 Jef D. Boeke, Ph.D. Additional Information |
Key Publications
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. [Epub ahead of print] 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
