-
1
-
-
0032489015
-
The cell as a collection of protein machines: Preparing the next generation of molecular biologists
-
Alberts, B. (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294
-
(1998)
Cell
, vol.92
, pp. 291-294
-
-
Alberts, B.1
-
2
-
-
42949089155
-
Making the most of high-throughput protein-interaction data
-
Gentleman, R., and Huber, W. (2007) Making the most of high-throughput protein-interaction data. Genome Biol. 8, 112
-
(2007)
Genome Biol.
, vol.8
, pp. 112
-
-
Gentleman, R.1
Huber, W.2
-
3
-
-
38049079362
-
Protein-protein interaction networks and biology-what's the connection?
-
Hakes, L., Pinney, J. W., Robertson, D. L., and Lovell, S. C. (2008) Protein-protein interaction networks and biology-what's the connection? Nat. Biotechnol. 26, 69-72
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 69-72
-
-
Hakes, L.1
Pinney, J.W.2
Robertson, D.L.3
Lovell, S.C.4
-
4
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
DOI 10.1038/415141a
-
Gavin, A. C., Bösche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., Remor, M., Höfert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., and Superti-Furga, G. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (Pubitemid 34059510)
-
(2002)
Nature
, vol.415
, Issue.6868
, pp. 141-147
-
-
Gavin, A.-C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.-M.9
Cruciat, C.-M.10
Remor, M.11
Hofert, C.12
Schelder, M.13
Brajenovic, M.14
Ruffner, H.15
Merino, A.16
Klein, K.17
Hudak, M.18
Dickson, D.19
Rudi, T.20
Gnau, V.21
Bauch, A.22
Bastuck, S.23
Huhse, B.24
Leutwein, C.25
Heurtier, M.-A.26
Copley, R.R.27
Edelmann, A.28
Querfurth, E.29
Rybin, V.30
Drewes, G.31
Raida, M.32
Bouwmeester, T.33
Bork, P.34
Seraphin, B.35
Kuster, B.36
Neubauer, G.37
Superti-Furga, G.38
more..
-
5
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
DOI 10.1038/415180a
-
Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A. R., Sassi, H., Nielsen, P. A., Rasmussen, K. J., Andersen, J. R., Johansen, L. E., Hansen, L. H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sørensen, B. D., Matthiesen, J., Hendrickson, R. C., Gleeson, F., Pawson, T., Moran, M. F., Durocher, D., Mann, M., Hogue, C. W., Figeys, D., and Tyers, M. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (Pubitemid 34059520)
-
(2002)
Nature
, vol.415
, Issue.6868
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
Adams, S.-L.6
Millar, A.7
Taylor, P.8
Bennett, K.9
Boutilier, K.10
Yang, L.11
Wolting, C.12
Donaldson, I.13
Schandorff, S.14
Shewnarane, J.15
Vo, M.16
Taggart, J.17
Goudreault, M.18
Muskat, B.19
Alfarano, C.20
Dewar, D.21
Lin, Z.22
Michalickova, K.23
Willems, A.R.24
Sassi, H.25
Nielsen, P.A.26
Rasmussen, K.J.27
Andersen, J.R.28
Johansen, L.E.29
Hansen, L.H.30
Jespersen, H.31
Podtelejnikov, A.32
Nielsen, E.33
Crawford, J.34
Poulsen, V.35
Sorensen, B.D.36
Matthiesen, J.37
Hendrickson, R.C.38
Gleeson, F.39
Pawson, T.40
Moran, M.F.41
Durocher, D.42
Mann, M.43
Hogue, C.W.V.44
Figeys, D.45
Tyers, M.46
more..
-
6
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., Edelmann, A., Heurtier, M. A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A. M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J. M., Kuster, B., Bork, P., Russell, R. B., and Superti-Furga, G. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
Rau, C.7
Jensen, L.J.8
Bastuck, S.9
Dümpelfeld, B.10
Edelmann, A.11
Heurtier, M.A.12
Hoffman, V.13
Hoefert, C.14
Klein, K.15
Hudak, M.16
Michon, A.M.17
Schelder, M.18
Schirle, M.19
Remor, M.20
Rudi, T.21
Hooper, S.22
Bauer, A.23
Bouwmeester, T.24
Casari, G.25
Drewes, G.26
Neubauer, G.27
Rick, J.M.28
Kuster, B.29
Bork, P.30
Russell, R.B.31
Superti-Furga, G.32
more..
-
7
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A. P., Punna, T., Peregrin-Alvarez, J. M., Shales, M., Zhang, X., Davey, M., Robinson, M. D., Paccanaro, A., Bray, J. E., Sheung, A., Beattie, B., Richards, D. P., Canadien, V., Lalev, A., Mena, F., Wong, P., Starostine, A., Canete, M. M., Vlasblom, J., Wu, S., Orsi, C., Collins, S. R., Chandran, S., Haw, R., Rilstone, J. J., Gandi, K., Thompson, N. J., Musso, G., St Onge, P., Ghanny, S., Lam, M. H., Butland, G., Altaf-Ul, A. M., Kanaya, S., Shilatifard, A., O'Shea, E., Weissman, J. S., Ingles, C. J., Hughes, T. R., Parkinson, J., Gerstein, M., Wodak, S. J., Emili, A., and Greenblatt, J. F. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
Li, J.7
Pu, S.8
Datta, N.9
Tikuisis, A.P.10
Punna, T.11
Peregrin-Alvarez, J.M.12
Shales, M.13
Zhang, X.14
Davey, M.15
Robinson, M.D.16
Paccanaro, A.17
Bray, J.E.18
Sheung, A.19
Beattie, B.20
Richards, D.P.21
Canadien, V.22
Lalev, A.23
Mena, F.24
Wong, P.25
Starostine, A.26
Canete, M.M.27
Vlasblom, J.28
Wu, S.29
Orsi, C.30
Collins, S.R.31
Chandran, S.32
Haw, R.33
Rilstone, J.J.34
Gandi, K.35
Thompson, N.J.36
Musso, G.37
St Onge, P.38
Ghanny, S.39
Lam, M.H.40
Butland, G.41
Altaf-Ul, A.M.42
Kanaya, S.43
Shilatifard, A.44
O'Shea, E.45
Weissman, J.S.46
Ingles, C.J.47
Hughes, T.R.48
Parkinson, J.49
Gerstein, M.50
Wodak, S.J.51
Emili, A.52
Greenblatt, J.F.53
more..
-
8
-
-
45849110261
-
An in vivo map of the yeast protein interactome
-
DOI 10.1126/science.1153878
-
Tarassov, K., Messier, V., Landry, C. R., Radinovic, S., Serna Molina, M. M., Shames, I., Malitskaya, Y., Vogel, J., Bussey, H., and Michnick, S. W. (2008) An in vivo map of the yeast protein interactome. Science 320, 1465-1470 (Pubitemid 351929421)
-
(2008)
Science
, vol.320
, Issue.5882
, pp. 1465-1470
-
-
Tarassov, K.1
Messier, V.2
Landry, C.R.3
Radinovic, S.4
Serna, M.M.M.5
Shames, I.6
Malitskaya, Y.7
Vogel, J.8
Bussey, H.9
Michnick, S.W.10
-
9
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
DOI 10.1073/pnas.061034498
-
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U.S.A. 98, 4569-4574 (Pubitemid 32295017)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.8
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
10
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
DOI 10.1038/35001009
-
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J. M. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (Pubitemid 30103994)
-
(2000)
Nature
, vol.403
, Issue.6770
, pp. 623-627
-
-
Uetz, P.1
Glot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
Lockshon, D.7
Narayan, V.8
Srinivasan, M.9
Pochart, P.10
Qureshi-Emlli, A.11
Li, Y.12
Godwin, B.13
Conover, D.14
Kalbfleisch, T.15
Vijayadamodar, G.16
Yang, M.17
Johnston, M.18
Fields, S.19
Rothberg, J.M.20
more..
-
11
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
Yu, H., Braun, P., Yildirim, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., Hao, T., Rual, J. F., Dricot, A., Vazquez, A., Murray, R. R., Simon, C., Tardivo, L., Tam, S., Svrzikapa, N., Fan, C., de Smet, A. S., Motyl, A., Hudson, M. E., Park, J., Xin, X., Cusick, M. E., Moore, T., Boone, C., Snyder, M., Roth, F. P., Barabasi, A. L., Tavernier, J., Hill, D. E., and Vidal, M. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322, 104-110
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
Braun, P.2
Yildirim, M.A.3
Lemmens, I.4
Venkatesan, K.5
Sahalie, J.6
Hirozane-Kishikawa, T.7
Gebreab, F.8
Li, N.9
Simonis, N.10
Hao, T.11
Rual, J.F.12
Dricot, A.13
Vazquez, A.14
Murray, R.R.15
Simon, C.16
Tardivo, L.17
Tam, S.18
Svrzikapa, N.19
Fan, C.20
De Smet, A.S.21
Motyl, A.22
Hudson, M.E.23
Park, J.24
Xin, X.25
Cusick, M.E.26
Moore, T.27
Boone, C.28
Snyder, M.29
Roth, F.P.30
Barabasi, A.L.31
Tavernier, J.32
Hill, D.E.33
Vidal, M.34
more..
-
12
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S., and Bork, P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403 (Pubitemid 34563526)
-
(2002)
Nature
, vol.417
, Issue.6887
, pp. 399-403
-
-
Von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
13
-
-
0347473809
-
Gaining confidence in high-throughput protein interaction networks
-
DOI 10.1038/nbt924
-
Bader, J. S., Chaudhuri, A., Rothberg, J. M., and Chant, J. (2004) Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol. 22, 78-85 (Pubitemid 38057960)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.1
, pp. 78-85
-
-
Bader, J.S.1
Chaudhuri, A.2
Rothberg, J.M.3
Chant, J.4
-
14
-
-
70349658775
-
A novel scoring approach for protein co-purification data reveals high interaction specificity
-
Yu, X., Ivanic, J., Wallqvist, A., and Reifman, J. (2009) A novel scoring approach for protein co-purification data reveals high interaction specificity. PLoS Comput. Biol. 5, e1000515
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Yu, X.1
Ivanic, J.2
Wallqvist, A.3
Reifman, J.4
-
15
-
-
48249147450
-
Probing the extent of randomness in protein interaction networks
-
Ivanic, J., Wallqvist, A., and Reifman, J. (2008) Probing the extent of randomness in protein interaction networks. PLoS Comput. Biol. 4, e1000114
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Ivanic, J.1
Wallqvist, A.2
Reifman, J.3
-
16
-
-
27644576841
-
High-throughput two-hybrid analysis. The promise and the peril
-
Fields, S. (2005) High-throughput two-hybrid analysis. The promise and the peril. FEBS J. 272, 5391-5399
-
(2005)
FEBS J.
, vol.272
, pp. 5391-5399
-
-
Fields, S.1
-
17
-
-
67649663886
-
Yeast two-hybrid, a powerful tool for systems biology
-
Brückner, A., Polge, C., Lentze, N., Auerbach, D., and Schlattner, U. (2009) Yeast two-hybrid, a powerful tool for systems biology. Int. J. Mol. Sci. 10, 2763-2788
-
(2009)
Int. J. Mol. Sci.
, vol.10
, pp. 2763-2788
-
-
Brückner, A.1
Polge, C.2
Lentze, N.3
Auerbach, D.4
Schlattner, U.5
-
18
-
-
73249129711
-
Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins
-
Rajagopala, S. V., Hughes, K. T., and Uetz, P. (2009) Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins. Proteomics 9, 5296-5302
-
(2009)
Proteomics
, vol.9
, pp. 5296-5302
-
-
Rajagopala, S.V.1
Hughes, K.T.2
Uetz, P.3
-
19
-
-
59149103076
-
Challenges and rewards of interaction proteomics
-
Wodak, S. J., Pu, S., Vlasblom, J., and Séraphin, B. (2009) Challenges and rewards of interaction proteomics. Mol. Cell. Proteomics 8, 3-18
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 3-18
-
-
Wodak, S.J.1
Pu, S.2
Vlasblom, J.3
Séraphin, B.4
-
20
-
-
34147121646
-
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
-
DOI 10.1074/mcp.M600381-MCP200
-
Collins, S. R., Kemmeren, P., Zhao, X. C., Greenblatt, J. F., Spencer, F., Holstege, F. C., Weissman, J. S., and Krogan, N. J. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics 6, 439-450 (Pubitemid 46554539)
-
(2007)
Molecular and Cellular Proteomics
, vol.6
, Issue.3
, pp. 439-450
-
-
Collins, S.R.1
Kemmeren, P.2
Zhao, X.-C.3
Greenblatt, J.F.4
Spencer, F.5
Hoolstege, F.C.P.6
Weissman, J.S.7
Krogan, N.J.8
-
21
-
-
34547787599
-
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
-
Hart, G. T., Lee, I., and Marcotte, E. R. (2007) A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics 8, 236
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 236
-
-
Hart, G.T.1
Lee, I.2
Marcotte, E.R.3
-
22
-
-
79551523294
-
Interactive proteomics research technologies: Recent applications and advances
-
Petschnigg, J., Snider, J., and Stagljar, I. (2011) Interactive proteomics research technologies: recent applications and advances. Curr. Opin. Biotechnol. 22, 50-58
-
(2011)
Curr. Opin. Biotechnol.
, vol.22
, pp. 50-58
-
-
Petschnigg, J.1
Snider, J.2
Stagljar, I.3
-
23
-
-
33748202182
-
Functional clustering of yeast proteins from the protein-protein interaction network
-
Sen, T. Z., Kloczkowski, A., and Jernigan, R. L. (2006) Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics 7, 355
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 355
-
-
Sen, T.Z.1
Kloczkowski, A.2
Jernigan, R.L.3
-
24
-
-
33748464764
-
Combining functional and topological properties to identify core modules in protein interaction networks
-
DOI 10.1002/prot.21071
-
Lubovac, Z., Gamalielsson, J., and Olsson, B. (2006) Combining functional and topological properties to identify core modules in protein interaction networks. Proteins 64, 948-959 (Pubitemid 44420936)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.64
, Issue.4
, pp. 948-959
-
-
Lubovac, Z.1
Gamalielsson, J.2
Olsson, B.3
-
25
-
-
34548742517
-
Identification of functional modules using network topology and high-throughput data
-
Ulitsky, I., and Shamir, R. (2007) Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol. 1, 8
-
(2007)
BMC Syst. Biol.
, vol.1
, pp. 8
-
-
Ulitsky, I.1
Shamir, R.2
-
26
-
-
65349187039
-
Energetic determinants of protein binding specificity: Insights into protein interaction networks
-
Carbonell, P., Nussinov, R., and del Sol, A. (2009) Energetic determinants of protein binding specificity: insights into protein interaction networks. Proteomics 9, 1744-1753
-
(2009)
Proteomics
, vol.9
, pp. 1744-1753
-
-
Carbonell, P.1
Nussinov, R.2
Del Sol, A.3
-
27
-
-
79551667508
-
Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks
-
Johnson, M. E., and Hummer, G. (2010) Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proc. Natl. Acad. Sci. U.S.A. 108, 603-608
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 603-608
-
-
Johnson, M.E.1
Hummer, G.2
-
28
-
-
33746834184
-
Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences
-
DOI 10.1073/pnas.0604316103
-
Shi, Y. Y., Miller, G. A., Qian, H., and Bomsztyk, K. (2006) Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences. Proc. Natl. Acad. Sci. U.S.A. 103, 11527-11532 (Pubitemid 44182485)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.31
, pp. 11527-11532
-
-
Shi, Y.Y.1
Miller, G.A.2
Qian, H.3
Bomsztyk, K.4
-
29
-
-
77952596213
-
Structural interpretation of protein-protein interaction network
-
Katebi, A. R., Kloczkowski, A., and Jernigan, R. L. (2010) Structural interpretation of protein-protein interaction network. BMC Struct. Biol. 10, Suppl 1, S4
-
(2010)
BMC Struct. Biol.
, vol.10
, Issue.SUPPL. 1
-
-
Katebi, A.R.1
Kloczkowski, A.2
Jernigan, R.L.3
-
30
-
-
77950353931
-
Toward the dynamic interactome: It's about time
-
Przytycka, T. M., Singh, M., and Slonim, D. K. (2010) Toward the dynamic interactome: it's about time. Brief Bioinform. 11, 15-29
-
(2010)
Brief Bioinform.
, vol.11
, pp. 15-29
-
-
Przytycka, T.M.1
Singh, M.2
Slonim, D.K.3
-
31
-
-
9144242935
-
MIPS: Analysis and annotation of proteins from whole genomes
-
Mewes, H. W., Amid, C., Arnold, R., Frishman, D., Göldener, U., Mannhaupt, G., Münsterkötter, M., Pagel, P., Strack, N., Stümpflen, V., Warfsmann, J., and Ruepp, A. (2004) MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 32, D41-44 (Pubitemid 38081600)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Mewes, H.W.1
Amid, C.2
Arnold, R.3
Frishman, D.4
Guldener, U.5
Mannhaupt, G.6
Munsterkotter, M.7
Pagel, P.8
Strack, N.9
Stumpflen, V.10
Warfsmann, J.11
Ruepp, A.12
-
32
-
-
78651331299
-
MIPS: Curated databases and comprehensive secondary data resources in 2010
-
Mewes, H. W., Ruepp, A., Theis, F., Rattei, T., Walter, M., Frishman, D., Suhre, K., Spannagl, M., Mayer, K. F., Stümpflen, V., and Antonov, A. (2011) MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res. 39, D220-224
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Mewes, H.W.1
Ruepp, A.2
Theis, F.3
Rattei, T.4
Walter, M.5
Frishman, D.6
Suhre, K.7
Spannagl, M.8
Mayer, K.F.9
Stümpflen, V.10
Antonov, A.11
-
33
-
-
70350482286
-
Evolution of biomolecular networks: Lessons from metabolic and protein interactions
-
Yamada, T., and Bork, P. (2009) Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat. Rev. Mol. Cell Biol. 10, 791-803
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 791-803
-
-
Yamada, T.1
Bork, P.2
-
34
-
-
33847744247
-
How complete are current yeast and human protein-interaction networks?
-
Hart, G. T., Ramani, A. K., and Marcotte, E. M. (2006) How complete are current yeast and human protein-interaction networks? Genome Biol. 7, 120
-
(2006)
Genome Biol.
, vol.7
, pp. 120
-
-
Hart, G.T.1
Ramani, A.K.2
Marcotte, E.M.3
-
35
-
-
78650274124
-
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size
-
Sambourg, L., and Thierry-Mieg, N. (2010) New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size. BMC Bioinformatics 11, 605
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 605
-
-
Sambourg, L.1
Thierry-Mieg, N.2
-
36
-
-
1342330546
-
Functional topology in a network of protein interactions
-
DOI 10.1093/bioinformatics/btg415
-
Przulj, N., Wigle, D. A., and Jurisica, I. (2004) Functional topology in a network of protein interactions. Bioinformatics 20, 340-348 (Pubitemid 38262765)
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 340-348
-
-
Przulj, N.1
Wigle, D.A.2
Jurisica, I.3
-
37
-
-
33644878150
-
MPact: The MIPS protein interaction resource on yeast
-
Güldener, U., Münsterkötter, M., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H. W., and Stümpflen, V. (2006) MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 34, D436-441
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Güldener, U.1
Münsterkötter, M.2
Oesterheld, M.3
Pagel, P.4
Ruepp, A.5
Mewes, H.W.6
Stümpflen, V.7
-
38
-
-
78650808055
-
Unraveling the conundrum of seemingly discordant protein-protein interaction datasets
-
Gupta, S., Wallqvist, A., Bondugula, R., Ivanic, J., and Reifman, J. (2010) Unraveling the conundrum of seemingly discordant protein-protein interaction datasets. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2010, 783-786
-
(2010)
Conf. Proc. IEEE Eng. Med. Biol. Soc.
, vol.2010
, pp. 783-786
-
-
Gupta, S.1
Wallqvist, A.2
Bondugula, R.3
Ivanic, J.4
Reifman, J.5
-
39
-
-
9144242935
-
MIPS: Analysis and annotation of proteins from whole genomes
-
Mewes, H. W., Amid, C., Arnold, R., Frishman, D., Güldener, U., Mannhaupt, G., Münsterkötter, M., Pagel, P., Strack, N., Stumpflen, V., Warfsmann, J., and Ruepp, A. (2004) MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 32, D41-44 (Pubitemid 38081600)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Mewes, H.W.1
Amid, C.2
Arnold, R.3
Frishman, D.4
Guldener, U.5
Mannhaupt, G.6
Munsterkotter, M.7
Pagel, P.8
Strack, N.9
Stumpflen, V.10
Warfsmann, J.11
Ruepp, A.12
-
40
-
-
77957352573
-
The bait compatibility index: Computational bait selection for interaction proteomics experiments
-
Saha, S., Kaur, P., and Ewing, R. M. (2010) The bait compatibility index: computational bait selection for interaction proteomics experiments. J. Proteome Res 9, 4972-4981
-
(2010)
J. Proteome Res
, vol.9
, pp. 4972-4981
-
-
Saha, S.1
Kaur, P.2
Ewing, R.M.3
-
41
-
-
1542346419
-
Chromatin remodeling by RNA polymerases
-
DOI 10.1016/j.tibs.2004.01.003, PII S0968000404000180
-
Studitsky, V. M., Walter, W., Kireeva, M., Kashlev, M., and Felsenfeld, G. (2004) Chromatin remodeling by RNA polymerases. Trends Biochem. Sci 29, 127-135 (Pubitemid 38314858)
-
(2004)
Trends in Biochemical Sciences
, vol.29
, Issue.3
, pp. 127-135
-
-
Studitsky, V.M.1
Walter, W.2
Kireeva, M.3
Kashlev, M.4
Felsenfeld, G.5
-
42
-
-
70249142494
-
Cooperation between the INO80 complex and histone chaperones determines adaptation of stress gene transcription in the yeast Saccharomyces cerevisiae
-
Klopf, E., Paskova, L., Solé, C., Mas, G., Petryshyn, A., Posas, F., Wintersberger, U., Ammerer, G., and Schüller, C. (2009) Cooperation between the INO80 complex and histone chaperones determines adaptation of stress gene transcription in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 29, 4994-5007
-
(2009)
Mol. Cell. Biol.
, vol.29
, pp. 4994-5007
-
-
Klopf, E.1
Paskova, L.2
Solé, C.3
Mas, G.4
Petryshyn, A.5
Posas, F.6
Wintersberger, U.7
Ammerer, G.8
Schüller, C.9
-
43
-
-
77950619158
-
Activation of a poised RNAPII-dependent promoter requires both SAGA and mediator
-
Lee, S. K., Fletcher, A. G., Zhang, L., Chen, X., Fischbeck, J. A., and Stargell, L. A. (2010) Activation of a poised RNAPII-dependent promoter requires both SAGA and mediator. Genetics 184, 659-672
-
(2010)
Genetics
, vol.184
, pp. 659-672
-
-
Lee, S.K.1
Fletcher, A.G.2
Zhang, L.3
Chen, X.4
Fischbeck, J.A.5
Stargell, L.A.6
-
44
-
-
1342346531
-
Structural and Functional Conservation of the NuA4 Histone Acetyltransferase Complex from Yeast to Humans
-
DOI 10.1128/MCB.24.5.1884-1896.2004
-
Doyon, Y., Selleck, W., Lane, W. S., Tan, S., and Côté, J. (2004) Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Mol. Cell. Biol. 24, 1884-1896 (Pubitemid 38248930)
-
(2004)
Molecular and Cellular Biology
, vol.24
, Issue.5
, pp. 1884-1896
-
-
Doyon, Y.1
Selleck, W.2
Lane, W.S.3
Tan, S.4
Cote, J.5
-
45
-
-
0032589574
-
II-containing complexes TFIID and TFTC
-
Brand, M., Leurent, C., Mallouh, V., Tora, L., and Schultz, P. (1999) Three-dimensional structures of the TAFII-containing complexes TFIID and TFTC. Science 286, 2151-2153 (Pubitemid 129516288)
-
(1999)
Science
, vol.286
, Issue.5447
, pp. 2151-2153
-
-
Brand, M.1
Leurent, C.2
Mallouh, V.3
Tora, L.4
Schultz, P.5
-
46
-
-
17644397037
-
Interdependent recruitment of SAGA and Srb mediator by transcriptional activator Gcn4p
-
DOI 10.1128/MCB.25.9.3461-3474.2005
-
Qiu, H., Hu, C., Zhang, F., Hwang, G. J., Swanson, M. J., Boonchird, C., and Hinnebusch, A. G. (2005) Interdependent recruitment of SAGA and Srb mediator by transcriptional activator Gcn4p. Mol. Cell. Biol. 25, 3461-3474 (Pubitemid 40559555)
-
(2005)
Molecular and Cellular Biology
, vol.25
, Issue.9
, pp. 3461-3474
-
-
Qiu, H.1
Hu, C.2
Zhang, F.3
Gwo, J.H.4
Swanson, M.J.5
Boonchird, C.6
Hinnebusch, A.G.7
-
47
-
-
0031858914
-
SGD: Saccharomyces genome database
-
DOI 10.1093/nar/26.1.73
-
Cherry, J. M., Adler, C., Ball, C., Chervitz, S. A., Dwight, S. S., Hester, E. T., Jia, Y., Juvik, G., Roe, T., Schroeder, M., Weng, S., and Botstein, D. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26, 73-79 (Pubitemid 28295265)
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.1
, pp. 73-79
-
-
Cherry, J.M.1
Adler, C.2
Ball, C.3
Chervitz, S.A.4
Dwight, S.S.5
Hester, E.T.6
Jia, Y.7
Juvik, G.8
Roe, T.9
Schroeder, M.10
Weng, S.11
Botstein, D.12
-
48
-
-
0036141992
-
Relating whole-genome expression data with protein-protein interactions
-
DOI 10.1101/gr.205602
-
Jansen, R., Greenbaum, D., and Gerstein, M. (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res. 12, 37-46 (Pubitemid 34065588)
-
(2002)
Genome Research
, vol.12
, Issue.1
, pp. 37-46
-
-
Jansen, R.1
Greenbaum, D.2
Gerstein, M.3
-
49
-
-
67149141471
-
Influence of protein abundance on high-throughput protein-protein interaction detection
-
Ivanic, J., Yu, X., Wallqvist, A., and Reifman, J. (2009) Influence of protein abundance on high-throughput protein-protein interaction detection. PLoS One 4, e5815
-
(2009)
PLoS One
, vol.4
-
-
Ivanic, J.1
Yu, X.2
Wallqvist, A.3
Reifman, J.4
-
50
-
-
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
-
51
-
-
0035799707
-
Lethality and centrality in protein networks
-
DOI 10.1038/35075138
-
Jeong, H., Mason, S. P., Barabási, A. L., and Oltvai, Z. N. (2001) Lethality and centrality in protein networks. Nature 411, 41-42 (Pubitemid 32428180)
-
(2001)
Nature
, vol.411
, Issue.6833
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabasi, A.-L.3
Oltvai, Z.N.4
-
52
-
-
33746631391
-
Evolutionary and physiological importance of hub proteins
-
Batada, N. N., Hurst, L. D., and Tyers, M. (2006) Evolutionary and physiological importance of hub proteins. PLoS Comput. Biol. 2, e88
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Batada, N.N.1
Hurst, L.D.2
Tyers, M.3
-
53
-
-
16344381521
-
Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
-
DOI 10.1093/molbev/msi072
-
Hahn, M. W., and Kern, A. D. (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol. Biol. Evol. 22, 803-806 (Pubitemid 40471393)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.4
, pp. 803-806
-
-
Hahn, M.W.1
Kern, A.D.2
-
54
-
-
0034721164
-
Error and attack tolerance of complex networks
-
DOI 10.1038/35019019
-
Albert, R., Jeong, H., and Barabasi, A. L. (2000) Error and attack tolerance of complex networks. Nature 406, 378-382 (Pubitemid 30625551)
-
(2000)
Nature
, vol.406
, Issue.6794
, pp. 378-382
-
-
Albert, R.1
Jeong, H.2
Barabasi, A.-L.3
-
55
-
-
33745712594
-
Why do hubs tend to be essential in protein networks?
-
He, X., and Zhang, J. (2006) Why do hubs tend to be essential in protein networks? PLoS Genet. 2, e88
-
(2006)
PLoS Genet.
, vol.2
-
-
He, X.1
Zhang, J.2
-
56
-
-
50949092459
-
Why do hubs in the yeast protein interaction network tend to be essential: Reexamining the connection between the network topology and essentiality
-
Zotenko, E., Mestre, J., O'Leary, D. P., and Przytycka, T. M. (2008) Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput. Biol. 4, e1000140
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Zotenko, E.1
Mestre, J.2
O'Leary, D.P.3
Przytycka, T.M.4
-
57
-
-
67649641077
-
A complex-based reconstruction of the Saccharomyces cerevisiae interactome
-
Wang, H., Kakaradov, B., Collins, S. R., Karotki, L., Fiedler, D., Shales, M., Shokat, K. M., Walther, T. C., Krogan, N. J., and Koller, D. (2009) A complex-based reconstruction of the Saccharomyces cerevisiae interactome. Mol. Cell. Proteomics 8, 1361-1381
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 1361-1381
-
-
Wang, H.1
Kakaradov, B.2
Collins, S.R.3
Karotki, L.4
Fiedler, D.5
Shales, M.6
Shokat, K.M.7
Walther, T.C.8
Krogan, N.J.9
Koller, D.10
-
58
-
-
33751395622
-
The value of high quality protein-protein interaction networks for systems biology
-
DOI 10.1016/j.cbpa.2006.10.005, PII S1367593106001578
-
Stelzl, U., and Wanker, E. E. (2006) The value of high quality protein-protein interaction networks for systems biology. Curr. Opin. Chem. Biol. 10, 551-558 (Pubitemid 44821895)
-
(2006)
Current Opinion in Chemical Biology
, vol.10
, Issue.6
, pp. 551-558
-
-
Stelzl, U.1
Wanker, E.E.2
-
59
-
-
34347374044
-
Universal strategies in research and drug discovery based on protein-fragment complementation assays
-
DOI 10.1038/nrd2311, PII NRD2311
-
Michnick, S. W., Ear, P. H., Manderson, E. N., Remy, I., and Stefan, E. (2007) Universal strategies in research and drug discovery based on protein-fragment complementation assays. Nat. Rev. Drug Discov. 6, 569-582 (Pubitemid 47019445)
-
(2007)
Nature Reviews Drug Discovery
, vol.6
, Issue.7
, pp. 569-582
-
-
Michnick, S.W.1
Ear, P.H.2
Manderson, E.N.3
Remy, I.4
Stefan, E.5
-
60
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
DOI 10.1073/pnas.061034498
-
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U.S.A. 98, 4569-4574 (Pubitemid 32295017)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.8
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
|