-
1
-
-
0347506028
-
It is all about metabolic fluxes
-
DOI 10.1128/JB.185.24.7031-7035.2003
-
Nielsen J (2003) It is all about metabolic fluxes. J Bacteriol 185: 7031-7035. (Pubitemid 37521234)
-
(2003)
Journal of Bacteriology
, vol.185
, Issue.24
, pp. 7031-7035
-
-
Nielsen, J.1
-
2
-
-
79961179947
-
Synergies between synthetic biology and metabolic engineering
-
Nielsen J, Keasling JD (2011) Synergies between synthetic biology and metabolic engineering. Nat Biotechnol 29: 693-695.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 693-695
-
-
Nielsen, J.1
Keasling, J.D.2
-
3
-
-
0028108519
-
Metabolic flux balancing: Basic concepts, scientific and practical use
-
Varma A, Palsson B (1994) Metabolic flux balancing: basic concepts, scientific and practical use. Nat Biotechnol 12: 994-998.
-
(1994)
Nat Biotechnol
, vol.12
, pp. 994-998
-
-
Varma, A.1
Palsson, B.2
-
4
-
-
0037385718
-
Genome-scale microbial in silico models: The constraints-based approach
-
DOI 10.1016/S0167-7799(03)00030-1, PII S0167779903000301
-
Price N, Papin J, Schilling C, Palsson B (2003) Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 21: 162-169. (Pubitemid 36397984)
-
(2003)
Trends in Biotechnology
, vol.21
, Issue.4
, pp. 162-169
-
-
Price, N.D.1
Papin, J.A.2
Schilling, C.H.3
Palsson, B.O.4
-
5
-
-
70449592325
-
Enhancing sesquiterpene production in saccharomyces cerevisiae through in silico driven metabolic engineering
-
Asadollahi MA, Maury J, Patil KR, Schalk M, Clark A, Nielsen J (2009) Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab Eng 11: 328-334.
-
(2009)
Metab Eng
, vol.11
, pp. 328-334
-
-
Asadollahi, M.A.1
Maury, J.2
Patil, K.R.3
Schalk, M.4
Clark, A.5
Nielsen, J.6
-
7
-
-
79952106791
-
From zero to hero - Design-based systems metabolic engineering of corynebacterium glutamicum for l-lysine production
-
Becker J, Zelder O, Hafner S, Schroder H, Wittmann C (2011) From zero to hero - design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production. Metab Eng 13: 159-68.
-
(2011)
Metab Eng
, vol.13
, pp. 159-168
-
-
Becker, J.1
Zelder, O.2
Hafner, S.3
Schroder, H.4
Wittmann, C.5
-
8
-
-
70349770739
-
Constraints-based genome-scale metabolic simulation for systems metabolic engineering
-
Park JM, Kim TY, Lee SY (2009) Constraints-based genome-scale metabolic simulation for systems metabolic engineering. Biotechnol Adv 27: 979-988.
-
(2009)
Biotechnol Adv
, vol.27
, pp. 979-988
-
-
Park, J.M.1
Kim, T.Y.2
Lee, S.Y.3
-
9
-
-
84863532131
-
Truncated branch and bound achieves efficient constraint-based genetic design
-
Egen D, Lun DS (2012) Truncated branch and bound achieves efficient constraint-based genetic design Bioinformatics 28: 1619-1623.
-
(2012)
Bioinformatics
, vol.28
, pp. 1619-1623
-
-
Egen, D.1
Lun, D.S.2
-
10
-
-
69249146187
-
Large-scale identification of genetic design strategies using local search
-
Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA et al. (2009) Large-scale identification of genetic design strategies using local search. Mol Syst Biol 5:296.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 296
-
-
Lun, D.S.1
Rockwell, G.2
Guido, N.J.3
Baym, M.4
Kelner, J.A.5
-
11
-
-
84865075156
-
Flux variability scanning based on enforced objective flux for identifying gene amplification targets
-
Park JM, Park HM, Kim WJ, Kim HU, Kim TY (2012) Flux variability scanning based on enforced objective flux for identifying gene amplification targets. BMC Syst Biol 6:106.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 106
-
-
Park, J.M.1
Park, H.M.2
Kim, W.J.3
Kim, H.U.4
Kim, T.Y.5
-
12
-
-
77952585143
-
Casop: A computational approach for strain optimization aiming at high productivity
-
Hadicke O, Klamt S (2010) CASOP: a computational approach for strain optimization aiming at high productivity. J Biotechnol 147: 88-101.
-
(2010)
J Biotechnol
, vol.147
, pp. 88-101
-
-
Hadicke, O.1
Klamt, S.2
-
13
-
-
74549189949
-
Flux design: In silico design of cell factories based on correlation of pathway fluxes to desired properties
-
Melzer G, Esfandabadi ME, Franco-Lara E, Wittmann C (2009) Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst Biol 3:120.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 120
-
-
Melzer, G.1
Esfandabadi, M.E.2
Franco-Lara, E.3
Wittmann, C.4
-
14
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: The cobra toolbox v2.0
-
Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6:1290-12307.
-
(2011)
Nat Protoc
, vol.6
, pp. 1290-12307
-
-
Schellenberger, J.1
Que, R.2
Fleming, R.M.3
Thiele, I.4
Orth, J.D.5
-
15
-
-
77950960250
-
Optflux: An open-source software platform for in silico metabolic engineering
-
Rocha I, Maia P, Evangelista P, Vilaca P, Soares S (2010) OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst Biol 4:45.
-
(2010)
BMC Syst Biol
, vol.4
, pp. 45
-
-
Rocha, I.1
Maia, P.2
Evangelista, P.3
Vilaca, P.4
Soares, S.5
-
17
-
-
0015989446
-
Linear steady-state treatment of enzymatic chains - General properties, control and effector strength
-
Heinrich R, Rapoport TA (1974) Linear Steady-State Treatment of Enzymatic Chains - General Properties, Control and Effector Strength. Eur J Biochem 42: 89-95.
-
(1974)
Eur J Biochem
, vol.42
, pp. 89-95
-
-
Heinrich, R.1
Rapoport, T.A.2
-
18
-
-
78650218972
-
Modeling of uncertainties in biochemical reactions
-
Miskovic L, Hatzimanikatis V (2011) Modeling of uncertainties in biochemical reactions. Biotechnol Bioeng 108: 413-423.
-
(2011)
Biotechnol Bioeng
, vol.108
, pp. 413-423
-
-
Miskovic, L.1
Hatzimanikatis, V.2
-
19
-
-
10044224601
-
Metabolic control analysis under uncertainty: Framework development and case studies
-
DOI 10.1529/biophysj.104.048090
-
Wang L, Birol I, Hatzimanikatis V (2004) Metabolic control analysis under uncertainty: framework development and case studies. BiophysJ87: 3750-3763. (Pubitemid 39602883)
-
(2004)
Biophysical Journal
, vol.87
, Issue.6
, pp. 3750-3763
-
-
Wang, L.1
Birol, I.2
Hatzimanikatis, V.3
-
20
-
-
84857702241
-
Metabolic ensemble modeling for strain engineers
-
Tan Y, Liao JC (2012) Metabolic ensemble modeling for strain engineers. Biotechnol J 7: 343-353.
-
(2012)
Biotechnol J
, vol.7
, pp. 343-353
-
-
Tan, Y.1
Liao, J.C.2
-
21
-
-
70149091494
-
Ensemble modeling for aromatic production in escherichia coli
-
Rizk ML, Liao JC (2009) Ensemble modeling for aromatic production in Escherichia coli. PLoS One 4: e6903.
-
(2009)
PLoS One
, vol.4
-
-
Rizk, M.L.1
Liao, J.C.2
-
22
-
-
0141684666
-
Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics
-
DOI 10.1016/S1096-7176(03)00025-9
-
Visser D, Heijnen JJ (2003) Dynamic simulation and metabolic re¬design of a branched pathway using linlog kinetics. Metab Eng 5: 164-176. (Pubitemid 37124115)
-
(2003)
Metabolic Engineering
, vol.5
, Issue.3
, pp. 164-176
-
-
Visser, D.1
Heijnen, J.J.2
-
24
-
-
33846617808
-
Bringing metabolic networks to life: Convenience rate law and thermodynamic constraints
-
Liebermeister W, Klipp E (2006) Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor BiolMedMod3: 41.
-
(2006)
Theor BiolMedMod
, vol.3
, pp. 41
-
-
Liebermeister, W.1
Klipp, E.2
-
25
-
-
0014733809
-
Biochemical systems analysis. Iii. Dynamic solutions using a power-law approximation
-
Savageau M (1970) Biochemical systems analysis. III. Dynamic solutions using a power-law approximation. J Theor Biol 26:215-226.
-
(1970)
J Theor Biol
, vol.26
, pp. 215-226
-
-
Savageau, M.1
-
26
-
-
77952953154
-
Hybrid dynamic modeling of escherichia coli central metabolic network combining michaelis-menten and approximate kinetic equations
-
Costa RS, Machado D, Rocha I, Ferreira EC (2010) Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. Biosystems. 100: 150-157.
-
(2010)
Biosystems.
, vol.100
, pp. 150-157
-
-
Costa, R.S.1
Machado, D.2
Rocha, I.3
Ferreira, E.C.4
-
27
-
-
58149156532
-
Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws - A promising method for speeding up the kinetic modelling of complex metabolic networks
-
Bulik S, Grimbs S, Huthmacher C, Selbig J, Holzhutter HG (2009) Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws - a promising method for speeding up the kinetic modelling of complex metabolic networks. FEBS J 276(2):410-424.
-
(2009)
FEBS J
, vol.276
, Issue.2
, pp. 410-424
-
-
Bulik, S.1
Grimbs, S.2
Huthmacher, C.3
Selbig, J.4
Holzhutter, H.G.5
-
28
-
-
79955137362
-
An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data
-
Canelas AB, Ras C, Ten Pierick A, van Gulik WM, Heijnen JJ (2011) An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data. Metab Eng 13: 294-306.
-
(2011)
Metab Eng
, vol.13
, pp. 294-306
-
-
Canelas, A.B.1
Ras, C.2
Ten Pierick, A.3
Van Gulik, W.M.4
Heijnen, J.J.5
-
29
-
-
79953162662
-
Escherichia coli w as a new platform strain for the enhanced production of l-valine by systems metabolic engineering
-
Park JH, Jang YS, Lee JW, Lee SY (2011) Escherichia coli W as a new platform strain for the enhanced production of L-valine by systems metabolic engineering. Biotechnol Bioeng 108: 1140-1147.
-
(2011)
Biotechnol Bioeng
, vol.108
, pp. 1140-1147
-
-
Park, J.H.1
Jang, Y.S.2
Lee, J.W.3
Lee, S.Y.4
-
30
-
-
29144524991
-
Engineering of solvent-tolerant pseudomonas putida S12 for bioproduction of phenol from glucose
-
DOI 10.1128/AEM.71.12.8221-8227.2005
-
Wierckx NJ, Ballerstedt H, de Bont JA, Wery J (2005) Engineering of solvent-tolerant Pseudomonas putida S12 for bioproduction of phenol from glucose. Appl Environ Microbiol 71: 8221-8227. (Pubitemid 41803948)
-
(2005)
Applied and Environmental Microbiology
, vol.71
, Issue.12
, pp. 8221-8227
-
-
Wierckx, N.J.P.1
Ballerstedt, H.2
De Bont, J.A.M.3
Wery, J.4
-
31
-
-
68049135724
-
Engineering alternative butanol production platforms in heterologous bacteria
-
Nielsen DR, Leonard E, Yoon SH, Tseng HC, Yuan C (2009) Engineering alternative butanol production platforms in heterologous bacteria. Metab Eng 11: 262-273.
-
(2009)
Metab Eng
, vol.11
, pp. 262-273
-
-
Nielsen, D.R.1
Leonard, E.2
Yoon, S.H.3
Tseng, H.C.4
Yuan, C.5
-
32
-
-
78751638661
-
Engineering cyanobacteria to generate high-value products
-
Ducat DC, Way JC, Silver PA (2011) Engineering cyanobacteria to generate high-value products. Trends Biotechnol 29: 95-103.
-
(2011)
Trends Biotechnol
, vol.29
, pp. 95-103
-
-
Ducat, D.C.1
Way, J.C.2
Silver, P.A.3
-
33
-
-
84863630261
-
Pathway engineering and synthetic biology using acetogens
-
Schiel-Bengelsdorf B, Diirre P (2012) Pathway engineering and synthetic biology using acetogens. FEBS Lett 586: 2191-2198.
-
(2012)
FEBS Lett
, vol.586
, pp. 2191-2198
-
-
Schiel-Bengelsdorf, B.1
Diirre, P.2
-
34
-
-
79955675417
-
Electrosynthesis of organic compounds from carbon dioxide is catalyzed by a diversity of acetogenic microorganisms
-
Nevin KP, Hensley SA, Franks AE, Summers ZM, Ou J (2011) Electrosynthesis of organic compounds from carbon dioxide is catalyzed by a diversity of acetogenic microorganisms. Appl Environ Microbiol 77: 2882-2886.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 2882-2886
-
-
Nevin, K.P.1
Hensley, S.A.2
Franks, A.E.3
Summers, Z.M.4
Ou, J.5
-
35
-
-
84859358212
-
Modelling cyanobacteria: From metabolism to integrative models of phototrophic growth
-
Steuer R, Knoop H, Machne R (2012) Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth. J Exp Bot 63: 2259-2274.
-
(2012)
J Exp Bot
, vol.63
, pp. 2259-2274
-
-
Steuer, R.1
Knoop, H.2
Machne, R.3
-
36
-
-
67650573077
-
Ibsull03: A new genome-scale metabolic model of bacillus subtilis based on seed annotations
-
Henry CS, Zinner JF, Cohoon MP, Stevens RL (2009) iBsull03: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol 10: R69.
-
(2009)
Genome Biol
, vol.10
-
-
Henry, C.S.1
Zinner, J.F.2
Cohoon, M.P.3
Stevens, R.L.4
-
37
-
-
33747620056
-
Accelerating the reconstruction of genome-scale metabolic networks
-
Notebaart RA, van Enckevort FH, Francke C, Siezen RJ, Teusink B (2006) Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics 7:296.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 296
-
-
Notebaart, R.A.1
Van Enckevort, F.H.2
Francke, C.3
Siezen, R.J.4
Teusink, B.5
-
38
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele I, Palsson BO (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5: 93-121.
-
(2010)
Nat Protoc
, vol.5
, pp. 93-121
-
-
Thiele, I.1
Palsson, B.O.2
-
39
-
-
84859199206
-
Genome-scale metabolic reconstructions of pichia stipitis and pichia pastoris and in silico evaluation of their potentials
-
Caspeta L, Shoaie S, Agren R, Nookaew I, Nielsen J (2012) Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst Biol 6: 24.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 24
-
-
Caspeta, L.1
Shoaie, S.2
Agren, R.3
Nookaew, I.4
Nielsen, J.5
-
41
-
-
17444382016
-
Exploring the diversity of complex metabolic networks
-
DOI 10.1093/bioinformatics/bti213
-
Hatzimanikatis V, Li C, Ionita JA, Henry CS, Jankowski MD et al. (2005) Exploring the diversity of complex metabolic networks. Bioinformatics21: 1603-1609. (Pubitemid 40542718)
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1603-1609
-
-
Hatzimanikatis, V.1
Li, C.2
Ionita, J.A.3
Henry, C.S.4
Jankowski, M.D.5
Broadbelt, L.6
-
42
-
-
83555163791
-
Integrating computational methods to retrofit enzymes to synthetic pathways
-
Brunk E, Neri M, Tavernelli I, Hatzimanikatis V, Rothlisberger U (2012) Integrating computational methods to retrofit enzymes to synthetic pathways. Biotechnol Bioeng 109: 572-582.
-
(2012)
Biotechnol Bioeng
, vol.109
, pp. 572-582
-
-
Brunk, E.1
Neri, M.2
Tavernelli, I.3
Hatzimanikatis, V.4
Rothlisberger, U.5
-
43
-
-
0000029295
-
On elementary flux modes in biochemical reaction systems at steady state
-
Schuster S, Hilgetag C (1994) On elementary flux modes in biochemical reaction systems at steady state. J Biol Syst 2: 165-182.
-
(1994)
J Biol Syst
, vol.2
, pp. 165-182
-
-
Schuster, S.1
Hilgetag, C.2
-
44
-
-
79951528622
-
Exploring metabolic pathways in genome-scale networks via generating flux modes
-
Rezola A, de Figueiredo LF, Brock M, Pey J, Podhorski A (2011) Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinformatics 27: 534-540.
-
(2011)
Bioinformatics
, vol.27
, pp. 534-540
-
-
Rezola, A.1
De Figueiredo, L.F.2
Brock, M.3
Pey, J.4
Podhorski, A.5
-
45
-
-
79961176618
-
Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks
-
Chan SH, Ji P (2011) Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks. Bioinformatics 27:2256-2262.
-
(2011)
Bioinformatics
, vol.27
, pp. 2256-2262
-
-
Chan, S.H.1
Ji, P.2
-
46
-
-
52949098408
-
Large-scale computation of elementary flux modes with bit pattern trees
-
Terzer M. Stelling J (2008) Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 24: 2229-2235.
-
(2008)
Bioinformatics
, vol.24
, pp. 2229-2235
-
-
Terzer, M.1
Stelling, J.2
-
47
-
-
84856579358
-
Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms
-
Carbonell P, Fichera D, Pandit SB, Faulon JL (2012) Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Syst Biol 6: 10.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 10
-
-
Carbonell, P.1
Fichera, D.2
Pandit, S.B.3
Faulon, J.L.4
-
48
-
-
8744224466
-
OptStrain: A computational framework for redesign of microbial production systems
-
DOI 10.1101/gr.2872004
-
Pharkya P, Burgard AP, Maranas CD (2004) OptStrain: a computational framework for redesign of microbial production systems. Genome Res 14: 2367-2376. (Pubitemid 39517344)
-
(2004)
Genome Research
, vol.14
, Issue.11
, pp. 2367-2376
-
-
Pharkya, P.1
Burgard, A.P.2
Maranas, C.D.3
-
49
-
-
70749083404
-
Inferring branching pathways in genome-scale metabolic networks
-
Pitkanen E, Jouhten P, Rousu J (2009) Inferring branching pathways in genome-scale metabolic networks. BMC Syst Biol 3:103.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 103
-
-
Pitkanen, E.1
Jouhten, P.2
Rousu, J.3
-
51
-
-
33644874819
-
From genomics to chemical genomics: New developments in kegg
-
(Database issue
-
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34(Database issue): D354-357.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Hattori, M.3
Aoki-Kinoshita, K.F.4
Itoh, M.5
-
52
-
-
78651301358
-
Computing atom mappings for biochemical reactions without subgraph isomorphism
-
Heinonen M, Lappalainen S, Mielikainen T, Rousu J (2011) Computing atom mappings for biochemical reactions without subgraph isomorphism. J Comput Biol 18: 43-58.
-
(2011)
J Comput Biol
, vol.18
, pp. 43-58
-
-
Heinonen, M.1
Lappalainen, S.2
Mielikainen, T.3
Rousu, J.4
-
53
-
-
33847797256
-
Thermodynamics-based metabolic flux analysis
-
DOI 10.1529/biophysj.106.093138
-
Henry CS, Broadbelt LJ, Hatzimanikatis V (2007) Thermodynamics-based metabolic flux analysis. Biophys J 92: 1792 - 1805. (Pubitemid 46393490)
-
(2007)
Biophysical Journal
, vol.92
, Issue.5
, pp. 1792-1805
-
-
Henry, C.S.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
54
-
-
77953578214
-
Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate
-
Henry C S, Broadbelt L J, Hatzimanikatis V (2010) Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-Hydroxypropanoate Biotechnol Bioeng 106: 462- 473.
-
(2010)
Biotechnol Bioeng
, vol.106
, pp. 462-473
-
-
Henry, C.S.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
55
-
-
51049107514
-
Group contribution method for thermodynamic analysis of complex metabolic networks
-
Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V (2008) Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 95: 1487-1499.
-
(2008)
Biophys J
, vol.95
, pp. 1487-1499
-
-
Jankowski, M.D.1
Henry, C.S.2
Broadbelt, L.J.3
Hatzimanikatis, V.4
-
56
-
-
84865136870
-
An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
-
Noor E, Bar-Even A, Flamholz A, Lubling Y, Davidi D et al. (2012) An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics 28: 2037-2044.
-
(2012)
Bioinformatics
, vol.28
, pp. 2037-2044
-
-
Noor, E.1
Bar-Even, A.2
Flamholz, A.3
Lubling, Y.4
Davidi, D.5
-
57
-
-
84860819691
-
An in silico platform for the design of heterologous pathways in nonnative metabolite production
-
Chatsurachai S, Furusawa C, Shimizu H (2012) An in silico platform for the design of heterologous pathways in nonnative metabolite production. BMC Bioinformatics 13: 93.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 93
-
-
Chatsurachai, S.1
Furusawa, C.2
Shimizu, H.3
-
58
-
-
80055098735
-
Hydrophobicity and charge shape cellular metabolite concentrations
-
Bar-Even A, Noor E, Flamholz A, Buescher JM, Milo R (2011) Hydrophobicity and charge shape cellular metabolite concentrations. PLoS Comput Biol 7: el002166.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Bar-Even, A.1
Noor, E.2
Flamholz, A.3
Buescher, J.M.4
Milo, R.5
-
59
-
-
84869875863
-
Designing biological compartmentalization
-
In press
-
Chen AH, Silver PA (2012) Designing biological compartmentalization. Trends Cell Biol. In press.
-
(2012)
Trends Cell Biol.
-
-
Chen, A.H.1
Silver, P.A.2
-
60
-
-
84859776222
-
The future of metabolic engineering and synthetic biology towards a systematic practice
-
Yadav VG, De Mey M, Lim CG, Ajikumar PK, Stephanopoulos G (2012) The future of metabolic engineering and synthetic biology: towards a systematic practice. Metab Eng 14: 233-241.
-
(2012)
Metab Eng
, vol.14
, pp. 233-241
-
-
Yadav, V.G.1
De Mey, M.2
Lim, C.G.3
Ajikumar, P.K.4
Stephanopoulos, G.5
-
61
-
-
77955852574
-
A model for improving microbial biofuel production using a synthetic feedback loop
-
Dunlop MJ, Keasling JD, Mukhopadhyay A (2010) A model for improving microbial biofuel production using a synthetic feedback loop. Syst Synth Biol 4: 95-104.
-
(2010)
Syst Synth Biol
, vol.4
, pp. 95-104
-
-
Dunlop, M.J.1
Keasling, J.D.2
Mukhopadhyay, A.3
-
62
-
-
84858609338
-
Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology
-
Blount BA, Weenink T, Vasylechko S, Ellis T (2012) Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS One 7: e33279.
-
(2012)
PLoS One
, vol.7
-
-
Blount, B.A.1
Weenink, T.2
Vasylechko, S.3
Ellis, T.4
-
63
-
-
84864634066
-
A synthetic biology framework for programming eukaryotic transcription functions
-
Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC et al. (2012) A synthetic biology framework for programming eukaryotic transcription functions. Cell 150: 647-658.
-
(2012)
Cell
, vol.150
, pp. 647-658
-
-
Khalil, A.S.1
Lu, T.K.2
Bashor, C.J.3
Ramirez, C.L.4
Pyenson, N.C.5
-
64
-
-
0036708443
-
Dynamic Flux Balance Analysis of diauxic growth in Escherichia coli
-
Mahadevan R, Edwards JS, Doyle FJ (2002) Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys J 83: 1331-1340. (Pubitemid 34977706)
-
(2002)
Biophysical Journal
, vol.83
, Issue.3
, pp. 1331-1340
-
-
Mahadevan, R.1
Edwards, J.S.2
Doyle III, F.J.3
-
65
-
-
33749996165
-
Optimization of fed-batch Saccharomyces cerevisiae fermentation using dynamic flux balance models
-
DOI 10.1021/bp060059v
-
Hjersted JL, Henson MA (2006) Optimization of fed-batch Saccharomyces cerevisiae fermentation using dynamic flux balance models. Biotechnol Prog 22: 1239-1248. (Pubitemid 44568797)
-
(2006)
Biotechnology Progress
, vol.22
, Issue.5
, pp. 1239-1248
-
-
Hjersted, J.L.1
Henson, M.A.2
-
67
-
-
80455156250
-
Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in saccharomyces cerevisiae
-
Ghosh A, Zhao H, Price ND (2011) Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. PLoS One 6: e27316.
-
(2011)
PLoS One
, vol.6
-
-
Ghosh, A.1
Zhao, H.2
Price, N.D.3
-
68
-
-
84865978199
-
Dynamic flux balance analysis of the metabolism of saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis
-
doi: 10.1111/j.l742-4658.2012.08649.x
-
Jouhten P, Wiebe M, Penttila M (2012) Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis. FEBS J doi: 10.1111/j.l742-4658.2012.08649.x.
-
(2012)
FEBS J
-
-
Jouhten, P.1
Wiebe, M.2
Penttila, M.3
-
69
-
-
34447308322
-
Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture
-
DOI 10.1002/bit.21332
-
Hjersted JL, Henson MA, Mahadevan R (2007) Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture. Biotechnol Bioeng 97:1190-1204. (Pubitemid 47195316)
-
(2007)
Biotechnology and Bioengineering
, vol.97
, Issue.5
, pp. 1190-1204
-
-
Hjersted, J.L.1
Henson, M.A.2
Mahadevan, R.3
-
70
-
-
84864318798
-
Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters
-
Moisset P, Vaisman D, Cintolesi A, Urrutia J, Rapaport I (2012) Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters. Biotechnol Bioeng 109: 2325-2339.
-
(2012)
Biotechnol Bioeng
, vol.109
, pp. 2325-2339
-
-
Moisset, P.1
Vaisman, D.2
Cintolesi, A.3
Urrutia, J.4
Rapaport, I.5
-
71
-
-
77949385752
-
Bacterial adaptation through distributed sensing of metabolic fluxes
-
Kotte O, Zaugg JB, Heinemann M (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 6: 355.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 355
-
-
Kotte, O.1
Zaugg, J.B.2
Heinemann, M.3
-
72
-
-
77954724818
-
Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing
-
Salimi F, Zhuang K, Mahadevan R (2010) Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol J 5: 726-738.
-
(2010)
Biotechnol J
, vol.5
, pp. 726-738
-
-
Salimi, F.1
Zhuang, K.2
Mahadevan, R.3
-
73
-
-
84055200869
-
Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered escherichia coli
-
Bokinsky G, Peralta-Yahya PP, George A, Holmes BM, Steen EJ et al. (2011) Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc Nad Acad Sci U SA 108: 19949-19954.
-
(2011)
Proc Nad Acad Sci U SA
, vol.108
, pp. 19949-19954
-
-
Bokinsky, G.1
Peralta-Yahya, P.P.2
George, A.3
Holmes, B.M.4
Steen, E.J.5
-
74
-
-
0242574984
-
In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism
-
DOI 10.1101/gr.1212003
-
Arita M (2003) In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res 13: 2455-66. (Pubitemid 37428270)
-
(2003)
Genome Research
, vol.13
, Issue.11
, pp. 2455-2466
-
-
Arita, M.1
-
75
-
-
79954459893
-
Construction of an e. Coli genome-scale atom mapping model for mfa calculations
-
Ravikirthi P, Suthers PF, Maranas CD (2011) Construction of an E. Coli genome-scale atom mapping model for MFA calculations. Biotechnol Bioeng 108: 1372-1382.
-
(2011)
Biotechnol Bioeng
, vol.108
, pp. 1372-1382
-
-
Ravikirthi, P.1
Suthers, P.F.2
Maranas, C.D.3
-
76
-
-
4243829380
-
Bidirectional reaction steps in metabolic networks: IV. Optimal design of isotopomer labeling experiments
-
DOI 10.1002/(SICI)1097-0290(1999)66:2<86: :AID-BIT2>3.0.CO;2-A
-
Mollney M, Wiechert W, Kownatzki D, de Graaf AA (1999) Bidirectional reaction steps in metabolic networks: IV.Optimal design of isotopomer labeling experiments. Biotechnol Bioeng 66: 86-103. (Pubitemid 32262269)
-
(1999)
Biotechnology and Bioengineering
, vol.66
, Issue.2
, pp. 86-103
-
-
Mollney, M.1
Wiechert, W.2
Kownatzki, D.3
De Graaf, A.A.4
-
77
-
-
84856291750
-
Predicting outcomes of steady-state 13c isotope tracing experiments using monte carlo sampling
-
Schellenberger J, Zielinski DC, Choi W, Madireddi S, Portnoy V et al. (2012) Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. BMC Syst Biol 6:9.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 9
-
-
Schellenberger, J.1
Zielinski, D.C.2
Choi, W.3
Madireddi, S.4
Portnoy, V.5
-
78
-
-
33845679072
-
Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions
-
DOI 10.1016/j.ymben.2006.09.001, PII S109671760600084X
-
Antoniewicz MR, Kelleher JK, Stephanopoulos G (2007) Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng 9: 68-86. (Pubitemid 44960874)
-
(2007)
Metabolic Engineering
, vol.9
, Issue.1
, pp. 68-86
-
-
Antoniewicz, M.R.1
Kelleher, J.K.2
Stephanopoulos, G.3
-
79
-
-
84861008392
-
Rational design of 13c-labeling experiments for metabolic flux analysis in mammalian cells
-
Crown SB, Ahn WS, Antoniewicz MR (2012) Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells. BMC Syst Biol 6: 43.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 43
-
-
Crown, S.B.1
Ahn, W.S.2
Antoniewicz, M.R.3
-
80
-
-
56149101337
-
Fid: A software for ab initio structural identification of product ions from tandem mass spectrometric data
-
Heinonen M, Rantanen A, Mielikainen T, Kokkonen J, Kiuru J et al. (2008) FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Commun Mass Spectrom 22: 3043-3052.
-
(2008)
Rapid Commun Mass Spectrom
, vol.22
, pp. 3043-3052
-
-
Heinonen, M.1
Rantanen, A.2
Mielikainen, T.3
Kokkonen, J.4
Kiuru, J.5
-
81
-
-
77952302069
-
In silico fragmentation for computer assisted identification of metabolite mass spectra
-
WolfS, Schmidt S, Miiller-Hannemann M, Neumann S (2010) In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics 11: 148.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 148
-
-
Wolf, S.1
Schmidt, S.2
Miiller-Hannemann, M.3
Neumann, S.4
-
82
-
-
0029146299
-
Biosynthetically directed fractional 13c-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism
-
Szyperski T (1995) Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. Eur J Biochem 232: 433-448.
-
(1995)
Eur J Biochem
, vol.232
, pp. 433-448
-
-
Szyperski, T.1
-
83
-
-
0034741985
-
13C metabolic flux analysis
-
DOI 10.1006/mben.2001.0188
-
Wiechert W, Mollney M, Petersen S, de Graaf AA (2001) A universal framework for 13C metabolic flux analysis. Metab Eng 3: 265-283. (Pubitemid 32748170)
-
(2001)
Metabolic Engineering
, vol.3
, Issue.3
, pp. 265-283
-
-
Wiechert, W.1
Mollney, M.2
Petersen, S.3
De Graaf, A.A.4
-
84
-
-
1642538406
-
13C constraints
-
DOI 10.1016/j.ab.2003.10.036
-
Fischer E, Zamboni N, Sauer U (2004) High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem 325: 308-316. (Pubitemid 38134368)
-
(2004)
Analytical Biochemistry
, vol.325
, Issue.2
, pp. 308-316
-
-
Fischer, E.1
Zamboni, N.2
Sauer, U.3
-
85
-
-
49549104162
-
Oxygen dependence of metabolic fluxes and energy generation of saccharomyces cerevisiae cen.Pk113-1a
-
Jouhten P, Rintala E, Huuskonen A, Tamminen A, Toivari M et al. (2008) Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A. BMC Syst Biol 2:60.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 60
-
-
Jouhten, P.1
Rintala, E.2
Huuskonen, A.3
Tamminen, A.4
Toivari, M.5
-
86
-
-
45749090110
-
An analytic and systematic framework for estimating metabolic flux ratios from 13c tracer experiments
-
Rantanen A, Rousu J, Jouhten P, Zamboni N, Maaheimo H et al. (2008) An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments.BMC Bioinformatics 9: 266.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 266
-
-
Rantanen, A.1
Rousu, J.2
Jouhten, P.3
Zamboni, N.4
Maaheimo, H.5
-
87
-
-
25444489844
-
Fiatflux - A software for metabolic flux analysis from 13c-glucose experiments
-
Zamboni N, Fischer E, Sauer U (2005) FiatFlux - a software for metabolic flux analysis from 13C-glucose experiments.BMC Bioinformatics 6: 209.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 209
-
-
Zamboni, N.1
Fischer, E.2
Sauer, U.3
-
88
-
-
84855258472
-
The ethylmalonyl-coa pathway is used in place of the glyoxylate cycle by methylobacterium extorquens ami during growth on acetate
-
Schneider K, Peyraud R, Kiefer P, Christen P, Delmotte N (2012) The ethylmalonyl-CoA pathway is used in place of the glyoxylate cycle by Methylobacterium extorquens AMI during growth on acetate. J Biol Chem 287: 757-766.
-
(2012)
J Biol Chem
, vol.287
, pp. 757-766
-
-
Schneider, K.1
Peyraud, R.2
Kiefer, P.3
Christen, P.4
Delmotte, N.5
-
89
-
-
34249007773
-
13C-Labeled metabolic flux analysis of a fed-batch culture of elutriated Saccharomyces cerevisiae
-
DOI 10.1111/j.1567-1364.2006.00199.x
-
Costenoble R, Miiller D, Barl T, van Gulik WM, van Winden WA (2007) 13C-Labeled metabolic flux analysis of a fed-batch culture of elutriated Saccharomyces cerevisiae, FEMS Yeast Res 7: 511-526. (Pubitemid 46788672)
-
(2007)
FEMS Yeast Research
, vol.7
, Issue.4
, pp. 511-526
-
-
Costenoble, R.1
Muller, D.2
Barl, T.3
Van Gulik, W.M.4
Van Winden, W.A.5
Reuss, M.6
Heijnen, J.J.7
-
90
-
-
80052644208
-
Metabolite channeling and compartmentation in the human cell line age1. Hn determined by 13c labeling experiments and 13c metabolic flux analysis
-
Niklas J, Sandig V, Heinzle E (2011) Metabolite channeling and compartmentation in the human cell line AGE1 .HN determined by 13C labeling experiments and 13C metabolic flux analysis. J Biosci Bioengll2: 616-623.
-
(2011)
J Biosci Bioengll
, vol.2
, pp. 616-623
-
-
Niklas, J.1
Sandig, V.2
Heinzle, E.3
-
91
-
-
66949164842
-
Openflux: Efficient modelling software for 13c-based metabolic flux analysis
-
Quek LE, Wittmann C, Nielsen LK, Kromer JO (2009) OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis. Microb Cell Fact 8:25.
-
(2009)
Microb Cell Fact
, vol.8
, pp. 25
-
-
Quek, L.E.1
Wittmann, C.2
Nielsen, L.K.3
Kromer, J.O.4
-
92
-
-
25444467580
-
Large-scale 13c-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast
-
Blank LM, Kuepfer L, Sauer U (2005) Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol. 6: R49.
-
(2005)
Genome Biol
, vol.6
-
-
Blank, L.M.1
Kuepfer, L.2
Sauer, U.3
-
93
-
-
76749140314
-
Improved computational performance of mfa using elementary metabolite units and flux coupling
-
Suthers PF, Chang YJ, Maranas CD (2010) Improved computational performance of MFA using elementary metabolite units and flux coupling. Metab Eng 12: 123-128.
-
(2010)
Metab Eng
, vol.12
, pp. 123-128
-
-
Suthers, P.F.1
Chang, Y.J.2
Maranas, C.D.3
-
94
-
-
84860855750
-
Application of targeted proteomics to metabolically engineered escherichia coli
-
Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD et al. (2012) Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics 12: 1289-1299.
-
(2012)
Proteomics
, vol.12
, pp. 1289-1299
-
-
Singh, P.1
Batth, T.S.2
Juminaga, D.3
Dahl, R.H.4
Keasling, J.D.5
-
95
-
-
51349092391
-
Network-based prediction of human tissue-specific metabolism
-
Shlomi T, Cabili MN, Herrgard MJ, Palsson BO, Ruppin E (2008) Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 26: 1003-1010.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1003-1010
-
-
Shlomi, T.1
Cabili, M.N.2
Herrgard, M.J.3
Palsson, B.O.4
Ruppin, E.5
-
97
-
-
78650571311
-
Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux
-
Tan Y, Rivera JG, Contador CA, Asenjo JA, Liao JC (2011) Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux.Metab Eng 13: 60-75.
-
(2011)
Metab Eng
, vol.13
, pp. 60-75
-
-
Tan, Y.1
Rivera, J.G.2
Contador, C.A.3
Asenjo, J.A.4
Liao, J.C.5
|