TORC1 regulates the transcriptional response to glucose and developmental cycle via the Tap42-Sit4-Rrd1/2 pathway in Saccharomyces cerevisiae

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

Livak, K. J., & Schmittgen, T. D. (2001) · Methods · doi:10.1006/meth.2001.1262 · Cited by 180,860 · see citing works

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works

HISAT: a fast spliced aligner with low memory requirements

Kim, D., Langmead, B., & Salzberg, S. L. (2015) · Nature Methods · doi:10.1038/nmeth.3317 · Cited by 24,112 · see citing works

HTSeq—a Python framework to work with high-throughput sequencing data

Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464 · see citing works

Repertoires of Autophagy in the Pathogenesis of Ocular Diseases

Li, Y., Jiang, Q. L., Cao, G.-F., Yao, J., & Yan, B. (2015) · Cellular Physiology and Biochemistry · doi:10.1159/000373980 · Cited by 16,351 · see citing works

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108 · see citing works

REVIGO summarizes and visualizes long lists of gene ontology terms

Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021800 · Cited by 6,264 · see citing works

mTOR: from growth signal integration to cancer, diabetes and ageing

Zoncu, R., Efeyan, A., & Sabatini, D. M. (2011) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3025 · Cited by 3,941 · see citing works

Mutation of the mouse klotho gene leads to a syndrome resembling ageing

Kuro-o, M., Matsumura, Y., Aizawa, H., Kawaguchi, H., Suga, T., Utsugi, T., Ohyama, Y., Kurabayashi, M., Kaname, T., Kume, E., et al. (1997) · Nature · doi:10.1038/36285 · Cited by 3,837 · see citing works

Targets for Cell Cycle Arrest by the Immunosuppressant Rapamycin in Yeast

Heitman, J., Movva, N. R., & Hall, M. N. (1991) · Science · doi:10.1126/science.1715094 · Cited by 2,010 · see citing works

Regulation of TORC1 by Rag GTPases in nutrient response

Kim, E., Goraksha-Hicks, P., Li, L., Neufeld, T. P., & Guan, K.-L. (2008) · Nature Cell Biology · doi:10.1038/ncb1753 · Cited by 1,349 · see citing works

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

Zhao, S., Fung‐Leung, W., Bittner, A., Ngo, K., & Liu, X. (2014) · PLoS ONE · doi:10.1371/journal.pone.0078644 · Cited by 945 · see citing works

Target of Rapamycin (TOR) in Nutrient Signaling and Growth Control

Loewith, R., & Hall, M. (2011) · Genetics · doi:10.1534/genetics.111.133363 · Cited by 894 · see citing works

Glucose–TOR signalling reprograms the transcriptome and activates meristems

Xiong, Y., McCormack, M., Li, L., Hall, Q., Xiang, C., & Sheen, J. (2013) · Nature · doi:10.1038/nature12030 · Cited by 811 · see citing works

Sch9 Is a Major Target of TORC1 in Saccharomyces cerevisiae

Urban, J., Soulard, A., Huber, A., Lippman, S., Mukhopadhyay, D., Deloche, O., Wanke, V., Anrather, D., Ammerer, G., Riezman, H., et al. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.04.020 · Cited by 798 · see citing works

Nutritional Control of Growth and Development in Yeast

Broach, J. R. (2012) · Genetics · doi:10.1534/genetics.111.135731 · Cited by 710 · see citing works

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

Breitkreutz, A., Choi, H., Sharom, J. R., Boucher, L., Neduva, V., Larsen, B. G., Lin, Z., Breitkreutz, B., Stark, C., Liu, G., et al. (2010) · Science · doi:10.1126/science.1176495 · Cited by 686 · see citing works

Nutrients, via the Tor proteins, stimulate the association of Tap42 with type 2A phosphatases.Preprint

Como, C. J. D., & Arndt, K. T. (1996) · Genes & Development · doi:10.1101/gad.10.15.1904 · Cited by 494 · see citing works

The Vam6 GEF Controls TORC1 by Activating the EGO Complex

Binda, M., Gulli, M., Bonfils, G., Panchaud, N., Urban, J., Sturgill, T. W., Loewith, R., & VIRGILIO, C. D. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.06.033 · Cited by 432 · see citing works

DNA sequence and characterization of the S. cerevisiae gene encoding adenylate cyclase

Kataoka, T., Broek, D., & Wigler, M. H. (1985) · Cell · doi:10.1016/0092-8674(85)90179-5 · Cited by 425 · see citing works

Leucyl-tRNA Synthetase Controls TORC1 via the EGO Complex

Bonfils, G., Jaquenoud, M., Bontron, S., Ostrowicz, C. W., Ungermann, C., & VIRGILIO, C. D. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.02.009 · Cited by 338 · see citing works

GPR1 encodes a putative G protein‐coupled receptor that associates with the Gpa2p Gα subunit and functions in a Ras‐independent pathway

Xue, Y., Batlle, M., & Hirsch, J. P. (1998) · The EMBO Journal · doi:10.1093/emboj/17.7.1996 · Cited by 306 · see citing works

Translational control by TOR and TAP42 through dephosphorylation of eIF2α kinase GCN2Preprint

Cherkasova, V. A., & Hinnebusch, A. G. (2003) · Genes & Development · doi:10.1101/gad.1069003 · Cited by 290 · see citing works

Amino Acid Deprivation Inhibits TORC1 Through a GTPase-Activating Protein Complex for the Rag Family GTPase Gtr1

Panchaud, N., Gulli, M., & VIRGILIO, C. D. (2013) · Science Signaling · doi:10.1126/scisignal.2004112 · Cited by 290 · see citing works

The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates

Soulard, A., Cremonesi, A., Moes, S., Schütz, F., Jenö, P., & Hall, M. N. (2010) · Molecular Biology of the Cell · doi:10.1091/mbc.e10-03-0182 · Cited by 260 · see citing works

Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins

Shamji, A. F., Kuruvilla, F. G., & Schreiber, S. L. (2000) · Current Biology · doi:10.1016/s0960-9822(00)00866-6 · Cited by 234 · see citing works

A Basic Helix-Loop-Helix–Leucine Zipper Transcription Complex in Yeast Functions in a Signaling Pathway from Mitochondria to the Nucleus

Jia, Y., Rothermel, B., Thornton, J., & Butow, R. A. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.3.1110 · Cited by 219 · see citing works

Glucose regulates transcription in yeast through a network of signaling pathways

Zaman, S., Lippman, S. I., Schneper, L. M., Slonim, N., & Broach, J. R. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.2 · Cited by 217 · see citing works

The Function of Ras Genes in Saccharomyces Cerevisiae

Broach, J. R., & Deschenes, R. J. (1990) · Advances in cancer research · doi:10.1016/s0065-230x(08)60809-x · Cited by 213 · see citing works

Gpa2p, a G-protein α-Subunit, Regulates Growth and Pseudohyphal Development in Saccharomyces cerevisiae via a cAMP-dependent Mechanism

Kübler, E., Mösch, H., Rupp, S., & Lisanti, M. P. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.33.20321 · Cited by 193 · see citing works

Multiple Roles of Tap42 in Mediating Rapamycin-Induced Transcriptional Changes in Yeast

Düvel, K., Santhanam, A. N., Garrett, S., Schneper, L. M., & Broach, J. R. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00228-4 · Cited by 164 · see citing works

Amino Acids Stimulate TORC1 through Lst4-Lst7, a GTPase-Activating Protein Complex for the Rag Family GTPase Gtr2

Péli-Gulli, M.-P., Sardu, A., Panchaud, N., Raucci, S., & De Virgilio, C. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.08.059 · Cited by 157 · see citing works

Ras and Gpa2 Mediate One Branch of a Redundant Glucose Signaling Pathway in Yeast

Wāng, Y., Pierce, M. M., Schneper, L. M., Guldal, C. G., Zhang, X., Tavazoie, S., & Broach, J. R. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020128 · Cited by 153 · see citing works

A Genome-Wide Screen for Regulators of TORC1 in Response to Amino Acid Starvation Reveals a Conserved Npr2/3 Complex

Neklesa, T. K., & Davis, R. W. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000515 · Cited by 151 · see citing works

Cytosolic pH Regulates Cell Growth through Distinct GTPases, Arf1 and Gtr1, to Promote Ras/PKA and TORC1 Activity

Dechant, R. C., Saad, S., Ibáñez, A. J., & Peter, M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.002 · Cited by 135 · see citing works

State Transitions in the TORC1 Signaling Pathway and Information Processing in Saccharomyces cerevisiae

Hallett, J. E. H., Luo, X., & Capaldi, A. P. (2014) · Genetics · doi:10.1534/genetics.114.168369 · Cited by 128 · see citing works

Yeast spore germination: a requirement for Ras protein activity during re‐entry into the cell cycle

Herman, P. K., & Rine, J. (1997) · The EMBO Journal · doi:10.1093/emboj/16.20.6171 · Cited by 122 · see citing works

TORC1 organized in inhibited domains (TOROIDs) regulate TORC1 activity

Prouteau, M., Desfosses, A., Sieben, C., Bourgoint, C., Mozaffari, N. L., Demurtas, D., MITRA, A. K., Guichard, P., Manley, S., & Loewith, R. (2017) · Nature · doi:10.1038/nature24021 · Cited by 117 · see citing works

Snf1/AMPK promotes the formation of Kog1/Raptor-bodies to increase the activation threshold of TORC1 in budding yeast

Hallett, J. E. H., Luo, X., & Capaldi, A. P. (2015) · eLife · doi:10.7554/elife.09181 · Cited by 106 · see citing works

The Yeast GATA Factor Gat1 Occupies a Central Position in Nitrogen Catabolite Repression-Sensitive Gene Activation

Georis, I., Feller, A., Vierendeels, F., & Dubois, E. L. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.00399-09 · Cited by 85 · see citing works

Conserved regulators of Rag GTPases orchestrate amino acid-dependent TORC1 signaling

Powis, K., & Virgilio, C. D. (2016) · Cell Discovery · doi:10.1038/celldisc.2015.49 · Cited by 83 · see citing works

Integrated TORC1 and PKA signaling control the temporal activation of glucose-induced gene expression in yeast

Kunkel, J., Luo, X., & Capaldi, A. P. (2019) · Nature Communications · doi:10.1038/s41467-019-11540-y · Cited by 79 · see citing works

Spore germination in Saccharomyces cerevisiae: global gene expression patterns and cell cycle landmarks

Joseph-Strauss, D., Zenvirth, D., Simchen, G., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-11-r241 · Cited by 65 · see citing works

Cytoplasmic Compartmentation of Gln3 during Nitrogen Catabolite Repression and the Mechanism of Its Nuclear Localization during Carbon Starvation in Saccharomyces cerevisiae

Cox, K. H., Tate, J. J., & Cooper, T. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m204879200 · Cited by 63 · see citing works

Protein Kinase A, TOR, and Glucose Transport Control the Response to Nutrient Repletion in Saccharomyces cerevisiae

Slattery, M. G., Liko, D., & Heideman, W. (2007) · Eukaryotic Cell · doi:10.1128/ec.00334-07 · Cited by 62 · see citing works

Antagonistic Interactions Between the cAMP-Dependent Protein Kinase and Tor Signaling Pathways Modulate Cell Growth inSaccharomyces cerevisiae

Ramachandran, V., & Herman, P. K. (2010) · Genetics · doi:10.1534/genetics.110.123372 · Cited by 59 · see citing works

INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division

Gowans, G. J., Schep, A. N., Wong, K. M., King, D. A., Greenleaf, W. J., & Morrison, A. J. (2018) · Cell Reports · doi:10.1016/j.celrep.2017.12.079 · Cited by 49 · see citing works

The Yeast Phosphotyrosyl Phosphatase Activator Is Part of the Tap42–Phosphatase Complexes

Zheng, Y., & Jiang, Y. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-09-0797 · Cited by 45 · see citing works

Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response

Geijer, C., Pirkov, I., Vongsangnak, W., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-554 · Cited by 31 · see citing works

Nitrogen Starvation and TorC1 Inhibition Differentially Affect Nuclear Localization of the Gln3 and Gat1 Transcription Factors Through the Rare Glutamine tRNACUG in Saccharomyces cerevisiae

Tate, J. J., Rai, R., & Cooper, T. (2014) · Genetics · doi:10.1534/genetics.114.173831 · Cited by 20 · see citing works

Divergent mitochondrial responses and metabolic signal pathways secure the azole resistance in Crabtree-positive and negative <i>Candida</i> species

Zhou, M., Peng, J., Ren, K., Yu, Y., Li, D., She, X., & Liu, W. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.04042-23 · Cited by 13 · see citing works

Evolution, heterologous expression of CAZymes and gene deletion in "Saccharomyces cerevisiae" for 2G-ethanol

Lopes, A. M. M. (2020) · doi:10.47749/t/unicamp.2020.1237698

Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-κB

Haustead, D. J., Stevenson, A. W., Saxena, V., Marriage, F., Firth, M. J., Silla, R. C., Martin, L., Adcroft, K. F., Rea, S. M., Day, P. J., et al. (2016) · Scientific Reports · doi:10.1038/srep26846 · Cited by 59 · see citing works

Physical and biochemical properties of freeze-tolerant mutants of a yeast Saccharomyces cerevisiae

Matsutani, K., Fukuda, Y., Murata, K., et al. (1990) · Journal of Fermentation and Bioengineering · doi:10.1016/0922-338x(90)90063-3 · Cited by 15 · see citing works

Adaptation mechanism of yeast to extreme environments: Construction of salt-tolerance mutants of the yeast Saccharomyces cerevisiae

Matsutani, K., Fukuda, Y., Murata, K., et al. (1992) · Journal of Fermentation and Bioengineering · doi:10.1016/0922-338x(92)90166-r · Cited by 16 · see citing works

Total Lipid Extraction from Baker's yeast (Saccharomyces cerevisiae) v2Preprint

Olayide, I., & Rieth, M. D. (2022) · doi:10.17504/protocols.io.b4h8qt9w