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Fan","year":"2016","journal-title":"Nature methods"},{"issue":"10","key":"ref55","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1038\/ncb1174","article-title":"Hog1 mediates cell-cycle arrest in G1 phase by the dual targeting of Sic1","volume":"6","author":"X Escote","year":"2004","journal-title":"Nature cell biology"},{"issue":"9","key":"ref56","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1128\/MCB.01279-14","article-title":"Hog1 targets Whi5 and Msa1 transcription factors to downregulate cyclin expression upon stress","volume":"35","author":"A Gonzalez-Novo","year":"2015","journal-title":"Molecular and cellular biology"},{"issue":"10","key":"ref57","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1091\/mbc.12.10.2987","article-title":"Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p","volume":"12","author":"AP Gasch","year":"2001","journal-title":"Molecular biology of the 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Genes & development"},{"issue":"1\u20132","key":"ref71","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1093\/emboj\/21.1.135","article-title":"Acute glucose starvation activates the nuclear localization signal of a stress-specific yeast transcription factor","volume":"21","author":"W Gorner","year":"2002","journal-title":"The EMBO journal"},{"issue":"18","key":"ref72","doi-asserted-by":"crossref","first-page":"2189","DOI":"10.1016\/j.cub.2014.07.076","article-title":"Pulsatile dynamics in the yeast proteome","volume":"24","author":"CK Dalal","year":"2014","journal-title":"Current biology: CB"},{"issue":"5","key":"ref73","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1091\/mbc.E10-04-0352","article-title":"Proteasomal degradation of Sfp1 contributes to the repression of ribosome biogenesis during starvation and is mediated by the proteasome activator Blm10","volume":"22","author":"AD Lopez","year":"2011","journal-title":"Molecular biology of the 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translocation","volume":"339","author":"N Hao","year":"2013","journal-title":"Science (New York, NY"},{"issue":"7","key":"ref84","doi-asserted-by":"crossref","first-page":"R269","DOI":"10.1016\/j.cub.2016.02.058","article-title":"Encoding four gene expression programs in the activation dynamics of a single transcription factor","volume":"26","author":"Hansen AS","year":"2016","journal-title":"Current biology: CB"},{"issue":"12","key":"ref85","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1016\/j.cub.2007.05.032","article-title":"Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: evidence for periodic PKA activation","volume":"17","author":"C Garmendia-Torres","year":"2007","journal-title":"Current biology: CB"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1038\/msb.2013.56","article-title":"Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression","volume":"9","author":"Hansen AS","year":"2013","journal-title":"Molecular systems biology"},{"issue":"8","key":"ref87","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1016\/j.celrep.2015.07.035","article-title":"cis Determinants of Promoter Threshold and Activation Timescale","volume":"12","author":"Hansen AS","year":"2015","journal-title":"Cell reports"},{"issue":"7192","key":"ref88","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/nature06867","article-title":"Chromatin decouples promoter threshold from dynamic range","volume":"453","author":"FH Lam","year":"2008","journal-title":"Nature"},{"issue":"7","key":"ref89","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1016\/j.cell.2004.11.047","article-title":"TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1","volume":"119","author":"DE Martin","year":"2004","journal-title":"Cell"},{"issue":"3","key":"ref90","doi-asserted-by":"crossref","first-page":"1920","DOI":"10.1128\/MCB.14.3.1920","article-title":"Protein kinase A mediates growth-regulated expression of yeast ribosomal protein genes by modulating RAP1 transcriptional activity","volume":"14","author":"C Klein","year":"1994","journal-title":"Molecular and cellular biology"},{"issue":"13","key":"ref91","doi-asserted-by":"crossref","first-page":"3556","DOI":"10.1093\/emboj\/17.13.3556","article-title":"Yeast PKA represses Msn2p\/Msn4p-dependent gene expression to regulate growth, stress response and glycogen accumulation","volume":"17","author":"A Smith","year":"1998","journal-title":"The EMBO journal"},{"issue":"6762","key":"ref92","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1038\/45287","article-title":"The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors","volume":"402","author":"T Beck","year":"1999","journal-title":"Nature"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"759","DOI":"10.15252\/msb.20145120","article-title":"Pathway connectivity and signaling coordination in the yeast stress-activated signaling network","volume":"10","author":"D Chasman","year":"2014","journal-title":"Molecular systems biology"},{"issue":"4","key":"ref94","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1007\/s00294-015-0491-0","article-title":"Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling","volume":"61","author":"YH Ho","year":"2015","journal-title":"Current genetics"},{"issue":"4","key":"ref95","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/j.molcel.2016.04.026","article-title":"Cyclin-Dependent Kinase Co-Ordinates Carbohydrate Metabolism and Cell Cycle in S. cerevisiae","volume":"62","author":"G Zhao","year":"2016","journal-title":"Molecular cell"},{"issue":"4","key":"ref96","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1016\/j.molcel.2016.02.017","article-title":"The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression","volume":"62","author":"JC Ewald","year":"2016","journal-title":"Molecular cell"},{"issue":"26","key":"ref97","doi-asserted-by":"crossref","first-page":"10450","DOI":"10.1073\/pnas.1200067109","article-title":"Cdc28 kinase activity regulates the basal transcription machinery at a subset of genes","volume":"109","author":"P Chymkowitch","year":"2012","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"44","key":"ref98","doi-asserted-by":"crossref","first-page":"31689","DOI":"10.1074\/jbc.M113.500488","article-title":"Balanced production of ribosome components is required for proper G1\/S transition in Saccharomyces cerevisiae","volume":"288","author":"F Gomez-Herreros","year":"2013","journal-title":"The Journal of biological chemistry"},{"issue":"3","key":"ref99","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1091\/mbc.E06-06-0512","article-title":"Ribosome biogenesis is sensed at the Start cell cycle checkpoint","volume":"18","author":"KA Bernstein","year":"2007","journal-title":"Molecular biology of the cell"},{"issue":"24","key":"ref100","doi-asserted-by":"crossref","first-page":"3442","DOI":"10.1080\/15384101.2016.1248006","article-title":"Persistence to anti-cancer treatments in the stationary to proliferating transition","volume":"15","author":"S Pearl Mizrahi","year":"2016","journal-title":"Cell Cycle"},{"issue":"8","key":"ref101","doi-asserted-by":"crossref","first-page":"a000935","DOI":"10.1101\/cshperspect.a000935","article-title":"Transcriptional regulation by p53","volume":"2","author":"R Beckerman","year":"2010","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"11","key":"ref102","doi-asserted-by":"crossref","first-page":"3112","DOI":"10.1093\/emboj\/17.11.3112","article-title":"p53 is a general repressor of RNA polymerase III transcription","volume":"17","author":"CA Cairns","year":"1998","journal-title":"The EMBO journal"},{"issue":"4","key":"ref103","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1038\/sj.onc.1202402","article-title":"p53 represses ribosomal gene transcription","volume":"18","author":"A Budde","year":"1999","journal-title":"Oncogene"},{"issue":"8","key":"ref104","doi-asserted-by":"crossref","first-page":"e1003726","DOI":"10.1371\/journal.pgen.1003726","article-title":"Characterization of the p53 cistrome\u2014DNA binding cooperativity dissects p53's tumor suppressor functions","volume":"9","author":"K Schlereth","year":"2013","journal-title":"PLoS Genet"},{"issue":"6087","key":"ref105","doi-asserted-by":"crossref","first-page":"1440","DOI":"10.1126\/science.1218351","article-title":"p53 dynamics control cell fate","volume":"336","author":"JE Purvis","year":"2012","journal-title":"Science (New York, NY"},{"issue":"6278","key":"ref106","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1126\/science.aac5610","article-title":"Schedule-dependent interaction between anticancer treatments","volume":"351","author":"SH Chen","year":"2016","journal-title":"Science (New York, NY"},{"issue":"1","key":"ref107","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.cell.2010.05.031","article-title":"Basal dynamics of p53 reveal transcriptionally attenuated pulses in cycling cells","volume":"142","author":"A Loewer","year":"2010","journal-title":"Cell"},{"issue":"6959","key":"ref108","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/nature02046","article-title":"Global analysis of protein expression in yeast","volume":"425","author":"S Ghaemmaghami","year":"2003","journal-title":"Nature"},{"issue":"5","key":"ref109","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"H Li","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/s13059-016-0888-1","article-title":"Classification of low quality cells from single-cell RNA-seq data","volume":"17","author":"T Ilicic","year":"2016","journal-title":"Genome biology"},{"issue":"6","key":"ref111","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1038\/nmeth.4263","article-title":"SCnorm: robust normalization of single-cell RNA-seq data","volume":"14","author":"R Bacher","year":"2017","journal-title":"Nature methods"},{"issue":"1","key":"ref112","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controllign the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"Journal of the Royal Statistical Society"},{"issue":"25","key":"ref113","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","article-title":"Cluster analysis and display of genome-wide expression patterns","volume":"95","author":"MB Eisen","year":"1998","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"9","key":"ref114","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1128\/MCB.06170-11","article-title":"Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators","volume":"32","author":"DJ Huebert","year":"2012","journal-title":"Molecular and cellular biology"},{"issue":"7004","key":"ref115","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nature02800","article-title":"Transcriptional regulatory code of a eukaryotic genome","volume":"431","author":"CT Harbison","year":"2004","journal-title":"Nature"},{"key":"ref116","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-7-113","article-title":"An improved map of conserved regulatory sites for Saccharomyces cerevisiae","volume":"7","author":"K MacIsaac","year":"2006","journal-title":"BMC bioinformatics"},{"issue":"4","key":"ref117","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1016\/j.molcel.2011.01.015","article-title":"A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces","volume":"41","author":"BJ Venters","year":"2011","journal-title":"Molecular cell"},{"key":"ref118","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkq964","article-title":"YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface","volume":"39","author":"D Abdulrehman","year":"2011","journal-title":"Nucleic acids research"},{"issue":"76","key":"ref119","first-page":"e50382","article-title":"Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae","author":"RS McIsaac","year":"2013","journal-title":"Journal of visualized experiments: JoVE"},{"issue":"10","key":"ref120","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1038\/nmeth.1253","article-title":"Imaging individual mRNA molecules using multiple singly labeled probes","volume":"5","author":"A Raj","year":"2008","journal-title":"Nature methods"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/978-1-62703-311-4_8","article-title":"CellProfiler and KNIME: open source tools for high content screening","volume":"986","author":"M Stoter","year":"2013","journal-title":"Methods Mol Biol"},{"issue":"7","key":"ref122","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"J Schindelin","year":"2012","journal-title":"Nature methods"},{"key":"ref123","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1006\/jcis.1996.0217","article-title":"Methods of Digital Video Microscopy for Colloidal Studies","volume":"179","author":"JC Crocker","year":"1996","journal-title":"J Colloid Interface Sci"},{"issue":"7212","key":"ref124","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1038\/nature07292","article-title":"Frequency-modulated nuclear localization bursts coordinate 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