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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)
51
Tennen RI, Haye JE, Wijayatilake HD, Arlow T, Ponzio D, Gammie AE. Cell-cycle and DNA damage regulation of the DNA mismatch repair protein Msh2 occurs at the transcriptional and post-transcriptional level. DNA Repair (Amst) 2013;12:97-109. [PMID: 23261051 PMCID: PMC3749301 DOI: 10.1016/j.dnarep.2012.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 10/03/2012] [Accepted: 11/06/2012] [Indexed: 12/13/2022]
52
Bean GJ, Ideker T. Differential analysis of high-throughput quantitative genetic interaction data. Genome Biol 2012;13:R123. [PMID: 23268787 PMCID: PMC4056373 DOI: 10.1186/gb-2012-13-12-r123] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/15/2012] [Accepted: 12/26/2012] [Indexed: 11/10/2022]  Open
53
Michoel T, Nachtergaele B. Alignment and integration of complex networks by hypergraph-based spectral clustering. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012;86:056111. [PMID: 23214847 DOI: 10.1103/physreve.86.056111] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Indexed: 06/01/2023]
54
Regulatory network structure as a dominant determinant of transcription factor evolutionary rate. PLoS Comput Biol 2012;8:e1002734. [PMID: 23093926 PMCID: PMC3475661 DOI: 10.1371/journal.pcbi.1002734] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 08/21/2012] [Indexed: 01/10/2023]  Open
55
Yang TH, Wu WS. Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. BMC SYSTEMS BIOLOGY 2012;6:102. [PMID: 22898448 PMCID: PMC3465233 DOI: 10.1186/1752-0509-6-102] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 08/02/2012] [Indexed: 12/17/2022]
56
Hasdemir D, Smits GJ, Westerhuis JA, Smilde AK. Topology of transcriptional regulatory networks: testing and improving. PLoS One 2012;7:e40082. [PMID: 22844399 PMCID: PMC3402518 DOI: 10.1371/journal.pone.0040082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/05/2012] [Indexed: 12/03/2022]  Open
57
Smith KT, Workman JL. Chromatin proteins: key responders to stress. PLoS Biol 2012;10:e1001371. [PMID: 22859908 PMCID: PMC3409139 DOI: 10.1371/journal.pbio.1001371] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
58
Wen Z, Liu ZP, Yan Y, Piao G, Liu Z, Wu J, Chen L. Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle. PLoS One 2012;7:e41854. [PMID: 22848637 PMCID: PMC3405030 DOI: 10.1371/journal.pone.0041854] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]  Open
59
Shayeghi N, Ng T, Coolen A. Direct Response Analysis in cellular signalling networks. J Theor Biol 2012;304:219-25. [DOI: 10.1016/j.jtbi.2012.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 03/17/2012] [Accepted: 04/02/2012] [Indexed: 11/25/2022]
60
Wittenburg LA, Ptitsyn AA, Thamm DH. A systems biology approach to identify molecular pathways altered by HDAC inhibition in osteosarcoma. J Cell Biochem 2012;113:773-83. [PMID: 21976144 DOI: 10.1002/jcb.23403] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
61
Systems genetics: challenges and developing strategies. Biologia (Bratisl) 2012. [DOI: 10.2478/s11756-012-0026-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
62
Akatsuka S, Toyokuni S. Genome-wide assessment of oxidatively generated DNA damage. Free Radic Res 2012;46:523-30. [PMID: 22034856 DOI: 10.3109/10715762.2011.633212] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
63
Ideker T, Krogan NJ. Differential network biology. Mol Syst Biol 2012;8:565. [PMID: 22252388 PMCID: PMC3296360 DOI: 10.1038/msb.2011.99] [Citation(s) in RCA: 539] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 12/06/2011] [Indexed: 01/22/2023]  Open
64
Gordân R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol 2011;12:R125. [PMID: 22189060 PMCID: PMC3334620 DOI: 10.1186/gb-2011-12-12-r125] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/09/2011] [Accepted: 12/21/2011] [Indexed: 11/24/2022]  Open
65
de Boer CG, Hughes TR. YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res 2011;40:D169-79. [PMID: 22102575 PMCID: PMC3245003 DOI: 10.1093/nar/gkr993] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
66
Amit I, Regev A, Hacohen N. Strategies to discover regulatory circuits of the mammalian immune system. Nat Rev Immunol 2011;11:873-80. [PMID: 22094988 PMCID: PMC3747038 DOI: 10.1038/nri3109] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
67
Construction of regulatory networks using expression time-series data of a genotyped population. Proc Natl Acad Sci U S A 2011;108:19436-41. [PMID: 22084118 DOI: 10.1073/pnas.1116442108] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
68
Transcriptional regulation and the diversification of metabolism in wine yeast strains. Genetics 2011;190:251-61. [PMID: 22042577 DOI: 10.1534/genetics.111.132720] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
69
Systems analysis of ATF3 in stress response and cancer reveals opposing effects on pro-apoptotic genes in p53 pathway. PLoS One 2011;6:e26848. [PMID: 22046379 PMCID: PMC3202577 DOI: 10.1371/journal.pone.0026848] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 10/04/2011] [Indexed: 12/31/2022]  Open
70
Svensson JP, Pesudo LQ, Fry RC, Adeleye YA, Carmichael P, Samson LD. Genomic phenotyping of the essential and non-essential yeast genome detects novel pathways for alkylation resistance. BMC SYSTEMS BIOLOGY 2011;5:157. [PMID: 21978764 PMCID: PMC3213080 DOI: 10.1186/1752-0509-5-157] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 10/06/2011] [Indexed: 11/10/2022]
71
Cho BK, Palsson B, Zengler K. Deciphering the regulatory codes in bacterial genomes. Biotechnol J 2011;6:1052-63. [PMID: 21845736 DOI: 10.1002/biot.201000349] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/30/2011] [Accepted: 07/25/2011] [Indexed: 12/24/2022]
72
Zhang B, Shi Z, Duncan DT, Prodduturi N, Marnett LJ, Liebler DC. Relating protein adduction to gene expression changes: a systems approach. MOLECULAR BIOSYSTEMS 2011;7:2118-27. [PMID: 21594272 PMCID: PMC3659419 DOI: 10.1039/c1mb05014a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
73
Szczurek E, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J, Vingron M. Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. BMC Bioinformatics 2011;12:249. [PMID: 21693013 PMCID: PMC3236061 DOI: 10.1186/1471-2105-12-249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 06/21/2011] [Indexed: 12/17/2022]  Open
74
Bai L, Ondracka A, Cross FR. Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter. Mol Cell 2011;42:465-76. [PMID: 21596311 PMCID: PMC3119483 DOI: 10.1016/j.molcel.2011.03.028] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 03/12/2011] [Accepted: 03/30/2011] [Indexed: 01/29/2023]
75
Tsaponina O, Barsoum E, Åström SU, Chabes A. Ixr1 is required for the expression of the ribonucleotide reductase Rnr1 and maintenance of dNTP pools. PLoS Genet 2011;7:e1002061. [PMID: 21573136 PMCID: PMC3088718 DOI: 10.1371/journal.pgen.1002061] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 03/14/2011] [Indexed: 12/29/2022]  Open
76
Elad T, Lee JH, Belkin S, Gu MB. Microbial whole-cell arrays. Microb Biotechnol 2011;1:137-48. [PMID: 21261831 PMCID: PMC3864447 DOI: 10.1111/j.1751-7915.2007.00021.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
77
Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Mol Syst Biol 2011;6:432. [PMID: 21119627 PMCID: PMC3010106 DOI: 10.1038/msb.2010.91] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 10/02/2010] [Indexed: 01/17/2023]  Open
78
Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysates. Appl Microbiol Biotechnol 2011;90:809-25. [DOI: 10.1007/s00253-011-3167-9] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 12/16/2010] [Accepted: 02/09/2011] [Indexed: 10/18/2022]
79
Tian C, Li J, Glass NL. Exploring the bZIP transcription factor regulatory network in Neurospora crassa. MICROBIOLOGY (READING, ENGLAND) 2011;157:747-759. [PMID: 21081763 PMCID: PMC3081083 DOI: 10.1099/mic.0.045468-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/08/2010] [Accepted: 11/14/2010] [Indexed: 11/18/2022]
80
Dyavaiah M, Rooney JP, Chittur SV, Lin Q, Begley TJ. Autophagy-dependent regulation of the DNA damage response protein ribonucleotide reductase 1. Mol Cancer Res 2011;9:462-75. [PMID: 21343333 DOI: 10.1158/1541-7786.mcr-10-0473] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
81
Rajan S, Djambazian H, Dang HCP, Sladek R, Hudson TJ. The living microarray: a high-throughput platform for measuring transcription dynamics in single cells. BMC Genomics 2011;12:115. [PMID: 21324195 PMCID: PMC3050818 DOI: 10.1186/1471-2164-12-115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 02/16/2011] [Indexed: 12/15/2022]  Open
82
Ament SA, Wang Y, Robinson GE. Nutritional regulation of division of labor in honey bees: toward a systems biology perspective. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011;2:566-576. [PMID: 20836048 DOI: 10.1002/wsbm.73] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
83
Liu Q, Tan Y, Huang T, Ding G, Tu Z, Liu L, Li Y, Dai H, Xie L. TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. BMC Bioinformatics 2010;11 Suppl 11:S5. [PMID: 21172055 PMCID: PMC3024863 DOI: 10.1186/1471-2105-11-s11-s5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
84
Ma M, Liu ZL. Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae. BMC Genomics 2010;11:660. [PMID: 21106074 PMCID: PMC3091778 DOI: 10.1186/1471-2164-11-660] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 11/24/2010] [Indexed: 11/16/2022]  Open
85
Functional genomics complements quantitative genetics in identifying disease-gene associations. PLoS Comput Biol 2010;6:e1000991. [PMID: 21085640 PMCID: PMC2978695 DOI: 10.1371/journal.pcbi.1000991] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 10/07/2010] [Indexed: 11/25/2022]  Open
86
Sequential recruitment of SAGA and TFIID in a genomic response to DNA damage in Saccharomyces cerevisiae. Mol Cell Biol 2010;31:190-202. [PMID: 20956559 DOI: 10.1128/mcb.00317-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
87
Wang Y, Franzosa EA, Zhang XS, Xia Y. Protein evolution in yeast transcription factor subnetworks. Nucleic Acids Res 2010;38:5959-69. [PMID: 20466810 PMCID: PMC2952844 DOI: 10.1093/nar/gkq353] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 04/21/2010] [Accepted: 04/22/2010] [Indexed: 01/08/2023]  Open
88
Lelandais G, Devaux F. Comparative Functional Genomics of Stress Responses in Yeasts. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010;14:501-15. [DOI: 10.1089/omi.2010.0029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
89
JIANG LH, LI YX, LIU Q. Reconstruction of Gene Regulatory Networks by Integrating ChIP-chip, Knock out and Expression Data*. PROG BIOCHEM BIOPHYS 2010. [DOI: 10.3724/sp.j.1206.2010.00184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
90
Cavalieri D. Evolution of transcriptional regulatory networks in yeast populations. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010;2:324-335. [PMID: 20836032 DOI: 10.1002/wsbm.68] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
91
Luo F, Liu J, Li J. Discovering conditional co-regulated protein complexes by integrating diverse data sources. BMC SYSTEMS BIOLOGY 2010;4 Suppl 2:S4. [PMID: 20840731 PMCID: PMC2982691 DOI: 10.1186/1752-0509-4-s2-s4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
92
Batenchuk C, Tepliakova L, Kaern M. Identification of response-modulated genetic interactions by sensitivity-based epistatic analysis. BMC Genomics 2010;11:493. [PMID: 20831804 PMCID: PMC2996989 DOI: 10.1186/1471-2164-11-493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 09/10/2010] [Indexed: 01/14/2023]  Open
93
Akatsuka S, Toyokuni S. Genome-scale approaches to investigate oxidative DNA damage. J Clin Biochem Nutr 2010;47:91-7. [PMID: 20838563 PMCID: PMC2935159 DOI: 10.3164/jcbn.10-38r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 04/10/2010] [Indexed: 12/22/2022]  Open
94
Inference of the Molecular Mechanism of Action from Genetic Interaction and Gene Expression Data. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010;14:357-67. [DOI: 10.1089/omi.2009.0144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
95
Smith AM, Ammar R, Nislow C, Giaever G. A survey of yeast genomic assays for drug and target discovery. Pharmacol Ther 2010;127:156-64. [PMID: 20546776 PMCID: PMC2923554 DOI: 10.1016/j.pharmthera.2010.04.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 04/28/2010] [Indexed: 01/01/2023]
96
Zhang J, Olsson L, Nielsen J. The β-subunits of the Snf1 kinase in Saccharomyces cerevisiae, Gal83 and Sip2, but not Sip1, are redundant in glucose derepression and regulation of sterol biosynthesis. Mol Microbiol 2010;77:371-83. [DOI: 10.1111/j.1365-2958.2010.07209.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
97
Carter GW, Rush CG, Uygun F, Sakhanenko NA, Galas DJ, Galitski T. A systems-biology approach to modular genetic complexity. CHAOS (WOODBURY, N.Y.) 2010;20:026102. [PMID: 20590331 PMCID: PMC2909309 DOI: 10.1063/1.3455183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 05/26/2010] [Indexed: 05/29/2023]
98
Ren X, Zhou X, Wu LY, Zhang XS. An information-flow-based model with dissipation, saturation and direction for active pathway inference. BMC SYSTEMS BIOLOGY 2010;4:72. [PMID: 20504374 PMCID: PMC2890502 DOI: 10.1186/1752-0509-4-72] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 05/27/2010] [Indexed: 11/25/2022]
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Rodrigues-Pousada C, Menezes RA, Pimentel C. The Yap family and its role in stress response. Yeast 2010;27:245-58. [DOI: 10.1002/yea.1752] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
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Joshi A, Van Parys T, Van de Peer Y, Michoel T. Characterizing regulatory path motifs in integrated networks using perturbational data. Genome Biol 2010;11:R32. [PMID: 20230615 PMCID: PMC2864572 DOI: 10.1186/gb-2010-11-3-r32] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 10/01/2009] [Accepted: 03/11/2010] [Indexed: 01/12/2023]  Open
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