-
1
-
-
6044265058
-
Integration of gene expression data into genome-scale metabolic models
-
Akesson, M., J. Forster, and J. Nielsen. 2004. Integration of gene expression data into genome-scale metabolic models. Metab. Eng. 6:285-293.
-
(2004)
Metab. Eng.
, vol.6
, pp. 285-293
-
-
Akesson, M.1
Forster, J.2
Nielsen, J.3
-
2
-
-
34250620817
-
Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration
-
Alvarez-Ortega, C., and C. S. Harwood. 2007. Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration. Mol. Microbiol. 65:153-165.
-
(2007)
Mol. Microbiol.
, vol.65
, pp. 153-165
-
-
Alvarez-Ortega, C.1
Harwood, C.S.2
-
3
-
-
34347258175
-
Quantitative prediction of cellular metabolism with constraint- Based models: The COBRA toolbox
-
Becker, S. A., A. M. Feist, M. L. Mo, G. Hannum, B. O. Palsson, and M. J. Herrgard. 2007. Quantitative prediction of cellular metabolism with constraint- based models: the COBRA toolbox. Nat. Protoc. 2:727-738.
-
(2007)
Nat. Protoc.
, 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
-
4
-
-
44949225040
-
Context-specific metabolic networks are consistent with experiments
-
Becker, S. A., and B. O. Palsson. 2008. Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol. 4:e1000082.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Becker, S.A.1
Palsson, B.O.2
-
5
-
-
70049110173
-
Interpreting expression data with metabolic flux models: Predicting Mycobacterium tuberculosis mycolic acid production
-
Colijn, C., A. Brandes, J. Zucker, D. S. Lun, B. Weiner, M. R. Farhat, T. Y. Cheng, D. B. Moody, M. Murray, and J. E. Galagan. 2009. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput. Biol. 5:e1000489.
-
(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
-
6
-
-
0037008673
-
Transcriptional regulation in constraints- Based metabolic models of Escherichia coli
-
Covert, M. W., and B. O. Palsson. 2002. Transcriptional regulation in constraints- based metabolic models of Escherichia coli. J. Biol. Chem. 277: 28058-28064.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 28058-28064
-
-
Covert, M.W.1
Palsson, B.O.2
-
7
-
-
34247333058
-
Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients
-
D'Argenio, D. A., M. Wu, L. R. Hoffman, H. D. Kulasekara, E. Deziel, E. E. Smith, H. Nguyen, R. K. Ernst, T. J. Larson Freeman, D. H. Spencer, M. Brittnacher, H. S. Hayden, S. Selgrade, M. Klausen, D. R. Goodlett, J. L. Burns, B. W. Ramsey, and S. I. Miller. 2007. Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients. Mol. Microbiol. 64:512-533.
-
(2007)
Mol. Microbiol.
, vol.64
, pp. 512-533
-
-
D'Argenio, D.A.1
Wu, M.2
Hoffman, L.R.3
Kulasekara, H.D.4
Deziel, E.5
Smith, E.E.6
Nguyen, H.7
Ernst, R.K.8
Larson Freeman, T.J.9
Spencer, D.H.10
Brittnacher, M.11
Hayden, H.S.12
Selgrade, S.13
Klausen, M.14
Goodlett, D.R.15
Burns, J.L.16
Ramsey, B.W.17
Miller, S.I.18
-
8
-
-
0028046468
-
Mucoid-to-nonmucoid conversion in alginate-producing Pseudomonas aeruginosa often results from spontaneous mutations in algT, encoding a putative alternate sigma factor, and shows evidence for autoregulation
-
DeVries, C. A., and D. E. Ohman. 1994. Mucoid-to-nonmucoid conversion in alginate-producing Pseudomonas aeruginosa often results from spontaneous mutations in algT, encoding a putative alternate sigma factor, and shows evidence for autoregulation. J. Bacteriol. 176:6677-6687.
-
(1994)
J. Bacteriol.
, vol.176
, pp. 6677-6687
-
-
DeVries, C.A.1
Ohman, D.E.2
-
9
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist, A. M., M. J. Herrgard, I. Thiele, J. L. Reed, and B. O. Palsson. 2009. Reconstruction of biochemical networks in microorganisms. Nat. Rev. Microbiol. 7:129-143.
-
(2009)
Nat. Rev. Microbiol.
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.O.5
-
10
-
-
6944224154
-
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
-
Fong, S. S., and B. O. Palsson. 2004. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat. Genet. 36:1056-1058.
-
(2004)
Nat. Genet.
, vol.36
, pp. 1056-1058
-
-
Fong, S.S.1
Palsson, B.O.2
-
11
-
-
33644865643
-
Impact of quorum sensing on fitness of Pseudomonas aeruginosa
-
Heurlier, K., V. Denervaud, and D. Haas. 2006. Impact of quorum sensing on fitness of Pseudomonas aeruginosa. Int. J. Med. Microbiol. 296:93-102.
-
(2006)
Int. J. Med. Microbiol.
, vol.296
, pp. 93-102
-
-
Heurlier, K.1
Denervaud, V.2
Haas, D.3
-
12
-
-
67650685860
-
Dynamics of adaptive microevolution of hypermutable Pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic fibrosis
-
Hoboth, C., R. Hoffmann, A. Eichner, C. Henke, S. Schmoldt, A. Imhof, J. Heesemann, and M. Hogardt. 2009. Dynamics of adaptive microevolution of hypermutable Pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic fibrosis. J. Infect. Dis. 200:118-130.
-
(2009)
J. Infect. Dis.
, vol.200
, pp. 118-130
-
-
Hoboth, C.1
Hoffmann, R.2
Eichner, A.3
Henke, C.4
Schmoldt, S.5
Imhof, A.6
Heesemann, J.7
Hogardt, M.8
-
13
-
-
33845623880
-
Stage-specific adaptation of hypermutable Pseudomonas aeruginosa isolates during chronic pulmonary infection in patients with cystic fibrosis
-
Hogardt, M., C. Hoboth, S. Schmoldt, C. Henke, L. Bader, and J. Heesemann. 2007. Stage-specific adaptation of hypermutable Pseudomonas aeruginosa isolates during chronic pulmonary infection in patients with cystic fibrosis. J. Infect. Dis. 195:70-80.
-
(2007)
J. Infect. Dis.
, vol.195
, pp. 70-80
-
-
Hogardt, M.1
Hoboth, C.2
Schmoldt, S.3
Henke, C.4
Bader, L.5
Heesemann, J.6
-
15
-
-
24344435852
-
Airway biofilms: Implications for pathogenesis and therapy of respiratory tract infections
-
Kobayashi, H. 2005. Airway biofilms: implications for pathogenesis and therapy of respiratory tract infections. Treat Respir. Med. 4:241-253.
-
(2005)
Treat Respir. Med.
, vol.4
, pp. 241-253
-
-
Kobayashi, H.1
-
16
-
-
67650447476
-
Fifteen years of microbial genomics: Meeting the challenges and fulfilling the dream
-
Kyrpides, N. C. 2009. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat. Biotechnol. 27:627-632.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 627-632
-
-
Kyrpides, N.C.1
-
18
-
-
0036128083
-
Pseudomonas-epithelial cell interactions dissected with DNA microarrays
-
Lory, S., and J. K. Ichikawa. 2002. Pseudomonas-epithelial cell interactions dissected with DNA microarrays. Chest 121:36S-39S.
-
(2002)
Chest
, vol.121
-
-
Lory, S.1
Ichikawa, J.K.2
-
19
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
-
Mahadevan, R., and C. H. Schilling. 2003. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5:264-276.
-
(2003)
Metab. Eng.
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
20
-
-
42949094250
-
Dynamics of Pseudomonas aeruginosa genome evolution
-
Mathee, K., G. Narasimhan, C. Valdes, X. Qiu, J. M. Matewish, M. Koehrsen, A. Rokas, C. N. Yandava, R. Engels, E. Zeng, R. Olavarietta, M. Doud, R. S. Smith, P. Montgomery, J. R. White, P. A. Godfrey, C. Kodira, B. Birren, J. E. Galagan, and S. Lory. 2008. Dynamics of Pseudomonas aeruginosa genome evolution. Proc. Natl. Acad. Sci. U. S. A. 105:3100-3105.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 3100-3105
-
-
Mathee, K.1
Narasimhan, G.2
Valdes, C.3
Qiu, X.4
Matewish, J.M.5
Koehrsen, M.6
Rokas, A.7
Yandava, C.N.8
Engels, R.9
Zeng, E.10
Olavarietta, R.11
Doud, M.12
Smith, R.S.13
Montgomery, P.14
White, J.R.15
Godfrey, P.A.16
Kodira, C.17
Birren, B.18
Galagan, J.E.19
Lory, S.20
more..
-
21
-
-
70449698364
-
Next-generation gap
-
McPherson, J. D. 2009. Next-generation gap. Nat. Methods 6:S2-S5.
-
(2009)
Nat. Methods
, vol.6
-
-
McPherson, J.D.1
-
22
-
-
66149122278
-
Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p
-
Moxley, J. F., M. C. Jewett, M. R. Antoniewicz, S. G. Villas-Boas, H. Alper, R. T. Wheeler, L. Tong, A. G. Hinnebusch, T. Ideker, J. Nielsen, and G. Stephanopoulos. 2009. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc. Natl. Acad. Sci. U. S. A. 106:6477-6482.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, 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
-
23
-
-
33846284918
-
Pseudomonas aeruginosa chronic colonization in cystic fibrosis patients
-
Murray, T. S., M. Egan, and B. I. Kazmierczak. 2007. Pseudomonas aeruginosa chronic colonization in cystic fibrosis patients. Curr. Opin. Pediatr. 19:83-88.
-
(2007)
Curr. Opin. Pediatr.
, vol.19
, pp. 83-88
-
-
Murray, T.S.1
Egan, M.2
Kazmierczak, B.I.3
-
24
-
-
65649126411
-
Flux balance analysis: Interrogating genome-scale metabolic networks
-
Oberhardt, M. A., A. K. Chavali, and J. A. Papin. 2009. Flux balance analysis: interrogating genome-scale metabolic networks. Methods Mol. Biol. 500:61-80.
-
(2009)
Methods Mol. Biol.
, vol.500
, pp. 61-80
-
-
Oberhardt, M.A.1
Chavali, A.K.2
Papin, J.A.3
-
26
-
-
41149163825
-
Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1
-
Oberhardt, M. A., J. Puchalka, K. E. Fryer, V. A. Martins dos Santos, and J. A. Papin. 2008. Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J. Bacteriol. 190:2790-2803.
-
(2008)
J. Bacteriol.
, vol.190
, pp. 2790-2803
-
-
Oberhardt, M.A.1
Puchalka, J.2
Fryer, K.E.3
Martins Dos Santos, V.A.4
Papin, J.A.5
-
27
-
-
35348934254
-
Genome-scale reconstruction of metabolic network in bacillus subtilis based on high-throughput phenotyping and gene essentiality data
-
Oh, Y. K., B. O. Palsson, S. M. Park, C. H. Schilling, and R. Mahadevan. 2007. Genome-scale reconstruction of metabolic network in bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J. Biol. Chem. 282:28791-28799.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 28791-28799
-
-
Oh, Y.K.1
Palsson, B.O.2
Park, S.M.3
Schilling, C.H.4
Mahadevan, R.5
-
28
-
-
0034685940
-
High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection
-
Oliver, A., R. Canton, P. Campo, F. Baquero, and J. Blazquez. 2000. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288:1251-1254.
-
(2000)
Science
, vol.288
, pp. 1251-1254
-
-
Oliver, A.1
Canton, R.2
Campo, P.3
Baquero, F.4
Blazquez, J.5
-
29
-
-
36549035760
-
Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum
-
Palmer, K. L., L. M. Aye, and M. Whiteley. 2007. Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum. J. Bacteriol. 189:8079-8087.
-
(2007)
J. Bacteriol.
, vol.189
, pp. 8079-8087
-
-
Palmer, K.L.1
Aye, L.M.2
Whiteley, M.3
-
30
-
-
17144382063
-
Understanding the control of Pseudomonas aeruginosa alginate synthesis and the prospects for management of chronic infections in cystic fibrosis
-
Ramsey, D. M., and D. J. Wozniak. 2005. Understanding the control of Pseudomonas aeruginosa alginate synthesis and the prospects for management of chronic infections in cystic fibrosis. Mol. Microbiol. 56:309-322.
-
(2005)
Mol. Microbiol.
, vol.56
, pp. 309-322
-
-
Ramsey, D.M.1
Wozniak, D.J.2
-
31
-
-
31144435316
-
Towards multidimensional genome annotation
-
Reed, J. L., I. Famili, I. Thiele, and B. O. Palsson. 2006. Towards multidimensional genome annotation. Nat. Rev. Genet. 7:130-141.
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 130-141
-
-
Reed, J.L.1
Famili, I.2
Thiele, I.3
Palsson, B.O.4
-
32
-
-
19644371239
-
Pathogen-host interactions in Pseudomonas aeruginosa pneumonia
-
Sadikot, R. T., T. S. Blackwell, J. W. Christman, and A. S. Prince. 2005. Pathogen-host interactions in Pseudomonas aeruginosa pneumonia. Am. J. Respir. Crit. Care Med. 171:1209-1223.
-
(2005)
Am. J. Respir. Crit. Care Med.
, vol.171
, pp. 1209-1223
-
-
Sadikot, R.T.1
Blackwell, T.S.2
Christman, J.W.3
Prince, A.S.4
-
34
-
-
51349092391
-
Network-based prediction of human tissue-specific metabolism
-
Shlomi, T., M. N. Cabili, M. J. Herrgard, B. O. Palsson, and E. Ruppin. 2008. Network-based prediction of human tissue-specific metabolism. Nat. Biotechnol. 26:1003-1010.
-
(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
-
35
-
-
33744814106
-
Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients
-
Smith, E. E., D. G. Buckley, Z. Wu, C. Saenphimmachak, L. R. Hoffman, D. A. D'Argenio, S. I. Miller, B. W. Ramsey, D. P. Speert, S. M. Moskowitz, J. L. Burns, R. Kaul, and M. V. Olson. 2006. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl. Acad. Sci. U. S. A. 103:8487-8492.
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, pp. 8487-8492
-
-
Smith, E.E.1
Buckley, D.G.2
Wu, Z.3
Saenphimmachak, C.4
Hoffman, L.R.5
D'Argenio, D.A.6
Miller, S.I.7
Ramsey, B.W.8
Speert, D.P.9
Moskowitz, S.M.10
Burns, J.L.11
Kaul, R.12
Olson, M.V.13
-
36
-
-
35648949942
-
In vivo evidence of Pseudomonas aeruginosa nutrient acquisition and pathogenesis in the lungs of cystic fibrosis patients
-
Son, M. S., W. J. Matthews, Jr., Y. Kang, D. T. Nguyen, and T. T. Hoang. 2007. In vivo evidence of Pseudomonas aeruginosa nutrient acquisition and pathogenesis in the lungs of cystic fibrosis patients. Infect. Immun. 75:5313-5324.
-
(2007)
Infect. Immun.
, vol.75
, pp. 5313-5324
-
-
Son, M.S.1
Matthews Jr., W.J.2
Kang, Y.3
Nguyen, D.T.4
Hoang, T.T.5
-
37
-
-
0034739007
-
Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen
-
Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener, M. J. Hickey, F. S. Brinkman, W. O. Hufnagle, D. J. Kowalik, M. Lagrou, R. L. Garber, L. Goltry, E. Tolentino, S. Westbrock-Wadman, Y. Yuan, L. L. Brody, S. N. Coulter, K. R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G. K. Wong, Z. Wu, I. T. Paulsen, J. Reizer, M. H. Saier, R. E. Hancock, S. Lory, and M. V. Olson. 2000. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406:959-964.
-
(2000)
Nature
, vol.406
, pp. 959-964
-
-
Stover, C.K.1
Pham, X.Q.2
Erwin, A.L.3
Mizoguchi, S.D.4
Warrener, P.5
Hickey, M.J.6
Brinkman, F.S.7
Hufnagle, W.O.8
Kowalik, D.J.9
Lagrou, M.10
Garber, R.L.11
Goltry, L.12
Tolentino, E.13
Westbrock-Wadman, S.14
Yuan, Y.15
Brody, L.L.16
Coulter, S.N.17
Folger, K.R.18
Kas, A.19
Larbig, K.20
Lim, R.21
Smith, K.22
Spencer, D.23
Wong, G.K.24
Wu, Z.25
Paulsen, I.T.26
Reizer, J.27
Saier, M.H.28
Hancock, R.E.29
Lory, S.30
Olson, M.V.31
more..
-
38
-
-
33846015888
-
Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model
-
Teusink, B., A. Wiersma, D. Molenaar, C. Francke, W. M. de Vos, R. J. Siezen, and E. J. Smid. 2006. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J. Biol. Chem. 281:40041-40048.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 40041-40048
-
-
Teusink, B.1
Wiersma, A.2
Molenaar, D.3
Francke, C.4
De Vos, W.M.5
Siezen, R.J.6
Smid, E.J.7
-
39
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher, V. G., R. Tibshirani, and G. Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 98:5116-5121.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
40
-
-
71349087490
-
A unifying view of 21st century systems biology
-
Vidal, M. 2009. A unifying view of 21st century systems biology. FEBS Lett. 583:3891-3894.
-
(2009)
FEBS Lett.
, vol.583
, pp. 3891-3894
-
-
Vidal, M.1
-
41
-
-
0036167851
-
Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients
-
Worlitzsch, D., R. Tarran, M. Ulrich, U. Schwab, A. Cekici, K. C. Meyer, P. Birrer, G. Bellon, J. Berger, T. Weiss, K. Botzenhart, J. R. Yankaskas, S. Randell, R. C. Boucher, and G. Doring. 2002. Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. J. Clin. Invest. 109:317-325.
-
(2002)
J. Clin. Invest.
, vol.109
, pp. 317-325
-
-
Worlitzsch, D.1
Tarran, R.2
Ulrich, M.3
Schwab, U.4
Cekici, A.5
Meyer, K.C.6
Birrer, P.7
Bellon, G.8
Berger, J.9
Weiss, T.10
Botzenhart, K.11
Yankaskas, J.R.12
Randell, S.13
Boucher, R.C.14
Doring, G.15
-
42
-
-
34347337394
-
Review of the literature examining the correlation among DNA microarray technologies
-
Yauk, C. L., and M. L. Berndt. 2007. Review of the literature examining the correlation among DNA microarray technologies. Environ. Mol. Mutagen. 48:380-394.
-
(2007)
Environ. Mol. Mutagen.
, vol.48
, pp. 380-394
-
-
Yauk, C.L.1
Berndt, M.L.2
|