Pan:Publications: Difference between revisions

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2005-2007:
2007-2009:
*Dai, Q., R. Fong, M. Saikia, D. Stephenson, Y.-T. Yu, Tao Pan & J.A. Piccirill: Identification of Recognition Residues for Ligation-Based Detection and Quantitation of Pseudouridine and N6-Methyladeonsine, Nucl. Acids Res. 35, 6322-6329 (2007).
 
*Netzer, N., J.M. Goodenbour, A. David, K.A. Dittmar, R.B. Jones, J.R. Schneider, D. Boone, E.M. Eves, M.R. Rosner, J.S. Gibbs, A. Embry, B. Dolan, S. Das, H. Hickman, P. Berglund, J.R. Bennink, J.W. Yewdell*, Tao Pan*: Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity, Nature, epub. Nov.25 (2009).
 
*Pavon-Eternod, M., M. Wei, Tao Pan*, Lawrence Kleiman*: Profiling non-lysyl tRNAs in HIV-1, RNA, in press (2009).
 
*Pavon-Eternod, M., S. Gomes, R. Geslain, Q. Dai, M. R. Rosner* & Tao Pan*: tRNA Over-expression in Breast Cancer and Functional Consequences, Nucl. Acids Res. epub. Sept.25 (2009).
 
*Zaborske, J.M., J. Narasimhan, L. Jiang, S.A. Wek, K.A. Dittmar, F. Freimoser, Tao Pan* & R.C. Wek*: Genome-wide analysis of tRNA charging and activation of the eIF2 kinase Gcn2p, J. Biol. Chem. 284, 25254-25267 (2009).
 
*Zhou, Y., J.M. Goodenbour, L.A. Godley, A. Wickrema* & Tao Pan*: High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma, Biochem. Biophys. Res. Comm. 385, 160-164 (2009).
 
*Dai, Q., M. Saikia, N-S. Li, Tao Pan* & J.A. Piccirilli*: Efficient Chemical Synthesis of AppDNA by Adenylation of Immobilized DNA-5-monophosphate, Organic Letters 11, 1067-1070 (2009).
 
*Qu, X-H., G. J. Smith, K.T. Lee, T. R. Sosnick, Tao Pan & N. F. Scherer: Single-Molecule Non-equilibrium Periodic Mg2+-concentration Jump Experiments Reveal Details of the Early Folding Pathways of a Large RNA, Proc. Natl. Acad. Sci. USA 105, 6602-6607 (2008).
 
*Smith, G.J., K.T. Lee, X-H. Qu, Z. Xie, J. Pesic, T.R. Sosnick, Tao Pan & N.F. Scherer: Discrete single molecule dynamics suggest relatively simple but rugged structure for a large collapsed-state RNA, J. Mol. Biol. 378, 941-951 (2008).
 
*Dai, Q., R. Fong, M. Saikia, D. Stephenson, Y.-T. Yu, Tao Pan* & J.A. Piccirilli*: Identification of Recognition Residues for Ligation-Based Detection and Quantitation of Pseudouridine and N6-Methyladeonsine, Nucl. Acids Res. 35, 6322-6329 (2007).


*Baird, N.J., X.-W. Fang, N. Srividya, Tao Pan & T. R. Sosnick: Folding of a universal ribozyme, the RNase P RNA. Q. Rev. Biophys. 40, 113-161 (2007). Review.
*Baird, N.J., X.-W. Fang, N. Srividya, Tao Pan & T. R. Sosnick: Folding of a universal ribozyme, the RNase P RNA. Q. Rev. Biophys. 40, 113-161 (2007). Review.


*Wong, T., T.R. Sosnick & Tao Pan: Folding of non-coding RNAs during transcription facilitated by pausing-induced non-native structures, Proc. Natl. Acad. Sci. USA 104, 17995-18000 (2007).
*Wong, T., T.R. Sosnick* & Tao Pan*: Folding of non-coding RNAs during transcription facilitated by pausing-induced non-native structures, Proc. Natl. Acad. Sci. USA 104, 17995-18000 (2007).


Selected older publications:
*Dittmar, K.A., J.M. Goodenbour & Tao Pan: Tissue specific differences in human transfer RNA expression. PLoS Genetics 2, 2107-2115 (e221, 2006).
*Dittmar, K.A., J.M. Goodenbour & Tao Pan: Tissue specific differences in human transfer RNA expression. PLoS Genetics 2, 2107-2115 (e221, 2006).


*Saikia, M., Q. Dai, W.A. Decatur, M.J. Fournier, J.A. Piccirilli & Tao Pan: A systematic, ligation based approach to study RNA modifications, RNA 12, 2025-2033 (2006).
*Saikia, M., Q. Dai, W.A. Decatur, M.J. Fournier, J.A. Piccirilli* & Tao Pan*: A systematic, ligation based approach to study RNA modifications, RNA 12, 2025-2033 (2006).


*Goodenbour, J.M. & Tao Pan: Diversity of tRNA genes in eukaryotes. Nucl. Acids Res. 34, 6137-46 (2006).
*Goodenbour, J.M. & Tao Pan: Diversity of tRNA genes in eukaryotes. Nucl. Acids Res. 34, 6137-46 (2006).
*Baird, N.J., N. Srividya, A. Krasilnikov, A. Mondragón, T. R. Sosnick & Tao Pan: Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium, RNA 12, 598-606 (2006).


*Tao Pan & T.R. Sosnick: RNA folding during transcription. Ann. Rev. Biophysics and Biomol. Dynamics 35, 161-175 (2006). Review.
*Tao Pan & T.R. Sosnick: RNA folding during transcription. Ann. Rev. Biophysics and Biomol. Dynamics 35, 161-175 (2006). Review.


*Baird NJ, Westhof E, Qin H, Pan T, Sosnick TR.  Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J Mol Biol. 352:712-22 (2005).  
*Baird NJ, Westhof E, Qin H, Pan T*, Sosnick TR*.  Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J Mol Biol. 352:712-22 (2005).  


*Torres-Larios A, Swinger KK, Krasilnikov AS, Pan T, Mondragon A. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437:584-7 (2005).
*Torres-Larios A, Swinger KK, Krasilnikov AS, Pan T, Mondragon A. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437:584-7 (2005).


*Le TT, Harlepp S, Guet CC, Dittmar K, Emonet T, Pan T, Cluzel P. Real-time RNA profiling within a single bacterium. Proc Natl Acad Sci USA 102:9160-4 (2005).
*Wong T, Sosnick TR, Pan T. Mechanistic insights on the folding of a large ribozyme during transcription. Biochemistry 44:7535-42 (2005).
*Dittmar KA, Sorensen MA, Elf J, Ehrenberg M, Pan T. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 6:151-7 (2005).  
*Dittmar KA, Sorensen MA, Elf J, Ehrenberg M, Pan T. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 6:151-7 (2005).  


*Smith GJ, Sosnick TR, Scherer NF, Pan T. Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. RNA 11:234-9 (2005).
Selected older publications:
*Krasilnikov AS, Xiao Y, Pan T, Mondragon A. Basis for structural diversity in homologous RNAs. Science 306:104-7 (2004).  
*Krasilnikov AS, Xiao Y, Pan T, Mondragon A. Basis for structural diversity in homologous RNAs. Science 306:104-7 (2004).  


Line 36: Line 44:
*Krasilnikov AS, Yang X, Pan T, Mondragon A. Crystal structure of the specificity domain of ribonuclease P. Nature 421:760-4 (2003).  
*Krasilnikov AS, Yang X, Pan T, Mondragon A. Crystal structure of the specificity domain of ribonuclease P. Nature 421:760-4 (2003).  
    
    
*Fang, X-W., P. Thiyagarajan, T.R. Sosnick & Tao Pan: The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc. Natl. Acad. Sci. USA 99, 8518-8523 (2002).
*Fang, X-W., P. Thiyagarajan, T.R. Sosnick* & Tao Pan*: The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc. Natl. Acad. Sci. USA 99, 8518-8523 (2002).


*Fang, X-W., B.L. Golden, K. Littrell, V. Shelton, P. Thiyagarajan, Tao Pan & T.R. Sosnick: The thermodynamic origin of the stability of a thermophilic ribozyme. Proc. Natl. Acad. Sci. USA 98, 4355-4360 (2001).
*Fang, X-W., B.L. Golden, K. Littrell, V. Shelton, P. Thiyagarajan, Tao Pan* & T.R. Sosnick*: The thermodynamic origin of the stability of a thermophilic ribozyme. Proc. Natl. Acad. Sci. USA 98, 4355-4360 (2001).


*Tao Pan, I. Artsimovitch, X-W. Fang, R. Landick & T.R. Sosnick: Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc. Natl. Acad. Sci. USA 96, 9545-9550 (1999).
*Tao Pan*, I. Artsimovitch, X-W. Fang, R. Landick & T.R. Sosnick*: Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc. Natl. Acad. Sci. USA 96, 9545-9550 (1999).




<font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]
<font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]

Revision as of 15:29, 25 November 2009

2007-2009:

  • Netzer, N., J.M. Goodenbour, A. David, K.A. Dittmar, R.B. Jones, J.R. Schneider, D. Boone, E.M. Eves, M.R. Rosner, J.S. Gibbs, A. Embry, B. Dolan, S. Das, H. Hickman, P. Berglund, J.R. Bennink, J.W. Yewdell*, Tao Pan*: Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity, Nature, epub. Nov.25 (2009).
  • Pavon-Eternod, M., M. Wei, Tao Pan*, Lawrence Kleiman*: Profiling non-lysyl tRNAs in HIV-1, RNA, in press (2009).
  • Pavon-Eternod, M., S. Gomes, R. Geslain, Q. Dai, M. R. Rosner* & Tao Pan*: tRNA Over-expression in Breast Cancer and Functional Consequences, Nucl. Acids Res. epub. Sept.25 (2009).
  • Zaborske, J.M., J. Narasimhan, L. Jiang, S.A. Wek, K.A. Dittmar, F. Freimoser, Tao Pan* & R.C. Wek*: Genome-wide analysis of tRNA charging and activation of the eIF2 kinase Gcn2p, J. Biol. Chem. 284, 25254-25267 (2009).
  • Zhou, Y., J.M. Goodenbour, L.A. Godley, A. Wickrema* & Tao Pan*: High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma, Biochem. Biophys. Res. Comm. 385, 160-164 (2009).
  • Dai, Q., M. Saikia, N-S. Li, Tao Pan* & J.A. Piccirilli*: Efficient Chemical Synthesis of AppDNA by Adenylation of Immobilized DNA-5-monophosphate, Organic Letters 11, 1067-1070 (2009).
  • Qu, X-H., G. J. Smith, K.T. Lee, T. R. Sosnick, Tao Pan & N. F. Scherer: Single-Molecule Non-equilibrium Periodic Mg2+-concentration Jump Experiments Reveal Details of the Early Folding Pathways of a Large RNA, Proc. Natl. Acad. Sci. USA 105, 6602-6607 (2008).
  • Smith, G.J., K.T. Lee, X-H. Qu, Z. Xie, J. Pesic, T.R. Sosnick, Tao Pan & N.F. Scherer: Discrete single molecule dynamics suggest relatively simple but rugged structure for a large collapsed-state RNA, J. Mol. Biol. 378, 941-951 (2008).
  • Dai, Q., R. Fong, M. Saikia, D. Stephenson, Y.-T. Yu, Tao Pan* & J.A. Piccirilli*: Identification of Recognition Residues for Ligation-Based Detection and Quantitation of Pseudouridine and N6-Methyladeonsine, Nucl. Acids Res. 35, 6322-6329 (2007).
  • Baird, N.J., X.-W. Fang, N. Srividya, Tao Pan & T. R. Sosnick: Folding of a universal ribozyme, the RNase P RNA. Q. Rev. Biophys. 40, 113-161 (2007). Review.
  • Wong, T., T.R. Sosnick* & Tao Pan*: Folding of non-coding RNAs during transcription facilitated by pausing-induced non-native structures, Proc. Natl. Acad. Sci. USA 104, 17995-18000 (2007).

Selected older publications:

  • Dittmar, K.A., J.M. Goodenbour & Tao Pan: Tissue specific differences in human transfer RNA expression. PLoS Genetics 2, 2107-2115 (e221, 2006).
  • Saikia, M., Q. Dai, W.A. Decatur, M.J. Fournier, J.A. Piccirilli* & Tao Pan*: A systematic, ligation based approach to study RNA modifications, RNA 12, 2025-2033 (2006).
  • Goodenbour, J.M. & Tao Pan: Diversity of tRNA genes in eukaryotes. Nucl. Acids Res. 34, 6137-46 (2006).
  • Tao Pan & T.R. Sosnick: RNA folding during transcription. Ann. Rev. Biophysics and Biomol. Dynamics 35, 161-175 (2006). Review.
  • Baird NJ, Westhof E, Qin H, Pan T*, Sosnick TR*. Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J Mol Biol. 352:712-22 (2005).
  • Torres-Larios A, Swinger KK, Krasilnikov AS, Pan T, Mondragon A. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437:584-7 (2005).
  • Dittmar KA, Sorensen MA, Elf J, Ehrenberg M, Pan T. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 6:151-7 (2005).
  • Krasilnikov AS, Xiao Y, Pan T, Mondragon A. Basis for structural diversity in homologous RNAs. Science 306:104-7 (2004).
  • Dittmar KA, Mobley EM, Radek AJ, Pan T. Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol. 337:31-47 (2004).
  • Krasilnikov AS, Yang X, Pan T, Mondragon A. Crystal structure of the specificity domain of ribonuclease P. Nature 421:760-4 (2003).
  • Fang, X-W., P. Thiyagarajan, T.R. Sosnick* & Tao Pan*: The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc. Natl. Acad. Sci. USA 99, 8518-8523 (2002).
  • Fang, X-W., B.L. Golden, K. Littrell, V. Shelton, P. Thiyagarajan, Tao Pan* & T.R. Sosnick*: The thermodynamic origin of the stability of a thermophilic ribozyme. Proc. Natl. Acad. Sci. USA 98, 4355-4360 (2001).
  • Tao Pan*, I. Artsimovitch, X-W. Fang, R. Landick & T.R. Sosnick*: Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc. Natl. Acad. Sci. USA 96, 9545-9550 (1999).


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