-
1
-
-
85015320169
-
Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals
-
1 Industrialization of Biology: A Roadmap to Accelerate the Advanced Manufacturing of Chemicals. The National Academies Press; 2015.
-
(2015)
The National Academies Press
-
-
-
2
-
-
0142027026
-
Metabolic engineering for the microbial production of 1,3-propanediol
-
2 Nakamura, C.E., Whited, G.M., Metabolic engineering for the microbial production of 1,3-propanediol. Curr Opin Biotechnol 14 (2003), 454–459.
-
(2003)
Curr Opin Biotechnol
, vol.14
, pp. 454-459
-
-
Nakamura, C.E.1
Whited, G.M.2
-
3
-
-
84901340681
-
Metabolic evolution of two reducing equivalent-conserving pathways for high-yield succinate production in Escherichia coli
-
3 Zhu, X., Tan, Z., Xu, H., Chen, J., Tang, J., Zhang, X., Metabolic evolution of two reducing equivalent-conserving pathways for high-yield succinate production in Escherichia coli. Metab Eng 24 (2014), 87–96.
-
(2014)
Metab Eng
, vol.24
, pp. 87-96
-
-
Zhu, X.1
Tan, Z.2
Xu, H.3
Chen, J.4
Tang, J.5
Zhang, X.6
-
4
-
-
79959374585
-
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
-
4 Yim, H., Haselbeck, R., Niu, W., Pujol-Baxley, C., Burgard, A., Boldt, J., Khandurina, J., Trawick, J.D., Osterhout, R.E., Stephen, R., et al. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 7 (2011), 445–452.
-
(2011)
Nat Chem Biol
, vol.7
, pp. 445-452
-
-
Yim, H.1
Haselbeck, R.2
Niu, W.3
Pujol-Baxley, C.4
Burgard, A.5
Boldt, J.6
Khandurina, J.7
Trawick, J.D.8
Osterhout, R.E.9
Stephen, R.10
-
5
-
-
84887622083
-
From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals
-
5 Van Dien, S., From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals. Curr Opin Biotechnol 24 (2013), 1061–1068.
-
(2013)
Curr Opin Biotechnol
, vol.24
, pp. 1061-1068
-
-
Van Dien, S.1
-
6
-
-
84943604629
-
Systems strategies for developing industrial microbial strains
-
6 Lee, S.Y., Kim, H.U., Systems strategies for developing industrial microbial strains. Nat Biotechnol 33 (2015), 1061–1072.
-
(2015)
Nat Biotechnol
, vol.33
, pp. 1061-1072
-
-
Lee, S.Y.1
Kim, H.U.2
-
7
-
-
84970035625
-
Synthetic and systems biology for microbial production of commodity chemicals
-
7 Chubukov, V., Mukhopadhyay, A., Petzold, C., Keasling, J., Martin, H.G., Synthetic and systems biology for microbial production of commodity chemicals. npj Syst Biol Appl 16009 (2016), 1–11.
-
(2016)
npj Syst Biol Appl
, vol.16009
, pp. 1-11
-
-
Chubukov, V.1
Mukhopadhyay, A.2
Petzold, C.3
Keasling, J.4
Martin, H.G.5
-
8
-
-
84865070369
-
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
-
8 Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., Charpentier, E., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337 (2012), 816–821.
-
(2012)
Science
, vol.337
, pp. 816-821
-
-
Jinek, M.1
Chylinski, K.2
Fonfara, I.3
Hauer, M.4
Doudna, J.A.5
Charpentier, E.6
-
9
-
-
84873729095
-
Multiplex genome engineering using CRISPR/Cas systems
-
9 Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339 (2013), 819–823.
-
(2013)
Science
, vol.339
, pp. 819-823
-
-
Cong, L.1
Ran, F.A.2
Cox, D.3
Lin, S.4
Barretto, R.5
Habib, N.6
Hsu, P.D.7
Wu, X.8
Jiang, W.9
Marraffini, L.A.10
-
10
-
-
68949161807
-
Programming cells by multiplex genome engineering and accelerated evolution
-
10 Wang, H.H., Isaacs, F.J., Carr, P.A., Sun, Z.Z., Xu, G., Forest, C.R., Church, G.M., Programming cells by multiplex genome engineering and accelerated evolution. Nature 460 (2009), 894–898.
-
(2009)
Nature
, vol.460
, pp. 894-898
-
-
Wang, H.H.1
Isaacs, F.J.2
Carr, P.A.3
Sun, Z.Z.4
Xu, G.5
Forest, C.R.6
Church, G.M.7
-
11
-
-
84952682854
-
CRISPR/Cas9 advances engineering of microbial cell factories
-
11 Jakočiūnas, T., Jensen, M.K., Keasling, J.D., CRISPR/Cas9 advances engineering of microbial cell factories. Metab Eng 34 (2016), 44–59.
-
(2016)
Metab Eng
, vol.34
, pp. 44-59
-
-
Jakočiūnas, T.1
Jensen, M.K.2
Keasling, J.D.3
-
12
-
-
84949524121
-
Seven gene deletions in seven days: fast generation of Escherichia coli strains tolerant to acetate and osmotic stress
-
12 Jensen, S.I., Lennen, R.M., Herrgård, M.J., Nielsen, A.T., Seven gene deletions in seven days: fast generation of Escherichia coli strains tolerant to acetate and osmotic stress. Sci Rep, 5, 2015, 17874.
-
(2015)
Sci Rep
, vol.5
, pp. 17874
-
-
Jensen, S.I.1
Lennen, R.M.2
Herrgård, M.J.3
Nielsen, A.T.4
-
13
-
-
84951061481
-
Pseudo-transition analysis identifies the key regulators of dynamic metabolic adaptations from steady-state data
-
Comprehensive multi-omic (transcriptomics, proteomics, metabolomics and fluxomics) characterization of E. coli wild-type strains and examples on how this can be used to understand engineered strains.
-
13• Gerosa, L., Haverkorn Van Rijsewijk, B.R.B., Christodoulou, D., Kochanowski, K., Schmidt, T.S.B., Noor, E., Sauer, U., Pseudo-transition analysis identifies the key regulators of dynamic metabolic adaptations from steady-state data. Cell Syst 1 (2015), 270–282 Comprehensive multi-omic (transcriptomics, proteomics, metabolomics and fluxomics) characterization of E. coli wild-type strains and examples on how this can be used to understand engineered strains.
-
(2015)
Cell Syst
, vol.1
, pp. 270-282
-
-
Gerosa, L.1
Haverkorn Van Rijsewijk, B.R.B.2
Christodoulou, D.3
Kochanowski, K.4
Schmidt, T.S.B.5
Noor, E.6
Sauer, U.7
-
14
-
-
84990961064
-
Functional metabolomics describes the yeast biosynthetic regulome
-
14 Mülleder, M., Calvani, E., Alam, M.T., Wang, R.K., Eckerstorfer, F., Zelezniak, A., Ralser, M., Functional metabolomics describes the yeast biosynthetic regulome. Cell 167 (2016), 553–565.
-
(2016)
Cell
, vol.167
, pp. 553-565
-
-
Mülleder, M.1
Calvani, E.2
Alam, M.T.3
Wang, R.K.4
Eckerstorfer, F.5
Zelezniak, A.6
Ralser, M.7
-
15
-
-
82255186724
-
Predicting phenotypic variation in yeast from individual genome sequences
-
15 Jelier, R., Semple, J.I., Garcia-Verdugo, R., Lehner, B., Predicting phenotypic variation in yeast from individual genome sequences. Nat Genet 43 (2011), 1270–1274.
-
(2011)
Nat Genet
, vol.43
, pp. 1270-1274
-
-
Jelier, R.1
Semple, J.I.2
Garcia-Verdugo, R.3
Lehner, B.4
-
16
-
-
84971661491
-
Analysis of genetic variation and potential applications in genome-scale metabolic modeling
-
16 Cardoso, J.G.R., Andersen, M.R., Herrgård, M.J., Sonnenschein, N., Analysis of genetic variation and potential applications in genome-scale metabolic modeling. Front Bioeng Biotechnol, 3, 2015, 13.
-
(2015)
Front Bioeng Biotechnol
, vol.3
, pp. 13
-
-
Cardoso, J.G.R.1
Andersen, M.R.2
Herrgård, M.J.3
Sonnenschein, N.4
-
17
-
-
84905668376
-
Improving fatty acids production by engineering dynamic pathway regulation and metabolic control
-
17 Xu, P., Li, L., Zhang, F., Stephanopoulos, G., Koffas, M., Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc Natl Acad Sci U S A 111 (2014), 11299–11304.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 11299-11304
-
-
Xu, P.1
Li, L.2
Zhang, F.3
Stephanopoulos, G.4
Koffas, M.5
-
18
-
-
84988353386
-
Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast
-
18 Skjoedt, M., Snoek, T., Kildegaard, K., Arovska, D., Eichenberger, M., Goedecke, T., Rajkumar, A., Zhang, J., Kristensen, M., Lehka, B., et al. Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast. Nat Chem Biol 12 (2016), 951–958.
-
(2016)
Nat Chem Biol
, vol.12
, pp. 951-958
-
-
Skjoedt, M.1
Snoek, T.2
Kildegaard, K.3
Arovska, D.4
Eichenberger, M.5
Goedecke, T.6
Rajkumar, A.7
Zhang, J.8
Kristensen, M.9
Lehka, B.10
-
19
-
-
34249934691
-
Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation
-
19 Park, J.H., Lee, K.H., Kim, T.Y., Lee, S.Y., Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci U S A 104 (2007), 7797–7802.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 7797-7802
-
-
Park, J.H.1
Lee, K.H.2
Kim, T.Y.3
Lee, S.Y.4
-
20
-
-
84969752776
-
Characterizing strain variation in engineered E. coli using a multi-omics-based workflow
-
Description of a systematic workflow for the analysis of targeted proteomics and metabolomics data on production strains incorporating the use of GEMs.
-
20•• Brunk, E., George, K.W., Alonso-Gutierrez, J., Thompson, M., Baidoo, E., Wang, G., Petzold, C.J., McCloskey, D., Monk, J., Yang, L., et al. Characterizing strain variation in engineered E. coli using a multi-omics-based workflow. Cell Syst 2 (2016), 335–346 Description of a systematic workflow for the analysis of targeted proteomics and metabolomics data on production strains incorporating the use of GEMs.
-
(2016)
Cell Syst
, vol.2
, pp. 335-346
-
-
Brunk, E.1
George, K.W.2
Alonso-Gutierrez, J.3
Thompson, M.4
Baidoo, E.5
Wang, G.6
Petzold, C.J.7
McCloskey, D.8
Monk, J.9
Yang, L.10
-
21
-
-
84960936931
-
Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway
-
21 Kildegaard, K.R., Jensen, N.B., Schneider, K., Czarnotta, E., Özdemir, E., Klein, T., Maury, J., Ebert, B.E., Christensen, H.B., Chen, Y., et al. Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway. Microb Cell Fact, 15, 2016, 53.
-
(2016)
Microb Cell Fact
, vol.15
, pp. 53
-
-
Kildegaard, K.R.1
Jensen, N.B.2
Schneider, K.3
Czarnotta, E.4
Özdemir, E.5
Klein, T.6
Maury, J.7
Ebert, B.E.8
Christensen, H.B.9
Chen, Y.10
-
22
-
-
84872409095
-
Increased lysine production by flux coupling of the tricarboxylic acid cycle and the lysine biosynthetic pathway—metabolic engineering of the availability of succinyl-CoA in Corynebacterium glutamicum
-
22 Kind, S., Becker, J., Wittmann, C., Increased lysine production by flux coupling of the tricarboxylic acid cycle and the lysine biosynthetic pathway—metabolic engineering of the availability of succinyl-CoA in Corynebacterium glutamicum. Metab Eng 15 (2013), 184–195.
-
(2013)
Metab Eng
, vol.15
, pp. 184-195
-
-
Kind, S.1
Becker, J.2
Wittmann, C.3
-
23
-
-
84991740197
-
Multi-omics quantification of species variation of Escherichia coli links molecular features with strain phenotypes
-
Genomic, transcriptomic, physiological and GEM-based characterization of seven different E. coli wild type strains that are commonly used in metabolic engineering.
-
23•• 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 3 (2016), 1–14 Genomic, transcriptomic, physiological and GEM-based characterization of seven different E. coli wild type strains that are commonly used in metabolic engineering.
-
(2016)
Cell Syst
, vol.3
, pp. 1-14
-
-
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
-
24
-
-
84952802569
-
A quantitative system-scale characterization of the metabolism of Clostridium acetobutylicum
-
24 Yoo, M., Bestel-Corre, G., Croux, C., Riviere, A., Meynial-Salles, I., Soucaille, P., A quantitative system-scale characterization of the metabolism of Clostridium acetobutylicum. MBio 6 (2015), e01808–e01815.
-
(2015)
MBio
, vol.6
, pp. e01808-e01815
-
-
Yoo, M.1
Bestel-Corre, G.2
Croux, C.3
Riviere, A.4
Meynial-Salles, I.5
Soucaille, P.6
-
25
-
-
84896932547
-
Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis
-
25 Kozak, B.U., van Rossum, H.M., Benjamin, K.R., Wu, L., Daran, J.M.G., Pronk, J.T., Van Maris, A.J.A., Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis. Metab Eng 21 (2014), 46–59.
-
(2014)
Metab Eng
, vol.21
, pp. 46-59
-
-
Kozak, B.U.1
van Rossum, H.M.2
Benjamin, K.R.3
Wu, L.4
Daran, J.M.G.5
Pronk, J.T.6
Van Maris, A.J.A.7
-
26
-
-
84907483760
-
Altered sterol composition renders yeast thermotolerant
-
Genomic, transcriptomic, and physiological analysis of evolved thermotolerant S. cerevisiae strains revealed a thermotolerance mechanism of altered membrane sterol composition.
-
26•• Caspeta, L., Chen, Y., Ghiaci, P., Feizi, A., Buskov, S., Hallström, B.M., Petranovic, D., Nielsen, J., Altered sterol composition renders yeast thermotolerant. Science 944 (2014), 75–78 Genomic, transcriptomic, and physiological analysis of evolved thermotolerant S. cerevisiae strains revealed a thermotolerance mechanism of altered membrane sterol composition.
-
(2014)
Science
, vol.944
, pp. 75-78
-
-
Caspeta, L.1
Chen, Y.2
Ghiaci, P.3
Feizi, A.4
Buskov, S.5
Hallström, B.M.6
Petranovic, D.7
Nielsen, J.8
-
27
-
-
84907862283
-
Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance
-
Elucidation of the mechanism of 3-hydroxypropionic acid tolerance in evolved S. cerevisiae isolates through transcriptomic analysis and genetic reconstructions.
-
27•• Kildegaard, K.R., Hallström, B.M., Blicher, T.H., Sonnenschein, N., Jensen, N.B., Sherstyk, S., Harrison, S.J., Maury, J., Herrgård, M.J., Juncker, A.S., et al. Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance. Metab Eng 26 (2014), 57–66 Elucidation of the mechanism of 3-hydroxypropionic acid tolerance in evolved S. cerevisiae isolates through transcriptomic analysis and genetic reconstructions.
-
(2014)
Metab Eng
, vol.26
, pp. 57-66
-
-
Kildegaard, K.R.1
Hallström, B.M.2
Blicher, T.H.3
Sonnenschein, N.4
Jensen, N.B.5
Sherstyk, S.6
Harrison, S.J.7
Maury, J.8
Herrgård, M.J.9
Juncker, A.S.10
-
28
-
-
84907020111
-
Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains
-
28 Lennen, R.M., Herrgård, M.J., Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains. Appl Environ Microbiol 80 (2014), 6223–6242.
-
(2014)
Appl Environ Microbiol
, vol.80
, pp. 6223-6242
-
-
Lennen, R.M.1
Herrgård, M.J.2
-
29
-
-
85015281028
-
Deep annotation of protein function across diverse bacteria from mutant phenotypes
-
29 Price, M.N., Wetmore, K.M., Waters, R.J., Callaghan, M., Ray, J., Kuehl, J.V., Melnyk, R.A., Lamson, J.S., Suh, Y., Esquivel, Z., et al. Deep annotation of protein function across diverse bacteria from mutant phenotypes. bioRxiv, 2016, 10.1101/072470.
-
(2016)
bioRxiv
-
-
Price, M.N.1
Wetmore, K.M.2
Waters, R.J.3
Callaghan, M.4
Ray, J.5
Kuehl, J.V.6
Melnyk, R.A.7
Lamson, J.S.8
Suh, Y.9
Esquivel, Z.10
-
30
-
-
84969916078
-
A comprehensive, CRISPR-based functional analysis of essential genes in bacteria
-
30 Peters, J.M., Colavin, A., Shi, H., Czarny, T.L., Larson, M.H., Wong, S., Hawkins, J.S., Lu, C.H.S., Koo, B.M., Marta, E., et al. A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell 165 (2016), 1493–1506.
-
(2016)
Cell
, vol.165
, pp. 1493-1506
-
-
Peters, J.M.1
Colavin, A.2
Shi, H.3
Czarny, T.L.4
Larson, M.H.5
Wong, S.6
Hawkins, J.S.7
Lu, C.H.S.8
Koo, B.M.9
Marta, E.10
-
31
-
-
84989852376
-
Rewriting yeast central carbon metabolism for industrial isoprenoid production
-
GEMs are effectively used for determining heterologous pathways leading to improved farnesene production.
-
31•• Meadows, A.L., Hawkins, K.M., Tsegaye, Y., Antipov, E., Kim, Y., Raetz, L., Dahl, R.H., Tai, A., Mahatdejkul-Meadows, T., Xu, L., et al. Rewriting yeast central carbon metabolism for industrial isoprenoid production. Nature 537 (2016), 694–697 GEMs are effectively used for determining heterologous pathways leading to improved farnesene production.
-
(2016)
Nature
, vol.537
, pp. 694-697
-
-
Meadows, A.L.1
Hawkins, K.M.2
Tsegaye, Y.3
Antipov, E.4
Kim, Y.5
Raetz, L.6
Dahl, R.H.7
Tai, A.8
Mahatdejkul-Meadows, T.9
Xu, L.10
-
32
-
-
85006511727
-
Engineering an NADPH/NADP+ redox biosensor in yeast
-
For the purpose of testing redox biosensor in vivo, the authors use a GEM of S. cerevisiae to predict single gene deletions that are likely to have an impact on the NAPH/NADP+ redox charge.
-
32• Zhang, J., Sonnenschein, N., Pihl, T.P.B., Pedersen, K.R., Jensen, M.K., Keasling, J.D., Engineering an NADPH/NADP+ redox biosensor in yeast. ACS Synth Biol 5 (2016), 1546–1556 For the purpose of testing redox biosensor in vivo, the authors use a GEM of S. cerevisiae to predict single gene deletions that are likely to have an impact on the NAPH/NADP+ redox charge.
-
(2016)
ACS Synth Biol
, vol.5
, pp. 1546-1556
-
-
Zhang, J.1
Sonnenschein, N.2
Pihl, T.P.B.3
Pedersen, K.R.4
Jensen, M.K.5
Keasling, J.D.6
-
33
-
-
84938074954
-
Co-evolution of strain design methods based on flux balance and elementary mode analysis
-
33 Machado, D., Herrgård, M., Co-evolution of strain design methods based on flux balance and elementary mode analysis. Metab Eng Commun 2 (2015), 85–92.
-
(2015)
Metab Eng Commun
, vol.2
, pp. 85-92
-
-
Machado, D.1
Herrgård, M.2
-
34
-
-
77950863401
-
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
-
34 Feist, A.M., Zielinski, D.C., Orth, J.D., Schellenberger, J., Herrgard Markus, J., Palsson, B.Ø., Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng 12 (2010), 173–186.
-
(2010)
Metab Eng
, vol.12
, pp. 173-186
-
-
Feist, A.M.1
Zielinski, D.C.2
Orth, J.D.3
Schellenberger, J.4
Herrgard Markus, J.5
Palsson, B.Ø.6
-
35
-
-
0242487787
-
Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
35 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 (2003), 647–657.
-
(2003)
Biotechnol Bioeng
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
36
-
-
30044437327
-
Evolutionary programming as a platform for in silico metabolic engineering
-
36 Patil, K.R., Rocha, I., Forster, J., Nielsen, J., Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinf, 6, 2005, 308.
-
(2005)
BMC Bioinf
, vol.6
, pp. 308
-
-
Patil, K.R.1
Rocha, I.2
Forster, J.3
Nielsen, J.4
-
37
-
-
77949495880
-
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
-
37 Tepper, N., Shlomi, T., Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 26 (2009), 536–543.
-
(2009)
Bioinformatics
, vol.26
, pp. 536-543
-
-
Tepper, N.1
Shlomi, T.2
-
38
-
-
84896731390
-
Enumeration of smallest intervention strategies in genome-scale metabolic networks
-
38 von Kamp, A., Klamt, S., Enumeration of smallest intervention strategies in genome-scale metabolic networks. PLoS Comput Biol, 10, 2014, e1003378.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003378
-
-
von Kamp, A.1
Klamt, S.2
-
39
-
-
84974657997
-
Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli
-
Iterative design and implementation of a high yield E. coli production strain for itaconic acid using minimal cut sets.
-
39•• Harder, B.-J., Bettenbrock, K., Klamt, S., Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli. Metab Eng 38 (2016), 29–37 Iterative design and implementation of a high yield E. coli production strain for itaconic acid using minimal cut sets.
-
(2016)
Metab Eng
, vol.38
, pp. 29-37
-
-
Harder, B.-J.1
Bettenbrock, K.2
Klamt, S.3
-
40
-
-
84901306814
-
Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
-
Systematic evaluation of methods for integration of transcriptome data with GEMs revealing that all methods do not surpass parsimonious flux balance analysis in predicting metabolic fluxes quantitatively.
-
40• Machado, D., Herrgård, M., Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput Biol, 10, 2014, e1003580 Systematic evaluation of methods for integration of transcriptome data with GEMs revealing that all methods do not surpass parsimonious flux balance analysis in predicting metabolic fluxes quantitatively.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003580
-
-
Machado, D.1
Herrgård, M.2
-
41
-
-
77955141026
-
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models
-
41 Lewis, N.E., Hixson, K.K., Conrad, T.M., Lerman, J.A., Charusanti, P., Polpitiya, A.D., Adkins, J.N., Schramm, G., Purvine, S.O., Lopez-Ferrer, D., et al. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol, 6, 2010.
-
(2010)
Mol Syst Biol
, vol.6
-
-
Lewis, N.E.1
Hixson, K.K.2
Conrad, T.M.3
Lerman, J.A.4
Charusanti, P.5
Polpitiya, A.D.6
Adkins, J.N.7
Schramm, G.8
Purvine, S.O.9
Lopez-Ferrer, D.10
-
42
-
-
84860806071
-
A network perspective on metabolic inconsistency
-
42 Sonnenschein, N., Golib Dzib, J.F., Lesne, A., Eilebrecht, S., Boulkroun, S., Zennaro, M.-C., Benecke, A., Hütt, M.-T., A network perspective on metabolic inconsistency. BMC Syst Biol 6 (2012), 41–53.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 41-53
-
-
Sonnenschein, N.1
Golib Dzib, J.F.2
Lesne, A.3
Eilebrecht, S.4
Boulkroun, S.5
Zennaro, M.-C.6
Benecke, A.7
Hütt, M.-T.8
-
43
-
-
84930227327
-
Using genome-scale models to predict biological capabilities
-
43 O'Brien, E.J., Monk, J.M., Palsson, B.O., Using genome-scale models to predict biological capabilities. Cell 161 (2015), 971–987.
-
(2015)
Cell
, vol.161
, pp. 971-987
-
-
O'Brien, E.J.1
Monk, J.M.2
Palsson, B.O.3
-
44
-
-
84990177186
-
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli
-
44 Kim, M., Rai, N., Zorraquino, V., Tagkopoulos, I., Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. Nat Commun, 7, 2016, 13090.
-
(2016)
Nat Commun
, vol.7
, pp. 13090
-
-
Kim, M.1
Rai, N.2
Zorraquino, V.3
Tagkopoulos, I.4
-
45
-
-
84901321053
-
Contribution of network donnectivity in determining the relationship between gene expression and metabolite concentration changes
-
At the reaction level, metabolite concentration and gene expression changes do not correlate. The authors find that only after taking the network and kinetic context into account they are able to predict changes in metabolite levels from gene expression data.
-
45• Zelezniak, A., Sheridan, S., Patil, K.R., Contribution of network donnectivity in determining the relationship between gene expression and metabolite concentration changes. PLoS Comput Biol, 10, 2014, e1003572 At the reaction level, metabolite concentration and gene expression changes do not correlate. The authors find that only after taking the network and kinetic context into account they are able to predict changes in metabolite levels from gene expression data.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003572
-
-
Zelezniak, A.1
Sheridan, S.2
Patil, K.R.3
-
46
-
-
84943573409
-
13C labeling data
-
13C labeling experiments into GEMs allowing the estimation of peripheral metabolic fluxes and this going beyond traditional metabolic flux analysis.
-
13C labeling experiments into GEMs allowing the estimation of peripheral metabolic fluxes and this going beyond traditional metabolic flux analysis.
-
(2015)
PLoS Comput Biol
, vol.11
, pp. 1-34
-
-
Martín, H.G.1
Kumar, V.S.2
Weaver, D.3
Ghosh, A.4
Chubukov, V.5
Mukhopadhyay, A.6
Arkin, A.7
Keasling, J.D.8
-
47
-
-
84963796141
-
Modeling method for increased precision and scope of directly measurable fluxes at a genome-scale
-
47 McCloskey, D., Young, J.D., Xu, S., Palsson, B.O., Feist, A.M., Modeling method for increased precision and scope of directly measurable fluxes at a genome-scale. Anal Chem 88 (2016), 3844–3852.
-
(2016)
Anal Chem
, vol.88
, pp. 3844-3852
-
-
McCloskey, D.1
Young, J.D.2
Xu, S.3
Palsson, B.O.4
Feist, A.M.5
-
48
-
-
84917705874
-
Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium
-
Foundational study using a robotic ALE system to obtain high-resolution fitness trajectories of E. coli evolved on minimal glucose medium.
-
48• 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 Foundational study using a robotic ALE system to obtain high-resolution fitness trajectories of E. coli evolved on minimal glucose medium.
-
(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
-
49
-
-
84928889593
-
Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol
-
49 Cheng, K.-K., Lee, B.-S., Masuda, T., Ito, T., Ikeda, K., Hirayama, A., Deng, L., Dong, J., Shimizu, K., Soga, T., et al. Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat Commun, 5, 2014, 3233.
-
(2014)
Nat Commun
, vol.5
, pp. 3233
-
-
Cheng, K.-K.1
Lee, B.-S.2
Masuda, T.3
Ito, T.4
Ikeda, K.5
Hirayama, A.6
Deng, L.7
Dong, J.8
Shimizu, K.9
Soga, T.10
-
50
-
-
84967180536
-
Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution
-
50 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
-
51
-
-
84856258903
-
The molecular diversity of adaptive convergence
-
51 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 335 (2012), 457–461.
-
(2012)
Science
, vol.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
-
52
-
-
84907269737
-
Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations
-
52 Sandberg, T.E., Pedersen, M., Lacroix, R.A., Ebrahim, A., Bonde, M., Herrgard, M.J., Palsson, B.O., Sommer, M., Feist, A.M., Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Mol Biol Evol 31 (2014), 2647–2662.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 2647-2662
-
-
Sandberg, T.E.1
Pedersen, M.2
Lacroix, R.A.3
Ebrahim, A.4
Bonde, M.5
Herrgard, M.J.6
Palsson, B.O.7
Sommer, M.8
Feist, A.M.9
-
53
-
-
84901358601
-
Evolved osmotolerant Escherichia coli mutants frequently exhibit defective N-acetylglucosamine catabolism and point mutations in cell shape-regulating protein MreB
-
53 Winkler, J.D., Garcia, C., Olson, M., Callaway, E., Kao, K.C., Evolved osmotolerant Escherichia coli mutants frequently exhibit defective N-acetylglucosamine catabolism and point mutations in cell shape-regulating protein MreB. Appl Environ Microbiol 80 (2014), 3729–3740.
-
(2014)
Appl Environ Microbiol
, vol.80
, pp. 3729-3740
-
-
Winkler, J.D.1
Garcia, C.2
Olson, M.3
Callaway, E.4
Kao, K.C.5
-
54
-
-
84898637077
-
Adaptation of Escherichia coli to elevated sodium concentrations increases cation tolerance and enables greater lactic acid production
-
54 Wu, X., Altman, R., Eiteman, M.A., Altman, E., Adaptation of Escherichia coli to elevated sodium concentrations increases cation tolerance and enables greater lactic acid production. Appl Environ Microbiol 80 (2014), 2880–2888.
-
(2014)
Appl Environ Microbiol
, vol.80
, pp. 2880-2888
-
-
Wu, X.1
Altman, R.2
Eiteman, M.A.3
Altman, E.4
-
55
-
-
84903458015
-
Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria
-
55 Haft, R.J.F., Keating, D.H., Schwaegler, T., Schwalbach, M.S., Vinokur, J., Tremaine, M., Peters, J.M., Kotlajich, M.V., Pohlmann, E.L., Ong, I.M., et al. Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria. Proc Natl Acad Sci U S A 111 (2014), e2576–e2585.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. e2576-e2585
-
-
Haft, R.J.F.1
Keating, D.H.2
Schwaegler, T.3
Schwalbach, M.S.4
Vinokur, J.5
Tremaine, M.6
Peters, J.M.7
Kotlajich, M.V.8
Pohlmann, E.L.9
Ong, I.M.10
-
56
-
-
84927514444
-
Evolution for exogenous octanoic acid tolerance improves carboxylic acid production and membrane integrity
-
56 Royce, L.A., Yoon, J.M., Chen, Y., Rickenbach, E., Shanks, J.V., Jarboe, L.R., Evolution for exogenous octanoic acid tolerance improves carboxylic acid production and membrane integrity. Metab Eng 29 (2015), 180–188.
-
(2015)
Metab Eng
, vol.29
, pp. 180-188
-
-
Royce, L.A.1
Yoon, J.M.2
Chen, Y.3
Rickenbach, E.4
Shanks, J.V.5
Jarboe, L.R.6
-
57
-
-
84959240103
-
Xylose fermentation by Saccharomyces cerevisiae: challenges and prospects
-
57 Moysés, D.N., Reis, V.C.B., de Almeida, J.R.M., de Moraes, L.M.P., Torres, F.A.G., Xylose fermentation by Saccharomyces cerevisiae: challenges and prospects. Int J Mol Sci, 17, 2016, 207.
-
(2016)
Int J Mol Sci
, vol.17
, pp. 207
-
-
Moysés, D.N.1
Reis, V.C.B.2
de Almeida, J.R.M.3
de Moraes, L.M.P.4
Torres, F.A.G.5
-
58
-
-
59949093124
-
Novel evolutionary engineering approach for accelerated utilization of glucose, xylose, and arabinose mixtures by engineered Saccharomyces cerevisiae strains
-
58 Wouter Wisselink, H., Toirkens, M.J., Wu, Q., Pronk, J.T., Van Maris, A.J.A., Novel evolutionary engineering approach for accelerated utilization of glucose, xylose, and arabinose mixtures by engineered Saccharomyces cerevisiae strains. Appl Environ Microbiol 75 (2009), 907–914.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 907-914
-
-
Wouter Wisselink, H.1
Toirkens, M.J.2
Wu, Q.3
Pronk, J.T.4
Van Maris, A.J.A.5
-
59
-
-
84955276048
-
Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae
-
59 Reider Apel, A., Ouellet, M., Szmidt-Middleton, H., Keasling, J.D., Mukhopadhyay, A., Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae. Sci Rep, 6, 2016, 19512.
-
(2016)
Sci Rep
, vol.6
, pp. 19512
-
-
Reider Apel, A.1
Ouellet, M.2
Szmidt-Middleton, H.3
Keasling, J.D.4
Mukhopadhyay, A.5
-
60
-
-
84976892364
-
2 in Escherichia coli
-
2 and pyruvate semi-autotroph through pathway manipulation followed by ALE using a dynamic selective pressure.
-
2 and pyruvate semi-autotroph through pathway manipulation followed by ALE using a dynamic selective pressure.
-
(2016)
Cell
, vol.166
, pp. 115-125
-
-
Antonovsky, N.1
Gleizer, S.2
Noor, E.3
Zohar, Y.4
Herz, E.5
Barenholz, U.6
Zelcbuch, L.7
Amram, S.8
Wides, A.9
Tepper, N.10
-
61
-
-
84982801326
-
Metabolic engineering of microbial competitive advantage for industrial fermentation processes
-
ALE was used to complement heterologous pathway expression to enable three microorganisms to utilise xenobiotic nitrogen and phosphorous sources as selective agents.
-
61• Shaw, A.J., Lam, F.H., Hamilton, M., Consiglio, A., MacEwen, K., Brevnova, E.E., Greenhagen, E., LaTouf, W.G., South, C.R., van Dijken, H., et al. Metabolic engineering of microbial competitive advantage for industrial fermentation processes. Science 353 (2016), 583–586 ALE was used to complement heterologous pathway expression to enable three microorganisms to utilise xenobiotic nitrogen and phosphorous sources as selective agents.
-
(2016)
Science
, vol.353
, pp. 583-586
-
-
Shaw, A.J.1
Lam, F.H.2
Hamilton, M.3
Consiglio, A.4
MacEwen, K.5
Brevnova, E.E.6
Greenhagen, E.7
LaTouf, W.G.8
South, C.R.9
van Dijken, H.10
-
62
-
-
84945388093
-
Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum
-
62 Mahr, R., Gätgens, C., Gätgens, J., Polen, T., Kalinowski, J., Frunzke, J., Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metab Eng 32 (2015), 184–194.
-
(2015)
Metab Eng
, vol.32
, pp. 184-194
-
-
Mahr, R.1
Gätgens, C.2
Gätgens, J.3
Polen, T.4
Kalinowski, J.5
Frunzke, J.6
-
63
-
-
84921476371
-
A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae
-
63 Lee, S.W., Oh, M.K., A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae. Metab Eng 28 (2015), 143–150.
-
(2015)
Metab Eng
, vol.28
, pp. 143-150
-
-
Lee, S.W.1
Oh, M.K.2
-
64
-
-
84919359797
-
Evolution-guided optimization of biosynthetic pathways
-
64 Raman, S., Rogers, J.K., Taylor, N.D., Church, G.M., Evolution-guided optimization of biosynthetic pathways. Proc Natl Acad Sci U S A 111 (2014), 17803–17808.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 17803-17808
-
-
Raman, S.1
Rogers, J.K.2
Taylor, N.D.3
Church, G.M.4
|