-
1
-
-
6944224154
-
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
-
10.1038/ng1432, 15448692
-
Fong SS, Palsson B. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 2004, 36:1056-1058. 10.1038/ng1432, 15448692.
-
(2004)
Nat Genet
, vol.36
, pp. 1056-1058
-
-
Fong, S.S.1
Palsson, B.2
-
2
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
10.1073/pnas.232349399, 137552, 12415116
-
Segrè D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 2002, 99:15112-15117. 10.1073/pnas.232349399, 137552, 12415116.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 15112-15117
-
-
Segrè, D.1
Vitkup, D.2
Church, G.M.3
-
3
-
-
19644386033
-
Regulatory on/off minimization of metabolic flux changes after genetic perturbations
-
10.1073/pnas.0406346102, 1140402, 15897462
-
Shlomi T, Berkman O, Ruppin E. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 2005, 102:7695-7700. 10.1073/pnas.0406346102, 1140402, 15897462.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 7695-7700
-
-
Shlomi, T.1
Berkman, O.2
Ruppin, E.3
-
4
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
10.1038/msb4100162, 1949037, 17625511
-
Schuetz R, Kuepfer L, Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 2007, 3:119. 10.1038/msb4100162, 1949037, 17625511.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
5
-
-
8744224466
-
OptStrain: A computational framework for redesign of microbial production systems
-
10.1101/gr.2872004, 525696, 15520298
-
Pharkya P, Burgard AP, Maranas CD. OptStrain: A computational framework for redesign of microbial production systems. Genome Res 2004, 14:2367-2376. 10.1101/gr.2872004, 525696, 15520298.
-
(2004)
Genome Res
, vol.14
, pp. 2367-2376
-
-
Pharkya, P.1
Burgard, A.P.2
Maranas, C.D.3
-
6
-
-
34249934691
-
Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation
-
10.1073/pnas.0702609104, 1857225, 17463081
-
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 USA 2007, 104:7797-7802. 10.1073/pnas.0702609104, 1857225, 17463081.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 7797-7802
-
-
Park, J.H.1
Lee, K.H.2
Kim, T.Y.3
Lee, S.Y.4
-
7
-
-
22844452835
-
Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets
-
10.1038/nbt1083, 15821729
-
Alper H, Miyaoku K, Stephanopoulos G. Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnol 2005, 23:612-616. 10.1038/nbt1083, 15821729.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 612-616
-
-
Alper, H.1
Miyaoku, K.2
Stephanopoulos, G.3
-
8
-
-
0242487787
-
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
10.1002/bit.10803, 14595777
-
Burgard AP, Pharkya P, Maranas CD. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003, 84:647-657. 10.1002/bit.10803, 14595777.
-
(2003)
Biotechnol Bioeng
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
9
-
-
25144505718
-
In silico design and adaptive evolution of Escherichia coli for production of lactic acid
-
10.1002/bit.20542, 15962337
-
Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson B. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 2005, 91:643-648. 10.1002/bit.20542, 15962337.
-
(2005)
Biotechnol Bioeng
, vol.91
, pp. 643-648
-
-
Fong, S.S.1
Burgard, A.P.2
Herring, C.D.3
Knight, E.M.4
Blattner, F.R.5
Maranas, C.D.6
Palsson, B.7
-
10
-
-
77954087740
-
Methods and organisms for the growth-coupled production of succinate
-
WO/2007/030830
-
Burgard AP, Van Dien SJ. Methods and organisms for the growth-coupled production of succinate. Patent 2007, WO/2007/030830.
-
(2007)
Patent
-
-
Burgard, A.P.1
Van Dien, S.J.2
-
11
-
-
30044437327
-
Evolutionary programming as a platform for in silico metabolic engineering
-
10.1186/1471-2105-6-308, 1327682, 16375763
-
Patil K, Rocha I, Forster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2005, 6:308. 10.1186/1471-2105-6-308, 1327682, 16375763.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 308
-
-
Patil, K.1
Rocha, I.2
Forster, J.3
Nielsen, J.4
-
12
-
-
29544436058
-
An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems
-
10.1016/j.ymben.2005.08.003, 16199194
-
Pharkya P, Maranas CD. An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 2006, 8:1-13. 10.1016/j.ymben.2005.08.003, 16199194.
-
(2006)
Metab Eng
, vol.8
, pp. 1-13
-
-
Pharkya, P.1
Maranas, C.D.2
-
13
-
-
69249146187
-
Large-scale identification of genetic design strategies using local search
-
10.1038/msb.2009.57, 2736654, 19690565
-
Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM. Large-scale identification of genetic design strategies using local search. Mol Syst Biol 2009, 5:296. 10.1038/msb.2009.57, 2736654, 19690565.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 296
-
-
Lun, D.S.1
Rockwell, G.2
Guido, N.J.3
Baym, M.4
Kelner, J.A.5
Berger, B.6
Galagan, J.E.7
Church, G.M.8
-
14
-
-
0037008673
-
Transcriptional regulation in constraints-based metabolic models of Escherichia coli
-
10.1074/jbc.M201691200, 12006566
-
Covert MW, Palsson B. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 2002, 277:28058-28064. 10.1074/jbc.M201691200, 12006566.
-
(2002)
J Biol Chem
, vol.277
, pp. 28058-28064
-
-
Covert, M.W.1
Palsson, B.2
-
15
-
-
34247183123
-
A genome-scale computational study of the interplay between transcriptional regulation and metabolism
-
10.1038/msb4100141, 1865583, 17437026
-
Shlomi T, Eisenberg Y, Sharan R, Ruppin E. A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol 2007, 3:101. 10.1038/msb4100141, 1865583, 17437026.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 101
-
-
Shlomi, T.1
Eisenberg, Y.2
Sharan, R.3
Ruppin, E.4
-
16
-
-
67650872959
-
Functional states of the genome-scale Escherichia Coli transcriptional regulatory system
-
10.1371/journal.pcbi.1000403, 2685017, 19503608
-
Gianchandani EP, Joyce AR, Palsson B, Papin JA. Functional states of the genome-scale Escherichia Coli transcriptional regulatory system. PLoS Comput Biol 2009, 5:e1000403. 10.1371/journal.pcbi.1000403, 2685017, 19503608.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Gianchandani, E.P.1
Joyce, A.R.2
Palsson, B.3
Papin, J.A.4
-
17
-
-
69249102097
-
Genome-scale gene/reaction essentiality and synthetic lethality analysis
-
10.1038/msb.2009.56, 2736653, 19690570
-
Suthers PF, Zomorrodi A, Maranas CD. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol 2009, 5:301. 10.1038/msb.2009.56, 2736653, 19690570.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 301
-
-
Suthers, P.F.1
Zomorrodi, A.2
Maranas, C.D.3
-
18
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
-
10.1186/gb-2003-4-9-r54, 193654, 12952533
-
Reed JL, Vo TD, Schilling CH, Palsson B. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4:R54. 10.1186/gb-2003-4-9-r54, 193654, 12952533.
-
(2003)
Genome Biol
, vol.4
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.4
-
19
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
10.1038/nature02456, 15129285
-
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson B. Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429:92-96. 10.1038/nature02456, 15129285.
-
(2004)
Nature
, vol.429
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
Reed, J.L.3
Herrgard, M.J.4
Palsson, B.5
-
20
-
-
38049001166
-
Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
-
10.1038/nature06450, 18172501
-
Atsumi S, Hanai T, Liao JC. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:86-89. 10.1038/nature06450, 18172501.
-
(2008)
Nature
, vol.451
, pp. 86-89
-
-
Atsumi, S.1
Hanai, T.2
Liao, J.C.3
-
21
-
-
0028146781
-
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
-
201879, 7986045
-
Varma A, Palsson B. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 1994, 60:3724-3731. 201879, 7986045.
-
(1994)
Appl Environ Microbiol
, vol.60
, pp. 3724-3731
-
-
Varma, A.1
Palsson, B.2
-
22
-
-
0028131269
-
An Escherichia coli K-12 tktA tktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth
-
196835, 7928977
-
Zhao G, Winkler ME. An Escherichia coli K-12 tktA tktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth. J Bacteriol 1994, 176:6134-6138. 196835, 7928977.
-
(1994)
J Bacteriol
, vol.176
, pp. 6134-6138
-
-
Zhao, G.1
Winkler, M.E.2
-
23
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
10.1038/msb4100155, 1911197, 17593909
-
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson B. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 2007, 3:121. 10.1038/msb4100155, 1911197, 17593909.
-
(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.9
-
24
-
-
33751567092
-
Experimental and computational assessment of conditionally essential genes in Escherichia coli
-
10.1128/JB.00740-06, 1698209, 17012394
-
Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson B, Agarwalla S. Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol 2006, 188:8259-8271. 10.1128/JB.00740-06, 1698209, 17012394.
-
(2006)
J Bacteriol
, vol.188
, pp. 8259-8271
-
-
Joyce, A.R.1
Reed, J.L.2
White, A.3
Edwards, R.4
Osterman, A.5
Baba, T.6
Mori, H.7
Lesely, S.A.8
Palsson, B.9
Agarwalla, S.10
-
25
-
-
31544450286
-
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection
-
2006.0008
-
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006, 2. 2006.0008.
-
(2006)
Mol Syst Biol
, vol.2
-
-
Baba, T.1
Ara, T.2
Hasegawa, M.3
Takai, Y.4
Okumura, Y.5
Baba, M.6
Datsenko, K.A.7
Tomita, M.8
Wanner, B.L.9
Mori, H.10
-
26
-
-
33947357776
-
Construction of an Escherichia coli K-12 mutant for homoethanologenic fermentation of glucose or xylose without foreign genes
-
10.1128/AEM.02456-06, 1828829, 17259366
-
Kim Y, Ingram LO, Shanmugam KT. Construction of an Escherichia coli K-12 mutant for homoethanologenic fermentation of glucose or xylose without foreign genes. Appl Environ Microbiol 2007, 73:1766-1771. 10.1128/AEM.02456-06, 1828829, 17259366.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 1766-1771
-
-
Kim, Y.1
Ingram, L.O.2
Shanmugam, K.T.3
-
27
-
-
0029975820
-
Stabilization of pet operon plasmids and ethanol production in Escherichia coli strains lacking lactate dehydrogenase and pyruvate formate-lyase activities
-
168284, 8953729
-
Hespell RB, Wyckoff H, Dien BS, Bothast RJ. Stabilization of pet operon plasmids and ethanol production in Escherichia coli strains lacking lactate dehydrogenase and pyruvate formate-lyase activities. Appl Environ Microbiol 1996, 62:4594-4597. 168284, 8953729.
-
(1996)
Appl Environ Microbiol
, vol.62
, pp. 4594-4597
-
-
Hespell, R.B.1
Wyckoff, H.2
Dien, B.S.3
Bothast, R.J.4
-
28
-
-
2442545374
-
The effect of pfl gene knockout on the metabolism for optically pure D-lactate production by Escherichia coli
-
10.1007/s00253-003-1499-9, 14673546
-
Zhu J, Shimizu K. The effect of pfl gene knockout on the metabolism for optically pure D-lactate production by Escherichia coli. Appl Microbiol Biotechnol 2004, 64:367-375. 10.1007/s00253-003-1499-9, 14673546.
-
(2004)
Appl Microbiol Biotechnol
, vol.64
, pp. 367-375
-
-
Zhu, J.1
Shimizu, K.2
-
29
-
-
15944366483
-
Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses
-
10.1002/bit.20381, 15669087
-
Levanon SS, San K-Y, Bennett GN. Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses. Biotechnol Bioeng 2005, 89:556-564. 10.1002/bit.20381, 15669087.
-
(2005)
Biotechnol Bioeng
, vol.89
, pp. 556-564
-
-
Levanon, S.S.1
San, K.-Y.2
Bennett, G.N.3
-
30
-
-
44349173795
-
Dihydrolipoamide dehydrogenase mutation alters the NADH sensitivity of pyruvate dehydrogenase complex of Escherichia coli K-12
-
10.1128/JB.00104-08, 2395023, 18375566
-
Kim Y, Ingram LO, Shanmugam KT. Dihydrolipoamide dehydrogenase mutation alters the NADH sensitivity of pyruvate dehydrogenase complex of Escherichia coli K-12. J Bacteriol 2008, 190:3851-3858. 10.1128/JB.00104-08, 2395023, 18375566.
-
(2008)
J Bacteriol
, vol.190
, pp. 3851-3858
-
-
Kim, Y.1
Ingram, L.O.2
Shanmugam, K.T.3
-
31
-
-
0037560068
-
The effect of acetate pathway mutations on the production of pyruvate in Escherichia coli
-
10.1007/s00253-003-1234-6, 12835924
-
Tomar A, Eiteman MA, Altman E. The effect of acetate pathway mutations on the production of pyruvate in Escherichia coli. Appl Microbiol Biotechnol 2003, 62:76-82. 10.1007/s00253-003-1234-6, 12835924.
-
(2003)
Appl Microbiol Biotechnol
, vol.62
, pp. 76-82
-
-
Tomar, A.1
Eiteman, M.A.2
Altman, E.3
-
32
-
-
1442306213
-
Engineering Escherichia coli for efficient conversion of glucose to pyruvate
-
10.1073/pnas.0308171100, 356934, 14982993
-
Causey TB, Shanmugam KT, Yomano LP, Ingram LO. Engineering Escherichia coli for efficient conversion of glucose to pyruvate. Proc Natl Acad Sci USA 2004, 101:2235-2240. 10.1073/pnas.0308171100, 356934, 14982993.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 2235-2240
-
-
Causey, T.B.1
Shanmugam, K.T.2
Yomano, L.P.3
Ingram, L.O.4
-
33
-
-
16344391449
-
Redistribution of metabolic fluxes in the central aerobic metabolic pathway of E. coli mutant strains with deletion of the ackA-pta and poxB pathways for the synthesis of isoamyl acetate
-
Dittrich CR, Vadali RV, Bennett GN, San K-Y. Redistribution of metabolic fluxes in the central aerobic metabolic pathway of E. coli mutant strains with deletion of the ackA-pta and poxB pathways for the synthesis of isoamyl acetate. Biotechnol Progr 2005, 21:627-631.
-
(2005)
Biotechnol Progr
, vol.21
, pp. 627-631
-
-
Dittrich, C.R.1
Vadali, R.V.2
Bennett, G.N.3
San, K.-Y.4
-
34
-
-
0031691147
-
Methylglyoxal production in bacteria: suicide or survival?
-
10.1007/s002030050635, 9732434
-
Ferguson GP, Tötemeyer S, MacLean MJ, Booth IR. Methylglyoxal production in bacteria: suicide or survival?. Arch Microbiol 1998, 170:209-218. 10.1007/s002030050635, 9732434.
-
(1998)
Arch Microbiol
, vol.170
, pp. 209-218
-
-
Ferguson, G.P.1
Tötemeyer, S.2
MacLean, M.J.3
Booth, I.R.4
-
35
-
-
26844512919
-
Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate:sugar phosphotransferase system
-
10.1186/1475-2859-4-14, 1156936, 15904518
-
Gosset G. Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate:sugar phosphotransferase system. Microb Cell Fact 2005, 4:14. 10.1186/1475-2859-4-14, 1156936, 15904518.
-
(2005)
Microb Cell Fact
, vol.4
, pp. 14
-
-
Gosset, G.1
-
36
-
-
0028129875
-
Why does Escherichia coli have two primary pathways for synthesis of glutamate?
-
196288, 7913929
-
Helling RB. Why does Escherichia coli have two primary pathways for synthesis of glutamate?. J Bacteriol 1994, 176:4664-4668. 196288, 7913929.
-
(1994)
J Bacteriol
, vol.176
, pp. 4664-4668
-
-
Helling, R.B.1
-
37
-
-
45749137679
-
Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses
-
10.1128/AEM.02708-07, 2446564, 18424547
-
Trinh CT, Unrean P, Srienc F. Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses. Appl Environ Microbiol 2008, 74:3634-3643. 10.1128/AEM.02708-07, 2446564, 18424547.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 3634-3643
-
-
Trinh, C.T.1
Unrean, P.2
Srienc, F.3
-
38
-
-
33751544539
-
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
-
10.1038/ng1906, 17086184
-
Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, Boom D, Cantor CR, Palsson BO. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 2006, 38:1406-1412. 10.1038/ng1906, 17086184.
-
(2006)
Nat Genet
, vol.38
, pp. 1406-1412
-
-
Herring, C.D.1
Raghunathan, A.2
Honisch, C.3
Patel, T.4
Applebee, M.K.5
Joyce, A.R.6
Albert, T.J.7
Blattner, F.R.8
Boom, D.9
Cantor, C.R.10
Palsson, B.O.11
-
39
-
-
0142152457
-
Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model
-
10.1128/JB.185.21.6400-6408.2003, 219384, 14563875
-
Fong SS, Marciniak JY, Palsson B. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J Bacteriol 2003, 185:6400-6408. 10.1128/JB.185.21.6400-6408.2003, 219384, 14563875.
-
(2003)
J Bacteriol
, vol.185
, pp. 6400-6408
-
-
Fong, S.S.1
Marciniak, J.Y.2
Palsson, B.3
-
40
-
-
25844495901
-
Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
-
10.1101/gr.3832305, 1240078, 16204189
-
Fong SS, Joyce AR, Palsson B. Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res 2005, 15:1365-1372. 10.1101/gr.3832305, 1240078, 16204189.
-
(2005)
Genome Res
, vol.15
, pp. 1365-1372
-
-
Fong, S.S.1
Joyce, A.R.2
Palsson, B.3
-
41
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
10.1126/science.1081900, 12843395
-
Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003, 301:102-105. 10.1126/science.1081900, 12843395.
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
42
-
-
70049110173
-
Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production
-
10.1371/journal.pcbi.1000489, 2726785, 19714220
-
Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol 2009, 5:e1000489. 10.1371/journal.pcbi.1000489, 2726785, 19714220.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Colijn, C.1
Brandes, A.2
Zucker, J.3
Lun, D.S.4
Weiner, B.5
Farhat, M.R.6
Cheng, T.Y.7
Moody, D.B.8
Murray, M.9
Galagan, J.E.10
-
43
-
-
51349092391
-
Network-based prediction of human tissue-specific metabolism
-
10.1038/nbt.1487, 18711341
-
Shlomi T, Cabili MN, Herrgard MJ, Palsson BO, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 2008, 26:1003-1010. 10.1038/nbt.1487, 18711341.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1003-1010
-
-
Shlomi, T.1
Cabili, M.N.2
Herrgard, M.J.3
Palsson, B.O.4
Ruppin, E.5
-
44
-
-
66149122278
-
Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p
-
10.1073/pnas.0811091106, 2672541, 19346491
-
Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci USA 2009, 106:6477-6482. 10.1073/pnas.0811091106, 2672541, 19346491.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 6477-6482
-
-
Moxley, J.F.1
Jewett, M.C.2
Antoniewicz, M.R.3
Villas-Boas, S.G.4
Alper, H.5
Wheeler, R.T.6
Tong, L.7
Hinnebusch, A.G.8
Ideker, T.9
Nielsen, J.10
Stephanopoulos, G.11
-
45
-
-
70449592325
-
Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
-
10.1016/j.ymben.2009.07.001, 19619667
-
Asadollahi MA, Maury J, Patil KR, Schalk M, Clark A, Nielsen J. Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab Eng 2009, 11:328-334. 10.1016/j.ymben.2009.07.001, 19619667.
-
(2009)
Metab Eng
, vol.11
, pp. 328-334
-
-
Asadollahi, M.A.1
Maury, J.2
Patil, K.R.3
Schalk, M.4
Clark, A.5
Nielsen, J.6
-
46
-
-
34548219522
-
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
-
10.1021/cr068309+, 2643304, 17636889
-
Rodionov DA. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev 2007, 107:3467-3497. 10.1021/cr068309+, 2643304, 17636889.
-
(2007)
Chem Rev
, vol.107
, pp. 3467-3497
-
-
Rodionov, D.A.1
-
47
-
-
33646920070
-
Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach
-
10.1371/journal.pcbi.0020052, 1463018,1463018, 16710450
-
Barrett CL, Palsson BO. Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol 2006, 2:e52. 10.1371/journal.pcbi.0020052, 1463018,1463018, 16710450.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Barrett, C.L.1
Palsson, B.O.2
-
48
-
-
34548499877
-
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing
-
10.1186/1471-2105-8-293, 1964768, 17683642
-
Rodriguez-Penagos C, Salgado H, Martinez-Flores I, Collado-Vides J. Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics 2007, 8:293. 10.1186/1471-2105-8-293, 1964768, 17683642.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 293
-
-
Rodriguez-Penagos, C.1
Salgado, H.2
Martinez-Flores, I.3
Collado-Vides, J.4
-
49
-
-
62649125796
-
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms
-
10.1186/1752-0509-3-8, 2653031, 19146695
-
Baumbach J, Rahmann S, Tauch A. Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst Biol 2009, 3:8. 10.1186/1752-0509-3-8, 2653031, 19146695.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 8
-
-
Baumbach, J.1
Rahmann, S.2
Tauch, A.3
-
50
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
10.1371/journal.pbio.0050008, 1764438,1764438, 17214507
-
Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007, 5:e8. 10.1371/journal.pbio.0050008, 1764438,1764438, 17214507.
-
(2007)
PLoS Biol
, vol.5
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
Kasif, S.7
Collins, J.J.8
Gardner, T.S.9
-
51
-
-
67249157808
-
Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes
-
10.1093/nar/gkp248, 2691844, 19383880
-
Zhang S, Xu M, Li S, Su Z. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Res 2009, 37:e72. 10.1093/nar/gkp248, 2691844, 19383880.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Zhang, S.1
Xu, M.2
Li, S.3
Su, Z.4
-
52
-
-
28444484981
-
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
-
10.1073/pnas.0505147102, 1297658, 16301543
-
Wang T, Stormo GD. Identifying the conserved network of cis-regulatory sites of a eukaryotic genome. Proc Natl Acad Sci USA 2005, 102:17400-17405. 10.1073/pnas.0505147102, 1297658, 16301543.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 17400-17405
-
-
Wang, T.1
Stormo, G.D.2
-
53
-
-
0346328227
-
Metabolic engineering for drug discovery and development
-
10.1038/nrd1256, 14654799
-
Khosla C, Keasling JD. Metabolic engineering for drug discovery and development. Nat Rev Drug Discov 2003, 2:1019-1025. 10.1038/nrd1256, 14654799.
-
(2003)
Nat Rev Drug Discov
, vol.2
, pp. 1019-1025
-
-
Khosla, C.1
Keasling, J.D.2
-
54
-
-
45149111660
-
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
-
10.1038/nbt1401, 18536691
-
Feist AM, Palsson B. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 2008, 26:659-667. 10.1038/nbt1401, 18536691.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 659-667
-
-
Feist, A.M.1
Palsson, B.2
-
55
-
-
70349281876
-
Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?
-
10.1038/nrmicro2186, 19756010
-
Alper H, Stephanopoulos G. Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?. Nat Rev Microbiol 2009, 7:715-723. 10.1038/nrmicro2186, 19756010.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 715-723
-
-
Alper, H.1
Stephanopoulos, G.2
|