Benjamin P. Tu, Ph.D. - Publications

Affiliations: 
2003 University of California, San Francisco, San Francisco, CA 
Area:
Proteomics, Protein Folding, and Prion-Based Inheritance in Disease and Normal Biology

57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Weiss CA, Hoberg JA, Liu K, Tu BP, Winkler WC. Single cell microscopy reveals that levels of cyclic di-GMP vary among subpopulations. Journal of Bacteriology. PMID 31138629 DOI: 10.1128/JB.00247-19  0.44
2019 Santos DA, Shi L, Tu BP, Weissman JS. Cycloheximide can distort measurements of mRNA levels and translation efficiency. Nucleic Acids Research. PMID 30916348 DOI: 10.1093/nar/gkz205  0.88
2018 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. Journal of Bacteriology. PMID 30249708 DOI: 10.1128/JB.00300-18  0.44
2017 Chen J, Sutter BM, Shi L, Tu BP. GATOR1 regulates nitrogenic cataplerotic reactions of the mitochondrial TCA cycle. Nature Chemical Biology. PMID 28920930 DOI: 10.1038/nchembio.2478  0.32
2017 Pendleton KE, Chen B, Liu K, Hunter OV, Xie Y, Tu BP, Conrad NK. The U6 snRNA m(6)A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention. Cell. 169: 824-835.e14. PMID 28525753 DOI: 10.1016/j.cell.2017.05.003  0.44
2016 Sato S, Jung H, Nakagawa T, Pawlosky R, Takeshima T, Lee WR, Sakiyama H, Laxman S, Wynn RM, Tu B, 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. The Journal of Biological Chemistry. PMID 26984404 DOI: 10.1074/jbc.M115.708982  0.88
2015 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 Reports. 13: 1868-1880. PMID 26655902 DOI: 10.1016/j.celrep.2015.10.043  0.88
2015 Savir Y, Tu BP, Springer M. Competitive inhibition can linearize dose-response and generate a linear rectifier. Cell Systems. 1: 238-245. PMID 26495436 DOI: 10.1016/j.cels.2015.09.001  0.88
2015 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 Reports. 12: 371-9. PMID 26166573 DOI: 10.1016/j.celrep.2015.06.042  0.88
2015 Huang Z, Cai L, Tu BP. Dietary control of chromatin. Current Opinion in Cell Biology. 34: 69-74. PMID 26094239 DOI: 10.1016/j.ceb.2015.05.004  0.88
2015 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 Reports. 11: 1638-50. PMID 26051939 DOI: 10.1016/j.celrep.2015.05.014  0.88
2015 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. Molecular Microbiology. 97: 1006-20. PMID 26043892 DOI: 10.1111/mmi.13083  0.88
2015 Shi L, Tu BP. Acetyl-CoA and the regulation of metabolism: mechanisms and consequences. Current Opinion in Cell Biology. 33: 125-31. PMID 25703630 DOI: 10.1016/j.ceb.2015.02.003  0.88
2014 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, et al. Acetate is a bioenergetic substrate for human glioblastoma and brain metastases. Cell. 159: 1603-14. PMID 25525878 DOI: 10.1016/j.cell.2014.11.025  0.88
2014 Comerford SA, Huang Z, Du X, Wang Y, Cai L, Witkiewicz AK, Walters H, Tantawy MN, Fu A, Manning HC, Horton JD, Hammer RE, McKnight SL, Tu BP. Acetate dependence of tumors. Cell. 159: 1591-602. PMID 25525877 DOI: 10.1016/j.cell.2014.11.020  0.88
2014 Laxman S, Sutter BM, Shi L, Tu BP. Npr2 inhibits TORC1 to prevent inappropriate utilization of glutamine for biosynthesis of nitrogen-containing metabolites. Science Signaling. 7: ra120. PMID 25515537 DOI: 10.1126/scisignal.2005948  0.88
2014 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. Nature Structural & Molecular Biology. 21: 854-63. PMID 25173176 DOI: 10.1038/nsmb.2881  0.88
2014 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. 10: 1702-11. PMID 25126732 DOI: 10.4161/auto.32122  0.88
2014 Shi L, Tu BP. Protein acetylation as a means to regulate protein function in tune with metabolic state. Biochemical Society Transactions. 42: 1037-42. PMID 25109999 DOI: 10.1042/BST20140135  0.88
2014 Laxman S, Tu BP, McKnight SL. Concerted effort: oscillations in global gene expression during nematode development. Molecular Cell. 53: 363-4. PMID 24507713 DOI: 10.1016/j.molcel.2014.01.023  0.88
2014 Laxman S, Sutter BM, Tu BP. Methionine is a signal of amino acid sufficiency that inhibits autophagy through the methylation of PP2A. Autophagy. 10: 386-7. PMID 24362312 DOI: 10.4161/auto.27485  0.88
2014 Tu BP, VanHook AM. Science Signaling Podcast: 16 December 2014 Science Signaling. 7. DOI: 10.1126/scisignal.aaa4034  0.88
2013 Cai L, McCormick MA, Kennedy BK, Tu BP. Integration of multiple nutrient cues and regulation of lifespan by ribosomal transcription factor Ifh1. Cell Reports. 4: 1063-71. PMID 24035395 DOI: 10.1016/j.celrep.2013.08.016  0.88
2013 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. 154: 416-29. PMID 23870129 DOI: 10.1016/j.cell.2013.06.043  0.88
2013 Sutter BM, Wu X, Laxman S, Tu BP. Methionine inhibits autophagy and promotes growth by inducing the SAM-responsive methylation of PP2A. Cell. 154: 403-15. PMID 23870128 DOI: 10.1016/j.cell.2013.06.041  0.88
2013 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, et al. Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase. Proceedings of the National Academy of Sciences of the United States of America. 110: 9728-33. PMID 23716694 DOI: 10.1073/pnas.1303220110  0.88
2013 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. Molecular Microbiology. 88: 846-61. PMID 23634831 DOI: 10.1111/mmi.12226  0.88
2013 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. Proceedings of the National Academy of Sciences of the United States of America. 110: 7318-23. PMID 23589851 DOI: 10.1073/pnas.1302490110  0.88
2012 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. Molecular Cell. 48: 231-41. PMID 22981860 DOI: 10.1016/j.molcel.2012.08.009  0.88
2012 Kaochar S, Tu BP. Gatekeepers of chromatin: Small metabolites elicit big changes in gene expression. Trends in Biochemical Sciences. 37: 477-83. PMID 22944281 DOI: 10.1016/j.tibs.2012.07.008  0.88
2012 Chen LY, Zhang Y, Zhang Q, Li H, Luo Z, Fang H, Kim SH, Qin L, Yotnda P, Xu J, Tu BP, Bai Y, Songyang Z. Mitochondrial localization of telomeric protein TIN2 links telomere regulation to metabolic control. Molecular Cell. 47: 839-50. PMID 22885005 DOI: 10.1016/j.molcel.2012.07.002  0.88
2012 Marin-Valencia I, Yang C, Mashimo T, Cho S, Baek H, Yang XL, Rajagopalan KN, Maddie M, Vemireddy V, Zhao Z, Cai L, Good L, Tu BP, Hatanpaa KJ, Mickey BE, et al. Analysis of tumor metabolism reveals mitochondrial glucose oxidation in genetically diverse human glioblastomas in the mouse brain in vivo. Cell Metabolism. 15: 827-37. PMID 22682223 DOI: 10.1016/j.cmet.2012.05.001  0.88
2012 Cai L, Tu BP. Driving the cell cycle through metabolism. Annual Review of Cell and Developmental Biology. 28: 59-87. PMID 22578140 DOI: 10.1146/annurev-cellbio-092910-154010  0.88
2012 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. The Journal of Cell Biology. 196: 315-26. PMID 22312003 DOI: 10.1083/jcb.201107058  0.88
2011 Laxman S, Tu BP. Multiple TORC1-associated proteins regulate nitrogen starvation-dependent cellular differentiation in Saccharomyces cerevisiae. Plos One. 6: e26081. PMID 22043304 DOI: 10.1371/journal.pone.0026081  0.88
2011 Wu X, Tu BP. Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the absence of nitrogen starvation. Molecular Biology of the Cell. 22: 4124-33. PMID 21900499 DOI: 10.1091/mbc.E11-06-0525  0.88
2011 Cai L, Tu BP. On acetyl-CoA as a gauge of cellular metabolic state. Cold Spring Harbor Symposia On Quantitative Biology. 76: 195-202. PMID 21900151 DOI: 10.1101/sqb.2011.76.010769  0.88
2011 Cai L, Tu BP. Acetyl-CoA drives the transcriptional growth program in yeast. Cell Cycle (Georgetown, Tex.). 10: 3045-6. PMID 21869612 DOI: 10.4161/cc.10.18.17000  0.88
2011 Cai L, Sutter BM, Li B, Tu BP. Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Molecular Cell. 42: 426-37. PMID 21596309 DOI: 10.1016/j.molcel.2011.05.004  0.88
2011 Humston EM, Dombek KM, Tu BP, Young ET, Synovec RE. Toward a global analysis of metabolites in regulatory mutants of yeast. Analytical and Bioanalytical Chemistry. 401: 2387-402. PMID 21416166 DOI: 10.1007/s00216-011-4800-2  0.88
2010 Laxman S, Tu BP. Systems approaches for the study of metabolic cycles in yeast. Current Opinion in Genetics & Development. 20: 599-604. PMID 21051220 DOI: 10.1016/j.gde.2010.09.008  0.88
2010 Tu BP. Ultradian metabolic cycles in yeast. Methods in Enzymology. 470: 857-66. PMID 20946838 DOI: 10.1016/S0076-6879(10)70035-5  0.88
2010 Laxman S, Sutter BM, Tu BP. Behavior of a metabolic cycling population at the single cell level as visualized by fluorescent gene expression reporters. Plos One. 5: e12595. PMID 20830298 DOI: 10.1371/journal.pone.0012595  0.88
2010 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. Molecular Biology of the Cell. 21: 1982-90. PMID 20427572 DOI: 10.1091/mbc.E10-01-0056  0.88
2009 Tu BP, McKnight SL. Evidence of carbon monoxide-mediated phase advancement of the yeast metabolic cycle. Proceedings of the National Academy of Sciences of the United States of America. 106: 14293-6. PMID 19706514 DOI: 10.1073/pnas.0907786106  0.88
2008 Mohler RE, Tu BP, Dombek KM, Hoggard JC, Young ET, Synovec RE. Identification and evaluation of cycling yeast metabolites in two-dimensional comprehensive gas chromatography-time-of-flight-mass spectrometry data. Journal of Chromatography. A. 1186: 401-11. PMID 18001745 DOI: 10.1016/j.chroma.2007.10.063  0.88
2007 Tu BP, McKnight SL. The yeast metabolic cycle: insights into the life of a eukaryotic cell. Cold Spring Harbor Symposia On Quantitative Biology. 72: 339-43. PMID 18419291 DOI: 10.1101/sqb.2007.72.019  0.88
2007 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. Proceedings of the National Academy of Sciences of the United States of America. 104: 16886-91. PMID 17940006 DOI: 10.1073/pnas.0708365104  0.88
2007 Rowicka M, Kudlicki A, Tu BP, Otwinowski Z. High-resolution timing of cell cycle-regulated gene expression. Proceedings of the National Academy of Sciences of the United States of America. 104: 16892-7. PMID 17827275 DOI: 10.1073/pnas.0706022104  0.88
2007 Chen Z, Odstrcil EA, Tu BP, McKnight SL. Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity. Science (New York, N.Y.). 316: 1916-9. PMID 17600220 DOI: 10.1126/science.1140958  0.88
2006 Tu BP, McKnight SL. Metabolic cycles as an underlying basis of biological oscillations. Nature Reviews. Molecular Cell Biology. 7: 696-701. PMID 16823381 DOI: 10.1038/nrm1980  0.88
2006 Tu BP, Kudlicki A, Rowicka M, McKnight SL. Let the data speak [3] Nature Reviews Molecular Cell Biology. 7: 1-2. DOI: 10.1038/nrm1980-c3  0.88
2005 Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science (New York, N.Y.). 310: 1152-8. PMID 16254148 DOI: 10.1126/science.1120499  0.88
2004 Tu BP, Weissman JS. Oxidative protein folding in eukaryotes: mechanisms and consequences. The Journal of Cell Biology. 164: 341-6. PMID 14757749 DOI: 10.1083/jcb.200311055  0.88
2002 Tu BP, Weissman JS. The FAD- and O(2)-dependent reaction cycle of Ero1-mediated oxidative protein folding in the endoplasmic reticulum. Molecular Cell. 10: 983-94. PMID 12453408 DOI: 10.1016/S1097-2765(02)00696-2  0.88
2000 Tu BP, Ho-Schleyer SC, Travers KJ, Weissman JS. Biochemical basis of oxidative protein folding in the endoplasmic reticulum. Science (New York, N.Y.). 290: 1571-4. PMID 11090354  0.88
1999 Tu BP, Wang JC. Protein footprinting at cysteines: probing ATP-modulated contacts in cysteine-substitution mutants of yeast DNA topoisomerase II. Proceedings of the National Academy of Sciences of the United States of America. 96: 4862-7. PMID 10220384 DOI: 10.1073/pnas.96.9.4862  0.88
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