-
1
-
-
1242319556
-
The metabolic world of Escherichia coli is not small
-
Arita M (2004) The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci 101:1543-1547.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 1543-1547
-
-
Arita, M.1
-
2
-
-
33745278855
-
Computational redesign of endonuclease DNA binding and cleavage specificity
-
Ashworth J, Havranek JJ, Duarte CM, Sussman D, Stoddard BL and Baker D (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441:656-659.
-
(2006)
Nature
, vol.441
, pp. 656-659
-
-
Ashworth, J.1
Havranek, J.J.2
Duarte, C.M.3
Sussman, D.4
Stoddard, B.L.5
Baker, D.6
-
3
-
-
0025895183
-
Toward a science of metabolic engineering
-
Bailey JE (1991) Toward a science of metabolic engineering. Science 252:1668-1675.
-
(1991)
Science
, vol.252
, pp. 1668-1675
-
-
Bailey, J.E.1
-
4
-
-
51749088153
-
MetaRoute: Fast search for relevant metabolic routes for interactive network navigation and visualization
-
Blum T and Kohlbacher O (2008) MetaRoute: Fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics 24:2108-2109.
-
(2008)
Bioinformatics
, vol.24
, pp. 2108-2109
-
-
Blum, T.1
Kohlbacher, O.2
-
6
-
-
67649786082
-
Towards the automated engineering of a synthetic genome
-
DOI: 10.1039/b904400k
-
Carrera J, Rodrigo G, Jaramillo A (2009b) Towards the automated engineering of a synthetic genome. Mol Biosyst DOI: 10.1039/b904400k.
-
(2009)
Mol Biosyst
-
-
Carrera, J.1
Rodrigo, G.2
Jaramillo, A.3
-
7
-
-
36249017917
-
Programming gene expression with combinatorial promoters
-
Cox RS, Surette MG and Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol Syst Biol 3:145.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 145
-
-
Cox, R.S.1
Surette, M.G.2
Elowitz, M.B.3
-
8
-
-
23144466440
-
Metabolic pathfinding: Inferring relevant pathways in biochemical networks
-
Croes D, Couche F, Wodak SJ and van Helden J (2005) Metabolic pathfinding: Inferring relevant pathways in biochemical networks. Nucleic Acids Res 33:W326-330.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Croes, D.1
Couche, F.2
Wodak, S.J.3
Van Helden, J.4
-
9
-
-
42549159572
-
OptCircuit: An optimization based method for computational design of genetic circuits
-
Dasika MS and Maranas CD (2008) OptCircuit: An optimization based method for computational design of genetic circuits. BMC Syst Biol 2:24.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 24
-
-
Dasika, M.S.1
Maranas, C.D.2
-
10
-
-
0347635508
-
Design of genetic networks with specified functions by evolution in silico
-
François P and Hakim V (2004) Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci 101:580-585.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 580-585
-
-
François, P.1
Hakim, V.2
-
11
-
-
84900899073
-
-
National center for biotechnology information, Data taken 20th November, 2008
-
Genbank (2008) National center for biotechnology information. A USA national resource of molecular biology information. http://www.ncbi.nlm.nih.gov/ Genbank/index.html. Data taken 20th November, 2008.
-
(2008)
A USA National Resource of Molecular Biology Information
-
-
-
12
-
-
34547609127
-
MetaPath Online: A web server implementation of the network expansion algorithm
-
Handorf T and Ebenhöh O (2007) MetaPath Online: A web server implementation of the network expansion algorithm. Nucleic Acids Res 35:W613-618.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Handorf, T.1
Ebenhöh, O.2
-
13
-
-
0035852623
-
Metabolic engineering of bacteria for environmental applications: Construction of pseudomonas strains for biodegradation of 2-chlorotoluene
-
Haro MA and de Lorenzo V (2001) Metabolic engineering of bacteria for environmental applications: Construction of pseudomonas strains for biodegradation of 2-chlorotoluene. J Biotechnol 85:103-113.
-
(2001)
J Biotechnol
, vol.85
, pp. 103-113
-
-
Haro, M.A.1
De Lorenzo, V.2
-
14
-
-
0037498035
-
Microbial pathway prediction: A functional group approach
-
Hou BK, Wackett LP and Ellis L B M (2003) Microbial pathway prediction: A functional group approach. J Chem Inf Comput Sci 43:1051-1057.
-
(2003)
J Chem Inf Comput Sci
, vol.43
, pp. 1051-1057
-
-
Hou, B.K.1
Wackett, L.P.2
Ellis, L.B.M.3
-
16
-
-
40449116114
-
De novo computational design of retro-aldol enzymes
-
Jiang L, Althoff EA, Clemente FR, Doyle L, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL and Baker D (2008) De novo computational design of retro-aldol enzymes. Science 319:1387-1391.
-
(2008)
Science
, vol.319
, pp. 1387-1391
-
-
Jiang, L.1
Althoff, E.A.2
Clemente, F.R.3
Doyle, L.4
Zanghellini, A.5
Gallaher, J.L.6
Betker, J.L.7
Tanaka, F.8
Barbas, C.F.9
Hilvert, D.10
Houk, K.N.11
Stoddard, B.L.12
Baker, D.13
-
17
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Kanehisa M and Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
18
-
-
27244436714
-
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
-
Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Ahrén D, Tsoka S, Darzentas N, Kunin V and Lçpez-Bigas N (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33:6083-6089.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
Ahrén, D.5
Tsoka, S.6
Darzentas, N.7
Kunin, V.8
Lçpez-Bigas, N.9
-
19
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL and Baker D (2008) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364-1368.
-
(2008)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
20
-
-
8744251043
-
Computational discovery of biochemical routes to specialty chemicals
-
Li C, Henry CS, Jankowski MD, Ionita JA, Hatzimanikatis V and Broadbelt LJ (2004) Computational discovery of biochemical routes to specialty chemicals. Chem Eng Sci 59:5051-5060.
-
(2004)
Chem Eng Sci
, vol.59
, pp. 5051-5060
-
-
Li, C.1
Henry, C.S.2
Jankowski, M.D.3
Ionita, J.A.4
Hatzimanikatis, V.5
Broadbelt, L.J.6
-
21
-
-
0038752617
-
Computational design of receptor and sensor proteins with novel functions
-
Looger LL, Dwyer MA, Smith JJ and Hellinga HW (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423:185-190.
-
(2003)
Nature
, vol.423
, pp. 185-190
-
-
Looger, L.L.1
Dwyer, M.A.2
Smith, J.J.3
Hellinga, H.W.4
-
22
-
-
50549103571
-
Computational design of synthetic gene circuits with composable parts
-
Marchisio MA and Stelling J (2008) Computational design of synthetic gene circuits with composable parts. Bioinformatics 24:1903-1910.
-
(2008)
Bioinformatics
, vol.24
, pp. 1903-1910
-
-
Marchisio, M.A.1
Stelling, J.2
-
23
-
-
0038391517
-
Engineering a mevalonate pathway in Escherichia coli for production of terpenoids
-
Martin JJ, Pitera DJ, Withers ST, Newman JD and Keasling JD (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21:796-802.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 796-802
-
-
Martin, J.J.1
Pitera, D.J.2
Withers, S.T.3
Newman, J.D.4
Keasling, J.D.5
-
24
-
-
7244219911
-
Evolving complex dynamics in electronic models of genetic networks
-
Mason J, Linsay P, Collins JJ and Glass L (2004) Evolving complex dynamics in electronic models of genetic networks. Chaos 14:707-715.
-
(2004)
Chaos
, vol.14
, pp. 707-715
-
-
Mason, J.1
Linsay, P.2
Collins, J.J.3
Glass, L.4
-
26
-
-
33746593012
-
In silico evolution of functional modules in biochemical networks
-
Paladugu SR, Chickarmane V, Deckard A, Frumkin JP, McCormack M and Sauro HM (2006) In silico evolution of functional modules in biochemical networks. IEE Proc Syst Biol 153:223-235.
-
(2006)
IEE Proc Syst Biol
, vol.153
, pp. 223-235
-
-
Paladugu, S.R.1
Chickarmane, V.2
Deckard, A.3
Frumkin, J.P.4
McCormack, M.5
Sauro, H.M.6
-
28
-
-
33645870422
-
Production of the antimalarial drug precursor artemisinic acid in engineered yeast
-
Ro DK, Paradise EM, Ouellet M, Fisher KJ, Ndungum JM, Ho KA, Eachus RA, Ham TS, Kirby J, Chang M C Y, Withers ST, Shiba Y, Sarpong R and Keasling JD (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440:940-943.
-
(2006)
Nature
, vol.440
, pp. 940-943
-
-
Ro, D.K.1
Paradise, E.M.2
Ouellet, M.3
Fisher, K.J.4
Ndungum, J.M.5
Ho, K.A.6
Eachus, R.A.7
Ham, T.S.8
Kirby, J.9
Chang, M.C.Y.10
Withers, S.T.11
Shiba, Y.12
Sarpong, R.13
Keasling, J.D.14
-
29
-
-
34547861255
-
Genetdes: Automatic design of transcriptional networks
-
Rodrigo G, Carrera J and Jaramillo A (2007a) Genetdes: Automatic design of transcriptional networks. Bioinformatics 23:1857-1858.
-
(2007)
Bioinformatics
, vol.23
, pp. 1857-1858
-
-
Rodrigo, G.1
Carrera, J.2
Jaramillo, A.3
-
31
-
-
54949140438
-
DESHARKY: Automatic design of metabolic pathways for optimal cell growth
-
Rodrigo G, Carrera J, Prather KJ and Jaramillo A (2008) DESHARKY: Automatic design of metabolic pathways for optimal cell growth. Bioinformatics 24:2554-2556.
-
(2008)
Bioinformatics
, vol.24
, pp. 2554-2556
-
-
Rodrigo, G.1
Carrera, J.2
Prather, K.J.3
Jaramillo, A.4
-
32
-
-
84900890436
-
Kemp elimination catalysts by computational enzyme design
-
Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS and Baker D (2008) Kemp elimination catalysts by computational enzyme design. Nature 9:1-6.
-
(2008)
Nature
, vol.9
, pp. 1-6
-
-
Röthlisberger, D.1
Khersonsky, O.2
Wollacott, A.M.3
Jiang, L.4
Betker, J.5
Gallaher, J.L.6
Althoff, E.A.7
Zanghellini, A.8
Dym, O.9
Albeck, S.10
Houk, K.N.11
Tawfik, D.S.12
Baker, D.13
-
33
-
-
0024694679
-
Overproduction of glycolytic enzymes in yeast
-
Schaaff I, Heinisch J and Zimmermann FK (1989) Overproduction of glycolytic enzymes in yeast. Yeast 5:285-290.
-
(1989)
Yeast
, vol.5
, pp. 285-290
-
-
Schaaff, I.1
Heinisch, J.2
Zimmermann, F.K.3
-
34
-
-
0345863907
-
BRENDA, the enzyme database: Updates and major new developments
-
Schomburg I, Chang A, Ebeling C, Gremse M, Huhn G and Schomburg D (2004) BRENDA, the enzyme database: Updates and major new developments. Nucleic Acids Res 1:D431-433.
-
(2004)
Nucleic Acids Res
, vol.1
-
-
Schomburg, I.1
Chang, A.2
Ebeling, C.3
Gremse, M.4
Huhn, G.5
Schomburg, D.6
-
36
-
-
45549085296
-
Predictive behavior within microbial genetic networks
-
Tagkopoulos I, Liu Y and Tavazoie S (2008) Predictive behavior within microbial genetic networks. Science 320:1313-1317.
-
(2008)
Science
, vol.320
, pp. 1313-1317
-
-
Tagkopoulos, I.1
Liu, Y.2
Tavazoie, S.3
-
37
-
-
54249113318
-
Higher-order cellular information processing with synthetic RNA devices
-
Win MN and Smolke CD (2008) Higher-order cellular information processing with synthetic RNA devices. Science 322:456-460.
-
(2008)
Science
, vol.322
, pp. 456-460
-
-
Win, M.N.1
Smolke, C.D.2
|