Pan:Publications: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
(9 intermediate revisions by the same user not shown)
Line 1: Line 1:
2004-2006:
2009-2012:
*Starck, S.R., V. Jiang, M. Pavon-Eternod, S. Prasad, B. McCarthy, Tao Pan, N. Shastri: Leucine-tRNA Initiates at CUG Start Codons for Protein Synthesis and Presentation by MHC Class I, Science 336, 1719-1723 (2012).


*Dittmar, K.A., J.M. Goodenbour & Tao Pan: Tissue specific differences in human transfer RNA expression. PLoS Genetics 2, 2107-2115 (e221, 2006).
*Novoa, E.M., M. Pavon Eternod, Tao Pan & L. Ribas de Pouplana: Two anticodon modifications shaped tRNA gene populations and genome structure in bacteria and eukaryotes, Cell 149, 202-13 (2012).
 
*Perdrizet, G.A., I. Artsimovitch, R. Furman, T. R. Sosnick*, Tao Pan*: Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch, Proc. Natl. Acad. Sci. USA 109, 3323-3328 (2012).
 
*Parisien, M., C-Q. Yi & Tao Pan*: Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons, RNA 18, 355-367 (2012).
 
*Geslain, R. & Tao Pan: tRNA: a vast reservoir of RNA molecules with unexpected regulatory function, Proc. Natl. Acad. Sci. 108, 16489-90 (2011) [Commentary].
 
*Jia, G-F.,Y. Fu, X. Zhao, Q. Dai, G-Q. Zheng, Y. Yang, C-Q. Yi, T. Lindahl, Tao Pan, Y-G. Yang  & C. He: N6-Methyladenosine in Nuclear RNA is a Major Substrate of the Obesity-Associated FTO, Nature Chem. Biol. 7, 885-887 (2011).
 
*Yi, C-Q. & Tao Pan: Cellular Dynamics of RNA modification, Acc. Chem. Res. 44, 1380-1388 (2011) [review].
 
*Jones, T.E., R.W. Alexander, Tao Pan*: Misacylation of specific non-methionyl-tRNAs by a bacterial methionyl-tRNA synthetases, Proc. Natl. Acad. Sci. USA, 108, 6933-6938 (2011).
 
*Dai, Q., C-X. Song, Tao Pan & C. He: Syntheses of Two 5-Hydroxymethyl-20-deoxycytidine Phosphoramidites with TBDMS as the 5-Hydroxymethyl Protecting Group and Their Incorporation into DNA, J. Org. Chem. 76, 4182-4188 (2011).
 
*Baird, N.J., S.J. Ludtke, H. Khant, W. Chiu, Tao Pan* & T.R. Sosnick*: A discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy, J. Am. Chem. Soc. 132, 16352-16353 (2010).
 
*Reiter, N.J., Osterman, A., Torres-Larios, A., Swinger, K.K., Tao Pan & Mondragon, A.: Crystal structure of a bacterial ribonuclease P holoenzyme in complex with tRNA, Nature 468, 784-791 (2010).
 
*Fu, Y., Q. Dai, W. Zhang, J. Ren, Tao Pan* & C. He*: The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the anticodon wobble base in tRNA, Angewandte Chemie (Int) 49, 8885-8888 (2010).
 
*Zaborske, J.M., X-C. Wu, R. C. Wek, Tao Pan*: Selective control of amino acid metabolism by the GCN2 eIF2 kinase pathway in Saccharomyces cerevisiae, BMC Biochemistry 11:e29 (2010).


*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).
*Zaborske, J.M. & Tao Pan: Genome-wide analysis of Aminoacylation (Charging) levels of tRNA Using Microarrays, J. Vis. Exp. 40, doi: 10.3791/2007 (2010) [Method].


*Goodenbour, J.M. & Tao Pan: Diversity of tRNA genes in eukaryotes. Nucl. Acids Res. 34, 6137-46 (2006).
*Saikia, M., Y. Fu, M. Pavon-Eternod, C. He & Tao Pan*: Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs, RNA, RNA 16, 1317-1327 (2010).


*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).
*Tuller, T., A. Carmi, K. Vestsigian, S. Navon, Y. Dorfan, J. Zaborske, Tao Pan, O. Dahan, I. Furman & Y. Pilpel: An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation, Cell 141, 344-354 (2010).


*Tao Pan & T.R. Sosnick: RNA folding during transcription. Ann. Rev. Biophysics and Biomol. Dynamics 35, 161-175 (2006). Review.
*Baird, N.J., H-P. Gong, S.S. Zaheer, K.F. Freed, Tao Pan* & T.R. Sosnick*: Extended structures in RNA folding intermediates are due to non-native interactions rather than electrostatic repulsion, J. Mol. Biol. 397, 1298-1306 (2010).


*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).  
*Geslain, R. & Tao Pan*: Functional analysis of human tRNA isodecoders, J. Mol. Biol. 396, 821-831 (2010).


*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).
*Pavon-Eternod, M., M. Wei, Tao Pan* & Lawrence Kleiman*: Profiling non-lysyl tRNAs in HIV-1, RNA 16, 267-273 (2010).


*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).  
*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 462, 522-526 (2009).


*Wong T, Sosnick TR, Pan T. Mechanistic insights on the folding of a large ribozyme during transcription. Biochemistry 44:7535-42 (2005).  
*Wong, T.N. & Tao Pan: RNA Folding during Transcription: Protocols and Studies. Methods in Enzymology 468, 167-193 (2009) [Method].
*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).  
*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. 37, 7268-7280 (2009).


*Krasilnikov AS, Xiao Y, Pan T, Mondragon A. Basis for structural diversity in homologous RNAs. Science 306:104-7 (2004).  
*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).


*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).
*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).


*Barrera A, Pan T. Interaction of the Bacillus subtilis RNase P with the 30S ribosomal subunit. RNA 10:482-92 (2004).  
*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).


*Xie Z, Srividya N, Sosnick TR, Pan T, Scherer NF.
Single-molecule studies highlight conformational heterogeneity in the early
folding steps of a large ribozyme. Proc Natl Acad Sci USA 101:534-9 (2004).


Selected older publications:
Selected older publications:
*Sosnick TR, Pan T. RNA folding: models and perspectives.
*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).
Curr Opin Struct Biol. 13:309-16 (2003). Review.  
 
*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).  
*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:Research positions|Research positions]] | [[Pan:Press|Press]] |  [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]

Revision as of 13:19, 20 July 2012

2009-2012:

  • Starck, S.R., V. Jiang, M. Pavon-Eternod, S. Prasad, B. McCarthy, Tao Pan, N. Shastri: Leucine-tRNA Initiates at CUG Start Codons for Protein Synthesis and Presentation by MHC Class I, Science 336, 1719-1723 (2012).
  • Novoa, E.M., M. Pavon Eternod, Tao Pan & L. Ribas de Pouplana: Two anticodon modifications shaped tRNA gene populations and genome structure in bacteria and eukaryotes, Cell 149, 202-13 (2012).
  • Perdrizet, G.A., I. Artsimovitch, R. Furman, T. R. Sosnick*, Tao Pan*: Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch, Proc. Natl. Acad. Sci. USA 109, 3323-3328 (2012).
  • Parisien, M., C-Q. Yi & Tao Pan*: Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons, RNA 18, 355-367 (2012).
  • Geslain, R. & Tao Pan: tRNA: a vast reservoir of RNA molecules with unexpected regulatory function, Proc. Natl. Acad. Sci. 108, 16489-90 (2011) [Commentary].
  • Jia, G-F.,Y. Fu, X. Zhao, Q. Dai, G-Q. Zheng, Y. Yang, C-Q. Yi, T. Lindahl, Tao Pan, Y-G. Yang & C. He: N6-Methyladenosine in Nuclear RNA is a Major Substrate of the Obesity-Associated FTO, Nature Chem. Biol. 7, 885-887 (2011).
  • Yi, C-Q. & Tao Pan: Cellular Dynamics of RNA modification, Acc. Chem. Res. 44, 1380-1388 (2011) [review].
  • Jones, T.E., R.W. Alexander, Tao Pan*: Misacylation of specific non-methionyl-tRNAs by a bacterial methionyl-tRNA synthetases, Proc. Natl. Acad. Sci. USA, 108, 6933-6938 (2011).
  • Dai, Q., C-X. Song, Tao Pan & C. He: Syntheses of Two 5-Hydroxymethyl-20-deoxycytidine Phosphoramidites with TBDMS as the 5-Hydroxymethyl Protecting Group and Their Incorporation into DNA, J. Org. Chem. 76, 4182-4188 (2011).
  • Baird, N.J., S.J. Ludtke, H. Khant, W. Chiu, Tao Pan* & T.R. Sosnick*: A discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy, J. Am. Chem. Soc. 132, 16352-16353 (2010).
  • Reiter, N.J., Osterman, A., Torres-Larios, A., Swinger, K.K., Tao Pan & Mondragon, A.: Crystal structure of a bacterial ribonuclease P holoenzyme in complex with tRNA, Nature 468, 784-791 (2010).
  • Fu, Y., Q. Dai, W. Zhang, J. Ren, Tao Pan* & C. He*: The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the anticodon wobble base in tRNA, Angewandte Chemie (Int) 49, 8885-8888 (2010).
  • Zaborske, J.M., X-C. Wu, R. C. Wek, Tao Pan*: Selective control of amino acid metabolism by the GCN2 eIF2 kinase pathway in Saccharomyces cerevisiae, BMC Biochemistry 11:e29 (2010).
  • Zaborske, J.M. & Tao Pan: Genome-wide analysis of Aminoacylation (Charging) levels of tRNA Using Microarrays, J. Vis. Exp. 40, doi: 10.3791/2007 (2010) [Method].
  • Saikia, M., Y. Fu, M. Pavon-Eternod, C. He & Tao Pan*: Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs, RNA, RNA 16, 1317-1327 (2010).
  • Tuller, T., A. Carmi, K. Vestsigian, S. Navon, Y. Dorfan, J. Zaborske, Tao Pan, O. Dahan, I. Furman & Y. Pilpel: An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation, Cell 141, 344-354 (2010).
  • Baird, N.J., H-P. Gong, S.S. Zaheer, K.F. Freed, Tao Pan* & T.R. Sosnick*: Extended structures in RNA folding intermediates are due to non-native interactions rather than electrostatic repulsion, J. Mol. Biol. 397, 1298-1306 (2010).
  • Geslain, R. & Tao Pan*: Functional analysis of human tRNA isodecoders, J. Mol. Biol. 396, 821-831 (2010).
  • Pavon-Eternod, M., M. Wei, Tao Pan* & Lawrence Kleiman*: Profiling non-lysyl tRNAs in HIV-1, RNA 16, 267-273 (2010).
  • 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 462, 522-526 (2009).
  • Wong, T.N. & Tao Pan: RNA Folding during Transcription: Protocols and Studies. Methods in Enzymology 468, 167-193 (2009) [Method].
  • 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. 37, 7268-7280 (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).


Selected older publications:

  • 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).
  • 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).


Main | What we do | Who we are | Research positions | Press | Publications | Protocols | Links | Contact us

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Pan:Publications&oldid=614952"