-
1
-
-
84874978130
-
Engineering plant metabolism into microbes: From systems biology to synthetic biology
-
Xu, P., Bhan, N., and Koffas, M. A. G. (2013) Engineering plant metabolism into microbes: From systems biology to synthetic biology Curr. Opin. Biotechnol. 24, 291-299 10.1016/j.copbio.2012.08.010
-
(2013)
Curr. Opin. Biotechnol.
, vol.24
, pp. 291-299
-
-
Xu, P.1
Bhan, N.2
Koffas, M.A.G.3
-
2
-
-
45149118469
-
Engineering BioBrick vectors from BioBrick parts
-
Shetty, R. P., Endy, D., and Knight, T. F. (2008) Engineering BioBrick vectors from BioBrick parts J. Biol. Eng. 2, 5 10.1186/1754-1611-2-5
-
(2008)
J. Biol. Eng.
, vol.2
, pp. 5
-
-
Shetty, R.P.1
Endy, D.2
Knight, T.F.3
-
3
-
-
84868263016
-
EPathBrick: A Synthetic Biology Platform for Engineering Metabolic Pathways in E. Coli
-
Xu, P., Vansiri, A., Bhan, N., and Koffas, M. a G. (2012) ePathBrick: A Synthetic Biology Platform for Engineering Metabolic Pathways in E. coli ACS Synth. Biol. 1, 256-66 10.1021/sb300016b
-
(2012)
ACS Synth. Biol.
, vol.1
, pp. 256-266
-
-
Xu, P.1
Vansiri, A.2
Bhan, N.3
Koffas, M.A.G.4
-
4
-
-
84931292024
-
EPathOptimize: A Combinatorial Approach for Transcriptional Balancing of Metabolic Pathways
-
Jones, J. A., Vernacchio, V. R., Lachance, D. M., Lebovich, M., Fu, L., Shirke, A. N., Schultz, V. L., Cress, B., Linhardt, R. J., and Koffas, M. A. G. (2015) ePathOptimize: A Combinatorial Approach for Transcriptional Balancing of Metabolic Pathways Sci. Rep. 5, 11301 10.1038/srep11301
-
(2015)
Sci. Rep.
, vol.5
, pp. 11301
-
-
Jones, J.A.1
Vernacchio, V.R.2
Lachance, D.M.3
Lebovich, M.4
Fu, L.5
Shirke, A.N.6
Schultz, V.L.7
Cress, B.8
Linhardt, R.J.9
Koffas, M.A.G.10
-
5
-
-
84921517479
-
Functional optimization of gene clusters by combinatorial design and assembly
-
Smanski, M. J., Bhatia, S., Zhao, D., Park, Y., B A Woodruff, L., Giannoukos, G., Ciulla, D., Busby, M., Calderon, J., Nicol, R., Gordon, D. B., Densmore, D., and Voigt, C. A. (2014) Functional optimization of gene clusters by combinatorial design and assembly Nat. Biotechnol. 32, 1241-1249 10.1038/nbt.3063
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 1241-1249
-
-
Smanski, M.J.1
Bhatia, S.2
Zhao, D.3
Park, Y.4
Woodruff L, B.A.5
Giannoukos, G.6
Ciulla, D.7
Busby, M.8
Calderon, J.9
Nicol, R.10
Gordon, D.B.11
Densmore, D.12
Voigt, C.A.13
-
6
-
-
77952915373
-
Construction and optimization of synthetic pathways in metabolic engineering
-
Na, D., Kim, T. Y., and Lee, S. Y. (2010) Construction and optimization of synthetic pathways in metabolic engineering Curr. Opin. Microbiol. 13, 363-370 10.1016/j.mib.2010.02.004
-
(2010)
Curr. Opin. Microbiol.
, vol.13
, pp. 363-370
-
-
Na, D.1
Kim, T.Y.2
Lee, S.Y.3
-
7
-
-
84866953925
-
Modular control of multiple pathways using engineered orthogonal T7 polymerases
-
Temme, K., Hill, R., Segall-Shapiro, T. H., Moser, F., and Voigt, C. A. (2012) Modular control of multiple pathways using engineered orthogonal T7 polymerases Nucleic Acids Res. 40, 8773-8781 10.1093/nar/gks597
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 8773-8781
-
-
Temme, K.1
Hill, R.2
Segall-Shapiro, T.H.3
Moser, F.4
Voigt, C.A.5
-
8
-
-
77951278557
-
Site-specific chromosomal integration of large synthetic constructs
-
Kuhlman, T. E. and Cox, E. C. (2010) Site-specific chromosomal integration of large synthetic constructs Nucleic Acids Res. 38, e92 10.1093/nar/gkp1193
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. e92
-
-
Kuhlman, T.E.1
Cox, E.C.2
-
9
-
-
0036429345
-
Estimating the instability parameters of plasmid-bearing cells. I. Chemostat culture
-
Ganusov, V. V. and Brilkov, A. V. (2002) Estimating the instability parameters of plasmid-bearing cells. I. Chemostat culture J. Theor. Biol. 219, 193-205 10.1006/jtbi.2002.3101
-
(2002)
J. Theor. Biol.
, vol.219
, pp. 193-205
-
-
Ganusov, V.V.1
Brilkov, A.V.2
-
10
-
-
0018403583
-
The influence of the growth environment on the stability of a drug resistance plasmid in Escherichia coli K12
-
Godwin, D. and Slater, J. H. (1979) The influence of the growth environment on the stability of a drug resistance plasmid in Escherichia coli K12 J. Gen. Microbiol. 111, 201-210 10.1099/00221287-111-1-201
-
(1979)
J. Gen. Microbiol.
, vol.111
, pp. 201-210
-
-
Godwin, D.1
Slater, J.H.2
-
11
-
-
78649712445
-
The continuing crisis in antibiotic resistance
-
French, G. L. (2010) The continuing crisis in antibiotic resistance Int. J. Antimicrob. Agents 36, S3-S7 10.1016/S0924-8579(10)70003-0
-
(2010)
Int. J. Antimicrob. Agents
, vol.36
, pp. S3-S7
-
-
French, G.L.1
-
12
-
-
78649709002
-
Coping with antibiotic resistance: The impending crisis
-
Gould, I. M. (2010) Coping with antibiotic resistance: The impending crisis Int. J. Antimicrob. Agents 36, S1-S2 10.1016/S0924-8579(10)00497-8
-
(2010)
Int. J. Antimicrob. Agents
, vol.36
, pp. S1-S2
-
-
Gould, I.M.1
-
13
-
-
81255157431
-
Tackling antibiotic resistance
-
Bush, K., Courvalin, P., Dantas, G., Davies, J., Eisenstein, B., Huovinen, P., Jacoby, G. A., Kishony, R., Kreiswirth, B. N., Kutter, E., Lerner, S. A., Levy, S., Lewis, K., Lomovskaya, O., Miller, J. H., Mobashery, S., Piddock, L. J., Projan, S., Thomas, C. M., Tomasz, A., Tulkens, P. M., Walsh, T. R., Watson, J. D., Witkowski, J., Witte, W., Wright, G., Yeh, P., and Zgurskaya, H. I. (2011) Tackling antibiotic resistance Nat. Rev. Microbiol. 9, 894-896 10.1038/nrmicro2693
-
(2011)
Nat. Rev. Microbiol.
, vol.9
, pp. 894-896
-
-
Bush, K.1
Courvalin, P.2
Dantas, G.3
Davies, J.4
Eisenstein, B.5
Huovinen, P.6
Jacoby, G.A.7
Kishony, R.8
Kreiswirth, B.N.9
Kutter, E.10
Lerner, S.A.11
Levy, S.12
Lewis, K.13
Lomovskaya, O.14
Miller, J.H.15
Mobashery, S.16
Piddock, L.J.17
Projan, S.18
Thomas, C.M.19
Tomasz, A.20
Tulkens, P.M.21
Walsh, T.R.22
Watson, J.D.23
Witkowski, J.24
Witte, W.25
Wright, G.26
Yeh, P.27
Zgurskaya, H.I.28
more..
-
14
-
-
84947474587
-
An integrated system for precise genome modification in Escherichia coli
-
Tas, H., Nguyen, C. T., Patel, R., Kim, N. H., and Kuhlman, T. E. (2015) An integrated system for precise genome modification in Escherichia coli PLoS One 10, 1-19 10.1371/journal.pone.0136963
-
(2015)
PLoS One
, vol.10
, pp. 1-19
-
-
Tas, H.1
Nguyen, C.T.2
Patel, R.3
Kim, N.H.4
Kuhlman, T.E.5
-
15
-
-
0034612342
-
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
-
Datsenko, K. A. and Wanner, B. L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products Proc. Natl. Acad. Sci. U. S. A. 97, 6640-6645 10.1073/pnas.120163297
-
(2000)
Proc. Natl. Acad. Sci. U. S. A.
, vol.97
, pp. 6640-6645
-
-
Datsenko, K.A.1
Wanner, B.L.2
-
16
-
-
84879225332
-
Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci
-
Sabri, S., Steen, J. A., Bongers, M., Nielsen, L. K., and Vickers, C. E. (2013) Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci Microb. Cell Fact. 12, 60 10.1186/1475-2859-12-60
-
(2013)
Microb. Cell Fact.
, vol.12
, pp. 60
-
-
Sabri, S.1
Steen, J.A.2
Bongers, M.3
Nielsen, L.K.4
Vickers, C.E.5
-
17
-
-
84868289569
-
Gene location and DNA density determine transcription factor distributions in Escherichia coli
-
Kuhlman, T. E. and Cox, E. C. (2012) Gene location and DNA density determine transcription factor distributions in Escherichia coli Mol. Syst. Biol. 8, 610 10.1038/msb.2012.42
-
(2012)
Mol. Syst. Biol.
, vol.8
, pp. 610
-
-
Kuhlman, T.E.1
Cox, E.C.2
-
18
-
-
84945944020
-
Sensitive cells: Enabling tools for static and dynamic control of microbial metabolic pathways
-
Cress, B. F., Trantas, E. A., Ververidis, F., Linhardt, R. J., and Koffas, M. A. G. (2015) Sensitive cells: Enabling tools for static and dynamic control of microbial metabolic pathways Curr. Opin. Biotechnol. 36, 205-214 10.1016/j.copbio.2015.09.007
-
(2015)
Curr. Opin. Biotechnol.
, vol.36
, pp. 205-214
-
-
Cress, B.F.1
Trantas, E.A.2
Ververidis, F.3
Linhardt, R.J.4
Koffas, M.A.G.5
-
19
-
-
0242487787
-
OptKnock: A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization
-
Burgard, A. P., Pharkya, P., and Maranas, C. D. (2003) OptKnock: A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization Biotechnol. Bioeng. 84, 647-657 10.1002/bit.10803
-
(2003)
Biotechnol. Bioeng.
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
20
-
-
84930971149
-
CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. Coli
-
Cress, B. F., Toparlak, O. D., Guleria, S., Lebovich, M., Stieglitz, J. T., Englaender, J. A., Jones, J. A., Linhardt, R. J., and Koffas, M. A. G. (2015) CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. coli ACS Synth. Biol. 4, 987-1000 10.1021/acssynbio.5b00012
-
(2015)
ACS Synth. Biol.
, vol.4
, pp. 987-1000
-
-
Cress, B.F.1
Toparlak, O.D.2
Guleria, S.3
Lebovich, M.4
Stieglitz, J.T.5
Englaender, J.A.6
Jones, J.A.7
Linhardt, R.J.8
Koffas, M.A.G.9
-
21
-
-
85117273619
-
Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model
-
Khodayari, A., Chowdhury, A., and Maranas, C. D. (2014) Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model Front. Bioeng. Biotechnol. 2, 76 10.3389/fbioe.2014.00076
-
(2014)
Front. Bioeng. Biotechnol.
, vol.2
, pp. 76
-
-
Khodayari, A.1
Chowdhury, A.2
Maranas, C.D.3
-
22
-
-
85012838041
-
Improving Metabolic Pathway Efficiency by Statistical Model-Based Multivariate Regulatory Metabolic Engineering
-
Xu, P., Rizzoni, E. A., Sul, S.-Y., and Stephanopoulos, G. (2016) Improving Metabolic Pathway Efficiency by Statistical Model-Based Multivariate Regulatory Metabolic Engineering ACS Synth. Biol. 10.1021/acssynbio.6b00187
-
(2016)
ACS Synth. Biol.
-
-
Xu, P.1
Rizzoni, E.A.2
Sul, S.-Y.3
Stephanopoulos, G.4
-
23
-
-
33845511743
-
Reconstitution of the myxothiazol biosynthetic gene cluster by red/ET recombination and heterologous expression in Myxococcus xanthus
-
Perlova, O., Fu, J., Kuhlmann, S., Krug, D., Stewart, A. F., Zhang, Y., and Muller, R. (2006) Reconstitution of the myxothiazol biosynthetic gene cluster by red/ET recombination and heterologous expression in Myxococcus xanthus Appl. Environ. Microbiol. 72, 7485-7494 10.1128/AEM.01503-06
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 7485-7494
-
-
Perlova, O.1
Fu, J.2
Kuhlmann, S.3
Krug, D.4
Stewart, A.F.5
Zhang, Y.6
Muller, R.7
-
24
-
-
84878546957
-
Comparative transcription profiling and in-depth characterization of plasmid-based and plasmid-free Escherichia coli expression systems under production conditions
-
Mairhofer, J., Scharl, T., Marisch, K., Cserjan-Puschmann, M., and Striedner, G. (2013) Comparative transcription profiling and in-depth characterization of plasmid-based and plasmid-free Escherichia coli expression systems under production conditions Appl. Environ. Microbiol. 79, 3802-3812 10.1128/AEM.00365-13
-
(2013)
Appl. Environ. Microbiol.
, vol.79
, pp. 3802-3812
-
-
Mairhofer, J.1
Scharl, T.2
Marisch, K.3
Cserjan-Puschmann, M.4
Striedner, G.5
-
25
-
-
84961223765
-
Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications
-
Wu, G., Yan, Q., Jones, J. A., Tang, Y. J., Fong, S. S., and Koffas, M. A. G. (2016) Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications Trends Biotechnol. 34, 652-664 10.1016/j.tibtech.2016.02.010
-
(2016)
Trends Biotechnol.
, vol.34
, pp. 652-664
-
-
Wu, G.1
Yan, Q.2
Jones, J.A.3
Tang, Y.J.4
Fong, S.S.5
Koffas, M.A.G.6
-
26
-
-
84997173327
-
Engineering Highly Efficient E. Coli strain for Mevalonate Fermentation by Chromosomal Integration
-
Wang, J., Niyompanich, S., Tai, Y.-S., Wang, J., Bai, W., Mahida, P., Gao, T., and Zhang, K. (2016) Engineering Highly Efficient E. coli strain for Mevalonate Fermentation by Chromosomal Integration Appl. Environ. Microbiol. 82, 7176 10.1128/AEM.02178-16
-
(2016)
Appl. Environ. Microbiol.
, vol.82
, pp. 7176
-
-
Wang, J.1
Niyompanich, S.2
Tai, Y.-S.3
Wang, J.4
Bai, W.5
Mahida, P.6
Gao, T.7
Zhang, K.8
-
27
-
-
84920161546
-
Improvement of catechin production in Escherichia coli through combinatorial metabolic engineering
-
Zhao, S., Jones, J. A., Lachance, D. M., Bhan, N., Khalidi, O., Venkataraman, S., Wang, Z., and Koffas, M. A. G. (2015) Improvement of catechin production in Escherichia coli through combinatorial metabolic engineering Metab. Eng. 28, 43-53 10.1016/j.ymben.2014.12.002
-
(2015)
Metab. Eng.
, vol.28
, pp. 43-53
-
-
Zhao, S.1
Jones, J.A.2
Lachance, D.M.3
Bhan, N.4
Khalidi, O.5
Venkataraman, S.6
Wang, Z.7
Koffas, M.A.G.8
-
28
-
-
84877804801
-
Modular optimization of multi-gene pathways for fatty acids production in E. Coli
-
Xu, P., Gu, Q., Wang, W., Wong, L., Bower, A. G. W., Collins, C. H., and Koffas, M. A. G. (2013) Modular optimization of multi-gene pathways for fatty acids production in E. coli Nat. Commun. 4, 1409 10.1038/ncomms2425
-
(2013)
Nat. Commun.
, vol.4
, pp. 1409
-
-
Xu, P.1
Gu, Q.2
Wang, W.3
Wong, L.4
Bower, A.G.W.5
Collins, C.H.6
Koffas, M.A.G.7
-
29
-
-
84911920717
-
Metabolic pathway balancing and its role in the production of biofuels and chemicals
-
Jones, J. A., Toparlak, O. D., and Koffas, M. A. G. (2015) Metabolic pathway balancing and its role in the production of biofuels and chemicals Curr. Opin. Biotechnol. 33, 52-59 10.1016/j.copbio.2014.11.013
-
(2015)
Curr. Opin. Biotechnol.
, vol.33
, pp. 52-59
-
-
Jones, J.A.1
Toparlak, O.D.2
Koffas, M.A.G.3
-
30
-
-
70349964350
-
Automated design of synthetic ribosome binding sites to control protein expression
-
Salis, H. M., Mirsky, E. A., and Voigt, C. A. (2009) Automated design of synthetic ribosome binding sites to control protein expression Nat. Biotechnol. 27, 946-50 10.1038/nbt.1568
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 946-950
-
-
Salis, H.M.1
Mirsky, E.A.2
Voigt, C.A.3
-
31
-
-
55249090459
-
Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition
-
Fu, J., Wenzel, S. C., Perlova, O., Wang, J., Gross, F., Tang, Z., Yin, Y., Stewart, A. F., Muller, R., and Zhang, Y. (2008) Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition Nucleic Acids Res. 36, e113 10.1093/nar/gkn499
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. e113
-
-
Fu, J.1
Wenzel, S.C.2
Perlova, O.3
Wang, J.4
Gross, F.5
Tang, Z.6
Yin, Y.7
Stewart, A.F.8
Muller, R.9
Zhang, Y.10
-
32
-
-
84987909959
-
Effect of Genome Position on Heterologous Gene Expression in Bacillus subtilis: An Unbiased Analysis
-
Sauer, C., Syvertsson, S., Bohorquez, L. C., Cruz, R., Harwood, C. R., van Rij, T., and Hamoen, L. W. (2016) Effect of Genome Position on Heterologous Gene Expression in Bacillus subtilis: An Unbiased Analysis ACS Synth. Biol. 5, 942 10.1021/acssynbio.6b00065
-
(2016)
ACS Synth. Biol.
, vol.5
, pp. 942
-
-
Sauer, C.1
Syvertsson, S.2
Bohorquez, L.C.3
Cruz, R.4
Harwood, C.R.5
Van Rij, T.6
Hamoen, L.W.7
-
33
-
-
84978492675
-
Rapid and Efficient One-Step Metabolic Pathway Integration in E. Coli
-
Bassalo, M. C., Garst, A. D., Halweg-Edwards, A. L., Grau, W. C., Domaille, D. W., Mutalik, V. K., Arkin, A. P., and Gill, R. T. (2016) Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli ACS Synth. Biol. 5, 561 10.1021/acssynbio.5b00187
-
(2016)
ACS Synth. Biol.
, vol.5
, pp. 561
-
-
Bassalo, M.C.1
Garst, A.D.2
Halweg-Edwards, A.L.3
Grau, W.C.4
Domaille, D.W.5
Mutalik, V.K.6
Arkin, A.P.7
Gill, R.T.8
-
34
-
-
84914129027
-
Production of chondroitin in metabolically engineered E. Coli
-
He, W., Fu, L., Li, G., Jones, J. A., Linhardt, R. J., and Koffas, M. (2015) Production of chondroitin in metabolically engineered E. coli Metab. Eng. 27, 92-100 10.1016/j.ymben.2014.11.003
-
(2015)
Metab. Eng.
, vol.27
, pp. 92-100
-
-
He, W.1
Fu, L.2
Li, G.3
Jones, J.A.4
Linhardt, R.J.5
Koffas, M.6
-
35
-
-
84890395226
-
Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay
-
Lee, M. E., Aswani, A., Han, A. S., Tomlin, C. J., and Dueber, J. E. (2013) Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay Nucleic Acids Res. 41, 10668-10678 10.1093/nar/gkt809
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 10668-10678
-
-
Lee, M.E.1
Aswani, A.2
Han, A.S.3
Tomlin, C.J.4
Dueber, J.E.5
-
36
-
-
0036193882
-
Crossing over between regions of limited homology in Escherichia coli: RecA-dependent and RecA-independent pathways
-
Lovett, S. T., Hurley, R. L., Sutera, V. A., Aubuchon, R. H., and Lebedeva, M. A. (2002) Crossing over between regions of limited homology in Escherichia coli: RecA-dependent and RecA-independent pathways Genetics 160, 851-859
-
(2002)
Genetics
, vol.160
, pp. 851-859
-
-
Lovett, S.T.1
Hurley, R.L.2
Sutera, V.A.3
Aubuchon, R.H.4
Lebedeva, M.A.5
-
37
-
-
84987903943
-
When Wavelengths Collide: Bias in Cell Abundance Measurements due to Expressed Fluorescent Proteins
-
Hecht, A. H., Endy, D., Salit, M., and Munson, M. S. (2016) When Wavelengths Collide: Bias in Cell Abundance Measurements due to Expressed Fluorescent Proteins ACS Synth. Biol. 5, 37010 10.1021/acssynbio.6b00072
-
(2016)
ACS Synth. Biol.
, vol.5
, pp. 37010
-
-
Hecht, A.H.1
Endy, D.2
Salit, M.3
Munson, M.S.4
-
38
-
-
84948179681
-
Optimization of naringenin and p-coumaric acid hydroxylation using the native E. Coli hydroxylase complex, HpaBC
-
Jones, J. A., Collins, S. M., Vernacchio, V. R., Lachance, D. M., and Koffas, M. A. G. (2016) Optimization of naringenin and p-coumaric acid hydroxylation using the native E. coli hydroxylase complex, HpaBC Biotechnol. Prog. 32, 21-25 10.1002/btpr.2185
-
(2016)
Biotechnol. Prog.
, vol.32
, pp. 21-25
-
-
Jones, J.A.1
Collins, S.M.2
Vernacchio, V.R.3
Lachance, D.M.4
Koffas, M.A.G.5
|