-
1
-
-
84941282441
-
Parallel labeling experiments for pathway elucidation and 13C metabolic flux analysis
-
Antoniewicz, M.R., Parallel labeling experiments for pathway elucidation and 13C metabolic flux analysis. Curr. Opin. Biotechnol. 36 (2015), 91–97.
-
(2015)
Curr. Opin. Biotechnol.
, vol.36
, pp. 91-97
-
-
Antoniewicz, M.R.1
-
2
-
-
35348941242
-
Accurate assessment of amino acid mass isotopomer distributions for metabolic flux analysis
-
Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., Accurate assessment of amino acid mass isotopomer distributions for metabolic flux analysis. Anal. Chem. 79 (2007), 7554–7559.
-
(2007)
Anal. Chem.
, vol.79
, pp. 7554-7559
-
-
Antoniewicz, M.R.1
Kelleher, J.K.2
Stephanopoulos, G.3
-
3
-
-
33845679072
-
Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions
-
Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab. Eng. 9 (2007), 68–86.
-
(2007)
Metab. Eng.
, vol.9
, pp. 68-86
-
-
Antoniewicz, M.R.1
Kelleher, J.K.2
Stephanopoulos, G.3
-
4
-
-
33745155105
-
Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements
-
Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab. Eng. 8 (2006), 324–337.
-
(2006)
Metab. Eng.
, vol.8
, pp. 324-337
-
-
Antoniewicz, M.R.1
Kelleher, J.K.2
Stephanopoulos, G.3
-
5
-
-
34249297627
-
Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol
-
Antoniewicz, M.R., Kraynie, D.F., Laffend, L. a., González-Lergier, J., Kelleher, J.K., Stephanopoulos, G., 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 (2007), 277–292.
-
(2007)
Metab. Eng.
, vol.9
, pp. 277-292
-
-
Antoniewicz, M.R.1
Kraynie, D.F.2
Laffend, L.A.3
González-Lergier, J.4
Kelleher, J.K.5
Stephanopoulos, G.6
-
6
-
-
78650647970
-
Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli
-
Atsumi, S., Wu, T.-Y., Machado, I.M.P., Huang, W.-C., Chen, P.-Y., Pellegrini, M., Liao, J.C., Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol. Syst. Biol. 6 (2010), 1–11.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 1-11
-
-
Atsumi, S.1
Wu, T.-Y.2
Machado, I.M.P.3
Huang, W.-C.4
Chen, P.-Y.5
Pellegrini, M.6
Liao, J.C.7
-
7
-
-
78649694766
-
Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene
-
Charusanti, P., Conrad, T.M., Knight, E.M., Venkataraman, K., Fong, N.L., Xie, B., Gao, Y., Palsson, B.Ø., Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene. PLoS Genet., 6, 2010, e1001186.
-
(2010)
PLoS Genet.
, vol.6
, pp. e1001186
-
-
Charusanti, P.1
Conrad, T.M.2
Knight, E.M.3
Venkataraman, K.4
Fong, N.L.5
Xie, B.6
Gao, Y.7
Palsson, B.Ø.8
-
8
-
-
78650574197
-
Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli
-
Chen, X., Alonso, A.P., Allen, D.K., Reed, J.L., Shachar-Hill, Y., Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli. Metab. Eng. 13 (2011), 38–48.
-
(2011)
Metab. Eng.
, vol.13
, pp. 38-48
-
-
Chen, X.1
Alonso, A.P.2
Allen, D.K.3
Reed, J.L.4
Shachar-Hill, Y.5
-
9
-
-
84952638985
-
13C metabolic flux analysis of the extremely thermophilic, fast growing, xylose-utilizing Geobacillus strain LC300
-
13C metabolic flux analysis of the extremely thermophilic, fast growing, xylose-utilizing Geobacillus strain LC300. Metab. Eng. 33 (2016), 148–157.
-
(2016)
Metab. Eng.
, vol.33
, pp. 148-157
-
-
Cordova, L.T.1
Antoniewicz, M.R.2
-
10
-
-
84943239543
-
Complete genome sequence, metabolic model construction and phenotypic characterization of Geobacillus LC300, an extremely thermophilic, fast growing, xylose-utilizing bacterium
-
Cordova, L.T., Long, C.P., Venkataramanan, P., Antoniewicz, M.R., Complete genome sequence, metabolic model construction and phenotypic characterization of Geobacillus LC300, an extremely thermophilic, fast growing, xylose-utilizing bacterium. Metab. Eng. 32 (2015), 74–81.
-
(2015)
Metab. Eng.
, vol.32
, pp. 74-81
-
-
Cordova, L.T.1
Long, C.P.2
Venkataramanan, P.3
Antoniewicz, M.R.4
-
11
-
-
84966700439
-
Co-utilization of glucose and xylose by evolved Thermus thermophilus LC113 strain elucidated by 13C metabolic flux analysis and whole genome sequencing
-
Cordova, L.T., Lu, J., Cipolla, R.M., Sandoval, N.R., Long, C.P., Antoniewicz, M.R., Co-utilization of glucose and xylose by evolved Thermus thermophilus LC113 strain elucidated by 13C metabolic flux analysis and whole genome sequencing. Metab. Eng. 37 (2016), 63–71.
-
(2016)
Metab. Eng.
, vol.37
, pp. 63-71
-
-
Cordova, L.T.1
Lu, J.2
Cipolla, R.M.3
Sandoval, N.R.4
Long, C.P.5
Antoniewicz, M.R.6
-
12
-
-
84973441412
-
13C metabolic flux analysis: a new precision and synergy scoring system
-
13C metabolic flux analysis: a new precision and synergy scoring system. Metab. Eng. 38 (2016), 10–18.
-
(2016)
Metab. Eng.
, vol.38
, pp. 10-18
-
-
Crown, S.B.1
Long, C.P.2
Antoniewicz, M.R.3
-
13
-
-
84922245805
-
Integrated 13C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli
-
Crown, S.B., Long, C.P., Antoniewicz, M.R., Integrated 13C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli. Metab. Eng. 28 (2015), 151–158.
-
(2015)
Metab. Eng.
, vol.28
, pp. 151-158
-
-
Crown, S.B.1
Long, C.P.2
Antoniewicz, M.R.3
-
14
-
-
0034625143
-
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities
-
Edwards, J.S., Palsson, B.O., The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA 97 (2000), 5528–5533.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 5528-5533
-
-
Edwards, J.S.1
Palsson, B.O.2
-
15
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V., Palsson, B.Ø., A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol., 3, 2007, 121.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, B.Ø.9
-
16
-
-
0029664919
-
Correction of 13C mass isotopomer distributions for natural stable isotope abundance
-
Fernandez, C. a., Des Rosiers, C., Previs, S.F., David, F., Brunengraber, H., Correction of 13C mass isotopomer distributions for natural stable isotope abundance. J. Mass Spectrom. 31 (1996), 255–262.
-
(1996)
J. Mass Spectrom.
, vol.31
, pp. 255-262
-
-
Fernandez, C.A.1
Des Rosiers, C.2
Previs, S.F.3
David, F.4
Brunengraber, H.5
-
17
-
-
33646362289
-
Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes
-
Fong, S.S., Nanchen, A., Palsson, B.O., Sauer, U., Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J. Biol. Chem. 281 (2006), 8024–8033.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 8024-8033
-
-
Fong, S.S.1
Nanchen, A.2
Palsson, B.O.3
Sauer, U.4
-
18
-
-
6944224154
-
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
-
Fong, S.S., Palsson, B.O., Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat. Genet. 36 (2004), 1056–1058.
-
(2004)
Nat. Genet.
, vol.36
, pp. 1056-1058
-
-
Fong, S.S.1
Palsson, B.O.2
-
19
-
-
84914124771
-
Comparison and analysis of objective functions in flux balance analysis
-
García Sánchez, C.E., Torres Sáez, R.G., Comparison and analysis of objective functions in flux balance analysis. Biotechnol. Prog. 30 (2014), 985–991.
-
(2014)
Biotechnol. Prog.
, vol.30
, pp. 985-991
-
-
García Sánchez, C.E.1
Torres Sáez, R.G.2
-
20
-
-
84995622089
-
Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis
-
Gonzalez, J.E., Long, C.P., Antoniewicz, M.R., Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis. Metab. Eng. 39 (2017), 9–18.
-
(2017)
Metab. Eng.
, vol.39
, pp. 9-18
-
-
Gonzalez, J.E.1
Long, C.P.2
Antoniewicz, M.R.3
-
21
-
-
33751544539
-
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
-
Herring, C.D., Raghunathan, A., Honisch, C., Patel, T., Applebee, M.K., Joyce, A.R., Albert, T.J., Blattner, F.R., van den Boom, D., Cantor, C.R., Palsson, B.O., Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat. Genet. 38 (2006), 1406–1412.
-
(2006)
Nat. Genet.
, vol.38
, pp. 1406-1412
-
-
Herring, C.D.1
Raghunathan, A.2
Honisch, C.3
Patel, T.4
Applebee, M.K.5
Joyce, A.R.6
Albert, T.J.7
Blattner, F.R.8
van den Boom, D.9
Cantor, C.R.10
Palsson, B.O.11
-
22
-
-
77957929240
-
Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress
-
Horinouchi, T., Tamaoka, K., Furusawa, C., Ono, N., Suzuki, S., Hirasawa, T., Yomo, T., Shimizu, H., Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress. BMC Genom., 11, 2010, 579.
-
(2010)
BMC Genom.
, vol.11
, pp. 579
-
-
Horinouchi, T.1
Tamaoka, K.2
Furusawa, C.3
Ono, N.4
Suzuki, S.5
Hirasawa, T.6
Yomo, T.7
Shimizu, H.8
-
23
-
-
20044377232
-
Genome coverage, literally speaking
-
Janssen, P., Goldovsky, L., Kunin, V., Darzentas, N., Ouzounis, C. a., Genome coverage, literally speaking. EMBO Rep. 6 (2005), 397–399.
-
(2005)
EMBO Rep.
, vol.6
, pp. 397-399
-
-
Janssen, P.1
Goldovsky, L.2
Kunin, V.3
Darzentas, N.4
Ouzounis, C.A.5
-
24
-
-
0027251266
-
The Escherichia coli K-12 “wild types” W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels
-
Jensen, K.F., The Escherichia coli K-12 “wild types” W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J. Bacteriol. 175 (1993), 3401–3407.
-
(1993)
J. Bacteriol.
, vol.175
, pp. 3401-3407
-
-
Jensen, K.F.1
-
25
-
-
84904317199
-
A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data
-
Khodayari, A., Zomorrodi, A.R., Liao, J.C., Maranas, C.D., A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data. Metab. Eng. 25 (2014), 50–62.
-
(2014)
Metab. Eng.
, vol.25
, pp. 50-62
-
-
Khodayari, A.1
Zomorrodi, A.R.2
Liao, J.C.3
Maranas, C.D.4
-
26
-
-
84917705874
-
Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium
-
LaCroix, R.A., Sandberg, T.E., O'Brien, E.J., Utrilla, J., Ebrahim, A., Guzman, G.I., Szubin, R., Palsson, B.O., Feist, A.M., Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Appl. Environ. Microbiol. 81 (2015), 17–30.
-
(2015)
Appl. Environ. Microbiol.
, vol.81
, pp. 17-30
-
-
LaCroix, R.A.1
Sandberg, T.E.2
O'Brien, E.J.3
Utrilla, J.4
Ebrahim, A.5
Guzman, G.I.6
Szubin, R.7
Palsson, B.O.8
Feist, A.M.9
-
27
-
-
77954265373
-
Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon source, L-l,2-propanediol
-
Lee, D.H., Palsson, B.O., Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon source, L-l,2-propanediol. Appl. Environ. Microbiol. 76 (2010), 4158–4168.
-
(2010)
Appl. Environ. Microbiol.
, vol.76
, pp. 4158-4168
-
-
Lee, D.H.1
Palsson, B.O.2
-
28
-
-
85030239584
-
-
Vibrio natriegens, a new genomic powerhouse. bioRxiv.
-
Lee, H.H., Ostrov, N., Wong, B.G., Gold, M.A., Khalil, A.S., Church, G.M., 2016. Vibrio natriegens, a new genomic powerhouse. bioRxiv.
-
(2016)
-
-
Lee, H.H.1
Ostrov, N.2
Wong, B.G.3
Gold, M.A.4
Khalil, A.S.5
Church, G.M.6
-
29
-
-
84884386184
-
COMPLETE-MFA: complementary parallel labeling experiments technique for metabolic flux analysis
-
Leighty, R.W., Antoniewicz, M.R., COMPLETE-MFA: complementary parallel labeling experiments technique for metabolic flux analysis. Metab. Eng. 20 (2013), 49–55.
-
(2013)
Metab. Eng.
, vol.20
, pp. 49-55
-
-
Leighty, R.W.1
Antoniewicz, M.R.2
-
30
-
-
84865597532
-
Parallel labeling experiments with [U-13C]glucose validate E. coli metabolic network model for 13C metabolic flux analysis
-
Leighty, R.W., Antoniewicz, M.R., Parallel labeling experiments with [U-13C]glucose validate E. coli metabolic network model for 13C metabolic flux analysis. Metab. Eng. 14 (2012), 533–541.
-
(2012)
Metab. Eng.
, vol.14
, pp. 533-541
-
-
Leighty, R.W.1
Antoniewicz, M.R.2
-
31
-
-
84907272917
-
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale
-
Liu, J.K., O Brien, E.J., Lerman, J. a., Zengler, K., Palsson, B.O., Feist, A.M., Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst. Biol., 8, 2014, 110.
-
(2014)
BMC Syst. Biol.
, vol.8
, pp. 110
-
-
Liu, J.K.1
O Brien, E.J.2
Lerman, J.A.3
Zengler, K.4
Palsson, B.O.5
Feist, A.M.6
-
32
-
-
84897083269
-
Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook
-
Long, C.P., Antoniewicz, M.R., Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook. Curr. Opin. Biotechnol. 28 (2014), 127–133.
-
(2014)
Curr. Opin. Biotechnol.
, vol.28
, pp. 127-133
-
-
Long, C.P.1
Antoniewicz, M.R.2
-
33
-
-
84907889105
-
Quantifying biomass composition by gas chromatography/mass spectrometry
-
Long, C.P., Antoniewicz, M.R., Quantifying biomass composition by gas chromatography/mass spectrometry. Anal. Chem. 86 (2014), 9423–9427.
-
(2014)
Anal. Chem.
, vol.86
, pp. 9423-9427
-
-
Long, C.P.1
Antoniewicz, M.R.2
-
34
-
-
84978249216
-
13C metabolic flux analysis of microbial and mammalian systems is enhanced with GC–MS measurements of glycogen and RNA labeling
-
Long, C.P., Au, J., Gonzalez, J.E., Antoniewicz, M.R., 13C metabolic flux analysis of microbial and mammalian systems is enhanced with GC–MS measurements of glycogen and RNA labeling. Metab. Eng. 38 (2016), 65–72.
-
(2016)
Metab. Eng.
, vol.38
, pp. 65-72
-
-
Long, C.P.1
Au, J.2
Gonzalez, J.E.3
Antoniewicz, M.R.4
-
35
-
-
85010992345
-
Enzyme I facilitates reverse flux from pyruvate to phosphoenolpyruvate in Escherichia coli
-
Long, C.P., Au, J., Sandoval, N.R., Gebreselassie, N.A., Antoniewicz, M.R., Enzyme I facilitates reverse flux from pyruvate to phosphoenolpyruvate in Escherichia coli. Nat. Commun., 8, 2017, 14316.
-
(2017)
Nat. Commun.
, vol.8
, pp. 14316
-
-
Long, C.P.1
Au, J.2
Sandoval, N.R.3
Gebreselassie, N.A.4
Antoniewicz, M.R.5
-
36
-
-
84973335042
-
Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism
-
Long, C.P., Gonzalez, J.E., Sandoval, N.R., Antoniewicz, M.R., Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism. Metab. Eng. 37 (2016), 102–113.
-
(2016)
Metab. Eng.
, vol.37
, pp. 102-113
-
-
Long, C.P.1
Gonzalez, J.E.2
Sandoval, N.R.3
Antoniewicz, M.R.4
-
37
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
Mahadevan, R., Schilling, C.H., The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5 (2003), 264–276.
-
(2003)
Metab. Eng.
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
38
-
-
84968754630
-
Measuring the composition and stable-isotope labeling of algal biomass carbohydrates via gas chromatography/mass spectrometry
-
McConnell, B.O., Antoniewicz, M.R., Measuring the composition and stable-isotope labeling of algal biomass carbohydrates via gas chromatography/mass spectrometry. Anal. Chem. 88 (2016), 4624–4628.
-
(2016)
Anal. Chem.
, vol.88
, pp. 4624-4628
-
-
McConnell, B.O.1
Antoniewicz, M.R.2
-
39
-
-
84991740197
-
Multi-omics quantification of species variation of escherichia coli links molecular features with strain phenotypes
-
Monk, J.M., Koza, A., Campodonico, M.A., Machado, D., Seoane, J.M., Palsson, B.O., Herrgård, M.J., Feist, A.M., Multi-omics quantification of species variation of escherichia coli links molecular features with strain phenotypes. Cell Syst., 2016, 238–251.
-
(2016)
Cell Syst.
, pp. 238-251
-
-
Monk, J.M.1
Koza, A.2
Campodonico, M.A.3
Machado, D.4
Seoane, J.M.5
Palsson, B.O.6
Herrgård, M.J.7
Feist, A.M.8
-
40
-
-
85008192136
-
Increased production of L-serine in Escherichia coli through adaptive laboratory evolution
-
Mundhada, H., Seoane, J.M., Schneider, K., Koza, A., Christensen, H.B., Klein, T., Phaneuf, P.V., Herrgard, M., Feist, A.M., Nielsen, A.T., Increased production of L-serine in Escherichia coli through adaptive laboratory evolution. Metab. Eng. 39 (2017), 141–150.
-
(2017)
Metab. Eng.
, vol.39
, pp. 141-150
-
-
Mundhada, H.1
Seoane, J.M.2
Schneider, K.3
Koza, A.4
Christensen, H.B.5
Klein, T.6
Phaneuf, P.V.7
Herrgard, M.8
Feist, A.M.9
Nielsen, A.T.10
-
41
-
-
13644259156
-
The energetic conversion competence of Escherichia coli during aerobic respiration studied by31P NMR using a circulating fermentation system
-
Noguchi, Y., Nakai, Y., Shimba, N., Toyosaki, H., Kawahara, Y., Sugimoto, S., Suzuki, E.I., The energetic conversion competence of Escherichia coli during aerobic respiration studied by31P NMR using a circulating fermentation system. J. Biochem. 136 (2004), 509–515, 10.1093/jb/mvh147.
-
(2004)
J. Biochem.
, vol.136
, pp. 509-515
-
-
Noguchi, Y.1
Nakai, Y.2
Shimba, N.3
Toyosaki, H.4
Kawahara, Y.5
Sugimoto, S.6
Suzuki, E.I.7
-
42
-
-
84885367114
-
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
-
O'Brien, E.J., Lerman, J.A., Chang, R.L., Hyduke, D.R., Palsson, B.Ø., Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol. Syst. Biol., 9, 2013, 693.
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 693
-
-
O'Brien, E.J.1
Lerman, J.A.2
Chang, R.L.3
Hyduke, D.R.4
Palsson, B.Ø.5
-
43
-
-
38349115629
-
Altered acetate metabolism and biomass production in several Escherichia coli mutants lacking rpoS-dependent metabolic pathway genes
-
Rahman, M., Shimizu, K., Altered acetate metabolism and biomass production in several Escherichia coli mutants lacking rpoS-dependent metabolic pathway genes. Mol. Biosyst. 4 (2008), 160–169.
-
(2008)
Mol. Biosyst.
, vol.4
, pp. 160-169
-
-
Rahman, M.1
Shimizu, K.2
-
44
-
-
84865711025
-
Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli
-
Reyes, L.H., Almario, M.P., Winkler, J., Orozco, M.M., Kao, K.C., Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli. Metab. Eng. 14 (2012), 579–590.
-
(2012)
Metab. Eng.
, vol.14
, pp. 579-590
-
-
Reyes, L.H.1
Almario, M.P.2
Winkler, J.3
Orozco, M.M.4
Kao, K.C.5
-
45
-
-
85020503243
-
Laboratory evolution to alternating substrate environments yields distinct phenotypic and genetic adaptive strategies
-
Sandberg, T.E., Lloyd, C.J., Palsson, B.O., Feist, A.M., Laboratory evolution to alternating substrate environments yields distinct phenotypic and genetic adaptive strategies. Appl. Environ. Microbiol., 2017, 00410–00417.
-
(2017)
Appl. Environ. Microbiol.
, pp. 00410-00417
-
-
Sandberg, T.E.1
Lloyd, C.J.2
Palsson, B.O.3
Feist, A.M.4
-
46
-
-
84962602150
-
Evolution of E. coli on [U-13C]glucose reveals a negligible isotopic influence on metabolism and physiology
-
Sandberg, T.E., Long, C.P., Gonzalez, J.E., Feist, A.M., Antoniewicz, M.R., Palsson, B.O., Evolution of E. coli on [U-13C]glucose reveals a negligible isotopic influence on metabolism and physiology. PLoS One, 11, 2016, e0151130.
-
(2016)
PLoS One
, vol.11
, pp. e0151130
-
-
Sandberg, T.E.1
Long, C.P.2
Gonzalez, J.E.3
Feist, A.M.4
Antoniewicz, M.R.5
Palsson, B.O.6
-
47
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
-
Schellenberger, J., Que, R., Fleming, R.M.T., Thiele, I., Orth, J.D., Feist, A.M., Zielinski, D.C., Bordbar, A., Lewis, N.E., Rahmanian, S., Kang, J., Hyduke, D.R., Palsson, B.Ø., Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 6 (2011), 1290–1307.
-
(2011)
Nat. Protoc.
, vol.6
, pp. 1290-1307
-
-
Schellenberger, J.1
Que, R.2
Fleming, R.M.T.3
Thiele, I.4
Orth, J.D.5
Feist, A.M.6
Zielinski, D.C.7
Bordbar, A.8
Lewis, N.E.9
Rahmanian, S.10
Kang, J.11
Hyduke, D.R.12
Palsson, B.Ø.13
-
48
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
Schuetz, R., Kuepfer, L., Sauer, U., Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol., 3, 2007, 119, 10.1038/msb4100162.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
49
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
Segre, D., Vitkup, D., Church, G.M., Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99 (2002), 15112–15117.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 15112-15117
-
-
Segre, D.1
Vitkup, D.2
Church, G.M.3
-
50
-
-
60549117294
-
Metabolic flux analysis of shewanella spp. Reveals evolutionary robustness in central carbon metabolism
-
Tang, Y.J., Martin, H.G., Dehal, P.S., Deutschbauer, A., Llora, X., Meadows, A., Arkin, A., Keasling, J.D., Metabolic flux analysis of shewanella spp. Reveals evolutionary robustness in central carbon metabolism. Biotechnol. Bioeng. 102 (2009), 1161–1169, 10.1002/bit.22129.
-
(2009)
Biotechnol. Bioeng.
, vol.102
, pp. 1161-1169
-
-
Tang, Y.J.1
Martin, H.G.2
Dehal, P.S.3
Deutschbauer, A.4
Llora, X.5
Meadows, A.6
Arkin, A.7
Keasling, J.D.8
-
51
-
-
78149245282
-
Genome-derived minimal metabolic models for Escherichia coli MG1655 with estimated in vivo respiratory ATP stoichiometry
-
Taymaz-Nikerel, H., Borujeni, A.E., Verheijen, P.J.T., Heijnen, J.J., van Gulik, W.M., Genome-derived minimal metabolic models for Escherichia coli MG1655 with estimated in vivo respiratory ATP stoichiometry. Biotechnol. Bioeng. 107 (2010), 369–381, 10.1002/bit.22802.
-
(2010)
Biotechnol. Bioeng.
, vol.107
, pp. 369-381
-
-
Taymaz-Nikerel, H.1
Borujeni, A.E.2
Verheijen, P.J.T.3
Heijnen, J.J.4
van Gulik, W.M.5
-
52
-
-
84856258903
-
The molecular diversity of adaptive convergence
-
Tenaillon, O., Rodriguez-Verdugo, A., Gaut, R.L., McDonald, P., Bennett, A.F., Long, A.D., Gaut, B.S., The molecular diversity of adaptive convergence. Science 80:335 (2012), 457–461.
-
(2012)
Science
, vol.80
, Issue.335
, pp. 457-461
-
-
Tenaillon, O.1
Rodriguez-Verdugo, A.2
Gaut, R.L.3
McDonald, P.4
Bennett, A.F.5
Long, A.D.6
Gaut, B.S.7
-
53
-
-
84967180536
-
Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution
-
Utrilla, J., O'Brien, E.J., Chen, K., McCloskey, D., Cheung, J., Wang, H., Armenta-Medina, D., Feist, A.M., Palsson, B.O., Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution. Cell Syst. 2 (2016), 260–271.
-
(2016)
Cell Syst.
, vol.2
, pp. 260-271
-
-
Utrilla, J.1
O'Brien, E.J.2
Chen, K.3
McCloskey, D.4
Cheung, J.5
Wang, H.6
Armenta-Medina, D.7
Feist, A.M.8
Palsson, B.O.9
-
54
-
-
79953789350
-
Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3)
-
Waegeman, H., Beauprez, J., Moens, H., Maertens, J., De Mey, M., Foulquié-Moreno, M.R., Heijnen, J.J., Charlier, D., Soetaert, W., Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3). BMC Microbiol., 2011, 11.
-
(2011)
BMC Microbiol.
, pp. 11
-
-
Waegeman, H.1
Beauprez, J.2
Moens, H.3
Maertens, J.4
De Mey, M.5
Foulquié-Moreno, M.R.6
Heijnen, J.J.7
Charlier, D.8
Soetaert, W.9
-
55
-
-
84856224805
-
Effect of iclR and arcA deletions on physiology and metabolic fluxes in Escherichia coli BL21 (DE3)
-
Waegeman, H., Maertens, J., Beauprez, J., De Mey, M., Soetaert, W., Effect of iclR and arcA deletions on physiology and metabolic fluxes in Escherichia coli BL21 (DE3). Biotechnol. Lett. 34 (2012), 329–337.
-
(2012)
Biotechnol. Lett.
, vol.34
, pp. 329-337
-
-
Waegeman, H.1
Maertens, J.2
Beauprez, J.3
De Mey, M.4
Soetaert, W.5
-
56
-
-
84964774521
-
Rapid prediction of bacterial heterotrophic fluxomics using machine learning and constraint programming
-
Wu, S.G., Wang, Y., Jiang, W., Oyetunde, T., Yao, R., Zhang, X., Shimizu, K., Tang, Y.J., Bao, F.S., Rapid prediction of bacterial heterotrophic fluxomics using machine learning and constraint programming. PLoS Comput. Biol., 2016, 12, 10.1371/journal.pcbi.1004838.
-
(2016)
PLoS Comput. Biol.
, pp. 12
-
-
Wu, S.G.1
Wang, Y.2
Jiang, W.3
Oyetunde, T.4
Yao, R.5
Zhang, X.6
Shimizu, K.7
Tang, Y.J.8
Bao, F.S.9
-
57
-
-
51049091904
-
Quantifying reductive carboxylation flux of glutamine to lipid in a brown adipocyte cell line
-
Yoo, H., Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., Quantifying reductive carboxylation flux of glutamine to lipid in a brown adipocyte cell line. J. Biol. Chem. 283:30 (2008), 20621–20627.
-
(2008)
J. Biol. Chem.
, vol.283
, Issue.30
, pp. 20621-20627
-
-
Yoo, H.1
Antoniewicz, M.R.2
Kelleher, J.K.3
Stephanopoulos, G.4
|