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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
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75 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
2024 Johnson Z, Wang Y, Sutter BM, Tu BP. Evidence for a hydrogen sulfide-sensing E3 ligase in yeast. Genetics. PMID 39378345 DOI: 10.1093/genetics/iyae154  0.305
2021 Liu K, Santos DA, Hussmann JA, Wang Y, Sutter BM, Weissman JS, Tu BP. Regulation of translation by methylation multiplicity of 18S rRNA. Cell Reports. 34: 108825. PMID 33691096 DOI: 10.1016/j.celrep.2021.108825  0.511
2021 Kato M, Tu BP, McKnight SL. Redox-mediated regulation of low complexity domain self-association. Current Opinion in Genetics & Development. 67: 111-118. PMID 33454579 DOI: 10.1016/j.gde.2020.12.006  0.539
2021 Liu K, Sutter BM, Tu BP. Autophagy sustains glutamate and aspartate synthesis in Saccharomyces cerevisiae during nitrogen starvation. Nature Communications. 12: 57. PMID 33397945 DOI: 10.1038/s41467-020-20253-6  0.313
2020 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 33144500 DOI: 10.1073/pnas.2012216117  0.717
2020 Zeinert RD, Baniasadi H, Tu BP, Chien P. The Lon Protease Links Nucleotide Metabolism with Proteotoxic Stress. Molecular Cell. PMID 32755596 DOI: 10.1016/J.Molcel.2020.07.011  0.591
2020 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, et al. Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence. Molecular Cell. PMID 32208170 DOI: 10.1016/J.Molcel.2020.03.004  0.36
2019 Cable J, Finley L, Tu BP, Patti GJ, Oliver TG, Vardhana S, Mana M, Ericksen R, Khare S, DeBerardinis R, Stockwell BR, Edinger A, Haigis M, Kaelin W. Leveraging insights into cancer metabolism-a symposium report. Annals of the New York Academy of Sciences. PMID 31792987 DOI: 10.1111/Nyas.14274  0.393
2019 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 Research. PMID 31745563 DOI: 10.1093/Nar/Gkz1098  0.382
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  0.314
2019 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. PMID 30982603 DOI: 10.1016/J.Cell.2019.02.044  0.603
2019 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. PMID 30982600 DOI: 10.1016/J.Cell.2019.02.043  0.389
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  0.533
2019 Ye C, Sutter BM, Wang Y, Kuang Z, 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. Molecular Cell. PMID 30772176 DOI: 10.1016/J.Molcel.2019.01.012  0.347
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  0.331
2018 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 30228117 DOI: 10.1073/Pnas.1806635115  0.602
2018 Ye C, Tu BP. Sink into the Epigenome: Histones as Repositories That Influence Cellular Metabolism. Trends in Endocrinology and Metabolism: Tem. PMID 30001904 DOI: 10.1016/J.Tem.2018.06.002  0.414
2018 Walsh CT, Tu BP, Tang Y. Correction to: Eight Kinetically Stable but Thermodynamically Activated Molecules that Power Cell Metabolism. Chemical Reviews. PMID 29620360 DOI: 10.1021/Acs.Chemrev.8B00181  0.327
2017 Walsh CT, Tu BP, Tang Y. Eight Kinetically Stable but Thermodynamically Activated Molecules that Power Cell Metabolism. Chemical Reviews. PMID 29272116 DOI: 10.1021/Acs.Chemrev.7B00510  0.391
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  0.399
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  0.368
2017 Ye C, Sutter BM, Wang Y, Kuang Z, Tu BP. A Metabolic Function for Phospholipid and Histone Methylation. Molecular Cell. PMID 28366644 DOI: 10.1016/J.Molcel.2017.02.026  0.343
2017 Lee CD, Tu BP. Metabolic influences on RNA biology and translation. Critical Reviews in Biochemistry and Molecular Biology. 1-9. PMID 28152618 DOI: 10.1080/10409238.2017.1283294  0.38
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  0.619
2016 Dutchak PA, Terpack S, Tu BP. Abstract B08: Altering cellular differentiation and energy metabolism by the mTORC1 inhibitor NPRL2 Molecular Cancer Research. 14. DOI: 10.1158/1557-3125.Devbiolca15-B08  0.391
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  0.365
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  0.637
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  0.41
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  0.361
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  0.37
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  0.458
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  0.593
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  0.675
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  0.401
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  0.333
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  0.431
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  0.671
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  0.662
2014 Tu BP, VanHook AM. Science Signaling Podcast: 16 December 2014 Science Signaling. 7. DOI: 10.1126/Scisignal.Aaa4034  0.405
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  0.414
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  0.674
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  0.634
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  0.594
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  0.412
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  0.411
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  0.462
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  0.399
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  0.418
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  0.35
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  0.433
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  0.314
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. Erratum: Analysis of tumor metabolism reveals mitochondrial glucose oxidation in genetically diverse human glioblastomas in the mouse brain in vivo (Cell Metabolism (2012) 16 (394-406)) Cell Metabolism. 16. DOI: 10.1016/J.Cmet.2012.10.010  0.361
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  0.645
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  0.39
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  0.426
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  0.459
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  0.399
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  0.45
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  0.642
2010 Tu BP. Ultradian metabolic cycles in yeast. Methods in Enzymology. 470: 857-66. PMID 20946838 DOI: 10.1016/S0076-6879(10)70035-5  0.425
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  0.642
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  0.395
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  0.647
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  0.304
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  0.645
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  0.635
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  0.375
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  0.627
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  0.606
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  0.484
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  0.65
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  0.514
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  0.569
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 DOI: 10.1126/Science.290.5496.1571  0.733
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  0.31
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