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Items: 28

1.

An Escherichia coli Nitrogen Starvation Response Is Important for Mutualistic Coexistence with Rhodopseudomonas palustris.

McCully AL, Behringer MG, Gliessman JR, Pilipenko EV, Mazny JL, Lynch M, Drummond DA, McKinlay JB.

Appl Environ Microbiol. 2018 Jul 2;84(14). pii: e00404-18. doi: 10.1128/AEM.00404-18. Print 2018 Jul 15.

PMID:
29728387
2.

Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response.

Riback JA, Katanski CD, Kear-Scott JL, Pilipenko EV, Rojek AE, Sosnick TR, Drummond DA.

Cell. 2017 Mar 9;168(6):1028-1040.e19. doi: 10.1016/j.cell.2017.02.027.

3.

Heat Shock Factor 1: From Fire Chief to Crowd-Control Specialist.

Triandafillou CG, Drummond DA.

Mol Cell. 2016 Jul 7;63(1):1-2. doi: 10.1016/j.molcel.2016.06.026.

4.

Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress.

Wallace EW, Kear-Scott JL, Pilipenko EV, Schwartz MH, Laskowski PR, Rojek AE, Katanski CD, Riback JA, Dion MF, Franks AM, Airoldi EM, Pan T, Budnik BA, Drummond DA.

Cell. 2015 Sep 10;162(6):1286-98. doi: 10.1016/j.cell.2015.08.041.

5.

Dying mRNA Tells a Story of Its Life.

Wallace EW, Drummond DA.

Cell. 2015 Jun 4;161(6):1246-8. doi: 10.1016/j.cell.2015.05.043.

6.

Estimating a structured covariance matrix from multi-lab measurements in high-throughput biology.

Franks AM, Csárdi G, Drummond DA, Airoldi EM.

J Am Stat Assoc. 2015 Mar 1;110(509):27-44.

7.

Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast.

Csárdi G, Franks A, Choi DS, Airoldi EM, Drummond DA.

PLoS Genet. 2015 May 7;11(5):e1005206. doi: 10.1371/journal.pgen.1005206. eCollection 2015 May.

8.

Correction: A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus.

Zaborske JM, Bauer DuMont VL, Wallace EW, Pan T, Aquadro CF, Drummond DA.

PLoS Biol. 2015 Apr 29;13(4):e1002150. doi: 10.1371/journal.pbio.1002150. eCollection 2015 Apr.

9.

A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus.

Zaborske JM, DuMont VL, Wallace EW, Pan T, Aquadro CF, Drummond DA.

PLoS Biol. 2014 Dec 9;12(12):e1002015. doi: 10.1371/journal.pbio.1002015. eCollection 2014 Dec. Erratum in: PLoS Biol. 2015 Apr;13(4):e1002150.

10.

Quantifying condition-dependent intracellular protein levels enables high-precision fitness estimates.

Geiler-Samerotte KA, Hashimoto T, Dion MF, Budnik BA, Airoldi EM, Drummond DA.

PLoS One. 2013 Sep 25;8(9):e75320. doi: 10.1371/journal.pone.0075320. eCollection 2013. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/9f5465d9-e9fa-4a80-84ca-9c9a3f6e82c7.

11.

Estimating selection on synonymous codon usage from noisy experimental data.

Wallace EW, Airoldi EM, Drummond DA.

Mol Biol Evol. 2013 Jun;30(6):1438-53. doi: 10.1093/molbev/mst051. Epub 2013 Mar 14.

12.

How infidelity creates a sticky situation.

Drummond DA.

Mol Cell. 2012 Dec 14;48(5):663-4. doi: 10.1016/j.molcel.2012.11.024.

13.

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, Marx CJ.

Mol Biol Evol. 2013 Mar;30(3):549-60. doi: 10.1093/molbev/mss273. Epub 2012 Dec 4.

14.

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):680-5. doi: 10.1073/pnas.1017570108. Epub 2010 Dec 27.

15.

Signatures of protein biophysics in coding sequence evolution.

Wilke CO, Drummond DA.

Curr Opin Struct Biol. 2010 Jun;20(3):385-9. doi: 10.1016/j.sbi.2010.03.004. Epub 2010 Apr 13. Review.

16.

Protein evolution: innovative chaps.

Drummond DA.

Curr Biol. 2009 Sep 15;19(17):R740-2. doi: 10.1016/j.cub.2009.07.039.

17.

The evolutionary consequences of erroneous protein synthesis.

Drummond DA, Wilke CO.

Nat Rev Genet. 2009 Oct;10(10):715-24. doi: 10.1038/nrg2662. Review.

18.

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

Drummond DA, Wilke CO.

Cell. 2008 Jul 25;134(2):341-52. doi: 10.1016/j.cell.2008.05.042.

19.

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. doi: 10.1007/s00239-008-9094-4. Epub 2008 Apr 1.

PMID:
18379715
20.

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.

PMID:
17721510
21.

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.

PMID:
16782762
22.

Population genetics of translational robustness.

Wilke CO, Drummond DA.

Genetics. 2006 May;173(1):473-81. Epub 2006 Feb 19.

23.

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.

PMID:
16237209
24.

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.

25.

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.

26.

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.

PMID:
15939434
27.

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.

28.

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.

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