-
1
-
-
84863662483
-
Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
-
Agren, R., Bordel, S., Mardinoglu, A., Pornputtapong, N., Nookaew, I., and Nielsen, J. (2012). Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput. Biol. 8:e1002518. doi: 10.1371/journal.pcbi.1002518
-
(2012)
PLoS Comput. Biol.
, vol.8
-
-
Agren, R.1
Bordel, S.2
Mardinoglu, A.3
Pornputtapong, N.4
Nookaew, I.5
Nielsen, J.6
-
2
-
-
84898663879
-
Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling
-
Agren, R., Mardinoglu, A., Asplund, A., Kampf, C., Uhlen, M., and Nielsen, J. (2014). Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Mol. Syst. Biol. 10, 721. doi: 10.1002/msb.145122
-
(2014)
Mol. Syst. Biol.
, vol.10
, pp. 721
-
-
Agren, R.1
Mardinoglu, A.2
Asplund, A.3
Kampf, C.4
Uhlen, M.5
Nielsen, J.6
-
3
-
-
80052406750
-
Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis
-
Ahn, S. Y., Jamshidi, N., Mo, M. L., Wu, W., Eraly, S. A., Dnyanmote, A., et al. (2011). Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis. J. Biol. Chem. 286, 31522-31531. doi: 10.1074/jbc.M111.272534
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 31522-31531
-
-
Ahn, S.Y.1
Jamshidi, N.2
Mo, M.L.3
Wu, W.4
Eraly, S.A.5
Dnyanmote, A.6
-
4
-
-
8144230574
-
Discrimination of modes of action of antifungal substances by use of metabolic footprinting
-
Allen, J., Davey, H. M., Broadhurst, D., Rowland, J. J., Oliver, S. G., and Kell, D. B. (2004). Discrimination of modes of action of antifungal substances by use of metabolic footprinting. Appl. Environ. Microbiol. 70, 6157-6165. doi: 10.1128/AEM.70.10.6157-6165.2004
-
(2004)
Appl. Environ. Microbiol.
, vol.70
, pp. 6157-6165
-
-
Allen, J.1
Davey, H.M.2
Broadhurst, D.3
Rowland, J.J.4
Oliver, S.G.5
Kell, D.B.6
-
5
-
-
84870853302
-
Contextualization procedure and modeling of monocyte specific TLR signaling
-
Aurich, M. K., and Thiele, I. (2012). Contextualization procedure and modeling of monocyte specific TLR signaling. PLoS ONE 7:e49978. doi: 10.1371/journal.pone.0049978
-
(2012)
PLoS ONE
, vol.7
-
-
Aurich, M.K.1
Thiele, I.2
-
6
-
-
84950258683
-
Computational modeling of human metabolism and its application to systems biomedicine
-
Aurich, M. K., and Thiele, I. (2016). Computational modeling of human metabolism and its application to systems biomedicine. Methods Mol. Biol. 1386, 253-281. doi: 10.1007/978-1-4939-3283-2_12
-
(2016)
Methods Mol. Biol.
, vol.1386
, pp. 253-281
-
-
Aurich, M.K.1
Thiele, I.2
-
7
-
-
84930373777
-
Prediction of intracellular metabolic states from extracellular metabolomic data
-
Aurich, M., Paglia, G., Rolfsson, Ó., Hrafnsdóttir, S., Magnúsdóttir, M., Stefaniak, M., et al. (2015). Prediction of intracellular metabolic states from extracellular metabolomic data. Metabolomics 11, 603-619. doi: 10.1007/s11306-014-0721-3
-
(2015)
Metabolomics
, vol.11
, pp. 603-619
-
-
Aurich, M.1
Paglia, G.2
Rolfsson, Ó.3
Hrafnsdóttir, S.4
Magnúsdóttir, M.5
Stefaniak, M.6
-
8
-
-
84919935837
-
Getting the right answers: understanding metabolomics challenges
-
Beisken, S., Eiden, M., and Salek, R. M. (2015). Getting the right answers: understanding metabolomics challenges. Expert Rev. Mol. Diagn. 15, 97-109. doi: 10.1586/14737159.2015.974562
-
(2015)
Expert Rev. Mol. Diagn.
, vol.15
, pp. 97-109
-
-
Beisken, S.1
Eiden, M.2
Salek, R.M.3
-
9
-
-
84866487453
-
Integration of expression data in genome-scale metabolic network reconstructions
-
Blazier, A. S., and Papin, J. A. (2012). Integration of expression data in genome-scale metabolic network reconstructions. Front. Physiol. 3:299. doi: 10.3389/fphys.2012.00299
-
(2012)
Front. Physiol.
, vol.3
, pp. 299
-
-
Blazier, A.S.1
Papin, J.A.2
-
10
-
-
84855929956
-
Using the reconstructed genome-scale human metabolic network to study physiology and pathology
-
Bordbar, A., and Palsson, B. O. (2012). Using the reconstructed genome-scale human metabolic network to study physiology and pathology. J. Intern. Med. 271, 131-141. doi: 10.1111/j.1365-2796.2011.02494.x
-
(2012)
J. Intern. Med.
, vol.271
, pp. 131-141
-
-
Bordbar, A.1
Palsson, B.O.2
-
11
-
-
77958537509
-
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
-
Bordbar, A., Lewis, N. E., Schellenberger, J., Palsson, B. O., and Jamshidi, N. (2010). Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol. Syst. Biol. 6, 422. doi: 10.1038/msb.2010.68
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 422
-
-
Bordbar, A.1
Lewis, N.E.2
Schellenberger, J.3
Palsson, B.O.4
Jamshidi, N.5
-
12
-
-
84863331725
-
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation
-
Bordbar, A., Mo, M. L., Nakayasu, E. S., Schrimpe-Rutledge, A. C., Kim, Y. M., Metz, T. O., et al. (2012). Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol. Syst. Biol. 8, 558. doi: 10.1038/msb.2012.21
-
(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
-
13
-
-
77954253893
-
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
-
Cottret, L., Wildridge, D., Vinson, F., Barrett, M. P., Charles, H., Sagot, M. F., et al. (2010). MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res. 38, W132-W137. doi: 10.1093/nar/gkq312
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W132-W137
-
-
Cottret, L.1
Wildridge, D.2
Vinson, F.3
Barrett, M.P.4
Charles, H.5
Sagot, M.F.6
-
14
-
-
77955518663
-
Cell culture metabolomics: applications and future directions
-
Cuperlovic-Culf, M., Barnett, D. A., Culf, A. S., and Chute, I. (2010). Cell culture metabolomics: applications and future directions. Drug Discov. Today 15, 610-621. doi: 10.1016/j.drudis.2010.06.012
-
(2010)
Drug Discov. Today
, vol.15
, pp. 610-621
-
-
Cuperlovic-Culf, M.1
Barnett, D.A.2
Culf, A.S.3
Chute, I.4
-
15
-
-
38549127678
-
ChEBI: a database and ontology for chemical entities of biological interest
-
Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., et al. (2008). ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344-D350. doi: 10.1093/nar/gkm791
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D344-D350
-
-
Degtyarenko, K.1
de Matos, P.2
Ennis, M.3
Hastings, J.4
Zbinden, M.5
McNaught, A.6
-
16
-
-
84890209181
-
Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia
-
Fan, J., Kamphorst, J. J., Mathew, R., Chung, M. K., White, E., Shlomi, T., et al. (2013). Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia. Mol. Syst. Biol. 9, 712. doi: 10.1038/msb.2013.65
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 712
-
-
Fan, J.1
Kamphorst, J.J.2
Mathew, R.3
Chung, M.K.4
White, E.5
Shlomi, T.6
-
17
-
-
84924020376
-
Pathomx: an interactive workflow-based tool for the analysis of metabolomic data
-
Fitzpatrick, M. A., McGrath, C. M., and Young, S. P. (2014). Pathomx: an interactive workflow-based tool for the analysis of metabolomic data. BMC Bioinform. 15:396. doi: 10.1186/s12859-014-0396-9
-
(2014)
BMC Bioinform.
, vol.15
, pp. 396
-
-
Fitzpatrick, M.A.1
McGrath, C.M.2
Young, S.P.3
-
18
-
-
80052580351
-
Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase
-
Frezza, C., Zheng, L., Folger, O., Rajagopalan, K. N., MacKenzie, E. D., Jerby, L., et al. (2011). Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. Nature 477, 225-228. doi: 10.1038/nature10363
-
(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
-
19
-
-
84899489010
-
Exometabolome analysis reveals hypoxia at the up-scaling of a Saccharomyces cerevisiae high-cell density fed-batch biopharmaceutical process
-
Fu, Z., Verderame, T. D., Leighton, J. M., Sampey, B. P., Appelbaum, E. R., Patel, P. S., et al. (2014). Exometabolome analysis reveals hypoxia at the up-scaling of a Saccharomyces cerevisiae high-cell density fed-batch biopharmaceutical process. Microb. Cell Fact. 13:32. doi: 10.1186/1475-2859-13-32
-
(2014)
Microb. Cell Fact.
, vol.13
, pp. 32
-
-
Fu, Z.1
Verderame, T.D.2
Leighton, J.M.3
Sampey, B.P.4
Appelbaum, E.R.5
Patel, P.S.6
-
20
-
-
84936890106
-
Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
-
Ghaffari, P., Mardinoglu, A., Asplund, A., Shoaie, S., Kampf, C., Uhlen, M., et al. (2015). Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling. Sci. Rep. 5:8183. doi: 10.1038/srep08183
-
(2015)
Sci. Rep.
, vol.5
, pp. 8183
-
-
Ghaffari, P.1
Mardinoglu, A.2
Asplund, A.3
Shoaie, S.4
Kampf, C.5
Uhlen, M.6
-
21
-
-
77957117220
-
Computationally efficient flux variability analysis
-
Gudmundsson, S., and Thiele, I. (2010). Computationally efficient flux variability analysis. BMC Bioinformatics 11:489. doi: 10.1186/1471-2105-11-489
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 489
-
-
Gudmundsson, S.1
Thiele, I.2
-
22
-
-
84908698705
-
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2
-
Haraldsdottir, H. S., Thiele, I., and Fleming, R. M. (2014). Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. J. Cheminform. 6:2. doi: 10.1186/1758-2946-6-2
-
(2014)
J. Cheminform.
, vol.6
, pp. 2
-
-
Haraldsdottir, H.S.1
Thiele, I.2
Fleming, R.M.3
-
23
-
-
84920265598
-
Transparency in metabolic network reconstruction enables scalable biological discovery
-
Heavner, B. D., and Price, N. D. (2015). Transparency in metabolic network reconstruction enables scalable biological discovery. Curr. Opin. Biotechnol. 34:105-109. doi: 10.1016/j.copbio.2014.12.010
-
(2015)
Curr. Opin. Biotechnol.
, vol.34
, pp. 105-109
-
-
Heavner, B.D.1
Price, N.D.2
-
24
-
-
84861420588
-
Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation
-
Jain, M., Nilsson, R., Sharma, S., Madhusudhan, N., Kitami, T., Souza, A. L., et al. (2012). Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation. Science 36, 1040-1044. doi: 10.1126/science.1218595
-
(2012)
Science
, vol.36
, pp. 1040-1044
-
-
Jain, M.1
Nilsson, R.2
Sharma, S.3
Madhusudhan, N.4
Kitami, T.5
Souza, A.L.6
-
25
-
-
83655183165
-
Individualized therapy of HHT driven by network analysis of metabolomic profiles
-
Jamshidi, N., Miller, F. J., Mandel, J., Evans, T., and Kuo, M. D. (2011). Individualized therapy of HHT driven by network analysis of metabolomic profiles. BMC Syst. Biol. 5:200. doi: 10.1186/1752-0509-5-200
-
(2011)
BMC Syst. Biol.
, vol.5
, pp. 200
-
-
Jamshidi, N.1
Miller, F.J.2
Mandel, J.3
Evans, T.4
Kuo, M.D.5
-
26
-
-
77956417789
-
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
-
Jerby, L., Shlomi, T., and Ruppin, E. (2010). Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol. Syst. Biol. 6:401. doi: 10.1038/msb.2010.56
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 401
-
-
Jerby, L.1
Shlomi, T.2
Ruppin, E.3
-
27
-
-
33644527950
-
The model organism as a system: integrating 'omics' data sets
-
Joyce, A. R., and Palsson, B. O. (2006). The model organism as a system: integrating 'omics' data sets. Nat. Rev. Mol. Cell Biol. 7, 198-210. doi: 10.1038/nrm1857
-
(2006)
Nat. Rev. Mol. Cell Biol.
, vol.7
, pp. 198-210
-
-
Joyce, A.R.1
Palsson, B.O.2
-
28
-
-
2942676743
-
Metabolomics and systems biology: making sense of the soup
-
Kell, D. B. (2004). Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7, 296-307. doi: 10.1016/j.mib.2004.04.012
-
(2004)
Curr. Opin. Microbiol.
, vol.7
, pp. 296-307
-
-
Kell, D.B.1
-
29
-
-
84861790964
-
The dynamic range of the human metabolome revealed by challenges
-
Krug, S., Kastenmuller, G., Stuckler, F., Rist, M. J., Skurk, T., Sailer, M., et al. (2012). The dynamic range of the human metabolome revealed by challenges. FASEB J. 26, 2607-2619. doi: 10.1096/fj.11-198093
-
(2012)
FASEB J.
, vol.26
, pp. 2607-2619
-
-
Krug, S.1
Kastenmuller, G.2
Stuckler, F.3
Rist, M.J.4
Skurk, T.5
Sailer, M.6
-
30
-
-
84922201382
-
Global profiling of metabolic adaptation to hypoxic stress in human glioblastoma cells
-
Kucharzewska, P., Christianson, H. C., and Belting, M. (2015). Global profiling of metabolic adaptation to hypoxic stress in human glioblastoma cells. PLoS ONE 10:e0116740. doi: 10.1371/journal.pone.0116740
-
(2015)
PLoS ONE
, vol.10
-
-
Kucharzewska, P.1
Christianson, H.C.2
Belting, M.3
-
31
-
-
84858439602
-
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
-
Lewis, N. E., Nagarajan, H., and Palsson, B. O. (2012). Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Microbiol. 10, 291-305. doi: 10.1038/nrmicro2737
-
(2012)
Nat. Rev. Microbiol.
, vol.10
, pp. 291-305
-
-
Lewis, N.E.1
Nagarajan, H.2
Palsson, B.O.3
-
32
-
-
84901306814
-
Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
-
Machado, D., and Herrgard, M. (2014). Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput. Biol. 10:e1003580. doi: 10.1371/journal.pcbi.1003580
-
(2014)
PLoS Comput. Biol.
, vol.10
-
-
Machado, D.1
Herrgard, M.2
-
33
-
-
84883787394
-
Integration of clinical data with a genome-scale metabolic model of the human adipocyte
-
Mardinoglu, A., Agren, R., Kampf, C., Asplund, A., Nookaew, I., Jacobson, P., et al. (2013). Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Mol. Syst. Biol. 9, 649. doi: 10.1038/msb.2013.5
-
(2013)
Mol. Syst. Biol.
, vol.9
, pp. 649
-
-
Mardinoglu, A.1
Agren, R.2
Kampf, C.3
Asplund, A.4
Nookaew, I.5
Jacobson, P.6
-
34
-
-
84898011025
-
Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease
-
Mardinoglu, A., Agren, R., Kampf, C., Asplund, A., Uhlen, M., and Nielsen, J. (2014b). Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nat. Commun. 5:3083. doi: 10.1038/ncomms4083
-
(2014)
Nat. Commun.
, vol.5
, pp. 3083
-
-
Mardinoglu, A.1
Agren, R.2
Kampf, C.3
Asplund, A.4
Uhlen, M.5
Nielsen, J.6
-
35
-
-
84908884352
-
Defining the human adipose tissue proteome to reveal metabolic alterations in obesity
-
Mardinoglu, A., Kampf, C., Asplund, A., Fagerberg, L., Hallstrom, B. M., Edlund, K., et al. (2014a). Defining the human adipose tissue proteome to reveal metabolic alterations in obesity. J. Proteome Res. 13, 5106-5119. doi: 10.1021/pr500586e
-
(2014)
J. Proteome Res.
, vol.13
, pp. 5106-5119
-
-
Mardinoglu, A.1
Kampf, C.2
Asplund, A.3
Fagerberg, L.4
Hallstrom, B.M.5
Edlund, K.6
-
36
-
-
84952863976
-
Updates in metabolomics tools and resources: 2014-2015
-
Misra, B. B., and van der Hooft, J. J. (2016). Updates in metabolomics tools and resources: 2014-2015. Electrophoresis 37, 86-110. doi: 10.1002/elps.201500417
-
(2016)
Electrophoresis
, vol.37
, pp. 86-110
-
-
Misra, B.B.1
van der Hooft, J.J.2
-
37
-
-
65649126379
-
Connecting extracellular metabolomic measurements to intracellular flux states in yeast
-
Mo, M. L., Palsson, B. O., and Herrgard, M. J. (2009). Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst. Biol. 3:37. doi: 10.1186/1752-0509-3-37
-
(2009)
BMC Syst. Biol.
, vol.3
, pp. 37
-
-
Mo, M.L.1
Palsson, B.O.2
Herrgard, M.J.3
-
38
-
-
0032919364
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M. (1999). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34. doi: 10.1093/nar/27.1.29
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
39
-
-
77749320898
-
What is flux balance analysis?
-
Orth, J. D., Thiele, I., and Palsson, B. O. (2010). What is flux balance analysis? Nat. Biotechnol. 28, 245-248. doi: 10.1038/nbt.1614
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 245-248
-
-
Orth, J.D.1
Thiele, I.2
Palsson, B.O.3
-
40
-
-
84856231790
-
Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS)
-
Paglia, G., Hrafnsdottir, S., Magnusdottir, M., Fleming, R. M., Thorlacius, S., Palsson, B. O., et al. (2012). Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS). Anal. Bioanal. Chem. 402, 1183-1198. doi: 10.1007/s00216-011-5556-4
-
(2012)
Anal. Bioanal. Chem.
, vol.402
, pp. 1183-1198
-
-
Paglia, G.1
Hrafnsdottir, S.2
Magnusdottir, M.3
Fleming, R.M.4
Thorlacius, S.5
Palsson, B.O.6
-
41
-
-
84897372328
-
Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits
-
Petersen, A. K., Zeilinger, S., Kastenmuller, G., Romisch-Margl, W., Brugger, M., Peters, A., et al. (2013). Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits. Hum. Mol. Genet. 23, 534-545. doi: 10.1093/hmg/ddt430
-
(2013)
Hum. Mol. Genet.
, vol.23
, pp. 534-545
-
-
Petersen, A.K.1
Zeilinger, S.2
Kastenmuller, G.3
Romisch-Margl, W.4
Brugger, M.5
Peters, A.6
-
42
-
-
8544235670
-
Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies
-
Price, N. D., Schellenberger, J., and Palsson, B. O. (2004). Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys. J. 87, 2172-2186. doi: 10.1529/biophysj.104.043000
-
(2004)
Biophys. J.
, vol.87
, pp. 2172-2186
-
-
Price, N.D.1
Schellenberger, J.2
Palsson, B.O.3
-
43
-
-
84897931922
-
Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease
-
Sahoo, S., Aurich, M. K., Jonsson, J. J., and Thiele, I. (2014). Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease. Front. Physiol. 5:91. doi: 10.3389/fphys.2014.00091
-
(2014)
Front. Physiol.
, vol.5
, pp. 91
-
-
Sahoo, S.1
Aurich, M.K.2
Jonsson, J.J.3
Thiele, I.4
-
44
-
-
77951880802
-
Metabolomics for functional genomics, systems biology, and biotechnology
-
Saito, K., and Matsuda, F. (2010). Metabolomics for functional genomics, systems biology, and biotechnology. Annu. Rev. Plant Biol. 61, 463-489. doi: 10.1146/annurev.arplant.043008.092035
-
(2010)
Annu. Rev. Plant Biol.
, vol.61
, pp. 463-489
-
-
Saito, K.1
Matsuda, F.2
-
45
-
-
65549092780
-
Use of randomized sampling for analysis of metabolic networks
-
Schellenberger, J., and Palsson, B. O. (2009). Use of randomized sampling for analysis of metabolic networks. J. Biol. Chem. 284, 5457-5461. doi: 10.1074/jbc.R800048200
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 5457-5461
-
-
Schellenberger, J.1
Palsson, B.O.2
-
46
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
-
Schellenberger, J., Que, R., Fleming, R. M., Thiele, I., Orth, J. D., Feist, A. M., et al. (2011). Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 6, 1290-1307. doi: 10.1038/nprot.2011.308
-
(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
-
47
-
-
84890092837
-
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data
-
Schmidt, B. J., Ebrahim, A., Metz, T. O., Adkins, J. N., Palsson, B. O., and Hyduke, D. R. (2013). GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics 29, 2900-2908. doi: 10.1093/bioinformatics/btt493
-
(2013)
Bioinformatics
, vol.29
, pp. 2900-2908
-
-
Schmidt, B.J.1
Ebrahim, A.2
Metz, T.O.3
Adkins, J.N.4
Palsson, B.O.5
Hyduke, D.R.6
-
48
-
-
84919381769
-
Integrating transcriptomics with metabolic modeling predicts biomarkers and drug targets for Alzheimer's disease
-
Stempler, S., Yizhak, K., and Ruppin, E. (2014). Integrating transcriptomics with metabolic modeling predicts biomarkers and drug targets for Alzheimer's disease. PLoS ONE 9:e105383. doi: 10.1371/journal.pone.0105383
-
(2014)
PLoS ONE
, vol.9
-
-
Stempler, S.1
Yizhak, K.2
Ruppin, E.3
-
49
-
-
78651467275
-
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
-
Thiele, I., Hyduke, D. R., Steeb, B., Fankam, G., Allen, D. K., Bazzani, S., et al. (2011). A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst. Biol. 5:8. doi: 10.1186/1752-0509-5-8
-
(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
-
50
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele, I., and Palsson, B. O. (2010). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc. 5, 93-121. doi: 10.1038/nprot.2009.203
-
(2010)
Nat. Protoc.
, vol.5
, pp. 93-121
-
-
Thiele, I.1
Palsson, B.O.2
-
51
-
-
15844387127
-
Candidate metabolic network states in human mitochondria
-
Thiele, I., Price, N. D., Vo, T. D., and Palsson, B. O. (2005). Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J. Biol. Chem. 280, 11683-11695. doi: 10.1074/jbc.M409072200
-
(2005)
Impact of diabetes, ischemia, and diet. J. Biol. Chem.
, vol.280
, pp. 11683-11695
-
-
Thiele, I.1
Price, N.D.2
Vo, T.D.3
Palsson, B.O.4
-
52
-
-
84877315835
-
A community-driven global reconstruction of human metabolism
-
Thiele, I., Swainston, N., Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., et al. (2013). A community-driven global reconstruction of human metabolism. Nat. Biotechnol. 31, 419-425. doi: 10.1038/nbt.2488
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 419-425
-
-
Thiele, I.1
Swainston, N.2
Fleming, R.M.3
Hoppe, A.4
Sahoo, S.5
Aurich, M.K.6
-
53
-
-
79960126760
-
rBioNet: a COBRA toolbox extension for reconstructing high-quality biochemical networks
-
Thorleifsson, S. G., and Thiele, I. (2011). rBioNet: a COBRA toolbox extension for reconstructing high-quality biochemical networks. Bioinformatics 27, 2009-2010. doi: 10.1093/bioinformatics/btr308
-
(2011)
Bioinformatics
, vol.27
, pp. 2009-2010
-
-
Thorleifsson, S.G.1
Thiele, I.2
-
54
-
-
84964754404
-
Improved metabolite identification with MIDAS and MAGMa through MS/MS spectral dataset-driven parameter optimization
-
Verdegem, D., Lambrechts, D., Carmeliet, P., and Ghesquière, B. (2016). Improved metabolite identification with MIDAS and MAGMa through MS/MS spectral dataset-driven parameter optimization. Metabolomics 12, 1-16. doi: 10.1007/s11306-016-1036-3
-
(2016)
Metabolomics
, vol.12
, pp. 1-16
-
-
Verdegem, D.1
Lambrechts, D.2
Carmeliet, P.3
Ghesquière, B.4
-
55
-
-
84896701551
-
Fast reconstruction of compact context-specific metabolic network models
-
Vlassis, N., Pacheco, M. P., and Sauter, T. (2014). Fast reconstruction of compact context-specific metabolic network models. PLoS Comput. Biol. 10:e1003424. doi: 10.1371/journal.pcbi.1003424
-
(2014)
PLoS Comput. Biol.
, vol.10
-
-
Vlassis, N.1
Pacheco, M.P.2
Sauter, T.3
-
56
-
-
84876148784
-
HMDB 3.0-The Human Metabolome Database in 2013
-
Wishart, D. S., Jewison, T., Guo, A. C., Wilson, M., Knox, C., Liu, Y., et al. (2013). HMDB 3.0-The Human Metabolome Database in 2013. Nucleic Acids Res. 41, D801-D807. doi: 10.1093/nar/gks1065
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D801-D807
-
-
Wishart, D.S.1
Jewison, T.2
Guo, A.C.3
Wilson, M.4
Knox, C.5
Liu, Y.6
-
57
-
-
84930377006
-
Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer
-
Yizhak, K., Gaude, E., Le Devedec, S., Waldman, Y. Y., Stein, G. Y., van de Water, B., et al. (2014). Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer. Elife 3:e03641. doi: 10.7554/eLife.03641
-
(2014)
Elife
, vol.3
-
-
Yizhak, K.1
Gaude, E.2
Le Devedec, S.3
Waldman, Y.Y.4
Stein, G.Y.5
van de Water, B.6
|