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For: Wang H, Mayhew D, Chen X, Johnston M, Mitra RD. Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins. Genome Res 2011;21:748-55. [PMID: 21471402 DOI: 10.1101/gr.114850.110] [Cited by in Crossref: 36] [Cited by in F6Publishing: 25] [Article Influence: 3.3] [Reference Citation Analysis]
Number Citing Articles
1 Zhou W, Dorrity MW, Bubb KL, Queitsch C, Fields S. Binding and Regulation of Transcription by Yeast Ste12 Variants To Drive Mating and Invasion Phenotypes. Genetics 2020;214:397-407. [PMID: 31810988 DOI: 10.1534/genetics.119.302929] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 0.7] [Reference Citation Analysis]
2 Policastro RA, Zentner GE. Enzymatic methods for genome-wide profiling of protein binding sites. Brief Funct Genomics 2018;17:138-45. [PMID: 29028882 DOI: 10.1093/bfgp/elx030] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
3 Mayhew D, Mitra RD. Transcription factor regulation and chromosome dynamics during pseudohyphal growth. Mol Biol Cell 2014;25:2669-76. [PMID: 25009286 DOI: 10.1091/mbc.E14-04-0871] [Cited by in Crossref: 9] [Cited by in F6Publishing: 6] [Article Influence: 1.1] [Reference Citation Analysis]
4 Cammack AJ, Moudgil A, Chen J, Vasek MJ, Shabsovich M, McCullough K, Yen A, Lagunas T, Maloney SE, He J, Chen X, Hooda M, Wilkinson MN, Miller TM, Mitra RD, Dougherty JD. A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues. Proc Natl Acad Sci U S A 2020;117:10003-14. [PMID: 32300008 DOI: 10.1073/pnas.1918241117] [Cited by in Crossref: 7] [Cited by in F6Publishing: 5] [Article Influence: 3.5] [Reference Citation Analysis]
5 Saleh MM, Tourigny JP, Zentner GE. Genome-Wide Profiling of Protein-DNA Interactions with Chromatin Endogenous Cleavage and High-Throughput Sequencing (ChEC-Seq ). Methods Mol Biol 2021;2351:289-303. [PMID: 34382196 DOI: 10.1007/978-1-0716-1597-3_16] [Reference Citation Analysis]
6 Grünberg S, Zentner GE. Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae. J Vis Exp 2017. [PMID: 28605389 DOI: 10.3791/55836] [Cited by in Crossref: 6] [Cited by in F6Publishing: 3] [Article Influence: 1.2] [Reference Citation Analysis]
7 Witchley JN, Basso P, Brimacombe CA, Abon NV, Noble SM. Recording of DNA-binding events reveals the importance of a repurposed Candida albicans regulatory network for gut commensalism. Cell Host Microbe 2021;29:1002-1013.e9. [PMID: 33915113 DOI: 10.1016/j.chom.2021.03.019] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 2.0] [Reference Citation Analysis]
8 Kang Y, Patel NR, Shively C, Recio PS, Chen X, Wranik BJ, Kim G, McIsaac RS, Mitra R, Brent MR. Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses. Genome Res 2020;30:459-71. [PMID: 32060051 DOI: 10.1101/gr.259655.119] [Cited by in Crossref: 11] [Cited by in F6Publishing: 6] [Article Influence: 5.5] [Reference Citation Analysis]
9 Chin BL, Ryan O, Lewitter F, Boone C, Fink GR. Genetic variation in Saccharomyces cerevisiae: circuit diversification in a signal transduction network. Genetics 2012;192:1523-32. [PMID: 23051644 DOI: 10.1534/genetics.112.145573] [Cited by in Crossref: 22] [Cited by in F6Publishing: 21] [Article Influence: 2.2] [Reference Citation Analysis]
10 Hew BE, Sato R, Mauro D, Stoytchev I, Owens JB. RNA-guided piggyBac transposition in human cells. Synth Biol (Oxf). 2019;4:ysz018. [PMID: 31355344 DOI: 10.1093/synbio/ysz018] [Cited by in Crossref: 15] [Cited by in F6Publishing: 14] [Article Influence: 5.0] [Reference Citation Analysis]
11 Ma CZ, Brent MR. Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data. Bioinformatics 2021;37:1234-45. [PMID: 33135076 DOI: 10.1093/bioinformatics/btaa947] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
12 Qi Z, Wilkinson MN, Chen X, Sankararaman S, Mayhew D, Mitra RD. An optimized, broadly applicable piggyBac transposon induction system. Nucleic Acids Res 2017;45:e55. [PMID: 28082389 DOI: 10.1093/nar/gkw1290] [Cited by in Crossref: 5] [Cited by in F6Publishing: 6] [Article Influence: 1.0] [Reference Citation Analysis]
13 Jain D, Baldi S, Zabel A, Straub T, Becker PB. Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments. Nucleic Acids Res 2015;43:6959-68. [PMID: 26117547 DOI: 10.1093/nar/gkv637] [Cited by in Crossref: 110] [Cited by in F6Publishing: 85] [Article Influence: 15.7] [Reference Citation Analysis]
14 Hughes TR, de Boer CG. Mapping yeast transcriptional networks. Genetics 2013;195:9-36. [PMID: 24018767 DOI: 10.1534/genetics.113.153262] [Cited by in Crossref: 64] [Cited by in F6Publishing: 49] [Article Influence: 8.0] [Reference Citation Analysis]
15 Wang H, Mayhew D, Chen X, Johnston M, Mitra RD. "Calling cards" for DNA-binding proteins in mammalian cells. Genetics 2012;190:941-9. [PMID: 22214611 DOI: 10.1534/genetics.111.137315] [Cited by in Crossref: 44] [Cited by in F6Publishing: 36] [Article Influence: 4.4] [Reference Citation Analysis]
16 Michael DG, Maier EJ, Brown H, Gish SR, Fiore C, Brown RH, Brent MR. Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast. Proc Natl Acad Sci U S A 2016;113:E7428-37. [PMID: 27810962 DOI: 10.1073/pnas.1603577113] [Cited by in Crossref: 23] [Cited by in F6Publishing: 18] [Article Influence: 3.8] [Reference Citation Analysis]
17 Moudgil A, Wilkinson MN, Chen X, He J, Cammack AJ, Vasek MJ, Lagunas T Jr, Qi Z, Lalli MA, Guo C, Morris SA, Dougherty JD, Mitra RD. Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells. Cell 2020;182:992-1008.e21. [PMID: 32710817 DOI: 10.1016/j.cell.2020.06.037] [Cited by in Crossref: 16] [Cited by in F6Publishing: 6] [Article Influence: 8.0] [Reference Citation Analysis]
18 Cuvier O, Fierz B. Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells. Nat Rev Genet 2017;18:457-72. [DOI: 10.1038/nrg.2017.28] [Cited by in Crossref: 44] [Cited by in F6Publishing: 33] [Article Influence: 8.8] [Reference Citation Analysis]
19 Styles EB, Founk KJ, Zamparo LA, Sing TL, Altintas D, Ribeyre C, Ribaud V, Rougemont J, Mayhew D, Costanzo M, Usaj M, Verster AJ, Koch EN, Novarina D, Graf M, Luke B, Muzi-Falconi M, Myers CL, Mitra RD, Shore D, Brown GW, Zhang Z, Boone C, Andrews BJ. Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci. Cell Syst 2016;3:264-277.e10. [PMID: 27617677 DOI: 10.1016/j.cels.2016.08.008] [Cited by in Crossref: 19] [Cited by in F6Publishing: 17] [Article Influence: 3.2] [Reference Citation Analysis]
20 Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin Z, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, Schwarzmuller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras A, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C. Global Gene Deletion Analysis Exploring Yeast Filamentous Growth. Science 2012;337:1353-6. [DOI: 10.1126/science.1224339] [Cited by in Crossref: 141] [Cited by in F6Publishing: 126] [Article Influence: 14.1] [Reference Citation Analysis]
21 Roy S, Thompson D. Evolution of regulatory networks in Candida glabrata: learning to live with the human host. FEMS Yeast Res 2015;15:fov087. [PMID: 26449820 DOI: 10.1093/femsyr/fov087] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 0.3] [Reference Citation Analysis]
22 Kfoury N, Qi Z, Prager BC, Wilkinson MN, Broestl L, Berrett KC, Moudgil A, Sankararaman S, Chen X, Gertz J, Rich JN, Mitra RD, Rubin JB. Brd4-bound enhancers drive cell-intrinsic sex differences in glioblastoma. Proc Natl Acad Sci U S A 2021;118:e2017148118. [PMID: 33850013 DOI: 10.1073/pnas.2017148118] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
23 Liu J, Shively CA, Mitra RD. Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays. Nucleic Acids Res 2020;48:e50. [PMID: 32133534 DOI: 10.1093/nar/gkaa141] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
24 Baller JA, Gao J, Voytas DF. Access to DNA establishes a secondary target site bias for the yeast retrotransposon Ty5. Proc Natl Acad Sci U S A 2011;108:20351-6. [PMID: 21788500 DOI: 10.1073/pnas.1103665108] [Cited by in Crossref: 19] [Cited by in F6Publishing: 19] [Article Influence: 1.7] [Reference Citation Analysis]
25 Shively CA, Liu J, Chen X, Loell K, Mitra RD. Homotypic cooperativity and collective binding are determinants of bHLH specificity and function. Proc Natl Acad Sci U S A 2019;116:16143-52. [PMID: 31341088 DOI: 10.1073/pnas.1818015116] [Cited by in Crossref: 13] [Cited by in F6Publishing: 9] [Article Influence: 4.3] [Reference Citation Analysis]
26 Rossbach D, Bryan DS, Hesselberth JR, Sclafani R. Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae. G3 (Bethesda) 2017;7:3757-74. [PMID: 28924058 DOI: 10.1534/g3.117.300223] [Cited by in Crossref: 5] [Article Influence: 1.0] [Reference Citation Analysis]
27 Siggers T, Reddy J, Barron B, Bulyk ML. Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding. Mol Cell 2014;55:640-8. [PMID: 25042805 DOI: 10.1016/j.molcel.2014.06.019] [Cited by in Crossref: 29] [Cited by in F6Publishing: 23] [Article Influence: 3.6] [Reference Citation Analysis]