-
1
-
-
45149111660
-
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
-
10.1038/nbt1401, 3108568, 18536691
-
Feist AM, Palsson BO. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 2008, 26:659-667. 10.1038/nbt1401, 3108568, 18536691.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 659-667
-
-
Feist, A.M.1
Palsson, B.O.2
-
2
-
-
84857058761
-
A systems-level approach for metabolic engineering of yeast cell factories
-
10.1111/j.1567-1364.2011.00779.x, 22188344
-
Kim IK, Roldao A, Siewers V, Nielsen J. A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 2012, 12:228-248. 10.1111/j.1567-1364.2011.00779.x, 22188344.
-
(2012)
FEMS Yeast Res
, vol.12
, pp. 228-248
-
-
Kim, I.K.1
Roldao, A.2
Siewers, V.3
Nielsen, J.4
-
3
-
-
0345824737
-
Network component analysis: reconstruction of regulatory signals in biological systems
-
10.1073/pnas.2136632100, 307600, 14673099
-
Liao JC, Boscolo R, Yang YL, Tran LM, Sabatti C, Roychowdhury VP. Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci USA 2003, 100:15522-15527. 10.1073/pnas.2136632100, 307600, 14673099.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 15522-15527
-
-
Liao, J.C.1
Boscolo, R.2
Yang, Y.L.3
Tran, L.M.4
Sabatti, C.5
Roychowdhury, V.P.6
-
4
-
-
34347250494
-
Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli
-
10.1073/pnas.0610888104, 1895976, 17494765
-
Hyduke DR, Jarboe LR, Tran LM, Chou KJ, Liao JC. Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli. Proc Natl Acad Sci USA 2007, 104:8484-8489. 10.1073/pnas.0610888104, 1895976, 17494765.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 8484-8489
-
-
Hyduke, D.R.1
Jarboe, L.R.2
Tran, L.M.3
Chou, K.J.4
Liao, J.C.5
-
5
-
-
77957742371
-
Trimming of mammalian transcriptional networks using network component analysis
-
Tran LM, Hyduke DR, Liao JC. Trimming of mammalian transcriptional networks using network component analysis. BMC Bioinforma 2010, 11:511.
-
(2010)
BMC Bioinforma
, vol.11
, pp. 511
-
-
Tran, L.M.1
Hyduke, D.R.2
Liao, J.C.3
-
6
-
-
0037008673
-
Transcriptional regulation in constraints-based metabolic models of Escherichia coli
-
10.1074/jbc.M201691200, 12006566
-
Covert MW, Palsson BO. 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.O.2
-
7
-
-
67650872959
-
Functional states of the genome-scale Escherichia coli transcriptional regulatory system
-
10.1371/journal.pcbi.1000403, 2685017, 19503608
-
Gianchandani EP, Joyce AR, Palsson BO, 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.O.3
Papin, J.A.4
-
8
-
-
63549148162
-
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization
-
10.1371/journal.pcbi.1000312, 2648898, 19282977
-
Thiele I, Jamshidi N, Fleming RM, Palsson BO. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol 2009, 5:e1000312. 10.1371/journal.pcbi.1000312, 2648898, 19282977.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Thiele, I.1
Jamshidi, N.2
Fleming, R.M.3
Palsson, B.O.4
-
9
-
-
77949773550
-
Towards genome-scale signalling-network reconstructions
-
Hyduke DR, Palsson BO. Towards genome-scale signalling-network reconstructions. Nat Rev Genet 2010, 11:297-307.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 297-307
-
-
Hyduke, D.R.1
Palsson, B.O.2
-
10
-
-
84864843180
-
In silico method for modelling metabolism and gene product expression at genome scale
-
Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun 2012, 3:929.
-
(2012)
Nat Commun
, vol.3
, pp. 929
-
-
Lerman, J.A.1
Hyduke, D.R.2
Latif, H.3
Portnoy, V.A.4
Lewis, N.E.5
Orth, J.D.6
Schrimpe-Rutledge, A.C.7
Smith, R.D.8
Adkins, J.N.9
Zengler, K.10
Palsson, B.O.11
-
11
-
-
41149087177
-
Impact of the solvent capacity constraint on E. coli metabolism
-
10.1186/1752-0509-2-7, 2270259, 18215292
-
Vazquez A, Beg QK, Demenezes MA, Ernst J, Bar-Joseph Z, Barabasi AL, Barabasi AL, Boros LG, Oltvai ZN. Impact of the solvent capacity constraint on E. coli metabolism. BMC Syst Biol 2008, 2:7. 10.1186/1752-0509-2-7, 2270259, 18215292.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 7
-
-
Vazquez, A.1
Beg, Q.K.2
Demenezes, M.A.3
Ernst, J.4
Bar-Joseph, Z.5
Barabasi, A.L.6
Barabasi, A.L.7
Boros, L.G.8
Oltvai, Z.N.9
-
12
-
-
33847797256
-
Thermodynamics-based metabolic flux analysis
-
10.1529/biophysj.106.093138, 1796839, 17172310
-
Henry CS, Broadbelt LJ, Hatzimanikatis V. Thermodynamics-based metabolic flux analysis. Biophys J 2007, 92:1792-1805. 10.1529/biophysj.106.093138, 1796839, 17172310.
-
(2007)
Biophys J
, vol.92
, pp. 1792-1805
-
-
Henry, C.S.1
Broadbelt, L.J.2
Hatzimanikatis, V.3
-
13
-
-
38549140094
-
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
-
10.1093/nar/gkn491, 2238961, 18158297
-
Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 2008, 36:D120-D124. 10.1093/nar/gkn491, 2238961, 18158297.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Gama-Castro, S.1
Jimenez-Jacinto, V.2
Peralta-Gil, M.3
Santos-Zavaleta, A.4
Penaloza-Spinola, M.I.5
Contreras-Moreira, B.6
Segura-Salazar, J.7
Muniz-Rascado, L.8
Martinez-Flores, I.9
Salgado, H.10
Bonavides-Martinez, C.11
Abreu-Goodger, C.12
Rodriguez-Penagos, C.13
Miranda-Rios, J.14
Morett, E.15
Merino, E.16
Huerta, A.M.17
Trevino-Quintanilla, L.18
Collado-Vides, J.19
-
14
-
-
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
-
15
-
-
80052580351
-
Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase
-
10.1038/nature10363, 21849978
-
Frezza C, Zheng L, Folger O, Rajagopalan KN, MacKenzie ED, Jerby L, Micaroni M, Chaneton B, Adam J, Hedley A, Kalna G, Tomlinson IP, Pollard PJ, Watson DG, Deberardinis RJ, Shlomi T, Ruppin E, Gottlieb E. Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. Nature 2011, 477:225-228. 10.1038/nature10363, 21849978.
-
(2011)
Nature
, vol.477
, pp. 225-228
-
-
Frezza, C.1
Zheng, L.2
Folger, O.3
Rajagopalan, K.N.4
MacKenzie, E.D.5
Jerby, L.6
Micaroni, M.7
Chaneton, B.8
Adam, J.9
Hedley, A.10
Kalna, G.11
Tomlinson, I.P.12
Pollard, P.J.13
Watson, D.G.14
Deberardinis, R.J.15
Shlomi, T.16
Ruppin, E.17
Gottlieb, E.18
-
16
-
-
84863331725
-
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation
-
3397418, 22735334
-
Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN, Hyduke DR, Adkins JN, Palsson BO. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol 2012, 8:558. 3397418, 22735334.
-
(2012)
Mol Syst Biol
, vol.8
, pp. 558
-
-
Bordbar, A.1
Mo, M.L.2
Nakayasu, E.S.3
Schrimpe-Rutledge, A.C.4
Kim, Y.M.5
Metz, T.O.6
Jones, M.B.7
Frank, B.C.8
Smith, R.D.9
Peterson, S.N.10
Hyduke, D.R.11
Adkins, J.N.12
Palsson, B.O.13
-
17
-
-
84872093417
-
Analysis of omics data with genome-scale models of metabolism
-
10.1039/c2mb25453k, 23247105
-
Hyduke DR, Lewis NE, Palsson BO. Analysis of omics data with genome-scale models of metabolism. Mol Biosyst 2013, 9:167-174. 10.1039/c2mb25453k, 23247105.
-
(2013)
Mol Biosyst
, vol.9
, pp. 167-174
-
-
Hyduke, D.R.1
Lewis, N.E.2
Palsson, B.O.3
-
18
-
-
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
-
19
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox v2.0
-
10.1038/nprot.2011.308, 3319681, 21886097
-
Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BO. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox v2.0. Nat Protoc 2011, 6:1290-1307. 10.1038/nprot.2011.308, 3319681, 21886097.
-
(2011)
Nat Protoc
, vol.6
, pp. 1290-1307
-
-
Schellenberger, J.1
Que, R.2
Fleming, R.M.3
Thiele, I.4
Orth, J.D.5
Feist, A.M.6
Zielinski, D.C.7
Bordbar, A.8
Lewis, N.E.9
Rahmanian, S.10
Kang, J.11
Hyduke, D.R.12
Palsson, B.O.13
-
20
-
-
84857192122
-
Computational tools for the synthetic design of biochemical pathways
-
10.1038/nrmicro2717, 22266781
-
Medema MH, van Raaphorst R, Takano E, Breitling R. Computational tools for the synthetic design of biochemical pathways. Nat Rev Microbiol 2012, 10:191-202. 10.1038/nrmicro2717, 22266781.
-
(2012)
Nat Rev Microbiol
, vol.10
, pp. 191-202
-
-
Medema, M.H.1
van Raaphorst, R.2
Takano, E.3
Breitling, R.4
-
21
-
-
10644250404
-
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
-
Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, Kovitz BL, Schilstra MJ, Funahashi A, Doyle JC, Kitano H. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Syst Biol (Stevenage) 2004, 1:41-53.
-
(2004)
Syst Biol (Stevenage)
, vol.1
, pp. 41-53
-
-
Hucka, M.1
Finney, A.2
Bornstein, B.J.3
Keating, S.M.4
Shapiro, B.E.5
Matthews, J.6
Kovitz, B.L.7
Schilstra, M.J.8
Funahashi, A.9
Doyle, J.C.10
Kitano, H.11
-
22
-
-
14544268137
-
Uncovering transcriptional regulation of metabolism by using metabolic network topology
-
10.1073/pnas.0406811102, 549453, 15710883
-
Patil KR, Nielsen J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci USA 2005, 102:2685-2689. 10.1073/pnas.0406811102, 549453, 15710883.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 2685-2689
-
-
Patil, K.R.1
Nielsen, J.2
-
24
-
-
79960375921
-
An application programming interface for Cell NetAnalyzer
-
10.1016/j.biosystems.2011.02.002, 21315797
-
Klamt S, von Kamp A. An application programming interface for Cell NetAnalyzer. Biosystems 2011, 105:162-168. 10.1016/j.biosystems.2011.02.002, 21315797.
-
(2011)
Biosystems
, vol.105
, pp. 162-168
-
-
Klamt, S.1
von Kamp, A.2
-
25
-
-
78651553577
-
FASIMU: flexible software for flux-balance computation series in large metabolic networks
-
Hoppe A, Hoffmann S, Gerasch A, Gille C, Holzhutter HG. FASIMU: flexible software for flux-balance computation series in large metabolic networks. BMC Bioinforma 2011, 12:28.
-
(2011)
BMC Bioinforma
, vol.12
, pp. 28
-
-
Hoppe, A.1
Hoffmann, S.2
Gerasch, A.3
Gille, C.4
Holzhutter, H.G.5
-
26
-
-
14644422159
-
Modelling cellular systems with PySCeS
-
10.1093/bioinformatics/bti046, 15454409
-
Olivier BG, Rohwer JM, Hofmeyr JH. Modelling cellular systems with PySCeS. Bioinformatics 2005, 21:560-561. 10.1093/bioinformatics/bti046, 15454409.
-
(2005)
Bioinformatics
, vol.21
, pp. 560-561
-
-
Olivier, B.G.1
Rohwer, J.M.2
Hofmeyr, J.H.3
-
27
-
-
84875973063
-
The RAVEN toolbox and its use for generating a genome-scale metabolic model for penicillium chrysogenum
-
10.1371/journal.pcbi.1002980, 3605104, 23555215
-
Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for penicillium chrysogenum. PLoS Comput Biol 2013, 9:e1002980. 10.1371/journal.pcbi.1002980, 3605104, 23555215.
-
(2013)
PLoS Comput Biol
, vol.9
-
-
Agren, R.1
Liu, L.2
Shoaie, S.3
Vongsangnak, W.4
Nookaew, I.5
Nielsen, J.6
-
28
-
-
47649105109
-
The systems biology research tool: evolvable open-source software
-
10.1186/1752-0509-2-55, 2446383, 18588708
-
Wright J, Wagner A. The systems biology research tool: evolvable open-source software. BMC Syst Biol 2008, 2:55. 10.1186/1752-0509-2-55, 2446383, 18588708.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 55
-
-
Wright, J.1
Wagner, A.2
-
30
-
-
78651467275
-
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
-
10.1186/1752-0509-5-8, 3032673, 21244678
-
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Ozdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjornsdottir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol 2011, 5:8. 10.1186/1752-0509-5-8, 3032673, 21244678.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 8
-
-
Thiele, I.1
Hyduke, D.R.2
Steeb, B.3
Fankam, G.4
Allen, D.K.5
Bazzani, S.6
Charusanti, P.7
Chen, F.C.8
Fleming, R.M.9
Hsiung, C.A.10
De Keersmaecker, S.C.11
Liao, Y.C.12
Marchal, K.13
Mo, M.L.14
Ozdemir, E.15
Raghunathan, A.16
Reed, J.L.17
Shin, S.I.18
Sigurbjornsdottir, S.19
Steinmann, J.20
Sudarsan, S.21
Swainston, N.22
Thijs, I.M.23
Zengler, K.24
Palsson, B.O.25
Adkins, J.N.26
Bumann, D.27
more..
-
31
-
-
80054069179
-
A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
-
3261703, 21988831
-
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BO. A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol Syst Biol 2011, 7:535. 3261703, 21988831.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 535
-
-
Orth, J.D.1
Conrad, T.M.2
Na, J.3
Lerman, J.A.4
Nam, H.5
Feist, A.M.6
Palsson, B.O.7
-
32
-
-
40749162829
-
LibSBML: an API library for SBML
-
10.1093/bioinformatics/btn051, 2517632, 18252737
-
Bornstein BJ, Keating SM, Jouraku A, Hucka M. LibSBML: an API library for SBML. Bioinformatics 2008, 24:880-881. 10.1093/bioinformatics/btn051, 2517632, 18252737.
-
(2008)
Bioinformatics
, vol.24
, pp. 880-881
-
-
Bornstein, B.J.1
Keating, S.M.2
Jouraku, A.3
Hucka, M.4
-
33
-
-
77956696072
-
High-throughput generation, optimization and analysis of genome-scale metabolic models
-
10.1038/nbt.1672, 20802497
-
Henry CS, Dejongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 2010, 28:977-982. 10.1038/nbt.1672, 20802497.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 977-982
-
-
Henry, C.S.1
Dejongh, M.2
Best, A.A.3
Frybarger, P.M.4
Linsay, B.5
Stevens, R.L.6
-
34
-
-
77953934646
-
BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models
-
10.1186/1752-0509-4-92, 2909940, 20587024
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novere N, Laibe C. BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010, 4:92. 10.1186/1752-0509-4-92, 2909940, 20587024.
-
(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.I.10
Snoep, J.L.11
Hucka, M.12
Le Novere, N.13
Laibe, C.14
-
35
-
-
77749320898
-
What is flux balance analysis?
-
10.1038/nbt.1614, 3108565, 20212490
-
Orth JD, Thiele I, Palsson BO. What is flux balance analysis?. Nat Biotechnol 2010, 28:245-248. 10.1038/nbt.1614, 3108565, 20212490.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 245-248
-
-
Orth, J.D.1
Thiele, I.2
Palsson, B.O.3
-
36
-
-
0032800559
-
PH-dependent secretion of SseB, a product of the SPI-2 type III secretion system of Salmonella typhimurium
-
10.1046/j.1365-2958.1999.01527.x, 10447889
-
Beuzon CR, Banks G, Deiwick J, Hensel M, Holden DW. pH-dependent secretion of SseB, a product of the SPI-2 type III secretion system of Salmonella typhimurium. Mol Microbiol 1999, 33:806-816. 10.1046/j.1365-2958.1999.01527.x, 10447889.
-
(1999)
Mol Microbiol
, vol.33
, pp. 806-816
-
-
Beuzon, C.R.1
Banks, G.2
Deiwick, J.3
Hensel, M.4
Holden, D.W.5
-
37
-
-
0001140586
-
Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium
-
10.1099/00221287-19-3-592, 13611202
-
Schaechter M, Maaloe O, Kjeldgaard NO. Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium. J Gen Microbiol 1958, 19:592-606. 10.1099/00221287-19-3-592, 13611202.
-
(1958)
J Gen Microbiol
, vol.19
, pp. 592-606
-
-
Schaechter, M.1
Maaloe, O.2
Kjeldgaard, N.O.3
-
38
-
-
0343035686
-
Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements
-
10.1002/(SICI)1097-0290(19971120)56:4<398::AID-BIT6>3.0.CO;2-J, 18642243
-
Pramanik J, Keasling JD. Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol Bioeng 1997, 56:398-421. 10.1002/(SICI)1097-0290(19971120)56:4<398::AID-BIT6>3.0.CO;2-J, 18642243.
-
(1997)
Biotechnol Bioeng
, vol.56
, pp. 398-421
-
-
Pramanik, J.1
Keasling, J.D.2
-
39
-
-
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
-
40
-
-
79551676901
-
Elimination of thermodynamically infeasible loops in steady-state metabolic models
-
10.1016/j.bpj.2010.12.3707, 3030201, 21281568
-
Schellenberger J, Lewis NE, Palsson BO. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J 2011, 100:544-553. 10.1016/j.bpj.2010.12.3707, 3030201, 21281568.
-
(2011)
Biophys J
, vol.100
, pp. 544-553
-
-
Schellenberger, J.1
Lewis, N.E.2
Palsson, B.O.3
-
42
-
-
84881664821
-
-
mlabwrap http://mlabwrap.sourceforge.net.
-
mlabwrap
-
-
-
43
-
-
84858439602
-
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
-
3536058, 22367118
-
Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 2012, 10:291-305. 3536058, 22367118.
-
(2012)
Nat Rev Microbiol
, vol.10
, pp. 291-305
-
-
Lewis, N.E.1
Nagarajan, H.2
Palsson, B.O.3
-
44
-
-
84881664708
-
-
GLPK http://www.gnu.org/software/glpk.
-
GLPK
-
-
-
47
-
-
79960423002
-
JSBML: a flexible Java library for working with SBML
-
10.1093/bioinformatics/btr361, 3137227, 21697129
-
Drager A, Rodriguez N, Dumousseau M, Dorr A, Wrzodek C, Le Novere N, Zell A, Hucka M. JSBML: a flexible Java library for working with SBML. Bioinformatics 2011, 27:2167-2168. 10.1093/bioinformatics/btr361, 3137227, 21697129.
-
(2011)
Bioinformatics
, vol.27
, pp. 2167-2168
-
-
Drager, A.1
Rodriguez, N.2
Dumousseau, M.3
Dorr, A.4
Wrzodek, C.5
Le Novere, N.6
Zell, A.7
Hucka, M.8
-
48
-
-
84902140029
-
-
GLPK for Java http://glpk-java.sourceforge.net.
-
GLPK for Java
-
-
|