-
1
-
-
33847616949
-
Reproducible isolation of distinct, overlapping segments of the phosphoproteome
-
Bodenmiller, B., Mueller, L. N., Mueller, M., Domon, B., and Aebersold, R. (2007) Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat. Methods 4, 231-237
-
(2007)
Nat. Methods
, vol.4
, pp. 231-237
-
-
Bodenmiller, B.1
Mueller, L.N.2
Mueller, M.3
Domon, B.4
Aebersold, R.5
-
2
-
-
65349155149
-
Weak functional constraints on phosphoproteomes
-
Landry, C. R., Levy, E. D., and Michnick, S. W. (2009) Weak functional constraints on phosphoproteomes. Trends Genet. 25, 193-197
-
(2009)
Trends Genet.
, vol.25
, pp. 193-197
-
-
Landry, C.R.1
Levy, E.D.2
Michnick, S.W.3
-
3
-
-
48149087568
-
Non-functional phosphorylations?
-
Lienhard, G. E. (2008) Non-functional phosphorylations? Trends Biochem. Sci. 33, 351-352
-
(2008)
Trends Biochem. Sci.
, vol.33
, pp. 351-352
-
-
Lienhard, G.E.1
-
4
-
-
47849125967
-
A multidimensional chromatography technology for indepth phosphoproteome analysis
-
Albuquerque, C. P., Smolka, M. B., Payne, S. H., Bafna, V., Eng, J., and Zhou, H. (2008) A multidimensional chromatography technology for indepth phosphoproteome analysis. Mol. Cell. Proteomics 7, 1389-1396
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 1389-1396
-
-
Albuquerque, C.P.1
Smolka, M.B.2
Payne, S.H.3
Bafna, V.4
Eng, J.5
Zhou, H.6
-
5
-
-
67649972198
-
Evolution of phosphoregulation: Comparison of phosphorylation patterns across yeast species
-
Beltrao, P., Trinidad, J. C., Fiedler, D., Roguev, A., Lim, W. A., Shokat, K. M., Burlingame, A. L., and Krogan, N. J. (2009) Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol. 7, e1000134
-
(2009)
PLoS Biol.
, vol.7
-
-
Beltrao, P.1
Trinidad, J.C.2
Fiedler, D.3
Roguev, A.4
Lim, W.A.5
Shokat, K.M.6
Burlingame, A.L.7
Krogan, N.J.8
-
6
-
-
57449105428
-
PhosphoPep-a database of protein phosphorylation sites in model organisms
-
Bodenmiller, B., Campbell, D., Gerrits, B., Lam, H., Jovanovic, M., Picotti, P., Schlapbach, R., and Aebersold, R. (2008) PhosphoPep-a database of protein phosphorylation sites in model organisms. Nat. Biotechnol. 26, 1339-1340
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1339-1340
-
-
Bodenmiller, B.1
Campbell, D.2
Gerrits, B.3
Lam, H.4
Jovanovic, M.5
Picotti, P.6
Schlapbach, R.7
Aebersold, R.8
-
7
-
-
33847778786
-
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry
-
Chi, A., Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., and Hunt, D. F. (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl. Acad. Sci. USA 104, 2193-2198
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 2193-2198
-
-
Chi, A.1
Huttenhower, C.2
Geer, L.Y.3
Coon, J.J.4
Syka, J.E.5
Bai, D.L.6
Shabanowitz, J.7
Burke, D.J.8
Troyanskaya, O.G.9
Hunt, D.F.10
-
8
-
-
68549085023
-
High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast
-
Gnad, F., de Godoy, L. M., Cox, J., Neuhauser, N., Ren, S., Olsen, J. V., and Mann, M. (2009) High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast. Proteomics 9, 4642-4652
-
(2009)
Proteomics
, vol.9
, pp. 4642-4652
-
-
Gnad, F.1
De Godoy, L.M.2
Cox, J.3
Neuhauser, N.4
Ren, S.5
Olsen, J.V.6
Mann, M.7
-
9
-
-
15944377809
-
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway
-
Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P., Faergeman, N. J., Mann, M., and Jensen, O. N. (2005) Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 4, 310-327
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 310-327
-
-
Gruhler, A.1
Olsen, J.V.2
Mohammed, S.3
Mortensen, P.4
Faergeman, N.J.5
Mann, M.6
Jensen, O.N.7
-
10
-
-
70349546862
-
Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution
-
Holt, L. J., Tuch, B. B., Villén, J., Johnson, A. D., Gygi, S. P., and Morgan, D. O. (2009) Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science 325, 1682-1686
-
(2009)
Science
, vol.325
, pp. 1682-1686
-
-
Holt, L.J.1
Tuch, B.B.2
Villén, J.3
Johnson, A.D.4
Gygi, S.P.5
Morgan, D.O.6
-
11
-
-
69249240179
-
Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis
-
Huber, A., Bodenmiller, B., Uotila, A., Stahl, M., Wanka, S., Gerrits, B., Aebersold, R., and Loewith, R. (2009) Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev. 23, 1929-1943
-
(2009)
Genes Dev.
, vol.23
, pp. 1929-1943
-
-
Huber, A.1
Bodenmiller, B.2
Uotila, A.3
Stahl, M.4
Wanka, S.5
Gerrits, B.6
Aebersold, R.7
Loewith, R.8
-
12
-
-
33947584417
-
Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae
-
Li, X., Gerber, S. A., Rudner, A. D., Beausoleil, S. A., Haas, W., Villén, J., Elias, J. E., and Gygi, S. P. (2007) Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae. J. Proteome Res. 6, 1190-1197
-
(2007)
J. Proteome Res.
, vol.6
, pp. 1190-1197
-
-
Li, X.1
Gerber, S.A.2
Rudner, A.D.3
Beausoleil, S.A.4
Haas, W.5
Villén, J.6
Elias, J.E.7
Gygi, S.P.8
-
13
-
-
70349972517
-
Global analysis of the yeast osmotic stress response by quantitative proteomics
-
Soufi, B., Kelstrup, C. D., Stoehr, G., Fröhlich, F., Walther, T. C., and Olsen, J. V. (2009) Global analysis of the yeast osmotic stress response by quantitative proteomics. Mol. Biosyst. 5, 1337-1346
-
(2009)
Mol. Biosyst.
, vol.5
, pp. 1337-1346
-
-
Soufi, B.1
Kelstrup, C.D.2
Stoehr, G.3
Fröhlich, F.4
Walther, T.C.5
Olsen, J.V.6
-
14
-
-
78651296878
-
PhosphoGRID: A database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae
-
Stark, C., Su, T. C., Breitkreutz, A., Lourenco, P., Dahabieh, M., Breitkreutz, B. J., Tyers, M., and Sadowski, I. (2010) PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database 2010, bap026
-
(2010)
Database 2010
-
-
Stark, C.1
Su, T.C.2
Breitkreutz, A.3
Lourenco, P.4
Dahabieh, M.5
Breitkreutz, B.J.6
Tyers, M.7
Sadowski, I.8
-
15
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
16
-
-
55249096894
-
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
-
de Godoy, L. M., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., and Mann, M. (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254
-
(2008)
Nature
, vol.455
, pp. 1251-1254
-
-
De Godoy, L.M.1
Olsen, J.V.2
Cox, J.3
Nielsen, M.L.4
Hubner, N.C.5
Fröhlich, F.6
Walther, T.C.7
Mann, M.8
-
17
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425, 737-741
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
O'Shea, E.K.7
Weissman, J.S.8
-
18
-
-
79961013401
-
Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes
-
Wu, R., Dephoure, N., Haas, W., Huttlin, E. L., Zhai, B., Sowa, M. E., and Gygi, S. P. (2011) Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes. Mol. Cell. Proteomics 10, M111.009654
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Wu, R.1
Dephoure, N.2
Haas, W.3
Huttlin, E.L.4
Zhai, B.5
Sowa, M.E.6
Gygi, S.P.7
-
19
-
-
0345687191
-
The proteome of Saccharomyces cerevisiae mitochondria
-
Sickmann, A., Reinders, J., Wagner, Y., Joppich, C., Zahedi, R., Meyer, H. E., Schönfisch, B., Perschil, I., Chacinska, A., Guiard, B., Rehling, P., Pfanner, N., and Meisinger, C. (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc. Natl. Acad. Sci. USA 100, 13207-13212
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13207-13212
-
-
Sickmann, A.1
Reinders, J.2
Wagner, Y.3
Joppich, C.4
Zahedi, R.5
Meyer, H.E.6
Schönfisch, B.7
Perschil, I.8
Chacinska, A.9
Guiard, B.10
Rehling, P.11
Pfanner, N.12
Meisinger, C.13
-
20
-
-
33748377124
-
Quantification of protein half-lives in the budding yeast proteome
-
Belle, A., Tanay, A., Bitincka, L., Shamir, R., and O'Shea, E. K. (2006) Quantification of protein half-lives in the budding yeast proteome. Proc. Natl. Acad. Sci. USA 103, 13004-13009
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 13004-13009
-
-
Belle, A.1
Tanay, A.2
Bitincka, L.3
Shamir, R.4
O'Shea, E.K.5
-
21
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman, J. R., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., and Weissman, J. S. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840-846
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.1
Ghaemmaghami, S.2
Ihmels, J.3
Breslow, D.K.4
Noble, M.5
DeRisi, J.L.6
Weissman, J.S.7
-
22
-
-
28444460297
-
Global analysis of protein phosphorylation in yeast
-
Ptacek, J., Devgan, G., Michaud, G., Zhu, H., Zhu, X., Fasolo, J., Guo, H., Jona, G., Breitkreutz, A., Sopko, R., McCartney, R. R., Schmidt, M. C., Rachidi, N., Lee, S. J., Mah, A. S., Meng, L., Stark, M. J., Stern, D. F., De Virgilio, C., Tyers, M., Andrews, B., Gerstein, M., Schweitzer, B., Predki, P. F., and Snyder, M. (2005) Global analysis of protein phosphorylation in yeast. Nature 438, 679-684
-
(2005)
Nature
, vol.438
, pp. 679-684
-
-
Ptacek, J.1
Devgan, G.2
Michaud, G.3
Zhu, H.4
Zhu, X.5
Fasolo, J.6
Guo, H.7
Jona, G.8
Breitkreutz, A.9
Sopko, R.10
McCartney, R.R.11
Schmidt, M.C.12
Rachidi, N.13
Lee, S.J.14
Mah, A.S.15
Meng, L.16
Stark, M.J.17
Stern, D.F.18
De Virgilio, C.19
Tyers, M.20
Andrews, B.21
Gerstein, M.22
Schweitzer, B.23
Predki, P.F.24
Snyder, M.25
more..
-
23
-
-
24044440971
-
BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
-
Maere, S., Heymans, K., and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21, 3448-3449
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.3
-
24
-
-
36749053957
-
Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase
-
Reinders, J., Wagner, K., Zahedi, R. P., Stojanovski, D., Eyrich, B., van der Laan, M., Rehling, P., Sickmann, A., Pfanner, N., and Meisinger, C. (2007) Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase. Mol. Cell. Proteomics 6, 1896-1906
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 1896-1906
-
-
Reinders, J.1
Wagner, K.2
Zahedi, R.P.3
Stojanovski, D.4
Eyrich, B.5
Van Der Laan, M.6
Rehling, P.7
Sickmann, A.8
Pfanner, N.9
Meisinger, C.10
-
25
-
-
33745851905
-
Toward the complete yeast mitochondrial proteome: Multidimensional separation techniques for mitochondrial proteomics
-
Reinders, J., Zahedi, R. P., Pfanner, N., Meisinger, C., and Sickmann, A. (2006) Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J. Proteome Res. 5, 1543-1554
-
(2006)
J. Proteome Res.
, vol.5
, pp. 1543-1554
-
-
Reinders, J.1
Zahedi, R.P.2
Pfanner, N.3
Meisinger, C.4
Sickmann, A.5
-
26
-
-
75149190104
-
Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 reveals a tight link between tyrosine phosphorylation and virulence
-
Lin, M. H., Hsu, T. L., Lin, S. Y., Pan, Y. J., Jan, J. T., Wang, J. T., Khoo, K. H., and Wu, S. H. (2009) Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 reveals a tight link between tyrosine phosphorylation and virulence. Mol. Cell. Proteomics 8, 2613-2623
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 2613-2623
-
-
Lin, M.H.1
Hsu, T.L.2
Lin, S.Y.3
Pan, Y.J.4
Jan, J.T.5
Wang, J.T.6
Khoo, K.H.7
Wu, S.H.8
-
27
-
-
39749166860
-
Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation
-
Macek, B., Gnad, F., Soufi, B., Kumar, C., Olsen, J. V., Mijakovic, I., and Mann, M. (2008) Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell. Proteomics 7, 299-307
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 299-307
-
-
Macek, B.1
Gnad, F.2
Soufi, B.3
Kumar, C.4
Olsen, J.V.5
Mijakovic, I.6
Mann, M.7
-
28
-
-
34247325212
-
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis
-
Macek, B., Mijakovic, I., Olsen, J. V., Gnad, F., Kumar, C., Jensen, P. R., and Mann, M. (2007) The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6, 697-707
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 697-707
-
-
Macek, B.1
Mijakovic, I.2
Olsen, J.V.3
Gnad, F.4
Kumar, C.5
Jensen, P.R.6
Mann, M.7
-
29
-
-
77954696406
-
Analysis of the phosphoproteome of the multicellular bacterium Streptomyces coelicolor A3(2) by protein/peptide fractionation, phosphopeptide enrichment and high-accuracy mass spectrometry
-
Parker, J. L., Jones, A. M., Serazetdinova, L., Saalbach, G., Bibb, M. J., and Naldrett, M. J. (2010) Analysis of the phosphoproteome of the multicellular bacterium Streptomyces coelicolor A3(2) by protein/peptide fractionation, phosphopeptide enrichment and high-accuracy mass spectrometry. Proteomics 10, 2486-2497
-
(2010)
Proteomics
, vol.10
, pp. 2486-2497
-
-
Parker, J.L.1
Jones, A.M.2
Serazetdinova, L.3
Saalbach, G.4
Bibb, M.J.5
Naldrett, M.J.6
-
30
-
-
77952132933
-
Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases
-
Prisic, S., Dankwa, S., Schwartz, D., Chou, M. F., Locasale, J. W., Kang, C. M., Bemis, G., Church, G. M., Steen, H., and Husson, R. N. (2010) Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. Proc. Natl. Acad. Sci. USA 107, 7521-7526
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 7521-7526
-
-
Prisic, S.1
Dankwa, S.2
Schwartz, D.3
Chou, M.F.4
Locasale, J.W.5
Kang, C.M.6
Bemis, G.7
Church, G.M.8
Steen, H.9
Husson, R.N.10
-
31
-
-
66449094321
-
Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species
-
Ravichandran, A., Sugiyama, N., Tomita, M., Swarup, S., and Ishihama, Y. (2009) Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species. Proteomics 9, 2764-2775
-
(2009)
Proteomics
, vol.9
, pp. 2764-2775
-
-
Ravichandran, A.1
Sugiyama, N.2
Tomita, M.3
Swarup, S.4
Ishihama, Y.5
-
32
-
-
77953160473
-
The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: Analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases
-
Schmidl, S. R., Gronau, K., Pietack, N., Hecker, M., Becher, D., and Stülke, J. (2010) The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases. Mol. Cell. Proteomics 9, 1228-1242
-
(2010)
Mol. Cell. Proteomics
, vol.9
, pp. 1228-1242
-
-
Schmidl, S.R.1
Gronau, K.2
Pietack, N.3
Hecker, M.4
Becher, D.5
Stülke, J.6
-
33
-
-
52649125713
-
The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins
-
Soufi, B., Gnad, F., Jensen, P. R., Petranovic, D., Mann, M., Mijakovic, I., and Macek, B. (2008) The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins. Proteomics 8, 3486-3493
-
(2008)
Proteomics
, vol.8
, pp. 3486-3493
-
-
Soufi, B.1
Gnad, F.2
Jensen, P.R.3
Petranovic, D.4
Mann, M.5
Mijakovic, I.6
Macek, B.7
-
34
-
-
73649133664
-
Phosphoproteomic analysis reveals the multiple roles of phosphorylation in pathogenic bacterium Streptococcus pneumoniae
-
Sun, X., Ge, F., Xiao, C. L., Yin, X. F., Ge, R., Zhang, L. H., and He, Q. Y. (2010) Phosphoproteomic analysis reveals the multiple roles of phosphorylation in pathogenic bacterium Streptococcus pneumoniae. J. Proteome Res. 9, 275-282
-
(2010)
J. Proteome Res.
, vol.9
, pp. 275-282
-
-
Sun, X.1
Ge, F.2
Xiao, C.L.3
Yin, X.F.4
Ge, R.5
Zhang, L.H.6
He, Q.Y.7
-
35
-
-
2342473198
-
The importance of intrinsic disorder for protein phosphorylation
-
Iakoucheva, L. M., Radivojac, P., Brown, C. J., O'Connor, T. R., Sikes, J. G., Obradovic, Z., and Dunker, A. K. (2004) The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. 32, 1037-1049
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1037-1049
-
-
Iakoucheva, L.M.1
Radivojac, P.2
Brown, C.J.3
O'Connor, T.R.4
Sikes, J.G.5
Obradovic, Z.6
Dunker, A.K.7
-
36
-
-
33745289067
-
Length-dependent prediction of protein intrinsic disorder
-
Peng, K., Radivojac, P., Vucetic, S., Dunker, A. K., and Obradovic, Z. (2006) Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 7, 208
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 208
-
-
Peng, K.1
Radivojac, P.2
Vucetic, S.3
Dunker, A.K.4
Obradovic, Z.5
-
37
-
-
57149116929
-
Tight regulation of unstructured proteins: From transcript synthesis to protein degradation
-
Gsponer, J., Futschik, M. E., Teichmann, S. A., and Babu, M. M. (2008) Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science 322, 1365-1368
-
(2008)
Science
, vol.322
, pp. 1365-1368
-
-
Gsponer, J.1
Futschik, M.E.2
Teichmann, S.A.3
Babu, M.M.4
-
38
-
-
3042662113
-
In silico proteome analysis to facilitate proteomics experiments using mass spectrometry
-
Cagney, G., Amiri, S., Premawaradena, T., Lindo, M., and Emili, A. (2003) In silico proteome analysis to facilitate proteomics experiments using mass spectrometry. Proteome Sci. 1, 5
-
(2003)
Proteome Sci.
, vol.1
, pp. 5
-
-
Cagney, G.1
Amiri, S.2
Premawaradena, T.3
Lindo, M.4
Emili, A.5
-
39
-
-
34248576306
-
NetPhos-Yeast: Prediction of protein phosphorylation sites in yeast
-
Ingrell, C. R., Miller, M. L., Jensen, O. N., and Blom, N. (2007) NetPhos-Yeast: prediction of protein phosphorylation sites in yeast. Bioinformatics 23, 895-897
-
(2007)
Bioinformatics
, vol.23
, pp. 895-897
-
-
Ingrell, C.R.1
Miller, M.L.2
Jensen, O.N.3
Blom, N.4
-
40
-
-
77952986553
-
Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs
-
Mok, J., Kim, P. M., Lam, H. Y., Piccirillo, S., Zhou, X., Jeschke, G. R., Sheridan, D. L., Parker, S. A., Desai, V., Jwa, M., Cameroni, E., Niu, H., Good, M., Remenyi, A., Ma, J. L., Sheu, Y. J., Sassi, H. E., Sopko, R., Chan, C. S., De Virgilio, C., Hollingsworth, N. M., Lim, W. A., Stern, D. F., Stillman, B., Andrews, B. J., Gerstein, M. B., Snyder, M., and Turk, B. E. (2010) Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci. Signal. 3, ra12
-
(2010)
Sci. Signal.
, vol.3
-
-
Mok, J.1
Kim, P.M.2
Lam, H.Y.3
Piccirillo, S.4
Zhou, X.5
Jeschke, G.R.6
Sheridan, D.L.7
Parker, S.A.8
Desai, V.9
Jwa, M.10
Cameroni, E.11
Niu, H.12
Good, M.13
Remenyi, A.14
Ma, J.L.15
Sheu, Y.J.16
Sassi, H.E.17
Sopko, R.18
Chan, C.S.19
De Virgilio, C.20
Hollingsworth, N.M.21
Lim, W.A.22
Stern, D.F.23
Stillman, B.24
Andrews, B.J.25
Gerstein, M.B.26
Snyder, M.27
Turk, B.E.28
more..
-
41
-
-
79551539500
-
Integrative features of the yeast phosphoproteome and protein-protein interaction map
-
Yachie, N., Saito, R., Sugiyama, N., Tomita, M., and Ishihama, Y. (2011) Integrative features of the yeast phosphoproteome and protein-protein interaction map. PLoS Comput. Biol. 7, e1001064
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Yachie, N.1
Saito, R.2
Sugiyama, N.3
Tomita, M.4
Ishihama, Y.5
-
42
-
-
0036806311
-
Evolution of protein kinase signaling from yeast to man
-
Manning, G., Plowman, G. D., Hunter, T., and Sudarsanam, S. (2002) Evolution of protein kinase signaling from yeast to man. Trends Biochem. Sci. 27, 514-520
-
(2002)
Trends Biochem. Sci.
, vol.27
, pp. 514-520
-
-
Manning, G.1
Plowman, G.D.2
Hunter, T.3
Sudarsanam, S.4
-
43
-
-
0037119988
-
Sec16p potentiates the action of COPII proteins to bud transport vesicles
-
Supek, F., Madden, D. T., Hamamoto, S., Orci, L., and Schekman, R. (2002) Sec16p potentiates the action of COPII proteins to bud transport vesicles. J. Cell Biol. 158, 1029-1038
-
(2002)
J. Cell Biol.
, vol.158
, pp. 1029-1038
-
-
Supek, F.1
Madden, D.T.2
Hamamoto, S.3
Orci, L.4
Schekman, R.5
-
44
-
-
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., and Ishihama, Y. (2009) In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. Mol. Cell. Proteomics 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
-
45
-
-
34548501747
-
Natural history and evolutionary principles of gene duplication in fungi
-
Wapinski, I., Pfeffer, A., Friedman, N., and Regev, A. (2007) Natural history and evolutionary principles of gene duplication in fungi. Nature 449, 54-61
-
(2007)
Nature
, vol.449
, pp. 54-61
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
Regev, A.4
-
46
-
-
25844471721
-
The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
-
Byrne, K. P., and Wolfe, K. H. (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15, 1456-1461
-
(2005)
Genome Res.
, vol.15
, pp. 1456-1461
-
-
Byrne, K.P.1
Wolfe, K.H.2
-
47
-
-
0037173615
-
Functional profiling of the Saccharomyces cerevisiae genome
-
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., Arkin, A. P., Astromoff, A., El-Bakkoury, M., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., Davis, K., Deutschbauer, A., Entian, K. D., Flaherty, P., Foury, F., Garfinkel, D. J., Gerstein, M., Gotte, D., Guldener, U., Hegemann, J. H., Hempel, S., Herman, Z., Jaramillo, D. F., Kelly, D. E., Kelly, S. L., Kötter, P., LaBonte, D., Lamb, D. C., Lan, N., Liang, H., Liao, H., Liu, L., Luo, C., Lussier, M., Mao, R., Menard, P., Ooi, S. L., Revuelta, J. L., Roberts, C. J., Rose, M., Ross-Macdonald, P., Scherens, B., Schimmack, G., Shafer, B., Shoemaker, D. D., Sookhai-Mahadeo, S., Storms, R. K., Strathern, J. N., Valle, G., Voet, M., Volckaert, G., Wang, C. Y., Ward, T. R., Wilhelmy, J., Winzeler, E. A., Yang, Y., Yen, G., Youngman, E., Yu, K., Bussey, H., Boeke, J. D., Snyder, M., Philippsen, P., Davis, R. W., and Johnston, M. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391
-
(2002)
Nature
, vol.418
, pp. 387-391
-
-
Giaever, G.1
Chu, A.M.2
Ni, L.3
Connelly, C.4
Riles, L.5
Véronneau, S.6
Dow, S.7
Lucau-Danila, A.8
Anderson, K.9
André, B.10
Arkin, A.P.11
Astromoff, A.12
El-Bakkoury, M.13
Bangham, R.14
Benito, R.15
Brachat, S.16
Campanaro, S.17
Curtiss, M.18
Davis, K.19
Deutschbauer, A.20
Entian, K.D.21
Flaherty, P.22
Foury, F.23
Garfinkel, D.J.24
Gerstein, M.25
Gotte, D.26
Guldener, U.27
Hegemann, J.H.28
Hempel, S.29
Herman, Z.30
Jaramillo, D.F.31
Kelly, D.E.32
Kelly, S.L.33
Kötter, P.34
LaBonte, D.35
Lamb, D.C.36
Lan, N.37
Liang, H.38
Liao, H.39
Liu, L.40
Luo, C.41
Lussier, M.42
Mao, R.43
Menard, P.44
Ooi, S.L.45
Revuelta, J.L.46
Roberts, C.J.47
Rose, M.48
Ross-Macdonald, P.49
Scherens, B.50
Schimmack, G.51
Shafer, B.52
Shoemaker, D.D.53
Sookhai-Mahadeo, S.54
Storms, R.K.55
Strathern, J.N.56
Valle, G.57
Voet, M.58
Volckaert, G.59
Wang, C.Y.60
Ward, T.R.61
Wilhelmy, J.62
Winzeler, E.A.63
Yang, Y.64
Yen, G.65
Youngman, E.66
Yu, K.67
Bussey, H.68
Boeke, J.D.69
Snyder, M.70
Philippsen, P.71
Davis, R.W.72
Johnston, M.73
more..
-
48
-
-
68449090023
-
Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions
-
Pache, R. A., Babu, M. M., and Aloy, P. (2009) Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions. BMC Syst. Biol. 3, 74
-
(2009)
BMC Syst. Biol.
, vol.3
, pp. 74
-
-
Pache, R.A.1
Babu, M.M.2
Aloy, P.3
-
49
-
-
0036699060
-
Systematic screen for human disease genes in yeast
-
Steinmetz, L. M., Scharfe, C., Deutschbauer, A. M., Mokranjac, D., Herman, Z. S., Jones, T., Chu, A. M., Giaever, G., Prokisch, H., Oefner, P. J., and Davis, R. W. (2002) Systematic screen for human disease genes in yeast. Nat. Genet. 31, 400-404
-
(2002)
Nat. Genet.
, vol.31
, pp. 400-404
-
-
Steinmetz, L.M.1
Scharfe, C.2
Deutschbauer, A.M.3
Mokranjac, D.4
Herman, Z.S.5
Jones, T.6
Chu, A.M.7
Giaever, G.8
Prokisch, H.9
Oefner, P.J.10
Davis, R.W.11
-
50
-
-
77649268965
-
Posttranslational regulation impacts the fate of duplicated genes
-
Amoutzias, G. D., He, Y., Gordon, J., Mossialos, D., Oliver, S. G., and Van de Peer, Y. (2010) Posttranslational regulation impacts the fate of duplicated genes. Proc. Natl. Acad. Sci. USA 107, 2967-2971
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 2967-2971
-
-
Amoutzias, G.D.1
He, Y.2
Gordon, J.3
Mossialos, D.4
Oliver, S.G.5
Van De Peer, Y.6
-
51
-
-
45449093756
-
Comparison of transcription regulatory interactions inferred from high-throughput methods: What do they reveal?
-
Balaji, S., Iyer, L. M., Babu, M. M., and Aravind, L. (2008) Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal? Trends Genet. 24, 319-323
-
(2008)
Trends Genet.
, vol.24
, pp. 319-323
-
-
Balaji, S.1
Iyer, L.M.2
Babu, M.M.3
Aravind, L.4
-
52
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., Hannett, N. M., Tagne, J. B., Reynolds, D. B., Yoo, J., Jennings, E. G., Zeitlinger, J., Pokholok, D. K., Kellis, M., Rolfe, P. A., Takusagawa, K. T., Lander, E. S., Gifford, D. K., Fraenkel, E., and Young, R. A. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
Jennings, E.G.11
Zeitlinger, J.12
Pokholok, D.K.13
Kellis, M.14
Rolfe, P.A.15
Takusagawa, K.T.16
Lander, E.S.17
Gifford, D.K.18
Fraenkel, E.19
Young, R.A.20
more..
-
53
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., Zeitlinger, J., Jennings, E. G., Murray, H. L., Gordon, D. B., Ren, B., Wyrick, J. J., Tagne, J. B., Volkert, T. L., Fraenkel, E., Gifford, D. K., and Young, R. A. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
54
-
-
0041706156
-
A proteomics approach to understanding protein ubiquitination
-
Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C., Cheng, D., Marsischky, G., Roelofs, J., Finley, D., and Gygi, S. P. (2003) A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21, 921-926
-
(2003)
Nat. Biotechnol.
, vol.21
, pp. 921-926
-
-
Peng, J.1
Schwartz, D.2
Elias, J.E.3
Thoreen, C.C.4
Cheng, D.5
Marsischky, G.6
Roelofs, J.7
Finley, D.8
Gygi, S.P.9
-
55
-
-
75649111192
-
The genetic landscape of a cell
-
Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., Koh, J. L., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. Y., Liang, W., Marback, M., Paw, J., San Luis, B. J., Shuteriqi, E., Tong, A. H., van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C. (2010) The genetic landscape of a cell. Science 327, 425-431
-
(2010)
Science
, vol.327
, pp. 425-431
-
-
Costanzo, M.1
Baryshnikova, A.2
Bellay, J.3
Kim, Y.4
Spear, E.D.5
Sevier, C.S.6
Ding, H.7
Koh, J.L.8
Toufighi, K.9
Mostafavi, S.10
Prinz, J.11
St Onge, R.P.12
VanderSluis, B.13
Makhnevych, T.14
Vizeacoumar, F.J.15
Alizadeh, S.16
Bahr, S.17
Brost, R.L.18
Chen, Y.19
Cokol, M.20
Deshpande, R.21
Li, Z.22
Lin, Z.Y.23
Liang, W.24
Marback, M.25
Paw, J.26
San Luis, B.J.27
Shuteriqi, E.28
Tong, A.H.29
Van Dyk, N.30
Wallace, I.M.31
Whitney, J.A.32
Weirauch, M.T.33
Zhong, G.34
Zhu, H.35
Houry, W.A.36
Brudno, M.37
Ragibizadeh, S.38
Papp, B.39
Pál, C.40
Roth, F.P.41
Giaever, G.42
Nislow, C.43
Troyanskaya, O.G.44
Bussey, H.45
Bader, G.D.46
Gingras, A.C.47
Morris, Q.D.48
Kim, P.M.49
Kaiser, C.A.50
Myers, C.L.51
Andrews, B.J.52
Boone, C.53
more..
-
56
-
-
33750238153
-
Stratus not altocumulus: A new view of the yeast protein interaction network
-
Batada, N. N., Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B. J., Hurst, L. D., and Tyers, M. (2006) Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol. 4, e317
-
(2006)
PLoS Biol.
, vol.4
-
-
Batada, N.N.1
Reguly, T.2
Breitkreutz, A.3
Boucher, L.4
Breitkreutz, B.J.5
Hurst, L.D.6
Tyers, M.7
-
57
-
-
79551521494
-
Measuring the evolutionary rewiring of biological networks
-
Shou, C., Bhardwaj, N., Lam, H. Y., Yan, K. K., Kim, P. M., Snyder, M., and Gerstein, M. B. (2011) Measuring the evolutionary rewiring of biological networks. PLoS Comput. Biol. 7, e1001050
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Shou, C.1
Bhardwaj, N.2
Lam, H.Y.3
Yan, K.K.4
Kim, P.M.5
Snyder, M.6
Gerstein, M.B.7
-
58
-
-
77649117952
-
Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data
-
Schweiger, R., and Linial, M. (2010) Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data. Biol. Direct 5, 6
-
(2010)
Biol. Direct
, vol.5
, pp. 6
-
-
Schweiger, R.1
Linial, M.2
-
59
-
-
26844571282
-
Multisite protein phosphorylation makes a good threshold but can be a poor switch
-
Gunawardena, J. (2005) Multisite protein phosphorylation makes a good threshold but can be a poor switch. Proc. Natl. Acad. Sci. USA 102, 14617-14622
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 14617-14622
-
-
Gunawardena, J.1
-
60
-
-
0035969559
-
Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication
-
Nash, P., Tang, X., Orlicky, S., Chen, Q., Gertler, F. B., Mendenhall, M. D., Sicheri, F., Pawson, T., and Tyers, M. (2001) Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature 414, 514-521
-
(2001)
Nature
, vol.414
, pp. 514-521
-
-
Nash, P.1
Tang, X.2
Orlicky, S.3
Chen, Q.4
Gertler, F.B.5
Mendenhall, M.D.6
Sicheri, F.7
Pawson, T.8
Tyers, M.9
-
61
-
-
34250743173
-
Systematic discovery of in vivo phosphorylation networks
-
Linding, R., Jensen, L. J., Ostheimer, G. J., van Vugt, M. A., Jørgensen, C., Miron, I. M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J. G., Samson, L. D., Woodgett, J. R., Russell, R. B., Bork, P., Yaffe, M. B., and Pawson, T. (2007) Systematic discovery of in vivo phosphorylation networks. Cell 129, 1415-1426
-
(2007)
Cell
, vol.129
, pp. 1415-1426
-
-
Linding, R.1
Jensen, L.J.2
Ostheimer, G.J.3
Van Vugt, M.A.4
Jørgensen, C.5
Miron, I.M.6
Diella, F.7
Colwill, K.8
Taylor, L.9
Elder, K.10
Metalnikov, P.11
Nguyen, V.12
Pasculescu, A.13
Jin, J.14
Park, J.G.15
Samson, L.D.16
Woodgett, J.R.17
Russell, R.B.18
Bork, P.19
Yaffe, M.B.20
Pawson, T.21
more..
-
62
-
-
79959938207
-
Recruitment interactions can override catalytic interactions in determining the functional identity of a protein kinase
-
Won, A. P., Garbarino, J. E., and Lim, W. A. (2011) Recruitment interactions can override catalytic interactions in determining the functional identity of a protein kinase. Proc. Natl. Acad. Sci. USA 108, 9809-9814
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 9809-9814
-
-
Won, A.P.1
Garbarino, J.E.2
Lim, W.A.3
-
63
-
-
36749051222
-
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites
-
Moses, A. M., Liku, M. E., Li, J. J., and Durbin, R. (2007) Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. Proc. Natl. Acad. Sci. USA 104, 17713-17718
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 17713-17718
-
-
Moses, A.M.1
Liku, M.E.2
Li, J.J.3
Durbin, R.4
|