-
2
-
-
24944546402
-
Biotechnology - a sustainable alternative for chemical industry
-
10.1016/j.biotechadv.2005.03.004, 15919172
-
Gavrilescu M, Chisti Y. Biotechnology - a sustainable alternative for chemical industry. Biotechnology Advances 2005, 23:471-499. 10.1016/j.biotechadv.2005.03.004, 15919172.
-
(2005)
Biotechnology Advances
, vol.23
, pp. 471-499
-
-
Gavrilescu, M.1
Chisti, Y.2
-
3
-
-
33847030736
-
Industrial biotechnology for the production of bio-based chemicals - a cradle-to-grave perspective
-
10.1016/j.tibtech.2007.01.001, 17234288
-
Hatti-Kaul R, Tornvall U, Gustafsson L, Borjesson P. Industrial biotechnology for the production of bio-based chemicals - a cradle-to-grave perspective. Trends in Biotechnology 2007, 25:119-124. 10.1016/j.tibtech.2007.01.001, 17234288.
-
(2007)
Trends in Biotechnology
, vol.25
, pp. 119-124
-
-
Hatti-Kaul, R.1
Tornvall, U.2
Gustafsson, L.3
Borjesson, P.4
-
4
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
-
10.1038/73786, 10700151
-
Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnology 2000, 18:326-332. 10.1038/73786, 10700151.
-
(2000)
Nature Biotechnology
, vol.18
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
5
-
-
33847073370
-
Expanding the metabolic engineering toolbox: more options to engineer cells
-
10.1016/j.tibtech.2007.01.003, 17254656
-
Tyo KE, Alper HS, Stephanopoulos GN. Expanding the metabolic engineering toolbox: more options to engineer cells. Trends in Biotechnology 2007, 25:132-137. 10.1016/j.tibtech.2007.01.003, 17254656.
-
(2007)
Trends in Biotechnology
, vol.25
, pp. 132-137
-
-
Tyo, K.E.1
Alper, H.S.2
Stephanopoulos, G.N.3
-
7
-
-
0242487787
-
A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
10.1002/bit.10803, 14595777
-
Burgard AP, Pharkya P, Maranas CD. A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnology and Bioengineering 2003, 84:647-657. 10.1002/bit.10803, 14595777.
-
(2003)
Biotechnology and Bioengineering
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
8
-
-
30044437327
-
Evolutionary programming as a platform for in silico metabolic engineering
-
10.1186/1471-2105-6-308, 1327682, 16375763
-
Patil KR, 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.R.1
Rocha, I.2
Forster, J.3
Nielsen, J.4
-
9
-
-
58149307906
-
Natural computation meta-heuristics for the in silico optimization of microbial strains
-
10.1186/1471-2105-9-499, 2612012, 19038030
-
Rocha M, Maia P, Mendes R, Pinto JP, Ferreira EC, Nielsen J, Patil KR, Rocha I. Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics 2008, 9:499. 10.1186/1471-2105-9-499, 2612012, 19038030.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 499
-
-
Rocha, M.1
Maia, P.2
Mendes, R.3
Pinto, J.P.4
Ferreira, E.C.5
Nielsen, J.6
Patil, K.R.7
Rocha, I.8
-
10
-
-
0034816558
-
Reflections on the scope and the future of metabolic engineering and its connections to functional genomics and drug discovery
-
10.1006/mben.2001.0184, 11289787
-
Bailey JE. Reflections on the scope and the future of metabolic engineering and its connections to functional genomics and drug discovery. Metabolic Engineering 2001, 3:111-114. 10.1006/mben.2001.0184, 11289787.
-
(2001)
Metabolic Engineering
, vol.3
, pp. 111-114
-
-
Bailey, J.E.1
-
11
-
-
0037316342
-
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
-
10.1093/bioinformatics/19.2.261, 12538248
-
Klamt S, Stelling J, Ginkel M, Gilles ED. FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 2003, 19:261-269. 10.1093/bioinformatics/19.2.261, 12538248.
-
(2003)
Bioinformatics
, vol.19
, pp. 261-269
-
-
Klamt, S.1
Stelling, J.2
Ginkel, M.3
Gilles, E.D.4
-
12
-
-
0242475329
-
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis
-
10.1093/bioinformatics/btg271, 14594721
-
Lee DY, Yun H, Park S, Lee SY. MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics 2003, 19:2144-2146. 10.1093/bioinformatics/btg271, 14594721.
-
(2003)
Bioinformatics
, vol.19
, pp. 2144-2146
-
-
Lee, D.Y.1
Yun, H.2
Park, S.3
Lee, S.Y.4
-
13
-
-
34447551397
-
Structural and functional analysis of cellular networks with CellNetAnalyzer
-
10.1186/1752-0509-1-2, 1847467, 17408509
-
Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 2007, 1:2. 10.1186/1752-0509-1-2, 1847467, 17408509.
-
(2007)
BMC Systems Biology
, vol.1
, pp. 2
-
-
Klamt, S.1
Saez-Rodriguez, J.2
Gilles, E.D.3
-
14
-
-
34347258175
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
-
10.1038/nprot.2007.99, 17406635
-
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nature Protocols 2007, 2:727-738. 10.1038/nprot.2007.99, 17406635.
-
(2007)
Nature Protocols
, vol.2
, pp. 727-738
-
-
Becker, S.A.1
Feist, A.M.2
Mo, M.L.3
Hannum, G.4
Palsson, B.O.5
Herrgard, M.J.6
-
15
-
-
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 Systems Biology 2008, 2:55. 10.1186/1752-0509-2-55, 2446383, 18588708.
-
(2008)
BMC Systems Biology
, vol.2
, pp. 55
-
-
Wright, J.1
Wagner, A.2
-
16
-
-
35248849697
-
Integrated network reconstruction, visualization and analysis using YANAsquare
-
10.1186/1471-2105-8-313, 2020486, 17725829
-
Schwarz R, Liang C, Kaleta C, Kühnel M, Hoffmann E, Kuznetsov S, Hecker M, Griffiths G, Schuster S, Dandekar T. Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics 2007, 8:313. 10.1186/1471-2105-8-313, 2020486, 17725829.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 313
-
-
Schwarz, R.1
Liang, C.2
Kaleta, C.3
Kühnel, M.4
Hoffmann, E.5
Kuznetsov, S.6
Hecker, M.7
Griffiths, G.8
Schuster, S.9
Dandekar, T.10
-
17
-
-
33645536317
-
SNA-a toolbox for the stoichiometric analysis of metabolic networks
-
Urbanczik R. SNA-a toolbox for the stoichiometric analysis of metabolic networks. BMC Bioinformatics 2007, 7:129.
-
(2007)
BMC Bioinformatics
, vol.7
, pp. 129
-
-
Urbanczik, R.1
-
18
-
-
40549127097
-
Design and application of genome-scale reconstructed metabolic models
-
Rocha I, Forster J, Nielsen J. Design and application of genome-scale reconstructed metabolic models. Methods Molecular Biology 2008, 416:409-431.
-
(2008)
Methods Molecular Biology
, vol.416
, pp. 409-431
-
-
Rocha, I.1
Forster, J.2
Nielsen, J.3
-
19
-
-
0037342537
-
The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models
-
10.1093/bioinformatics/btg015, 12611808
-
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel G, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr J-H, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, et al. The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531. 10.1093/bioinformatics/btg015, 12611808.
-
(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
Cuellar, A.A.11
Dronov, S.12
Gilles, E.D.13
Ginkel, G.14
Gor, V.15
Goryanin, I.I.16
Hedley, W.J.17
Hodgman, T.C.18
Hofmeyr, J.-.H.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Le Novère, N.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
more..
-
20
-
-
23444439817
-
Using process diagrams for the graphical representation of biological networks
-
10.1038/nbt1111, 16082367
-
Kitano H, Funahashi A, Matsuoka Y, Oda K. Using process diagrams for the graphical representation of biological networks. Nature Biotechnology 2005, 23:961-966. 10.1038/nbt1111, 16082367.
-
(2005)
Nature Biotechnology
, vol.23
, pp. 961-966
-
-
Kitano, H.1
Funahashi, A.2
Matsuoka, Y.3
Oda, K.4
-
21
-
-
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. PNAS 2002, 99:15112-15117. 10.1073/pnas.232349399, 137552, 12415116.
-
(2002)
PNAS
, vol.99
, pp. 15112-15117
-
-
Segre, D.1
Vitkup, D.2
Church, G.M.3
-
22
-
-
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. PNAS 2005, 102:7695-7700. 10.1073/pnas.0406346102, 1140402, 15897462.
-
(2005)
PNAS
, vol.102
, pp. 7695-7700
-
-
Shlomi, T.1
Berkman, O.2
Ruppin, E.3
-
23
-
-
77952673317
-
Jung Java Library
-
Jung Java Library. , http://jung.sourceforge.net/
-
-
-
-
24
-
-
57349104476
-
GNU Linear Programming Kit (GLPK)
-
GNU Linear Programming Kit (GLPK). , http://www.gnu.org/software/glpk
-
-
-
-
25
-
-
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
-
26
-
-
77952673702
-
AI Bench
-
AI Bench. , http://www.aibench.org
-
-
-
-
27
-
-
33747856186
-
Metatool 5.0: fast and flexible elementary modes analysis
-
10.1093/bioinformatics/btl267, 16731697
-
von Kamp A, Schuster S. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 2006, 22:1930-1. 10.1093/bioinformatics/btl267, 16731697.
-
(2006)
Bioinformatics
, vol.22
, pp. 1930-1931
-
-
von Kamp, A.1
Schuster, S.2
-
28
-
-
33644877164
-
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
10.1093/nar/gkj092, 1347454, 16381960
-
Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 2006, 34:D689-D691. 10.1093/nar/gkj092, 1347454, 16381960.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Le Novere, N.1
Bornstein, B.2
Broicher, A.3
Courtot, M.4
Donizelli, M.5
Dharuri, H.6
Li, L.7
Sauro, H.8
Schilstra, M.9
Shapiro, B.10
Snoep, J.L.11
Hucka, M.12
-
29
-
-
84901180915
-
BiGG database
-
BiGG database. , http://bigg.ucsd.edu/
-
-
-
-
30
-
-
0036001069
-
Metabolic modelling of microbes: the flux-balance approach
-
10.1046/j.1462-2920.2002.00282.x, 12000313
-
Edwards JS, Covert M, Palsson B. Metabolic modelling of microbes: the flux-balance approach. Environmental Microbiology 2002, 4:133-140. 10.1046/j.1462-2920.2002.00282.x, 12000313.
-
(2002)
Environmental Microbiology
, vol.4
, pp. 133-140
-
-
Edwards, J.S.1
Covert, M.2
Palsson, B.3
-
31
-
-
0037079023
-
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
-
10.1038/nature01149, 12432395
-
Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420:186-189. 10.1038/nature01149, 12432395.
-
(2002)
Nature
, vol.420
, pp. 186-189
-
-
Ibarra, R.U.1
Edwards, J.S.2
Palsson, B.O.3
-
32
-
-
77949495880
-
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
-
10.1093/bioinformatics/btp704, 20031969
-
Tepper N, Shlomi T. Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 2010, 26(4):536-543. 10.1093/bioinformatics/btp704, 20031969.
-
(2010)
Bioinformatics
, vol.26
, Issue.4
, pp. 536-543
-
-
Tepper, N.1
Shlomi, T.2
-
33
-
-
52949098408
-
Large scale computation of elementary flux modes with bit pattern trees
-
10.1093/bioinformatics/btn401, 18676417
-
Terzer M, Stelling J. Large scale computation of elementary flux modes with bit pattern trees. Bioinformatics 2008, 24(19):2229-35. 10.1093/bioinformatics/btn401, 18676417.
-
(2008)
Bioinformatics
, vol.24
, Issue.19
, pp. 2229-2235
-
-
Terzer, M.1
Stelling, J.2
-
34
-
-
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 BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biology 2003, 4:R54. 10.1186/gb-2003-4-9-r54, 193654, 12952533.
-
(2003)
Genome Biology
, vol.4
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.O.4
-
35
-
-
0642343749
-
In Silico metabolic pathway analysis and design: succinic acid production by metabolically engineered Escherichia coli as an example
-
Lee SY, Hong SH, Moon SY. In Silico metabolic pathway analysis and design: succinic acid production by metabolically engineered Escherichia coli as an example. Genome Informatics 2002, 13:214-223.
-
(2002)
Genome Informatics
, vol.13
, pp. 214-223
-
-
Lee, S.Y.1
Hong, S.H.2
Moon, S.Y.3
-
36
-
-
12744254193
-
Genetic reconstruction of the aerobic central metabolism in Escherichia coli for the absolute aerobic production of succinate
-
10.1002/bit.20298, 15543598
-
Lin H, Bennett GN, San KY. Genetic reconstruction of the aerobic central metabolism in Escherichia coli for the absolute aerobic production of succinate. Biotechnology and Bioengineering 2005, 89:148-156. 10.1002/bit.20298, 15543598.
-
(2005)
Biotechnology and Bioengineering
, vol.89
, pp. 148-156
-
-
Lin, H.1
Bennett, G.N.2
San, K.Y.3
-
37
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
10.1101/gr.1239303, 403769, 14597658
-
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
-
(2003)
Genome Research
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
38
-
-
0042283712
-
Systems Biology Workbench
-
Systems Biology Workbench. , http://sbw.sourceforge.net/
-
-
-
-
39
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
10.1093/nar/28.1.27, 102409, 10592173
-
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
-
(2000)
Nucleic Acids Research
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
40
-
-
84871170033
-
BioCyc database collection
-
BioCyc database collection. , http://biocyc.org
-
-
-
|