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Items: 1 to 50 of 106

1.

Selection for Protein Stability Enriches for Epistatic Interactions.

Posfai A, Zhou J, Plotkin JB, Kinney JB, McCandlish DM.

Genes (Basel). 2018 Aug 21;9(9). pii: E423. doi: 10.3390/genes9090423.

2.

Codon usage influences fitness through RNA toxicity.

Mittal P, Brindle J, Stephen J, Plotkin JB, Kudla G.

Proc Natl Acad Sci U S A. 2018 Aug 21;115(34):8639-8644. doi: 10.1073/pnas.1810022115. Epub 2018 Aug 6. Erratum in: Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):E9753.

3.

Beyond words: What can help first year medical students practice effective empathic communication?

Plotkin JB, Shochet R.

Patient Educ Couns. 2018 Nov;101(11):2005-2010. doi: 10.1016/j.pec.2018.07.013. Epub 2018 Jul 19.

PMID:
30078499
4.

Inferring the shape of global epistasis.

Otwinowski J, McCandlish DM, Plotkin JB.

Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):E7550-E7558. doi: 10.1073/pnas.1804015115. Epub 2018 Jul 23.

PMID:
30037990
5.

Phenotypic plasticity promotes recombination and gene clustering in periodic environments.

Gulisija D, Plotkin JB.

Nat Commun. 2017 Dec 11;8(1):2041. doi: 10.1038/s41467-017-01952-z.

6.

Detecting evolutionary forces in language change.

Newberry MG, Ahern CA, Clark R, Plotkin JB.

Nature. 2017 Nov 9;551(7679):223-226. doi: 10.1038/nature24455. Epub 2017 Nov 1.

PMID:
29088703
7.

riboviz: analysis and visualization of ribosome profiling datasets.

Carja O, Xing T, Wallace EWJ, Plotkin JB, Shah P.

BMC Bioinformatics. 2017 Oct 25;18(1):461. doi: 10.1186/s12859-017-1873-8.

8.

Molecular evolution: No escape from the tangled bank.

Plotkin JB.

Nature. 2017 Nov 2;551(7678):42-43. doi: 10.1038/nature24152. Epub 2017 Oct 18. No abstract available.

PMID:
29045393
9.

The evolutionary advantage of heritable phenotypic heterogeneity.

Carja O, Plotkin JB.

Sci Rep. 2017 Jul 11;7(1):5090. doi: 10.1038/s41598-017-05214-2.

10.

Evolutionary consequences of behavioral diversity.

Stewart AJ, Parsons TL, Plotkin JB.

Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):E7003-E7009. doi: 10.1073/pnas.1608990113. Epub 2016 Oct 24.

11.

Assortative mating can impede or facilitate fixation of underdominant alleles.

Newberry MG, McCandlish DM, Plotkin JB.

Theor Popul Biol. 2016 Dec;112:14-21. doi: 10.1016/j.tpb.2016.07.003. Epub 2016 Aug 3.

12.

Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections.

Nourmohammad A, Otwinowski J, Plotkin JB.

PLoS Genet. 2016 Jul 21;12(7):e1006171. doi: 10.1371/journal.pgen.1006171. eCollection 2016 Jul.

13.

Small groups and long memories promote cooperation.

Stewart AJ, Plotkin JB.

Sci Rep. 2016 Jun 1;6:26889. doi: 10.1038/srep26889.

14.

Epistasis and the Dynamics of Reversion in Molecular Evolution.

McCandlish DM, Shah P, Plotkin JB.

Genetics. 2016 Jul;203(3):1335-51. doi: 10.1534/genetics.116.188961. Epub 2016 May 18.

15.

Transcriptional errors and the drift barrier.

McCandlish DM, Plotkin JB.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3136-8. doi: 10.1073/pnas.1601785113. Epub 2016 Mar 10. No abstract available.

16.

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation.

Weinberg DE, Shah P, Eichhorn SW, Hussmann JA, Plotkin JB, Bartel DP.

Cell Rep. 2016 Feb 23;14(7):1787-1799. doi: 10.1016/j.celrep.2016.01.043. Epub 2016 Feb 11.

17.

Phenotypic Plasticity Promotes Balanced Polymorphism in Periodic Environments by a Genomic Storage Effect.

Gulisija D, Kim Y, Plotkin JB.

Genetics. 2016 Apr;202(4):1437-48. doi: 10.1534/genetics.115.185702. Epub 2016 Feb 8.

18.

Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution.

Kumar MS, Plotkin JB, Hannenhalli S.

PLoS Comput Biol. 2015 Nov 6;11(11):e1004603. doi: 10.1371/journal.pcbi.1004603. eCollection 2015 Nov.

19.

Coordinated Evolution of Influenza A Surface Proteins.

Neverov AD, Kryazhimskiy S, Plotkin JB, Bazykin GA.

PLoS Genet. 2015 Aug 6;11(8):e1005404. doi: 10.1371/journal.pgen.1005404. eCollection 2015 Aug.

20.

Detecting epistasis from an ensemble of adapting populations.

McCandlish DM, Otwinowski J, Plotkin JB.

Evolution. 2015 Sep;69(9):2359-70. doi: 10.1111/evo.12735. Epub 2015 Aug 20.

21.

Contingency and entrenchment in protein evolution under purifying selection.

Shah P, McCandlish DM, Plotkin JB.

Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):E3226-35. doi: 10.1073/pnas.1412933112. Epub 2015 Jun 8.

22.

Experimentally guided models reveal replication principles that shape the mutation distribution of RNA viruses.

Schulte MB, Draghi JA, Plotkin JB, Andino R.

Elife. 2015 Jan 30;4. doi: 10.7554/eLife.03753.

23.

Formal properties of the probability of fixation: identities, inequalities and approximations.

McCandlish DM, Epstein CL, Plotkin JB.

Theor Popul Biol. 2015 Feb;99:98-113. doi: 10.1016/j.tpb.2014.11.004. Epub 2014 Nov 20.

PMID:
25450112
24.

Collapse of cooperation in evolving games.

Stewart AJ, Plotkin JB.

Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):17558-63. doi: 10.1073/pnas.1408618111. Epub 2014 Nov 24.

25.

Inferring fitness landscapes by regression produces biased estimates of epistasis.

Otwinowski J, Plotkin JB.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2301-9. doi: 10.1073/pnas.1400849111. Epub 2014 May 19.

26.

The equilibrium allele frequency distribution for a population with reproductive skew.

Der R, Plotkin JB.

Genetics. 2014 Apr;196(4):1199-216. doi: 10.1534/genetics.114.161422. Epub 2014 Jan 28.

27.

The inevitability of unconditionally deleterious substitutions during adaptation.

McCandlish DM, Epstein CL, Plotkin JB.

Evolution. 2014 May;68(5):1351-64. doi: 10.1111/evo.12350. Epub 2014 Mar 4.

PMID:
24410330
28.

Identifying signatures of selection in genetic time series.

Feder AF, Kryazhimskiy S, Plotkin JB.

Genetics. 2014 Feb;196(2):509-22. doi: 10.1534/genetics.113.158220. Epub 2013 Dec 6.

29.

Selection biases the prevalence and type of epistasis along adaptive trajectories.

Draghi JA, Plotkin JB.

Evolution. 2013 Nov;67(11):3120-31. doi: 10.1111/evo.12192. Epub 2013 Jul 4.

PMID:
24151997
30.

From extortion to generosity, evolution in the Iterated Prisoner's Dilemma.

Stewart AJ, Plotkin JB.

Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15348-53. doi: 10.1073/pnas.1306246110. Epub 2013 Sep 3.

31.

The evolution of genetic architectures underlying quantitative traits.

Rajon E, Plotkin JB.

Proc Biol Sci. 2013 Aug 28;280(1769):20131552. doi: 10.1098/rspb.2013.1552. Print 2013 Oct 22.

32.

Plaque disruption during transcatheter aortic valve replacement.

Plotkin JB, Siegel RJ, Beigel R.

Eur Heart J Cardiovasc Imaging. 2014 Jan;15(1):117. doi: 10.1093/ehjci/jet151. Epub 2013 Aug 22. No abstract available.

PMID:
23970763
33.

The evolution of complex gene regulation by low-specificity binding sites.

Stewart AJ, Plotkin JB.

Proc Biol Sci. 2013 Aug 14;280(1768):20131313. doi: 10.1098/rspb.2013.1313. Print 2013 Oct 7.

34.

Misdiagnosis by transoesophageal echo of post-operative cardiac thrombus and tamponade due to Surgicel® Fibrillar.

Dela Cruz SG, Plotkin JB, Esmailian F, Beigel R, Siegel RJ.

Eur Heart J Cardiovasc Imaging. 2014 Jan;15(1):114. doi: 10.1093/ehjci/jet126. Epub 2013 Aug 2. No abstract available.

PMID:
23913333
35.

Immune history shapes specificity of pandemic H1N1 influenza antibody responses.

Li Y, Myers JL, Bostick DL, Sullivan CB, Madara J, Linderman SL, Liu Q, Carter DM, Wrammert J, Esposito S, Principi N, Plotkin JB, Ross TM, Ahmed R, Wilson PC, Hensley SE.

J Exp Med. 2013 Jul 29;210(8):1493-500. doi: 10.1084/jem.20130212. Epub 2013 Jul 15.

36.

Single hemagglutinin mutations that alter both antigenicity and receptor binding avidity influence influenza virus antigenic clustering.

Li Y, Bostick DL, Sullivan CB, Myers JL, Griesemer SB, Stgeorge K, Plotkin JB, Hensley SE.

J Virol. 2013 Sep;87(17):9904-10. doi: 10.1128/JVI.01023-13. Epub 2013 Jul 3.

37.

Rate-limiting steps in yeast protein translation.

Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB.

Cell. 2013 Jun 20;153(7):1589-601. doi: 10.1016/j.cell.2013.05.049.

38.

The role of epistasis in protein evolution.

McCandlish DM, Rajon E, Shah P, Ding Y, Plotkin JB.

Nature. 2013 May 30;497(7451):E1-2; discussion E2-3. doi: 10.1038/nature12219. No abstract available.

PMID:
23719465
39.

Consequences of defaunation for a tropical tree community.

Harrison RD, Tan S, Plotkin JB, Slik F, Detto M, Brenes T, Itoh A, Davies SJ.

Ecol Lett. 2013 May;16(5):687-94. doi: 10.1111/ele.12102. Epub 2013 Mar 12.

PMID:
23489437
40.

Weak 5'-mRNA secondary structures in short eukaryotic genes.

Ding Y, Shah P, Plotkin JB.

Genome Biol Evol. 2012;4(10):1046-53. doi: 10.1093/gbe/evs082.

41.

The population genetics of cooperative gene regulation.

Stewart AJ, Seymour RM, Pomiankowski A, Plotkin JB.

BMC Evol Biol. 2012 Sep 6;12:173. doi: 10.1186/1471-2148-12-173.

42.

Why transcription factor binding sites are ten nucleotides long.

Stewart AJ, Hannenhalli S, Plotkin JB.

Genetics. 2012 Nov;192(3):973-85. doi: 10.1534/genetics.112.143370. Epub 2012 Aug 10. Erratum in: Genetics. 2013 Apr;193(4):1311. Hannenhalli, Sridhar [added].

43.

Explosive radiation of a bacterial species group.

Morlon H, Kemps BD, Plotkin JB, Brisson D.

Evolution. 2012 Aug;66(8):2577-86. doi: 10.1111/j.1558-5646.2012.01598.x. Epub 2012 Mar 12.

44.

Evolution, safety, and highly pathogenic influenza viruses.

Lipsitch M, Plotkin JB, Simonsen L, Bloom B.

Science. 2012 Jun 22;336(6088):1529-31. doi: 10.1126/science.1223204.

45.

Extortion and cooperation in the Prisoner's Dilemma.

Stewart AJ, Plotkin JB.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10134-5. doi: 10.1073/pnas.1208087109. Epub 2012 Jun 18. No abstract available.

46.

Structure and age jointly influence rates of protein evolution.

Toll-Riera M, Bostick D, AlbĂ  MM, Plotkin JB.

PLoS Comput Biol. 2012 May;8(5):e1002542. doi: 10.1371/journal.pcbi.1002542. Epub 2012 May 31.

47.

Dynamics of neutral and selected alleles when the offspring distribution is skewed.

Der R, Epstein C, Plotkin JB.

Genetics. 2012 Aug;191(4):1331-44. doi: 10.1534/genetics.112.140038. Epub 2012 Jun 1.

48.

Environmental robustness and the adaptability of populations.

Stewart AJ, Parsons TL, Plotkin JB.

Evolution. 2012 May;66(5):1598-612. doi: 10.1111/j.1558-5646.2011.01526.x. Epub 2012 Jan 11.

PMID:
22519793
49.

The structure of allelic diversity in the presence of purifying selection.

Desai MM, Nicolaisen LE, Walczak AM, Plotkin JB.

Theor Popul Biol. 2012 Mar;81(2):144-57. doi: 10.1016/j.tpb.2011.12.002. Epub 2011 Dec 16.

50.

The structure of genealogies in the presence of purifying selection: a fitness-class coalescent.

Walczak AM, Nicolaisen LE, Plotkin JB, Desai MM.

Genetics. 2012 Feb;190(2):753-79. doi: 10.1534/genetics.111.134544. Epub 2011 Nov 30.

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