Publications

Miles S, Breeden LL. (2016) A common strategy for initiating the transition from proliferation to quiescence. Current Genetics, doi:10.1007/s00294-016-0640-0. PMID: 27544284.
Abstract

Miles S, Croxford MW, Abeysinghe AP, Breeden LL. (2016) Msa1 and Msa2 Modulate G1-Specific Transcription to Promote G1 Arrest and the Transition to Quiescence in Budding Yeast. PLoS Genet. doi: 10.1371/journal.pgen. 1006088. PMCID: PMC4894574.
Abstract

McKnight JN, Breeden LL, Tsukiyama T. (2015) A molecular off switch for transcriptional quiescence. Cell Cycle. doi:10.1080/15384101.2015.1112618. PMCID: PMC4825787.
Abstract

McKnight JN, Boerma JW, Breeden LL, Tsukiyama T. (2015) Global promoter targeting of a conserved lysine deacetylase for transcriptional shutoff during quiescence entry. Mol. Cell 59, 1-12 Sep 3 2015 doi:10.1016/j.molcel.2015.07.014. PMCID: PMC4560983.
Abstract

Li L, Miles S, Breeden LL. (2015) A genetic screen for Saccharomyces cerevisiae mutants that fail to enter quiescence. G3 (Bethesda) Jun 10. pii: g3.115.019091. doi: 10.1534/g3.115.019091. PMCID: PMC4528334.
Abstract

Qin LX, Breeden LL, Self SG. (2014) Finding gene clusters for a replicated time course study. BMC Res Notes.  Jan 24;7:60. doi: 10.1186/1756-0500-7-60. PMCID: PMC3906880.
Abstract

Miles, S., Li, L., Davison, J., and LL Breeden. (2013) Xbp1 directs global repression of budding yeast transcription during the transition to quiescence and is important for the longevity and reversibility of the quiescent state.  PLOS Genetics 9(10):e1003854.  PMID: 24204289.
Abstract

Li L, Miles S, Melville Z, Prasad A, Bradley G, Breeden LL. (2013) Key events during the transition from rapid growth to quiescence in budding yeast require posttranscriptional regulators. Mol Biol Cell. Dec;24(23):3697-709. doi: 10.1091/mbc.E13-05-0241. PMID: 24088570.
Abstract

Li, L., Lu, Y., Qin, L. Bar-Joseph, Z., Werner-Washburne, M., Breeden LL. (2009) Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. Mol. Biol. Cell 20:3851-3864. PMC2735484.
Abstract

Lu, Y., Mahony, S., Benos, P., Rosenfeld, R., Simon, I., Breeden LL, Bar-Joseph, Z. (2007) Combined analysis reveals a core set of cycling genes, Genome Biology 8:R146-R157 , PMC2323241.
Abstract

Braun, K, Breeden LL. (2007) Nascent transcription of MCM2-7 is important for nuclear localizaation of the minichromosome maintenance complex in G1, Molecular Biology of the Cell, 18, 1447, PMC1838970.
Abstract

Pramila, T, Wu, W, Miles, S, Noble, WS, Breeden LL. (2006) The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle, Genes Dev., 15(20)2266-78, PMC1553209.
Abstract

Guo, Y, Breeden LL. (2006) Analysis of cellular responses to Aflatoxin B1in yeast expressing cytochrome P450 1A2 using cDNA microarrays, Mutation Research, 593, 121-142, PMID:16122766.
Abstract

Zhou, C, Wakefield, J, Breeden LL. (2006) Bayesian analysis of cell cycle gene expression data, Bayesian Inference for Gene Expression and Proteomics, Cambridge University Press, 1-24.
Paper

Li, L, Quinton, T, Miles, S, Breeden, LL. (2005) Genetic interactions between mediator and the late G1-specific transcription factor Swi6 in Saccharomyces cerevisiae, Genetics, 171(2)477-88, PMCID:PMC1456765.
Abstract

Guo Y, Breeden LL, Zarbl H, Preston BD, Eaton DL. (2005) Expression of a human cytochrome p450 in yeast permits analysis of pathways for response to and repair of aflatoxin-induced DNA damage, Molecular and Cellular Biology, 25(14)5823-33, PMCID: PMC1168797.
Abstract

Mai, B., Breeden LL. (2005) Identification of target genes of a yeast transcriptional repressor, Methods in Molecular Biology. Published.
Paper

Schaefer JB, Breeden LL (Jun 2004) RB from a bud's eye view, Cell, 117(7)849-50. PMID:15210104.
Abstract

Sidorova JM, Breeden LL (Nov 2003) Precocious G1/S transitions and genomic instability: the origin connection, Mutation Research, 532(1-2)5-19. PMID:14643425.
Abstract

Sidorova JM, Breeden LL (May 2003) Rad53 checkpoint kinase phosphorylation site preference identified in the Swi6 protein of Saccharomyces cerevisiae, Molecular and Cellular Biology, 23(10)3405-16, PMCID:PMC164756.
Abstract

Breeden L.L., Periodic Transcription: A Cycle within a Cycle, Current Biology, 12, 6 Jan 2003, PMID:12526763.
Abstract

Pramila, T., Miles, S., GuhaThakurta, D., Jemiolo, D., and L. Breeden (1 Dec 2002) Conserved homeodomain proteins interact with MADS box protein Mcm1 to restrict ECB-dependent transcription to the M/G1 phase of the cell cycle, Genes and Development, 16, 3034-3045, PMCID: PMC187489.
Abstract

Sidorova JM, Breeden LL (January 2002) Precocious S-phase entry in budding yeast prolongs replicative state and increases dependence upon Rad53 for viability, Genetics, 160(1)123-36, PMCID: PMC1461931.
Abstract

Mai B, Miles S, Breeden LL (January 2002) Characterization of the ECB binding complex responsible for the M/G(1)-specific transcription of CLN3 and SWI4, Molecular and Cellular Biology, 22(2)430-41, PMCID: PMC139728.
Abstract

MacKay VL, Mai B, Waters L, Breeden LL (July 2001) Early cell cycle box-mediated transcription of CLN3 and SWI4 contributes to the proper timing of the G(1)-to-S transition in budding yeast, Molecular and Cellular Biology, 21(13)4140-8, PMCID: PMC87075.
Abstract

Zhao LP, Prentice R, Breeden L, Statistical modeling of large microarray data sets to identify stimulus-response profiles, Proceedings of the National Academy of Sciences (USA), 98(10):5631-6, 2001, PMCID: PMC33264.
Abstract

Breeden LL (2000) Cyclin transcription: Timing is everything, Current Biology, 10(16)R586-8, PMID: 10985373.
Abstract

Mai B, Breeden LL (Jan 2000) CLN1 and its repression by Xbp1 are important for efficient sporulation in budding yeast, Molecular and Cellular Biology, 20(2)478-87, PMCID: PMC85107.
Abstract

Sidorova J, Breeden LL (Jan 1999) The MSN1 and NHP6A genes suppress SWI6 defects in Saccharomyces cerevisiae, Genetics, 151(1)45-55, PMCID: PMC1460468.
Abstract

Ewaskow SP, Sidorova JM, Hendle J, Emery JC, Lycan DE, Zhang KY, Breeden LL (March 1998) Mutation and modeling analysis of the Saccharomyces cerevisiae Swi6 ankyrin repeats, Biochemistry, 37(13)4437-50, PMID: 9521763.
Abstract

Mai B, Breeden L (November 1997) Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family, Molecular and Cellular Biology, 17(11)6491-501, PMCID: PMC232502.
Abstract

Sidorova JM, Breeden LL (November 1997) Rad53-dependent phosphorylation of Swi6 and down-regulation of CLN1 and CLN2 transcription occur in response to DNA damage in Saccharomyces cerevisiae, Genes and Development, 11(22)3032-45, PMCID: PMC316703.
Abstract

McInerny CJ, Partridge JF, Mikesell GE, Creemer DP, Breeden LL (May 1997) A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription, Genes and Development, 11(10)1277-88, PMID: 9171372.
Abstract

Partridge JF, Mikesell GE, Breeden LL (April 1997) Cell cycle-dependent transcription of CLN1 involves swi4 binding to MCB-like elements, Journal of Biological Chemistry, 272(14)9071-7, PMID: 9083033.
Abstract

Breeden LL, Alpha-factor synchronization of budding yeast, Methods in Enzymology, 283, 332-41, 1997, PMID: 9251031.
Abstract

Lycan DE, Stafford KA, Bollinger W, Breeden LL (May 1996) A new Saccharomyces cerevisiae ankyrin repeat-encoding gene required for a normal rate of cell proliferation, Gene, 171(1)33-40, PMID: 8675027.
Abstract

Breeden L, Start-specific transcription in yeast, Current Topics in Microbiology and Immunology, 208, 95-127, 1996. PMID: 8575215.
Abstract

Sidorova JM, Mikesell GE, Breeden LL (December 1995) Cell cycle-regulated phosphorylation of Swi6 controls its nuclear localization, Molecular Biology of the Cell, 6(12)1641-58, PMCID: PMC301322.
Abstract

Lycan D, Mikesell G, Bunger M, Breeden L (November 1994) Differential effects of Cdc68 on cell cycle-regulated promoters in Saccharomyces cerevisiae, Molecular and Cellular Biology, 14(11)7455-65, PMCID: PMC359281.
Abstract

Foster R, Mikesell GE, Breeden L (June 1993) Multiple SW16-dependent cis-acting elements control SWI4 transcription through the cell cycle, Molecular and Cellular Biology, 13(6)3792-801, PMCID: PMC359864.
Abstract

Sidorova J, Breeden L (February 1993) Analysis of the SW14/SW16 protein complex, which directs G1/S-specific transcription in Saccharomyces cerevisiae, Molecular and Cellular Biology, 13(2)1069-77, PMCID: PMC358992.
Abstract

Lowndes NF, Johnson AL, Breeden L, Johnston LH (June 1992) SWI6 protein is required for transcription of the periodically expressed DNA synthesis genes in budding yeast, Nature, 357(6378)505-8, PMID:1608450.
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Breeden L, Mikesell GE (July 1991) Cell cycle-specific expression of the SWI4 transcription factor is required for the cell cycle regulation of HO transcription, Genes and Development, 5(7)1183-90, PMID: 2065973.
Abstract

Breeden L (September 1988) Cell cycle-regulated promoters in budding yeast, Trends in Genetics, 4(9)249-53, PMID: 3070871.
Abstract

Breeden L, Nasmyth K (October 1987) Similarity between cell-cycle genes of budding yeast and fission yeast and the Notch gene of Drosophila, Nature, 329(6140)651-4, PMID: 2821408.
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Smith D, Breeden L, Farrell E, Yarus M (June 1987) The bases of the tRNA anticodon loop are independent by genetic criteria, Nucleic Acids Research, 15(11)4669-86, PMCID: PMC340888.
Abstract

Breeden L, Nasmyth K (February 1987) Cell cycle control of the yeast HO gene: cis- and trans-acting regulators, Cell, 48(3)389-97, PMID: 3542227.
Abstract

Yarus M, Cline SW, Wier P, Breeden L, Thompson RC (November 1986) Actions of the anticodon arm in translation on the phenotypes of RNA mutants, Journal of Molecular Biology, 192(2)235-55, PMID: 2435916.
Abstract

Brand AH, Breeden L, Abraham J, Sternglanz R, Nasmyth K (May 1985) Characterization of a 'silencer' in yeast: a DNA sequence with properties opposite to those of a transcriptional enhancer, Cell, 41(1)41-8, PMID: 3888409.
Abstract

Breeden L, Nasmyth K, Regulation of the yeast HO gene, Cold Spring Harbor Symposia On Quantitative Biology, 50, 643-50, 1985, PMID: 3938367.
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Yarus M, Breeden L (September 1981) Mutants of Su+7 tRNA include a functional tRNA with an altered T pseudo uracil CG sequence, Cell, 25(3)815-23, PMID: 7285119.
Abstract

Breeden L, Yarus M (1980) Mutations that overcome plasmid-mediated relaxation affect (p)ppGpp, Molecular and General Genetics, 179(1)119-24, PMID: 6161292.
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Breeden L, Yarus M, Cline S (1980) A cloned suppressor tRNA gene relaxes stringent control, Molecular and General Genetics, 179(1)125-33, PMID: 6256603.
Abstract