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For: Sardiu ME, Gilmore JM, Carrozza MJ, Li B, Workman JL, Florens L, Washburn MP. Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics. PLoS One 2009;4:e7310. [PMID: 19806189 PMCID: PMC2751824 DOI: 10.1371/journal.pone.0007310] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 09/07/2009] [Indexed: 11/19/2022]  Open
Number Cited by Other Article(s)
1
Hao H, Lian Y, Ren C, Yang S, Zhao M, Bo T, Xu J, Wang W. RebL1 is required for macronuclear structure stability and gametogenesis in Tetrahymena thermophila. MARINE LIFE SCIENCE & TECHNOLOGY 2024;6:183-197. [PMID: 38827131 PMCID: PMC11136921 DOI: 10.1007/s42995-024-00219-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 03/01/2024] [Indexed: 06/04/2024]
2
Pons C, van Leeuwen J. Meta-analysis of dispensable essential genes and their interactions with bypass suppressors. Life Sci Alliance 2024;7:e202302192. [PMID: 37918966 PMCID: PMC10622647 DOI: 10.26508/lsa.202302192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]  Open
3
Patel AB, Qing J, Tam KH, Zaman S, Luiso M, Radhakrishnan I, He Y. Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Nat Commun 2023;14:3061. [PMID: 37244892 PMCID: PMC10224958 DOI: 10.1038/s41467-023-38687-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/11/2023] [Indexed: 05/29/2023]  Open
4
Opposing Roles of FACT for Euchromatin and Heterochromatin in Yeast. Biomolecules 2023;13:biom13020377. [PMID: 36830746 PMCID: PMC9953268 DOI: 10.3390/biom13020377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]  Open
5
Xu H, Ye M, Xia A, Jiang H, Huang P, Liu H, Hou R, Wang Q, Li D, Xu JR, Jiang C. The Fng3 ING protein regulates H3 acetylation and H4 deacetylation by interacting with two distinct histone-modifying complexes. THE NEW PHYTOLOGIST 2022;235:2350-2364. [PMID: 35653584 DOI: 10.1111/nph.18294] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/30/2022] [Indexed: 05/26/2023]
6
Amoiradaki K, Bunting KR, Paine KM, Ayre JE, Hogg K, Laidlaw KME, MacDonald C. The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast. Int J Mol Sci 2021;22:12477. [PMID: 34830359 PMCID: PMC8617818 DOI: 10.3390/ijms222212477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022]  Open
7
Sardiu ME, Florens L, Washburn MP. Generating topological protein interaction scores and data visualization with TopS. Methods 2019;184:13-18. [PMID: 31476375 DOI: 10.1016/j.ymeth.2019.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 12/17/2022]  Open
8
Lee BB, Choi A, Kim JH, Jun Y, Woo H, Ha SD, Yoon CY, Hwang JT, Steinmetz L, Buratowski S, Lee S, Kim HY, Kim T. Rpd3L HDAC links H3K4me3 to transcriptional repression memory. Nucleic Acids Res 2019;46:8261-8274. [PMID: 29982589 PMCID: PMC6144869 DOI: 10.1093/nar/gky573] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/14/2018] [Indexed: 11/13/2022]  Open
9
Sardiu ME, Gilmore JM, Groppe B, Florens L, Washburn MP. Identification of Topological Network Modules in Perturbed Protein Interaction Networks. Sci Rep 2017;7:43845. [PMID: 28272416 PMCID: PMC5341041 DOI: 10.1038/srep43845] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/30/2017] [Indexed: 12/31/2022]  Open
10
Lakshminarasimhan M, Boanca G, Banks CAS, Hattem GL, Gabriel AE, Groppe BD, Smoyer C, Malanowski KE, Peak A, Florens L, Washburn MP. Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components. Mol Cell Proteomics 2016;15:960-74. [PMID: 26831523 DOI: 10.1074/mcp.m115.053165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 11/06/2022]  Open
11
Ruan C, Cui H, Lee CH, Li S, Li B. Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex. J Biol Chem 2016;291:5428-38. [PMID: 26747610 DOI: 10.1074/jbc.m115.703637] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Indexed: 12/29/2022]  Open
12
Sardiu ME, Smith KT, Groppe BD, Gilmore JM, Saraf A, Egidy R, Peak A, Seidel CW, Florens L, Workman JL, Washburn MP. Suberoylanilide hydroxamic acid (SAHA)-induced dynamics of a human histone deacetylase protein interaction network. Mol Cell Proteomics 2014;13:3114-25. [PMID: 25073741 DOI: 10.1074/mcp.m113.037127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
13
Bypassing the requirement for an essential MYST acetyltransferase. Genetics 2014;197:851-63. [PMID: 24831819 DOI: 10.1534/genetics.114.165894] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
14
Mosley AL, Hunter GO, Sardiu ME, Smolle M, Workman JL, Florens L, Washburn MP. Quantitative proteomics demonstrates that the RNA polymerase II subunits Rpb4 and Rpb7 dissociate during transcriptional elongation. Mol Cell Proteomics 2013;12:1530-8. [PMID: 23418395 DOI: 10.1074/mcp.m112.024034] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
15
White EA, Howley PM. Proteomic approaches to the study of papillomavirus-host interactions. Virology 2013;435:57-69. [PMID: 23217616 PMCID: PMC3522865 DOI: 10.1016/j.virol.2012.09.046] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 09/30/2012] [Indexed: 01/22/2023]
16
Nesvizhskii AI. Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 2012;12:1639-55. [PMID: 22611043 DOI: 10.1002/pmic.201100537] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
17
Kaluarachchi Duffy S, Friesen H, Baryshnikova A, Lambert JP, Chong YT, Figeys D, Andrews B. Exploring the yeast acetylome using functional genomics. Cell 2012;149:936-48. [PMID: 22579291 DOI: 10.1016/j.cell.2012.02.064] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 01/24/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
18
Gingras AC, Raught B. Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions. FEBS Lett 2012;586:2723-31. [PMID: 22710165 DOI: 10.1016/j.febslet.2012.03.065] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 03/30/2012] [Accepted: 03/30/2012] [Indexed: 10/28/2022]
19
Fang L, Kaake RM, Patel VR, Yang Y, Baldi P, Huang L. Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy. Mol Cell Proteomics 2012;11:138-47. [PMID: 22474085 DOI: 10.1074/mcp.m111.016352] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
20
Gilmore JM, Sardiu ME, Venkatesh S, Stutzman B, Peak A, Seidel CW, Workman JL, Florens L, Washburn MP. Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses. Mol Cell Proteomics 2011;11:M111.011544. [PMID: 22199229 DOI: 10.1074/mcp.m111.011544] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
21
Remmerie N, De Vijlder T, Valkenborg D, Laukens K, Smets K, Vreeken J, Mertens I, Carpentier SC, Panis B, De Jaeger G, Blust R, Prinsen E, Witters E. Unraveling tobacco BY-2 protein complexes with BN PAGE/LC-MS/MS and clustering methods. J Proteomics 2011;74:1201-17. [PMID: 21443973 DOI: 10.1016/j.jprot.2011.03.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/13/2011] [Accepted: 03/21/2011] [Indexed: 11/26/2022]
22
Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes. Mol Syst Biol 2011;7:503. [PMID: 21734642 PMCID: PMC3159981 DOI: 10.1038/msb.2011.40] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 05/22/2011] [Indexed: 12/12/2022]  Open
23
Sardiu ME, Washburn MP. Building protein-protein interaction networks with proteomics and informatics tools. J Biol Chem 2011;286:23645-51. [PMID: 21566121 DOI: 10.1074/jbc.r110.174052] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
24
Ning Z, Zhou H, Wang F, Abu-Farha M, Figeys D. Analytical Aspects of Proteomics: 2009–2010. Anal Chem 2011;83:4407-26. [DOI: 10.1021/ac200857t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
25
Ramisetty SR, Washburn MP. Unraveling the dynamics of protein interactions with quantitative mass spectrometry. Crit Rev Biochem Mol Biol 2011;46:216-28. [PMID: 21438726 DOI: 10.3109/10409238.2011.567244] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
26
Construction of protein interaction networks based on the label-free quantitative proteomics. Methods Mol Biol 2011;781:71-85. [PMID: 21877278 DOI: 10.1007/978-1-61779-276-2_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
27
Mosley AL, Sardiu ME, Pattenden SG, Workman JL, Florens L, Washburn MP. Highly reproducible label free quantitative proteomic analysis of RNA polymerase complexes. Mol Cell Proteomics 2010;10:M110.000687. [PMID: 21048197 DOI: 10.1074/mcp.m110.000687] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
28
Washburn MP. Driving biochemical discovery with quantitative proteomics. Trends Biochem Sci 2010;36:170-7. [PMID: 20880711 DOI: 10.1016/j.tibs.2010.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 08/31/2010] [Accepted: 09/01/2010] [Indexed: 11/26/2022]
29
Cooper B, Feng J, Garrett WM. Relative, label-free protein quantitation: spectral counting error statistics from nine replicate MudPIT samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010;21:1534-46. [PMID: 20541435 DOI: 10.1016/j.jasms.2010.05.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 04/30/2010] [Accepted: 05/03/2010] [Indexed: 05/03/2023]
30
Zhang Y, Wen Z, Washburn MP, Florens L. Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Anal Chem 2010;82:2272-81. [PMID: 20166708 DOI: 10.1021/ac9023999] [Citation(s) in RCA: 297] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
31
Kaake RM, Wang X, Huang L. Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. Mol Cell Proteomics 2010;9:1650-65. [PMID: 20445003 DOI: 10.1074/mcp.r110.000265] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
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