-
1
-
-
20644467467
-
Systems biotechnology for strain improvement
-
Lee, S.Y., Lee, D.-Y. and Kim, T.Y. (2005) Systems biotechnology for strain improvement. Trends Biotechnol., 23, 349-358.
-
(2005)
Trends Biotechnol
, vol.23
, pp. 349-358
-
-
Lee, S.Y.1
Lee, D.-Y.2
Kim, T.Y.3
-
2
-
-
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.
-
(2012)
Front. Physiol
, vol.3
, pp. 299
-
-
Blazier, A.S.1
Papin, J.A.2
-
3
-
-
84924935721
-
Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization
-
Jha, A.K., Huang, S.C.-C., Sergushichev, A., Lampropoulou, V., Ivanova, Y., Loginicheva, E., Chmielewski, K., Stewart, K.M., Ashall, J., Everts, B. et al. (2015) Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization. Immunity, 42, 419-430.
-
(2015)
Immunity
, vol.42
, pp. 419-430
-
-
Jha, A.K.1
Huang, S.C.-C.2
Sergushichev, A.3
Lampropoulou, V.4
Ivanova, Y.5
Loginicheva, E.6
Chmielewski, K.7
Stewart, K.M.8
Ashall, J.9
Everts, B.10
-
4
-
-
84944889945
-
Mitochondrial phosphoenolpyruvate carboxykinase regulates metabolic adaptation and enables glucose-independent tumor growth
-
Vincent, E.E., Sergushichev, A., Griss, T., Gingras, M., Samborska, B., Ntimbane, T., Coelho, P.P., Blagih, J., Raissi, T.C., Choinière, L. et al. (2015) Mitochondrial phosphoenolpyruvate carboxykinase regulates metabolic adaptation and enables glucose-independent tumor growth. Mol. Cell, 60, 195-207.
-
(2015)
Mol. Cell
, vol.60
, pp. 195-207
-
-
Vincent, E.E.1
Sergushichev, A.2
Griss, T.3
Gingras, M.4
Samborska, B.5
Ntimbane, T.6
Coelho, P.P.7
Blagih, J.8
Raissi, T.C.9
Choinière, L.10
-
5
-
-
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., Jones, M.B., Frank, B.C., Smith, R.D., Peterson, S.N. et al. (2012) Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol. Syst. Biol., 8, 558.
-
(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
Jones, M.B.7
Frank, B.C.8
Smith, R.D.9
Peterson, S.N.10
-
6
-
-
77954197778
-
Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model
-
Yizhak, K., Benyamini, T., Liebermeister, W., Ruppin, E. and Shlomi, T. (2010) Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics, 26, i255-i260.
-
(2010)
Bioinformatics
, vol.26
, pp. i255-i260
-
-
Yizhak, K.1
Benyamini, T.2
Liebermeister, W.3
Ruppin, E.4
Shlomi, T.5
-
7
-
-
84864479791
-
MetaboAnalyst 2.0-a comprehensive server for metabolomic data analysis
-
Xia, J., Mandal, R., Sinelnikov, I. V, Broadhurst, D. and Wishart, D.S. (2012) MetaboAnalyst 2.0-a comprehensive server for metabolomic data analysis. Nucleic Acids Res., 40, W127-W133.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. W127-W133
-
-
Xia, J.1
Mandal, R.2
Sinelnikov, I. V3
Broadhurst, D.4
Wishart, D.S.5
-
8
-
-
84897674937
-
iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis
-
Sun, H., Wang, H., Zhu, R., Tang, K., Gong, Q., Cui, J., Cao, Z. and Liu, Q. (2014) iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis. Bioinformatics, 30, 737-739.
-
(2014)
Bioinformatics
, vol.30
, pp. 737-739
-
-
Sun, H.1
Wang, H.2
Zhu, R.3
Tang, K.4
Gong, Q.5
Cui, J.6
Cao, Z.7
Liu, Q.8
-
9
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
(Suppl. 1)
-
Ideker, T., Ozier, O., Schwikowski, B. and Siegel, A.F. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18(Suppl. 1), S233-S240.
-
(2002)
Bioinformatics
, vol.18
, pp. S233-S240
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
10
-
-
84925344291
-
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape
-
Alcaraz, N., Pauling, J., Batra, R., Barbosa, E., Junge, A., Christensen, A.G.L., Azevedo, V., Ditzel, H.J. and Baumbach, J. (2014) KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. BMC Syst. Biol., 8, 1-6.
-
(2014)
BMC Syst. Biol
, vol.8
, pp. 1-6
-
-
Alcaraz, N.1
Pauling, J.2
Batra, R.3
Barbosa, E.4
Junge, A.5
Christensen, A.G.L.6
Azevedo, V.7
Ditzel, H.J.8
Baumbach, J.9
-
11
-
-
21844472259
-
Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics
-
Hirai, M.Y., Klein, M., Fujikawa, Y., Yano, M., Goodenowe, D.B., Yamazaki, Y., Kanaya, S., Nakamura, Y., Kitayama, M., Suzuki, H. et al. (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. J. Biol. Chem., 280, 25590-25595.
-
(2005)
J. Biol. Chem
, vol.280
, pp. 25590-25595
-
-
Hirai, M.Y.1
Klein, M.2
Fujikawa, Y.3
Yano, M.4
Goodenowe, D.B.5
Yamazaki, Y.6
Kanaya, S.7
Nakamura, Y.8
Kitayama, M.9
Suzuki, H.10
-
12
-
-
84964694431
-
Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content
-
Kling, T., Johansson, P., Sanchez, J., Marinescu, V.D., Jörnsten, R. and Nelander, S. (2015) Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content. Nucleic Acids Res., 43, e98.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. e98
-
-
Kling, T.1
Johansson, P.2
Sanchez, J.3
Marinescu, V.D.4
Jörnsten, R.5
Nelander, S.6
-
13
-
-
84859959092
-
Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation
-
Zhu, J., Sova, P., Xu, Q., Dombek, K.M., Xu, E.Y., Vu, H., Tu, Z., Brem, R.B., Bumgarner, R.E. and Schadt, E.E. (2012) Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. PLoS Biol., 10, e1001301.
-
(2012)
PLoS Biol
, vol.10
, pp. e1001301
-
-
Zhu, J.1
Sova, P.2
Xu, Q.3
Dombek, K.M.4
Xu, E.Y.5
Vu, H.6
Tu, Z.7
Brem, R.B.8
Bumgarner, R.E.9
Schadt, E.E.10
-
14
-
-
84862297319
-
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum
-
Beisser, D., Grohme, M.A., Kopka, J., Frohme, M., Schill, R.O., Hengherr, S., Dandekar, T., Klau, G.W., Dittrich, M. and Müller, T. (2012) Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Syst. Biol., 6, 1-13.
-
(2012)
BMC Syst. Biol
, vol.6
, pp. 1-13
-
-
Beisser, D.1
Grohme, M.A.2
Kopka, J.3
Frohme, M.4
Schill, R.O.5
Hengherr, S.6
Dandekar, T.7
Klau, G.W.8
Dittrich, M.9
Müller, T.10
-
15
-
-
84897943328
-
Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software
-
Landesfeind, M., Kaever, A., Feussner, K., Thurow, C., Gatz, C., Feussner, I. and Meinicke, P. (2014) Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software. PeerJ, 2, e239.
-
(2014)
PeerJ
, vol.2
, pp. e239
-
-
Landesfeind, M.1
Kaever, A.2
Feussner, K.3
Thurow, C.4
Gatz, C.5
Feussner, I.6
Meinicke, P.7
-
16
-
-
84856562561
-
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data
-
Karnovsky, A., Weymouth, T., Hull, T., Tarcea, V.G., Scardoni, G., Laudanna, C., Sartor, M.A., Stringer, K.A., Jagadish, H.V., Burant, C. et al. (2012) Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. Bioinformatics, 28, 373-380.
-
(2012)
Bioinformatics
, vol.28
, pp. 373-380
-
-
Karnovsky, A.1
Weymouth, T.2
Hull, T.3
Tarcea, V.G.4
Scardoni, G.5
Laudanna, C.6
Sartor, M.A.7
Stringer, K.A.8
Jagadish, H.V.9
Burant, C.10
-
17
-
-
84893854125
-
Untargeted LC-MS metabolomics of bronchoalveolar lavage fluid differentiates acute respiratory distress syndrome from health
-
Evans, C.R., Karnovsky, A., Kovach, M.A., Standiford, T.J., Burant, C.F. and Stringer, K.A. (2014) Untargeted LC-MS metabolomics of bronchoalveolar lavage fluid differentiates acute respiratory distress syndrome from health. J. Proteome Res., 13, 640-649.
-
(2014)
J. Proteome Res
, vol.13
, pp. 640-649
-
-
Evans, C.R.1
Karnovsky, A.2
Kovach, M.A.3
Standiford, T.J.4
Burant, C.F.5
Stringer, K.A.6
-
18
-
-
46249128543
-
Identifying functional modules in protein-protein interaction networks: an integrated exact approach
-
Dittrich, M.T., Klau, G.W., Rosenwald, A., Dandekar, T. and Müller, T. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics, 24, i223-i231.
-
(2008)
Bioinformatics
, vol.24
, pp. i223-i231
-
-
Dittrich, M.T.1
Klau, G.W.2
Rosenwald, A.3
Dandekar, T.4
Müller, T.5
-
20
-
-
84864131140
-
Robustness and accuracy of functional modules in integrated network analysis
-
Beisser, D., Brunkhorst, S., Dandekar, T., Klau, G.W., Dittrich, M.T. and Müller, T. (2012) Robustness and accuracy of functional modules in integrated network analysis. Bioinformatics, 28, 1887-1894.
-
(2012)
Bioinformatics
, vol.28
, pp. 1887-1894
-
-
Beisser, D.1
Brunkhorst, S.2
Dandekar, T.3
Klau, G.W.4
Dittrich, M.T.5
Müller, T.6
-
21
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa, M. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
-
22
-
-
33846088138
-
HMDB: the human metabolome database
-
Wishart, D.S., Tzur, D., Knox, C., Eisner, R., Guo, A.C., Young, N., Cheng, D., Jewell, K., Arndt, D., Sawhney, S. et al. (2007) HMDB: the human metabolome database. Nucleic Acids Res., 35, D521-D526.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D521-D526
-
-
Wishart, D.S.1
Tzur, D.2
Knox, C.3
Eisner, R.4
Guo, A.C.5
Young, N.6
Cheng, D.7
Jewell, K.8
Arndt, D.9
Sawhney, S.10
-
23
-
-
84926507971
-
limma powers differential expression analyses for RNA-sequencing and microarray studies
-
Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W. and Smyth, G.K. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, e47.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. e47
-
-
Ritchie, M.E.1
Phipson, B.2
Wu, D.3
Hu, Y.4
Law, C.W.5
Shi, W.6
Smyth, G.K.7
-
24
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M.I., Huber, W. and Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 1-21.
-
(2014)
Genome Biol
, vol.15
, pp. 1-21
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
25
-
-
84879055437
-
Enhanced compact models for the connected subgraph problem and for the shortest path problem in digraphs with negative cycles
-
Haouari, M., Maculan, N. and Mrad, M. (2013) Enhanced compact models for the connected subgraph problem and for the shortest path problem in digraphs with negative cycles. Comput. Oper. Res., 40, 2485-2492.
-
(2013)
Comput. Oper. Res
, vol.40
, pp. 2485-2492
-
-
Haouari, M.1
Maculan, N.2
Mrad, M.3
-
26
-
-
84929191992
-
Aerobic glycolysis tunes YAP/TAZ transcriptional activity
-
Enzo, E., Santinon, G., Pocaterra, A., Aragona, M., Bresolin, S., Forcato, M., Grifoni, D., Pession, A., Zanconato, F., Guzzo, G. et al. (2015) Aerobic glycolysis tunes YAP/TAZ transcriptional activity. EMBO J., 34, 1349-1370.
-
(2015)
EMBO J
, vol.34
, pp. 1349-1370
-
-
Enzo, E.1
Santinon, G.2
Pocaterra, A.3
Aragona, M.4
Bresolin, S.5
Forcato, M.6
Grifoni, D.7
Pession, A.8
Zanconato, F.9
Guzzo, G.10
-
27
-
-
0141688316
-
Glucose deprivation induces mitochondrial dysfunction and oxidative stress in PC12 cell line
-
Liu, Y., Song, X.-D., Liu, W., Zhang, T.-Y. and Zuo, J. (2003) Glucose deprivation induces mitochondrial dysfunction and oxidative stress in PC12 cell line. J. Cell. Mol. Med., 7, 49-56.
-
(2003)
J. Cell. Mol. Med
, vol.7
, pp. 49-56
-
-
Liu, Y.1
Song, X.-D.2
Liu, W.3
Zhang, T.-Y.4
Zuo, J.5
-
28
-
-
84855453655
-
Glucose-independent glutamine metabolism via TCA cycling for proliferation and survival in B cells
-
Le, A., Lane, A.N., Hamaker, M., Bose, S., Gouw, A., Barbi, J., Tsukamoto, T., Rojas, C.J., Slusher, B.S., Zhang, H. et al. (2012) Glucose-independent glutamine metabolism via TCA cycling for proliferation and survival in B cells. Cell Metab., 15, 110-121
-
(2012)
Cell Metab
, vol.15
, pp. 110-121
-
-
Le, A.1
Lane, A.N.2
Hamaker, M.3
Bose, S.4
Gouw, A.5
Barbi, J.6
Tsukamoto, T.7
Rojas, C.J.8
Slusher, B.S.9
Zhang, H.10
|