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Volumn 14, Issue 3, 2019, Pages 639-702

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(55)  Heirendt, Laurent a   Arreckx, Sylvain a   Pfau, Thomas a   Mendoza, Sebastián N b   Richelle, Anne c   Heinken, Almut a   Haraldsdóttir, Hulda S a   Wachowiak, Jacek a   Keating, Sarah M d   Vlasov, Vanja a   Magnusdóttir, Stefania a   Ng, Chiam Yu e   Preciat, German a   Žagare, Alise a   Chan, Siu H J e   Aurich, Maike K a   Clancy, Catherine M a   Modamio, Jennifer a   Sauls, John T f   Noronha, Alberto a   more..


Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOMEDICINE; BIOTECHNOLOGY; EXPERIMENTAL DESIGN; NAJA; NONHUMAN; PREDICTION; QUANTITATIVE ANALYSIS; SOFTWARE; SYSTEMS BIOLOGY; BIOLOGICAL MODEL; GENOME; METABOLISM;

EID: 85061915038     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/s41596-018-0098-2     Document Type: Article
Times cited : (780)

References (155)
  • 2
    • 84930227327 scopus 로고    scopus 로고
    • Using genome-scale models to predict biological capabilities
    • PID: 26000478
    • O’Brien, E. J., Monk, J. M. & Palsson, B. O. Using genome-scale models to predict biological capabilities. Cell 161, 971–987 (2015).
    • (2015) Cell , vol.161 , pp. 971-987
    • O’Brien, E.J.1    Monk, J.M.2    Palsson, B.O.3
  • 3
    • 34347258175 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
    • COI: 1:CAS:528:DC%2BD2sXhtFGntbfI, PID: 17406635
    • Becker, S. A. et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat. Protoc. 2, 727–738 (2007).
    • (2007) Nat. Protoc. , vol.2 , pp. 727-738
    • Becker, S.A.1
  • 4
    • 79551662521 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
    • Schellenberger, J. et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 6, 1290–1307 (2011).
    • (2011) Nat. Protoc. , vol.6 , pp. 1290-1307
    • Schellenberger, J.1
  • 5
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
    • &
    • Lewis, N. E., Nagarajan, H. & Palsson, B. O. Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Microbiol. 10, 291–305 (2012).
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 6
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • COI: 1:CAS:528:DC%2BC3cXks12hsA%3D%3D, PID: 20057383
    • Thiele, I. & Palsson, B. Ø. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc. 5, 93–121 (2010).
    • (2010) Nat. Protoc. , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 7
    • 79956099883 scopus 로고    scopus 로고
    • Social engineering for virtual ‘big science’ in systems biology
    • COI: 1:CAS:528:DC%2BC3MXmtF2ksrw%3D, PID: 21587248
    • Kitano, H., Ghosh, S. & Matsuoka, Y. Social engineering for virtual ‘big science’ in systems biology. Nat. Chem. Biol. 7, 323–326 (2011).
    • (2011) Nat. Chem. Biol. , vol.7 , pp. 323-326
    • Kitano, H.1    Ghosh, S.2    Matsuoka, Y.3
  • 8
    • 84892788440 scopus 로고    scopus 로고
    • Constraint-based models predict metabolic and associated cellular functions
    • COI: 1:CAS:528:DC%2BC2cXotFKmtg%3D%3D, PID: 24430943
    • Bordbar, A., Monk, J. M., King, Z. A. & Palsson, B. O. Constraint-based models predict metabolic and associated cellular functions. Nat. Rev. Genet. 15, 107–120 (2014).
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 107-120
    • Bordbar, A.1    Monk, J.M.2    King, Z.A.3    Palsson, B.O.4
  • 9
    • 84964043843 scopus 로고    scopus 로고
    • In silico constraint-based strain optimization methods: the quest for optimal cell factories
    • PID: 26609052
    • Maia, P., Rocha, M. & Rocha, I. In silico constraint-based strain optimization methods: the quest for optimal cell factories. Microbiol. Mol. Biol. Rev. 80, 45–67 (2016).
    • (2016) Microbiol. Mol. Biol. Rev. , vol.80 , pp. 45-67
    • Maia, P.1    Rocha, M.2    Rocha, I.3
  • 10
    • 84996956349 scopus 로고    scopus 로고
    • A consensus genome-scale reconstruction of Chinese hamster ovary cell metabolism
    • COI: 1:CAS:528:DC%2BC2sXhtFalsr4%3D, PID: 27883890
    • Hefzi, H. et al. A consensus genome-scale reconstruction of Chinese hamster ovary cell metabolism. Cell Syst. 3, 434–443.e8 (2016).
    • (2016) Cell Syst. , vol.3 , pp. 434-443.e8
    • Hefzi, H.1
  • 11
    • 85019561406 scopus 로고    scopus 로고
    • Mammalian systems biotechnology reveals global cellular adaptations in a recombinant CHO cell line
    • COI: 1:CAS:528:DC%2BC2sXosFSnt7g%3D, PID: 28544881
    • Yusufi, F. N. K. et al. Mammalian systems biotechnology reveals global cellular adaptations in a recombinant CHO cell line. Cell Syst. 4, 530–542.e6 (2017).
    • (2017) Cell Syst. , vol.4 , pp. 530-542.e6
    • Yusufi, F.N.K.1
  • 12
    • 78751584992 scopus 로고    scopus 로고
    • Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
    • PID: 20668487
    • Zhuang, K. et al. Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME J 5, 305–316 (2011).
    • (2011) ISME J , vol.5 , pp. 305-316
    • Zhuang, K.1
  • 13
    • 33645288016 scopus 로고    scopus 로고
    • Systems biology of the human red blood cell
    • COI: 1:CAS:528:DC%2BD28XivVGrsb8%3D, PID: 16533612
    • Jamshidi, N. & Palsson, B. Ø. Systems biology of the human red blood cell. Blood Cells Mol. Dis. 36, 239–247 (2006).
    • (2006) Blood Cells Mol. Dis. , vol.36 , pp. 239-247
    • Jamshidi, N.1    Palsson, B.O.2
  • 14
    • 84886670153 scopus 로고    scopus 로고
    • Model-based identification of drug targets that revert disrupted metabolism and its application to ageing
    • PID: 24153335
    • Yizhak, K., Gabay, O., Cohen, H. & Ruppin, E. Model-based identification of drug targets that revert disrupted metabolism and its application to ageing. Nat. Commun. 4, 2632 (2013).
    • (2013) Nat. Commun. , vol.4
    • Yizhak, K.1    Gabay, O.2    Cohen, H.3    Ruppin, E.4
  • 15
    • 66249132328 scopus 로고    scopus 로고
    • Predicting metabolic biomarkers of human inborn errors of metabolism
    • PID: 19401675
    • Shlomi, T., Cabili, M. N. & Ruppin, E. Predicting metabolic biomarkers of human inborn errors of metabolism. Mol. Syst. Biol. 5, 263 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 263
    • Shlomi, T.1    Cabili, M.N.2    Ruppin, E.3
  • 16
    • 84865768271 scopus 로고    scopus 로고
    • A compendium of inborn errors of metabolism mapped onto the human metabolic network
    • COI: 1:CAS:528:DC%2BC38Xht1ygtbbE, PID: 22699794
    • Sahoo, S., Franzson, L., Jonsson, J. J. & Thiele, I. A compendium of inborn errors of metabolism mapped onto the human metabolic network. Mol. Biosyst. 8, 2545–2558 (2012).
    • (2012) Mol. Biosyst. , vol.8 , pp. 2545-2558
    • Sahoo, S.1    Franzson, L.2    Jonsson, J.J.3    Thiele, I.4
  • 17
    • 84877315835 scopus 로고    scopus 로고
    • A community-driven global reconstruction of human metabolism
    • COI: 1:CAS:528:DC%2BC3sXjtlKgtbk%3D, PID: 23455439
    • Thiele, I. et al. A community-driven global reconstruction of human metabolism. Nat. Biotechnol. 31, 419–425 (2013).
    • (2013) Nat. Biotechnol. , vol.31 , pp. 419-425
    • Thiele, I.1
  • 18
    • 84881604631 scopus 로고    scopus 로고
    • A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient
    • COI: 1:CAS:528:DC%2BC3sXmvFOmsL0%3D, PID: 23464878
    • Pagliarini, R. & di Bernardo, D. A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient. J. Comput. Biol. 20, 383–397 (2013).
    • (2013) J. Comput. Biol. , vol.20 , pp. 383-397
    • Pagliarini, R.1    di Bernardo, D.2
  • 19
    • 84962140627 scopus 로고    scopus 로고
    • Metabolic network prediction of drug side effects
    • COI: 1:CAS:528:DC%2BC2sXhtFaksrc%3D, PID: 27135366
    • Shaked, I., Oberhardt, M. A., Atias, N., Sharan, R. & Ruppin, E. Metabolic network prediction of drug side effects. Cell Syst. 2, 209–213 (2016).
    • (2016) Cell Syst. , vol.2 , pp. 209-213
    • Shaked, I.1    Oberhardt, M.A.2    Atias, N.3    Sharan, R.4    Ruppin, E.5
  • 20
    • 78049445175 scopus 로고    scopus 로고
    • Drug off-target effects predicted using structural analysis in the context of a metabolic network model
    • &
    • Chang, R. L., Xie, L., Xie, L., Bourne, P. E. & Palsson, B. Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput. Biol. 6, e1000938 (2010).
    • (2010) PLoS Comput. Biol. , vol.6
    • Chang, R.L.1    Xie, L.2    Xie, L.3    Bourne, P.E.4    Palsson, B.5
  • 21
    • 33751356224 scopus 로고    scopus 로고
    • Systems biology, metabolic modelling and metabolomics in drug discovery and development
    • COI: 1:CAS:528:DC%2BD28Xht1eqtb%2FK, PID: 17129827
    • Kell, D. B. Systems biology, metabolic modelling and metabolomics in drug discovery and development. Drug Discov. Today 11, 1085–1092 (2006).
    • (2006) Drug Discov. Today , vol.11 , pp. 1085-1092
    • Kell, D.B.1
  • 22
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • COI: 1:CAS:528:DC%2BD2sXitVaqu7w%3D, PID: 17267599
    • Duarte, N. C. et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. USA 104, 1777–1782 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 1777-1782
    • Duarte, N.C.1
  • 23
    • 84976345862 scopus 로고    scopus 로고
    • Recon 2.2: from reconstruction to model of human metabolism
    • PID: 27358602
    • Swainston, N. et al. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics 12, 109 (2016).
    • (2016) Metabolomics , vol.12
    • Swainston, N.1
  • 24
    • 84943164994 scopus 로고    scopus 로고
    • Human metabolic atlas: An online resource for human metabolism
    • bav068
    • Pornputtapong, N., Nookaew, I. & Nielsen, J. Human metabolic atlas: an online resource for human metabolism. Database 2015, bav068 (2015).
    • (2015) Database 2015
    • Pornputtapong, N.1    Nookaew, I.2    Nielsen, J.3
  • 25
    • 85010962151 scopus 로고    scopus 로고
    • Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism
    • COI: 1:CAS:528:DC%2BC2sXhs1Gms7o%3D, PID: 28120890
    • Zielinski, D. C. et al. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Sci. Rep. 7, 41241 (2017).
    • (2017) Sci. Rep. , vol.7
    • Zielinski, D.C.1
  • 26
    • 84898011025 scopus 로고    scopus 로고
    • Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease
    • PID: 24419221
    • Mardinoglu, A. et al. Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nat. Commun. 5, 3083 (2014).
    • (2014) Nat. Commun. , vol.5
    • Mardinoglu, A.1
  • 27
    • 84865432555 scopus 로고    scopus 로고
    • CardioNet: a human metabolic network suited for the study of cardiomyocyte metabolism
    • PID: 22929619
    • Karlstädt, A. et al. CardioNet: a human metabolic network suited for the study of cardiomyocyte metabolism. BMC Syst. Biol. 6, 114 (2012).
    • (2012) BMC Syst. Biol. , vol.6
    • Karlstädt, A.1
  • 28
    • 77956407882 scopus 로고    scopus 로고
    • HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology
    • PID: 20823849
    • Gille, C. et al. HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol. Syst. Biol. 6, 411 (2010).
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 411
    • Gille, C.1
  • 30
    • 80054969621 scopus 로고    scopus 로고
    • A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
    • PID: 22041191
    • Bordbar, A. et al. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst. Biol. 5, 180 (2011).
    • (2011) BMC Syst. Biol. , vol.5
    • Bordbar, A.1
  • 31
    • 84930377006 scopus 로고    scopus 로고
    • Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer
    • Yizhak, K. et al. Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer. Elife 3, e03641 (2014).
    • (2014) Elife , vol.3
    • Yizhak, K.1
  • 32
    • 84883787394 scopus 로고    scopus 로고
    • Integration of clinical data with a genome-scale metabolic model of the human adipocyte
    • COI: 1:CAS:528:DC%2BC3sXhtFSqsbjI, PID: 23511207
    • Mardinoglu, A. et al. Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Mol. Syst. Biol. 9, 649 (2013).
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 649
    • Mardinoglu, A.1
  • 33
    • 84951056186 scopus 로고    scopus 로고
    • Personalized whole-cell kinetic models of metabolism for discovery in genomics and pharmacodynamics
    • COI: 1:CAS:528:DC%2BC2sXhtFaltLY%3D, PID: 27136057
    • Bordbar, A. et al. Personalized whole-cell kinetic models of metabolism for discovery in genomics and pharmacodynamics. Cell Syst. 1, 283–292 (2015).
    • (2015) Cell Syst. , vol.1 , pp. 283-292
    • Bordbar, A.1
  • 34
    • 84938586730 scopus 로고    scopus 로고
    • Quantifying diet-induced metabolic changes of the human gut microbiome
    • COI: 1:CAS:528:DC%2BC2MXht1Chs7nN, PID: 26244934
    • Shoaie, S. et al. Quantifying diet-induced metabolic changes of the human gut microbiome. Cell Metab. 22, 320–331 (2015).
    • (2015) Cell Metab. , vol.22 , pp. 320-331
    • Shoaie, S.1
  • 35
    • 84881086390 scopus 로고    scopus 로고
    • To supplement or not to supplement: a metabolic network framework for human nutritional supplements
    • COI: 1:CAS:528:DC%2BC3sXhtlSmsLjO, PID: 23967053
    • Nogiec, C. D. & Kasif, S. To supplement or not to supplement: a metabolic network framework for human nutritional supplements. PLoS ONE 8, e68751 (2013).
    • (2013) PLoS ONE , vol.8
    • Nogiec, C.D.1    Kasif, S.2
  • 36
    • 84871588520 scopus 로고    scopus 로고
    • Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
    • PID: 23022739
    • Heinken, A., Sahoo, S., Fleming, R. M. T. & Thiele, I. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes 4, 28–40 (2013).
    • (2013) Gut Microbes , vol.4 , pp. 28-40
    • Heinken, A.1    Sahoo, S.2    Fleming, R.M.T.3    Thiele, I.4
  • 37
    • 84906052535 scopus 로고    scopus 로고
    • Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe
    • PID: 25002542
    • Heinken, A. et al. Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J. Bacteriol. 196, 3289–3302 (2014).
    • (2014) J. Bacteriol. , vol.196 , pp. 3289-3302
    • Heinken, A.1
  • 38
    • 85011094697 scopus 로고    scopus 로고
    • Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
    • PID: 27893703
    • Magnúsdóttir, S. et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat. Biotechnol. 35, 81–89 (2017).
    • (2017) Nat. Biotechnol. , vol.35 , pp. 81-89
    • Magnúsdóttir, S.1
  • 39
    • 84892991094 scopus 로고    scopus 로고
    • Software applications for flux balance analysis
    • PID: 23131418
    • Lakshmanan, M., Koh, G., Chung, B. K. S. & Lee, D.-Y. Software applications for flux balance analysis. Brief Bioinform. 15, 108–122 (2014).
    • (2014) Brief Bioinform. , vol.15 , pp. 108-122
    • Lakshmanan, M.1    Koh, G.2    Chung, B.K.S.3    Lee, D.Y.4
  • 40
    • 84881152495 scopus 로고    scopus 로고
    • COBRApy: constraints-based reconstruction and analysis for Python
    • PID: 23927696
    • Ebrahim, A., Lerman, J. A., Palsson, B. O. & Hyduke, D. R. COBRApy: constraints-based reconstruction and analysis for Python. BMC Syst. Biol. 7, 74 (2013).
    • (2013) BMC Syst. Biol. , vol.7
    • Ebrahim, A.1    Lerman, J.A.2    Palsson, B.O.3    Hyduke, D.R.4
  • 41
    • 85049776867 scopus 로고    scopus 로고
    • The United States Department of Energy Systems Biology Knowledgebase
    • Arkin, A. P. et al. The United States Department of Energy Systems Biology Knowledgebase. Nat. Biotechnol. 36, 566–569 (2018).
    • (2018) Nat. Biotechnol. , vol.36 , pp. 566-569
    • Arkin, A.P.1
  • 42
    • 85019711682 scopus 로고    scopus 로고
    • DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia
    • COI: 1:CAS:528:DC%2BC1cXitFOht7%2FO, PID: 28453682
    • Heirendt, L., Thiele, I. & Fleming, R. M. T. DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia. Bioinformatics 33, 1421–1423 (2017).
    • (2017) Bioinformatics , vol.33 , pp. 1421-1423
    • Heirendt, L.1    Thiele, I.2    Fleming, R.M.T.3
  • 43
    • 84856568013 scopus 로고    scopus 로고
    • Construction and completion of flux balance models from pathway databases
    • COI: 1:CAS:528:DC%2BC38XhvVeqs70%3D, PID: 22262672
    • Latendresse, M., Krummenacker, M., Trupp, M. & Karp, P. D. Construction and completion of flux balance models from pathway databases. Bioinformatics 28, 388–396 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 388-396
    • Latendresse, M.1    Krummenacker, M.2    Trupp, M.3    Karp, P.D.4
  • 44
    • 84995776550 scopus 로고    scopus 로고
    • Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
    • COI: 1:CAS:528:DC%2BC1cXlsVSqsrw%3D, PID: 26454094
    • Karp, P. D. et al. Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform. 17, 877–890 (2016).
    • (2016) Brief Bioinform. , vol.17 , pp. 877-890
    • Karp, P.D.1
  • 45
  • 46
    • 84857392540 scopus 로고    scopus 로고
    • The case for open computer programs
    • COI: 1:CAS:528:DC%2BC38Xis1ert74%3D, PID: 22358837
    • Ince, D. C., Hatton, L. & Graham-Cumming, J. The case for open computer programs. Nature 482, 485–488 (2012).
    • (2012) Nature , vol.482 , pp. 485-488
    • Ince, D.C.1    Hatton, L.2    Graham-Cumming, J.3
  • 47
    • 79551582182 scopus 로고    scopus 로고
    • SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks
    • COI: 1:CAS:528:DC%2BC3MXhs1Gis7c%3D, PID: 21148545
    • Gevorgyan, A., Bushell, M. E., Avignone-Rossa, C. & Kierzek, A. M. SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks. Bioinformatics 27, 433–434 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 433-434
    • Gevorgyan, A.1    Bushell, M.E.2    Avignone-Rossa, C.3    Kierzek, A.M.4
  • 48
    • 79960126760 scopus 로고    scopus 로고
    • rBioNet: a COBRA toolbox extension for reconstructing high-quality biochemical networks
    • &
    • Thorleifsson, S. G. & Thiele, I. rBioNet: a COBRA toolbox extension for reconstructing high-quality biochemical networks. Bioinformatics 27, 2009–2010 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2009-2010
    • Thorleifsson, S.G.1    Thiele, I.2
  • 49
    • 84897382623 scopus 로고    scopus 로고
    • Assimilating genome-scale metabolic reconstructions with modelBorgifier
    • COI: 1:CAS:528:DC%2BC2cXltFKjsL0%3D, PID: 24371155
    • Sauls, J. T. & Buescher, J. M. Assimilating genome-scale metabolic reconstructions with modelBorgifier. Bioinformatics 30, 1036–1038 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 1036-1038
    • Sauls, J.T.1    Buescher, J.M.2
  • 50
    • 85024403074 scopus 로고    scopus 로고
    • ReconMap: an interactive visualization of human metabolism
    • COI: 1:CAS:528:DC%2BC1cXitFSgtrnN, PID: 27993782
    • Noronha, A. et al. ReconMap: an interactive visualization of human metabolism. Bioinformatics 33, 605–607 (2017).
    • (2017) Bioinformatics , vol.33 , pp. 605-607
    • Noronha, A.1
  • 51
    • 85028318822 scopus 로고    scopus 로고
    • MINERVA—a platform for visualization and curation of molecular interaction networks
    • PID: 28725475
    • Gawron, P. et al. MINERVA—a platform for visualization and curation of molecular interaction networks. npj Syst. Biol. Appl. 2, 16020 (2016).
    • (2016) npj Syst. Biol. Appl. , vol.2
    • Gawron, P.1
  • 52
    • 14644422159 scopus 로고    scopus 로고
    • Modelling cellular systems with PySCeS
    • COI: 1:CAS:528:DC%2BD2MXhsFSgurs%3D, PID: 15454409
    • Olivier, B. G., Rohwer, J. M. & Hofmeyr, J.-H. S. Modelling cellular systems with PySCeS. Bioinformatics 21, 560–561 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 560-561
    • Olivier, B.G.1    Rohwer, J.M.2    Hofmeyr, J.H.S.3
  • 54
    • 85010036575 scopus 로고    scopus 로고
    • Reliable and efficient solution of genome-scale models of metabolism and macromolecular expression
    • COI: 1:CAS:528:DC%2BC2sXhtlalur4%3D, PID: 28098205
    • Ma, D. et al. Reliable and efficient solution of genome-scale models of metabolism and macromolecular expression. Sci. Rep. 7, 40863 (2017).
    • (2017) Sci. Rep. , vol.7
    • Ma, D.1
  • 55
    • 34447551397 scopus 로고    scopus 로고
    • Structural and functional analysis of cellular networks with CellNetAnalyzer
    • PID: 17408509
    • Klamt, S., Saez-Rodriguez, J. & Gilles, E. D. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1, 2 (2007).
    • (2007) BMC Syst. Biol. , vol.1
    • Klamt, S.1    Saez-Rodriguez, J.2    Gilles, E.D.3
  • 56
    • 79960375921 scopus 로고    scopus 로고
    • An application programming interface for CellNetAnalyzer
    • COI: 1:CAS:528:DC%2BC3MXptFahurY%3D, PID: 21315797
    • Klamt, S. & von Kamp, A. An application programming interface for CellNetAnalyzer. Biosystems 105, 162–168 (2011).
    • (2011) Biosystems , vol.105 , pp. 162-168
    • Klamt, S.1    von Kamp, A.2
  • 57
    • 85028921426 scopus 로고    scopus 로고
    • An in-silico approach to predict and exploit synthetic lethality in cancer metabolism
    • Apaolaza, I. et al. An in-silico approach to predict and exploit synthetic lethality in cancer metabolism. Nat. Commun. 8, 459 (2017).
    • (2017) Nat. Commun. , vol.8 , pp. 459
    • Apaolaza, I.1
  • 59
    • 84908326327 scopus 로고    scopus 로고
    • Bilevel optimization techniques in computational strain design
    • COI: 1:CAS:528:DC%2BC2cXhtFOrsrvP
    • Chowdhury, A., Zomorrodi, A. R. & Maranas, C. D. Bilevel optimization techniques in computational strain design. Comp. Chem. Eng. 72, 363–372 (2015).
    • (2015) Comp. Chem. Eng. , vol.72 , pp. 363-372
    • Chowdhury, A.1    Zomorrodi, A.R.2    Maranas, C.D.3
  • 60
    • 84866975246 scopus 로고    scopus 로고
    • Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage
    • COI: 1:CAS:528:DC%2BC38XhsFWgs7jE, PID: 23029152
    • Thiele, I. et al. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS ONE 7, e45635 (2012).
    • (2012) PLoS ONE , vol.7
    • Thiele, I.1
  • 61
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    • PID: 17593909
    • Feist, A. M. et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 3, 121 (2007).
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 121
    • Feist, A.M.1
  • 62
    • 63549148162 scopus 로고    scopus 로고
    • Genome-scale reconstruction of Escherichia coli’s transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization
    • PID: 19282977
    • Thiele, I., Jamshidi, N., Fleming, R. M. T. & Palsson, B. Ø. Genome-scale reconstruction of Escherichia coli’s transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput. Biol. 5, e1000312 (2009).
    • (2009) PLoS Comput. Biol. , vol.5
    • Thiele, I.1    Jamshidi, N.2    Fleming, R.M.T.3    Palsson, B.O.4
  • 63
    • 84940499594 scopus 로고    scopus 로고
    • Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
    • COI: 1:CAS:528:DC%2BC2MXhtlSit7zM, PID: 26261351
    • Yang, L. et al. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proc. Natl. Acad. Sci. USA 112, 10810–10815 (2015).
    • (2015) Proc. Natl. Acad. Sci. USA , vol.112 , pp. 10810-10815
    • Yang, L.1
  • 64
    • 40749162829 scopus 로고    scopus 로고
    • LibSBML: an API library for SBML
    • COI: 1:CAS:528:DC%2BD1cXjsVakuro%3D, PID: 18252737
    • Bornstein, B. J., Keating, S. M., Jouraku, A. & Hucka, M. LibSBML: an API library for SBML. Bioinformatics 24, 880–881 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 880-881
    • Bornstein, B.J.1    Keating, S.M.2    Jouraku, A.3    Hucka, M.4
  • 65
    • 84988890296 scopus 로고    scopus 로고
    • MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models
    • Aurich, M. K., Fleming, R. M. T. & Thiele, I. MetaboTools: a comprehensive toolbox for analysis of genome-scale metabolic models. Front. Physiol. 7, 327 (2016).
    • (2016) Front. Physiol. , vol.7 , pp. 327
    • Aurich, M.K.1    Fleming, R.M.T.2    Thiele, I.3
  • 66
    • 85042916724 scopus 로고    scopus 로고
    • Recon 3D: A resource enabling a three-dimensional view of gene variation in human metabolism
    • Brunk, E. et al. Recon 3D: a resource enabling a three-dimensional view of gene variation in human metabolism. Nat. Biotechnol. 36, 272–281 (2018).
    • (2018) Nat. Biotechnol. , vol.36 , pp. 272-281
    • Brunk, E.1
  • 67
    • 84947073615 scopus 로고    scopus 로고
    • Solving multiscale linear programs using the simplex method in quadruple precision
    • Al-Baali, M., Grandinetti, L., Purnama, A., Springer International Publishing, Cham, Switzerland
    • Ma, D. & Saunders, M. A. Solving multiscale linear programs using the simplex method in quadruple precision. in Numerical Analysis and Optimization, Vol. 134 (eds. Al-Baali, M., Grandinetti, L. & Purnama, A.) 223–235 (Springer International Publishing, Cham, Switzerland, 2015).
    • (2015) Numerical Analysis and Optimization , vol.134 , pp. 223-235
    • Ma, D.1    Saunders, M.A.2
  • 68
    • 84866544764 scopus 로고    scopus 로고
    • Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration
    • &
    • Fleming, R. M. T. & Thiele, I. Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration. J. Theor. Biol. 314, 173–181 (2012).
    • (2012) J. Theor. Biol. , vol.314 , pp. 173-181
    • Fleming, R.M.T.1    Thiele, I.2
  • 69
    • 52949144612 scopus 로고    scopus 로고
    • Detection of stoichiometric inconsistencies in biomolecular models
    • COI: 1:CAS:528:DC%2BD1cXhtFOgs77P, PID: 18697772
    • Gevorgyan, A., Poolman, M. G. & Fell, D. A. Detection of stoichiometric inconsistencies in biomolecular models. Bioinformatics 24, 2245–2251 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 2245-2251
    • Gevorgyan, A.1    Poolman, M.G.2    Fell, D.A.3
  • 70
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • COI: 1:CAS:528:DC%2BC3cXivV2rtL4%3D, PID: 20212490
    • Orth, J. D., Thiele, I. & Palsson, B. Ø. What is flux balance analysis? Nat. Biotechnol. 28, 245–248 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 245-248
    • Orth, J.D.1    Thiele, I.2    Palsson, B.O.3
  • 71
    • 77952886804 scopus 로고    scopus 로고
    • The biomass objective function
    • COI: 1:CAS:528:DC%2BC3cXntVSlu7w%3D, PID: 20430689
    • Feist, A. M. & Palsson, B. O. The biomass objective function. Curr. Opin. Microbiol. 13, 344–349 (2010).
    • (2010) Curr. Opin. Microbiol. , vol.13 , pp. 344-349
    • Feist, A.M.1    Palsson, B.O.2
  • 72
    • 0022350091 scopus 로고
    • The game of the pentose phosphate cycle
    • PID: 4079448
    • Meléndez-Hevia, E. & Isidoro, A. The game of the pentose phosphate cycle. J. Theor. Biol. 117, 251–263 (1985).
    • (1985) J. Theor. Biol. , vol.117 , pp. 251-263
    • Meléndez-Hevia, E.1    Isidoro, A.2
  • 73
    • 78651335279 scopus 로고    scopus 로고
    • Systematizing the generation of missing metabolic knowledge
    • COI: 1:CAS:528:DC%2BC3cXhtFSisr7L, PID: 20589842
    • Orth, J. D. & Palsson, B. Ø. Systematizing the generation of missing metabolic knowledge. Biotechnol. Bioeng. 107, 403–412 (2010).
    • (2010) Biotechnol. Bioeng. , vol.107 , pp. 403-412
    • Orth, J.D.1    Palsson, B.O.2
  • 74
    • 84861125789 scopus 로고    scopus 로고
    • Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
    • PID: 22569339
    • Yamada, T. et al. Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Mol. Syst. Biol. 8, 581 (2012).
    • (2012) Mol. Syst. Biol. , vol.8 , pp. 581
    • Yamada, T.1
  • 75
    • 84879911126 scopus 로고    scopus 로고
    • Simple topological properties predict functional misannotations in a metabolic network
    • COI: 1:CAS:528:DC%2BC3sXhtVakt7%2FF, PID: 23812979
    • Liberal, R. & Pinney, J. W. Simple topological properties predict functional misannotations in a metabolic network. Bioinformatics 29, i154–i161 (2013).
    • (2013) Bioinformatics , vol.29 , pp. i154-i161
    • Liberal, R.1    Pinney, J.W.2
  • 76
    • 33751226921 scopus 로고    scopus 로고
    • Systems approach to refining genome annotation
    • COI: 1:CAS:528:DC%2BD28Xht1Ojsr%2FE, PID: 17088549
    • Reed, J. L. et al. Systems approach to refining genome annotation. Proc. Natl. Acad. Sci. USA 103, 17480–17484 (2006).
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 17480-17484
    • Reed, J.L.1
  • 77
    • 84862159261 scopus 로고    scopus 로고
    • Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
    • PID: 22548736
    • Orth, J. D. & Palsson, B. Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst. Biol. 6, 30 (2012).
    • (2012) BMC Syst. Biol. , vol.6
    • Orth, J.D.1    Palsson, B.2
  • 78
    • 80051537012 scopus 로고    scopus 로고
    • Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism
    • PID: 21811229
    • Chang, R. L. et al. Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol. Syst. Biol. 7, 518 (2011).
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 518
    • Chang, R.L.1
  • 79
    • 80053375237 scopus 로고    scopus 로고
    • The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
    • PID: 21962087
    • Rolfsson, O., Palsson, B. Ø. & Thiele, I. The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst. Biol. 5, 155 (2011).
    • (2011) BMC Syst. Biol. , vol.5
    • Rolfsson, O.1    Palsson, B.O.2    Thiele, I.3
  • 80
    • 84871458276 scopus 로고    scopus 로고
    • Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity
    • COI: 1:CAS:528:DC%2BC38XhvVelurvN, PID: 23067238
    • Rolfsson, Ó., Paglia, G., Magnusdóttir, M., Palsson, B. Ø. & Thiele, I. Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity. Biochem. J. 449, 427–435 (2013).
    • (2013) Biochem. J. , vol.449 , pp. 427-435
    • Rolfsson, O.1    Paglia, G.2    Magnusdóttir, M.3    Palsson, B.O.4    Thiele, I.5
  • 81
    • 34547676311 scopus 로고    scopus 로고
    • Optimization based automated curation of metabolic reconstructions
    • PID: 17584497
    • Satish Kumar, V., Dasika, M. S. & Maranas, C. D. Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8, 212 (2007).
    • (2007) BMC Bioinformatics , vol.8
    • Satish Kumar, V.1    Dasika, M.S.2    Maranas, C.D.3
  • 82
    • 84907026934 scopus 로고    scopus 로고
    • fastGapFill: efficient gap filling in metabolic networks
    • &
    • Thiele, I., Vlassis, N. & Fleming, R. M. T. fastGapFill: efficient gap filling in metabolic networks. Bioinformatics 30, 2529–2531 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 2529-2531
    • Thiele, I.1    Vlassis, N.2    Fleming, R.M.T.3
  • 83
    • 84918789208 scopus 로고    scopus 로고
    • MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis
    • PID: 25315283
    • Willemsen, A. M. et al. MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Mol. Biosyst. 11, 137–145 (2014).
    • (2014) Mol. Biosyst. , vol.11 , pp. 137-145
    • Willemsen, A.M.1
  • 84
    • 84923516679 scopus 로고    scopus 로고
    • Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment
    • COI: 1:CAS:528:DC%2BC2MXjtFaks70%3D, PID: 25600836
    • Kleessen, S., Irgang, S., Klie, S., Giavalisco, P. & Nikoloski, Z. Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment. Plant J. 81, 822–835 (2015).
    • (2015) Plant J. , vol.81 , pp. 822-835
    • Kleessen, S.1    Irgang, S.2    Klie, S.3    Giavalisco, P.4    Nikoloski, Z.5
  • 85
    • 85017208176 scopus 로고    scopus 로고
    • Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics
    • PID: 28387366
    • Bordbar, A. et al. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. Sci. Rep. 7, 46249 (2017).
    • (2017) Sci. Rep. , vol.7
    • Bordbar, A.1
  • 86
    • 84866487453 scopus 로고    scopus 로고
    • Integration of expression data in genome-scale metabolic network reconstructions
    • Blazier, A. S. & Papin, J. A. Integration of expression data in genome-scale metabolic network reconstructions. Front. Physiol. 3, 299 (2012).
    • (2012) Front. Physiol. , vol.3 , pp. 299
    • Blazier, A.S.1    Papin, J.A.2
  • 87
    • 85012870351 scopus 로고    scopus 로고
    • A systematic evaluation of methods for tailoring genome-scale metabolic models
    • COI: 1:CAS:528:DC%2BC2sXkvFWktbc%3D, PID: 28215528
    • Opdam, S. et al. A systematic evaluation of methods for tailoring genome-scale metabolic models. Cell Syst. 4, 318–329.e6 (2017).
    • (2017) Cell Syst. , vol.4 , pp. 318-329.e6
    • Opdam, S.1
  • 88
    • 84907288908 scopus 로고    scopus 로고
    • Generalized framework for context-specific metabolic model extraction methods
    • Estévez, S. R. & Nikoloski, Z. Generalized framework for context-specific metabolic model extraction methods. Front. Plant Sci. 5, 491 (2014).
    • (2014) Front. Plant Sci. , vol.5 , pp. 491
    • Estévez, S.R.1    Nikoloski, Z.2
  • 89
    • 84896701551 scopus 로고    scopus 로고
    • Fast reconstruction of compact context-specific metabolic network models
    • PID: 24453953
    • Vlassis, N., Pacheco, M. P. & Sauter, T. Fast reconstruction of compact context-specific metabolic network models. PLoS Comput. Biol. 10, e1003424 (2014).
    • (2014) PLoS Comput. Biol. , vol.10
    • Vlassis, N.1    Pacheco, M.P.2    Sauter, T.3
  • 90
    • 44949225040 scopus 로고    scopus 로고
    • Context-specific metabolic networks are consistent with experiments
    • PID: 18483554
    • Becker, S. A. & Palsson, B. O. Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol. 4, e1000082 (2008).
    • (2008) PLoS Comput. Biol. , vol.4
    • Becker, S.A.1    Palsson, B.O.2
  • 91
    • 79951745716 scopus 로고    scopus 로고
    • iMAT: an integrative metabolic analysis tool
    • COI: 1:CAS:528:DC%2BC3cXhsFamtr7P, PID: 21081510
    • Zur, H., Ruppin, E. & Shlomi, T. iMAT: an integrative metabolic analysis tool. Bioinformatics 26, 3140–3142 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 3140-3142
    • Zur, H.1    Ruppin, E.2    Shlomi, T.3
  • 92
    • 84863662483 scopus 로고    scopus 로고
    • Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
    • COI: 1:CAS:528:DC%2BC38XnvFSns78%3D
    • Agren, R. et al. Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comp. Biol. 8, e1002518 (2012).
    • (2012) PLoS Comp. Biol. , vol.8
    • Agren, R.1
  • 93
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
    • PID: 20823844
    • Jerby, L., Shlomi, T. & Ruppin, E. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol. Syst. Biol. 6, 401 (2010).
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 94
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • PID: 23234303
    • Wang, Y., Eddy, J. A. & Price, N. D. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst. Biol. 6, 153 (2012).
    • (2012) BMC Syst. Biol. , vol.6
    • Wang, Y.1    Eddy, J.A.2    Price, N.D.3
  • 95
    • 62349088991 scopus 로고    scopus 로고
    • On the use of protein turnover and half-lives
    • PID: 18923400
    • Kuhar, M. J. On the use of protein turnover and half-lives. Neuropsychopharmacology 34, 1172–1173 (2008).
    • (2008) Neuropsychopharmacology , vol.34 , pp. 1172-1173
    • Kuhar, M.J.1
  • 97
    • 0000029295 scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • Schuster, S. & Hilgetag, C. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 02, 165–182 (1994).
    • (1994) J. Biol. Syst. , vol.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 98
    • 0034615791 scopus 로고    scopus 로고
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
    • COI: 1:CAS:528:DC%2BD3cXhs12hsLs%3D, PID: 10716907
    • Schilling, C. H., Letscher, D. & Palsson, B. Ø. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203, 229–248 (2000).
    • (2000) J. Theor. Biol. , vol.203 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 99
    • 85018301681 scopus 로고    scopus 로고
    • From elementary flux modes to elementary flux vectors: metabolic pathway analysis with arbitrary linear flux constraints
    • PID: 28406903
    • Klamt, S. et al. From elementary flux modes to elementary flux vectors: metabolic pathway analysis with arbitrary linear flux constraints. PLoS Comput. Biol. 13, e1005409 (2017).
    • (2017) PLoS Comput. Biol. , vol.13
    • Klamt, S.1
  • 100
    • 84905403664 scopus 로고    scopus 로고
    • Minimal metabolic pathway structure is consistent with associated biomolecular interactions
    • PID: 24987116
    • Bordbar, A. et al. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol. Syst. Biol. 10, 737 (2014).
    • (2014) Mol. Syst. Biol. , vol.10 , pp. 737
    • Bordbar, A.1
  • 101
    • 77957117220 scopus 로고    scopus 로고
    • Computationally efficient flux variability analysis
    • PID: 20920235
    • Gudmundsson, S. & Thiele, I. Computationally efficient flux variability analysis. BMC Bioinformatics 11, 489 (2010).
    • (2010) BMC Bioinformatics , vol.11
    • Gudmundsson, S.1    Thiele, I.2
  • 102
    • 85021377998 scopus 로고    scopus 로고
    • CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models
    • PID: 28158334
    • Haraldsdóttir, H. S., Cousins, B., Thiele, I., Fleming, R. M. T. & Vempala, S. CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models. Bioinformatics 33, 1741–1743 (2017).
    • (2017) Bioinformatics , vol.33 , pp. 1741-1743
    • Haraldsdóttir, H.S.1    Cousins, B.2    Thiele, I.3    Fleming, R.M.T.4    Vempala, S.5
  • 103
    • 85049450891 scopus 로고    scopus 로고
    • Gaussian cooling and algorithms for volume and Gaussian volume
    • Cousins, B. & Vempala, S. Gaussian cooling and algorithms for volume and Gaussian volume. SIAM J. Comput. 47, 1237–1273 (2018).
    • (2018) SIAM J. Comput. , vol.47 , pp. 1237-1273
    • Cousins, B.1    Vempala, S.2
  • 104
    • 85061894814 scopus 로고    scopus 로고
    • A practical volume algorithm
    • Cousins, B. & Vempala, S. A practical volume algorithm. Math. Prog. Comp. 8, 1–28 (2015).
    • (2015) Math. Prog. Comp. , vol.8 , pp. 1-28
    • Cousins, B.1    Vempala, S.2
  • 105
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • COI: 1:CAS:528:DC%2BD3sXptFWmsL0%3D, PID: 14595777
    • Burgard, A. P., Pharkya, P. & Maranas, C. D. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84, 647–657 (2003).
    • (2003) Biotechnol. Bioeng. , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 106
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • PID: 1327682
    • Patil, K. R., Rocha, I., Förster, J. & Nielsen, J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6, 308 (2005).
    • (2005) BMC Bioinformatics , vol.6
    • Patil, K.R.1    Rocha, I.2    Förster, J.3    Nielsen, J.4
  • 107
    • 69249146187 scopus 로고    scopus 로고
    • Large-scale identification of genetic design strategies using local search
    • PID: 19690565
    • Lun, D. S. et al. Large-scale identification of genetic design strategies using local search. Mol. Syst. Biol. 5, 296 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 296
    • Lun, D.S.1
  • 108
    • 77954590959 scopus 로고    scopus 로고
    • OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions
    • PID: 20419153
    • Ranganathan, S., Suthers, P. F. & Maranas, C. D. OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput. Biol. 6, e1000744 (2010).
    • (2010) PLoS Comput. Biol. , vol.6
    • Ranganathan, S.1    Suthers, P.F.2    Maranas, C.D.3
  • 109
    • 34249297627 scopus 로고    scopus 로고
    • Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol
    • COI: 1:CAS:528:DC%2BD2sXlvFSisrs%3D, PID: 17400499
    • Antoniewicz, M. R. et al. Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. Metab. Eng. 9, 277–292 (2007).
    • (2007) Metab. Eng. , vol.9 , pp. 277-292
    • Antoniewicz, M.R.1
  • 110
    • 84908698705 scopus 로고    scopus 로고
    • Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: Application to Recon 2
    • Haraldsdóttir, H. S., Thiele, I. & Fleming, R. M. T. Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. J. Cheminform. 6, 2 (2014).
    • (2014) J. Cheminform. , vol.6 , pp. 2
    • Haraldsdóttir, H.S.1    Thiele, I.2    Fleming, R.M.T.3
  • 111
    • 85027856736 scopus 로고    scopus 로고
    • Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
    • PID: 29086112
    • Preciat Gonzalez, G. A. et al. Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. J. Cheminform. 9, 39 (2017).
    • (2017) J. Cheminform. , vol.9 , pp. 39
    • Preciat Gonzalez, G.A.1
  • 112
    • 84979586933 scopus 로고    scopus 로고
    • PubChem substance and compound databases
    • COI: 1:CAS:528:DC%2BC2sXhtV2gu7bE
    • Kim, S. et al. PubChem substance and compound databases. Nucleic Acids Res. 44, D1202–D1213 (2016).
    • (2016) Nucleic Acids Res. , vol.44 , pp. D1202-D1213
    • Kim, S.1
  • 113
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 114
    • 84876560358 scopus 로고    scopus 로고
    • The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
    • COI: 1:CAS:528:DC%2BC38XhvV2ktrjE, PID: 23180789
    • Hastings, J. et al. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 41, D456–D463 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D456-D463
    • Hastings, J.1
  • 115
    • 33846058198 scopus 로고    scopus 로고
    • LMSD: LIPID MAPS structure database
    • COI: 1:CAS:528:DC%2BD2sXivFGktQ%3D%3D, PID: 17098933
    • Sud, M. et al. LMSD: LIPID MAPS structure database. Nucleic Acids Res. 35, D527–D532 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. D527-D532
    • Sud, M.1
  • 117
    • 84869114811 scopus 로고    scopus 로고
    • ChemSpider—building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry
    • &
    • Williams, A. J., Tkachenko, V., Golotvin, S., Kidd, R. & McCann, G. ChemSpider—building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry. J. Cheminform. 2, O16 (2010).
    • (2010) J. Cheminform. , vol.2 , pp. O16
    • Williams, A.J.1    Tkachenko, V.2    Golotvin, S.3    Kidd, R.4    McCann, G.5
  • 118
    • 33846088138 scopus 로고    scopus 로고
    • HMDB: the Human Metabolome Database
    • COI: 1:CAS:528:DC%2BD2sXivFKhtA%3D%3D, PID: 17202168
    • Wishart, D. S. et al. HMDB: the Human Metabolome Database. Nucleic Acids Res. 35, D521–D526 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. D521-D526
    • Wishart, D.S.1
  • 119
    • 85007211750 scopus 로고    scopus 로고
    • Reaction Decoder Tool (RDT): extracting features from chemical reactions
    • PID: 27153692
    • Rahman, S. A. et al. Reaction Decoder Tool (RDT): extracting features from chemical reactions. Bioinformatics 32, 2065–2066 (2016).
    • (2016) Bioinformatics , vol.32 , pp. 2065-2066
    • Rahman, S.A.1
  • 120
    • 84919681581 scopus 로고    scopus 로고
    • CLCA: maximum common molecular substructure queries within the MetRxn Database
    • COI: 1:CAS:528:DC%2BC2cXhvFGkurjE, PID: 25412255
    • Kumar, A. & Maranas, C. D. CLCA: maximum common molecular substructure queries within the MetRxn Database. J. Chem. Inf. Model. 54, 3417–3438 (2014).
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 3417-3438
    • Kumar, A.1    Maranas, C.D.2
  • 121
    • 67649994019 scopus 로고    scopus 로고
    • Generalized reaction patterns for prediction of unknown enzymatic reactions
    • COI: 1:CAS:528:DC%2BC3cXlvFOnu7o%3D, PID: 19425130
    • Shimizu, Y., Hattori, M., Goto, S. & Kanehisa, M. Generalized reaction patterns for prediction of unknown enzymatic reactions. Genome Inform. 20, 149–158 (2008).
    • (2008) Genome Inform. , vol.20 , pp. 149-158
    • Shimizu, Y.1    Hattori, M.2    Goto, S.3    Kanehisa, M.4
  • 122
    • 84999700139 scopus 로고    scopus 로고
    • Identification of conserved moieties in metabolic networks by graph theoretical analysis of atom transition networks
    • PID: 27870845
    • Haraldsdóttir, H. S. & Fleming, R. M. T. Identification of conserved moieties in metabolic networks by graph theoretical analysis of atom transition networks. PLoS Comput. Biol. 12, e1004999 (2016).
    • (2016) PLoS Comput. Biol. , vol.12
    • Haraldsdóttir, H.S.1    Fleming, R.M.T.2
  • 124
    • 78650541419 scopus 로고    scopus 로고
    • von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
    • COI: 1:CAS:528:DC%2BC3cXhs1ajurvL, PID: 21115436
    • Fleming, R. M. T. & Thiele, I. von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics 27, 142–143 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 142-143
    • Fleming, R.M.T.1    Thiele, I.2
  • 125
    • 70350560332 scopus 로고    scopus 로고
    • Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli
    • COI: 1:CAS:528:DC%2BD1MXhtlWitrrJ, PID: 19783351
    • Fleming, R. M. T., Thiele, I. & Nasheuer, H. P. Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophys. Chem. 145, 47–56 (2009).
    • (2009) Biophys. Chem. , vol.145 , pp. 47-56
    • Fleming, R.M.T.1    Thiele, I.2    Nasheuer, H.P.3
  • 126
    • 84859920505 scopus 로고    scopus 로고
    • Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction
    • PID: 22768925
    • Haraldsdóttir, H. S., Thiele, I. & Fleming, R. M. T. Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction. Biophys. J. 102, 1703–1711 (2012).
    • (2012) Biophys. J. , vol.102 , pp. 1703-1711
    • Haraldsdóttir, H.S.1    Thiele, I.2    Fleming, R.M.T.3
  • 127
    • 84880781653 scopus 로고    scopus 로고
    • Consistent estimation of Gibbs energy using component contributions
    • COI: 1:CAS:528:DC%2BC3sXht1CmsbnN, PID: 23874165
    • Noor, E., Haraldsdóttir, H. S., Milo, R. & Fleming, R. M. T. Consistent estimation of Gibbs energy using component contributions. PLoS Comput. Biol. 9, e1003098 (2013).
    • (2013) PLoS Comput. Biol. , vol.9
    • Noor, E.1    Haraldsdóttir, H.S.2    Milo, R.3    Fleming, R.M.T.4
  • 128
    • 80054052364 scopus 로고    scopus 로고
    • A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks
    • COI: 1:STN:280:DC%2BC3MbovVWmsA%3D%3D, PID: 21983269
    • Fleming, R. M. T., Maes, C. M., Saunders, M. A., Ye, Y. & Palsson, B. Ø. A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks. J. Theor. Biol. 292, 71–77 (2012).
    • (2012) J. Theor. Biol. , vol.292 , pp. 71-77
    • Fleming, R.M.T.1    Maes, C.M.2    Saunders, M.A.3    Ye, Y.4    Palsson, B.O.5
  • 129
    • 0036286631 scopus 로고    scopus 로고
    • Energy balance for analysis of complex metabolic networks
    • &
    • Beard, D. A., Liang, S.-D. & Qian, H. Energy balance for analysis of complex metabolic networks. Biophys. J. 83, 79–86 (2002).
    • (2002) Biophys. J. , vol.83 , pp. 79-86
    • Beard, D.A.1    Liang, S.-D.2    Qian, H.3
  • 130
    • 17244378347 scopus 로고    scopus 로고
    • Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium
    • COI: 1:CAS:528:DC%2BD2MXjt1Sqsbo%3D, PID: 15829355
    • Qian, H. & Beard, D. A. Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. Biophys. Chem. 114, 213–220 (2005).
    • (2005) Biophys. Chem. , vol.114 , pp. 213-220
    • Qian, H.1    Beard, D.A.2
  • 131
    • 77952643400 scopus 로고    scopus 로고
    • Integrated stoichiometric, thermo- dynamic and kinetic modelling of steady state metabolism
    • COI: 1:STN:280:DC%2BC3czisVersg%3D%3D, PID: 20230840
    • Fleming, R. M. T., Thiele, I., Provan, G. & Nasheuer, H. P. Integrated stoichiometric, thermo- dynamic and kinetic modelling of steady state metabolism. J. Theor. Biol. 264, 683–692 (2010).
    • (2010) J. Theor. Biol. , vol.264 , pp. 683-692
    • Fleming, R.M.T.1    Thiele, I.2    Provan, G.3    Nasheuer, H.P.4
  • 132
    • 79551676901 scopus 로고    scopus 로고
    • Elimination of thermodynamically infeasible loops in steady-state metabolic models
    • COI: 1:CAS:528:DC%2BC3MXhtlGgtbg%3D, PID: 21281568
    • Schellenberger, J., Lewis, N. E. & Palsson, B. Ø. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys. J. 100, 544–553 (2011).
    • (2011) Biophys. J. , vol.100 , pp. 544-553
    • Schellenberger, J.1    Lewis, N.E.2    Palsson, B.O.3
  • 133
    • 77952952952 scopus 로고    scopus 로고
    • Network thermodynamics in the post-genomic era
    • COI: 1:CAS:528:DC%2BC3cXntVSlu70%3D, PID: 20378394
    • Soh, K. C. & Hatzimanikatis, V. Network thermodynamics in the post-genomic era. Curr. Opin. Microbiol. 13, 350–357 (2010).
    • (2010) Curr. Opin. Microbiol. , vol.13 , pp. 350-357
    • Soh, K.C.1    Hatzimanikatis, V.2
  • 134
    • 84984653600 scopus 로고    scopus 로고
    • Conditions for duality between fluxes and concentrations in biochemical networks
    • COI: 1:CAS:528:DC%2BC28XhsVeltLvJ, PID: 27345817
    • Fleming, R. M. T., Vlassis, N., Thiele, I. & Saunders, M. A. Conditions for duality between fluxes and concentrations in biochemical networks. J. Theor. Biol. 409, 1–10 (2016).
    • (2016) J. Theor. Biol. , vol.409 , pp. 1-10
    • Fleming, R.M.T.1    Vlassis, N.2    Thiele, I.3    Saunders, M.A.4
  • 135
    • 85024478699 scopus 로고    scopus 로고
    • Accelerating the DC algorithm for smooth functions
    • ​Aragón Artacho, F.J., Fleming, R. M. T. & Vuong, P. T. Accelerating the DC algorithm for smooth functions. Math. Program. 169, 95–118 (2018).
    • (2018) Math. Program , vol.169 , pp. 95-118
    • Aragón Artacho, F.J.1    Fleming, R.M.T.2    Vuong, P.T.3
  • 136
    • 85061906738 scopus 로고    scopus 로고
    • Globally convergent algorithms for finding zeros of duplomonotone mappings
    • Artacho, F. J. A. & Fleming, R. M. T. Globally convergent algorithms for finding zeros of duplomonotone mappings. Optim. Lett. 9, 1–16 (2014).
    • (2014) Optim. Lett. , vol.9 , pp. 1-16
    • Artacho, F.J.A.1    Fleming, R.M.T.2
  • 138
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • COI: 1:CAS:528:DC%2BD3sXovFWrtr4%3D, PID: 14597658
    • Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
    • (2003) Genome Res. , vol.13 , pp. 2498-2504
    • Shannon, P.1
  • 139
    • 84940751701 scopus 로고    scopus 로고
    • Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways
    • PID: 26313928
    • King, Z. A. et al. Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS Comput. Biol. 11, e1004321 (2015).
    • (2015) PLoS Comput. Biol. , vol.11
    • King, Z.A.1
  • 140
    • 84885007150 scopus 로고    scopus 로고
    • NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
    • PID: 24099179
    • Kuperstein, I. et al. NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst. Biol. 7, 100 (2013).
    • (2013) BMC Syst. Biol. , vol.7
    • Kuperstein, I.1
  • 141
    • 84863432704 scopus 로고    scopus 로고
    • Paint4net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism
    • COI: 1:CAS:528:DC%2BC38XkvFyqsLs%3D, PID: 22446067
    • Kostromins, A. & Stalidzans, E. Paint4net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism. Biosystems 109, 233–239 (2012).
    • (2012) Biosystems , vol.109 , pp. 233-239
    • Kostromins, A.1    Stalidzans, E.2
  • 142
    • 84930373777 scopus 로고    scopus 로고
    • Prediction of intracellular metabolic states from extracellular metabolomic data
    • PID: 25972769
    • Aurich, M. K. et al. Prediction of intracellular metabolic states from extracellular metabolomic data. Metabolomics 11, 603–619 (2014).
    • (2014) Metabolomics , vol.11 , pp. 603-619
    • Aurich, M.K.1
  • 143
    • 85052707536 scopus 로고    scopus 로고
    • Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients
    • PID: 28725472
    • Guebila, M. B. & Thiele, I. Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients. npj Syst. Biol. Appl. 2, 16013 (2016).
    • (2016) npj Syst. Biol. Appl. , vol.2
    • Guebila, M.B.1    Thiele, I.2
  • 144
    • 84880860962 scopus 로고    scopus 로고
    • Robust flux balance analysis of multiscale biochemical reaction networks
    • Sun, Y., Fleming, R. M. T., Thiele, I. & Saunders, M. A. Robust flux balance analysis of multiscale biochemical reaction networks. BMC Bioinformatics 14, 240 (2013).
    • (2013) BMC Bioinformatics , vol.14 , pp. 240
    • Sun, Y.1    Fleming, R.M.T.2    Thiele, I.3    Saunders, M.A.4
  • 145
    • 77955141026 scopus 로고    scopus 로고
    • Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models
    • PID: 20664636
    • Lewis, N. E. et al. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol. Syst. Biol. 6, 390 (2010).
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 390
    • Lewis, N.E.1
  • 146
    • 77952774546 scopus 로고    scopus 로고
    • Functional characterization of alternate optimal solutions of Escherichia coli’s transcriptional and translational machinery
    • COI: 1:CAS:528:DC%2BC3cXosFCis7g%3D, PID: 20483314
    • Thiele, I., Fleming, R. M. T., Bordbar, A., Schellenberger, J. & Palsson, B. Ø. Functional characterization of alternate optimal solutions of Escherichia coli’s transcriptional and translational machinery. Biophys. J. 98, 2072–2081 (2010).
    • (2010) Biophys. J. , vol.98 , pp. 2072-2081
    • Thiele, I.1    Fleming, R.M.T.2    Bordbar, A.3    Schellenberger, J.4    Palsson, B.O.5
  • 147
    • 84856566482 scopus 로고    scopus 로고
    • Minimal cut sets in a metabolic network are elementary modes in a dual network
    • COI: 1:CAS:528:DC%2BC38XhvVertrs%3D, PID: 22190691
    • Ballerstein, K., von Kamp, A., Klamt, S. & Haus, U.-U. Minimal cut sets in a metabolic network are elementary modes in a dual network. Bioinformatics 28, 381–387 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 381-387
    • Ballerstein, K.1    von Kamp, A.2    Klamt, S.3    Haus, U.U.4
  • 148
    • 84896731390 scopus 로고    scopus 로고
    • Enumeration of smallest intervention strategies in genome-scale metabolic networks
    • von Kamp, A. & Klamt, S. Enumeration of smallest intervention strategies in genome-scale metabolic networks. PLoS Comput. Biol. 10, e1003378 (2014).
    • (2014) PLoS Comput. Biol. , vol.10
    • von Kamp, A.1    Klamt, S.2
  • 149
    • 84894315212 scopus 로고    scopus 로고
    • Integrating pathways of Parkinson’s disease in a molecular interaction map
    • COI: 1:CAS:528:DC%2BC2cXitFOltr4%3D, PID: 23832570
    • Fujita, K. A. et al. Integrating pathways of Parkinson’s disease in a molecular interaction map. Mol. Neurobiol. 49, 88–102 (2014).
    • (2014) Mol. Neurobiol. , vol.49 , pp. 88-102
    • Fujita, K.A.1
  • 150
    • 84875973063 scopus 로고    scopus 로고
    • The RAVEN Toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
    • COI: 1:CAS:528:DC%2BC3sXlvVamurw%3D, PID: 23555215
    • Agren, R. et al. The RAVEN Toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput. Biol. 9, e1002980 (2013).
    • (2013) PLoS Comput. Biol. , vol.9
    • Agren, R.1
  • 151
    • 70350029519 scopus 로고    scopus 로고
    • FBA-SimVis: interactive visualization of constraint-based metabolic models
    • COI: 1:CAS:528:DC%2BD1MXht1Glsr3L, PID: 19578041
    • Grafahrend-Belau, E., Klukas, C., Junker, B. H. & Schreiber, F. FBA-SimVis: interactive visualization of constraint-based metabolic models. Bioinformatics 25, 2755–2757 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2755-2757
    • Grafahrend-Belau, E.1    Klukas, C.2    Junker, B.H.3    Schreiber, F.4
  • 152
    • 77950960250 scopus 로고    scopus 로고
    • OptFlux: an open-source software platform for in silico metabolic engineering
    • PID: 20403172
    • Rocha, I. et al. OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst. Biol. 4, 45 (2010).
    • (2010) BMC Syst. Biol. , vol.4
    • Rocha, I.1
  • 153
    • 33747193585 scopus 로고    scopus 로고
    • ScrumPy: metabolic modelling with Python
    • Poolman, M. G. ScrumPy: metabolic modelling with Python. Syst. Biol. 153, 375–378 (2006).
    • (2006) Syst. Biol. , vol.153 , pp. 375-378
    • Poolman, M.G.1
  • 154
    • 78651553577 scopus 로고    scopus 로고
    • FASIMU: flexible software for flux-balance computation series in large metabolic networks
    • PID: 21255455
    • Hoppe, A., Hoffmann, S., Gerasch, A., Gille, C. & Holzhütter, H.-G. FASIMU: flexible software for flux-balance computation series in large metabolic networks. BMC Bioinformatics 12, 28 (2011).
    • (2011) BMC Bioinformatics , vol.12
    • Hoppe, A.1    Hoffmann, S.2    Gerasch, A.3    Gille, C.4    Holzhütter, H.G.5
  • 155
    • 84856247380 scopus 로고    scopus 로고
    • FAME, the flux analysis and modeling environment
    • PID: 22289213
    • Boele, J., Olivier, B. G. & Teusink, B. FAME, the flux analysis and modeling environment. BMC Syst. Biol. 6, 8 (2012).
    • (2012) BMC Syst. Biol. , vol.6
    • Boele, J.1    Olivier, B.G.2    Teusink, B.3


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