76. Hsieh WC, Sutter BM, Ruess H, Barnes SD, Malladi VS, Tu BP. Glucose starvation induces a switch in the histone acetylome for activation of gluconeogenic and fat metabolism genes. Mol Cell. 2022 Jan 6;82:60-74.

75. Xue J, Han Y, Baniasadi H, Zeng W, Pei J, Grishin NV, Wang J, Tu BP, Jiang Y. TMEM120A is a coenzyme A-binding membrane protein with structural similarities to ELOVL fatty acid elongase. Elife. 2021 Aug 10;10:e71220.

74. Scarborough AM, Flaherty JN, Hunter OV, Liu K, Kumar A, Xing C, Tu BP, Conrad NK. SAM homeostasis is regulated by CFIm-mediated splicing of MAT2A. Elife. 2021 May 5;10:e64930.

73. Kato M, Tu BP, McKnight SL. Redox-mediated regulation of low complexity domain self-association. Curr Opin Genet Dev. 2021 Apr;67:111-118.

72. Liu K, Santos D, Hussmann J, Sutter BM, Wang Y, Weissman JS, Tu BP. Regulation of translation by methylation multiplicity of 18S rRNA. Cell Rep. 2021 Mar 9;34(10):108825.

71. Liu K, Sutter BM, Tu BP. Autophagy sustains glutamate and aspartate synthesis in Saccharomyces cerevisiae during nitrogen starvation. Nat Commun. 2021 Jan 4;12(1):57. doi: 10.1038/s41467-020-20253-6.

70. Lin Y, Zhou X, Kato M, Liu D, Ghaemmaghami S, Tu BP, McKnight SL. Redox-mediated regulation of an evolutionarily conserved cross-β structure formed by the TDP43 low complexity domain. Proc Natl Acad Sci USA. 2020 Nov 17;117(46):28727-28734.

69. Zeinert RD, Baniasadi H, Tu BP, Chien P. The Lon Protease Links Nucleotide Metabolism with Proteotoxic Stress. Mol Cell. 2020 Sep 3;79(5):758-767.e6.

68. Haws SA, Yu D, Ye C, Wille CK, Nguyen LC, Krautkramer KA, Tomasiewicz JL, Yang SE, Miller BR, Liu WH, Igarashi K, Sridharan R, Tu BP, Cryns VL, Lamming DW, Denu JM. Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence. Mol Cell. 2020 Apr 16;78(2):210-223.e8.

67. Agmon N, Temple J, Tang Z, Schraink T, Baron M, Chen J, Mita P, Martin JA, Tu BP, Yanai I, Fenyö D, Boeke JD. Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast. Nucleic Acids Res. 2020 Jan 10;48(1):486-499.

66. Weiss CA, Hoberg JA, Liu K, Tu BP, Winkler WC. Single-cell microscopy reveals that levels of cyclic di-GMP vary among Bacillus subtilis subpopulations. J Bacteriol. 2019 Jul 24;201(16). pii: e00247-19.

65. Kato M, Yang YS, Sutter BM, Wang Y, McKnight SL, Tu BP. Redox state controls phase separation of the yeast ataxin-2 protein via reversible oxidation of its methionine-rich low complexity domain. Cell. 2019 Apr 18;177(3):711-721.

64. Yang YS, Kato M, Wu X, Litsios A, Sutter BM, Wang Y, Hsu CH, Wood NE, Lemoff A, Mirzaei H, Heinemann M, Tu BP. Yeast ataxin-2 forms an intracellular condensate required for the inhibition of TORC1 signaling during respiratory growth. Cell. 2019 Apr 18;177(3):697-710.

63. Santos DA, Shi L, Tu BP, Weissman JS. Cycloheximide can distort measurements of mRNA levels and translation efficiency. Nucleic Acids Res.  2019 Jun 4;47(10):4974-4985.

62. Ye C, Sutter BM, Wang Y, Zhao X, Yu Y, Tu BP. Demethylation of the protein phosphatase PP2A promotes demethylation of histones to enable their function as a methyl group sink. Mol Cell. 2019 Mar 21;73(6):1115-1126.

61. Orr MW, Weiss CA, Severin GB, Turdiev H, Kim SK, Turdiev A, Liu K, Tu BP, Waters CM, Winkler WC, Lee VT. A subset of exoribonucleases serve as degradative enzymes for pGpG in c-di-GMP signaling. J Bacteriol. 2018 Nov 26;200(24). pii: e00300-18.

60. Huang Z, Zhang M, Plec AA, Estill SJ, Cai L, Repa JJ, McKnight SL, Tu BP. ACSS2 promotes systemic fat storage and utilization through selective regulation of genes involved in lipid metabolism. Proc Natl Acad Sci USA. 2018 Oct 2;115(40):E9499-9506.  

59. Ye C, Tu BP. Sink into the epigenome: histones as repositories that influence cellular metabolism. Trends Endocrinol Metab. 2018 Sep; 29(9):626-637.

58. Dutchak PA, Estill SJ, Plec AA, Zhao X, Yang C, Chen J, Ko B, Deberardinis RJ, Yu Y, Tu BP. Loss of a negative regulator of mTORC1 induces aerobic glycolysis and altered fibre composition in skeletal muscle, Cell Rep. 2018 May 15;23(7):1907-1914. 

57. Walsh CT, Tu BP, Tang Y. Eight kinetically stable but thermodynamically activated molecules that power cell metabolism. Chem Rev. 2018 Feb 28; 118(4): 1460-1494.

56. Chen J, Sutter BM, Shi L, Tu BP. GATOR1 regulates nitrogenic cataplerotic reactions of the mitochondrial TCA cycle. Nat Chem Biol. 2017 Nov;13(11):1179-1186.

55. Pendleton KE, Chen B, Liu K, Hunter OV, Xie Y, Tu BP, Conrad NK. The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell. 2017 May 18;169(5):824-835.

54. Ye C, Sutter BM, Wang Y, Kuang Z, Tu BP. A metabolic function for phospholipid and histone methylation. Mol Cell. 2017 Apr 20;66(2):180-193.

53. Agmon N, Tang Z, Yang K, Sutter B, Ikushima S, Cai Y, Caravelli K, Martin JA, Sun X, Choi WJ, Zhang A, Stracquadanio G, Hao H, Tu BP, Fenyo D, Bader JS, Boeke JD. Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 2017 Feb 21;114(8):E1470-E1479.

52. Lee CD, Tu BP. Metabolic influences on RNA biology and translation. Crit Rev Biochem Mol Biol. 2017 Apr;52(2):176-184.

51. Sato S, Jung H, Nakagawa T, Pawlosky R, Takeshima T, Lee WR, Sakiyama H, Laxman S, Wynn RM, Tu BP, MacMillan JB, De Brabander JK, Veech RL, Uyeda K. Metabolite regulation of nuclear localization of carbohydrate-response element-binding protein (ChREBP): role of AMP as an allosteric inhibitor. J Biol Chem. 2016 May 13;291(20):10515-27.

50. Wang GZ, Hickey SL, Shi L, Huang HC, Nakashe P, Koike N, Tu BP, Takahashi JS, Konopka G. Cycling transcriptional networks optimize energy utilization on a genome scale. Cell Rep. 2015 Dec 1;13(9):1868-80.

49. Savir Y, Tu BP, Springer M. Competitive inhibition can linearize dose-response and generate a linear rectifier. Cell Syst. 2015 Sep 23;1(3):238-245.

48. Dutchak PA, Laxman S, Estill SJ, Wang C, Wang Y, Wang Y, Bulut GB, Gao J, Huang LJ, Tu BP. Regulation of hematopoiesis and methionine homeostasis by mTORC1 inhibitor NPRL2. Cell Rep. 2015 Jul 21;12:371-9. 

47. Huang Z, Cai L, Tu BP. Dietary control of chromatin. Curr Opin Cell Biol. 2015 Jun 18;34:69-74.

46. Lee CD, Tu BP. Glucose-regulated phosphorylation of the PUF protein Puf3 regulates the translational fate of its bound mRNAs and association with RNA granules. Cell Rep. 2015 Jun 16;11:1638-50.

45. Li Q, Leija C, Rijo-Ferreira F, Chen J, Cestari I, Stuart K, Tu BP, Phillips MA. GMP synthase is essential for viability and infectivity of Trypanosoma brucei despite a redundant purine salvage pathway. Mol Microbiol. 2015 Sep;97(5):1006-20.

44. Shi L, Tu BP. Acetyl-CoA and the regulation of metabolism: mechanisms and consequences. Curr Opin Cell Biol. 2015 Feb 19;33C:125-131.

43. Mashimo T, Pichumani K, Vemireddy V, Hatanpaa KJ, Singh DK, Sirasanagandla S, Nannepaga S, Piccirillo SG, Kovacs Z, Foong C, Huang Z, Barnett S, Mickey BE, DeBerardinis RJ, Tu BP, Maher EA, Bachoo RM. Acetate is a bioenergetic substrate for human glioblastoma and brain metastases. Cell. 2014;159:1603-14.

42. Comerford SA, Huang Z, Du X, Wang Y, Cai L, Witkiewicz A, Walters H, Tantawy MN, Fu A, Manning HC, Horton JD, Hammer RE, McKnight SL*, Tu BP*. Acetate dependence of tumors. Cell. 2014;159:1591-602.

41. Laxman S, Sutter BM, Shi L, Tu BP. Npr2 inhibits TORC1 to prevent inappropriate utilization of glutamine for biosynthesis of nitrogen-containing metabolites. Sci Signal. 2014;7:ra120.

40. Kuang Z, Cai L, Zhang X, Ji H, Tu BP*, Boeke JD*. High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat Struct Mol Biol. 2014;21:854-63.

39. An Z, Tassa A, Thomas C, Zhong R, Xiao G, Fotedar R, Tu BP, Klionsky DJ, Levine B. Autophagy is required for G1/G0 quiescence in response to nitrogen starvation in Saccharomyces cerevisiae. Autophagy. 2014;10:1702-11.

38. Shi L, Tu BP. Protein acetylation as a means to regulate protein function in tune with metabolic state. Biochem Soc Trans. 2014;42:1037-1042.

37. Laxman S, Tu BP, McKnight SL. Concerted effort: oscillations in global gene expression during nematode development. Mol Cell. 2014;53:363-4.

36. Laxman S, Sutter BM, Tu BP. Methionine is a signal of amino acid sufficiency that inhibits autophagy through the methylation of PP2A. Autophagy. 2014;10:386-7.

35. Cai L, McCormick MA, Kennedy BK, Tu BP. Integration of multiple nutrient cues and regulation of lifespan by ribosomal transcription factor Ifh1p. Cell Rep. 2013;4:1063-71.

34. Laxman S, Sutter BM, Wu X, Kumar S, Guo X, Trudgian DC, Mirzaei H, Tu BP. Sulfur amino acids regulate translational capacity and metabolic homeostasis through modulation of tRNA thiolation. Cell. 2013;154:416-29.

33. Sutter BM, Wu X, Laxman S, Tu BP. Methionine inhibits autophagy and promotes growth by inducing the SAM-responsive methylation of PP2A. Cell. 2013;154:403-15.

32. Tso SC, Qi X, Gui WJ, Chuang JL, Morlock LK, Wallace AL, Ahmed K, Laxman S, Campeau PM, Lee BH, Hutson SM, Tu BP, Williams NS, Tambar UK, Wynn RM, Chuang DT. Structure-based design of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase. Proc Natl Acad Sci USA. 2013;110:9728-33. 

31. Xiao Y, Nguyen S, Kim SH, Volkov OA, Tu BP, Phillips MA. Product feedback regulation implicated in translational control of the Trypanosoma brucei S-adenosylmethionine decarboxylase regulatory subunit prozyme. Mol Microbiol. 2013;88:846-61.

30. Shi L, Tu BP. Acetyl-CoA induces transcription of the key G1 cyclin CLN3 to promote entry into the cell division cycle in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 2013;110:7318-23.

29. Kriel A, Bittner AN, Kim SH, Liu K, Tehranchi AK, Zou WY, Rendon S, Chen R, Tu BP, Wang JD. Direct regulation of GTP homeostasis by (p)ppGpp: a critical component of viability and stress resistance. Mol Cell. 2012;48:231-41.

28. Chen LY, Zhang Y, Zhang Q, Li H, Luo Z, Fang H, Kim SH, Qin L, Yotnda P, Xu J, Tu BP, Bai Y, Sonyang Z. Mitochondrial localization of telomeric protein TIN2 links telomere regulation to metabolic control. Mol Cell. 2012;47:839-50.  

27. Kaochar S, Tu BP. Gatekeepers of chromatin: small metabolites elicit big changes in gene expression. Trends Biochem Sci. 2012;37:477-83.

26. Cai L, Tu BP. Driving the cell cycle through metabolism. Annu Rev Cell Dev Biol. 2012;28:59-87.

25. Marin-Valencia I, Yang C, Mashimo T, Cho S, Baek H, Yang XL, Rajagopalan KN, Maddie M, Vemireddy V, Cai L, Good L, Tu BP, Hatanpaa K, Mickey BE, Mates JM, Pascual JM, Maher EA, Malloy CR, DeBerardinis RJ, Bachoo RM. Analysis of tumor metabolism reveals mitochondrial glucose oxidation in genetically diverse human glioblastomas in the mouse brain in vivo. Cell Metabolism. 2012;15:827-37.

24. Zhang L, Das P, Schmolke M, Manicassamy B, Wang Y, Deng X, Cai L, Tu BP, Forst CV, Roth MG, Levy DE, García-Sastre A, de Brabander J, Phillips MA, Fontoura BM. Inhibition of pyrimidine synthesis reverses viral virulence factor-mediated block of mRNA nuclear export. J Cell Biol. 2012;196:315-26.

23. Laxman S, Tu BP. Multiple TORC1-associated proteins regulate nitrogen starvation-dependent cellular differentiation in Saccharomyces cerevisiae. PLoS One. 2011;6:e26081.

22. Wu X, Tu BP. Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the absence of nitrogen starvation. Mol Biol Cell. 2011;22:4124-33.

21. Cai L, Tu BP. On acetyl-CoA as a gauge of cellular metabolic state. Cold Spring Harb Symp Quant Biol. 2011;76:195-202.

20. Cai L, Tu BP. Acetyl-CoA drives the transcriptional growth program in yeast. Cell Cycle. 2011;10:3045-6.

19. Cai L, Sutter BM, Li B, Tu BP. Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol Cell. 2011;42:426-37.

18. Humston EM, Dombek KM, Tu BP, Young ET, Synovec RE. Toward a global analysis of metabolites in regulatory mutants of yeast. Anal Bioanal Chem. 2011;401:2387-402.

17. Laxman S, Tu BP. Systems approaches for the study of metabolic cycles in yeast. Curr Opin Genet Dev. 2010; 20:599-604.

16. Laxman S, Sutter BM, Tu BP. Behavior of a metabolic cycling yeast population at the single cell level as visualized using fluorescent reporters. PLoS One. 2010;5:e12595. 

15. Shi L, Sutter BM, Ye X, Tu BP. Trehalose is a key determinant of the quiescent metabolic state that fuels cell cycle progression upon return to growth. Mol Biol Cell. 2010;21:1982-90.

14. Tu BP. Ultradian metabolic cycles in yeast. Methods Enzymol. 2010;470:857-66.

**************************

13. Tu BP*, McKnight SL*. Evidence of carbon monoxide-mediated phase advancement of the yeast metabolic cycle. Proc Natl Acad Sci USA. 2009;106:14293-6.

12. Mohler RE, Tu BP, Dombek KM, Hoggard JC, Young ET, Synovec RE. Identification and evaluation of cycling metabolites in two-dimensional comprehensive gas chromatography-time-of-flight mass spectrometry data. J Chromatogr A. 2008;1186:401-11.

11. Tu BP, McKnight SL. The yeast metabolic cycle: insights into the life of a eukaryotic cell. Cold Spring Harb Symp Quant Biol. 2007;72:339-43.

10. Tu BP*, Mohler RE, Liu JC, Dombek KM, Young ET, Synovec RE, McKnight SL*. Cyclic changes in metabolic state during the life of a yeast cell. Proc Natl Acad Sci USA. 2007;104:16886-91.

9.  Rowicka M, Kudlicki A, Tu BP, Otwinowski Z. High-resolution timing of cell cycle-regulated gene expression. Proc Natl Acad Sci USA. 2007;104:16892-7.

8.  Chen Z, Odstrcil EA, Tu BP, McKnight SL. Restriction of nuclear DNA replication to the reductive phase of the metabolic cycle protects genome integrity. Science. 2007;316:1916-9. 

7.  Tu BP, McKnight SL. Metabolic cycles as an underlying basis of biological oscillations. Nat Rev Mol Cell Biol. 2006;7:696-701.

6.  Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: Temporal     compartmentalization of cellular processes. Science. 2005;310:1152-8.

5.  Tu BP, Weissman JS. Oxidative protein folding in eukaryotes: mechanisms and consequences. J Cell Biol. 2004;164:341-6.

4.  Tu BP, Weissman JS. The FAD and O2-dependent reaction cycle of Ero1-mediated oxidative protein folding in the endoplasmic reticulum. Mol Cell. 2002;10:983-94.

3.  Tu BP, Ho-Schleyer SC, Travers KJ, Weissman JS. Biochemical basis of oxidative protein folding in the endoplasmic reticulum. Science. 2000;290:1571-4.

2.  Tu BP, Wang JC. Protein footprinting at cysteines: probing ATP-modulated contacts in cysteine-substitution mutants of yeast DNA topoisomerase II. Proc Natl Acad Sci USA. 1999;96:4862-7.

1.  Tse B, Blazey CM, Tu B, Balkovec. Determination of the absolute stereochemistry of (-)-galbonolide A. J Org Chem. 1997;62:3236-41.