-
1
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO, (2009) Reconstruction of biochemical networks in microorganisms. Nature Reviews: Microbiology 7: 129-143.
-
(2009)
Nature Reviews: Microbiology
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.O.5
-
3
-
-
9544253891
-
Genome-scale models of microbial cells: evaluating the consequences of constraints
-
Price ND, Reed JL, Palsson BO, (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature Reviews: Microbiology 2: 886-897.
-
(2004)
Nature Reviews: Microbiology
, vol.2
, pp. 886-897
-
-
Price, N.D.1
Reed, J.L.2
Palsson, B.O.3
-
4
-
-
78650900723
-
The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli
-
Archer CT, Kim JF, Jeong H, Park JH, Vickers CE, et al. (2011) The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics 12: 9.
-
(2011)
BMC Genomics
, vol.12
, pp. 9
-
-
Archer, C.T.1
Kim, J.F.2
Jeong, H.3
Park, J.H.4
Vickers, C.E.5
-
5
-
-
78751556862
-
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery
-
Kim HU, Kim SY, Jeong H, Kim TY, Kim JJ, et al. (2011) Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Molecular Systems Biology 7: 460.
-
(2011)
Molecular Systems Biology
, vol.7
, pp. 460
-
-
Kim, H.U.1
Kim, S.Y.2
Jeong, H.3
Kim, T.Y.4
Kim, J.J.5
-
6
-
-
77956696072
-
High-throughput generation, optimization and analysis of genome-scale metabolic models
-
Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, et al. (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nature Biotechnology 28: 969-974.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 969-974
-
-
Henry, C.S.1
DeJongh, M.2
Best, A.A.3
Frybarger, P.M.4
Linsay, B.5
-
7
-
-
53749085229
-
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
-
Herrgard MJ, Swainston N, Dobson PD, Dunn WB, Arga KY, et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 26: 1155-1160.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 1155-1160
-
-
Herrgard, M.J.1
Swainston, N.2
Dobson, P.D.3
Dunn, W.B.4
Arga, K.Y.5
-
8
-
-
78651467275
-
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
-
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, et al. (2011) A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Systems Biology 5: 8.
-
(2011)
BMC Systems Biology
, vol.5
, pp. 8
-
-
Thiele, I.1
Hyduke, D.R.2
Steeb, B.3
Fankam, G.4
Allen, D.K.5
-
10
-
-
77951612556
-
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
-
Schellenberger J, Park JO, Conrad TM, Palsson BO, (2010) BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11: 213.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson, B.O.4
-
11
-
-
75549090505
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, et al. (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research 38: D473-D479.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Caspi, R.1
Altman, T.2
Dale, J.M.3
Dreher, K.4
Fulcher, C.A.5
-
12
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28: 27-30.
-
(2000)
Nucleic Acids Research
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
13
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek RA, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research 33: 5691-5702.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.A.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
-
14
-
-
75849133666
-
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
-
Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, et al. (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Briefings in Bioinformatics 11: 40-79.
-
(2010)
Briefings in Bioinformatics
, vol.11
, pp. 40-79
-
-
Karp, P.D.1
Paley, S.M.2
Krummenacker, M.3
Latendresse, M.4
Dale, J.M.5
-
16
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology 3: 121.
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
-
17
-
-
2342648924
-
Integrating high-throughput and computational data
-
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO, (2004) Integrating high-throughput and computational data. Nature 429: 92-96.
-
(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.O.5
-
18
-
-
33751226921
-
Systems approach to refining genome annotation
-
Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, et al. (2006) Systems approach to refining genome annotation. Proceedings of the National Academy of Sciences of the United States of America 103: 17480-17484.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, pp. 17480-17484
-
-
Reed, J.L.1
Patel, T.R.2
Chen, K.H.3
Joyce, A.R.4
Applebee, M.K.5
-
19
-
-
25144505718
-
In silico design and adaptive evolution of Escherichia coli for production of lactic acid
-
Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, et al. (2005) In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnology and Bioengineering 91: 643-648.
-
(2005)
Biotechnology and Bioengineering
, 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
-
20
-
-
18844392599
-
Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
-
Alper H, Jin YS, Moxley JF, Stephanopoulos GN, (2005) Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metabolic Engineering 7: 155-164.
-
(2005)
Metabolic Engineering
, vol.7
, pp. 155-164
-
-
Alper, H.1
Jin, Y.S.2
Moxley, J.F.3
Stephanopoulos, G.N.4
-
21
-
-
29144484729
-
Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation
-
Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, et al. (2005) Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Applied and Environmental Microbiology 71: 7880-7887.
-
(2005)
Applied and Environmental Microbiology
, vol.71
, pp. 7880-7887
-
-
Lee, S.J.1
Lee, D.Y.2
Kim, T.Y.3
Kim, B.H.4
Lee, J.5
-
22
-
-
78650595035
-
Manipulating redox and ATP balancing for improved production of succinate in E. coli
-
Singh A, Cher Soh K, Hatzimanikatis V, Gill RT, (2011) Manipulating redox and ATP balancing for improved production of succinate in E. coli. Metabolic Engineering 13: 76-81.
-
(2011)
Metabolic Engineering
, vol.13
, pp. 76-81
-
-
Singh, A.1
Cher Soh, K.2
Hatzimanikatis, V.3
Gill, R.T.4
-
23
-
-
84859830554
-
Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142
-
in press
-
Vu T, Stolyar SM, Pinchuk GE, Hill EA, Kucek LA, et al. (1142) Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142. PLoS Computational Biology in press.
-
(1142)
PLoS Computational Biology
-
-
Vu, T.1
Stolyar, S.M.2
Pinchuk, G.E.3
Hill, E.A.4
Kucek, L.A.5
-
24
-
-
71849086611
-
Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde
-
Atsumi S, Higashide W, Liao JC, (2009) Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nature Biotechnology 27: 1177-1180.
-
(2009)
Nature Biotechnology
, vol.27
, pp. 1177-1180
-
-
Atsumi, S.1
Higashide, W.2
Liao, J.C.3
-
25
-
-
70449336249
-
Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the model organism
-
Lindberg P, Park S, Melis A, (2010) Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the model organism. Metabolic Engineering 12: 70-79.
-
(2010)
Metabolic Engineering
, vol.12
, pp. 70-79
-
-
Lindberg, P.1
Park, S.2
Melis, A.3
-
27
-
-
79952106852
-
Photosynthesis driven conversion of carbon dioxide to fatty alcohols and hydrocarbons in cyanobacteria
-
Tan X, Yao L, Gao Q, Wang W, Qi F, et al. (2011) Photosynthesis driven conversion of carbon dioxide to fatty alcohols and hydrocarbons in cyanobacteria. Metabolic Engineering 13: 169-176.
-
(2011)
Metabolic Engineering
, vol.13
, pp. 169-176
-
-
Tan, X.1
Yao, L.2
Gao, Q.3
Wang, W.4
Qi, F.5
-
28
-
-
34447317247
-
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets
-
Jamshidi N, Palsson BO, (2007) Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Systems Biology 1: 26.
-
(2007)
BMC Systems Biology
, vol.1
, pp. 26
-
-
Jamshidi, N.1
Palsson, B.O.2
-
29
-
-
17844405878
-
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation
-
Becker SA, Palsson BO, (2005) Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiology 5: 8.
-
(2005)
BMC Microbiology
, vol.5
, pp. 8
-
-
Becker, S.A.1
Palsson, B.O.2
-
30
-
-
36248994803
-
The targets of currently used antibacterial agents: lessons for drug discovery
-
Lange RP, Locher HH, Wyss PC, Then RL, (2007) The targets of currently used antibacterial agents: lessons for drug discovery. Current Pharmaceutical Design 13: 3140-3154.
-
(2007)
Current Pharmaceutical Design
, vol.13
, pp. 3140-3154
-
-
Lange, R.P.1
Locher, H.H.2
Wyss, P.C.3
Then, R.L.4
-
31
-
-
0026760182
-
The Crisis in Antibiotic Resistance
-
Neu HC, (1992) The Crisis in Antibiotic Resistance. Science 257: 1064-1073.
-
(1992)
Science
, vol.257
, pp. 1064-1073
-
-
Neu, H.C.1
-
32
-
-
15744372279
-
Mechanisms of action of newer antibiotics for Gram-positive pathogens
-
Hancock REW, (2005) Mechanisms of action of newer antibiotics for Gram-positive pathogens. The Lancet Infectious Diseases 5: 209-218.
-
(2005)
The Lancet Infectious Diseases
, vol.5
, pp. 209-218
-
-
Hancock, R.E.W.1
-
33
-
-
0345839252
-
Where will new antibiotics come from?
-
Walsh CT, (2003) Where will new antibiotics come from? Nature Reviews: Microbiology 1: 65-70.
-
(2003)
Nature Reviews: Microbiology
, vol.1
, pp. 65-70
-
-
Walsh, C.T.1
-
34
-
-
55049136420
-
Has nature already identified all useful antibacterial targets?
-
Bumann D, (2008) Has nature already identified all useful antibacterial targets? Current Opinion in Microbiology 11: 387-392.
-
(2008)
Current Opinion in Microbiology
, vol.11
, pp. 387-392
-
-
Bumann, D.1
-
35
-
-
77951552860
-
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
-
Kim J, Reed JL, (2010) OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Systems Biology 4: 53.
-
(2010)
BMC Systems Biology
, vol.4
, pp. 53
-
-
Kim, J.1
Reed, J.L.2
-
36
-
-
45149111660
-
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
-
Feist AM, Palsson BO, (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nature Biotechnology 26: 659-667.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 659-667
-
-
Feist, A.M.1
Palsson, B.O.2
-
37
-
-
67449162060
-
Genome-scale modeling of Synechocystis sp. PCC 6803 and prediction of pathway insertion
-
Fu P, (2009) Genome-scale modeling of Synechocystis sp. PCC 6803 and prediction of pathway insertion. Journal of Chemical Technology & Biotechnology 84: 473-483.
-
(2009)
Journal of Chemical Technology & Biotechnology
, vol.84
, pp. 473-483
-
-
Fu, P.1
-
38
-
-
77956710803
-
The metabolic network of Synechocystis sp. PCC 6803: Systemic properties of autotrophic growth
-
Knoop H, Zilliges Y, Lockau W, Steuer R, (2010) The metabolic network of Synechocystis sp. PCC 6803: Systemic properties of autotrophic growth. Plant Physiology 154: 410-422.
-
(2010)
Plant Physiology
, vol.154
, pp. 410-422
-
-
Knoop, H.1
Zilliges, Y.2
Lockau, W.3
Steuer, R.4
-
39
-
-
78349292275
-
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
-
Montagud A, Navarro E, Fernandez de Cordoba P, Urchueguia JF, Patil KR, (2010) Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. BMC Systems Biology 4: 156.
-
(2010)
BMC Systems Biology
, vol.4
, pp. 156
-
-
Montagud, A.1
Navarro, E.2
Fernandez de Cordoba, P.3
Urchueguia, J.F.4
Patil, K.R.5
-
40
-
-
33846910173
-
Global reconstruction of the human metabolic network based on genomic and bibliomic data
-
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, et al. (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences of the United States of America 104: 1777-1782.
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, pp. 1777-1782
-
-
Duarte, N.C.1
Becker, S.A.2
Jamshidi, N.3
Thiele, I.4
Mo, M.L.5
-
41
-
-
0000437775
-
D-Alanyl-D-alanine Ligases and the Molecular Mechanism of Vancomycin Resistance
-
Wright GD, Walsh CT, (1992) D-Alanyl-D-alanine Ligases and the Molecular Mechanism of Vancomycin Resistance. Accounts of Chemical Research 25: 468-473.
-
(1992)
Accounts of Chemical Research
, vol.25
, pp. 468-473
-
-
Wright, G.D.1
Walsh, C.T.2
-
42
-
-
0029943128
-
Molecular Mechanisms of Drug Resistance in Mycobacterium Tuberculosis
-
Blanchard JS, (1996) Molecular Mechanisms of Drug Resistance in Mycobacterium Tuberculosis. Annual Review of Biochemistry 65: 215-239.
-
(1996)
Annual Review of Biochemistry
, vol.65
, pp. 215-239
-
-
Blanchard, J.S.1
-
43
-
-
0033834868
-
Pyrazinamide inhibits the eukaryotic-like fatty acid synthetase I (FASI) of Mycobacterium tuberculosis
-
Zimhony O, Cox JS, Welch JT, Vilchèze C, Jacobs WR Jr, (2000) Pyrazinamide inhibits the eukaryotic-like fatty acid synthetase I (FASI) of Mycobacterium tuberculosis. Nature Medicine 6: 1043-1047.
-
(2000)
Nature Medicine
, vol.6
, pp. 1043-1047
-
-
Zimhony, O.1
Cox, J.S.2
Welch, J.T.3
Vilchèze, C.4
Jacobs Jr., W.R.5
-
44
-
-
0242437861
-
Mode of action of pyrazinamide: disruption of Mycobacterium tuberculosis membrane transport and energetics by pyrazinoic acid
-
Zhang Y, Wade MM, Scorpio A, Zhang H, Sun Z, (2003) Mode of action of pyrazinamide: disruption of Mycobacterium tuberculosis membrane transport and energetics by pyrazinoic acid. The Journal of Antimicrobial Chemotherapy 52: 790-795.
-
(2003)
The Journal of Antimicrobial Chemotherapy
, vol.52
, pp. 790-795
-
-
Zhang, Y.1
Wade, M.M.2
Scorpio, A.3
Zhang, H.4
Sun, Z.5
-
45
-
-
0036232990
-
Purification, Characterization, and Identification of Novel Inhibitors of the Beta-Ketoacyl-Acyl Carrier Protein Synthase III (FabH) from Staphylococcus aureus
-
He X, Reynolds KA, (2002) Purification, Characterization, and Identification of Novel Inhibitors of the Beta-Ketoacyl-Acyl Carrier Protein Synthase III (FabH) from Staphylococcus aureus. Antimicrobial Agents and Chemotherapy 46: 1310-1318.
-
(2002)
Antimicrobial Agents and Chemotherapy
, vol.46
, pp. 1310-1318
-
-
He, X.1
Reynolds, K.A.2
-
46
-
-
20144370577
-
Structure-based design, synthesis, and study of potent inhibitors of beta-ketoacyl-acyl carrier protein synthase III as potential antimicrobial agents
-
Nie Z, Perretta C, Lu J, Su Y, Margosiak S, et al. (2005) Structure-based design, synthesis, and study of potent inhibitors of beta-ketoacyl-acyl carrier protein synthase III as potential antimicrobial agents. Journal of Medicinal Chemistry 48: 1596-1609.
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, pp. 1596-1609
-
-
Nie, Z.1
Perretta, C.2
Lu, J.3
Su, Y.4
Margosiak, S.5
-
47
-
-
60249099423
-
Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis
-
Arora P, Goyal A, Natarajan VT, Rajakumara E, Tyagi A, et al. (2009) Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis. Nature Chemical Biology 5: 166-173.
-
(2009)
Nature Chemical Biology
, vol.5
, pp. 166-173
-
-
Arora, P.1
Goyal, A.2
Natarajan, V.T.3
Rajakumara, E.4
Tyagi, A.5
-
48
-
-
0023139623
-
Antimicrobial resistance of Staphylococcus aureus: genetic basis
-
Lyon BR, Skurray R, (1987) Antimicrobial resistance of Staphylococcus aureus: genetic basis. Microbiological Reviews 51: 88-134.
-
(1987)
Microbiological Reviews
, vol.51
, pp. 88-134
-
-
Lyon, B.R.1
Skurray, R.2
-
49
-
-
78650115180
-
Characterization of nicotinamidases: steady state kinetic parameters, classwide inhibition by nicotinaldehydes, and catalytic mechanism
-
French JB, Cen Y, Vrablik TL, Xu P, Allen E, et al. (2010) Characterization of nicotinamidases: steady state kinetic parameters, classwide inhibition by nicotinaldehydes, and catalytic mechanism. Biochemistry 49: 10421-10439.
-
(2010)
Biochemistry
, vol.49
, pp. 10421-10439
-
-
French, J.B.1
Cen, Y.2
Vrablik, T.L.3
Xu, P.4
Allen, E.5
-
50
-
-
51849155973
-
Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: structureactivity relationships of the nucleobase domain of 5′-O-[N-(salicyl)sulfamoyl]adenosine
-
Neres J, Labello NP, Somu RV, Boshoff HIM, Wilson DJ, et al. (2008) Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: structureactivity relationships of the nucleobase domain of 5′-O-[N-(salicyl)sulfamoyl]adenosine. Journal of Medicinal Chemistry 51: 5349-5370.
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, pp. 5349-5370
-
-
Neres, J.1
Labello, N.P.2
Somu, R.V.3
Boshoff, H.I.M.4
Wilson, D.J.5
-
51
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
-
(1990)
Journal of Molecular Biology
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
52
-
-
0141519279
-
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
-
Li L, Stoeckert CJ Jr, Roos DS, (2003) OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Research 13: 2178-2189.
-
(2003)
Genome Research
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert Jr., C.J.2
Roos, D.S.3
-
53
-
-
65649105134
-
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction
-
Raghunathan A, Reed JL, Shin S, Palsson BO, Daeer S, (2009) Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Systems Biology 3: 38.
-
(2009)
BMC Systems Biology
, vol.3
, pp. 38
-
-
Raghunathan, A.1
Reed, J.L.2
Shin, S.3
Palsson, B.O.4
Daeer, S.5
-
54
-
-
60849099919
-
Genome-scale constraint-based modeling of Geobacter metallireducens
-
Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, et al. (2009) Genome-scale constraint-based modeling of Geobacter metallireducens. BMC Systems Biology 3: 15.
-
(2009)
BMC Systems Biology
, vol.3
, pp. 15
-
-
Sun, J.1
Sayyar, B.2
Butler, J.E.3
Pharkya, P.4
Fahland, T.R.5
-
55
-
-
77955495197
-
Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation
-
Pinchuk GE, Hill EA, Geydebrekht OV, De Ingeniis J, Zhang X, et al. (2010) Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation. PLoS Computational Biology 6: e1000822.
-
(2010)
PLoS Computational Biology
, vol.6
-
-
Pinchuk, G.E.1
Hill, E.A.2
Geydebrekht, O.V.3
De Ingeniis, J.4
Zhang, X.5
-
56
-
-
78650389698
-
Constraint-based modeling analysis of the metabolism of two Pelobacter species
-
Sun J, Haveman SA, Bui OT, Fahland TR, Lovley DR, (2010) Constraint-based modeling analysis of the metabolism of two Pelobacter species. BMC Systems Biology 4: 174.
-
(2010)
BMC Systems Biology
, vol.4
, pp. 174
-
-
Sun, J.1
Haveman, S.A.2
Bui, O.T.3
Fahland, T.R.4
Lovley, D.R.5
-
57
-
-
79851515763
-
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans
-
Satish Kumar V, Ferry JG, Maranas CD, (2011) Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. BMC Systems Biology 5: 28.
-
(2011)
BMC Systems Biology
, vol.5
, pp. 28
-
-
Satish Kumar, V.1
Ferry, J.G.2
Maranas, C.D.3
-
58
-
-
8744224466
-
OptStrain: A computational framework for redesign of microbial production systems
-
Pharkya P, Burgard AP, Maranas CD, (2004) OptStrain: A computational framework for redesign of microbial production systems. Genome Research 14: 2367-2376.
-
(2004)
Genome Research
, vol.14
, pp. 2367-2376
-
-
Pharkya, P.1
Burgard, A.P.2
Maranas, C.D.3
-
59
-
-
30044437327
-
Evolutionary programming as a platform for in silico metabolic engineering
-
Patil KR, Rocha I, Förster J, Nielsen J, (2005) Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6: 308.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 308
-
-
Patil, K.R.1
Rocha, I.2
Förster, J.3
Nielsen, J.4
-
60
-
-
29544436058
-
An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems
-
Pharkya P, Maranas CD, (2006) An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metabolic Engineering 8: 1-13.
-
(2006)
Metabolic Engineering
, vol.8
, pp. 1-13
-
-
Pharkya, P.1
Maranas, C.D.2
-
61
-
-
69249146187
-
Large-scale identification of genetic design strategies using local search
-
Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, et al. (2009) Large-scale identification of genetic design strategies using local search. Molecular Systems Biology 5: 296.
-
(2009)
Molecular Systems Biology
, vol.5
, pp. 296
-
-
Lun, D.S.1
Rockwell, G.2
Guido, N.J.3
Baym, M.4
Kelner, J.A.5
-
62
-
-
77954590959
-
OptForce: An optimization procedure for identifying all genetic manipulations leading to targeted overproductions
-
Ranganathan S, Suthers PF, Maranas CD, (2010) OptForce: An optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Computational Biology 6: e1000744.
-
(2010)
PLoS Computational Biology
, vol.6
-
-
Ranganathan, S.1
Suthers, P.F.2
Maranas, C.D.3
-
63
-
-
79955145774
-
EMILiO: A Fast Algorithm for Genome-Scale Strain Design
-
Yang L, Cluett WR, Mahadevan R, (2011) EMILiO: A Fast Algorithm for Genome-Scale Strain Design. Metabolic Engineering 13: 272-281.
-
(2011)
Metabolic Engineering
, vol.13
, pp. 272-281
-
-
Yang, L.1
Cluett, W.R.2
Mahadevan, R.3
-
65
-
-
77951530463
-
Linear Programming with Matlab
-
Society for Industrial Mathematics
-
Ferris MC, Mangasarian OL, Wright SJ, (2008) Linear Programming with Matlab. Society for Industrial Mathematics.
-
(2008)
-
-
Ferris, M.C.1
Mangasarian, O.L.2
Wright, S.J.3
-
66
-
-
0242487787
-
OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
-
Burgard AP, Pharkya P, Maranas CD, (2003) OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnology and Bioengineering 84: 647-657.
-
(2003)
Biotechnology and Bioengineering
, vol.84
, pp. 647-657
-
-
Burgard, A.P.1
Pharkya, P.2
Maranas, C.D.3
-
67
-
-
77949495880
-
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
-
Tepper N, Shlomi T, (2010) Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 26: 536-543.
-
(2010)
Bioinformatics
, vol.26
, pp. 536-543
-
-
Tepper, N.1
Shlomi, T.2
-
68
-
-
0004046678
-
Model Building in Mathematical Programming
-
Wiley, 4 edition
-
Williams HP, (1999) Model Building in Mathematical Programming. Wiley, 4 edition.
-
(1999)
-
-
Williams, H.P.1
-
69
-
-
0034798879
-
Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments
-
Burgard AP, Vaidyaraman S, Maranas CD, (2001) Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnology Progress 17: 791-797.
-
(2001)
Biotechnology Progress
, vol.17
, pp. 791-797
-
-
Burgard, A.P.1
Vaidyaraman, S.2
Maranas, C.D.3
-
70
-
-
77950863401
-
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
-
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, et al. (2010) Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metabolic Engineering 12: 173-186.
-
(2010)
Metabolic Engineering
, vol.12
, pp. 173-186
-
-
Feist, A.M.1
Zielinski, D.C.2
Orth, J.D.3
Schellenberger, J.4
Herrgard, M.J.5
-
71
-
-
80052573483
-
Large-scale bi-level strain design approaches and mixedinteger programming solution techniques
-
Kim J, Reed JL, Maravelias CT, (2011) Large-scale bi-level strain design approaches and mixedinteger programming solution techniques. PloS ONE 6: e24162.
-
(2011)
PloS ONE
, vol.6
-
-
Kim, J.1
Reed, J.L.2
Maravelias, C.T.3
-
72
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
Mahadevan R, Schilling CH, (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metabolic Engineering 5: 264-276.
-
(2003)
Metabolic Engineering
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
73
-
-
25444439861
-
GenBank
-
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW, (2010) GenBank. Nucleic Acids Research 39: 32-37.
-
(2010)
Nucleic Acids Research
, vol.39
, pp. 32-37
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Sayers, E.W.5
-
74
-
-
0029060966
-
Acyl-lipid desaturases and their importance in the tolerance and acclimatization to cold of cyanobacteria
-
Murata N, Wadat H, (1995) Acyl-lipid desaturases and their importance in the tolerance and acclimatization to cold of cyanobacteria. Biochemical Journal 308: 1-8.
-
(1995)
Biochemical Journal
, vol.308
, pp. 1-8
-
-
Murata, N.1
Wadat, H.2
-
75
-
-
0031934655
-
Alteration of low-temperature susceptibility of the cyanobacterium Synechococcus sp. PCC 7002 by genetic manipulation of membrane lipid unsaturation
-
Sakamoto T, Shen G, Higashi S, Murata N, Bryant DA, (1998) Alteration of low-temperature susceptibility of the cyanobacterium Synechococcus sp. PCC 7002 by genetic manipulation of membrane lipid unsaturation. Archives of Microbiology 169: 20-28.
-
(1998)
Archives of Microbiology
, vol.169
, pp. 20-28
-
-
Sakamoto, T.1
Shen, G.2
Higashi, S.3
Murata, N.4
Bryant, D.A.5
-
77
-
-
28844474830
-
Flux balance analysis of photoautotrophic metabolism
-
Shastri AA, Morgan JA, (2005) Flux balance analysis of photoautotrophic metabolism. Biotechnology Progress 21: 1617-1626.
-
(2005)
Biotechnology Progress
, vol.21
, pp. 1617-1626
-
-
Shastri, A.A.1
Morgan, J.A.2
|