-
1
-
-
39449095000
-
Stoichiometric modelling of cell metabolism
-
10.1263/jbb.105.1, 18295713
-
Llaneras F, Pico J. Stoichiometric modelling of cell metabolism. J Biosci Bioeng 2008, 105:1-11. 10.1263/jbb.105.1, 18295713.
-
(2008)
J Biosci Bioeng
, vol.105
, pp. 1-11
-
-
Llaneras, F.1
Pico, J.2
-
2
-
-
0003490410
-
-
Reading, Mass.: Addison-Wesley Pub
-
Strogatz SH. Nonlinear dynamics and Chaos: with applications to physics, biology, chemistry, and engineering 1994, Reading, Mass.: Addison-Wesley Pub.
-
(1994)
Nonlinear dynamics and Chaos: with applications to physics, biology, chemistry, and engineering
-
-
Strogatz, S.H.1
-
3
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
10.1073/pnas.232349399, 137552, 12415116
-
Segre 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
-
-
Segre, D.1
Vitkup, D.2
Church, G.M.3
-
6
-
-
0028146781
-
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
-
201879, 7986045
-
Varma A, Palsson BO. 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.O.2
-
7
-
-
44949225040
-
Context-specific metabolic networks are consistent with experiments
-
10.1371/journal.pcbi.1000082, 2366062, 18483554
-
Becker SA, Palsson BO. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 2008, 4:e1000082. 10.1371/journal.pcbi.1000082, 2366062, 18483554.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Becker, S.A.1
Palsson, B.O.2
-
8
-
-
67449096729
-
Flux balance analysis of biological systems: applications and challenges
-
10.1093/bib/bbp011, 19287049
-
Raman K, Chandra N. Flux balance analysis of biological systems: applications and challenges. Brief Bioinform 2009, 10:435-449. 10.1093/bib/bbp011, 19287049.
-
(2009)
Brief Bioinform
, vol.10
, pp. 435-449
-
-
Raman, K.1
Chandra, N.2
-
9
-
-
9544253891
-
Genome-scale models of microbial cells: evaluating the consequences of constraints
-
10.1038/nrmicro1023, 15494745
-
Price ND, Reed JL, Palsson BO. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2004, 2:886-897. 10.1038/nrmicro1023, 15494745.
-
(2004)
Nat Rev Microbiol
, vol.2
, pp. 886-897
-
-
Price, N.D.1
Reed, J.L.2
Palsson, B.O.3
-
10
-
-
65649126411
-
Flux balance analysis: interrogating genome-scale metabolic networks
-
Oberhardt MA, Chavali AK, Papin JA. Flux balance analysis: interrogating genome-scale metabolic networks. Methods Mol Biol 2009, 500:61-80.
-
(2009)
Methods Mol Biol
, vol.500
, pp. 61-80
-
-
Oberhardt, M.A.1
Chavali, A.K.2
Papin, J.A.3
-
11
-
-
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
-
12
-
-
39149119221
-
Predicting synthetic rescues in metabolic networks
-
10.1038/msb.2008.1, 2267730, 18277384
-
Motter AE, Gulbahce N, Almaas E, Barabasi AL. Predicting synthetic rescues in metabolic networks. Mol Syst Biol 2008, 4:168. 10.1038/msb.2008.1, 2267730, 18277384.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 168
-
-
Motter, A.E.1
Gulbahce, N.2
Almaas, E.3
Barabasi, A.L.4
-
13
-
-
23644452487
-
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants
-
10.1128/JB.187.16.5818-5830.2005, 1196094, 16077130
-
Thiele I, Vo TD, Price ND, Palsson BO. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol 2005, 187:5818-5830. 10.1128/JB.187.16.5818-5830.2005, 1196094, 16077130.
-
(2005)
J Bacteriol
, vol.187
, pp. 5818-5830
-
-
Thiele, I.1
Vo, T.D.2
Price, N.D.3
Palsson, B.O.4
-
14
-
-
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
-
15
-
-
18744380689
-
Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities
-
10.1093/bioinformatics/bti245, 15671116
-
Imielinski M, Belta C, Halasz A, Rubin H. Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities. Bioinformatics 2005, 21:2008-2016. 10.1093/bioinformatics/bti245, 15671116.
-
(2005)
Bioinformatics
, vol.21
, pp. 2008-2016
-
-
Imielinski, M.1
Belta, C.2
Halasz, A.3
Rubin, H.4
-
16
-
-
35348893696
-
Metabolite essentiality elucidates robustness of Escherichia coli metabolism
-
10.1073/pnas.0703262104, 1947999,1947999, 17698812
-
Kim PJ, Lee DY, Kim TY, Lee KH, Jeong H, Lee SY, Park S. Metabolite essentiality elucidates robustness of Escherichia coli metabolism. Proc Natl Acad Sci USA 2007, 104:13638-13642. 10.1073/pnas.0703262104, 1947999,1947999, 17698812.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 13638-13642
-
-
Kim, P.J.1
Lee, D.Y.2
Kim, T.Y.3
Lee, K.H.4
Jeong, H.5
Lee, S.Y.6
Park, S.7
-
17
-
-
73849129785
-
Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks
-
Kim TY, Kim HU, Lee SY. Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks. Metab Eng 2009,
-
(2009)
Metab Eng
-
-
Kim, T.Y.1
Kim, H.U.2
Lee, S.Y.3
-
18
-
-
0038434059
-
Metabolites: a helping hand for pathway evolution?
-
10.1016/S0968-0004(03)00114-2, 12826406
-
Schmidt S, Sunyaev S, Bork P, Dandekar T. Metabolites: a helping hand for pathway evolution?. Trends Biochem Sci 2003, 28:336-341. 10.1016/S0968-0004(03)00114-2, 12826406.
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 336-341
-
-
Schmidt, S.1
Sunyaev, S.2
Bork, P.3
Dandekar, T.4
-
19
-
-
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 BO. 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.O.9
-
21
-
-
0027223982
-
Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates
-
182307, 8368835
-
Varma A, Boesch BW, Palsson BO. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol 1993, 59:2465-2473. 182307, 8368835.
-
(1993)
Appl Environ Microbiol
, vol.59
, pp. 2465-2473
-
-
Varma, A.1
Boesch, B.W.2
Palsson, B.O.3
-
22
-
-
0042093610
-
The connectivity structure, giant strong component and centrality of metabolic networks
-
10.1093/bioinformatics/btg177, 12874056
-
Ma HW, Zeng AP. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003, 19:1423-1430. 10.1093/bioinformatics/btg177, 12874056.
-
(2003)
Bioinformatics
, vol.19
, pp. 1423-1430
-
-
Ma, H.W.1
Zeng, A.P.2
-
23
-
-
1242274402
-
Flux coupling analysis of genome-scale metabolic network reconstructions
-
10.1101/gr.1926504, 327106, 14718379
-
Burgard AP, Nikolaev EV, Schilling CH, Maranas CD. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res 2004, 14:301-312. 10.1101/gr.1926504, 327106, 14718379.
-
(2004)
Genome Res
, vol.14
, pp. 301-312
-
-
Burgard, A.P.1
Nikolaev, E.V.2
Schilling, C.H.3
Maranas, C.D.4
-
24
-
-
0034615791
-
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
-
10.1006/jtbi.2000.1073, 10716907
-
Schilling CH, Letscher D, Palsson BO. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol 2000, 203:229-248. 10.1006/jtbi.2000.1073, 10716907.
-
(2000)
J Theor Biol
, vol.203
, pp. 229-248
-
-
Schilling, C.H.1
Letscher, D.2
Palsson, B.O.3
-
25
-
-
0141504252
-
Experimental determination and system level analysis of essential genes in Escherichia coli MG1655
-
10.1128/JB.185.19.5673-5684.2003, 193955, 13129938
-
Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, et al. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 2003, 185:5673-5684. 10.1128/JB.185.19.5673-5684.2003, 193955, 13129938.
-
(2003)
J Bacteriol
, vol.185
, pp. 5673-5684
-
-
Gerdes, S.Y.1
Scholle, M.D.2
Campbell, J.W.3
Balazsi, G.4
Ravasz, E.5
Daugherty, M.D.6
Somera, A.L.7
Kyrpides, N.C.8
Anderson, I.9
Gelfand, M.S.10
-
26
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
10.1016/j.ymben.2003.09.002, 14642354
-
Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 2003, 5:264-276. 10.1016/j.ymben.2003.09.002, 14642354.
-
(2003)
Metab Eng
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
28
-
-
34547676311
-
Optimization based automated curation of metabolic reconstructions
-
10.1186/1471-2105-8-212, 1933441, 17584497
-
Satish Kumar V, Dasika MS, Maranas CD. Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 2007, 8:212. 10.1186/1471-2105-8-212, 1933441, 17584497.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 212
-
-
Satish Kumar, V.1
Dasika, M.S.2
Maranas, C.D.3
-
29
-
-
29144484729
-
Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation
-
10.1128/AEM.71.12.7880-7887.2005, 1317394, 16332763
-
Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY. Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl Environ Microbiol 2005, 71:7880-7887. 10.1128/AEM.71.12.7880-7887.2005, 1317394, 16332763.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 7880-7887
-
-
Lee, S.J.1
Lee, D.Y.2
Kim, T.Y.3
Kim, B.H.4
Lee, J.5
Lee, S.Y.6
|