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Rev"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1128\/JB.143.3.1384-1394.1980","article-title":"Reserve carbohydrate metabolism in Saccharomyces cerevisiae: responses to nutrient limitation","volume":"143","author":"SH Lillie","year":"1980","journal-title":"J Bacteriol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/S0968-0004(00)88990-2","article-title":"The SWI-SNF complex: a chromatin remodeling machine?","volume":"20","author":"CL Peterson","year":"1995","journal-title":"Trends Biochem Sci"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"4240","DOI":"10.1128\/MCB.15.8.4240","article-title":"SNF11, a new component of the yeast SNF-SWI complex that interacts with a conserved region of SNF2","volume":"15","author":"I Treich","year":"1995","journal-title":"Mol Cell Biol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"e1004084","DOI":"10.1371\/journal.pgen.1004084","article-title":"A comprehensive 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Yen","year":"2003","journal-title":"Yeast"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"3441","DOI":"10.1128\/MCB.01643-06","article-title":"mRNAs encoding polarity and exocytosis factors are cotransported with the cortical endoplasmic reticulum to the incipient bud in Saccharomyces cerevisiae","volume":"27","author":"S Aronov","year":"2007","journal-title":"Mol Cell Biol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"D502","DOI":"10.1093\/nar\/gkp820","article-title":"DRYGIN: a database of quantitative genetic interaction networks in yeast","volume":"38","author":"JL Koh","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/S0968-0004(99)01460-7","article-title":"The economics of ribosome biosynthesis in yeast","volume":"24","author":"JR Warner","year":"1999","journal-title":"Trends Biochem 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Yoshikawa","year":"2011","journal-title":"Yeast"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1101\/gad.458008","article-title":"A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae","volume":"22","author":"J Berretta","year":"2008","journal-title":"Genes Dev"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1101\/gad.522509","article-title":"Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae","volume":"23","author":"J Camblong","year":"2009","journal-title":"Genes Dev"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM 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Res"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v032.i06","article-title":"mixtools: An R Package for Analyzing Finite Mixture Models","volume":"32","author":"T Benaglia","year":"2009","journal-title":"J Stat Softw"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"key":"ref84","article-title":"cluster: Cluster Analysis Basics and Extensions","author":"M Maechler","year":"2016"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"e53958","DOI":"10.1371\/journal.pone.0053958","article-title":"A Yeast Purification System for Human Translation Initiation Factors eIF2 and eIF2B epsilon and Their Use in the Diagnosis of CACH\/VWM Disease","volume":"8","author":"RA de Almeida","year":"2013","journal-title":"PLoS One"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1093\/genetics\/122.1.19","article-title":"A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in <italic>Saccharomyces cerevisiae<\/italic>","volume":"122","author":"RS Sikorski","year":"1989","journal-title":"Genetics"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/0378-1119(95)00037-7","article-title":"Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds","volume":"156","author":"D Mumberg","year":"1995","journal-title":"Gene"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/B978-0-12-385120-8.00015-2","article-title":"Enzymatic Assembly of Overlapping DNA Fragments","volume":"498","author":"DG Gibson","year":"2011","journal-title":"Method Enzymol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"3577","DOI":"10.1093\/nar\/26.15.3577","article-title":"Assessment of aryl hydrocarbon receptor complex interactions using pBEVY plasmids: expression vectors with bi-directional promoters for use in Saccharomyces cerevisiae","volume":"26","author":"CA Miller","year":"1998","journal-title":"Nucleic Acids Res"},{"key":"ref90","unstructured":"RStudio-Team (2016) RStudio: Integrated development for R. URL <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.rstudio.com\/\" xlink:type=\"simple\">https:\/\/www.rstudio.com\/<\/ext-link>."},{"key":"ref91","unstructured":"Chang W, Cheng J, Allaire JJ, Xie Y, McPherson J (2017) shiny: Web application framework for R. URL <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/cran.r-project.org\/package=shiny\" xlink:type=\"simple\">https:\/\/cran.r-project.org\/package=shiny<\/ext-link>."},{"key":"ref92","unstructured":"Allaire JJ, Cheng J, Xie Y, McPherson J, Chang W, et al. (2017) rmarkdown: Dynamic documents for R. URL <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/cran.r-project.org\/package=rmarkdown\" xlink:type=\"simple\">https:\/\/cran.r-project.org\/package=rmarkdown<\/ext-link>."},{"key":"ref93","unstructured":"R-Development-Core-Team (2008) R: A language and environment for statistical computing. URL <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.r-project.org\/\" xlink:type=\"simple\">https:\/\/www.r-project.org\/<\/ext-link>."}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1007253","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,3,22]],"date-time":"2018-03-22T00:00:00Z","timestamp":1521676800000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1007253","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T15:29:57Z","timestamp":1693582197000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1007253"}},"subtitle":[],"editor":[{"given":"Michael","family":"Snyder","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,3,12]]},"references-count":93,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2018,3,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1007253","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pgen.1007253","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,3,12]]}}}