-
1
-
-
78650829303
-
Systems biology of industrial microorganisms
-
Papini,M., Salazar,M. and Nielsen,J. (2010) Systems biology of industrial microorganisms. Adv. Biochem. Eng. Biotechnol., 120, 51-99.
-
(2010)
Adv. Biochem. Eng. Biotechnol.
, vol.120
, pp. 51-99
-
-
Papini, M.1
Salazar, M.2
Nielsen, J.3
-
2
-
-
84862207929
-
Expanding the chemical palate of cells by combining systems biology and metabolic engineering
-
Curran,K.A. and Alper,H.S. (2012) Expanding the chemical palate of cells by combining systems biology and metabolic engineering. Metab. Eng., 14, 289-297.
-
(2012)
Metab. Eng.
, vol.14
, pp. 289-297
-
-
Curran, K.A.1
Alper, H.S.2
-
3
-
-
84876784070
-
High-level semi-synthetic production of the potent antimalarial artemisinin
-
Paddon,C.J., Westfall,P.J., Pitera,D.J., Benjamin,K., Fisher,K., McPhee,D., Leavell,M.D., Tai,A., Main,A., Eng,D. et al. (2013) High-level semi-synthetic production of the potent antimalarial artemisinin. Nature, 496, 528-532.
-
(2013)
Nature
, vol.496
, pp. 528-532
-
-
Paddon, C.J.1
Westfall, P.J.2
Pitera, D.J.3
Benjamin, K.4
Fisher, K.5
McPhee, D.6
Leavell, M.D.7
Tai, A.8
Main, A.9
Eng, D.10
-
4
-
-
77957329119
-
Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli
-
Ajikumar,P.K., Xiao,W.-H., Tyo,K.E.J., Wang,Y., Simeon,F., Leonard,E., Mucha,O., Phon,T.H., Pfeifer,B. and Stephanopoulos,G. (2010) Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science, 330, 70-74.
-
(2010)
Science
, vol.330
, pp. 70-74
-
-
Ajikumar, P.K.1
Xiao, W.-H.2
Tyo, K.E.J.3
Wang, Y.4
Simeon, F.5
Leonard, E.6
Mucha, O.7
Phon, T.H.8
Pfeifer, B.9
Stephanopoulos, G.10
-
5
-
-
80051551391
-
Microbial production of isoprenoids
-
Chandran,S.S., Kealey,J.T. and Reeves,C.D. (2011) Microbial production of isoprenoids. Process Biochem., 46, 1703-1710.
-
(2011)
Process Biochem.
, vol.46
, pp. 1703-1710
-
-
Chandran, S.S.1
Kealey, J.T.2
Reeves, C.D.3
-
6
-
-
79958715193
-
Optimization of a heterologous pathway for the production of flavonoids from glucose
-
Santos,C.N., Koffas,M. and Stephanopoulos,G. (2011) Optimization of a heterologous pathway for the production of flavonoids from glucose. Metab. Eng., 13, 392-400.
-
(2011)
Metab. Eng.
, vol.13
, pp. 392-400
-
-
Santos, C.N.1
Koffas, M.2
Stephanopoulos, G.3
-
7
-
-
79961116083
-
A retrosynthetic biology approach to metabolic pathway design for therapeutic production
-
Carbonell,P., Planson,A.-G., Fichera,D. and Faulon,J.-L. (2011) A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst. Biol., 5, 122.
-
(2011)
BMC Syst. Biol.
, vol.5
, pp. 122
-
-
Carbonell, P.1
Planson, A.-G.2
Fichera, D.3
Faulon, J.-L.4
-
8
-
-
77953329895
-
Prediction of novel synthetic pathways for the production of desired chemicals
-
Cho,A., Yun,H., Park,J.H., Lee,S.Y. and Park,S. (2010) Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst. Biol., 4, 35.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 35
-
-
Cho, A.1
Yun, H.2
Park, J.H.3
Lee, S.Y.4
Park, S.5
-
9
-
-
17444382016
-
Exploring the diversity of complex metabolic networks
-
Hatzimanikatis,V., Li,C., Ionita,J.a., Henry,C.S., Jankowski,M.D. and Broadbelt,L.J. (2005) Exploring the diversity of complex metabolic networks. Bioinformatics, 21, 1603-1609.
-
(2005)
Bioinformatics
, vol.21
, pp. 1603-1609
-
-
Hatzimanikatis, V.1
Li, C.2
Ionita, J.A.3
Henry, C.S.4
Jankowski, M.D.5
Broadbelt, L.J.6
-
10
-
-
34247131307
-
Enzyme promiscuity: Mechanism and applications
-
Hult,K. and Berglund,P. (2007) Enzyme promiscuity: mechanism and applications. Trends Biotechnol., 25, 231-238.
-
(2007)
Trends Biotechnol.
, vol.25
, pp. 231-238
-
-
Hult, K.1
Berglund, P.2
-
11
-
-
77955353890
-
Molecular signatures-based prediction of enzyme promiscuity
-
Carbonell,P. and Faulon,J.-L. (2010) Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics, 26, 2012-2019.
-
(2010)
Bioinformatics
, vol.26
, pp. 2012-2019
-
-
Carbonell, P.1
Faulon, J.-L.2
-
12
-
-
83755171600
-
Origins of specificity and promiscuity in metabolic networks
-
Carbonell,P., Lecointre,G. and Faulon,J.-L. (2011) Origins of specificity and promiscuity in metabolic networks. J. Biol. Chem., 286, 43994-44004.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 43994-44004
-
-
Carbonell, P.1
Lecointre, G.2
Faulon, J.-L.3
-
13
-
-
59849106371
-
Protein promiscuity and its implications for biotechnology
-
Nobeli,I., Favia,A.D. and Thornton,J.M. (2009) Protein promiscuity and its implications for biotechnology. Nat. Biotechnol., 27, 157-167.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 157-167
-
-
Nobeli, I.1
Favia, A.D.2
Thornton, J.M.3
-
14
-
-
84894174799
-
Enzyme recruitment and its role in metabolic expansion
-
Schulenburg,C. and Miller,B.G. (2014) Enzyme recruitment and its role in metabolic expansion. Biochemistry, 53, 836-845.
-
(2014)
Biochemistry
, vol.53
, pp. 836-845
-
-
Schulenburg, C.1
Miller, B.G.2
-
15
-
-
84860490976
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
Caspi,R., Altman,T., Dreher,K., Fulcher,C.A., Subhraveti,P., Keseler,I.M., Kothari,A., Krummenacker,M., Latendresse,M., Mueller,L.A. et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 40, D742-D753.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Caspi, R.1
Altman, T.2
Dreher, K.3
Fulcher, C.A.4
Subhraveti, P.5
Keseler, I.M.6
Kothari, A.7
Krummenacker, M.8
Latendresse, M.9
Mueller, L.A.10
-
16
-
-
84858983547
-
KEGG for integration and interpretation of large-scale molecular data sets
-
Kanehisa,M., Goto,S., Sato,Y., Furumichi,M. and Tanabe,M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Furumichi, M.4
Tanabe, M.5
-
17
-
-
84876522835
-
BRENDA in 2013: Integrated reactions, kinetic data, enzyme function data, improved disease classification: New options and contents in BRENDA
-
Schomburg,I., Chang,A., Placzek,S., Söhngen,C., Rother,M., Lang,M., Munaretto,C., Ulas,S., Stelzer,M., Grote,A. et al. (2013) BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res., 41, D764-D772.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Schomburg, I.1
Chang, A.2
Placzek, S.3
Söhngen, C.4
Rother, M.5
Lang, M.6
Munaretto, C.7
Ulas, S.8
Stelzer, M.9
Grote, A.10
-
18
-
-
84876560358
-
The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013
-
Hastings,J., de Matos,P., Dekker,A., Ennis,M., Harsha,B., Kale,N., Muthukrishnan,V., Owen,G., Turner,S., Williams,M. et al. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res., 41, D456-D463.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Hastings, J.1
De Matos, P.2
Dekker, A.3
Ennis, M.4
Harsha, B.5
Kale, N.6
Muthukrishnan, V.7
Owen, G.8
Turner, S.9
Williams, M.10
-
19
-
-
84862220951
-
Rhea - A manually curated resource of biochemical reactions
-
Alcantara,R., Axelsen,K.B., Morgat,A., Belda,E., Coudert,E., Bridge,A., Cao,H., de Matos,P., Ennis,M., Turner,S. et al. (2012) Rhea-a manually curated resource of biochemical reactions. Nucleic Acids Res., 40, D754-D760.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Alcantara, R.1
Axelsen, K.B.2
Morgat, A.3
Belda, E.4
Coudert, E.5
Bridge, A.6
Cao, H.7
De Matos, P.8
Ennis, M.9
Turner, S.10
-
20
-
-
77954268488
-
PathPred: An enzyme-catalyzed metabolic pathway prediction server
-
Moriya,Y., Shigemizu,D., Hattori,M., Tokimatstu,T., Kotera,M., Goto,S. and Kanehisa,M. (2010) PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res., 38, W138-W143.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Moriya, Y.1
Shigemizu, D.2
Hattori, M.3
Tokimatstu, T.4
Kotera, M.5
Goto, S.6
Kanehisa, M.7
-
21
-
-
11444249446
-
Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions
-
Kotera,M., Okuno,Y., Hattori,M., Goto,S. and Kanehisa,M. (2004) Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J. Am. Chem. Soc, 126, 16487-16498.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 16487-16498
-
-
Kotera, M.1
Okuno, Y.2
Hattori, M.3
Goto, S.4
Kanehisa, M.5
-
22
-
-
84878862372
-
Metabolic tinker: An online tool for guiding the design of synthetic metabolic pathways
-
McClymont,K. and Soyer,O.S. (2013) Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. Nucleic Acids Res., 41, e113-e113.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
McClymont, K.1
Soyer, O.S.2
-
23
-
-
67849083088
-
FMM: A web server for metabolic pathway reconstruction and comparative analysis
-
Chou,C.-H., Chang,W.-C., Chiu,C.-M., Huang,C.-C. and Huang,H.-D. (2009) FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res., 37, W129-W134.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Chou, C.-H.1
Chang, W.-C.2
Chiu, C.-M.3
Huang, C.-C.4
Huang, H.-D.5
-
24
-
-
84876554425
-
Stereo signature molecular descriptor
-
Carbonell,P., Carlsson,L. and Faulon,J.-L. (2013) Stereo signature molecular descriptor. J. Chem. Inf. Model, 53, 887-897.
-
(2013)
J. Chem. Inf. Model
, vol.53
, pp. 887-897
-
-
Carbonell, P.1
Carlsson, L.2
Faulon, J.-L.3
-
25
-
-
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. and Palsson,B.O. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol., 3, 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.O.9
-
26
-
-
77953934646
-
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
Li,C., Donizelli,M., Rodriguez,N., Dharuri,H., Endler,L., Chelliah,V., Li,L., He,E., Henry,A., Stefan,M. et al. (2010) BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol., 4, 92.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.8
Henry, A.9
Stefan, M.10
-
27
-
-
84899702032
-
Retropath: Automated pipeline for embedded metabolic circuits
-
doi:10.1021/sb4001273
-
Carbonell,P., Parutto,P., Baudier,C., Junot,C. and Faulon,J.-L. (2013) Retropath: automated pipeline for embedded metabolic circuits. ACS Synth. Biol., doi:10.1021/sb4001273.
-
(2013)
ACS Synth. Biol.
-
-
Carbonell, P.1
Parutto, P.2
Baudier, C.3
Junot, C.4
Faulon, J.-L.5
-
29
-
-
80053512597
-
Open Babel: An open chemical toolbox
-
O'Boyle,N.M., Banck,M., James,C.A., Morley,C., Vandermeersch,T. and Hutchison,G.R. (2011) Open Babel: an open chemical toolbox. J. Cheminform., 3, 33.
-
(2011)
J. Cheminform.
, vol.3
, pp. 33
-
-
O'boyle, N.M.1
Banck, M.2
James, C.A.3
Morley, C.4
Vandermeersch, T.5
Hutchison, G.R.6
-
30
-
-
84892965416
-
Software applications toward quantitative metabolic flux analysis and modeling
-
Dandekar,T., Fieselmann,A., Majeed,S. and Ahmed,Z. (2012) Software applications toward quantitative metabolic flux analysis and modeling. Brief. Bioinform., 15, 91-107.
-
(2012)
Brief. Bioinform.
, vol.15
, pp. 91-107
-
-
Dandekar, T.1
Fieselmann, A.2
Majeed, S.3
Ahmed, Z.4
-
31
-
-
38349114038
-
Genome scale enzyme-metabolite and drugtarget interaction predictions using the signature molecular descriptor
-
Faulon,J.-L., Misra,M., Martin,S., Sale,K. and Sapra,R. (2008) Genome scale enzyme-metabolite and drugtarget interaction predictions using the signature molecular descriptor. Bioinformatics, 24, 225-233.
-
(2008)
Bioinformatics
, vol.24
, pp. 225-233
-
-
Faulon, J.-L.1
Misra, M.2
Martin, S.3
Sale, K.4
Sapra, R.5
-
32
-
-
84855946759
-
Compound toxicity screening and structure-activity relationship modeling in Escherichia coli
-
Planson,A.-G., Carbonell,P., Paillard,E., Pollet,N. and Faulon,J.-L. (2012) Compound toxicity screening and structure-activity relationship modeling in Escherichia coli. Biotechnol. Bioeng., 109, 846-850.
-
(2012)
Biotechnol. Bioeng.
, vol.109
, pp. 846-850
-
-
Planson, A.-G.1
Carbonell, P.2
Paillard, E.3
Pollet, N.4
Faulon, J.-L.5
-
33
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka,M., Finney,A., Sauro,H.M., Bolouri,H., Doyle,J.C., Kitano,H., Arkin,A.P., Bornstein,B.J., Bray,D., Cornish-Bowden,A. et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
-
34
-
-
84896831202
-
A methodology to annotate systems biology markup language models with the synthetic biology open language
-
Roehner,N. and Myers,C.J. (2014) A methodology to annotate systems biology markup language models with the synthetic biology open language. ACS Synth. Biol., 3, 57-66.
-
(2014)
ACS Synth. Biol.
, vol.3
, pp. 57-66
-
-
Roehner, N.1
Myers, C.J.2
-
35
-
-
52949098408
-
Large-scale computation of elementary flux modes with bit pattern trees
-
Terzer,M. and Stelling,J. (2008) Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics, 24, 2229-2235.
-
(2008)
Bioinformatics
, vol.24
, pp. 2229-2235
-
-
Terzer, M.1
Stelling, J.2
-
36
-
-
84856579358
-
Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms
-
Carbonell,P., Fichera,D., Pandit,S. and Faulon,J.L. (2012) Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Syst. Biol., 6, 10.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 10
-
-
Carbonell, P.1
Fichera, D.2
Pandit, S.3
Faulon, J.L.4
-
37
-
-
35748979142
-
Microbial production of natural raspberry ketone
-
Beekwilder,J., van der Meer,I.M., Sibbesen,O., Broekgaarden,M., Qvist,I., Mikkelsen,J.D. and Hall,R.D. (2007) Microbial production of natural raspberry ketone. Biotechnol. J., 2, 1270-1279.
-
(2007)
Biotechnol. J.
, vol.2
, pp. 1270-1279
-
-
Beekwilder, J.1
Van Der Meer, I.M.2
Sibbesen, O.3
Broekgaarden, M.4
Qvist, I.5
Mikkelsen, J.D.6
Hall, R.D.7
|