Bernhard O. BMC Bioinformatics, Vol. 1, Issue 1, p. 1471-2105 https://doi.org/10.1186/1471-2105-1-1	journal	July 2000
Predicting biological system objectives de novo from internal state measurements Gianchandani, Erwin P.; Oberhardt, Matthew A.; Burgard, Anthony P. BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-43	journal	January 2008
Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis Valdés, Jorge; Veloso, Felipe; Jedlicki, Eugenia BMC Genomics, Vol. 4, Issue 1 https://doi.org/10.1186/1471-2164-4-51	journal	December 2003
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
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
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
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
Studies on hydrogen production by continuous culture system of hydrogen-producing anaerobic bacteria Kataoka, Naoaki; Miya, Akiko; Kiriyama, Koichi Water Science and Technology, Vol. 36, Issue 6-7 https://doi.org/10.2166/wst.1997.0573	journal	September 1997

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