Drummond:Publications: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
Dadrummond (talk | contribs) No edit summary |
Dadrummond (talk | contribs) (→Research: queuosine paper) |
||
(15 intermediate revisions by the same user not shown) | |||
Line 3: | Line 3: | ||
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]. | 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 == | == Research == | ||
#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| | #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]. | ||
#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:// | #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. | #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 | #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. | #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. | #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://www.f1000biology.com/article/id/1029629 Faculty of 1000 | #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 | #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. | #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 | #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. | #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 | #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 == | == 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. | #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. | #Protein evolution: innovative chaps. Drummond DA. <em>Curr Biol.</em> 2009 Sep 15;19(17):R740-2. |
Revision as of 10:55, 10 December 2014
Find our papers on PubMed or 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, PLoS Biology, 12(12):e1002015, 2014. 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. Journal of the American Statistical Association, 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. PLoS One 8(9): e75320. Epub 2013 Sept 25, doi:10.1371/journal.pone.0075320 HTML, PDF.
- 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
- 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
- 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. - 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. - 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.
- 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
- 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.
- Population genetics of translational robustness. Wilke CO, Drummond DA. Genetics. 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. Mol Biol Evol. 2006 Feb;23(2):327-37. Epub 2005 Oct 19. MBE Early Citation Classic 2013 Faculty of 1000 recommended
- 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
- 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.
- 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
- 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.
- 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
- How infidelity creates a sticky situation. Drummond DA. Molecular Cell. 2012 48(5): 663–664. Preview of Ling et al..
- 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.
- Protein evolution: innovative chaps. Drummond DA. Curr Biol. 2009 Sep 15;19(17):R740-2.
- The evolutionary consequences of erroneous protein synthesis. Drummond DA, Wilke CO. Nat Rev Genet. 2009 Oct;10(10):715-24. Review.