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Jef Boeke, Ph.D.: Key Publications

JEF D. BOEKE, Ph.D.
Jef D. Boeke, Ph.D.

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Key Publications

Ng TM, Lenstra TL, Duggan N, Jiang S, Ceto S, Holstege FC, Dai J, Boeke JD, Biggins S. (2013). Kinetochore function and chromosome segregation rely on critical residues in histones H3 and H4 in budding yeast. Genetics. 195(3):795-807.  PubMed Link

Fiedler KL, Bheda P, Dai J, Boeke JD, Wolberger C, Cotter RJ. (2013). A quantitative analysis of histone methylation and acetylation isoforms from their deuteroacetylated derivatives: application to a series of knockout mutants. J Mass Spectrom. 48(5):608-615.  PubMed Link

Bheda P, Swatkoski S, Fiedler KL, Boeke JD, Cotter RJ, Wolberger C. (2012). Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2. Proc Natl Acad Sci U S A. 109, E916-925.  PubMed Link

Darby MM, Serebreni L, Pan X, Boeke JD, Corden JL. (2012). The Saccharomyces cerevisiae Nrd1-Nab3 Transcription Termination Pathway Acts in Opposition to Ras  Signaling and Mediates Response to Nutrient Depletion. Mol Cell Biol. 32, 1762-1775.  PubMed Link

Xie Z, Dai J, Dai L, Tan M, Cheng Z, Wu Y, Boeke JD, Zhao Y. (2012). Lysine succinylation and lysine malonylation in histones. Mol Cell Proteomics. 11, 100-107.  PubMed Link

HOT PAPER!
Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z, Lu JY, Khor CN, Lin CL, Bader JS, Irizarry R, Boeke JD. (2012). Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 482, 251-255.  PubMed Link

Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, Hu J, Hu S, Vera C, Bayron-Poueymiroy D, Rivera-Pacheco ZA, Ramos L, Torres-Castro C, Qian J, Bonaventura J, Boeke JD, Yap WY, Pino I, Eichinger DJ, Zhu H, Blackshaw S. (2012). Rapid  identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics.11, O111.016253.  PubMed Link

Sims JJ, Scavone F, Cooper EM, Kane LA, Youle RJ, Boeke JD, Cohen RE. (2012). Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of  cellular ubiquitin signaling. Nat Methods. 9, 303-309.  PubMed Link

Dai J, Boeke JD. (2011). Strain construction and screening methods for a yeast histone H3/H4 mutant library. Methods Mol Biol. 833, 1-14.  PubMed Link

Lu JY, Lin YY, Zhu H, Chuang LM, Boeke JD. (2011). Protein acetylation and aging. Aging (Albany NY). 3, 911-912.  PubMed Link

HOT PAPER!
Lu JY, Lin YY, Sheu JC, Wu JT, Lee FJ, Chen Y, Lin MI, Chiang FT, Tai TY, Berger SL, Zhao Y, Tsai KS, Zhu H, Chuang LM, Boeke JD. (2011). Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell. 146, 969-979.  PubMed Link

Hyland EM, Molina H, Poorey K, Jie C, Xie Z, Dai J, Qian J, Bekiranov S, Auble DT, Pandey A, Boeke JD. (2011). An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae. Genes Dev. 25, 1306-1319.  PubMed Link

Yu Q, Olsen L, Zhang X, Boeke JD, Bi X. (2011). Differential contributions of histone H3 and H4 residues to heterochromatin structure. Genetics. 188, 291-308.  PubMed Link

HOT PAPER!
Barnett BP, Hwang Y, Taylor MS, Kirchner H, Pfluger PT, Bernard V, Lin YY, Bowers EM, Mukherjee C, Song WJ, Longo PA, Leahy DJ, Hussain MA, Tschöp MH, Boeke JD, Cole PA. (2010). Glucose and weight control in mice with a designed ghrelin O-acyltransferase inhibitor. Science. 330, 1689-1692PubMed Link

Pan X, Reissman S, Douglas NR, Huang Z, Yuan DS, Wang X, McCaffery JM, Frydman J, Boeke JD. (2010). Trivalent arsenic inhibits the functions of chaperonin complex. Genetics. 186, 725-734.  PubMed Link

Ben-Aroya S, Pan X, Boeke JD, Hieter P. (2010). Making temperature-sensitive mutants. Methods in Enzymol. 470, 181-204.  PubMed Link

Matecic M, Smith DL, Pan X, Maqani N, Bekiranov S, Boeke JD, Smith JS. (2010). A microarray-based genetic screen for yeast chronological aging factors. PLoS Genet. 6(4):e1000921.  PubMed Link

Cooper EM, Boeke JD, Cohen RE. (2010). Specificity of the BRISC deubiquitinating enzyme is not due to selective binding to Lys63-linked polyubiquitin. J Biol Chem. 285, 10344-10352.  PubMed Link

Norris A, Boeke JD. (2010). Silent information regulator 3: the Goldilocks of the silencing complex. Genes Dev. 2, 115-122. Review.  PubMed Link

Luo J, Xu X, Hall H, Hyland EM, Boeke JD, Hazbun T, Kuo MH. (2009). Histone H3 exerts a key function in mitotic checkpoint control. Mol Cell Biol. 30, 537-549PubMed Link

HOT PAPER!
Lin Y-Y, Lu J-Y, Zhang J, Walter W, Dang W, Wan J, Tao S-C, Qian J, Zhao Y, Boeke JD, Berger SL, Zhu H. (2009). Protein acetylation microarray reveals NuA4 controls key metabolic target regulating gluconeogenesis. Cell. 136, 1073-1084.  PubMed Link

Huang H, Maertens AM, Hyland E, Dai J, Norris A, Boeke JD, Bader JS. (2009). HistoneHits: a database for histone mutations and their phenotypes. Genome Res. 19, 674-681.  PubMed Link

Norris A, Bianchet MA, Boeke JD. (2008). Compensatory interactions between Sir3p and the nucleosomal LRS surface imply their direct interaction. PLoS Genet.4(12), e1000301.  PubMed Link

HOT PAPER!
Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS. (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, 1991-2004.  PubMed Link

HOT PAPER!
Dai J, Hyland EM, Yuan DS, Huang H, Bader JS, Boeke JD. (2008). Probing nucleosome function:  A highly versatile library of synthetic histone H3 and H4 mutants. Cell. 134, 1066-1078.  PubMed Link

HOT PAPER!
Ben-Aroya S, Coombes C, Kwok T, O’Donnell KA, Boeke JD, Hieter P. (2008). Towards a comprehensive temperature sensitive mutant repository of the essential genes of Saccharomyces cerevisiae. Molecular Cell. 30, 248-258.  PubMed Link

Celic I, Verreault A, Boeke JD. (2008). Histone H3 K56 hyperacetylation perturbs replisomes and causes DNA damage. Genetics. 179,1769-1784.  PubMed Link

Huang Z, Sucgang RS, Lin YY, Shi X, Boeke JD, Pan X. (2008). Plasmid-chromosome shuffling for non-deletion alleles in yeast. Nature Methods. 5, 167-169.  PubMed Link

Li F, Dong J,  Pan X, Oum JH,  Boeke JD, Lee SE. (2008). Microarray-based genetic screen defined defines SAW1, a new gene required for the Rad1/Rad10-dependent processing of recombination intermediates. Mol. Cell. 30, 325-335.  PubMed Link

HOT PAPER!
Lin YY, Qi Y, Lu JY, Pan X, Yuan DS, Zhao Y, Bader JS, Boeke JD. (2008). A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes Dev. 22, 2062-2074.  PubMed Link

Meluh, P, Pan X, Yuan DS, Tiffany C, Chen O, Sookhai-Mahadeo S, Wang S, Peyser B, Irizarry R, Spencer F, Boeke JD. (2008). Analysis of genetic interactions on a genome-wide scale in budding yeast. Methods Mol. Biol. 416, 221-247.  PubMed Link

Pan X, Yuan D, Ye P, Bader J, Boeke JD. (2008). Response to Dr. Stephen Cooper’s ‘On the use of metaphor to understand, explain, or rationalize redundant genes in yeast’.  FEMS Yeast Res. 8, 349-350.  PubMed Link

Wheelan SJ, Martínez Murillo F, Boeke JD. (2008). The incredible shrinking world of DNA microarrays.  Molecular Biosystems. 4, 726-732.  PubMed Link

Sulek M, Yarrington R, McGibbon G, Boeke JD, Junop M. (2007). A critical role for the C-terminus of Nej1 protein in Lif1p assocation, DNA binding and non-homologous end-joining. DNA Repair (Amst). 6, 1805-1818.  PubMed Link

Zurita-Martinez SA, Puria R, Pan X, Boeke JD, Cardenas ME. (2007). Efficient Tor signaling requires a functional Class C Vps protein complex in Saccharomyces cerevisiae. Genetics. 176, 2139-2150.  PubMed Link

Celic I, Masumoto H, Griffith WP, Meluh P, Cotter RJ, Boeke JD, Verreault A. (2006). The sirtuins Hst3 and Hst4p preserve genome integrity by controlling histone H3 lysine 56 deacetylation. Current Biology 16:1280-1289.  PubMed Link

Fry CJ, Norris A, Cosgrove M, Boeke JD, Peterson CL. (2006). The LRS and SIN domains:  Two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing. Mol. Cell Biol. 26, 9045-9059.  PubMed Link

Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 38, 285-293.  PubMed Link

Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD. (2006). Global synthetic-lethality analysis and yeast functional profiling. Trends Genet. 22, 56-63.  PubMed Link

Pan X, Yuan DS, Ooi S-L, Wang X, Sookhai-Mahadeo S, Meluh P, Boeke JD. (2006). dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods. 41, 206-221.  PubMed Link

Richardson SM, Wheelan SJ, Yarrington RM, Boeke JD. (2006). GeneDesign: Rapid, Automated Design of Multikilobase Synthetic Genes. Genome Res. 16, 550-556.  PubMed Link

Sauve AA, Wolberger C, Schramm VL, Boeke JD. (2006). The biochemistry of sirtuins.  Ann. Rev. Bioch. 75, 435-465.  PubMed Link

Wheelan SJ, Martínez-Murillo F, Irizarry R, Boeke JD. (2006). Stacking the deck: double-tiled DNA microarrays. Nature Methods. 3, 903-907.  PubMed Link

Takahashi H, McCaffery JM, Irizarry RA, Boeke JD. (2006). Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Molecular Cell. 23, 207-17.  PubMed Link

Ooi SL, Pan X,  Peyser B, Ye P, Meluh P, Yuan D, Irizarry R, Bader JS, Spencer F, Boeke JD. (2006). Global synthetic lethality analysis and yeast functional profiling. Trends Genet, 22, 56-63.  PubMed Link

Ye P, Peyser BP, Pan X, Boeke JD, Spencer FA, Bader JS. (2005). Gene function prediction from congruent synthetic lethal interactions in yeast.  Molecular Systems Biology. 1, 2005.0026.  PubMed Link

HOT PAPER!
Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. (2005). A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell. 124: 1069-1081.  PubMed Link

Hyland, EM, Cosgrove, MS, Molina, H, Wang, D, Pandey, A, Cotter, R, Boeke, JD. (2005). Insights into the Role of Histone H3 and Histone H4 Core Modifiable Residues in Saccharomyces cerevisiae. Mol. Cell. Biol. 25, 10060-10070.  PubMed Link

Peyser BD, Irizarry RA, Tiffany CW, Chen O, Yuan DS, Boeke JD, Spencer FA. (2005). Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Res. 33, e140.  PubMed Link

Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA, Irizarry RA, Boeke JD. (2005). Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic Acids Res. 33, e103  PubMed Link

Cosgrove, M.S., Boeke, J.D., Wolberger, C. (2004) Regulated nucleosome mobility and the histone code. Nature Struct. Mol. Biol. 11:1037-43. PubMed link

Arevalo-Rodriguez, M. Pan, X., Boeke, J.D. and Heitman, J. (2004) FKBP12 controls aspartate pathway  flux in Saccharomyces cerevisiae to prevent toxic intermediate accumulation.  Euk. Cell. 3:1287-1296. PubMed link

Avalos, J.L., Boeke, J.D. and Wolberger, C. (2004) Structural basis for the mechanism and regulation of Sir2 enzymes. Moecular. Cell 13: 639-648.  PubMed link

Pan, X., Yuan, D.S., Xiang, D., Wang, X., Sookhai-Mahadeo, S., Hieter, P., Spencer, F., Boeke, J.S. (2004). A robust toolkit for wiring genome-wide genetic networks in yeast, Molecular Cell 16:487-496 PubMed link

Ooi, S.-L., Shoemaker, D. Boeke, J.D. (2003) DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray.  Nature Genetics 35:277-286.  PubMed link

Irizarry, R., Ooi, S.L. Wu, Z., and Boeke J.D. (2003) Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants Statist. App. Genet. Mol. Biol.  2:1-17

Starai, V. J., Takahashi, H., Boeke, J. D., and Escalante-Semerena, J. C. (2003). Short-chain fatty acid activation by acyl-Coenzyme A synthetases requires Sir2 protein function. Genetics 163:545-555. PubMed link

Starai, V. J., Celic, I., Cole, R. N., Boeke, J. D., and Escalante-Semerena, J. C. (2002). Sir2-dependent activation of acetyl-coenzyme A synthetase by deacetylation of an active site lysine residue. Science 298:2390-2392.  PubMed link

Onyango, P., Celic, I., McCaffery, J. M., Boeke, J.D., and Feinberg, A. P. (2002). SIRT3, a human SIR2 homologue, is an NAD-dependent deacetylase localized to mitochondria. Proc. Natl. Acad. Sci. USA 99, 13653-13658.  PubMed link

Giaever, G., et al. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-91. PubMed link

Avalos, J. L., Celic, I., Muhammad, S., Cosgrove, M. S., Boeke, J. D., and Wolberger, C. (2002). Structure of a Sir2 enzyme bound to an acetylated p53 peptide. Mol. Cell 10, 523-535. PubMed link

Park, J., Cosgrove, M., Youngman, E., Wolberger, C., and Boeke, J. D. (2002). A core nucleosome surface critical for transcriptional silencing. Nature Genet. 32,273-279. PubMed link

Sandmeier, J. J., Celic, I., Boeke, J. D., and Smith, J. S. (2002). Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD+ salvage pathway. Genetics 160, 877-889. PubMed link

Smith, J. S., Avalos, J., Celic, I., Muhammad, S., Wolberger, C., and Boeke, J. D. (2002). The SIR2 family of NAD+-dependent protein deacetylases. Meth Enzymol 353, 282-300. PubMed link

Sauve, A., Celic, I., Avalos, J., Deng, H., Boeke, J.D. and Schramm, V. L. (2001). The chemistry of gene silencing: the mechanism of NAD+-dependent deacetylation of histones and p53. Biochemistry, 40: 15456-15463. PubMed link

Ooi, S.-L., Shoemaker, D., and Boeke, J. D. (2001). A genome-wide DNA microarray-based genetic screen for components of the nonhomologous end-joining pathway in Saccharomyces cerevisiae. Science 294:2552-2556.   PubMed link

Smith, J. S., Brachmann, C. B., Celic, I., Kenna, M. A., Muhammad, S., Starai, V. C., Avalos, J., Escalante-Semerena, J. C., Grubmeyer, C., Wolberger, C., and Boeke, J. D. (2000). A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family Proc Natl Acad Sci 97: 6658-6663.  PubMed link

Fink, G. R., and Boeke, J. D. (1999). Yeast, an experimental organism for all times. ASM News 61, 89-95. 

Winzeler, E. A., et al. (1999). Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science, 285:901-906. PubMed link

Smith, J. S., Caputo, E., and Boeke, J. D. (1999). A genetic screen for ribosomal silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol. Cell. Biol. 19, 3184-3197.  PubMed link

Brachmann, C. B., Davies, A., Cost G.J., Caputo, E., Li, J., Hieter, P., and Boeke, J. D. (1998). Designer deletion strains derived from Saccharomyces cerevisiae S288C:  a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 114-132.  PubMed link

Brachmann, R. K., and Boeke, J. D. (1997). Tag games in yeast: the two hybrid system and beyond. Curr. Op. Biotech. 8, 561-568. PubMed link

Basrai, M. A., Hieter, P., and Boeke, J. D. (1997). Small Open Reading Frames: beautiful needles in the haystack. Genome Res. 7, 768-771.  PubMed link

Smith, J. S. and J. D. Boeke. (1997) An unusual form of silencing in yeast ribosomal DNA. Genes Dev. 11:241-254.  PubMed link


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