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For: Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A systems approach to mapping DNA damage response pathways. Science 2006;312:1054-9. [PMID: 16709784 PMCID: PMC2811083 DOI: 10.1126/science.1122088] [Citation(s) in RCA: 203] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Number Cited by Other Article(s)
151
Feala JD, Omens JH, Paternostro G, McCulloch AD. Discovering Regulators of the Drosophila Cardiac Hypoxia Response Using Automated Phenotyping Technology. Ann N Y Acad Sci 2008;1123:169-77. [DOI: 10.1196/annals.1420.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
152
Yeast adaptation to mancozeb involves the up-regulation of FLR1 under the coordinate control of Yap1, Rpn4, Pdr3, and Yrr1. Biochem Biophys Res Commun 2008;367:249-55. [DOI: 10.1016/j.bbrc.2007.12.056] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 12/07/2007] [Indexed: 11/19/2022]
153
Tan K, Feizi H, Luo C, Fan SH, Ravasi T, Ideker TG. A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. Proc Natl Acad Sci U S A 2008;105:2934-9. [PMID: 18287073 PMCID: PMC2268563 DOI: 10.1073/pnas.0708670105] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Indexed: 11/18/2022]  Open
154
Pache RA, Zanzoni A, Naval J, Mas JM, Aloy P. Towards a molecular characterisation of pathological pathways. FEBS Lett 2008;582:1259-65. [PMID: 18282477 DOI: 10.1016/j.febslet.2008.02.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Accepted: 02/08/2008] [Indexed: 01/07/2023]
155
Amundson SA. Functional genomics in radiation biology: a gateway to cellular systems-level studies. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2008;47:25-31. [PMID: 17973116 DOI: 10.1007/s00411-007-0140-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 10/17/2007] [Indexed: 05/23/2023]
156
Hwang W, Cho YR, Zhang A, Ramanathan M. CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions. BMC Bioinformatics 2008;9:64. [PMID: 18230159 PMCID: PMC2253513 DOI: 10.1186/1471-2105-9-64] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 01/29/2008] [Indexed: 11/10/2022]  Open
157
Borecka-Melkusova S, Kozovska Z, Hikkel I, Dzugasova V, Subik J. RPD3 and ROM2 are required for multidrug resistance in Saccharomyces cerevisiae. FEMS Yeast Res 2008;8:414-24. [DOI: 10.1111/j.1567-1364.2007.00352.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
158
Gracey AY. Interpreting physiological responses to environmental change through gene expression profiling. ACTA ACUST UNITED AC 2008;210:1584-92. [PMID: 17449823 DOI: 10.1242/jeb.004333] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
159
Liebler DC. Protein damage by reactive electrophiles: targets and consequences. Chem Res Toxicol 2008;21:117-28. [PMID: 18052106 PMCID: PMC2533766 DOI: 10.1021/tx700235t] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
160
Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray. Methods Mol Biol 2008;439:131-45. [PMID: 18370100 DOI: 10.1007/978-1-59745-188-8_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
161
Song EJ, Babar SME, Oh E, Hasan MN, Hong HM, Yoo YS. CE at the omics level: Towards systems biology – An update. Electrophoresis 2008;29:129-42. [DOI: 10.1002/elps.200700467] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
162
Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, Pilpel Y. Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol 2008. [PMID: 18854817 DOI: 10.1037/msb.2008.59] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]  Open
163
Begley U, Dyavaiah M, Patil A, Rooney JP, DiRenzo D, Young CM, Conklin DS, Zitomer RS, Begley TJ. Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol Cell 2007;28:860-70. [PMID: 18082610 PMCID: PMC2211415 DOI: 10.1016/j.molcel.2007.09.021] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Revised: 07/26/2007] [Accepted: 09/26/2007] [Indexed: 10/22/2022]
164
Monteiro PT, Mendes ND, Teixeira MC, d'Orey S, Tenreiro S, Mira NP, Pais H, Francisco AP, Carvalho AM, Lourenço AB, Sá-Correia I, Oliveira AL, Freitas AT. YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res 2007;36:D132-6. [PMID: 18032429 PMCID: PMC2238916 DOI: 10.1093/nar/gkm976] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
165
Burgis NE, Samson LD. The protein degradation response of Saccharomyces cerevisiae to classical DNA-damaging agents. Chem Res Toxicol 2007;20:1843-53. [PMID: 18020423 DOI: 10.1021/tx700126e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
166
Pierce SE, Davis RW, Nislow C, Giaever G. Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protoc 2007;2:2958-74. [DOI: 10.1038/nprot.2007.427] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
167
Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L, Leslie C. Learning regulatory programs that accurately predict differential expression with MEDUSA. Ann N Y Acad Sci 2007;1115:178-202. [PMID: 17934055 DOI: 10.1196/annals.1407.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
168
Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet 2007;8:699-710. [PMID: 17703239 PMCID: PMC2811081 DOI: 10.1038/nrg2144] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
169
Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. ACTA ACUST UNITED AC 2007;23:i359-66. [PMID: 17646318 DOI: 10.1093/bioinformatics/btm170] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
170
Cho BK, Charusanti P, Herrgård MJ, Palsson BO. Microbial regulatory and metabolic networks. Curr Opin Biotechnol 2007;18:360-4. [PMID: 17719767 DOI: 10.1016/j.copbio.2007.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 07/12/2007] [Indexed: 11/18/2022]
171
Dardalhon M, Lin W, Nicolas A, Averbeck D. Specific transcriptional responses induced by 8-methoxypsoralen and UVA in yeast. FEMS Yeast Res 2007;7:866-78. [PMID: 17608707 PMCID: PMC2040189 DOI: 10.1111/j.1567-1364.2007.00270.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]  Open
172
Qi Y, Ge H. Modularity and dynamics of cellular networks. PLoS Comput Biol 2007;2:e174. [PMID: 17196032 PMCID: PMC1761653 DOI: 10.1371/journal.pcbi.0020174] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
173
Carter GW, Prinz S, Neou C, Shelby JP, Marzolf B, Thorsson V, Galitski T. Prediction of phenotype and gene expression for combinations of mutations. Mol Syst Biol 2007;3:96. [PMID: 17389876 PMCID: PMC1847951 DOI: 10.1038/msb4100137] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 02/09/2007] [Indexed: 02/06/2023]  Open
174
King AA, Shaughnessy DT, Mure K, Leszczynska J, Ward WO, Umbach DM, Xu Z, Ducharme D, Taylor JA, DeMarini DM, Klein CB. Antimutagenicity of cinnamaldehyde and vanillin in human cells: Global gene expression and possible role of DNA damage and repair. Mutat Res 2007;616:60-9. [PMID: 17178418 PMCID: PMC1955325 DOI: 10.1016/j.mrfmmm.2006.11.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
175
Steinfeld I, Shamir R, Kupiec M. A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription. Nat Genet 2007;39:303-9. [PMID: 17325681 DOI: 10.1038/ng1965] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
176
Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D. How to infer gene networks from expression profiles. Mol Syst Biol 2007;3:78. [PMID: 17299415 PMCID: PMC1828749 DOI: 10.1038/msb4100120] [Citation(s) in RCA: 351] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Accepted: 12/18/2006] [Indexed: 02/01/2023]  Open
177
van Vugt JJFA, Ranes M, Campsteijn C, Logie C. The ins and outs of ATP-dependent chromatin remodeling in budding yeast: biophysical and proteomic perspectives. ACTA ACUST UNITED AC 2007;1769:153-71. [PMID: 17395283 DOI: 10.1016/j.bbaexp.2007.01.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 01/22/2007] [Accepted: 01/29/2007] [Indexed: 11/30/2022]
178
Maerkl SJ, Quake SR. A systems approach to measuring the binding energy landscapes of transcription factors. Science 2007;315:233-7. [PMID: 17218526 DOI: 10.1126/science.1131007] [Citation(s) in RCA: 408] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
179
Cagney G, Alvaro D, Reid RJD, Thorpe PH, Rothstein R, Krogan NJ. Functional genomics of the yeast DNA-damage response. Genome Biol 2007;7:233. [PMID: 16959047 PMCID: PMC1794544 DOI: 10.1186/gb-2006-7-9-233] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
180
Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z. Reconstructing dynamic regulatory maps. Mol Syst Biol 2007;3:74. [PMID: 17224918 PMCID: PMC1800355 DOI: 10.1038/msb4100115] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Accepted: 11/15/2006] [Indexed: 02/07/2023]  Open
181
Tegnér J, Nilsson R, Bajic VB, Björkegren J, Ravasi. T. Systems biology of innate immunity. Cell Immunol 2006;244:105-9. [PMID: 17433274 PMCID: PMC1947944 DOI: 10.1016/j.cellimm.2007.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 01/31/2007] [Indexed: 02/07/2023]
182
Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to methyl methanesulfonate and ionizing radiation. BMC Genomics 2006;7:305. [PMID: 17140446 PMCID: PMC1698923 DOI: 10.1186/1471-2164-7-305] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2006] [Accepted: 12/01/2006] [Indexed: 11/10/2022]  Open
183
Sauer U. Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol 2006;2:62. [PMID: 17102807 PMCID: PMC1682028 DOI: 10.1038/msb4100109] [Citation(s) in RCA: 490] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 10/06/2006] [Indexed: 01/08/2023]  Open
184
Hart CE, Mjolsness E, Wold BJ. Connectivity in the yeast cell cycle transcription network: inferences from neural networks. PLoS Comput Biol 2006;2:e169. [PMID: 17194216 PMCID: PMC1761652 DOI: 10.1371/journal.pcbi.0020169] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Accepted: 10/30/2006] [Indexed: 02/02/2023]  Open
185
Walhout AJM. Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res 2006;16:1445-54. [PMID: 17053092 DOI: 10.1101/gr.5321506] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
186
Farkas IJ, Beg QK, Oltvai ZN. Exploring transcriptional regulatory networks in the worm. Cell 2006;125:1032-4. [PMID: 16777593 DOI: 10.1016/j.cell.2006.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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