Taba MR, et al. (1991) Changes in a SWI4,6-DNA-binding complex occur at the time of HO gene activation in yeast. Genes Dev 5(11):2000-13 |
Poirel CL, et al. (2013) Top-down network analysis to drive bottom-up modeling of physiological processes. J Comput Biol 20(5):409-18 |
Dyczkowski J and Vingron M (2005) Comparative analysis of cell cycle regulated genes in eukaryotes. Genome Inform Ser Workshop Genome Inform 16(1):125-31 |
Igual JC, et al. (1996) Coordinated regulation of gene expression by the cell cycle transcription factor Swi4 and the protein kinase C MAP kinase pathway for yeast cell integrity. EMBO J 15(18):5001-13 |
Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6():420 |
Haase SB and Wittenberg C (2014) Topology and control of the cell-cycle-regulated transcriptional circuitry. Genetics 196(1):65-90 |
Mager WH and Siderius M (2002) Novel insights into the osmotic stress response of yeast. FEMS Yeast Res 2(3):251-7 |
Shaner L, et al. (2008) The Hsp110 protein chaperone Sse1 is required for yeast cell wall integrity and morphogenesis. Curr Genet 54(1):1-11 |
Andrews BJ and Herskowitz I (1989) The yeast SWI4 protein contains a motif present in developmental regulators and is part of a complex involved in cell-cycle-dependent transcription. Nature 342(6251):830-3 |
Breeden L and Nasmyth K (1987) Similarity between cell-cycle genes of budding yeast and fission yeast and the Notch gene of Drosophila. Nature 329(6140):651-4 |
Cross FR, et al. (1994) Role of Swi4 in cell cycle regulation of CLN2 expression. Mol Cell Biol 14(7):4779-87 |
Ewaskow SP, et al. (1998) Mutation and modeling analysis of the Saccharomyces cerevisiae Swi6 ankyrin repeats. Biochemistry 37(13):4437-50 |
Levine K, et al. (1996) Saccharomyces cerevisiae G1 cyclins differ in their intrinsic functional specificities. Mol Cell Biol 16(12):6794-803 |
Wang H, et al. (2011) Yeast cell cycle transcription factors identification by variable selection criteria. Gene 485(2):172-6 |
Zhao Y, et al. (2015) The APSES family proteins in fungi: Characterizations, evolution and functions. Fungal Genet Biol 81():271-80 |
Xiao Y and Segal MR (2009) Identification of yeast transcriptional regulation networks using multivariate random forests. PLoS Comput Biol 5(6):e1000414 |
Mathiasen DP and Lisby M (2014) Cell cycle regulation of homologous recombination in Saccharomyces cerevisiae. FEMS Microbiol Rev 38(2):172-84 |
Cook M and Tyers M (2007) Size control goes global. Curr Opin Biotechnol 18(4):341-50 |
Sidorova J and Breeden L (1993) Analysis of the SWI4/SWI6 protein complex, which directs G1/S-specific transcription in Saccharomyces cerevisiae. Mol Cell Biol 13(2):1069-77 |
Busnelli S, et al. (2013) Snf1/AMPK promotes SBF and MBF-dependent transcription in budding yeast. Biochim Biophys Acta 1833(12):3254-64 |
Imamura Y, et al. (2014) 3,6-Epidioxy-1,10-bisaboladiene inhibits G1 -specific transcription through Swi4/Swi6 and Mbp1/Swi6 via the Hog1 stress pathway in yeast. FEBS J 281(20):4612-21 |
Merrill GF, et al. (1992) DNA synthesis control in yeast: an evolutionarily conserved mechanism for regulating DNA synthesis genes? Bioessays 14(12):823-30 |
Iyer VR, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409(6819):533-8 |
Sedgwick SG, et al. (1998) Structural and functional architecture of the yeast cell-cycle transcription factor swi6. J Mol Biol 281(5):763-75 |
Travesa A, et al. (2013) Repression of G1/S transcription is mediated via interaction of the GTB motifs of Nrm1 and Whi5 with Swi6. Mol Cell Biol 33(8):1476-86 |
Ferrezuelo F, et al. (2010) The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle. Genome Biol 11(6):R67 |
Aranda A and Proudfoot N (2001) Transcriptional termination factors for RNA polymerase II in yeast. Mol Cell 7(5):1003-11 |
Hamann T (2015) The plant cell wall integrity maintenance mechanism - A case study of a cell wall plasma membrane signaling network. Phytochemistry 112():100-109 |
Taberner FJ and Igual JC (2010) Yeast karyopherin Kap95 is required for cell cycle progression at Start. BMC Cell Biol 11():47 |
Ashe M, et al. (2008) The SBF- and MBF-associated Protein Msa1 Is Required for Proper Timing of G1-specific Transcription in Saccharomyces cerevisiae. J Biol Chem 283(10):6040-9 |
Harrington LA and Andrews BJ (1996) Binding to the yeast SwI4,6-dependent cell cycle box, CACGAAA, is cell cycle regulated in vivo. Nucleic Acids Res 24(4):558-65 |
Cross F and McKinney J (1992) Is START a switch? Ciba Found Symp 170:20-5; discussion 25-9 |
Jorgensen P and Tyers M (2004) How cells coordinate growth and division. Curr Biol 14(23):R1014-27 |
Tsankov AM, et al. (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8(7):e1000414 |
Elsztein C, et al. (2011) The resistance of the yeast Saccharomyces cerevisiae to the biocide polyhexamethylene biguanide: involvement of cell wall integrity pathway and emerging role for YAP1. BMC Mol Biol 12(1):38 |
Lai LC, et al. (2008) Comparison of the transcriptomic "stress response" evoked by antimycin A and oxygen deprivation in saccharomyces cerevisiae. BMC Genomics 9:627 |
Enserink JM, et al. (2006) Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiae. J Cell Biol 175(5):729-41 |
Lau KY, et al. (2007) Function constrains network architecture and dynamics: a case study on the yeast cell cycle Boolean network. Phys Rev E Stat Nonlin Soft Matter Phys 75(5 Pt 1):051907 |
Malagon F and Jensen TH (2008) The T body, a new cytoplasmic RNA granule in Saccharomyces cerevisiae. Mol Cell Biol 28(19):6022-32 |
de Bruin RA, et al. (2008) Stb1 collaborates with other regulators to modulate the G1-specific transcriptional circuit. Mol Cell Biol 28(22):6919-28 |
Taylor IA, et al. (2000) Characterization of the DNA-binding domains from the yeast cell-cycle transcription factors Mbp1 and Swi4. Biochemistry 39(14):3943-54 |
Holloway DT, et al. (2007) Machine learning for regulatory analysis and transcription factor target prediction in yeast. Syst Synth Biol 1(1):25-46 |
Bean JM, et al. (2005) High functional overlap between MluI cell-cycle box binding factor and Swi4/6 cell-cycle box binding factor in the G1/S transcriptional program in Saccharomyces cerevisiae. Genetics 171(1):49-61 |
Tong AH, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303(5659):808-13 |
Lai FJ, et al. (2014) A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Syst Biol 8 Suppl 4():S9 |
Kim KY, et al. (2010) Yeast Mpk1 cell wall integrity mitogen-activated protein kinase regulates nucleocytoplasmic shuttling of the Swi6 transcriptional regulator. Mol Biol Cell 21(9):1609-19 |
Chin SL, et al. (2012) Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators. FEBS J 279(6):1119-30 |
Amon A, et al. (1993) Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins. Cell 74(6):993-1007 |
Simon I, et al. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697-708 |
Andrews BJ and Moore LA (1992) Interaction of the yeast Swi4 and Swi6 cell cycle regulatory proteins in vitro. Proc Natl Acad Sci U S A 89(24):11852-6 |
Tripodi F, et al. (2013) Protein Kinase CK2 Holoenzyme Promotes Start-Specific Transcription in Saccharomyces cerevisiae. Eukaryot Cell 12(9):1271-80 |
Machado AK, et al. (1997) Thioredoxin reductase-dependent inhibition of MCB cell cycle box activity in Saccharomyces cerevisiae. J Biol Chem 272(27):17045-54 |
Tuglus C and van der Laan MJ (2011) Repeated measures semiparametric regression using targeted maximum likelihood methodology with application to transcription factor activity discovery. Stat Appl Genet Mol Biol 10(1):Article2 |
Flick K and Wittenberg C (2005) Multiple pathways for suppression of mutants affecting G1-specific transcription in Saccharomyces cerevisiae. Genetics 169(1):37-49 |
Li L, et al. (2005) Genetic interactions between mediator and the late G1-specific transcription factor Swi6 in Saccharomyces cerevisiae. Genetics 171(2):477-88 |
Cosma MP, et al. (1999) Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell 97(3):299-311 |
Becskei A, et al. (2005) Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat Genet 37(9):937-44 |
Garcia R, et al. (2004) The global transcriptional response to transient cell wall damage in Saccharomyces cerevisiae and its regulation by the cell integrity signaling pathway. J Biol Chem 279(15):15183-95 |
Epstein CB and Cross FR (1994) Genes that can bypass the CLN requirement for Saccharomyces cerevisiae cell cycle START. Mol Cell Biol 14(3):2041-7 |
Wu WS and Li WH (2008) Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics 9:522 |
Toone WM, et al. (1995) Rme1, a negative regulator of meiosis, is also a positive activator of G1 cyclin gene expression. EMBO J 14(23):5824-32 |
Tanaka K, et al. (1992) A new cdc gene required for S phase entry of Schizosaccharomyces pombe encodes a protein similar to the cdc 10+ and SWI4 gene products. EMBO J 11(13):4923-32 |
Yarrington RM, et al. (2015) Spatiotemporal cascade of transcription factor binding required for promoter activation. Mol Cell Biol 35(4):688-98 |
Tennen RI, et al. (2013) Cell-cycle and DNA damage regulation of the DNA mismatch repair protein Msh2 occurs at the transcriptional and post-transcriptional level. DNA Repair (Amst) 12(2):97-109 |
Golla U, et al. (2015) Molecular Cytotoxicity Mechanisms of Allyl Alcohol (Acrolein) in Budding Yeast. Chem Res Toxicol 28(6):1246-64 |
Morgan BA, et al. (1995) A yeast transcription factor bypassing the requirement for SBF and DSC1/MBF in budding yeast has homology to bacterial signal transduction proteins. EMBO J 14(22):5679-89 |
Noor A, et al. (2013) ROBNCA: robust network component analysis for recovering transcription factor activities. Bioinformatics 29(19):2410-8 |
Moll T, et al. (1992) SWI6 is a regulatory subunit of two different cell cycle START-dependent transcription factors in Saccharomyces cerevisiae. J Cell Sci Suppl 16:87-96 |
Moll T, et al. (1993) Transcription factors important for starting the cell cycle in yeast. Philos Trans R Soc Lond B Biol Sci 340(1293):351-60 |
Chavel CA, et al. (2010) Multiple signals converge on a differentiation MAPK pathway. PLoS Genet 6(3):e1000883 |
Stevens SW, et al. (2002) Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol Cell 9(1):31-44 |
Breeden LL (2003) Periodic transcription: a cycle within a cycle. Curr Biol 13(1):R31-8 |
Vohradsky J (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40(15):7096-103 |
Breeden L and Nasmyth K (1987) Cell cycle control of the yeast HO gene: cis- and trans-acting regulators. Cell 48(3):389-97 |
Queralt E and Igual JC (2005) Functional connection between the Clb5 cyclin, the protein kinase C pathway and the Swi4 transcription factor in Saccharomyces cerevisiae. Genetics 171(4):1485-98 |
Gormley M, et al. (2011) An integrated framework to model cellular phenotype as a component of biochemical networks. Adv Bioinformatics 2011():608295 |
Haarer B, et al. (2013) Actin dosage lethality screening in yeast mediated by selective ploidy ablation reveals links to urmylation/wobble codon recognition and chromosome stability. G3 (Bethesda) 3(3):553-61 |
Galdieri L, et al. (2016) Reduced histone expression or defect in chromatin assembly induce respiration. Mol Cell Biol () |
Koch C, et al. (1999) A role for Ctr9p and Paf1p in the regulation G1 cyclin expression in yeast. Nucleic Acids Res 27(10):2126-34 |
Corcoles-Saez I, et al. (2012) Low temperature highlights the functional role of the cell wall integrity pathway in the regulation of growth in Saccharomyces cerevisiae. Biochem J 446(3):477-88 |
Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
Wang G, et al. (2010) Process-based network decomposition reveals backbone motif structure. Proc Natl Acad Sci U S A 107(23):10478-83 |
Foster R, et al. (1993) Multiple SWI6-dependent cis-acting elements control SWI4 transcription through the cell cycle. Mol Cell Biol 13(6):3792-801 |
Heinisch JJ, et al. (1999) The protein kinase C-mediated MAP kinase pathway involved in the maintenance of cellular integrity in Saccharomyces cerevisiae. Mol Microbiol 32(4):671-80 |
Yu Y, et al. (2003) Regulation of TATA-binding protein binding by the SAGA complex and the Nhp6 high-mobility group protein. Mol Cell Biol 23(6):1910-21 |
Wijnen H, et al. (2002) The G(1) cyclin Cln3 promotes cell cycle entry via the transcription factor Swi6. Mol Cell Biol 22(12):4402-18 |
Ruotolo R, et al. (2010) Chemogenomic profiling of the cellular effects associated with histone H3 acetylation impairment by a quinoline-derived compound. Genomics 96(5):272-80 |
Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458 |
Taoka M, et al. (1992) A rat cerebellar protein containing the cdc10/SWI6 motif. Eur J Biochem 207(2):615-20 |
Andrews BJ and Herskowitz I (1989) Identification of a DNA binding factor involved in cell-cycle control of the yeast HO gene. Cell 57(1):21-9 |
Chen H, et al. (2014) Highly sensitive inference of time-delayed gene regulation by network deconvolution. BMC Syst Biol 8 Suppl 4():S6 |
Artiles K, et al. (2009) The Rts1 regulatory subunit of protein phosphatase 2A is required for control of G1 cyclin transcription and nutrient modulation of cell size. PLoS Genet 5(11):e1000727 |
Rodriguez-Pena JM, et al. (2010) The high-osmolarity glycerol (HOG) and cell wall integrity (CWI) signalling pathways interplay: a yeast dialogue between MAPK routes. Yeast 27(8):495-502 |
Lai LC, et al. (2006) Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryot Cell 5(9):1468-89 |
Flick K, et al. (1998) Regulation of cell size by glucose is exerted via repression of the CLN1 promoter. Mol Cell Biol 18(5):2492-501 |
Ernst J, et al. (2007) Reconstructing dynamic regulatory maps. Mol Syst Biol 3():74 |
Wu WS, et al. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7(1):421 |
Huang SS and Fraenkel E (2012) Swimming Upstream: Identifying Proteomic Signals that Drive Transcriptional Changes using the Interactome and Multiple "-Omics" Datasets. Methods Cell Biol 110():57-80 |
Shohat-Tal A and Eshel D (2011) Cell cycle regulators interact with pathways that modulate microtubule stability in Saccharomyces cerevisiae. Eukaryot Cell 10(12):1705-13 |
Serrano R, et al. (2006) Signaling alkaline pH stress in the yeast Saccharomyces cerevisiae through the Wsc1 cell surface sensor and the Slt2 MAPK pathway. J Biol Chem 281(52):39785-95 |
Chen KC, et al. (2000) Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol Biol Cell 11(1):369-91 |
Dohrmann PR, et al. (1992) Parallel pathways of gene regulation: homologous regulators SWI5 and ACE2 differentially control transcription of HO and chitinase. Genes Dev 6(1):93-104 |
Moretto F, et al. (2013) A pharmaco-epistasis strategy reveals a new cell size controlling pathway in yeast. Mol Syst Biol 9():707 |
Choy JS, et al. (2015) A Genome-Wide Screen with Nicotinamide to Identify Sirtuin-Dependent Pathways in Saccharomyces cerevisiae. G3 (Bethesda) 6(2):485-94 |
Nadeem FK, et al. (2006) Pol5p, a novel binding partner to Cdc10p in fission yeast involved in rRNA production. Mol Genet Genomics 276(4):391-401 |
Koc A, et al. (2003) Replication-independent MCB gene induction and deoxyribonucleotide accumulation at G1/S in Saccharomyces cerevisiae. J Biol Chem 278(11):9345-52 |
Bermejo C, et al. (2008) The Sequential Activation of the Yeast HOG and SLT2 Pathways Is Required for Cell Survival to Cell Wall Stress. Mol Biol Cell 19(3):1113-24 |
Yu H and Gerstein M (2006) Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A 103(40):14724-31 |
Ouedraogo JP, et al. (2011) Survival Strategies of Yeast and Filamentous Fungi against the Antifungal Protein AFP. J Biol Chem 286(16):13859-68 |
Horak CE, et al. (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16(23):3017-33 |
de Lichtenberg U, et al. (2005) New weakly expressed cell cycle-regulated genes in yeast. Yeast 22(15):1191-201 |
Coic E, et al. (2006) Cell cycle-dependent regulation of Saccharomyces cerevisiae donor preference during mating-type switching by SBF (Swi4/Swi6) and Fkh1. Mol Cell Biol 26(14):5470-80 |
Wang H, et al. (2009) Recruitment of Cln3 cyclin to promoters controls cell cycle entry via histone deacetylase and other targets. PLoS Biol 7(9):e1000189 |
Huang D, et al. (2009) Dual regulation by pairs of cyclin-dependent protein kinases and histone deacetylases controls G1 transcription in budding yeast. PLoS Biol 7(9):e1000188 |
Verma R, et al. (1992) Regulation of the yeast DNA replication genes through the Mlu I cell cycle box is dependent on SWI6. Proc Natl Acad Sci U S A 89(20):9479-83 |
LaFayette SL, et al. (2010) PKC signaling regulates drug resistance of the fungal pathogen Candida albicans via circuitry comprised of Mkc1, calcineurin, and Hsp90.LID - e1001069 [pii] PLoS Pathog 6(8) |
Levin DE (2011) Regulation of Cell Wall Biogenesis in Saccharomyces cerevisiae: The Cell Wall Integrity Signaling Pathway. Genetics 189(4):1145-75 |
Taberner FJ, et al. (2009) Spatial regulation of the start repressor Whi5. Cell Cycle 8(18):3010-8 |
Heinisch JJ and Dufrene YF (2010) Is there anyone out there?-Single-molecule atomic force microscopy meets yeast genetics to study sensor functions. Integr Biol (Camb) 2(9):408-15 |
Yu Y, et al. (2000) Architectural transcription factors and the SAGA complex function in parallel pathways to activate transcription. Mol Cell Biol 20(7):2350-7 |
Madden K, et al. (1997) SBF cell cycle regulator as a target of the yeast PKC-MAP kinase pathway. Science 275(5307):1781-4 |
Rodicio R and Heinisch JJ (2010) Together we are strong-cell wall integrity sensors in yeasts. Yeast 27(8):531-40 |
Ho U, et al. (1997) Role of the casein kinase I isoform, Hrr25, and the cell cycle-regulatory transcription factor, SBF, in the transcriptional response to DNA damage in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 94(2):581-6 |
Workman CT, et al. (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-9 |
Alarcon T and Tindall MJ (2007) Modelling cell growth and its modulation of the G1/S transition. Bull Math Biol 69(1):197-214 |
de Nadal E and Posas F (2011) Elongating under Stress. Genet Res Int 2011():326286 |
Venters BJ, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92 |
Qi Y, et al. (2008) Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res 18(12):1991-2004 |
Wijnen H and Futcher B (1999) Genetic analysis of the shared role of CLN3 and BCK2 at the G(1)-S transition in Saccharomyces cerevisiae. Genetics 153(3):1131-43 |
Sillje HH, et al. (1997) Effects of different carbon fluxes on G1 phase duration, cyclin expression, and reserve carbohydrate metabolism in Saccharomyces cerevisiae. J Bacteriol 179(21):6560-5 |
Urnov FD (2002) A feel for the template: zinc finger protein transcription factors and chromatin. Biochem Cell Biol 80(3):321-33 |
Dionne I, et al. (2013) Cell cycle-dependent transcription factors control the expression of yeast telomerase RNA. RNA 19(7):992-1002 |
Schmoller KM and Skotheim JM (2015) The Biosynthetic Basis of Cell Size Control. Trends Cell Biol 25(12):793-802 |
Queralt E and Igual JC (2004) Functional distinction between Cln1p and Cln2p cyclins in the control of the Saccharomyces cerevisiae mitotic cycle. Genetics 168(1):129-40 |
Mao K, et al. (2011) Two MAPK-signaling pathways are required for mitophagy in Saccharomyces cerevisiae. J Cell Biol 193(4):755-67 |
Maraziotis I, et al. (2005) Gene networks inference from expression data using a recurrent neuro-fuzzy approach. Conf Proc IEEE Eng Med Biol Soc 5:4834-7 |
Gustin MC, et al. (1998) MAP kinase pathways in the yeast Saccharomyces cerevisiae. Microbiol Mol Biol Rev 62(4):1264-300 |
Bristow SL, et al. (2014) Cell cycle-regulated transcription: effectively using a genomics toolbox. Methods Mol Biol 1170():3-27 |
Kim KY, et al. (2008) Yeast Mpk1 mitogen-activated protein kinase activates transcription through Swi4/Swi6 by a noncatalytic mechanism that requires upstream signal. Mol Cell Biol 28(8):2579-89 |
Porter SE, et al. (2002) The yeast pafl-rNA polymerase II complex is required for full expression of a subset of cell cycle-regulated genes. Eukaryot Cell 1(5):830-42 |
Zhao XM, et al. (2008) Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Res 36(9):e48 |
Stuart D and Wittenberg C (1994) Cell cycle-dependent transcription of CLN2 is conferred by multiple distinct cis-acting regulatory elements. Mol Cell Biol 14(7):4788-801 |
Dirick L, et al. (1992) A central role for SWI6 in modulating cell cycle Start-specific transcription in yeast. Nature 357(6378):508-13 |
Lowndes NF, et al. (1992) SWI6 protein is required for transcription of the periodically expressed DNA synthesis genes in budding yeast. Nature 357(6378):505-8 |
Gong J and Siede W (2009) SBF transcription factor complex positively regulates UV mutagenesis in Saccharomyces cerevisiae. Biochem Biophys Res Commun 379(4):1009-14 |
Banerjee N and Zhang MQ (2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res 31(23):7024-31 |
Chen T and Li F (2009) Identifying cell cycle regulators and combinatorial interactions among transcription factors with microarray data and ChIP-chip data. Int J Bioinform Res Appl 5(6):625-46 |
Toone WM, et al. (1997) Getting started: regulating the initiation of DNA replication in yeast. Annu Rev Microbiol 51:125-49 |
Tomson BN and Arndt KM (2013) The many roles of the conserved eukaryotic Paf1 complex in regulating transcription, histone modifications, and disease states. Biochim Biophys Acta 1829(1):116-26 |
Ho Y, et al. (1999) Regulation of transcription at the Saccharomyces cerevisiae start transition by Stb1, a Swi6-binding protein. Mol Cell Biol 19(8):5267-78 |
Bertoli C, et al. (2013) Control of cell cycle transcription during G1 and S phases. Nat Rev Mol Cell Biol 14(8):518-28 |
Siegmund RF and Nasmyth KA (1996) The Saccharomyces cerevisiae Start-specific transcription factor Swi4 interacts through the ankyrin repeats with the mitotic Clb2/Cdc28 kinase and through its conserved carboxy terminus with Swi6. Mol Cell Biol 16(6):2647 |
Wang RS, et al. (2007) Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics 23(22):3056-3064 |
Koch C, et al. (1993) A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science 261(5128):1551-7 |
Hart CE, et al. (2005) A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data. Nucleic Acids Res 33(8):2580-94 |
Santisteban MS, et al. (1997) Histone octamer function in vivo: mutations in the dimer-tetramer interfaces disrupt both gene activation and repression. EMBO J 16(9):2493-506 |
MacKay VL, et al. (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. Mol Cell Biol 21(13):4140-8 |
Lai WK and Buck MJ (2013) An integrative approach to understanding the combinatorial histone code at functional elements. Bioinformatics 29(18):2231-7 |
Tahara S, et al. (1998) Functional domains of rep2, a transcriptional activator subunit for Res2-Cdc10, controlling the cell cycle "start". Mol Biol Cell 9(6):1577-88 |
Breeden L (1996) Start-specific transcription in yeast. Curr Top Microbiol Immunol 208():95-127 |
Cote P, et al. (2009) Transcriptional analysis of the Candida albicans cell cycle. Mol Biol Cell 20(14):3363-73 |
Bhoite LT, et al. (2001) The Swi5 activator recruits the Mediator complex to the HO promoter without RNA polymerase II. Genes Dev 15(18):2457-69 |
Tanaka K and Okayama H (2000) A pcl-like cyclin activates the Res2p-Cdc10p cell cycle "start" transcriptional factor complex in fission yeast. Mol Biol Cell 11(9):2845-62 |
Stephan O and Koch C (2009) Sin3 is involved in cell size control at Start in Saccharomyces cerevisiae. FEBS J 276(14):3810-24 |
To CC and Vohradsky J (2010) Measurement variation determines the gene network topology reconstructed from experimental data: a case study of the yeast cyclin network. FASEB J 24(9):3468-78 |
Haber JE (2012) Mating-Type Genes and MAT Switching in Saccharomyces cerevisiae. Genetics 191(1):33-64 |
Kato M, et al. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5(8):R56 |
Kang X, et al. (2014) Pump-free multi-well-based microfluidic system for high-throughput analysis of size-control relative genes in budding yeast. Integr Biol (Camb) 6(7):685-93 |
Primig M, et al. (1992) Anatomy of a transcription factor important for the start of the cell cycle in Saccharomyces cerevisiae. Nature 358(6387):593-7 |
Stillman DJ (2013) Dancing the cell cycle two-step: regulation of yeast G1-cell-cycle genes by chromatin structure. Trends Biochem Sci 38(9):467-75 |
de Bruin RA, et al. (2004) Cln3 activates G1-specific transcription via phosphorylation of the SBF bound repressor Whi5. Cell 117(7):887-98 |
Sidorova JM and Breeden LL (1997) Rad53-dependent phosphorylation of Swi6 and down-regulation of CLN1 and CLN2 transcription occur in response to DNA damage in Saccharomyces cerevisiae. Genes Dev 11(22):3032-45 |
Hussein B, et al. (2011) G1/S Transcription Factor Orthologues Swi4p and Swi6p Are Important but Not Essential for Cell Proliferation and Influence Hyphal Development in the Fungal Pathogen Candida albicans. Eukaryot Cell 10(3):384-97 |
Moriya H, et al. (2011) Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico. Mol Syst Biol 7():556 |
Baetz K, et al. (2001) Transcriptional coregulation by the cell integrity mitogen-activated protein kinase Slt2 and the cell cycle regulator Swi4. Mol Cell Biol 21(19):6515-28 |
Gallo CA, et al. (2011) Discovering Time-Lagged Rules from Microarray Data using Gene Profile Classifiers. BMC Bioinformatics 12(1):123 |
Harris MR, et al. (2013) Binding specificity of the G1/S transcriptional regulators in budding yeast. PLoS One 8(4):e61059 |
Laman H, et al. (1995) Disturbance of normal cell cycle progression enhances the establishment of transcriptional silencing in Saccharomyces cerevisiae. Mol Cell Biol 15(7):3608-17 |
Nishida N, et al. (2014) Activation of signaling pathways related to cell wall integrity and multidrug resistance by organic solvent in Saccharomyces cerevisiae. Curr Genet 60(3):149-62 |
Liu N, et al. (2013) The transcription cofactor FgSwi6 plays a role in growth and development, carbendazim sensitivity, cellulose utilization, lithium tolerance, deoxynivalenol production and virulence in the filamentous fungus Fusarium graminearum. Funga |
Kaluarachchi Duffy S, et al. (2012) Exploring the yeast acetylome using functional genomics. Cell 149(4):936-48 |
Galbraith SJ, et al. (2006) Transcriptome network component analysis with limited microarray data. Bioinformatics 22(15):1886-94 |
Kumar A and Snyder M (2001) Emerging technologies in yeast genomics. Nat Rev Genet 2(4):302-12 |
Zanders ED (2000) Gene expression analysis as an aid to the identification of drug targets. Pharmacogenomics 1(4):375-84 |
Nasmyth K and Dirick L (1991) The role of SWI4 and SWI6 in the activity of G1 cyclins in yeast. Cell 66(5):995-1013 |
Bai L, et al. (2010) Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Dev Cell 18(4):544-55 |
Manioudaki ME and Poirazi P (2013) Modeling regulatory cascades using Artificial Neural Networks: the case of transcriptional regulatory networks shaped during the yeast stress response. Front Genet 4():110 |
Andrews BJ and Mason SW (1993) Gene expression and the cell cycle: a family affair. Science 261(5128):1543-4 |
Benanti JA (2015) Create, activate, destroy, repeat: Cdk1 controls proliferation by limiting transcription factor activity. Curr Genet () |
Ogas J, et al. (1991) Transcriptional activation of CLN1, CLN2, and a putative new G1 cyclin (HCS26) by SWI4, a positive regulator of G1-specific transcription. Cell 66(5):1015-26 |
Sherlock G and Rosamond J (1993) Starting to cycle: G1 controls regulating cell division in budding yeast. J Gen Microbiol 139(11):2531-41 |
Truman AW, et al. (2007) In the yeast heat shock response, Hsf1-directed induction of Hsp90 facilitates the activation of the Slt2 (Mpk1) mitogen-activated protein kinase required for cell integrity. Eukaryot Cell 6(4):744-52 |
Ozonov EA and van Nimwegen E (2013) Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. PLoS Comput Biol 9(8):e1003181 |
Koch C, et al. (1996) Switching transcription on and off during the yeast cell cycle: Cln/Cdc28 kinases activate bound transcription factor SBF (Swi4/Swi6) at start, whereas Clb/Cdc28 kinases displace it from the promoter in G2. Genes Dev 10(2):129-41 |
Fujioka T, et al. (2007) MpkA-Dependent and -Independent Cell Wall Integrity Signaling in Aspergillus nidulans. Eukaryot Cell 6(8):1497-510 |
Nasmyth K (1993) Regulating the HO endonuclease in yeast. Curr Opin Genet Dev 3(2):286-94 |
Andrews BJ and Moore L (1992) Mutational analysis of a DNA sequence involved in linking gene expression to the cell cycle. Biochem Cell Biol 70(10-11):1073-80 |
Breeden L and Mikesell G (1994) Three independent forms of regulation affect expression of HO, CLN1 and CLN2 during the cell cycle of Saccharomyces cerevisiae. Genetics 138(4):1015-24 |
Chen G, et al. (2007) Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol 8(1):R4 |
Dirick L, et al. (1995) Roles and regulation of Cln-Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. EMBO J 14(19):4803-13 |
Cooper K (2006) Rb, whi it's not just for metazoans anymore. Oncogene 25(38):5228-32 |
Spivak AT and Stormo GD (2016) Combinatorial cis-Regulation in Saccharomyces Species. G3 (Bethesda) () |
de Lucena RM, et al. (2012) Participation of CWI, HOG and Calcineurin pathways in the tolerance of Saccharomyces cerevisiae to low pH by inorganic acid. J Appl Microbiol 113(3):629-40 |
Alberghina L, et al. (2009) Molecular networks and system-level properties. J Biotechnol 144(3):224-33 |
Millar JB (2002) A genomic approach to studying cell-size homeostasis in yeast. Genome Biol 3(10):REVIEWS1028 |
Costanzo M, et al. (2003) G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol Cell Biol 23(14):5064-77 |
Eriksson PR, et al. (2011) Spt10 and Swi4 Control the Timing of Histone H2A/H2B Gene Activation in Budding Yeast. Mol Cell Biol 31(3):557-72 |
Queralt E and Igual JC (2003) Cell cycle activation of the Swi6p transcription factor is linked to nucleocytoplasmic shuttling. Mol Cell Biol 23(9):3126-40 |
Hess D and Winston F (2005) Evidence that Spt10 and Spt21 of Saccharomyces cerevisiae play distinct roles in vivo and functionally interact with MCB-binding factor, SCB-binding factor and Snf1. Genetics 170(1):87-94 |
Cai L and Tu BP (2012) Driving the cell cycle through metabolism. Annu Rev Cell Dev Biol 28():59-87 |
Goh WS, et al. (2010) Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PLoS Comput Biol 6(1):e1000649 |
Wright J, et al. (2013) A growing role for hypertrophy in senescence. FEMS Yeast Res 13(1):2-6 |
Wagner A (1997) A computational genomics approach to the identification of gene networks. Nucleic Acids Res 25(18):3594-604 |
Lyu S (2009) Combining boolean method with delay times for determining behaviors of biological networks. Conf Proc IEEE Eng Med Biol Soc 1():4884-7 |
Manderson EN, et al. (2008) A Novel Genetic Screen Implicates Elm1 in the Inactivation of the Yeast Transcription Factor SBF. PLoS One 3(1):e1500 |
Swamy KB, et al. (2009) Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 37(21):6991-7001 |
Kim KY and Levin DE (2010) Transcriptional reporters for genes activated by cell wall stress through a non-catalytic mechanism involving Mpk1 and SBF. Yeast 27(8):541-8 |
Manukyan A, et al. (2008) Ccr4 Alters Cell Size in Yeast by Modulating the Timing of CLN1 and CLN2 Expression. Genetics 179(1):345-57 |
Yu X, et al. (2006) Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res 34(3):917-27 |
Busti S, et al. (2010) Glucose signaling-mediated coordination of cell growth and cell cycle in Saccharomyces cerevisiae. Sensors (Basel) 10(6):6195-240 |
Turner JJ, et al. (2012) Cell size control in yeast. Curr Biol 22(9):R350-9 |
Alter O and Golub GH (2004) Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription. Proc Natl Acad Sci U S A 101(47):16577-82 |
Koch C and Nasmyth K (1994) Cell cycle regulated transcription in yeast. Curr Opin Cell Biol 6(3):451-9 |
Breeden L and Mikesell GE (1991) Cell cycle-specific expression of the SWI4 transcription factor is required for the cell cycle regulation of HO transcription. Genes Dev 5(7):1183-90 |
Bonilla M and Cunningham KW (2003) Mitogen-activated protein kinase stimulation of Ca(2+) signaling is required for survival of endoplasmic reticulum stress in yeast. Mol Biol Cell 14(10):4296-305 |
Xiong B, et al. (2015) Cadmium induces the activation of cell wall integrity pathway in budding yeast. Chem Biol Interact 240():316-23 |
Eriksson PR, et al. (2012) Regulation of histone gene expression in budding yeast. Genetics 191(1):7-20 |
Smolka MB, et al. (2006) An FHA domain-mediated protein interaction network of Rad53 reveals its role in polarized cell growth. J Cell Biol 175(5):743-53 |
Hansen L, et al. (2012) Differences in local genomic context of bound and unbound motifs. Gene 506(1):125-34 |
Lycan D, et al. (1994) Differential effects of Cdc68 on cell cycle-regulated promoters in Saccharomyces cerevisiae. Mol Cell Biol 14(11):7455-65 |
McInerny CJ (2011) Cell cycle regulated gene expression in yeasts. Adv Genet 73():51-85 |
Huang SS and Fraenkel E (2009) Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal 2(81):ra40 |
O'Donnell AF, et al. (2009) New mutant versions of yeast FACT subunit Spt16 affect cell integrity. Mol Genet Genomics 282(5):487-502 |
Braunewell S and Bornholdt S (2007) Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity. J Theor Biol 245(4):638-43 |
Lu Y, et al. (2007) Combined analysis reveals a core set of cycling genes. Genome Biol 8(7):R146 |
Leem SH, et al. (1994) The yeast Saccharomyces cerevisiae DNA polymerase IV: possible involvement in double strand break DNA repair. Nucleic Acids Res 22(15):3011-7 |
Partridge JF, et al. (1997) Cell cycle-dependent transcription of CLN1 involves swi4 binding to MCB-like elements. J Biol Chem 272(14):9071-7 |
Dynlacht BD (1997) Regulation of transcription by proteins that control the cell cycle. Nature 389(6647):149-52 |
Takahata S, et al. (2009) The E2F functional analogue SBF recruits the Rpd3(L) HDAC, via Whi5 and Stb1, and the FACT chromatin reorganizer, to yeast G1 cyclin promoters. EMBO J 28(21):3378-89 |
Bi E and Park HO (2012) Cell polarization and cytokinesis in budding yeast. Genetics 191(2):347-87 |
Wang X, et al. (2011) Nucleosomes and the accessibility problem. Trends Genet 27(12):487-92 |
Enserink JM and Kolodner RD (2012) What makes the engine hum: Rad6, a cell cycle supercharger. Cell Cycle 11(2):249-52 |
Ear PH and Michnick SW (2009) A general life-death selection strategy for dissecting protein functions. Nat Methods 6(11):813-6 |
Schulze JM, et al. (2009) Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation. Mol Cell 35(5):626-41 |
Baetz K and Andrews B (1999) Regulation of cell cycle transcription factor Swi4 through auto-inhibition of DNA binding. Mol Cell Biol 19(10):6729-41 |
Aucher W, et al. (2010) A Strategy for Interaction Site Prediction between Phospho-binding Modules and their Partners Identified from Proteomic Data. Mol Cell Proteomics 9(12):2745-59 |
Luscombe NM, et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006):308-12 |
Costanzo M, et al. (2004) CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast. Cell 117(7):899-913 |
Ofir A, et al. (2012) Role of a Candida albicans Nrm1/Whi5 homologue in cell cycle gene expression and DNA replication stress response. Mol Microbiol 84(4):778-94 |
Arino J (2010) Integrative Responses to High pH Stress in S. cerevisiae. OMICS 14(5):517-23 |
Moriya H, et al. (2006) In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae. PLoS Genet 2(7):e111 |
Bahler J (2005) Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69-94 |
Verdicchio MP and Kim S (2011) Identifying targets for intervention by analyzing basins of attraction. Pac Symp Biocomput ():350-61 |
de Bruin RA, et al. (2006) Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback. Mol Cell 23(4):483-96 |
Galdieri L, et al. (2014) Protein acetylation and acetyl coenzyme a metabolism in budding yeast. Eukaryot Cell 13(12):1472-83 |
Jendretzki A, et al. (2011) How do I begin? Sensing extracellular stress to maintain yeast cell wall integrity. Eur J Cell Biol 90(9):740-4 |