-
2
-
-
84930227327
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
29
-
-
85028077640
-
Constraint based modeling going multicellular
-
Martins Conde Pdo, R., Sauter, T. & Pfau, T. Constraint based modeling going multicellular. Front. Mol. Biosci. 3, 3 (2016).
-
(2016)
Front. Mol. Biosci.
, vol.3
, pp. 3
-
-
Martins Conde Pdo, R.1
Sauter, T.2
Pfau, T.3
-
30
-
-
80054969621
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
-
84887264733
-
Ten simple rules for reproducible computational research
-
PID: 24204232
-
Sandve, G. K., Nekrutenko, A., Taylor, J. & Hovig, E. Ten simple rules for reproducible computational research. PLoS Comput. Biol. 9, e1003285 (2013).
-
(2013)
PLoS Comput. Biol.
, vol.9
-
-
Sandve, G.K.1
Nekrutenko, A.2
Taylor, J.3
Hovig, E.4
-
46
-
-
84857392540
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
53
-
-
84887364569
-
Sybil—efficient constraint-based modelling in R
-
&
-
Gelius-Dietrich, G., Desouki, A. A., Fritzemeier, C. J. & Lercher, M. J. Sybil—efficient constraint-based modelling in R. BMC Syst. Biol. 7, 125 (2013).
-
(2013)
BMC Syst. Biol.
, vol.7
, pp. 125
-
-
Gelius-Dietrich, G.1
Desouki, A.A.2
Fritzemeier, C.J.3
Lercher, M.J.4
-
54
-
-
85010036575
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
105
-
-
0242487787
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
116
-
-
0036457996
-
The system architecture of the BioPath system
-
COI: 1:CAS:528:DC%2BD38Xpsl2ks7c%3D, PID: 12542424
-
Forster, M., Pick, A., Raitner, M., Schreiber, F. & Brandenburg, F. J. The system architecture of the BioPath system. In Silico Biol. 2, 415–426 (2002).
-
(2002)
In Silico Biol.
, vol.2
, pp. 415-426
-
-
Forster, M.1
Pick, A.2
Raitner, M.3
Schreiber, F.4
Brandenburg, F.J.5
-
117
-
-
84869114811
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
137
-
-
85054302038
-
-
Ahookhosh, M., Aragón, F. J., Fleming, R. M. T. & Vuong, P. T. Local convergence of Levenberg-Marquardt methods under Hölder metric subregularity. Preprint at https://arxiv.org/abs/1703.07461 (2017).
-
(2017)
Local Convergence of Levenberg-Marquardt Methods under Hölder Metric Subregularity
-
-
Ahookhosh, M.1
Aragón, F.J.2
Fleming, R.M.T.3
Vuong, P.T.4
-
138
-
-
0242490780
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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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