-
1
-
-
33746930864
-
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
-
Keller, A., Eng, J., Zhang, N., Li, X. J., Aebersold, R., A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1, 2005.0017.
-
(2005)
Mol. Syst. Biol.
, vol.1
, pp. 20050017
-
-
Keller, A.1
Eng, J.2
Zhang, N.3
Li, X.J.4
Aebersold, R.5
-
2
-
-
33846706581
-
TOPP - the OpenMS proteomics pipeline
-
Kohlbacher, O., Reinert, K., Gropl, C., Lange, E. et al., TOPP - the OpenMS proteomics pipeline. Bioinformatics 2007, 23, e191-e197.
-
(2007)
Bioinformatics
, vol.23
-
-
Kohlbacher, O.1
Reinert, K.2
Gropl, C.3
Lange, E.4
-
3
-
-
39049184740
-
Virtual Expert Mass Spectrometrist v3.0: an integrated tool for proteome analysis
-
Matthiesen, R., Virtual Expert Mass Spectrometrist v3.0: an integrated tool for proteome analysis. Methods Mol. Biol. 2007, 367, 121-138.
-
(2007)
Methods Mol. Biol.
, vol.367
, pp. 121-138
-
-
Matthiesen, R.1
-
4
-
-
61449238279
-
Prequips - an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data
-
Gehlenborg, N., Yan, W., Lee, I. Y., Yoo, H. et al., Prequips - an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics 2009, 25, 682-683.
-
(2009)
Bioinformatics
, vol.25
, pp. 682-683
-
-
Gehlenborg, N.1
Yan, W.2
Lee, I.Y.3
Yoo, H.4
-
5
-
-
77952972294
-
HTAPP: High-throughput autonomous proteomic pipeline
-
Yu, K., Salomon, A. R., HTAPP: High-throughput autonomous proteomic pipeline. Proteomics 2010, 10, 2113-2122.
-
(2010)
Proteomics
, vol.10
, pp. 2113-2122
-
-
Yu, K.1
Salomon, A.R.2
-
6
-
-
9144233086
-
PEDRo: a database for storing, searching and disseminating experimental proteomics data
-
Garwood, K., McLaughlin, T., Garwood, C., Joens, S. et al., PEDRo: a database for storing, searching and disseminating experimental proteomics data. Biomed. Chromatogr. Genomics 2004, 5, 68.
-
(2004)
Biomed. Chromatogr. Genomics
, vol.5
, pp. 68
-
-
Garwood, K.1
McLaughlin, T.2
Garwood, C.3
Joens, S.4
-
7
-
-
33645461851
-
PRISM: a data management system for high-throughput proteomics
-
Kiebel, G. R., Auberry, K. J., Jaitly, N., Clark, D. A. et al., PRISM: a data management system for high-throughput proteomics. Proteomics 2006, 6, 1783-1790.
-
(2006)
Proteomics
, vol.6
, pp. 1783-1790
-
-
Kiebel, G.R.1
Auberry, K.J.2
Jaitly, N.3
Clark, D.A.4
-
8
-
-
34547907397
-
myProMS, a web server for management and validation of mass spectrometry-based proteomic data
-
Poullet, P., Carpentier, S., Barillot, E., myProMS, a web server for management and validation of mass spectrometry-based proteomic data. Proteomics 2007, 7, 2553-2556.
-
(2007)
Proteomics
, vol.7
, pp. 2553-2556
-
-
Poullet, P.1
Carpentier, S.2
Barillot, E.3
-
9
-
-
34447260760
-
MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data
-
Hartler, J., Thallinger, G. G., Stocker, G., Sturn, A. et al., MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data. Biomed. Chromatogr. Bioinformatics 2007, 8, 197.
-
(2007)
Biomed. Chromatogr. Bioinformatics
, vol.8
, pp. 197
-
-
Hartler, J.1
Thallinger, G.G.2
Stocker, G.3
Sturn, A.4
-
10
-
-
34250808391
-
PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories
-
Howes, C. G., Foster, L. J., PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories. Proteome Sci. 2007, 5, 8.
-
(2007)
Proteome Sci.
, vol.5
, pp. 8
-
-
Howes, C.G.1
Foster, L.J.2
-
11
-
-
73249117392
-
PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information
-
Yu, K., Salomon, A. R., PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information. Proteomics 2009, 9, 5350-5358.
-
(2009)
Proteomics
, vol.9
, pp. 5350-5358
-
-
Yu, K.1
Salomon, A.R.2
-
12
-
-
33645801199
-
2DDB - a bioinformatics solution for analysis of quantitative proteomics data
-
Malmstrom, L., Marko-Varga, G., Westergren-Thorsson, G., Laurell, T., Malmstrom, J., 2DDB - a bioinformatics solution for analysis of quantitative proteomics data. Biomed. Chromatogr. Bioinformatics 2006, 7, 158.
-
(2006)
Biomed. Chromatogr. Bioinformatics
, vol.7
, pp. 158
-
-
Malmstrom, L.1
Marko-Varga, G.2
Westergren-Thorsson, G.3
Laurell, T.4
Malmstrom, J.5
-
13
-
-
75949113358
-
Qupe - a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments
-
Albaum, S. P., Neuweger, H., Franzel, B., Lange, S. et al., Qupe - a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics 2009, 25, 3128-3134.
-
(2009)
Bioinformatics
, vol.25
, pp. 3128-3134
-
-
Albaum, S.P.1
Neuweger, H.2
Franzel, B.3
Lange, S.4
-
14
-
-
1842424944
-
The need for a public proteomics repository (commentary)
-
Prince, J. T., Carlson, M. W., Wang, R., Lu, P., Marcotte, E. M., The need for a public proteomics repository (commentary). Nat. Biotechnol. 2004, 22, 471-472.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 471-472
-
-
Prince, J.T.1
Carlson, M.W.2
Wang, R.3
Lu, P.4
Marcotte, E.M.5
-
15
-
-
38549117407
-
PRIDE: new developments and new datasets
-
Jones, P., Cote, R. G., Cho, S. Y., Klie, S. et al., PRIDE: new developments and new datasets. Nucleic Acids Res. 2008, 36, D878-D883.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Jones, P.1
Cote, R.G.2
Cho, S.Y.3
Klie, S.4
-
16
-
-
11144320641
-
Open source system for analyzing, validating, and storing protein identification data
-
Craig, R., Cortens, J. P., Beavis, R. C., Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004, 3, 1234-1242.
-
(2004)
J. Proteome Res.
, vol.3
, pp. 1234-1242
-
-
Craig, R.1
Cortens, J.P.2
Beavis, R.C.3
-
17
-
-
43049127826
-
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
-
Deutsch, E. W., Lam, H., Aebersold, R., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9, 429-434.
-
(2008)
EMBO Rep.
, vol.9
, pp. 429-434
-
-
Deutsch, E.W.1
Lam, H.2
Aebersold, R.3
-
18
-
-
38949210266
-
Human Proteinpedia enables sharing of human protein data
-
Mathivanan, S., Ahmed, M., Ahn, N. G., Alexandre, H. et al., Human Proteinpedia enables sharing of human protein data. Nat. Biotechnol. 2008, 26, 164-167.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 164-167
-
-
Mathivanan, S.1
Ahmed, M.2
Ahn, N.G.3
Alexandre, H.4
-
19
-
-
67650479361
-
NCBI Peptidome: a new public repository for mass spectrometry peptide identifications
-
Slotta, D. J., Barrett, T., Edgar, R., NCBI Peptidome: a new public repository for mass spectrometry peptide identifications. Nat. Biotechnol. 2009, 27, 600-601.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 600-601
-
-
Slotta, D.J.1
Barrett, T.2
Edgar, R.3
-
20
-
-
41349094093
-
Tranche: secure decentralized data storage for the proteomics community
-
Falkner, JA, A. P., Tranche: secure decentralized data storage for the proteomics community. J. Biomol. Tech. 2007, 18, 3.
-
(2007)
J. Biomol. Tech.
, vol.18
, pp. 3
-
-
Falkner, J.A.1
A., P.2
-
21
-
-
2942598149
-
PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation
-
Hornbeck, P. V., Chabra, I., Kornhauser, J. M., Skrzypek, E., Zhang, B., PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 2004, 4, 1551-1561.
-
(2004)
Proteomics
, vol.4
, pp. 1551-1561
-
-
Hornbeck, P.V.1
Chabra, I.2
Kornhauser, J.M.3
Skrzypek, E.4
Zhang, B.5
-
22
-
-
38549092088
-
Phospho.ELM: a database of phosphorylation sites - update 2008
-
Diella, F., Gould, C. M., Chica, C., Via, A., Gibson, T. J., Phospho.ELM: a database of phosphorylation sites - update 2008. Nucleic Acids Res. 2008, 36, D240-D244.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Diella, F.1
Gould, C.M.2
Chica, C.3
Via, A.4
Gibson, T.J.5
-
23
-
-
44149105911
-
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
-
Gnad, F., Ren, S., Cox, J., Olsen, J. V. et al., PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol. 2007, 8, R250.
-
(2007)
Genome Biol.
, vol.8
-
-
Gnad, F.1
Ren, S.2
Cox, J.3
Olsen, J.V.4
-
24
-
-
57449105428
-
PhosphoPep - a database of protein phosphorylation sites in model organisms
-
Bodenmiller, B., Campbell, D., Gerrits, B., Lam, H. et al., PhosphoPep - a database of protein phosphorylation sites in model organisms. Nat. Biotechnol. 2008, 26, 1339-1340.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1339-1340
-
-
Bodenmiller, B.1
Campbell, D.2
Gerrits, B.3
Lam, H.4
-
25
-
-
68049108471
-
LymPHOS: design of a phosphosite database of primary human T cells
-
Ovelleiro, D., Carrascal, M., Casas, V., Abian, J., LymPHOS: design of a phosphosite database of primary human T cells. Proteomics 2009, 9, 3741-3751.
-
(2009)
Proteomics
, vol.9
, pp. 3741-3751
-
-
Ovelleiro, D.1
Carrascal, M.2
Casas, V.3
Abian, J.4
-
26
-
-
0042622251
-
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
-
Obenauer, J. C., Cantley, L. C., Yaffe, M. B., Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 2003, 31, 3635-3641.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3635-3641
-
-
Obenauer, J.C.1
Cantley, L.C.2
Yaffe, M.B.3
-
27
-
-
34547555987
-
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns
-
Wong, Y. H., Lee, T. Y., Liang, H. K., Huang, C. M. et al., KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res. 2007, 35, W588-W594.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Wong, Y.H.1
Lee, T.Y.2
Liang, H.K.3
Huang, C.M.4
-
28
-
-
33645758540
-
PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory
-
Xue, Y., Li, A., Wang, L., Feng, H., Yao, X., PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. Biomed. Chromatogr. Bioinformatics 2006, 7, 163.
-
(2006)
Biomed. Chromatogr. Bioinformatics
, vol.7
, pp. 163
-
-
Xue, Y.1
Li, A.2
Wang, L.3
Feng, H.4
Yao, X.5
-
29
-
-
71049118572
-
SysPTM: a systematic resource for proteomic research on post-translational modifications
-
Li, H., Xing, X., Ding, G., Li, Q. et al., SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol. Cell. Proteomics 2009, 8, 1839-1849.
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 1839-1849
-
-
Li, H.1
Xing, X.2
Ding, G.3
Li, Q.4
-
30
-
-
78149309682
-
PTMScout: A web resource for analysis of high-throughput post-translational proteomic studies
-
Naegle, K. M., Gymrek, M., Joughin, B. A., Wagner, J. P. et al., PTMScout: A web resource for analysis of high-throughput post-translational proteomic studies. Mol. Cell. Proteomics 2010, 9, 2558-2570.
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 2558-2570
-
-
Naegle, K.M.1
Gymrek, M.2
Joughin, B.A.3
Wagner, J.P.4
-
31
-
-
38549146894
-
The Pfam protein families database
-
Finn, R. D., Tate, J., Mistry, J., Coggill, P. C. et al., The Pfam protein families database. Nucleic Acids Res. 2008, 36, D281-D288.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Finn, R.D.1
Tate, J.2
Mistry, J.3
Coggill, P.C.4
-
32
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M., The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004, 32, D277-D280.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
33
-
-
34248640261
-
Highly selective enrichment of phosphorylated peptides using titanium dioxide
-
Thingholm, T. E., Jorgensen, T. J., Jensen, O. N., Larsen, M. R., Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat. Protoc. 2006, 1, 1929-1935.
-
(2006)
Nat. Protoc.
, vol.1
, pp. 1929-1935
-
-
Thingholm, T.E.1
Jorgensen, T.J.2
Jensen, O.N.3
Larsen, M.R.4
-
34
-
-
42649142332
-
Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: application to cell signaling events of interferon-gamma-stimulated macrophages
-
Marcantonio, M., Trost, M., Courcelles, M., Desjardins, M., Thibault, P., Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: application to cell signaling events of interferon-gamma-stimulated macrophages. Mol. Cell. Proteomics 2008, 7, 645-660.
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 645-660
-
-
Marcantonio, M.1
Trost, M.2
Courcelles, M.3
Desjardins, M.4
Thibault, P.5
-
35
-
-
3042818018
-
The International Protein Index: an integrated database for proteomics experiments
-
Kersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y. et al., The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4, 1985-1988.
-
(2004)
Proteomics
, vol.4
, pp. 1985-1988
-
-
Kersey, P.J.1
Duarte, J.2
Williams, A.3
Karavidopoulou, Y.4
-
36
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M. C. et al., The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003, 31, 365-370.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.C.4
-
37
-
-
58149178579
-
NCBI Reference Sequences: current status, policy and new initiatives
-
Pruitt, K. D., Tatusova, T., Klimke, W., Maglott, D. R., NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 2009, 37, D32-D36.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Pruitt, K.D.1
Tatusova, T.2
Klimke, W.3
Maglott, D.R.4
-
38
-
-
0032619552
-
Protein identification and analysis tools in the ExPASy server
-
Wilkins, M. R., Gasteiger, E., Bairoch, A., Sanchez, J. C. et al., Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol. 1999, 112, 531-552.
-
(1999)
Methods Mol. Biol.
, vol.112
, pp. 531-552
-
-
Wilkins, M.R.1
Gasteiger, E.2
Bairoch, A.3
Sanchez, J.C.4
-
39
-
-
34248531753
-
Locating proteins in the cell using TargetP, SignalP and related tools
-
Emanuelsson, O., Brunak, S., von Heijne, G., Nielsen, H., Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2007, 2, 953-971.
-
(2007)
Nat. Protoc.
, vol.2
, pp. 953-971
-
-
Emanuelsson, O.1
Brunak, S.2
von Heijne, G.3
Nielsen, H.4
-
40
-
-
0031614678
-
A hidden Markov model for predicting transmembrane helices in protein sequences
-
Sonnhammer, E. L., von Heijne, G., Krogh, A., A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1998, 6, 175-182.
-
(1998)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.6
, pp. 175-182
-
-
Sonnhammer, E.L.1
von Heijne, G.2
Krogh, A.3
-
41
-
-
58149203231
-
InterPro: the integrative protein signature database
-
Hunter, S., Apweiler, R., Attwood, T. K., Bairoch, A. et al., InterPro: the integrative protein signature database. Nucleic Acids Res. 2009, 37, D211-D215.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Hunter, S.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
-
42
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar, R. C., MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
43
-
-
63049086405
-
Artifactual sulfation of silver-stained proteins: implications for the assignment of phosphorylation and sulfation sites
-
Gharib, M., Marcantonio, M., Lehmann, S. G., Courcelles, M. et al., Artifactual sulfation of silver-stained proteins: implications for the assignment of phosphorylation and sulfation sites. Mol. Cell. Proteomics 2009, 8, 506-518.
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 506-518
-
-
Gharib, M.1
Marcantonio, M.2
Lehmann, S.G.3
Courcelles, M.4
-
44
-
-
33750456519
-
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
-
Olsen, J. V., Blagoev, B., Gnad, F., Macek, B. et al., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648.
-
(2006)
Cell
, vol.127
, pp. 635-648
-
-
Olsen, J.V.1
Blagoev, B.2
Gnad, F.3
Macek, B.4
-
45
-
-
33947103658
-
A curated compendium of phosphorylation motifs
-
Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R. et al., A curated compendium of phosphorylation motifs. Nat. Biotechnol. 2007, 25, 285-286.
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 285-286
-
-
Amanchy, R.1
Periaswamy, B.2
Mathivanan, S.3
Reddy, R.4
-
46
-
-
38549086310
-
PepCyber:P∼PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains
-
Gong, W., Zhou, D., Ren, Y., Wang, Y. et al., PepCyber:P∼PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains. Nucleic Acids Res. 2008, 36, D679-D683.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Gong, W.1
Zhou, D.2
Ren, Y.3
Wang, Y.4
-
47
-
-
38549109487
-
NetworKIN: a resource for exploring cellular phosphorylation networks
-
Linding, R., Jensen, L. J., Pasculescu, A., Olhovsky, M. et al., NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res. 2008, 36, D695-D699.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Linding, R.1
Jensen, L.J.2
Pasculescu, A.3
Olhovsky, M.4
-
48
-
-
27944499451
-
An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets
-
Schwartz, D., Gygi, S. P., An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat. Biotechnol. 2005, 23, 1391-1398.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 1391-1398
-
-
Schwartz, D.1
Gygi, S.P.2
-
49
-
-
58049204428
-
Discovery of phosphorylation motif mixtures in phosphoproteomics data
-
Ritz, A., Shakhnarovich, G., Salomon, A. R., Raphael, B. J., Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinformatics 2009, 25, 14-21.
-
(2009)
Bioinformatics
, vol.25
, pp. 14-21
-
-
Ritz, A.1
Shakhnarovich, G.2
Salomon, A.R.3
Raphael, B.J.4
-
50
-
-
23144465987
-
SCRATCH: a protein structure and structural feature prediction server
-
Cheng, J., Randall, A. Z., Sweredoski, M. J., Baldi, P., SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. 2005, 33, W72-W76.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Cheng, J.1
Randall, A.Z.2
Sweredoski, M.J.3
Baldi, P.4
-
51
-
-
75149164436
-
PreDisorder: ab initio sequence-based prediction of protein disordered regions
-
Deng, X., Eickholt, J., Cheng, J., PreDisorder: ab initio sequence-based prediction of protein disordered regions. Biomed. Chromatogr. Bioinformatics 2009, 10, 436.
-
(2009)
Biomed. Chromatogr. Bioinformatics
, vol.10
, pp. 436
-
-
Deng, X.1
Eickholt, J.2
Cheng, J.3
-
52
-
-
0037249644
-
NLSdb: database of nuclear localization signals
-
Nair, R., Carter, P., Rost, B., NLSdb: database of nuclear localization signals. Nucleic Acids Res. 2003, 31, 397-399.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 397-399
-
-
Nair, R.1
Carter, P.2
Rost, B.3
-
53
-
-
56149103088
-
Nuclear export signal consensus sequences defined using a localization-based yeast selection system
-
Kosugi, S., Hasebe, M., Tomita, M., Yanagawa, H., Nuclear export signal consensus sequences defined using a localization-based yeast selection system. Traffic 2008, 9, 2053-2062.
-
(2008)
Traffic
, vol.9
, pp. 2053-2062
-
-
Kosugi, S.1
Hasebe, M.2
Tomita, M.3
Yanagawa, H.4
-
54
-
-
13644257223
-
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
-
Julenius, K., Molgaard, A., Gupta, R., Brunak, S., Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology 2005, 15, 153-164.
-
(2005)
Glycobiology
, vol.15
, pp. 153-164
-
-
Julenius, K.1
Molgaard, A.2
Gupta, R.3
Brunak, S.4
-
55
-
-
0036370537
-
Prediction of glycosylation across the human proteome and the correlation to protein function
-
Gupta, R., Brunak, S., Prediction of glycosylation across the human proteome and the correlation to protein function. Pac. Symp. Biocomput. 2002, 7, 310-322.
-
(2002)
Pac. Symp. Biocomput.
, vol.7
, pp. 310-322
-
-
Gupta, R.1
Brunak, S.2
-
56
-
-
79959718857
-
-
6th US HUPO Annual Meeting, Denver, CO
-
Hu, Z.-Z., 6th US HUPO Annual Meeting, Denver, CO 2010.
-
(2010)
-
-
Hu, Z.-Z.1
-
57
-
-
65349155149
-
Weak functional constraints on phosphoproteomes
-
Landry, C. R., Levy, E. D., Michnick, S. W., Weak functional constraints on phosphoproteomes. Trends Genet. 2009, 25, 193-197.
-
(2009)
Trends Genet.
, vol.25
, pp. 193-197
-
-
Landry, C.R.1
Levy, E.D.2
Michnick, S.W.3
-
58
-
-
67449104195
-
In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution
-
Yachie, N., Saito, R., Sugahara, J., Tomita, M., Ishihama, Y., In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. Mol. Cell. Proteomics 2009, 8, 1061-1071.
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 1061-1071
-
-
Yachie, N.1
Saito, R.2
Sugahara, J.3
Tomita, M.4
Ishihama, Y.5
-
59
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J., Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
60
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T. F., Waterman, M. S., Identification of common molecular subsequences. J. Mol. Biol. 1981, 147, 195-197.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
61
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson, W. R., Lipman, D. J., Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 1988, 85, 2444-2448.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
62
-
-
38549122308
-
InParanoid 6: eukaryotic ortholog clusters with inparalogs
-
Berglund, A. C., Sjolund, E., Ostlund, G., Sonnhammer, E. L., InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 2008, 36, D263-D266.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Berglund, A.C.1
Sjolund, E.2
Ostlund, G.3
Sonnhammer, E.L.4
-
63
-
-
0034069495
-
Gene ontology: tool for the unification of biology
-
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D. et al., Gene ontology: tool for the unification of biology. Gene Ontol. Consortium Nat. Genet. 2000, 25, 25-29.
-
(2000)
Gene Ontol. Consortium Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
-
64
-
-
58149193234
-
STRING 8 - a global view on proteins and their functional interactions in 630 organisms
-
Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S. et al., STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 2009, 37, D412-D416.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Jensen, L.J.1
Kuhn, M.2
Stark, M.3
Chaffron, S.4
-
65
-
-
27644467857
-
Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae
-
Hyland, E. M., Cosgrove, M. S., Molina, H., Wang, D. et al., Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Mol. Cell. Biol. 2005, 25, 10060-10070.
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 10060-10070
-
-
Hyland, E.M.1
Cosgrove, M.S.2
Molina, H.3
Wang, D.4
-
66
-
-
0029032249
-
The regulation of AP-1 activity by mitogen-activated protein kinases
-
Karin, M., The regulation of AP-1 activity by mitogen-activated protein kinases. J. Biol. Chem. 1995, 270, 16483-16486.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 16483-16486
-
-
Karin, M.1
-
67
-
-
0032523934
-
Phosphorylation of spliceosomal protein SAP 155 coupled with splicing catalysis
-
Wang, C., Chua, K., Seghezzi, W., Lees, E. et al., Phosphorylation of spliceosomal protein SAP 155 coupled with splicing catalysis. Genes Dev. 1998, 12, 1409-1414.
-
(1998)
Genes Dev.
, vol.12
, pp. 1409-1414
-
-
Wang, C.1
Chua, K.2
Seghezzi, W.3
Lees, E.4
-
68
-
-
26244435980
-
CDK phosphorylation of a novel NLS-NES module distributed between two subunits of the Mcm2-7 complex prevents chromosomal rereplication
-
Liku, M. E., Nguyen, V. Q., Rosales, A. W., Irie, K., Li, J. J., CDK phosphorylation of a novel NLS-NES module distributed between two subunits of the Mcm2-7 complex prevents chromosomal rereplication. Mol. Biol. Cell 2005, 16, 5026-5039.
-
(2005)
Mol. Biol. Cell
, vol.16
, pp. 5026-5039
-
-
Liku, M.E.1
Nguyen, V.Q.2
Rosales, A.W.3
Irie, K.4
Li, J.J.5
-
69
-
-
77949523576
-
Dissecting the signaling events that impact classical nuclear import and target nuclear transport factors
-
Kodiha, M., Tran, D., Morogan, A., Qian, C., Stochaj, U., Dissecting the signaling events that impact classical nuclear import and target nuclear transport factors. PLoS One 2009, 4, e8420.
-
(2009)
PLoS One
, vol.4
-
-
Kodiha, M.1
Tran, D.2
Morogan, A.3
Qian, C.4
Stochaj, U.5
-
70
-
-
45849104555
-
14-3-3 Proteins: a family of versatile molecular regulators
-
Obsilova, V., Silhan, J., Boura, E., Teisinger, J., Obsil, T., 14-3-3 Proteins: a family of versatile molecular regulators. Physiol. Res. 2008, 57, S11-S21.
-
(2008)
Physiol. Res.
, vol.57
-
-
Obsilova, V.1
Silhan, J.2
Boura, E.3
Teisinger, J.4
Obsil, T.5
-
71
-
-
0028844188
-
O-linked N-acetylglucosamine: the "yin-yang" of Ser/Thr phosphorylation? Nuclear and cytoplasmic glycosylation
-
Hart, G. W., Greis, K. D., Dong, L. Y., Blomberg, M. A. et al., O-linked N-acetylglucosamine: the "yin-yang" of Ser/Thr phosphorylation? Nuclear and cytoplasmic glycosylation. Adv. Exp. Med. Biol. 1995, 376, 115-123.
-
(1995)
Adv. Exp. Med. Biol.
, vol.376
, pp. 115-123
-
-
Hart, G.W.1
Greis, K.D.2
Dong, L.Y.3
Blomberg, M.A.4
-
72
-
-
0030200110
-
PEST sequences and regulation by proteolysis
-
Rechsteiner, M., Rogers, S. W., PEST sequences and regulation by proteolysis. Trends Biochem. Sci. 1996, 21, 267-271.
-
(1996)
Trends Biochem. Sci.
, vol.21
, pp. 267-271
-
-
Rechsteiner, M.1
Rogers, S.W.2
-
73
-
-
30744474699
-
Global identification of O-GlcNAc-modified proteins
-
Nandi, A., Sprung, R., Barma, D. K., Zhao, Y. et al., Global identification of O-GlcNAc-modified proteins. Anal. Chem. 2006, 78, 452-458.
-
(2006)
Anal. Chem.
, vol.78
, pp. 452-458
-
-
Nandi, A.1
Sprung, R.2
Barma, D.K.3
Zhao, Y.4
-
74
-
-
2942615089
-
The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit
-
Klein, D. J., Moore, P. B., Steitz, T. A., The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol. 2004, 340, 141-177.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 141-177
-
-
Klein, D.J.1
Moore, P.B.2
Steitz, T.A.3
-
75
-
-
0035865683
-
Changes in intracellular calpastatin localization are mediated by reversible phosphorylation
-
Averna, M., de Tullio, R., Passalacqua, M., Salamino, F. et al., Changes in intracellular calpastatin localization are mediated by reversible phosphorylation. Biochem. J. 2001, 354, 25-30.
-
(2001)
Biochem. J.
, vol.354
, pp. 25-30
-
-
Averna, M.1
de Tullio, R.2
Passalacqua, M.3
Salamino, F.4
-
76
-
-
77955957347
-
Evolution of characterized phosphorylation sites in budding yeast
-
Ba, A. N., Moses, A. M., Evolution of characterized phosphorylation sites in budding yeast. Mol. Biol. Evol. 2010, 27, 2027-2037.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 2027-2037
-
-
Ba, A.N.1
Moses, A.M.2
-
77
-
-
67649972198
-
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species
-
Beltrao, P., Trinidad, J. C., Fiedler, D., Roguev, A. et al., Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol. 2009, 7, e1000134.
-
(2009)
PLoS Biol.
, vol.7
-
-
Beltrao, P.1
Trinidad, J.C.2
Fiedler, D.3
Roguev, A.4
-
78
-
-
77958606998
-
Molecular characterization of the evolution of phagosomes
-
Boulais, J., Trost, M., Landry, C. R., Dieckmann, R. et al., Molecular characterization of the evolution of phagosomes. Mol. Syst. Biol. 2010, 6, 423.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 423
-
-
Boulais, J.1
Trost, M.2
Landry, C.R.3
Dieckmann, R.4
-
79
-
-
0032502785
-
Regulation of connexin-43 gap junctional intercellular communication by mitogen-activated protein kinase
-
Warn-Cramer, B. J., Cottrell, G. T., Burt, J. M., Lau, A. F., Regulation of connexin-43 gap junctional intercellular communication by mitogen-activated protein kinase. J. Biol. Chem. 1998, 273, 9188-9196.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 9188-9196
-
-
Warn-Cramer, B.J.1
Cottrell, G.T.2
Burt, J.M.3
Lau, A.F.4
-
80
-
-
0037160066
-
Casein kinase 1 regulates connexin-43 gap junction assembly
-
Cooper, C. D., Lampe, P. D., Casein kinase 1 regulates connexin-43 gap junction assembly. J. Biol. Chem. 2002, 277, 44962-44968.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 44962-44968
-
-
Cooper, C.D.1
Lampe, P.D.2
-
81
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
-
Keller, A., Nesvizhskii, A. I., Kolker, E., Aebersold, R., Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74, 5383-5392.
-
(2002)
Anal. Chem.
, vol.74
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.I.2
Kolker, E.3
Aebersold, R.4
|