-
1
-
-
84860405978
-
Mathematical models of cell factories: Moving towards the core of industrial biotechnology
-
Cvijovic M, Bordel S, Nielsen J. Mathematical models of cell factories: Moving towards the core of industrial biotechnology. Microb Biotechnol 2011;4(5):572-584.
-
(2011)
Microb Biotechnol
, vol.4
, Issue.5
, pp. 572-584
-
-
Cvijovic, M.1
Bordel, S.2
Nielsen, J.3
-
2
-
-
84873997973
-
Genome-scale metabolic model in guiding metabolic engineering of microbial improvement
-
Xu C, Liu L, Zhang Z, et al. Genome-scale metabolic model in guiding metabolic engineering of microbial improvement. Appl Microbiol Biotechnol 2013;97:519-539.
-
(2013)
Appl Microbiol Biotechnol
, vol.97
, pp. 519-539
-
-
Xu, C.1
Liu, L.2
Zhang, Z.3
-
3
-
-
84859776222
-
The future of metabolic engineering and synthetic biology: Towards a systematic practice
-
Yadav VG, De Mey M, Lim CG, et al. The future of metabolic engineering and synthetic biology: Towards a systematic practice. Metab Eng 2012;14:233-241.
-
(2012)
Metab Eng
, vol.14
, pp. 233-241
-
-
Yadav, V.G.1
De Mey, M.2
Lim, C.G.3
-
4
-
-
84875973063
-
The RAVEN toolbox and its use for generating a genome-scale metabolic model for penicillium chrysogenum
-
Agren R, Liu L, Shoaie S, et al. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol 2013;9(3):e1002980.
-
(2013)
PLoS Comput Biol
, vol.9
, Issue.3
-
-
Agren, R.1
Liu, L.2
Shoaie, S.3
-
5
-
-
0343035686
-
Stoichiometric model of Escherichia coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements
-
DOI 10.1002/(SICI)1097-0290(19971120)56:4<398::AID-BIT6>3.0.CO;2-J
-
Pramanik J, Keasling JD. Stoichiometric model of Escherichia coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotech Bioeng 1997;56(4):398-421. (Pubitemid 27468936)
-
(1997)
Biotechnology and Bioengineering
, vol.56
, Issue.4
, pp. 398-421
-
-
Pramanik, J.1
Keasling, J.D.2
-
6
-
-
0036330798
-
Genome-scale metabolic model of Helicobacter pylori 26695
-
DOI 10.1128/JB.184.16.4582-4593.2002
-
Schilling CH, Covert MW, Famili I, et al. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 2002;184(16):4582-4593. (Pubitemid 34832586)
-
(2002)
Journal of Bacteriology
, vol.184
, Issue.16
, pp. 4582-4593
-
-
Schilling, C.H.1
Covert, M.W.2
Famili, I.3
Church, G.M.4
Edwards, J.S.5
Palsson, B.O.6
-
7
-
-
0036350955
-
The genome-scale metabolic extreme pathway structure in Haemophilus influenza shows significant network redundancy
-
Papin JA, Price ND, Edwards JS, Palsson BO. The genome-scale metabolic extreme pathway structure in Haemophilus influenza shows significant network redundancy. J Theor Biol 2002;215:67-82.
-
(2002)
J Theor Biol
, vol.215
, pp. 67-82
-
-
Papin, J.A.1
Price, N.D.2
Edwards, J.S.3
Palsson, B.O.4
-
8
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
DOI 10.1101/gr.234503
-
Forster J, Famili I, Fu PC, et al. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003;13:244-253. (Pubitemid 36581837)
-
(2003)
Genome Research
, vol.13
, Issue.2
, pp. 244-253
-
-
Forster, J.1
Famili, I.2
Fu, P.3
Palsson, B.O.4
Nielsen, J.5
-
9
-
-
77950960250
-
OptFlux: An open-source software platform for in silico metabolic engineering
-
Rocha I, Maia P, Evangelista P, et al. OptFlux: An open-source software platform for in silico metabolic engineering. BMC Sys Biol 2010;4:45.
-
(2010)
BMC Sys Biol
, vol.4
, pp. 45
-
-
Rocha, I.1
Maia, P.2
Evangelista, P.3
-
10
-
-
84864932596
-
Fifteen years of large scale metabolic modeling of yeast: Developments and impacts
-
Osterlund T, Nookaew I, Nielsen J. Fifteen years of large scale metabolic modeling of yeast: Developments and impacts. Biotech Adv 2012;30:979-988.
-
(2012)
Biotech Adv
, vol.30
, pp. 979-988
-
-
Osterlund, T.1
Nookaew, I.2
Nielsen, J.3
-
11
-
-
84870293949
-
Artificial biosynthesis of phenylpropanoic acids in a tyrosine overproducing Escherichia coli strain
-
Kang SY, Choi O, Lee JK, et al. Artificial biosynthesis of phenylpropanoic acids in a tyrosine overproducing Escherichia coli strain. Microb Cell Fact 2012;11:153.
-
(2012)
Microb Cell Fact
, vol.11
, pp. 153
-
-
Kang, S.Y.1
Choi, O.2
Lee, J.K.3
-
12
-
-
84862207929
-
Expanding the chemical palate of cells by combining systems biology and metabolic engineering
-
Curran KA, Alper HS. Expanding the chemical palate of cells by combining systems biology and metabolic engineering. Metab Eng 2012;14:289-297.
-
(2012)
Metab Eng
, vol.14
, pp. 289-297
-
-
Curran, K.A.1
Alper, H.S.2
-
15
-
-
84864955882
-
Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches
-
Jang YS, Park JM, Choi S, et al. Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches. Biotechnol Adv 2012;30(5):989-1000.
-
(2012)
Biotechnol Adv
, vol.30
, Issue.5
, pp. 989-1000
-
-
Jang, Y.S.1
Park, J.M.2
Choi, S.3
-
18
-
-
75749144228
-
Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE
-
Kim HU, Kim TY, Lee SY. Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE. Mol Biosyst 2010;6:339-348.
-
(2010)
Mol Biosyst
, vol.6
, pp. 339-348
-
-
Kim, H.U.1
Kim, T.Y.2
Lee, S.Y.3
-
19
-
-
3843128481
-
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
-
DOI 10.1101/gr.2250904
-
Duarte NC, Herrgard MJ, Palsson BO. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 2004;14:1298-1309. (Pubitemid 39036129)
-
(2004)
Genome Research
, vol.14
, Issue.7
, pp. 1298-1309
-
-
Duarte, N.C.1
Herrgard, M.J.2
Palsson, B.O.3
-
20
-
-
1242283921
-
Use of genome-scale microbial models for metabolic engineering
-
DOI 10.1016/j.copbio.2003.11.003
-
Patil KR, A.kesson M, Nielsen J. Use of genome-scale microbial models for metabolic engineering. Curr Op Biotechnol 2004;15:64-69. (Pubitemid 38224252)
-
(2004)
Current Opinion in Biotechnology
, vol.15
, Issue.1
, pp. 64-69
-
-
Patil, K.R.1
Akesson, M.2
Nielsen, J.3
-
21
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist AM, Herrgard MJ, Thiele I, et al. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 2009;7:129-143.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
-
22
-
-
84861898310
-
IMG: The integrated microbial genomes database and comparative analysis system
-
Markowitz VM, Min I, Chen A, et al. IMG: The integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 2012;40:D115-D122.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Markowitz, V.M.1
Min, I.2
Chen, A.3
-
24
-
-
58149203228
-
SUPERFAMILY: Sophisticated comparative genomics, data mining, visualization and phylogeny
-
Wilson D, Pethica R, Zhou Y, et al. SUPERFAMILY: Sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res 2009;37:D380-D386.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Wilson, D.1
Pethica, R.2
Zhou, Y.3
-
25
-
-
38049007503
-
Multidimensional annotation of the Escherichia coli K-12 genome
-
Karp PD, Keseler IM, Shearer A, et al. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 2007;35(22):7577-7590.
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.22
, pp. 7577-7590
-
-
Karp, P.D.1
Keseler, I.M.2
Shearer, A.3
-
26
-
-
84858588614
-
Saccharomyces Genome Database: The genomics resource of budding yeast
-
Cherry JM, Hong EL, Amundsen C, et al. Saccharomyces Genome Database: The genomics resource of budding yeast. Nucleic Acids Res 2012;40:D700-D705.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Cherry, J.M.1
Hong, E.L.2
Amundsen, C.3
-
27
-
-
13444306676
-
CYGD: The comprehensive yeast genome database
-
DOI 10.1093/nar/gki053
-
Guldener U, Munsterkotter M, Kastenmuller G, et al. CYGD: The comprehensive yeast genome database. Nucleic Acids Res 2005;33:D364-D368. (Pubitemid 40207896)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Guldener, U.1
Munsterkotter, M.2
Kastenmuller, G.3
Strack, N.4
Van Helden, J.5
Lemer, C.6
Richelles, J.7
Wodak, S.J.8
Garcia-Martinez, J.9
Perez-Ortin, J.E.10
Michael, H.11
Kaps, A.12
Talla, E.13
Dujon, B.14
Andre, B.15
Souciet, J.L.16
De Montigny, J.17
Bon, E.18
Gaillardin, C.19
Mewes, H.W.20
more..
-
28
-
-
77954401189
-
YeastWeb: A workset-centric web resource for gene family analysis in yeast
-
Chu Y, Yuan X, Guo Y, et al. YeastWeb: A workset-centric web resource for gene family analysis in yeast. BMC Genomics 2010;11:429.
-
(2010)
BMC Genomics
, vol.11
, pp. 429
-
-
Chu, Y.1
Yuan, X.2
Guo, Y.3
-
29
-
-
38549176698
-
CFGP: A web-based, comparative fungal genomics platform
-
DOI 10.1093/nar/gkm758
-
Park JH, Park B, Jung K, et al. CFGP: A web-based, comparative fungal genomics platform. Nucleic Acids Res 2008;36:D562-D571. (Pubitemid 351149786)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Park, J.1
Park, B.2
Jung, K.3
Jang, S.4
Yu, K.5
Choi, J.6
Kong, S.7
Park, J.8
Kim, S.9
Kim, H.10
Kim, S.11
Kim, J.F.12
Blair, J.E.13
Lee, K.14
Kang, S.15
Lee, Y.-H.16
-
30
-
-
33644877429
-
Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeast
-
Sherman D, Durrens P, Iragne F, et al. Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeast. Nucleic Acids Res 2006;34:D432-D435.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Sherman, D.1
Durrens, P.2
Iragne, F.3
-
31
-
-
84862234237
-
DBTSS: DataBase of Transciptional Start Sites progress report in 2012
-
Yamashita R, Sugano S, Suzuki Y, Nakai K. DBTSS: DataBase of Transciptional Start Sites progress report in 2012. Nucleic Acids Res 2012;40:D150-D154.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Yamashita, R.1
Sugano, S.2
Suzuki, Y.3
Nakai, K.4
-
33
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000;28(1):27-30. (Pubitemid 30047706)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
34
-
-
78651330012
-
BRENDA, the enzyme information system in 2011
-
Scheer M, Grote A, Chang A, et al. BRENDA, the enzyme information system in 2011. Nucleic Acids Res 2011;39:D670-D676.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Scheer, M.1
Grote, A.2
Chang, A.3
-
35
-
-
33644877904
-
MetaCyc: A multiorganism database of metabolic pathways and enzymes
-
Caspi R, Foerster H, Fulcher CA, et al. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 2006;34:D511-D516.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Caspi, R.1
Foerster, H.2
Fulcher, C.A.3
-
36
-
-
34248632008
-
Toward the automated generation of genome-scale metabolic networks in the SEED
-
DeJongh M, Formsma K, Boillot P, et al. Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007;8:139.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 139
-
-
Dejongh, M.1
Formsma, K.2
Boillot, P.3
-
39
-
-
78651345652
-
The RCSB Protein Data Bank: Redesigned web site and web services
-
Rose PW, Beran B, Bi C, et al. The RCSB Protein Data Bank: Redesigned web site and web services. Nucleic Acids Res 2011;39:D392-D401.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Rose, P.W.1
Beran, B.2
Bi, C.3
-
40
-
-
41149105489
-
Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger
-
DOI 10.1038/msb.2008.12, PII MSB200812
-
Andersen M, Nielsen M, Nielsen J. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol 2008;4:178. (Pubitemid 351441042)
-
(2008)
Molecular Systems Biology
, vol.4
, pp. 178
-
-
Andersen, M.R.1
Nielsen, M.L.2
Nielsen, J.3
-
41
-
-
0032485833
-
Metabolic engineering: Techniques for analysis of targets for genetic manipulations
-
DOI 10.1002/(SICI)1097-0290(19980420)58:2/3<125::AID-BIT3>3.0.CO;2- N
-
Nielsen J. Metabolic engineering: Techniques for analysis of targets for genetic manipulations. Biotechnol Bioeng 1998;58(2-3):125-132. (Pubitemid 28136368)
-
(1998)
Biotechnology and Bioengineering
, vol.58
, Issue.2-3
, pp. 125-132
-
-
Nielsen, J.1
-
43
-
-
0042816453
-
Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae
-
Forster J, Famili I, Palsson BO, Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS 2003;7(2):193-202. (Pubitemid 36896124)
-
(2003)
OMICS A Journal of Integrative Biology
, vol.7
, Issue.2
, pp. 193-202
-
-
Forster, J.1
Famili, I.2
Palsson, B.O.3
Nielsen, J.4
-
44
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele I, Palsson BO. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 2010;5:93-121.
-
(2010)
Nat Protoc
, vol.5
, pp. 93-121
-
-
Thiele, I.1
Palsson, B.O.2
-
45
-
-
84862777085
-
Computational tools for metabolic engineering
-
Copeland WB, Bartley BA, Chandran D, et al. Computational tools for metabolic engineering. Metab Eng 2012;14:270-280.
-
(2012)
Metab Eng
, vol.14
, pp. 270-280
-
-
Copeland, W.B.1
Bartley, B.A.2
Chandran, D.3
-
46
-
-
0037075690
-
Modeling and simulation: Tools for metabolic engineering
-
DOI 10.1016/S0168-1656(01)00418-7, PII S0168165601004187
-
Wiechert W. Modeling and simulation: Tools for metabolic engineering. J Biotechnol 2002;94:37-63. (Pubitemid 34127667)
-
(2002)
Journal of Biotechnology
, vol.94
, Issue.1
, pp. 37-63
-
-
Wiechert, W.1
-
47
-
-
84859772410
-
Synthetic biology and the development of tools for metabolic engineering
-
Keasling JD. Synthetic biology and the development of tools for metabolic engineering. Metab Eng 2012;14:189-195.
-
(2012)
Metab Eng
, vol.14
, pp. 189-195
-
-
Keasling, J.D.1
-
48
-
-
41049102359
-
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
-
Oliveira AP, Patil KR, Nielsen J. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Sys Biol 2008;2:17.
-
(2008)
BMC Sys Biol
, vol.2
, pp. 17
-
-
Oliveira, A.P.1
Patil, K.R.2
Nielsen, J.3
-
50
-
-
44849094233
-
Improved annotation through genomescale metabolic modeling of Aspergillus oryzae
-
Vongsangnaki W, Olsen P, Hansen K, et al. Improved annotation through genomescale metabolic modeling of Aspergillus oryzae. BMC Genomics 2008; 9:245.
-
(2008)
BMC Genomics
, vol.9
, pp. 245
-
-
Vongsangnaki, W.1
Olsen, P.2
Hansen, K.3
-
51
-
-
30044437327
-
Evolutionary programming as a platform for in silico metabolic engineering
-
Patil KR, Rocha I, Forster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2005;6:308.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 308
-
-
Patil, K.R.1
Rocha, I.2
Forster, J.3
Nielsen, J.4
-
53
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0
-
Schellenberger J, Que R, Fleming RMT, et al. Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0. Nat Prot 2011;6:1290-1307.
-
(2011)
Nat Prot
, vol.6
, pp. 1290-1307
-
-
Schellenberger, J.1
Que, R.2
Rmt, F.3
-
54
-
-
80053175304
-
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks
-
Jensen PA, Lutz KA, Papin JA. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Syst Biol 2011;5:147.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 147
-
-
Jensen, P.A.1
Lutz, K.A.2
Papin, J.A.3
-
55
-
-
79955145774
-
EMILiO: A fast algorithm for genome-scale strain design
-
Yang L, Cluett WR, Mahadevan R. EMILiO: A fast algorithm for genome-scale strain design. Metab Eng 2011;13:272-281.
-
(2011)
Metab Eng
, vol.13
, pp. 272-281
-
-
Yang, L.1
Cluett, W.R.2
Mahadevan, R.3
-
58
-
-
0242487787
-
OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
DOI 10.1002/bit.10803
-
Burgard AP, Pharkya P, Maranas CD. OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotech Bioeng 2003;84(6):647-657. (Pubitemid 37420336)
-
(2003)
Biotechnology and Bioengineering
, vol.84
, Issue.6
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
59
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 2004;5(10):R80.
-
(2004)
Genome Biol
, vol.5
, Issue.10
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
-
60
-
-
75549084894
-
PANTHER version 7: Improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
-
Mi H, Dong Q, Muruganujan A, et al. PANTHER version 7: Improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res 2010;38:D204-D210.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Mi, H.1
Dong, Q.2
Muruganujan, A.3
-
62
-
-
60649101258
-
The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results
-
Braisted JC, Kuntumalla S, Vogel C, et al. The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics 2008;9:529.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 529
-
-
Braisted, J.C.1
Kuntumalla, S.2
Vogel, C.3
-
63
-
-
0036138754
-
Peptide sequence motif analysis of tandem MS data with the SALSA Algorithm
-
DOI 10.1021/ac0155512
-
Liebler DC, Hansen BT, Davey SW, et al. Peptide sequence motif analysis of tandem MS data with the SALSA algorithm. Anal Chem 2002;74:203-210. (Pubitemid 34044445)
-
(2002)
Analytical Chemistry
, vol.74
, Issue.1
, pp. 203-210
-
-
Liebler, D.C.1
Hansen, B.T.2
Davey, S.W.3
Tiscareno, L.4
Mason, D.E.5
-
64
-
-
84867045160
-
Current challenges in software solutions for mass spectrometry-based quantitative proteomics
-
Cappadona S, Baker PR, Cutillas PR, et al. Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids 2012;43:1087-1108.
-
(2012)
Amino Acids
, vol.43
, pp. 1087-1108
-
-
Cappadona, S.1
Baker, P.R.2
Cutillas, P.R.3
-
65
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright AJ, Van Dogen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002;30(7):1575-1584. (Pubitemid 34679732)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
66
-
-
84862221167
-
SMART 7: Recent updates to the protein domain annotation resource
-
Letunic I, Doerks T, Bork P. SMART 7: Recent updates to the protein domain annotation resource. Nucleic Acids Res 2012;40:D302-D305.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Letunic, I.1
Doerks, T.2
Bork, P.3
-
67
-
-
78049255973
-
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
-
Chandrasekaran S, Price ND. Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci 2010;107(41):17845-17850.
-
(2010)
Proc Natl Acad Sci
, vol.107
, Issue.41
, pp. 17845-17850
-
-
Chandrasekaran, S.1
Price, N.D.2
-
69
-
-
33644832381
-
In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production
-
DOI 10.1016/j.ymben.2005.09.007, PII S1096717605000789
-
Bro C, Regenberg B, Forster J, Nielsen J. In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng 2006;8(2):102-111. (Pubitemid 43356393)
-
(2006)
Metabolic Engineering
, vol.8
, Issue.2
, pp. 102-111
-
-
Bro, C.1
Regenberg, B.2
Forster, J.3
Nielsen, J.4
-
71
-
-
50249115104
-
Dynamic metabolic engineering for increasing bioprocess productivity
-
Anesiadis N, Cluett WR, Mahadevan R. Dynamic metabolic engineering for increasing bioprocess productivity. Metab Eng 2008;10:255-266.
-
(2008)
Metab Eng
, vol.10
, pp. 255-266
-
-
Anesiadis, N.1
Cluett, W.R.2
Mahadevan, R.3
-
72
-
-
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. Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture. Biotechnol Bioeng 2007;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
-
73
-
-
78549287163
-
The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies
-
Lee KY, Park JM, Kim TY, et al. The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. Microb Cell Fact 2010;9:94.
-
(2010)
Microb Cell Fact
, vol.9
, pp. 94
-
-
Lee, K.Y.1
Park, J.M.2
Kim, T.Y.3
-
74
-
-
77954732846
-
Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions
-
Ranganathan S, Maranas CD. Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions. Biotechnol J 2010;5:716-725.
-
(2010)
Biotechnol J
, vol.5
, pp. 716-725
-
-
Ranganathan, S.1
Maranas, C.D.2
-
75
-
-
79952589723
-
Engineering butanol-tolerance in Escherichia coli with artificial transcription factor libraries
-
Lee JY, Yang KS, Jang SA, et al. Engineering butanol-tolerance in Escherichia coli with artificial transcription factor libraries. Biotechnol Bioeng 2011;108:742-749.
-
(2011)
Biotechnol Bioeng
, vol.108
, pp. 742-749
-
-
Lee, J.Y.1
Yang, K.S.2
Jang, S.A.3
-
76
-
-
77950857795
-
A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing
-
Borden JR, Jones SW, Indurthi D, et al. A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing. Metab Eng 2010;12:268-281.
-
(2010)
Metab Eng
, vol.12
, pp. 268-281
-
-
Borden, J.R.1
Jones, S.W.2
Indurthi, D.3
-
77
-
-
80052625837
-
Metabolic engineering of Clostridium acetobutylicum: Recent advances to improve butanol production
-
Lutke-Eversloh T, Bahl, H. Metabolic engineering of Clostridium acetobutylicum: Recent advances to improve butanol production. Curr Opin Biotechnol 2011;22:634-647.
-
(2011)
Curr Opin Biotechnol
, vol.22
, pp. 634-647
-
-
Lutke-Eversloh, T.1
Bahl, H.2
-
78
-
-
77953076065
-
Reconstructing the clostridial n-butanol metabolic pathway in Lactobacillus brevis
-
Berezina OV, Zakharova NV, Brandt A, et al. Reconstructing the clostridial n-butanol metabolic pathway in Lactobacillus brevis. Appl Microbiol Biotechnol 2010;87:635-646.
-
(2010)
Appl Microbiol Biotechnol
, vol.87
, pp. 635-646
-
-
Berezina, O.V.1
Zakharova, N.V.2
Brandt, A.3
-
79
-
-
36849002434
-
Systems metabolic engineering of Escherichia coli for L-threonine production
-
Lee KH, Park JH, Kim TY, et al. Systems metabolic engineering of Escherichia coli for L-threonine production. Mol Syst Biol 2007;3:149.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 149
-
-
Lee, K.H.1
Park, J.H.2
Kim, T.Y.3
-
80
-
-
34249934691
-
Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation
-
Park JH, Lee KH, Kim TY, Lee SY. 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 2007;104:7797-7802.
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 7797-7802
-
-
Park, J.H.1
Lee, K.H.2
Kim, T.Y.3
Lee, S.Y.4
-
81
-
-
79952578981
-
Fed-batch culture of Escherichia coli for L-valine production based on in silico flux response analysis
-
Park JH, Kim TY, Lee KH, Lee SY. Fed-batch culture of Escherichia coli for L-valine production based on in silico flux response analysis. Biotechnol Bioeng 2011;108:934-946.
-
(2011)
Biotechnol Bioeng
, vol.108
, pp. 934-946
-
-
Park, J.H.1
Kim, T.Y.2
Lee, K.H.3
Lee, S.Y.4
-
82
-
-
79952106791
-
From zero to hero: Design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production
-
Becker JV, Zelder O, Hafner S, et al. From zero to hero: Design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production. Metab Eng 2011;13:159-168.
-
(2011)
Metab Eng
, vol.13
, pp. 159-168
-
-
Becker, J.V.1
Zelder, O.2
Hafner, S.3
-
83
-
-
0242267924
-
Reconstruction of the central carbon metabolism of Aspergillus niger
-
DOI 10.1046/j.1432-1033.2003.03798.x
-
David H, Akesson M, Nielsen J. Reconstruction of the central carbon metabolism of Aspergillus niger. Eur J Biochem 2003;270:4243-4253. (Pubitemid 37340342)
-
(2003)
European Journal of Biochemistry
, vol.270
, Issue.21
, pp. 4243-4253
-
-
David, H.1
Akesson, M.2
Nielsen, J.3
-
84
-
-
0034610099
-
Metabolism of citric acid production by Aspergillus niger: Model definition, steady-state analysis and constrained optimization of citric acid production rate
-
Alvarez-Vasquez F, González-Alcon C, Torres NV. Metabolism of citric acid production by Aspergillus niger: Model definition, steady-state analysis and constrained optimization of citric acid production rate. Biotechnol Bioeng 2000;70(1):82-108.
-
(2000)
Biotechnol Bioeng
, vol.70
, Issue.1
, pp. 82-108
-
-
Alvarez-Vasquez, F.1
González-Alcon, C.2
Torres, N.V.3
-
85
-
-
84872655172
-
Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory
-
Otero JM, Cimini D, Patil KR, et al. Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory. PLoS ONE 2013;8(1): e54144.
-
(2013)
PLoS ONE
, vol.8
, Issue.1
-
-
Otero, J.M.1
Cimini, D.2
Patil, K.R.3
-
86
-
-
84879236195
-
Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production
-
doi: 10.1007/s10295-013-1269-3
-
Agren R, Otero JM, Nielsen J. Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production. J Ind Microbiol Biotechnol 2013;doi: 10.1007/s10295-013-1269-3.
-
(2013)
J Ind Microbiol Biotechnol
-
-
Agren, R.1
Otero, J.M.2
Nielsen, J.3
-
87
-
-
33747369422
-
Batch culture characterization and metabolic flux analysis of succinate-producing Escherichia coli strains
-
DOI 10.1016/j.ymben.2005.11.004, PII S109671760500100X
-
Sanchez AM, Bennett GN, San KY. Batch culture characterization and metabolic flux analysis of succinate-producing Escherichia coli strains. Metab Eng 2006;8:209-226. (Pubitemid 44382420)
-
(2006)
Metabolic Engineering
, vol.8
, Issue.3
, pp. 209-226
-
-
Sanchez, A.M.1
Bennett, G.N.2
San, K.-Y.3
-
88
-
-
34249297627
-
Metabolic flux analysis in a nonstationary system: Fed-batch fermentation of a high yielding strain of E. Coli producing 1,3-propanediol
-
DOI 10.1016/j.ymben.2007.01.003, PII S1096717607000122
-
Antoniewicz MR, Kraynie DF, Laffend LA, et al. Metabolic flux analysis in a nonstationary system: Fed-batch fermentation of a high yielding strain of E. Coli producing 1,3-propanediol. Metab Eng 2007;9:277-292. (Pubitemid 46809526)
-
(2007)
Metabolic Engineering
, vol.9
, Issue.3
, pp. 277-292
-
-
Antoniewicz, M.R.1
Kraynie, D.F.2
Laffend, L.A.3
Gonzalez-Lergier, J.4
Kelleher, J.K.5
Stephanopoulos, G.6
-
89
-
-
79959374585
-
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
-
Yim H, Haselbeck R, Niu W, et al. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 2011;7:445-452.
-
(2011)
Nat Chem Biol
, vol.7
, pp. 445-452
-
-
Yim, H.1
Haselbeck, R.2
Niu, W.3
-
90
-
-
84859199206
-
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials
-
Caspeta L, Shoaie S, Agren R, et al. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst Biol 2012;6:4.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 4
-
-
Caspeta, L.1
Shoaie, S.2
Agren, R.3
-
91
-
-
80052021573
-
Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA
-
Xu P, Ranganathan S, Fowler ZL, et al. Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab Eng 2011;13:578-587.
-
(2011)
Metab Eng
, vol.13
, pp. 578-587
-
-
Xu, P.1
Ranganathan, S.2
Fowler, Z.L.3
-
92
-
-
0036207217
-
Application of metabolic engineering to improve both the production and use of biotech indigo
-
Berry A, Dodge TC, Pepsin M, Weyler W. Application of metabolic engineering to improve both the production and use of biotech indigo. J Ind Microbiol Biotechnol 2002;28:127-133. (Pubitemid 34264061)
-
(2002)
Journal of Industrial Microbiology and Biotechnology
, vol.28
, Issue.3
, pp. 127-133
-
-
Berry, A.1
Dodge, T.2
Pepsin, M.3
Weyler, W.4
-
93
-
-
73949094856
-
Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers
-
Jung YK, Kim TY, Park SJ, Lee SY. Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers. Biotechnol Bioeng 2010;105:161-171.
-
(2010)
Biotechnol Bioeng
, vol.105
, pp. 161-171
-
-
Jung, Y.K.1
Kim, T.Y.2
Park, S.J.3
Lee, S.Y.4
-
94
-
-
22844452835
-
Construction of lycopene-overproducing E. Coli strains by combining systematic and combinatorial gene knockout targets
-
DOI 10.1038/nbt1083
-
Alper H, Miyaoku K, Stephanopoulos G. Construction of lycopeneoverproducing E. Coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnol 2005;23:612-616. (Pubitemid 41724901)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.5
, pp. 612-616
-
-
Alper, H.1
Miyaoku, K.2
Stephanopoulos, G.3
-
95
-
-
41049115923
-
Uncovering the gene knockout landscape for improved lycopene production in E. Coli
-
Alper H, Stephanopoulos G. Uncovering the gene knockout landscape for improved lycopene production in E. Coli. Appl Microbiol Biotechnol 2008;78:801-810.
-
(2008)
Appl Microbiol Biotechnol
, vol.78
, pp. 801-810
-
-
Alper, H.1
Stephanopoulos, G.2
-
96
-
-
78049460641
-
Improved vanillin production in baker's yeast through in silico design
-
Brochado AR, Matos C, Moller BL, et al. Improved vanillin production in baker's yeast through in silico design. Microb Cell Factor 2010;9:84.
-
(2010)
Microb Cell Factor
, vol.9
, pp. 84
-
-
Brochado, A.R.1
Matos, C.2
Moller, B.L.3
-
97
-
-
70449592325
-
Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
-
Asadollahi MA, Maury J, Patil KR, et al. Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab Eng 2009;11:328-334.
-
(2009)
Metab Eng
, vol.11
, pp. 328-334
-
-
Asadollahi, M.A.1
Maury, J.2
Patil, K.R.3
-
98
-
-
29044432251
-
Metabolic flux analysis of HEK-293 cells in perfusion cultures for the production of adenoviral vectors
-
DOI 10.1016/j.ymben.2005.08.002, PII S1096717605000686
-
Henry O, Perrier M, Kamen A. Metabolic flux analysis of HEK-293 cells in perfusion cultures for the production of adenoviral vectors. Metab Eng 2005;7:467-476. (Pubitemid 41790475)
-
(2005)
Metabolic Engineering
, vol.7
, Issue.5-6
, pp. 467-476
-
-
Henry, O.1
Perrier, M.2
Kamen, A.3
-
99
-
-
1642576078
-
Reconstitution of the entry point of plant phenylpropanoid metabolism in yeast (Saccharomyces cerevisiae): Implications for control of metabolic flux into the phenylpropanoid pathway
-
DOI 10.1074/jbc.M309951200
-
Ro DK, Douglas CJ. Reconstitution of the entry point of plant phenylpropanoid metabolism in yeast (Saccharomyces cerevisiae): Implications for control of metabolic flux into the phenylpropanoid pathway. J Biol Chem 2004;279:2600-2607. (Pubitemid 38114246)
-
(2004)
Journal of Biological Chemistry
, vol.279
, Issue.4
, pp. 2600-2607
-
-
Ro, D.-K.1
Douglas, C.J.2
-
100
-
-
0031256338
-
Classification of fermented foods: Worldwide review of household fermentation techniques
-
PII S0956713597000509
-
Steinkraus KH. Classification of fermented foods: Worldwide review of household fermentation techniques. Food Control 1997;8(5-6):311-317. (Pubitemid 127162023)
-
(1997)
Food Control
, vol.8
, Issue.5-6
, pp. 311-317
-
-
Steinkraus, K.H.1
-
101
-
-
4544372921
-
A genome-wide transcription analysis of a fungal riboflavin overproducer
-
DOI 10.1016/j.jbiotec.2004.03.025, PII S0168165604003062
-
Karos M, Vilarino C, Bollschweiler C, Revuelta JL. A genome-wide transcription analysis of a fungal riboflavin overproducer. J Biotechnol 2004;113:69-76. (Pubitemid 39237071)
-
(2004)
Journal of Biotechnology
, vol.113
, Issue.1-3
, pp. 69-76
-
-
Karos, M.1
Vilarino, C.2
Bollschweiler, C.3
Revuelta, J.L.4
-
102
-
-
84864186953
-
Metabolic engineering of Saccharomyces cerevisiae: A key cell factory platform for future biorefineries
-
Hong KK, Nielsen, J. Metabolic engineering of Saccharomyces cerevisiae: A key cell factory platform for future biorefineries. Cell Mol Life Sci 2012;69:2671-2690.
-
(2012)
Cell Mol Life Sci
, vol.69
, pp. 2671-2690
-
-
Hong, K.K.1
Nielsen, J.2
|