-
1
-
-
77951612556
-
BiGG: A biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions
-
20426874
-
Schellenberger J, Park JO, Conrad TM, Palsson BØ. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics. 2010;11:213. doi: 10. 1186/1471-2105-11-213 PMID: 20426874
-
(2010)
BMC Bioinformatics.
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.M.3
Palsson BØ4
-
2
-
-
84859346785
-
Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: Lessons from an Arabidopsis cell culture and other systems
-
22140245
-
Kruger NJ, Masakapalli SK, Ratcliffe RG. Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: Lessons from an Arabidopsis cell culture and other systems. Journal of Experimental Botany. 2012. pp. 2309-2323. doi: 10.1093/jxb/err382 PMID: 22140245
-
(2012)
Journal of Experimental Botany
, pp. 2309-2323
-
-
Kruger, N.J.1
Masakapalli, S.K.2
Ratcliffe, R.G.3
-
3
-
-
79954459893
-
Construction of an E. Coli genome-scale atom mapping model for MFA calculations
-
21328316
-
Ravikirthi P, Suthers PF, Maranas CD. Construction of an E. Coli genome-scale atom mapping model for MFA calculations. Biotechnol Bioeng. 2011;108:1372-1382. doi: 10.1002/bit.23070 PMID: 21328316
-
(2011)
Biotechnol Bioeng.
, vol.108
, pp. 1372-1382
-
-
Ravikirthi, P.1
Suthers, P.F.2
Maranas, C.D.3
-
4
-
-
80555122963
-
Mapping photoautotrophic metabolism with isotopically nonstationary (13) C flux analysis
-
21907300
-
Young JD, Shastri AA, Stephanopoulos G, Morgan JA. Mapping photoautotrophic metabolism with isotopically nonstationary (13) C flux analysis. Metab Eng. 2011;13:656-65. doi: 10.1016/j.ymben. 2011. 08.002 PMID: 21907300
-
(2011)
Metab Eng.
, vol.13
, pp. 656-665
-
-
Young, J.D.1
Shastri, A.A.2
Stephanopoulos, G.3
Morgan, J.A.4
-
5
-
-
84872093417
-
Analysis of omics data with genome-scale models of metabolism
-
23247105
-
Hyduke DR, Lewis NE, Palsson BØ. Analysis of omics data with genome-scale models of metabolism. Mol Biosyst. 2013;9:167-74. doi: 10.1039/c2mb25453k PMID: 23247105
-
(2013)
Mol Biosyst.
, vol.9
, pp. 167-174
-
-
Hyduke, D.R.1
Lewis, N.E.2
Palsson BØ3
-
6
-
-
84866487453
-
Integration of expression data in genome-scale metabolic network reconstructions
-
Blazier AS, Papin JA. Integration of expression data in genome-scale metabolic network reconstructions. Frontiers in Physiology. 2012. doi: 10.3389/fphys.2012.00299
-
(2012)
Frontiers in Physiology
-
-
Blazier, A.S.1
Papin, J.A.2
-
7
-
-
84885218166
-
Multiscale metabolic modeling: Dynamic flux balance analysis on a whole-plant scale
-
23926077
-
Grafahrend-Belau E, Junker A, Eschenröder A, Müller J, Schreiber F, Junker BH. Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale. Plant Physiol. 2013;163:637-47. doi: 10.1104/pp. 113.224006 PMID: 23926077
-
(2013)
Plant Physiol.
, vol.163
, pp. 637-647
-
-
Grafahrend-Belau, E.1
Junker, A.2
Eschenröder, A.3
Müller, J.4
Schreiber, F.5
Junker, B.H.6
-
8
-
-
78649796264
-
C4GEM, a genome-scale metabolic model to study C4 plant metabolism
-
20974891
-
Dal'Molin CG de O, Quek L-E, Palfreyman RW, Brumbley SM, Nielsen LK. C4GEM, a genome-scale metabolic model to study C4 plant metabolism. Plant Physiol. 2010;154:1871-1885. doi: 10.1104/pp. 110.166488 PMID: 20974891
-
(2010)
Plant Physiol.
, vol.154
, pp. 1871-1885
-
-
De Dal'Molin, C.G.O.1
Quek, L.-E.2
Palfreyman, R.W.3
Brumbley, S.M.4
Nielsen, L.K.5
-
9
-
-
84901306814
-
Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
-
24762745
-
Machado D, Herrgård M. Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput Biol. 2014;10:e1003580. Available: http://www.ncbi.nlm.nih.gov/pubmed/24762745. doi: 10.1371/journal.pcbi.1003580 PMID: 24762745
-
(2014)
PLoS Comput Biol.
, vol.10
, pp. e1003580
-
-
Machado, D.1
Herrgård, M.2
-
10
-
-
84907288908
-
Generalized framework for context-specific metabolic model extraction methods
-
Robaina Estévez S, Nikoloski Z. Generalized framework for context-specific metabolic model extraction methods. Front Plant Sci. 2014;5. doi: 10.3389/fpls.2014.00491
-
(2014)
Front Plant Sci.
, pp. 5
-
-
Robaina Estévez, S.1
Nikoloski, Z.2
-
11
-
-
44949225040
-
Context-specific metabolic networks are consistent with experiments
-
Becker SA, Palsson BO. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol. 2008;4.
-
(2008)
PLoS Comput Biol.
, pp. 4
-
-
Becker, S.A.1
Palsson, B.O.2
-
12
-
-
84890092837
-
GIM3E: Condition-specific models of cellular metabolism developed from metabolomics and expression data
-
23975765
-
Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson B, Hyduke DR. GIM3E: Condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics. 2013;29:2900-2908. doi: 10.1093/bioinformatics/btt493 PMID: 23975765
-
(2013)
Bioinformatics.
, vol.29
, pp. 2900-2908
-
-
Schmidt, B.J.1
Ebrahim, A.2
Metz, T.O.3
Adkins, J.N.4
Palsson, B.5
Hyduke, D.R.6
-
13
-
-
77749320898
-
What is flux balance analysis?
-
20212490
-
Orth JD, Thiele I, Palsson BØ. What is flux balance analysis? Nat Biotechnol. 2010;28:245-248. doi: 10.1038/nbt.1614 PMID: 20212490
-
(2010)
Nat Biotechnol.
, vol.28
, pp. 245-248
-
-
Orth, J.D.1
Thiele, I.2
Palsson BØ3
-
14
-
-
51349092391
-
Network-based prediction of human tissuespecific metabolism
-
18711341
-
Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. Network-based prediction of human tissuespecific metabolism. Nat Biotechnol. 2008;26:1003-1010. doi: 10.1038/nbt.1487 PMID: 18711341
-
(2008)
Nat Biotechnol.
, vol.26
, pp. 1003-1010
-
-
Shlomi, T.1
Cabili, M.N.2
Herrgård, M.J.3
Palsson B.Ø.4
Ruppin, E.5
-
15
-
-
84863662483
-
Reconstruction of genomescale active metabolic networks for 69 human cell types and 16 cancer types using INIT
-
Agren R, Bordel S, Mardinoglu A, Pornputtapong N, Nookaew I, Nielsen J. Reconstruction of genomescale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput Biol. 2012;8.
-
(2012)
PLoS Comput Biol.
, pp. 8
-
-
Agren, R.1
Bordel, S.2
Mardinoglu, A.3
Pornputtapong, N.4
Nookaew, I.5
Nielsen, J.6
-
16
-
-
84898663879
-
Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling
-
24646661
-
Agren R, Mardinoglu A, Asplund A, Kampf C, Uhlen M, Nielsen J. Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Mol Syst Biol. 2014;10:721. doi: 10.1002/msb.145122 PMID: 24646661
-
(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
-
17
-
-
77956417789
-
Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism
-
20823844
-
Jerby L, Shlomi T, Ruppin E. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol. 2010;6:401. doi: 10.1038/msb.2010.56 PMID: 20823844
-
(2010)
Mol Syst Biol.
, vol.6
, pp. 401
-
-
Jerby, L.1
Shlomi, T.2
Ruppin, E.3
-
18
-
-
84870933131
-
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
-
23234303
-
Wang Y, Eddy J A, Price ND. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol. 2012;6:153. doi: 10.1186/1752-0509-6-153 PMID: 23234303
-
(2012)
BMC Syst Biol.
, vol.6
, pp. 153
-
-
Wang, Y.1
Eddy, J.A.2
Price, N.D.3
-
19
-
-
84896701551
-
Fast reconstruction of compact context-specific metabolic network models
-
Vlassis N, Pacheco MP, Sauter T. Fast Reconstruction of Compact Context-Specific Metabolic Network Models. PLoS Comput Biol. 2014;10.
-
(2014)
PLoS Comput Biol.
, pp. 10
-
-
Vlassis, N.1
Pacheco, M.P.2
Sauter, T.3
-
20
-
-
84858439602
-
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
-
Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nature Reviews Microbiology. 2012. doi: 10.1038/nrmicro2737
-
(2012)
Nature Reviews Microbiology
-
-
Lewis, N.E.1
Nagarajan, H.2
Palsson, B.O.3
-
21
-
-
34548275795
-
The Dantzig selector: Statistical estimation when p is much larger than n
-
Candes E, Tao T. The Dantzig selector: Statistical estimation when p is much larger than n. Ann Stat. 2007;35:2313-2351. doi: 10.1214/009053606000001523
-
(2007)
Ann Stat.
, vol.35
, pp. 2313-2351
-
-
Candes, E.1
Tao, T.2
-
23
-
-
16244401458
-
Regularization and variable selection via the elastic net
-
Zou H, Hastie T. Regularization and variable selection via the elastic net. J R Stat Soc Ser B Stat Methodol. 2005;67:301-320. doi: 10.1111/j.1467-9868.2005.00503.x
-
(2005)
J R Stat Soc Ser B Stat Methodol.
, vol.67
, pp. 301-320
-
-
Zou, H.1
Hastie, T.2
-
24
-
-
85194972808
-
Regression Selection and Shrinkage via the Lasso
-
Tibshirani R. Regression Selection and Shrinkage via the Lasso. J R Stat Soc B. 1994;58:267-288.
-
(1994)
J R Stat Soc B
, vol.58
, pp. 267-288
-
-
Tibshirani, R.1
-
26
-
-
58349104057
-
Least angle and L1 penalized regression: A review
-
Hesterberg T, Choi NH, Meier L, Fraley C. Least Angle and L1 Penalized Regression: A Review. Stat Surv. 2008;2:61-93. doi: 10.1214/08-SS035
-
(2008)
Stat Surv.
, vol.2
, pp. 61-93
-
-
Hesterberg, T.1
Choi, N.H.2
Meier, L.3
Fraley, C.4
-
27
-
-
84941305055
-
Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach
-
abs/1205.1:1-15
-
Pan W, Yuan Y, Stan G. Reconstruction of arbitrary biochemical reaction networks: a compressive sensing approach. CoRR. 2012; abs/1205.1:1-15. Available: http://arxiv.org/abs/1205.1720.
-
(2012)
CoRR.
-
-
Pan, W.1
Yuan, Y.2
Stan, G.3
-
29
-
-
80053175304
-
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks
-
21943338
-
Jensen PA, Lutz KA, Papin JA. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Systems Biology. 2011. p. 147. doi: 10. 1186/1752-0509-5-147 PMID: 21943338
-
(2011)
BMC Systems Biology
, pp. 147
-
-
Jensen, P.A.1
Lutz, K.A.2
Papin, J.A.3
-
31
-
-
84976895733
-
COBRA Toolbox 2.0
-
Hyduke D, Schellenberger J, Que R, Fleming R, Thiele I, Orth J, et al. COBRA Toolbox 2.0. Protocol Exchange. 2011. doi: 10.1038/protex.2011.234
-
(2011)
Protocol Exchange.
-
-
Hyduke, D.1
Schellenberger, J.2
Que, R.3
Fleming, R.4
Thiele, I.5
Orth, J.6
-
32
-
-
33846910173
-
Global reconstruction of the human metabolic network based on genomic and bibliomic data
-
17267599
-
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A. 2007;104:1777-1782. doi: 10.1073/pnas.0610772104 PMID: 17267599
-
(2007)
Proc Natl Acad Sci U S A.
, vol.104
, pp. 1777-1782
-
-
Duarte, N.C.1
Becker, S.A.2
Jamshidi, N.3
Thiele, I.4
Mo, M.L.5
Vo, T.D.6
-
33
-
-
79951745716
-
IMAT: An integrative metabolic analysis tool
-
21081510
-
Zur H, Ruppin E, Shlomi T. iMAT: An integrative metabolic analysis tool. Bioinformatics. 2010;26:3140-3142. doi: 10.1093/bioinformatics/btq602 PMID: 21081510
-
(2010)
Bioinformatics.
, vol.26
, pp. 3140-3142
-
-
Zur, H.1
Ruppin, E.2
Shlomi, T.3
-
34
-
-
84877315835
-
A community-driven global reconstruction of human metabolism
-
23455439
-
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, et al. A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013;31:419-25. doi: 10.1038/nbt.2488 PMID: 23455439
-
(2013)
Nat Biotechnol.
, vol.31
, pp. 419-425
-
-
Thiele, I.1
Swainston, N.2
Fleming, R.M.T.3
Hoppe, A.4
Sahoo, S.5
Aurich, M.K.6
-
35
-
-
84859740873
-
RNA-Seq Atlas -A reference database for gene expression profiling in normal tissue by next-generation sequencing
-
22345621
-
Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A. RNA-Seq Atlas-a reference database for gene expression profiling in normal tissue by next-generation sequencing. Bioinformatics. 2012;28:1184-1185. doi: 10.1093/bioinformatics/bts084 PMID: 22345621
-
(2012)
Bioinformatics.
, vol.28
, pp. 1184-1185
-
-
Krupp, M.1
Marquardt, J.U.2
Sahin, U.3
Galle, P.R.4
Castle, J.5
Teufel, A.6
-
36
-
-
84862301363
-
Improving metabolic flux predictions using absolute gene expression data
-
Lee D, Smallbone K, Dunn WB, Murabito E, Winder CL, Kell DB, et al. Improving metabolic flux predictions using absolute gene expression data. BMC Syst Biol. BMC Systems Biology; 2012;6:73. doi: 10. 1186/1752-0509-6-73
-
(2012)
BMC Syst Biol. BMC Systems Biology
, vol.6
, pp. 73
-
-
Lee, D.1
Smallbone, K.2
Dunn, W.B.3
Murabito, E.4
Winder, C.L.5
Kell, D.B.6
-
38
-
-
84920269464
-
Tissue-based map of the human proteome
-
Uhlén M et al. Tissue-based map of the human proteome. Science (80-). 2015;347. doi: 10.1126/science.1260419
-
(2015)
Science
, Issue.80
, pp. 347
-
-
Uhlén, M.1
-
39
-
-
84941305058
-
-
BioMart (Ensembl) [Internet]. Available: http://www.ensembl.org/biomart/martview/2a3c1aa45a4126aa9947f83d577eee2b.
-
-
-
BioMart (Ensembl) [Internet]1
-
40
-
-
33144474263
-
Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae
-
16467155
-
Rossell S, Van Der Weijden CC, Lindenbergh A, Van Tuijl A, Francke C, Bakker BM, et al. Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2006;103:2166-2171. doi: 10.1073/pnas.0509831103 PMID: 16467155
-
(2006)
Proc Natl Acad Sci U S A.
, vol.103
, pp. 2166-2171
-
-
Rossell, S.1
Van Der Weijden, C.C.2
Lindenbergh, A.3
Van Tuijl, A.4
Francke, C.5
Bakker, B.M.6
-
41
-
-
66149122278
-
Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p
-
19346491
-
Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, et al. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A. 2009;106:6477-6482. doi: 10.1073/pnas.0811091106 PMID: 19346491
-
(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
-
42
-
-
1642457253
-
The effects of alternate optimal solutions in constraint-based genomescale metabolic models
-
14642354
-
Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genomescale metabolic models. Metab Eng. 2003;5:264-276. PMID: 14642354
-
(2003)
Metab Eng.
, vol.5
, pp. 264-276
-
-
Mahadevan, R.1
Schilling, C.H.2
-
43
-
-
34250616386
-
Fatty acid metabolism in adipose tissue, muscle and liver in health and disease
-
17144882
-
Frayn KN, Arner P, Yki-Järvinen H. Fatty acid metabolism in adipose tissue, muscle and liver in health and disease. Essays Biochem. 2006;42:89-103. doi: 10.1042/bse0420089 PMID: 17144882
-
(2006)
Essays Biochem.
, vol.42
, pp. 89-103
-
-
Frayn, K.N.1
Arner, P.2
Yki-Järvinen, H.3
-
44
-
-
17444419341
-
Role of glutathione transport processes in kidney function
-
Lash LH. Role of glutathione transport processes in kidney function. Toxicology and Applied Pharmacology. 2005. pp. 329-342. doi: 10.1016/j.taap. 2004.10.004
-
(2005)
Toxicology and Applied Pharmacology
, pp. 329-342
-
-
Lash, L.H.1
|