Drummond:Publications

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Research

1. Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast. Csárdi G, Franks AM, Choi DS, Airoldi EM, and Drummond DA, PLoS Genetics, in press, 2015. preprint.
2. 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.
3. Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology. Franks AM, Csárdi G, Drummond AD, Airoldi EM. Journal of the American Statistical Association, in press, 2014.
4. 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.
   
5. 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
6. 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
7. 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.
8. 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.
9. 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.
10. 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
11. 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.
12. Population genetics of translational robustness. Wilke CO, Drummond DA. Genetics. 2006 May;173(1):473-81. Epub 2006 Feb 19.
13. 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
14. 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
15. 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.
16. 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
17. 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.
18. 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.