-
1
-
-
84859242507
-
How advancement in biological network analysis methods empowers proteomics
-
Goh, W. W.; Lee, Y. H.; Chung, M.; Wong, L. How advancement in biological network analysis methods empowers proteomics Proteomics 2012, 12, 550-63
-
(2012)
Proteomics
, vol.12
, pp. 550-563
-
-
Goh, W.W.1
Lee, Y.H.2
Chung, M.3
Wong, L.4
-
2
-
-
80655131079
-
Subcellular tissue proteomics of hepatocellular carcinoma for molecular signature discovery
-
Lee, Y. Y.; McKinney, K. Q.; Ghosh, S.; Iannitti, D. A.; Martinie, J. B.; Caballes, F. R.; Russo, M. W.; Ahrens, W. A.; Lundgren, D. H.; Han, D. K.; Bonkovsky, H. L.; Hwang, S. I. Subcellular tissue proteomics of hepatocellular carcinoma for molecular signature discovery J. Proteome Res. 2011, 10 (11) 5070-83
-
(2011)
J. Proteome Res.
, vol.10
, Issue.11
, pp. 5070-5083
-
-
Lee, Y.Y.1
McKinney, K.Q.2
Ghosh, S.3
Iannitti, D.A.4
Martinie, J.B.5
Caballes, F.R.6
Russo, M.W.7
Ahrens, W.A.8
Lundgren, D.H.9
Han, D.K.10
Bonkovsky, H.L.11
Hwang, S.I.12
-
3
-
-
79954471161
-
Nano-LC-MS/MS based proteomics of hepatocellular carcinoma cells compared to Chang liver cells and tanshinone IIA induction
-
Long, X.; Zhang, J.; Zhang, Y.; Yao, J.; Cai, Z.; Yang, P. Nano-LC-MS/MS based proteomics of hepatocellular carcinoma cells compared to Chang liver cells and tanshinone IIA induction Mol. Biosyst. 2011, 7 (5) 1728-41
-
(2011)
Mol. Biosyst.
, vol.7
, Issue.5
, pp. 1728-1741
-
-
Long, X.1
Zhang, J.2
Zhang, Y.3
Yao, J.4
Cai, Z.5
Yang, P.6
-
4
-
-
84887625418
-
Networks in proteomics analysis of cancer
-
10.1016/j.copbio.2013.02.011
-
Goh, W. W.; Wong, L. Networks in proteomics analysis of cancer Curr. Opin. Biotechnol. 2013, 10.1016/j.copbio.2013.02.011
-
(2013)
Curr. Opin. Biotechnol.
-
-
Goh, W.W.1
Wong, L.2
-
5
-
-
33645830948
-
CFinder: Locating cliques and overlapping modules in biological networks
-
Adamcsek, B.; Palla, G.; Farkas, I. J.; Derenyi, I.; Vicsek, T. CFinder: locating cliques and overlapping modules in biological networks Bioinformatics 2006, 22 (8) 1021-3
-
(2006)
Bioinformatics
, vol.22
, Issue.8
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.J.3
Derenyi, I.4
Vicsek, T.5
-
6
-
-
69249122100
-
Network-assisted protein identification and data interpretation in shotgun proteomics
-
Li, J.; Zimmerman, L. J.; Park, B. H.; Tabb, D. L.; Liebler, D. C.; Zhang, B. Network-assisted protein identification and data interpretation in shotgun proteomics Mol. Syst. Biol. 2009, 5, 303
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 303
-
-
Li, J.1
Zimmerman, L.J.2
Park, B.H.3
Tabb, D.L.4
Liebler, D.C.5
Zhang, B.6
-
7
-
-
79955797347
-
Network-based pipeline for analyzing MS data: An application toward liver cancer
-
Goh, W. W.; Lee, Y. H.; Zubaidah, R. M.; Jin, J.; Dong, D.; Lin, Q.; Chung, M. C.; Wong, L. Network-based pipeline for analyzing MS data: an application toward liver cancer J. Proteome Res. 2011, 10 (5) 2261-72
-
(2011)
J. Proteome Res.
, vol.10
, Issue.5
, pp. 2261-2272
-
-
Goh, W.W.1
Lee, Y.H.2
Zubaidah, R.M.3
Jin, J.4
Dong, D.5
Lin, Q.6
Chung, M.C.7
Wong, L.8
-
9
-
-
80055090025
-
Detours, V., Most random gene expression signatures are significantly associated with breast cancer outcome
-
Venet, D.; Dumont, J. E. Detours, V., Most random gene expression signatures are significantly associated with breast cancer outcome PLoS Comput. Biol. 2011, 7 (10) e1002240
-
(2011)
PLoS Comput. Biol.
, vol.7
, Issue.10
, pp. 1002240
-
-
Venet, D.1
Dumont, J.E.2
-
10
-
-
77950672712
-
Network-based Identification of novel cancer genes
-
Ostlund, G.; Lindskog, M.; Sonnhammer, E. L. Network-based Identification of novel cancer genes Mol. Cell. Proteomics 2010, 9 (4) 648-55
-
(2010)
Mol. Cell. Proteomics
, vol.9
, Issue.4
, pp. 648-655
-
-
Ostlund, G.1
Lindskog, M.2
Sonnhammer, E.L.3
-
11
-
-
84872184001
-
Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies
-
Goh, W. W.; Fan, M.; Low, H. S.; Sergot, M.; Wong, L. Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies BMC Genomics 2013, 14 (1) 35
-
(2013)
BMC Genomics
, vol.14
, Issue.1
, pp. 35
-
-
Goh, W.W.1
Fan, M.2
Low, H.S.3
Sergot, M.4
Wong, L.5
-
12
-
-
84863260908
-
Proteomics signature profiling (PSP): A novel contextualization approach for cancer proteomics
-
Goh, W. W.; Lee, Y. H.; Ramdzan, Z. M.; Sergot, M. J.; Chung, M.; Wong, L. Proteomics signature profiling (PSP): a novel contextualization approach for cancer proteomics J. Proteome Res. 2012, 11 (3) 1571-81
-
(2012)
J. Proteome Res.
, vol.11
, Issue.3
, pp. 1571-1581
-
-
Goh, W.W.1
Lee, Y.H.2
Ramdzan, Z.M.3
Sergot, M.J.4
Chung, M.5
Wong, L.6
-
13
-
-
38649140454
-
The histone deacetylase inhibitor valproic acid enhances acquisition, extinction, and reconsolidation of conditioned fear
-
Bredy, T. W.; Barad, M. The histone deacetylase inhibitor valproic acid enhances acquisition, extinction, and reconsolidation of conditioned fear Learn. Mem. 2008, 15 (1) 39-45
-
(2008)
Learn. Mem.
, vol.15
, Issue.1
, pp. 39-45
-
-
Bredy, T.W.1
Barad, M.2
-
14
-
-
33748423722
-
Epigenetic alchemy for cell fate conversion
-
Kondo, T. Epigenetic alchemy for cell fate conversion Curr. Opin. Genet. Dev. 2006, 16 (5) 502-7
-
(2006)
Curr. Opin. Genet. Dev.
, vol.16
, Issue.5
, pp. 502-507
-
-
Kondo, T.1
-
15
-
-
9344252804
-
Histone deacetylase inhibition-mediated neuronal differentiation of multipotent adult neural progenitor cells
-
Hsieh, J.; Nakashima, K.; Kuwabara, T.; Mejia, E.; Gage, F. H. Histone deacetylase inhibition-mediated neuronal differentiation of multipotent adult neural progenitor cells Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (47) 16659-64
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, Issue.47
, pp. 16659-16664
-
-
Hsieh, J.1
Nakashima, K.2
Kuwabara, T.3
Mejia, E.4
Gage, F.H.5
-
16
-
-
75749138038
-
Valproate and amitriptyline exert common and divergent influences on global and gene promoter-specific chromatin modifications in rat primary astrocytes
-
Perisic, T.; Zimmermann, N.; Kirmeier, T.; Asmus, M.; Tuorto, F.; Uhr, M.; Holsboer, F.; Rein, T.; Zschocke, J. Valproate and amitriptyline exert common and divergent influences on global and gene promoter-specific chromatin modifications in rat primary astrocytes Neuropsychopharmacology 2010, 35 (3) 792-805
-
(2010)
Neuropsychopharmacology
, vol.35
, Issue.3
, pp. 792-805
-
-
Perisic, T.1
Zimmermann, N.2
Kirmeier, T.3
Asmus, M.4
Tuorto, F.5
Uhr, M.6
Holsboer, F.7
Rein, T.8
Zschocke, J.9
-
17
-
-
77953737800
-
Epigenetic treatments of adult rats promote recovery from visual acuity deficits induced by long-term monocular deprivation
-
Silingardi, D.; Scali, M.; Belluomini, G.; Pizzorusso, T. Epigenetic treatments of adult rats promote recovery from visual acuity deficits induced by long-term monocular deprivation Eur. J. Neurosci. 2010, 31 (12) 2185-92
-
(2010)
Eur. J. Neurosci.
, vol.31
, Issue.12
, pp. 2185-2192
-
-
Silingardi, D.1
Scali, M.2
Belluomini, G.3
Pizzorusso, T.4
-
18
-
-
33847150936
-
Developmental downregulation of histone posttranslational modifications regulates visual cortical plasticity
-
Putignano, E.; Lonetti, G.; Cancedda, L.; Ratto, G.; Costa, M.; Maffei, L.; Pizzorusso, T. Developmental downregulation of histone posttranslational modifications regulates visual cortical plasticity Neuron 2007, 53 (5) 747-59
-
(2007)
Neuron
, vol.53
, Issue.5
, pp. 747-759
-
-
Putignano, E.1
Lonetti, G.2
Cancedda, L.3
Ratto, G.4
Costa, M.5
Maffei, L.6
Pizzorusso, T.7
-
19
-
-
84857171467
-
The role of miRNAs in complex formation and control
-
Goh, W. W.; Oikawa, H.; Sng, J. C.; Sergot, M.; Wong, L. The role of miRNAs in complex formation and control Bioinformatics 2012, 28 (4) 453-6
-
(2012)
Bioinformatics
, vol.28
, Issue.4
, pp. 453-456
-
-
Goh, W.W.1
Oikawa, H.2
Sng, J.C.3
Sergot, M.4
Wong, L.5
-
20
-
-
3042818018
-
The International Protein Index: An integrated database for proteomics experiments
-
Kersey, P. J.; Duarte, J.; Williams, A.; Karavidopoulou, Y.; Birney, E.; Apweiler, R. The International Protein Index: an integrated database for proteomics experiments Proteomics 2004, 4 (7) 1985-8
-
(2004)
Proteomics
, vol.4
, Issue.7
, pp. 1985-1988
-
-
Kersey, P.J.1
Duarte, J.2
Williams, A.3
Karavidopoulou, Y.4
Birney, E.5
Apweiler, R.6
-
21
-
-
33847630405
-
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
-
Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat. Methods 2007, 4 (3) 207-14
-
(2007)
Nat. Methods
, vol.4
, Issue.3
, pp. 207-214
-
-
Elias, J.E.1
Gygi, S.P.2
-
22
-
-
73649107287
-
Phenotyping of an in vitro model of ischemic penumbra by iTRAQ-based shotgun quantitative proteomics
-
Datta, A.; Park, J. E.; Li, X.; Zhang, H.; Ho, Z. S.; Heese, K.; Lim, S. K.; Tam, J. P.; Sze, S. K. Phenotyping of an in vitro model of ischemic penumbra by iTRAQ-based shotgun quantitative proteomics J. Proteome Res. 2010, 9 (1) 472-84
-
(2010)
J. Proteome Res.
, vol.9
, Issue.1
, pp. 472-484
-
-
Datta, A.1
Park, J.E.2
Li, X.3
Zhang, H.4
Ho, Z.S.5
Heese, K.6
Lim, S.K.7
Tam, J.P.8
Sze, S.K.9
-
23
-
-
77951666584
-
A mouse protein interactome through combined literature mining with multiple sources of interaction evidence
-
Li, X.; Cai, H.; Xu, J.; Ying, S.; Zhang, Y. A mouse protein interactome through combined literature mining with multiple sources of interaction evidence Amino Acids 2010, 38 (4) 1237-52
-
(2010)
Amino Acids
, vol.38
, Issue.4
, pp. 1237-1252
-
-
Li, X.1
Cai, H.2
Xu, J.3
Ying, S.4
Zhang, Y.5
-
24
-
-
33845220382
-
IntNetDB v1.0: An integrated protein-protein interaction network database generated by a probabilistic model
-
Xia, K.; Dong, D.; Han, J. D. IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model BMC Bioinformatics 2006, 7, 508
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 508
-
-
Xia, K.1
Dong, D.2
Han, J.D.3
-
25
-
-
77951967208
-
SPICi: A fast clustering algorithm for large biological networks
-
Jiang, P.; Singh, M. SPICi: a fast clustering algorithm for large biological networks Bioinformatics 2010, 26 (8) 1105-11
-
(2010)
Bioinformatics
, vol.26
, Issue.8
, pp. 1105-1111
-
-
Jiang, P.1
Singh, M.2
-
26
-
-
75549091794
-
CORUM: The comprehensive resource of mammalian protein complexes-2009
-
Ruepp, A.; Waegele, B.; Lechner, M.; Brauner, B.; Dunger-Kaltenbach, I.; Fobo, G.; Frishman, G.; Montrone, C.; Mewes, H. W. CORUM: the comprehensive resource of mammalian protein complexes-2009 Nucleic Acids Res. 2010, 38, D497-501
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 497-501
-
-
Ruepp, A.1
Waegele, B.2
Lechner, M.3
Brauner, B.4
Dunger-Kaltenbach, I.5
Fobo, G.6
Frishman, G.7
Montrone, C.8
Mewes, H.W.9
-
27
-
-
34447249019
-
An essential switch in subunit composition of a chromatin remodeling complex during neural development
-
Lessard, J.; Wu, J. I.; Ranish, J. A.; Wan, M.; Winslow, M. M.; Staahl, B. T.; Wu, H.; Aebersold, R.; Graef, I. A.; Crabtree, G. R. An essential switch in subunit composition of a chromatin remodeling complex during neural development Neuron 2007, 55 (2) 201-15
-
(2007)
Neuron
, vol.55
, Issue.2
, pp. 201-215
-
-
Lessard, J.1
Wu, J.I.2
Ranish, J.A.3
Wan, M.4
Winslow, M.M.5
Staahl, B.T.6
Wu, H.7
Aebersold, R.8
Graef, I.A.9
Crabtree, G.R.10
-
28
-
-
79953777487
-
Experience-dependent retinogeniculate synapse remodeling is abnormal in MeCP2-deficient mice
-
Noutel, J.; Hong, Y. K.; Leu, B.; Kang, E.; Chen, C. Experience-dependent retinogeniculate synapse remodeling is abnormal in MeCP2-deficient mice Neuron 2011, 70 (1) 35-42
-
(2011)
Neuron
, vol.70
, Issue.1
, pp. 35-42
-
-
Noutel, J.1
Hong, Y.K.2
Leu, B.3
Kang, E.4
Chen, C.5
-
29
-
-
33846840971
-
Obligatory role of NR2A for metaplasticity in visual cortex
-
Philpot, B. D.; Cho, K. K.; Bear, M. F. Obligatory role of NR2A for metaplasticity in visual cortex Neuron 2007, 53 (4) 495-502
-
(2007)
Neuron
, vol.53
, Issue.4
, pp. 495-502
-
-
Philpot, B.D.1
Cho, K.K.2
Bear, M.F.3
-
30
-
-
0037418328
-
Separable features of visual cortical plasticity revealed by N-methyl-D-aspartate receptor 2A signaling
-
Fagiolini, M.; Katagiri, H.; Miyamoto, H.; Mori, H.; Grant, S. G.; Mishina, M.; Hensch, T. K. Separable features of visual cortical plasticity revealed by N-methyl-D-aspartate receptor 2A signaling Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (5) 2854-9
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, Issue.5
, pp. 2854-2859
-
-
Fagiolini, M.1
Katagiri, H.2
Miyamoto, H.3
Mori, H.4
Grant, S.G.5
Mishina, M.6
Hensch, T.K.7
-
31
-
-
65549123471
-
HDAC2 negatively regulates memory formation and synaptic plasticity
-
Guan, J. S.; Haggarty, S. J.; Giacometti, E.; Dannenberg, J. H.; Joseph, N.; Gao, J.; Nieland, T. J.; Zhou, Y.; Wang, X.; Mazitschek, R.; Bradner, J. E.; DePinho, R. A.; Jaenisch, R.; Tsai, L. H. HDAC2 negatively regulates memory formation and synaptic plasticity Nature 2009, 459 (7243) 55-60
-
(2009)
Nature
, vol.459
, Issue.7243
, pp. 55-60
-
-
Guan, J.S.1
Haggarty, S.J.2
Giacometti, E.3
Dannenberg, J.H.4
Joseph, N.5
Gao, J.6
Nieland, T.J.7
Zhou, Y.8
Wang, X.9
Mazitschek, R.10
Bradner, J.E.11
Depinho, R.A.12
Jaenisch, R.13
Tsai, L.H.14
-
32
-
-
0037380768
-
Fluorescent two-dimensional difference gel electrophoresis and mass spectrometry identify age-related protein expression differences for the primary visual cortex of kitten and adult cat
-
Van den Bergh, G.; Clerens, S.; Cnops, L.; Vandesande, F.; Arckens, L. Fluorescent two-dimensional difference gel electrophoresis and mass spectrometry identify age-related protein expression differences for the primary visual cortex of kitten and adult cat J. Neurochem. 2003, 85 (1) 193-205
-
(2003)
J. Neurochem.
, vol.85
, Issue.1
, pp. 193-205
-
-
Van Den Bergh, G.1
Clerens, S.2
Cnops, L.3
Vandesande, F.4
Arckens, L.5
-
33
-
-
84877121966
-
-
In submission.
-
Lim, V.; Goh, W.; Wong, L.; Sng, J., Downregulation of HDAC1 by valproic acid improves visual acuity in adult visual cortex. 2013, In submission.
-
(2013)
Downregulation of HDAC1 by Valproic Acid Improves Visual Acuity in Adult Visual Cortex
-
-
Lim, V.1
Goh, W.2
Wong, L.3
Sng, J.4
-
34
-
-
78149475575
-
Regulation of the postsynaptic cytoskeleton: Roles in development, plasticity, and disorders
-
Svitkina, T.; Lin, W. H.; Webb, D. J.; Yasuda, R.; Wayman, G. A.; Van Aelst, L.; Soderling, S. H. Regulation of the postsynaptic cytoskeleton: roles in development, plasticity, and disorders J. Neurosci. 2010, 30 (45) 14937-42
-
(2010)
J. Neurosci.
, vol.30
, Issue.45
, pp. 14937-14942
-
-
Svitkina, T.1
Lin, W.H.2
Webb, D.J.3
Yasuda, R.4
Wayman, G.A.5
Van Aelst, L.6
Soderling, S.H.7
-
35
-
-
33748166139
-
Actin-dependent activation of presynaptic silent synapses contributes to long-term synaptic plasticity in developing hippocampal neurons
-
Yao, J.; Qi, J.; Chen, G. Actin-dependent activation of presynaptic silent synapses contributes to long-term synaptic plasticity in developing hippocampal neurons J. Neurosci. 2006, 26 (31) 8137-47
-
(2006)
J. Neurosci.
, vol.26
, Issue.31
, pp. 8137-8147
-
-
Yao, J.1
Qi, J.2
Chen, G.3
-
36
-
-
80054738314
-
Activation of Rho GTPases triggers structural remodeling and functional plasticity in the adult rat visual cortex
-
Cerri, C.; Fabbri, A.; Vannini, E.; Spolidoro, M.; Costa, M.; Maffei, L.; Fiorentini, C.; Caleo, M. Activation of Rho GTPases triggers structural remodeling and functional plasticity in the adult rat visual cortex J. Neurosci. 2011, 31 (42) 15163-72
-
(2011)
J. Neurosci.
, vol.31
, Issue.42
, pp. 15163-15172
-
-
Cerri, C.1
Fabbri, A.2
Vannini, E.3
Spolidoro, M.4
Costa, M.5
Maffei, L.6
Fiorentini, C.7
Caleo, M.8
-
37
-
-
0035807975
-
Mechanisms underlying rapid experience-dependent plasticity in the human visual cortex
-
Boroojerdi, B.; Battaglia, F.; Muellbacher, W.; Cohen, L. G. Mechanisms underlying rapid experience-dependent plasticity in the human visual cortex Proc. Natl. Acad. Sci. U.S.A. 2001, 98 (25) 14698-701
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, Issue.25
, pp. 14698-14701
-
-
Boroojerdi, B.1
Battaglia, F.2
Muellbacher, W.3
Cohen, L.G.4
-
38
-
-
84863011342
-
Pull-push neuromodulation of LTP and LTD enables bidirectional experience-induced synaptic scaling in visual cortex
-
Huang, S.; Trevino, M.; He, K.; Ardiles, A.; Pasquale, R.; Guo, Y.; Palacios, A.; Huganir, R.; Kirkwood, A. Pull-push neuromodulation of LTP and LTD enables bidirectional experience-induced synaptic scaling in visual cortex Neuron 2012, 73 (3) 497-510
-
(2012)
Neuron
, vol.73
, Issue.3
, pp. 497-510
-
-
Huang, S.1
Trevino, M.2
He, K.3
Ardiles, A.4
Pasquale, R.5
Guo, Y.6
Palacios, A.7
Huganir, R.8
Kirkwood, A.9
-
39
-
-
33845882992
-
Activity-dependent regulation of NR2B translation contributes to metaplasticity in mouse visual cortex
-
Chen, W. S.; Bear, M. F. Activity-dependent regulation of NR2B translation contributes to metaplasticity in mouse visual cortex Neuropharmacology 2007, 52 (1) 200-14
-
(2007)
Neuropharmacology
, vol.52
, Issue.1
, pp. 200-214
-
-
Chen, W.S.1
Bear, M.F.2
-
40
-
-
0038222587
-
Bidirectional synaptic plasticity: From theory to reality
-
Bear, M. F. Bidirectional synaptic plasticity: from theory to reality Philos. Trans. R. Soc., B 2003, 358 (1432) 649-55
-
(2003)
Philos. Trans. R. Soc., B
, vol.358
, Issue.1432
, pp. 649-655
-
-
Bear, M.F.1
-
41
-
-
1542408736
-
Specific GABAA circuits for visual cortical plasticity
-
Fagiolini, M.; Fritschy, J. M.; Low, K.; Mohler, H.; Rudolph, U.; Hensch, T. K. Specific GABAA circuits for visual cortical plasticity Science 2004, 303 (5664) 1681-3
-
(2004)
Science
, vol.303
, Issue.5664
, pp. 1681-1683
-
-
Fagiolini, M.1
Fritschy, J.M.2
Low, K.3
Mohler, H.4
Rudolph, U.5
Hensch, T.K.6
-
42
-
-
42349094651
-
The antidepressant fluoxetine restores plasticity in the adult visual cortex
-
Maya Vetencourt, J. F.; Sale, A.; Viegi, A.; Baroncelli, L.; De Pasquale, R.; O'Leary, O. F.; Castren, E.; Maffei, L. The antidepressant fluoxetine restores plasticity in the adult visual cortex Science 2008, 320 (5874) 385-8
-
(2008)
Science
, vol.320
, Issue.5874
, pp. 385-388
-
-
Maya Vetencourt, J.F.1
Sale, A.2
Viegi, A.3
Baroncelli, L.4
De Pasquale, R.5
O'Leary, O.F.6
Castren, E.7
Maffei, L.8
|