-
1
-
-
84871297843
-
Next-generation proteomics: Towards an integrative view of proteome dynamics
-
Altelaar, A. F. M., Munoz, J. and Heck, A. J. R. Next-generation proteomics: towards an integrative view of proteome dynamics. Nat. Rev. Genet. 14, 35-48 (2013).
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 35-48
-
-
Altelaar, A.F.M.1
Munoz, J.2
Heck, A.J.R.3
-
2
-
-
77952956167
-
Decoding signalling networks by mass spectrometry-based proteomics
-
Choudhary, C. and Mann, M. Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. Mol. Cell. Biol. 11, 427-439 (2010).
-
(2010)
Nat. Rev. Mol. Cell. Biol.
, vol.11
, pp. 427-439
-
-
Choudhary, C.1
Mann, M.2
-
3
-
-
84861860481
-
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis
-
Gillet, L. C. et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11, O111.016717 (2012).
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. O111-016717
-
-
Gillet, L.C.1
-
4
-
-
68949206409
-
Applying mass spectrometry-based proteomics to genetics, genomics and network biology
-
Gstaiger, M. and Aebersold, R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat. Rev. Genet. 10, 617-627 (2009).
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 617-627
-
-
Gstaiger, M.1
Aebersold, R.2
-
5
-
-
34548522775
-
Advances in proteomic workflows for systems biology
-
Malmstroem, J., Lee, H. and Aebersold, R. Advances in proteomic workflows for systems biology. Curr. Opin. Biotechnol. 18, 378-384 (2007).
-
(2007)
Curr. Opin. Biotechnol.
, vol.18
, pp. 378-384
-
-
Malmstroem, J.1
Lee, H.2
Aebersold, R.3
-
6
-
-
68749094119
-
Full dynamic range proteome analysis of s. Cerevisiae by targeted proteomics
-
Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B. and Aebersold, R. Full dynamic range proteome analysis of s. cerevisiae by targeted proteomics. Cell 138, 795-806 (2009).
-
(2009)
Cell
, vol.138
, pp. 795-806
-
-
Picotti, P.1
Bodenmiller, B.2
Mueller, L.N.3
Domon, B.4
Aebersold, R.5
-
7
-
-
67349196123
-
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
-
Bell, A. W. et al. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat. Methods 6, 423-430 (2009).
-
(2009)
Nat. Methods
, vol.6
, pp. 423-430
-
-
Bell, A.W.1
-
8
-
-
84861897793
-
Mass spectrometry-based proteomics and network biology
-
Bensimon, A., Heck, A. J. R. and Aebersold, R. Mass spectrometry-based proteomics and network biology. Annu. Rev. Biochem. 81, 379-405 (2012).
-
(2012)
Annu. Rev. Biochem.
, vol.81
, pp. 379-405
-
-
Bensimon, A.1
Heck, A.J.R.2
Aebersold, R.3
-
9
-
-
78651083717
-
A self-validating quantitative mass spectrometry method for assessing the accuracy of high-content phosphoproteomic experiments
-
Casado, P. and Cutillas, P. R. A self-validating quantitative mass spectrometry method for assessing the accuracy of high-content phosphoproteomic experiments. Mol. Cell. Proteomics 10, M110.003079 (2011).
-
(2011)
Mol. Cell. Proteomics
, vol.10
, pp. M110-003079
-
-
Casado, P.1
Cutillas, P.R.2
-
10
-
-
77956304093
-
Mass spectrometry in high-throughput proteomics: Ready for the big time
-
Nilsson, T. et al. Mass spectrometry in high-throughput proteomics: ready for the big time. Nat. Methods 7, 681-685 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 681-685
-
-
Nilsson, T.1
-
11
-
-
76149142168
-
Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry
-
Tabb, D. L. et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J. Proteome Res. 9, 761-776 (2010).
-
(2010)
J. Proteome Res.
, vol.9
, pp. 761-776
-
-
Tabb, D.L.1
-
12
-
-
84875699641
-
Kinase-substrate enrichment analysis provides insights into the heterogeneity of signalling pathway activation in leukemia cells
-
Casado, P. et al. Kinase-substrate enrichment analysis provides insights into the heterogeneity of signalling pathway activation in leukemia cells. Sci. Signal. 6, rs6 (2013).
-
(2013)
Sci. Signal.
, vol.6
, pp. rs6
-
-
Casado, P.1
-
13
-
-
78650632764
-
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast
-
Bodenmiller, B. et al. Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci. Signal. 3, rs4 (2010).
-
(2010)
Sci. Signal.
, vol.3
, pp. rs4
-
-
Bodenmiller, B.1
-
14
-
-
75849156133
-
Simplistic pathways or complex networks?
-
Jorgensen, C. and Linding, R. Simplistic pathways or complex networks? Curr. Opin. Genet. Dev. 20, 15-22 (2010).
-
(2010)
Curr. Opin. Genet. Dev.
, vol.20
, pp. 15-22
-
-
Jorgensen, C.1
Linding, R.2
-
15
-
-
20444383859
-
Protein phosphorylation in signalling-50 years and counting
-
Pawson, T. and Scott, J. D. Protein phosphorylation in signalling-50 years and counting. Trends. Biochem. Sci. 30, 286-290 (2005).
-
(2005)
Trends. Biochem. Sci.
, vol.30
, pp. 286-290
-
-
Pawson, T.1
Scott, J.D.2
-
17
-
-
84855921201
-
Modeling signalling networks using high-throughput phospho-proteomics
-
Terfve, C. and Saez-Rodriguez, J. Modeling signalling networks using high-throughput phospho-proteomics. Adv. Exp. Med. Biol. 736, 19-57 (2012).
-
(2012)
Adv. Exp. Med. Biol.
, vol.736
, pp. 19-57
-
-
Terfve, C.1
Saez-Rodriguez, J.2
-
18
-
-
75849125610
-
Quantifying oncogenic phosphotyrosine signalling networks through systems biology
-
Del Rosario, A. M. and White, F. M. Quantifying oncogenic phosphotyrosine signalling networks through systems biology. Curr. Opin. Genet. Dev. 20, 23-30 (2010).
-
(2010)
Curr. Opin. Genet. Dev.
, vol.20
, pp. 23-30
-
-
Del Rosario, A.M.1
White, F.M.2
-
19
-
-
78149309682
-
PTMScout, a web resource for analysis of high throughput post-translational proteomics studies
-
Naegle, K. M. et al. PTMScout, a web resource for analysis of high throughput post-translational proteomics studies. Mol. Cell. Proteomics 9, 2558-2570 (2011).
-
(2011)
Mol. Cell. Proteomics
, vol.9
, pp. 2558-2570
-
-
Naegle, K.M.1
-
20
-
-
84934965093
-
Empirical inference of circuitry and plasticity in a kinase signalling network
-
Wilkes, E. H., Terfve, C., Gribben, J. G., Saez-Rodriguez, J. and Cutillas, P. R. Empirical inference of circuitry and plasticity in a kinase signalling network. Proc. Natl Acad. Sci. USA 112, 7719-7724 (2015).
-
(2015)
Proc. Natl Acad. Sci. USA
, vol.112
, pp. 7719-7724
-
-
Wilkes, E.H.1
Terfve, C.2
Gribben, J.G.3
Saez-Rodriguez, J.4
Cutillas, P.R.5
-
21
-
-
77950943011
-
Logicbased models for the analysis of cell signalling networks
-
Morris, M. K., Saez-Rodriguez, J., Sorger, P. K. and Laffenburger, D. A. Logicbased models for the analysis of cell signalling networks. Biochemistry 49, 3216-3224 (2010).
-
(2010)
Biochemistry
, vol.49
, pp. 3216-3224
-
-
Morris, M.K.1
Saez-Rodriguez, J.2
Sorger, P.K.3
Laffenburger, D.A.4
-
22
-
-
77949773550
-
Towards genome-scale signalling-network reconstructions
-
Hyduke, D. R. and Palsson, B. Towards genome-scale signalling-network reconstructions. Nat. Rev. Genet. 11, 297-307 (2010).
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 297-307
-
-
Hyduke, D.R.1
Palsson, B.2
-
23
-
-
71449120701
-
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
-
Saez-Rodriguez, J. et al. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol. Syst. Biol. 5, 331 (2009).
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 331
-
-
Saez-Rodriguez, J.1
-
24
-
-
84859778293
-
MTOR signalling in growth control and disease
-
Laplante, M. and Sabatini, D. M. mTOR signalling in growth control and disease. Cell 149, 274-293 (2012).
-
(2012)
Cell
, vol.149
, pp. 274-293
-
-
Laplante, M.1
Sabatini, D.M.2
-
25
-
-
12644284504
-
The consensus motif for phosphorylation by cyclin D1-Cdk4 is different from that for phosphorylation by cyclin A/E-cdk2
-
Kitawaga, M. et al. The consensus motif for phosphorylation by cyclin D1-Cdk4 is different from that for phosphorylation by cyclin A/E-cdk2. EMBO J. 15, 7060-7069 (1996).
-
(1996)
EMBO J.
, vol.15
, pp. 7060-7069
-
-
Kitawaga, M.1
-
26
-
-
79958696694
-
The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signalling
-
Hsu, P. P. et al. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signalling. Science 332, 1317-1322 (2011).
-
(2011)
Science
, vol.332
, pp. 1317-1322
-
-
Hsu, P.P.1
-
27
-
-
84873598070
-
Simultaneous reconstruction of multiple signalling pathways via the prize-collecting steiner forest problem
-
Tuncbag, N. et al. Simultaneous reconstruction of multiple signalling pathways via the prize-collecting steiner forest problem. J. Comput. Biol. 20, 124-136 (2013).
-
(2013)
J. Comput. Biol.
, vol.20
, pp. 124-136
-
-
Tuncbag, N.1
-
28
-
-
84873392956
-
Linking the signalling cascades and dynamic regulatory networks controlling stress responses
-
Gitter, A., Carmi, M., Barkai, N. and Bar-Joseph, Z. Linking the signalling cascades and dynamic regulatory networks controlling stress responses. Genome Res. 23, 365-376 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 365-376
-
-
Gitter, A.1
Carmi, M.2
Barkai, N.3
Bar-Joseph, Z.4
-
29
-
-
84874419781
-
SAMNet: A networkbased approach to integrate multi-dimensional high throughput datasets
-
Gosline, S. J. C., Spencer, S. J., Ursu, O. and Fraenkel, E. SAMNet: a networkbased approach to integrate multi-dimensional high throughput datasets. Integr. Biol. 4, 1415-1427 (2012).
-
(2012)
Integr. Biol.
, vol.4
, pp. 1415-1427
-
-
Gosline, S.J.C.1
Spencer, S.J.2
Ursu, O.3
Fraenkel, E.4
-
30
-
-
84874766054
-
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signalling
-
Huang, S.-S. et al. Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signalling. PLoS Comput. Biol. 9, e1002887 (2013).
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002887
-
-
Huang, S.-S.1
-
31
-
-
79960008610
-
ResponseNet: Revealing signalling and regulatory networks linking genetic and transcriptomic screening data
-
Lan, A. et al. ResponseNet: revealing signalling and regulatory networks linking genetic and transcriptomic screening data. Nucleic Acids Res. 39, W424-W429 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W424-W429
-
-
Lan, A.1
-
32
-
-
62549145762
-
Toward accurate reconstruction of functional protein networks
-
Yosef, N. et al. Toward accurate reconstruction of functional protein networks. Mol. Syst. Biol. 5, 248 (2009).
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 248
-
-
Yosef, N.1
-
33
-
-
84876515907
-
STRING v9.1: Protein-protein interaction networks, with increased coverage and integration
-
Franceschini, A. et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41, D808-D815 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D808-D815
-
-
Franceschini, A.1
-
34
-
-
33846554088
-
Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data
-
Kumar, N., Wolf-Yadlin, A., White, F. M. and Lauffenburger, D. A. Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput. Biol. 3, e4 (2007).
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. e4
-
-
Kumar, N.1
Wolf-Yadlin, A.2
White, F.M.3
Lauffenburger, D.A.4
-
35
-
-
69849101988
-
Maximum entropy reconstructions of dynamic signalling networks from quantitative proteomics data
-
Locasale, J. W. and Wolf-Yadlin, A. Maximum entropy reconstructions of dynamic signalling networks from quantitative proteomics data. PLoS ONE 4, e6522 (2009).
-
(2009)
PLoS ONE
, vol.4
, pp. e6522
-
-
Locasale, J.W.1
Wolf-Yadlin, A.2
-
36
-
-
84879533104
-
Towards systematic discovery of signalling networks in budding yeast filamentous growth stress response using interventional phosphorylation data
-
Zhang, Y., Kweon, H. K., Shively, C., Kumar, A. and Andrews, P. C. Towards systematic discovery of signalling networks in budding yeast filamentous growth stress response using interventional phosphorylation data. PLoS Comput. Biol. 9, e1003077 (2013).
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1003077
-
-
Zhang, Y.1
Kweon, H.K.2
Shively, C.3
Kumar, A.4
Andrews, P.C.5
-
37
-
-
84855974398
-
An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells
-
Santra, T., Kholodenko, B. and Kolch, W. An integrated bayesian framework for identifying phosphorylation networks in stimulated cells. Adv. Exp. Med. Biol. 736, 59-80 (2012).
-
(2012)
Adv. Exp. Med. Biol.
, vol.736
, pp. 59-80
-
-
Santra, T.1
Kholodenko, B.2
Kolch, W.3
-
38
-
-
34848822499
-
Quantitative profile of five murine core proteomes using label-free functional proteomics
-
Cutillas, P. R. and Vanhaesebroeck, B. Quantitative profile of five murine core proteomes using label-free functional proteomics. Mol. Cell. Proteomics 6, 1560-1573 (2007).
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 1560-1573
-
-
Cutillas, P.R.1
Vanhaesebroeck, B.2
-
39
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
|