Drummond:Publications: Difference between revisions

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Find our papers on [http://www.ncbi.nlm.nih.gov/pubmed?term=drummond%20da PubMed] or [http://pubget.com/search?q=author:%22d.+allan+drummond%22 PubGet].
== Research ==
#A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus. Zaborske J, Bauer-DuMont VL, Wallace EWJ, Pan T, Aquadro CF, and Drummond DA, <em>PLoS Biology</em>, 12(12):e1002015, 2014. [http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002015 Full text].
#Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology. Franks AM, Csárdi G, Drummond AD, Airoldi EM. Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology. <em>Journal of the American Statistical Association</em>, in press, 2014.
#Quantifying condition-dependent intracellular protein levels enables high-precision fitness estimates. Geiler-Samerotte KA, Hashimoto T, Dion MF, Budnik BA, Airoldi EM, and Drummond DA. <em>PLoS One</em> 8(9): e75320. Epub 2013 Sept 25, doi:10.1371/journal.pone.0075320 [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075320 HTML], [http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0075320&representation=PDF PDF].<br/>
#Estimating selection on synonymous codon usage from noisy experimental data. Wallace EWJ, Airoldi EM, and Drummond DA. <em>Molecular Biology & Evolution</em>, 2013 Jun 30(6):1438–1453. Epub 2013 Mar 14, doi:10.1093/molbev/mst051. [http://f1000.com/prime/718042321 Faculty of 1000 recommended]
#Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme. Agashe D, Martinez-Gomez NC, Drummond DA, and Marx CJ. <em>Molecular Biology & Evolution</em>, 2013 Mar 30(3):549-60. doi:10.1093/molbev/mss273. [http://f1000.com/prime/717989786 Faculty of 1000 recommended]
#Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast.  Geiler-Samerotte KA, Dion MF, Budnik BA, Wang SM, Hartl DL, Drummond DA.  <em>Proc Natl Acad Sci U S A.</em> 2011 Jan 11;108(2):680–685.  Epub  2010 Dec 27. <br/> [http://www.pnas.org/content/108/2/680.full.pdf PDF], [http://www.pnas.org/content/108/2/680.full.pdf+html PDF+HTML], [[Drummond:MisfoldingCost2010|Supporting page]].
#Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Drummond DA, Wilke CO. <em>Cell.</em> 2008 Jul 25;134(2):341-52. [http://f1000.com/prime/1122806 Faculty of 1000 recommended] <br/> Preview by [http://www.cell.com/content/article/abstract?uid=PIIS0092867408008829 Powers and Balch].  [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2696314 Full text], [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2696314/bin/NIHMS61423-supplement-01.pdf supplementary materials], [[Drummond:MistranslationInducedMisfolding2008|supporting page]]. 
#Contact density affects protein evolutionary rate from bacteria to animals.  Zhou T, Drummond DA, Wilke CO.  <em>J Mol Evol.</em> 2008 Apr;66(4):395-404. Epub 2008 Apr 1.
#A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments. Li Y, Drummond DA, Sawayama AM, Snow CD, Bloom JD, Arnold FH. <em>Nat Biotechnol.</em> 2007 Sep;25(9):1051-6. Epub 2007 Aug 26. Erratum in: Nat Biotechnol. 2007 Dec;25(12):1488.  [http://www.f1000biology.com/article/id/1091770 Faculty of 1000 recommended]
#Structural determinants of the rate of protein evolution in yeast. Bloom JD, Drummond DA, Arnold FH, Wilke CO. <em>Mol Biol Evol.</em> 2006 Sep;23(9):1751-61. Epub 2006 Jun 16.
#Population genetics of translational robustness. Wilke CO, Drummond DA. <em>Genetics.</em> 2006 May;173(1):473-81. Epub 2006 Feb 19.
#A single determinant dominates the rate of yeast protein evolution. Drummond DA, Raval A, Wilke CO. <em>Mol Biol Evol.</em> 2006 Feb;23(2):327-37. Epub 2005 Oct 19. [http://mbe.oxfordjournals.org/content/30/1/3.full.pdf+html MBE Early Citation Classic 2013] [http://www.f1000biology.com/article/id/1029629 Faculty of 1000 recommended]
#Why highly expressed proteins evolve slowly. Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. <em>Proc Natl Acad Sci U S A.</em> 2005 Oct 4;102(40):14338-43. Epub 2005 Sep 21. [http://www.f1000biology.com/article/id/1029543 Faculty of 1000 recommended]
#Predicting the tolerance of proteins to random amino acid substitution. Wilke CO, Bloom JD, Drummond DA, Raval A. <em>Biophys J.</em> 2005 Dec;89(6):3714-20. Epub 2005 Sep 8.
#Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins. Drummond DA, Iverson BL, Georgiou G, Arnold FH. <em>J Mol Biol.</em> 2005 Jul 22;350(4):806-16. [http://www.f1000biology.com/article/id/1021960 Faculty of 1000 recommended]
#On the conservative nature of intragenic recombination. Drummond DA, Silberg JJ, Meyer MM, Wilke CO, Arnold FH. <em>Proc Natl Acad Sci U S A.</em> 2005 Apr 12;102(15):5380-5. Epub 2005 Apr 4.
#Thermodynamic prediction of protein neutrality. Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH. <em>Proc Natl Acad Sci U S A.</em> 2005 Jan 18;102(3):606-11. Epub 2005 Jan 11. [http://www.f1000biology.com/article/id/1030269 Faculty of 1000 recommended]
== Reviews ==
#How infidelity creates a sticky situation. Drummond DA. <em>Molecular Cell.</em> 2012 48(5): 663–664. Preview of Ling <em>et al.</em>.
#Signatures of protein biophysics in coding sequence evolution. Wilke CO, Drummond DA. <em>Curr Opin Struct Biol.</em> 2010 Jun;20(3):385-9. Epub 2010 Apr 13. Review.
#Protein evolution: innovative chaps. Drummond DA. <em>Curr Biol.</em> 2009 Sep 15;19(17):R740-2.
#The evolutionary consequences of erroneous protein synthesis. Drummond DA, Wilke CO. <em>Nat Rev Genet.</em> 2009 Oct;10(10):715-24. Review.
<!-- Awaiting return of biblio
==Peer-Reviewed Publications==
==Peer-Reviewed Publications==
 
<em>If this page seems strange and garbled, it's because OpenWetWare is currently chasing a bug in the software that properly renders citations.  In the meantime, you can find our papers indexed on [http://www.ncbi.nlm.nih.gov/pubmed?term=drummond%20da PubMed].
<biblio>
<biblio>
#Geiler-Samerotte-PNAS-2010 in press
#Drummond-NRG-2009 pmid=19763154
#Drummond-Cell-2008 pmid=18662548
//Preview by [http://www.cell.com/content/article/abstract?uid=PIIS0092867408008829 Powers and Balch]<br/>Download [[Media:Drummond08-MisfoldingPreprint.pdf|preprint PDF]], [[Media:Drummond08-MisfoldingPreprintSuppl.pdf|supplementary materials]], [[Drummond:Research#Mistranslation-induced_misfolding_and_gene_evolution|data]]<br/>[http://www.f1000biology.com/article/id/1122806 Faculty of 1000 rated]
#Zhou-JMolEv-2008 pmid=18379715
#Li-NBT-2007 pmid=17721510
// [http://www.f1000biology.com/article/id/1091770 Faculty of 1000 rated]
#Bloom-MBE-2006 pmid=16782762
#Bloom-MBE-2006 pmid=16782762
#Wilke-Genetics-2006 pmid=16489231
#Wilke-Genetics-2006 pmid=16489231
#Drummond-MBE-2006 pmid=16237209
#Drummond-MBE-2006 pmid=16237209
// [http://www.f1000biology.com/article/id/1029629 Faculty of 1000 rated]
#Drummond-PNAS-2005b pmid=16176987
#Drummond-PNAS-2005b pmid=16176987
// [http://www.f1000biology.com/article/id/1029543 Faculty of 1000 rated]
#Wilke-BiophysJ-2005 pmid=16150971
#Wilke-BiophysJ-2005 pmid=16150971
#Drummond-JMB-2005 pmid=15939434
#Drummond-JMB-2005 pmid=15939434
// [http://www.f1000biology.com/article/id/1021960 Faculty of 1000 rated]
#Drummond-PNAS-2005a pmid=15809422
#Drummond-PNAS-2005a pmid=15809422
#Bloom-PNAS-2005 pmid=15644440
#Bloom-PNAS-2005 pmid=15644440
// [http://www.f1000biology.com/article/id/1030269 Faculty of 1000 rated]
</biblio>
</biblio>


<!--
==Commentary==
 
<biblio>
<p class="publication">
#Wilke-CurStr-2010 pmid=20395125
Bloom, J.D., Drummond, D.A., Arnold, F.H., and Wilke, C.O., "Structural determinants of the rate of protein evolution in yeast," Molecular Biology and Evolution 23(9):1751&ndash;1761 (2006).
#Drummond-CurBio-2009 pmid=19906575
</p>
</biblio>
 
<p class="publication">
Wilke, C.O. and Drummond, D.A., "Population genetics of translational robustness," Genetics 173:473&ndash;481 (2006).
</p>
<p class="publication">
Drummond, D.A., Raval, A., and Wilke, C.O., "A single determinant dominates the rate of yeast protein evolution," Molecular Biology and Evolution 23(2):327&ndash;337 (2006). (Faculty of 1000 rated 6.4: Must Read)
</p>
 
<p class="publication">
Drummond, D.A., Bloom, J.D., Adami, C., Wilke, C.O., and Arnold, F.H., "Why highly expressed proteins evolve slowly," Proc. Nat'l. Acad. Sci. USA 102(40):14338&ndash;14343 (2005). (Nature Research Highlights and J. Cell Biol. Research Roundup selection; #1 most-read PNAS paper, Oct. 2005; Faculty of 1000 rated 6.4: Must Read.)
</p>
 
<p class="publication">
Wilke, C.O., Bloom, J.D., Drummond, D.A., and Raval, A., "Predicting the tolerance of proteins to random amino acid substitution," Biophysical Journal 89(6):3714&ndash;3720 (2005).
</p>
 
<p class="publication">
Drummond, D.A., Iverson, B.L., Georgiou, G.G., and Arnold, F.H., "Why high-error-rate mutagenesis libraries are enriched in functional and improved proteins," Journal of Molecular Biology 350(4):806&ndash;816 (2005). (Faculty of 1000 rated 3.0: Recommended)
</p>
 
<p class="publication">
Drummond, D.A., Silberg, J.J., Meyer, M.M., Wilke, C.O., and Arnold, F.H., "On the conservative nature of intragenic recombination," Proc. Nat'l. Acad. Sci. USA 102(15):5380&ndash;5385 (2005).
</p>
 
<p class="publication">
Bloom, J.D., Silberg, J.J., Wilke, C.O., Drummond, D.A., Adami, C., and Arnold, F.H., "Thermodynamic prediction of protein neutrality," Proc. Nat'l. Acad. Sci. USA 102(3):606&ndash;611 (2005).  (Faculty of 1000 rated 3.0: Recommended)
 
</p>
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</div>
{{Drummond_Bottom}}

Revision as of 10:55, 10 December 2014

We've moved to http://drummondlab.org.

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Find our papers on PubMed or PubGet.

Research

  1. A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus. Zaborske J, Bauer-DuMont VL, Wallace EWJ, Pan T, Aquadro CF, and Drummond DA, PLoS Biology, 12(12):e1002015, 2014. Full text.
  2. Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology. Franks AM, Csárdi G, Drummond AD, Airoldi EM. Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology. Journal of the American Statistical Association, in press, 2014.
  3. Quantifying condition-dependent intracellular protein levels enables high-precision fitness estimates. Geiler-Samerotte KA, Hashimoto T, Dion MF, Budnik BA, Airoldi EM, and Drummond DA. PLoS One 8(9): e75320. Epub 2013 Sept 25, doi:10.1371/journal.pone.0075320 HTML, PDF.
  4. Estimating selection on synonymous codon usage from noisy experimental data. Wallace EWJ, Airoldi EM, and Drummond DA. Molecular Biology & Evolution, 2013 Jun 30(6):1438–1453. Epub 2013 Mar 14, doi:10.1093/molbev/mst051. Faculty of 1000 recommended
  5. Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme. Agashe D, Martinez-Gomez NC, Drummond DA, and Marx CJ. Molecular Biology & Evolution, 2013 Mar 30(3):549-60. doi:10.1093/molbev/mss273. Faculty of 1000 recommended
  6. Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Geiler-Samerotte KA, Dion MF, Budnik BA, Wang SM, Hartl DL, Drummond DA. Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):680–685. Epub 2010 Dec 27.
    PDF, PDF+HTML, Supporting page.
  7. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Drummond DA, Wilke CO. Cell. 2008 Jul 25;134(2):341-52. Faculty of 1000 recommended
    Preview by Powers and Balch. Full text, supplementary materials, supporting page.
  8. Contact density affects protein evolutionary rate from bacteria to animals. Zhou T, Drummond DA, Wilke CO. J Mol Evol. 2008 Apr;66(4):395-404. Epub 2008 Apr 1.
  9. A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments. Li Y, Drummond DA, Sawayama AM, Snow CD, Bloom JD, Arnold FH. Nat Biotechnol. 2007 Sep;25(9):1051-6. Epub 2007 Aug 26. Erratum in: Nat Biotechnol. 2007 Dec;25(12):1488. Faculty of 1000 recommended
  10. Structural determinants of the rate of protein evolution in yeast. Bloom JD, Drummond DA, Arnold FH, Wilke CO. Mol Biol Evol. 2006 Sep;23(9):1751-61. Epub 2006 Jun 16.
  11. Population genetics of translational robustness. Wilke CO, Drummond DA. Genetics. 2006 May;173(1):473-81. Epub 2006 Feb 19.
  12. A single determinant dominates the rate of yeast protein evolution. Drummond DA, Raval A, Wilke CO. Mol Biol Evol. 2006 Feb;23(2):327-37. Epub 2005 Oct 19. MBE Early Citation Classic 2013 Faculty of 1000 recommended
  13. Why highly expressed proteins evolve slowly. Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14338-43. Epub 2005 Sep 21. Faculty of 1000 recommended
  14. Predicting the tolerance of proteins to random amino acid substitution. Wilke CO, Bloom JD, Drummond DA, Raval A. Biophys J. 2005 Dec;89(6):3714-20. Epub 2005 Sep 8.
  15. Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins. Drummond DA, Iverson BL, Georgiou G, Arnold FH. J Mol Biol. 2005 Jul 22;350(4):806-16. Faculty of 1000 recommended
  16. On the conservative nature of intragenic recombination. Drummond DA, Silberg JJ, Meyer MM, Wilke CO, Arnold FH. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5380-5. Epub 2005 Apr 4.
  17. Thermodynamic prediction of protein neutrality. Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH. Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):606-11. Epub 2005 Jan 11. Faculty of 1000 recommended

Reviews

  1. How infidelity creates a sticky situation. Drummond DA. Molecular Cell. 2012 48(5): 663–664. Preview of Ling et al..
  2. Signatures of protein biophysics in coding sequence evolution. Wilke CO, Drummond DA. Curr Opin Struct Biol. 2010 Jun;20(3):385-9. Epub 2010 Apr 13. Review.
  3. Protein evolution: innovative chaps. Drummond DA. Curr Biol. 2009 Sep 15;19(17):R740-2.
  4. The evolutionary consequences of erroneous protein synthesis. Drummond DA, Wilke CO. Nat Rev Genet. 2009 Oct;10(10):715-24. Review.


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